diff --git a/acmc/logging_config.py b/acmc/logging_config.py
index 735365a38a5ac3d653f2ea04d48c93a94d7815ba..86aee5a424645ce549cc04954d62f619c16e1193 100644
--- a/acmc/logging_config.py
+++ b/acmc/logging_config.py
@@ -4,20 +4,7 @@ import logging
DEFAULT_LOG_FILE = "acmc.log"
-# TODO: Determine if bcolours is still needed considering use of logging not print
-class bcolors: # for printing coloured text
- HEADER = "\033[95m"
- OKBLUE = "\033[94m"
- OKCYAN = "\033[96m"
- OKGREEN = "\033[92m"
- WARNING = "\033[93m"
- FAIL = "\033[91m"
- ENDC = "\033[0m"
- BOLD = "\033[1m"
- UNDERLINE = "\033[4m"
-
-
-def setup_logger(log_level=logging.INFO):
+def setup_logger(log_level: int = logging.INFO):
"""Sets up logger as a singleton outputing to file and sysout syserr"""
# Create a logger
logger = logging.getLogger("acmc_logger")
@@ -49,7 +36,7 @@ def setup_logger(log_level=logging.INFO):
return logger
-def set_log_level(log_level):
+def set_log_level(log_level: int):
"""Sets the log level for the acmc logger"""
logger = logging.getLogger("acmc_logger")
logger.setLevel(log_level) # Set logger level
diff --git a/acmc/main.py b/acmc/main.py
index 72ce3948011c83032d3b8f129236c1995661b02b..5b071fc2cbc6de723285b19e7f5467ad4169a3af 100644
--- a/acmc/main.py
+++ b/acmc/main.py
@@ -8,35 +8,35 @@ from acmc import trud, omop, phen, parse, logging_config as lc
# setup logging
logger = lc.setup_logger()
-DEFAULT_WORKING_PATH = Path("./workspace")
+DEFAULT_WORKSPACE_PATH = Path("./workspace")
-def trud_install(args):
+def trud_install(args: argparse.Namespace):
"""Handle the `trud install` command."""
trud.install()
-def omop_install(args):
+def omop_install(args: argparse.Namespace):
"""Handle the `omop install` command."""
omop.install(args.omop_zip_file, args.version)
-def omop_clear(args):
+def omop_clear(args: argparse.Namespace):
"""Handle the `omop clear` command."""
omop.clear(omop.DB_PATH)
-def omop_delete(args):
+def omop_delete(args: argparse.Namespace):
"""Handle the `omop delete` command."""
omop.delete(omop.DB_PATH)
-def phen_init(args):
+def phen_init(args: argparse.Namespace):
"""Handle the `phen init` command."""
phen.init(args.phen_dir, args.remote_url)
-def phen_fork(args):
+def phen_fork(args: argparse.Namespace):
"""Handle the `phen fork` command."""
phen.fork(
args.phen_dir,
@@ -46,32 +46,32 @@ def phen_fork(args):
)
-def phen_validate(args):
+def phen_validate(args: argparse.Namespace):
"""Handle the `phen validate` command."""
phen.validate(args.phen_dir)
-def phen_map(args):
+def phen_map(args: argparse.Namespace):
"""Handle the `phen map` command."""
phen.map(args.phen_dir, args.target_coding)
-def phen_export(args):
+def phen_export(args: argparse.Namespace):
"""Handle the `phen copy` command."""
phen.export(args.phen_dir, args.version)
-def phen_publish(args):
+def phen_publish(args: argparse.Namespace):
"""Handle the `phen publish` command."""
phen.publish(args.phen_dir, args.msg, args.remote_url, args.increment)
-def phen_copy(args):
+def phen_copy(args: argparse.Namespace):
"""Handle the `phen copy` command."""
phen.copy(args.phen_dir, args.target_dir, args.version)
-def phen_diff(args):
+def phen_diff(args: argparse.Namespace):
"""Handle the `phen diff` command."""
phen.diff(args.phen_dir, args.version, args.old_phen_dir, args.old_version)
@@ -276,7 +276,7 @@ def main():
"-td",
"--target-dir",
type=str,
- default=str(DEFAULT_WORKING_PATH.resolve()),
+ default=str(DEFAULT_WORKSPACE_PATH.resolve()),
help="Target directory for the copy",
)
phen_copy_parser.add_argument(
diff --git a/acmc/omop.py b/acmc/omop.py
index a66607463beb8f16e7a1c8b55facfba6440bd887..b6e443b600579e4afde1d289401b5af52641495d 100644
--- a/acmc/omop.py
+++ b/acmc/omop.py
@@ -57,7 +57,7 @@ omop_vocab_types = {
# Populate SQLite3 Database with default OMOP CONCEPTS
-def install(omop_zip_file, version):
+def install(omop_zip_file: str, version: str):
"""Installs the OMOP release csv files in a file-based sql database"""
logger.info(f"Installing OMOP from zip file: {omop_zip_file}")
omop_zip_path = Path(omop_zip_file)
@@ -119,7 +119,7 @@ def install(omop_zip_file, version):
logger.info(f"OMOP installation completed")
-def write_version_file(version):
+def write_version_file(version: str):
"""Writes the OMOP vocaburaries and version to a file"""
vocabularies["version"] = version
with open(VERSION_PATH, "w") as file:
@@ -133,12 +133,11 @@ def write_version_file(version):
)
-def clear(db_path):
+def clear(db_path: Path):
"""Clears the OMOP sql database"""
logger.info(f"Clearing OMOP data from database")
- omop_db_path = Path(db_path)
- if not omop_db_path.is_file():
- raise FileNotFoundError(f"Error: OMOP DB file '{omop_db_path}' does not exist.")
+ if not db_path.is_file():
+ raise FileNotFoundError(f"Error: OMOP DB file '{db_path}' does not exist.")
conn = sqlite3.connect(db_path)
cur = conn.cursor()
cur.execute("SELECT name FROM sqlite_master WHERE type='table';")
@@ -154,18 +153,17 @@ def clear(db_path):
logger.info(f"OMOP database cleared")
-def delete(db_path):
+def delete(db_path: Path):
"""Deletes the OMOP sql database"""
logger.info(f"Deleting OMOP database")
- omop_db_path = Path(db_path)
- if not omop_db_path.is_file():
- raise FileNotFoundError(f"Error: OMOP DB file '{omop_db_path}' does not exist.")
+ if not db_path.is_file():
+ raise FileNotFoundError(f"Error: OMOP DB file '{db_path}' does not exist.")
- omop_db_path.unlink()
+ db_path.unlink()
logger.info(f"OMOP database deleted")
-def table_exists(cursor, table_name):
+def table_exists(cursor: sqlite3.Cursor, table_name: str) -> bool:
# Query to check if the table exists
cursor.execute(
"""
@@ -182,7 +180,7 @@ def table_exists(cursor, table_name):
return result is not None
-def vocab_exists(cursor, vocab_id):
+def vocab_exists(cursor: sqlite3.Cursor, vocab_id: str) -> bool:
# Query to check if the table exists
cursor.execute(
"""
@@ -199,7 +197,7 @@ def vocab_exists(cursor, vocab_id):
return result is not None
-def concept_set_exist(cursor, concept_set_name):
+def concept_set_exist(cursor: sqlite3.Cursor, concept_set_name: str) -> bool:
query = f"SELECT EXISTS (SELECT 1 FROM CONCEPT_SET WHERE concept_set_name = ?)"
cursor.execute(query, (concept_set_name,))
@@ -208,7 +206,7 @@ def concept_set_exist(cursor, concept_set_name):
return cursor.fetchone()[0] == 1
-def export(map_path, export_path, version, omop_metadata):
+def export(map_path: Path, export_path: Path, version: str, omop_metadata) -> Path:
logger.debug(f"exporting with metadata {omop_metadata} at version {version}")
# copy the baseline omop database
@@ -269,7 +267,7 @@ def export(map_path, export_path, version, omop_metadata):
for concept_set_name, grp in df.groupby("CONCEPT_SET"):
# create Concept_Set
- if not concept_set_exist(cur, concept_set_name):
+ if not concept_set_exist(cur, str(concept_set_name)):
cur.execute(
f"INSERT INTO CONCEPT_SET (concept_set_name, vocabulary_id) VALUES ('{concept_set_name}', '{omop_metadata['vocabulary_id']}');"
)
diff --git a/acmc/parse.py b/acmc/parse.py
index 798a10ba743f3d5e939e9ebd7037eb43bf21aaba..2542ceab4fd3230365c3a8146e6bb1c78f2f9e90 100644
--- a/acmc/parse.py
+++ b/acmc/parse.py
@@ -1,7 +1,8 @@
import pandas as pd
import numpy as np
import os
-from typing import Callable
+from typing import Callable, Optional, Tuple
+from pathlib import Path
from acmc import trud, logging_config as lc
@@ -46,32 +47,36 @@ class Proto:
pd.Series,
], # The first lambda function: takes a list and returns a pd.Series of booleans
Callable[
- [list, str],
+ [list, Path],
None,
], # The second lambda function: takes a list and a string, and returns nothing
]
]
- def __init__(self, name, trud_codes_path=None):
+ def __init__(self, name: str, trud_codes_path: Optional[Path] = None):
if trud_codes_path is not None:
if trud_codes_path.is_file():
- self.trud_codes_path = trud_codes_path
- self.db = pd.read_parquet(self.trud_codes_path)
+ self.trud_codes_path: Path = trud_codes_path
+ self.db: pd.DataFrame = pd.read_parquet(self.trud_codes_path)
else:
raise FileNotFoundError(
f"Error: Read2 code file '{trud_codes_path}' does not exist. Please ensure you have installed TRUD correctly"
)
- self.name = name
+ self.name: str = name
- def raise_exception(self, ex):
+ def raise_exception(self, ex: Exception):
"""Raises an exception inside a lambda function. Python does not allow using raise statement inside lambda because lambda can only contain expressions, not statements. Using raise_exception not raise_ as it's more explict"""
raise ex
- def in_database(self, codes, db, col):
+ def in_database(
+ self, codes: pd.DataFrame, db: pd.DataFrame, col: str
+ ) -> pd.DataFrame:
return codes.isin(db[col])
- def process(self, codes, codes_file):
+ def process(
+ self, codes: pd.DataFrame, codes_file: Path
+ ) -> Tuple[pd.DataFrame, list]:
"""identify issues that do not pass and fix them with define/d process"""
errors = []
# Iter through each item in check.
@@ -93,7 +98,7 @@ class Proto:
return codes, errors
- def verify(self, codes, codes_file):
+ def verify(self, codes: pd.DataFrame, codes_file: Path):
"""verify codes in codes file"""
conds = np.array([])
@@ -333,7 +338,7 @@ class Icd10(Proto):
# )
]
- def trim_icd10(codes):
+ def trim_icd10(codes: pd.DataFrame) -> pd.DataFrame:
codes = codes.str[:4]
return codes
@@ -538,7 +543,7 @@ class Cprd(Proto):
class CodeTypeParser:
"""A class used in InvalidCodesException to report an error if a code parser check fails"""
- def __init__(self, trud_processed_dir=trud.PROCESSED_PATH):
+ def __init__(self, trud_processed_dir: Path = trud.PROCESSED_PATH):
if not trud_processed_dir.exists() or not trud_processed_dir.is_dir():
raise FileNotFoundError(
diff --git a/acmc/phen.py b/acmc/phen.py
index 86131c282a72b4bf5cc8ea2fb0f723ba2cebac9e..8b5144b8a7045110db5f630b77e37d1d61887f45 100644
--- a/acmc/phen.py
+++ b/acmc/phen.py
@@ -13,10 +13,12 @@ import logging
import requests
import yaml
import semver
+from git import Repo
from cerberus import Validator
from deepdiff import DeepDiff
from pathlib import Path
from urllib.parse import urlparse, urlunparse
+from typing import Tuple, Set, Any
import acmc
from acmc import trud, omop, parse, util
@@ -125,7 +127,7 @@ class PhenValidationException(Exception):
self.validation_errors = validation_errors
-def construct_git_url(remote_url):
+def construct_git_url(remote_url: str):
"""Constructs a git url for github or gitlab including a PAT token environment variable"""
# check the url
parsed_url = urlparse(remote_url)
@@ -162,15 +164,15 @@ def construct_git_url(remote_url):
)
-def create_empty_git_dir(path):
+def create_empty_git_dir(path: Path):
"""Creates a directory with a .gitkeep file so that it's tracked in git"""
path.mkdir(exist_ok=True)
keep_path = path / ".gitkeep"
keep_path.touch(exist_ok=True)
-def check_delete_dir(path, msg):
- """Checks on the command line if a user wants to delete a directory
+def check_delete_dir(path: Path, msg: str) -> bool:
+ """Checks on the command line if a user wants to delete a directory
Args:
path (Path): path of the directory to be deleted
@@ -191,7 +193,9 @@ def check_delete_dir(path, msg):
return deleted
-def fork(phen_dir, upstream_url, upstream_version, new_origin_url=None):
+def fork(
+ phen_dir: str, upstream_url: str, upstream_version: str, new_origin_url: str = None
+):
"""Forks an upstream phenotype in a remote repo at a specific version to a local director, and optionally sets to a new remote origin"
Args:
@@ -253,7 +257,7 @@ def fork(phen_dir, upstream_url, upstream_version, new_origin_url=None):
)
# Validate the phenotype is compatible with the acmc tool
- validate(phen_path)
+ validate(str(phen_path.resolve()))
# Delete each tag locally
tags = repo.tags
@@ -263,7 +267,8 @@ def fork(phen_dir, upstream_url, upstream_version, new_origin_url=None):
# Add upstream remote
repo.create_remote("upstream", upstream_url)
- repo.delete_remote("origin") # Remove existing origin
+ remote = repo.remotes["origin"]
+ repo.delete_remote(remote) # Remove existing origin
# Optionally set a new origin remote
if new_origin_url:
@@ -282,7 +287,7 @@ def fork(phen_dir, upstream_url, upstream_version, new_origin_url=None):
raise ValueError(f"Error occurred during repository fork: {str(e)}")
-def init(phen_dir, remote_url):
+def init(phen_dir: str, remote_url: str):
"""Initial phenotype directory as git repo with standard structure"""
logger.info(f"Initialising Phenotype in directory: {phen_dir}")
phen_path = Path(phen_dir)
@@ -303,7 +308,7 @@ def init(phen_dir, remote_url):
return
# Initialise repo from local or remote
- repo = None
+ repo: Repo
# if remote then clone the repo otherwise init a local repo
if remote_url != None:
# add PAT token to the URL
@@ -312,8 +317,9 @@ def init(phen_dir, remote_url):
# clone the repo
repo = git.cmd.Git()
repo.clone(git_url, phen_path)
+
# open repo
- repo = git.Repo(phen_path)
+ repo = Repo(phen_path)
# check if there are any commits (new repo has no commits)
if (
len(repo.branches) == 0 or repo.head.is_detached
@@ -411,7 +417,7 @@ def init(phen_dir, remote_url):
logger.info(f"Phenotype initialised successfully")
-def validate(phen_dir):
+def validate(phen_dir: str):
"""Validates the phenotype directory is a git repo with standard structure"""
logger.info(f"Validating phenotype: {phen_dir}")
phen_path = Path(phen_dir)
@@ -524,7 +530,7 @@ def validate(phen_dir):
logger.info(f"Phenotype validated successfully")
-def read_table_file(path, excel_sheet=None):
+def read_table_file(path: Path, excel_sheet: str = ""):
"""
Load Code List File
"""
@@ -533,21 +539,21 @@ def read_table_file(path, excel_sheet=None):
if path.suffix == ".csv":
df = pd.read_csv(path, dtype=str)
elif path.suffix == ".xlsx" or path.suffix == ".xls":
- if excel_sheet:
+ if excel_sheet != "":
df = pd.read_excel(path, sheet_name=excel_sheet, dtype=str)
else:
df = pd.read_excel(path, dtype=str)
elif path.suffix == ".dta":
- df = pd.read_stata(path, dtype=str)
+ df = pd.read_stata(path)
else:
raise ValueError(
- f"Unsupported filetype {codes_file_path.suffix}, only support{CODE_FILE_TYPES} code file types"
+ f"Unsupported filetype {path.suffix}, only support{CODE_FILE_TYPES} code file types"
)
return df
-def process_actions(df, concept_set):
+def process_actions(df: pd.DataFrame, concept_set: dict) -> pd.DataFrame:
# Perform Structural Changes to file before preprocessing
logger.debug("Processing file structural actions")
if (
@@ -573,7 +579,9 @@ def process_actions(df, concept_set):
# Perform QA Checks on columns individually and append to df
-def preprocess_source_concepts(df, concept_set, code_file_path):
+def preprocess_source_concepts(
+ df: pd.DataFrame, concept_set: dict, code_file_path: Path
+) -> Tuple[pd.DataFrame, list]:
"""Parses each column individually - Order and length will not be preserved!"""
out = pd.DataFrame([]) # create output df to append to
code_errors = [] # list of errors from processing
@@ -613,12 +621,14 @@ def preprocess_source_concepts(df, concept_set, code_file_path):
return out, code_errors
-def get_code_type_from_col_name(col_name):
+def get_code_type_from_col_name(col_name: str):
return col_name.split("_")[0]
# Translate Df with multiple codes into single code type Series
-def translate_codes(source_df, target_code_type, concept_name):
+def translate_codes(
+ source_df: pd.DataFrame, target_code_type: str, concept_name: str
+) -> pd.DataFrame:
"""Translates each source code type the source coding list into a target type and returns all conversions as a concept set"""
# codes = pd.DataFrame([], dtype=str)
@@ -681,7 +691,9 @@ def translate_codes(source_df, target_code_type, concept_name):
return codes
-def sql_row_exist(conn, table, column, value):
+def sql_row_exist(
+ conn: sqlite3.Connection, table: str, column: str, value: str
+) -> bool:
# Execute and check if a result exists
cur = conn.cursor()
query = f"SELECT 1 FROM {table} WHERE {column} = ? LIMIT 1;"
@@ -691,7 +703,7 @@ def sql_row_exist(conn, table, column, value):
return exists
-def write_code_errors(code_errors, code_errors_path):
+def write_code_errors(code_errors: list, code_errors_path: Path):
err_df = pd.DataFrame(
[
{
@@ -709,7 +721,7 @@ def write_code_errors(code_errors, code_errors_path):
err_df.to_csv(code_errors_path, index=False, mode="w")
-def write_vocab_version(phen_path):
+def write_vocab_version(phen_path: Path):
# write the vocab version files
if not trud.VERSION_PATH.exists():
@@ -748,7 +760,7 @@ def write_vocab_version(phen_path):
)
-def map(phen_dir, target_code_type):
+def map(phen_dir: str, target_code_type: str):
logger.info(f"Processing phenotype: {phen_dir}")
# Validate configuration
@@ -780,7 +792,7 @@ def map(phen_dir, target_code_type):
logger.info(f"Phenotype processed successfully")
-def map_target_code_type(phen_path, phenotype, target_code_type):
+def map_target_code_type(phen_path: Path, phenotype: dict, target_code_type: str):
logger.debug(f"Target coding format: {target_code_type}")
concepts_path = phen_path / CONCEPTS_DIR
# Create output dataframe
@@ -859,7 +871,7 @@ def map_target_code_type(phen_path, phenotype, target_code_type):
if len(out.index) == 0:
logger.error(f"No output after map processing")
raise Exception(
- f"No output after map processing, check config {str(config_path.resolve())}"
+ f"No output after map processing, check config {str(phen_path.resolve())}"
)
# final processing
@@ -939,7 +951,9 @@ def map_target_code_type(phen_path, phenotype, target_code_type):
logger.info(f"Phenotype processed target code type {target_code_type}")
-def generate_version_tag(repo, increment=DEFAULT_VERSION_INC, use_v_prefix=False):
+def generate_version_tag(
+ repo: git.Repo, increment: str = DEFAULT_VERSION_INC, use_v_prefix: bool = False
+) -> str:
# Get all valid semantic version tags
versions = []
for tag in repo.tags:
@@ -967,7 +981,9 @@ def generate_version_tag(repo, increment=DEFAULT_VERSION_INC, use_v_prefix=False
return new_version_str
-def publish(phen_dir, msg, remote_url, increment=DEFAULT_VERSION_INC):
+def publish(
+ phen_dir: str, msg: str, remote_url: str, increment: str = DEFAULT_VERSION_INC
+):
"""Publishes updates to the phenotype by commiting all changes to the repo directory"""
# Validate config
@@ -1037,14 +1053,15 @@ def publish(phen_dir, msg, remote_url, increment=DEFAULT_VERSION_INC):
else:
logger.debug("Remote 'origin' is not set")
except Exception as e:
- repo.delete_tag(new_version_str)
+ tag_ref = repo.tags[new_version_str]
+ repo.delete_tag(tag_ref)
repo.git.reset("--soft", "HEAD~1")
raise e
logger.info(f"Phenotype published successfully")
-def export(phen_dir, version):
+def export(phen_dir: str, version: str):
"""Exports a phen repo at a specific tagged version into a target directory"""
logger.info(f"Exporting phenotype {phen_dir} at version {version}")
@@ -1080,7 +1097,7 @@ def export(phen_dir, version):
logger.info(f"Phenotype exported successfully")
-def copy(phen_dir, target_dir, version):
+def copy(phen_dir: str, target_dir: str, version: str):
"""Copys a phen repo at a specific tagged version into a target directory"""
# Validate
@@ -1129,7 +1146,7 @@ def copy(phen_dir, target_dir, version):
# Convert concept_sets list into dictionaries
-def extract_concepts(config_data):
+def extract_concepts(config_data: dict) -> Tuple[dict, Set[str]]:
"""Extracts concepts as {name: file_path} dictionary and a name set."""
concepts_dict = {
item["name"]: item["file"]["path"]
@@ -1139,7 +1156,7 @@ def extract_concepts(config_data):
return concepts_dict, name_set
-def extract_clean_deepdiff_keys(diff, key_type):
+def extract_clean_deepdiff_keys(diff: dict, key_type: str) -> Set[Any]:
"""
Extracts clean keys from a DeepDiff dictionary.
@@ -1150,7 +1167,7 @@ def extract_clean_deepdiff_keys(diff, key_type):
return {key.split("root['")[1].split("']")[0] for key in diff.get(key_type, [])}
-def diff_config(old_config, new_config):
+def diff_config(old_config: dict, new_config: dict) -> str:
report = f"\n# Changes to phenotype configuration\n"
report += f"This compares changes in the phenotype configuration including added, removed and renamed concept sets and changes to concept set source concept code file paths\n\n"
@@ -1225,7 +1242,7 @@ def diff_config(old_config, new_config):
return report
-def diff_map_files(old_map_path, new_map_path):
+def diff_map_files(old_map_path: Path, new_map_path: Path) -> str:
old_output_files = [
file.name
for file in old_map_path.iterdir()
@@ -1292,7 +1309,13 @@ def diff_map_files(old_map_path, new_map_path):
return report
-def diff_phen(new_phen_path, new_version, old_phen_path, old_version, report_path):
+def diff_phen(
+ new_phen_path: Path,
+ new_version: str,
+ old_phen_path: Path,
+ old_version: str,
+ report_path: Path,
+):
"""Compare the differences between two versions of a phenotype"""
# validate phenotypes
@@ -1302,11 +1325,11 @@ def diff_phen(new_phen_path, new_version, old_phen_path, old_version, report_pat
validate(str(new_phen_path.resolve()))
# get old and new config
- old_config = old_phen_path / CONFIG_FILE
- with old_config.open("r") as file:
+ old_config_path = old_phen_path / CONFIG_FILE
+ with old_config_path.open("r") as file:
old_config = yaml.safe_load(file)
- new_config = new_phen_path / CONFIG_FILE
- with new_config.open("r") as file:
+ new_config_path = new_phen_path / CONFIG_FILE
+ with new_config_path.open("r") as file:
new_config = yaml.safe_load(file)
# write report heading
@@ -1339,7 +1362,7 @@ def diff_phen(new_phen_path, new_version, old_phen_path, old_version, report_pat
logger.info(f"Phenotypes diff'd successfully")
-def diff(phen_dir, version, old_phen_dir, old_version):
+def diff(phen_dir: str, version: str, old_phen_dir: str, old_version: str):
# make tmp directory .acmc
timestamp = time.strftime("%Y%m%d_%H%M%S")
temp_dir = Path(f".acmc/diff_{timestamp}")
diff --git a/acmc/trud.py b/acmc/trud.py
index 08f5c4ad1eae64927955f01b4a162583e492f153..65a3cd3af62439600d7cb5990c0654e81c4d71d9 100644
--- a/acmc/trud.py
+++ b/acmc/trud.py
@@ -24,12 +24,7 @@ DOWNLOADS_PATH = VOCAB_PATH / "downloads"
PROCESSED_PATH = VOCAB_PATH / "processed"
-def error_exit(message):
- logger.error(message, "error")
- sys.exit(1)
-
-
-def get_releases(item_id, API_KEY, latest=False):
+def get_releases(item_id: str, API_KEY: str, latest=False) -> list:
"""Retrieve release information for an item from the TRUD API."""
url = f"https://{FQDN}/trud/api/v1/keys/{API_KEY}/items/{item_id}/releases"
if latest:
@@ -37,20 +32,27 @@ def get_releases(item_id, API_KEY, latest=False):
response = requests.get(url)
if response.status_code != 200:
- error_exit(
+ logger.error(
f"Failed to fetch releases for item {item_id}. Status code: {response.status_code}, error {response.json()['message']}. If no releases found for API key, please ensure you are subscribed to the data release and that it is not pending approval"
)
+ response.raise_for_status()
data = response.json()
if data.get("message") != "OK":
- error_exit(data.get("message", "Unknown error occurred"))
+ msg = f"Unknown error occurred {data.get('message')}"
+ logger.error(msg)
+ raise Exception(msg)
return data.get("releases", [])
def download_release_file(
- item_id, release_ordinal, release, file_json_prefix, file_type=None
-):
+ item_id: str,
+ release_ordinal: str,
+ release: dict,
+ file_json_prefix: str,
+ file_type=None,
+) -> Path:
"""Download specified file type for a given release of an item."""
# check folder is a directory
@@ -65,7 +67,7 @@ def download_release_file(
file_destination = DOWNLOADS_PATH / file_name
if not file_url or not file_name:
- error_exit(
+ raise ValueError(
f"Missing {file_type} file information for release {release_ordinal} of item {item_id}."
)
@@ -77,11 +79,13 @@ def download_release_file(
if response.status_code == 200:
with open(file_destination, "wb") as f:
f.write(response.content)
- return file_destination
else:
- error_exit(
+ logger.error(
f"Failed to download {file_type} file for item {item_id}. Status code: {response.status_code}"
)
+ response.raise_for_status()
+
+ return file_destination
def validate_download_hash(file_destination: str, item_hash: str):
@@ -91,9 +95,9 @@ def validate_download_hash(file_destination: str, item_hash: str):
if hash.upper() == item_hash.upper():
logger.debug(f"Verified hash of {file_destination} {hash}")
else:
- error_exit(
- f"Could not validate origin of {file_destination}. The SHA-256 hash should be: {item_hash}, but got {hash} instead"
- )
+ msg = f"Could not validate origin of {file_destination}. The SHA-256 hash should be: {item_hash}, but got {hash} instead"
+ logger.error(msg)
+ raise ValueError(msg)
def unzip_download(file_destination: str):
@@ -400,7 +404,7 @@ def install():
releases = get_releases(item_id, API_KEY=api_key, latest=items_latest)
if not releases:
- error_exit(f"No releases found for item {item_id}.")
+ raise ValueError(f"No releases found for item {item_id}.")
# Process each release in reverse order
for release_ordinal, release in enumerate(releases[::-1], 1):
diff --git a/docs/api.md b/docs/api.md
deleted file mode 100644
index fe113c6a1500759d413611699ecd0b4002ec9902..0000000000000000000000000000000000000000
--- a/docs/api.md
+++ /dev/null
@@ -1,3 +0,0 @@
-# API Reference
-
-::: acmc.module_name
\ No newline at end of file
diff --git a/docs/api/acmc.html b/docs/api/acmc.html
new file mode 100644
index 0000000000000000000000000000000000000000..7fb0357e7df7298fcf5b2846ddb12b75f7af2d2c
--- /dev/null
+++ b/docs/api/acmc.html
@@ -0,0 +1,249 @@
+<!doctype html>
+<html lang="en">
+<head>
+ <meta charset="utf-8">
+ <meta name="viewport" content="width=device-width, initial-scale=1">
+ <meta name="generator" content="pdoc 15.0.1"/>
+ <title>acmc API documentation</title>
+
+ <style>/*! * Bootstrap Reboot v5.0.0 (https://getbootstrap.com/) * Copyright 2011-2021 The Bootstrap Authors * Copyright 2011-2021 Twitter, Inc. * Licensed under MIT (https://github.com/twbs/bootstrap/blob/main/LICENSE) * Forked from Normalize.css, licensed MIT (https://github.com/necolas/normalize.css/blob/master/LICENSE.md) */*,::after,::before{box-sizing:border-box}@media (prefers-reduced-motion:no-preference){:root{scroll-behavior:smooth}}body{margin:0;font-family:system-ui,-apple-system,"Segoe UI",Roboto,"Helvetica Neue",Arial,"Noto Sans","Liberation Sans",sans-serif,"Apple Color Emoji","Segoe UI Emoji","Segoe UI Symbol","Noto Color Emoji";font-size:1rem;font-weight:400;line-height:1.5;color:#212529;background-color:#fff;-webkit-text-size-adjust:100%;-webkit-tap-highlight-color:transparent}hr{margin:1rem 0;color:inherit;background-color:currentColor;border:0;opacity:.25}hr:not([size]){height:1px}h1,h2,h3,h4,h5,h6{margin-top:0;margin-bottom:.5rem;font-weight:500;line-height:1.2}h1{font-size:calc(1.375rem + 1.5vw)}@media (min-width:1200px){h1{font-size:2.5rem}}h2{font-size:calc(1.325rem + .9vw)}@media (min-width:1200px){h2{font-size:2rem}}h3{font-size:calc(1.3rem + .6vw)}@media (min-width:1200px){h3{font-size:1.75rem}}h4{font-size:calc(1.275rem + .3vw)}@media (min-width:1200px){h4{font-size:1.5rem}}h5{font-size:1.25rem}h6{font-size:1rem}p{margin-top:0;margin-bottom:1rem}abbr[data-bs-original-title],abbr[title]{-webkit-text-decoration:underline dotted;text-decoration:underline dotted;cursor:help;-webkit-text-decoration-skip-ink:none;text-decoration-skip-ink:none}address{margin-bottom:1rem;font-style:normal;line-height:inherit}ol,ul{padding-left:2rem}dl,ol,ul{margin-top:0;margin-bottom:1rem}ol ol,ol ul,ul ol,ul ul{margin-bottom:0}dt{font-weight:700}dd{margin-bottom:.5rem;margin-left:0}blockquote{margin:0 0 1rem}b,strong{font-weight:bolder}small{font-size:.875em}mark{padding:.2em;background-color:#fcf8e3}sub,sup{position:relative;font-size:.75em;line-height:0;vertical-align:baseline}sub{bottom:-.25em}sup{top:-.5em}a{color:#0d6efd;text-decoration:underline}a:hover{color:#0a58ca}a:not([href]):not([class]),a:not([href]):not([class]):hover{color:inherit;text-decoration:none}code,kbd,pre,samp{font-family:SFMono-Regular,Menlo,Monaco,Consolas,"Liberation Mono","Courier New",monospace;font-size:1em;direction:ltr;unicode-bidi:bidi-override}pre{display:block;margin-top:0;margin-bottom:1rem;overflow:auto;font-size:.875em}pre code{font-size:inherit;color:inherit;word-break:normal}code{font-size:.875em;color:#d63384;word-wrap:break-word}a>code{color:inherit}kbd{padding:.2rem .4rem;font-size:.875em;color:#fff;background-color:#212529;border-radius:.2rem}kbd kbd{padding:0;font-size:1em;font-weight:700}figure{margin:0 0 1rem}img,svg{vertical-align:middle}table{caption-side:bottom;border-collapse:collapse}caption{padding-top:.5rem;padding-bottom:.5rem;color:#6c757d;text-align:left}th{text-align:inherit;text-align:-webkit-match-parent}tbody,td,tfoot,th,thead,tr{border-color:inherit;border-style:solid;border-width:0}label{display:inline-block}button{border-radius:0}button:focus:not(:focus-visible){outline:0}button,input,optgroup,select,textarea{margin:0;font-family:inherit;font-size:inherit;line-height:inherit}button,select{text-transform:none}[role=button]{cursor:pointer}select{word-wrap:normal}select:disabled{opacity:1}[list]::-webkit-calendar-picker-indicator{display:none}[type=button],[type=reset],[type=submit],button{-webkit-appearance:button}[type=button]:not(:disabled),[type=reset]:not(:disabled),[type=submit]:not(:disabled),button:not(:disabled){cursor:pointer}::-moz-focus-inner{padding:0;border-style:none}textarea{resize:vertical}fieldset{min-width:0;padding:0;margin:0;border:0}legend{float:left;width:100%;padding:0;margin-bottom:.5rem;font-size:calc(1.275rem + .3vw);line-height:inherit}@media (min-width:1200px){legend{font-size:1.5rem}}legend+*{clear:left}::-webkit-datetime-edit-day-field,::-webkit-datetime-edit-fields-wrapper,::-webkit-datetime-edit-hour-field,::-webkit-datetime-edit-minute,::-webkit-datetime-edit-month-field,::-webkit-datetime-edit-text,::-webkit-datetime-edit-year-field{padding:0}::-webkit-inner-spin-button{height:auto}[type=search]{outline-offset:-2px;-webkit-appearance:textfield}::-webkit-search-decoration{-webkit-appearance:none}::-webkit-color-swatch-wrapper{padding:0}::file-selector-button{font:inherit}::-webkit-file-upload-button{font:inherit;-webkit-appearance:button}output{display:inline-block}iframe{border:0}summary{display:list-item;cursor:pointer}progress{vertical-align:baseline}[hidden]{display:none!important}</style>
+ <style>/*! syntax-highlighting.css */pre{line-height:125%;}span.linenos{color:inherit; background-color:transparent; padding-left:5px; padding-right:20px;}.pdoc-code .hll{background-color:#ffffcc}.pdoc-code{background:#f8f8f8;}.pdoc-code .c{color:#3D7B7B; font-style:italic}.pdoc-code .err{border:1px solid #FF0000}.pdoc-code .k{color:#008000; font-weight:bold}.pdoc-code .o{color:#666666}.pdoc-code .ch{color:#3D7B7B; font-style:italic}.pdoc-code .cm{color:#3D7B7B; font-style:italic}.pdoc-code .cp{color:#9C6500}.pdoc-code .cpf{color:#3D7B7B; font-style:italic}.pdoc-code .c1{color:#3D7B7B; font-style:italic}.pdoc-code .cs{color:#3D7B7B; font-style:italic}.pdoc-code .gd{color:#A00000}.pdoc-code .ge{font-style:italic}.pdoc-code .gr{color:#E40000}.pdoc-code .gh{color:#000080; font-weight:bold}.pdoc-code .gi{color:#008400}.pdoc-code .go{color:#717171}.pdoc-code .gp{color:#000080; font-weight:bold}.pdoc-code .gs{font-weight:bold}.pdoc-code .gu{color:#800080; font-weight:bold}.pdoc-code .gt{color:#0044DD}.pdoc-code .kc{color:#008000; font-weight:bold}.pdoc-code .kd{color:#008000; font-weight:bold}.pdoc-code .kn{color:#008000; font-weight:bold}.pdoc-code .kp{color:#008000}.pdoc-code .kr{color:#008000; font-weight:bold}.pdoc-code .kt{color:#B00040}.pdoc-code .m{color:#666666}.pdoc-code .s{color:#BA2121}.pdoc-code .na{color:#687822}.pdoc-code .nb{color:#008000}.pdoc-code .nc{color:#0000FF; font-weight:bold}.pdoc-code .no{color:#880000}.pdoc-code .nd{color:#AA22FF}.pdoc-code .ni{color:#717171; font-weight:bold}.pdoc-code .ne{color:#CB3F38; font-weight:bold}.pdoc-code .nf{color:#0000FF}.pdoc-code .nl{color:#767600}.pdoc-code .nn{color:#0000FF; font-weight:bold}.pdoc-code .nt{color:#008000; font-weight:bold}.pdoc-code .nv{color:#19177C}.pdoc-code .ow{color:#AA22FF; font-weight:bold}.pdoc-code .w{color:#bbbbbb}.pdoc-code .mb{color:#666666}.pdoc-code .mf{color:#666666}.pdoc-code .mh{color:#666666}.pdoc-code .mi{color:#666666}.pdoc-code .mo{color:#666666}.pdoc-code .sa{color:#BA2121}.pdoc-code .sb{color:#BA2121}.pdoc-code .sc{color:#BA2121}.pdoc-code .dl{color:#BA2121}.pdoc-code .sd{color:#BA2121; font-style:italic}.pdoc-code .s2{color:#BA2121}.pdoc-code .se{color:#AA5D1F; font-weight:bold}.pdoc-code .sh{color:#BA2121}.pdoc-code .si{color:#A45A77; font-weight:bold}.pdoc-code .sx{color:#008000}.pdoc-code .sr{color:#A45A77}.pdoc-code .s1{color:#BA2121}.pdoc-code .ss{color:#19177C}.pdoc-code .bp{color:#008000}.pdoc-code .fm{color:#0000FF}.pdoc-code .vc{color:#19177C}.pdoc-code .vg{color:#19177C}.pdoc-code .vi{color:#19177C}.pdoc-code .vm{color:#19177C}.pdoc-code .il{color:#666666}</style>
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+ </a>
+</div>
+ </nav>
+ <main class="pdoc">
+ <section class="module-info">
+ <h1 class="modulename">
+acmc </h1>
+
+
+ <input id="mod-acmc-view-source" class="view-source-toggle-state" type="checkbox" aria-hidden="true" tabindex="-1">
+
+ <label class="view-source-button" for="mod-acmc-view-source"><span>View Source</span></label>
+
+ <div class="pdoc-code codehilite"><pre><span></span><span id="L-1"><a href="#L-1"><span class="linenos">1</span></a><span class="kn">from</span><span class="w"> </span><span class="nn">importlib.metadata</span><span class="w"> </span><span class="kn">import</span> <span class="n">version</span>
+</span><span id="L-2"><a href="#L-2"><span class="linenos">2</span></a>
+</span><span id="L-3"><a href="#L-3"><span class="linenos">3</span></a><span class="n">__version__</span> <span class="o">=</span> <span class="n">version</span><span class="p">(</span><span class="s2">"acmc"</span><span class="p">)</span>
+</span></pre></div>
+
+
+ </section>
+ </main>
+<script>
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diff --git a/docs/api/acmc/logging_config.html b/docs/api/acmc/logging_config.html
new file mode 100644
index 0000000000000000000000000000000000000000..a844e4d8294181d98be83eff2c6a61e5f6d98680
--- /dev/null
+++ b/docs/api/acmc/logging_config.html
@@ -0,0 +1,384 @@
+<!doctype html>
+<html lang="en">
+<head>
+ <meta charset="utf-8">
+ <meta name="viewport" content="width=device-width, initial-scale=1">
+ <meta name="generator" content="pdoc 15.0.1"/>
+ <title>acmc.logging_config API documentation</title>
+
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+ <h2>API Documentation</h2>
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+ <a class="variable" href="#DEFAULT_LOG_FILE">DEFAULT_LOG_FILE</a>
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+ <a class="function" href="#setup_logger">setup_logger</a>
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+ </a>
+</div>
+ </nav>
+ <main class="pdoc">
+ <section class="module-info">
+ <h1 class="modulename">
+<a href="./../acmc.html">acmc</a><wbr>.logging_config </h1>
+
+
+ <input id="mod-logging_config-view-source" class="view-source-toggle-state" type="checkbox" aria-hidden="true" tabindex="-1">
+
+ <label class="view-source-button" for="mod-logging_config-view-source"><span>View Source</span></label>
+
+ <div class="pdoc-code codehilite"><pre><span></span><span id="L-1"><a href="#L-1"><span class="linenos"> 1</span></a><span class="kn">import</span><span class="w"> </span><span class="nn">pandas</span><span class="w"> </span><span class="k">as</span><span class="w"> </span><span class="nn">pd</span>
+</span><span id="L-2"><a href="#L-2"><span class="linenos"> 2</span></a><span class="kn">import</span><span class="w"> </span><span class="nn">logging</span>
+</span><span id="L-3"><a href="#L-3"><span class="linenos"> 3</span></a>
+</span><span id="L-4"><a href="#L-4"><span class="linenos"> 4</span></a><span class="n">DEFAULT_LOG_FILE</span> <span class="o">=</span> <span class="s2">"acmc.log"</span>
+</span><span id="L-5"><a href="#L-5"><span class="linenos"> 5</span></a>
+</span><span id="L-6"><a href="#L-6"><span class="linenos"> 6</span></a>
+</span><span id="L-7"><a href="#L-7"><span class="linenos"> 7</span></a><span class="k">def</span><span class="w"> </span><span class="nf">setup_logger</span><span class="p">(</span><span class="n">log_level</span><span class="p">:</span> <span class="nb">int</span> <span class="o">=</span> <span class="n">logging</span><span class="o">.</span><span class="n">INFO</span><span class="p">):</span>
+</span><span id="L-8"><a href="#L-8"><span class="linenos"> 8</span></a><span class="w"> </span><span class="sd">"""Sets up logger as a singleton outputing to file and sysout syserr"""</span>
+</span><span id="L-9"><a href="#L-9"><span class="linenos"> 9</span></a> <span class="c1"># Create a logger</span>
+</span><span id="L-10"><a href="#L-10"><span class="linenos">10</span></a> <span class="n">logger</span> <span class="o">=</span> <span class="n">logging</span><span class="o">.</span><span class="n">getLogger</span><span class="p">(</span><span class="s2">"acmc_logger"</span><span class="p">)</span>
+</span><span id="L-11"><a href="#L-11"><span class="linenos">11</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">setLevel</span><span class="p">(</span><span class="n">logging</span><span class="o">.</span><span class="n">INFO</span><span class="p">)</span>
+</span><span id="L-12"><a href="#L-12"><span class="linenos">12</span></a>
+</span><span id="L-13"><a href="#L-13"><span class="linenos">13</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="n">logger</span><span class="o">.</span><span class="n">hasHandlers</span><span class="p">():</span>
+</span><span id="L-14"><a href="#L-14"><span class="linenos">14</span></a> <span class="c1"># Create a file handler that logs to a file</span>
+</span><span id="L-15"><a href="#L-15"><span class="linenos">15</span></a> <span class="n">file_handler</span> <span class="o">=</span> <span class="n">logging</span><span class="o">.</span><span class="n">FileHandler</span><span class="p">(</span><span class="n">DEFAULT_LOG_FILE</span><span class="p">)</span>
+</span><span id="L-16"><a href="#L-16"><span class="linenos">16</span></a> <span class="n">file_handler</span><span class="o">.</span><span class="n">setLevel</span><span class="p">(</span><span class="n">logging</span><span class="o">.</span><span class="n">INFO</span><span class="p">)</span>
+</span><span id="L-17"><a href="#L-17"><span class="linenos">17</span></a>
+</span><span id="L-18"><a href="#L-18"><span class="linenos">18</span></a> <span class="c1"># Create a stream handler that prints to the console</span>
+</span><span id="L-19"><a href="#L-19"><span class="linenos">19</span></a> <span class="n">stream_handler</span> <span class="o">=</span> <span class="n">logging</span><span class="o">.</span><span class="n">StreamHandler</span><span class="p">()</span>
+</span><span id="L-20"><a href="#L-20"><span class="linenos">20</span></a> <span class="n">stream_handler</span><span class="o">.</span><span class="n">setLevel</span><span class="p">(</span><span class="n">logging</span><span class="o">.</span><span class="n">INFO</span><span class="p">)</span>
+</span><span id="L-21"><a href="#L-21"><span class="linenos">21</span></a>
+</span><span id="L-22"><a href="#L-22"><span class="linenos">22</span></a> <span class="c1"># Create a formatter for how the log messages should look</span>
+</span><span id="L-23"><a href="#L-23"><span class="linenos">23</span></a>
+</span><span id="L-24"><a href="#L-24"><span class="linenos">24</span></a> <span class="c1"># Add the formatter to both handlers</span>
+</span><span id="L-25"><a href="#L-25"><span class="linenos">25</span></a> <span class="n">file_formatter</span> <span class="o">=</span> <span class="n">logging</span><span class="o">.</span><span class="n">Formatter</span><span class="p">(</span>
+</span><span id="L-26"><a href="#L-26"><span class="linenos">26</span></a> <span class="s2">"</span><span class="si">%(asctime)s</span><span class="s2"> - - </span><span class="si">%(levelname)s</span><span class="s2"> - </span><span class="si">%(message)s</span><span class="s2">"</span>
+</span><span id="L-27"><a href="#L-27"><span class="linenos">27</span></a> <span class="p">)</span>
+</span><span id="L-28"><a href="#L-28"><span class="linenos">28</span></a> <span class="n">file_handler</span><span class="o">.</span><span class="n">setFormatter</span><span class="p">(</span><span class="n">file_formatter</span><span class="p">)</span>
+</span><span id="L-29"><a href="#L-29"><span class="linenos">29</span></a> <span class="n">stream_formatter</span> <span class="o">=</span> <span class="n">logging</span><span class="o">.</span><span class="n">Formatter</span><span class="p">(</span><span class="s2">"[</span><span class="si">%(levelname)s</span><span class="s2">] - </span><span class="si">%(message)s</span><span class="s2">"</span><span class="p">)</span>
+</span><span id="L-30"><a href="#L-30"><span class="linenos">30</span></a> <span class="n">stream_handler</span><span class="o">.</span><span class="n">setFormatter</span><span class="p">(</span><span class="n">stream_formatter</span><span class="p">)</span>
+</span><span id="L-31"><a href="#L-31"><span class="linenos">31</span></a>
+</span><span id="L-32"><a href="#L-32"><span class="linenos">32</span></a> <span class="c1"># Add the handlers to the logger</span>
+</span><span id="L-33"><a href="#L-33"><span class="linenos">33</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">addHandler</span><span class="p">(</span><span class="n">file_handler</span><span class="p">)</span>
+</span><span id="L-34"><a href="#L-34"><span class="linenos">34</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">addHandler</span><span class="p">(</span><span class="n">stream_handler</span><span class="p">)</span>
+</span><span id="L-35"><a href="#L-35"><span class="linenos">35</span></a>
+</span><span id="L-36"><a href="#L-36"><span class="linenos">36</span></a> <span class="k">return</span> <span class="n">logger</span>
+</span><span id="L-37"><a href="#L-37"><span class="linenos">37</span></a>
+</span><span id="L-38"><a href="#L-38"><span class="linenos">38</span></a>
+</span><span id="L-39"><a href="#L-39"><span class="linenos">39</span></a><span class="k">def</span><span class="w"> </span><span class="nf">set_log_level</span><span class="p">(</span><span class="n">log_level</span><span class="p">:</span> <span class="nb">int</span><span class="p">):</span>
+</span><span id="L-40"><a href="#L-40"><span class="linenos">40</span></a><span class="w"> </span><span class="sd">"""Sets the log level for the acmc logger"""</span>
+</span><span id="L-41"><a href="#L-41"><span class="linenos">41</span></a> <span class="n">logger</span> <span class="o">=</span> <span class="n">logging</span><span class="o">.</span><span class="n">getLogger</span><span class="p">(</span><span class="s2">"acmc_logger"</span><span class="p">)</span>
+</span><span id="L-42"><a href="#L-42"><span class="linenos">42</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">setLevel</span><span class="p">(</span><span class="n">log_level</span><span class="p">)</span> <span class="c1"># Set logger level</span>
+</span><span id="L-43"><a href="#L-43"><span class="linenos">43</span></a>
+</span><span id="L-44"><a href="#L-44"><span class="linenos">44</span></a> <span class="c1"># Also update handlers to match the new level</span>
+</span><span id="L-45"><a href="#L-45"><span class="linenos">45</span></a> <span class="k">for</span> <span class="n">handler</span> <span class="ow">in</span> <span class="n">logger</span><span class="o">.</span><span class="n">handlers</span><span class="p">:</span>
+</span><span id="L-46"><a href="#L-46"><span class="linenos">46</span></a> <span class="n">handler</span><span class="o">.</span><span class="n">setLevel</span><span class="p">(</span><span class="n">log_level</span><span class="p">)</span>
+</span></pre></div>
+
+
+ </section>
+ <section id="DEFAULT_LOG_FILE">
+ <div class="attr variable">
+ <span class="name">DEFAULT_LOG_FILE</span> =
+<span class="default_value">'acmc.log'</span>
+
+
+ </div>
+ <a class="headerlink" href="#DEFAULT_LOG_FILE"></a>
+
+
+
+ </section>
+ <section id="setup_logger">
+ <input id="setup_logger-view-source" class="view-source-toggle-state" type="checkbox" aria-hidden="true" tabindex="-1">
+<div class="attr function">
+
+ <span class="def">def</span>
+ <span class="name">setup_logger</span><span class="signature pdoc-code condensed">(<span class="param"><span class="n">log_level</span><span class="p">:</span> <span class="nb">int</span> <span class="o">=</span> <span class="mi">20</span></span><span class="return-annotation">):</span></span>
+
+ <label class="view-source-button" for="setup_logger-view-source"><span>View Source</span></label>
+
+ </div>
+ <a class="headerlink" href="#setup_logger"></a>
+ <div class="pdoc-code codehilite"><pre><span></span><span id="setup_logger-8"><a href="#setup_logger-8"><span class="linenos"> 8</span></a><span class="k">def</span><span class="w"> </span><span class="nf">setup_logger</span><span class="p">(</span><span class="n">log_level</span><span class="p">:</span> <span class="nb">int</span> <span class="o">=</span> <span class="n">logging</span><span class="o">.</span><span class="n">INFO</span><span class="p">):</span>
+</span><span id="setup_logger-9"><a href="#setup_logger-9"><span class="linenos"> 9</span></a><span class="w"> </span><span class="sd">"""Sets up logger as a singleton outputing to file and sysout syserr"""</span>
+</span><span id="setup_logger-10"><a href="#setup_logger-10"><span class="linenos">10</span></a> <span class="c1"># Create a logger</span>
+</span><span id="setup_logger-11"><a href="#setup_logger-11"><span class="linenos">11</span></a> <span class="n">logger</span> <span class="o">=</span> <span class="n">logging</span><span class="o">.</span><span class="n">getLogger</span><span class="p">(</span><span class="s2">"acmc_logger"</span><span class="p">)</span>
+</span><span id="setup_logger-12"><a href="#setup_logger-12"><span class="linenos">12</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">setLevel</span><span class="p">(</span><span class="n">logging</span><span class="o">.</span><span class="n">INFO</span><span class="p">)</span>
+</span><span id="setup_logger-13"><a href="#setup_logger-13"><span class="linenos">13</span></a>
+</span><span id="setup_logger-14"><a href="#setup_logger-14"><span class="linenos">14</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="n">logger</span><span class="o">.</span><span class="n">hasHandlers</span><span class="p">():</span>
+</span><span id="setup_logger-15"><a href="#setup_logger-15"><span class="linenos">15</span></a> <span class="c1"># Create a file handler that logs to a file</span>
+</span><span id="setup_logger-16"><a href="#setup_logger-16"><span class="linenos">16</span></a> <span class="n">file_handler</span> <span class="o">=</span> <span class="n">logging</span><span class="o">.</span><span class="n">FileHandler</span><span class="p">(</span><span class="n">DEFAULT_LOG_FILE</span><span class="p">)</span>
+</span><span id="setup_logger-17"><a href="#setup_logger-17"><span class="linenos">17</span></a> <span class="n">file_handler</span><span class="o">.</span><span class="n">setLevel</span><span class="p">(</span><span class="n">logging</span><span class="o">.</span><span class="n">INFO</span><span class="p">)</span>
+</span><span id="setup_logger-18"><a href="#setup_logger-18"><span class="linenos">18</span></a>
+</span><span id="setup_logger-19"><a href="#setup_logger-19"><span class="linenos">19</span></a> <span class="c1"># Create a stream handler that prints to the console</span>
+</span><span id="setup_logger-20"><a href="#setup_logger-20"><span class="linenos">20</span></a> <span class="n">stream_handler</span> <span class="o">=</span> <span class="n">logging</span><span class="o">.</span><span class="n">StreamHandler</span><span class="p">()</span>
+</span><span id="setup_logger-21"><a href="#setup_logger-21"><span class="linenos">21</span></a> <span class="n">stream_handler</span><span class="o">.</span><span class="n">setLevel</span><span class="p">(</span><span class="n">logging</span><span class="o">.</span><span class="n">INFO</span><span class="p">)</span>
+</span><span id="setup_logger-22"><a href="#setup_logger-22"><span class="linenos">22</span></a>
+</span><span id="setup_logger-23"><a href="#setup_logger-23"><span class="linenos">23</span></a> <span class="c1"># Create a formatter for how the log messages should look</span>
+</span><span id="setup_logger-24"><a href="#setup_logger-24"><span class="linenos">24</span></a>
+</span><span id="setup_logger-25"><a href="#setup_logger-25"><span class="linenos">25</span></a> <span class="c1"># Add the formatter to both handlers</span>
+</span><span id="setup_logger-26"><a href="#setup_logger-26"><span class="linenos">26</span></a> <span class="n">file_formatter</span> <span class="o">=</span> <span class="n">logging</span><span class="o">.</span><span class="n">Formatter</span><span class="p">(</span>
+</span><span id="setup_logger-27"><a href="#setup_logger-27"><span class="linenos">27</span></a> <span class="s2">"</span><span class="si">%(asctime)s</span><span class="s2"> - - </span><span class="si">%(levelname)s</span><span class="s2"> - </span><span class="si">%(message)s</span><span class="s2">"</span>
+</span><span id="setup_logger-28"><a href="#setup_logger-28"><span class="linenos">28</span></a> <span class="p">)</span>
+</span><span id="setup_logger-29"><a href="#setup_logger-29"><span class="linenos">29</span></a> <span class="n">file_handler</span><span class="o">.</span><span class="n">setFormatter</span><span class="p">(</span><span class="n">file_formatter</span><span class="p">)</span>
+</span><span id="setup_logger-30"><a href="#setup_logger-30"><span class="linenos">30</span></a> <span class="n">stream_formatter</span> <span class="o">=</span> <span class="n">logging</span><span class="o">.</span><span class="n">Formatter</span><span class="p">(</span><span class="s2">"[</span><span class="si">%(levelname)s</span><span class="s2">] - </span><span class="si">%(message)s</span><span class="s2">"</span><span class="p">)</span>
+</span><span id="setup_logger-31"><a href="#setup_logger-31"><span class="linenos">31</span></a> <span class="n">stream_handler</span><span class="o">.</span><span class="n">setFormatter</span><span class="p">(</span><span class="n">stream_formatter</span><span class="p">)</span>
+</span><span id="setup_logger-32"><a href="#setup_logger-32"><span class="linenos">32</span></a>
+</span><span id="setup_logger-33"><a href="#setup_logger-33"><span class="linenos">33</span></a> <span class="c1"># Add the handlers to the logger</span>
+</span><span id="setup_logger-34"><a href="#setup_logger-34"><span class="linenos">34</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">addHandler</span><span class="p">(</span><span class="n">file_handler</span><span class="p">)</span>
+</span><span id="setup_logger-35"><a href="#setup_logger-35"><span class="linenos">35</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">addHandler</span><span class="p">(</span><span class="n">stream_handler</span><span class="p">)</span>
+</span><span id="setup_logger-36"><a href="#setup_logger-36"><span class="linenos">36</span></a>
+</span><span id="setup_logger-37"><a href="#setup_logger-37"><span class="linenos">37</span></a> <span class="k">return</span> <span class="n">logger</span>
+</span></pre></div>
+
+
+ <div class="docstring"><p>Sets up logger as a singleton outputing to file and sysout syserr</p>
+</div>
+
+
+ </section>
+ <section id="set_log_level">
+ <input id="set_log_level-view-source" class="view-source-toggle-state" type="checkbox" aria-hidden="true" tabindex="-1">
+<div class="attr function">
+
+ <span class="def">def</span>
+ <span class="name">set_log_level</span><span class="signature pdoc-code condensed">(<span class="param"><span class="n">log_level</span><span class="p">:</span> <span class="nb">int</span></span><span class="return-annotation">):</span></span>
+
+ <label class="view-source-button" for="set_log_level-view-source"><span>View Source</span></label>
+
+ </div>
+ <a class="headerlink" href="#set_log_level"></a>
+ <div class="pdoc-code codehilite"><pre><span></span><span id="set_log_level-40"><a href="#set_log_level-40"><span class="linenos">40</span></a><span class="k">def</span><span class="w"> </span><span class="nf">set_log_level</span><span class="p">(</span><span class="n">log_level</span><span class="p">:</span> <span class="nb">int</span><span class="p">):</span>
+</span><span id="set_log_level-41"><a href="#set_log_level-41"><span class="linenos">41</span></a><span class="w"> </span><span class="sd">"""Sets the log level for the acmc logger"""</span>
+</span><span id="set_log_level-42"><a href="#set_log_level-42"><span class="linenos">42</span></a> <span class="n">logger</span> <span class="o">=</span> <span class="n">logging</span><span class="o">.</span><span class="n">getLogger</span><span class="p">(</span><span class="s2">"acmc_logger"</span><span class="p">)</span>
+</span><span id="set_log_level-43"><a href="#set_log_level-43"><span class="linenos">43</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">setLevel</span><span class="p">(</span><span class="n">log_level</span><span class="p">)</span> <span class="c1"># Set logger level</span>
+</span><span id="set_log_level-44"><a href="#set_log_level-44"><span class="linenos">44</span></a>
+</span><span id="set_log_level-45"><a href="#set_log_level-45"><span class="linenos">45</span></a> <span class="c1"># Also update handlers to match the new level</span>
+</span><span id="set_log_level-46"><a href="#set_log_level-46"><span class="linenos">46</span></a> <span class="k">for</span> <span class="n">handler</span> <span class="ow">in</span> <span class="n">logger</span><span class="o">.</span><span class="n">handlers</span><span class="p">:</span>
+</span><span id="set_log_level-47"><a href="#set_log_level-47"><span class="linenos">47</span></a> <span class="n">handler</span><span class="o">.</span><span class="n">setLevel</span><span class="p">(</span><span class="n">log_level</span><span class="p">)</span>
+</span></pre></div>
+
+
+ <div class="docstring"><p>Sets the log level for the acmc logger</p>
+</div>
+
+
+ </section>
+ </main>
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diff --git a/docs/api/acmc/main.html b/docs/api/acmc/main.html
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+<!doctype html>
+<html lang="en">
+<head>
+ <meta charset="utf-8">
+ <meta name="viewport" content="width=device-width, initial-scale=1">
+ <meta name="generator" content="pdoc 15.0.1"/>
+ <title>acmc.main API documentation</title>
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+ <style>/*! theme.css */:root{--pdoc-background:#fff;}.pdoc{--text:#212529;--muted:#6c757d;--link:#3660a5;--link-hover:#1659c5;--code:#f8f8f8;--active:#fff598;--accent:#eee;--accent2:#c1c1c1;--nav-hover:rgba(255, 255, 255, 0.5);--name:#0066BB;--def:#008800;--annotation:#007020;}</style>
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+ <style>/*! custom.css */</style></head>
+<body>
+ <nav class="pdoc">
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+ <input id="togglestate" type="checkbox" aria-hidden="true" tabindex="-1">
+ <div> <a class="pdoc-button module-list-button" href="../acmc.html">
+<svg xmlns="http://www.w3.org/2000/svg" width="16" height="16" fill="currentColor" class="bi bi-box-arrow-in-left" viewBox="0 0 16 16">
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+</svg> acmc</a>
+
+
+ <input type="search" placeholder="Search..." role="searchbox" aria-label="search"
+ pattern=".+" required>
+
+
+
+ <h2>API Documentation</h2>
+ <ul class="memberlist">
+ <li>
+ <a class="variable" href="#logger">logger</a>
+ </li>
+ <li>
+ <a class="variable" href="#DEFAULT_WORKSPACE_PATH">DEFAULT_WORKSPACE_PATH</a>
+ </li>
+ <li>
+ <a class="function" href="#trud_install">trud_install</a>
+ </li>
+ <li>
+ <a class="function" href="#omop_install">omop_install</a>
+ </li>
+ <li>
+ <a class="function" href="#omop_clear">omop_clear</a>
+ </li>
+ <li>
+ <a class="function" href="#omop_delete">omop_delete</a>
+ </li>
+ <li>
+ <a class="function" href="#phen_init">phen_init</a>
+ </li>
+ <li>
+ <a class="function" href="#phen_fork">phen_fork</a>
+ </li>
+ <li>
+ <a class="function" href="#phen_validate">phen_validate</a>
+ </li>
+ <li>
+ <a class="function" href="#phen_map">phen_map</a>
+ </li>
+ <li>
+ <a class="function" href="#phen_export">phen_export</a>
+ </li>
+ <li>
+ <a class="function" href="#phen_publish">phen_publish</a>
+ </li>
+ <li>
+ <a class="function" href="#phen_copy">phen_copy</a>
+ </li>
+ <li>
+ <a class="function" href="#phen_diff">phen_diff</a>
+ </li>
+ <li>
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+ <div class="pdoc-code codehilite"><pre><span></span><span id="L-1"><a href="#L-1"><span class="linenos"> 1</span></a><span class="kn">import</span><span class="w"> </span><span class="nn">argparse</span>
+</span><span id="L-2"><a href="#L-2"><span class="linenos"> 2</span></a><span class="kn">import</span><span class="w"> </span><span class="nn">logging</span>
+</span><span id="L-3"><a href="#L-3"><span class="linenos"> 3</span></a><span class="kn">from</span><span class="w"> </span><span class="nn">pathlib</span><span class="w"> </span><span class="kn">import</span> <span class="n">Path</span>
+</span><span id="L-4"><a href="#L-4"><span class="linenos"> 4</span></a>
+</span><span id="L-5"><a href="#L-5"><span class="linenos"> 5</span></a><span class="kn">import</span><span class="w"> </span><span class="nn">acmc</span>
+</span><span id="L-6"><a href="#L-6"><span class="linenos"> 6</span></a><span class="kn">from</span><span class="w"> </span><span class="nn">acmc</span><span class="w"> </span><span class="kn">import</span> <span class="n">trud</span><span class="p">,</span> <span class="n">omop</span><span class="p">,</span> <span class="n">phen</span><span class="p">,</span> <span class="n">parse</span><span class="p">,</span> <span class="n">logging_config</span> <span class="k">as</span> <span class="n">lc</span>
+</span><span id="L-7"><a href="#L-7"><span class="linenos"> 7</span></a>
+</span><span id="L-8"><a href="#L-8"><span class="linenos"> 8</span></a><span class="c1"># setup logging</span>
+</span><span id="L-9"><a href="#L-9"><span class="linenos"> 9</span></a><span class="n">logger</span> <span class="o">=</span> <span class="n">lc</span><span class="o">.</span><span class="n">setup_logger</span><span class="p">()</span>
+</span><span id="L-10"><a href="#L-10"><span class="linenos"> 10</span></a>
+</span><span id="L-11"><a href="#L-11"><span class="linenos"> 11</span></a><span class="n">DEFAULT_WORKSPACE_PATH</span> <span class="o">=</span> <span class="n">Path</span><span class="p">(</span><span class="s2">"./workspace"</span><span class="p">)</span>
+</span><span id="L-12"><a href="#L-12"><span class="linenos"> 12</span></a>
+</span><span id="L-13"><a href="#L-13"><span class="linenos"> 13</span></a>
+</span><span id="L-14"><a href="#L-14"><span class="linenos"> 14</span></a><span class="k">def</span><span class="w"> </span><span class="nf">trud_install</span><span class="p">(</span><span class="n">args</span><span class="p">:</span> <span class="n">argparse</span><span class="o">.</span><span class="n">Namespace</span><span class="p">):</span>
+</span><span id="L-15"><a href="#L-15"><span class="linenos"> 15</span></a><span class="w"> </span><span class="sd">"""Handle the `trud install` command."""</span>
+</span><span id="L-16"><a href="#L-16"><span class="linenos"> 16</span></a> <span class="n">trud</span><span class="o">.</span><span class="n">install</span><span class="p">()</span>
+</span><span id="L-17"><a href="#L-17"><span class="linenos"> 17</span></a>
+</span><span id="L-18"><a href="#L-18"><span class="linenos"> 18</span></a>
+</span><span id="L-19"><a href="#L-19"><span class="linenos"> 19</span></a><span class="k">def</span><span class="w"> </span><span class="nf">omop_install</span><span class="p">(</span><span class="n">args</span><span class="p">:</span> <span class="n">argparse</span><span class="o">.</span><span class="n">Namespace</span><span class="p">):</span>
+</span><span id="L-20"><a href="#L-20"><span class="linenos"> 20</span></a><span class="w"> </span><span class="sd">"""Handle the `omop install` command."""</span>
+</span><span id="L-21"><a href="#L-21"><span class="linenos"> 21</span></a> <span class="n">omop</span><span class="o">.</span><span class="n">install</span><span class="p">(</span><span class="n">args</span><span class="o">.</span><span class="n">omop_zip_file</span><span class="p">,</span> <span class="n">args</span><span class="o">.</span><span class="n">version</span><span class="p">)</span>
+</span><span id="L-22"><a href="#L-22"><span class="linenos"> 22</span></a>
+</span><span id="L-23"><a href="#L-23"><span class="linenos"> 23</span></a>
+</span><span id="L-24"><a href="#L-24"><span class="linenos"> 24</span></a><span class="k">def</span><span class="w"> </span><span class="nf">omop_clear</span><span class="p">(</span><span class="n">args</span><span class="p">:</span> <span class="n">argparse</span><span class="o">.</span><span class="n">Namespace</span><span class="p">):</span>
+</span><span id="L-25"><a href="#L-25"><span class="linenos"> 25</span></a><span class="w"> </span><span class="sd">"""Handle the `omop clear` command."""</span>
+</span><span id="L-26"><a href="#L-26"><span class="linenos"> 26</span></a> <span class="n">omop</span><span class="o">.</span><span class="n">clear</span><span class="p">(</span><span class="n">omop</span><span class="o">.</span><span class="n">DB_PATH</span><span class="p">)</span>
+</span><span id="L-27"><a href="#L-27"><span class="linenos"> 27</span></a>
+</span><span id="L-28"><a href="#L-28"><span class="linenos"> 28</span></a>
+</span><span id="L-29"><a href="#L-29"><span class="linenos"> 29</span></a><span class="k">def</span><span class="w"> </span><span class="nf">omop_delete</span><span class="p">(</span><span class="n">args</span><span class="p">:</span> <span class="n">argparse</span><span class="o">.</span><span class="n">Namespace</span><span class="p">):</span>
+</span><span id="L-30"><a href="#L-30"><span class="linenos"> 30</span></a><span class="w"> </span><span class="sd">"""Handle the `omop delete` command."""</span>
+</span><span id="L-31"><a href="#L-31"><span class="linenos"> 31</span></a> <span class="n">omop</span><span class="o">.</span><span class="n">delete</span><span class="p">(</span><span class="n">omop</span><span class="o">.</span><span class="n">DB_PATH</span><span class="p">)</span>
+</span><span id="L-32"><a href="#L-32"><span class="linenos"> 32</span></a>
+</span><span id="L-33"><a href="#L-33"><span class="linenos"> 33</span></a>
+</span><span id="L-34"><a href="#L-34"><span class="linenos"> 34</span></a><span class="k">def</span><span class="w"> </span><span class="nf">phen_init</span><span class="p">(</span><span class="n">args</span><span class="p">:</span> <span class="n">argparse</span><span class="o">.</span><span class="n">Namespace</span><span class="p">):</span>
+</span><span id="L-35"><a href="#L-35"><span class="linenos"> 35</span></a><span class="w"> </span><span class="sd">"""Handle the `phen init` command."""</span>
+</span><span id="L-36"><a href="#L-36"><span class="linenos"> 36</span></a> <span class="n">phen</span><span class="o">.</span><span class="n">init</span><span class="p">(</span><span class="n">args</span><span class="o">.</span><span class="n">phen_dir</span><span class="p">,</span> <span class="n">args</span><span class="o">.</span><span class="n">remote_url</span><span class="p">)</span>
+</span><span id="L-37"><a href="#L-37"><span class="linenos"> 37</span></a>
+</span><span id="L-38"><a href="#L-38"><span class="linenos"> 38</span></a>
+</span><span id="L-39"><a href="#L-39"><span class="linenos"> 39</span></a><span class="k">def</span><span class="w"> </span><span class="nf">phen_fork</span><span class="p">(</span><span class="n">args</span><span class="p">:</span> <span class="n">argparse</span><span class="o">.</span><span class="n">Namespace</span><span class="p">):</span>
+</span><span id="L-40"><a href="#L-40"><span class="linenos"> 40</span></a><span class="w"> </span><span class="sd">"""Handle the `phen fork` command."""</span>
+</span><span id="L-41"><a href="#L-41"><span class="linenos"> 41</span></a> <span class="n">phen</span><span class="o">.</span><span class="n">fork</span><span class="p">(</span>
+</span><span id="L-42"><a href="#L-42"><span class="linenos"> 42</span></a> <span class="n">args</span><span class="o">.</span><span class="n">phen_dir</span><span class="p">,</span>
+</span><span id="L-43"><a href="#L-43"><span class="linenos"> 43</span></a> <span class="n">args</span><span class="o">.</span><span class="n">upstream_url</span><span class="p">,</span>
+</span><span id="L-44"><a href="#L-44"><span class="linenos"> 44</span></a> <span class="n">args</span><span class="o">.</span><span class="n">upstream_version</span><span class="p">,</span>
+</span><span id="L-45"><a href="#L-45"><span class="linenos"> 45</span></a> <span class="n">new_origin_url</span><span class="o">=</span><span class="n">args</span><span class="o">.</span><span class="n">remote_url</span><span class="p">,</span>
+</span><span id="L-46"><a href="#L-46"><span class="linenos"> 46</span></a> <span class="p">)</span>
+</span><span id="L-47"><a href="#L-47"><span class="linenos"> 47</span></a>
+</span><span id="L-48"><a href="#L-48"><span class="linenos"> 48</span></a>
+</span><span id="L-49"><a href="#L-49"><span class="linenos"> 49</span></a><span class="k">def</span><span class="w"> </span><span class="nf">phen_validate</span><span class="p">(</span><span class="n">args</span><span class="p">:</span> <span class="n">argparse</span><span class="o">.</span><span class="n">Namespace</span><span class="p">):</span>
+</span><span id="L-50"><a href="#L-50"><span class="linenos"> 50</span></a><span class="w"> </span><span class="sd">"""Handle the `phen validate` command."""</span>
+</span><span id="L-51"><a href="#L-51"><span class="linenos"> 51</span></a> <span class="n">phen</span><span class="o">.</span><span class="n">validate</span><span class="p">(</span><span class="n">args</span><span class="o">.</span><span class="n">phen_dir</span><span class="p">)</span>
+</span><span id="L-52"><a href="#L-52"><span class="linenos"> 52</span></a>
+</span><span id="L-53"><a href="#L-53"><span class="linenos"> 53</span></a>
+</span><span id="L-54"><a href="#L-54"><span class="linenos"> 54</span></a><span class="k">def</span><span class="w"> </span><span class="nf">phen_map</span><span class="p">(</span><span class="n">args</span><span class="p">:</span> <span class="n">argparse</span><span class="o">.</span><span class="n">Namespace</span><span class="p">):</span>
+</span><span id="L-55"><a href="#L-55"><span class="linenos"> 55</span></a><span class="w"> </span><span class="sd">"""Handle the `phen map` command."""</span>
+</span><span id="L-56"><a href="#L-56"><span class="linenos"> 56</span></a> <span class="n">phen</span><span class="o">.</span><span class="n">map</span><span class="p">(</span><span class="n">args</span><span class="o">.</span><span class="n">phen_dir</span><span class="p">,</span> <span class="n">args</span><span class="o">.</span><span class="n">target_coding</span><span class="p">)</span>
+</span><span id="L-57"><a href="#L-57"><span class="linenos"> 57</span></a>
+</span><span id="L-58"><a href="#L-58"><span class="linenos"> 58</span></a>
+</span><span id="L-59"><a href="#L-59"><span class="linenos"> 59</span></a><span class="k">def</span><span class="w"> </span><span class="nf">phen_export</span><span class="p">(</span><span class="n">args</span><span class="p">:</span> <span class="n">argparse</span><span class="o">.</span><span class="n">Namespace</span><span class="p">):</span>
+</span><span id="L-60"><a href="#L-60"><span class="linenos"> 60</span></a><span class="w"> </span><span class="sd">"""Handle the `phen copy` command."""</span>
+</span><span id="L-61"><a href="#L-61"><span class="linenos"> 61</span></a> <span class="n">phen</span><span class="o">.</span><span class="n">export</span><span class="p">(</span><span class="n">args</span><span class="o">.</span><span class="n">phen_dir</span><span class="p">,</span> <span class="n">args</span><span class="o">.</span><span class="n">version</span><span class="p">)</span>
+</span><span id="L-62"><a href="#L-62"><span class="linenos"> 62</span></a>
+</span><span id="L-63"><a href="#L-63"><span class="linenos"> 63</span></a>
+</span><span id="L-64"><a href="#L-64"><span class="linenos"> 64</span></a><span class="k">def</span><span class="w"> </span><span class="nf">phen_publish</span><span class="p">(</span><span class="n">args</span><span class="p">:</span> <span class="n">argparse</span><span class="o">.</span><span class="n">Namespace</span><span class="p">):</span>
+</span><span id="L-65"><a href="#L-65"><span class="linenos"> 65</span></a><span class="w"> </span><span class="sd">"""Handle the `phen publish` command."""</span>
+</span><span id="L-66"><a href="#L-66"><span class="linenos"> 66</span></a> <span class="n">phen</span><span class="o">.</span><span class="n">publish</span><span class="p">(</span><span class="n">args</span><span class="o">.</span><span class="n">phen_dir</span><span class="p">,</span> <span class="n">args</span><span class="o">.</span><span class="n">msg</span><span class="p">,</span> <span class="n">args</span><span class="o">.</span><span class="n">remote_url</span><span class="p">,</span> <span class="n">args</span><span class="o">.</span><span class="n">increment</span><span class="p">)</span>
+</span><span id="L-67"><a href="#L-67"><span class="linenos"> 67</span></a>
+</span><span id="L-68"><a href="#L-68"><span class="linenos"> 68</span></a>
+</span><span id="L-69"><a href="#L-69"><span class="linenos"> 69</span></a><span class="k">def</span><span class="w"> </span><span class="nf">phen_copy</span><span class="p">(</span><span class="n">args</span><span class="p">:</span> <span class="n">argparse</span><span class="o">.</span><span class="n">Namespace</span><span class="p">):</span>
+</span><span id="L-70"><a href="#L-70"><span class="linenos"> 70</span></a><span class="w"> </span><span class="sd">"""Handle the `phen copy` command."""</span>
+</span><span id="L-71"><a href="#L-71"><span class="linenos"> 71</span></a> <span class="n">phen</span><span class="o">.</span><span class="n">copy</span><span class="p">(</span><span class="n">args</span><span class="o">.</span><span class="n">phen_dir</span><span class="p">,</span> <span class="n">args</span><span class="o">.</span><span class="n">target_dir</span><span class="p">,</span> <span class="n">args</span><span class="o">.</span><span class="n">version</span><span class="p">)</span>
+</span><span id="L-72"><a href="#L-72"><span class="linenos"> 72</span></a>
+</span><span id="L-73"><a href="#L-73"><span class="linenos"> 73</span></a>
+</span><span id="L-74"><a href="#L-74"><span class="linenos"> 74</span></a><span class="k">def</span><span class="w"> </span><span class="nf">phen_diff</span><span class="p">(</span><span class="n">args</span><span class="p">:</span> <span class="n">argparse</span><span class="o">.</span><span class="n">Namespace</span><span class="p">):</span>
+</span><span id="L-75"><a href="#L-75"><span class="linenos"> 75</span></a><span class="w"> </span><span class="sd">"""Handle the `phen diff` command."""</span>
+</span><span id="L-76"><a href="#L-76"><span class="linenos"> 76</span></a> <span class="n">phen</span><span class="o">.</span><span class="n">diff</span><span class="p">(</span><span class="n">args</span><span class="o">.</span><span class="n">phen_dir</span><span class="p">,</span> <span class="n">args</span><span class="o">.</span><span class="n">version</span><span class="p">,</span> <span class="n">args</span><span class="o">.</span><span class="n">old_phen_dir</span><span class="p">,</span> <span class="n">args</span><span class="o">.</span><span class="n">old_version</span><span class="p">)</span>
+</span><span id="L-77"><a href="#L-77"><span class="linenos"> 77</span></a>
+</span><span id="L-78"><a href="#L-78"><span class="linenos"> 78</span></a>
+</span><span id="L-79"><a href="#L-79"><span class="linenos"> 79</span></a><span class="k">def</span><span class="w"> </span><span class="nf">main</span><span class="p">():</span>
+</span><span id="L-80"><a href="#L-80"><span class="linenos"> 80</span></a> <span class="n">parser</span> <span class="o">=</span> <span class="n">argparse</span><span class="o">.</span><span class="n">ArgumentParser</span><span class="p">(</span><span class="n">description</span><span class="o">=</span><span class="s2">"ACMC command-line tool"</span><span class="p">)</span>
+</span><span id="L-81"><a href="#L-81"><span class="linenos"> 81</span></a> <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s2">"--debug"</span><span class="p">,</span> <span class="n">action</span><span class="o">=</span><span class="s2">"store_true"</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s2">"Enable debug mode"</span><span class="p">)</span>
+</span><span id="L-82"><a href="#L-82"><span class="linenos"> 82</span></a> <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span>
+</span><span id="L-83"><a href="#L-83"><span class="linenos"> 83</span></a> <span class="s2">"--version"</span><span class="p">,</span> <span class="n">action</span><span class="o">=</span><span class="s2">"version"</span><span class="p">,</span> <span class="n">version</span><span class="o">=</span><span class="sa">f</span><span class="s2">"acmc </span><span class="si">{</span><span class="n">acmc</span><span class="o">.</span><span class="n">__version__</span><span class="si">}</span><span class="s2">"</span>
+</span><span id="L-84"><a href="#L-84"><span class="linenos"> 84</span></a> <span class="p">)</span>
+</span><span id="L-85"><a href="#L-85"><span class="linenos"> 85</span></a>
+</span><span id="L-86"><a href="#L-86"><span class="linenos"> 86</span></a> <span class="c1"># Top-level commands</span>
+</span><span id="L-87"><a href="#L-87"><span class="linenos"> 87</span></a> <span class="n">subparsers</span> <span class="o">=</span> <span class="n">parser</span><span class="o">.</span><span class="n">add_subparsers</span><span class="p">(</span>
+</span><span id="L-88"><a href="#L-88"><span class="linenos"> 88</span></a> <span class="n">dest</span><span class="o">=</span><span class="s2">"command"</span><span class="p">,</span> <span class="n">required</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s2">"Available commands"</span>
+</span><span id="L-89"><a href="#L-89"><span class="linenos"> 89</span></a> <span class="p">)</span>
+</span><span id="L-90"><a href="#L-90"><span class="linenos"> 90</span></a>
+</span><span id="L-91"><a href="#L-91"><span class="linenos"> 91</span></a> <span class="c1">### TRUD Command ###</span>
+</span><span id="L-92"><a href="#L-92"><span class="linenos"> 92</span></a> <span class="n">trud_parser</span> <span class="o">=</span> <span class="n">subparsers</span><span class="o">.</span><span class="n">add_parser</span><span class="p">(</span><span class="s2">"trud"</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s2">"TRUD commands"</span><span class="p">)</span>
+</span><span id="L-93"><a href="#L-93"><span class="linenos"> 93</span></a> <span class="n">trud_subparsers</span> <span class="o">=</span> <span class="n">trud_parser</span><span class="o">.</span><span class="n">add_subparsers</span><span class="p">(</span>
+</span><span id="L-94"><a href="#L-94"><span class="linenos"> 94</span></a> <span class="n">dest</span><span class="o">=</span><span class="s2">"subcommand"</span><span class="p">,</span> <span class="n">required</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s2">"TRUD subcommands"</span>
+</span><span id="L-95"><a href="#L-95"><span class="linenos"> 95</span></a> <span class="p">)</span>
+</span><span id="L-96"><a href="#L-96"><span class="linenos"> 96</span></a>
+</span><span id="L-97"><a href="#L-97"><span class="linenos"> 97</span></a> <span class="c1"># trud install</span>
+</span><span id="L-98"><a href="#L-98"><span class="linenos"> 98</span></a> <span class="n">trud_install_parser</span> <span class="o">=</span> <span class="n">trud_subparsers</span><span class="o">.</span><span class="n">add_parser</span><span class="p">(</span>
+</span><span id="L-99"><a href="#L-99"><span class="linenos"> 99</span></a> <span class="s2">"install"</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s2">"Install TRUD components"</span>
+</span><span id="L-100"><a href="#L-100"><span class="linenos">100</span></a> <span class="p">)</span>
+</span><span id="L-101"><a href="#L-101"><span class="linenos">101</span></a> <span class="n">trud_install_parser</span><span class="o">.</span><span class="n">set_defaults</span><span class="p">(</span><span class="n">func</span><span class="o">=</span><span class="n">trud_install</span><span class="p">)</span>
+</span><span id="L-102"><a href="#L-102"><span class="linenos">102</span></a>
+</span><span id="L-103"><a href="#L-103"><span class="linenos">103</span></a> <span class="c1">### OMOP Command ###</span>
+</span><span id="L-104"><a href="#L-104"><span class="linenos">104</span></a> <span class="n">omop_parser</span> <span class="o">=</span> <span class="n">subparsers</span><span class="o">.</span><span class="n">add_parser</span><span class="p">(</span><span class="s2">"omop"</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s2">"OMOP commands"</span><span class="p">)</span>
+</span><span id="L-105"><a href="#L-105"><span class="linenos">105</span></a> <span class="n">omop_subparsers</span> <span class="o">=</span> <span class="n">omop_parser</span><span class="o">.</span><span class="n">add_subparsers</span><span class="p">(</span>
+</span><span id="L-106"><a href="#L-106"><span class="linenos">106</span></a> <span class="n">dest</span><span class="o">=</span><span class="s2">"subcommand"</span><span class="p">,</span> <span class="n">required</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s2">"OMOP subcommands"</span>
+</span><span id="L-107"><a href="#L-107"><span class="linenos">107</span></a> <span class="p">)</span>
+</span><span id="L-108"><a href="#L-108"><span class="linenos">108</span></a>
+</span><span id="L-109"><a href="#L-109"><span class="linenos">109</span></a> <span class="c1"># omop install</span>
+</span><span id="L-110"><a href="#L-110"><span class="linenos">110</span></a> <span class="n">omop_install_parser</span> <span class="o">=</span> <span class="n">omop_subparsers</span><span class="o">.</span><span class="n">add_parser</span><span class="p">(</span>
+</span><span id="L-111"><a href="#L-111"><span class="linenos">111</span></a> <span class="s2">"install"</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s2">"Install OMOP codes within database"</span>
+</span><span id="L-112"><a href="#L-112"><span class="linenos">112</span></a> <span class="p">)</span>
+</span><span id="L-113"><a href="#L-113"><span class="linenos">113</span></a> <span class="n">omop_install_parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span>
+</span><span id="L-114"><a href="#L-114"><span class="linenos">114</span></a> <span class="s2">"-f"</span><span class="p">,</span> <span class="s2">"--omop-zip-file"</span><span class="p">,</span> <span class="n">required</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s2">"Path to downloaded OMOP zip file"</span>
+</span><span id="L-115"><a href="#L-115"><span class="linenos">115</span></a> <span class="p">)</span>
+</span><span id="L-116"><a href="#L-116"><span class="linenos">116</span></a> <span class="n">omop_install_parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span>
+</span><span id="L-117"><a href="#L-117"><span class="linenos">117</span></a> <span class="s2">"-v"</span><span class="p">,</span> <span class="s2">"--version"</span><span class="p">,</span> <span class="n">required</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s2">"OMOP vocabularies release version"</span>
+</span><span id="L-118"><a href="#L-118"><span class="linenos">118</span></a> <span class="p">)</span>
+</span><span id="L-119"><a href="#L-119"><span class="linenos">119</span></a> <span class="n">omop_install_parser</span><span class="o">.</span><span class="n">set_defaults</span><span class="p">(</span><span class="n">func</span><span class="o">=</span><span class="n">omop_install</span><span class="p">)</span>
+</span><span id="L-120"><a href="#L-120"><span class="linenos">120</span></a>
+</span><span id="L-121"><a href="#L-121"><span class="linenos">121</span></a> <span class="c1"># omop clear</span>
+</span><span id="L-122"><a href="#L-122"><span class="linenos">122</span></a> <span class="n">omop_clear_parser</span> <span class="o">=</span> <span class="n">omop_subparsers</span><span class="o">.</span><span class="n">add_parser</span><span class="p">(</span>
+</span><span id="L-123"><a href="#L-123"><span class="linenos">123</span></a> <span class="s2">"clear"</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s2">"Clear OMOP data from database"</span>
+</span><span id="L-124"><a href="#L-124"><span class="linenos">124</span></a> <span class="p">)</span>
+</span><span id="L-125"><a href="#L-125"><span class="linenos">125</span></a> <span class="n">omop_clear_parser</span><span class="o">.</span><span class="n">set_defaults</span><span class="p">(</span><span class="n">func</span><span class="o">=</span><span class="n">omop_clear</span><span class="p">)</span>
+</span><span id="L-126"><a href="#L-126"><span class="linenos">126</span></a>
+</span><span id="L-127"><a href="#L-127"><span class="linenos">127</span></a> <span class="c1"># omop delete</span>
+</span><span id="L-128"><a href="#L-128"><span class="linenos">128</span></a> <span class="n">omop_delete_parser</span> <span class="o">=</span> <span class="n">omop_subparsers</span><span class="o">.</span><span class="n">add_parser</span><span class="p">(</span>
+</span><span id="L-129"><a href="#L-129"><span class="linenos">129</span></a> <span class="s2">"delete"</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s2">"Delete OMOP database"</span>
+</span><span id="L-130"><a href="#L-130"><span class="linenos">130</span></a> <span class="p">)</span>
+</span><span id="L-131"><a href="#L-131"><span class="linenos">131</span></a> <span class="n">omop_delete_parser</span><span class="o">.</span><span class="n">set_defaults</span><span class="p">(</span><span class="n">func</span><span class="o">=</span><span class="n">omop_delete</span><span class="p">)</span>
+</span><span id="L-132"><a href="#L-132"><span class="linenos">132</span></a>
+</span><span id="L-133"><a href="#L-133"><span class="linenos">133</span></a> <span class="c1">### PHEN Command ###</span>
+</span><span id="L-134"><a href="#L-134"><span class="linenos">134</span></a> <span class="n">phen_parser</span> <span class="o">=</span> <span class="n">subparsers</span><span class="o">.</span><span class="n">add_parser</span><span class="p">(</span><span class="s2">"phen"</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s2">"Phen commands"</span><span class="p">)</span>
+</span><span id="L-135"><a href="#L-135"><span class="linenos">135</span></a> <span class="n">phen_subparsers</span> <span class="o">=</span> <span class="n">phen_parser</span><span class="o">.</span><span class="n">add_subparsers</span><span class="p">(</span>
+</span><span id="L-136"><a href="#L-136"><span class="linenos">136</span></a> <span class="n">dest</span><span class="o">=</span><span class="s2">"subcommand"</span><span class="p">,</span> <span class="n">required</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s2">"Phen subcommands"</span>
+</span><span id="L-137"><a href="#L-137"><span class="linenos">137</span></a> <span class="p">)</span>
+</span><span id="L-138"><a href="#L-138"><span class="linenos">138</span></a>
+</span><span id="L-139"><a href="#L-139"><span class="linenos">139</span></a> <span class="c1"># phen init</span>
+</span><span id="L-140"><a href="#L-140"><span class="linenos">140</span></a> <span class="n">phen_init_parser</span> <span class="o">=</span> <span class="n">phen_subparsers</span><span class="o">.</span><span class="n">add_parser</span><span class="p">(</span>
+</span><span id="L-141"><a href="#L-141"><span class="linenos">141</span></a> <span class="s2">"init"</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s2">"Initiatise phenotype directory"</span>
+</span><span id="L-142"><a href="#L-142"><span class="linenos">142</span></a> <span class="p">)</span>
+</span><span id="L-143"><a href="#L-143"><span class="linenos">143</span></a> <span class="n">phen_init_parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span>
+</span><span id="L-144"><a href="#L-144"><span class="linenos">144</span></a> <span class="s2">"-d"</span><span class="p">,</span>
+</span><span id="L-145"><a href="#L-145"><span class="linenos">145</span></a> <span class="s2">"--phen-dir"</span><span class="p">,</span>
+</span><span id="L-146"><a href="#L-146"><span class="linenos">146</span></a> <span class="nb">type</span><span class="o">=</span><span class="nb">str</span><span class="p">,</span>
+</span><span id="L-147"><a href="#L-147"><span class="linenos">147</span></a> <span class="n">default</span><span class="o">=</span><span class="nb">str</span><span class="p">(</span><span class="n">phen</span><span class="o">.</span><span class="n">DEFAULT_PHEN_PATH</span><span class="o">.</span><span class="n">resolve</span><span class="p">()),</span>
+</span><span id="L-148"><a href="#L-148"><span class="linenos">148</span></a> <span class="n">help</span><span class="o">=</span><span class="s2">"(Optional) Local phenotype workspace directory (default is ./workspace/phen)."</span><span class="p">,</span>
+</span><span id="L-149"><a href="#L-149"><span class="linenos">149</span></a> <span class="p">)</span>
+</span><span id="L-150"><a href="#L-150"><span class="linenos">150</span></a> <span class="n">phen_init_parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span>
+</span><span id="L-151"><a href="#L-151"><span class="linenos">151</span></a> <span class="s2">"-r"</span><span class="p">,</span>
+</span><span id="L-152"><a href="#L-152"><span class="linenos">152</span></a> <span class="s2">"--remote_url"</span><span class="p">,</span>
+</span><span id="L-153"><a href="#L-153"><span class="linenos">153</span></a> <span class="n">help</span><span class="o">=</span><span class="s2">"(Optional) URL to repository where the phenotype will be published."</span><span class="p">,</span>
+</span><span id="L-154"><a href="#L-154"><span class="linenos">154</span></a> <span class="p">)</span>
+</span><span id="L-155"><a href="#L-155"><span class="linenos">155</span></a> <span class="n">phen_init_parser</span><span class="o">.</span><span class="n">set_defaults</span><span class="p">(</span><span class="n">func</span><span class="o">=</span><span class="n">phen_init</span><span class="p">)</span>
+</span><span id="L-156"><a href="#L-156"><span class="linenos">156</span></a>
+</span><span id="L-157"><a href="#L-157"><span class="linenos">157</span></a> <span class="c1"># phen fork</span>
+</span><span id="L-158"><a href="#L-158"><span class="linenos">158</span></a> <span class="n">phen_fork_parser</span> <span class="o">=</span> <span class="n">phen_subparsers</span><span class="o">.</span><span class="n">add_parser</span><span class="p">(</span>
+</span><span id="L-159"><a href="#L-159"><span class="linenos">159</span></a> <span class="s2">"fork"</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s2">"Fork an existing phenotype"</span>
+</span><span id="L-160"><a href="#L-160"><span class="linenos">160</span></a> <span class="p">)</span>
+</span><span id="L-161"><a href="#L-161"><span class="linenos">161</span></a> <span class="n">phen_fork_parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span>
+</span><span id="L-162"><a href="#L-162"><span class="linenos">162</span></a> <span class="s2">"-d"</span><span class="p">,</span>
+</span><span id="L-163"><a href="#L-163"><span class="linenos">163</span></a> <span class="s2">"--phen-dir"</span><span class="p">,</span>
+</span><span id="L-164"><a href="#L-164"><span class="linenos">164</span></a> <span class="nb">type</span><span class="o">=</span><span class="nb">str</span><span class="p">,</span>
+</span><span id="L-165"><a href="#L-165"><span class="linenos">165</span></a> <span class="n">default</span><span class="o">=</span><span class="nb">str</span><span class="p">(</span><span class="n">phen</span><span class="o">.</span><span class="n">DEFAULT_PHEN_PATH</span><span class="o">.</span><span class="n">resolve</span><span class="p">()),</span>
+</span><span id="L-166"><a href="#L-166"><span class="linenos">166</span></a> <span class="n">help</span><span class="o">=</span><span class="s2">"(Optional) Local phenotype workspace directory (default is ./workspace/phen)."</span><span class="p">,</span>
+</span><span id="L-167"><a href="#L-167"><span class="linenos">167</span></a> <span class="p">)</span>
+</span><span id="L-168"><a href="#L-168"><span class="linenos">168</span></a> <span class="n">phen_fork_parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span>
+</span><span id="L-169"><a href="#L-169"><span class="linenos">169</span></a> <span class="s2">"-r"</span><span class="p">,</span>
+</span><span id="L-170"><a href="#L-170"><span class="linenos">170</span></a> <span class="s2">"--remote_url"</span><span class="p">,</span>
+</span><span id="L-171"><a href="#L-171"><span class="linenos">171</span></a> <span class="n">help</span><span class="o">=</span><span class="s2">"(Optional) URL to repository where the forked phenotype will be published."</span><span class="p">,</span>
+</span><span id="L-172"><a href="#L-172"><span class="linenos">172</span></a> <span class="p">)</span>
+</span><span id="L-173"><a href="#L-173"><span class="linenos">173</span></a> <span class="n">phen_fork_parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span>
+</span><span id="L-174"><a href="#L-174"><span class="linenos">174</span></a> <span class="s2">"-u"</span><span class="p">,</span>
+</span><span id="L-175"><a href="#L-175"><span class="linenos">175</span></a> <span class="s2">"--upstream-url"</span><span class="p">,</span>
+</span><span id="L-176"><a href="#L-176"><span class="linenos">176</span></a> <span class="n">required</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span>
+</span><span id="L-177"><a href="#L-177"><span class="linenos">177</span></a> <span class="n">help</span><span class="o">=</span><span class="s2">"(Required) URL to the phenotype repository to fork."</span><span class="p">,</span>
+</span><span id="L-178"><a href="#L-178"><span class="linenos">178</span></a> <span class="p">)</span>
+</span><span id="L-179"><a href="#L-179"><span class="linenos">179</span></a> <span class="n">phen_fork_parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span>
+</span><span id="L-180"><a href="#L-180"><span class="linenos">180</span></a> <span class="s2">"-v"</span><span class="p">,</span>
+</span><span id="L-181"><a href="#L-181"><span class="linenos">181</span></a> <span class="s2">"--upstream-version"</span><span class="p">,</span>
+</span><span id="L-182"><a href="#L-182"><span class="linenos">182</span></a> <span class="n">required</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span>
+</span><span id="L-183"><a href="#L-183"><span class="linenos">183</span></a> <span class="n">help</span><span class="o">=</span><span class="s2">"(Required) Phenotype version to fork."</span><span class="p">,</span>
+</span><span id="L-184"><a href="#L-184"><span class="linenos">184</span></a> <span class="p">)</span>
+</span><span id="L-185"><a href="#L-185"><span class="linenos">185</span></a> <span class="n">phen_fork_parser</span><span class="o">.</span><span class="n">set_defaults</span><span class="p">(</span><span class="n">func</span><span class="o">=</span><span class="n">phen_fork</span><span class="p">)</span>
+</span><span id="L-186"><a href="#L-186"><span class="linenos">186</span></a>
+</span><span id="L-187"><a href="#L-187"><span class="linenos">187</span></a> <span class="c1"># phen validate</span>
+</span><span id="L-188"><a href="#L-188"><span class="linenos">188</span></a> <span class="n">phen_validate_parser</span> <span class="o">=</span> <span class="n">phen_subparsers</span><span class="o">.</span><span class="n">add_parser</span><span class="p">(</span>
+</span><span id="L-189"><a href="#L-189"><span class="linenos">189</span></a> <span class="s2">"validate"</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s2">"Validate phenotype configuration"</span>
+</span><span id="L-190"><a href="#L-190"><span class="linenos">190</span></a> <span class="p">)</span>
+</span><span id="L-191"><a href="#L-191"><span class="linenos">191</span></a> <span class="n">phen_validate_parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span>
+</span><span id="L-192"><a href="#L-192"><span class="linenos">192</span></a> <span class="s2">"-d"</span><span class="p">,</span>
+</span><span id="L-193"><a href="#L-193"><span class="linenos">193</span></a> <span class="s2">"--phen-dir"</span><span class="p">,</span>
+</span><span id="L-194"><a href="#L-194"><span class="linenos">194</span></a> <span class="nb">type</span><span class="o">=</span><span class="nb">str</span><span class="p">,</span>
+</span><span id="L-195"><a href="#L-195"><span class="linenos">195</span></a> <span class="n">default</span><span class="o">=</span><span class="nb">str</span><span class="p">(</span><span class="n">phen</span><span class="o">.</span><span class="n">DEFAULT_PHEN_PATH</span><span class="o">.</span><span class="n">resolve</span><span class="p">()),</span>
+</span><span id="L-196"><a href="#L-196"><span class="linenos">196</span></a> <span class="n">help</span><span class="o">=</span><span class="s2">"(Optional) Local phenotype workspace directory (default is ./workspace/phen)."</span><span class="p">,</span>
+</span><span id="L-197"><a href="#L-197"><span class="linenos">197</span></a> <span class="p">)</span>
+</span><span id="L-198"><a href="#L-198"><span class="linenos">198</span></a> <span class="n">phen_validate_parser</span><span class="o">.</span><span class="n">set_defaults</span><span class="p">(</span><span class="n">func</span><span class="o">=</span><span class="n">phen_validate</span><span class="p">)</span>
+</span><span id="L-199"><a href="#L-199"><span class="linenos">199</span></a>
+</span><span id="L-200"><a href="#L-200"><span class="linenos">200</span></a> <span class="c1"># phen map</span>
+</span><span id="L-201"><a href="#L-201"><span class="linenos">201</span></a> <span class="n">phen_map_parser</span> <span class="o">=</span> <span class="n">phen_subparsers</span><span class="o">.</span><span class="n">add_parser</span><span class="p">(</span><span class="s2">"map"</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s2">"Process phen mapping"</span><span class="p">)</span>
+</span><span id="L-202"><a href="#L-202"><span class="linenos">202</span></a> <span class="n">phen_map_parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span>
+</span><span id="L-203"><a href="#L-203"><span class="linenos">203</span></a> <span class="s2">"-d"</span><span class="p">,</span>
+</span><span id="L-204"><a href="#L-204"><span class="linenos">204</span></a> <span class="s2">"--phen-dir"</span><span class="p">,</span>
+</span><span id="L-205"><a href="#L-205"><span class="linenos">205</span></a> <span class="nb">type</span><span class="o">=</span><span class="nb">str</span><span class="p">,</span>
+</span><span id="L-206"><a href="#L-206"><span class="linenos">206</span></a> <span class="n">default</span><span class="o">=</span><span class="nb">str</span><span class="p">(</span><span class="n">phen</span><span class="o">.</span><span class="n">DEFAULT_PHEN_PATH</span><span class="o">.</span><span class="n">resolve</span><span class="p">()),</span>
+</span><span id="L-207"><a href="#L-207"><span class="linenos">207</span></a> <span class="n">help</span><span class="o">=</span><span class="s2">"(Optional) Local phenotype workspace directory (default is ./workspace/phen)."</span><span class="p">,</span>
+</span><span id="L-208"><a href="#L-208"><span class="linenos">208</span></a> <span class="p">)</span>
+</span><span id="L-209"><a href="#L-209"><span class="linenos">209</span></a> <span class="n">phen_map_parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span>
+</span><span id="L-210"><a href="#L-210"><span class="linenos">210</span></a> <span class="s2">"-t"</span><span class="p">,</span>
+</span><span id="L-211"><a href="#L-211"><span class="linenos">211</span></a> <span class="s2">"--target-coding"</span><span class="p">,</span>
+</span><span id="L-212"><a href="#L-212"><span class="linenos">212</span></a> <span class="n">choices</span><span class="o">=</span><span class="n">parse</span><span class="o">.</span><span class="n">SUPPORTED_CODE_TYPES</span><span class="p">,</span>
+</span><span id="L-213"><a href="#L-213"><span class="linenos">213</span></a> <span class="n">help</span><span class="o">=</span><span class="sa">f</span><span class="s2">"Specify the target coding </span><span class="si">{</span><span class="n">parse</span><span class="o">.</span><span class="n">SUPPORTED_CODE_TYPES</span><span class="si">}</span><span class="s2">"</span><span class="p">,</span>
+</span><span id="L-214"><a href="#L-214"><span class="linenos">214</span></a> <span class="p">)</span>
+</span><span id="L-215"><a href="#L-215"><span class="linenos">215</span></a> <span class="n">phen_map_parser</span><span class="o">.</span><span class="n">set_defaults</span><span class="p">(</span><span class="n">func</span><span class="o">=</span><span class="n">phen_map</span><span class="p">)</span>
+</span><span id="L-216"><a href="#L-216"><span class="linenos">216</span></a>
+</span><span id="L-217"><a href="#L-217"><span class="linenos">217</span></a> <span class="c1"># phen export</span>
+</span><span id="L-218"><a href="#L-218"><span class="linenos">218</span></a> <span class="n">phen_export_parser</span> <span class="o">=</span> <span class="n">phen_subparsers</span><span class="o">.</span><span class="n">add_parser</span><span class="p">(</span>
+</span><span id="L-219"><a href="#L-219"><span class="linenos">219</span></a> <span class="s2">"export"</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s2">"Export phen to OMOP database"</span>
+</span><span id="L-220"><a href="#L-220"><span class="linenos">220</span></a> <span class="p">)</span>
+</span><span id="L-221"><a href="#L-221"><span class="linenos">221</span></a> <span class="n">phen_export_parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span>
+</span><span id="L-222"><a href="#L-222"><span class="linenos">222</span></a> <span class="s2">"-d"</span><span class="p">,</span>
+</span><span id="L-223"><a href="#L-223"><span class="linenos">223</span></a> <span class="s2">"--phen-dir"</span><span class="p">,</span>
+</span><span id="L-224"><a href="#L-224"><span class="linenos">224</span></a> <span class="nb">type</span><span class="o">=</span><span class="nb">str</span><span class="p">,</span>
+</span><span id="L-225"><a href="#L-225"><span class="linenos">225</span></a> <span class="n">default</span><span class="o">=</span><span class="nb">str</span><span class="p">(</span><span class="n">phen</span><span class="o">.</span><span class="n">DEFAULT_PHEN_PATH</span><span class="o">.</span><span class="n">resolve</span><span class="p">()),</span>
+</span><span id="L-226"><a href="#L-226"><span class="linenos">226</span></a> <span class="n">help</span><span class="o">=</span><span class="s2">"(Optional) Local phenotype workspace directory (default is ./workspace/phen)."</span><span class="p">,</span>
+</span><span id="L-227"><a href="#L-227"><span class="linenos">227</span></a> <span class="p">)</span>
+</span><span id="L-228"><a href="#L-228"><span class="linenos">228</span></a> <span class="n">phen_export_parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span>
+</span><span id="L-229"><a href="#L-229"><span class="linenos">229</span></a> <span class="s2">"-v"</span><span class="p">,</span>
+</span><span id="L-230"><a href="#L-230"><span class="linenos">230</span></a> <span class="s2">"--version"</span><span class="p">,</span>
+</span><span id="L-231"><a href="#L-231"><span class="linenos">231</span></a> <span class="nb">type</span><span class="o">=</span><span class="nb">str</span><span class="p">,</span>
+</span><span id="L-232"><a href="#L-232"><span class="linenos">232</span></a> <span class="n">default</span><span class="o">=</span><span class="s2">"latest"</span><span class="p">,</span>
+</span><span id="L-233"><a href="#L-233"><span class="linenos">233</span></a> <span class="n">help</span><span class="o">=</span><span class="s2">"Phenotype version to export, defaults to the latest version"</span><span class="p">,</span>
+</span><span id="L-234"><a href="#L-234"><span class="linenos">234</span></a> <span class="p">)</span>
+</span><span id="L-235"><a href="#L-235"><span class="linenos">235</span></a> <span class="n">phen_export_parser</span><span class="o">.</span><span class="n">set_defaults</span><span class="p">(</span><span class="n">func</span><span class="o">=</span><span class="n">phen_export</span><span class="p">)</span>
+</span><span id="L-236"><a href="#L-236"><span class="linenos">236</span></a>
+</span><span id="L-237"><a href="#L-237"><span class="linenos">237</span></a> <span class="c1"># phen publish</span>
+</span><span id="L-238"><a href="#L-238"><span class="linenos">238</span></a> <span class="n">phen_publish_parser</span> <span class="o">=</span> <span class="n">phen_subparsers</span><span class="o">.</span><span class="n">add_parser</span><span class="p">(</span>
+</span><span id="L-239"><a href="#L-239"><span class="linenos">239</span></a> <span class="s2">"publish"</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s2">"Publish phenotype configuration"</span>
+</span><span id="L-240"><a href="#L-240"><span class="linenos">240</span></a> <span class="p">)</span>
+</span><span id="L-241"><a href="#L-241"><span class="linenos">241</span></a> <span class="n">phen_publish_parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span>
+</span><span id="L-242"><a href="#L-242"><span class="linenos">242</span></a> <span class="s2">"-d"</span><span class="p">,</span>
+</span><span id="L-243"><a href="#L-243"><span class="linenos">243</span></a> <span class="s2">"--phen-dir"</span><span class="p">,</span>
+</span><span id="L-244"><a href="#L-244"><span class="linenos">244</span></a> <span class="nb">type</span><span class="o">=</span><span class="nb">str</span><span class="p">,</span>
+</span><span id="L-245"><a href="#L-245"><span class="linenos">245</span></a> <span class="n">default</span><span class="o">=</span><span class="nb">str</span><span class="p">(</span><span class="n">phen</span><span class="o">.</span><span class="n">DEFAULT_PHEN_PATH</span><span class="o">.</span><span class="n">resolve</span><span class="p">()),</span>
+</span><span id="L-246"><a href="#L-246"><span class="linenos">246</span></a> <span class="n">help</span><span class="o">=</span><span class="s2">"(Optional) Local phenotype workspace directory (default is ./workspace/phen)."</span><span class="p">,</span>
+</span><span id="L-247"><a href="#L-247"><span class="linenos">247</span></a> <span class="p">)</span>
+</span><span id="L-248"><a href="#L-248"><span class="linenos">248</span></a> <span class="n">phen_publish_parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span>
+</span><span id="L-249"><a href="#L-249"><span class="linenos">249</span></a> <span class="s2">"-i"</span><span class="p">,</span>
+</span><span id="L-250"><a href="#L-250"><span class="linenos">250</span></a> <span class="s2">"--increment"</span><span class="p">,</span>
+</span><span id="L-251"><a href="#L-251"><span class="linenos">251</span></a> <span class="nb">type</span><span class="o">=</span><span class="nb">str</span><span class="p">,</span>
+</span><span id="L-252"><a href="#L-252"><span class="linenos">252</span></a> <span class="n">default</span><span class="o">=</span><span class="n">phen</span><span class="o">.</span><span class="n">DEFAULT_VERSION_INC</span><span class="p">,</span>
+</span><span id="L-253"><a href="#L-253"><span class="linenos">253</span></a> <span class="n">choices</span><span class="o">=</span><span class="n">phen</span><span class="o">.</span><span class="n">SEMANTIC_VERSION_TYPES</span><span class="p">,</span>
+</span><span id="L-254"><a href="#L-254"><span class="linenos">254</span></a> <span class="n">help</span><span class="o">=</span><span class="sa">f</span><span class="s2">"Version increment: </span><span class="si">{</span><span class="n">phen</span><span class="o">.</span><span class="n">SEMANTIC_VERSION_TYPES</span><span class="si">}</span><span class="s2">, default is </span><span class="si">{</span><span class="n">phen</span><span class="o">.</span><span class="n">DEFAULT_VERSION_INC</span><span class="si">}</span><span class="s2"> increment"</span><span class="p">,</span>
+</span><span id="L-255"><a href="#L-255"><span class="linenos">255</span></a> <span class="p">)</span>
+</span><span id="L-256"><a href="#L-256"><span class="linenos">256</span></a> <span class="n">phen_publish_parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span>
+</span><span id="L-257"><a href="#L-257"><span class="linenos">257</span></a> <span class="s2">"-m"</span><span class="p">,</span> <span class="s2">"--msg"</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s2">"Message to include with the published version"</span>
+</span><span id="L-258"><a href="#L-258"><span class="linenos">258</span></a> <span class="p">)</span>
+</span><span id="L-259"><a href="#L-259"><span class="linenos">259</span></a> <span class="n">phen_publish_parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span>
+</span><span id="L-260"><a href="#L-260"><span class="linenos">260</span></a> <span class="s2">"-r"</span><span class="p">,</span> <span class="s2">"--remote_url"</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s2">"URL to remote git repository"</span>
+</span><span id="L-261"><a href="#L-261"><span class="linenos">261</span></a> <span class="p">)</span>
+</span><span id="L-262"><a href="#L-262"><span class="linenos">262</span></a> <span class="n">phen_publish_parser</span><span class="o">.</span><span class="n">set_defaults</span><span class="p">(</span><span class="n">func</span><span class="o">=</span><span class="n">phen_publish</span><span class="p">)</span>
+</span><span id="L-263"><a href="#L-263"><span class="linenos">263</span></a>
+</span><span id="L-264"><a href="#L-264"><span class="linenos">264</span></a> <span class="c1"># phen copy</span>
+</span><span id="L-265"><a href="#L-265"><span class="linenos">265</span></a> <span class="n">phen_copy_parser</span> <span class="o">=</span> <span class="n">phen_subparsers</span><span class="o">.</span><span class="n">add_parser</span><span class="p">(</span>
+</span><span id="L-266"><a href="#L-266"><span class="linenos">266</span></a> <span class="s2">"copy"</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s2">"Publish phenotype configuration"</span>
+</span><span id="L-267"><a href="#L-267"><span class="linenos">267</span></a> <span class="p">)</span>
+</span><span id="L-268"><a href="#L-268"><span class="linenos">268</span></a> <span class="n">phen_copy_parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span>
+</span><span id="L-269"><a href="#L-269"><span class="linenos">269</span></a> <span class="s2">"-d"</span><span class="p">,</span>
+</span><span id="L-270"><a href="#L-270"><span class="linenos">270</span></a> <span class="s2">"--phen-dir"</span><span class="p">,</span>
+</span><span id="L-271"><a href="#L-271"><span class="linenos">271</span></a> <span class="nb">type</span><span class="o">=</span><span class="nb">str</span><span class="p">,</span>
+</span><span id="L-272"><a href="#L-272"><span class="linenos">272</span></a> <span class="n">default</span><span class="o">=</span><span class="nb">str</span><span class="p">(</span><span class="n">phen</span><span class="o">.</span><span class="n">DEFAULT_PHEN_PATH</span><span class="o">.</span><span class="n">resolve</span><span class="p">()),</span>
+</span><span id="L-273"><a href="#L-273"><span class="linenos">273</span></a> <span class="n">help</span><span class="o">=</span><span class="s2">"(Optional) Local phenotype workspace directory (default is ./workspace/phen)."</span><span class="p">,</span>
+</span><span id="L-274"><a href="#L-274"><span class="linenos">274</span></a> <span class="p">)</span>
+</span><span id="L-275"><a href="#L-275"><span class="linenos">275</span></a> <span class="n">phen_copy_parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span>
+</span><span id="L-276"><a href="#L-276"><span class="linenos">276</span></a> <span class="s2">"-td"</span><span class="p">,</span>
+</span><span id="L-277"><a href="#L-277"><span class="linenos">277</span></a> <span class="s2">"--target-dir"</span><span class="p">,</span>
+</span><span id="L-278"><a href="#L-278"><span class="linenos">278</span></a> <span class="nb">type</span><span class="o">=</span><span class="nb">str</span><span class="p">,</span>
+</span><span id="L-279"><a href="#L-279"><span class="linenos">279</span></a> <span class="n">default</span><span class="o">=</span><span class="nb">str</span><span class="p">(</span><span class="n">DEFAULT_WORKSPACE_PATH</span><span class="o">.</span><span class="n">resolve</span><span class="p">()),</span>
+</span><span id="L-280"><a href="#L-280"><span class="linenos">280</span></a> <span class="n">help</span><span class="o">=</span><span class="s2">"Target directory for the copy"</span><span class="p">,</span>
+</span><span id="L-281"><a href="#L-281"><span class="linenos">281</span></a> <span class="p">)</span>
+</span><span id="L-282"><a href="#L-282"><span class="linenos">282</span></a> <span class="n">phen_copy_parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span>
+</span><span id="L-283"><a href="#L-283"><span class="linenos">283</span></a> <span class="s2">"-v"</span><span class="p">,</span>
+</span><span id="L-284"><a href="#L-284"><span class="linenos">284</span></a> <span class="s2">"--version"</span><span class="p">,</span>
+</span><span id="L-285"><a href="#L-285"><span class="linenos">285</span></a> <span class="nb">type</span><span class="o">=</span><span class="nb">str</span><span class="p">,</span>
+</span><span id="L-286"><a href="#L-286"><span class="linenos">286</span></a> <span class="n">default</span><span class="o">=</span><span class="s2">"latest"</span><span class="p">,</span>
+</span><span id="L-287"><a href="#L-287"><span class="linenos">287</span></a> <span class="n">help</span><span class="o">=</span><span class="s2">"Phenotype version to copy, defaults to the latest version"</span><span class="p">,</span>
+</span><span id="L-288"><a href="#L-288"><span class="linenos">288</span></a> <span class="p">)</span>
+</span><span id="L-289"><a href="#L-289"><span class="linenos">289</span></a> <span class="n">phen_copy_parser</span><span class="o">.</span><span class="n">set_defaults</span><span class="p">(</span><span class="n">func</span><span class="o">=</span><span class="n">phen_copy</span><span class="p">)</span>
+</span><span id="L-290"><a href="#L-290"><span class="linenos">290</span></a>
+</span><span id="L-291"><a href="#L-291"><span class="linenos">291</span></a> <span class="c1"># phen diff</span>
+</span><span id="L-292"><a href="#L-292"><span class="linenos">292</span></a> <span class="n">phen_diff_parser</span> <span class="o">=</span> <span class="n">phen_subparsers</span><span class="o">.</span><span class="n">add_parser</span><span class="p">(</span>
+</span><span id="L-293"><a href="#L-293"><span class="linenos">293</span></a> <span class="s2">"diff"</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s2">"Publish phenotype configuration"</span>
+</span><span id="L-294"><a href="#L-294"><span class="linenos">294</span></a> <span class="p">)</span>
+</span><span id="L-295"><a href="#L-295"><span class="linenos">295</span></a> <span class="n">phen_diff_parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span>
+</span><span id="L-296"><a href="#L-296"><span class="linenos">296</span></a> <span class="s2">"-d"</span><span class="p">,</span>
+</span><span id="L-297"><a href="#L-297"><span class="linenos">297</span></a> <span class="s2">"--phen-dir"</span><span class="p">,</span>
+</span><span id="L-298"><a href="#L-298"><span class="linenos">298</span></a> <span class="nb">type</span><span class="o">=</span><span class="nb">str</span><span class="p">,</span>
+</span><span id="L-299"><a href="#L-299"><span class="linenos">299</span></a> <span class="n">default</span><span class="o">=</span><span class="nb">str</span><span class="p">(</span><span class="n">phen</span><span class="o">.</span><span class="n">DEFAULT_PHEN_PATH</span><span class="o">.</span><span class="n">resolve</span><span class="p">()),</span>
+</span><span id="L-300"><a href="#L-300"><span class="linenos">300</span></a> <span class="n">help</span><span class="o">=</span><span class="s2">"(Optional) Local phenotype workspace directory (default is ./workspace/phen)."</span><span class="p">,</span>
+</span><span id="L-301"><a href="#L-301"><span class="linenos">301</span></a> <span class="p">)</span>
+</span><span id="L-302"><a href="#L-302"><span class="linenos">302</span></a> <span class="n">phen_diff_parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span>
+</span><span id="L-303"><a href="#L-303"><span class="linenos">303</span></a> <span class="s2">"-v"</span><span class="p">,</span>
+</span><span id="L-304"><a href="#L-304"><span class="linenos">304</span></a> <span class="s2">"--version"</span><span class="p">,</span>
+</span><span id="L-305"><a href="#L-305"><span class="linenos">305</span></a> <span class="n">default</span><span class="o">=</span><span class="s2">"latest"</span><span class="p">,</span>
+</span><span id="L-306"><a href="#L-306"><span class="linenos">306</span></a> <span class="n">help</span><span class="o">=</span><span class="s2">"Phenotype version to compare with an old version, defaults to the HEAD of the workspace directory"</span><span class="p">,</span>
+</span><span id="L-307"><a href="#L-307"><span class="linenos">307</span></a> <span class="p">)</span>
+</span><span id="L-308"><a href="#L-308"><span class="linenos">308</span></a> <span class="n">phen_diff_parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span>
+</span><span id="L-309"><a href="#L-309"><span class="linenos">309</span></a> <span class="s2">"-od"</span><span class="p">,</span>
+</span><span id="L-310"><a href="#L-310"><span class="linenos">310</span></a> <span class="s2">"--old-phen-dir"</span><span class="p">,</span>
+</span><span id="L-311"><a href="#L-311"><span class="linenos">311</span></a> <span class="nb">type</span><span class="o">=</span><span class="nb">str</span><span class="p">,</span>
+</span><span id="L-312"><a href="#L-312"><span class="linenos">312</span></a> <span class="n">default</span><span class="o">=</span><span class="nb">str</span><span class="p">(</span><span class="n">phen</span><span class="o">.</span><span class="n">DEFAULT_PHEN_PATH</span><span class="o">.</span><span class="n">resolve</span><span class="p">()),</span>
+</span><span id="L-313"><a href="#L-313"><span class="linenos">313</span></a> <span class="n">help</span><span class="o">=</span><span class="s2">"Directory for the old phenotype version, defaults to workspace directory"</span><span class="p">,</span>
+</span><span id="L-314"><a href="#L-314"><span class="linenos">314</span></a> <span class="p">)</span>
+</span><span id="L-315"><a href="#L-315"><span class="linenos">315</span></a> <span class="n">phen_diff_parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span>
+</span><span id="L-316"><a href="#L-316"><span class="linenos">316</span></a> <span class="s2">"-ov"</span><span class="p">,</span>
+</span><span id="L-317"><a href="#L-317"><span class="linenos">317</span></a> <span class="s2">"--old-version"</span><span class="p">,</span>
+</span><span id="L-318"><a href="#L-318"><span class="linenos">318</span></a> <span class="n">required</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span>
+</span><span id="L-319"><a href="#L-319"><span class="linenos">319</span></a> <span class="n">help</span><span class="o">=</span><span class="s2">"Old phenotype version to compare with the changed version"</span><span class="p">,</span>
+</span><span id="L-320"><a href="#L-320"><span class="linenos">320</span></a> <span class="p">)</span>
+</span><span id="L-321"><a href="#L-321"><span class="linenos">321</span></a> <span class="n">phen_diff_parser</span><span class="o">.</span><span class="n">set_defaults</span><span class="p">(</span><span class="n">func</span><span class="o">=</span><span class="n">phen_diff</span><span class="p">)</span>
+</span><span id="L-322"><a href="#L-322"><span class="linenos">322</span></a>
+</span><span id="L-323"><a href="#L-323"><span class="linenos">323</span></a> <span class="c1"># Parse arguments</span>
+</span><span id="L-324"><a href="#L-324"><span class="linenos">324</span></a> <span class="n">args</span> <span class="o">=</span> <span class="n">parser</span><span class="o">.</span><span class="n">parse_args</span><span class="p">()</span>
+</span><span id="L-325"><a href="#L-325"><span class="linenos">325</span></a>
+</span><span id="L-326"><a href="#L-326"><span class="linenos">326</span></a> <span class="c1"># setup logging</span>
+</span><span id="L-327"><a href="#L-327"><span class="linenos">327</span></a> <span class="k">if</span> <span class="n">args</span><span class="o">.</span><span class="n">debug</span><span class="p">:</span>
+</span><span id="L-328"><a href="#L-328"><span class="linenos">328</span></a> <span class="n">lc</span><span class="o">.</span><span class="n">set_log_level</span><span class="p">(</span><span class="n">logging</span><span class="o">.</span><span class="n">DEBUG</span><span class="p">)</span>
+</span><span id="L-329"><a href="#L-329"><span class="linenos">329</span></a>
+</span><span id="L-330"><a href="#L-330"><span class="linenos">330</span></a> <span class="c1"># Call the function associated with the command</span>
+</span><span id="L-331"><a href="#L-331"><span class="linenos">331</span></a> <span class="n">args</span><span class="o">.</span><span class="n">func</span><span class="p">(</span><span class="n">args</span><span class="p">)</span>
+</span><span id="L-332"><a href="#L-332"><span class="linenos">332</span></a>
+</span><span id="L-333"><a href="#L-333"><span class="linenos">333</span></a>
+</span><span id="L-334"><a href="#L-334"><span class="linenos">334</span></a><span class="k">if</span> <span class="vm">__name__</span> <span class="o">==</span> <span class="s2">"__main__"</span><span class="p">:</span>
+</span><span id="L-335"><a href="#L-335"><span class="linenos">335</span></a> <span class="n">main</span><span class="p">()</span>
+</span></pre></div>
+
+
+ </section>
+ <section id="logger">
+ <div class="attr variable">
+ <span class="name">logger</span> =
+<span class="default_value"><Logger acmc_logger (INFO)></span>
+
+
+ </div>
+ <a class="headerlink" href="#logger"></a>
+
+
+
+ </section>
+ <section id="DEFAULT_WORKSPACE_PATH">
+ <div class="attr variable">
+ <span class="name">DEFAULT_WORKSPACE_PATH</span> =
+<span class="default_value">PosixPath('workspace')</span>
+
+
+ </div>
+ <a class="headerlink" href="#DEFAULT_WORKSPACE_PATH"></a>
+
+
+
+ </section>
+ <section id="trud_install">
+ <input id="trud_install-view-source" class="view-source-toggle-state" type="checkbox" aria-hidden="true" tabindex="-1">
+<div class="attr function">
+
+ <span class="def">def</span>
+ <span class="name">trud_install</span><span class="signature pdoc-code condensed">(<span class="param"><span class="n">args</span><span class="p">:</span> <span class="n">argparse</span><span class="o">.</span><span class="n">Namespace</span></span><span class="return-annotation">):</span></span>
+
+ <label class="view-source-button" for="trud_install-view-source"><span>View Source</span></label>
+
+ </div>
+ <a class="headerlink" href="#trud_install"></a>
+ <div class="pdoc-code codehilite"><pre><span></span><span id="trud_install-15"><a href="#trud_install-15"><span class="linenos">15</span></a><span class="k">def</span><span class="w"> </span><span class="nf">trud_install</span><span class="p">(</span><span class="n">args</span><span class="p">:</span> <span class="n">argparse</span><span class="o">.</span><span class="n">Namespace</span><span class="p">):</span>
+</span><span id="trud_install-16"><a href="#trud_install-16"><span class="linenos">16</span></a><span class="w"> </span><span class="sd">"""Handle the `trud install` command."""</span>
+</span><span id="trud_install-17"><a href="#trud_install-17"><span class="linenos">17</span></a> <span class="n">trud</span><span class="o">.</span><span class="n">install</span><span class="p">()</span>
+</span></pre></div>
+
+
+ <div class="docstring"><p>Handle the <code>trud install</code> command.</p>
+</div>
+
+
+ </section>
+ <section id="omop_install">
+ <input id="omop_install-view-source" class="view-source-toggle-state" type="checkbox" aria-hidden="true" tabindex="-1">
+<div class="attr function">
+
+ <span class="def">def</span>
+ <span class="name">omop_install</span><span class="signature pdoc-code condensed">(<span class="param"><span class="n">args</span><span class="p">:</span> <span class="n">argparse</span><span class="o">.</span><span class="n">Namespace</span></span><span class="return-annotation">):</span></span>
+
+ <label class="view-source-button" for="omop_install-view-source"><span>View Source</span></label>
+
+ </div>
+ <a class="headerlink" href="#omop_install"></a>
+ <div class="pdoc-code codehilite"><pre><span></span><span id="omop_install-20"><a href="#omop_install-20"><span class="linenos">20</span></a><span class="k">def</span><span class="w"> </span><span class="nf">omop_install</span><span class="p">(</span><span class="n">args</span><span class="p">:</span> <span class="n">argparse</span><span class="o">.</span><span class="n">Namespace</span><span class="p">):</span>
+</span><span id="omop_install-21"><a href="#omop_install-21"><span class="linenos">21</span></a><span class="w"> </span><span class="sd">"""Handle the `omop install` command."""</span>
+</span><span id="omop_install-22"><a href="#omop_install-22"><span class="linenos">22</span></a> <span class="n">omop</span><span class="o">.</span><span class="n">install</span><span class="p">(</span><span class="n">args</span><span class="o">.</span><span class="n">omop_zip_file</span><span class="p">,</span> <span class="n">args</span><span class="o">.</span><span class="n">version</span><span class="p">)</span>
+</span></pre></div>
+
+
+ <div class="docstring"><p>Handle the <code>omop install</code> command.</p>
+</div>
+
+
+ </section>
+ <section id="omop_clear">
+ <input id="omop_clear-view-source" class="view-source-toggle-state" type="checkbox" aria-hidden="true" tabindex="-1">
+<div class="attr function">
+
+ <span class="def">def</span>
+ <span class="name">omop_clear</span><span class="signature pdoc-code condensed">(<span class="param"><span class="n">args</span><span class="p">:</span> <span class="n">argparse</span><span class="o">.</span><span class="n">Namespace</span></span><span class="return-annotation">):</span></span>
+
+ <label class="view-source-button" for="omop_clear-view-source"><span>View Source</span></label>
+
+ </div>
+ <a class="headerlink" href="#omop_clear"></a>
+ <div class="pdoc-code codehilite"><pre><span></span><span id="omop_clear-25"><a href="#omop_clear-25"><span class="linenos">25</span></a><span class="k">def</span><span class="w"> </span><span class="nf">omop_clear</span><span class="p">(</span><span class="n">args</span><span class="p">:</span> <span class="n">argparse</span><span class="o">.</span><span class="n">Namespace</span><span class="p">):</span>
+</span><span id="omop_clear-26"><a href="#omop_clear-26"><span class="linenos">26</span></a><span class="w"> </span><span class="sd">"""Handle the `omop clear` command."""</span>
+</span><span id="omop_clear-27"><a href="#omop_clear-27"><span class="linenos">27</span></a> <span class="n">omop</span><span class="o">.</span><span class="n">clear</span><span class="p">(</span><span class="n">omop</span><span class="o">.</span><span class="n">DB_PATH</span><span class="p">)</span>
+</span></pre></div>
+
+
+ <div class="docstring"><p>Handle the <code>omop clear</code> command.</p>
+</div>
+
+
+ </section>
+ <section id="omop_delete">
+ <input id="omop_delete-view-source" class="view-source-toggle-state" type="checkbox" aria-hidden="true" tabindex="-1">
+<div class="attr function">
+
+ <span class="def">def</span>
+ <span class="name">omop_delete</span><span class="signature pdoc-code condensed">(<span class="param"><span class="n">args</span><span class="p">:</span> <span class="n">argparse</span><span class="o">.</span><span class="n">Namespace</span></span><span class="return-annotation">):</span></span>
+
+ <label class="view-source-button" for="omop_delete-view-source"><span>View Source</span></label>
+
+ </div>
+ <a class="headerlink" href="#omop_delete"></a>
+ <div class="pdoc-code codehilite"><pre><span></span><span id="omop_delete-30"><a href="#omop_delete-30"><span class="linenos">30</span></a><span class="k">def</span><span class="w"> </span><span class="nf">omop_delete</span><span class="p">(</span><span class="n">args</span><span class="p">:</span> <span class="n">argparse</span><span class="o">.</span><span class="n">Namespace</span><span class="p">):</span>
+</span><span id="omop_delete-31"><a href="#omop_delete-31"><span class="linenos">31</span></a><span class="w"> </span><span class="sd">"""Handle the `omop delete` command."""</span>
+</span><span id="omop_delete-32"><a href="#omop_delete-32"><span class="linenos">32</span></a> <span class="n">omop</span><span class="o">.</span><span class="n">delete</span><span class="p">(</span><span class="n">omop</span><span class="o">.</span><span class="n">DB_PATH</span><span class="p">)</span>
+</span></pre></div>
+
+
+ <div class="docstring"><p>Handle the <code>omop delete</code> command.</p>
+</div>
+
+
+ </section>
+ <section id="phen_init">
+ <input id="phen_init-view-source" class="view-source-toggle-state" type="checkbox" aria-hidden="true" tabindex="-1">
+<div class="attr function">
+
+ <span class="def">def</span>
+ <span class="name">phen_init</span><span class="signature pdoc-code condensed">(<span class="param"><span class="n">args</span><span class="p">:</span> <span class="n">argparse</span><span class="o">.</span><span class="n">Namespace</span></span><span class="return-annotation">):</span></span>
+
+ <label class="view-source-button" for="phen_init-view-source"><span>View Source</span></label>
+
+ </div>
+ <a class="headerlink" href="#phen_init"></a>
+ <div class="pdoc-code codehilite"><pre><span></span><span id="phen_init-35"><a href="#phen_init-35"><span class="linenos">35</span></a><span class="k">def</span><span class="w"> </span><span class="nf">phen_init</span><span class="p">(</span><span class="n">args</span><span class="p">:</span> <span class="n">argparse</span><span class="o">.</span><span class="n">Namespace</span><span class="p">):</span>
+</span><span id="phen_init-36"><a href="#phen_init-36"><span class="linenos">36</span></a><span class="w"> </span><span class="sd">"""Handle the `phen init` command."""</span>
+</span><span id="phen_init-37"><a href="#phen_init-37"><span class="linenos">37</span></a> <span class="n">phen</span><span class="o">.</span><span class="n">init</span><span class="p">(</span><span class="n">args</span><span class="o">.</span><span class="n">phen_dir</span><span class="p">,</span> <span class="n">args</span><span class="o">.</span><span class="n">remote_url</span><span class="p">)</span>
+</span></pre></div>
+
+
+ <div class="docstring"><p>Handle the <code>phen init</code> command.</p>
+</div>
+
+
+ </section>
+ <section id="phen_fork">
+ <input id="phen_fork-view-source" class="view-source-toggle-state" type="checkbox" aria-hidden="true" tabindex="-1">
+<div class="attr function">
+
+ <span class="def">def</span>
+ <span class="name">phen_fork</span><span class="signature pdoc-code condensed">(<span class="param"><span class="n">args</span><span class="p">:</span> <span class="n">argparse</span><span class="o">.</span><span class="n">Namespace</span></span><span class="return-annotation">):</span></span>
+
+ <label class="view-source-button" for="phen_fork-view-source"><span>View Source</span></label>
+
+ </div>
+ <a class="headerlink" href="#phen_fork"></a>
+ <div class="pdoc-code codehilite"><pre><span></span><span id="phen_fork-40"><a href="#phen_fork-40"><span class="linenos">40</span></a><span class="k">def</span><span class="w"> </span><span class="nf">phen_fork</span><span class="p">(</span><span class="n">args</span><span class="p">:</span> <span class="n">argparse</span><span class="o">.</span><span class="n">Namespace</span><span class="p">):</span>
+</span><span id="phen_fork-41"><a href="#phen_fork-41"><span class="linenos">41</span></a><span class="w"> </span><span class="sd">"""Handle the `phen fork` command."""</span>
+</span><span id="phen_fork-42"><a href="#phen_fork-42"><span class="linenos">42</span></a> <span class="n">phen</span><span class="o">.</span><span class="n">fork</span><span class="p">(</span>
+</span><span id="phen_fork-43"><a href="#phen_fork-43"><span class="linenos">43</span></a> <span class="n">args</span><span class="o">.</span><span class="n">phen_dir</span><span class="p">,</span>
+</span><span id="phen_fork-44"><a href="#phen_fork-44"><span class="linenos">44</span></a> <span class="n">args</span><span class="o">.</span><span class="n">upstream_url</span><span class="p">,</span>
+</span><span id="phen_fork-45"><a href="#phen_fork-45"><span class="linenos">45</span></a> <span class="n">args</span><span class="o">.</span><span class="n">upstream_version</span><span class="p">,</span>
+</span><span id="phen_fork-46"><a href="#phen_fork-46"><span class="linenos">46</span></a> <span class="n">new_origin_url</span><span class="o">=</span><span class="n">args</span><span class="o">.</span><span class="n">remote_url</span><span class="p">,</span>
+</span><span id="phen_fork-47"><a href="#phen_fork-47"><span class="linenos">47</span></a> <span class="p">)</span>
+</span></pre></div>
+
+
+ <div class="docstring"><p>Handle the <code>phen fork</code> command.</p>
+</div>
+
+
+ </section>
+ <section id="phen_validate">
+ <input id="phen_validate-view-source" class="view-source-toggle-state" type="checkbox" aria-hidden="true" tabindex="-1">
+<div class="attr function">
+
+ <span class="def">def</span>
+ <span class="name">phen_validate</span><span class="signature pdoc-code condensed">(<span class="param"><span class="n">args</span><span class="p">:</span> <span class="n">argparse</span><span class="o">.</span><span class="n">Namespace</span></span><span class="return-annotation">):</span></span>
+
+ <label class="view-source-button" for="phen_validate-view-source"><span>View Source</span></label>
+
+ </div>
+ <a class="headerlink" href="#phen_validate"></a>
+ <div class="pdoc-code codehilite"><pre><span></span><span id="phen_validate-50"><a href="#phen_validate-50"><span class="linenos">50</span></a><span class="k">def</span><span class="w"> </span><span class="nf">phen_validate</span><span class="p">(</span><span class="n">args</span><span class="p">:</span> <span class="n">argparse</span><span class="o">.</span><span class="n">Namespace</span><span class="p">):</span>
+</span><span id="phen_validate-51"><a href="#phen_validate-51"><span class="linenos">51</span></a><span class="w"> </span><span class="sd">"""Handle the `phen validate` command."""</span>
+</span><span id="phen_validate-52"><a href="#phen_validate-52"><span class="linenos">52</span></a> <span class="n">phen</span><span class="o">.</span><span class="n">validate</span><span class="p">(</span><span class="n">args</span><span class="o">.</span><span class="n">phen_dir</span><span class="p">)</span>
+</span></pre></div>
+
+
+ <div class="docstring"><p>Handle the <code>phen validate</code> command.</p>
+</div>
+
+
+ </section>
+ <section id="phen_map">
+ <input id="phen_map-view-source" class="view-source-toggle-state" type="checkbox" aria-hidden="true" tabindex="-1">
+<div class="attr function">
+
+ <span class="def">def</span>
+ <span class="name">phen_map</span><span class="signature pdoc-code condensed">(<span class="param"><span class="n">args</span><span class="p">:</span> <span class="n">argparse</span><span class="o">.</span><span class="n">Namespace</span></span><span class="return-annotation">):</span></span>
+
+ <label class="view-source-button" for="phen_map-view-source"><span>View Source</span></label>
+
+ </div>
+ <a class="headerlink" href="#phen_map"></a>
+ <div class="pdoc-code codehilite"><pre><span></span><span id="phen_map-55"><a href="#phen_map-55"><span class="linenos">55</span></a><span class="k">def</span><span class="w"> </span><span class="nf">phen_map</span><span class="p">(</span><span class="n">args</span><span class="p">:</span> <span class="n">argparse</span><span class="o">.</span><span class="n">Namespace</span><span class="p">):</span>
+</span><span id="phen_map-56"><a href="#phen_map-56"><span class="linenos">56</span></a><span class="w"> </span><span class="sd">"""Handle the `phen map` command."""</span>
+</span><span id="phen_map-57"><a href="#phen_map-57"><span class="linenos">57</span></a> <span class="n">phen</span><span class="o">.</span><span class="n">map</span><span class="p">(</span><span class="n">args</span><span class="o">.</span><span class="n">phen_dir</span><span class="p">,</span> <span class="n">args</span><span class="o">.</span><span class="n">target_coding</span><span class="p">)</span>
+</span></pre></div>
+
+
+ <div class="docstring"><p>Handle the <code>phen map</code> command.</p>
+</div>
+
+
+ </section>
+ <section id="phen_export">
+ <input id="phen_export-view-source" class="view-source-toggle-state" type="checkbox" aria-hidden="true" tabindex="-1">
+<div class="attr function">
+
+ <span class="def">def</span>
+ <span class="name">phen_export</span><span class="signature pdoc-code condensed">(<span class="param"><span class="n">args</span><span class="p">:</span> <span class="n">argparse</span><span class="o">.</span><span class="n">Namespace</span></span><span class="return-annotation">):</span></span>
+
+ <label class="view-source-button" for="phen_export-view-source"><span>View Source</span></label>
+
+ </div>
+ <a class="headerlink" href="#phen_export"></a>
+ <div class="pdoc-code codehilite"><pre><span></span><span id="phen_export-60"><a href="#phen_export-60"><span class="linenos">60</span></a><span class="k">def</span><span class="w"> </span><span class="nf">phen_export</span><span class="p">(</span><span class="n">args</span><span class="p">:</span> <span class="n">argparse</span><span class="o">.</span><span class="n">Namespace</span><span class="p">):</span>
+</span><span id="phen_export-61"><a href="#phen_export-61"><span class="linenos">61</span></a><span class="w"> </span><span class="sd">"""Handle the `phen copy` command."""</span>
+</span><span id="phen_export-62"><a href="#phen_export-62"><span class="linenos">62</span></a> <span class="n">phen</span><span class="o">.</span><span class="n">export</span><span class="p">(</span><span class="n">args</span><span class="o">.</span><span class="n">phen_dir</span><span class="p">,</span> <span class="n">args</span><span class="o">.</span><span class="n">version</span><span class="p">)</span>
+</span></pre></div>
+
+
+ <div class="docstring"><p>Handle the <code>phen copy</code> command.</p>
+</div>
+
+
+ </section>
+ <section id="phen_publish">
+ <input id="phen_publish-view-source" class="view-source-toggle-state" type="checkbox" aria-hidden="true" tabindex="-1">
+<div class="attr function">
+
+ <span class="def">def</span>
+ <span class="name">phen_publish</span><span class="signature pdoc-code condensed">(<span class="param"><span class="n">args</span><span class="p">:</span> <span class="n">argparse</span><span class="o">.</span><span class="n">Namespace</span></span><span class="return-annotation">):</span></span>
+
+ <label class="view-source-button" for="phen_publish-view-source"><span>View Source</span></label>
+
+ </div>
+ <a class="headerlink" href="#phen_publish"></a>
+ <div class="pdoc-code codehilite"><pre><span></span><span id="phen_publish-65"><a href="#phen_publish-65"><span class="linenos">65</span></a><span class="k">def</span><span class="w"> </span><span class="nf">phen_publish</span><span class="p">(</span><span class="n">args</span><span class="p">:</span> <span class="n">argparse</span><span class="o">.</span><span class="n">Namespace</span><span class="p">):</span>
+</span><span id="phen_publish-66"><a href="#phen_publish-66"><span class="linenos">66</span></a><span class="w"> </span><span class="sd">"""Handle the `phen publish` command."""</span>
+</span><span id="phen_publish-67"><a href="#phen_publish-67"><span class="linenos">67</span></a> <span class="n">phen</span><span class="o">.</span><span class="n">publish</span><span class="p">(</span><span class="n">args</span><span class="o">.</span><span class="n">phen_dir</span><span class="p">,</span> <span class="n">args</span><span class="o">.</span><span class="n">msg</span><span class="p">,</span> <span class="n">args</span><span class="o">.</span><span class="n">remote_url</span><span class="p">,</span> <span class="n">args</span><span class="o">.</span><span class="n">increment</span><span class="p">)</span>
+</span></pre></div>
+
+
+ <div class="docstring"><p>Handle the <code>phen publish</code> command.</p>
+</div>
+
+
+ </section>
+ <section id="phen_copy">
+ <input id="phen_copy-view-source" class="view-source-toggle-state" type="checkbox" aria-hidden="true" tabindex="-1">
+<div class="attr function">
+
+ <span class="def">def</span>
+ <span class="name">phen_copy</span><span class="signature pdoc-code condensed">(<span class="param"><span class="n">args</span><span class="p">:</span> <span class="n">argparse</span><span class="o">.</span><span class="n">Namespace</span></span><span class="return-annotation">):</span></span>
+
+ <label class="view-source-button" for="phen_copy-view-source"><span>View Source</span></label>
+
+ </div>
+ <a class="headerlink" href="#phen_copy"></a>
+ <div class="pdoc-code codehilite"><pre><span></span><span id="phen_copy-70"><a href="#phen_copy-70"><span class="linenos">70</span></a><span class="k">def</span><span class="w"> </span><span class="nf">phen_copy</span><span class="p">(</span><span class="n">args</span><span class="p">:</span> <span class="n">argparse</span><span class="o">.</span><span class="n">Namespace</span><span class="p">):</span>
+</span><span id="phen_copy-71"><a href="#phen_copy-71"><span class="linenos">71</span></a><span class="w"> </span><span class="sd">"""Handle the `phen copy` command."""</span>
+</span><span id="phen_copy-72"><a href="#phen_copy-72"><span class="linenos">72</span></a> <span class="n">phen</span><span class="o">.</span><span class="n">copy</span><span class="p">(</span><span class="n">args</span><span class="o">.</span><span class="n">phen_dir</span><span class="p">,</span> <span class="n">args</span><span class="o">.</span><span class="n">target_dir</span><span class="p">,</span> <span class="n">args</span><span class="o">.</span><span class="n">version</span><span class="p">)</span>
+</span></pre></div>
+
+
+ <div class="docstring"><p>Handle the <code>phen copy</code> command.</p>
+</div>
+
+
+ </section>
+ <section id="phen_diff">
+ <input id="phen_diff-view-source" class="view-source-toggle-state" type="checkbox" aria-hidden="true" tabindex="-1">
+<div class="attr function">
+
+ <span class="def">def</span>
+ <span class="name">phen_diff</span><span class="signature pdoc-code condensed">(<span class="param"><span class="n">args</span><span class="p">:</span> <span class="n">argparse</span><span class="o">.</span><span class="n">Namespace</span></span><span class="return-annotation">):</span></span>
+
+ <label class="view-source-button" for="phen_diff-view-source"><span>View Source</span></label>
+
+ </div>
+ <a class="headerlink" href="#phen_diff"></a>
+ <div class="pdoc-code codehilite"><pre><span></span><span id="phen_diff-75"><a href="#phen_diff-75"><span class="linenos">75</span></a><span class="k">def</span><span class="w"> </span><span class="nf">phen_diff</span><span class="p">(</span><span class="n">args</span><span class="p">:</span> <span class="n">argparse</span><span class="o">.</span><span class="n">Namespace</span><span class="p">):</span>
+</span><span id="phen_diff-76"><a href="#phen_diff-76"><span class="linenos">76</span></a><span class="w"> </span><span class="sd">"""Handle the `phen diff` command."""</span>
+</span><span id="phen_diff-77"><a href="#phen_diff-77"><span class="linenos">77</span></a> <span class="n">phen</span><span class="o">.</span><span class="n">diff</span><span class="p">(</span><span class="n">args</span><span class="o">.</span><span class="n">phen_dir</span><span class="p">,</span> <span class="n">args</span><span class="o">.</span><span class="n">version</span><span class="p">,</span> <span class="n">args</span><span class="o">.</span><span class="n">old_phen_dir</span><span class="p">,</span> <span class="n">args</span><span class="o">.</span><span class="n">old_version</span><span class="p">)</span>
+</span></pre></div>
+
+
+ <div class="docstring"><p>Handle the <code>phen diff</code> command.</p>
+</div>
+
+
+ </section>
+ <section id="main">
+ <input id="main-view-source" class="view-source-toggle-state" type="checkbox" aria-hidden="true" tabindex="-1">
+<div class="attr function">
+
+ <span class="def">def</span>
+ <span class="name">main</span><span class="signature pdoc-code condensed">(<span class="return-annotation">):</span></span>
+
+ <label class="view-source-button" for="main-view-source"><span>View Source</span></label>
+
+ </div>
+ <a class="headerlink" href="#main"></a>
+ <div class="pdoc-code codehilite"><pre><span></span><span id="main-80"><a href="#main-80"><span class="linenos"> 80</span></a><span class="k">def</span><span class="w"> </span><span class="nf">main</span><span class="p">():</span>
+</span><span id="main-81"><a href="#main-81"><span class="linenos"> 81</span></a> <span class="n">parser</span> <span class="o">=</span> <span class="n">argparse</span><span class="o">.</span><span class="n">ArgumentParser</span><span class="p">(</span><span class="n">description</span><span class="o">=</span><span class="s2">"ACMC command-line tool"</span><span class="p">)</span>
+</span><span id="main-82"><a href="#main-82"><span class="linenos"> 82</span></a> <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s2">"--debug"</span><span class="p">,</span> <span class="n">action</span><span class="o">=</span><span class="s2">"store_true"</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s2">"Enable debug mode"</span><span class="p">)</span>
+</span><span id="main-83"><a href="#main-83"><span class="linenos"> 83</span></a> <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span>
+</span><span id="main-84"><a href="#main-84"><span class="linenos"> 84</span></a> <span class="s2">"--version"</span><span class="p">,</span> <span class="n">action</span><span class="o">=</span><span class="s2">"version"</span><span class="p">,</span> <span class="n">version</span><span class="o">=</span><span class="sa">f</span><span class="s2">"acmc </span><span class="si">{</span><span class="n">acmc</span><span class="o">.</span><span class="n">__version__</span><span class="si">}</span><span class="s2">"</span>
+</span><span id="main-85"><a href="#main-85"><span class="linenos"> 85</span></a> <span class="p">)</span>
+</span><span id="main-86"><a href="#main-86"><span class="linenos"> 86</span></a>
+</span><span id="main-87"><a href="#main-87"><span class="linenos"> 87</span></a> <span class="c1"># Top-level commands</span>
+</span><span id="main-88"><a href="#main-88"><span class="linenos"> 88</span></a> <span class="n">subparsers</span> <span class="o">=</span> <span class="n">parser</span><span class="o">.</span><span class="n">add_subparsers</span><span class="p">(</span>
+</span><span id="main-89"><a href="#main-89"><span class="linenos"> 89</span></a> <span class="n">dest</span><span class="o">=</span><span class="s2">"command"</span><span class="p">,</span> <span class="n">required</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s2">"Available commands"</span>
+</span><span id="main-90"><a href="#main-90"><span class="linenos"> 90</span></a> <span class="p">)</span>
+</span><span id="main-91"><a href="#main-91"><span class="linenos"> 91</span></a>
+</span><span id="main-92"><a href="#main-92"><span class="linenos"> 92</span></a> <span class="c1">### TRUD Command ###</span>
+</span><span id="main-93"><a href="#main-93"><span class="linenos"> 93</span></a> <span class="n">trud_parser</span> <span class="o">=</span> <span class="n">subparsers</span><span class="o">.</span><span class="n">add_parser</span><span class="p">(</span><span class="s2">"trud"</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s2">"TRUD commands"</span><span class="p">)</span>
+</span><span id="main-94"><a href="#main-94"><span class="linenos"> 94</span></a> <span class="n">trud_subparsers</span> <span class="o">=</span> <span class="n">trud_parser</span><span class="o">.</span><span class="n">add_subparsers</span><span class="p">(</span>
+</span><span id="main-95"><a href="#main-95"><span class="linenos"> 95</span></a> <span class="n">dest</span><span class="o">=</span><span class="s2">"subcommand"</span><span class="p">,</span> <span class="n">required</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s2">"TRUD subcommands"</span>
+</span><span id="main-96"><a href="#main-96"><span class="linenos"> 96</span></a> <span class="p">)</span>
+</span><span id="main-97"><a href="#main-97"><span class="linenos"> 97</span></a>
+</span><span id="main-98"><a href="#main-98"><span class="linenos"> 98</span></a> <span class="c1"># trud install</span>
+</span><span id="main-99"><a href="#main-99"><span class="linenos"> 99</span></a> <span class="n">trud_install_parser</span> <span class="o">=</span> <span class="n">trud_subparsers</span><span class="o">.</span><span class="n">add_parser</span><span class="p">(</span>
+</span><span id="main-100"><a href="#main-100"><span class="linenos">100</span></a> <span class="s2">"install"</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s2">"Install TRUD components"</span>
+</span><span id="main-101"><a href="#main-101"><span class="linenos">101</span></a> <span class="p">)</span>
+</span><span id="main-102"><a href="#main-102"><span class="linenos">102</span></a> <span class="n">trud_install_parser</span><span class="o">.</span><span class="n">set_defaults</span><span class="p">(</span><span class="n">func</span><span class="o">=</span><span class="n">trud_install</span><span class="p">)</span>
+</span><span id="main-103"><a href="#main-103"><span class="linenos">103</span></a>
+</span><span id="main-104"><a href="#main-104"><span class="linenos">104</span></a> <span class="c1">### OMOP Command ###</span>
+</span><span id="main-105"><a href="#main-105"><span class="linenos">105</span></a> <span class="n">omop_parser</span> <span class="o">=</span> <span class="n">subparsers</span><span class="o">.</span><span class="n">add_parser</span><span class="p">(</span><span class="s2">"omop"</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s2">"OMOP commands"</span><span class="p">)</span>
+</span><span id="main-106"><a href="#main-106"><span class="linenos">106</span></a> <span class="n">omop_subparsers</span> <span class="o">=</span> <span class="n">omop_parser</span><span class="o">.</span><span class="n">add_subparsers</span><span class="p">(</span>
+</span><span id="main-107"><a href="#main-107"><span class="linenos">107</span></a> <span class="n">dest</span><span class="o">=</span><span class="s2">"subcommand"</span><span class="p">,</span> <span class="n">required</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s2">"OMOP subcommands"</span>
+</span><span id="main-108"><a href="#main-108"><span class="linenos">108</span></a> <span class="p">)</span>
+</span><span id="main-109"><a href="#main-109"><span class="linenos">109</span></a>
+</span><span id="main-110"><a href="#main-110"><span class="linenos">110</span></a> <span class="c1"># omop install</span>
+</span><span id="main-111"><a href="#main-111"><span class="linenos">111</span></a> <span class="n">omop_install_parser</span> <span class="o">=</span> <span class="n">omop_subparsers</span><span class="o">.</span><span class="n">add_parser</span><span class="p">(</span>
+</span><span id="main-112"><a href="#main-112"><span class="linenos">112</span></a> <span class="s2">"install"</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s2">"Install OMOP codes within database"</span>
+</span><span id="main-113"><a href="#main-113"><span class="linenos">113</span></a> <span class="p">)</span>
+</span><span id="main-114"><a href="#main-114"><span class="linenos">114</span></a> <span class="n">omop_install_parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span>
+</span><span id="main-115"><a href="#main-115"><span class="linenos">115</span></a> <span class="s2">"-f"</span><span class="p">,</span> <span class="s2">"--omop-zip-file"</span><span class="p">,</span> <span class="n">required</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s2">"Path to downloaded OMOP zip file"</span>
+</span><span id="main-116"><a href="#main-116"><span class="linenos">116</span></a> <span class="p">)</span>
+</span><span id="main-117"><a href="#main-117"><span class="linenos">117</span></a> <span class="n">omop_install_parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span>
+</span><span id="main-118"><a href="#main-118"><span class="linenos">118</span></a> <span class="s2">"-v"</span><span class="p">,</span> <span class="s2">"--version"</span><span class="p">,</span> <span class="n">required</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s2">"OMOP vocabularies release version"</span>
+</span><span id="main-119"><a href="#main-119"><span class="linenos">119</span></a> <span class="p">)</span>
+</span><span id="main-120"><a href="#main-120"><span class="linenos">120</span></a> <span class="n">omop_install_parser</span><span class="o">.</span><span class="n">set_defaults</span><span class="p">(</span><span class="n">func</span><span class="o">=</span><span class="n">omop_install</span><span class="p">)</span>
+</span><span id="main-121"><a href="#main-121"><span class="linenos">121</span></a>
+</span><span id="main-122"><a href="#main-122"><span class="linenos">122</span></a> <span class="c1"># omop clear</span>
+</span><span id="main-123"><a href="#main-123"><span class="linenos">123</span></a> <span class="n">omop_clear_parser</span> <span class="o">=</span> <span class="n">omop_subparsers</span><span class="o">.</span><span class="n">add_parser</span><span class="p">(</span>
+</span><span id="main-124"><a href="#main-124"><span class="linenos">124</span></a> <span class="s2">"clear"</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s2">"Clear OMOP data from database"</span>
+</span><span id="main-125"><a href="#main-125"><span class="linenos">125</span></a> <span class="p">)</span>
+</span><span id="main-126"><a href="#main-126"><span class="linenos">126</span></a> <span class="n">omop_clear_parser</span><span class="o">.</span><span class="n">set_defaults</span><span class="p">(</span><span class="n">func</span><span class="o">=</span><span class="n">omop_clear</span><span class="p">)</span>
+</span><span id="main-127"><a href="#main-127"><span class="linenos">127</span></a>
+</span><span id="main-128"><a href="#main-128"><span class="linenos">128</span></a> <span class="c1"># omop delete</span>
+</span><span id="main-129"><a href="#main-129"><span class="linenos">129</span></a> <span class="n">omop_delete_parser</span> <span class="o">=</span> <span class="n">omop_subparsers</span><span class="o">.</span><span class="n">add_parser</span><span class="p">(</span>
+</span><span id="main-130"><a href="#main-130"><span class="linenos">130</span></a> <span class="s2">"delete"</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s2">"Delete OMOP database"</span>
+</span><span id="main-131"><a href="#main-131"><span class="linenos">131</span></a> <span class="p">)</span>
+</span><span id="main-132"><a href="#main-132"><span class="linenos">132</span></a> <span class="n">omop_delete_parser</span><span class="o">.</span><span class="n">set_defaults</span><span class="p">(</span><span class="n">func</span><span class="o">=</span><span class="n">omop_delete</span><span class="p">)</span>
+</span><span id="main-133"><a href="#main-133"><span class="linenos">133</span></a>
+</span><span id="main-134"><a href="#main-134"><span class="linenos">134</span></a> <span class="c1">### PHEN Command ###</span>
+</span><span id="main-135"><a href="#main-135"><span class="linenos">135</span></a> <span class="n">phen_parser</span> <span class="o">=</span> <span class="n">subparsers</span><span class="o">.</span><span class="n">add_parser</span><span class="p">(</span><span class="s2">"phen"</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s2">"Phen commands"</span><span class="p">)</span>
+</span><span id="main-136"><a href="#main-136"><span class="linenos">136</span></a> <span class="n">phen_subparsers</span> <span class="o">=</span> <span class="n">phen_parser</span><span class="o">.</span><span class="n">add_subparsers</span><span class="p">(</span>
+</span><span id="main-137"><a href="#main-137"><span class="linenos">137</span></a> <span class="n">dest</span><span class="o">=</span><span class="s2">"subcommand"</span><span class="p">,</span> <span class="n">required</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s2">"Phen subcommands"</span>
+</span><span id="main-138"><a href="#main-138"><span class="linenos">138</span></a> <span class="p">)</span>
+</span><span id="main-139"><a href="#main-139"><span class="linenos">139</span></a>
+</span><span id="main-140"><a href="#main-140"><span class="linenos">140</span></a> <span class="c1"># phen init</span>
+</span><span id="main-141"><a href="#main-141"><span class="linenos">141</span></a> <span class="n">phen_init_parser</span> <span class="o">=</span> <span class="n">phen_subparsers</span><span class="o">.</span><span class="n">add_parser</span><span class="p">(</span>
+</span><span id="main-142"><a href="#main-142"><span class="linenos">142</span></a> <span class="s2">"init"</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s2">"Initiatise phenotype directory"</span>
+</span><span id="main-143"><a href="#main-143"><span class="linenos">143</span></a> <span class="p">)</span>
+</span><span id="main-144"><a href="#main-144"><span class="linenos">144</span></a> <span class="n">phen_init_parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span>
+</span><span id="main-145"><a href="#main-145"><span class="linenos">145</span></a> <span class="s2">"-d"</span><span class="p">,</span>
+</span><span id="main-146"><a href="#main-146"><span class="linenos">146</span></a> <span class="s2">"--phen-dir"</span><span class="p">,</span>
+</span><span id="main-147"><a href="#main-147"><span class="linenos">147</span></a> <span class="nb">type</span><span class="o">=</span><span class="nb">str</span><span class="p">,</span>
+</span><span id="main-148"><a href="#main-148"><span class="linenos">148</span></a> <span class="n">default</span><span class="o">=</span><span class="nb">str</span><span class="p">(</span><span class="n">phen</span><span class="o">.</span><span class="n">DEFAULT_PHEN_PATH</span><span class="o">.</span><span class="n">resolve</span><span class="p">()),</span>
+</span><span id="main-149"><a href="#main-149"><span class="linenos">149</span></a> <span class="n">help</span><span class="o">=</span><span class="s2">"(Optional) Local phenotype workspace directory (default is ./workspace/phen)."</span><span class="p">,</span>
+</span><span id="main-150"><a href="#main-150"><span class="linenos">150</span></a> <span class="p">)</span>
+</span><span id="main-151"><a href="#main-151"><span class="linenos">151</span></a> <span class="n">phen_init_parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span>
+</span><span id="main-152"><a href="#main-152"><span class="linenos">152</span></a> <span class="s2">"-r"</span><span class="p">,</span>
+</span><span id="main-153"><a href="#main-153"><span class="linenos">153</span></a> <span class="s2">"--remote_url"</span><span class="p">,</span>
+</span><span id="main-154"><a href="#main-154"><span class="linenos">154</span></a> <span class="n">help</span><span class="o">=</span><span class="s2">"(Optional) URL to repository where the phenotype will be published."</span><span class="p">,</span>
+</span><span id="main-155"><a href="#main-155"><span class="linenos">155</span></a> <span class="p">)</span>
+</span><span id="main-156"><a href="#main-156"><span class="linenos">156</span></a> <span class="n">phen_init_parser</span><span class="o">.</span><span class="n">set_defaults</span><span class="p">(</span><span class="n">func</span><span class="o">=</span><span class="n">phen_init</span><span class="p">)</span>
+</span><span id="main-157"><a href="#main-157"><span class="linenos">157</span></a>
+</span><span id="main-158"><a href="#main-158"><span class="linenos">158</span></a> <span class="c1"># phen fork</span>
+</span><span id="main-159"><a href="#main-159"><span class="linenos">159</span></a> <span class="n">phen_fork_parser</span> <span class="o">=</span> <span class="n">phen_subparsers</span><span class="o">.</span><span class="n">add_parser</span><span class="p">(</span>
+</span><span id="main-160"><a href="#main-160"><span class="linenos">160</span></a> <span class="s2">"fork"</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s2">"Fork an existing phenotype"</span>
+</span><span id="main-161"><a href="#main-161"><span class="linenos">161</span></a> <span class="p">)</span>
+</span><span id="main-162"><a href="#main-162"><span class="linenos">162</span></a> <span class="n">phen_fork_parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span>
+</span><span id="main-163"><a href="#main-163"><span class="linenos">163</span></a> <span class="s2">"-d"</span><span class="p">,</span>
+</span><span id="main-164"><a href="#main-164"><span class="linenos">164</span></a> <span class="s2">"--phen-dir"</span><span class="p">,</span>
+</span><span id="main-165"><a href="#main-165"><span class="linenos">165</span></a> <span class="nb">type</span><span class="o">=</span><span class="nb">str</span><span class="p">,</span>
+</span><span id="main-166"><a href="#main-166"><span class="linenos">166</span></a> <span class="n">default</span><span class="o">=</span><span class="nb">str</span><span class="p">(</span><span class="n">phen</span><span class="o">.</span><span class="n">DEFAULT_PHEN_PATH</span><span class="o">.</span><span class="n">resolve</span><span class="p">()),</span>
+</span><span id="main-167"><a href="#main-167"><span class="linenos">167</span></a> <span class="n">help</span><span class="o">=</span><span class="s2">"(Optional) Local phenotype workspace directory (default is ./workspace/phen)."</span><span class="p">,</span>
+</span><span id="main-168"><a href="#main-168"><span class="linenos">168</span></a> <span class="p">)</span>
+</span><span id="main-169"><a href="#main-169"><span class="linenos">169</span></a> <span class="n">phen_fork_parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span>
+</span><span id="main-170"><a href="#main-170"><span class="linenos">170</span></a> <span class="s2">"-r"</span><span class="p">,</span>
+</span><span id="main-171"><a href="#main-171"><span class="linenos">171</span></a> <span class="s2">"--remote_url"</span><span class="p">,</span>
+</span><span id="main-172"><a href="#main-172"><span class="linenos">172</span></a> <span class="n">help</span><span class="o">=</span><span class="s2">"(Optional) URL to repository where the forked phenotype will be published."</span><span class="p">,</span>
+</span><span id="main-173"><a href="#main-173"><span class="linenos">173</span></a> <span class="p">)</span>
+</span><span id="main-174"><a href="#main-174"><span class="linenos">174</span></a> <span class="n">phen_fork_parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span>
+</span><span id="main-175"><a href="#main-175"><span class="linenos">175</span></a> <span class="s2">"-u"</span><span class="p">,</span>
+</span><span id="main-176"><a href="#main-176"><span class="linenos">176</span></a> <span class="s2">"--upstream-url"</span><span class="p">,</span>
+</span><span id="main-177"><a href="#main-177"><span class="linenos">177</span></a> <span class="n">required</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span>
+</span><span id="main-178"><a href="#main-178"><span class="linenos">178</span></a> <span class="n">help</span><span class="o">=</span><span class="s2">"(Required) URL to the phenotype repository to fork."</span><span class="p">,</span>
+</span><span id="main-179"><a href="#main-179"><span class="linenos">179</span></a> <span class="p">)</span>
+</span><span id="main-180"><a href="#main-180"><span class="linenos">180</span></a> <span class="n">phen_fork_parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span>
+</span><span id="main-181"><a href="#main-181"><span class="linenos">181</span></a> <span class="s2">"-v"</span><span class="p">,</span>
+</span><span id="main-182"><a href="#main-182"><span class="linenos">182</span></a> <span class="s2">"--upstream-version"</span><span class="p">,</span>
+</span><span id="main-183"><a href="#main-183"><span class="linenos">183</span></a> <span class="n">required</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span>
+</span><span id="main-184"><a href="#main-184"><span class="linenos">184</span></a> <span class="n">help</span><span class="o">=</span><span class="s2">"(Required) Phenotype version to fork."</span><span class="p">,</span>
+</span><span id="main-185"><a href="#main-185"><span class="linenos">185</span></a> <span class="p">)</span>
+</span><span id="main-186"><a href="#main-186"><span class="linenos">186</span></a> <span class="n">phen_fork_parser</span><span class="o">.</span><span class="n">set_defaults</span><span class="p">(</span><span class="n">func</span><span class="o">=</span><span class="n">phen_fork</span><span class="p">)</span>
+</span><span id="main-187"><a href="#main-187"><span class="linenos">187</span></a>
+</span><span id="main-188"><a href="#main-188"><span class="linenos">188</span></a> <span class="c1"># phen validate</span>
+</span><span id="main-189"><a href="#main-189"><span class="linenos">189</span></a> <span class="n">phen_validate_parser</span> <span class="o">=</span> <span class="n">phen_subparsers</span><span class="o">.</span><span class="n">add_parser</span><span class="p">(</span>
+</span><span id="main-190"><a href="#main-190"><span class="linenos">190</span></a> <span class="s2">"validate"</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s2">"Validate phenotype configuration"</span>
+</span><span id="main-191"><a href="#main-191"><span class="linenos">191</span></a> <span class="p">)</span>
+</span><span id="main-192"><a href="#main-192"><span class="linenos">192</span></a> <span class="n">phen_validate_parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span>
+</span><span id="main-193"><a href="#main-193"><span class="linenos">193</span></a> <span class="s2">"-d"</span><span class="p">,</span>
+</span><span id="main-194"><a href="#main-194"><span class="linenos">194</span></a> <span class="s2">"--phen-dir"</span><span class="p">,</span>
+</span><span id="main-195"><a href="#main-195"><span class="linenos">195</span></a> <span class="nb">type</span><span class="o">=</span><span class="nb">str</span><span class="p">,</span>
+</span><span id="main-196"><a href="#main-196"><span class="linenos">196</span></a> <span class="n">default</span><span class="o">=</span><span class="nb">str</span><span class="p">(</span><span class="n">phen</span><span class="o">.</span><span class="n">DEFAULT_PHEN_PATH</span><span class="o">.</span><span class="n">resolve</span><span class="p">()),</span>
+</span><span id="main-197"><a href="#main-197"><span class="linenos">197</span></a> <span class="n">help</span><span class="o">=</span><span class="s2">"(Optional) Local phenotype workspace directory (default is ./workspace/phen)."</span><span class="p">,</span>
+</span><span id="main-198"><a href="#main-198"><span class="linenos">198</span></a> <span class="p">)</span>
+</span><span id="main-199"><a href="#main-199"><span class="linenos">199</span></a> <span class="n">phen_validate_parser</span><span class="o">.</span><span class="n">set_defaults</span><span class="p">(</span><span class="n">func</span><span class="o">=</span><span class="n">phen_validate</span><span class="p">)</span>
+</span><span id="main-200"><a href="#main-200"><span class="linenos">200</span></a>
+</span><span id="main-201"><a href="#main-201"><span class="linenos">201</span></a> <span class="c1"># phen map</span>
+</span><span id="main-202"><a href="#main-202"><span class="linenos">202</span></a> <span class="n">phen_map_parser</span> <span class="o">=</span> <span class="n">phen_subparsers</span><span class="o">.</span><span class="n">add_parser</span><span class="p">(</span><span class="s2">"map"</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s2">"Process phen mapping"</span><span class="p">)</span>
+</span><span id="main-203"><a href="#main-203"><span class="linenos">203</span></a> <span class="n">phen_map_parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span>
+</span><span id="main-204"><a href="#main-204"><span class="linenos">204</span></a> <span class="s2">"-d"</span><span class="p">,</span>
+</span><span id="main-205"><a href="#main-205"><span class="linenos">205</span></a> <span class="s2">"--phen-dir"</span><span class="p">,</span>
+</span><span id="main-206"><a href="#main-206"><span class="linenos">206</span></a> <span class="nb">type</span><span class="o">=</span><span class="nb">str</span><span class="p">,</span>
+</span><span id="main-207"><a href="#main-207"><span class="linenos">207</span></a> <span class="n">default</span><span class="o">=</span><span class="nb">str</span><span class="p">(</span><span class="n">phen</span><span class="o">.</span><span class="n">DEFAULT_PHEN_PATH</span><span class="o">.</span><span class="n">resolve</span><span class="p">()),</span>
+</span><span id="main-208"><a href="#main-208"><span class="linenos">208</span></a> <span class="n">help</span><span class="o">=</span><span class="s2">"(Optional) Local phenotype workspace directory (default is ./workspace/phen)."</span><span class="p">,</span>
+</span><span id="main-209"><a href="#main-209"><span class="linenos">209</span></a> <span class="p">)</span>
+</span><span id="main-210"><a href="#main-210"><span class="linenos">210</span></a> <span class="n">phen_map_parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span>
+</span><span id="main-211"><a href="#main-211"><span class="linenos">211</span></a> <span class="s2">"-t"</span><span class="p">,</span>
+</span><span id="main-212"><a href="#main-212"><span class="linenos">212</span></a> <span class="s2">"--target-coding"</span><span class="p">,</span>
+</span><span id="main-213"><a href="#main-213"><span class="linenos">213</span></a> <span class="n">choices</span><span class="o">=</span><span class="n">parse</span><span class="o">.</span><span class="n">SUPPORTED_CODE_TYPES</span><span class="p">,</span>
+</span><span id="main-214"><a href="#main-214"><span class="linenos">214</span></a> <span class="n">help</span><span class="o">=</span><span class="sa">f</span><span class="s2">"Specify the target coding </span><span class="si">{</span><span class="n">parse</span><span class="o">.</span><span class="n">SUPPORTED_CODE_TYPES</span><span class="si">}</span><span class="s2">"</span><span class="p">,</span>
+</span><span id="main-215"><a href="#main-215"><span class="linenos">215</span></a> <span class="p">)</span>
+</span><span id="main-216"><a href="#main-216"><span class="linenos">216</span></a> <span class="n">phen_map_parser</span><span class="o">.</span><span class="n">set_defaults</span><span class="p">(</span><span class="n">func</span><span class="o">=</span><span class="n">phen_map</span><span class="p">)</span>
+</span><span id="main-217"><a href="#main-217"><span class="linenos">217</span></a>
+</span><span id="main-218"><a href="#main-218"><span class="linenos">218</span></a> <span class="c1"># phen export</span>
+</span><span id="main-219"><a href="#main-219"><span class="linenos">219</span></a> <span class="n">phen_export_parser</span> <span class="o">=</span> <span class="n">phen_subparsers</span><span class="o">.</span><span class="n">add_parser</span><span class="p">(</span>
+</span><span id="main-220"><a href="#main-220"><span class="linenos">220</span></a> <span class="s2">"export"</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s2">"Export phen to OMOP database"</span>
+</span><span id="main-221"><a href="#main-221"><span class="linenos">221</span></a> <span class="p">)</span>
+</span><span id="main-222"><a href="#main-222"><span class="linenos">222</span></a> <span class="n">phen_export_parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span>
+</span><span id="main-223"><a href="#main-223"><span class="linenos">223</span></a> <span class="s2">"-d"</span><span class="p">,</span>
+</span><span id="main-224"><a href="#main-224"><span class="linenos">224</span></a> <span class="s2">"--phen-dir"</span><span class="p">,</span>
+</span><span id="main-225"><a href="#main-225"><span class="linenos">225</span></a> <span class="nb">type</span><span class="o">=</span><span class="nb">str</span><span class="p">,</span>
+</span><span id="main-226"><a href="#main-226"><span class="linenos">226</span></a> <span class="n">default</span><span class="o">=</span><span class="nb">str</span><span class="p">(</span><span class="n">phen</span><span class="o">.</span><span class="n">DEFAULT_PHEN_PATH</span><span class="o">.</span><span class="n">resolve</span><span class="p">()),</span>
+</span><span id="main-227"><a href="#main-227"><span class="linenos">227</span></a> <span class="n">help</span><span class="o">=</span><span class="s2">"(Optional) Local phenotype workspace directory (default is ./workspace/phen)."</span><span class="p">,</span>
+</span><span id="main-228"><a href="#main-228"><span class="linenos">228</span></a> <span class="p">)</span>
+</span><span id="main-229"><a href="#main-229"><span class="linenos">229</span></a> <span class="n">phen_export_parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span>
+</span><span id="main-230"><a href="#main-230"><span class="linenos">230</span></a> <span class="s2">"-v"</span><span class="p">,</span>
+</span><span id="main-231"><a href="#main-231"><span class="linenos">231</span></a> <span class="s2">"--version"</span><span class="p">,</span>
+</span><span id="main-232"><a href="#main-232"><span class="linenos">232</span></a> <span class="nb">type</span><span class="o">=</span><span class="nb">str</span><span class="p">,</span>
+</span><span id="main-233"><a href="#main-233"><span class="linenos">233</span></a> <span class="n">default</span><span class="o">=</span><span class="s2">"latest"</span><span class="p">,</span>
+</span><span id="main-234"><a href="#main-234"><span class="linenos">234</span></a> <span class="n">help</span><span class="o">=</span><span class="s2">"Phenotype version to export, defaults to the latest version"</span><span class="p">,</span>
+</span><span id="main-235"><a href="#main-235"><span class="linenos">235</span></a> <span class="p">)</span>
+</span><span id="main-236"><a href="#main-236"><span class="linenos">236</span></a> <span class="n">phen_export_parser</span><span class="o">.</span><span class="n">set_defaults</span><span class="p">(</span><span class="n">func</span><span class="o">=</span><span class="n">phen_export</span><span class="p">)</span>
+</span><span id="main-237"><a href="#main-237"><span class="linenos">237</span></a>
+</span><span id="main-238"><a href="#main-238"><span class="linenos">238</span></a> <span class="c1"># phen publish</span>
+</span><span id="main-239"><a href="#main-239"><span class="linenos">239</span></a> <span class="n">phen_publish_parser</span> <span class="o">=</span> <span class="n">phen_subparsers</span><span class="o">.</span><span class="n">add_parser</span><span class="p">(</span>
+</span><span id="main-240"><a href="#main-240"><span class="linenos">240</span></a> <span class="s2">"publish"</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s2">"Publish phenotype configuration"</span>
+</span><span id="main-241"><a href="#main-241"><span class="linenos">241</span></a> <span class="p">)</span>
+</span><span id="main-242"><a href="#main-242"><span class="linenos">242</span></a> <span class="n">phen_publish_parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span>
+</span><span id="main-243"><a href="#main-243"><span class="linenos">243</span></a> <span class="s2">"-d"</span><span class="p">,</span>
+</span><span id="main-244"><a href="#main-244"><span class="linenos">244</span></a> <span class="s2">"--phen-dir"</span><span class="p">,</span>
+</span><span id="main-245"><a href="#main-245"><span class="linenos">245</span></a> <span class="nb">type</span><span class="o">=</span><span class="nb">str</span><span class="p">,</span>
+</span><span id="main-246"><a href="#main-246"><span class="linenos">246</span></a> <span class="n">default</span><span class="o">=</span><span class="nb">str</span><span class="p">(</span><span class="n">phen</span><span class="o">.</span><span class="n">DEFAULT_PHEN_PATH</span><span class="o">.</span><span class="n">resolve</span><span class="p">()),</span>
+</span><span id="main-247"><a href="#main-247"><span class="linenos">247</span></a> <span class="n">help</span><span class="o">=</span><span class="s2">"(Optional) Local phenotype workspace directory (default is ./workspace/phen)."</span><span class="p">,</span>
+</span><span id="main-248"><a href="#main-248"><span class="linenos">248</span></a> <span class="p">)</span>
+</span><span id="main-249"><a href="#main-249"><span class="linenos">249</span></a> <span class="n">phen_publish_parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span>
+</span><span id="main-250"><a href="#main-250"><span class="linenos">250</span></a> <span class="s2">"-i"</span><span class="p">,</span>
+</span><span id="main-251"><a href="#main-251"><span class="linenos">251</span></a> <span class="s2">"--increment"</span><span class="p">,</span>
+</span><span id="main-252"><a href="#main-252"><span class="linenos">252</span></a> <span class="nb">type</span><span class="o">=</span><span class="nb">str</span><span class="p">,</span>
+</span><span id="main-253"><a href="#main-253"><span class="linenos">253</span></a> <span class="n">default</span><span class="o">=</span><span class="n">phen</span><span class="o">.</span><span class="n">DEFAULT_VERSION_INC</span><span class="p">,</span>
+</span><span id="main-254"><a href="#main-254"><span class="linenos">254</span></a> <span class="n">choices</span><span class="o">=</span><span class="n">phen</span><span class="o">.</span><span class="n">SEMANTIC_VERSION_TYPES</span><span class="p">,</span>
+</span><span id="main-255"><a href="#main-255"><span class="linenos">255</span></a> <span class="n">help</span><span class="o">=</span><span class="sa">f</span><span class="s2">"Version increment: </span><span class="si">{</span><span class="n">phen</span><span class="o">.</span><span class="n">SEMANTIC_VERSION_TYPES</span><span class="si">}</span><span class="s2">, default is </span><span class="si">{</span><span class="n">phen</span><span class="o">.</span><span class="n">DEFAULT_VERSION_INC</span><span class="si">}</span><span class="s2"> increment"</span><span class="p">,</span>
+</span><span id="main-256"><a href="#main-256"><span class="linenos">256</span></a> <span class="p">)</span>
+</span><span id="main-257"><a href="#main-257"><span class="linenos">257</span></a> <span class="n">phen_publish_parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span>
+</span><span id="main-258"><a href="#main-258"><span class="linenos">258</span></a> <span class="s2">"-m"</span><span class="p">,</span> <span class="s2">"--msg"</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s2">"Message to include with the published version"</span>
+</span><span id="main-259"><a href="#main-259"><span class="linenos">259</span></a> <span class="p">)</span>
+</span><span id="main-260"><a href="#main-260"><span class="linenos">260</span></a> <span class="n">phen_publish_parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span>
+</span><span id="main-261"><a href="#main-261"><span class="linenos">261</span></a> <span class="s2">"-r"</span><span class="p">,</span> <span class="s2">"--remote_url"</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s2">"URL to remote git repository"</span>
+</span><span id="main-262"><a href="#main-262"><span class="linenos">262</span></a> <span class="p">)</span>
+</span><span id="main-263"><a href="#main-263"><span class="linenos">263</span></a> <span class="n">phen_publish_parser</span><span class="o">.</span><span class="n">set_defaults</span><span class="p">(</span><span class="n">func</span><span class="o">=</span><span class="n">phen_publish</span><span class="p">)</span>
+</span><span id="main-264"><a href="#main-264"><span class="linenos">264</span></a>
+</span><span id="main-265"><a href="#main-265"><span class="linenos">265</span></a> <span class="c1"># phen copy</span>
+</span><span id="main-266"><a href="#main-266"><span class="linenos">266</span></a> <span class="n">phen_copy_parser</span> <span class="o">=</span> <span class="n">phen_subparsers</span><span class="o">.</span><span class="n">add_parser</span><span class="p">(</span>
+</span><span id="main-267"><a href="#main-267"><span class="linenos">267</span></a> <span class="s2">"copy"</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s2">"Publish phenotype configuration"</span>
+</span><span id="main-268"><a href="#main-268"><span class="linenos">268</span></a> <span class="p">)</span>
+</span><span id="main-269"><a href="#main-269"><span class="linenos">269</span></a> <span class="n">phen_copy_parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span>
+</span><span id="main-270"><a href="#main-270"><span class="linenos">270</span></a> <span class="s2">"-d"</span><span class="p">,</span>
+</span><span id="main-271"><a href="#main-271"><span class="linenos">271</span></a> <span class="s2">"--phen-dir"</span><span class="p">,</span>
+</span><span id="main-272"><a href="#main-272"><span class="linenos">272</span></a> <span class="nb">type</span><span class="o">=</span><span class="nb">str</span><span class="p">,</span>
+</span><span id="main-273"><a href="#main-273"><span class="linenos">273</span></a> <span class="n">default</span><span class="o">=</span><span class="nb">str</span><span class="p">(</span><span class="n">phen</span><span class="o">.</span><span class="n">DEFAULT_PHEN_PATH</span><span class="o">.</span><span class="n">resolve</span><span class="p">()),</span>
+</span><span id="main-274"><a href="#main-274"><span class="linenos">274</span></a> <span class="n">help</span><span class="o">=</span><span class="s2">"(Optional) Local phenotype workspace directory (default is ./workspace/phen)."</span><span class="p">,</span>
+</span><span id="main-275"><a href="#main-275"><span class="linenos">275</span></a> <span class="p">)</span>
+</span><span id="main-276"><a href="#main-276"><span class="linenos">276</span></a> <span class="n">phen_copy_parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span>
+</span><span id="main-277"><a href="#main-277"><span class="linenos">277</span></a> <span class="s2">"-td"</span><span class="p">,</span>
+</span><span id="main-278"><a href="#main-278"><span class="linenos">278</span></a> <span class="s2">"--target-dir"</span><span class="p">,</span>
+</span><span id="main-279"><a href="#main-279"><span class="linenos">279</span></a> <span class="nb">type</span><span class="o">=</span><span class="nb">str</span><span class="p">,</span>
+</span><span id="main-280"><a href="#main-280"><span class="linenos">280</span></a> <span class="n">default</span><span class="o">=</span><span class="nb">str</span><span class="p">(</span><span class="n">DEFAULT_WORKSPACE_PATH</span><span class="o">.</span><span class="n">resolve</span><span class="p">()),</span>
+</span><span id="main-281"><a href="#main-281"><span class="linenos">281</span></a> <span class="n">help</span><span class="o">=</span><span class="s2">"Target directory for the copy"</span><span class="p">,</span>
+</span><span id="main-282"><a href="#main-282"><span class="linenos">282</span></a> <span class="p">)</span>
+</span><span id="main-283"><a href="#main-283"><span class="linenos">283</span></a> <span class="n">phen_copy_parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span>
+</span><span id="main-284"><a href="#main-284"><span class="linenos">284</span></a> <span class="s2">"-v"</span><span class="p">,</span>
+</span><span id="main-285"><a href="#main-285"><span class="linenos">285</span></a> <span class="s2">"--version"</span><span class="p">,</span>
+</span><span id="main-286"><a href="#main-286"><span class="linenos">286</span></a> <span class="nb">type</span><span class="o">=</span><span class="nb">str</span><span class="p">,</span>
+</span><span id="main-287"><a href="#main-287"><span class="linenos">287</span></a> <span class="n">default</span><span class="o">=</span><span class="s2">"latest"</span><span class="p">,</span>
+</span><span id="main-288"><a href="#main-288"><span class="linenos">288</span></a> <span class="n">help</span><span class="o">=</span><span class="s2">"Phenotype version to copy, defaults to the latest version"</span><span class="p">,</span>
+</span><span id="main-289"><a href="#main-289"><span class="linenos">289</span></a> <span class="p">)</span>
+</span><span id="main-290"><a href="#main-290"><span class="linenos">290</span></a> <span class="n">phen_copy_parser</span><span class="o">.</span><span class="n">set_defaults</span><span class="p">(</span><span class="n">func</span><span class="o">=</span><span class="n">phen_copy</span><span class="p">)</span>
+</span><span id="main-291"><a href="#main-291"><span class="linenos">291</span></a>
+</span><span id="main-292"><a href="#main-292"><span class="linenos">292</span></a> <span class="c1"># phen diff</span>
+</span><span id="main-293"><a href="#main-293"><span class="linenos">293</span></a> <span class="n">phen_diff_parser</span> <span class="o">=</span> <span class="n">phen_subparsers</span><span class="o">.</span><span class="n">add_parser</span><span class="p">(</span>
+</span><span id="main-294"><a href="#main-294"><span class="linenos">294</span></a> <span class="s2">"diff"</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s2">"Publish phenotype configuration"</span>
+</span><span id="main-295"><a href="#main-295"><span class="linenos">295</span></a> <span class="p">)</span>
+</span><span id="main-296"><a href="#main-296"><span class="linenos">296</span></a> <span class="n">phen_diff_parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span>
+</span><span id="main-297"><a href="#main-297"><span class="linenos">297</span></a> <span class="s2">"-d"</span><span class="p">,</span>
+</span><span id="main-298"><a href="#main-298"><span class="linenos">298</span></a> <span class="s2">"--phen-dir"</span><span class="p">,</span>
+</span><span id="main-299"><a href="#main-299"><span class="linenos">299</span></a> <span class="nb">type</span><span class="o">=</span><span class="nb">str</span><span class="p">,</span>
+</span><span id="main-300"><a href="#main-300"><span class="linenos">300</span></a> <span class="n">default</span><span class="o">=</span><span class="nb">str</span><span class="p">(</span><span class="n">phen</span><span class="o">.</span><span class="n">DEFAULT_PHEN_PATH</span><span class="o">.</span><span class="n">resolve</span><span class="p">()),</span>
+</span><span id="main-301"><a href="#main-301"><span class="linenos">301</span></a> <span class="n">help</span><span class="o">=</span><span class="s2">"(Optional) Local phenotype workspace directory (default is ./workspace/phen)."</span><span class="p">,</span>
+</span><span id="main-302"><a href="#main-302"><span class="linenos">302</span></a> <span class="p">)</span>
+</span><span id="main-303"><a href="#main-303"><span class="linenos">303</span></a> <span class="n">phen_diff_parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span>
+</span><span id="main-304"><a href="#main-304"><span class="linenos">304</span></a> <span class="s2">"-v"</span><span class="p">,</span>
+</span><span id="main-305"><a href="#main-305"><span class="linenos">305</span></a> <span class="s2">"--version"</span><span class="p">,</span>
+</span><span id="main-306"><a href="#main-306"><span class="linenos">306</span></a> <span class="n">default</span><span class="o">=</span><span class="s2">"latest"</span><span class="p">,</span>
+</span><span id="main-307"><a href="#main-307"><span class="linenos">307</span></a> <span class="n">help</span><span class="o">=</span><span class="s2">"Phenotype version to compare with an old version, defaults to the HEAD of the workspace directory"</span><span class="p">,</span>
+</span><span id="main-308"><a href="#main-308"><span class="linenos">308</span></a> <span class="p">)</span>
+</span><span id="main-309"><a href="#main-309"><span class="linenos">309</span></a> <span class="n">phen_diff_parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span>
+</span><span id="main-310"><a href="#main-310"><span class="linenos">310</span></a> <span class="s2">"-od"</span><span class="p">,</span>
+</span><span id="main-311"><a href="#main-311"><span class="linenos">311</span></a> <span class="s2">"--old-phen-dir"</span><span class="p">,</span>
+</span><span id="main-312"><a href="#main-312"><span class="linenos">312</span></a> <span class="nb">type</span><span class="o">=</span><span class="nb">str</span><span class="p">,</span>
+</span><span id="main-313"><a href="#main-313"><span class="linenos">313</span></a> <span class="n">default</span><span class="o">=</span><span class="nb">str</span><span class="p">(</span><span class="n">phen</span><span class="o">.</span><span class="n">DEFAULT_PHEN_PATH</span><span class="o">.</span><span class="n">resolve</span><span class="p">()),</span>
+</span><span id="main-314"><a href="#main-314"><span class="linenos">314</span></a> <span class="n">help</span><span class="o">=</span><span class="s2">"Directory for the old phenotype version, defaults to workspace directory"</span><span class="p">,</span>
+</span><span id="main-315"><a href="#main-315"><span class="linenos">315</span></a> <span class="p">)</span>
+</span><span id="main-316"><a href="#main-316"><span class="linenos">316</span></a> <span class="n">phen_diff_parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span>
+</span><span id="main-317"><a href="#main-317"><span class="linenos">317</span></a> <span class="s2">"-ov"</span><span class="p">,</span>
+</span><span id="main-318"><a href="#main-318"><span class="linenos">318</span></a> <span class="s2">"--old-version"</span><span class="p">,</span>
+</span><span id="main-319"><a href="#main-319"><span class="linenos">319</span></a> <span class="n">required</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span>
+</span><span id="main-320"><a href="#main-320"><span class="linenos">320</span></a> <span class="n">help</span><span class="o">=</span><span class="s2">"Old phenotype version to compare with the changed version"</span><span class="p">,</span>
+</span><span id="main-321"><a href="#main-321"><span class="linenos">321</span></a> <span class="p">)</span>
+</span><span id="main-322"><a href="#main-322"><span class="linenos">322</span></a> <span class="n">phen_diff_parser</span><span class="o">.</span><span class="n">set_defaults</span><span class="p">(</span><span class="n">func</span><span class="o">=</span><span class="n">phen_diff</span><span class="p">)</span>
+</span><span id="main-323"><a href="#main-323"><span class="linenos">323</span></a>
+</span><span id="main-324"><a href="#main-324"><span class="linenos">324</span></a> <span class="c1"># Parse arguments</span>
+</span><span id="main-325"><a href="#main-325"><span class="linenos">325</span></a> <span class="n">args</span> <span class="o">=</span> <span class="n">parser</span><span class="o">.</span><span class="n">parse_args</span><span class="p">()</span>
+</span><span id="main-326"><a href="#main-326"><span class="linenos">326</span></a>
+</span><span id="main-327"><a href="#main-327"><span class="linenos">327</span></a> <span class="c1"># setup logging</span>
+</span><span id="main-328"><a href="#main-328"><span class="linenos">328</span></a> <span class="k">if</span> <span class="n">args</span><span class="o">.</span><span class="n">debug</span><span class="p">:</span>
+</span><span id="main-329"><a href="#main-329"><span class="linenos">329</span></a> <span class="n">lc</span><span class="o">.</span><span class="n">set_log_level</span><span class="p">(</span><span class="n">logging</span><span class="o">.</span><span class="n">DEBUG</span><span class="p">)</span>
+</span><span id="main-330"><a href="#main-330"><span class="linenos">330</span></a>
+</span><span id="main-331"><a href="#main-331"><span class="linenos">331</span></a> <span class="c1"># Call the function associated with the command</span>
+</span><span id="main-332"><a href="#main-332"><span class="linenos">332</span></a> <span class="n">args</span><span class="o">.</span><span class="n">func</span><span class="p">(</span><span class="n">args</span><span class="p">)</span>
+</span></pre></div>
+
+
+
+
+ </section>
+ </main>
+<script>
+ function escapeHTML(html) {
+ return document.createElement('div').appendChild(document.createTextNode(html)).parentNode.innerHTML;
+ }
+
+ const originalContent = document.querySelector("main.pdoc");
+ let currentContent = originalContent;
+
+ function setContent(innerHTML) {
+ let elem;
+ if (innerHTML) {
+ elem = document.createElement("main");
+ elem.classList.add("pdoc");
+ elem.innerHTML = innerHTML;
+ } else {
+ elem = originalContent;
+ }
+ if (currentContent !== elem) {
+ currentContent.replaceWith(elem);
+ currentContent = elem;
+ }
+ }
+
+ function getSearchTerm() {
+ return (new URL(window.location)).searchParams.get("search");
+ }
+
+ const searchBox = document.querySelector(".pdoc input[type=search]");
+ searchBox.addEventListener("input", function () {
+ let url = new URL(window.location);
+ if (searchBox.value.trim()) {
+ url.hash = "";
+ url.searchParams.set("search", searchBox.value);
+ } else {
+ url.searchParams.delete("search");
+ }
+ history.replaceState("", "", url.toString());
+ onInput();
+ });
+ window.addEventListener("popstate", onInput);
+
+
+ let search, searchErr;
+
+ async function initialize() {
+ try {
+ search = await new Promise((resolve, reject) => {
+ const script = document.createElement("script");
+ script.type = "text/javascript";
+ script.async = true;
+ script.onload = () => resolve(window.pdocSearch);
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+ document.getElementsByTagName("head")[0].appendChild(script);
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+ } catch (e) {
+ console.error("Cannot fetch pdoc search index");
+ searchErr = "Cannot fetch search index.";
+ }
+ onInput();
+
+ document.querySelector("nav.pdoc").addEventListener("click", e => {
+ if (e.target.hash) {
+ searchBox.value = "";
+ searchBox.dispatchEvent(new Event("input"));
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+ });
+ }
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+ function onInput() {
+ setContent((() => {
+ const term = getSearchTerm();
+ if (!term) {
+ return null
+ }
+ if (searchErr) {
+ return `<h3>Error: ${searchErr}</h3>`
+ }
+ if (!search) {
+ return "<h3>Searching...</h3>"
+ }
+
+ window.scrollTo({top: 0, left: 0, behavior: 'auto'});
+
+ const results = search(term);
+
+ let html;
+ if (results.length === 0) {
+ html = `No search results for '${escapeHTML(term)}'.`
+ } else {
+ html = `<h4>${results.length} search result${results.length > 1 ? "s" : ""} for '${escapeHTML(term)}'.</h4>`;
+ }
+ for (let result of results.slice(0, 10)) {
+ let doc = result.doc;
+ let url = `../${doc.modulename.replaceAll(".", "/")}.html`;
+ if (doc.qualname) {
+ url += `#${doc.qualname}`;
+ }
+
+ let heading;
+ switch (result.doc.kind) {
+ case "function":
+ if (doc.fullname.endsWith(".__init__")) {
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diff --git a/docs/api/acmc/omop.html b/docs/api/acmc/omop.html
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+ </li>
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+ <a class="variable" href="#VOCAB_PATH">VOCAB_PATH</a>
+ </li>
+ <li>
+ <a class="variable" href="#OMOP_CDM_Version">OMOP_CDM_Version</a>
+ </li>
+ <li>
+ <a class="variable" href="#OMOP_DB_FILENAME">OMOP_DB_FILENAME</a>
+ </li>
+ <li>
+ <a class="variable" href="#DB_PATH">DB_PATH</a>
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+ <a class="function" href="#table_exists">table_exists</a>
+ </li>
+ <li>
+ <a class="function" href="#vocab_exists">vocab_exists</a>
+ </li>
+ <li>
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+ <section class="module-info">
+ <h1 class="modulename">
+<a href="./../acmc.html">acmc</a><wbr>.omop </h1>
+
+
+ <input id="mod-omop-view-source" class="view-source-toggle-state" type="checkbox" aria-hidden="true" tabindex="-1">
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+ <label class="view-source-button" for="mod-omop-view-source"><span>View Source</span></label>
+
+ <div class="pdoc-code codehilite"><pre><span></span><span id="L-1"><a href="#L-1"><span class="linenos"> 1</span></a><span class="kn">import</span><span class="w"> </span><span class="nn">os</span>
+</span><span id="L-2"><a href="#L-2"><span class="linenos"> 2</span></a><span class="kn">import</span><span class="w"> </span><span class="nn">argparse</span>
+</span><span id="L-3"><a href="#L-3"><span class="linenos"> 3</span></a><span class="kn">import</span><span class="w"> </span><span class="nn">sqlite3</span>
+</span><span id="L-4"><a href="#L-4"><span class="linenos"> 4</span></a><span class="kn">import</span><span class="w"> </span><span class="nn">pandas</span><span class="w"> </span><span class="k">as</span><span class="w"> </span><span class="nn">pd</span>
+</span><span id="L-5"><a href="#L-5"><span class="linenos"> 5</span></a><span class="kn">import</span><span class="w"> </span><span class="nn">logging</span>
+</span><span id="L-6"><a href="#L-6"><span class="linenos"> 6</span></a><span class="kn">import</span><span class="w"> </span><span class="nn">zipfile</span>
+</span><span id="L-7"><a href="#L-7"><span class="linenos"> 7</span></a><span class="kn">import</span><span class="w"> </span><span class="nn">shutil</span>
+</span><span id="L-8"><a href="#L-8"><span class="linenos"> 8</span></a><span class="kn">import</span><span class="w"> </span><span class="nn">json</span>
+</span><span id="L-9"><a href="#L-9"><span class="linenos"> 9</span></a><span class="kn">import</span><span class="w"> </span><span class="nn">yaml</span>
+</span><span id="L-10"><a href="#L-10"><span class="linenos"> 10</span></a><span class="kn">from</span><span class="w"> </span><span class="nn">pathlib</span><span class="w"> </span><span class="kn">import</span> <span class="n">Path</span>
+</span><span id="L-11"><a href="#L-11"><span class="linenos"> 11</span></a>
+</span><span id="L-12"><a href="#L-12"><span class="linenos"> 12</span></a><span class="kn">from</span><span class="w"> </span><span class="nn">acmc</span><span class="w"> </span><span class="kn">import</span> <span class="n">util</span><span class="p">,</span> <span class="n">logging_config</span>
+</span><span id="L-13"><a href="#L-13"><span class="linenos"> 13</span></a>
+</span><span id="L-14"><a href="#L-14"><span class="linenos"> 14</span></a><span class="c1"># setup logging</span>
+</span><span id="L-15"><a href="#L-15"><span class="linenos"> 15</span></a><span class="n">logger</span> <span class="o">=</span> <span class="n">logging_config</span><span class="o">.</span><span class="n">setup_logger</span><span class="p">()</span>
+</span><span id="L-16"><a href="#L-16"><span class="linenos"> 16</span></a>
+</span><span id="L-17"><a href="#L-17"><span class="linenos"> 17</span></a><span class="c1"># constants</span>
+</span><span id="L-18"><a href="#L-18"><span class="linenos"> 18</span></a><span class="n">VOCAB_PATH</span> <span class="o">=</span> <span class="n">Path</span><span class="p">(</span><span class="s2">"./vocab/omop"</span><span class="p">)</span>
+</span><span id="L-19"><a href="#L-19"><span class="linenos"> 19</span></a><span class="n">OMOP_CDM_Version</span> <span class="o">=</span> <span class="s2">"54"</span>
+</span><span id="L-20"><a href="#L-20"><span class="linenos"> 20</span></a><span class="n">OMOP_DB_FILENAME</span> <span class="o">=</span> <span class="sa">f</span><span class="s2">"omop_</span><span class="si">{</span><span class="n">OMOP_CDM_Version</span><span class="si">}</span><span class="s2">.sqlite"</span>
+</span><span id="L-21"><a href="#L-21"><span class="linenos"> 21</span></a><span class="n">DB_PATH</span> <span class="o">=</span> <span class="n">VOCAB_PATH</span> <span class="o">/</span> <span class="n">OMOP_DB_FILENAME</span>
+</span><span id="L-22"><a href="#L-22"><span class="linenos"> 22</span></a><span class="n">VERSION_FILE</span> <span class="o">=</span> <span class="s2">"omop_version.yaml"</span>
+</span><span id="L-23"><a href="#L-23"><span class="linenos"> 23</span></a><span class="n">VERSION_PATH</span> <span class="o">=</span> <span class="n">VOCAB_PATH</span> <span class="o">/</span> <span class="n">VERSION_FILE</span>
+</span><span id="L-24"><a href="#L-24"><span class="linenos"> 24</span></a><span class="n">EXPORT_FILE</span> <span class="o">=</span> <span class="sa">f</span><span class="s2">"omop_</span><span class="si">{</span><span class="n">OMOP_CDM_Version</span><span class="si">}</span><span class="s2">_export.sqlite"</span>
+</span><span id="L-25"><a href="#L-25"><span class="linenos"> 25</span></a>
+</span><span id="L-26"><a href="#L-26"><span class="linenos"> 26</span></a><span class="n">vocabularies</span> <span class="o">=</span> <span class="p">{</span>
+</span><span id="L-27"><a href="#L-27"><span class="linenos"> 27</span></a> <span class="s2">"source"</span><span class="p">:</span> <span class="s2">"OHDSI Athena"</span><span class="p">,</span>
+</span><span id="L-28"><a href="#L-28"><span class="linenos"> 28</span></a> <span class="s2">"url"</span><span class="p">:</span> <span class="s2">"https://athena.ohdsi.org/vocabulary/list"</span><span class="p">,</span>
+</span><span id="L-29"><a href="#L-29"><span class="linenos"> 29</span></a> <span class="s2">"cdm_version"</span><span class="p">:</span> <span class="n">OMOP_CDM_Version</span><span class="p">,</span>
+</span><span id="L-30"><a href="#L-30"><span class="linenos"> 30</span></a> <span class="s2">"version"</span><span class="p">:</span> <span class="s2">""</span><span class="p">,</span>
+</span><span id="L-31"><a href="#L-31"><span class="linenos"> 31</span></a> <span class="s2">"vocabularies"</span><span class="p">:</span> <span class="p">[</span>
+</span><span id="L-32"><a href="#L-32"><span class="linenos"> 32</span></a> <span class="p">{</span><span class="s2">"id"</span><span class="p">:</span> <span class="mi">1</span><span class="p">,</span> <span class="s2">"name"</span><span class="p">:</span> <span class="s2">"SNOMED"</span><span class="p">},</span> <span class="c1"># No license required</span>
+</span><span id="L-33"><a href="#L-33"><span class="linenos"> 33</span></a> <span class="p">{</span><span class="s2">"id"</span><span class="p">:</span> <span class="mi">2</span><span class="p">,</span> <span class="s2">"name"</span><span class="p">:</span> <span class="s2">"ICD9CM"</span><span class="p">},</span> <span class="c1"># No license required</span>
+</span><span id="L-34"><a href="#L-34"><span class="linenos"> 34</span></a> <span class="p">{</span><span class="s2">"id"</span><span class="p">:</span> <span class="mi">17</span><span class="p">,</span> <span class="s2">"name"</span><span class="p">:</span> <span class="s2">"Readv2"</span><span class="p">},</span> <span class="c1"># No license required</span>
+</span><span id="L-35"><a href="#L-35"><span class="linenos"> 35</span></a> <span class="p">{</span><span class="s2">"id"</span><span class="p">:</span> <span class="mi">21</span><span class="p">,</span> <span class="s2">"name"</span><span class="p">:</span> <span class="s2">"ATC"</span><span class="p">},</span> <span class="c1"># No license required</span>
+</span><span id="L-36"><a href="#L-36"><span class="linenos"> 36</span></a> <span class="p">{</span><span class="s2">"id"</span><span class="p">:</span> <span class="mi">55</span><span class="p">,</span> <span class="s2">"name"</span><span class="p">:</span> <span class="s2">"OPCS4"</span><span class="p">},</span> <span class="c1"># No license required</span>
+</span><span id="L-37"><a href="#L-37"><span class="linenos"> 37</span></a> <span class="p">{</span><span class="s2">"id"</span><span class="p">:</span> <span class="mi">57</span><span class="p">,</span> <span class="s2">"name"</span><span class="p">:</span> <span class="s2">"HES Specialty"</span><span class="p">},</span> <span class="c1"># No license required</span>
+</span><span id="L-38"><a href="#L-38"><span class="linenos"> 38</span></a> <span class="p">{</span><span class="s2">"id"</span><span class="p">:</span> <span class="mi">70</span><span class="p">,</span> <span class="s2">"name"</span><span class="p">:</span> <span class="s2">"ICD10CM"</span><span class="p">},</span> <span class="c1"># No license required</span>
+</span><span id="L-39"><a href="#L-39"><span class="linenos"> 39</span></a> <span class="p">{</span><span class="s2">"id"</span><span class="p">:</span> <span class="mi">75</span><span class="p">,</span> <span class="s2">"name"</span><span class="p">:</span> <span class="s2">"dm+d"</span><span class="p">},</span> <span class="c1"># No license required</span>
+</span><span id="L-40"><a href="#L-40"><span class="linenos"> 40</span></a> <span class="p">{</span><span class="s2">"id"</span><span class="p">:</span> <span class="mi">144</span><span class="p">,</span> <span class="s2">"name"</span><span class="p">:</span> <span class="s2">"UK Biobank"</span><span class="p">},</span> <span class="c1"># No license required</span>
+</span><span id="L-41"><a href="#L-41"><span class="linenos"> 41</span></a> <span class="p">{</span><span class="s2">"id"</span><span class="p">:</span> <span class="mi">154</span><span class="p">,</span> <span class="s2">"name"</span><span class="p">:</span> <span class="s2">"NHS Ethnic Category"</span><span class="p">},</span> <span class="c1"># No license required</span>
+</span><span id="L-42"><a href="#L-42"><span class="linenos"> 42</span></a> <span class="p">{</span><span class="s2">"id"</span><span class="p">:</span> <span class="mi">155</span><span class="p">,</span> <span class="s2">"name"</span><span class="p">:</span> <span class="s2">"NHS Place of Service"</span><span class="p">},</span> <span class="c1"># No license required</span>
+</span><span id="L-43"><a href="#L-43"><span class="linenos"> 43</span></a> <span class="p">],</span>
+</span><span id="L-44"><a href="#L-44"><span class="linenos"> 44</span></a> <span class="s2">"tables"</span><span class="p">:</span> <span class="p">[],</span>
+</span><span id="L-45"><a href="#L-45"><span class="linenos"> 45</span></a><span class="p">}</span>
+</span><span id="L-46"><a href="#L-46"><span class="linenos"> 46</span></a>
+</span><span id="L-47"><a href="#L-47"><span class="linenos"> 47</span></a><span class="n">omop_vocab_types</span> <span class="o">=</span> <span class="p">{</span>
+</span><span id="L-48"><a href="#L-48"><span class="linenos"> 48</span></a> <span class="s2">"read2"</span><span class="p">:</span> <span class="s2">"Read"</span><span class="p">,</span>
+</span><span id="L-49"><a href="#L-49"><span class="linenos"> 49</span></a> <span class="s2">"read3"</span><span class="p">:</span> <span class="kc">None</span><span class="p">,</span>
+</span><span id="L-50"><a href="#L-50"><span class="linenos"> 50</span></a> <span class="s2">"icd10"</span><span class="p">:</span> <span class="s2">"ICD10CM"</span><span class="p">,</span>
+</span><span id="L-51"><a href="#L-51"><span class="linenos"> 51</span></a> <span class="s2">"snomed"</span><span class="p">:</span> <span class="s2">"SNOMED"</span><span class="p">,</span>
+</span><span id="L-52"><a href="#L-52"><span class="linenos"> 52</span></a> <span class="s2">"opcs4"</span><span class="p">:</span> <span class="s2">"OPCS4"</span><span class="p">,</span>
+</span><span id="L-53"><a href="#L-53"><span class="linenos"> 53</span></a> <span class="s2">"atc"</span><span class="p">:</span> <span class="s2">"ATC"</span><span class="p">,</span>
+</span><span id="L-54"><a href="#L-54"><span class="linenos"> 54</span></a> <span class="s2">"med"</span><span class="p">:</span> <span class="kc">None</span><span class="p">,</span>
+</span><span id="L-55"><a href="#L-55"><span class="linenos"> 55</span></a> <span class="s2">"cprd"</span><span class="p">:</span> <span class="kc">None</span><span class="p">,</span>
+</span><span id="L-56"><a href="#L-56"><span class="linenos"> 56</span></a><span class="p">}</span>
+</span><span id="L-57"><a href="#L-57"><span class="linenos"> 57</span></a>
+</span><span id="L-58"><a href="#L-58"><span class="linenos"> 58</span></a>
+</span><span id="L-59"><a href="#L-59"><span class="linenos"> 59</span></a><span class="c1"># Populate SQLite3 Database with default OMOP CONCEPTS</span>
+</span><span id="L-60"><a href="#L-60"><span class="linenos"> 60</span></a><span class="k">def</span><span class="w"> </span><span class="nf">install</span><span class="p">(</span><span class="n">omop_zip_file</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">version</span><span class="p">:</span> <span class="nb">str</span><span class="p">):</span>
+</span><span id="L-61"><a href="#L-61"><span class="linenos"> 61</span></a><span class="w"> </span><span class="sd">"""Installs the OMOP release csv files in a file-based sql database"""</span>
+</span><span id="L-62"><a href="#L-62"><span class="linenos"> 62</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Installing OMOP from zip file: </span><span class="si">{</span><span class="n">omop_zip_file</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+</span><span id="L-63"><a href="#L-63"><span class="linenos"> 63</span></a> <span class="n">omop_zip_path</span> <span class="o">=</span> <span class="n">Path</span><span class="p">(</span><span class="n">omop_zip_file</span><span class="p">)</span>
+</span><span id="L-64"><a href="#L-64"><span class="linenos"> 64</span></a>
+</span><span id="L-65"><a href="#L-65"><span class="linenos"> 65</span></a> <span class="c1"># Check if the file exists and is a ZIP file</span>
+</span><span id="L-66"><a href="#L-66"><span class="linenos"> 66</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="n">omop_zip_path</span><span class="o">.</span><span class="n">exists</span><span class="p">():</span>
+</span><span id="L-67"><a href="#L-67"><span class="linenos"> 67</span></a> <span class="n">msg</span> <span class="o">=</span> <span class="sa">f</span><span class="s2">"</span><span class="si">{</span><span class="n">omop_zip_path</span><span class="si">}</span><span class="s2"> does not exist."</span>
+</span><span id="L-68"><a href="#L-68"><span class="linenos"> 68</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">error</span><span class="p">(</span><span class="n">msg</span><span class="p">)</span>
+</span><span id="L-69"><a href="#L-69"><span class="linenos"> 69</span></a> <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="n">msg</span><span class="p">)</span>
+</span><span id="L-70"><a href="#L-70"><span class="linenos"> 70</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="n">zipfile</span><span class="o">.</span><span class="n">is_zipfile</span><span class="p">(</span><span class="n">omop_zip_path</span><span class="p">):</span>
+</span><span id="L-71"><a href="#L-71"><span class="linenos"> 71</span></a> <span class="n">msg</span> <span class="o">=</span> <span class="sa">f</span><span class="s2">"Error: </span><span class="si">{</span><span class="n">omop_zip_path</span><span class="si">}</span><span class="s2"> is not a valid ZIP file."</span>
+</span><span id="L-72"><a href="#L-72"><span class="linenos"> 72</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">error</span><span class="p">(</span><span class="n">msg</span><span class="p">)</span>
+</span><span id="L-73"><a href="#L-73"><span class="linenos"> 73</span></a> <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="n">msg</span><span class="p">)</span>
+</span><span id="L-74"><a href="#L-74"><span class="linenos"> 74</span></a>
+</span><span id="L-75"><a href="#L-75"><span class="linenos"> 75</span></a> <span class="c1"># check codes directory exists and if not create it</span>
+</span><span id="L-76"><a href="#L-76"><span class="linenos"> 76</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="n">VOCAB_PATH</span><span class="o">.</span><span class="n">exists</span><span class="p">():</span>
+</span><span id="L-77"><a href="#L-77"><span class="linenos"> 77</span></a> <span class="n">VOCAB_PATH</span><span class="o">.</span><span class="n">mkdir</span><span class="p">(</span><span class="n">parents</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+</span><span id="L-78"><a href="#L-78"><span class="linenos"> 78</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="sa">f</span><span class="s2">"OMOP directory '</span><span class="si">{</span><span class="n">VOCAB_PATH</span><span class="si">}</span><span class="s2">' created."</span><span class="p">)</span>
+</span><span id="L-79"><a href="#L-79"><span class="linenos"> 79</span></a> <span class="k">else</span><span class="p">:</span>
+</span><span id="L-80"><a href="#L-80"><span class="linenos"> 80</span></a> <span class="c1"># removing existing OMOP files</span>
+</span><span id="L-81"><a href="#L-81"><span class="linenos"> 81</span></a> <span class="n">csv_files</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="n">VOCAB_PATH</span><span class="o">.</span><span class="n">glob</span><span class="p">(</span><span class="s2">"*.csv"</span><span class="p">))</span>
+</span><span id="L-82"><a href="#L-82"><span class="linenos"> 82</span></a> <span class="k">for</span> <span class="n">file</span> <span class="ow">in</span> <span class="n">csv_files</span><span class="p">:</span>
+</span><span id="L-83"><a href="#L-83"><span class="linenos"> 83</span></a> <span class="n">file</span><span class="o">.</span><span class="n">unlink</span><span class="p">()</span>
+</span><span id="L-84"><a href="#L-84"><span class="linenos"> 84</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Deleted OMOP csv file: </span><span class="si">{</span><span class="n">file</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+</span><span id="L-85"><a href="#L-85"><span class="linenos"> 85</span></a>
+</span><span id="L-86"><a href="#L-86"><span class="linenos"> 86</span></a> <span class="c1"># Extract ZIP contents</span>
+</span><span id="L-87"><a href="#L-87"><span class="linenos"> 87</span></a> <span class="k">with</span> <span class="n">zipfile</span><span class="o">.</span><span class="n">ZipFile</span><span class="p">(</span><span class="n">omop_zip_path</span><span class="p">,</span> <span class="s2">"r"</span><span class="p">)</span> <span class="k">as</span> <span class="n">zip_ref</span><span class="p">:</span>
+</span><span id="L-88"><a href="#L-88"><span class="linenos"> 88</span></a> <span class="n">zip_ref</span><span class="o">.</span><span class="n">extractall</span><span class="p">(</span><span class="n">VOCAB_PATH</span><span class="p">)</span>
+</span><span id="L-89"><a href="#L-89"><span class="linenos"> 89</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Extracted OMOP zip file </span><span class="si">{</span><span class="n">omop_zip_path</span><span class="si">}</span><span class="s2"> to </span><span class="si">{</span><span class="n">VOCAB_PATH</span><span class="si">}</span><span class="s2">/"</span><span class="p">)</span>
+</span><span id="L-90"><a href="#L-90"><span class="linenos"> 90</span></a>
+</span><span id="L-91"><a href="#L-91"><span class="linenos"> 91</span></a> <span class="c1"># connect to database, if it does not exist it will be created</span>
+</span><span id="L-92"><a href="#L-92"><span class="linenos"> 92</span></a> <span class="n">conn</span> <span class="o">=</span> <span class="n">sqlite3</span><span class="o">.</span><span class="n">connect</span><span class="p">(</span><span class="n">DB_PATH</span><span class="p">)</span>
+</span><span id="L-93"><a href="#L-93"><span class="linenos"> 93</span></a> <span class="c1"># Iterate through files in the folder</span>
+</span><span id="L-94"><a href="#L-94"><span class="linenos"> 94</span></a> <span class="n">csv_files</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="n">VOCAB_PATH</span><span class="o">.</span><span class="n">glob</span><span class="p">(</span><span class="s2">"*.csv"</span><span class="p">))</span>
+</span><span id="L-95"><a href="#L-95"><span class="linenos"> 95</span></a> <span class="n">total_tables_count</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">csv_files</span><span class="p">)</span>
+</span><span id="L-96"><a href="#L-96"><span class="linenos"> 96</span></a> <span class="n">table_count</span> <span class="o">=</span> <span class="mi">1</span>
+</span><span id="L-97"><a href="#L-97"><span class="linenos"> 97</span></a> <span class="k">for</span> <span class="n">filename</span> <span class="ow">in</span> <span class="n">csv_files</span><span class="p">:</span>
+</span><span id="L-98"><a href="#L-98"><span class="linenos"> 98</span></a> <span class="k">try</span><span class="p">:</span>
+</span><span id="L-99"><a href="#L-99"><span class="linenos"> 99</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span>
+</span><span id="L-100"><a href="#L-100"><span class="linenos">100</span></a> <span class="sa">f</span><span class="s2">"Processing </span><span class="si">{</span><span class="n">table_count</span><span class="si">}</span><span class="s2"> of </span><span class="si">{</span><span class="n">total_tables_count</span><span class="si">}</span><span class="s2"> tables: </span><span class="si">{</span><span class="n">filename</span><span class="si">}</span><span class="s2">"</span>
+</span><span id="L-101"><a href="#L-101"><span class="linenos">101</span></a> <span class="p">)</span>
+</span><span id="L-102"><a href="#L-102"><span class="linenos">102</span></a> <span class="c1"># read the CSV file with the specified delimiter</span>
+</span><span id="L-103"><a href="#L-103"><span class="linenos">103</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">read_csv</span><span class="p">(</span><span class="n">filename</span><span class="p">,</span> <span class="n">delimiter</span><span class="o">=</span><span class="s2">"</span><span class="se">\t</span><span class="s2">"</span><span class="p">,</span> <span class="n">low_memory</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span>
+</span><span id="L-104"><a href="#L-104"><span class="linenos">104</span></a>
+</span><span id="L-105"><a href="#L-105"><span class="linenos">105</span></a> <span class="c1"># export Table to sqlite db</span>
+</span><span id="L-106"><a href="#L-106"><span class="linenos">106</span></a> <span class="n">df</span><span class="o">.</span><span class="n">to_sql</span><span class="p">(</span><span class="n">filename</span><span class="o">.</span><span class="n">stem</span><span class="p">,</span> <span class="n">conn</span><span class="p">,</span> <span class="n">if_exists</span><span class="o">=</span><span class="s2">"replace"</span><span class="p">,</span> <span class="n">index</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span>
+</span><span id="L-107"><a href="#L-107"><span class="linenos">107</span></a>
+</span><span id="L-108"><a href="#L-108"><span class="linenos">108</span></a> <span class="c1"># add to the metadata</span>
+</span><span id="L-109"><a href="#L-109"><span class="linenos">109</span></a> <span class="n">vocabularies</span><span class="p">[</span><span class="s2">"tables"</span><span class="p">]</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">filename</span><span class="o">.</span><span class="n">stem</span><span class="p">)</span>
+</span><span id="L-110"><a href="#L-110"><span class="linenos">110</span></a> <span class="n">table_count</span> <span class="o">=</span> <span class="n">table_count</span> <span class="o">+</span> <span class="mi">1</span>
+</span><span id="L-111"><a href="#L-111"><span class="linenos">111</span></a> <span class="k">except</span> <span class="ne">Exception</span> <span class="k">as</span> <span class="n">e</span><span class="p">:</span>
+</span><span id="L-112"><a href="#L-112"><span class="linenos">112</span></a> <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Error reading file </span><span class="si">{</span><span class="n">filename</span><span class="si">}</span><span class="s2">: </span><span class="si">{</span><span class="n">e</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+</span><span id="L-113"><a href="#L-113"><span class="linenos">113</span></a>
+</span><span id="L-114"><a href="#L-114"><span class="linenos">114</span></a> <span class="n">conn</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
+</span><span id="L-115"><a href="#L-115"><span class="linenos">115</span></a>
+</span><span id="L-116"><a href="#L-116"><span class="linenos">116</span></a> <span class="c1"># write version file</span>
+</span><span id="L-117"><a href="#L-117"><span class="linenos">117</span></a> <span class="n">write_version_file</span><span class="p">(</span><span class="n">version</span><span class="p">)</span>
+</span><span id="L-118"><a href="#L-118"><span class="linenos">118</span></a>
+</span><span id="L-119"><a href="#L-119"><span class="linenos">119</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"OMOP installation completed"</span><span class="p">)</span>
+</span><span id="L-120"><a href="#L-120"><span class="linenos">120</span></a>
+</span><span id="L-121"><a href="#L-121"><span class="linenos">121</span></a>
+</span><span id="L-122"><a href="#L-122"><span class="linenos">122</span></a><span class="k">def</span><span class="w"> </span><span class="nf">write_version_file</span><span class="p">(</span><span class="n">version</span><span class="p">:</span> <span class="nb">str</span><span class="p">):</span>
+</span><span id="L-123"><a href="#L-123"><span class="linenos">123</span></a><span class="w"> </span><span class="sd">"""Writes the OMOP vocaburaries and version to a file"""</span>
+</span><span id="L-124"><a href="#L-124"><span class="linenos">124</span></a> <span class="n">vocabularies</span><span class="p">[</span><span class="s2">"version"</span><span class="p">]</span> <span class="o">=</span> <span class="n">version</span>
+</span><span id="L-125"><a href="#L-125"><span class="linenos">125</span></a> <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">VERSION_PATH</span><span class="p">,</span> <span class="s2">"w"</span><span class="p">)</span> <span class="k">as</span> <span class="n">file</span><span class="p">:</span>
+</span><span id="L-126"><a href="#L-126"><span class="linenos">126</span></a> <span class="n">yaml</span><span class="o">.</span><span class="n">dump</span><span class="p">(</span>
+</span><span id="L-127"><a href="#L-127"><span class="linenos">127</span></a> <span class="n">vocabularies</span><span class="p">,</span>
+</span><span id="L-128"><a href="#L-128"><span class="linenos">128</span></a> <span class="n">file</span><span class="p">,</span>
+</span><span id="L-129"><a href="#L-129"><span class="linenos">129</span></a> <span class="n">Dumper</span><span class="o">=</span><span class="n">util</span><span class="o">.</span><span class="n">QuotedDumper</span><span class="p">,</span>
+</span><span id="L-130"><a href="#L-130"><span class="linenos">130</span></a> <span class="n">default_flow_style</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span>
+</span><span id="L-131"><a href="#L-131"><span class="linenos">131</span></a> <span class="n">sort_keys</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span>
+</span><span id="L-132"><a href="#L-132"><span class="linenos">132</span></a> <span class="n">default_style</span><span class="o">=</span><span class="s1">'"'</span><span class="p">,</span>
+</span><span id="L-133"><a href="#L-133"><span class="linenos">133</span></a> <span class="p">)</span>
+</span><span id="L-134"><a href="#L-134"><span class="linenos">134</span></a>
+</span><span id="L-135"><a href="#L-135"><span class="linenos">135</span></a>
+</span><span id="L-136"><a href="#L-136"><span class="linenos">136</span></a><span class="k">def</span><span class="w"> </span><span class="nf">clear</span><span class="p">(</span><span class="n">db_path</span><span class="p">:</span> <span class="n">Path</span><span class="p">):</span>
+</span><span id="L-137"><a href="#L-137"><span class="linenos">137</span></a><span class="w"> </span><span class="sd">"""Clears the OMOP sql database"""</span>
+</span><span id="L-138"><a href="#L-138"><span class="linenos">138</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Clearing OMOP data from database"</span><span class="p">)</span>
+</span><span id="L-139"><a href="#L-139"><span class="linenos">139</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="n">db_path</span><span class="o">.</span><span class="n">is_file</span><span class="p">():</span>
+</span><span id="L-140"><a href="#L-140"><span class="linenos">140</span></a> <span class="k">raise</span> <span class="ne">FileNotFoundError</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Error: OMOP DB file '</span><span class="si">{</span><span class="n">db_path</span><span class="si">}</span><span class="s2">' does not exist."</span><span class="p">)</span>
+</span><span id="L-141"><a href="#L-141"><span class="linenos">141</span></a> <span class="n">conn</span> <span class="o">=</span> <span class="n">sqlite3</span><span class="o">.</span><span class="n">connect</span><span class="p">(</span><span class="n">db_path</span><span class="p">)</span>
+</span><span id="L-142"><a href="#L-142"><span class="linenos">142</span></a> <span class="n">cur</span> <span class="o">=</span> <span class="n">conn</span><span class="o">.</span><span class="n">cursor</span><span class="p">()</span>
+</span><span id="L-143"><a href="#L-143"><span class="linenos">143</span></a> <span class="n">cur</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s2">"SELECT name FROM sqlite_master WHERE type='table';"</span><span class="p">)</span>
+</span><span id="L-144"><a href="#L-144"><span class="linenos">144</span></a>
+</span><span id="L-145"><a href="#L-145"><span class="linenos">145</span></a> <span class="c1"># Fetch and print table names</span>
+</span><span id="L-146"><a href="#L-146"><span class="linenos">146</span></a> <span class="n">tables</span> <span class="o">=</span> <span class="n">cur</span><span class="o">.</span><span class="n">fetchall</span><span class="p">()</span>
+</span><span id="L-147"><a href="#L-147"><span class="linenos">147</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="s2">"Tables in database:"</span><span class="p">,</span> <span class="p">[</span><span class="n">table</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="k">for</span> <span class="n">table</span> <span class="ow">in</span> <span class="n">tables</span><span class="p">])</span>
+</span><span id="L-148"><a href="#L-148"><span class="linenos">148</span></a>
+</span><span id="L-149"><a href="#L-149"><span class="linenos">149</span></a> <span class="c1"># cur.execute("DROP TABLE CONCEPT_SET;")</span>
+</span><span id="L-150"><a href="#L-150"><span class="linenos">150</span></a> <span class="c1"># cur.execute("DROP TABLE CONCEPT_SET_ITEM;")</span>
+</span><span id="L-151"><a href="#L-151"><span class="linenos">151</span></a>
+</span><span id="L-152"><a href="#L-152"><span class="linenos">152</span></a> <span class="n">conn</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
+</span><span id="L-153"><a href="#L-153"><span class="linenos">153</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"OMOP database cleared"</span><span class="p">)</span>
+</span><span id="L-154"><a href="#L-154"><span class="linenos">154</span></a>
+</span><span id="L-155"><a href="#L-155"><span class="linenos">155</span></a>
+</span><span id="L-156"><a href="#L-156"><span class="linenos">156</span></a><span class="k">def</span><span class="w"> </span><span class="nf">delete</span><span class="p">(</span><span class="n">db_path</span><span class="p">:</span> <span class="n">Path</span><span class="p">):</span>
+</span><span id="L-157"><a href="#L-157"><span class="linenos">157</span></a><span class="w"> </span><span class="sd">"""Deletes the OMOP sql database"""</span>
+</span><span id="L-158"><a href="#L-158"><span class="linenos">158</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Deleting OMOP database"</span><span class="p">)</span>
+</span><span id="L-159"><a href="#L-159"><span class="linenos">159</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="n">db_path</span><span class="o">.</span><span class="n">is_file</span><span class="p">():</span>
+</span><span id="L-160"><a href="#L-160"><span class="linenos">160</span></a> <span class="k">raise</span> <span class="ne">FileNotFoundError</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Error: OMOP DB file '</span><span class="si">{</span><span class="n">db_path</span><span class="si">}</span><span class="s2">' does not exist."</span><span class="p">)</span>
+</span><span id="L-161"><a href="#L-161"><span class="linenos">161</span></a>
+</span><span id="L-162"><a href="#L-162"><span class="linenos">162</span></a> <span class="n">db_path</span><span class="o">.</span><span class="n">unlink</span><span class="p">()</span>
+</span><span id="L-163"><a href="#L-163"><span class="linenos">163</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"OMOP database deleted"</span><span class="p">)</span>
+</span><span id="L-164"><a href="#L-164"><span class="linenos">164</span></a>
+</span><span id="L-165"><a href="#L-165"><span class="linenos">165</span></a>
+</span><span id="L-166"><a href="#L-166"><span class="linenos">166</span></a><span class="k">def</span><span class="w"> </span><span class="nf">table_exists</span><span class="p">(</span><span class="n">cursor</span><span class="p">:</span> <span class="n">sqlite3</span><span class="o">.</span><span class="n">Cursor</span><span class="p">,</span> <span class="n">table_name</span><span class="p">:</span> <span class="nb">str</span><span class="p">)</span> <span class="o">-></span> <span class="nb">bool</span><span class="p">:</span>
+</span><span id="L-167"><a href="#L-167"><span class="linenos">167</span></a> <span class="c1"># Query to check if the table exists</span>
+</span><span id="L-168"><a href="#L-168"><span class="linenos">168</span></a> <span class="n">cursor</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span>
+</span><span id="L-169"><a href="#L-169"><span class="linenos">169</span></a><span class="w"> </span><span class="sd">"""</span>
+</span><span id="L-170"><a href="#L-170"><span class="linenos">170</span></a><span class="sd"> SELECT name</span>
+</span><span id="L-171"><a href="#L-171"><span class="linenos">171</span></a><span class="sd"> FROM sqlite_master</span>
+</span><span id="L-172"><a href="#L-172"><span class="linenos">172</span></a><span class="sd"> WHERE type='table' AND name=?</span>
+</span><span id="L-173"><a href="#L-173"><span class="linenos">173</span></a><span class="sd"> """</span><span class="p">,</span>
+</span><span id="L-174"><a href="#L-174"><span class="linenos">174</span></a> <span class="p">(</span><span class="n">table_name</span><span class="p">,),</span>
+</span><span id="L-175"><a href="#L-175"><span class="linenos">175</span></a> <span class="p">)</span>
+</span><span id="L-176"><a href="#L-176"><span class="linenos">176</span></a>
+</span><span id="L-177"><a href="#L-177"><span class="linenos">177</span></a> <span class="c1"># Fetch the result</span>
+</span><span id="L-178"><a href="#L-178"><span class="linenos">178</span></a> <span class="n">result</span> <span class="o">=</span> <span class="n">cursor</span><span class="o">.</span><span class="n">fetchone</span><span class="p">()</span>
+</span><span id="L-179"><a href="#L-179"><span class="linenos">179</span></a>
+</span><span id="L-180"><a href="#L-180"><span class="linenos">180</span></a> <span class="k">return</span> <span class="n">result</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span>
+</span><span id="L-181"><a href="#L-181"><span class="linenos">181</span></a>
+</span><span id="L-182"><a href="#L-182"><span class="linenos">182</span></a>
+</span><span id="L-183"><a href="#L-183"><span class="linenos">183</span></a><span class="k">def</span><span class="w"> </span><span class="nf">vocab_exists</span><span class="p">(</span><span class="n">cursor</span><span class="p">:</span> <span class="n">sqlite3</span><span class="o">.</span><span class="n">Cursor</span><span class="p">,</span> <span class="n">vocab_id</span><span class="p">:</span> <span class="nb">str</span><span class="p">)</span> <span class="o">-></span> <span class="nb">bool</span><span class="p">:</span>
+</span><span id="L-184"><a href="#L-184"><span class="linenos">184</span></a> <span class="c1"># Query to check if the table exists</span>
+</span><span id="L-185"><a href="#L-185"><span class="linenos">185</span></a> <span class="n">cursor</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span>
+</span><span id="L-186"><a href="#L-186"><span class="linenos">186</span></a><span class="w"> </span><span class="sd">"""</span>
+</span><span id="L-187"><a href="#L-187"><span class="linenos">187</span></a><span class="sd"> SELECT vocabulary_id </span>
+</span><span id="L-188"><a href="#L-188"><span class="linenos">188</span></a><span class="sd"> FROM VOCABULARY</span>
+</span><span id="L-189"><a href="#L-189"><span class="linenos">189</span></a><span class="sd"> WHERE vocabulary_id=?</span>
+</span><span id="L-190"><a href="#L-190"><span class="linenos">190</span></a><span class="sd"> """</span><span class="p">,</span>
+</span><span id="L-191"><a href="#L-191"><span class="linenos">191</span></a> <span class="p">(</span><span class="n">vocab_id</span><span class="p">,),</span>
+</span><span id="L-192"><a href="#L-192"><span class="linenos">192</span></a> <span class="p">)</span>
+</span><span id="L-193"><a href="#L-193"><span class="linenos">193</span></a>
+</span><span id="L-194"><a href="#L-194"><span class="linenos">194</span></a> <span class="c1"># Fetch the result</span>
+</span><span id="L-195"><a href="#L-195"><span class="linenos">195</span></a> <span class="n">result</span> <span class="o">=</span> <span class="n">cursor</span><span class="o">.</span><span class="n">fetchone</span><span class="p">()</span>
+</span><span id="L-196"><a href="#L-196"><span class="linenos">196</span></a>
+</span><span id="L-197"><a href="#L-197"><span class="linenos">197</span></a> <span class="k">return</span> <span class="n">result</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span>
+</span><span id="L-198"><a href="#L-198"><span class="linenos">198</span></a>
+</span><span id="L-199"><a href="#L-199"><span class="linenos">199</span></a>
+</span><span id="L-200"><a href="#L-200"><span class="linenos">200</span></a><span class="k">def</span><span class="w"> </span><span class="nf">concept_set_exist</span><span class="p">(</span><span class="n">cursor</span><span class="p">:</span> <span class="n">sqlite3</span><span class="o">.</span><span class="n">Cursor</span><span class="p">,</span> <span class="n">concept_set_name</span><span class="p">:</span> <span class="nb">str</span><span class="p">)</span> <span class="o">-></span> <span class="nb">bool</span><span class="p">:</span>
+</span><span id="L-201"><a href="#L-201"><span class="linenos">201</span></a>
+</span><span id="L-202"><a href="#L-202"><span class="linenos">202</span></a> <span class="n">query</span> <span class="o">=</span> <span class="sa">f</span><span class="s2">"SELECT EXISTS (SELECT 1 FROM CONCEPT_SET WHERE concept_set_name = ?)"</span>
+</span><span id="L-203"><a href="#L-203"><span class="linenos">203</span></a> <span class="n">cursor</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="n">query</span><span class="p">,</span> <span class="p">(</span><span class="n">concept_set_name</span><span class="p">,))</span>
+</span><span id="L-204"><a href="#L-204"><span class="linenos">204</span></a>
+</span><span id="L-205"><a href="#L-205"><span class="linenos">205</span></a> <span class="c1"># 1 if exists, 0 otherwise</span>
+</span><span id="L-206"><a href="#L-206"><span class="linenos">206</span></a> <span class="k">return</span> <span class="n">cursor</span><span class="o">.</span><span class="n">fetchone</span><span class="p">()[</span><span class="mi">0</span><span class="p">]</span> <span class="o">==</span> <span class="mi">1</span>
+</span><span id="L-207"><a href="#L-207"><span class="linenos">207</span></a>
+</span><span id="L-208"><a href="#L-208"><span class="linenos">208</span></a>
+</span><span id="L-209"><a href="#L-209"><span class="linenos">209</span></a><span class="k">def</span><span class="w"> </span><span class="nf">export</span><span class="p">(</span><span class="n">map_path</span><span class="p">:</span> <span class="n">Path</span><span class="p">,</span> <span class="n">export_path</span><span class="p">:</span> <span class="n">Path</span><span class="p">,</span> <span class="n">version</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">omop_metadata</span><span class="p">)</span> <span class="o">-></span> <span class="n">Path</span><span class="p">:</span>
+</span><span id="L-210"><a href="#L-210"><span class="linenos">210</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="sa">f</span><span class="s2">"exporting with metadata </span><span class="si">{</span><span class="n">omop_metadata</span><span class="si">}</span><span class="s2"> at version </span><span class="si">{</span><span class="n">version</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+</span><span id="L-211"><a href="#L-211"><span class="linenos">211</span></a>
+</span><span id="L-212"><a href="#L-212"><span class="linenos">212</span></a> <span class="c1"># copy the baseline omop database</span>
+</span><span id="L-213"><a href="#L-213"><span class="linenos">213</span></a> <span class="n">export_db_path</span> <span class="o">=</span> <span class="n">export_path</span> <span class="o">/</span> <span class="n">EXPORT_FILE</span>
+</span><span id="L-214"><a href="#L-214"><span class="linenos">214</span></a> <span class="n">shutil</span><span class="o">.</span><span class="n">copy</span><span class="p">(</span><span class="n">DB_PATH</span><span class="p">,</span> <span class="n">export_db_path</span><span class="p">)</span>
+</span><span id="L-215"><a href="#L-215"><span class="linenos">215</span></a>
+</span><span id="L-216"><a href="#L-216"><span class="linenos">216</span></a> <span class="c1"># connect to db</span>
+</span><span id="L-217"><a href="#L-217"><span class="linenos">217</span></a> <span class="n">conn</span> <span class="o">=</span> <span class="n">sqlite3</span><span class="o">.</span><span class="n">connect</span><span class="p">(</span><span class="n">export_db_path</span><span class="p">)</span>
+</span><span id="L-218"><a href="#L-218"><span class="linenos">218</span></a> <span class="n">cur</span> <span class="o">=</span> <span class="n">conn</span><span class="o">.</span><span class="n">cursor</span><span class="p">()</span>
+</span><span id="L-219"><a href="#L-219"><span class="linenos">219</span></a>
+</span><span id="L-220"><a href="#L-220"><span class="linenos">220</span></a> <span class="c1"># Create VOCABULARY</span>
+</span><span id="L-221"><a href="#L-221"><span class="linenos">221</span></a> <span class="n">df_test</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">(</span>
+</span><span id="L-222"><a href="#L-222"><span class="linenos">222</span></a> <span class="p">[</span>
+</span><span id="L-223"><a href="#L-223"><span class="linenos">223</span></a> <span class="p">{</span>
+</span><span id="L-224"><a href="#L-224"><span class="linenos">224</span></a> <span class="s2">"vocabulary_id"</span><span class="p">:</span> <span class="n">omop_metadata</span><span class="p">[</span><span class="s2">"vocabulary_id"</span><span class="p">],</span>
+</span><span id="L-225"><a href="#L-225"><span class="linenos">225</span></a> <span class="s2">"vocabulary_name"</span><span class="p">:</span> <span class="n">omop_metadata</span><span class="p">[</span><span class="s2">"vocabulary_name"</span><span class="p">],</span>
+</span><span id="L-226"><a href="#L-226"><span class="linenos">226</span></a> <span class="s2">"vocabulary_reference"</span><span class="p">:</span> <span class="n">omop_metadata</span><span class="p">[</span><span class="s2">"vocabulary_reference"</span><span class="p">],</span>
+</span><span id="L-227"><a href="#L-227"><span class="linenos">227</span></a> <span class="s2">"vocabulary_version"</span><span class="p">:</span> <span class="n">version</span><span class="p">,</span>
+</span><span id="L-228"><a href="#L-228"><span class="linenos">228</span></a> <span class="c1"># "vocabulary_concept_id": 0,</span>
+</span><span id="L-229"><a href="#L-229"><span class="linenos">229</span></a> <span class="p">}</span>
+</span><span id="L-230"><a href="#L-230"><span class="linenos">230</span></a> <span class="p">]</span>
+</span><span id="L-231"><a href="#L-231"><span class="linenos">231</span></a> <span class="p">)</span>
+</span><span id="L-232"><a href="#L-232"><span class="linenos">232</span></a> <span class="n">df_test</span><span class="o">.</span><span class="n">to_sql</span><span class="p">(</span><span class="s2">"VOCABULARY"</span><span class="p">,</span> <span class="n">conn</span><span class="p">,</span> <span class="n">if_exists</span><span class="o">=</span><span class="s2">"append"</span><span class="p">,</span> <span class="n">index</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span>
+</span><span id="L-233"><a href="#L-233"><span class="linenos">233</span></a>
+</span><span id="L-234"><a href="#L-234"><span class="linenos">234</span></a> <span class="c1"># Create CONCEPT_SET</span>
+</span><span id="L-235"><a href="#L-235"><span class="linenos">235</span></a> <span class="n">cur</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span>
+</span><span id="L-236"><a href="#L-236"><span class="linenos">236</span></a><span class="w"> </span><span class="sd">"""</span>
+</span><span id="L-237"><a href="#L-237"><span class="linenos">237</span></a><span class="sd"> CREATE TABLE CONCEPT_SET (</span>
+</span><span id="L-238"><a href="#L-238"><span class="linenos">238</span></a><span class="sd"> concept_set_id INTEGER PRIMARY KEY AUTOINCREMENT, -- Unique identifier for each concept set</span>
+</span><span id="L-239"><a href="#L-239"><span class="linenos">239</span></a><span class="sd"> atlas_id INTEGER, -- Unique identifier generated by ATLAS</span>
+</span><span id="L-240"><a href="#L-240"><span class="linenos">240</span></a><span class="sd"> concept_set_name TEXT, -- Optional name for the concept set</span>
+</span><span id="L-241"><a href="#L-241"><span class="linenos">241</span></a><span class="sd"> concept_set_description TEXT, -- Optional description for the concept set</span>
+</span><span id="L-242"><a href="#L-242"><span class="linenos">242</span></a><span class="sd"> vocabulary_id TEXT NOT NULL, -- Foreign key to VOCABULARY table</span>
+</span><span id="L-243"><a href="#L-243"><span class="linenos">243</span></a><span class="sd"> FOREIGN KEY (vocabulary_id) REFERENCES VOCABULARY(vocabulary_id)</span>
+</span><span id="L-244"><a href="#L-244"><span class="linenos">244</span></a><span class="sd"> );"""</span>
+</span><span id="L-245"><a href="#L-245"><span class="linenos">245</span></a> <span class="p">)</span>
+</span><span id="L-246"><a href="#L-246"><span class="linenos">246</span></a>
+</span><span id="L-247"><a href="#L-247"><span class="linenos">247</span></a> <span class="c1"># Create CONCEPT_SET_ITEM</span>
+</span><span id="L-248"><a href="#L-248"><span class="linenos">248</span></a> <span class="n">cur</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span>
+</span><span id="L-249"><a href="#L-249"><span class="linenos">249</span></a><span class="w"> </span><span class="sd">"""</span>
+</span><span id="L-250"><a href="#L-250"><span class="linenos">250</span></a><span class="sd"> CREATE TABLE CONCEPT_SET_ITEM (</span>
+</span><span id="L-251"><a href="#L-251"><span class="linenos">251</span></a><span class="sd"> concept_set_item_id INTEGER PRIMARY KEY AUTOINCREMENT, -- Unique identifier for each mapping</span>
+</span><span id="L-252"><a href="#L-252"><span class="linenos">252</span></a><span class="sd"> concept_set_id INTEGER NOT NULL, -- Foreign key to CONCEPT_SET table</span>
+</span><span id="L-253"><a href="#L-253"><span class="linenos">253</span></a><span class="sd"> concept_id INTEGER NOT NULL, -- Foreign key to CONCEPT table</span>
+</span><span id="L-254"><a href="#L-254"><span class="linenos">254</span></a><span class="sd"> FOREIGN KEY (concept_set_id) REFERENCES CONCEPT_SET(concept_set_id),</span>
+</span><span id="L-255"><a href="#L-255"><span class="linenos">255</span></a><span class="sd"> FOREIGN KEY (concept_id) REFERENCES CONCEPT(concept_id)</span>
+</span><span id="L-256"><a href="#L-256"><span class="linenos">256</span></a><span class="sd"> );"""</span>
+</span><span id="L-257"><a href="#L-257"><span class="linenos">257</span></a> <span class="p">)</span>
+</span><span id="L-258"><a href="#L-258"><span class="linenos">258</span></a>
+</span><span id="L-259"><a href="#L-259"><span class="linenos">259</span></a> <span class="c1"># read map files</span>
+</span><span id="L-260"><a href="#L-260"><span class="linenos">260</span></a> <span class="n">map_files</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="n">map_path</span><span class="o">.</span><span class="n">glob</span><span class="p">(</span><span class="s2">"*.csv"</span><span class="p">))</span>
+</span><span id="L-261"><a href="#L-261"><span class="linenos">261</span></a> <span class="n">total</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">map_files</span><span class="p">)</span>
+</span><span id="L-262"><a href="#L-262"><span class="linenos">262</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Exporting </span><span class="si">{</span><span class="n">total</span><span class="si">}</span><span class="s2"> map files"</span><span class="p">)</span>
+</span><span id="L-263"><a href="#L-263"><span class="linenos">263</span></a> <span class="k">for</span> <span class="n">index</span><span class="p">,</span> <span class="n">map_file</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">map_files</span><span class="p">):</span>
+</span><span id="L-264"><a href="#L-264"><span class="linenos">264</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Processing </span><span class="si">{</span><span class="n">index</span><span class="o">+</span><span class="mi">1</span><span class="si">}</span><span class="s2"> of </span><span class="si">{</span><span class="n">total</span><span class="si">}</span><span class="s2">: </span><span class="si">{</span><span class="n">map_file</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+</span><span id="L-265"><a href="#L-265"><span class="linenos">265</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">read_csv</span><span class="p">(</span><span class="n">map_file</span><span class="p">)</span>
+</span><span id="L-266"><a href="#L-266"><span class="linenos">266</span></a>
+</span><span id="L-267"><a href="#L-267"><span class="linenos">267</span></a> <span class="k">for</span> <span class="n">concept_set_name</span><span class="p">,</span> <span class="n">grp</span> <span class="ow">in</span> <span class="n">df</span><span class="o">.</span><span class="n">groupby</span><span class="p">(</span><span class="s2">"CONCEPT_SET"</span><span class="p">):</span>
+</span><span id="L-268"><a href="#L-268"><span class="linenos">268</span></a>
+</span><span id="L-269"><a href="#L-269"><span class="linenos">269</span></a> <span class="c1"># create Concept_Set</span>
+</span><span id="L-270"><a href="#L-270"><span class="linenos">270</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="n">concept_set_exist</span><span class="p">(</span><span class="n">cur</span><span class="p">,</span> <span class="nb">str</span><span class="p">(</span><span class="n">concept_set_name</span><span class="p">)):</span>
+</span><span id="L-271"><a href="#L-271"><span class="linenos">271</span></a> <span class="n">cur</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span>
+</span><span id="L-272"><a href="#L-272"><span class="linenos">272</span></a> <span class="sa">f</span><span class="s2">"INSERT INTO CONCEPT_SET (concept_set_name, vocabulary_id) VALUES ('</span><span class="si">{</span><span class="n">concept_set_name</span><span class="si">}</span><span class="s2">', '</span><span class="si">{</span><span class="n">omop_metadata</span><span class="p">[</span><span class="s1">'vocabulary_id'</span><span class="p">]</span><span class="si">}</span><span class="s2">');"</span>
+</span><span id="L-273"><a href="#L-273"><span class="linenos">273</span></a> <span class="p">)</span>
+</span><span id="L-274"><a href="#L-274"><span class="linenos">274</span></a> <span class="k">else</span><span class="p">:</span>
+</span><span id="L-275"><a href="#L-275"><span class="linenos">275</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Concept_set </span><span class="si">{</span><span class="n">concept_set_name</span><span class="si">}</span><span class="s2"> already exists"</span><span class="p">)</span>
+</span><span id="L-276"><a href="#L-276"><span class="linenos">276</span></a> <span class="c1"># TODO: ask to remove old concept_set?</span>
+</span><span id="L-277"><a href="#L-277"><span class="linenos">277</span></a>
+</span><span id="L-278"><a href="#L-278"><span class="linenos">278</span></a> <span class="c1"># get Concept_set_Id</span>
+</span><span id="L-279"><a href="#L-279"><span class="linenos">279</span></a> <span class="n">query</span> <span class="o">=</span> <span class="s2">"SELECT concept_set_id FROM CONCEPT_SET WHERE concept_set_name = ? AND vocabulary_id = ?;"</span>
+</span><span id="L-280"><a href="#L-280"><span class="linenos">280</span></a> <span class="n">target_code_type</span> <span class="o">=</span> <span class="n">map_file</span><span class="o">.</span><span class="n">stem</span>
+</span><span id="L-281"><a href="#L-281"><span class="linenos">281</span></a> <span class="n">cur</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span>
+</span><span id="L-282"><a href="#L-282"><span class="linenos">282</span></a> <span class="n">query</span><span class="p">,</span>
+</span><span id="L-283"><a href="#L-283"><span class="linenos">283</span></a> <span class="p">(</span>
+</span><span id="L-284"><a href="#L-284"><span class="linenos">284</span></a> <span class="n">concept_set_name</span><span class="p">,</span>
+</span><span id="L-285"><a href="#L-285"><span class="linenos">285</span></a> <span class="n">omop_metadata</span><span class="p">[</span><span class="s2">"vocabulary_id"</span><span class="p">],</span>
+</span><span id="L-286"><a href="#L-286"><span class="linenos">286</span></a> <span class="p">),</span>
+</span><span id="L-287"><a href="#L-287"><span class="linenos">287</span></a> <span class="p">)</span>
+</span><span id="L-288"><a href="#L-288"><span class="linenos">288</span></a> <span class="c1"># FAILS HERE WITH NONE REUR</span>
+</span><span id="L-289"><a href="#L-289"><span class="linenos">289</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="sa">f</span><span class="s2">"target code type </span><span class="si">{</span><span class="n">target_code_type</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+</span><span id="L-290"><a href="#L-290"><span class="linenos">290</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="sa">f</span><span class="s2">"omop code type </span><span class="si">{</span><span class="n">omop_vocab_types</span><span class="p">[</span><span class="n">target_code_type</span><span class="p">]</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+</span><span id="L-291"><a href="#L-291"><span class="linenos">291</span></a> <span class="n">concept_set_id</span> <span class="o">=</span> <span class="n">cur</span><span class="o">.</span><span class="n">fetchone</span><span class="p">()[</span><span class="mi">0</span><span class="p">]</span>
+</span><span id="L-292"><a href="#L-292"><span class="linenos">292</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="sa">f</span><span class="s2">"concept set id </span><span class="si">{</span><span class="n">concept_set_id</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+</span><span id="L-293"><a href="#L-293"><span class="linenos">293</span></a>
+</span><span id="L-294"><a href="#L-294"><span class="linenos">294</span></a> <span class="c1"># get corresponing Concept_id (OMOP) for each Concept_code (e.g. SNOMED)</span>
+</span><span id="L-295"><a href="#L-295"><span class="linenos">295</span></a> <span class="n">concept_codes</span> <span class="o">=</span> <span class="s2">"'"</span> <span class="o">+</span> <span class="s2">"', '"</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="nb">list</span><span class="p">(</span><span class="n">grp</span><span class="p">[</span><span class="s2">"CONCEPT"</span><span class="p">]</span><span class="o">.</span><span class="n">astype</span><span class="p">(</span><span class="nb">str</span><span class="p">)))</span> <span class="o">+</span> <span class="s2">"'"</span>
+</span><span id="L-296"><a href="#L-296"><span class="linenos">296</span></a> <span class="n">query</span> <span class="o">=</span> <span class="sa">f</span><span class="s2">"SELECT concept_id FROM CONCEPT WHERE vocabulary_id = ? AND concept_code IN (</span><span class="si">{</span><span class="n">concept_codes</span><span class="si">}</span><span class="s2">);"</span>
+</span><span id="L-297"><a href="#L-297"><span class="linenos">297</span></a> <span class="n">cur</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="n">query</span><span class="p">,</span> <span class="p">(</span><span class="n">omop_vocab_types</span><span class="p">[</span><span class="n">target_code_type</span><span class="p">],))</span>
+</span><span id="L-298"><a href="#L-298"><span class="linenos">298</span></a> <span class="n">df_out</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">(</span><span class="n">cur</span><span class="o">.</span><span class="n">fetchall</span><span class="p">(),</span> <span class="n">columns</span><span class="o">=</span><span class="p">[</span><span class="s2">"concept_id"</span><span class="p">])</span>
+</span><span id="L-299"><a href="#L-299"><span class="linenos">299</span></a>
+</span><span id="L-300"><a href="#L-300"><span class="linenos">300</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="nb">len</span><span class="p">(</span><span class="n">grp</span><span class="p">)</span> <span class="o">==</span> <span class="nb">len</span><span class="p">(</span><span class="n">df_out</span><span class="p">):</span>
+</span><span id="L-301"><a href="#L-301"><span class="linenos">301</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">error</span><span class="p">(</span>
+</span><span id="L-302"><a href="#L-302"><span class="linenos">302</span></a> <span class="sa">f</span><span class="s2">"ERROR: Some </span><span class="si">{</span><span class="n">omop_vocab_types</span><span class="p">[</span><span class="n">target_code_type</span><span class="p">]</span><span class="si">}</span><span class="s2"> Codes do not exist in OMOP Database"</span>
+</span><span id="L-303"><a href="#L-303"><span class="linenos">303</span></a> <span class="p">)</span>
+</span><span id="L-304"><a href="#L-304"><span class="linenos">304</span></a>
+</span><span id="L-305"><a href="#L-305"><span class="linenos">305</span></a> <span class="c1"># Create Concept_set_item</span>
+</span><span id="L-306"><a href="#L-306"><span class="linenos">306</span></a> <span class="n">df_out</span><span class="p">[</span><span class="s2">"concept_set_id"</span><span class="p">]</span> <span class="o">=</span> <span class="n">concept_set_id</span>
+</span><span id="L-307"><a href="#L-307"><span class="linenos">307</span></a> <span class="n">df_out</span><span class="o">.</span><span class="n">to_sql</span><span class="p">(</span><span class="s2">"CONCEPT_SET_ITEM"</span><span class="p">,</span> <span class="n">conn</span><span class="p">,</span> <span class="n">if_exists</span><span class="o">=</span><span class="s2">"append"</span><span class="p">,</span> <span class="n">index</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span>
+</span><span id="L-308"><a href="#L-308"><span class="linenos">308</span></a>
+</span><span id="L-309"><a href="#L-309"><span class="linenos">309</span></a> <span class="c1"># Output all tables to CSV</span>
+</span><span id="L-310"><a href="#L-310"><span class="linenos">310</span></a> <span class="c1"># Get the list of all tables</span>
+</span><span id="L-311"><a href="#L-311"><span class="linenos">311</span></a> <span class="n">cur</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s2">"SELECT name FROM sqlite_master WHERE type='table';"</span><span class="p">)</span>
+</span><span id="L-312"><a href="#L-312"><span class="linenos">312</span></a> <span class="n">tables</span> <span class="o">=</span> <span class="n">cur</span><span class="o">.</span><span class="n">fetchall</span><span class="p">()</span> <span class="c1"># List of tables</span>
+</span><span id="L-313"><a href="#L-313"><span class="linenos">313</span></a>
+</span><span id="L-314"><a href="#L-314"><span class="linenos">314</span></a> <span class="c1"># Export each table to a separate CSV file</span>
+</span><span id="L-315"><a href="#L-315"><span class="linenos">315</span></a> <span class="k">for</span> <span class="n">table</span> <span class="ow">in</span> <span class="n">tables</span><span class="p">:</span>
+</span><span id="L-316"><a href="#L-316"><span class="linenos">316</span></a> <span class="n">table_name</span> <span class="o">=</span> <span class="n">table</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
+</span><span id="L-317"><a href="#L-317"><span class="linenos">317</span></a> <span class="c1"># ignore SQLite's internal system table</span>
+</span><span id="L-318"><a href="#L-318"><span class="linenos">318</span></a> <span class="k">if</span> <span class="n">table_name</span> <span class="o">!=</span> <span class="s2">"sqlite_sequence"</span><span class="p">:</span>
+</span><span id="L-319"><a href="#L-319"><span class="linenos">319</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">read_sql_query</span><span class="p">(</span><span class="sa">f</span><span class="s2">"SELECT * FROM </span><span class="si">{</span><span class="n">table_name</span><span class="si">}</span><span class="s2">"</span><span class="p">,</span> <span class="n">conn</span><span class="p">)</span>
+</span><span id="L-320"><a href="#L-320"><span class="linenos">320</span></a> <span class="n">output_file</span> <span class="o">=</span> <span class="sa">f</span><span class="s2">"</span><span class="si">{</span><span class="n">table_name</span><span class="si">}</span><span class="s2">.csv"</span>
+</span><span id="L-321"><a href="#L-321"><span class="linenos">321</span></a> <span class="n">output_path</span> <span class="o">=</span> <span class="n">export_path</span> <span class="o">/</span> <span class="n">output_file</span>
+</span><span id="L-322"><a href="#L-322"><span class="linenos">322</span></a> <span class="n">df</span><span class="o">.</span><span class="n">to_csv</span><span class="p">(</span><span class="n">output_path</span><span class="p">,</span> <span class="n">index</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span> <span class="c1"># Save as CSV</span>
+</span><span id="L-323"><a href="#L-323"><span class="linenos">323</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Exported </span><span class="si">{</span><span class="n">table_name</span><span class="si">}</span><span class="s2"> to </span><span class="si">{</span><span class="n">table_name</span><span class="si">}</span><span class="s2">.csv"</span><span class="p">)</span>
+</span><span id="L-324"><a href="#L-324"><span class="linenos">324</span></a>
+</span><span id="L-325"><a href="#L-325"><span class="linenos">325</span></a> <span class="n">conn</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
+</span><span id="L-326"><a href="#L-326"><span class="linenos">326</span></a>
+</span><span id="L-327"><a href="#L-327"><span class="linenos">327</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Created export db successfully"</span><span class="p">)</span>
+</span><span id="L-328"><a href="#L-328"><span class="linenos">328</span></a>
+</span><span id="L-329"><a href="#L-329"><span class="linenos">329</span></a> <span class="k">return</span> <span class="n">export_db_path</span>
+</span></pre></div>
+
+
+ </section>
+ <section id="logger">
+ <div class="attr variable">
+ <span class="name">logger</span> =
+<span class="default_value"><Logger acmc_logger (INFO)></span>
+
+
+ </div>
+ <a class="headerlink" href="#logger"></a>
+
+
+
+ </section>
+ <section id="VOCAB_PATH">
+ <div class="attr variable">
+ <span class="name">VOCAB_PATH</span> =
+<span class="default_value">PosixPath('vocab/omop')</span>
+
+
+ </div>
+ <a class="headerlink" href="#VOCAB_PATH"></a>
+
+
+
+ </section>
+ <section id="OMOP_CDM_Version">
+ <div class="attr variable">
+ <span class="name">OMOP_CDM_Version</span> =
+<span class="default_value">'54'</span>
+
+
+ </div>
+ <a class="headerlink" href="#OMOP_CDM_Version"></a>
+
+
+
+ </section>
+ <section id="OMOP_DB_FILENAME">
+ <div class="attr variable">
+ <span class="name">OMOP_DB_FILENAME</span> =
+<span class="default_value">'omop_54.sqlite'</span>
+
+
+ </div>
+ <a class="headerlink" href="#OMOP_DB_FILENAME"></a>
+
+
+
+ </section>
+ <section id="DB_PATH">
+ <div class="attr variable">
+ <span class="name">DB_PATH</span> =
+<span class="default_value">PosixPath('vocab/omop/omop_54.sqlite')</span>
+
+
+ </div>
+ <a class="headerlink" href="#DB_PATH"></a>
+
+
+
+ </section>
+ <section id="VERSION_FILE">
+ <div class="attr variable">
+ <span class="name">VERSION_FILE</span> =
+<span class="default_value">'omop_version.yaml'</span>
+
+
+ </div>
+ <a class="headerlink" href="#VERSION_FILE"></a>
+
+
+
+ </section>
+ <section id="VERSION_PATH">
+ <div class="attr variable">
+ <span class="name">VERSION_PATH</span> =
+<span class="default_value">PosixPath('vocab/omop/omop_version.yaml')</span>
+
+
+ </div>
+ <a class="headerlink" href="#VERSION_PATH"></a>
+
+
+
+ </section>
+ <section id="EXPORT_FILE">
+ <div class="attr variable">
+ <span class="name">EXPORT_FILE</span> =
+<span class="default_value">'omop_54_export.sqlite'</span>
+
+
+ </div>
+ <a class="headerlink" href="#EXPORT_FILE"></a>
+
+
+
+ </section>
+ <section id="vocabularies">
+ <div class="attr variable">
+ <span class="name">vocabularies</span> =
+<input id="vocabularies-view-value" class="view-value-toggle-state" type="checkbox" aria-hidden="true" tabindex="-1">
+ <label class="view-value-button pdoc-button" for="vocabularies-view-value"></label><span class="default_value">{'source': 'OHDSI Athena', 'url': 'https://athena.ohdsi.org/vocabulary/list', 'cdm_version': '54', 'version': '', 'vocabularies': [{'id': 1, 'name': 'SNOMED'}, {'id': 2, 'name': 'ICD9CM'}, {'id': 17, 'name': 'Readv2'}, {'id': 21, 'name': 'ATC'}, {'id': 55, 'name': 'OPCS4'}, {'id': 57, 'name': 'HES Specialty'}, {'id': 70, 'name': 'ICD10CM'}, {'id': 75, 'name': 'dm+d'}, {'id': 144, 'name': 'UK Biobank'}, {'id': 154, 'name': 'NHS Ethnic Category'}, {'id': 155, 'name': 'NHS Place of Service'}], 'tables': []}</span>
+
+
+ </div>
+ <a class="headerlink" href="#vocabularies"></a>
+
+
+
+ </section>
+ <section id="omop_vocab_types">
+ <div class="attr variable">
+ <span class="name">omop_vocab_types</span> =
+<input id="omop_vocab_types-view-value" class="view-value-toggle-state" type="checkbox" aria-hidden="true" tabindex="-1">
+ <label class="view-value-button pdoc-button" for="omop_vocab_types-view-value"></label><span class="default_value">{'read2': 'Read', 'read3': None, 'icd10': 'ICD10CM', 'snomed': 'SNOMED', 'opcs4': 'OPCS4', 'atc': 'ATC', 'med': None, 'cprd': None}</span>
+
+
+ </div>
+ <a class="headerlink" href="#omop_vocab_types"></a>
+
+
+
+ </section>
+ <section id="install">
+ <input id="install-view-source" class="view-source-toggle-state" type="checkbox" aria-hidden="true" tabindex="-1">
+<div class="attr function">
+
+ <span class="def">def</span>
+ <span class="name">install</span><span class="signature pdoc-code condensed">(<span class="param"><span class="n">omop_zip_file</span><span class="p">:</span> <span class="nb">str</span>, </span><span class="param"><span class="n">version</span><span class="p">:</span> <span class="nb">str</span></span><span class="return-annotation">):</span></span>
+
+ <label class="view-source-button" for="install-view-source"><span>View Source</span></label>
+
+ </div>
+ <a class="headerlink" href="#install"></a>
+ <div class="pdoc-code codehilite"><pre><span></span><span id="install-61"><a href="#install-61"><span class="linenos"> 61</span></a><span class="k">def</span><span class="w"> </span><span class="nf">install</span><span class="p">(</span><span class="n">omop_zip_file</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">version</span><span class="p">:</span> <span class="nb">str</span><span class="p">):</span>
+</span><span id="install-62"><a href="#install-62"><span class="linenos"> 62</span></a><span class="w"> </span><span class="sd">"""Installs the OMOP release csv files in a file-based sql database"""</span>
+</span><span id="install-63"><a href="#install-63"><span class="linenos"> 63</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Installing OMOP from zip file: </span><span class="si">{</span><span class="n">omop_zip_file</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+</span><span id="install-64"><a href="#install-64"><span class="linenos"> 64</span></a> <span class="n">omop_zip_path</span> <span class="o">=</span> <span class="n">Path</span><span class="p">(</span><span class="n">omop_zip_file</span><span class="p">)</span>
+</span><span id="install-65"><a href="#install-65"><span class="linenos"> 65</span></a>
+</span><span id="install-66"><a href="#install-66"><span class="linenos"> 66</span></a> <span class="c1"># Check if the file exists and is a ZIP file</span>
+</span><span id="install-67"><a href="#install-67"><span class="linenos"> 67</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="n">omop_zip_path</span><span class="o">.</span><span class="n">exists</span><span class="p">():</span>
+</span><span id="install-68"><a href="#install-68"><span class="linenos"> 68</span></a> <span class="n">msg</span> <span class="o">=</span> <span class="sa">f</span><span class="s2">"</span><span class="si">{</span><span class="n">omop_zip_path</span><span class="si">}</span><span class="s2"> does not exist."</span>
+</span><span id="install-69"><a href="#install-69"><span class="linenos"> 69</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">error</span><span class="p">(</span><span class="n">msg</span><span class="p">)</span>
+</span><span id="install-70"><a href="#install-70"><span class="linenos"> 70</span></a> <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="n">msg</span><span class="p">)</span>
+</span><span id="install-71"><a href="#install-71"><span class="linenos"> 71</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="n">zipfile</span><span class="o">.</span><span class="n">is_zipfile</span><span class="p">(</span><span class="n">omop_zip_path</span><span class="p">):</span>
+</span><span id="install-72"><a href="#install-72"><span class="linenos"> 72</span></a> <span class="n">msg</span> <span class="o">=</span> <span class="sa">f</span><span class="s2">"Error: </span><span class="si">{</span><span class="n">omop_zip_path</span><span class="si">}</span><span class="s2"> is not a valid ZIP file."</span>
+</span><span id="install-73"><a href="#install-73"><span class="linenos"> 73</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">error</span><span class="p">(</span><span class="n">msg</span><span class="p">)</span>
+</span><span id="install-74"><a href="#install-74"><span class="linenos"> 74</span></a> <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="n">msg</span><span class="p">)</span>
+</span><span id="install-75"><a href="#install-75"><span class="linenos"> 75</span></a>
+</span><span id="install-76"><a href="#install-76"><span class="linenos"> 76</span></a> <span class="c1"># check codes directory exists and if not create it</span>
+</span><span id="install-77"><a href="#install-77"><span class="linenos"> 77</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="n">VOCAB_PATH</span><span class="o">.</span><span class="n">exists</span><span class="p">():</span>
+</span><span id="install-78"><a href="#install-78"><span class="linenos"> 78</span></a> <span class="n">VOCAB_PATH</span><span class="o">.</span><span class="n">mkdir</span><span class="p">(</span><span class="n">parents</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+</span><span id="install-79"><a href="#install-79"><span class="linenos"> 79</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="sa">f</span><span class="s2">"OMOP directory '</span><span class="si">{</span><span class="n">VOCAB_PATH</span><span class="si">}</span><span class="s2">' created."</span><span class="p">)</span>
+</span><span id="install-80"><a href="#install-80"><span class="linenos"> 80</span></a> <span class="k">else</span><span class="p">:</span>
+</span><span id="install-81"><a href="#install-81"><span class="linenos"> 81</span></a> <span class="c1"># removing existing OMOP files</span>
+</span><span id="install-82"><a href="#install-82"><span class="linenos"> 82</span></a> <span class="n">csv_files</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="n">VOCAB_PATH</span><span class="o">.</span><span class="n">glob</span><span class="p">(</span><span class="s2">"*.csv"</span><span class="p">))</span>
+</span><span id="install-83"><a href="#install-83"><span class="linenos"> 83</span></a> <span class="k">for</span> <span class="n">file</span> <span class="ow">in</span> <span class="n">csv_files</span><span class="p">:</span>
+</span><span id="install-84"><a href="#install-84"><span class="linenos"> 84</span></a> <span class="n">file</span><span class="o">.</span><span class="n">unlink</span><span class="p">()</span>
+</span><span id="install-85"><a href="#install-85"><span class="linenos"> 85</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Deleted OMOP csv file: </span><span class="si">{</span><span class="n">file</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+</span><span id="install-86"><a href="#install-86"><span class="linenos"> 86</span></a>
+</span><span id="install-87"><a href="#install-87"><span class="linenos"> 87</span></a> <span class="c1"># Extract ZIP contents</span>
+</span><span id="install-88"><a href="#install-88"><span class="linenos"> 88</span></a> <span class="k">with</span> <span class="n">zipfile</span><span class="o">.</span><span class="n">ZipFile</span><span class="p">(</span><span class="n">omop_zip_path</span><span class="p">,</span> <span class="s2">"r"</span><span class="p">)</span> <span class="k">as</span> <span class="n">zip_ref</span><span class="p">:</span>
+</span><span id="install-89"><a href="#install-89"><span class="linenos"> 89</span></a> <span class="n">zip_ref</span><span class="o">.</span><span class="n">extractall</span><span class="p">(</span><span class="n">VOCAB_PATH</span><span class="p">)</span>
+</span><span id="install-90"><a href="#install-90"><span class="linenos"> 90</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Extracted OMOP zip file </span><span class="si">{</span><span class="n">omop_zip_path</span><span class="si">}</span><span class="s2"> to </span><span class="si">{</span><span class="n">VOCAB_PATH</span><span class="si">}</span><span class="s2">/"</span><span class="p">)</span>
+</span><span id="install-91"><a href="#install-91"><span class="linenos"> 91</span></a>
+</span><span id="install-92"><a href="#install-92"><span class="linenos"> 92</span></a> <span class="c1"># connect to database, if it does not exist it will be created</span>
+</span><span id="install-93"><a href="#install-93"><span class="linenos"> 93</span></a> <span class="n">conn</span> <span class="o">=</span> <span class="n">sqlite3</span><span class="o">.</span><span class="n">connect</span><span class="p">(</span><span class="n">DB_PATH</span><span class="p">)</span>
+</span><span id="install-94"><a href="#install-94"><span class="linenos"> 94</span></a> <span class="c1"># Iterate through files in the folder</span>
+</span><span id="install-95"><a href="#install-95"><span class="linenos"> 95</span></a> <span class="n">csv_files</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="n">VOCAB_PATH</span><span class="o">.</span><span class="n">glob</span><span class="p">(</span><span class="s2">"*.csv"</span><span class="p">))</span>
+</span><span id="install-96"><a href="#install-96"><span class="linenos"> 96</span></a> <span class="n">total_tables_count</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">csv_files</span><span class="p">)</span>
+</span><span id="install-97"><a href="#install-97"><span class="linenos"> 97</span></a> <span class="n">table_count</span> <span class="o">=</span> <span class="mi">1</span>
+</span><span id="install-98"><a href="#install-98"><span class="linenos"> 98</span></a> <span class="k">for</span> <span class="n">filename</span> <span class="ow">in</span> <span class="n">csv_files</span><span class="p">:</span>
+</span><span id="install-99"><a href="#install-99"><span class="linenos"> 99</span></a> <span class="k">try</span><span class="p">:</span>
+</span><span id="install-100"><a href="#install-100"><span class="linenos">100</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span>
+</span><span id="install-101"><a href="#install-101"><span class="linenos">101</span></a> <span class="sa">f</span><span class="s2">"Processing </span><span class="si">{</span><span class="n">table_count</span><span class="si">}</span><span class="s2"> of </span><span class="si">{</span><span class="n">total_tables_count</span><span class="si">}</span><span class="s2"> tables: </span><span class="si">{</span><span class="n">filename</span><span class="si">}</span><span class="s2">"</span>
+</span><span id="install-102"><a href="#install-102"><span class="linenos">102</span></a> <span class="p">)</span>
+</span><span id="install-103"><a href="#install-103"><span class="linenos">103</span></a> <span class="c1"># read the CSV file with the specified delimiter</span>
+</span><span id="install-104"><a href="#install-104"><span class="linenos">104</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">read_csv</span><span class="p">(</span><span class="n">filename</span><span class="p">,</span> <span class="n">delimiter</span><span class="o">=</span><span class="s2">"</span><span class="se">\t</span><span class="s2">"</span><span class="p">,</span> <span class="n">low_memory</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span>
+</span><span id="install-105"><a href="#install-105"><span class="linenos">105</span></a>
+</span><span id="install-106"><a href="#install-106"><span class="linenos">106</span></a> <span class="c1"># export Table to sqlite db</span>
+</span><span id="install-107"><a href="#install-107"><span class="linenos">107</span></a> <span class="n">df</span><span class="o">.</span><span class="n">to_sql</span><span class="p">(</span><span class="n">filename</span><span class="o">.</span><span class="n">stem</span><span class="p">,</span> <span class="n">conn</span><span class="p">,</span> <span class="n">if_exists</span><span class="o">=</span><span class="s2">"replace"</span><span class="p">,</span> <span class="n">index</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span>
+</span><span id="install-108"><a href="#install-108"><span class="linenos">108</span></a>
+</span><span id="install-109"><a href="#install-109"><span class="linenos">109</span></a> <span class="c1"># add to the metadata</span>
+</span><span id="install-110"><a href="#install-110"><span class="linenos">110</span></a> <span class="n">vocabularies</span><span class="p">[</span><span class="s2">"tables"</span><span class="p">]</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">filename</span><span class="o">.</span><span class="n">stem</span><span class="p">)</span>
+</span><span id="install-111"><a href="#install-111"><span class="linenos">111</span></a> <span class="n">table_count</span> <span class="o">=</span> <span class="n">table_count</span> <span class="o">+</span> <span class="mi">1</span>
+</span><span id="install-112"><a href="#install-112"><span class="linenos">112</span></a> <span class="k">except</span> <span class="ne">Exception</span> <span class="k">as</span> <span class="n">e</span><span class="p">:</span>
+</span><span id="install-113"><a href="#install-113"><span class="linenos">113</span></a> <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Error reading file </span><span class="si">{</span><span class="n">filename</span><span class="si">}</span><span class="s2">: </span><span class="si">{</span><span class="n">e</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+</span><span id="install-114"><a href="#install-114"><span class="linenos">114</span></a>
+</span><span id="install-115"><a href="#install-115"><span class="linenos">115</span></a> <span class="n">conn</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
+</span><span id="install-116"><a href="#install-116"><span class="linenos">116</span></a>
+</span><span id="install-117"><a href="#install-117"><span class="linenos">117</span></a> <span class="c1"># write version file</span>
+</span><span id="install-118"><a href="#install-118"><span class="linenos">118</span></a> <span class="n">write_version_file</span><span class="p">(</span><span class="n">version</span><span class="p">)</span>
+</span><span id="install-119"><a href="#install-119"><span class="linenos">119</span></a>
+</span><span id="install-120"><a href="#install-120"><span class="linenos">120</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"OMOP installation completed"</span><span class="p">)</span>
+</span></pre></div>
+
+
+ <div class="docstring"><p>Installs the OMOP release csv files in a file-based sql database</p>
+</div>
+
+
+ </section>
+ <section id="write_version_file">
+ <input id="write_version_file-view-source" class="view-source-toggle-state" type="checkbox" aria-hidden="true" tabindex="-1">
+<div class="attr function">
+
+ <span class="def">def</span>
+ <span class="name">write_version_file</span><span class="signature pdoc-code condensed">(<span class="param"><span class="n">version</span><span class="p">:</span> <span class="nb">str</span></span><span class="return-annotation">):</span></span>
+
+ <label class="view-source-button" for="write_version_file-view-source"><span>View Source</span></label>
+
+ </div>
+ <a class="headerlink" href="#write_version_file"></a>
+ <div class="pdoc-code codehilite"><pre><span></span><span id="write_version_file-123"><a href="#write_version_file-123"><span class="linenos">123</span></a><span class="k">def</span><span class="w"> </span><span class="nf">write_version_file</span><span class="p">(</span><span class="n">version</span><span class="p">:</span> <span class="nb">str</span><span class="p">):</span>
+</span><span id="write_version_file-124"><a href="#write_version_file-124"><span class="linenos">124</span></a><span class="w"> </span><span class="sd">"""Writes the OMOP vocaburaries and version to a file"""</span>
+</span><span id="write_version_file-125"><a href="#write_version_file-125"><span class="linenos">125</span></a> <span class="n">vocabularies</span><span class="p">[</span><span class="s2">"version"</span><span class="p">]</span> <span class="o">=</span> <span class="n">version</span>
+</span><span id="write_version_file-126"><a href="#write_version_file-126"><span class="linenos">126</span></a> <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">VERSION_PATH</span><span class="p">,</span> <span class="s2">"w"</span><span class="p">)</span> <span class="k">as</span> <span class="n">file</span><span class="p">:</span>
+</span><span id="write_version_file-127"><a href="#write_version_file-127"><span class="linenos">127</span></a> <span class="n">yaml</span><span class="o">.</span><span class="n">dump</span><span class="p">(</span>
+</span><span id="write_version_file-128"><a href="#write_version_file-128"><span class="linenos">128</span></a> <span class="n">vocabularies</span><span class="p">,</span>
+</span><span id="write_version_file-129"><a href="#write_version_file-129"><span class="linenos">129</span></a> <span class="n">file</span><span class="p">,</span>
+</span><span id="write_version_file-130"><a href="#write_version_file-130"><span class="linenos">130</span></a> <span class="n">Dumper</span><span class="o">=</span><span class="n">util</span><span class="o">.</span><span class="n">QuotedDumper</span><span class="p">,</span>
+</span><span id="write_version_file-131"><a href="#write_version_file-131"><span class="linenos">131</span></a> <span class="n">default_flow_style</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span>
+</span><span id="write_version_file-132"><a href="#write_version_file-132"><span class="linenos">132</span></a> <span class="n">sort_keys</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span>
+</span><span id="write_version_file-133"><a href="#write_version_file-133"><span class="linenos">133</span></a> <span class="n">default_style</span><span class="o">=</span><span class="s1">'"'</span><span class="p">,</span>
+</span><span id="write_version_file-134"><a href="#write_version_file-134"><span class="linenos">134</span></a> <span class="p">)</span>
+</span></pre></div>
+
+
+ <div class="docstring"><p>Writes the OMOP vocaburaries and version to a file</p>
+</div>
+
+
+ </section>
+ <section id="clear">
+ <input id="clear-view-source" class="view-source-toggle-state" type="checkbox" aria-hidden="true" tabindex="-1">
+<div class="attr function">
+
+ <span class="def">def</span>
+ <span class="name">clear</span><span class="signature pdoc-code condensed">(<span class="param"><span class="n">db_path</span><span class="p">:</span> <span class="n">pathlib</span><span class="o">.</span><span class="n">Path</span></span><span class="return-annotation">):</span></span>
+
+ <label class="view-source-button" for="clear-view-source"><span>View Source</span></label>
+
+ </div>
+ <a class="headerlink" href="#clear"></a>
+ <div class="pdoc-code codehilite"><pre><span></span><span id="clear-137"><a href="#clear-137"><span class="linenos">137</span></a><span class="k">def</span><span class="w"> </span><span class="nf">clear</span><span class="p">(</span><span class="n">db_path</span><span class="p">:</span> <span class="n">Path</span><span class="p">):</span>
+</span><span id="clear-138"><a href="#clear-138"><span class="linenos">138</span></a><span class="w"> </span><span class="sd">"""Clears the OMOP sql database"""</span>
+</span><span id="clear-139"><a href="#clear-139"><span class="linenos">139</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Clearing OMOP data from database"</span><span class="p">)</span>
+</span><span id="clear-140"><a href="#clear-140"><span class="linenos">140</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="n">db_path</span><span class="o">.</span><span class="n">is_file</span><span class="p">():</span>
+</span><span id="clear-141"><a href="#clear-141"><span class="linenos">141</span></a> <span class="k">raise</span> <span class="ne">FileNotFoundError</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Error: OMOP DB file '</span><span class="si">{</span><span class="n">db_path</span><span class="si">}</span><span class="s2">' does not exist."</span><span class="p">)</span>
+</span><span id="clear-142"><a href="#clear-142"><span class="linenos">142</span></a> <span class="n">conn</span> <span class="o">=</span> <span class="n">sqlite3</span><span class="o">.</span><span class="n">connect</span><span class="p">(</span><span class="n">db_path</span><span class="p">)</span>
+</span><span id="clear-143"><a href="#clear-143"><span class="linenos">143</span></a> <span class="n">cur</span> <span class="o">=</span> <span class="n">conn</span><span class="o">.</span><span class="n">cursor</span><span class="p">()</span>
+</span><span id="clear-144"><a href="#clear-144"><span class="linenos">144</span></a> <span class="n">cur</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s2">"SELECT name FROM sqlite_master WHERE type='table';"</span><span class="p">)</span>
+</span><span id="clear-145"><a href="#clear-145"><span class="linenos">145</span></a>
+</span><span id="clear-146"><a href="#clear-146"><span class="linenos">146</span></a> <span class="c1"># Fetch and print table names</span>
+</span><span id="clear-147"><a href="#clear-147"><span class="linenos">147</span></a> <span class="n">tables</span> <span class="o">=</span> <span class="n">cur</span><span class="o">.</span><span class="n">fetchall</span><span class="p">()</span>
+</span><span id="clear-148"><a href="#clear-148"><span class="linenos">148</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="s2">"Tables in database:"</span><span class="p">,</span> <span class="p">[</span><span class="n">table</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="k">for</span> <span class="n">table</span> <span class="ow">in</span> <span class="n">tables</span><span class="p">])</span>
+</span><span id="clear-149"><a href="#clear-149"><span class="linenos">149</span></a>
+</span><span id="clear-150"><a href="#clear-150"><span class="linenos">150</span></a> <span class="c1"># cur.execute("DROP TABLE CONCEPT_SET;")</span>
+</span><span id="clear-151"><a href="#clear-151"><span class="linenos">151</span></a> <span class="c1"># cur.execute("DROP TABLE CONCEPT_SET_ITEM;")</span>
+</span><span id="clear-152"><a href="#clear-152"><span class="linenos">152</span></a>
+</span><span id="clear-153"><a href="#clear-153"><span class="linenos">153</span></a> <span class="n">conn</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
+</span><span id="clear-154"><a href="#clear-154"><span class="linenos">154</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"OMOP database cleared"</span><span class="p">)</span>
+</span></pre></div>
+
+
+ <div class="docstring"><p>Clears the OMOP sql database</p>
+</div>
+
+
+ </section>
+ <section id="delete">
+ <input id="delete-view-source" class="view-source-toggle-state" type="checkbox" aria-hidden="true" tabindex="-1">
+<div class="attr function">
+
+ <span class="def">def</span>
+ <span class="name">delete</span><span class="signature pdoc-code condensed">(<span class="param"><span class="n">db_path</span><span class="p">:</span> <span class="n">pathlib</span><span class="o">.</span><span class="n">Path</span></span><span class="return-annotation">):</span></span>
+
+ <label class="view-source-button" for="delete-view-source"><span>View Source</span></label>
+
+ </div>
+ <a class="headerlink" href="#delete"></a>
+ <div class="pdoc-code codehilite"><pre><span></span><span id="delete-157"><a href="#delete-157"><span class="linenos">157</span></a><span class="k">def</span><span class="w"> </span><span class="nf">delete</span><span class="p">(</span><span class="n">db_path</span><span class="p">:</span> <span class="n">Path</span><span class="p">):</span>
+</span><span id="delete-158"><a href="#delete-158"><span class="linenos">158</span></a><span class="w"> </span><span class="sd">"""Deletes the OMOP sql database"""</span>
+</span><span id="delete-159"><a href="#delete-159"><span class="linenos">159</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Deleting OMOP database"</span><span class="p">)</span>
+</span><span id="delete-160"><a href="#delete-160"><span class="linenos">160</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="n">db_path</span><span class="o">.</span><span class="n">is_file</span><span class="p">():</span>
+</span><span id="delete-161"><a href="#delete-161"><span class="linenos">161</span></a> <span class="k">raise</span> <span class="ne">FileNotFoundError</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Error: OMOP DB file '</span><span class="si">{</span><span class="n">db_path</span><span class="si">}</span><span class="s2">' does not exist."</span><span class="p">)</span>
+</span><span id="delete-162"><a href="#delete-162"><span class="linenos">162</span></a>
+</span><span id="delete-163"><a href="#delete-163"><span class="linenos">163</span></a> <span class="n">db_path</span><span class="o">.</span><span class="n">unlink</span><span class="p">()</span>
+</span><span id="delete-164"><a href="#delete-164"><span class="linenos">164</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"OMOP database deleted"</span><span class="p">)</span>
+</span></pre></div>
+
+
+ <div class="docstring"><p>Deletes the OMOP sql database</p>
+</div>
+
+
+ </section>
+ <section id="table_exists">
+ <input id="table_exists-view-source" class="view-source-toggle-state" type="checkbox" aria-hidden="true" tabindex="-1">
+<div class="attr function">
+
+ <span class="def">def</span>
+ <span class="name">table_exists</span><span class="signature pdoc-code condensed">(<span class="param"><span class="n">cursor</span><span class="p">:</span> <span class="n">sqlite3</span><span class="o">.</span><span class="n">Cursor</span>, </span><span class="param"><span class="n">table_name</span><span class="p">:</span> <span class="nb">str</span></span><span class="return-annotation">) -> <span class="nb">bool</span>:</span></span>
+
+ <label class="view-source-button" for="table_exists-view-source"><span>View Source</span></label>
+
+ </div>
+ <a class="headerlink" href="#table_exists"></a>
+ <div class="pdoc-code codehilite"><pre><span></span><span id="table_exists-167"><a href="#table_exists-167"><span class="linenos">167</span></a><span class="k">def</span><span class="w"> </span><span class="nf">table_exists</span><span class="p">(</span><span class="n">cursor</span><span class="p">:</span> <span class="n">sqlite3</span><span class="o">.</span><span class="n">Cursor</span><span class="p">,</span> <span class="n">table_name</span><span class="p">:</span> <span class="nb">str</span><span class="p">)</span> <span class="o">-></span> <span class="nb">bool</span><span class="p">:</span>
+</span><span id="table_exists-168"><a href="#table_exists-168"><span class="linenos">168</span></a> <span class="c1"># Query to check if the table exists</span>
+</span><span id="table_exists-169"><a href="#table_exists-169"><span class="linenos">169</span></a> <span class="n">cursor</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span>
+</span><span id="table_exists-170"><a href="#table_exists-170"><span class="linenos">170</span></a><span class="w"> </span><span class="sd">"""</span>
+</span><span id="table_exists-171"><a href="#table_exists-171"><span class="linenos">171</span></a><span class="sd"> SELECT name</span>
+</span><span id="table_exists-172"><a href="#table_exists-172"><span class="linenos">172</span></a><span class="sd"> FROM sqlite_master</span>
+</span><span id="table_exists-173"><a href="#table_exists-173"><span class="linenos">173</span></a><span class="sd"> WHERE type='table' AND name=?</span>
+</span><span id="table_exists-174"><a href="#table_exists-174"><span class="linenos">174</span></a><span class="sd"> """</span><span class="p">,</span>
+</span><span id="table_exists-175"><a href="#table_exists-175"><span class="linenos">175</span></a> <span class="p">(</span><span class="n">table_name</span><span class="p">,),</span>
+</span><span id="table_exists-176"><a href="#table_exists-176"><span class="linenos">176</span></a> <span class="p">)</span>
+</span><span id="table_exists-177"><a href="#table_exists-177"><span class="linenos">177</span></a>
+</span><span id="table_exists-178"><a href="#table_exists-178"><span class="linenos">178</span></a> <span class="c1"># Fetch the result</span>
+</span><span id="table_exists-179"><a href="#table_exists-179"><span class="linenos">179</span></a> <span class="n">result</span> <span class="o">=</span> <span class="n">cursor</span><span class="o">.</span><span class="n">fetchone</span><span class="p">()</span>
+</span><span id="table_exists-180"><a href="#table_exists-180"><span class="linenos">180</span></a>
+</span><span id="table_exists-181"><a href="#table_exists-181"><span class="linenos">181</span></a> <span class="k">return</span> <span class="n">result</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span>
+</span></pre></div>
+
+
+
+
+ </section>
+ <section id="vocab_exists">
+ <input id="vocab_exists-view-source" class="view-source-toggle-state" type="checkbox" aria-hidden="true" tabindex="-1">
+<div class="attr function">
+
+ <span class="def">def</span>
+ <span class="name">vocab_exists</span><span class="signature pdoc-code condensed">(<span class="param"><span class="n">cursor</span><span class="p">:</span> <span class="n">sqlite3</span><span class="o">.</span><span class="n">Cursor</span>, </span><span class="param"><span class="n">vocab_id</span><span class="p">:</span> <span class="nb">str</span></span><span class="return-annotation">) -> <span class="nb">bool</span>:</span></span>
+
+ <label class="view-source-button" for="vocab_exists-view-source"><span>View Source</span></label>
+
+ </div>
+ <a class="headerlink" href="#vocab_exists"></a>
+ <div class="pdoc-code codehilite"><pre><span></span><span id="vocab_exists-184"><a href="#vocab_exists-184"><span class="linenos">184</span></a><span class="k">def</span><span class="w"> </span><span class="nf">vocab_exists</span><span class="p">(</span><span class="n">cursor</span><span class="p">:</span> <span class="n">sqlite3</span><span class="o">.</span><span class="n">Cursor</span><span class="p">,</span> <span class="n">vocab_id</span><span class="p">:</span> <span class="nb">str</span><span class="p">)</span> <span class="o">-></span> <span class="nb">bool</span><span class="p">:</span>
+</span><span id="vocab_exists-185"><a href="#vocab_exists-185"><span class="linenos">185</span></a> <span class="c1"># Query to check if the table exists</span>
+</span><span id="vocab_exists-186"><a href="#vocab_exists-186"><span class="linenos">186</span></a> <span class="n">cursor</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span>
+</span><span id="vocab_exists-187"><a href="#vocab_exists-187"><span class="linenos">187</span></a><span class="w"> </span><span class="sd">"""</span>
+</span><span id="vocab_exists-188"><a href="#vocab_exists-188"><span class="linenos">188</span></a><span class="sd"> SELECT vocabulary_id </span>
+</span><span id="vocab_exists-189"><a href="#vocab_exists-189"><span class="linenos">189</span></a><span class="sd"> FROM VOCABULARY</span>
+</span><span id="vocab_exists-190"><a href="#vocab_exists-190"><span class="linenos">190</span></a><span class="sd"> WHERE vocabulary_id=?</span>
+</span><span id="vocab_exists-191"><a href="#vocab_exists-191"><span class="linenos">191</span></a><span class="sd"> """</span><span class="p">,</span>
+</span><span id="vocab_exists-192"><a href="#vocab_exists-192"><span class="linenos">192</span></a> <span class="p">(</span><span class="n">vocab_id</span><span class="p">,),</span>
+</span><span id="vocab_exists-193"><a href="#vocab_exists-193"><span class="linenos">193</span></a> <span class="p">)</span>
+</span><span id="vocab_exists-194"><a href="#vocab_exists-194"><span class="linenos">194</span></a>
+</span><span id="vocab_exists-195"><a href="#vocab_exists-195"><span class="linenos">195</span></a> <span class="c1"># Fetch the result</span>
+</span><span id="vocab_exists-196"><a href="#vocab_exists-196"><span class="linenos">196</span></a> <span class="n">result</span> <span class="o">=</span> <span class="n">cursor</span><span class="o">.</span><span class="n">fetchone</span><span class="p">()</span>
+</span><span id="vocab_exists-197"><a href="#vocab_exists-197"><span class="linenos">197</span></a>
+</span><span id="vocab_exists-198"><a href="#vocab_exists-198"><span class="linenos">198</span></a> <span class="k">return</span> <span class="n">result</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span>
+</span></pre></div>
+
+
+
+
+ </section>
+ <section id="concept_set_exist">
+ <input id="concept_set_exist-view-source" class="view-source-toggle-state" type="checkbox" aria-hidden="true" tabindex="-1">
+<div class="attr function">
+
+ <span class="def">def</span>
+ <span class="name">concept_set_exist</span><span class="signature pdoc-code condensed">(<span class="param"><span class="n">cursor</span><span class="p">:</span> <span class="n">sqlite3</span><span class="o">.</span><span class="n">Cursor</span>, </span><span class="param"><span class="n">concept_set_name</span><span class="p">:</span> <span class="nb">str</span></span><span class="return-annotation">) -> <span class="nb">bool</span>:</span></span>
+
+ <label class="view-source-button" for="concept_set_exist-view-source"><span>View Source</span></label>
+
+ </div>
+ <a class="headerlink" href="#concept_set_exist"></a>
+ <div class="pdoc-code codehilite"><pre><span></span><span id="concept_set_exist-201"><a href="#concept_set_exist-201"><span class="linenos">201</span></a><span class="k">def</span><span class="w"> </span><span class="nf">concept_set_exist</span><span class="p">(</span><span class="n">cursor</span><span class="p">:</span> <span class="n">sqlite3</span><span class="o">.</span><span class="n">Cursor</span><span class="p">,</span> <span class="n">concept_set_name</span><span class="p">:</span> <span class="nb">str</span><span class="p">)</span> <span class="o">-></span> <span class="nb">bool</span><span class="p">:</span>
+</span><span id="concept_set_exist-202"><a href="#concept_set_exist-202"><span class="linenos">202</span></a>
+</span><span id="concept_set_exist-203"><a href="#concept_set_exist-203"><span class="linenos">203</span></a> <span class="n">query</span> <span class="o">=</span> <span class="sa">f</span><span class="s2">"SELECT EXISTS (SELECT 1 FROM CONCEPT_SET WHERE concept_set_name = ?)"</span>
+</span><span id="concept_set_exist-204"><a href="#concept_set_exist-204"><span class="linenos">204</span></a> <span class="n">cursor</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="n">query</span><span class="p">,</span> <span class="p">(</span><span class="n">concept_set_name</span><span class="p">,))</span>
+</span><span id="concept_set_exist-205"><a href="#concept_set_exist-205"><span class="linenos">205</span></a>
+</span><span id="concept_set_exist-206"><a href="#concept_set_exist-206"><span class="linenos">206</span></a> <span class="c1"># 1 if exists, 0 otherwise</span>
+</span><span id="concept_set_exist-207"><a href="#concept_set_exist-207"><span class="linenos">207</span></a> <span class="k">return</span> <span class="n">cursor</span><span class="o">.</span><span class="n">fetchone</span><span class="p">()[</span><span class="mi">0</span><span class="p">]</span> <span class="o">==</span> <span class="mi">1</span>
+</span></pre></div>
+
+
+
+
+ </section>
+ <section id="export">
+ <input id="export-view-source" class="view-source-toggle-state" type="checkbox" aria-hidden="true" tabindex="-1">
+<div class="attr function">
+
+ <span class="def">def</span>
+ <span class="name">export</span><span class="signature pdoc-code multiline">(<span class="param"> <span class="n">map_path</span><span class="p">:</span> <span class="n">pathlib</span><span class="o">.</span><span class="n">Path</span>,</span><span class="param"> <span class="n">export_path</span><span class="p">:</span> <span class="n">pathlib</span><span class="o">.</span><span class="n">Path</span>,</span><span class="param"> <span class="n">version</span><span class="p">:</span> <span class="nb">str</span>,</span><span class="param"> <span class="n">omop_metadata</span></span><span class="return-annotation">) -> <span class="n">pathlib</span><span class="o">.</span><span class="n">Path</span>:</span></span>
+
+ <label class="view-source-button" for="export-view-source"><span>View Source</span></label>
+
+ </div>
+ <a class="headerlink" href="#export"></a>
+ <div class="pdoc-code codehilite"><pre><span></span><span id="export-210"><a href="#export-210"><span class="linenos">210</span></a><span class="k">def</span><span class="w"> </span><span class="nf">export</span><span class="p">(</span><span class="n">map_path</span><span class="p">:</span> <span class="n">Path</span><span class="p">,</span> <span class="n">export_path</span><span class="p">:</span> <span class="n">Path</span><span class="p">,</span> <span class="n">version</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">omop_metadata</span><span class="p">)</span> <span class="o">-></span> <span class="n">Path</span><span class="p">:</span>
+</span><span id="export-211"><a href="#export-211"><span class="linenos">211</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="sa">f</span><span class="s2">"exporting with metadata </span><span class="si">{</span><span class="n">omop_metadata</span><span class="si">}</span><span class="s2"> at version </span><span class="si">{</span><span class="n">version</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+</span><span id="export-212"><a href="#export-212"><span class="linenos">212</span></a>
+</span><span id="export-213"><a href="#export-213"><span class="linenos">213</span></a> <span class="c1"># copy the baseline omop database</span>
+</span><span id="export-214"><a href="#export-214"><span class="linenos">214</span></a> <span class="n">export_db_path</span> <span class="o">=</span> <span class="n">export_path</span> <span class="o">/</span> <span class="n">EXPORT_FILE</span>
+</span><span id="export-215"><a href="#export-215"><span class="linenos">215</span></a> <span class="n">shutil</span><span class="o">.</span><span class="n">copy</span><span class="p">(</span><span class="n">DB_PATH</span><span class="p">,</span> <span class="n">export_db_path</span><span class="p">)</span>
+</span><span id="export-216"><a href="#export-216"><span class="linenos">216</span></a>
+</span><span id="export-217"><a href="#export-217"><span class="linenos">217</span></a> <span class="c1"># connect to db</span>
+</span><span id="export-218"><a href="#export-218"><span class="linenos">218</span></a> <span class="n">conn</span> <span class="o">=</span> <span class="n">sqlite3</span><span class="o">.</span><span class="n">connect</span><span class="p">(</span><span class="n">export_db_path</span><span class="p">)</span>
+</span><span id="export-219"><a href="#export-219"><span class="linenos">219</span></a> <span class="n">cur</span> <span class="o">=</span> <span class="n">conn</span><span class="o">.</span><span class="n">cursor</span><span class="p">()</span>
+</span><span id="export-220"><a href="#export-220"><span class="linenos">220</span></a>
+</span><span id="export-221"><a href="#export-221"><span class="linenos">221</span></a> <span class="c1"># Create VOCABULARY</span>
+</span><span id="export-222"><a href="#export-222"><span class="linenos">222</span></a> <span class="n">df_test</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">(</span>
+</span><span id="export-223"><a href="#export-223"><span class="linenos">223</span></a> <span class="p">[</span>
+</span><span id="export-224"><a href="#export-224"><span class="linenos">224</span></a> <span class="p">{</span>
+</span><span id="export-225"><a href="#export-225"><span class="linenos">225</span></a> <span class="s2">"vocabulary_id"</span><span class="p">:</span> <span class="n">omop_metadata</span><span class="p">[</span><span class="s2">"vocabulary_id"</span><span class="p">],</span>
+</span><span id="export-226"><a href="#export-226"><span class="linenos">226</span></a> <span class="s2">"vocabulary_name"</span><span class="p">:</span> <span class="n">omop_metadata</span><span class="p">[</span><span class="s2">"vocabulary_name"</span><span class="p">],</span>
+</span><span id="export-227"><a href="#export-227"><span class="linenos">227</span></a> <span class="s2">"vocabulary_reference"</span><span class="p">:</span> <span class="n">omop_metadata</span><span class="p">[</span><span class="s2">"vocabulary_reference"</span><span class="p">],</span>
+</span><span id="export-228"><a href="#export-228"><span class="linenos">228</span></a> <span class="s2">"vocabulary_version"</span><span class="p">:</span> <span class="n">version</span><span class="p">,</span>
+</span><span id="export-229"><a href="#export-229"><span class="linenos">229</span></a> <span class="c1"># "vocabulary_concept_id": 0,</span>
+</span><span id="export-230"><a href="#export-230"><span class="linenos">230</span></a> <span class="p">}</span>
+</span><span id="export-231"><a href="#export-231"><span class="linenos">231</span></a> <span class="p">]</span>
+</span><span id="export-232"><a href="#export-232"><span class="linenos">232</span></a> <span class="p">)</span>
+</span><span id="export-233"><a href="#export-233"><span class="linenos">233</span></a> <span class="n">df_test</span><span class="o">.</span><span class="n">to_sql</span><span class="p">(</span><span class="s2">"VOCABULARY"</span><span class="p">,</span> <span class="n">conn</span><span class="p">,</span> <span class="n">if_exists</span><span class="o">=</span><span class="s2">"append"</span><span class="p">,</span> <span class="n">index</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span>
+</span><span id="export-234"><a href="#export-234"><span class="linenos">234</span></a>
+</span><span id="export-235"><a href="#export-235"><span class="linenos">235</span></a> <span class="c1"># Create CONCEPT_SET</span>
+</span><span id="export-236"><a href="#export-236"><span class="linenos">236</span></a> <span class="n">cur</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span>
+</span><span id="export-237"><a href="#export-237"><span class="linenos">237</span></a><span class="w"> </span><span class="sd">"""</span>
+</span><span id="export-238"><a href="#export-238"><span class="linenos">238</span></a><span class="sd"> CREATE TABLE CONCEPT_SET (</span>
+</span><span id="export-239"><a href="#export-239"><span class="linenos">239</span></a><span class="sd"> concept_set_id INTEGER PRIMARY KEY AUTOINCREMENT, -- Unique identifier for each concept set</span>
+</span><span id="export-240"><a href="#export-240"><span class="linenos">240</span></a><span class="sd"> atlas_id INTEGER, -- Unique identifier generated by ATLAS</span>
+</span><span id="export-241"><a href="#export-241"><span class="linenos">241</span></a><span class="sd"> concept_set_name TEXT, -- Optional name for the concept set</span>
+</span><span id="export-242"><a href="#export-242"><span class="linenos">242</span></a><span class="sd"> concept_set_description TEXT, -- Optional description for the concept set</span>
+</span><span id="export-243"><a href="#export-243"><span class="linenos">243</span></a><span class="sd"> vocabulary_id TEXT NOT NULL, -- Foreign key to VOCABULARY table</span>
+</span><span id="export-244"><a href="#export-244"><span class="linenos">244</span></a><span class="sd"> FOREIGN KEY (vocabulary_id) REFERENCES VOCABULARY(vocabulary_id)</span>
+</span><span id="export-245"><a href="#export-245"><span class="linenos">245</span></a><span class="sd"> );"""</span>
+</span><span id="export-246"><a href="#export-246"><span class="linenos">246</span></a> <span class="p">)</span>
+</span><span id="export-247"><a href="#export-247"><span class="linenos">247</span></a>
+</span><span id="export-248"><a href="#export-248"><span class="linenos">248</span></a> <span class="c1"># Create CONCEPT_SET_ITEM</span>
+</span><span id="export-249"><a href="#export-249"><span class="linenos">249</span></a> <span class="n">cur</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span>
+</span><span id="export-250"><a href="#export-250"><span class="linenos">250</span></a><span class="w"> </span><span class="sd">"""</span>
+</span><span id="export-251"><a href="#export-251"><span class="linenos">251</span></a><span class="sd"> CREATE TABLE CONCEPT_SET_ITEM (</span>
+</span><span id="export-252"><a href="#export-252"><span class="linenos">252</span></a><span class="sd"> concept_set_item_id INTEGER PRIMARY KEY AUTOINCREMENT, -- Unique identifier for each mapping</span>
+</span><span id="export-253"><a href="#export-253"><span class="linenos">253</span></a><span class="sd"> concept_set_id INTEGER NOT NULL, -- Foreign key to CONCEPT_SET table</span>
+</span><span id="export-254"><a href="#export-254"><span class="linenos">254</span></a><span class="sd"> concept_id INTEGER NOT NULL, -- Foreign key to CONCEPT table</span>
+</span><span id="export-255"><a href="#export-255"><span class="linenos">255</span></a><span class="sd"> FOREIGN KEY (concept_set_id) REFERENCES CONCEPT_SET(concept_set_id),</span>
+</span><span id="export-256"><a href="#export-256"><span class="linenos">256</span></a><span class="sd"> FOREIGN KEY (concept_id) REFERENCES CONCEPT(concept_id)</span>
+</span><span id="export-257"><a href="#export-257"><span class="linenos">257</span></a><span class="sd"> );"""</span>
+</span><span id="export-258"><a href="#export-258"><span class="linenos">258</span></a> <span class="p">)</span>
+</span><span id="export-259"><a href="#export-259"><span class="linenos">259</span></a>
+</span><span id="export-260"><a href="#export-260"><span class="linenos">260</span></a> <span class="c1"># read map files</span>
+</span><span id="export-261"><a href="#export-261"><span class="linenos">261</span></a> <span class="n">map_files</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="n">map_path</span><span class="o">.</span><span class="n">glob</span><span class="p">(</span><span class="s2">"*.csv"</span><span class="p">))</span>
+</span><span id="export-262"><a href="#export-262"><span class="linenos">262</span></a> <span class="n">total</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">map_files</span><span class="p">)</span>
+</span><span id="export-263"><a href="#export-263"><span class="linenos">263</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Exporting </span><span class="si">{</span><span class="n">total</span><span class="si">}</span><span class="s2"> map files"</span><span class="p">)</span>
+</span><span id="export-264"><a href="#export-264"><span class="linenos">264</span></a> <span class="k">for</span> <span class="n">index</span><span class="p">,</span> <span class="n">map_file</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">map_files</span><span class="p">):</span>
+</span><span id="export-265"><a href="#export-265"><span class="linenos">265</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Processing </span><span class="si">{</span><span class="n">index</span><span class="o">+</span><span class="mi">1</span><span class="si">}</span><span class="s2"> of </span><span class="si">{</span><span class="n">total</span><span class="si">}</span><span class="s2">: </span><span class="si">{</span><span class="n">map_file</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+</span><span id="export-266"><a href="#export-266"><span class="linenos">266</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">read_csv</span><span class="p">(</span><span class="n">map_file</span><span class="p">)</span>
+</span><span id="export-267"><a href="#export-267"><span class="linenos">267</span></a>
+</span><span id="export-268"><a href="#export-268"><span class="linenos">268</span></a> <span class="k">for</span> <span class="n">concept_set_name</span><span class="p">,</span> <span class="n">grp</span> <span class="ow">in</span> <span class="n">df</span><span class="o">.</span><span class="n">groupby</span><span class="p">(</span><span class="s2">"CONCEPT_SET"</span><span class="p">):</span>
+</span><span id="export-269"><a href="#export-269"><span class="linenos">269</span></a>
+</span><span id="export-270"><a href="#export-270"><span class="linenos">270</span></a> <span class="c1"># create Concept_Set</span>
+</span><span id="export-271"><a href="#export-271"><span class="linenos">271</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="n">concept_set_exist</span><span class="p">(</span><span class="n">cur</span><span class="p">,</span> <span class="nb">str</span><span class="p">(</span><span class="n">concept_set_name</span><span class="p">)):</span>
+</span><span id="export-272"><a href="#export-272"><span class="linenos">272</span></a> <span class="n">cur</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span>
+</span><span id="export-273"><a href="#export-273"><span class="linenos">273</span></a> <span class="sa">f</span><span class="s2">"INSERT INTO CONCEPT_SET (concept_set_name, vocabulary_id) VALUES ('</span><span class="si">{</span><span class="n">concept_set_name</span><span class="si">}</span><span class="s2">', '</span><span class="si">{</span><span class="n">omop_metadata</span><span class="p">[</span><span class="s1">'vocabulary_id'</span><span class="p">]</span><span class="si">}</span><span class="s2">');"</span>
+</span><span id="export-274"><a href="#export-274"><span class="linenos">274</span></a> <span class="p">)</span>
+</span><span id="export-275"><a href="#export-275"><span class="linenos">275</span></a> <span class="k">else</span><span class="p">:</span>
+</span><span id="export-276"><a href="#export-276"><span class="linenos">276</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Concept_set </span><span class="si">{</span><span class="n">concept_set_name</span><span class="si">}</span><span class="s2"> already exists"</span><span class="p">)</span>
+</span><span id="export-277"><a href="#export-277"><span class="linenos">277</span></a> <span class="c1"># TODO: ask to remove old concept_set?</span>
+</span><span id="export-278"><a href="#export-278"><span class="linenos">278</span></a>
+</span><span id="export-279"><a href="#export-279"><span class="linenos">279</span></a> <span class="c1"># get Concept_set_Id</span>
+</span><span id="export-280"><a href="#export-280"><span class="linenos">280</span></a> <span class="n">query</span> <span class="o">=</span> <span class="s2">"SELECT concept_set_id FROM CONCEPT_SET WHERE concept_set_name = ? AND vocabulary_id = ?;"</span>
+</span><span id="export-281"><a href="#export-281"><span class="linenos">281</span></a> <span class="n">target_code_type</span> <span class="o">=</span> <span class="n">map_file</span><span class="o">.</span><span class="n">stem</span>
+</span><span id="export-282"><a href="#export-282"><span class="linenos">282</span></a> <span class="n">cur</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span>
+</span><span id="export-283"><a href="#export-283"><span class="linenos">283</span></a> <span class="n">query</span><span class="p">,</span>
+</span><span id="export-284"><a href="#export-284"><span class="linenos">284</span></a> <span class="p">(</span>
+</span><span id="export-285"><a href="#export-285"><span class="linenos">285</span></a> <span class="n">concept_set_name</span><span class="p">,</span>
+</span><span id="export-286"><a href="#export-286"><span class="linenos">286</span></a> <span class="n">omop_metadata</span><span class="p">[</span><span class="s2">"vocabulary_id"</span><span class="p">],</span>
+</span><span id="export-287"><a href="#export-287"><span class="linenos">287</span></a> <span class="p">),</span>
+</span><span id="export-288"><a href="#export-288"><span class="linenos">288</span></a> <span class="p">)</span>
+</span><span id="export-289"><a href="#export-289"><span class="linenos">289</span></a> <span class="c1"># FAILS HERE WITH NONE REUR</span>
+</span><span id="export-290"><a href="#export-290"><span class="linenos">290</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="sa">f</span><span class="s2">"target code type </span><span class="si">{</span><span class="n">target_code_type</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+</span><span id="export-291"><a href="#export-291"><span class="linenos">291</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="sa">f</span><span class="s2">"omop code type </span><span class="si">{</span><span class="n">omop_vocab_types</span><span class="p">[</span><span class="n">target_code_type</span><span class="p">]</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+</span><span id="export-292"><a href="#export-292"><span class="linenos">292</span></a> <span class="n">concept_set_id</span> <span class="o">=</span> <span class="n">cur</span><span class="o">.</span><span class="n">fetchone</span><span class="p">()[</span><span class="mi">0</span><span class="p">]</span>
+</span><span id="export-293"><a href="#export-293"><span class="linenos">293</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="sa">f</span><span class="s2">"concept set id </span><span class="si">{</span><span class="n">concept_set_id</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+</span><span id="export-294"><a href="#export-294"><span class="linenos">294</span></a>
+</span><span id="export-295"><a href="#export-295"><span class="linenos">295</span></a> <span class="c1"># get corresponing Concept_id (OMOP) for each Concept_code (e.g. SNOMED)</span>
+</span><span id="export-296"><a href="#export-296"><span class="linenos">296</span></a> <span class="n">concept_codes</span> <span class="o">=</span> <span class="s2">"'"</span> <span class="o">+</span> <span class="s2">"', '"</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="nb">list</span><span class="p">(</span><span class="n">grp</span><span class="p">[</span><span class="s2">"CONCEPT"</span><span class="p">]</span><span class="o">.</span><span class="n">astype</span><span class="p">(</span><span class="nb">str</span><span class="p">)))</span> <span class="o">+</span> <span class="s2">"'"</span>
+</span><span id="export-297"><a href="#export-297"><span class="linenos">297</span></a> <span class="n">query</span> <span class="o">=</span> <span class="sa">f</span><span class="s2">"SELECT concept_id FROM CONCEPT WHERE vocabulary_id = ? AND concept_code IN (</span><span class="si">{</span><span class="n">concept_codes</span><span class="si">}</span><span class="s2">);"</span>
+</span><span id="export-298"><a href="#export-298"><span class="linenos">298</span></a> <span class="n">cur</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="n">query</span><span class="p">,</span> <span class="p">(</span><span class="n">omop_vocab_types</span><span class="p">[</span><span class="n">target_code_type</span><span class="p">],))</span>
+</span><span id="export-299"><a href="#export-299"><span class="linenos">299</span></a> <span class="n">df_out</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">(</span><span class="n">cur</span><span class="o">.</span><span class="n">fetchall</span><span class="p">(),</span> <span class="n">columns</span><span class="o">=</span><span class="p">[</span><span class="s2">"concept_id"</span><span class="p">])</span>
+</span><span id="export-300"><a href="#export-300"><span class="linenos">300</span></a>
+</span><span id="export-301"><a href="#export-301"><span class="linenos">301</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="nb">len</span><span class="p">(</span><span class="n">grp</span><span class="p">)</span> <span class="o">==</span> <span class="nb">len</span><span class="p">(</span><span class="n">df_out</span><span class="p">):</span>
+</span><span id="export-302"><a href="#export-302"><span class="linenos">302</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">error</span><span class="p">(</span>
+</span><span id="export-303"><a href="#export-303"><span class="linenos">303</span></a> <span class="sa">f</span><span class="s2">"ERROR: Some </span><span class="si">{</span><span class="n">omop_vocab_types</span><span class="p">[</span><span class="n">target_code_type</span><span class="p">]</span><span class="si">}</span><span class="s2"> Codes do not exist in OMOP Database"</span>
+</span><span id="export-304"><a href="#export-304"><span class="linenos">304</span></a> <span class="p">)</span>
+</span><span id="export-305"><a href="#export-305"><span class="linenos">305</span></a>
+</span><span id="export-306"><a href="#export-306"><span class="linenos">306</span></a> <span class="c1"># Create Concept_set_item</span>
+</span><span id="export-307"><a href="#export-307"><span class="linenos">307</span></a> <span class="n">df_out</span><span class="p">[</span><span class="s2">"concept_set_id"</span><span class="p">]</span> <span class="o">=</span> <span class="n">concept_set_id</span>
+</span><span id="export-308"><a href="#export-308"><span class="linenos">308</span></a> <span class="n">df_out</span><span class="o">.</span><span class="n">to_sql</span><span class="p">(</span><span class="s2">"CONCEPT_SET_ITEM"</span><span class="p">,</span> <span class="n">conn</span><span class="p">,</span> <span class="n">if_exists</span><span class="o">=</span><span class="s2">"append"</span><span class="p">,</span> <span class="n">index</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span>
+</span><span id="export-309"><a href="#export-309"><span class="linenos">309</span></a>
+</span><span id="export-310"><a href="#export-310"><span class="linenos">310</span></a> <span class="c1"># Output all tables to CSV</span>
+</span><span id="export-311"><a href="#export-311"><span class="linenos">311</span></a> <span class="c1"># Get the list of all tables</span>
+</span><span id="export-312"><a href="#export-312"><span class="linenos">312</span></a> <span class="n">cur</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="s2">"SELECT name FROM sqlite_master WHERE type='table';"</span><span class="p">)</span>
+</span><span id="export-313"><a href="#export-313"><span class="linenos">313</span></a> <span class="n">tables</span> <span class="o">=</span> <span class="n">cur</span><span class="o">.</span><span class="n">fetchall</span><span class="p">()</span> <span class="c1"># List of tables</span>
+</span><span id="export-314"><a href="#export-314"><span class="linenos">314</span></a>
+</span><span id="export-315"><a href="#export-315"><span class="linenos">315</span></a> <span class="c1"># Export each table to a separate CSV file</span>
+</span><span id="export-316"><a href="#export-316"><span class="linenos">316</span></a> <span class="k">for</span> <span class="n">table</span> <span class="ow">in</span> <span class="n">tables</span><span class="p">:</span>
+</span><span id="export-317"><a href="#export-317"><span class="linenos">317</span></a> <span class="n">table_name</span> <span class="o">=</span> <span class="n">table</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
+</span><span id="export-318"><a href="#export-318"><span class="linenos">318</span></a> <span class="c1"># ignore SQLite's internal system table</span>
+</span><span id="export-319"><a href="#export-319"><span class="linenos">319</span></a> <span class="k">if</span> <span class="n">table_name</span> <span class="o">!=</span> <span class="s2">"sqlite_sequence"</span><span class="p">:</span>
+</span><span id="export-320"><a href="#export-320"><span class="linenos">320</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">read_sql_query</span><span class="p">(</span><span class="sa">f</span><span class="s2">"SELECT * FROM </span><span class="si">{</span><span class="n">table_name</span><span class="si">}</span><span class="s2">"</span><span class="p">,</span> <span class="n">conn</span><span class="p">)</span>
+</span><span id="export-321"><a href="#export-321"><span class="linenos">321</span></a> <span class="n">output_file</span> <span class="o">=</span> <span class="sa">f</span><span class="s2">"</span><span class="si">{</span><span class="n">table_name</span><span class="si">}</span><span class="s2">.csv"</span>
+</span><span id="export-322"><a href="#export-322"><span class="linenos">322</span></a> <span class="n">output_path</span> <span class="o">=</span> <span class="n">export_path</span> <span class="o">/</span> <span class="n">output_file</span>
+</span><span id="export-323"><a href="#export-323"><span class="linenos">323</span></a> <span class="n">df</span><span class="o">.</span><span class="n">to_csv</span><span class="p">(</span><span class="n">output_path</span><span class="p">,</span> <span class="n">index</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span> <span class="c1"># Save as CSV</span>
+</span><span id="export-324"><a href="#export-324"><span class="linenos">324</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Exported </span><span class="si">{</span><span class="n">table_name</span><span class="si">}</span><span class="s2"> to </span><span class="si">{</span><span class="n">table_name</span><span class="si">}</span><span class="s2">.csv"</span><span class="p">)</span>
+</span><span id="export-325"><a href="#export-325"><span class="linenos">325</span></a>
+</span><span id="export-326"><a href="#export-326"><span class="linenos">326</span></a> <span class="n">conn</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
+</span><span id="export-327"><a href="#export-327"><span class="linenos">327</span></a>
+</span><span id="export-328"><a href="#export-328"><span class="linenos">328</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Created export db successfully"</span><span class="p">)</span>
+</span><span id="export-329"><a href="#export-329"><span class="linenos">329</span></a>
+</span><span id="export-330"><a href="#export-330"><span class="linenos">330</span></a> <span class="k">return</span> <span class="n">export_db_path</span>
+</span></pre></div>
+
+
+
+
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\ No newline at end of file
diff --git a/docs/api/acmc/parse.html b/docs/api/acmc/parse.html
new file mode 100644
index 0000000000000000000000000000000000000000..7799b9fa21e05e4b21938af15df06aace8ca321a
--- /dev/null
+++ b/docs/api/acmc/parse.html
@@ -0,0 +1,2240 @@
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+</svg> acmc</a>
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+ pattern=".+" required>
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+
+
+ <h2>API Documentation</h2>
+ <ul class="memberlist">
+ <li>
+ <a class="variable" href="#logger">logger</a>
+ </li>
+ <li>
+ <a class="variable" href="#SUPPORTED_CODE_TYPES">SUPPORTED_CODE_TYPES</a>
+ </li>
+ <li>
+ <a class="class" href="#CodesError">CodesError</a>
+ <ul class="memberlist">
+ <li>
+ <a class="function" href="#CodesError.__init__">CodesError</a>
+ </li>
+ </ul>
+
+ </li>
+ <li>
+ <a class="class" href="#InvalidCodesException">InvalidCodesException</a>
+ <ul class="memberlist">
+ <li>
+ <a class="function" href="#InvalidCodesException.__init__">InvalidCodesException</a>
+ </li>
+ <li>
+ <a class="variable" href="#InvalidCodesException.error">error</a>
+ </li>
+ </ul>
+
+ </li>
+ <li>
+ <a class="class" href="#Proto">Proto</a>
+ <ul class="memberlist">
+ <li>
+ <a class="function" href="#Proto.__init__">Proto</a>
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+ <li>
+ <a class="variable" href="#Proto.checks">checks</a>
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+ <li>
+ <a class="variable" href="#Proto.name">name</a>
+ </li>
+ <li>
+ <a class="function" href="#Proto.raise_exception">raise_exception</a>
+ </li>
+ <li>
+ <a class="function" href="#Proto.in_database">in_database</a>
+ </li>
+ <li>
+ <a class="function" href="#Proto.process">process</a>
+ </li>
+ <li>
+ <a class="function" href="#Proto.verify">verify</a>
+ </li>
+ </ul>
+
+ </li>
+ <li>
+ <a class="class" href="#Read2">Read2</a>
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+ <li>
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+ </li>
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+
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+ <li>
+ <a class="variable" href="#Read3.checks">checks</a>
+ </li>
+ </ul>
+
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+ <li>
+ <a class="class" href="#Icd10">Icd10</a>
+ <ul class="memberlist">
+ <li>
+ <a class="variable" href="#Icd10.checks">checks</a>
+ </li>
+ <li>
+ <a class="function" href="#Icd10.trim_icd10">trim_icd10</a>
+ </li>
+ </ul>
+
+ </li>
+ <li>
+ <a class="class" href="#Snomed">Snomed</a>
+ <ul class="memberlist">
+ <li>
+ <a class="variable" href="#Snomed.checks">checks</a>
+ </li>
+ </ul>
+
+ </li>
+ <li>
+ <a class="class" href="#Opcs4">Opcs4</a>
+ <ul class="memberlist">
+ <li>
+ <a class="variable" href="#Opcs4.checks">checks</a>
+ </li>
+ </ul>
+
+ </li>
+ <li>
+ <a class="class" href="#Atc">Atc</a>
+ <ul class="memberlist">
+ <li>
+ <a class="variable" href="#Atc.checks">checks</a>
+ </li>
+ </ul>
+
+ </li>
+ <li>
+ <a class="class" href="#Med">Med</a>
+ <ul class="memberlist">
+ <li>
+ <a class="variable" href="#Med.checks">checks</a>
+ </li>
+ </ul>
+
+ </li>
+ <li>
+ <a class="class" href="#Cprd">Cprd</a>
+ <ul class="memberlist">
+ <li>
+ <a class="variable" href="#Cprd.checks">checks</a>
+ </li>
+ </ul>
+
+ </li>
+ <li>
+ <a class="class" href="#CodeTypeParser">CodeTypeParser</a>
+ <ul class="memberlist">
+ <li>
+ <a class="function" href="#CodeTypeParser.__init__">CodeTypeParser</a>
+ </li>
+ <li>
+ <a class="variable" href="#CodeTypeParser.code_types">code_types</a>
+ </li>
+ </ul>
+
+ </li>
+ </ul>
+
+
+
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+ <h1 class="modulename">
+<a href="./../acmc.html">acmc</a><wbr>.parse </h1>
+
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+ <input id="mod-parse-view-source" class="view-source-toggle-state" type="checkbox" aria-hidden="true" tabindex="-1">
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+
+ <div class="pdoc-code codehilite"><pre><span></span><span id="L-1"><a href="#L-1"><span class="linenos"> 1</span></a><span class="kn">import</span><span class="w"> </span><span class="nn">pandas</span><span class="w"> </span><span class="k">as</span><span class="w"> </span><span class="nn">pd</span>
+</span><span id="L-2"><a href="#L-2"><span class="linenos"> 2</span></a><span class="kn">import</span><span class="w"> </span><span class="nn">numpy</span><span class="w"> </span><span class="k">as</span><span class="w"> </span><span class="nn">np</span>
+</span><span id="L-3"><a href="#L-3"><span class="linenos"> 3</span></a><span class="kn">import</span><span class="w"> </span><span class="nn">os</span>
+</span><span id="L-4"><a href="#L-4"><span class="linenos"> 4</span></a><span class="kn">from</span><span class="w"> </span><span class="nn">typing</span><span class="w"> </span><span class="kn">import</span> <span class="n">Callable</span><span class="p">,</span> <span class="n">Optional</span><span class="p">,</span> <span class="n">Tuple</span>
+</span><span id="L-5"><a href="#L-5"><span class="linenos"> 5</span></a><span class="kn">from</span><span class="w"> </span><span class="nn">pathlib</span><span class="w"> </span><span class="kn">import</span> <span class="n">Path</span>
+</span><span id="L-6"><a href="#L-6"><span class="linenos"> 6</span></a>
+</span><span id="L-7"><a href="#L-7"><span class="linenos"> 7</span></a><span class="kn">from</span><span class="w"> </span><span class="nn">acmc</span><span class="w"> </span><span class="kn">import</span> <span class="n">trud</span><span class="p">,</span> <span class="n">logging_config</span> <span class="k">as</span> <span class="n">lc</span>
+</span><span id="L-8"><a href="#L-8"><span class="linenos"> 8</span></a>
+</span><span id="L-9"><a href="#L-9"><span class="linenos"> 9</span></a><span class="c1"># setup logging</span>
+</span><span id="L-10"><a href="#L-10"><span class="linenos"> 10</span></a><span class="n">logger</span> <span class="o">=</span> <span class="n">lc</span><span class="o">.</span><span class="n">setup_logger</span><span class="p">()</span>
+</span><span id="L-11"><a href="#L-11"><span class="linenos"> 11</span></a>
+</span><span id="L-12"><a href="#L-12"><span class="linenos"> 12</span></a><span class="c1"># Define allowed values</span>
+</span><span id="L-13"><a href="#L-13"><span class="linenos"> 13</span></a><span class="n">SUPPORTED_CODE_TYPES</span> <span class="o">=</span> <span class="p">{</span><span class="s2">"read2"</span><span class="p">,</span> <span class="s2">"read3"</span><span class="p">,</span> <span class="s2">"icd10"</span><span class="p">,</span> <span class="s2">"snomed"</span><span class="p">,</span> <span class="s2">"opcs4"</span><span class="p">,</span> <span class="s2">"atc"</span><span class="p">}</span>
+</span><span id="L-14"><a href="#L-14"><span class="linenos"> 14</span></a>
+</span><span id="L-15"><a href="#L-15"><span class="linenos"> 15</span></a>
+</span><span id="L-16"><a href="#L-16"><span class="linenos"> 16</span></a><span class="k">class</span><span class="w"> </span><span class="nc">CodesError</span><span class="p">:</span>
+</span><span id="L-17"><a href="#L-17"><span class="linenos"> 17</span></a><span class="w"> </span><span class="sd">"""A class used in InvalidCodesException to report an error if a code parser check fails"""</span>
+</span><span id="L-18"><a href="#L-18"><span class="linenos"> 18</span></a>
+</span><span id="L-19"><a href="#L-19"><span class="linenos"> 19</span></a> <span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">message</span><span class="p">,</span> <span class="n">codes</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">codes_file</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">mask</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">code_type</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
+</span><span id="L-20"><a href="#L-20"><span class="linenos"> 20</span></a> <span class="c1"># initialise class variables with provided parameters</span>
+</span><span id="L-21"><a href="#L-21"><span class="linenos"> 21</span></a> <span class="k">for</span> <span class="n">key</span><span class="p">,</span> <span class="n">value</span> <span class="ow">in</span> <span class="nb">locals</span><span class="p">()</span><span class="o">.</span><span class="n">items</span><span class="p">():</span>
+</span><span id="L-22"><a href="#L-22"><span class="linenos"> 22</span></a> <span class="k">if</span> <span class="n">key</span> <span class="o">!=</span> <span class="s2">"self"</span><span class="p">:</span>
+</span><span id="L-23"><a href="#L-23"><span class="linenos"> 23</span></a> <span class="nb">setattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">key</span><span class="p">,</span> <span class="n">value</span><span class="p">)</span>
+</span><span id="L-24"><a href="#L-24"><span class="linenos"> 24</span></a>
+</span><span id="L-25"><a href="#L-25"><span class="linenos"> 25</span></a>
+</span><span id="L-26"><a href="#L-26"><span class="linenos"> 26</span></a><span class="k">class</span><span class="w"> </span><span class="nc">InvalidCodesException</span><span class="p">(</span><span class="ne">Exception</span><span class="p">):</span>
+</span><span id="L-27"><a href="#L-27"><span class="linenos"> 27</span></a><span class="w"> </span><span class="sd">"""Custom exception class raised when invalid codes are found that cannot be resolved by processing"""</span>
+</span><span id="L-28"><a href="#L-28"><span class="linenos"> 28</span></a>
+</span><span id="L-29"><a href="#L-29"><span class="linenos"> 29</span></a> <span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">error</span><span class="p">):</span>
+</span><span id="L-30"><a href="#L-30"><span class="linenos"> 30</span></a> <span class="nb">super</span><span class="p">()</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="n">error</span><span class="o">.</span><span class="n">message</span><span class="p">)</span>
+</span><span id="L-31"><a href="#L-31"><span class="linenos"> 31</span></a> <span class="bp">self</span><span class="o">.</span><span class="n">error</span> <span class="o">=</span> <span class="n">error</span>
+</span><span id="L-32"><a href="#L-32"><span class="linenos"> 32</span></a>
+</span><span id="L-33"><a href="#L-33"><span class="linenos"> 33</span></a>
+</span><span id="L-34"><a href="#L-34"><span class="linenos"> 34</span></a><span class="k">class</span><span class="w"> </span><span class="nc">Proto</span><span class="p">:</span>
+</span><span id="L-35"><a href="#L-35"><span class="linenos"> 35</span></a><span class="w"> </span><span class="sd">"""</span>
+</span><span id="L-36"><a href="#L-36"><span class="linenos"> 36</span></a><span class="sd"> Define checks as list of 3 tuple: (Message, Condition, Process)</span>
+</span><span id="L-37"><a href="#L-37"><span class="linenos"> 37</span></a><span class="sd"> - Message = The name of the condition (what is printed and logged)</span>
+</span><span id="L-38"><a href="#L-38"><span class="linenos"> 38</span></a><span class="sd"> - Condition = True if Passed, and False if Failed</span>
+</span><span id="L-39"><a href="#L-39"><span class="linenos"> 39</span></a><span class="sd"> - Process = Aims to resolve all issues that stop condition from passing (Do not change index!)</span>
+</span><span id="L-40"><a href="#L-40"><span class="linenos"> 40</span></a><span class="sd"> """</span>
+</span><span id="L-41"><a href="#L-41"><span class="linenos"> 41</span></a>
+</span><span id="L-42"><a href="#L-42"><span class="linenos"> 42</span></a> <span class="n">checks</span><span class="p">:</span> <span class="nb">list</span><span class="p">[</span>
+</span><span id="L-43"><a href="#L-43"><span class="linenos"> 43</span></a> <span class="nb">tuple</span><span class="p">[</span>
+</span><span id="L-44"><a href="#L-44"><span class="linenos"> 44</span></a> <span class="nb">str</span><span class="p">,</span> <span class="c1"># The description, e.g., "Not Empty"</span>
+</span><span id="L-45"><a href="#L-45"><span class="linenos"> 45</span></a> <span class="n">Callable</span><span class="p">[</span>
+</span><span id="L-46"><a href="#L-46"><span class="linenos"> 46</span></a> <span class="p">[</span><span class="nb">list</span><span class="p">],</span>
+</span><span id="L-47"><a href="#L-47"><span class="linenos"> 47</span></a> <span class="n">pd</span><span class="o">.</span><span class="n">Series</span><span class="p">,</span>
+</span><span id="L-48"><a href="#L-48"><span class="linenos"> 48</span></a> <span class="p">],</span> <span class="c1"># The first lambda function: takes a list and returns a pd.Series of booleans</span>
+</span><span id="L-49"><a href="#L-49"><span class="linenos"> 49</span></a> <span class="n">Callable</span><span class="p">[</span>
+</span><span id="L-50"><a href="#L-50"><span class="linenos"> 50</span></a> <span class="p">[</span><span class="nb">list</span><span class="p">,</span> <span class="n">Path</span><span class="p">],</span>
+</span><span id="L-51"><a href="#L-51"><span class="linenos"> 51</span></a> <span class="kc">None</span><span class="p">,</span>
+</span><span id="L-52"><a href="#L-52"><span class="linenos"> 52</span></a> <span class="p">],</span> <span class="c1"># The second lambda function: takes a list and a string, and returns nothing</span>
+</span><span id="L-53"><a href="#L-53"><span class="linenos"> 53</span></a> <span class="p">]</span>
+</span><span id="L-54"><a href="#L-54"><span class="linenos"> 54</span></a> <span class="p">]</span>
+</span><span id="L-55"><a href="#L-55"><span class="linenos"> 55</span></a>
+</span><span id="L-56"><a href="#L-56"><span class="linenos"> 56</span></a> <span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">name</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">trud_codes_path</span><span class="p">:</span> <span class="n">Optional</span><span class="p">[</span><span class="n">Path</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
+</span><span id="L-57"><a href="#L-57"><span class="linenos"> 57</span></a> <span class="k">if</span> <span class="n">trud_codes_path</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+</span><span id="L-58"><a href="#L-58"><span class="linenos"> 58</span></a> <span class="k">if</span> <span class="n">trud_codes_path</span><span class="o">.</span><span class="n">is_file</span><span class="p">():</span>
+</span><span id="L-59"><a href="#L-59"><span class="linenos"> 59</span></a> <span class="bp">self</span><span class="o">.</span><span class="n">trud_codes_path</span><span class="p">:</span> <span class="n">Path</span> <span class="o">=</span> <span class="n">trud_codes_path</span>
+</span><span id="L-60"><a href="#L-60"><span class="linenos"> 60</span></a> <span class="bp">self</span><span class="o">.</span><span class="n">db</span><span class="p">:</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">read_parquet</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">trud_codes_path</span><span class="p">)</span>
+</span><span id="L-61"><a href="#L-61"><span class="linenos"> 61</span></a> <span class="k">else</span><span class="p">:</span>
+</span><span id="L-62"><a href="#L-62"><span class="linenos"> 62</span></a> <span class="k">raise</span> <span class="ne">FileNotFoundError</span><span class="p">(</span>
+</span><span id="L-63"><a href="#L-63"><span class="linenos"> 63</span></a> <span class="sa">f</span><span class="s2">"Error: Read2 code file '</span><span class="si">{</span><span class="n">trud_codes_path</span><span class="si">}</span><span class="s2">' does not exist. Please ensure you have installed TRUD correctly"</span>
+</span><span id="L-64"><a href="#L-64"><span class="linenos"> 64</span></a> <span class="p">)</span>
+</span><span id="L-65"><a href="#L-65"><span class="linenos"> 65</span></a>
+</span><span id="L-66"><a href="#L-66"><span class="linenos"> 66</span></a> <span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="n">name</span>
+</span><span id="L-67"><a href="#L-67"><span class="linenos"> 67</span></a>
+</span><span id="L-68"><a href="#L-68"><span class="linenos"> 68</span></a> <span class="k">def</span><span class="w"> </span><span class="nf">raise_exception</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">ex</span><span class="p">:</span> <span class="ne">Exception</span><span class="p">):</span>
+</span><span id="L-69"><a href="#L-69"><span class="linenos"> 69</span></a><span class="w"> </span><span class="sd">"""Raises an exception inside a lambda function. Python does not allow using raise statement inside lambda because lambda can only contain expressions, not statements. Using raise_exception not raise_ as it's more explict"""</span>
+</span><span id="L-70"><a href="#L-70"><span class="linenos"> 70</span></a> <span class="k">raise</span> <span class="n">ex</span>
+</span><span id="L-71"><a href="#L-71"><span class="linenos"> 71</span></a>
+</span><span id="L-72"><a href="#L-72"><span class="linenos"> 72</span></a> <span class="k">def</span><span class="w"> </span><span class="nf">in_database</span><span class="p">(</span>
+</span><span id="L-73"><a href="#L-73"><span class="linenos"> 73</span></a> <span class="bp">self</span><span class="p">,</span> <span class="n">codes</span><span class="p">:</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">,</span> <span class="n">db</span><span class="p">:</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">,</span> <span class="n">col</span><span class="p">:</span> <span class="nb">str</span>
+</span><span id="L-74"><a href="#L-74"><span class="linenos"> 74</span></a> <span class="p">)</span> <span class="o">-></span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">:</span>
+</span><span id="L-75"><a href="#L-75"><span class="linenos"> 75</span></a> <span class="k">return</span> <span class="n">codes</span><span class="o">.</span><span class="n">isin</span><span class="p">(</span><span class="n">db</span><span class="p">[</span><span class="n">col</span><span class="p">])</span>
+</span><span id="L-76"><a href="#L-76"><span class="linenos"> 76</span></a>
+</span><span id="L-77"><a href="#L-77"><span class="linenos"> 77</span></a> <span class="k">def</span><span class="w"> </span><span class="nf">process</span><span class="p">(</span>
+</span><span id="L-78"><a href="#L-78"><span class="linenos"> 78</span></a> <span class="bp">self</span><span class="p">,</span> <span class="n">codes</span><span class="p">:</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">,</span> <span class="n">codes_file</span><span class="p">:</span> <span class="n">Path</span>
+</span><span id="L-79"><a href="#L-79"><span class="linenos"> 79</span></a> <span class="p">)</span> <span class="o">-></span> <span class="n">Tuple</span><span class="p">[</span><span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">,</span> <span class="nb">list</span><span class="p">]:</span>
+</span><span id="L-80"><a href="#L-80"><span class="linenos"> 80</span></a><span class="w"> </span><span class="sd">"""identify issues that do not pass and fix them with define/d process"""</span>
+</span><span id="L-81"><a href="#L-81"><span class="linenos"> 81</span></a> <span class="n">errors</span> <span class="o">=</span> <span class="p">[]</span>
+</span><span id="L-82"><a href="#L-82"><span class="linenos"> 82</span></a> <span class="c1"># Iter through each item in check.</span>
+</span><span id="L-83"><a href="#L-83"><span class="linenos"> 83</span></a> <span class="k">for</span> <span class="n">msg</span><span class="p">,</span> <span class="n">cond</span><span class="p">,</span> <span class="n">fix</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">checks</span><span class="p">:</span>
+</span><span id="L-84"><a href="#L-84"><span class="linenos"> 84</span></a> <span class="c1"># Check if any codes fail the check to False</span>
+</span><span id="L-85"><a href="#L-85"><span class="linenos"> 85</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="n">cond</span><span class="p">(</span><span class="n">codes</span><span class="p">)</span><span class="o">.</span><span class="n">all</span><span class="p">():</span>
+</span><span id="L-86"><a href="#L-86"><span class="linenos"> 86</span></a> <span class="c1"># Log the number of codes that failed</span>
+</span><span id="L-87"><a href="#L-87"><span class="linenos"> 87</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span>
+</span><span id="L-88"><a href="#L-88"><span class="linenos"> 88</span></a> <span class="sa">f</span><span class="s2">"Check: </span><span class="si">{</span><span class="n">msg</span><span class="si">}</span><span class="s2"> </span><span class="si">{</span><span class="p">(</span><span class="o">~</span><span class="n">cond</span><span class="p">(</span><span class="n">codes</span><span class="p">))</span><span class="o">.</span><span class="n">sum</span><span class="p">()</span><span class="si">}</span><span class="s2"> failed, trying to fix"</span>
+</span><span id="L-89"><a href="#L-89"><span class="linenos"> 89</span></a> <span class="p">)</span>
+</span><span id="L-90"><a href="#L-90"><span class="linenos"> 90</span></a> <span class="c1"># try fix errors by running lamba "process" function</span>
+</span><span id="L-91"><a href="#L-91"><span class="linenos"> 91</span></a> <span class="k">try</span><span class="p">:</span>
+</span><span id="L-92"><a href="#L-92"><span class="linenos"> 92</span></a> <span class="n">codes</span> <span class="o">=</span> <span class="n">fix</span><span class="p">(</span><span class="n">codes</span><span class="p">,</span> <span class="n">codes_file</span><span class="p">)</span>
+</span><span id="L-93"><a href="#L-93"><span class="linenos"> 93</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Check: Fixed"</span><span class="p">)</span>
+</span><span id="L-94"><a href="#L-94"><span class="linenos"> 94</span></a> <span class="k">except</span> <span class="n">InvalidCodesException</span> <span class="k">as</span> <span class="n">ex</span><span class="p">:</span>
+</span><span id="L-95"><a href="#L-95"><span class="linenos"> 95</span></a> <span class="n">errors</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">ex</span><span class="o">.</span><span class="n">error</span><span class="p">)</span>
+</span><span id="L-96"><a href="#L-96"><span class="linenos"> 96</span></a> <span class="k">else</span><span class="p">:</span>
+</span><span id="L-97"><a href="#L-97"><span class="linenos"> 97</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Check: passed"</span><span class="p">)</span>
+</span><span id="L-98"><a href="#L-98"><span class="linenos"> 98</span></a>
+</span><span id="L-99"><a href="#L-99"><span class="linenos"> 99</span></a> <span class="k">return</span> <span class="n">codes</span><span class="p">,</span> <span class="n">errors</span>
+</span><span id="L-100"><a href="#L-100"><span class="linenos">100</span></a>
+</span><span id="L-101"><a href="#L-101"><span class="linenos">101</span></a> <span class="k">def</span><span class="w"> </span><span class="nf">verify</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">codes</span><span class="p">:</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">,</span> <span class="n">codes_file</span><span class="p">:</span> <span class="n">Path</span><span class="p">):</span>
+</span><span id="L-102"><a href="#L-102"><span class="linenos">102</span></a><span class="w"> </span><span class="sd">"""verify codes in codes file"""</span>
+</span><span id="L-103"><a href="#L-103"><span class="linenos">103</span></a> <span class="n">conds</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([])</span>
+</span><span id="L-104"><a href="#L-104"><span class="linenos">104</span></a>
+</span><span id="L-105"><a href="#L-105"><span class="linenos">105</span></a> <span class="c1"># Iter through each item in check.</span>
+</span><span id="L-106"><a href="#L-106"><span class="linenos">106</span></a> <span class="k">for</span> <span class="n">msg</span><span class="p">,</span> <span class="n">cond</span><span class="p">,</span> <span class="n">process</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">checks</span><span class="p">:</span>
+</span><span id="L-107"><a href="#L-107"><span class="linenos">107</span></a> <span class="c1"># run conditional check</span>
+</span><span id="L-108"><a href="#L-108"><span class="linenos">108</span></a> <span class="n">out</span> <span class="o">=</span> <span class="n">cond</span><span class="p">(</span><span class="n">codes</span><span class="p">)</span>
+</span><span id="L-109"><a href="#L-109"><span class="linenos">109</span></a> <span class="n">conds</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">conds</span><span class="p">,</span> <span class="n">out</span><span class="o">.</span><span class="n">all</span><span class="p">())</span>
+</span><span id="L-110"><a href="#L-110"><span class="linenos">110</span></a>
+</span><span id="L-111"><a href="#L-111"><span class="linenos">111</span></a> <span class="k">return</span> <span class="n">conds</span>
+</span><span id="L-112"><a href="#L-112"><span class="linenos">112</span></a>
+</span><span id="L-113"><a href="#L-113"><span class="linenos">113</span></a>
+</span><span id="L-114"><a href="#L-114"><span class="linenos">114</span></a><span class="k">class</span><span class="w"> </span><span class="nc">Read2</span><span class="p">(</span><span class="n">Proto</span><span class="p">):</span>
+</span><span id="L-115"><a href="#L-115"><span class="linenos">115</span></a><span class="w"> </span><span class="sd">"""This Read2 class extends Proto, adding custom validation checks for a dataset of "Read2" codes. It ensures that the dataset is loaded, validates the codes based on several rules, and applies corrections or logs errors when necessary."""</span>
+</span><span id="L-116"><a href="#L-116"><span class="linenos">116</span></a>
+</span><span id="L-117"><a href="#L-117"><span class="linenos">117</span></a> <span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+</span><span id="L-118"><a href="#L-118"><span class="linenos">118</span></a> <span class="nb">super</span><span class="p">()</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="s2">"read2"</span><span class="p">,</span> <span class="n">trud</span><span class="o">.</span><span class="n">PROCESSED_PATH</span> <span class="o">/</span> <span class="s2">"read2.parquet"</span><span class="p">)</span>
+</span><span id="L-119"><a href="#L-119"><span class="linenos">119</span></a>
+</span><span id="L-120"><a href="#L-120"><span class="linenos">120</span></a> <span class="c1"># validate checks</span>
+</span><span id="L-121"><a href="#L-121"><span class="linenos">121</span></a> <span class="bp">self</span><span class="o">.</span><span class="n">checks</span> <span class="o">=</span> <span class="p">[</span>
+</span><span id="L-122"><a href="#L-122"><span class="linenos">122</span></a> <span class="p">(</span>
+</span><span id="L-123"><a href="#L-123"><span class="linenos">123</span></a> <span class="c1"># check codes are not empty, if empty throw an exception</span>
+</span><span id="L-124"><a href="#L-124"><span class="linenos">124</span></a> <span class="s2">"Not Empty"</span><span class="p">,</span>
+</span><span id="L-125"><a href="#L-125"><span class="linenos">125</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">:</span> <span class="n">pd</span><span class="o">.</span><span class="n">Series</span><span class="p">([</span><span class="nb">len</span><span class="p">(</span><span class="n">codes</span><span class="p">)</span> <span class="o">></span> <span class="mi">0</span><span class="p">]),</span>
+</span><span id="L-126"><a href="#L-126"><span class="linenos">126</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">,</span> <span class="n">codes_file</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">raise_exception</span><span class="p">(</span>
+</span><span id="L-127"><a href="#L-127"><span class="linenos">127</span></a> <span class="n">InvalidCodesException</span><span class="p">(</span>
+</span><span id="L-128"><a href="#L-128"><span class="linenos">128</span></a> <span class="n">CodesError</span><span class="p">(</span>
+</span><span id="L-129"><a href="#L-129"><span class="linenos">129</span></a> <span class="sa">f</span><span class="s2">"Code list is empty"</span><span class="p">,</span>
+</span><span id="L-130"><a href="#L-130"><span class="linenos">130</span></a> <span class="n">codes</span><span class="o">=</span><span class="n">codes</span><span class="p">,</span>
+</span><span id="L-131"><a href="#L-131"><span class="linenos">131</span></a> <span class="n">codes_file</span><span class="o">=</span><span class="n">codes_file</span><span class="p">,</span>
+</span><span id="L-132"><a href="#L-132"><span class="linenos">132</span></a> <span class="n">mask</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
+</span><span id="L-133"><a href="#L-133"><span class="linenos">133</span></a> <span class="n">code_type</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">,</span>
+</span><span id="L-134"><a href="#L-134"><span class="linenos">134</span></a> <span class="p">)</span>
+</span><span id="L-135"><a href="#L-135"><span class="linenos">135</span></a> <span class="p">)</span>
+</span><span id="L-136"><a href="#L-136"><span class="linenos">136</span></a> <span class="p">),</span>
+</span><span id="L-137"><a href="#L-137"><span class="linenos">137</span></a> <span class="p">),</span>
+</span><span id="L-138"><a href="#L-138"><span class="linenos">138</span></a> <span class="p">(</span>
+</span><span id="L-139"><a href="#L-139"><span class="linenos">139</span></a> <span class="c1"># check codes <5 characters, if too short pads it with . (dots) to reach 5 characters</span>
+</span><span id="L-140"><a href="#L-140"><span class="linenos">140</span></a> <span class="s2">"Too Short"</span><span class="p">,</span>
+</span><span id="L-141"><a href="#L-141"><span class="linenos">141</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">:</span> <span class="o">~</span><span class="p">(</span><span class="n">codes</span><span class="o">.</span><span class="n">str</span><span class="o">.</span><span class="n">len</span><span class="p">()</span> <span class="o"><</span> <span class="mi">5</span><span class="p">),</span>
+</span><span id="L-142"><a href="#L-142"><span class="linenos">142</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">,</span> <span class="n">codes_file</span><span class="p">:</span> <span class="n">codes</span><span class="o">.</span><span class="n">str</span><span class="o">.</span><span class="n">pad</span><span class="p">(</span>
+</span><span id="L-143"><a href="#L-143"><span class="linenos">143</span></a> <span class="n">width</span><span class="o">=</span><span class="mi">5</span><span class="p">,</span> <span class="n">side</span><span class="o">=</span><span class="s2">"right"</span><span class="p">,</span> <span class="n">fillchar</span><span class="o">=</span><span class="s2">"."</span>
+</span><span id="L-144"><a href="#L-144"><span class="linenos">144</span></a> <span class="p">),</span>
+</span><span id="L-145"><a href="#L-145"><span class="linenos">145</span></a> <span class="p">),</span>
+</span><span id="L-146"><a href="#L-146"><span class="linenos">146</span></a> <span class="p">(</span>
+</span><span id="L-147"><a href="#L-147"><span class="linenos">147</span></a> <span class="c1"># check codes > 5 characters, If too long, truncates them to 5 characters</span>
+</span><span id="L-148"><a href="#L-148"><span class="linenos">148</span></a> <span class="s2">"Too Long"</span><span class="p">,</span>
+</span><span id="L-149"><a href="#L-149"><span class="linenos">149</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">:</span> <span class="o">~</span><span class="p">(</span><span class="n">codes</span><span class="o">.</span><span class="n">str</span><span class="o">.</span><span class="n">len</span><span class="p">()</span> <span class="o">></span> <span class="mi">5</span><span class="p">),</span>
+</span><span id="L-150"><a href="#L-150"><span class="linenos">150</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">,</span> <span class="n">codes_file</span><span class="p">:</span> <span class="n">codes</span><span class="o">.</span><span class="n">str</span><span class="p">[:</span><span class="mi">5</span><span class="p">],</span>
+</span><span id="L-151"><a href="#L-151"><span class="linenos">151</span></a> <span class="p">),</span>
+</span><span id="L-152"><a href="#L-152"><span class="linenos">152</span></a> <span class="p">(</span>
+</span><span id="L-153"><a href="#L-153"><span class="linenos">153</span></a> <span class="c1"># checks codes contain numbers, or dots (.), if not logs invalid code error</span>
+</span><span id="L-154"><a href="#L-154"><span class="linenos">154</span></a> <span class="s2">"Alphanumeric Dot"</span><span class="p">,</span>
+</span><span id="L-155"><a href="#L-155"><span class="linenos">155</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">:</span> <span class="n">codes</span><span class="o">.</span><span class="n">str</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="sa">r</span><span class="s2">"^[a-zA-Z0-9.]+$"</span><span class="p">),</span>
+</span><span id="L-156"><a href="#L-156"><span class="linenos">156</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">,</span> <span class="n">codes_file</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">raise_exception</span><span class="p">(</span>
+</span><span id="L-157"><a href="#L-157"><span class="linenos">157</span></a> <span class="n">InvalidCodesException</span><span class="p">(</span>
+</span><span id="L-158"><a href="#L-158"><span class="linenos">158</span></a> <span class="n">CodesError</span><span class="p">(</span>
+</span><span id="L-159"><a href="#L-159"><span class="linenos">159</span></a> <span class="sa">f</span><span class="s2">"Illegal code format, not alphanumeric dot"</span><span class="p">,</span>
+</span><span id="L-160"><a href="#L-160"><span class="linenos">160</span></a> <span class="n">codes</span><span class="o">=</span><span class="n">codes</span><span class="p">,</span>
+</span><span id="L-161"><a href="#L-161"><span class="linenos">161</span></a> <span class="n">codes_file</span><span class="o">=</span><span class="n">codes_file</span><span class="p">,</span>
+</span><span id="L-162"><a href="#L-162"><span class="linenos">162</span></a> <span class="n">mask</span><span class="o">=</span><span class="n">codes</span><span class="o">.</span><span class="n">str</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="sa">r</span><span class="s2">"^[a-zA-Z0-9.]+$"</span><span class="p">),</span>
+</span><span id="L-163"><a href="#L-163"><span class="linenos">163</span></a> <span class="n">code_type</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">,</span>
+</span><span id="L-164"><a href="#L-164"><span class="linenos">164</span></a> <span class="p">)</span>
+</span><span id="L-165"><a href="#L-165"><span class="linenos">165</span></a> <span class="p">)</span>
+</span><span id="L-166"><a href="#L-166"><span class="linenos">166</span></a> <span class="p">),</span>
+</span><span id="L-167"><a href="#L-167"><span class="linenos">167</span></a> <span class="p">),</span>
+</span><span id="L-168"><a href="#L-168"><span class="linenos">168</span></a> <span class="p">(</span>
+</span><span id="L-169"><a href="#L-169"><span class="linenos">169</span></a> <span class="c1"># checks code exists in self.db (the Read2 dataset). If missing log invalid codes.</span>
+</span><span id="L-170"><a href="#L-170"><span class="linenos">170</span></a> <span class="s2">"In Database"</span><span class="p">,</span>
+</span><span id="L-171"><a href="#L-171"><span class="linenos">171</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">in_database</span><span class="p">(</span><span class="n">codes</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">db</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">),</span>
+</span><span id="L-172"><a href="#L-172"><span class="linenos">172</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">,</span> <span class="n">codes_file</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">raise_exception</span><span class="p">(</span>
+</span><span id="L-173"><a href="#L-173"><span class="linenos">173</span></a> <span class="n">InvalidCodesException</span><span class="p">(</span>
+</span><span id="L-174"><a href="#L-174"><span class="linenos">174</span></a> <span class="n">CodesError</span><span class="p">(</span>
+</span><span id="L-175"><a href="#L-175"><span class="linenos">175</span></a> <span class="sa">f</span><span class="s2">"Codes do not exist in database"</span><span class="p">,</span>
+</span><span id="L-176"><a href="#L-176"><span class="linenos">176</span></a> <span class="n">codes</span><span class="o">=</span><span class="n">codes</span><span class="p">,</span>
+</span><span id="L-177"><a href="#L-177"><span class="linenos">177</span></a> <span class="n">codes_file</span><span class="o">=</span><span class="n">codes_file</span><span class="p">,</span>
+</span><span id="L-178"><a href="#L-178"><span class="linenos">178</span></a> <span class="n">mask</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">in_database</span><span class="p">(</span><span class="n">codes</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">db</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">),</span>
+</span><span id="L-179"><a href="#L-179"><span class="linenos">179</span></a> <span class="n">code_type</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">,</span>
+</span><span id="L-180"><a href="#L-180"><span class="linenos">180</span></a> <span class="p">)</span>
+</span><span id="L-181"><a href="#L-181"><span class="linenos">181</span></a> <span class="p">)</span>
+</span><span id="L-182"><a href="#L-182"><span class="linenos">182</span></a> <span class="p">),</span>
+</span><span id="L-183"><a href="#L-183"><span class="linenos">183</span></a> <span class="p">),</span>
+</span><span id="L-184"><a href="#L-184"><span class="linenos">184</span></a> <span class="p">]</span>
+</span><span id="L-185"><a href="#L-185"><span class="linenos">185</span></a>
+</span><span id="L-186"><a href="#L-186"><span class="linenos">186</span></a>
+</span><span id="L-187"><a href="#L-187"><span class="linenos">187</span></a><span class="k">class</span><span class="w"> </span><span class="nc">Read3</span><span class="p">(</span><span class="n">Proto</span><span class="p">):</span>
+</span><span id="L-188"><a href="#L-188"><span class="linenos">188</span></a> <span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+</span><span id="L-189"><a href="#L-189"><span class="linenos">189</span></a> <span class="nb">super</span><span class="p">()</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="s2">"Read3"</span><span class="p">,</span> <span class="n">trud</span><span class="o">.</span><span class="n">PROCESSED_PATH</span> <span class="o">/</span> <span class="s2">"read3.parquet"</span><span class="p">)</span>
+</span><span id="L-190"><a href="#L-190"><span class="linenos">190</span></a>
+</span><span id="L-191"><a href="#L-191"><span class="linenos">191</span></a> <span class="bp">self</span><span class="o">.</span><span class="n">checks</span> <span class="o">=</span> <span class="p">[</span>
+</span><span id="L-192"><a href="#L-192"><span class="linenos">192</span></a> <span class="p">(</span>
+</span><span id="L-193"><a href="#L-193"><span class="linenos">193</span></a> <span class="s2">"Not Empty"</span><span class="p">,</span>
+</span><span id="L-194"><a href="#L-194"><span class="linenos">194</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">:</span> <span class="n">pd</span><span class="o">.</span><span class="n">Series</span><span class="p">([</span><span class="nb">len</span><span class="p">(</span><span class="n">codes</span><span class="p">)</span> <span class="o">></span> <span class="mi">0</span><span class="p">]),</span>
+</span><span id="L-195"><a href="#L-195"><span class="linenos">195</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">,</span> <span class="n">codes_file</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">raise_exception</span><span class="p">(</span>
+</span><span id="L-196"><a href="#L-196"><span class="linenos">196</span></a> <span class="n">InvalidCodesException</span><span class="p">(</span>
+</span><span id="L-197"><a href="#L-197"><span class="linenos">197</span></a> <span class="n">CodesError</span><span class="p">(</span>
+</span><span id="L-198"><a href="#L-198"><span class="linenos">198</span></a> <span class="sa">f</span><span class="s2">"Code list is empty"</span><span class="p">,</span>
+</span><span id="L-199"><a href="#L-199"><span class="linenos">199</span></a> <span class="n">codes</span><span class="o">=</span><span class="n">codes</span><span class="p">,</span>
+</span><span id="L-200"><a href="#L-200"><span class="linenos">200</span></a> <span class="n">codes_file</span><span class="o">=</span><span class="n">codes_file</span><span class="p">,</span>
+</span><span id="L-201"><a href="#L-201"><span class="linenos">201</span></a> <span class="n">mask</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
+</span><span id="L-202"><a href="#L-202"><span class="linenos">202</span></a> <span class="n">code_type</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">,</span>
+</span><span id="L-203"><a href="#L-203"><span class="linenos">203</span></a> <span class="p">)</span>
+</span><span id="L-204"><a href="#L-204"><span class="linenos">204</span></a> <span class="p">)</span>
+</span><span id="L-205"><a href="#L-205"><span class="linenos">205</span></a> <span class="p">),</span>
+</span><span id="L-206"><a href="#L-206"><span class="linenos">206</span></a> <span class="p">),</span>
+</span><span id="L-207"><a href="#L-207"><span class="linenos">207</span></a> <span class="p">(</span>
+</span><span id="L-208"><a href="#L-208"><span class="linenos">208</span></a> <span class="s2">"Too Short"</span><span class="p">,</span>
+</span><span id="L-209"><a href="#L-209"><span class="linenos">209</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">:</span> <span class="o">~</span><span class="p">(</span><span class="n">codes</span><span class="o">.</span><span class="n">str</span><span class="o">.</span><span class="n">len</span><span class="p">()</span> <span class="o"><</span> <span class="mi">5</span><span class="p">),</span>
+</span><span id="L-210"><a href="#L-210"><span class="linenos">210</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">,</span> <span class="n">codes_file</span><span class="p">:</span> <span class="n">codes</span><span class="o">.</span><span class="n">str</span><span class="o">.</span><span class="n">pad</span><span class="p">(</span>
+</span><span id="L-211"><a href="#L-211"><span class="linenos">211</span></a> <span class="n">width</span><span class="o">=</span><span class="mi">5</span><span class="p">,</span> <span class="n">side</span><span class="o">=</span><span class="s2">"right"</span><span class="p">,</span> <span class="n">fillchar</span><span class="o">=</span><span class="s2">"."</span>
+</span><span id="L-212"><a href="#L-212"><span class="linenos">212</span></a> <span class="p">),</span>
+</span><span id="L-213"><a href="#L-213"><span class="linenos">213</span></a> <span class="p">),</span>
+</span><span id="L-214"><a href="#L-214"><span class="linenos">214</span></a> <span class="p">(</span>
+</span><span id="L-215"><a href="#L-215"><span class="linenos">215</span></a> <span class="s2">"Too Long"</span><span class="p">,</span>
+</span><span id="L-216"><a href="#L-216"><span class="linenos">216</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">:</span> <span class="o">~</span><span class="p">(</span><span class="n">codes</span><span class="o">.</span><span class="n">str</span><span class="o">.</span><span class="n">len</span><span class="p">()</span> <span class="o">></span> <span class="mi">5</span><span class="p">),</span>
+</span><span id="L-217"><a href="#L-217"><span class="linenos">217</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">,</span> <span class="n">codes_file</span><span class="p">:</span> <span class="n">codes</span><span class="o">.</span><span class="n">str</span><span class="p">[:</span><span class="mi">5</span><span class="p">],</span>
+</span><span id="L-218"><a href="#L-218"><span class="linenos">218</span></a> <span class="p">),</span>
+</span><span id="L-219"><a href="#L-219"><span class="linenos">219</span></a> <span class="p">(</span>
+</span><span id="L-220"><a href="#L-220"><span class="linenos">220</span></a> <span class="s2">"Alphanumeric Dot"</span><span class="p">,</span>
+</span><span id="L-221"><a href="#L-221"><span class="linenos">221</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">:</span> <span class="n">codes</span><span class="o">.</span><span class="n">str</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="sa">r</span><span class="s2">"^[a-zA-Z0-9.]+$"</span><span class="p">),</span>
+</span><span id="L-222"><a href="#L-222"><span class="linenos">222</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">,</span> <span class="n">codes_file</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">raise_exception</span><span class="p">(</span>
+</span><span id="L-223"><a href="#L-223"><span class="linenos">223</span></a> <span class="n">InvalidCodesException</span><span class="p">(</span>
+</span><span id="L-224"><a href="#L-224"><span class="linenos">224</span></a> <span class="n">CodesError</span><span class="p">(</span>
+</span><span id="L-225"><a href="#L-225"><span class="linenos">225</span></a> <span class="sa">f</span><span class="s2">"QA Alphanumeric Dot"</span><span class="p">,</span>
+</span><span id="L-226"><a href="#L-226"><span class="linenos">226</span></a> <span class="n">codes</span><span class="o">=</span><span class="n">codes</span><span class="p">,</span>
+</span><span id="L-227"><a href="#L-227"><span class="linenos">227</span></a> <span class="n">codes_file</span><span class="o">=</span><span class="n">codes_file</span><span class="p">,</span>
+</span><span id="L-228"><a href="#L-228"><span class="linenos">228</span></a> <span class="n">check_regex</span><span class="o">=</span><span class="n">codes</span><span class="o">.</span><span class="n">str</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="sa">r</span><span class="s2">"^[a-zA-Z0-9.]+$"</span><span class="p">),</span>
+</span><span id="L-229"><a href="#L-229"><span class="linenos">229</span></a> <span class="n">code_type</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">,</span>
+</span><span id="L-230"><a href="#L-230"><span class="linenos">230</span></a> <span class="p">)</span>
+</span><span id="L-231"><a href="#L-231"><span class="linenos">231</span></a> <span class="p">)</span>
+</span><span id="L-232"><a href="#L-232"><span class="linenos">232</span></a> <span class="p">),</span>
+</span><span id="L-233"><a href="#L-233"><span class="linenos">233</span></a> <span class="p">),</span>
+</span><span id="L-234"><a href="#L-234"><span class="linenos">234</span></a> <span class="p">(</span>
+</span><span id="L-235"><a href="#L-235"><span class="linenos">235</span></a> <span class="s2">"In Database"</span><span class="p">,</span>
+</span><span id="L-236"><a href="#L-236"><span class="linenos">236</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">in_database</span><span class="p">(</span><span class="n">codes</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">db</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">),</span>
+</span><span id="L-237"><a href="#L-237"><span class="linenos">237</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">,</span> <span class="n">codes_file</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">raise_exception</span><span class="p">(</span>
+</span><span id="L-238"><a href="#L-238"><span class="linenos">238</span></a> <span class="n">InvalidCodesException</span><span class="p">(</span>
+</span><span id="L-239"><a href="#L-239"><span class="linenos">239</span></a> <span class="n">CodesError</span><span class="p">(</span>
+</span><span id="L-240"><a href="#L-240"><span class="linenos">240</span></a> <span class="sa">f</span><span class="s2">"QA In Database"</span><span class="p">,</span>
+</span><span id="L-241"><a href="#L-241"><span class="linenos">241</span></a> <span class="n">codes</span><span class="o">=</span><span class="n">codes</span><span class="p">,</span>
+</span><span id="L-242"><a href="#L-242"><span class="linenos">242</span></a> <span class="n">codes_file</span><span class="o">=</span><span class="n">codes_file</span><span class="p">,</span>
+</span><span id="L-243"><a href="#L-243"><span class="linenos">243</span></a> <span class="n">check_regex</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">in_database</span><span class="p">(</span><span class="n">codes</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">db</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">),</span>
+</span><span id="L-244"><a href="#L-244"><span class="linenos">244</span></a> <span class="n">code_type</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">,</span>
+</span><span id="L-245"><a href="#L-245"><span class="linenos">245</span></a> <span class="p">)</span>
+</span><span id="L-246"><a href="#L-246"><span class="linenos">246</span></a> <span class="p">)</span>
+</span><span id="L-247"><a href="#L-247"><span class="linenos">247</span></a> <span class="p">),</span>
+</span><span id="L-248"><a href="#L-248"><span class="linenos">248</span></a> <span class="p">),</span>
+</span><span id="L-249"><a href="#L-249"><span class="linenos">249</span></a> <span class="p">]</span>
+</span><span id="L-250"><a href="#L-250"><span class="linenos">250</span></a>
+</span><span id="L-251"><a href="#L-251"><span class="linenos">251</span></a>
+</span><span id="L-252"><a href="#L-252"><span class="linenos">252</span></a><span class="k">class</span><span class="w"> </span><span class="nc">Icd10</span><span class="p">(</span><span class="n">Proto</span><span class="p">):</span>
+</span><span id="L-253"><a href="#L-253"><span class="linenos">253</span></a> <span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+</span><span id="L-254"><a href="#L-254"><span class="linenos">254</span></a> <span class="nb">super</span><span class="p">()</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="s2">"icd10"</span><span class="p">,</span> <span class="n">trud</span><span class="o">.</span><span class="n">PROCESSED_PATH</span> <span class="o">/</span> <span class="s2">"icd10.parquet"</span><span class="p">)</span>
+</span><span id="L-255"><a href="#L-255"><span class="linenos">255</span></a>
+</span><span id="L-256"><a href="#L-256"><span class="linenos">256</span></a> <span class="bp">self</span><span class="o">.</span><span class="n">checks</span> <span class="o">=</span> <span class="p">[</span>
+</span><span id="L-257"><a href="#L-257"><span class="linenos">257</span></a> <span class="p">(</span>
+</span><span id="L-258"><a href="#L-258"><span class="linenos">258</span></a> <span class="s2">"Not Empty"</span><span class="p">,</span>
+</span><span id="L-259"><a href="#L-259"><span class="linenos">259</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">:</span> <span class="n">pd</span><span class="o">.</span><span class="n">Series</span><span class="p">([</span><span class="nb">len</span><span class="p">(</span><span class="n">codes</span><span class="p">)</span> <span class="o">></span> <span class="mi">0</span><span class="p">]),</span>
+</span><span id="L-260"><a href="#L-260"><span class="linenos">260</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">,</span> <span class="n">codes_file</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">raise_exception</span><span class="p">(</span>
+</span><span id="L-261"><a href="#L-261"><span class="linenos">261</span></a> <span class="n">InvalidCodesException</span><span class="p">(</span>
+</span><span id="L-262"><a href="#L-262"><span class="linenos">262</span></a> <span class="n">CodesError</span><span class="p">(</span>
+</span><span id="L-263"><a href="#L-263"><span class="linenos">263</span></a> <span class="sa">f</span><span class="s2">"Code list is empty </span><span class="si">{</span><span class="n">codes_file</span><span class="si">}</span><span class="s2">"</span><span class="p">,</span>
+</span><span id="L-264"><a href="#L-264"><span class="linenos">264</span></a> <span class="n">codes</span><span class="o">=</span><span class="n">codes</span><span class="p">,</span>
+</span><span id="L-265"><a href="#L-265"><span class="linenos">265</span></a> <span class="n">codes_file</span><span class="o">=</span><span class="n">codes_file</span><span class="p">,</span>
+</span><span id="L-266"><a href="#L-266"><span class="linenos">266</span></a> <span class="n">mask</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
+</span><span id="L-267"><a href="#L-267"><span class="linenos">267</span></a> <span class="n">code_type</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">,</span>
+</span><span id="L-268"><a href="#L-268"><span class="linenos">268</span></a> <span class="p">)</span>
+</span><span id="L-269"><a href="#L-269"><span class="linenos">269</span></a> <span class="p">)</span>
+</span><span id="L-270"><a href="#L-270"><span class="linenos">270</span></a> <span class="p">),</span>
+</span><span id="L-271"><a href="#L-271"><span class="linenos">271</span></a> <span class="p">),</span>
+</span><span id="L-272"><a href="#L-272"><span class="linenos">272</span></a> <span class="p">(</span>
+</span><span id="L-273"><a href="#L-273"><span class="linenos">273</span></a> <span class="s2">"Too Short"</span><span class="p">,</span>
+</span><span id="L-274"><a href="#L-274"><span class="linenos">274</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">:</span> <span class="o">~</span><span class="p">(</span><span class="n">codes</span><span class="o">.</span><span class="n">str</span><span class="o">.</span><span class="n">len</span><span class="p">()</span> <span class="o"><</span> <span class="mi">3</span><span class="p">),</span>
+</span><span id="L-275"><a href="#L-275"><span class="linenos">275</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">,</span> <span class="n">codes_file</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">raise_exception</span><span class="p">(</span>
+</span><span id="L-276"><a href="#L-276"><span class="linenos">276</span></a> <span class="n">InvalidCodesException</span><span class="p">(</span>
+</span><span id="L-277"><a href="#L-277"><span class="linenos">277</span></a> <span class="n">CodesError</span><span class="p">(</span>
+</span><span id="L-278"><a href="#L-278"><span class="linenos">278</span></a> <span class="sa">f</span><span class="s2">"QA Too Short"</span><span class="p">,</span>
+</span><span id="L-279"><a href="#L-279"><span class="linenos">279</span></a> <span class="n">codes</span><span class="o">=</span><span class="n">codes</span><span class="p">,</span>
+</span><span id="L-280"><a href="#L-280"><span class="linenos">280</span></a> <span class="n">codes_file</span><span class="o">=</span><span class="n">codes_file</span><span class="p">,</span>
+</span><span id="L-281"><a href="#L-281"><span class="linenos">281</span></a> <span class="n">mask</span><span class="o">=~</span><span class="p">(</span><span class="n">codes</span><span class="o">.</span><span class="n">str</span><span class="o">.</span><span class="n">len</span><span class="p">()</span> <span class="o"><</span> <span class="mi">3</span><span class="p">),</span>
+</span><span id="L-282"><a href="#L-282"><span class="linenos">282</span></a> <span class="n">code_type</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">,</span>
+</span><span id="L-283"><a href="#L-283"><span class="linenos">283</span></a> <span class="p">)</span>
+</span><span id="L-284"><a href="#L-284"><span class="linenos">284</span></a> <span class="p">)</span>
+</span><span id="L-285"><a href="#L-285"><span class="linenos">285</span></a> <span class="p">),</span>
+</span><span id="L-286"><a href="#L-286"><span class="linenos">286</span></a> <span class="p">),</span>
+</span><span id="L-287"><a href="#L-287"><span class="linenos">287</span></a> <span class="p">(</span>
+</span><span id="L-288"><a href="#L-288"><span class="linenos">288</span></a> <span class="s2">"Has Dot"</span><span class="p">,</span>
+</span><span id="L-289"><a href="#L-289"><span class="linenos">289</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">:</span> <span class="o">~</span><span class="p">(</span><span class="n">codes</span><span class="o">.</span><span class="n">str</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="sa">r</span><span class="s2">".*\..*"</span><span class="p">)),</span> <span class="c1"># check if contains dot</span>
+</span><span id="L-290"><a href="#L-290"><span class="linenos">290</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">,</span> <span class="n">codes_file</span><span class="p">:</span> <span class="n">codes</span><span class="o">.</span><span class="n">str</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span>
+</span><span id="L-291"><a href="#L-291"><span class="linenos">291</span></a> <span class="s2">"."</span><span class="p">,</span> <span class="s2">""</span>
+</span><span id="L-292"><a href="#L-292"><span class="linenos">292</span></a> <span class="p">),</span> <span class="c1"># delete any dots in string</span>
+</span><span id="L-293"><a href="#L-293"><span class="linenos">293</span></a> <span class="c1"># lambda codes : codes.str.split('\.').apply(lambda ls: ls[0]) #only get part before dot</span>
+</span><span id="L-294"><a href="#L-294"><span class="linenos">294</span></a> <span class="p">),</span>
+</span><span id="L-295"><a href="#L-295"><span class="linenos">295</span></a> <span class="p">(</span>
+</span><span id="L-296"><a href="#L-296"><span class="linenos">296</span></a> <span class="s2">"Alphanumeric Capital"</span><span class="p">,</span>
+</span><span id="L-297"><a href="#L-297"><span class="linenos">297</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">:</span> <span class="n">codes</span><span class="o">.</span><span class="n">str</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="sa">r</span><span class="s2">"^[A-Z0-9]+$"</span><span class="p">),</span>
+</span><span id="L-298"><a href="#L-298"><span class="linenos">298</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">,</span> <span class="n">codes_file</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">raise_exception</span><span class="p">(</span>
+</span><span id="L-299"><a href="#L-299"><span class="linenos">299</span></a> <span class="n">InvalidCodesException</span><span class="p">(</span>
+</span><span id="L-300"><a href="#L-300"><span class="linenos">300</span></a> <span class="n">CodesError</span><span class="p">(</span>
+</span><span id="L-301"><a href="#L-301"><span class="linenos">301</span></a> <span class="sa">f</span><span class="s2">"QA Alphanumeric Capital"</span><span class="p">,</span>
+</span><span id="L-302"><a href="#L-302"><span class="linenos">302</span></a> <span class="n">codes</span><span class="o">=</span><span class="n">codes</span><span class="p">,</span>
+</span><span id="L-303"><a href="#L-303"><span class="linenos">303</span></a> <span class="n">codes_file</span><span class="o">=</span><span class="n">codes_file</span><span class="p">,</span>
+</span><span id="L-304"><a href="#L-304"><span class="linenos">304</span></a> <span class="n">mask</span><span class="o">=</span><span class="n">codes</span><span class="o">.</span><span class="n">str</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="sa">r</span><span class="s2">"^[A-Z0-9]+$"</span><span class="p">),</span>
+</span><span id="L-305"><a href="#L-305"><span class="linenos">305</span></a> <span class="n">code_type</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">,</span>
+</span><span id="L-306"><a href="#L-306"><span class="linenos">306</span></a> <span class="p">)</span>
+</span><span id="L-307"><a href="#L-307"><span class="linenos">307</span></a> <span class="p">)</span>
+</span><span id="L-308"><a href="#L-308"><span class="linenos">308</span></a> <span class="p">),</span>
+</span><span id="L-309"><a href="#L-309"><span class="linenos">309</span></a> <span class="p">),</span>
+</span><span id="L-310"><a href="#L-310"><span class="linenos">310</span></a> <span class="p">(</span>
+</span><span id="L-311"><a href="#L-311"><span class="linenos">311</span></a> <span class="s2">"In Database"</span><span class="p">,</span>
+</span><span id="L-312"><a href="#L-312"><span class="linenos">312</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">:</span> <span class="o">~</span><span class="p">(</span>
+</span><span id="L-313"><a href="#L-313"><span class="linenos">313</span></a> <span class="o">~</span><span class="bp">self</span><span class="o">.</span><span class="n">in_database</span><span class="p">(</span><span class="n">codes</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">db</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">)</span>
+</span><span id="L-314"><a href="#L-314"><span class="linenos">314</span></a> <span class="o">&</span> <span class="o">~</span><span class="bp">self</span><span class="o">.</span><span class="n">in_database</span><span class="p">(</span><span class="n">codes</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">db</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">name</span> <span class="o">+</span> <span class="s2">"_alt"</span><span class="p">)</span>
+</span><span id="L-315"><a href="#L-315"><span class="linenos">315</span></a> <span class="p">),</span>
+</span><span id="L-316"><a href="#L-316"><span class="linenos">316</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">,</span> <span class="n">codes_file</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">raise_exception</span><span class="p">(</span>
+</span><span id="L-317"><a href="#L-317"><span class="linenos">317</span></a> <span class="n">InvalidCodesException</span><span class="p">(</span>
+</span><span id="L-318"><a href="#L-318"><span class="linenos">318</span></a> <span class="n">CodesError</span><span class="p">(</span>
+</span><span id="L-319"><a href="#L-319"><span class="linenos">319</span></a> <span class="sa">f</span><span class="s2">"QA In Database"</span><span class="p">,</span>
+</span><span id="L-320"><a href="#L-320"><span class="linenos">320</span></a> <span class="n">codes</span><span class="o">=</span><span class="n">codes</span><span class="p">,</span>
+</span><span id="L-321"><a href="#L-321"><span class="linenos">321</span></a> <span class="n">codes_file</span><span class="o">=</span><span class="n">codes_file</span><span class="p">,</span>
+</span><span id="L-322"><a href="#L-322"><span class="linenos">322</span></a> <span class="n">mask</span><span class="o">=~</span><span class="p">(</span>
+</span><span id="L-323"><a href="#L-323"><span class="linenos">323</span></a> <span class="o">~</span><span class="bp">self</span><span class="o">.</span><span class="n">in_database</span><span class="p">(</span><span class="n">codes</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">db</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">)</span>
+</span><span id="L-324"><a href="#L-324"><span class="linenos">324</span></a> <span class="o">&</span> <span class="o">~</span><span class="bp">self</span><span class="o">.</span><span class="n">in_database</span><span class="p">(</span><span class="n">codes</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">db</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">name</span> <span class="o">+</span> <span class="s2">"_alt"</span><span class="p">)</span>
+</span><span id="L-325"><a href="#L-325"><span class="linenos">325</span></a> <span class="p">),</span>
+</span><span id="L-326"><a href="#L-326"><span class="linenos">326</span></a> <span class="n">code_type</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">,</span>
+</span><span id="L-327"><a href="#L-327"><span class="linenos">327</span></a> <span class="p">)</span>
+</span><span id="L-328"><a href="#L-328"><span class="linenos">328</span></a> <span class="p">)</span>
+</span><span id="L-329"><a href="#L-329"><span class="linenos">329</span></a> <span class="p">),</span>
+</span><span id="L-330"><a href="#L-330"><span class="linenos">330</span></a> <span class="p">),</span>
+</span><span id="L-331"><a href="#L-331"><span class="linenos">331</span></a> <span class="c1"># (</span>
+</span><span id="L-332"><a href="#L-332"><span class="linenos">332</span></a> <span class="c1"># "ICD10 Regex",</span>
+</span><span id="L-333"><a href="#L-333"><span class="linenos">333</span></a> <span class="c1"># lambda codes : codes.str.match("[a-zA-Z][0-9][0-9]\.?[a-zA-Z0-9]*$"), #Alpha, Num, Num , Dot?, 4xAlphNum*</span>
+</span><span id="L-334"><a href="#L-334"><span class="linenos">334</span></a> <span class="c1"># lambda codes : lc.log_invalid_code(codes,</span>
+</span><span id="L-335"><a href="#L-335"><span class="linenos">335</span></a> <span class="c1"># codes.str.match("[a-zA-Z][0-9][0-9]\.?[a-zA-Z0-9]*$"), #Log non-matching rows</span>
+</span><span id="L-336"><a href="#L-336"><span class="linenos">336</span></a> <span class="c1"># code_type="icd10",</span>
+</span><span id="L-337"><a href="#L-337"><span class="linenos">337</span></a> <span class="c1">#</span>
+</span><span id="L-338"><a href="#L-338"><span class="linenos">338</span></a> <span class="c1"># )</span>
+</span><span id="L-339"><a href="#L-339"><span class="linenos">339</span></a> <span class="p">]</span>
+</span><span id="L-340"><a href="#L-340"><span class="linenos">340</span></a>
+</span><span id="L-341"><a href="#L-341"><span class="linenos">341</span></a> <span class="k">def</span><span class="w"> </span><span class="nf">trim_icd10</span><span class="p">(</span><span class="n">codes</span><span class="p">:</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">)</span> <span class="o">-></span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">:</span>
+</span><span id="L-342"><a href="#L-342"><span class="linenos">342</span></a> <span class="n">codes</span> <span class="o">=</span> <span class="n">codes</span><span class="o">.</span><span class="n">str</span><span class="p">[:</span><span class="mi">4</span><span class="p">]</span>
+</span><span id="L-343"><a href="#L-343"><span class="linenos">343</span></a> <span class="k">return</span> <span class="n">codes</span>
+</span><span id="L-344"><a href="#L-344"><span class="linenos">344</span></a>
+</span><span id="L-345"><a href="#L-345"><span class="linenos">345</span></a>
+</span><span id="L-346"><a href="#L-346"><span class="linenos">346</span></a><span class="k">class</span><span class="w"> </span><span class="nc">Snomed</span><span class="p">(</span><span class="n">Proto</span><span class="p">):</span>
+</span><span id="L-347"><a href="#L-347"><span class="linenos">347</span></a> <span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+</span><span id="L-348"><a href="#L-348"><span class="linenos">348</span></a> <span class="nb">super</span><span class="p">()</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="s2">"snomed"</span><span class="p">,</span> <span class="n">trud</span><span class="o">.</span><span class="n">PROCESSED_PATH</span> <span class="o">/</span> <span class="s2">"snomed.parquet"</span><span class="p">)</span>
+</span><span id="L-349"><a href="#L-349"><span class="linenos">349</span></a>
+</span><span id="L-350"><a href="#L-350"><span class="linenos">350</span></a> <span class="bp">self</span><span class="o">.</span><span class="n">checks</span> <span class="o">=</span> <span class="p">[</span>
+</span><span id="L-351"><a href="#L-351"><span class="linenos">351</span></a> <span class="c1"># (</span>
+</span><span id="L-352"><a href="#L-352"><span class="linenos">352</span></a> <span class="c1"># "Not Empty",</span>
+</span><span id="L-353"><a href="#L-353"><span class="linenos">353</span></a> <span class="c1"># lambda codes : pd.Series([len(codes) > 0]),</span>
+</span><span id="L-354"><a href="#L-354"><span class="linenos">354</span></a> <span class="c1"># lambda codes : raise_exception(Exception("Code List is Empty"))</span>
+</span><span id="L-355"><a href="#L-355"><span class="linenos">355</span></a> <span class="c1"># ),</span>
+</span><span id="L-356"><a href="#L-356"><span class="linenos">356</span></a> <span class="p">(</span>
+</span><span id="L-357"><a href="#L-357"><span class="linenos">357</span></a> <span class="s2">"Too Short"</span><span class="p">,</span>
+</span><span id="L-358"><a href="#L-358"><span class="linenos">358</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">:</span> <span class="o">~</span><span class="p">(</span><span class="n">codes</span><span class="o">.</span><span class="n">str</span><span class="o">.</span><span class="n">len</span><span class="p">()</span> <span class="o"><</span> <span class="mi">6</span><span class="p">),</span>
+</span><span id="L-359"><a href="#L-359"><span class="linenos">359</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">,</span> <span class="n">codes_file</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">raise_exception</span><span class="p">(</span>
+</span><span id="L-360"><a href="#L-360"><span class="linenos">360</span></a> <span class="n">InvalidCodesException</span><span class="p">(</span>
+</span><span id="L-361"><a href="#L-361"><span class="linenos">361</span></a> <span class="n">CodesError</span><span class="p">(</span>
+</span><span id="L-362"><a href="#L-362"><span class="linenos">362</span></a> <span class="sa">f</span><span class="s2">"QA Too Short"</span><span class="p">,</span>
+</span><span id="L-363"><a href="#L-363"><span class="linenos">363</span></a> <span class="n">codes</span><span class="o">=</span><span class="n">codes</span><span class="p">,</span>
+</span><span id="L-364"><a href="#L-364"><span class="linenos">364</span></a> <span class="n">codes_file</span><span class="o">=</span><span class="n">codes_file</span><span class="p">,</span>
+</span><span id="L-365"><a href="#L-365"><span class="linenos">365</span></a> <span class="n">mask</span><span class="o">=~</span><span class="p">(</span><span class="n">codes</span><span class="o">.</span><span class="n">str</span><span class="o">.</span><span class="n">len</span><span class="p">()</span> <span class="o"><</span> <span class="mi">6</span><span class="p">),</span>
+</span><span id="L-366"><a href="#L-366"><span class="linenos">366</span></a> <span class="n">code_type</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">,</span>
+</span><span id="L-367"><a href="#L-367"><span class="linenos">367</span></a> <span class="p">)</span>
+</span><span id="L-368"><a href="#L-368"><span class="linenos">368</span></a> <span class="p">)</span>
+</span><span id="L-369"><a href="#L-369"><span class="linenos">369</span></a> <span class="p">),</span>
+</span><span id="L-370"><a href="#L-370"><span class="linenos">370</span></a> <span class="p">),</span>
+</span><span id="L-371"><a href="#L-371"><span class="linenos">371</span></a> <span class="p">(</span>
+</span><span id="L-372"><a href="#L-372"><span class="linenos">372</span></a> <span class="s2">"Too Long"</span><span class="p">,</span>
+</span><span id="L-373"><a href="#L-373"><span class="linenos">373</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">:</span> <span class="o">~</span><span class="p">(</span><span class="n">codes</span><span class="o">.</span><span class="n">str</span><span class="o">.</span><span class="n">len</span><span class="p">()</span> <span class="o">></span> <span class="mi">18</span><span class="p">),</span>
+</span><span id="L-374"><a href="#L-374"><span class="linenos">374</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">,</span> <span class="n">codes_file</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">raise_exception</span><span class="p">(</span>
+</span><span id="L-375"><a href="#L-375"><span class="linenos">375</span></a> <span class="n">InvalidCodesException</span><span class="p">(</span>
+</span><span id="L-376"><a href="#L-376"><span class="linenos">376</span></a> <span class="n">CodesError</span><span class="p">(</span>
+</span><span id="L-377"><a href="#L-377"><span class="linenos">377</span></a> <span class="sa">f</span><span class="s2">"QA Too Long"</span><span class="p">,</span>
+</span><span id="L-378"><a href="#L-378"><span class="linenos">378</span></a> <span class="n">codes</span><span class="o">=</span><span class="n">codes</span><span class="p">,</span>
+</span><span id="L-379"><a href="#L-379"><span class="linenos">379</span></a> <span class="n">codes_file</span><span class="o">=</span><span class="n">codes_file</span><span class="p">,</span>
+</span><span id="L-380"><a href="#L-380"><span class="linenos">380</span></a> <span class="n">mask</span><span class="o">=~</span><span class="p">(</span><span class="n">codes</span><span class="o">.</span><span class="n">str</span><span class="o">.</span><span class="n">len</span><span class="p">()</span> <span class="o">></span> <span class="mi">18</span><span class="p">),</span>
+</span><span id="L-381"><a href="#L-381"><span class="linenos">381</span></a> <span class="n">code_type</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">,</span>
+</span><span id="L-382"><a href="#L-382"><span class="linenos">382</span></a> <span class="p">)</span>
+</span><span id="L-383"><a href="#L-383"><span class="linenos">383</span></a> <span class="p">)</span>
+</span><span id="L-384"><a href="#L-384"><span class="linenos">384</span></a> <span class="p">),</span>
+</span><span id="L-385"><a href="#L-385"><span class="linenos">385</span></a> <span class="p">),</span>
+</span><span id="L-386"><a href="#L-386"><span class="linenos">386</span></a> <span class="p">(</span>
+</span><span id="L-387"><a href="#L-387"><span class="linenos">387</span></a> <span class="s2">"Numeric"</span><span class="p">,</span>
+</span><span id="L-388"><a href="#L-388"><span class="linenos">388</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">:</span> <span class="n">codes</span><span class="o">.</span><span class="n">str</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="sa">r</span><span class="s2">"[0-9]+$"</span><span class="p">),</span>
+</span><span id="L-389"><a href="#L-389"><span class="linenos">389</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">,</span> <span class="n">codes_file</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">raise_exception</span><span class="p">(</span>
+</span><span id="L-390"><a href="#L-390"><span class="linenos">390</span></a> <span class="n">InvalidCodesException</span><span class="p">(</span>
+</span><span id="L-391"><a href="#L-391"><span class="linenos">391</span></a> <span class="n">CodesError</span><span class="p">(</span>
+</span><span id="L-392"><a href="#L-392"><span class="linenos">392</span></a> <span class="sa">f</span><span class="s2">"QA Numeric"</span><span class="p">,</span>
+</span><span id="L-393"><a href="#L-393"><span class="linenos">393</span></a> <span class="n">codes</span><span class="o">=</span><span class="n">codes</span><span class="p">,</span>
+</span><span id="L-394"><a href="#L-394"><span class="linenos">394</span></a> <span class="n">codes_file</span><span class="o">=</span><span class="n">codes_file</span><span class="p">,</span>
+</span><span id="L-395"><a href="#L-395"><span class="linenos">395</span></a> <span class="n">mask</span><span class="o">=</span><span class="n">codes</span><span class="o">.</span><span class="n">str</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="sa">r</span><span class="s2">"[0-9]+$"</span><span class="p">),</span>
+</span><span id="L-396"><a href="#L-396"><span class="linenos">396</span></a> <span class="n">code_type</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">,</span>
+</span><span id="L-397"><a href="#L-397"><span class="linenos">397</span></a> <span class="p">)</span>
+</span><span id="L-398"><a href="#L-398"><span class="linenos">398</span></a> <span class="p">)</span>
+</span><span id="L-399"><a href="#L-399"><span class="linenos">399</span></a> <span class="p">),</span>
+</span><span id="L-400"><a href="#L-400"><span class="linenos">400</span></a> <span class="p">),</span>
+</span><span id="L-401"><a href="#L-401"><span class="linenos">401</span></a> <span class="c1"># (</span>
+</span><span id="L-402"><a href="#L-402"><span class="linenos">402</span></a> <span class="c1"># "Is Integer",</span>
+</span><span id="L-403"><a href="#L-403"><span class="linenos">403</span></a> <span class="c1"># lambda codes : codes.dtype == int,</span>
+</span><span id="L-404"><a href="#L-404"><span class="linenos">404</span></a> <span class="c1"># lambda codes : codes.astype(int) #Convert to integer</span>
+</span><span id="L-405"><a href="#L-405"><span class="linenos">405</span></a> <span class="c1"># ),</span>
+</span><span id="L-406"><a href="#L-406"><span class="linenos">406</span></a> <span class="p">(</span>
+</span><span id="L-407"><a href="#L-407"><span class="linenos">407</span></a> <span class="s2">"In Database"</span><span class="p">,</span>
+</span><span id="L-408"><a href="#L-408"><span class="linenos">408</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">in_database</span><span class="p">(</span><span class="n">codes</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">db</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">),</span>
+</span><span id="L-409"><a href="#L-409"><span class="linenos">409</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">,</span> <span class="n">codes_file</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">raise_exception</span><span class="p">(</span>
+</span><span id="L-410"><a href="#L-410"><span class="linenos">410</span></a> <span class="n">InvalidCodesException</span><span class="p">(</span>
+</span><span id="L-411"><a href="#L-411"><span class="linenos">411</span></a> <span class="n">CodesError</span><span class="p">(</span>
+</span><span id="L-412"><a href="#L-412"><span class="linenos">412</span></a> <span class="sa">f</span><span class="s2">"QA In Database"</span><span class="p">,</span>
+</span><span id="L-413"><a href="#L-413"><span class="linenos">413</span></a> <span class="n">codes</span><span class="o">=</span><span class="n">codes</span><span class="p">,</span>
+</span><span id="L-414"><a href="#L-414"><span class="linenos">414</span></a> <span class="n">codes_file</span><span class="o">=</span><span class="n">codes_file</span><span class="p">,</span>
+</span><span id="L-415"><a href="#L-415"><span class="linenos">415</span></a> <span class="n">mask</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">in_database</span><span class="p">(</span><span class="n">codes</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">db</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">),</span>
+</span><span id="L-416"><a href="#L-416"><span class="linenos">416</span></a> <span class="n">code_type</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">,</span>
+</span><span id="L-417"><a href="#L-417"><span class="linenos">417</span></a> <span class="p">)</span>
+</span><span id="L-418"><a href="#L-418"><span class="linenos">418</span></a> <span class="p">)</span>
+</span><span id="L-419"><a href="#L-419"><span class="linenos">419</span></a> <span class="p">),</span>
+</span><span id="L-420"><a href="#L-420"><span class="linenos">420</span></a> <span class="p">),</span>
+</span><span id="L-421"><a href="#L-421"><span class="linenos">421</span></a> <span class="p">]</span>
+</span><span id="L-422"><a href="#L-422"><span class="linenos">422</span></a>
+</span><span id="L-423"><a href="#L-423"><span class="linenos">423</span></a>
+</span><span id="L-424"><a href="#L-424"><span class="linenos">424</span></a><span class="k">class</span><span class="w"> </span><span class="nc">Opcs4</span><span class="p">(</span><span class="n">Proto</span><span class="p">):</span>
+</span><span id="L-425"><a href="#L-425"><span class="linenos">425</span></a> <span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+</span><span id="L-426"><a href="#L-426"><span class="linenos">426</span></a> <span class="nb">super</span><span class="p">()</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="s2">"opcs4"</span><span class="p">,</span> <span class="n">trud</span><span class="o">.</span><span class="n">PROCESSED_PATH</span> <span class="o">/</span> <span class="s2">"opcs4.parquet"</span><span class="p">)</span>
+</span><span id="L-427"><a href="#L-427"><span class="linenos">427</span></a>
+</span><span id="L-428"><a href="#L-428"><span class="linenos">428</span></a> <span class="bp">self</span><span class="o">.</span><span class="n">checks</span> <span class="o">=</span> <span class="p">[</span>
+</span><span id="L-429"><a href="#L-429"><span class="linenos">429</span></a> <span class="p">(</span>
+</span><span id="L-430"><a href="#L-430"><span class="linenos">430</span></a> <span class="s2">"Not Empty"</span><span class="p">,</span>
+</span><span id="L-431"><a href="#L-431"><span class="linenos">431</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">:</span> <span class="n">pd</span><span class="o">.</span><span class="n">Series</span><span class="p">([</span><span class="nb">len</span><span class="p">(</span><span class="n">codes</span><span class="p">)</span> <span class="o">></span> <span class="mi">0</span><span class="p">]),</span>
+</span><span id="L-432"><a href="#L-432"><span class="linenos">432</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">,</span> <span class="n">codes_file</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">raise_exception</span><span class="p">(</span>
+</span><span id="L-433"><a href="#L-433"><span class="linenos">433</span></a> <span class="n">InvalidCodesException</span><span class="p">(</span>
+</span><span id="L-434"><a href="#L-434"><span class="linenos">434</span></a> <span class="n">CodesError</span><span class="p">(</span>
+</span><span id="L-435"><a href="#L-435"><span class="linenos">435</span></a> <span class="sa">f</span><span class="s2">"Code list is empty"</span><span class="p">,</span>
+</span><span id="L-436"><a href="#L-436"><span class="linenos">436</span></a> <span class="n">codes</span><span class="o">=</span><span class="n">codes</span><span class="p">,</span>
+</span><span id="L-437"><a href="#L-437"><span class="linenos">437</span></a> <span class="n">codes_file</span><span class="o">=</span><span class="n">codes_file</span><span class="p">,</span>
+</span><span id="L-438"><a href="#L-438"><span class="linenos">438</span></a> <span class="n">mask</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
+</span><span id="L-439"><a href="#L-439"><span class="linenos">439</span></a> <span class="n">code_type</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">,</span>
+</span><span id="L-440"><a href="#L-440"><span class="linenos">440</span></a> <span class="p">)</span>
+</span><span id="L-441"><a href="#L-441"><span class="linenos">441</span></a> <span class="p">)</span>
+</span><span id="L-442"><a href="#L-442"><span class="linenos">442</span></a> <span class="p">),</span>
+</span><span id="L-443"><a href="#L-443"><span class="linenos">443</span></a> <span class="p">),</span>
+</span><span id="L-444"><a href="#L-444"><span class="linenos">444</span></a> <span class="p">(</span>
+</span><span id="L-445"><a href="#L-445"><span class="linenos">445</span></a> <span class="s2">"In Database"</span><span class="p">,</span>
+</span><span id="L-446"><a href="#L-446"><span class="linenos">446</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">in_database</span><span class="p">(</span><span class="n">codes</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">db</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">),</span>
+</span><span id="L-447"><a href="#L-447"><span class="linenos">447</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">,</span> <span class="n">codes_file</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">raise_exception</span><span class="p">(</span>
+</span><span id="L-448"><a href="#L-448"><span class="linenos">448</span></a> <span class="n">InvalidCodesException</span><span class="p">(</span>
+</span><span id="L-449"><a href="#L-449"><span class="linenos">449</span></a> <span class="n">CodesError</span><span class="p">(</span>
+</span><span id="L-450"><a href="#L-450"><span class="linenos">450</span></a> <span class="sa">f</span><span class="s2">"QA In Database"</span><span class="p">,</span>
+</span><span id="L-451"><a href="#L-451"><span class="linenos">451</span></a> <span class="n">codes</span><span class="o">=</span><span class="n">codes</span><span class="p">,</span>
+</span><span id="L-452"><a href="#L-452"><span class="linenos">452</span></a> <span class="n">codes_file</span><span class="o">=</span><span class="n">codes_file</span><span class="p">,</span>
+</span><span id="L-453"><a href="#L-453"><span class="linenos">453</span></a> <span class="n">mask</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">in_database</span><span class="p">(</span><span class="n">codes</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">db</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">),</span>
+</span><span id="L-454"><a href="#L-454"><span class="linenos">454</span></a> <span class="n">code_type</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">,</span>
+</span><span id="L-455"><a href="#L-455"><span class="linenos">455</span></a> <span class="p">)</span>
+</span><span id="L-456"><a href="#L-456"><span class="linenos">456</span></a> <span class="p">)</span>
+</span><span id="L-457"><a href="#L-457"><span class="linenos">457</span></a> <span class="p">),</span>
+</span><span id="L-458"><a href="#L-458"><span class="linenos">458</span></a> <span class="p">),</span>
+</span><span id="L-459"><a href="#L-459"><span class="linenos">459</span></a> <span class="p">]</span>
+</span><span id="L-460"><a href="#L-460"><span class="linenos">460</span></a>
+</span><span id="L-461"><a href="#L-461"><span class="linenos">461</span></a>
+</span><span id="L-462"><a href="#L-462"><span class="linenos">462</span></a><span class="k">class</span><span class="w"> </span><span class="nc">Atc</span><span class="p">(</span><span class="n">Proto</span><span class="p">):</span>
+</span><span id="L-463"><a href="#L-463"><span class="linenos">463</span></a> <span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+</span><span id="L-464"><a href="#L-464"><span class="linenos">464</span></a> <span class="nb">super</span><span class="p">()</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="s2">"atc"</span><span class="p">,</span> <span class="n">trud_codes_path</span><span class="o">=</span><span class="kc">None</span><span class="p">)</span>
+</span><span id="L-465"><a href="#L-465"><span class="linenos">465</span></a> <span class="bp">self</span><span class="o">.</span><span class="n">checks</span> <span class="o">=</span> <span class="p">[</span>
+</span><span id="L-466"><a href="#L-466"><span class="linenos">466</span></a> <span class="p">(</span>
+</span><span id="L-467"><a href="#L-467"><span class="linenos">467</span></a> <span class="s2">"Not Empty"</span><span class="p">,</span>
+</span><span id="L-468"><a href="#L-468"><span class="linenos">468</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">:</span> <span class="n">pd</span><span class="o">.</span><span class="n">Series</span><span class="p">([</span><span class="nb">len</span><span class="p">(</span><span class="n">codes</span><span class="p">)</span> <span class="o">></span> <span class="mi">0</span><span class="p">]),</span>
+</span><span id="L-469"><a href="#L-469"><span class="linenos">469</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">,</span> <span class="n">codes_file</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">raise_exception</span><span class="p">(</span>
+</span><span id="L-470"><a href="#L-470"><span class="linenos">470</span></a> <span class="n">InvalidCodesException</span><span class="p">(</span>
+</span><span id="L-471"><a href="#L-471"><span class="linenos">471</span></a> <span class="n">CodesError</span><span class="p">(</span>
+</span><span id="L-472"><a href="#L-472"><span class="linenos">472</span></a> <span class="sa">f</span><span class="s2">"Code list is empty"</span><span class="p">,</span>
+</span><span id="L-473"><a href="#L-473"><span class="linenos">473</span></a> <span class="n">codes</span><span class="o">=</span><span class="n">codes</span><span class="p">,</span>
+</span><span id="L-474"><a href="#L-474"><span class="linenos">474</span></a> <span class="n">codes_file</span><span class="o">=</span><span class="n">codes_file</span><span class="p">,</span>
+</span><span id="L-475"><a href="#L-475"><span class="linenos">475</span></a> <span class="n">mask</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
+</span><span id="L-476"><a href="#L-476"><span class="linenos">476</span></a> <span class="n">code_type</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">,</span>
+</span><span id="L-477"><a href="#L-477"><span class="linenos">477</span></a> <span class="p">)</span>
+</span><span id="L-478"><a href="#L-478"><span class="linenos">478</span></a> <span class="p">)</span>
+</span><span id="L-479"><a href="#L-479"><span class="linenos">479</span></a> <span class="p">),</span>
+</span><span id="L-480"><a href="#L-480"><span class="linenos">480</span></a> <span class="p">),</span>
+</span><span id="L-481"><a href="#L-481"><span class="linenos">481</span></a> <span class="p">(</span>
+</span><span id="L-482"><a href="#L-482"><span class="linenos">482</span></a> <span class="s2">"Alphanumeric Capital"</span><span class="p">,</span>
+</span><span id="L-483"><a href="#L-483"><span class="linenos">483</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">:</span> <span class="n">codes</span><span class="o">.</span><span class="n">str</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="sa">r</span><span class="s2">"^[A-Z0-9]+$"</span><span class="p">),</span>
+</span><span id="L-484"><a href="#L-484"><span class="linenos">484</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">,</span> <span class="n">codes_file</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">raise_exception</span><span class="p">(</span>
+</span><span id="L-485"><a href="#L-485"><span class="linenos">485</span></a> <span class="n">InvalidCodesException</span><span class="p">(</span>
+</span><span id="L-486"><a href="#L-486"><span class="linenos">486</span></a> <span class="n">CodesError</span><span class="p">(</span>
+</span><span id="L-487"><a href="#L-487"><span class="linenos">487</span></a> <span class="sa">f</span><span class="s2">"QA Alphanumeric Capital"</span><span class="p">,</span>
+</span><span id="L-488"><a href="#L-488"><span class="linenos">488</span></a> <span class="n">codes</span><span class="o">=</span><span class="n">codes</span><span class="p">,</span>
+</span><span id="L-489"><a href="#L-489"><span class="linenos">489</span></a> <span class="n">codes_file</span><span class="o">=</span><span class="n">codes_file</span><span class="p">,</span>
+</span><span id="L-490"><a href="#L-490"><span class="linenos">490</span></a> <span class="n">mask</span><span class="o">=</span><span class="n">codes</span><span class="o">.</span><span class="n">str</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="sa">r</span><span class="s2">"^[A-Z0-9]+$"</span><span class="p">),</span>
+</span><span id="L-491"><a href="#L-491"><span class="linenos">491</span></a> <span class="n">code_type</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">,</span>
+</span><span id="L-492"><a href="#L-492"><span class="linenos">492</span></a> <span class="p">)</span>
+</span><span id="L-493"><a href="#L-493"><span class="linenos">493</span></a> <span class="p">)</span>
+</span><span id="L-494"><a href="#L-494"><span class="linenos">494</span></a> <span class="p">),</span>
+</span><span id="L-495"><a href="#L-495"><span class="linenos">495</span></a> <span class="p">),</span>
+</span><span id="L-496"><a href="#L-496"><span class="linenos">496</span></a> <span class="p">]</span>
+</span><span id="L-497"><a href="#L-497"><span class="linenos">497</span></a>
+</span><span id="L-498"><a href="#L-498"><span class="linenos">498</span></a>
+</span><span id="L-499"><a href="#L-499"><span class="linenos">499</span></a><span class="k">class</span><span class="w"> </span><span class="nc">Med</span><span class="p">(</span><span class="n">Proto</span><span class="p">):</span>
+</span><span id="L-500"><a href="#L-500"><span class="linenos">500</span></a> <span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+</span><span id="L-501"><a href="#L-501"><span class="linenos">501</span></a> <span class="nb">super</span><span class="p">()</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="s2">"med"</span><span class="p">,</span> <span class="n">trud_codes_path</span><span class="o">=</span><span class="kc">None</span><span class="p">)</span>
+</span><span id="L-502"><a href="#L-502"><span class="linenos">502</span></a> <span class="bp">self</span><span class="o">.</span><span class="n">checks</span> <span class="o">=</span> <span class="p">[</span>
+</span><span id="L-503"><a href="#L-503"><span class="linenos">503</span></a> <span class="p">(</span>
+</span><span id="L-504"><a href="#L-504"><span class="linenos">504</span></a> <span class="s2">"Not Empty"</span><span class="p">,</span>
+</span><span id="L-505"><a href="#L-505"><span class="linenos">505</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">:</span> <span class="n">pd</span><span class="o">.</span><span class="n">Series</span><span class="p">([</span><span class="nb">len</span><span class="p">(</span><span class="n">codes</span><span class="p">)</span> <span class="o">></span> <span class="mi">0</span><span class="p">]),</span>
+</span><span id="L-506"><a href="#L-506"><span class="linenos">506</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">,</span> <span class="n">codes_file</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">raise_exception</span><span class="p">(</span>
+</span><span id="L-507"><a href="#L-507"><span class="linenos">507</span></a> <span class="n">InvalidCodesException</span><span class="p">(</span>
+</span><span id="L-508"><a href="#L-508"><span class="linenos">508</span></a> <span class="n">CodesError</span><span class="p">(</span>
+</span><span id="L-509"><a href="#L-509"><span class="linenos">509</span></a> <span class="sa">f</span><span class="s2">"Code list is empty"</span><span class="p">,</span>
+</span><span id="L-510"><a href="#L-510"><span class="linenos">510</span></a> <span class="n">codes</span><span class="o">=</span><span class="n">codes</span><span class="p">,</span>
+</span><span id="L-511"><a href="#L-511"><span class="linenos">511</span></a> <span class="n">codes_file</span><span class="o">=</span><span class="n">codes_file</span><span class="p">,</span>
+</span><span id="L-512"><a href="#L-512"><span class="linenos">512</span></a> <span class="n">mask</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
+</span><span id="L-513"><a href="#L-513"><span class="linenos">513</span></a> <span class="n">code_type</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">,</span>
+</span><span id="L-514"><a href="#L-514"><span class="linenos">514</span></a> <span class="p">)</span>
+</span><span id="L-515"><a href="#L-515"><span class="linenos">515</span></a> <span class="p">)</span>
+</span><span id="L-516"><a href="#L-516"><span class="linenos">516</span></a> <span class="p">),</span>
+</span><span id="L-517"><a href="#L-517"><span class="linenos">517</span></a> <span class="p">)</span>
+</span><span id="L-518"><a href="#L-518"><span class="linenos">518</span></a> <span class="p">]</span>
+</span><span id="L-519"><a href="#L-519"><span class="linenos">519</span></a>
+</span><span id="L-520"><a href="#L-520"><span class="linenos">520</span></a>
+</span><span id="L-521"><a href="#L-521"><span class="linenos">521</span></a><span class="k">class</span><span class="w"> </span><span class="nc">Cprd</span><span class="p">(</span><span class="n">Proto</span><span class="p">):</span>
+</span><span id="L-522"><a href="#L-522"><span class="linenos">522</span></a> <span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+</span><span id="L-523"><a href="#L-523"><span class="linenos">523</span></a> <span class="nb">super</span><span class="p">()</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="s2">"cprd"</span><span class="p">,</span> <span class="n">trud_codes_path</span><span class="o">=</span><span class="kc">None</span><span class="p">)</span>
+</span><span id="L-524"><a href="#L-524"><span class="linenos">524</span></a> <span class="bp">self</span><span class="o">.</span><span class="n">checks</span> <span class="o">=</span> <span class="p">[</span>
+</span><span id="L-525"><a href="#L-525"><span class="linenos">525</span></a> <span class="p">(</span>
+</span><span id="L-526"><a href="#L-526"><span class="linenos">526</span></a> <span class="s2">"Not Empty"</span><span class="p">,</span>
+</span><span id="L-527"><a href="#L-527"><span class="linenos">527</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">:</span> <span class="n">pd</span><span class="o">.</span><span class="n">Series</span><span class="p">([</span><span class="nb">len</span><span class="p">(</span><span class="n">codes</span><span class="p">)</span> <span class="o">></span> <span class="mi">0</span><span class="p">]),</span>
+</span><span id="L-528"><a href="#L-528"><span class="linenos">528</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">,</span> <span class="n">codes_file</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">raise_exception</span><span class="p">(</span>
+</span><span id="L-529"><a href="#L-529"><span class="linenos">529</span></a> <span class="n">InvalidCodesException</span><span class="p">(</span>
+</span><span id="L-530"><a href="#L-530"><span class="linenos">530</span></a> <span class="n">CodesError</span><span class="p">(</span>
+</span><span id="L-531"><a href="#L-531"><span class="linenos">531</span></a> <span class="sa">f</span><span class="s2">"Code list is empty"</span><span class="p">,</span>
+</span><span id="L-532"><a href="#L-532"><span class="linenos">532</span></a> <span class="n">codes</span><span class="o">=</span><span class="n">codes</span><span class="p">,</span>
+</span><span id="L-533"><a href="#L-533"><span class="linenos">533</span></a> <span class="n">codes_file</span><span class="o">=</span><span class="n">codes_file</span><span class="p">,</span>
+</span><span id="L-534"><a href="#L-534"><span class="linenos">534</span></a> <span class="n">mask</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
+</span><span id="L-535"><a href="#L-535"><span class="linenos">535</span></a> <span class="n">code_type</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">,</span>
+</span><span id="L-536"><a href="#L-536"><span class="linenos">536</span></a> <span class="p">)</span>
+</span><span id="L-537"><a href="#L-537"><span class="linenos">537</span></a> <span class="p">)</span>
+</span><span id="L-538"><a href="#L-538"><span class="linenos">538</span></a> <span class="p">),</span>
+</span><span id="L-539"><a href="#L-539"><span class="linenos">539</span></a> <span class="p">)</span>
+</span><span id="L-540"><a href="#L-540"><span class="linenos">540</span></a> <span class="p">]</span>
+</span><span id="L-541"><a href="#L-541"><span class="linenos">541</span></a>
+</span><span id="L-542"><a href="#L-542"><span class="linenos">542</span></a>
+</span><span id="L-543"><a href="#L-543"><span class="linenos">543</span></a><span class="k">class</span><span class="w"> </span><span class="nc">CodeTypeParser</span><span class="p">:</span>
+</span><span id="L-544"><a href="#L-544"><span class="linenos">544</span></a><span class="w"> </span><span class="sd">"""A class used in InvalidCodesException to report an error if a code parser check fails"""</span>
+</span><span id="L-545"><a href="#L-545"><span class="linenos">545</span></a>
+</span><span id="L-546"><a href="#L-546"><span class="linenos">546</span></a> <span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">trud_processed_dir</span><span class="p">:</span> <span class="n">Path</span> <span class="o">=</span> <span class="n">trud</span><span class="o">.</span><span class="n">PROCESSED_PATH</span><span class="p">):</span>
+</span><span id="L-547"><a href="#L-547"><span class="linenos">547</span></a>
+</span><span id="L-548"><a href="#L-548"><span class="linenos">548</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="n">trud_processed_dir</span><span class="o">.</span><span class="n">exists</span><span class="p">()</span> <span class="ow">or</span> <span class="ow">not</span> <span class="n">trud_processed_dir</span><span class="o">.</span><span class="n">is_dir</span><span class="p">():</span>
+</span><span id="L-549"><a href="#L-549"><span class="linenos">549</span></a> <span class="k">raise</span> <span class="ne">FileNotFoundError</span><span class="p">(</span>
+</span><span id="L-550"><a href="#L-550"><span class="linenos">550</span></a> <span class="sa">f</span><span class="s2">"Cannot initialise parsers as the TRUD processed directory </span><span class="si">{</span><span class="n">trud_processed_dir</span><span class="si">}</span><span class="s2"> does not exist, please check that TRUD has been installed: acmc trud install"</span>
+</span><span id="L-551"><a href="#L-551"><span class="linenos">551</span></a> <span class="p">)</span>
+</span><span id="L-552"><a href="#L-552"><span class="linenos">552</span></a>
+</span><span id="L-553"><a href="#L-553"><span class="linenos">553</span></a> <span class="bp">self</span><span class="o">.</span><span class="n">code_types</span> <span class="o">=</span> <span class="p">{</span>
+</span><span id="L-554"><a href="#L-554"><span class="linenos">554</span></a> <span class="s2">"read2"</span><span class="p">:</span> <span class="n">Read2</span><span class="p">(),</span>
+</span><span id="L-555"><a href="#L-555"><span class="linenos">555</span></a> <span class="s2">"read3"</span><span class="p">:</span> <span class="n">Read3</span><span class="p">(),</span>
+</span><span id="L-556"><a href="#L-556"><span class="linenos">556</span></a> <span class="s2">"icd10"</span><span class="p">:</span> <span class="n">Icd10</span><span class="p">(),</span>
+</span><span id="L-557"><a href="#L-557"><span class="linenos">557</span></a> <span class="s2">"snomed"</span><span class="p">:</span> <span class="n">Snomed</span><span class="p">(),</span>
+</span><span id="L-558"><a href="#L-558"><span class="linenos">558</span></a> <span class="s2">"opcs4"</span><span class="p">:</span> <span class="n">Opcs4</span><span class="p">(),</span>
+</span><span id="L-559"><a href="#L-559"><span class="linenos">559</span></a> <span class="s2">"atc"</span><span class="p">:</span> <span class="n">Atc</span><span class="p">(),</span>
+</span><span id="L-560"><a href="#L-560"><span class="linenos">560</span></a> <span class="s2">"med"</span><span class="p">:</span> <span class="n">Med</span><span class="p">(),</span>
+</span><span id="L-561"><a href="#L-561"><span class="linenos">561</span></a> <span class="s2">"cprd"</span><span class="p">:</span> <span class="n">Cprd</span><span class="p">(),</span>
+</span><span id="L-562"><a href="#L-562"><span class="linenos">562</span></a> <span class="p">}</span>
+</span></pre></div>
+
+
+ </section>
+ <section id="logger">
+ <div class="attr variable">
+ <span class="name">logger</span> =
+<span class="default_value"><Logger acmc_logger (INFO)></span>
+
+
+ </div>
+ <a class="headerlink" href="#logger"></a>
+
+
+
+ </section>
+ <section id="SUPPORTED_CODE_TYPES">
+ <div class="attr variable">
+ <span class="name">SUPPORTED_CODE_TYPES</span> =
+<span class="default_value">{'opcs4', 'icd10', 'read3', 'snomed', 'read2', 'atc'}</span>
+
+
+ </div>
+ <a class="headerlink" href="#SUPPORTED_CODE_TYPES"></a>
+
+
+
+ </section>
+ <section id="CodesError">
+ <input id="CodesError-view-source" class="view-source-toggle-state" type="checkbox" aria-hidden="true" tabindex="-1">
+<div class="attr class">
+
+ <span class="def">class</span>
+ <span class="name">CodesError</span>:
+
+ <label class="view-source-button" for="CodesError-view-source"><span>View Source</span></label>
+
+ </div>
+ <a class="headerlink" href="#CodesError"></a>
+ <div class="pdoc-code codehilite"><pre><span></span><span id="CodesError-17"><a href="#CodesError-17"><span class="linenos">17</span></a><span class="k">class</span><span class="w"> </span><span class="nc">CodesError</span><span class="p">:</span>
+</span><span id="CodesError-18"><a href="#CodesError-18"><span class="linenos">18</span></a><span class="w"> </span><span class="sd">"""A class used in InvalidCodesException to report an error if a code parser check fails"""</span>
+</span><span id="CodesError-19"><a href="#CodesError-19"><span class="linenos">19</span></a>
+</span><span id="CodesError-20"><a href="#CodesError-20"><span class="linenos">20</span></a> <span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">message</span><span class="p">,</span> <span class="n">codes</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">codes_file</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">mask</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">code_type</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
+</span><span id="CodesError-21"><a href="#CodesError-21"><span class="linenos">21</span></a> <span class="c1"># initialise class variables with provided parameters</span>
+</span><span id="CodesError-22"><a href="#CodesError-22"><span class="linenos">22</span></a> <span class="k">for</span> <span class="n">key</span><span class="p">,</span> <span class="n">value</span> <span class="ow">in</span> <span class="nb">locals</span><span class="p">()</span><span class="o">.</span><span class="n">items</span><span class="p">():</span>
+</span><span id="CodesError-23"><a href="#CodesError-23"><span class="linenos">23</span></a> <span class="k">if</span> <span class="n">key</span> <span class="o">!=</span> <span class="s2">"self"</span><span class="p">:</span>
+</span><span id="CodesError-24"><a href="#CodesError-24"><span class="linenos">24</span></a> <span class="nb">setattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">key</span><span class="p">,</span> <span class="n">value</span><span class="p">)</span>
+</span></pre></div>
+
+
+ <div class="docstring"><p>A class used in InvalidCodesException to report an error if a code parser check fails</p>
+</div>
+
+
+ <div id="CodesError.__init__" class="classattr">
+ <input id="CodesError.__init__-view-source" class="view-source-toggle-state" type="checkbox" aria-hidden="true" tabindex="-1">
+<div class="attr function">
+
+ <span class="name">CodesError</span><span class="signature pdoc-code condensed">(<span class="param"><span class="n">message</span>, </span><span class="param"><span class="n">codes</span><span class="o">=</span><span class="kc">None</span>, </span><span class="param"><span class="n">codes_file</span><span class="o">=</span><span class="kc">None</span>, </span><span class="param"><span class="n">mask</span><span class="o">=</span><span class="kc">None</span>, </span><span class="param"><span class="n">code_type</span><span class="o">=</span><span class="kc">None</span></span>)</span>
+
+ <label class="view-source-button" for="CodesError.__init__-view-source"><span>View Source</span></label>
+
+ </div>
+ <a class="headerlink" href="#CodesError.__init__"></a>
+ <div class="pdoc-code codehilite"><pre><span></span><span id="CodesError.__init__-20"><a href="#CodesError.__init__-20"><span class="linenos">20</span></a> <span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">message</span><span class="p">,</span> <span class="n">codes</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">codes_file</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">mask</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">code_type</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
+</span><span id="CodesError.__init__-21"><a href="#CodesError.__init__-21"><span class="linenos">21</span></a> <span class="c1"># initialise class variables with provided parameters</span>
+</span><span id="CodesError.__init__-22"><a href="#CodesError.__init__-22"><span class="linenos">22</span></a> <span class="k">for</span> <span class="n">key</span><span class="p">,</span> <span class="n">value</span> <span class="ow">in</span> <span class="nb">locals</span><span class="p">()</span><span class="o">.</span><span class="n">items</span><span class="p">():</span>
+</span><span id="CodesError.__init__-23"><a href="#CodesError.__init__-23"><span class="linenos">23</span></a> <span class="k">if</span> <span class="n">key</span> <span class="o">!=</span> <span class="s2">"self"</span><span class="p">:</span>
+</span><span id="CodesError.__init__-24"><a href="#CodesError.__init__-24"><span class="linenos">24</span></a> <span class="nb">setattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">key</span><span class="p">,</span> <span class="n">value</span><span class="p">)</span>
+</span></pre></div>
+
+
+
+
+ </div>
+ </section>
+ <section id="InvalidCodesException">
+ <input id="InvalidCodesException-view-source" class="view-source-toggle-state" type="checkbox" aria-hidden="true" tabindex="-1">
+<div class="attr class">
+
+ <span class="def">class</span>
+ <span class="name">InvalidCodesException</span><wbr>(<span class="base">builtins.Exception</span>):
+
+ <label class="view-source-button" for="InvalidCodesException-view-source"><span>View Source</span></label>
+
+ </div>
+ <a class="headerlink" href="#InvalidCodesException"></a>
+ <div class="pdoc-code codehilite"><pre><span></span><span id="InvalidCodesException-27"><a href="#InvalidCodesException-27"><span class="linenos">27</span></a><span class="k">class</span><span class="w"> </span><span class="nc">InvalidCodesException</span><span class="p">(</span><span class="ne">Exception</span><span class="p">):</span>
+</span><span id="InvalidCodesException-28"><a href="#InvalidCodesException-28"><span class="linenos">28</span></a><span class="w"> </span><span class="sd">"""Custom exception class raised when invalid codes are found that cannot be resolved by processing"""</span>
+</span><span id="InvalidCodesException-29"><a href="#InvalidCodesException-29"><span class="linenos">29</span></a>
+</span><span id="InvalidCodesException-30"><a href="#InvalidCodesException-30"><span class="linenos">30</span></a> <span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">error</span><span class="p">):</span>
+</span><span id="InvalidCodesException-31"><a href="#InvalidCodesException-31"><span class="linenos">31</span></a> <span class="nb">super</span><span class="p">()</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="n">error</span><span class="o">.</span><span class="n">message</span><span class="p">)</span>
+</span><span id="InvalidCodesException-32"><a href="#InvalidCodesException-32"><span class="linenos">32</span></a> <span class="bp">self</span><span class="o">.</span><span class="n">error</span> <span class="o">=</span> <span class="n">error</span>
+</span></pre></div>
+
+
+ <div class="docstring"><p>Custom exception class raised when invalid codes are found that cannot be resolved by processing</p>
+</div>
+
+
+ <div id="InvalidCodesException.__init__" class="classattr">
+ <input id="InvalidCodesException.__init__-view-source" class="view-source-toggle-state" type="checkbox" aria-hidden="true" tabindex="-1">
+<div class="attr function">
+
+ <span class="name">InvalidCodesException</span><span class="signature pdoc-code condensed">(<span class="param"><span class="n">error</span></span>)</span>
+
+ <label class="view-source-button" for="InvalidCodesException.__init__-view-source"><span>View Source</span></label>
+
+ </div>
+ <a class="headerlink" href="#InvalidCodesException.__init__"></a>
+ <div class="pdoc-code codehilite"><pre><span></span><span id="InvalidCodesException.__init__-30"><a href="#InvalidCodesException.__init__-30"><span class="linenos">30</span></a> <span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">error</span><span class="p">):</span>
+</span><span id="InvalidCodesException.__init__-31"><a href="#InvalidCodesException.__init__-31"><span class="linenos">31</span></a> <span class="nb">super</span><span class="p">()</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="n">error</span><span class="o">.</span><span class="n">message</span><span class="p">)</span>
+</span><span id="InvalidCodesException.__init__-32"><a href="#InvalidCodesException.__init__-32"><span class="linenos">32</span></a> <span class="bp">self</span><span class="o">.</span><span class="n">error</span> <span class="o">=</span> <span class="n">error</span>
+</span></pre></div>
+
+
+
+
+ </div>
+ <div id="InvalidCodesException.error" class="classattr">
+ <div class="attr variable">
+ <span class="name">error</span>
+
+
+ </div>
+ <a class="headerlink" href="#InvalidCodesException.error"></a>
+
+
+
+ </div>
+ </section>
+ <section id="Proto">
+ <input id="Proto-view-source" class="view-source-toggle-state" type="checkbox" aria-hidden="true" tabindex="-1">
+<div class="attr class">
+
+ <span class="def">class</span>
+ <span class="name">Proto</span>:
+
+ <label class="view-source-button" for="Proto-view-source"><span>View Source</span></label>
+
+ </div>
+ <a class="headerlink" href="#Proto"></a>
+ <div class="pdoc-code codehilite"><pre><span></span><span id="Proto-35"><a href="#Proto-35"><span class="linenos"> 35</span></a><span class="k">class</span><span class="w"> </span><span class="nc">Proto</span><span class="p">:</span>
+</span><span id="Proto-36"><a href="#Proto-36"><span class="linenos"> 36</span></a><span class="w"> </span><span class="sd">"""</span>
+</span><span id="Proto-37"><a href="#Proto-37"><span class="linenos"> 37</span></a><span class="sd"> Define checks as list of 3 tuple: (Message, Condition, Process)</span>
+</span><span id="Proto-38"><a href="#Proto-38"><span class="linenos"> 38</span></a><span class="sd"> - Message = The name of the condition (what is printed and logged)</span>
+</span><span id="Proto-39"><a href="#Proto-39"><span class="linenos"> 39</span></a><span class="sd"> - Condition = True if Passed, and False if Failed</span>
+</span><span id="Proto-40"><a href="#Proto-40"><span class="linenos"> 40</span></a><span class="sd"> - Process = Aims to resolve all issues that stop condition from passing (Do not change index!)</span>
+</span><span id="Proto-41"><a href="#Proto-41"><span class="linenos"> 41</span></a><span class="sd"> """</span>
+</span><span id="Proto-42"><a href="#Proto-42"><span class="linenos"> 42</span></a>
+</span><span id="Proto-43"><a href="#Proto-43"><span class="linenos"> 43</span></a> <span class="n">checks</span><span class="p">:</span> <span class="nb">list</span><span class="p">[</span>
+</span><span id="Proto-44"><a href="#Proto-44"><span class="linenos"> 44</span></a> <span class="nb">tuple</span><span class="p">[</span>
+</span><span id="Proto-45"><a href="#Proto-45"><span class="linenos"> 45</span></a> <span class="nb">str</span><span class="p">,</span> <span class="c1"># The description, e.g., "Not Empty"</span>
+</span><span id="Proto-46"><a href="#Proto-46"><span class="linenos"> 46</span></a> <span class="n">Callable</span><span class="p">[</span>
+</span><span id="Proto-47"><a href="#Proto-47"><span class="linenos"> 47</span></a> <span class="p">[</span><span class="nb">list</span><span class="p">],</span>
+</span><span id="Proto-48"><a href="#Proto-48"><span class="linenos"> 48</span></a> <span class="n">pd</span><span class="o">.</span><span class="n">Series</span><span class="p">,</span>
+</span><span id="Proto-49"><a href="#Proto-49"><span class="linenos"> 49</span></a> <span class="p">],</span> <span class="c1"># The first lambda function: takes a list and returns a pd.Series of booleans</span>
+</span><span id="Proto-50"><a href="#Proto-50"><span class="linenos"> 50</span></a> <span class="n">Callable</span><span class="p">[</span>
+</span><span id="Proto-51"><a href="#Proto-51"><span class="linenos"> 51</span></a> <span class="p">[</span><span class="nb">list</span><span class="p">,</span> <span class="n">Path</span><span class="p">],</span>
+</span><span id="Proto-52"><a href="#Proto-52"><span class="linenos"> 52</span></a> <span class="kc">None</span><span class="p">,</span>
+</span><span id="Proto-53"><a href="#Proto-53"><span class="linenos"> 53</span></a> <span class="p">],</span> <span class="c1"># The second lambda function: takes a list and a string, and returns nothing</span>
+</span><span id="Proto-54"><a href="#Proto-54"><span class="linenos"> 54</span></a> <span class="p">]</span>
+</span><span id="Proto-55"><a href="#Proto-55"><span class="linenos"> 55</span></a> <span class="p">]</span>
+</span><span id="Proto-56"><a href="#Proto-56"><span class="linenos"> 56</span></a>
+</span><span id="Proto-57"><a href="#Proto-57"><span class="linenos"> 57</span></a> <span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">name</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">trud_codes_path</span><span class="p">:</span> <span class="n">Optional</span><span class="p">[</span><span class="n">Path</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
+</span><span id="Proto-58"><a href="#Proto-58"><span class="linenos"> 58</span></a> <span class="k">if</span> <span class="n">trud_codes_path</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+</span><span id="Proto-59"><a href="#Proto-59"><span class="linenos"> 59</span></a> <span class="k">if</span> <span class="n">trud_codes_path</span><span class="o">.</span><span class="n">is_file</span><span class="p">():</span>
+</span><span id="Proto-60"><a href="#Proto-60"><span class="linenos"> 60</span></a> <span class="bp">self</span><span class="o">.</span><span class="n">trud_codes_path</span><span class="p">:</span> <span class="n">Path</span> <span class="o">=</span> <span class="n">trud_codes_path</span>
+</span><span id="Proto-61"><a href="#Proto-61"><span class="linenos"> 61</span></a> <span class="bp">self</span><span class="o">.</span><span class="n">db</span><span class="p">:</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">read_parquet</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">trud_codes_path</span><span class="p">)</span>
+</span><span id="Proto-62"><a href="#Proto-62"><span class="linenos"> 62</span></a> <span class="k">else</span><span class="p">:</span>
+</span><span id="Proto-63"><a href="#Proto-63"><span class="linenos"> 63</span></a> <span class="k">raise</span> <span class="ne">FileNotFoundError</span><span class="p">(</span>
+</span><span id="Proto-64"><a href="#Proto-64"><span class="linenos"> 64</span></a> <span class="sa">f</span><span class="s2">"Error: Read2 code file '</span><span class="si">{</span><span class="n">trud_codes_path</span><span class="si">}</span><span class="s2">' does not exist. Please ensure you have installed TRUD correctly"</span>
+</span><span id="Proto-65"><a href="#Proto-65"><span class="linenos"> 65</span></a> <span class="p">)</span>
+</span><span id="Proto-66"><a href="#Proto-66"><span class="linenos"> 66</span></a>
+</span><span id="Proto-67"><a href="#Proto-67"><span class="linenos"> 67</span></a> <span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="n">name</span>
+</span><span id="Proto-68"><a href="#Proto-68"><span class="linenos"> 68</span></a>
+</span><span id="Proto-69"><a href="#Proto-69"><span class="linenos"> 69</span></a> <span class="k">def</span><span class="w"> </span><span class="nf">raise_exception</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">ex</span><span class="p">:</span> <span class="ne">Exception</span><span class="p">):</span>
+</span><span id="Proto-70"><a href="#Proto-70"><span class="linenos"> 70</span></a><span class="w"> </span><span class="sd">"""Raises an exception inside a lambda function. Python does not allow using raise statement inside lambda because lambda can only contain expressions, not statements. Using raise_exception not raise_ as it's more explict"""</span>
+</span><span id="Proto-71"><a href="#Proto-71"><span class="linenos"> 71</span></a> <span class="k">raise</span> <span class="n">ex</span>
+</span><span id="Proto-72"><a href="#Proto-72"><span class="linenos"> 72</span></a>
+</span><span id="Proto-73"><a href="#Proto-73"><span class="linenos"> 73</span></a> <span class="k">def</span><span class="w"> </span><span class="nf">in_database</span><span class="p">(</span>
+</span><span id="Proto-74"><a href="#Proto-74"><span class="linenos"> 74</span></a> <span class="bp">self</span><span class="p">,</span> <span class="n">codes</span><span class="p">:</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">,</span> <span class="n">db</span><span class="p">:</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">,</span> <span class="n">col</span><span class="p">:</span> <span class="nb">str</span>
+</span><span id="Proto-75"><a href="#Proto-75"><span class="linenos"> 75</span></a> <span class="p">)</span> <span class="o">-></span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">:</span>
+</span><span id="Proto-76"><a href="#Proto-76"><span class="linenos"> 76</span></a> <span class="k">return</span> <span class="n">codes</span><span class="o">.</span><span class="n">isin</span><span class="p">(</span><span class="n">db</span><span class="p">[</span><span class="n">col</span><span class="p">])</span>
+</span><span id="Proto-77"><a href="#Proto-77"><span class="linenos"> 77</span></a>
+</span><span id="Proto-78"><a href="#Proto-78"><span class="linenos"> 78</span></a> <span class="k">def</span><span class="w"> </span><span class="nf">process</span><span class="p">(</span>
+</span><span id="Proto-79"><a href="#Proto-79"><span class="linenos"> 79</span></a> <span class="bp">self</span><span class="p">,</span> <span class="n">codes</span><span class="p">:</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">,</span> <span class="n">codes_file</span><span class="p">:</span> <span class="n">Path</span>
+</span><span id="Proto-80"><a href="#Proto-80"><span class="linenos"> 80</span></a> <span class="p">)</span> <span class="o">-></span> <span class="n">Tuple</span><span class="p">[</span><span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">,</span> <span class="nb">list</span><span class="p">]:</span>
+</span><span id="Proto-81"><a href="#Proto-81"><span class="linenos"> 81</span></a><span class="w"> </span><span class="sd">"""identify issues that do not pass and fix them with define/d process"""</span>
+</span><span id="Proto-82"><a href="#Proto-82"><span class="linenos"> 82</span></a> <span class="n">errors</span> <span class="o">=</span> <span class="p">[]</span>
+</span><span id="Proto-83"><a href="#Proto-83"><span class="linenos"> 83</span></a> <span class="c1"># Iter through each item in check.</span>
+</span><span id="Proto-84"><a href="#Proto-84"><span class="linenos"> 84</span></a> <span class="k">for</span> <span class="n">msg</span><span class="p">,</span> <span class="n">cond</span><span class="p">,</span> <span class="n">fix</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">checks</span><span class="p">:</span>
+</span><span id="Proto-85"><a href="#Proto-85"><span class="linenos"> 85</span></a> <span class="c1"># Check if any codes fail the check to False</span>
+</span><span id="Proto-86"><a href="#Proto-86"><span class="linenos"> 86</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="n">cond</span><span class="p">(</span><span class="n">codes</span><span class="p">)</span><span class="o">.</span><span class="n">all</span><span class="p">():</span>
+</span><span id="Proto-87"><a href="#Proto-87"><span class="linenos"> 87</span></a> <span class="c1"># Log the number of codes that failed</span>
+</span><span id="Proto-88"><a href="#Proto-88"><span class="linenos"> 88</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span>
+</span><span id="Proto-89"><a href="#Proto-89"><span class="linenos"> 89</span></a> <span class="sa">f</span><span class="s2">"Check: </span><span class="si">{</span><span class="n">msg</span><span class="si">}</span><span class="s2"> </span><span class="si">{</span><span class="p">(</span><span class="o">~</span><span class="n">cond</span><span class="p">(</span><span class="n">codes</span><span class="p">))</span><span class="o">.</span><span class="n">sum</span><span class="p">()</span><span class="si">}</span><span class="s2"> failed, trying to fix"</span>
+</span><span id="Proto-90"><a href="#Proto-90"><span class="linenos"> 90</span></a> <span class="p">)</span>
+</span><span id="Proto-91"><a href="#Proto-91"><span class="linenos"> 91</span></a> <span class="c1"># try fix errors by running lamba "process" function</span>
+</span><span id="Proto-92"><a href="#Proto-92"><span class="linenos"> 92</span></a> <span class="k">try</span><span class="p">:</span>
+</span><span id="Proto-93"><a href="#Proto-93"><span class="linenos"> 93</span></a> <span class="n">codes</span> <span class="o">=</span> <span class="n">fix</span><span class="p">(</span><span class="n">codes</span><span class="p">,</span> <span class="n">codes_file</span><span class="p">)</span>
+</span><span id="Proto-94"><a href="#Proto-94"><span class="linenos"> 94</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Check: Fixed"</span><span class="p">)</span>
+</span><span id="Proto-95"><a href="#Proto-95"><span class="linenos"> 95</span></a> <span class="k">except</span> <span class="n">InvalidCodesException</span> <span class="k">as</span> <span class="n">ex</span><span class="p">:</span>
+</span><span id="Proto-96"><a href="#Proto-96"><span class="linenos"> 96</span></a> <span class="n">errors</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">ex</span><span class="o">.</span><span class="n">error</span><span class="p">)</span>
+</span><span id="Proto-97"><a href="#Proto-97"><span class="linenos"> 97</span></a> <span class="k">else</span><span class="p">:</span>
+</span><span id="Proto-98"><a href="#Proto-98"><span class="linenos"> 98</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Check: passed"</span><span class="p">)</span>
+</span><span id="Proto-99"><a href="#Proto-99"><span class="linenos"> 99</span></a>
+</span><span id="Proto-100"><a href="#Proto-100"><span class="linenos">100</span></a> <span class="k">return</span> <span class="n">codes</span><span class="p">,</span> <span class="n">errors</span>
+</span><span id="Proto-101"><a href="#Proto-101"><span class="linenos">101</span></a>
+</span><span id="Proto-102"><a href="#Proto-102"><span class="linenos">102</span></a> <span class="k">def</span><span class="w"> </span><span class="nf">verify</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">codes</span><span class="p">:</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">,</span> <span class="n">codes_file</span><span class="p">:</span> <span class="n">Path</span><span class="p">):</span>
+</span><span id="Proto-103"><a href="#Proto-103"><span class="linenos">103</span></a><span class="w"> </span><span class="sd">"""verify codes in codes file"""</span>
+</span><span id="Proto-104"><a href="#Proto-104"><span class="linenos">104</span></a> <span class="n">conds</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([])</span>
+</span><span id="Proto-105"><a href="#Proto-105"><span class="linenos">105</span></a>
+</span><span id="Proto-106"><a href="#Proto-106"><span class="linenos">106</span></a> <span class="c1"># Iter through each item in check.</span>
+</span><span id="Proto-107"><a href="#Proto-107"><span class="linenos">107</span></a> <span class="k">for</span> <span class="n">msg</span><span class="p">,</span> <span class="n">cond</span><span class="p">,</span> <span class="n">process</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">checks</span><span class="p">:</span>
+</span><span id="Proto-108"><a href="#Proto-108"><span class="linenos">108</span></a> <span class="c1"># run conditional check</span>
+</span><span id="Proto-109"><a href="#Proto-109"><span class="linenos">109</span></a> <span class="n">out</span> <span class="o">=</span> <span class="n">cond</span><span class="p">(</span><span class="n">codes</span><span class="p">)</span>
+</span><span id="Proto-110"><a href="#Proto-110"><span class="linenos">110</span></a> <span class="n">conds</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">conds</span><span class="p">,</span> <span class="n">out</span><span class="o">.</span><span class="n">all</span><span class="p">())</span>
+</span><span id="Proto-111"><a href="#Proto-111"><span class="linenos">111</span></a>
+</span><span id="Proto-112"><a href="#Proto-112"><span class="linenos">112</span></a> <span class="k">return</span> <span class="n">conds</span>
+</span></pre></div>
+
+
+ <div class="docstring"><p>Define checks as list of 3 tuple: (Message, Condition, Process)</p>
+
+<ul>
+<li>Message = The name of the condition (what is printed and logged)</li>
+<li>Condition = True if Passed, and False if Failed</li>
+<li>Process = Aims to resolve all issues that stop condition from passing (Do not change index!)</li>
+</ul>
+</div>
+
+
+ <div id="Proto.__init__" class="classattr">
+ <input id="Proto.__init__-view-source" class="view-source-toggle-state" type="checkbox" aria-hidden="true" tabindex="-1">
+<div class="attr function">
+
+ <span class="name">Proto</span><span class="signature pdoc-code condensed">(<span class="param"><span class="n">name</span><span class="p">:</span> <span class="nb">str</span>, </span><span class="param"><span class="n">trud_codes_path</span><span class="p">:</span> <span class="n">Optional</span><span class="p">[</span><span class="n">pathlib</span><span class="o">.</span><span class="n">Path</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span></span>)</span>
+
+ <label class="view-source-button" for="Proto.__init__-view-source"><span>View Source</span></label>
+
+ </div>
+ <a class="headerlink" href="#Proto.__init__"></a>
+ <div class="pdoc-code codehilite"><pre><span></span><span id="Proto.__init__-57"><a href="#Proto.__init__-57"><span class="linenos">57</span></a> <span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">name</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">trud_codes_path</span><span class="p">:</span> <span class="n">Optional</span><span class="p">[</span><span class="n">Path</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
+</span><span id="Proto.__init__-58"><a href="#Proto.__init__-58"><span class="linenos">58</span></a> <span class="k">if</span> <span class="n">trud_codes_path</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+</span><span id="Proto.__init__-59"><a href="#Proto.__init__-59"><span class="linenos">59</span></a> <span class="k">if</span> <span class="n">trud_codes_path</span><span class="o">.</span><span class="n">is_file</span><span class="p">():</span>
+</span><span id="Proto.__init__-60"><a href="#Proto.__init__-60"><span class="linenos">60</span></a> <span class="bp">self</span><span class="o">.</span><span class="n">trud_codes_path</span><span class="p">:</span> <span class="n">Path</span> <span class="o">=</span> <span class="n">trud_codes_path</span>
+</span><span id="Proto.__init__-61"><a href="#Proto.__init__-61"><span class="linenos">61</span></a> <span class="bp">self</span><span class="o">.</span><span class="n">db</span><span class="p">:</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">read_parquet</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">trud_codes_path</span><span class="p">)</span>
+</span><span id="Proto.__init__-62"><a href="#Proto.__init__-62"><span class="linenos">62</span></a> <span class="k">else</span><span class="p">:</span>
+</span><span id="Proto.__init__-63"><a href="#Proto.__init__-63"><span class="linenos">63</span></a> <span class="k">raise</span> <span class="ne">FileNotFoundError</span><span class="p">(</span>
+</span><span id="Proto.__init__-64"><a href="#Proto.__init__-64"><span class="linenos">64</span></a> <span class="sa">f</span><span class="s2">"Error: Read2 code file '</span><span class="si">{</span><span class="n">trud_codes_path</span><span class="si">}</span><span class="s2">' does not exist. Please ensure you have installed TRUD correctly"</span>
+</span><span id="Proto.__init__-65"><a href="#Proto.__init__-65"><span class="linenos">65</span></a> <span class="p">)</span>
+</span><span id="Proto.__init__-66"><a href="#Proto.__init__-66"><span class="linenos">66</span></a>
+</span><span id="Proto.__init__-67"><a href="#Proto.__init__-67"><span class="linenos">67</span></a> <span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="n">name</span>
+</span></pre></div>
+
+
+
+
+ </div>
+ <div id="Proto.checks" class="classattr">
+ <div class="attr variable">
+ <span class="name">checks</span><span class="annotation">: list[tuple[str, typing.Callable[[list], pandas.core.series.Series], typing.Callable[[list, pathlib.Path], NoneType]]]</span>
+
+
+ </div>
+ <a class="headerlink" href="#Proto.checks"></a>
+
+
+
+ </div>
+ <div id="Proto.name" class="classattr">
+ <div class="attr variable">
+ <span class="name">name</span><span class="annotation">: str</span>
+
+
+ </div>
+ <a class="headerlink" href="#Proto.name"></a>
+
+
+
+ </div>
+ <div id="Proto.raise_exception" class="classattr">
+ <input id="Proto.raise_exception-view-source" class="view-source-toggle-state" type="checkbox" aria-hidden="true" tabindex="-1">
+<div class="attr function">
+
+ <span class="def">def</span>
+ <span class="name">raise_exception</span><span class="signature pdoc-code condensed">(<span class="param"><span class="bp">self</span>, </span><span class="param"><span class="n">ex</span><span class="p">:</span> <span class="ne">Exception</span></span><span class="return-annotation">):</span></span>
+
+ <label class="view-source-button" for="Proto.raise_exception-view-source"><span>View Source</span></label>
+
+ </div>
+ <a class="headerlink" href="#Proto.raise_exception"></a>
+ <div class="pdoc-code codehilite"><pre><span></span><span id="Proto.raise_exception-69"><a href="#Proto.raise_exception-69"><span class="linenos">69</span></a> <span class="k">def</span><span class="w"> </span><span class="nf">raise_exception</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">ex</span><span class="p">:</span> <span class="ne">Exception</span><span class="p">):</span>
+</span><span id="Proto.raise_exception-70"><a href="#Proto.raise_exception-70"><span class="linenos">70</span></a><span class="w"> </span><span class="sd">"""Raises an exception inside a lambda function. Python does not allow using raise statement inside lambda because lambda can only contain expressions, not statements. Using raise_exception not raise_ as it's more explict"""</span>
+</span><span id="Proto.raise_exception-71"><a href="#Proto.raise_exception-71"><span class="linenos">71</span></a> <span class="k">raise</span> <span class="n">ex</span>
+</span></pre></div>
+
+
+ <div class="docstring"><p>Raises an exception inside a lambda function. Python does not allow using raise statement inside lambda because lambda can only contain expressions, not statements. Using raise_exception not raise_ as it's more explict</p>
+</div>
+
+
+ </div>
+ <div id="Proto.in_database" class="classattr">
+ <input id="Proto.in_database-view-source" class="view-source-toggle-state" type="checkbox" aria-hidden="true" tabindex="-1">
+<div class="attr function">
+
+ <span class="def">def</span>
+ <span class="name">in_database</span><span class="signature pdoc-code multiline">(<span class="param"> <span class="bp">self</span>,</span><span class="param"> <span class="n">codes</span><span class="p">:</span> <span class="n">pandas</span><span class="o">.</span><span class="n">core</span><span class="o">.</span><span class="n">frame</span><span class="o">.</span><span class="n">DataFrame</span>,</span><span class="param"> <span class="n">db</span><span class="p">:</span> <span class="n">pandas</span><span class="o">.</span><span class="n">core</span><span class="o">.</span><span class="n">frame</span><span class="o">.</span><span class="n">DataFrame</span>,</span><span class="param"> <span class="n">col</span><span class="p">:</span> <span class="nb">str</span></span><span class="return-annotation">) -> <span class="n">pandas</span><span class="o">.</span><span class="n">core</span><span class="o">.</span><span class="n">frame</span><span class="o">.</span><span class="n">DataFrame</span>:</span></span>
+
+ <label class="view-source-button" for="Proto.in_database-view-source"><span>View Source</span></label>
+
+ </div>
+ <a class="headerlink" href="#Proto.in_database"></a>
+ <div class="pdoc-code codehilite"><pre><span></span><span id="Proto.in_database-73"><a href="#Proto.in_database-73"><span class="linenos">73</span></a> <span class="k">def</span><span class="w"> </span><span class="nf">in_database</span><span class="p">(</span>
+</span><span id="Proto.in_database-74"><a href="#Proto.in_database-74"><span class="linenos">74</span></a> <span class="bp">self</span><span class="p">,</span> <span class="n">codes</span><span class="p">:</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">,</span> <span class="n">db</span><span class="p">:</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">,</span> <span class="n">col</span><span class="p">:</span> <span class="nb">str</span>
+</span><span id="Proto.in_database-75"><a href="#Proto.in_database-75"><span class="linenos">75</span></a> <span class="p">)</span> <span class="o">-></span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">:</span>
+</span><span id="Proto.in_database-76"><a href="#Proto.in_database-76"><span class="linenos">76</span></a> <span class="k">return</span> <span class="n">codes</span><span class="o">.</span><span class="n">isin</span><span class="p">(</span><span class="n">db</span><span class="p">[</span><span class="n">col</span><span class="p">])</span>
+</span></pre></div>
+
+
+
+
+ </div>
+ <div id="Proto.process" class="classattr">
+ <input id="Proto.process-view-source" class="view-source-toggle-state" type="checkbox" aria-hidden="true" tabindex="-1">
+<div class="attr function">
+
+ <span class="def">def</span>
+ <span class="name">process</span><span class="signature pdoc-code multiline">(<span class="param"> <span class="bp">self</span>,</span><span class="param"> <span class="n">codes</span><span class="p">:</span> <span class="n">pandas</span><span class="o">.</span><span class="n">core</span><span class="o">.</span><span class="n">frame</span><span class="o">.</span><span class="n">DataFrame</span>,</span><span class="param"> <span class="n">codes_file</span><span class="p">:</span> <span class="n">pathlib</span><span class="o">.</span><span class="n">Path</span></span><span class="return-annotation">) -> <span class="n">Tuple</span><span class="p">[</span><span class="n">pandas</span><span class="o">.</span><span class="n">core</span><span class="o">.</span><span class="n">frame</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">,</span> <span class="nb">list</span><span class="p">]</span>:</span></span>
+
+ <label class="view-source-button" for="Proto.process-view-source"><span>View Source</span></label>
+
+ </div>
+ <a class="headerlink" href="#Proto.process"></a>
+ <div class="pdoc-code codehilite"><pre><span></span><span id="Proto.process-78"><a href="#Proto.process-78"><span class="linenos"> 78</span></a> <span class="k">def</span><span class="w"> </span><span class="nf">process</span><span class="p">(</span>
+</span><span id="Proto.process-79"><a href="#Proto.process-79"><span class="linenos"> 79</span></a> <span class="bp">self</span><span class="p">,</span> <span class="n">codes</span><span class="p">:</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">,</span> <span class="n">codes_file</span><span class="p">:</span> <span class="n">Path</span>
+</span><span id="Proto.process-80"><a href="#Proto.process-80"><span class="linenos"> 80</span></a> <span class="p">)</span> <span class="o">-></span> <span class="n">Tuple</span><span class="p">[</span><span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">,</span> <span class="nb">list</span><span class="p">]:</span>
+</span><span id="Proto.process-81"><a href="#Proto.process-81"><span class="linenos"> 81</span></a><span class="w"> </span><span class="sd">"""identify issues that do not pass and fix them with define/d process"""</span>
+</span><span id="Proto.process-82"><a href="#Proto.process-82"><span class="linenos"> 82</span></a> <span class="n">errors</span> <span class="o">=</span> <span class="p">[]</span>
+</span><span id="Proto.process-83"><a href="#Proto.process-83"><span class="linenos"> 83</span></a> <span class="c1"># Iter through each item in check.</span>
+</span><span id="Proto.process-84"><a href="#Proto.process-84"><span class="linenos"> 84</span></a> <span class="k">for</span> <span class="n">msg</span><span class="p">,</span> <span class="n">cond</span><span class="p">,</span> <span class="n">fix</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">checks</span><span class="p">:</span>
+</span><span id="Proto.process-85"><a href="#Proto.process-85"><span class="linenos"> 85</span></a> <span class="c1"># Check if any codes fail the check to False</span>
+</span><span id="Proto.process-86"><a href="#Proto.process-86"><span class="linenos"> 86</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="n">cond</span><span class="p">(</span><span class="n">codes</span><span class="p">)</span><span class="o">.</span><span class="n">all</span><span class="p">():</span>
+</span><span id="Proto.process-87"><a href="#Proto.process-87"><span class="linenos"> 87</span></a> <span class="c1"># Log the number of codes that failed</span>
+</span><span id="Proto.process-88"><a href="#Proto.process-88"><span class="linenos"> 88</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span>
+</span><span id="Proto.process-89"><a href="#Proto.process-89"><span class="linenos"> 89</span></a> <span class="sa">f</span><span class="s2">"Check: </span><span class="si">{</span><span class="n">msg</span><span class="si">}</span><span class="s2"> </span><span class="si">{</span><span class="p">(</span><span class="o">~</span><span class="n">cond</span><span class="p">(</span><span class="n">codes</span><span class="p">))</span><span class="o">.</span><span class="n">sum</span><span class="p">()</span><span class="si">}</span><span class="s2"> failed, trying to fix"</span>
+</span><span id="Proto.process-90"><a href="#Proto.process-90"><span class="linenos"> 90</span></a> <span class="p">)</span>
+</span><span id="Proto.process-91"><a href="#Proto.process-91"><span class="linenos"> 91</span></a> <span class="c1"># try fix errors by running lamba "process" function</span>
+</span><span id="Proto.process-92"><a href="#Proto.process-92"><span class="linenos"> 92</span></a> <span class="k">try</span><span class="p">:</span>
+</span><span id="Proto.process-93"><a href="#Proto.process-93"><span class="linenos"> 93</span></a> <span class="n">codes</span> <span class="o">=</span> <span class="n">fix</span><span class="p">(</span><span class="n">codes</span><span class="p">,</span> <span class="n">codes_file</span><span class="p">)</span>
+</span><span id="Proto.process-94"><a href="#Proto.process-94"><span class="linenos"> 94</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Check: Fixed"</span><span class="p">)</span>
+</span><span id="Proto.process-95"><a href="#Proto.process-95"><span class="linenos"> 95</span></a> <span class="k">except</span> <span class="n">InvalidCodesException</span> <span class="k">as</span> <span class="n">ex</span><span class="p">:</span>
+</span><span id="Proto.process-96"><a href="#Proto.process-96"><span class="linenos"> 96</span></a> <span class="n">errors</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">ex</span><span class="o">.</span><span class="n">error</span><span class="p">)</span>
+</span><span id="Proto.process-97"><a href="#Proto.process-97"><span class="linenos"> 97</span></a> <span class="k">else</span><span class="p">:</span>
+</span><span id="Proto.process-98"><a href="#Proto.process-98"><span class="linenos"> 98</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Check: passed"</span><span class="p">)</span>
+</span><span id="Proto.process-99"><a href="#Proto.process-99"><span class="linenos"> 99</span></a>
+</span><span id="Proto.process-100"><a href="#Proto.process-100"><span class="linenos">100</span></a> <span class="k">return</span> <span class="n">codes</span><span class="p">,</span> <span class="n">errors</span>
+</span></pre></div>
+
+
+ <div class="docstring"><p>identify issues that do not pass and fix them with define/d process</p>
+</div>
+
+
+ </div>
+ <div id="Proto.verify" class="classattr">
+ <input id="Proto.verify-view-source" class="view-source-toggle-state" type="checkbox" aria-hidden="true" tabindex="-1">
+<div class="attr function">
+
+ <span class="def">def</span>
+ <span class="name">verify</span><span class="signature pdoc-code condensed">(<span class="param"><span class="bp">self</span>, </span><span class="param"><span class="n">codes</span><span class="p">:</span> <span class="n">pandas</span><span class="o">.</span><span class="n">core</span><span class="o">.</span><span class="n">frame</span><span class="o">.</span><span class="n">DataFrame</span>, </span><span class="param"><span class="n">codes_file</span><span class="p">:</span> <span class="n">pathlib</span><span class="o">.</span><span class="n">Path</span></span><span class="return-annotation">):</span></span>
+
+ <label class="view-source-button" for="Proto.verify-view-source"><span>View Source</span></label>
+
+ </div>
+ <a class="headerlink" href="#Proto.verify"></a>
+ <div class="pdoc-code codehilite"><pre><span></span><span id="Proto.verify-102"><a href="#Proto.verify-102"><span class="linenos">102</span></a> <span class="k">def</span><span class="w"> </span><span class="nf">verify</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">codes</span><span class="p">:</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">,</span> <span class="n">codes_file</span><span class="p">:</span> <span class="n">Path</span><span class="p">):</span>
+</span><span id="Proto.verify-103"><a href="#Proto.verify-103"><span class="linenos">103</span></a><span class="w"> </span><span class="sd">"""verify codes in codes file"""</span>
+</span><span id="Proto.verify-104"><a href="#Proto.verify-104"><span class="linenos">104</span></a> <span class="n">conds</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([])</span>
+</span><span id="Proto.verify-105"><a href="#Proto.verify-105"><span class="linenos">105</span></a>
+</span><span id="Proto.verify-106"><a href="#Proto.verify-106"><span class="linenos">106</span></a> <span class="c1"># Iter through each item in check.</span>
+</span><span id="Proto.verify-107"><a href="#Proto.verify-107"><span class="linenos">107</span></a> <span class="k">for</span> <span class="n">msg</span><span class="p">,</span> <span class="n">cond</span><span class="p">,</span> <span class="n">process</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">checks</span><span class="p">:</span>
+</span><span id="Proto.verify-108"><a href="#Proto.verify-108"><span class="linenos">108</span></a> <span class="c1"># run conditional check</span>
+</span><span id="Proto.verify-109"><a href="#Proto.verify-109"><span class="linenos">109</span></a> <span class="n">out</span> <span class="o">=</span> <span class="n">cond</span><span class="p">(</span><span class="n">codes</span><span class="p">)</span>
+</span><span id="Proto.verify-110"><a href="#Proto.verify-110"><span class="linenos">110</span></a> <span class="n">conds</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">conds</span><span class="p">,</span> <span class="n">out</span><span class="o">.</span><span class="n">all</span><span class="p">())</span>
+</span><span id="Proto.verify-111"><a href="#Proto.verify-111"><span class="linenos">111</span></a>
+</span><span id="Proto.verify-112"><a href="#Proto.verify-112"><span class="linenos">112</span></a> <span class="k">return</span> <span class="n">conds</span>
+</span></pre></div>
+
+
+ <div class="docstring"><p>verify codes in codes file</p>
+</div>
+
+
+ </div>
+ </section>
+ <section id="Read2">
+ <input id="Read2-view-source" class="view-source-toggle-state" type="checkbox" aria-hidden="true" tabindex="-1">
+<div class="attr class">
+
+ <span class="def">class</span>
+ <span class="name">Read2</span><wbr>(<span class="base"><a href="#Proto">Proto</a></span>):
+
+ <label class="view-source-button" for="Read2-view-source"><span>View Source</span></label>
+
+ </div>
+ <a class="headerlink" href="#Read2"></a>
+ <div class="pdoc-code codehilite"><pre><span></span><span id="Read2-115"><a href="#Read2-115"><span class="linenos">115</span></a><span class="k">class</span><span class="w"> </span><span class="nc">Read2</span><span class="p">(</span><span class="n">Proto</span><span class="p">):</span>
+</span><span id="Read2-116"><a href="#Read2-116"><span class="linenos">116</span></a><span class="w"> </span><span class="sd">"""This Read2 class extends Proto, adding custom validation checks for a dataset of "Read2" codes. It ensures that the dataset is loaded, validates the codes based on several rules, and applies corrections or logs errors when necessary."""</span>
+</span><span id="Read2-117"><a href="#Read2-117"><span class="linenos">117</span></a>
+</span><span id="Read2-118"><a href="#Read2-118"><span class="linenos">118</span></a> <span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+</span><span id="Read2-119"><a href="#Read2-119"><span class="linenos">119</span></a> <span class="nb">super</span><span class="p">()</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="s2">"read2"</span><span class="p">,</span> <span class="n">trud</span><span class="o">.</span><span class="n">PROCESSED_PATH</span> <span class="o">/</span> <span class="s2">"read2.parquet"</span><span class="p">)</span>
+</span><span id="Read2-120"><a href="#Read2-120"><span class="linenos">120</span></a>
+</span><span id="Read2-121"><a href="#Read2-121"><span class="linenos">121</span></a> <span class="c1"># validate checks</span>
+</span><span id="Read2-122"><a href="#Read2-122"><span class="linenos">122</span></a> <span class="bp">self</span><span class="o">.</span><span class="n">checks</span> <span class="o">=</span> <span class="p">[</span>
+</span><span id="Read2-123"><a href="#Read2-123"><span class="linenos">123</span></a> <span class="p">(</span>
+</span><span id="Read2-124"><a href="#Read2-124"><span class="linenos">124</span></a> <span class="c1"># check codes are not empty, if empty throw an exception</span>
+</span><span id="Read2-125"><a href="#Read2-125"><span class="linenos">125</span></a> <span class="s2">"Not Empty"</span><span class="p">,</span>
+</span><span id="Read2-126"><a href="#Read2-126"><span class="linenos">126</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">:</span> <span class="n">pd</span><span class="o">.</span><span class="n">Series</span><span class="p">([</span><span class="nb">len</span><span class="p">(</span><span class="n">codes</span><span class="p">)</span> <span class="o">></span> <span class="mi">0</span><span class="p">]),</span>
+</span><span id="Read2-127"><a href="#Read2-127"><span class="linenos">127</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">,</span> <span class="n">codes_file</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">raise_exception</span><span class="p">(</span>
+</span><span id="Read2-128"><a href="#Read2-128"><span class="linenos">128</span></a> <span class="n">InvalidCodesException</span><span class="p">(</span>
+</span><span id="Read2-129"><a href="#Read2-129"><span class="linenos">129</span></a> <span class="n">CodesError</span><span class="p">(</span>
+</span><span id="Read2-130"><a href="#Read2-130"><span class="linenos">130</span></a> <span class="sa">f</span><span class="s2">"Code list is empty"</span><span class="p">,</span>
+</span><span id="Read2-131"><a href="#Read2-131"><span class="linenos">131</span></a> <span class="n">codes</span><span class="o">=</span><span class="n">codes</span><span class="p">,</span>
+</span><span id="Read2-132"><a href="#Read2-132"><span class="linenos">132</span></a> <span class="n">codes_file</span><span class="o">=</span><span class="n">codes_file</span><span class="p">,</span>
+</span><span id="Read2-133"><a href="#Read2-133"><span class="linenos">133</span></a> <span class="n">mask</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
+</span><span id="Read2-134"><a href="#Read2-134"><span class="linenos">134</span></a> <span class="n">code_type</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">,</span>
+</span><span id="Read2-135"><a href="#Read2-135"><span class="linenos">135</span></a> <span class="p">)</span>
+</span><span id="Read2-136"><a href="#Read2-136"><span class="linenos">136</span></a> <span class="p">)</span>
+</span><span id="Read2-137"><a href="#Read2-137"><span class="linenos">137</span></a> <span class="p">),</span>
+</span><span id="Read2-138"><a href="#Read2-138"><span class="linenos">138</span></a> <span class="p">),</span>
+</span><span id="Read2-139"><a href="#Read2-139"><span class="linenos">139</span></a> <span class="p">(</span>
+</span><span id="Read2-140"><a href="#Read2-140"><span class="linenos">140</span></a> <span class="c1"># check codes <5 characters, if too short pads it with . (dots) to reach 5 characters</span>
+</span><span id="Read2-141"><a href="#Read2-141"><span class="linenos">141</span></a> <span class="s2">"Too Short"</span><span class="p">,</span>
+</span><span id="Read2-142"><a href="#Read2-142"><span class="linenos">142</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">:</span> <span class="o">~</span><span class="p">(</span><span class="n">codes</span><span class="o">.</span><span class="n">str</span><span class="o">.</span><span class="n">len</span><span class="p">()</span> <span class="o"><</span> <span class="mi">5</span><span class="p">),</span>
+</span><span id="Read2-143"><a href="#Read2-143"><span class="linenos">143</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">,</span> <span class="n">codes_file</span><span class="p">:</span> <span class="n">codes</span><span class="o">.</span><span class="n">str</span><span class="o">.</span><span class="n">pad</span><span class="p">(</span>
+</span><span id="Read2-144"><a href="#Read2-144"><span class="linenos">144</span></a> <span class="n">width</span><span class="o">=</span><span class="mi">5</span><span class="p">,</span> <span class="n">side</span><span class="o">=</span><span class="s2">"right"</span><span class="p">,</span> <span class="n">fillchar</span><span class="o">=</span><span class="s2">"."</span>
+</span><span id="Read2-145"><a href="#Read2-145"><span class="linenos">145</span></a> <span class="p">),</span>
+</span><span id="Read2-146"><a href="#Read2-146"><span class="linenos">146</span></a> <span class="p">),</span>
+</span><span id="Read2-147"><a href="#Read2-147"><span class="linenos">147</span></a> <span class="p">(</span>
+</span><span id="Read2-148"><a href="#Read2-148"><span class="linenos">148</span></a> <span class="c1"># check codes > 5 characters, If too long, truncates them to 5 characters</span>
+</span><span id="Read2-149"><a href="#Read2-149"><span class="linenos">149</span></a> <span class="s2">"Too Long"</span><span class="p">,</span>
+</span><span id="Read2-150"><a href="#Read2-150"><span class="linenos">150</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">:</span> <span class="o">~</span><span class="p">(</span><span class="n">codes</span><span class="o">.</span><span class="n">str</span><span class="o">.</span><span class="n">len</span><span class="p">()</span> <span class="o">></span> <span class="mi">5</span><span class="p">),</span>
+</span><span id="Read2-151"><a href="#Read2-151"><span class="linenos">151</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">,</span> <span class="n">codes_file</span><span class="p">:</span> <span class="n">codes</span><span class="o">.</span><span class="n">str</span><span class="p">[:</span><span class="mi">5</span><span class="p">],</span>
+</span><span id="Read2-152"><a href="#Read2-152"><span class="linenos">152</span></a> <span class="p">),</span>
+</span><span id="Read2-153"><a href="#Read2-153"><span class="linenos">153</span></a> <span class="p">(</span>
+</span><span id="Read2-154"><a href="#Read2-154"><span class="linenos">154</span></a> <span class="c1"># checks codes contain numbers, or dots (.), if not logs invalid code error</span>
+</span><span id="Read2-155"><a href="#Read2-155"><span class="linenos">155</span></a> <span class="s2">"Alphanumeric Dot"</span><span class="p">,</span>
+</span><span id="Read2-156"><a href="#Read2-156"><span class="linenos">156</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">:</span> <span class="n">codes</span><span class="o">.</span><span class="n">str</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="sa">r</span><span class="s2">"^[a-zA-Z0-9.]+$"</span><span class="p">),</span>
+</span><span id="Read2-157"><a href="#Read2-157"><span class="linenos">157</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">,</span> <span class="n">codes_file</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">raise_exception</span><span class="p">(</span>
+</span><span id="Read2-158"><a href="#Read2-158"><span class="linenos">158</span></a> <span class="n">InvalidCodesException</span><span class="p">(</span>
+</span><span id="Read2-159"><a href="#Read2-159"><span class="linenos">159</span></a> <span class="n">CodesError</span><span class="p">(</span>
+</span><span id="Read2-160"><a href="#Read2-160"><span class="linenos">160</span></a> <span class="sa">f</span><span class="s2">"Illegal code format, not alphanumeric dot"</span><span class="p">,</span>
+</span><span id="Read2-161"><a href="#Read2-161"><span class="linenos">161</span></a> <span class="n">codes</span><span class="o">=</span><span class="n">codes</span><span class="p">,</span>
+</span><span id="Read2-162"><a href="#Read2-162"><span class="linenos">162</span></a> <span class="n">codes_file</span><span class="o">=</span><span class="n">codes_file</span><span class="p">,</span>
+</span><span id="Read2-163"><a href="#Read2-163"><span class="linenos">163</span></a> <span class="n">mask</span><span class="o">=</span><span class="n">codes</span><span class="o">.</span><span class="n">str</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="sa">r</span><span class="s2">"^[a-zA-Z0-9.]+$"</span><span class="p">),</span>
+</span><span id="Read2-164"><a href="#Read2-164"><span class="linenos">164</span></a> <span class="n">code_type</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">,</span>
+</span><span id="Read2-165"><a href="#Read2-165"><span class="linenos">165</span></a> <span class="p">)</span>
+</span><span id="Read2-166"><a href="#Read2-166"><span class="linenos">166</span></a> <span class="p">)</span>
+</span><span id="Read2-167"><a href="#Read2-167"><span class="linenos">167</span></a> <span class="p">),</span>
+</span><span id="Read2-168"><a href="#Read2-168"><span class="linenos">168</span></a> <span class="p">),</span>
+</span><span id="Read2-169"><a href="#Read2-169"><span class="linenos">169</span></a> <span class="p">(</span>
+</span><span id="Read2-170"><a href="#Read2-170"><span class="linenos">170</span></a> <span class="c1"># checks code exists in self.db (the Read2 dataset). If missing log invalid codes.</span>
+</span><span id="Read2-171"><a href="#Read2-171"><span class="linenos">171</span></a> <span class="s2">"In Database"</span><span class="p">,</span>
+</span><span id="Read2-172"><a href="#Read2-172"><span class="linenos">172</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">in_database</span><span class="p">(</span><span class="n">codes</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">db</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">),</span>
+</span><span id="Read2-173"><a href="#Read2-173"><span class="linenos">173</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">,</span> <span class="n">codes_file</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">raise_exception</span><span class="p">(</span>
+</span><span id="Read2-174"><a href="#Read2-174"><span class="linenos">174</span></a> <span class="n">InvalidCodesException</span><span class="p">(</span>
+</span><span id="Read2-175"><a href="#Read2-175"><span class="linenos">175</span></a> <span class="n">CodesError</span><span class="p">(</span>
+</span><span id="Read2-176"><a href="#Read2-176"><span class="linenos">176</span></a> <span class="sa">f</span><span class="s2">"Codes do not exist in database"</span><span class="p">,</span>
+</span><span id="Read2-177"><a href="#Read2-177"><span class="linenos">177</span></a> <span class="n">codes</span><span class="o">=</span><span class="n">codes</span><span class="p">,</span>
+</span><span id="Read2-178"><a href="#Read2-178"><span class="linenos">178</span></a> <span class="n">codes_file</span><span class="o">=</span><span class="n">codes_file</span><span class="p">,</span>
+</span><span id="Read2-179"><a href="#Read2-179"><span class="linenos">179</span></a> <span class="n">mask</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">in_database</span><span class="p">(</span><span class="n">codes</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">db</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">),</span>
+</span><span id="Read2-180"><a href="#Read2-180"><span class="linenos">180</span></a> <span class="n">code_type</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">,</span>
+</span><span id="Read2-181"><a href="#Read2-181"><span class="linenos">181</span></a> <span class="p">)</span>
+</span><span id="Read2-182"><a href="#Read2-182"><span class="linenos">182</span></a> <span class="p">)</span>
+</span><span id="Read2-183"><a href="#Read2-183"><span class="linenos">183</span></a> <span class="p">),</span>
+</span><span id="Read2-184"><a href="#Read2-184"><span class="linenos">184</span></a> <span class="p">),</span>
+</span><span id="Read2-185"><a href="#Read2-185"><span class="linenos">185</span></a> <span class="p">]</span>
+</span></pre></div>
+
+
+ <div class="docstring"><p>This Read2 class extends Proto, adding custom validation checks for a dataset of "Read2" codes. It ensures that the dataset is loaded, validates the codes based on several rules, and applies corrections or logs errors when necessary.</p>
+</div>
+
+
+ <div id="Read2.checks" class="classattr">
+ <div class="attr variable">
+ <span class="name">checks</span>
+
+
+ </div>
+ <a class="headerlink" href="#Read2.checks"></a>
+
+
+
+ </div>
+ <div class="inherited">
+ <h5>Inherited Members</h5>
+ <dl>
+ <div><dt><a href="#Proto">Proto</a></dt>
+ <dd id="Read2.name" class="variable"><a href="#Proto.name">name</a></dd>
+ <dd id="Read2.raise_exception" class="function"><a href="#Proto.raise_exception">raise_exception</a></dd>
+ <dd id="Read2.in_database" class="function"><a href="#Proto.in_database">in_database</a></dd>
+ <dd id="Read2.process" class="function"><a href="#Proto.process">process</a></dd>
+ <dd id="Read2.verify" class="function"><a href="#Proto.verify">verify</a></dd>
+
+ </div>
+ </dl>
+ </div>
+ </section>
+ <section id="Read3">
+ <input id="Read3-view-source" class="view-source-toggle-state" type="checkbox" aria-hidden="true" tabindex="-1">
+<div class="attr class">
+
+ <span class="def">class</span>
+ <span class="name">Read3</span><wbr>(<span class="base"><a href="#Proto">Proto</a></span>):
+
+ <label class="view-source-button" for="Read3-view-source"><span>View Source</span></label>
+
+ </div>
+ <a class="headerlink" href="#Read3"></a>
+ <div class="pdoc-code codehilite"><pre><span></span><span id="Read3-188"><a href="#Read3-188"><span class="linenos">188</span></a><span class="k">class</span><span class="w"> </span><span class="nc">Read3</span><span class="p">(</span><span class="n">Proto</span><span class="p">):</span>
+</span><span id="Read3-189"><a href="#Read3-189"><span class="linenos">189</span></a> <span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+</span><span id="Read3-190"><a href="#Read3-190"><span class="linenos">190</span></a> <span class="nb">super</span><span class="p">()</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="s2">"Read3"</span><span class="p">,</span> <span class="n">trud</span><span class="o">.</span><span class="n">PROCESSED_PATH</span> <span class="o">/</span> <span class="s2">"read3.parquet"</span><span class="p">)</span>
+</span><span id="Read3-191"><a href="#Read3-191"><span class="linenos">191</span></a>
+</span><span id="Read3-192"><a href="#Read3-192"><span class="linenos">192</span></a> <span class="bp">self</span><span class="o">.</span><span class="n">checks</span> <span class="o">=</span> <span class="p">[</span>
+</span><span id="Read3-193"><a href="#Read3-193"><span class="linenos">193</span></a> <span class="p">(</span>
+</span><span id="Read3-194"><a href="#Read3-194"><span class="linenos">194</span></a> <span class="s2">"Not Empty"</span><span class="p">,</span>
+</span><span id="Read3-195"><a href="#Read3-195"><span class="linenos">195</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">:</span> <span class="n">pd</span><span class="o">.</span><span class="n">Series</span><span class="p">([</span><span class="nb">len</span><span class="p">(</span><span class="n">codes</span><span class="p">)</span> <span class="o">></span> <span class="mi">0</span><span class="p">]),</span>
+</span><span id="Read3-196"><a href="#Read3-196"><span class="linenos">196</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">,</span> <span class="n">codes_file</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">raise_exception</span><span class="p">(</span>
+</span><span id="Read3-197"><a href="#Read3-197"><span class="linenos">197</span></a> <span class="n">InvalidCodesException</span><span class="p">(</span>
+</span><span id="Read3-198"><a href="#Read3-198"><span class="linenos">198</span></a> <span class="n">CodesError</span><span class="p">(</span>
+</span><span id="Read3-199"><a href="#Read3-199"><span class="linenos">199</span></a> <span class="sa">f</span><span class="s2">"Code list is empty"</span><span class="p">,</span>
+</span><span id="Read3-200"><a href="#Read3-200"><span class="linenos">200</span></a> <span class="n">codes</span><span class="o">=</span><span class="n">codes</span><span class="p">,</span>
+</span><span id="Read3-201"><a href="#Read3-201"><span class="linenos">201</span></a> <span class="n">codes_file</span><span class="o">=</span><span class="n">codes_file</span><span class="p">,</span>
+</span><span id="Read3-202"><a href="#Read3-202"><span class="linenos">202</span></a> <span class="n">mask</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
+</span><span id="Read3-203"><a href="#Read3-203"><span class="linenos">203</span></a> <span class="n">code_type</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">,</span>
+</span><span id="Read3-204"><a href="#Read3-204"><span class="linenos">204</span></a> <span class="p">)</span>
+</span><span id="Read3-205"><a href="#Read3-205"><span class="linenos">205</span></a> <span class="p">)</span>
+</span><span id="Read3-206"><a href="#Read3-206"><span class="linenos">206</span></a> <span class="p">),</span>
+</span><span id="Read3-207"><a href="#Read3-207"><span class="linenos">207</span></a> <span class="p">),</span>
+</span><span id="Read3-208"><a href="#Read3-208"><span class="linenos">208</span></a> <span class="p">(</span>
+</span><span id="Read3-209"><a href="#Read3-209"><span class="linenos">209</span></a> <span class="s2">"Too Short"</span><span class="p">,</span>
+</span><span id="Read3-210"><a href="#Read3-210"><span class="linenos">210</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">:</span> <span class="o">~</span><span class="p">(</span><span class="n">codes</span><span class="o">.</span><span class="n">str</span><span class="o">.</span><span class="n">len</span><span class="p">()</span> <span class="o"><</span> <span class="mi">5</span><span class="p">),</span>
+</span><span id="Read3-211"><a href="#Read3-211"><span class="linenos">211</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">,</span> <span class="n">codes_file</span><span class="p">:</span> <span class="n">codes</span><span class="o">.</span><span class="n">str</span><span class="o">.</span><span class="n">pad</span><span class="p">(</span>
+</span><span id="Read3-212"><a href="#Read3-212"><span class="linenos">212</span></a> <span class="n">width</span><span class="o">=</span><span class="mi">5</span><span class="p">,</span> <span class="n">side</span><span class="o">=</span><span class="s2">"right"</span><span class="p">,</span> <span class="n">fillchar</span><span class="o">=</span><span class="s2">"."</span>
+</span><span id="Read3-213"><a href="#Read3-213"><span class="linenos">213</span></a> <span class="p">),</span>
+</span><span id="Read3-214"><a href="#Read3-214"><span class="linenos">214</span></a> <span class="p">),</span>
+</span><span id="Read3-215"><a href="#Read3-215"><span class="linenos">215</span></a> <span class="p">(</span>
+</span><span id="Read3-216"><a href="#Read3-216"><span class="linenos">216</span></a> <span class="s2">"Too Long"</span><span class="p">,</span>
+</span><span id="Read3-217"><a href="#Read3-217"><span class="linenos">217</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">:</span> <span class="o">~</span><span class="p">(</span><span class="n">codes</span><span class="o">.</span><span class="n">str</span><span class="o">.</span><span class="n">len</span><span class="p">()</span> <span class="o">></span> <span class="mi">5</span><span class="p">),</span>
+</span><span id="Read3-218"><a href="#Read3-218"><span class="linenos">218</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">,</span> <span class="n">codes_file</span><span class="p">:</span> <span class="n">codes</span><span class="o">.</span><span class="n">str</span><span class="p">[:</span><span class="mi">5</span><span class="p">],</span>
+</span><span id="Read3-219"><a href="#Read3-219"><span class="linenos">219</span></a> <span class="p">),</span>
+</span><span id="Read3-220"><a href="#Read3-220"><span class="linenos">220</span></a> <span class="p">(</span>
+</span><span id="Read3-221"><a href="#Read3-221"><span class="linenos">221</span></a> <span class="s2">"Alphanumeric Dot"</span><span class="p">,</span>
+</span><span id="Read3-222"><a href="#Read3-222"><span class="linenos">222</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">:</span> <span class="n">codes</span><span class="o">.</span><span class="n">str</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="sa">r</span><span class="s2">"^[a-zA-Z0-9.]+$"</span><span class="p">),</span>
+</span><span id="Read3-223"><a href="#Read3-223"><span class="linenos">223</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">,</span> <span class="n">codes_file</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">raise_exception</span><span class="p">(</span>
+</span><span id="Read3-224"><a href="#Read3-224"><span class="linenos">224</span></a> <span class="n">InvalidCodesException</span><span class="p">(</span>
+</span><span id="Read3-225"><a href="#Read3-225"><span class="linenos">225</span></a> <span class="n">CodesError</span><span class="p">(</span>
+</span><span id="Read3-226"><a href="#Read3-226"><span class="linenos">226</span></a> <span class="sa">f</span><span class="s2">"QA Alphanumeric Dot"</span><span class="p">,</span>
+</span><span id="Read3-227"><a href="#Read3-227"><span class="linenos">227</span></a> <span class="n">codes</span><span class="o">=</span><span class="n">codes</span><span class="p">,</span>
+</span><span id="Read3-228"><a href="#Read3-228"><span class="linenos">228</span></a> <span class="n">codes_file</span><span class="o">=</span><span class="n">codes_file</span><span class="p">,</span>
+</span><span id="Read3-229"><a href="#Read3-229"><span class="linenos">229</span></a> <span class="n">check_regex</span><span class="o">=</span><span class="n">codes</span><span class="o">.</span><span class="n">str</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="sa">r</span><span class="s2">"^[a-zA-Z0-9.]+$"</span><span class="p">),</span>
+</span><span id="Read3-230"><a href="#Read3-230"><span class="linenos">230</span></a> <span class="n">code_type</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">,</span>
+</span><span id="Read3-231"><a href="#Read3-231"><span class="linenos">231</span></a> <span class="p">)</span>
+</span><span id="Read3-232"><a href="#Read3-232"><span class="linenos">232</span></a> <span class="p">)</span>
+</span><span id="Read3-233"><a href="#Read3-233"><span class="linenos">233</span></a> <span class="p">),</span>
+</span><span id="Read3-234"><a href="#Read3-234"><span class="linenos">234</span></a> <span class="p">),</span>
+</span><span id="Read3-235"><a href="#Read3-235"><span class="linenos">235</span></a> <span class="p">(</span>
+</span><span id="Read3-236"><a href="#Read3-236"><span class="linenos">236</span></a> <span class="s2">"In Database"</span><span class="p">,</span>
+</span><span id="Read3-237"><a href="#Read3-237"><span class="linenos">237</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">in_database</span><span class="p">(</span><span class="n">codes</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">db</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">),</span>
+</span><span id="Read3-238"><a href="#Read3-238"><span class="linenos">238</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">,</span> <span class="n">codes_file</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">raise_exception</span><span class="p">(</span>
+</span><span id="Read3-239"><a href="#Read3-239"><span class="linenos">239</span></a> <span class="n">InvalidCodesException</span><span class="p">(</span>
+</span><span id="Read3-240"><a href="#Read3-240"><span class="linenos">240</span></a> <span class="n">CodesError</span><span class="p">(</span>
+</span><span id="Read3-241"><a href="#Read3-241"><span class="linenos">241</span></a> <span class="sa">f</span><span class="s2">"QA In Database"</span><span class="p">,</span>
+</span><span id="Read3-242"><a href="#Read3-242"><span class="linenos">242</span></a> <span class="n">codes</span><span class="o">=</span><span class="n">codes</span><span class="p">,</span>
+</span><span id="Read3-243"><a href="#Read3-243"><span class="linenos">243</span></a> <span class="n">codes_file</span><span class="o">=</span><span class="n">codes_file</span><span class="p">,</span>
+</span><span id="Read3-244"><a href="#Read3-244"><span class="linenos">244</span></a> <span class="n">check_regex</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">in_database</span><span class="p">(</span><span class="n">codes</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">db</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">),</span>
+</span><span id="Read3-245"><a href="#Read3-245"><span class="linenos">245</span></a> <span class="n">code_type</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">,</span>
+</span><span id="Read3-246"><a href="#Read3-246"><span class="linenos">246</span></a> <span class="p">)</span>
+</span><span id="Read3-247"><a href="#Read3-247"><span class="linenos">247</span></a> <span class="p">)</span>
+</span><span id="Read3-248"><a href="#Read3-248"><span class="linenos">248</span></a> <span class="p">),</span>
+</span><span id="Read3-249"><a href="#Read3-249"><span class="linenos">249</span></a> <span class="p">),</span>
+</span><span id="Read3-250"><a href="#Read3-250"><span class="linenos">250</span></a> <span class="p">]</span>
+</span></pre></div>
+
+
+ <div class="docstring"><p>Define checks as list of 3 tuple: (Message, Condition, Process)</p>
+
+<ul>
+<li>Message = The name of the condition (what is printed and logged)</li>
+<li>Condition = True if Passed, and False if Failed</li>
+<li>Process = Aims to resolve all issues that stop condition from passing (Do not change index!)</li>
+</ul>
+</div>
+
+
+ <div id="Read3.checks" class="classattr">
+ <div class="attr variable">
+ <span class="name">checks</span>
+
+
+ </div>
+ <a class="headerlink" href="#Read3.checks"></a>
+
+
+
+ </div>
+ <div class="inherited">
+ <h5>Inherited Members</h5>
+ <dl>
+ <div><dt><a href="#Proto">Proto</a></dt>
+ <dd id="Read3.name" class="variable"><a href="#Proto.name">name</a></dd>
+ <dd id="Read3.raise_exception" class="function"><a href="#Proto.raise_exception">raise_exception</a></dd>
+ <dd id="Read3.in_database" class="function"><a href="#Proto.in_database">in_database</a></dd>
+ <dd id="Read3.process" class="function"><a href="#Proto.process">process</a></dd>
+ <dd id="Read3.verify" class="function"><a href="#Proto.verify">verify</a></dd>
+
+ </div>
+ </dl>
+ </div>
+ </section>
+ <section id="Icd10">
+ <input id="Icd10-view-source" class="view-source-toggle-state" type="checkbox" aria-hidden="true" tabindex="-1">
+<div class="attr class">
+
+ <span class="def">class</span>
+ <span class="name">Icd10</span><wbr>(<span class="base"><a href="#Proto">Proto</a></span>):
+
+ <label class="view-source-button" for="Icd10-view-source"><span>View Source</span></label>
+
+ </div>
+ <a class="headerlink" href="#Icd10"></a>
+ <div class="pdoc-code codehilite"><pre><span></span><span id="Icd10-253"><a href="#Icd10-253"><span class="linenos">253</span></a><span class="k">class</span><span class="w"> </span><span class="nc">Icd10</span><span class="p">(</span><span class="n">Proto</span><span class="p">):</span>
+</span><span id="Icd10-254"><a href="#Icd10-254"><span class="linenos">254</span></a> <span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+</span><span id="Icd10-255"><a href="#Icd10-255"><span class="linenos">255</span></a> <span class="nb">super</span><span class="p">()</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="s2">"icd10"</span><span class="p">,</span> <span class="n">trud</span><span class="o">.</span><span class="n">PROCESSED_PATH</span> <span class="o">/</span> <span class="s2">"icd10.parquet"</span><span class="p">)</span>
+</span><span id="Icd10-256"><a href="#Icd10-256"><span class="linenos">256</span></a>
+</span><span id="Icd10-257"><a href="#Icd10-257"><span class="linenos">257</span></a> <span class="bp">self</span><span class="o">.</span><span class="n">checks</span> <span class="o">=</span> <span class="p">[</span>
+</span><span id="Icd10-258"><a href="#Icd10-258"><span class="linenos">258</span></a> <span class="p">(</span>
+</span><span id="Icd10-259"><a href="#Icd10-259"><span class="linenos">259</span></a> <span class="s2">"Not Empty"</span><span class="p">,</span>
+</span><span id="Icd10-260"><a href="#Icd10-260"><span class="linenos">260</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">:</span> <span class="n">pd</span><span class="o">.</span><span class="n">Series</span><span class="p">([</span><span class="nb">len</span><span class="p">(</span><span class="n">codes</span><span class="p">)</span> <span class="o">></span> <span class="mi">0</span><span class="p">]),</span>
+</span><span id="Icd10-261"><a href="#Icd10-261"><span class="linenos">261</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">,</span> <span class="n">codes_file</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">raise_exception</span><span class="p">(</span>
+</span><span id="Icd10-262"><a href="#Icd10-262"><span class="linenos">262</span></a> <span class="n">InvalidCodesException</span><span class="p">(</span>
+</span><span id="Icd10-263"><a href="#Icd10-263"><span class="linenos">263</span></a> <span class="n">CodesError</span><span class="p">(</span>
+</span><span id="Icd10-264"><a href="#Icd10-264"><span class="linenos">264</span></a> <span class="sa">f</span><span class="s2">"Code list is empty </span><span class="si">{</span><span class="n">codes_file</span><span class="si">}</span><span class="s2">"</span><span class="p">,</span>
+</span><span id="Icd10-265"><a href="#Icd10-265"><span class="linenos">265</span></a> <span class="n">codes</span><span class="o">=</span><span class="n">codes</span><span class="p">,</span>
+</span><span id="Icd10-266"><a href="#Icd10-266"><span class="linenos">266</span></a> <span class="n">codes_file</span><span class="o">=</span><span class="n">codes_file</span><span class="p">,</span>
+</span><span id="Icd10-267"><a href="#Icd10-267"><span class="linenos">267</span></a> <span class="n">mask</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
+</span><span id="Icd10-268"><a href="#Icd10-268"><span class="linenos">268</span></a> <span class="n">code_type</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">,</span>
+</span><span id="Icd10-269"><a href="#Icd10-269"><span class="linenos">269</span></a> <span class="p">)</span>
+</span><span id="Icd10-270"><a href="#Icd10-270"><span class="linenos">270</span></a> <span class="p">)</span>
+</span><span id="Icd10-271"><a href="#Icd10-271"><span class="linenos">271</span></a> <span class="p">),</span>
+</span><span id="Icd10-272"><a href="#Icd10-272"><span class="linenos">272</span></a> <span class="p">),</span>
+</span><span id="Icd10-273"><a href="#Icd10-273"><span class="linenos">273</span></a> <span class="p">(</span>
+</span><span id="Icd10-274"><a href="#Icd10-274"><span class="linenos">274</span></a> <span class="s2">"Too Short"</span><span class="p">,</span>
+</span><span id="Icd10-275"><a href="#Icd10-275"><span class="linenos">275</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">:</span> <span class="o">~</span><span class="p">(</span><span class="n">codes</span><span class="o">.</span><span class="n">str</span><span class="o">.</span><span class="n">len</span><span class="p">()</span> <span class="o"><</span> <span class="mi">3</span><span class="p">),</span>
+</span><span id="Icd10-276"><a href="#Icd10-276"><span class="linenos">276</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">,</span> <span class="n">codes_file</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">raise_exception</span><span class="p">(</span>
+</span><span id="Icd10-277"><a href="#Icd10-277"><span class="linenos">277</span></a> <span class="n">InvalidCodesException</span><span class="p">(</span>
+</span><span id="Icd10-278"><a href="#Icd10-278"><span class="linenos">278</span></a> <span class="n">CodesError</span><span class="p">(</span>
+</span><span id="Icd10-279"><a href="#Icd10-279"><span class="linenos">279</span></a> <span class="sa">f</span><span class="s2">"QA Too Short"</span><span class="p">,</span>
+</span><span id="Icd10-280"><a href="#Icd10-280"><span class="linenos">280</span></a> <span class="n">codes</span><span class="o">=</span><span class="n">codes</span><span class="p">,</span>
+</span><span id="Icd10-281"><a href="#Icd10-281"><span class="linenos">281</span></a> <span class="n">codes_file</span><span class="o">=</span><span class="n">codes_file</span><span class="p">,</span>
+</span><span id="Icd10-282"><a href="#Icd10-282"><span class="linenos">282</span></a> <span class="n">mask</span><span class="o">=~</span><span class="p">(</span><span class="n">codes</span><span class="o">.</span><span class="n">str</span><span class="o">.</span><span class="n">len</span><span class="p">()</span> <span class="o"><</span> <span class="mi">3</span><span class="p">),</span>
+</span><span id="Icd10-283"><a href="#Icd10-283"><span class="linenos">283</span></a> <span class="n">code_type</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">,</span>
+</span><span id="Icd10-284"><a href="#Icd10-284"><span class="linenos">284</span></a> <span class="p">)</span>
+</span><span id="Icd10-285"><a href="#Icd10-285"><span class="linenos">285</span></a> <span class="p">)</span>
+</span><span id="Icd10-286"><a href="#Icd10-286"><span class="linenos">286</span></a> <span class="p">),</span>
+</span><span id="Icd10-287"><a href="#Icd10-287"><span class="linenos">287</span></a> <span class="p">),</span>
+</span><span id="Icd10-288"><a href="#Icd10-288"><span class="linenos">288</span></a> <span class="p">(</span>
+</span><span id="Icd10-289"><a href="#Icd10-289"><span class="linenos">289</span></a> <span class="s2">"Has Dot"</span><span class="p">,</span>
+</span><span id="Icd10-290"><a href="#Icd10-290"><span class="linenos">290</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">:</span> <span class="o">~</span><span class="p">(</span><span class="n">codes</span><span class="o">.</span><span class="n">str</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="sa">r</span><span class="s2">".*\..*"</span><span class="p">)),</span> <span class="c1"># check if contains dot</span>
+</span><span id="Icd10-291"><a href="#Icd10-291"><span class="linenos">291</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">,</span> <span class="n">codes_file</span><span class="p">:</span> <span class="n">codes</span><span class="o">.</span><span class="n">str</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span>
+</span><span id="Icd10-292"><a href="#Icd10-292"><span class="linenos">292</span></a> <span class="s2">"."</span><span class="p">,</span> <span class="s2">""</span>
+</span><span id="Icd10-293"><a href="#Icd10-293"><span class="linenos">293</span></a> <span class="p">),</span> <span class="c1"># delete any dots in string</span>
+</span><span id="Icd10-294"><a href="#Icd10-294"><span class="linenos">294</span></a> <span class="c1"># lambda codes : codes.str.split('\.').apply(lambda ls: ls[0]) #only get part before dot</span>
+</span><span id="Icd10-295"><a href="#Icd10-295"><span class="linenos">295</span></a> <span class="p">),</span>
+</span><span id="Icd10-296"><a href="#Icd10-296"><span class="linenos">296</span></a> <span class="p">(</span>
+</span><span id="Icd10-297"><a href="#Icd10-297"><span class="linenos">297</span></a> <span class="s2">"Alphanumeric Capital"</span><span class="p">,</span>
+</span><span id="Icd10-298"><a href="#Icd10-298"><span class="linenos">298</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">:</span> <span class="n">codes</span><span class="o">.</span><span class="n">str</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="sa">r</span><span class="s2">"^[A-Z0-9]+$"</span><span class="p">),</span>
+</span><span id="Icd10-299"><a href="#Icd10-299"><span class="linenos">299</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">,</span> <span class="n">codes_file</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">raise_exception</span><span class="p">(</span>
+</span><span id="Icd10-300"><a href="#Icd10-300"><span class="linenos">300</span></a> <span class="n">InvalidCodesException</span><span class="p">(</span>
+</span><span id="Icd10-301"><a href="#Icd10-301"><span class="linenos">301</span></a> <span class="n">CodesError</span><span class="p">(</span>
+</span><span id="Icd10-302"><a href="#Icd10-302"><span class="linenos">302</span></a> <span class="sa">f</span><span class="s2">"QA Alphanumeric Capital"</span><span class="p">,</span>
+</span><span id="Icd10-303"><a href="#Icd10-303"><span class="linenos">303</span></a> <span class="n">codes</span><span class="o">=</span><span class="n">codes</span><span class="p">,</span>
+</span><span id="Icd10-304"><a href="#Icd10-304"><span class="linenos">304</span></a> <span class="n">codes_file</span><span class="o">=</span><span class="n">codes_file</span><span class="p">,</span>
+</span><span id="Icd10-305"><a href="#Icd10-305"><span class="linenos">305</span></a> <span class="n">mask</span><span class="o">=</span><span class="n">codes</span><span class="o">.</span><span class="n">str</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="sa">r</span><span class="s2">"^[A-Z0-9]+$"</span><span class="p">),</span>
+</span><span id="Icd10-306"><a href="#Icd10-306"><span class="linenos">306</span></a> <span class="n">code_type</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">,</span>
+</span><span id="Icd10-307"><a href="#Icd10-307"><span class="linenos">307</span></a> <span class="p">)</span>
+</span><span id="Icd10-308"><a href="#Icd10-308"><span class="linenos">308</span></a> <span class="p">)</span>
+</span><span id="Icd10-309"><a href="#Icd10-309"><span class="linenos">309</span></a> <span class="p">),</span>
+</span><span id="Icd10-310"><a href="#Icd10-310"><span class="linenos">310</span></a> <span class="p">),</span>
+</span><span id="Icd10-311"><a href="#Icd10-311"><span class="linenos">311</span></a> <span class="p">(</span>
+</span><span id="Icd10-312"><a href="#Icd10-312"><span class="linenos">312</span></a> <span class="s2">"In Database"</span><span class="p">,</span>
+</span><span id="Icd10-313"><a href="#Icd10-313"><span class="linenos">313</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">:</span> <span class="o">~</span><span class="p">(</span>
+</span><span id="Icd10-314"><a href="#Icd10-314"><span class="linenos">314</span></a> <span class="o">~</span><span class="bp">self</span><span class="o">.</span><span class="n">in_database</span><span class="p">(</span><span class="n">codes</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">db</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">)</span>
+</span><span id="Icd10-315"><a href="#Icd10-315"><span class="linenos">315</span></a> <span class="o">&</span> <span class="o">~</span><span class="bp">self</span><span class="o">.</span><span class="n">in_database</span><span class="p">(</span><span class="n">codes</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">db</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">name</span> <span class="o">+</span> <span class="s2">"_alt"</span><span class="p">)</span>
+</span><span id="Icd10-316"><a href="#Icd10-316"><span class="linenos">316</span></a> <span class="p">),</span>
+</span><span id="Icd10-317"><a href="#Icd10-317"><span class="linenos">317</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">,</span> <span class="n">codes_file</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">raise_exception</span><span class="p">(</span>
+</span><span id="Icd10-318"><a href="#Icd10-318"><span class="linenos">318</span></a> <span class="n">InvalidCodesException</span><span class="p">(</span>
+</span><span id="Icd10-319"><a href="#Icd10-319"><span class="linenos">319</span></a> <span class="n">CodesError</span><span class="p">(</span>
+</span><span id="Icd10-320"><a href="#Icd10-320"><span class="linenos">320</span></a> <span class="sa">f</span><span class="s2">"QA In Database"</span><span class="p">,</span>
+</span><span id="Icd10-321"><a href="#Icd10-321"><span class="linenos">321</span></a> <span class="n">codes</span><span class="o">=</span><span class="n">codes</span><span class="p">,</span>
+</span><span id="Icd10-322"><a href="#Icd10-322"><span class="linenos">322</span></a> <span class="n">codes_file</span><span class="o">=</span><span class="n">codes_file</span><span class="p">,</span>
+</span><span id="Icd10-323"><a href="#Icd10-323"><span class="linenos">323</span></a> <span class="n">mask</span><span class="o">=~</span><span class="p">(</span>
+</span><span id="Icd10-324"><a href="#Icd10-324"><span class="linenos">324</span></a> <span class="o">~</span><span class="bp">self</span><span class="o">.</span><span class="n">in_database</span><span class="p">(</span><span class="n">codes</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">db</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">)</span>
+</span><span id="Icd10-325"><a href="#Icd10-325"><span class="linenos">325</span></a> <span class="o">&</span> <span class="o">~</span><span class="bp">self</span><span class="o">.</span><span class="n">in_database</span><span class="p">(</span><span class="n">codes</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">db</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">name</span> <span class="o">+</span> <span class="s2">"_alt"</span><span class="p">)</span>
+</span><span id="Icd10-326"><a href="#Icd10-326"><span class="linenos">326</span></a> <span class="p">),</span>
+</span><span id="Icd10-327"><a href="#Icd10-327"><span class="linenos">327</span></a> <span class="n">code_type</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">,</span>
+</span><span id="Icd10-328"><a href="#Icd10-328"><span class="linenos">328</span></a> <span class="p">)</span>
+</span><span id="Icd10-329"><a href="#Icd10-329"><span class="linenos">329</span></a> <span class="p">)</span>
+</span><span id="Icd10-330"><a href="#Icd10-330"><span class="linenos">330</span></a> <span class="p">),</span>
+</span><span id="Icd10-331"><a href="#Icd10-331"><span class="linenos">331</span></a> <span class="p">),</span>
+</span><span id="Icd10-332"><a href="#Icd10-332"><span class="linenos">332</span></a> <span class="c1"># (</span>
+</span><span id="Icd10-333"><a href="#Icd10-333"><span class="linenos">333</span></a> <span class="c1"># "ICD10 Regex",</span>
+</span><span id="Icd10-334"><a href="#Icd10-334"><span class="linenos">334</span></a> <span class="c1"># lambda codes : codes.str.match("[a-zA-Z][0-9][0-9]\.?[a-zA-Z0-9]*$"), #Alpha, Num, Num , Dot?, 4xAlphNum*</span>
+</span><span id="Icd10-335"><a href="#Icd10-335"><span class="linenos">335</span></a> <span class="c1"># lambda codes : lc.log_invalid_code(codes,</span>
+</span><span id="Icd10-336"><a href="#Icd10-336"><span class="linenos">336</span></a> <span class="c1"># codes.str.match("[a-zA-Z][0-9][0-9]\.?[a-zA-Z0-9]*$"), #Log non-matching rows</span>
+</span><span id="Icd10-337"><a href="#Icd10-337"><span class="linenos">337</span></a> <span class="c1"># code_type="icd10",</span>
+</span><span id="Icd10-338"><a href="#Icd10-338"><span class="linenos">338</span></a> <span class="c1">#</span>
+</span><span id="Icd10-339"><a href="#Icd10-339"><span class="linenos">339</span></a> <span class="c1"># )</span>
+</span><span id="Icd10-340"><a href="#Icd10-340"><span class="linenos">340</span></a> <span class="p">]</span>
+</span><span id="Icd10-341"><a href="#Icd10-341"><span class="linenos">341</span></a>
+</span><span id="Icd10-342"><a href="#Icd10-342"><span class="linenos">342</span></a> <span class="k">def</span><span class="w"> </span><span class="nf">trim_icd10</span><span class="p">(</span><span class="n">codes</span><span class="p">:</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">)</span> <span class="o">-></span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">:</span>
+</span><span id="Icd10-343"><a href="#Icd10-343"><span class="linenos">343</span></a> <span class="n">codes</span> <span class="o">=</span> <span class="n">codes</span><span class="o">.</span><span class="n">str</span><span class="p">[:</span><span class="mi">4</span><span class="p">]</span>
+</span><span id="Icd10-344"><a href="#Icd10-344"><span class="linenos">344</span></a> <span class="k">return</span> <span class="n">codes</span>
+</span></pre></div>
+
+
+ <div class="docstring"><p>Define checks as list of 3 tuple: (Message, Condition, Process)</p>
+
+<ul>
+<li>Message = The name of the condition (what is printed and logged)</li>
+<li>Condition = True if Passed, and False if Failed</li>
+<li>Process = Aims to resolve all issues that stop condition from passing (Do not change index!)</li>
+</ul>
+</div>
+
+
+ <div id="Icd10.checks" class="classattr">
+ <div class="attr variable">
+ <span class="name">checks</span>
+
+
+ </div>
+ <a class="headerlink" href="#Icd10.checks"></a>
+
+
+
+ </div>
+ <div id="Icd10.trim_icd10" class="classattr">
+ <input id="Icd10.trim_icd10-view-source" class="view-source-toggle-state" type="checkbox" aria-hidden="true" tabindex="-1">
+<div class="attr function">
+
+ <span class="def">def</span>
+ <span class="name">trim_icd10</span><span class="signature pdoc-code condensed">(<span class="param"><span class="n">codes</span><span class="p">:</span> <span class="n">pandas</span><span class="o">.</span><span class="n">core</span><span class="o">.</span><span class="n">frame</span><span class="o">.</span><span class="n">DataFrame</span></span><span class="return-annotation">) -> <span class="n">pandas</span><span class="o">.</span><span class="n">core</span><span class="o">.</span><span class="n">frame</span><span class="o">.</span><span class="n">DataFrame</span>:</span></span>
+
+ <label class="view-source-button" for="Icd10.trim_icd10-view-source"><span>View Source</span></label>
+
+ </div>
+ <a class="headerlink" href="#Icd10.trim_icd10"></a>
+ <div class="pdoc-code codehilite"><pre><span></span><span id="Icd10.trim_icd10-342"><a href="#Icd10.trim_icd10-342"><span class="linenos">342</span></a> <span class="k">def</span><span class="w"> </span><span class="nf">trim_icd10</span><span class="p">(</span><span class="n">codes</span><span class="p">:</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">)</span> <span class="o">-></span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">:</span>
+</span><span id="Icd10.trim_icd10-343"><a href="#Icd10.trim_icd10-343"><span class="linenos">343</span></a> <span class="n">codes</span> <span class="o">=</span> <span class="n">codes</span><span class="o">.</span><span class="n">str</span><span class="p">[:</span><span class="mi">4</span><span class="p">]</span>
+</span><span id="Icd10.trim_icd10-344"><a href="#Icd10.trim_icd10-344"><span class="linenos">344</span></a> <span class="k">return</span> <span class="n">codes</span>
+</span></pre></div>
+
+
+
+
+ </div>
+ <div class="inherited">
+ <h5>Inherited Members</h5>
+ <dl>
+ <div><dt><a href="#Proto">Proto</a></dt>
+ <dd id="Icd10.name" class="variable"><a href="#Proto.name">name</a></dd>
+ <dd id="Icd10.raise_exception" class="function"><a href="#Proto.raise_exception">raise_exception</a></dd>
+ <dd id="Icd10.in_database" class="function"><a href="#Proto.in_database">in_database</a></dd>
+ <dd id="Icd10.process" class="function"><a href="#Proto.process">process</a></dd>
+ <dd id="Icd10.verify" class="function"><a href="#Proto.verify">verify</a></dd>
+
+ </div>
+ </dl>
+ </div>
+ </section>
+ <section id="Snomed">
+ <input id="Snomed-view-source" class="view-source-toggle-state" type="checkbox" aria-hidden="true" tabindex="-1">
+<div class="attr class">
+
+ <span class="def">class</span>
+ <span class="name">Snomed</span><wbr>(<span class="base"><a href="#Proto">Proto</a></span>):
+
+ <label class="view-source-button" for="Snomed-view-source"><span>View Source</span></label>
+
+ </div>
+ <a class="headerlink" href="#Snomed"></a>
+ <div class="pdoc-code codehilite"><pre><span></span><span id="Snomed-347"><a href="#Snomed-347"><span class="linenos">347</span></a><span class="k">class</span><span class="w"> </span><span class="nc">Snomed</span><span class="p">(</span><span class="n">Proto</span><span class="p">):</span>
+</span><span id="Snomed-348"><a href="#Snomed-348"><span class="linenos">348</span></a> <span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+</span><span id="Snomed-349"><a href="#Snomed-349"><span class="linenos">349</span></a> <span class="nb">super</span><span class="p">()</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="s2">"snomed"</span><span class="p">,</span> <span class="n">trud</span><span class="o">.</span><span class="n">PROCESSED_PATH</span> <span class="o">/</span> <span class="s2">"snomed.parquet"</span><span class="p">)</span>
+</span><span id="Snomed-350"><a href="#Snomed-350"><span class="linenos">350</span></a>
+</span><span id="Snomed-351"><a href="#Snomed-351"><span class="linenos">351</span></a> <span class="bp">self</span><span class="o">.</span><span class="n">checks</span> <span class="o">=</span> <span class="p">[</span>
+</span><span id="Snomed-352"><a href="#Snomed-352"><span class="linenos">352</span></a> <span class="c1"># (</span>
+</span><span id="Snomed-353"><a href="#Snomed-353"><span class="linenos">353</span></a> <span class="c1"># "Not Empty",</span>
+</span><span id="Snomed-354"><a href="#Snomed-354"><span class="linenos">354</span></a> <span class="c1"># lambda codes : pd.Series([len(codes) > 0]),</span>
+</span><span id="Snomed-355"><a href="#Snomed-355"><span class="linenos">355</span></a> <span class="c1"># lambda codes : raise_exception(Exception("Code List is Empty"))</span>
+</span><span id="Snomed-356"><a href="#Snomed-356"><span class="linenos">356</span></a> <span class="c1"># ),</span>
+</span><span id="Snomed-357"><a href="#Snomed-357"><span class="linenos">357</span></a> <span class="p">(</span>
+</span><span id="Snomed-358"><a href="#Snomed-358"><span class="linenos">358</span></a> <span class="s2">"Too Short"</span><span class="p">,</span>
+</span><span id="Snomed-359"><a href="#Snomed-359"><span class="linenos">359</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">:</span> <span class="o">~</span><span class="p">(</span><span class="n">codes</span><span class="o">.</span><span class="n">str</span><span class="o">.</span><span class="n">len</span><span class="p">()</span> <span class="o"><</span> <span class="mi">6</span><span class="p">),</span>
+</span><span id="Snomed-360"><a href="#Snomed-360"><span class="linenos">360</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">,</span> <span class="n">codes_file</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">raise_exception</span><span class="p">(</span>
+</span><span id="Snomed-361"><a href="#Snomed-361"><span class="linenos">361</span></a> <span class="n">InvalidCodesException</span><span class="p">(</span>
+</span><span id="Snomed-362"><a href="#Snomed-362"><span class="linenos">362</span></a> <span class="n">CodesError</span><span class="p">(</span>
+</span><span id="Snomed-363"><a href="#Snomed-363"><span class="linenos">363</span></a> <span class="sa">f</span><span class="s2">"QA Too Short"</span><span class="p">,</span>
+</span><span id="Snomed-364"><a href="#Snomed-364"><span class="linenos">364</span></a> <span class="n">codes</span><span class="o">=</span><span class="n">codes</span><span class="p">,</span>
+</span><span id="Snomed-365"><a href="#Snomed-365"><span class="linenos">365</span></a> <span class="n">codes_file</span><span class="o">=</span><span class="n">codes_file</span><span class="p">,</span>
+</span><span id="Snomed-366"><a href="#Snomed-366"><span class="linenos">366</span></a> <span class="n">mask</span><span class="o">=~</span><span class="p">(</span><span class="n">codes</span><span class="o">.</span><span class="n">str</span><span class="o">.</span><span class="n">len</span><span class="p">()</span> <span class="o"><</span> <span class="mi">6</span><span class="p">),</span>
+</span><span id="Snomed-367"><a href="#Snomed-367"><span class="linenos">367</span></a> <span class="n">code_type</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">,</span>
+</span><span id="Snomed-368"><a href="#Snomed-368"><span class="linenos">368</span></a> <span class="p">)</span>
+</span><span id="Snomed-369"><a href="#Snomed-369"><span class="linenos">369</span></a> <span class="p">)</span>
+</span><span id="Snomed-370"><a href="#Snomed-370"><span class="linenos">370</span></a> <span class="p">),</span>
+</span><span id="Snomed-371"><a href="#Snomed-371"><span class="linenos">371</span></a> <span class="p">),</span>
+</span><span id="Snomed-372"><a href="#Snomed-372"><span class="linenos">372</span></a> <span class="p">(</span>
+</span><span id="Snomed-373"><a href="#Snomed-373"><span class="linenos">373</span></a> <span class="s2">"Too Long"</span><span class="p">,</span>
+</span><span id="Snomed-374"><a href="#Snomed-374"><span class="linenos">374</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">:</span> <span class="o">~</span><span class="p">(</span><span class="n">codes</span><span class="o">.</span><span class="n">str</span><span class="o">.</span><span class="n">len</span><span class="p">()</span> <span class="o">></span> <span class="mi">18</span><span class="p">),</span>
+</span><span id="Snomed-375"><a href="#Snomed-375"><span class="linenos">375</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">,</span> <span class="n">codes_file</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">raise_exception</span><span class="p">(</span>
+</span><span id="Snomed-376"><a href="#Snomed-376"><span class="linenos">376</span></a> <span class="n">InvalidCodesException</span><span class="p">(</span>
+</span><span id="Snomed-377"><a href="#Snomed-377"><span class="linenos">377</span></a> <span class="n">CodesError</span><span class="p">(</span>
+</span><span id="Snomed-378"><a href="#Snomed-378"><span class="linenos">378</span></a> <span class="sa">f</span><span class="s2">"QA Too Long"</span><span class="p">,</span>
+</span><span id="Snomed-379"><a href="#Snomed-379"><span class="linenos">379</span></a> <span class="n">codes</span><span class="o">=</span><span class="n">codes</span><span class="p">,</span>
+</span><span id="Snomed-380"><a href="#Snomed-380"><span class="linenos">380</span></a> <span class="n">codes_file</span><span class="o">=</span><span class="n">codes_file</span><span class="p">,</span>
+</span><span id="Snomed-381"><a href="#Snomed-381"><span class="linenos">381</span></a> <span class="n">mask</span><span class="o">=~</span><span class="p">(</span><span class="n">codes</span><span class="o">.</span><span class="n">str</span><span class="o">.</span><span class="n">len</span><span class="p">()</span> <span class="o">></span> <span class="mi">18</span><span class="p">),</span>
+</span><span id="Snomed-382"><a href="#Snomed-382"><span class="linenos">382</span></a> <span class="n">code_type</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">,</span>
+</span><span id="Snomed-383"><a href="#Snomed-383"><span class="linenos">383</span></a> <span class="p">)</span>
+</span><span id="Snomed-384"><a href="#Snomed-384"><span class="linenos">384</span></a> <span class="p">)</span>
+</span><span id="Snomed-385"><a href="#Snomed-385"><span class="linenos">385</span></a> <span class="p">),</span>
+</span><span id="Snomed-386"><a href="#Snomed-386"><span class="linenos">386</span></a> <span class="p">),</span>
+</span><span id="Snomed-387"><a href="#Snomed-387"><span class="linenos">387</span></a> <span class="p">(</span>
+</span><span id="Snomed-388"><a href="#Snomed-388"><span class="linenos">388</span></a> <span class="s2">"Numeric"</span><span class="p">,</span>
+</span><span id="Snomed-389"><a href="#Snomed-389"><span class="linenos">389</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">:</span> <span class="n">codes</span><span class="o">.</span><span class="n">str</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="sa">r</span><span class="s2">"[0-9]+$"</span><span class="p">),</span>
+</span><span id="Snomed-390"><a href="#Snomed-390"><span class="linenos">390</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">,</span> <span class="n">codes_file</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">raise_exception</span><span class="p">(</span>
+</span><span id="Snomed-391"><a href="#Snomed-391"><span class="linenos">391</span></a> <span class="n">InvalidCodesException</span><span class="p">(</span>
+</span><span id="Snomed-392"><a href="#Snomed-392"><span class="linenos">392</span></a> <span class="n">CodesError</span><span class="p">(</span>
+</span><span id="Snomed-393"><a href="#Snomed-393"><span class="linenos">393</span></a> <span class="sa">f</span><span class="s2">"QA Numeric"</span><span class="p">,</span>
+</span><span id="Snomed-394"><a href="#Snomed-394"><span class="linenos">394</span></a> <span class="n">codes</span><span class="o">=</span><span class="n">codes</span><span class="p">,</span>
+</span><span id="Snomed-395"><a href="#Snomed-395"><span class="linenos">395</span></a> <span class="n">codes_file</span><span class="o">=</span><span class="n">codes_file</span><span class="p">,</span>
+</span><span id="Snomed-396"><a href="#Snomed-396"><span class="linenos">396</span></a> <span class="n">mask</span><span class="o">=</span><span class="n">codes</span><span class="o">.</span><span class="n">str</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="sa">r</span><span class="s2">"[0-9]+$"</span><span class="p">),</span>
+</span><span id="Snomed-397"><a href="#Snomed-397"><span class="linenos">397</span></a> <span class="n">code_type</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">,</span>
+</span><span id="Snomed-398"><a href="#Snomed-398"><span class="linenos">398</span></a> <span class="p">)</span>
+</span><span id="Snomed-399"><a href="#Snomed-399"><span class="linenos">399</span></a> <span class="p">)</span>
+</span><span id="Snomed-400"><a href="#Snomed-400"><span class="linenos">400</span></a> <span class="p">),</span>
+</span><span id="Snomed-401"><a href="#Snomed-401"><span class="linenos">401</span></a> <span class="p">),</span>
+</span><span id="Snomed-402"><a href="#Snomed-402"><span class="linenos">402</span></a> <span class="c1"># (</span>
+</span><span id="Snomed-403"><a href="#Snomed-403"><span class="linenos">403</span></a> <span class="c1"># "Is Integer",</span>
+</span><span id="Snomed-404"><a href="#Snomed-404"><span class="linenos">404</span></a> <span class="c1"># lambda codes : codes.dtype == int,</span>
+</span><span id="Snomed-405"><a href="#Snomed-405"><span class="linenos">405</span></a> <span class="c1"># lambda codes : codes.astype(int) #Convert to integer</span>
+</span><span id="Snomed-406"><a href="#Snomed-406"><span class="linenos">406</span></a> <span class="c1"># ),</span>
+</span><span id="Snomed-407"><a href="#Snomed-407"><span class="linenos">407</span></a> <span class="p">(</span>
+</span><span id="Snomed-408"><a href="#Snomed-408"><span class="linenos">408</span></a> <span class="s2">"In Database"</span><span class="p">,</span>
+</span><span id="Snomed-409"><a href="#Snomed-409"><span class="linenos">409</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">in_database</span><span class="p">(</span><span class="n">codes</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">db</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">),</span>
+</span><span id="Snomed-410"><a href="#Snomed-410"><span class="linenos">410</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">,</span> <span class="n">codes_file</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">raise_exception</span><span class="p">(</span>
+</span><span id="Snomed-411"><a href="#Snomed-411"><span class="linenos">411</span></a> <span class="n">InvalidCodesException</span><span class="p">(</span>
+</span><span id="Snomed-412"><a href="#Snomed-412"><span class="linenos">412</span></a> <span class="n">CodesError</span><span class="p">(</span>
+</span><span id="Snomed-413"><a href="#Snomed-413"><span class="linenos">413</span></a> <span class="sa">f</span><span class="s2">"QA In Database"</span><span class="p">,</span>
+</span><span id="Snomed-414"><a href="#Snomed-414"><span class="linenos">414</span></a> <span class="n">codes</span><span class="o">=</span><span class="n">codes</span><span class="p">,</span>
+</span><span id="Snomed-415"><a href="#Snomed-415"><span class="linenos">415</span></a> <span class="n">codes_file</span><span class="o">=</span><span class="n">codes_file</span><span class="p">,</span>
+</span><span id="Snomed-416"><a href="#Snomed-416"><span class="linenos">416</span></a> <span class="n">mask</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">in_database</span><span class="p">(</span><span class="n">codes</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">db</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">),</span>
+</span><span id="Snomed-417"><a href="#Snomed-417"><span class="linenos">417</span></a> <span class="n">code_type</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">,</span>
+</span><span id="Snomed-418"><a href="#Snomed-418"><span class="linenos">418</span></a> <span class="p">)</span>
+</span><span id="Snomed-419"><a href="#Snomed-419"><span class="linenos">419</span></a> <span class="p">)</span>
+</span><span id="Snomed-420"><a href="#Snomed-420"><span class="linenos">420</span></a> <span class="p">),</span>
+</span><span id="Snomed-421"><a href="#Snomed-421"><span class="linenos">421</span></a> <span class="p">),</span>
+</span><span id="Snomed-422"><a href="#Snomed-422"><span class="linenos">422</span></a> <span class="p">]</span>
+</span></pre></div>
+
+
+ <div class="docstring"><p>Define checks as list of 3 tuple: (Message, Condition, Process)</p>
+
+<ul>
+<li>Message = The name of the condition (what is printed and logged)</li>
+<li>Condition = True if Passed, and False if Failed</li>
+<li>Process = Aims to resolve all issues that stop condition from passing (Do not change index!)</li>
+</ul>
+</div>
+
+
+ <div id="Snomed.checks" class="classattr">
+ <div class="attr variable">
+ <span class="name">checks</span>
+
+
+ </div>
+ <a class="headerlink" href="#Snomed.checks"></a>
+
+
+
+ </div>
+ <div class="inherited">
+ <h5>Inherited Members</h5>
+ <dl>
+ <div><dt><a href="#Proto">Proto</a></dt>
+ <dd id="Snomed.name" class="variable"><a href="#Proto.name">name</a></dd>
+ <dd id="Snomed.raise_exception" class="function"><a href="#Proto.raise_exception">raise_exception</a></dd>
+ <dd id="Snomed.in_database" class="function"><a href="#Proto.in_database">in_database</a></dd>
+ <dd id="Snomed.process" class="function"><a href="#Proto.process">process</a></dd>
+ <dd id="Snomed.verify" class="function"><a href="#Proto.verify">verify</a></dd>
+
+ </div>
+ </dl>
+ </div>
+ </section>
+ <section id="Opcs4">
+ <input id="Opcs4-view-source" class="view-source-toggle-state" type="checkbox" aria-hidden="true" tabindex="-1">
+<div class="attr class">
+
+ <span class="def">class</span>
+ <span class="name">Opcs4</span><wbr>(<span class="base"><a href="#Proto">Proto</a></span>):
+
+ <label class="view-source-button" for="Opcs4-view-source"><span>View Source</span></label>
+
+ </div>
+ <a class="headerlink" href="#Opcs4"></a>
+ <div class="pdoc-code codehilite"><pre><span></span><span id="Opcs4-425"><a href="#Opcs4-425"><span class="linenos">425</span></a><span class="k">class</span><span class="w"> </span><span class="nc">Opcs4</span><span class="p">(</span><span class="n">Proto</span><span class="p">):</span>
+</span><span id="Opcs4-426"><a href="#Opcs4-426"><span class="linenos">426</span></a> <span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+</span><span id="Opcs4-427"><a href="#Opcs4-427"><span class="linenos">427</span></a> <span class="nb">super</span><span class="p">()</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="s2">"opcs4"</span><span class="p">,</span> <span class="n">trud</span><span class="o">.</span><span class="n">PROCESSED_PATH</span> <span class="o">/</span> <span class="s2">"opcs4.parquet"</span><span class="p">)</span>
+</span><span id="Opcs4-428"><a href="#Opcs4-428"><span class="linenos">428</span></a>
+</span><span id="Opcs4-429"><a href="#Opcs4-429"><span class="linenos">429</span></a> <span class="bp">self</span><span class="o">.</span><span class="n">checks</span> <span class="o">=</span> <span class="p">[</span>
+</span><span id="Opcs4-430"><a href="#Opcs4-430"><span class="linenos">430</span></a> <span class="p">(</span>
+</span><span id="Opcs4-431"><a href="#Opcs4-431"><span class="linenos">431</span></a> <span class="s2">"Not Empty"</span><span class="p">,</span>
+</span><span id="Opcs4-432"><a href="#Opcs4-432"><span class="linenos">432</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">:</span> <span class="n">pd</span><span class="o">.</span><span class="n">Series</span><span class="p">([</span><span class="nb">len</span><span class="p">(</span><span class="n">codes</span><span class="p">)</span> <span class="o">></span> <span class="mi">0</span><span class="p">]),</span>
+</span><span id="Opcs4-433"><a href="#Opcs4-433"><span class="linenos">433</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">,</span> <span class="n">codes_file</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">raise_exception</span><span class="p">(</span>
+</span><span id="Opcs4-434"><a href="#Opcs4-434"><span class="linenos">434</span></a> <span class="n">InvalidCodesException</span><span class="p">(</span>
+</span><span id="Opcs4-435"><a href="#Opcs4-435"><span class="linenos">435</span></a> <span class="n">CodesError</span><span class="p">(</span>
+</span><span id="Opcs4-436"><a href="#Opcs4-436"><span class="linenos">436</span></a> <span class="sa">f</span><span class="s2">"Code list is empty"</span><span class="p">,</span>
+</span><span id="Opcs4-437"><a href="#Opcs4-437"><span class="linenos">437</span></a> <span class="n">codes</span><span class="o">=</span><span class="n">codes</span><span class="p">,</span>
+</span><span id="Opcs4-438"><a href="#Opcs4-438"><span class="linenos">438</span></a> <span class="n">codes_file</span><span class="o">=</span><span class="n">codes_file</span><span class="p">,</span>
+</span><span id="Opcs4-439"><a href="#Opcs4-439"><span class="linenos">439</span></a> <span class="n">mask</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
+</span><span id="Opcs4-440"><a href="#Opcs4-440"><span class="linenos">440</span></a> <span class="n">code_type</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">,</span>
+</span><span id="Opcs4-441"><a href="#Opcs4-441"><span class="linenos">441</span></a> <span class="p">)</span>
+</span><span id="Opcs4-442"><a href="#Opcs4-442"><span class="linenos">442</span></a> <span class="p">)</span>
+</span><span id="Opcs4-443"><a href="#Opcs4-443"><span class="linenos">443</span></a> <span class="p">),</span>
+</span><span id="Opcs4-444"><a href="#Opcs4-444"><span class="linenos">444</span></a> <span class="p">),</span>
+</span><span id="Opcs4-445"><a href="#Opcs4-445"><span class="linenos">445</span></a> <span class="p">(</span>
+</span><span id="Opcs4-446"><a href="#Opcs4-446"><span class="linenos">446</span></a> <span class="s2">"In Database"</span><span class="p">,</span>
+</span><span id="Opcs4-447"><a href="#Opcs4-447"><span class="linenos">447</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">in_database</span><span class="p">(</span><span class="n">codes</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">db</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">),</span>
+</span><span id="Opcs4-448"><a href="#Opcs4-448"><span class="linenos">448</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">,</span> <span class="n">codes_file</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">raise_exception</span><span class="p">(</span>
+</span><span id="Opcs4-449"><a href="#Opcs4-449"><span class="linenos">449</span></a> <span class="n">InvalidCodesException</span><span class="p">(</span>
+</span><span id="Opcs4-450"><a href="#Opcs4-450"><span class="linenos">450</span></a> <span class="n">CodesError</span><span class="p">(</span>
+</span><span id="Opcs4-451"><a href="#Opcs4-451"><span class="linenos">451</span></a> <span class="sa">f</span><span class="s2">"QA In Database"</span><span class="p">,</span>
+</span><span id="Opcs4-452"><a href="#Opcs4-452"><span class="linenos">452</span></a> <span class="n">codes</span><span class="o">=</span><span class="n">codes</span><span class="p">,</span>
+</span><span id="Opcs4-453"><a href="#Opcs4-453"><span class="linenos">453</span></a> <span class="n">codes_file</span><span class="o">=</span><span class="n">codes_file</span><span class="p">,</span>
+</span><span id="Opcs4-454"><a href="#Opcs4-454"><span class="linenos">454</span></a> <span class="n">mask</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">in_database</span><span class="p">(</span><span class="n">codes</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">db</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">),</span>
+</span><span id="Opcs4-455"><a href="#Opcs4-455"><span class="linenos">455</span></a> <span class="n">code_type</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">,</span>
+</span><span id="Opcs4-456"><a href="#Opcs4-456"><span class="linenos">456</span></a> <span class="p">)</span>
+</span><span id="Opcs4-457"><a href="#Opcs4-457"><span class="linenos">457</span></a> <span class="p">)</span>
+</span><span id="Opcs4-458"><a href="#Opcs4-458"><span class="linenos">458</span></a> <span class="p">),</span>
+</span><span id="Opcs4-459"><a href="#Opcs4-459"><span class="linenos">459</span></a> <span class="p">),</span>
+</span><span id="Opcs4-460"><a href="#Opcs4-460"><span class="linenos">460</span></a> <span class="p">]</span>
+</span></pre></div>
+
+
+ <div class="docstring"><p>Define checks as list of 3 tuple: (Message, Condition, Process)</p>
+
+<ul>
+<li>Message = The name of the condition (what is printed and logged)</li>
+<li>Condition = True if Passed, and False if Failed</li>
+<li>Process = Aims to resolve all issues that stop condition from passing (Do not change index!)</li>
+</ul>
+</div>
+
+
+ <div id="Opcs4.checks" class="classattr">
+ <div class="attr variable">
+ <span class="name">checks</span>
+
+
+ </div>
+ <a class="headerlink" href="#Opcs4.checks"></a>
+
+
+
+ </div>
+ <div class="inherited">
+ <h5>Inherited Members</h5>
+ <dl>
+ <div><dt><a href="#Proto">Proto</a></dt>
+ <dd id="Opcs4.name" class="variable"><a href="#Proto.name">name</a></dd>
+ <dd id="Opcs4.raise_exception" class="function"><a href="#Proto.raise_exception">raise_exception</a></dd>
+ <dd id="Opcs4.in_database" class="function"><a href="#Proto.in_database">in_database</a></dd>
+ <dd id="Opcs4.process" class="function"><a href="#Proto.process">process</a></dd>
+ <dd id="Opcs4.verify" class="function"><a href="#Proto.verify">verify</a></dd>
+
+ </div>
+ </dl>
+ </div>
+ </section>
+ <section id="Atc">
+ <input id="Atc-view-source" class="view-source-toggle-state" type="checkbox" aria-hidden="true" tabindex="-1">
+<div class="attr class">
+
+ <span class="def">class</span>
+ <span class="name">Atc</span><wbr>(<span class="base"><a href="#Proto">Proto</a></span>):
+
+ <label class="view-source-button" for="Atc-view-source"><span>View Source</span></label>
+
+ </div>
+ <a class="headerlink" href="#Atc"></a>
+ <div class="pdoc-code codehilite"><pre><span></span><span id="Atc-463"><a href="#Atc-463"><span class="linenos">463</span></a><span class="k">class</span><span class="w"> </span><span class="nc">Atc</span><span class="p">(</span><span class="n">Proto</span><span class="p">):</span>
+</span><span id="Atc-464"><a href="#Atc-464"><span class="linenos">464</span></a> <span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+</span><span id="Atc-465"><a href="#Atc-465"><span class="linenos">465</span></a> <span class="nb">super</span><span class="p">()</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="s2">"atc"</span><span class="p">,</span> <span class="n">trud_codes_path</span><span class="o">=</span><span class="kc">None</span><span class="p">)</span>
+</span><span id="Atc-466"><a href="#Atc-466"><span class="linenos">466</span></a> <span class="bp">self</span><span class="o">.</span><span class="n">checks</span> <span class="o">=</span> <span class="p">[</span>
+</span><span id="Atc-467"><a href="#Atc-467"><span class="linenos">467</span></a> <span class="p">(</span>
+</span><span id="Atc-468"><a href="#Atc-468"><span class="linenos">468</span></a> <span class="s2">"Not Empty"</span><span class="p">,</span>
+</span><span id="Atc-469"><a href="#Atc-469"><span class="linenos">469</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">:</span> <span class="n">pd</span><span class="o">.</span><span class="n">Series</span><span class="p">([</span><span class="nb">len</span><span class="p">(</span><span class="n">codes</span><span class="p">)</span> <span class="o">></span> <span class="mi">0</span><span class="p">]),</span>
+</span><span id="Atc-470"><a href="#Atc-470"><span class="linenos">470</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">,</span> <span class="n">codes_file</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">raise_exception</span><span class="p">(</span>
+</span><span id="Atc-471"><a href="#Atc-471"><span class="linenos">471</span></a> <span class="n">InvalidCodesException</span><span class="p">(</span>
+</span><span id="Atc-472"><a href="#Atc-472"><span class="linenos">472</span></a> <span class="n">CodesError</span><span class="p">(</span>
+</span><span id="Atc-473"><a href="#Atc-473"><span class="linenos">473</span></a> <span class="sa">f</span><span class="s2">"Code list is empty"</span><span class="p">,</span>
+</span><span id="Atc-474"><a href="#Atc-474"><span class="linenos">474</span></a> <span class="n">codes</span><span class="o">=</span><span class="n">codes</span><span class="p">,</span>
+</span><span id="Atc-475"><a href="#Atc-475"><span class="linenos">475</span></a> <span class="n">codes_file</span><span class="o">=</span><span class="n">codes_file</span><span class="p">,</span>
+</span><span id="Atc-476"><a href="#Atc-476"><span class="linenos">476</span></a> <span class="n">mask</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
+</span><span id="Atc-477"><a href="#Atc-477"><span class="linenos">477</span></a> <span class="n">code_type</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">,</span>
+</span><span id="Atc-478"><a href="#Atc-478"><span class="linenos">478</span></a> <span class="p">)</span>
+</span><span id="Atc-479"><a href="#Atc-479"><span class="linenos">479</span></a> <span class="p">)</span>
+</span><span id="Atc-480"><a href="#Atc-480"><span class="linenos">480</span></a> <span class="p">),</span>
+</span><span id="Atc-481"><a href="#Atc-481"><span class="linenos">481</span></a> <span class="p">),</span>
+</span><span id="Atc-482"><a href="#Atc-482"><span class="linenos">482</span></a> <span class="p">(</span>
+</span><span id="Atc-483"><a href="#Atc-483"><span class="linenos">483</span></a> <span class="s2">"Alphanumeric Capital"</span><span class="p">,</span>
+</span><span id="Atc-484"><a href="#Atc-484"><span class="linenos">484</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">:</span> <span class="n">codes</span><span class="o">.</span><span class="n">str</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="sa">r</span><span class="s2">"^[A-Z0-9]+$"</span><span class="p">),</span>
+</span><span id="Atc-485"><a href="#Atc-485"><span class="linenos">485</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">,</span> <span class="n">codes_file</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">raise_exception</span><span class="p">(</span>
+</span><span id="Atc-486"><a href="#Atc-486"><span class="linenos">486</span></a> <span class="n">InvalidCodesException</span><span class="p">(</span>
+</span><span id="Atc-487"><a href="#Atc-487"><span class="linenos">487</span></a> <span class="n">CodesError</span><span class="p">(</span>
+</span><span id="Atc-488"><a href="#Atc-488"><span class="linenos">488</span></a> <span class="sa">f</span><span class="s2">"QA Alphanumeric Capital"</span><span class="p">,</span>
+</span><span id="Atc-489"><a href="#Atc-489"><span class="linenos">489</span></a> <span class="n">codes</span><span class="o">=</span><span class="n">codes</span><span class="p">,</span>
+</span><span id="Atc-490"><a href="#Atc-490"><span class="linenos">490</span></a> <span class="n">codes_file</span><span class="o">=</span><span class="n">codes_file</span><span class="p">,</span>
+</span><span id="Atc-491"><a href="#Atc-491"><span class="linenos">491</span></a> <span class="n">mask</span><span class="o">=</span><span class="n">codes</span><span class="o">.</span><span class="n">str</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="sa">r</span><span class="s2">"^[A-Z0-9]+$"</span><span class="p">),</span>
+</span><span id="Atc-492"><a href="#Atc-492"><span class="linenos">492</span></a> <span class="n">code_type</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">,</span>
+</span><span id="Atc-493"><a href="#Atc-493"><span class="linenos">493</span></a> <span class="p">)</span>
+</span><span id="Atc-494"><a href="#Atc-494"><span class="linenos">494</span></a> <span class="p">)</span>
+</span><span id="Atc-495"><a href="#Atc-495"><span class="linenos">495</span></a> <span class="p">),</span>
+</span><span id="Atc-496"><a href="#Atc-496"><span class="linenos">496</span></a> <span class="p">),</span>
+</span><span id="Atc-497"><a href="#Atc-497"><span class="linenos">497</span></a> <span class="p">]</span>
+</span></pre></div>
+
+
+ <div class="docstring"><p>Define checks as list of 3 tuple: (Message, Condition, Process)</p>
+
+<ul>
+<li>Message = The name of the condition (what is printed and logged)</li>
+<li>Condition = True if Passed, and False if Failed</li>
+<li>Process = Aims to resolve all issues that stop condition from passing (Do not change index!)</li>
+</ul>
+</div>
+
+
+ <div id="Atc.checks" class="classattr">
+ <div class="attr variable">
+ <span class="name">checks</span>
+
+
+ </div>
+ <a class="headerlink" href="#Atc.checks"></a>
+
+
+
+ </div>
+ <div class="inherited">
+ <h5>Inherited Members</h5>
+ <dl>
+ <div><dt><a href="#Proto">Proto</a></dt>
+ <dd id="Atc.name" class="variable"><a href="#Proto.name">name</a></dd>
+ <dd id="Atc.raise_exception" class="function"><a href="#Proto.raise_exception">raise_exception</a></dd>
+ <dd id="Atc.in_database" class="function"><a href="#Proto.in_database">in_database</a></dd>
+ <dd id="Atc.process" class="function"><a href="#Proto.process">process</a></dd>
+ <dd id="Atc.verify" class="function"><a href="#Proto.verify">verify</a></dd>
+
+ </div>
+ </dl>
+ </div>
+ </section>
+ <section id="Med">
+ <input id="Med-view-source" class="view-source-toggle-state" type="checkbox" aria-hidden="true" tabindex="-1">
+<div class="attr class">
+
+ <span class="def">class</span>
+ <span class="name">Med</span><wbr>(<span class="base"><a href="#Proto">Proto</a></span>):
+
+ <label class="view-source-button" for="Med-view-source"><span>View Source</span></label>
+
+ </div>
+ <a class="headerlink" href="#Med"></a>
+ <div class="pdoc-code codehilite"><pre><span></span><span id="Med-500"><a href="#Med-500"><span class="linenos">500</span></a><span class="k">class</span><span class="w"> </span><span class="nc">Med</span><span class="p">(</span><span class="n">Proto</span><span class="p">):</span>
+</span><span id="Med-501"><a href="#Med-501"><span class="linenos">501</span></a> <span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+</span><span id="Med-502"><a href="#Med-502"><span class="linenos">502</span></a> <span class="nb">super</span><span class="p">()</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="s2">"med"</span><span class="p">,</span> <span class="n">trud_codes_path</span><span class="o">=</span><span class="kc">None</span><span class="p">)</span>
+</span><span id="Med-503"><a href="#Med-503"><span class="linenos">503</span></a> <span class="bp">self</span><span class="o">.</span><span class="n">checks</span> <span class="o">=</span> <span class="p">[</span>
+</span><span id="Med-504"><a href="#Med-504"><span class="linenos">504</span></a> <span class="p">(</span>
+</span><span id="Med-505"><a href="#Med-505"><span class="linenos">505</span></a> <span class="s2">"Not Empty"</span><span class="p">,</span>
+</span><span id="Med-506"><a href="#Med-506"><span class="linenos">506</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">:</span> <span class="n">pd</span><span class="o">.</span><span class="n">Series</span><span class="p">([</span><span class="nb">len</span><span class="p">(</span><span class="n">codes</span><span class="p">)</span> <span class="o">></span> <span class="mi">0</span><span class="p">]),</span>
+</span><span id="Med-507"><a href="#Med-507"><span class="linenos">507</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">,</span> <span class="n">codes_file</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">raise_exception</span><span class="p">(</span>
+</span><span id="Med-508"><a href="#Med-508"><span class="linenos">508</span></a> <span class="n">InvalidCodesException</span><span class="p">(</span>
+</span><span id="Med-509"><a href="#Med-509"><span class="linenos">509</span></a> <span class="n">CodesError</span><span class="p">(</span>
+</span><span id="Med-510"><a href="#Med-510"><span class="linenos">510</span></a> <span class="sa">f</span><span class="s2">"Code list is empty"</span><span class="p">,</span>
+</span><span id="Med-511"><a href="#Med-511"><span class="linenos">511</span></a> <span class="n">codes</span><span class="o">=</span><span class="n">codes</span><span class="p">,</span>
+</span><span id="Med-512"><a href="#Med-512"><span class="linenos">512</span></a> <span class="n">codes_file</span><span class="o">=</span><span class="n">codes_file</span><span class="p">,</span>
+</span><span id="Med-513"><a href="#Med-513"><span class="linenos">513</span></a> <span class="n">mask</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
+</span><span id="Med-514"><a href="#Med-514"><span class="linenos">514</span></a> <span class="n">code_type</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">,</span>
+</span><span id="Med-515"><a href="#Med-515"><span class="linenos">515</span></a> <span class="p">)</span>
+</span><span id="Med-516"><a href="#Med-516"><span class="linenos">516</span></a> <span class="p">)</span>
+</span><span id="Med-517"><a href="#Med-517"><span class="linenos">517</span></a> <span class="p">),</span>
+</span><span id="Med-518"><a href="#Med-518"><span class="linenos">518</span></a> <span class="p">)</span>
+</span><span id="Med-519"><a href="#Med-519"><span class="linenos">519</span></a> <span class="p">]</span>
+</span></pre></div>
+
+
+ <div class="docstring"><p>Define checks as list of 3 tuple: (Message, Condition, Process)</p>
+
+<ul>
+<li>Message = The name of the condition (what is printed and logged)</li>
+<li>Condition = True if Passed, and False if Failed</li>
+<li>Process = Aims to resolve all issues that stop condition from passing (Do not change index!)</li>
+</ul>
+</div>
+
+
+ <div id="Med.checks" class="classattr">
+ <div class="attr variable">
+ <span class="name">checks</span>
+
+
+ </div>
+ <a class="headerlink" href="#Med.checks"></a>
+
+
+
+ </div>
+ <div class="inherited">
+ <h5>Inherited Members</h5>
+ <dl>
+ <div><dt><a href="#Proto">Proto</a></dt>
+ <dd id="Med.name" class="variable"><a href="#Proto.name">name</a></dd>
+ <dd id="Med.raise_exception" class="function"><a href="#Proto.raise_exception">raise_exception</a></dd>
+ <dd id="Med.in_database" class="function"><a href="#Proto.in_database">in_database</a></dd>
+ <dd id="Med.process" class="function"><a href="#Proto.process">process</a></dd>
+ <dd id="Med.verify" class="function"><a href="#Proto.verify">verify</a></dd>
+
+ </div>
+ </dl>
+ </div>
+ </section>
+ <section id="Cprd">
+ <input id="Cprd-view-source" class="view-source-toggle-state" type="checkbox" aria-hidden="true" tabindex="-1">
+<div class="attr class">
+
+ <span class="def">class</span>
+ <span class="name">Cprd</span><wbr>(<span class="base"><a href="#Proto">Proto</a></span>):
+
+ <label class="view-source-button" for="Cprd-view-source"><span>View Source</span></label>
+
+ </div>
+ <a class="headerlink" href="#Cprd"></a>
+ <div class="pdoc-code codehilite"><pre><span></span><span id="Cprd-522"><a href="#Cprd-522"><span class="linenos">522</span></a><span class="k">class</span><span class="w"> </span><span class="nc">Cprd</span><span class="p">(</span><span class="n">Proto</span><span class="p">):</span>
+</span><span id="Cprd-523"><a href="#Cprd-523"><span class="linenos">523</span></a> <span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+</span><span id="Cprd-524"><a href="#Cprd-524"><span class="linenos">524</span></a> <span class="nb">super</span><span class="p">()</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="s2">"cprd"</span><span class="p">,</span> <span class="n">trud_codes_path</span><span class="o">=</span><span class="kc">None</span><span class="p">)</span>
+</span><span id="Cprd-525"><a href="#Cprd-525"><span class="linenos">525</span></a> <span class="bp">self</span><span class="o">.</span><span class="n">checks</span> <span class="o">=</span> <span class="p">[</span>
+</span><span id="Cprd-526"><a href="#Cprd-526"><span class="linenos">526</span></a> <span class="p">(</span>
+</span><span id="Cprd-527"><a href="#Cprd-527"><span class="linenos">527</span></a> <span class="s2">"Not Empty"</span><span class="p">,</span>
+</span><span id="Cprd-528"><a href="#Cprd-528"><span class="linenos">528</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">:</span> <span class="n">pd</span><span class="o">.</span><span class="n">Series</span><span class="p">([</span><span class="nb">len</span><span class="p">(</span><span class="n">codes</span><span class="p">)</span> <span class="o">></span> <span class="mi">0</span><span class="p">]),</span>
+</span><span id="Cprd-529"><a href="#Cprd-529"><span class="linenos">529</span></a> <span class="k">lambda</span> <span class="n">codes</span><span class="p">,</span> <span class="n">codes_file</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">raise_exception</span><span class="p">(</span>
+</span><span id="Cprd-530"><a href="#Cprd-530"><span class="linenos">530</span></a> <span class="n">InvalidCodesException</span><span class="p">(</span>
+</span><span id="Cprd-531"><a href="#Cprd-531"><span class="linenos">531</span></a> <span class="n">CodesError</span><span class="p">(</span>
+</span><span id="Cprd-532"><a href="#Cprd-532"><span class="linenos">532</span></a> <span class="sa">f</span><span class="s2">"Code list is empty"</span><span class="p">,</span>
+</span><span id="Cprd-533"><a href="#Cprd-533"><span class="linenos">533</span></a> <span class="n">codes</span><span class="o">=</span><span class="n">codes</span><span class="p">,</span>
+</span><span id="Cprd-534"><a href="#Cprd-534"><span class="linenos">534</span></a> <span class="n">codes_file</span><span class="o">=</span><span class="n">codes_file</span><span class="p">,</span>
+</span><span id="Cprd-535"><a href="#Cprd-535"><span class="linenos">535</span></a> <span class="n">mask</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
+</span><span id="Cprd-536"><a href="#Cprd-536"><span class="linenos">536</span></a> <span class="n">code_type</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">name</span><span class="p">,</span>
+</span><span id="Cprd-537"><a href="#Cprd-537"><span class="linenos">537</span></a> <span class="p">)</span>
+</span><span id="Cprd-538"><a href="#Cprd-538"><span class="linenos">538</span></a> <span class="p">)</span>
+</span><span id="Cprd-539"><a href="#Cprd-539"><span class="linenos">539</span></a> <span class="p">),</span>
+</span><span id="Cprd-540"><a href="#Cprd-540"><span class="linenos">540</span></a> <span class="p">)</span>
+</span><span id="Cprd-541"><a href="#Cprd-541"><span class="linenos">541</span></a> <span class="p">]</span>
+</span></pre></div>
+
+
+ <div class="docstring"><p>Define checks as list of 3 tuple: (Message, Condition, Process)</p>
+
+<ul>
+<li>Message = The name of the condition (what is printed and logged)</li>
+<li>Condition = True if Passed, and False if Failed</li>
+<li>Process = Aims to resolve all issues that stop condition from passing (Do not change index!)</li>
+</ul>
+</div>
+
+
+ <div id="Cprd.checks" class="classattr">
+ <div class="attr variable">
+ <span class="name">checks</span>
+
+
+ </div>
+ <a class="headerlink" href="#Cprd.checks"></a>
+
+
+
+ </div>
+ <div class="inherited">
+ <h5>Inherited Members</h5>
+ <dl>
+ <div><dt><a href="#Proto">Proto</a></dt>
+ <dd id="Cprd.name" class="variable"><a href="#Proto.name">name</a></dd>
+ <dd id="Cprd.raise_exception" class="function"><a href="#Proto.raise_exception">raise_exception</a></dd>
+ <dd id="Cprd.in_database" class="function"><a href="#Proto.in_database">in_database</a></dd>
+ <dd id="Cprd.process" class="function"><a href="#Proto.process">process</a></dd>
+ <dd id="Cprd.verify" class="function"><a href="#Proto.verify">verify</a></dd>
+
+ </div>
+ </dl>
+ </div>
+ </section>
+ <section id="CodeTypeParser">
+ <input id="CodeTypeParser-view-source" class="view-source-toggle-state" type="checkbox" aria-hidden="true" tabindex="-1">
+<div class="attr class">
+
+ <span class="def">class</span>
+ <span class="name">CodeTypeParser</span>:
+
+ <label class="view-source-button" for="CodeTypeParser-view-source"><span>View Source</span></label>
+
+ </div>
+ <a class="headerlink" href="#CodeTypeParser"></a>
+ <div class="pdoc-code codehilite"><pre><span></span><span id="CodeTypeParser-544"><a href="#CodeTypeParser-544"><span class="linenos">544</span></a><span class="k">class</span><span class="w"> </span><span class="nc">CodeTypeParser</span><span class="p">:</span>
+</span><span id="CodeTypeParser-545"><a href="#CodeTypeParser-545"><span class="linenos">545</span></a><span class="w"> </span><span class="sd">"""A class used in InvalidCodesException to report an error if a code parser check fails"""</span>
+</span><span id="CodeTypeParser-546"><a href="#CodeTypeParser-546"><span class="linenos">546</span></a>
+</span><span id="CodeTypeParser-547"><a href="#CodeTypeParser-547"><span class="linenos">547</span></a> <span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">trud_processed_dir</span><span class="p">:</span> <span class="n">Path</span> <span class="o">=</span> <span class="n">trud</span><span class="o">.</span><span class="n">PROCESSED_PATH</span><span class="p">):</span>
+</span><span id="CodeTypeParser-548"><a href="#CodeTypeParser-548"><span class="linenos">548</span></a>
+</span><span id="CodeTypeParser-549"><a href="#CodeTypeParser-549"><span class="linenos">549</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="n">trud_processed_dir</span><span class="o">.</span><span class="n">exists</span><span class="p">()</span> <span class="ow">or</span> <span class="ow">not</span> <span class="n">trud_processed_dir</span><span class="o">.</span><span class="n">is_dir</span><span class="p">():</span>
+</span><span id="CodeTypeParser-550"><a href="#CodeTypeParser-550"><span class="linenos">550</span></a> <span class="k">raise</span> <span class="ne">FileNotFoundError</span><span class="p">(</span>
+</span><span id="CodeTypeParser-551"><a href="#CodeTypeParser-551"><span class="linenos">551</span></a> <span class="sa">f</span><span class="s2">"Cannot initialise parsers as the TRUD processed directory </span><span class="si">{</span><span class="n">trud_processed_dir</span><span class="si">}</span><span class="s2"> does not exist, please check that TRUD has been installed: acmc trud install"</span>
+</span><span id="CodeTypeParser-552"><a href="#CodeTypeParser-552"><span class="linenos">552</span></a> <span class="p">)</span>
+</span><span id="CodeTypeParser-553"><a href="#CodeTypeParser-553"><span class="linenos">553</span></a>
+</span><span id="CodeTypeParser-554"><a href="#CodeTypeParser-554"><span class="linenos">554</span></a> <span class="bp">self</span><span class="o">.</span><span class="n">code_types</span> <span class="o">=</span> <span class="p">{</span>
+</span><span id="CodeTypeParser-555"><a href="#CodeTypeParser-555"><span class="linenos">555</span></a> <span class="s2">"read2"</span><span class="p">:</span> <span class="n">Read2</span><span class="p">(),</span>
+</span><span id="CodeTypeParser-556"><a href="#CodeTypeParser-556"><span class="linenos">556</span></a> <span class="s2">"read3"</span><span class="p">:</span> <span class="n">Read3</span><span class="p">(),</span>
+</span><span id="CodeTypeParser-557"><a href="#CodeTypeParser-557"><span class="linenos">557</span></a> <span class="s2">"icd10"</span><span class="p">:</span> <span class="n">Icd10</span><span class="p">(),</span>
+</span><span id="CodeTypeParser-558"><a href="#CodeTypeParser-558"><span class="linenos">558</span></a> <span class="s2">"snomed"</span><span class="p">:</span> <span class="n">Snomed</span><span class="p">(),</span>
+</span><span id="CodeTypeParser-559"><a href="#CodeTypeParser-559"><span class="linenos">559</span></a> <span class="s2">"opcs4"</span><span class="p">:</span> <span class="n">Opcs4</span><span class="p">(),</span>
+</span><span id="CodeTypeParser-560"><a href="#CodeTypeParser-560"><span class="linenos">560</span></a> <span class="s2">"atc"</span><span class="p">:</span> <span class="n">Atc</span><span class="p">(),</span>
+</span><span id="CodeTypeParser-561"><a href="#CodeTypeParser-561"><span class="linenos">561</span></a> <span class="s2">"med"</span><span class="p">:</span> <span class="n">Med</span><span class="p">(),</span>
+</span><span id="CodeTypeParser-562"><a href="#CodeTypeParser-562"><span class="linenos">562</span></a> <span class="s2">"cprd"</span><span class="p">:</span> <span class="n">Cprd</span><span class="p">(),</span>
+</span><span id="CodeTypeParser-563"><a href="#CodeTypeParser-563"><span class="linenos">563</span></a> <span class="p">}</span>
+</span></pre></div>
+
+
+ <div class="docstring"><p>A class used in InvalidCodesException to report an error if a code parser check fails</p>
+</div>
+
+
+ <div id="CodeTypeParser.__init__" class="classattr">
+ <input id="CodeTypeParser.__init__-view-source" class="view-source-toggle-state" type="checkbox" aria-hidden="true" tabindex="-1">
+<div class="attr function">
+
+ <span class="name">CodeTypeParser</span><span class="signature pdoc-code condensed">(<span class="param"><span class="n">trud_processed_dir</span><span class="p">:</span> <span class="n">pathlib</span><span class="o">.</span><span class="n">Path</span> <span class="o">=</span> <span class="n">PosixPath</span><span class="p">(</span><span class="s1">'vocab/trud/processed'</span><span class="p">)</span></span>)</span>
+
+ <label class="view-source-button" for="CodeTypeParser.__init__-view-source"><span>View Source</span></label>
+
+ </div>
+ <a class="headerlink" href="#CodeTypeParser.__init__"></a>
+ <div class="pdoc-code codehilite"><pre><span></span><span id="CodeTypeParser.__init__-547"><a href="#CodeTypeParser.__init__-547"><span class="linenos">547</span></a> <span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">trud_processed_dir</span><span class="p">:</span> <span class="n">Path</span> <span class="o">=</span> <span class="n">trud</span><span class="o">.</span><span class="n">PROCESSED_PATH</span><span class="p">):</span>
+</span><span id="CodeTypeParser.__init__-548"><a href="#CodeTypeParser.__init__-548"><span class="linenos">548</span></a>
+</span><span id="CodeTypeParser.__init__-549"><a href="#CodeTypeParser.__init__-549"><span class="linenos">549</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="n">trud_processed_dir</span><span class="o">.</span><span class="n">exists</span><span class="p">()</span> <span class="ow">or</span> <span class="ow">not</span> <span class="n">trud_processed_dir</span><span class="o">.</span><span class="n">is_dir</span><span class="p">():</span>
+</span><span id="CodeTypeParser.__init__-550"><a href="#CodeTypeParser.__init__-550"><span class="linenos">550</span></a> <span class="k">raise</span> <span class="ne">FileNotFoundError</span><span class="p">(</span>
+</span><span id="CodeTypeParser.__init__-551"><a href="#CodeTypeParser.__init__-551"><span class="linenos">551</span></a> <span class="sa">f</span><span class="s2">"Cannot initialise parsers as the TRUD processed directory </span><span class="si">{</span><span class="n">trud_processed_dir</span><span class="si">}</span><span class="s2"> does not exist, please check that TRUD has been installed: acmc trud install"</span>
+</span><span id="CodeTypeParser.__init__-552"><a href="#CodeTypeParser.__init__-552"><span class="linenos">552</span></a> <span class="p">)</span>
+</span><span id="CodeTypeParser.__init__-553"><a href="#CodeTypeParser.__init__-553"><span class="linenos">553</span></a>
+</span><span id="CodeTypeParser.__init__-554"><a href="#CodeTypeParser.__init__-554"><span class="linenos">554</span></a> <span class="bp">self</span><span class="o">.</span><span class="n">code_types</span> <span class="o">=</span> <span class="p">{</span>
+</span><span id="CodeTypeParser.__init__-555"><a href="#CodeTypeParser.__init__-555"><span class="linenos">555</span></a> <span class="s2">"read2"</span><span class="p">:</span> <span class="n">Read2</span><span class="p">(),</span>
+</span><span id="CodeTypeParser.__init__-556"><a href="#CodeTypeParser.__init__-556"><span class="linenos">556</span></a> <span class="s2">"read3"</span><span class="p">:</span> <span class="n">Read3</span><span class="p">(),</span>
+</span><span id="CodeTypeParser.__init__-557"><a href="#CodeTypeParser.__init__-557"><span class="linenos">557</span></a> <span class="s2">"icd10"</span><span class="p">:</span> <span class="n">Icd10</span><span class="p">(),</span>
+</span><span id="CodeTypeParser.__init__-558"><a href="#CodeTypeParser.__init__-558"><span class="linenos">558</span></a> <span class="s2">"snomed"</span><span class="p">:</span> <span class="n">Snomed</span><span class="p">(),</span>
+</span><span id="CodeTypeParser.__init__-559"><a href="#CodeTypeParser.__init__-559"><span class="linenos">559</span></a> <span class="s2">"opcs4"</span><span class="p">:</span> <span class="n">Opcs4</span><span class="p">(),</span>
+</span><span id="CodeTypeParser.__init__-560"><a href="#CodeTypeParser.__init__-560"><span class="linenos">560</span></a> <span class="s2">"atc"</span><span class="p">:</span> <span class="n">Atc</span><span class="p">(),</span>
+</span><span id="CodeTypeParser.__init__-561"><a href="#CodeTypeParser.__init__-561"><span class="linenos">561</span></a> <span class="s2">"med"</span><span class="p">:</span> <span class="n">Med</span><span class="p">(),</span>
+</span><span id="CodeTypeParser.__init__-562"><a href="#CodeTypeParser.__init__-562"><span class="linenos">562</span></a> <span class="s2">"cprd"</span><span class="p">:</span> <span class="n">Cprd</span><span class="p">(),</span>
+</span><span id="CodeTypeParser.__init__-563"><a href="#CodeTypeParser.__init__-563"><span class="linenos">563</span></a> <span class="p">}</span>
+</span></pre></div>
+
+
+
+
+ </div>
+ <div id="CodeTypeParser.code_types" class="classattr">
+ <div class="attr variable">
+ <span class="name">code_types</span>
+
+
+ </div>
+ <a class="headerlink" href="#CodeTypeParser.code_types"></a>
+
+
+
+ </div>
+ </section>
+ </main>
+<script>
+ function escapeHTML(html) {
+ return document.createElement('div').appendChild(document.createTextNode(html)).parentNode.innerHTML;
+ }
+
+ const originalContent = document.querySelector("main.pdoc");
+ let currentContent = originalContent;
+
+ function setContent(innerHTML) {
+ let elem;
+ if (innerHTML) {
+ elem = document.createElement("main");
+ elem.classList.add("pdoc");
+ elem.innerHTML = innerHTML;
+ } else {
+ elem = originalContent;
+ }
+ if (currentContent !== elem) {
+ currentContent.replaceWith(elem);
+ currentContent = elem;
+ }
+ }
+
+ function getSearchTerm() {
+ return (new URL(window.location)).searchParams.get("search");
+ }
+
+ const searchBox = document.querySelector(".pdoc input[type=search]");
+ searchBox.addEventListener("input", function () {
+ let url = new URL(window.location);
+ if (searchBox.value.trim()) {
+ url.hash = "";
+ url.searchParams.set("search", searchBox.value);
+ } else {
+ url.searchParams.delete("search");
+ }
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diff --git a/docs/api/acmc/phen.html b/docs/api/acmc/phen.html
new file mode 100644
index 0000000000000000000000000000000000000000..ac8f1478fcb3bc7fb23b0e82ca2f3115e8ffa536
--- /dev/null
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+ <style>/*! custom.css */</style></head>
+<body>
+ <nav class="pdoc">
+ <label id="navtoggle" for="togglestate" class="pdoc-button"><svg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 30 30'><path stroke-linecap='round' stroke="currentColor" stroke-miterlimit='10' stroke-width='2' d='M4 7h22M4 15h22M4 23h22'/></svg></label>
+ <input id="togglestate" type="checkbox" aria-hidden="true" tabindex="-1">
+ <div> <a class="pdoc-button module-list-button" href="../acmc.html">
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+</svg> acmc</a>
+
+
+ <input type="search" placeholder="Search..." role="searchbox" aria-label="search"
+ pattern=".+" required>
+
+
+
+ <h2>API Documentation</h2>
+ <ul class="memberlist">
+ <li>
+ <a class="variable" href="#logger">logger</a>
+ </li>
+ <li>
+ <a class="variable" href="#PHEN_DIR">PHEN_DIR</a>
+ </li>
+ <li>
+ <a class="variable" href="#DEFAULT_PHEN_PATH">DEFAULT_PHEN_PATH</a>
+ </li>
+ <li>
+ <a class="variable" href="#CONCEPTS_DIR">CONCEPTS_DIR</a>
+ </li>
+ <li>
+ <a class="variable" href="#MAP_DIR">MAP_DIR</a>
+ </li>
+ <li>
+ <a class="variable" href="#CONCEPT_SET_DIR">CONCEPT_SET_DIR</a>
+ </li>
+ <li>
+ <a class="variable" href="#CSV_PATH">CSV_PATH</a>
+ </li>
+ <li>
+ <a class="variable" href="#OMOP_PATH">OMOP_PATH</a>
+ </li>
+ <li>
+ <a class="variable" href="#DEFAULT_PHEN_DIR_LIST">DEFAULT_PHEN_DIR_LIST</a>
+ </li>
+ <li>
+ <a class="variable" href="#CONFIG_FILE">CONFIG_FILE</a>
+ </li>
+ <li>
+ <a class="variable" href="#VOCAB_VERSION_FILE">VOCAB_VERSION_FILE</a>
+ </li>
+ <li>
+ <a class="variable" href="#SEMANTIC_VERSION_TYPES">SEMANTIC_VERSION_TYPES</a>
+ </li>
+ <li>
+ <a class="variable" href="#DEFAULT_VERSION_INC">DEFAULT_VERSION_INC</a>
+ </li>
+ <li>
+ <a class="variable" href="#DEFAULT_GIT_BRANCH">DEFAULT_GIT_BRANCH</a>
+ </li>
+ <li>
+ <a class="variable" href="#SPLIT_COL_ACTION">SPLIT_COL_ACTION</a>
+ </li>
+ <li>
+ <a class="variable" href="#CODES_COL_ACTION">CODES_COL_ACTION</a>
+ </li>
+ <li>
+ <a class="variable" href="#DIVIDE_COL_ACTION">DIVIDE_COL_ACTION</a>
+ </li>
+ <li>
+ <a class="variable" href="#COL_ACTIONS">COL_ACTIONS</a>
+ </li>
+ <li>
+ <a class="variable" href="#CODE_FILE_TYPES">CODE_FILE_TYPES</a>
+ </li>
+ <li>
+ <a class="variable" href="#SOURCE_COL_SUFFIX">SOURCE_COL_SUFFIX</a>
+ </li>
+ <li>
+ <a class="variable" href="#TARGET_COL_SUFFIX">TARGET_COL_SUFFIX</a>
+ </li>
+ <li>
+ <a class="variable" href="#CONFIG_SCHEMA">CONFIG_SCHEMA</a>
+ </li>
+ <li>
+ <a class="class" href="#PhenValidationException">PhenValidationException</a>
+ <ul class="memberlist">
+ <li>
+ <a class="function" href="#PhenValidationException.__init__">PhenValidationException</a>
+ </li>
+ <li>
+ <a class="variable" href="#PhenValidationException.validation_errors">validation_errors</a>
+ </li>
+ </ul>
+
+ </li>
+ <li>
+ <a class="function" href="#construct_git_url">construct_git_url</a>
+ </li>
+ <li>
+ <a class="function" href="#create_empty_git_dir">create_empty_git_dir</a>
+ </li>
+ <li>
+ <a class="function" href="#check_delete_dir">check_delete_dir</a>
+ </li>
+ <li>
+ <a class="function" href="#fork">fork</a>
+ </li>
+ <li>
+ <a class="function" href="#init">init</a>
+ </li>
+ <li>
+ <a class="function" href="#validate">validate</a>
+ </li>
+ <li>
+ <a class="function" href="#read_table_file">read_table_file</a>
+ </li>
+ <li>
+ <a class="function" href="#process_actions">process_actions</a>
+ </li>
+ <li>
+ <a class="function" href="#preprocess_source_concepts">preprocess_source_concepts</a>
+ </li>
+ <li>
+ <a class="function" href="#get_code_type_from_col_name">get_code_type_from_col_name</a>
+ </li>
+ <li>
+ <a class="function" href="#translate_codes">translate_codes</a>
+ </li>
+ <li>
+ <a class="function" href="#sql_row_exist">sql_row_exist</a>
+ </li>
+ <li>
+ <a class="function" href="#write_code_errors">write_code_errors</a>
+ </li>
+ <li>
+ <a class="function" href="#write_vocab_version">write_vocab_version</a>
+ </li>
+ <li>
+ <a class="function" href="#map">map</a>
+ </li>
+ <li>
+ <a class="function" href="#map_target_code_type">map_target_code_type</a>
+ </li>
+ <li>
+ <a class="function" href="#generate_version_tag">generate_version_tag</a>
+ </li>
+ <li>
+ <a class="function" href="#publish">publish</a>
+ </li>
+ <li>
+ <a class="function" href="#export">export</a>
+ </li>
+ <li>
+ <a class="function" href="#copy">copy</a>
+ </li>
+ <li>
+ <a class="function" href="#extract_concepts">extract_concepts</a>
+ </li>
+ <li>
+ <a class="function" href="#extract_clean_deepdiff_keys">extract_clean_deepdiff_keys</a>
+ </li>
+ <li>
+ <a class="function" href="#diff_config">diff_config</a>
+ </li>
+ <li>
+ <a class="function" href="#diff_map_files">diff_map_files</a>
+ </li>
+ <li>
+ <a class="function" href="#diff_phen">diff_phen</a>
+ </li>
+ <li>
+ <a class="function" href="#diff">diff</a>
+ </li>
+ </ul>
+
+
+
+ <a class="attribution" title="pdoc: Python API documentation generator" href="https://pdoc.dev" target="_blank">
+ built with <span class="visually-hidden">pdoc</span><img
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+<a href="./../acmc.html">acmc</a><wbr>.phen </h1>
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+
+ <div class="pdoc-code codehilite"><pre><span></span><span id="L-1"><a href="#L-1"><span class="linenos"> 1</span></a><span class="kn">import</span><span class="w"> </span><span class="nn">argparse</span>
+</span><span id="L-2"><a href="#L-2"><span class="linenos"> 2</span></a><span class="kn">import</span><span class="w"> </span><span class="nn">pandas</span><span class="w"> </span><span class="k">as</span><span class="w"> </span><span class="nn">pd</span>
+</span><span id="L-3"><a href="#L-3"><span class="linenos"> 3</span></a><span class="kn">import</span><span class="w"> </span><span class="nn">numpy</span><span class="w"> </span><span class="k">as</span><span class="w"> </span><span class="nn">np</span>
+</span><span id="L-4"><a href="#L-4"><span class="linenos"> 4</span></a><span class="kn">import</span><span class="w"> </span><span class="nn">json</span>
+</span><span id="L-5"><a href="#L-5"><span class="linenos"> 5</span></a><span class="kn">import</span><span class="w"> </span><span class="nn">os</span>
+</span><span id="L-6"><a href="#L-6"><span class="linenos"> 6</span></a><span class="kn">import</span><span class="w"> </span><span class="nn">sqlite3</span>
+</span><span id="L-7"><a href="#L-7"><span class="linenos"> 7</span></a><span class="kn">import</span><span class="w"> </span><span class="nn">sys</span>
+</span><span id="L-8"><a href="#L-8"><span class="linenos"> 8</span></a><span class="kn">import</span><span class="w"> </span><span class="nn">shutil</span>
+</span><span id="L-9"><a href="#L-9"><span class="linenos"> 9</span></a><span class="kn">import</span><span class="w"> </span><span class="nn">time</span>
+</span><span id="L-10"><a href="#L-10"><span class="linenos"> 10</span></a><span class="kn">import</span><span class="w"> </span><span class="nn">git</span>
+</span><span id="L-11"><a href="#L-11"><span class="linenos"> 11</span></a><span class="kn">import</span><span class="w"> </span><span class="nn">re</span>
+</span><span id="L-12"><a href="#L-12"><span class="linenos"> 12</span></a><span class="kn">import</span><span class="w"> </span><span class="nn">logging</span>
+</span><span id="L-13"><a href="#L-13"><span class="linenos"> 13</span></a><span class="kn">import</span><span class="w"> </span><span class="nn">requests</span>
+</span><span id="L-14"><a href="#L-14"><span class="linenos"> 14</span></a><span class="kn">import</span><span class="w"> </span><span class="nn">yaml</span>
+</span><span id="L-15"><a href="#L-15"><span class="linenos"> 15</span></a><span class="kn">import</span><span class="w"> </span><span class="nn">semver</span>
+</span><span id="L-16"><a href="#L-16"><span class="linenos"> 16</span></a><span class="kn">from</span><span class="w"> </span><span class="nn">git</span><span class="w"> </span><span class="kn">import</span> <span class="n">Repo</span>
+</span><span id="L-17"><a href="#L-17"><span class="linenos"> 17</span></a><span class="kn">from</span><span class="w"> </span><span class="nn">cerberus</span><span class="w"> </span><span class="kn">import</span> <span class="n">Validator</span>
+</span><span id="L-18"><a href="#L-18"><span class="linenos"> 18</span></a><span class="kn">from</span><span class="w"> </span><span class="nn">deepdiff</span><span class="w"> </span><span class="kn">import</span> <span class="n">DeepDiff</span>
+</span><span id="L-19"><a href="#L-19"><span class="linenos"> 19</span></a><span class="kn">from</span><span class="w"> </span><span class="nn">pathlib</span><span class="w"> </span><span class="kn">import</span> <span class="n">Path</span>
+</span><span id="L-20"><a href="#L-20"><span class="linenos"> 20</span></a><span class="kn">from</span><span class="w"> </span><span class="nn">urllib.parse</span><span class="w"> </span><span class="kn">import</span> <span class="n">urlparse</span><span class="p">,</span> <span class="n">urlunparse</span>
+</span><span id="L-21"><a href="#L-21"><span class="linenos"> 21</span></a><span class="kn">from</span><span class="w"> </span><span class="nn">typing</span><span class="w"> </span><span class="kn">import</span> <span class="n">Tuple</span><span class="p">,</span> <span class="n">Set</span><span class="p">,</span> <span class="n">Any</span>
+</span><span id="L-22"><a href="#L-22"><span class="linenos"> 22</span></a>
+</span><span id="L-23"><a href="#L-23"><span class="linenos"> 23</span></a><span class="kn">import</span><span class="w"> </span><span class="nn">acmc</span>
+</span><span id="L-24"><a href="#L-24"><span class="linenos"> 24</span></a><span class="kn">from</span><span class="w"> </span><span class="nn">acmc</span><span class="w"> </span><span class="kn">import</span> <span class="n">trud</span><span class="p">,</span> <span class="n">omop</span><span class="p">,</span> <span class="n">parse</span><span class="p">,</span> <span class="n">util</span>
+</span><span id="L-25"><a href="#L-25"><span class="linenos"> 25</span></a>
+</span><span id="L-26"><a href="#L-26"><span class="linenos"> 26</span></a><span class="c1"># setup logging</span>
+</span><span id="L-27"><a href="#L-27"><span class="linenos"> 27</span></a><span class="kn">import</span><span class="w"> </span><span class="nn">acmc.logging_config</span><span class="w"> </span><span class="k">as</span><span class="w"> </span><span class="nn">lc</span>
+</span><span id="L-28"><a href="#L-28"><span class="linenos"> 28</span></a>
+</span><span id="L-29"><a href="#L-29"><span class="linenos"> 29</span></a><span class="n">logger</span> <span class="o">=</span> <span class="n">lc</span><span class="o">.</span><span class="n">setup_logger</span><span class="p">()</span>
+</span><span id="L-30"><a href="#L-30"><span class="linenos"> 30</span></a>
+</span><span id="L-31"><a href="#L-31"><span class="linenos"> 31</span></a><span class="n">pd</span><span class="o">.</span><span class="n">set_option</span><span class="p">(</span><span class="s2">"mode.chained_assignment"</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span>
+</span><span id="L-32"><a href="#L-32"><span class="linenos"> 32</span></a>
+</span><span id="L-33"><a href="#L-33"><span class="linenos"> 33</span></a><span class="n">PHEN_DIR</span> <span class="o">=</span> <span class="s2">"phen"</span>
+</span><span id="L-34"><a href="#L-34"><span class="linenos"> 34</span></a><span class="n">DEFAULT_PHEN_PATH</span> <span class="o">=</span> <span class="n">Path</span><span class="p">(</span><span class="s2">"./workspace"</span><span class="p">)</span> <span class="o">/</span> <span class="n">PHEN_DIR</span>
+</span><span id="L-35"><a href="#L-35"><span class="linenos"> 35</span></a>
+</span><span id="L-36"><a href="#L-36"><span class="linenos"> 36</span></a><span class="n">CONCEPTS_DIR</span> <span class="o">=</span> <span class="s2">"concepts"</span>
+</span><span id="L-37"><a href="#L-37"><span class="linenos"> 37</span></a><span class="n">MAP_DIR</span> <span class="o">=</span> <span class="s2">"map"</span>
+</span><span id="L-38"><a href="#L-38"><span class="linenos"> 38</span></a><span class="n">CONCEPT_SET_DIR</span> <span class="o">=</span> <span class="s2">"concept-sets"</span>
+</span><span id="L-39"><a href="#L-39"><span class="linenos"> 39</span></a><span class="n">CSV_PATH</span> <span class="o">=</span> <span class="n">Path</span><span class="p">(</span><span class="n">CONCEPT_SET_DIR</span><span class="p">)</span> <span class="o">/</span> <span class="s2">"csv"</span>
+</span><span id="L-40"><a href="#L-40"><span class="linenos"> 40</span></a><span class="n">OMOP_PATH</span> <span class="o">=</span> <span class="n">Path</span><span class="p">(</span><span class="n">CONCEPT_SET_DIR</span><span class="p">)</span> <span class="o">/</span> <span class="s2">"omop"</span>
+</span><span id="L-41"><a href="#L-41"><span class="linenos"> 41</span></a><span class="n">DEFAULT_PHEN_DIR_LIST</span> <span class="o">=</span> <span class="p">[</span><span class="n">CONCEPTS_DIR</span><span class="p">,</span> <span class="n">MAP_DIR</span><span class="p">,</span> <span class="n">CONCEPT_SET_DIR</span><span class="p">]</span>
+</span><span id="L-42"><a href="#L-42"><span class="linenos"> 42</span></a><span class="n">CONFIG_FILE</span> <span class="o">=</span> <span class="s2">"config.yaml"</span>
+</span><span id="L-43"><a href="#L-43"><span class="linenos"> 43</span></a><span class="n">VOCAB_VERSION_FILE</span> <span class="o">=</span> <span class="s2">"vocab_version.yaml"</span>
+</span><span id="L-44"><a href="#L-44"><span class="linenos"> 44</span></a><span class="n">SEMANTIC_VERSION_TYPES</span> <span class="o">=</span> <span class="p">[</span><span class="s2">"major"</span><span class="p">,</span> <span class="s2">"minor"</span><span class="p">,</span> <span class="s2">"patch"</span><span class="p">]</span>
+</span><span id="L-45"><a href="#L-45"><span class="linenos"> 45</span></a><span class="n">DEFAULT_VERSION_INC</span> <span class="o">=</span> <span class="s2">"patch"</span>
+</span><span id="L-46"><a href="#L-46"><span class="linenos"> 46</span></a>
+</span><span id="L-47"><a href="#L-47"><span class="linenos"> 47</span></a><span class="n">DEFAULT_GIT_BRANCH</span> <span class="o">=</span> <span class="s2">"main"</span>
+</span><span id="L-48"><a href="#L-48"><span class="linenos"> 48</span></a>
+</span><span id="L-49"><a href="#L-49"><span class="linenos"> 49</span></a><span class="n">SPLIT_COL_ACTION</span> <span class="o">=</span> <span class="s2">"split_col"</span>
+</span><span id="L-50"><a href="#L-50"><span class="linenos"> 50</span></a><span class="n">CODES_COL_ACTION</span> <span class="o">=</span> <span class="s2">"codes_col"</span>
+</span><span id="L-51"><a href="#L-51"><span class="linenos"> 51</span></a><span class="n">DIVIDE_COL_ACTION</span> <span class="o">=</span> <span class="s2">"divide_col"</span>
+</span><span id="L-52"><a href="#L-52"><span class="linenos"> 52</span></a><span class="n">COL_ACTIONS</span> <span class="o">=</span> <span class="p">[</span><span class="n">SPLIT_COL_ACTION</span><span class="p">,</span> <span class="n">CODES_COL_ACTION</span><span class="p">,</span> <span class="n">DIVIDE_COL_ACTION</span><span class="p">]</span>
+</span><span id="L-53"><a href="#L-53"><span class="linenos"> 53</span></a>
+</span><span id="L-54"><a href="#L-54"><span class="linenos"> 54</span></a><span class="n">CODE_FILE_TYPES</span> <span class="o">=</span> <span class="p">[</span><span class="s2">".xlsx"</span><span class="p">,</span> <span class="s2">".xls"</span><span class="p">,</span> <span class="s2">".csv"</span><span class="p">]</span>
+</span><span id="L-55"><a href="#L-55"><span class="linenos"> 55</span></a><span class="n">SOURCE_COL_SUFFIX</span> <span class="o">=</span> <span class="s2">"_acmc_source"</span>
+</span><span id="L-56"><a href="#L-56"><span class="linenos"> 56</span></a><span class="n">TARGET_COL_SUFFIX</span> <span class="o">=</span> <span class="s2">"_acmc_target"</span>
+</span><span id="L-57"><a href="#L-57"><span class="linenos"> 57</span></a>
+</span><span id="L-58"><a href="#L-58"><span class="linenos"> 58</span></a><span class="c1"># config.yaml schema</span>
+</span><span id="L-59"><a href="#L-59"><span class="linenos"> 59</span></a><span class="n">CONFIG_SCHEMA</span> <span class="o">=</span> <span class="p">{</span>
+</span><span id="L-60"><a href="#L-60"><span class="linenos"> 60</span></a> <span class="s2">"phenotype"</span><span class="p">:</span> <span class="p">{</span>
+</span><span id="L-61"><a href="#L-61"><span class="linenos"> 61</span></a> <span class="s2">"type"</span><span class="p">:</span> <span class="s2">"dict"</span><span class="p">,</span>
+</span><span id="L-62"><a href="#L-62"><span class="linenos"> 62</span></a> <span class="s2">"required"</span><span class="p">:</span> <span class="kc">True</span><span class="p">,</span>
+</span><span id="L-63"><a href="#L-63"><span class="linenos"> 63</span></a> <span class="s2">"schema"</span><span class="p">:</span> <span class="p">{</span>
+</span><span id="L-64"><a href="#L-64"><span class="linenos"> 64</span></a> <span class="s2">"version"</span><span class="p">:</span> <span class="p">{</span>
+</span><span id="L-65"><a href="#L-65"><span class="linenos"> 65</span></a> <span class="s2">"type"</span><span class="p">:</span> <span class="s2">"string"</span><span class="p">,</span>
+</span><span id="L-66"><a href="#L-66"><span class="linenos"> 66</span></a> <span class="s2">"required"</span><span class="p">:</span> <span class="kc">True</span><span class="p">,</span>
+</span><span id="L-67"><a href="#L-67"><span class="linenos"> 67</span></a> <span class="s2">"regex"</span><span class="p">:</span> <span class="sa">r</span><span class="s2">"^\d+\.\d+\.\d+$"</span><span class="p">,</span> <span class="c1"># Enforces 'vN.N.N' format</span>
+</span><span id="L-68"><a href="#L-68"><span class="linenos"> 68</span></a> <span class="p">},</span>
+</span><span id="L-69"><a href="#L-69"><span class="linenos"> 69</span></a> <span class="s2">"omop"</span><span class="p">:</span> <span class="p">{</span>
+</span><span id="L-70"><a href="#L-70"><span class="linenos"> 70</span></a> <span class="s2">"type"</span><span class="p">:</span> <span class="s2">"dict"</span><span class="p">,</span>
+</span><span id="L-71"><a href="#L-71"><span class="linenos"> 71</span></a> <span class="s2">"required"</span><span class="p">:</span> <span class="kc">True</span><span class="p">,</span>
+</span><span id="L-72"><a href="#L-72"><span class="linenos"> 72</span></a> <span class="s2">"schema"</span><span class="p">:</span> <span class="p">{</span>
+</span><span id="L-73"><a href="#L-73"><span class="linenos"> 73</span></a> <span class="s2">"vocabulary_id"</span><span class="p">:</span> <span class="p">{</span><span class="s2">"type"</span><span class="p">:</span> <span class="s2">"string"</span><span class="p">,</span> <span class="s2">"required"</span><span class="p">:</span> <span class="kc">True</span><span class="p">},</span>
+</span><span id="L-74"><a href="#L-74"><span class="linenos"> 74</span></a> <span class="s2">"vocabulary_name"</span><span class="p">:</span> <span class="p">{</span><span class="s2">"type"</span><span class="p">:</span> <span class="s2">"string"</span><span class="p">,</span> <span class="s2">"required"</span><span class="p">:</span> <span class="kc">True</span><span class="p">},</span>
+</span><span id="L-75"><a href="#L-75"><span class="linenos"> 75</span></a> <span class="s2">"vocabulary_reference"</span><span class="p">:</span> <span class="p">{</span>
+</span><span id="L-76"><a href="#L-76"><span class="linenos"> 76</span></a> <span class="s2">"type"</span><span class="p">:</span> <span class="s2">"string"</span><span class="p">,</span>
+</span><span id="L-77"><a href="#L-77"><span class="linenos"> 77</span></a> <span class="s2">"required"</span><span class="p">:</span> <span class="kc">True</span><span class="p">,</span>
+</span><span id="L-78"><a href="#L-78"><span class="linenos"> 78</span></a> <span class="s2">"regex"</span><span class="p">:</span> <span class="sa">r</span><span class="s2">"^https?://.*"</span><span class="p">,</span> <span class="c1"># Ensures it's a URL</span>
+</span><span id="L-79"><a href="#L-79"><span class="linenos"> 79</span></a> <span class="p">},</span>
+</span><span id="L-80"><a href="#L-80"><span class="linenos"> 80</span></a> <span class="p">},</span>
+</span><span id="L-81"><a href="#L-81"><span class="linenos"> 81</span></a> <span class="p">},</span>
+</span><span id="L-82"><a href="#L-82"><span class="linenos"> 82</span></a> <span class="s2">"map"</span><span class="p">:</span> <span class="p">{</span>
+</span><span id="L-83"><a href="#L-83"><span class="linenos"> 83</span></a> <span class="s2">"type"</span><span class="p">:</span> <span class="s2">"list"</span><span class="p">,</span>
+</span><span id="L-84"><a href="#L-84"><span class="linenos"> 84</span></a> <span class="s2">"schema"</span><span class="p">:</span> <span class="p">{</span>
+</span><span id="L-85"><a href="#L-85"><span class="linenos"> 85</span></a> <span class="s2">"type"</span><span class="p">:</span> <span class="s2">"string"</span><span class="p">,</span>
+</span><span id="L-86"><a href="#L-86"><span class="linenos"> 86</span></a> <span class="s2">"allowed"</span><span class="p">:</span> <span class="nb">list</span><span class="p">(</span>
+</span><span id="L-87"><a href="#L-87"><span class="linenos"> 87</span></a> <span class="n">parse</span><span class="o">.</span><span class="n">SUPPORTED_CODE_TYPES</span>
+</span><span id="L-88"><a href="#L-88"><span class="linenos"> 88</span></a> <span class="p">),</span> <span class="c1"># Ensure only predefined values are allowed</span>
+</span><span id="L-89"><a href="#L-89"><span class="linenos"> 89</span></a> <span class="p">},</span>
+</span><span id="L-90"><a href="#L-90"><span class="linenos"> 90</span></a> <span class="p">},</span>
+</span><span id="L-91"><a href="#L-91"><span class="linenos"> 91</span></a> <span class="s2">"concept_sets"</span><span class="p">:</span> <span class="p">{</span>
+</span><span id="L-92"><a href="#L-92"><span class="linenos"> 92</span></a> <span class="s2">"type"</span><span class="p">:</span> <span class="s2">"list"</span><span class="p">,</span>
+</span><span id="L-93"><a href="#L-93"><span class="linenos"> 93</span></a> <span class="s2">"required"</span><span class="p">:</span> <span class="kc">True</span><span class="p">,</span>
+</span><span id="L-94"><a href="#L-94"><span class="linenos"> 94</span></a> <span class="s2">"schema"</span><span class="p">:</span> <span class="p">{</span>
+</span><span id="L-95"><a href="#L-95"><span class="linenos"> 95</span></a> <span class="s2">"type"</span><span class="p">:</span> <span class="s2">"dict"</span><span class="p">,</span>
+</span><span id="L-96"><a href="#L-96"><span class="linenos"> 96</span></a> <span class="s2">"schema"</span><span class="p">:</span> <span class="p">{</span>
+</span><span id="L-97"><a href="#L-97"><span class="linenos"> 97</span></a> <span class="s2">"name"</span><span class="p">:</span> <span class="p">{</span><span class="s2">"type"</span><span class="p">:</span> <span class="s2">"string"</span><span class="p">,</span> <span class="s2">"required"</span><span class="p">:</span> <span class="kc">True</span><span class="p">},</span>
+</span><span id="L-98"><a href="#L-98"><span class="linenos"> 98</span></a> <span class="s2">"file"</span><span class="p">:</span> <span class="p">{</span>
+</span><span id="L-99"><a href="#L-99"><span class="linenos"> 99</span></a> <span class="s2">"type"</span><span class="p">:</span> <span class="s2">"dict"</span><span class="p">,</span>
+</span><span id="L-100"><a href="#L-100"><span class="linenos"> 100</span></a> <span class="s2">"required"</span><span class="p">:</span> <span class="kc">False</span><span class="p">,</span>
+</span><span id="L-101"><a href="#L-101"><span class="linenos"> 101</span></a> <span class="s2">"schema"</span><span class="p">:</span> <span class="p">{</span>
+</span><span id="L-102"><a href="#L-102"><span class="linenos"> 102</span></a> <span class="s2">"path"</span><span class="p">:</span> <span class="p">{</span><span class="s2">"type"</span><span class="p">:</span> <span class="s2">"string"</span><span class="p">,</span> <span class="s2">"required"</span><span class="p">:</span> <span class="kc">True</span><span class="p">},</span>
+</span><span id="L-103"><a href="#L-103"><span class="linenos"> 103</span></a> <span class="s2">"columns"</span><span class="p">:</span> <span class="p">{</span><span class="s2">"type"</span><span class="p">:</span> <span class="s2">"dict"</span><span class="p">,</span> <span class="s2">"required"</span><span class="p">:</span> <span class="kc">True</span><span class="p">},</span>
+</span><span id="L-104"><a href="#L-104"><span class="linenos"> 104</span></a> <span class="s2">"category"</span><span class="p">:</span> <span class="p">{</span>
+</span><span id="L-105"><a href="#L-105"><span class="linenos"> 105</span></a> <span class="s2">"type"</span><span class="p">:</span> <span class="s2">"string"</span>
+</span><span id="L-106"><a href="#L-106"><span class="linenos"> 106</span></a> <span class="p">},</span> <span class="c1"># Optional but must be string if present</span>
+</span><span id="L-107"><a href="#L-107"><span class="linenos"> 107</span></a> <span class="s2">"actions"</span><span class="p">:</span> <span class="p">{</span>
+</span><span id="L-108"><a href="#L-108"><span class="linenos"> 108</span></a> <span class="s2">"type"</span><span class="p">:</span> <span class="s2">"dict"</span><span class="p">,</span>
+</span><span id="L-109"><a href="#L-109"><span class="linenos"> 109</span></a> <span class="s2">"schema"</span><span class="p">:</span> <span class="p">{</span><span class="s2">"divide_col"</span><span class="p">:</span> <span class="p">{</span><span class="s2">"type"</span><span class="p">:</span> <span class="s2">"string"</span><span class="p">}},</span>
+</span><span id="L-110"><a href="#L-110"><span class="linenos"> 110</span></a> <span class="p">},</span>
+</span><span id="L-111"><a href="#L-111"><span class="linenos"> 111</span></a> <span class="p">},</span>
+</span><span id="L-112"><a href="#L-112"><span class="linenos"> 112</span></a> <span class="p">},</span>
+</span><span id="L-113"><a href="#L-113"><span class="linenos"> 113</span></a> <span class="s2">"metadata"</span><span class="p">:</span> <span class="p">{</span><span class="s2">"type"</span><span class="p">:</span> <span class="s2">"dict"</span><span class="p">,</span> <span class="s2">"required"</span><span class="p">:</span> <span class="kc">True</span><span class="p">},</span>
+</span><span id="L-114"><a href="#L-114"><span class="linenos"> 114</span></a> <span class="p">},</span>
+</span><span id="L-115"><a href="#L-115"><span class="linenos"> 115</span></a> <span class="p">},</span>
+</span><span id="L-116"><a href="#L-116"><span class="linenos"> 116</span></a> <span class="p">},</span>
+</span><span id="L-117"><a href="#L-117"><span class="linenos"> 117</span></a> <span class="p">},</span>
+</span><span id="L-118"><a href="#L-118"><span class="linenos"> 118</span></a> <span class="p">}</span>
+</span><span id="L-119"><a href="#L-119"><span class="linenos"> 119</span></a><span class="p">}</span>
+</span><span id="L-120"><a href="#L-120"><span class="linenos"> 120</span></a>
+</span><span id="L-121"><a href="#L-121"><span class="linenos"> 121</span></a>
+</span><span id="L-122"><a href="#L-122"><span class="linenos"> 122</span></a><span class="k">class</span><span class="w"> </span><span class="nc">PhenValidationException</span><span class="p">(</span><span class="ne">Exception</span><span class="p">):</span>
+</span><span id="L-123"><a href="#L-123"><span class="linenos"> 123</span></a><span class="w"> </span><span class="sd">"""Custom exception class raised when validation errors in phenotype configuration file"""</span>
+</span><span id="L-124"><a href="#L-124"><span class="linenos"> 124</span></a>
+</span><span id="L-125"><a href="#L-125"><span class="linenos"> 125</span></a> <span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">message</span><span class="p">,</span> <span class="n">validation_errors</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
+</span><span id="L-126"><a href="#L-126"><span class="linenos"> 126</span></a> <span class="nb">super</span><span class="p">()</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="n">message</span><span class="p">)</span>
+</span><span id="L-127"><a href="#L-127"><span class="linenos"> 127</span></a> <span class="bp">self</span><span class="o">.</span><span class="n">validation_errors</span> <span class="o">=</span> <span class="n">validation_errors</span>
+</span><span id="L-128"><a href="#L-128"><span class="linenos"> 128</span></a>
+</span><span id="L-129"><a href="#L-129"><span class="linenos"> 129</span></a>
+</span><span id="L-130"><a href="#L-130"><span class="linenos"> 130</span></a><span class="k">def</span><span class="w"> </span><span class="nf">construct_git_url</span><span class="p">(</span><span class="n">remote_url</span><span class="p">:</span> <span class="nb">str</span><span class="p">):</span>
+</span><span id="L-131"><a href="#L-131"><span class="linenos"> 131</span></a><span class="w"> </span><span class="sd">"""Constructs a git url for github or gitlab including a PAT token environment variable"""</span>
+</span><span id="L-132"><a href="#L-132"><span class="linenos"> 132</span></a> <span class="c1"># check the url</span>
+</span><span id="L-133"><a href="#L-133"><span class="linenos"> 133</span></a> <span class="n">parsed_url</span> <span class="o">=</span> <span class="n">urlparse</span><span class="p">(</span><span class="n">remote_url</span><span class="p">)</span>
+</span><span id="L-134"><a href="#L-134"><span class="linenos"> 134</span></a>
+</span><span id="L-135"><a href="#L-135"><span class="linenos"> 135</span></a> <span class="c1"># if github in the URL otherwise assume it's gitlab, if we want to use others such as codeberg we'd</span>
+</span><span id="L-136"><a href="#L-136"><span class="linenos"> 136</span></a> <span class="c1"># need to update this function if the URL scheme is different.</span>
+</span><span id="L-137"><a href="#L-137"><span class="linenos"> 137</span></a> <span class="k">if</span> <span class="s2">"github.com"</span> <span class="ow">in</span> <span class="n">parsed_url</span><span class="o">.</span><span class="n">netloc</span><span class="p">:</span>
+</span><span id="L-138"><a href="#L-138"><span class="linenos"> 138</span></a> <span class="c1"># get GitHub PAT from environment variable</span>
+</span><span id="L-139"><a href="#L-139"><span class="linenos"> 139</span></a> <span class="n">auth</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">getenv</span><span class="p">(</span><span class="s2">"ACMC_GITHUB_PAT"</span><span class="p">)</span>
+</span><span id="L-140"><a href="#L-140"><span class="linenos"> 140</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="n">auth</span><span class="p">:</span>
+</span><span id="L-141"><a href="#L-141"><span class="linenos"> 141</span></a> <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span>
+</span><span id="L-142"><a href="#L-142"><span class="linenos"> 142</span></a> <span class="s2">"GitHub PAT not found. Set the ACMC_GITHUB_PAT environment variable."</span>
+</span><span id="L-143"><a href="#L-143"><span class="linenos"> 143</span></a> <span class="p">)</span>
+</span><span id="L-144"><a href="#L-144"><span class="linenos"> 144</span></a> <span class="k">else</span><span class="p">:</span>
+</span><span id="L-145"><a href="#L-145"><span class="linenos"> 145</span></a> <span class="c1"># get GitLab PAT from environment variable</span>
+</span><span id="L-146"><a href="#L-146"><span class="linenos"> 146</span></a> <span class="n">auth</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">getenv</span><span class="p">(</span><span class="s2">"ACMC_GITLAB_PAT"</span><span class="p">)</span>
+</span><span id="L-147"><a href="#L-147"><span class="linenos"> 147</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="n">auth</span><span class="p">:</span>
+</span><span id="L-148"><a href="#L-148"><span class="linenos"> 148</span></a> <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span>
+</span><span id="L-149"><a href="#L-149"><span class="linenos"> 149</span></a> <span class="s2">"GitLab PAT not found. Set the ACMC_GITLAB_PAT environment variable."</span>
+</span><span id="L-150"><a href="#L-150"><span class="linenos"> 150</span></a> <span class="p">)</span>
+</span><span id="L-151"><a href="#L-151"><span class="linenos"> 151</span></a> <span class="n">auth</span> <span class="o">=</span> <span class="sa">f</span><span class="s2">"oauth2:</span><span class="si">{</span><span class="n">auth</span><span class="si">}</span><span class="s2">"</span>
+</span><span id="L-152"><a href="#L-152"><span class="linenos"> 152</span></a>
+</span><span id="L-153"><a href="#L-153"><span class="linenos"> 153</span></a> <span class="c1"># Construct the new URL with credentials</span>
+</span><span id="L-154"><a href="#L-154"><span class="linenos"> 154</span></a> <span class="n">new_netloc</span> <span class="o">=</span> <span class="sa">f</span><span class="s2">"</span><span class="si">{</span><span class="n">auth</span><span class="si">}</span><span class="s2">@</span><span class="si">{</span><span class="n">parsed_url</span><span class="o">.</span><span class="n">netloc</span><span class="si">}</span><span class="s2">"</span>
+</span><span id="L-155"><a href="#L-155"><span class="linenos"> 155</span></a> <span class="k">return</span> <span class="n">urlunparse</span><span class="p">(</span>
+</span><span id="L-156"><a href="#L-156"><span class="linenos"> 156</span></a> <span class="p">(</span>
+</span><span id="L-157"><a href="#L-157"><span class="linenos"> 157</span></a> <span class="n">parsed_url</span><span class="o">.</span><span class="n">scheme</span><span class="p">,</span>
+</span><span id="L-158"><a href="#L-158"><span class="linenos"> 158</span></a> <span class="n">new_netloc</span><span class="p">,</span>
+</span><span id="L-159"><a href="#L-159"><span class="linenos"> 159</span></a> <span class="n">parsed_url</span><span class="o">.</span><span class="n">path</span><span class="p">,</span>
+</span><span id="L-160"><a href="#L-160"><span class="linenos"> 160</span></a> <span class="n">parsed_url</span><span class="o">.</span><span class="n">params</span><span class="p">,</span>
+</span><span id="L-161"><a href="#L-161"><span class="linenos"> 161</span></a> <span class="n">parsed_url</span><span class="o">.</span><span class="n">query</span><span class="p">,</span>
+</span><span id="L-162"><a href="#L-162"><span class="linenos"> 162</span></a> <span class="n">parsed_url</span><span class="o">.</span><span class="n">fragment</span><span class="p">,</span>
+</span><span id="L-163"><a href="#L-163"><span class="linenos"> 163</span></a> <span class="p">)</span>
+</span><span id="L-164"><a href="#L-164"><span class="linenos"> 164</span></a> <span class="p">)</span>
+</span><span id="L-165"><a href="#L-165"><span class="linenos"> 165</span></a>
+</span><span id="L-166"><a href="#L-166"><span class="linenos"> 166</span></a>
+</span><span id="L-167"><a href="#L-167"><span class="linenos"> 167</span></a><span class="k">def</span><span class="w"> </span><span class="nf">create_empty_git_dir</span><span class="p">(</span><span class="n">path</span><span class="p">:</span> <span class="n">Path</span><span class="p">):</span>
+</span><span id="L-168"><a href="#L-168"><span class="linenos"> 168</span></a><span class="w"> </span><span class="sd">"""Creates a directory with a .gitkeep file so that it's tracked in git"""</span>
+</span><span id="L-169"><a href="#L-169"><span class="linenos"> 169</span></a> <span class="n">path</span><span class="o">.</span><span class="n">mkdir</span><span class="p">(</span><span class="n">exist_ok</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+</span><span id="L-170"><a href="#L-170"><span class="linenos"> 170</span></a> <span class="n">keep_path</span> <span class="o">=</span> <span class="n">path</span> <span class="o">/</span> <span class="s2">".gitkeep"</span>
+</span><span id="L-171"><a href="#L-171"><span class="linenos"> 171</span></a> <span class="n">keep_path</span><span class="o">.</span><span class="n">touch</span><span class="p">(</span><span class="n">exist_ok</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+</span><span id="L-172"><a href="#L-172"><span class="linenos"> 172</span></a>
+</span><span id="L-173"><a href="#L-173"><span class="linenos"> 173</span></a>
+</span><span id="L-174"><a href="#L-174"><span class="linenos"> 174</span></a><span class="k">def</span><span class="w"> </span><span class="nf">check_delete_dir</span><span class="p">(</span><span class="n">path</span><span class="p">:</span> <span class="n">Path</span><span class="p">,</span> <span class="n">msg</span><span class="p">:</span> <span class="nb">str</span><span class="p">)</span> <span class="o">-></span> <span class="nb">bool</span><span class="p">:</span>
+</span><span id="L-175"><a href="#L-175"><span class="linenos"> 175</span></a><span class="w"> </span><span class="sd">"""Checks on the command line if a user wants to delete a directory</span>
+</span><span id="L-176"><a href="#L-176"><span class="linenos"> 176</span></a>
+</span><span id="L-177"><a href="#L-177"><span class="linenos"> 177</span></a><span class="sd"> Args:</span>
+</span><span id="L-178"><a href="#L-178"><span class="linenos"> 178</span></a><span class="sd"> path (Path): path of the directory to be deleted</span>
+</span><span id="L-179"><a href="#L-179"><span class="linenos"> 179</span></a><span class="sd"> msg (str): message to be displayed to the user</span>
+</span><span id="L-180"><a href="#L-180"><span class="linenos"> 180</span></a>
+</span><span id="L-181"><a href="#L-181"><span class="linenos"> 181</span></a><span class="sd"> Returns:</span>
+</span><span id="L-182"><a href="#L-182"><span class="linenos"> 182</span></a><span class="sd"> Boolean: True if deleted</span>
+</span><span id="L-183"><a href="#L-183"><span class="linenos"> 183</span></a><span class="sd"> """</span>
+</span><span id="L-184"><a href="#L-184"><span class="linenos"> 184</span></a> <span class="n">deleted</span> <span class="o">=</span> <span class="kc">False</span>
+</span><span id="L-185"><a href="#L-185"><span class="linenos"> 185</span></a>
+</span><span id="L-186"><a href="#L-186"><span class="linenos"> 186</span></a> <span class="n">user_input</span> <span class="o">=</span> <span class="nb">input</span><span class="p">(</span><span class="sa">f</span><span class="s2">"</span><span class="si">{</span><span class="n">msg</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span>
+</span><span id="L-187"><a href="#L-187"><span class="linenos"> 187</span></a> <span class="k">if</span> <span class="n">user_input</span> <span class="ow">in</span> <span class="p">[</span><span class="s2">"yes"</span><span class="p">,</span> <span class="s2">"y"</span><span class="p">]:</span>
+</span><span id="L-188"><a href="#L-188"><span class="linenos"> 188</span></a> <span class="n">shutil</span><span class="o">.</span><span class="n">rmtree</span><span class="p">(</span><span class="n">path</span><span class="p">)</span>
+</span><span id="L-189"><a href="#L-189"><span class="linenos"> 189</span></a> <span class="n">deleted</span> <span class="o">=</span> <span class="kc">True</span>
+</span><span id="L-190"><a href="#L-190"><span class="linenos"> 190</span></a> <span class="k">else</span><span class="p">:</span>
+</span><span id="L-191"><a href="#L-191"><span class="linenos"> 191</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">"Directory was not deleted."</span><span class="p">)</span>
+</span><span id="L-192"><a href="#L-192"><span class="linenos"> 192</span></a>
+</span><span id="L-193"><a href="#L-193"><span class="linenos"> 193</span></a> <span class="k">return</span> <span class="n">deleted</span>
+</span><span id="L-194"><a href="#L-194"><span class="linenos"> 194</span></a>
+</span><span id="L-195"><a href="#L-195"><span class="linenos"> 195</span></a>
+</span><span id="L-196"><a href="#L-196"><span class="linenos"> 196</span></a><span class="k">def</span><span class="w"> </span><span class="nf">fork</span><span class="p">(</span>
+</span><span id="L-197"><a href="#L-197"><span class="linenos"> 197</span></a> <span class="n">phen_dir</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">upstream_url</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">upstream_version</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">new_origin_url</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="kc">None</span>
+</span><span id="L-198"><a href="#L-198"><span class="linenos"> 198</span></a><span class="p">):</span>
+</span><span id="L-199"><a href="#L-199"><span class="linenos"> 199</span></a><span class="w"> </span><span class="sd">"""Forks an upstream phenotype in a remote repo at a specific version to a local director, and optionally sets to a new remote origin"</span>
+</span><span id="L-200"><a href="#L-200"><span class="linenos"> 200</span></a>
+</span><span id="L-201"><a href="#L-201"><span class="linenos"> 201</span></a><span class="sd"> Args:</span>
+</span><span id="L-202"><a href="#L-202"><span class="linenos"> 202</span></a><span class="sd"> phen_dir (str): local directory path where the upstream repo is to be cloned</span>
+</span><span id="L-203"><a href="#L-203"><span class="linenos"> 203</span></a><span class="sd"> upstream_url (str): url to the upstream repo</span>
+</span><span id="L-204"><a href="#L-204"><span class="linenos"> 204</span></a><span class="sd"> upstream_version (str): version in the upstream repo to clone</span>
+</span><span id="L-205"><a href="#L-205"><span class="linenos"> 205</span></a><span class="sd"> new_origin_url (str, optional): url of the remote repo to set as the new origin. Defaults to None.</span>
+</span><span id="L-206"><a href="#L-206"><span class="linenos"> 206</span></a>
+</span><span id="L-207"><a href="#L-207"><span class="linenos"> 207</span></a><span class="sd"> Raises:</span>
+</span><span id="L-208"><a href="#L-208"><span class="linenos"> 208</span></a><span class="sd"> ValueError: if the specified version is not in the upstream repo</span>
+</span><span id="L-209"><a href="#L-209"><span class="linenos"> 209</span></a><span class="sd"> ValueError: if the upstream repo is not a valid phenotype repo</span>
+</span><span id="L-210"><a href="#L-210"><span class="linenos"> 210</span></a><span class="sd"> ValueError: if there's any other problems with Git</span>
+</span><span id="L-211"><a href="#L-211"><span class="linenos"> 211</span></a><span class="sd"> """</span>
+</span><span id="L-212"><a href="#L-212"><span class="linenos"> 212</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span>
+</span><span id="L-213"><a href="#L-213"><span class="linenos"> 213</span></a> <span class="sa">f</span><span class="s2">"Forking upstream repo </span><span class="si">{</span><span class="n">upstream_url</span><span class="si">}</span><span class="s2"> </span><span class="si">{</span><span class="n">upstream_version</span><span class="si">}</span><span class="s2"> into directory: </span><span class="si">{</span><span class="n">phen_dir</span><span class="si">}</span><span class="s2">"</span>
+</span><span id="L-214"><a href="#L-214"><span class="linenos"> 214</span></a> <span class="p">)</span>
+</span><span id="L-215"><a href="#L-215"><span class="linenos"> 215</span></a>
+</span><span id="L-216"><a href="#L-216"><span class="linenos"> 216</span></a> <span class="n">phen_path</span> <span class="o">=</span> <span class="n">Path</span><span class="p">(</span><span class="n">phen_dir</span><span class="p">)</span>
+</span><span id="L-217"><a href="#L-217"><span class="linenos"> 217</span></a> <span class="c1"># check if directory already exists and ask user if they want to recreate it</span>
+</span><span id="L-218"><a href="#L-218"><span class="linenos"> 218</span></a> <span class="k">if</span> <span class="p">(</span>
+</span><span id="L-219"><a href="#L-219"><span class="linenos"> 219</span></a> <span class="n">phen_path</span><span class="o">.</span><span class="n">exists</span><span class="p">()</span> <span class="ow">and</span> <span class="n">phen_path</span><span class="o">.</span><span class="n">is_dir</span><span class="p">()</span>
+</span><span id="L-220"><a href="#L-220"><span class="linenos"> 220</span></a> <span class="p">):</span> <span class="c1"># Check if it exists and is a directory</span>
+</span><span id="L-221"><a href="#L-221"><span class="linenos"> 221</span></a> <span class="n">configure</span> <span class="o">=</span> <span class="n">check_delete_dir</span><span class="p">(</span>
+</span><span id="L-222"><a href="#L-222"><span class="linenos"> 222</span></a> <span class="n">phen_path</span><span class="p">,</span>
+</span><span id="L-223"><a href="#L-223"><span class="linenos"> 223</span></a> <span class="sa">f</span><span class="s2">"The phen directory already exists. Do you want to reinitialise? (yes/no): "</span><span class="p">,</span>
+</span><span id="L-224"><a href="#L-224"><span class="linenos"> 224</span></a> <span class="p">)</span>
+</span><span id="L-225"><a href="#L-225"><span class="linenos"> 225</span></a> <span class="k">else</span><span class="p">:</span>
+</span><span id="L-226"><a href="#L-226"><span class="linenos"> 226</span></a> <span class="n">configure</span> <span class="o">=</span> <span class="kc">True</span>
+</span><span id="L-227"><a href="#L-227"><span class="linenos"> 227</span></a>
+</span><span id="L-228"><a href="#L-228"><span class="linenos"> 228</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="n">configure</span><span class="p">:</span>
+</span><span id="L-229"><a href="#L-229"><span class="linenos"> 229</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Exiting, phenotype not initiatised"</span><span class="p">)</span>
+</span><span id="L-230"><a href="#L-230"><span class="linenos"> 230</span></a> <span class="k">return</span>
+</span><span id="L-231"><a href="#L-231"><span class="linenos"> 231</span></a>
+</span><span id="L-232"><a href="#L-232"><span class="linenos"> 232</span></a> <span class="k">try</span><span class="p">:</span>
+</span><span id="L-233"><a href="#L-233"><span class="linenos"> 233</span></a> <span class="c1"># Clone repo</span>
+</span><span id="L-234"><a href="#L-234"><span class="linenos"> 234</span></a> <span class="n">git_url</span> <span class="o">=</span> <span class="n">construct_git_url</span><span class="p">(</span><span class="n">upstream_url</span><span class="p">)</span>
+</span><span id="L-235"><a href="#L-235"><span class="linenos"> 235</span></a> <span class="n">repo</span> <span class="o">=</span> <span class="n">git</span><span class="o">.</span><span class="n">Repo</span><span class="o">.</span><span class="n">clone_from</span><span class="p">(</span><span class="n">git_url</span><span class="p">,</span> <span class="n">phen_path</span><span class="p">)</span>
+</span><span id="L-236"><a href="#L-236"><span class="linenos"> 236</span></a>
+</span><span id="L-237"><a href="#L-237"><span class="linenos"> 237</span></a> <span class="c1"># Fetch all branches and tags</span>
+</span><span id="L-238"><a href="#L-238"><span class="linenos"> 238</span></a> <span class="n">repo</span><span class="o">.</span><span class="n">remotes</span><span class="o">.</span><span class="n">origin</span><span class="o">.</span><span class="n">fetch</span><span class="p">()</span>
+</span><span id="L-239"><a href="#L-239"><span class="linenos"> 239</span></a>
+</span><span id="L-240"><a href="#L-240"><span class="linenos"> 240</span></a> <span class="c1"># Check if the version exists</span>
+</span><span id="L-241"><a href="#L-241"><span class="linenos"> 241</span></a> <span class="n">available_refs</span> <span class="o">=</span> <span class="p">[</span><span class="n">ref</span><span class="o">.</span><span class="n">name</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s2">"/"</span><span class="p">)[</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span> <span class="k">for</span> <span class="n">ref</span> <span class="ow">in</span> <span class="n">repo</span><span class="o">.</span><span class="n">references</span><span class="p">]</span>
+</span><span id="L-242"><a href="#L-242"><span class="linenos"> 242</span></a> <span class="k">if</span> <span class="n">upstream_version</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">available_refs</span><span class="p">:</span>
+</span><span id="L-243"><a href="#L-243"><span class="linenos"> 243</span></a> <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span>
+</span><span id="L-244"><a href="#L-244"><span class="linenos"> 244</span></a> <span class="sa">f</span><span class="s2">"Version '</span><span class="si">{</span><span class="n">upstream_version</span><span class="si">}</span><span class="s2">' not found in the repository: </span><span class="si">{</span><span class="n">upstream_url</span><span class="si">}</span><span class="s2">."</span>
+</span><span id="L-245"><a href="#L-245"><span class="linenos"> 245</span></a> <span class="p">)</span>
+</span><span id="L-246"><a href="#L-246"><span class="linenos"> 246</span></a>
+</span><span id="L-247"><a href="#L-247"><span class="linenos"> 247</span></a> <span class="c1"># Checkout the specified version</span>
+</span><span id="L-248"><a href="#L-248"><span class="linenos"> 248</span></a> <span class="n">repo</span><span class="o">.</span><span class="n">git</span><span class="o">.</span><span class="n">checkout</span><span class="p">(</span><span class="n">upstream_version</span><span class="p">)</span>
+</span><span id="L-249"><a href="#L-249"><span class="linenos"> 249</span></a> <span class="n">main_branch</span> <span class="o">=</span> <span class="n">repo</span><span class="o">.</span><span class="n">heads</span><span class="p">[</span><span class="n">DEFAULT_GIT_BRANCH</span><span class="p">]</span>
+</span><span id="L-250"><a href="#L-250"><span class="linenos"> 250</span></a> <span class="n">main_branch</span><span class="o">.</span><span class="n">checkout</span><span class="p">()</span>
+</span><span id="L-251"><a href="#L-251"><span class="linenos"> 251</span></a>
+</span><span id="L-252"><a href="#L-252"><span class="linenos"> 252</span></a> <span class="c1"># Check if 'config.yaml' exists in the root directory</span>
+</span><span id="L-253"><a href="#L-253"><span class="linenos"> 253</span></a> <span class="n">config_path</span> <span class="o">=</span> <span class="n">phen_path</span> <span class="o">/</span> <span class="s2">"config.yaml"</span>
+</span><span id="L-254"><a href="#L-254"><span class="linenos"> 254</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">isfile</span><span class="p">(</span><span class="n">config_path</span><span class="p">):</span>
+</span><span id="L-255"><a href="#L-255"><span class="linenos"> 255</span></a> <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span>
+</span><span id="L-256"><a href="#L-256"><span class="linenos"> 256</span></a> <span class="sa">f</span><span class="s2">"The forked repository is not a valid ACMC repo because 'config.yaml' is missing in the root directory."</span>
+</span><span id="L-257"><a href="#L-257"><span class="linenos"> 257</span></a> <span class="p">)</span>
+</span><span id="L-258"><a href="#L-258"><span class="linenos"> 258</span></a>
+</span><span id="L-259"><a href="#L-259"><span class="linenos"> 259</span></a> <span class="c1"># Validate the phenotype is compatible with the acmc tool</span>
+</span><span id="L-260"><a href="#L-260"><span class="linenos"> 260</span></a> <span class="n">validate</span><span class="p">(</span><span class="nb">str</span><span class="p">(</span><span class="n">phen_path</span><span class="o">.</span><span class="n">resolve</span><span class="p">()))</span>
+</span><span id="L-261"><a href="#L-261"><span class="linenos"> 261</span></a>
+</span><span id="L-262"><a href="#L-262"><span class="linenos"> 262</span></a> <span class="c1"># Delete each tag locally</span>
+</span><span id="L-263"><a href="#L-263"><span class="linenos"> 263</span></a> <span class="n">tags</span> <span class="o">=</span> <span class="n">repo</span><span class="o">.</span><span class="n">tags</span>
+</span><span id="L-264"><a href="#L-264"><span class="linenos"> 264</span></a> <span class="k">for</span> <span class="n">tag</span> <span class="ow">in</span> <span class="n">tags</span><span class="p">:</span>
+</span><span id="L-265"><a href="#L-265"><span class="linenos"> 265</span></a> <span class="n">repo</span><span class="o">.</span><span class="n">delete_tag</span><span class="p">(</span><span class="n">tag</span><span class="p">)</span>
+</span><span id="L-266"><a href="#L-266"><span class="linenos"> 266</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Deleted tags from forked repo: </span><span class="si">{</span><span class="n">tag</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+</span><span id="L-267"><a href="#L-267"><span class="linenos"> 267</span></a>
+</span><span id="L-268"><a href="#L-268"><span class="linenos"> 268</span></a> <span class="c1"># Add upstream remote</span>
+</span><span id="L-269"><a href="#L-269"><span class="linenos"> 269</span></a> <span class="n">repo</span><span class="o">.</span><span class="n">create_remote</span><span class="p">(</span><span class="s2">"upstream"</span><span class="p">,</span> <span class="n">upstream_url</span><span class="p">)</span>
+</span><span id="L-270"><a href="#L-270"><span class="linenos"> 270</span></a> <span class="n">remote</span> <span class="o">=</span> <span class="n">repo</span><span class="o">.</span><span class="n">remotes</span><span class="p">[</span><span class="s2">"origin"</span><span class="p">]</span>
+</span><span id="L-271"><a href="#L-271"><span class="linenos"> 271</span></a> <span class="n">repo</span><span class="o">.</span><span class="n">delete_remote</span><span class="p">(</span><span class="n">remote</span><span class="p">)</span> <span class="c1"># Remove existing origin</span>
+</span><span id="L-272"><a href="#L-272"><span class="linenos"> 272</span></a>
+</span><span id="L-273"><a href="#L-273"><span class="linenos"> 273</span></a> <span class="c1"># Optionally set a new origin remote</span>
+</span><span id="L-274"><a href="#L-274"><span class="linenos"> 274</span></a> <span class="k">if</span> <span class="n">new_origin_url</span><span class="p">:</span>
+</span><span id="L-275"><a href="#L-275"><span class="linenos"> 275</span></a> <span class="n">git_url</span> <span class="o">=</span> <span class="n">construct_git_url</span><span class="p">(</span><span class="n">new_origin_url</span><span class="p">)</span>
+</span><span id="L-276"><a href="#L-276"><span class="linenos"> 276</span></a> <span class="n">repo</span><span class="o">.</span><span class="n">create_remote</span><span class="p">(</span><span class="s2">"origin"</span><span class="p">,</span> <span class="n">git_url</span><span class="p">)</span>
+</span><span id="L-277"><a href="#L-277"><span class="linenos"> 277</span></a> <span class="n">repo</span><span class="o">.</span><span class="n">git</span><span class="o">.</span><span class="n">push</span><span class="p">(</span><span class="s2">"--set-upstream"</span><span class="p">,</span> <span class="s2">"origin"</span><span class="p">,</span> <span class="s2">"main"</span><span class="p">)</span>
+</span><span id="L-278"><a href="#L-278"><span class="linenos"> 278</span></a>
+</span><span id="L-279"><a href="#L-279"><span class="linenos"> 279</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Repository forked successfully at </span><span class="si">{</span><span class="n">phen_path</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+</span><span id="L-280"><a href="#L-280"><span class="linenos"> 280</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Upstream set to </span><span class="si">{</span><span class="n">upstream_url</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+</span><span id="L-281"><a href="#L-281"><span class="linenos"> 281</span></a> <span class="k">if</span> <span class="n">new_origin_url</span><span class="p">:</span>
+</span><span id="L-282"><a href="#L-282"><span class="linenos"> 282</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Origin set to </span><span class="si">{</span><span class="n">new_origin_url</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+</span><span id="L-283"><a href="#L-283"><span class="linenos"> 283</span></a>
+</span><span id="L-284"><a href="#L-284"><span class="linenos"> 284</span></a> <span class="k">except</span> <span class="ne">Exception</span> <span class="k">as</span> <span class="n">e</span><span class="p">:</span>
+</span><span id="L-285"><a href="#L-285"><span class="linenos"> 285</span></a> <span class="k">if</span> <span class="n">phen_path</span><span class="o">.</span><span class="n">exists</span><span class="p">():</span>
+</span><span id="L-286"><a href="#L-286"><span class="linenos"> 286</span></a> <span class="n">shutil</span><span class="o">.</span><span class="n">rmtree</span><span class="p">(</span><span class="n">phen_path</span><span class="p">)</span>
+</span><span id="L-287"><a href="#L-287"><span class="linenos"> 287</span></a> <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Error occurred during repository fork: </span><span class="si">{</span><span class="nb">str</span><span class="p">(</span><span class="n">e</span><span class="p">)</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+</span><span id="L-288"><a href="#L-288"><span class="linenos"> 288</span></a>
+</span><span id="L-289"><a href="#L-289"><span class="linenos"> 289</span></a>
+</span><span id="L-290"><a href="#L-290"><span class="linenos"> 290</span></a><span class="k">def</span><span class="w"> </span><span class="nf">init</span><span class="p">(</span><span class="n">phen_dir</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">remote_url</span><span class="p">:</span> <span class="nb">str</span><span class="p">):</span>
+</span><span id="L-291"><a href="#L-291"><span class="linenos"> 291</span></a><span class="w"> </span><span class="sd">"""Initial phenotype directory as git repo with standard structure"""</span>
+</span><span id="L-292"><a href="#L-292"><span class="linenos"> 292</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Initialising Phenotype in directory: </span><span class="si">{</span><span class="n">phen_dir</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+</span><span id="L-293"><a href="#L-293"><span class="linenos"> 293</span></a> <span class="n">phen_path</span> <span class="o">=</span> <span class="n">Path</span><span class="p">(</span><span class="n">phen_dir</span><span class="p">)</span>
+</span><span id="L-294"><a href="#L-294"><span class="linenos"> 294</span></a>
+</span><span id="L-295"><a href="#L-295"><span class="linenos"> 295</span></a> <span class="c1"># check if directory already exists and ask user if they want to recreate it</span>
+</span><span id="L-296"><a href="#L-296"><span class="linenos"> 296</span></a> <span class="k">if</span> <span class="p">(</span>
+</span><span id="L-297"><a href="#L-297"><span class="linenos"> 297</span></a> <span class="n">phen_path</span><span class="o">.</span><span class="n">exists</span><span class="p">()</span> <span class="ow">and</span> <span class="n">phen_path</span><span class="o">.</span><span class="n">is_dir</span><span class="p">()</span>
+</span><span id="L-298"><a href="#L-298"><span class="linenos"> 298</span></a> <span class="p">):</span> <span class="c1"># Check if it exists and is a directory</span>
+</span><span id="L-299"><a href="#L-299"><span class="linenos"> 299</span></a> <span class="n">configure</span> <span class="o">=</span> <span class="n">check_delete_dir</span><span class="p">(</span>
+</span><span id="L-300"><a href="#L-300"><span class="linenos"> 300</span></a> <span class="n">phen_path</span><span class="p">,</span>
+</span><span id="L-301"><a href="#L-301"><span class="linenos"> 301</span></a> <span class="sa">f</span><span class="s2">"The phen directory already exists. Do you want to reinitialise? (yes/no): "</span><span class="p">,</span>
+</span><span id="L-302"><a href="#L-302"><span class="linenos"> 302</span></a> <span class="p">)</span>
+</span><span id="L-303"><a href="#L-303"><span class="linenos"> 303</span></a> <span class="k">else</span><span class="p">:</span>
+</span><span id="L-304"><a href="#L-304"><span class="linenos"> 304</span></a> <span class="n">configure</span> <span class="o">=</span> <span class="kc">True</span>
+</span><span id="L-305"><a href="#L-305"><span class="linenos"> 305</span></a>
+</span><span id="L-306"><a href="#L-306"><span class="linenos"> 306</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="n">configure</span><span class="p">:</span>
+</span><span id="L-307"><a href="#L-307"><span class="linenos"> 307</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Exiting, phenotype not initiatised"</span><span class="p">)</span>
+</span><span id="L-308"><a href="#L-308"><span class="linenos"> 308</span></a> <span class="k">return</span>
+</span><span id="L-309"><a href="#L-309"><span class="linenos"> 309</span></a>
+</span><span id="L-310"><a href="#L-310"><span class="linenos"> 310</span></a> <span class="c1"># Initialise repo from local or remote</span>
+</span><span id="L-311"><a href="#L-311"><span class="linenos"> 311</span></a> <span class="n">repo</span><span class="p">:</span> <span class="n">Repo</span>
+</span><span id="L-312"><a href="#L-312"><span class="linenos"> 312</span></a> <span class="c1"># if remote then clone the repo otherwise init a local repo</span>
+</span><span id="L-313"><a href="#L-313"><span class="linenos"> 313</span></a> <span class="k">if</span> <span class="n">remote_url</span> <span class="o">!=</span> <span class="kc">None</span><span class="p">:</span>
+</span><span id="L-314"><a href="#L-314"><span class="linenos"> 314</span></a> <span class="c1"># add PAT token to the URL</span>
+</span><span id="L-315"><a href="#L-315"><span class="linenos"> 315</span></a> <span class="n">git_url</span> <span class="o">=</span> <span class="n">construct_git_url</span><span class="p">(</span><span class="n">remote_url</span><span class="p">)</span>
+</span><span id="L-316"><a href="#L-316"><span class="linenos"> 316</span></a>
+</span><span id="L-317"><a href="#L-317"><span class="linenos"> 317</span></a> <span class="c1"># clone the repo</span>
+</span><span id="L-318"><a href="#L-318"><span class="linenos"> 318</span></a> <span class="n">repo</span> <span class="o">=</span> <span class="n">git</span><span class="o">.</span><span class="n">cmd</span><span class="o">.</span><span class="n">Git</span><span class="p">()</span>
+</span><span id="L-319"><a href="#L-319"><span class="linenos"> 319</span></a> <span class="n">repo</span><span class="o">.</span><span class="n">clone</span><span class="p">(</span><span class="n">git_url</span><span class="p">,</span> <span class="n">phen_path</span><span class="p">)</span>
+</span><span id="L-320"><a href="#L-320"><span class="linenos"> 320</span></a>
+</span><span id="L-321"><a href="#L-321"><span class="linenos"> 321</span></a> <span class="c1"># open repo</span>
+</span><span id="L-322"><a href="#L-322"><span class="linenos"> 322</span></a> <span class="n">repo</span> <span class="o">=</span> <span class="n">Repo</span><span class="p">(</span><span class="n">phen_path</span><span class="p">)</span>
+</span><span id="L-323"><a href="#L-323"><span class="linenos"> 323</span></a> <span class="c1"># check if there are any commits (new repo has no commits)</span>
+</span><span id="L-324"><a href="#L-324"><span class="linenos"> 324</span></a> <span class="k">if</span> <span class="p">(</span>
+</span><span id="L-325"><a href="#L-325"><span class="linenos"> 325</span></a> <span class="nb">len</span><span class="p">(</span><span class="n">repo</span><span class="o">.</span><span class="n">branches</span><span class="p">)</span> <span class="o">==</span> <span class="mi">0</span> <span class="ow">or</span> <span class="n">repo</span><span class="o">.</span><span class="n">head</span><span class="o">.</span><span class="n">is_detached</span>
+</span><span id="L-326"><a href="#L-326"><span class="linenos"> 326</span></a> <span class="p">):</span> <span class="c1"># Handle detached HEAD (e.g., after init)</span>
+</span><span id="L-327"><a href="#L-327"><span class="linenos"> 327</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="s2">"The phen repository has no commits yet."</span><span class="p">)</span>
+</span><span id="L-328"><a href="#L-328"><span class="linenos"> 328</span></a> <span class="n">commit_count</span> <span class="o">=</span> <span class="mi">0</span>
+</span><span id="L-329"><a href="#L-329"><span class="linenos"> 329</span></a> <span class="k">else</span><span class="p">:</span>
+</span><span id="L-330"><a href="#L-330"><span class="linenos"> 330</span></a> <span class="c1"># Get the total number of commits in the default branch</span>
+</span><span id="L-331"><a href="#L-331"><span class="linenos"> 331</span></a> <span class="n">commit_count</span> <span class="o">=</span> <span class="nb">sum</span><span class="p">(</span><span class="mi">1</span> <span class="k">for</span> <span class="n">_</span> <span class="ow">in</span> <span class="n">repo</span><span class="o">.</span><span class="n">iter_commits</span><span class="p">())</span>
+</span><span id="L-332"><a href="#L-332"><span class="linenos"> 332</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Repo has previous commits: </span><span class="si">{</span><span class="n">commit_count</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+</span><span id="L-333"><a href="#L-333"><span class="linenos"> 333</span></a> <span class="k">else</span><span class="p">:</span>
+</span><span id="L-334"><a href="#L-334"><span class="linenos"> 334</span></a> <span class="c1"># local repo, create the directories and init</span>
+</span><span id="L-335"><a href="#L-335"><span class="linenos"> 335</span></a> <span class="n">phen_path</span><span class="o">.</span><span class="n">mkdir</span><span class="p">(</span><span class="n">parents</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">exist_ok</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+</span><span id="L-336"><a href="#L-336"><span class="linenos"> 336</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Phen directory '</span><span class="si">{</span><span class="n">phen_path</span><span class="si">}</span><span class="s2">' has been created."</span><span class="p">)</span>
+</span><span id="L-337"><a href="#L-337"><span class="linenos"> 337</span></a> <span class="n">repo</span> <span class="o">=</span> <span class="n">git</span><span class="o">.</span><span class="n">Repo</span><span class="o">.</span><span class="n">init</span><span class="p">(</span><span class="n">phen_path</span><span class="p">)</span>
+</span><span id="L-338"><a href="#L-338"><span class="linenos"> 338</span></a> <span class="n">commit_count</span> <span class="o">=</span> <span class="mi">0</span>
+</span><span id="L-339"><a href="#L-339"><span class="linenos"> 339</span></a>
+</span><span id="L-340"><a href="#L-340"><span class="linenos"> 340</span></a> <span class="n">phen_path</span> <span class="o">=</span> <span class="n">phen_path</span><span class="o">.</span><span class="n">resolve</span><span class="p">()</span>
+</span><span id="L-341"><a href="#L-341"><span class="linenos"> 341</span></a> <span class="c1"># initialise empty repos</span>
+</span><span id="L-342"><a href="#L-342"><span class="linenos"> 342</span></a> <span class="k">if</span> <span class="n">commit_count</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
+</span><span id="L-343"><a href="#L-343"><span class="linenos"> 343</span></a> <span class="c1"># create initial commit</span>
+</span><span id="L-344"><a href="#L-344"><span class="linenos"> 344</span></a> <span class="n">initial_file_path</span> <span class="o">=</span> <span class="n">phen_path</span> <span class="o">/</span> <span class="s2">"README.md"</span>
+</span><span id="L-345"><a href="#L-345"><span class="linenos"> 345</span></a> <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">initial_file_path</span><span class="p">,</span> <span class="s2">"w"</span><span class="p">)</span> <span class="k">as</span> <span class="n">file</span><span class="p">:</span>
+</span><span id="L-346"><a href="#L-346"><span class="linenos"> 346</span></a> <span class="n">file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span>
+</span><span id="L-347"><a href="#L-347"><span class="linenos"> 347</span></a> <span class="s2">"# Initial commit</span><span class="se">\n</span><span class="s2">This is the first commit in the phen repository.</span><span class="se">\n</span><span class="s2">"</span>
+</span><span id="L-348"><a href="#L-348"><span class="linenos"> 348</span></a> <span class="p">)</span>
+</span><span id="L-349"><a href="#L-349"><span class="linenos"> 349</span></a> <span class="n">repo</span><span class="o">.</span><span class="n">index</span><span class="o">.</span><span class="n">add</span><span class="p">([</span><span class="n">initial_file_path</span><span class="p">])</span>
+</span><span id="L-350"><a href="#L-350"><span class="linenos"> 350</span></a> <span class="n">repo</span><span class="o">.</span><span class="n">index</span><span class="o">.</span><span class="n">commit</span><span class="p">(</span><span class="s2">"Initial commit"</span><span class="p">)</span>
+</span><span id="L-351"><a href="#L-351"><span class="linenos"> 351</span></a> <span class="n">commit_count</span> <span class="o">=</span> <span class="mi">1</span>
+</span><span id="L-352"><a href="#L-352"><span class="linenos"> 352</span></a>
+</span><span id="L-353"><a href="#L-353"><span class="linenos"> 353</span></a> <span class="c1"># Checkout the phens default branch, creating it if it does not exist</span>
+</span><span id="L-354"><a href="#L-354"><span class="linenos"> 354</span></a> <span class="k">if</span> <span class="n">DEFAULT_GIT_BRANCH</span> <span class="ow">in</span> <span class="n">repo</span><span class="o">.</span><span class="n">branches</span><span class="p">:</span>
+</span><span id="L-355"><a href="#L-355"><span class="linenos"> 355</span></a> <span class="n">main_branch</span> <span class="o">=</span> <span class="n">repo</span><span class="o">.</span><span class="n">heads</span><span class="p">[</span><span class="n">DEFAULT_GIT_BRANCH</span><span class="p">]</span>
+</span><span id="L-356"><a href="#L-356"><span class="linenos"> 356</span></a> <span class="n">main_branch</span><span class="o">.</span><span class="n">checkout</span><span class="p">()</span>
+</span><span id="L-357"><a href="#L-357"><span class="linenos"> 357</span></a> <span class="k">else</span><span class="p">:</span>
+</span><span id="L-358"><a href="#L-358"><span class="linenos"> 358</span></a> <span class="n">main_branch</span> <span class="o">=</span> <span class="n">repo</span><span class="o">.</span><span class="n">create_head</span><span class="p">(</span><span class="n">DEFAULT_GIT_BRANCH</span><span class="p">)</span>
+</span><span id="L-359"><a href="#L-359"><span class="linenos"> 359</span></a> <span class="n">main_branch</span><span class="o">.</span><span class="n">checkout</span><span class="p">()</span>
+</span><span id="L-360"><a href="#L-360"><span class="linenos"> 360</span></a>
+</span><span id="L-361"><a href="#L-361"><span class="linenos"> 361</span></a> <span class="c1"># if the phen path does not contain the config file then initialise the phen type</span>
+</span><span id="L-362"><a href="#L-362"><span class="linenos"> 362</span></a> <span class="n">config_path</span> <span class="o">=</span> <span class="n">phen_path</span> <span class="o">/</span> <span class="n">CONFIG_FILE</span>
+</span><span id="L-363"><a href="#L-363"><span class="linenos"> 363</span></a> <span class="k">if</span> <span class="n">config_path</span><span class="o">.</span><span class="n">exists</span><span class="p">():</span>
+</span><span id="L-364"><a href="#L-364"><span class="linenos"> 364</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Phenotype configuration files already exist"</span><span class="p">)</span>
+</span><span id="L-365"><a href="#L-365"><span class="linenos"> 365</span></a> <span class="k">return</span>
+</span><span id="L-366"><a href="#L-366"><span class="linenos"> 366</span></a>
+</span><span id="L-367"><a href="#L-367"><span class="linenos"> 367</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">"Creating phen directory structure and config files"</span><span class="p">)</span>
+</span><span id="L-368"><a href="#L-368"><span class="linenos"> 368</span></a> <span class="k">for</span> <span class="n">d</span> <span class="ow">in</span> <span class="n">DEFAULT_PHEN_DIR_LIST</span><span class="p">:</span>
+</span><span id="L-369"><a href="#L-369"><span class="linenos"> 369</span></a> <span class="n">create_empty_git_dir</span><span class="p">(</span><span class="n">phen_path</span> <span class="o">/</span> <span class="n">d</span><span class="p">)</span>
+</span><span id="L-370"><a href="#L-370"><span class="linenos"> 370</span></a>
+</span><span id="L-371"><a href="#L-371"><span class="linenos"> 371</span></a> <span class="c1"># create empty phen config file</span>
+</span><span id="L-372"><a href="#L-372"><span class="linenos"> 372</span></a> <span class="n">config</span> <span class="o">=</span> <span class="p">{</span>
+</span><span id="L-373"><a href="#L-373"><span class="linenos"> 373</span></a> <span class="s2">"phenotype"</span><span class="p">:</span> <span class="p">{</span>
+</span><span id="L-374"><a href="#L-374"><span class="linenos"> 374</span></a> <span class="s2">"version"</span><span class="p">:</span> <span class="s2">"0.0.0"</span><span class="p">,</span>
+</span><span id="L-375"><a href="#L-375"><span class="linenos"> 375</span></a> <span class="s2">"omop"</span><span class="p">:</span> <span class="p">{</span>
+</span><span id="L-376"><a href="#L-376"><span class="linenos"> 376</span></a> <span class="s2">"vocabulary_id"</span><span class="p">:</span> <span class="s2">""</span><span class="p">,</span>
+</span><span id="L-377"><a href="#L-377"><span class="linenos"> 377</span></a> <span class="s2">"vocabulary_name"</span><span class="p">:</span> <span class="s2">""</span><span class="p">,</span>
+</span><span id="L-378"><a href="#L-378"><span class="linenos"> 378</span></a> <span class="s2">"vocabulary_reference"</span><span class="p">:</span> <span class="s2">""</span><span class="p">,</span>
+</span><span id="L-379"><a href="#L-379"><span class="linenos"> 379</span></a> <span class="p">},</span>
+</span><span id="L-380"><a href="#L-380"><span class="linenos"> 380</span></a> <span class="s2">"translate"</span><span class="p">:</span> <span class="p">[],</span>
+</span><span id="L-381"><a href="#L-381"><span class="linenos"> 381</span></a> <span class="s2">"concept_sets"</span><span class="p">:</span> <span class="p">[],</span>
+</span><span id="L-382"><a href="#L-382"><span class="linenos"> 382</span></a> <span class="p">}</span>
+</span><span id="L-383"><a href="#L-383"><span class="linenos"> 383</span></a> <span class="p">}</span>
+</span><span id="L-384"><a href="#L-384"><span class="linenos"> 384</span></a>
+</span><span id="L-385"><a href="#L-385"><span class="linenos"> 385</span></a> <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">phen_path</span> <span class="o">/</span> <span class="n">CONFIG_FILE</span><span class="p">,</span> <span class="s2">"w"</span><span class="p">)</span> <span class="k">as</span> <span class="n">file</span><span class="p">:</span>
+</span><span id="L-386"><a href="#L-386"><span class="linenos"> 386</span></a> <span class="n">yaml</span><span class="o">.</span><span class="n">dump</span><span class="p">(</span>
+</span><span id="L-387"><a href="#L-387"><span class="linenos"> 387</span></a> <span class="n">config</span><span class="p">,</span>
+</span><span id="L-388"><a href="#L-388"><span class="linenos"> 388</span></a> <span class="n">file</span><span class="p">,</span>
+</span><span id="L-389"><a href="#L-389"><span class="linenos"> 389</span></a> <span class="n">Dumper</span><span class="o">=</span><span class="n">util</span><span class="o">.</span><span class="n">QuotedDumper</span><span class="p">,</span>
+</span><span id="L-390"><a href="#L-390"><span class="linenos"> 390</span></a> <span class="n">default_flow_style</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span>
+</span><span id="L-391"><a href="#L-391"><span class="linenos"> 391</span></a> <span class="n">sort_keys</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span>
+</span><span id="L-392"><a href="#L-392"><span class="linenos"> 392</span></a> <span class="n">default_style</span><span class="o">=</span><span class="s1">'"'</span><span class="p">,</span>
+</span><span id="L-393"><a href="#L-393"><span class="linenos"> 393</span></a> <span class="p">)</span>
+</span><span id="L-394"><a href="#L-394"><span class="linenos"> 394</span></a>
+</span><span id="L-395"><a href="#L-395"><span class="linenos"> 395</span></a> <span class="c1"># add git ignore</span>
+</span><span id="L-396"><a href="#L-396"><span class="linenos"> 396</span></a> <span class="n">ignore_content</span> <span class="o">=</span> <span class="s2">"""# Ignore SQLite database files</span>
+</span><span id="L-397"><a href="#L-397"><span class="linenos"> 397</span></a><span class="s2">*.db</span>
+</span><span id="L-398"><a href="#L-398"><span class="linenos"> 398</span></a><span class="s2">*.sqlite3</span>
+</span><span id="L-399"><a href="#L-399"><span class="linenos"> 399</span></a><span class="s2"> </span>
+</span><span id="L-400"><a href="#L-400"><span class="linenos"> 400</span></a><span class="s2"># Ignore SQLite journal and metadata files</span>
+</span><span id="L-401"><a href="#L-401"><span class="linenos"> 401</span></a><span class="s2">*.db-journal</span>
+</span><span id="L-402"><a href="#L-402"><span class="linenos"> 402</span></a><span class="s2">*.sqlite3-journal</span>
+</span><span id="L-403"><a href="#L-403"><span class="linenos"> 403</span></a>
+</span><span id="L-404"><a href="#L-404"><span class="linenos"> 404</span></a><span class="s2"># python</span>
+</span><span id="L-405"><a href="#L-405"><span class="linenos"> 405</span></a><span class="s2">.ipynb_checkpoints</span>
+</span><span id="L-406"><a href="#L-406"><span class="linenos"> 406</span></a><span class="s2"> """</span>
+</span><span id="L-407"><a href="#L-407"><span class="linenos"> 407</span></a> <span class="n">ignore_path</span> <span class="o">=</span> <span class="n">phen_path</span> <span class="o">/</span> <span class="s2">".gitignore"</span>
+</span><span id="L-408"><a href="#L-408"><span class="linenos"> 408</span></a> <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">ignore_path</span><span class="p">,</span> <span class="s2">"w"</span><span class="p">)</span> <span class="k">as</span> <span class="n">file</span><span class="p">:</span>
+</span><span id="L-409"><a href="#L-409"><span class="linenos"> 409</span></a> <span class="n">file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">ignore_content</span><span class="p">)</span>
+</span><span id="L-410"><a href="#L-410"><span class="linenos"> 410</span></a>
+</span><span id="L-411"><a href="#L-411"><span class="linenos"> 411</span></a> <span class="c1"># add to git repo and commit</span>
+</span><span id="L-412"><a href="#L-412"><span class="linenos"> 412</span></a> <span class="k">for</span> <span class="n">d</span> <span class="ow">in</span> <span class="n">DEFAULT_PHEN_DIR_LIST</span><span class="p">:</span>
+</span><span id="L-413"><a href="#L-413"><span class="linenos"> 413</span></a> <span class="n">repo</span><span class="o">.</span><span class="n">git</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">phen_path</span> <span class="o">/</span> <span class="n">d</span><span class="p">)</span>
+</span><span id="L-414"><a href="#L-414"><span class="linenos"> 414</span></a> <span class="n">repo</span><span class="o">.</span><span class="n">git</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="nb">all</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+</span><span id="L-415"><a href="#L-415"><span class="linenos"> 415</span></a> <span class="n">repo</span><span class="o">.</span><span class="n">index</span><span class="o">.</span><span class="n">commit</span><span class="p">(</span><span class="s2">"initialised the phen git repo."</span><span class="p">)</span>
+</span><span id="L-416"><a href="#L-416"><span class="linenos"> 416</span></a>
+</span><span id="L-417"><a href="#L-417"><span class="linenos"> 417</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Phenotype initialised successfully"</span><span class="p">)</span>
+</span><span id="L-418"><a href="#L-418"><span class="linenos"> 418</span></a>
+</span><span id="L-419"><a href="#L-419"><span class="linenos"> 419</span></a>
+</span><span id="L-420"><a href="#L-420"><span class="linenos"> 420</span></a><span class="k">def</span><span class="w"> </span><span class="nf">validate</span><span class="p">(</span><span class="n">phen_dir</span><span class="p">:</span> <span class="nb">str</span><span class="p">):</span>
+</span><span id="L-421"><a href="#L-421"><span class="linenos"> 421</span></a><span class="w"> </span><span class="sd">"""Validates the phenotype directory is a git repo with standard structure"""</span>
+</span><span id="L-422"><a href="#L-422"><span class="linenos"> 422</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Validating phenotype: </span><span class="si">{</span><span class="n">phen_dir</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+</span><span id="L-423"><a href="#L-423"><span class="linenos"> 423</span></a> <span class="n">phen_path</span> <span class="o">=</span> <span class="n">Path</span><span class="p">(</span><span class="n">phen_dir</span><span class="p">)</span>
+</span><span id="L-424"><a href="#L-424"><span class="linenos"> 424</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="n">phen_path</span><span class="o">.</span><span class="n">is_dir</span><span class="p">():</span>
+</span><span id="L-425"><a href="#L-425"><span class="linenos"> 425</span></a> <span class="k">raise</span> <span class="ne">NotADirectoryError</span><span class="p">(</span>
+</span><span id="L-426"><a href="#L-426"><span class="linenos"> 426</span></a> <span class="sa">f</span><span class="s2">"Error: '</span><span class="si">{</span><span class="nb">str</span><span class="p">(</span><span class="n">phen_path</span><span class="o">.</span><span class="n">resolve</span><span class="p">())</span><span class="si">}</span><span class="s2">' is not a directory"</span>
+</span><span id="L-427"><a href="#L-427"><span class="linenos"> 427</span></a> <span class="p">)</span>
+</span><span id="L-428"><a href="#L-428"><span class="linenos"> 428</span></a>
+</span><span id="L-429"><a href="#L-429"><span class="linenos"> 429</span></a> <span class="n">config_path</span> <span class="o">=</span> <span class="n">phen_path</span> <span class="o">/</span> <span class="n">CONFIG_FILE</span>
+</span><span id="L-430"><a href="#L-430"><span class="linenos"> 430</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="n">config_path</span><span class="o">.</span><span class="n">is_file</span><span class="p">():</span>
+</span><span id="L-431"><a href="#L-431"><span class="linenos"> 431</span></a> <span class="k">raise</span> <span class="ne">FileNotFoundError</span><span class="p">(</span>
+</span><span id="L-432"><a href="#L-432"><span class="linenos"> 432</span></a> <span class="sa">f</span><span class="s2">"Error: phen configuration file '</span><span class="si">{</span><span class="n">config_path</span><span class="si">}</span><span class="s2">' does not exist."</span>
+</span><span id="L-433"><a href="#L-433"><span class="linenos"> 433</span></a> <span class="p">)</span>
+</span><span id="L-434"><a href="#L-434"><span class="linenos"> 434</span></a>
+</span><span id="L-435"><a href="#L-435"><span class="linenos"> 435</span></a> <span class="n">concepts_path</span> <span class="o">=</span> <span class="n">phen_path</span> <span class="o">/</span> <span class="n">CONCEPTS_DIR</span>
+</span><span id="L-436"><a href="#L-436"><span class="linenos"> 436</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="n">concepts_path</span><span class="o">.</span><span class="n">is_dir</span><span class="p">():</span>
+</span><span id="L-437"><a href="#L-437"><span class="linenos"> 437</span></a> <span class="k">raise</span> <span class="ne">FileNotFoundError</span><span class="p">(</span>
+</span><span id="L-438"><a href="#L-438"><span class="linenos"> 438</span></a> <span class="sa">f</span><span class="s2">"Error: source concepts directory </span><span class="si">{</span><span class="n">concepts_path</span><span class="si">}</span><span class="s2"> does not exist."</span>
+</span><span id="L-439"><a href="#L-439"><span class="linenos"> 439</span></a> <span class="p">)</span>
+</span><span id="L-440"><a href="#L-440"><span class="linenos"> 440</span></a>
+</span><span id="L-441"><a href="#L-441"><span class="linenos"> 441</span></a> <span class="c1"># Calidate the directory is a git repo</span>
+</span><span id="L-442"><a href="#L-442"><span class="linenos"> 442</span></a> <span class="k">try</span><span class="p">:</span>
+</span><span id="L-443"><a href="#L-443"><span class="linenos"> 443</span></a> <span class="n">git</span><span class="o">.</span><span class="n">Repo</span><span class="p">(</span><span class="n">phen_path</span><span class="p">)</span>
+</span><span id="L-444"><a href="#L-444"><span class="linenos"> 444</span></a> <span class="k">except</span> <span class="p">(</span><span class="n">git</span><span class="o">.</span><span class="n">exc</span><span class="o">.</span><span class="n">InvalidGitRepositoryError</span><span class="p">,</span> <span class="n">git</span><span class="o">.</span><span class="n">exc</span><span class="o">.</span><span class="n">NoSuchPathError</span><span class="p">):</span>
+</span><span id="L-445"><a href="#L-445"><span class="linenos"> 445</span></a> <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Phen directory </span><span class="si">{</span><span class="n">phen_path</span><span class="si">}</span><span class="s2"> is not a git repo"</span><span class="p">)</span>
+</span><span id="L-446"><a href="#L-446"><span class="linenos"> 446</span></a>
+</span><span id="L-447"><a href="#L-447"><span class="linenos"> 447</span></a> <span class="c1"># Load configuration File</span>
+</span><span id="L-448"><a href="#L-448"><span class="linenos"> 448</span></a> <span class="k">if</span> <span class="n">config_path</span><span class="o">.</span><span class="n">suffix</span> <span class="o">==</span> <span class="s2">".yaml"</span><span class="p">:</span>
+</span><span id="L-449"><a href="#L-449"><span class="linenos"> 449</span></a> <span class="k">try</span><span class="p">:</span>
+</span><span id="L-450"><a href="#L-450"><span class="linenos"> 450</span></a> <span class="k">with</span> <span class="n">config_path</span><span class="o">.</span><span class="n">open</span><span class="p">(</span><span class="s2">"r"</span><span class="p">)</span> <span class="k">as</span> <span class="n">file</span><span class="p">:</span>
+</span><span id="L-451"><a href="#L-451"><span class="linenos"> 451</span></a> <span class="n">phenotype</span> <span class="o">=</span> <span class="n">yaml</span><span class="o">.</span><span class="n">safe_load</span><span class="p">(</span><span class="n">file</span><span class="p">)</span>
+</span><span id="L-452"><a href="#L-452"><span class="linenos"> 452</span></a>
+</span><span id="L-453"><a href="#L-453"><span class="linenos"> 453</span></a> <span class="n">validator</span> <span class="o">=</span> <span class="n">Validator</span><span class="p">(</span><span class="n">CONFIG_SCHEMA</span><span class="p">)</span>
+</span><span id="L-454"><a href="#L-454"><span class="linenos"> 454</span></a> <span class="k">if</span> <span class="n">validator</span><span class="o">.</span><span class="n">validate</span><span class="p">(</span><span class="n">phenotype</span><span class="p">):</span>
+</span><span id="L-455"><a href="#L-455"><span class="linenos"> 455</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="s2">"YAML structure is valid."</span><span class="p">)</span>
+</span><span id="L-456"><a href="#L-456"><span class="linenos"> 456</span></a> <span class="k">else</span><span class="p">:</span>
+</span><span id="L-457"><a href="#L-457"><span class="linenos"> 457</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">error</span><span class="p">(</span><span class="sa">f</span><span class="s2">"YAML structure validation failed: </span><span class="si">{</span><span class="n">validator</span><span class="o">.</span><span class="n">errors</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+</span><span id="L-458"><a href="#L-458"><span class="linenos"> 458</span></a> <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="sa">f</span><span class="s2">"YAML structure validation failed: </span><span class="si">{</span><span class="n">validator</span><span class="o">.</span><span class="n">errors</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+</span><span id="L-459"><a href="#L-459"><span class="linenos"> 459</span></a> <span class="k">except</span> <span class="n">yaml</span><span class="o">.</span><span class="n">YAMLError</span> <span class="k">as</span> <span class="n">e</span><span class="p">:</span>
+</span><span id="L-460"><a href="#L-460"><span class="linenos"> 460</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">error</span><span class="p">(</span><span class="sa">f</span><span class="s2">"YAML syntax error: </span><span class="si">{</span><span class="n">e</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+</span><span id="L-461"><a href="#L-461"><span class="linenos"> 461</span></a> <span class="k">raise</span> <span class="n">e</span>
+</span><span id="L-462"><a href="#L-462"><span class="linenos"> 462</span></a> <span class="k">else</span><span class="p">:</span>
+</span><span id="L-463"><a href="#L-463"><span class="linenos"> 463</span></a> <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span>
+</span><span id="L-464"><a href="#L-464"><span class="linenos"> 464</span></a> <span class="sa">f</span><span class="s2">"Unsupported configuration filetype: </span><span class="si">{</span><span class="nb">str</span><span class="p">(</span><span class="n">config_path</span><span class="o">.</span><span class="n">resolve</span><span class="p">())</span><span class="si">}</span><span class="s2">"</span>
+</span><span id="L-465"><a href="#L-465"><span class="linenos"> 465</span></a> <span class="p">)</span>
+</span><span id="L-466"><a href="#L-466"><span class="linenos"> 466</span></a>
+</span><span id="L-467"><a href="#L-467"><span class="linenos"> 467</span></a> <span class="c1"># initiatise</span>
+</span><span id="L-468"><a href="#L-468"><span class="linenos"> 468</span></a> <span class="n">validation_errors</span> <span class="o">=</span> <span class="p">[]</span>
+</span><span id="L-469"><a href="#L-469"><span class="linenos"> 469</span></a> <span class="n">phenotype</span> <span class="o">=</span> <span class="n">phenotype</span><span class="p">[</span><span class="s2">"phenotype"</span><span class="p">]</span>
+</span><span id="L-470"><a href="#L-470"><span class="linenos"> 470</span></a> <span class="n">code_types</span> <span class="o">=</span> <span class="n">parse</span><span class="o">.</span><span class="n">CodeTypeParser</span><span class="p">()</span><span class="o">.</span><span class="n">code_types</span>
+</span><span id="L-471"><a href="#L-471"><span class="linenos"> 471</span></a>
+</span><span id="L-472"><a href="#L-472"><span class="linenos"> 472</span></a> <span class="c1"># check the version number is of the format vn.n.n</span>
+</span><span id="L-473"><a href="#L-473"><span class="linenos"> 473</span></a> <span class="n">match</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="sa">r</span><span class="s2">"(\d+\.\d+\.\d+)"</span><span class="p">,</span> <span class="n">phenotype</span><span class="p">[</span><span class="s2">"version"</span><span class="p">])</span>
+</span><span id="L-474"><a href="#L-474"><span class="linenos"> 474</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="n">match</span><span class="p">:</span>
+</span><span id="L-475"><a href="#L-475"><span class="linenos"> 475</span></a> <span class="n">validation_errors</span><span class="o">.</span><span class="n">append</span><span class="p">(</span>
+</span><span id="L-476"><a href="#L-476"><span class="linenos"> 476</span></a> <span class="sa">f</span><span class="s2">"Invalid version format in configuration file: </span><span class="si">{</span><span class="n">phenotype</span><span class="p">[</span><span class="s1">'version'</span><span class="p">]</span><span class="si">}</span><span class="s2">"</span>
+</span><span id="L-477"><a href="#L-477"><span class="linenos"> 477</span></a> <span class="p">)</span>
+</span><span id="L-478"><a href="#L-478"><span class="linenos"> 478</span></a>
+</span><span id="L-479"><a href="#L-479"><span class="linenos"> 479</span></a> <span class="c1"># create a list of all the concept set names defined in the concept set configuration</span>
+</span><span id="L-480"><a href="#L-480"><span class="linenos"> 480</span></a> <span class="n">concept_set_names</span> <span class="o">=</span> <span class="p">[]</span>
+</span><span id="L-481"><a href="#L-481"><span class="linenos"> 481</span></a> <span class="k">for</span> <span class="n">item</span> <span class="ow">in</span> <span class="n">phenotype</span><span class="p">[</span><span class="s2">"concept_sets"</span><span class="p">]:</span>
+</span><span id="L-482"><a href="#L-482"><span class="linenos"> 482</span></a> <span class="k">if</span> <span class="n">item</span><span class="p">[</span><span class="s2">"name"</span><span class="p">]</span> <span class="ow">in</span> <span class="n">concept_set_names</span><span class="p">:</span>
+</span><span id="L-483"><a href="#L-483"><span class="linenos"> 483</span></a> <span class="n">validation_errors</span><span class="o">.</span><span class="n">append</span><span class="p">(</span>
+</span><span id="L-484"><a href="#L-484"><span class="linenos"> 484</span></a> <span class="sa">f</span><span class="s2">"Duplicate concept set defined in concept sets </span><span class="si">{</span><span class="n">item</span><span class="p">[</span><span class="s1">'name'</span><span class="p">]</span><span class="w"> </span><span class="si">}</span><span class="s2">"</span>
+</span><span id="L-485"><a href="#L-485"><span class="linenos"> 485</span></a> <span class="p">)</span>
+</span><span id="L-486"><a href="#L-486"><span class="linenos"> 486</span></a> <span class="k">else</span><span class="p">:</span>
+</span><span id="L-487"><a href="#L-487"><span class="linenos"> 487</span></a> <span class="n">concept_set_names</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">item</span><span class="p">[</span><span class="s2">"name"</span><span class="p">])</span>
+</span><span id="L-488"><a href="#L-488"><span class="linenos"> 488</span></a>
+</span><span id="L-489"><a href="#L-489"><span class="linenos"> 489</span></a> <span class="c1"># check codes definition</span>
+</span><span id="L-490"><a href="#L-490"><span class="linenos"> 490</span></a> <span class="k">for</span> <span class="n">item</span> <span class="ow">in</span> <span class="n">phenotype</span><span class="p">[</span><span class="s2">"concept_sets"</span><span class="p">]:</span>
+</span><span id="L-491"><a href="#L-491"><span class="linenos"> 491</span></a> <span class="c1"># check concepte code file exists</span>
+</span><span id="L-492"><a href="#L-492"><span class="linenos"> 492</span></a> <span class="n">concept_code_file_path</span> <span class="o">=</span> <span class="n">concepts_path</span> <span class="o">/</span> <span class="n">item</span><span class="p">[</span><span class="s2">"file"</span><span class="p">][</span><span class="s2">"path"</span><span class="p">]</span>
+</span><span id="L-493"><a href="#L-493"><span class="linenos"> 493</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="n">concept_code_file_path</span><span class="o">.</span><span class="n">exists</span><span class="p">():</span>
+</span><span id="L-494"><a href="#L-494"><span class="linenos"> 494</span></a> <span class="n">validation_errors</span><span class="o">.</span><span class="n">append</span><span class="p">(</span>
+</span><span id="L-495"><a href="#L-495"><span class="linenos"> 495</span></a> <span class="sa">f</span><span class="s2">"Coding file </span><span class="si">{</span><span class="nb">str</span><span class="p">(</span><span class="n">concept_code_file_path</span><span class="o">.</span><span class="n">resolve</span><span class="p">())</span><span class="si">}</span><span class="s2"> does not exist"</span>
+</span><span id="L-496"><a href="#L-496"><span class="linenos"> 496</span></a> <span class="p">)</span>
+</span><span id="L-497"><a href="#L-497"><span class="linenos"> 497</span></a>
+</span><span id="L-498"><a href="#L-498"><span class="linenos"> 498</span></a> <span class="c1"># check concepte code file is not empty</span>
+</span><span id="L-499"><a href="#L-499"><span class="linenos"> 499</span></a> <span class="k">if</span> <span class="n">concept_code_file_path</span><span class="o">.</span><span class="n">stat</span><span class="p">()</span><span class="o">.</span><span class="n">st_size</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
+</span><span id="L-500"><a href="#L-500"><span class="linenos"> 500</span></a> <span class="n">validation_errors</span><span class="o">.</span><span class="n">append</span><span class="p">(</span>
+</span><span id="L-501"><a href="#L-501"><span class="linenos"> 501</span></a> <span class="sa">f</span><span class="s2">"Coding file </span><span class="si">{</span><span class="nb">str</span><span class="p">(</span><span class="n">concept_code_file_path</span><span class="o">.</span><span class="n">resolve</span><span class="p">())</span><span class="si">}</span><span class="s2"> is an empty file"</span>
+</span><span id="L-502"><a href="#L-502"><span class="linenos"> 502</span></a> <span class="p">)</span>
+</span><span id="L-503"><a href="#L-503"><span class="linenos"> 503</span></a>
+</span><span id="L-504"><a href="#L-504"><span class="linenos"> 504</span></a> <span class="c1"># check code file type is supported</span>
+</span><span id="L-505"><a href="#L-505"><span class="linenos"> 505</span></a> <span class="k">if</span> <span class="n">concept_code_file_path</span><span class="o">.</span><span class="n">suffix</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">CODE_FILE_TYPES</span><span class="p">:</span>
+</span><span id="L-506"><a href="#L-506"><span class="linenos"> 506</span></a> <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span>
+</span><span id="L-507"><a href="#L-507"><span class="linenos"> 507</span></a> <span class="sa">f</span><span class="s2">"Unsupported filetype </span><span class="si">{</span><span class="n">concept_code_file_path</span><span class="o">.</span><span class="n">suffix</span><span class="si">}</span><span class="s2">, only support csv, xlsx, xls code file types"</span>
+</span><span id="L-508"><a href="#L-508"><span class="linenos"> 508</span></a> <span class="p">)</span>
+</span><span id="L-509"><a href="#L-509"><span class="linenos"> 509</span></a>
+</span><span id="L-510"><a href="#L-510"><span class="linenos"> 510</span></a> <span class="c1"># check columns specified are a supported medical coding type</span>
+</span><span id="L-511"><a href="#L-511"><span class="linenos"> 511</span></a> <span class="k">for</span> <span class="n">column</span> <span class="ow">in</span> <span class="n">item</span><span class="p">[</span><span class="s2">"file"</span><span class="p">][</span><span class="s2">"columns"</span><span class="p">]:</span>
+</span><span id="L-512"><a href="#L-512"><span class="linenos"> 512</span></a> <span class="k">if</span> <span class="n">column</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">code_types</span><span class="p">:</span>
+</span><span id="L-513"><a href="#L-513"><span class="linenos"> 513</span></a> <span class="n">validation_errors</span><span class="o">.</span><span class="n">append</span><span class="p">(</span>
+</span><span id="L-514"><a href="#L-514"><span class="linenos"> 514</span></a> <span class="sa">f</span><span class="s2">"Column type </span><span class="si">{</span><span class="n">column</span><span class="si">}</span><span class="s2"> for file </span><span class="si">{</span><span class="n">concept_code_file_path</span><span class="si">}</span><span class="s2"> is not supported"</span>
+</span><span id="L-515"><a href="#L-515"><span class="linenos"> 515</span></a> <span class="p">)</span>
+</span><span id="L-516"><a href="#L-516"><span class="linenos"> 516</span></a>
+</span><span id="L-517"><a href="#L-517"><span class="linenos"> 517</span></a> <span class="c1"># check the actions are supported</span>
+</span><span id="L-518"><a href="#L-518"><span class="linenos"> 518</span></a> <span class="k">if</span> <span class="s2">"actions"</span> <span class="ow">in</span> <span class="n">item</span><span class="p">[</span><span class="s2">"file"</span><span class="p">]:</span>
+</span><span id="L-519"><a href="#L-519"><span class="linenos"> 519</span></a> <span class="k">for</span> <span class="n">action</span> <span class="ow">in</span> <span class="n">item</span><span class="p">[</span><span class="s2">"file"</span><span class="p">][</span><span class="s2">"actions"</span><span class="p">]:</span>
+</span><span id="L-520"><a href="#L-520"><span class="linenos"> 520</span></a> <span class="k">if</span> <span class="n">action</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">COL_ACTIONS</span><span class="p">:</span>
+</span><span id="L-521"><a href="#L-521"><span class="linenos"> 521</span></a> <span class="n">validation_errors</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Action </span><span class="si">{</span><span class="n">action</span><span class="si">}</span><span class="s2"> is not supported"</span><span class="p">)</span>
+</span><span id="L-522"><a href="#L-522"><span class="linenos"> 522</span></a>
+</span><span id="L-523"><a href="#L-523"><span class="linenos"> 523</span></a> <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">validation_errors</span><span class="p">)</span> <span class="o">></span> <span class="mi">0</span><span class="p">:</span>
+</span><span id="L-524"><a href="#L-524"><span class="linenos"> 524</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">error</span><span class="p">(</span><span class="n">validation_errors</span><span class="p">)</span>
+</span><span id="L-525"><a href="#L-525"><span class="linenos"> 525</span></a> <span class="k">raise</span> <span class="n">PhenValidationException</span><span class="p">(</span>
+</span><span id="L-526"><a href="#L-526"><span class="linenos"> 526</span></a> <span class="sa">f</span><span class="s2">"Configuration file </span><span class="si">{</span><span class="nb">str</span><span class="p">(</span><span class="n">config_path</span><span class="o">.</span><span class="n">resolve</span><span class="p">())</span><span class="si">}</span><span class="s2"> failed validation"</span><span class="p">,</span>
+</span><span id="L-527"><a href="#L-527"><span class="linenos"> 527</span></a> <span class="n">validation_errors</span><span class="p">,</span>
+</span><span id="L-528"><a href="#L-528"><span class="linenos"> 528</span></a> <span class="p">)</span>
+</span><span id="L-529"><a href="#L-529"><span class="linenos"> 529</span></a>
+</span><span id="L-530"><a href="#L-530"><span class="linenos"> 530</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Phenotype validated successfully"</span><span class="p">)</span>
+</span><span id="L-531"><a href="#L-531"><span class="linenos"> 531</span></a>
+</span><span id="L-532"><a href="#L-532"><span class="linenos"> 532</span></a>
+</span><span id="L-533"><a href="#L-533"><span class="linenos"> 533</span></a><span class="k">def</span><span class="w"> </span><span class="nf">read_table_file</span><span class="p">(</span><span class="n">path</span><span class="p">:</span> <span class="n">Path</span><span class="p">,</span> <span class="n">excel_sheet</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="s2">""</span><span class="p">):</span>
+</span><span id="L-534"><a href="#L-534"><span class="linenos"> 534</span></a><span class="w"> </span><span class="sd">"""</span>
+</span><span id="L-535"><a href="#L-535"><span class="linenos"> 535</span></a><span class="sd"> Load Code List File</span>
+</span><span id="L-536"><a href="#L-536"><span class="linenos"> 536</span></a><span class="sd"> """</span>
+</span><span id="L-537"><a href="#L-537"><span class="linenos"> 537</span></a>
+</span><span id="L-538"><a href="#L-538"><span class="linenos"> 538</span></a> <span class="n">path</span> <span class="o">=</span> <span class="n">path</span><span class="o">.</span><span class="n">resolve</span><span class="p">()</span>
+</span><span id="L-539"><a href="#L-539"><span class="linenos"> 539</span></a> <span class="k">if</span> <span class="n">path</span><span class="o">.</span><span class="n">suffix</span> <span class="o">==</span> <span class="s2">".csv"</span><span class="p">:</span>
+</span><span id="L-540"><a href="#L-540"><span class="linenos"> 540</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">read_csv</span><span class="p">(</span><span class="n">path</span><span class="p">,</span> <span class="n">dtype</span><span class="o">=</span><span class="nb">str</span><span class="p">)</span>
+</span><span id="L-541"><a href="#L-541"><span class="linenos"> 541</span></a> <span class="k">elif</span> <span class="n">path</span><span class="o">.</span><span class="n">suffix</span> <span class="o">==</span> <span class="s2">".xlsx"</span> <span class="ow">or</span> <span class="n">path</span><span class="o">.</span><span class="n">suffix</span> <span class="o">==</span> <span class="s2">".xls"</span><span class="p">:</span>
+</span><span id="L-542"><a href="#L-542"><span class="linenos"> 542</span></a> <span class="k">if</span> <span class="n">excel_sheet</span> <span class="o">!=</span> <span class="s2">""</span><span class="p">:</span>
+</span><span id="L-543"><a href="#L-543"><span class="linenos"> 543</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">read_excel</span><span class="p">(</span><span class="n">path</span><span class="p">,</span> <span class="n">sheet_name</span><span class="o">=</span><span class="n">excel_sheet</span><span class="p">,</span> <span class="n">dtype</span><span class="o">=</span><span class="nb">str</span><span class="p">)</span>
+</span><span id="L-544"><a href="#L-544"><span class="linenos"> 544</span></a> <span class="k">else</span><span class="p">:</span>
+</span><span id="L-545"><a href="#L-545"><span class="linenos"> 545</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">read_excel</span><span class="p">(</span><span class="n">path</span><span class="p">,</span> <span class="n">dtype</span><span class="o">=</span><span class="nb">str</span><span class="p">)</span>
+</span><span id="L-546"><a href="#L-546"><span class="linenos"> 546</span></a> <span class="k">elif</span> <span class="n">path</span><span class="o">.</span><span class="n">suffix</span> <span class="o">==</span> <span class="s2">".dta"</span><span class="p">:</span>
+</span><span id="L-547"><a href="#L-547"><span class="linenos"> 547</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">read_stata</span><span class="p">(</span><span class="n">path</span><span class="p">)</span>
+</span><span id="L-548"><a href="#L-548"><span class="linenos"> 548</span></a> <span class="k">else</span><span class="p">:</span>
+</span><span id="L-549"><a href="#L-549"><span class="linenos"> 549</span></a> <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span>
+</span><span id="L-550"><a href="#L-550"><span class="linenos"> 550</span></a> <span class="sa">f</span><span class="s2">"Unsupported filetype </span><span class="si">{</span><span class="n">path</span><span class="o">.</span><span class="n">suffix</span><span class="si">}</span><span class="s2">, only support</span><span class="si">{</span><span class="n">CODE_FILE_TYPES</span><span class="si">}</span><span class="s2"> code file types"</span>
+</span><span id="L-551"><a href="#L-551"><span class="linenos"> 551</span></a> <span class="p">)</span>
+</span><span id="L-552"><a href="#L-552"><span class="linenos"> 552</span></a>
+</span><span id="L-553"><a href="#L-553"><span class="linenos"> 553</span></a> <span class="k">return</span> <span class="n">df</span>
+</span><span id="L-554"><a href="#L-554"><span class="linenos"> 554</span></a>
+</span><span id="L-555"><a href="#L-555"><span class="linenos"> 555</span></a>
+</span><span id="L-556"><a href="#L-556"><span class="linenos"> 556</span></a><span class="k">def</span><span class="w"> </span><span class="nf">process_actions</span><span class="p">(</span><span class="n">df</span><span class="p">:</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">,</span> <span class="n">concept_set</span><span class="p">:</span> <span class="nb">dict</span><span class="p">)</span> <span class="o">-></span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">:</span>
+</span><span id="L-557"><a href="#L-557"><span class="linenos"> 557</span></a> <span class="c1"># Perform Structural Changes to file before preprocessing</span>
+</span><span id="L-558"><a href="#L-558"><span class="linenos"> 558</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="s2">"Processing file structural actions"</span><span class="p">)</span>
+</span><span id="L-559"><a href="#L-559"><span class="linenos"> 559</span></a> <span class="k">if</span> <span class="p">(</span>
+</span><span id="L-560"><a href="#L-560"><span class="linenos"> 560</span></a> <span class="s2">"actions"</span> <span class="ow">in</span> <span class="n">concept_set</span><span class="p">[</span><span class="s2">"file"</span><span class="p">]</span>
+</span><span id="L-561"><a href="#L-561"><span class="linenos"> 561</span></a> <span class="ow">and</span> <span class="s2">"split_col"</span> <span class="ow">in</span> <span class="n">concept_set</span><span class="p">[</span><span class="s2">"file"</span><span class="p">][</span><span class="s2">"actions"</span><span class="p">]</span>
+</span><span id="L-562"><a href="#L-562"><span class="linenos"> 562</span></a> <span class="ow">and</span> <span class="s2">"codes_col"</span> <span class="ow">in</span> <span class="n">concept_set</span><span class="p">[</span><span class="s2">"file"</span><span class="p">][</span><span class="s2">"actions"</span><span class="p">]</span>
+</span><span id="L-563"><a href="#L-563"><span class="linenos"> 563</span></a> <span class="p">):</span>
+</span><span id="L-564"><a href="#L-564"><span class="linenos"> 564</span></a> <span class="n">split_col</span> <span class="o">=</span> <span class="n">concept_set</span><span class="p">[</span><span class="s2">"file"</span><span class="p">][</span><span class="s2">"actions"</span><span class="p">][</span><span class="s2">"split_col"</span><span class="p">]</span>
+</span><span id="L-565"><a href="#L-565"><span class="linenos"> 565</span></a> <span class="n">codes_col</span> <span class="o">=</span> <span class="n">concept_set</span><span class="p">[</span><span class="s2">"file"</span><span class="p">][</span><span class="s2">"actions"</span><span class="p">][</span><span class="s2">"codes_col"</span><span class="p">]</span>
+</span><span id="L-566"><a href="#L-566"><span class="linenos"> 566</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span>
+</span><span id="L-567"><a href="#L-567"><span class="linenos"> 567</span></a> <span class="s2">"Action: Splitting"</span><span class="p">,</span>
+</span><span id="L-568"><a href="#L-568"><span class="linenos"> 568</span></a> <span class="n">split_col</span><span class="p">,</span>
+</span><span id="L-569"><a href="#L-569"><span class="linenos"> 569</span></a> <span class="s2">"column into:"</span><span class="p">,</span>
+</span><span id="L-570"><a href="#L-570"><span class="linenos"> 570</span></a> <span class="n">df</span><span class="p">[</span><span class="n">split_col</span><span class="p">]</span><span class="o">.</span><span class="n">unique</span><span class="p">(),</span>
+</span><span id="L-571"><a href="#L-571"><span class="linenos"> 571</span></a> <span class="p">)</span>
+</span><span id="L-572"><a href="#L-572"><span class="linenos"> 572</span></a> <span class="n">codes</span> <span class="o">=</span> <span class="n">df</span><span class="p">[</span><span class="n">codes_col</span><span class="p">]</span>
+</span><span id="L-573"><a href="#L-573"><span class="linenos"> 573</span></a> <span class="n">oh</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">get_dummies</span><span class="p">(</span><span class="n">df</span><span class="p">[</span><span class="n">split_col</span><span class="p">],</span> <span class="n">dtype</span><span class="o">=</span><span class="nb">bool</span><span class="p">)</span> <span class="c1"># one hot encode</span>
+</span><span id="L-574"><a href="#L-574"><span class="linenos"> 574</span></a> <span class="n">oh</span> <span class="o">=</span> <span class="n">oh</span><span class="o">.</span><span class="n">where</span><span class="p">((</span><span class="n">oh</span> <span class="o">!=</span> <span class="kc">True</span><span class="p">),</span> <span class="n">codes</span><span class="p">,</span> <span class="n">axis</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span> <span class="c1"># fill in 1s with codes</span>
+</span><span id="L-575"><a href="#L-575"><span class="linenos"> 575</span></a> <span class="n">oh</span><span class="p">[</span><span class="n">oh</span> <span class="o">==</span> <span class="kc">False</span><span class="p">]</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">nan</span> <span class="c1"># replace 0s with None</span>
+</span><span id="L-576"><a href="#L-576"><span class="linenos"> 576</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">concat</span><span class="p">([</span><span class="n">df</span><span class="p">,</span> <span class="n">oh</span><span class="p">],</span> <span class="n">axis</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span> <span class="c1"># merge in new columns</span>
+</span><span id="L-577"><a href="#L-577"><span class="linenos"> 577</span></a>
+</span><span id="L-578"><a href="#L-578"><span class="linenos"> 578</span></a> <span class="k">return</span> <span class="n">df</span>
+</span><span id="L-579"><a href="#L-579"><span class="linenos"> 579</span></a>
+</span><span id="L-580"><a href="#L-580"><span class="linenos"> 580</span></a>
+</span><span id="L-581"><a href="#L-581"><span class="linenos"> 581</span></a><span class="c1"># Perform QA Checks on columns individually and append to df</span>
+</span><span id="L-582"><a href="#L-582"><span class="linenos"> 582</span></a><span class="k">def</span><span class="w"> </span><span class="nf">preprocess_source_concepts</span><span class="p">(</span>
+</span><span id="L-583"><a href="#L-583"><span class="linenos"> 583</span></a> <span class="n">df</span><span class="p">:</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">,</span> <span class="n">concept_set</span><span class="p">:</span> <span class="nb">dict</span><span class="p">,</span> <span class="n">code_file_path</span><span class="p">:</span> <span class="n">Path</span>
+</span><span id="L-584"><a href="#L-584"><span class="linenos"> 584</span></a><span class="p">)</span> <span class="o">-></span> <span class="n">Tuple</span><span class="p">[</span><span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">,</span> <span class="nb">list</span><span class="p">]:</span>
+</span><span id="L-585"><a href="#L-585"><span class="linenos"> 585</span></a><span class="w"> </span><span class="sd">"""Parses each column individually - Order and length will not be preserved!"""</span>
+</span><span id="L-586"><a href="#L-586"><span class="linenos"> 586</span></a> <span class="n">out</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">([])</span> <span class="c1"># create output df to append to</span>
+</span><span id="L-587"><a href="#L-587"><span class="linenos"> 587</span></a> <span class="n">code_errors</span> <span class="o">=</span> <span class="p">[]</span> <span class="c1"># list of errors from processing</span>
+</span><span id="L-588"><a href="#L-588"><span class="linenos"> 588</span></a>
+</span><span id="L-589"><a href="#L-589"><span class="linenos"> 589</span></a> <span class="c1"># remove unnamed columns due to extra commas, missing headers, or incorrect parsing</span>
+</span><span id="L-590"><a href="#L-590"><span class="linenos"> 590</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">df</span><span class="o">.</span><span class="n">drop</span><span class="p">(</span><span class="n">columns</span><span class="o">=</span><span class="p">[</span><span class="n">col</span> <span class="k">for</span> <span class="n">col</span> <span class="ow">in</span> <span class="n">df</span><span class="o">.</span><span class="n">columns</span> <span class="k">if</span> <span class="s2">"Unnamed"</span> <span class="ow">in</span> <span class="n">col</span><span class="p">])</span>
+</span><span id="L-591"><a href="#L-591"><span class="linenos"> 591</span></a>
+</span><span id="L-592"><a href="#L-592"><span class="linenos"> 592</span></a> <span class="c1"># Preprocess codes</span>
+</span><span id="L-593"><a href="#L-593"><span class="linenos"> 593</span></a> <span class="n">code_types</span> <span class="o">=</span> <span class="n">parse</span><span class="o">.</span><span class="n">CodeTypeParser</span><span class="p">()</span><span class="o">.</span><span class="n">code_types</span>
+</span><span id="L-594"><a href="#L-594"><span class="linenos"> 594</span></a> <span class="k">for</span> <span class="n">code_type</span> <span class="ow">in</span> <span class="n">concept_set</span><span class="p">[</span><span class="s2">"file"</span><span class="p">][</span><span class="s2">"columns"</span><span class="p">]:</span>
+</span><span id="L-595"><a href="#L-595"><span class="linenos"> 595</span></a> <span class="n">parser</span> <span class="o">=</span> <span class="n">code_types</span><span class="p">[</span><span class="n">code_type</span><span class="p">]</span>
+</span><span id="L-596"><a href="#L-596"><span class="linenos"> 596</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Processing </span><span class="si">{</span><span class="n">code_type</span><span class="si">}</span><span class="s2"> codes for </span><span class="si">{</span><span class="n">code_file_path</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+</span><span id="L-597"><a href="#L-597"><span class="linenos"> 597</span></a>
+</span><span id="L-598"><a href="#L-598"><span class="linenos"> 598</span></a> <span class="c1"># get codes by column name</span>
+</span><span id="L-599"><a href="#L-599"><span class="linenos"> 599</span></a> <span class="n">source_col_name</span> <span class="o">=</span> <span class="n">concept_set</span><span class="p">[</span><span class="s2">"file"</span><span class="p">][</span><span class="s2">"columns"</span><span class="p">][</span><span class="n">code_type</span><span class="p">]</span>
+</span><span id="L-600"><a href="#L-600"><span class="linenos"> 600</span></a> <span class="n">codes</span> <span class="o">=</span> <span class="n">df</span><span class="p">[</span><span class="n">source_col_name</span><span class="p">]</span><span class="o">.</span><span class="n">dropna</span><span class="p">()</span>
+</span><span id="L-601"><a href="#L-601"><span class="linenos"> 601</span></a> <span class="n">codes</span> <span class="o">=</span> <span class="n">codes</span><span class="o">.</span><span class="n">astype</span><span class="p">(</span><span class="nb">str</span><span class="p">)</span> <span class="c1"># convert to string</span>
+</span><span id="L-602"><a href="#L-602"><span class="linenos"> 602</span></a> <span class="n">codes</span> <span class="o">=</span> <span class="n">codes</span><span class="o">.</span><span class="n">str</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span> <span class="c1"># remove excess spaces</span>
+</span><span id="L-603"><a href="#L-603"><span class="linenos"> 603</span></a>
+</span><span id="L-604"><a href="#L-604"><span class="linenos"> 604</span></a> <span class="c1"># process codes, validating them using parser and returning the errors</span>
+</span><span id="L-605"><a href="#L-605"><span class="linenos"> 605</span></a> <span class="n">codes</span><span class="p">,</span> <span class="n">errors</span> <span class="o">=</span> <span class="n">parser</span><span class="o">.</span><span class="n">process</span><span class="p">(</span><span class="n">codes</span><span class="p">,</span> <span class="n">code_file_path</span><span class="p">)</span>
+</span><span id="L-606"><a href="#L-606"><span class="linenos"> 606</span></a> <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">errors</span><span class="p">)</span> <span class="o">></span> <span class="mi">0</span><span class="p">:</span>
+</span><span id="L-607"><a href="#L-607"><span class="linenos"> 607</span></a> <span class="n">code_errors</span><span class="o">.</span><span class="n">extend</span><span class="p">(</span><span class="n">errors</span><span class="p">)</span>
+</span><span id="L-608"><a href="#L-608"><span class="linenos"> 608</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">warning</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Codes validation failed with </span><span class="si">{</span><span class="nb">len</span><span class="p">(</span><span class="n">errors</span><span class="p">)</span><span class="si">}</span><span class="s2"> errors"</span><span class="p">)</span>
+</span><span id="L-609"><a href="#L-609"><span class="linenos"> 609</span></a>
+</span><span id="L-610"><a href="#L-610"><span class="linenos"> 610</span></a> <span class="c1"># add processed codes to df</span>
+</span><span id="L-611"><a href="#L-611"><span class="linenos"> 611</span></a> <span class="n">new_col_name</span> <span class="o">=</span> <span class="sa">f</span><span class="s2">"</span><span class="si">{</span><span class="n">source_col_name</span><span class="si">}</span><span class="s2">_SOURCE"</span>
+</span><span id="L-612"><a href="#L-612"><span class="linenos"> 612</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">df</span><span class="o">.</span><span class="n">rename</span><span class="p">(</span><span class="n">columns</span><span class="o">=</span><span class="p">{</span><span class="n">source_col_name</span><span class="p">:</span> <span class="n">new_col_name</span><span class="p">})</span>
+</span><span id="L-613"><a href="#L-613"><span class="linenos"> 613</span></a> <span class="n">process_codes</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">({</span><span class="n">code_type</span><span class="p">:</span> <span class="n">codes</span><span class="p">})</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">df</span><span class="p">)</span>
+</span><span id="L-614"><a href="#L-614"><span class="linenos"> 614</span></a> <span class="n">out</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">concat</span><span class="p">(</span>
+</span><span id="L-615"><a href="#L-615"><span class="linenos"> 615</span></a> <span class="p">[</span><span class="n">out</span><span class="p">,</span> <span class="n">process_codes</span><span class="p">],</span>
+</span><span id="L-616"><a href="#L-616"><span class="linenos"> 616</span></a> <span class="n">ignore_index</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span>
+</span><span id="L-617"><a href="#L-617"><span class="linenos"> 617</span></a> <span class="p">)</span>
+</span><span id="L-618"><a href="#L-618"><span class="linenos"> 618</span></a>
+</span><span id="L-619"><a href="#L-619"><span class="linenos"> 619</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="n">out</span><span class="o">.</span><span class="n">head</span><span class="p">())</span>
+</span><span id="L-620"><a href="#L-620"><span class="linenos"> 620</span></a>
+</span><span id="L-621"><a href="#L-621"><span class="linenos"> 621</span></a> <span class="k">return</span> <span class="n">out</span><span class="p">,</span> <span class="n">code_errors</span>
+</span><span id="L-622"><a href="#L-622"><span class="linenos"> 622</span></a>
+</span><span id="L-623"><a href="#L-623"><span class="linenos"> 623</span></a>
+</span><span id="L-624"><a href="#L-624"><span class="linenos"> 624</span></a><span class="k">def</span><span class="w"> </span><span class="nf">get_code_type_from_col_name</span><span class="p">(</span><span class="n">col_name</span><span class="p">:</span> <span class="nb">str</span><span class="p">):</span>
+</span><span id="L-625"><a href="#L-625"><span class="linenos"> 625</span></a> <span class="k">return</span> <span class="n">col_name</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s2">"_"</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span>
+</span><span id="L-626"><a href="#L-626"><span class="linenos"> 626</span></a>
+</span><span id="L-627"><a href="#L-627"><span class="linenos"> 627</span></a>
+</span><span id="L-628"><a href="#L-628"><span class="linenos"> 628</span></a><span class="c1"># Translate Df with multiple codes into single code type Series</span>
+</span><span id="L-629"><a href="#L-629"><span class="linenos"> 629</span></a><span class="k">def</span><span class="w"> </span><span class="nf">translate_codes</span><span class="p">(</span>
+</span><span id="L-630"><a href="#L-630"><span class="linenos"> 630</span></a> <span class="n">source_df</span><span class="p">:</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">,</span> <span class="n">target_code_type</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">concept_name</span><span class="p">:</span> <span class="nb">str</span>
+</span><span id="L-631"><a href="#L-631"><span class="linenos"> 631</span></a><span class="p">)</span> <span class="o">-></span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">:</span>
+</span><span id="L-632"><a href="#L-632"><span class="linenos"> 632</span></a><span class="w"> </span><span class="sd">"""Translates each source code type the source coding list into a target type and returns all conversions as a concept set"""</span>
+</span><span id="L-633"><a href="#L-633"><span class="linenos"> 633</span></a>
+</span><span id="L-634"><a href="#L-634"><span class="linenos"> 634</span></a> <span class="c1"># codes = pd.DataFrame([], dtype=str)</span>
+</span><span id="L-635"><a href="#L-635"><span class="linenos"> 635</span></a> <span class="n">codes</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">(</span>
+</span><span id="L-636"><a href="#L-636"><span class="linenos"> 636</span></a> <span class="n">columns</span><span class="o">=</span><span class="p">[</span><span class="s2">"SOURCE_CONCEPT"</span><span class="p">,</span> <span class="s2">"SOURCE_CONCEPT_TYPE"</span><span class="p">,</span> <span class="s2">"CONCEPT"</span><span class="p">],</span> <span class="n">dtype</span><span class="o">=</span><span class="s2">"string"</span>
+</span><span id="L-637"><a href="#L-637"><span class="linenos"> 637</span></a> <span class="p">)</span>
+</span><span id="L-638"><a href="#L-638"><span class="linenos"> 638</span></a> <span class="c1"># Convert codes to target type</span>
+</span><span id="L-639"><a href="#L-639"><span class="linenos"> 639</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Converting to target code type </span><span class="si">{</span><span class="n">target_code_type</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+</span><span id="L-640"><a href="#L-640"><span class="linenos"> 640</span></a>
+</span><span id="L-641"><a href="#L-641"><span class="linenos"> 641</span></a> <span class="k">for</span> <span class="n">source_code_type</span> <span class="ow">in</span> <span class="n">source_df</span><span class="o">.</span><span class="n">columns</span><span class="p">:</span>
+</span><span id="L-642"><a href="#L-642"><span class="linenos"> 642</span></a>
+</span><span id="L-643"><a href="#L-643"><span class="linenos"> 643</span></a> <span class="c1"># if target code type is the same as thet source code type, no translation, just appending source as target</span>
+</span><span id="L-644"><a href="#L-644"><span class="linenos"> 644</span></a> <span class="k">if</span> <span class="n">source_code_type</span> <span class="o">==</span> <span class="n">target_code_type</span><span class="p">:</span>
+</span><span id="L-645"><a href="#L-645"><span class="linenos"> 645</span></a> <span class="n">copy_df</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">(</span>
+</span><span id="L-646"><a href="#L-646"><span class="linenos"> 646</span></a> <span class="p">{</span>
+</span><span id="L-647"><a href="#L-647"><span class="linenos"> 647</span></a> <span class="s2">"SOURCE_CONCEPT"</span><span class="p">:</span> <span class="n">source_df</span><span class="p">[</span><span class="n">source_code_type</span><span class="p">],</span>
+</span><span id="L-648"><a href="#L-648"><span class="linenos"> 648</span></a> <span class="s2">"SOURCE_CONCEPT_TYPE"</span><span class="p">:</span> <span class="n">source_code_type</span><span class="p">,</span>
+</span><span id="L-649"><a href="#L-649"><span class="linenos"> 649</span></a> <span class="s2">"CONCEPT"</span><span class="p">:</span> <span class="n">source_df</span><span class="p">[</span><span class="n">source_code_type</span><span class="p">],</span>
+</span><span id="L-650"><a href="#L-650"><span class="linenos"> 650</span></a> <span class="p">}</span>
+</span><span id="L-651"><a href="#L-651"><span class="linenos"> 651</span></a> <span class="p">)</span>
+</span><span id="L-652"><a href="#L-652"><span class="linenos"> 652</span></a> <span class="n">codes</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">concat</span><span class="p">([</span><span class="n">codes</span><span class="p">,</span> <span class="n">copy_df</span><span class="p">])</span>
+</span><span id="L-653"><a href="#L-653"><span class="linenos"> 653</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span>
+</span><span id="L-654"><a href="#L-654"><span class="linenos"> 654</span></a> <span class="sa">f</span><span class="s2">"Target code type </span><span class="si">{</span><span class="n">target_code_type</span><span class="si">}</span><span class="s2"> is the same as source code type </span><span class="si">{</span><span class="nb">len</span><span class="p">(</span><span class="n">source_df</span><span class="p">)</span><span class="si">}</span><span class="s2">, copying codes rather than translating"</span>
+</span><span id="L-655"><a href="#L-655"><span class="linenos"> 655</span></a> <span class="p">)</span>
+</span><span id="L-656"><a href="#L-656"><span class="linenos"> 656</span></a> <span class="k">else</span><span class="p">:</span>
+</span><span id="L-657"><a href="#L-657"><span class="linenos"> 657</span></a> <span class="c1"># get the translation filename using source to target code types</span>
+</span><span id="L-658"><a href="#L-658"><span class="linenos"> 658</span></a> <span class="n">filename</span> <span class="o">=</span> <span class="sa">f</span><span class="s2">"</span><span class="si">{</span><span class="n">source_code_type</span><span class="si">}</span><span class="s2">_to_</span><span class="si">{</span><span class="n">target_code_type</span><span class="si">}</span><span class="s2">.parquet"</span>
+</span><span id="L-659"><a href="#L-659"><span class="linenos"> 659</span></a> <span class="n">map_path</span> <span class="o">=</span> <span class="n">trud</span><span class="o">.</span><span class="n">PROCESSED_PATH</span> <span class="o">/</span> <span class="n">filename</span>
+</span><span id="L-660"><a href="#L-660"><span class="linenos"> 660</span></a>
+</span><span id="L-661"><a href="#L-661"><span class="linenos"> 661</span></a> <span class="c1"># do the mapping if it exists</span>
+</span><span id="L-662"><a href="#L-662"><span class="linenos"> 662</span></a> <span class="k">if</span> <span class="n">map_path</span><span class="o">.</span><span class="n">exists</span><span class="p">():</span>
+</span><span id="L-663"><a href="#L-663"><span class="linenos"> 663</span></a> <span class="c1"># get mapping</span>
+</span><span id="L-664"><a href="#L-664"><span class="linenos"> 664</span></a> <span class="n">df_map</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">read_parquet</span><span class="p">(</span><span class="n">map_path</span><span class="p">)</span>
+</span><span id="L-665"><a href="#L-665"><span class="linenos"> 665</span></a>
+</span><span id="L-666"><a href="#L-666"><span class="linenos"> 666</span></a> <span class="c1"># do mapping</span>
+</span><span id="L-667"><a href="#L-667"><span class="linenos"> 667</span></a> <span class="n">translated_df</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">merge</span><span class="p">(</span>
+</span><span id="L-668"><a href="#L-668"><span class="linenos"> 668</span></a> <span class="n">source_df</span><span class="p">[</span><span class="n">source_code_type</span><span class="p">],</span> <span class="n">df_map</span><span class="p">,</span> <span class="n">how</span><span class="o">=</span><span class="s2">"left"</span>
+</span><span id="L-669"><a href="#L-669"><span class="linenos"> 669</span></a> <span class="p">)</span>
+</span><span id="L-670"><a href="#L-670"><span class="linenos"> 670</span></a>
+</span><span id="L-671"><a href="#L-671"><span class="linenos"> 671</span></a> <span class="c1"># normalise the output</span>
+</span><span id="L-672"><a href="#L-672"><span class="linenos"> 672</span></a> <span class="n">translated_df</span><span class="o">.</span><span class="n">columns</span> <span class="o">=</span> <span class="p">[</span><span class="s2">"SOURCE_CONCEPT"</span><span class="p">,</span> <span class="s2">"CONCEPT"</span><span class="p">]</span>
+</span><span id="L-673"><a href="#L-673"><span class="linenos"> 673</span></a> <span class="n">translated_df</span><span class="p">[</span><span class="s2">"SOURCE_CONCEPT_TYPE"</span><span class="p">]</span> <span class="o">=</span> <span class="n">source_code_type</span>
+</span><span id="L-674"><a href="#L-674"><span class="linenos"> 674</span></a>
+</span><span id="L-675"><a href="#L-675"><span class="linenos"> 675</span></a> <span class="c1"># add to list of codes</span>
+</span><span id="L-676"><a href="#L-676"><span class="linenos"> 676</span></a> <span class="n">codes</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">concat</span><span class="p">([</span><span class="n">codes</span><span class="p">,</span> <span class="n">translated_df</span><span class="p">])</span>
+</span><span id="L-677"><a href="#L-677"><span class="linenos"> 677</span></a>
+</span><span id="L-678"><a href="#L-678"><span class="linenos"> 678</span></a> <span class="k">else</span><span class="p">:</span>
+</span><span id="L-679"><a href="#L-679"><span class="linenos"> 679</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">warning</span><span class="p">(</span>
+</span><span id="L-680"><a href="#L-680"><span class="linenos"> 680</span></a> <span class="sa">f</span><span class="s2">"No mapping from </span><span class="si">{</span><span class="n">source_code_type</span><span class="si">}</span><span class="s2"> to </span><span class="si">{</span><span class="n">target_code_type</span><span class="si">}</span><span class="s2">, file </span><span class="si">{</span><span class="nb">str</span><span class="p">(</span><span class="n">map_path</span><span class="o">.</span><span class="n">resolve</span><span class="p">())</span><span class="si">}</span><span class="s2"> does not exist"</span>
+</span><span id="L-681"><a href="#L-681"><span class="linenos"> 681</span></a> <span class="p">)</span>
+</span><span id="L-682"><a href="#L-682"><span class="linenos"> 682</span></a>
+</span><span id="L-683"><a href="#L-683"><span class="linenos"> 683</span></a> <span class="n">codes</span> <span class="o">=</span> <span class="n">codes</span><span class="o">.</span><span class="n">dropna</span><span class="p">()</span> <span class="c1"># delete NaNs</span>
+</span><span id="L-684"><a href="#L-684"><span class="linenos"> 684</span></a>
+</span><span id="L-685"><a href="#L-685"><span class="linenos"> 685</span></a> <span class="c1"># added concept set type to output if any translations</span>
+</span><span id="L-686"><a href="#L-686"><span class="linenos"> 686</span></a> <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">codes</span><span class="o">.</span><span class="n">index</span><span class="p">)</span> <span class="o">></span> <span class="mi">0</span><span class="p">:</span>
+</span><span id="L-687"><a href="#L-687"><span class="linenos"> 687</span></a> <span class="n">codes</span><span class="p">[</span><span class="s2">"CONCEPT_SET"</span><span class="p">]</span> <span class="o">=</span> <span class="n">concept_name</span>
+</span><span id="L-688"><a href="#L-688"><span class="linenos"> 688</span></a> <span class="k">else</span><span class="p">:</span>
+</span><span id="L-689"><a href="#L-689"><span class="linenos"> 689</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="sa">f</span><span class="s2">"No codes converted with target code type </span><span class="si">{</span><span class="n">target_code_type</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+</span><span id="L-690"><a href="#L-690"><span class="linenos"> 690</span></a>
+</span><span id="L-691"><a href="#L-691"><span class="linenos"> 691</span></a> <span class="k">return</span> <span class="n">codes</span>
+</span><span id="L-692"><a href="#L-692"><span class="linenos"> 692</span></a>
+</span><span id="L-693"><a href="#L-693"><span class="linenos"> 693</span></a>
+</span><span id="L-694"><a href="#L-694"><span class="linenos"> 694</span></a><span class="k">def</span><span class="w"> </span><span class="nf">sql_row_exist</span><span class="p">(</span>
+</span><span id="L-695"><a href="#L-695"><span class="linenos"> 695</span></a> <span class="n">conn</span><span class="p">:</span> <span class="n">sqlite3</span><span class="o">.</span><span class="n">Connection</span><span class="p">,</span> <span class="n">table</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">column</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">value</span><span class="p">:</span> <span class="nb">str</span>
+</span><span id="L-696"><a href="#L-696"><span class="linenos"> 696</span></a><span class="p">)</span> <span class="o">-></span> <span class="nb">bool</span><span class="p">:</span>
+</span><span id="L-697"><a href="#L-697"><span class="linenos"> 697</span></a> <span class="c1"># Execute and check if a result exists</span>
+</span><span id="L-698"><a href="#L-698"><span class="linenos"> 698</span></a> <span class="n">cur</span> <span class="o">=</span> <span class="n">conn</span><span class="o">.</span><span class="n">cursor</span><span class="p">()</span>
+</span><span id="L-699"><a href="#L-699"><span class="linenos"> 699</span></a> <span class="n">query</span> <span class="o">=</span> <span class="sa">f</span><span class="s2">"SELECT 1 FROM </span><span class="si">{</span><span class="n">table</span><span class="si">}</span><span class="s2"> WHERE </span><span class="si">{</span><span class="n">column</span><span class="si">}</span><span class="s2"> = ? LIMIT 1;"</span>
+</span><span id="L-700"><a href="#L-700"><span class="linenos"> 700</span></a> <span class="n">cur</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="n">query</span><span class="p">,</span> <span class="p">(</span><span class="n">value</span><span class="p">,))</span>
+</span><span id="L-701"><a href="#L-701"><span class="linenos"> 701</span></a> <span class="n">exists</span> <span class="o">=</span> <span class="n">cur</span><span class="o">.</span><span class="n">fetchone</span><span class="p">()</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span>
+</span><span id="L-702"><a href="#L-702"><span class="linenos"> 702</span></a>
+</span><span id="L-703"><a href="#L-703"><span class="linenos"> 703</span></a> <span class="k">return</span> <span class="n">exists</span>
+</span><span id="L-704"><a href="#L-704"><span class="linenos"> 704</span></a>
+</span><span id="L-705"><a href="#L-705"><span class="linenos"> 705</span></a>
+</span><span id="L-706"><a href="#L-706"><span class="linenos"> 706</span></a><span class="k">def</span><span class="w"> </span><span class="nf">write_code_errors</span><span class="p">(</span><span class="n">code_errors</span><span class="p">:</span> <span class="nb">list</span><span class="p">,</span> <span class="n">code_errors_path</span><span class="p">:</span> <span class="n">Path</span><span class="p">):</span>
+</span><span id="L-707"><a href="#L-707"><span class="linenos"> 707</span></a> <span class="n">err_df</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">(</span>
+</span><span id="L-708"><a href="#L-708"><span class="linenos"> 708</span></a> <span class="p">[</span>
+</span><span id="L-709"><a href="#L-709"><span class="linenos"> 709</span></a> <span class="p">{</span>
+</span><span id="L-710"><a href="#L-710"><span class="linenos"> 710</span></a> <span class="s2">"CONCEPT"</span><span class="p">:</span> <span class="s2">", "</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">err</span><span class="o">.</span><span class="n">codes</span><span class="p">[</span><span class="o">~</span><span class="n">err</span><span class="o">.</span><span class="n">mask</span><span class="p">]</span><span class="o">.</span><span class="n">tolist</span><span class="p">()),</span>
+</span><span id="L-711"><a href="#L-711"><span class="linenos"> 711</span></a> <span class="s2">"VOCABULARY"</span><span class="p">:</span> <span class="n">err</span><span class="o">.</span><span class="n">code_type</span><span class="p">,</span>
+</span><span id="L-712"><a href="#L-712"><span class="linenos"> 712</span></a> <span class="s2">"SOURCE"</span><span class="p">:</span> <span class="n">err</span><span class="o">.</span><span class="n">codes_file</span><span class="p">,</span>
+</span><span id="L-713"><a href="#L-713"><span class="linenos"> 713</span></a> <span class="s2">"CAUSE"</span><span class="p">:</span> <span class="n">err</span><span class="o">.</span><span class="n">message</span><span class="p">,</span>
+</span><span id="L-714"><a href="#L-714"><span class="linenos"> 714</span></a> <span class="p">}</span>
+</span><span id="L-715"><a href="#L-715"><span class="linenos"> 715</span></a> <span class="k">for</span> <span class="n">err</span> <span class="ow">in</span> <span class="n">code_errors</span>
+</span><span id="L-716"><a href="#L-716"><span class="linenos"> 716</span></a> <span class="p">]</span>
+</span><span id="L-717"><a href="#L-717"><span class="linenos"> 717</span></a> <span class="p">)</span>
+</span><span id="L-718"><a href="#L-718"><span class="linenos"> 718</span></a>
+</span><span id="L-719"><a href="#L-719"><span class="linenos"> 719</span></a> <span class="n">err_df</span> <span class="o">=</span> <span class="n">err_df</span><span class="o">.</span><span class="n">drop_duplicates</span><span class="p">()</span> <span class="c1"># Remove Duplicates from Error file</span>
+</span><span id="L-720"><a href="#L-720"><span class="linenos"> 720</span></a> <span class="n">err_df</span> <span class="o">=</span> <span class="n">err_df</span><span class="o">.</span><span class="n">sort_values</span><span class="p">(</span><span class="n">by</span><span class="o">=</span><span class="p">[</span><span class="s2">"SOURCE"</span><span class="p">,</span> <span class="s2">"VOCABULARY"</span><span class="p">,</span> <span class="s2">"CONCEPT"</span><span class="p">])</span>
+</span><span id="L-721"><a href="#L-721"><span class="linenos"> 721</span></a> <span class="n">err_df</span><span class="o">.</span><span class="n">to_csv</span><span class="p">(</span><span class="n">code_errors_path</span><span class="p">,</span> <span class="n">index</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span> <span class="n">mode</span><span class="o">=</span><span class="s2">"w"</span><span class="p">)</span>
+</span><span id="L-722"><a href="#L-722"><span class="linenos"> 722</span></a>
+</span><span id="L-723"><a href="#L-723"><span class="linenos"> 723</span></a>
+</span><span id="L-724"><a href="#L-724"><span class="linenos"> 724</span></a><span class="k">def</span><span class="w"> </span><span class="nf">write_vocab_version</span><span class="p">(</span><span class="n">phen_path</span><span class="p">:</span> <span class="n">Path</span><span class="p">):</span>
+</span><span id="L-725"><a href="#L-725"><span class="linenos"> 725</span></a> <span class="c1"># write the vocab version files</span>
+</span><span id="L-726"><a href="#L-726"><span class="linenos"> 726</span></a>
+</span><span id="L-727"><a href="#L-727"><span class="linenos"> 727</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="n">trud</span><span class="o">.</span><span class="n">VERSION_PATH</span><span class="o">.</span><span class="n">exists</span><span class="p">():</span>
+</span><span id="L-728"><a href="#L-728"><span class="linenos"> 728</span></a> <span class="k">raise</span> <span class="ne">FileNotFoundError</span><span class="p">(</span>
+</span><span id="L-729"><a href="#L-729"><span class="linenos"> 729</span></a> <span class="sa">f</span><span class="s2">"TRUD version path </span><span class="si">{</span><span class="n">trud</span><span class="o">.</span><span class="n">VERSION_PATH</span><span class="si">}</span><span class="s2"> does not exist, please check TRUD is installed"</span>
+</span><span id="L-730"><a href="#L-730"><span class="linenos"> 730</span></a> <span class="p">)</span>
+</span><span id="L-731"><a href="#L-731"><span class="linenos"> 731</span></a>
+</span><span id="L-732"><a href="#L-732"><span class="linenos"> 732</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="n">omop</span><span class="o">.</span><span class="n">VERSION_PATH</span><span class="o">.</span><span class="n">exists</span><span class="p">():</span>
+</span><span id="L-733"><a href="#L-733"><span class="linenos"> 733</span></a> <span class="k">raise</span> <span class="ne">FileNotFoundError</span><span class="p">(</span>
+</span><span id="L-734"><a href="#L-734"><span class="linenos"> 734</span></a> <span class="sa">f</span><span class="s2">"OMOP version path </span><span class="si">{</span><span class="n">omop</span><span class="o">.</span><span class="n">VERSION_PATH</span><span class="si">}</span><span class="s2"> does not exist, please check OMOP is installed"</span>
+</span><span id="L-735"><a href="#L-735"><span class="linenos"> 735</span></a> <span class="p">)</span>
+</span><span id="L-736"><a href="#L-736"><span class="linenos"> 736</span></a>
+</span><span id="L-737"><a href="#L-737"><span class="linenos"> 737</span></a> <span class="k">with</span> <span class="n">trud</span><span class="o">.</span><span class="n">VERSION_PATH</span><span class="o">.</span><span class="n">open</span><span class="p">(</span><span class="s2">"r"</span><span class="p">)</span> <span class="k">as</span> <span class="n">file</span><span class="p">:</span>
+</span><span id="L-738"><a href="#L-738"><span class="linenos"> 738</span></a> <span class="n">trud_version</span> <span class="o">=</span> <span class="n">yaml</span><span class="o">.</span><span class="n">safe_load</span><span class="p">(</span><span class="n">file</span><span class="p">)</span>
+</span><span id="L-739"><a href="#L-739"><span class="linenos"> 739</span></a>
+</span><span id="L-740"><a href="#L-740"><span class="linenos"> 740</span></a> <span class="k">with</span> <span class="n">omop</span><span class="o">.</span><span class="n">VERSION_PATH</span><span class="o">.</span><span class="n">open</span><span class="p">(</span><span class="s2">"r"</span><span class="p">)</span> <span class="k">as</span> <span class="n">file</span><span class="p">:</span>
+</span><span id="L-741"><a href="#L-741"><span class="linenos"> 741</span></a> <span class="n">omop_version</span> <span class="o">=</span> <span class="n">yaml</span><span class="o">.</span><span class="n">safe_load</span><span class="p">(</span><span class="n">file</span><span class="p">)</span>
+</span><span id="L-742"><a href="#L-742"><span class="linenos"> 742</span></a>
+</span><span id="L-743"><a href="#L-743"><span class="linenos"> 743</span></a> <span class="c1"># Create the combined YAML structure</span>
+</span><span id="L-744"><a href="#L-744"><span class="linenos"> 744</span></a> <span class="n">version_data</span> <span class="o">=</span> <span class="p">{</span>
+</span><span id="L-745"><a href="#L-745"><span class="linenos"> 745</span></a> <span class="s2">"versions"</span><span class="p">:</span> <span class="p">{</span>
+</span><span id="L-746"><a href="#L-746"><span class="linenos"> 746</span></a> <span class="s2">"acmc"</span><span class="p">:</span> <span class="n">acmc</span><span class="o">.</span><span class="n">__version__</span><span class="p">,</span>
+</span><span id="L-747"><a href="#L-747"><span class="linenos"> 747</span></a> <span class="s2">"trud"</span><span class="p">:</span> <span class="n">trud_version</span><span class="p">,</span>
+</span><span id="L-748"><a href="#L-748"><span class="linenos"> 748</span></a> <span class="s2">"omop"</span><span class="p">:</span> <span class="n">omop_version</span><span class="p">,</span>
+</span><span id="L-749"><a href="#L-749"><span class="linenos"> 749</span></a> <span class="p">}</span>
+</span><span id="L-750"><a href="#L-750"><span class="linenos"> 750</span></a> <span class="p">}</span>
+</span><span id="L-751"><a href="#L-751"><span class="linenos"> 751</span></a>
+</span><span id="L-752"><a href="#L-752"><span class="linenos"> 752</span></a> <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">phen_path</span> <span class="o">/</span> <span class="n">VOCAB_VERSION_FILE</span><span class="p">,</span> <span class="s2">"w"</span><span class="p">)</span> <span class="k">as</span> <span class="n">file</span><span class="p">:</span>
+</span><span id="L-753"><a href="#L-753"><span class="linenos"> 753</span></a> <span class="n">yaml</span><span class="o">.</span><span class="n">dump</span><span class="p">(</span>
+</span><span id="L-754"><a href="#L-754"><span class="linenos"> 754</span></a> <span class="n">version_data</span><span class="p">,</span>
+</span><span id="L-755"><a href="#L-755"><span class="linenos"> 755</span></a> <span class="n">file</span><span class="p">,</span>
+</span><span id="L-756"><a href="#L-756"><span class="linenos"> 756</span></a> <span class="n">Dumper</span><span class="o">=</span><span class="n">util</span><span class="o">.</span><span class="n">QuotedDumper</span><span class="p">,</span>
+</span><span id="L-757"><a href="#L-757"><span class="linenos"> 757</span></a> <span class="n">default_flow_style</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span>
+</span><span id="L-758"><a href="#L-758"><span class="linenos"> 758</span></a> <span class="n">sort_keys</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span>
+</span><span id="L-759"><a href="#L-759"><span class="linenos"> 759</span></a> <span class="n">default_style</span><span class="o">=</span><span class="s1">'"'</span><span class="p">,</span>
+</span><span id="L-760"><a href="#L-760"><span class="linenos"> 760</span></a> <span class="p">)</span>
+</span><span id="L-761"><a href="#L-761"><span class="linenos"> 761</span></a>
+</span><span id="L-762"><a href="#L-762"><span class="linenos"> 762</span></a>
+</span><span id="L-763"><a href="#L-763"><span class="linenos"> 763</span></a><span class="k">def</span><span class="w"> </span><span class="nf">map</span><span class="p">(</span><span class="n">phen_dir</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">target_code_type</span><span class="p">:</span> <span class="nb">str</span><span class="p">):</span>
+</span><span id="L-764"><a href="#L-764"><span class="linenos"> 764</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Processing phenotype: </span><span class="si">{</span><span class="n">phen_dir</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+</span><span id="L-765"><a href="#L-765"><span class="linenos"> 765</span></a>
+</span><span id="L-766"><a href="#L-766"><span class="linenos"> 766</span></a> <span class="c1"># Validate configuration</span>
+</span><span id="L-767"><a href="#L-767"><span class="linenos"> 767</span></a> <span class="n">validate</span><span class="p">(</span><span class="n">phen_dir</span><span class="p">)</span>
+</span><span id="L-768"><a href="#L-768"><span class="linenos"> 768</span></a>
+</span><span id="L-769"><a href="#L-769"><span class="linenos"> 769</span></a> <span class="c1"># initialise paths</span>
+</span><span id="L-770"><a href="#L-770"><span class="linenos"> 770</span></a> <span class="n">phen_path</span> <span class="o">=</span> <span class="n">Path</span><span class="p">(</span><span class="n">phen_dir</span><span class="p">)</span>
+</span><span id="L-771"><a href="#L-771"><span class="linenos"> 771</span></a> <span class="n">config_path</span> <span class="o">=</span> <span class="n">phen_path</span> <span class="o">/</span> <span class="n">CONFIG_FILE</span>
+</span><span id="L-772"><a href="#L-772"><span class="linenos"> 772</span></a>
+</span><span id="L-773"><a href="#L-773"><span class="linenos"> 773</span></a> <span class="c1"># load configuration</span>
+</span><span id="L-774"><a href="#L-774"><span class="linenos"> 774</span></a> <span class="k">with</span> <span class="n">config_path</span><span class="o">.</span><span class="n">open</span><span class="p">(</span><span class="s2">"r"</span><span class="p">)</span> <span class="k">as</span> <span class="n">file</span><span class="p">:</span>
+</span><span id="L-775"><a href="#L-775"><span class="linenos"> 775</span></a> <span class="n">config</span> <span class="o">=</span> <span class="n">yaml</span><span class="o">.</span><span class="n">safe_load</span><span class="p">(</span><span class="n">file</span><span class="p">)</span>
+</span><span id="L-776"><a href="#L-776"><span class="linenos"> 776</span></a> <span class="n">phenotype</span> <span class="o">=</span> <span class="n">config</span><span class="p">[</span><span class="s2">"phenotype"</span><span class="p">]</span>
+</span><span id="L-777"><a href="#L-777"><span class="linenos"> 777</span></a>
+</span><span id="L-778"><a href="#L-778"><span class="linenos"> 778</span></a> <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">phenotype</span><span class="p">[</span><span class="s2">"map"</span><span class="p">])</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
+</span><span id="L-779"><a href="#L-779"><span class="linenos"> 779</span></a> <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="sa">f</span><span class="s2">"No map codes defined in the phenotype configuration"</span><span class="p">)</span>
+</span><span id="L-780"><a href="#L-780"><span class="linenos"> 780</span></a>
+</span><span id="L-781"><a href="#L-781"><span class="linenos"> 781</span></a> <span class="k">if</span> <span class="n">target_code_type</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span> <span class="ow">and</span> <span class="n">target_code_type</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">phenotype</span><span class="p">[</span><span class="s2">"map"</span><span class="p">]:</span>
+</span><span id="L-782"><a href="#L-782"><span class="linenos"> 782</span></a> <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span>
+</span><span id="L-783"><a href="#L-783"><span class="linenos"> 783</span></a> <span class="sa">f</span><span class="s2">"Target code type </span><span class="si">{</span><span class="n">target_code_type</span><span class="si">}</span><span class="s2"> not in phenotype configuration map </span><span class="si">{</span><span class="n">phenotype</span><span class="p">[</span><span class="s1">'map'</span><span class="p">]</span><span class="si">}</span><span class="s2">"</span>
+</span><span id="L-784"><a href="#L-784"><span class="linenos"> 784</span></a> <span class="p">)</span>
+</span><span id="L-785"><a href="#L-785"><span class="linenos"> 785</span></a>
+</span><span id="L-786"><a href="#L-786"><span class="linenos"> 786</span></a> <span class="k">if</span> <span class="n">target_code_type</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+</span><span id="L-787"><a href="#L-787"><span class="linenos"> 787</span></a> <span class="n">map_target_code_type</span><span class="p">(</span><span class="n">phen_path</span><span class="p">,</span> <span class="n">phenotype</span><span class="p">,</span> <span class="n">target_code_type</span><span class="p">)</span>
+</span><span id="L-788"><a href="#L-788"><span class="linenos"> 788</span></a> <span class="k">else</span><span class="p">:</span>
+</span><span id="L-789"><a href="#L-789"><span class="linenos"> 789</span></a> <span class="k">for</span> <span class="n">t</span> <span class="ow">in</span> <span class="n">phenotype</span><span class="p">[</span><span class="s2">"map"</span><span class="p">]:</span>
+</span><span id="L-790"><a href="#L-790"><span class="linenos"> 790</span></a> <span class="n">map_target_code_type</span><span class="p">(</span><span class="n">phen_path</span><span class="p">,</span> <span class="n">phenotype</span><span class="p">,</span> <span class="n">t</span><span class="p">)</span>
+</span><span id="L-791"><a href="#L-791"><span class="linenos"> 791</span></a>
+</span><span id="L-792"><a href="#L-792"><span class="linenos"> 792</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Phenotype processed successfully"</span><span class="p">)</span>
+</span><span id="L-793"><a href="#L-793"><span class="linenos"> 793</span></a>
+</span><span id="L-794"><a href="#L-794"><span class="linenos"> 794</span></a>
+</span><span id="L-795"><a href="#L-795"><span class="linenos"> 795</span></a><span class="k">def</span><span class="w"> </span><span class="nf">map_target_code_type</span><span class="p">(</span><span class="n">phen_path</span><span class="p">:</span> <span class="n">Path</span><span class="p">,</span> <span class="n">phenotype</span><span class="p">:</span> <span class="nb">dict</span><span class="p">,</span> <span class="n">target_code_type</span><span class="p">:</span> <span class="nb">str</span><span class="p">):</span>
+</span><span id="L-796"><a href="#L-796"><span class="linenos"> 796</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Target coding format: </span><span class="si">{</span><span class="n">target_code_type</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+</span><span id="L-797"><a href="#L-797"><span class="linenos"> 797</span></a> <span class="n">concepts_path</span> <span class="o">=</span> <span class="n">phen_path</span> <span class="o">/</span> <span class="n">CONCEPTS_DIR</span>
+</span><span id="L-798"><a href="#L-798"><span class="linenos"> 798</span></a> <span class="c1"># Create output dataframe</span>
+</span><span id="L-799"><a href="#L-799"><span class="linenos"> 799</span></a> <span class="n">out</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">([])</span>
+</span><span id="L-800"><a href="#L-800"><span class="linenos"> 800</span></a> <span class="n">code_errors</span> <span class="o">=</span> <span class="p">[]</span>
+</span><span id="L-801"><a href="#L-801"><span class="linenos"> 801</span></a>
+</span><span id="L-802"><a href="#L-802"><span class="linenos"> 802</span></a> <span class="c1"># Process each folder in codes section</span>
+</span><span id="L-803"><a href="#L-803"><span class="linenos"> 803</span></a> <span class="k">for</span> <span class="n">concept_set</span> <span class="ow">in</span> <span class="n">phenotype</span><span class="p">[</span><span class="s2">"concept_sets"</span><span class="p">]:</span>
+</span><span id="L-804"><a href="#L-804"><span class="linenos"> 804</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="sa">f</span><span class="s2">"--- </span><span class="si">{</span><span class="n">concept_set</span><span class="p">[</span><span class="s1">'file'</span><span class="p">]</span><span class="si">}</span><span class="s2"> ---"</span><span class="p">)</span>
+</span><span id="L-805"><a href="#L-805"><span class="linenos"> 805</span></a>
+</span><span id="L-806"><a href="#L-806"><span class="linenos"> 806</span></a> <span class="c1"># Load code file</span>
+</span><span id="L-807"><a href="#L-807"><span class="linenos"> 807</span></a> <span class="n">codes_file_path</span> <span class="o">=</span> <span class="n">Path</span><span class="p">(</span><span class="n">concepts_path</span> <span class="o">/</span> <span class="n">concept_set</span><span class="p">[</span><span class="s2">"file"</span><span class="p">][</span><span class="s2">"path"</span><span class="p">])</span>
+</span><span id="L-808"><a href="#L-808"><span class="linenos"> 808</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">read_table_file</span><span class="p">(</span><span class="n">codes_file_path</span><span class="p">)</span>
+</span><span id="L-809"><a href="#L-809"><span class="linenos"> 809</span></a>
+</span><span id="L-810"><a href="#L-810"><span class="linenos"> 810</span></a> <span class="c1"># process structural actions</span>
+</span><span id="L-811"><a href="#L-811"><span class="linenos"> 811</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">process_actions</span><span class="p">(</span><span class="n">df</span><span class="p">,</span> <span class="n">concept_set</span><span class="p">)</span>
+</span><span id="L-812"><a href="#L-812"><span class="linenos"> 812</span></a>
+</span><span id="L-813"><a href="#L-813"><span class="linenos"> 813</span></a> <span class="c1"># preprocessing and validate of source concepts</span>
+</span><span id="L-814"><a href="#L-814"><span class="linenos"> 814</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="s2">"Processing and validating source concept codes"</span><span class="p">)</span>
+</span><span id="L-815"><a href="#L-815"><span class="linenos"> 815</span></a> <span class="n">df</span><span class="p">,</span> <span class="n">errors</span> <span class="o">=</span> <span class="n">preprocess_source_concepts</span><span class="p">(</span>
+</span><span id="L-816"><a href="#L-816"><span class="linenos"> 816</span></a> <span class="n">df</span><span class="p">,</span>
+</span><span id="L-817"><a href="#L-817"><span class="linenos"> 817</span></a> <span class="n">concept_set</span><span class="p">,</span>
+</span><span id="L-818"><a href="#L-818"><span class="linenos"> 818</span></a> <span class="n">codes_file_path</span><span class="p">,</span>
+</span><span id="L-819"><a href="#L-819"><span class="linenos"> 819</span></a> <span class="p">)</span>
+</span><span id="L-820"><a href="#L-820"><span class="linenos"> 820</span></a>
+</span><span id="L-821"><a href="#L-821"><span class="linenos"> 821</span></a> <span class="c1"># create df with just the source code columns</span>
+</span><span id="L-822"><a href="#L-822"><span class="linenos"> 822</span></a> <span class="n">source_column_names</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="n">concept_set</span><span class="p">[</span><span class="s2">"file"</span><span class="p">][</span><span class="s2">"columns"</span><span class="p">]</span><span class="o">.</span><span class="n">keys</span><span class="p">())</span>
+</span><span id="L-823"><a href="#L-823"><span class="linenos"> 823</span></a> <span class="n">source_df</span> <span class="o">=</span> <span class="n">df</span><span class="p">[</span><span class="n">source_column_names</span><span class="p">]</span>
+</span><span id="L-824"><a href="#L-824"><span class="linenos"> 824</span></a>
+</span><span id="L-825"><a href="#L-825"><span class="linenos"> 825</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="n">source_df</span><span class="o">.</span><span class="n">columns</span><span class="p">)</span>
+</span><span id="L-826"><a href="#L-826"><span class="linenos"> 826</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="n">source_df</span><span class="o">.</span><span class="n">head</span><span class="p">())</span>
+</span><span id="L-827"><a href="#L-827"><span class="linenos"> 827</span></a>
+</span><span id="L-828"><a href="#L-828"><span class="linenos"> 828</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Length of errors from preprocess_source_concepts </span><span class="si">{</span><span class="nb">len</span><span class="p">(</span><span class="n">errors</span><span class="p">)</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+</span><span id="L-829"><a href="#L-829"><span class="linenos"> 829</span></a> <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">errors</span><span class="p">)</span> <span class="o">></span> <span class="mi">0</span><span class="p">:</span>
+</span><span id="L-830"><a href="#L-830"><span class="linenos"> 830</span></a> <span class="n">code_errors</span><span class="o">.</span><span class="n">extend</span><span class="p">(</span><span class="n">errors</span><span class="p">)</span>
+</span><span id="L-831"><a href="#L-831"><span class="linenos"> 831</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="sa">f</span><span class="s2">" Length of code_errors </span><span class="si">{</span><span class="nb">len</span><span class="p">(</span><span class="n">code_errors</span><span class="p">)</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+</span><span id="L-832"><a href="#L-832"><span class="linenos"> 832</span></a>
+</span><span id="L-833"><a href="#L-833"><span class="linenos"> 833</span></a> <span class="c1"># Map source concepts codes to target codes</span>
+</span><span id="L-834"><a href="#L-834"><span class="linenos"> 834</span></a> <span class="c1"># if processing a source coding list with categorical data</span>
+</span><span id="L-835"><a href="#L-835"><span class="linenos"> 835</span></a> <span class="k">if</span> <span class="p">(</span>
+</span><span id="L-836"><a href="#L-836"><span class="linenos"> 836</span></a> <span class="s2">"actions"</span> <span class="ow">in</span> <span class="n">concept_set</span><span class="p">[</span><span class="s2">"file"</span><span class="p">]</span>
+</span><span id="L-837"><a href="#L-837"><span class="linenos"> 837</span></a> <span class="ow">and</span> <span class="s2">"divide_col"</span> <span class="ow">in</span> <span class="n">concept_set</span><span class="p">[</span><span class="s2">"file"</span><span class="p">][</span><span class="s2">"actions"</span><span class="p">]</span>
+</span><span id="L-838"><a href="#L-838"><span class="linenos"> 838</span></a> <span class="ow">and</span> <span class="nb">len</span><span class="p">(</span><span class="n">df</span><span class="p">)</span> <span class="o">></span> <span class="mi">0</span>
+</span><span id="L-839"><a href="#L-839"><span class="linenos"> 839</span></a> <span class="p">):</span>
+</span><span id="L-840"><a href="#L-840"><span class="linenos"> 840</span></a> <span class="n">divide_col</span> <span class="o">=</span> <span class="n">concept_set</span><span class="p">[</span><span class="s2">"file"</span><span class="p">][</span><span class="s2">"actions"</span><span class="p">][</span><span class="s2">"divide_col"</span><span class="p">]</span>
+</span><span id="L-841"><a href="#L-841"><span class="linenos"> 841</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Action: Dividing Table by </span><span class="si">{</span><span class="n">divide_col</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+</span><span id="L-842"><a href="#L-842"><span class="linenos"> 842</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="sa">f</span><span class="s2">"column into: </span><span class="si">{</span><span class="n">df</span><span class="p">[</span><span class="n">divide_col</span><span class="p">]</span><span class="o">.</span><span class="n">unique</span><span class="p">()</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+</span><span id="L-843"><a href="#L-843"><span class="linenos"> 843</span></a> <span class="n">df_grp</span> <span class="o">=</span> <span class="n">df</span><span class="o">.</span><span class="n">groupby</span><span class="p">(</span><span class="n">divide_col</span><span class="p">)</span>
+</span><span id="L-844"><a href="#L-844"><span class="linenos"> 844</span></a> <span class="k">for</span> <span class="n">cat</span><span class="p">,</span> <span class="n">grp</span> <span class="ow">in</span> <span class="n">df_grp</span><span class="p">:</span>
+</span><span id="L-845"><a href="#L-845"><span class="linenos"> 845</span></a> <span class="k">if</span> <span class="n">cat</span> <span class="o">==</span> <span class="n">concept_set</span><span class="p">[</span><span class="s2">"file"</span><span class="p">][</span><span class="s2">"category"</span><span class="p">]:</span>
+</span><span id="L-846"><a href="#L-846"><span class="linenos"> 846</span></a> <span class="n">grp</span> <span class="o">=</span> <span class="n">grp</span><span class="o">.</span><span class="n">drop</span><span class="p">(</span><span class="n">columns</span><span class="o">=</span><span class="p">[</span><span class="n">divide_col</span><span class="p">])</span> <span class="c1"># delete categorical column</span>
+</span><span id="L-847"><a href="#L-847"><span class="linenos"> 847</span></a> <span class="n">source_df</span> <span class="o">=</span> <span class="n">grp</span><span class="p">[</span><span class="n">source_column_names</span><span class="p">]</span>
+</span><span id="L-848"><a href="#L-848"><span class="linenos"> 848</span></a> <span class="n">trans_out</span> <span class="o">=</span> <span class="n">translate_codes</span><span class="p">(</span>
+</span><span id="L-849"><a href="#L-849"><span class="linenos"> 849</span></a> <span class="n">source_df</span><span class="p">,</span>
+</span><span id="L-850"><a href="#L-850"><span class="linenos"> 850</span></a> <span class="n">target_code_type</span><span class="o">=</span><span class="n">target_code_type</span><span class="p">,</span>
+</span><span id="L-851"><a href="#L-851"><span class="linenos"> 851</span></a> <span class="n">concept_name</span><span class="o">=</span><span class="n">concept_set</span><span class="p">[</span><span class="s2">"name"</span><span class="p">],</span>
+</span><span id="L-852"><a href="#L-852"><span class="linenos"> 852</span></a> <span class="p">)</span>
+</span><span id="L-853"><a href="#L-853"><span class="linenos"> 853</span></a> <span class="n">out</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">concat</span><span class="p">([</span><span class="n">out</span><span class="p">,</span> <span class="n">trans_out</span><span class="p">])</span>
+</span><span id="L-854"><a href="#L-854"><span class="linenos"> 854</span></a> <span class="k">else</span><span class="p">:</span>
+</span><span id="L-855"><a href="#L-855"><span class="linenos"> 855</span></a> <span class="n">source_df</span> <span class="o">=</span> <span class="n">df</span><span class="p">[</span><span class="n">source_column_names</span><span class="p">]</span>
+</span><span id="L-856"><a href="#L-856"><span class="linenos"> 856</span></a> <span class="n">trans_out</span> <span class="o">=</span> <span class="n">translate_codes</span><span class="p">(</span>
+</span><span id="L-857"><a href="#L-857"><span class="linenos"> 857</span></a> <span class="n">source_df</span><span class="p">,</span>
+</span><span id="L-858"><a href="#L-858"><span class="linenos"> 858</span></a> <span class="n">target_code_type</span><span class="o">=</span><span class="n">target_code_type</span><span class="p">,</span>
+</span><span id="L-859"><a href="#L-859"><span class="linenos"> 859</span></a> <span class="n">concept_name</span><span class="o">=</span><span class="n">concept_set</span><span class="p">[</span><span class="s2">"name"</span><span class="p">],</span>
+</span><span id="L-860"><a href="#L-860"><span class="linenos"> 860</span></a> <span class="p">)</span>
+</span><span id="L-861"><a href="#L-861"><span class="linenos"> 861</span></a> <span class="n">out</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">concat</span><span class="p">([</span><span class="n">out</span><span class="p">,</span> <span class="n">trans_out</span><span class="p">])</span>
+</span><span id="L-862"><a href="#L-862"><span class="linenos"> 862</span></a>
+</span><span id="L-863"><a href="#L-863"><span class="linenos"> 863</span></a> <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">code_errors</span><span class="p">)</span> <span class="o">></span> <span class="mi">0</span><span class="p">:</span>
+</span><span id="L-864"><a href="#L-864"><span class="linenos"> 864</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">error</span><span class="p">(</span><span class="sa">f</span><span class="s2">"The map processing has </span><span class="si">{</span><span class="nb">len</span><span class="p">(</span><span class="n">code_errors</span><span class="p">)</span><span class="si">}</span><span class="s2"> errors"</span><span class="p">)</span>
+</span><span id="L-865"><a href="#L-865"><span class="linenos"> 865</span></a> <span class="n">error_path</span> <span class="o">=</span> <span class="n">phen_path</span> <span class="o">/</span> <span class="n">MAP_DIR</span> <span class="o">/</span> <span class="s2">"errors"</span>
+</span><span id="L-866"><a href="#L-866"><span class="linenos"> 866</span></a> <span class="n">error_path</span><span class="o">.</span><span class="n">mkdir</span><span class="p">(</span><span class="n">parents</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">exist_ok</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+</span><span id="L-867"><a href="#L-867"><span class="linenos"> 867</span></a> <span class="n">error_filename</span> <span class="o">=</span> <span class="sa">f</span><span class="s2">"</span><span class="si">{</span><span class="n">target_code_type</span><span class="si">}</span><span class="s2">-code-errors.csv"</span>
+</span><span id="L-868"><a href="#L-868"><span class="linenos"> 868</span></a> <span class="n">write_code_errors</span><span class="p">(</span><span class="n">code_errors</span><span class="p">,</span> <span class="n">error_path</span> <span class="o">/</span> <span class="n">error_filename</span><span class="p">)</span>
+</span><span id="L-869"><a href="#L-869"><span class="linenos"> 869</span></a>
+</span><span id="L-870"><a href="#L-870"><span class="linenos"> 870</span></a> <span class="c1"># Check there is output from processing</span>
+</span><span id="L-871"><a href="#L-871"><span class="linenos"> 871</span></a> <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">out</span><span class="o">.</span><span class="n">index</span><span class="p">)</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
+</span><span id="L-872"><a href="#L-872"><span class="linenos"> 872</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">error</span><span class="p">(</span><span class="sa">f</span><span class="s2">"No output after map processing"</span><span class="p">)</span>
+</span><span id="L-873"><a href="#L-873"><span class="linenos"> 873</span></a> <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span>
+</span><span id="L-874"><a href="#L-874"><span class="linenos"> 874</span></a> <span class="sa">f</span><span class="s2">"No output after map processing, check config </span><span class="si">{</span><span class="nb">str</span><span class="p">(</span><span class="n">phen_path</span><span class="o">.</span><span class="n">resolve</span><span class="p">())</span><span class="si">}</span><span class="s2">"</span>
+</span><span id="L-875"><a href="#L-875"><span class="linenos"> 875</span></a> <span class="p">)</span>
+</span><span id="L-876"><a href="#L-876"><span class="linenos"> 876</span></a>
+</span><span id="L-877"><a href="#L-877"><span class="linenos"> 877</span></a> <span class="c1"># final processing</span>
+</span><span id="L-878"><a href="#L-878"><span class="linenos"> 878</span></a> <span class="n">out</span> <span class="o">=</span> <span class="n">out</span><span class="o">.</span><span class="n">reset_index</span><span class="p">(</span><span class="n">drop</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+</span><span id="L-879"><a href="#L-879"><span class="linenos"> 879</span></a> <span class="n">out</span> <span class="o">=</span> <span class="n">out</span><span class="o">.</span><span class="n">drop_duplicates</span><span class="p">(</span><span class="n">subset</span><span class="o">=</span><span class="p">[</span><span class="s2">"CONCEPT_SET"</span><span class="p">,</span> <span class="s2">"CONCEPT"</span><span class="p">])</span>
+</span><span id="L-880"><a href="#L-880"><span class="linenos"> 880</span></a> <span class="n">out</span> <span class="o">=</span> <span class="n">out</span><span class="o">.</span><span class="n">sort_values</span><span class="p">(</span><span class="n">by</span><span class="o">=</span><span class="p">[</span><span class="s2">"CONCEPT_SET"</span><span class="p">,</span> <span class="s2">"CONCEPT"</span><span class="p">])</span>
+</span><span id="L-881"><a href="#L-881"><span class="linenos"> 881</span></a>
+</span><span id="L-882"><a href="#L-882"><span class="linenos"> 882</span></a> <span class="n">out_count</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">out</span><span class="o">.</span><span class="n">index</span><span class="p">)</span>
+</span><span id="L-883"><a href="#L-883"><span class="linenos"> 883</span></a> <span class="c1"># added metadata</span>
+</span><span id="L-884"><a href="#L-884"><span class="linenos"> 884</span></a> <span class="c1"># Loop over each source_concept_type and perform the left join on all columns apart from source code columns</span>
+</span><span id="L-885"><a href="#L-885"><span class="linenos"> 885</span></a> <span class="n">result_list</span> <span class="o">=</span> <span class="p">[]</span>
+</span><span id="L-886"><a href="#L-886"><span class="linenos"> 886</span></a> <span class="n">source_column_names</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="n">concept_set</span><span class="p">[</span><span class="s2">"file"</span><span class="p">][</span><span class="s2">"columns"</span><span class="p">]</span><span class="o">.</span><span class="n">keys</span><span class="p">())</span>
+</span><span id="L-887"><a href="#L-887"><span class="linenos"> 887</span></a> <span class="k">for</span> <span class="n">source_concept_type</span> <span class="ow">in</span> <span class="n">source_column_names</span><span class="p">:</span>
+</span><span id="L-888"><a href="#L-888"><span class="linenos"> 888</span></a>
+</span><span id="L-889"><a href="#L-889"><span class="linenos"> 889</span></a> <span class="c1"># Filter output based on the current source_concept_type</span>
+</span><span id="L-890"><a href="#L-890"><span class="linenos"> 890</span></a> <span class="n">out_filtered_df</span> <span class="o">=</span> <span class="n">out</span><span class="p">[</span><span class="n">out</span><span class="p">[</span><span class="s2">"SOURCE_CONCEPT_TYPE"</span><span class="p">]</span> <span class="o">==</span> <span class="n">source_concept_type</span><span class="p">]</span>
+</span><span id="L-891"><a href="#L-891"><span class="linenos"> 891</span></a> <span class="n">filtered_count</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">out_filtered_df</span><span class="o">.</span><span class="n">index</span><span class="p">)</span>
+</span><span id="L-892"><a href="#L-892"><span class="linenos"> 892</span></a>
+</span><span id="L-893"><a href="#L-893"><span class="linenos"> 893</span></a> <span class="c1"># Remove the source type columns except the current type will leave the metadata and the join</span>
+</span><span id="L-894"><a href="#L-894"><span class="linenos"> 894</span></a> <span class="n">remove_types</span> <span class="o">=</span> <span class="p">[</span>
+</span><span id="L-895"><a href="#L-895"><span class="linenos"> 895</span></a> <span class="nb">type</span> <span class="k">for</span> <span class="nb">type</span> <span class="ow">in</span> <span class="n">source_column_names</span> <span class="k">if</span> <span class="nb">type</span> <span class="o">!=</span> <span class="n">source_concept_type</span>
+</span><span id="L-896"><a href="#L-896"><span class="linenos"> 896</span></a> <span class="p">]</span>
+</span><span id="L-897"><a href="#L-897"><span class="linenos"> 897</span></a> <span class="n">metadata_df</span> <span class="o">=</span> <span class="n">df</span><span class="o">.</span><span class="n">drop</span><span class="p">(</span><span class="n">columns</span><span class="o">=</span><span class="n">remove_types</span><span class="p">)</span>
+</span><span id="L-898"><a href="#L-898"><span class="linenos"> 898</span></a> <span class="n">metadata_df</span> <span class="o">=</span> <span class="n">metadata_df</span><span class="o">.</span><span class="n">rename</span><span class="p">(</span>
+</span><span id="L-899"><a href="#L-899"><span class="linenos"> 899</span></a> <span class="n">columns</span><span class="o">=</span><span class="p">{</span><span class="n">source_concept_type</span><span class="p">:</span> <span class="s2">"SOURCE_CONCEPT"</span><span class="p">}</span>
+</span><span id="L-900"><a href="#L-900"><span class="linenos"> 900</span></a> <span class="p">)</span>
+</span><span id="L-901"><a href="#L-901"><span class="linenos"> 901</span></a> <span class="n">metadata_df_count</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">metadata_df</span><span class="o">.</span><span class="n">index</span><span class="p">)</span>
+</span><span id="L-902"><a href="#L-902"><span class="linenos"> 902</span></a>
+</span><span id="L-903"><a href="#L-903"><span class="linenos"> 903</span></a> <span class="c1"># Perform the left join with df2 on SOURCE_CONCEPT to add the metadata</span>
+</span><span id="L-904"><a href="#L-904"><span class="linenos"> 904</span></a> <span class="n">result</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">merge</span><span class="p">(</span><span class="n">out_filtered_df</span><span class="p">,</span> <span class="n">metadata_df</span><span class="p">,</span> <span class="n">how</span><span class="o">=</span><span class="s2">"left"</span><span class="p">,</span> <span class="n">on</span><span class="o">=</span><span class="s2">"SOURCE_CONCEPT"</span><span class="p">)</span>
+</span><span id="L-905"><a href="#L-905"><span class="linenos"> 905</span></a> <span class="n">result_count</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">result</span><span class="o">.</span><span class="n">index</span><span class="p">)</span>
+</span><span id="L-906"><a href="#L-906"><span class="linenos"> 906</span></a>
+</span><span id="L-907"><a href="#L-907"><span class="linenos"> 907</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span>
+</span><span id="L-908"><a href="#L-908"><span class="linenos"> 908</span></a> <span class="sa">f</span><span class="s2">"Adding metadata for </span><span class="si">{</span><span class="n">source_concept_type</span><span class="si">}</span><span class="s2">: out_count </span><span class="si">{</span><span class="n">out_count</span><span class="si">}</span><span class="s2">, filtered_count </span><span class="si">{</span><span class="n">filtered_count</span><span class="si">}</span><span class="s2">, metadata_df_count </span><span class="si">{</span><span class="n">metadata_df_count</span><span class="si">}</span><span class="s2">, result_count </span><span class="si">{</span><span class="n">result_count</span><span class="si">}</span><span class="s2">"</span>
+</span><span id="L-909"><a href="#L-909"><span class="linenos"> 909</span></a> <span class="p">)</span>
+</span><span id="L-910"><a href="#L-910"><span class="linenos"> 910</span></a>
+</span><span id="L-911"><a href="#L-911"><span class="linenos"> 911</span></a> <span class="c1"># Append the result to the result_list</span>
+</span><span id="L-912"><a href="#L-912"><span class="linenos"> 912</span></a> <span class="n">result_list</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">result</span><span class="p">)</span>
+</span><span id="L-913"><a href="#L-913"><span class="linenos"> 913</span></a>
+</span><span id="L-914"><a href="#L-914"><span class="linenos"> 914</span></a> <span class="c1"># Concatenate all the results into a single DataFrame</span>
+</span><span id="L-915"><a href="#L-915"><span class="linenos"> 915</span></a> <span class="n">final_out</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">concat</span><span class="p">(</span><span class="n">result_list</span><span class="p">,</span> <span class="n">ignore_index</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+</span><span id="L-916"><a href="#L-916"><span class="linenos"> 916</span></a> <span class="n">final_out</span> <span class="o">=</span> <span class="n">final_out</span><span class="o">.</span><span class="n">drop_duplicates</span><span class="p">(</span><span class="n">subset</span><span class="o">=</span><span class="p">[</span><span class="s2">"CONCEPT_SET"</span><span class="p">,</span> <span class="s2">"CONCEPT"</span><span class="p">])</span>
+</span><span id="L-917"><a href="#L-917"><span class="linenos"> 917</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span>
+</span><span id="L-918"><a href="#L-918"><span class="linenos"> 918</span></a> <span class="sa">f</span><span class="s2">"Check metadata processing counts: before </span><span class="si">{</span><span class="nb">len</span><span class="p">(</span><span class="n">out</span><span class="o">.</span><span class="n">index</span><span class="p">)</span><span class="si">}</span><span class="s2"> : after </span><span class="si">{</span><span class="nb">len</span><span class="p">(</span><span class="n">final_out</span><span class="o">.</span><span class="n">index</span><span class="p">)</span><span class="si">}</span><span class="s2">"</span>
+</span><span id="L-919"><a href="#L-919"><span class="linenos"> 919</span></a> <span class="p">)</span>
+</span><span id="L-920"><a href="#L-920"><span class="linenos"> 920</span></a>
+</span><span id="L-921"><a href="#L-921"><span class="linenos"> 921</span></a> <span class="c1"># Save output to map directory</span>
+</span><span id="L-922"><a href="#L-922"><span class="linenos"> 922</span></a> <span class="n">output_filename</span> <span class="o">=</span> <span class="n">target_code_type</span> <span class="o">+</span> <span class="s2">".csv"</span>
+</span><span id="L-923"><a href="#L-923"><span class="linenos"> 923</span></a> <span class="n">map_path</span> <span class="o">=</span> <span class="n">phen_path</span> <span class="o">/</span> <span class="n">MAP_DIR</span> <span class="o">/</span> <span class="n">output_filename</span>
+</span><span id="L-924"><a href="#L-924"><span class="linenos"> 924</span></a> <span class="n">final_out</span><span class="o">.</span><span class="n">to_csv</span><span class="p">(</span><span class="n">map_path</span><span class="p">,</span> <span class="n">index</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span>
+</span><span id="L-925"><a href="#L-925"><span class="linenos"> 925</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Saved mapped concepts to </span><span class="si">{</span><span class="nb">str</span><span class="p">(</span><span class="n">map_path</span><span class="o">.</span><span class="n">resolve</span><span class="p">())</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+</span><span id="L-926"><a href="#L-926"><span class="linenos"> 926</span></a>
+</span><span id="L-927"><a href="#L-927"><span class="linenos"> 927</span></a> <span class="c1"># save concept sets as separate files</span>
+</span><span id="L-928"><a href="#L-928"><span class="linenos"> 928</span></a> <span class="n">concept_set_path</span> <span class="o">=</span> <span class="n">phen_path</span> <span class="o">/</span> <span class="n">CSV_PATH</span> <span class="o">/</span> <span class="n">target_code_type</span>
+</span><span id="L-929"><a href="#L-929"><span class="linenos"> 929</span></a>
+</span><span id="L-930"><a href="#L-930"><span class="linenos"> 930</span></a> <span class="c1"># empty the concept-set directory except for hiddle files, e.g. .git</span>
+</span><span id="L-931"><a href="#L-931"><span class="linenos"> 931</span></a> <span class="k">if</span> <span class="n">concept_set_path</span><span class="o">.</span><span class="n">exists</span><span class="p">():</span>
+</span><span id="L-932"><a href="#L-932"><span class="linenos"> 932</span></a> <span class="k">for</span> <span class="n">item</span> <span class="ow">in</span> <span class="n">concept_set_path</span><span class="o">.</span><span class="n">iterdir</span><span class="p">():</span>
+</span><span id="L-933"><a href="#L-933"><span class="linenos"> 933</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="n">item</span><span class="o">.</span><span class="n">name</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s2">"."</span><span class="p">):</span>
+</span><span id="L-934"><a href="#L-934"><span class="linenos"> 934</span></a> <span class="n">item</span><span class="o">.</span><span class="n">unlink</span><span class="p">()</span>
+</span><span id="L-935"><a href="#L-935"><span class="linenos"> 935</span></a> <span class="k">else</span><span class="p">:</span>
+</span><span id="L-936"><a href="#L-936"><span class="linenos"> 936</span></a> <span class="n">concept_set_path</span><span class="o">.</span><span class="n">mkdir</span><span class="p">(</span><span class="n">parents</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">exist_ok</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+</span><span id="L-937"><a href="#L-937"><span class="linenos"> 937</span></a>
+</span><span id="L-938"><a href="#L-938"><span class="linenos"> 938</span></a> <span class="c1"># write each concept as a separate file</span>
+</span><span id="L-939"><a href="#L-939"><span class="linenos"> 939</span></a> <span class="k">for</span> <span class="n">name</span><span class="p">,</span> <span class="n">concept</span> <span class="ow">in</span> <span class="n">final_out</span><span class="o">.</span><span class="n">groupby</span><span class="p">(</span><span class="s2">"CONCEPT_SET"</span><span class="p">):</span>
+</span><span id="L-940"><a href="#L-940"><span class="linenos"> 940</span></a> <span class="n">concept</span> <span class="o">=</span> <span class="n">concept</span><span class="o">.</span><span class="n">sort_values</span><span class="p">(</span><span class="n">by</span><span class="o">=</span><span class="s2">"CONCEPT"</span><span class="p">)</span> <span class="c1"># sort rows</span>
+</span><span id="L-941"><a href="#L-941"><span class="linenos"> 941</span></a> <span class="n">concept</span> <span class="o">=</span> <span class="n">concept</span><span class="o">.</span><span class="n">dropna</span><span class="p">(</span><span class="n">how</span><span class="o">=</span><span class="s2">"all"</span><span class="p">,</span> <span class="n">axis</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span> <span class="c1"># remove empty cols</span>
+</span><span id="L-942"><a href="#L-942"><span class="linenos"> 942</span></a> <span class="n">concept</span> <span class="o">=</span> <span class="n">concept</span><span class="o">.</span><span class="n">reindex</span><span class="p">(</span>
+</span><span id="L-943"><a href="#L-943"><span class="linenos"> 943</span></a> <span class="nb">sorted</span><span class="p">(</span><span class="n">concept</span><span class="o">.</span><span class="n">columns</span><span class="p">),</span> <span class="n">axis</span><span class="o">=</span><span class="mi">1</span>
+</span><span id="L-944"><a href="#L-944"><span class="linenos"> 944</span></a> <span class="p">)</span> <span class="c1"># sort cols alphabetically</span>
+</span><span id="L-945"><a href="#L-945"><span class="linenos"> 945</span></a> <span class="n">filename</span> <span class="o">=</span> <span class="sa">f</span><span class="s2">"</span><span class="si">{</span><span class="n">name</span><span class="si">}</span><span class="s2">.csv"</span>
+</span><span id="L-946"><a href="#L-946"><span class="linenos"> 946</span></a> <span class="n">concept_path</span> <span class="o">=</span> <span class="n">concept_set_path</span> <span class="o">/</span> <span class="n">filename</span>
+</span><span id="L-947"><a href="#L-947"><span class="linenos"> 947</span></a> <span class="n">concept</span><span class="o">.</span><span class="n">to_csv</span><span class="p">(</span><span class="n">concept_path</span><span class="p">,</span> <span class="n">index</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span>
+</span><span id="L-948"><a href="#L-948"><span class="linenos"> 948</span></a>
+</span><span id="L-949"><a href="#L-949"><span class="linenos"> 949</span></a> <span class="n">write_vocab_version</span><span class="p">(</span><span class="n">phen_path</span><span class="p">)</span>
+</span><span id="L-950"><a href="#L-950"><span class="linenos"> 950</span></a>
+</span><span id="L-951"><a href="#L-951"><span class="linenos"> 951</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Phenotype processed target code type </span><span class="si">{</span><span class="n">target_code_type</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+</span><span id="L-952"><a href="#L-952"><span class="linenos"> 952</span></a>
+</span><span id="L-953"><a href="#L-953"><span class="linenos"> 953</span></a>
+</span><span id="L-954"><a href="#L-954"><span class="linenos"> 954</span></a><span class="k">def</span><span class="w"> </span><span class="nf">generate_version_tag</span><span class="p">(</span>
+</span><span id="L-955"><a href="#L-955"><span class="linenos"> 955</span></a> <span class="n">repo</span><span class="p">:</span> <span class="n">git</span><span class="o">.</span><span class="n">Repo</span><span class="p">,</span> <span class="n">increment</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="n">DEFAULT_VERSION_INC</span><span class="p">,</span> <span class="n">use_v_prefix</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">False</span>
+</span><span id="L-956"><a href="#L-956"><span class="linenos"> 956</span></a><span class="p">)</span> <span class="o">-></span> <span class="nb">str</span><span class="p">:</span>
+</span><span id="L-957"><a href="#L-957"><span class="linenos"> 957</span></a> <span class="c1"># Get all valid semantic version tags</span>
+</span><span id="L-958"><a href="#L-958"><span class="linenos"> 958</span></a> <span class="n">versions</span> <span class="o">=</span> <span class="p">[]</span>
+</span><span id="L-959"><a href="#L-959"><span class="linenos"> 959</span></a> <span class="k">for</span> <span class="n">tag</span> <span class="ow">in</span> <span class="n">repo</span><span class="o">.</span><span class="n">tags</span><span class="p">:</span>
+</span><span id="L-960"><a href="#L-960"><span class="linenos"> 960</span></a> <span class="n">tag_name</span> <span class="o">=</span> <span class="p">(</span>
+</span><span id="L-961"><a href="#L-961"><span class="linenos"> 961</span></a> <span class="n">tag</span><span class="o">.</span><span class="n">name</span><span class="o">.</span><span class="n">lstrip</span><span class="p">(</span><span class="s2">"v"</span><span class="p">)</span> <span class="k">if</span> <span class="n">use_v_prefix</span> <span class="k">else</span> <span class="n">tag</span><span class="o">.</span><span class="n">name</span>
+</span><span id="L-962"><a href="#L-962"><span class="linenos"> 962</span></a> <span class="p">)</span> <span class="c1"># Remove 'v' if needed</span>
+</span><span id="L-963"><a href="#L-963"><span class="linenos"> 963</span></a> <span class="k">if</span> <span class="n">semver</span><span class="o">.</span><span class="n">Version</span><span class="o">.</span><span class="n">is_valid</span><span class="p">(</span><span class="n">tag_name</span><span class="p">):</span>
+</span><span id="L-964"><a href="#L-964"><span class="linenos"> 964</span></a> <span class="n">versions</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">semver</span><span class="o">.</span><span class="n">Version</span><span class="o">.</span><span class="n">parse</span><span class="p">(</span><span class="n">tag_name</span><span class="p">))</span>
+</span><span id="L-965"><a href="#L-965"><span class="linenos"> 965</span></a>
+</span><span id="L-966"><a href="#L-966"><span class="linenos"> 966</span></a> <span class="c1"># Determine the next version</span>
+</span><span id="L-967"><a href="#L-967"><span class="linenos"> 967</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="n">versions</span><span class="p">:</span>
+</span><span id="L-968"><a href="#L-968"><span class="linenos"> 968</span></a> <span class="n">new_version</span> <span class="o">=</span> <span class="n">semver</span><span class="o">.</span><span class="n">Version</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">1</span><span class="p">)</span>
+</span><span id="L-969"><a href="#L-969"><span class="linenos"> 969</span></a> <span class="k">else</span><span class="p">:</span>
+</span><span id="L-970"><a href="#L-970"><span class="linenos"> 970</span></a> <span class="n">latest_version</span> <span class="o">=</span> <span class="nb">max</span><span class="p">(</span><span class="n">versions</span><span class="p">)</span>
+</span><span id="L-971"><a href="#L-971"><span class="linenos"> 971</span></a> <span class="k">if</span> <span class="n">increment</span> <span class="o">==</span> <span class="s2">"major"</span><span class="p">:</span>
+</span><span id="L-972"><a href="#L-972"><span class="linenos"> 972</span></a> <span class="n">new_version</span> <span class="o">=</span> <span class="n">latest_version</span><span class="o">.</span><span class="n">bump_major</span><span class="p">()</span>
+</span><span id="L-973"><a href="#L-973"><span class="linenos"> 973</span></a> <span class="k">elif</span> <span class="n">increment</span> <span class="o">==</span> <span class="s2">"minor"</span><span class="p">:</span>
+</span><span id="L-974"><a href="#L-974"><span class="linenos"> 974</span></a> <span class="n">new_version</span> <span class="o">=</span> <span class="n">latest_version</span><span class="o">.</span><span class="n">bump_minor</span><span class="p">()</span>
+</span><span id="L-975"><a href="#L-975"><span class="linenos"> 975</span></a> <span class="k">else</span><span class="p">:</span>
+</span><span id="L-976"><a href="#L-976"><span class="linenos"> 976</span></a> <span class="n">new_version</span> <span class="o">=</span> <span class="n">latest_version</span><span class="o">.</span><span class="n">bump_patch</span><span class="p">()</span>
+</span><span id="L-977"><a href="#L-977"><span class="linenos"> 977</span></a>
+</span><span id="L-978"><a href="#L-978"><span class="linenos"> 978</span></a> <span class="c1"># Create the new tag</span>
+</span><span id="L-979"><a href="#L-979"><span class="linenos"> 979</span></a> <span class="n">new_version_str</span> <span class="o">=</span> <span class="sa">f</span><span class="s2">"v</span><span class="si">{</span><span class="n">new_version</span><span class="si">}</span><span class="s2">"</span> <span class="k">if</span> <span class="n">use_v_prefix</span> <span class="k">else</span> <span class="nb">str</span><span class="p">(</span><span class="n">new_version</span><span class="p">)</span>
+</span><span id="L-980"><a href="#L-980"><span class="linenos"> 980</span></a>
+</span><span id="L-981"><a href="#L-981"><span class="linenos"> 981</span></a> <span class="k">return</span> <span class="n">new_version_str</span>
+</span><span id="L-982"><a href="#L-982"><span class="linenos"> 982</span></a>
+</span><span id="L-983"><a href="#L-983"><span class="linenos"> 983</span></a>
+</span><span id="L-984"><a href="#L-984"><span class="linenos"> 984</span></a><span class="k">def</span><span class="w"> </span><span class="nf">publish</span><span class="p">(</span>
+</span><span id="L-985"><a href="#L-985"><span class="linenos"> 985</span></a> <span class="n">phen_dir</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">msg</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">remote_url</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">increment</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="n">DEFAULT_VERSION_INC</span>
+</span><span id="L-986"><a href="#L-986"><span class="linenos"> 986</span></a><span class="p">):</span>
+</span><span id="L-987"><a href="#L-987"><span class="linenos"> 987</span></a><span class="w"> </span><span class="sd">"""Publishes updates to the phenotype by commiting all changes to the repo directory"""</span>
+</span><span id="L-988"><a href="#L-988"><span class="linenos"> 988</span></a>
+</span><span id="L-989"><a href="#L-989"><span class="linenos"> 989</span></a> <span class="c1"># Validate config</span>
+</span><span id="L-990"><a href="#L-990"><span class="linenos"> 990</span></a> <span class="n">validate</span><span class="p">(</span><span class="n">phen_dir</span><span class="p">)</span>
+</span><span id="L-991"><a href="#L-991"><span class="linenos"> 991</span></a> <span class="n">phen_path</span> <span class="o">=</span> <span class="n">Path</span><span class="p">(</span><span class="n">phen_dir</span><span class="p">)</span>
+</span><span id="L-992"><a href="#L-992"><span class="linenos"> 992</span></a>
+</span><span id="L-993"><a href="#L-993"><span class="linenos"> 993</span></a> <span class="c1"># load git repo and set the branch</span>
+</span><span id="L-994"><a href="#L-994"><span class="linenos"> 994</span></a> <span class="n">repo</span> <span class="o">=</span> <span class="n">git</span><span class="o">.</span><span class="n">Repo</span><span class="p">(</span><span class="n">phen_path</span><span class="p">)</span>
+</span><span id="L-995"><a href="#L-995"><span class="linenos"> 995</span></a> <span class="k">if</span> <span class="n">DEFAULT_GIT_BRANCH</span> <span class="ow">in</span> <span class="n">repo</span><span class="o">.</span><span class="n">branches</span><span class="p">:</span>
+</span><span id="L-996"><a href="#L-996"><span class="linenos"> 996</span></a> <span class="n">main_branch</span> <span class="o">=</span> <span class="n">repo</span><span class="o">.</span><span class="n">heads</span><span class="p">[</span><span class="n">DEFAULT_GIT_BRANCH</span><span class="p">]</span>
+</span><span id="L-997"><a href="#L-997"><span class="linenos"> 997</span></a> <span class="n">main_branch</span><span class="o">.</span><span class="n">checkout</span><span class="p">()</span>
+</span><span id="L-998"><a href="#L-998"><span class="linenos"> 998</span></a> <span class="k">else</span><span class="p">:</span>
+</span><span id="L-999"><a href="#L-999"><span class="linenos"> 999</span></a> <span class="k">raise</span> <span class="ne">AttributeError</span><span class="p">(</span>
+</span><span id="L-1000"><a href="#L-1000"><span class="linenos">1000</span></a> <span class="sa">f</span><span class="s2">"Phen repo does not contain the default branch </span><span class="si">{</span><span class="n">DEFAULT_GIT_BRANCH</span><span class="si">}</span><span class="s2">"</span>
+</span><span id="L-1001"><a href="#L-1001"><span class="linenos">1001</span></a> <span class="p">)</span>
+</span><span id="L-1002"><a href="#L-1002"><span class="linenos">1002</span></a>
+</span><span id="L-1003"><a href="#L-1003"><span class="linenos">1003</span></a> <span class="c1"># check if any changes to publish</span>
+</span><span id="L-1004"><a href="#L-1004"><span class="linenos">1004</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="n">repo</span><span class="o">.</span><span class="n">is_dirty</span><span class="p">()</span> <span class="ow">and</span> <span class="ow">not</span> <span class="n">repo</span><span class="o">.</span><span class="n">untracked_files</span><span class="p">:</span>
+</span><span id="L-1005"><a href="#L-1005"><span class="linenos">1005</span></a> <span class="k">if</span> <span class="n">remote_url</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span> <span class="ow">and</span> <span class="s2">"origin"</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">repo</span><span class="o">.</span><span class="n">remotes</span><span class="p">:</span>
+</span><span id="L-1006"><a href="#L-1006"><span class="linenos">1006</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"First publish to remote url </span><span class="si">{</span><span class="n">remote_url</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+</span><span id="L-1007"><a href="#L-1007"><span class="linenos">1007</span></a> <span class="k">else</span><span class="p">:</span>
+</span><span id="L-1008"><a href="#L-1008"><span class="linenos">1008</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">"Nothing to publish, no changes to the repo"</span><span class="p">)</span>
+</span><span id="L-1009"><a href="#L-1009"><span class="linenos">1009</span></a> <span class="k">return</span>
+</span><span id="L-1010"><a href="#L-1010"><span class="linenos">1010</span></a>
+</span><span id="L-1011"><a href="#L-1011"><span class="linenos">1011</span></a> <span class="c1"># get next version</span>
+</span><span id="L-1012"><a href="#L-1012"><span class="linenos">1012</span></a> <span class="n">new_version_str</span> <span class="o">=</span> <span class="n">generate_version_tag</span><span class="p">(</span><span class="n">repo</span><span class="p">,</span> <span class="n">increment</span><span class="p">)</span>
+</span><span id="L-1013"><a href="#L-1013"><span class="linenos">1013</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"New version: </span><span class="si">{</span><span class="n">new_version_str</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+</span><span id="L-1014"><a href="#L-1014"><span class="linenos">1014</span></a>
+</span><span id="L-1015"><a href="#L-1015"><span class="linenos">1015</span></a> <span class="c1"># Write version in configuration file</span>
+</span><span id="L-1016"><a href="#L-1016"><span class="linenos">1016</span></a> <span class="n">config_path</span> <span class="o">=</span> <span class="n">phen_path</span> <span class="o">/</span> <span class="n">CONFIG_FILE</span>
+</span><span id="L-1017"><a href="#L-1017"><span class="linenos">1017</span></a> <span class="k">with</span> <span class="n">config_path</span><span class="o">.</span><span class="n">open</span><span class="p">(</span><span class="s2">"r"</span><span class="p">)</span> <span class="k">as</span> <span class="n">file</span><span class="p">:</span>
+</span><span id="L-1018"><a href="#L-1018"><span class="linenos">1018</span></a> <span class="n">config</span> <span class="o">=</span> <span class="n">yaml</span><span class="o">.</span><span class="n">safe_load</span><span class="p">(</span><span class="n">file</span><span class="p">)</span>
+</span><span id="L-1019"><a href="#L-1019"><span class="linenos">1019</span></a>
+</span><span id="L-1020"><a href="#L-1020"><span class="linenos">1020</span></a> <span class="n">config</span><span class="p">[</span><span class="s2">"phenotype"</span><span class="p">][</span><span class="s2">"version"</span><span class="p">]</span> <span class="o">=</span> <span class="n">new_version_str</span>
+</span><span id="L-1021"><a href="#L-1021"><span class="linenos">1021</span></a> <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">config_path</span><span class="p">,</span> <span class="s2">"w"</span><span class="p">)</span> <span class="k">as</span> <span class="n">file</span><span class="p">:</span>
+</span><span id="L-1022"><a href="#L-1022"><span class="linenos">1022</span></a> <span class="n">yaml</span><span class="o">.</span><span class="n">dump</span><span class="p">(</span>
+</span><span id="L-1023"><a href="#L-1023"><span class="linenos">1023</span></a> <span class="n">config</span><span class="p">,</span>
+</span><span id="L-1024"><a href="#L-1024"><span class="linenos">1024</span></a> <span class="n">file</span><span class="p">,</span>
+</span><span id="L-1025"><a href="#L-1025"><span class="linenos">1025</span></a> <span class="n">Dumper</span><span class="o">=</span><span class="n">util</span><span class="o">.</span><span class="n">QuotedDumper</span><span class="p">,</span>
+</span><span id="L-1026"><a href="#L-1026"><span class="linenos">1026</span></a> <span class="n">default_flow_style</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span>
+</span><span id="L-1027"><a href="#L-1027"><span class="linenos">1027</span></a> <span class="n">sort_keys</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span>
+</span><span id="L-1028"><a href="#L-1028"><span class="linenos">1028</span></a> <span class="n">default_style</span><span class="o">=</span><span class="s1">'"'</span><span class="p">,</span>
+</span><span id="L-1029"><a href="#L-1029"><span class="linenos">1029</span></a> <span class="p">)</span>
+</span><span id="L-1030"><a href="#L-1030"><span class="linenos">1030</span></a>
+</span><span id="L-1031"><a href="#L-1031"><span class="linenos">1031</span></a> <span class="c1"># Add and commit changes to repo including version updates</span>
+</span><span id="L-1032"><a href="#L-1032"><span class="linenos">1032</span></a> <span class="n">commit_message</span> <span class="o">=</span> <span class="sa">f</span><span class="s2">"Committing updates to phenotype </span><span class="si">{</span><span class="n">phen_path</span><span class="si">}</span><span class="s2">"</span>
+</span><span id="L-1033"><a href="#L-1033"><span class="linenos">1033</span></a> <span class="n">repo</span><span class="o">.</span><span class="n">git</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="s2">"--all"</span><span class="p">)</span>
+</span><span id="L-1034"><a href="#L-1034"><span class="linenos">1034</span></a> <span class="n">repo</span><span class="o">.</span><span class="n">index</span><span class="o">.</span><span class="n">commit</span><span class="p">(</span><span class="n">commit_message</span><span class="p">)</span>
+</span><span id="L-1035"><a href="#L-1035"><span class="linenos">1035</span></a>
+</span><span id="L-1036"><a href="#L-1036"><span class="linenos">1036</span></a> <span class="c1"># Add tag to the repo</span>
+</span><span id="L-1037"><a href="#L-1037"><span class="linenos">1037</span></a> <span class="n">repo</span><span class="o">.</span><span class="n">create_tag</span><span class="p">(</span><span class="n">new_version_str</span><span class="p">)</span>
+</span><span id="L-1038"><a href="#L-1038"><span class="linenos">1038</span></a>
+</span><span id="L-1039"><a href="#L-1039"><span class="linenos">1039</span></a> <span class="c1"># push to origin if a remote repo</span>
+</span><span id="L-1040"><a href="#L-1040"><span class="linenos">1040</span></a> <span class="k">if</span> <span class="n">remote_url</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span> <span class="ow">and</span> <span class="s2">"origin"</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">repo</span><span class="o">.</span><span class="n">remotes</span><span class="p">:</span>
+</span><span id="L-1041"><a href="#L-1041"><span class="linenos">1041</span></a> <span class="n">git_url</span> <span class="o">=</span> <span class="n">construct_git_url</span><span class="p">(</span><span class="n">remote_url</span><span class="p">)</span>
+</span><span id="L-1042"><a href="#L-1042"><span class="linenos">1042</span></a> <span class="n">repo</span><span class="o">.</span><span class="n">create_remote</span><span class="p">(</span><span class="s2">"origin"</span><span class="p">,</span> <span class="n">git_url</span><span class="p">)</span>
+</span><span id="L-1043"><a href="#L-1043"><span class="linenos">1043</span></a>
+</span><span id="L-1044"><a href="#L-1044"><span class="linenos">1044</span></a> <span class="k">try</span><span class="p">:</span>
+</span><span id="L-1045"><a href="#L-1045"><span class="linenos">1045</span></a> <span class="k">if</span> <span class="s2">"origin"</span> <span class="ow">in</span> <span class="n">repo</span><span class="o">.</span><span class="n">remotes</span><span class="p">:</span>
+</span><span id="L-1046"><a href="#L-1046"><span class="linenos">1046</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Remote 'origin' is set </span><span class="si">{</span><span class="n">repo</span><span class="o">.</span><span class="n">remotes</span><span class="o">.</span><span class="n">origin</span><span class="o">.</span><span class="n">url</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+</span><span id="L-1047"><a href="#L-1047"><span class="linenos">1047</span></a> <span class="n">origin</span> <span class="o">=</span> <span class="n">repo</span><span class="o">.</span><span class="n">remotes</span><span class="o">.</span><span class="n">origin</span>
+</span><span id="L-1048"><a href="#L-1048"><span class="linenos">1048</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Pushing main branch to remote repo"</span><span class="p">)</span>
+</span><span id="L-1049"><a href="#L-1049"><span class="linenos">1049</span></a> <span class="n">repo</span><span class="o">.</span><span class="n">git</span><span class="o">.</span><span class="n">push</span><span class="p">(</span><span class="s2">"--set-upstream"</span><span class="p">,</span> <span class="s2">"origin"</span><span class="p">,</span> <span class="s2">"main"</span><span class="p">)</span>
+</span><span id="L-1050"><a href="#L-1050"><span class="linenos">1050</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Pushing version tags to remote git repo"</span><span class="p">)</span>
+</span><span id="L-1051"><a href="#L-1051"><span class="linenos">1051</span></a> <span class="n">origin</span><span class="o">.</span><span class="n">push</span><span class="p">(</span><span class="n">tags</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+</span><span id="L-1052"><a href="#L-1052"><span class="linenos">1052</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="s2">"Changes pushed to 'origin'"</span><span class="p">)</span>
+</span><span id="L-1053"><a href="#L-1053"><span class="linenos">1053</span></a> <span class="k">else</span><span class="p">:</span>
+</span><span id="L-1054"><a href="#L-1054"><span class="linenos">1054</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="s2">"Remote 'origin' is not set"</span><span class="p">)</span>
+</span><span id="L-1055"><a href="#L-1055"><span class="linenos">1055</span></a> <span class="k">except</span> <span class="ne">Exception</span> <span class="k">as</span> <span class="n">e</span><span class="p">:</span>
+</span><span id="L-1056"><a href="#L-1056"><span class="linenos">1056</span></a> <span class="n">tag_ref</span> <span class="o">=</span> <span class="n">repo</span><span class="o">.</span><span class="n">tags</span><span class="p">[</span><span class="n">new_version_str</span><span class="p">]</span>
+</span><span id="L-1057"><a href="#L-1057"><span class="linenos">1057</span></a> <span class="n">repo</span><span class="o">.</span><span class="n">delete_tag</span><span class="p">(</span><span class="n">tag_ref</span><span class="p">)</span>
+</span><span id="L-1058"><a href="#L-1058"><span class="linenos">1058</span></a> <span class="n">repo</span><span class="o">.</span><span class="n">git</span><span class="o">.</span><span class="n">reset</span><span class="p">(</span><span class="s2">"--soft"</span><span class="p">,</span> <span class="s2">"HEAD~1"</span><span class="p">)</span>
+</span><span id="L-1059"><a href="#L-1059"><span class="linenos">1059</span></a> <span class="k">raise</span> <span class="n">e</span>
+</span><span id="L-1060"><a href="#L-1060"><span class="linenos">1060</span></a>
+</span><span id="L-1061"><a href="#L-1061"><span class="linenos">1061</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Phenotype published successfully"</span><span class="p">)</span>
+</span><span id="L-1062"><a href="#L-1062"><span class="linenos">1062</span></a>
+</span><span id="L-1063"><a href="#L-1063"><span class="linenos">1063</span></a>
+</span><span id="L-1064"><a href="#L-1064"><span class="linenos">1064</span></a><span class="k">def</span><span class="w"> </span><span class="nf">export</span><span class="p">(</span><span class="n">phen_dir</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">version</span><span class="p">:</span> <span class="nb">str</span><span class="p">):</span>
+</span><span id="L-1065"><a href="#L-1065"><span class="linenos">1065</span></a><span class="w"> </span><span class="sd">"""Exports a phen repo at a specific tagged version into a target directory"""</span>
+</span><span id="L-1066"><a href="#L-1066"><span class="linenos">1066</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Exporting phenotype </span><span class="si">{</span><span class="n">phen_dir</span><span class="si">}</span><span class="s2"> at version </span><span class="si">{</span><span class="n">version</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+</span><span id="L-1067"><a href="#L-1067"><span class="linenos">1067</span></a>
+</span><span id="L-1068"><a href="#L-1068"><span class="linenos">1068</span></a> <span class="c1"># validate configuration</span>
+</span><span id="L-1069"><a href="#L-1069"><span class="linenos">1069</span></a> <span class="n">validate</span><span class="p">(</span><span class="n">phen_dir</span><span class="p">)</span>
+</span><span id="L-1070"><a href="#L-1070"><span class="linenos">1070</span></a> <span class="n">phen_path</span> <span class="o">=</span> <span class="n">Path</span><span class="p">(</span><span class="n">phen_dir</span><span class="p">)</span>
+</span><span id="L-1071"><a href="#L-1071"><span class="linenos">1071</span></a>
+</span><span id="L-1072"><a href="#L-1072"><span class="linenos">1072</span></a> <span class="c1"># load configuration</span>
+</span><span id="L-1073"><a href="#L-1073"><span class="linenos">1073</span></a> <span class="n">config_path</span> <span class="o">=</span> <span class="n">phen_path</span> <span class="o">/</span> <span class="n">CONFIG_FILE</span>
+</span><span id="L-1074"><a href="#L-1074"><span class="linenos">1074</span></a> <span class="k">with</span> <span class="n">config_path</span><span class="o">.</span><span class="n">open</span><span class="p">(</span><span class="s2">"r"</span><span class="p">)</span> <span class="k">as</span> <span class="n">file</span><span class="p">:</span>
+</span><span id="L-1075"><a href="#L-1075"><span class="linenos">1075</span></a> <span class="n">config</span> <span class="o">=</span> <span class="n">yaml</span><span class="o">.</span><span class="n">safe_load</span><span class="p">(</span><span class="n">file</span><span class="p">)</span>
+</span><span id="L-1076"><a href="#L-1076"><span class="linenos">1076</span></a>
+</span><span id="L-1077"><a href="#L-1077"><span class="linenos">1077</span></a> <span class="n">map_path</span> <span class="o">=</span> <span class="n">phen_path</span> <span class="o">/</span> <span class="n">MAP_DIR</span>
+</span><span id="L-1078"><a href="#L-1078"><span class="linenos">1078</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="n">map_path</span><span class="o">.</span><span class="n">exists</span><span class="p">():</span>
+</span><span id="L-1079"><a href="#L-1079"><span class="linenos">1079</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">warning</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Map path does not exist '</span><span class="si">{</span><span class="n">map_path</span><span class="si">}</span><span class="s2">'"</span><span class="p">)</span>
+</span><span id="L-1080"><a href="#L-1080"><span class="linenos">1080</span></a>
+</span><span id="L-1081"><a href="#L-1081"><span class="linenos">1081</span></a> <span class="n">export_path</span> <span class="o">=</span> <span class="n">phen_path</span> <span class="o">/</span> <span class="n">OMOP_PATH</span>
+</span><span id="L-1082"><a href="#L-1082"><span class="linenos">1082</span></a> <span class="c1"># check export directory exists and if not create it</span>
+</span><span id="L-1083"><a href="#L-1083"><span class="linenos">1083</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="n">export_path</span><span class="o">.</span><span class="n">exists</span><span class="p">():</span>
+</span><span id="L-1084"><a href="#L-1084"><span class="linenos">1084</span></a> <span class="n">export_path</span><span class="o">.</span><span class="n">mkdir</span><span class="p">(</span><span class="n">parents</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+</span><span id="L-1085"><a href="#L-1085"><span class="linenos">1085</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="sa">f</span><span class="s2">"OMOP export directory '</span><span class="si">{</span><span class="n">export_path</span><span class="si">}</span><span class="s2">' created."</span><span class="p">)</span>
+</span><span id="L-1086"><a href="#L-1086"><span class="linenos">1086</span></a>
+</span><span id="L-1087"><a href="#L-1087"><span class="linenos">1087</span></a> <span class="c1"># omop export db</span>
+</span><span id="L-1088"><a href="#L-1088"><span class="linenos">1088</span></a> <span class="n">export_db_path</span> <span class="o">=</span> <span class="n">omop</span><span class="o">.</span><span class="n">export</span><span class="p">(</span>
+</span><span id="L-1089"><a href="#L-1089"><span class="linenos">1089</span></a> <span class="n">map_path</span><span class="p">,</span>
+</span><span id="L-1090"><a href="#L-1090"><span class="linenos">1090</span></a> <span class="n">export_path</span><span class="p">,</span>
+</span><span id="L-1091"><a href="#L-1091"><span class="linenos">1091</span></a> <span class="n">config</span><span class="p">[</span><span class="s2">"phenotype"</span><span class="p">][</span><span class="s2">"version"</span><span class="p">],</span>
+</span><span id="L-1092"><a href="#L-1092"><span class="linenos">1092</span></a> <span class="n">config</span><span class="p">[</span><span class="s2">"phenotype"</span><span class="p">][</span><span class="s2">"omop"</span><span class="p">],</span>
+</span><span id="L-1093"><a href="#L-1093"><span class="linenos">1093</span></a> <span class="p">)</span>
+</span><span id="L-1094"><a href="#L-1094"><span class="linenos">1094</span></a>
+</span><span id="L-1095"><a href="#L-1095"><span class="linenos">1095</span></a> <span class="c1"># write to tables</span>
+</span><span id="L-1096"><a href="#L-1096"><span class="linenos">1096</span></a> <span class="c1"># export as csv</span>
+</span><span id="L-1097"><a href="#L-1097"><span class="linenos">1097</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Phenotype exported successfully"</span><span class="p">)</span>
+</span><span id="L-1098"><a href="#L-1098"><span class="linenos">1098</span></a>
+</span><span id="L-1099"><a href="#L-1099"><span class="linenos">1099</span></a>
+</span><span id="L-1100"><a href="#L-1100"><span class="linenos">1100</span></a><span class="k">def</span><span class="w"> </span><span class="nf">copy</span><span class="p">(</span><span class="n">phen_dir</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">target_dir</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">version</span><span class="p">:</span> <span class="nb">str</span><span class="p">):</span>
+</span><span id="L-1101"><a href="#L-1101"><span class="linenos">1101</span></a><span class="w"> </span><span class="sd">"""Copys a phen repo at a specific tagged version into a target directory"""</span>
+</span><span id="L-1102"><a href="#L-1102"><span class="linenos">1102</span></a>
+</span><span id="L-1103"><a href="#L-1103"><span class="linenos">1103</span></a> <span class="c1"># Validate</span>
+</span><span id="L-1104"><a href="#L-1104"><span class="linenos">1104</span></a> <span class="n">validate</span><span class="p">(</span><span class="n">phen_dir</span><span class="p">)</span>
+</span><span id="L-1105"><a href="#L-1105"><span class="linenos">1105</span></a> <span class="n">phen_path</span> <span class="o">=</span> <span class="n">Path</span><span class="p">(</span><span class="n">phen_dir</span><span class="p">)</span>
+</span><span id="L-1106"><a href="#L-1106"><span class="linenos">1106</span></a>
+</span><span id="L-1107"><a href="#L-1107"><span class="linenos">1107</span></a> <span class="c1"># Check target directory exists</span>
+</span><span id="L-1108"><a href="#L-1108"><span class="linenos">1108</span></a> <span class="n">target_path</span> <span class="o">=</span> <span class="n">Path</span><span class="p">(</span><span class="n">target_dir</span><span class="p">)</span>
+</span><span id="L-1109"><a href="#L-1109"><span class="linenos">1109</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="n">target_path</span><span class="o">.</span><span class="n">exists</span><span class="p">():</span>
+</span><span id="L-1110"><a href="#L-1110"><span class="linenos">1110</span></a> <span class="k">raise</span> <span class="ne">FileNotFoundError</span><span class="p">(</span><span class="sa">f</span><span class="s2">"The target directory </span><span class="si">{</span><span class="n">target_path</span><span class="si">}</span><span class="s2"> does not exist"</span><span class="p">)</span>
+</span><span id="L-1111"><a href="#L-1111"><span class="linenos">1111</span></a>
+</span><span id="L-1112"><a href="#L-1112"><span class="linenos">1112</span></a> <span class="c1"># Set copy directory</span>
+</span><span id="L-1113"><a href="#L-1113"><span class="linenos">1113</span></a> <span class="n">copy_path</span> <span class="o">=</span> <span class="n">target_path</span> <span class="o">/</span> <span class="n">version</span>
+</span><span id="L-1114"><a href="#L-1114"><span class="linenos">1114</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Copying repo </span><span class="si">{</span><span class="n">phen_path</span><span class="si">}</span><span class="s2"> to </span><span class="si">{</span><span class="n">copy_path</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+</span><span id="L-1115"><a href="#L-1115"><span class="linenos">1115</span></a>
+</span><span id="L-1116"><a href="#L-1116"><span class="linenos">1116</span></a> <span class="k">if</span> <span class="p">(</span>
+</span><span id="L-1117"><a href="#L-1117"><span class="linenos">1117</span></a> <span class="n">copy_path</span><span class="o">.</span><span class="n">exists</span><span class="p">()</span> <span class="ow">and</span> <span class="n">copy_path</span><span class="o">.</span><span class="n">is_dir</span><span class="p">()</span>
+</span><span id="L-1118"><a href="#L-1118"><span class="linenos">1118</span></a> <span class="p">):</span> <span class="c1"># Check if it exists and is a directory</span>
+</span><span id="L-1119"><a href="#L-1119"><span class="linenos">1119</span></a> <span class="n">copy</span> <span class="o">=</span> <span class="n">check_delete_dir</span><span class="p">(</span>
+</span><span id="L-1120"><a href="#L-1120"><span class="linenos">1120</span></a> <span class="n">copy_path</span><span class="p">,</span>
+</span><span id="L-1121"><a href="#L-1121"><span class="linenos">1121</span></a> <span class="sa">f</span><span class="s2">"The directory </span><span class="si">{</span><span class="nb">str</span><span class="p">(</span><span class="n">copy_path</span><span class="o">.</span><span class="n">resolve</span><span class="p">())</span><span class="si">}</span><span class="s2"> already exists. Do you want to overwrite? (yes/no): "</span><span class="p">,</span>
+</span><span id="L-1122"><a href="#L-1122"><span class="linenos">1122</span></a> <span class="p">)</span>
+</span><span id="L-1123"><a href="#L-1123"><span class="linenos">1123</span></a> <span class="k">else</span><span class="p">:</span>
+</span><span id="L-1124"><a href="#L-1124"><span class="linenos">1124</span></a> <span class="n">copy</span> <span class="o">=</span> <span class="kc">True</span>
+</span><span id="L-1125"><a href="#L-1125"><span class="linenos">1125</span></a>
+</span><span id="L-1126"><a href="#L-1126"><span class="linenos">1126</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="n">copy</span><span class="p">:</span>
+</span><span id="L-1127"><a href="#L-1127"><span class="linenos">1127</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Not copying the version </span><span class="si">{</span><span class="n">version</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+</span><span id="L-1128"><a href="#L-1128"><span class="linenos">1128</span></a> <span class="k">return</span>
+</span><span id="L-1129"><a href="#L-1129"><span class="linenos">1129</span></a>
+</span><span id="L-1130"><a href="#L-1130"><span class="linenos">1130</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Cloning repo from </span><span class="si">{</span><span class="n">phen_path</span><span class="si">}</span><span class="s2"> into </span><span class="si">{</span><span class="n">copy_path</span><span class="si">}</span><span class="s2">..."</span><span class="p">)</span>
+</span><span id="L-1131"><a href="#L-1131"><span class="linenos">1131</span></a> <span class="n">repo</span> <span class="o">=</span> <span class="n">git</span><span class="o">.</span><span class="n">Repo</span><span class="o">.</span><span class="n">clone_from</span><span class="p">(</span><span class="n">phen_path</span><span class="p">,</span> <span class="n">copy_path</span><span class="p">)</span>
+</span><span id="L-1132"><a href="#L-1132"><span class="linenos">1132</span></a>
+</span><span id="L-1133"><a href="#L-1133"><span class="linenos">1133</span></a> <span class="c1"># Check out the latest commit or specified version</span>
+</span><span id="L-1134"><a href="#L-1134"><span class="linenos">1134</span></a> <span class="k">if</span> <span class="n">version</span><span class="p">:</span>
+</span><span id="L-1135"><a href="#L-1135"><span class="linenos">1135</span></a> <span class="c1"># Checkout a specific version (e.g., branch, tag, or commit hash)</span>
+</span><span id="L-1136"><a href="#L-1136"><span class="linenos">1136</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Checking out version </span><span class="si">{</span><span class="n">version</span><span class="si">}</span><span class="s2">..."</span><span class="p">)</span>
+</span><span id="L-1137"><a href="#L-1137"><span class="linenos">1137</span></a> <span class="n">repo</span><span class="o">.</span><span class="n">git</span><span class="o">.</span><span class="n">checkout</span><span class="p">(</span><span class="n">version</span><span class="p">)</span>
+</span><span id="L-1138"><a href="#L-1138"><span class="linenos">1138</span></a> <span class="k">else</span><span class="p">:</span>
+</span><span id="L-1139"><a href="#L-1139"><span class="linenos">1139</span></a> <span class="c1"># Checkout the latest commit (HEAD)</span>
+</span><span id="L-1140"><a href="#L-1140"><span class="linenos">1140</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Checking out the latest commit..."</span><span class="p">)</span>
+</span><span id="L-1141"><a href="#L-1141"><span class="linenos">1141</span></a> <span class="n">repo</span><span class="o">.</span><span class="n">git</span><span class="o">.</span><span class="n">checkout</span><span class="p">(</span><span class="s2">"HEAD"</span><span class="p">)</span>
+</span><span id="L-1142"><a href="#L-1142"><span class="linenos">1142</span></a>
+</span><span id="L-1143"><a href="#L-1143"><span class="linenos">1143</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Copied </span><span class="si">{</span><span class="n">phen_path</span><span class="si">}</span><span class="s2"> </span><span class="si">{</span><span class="n">repo</span><span class="o">.</span><span class="n">head</span><span class="o">.</span><span class="n">commit</span><span class="o">.</span><span class="n">hexsha</span><span class="p">[:</span><span class="mi">7</span><span class="p">]</span><span class="si">}</span><span class="s2"> in </span><span class="si">{</span><span class="n">copy_path</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+</span><span id="L-1144"><a href="#L-1144"><span class="linenos">1144</span></a>
+</span><span id="L-1145"><a href="#L-1145"><span class="linenos">1145</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Phenotype copied successfully"</span><span class="p">)</span>
+</span><span id="L-1146"><a href="#L-1146"><span class="linenos">1146</span></a>
+</span><span id="L-1147"><a href="#L-1147"><span class="linenos">1147</span></a>
+</span><span id="L-1148"><a href="#L-1148"><span class="linenos">1148</span></a><span class="c1"># Convert concept_sets list into dictionaries</span>
+</span><span id="L-1149"><a href="#L-1149"><span class="linenos">1149</span></a><span class="k">def</span><span class="w"> </span><span class="nf">extract_concepts</span><span class="p">(</span><span class="n">config_data</span><span class="p">:</span> <span class="nb">dict</span><span class="p">)</span> <span class="o">-></span> <span class="n">Tuple</span><span class="p">[</span><span class="nb">dict</span><span class="p">,</span> <span class="n">Set</span><span class="p">[</span><span class="nb">str</span><span class="p">]]:</span>
+</span><span id="L-1150"><a href="#L-1150"><span class="linenos">1150</span></a><span class="w"> </span><span class="sd">"""Extracts concepts as {name: file_path} dictionary and a name set."""</span>
+</span><span id="L-1151"><a href="#L-1151"><span class="linenos">1151</span></a> <span class="n">concepts_dict</span> <span class="o">=</span> <span class="p">{</span>
+</span><span id="L-1152"><a href="#L-1152"><span class="linenos">1152</span></a> <span class="n">item</span><span class="p">[</span><span class="s2">"name"</span><span class="p">]:</span> <span class="n">item</span><span class="p">[</span><span class="s2">"file"</span><span class="p">][</span><span class="s2">"path"</span><span class="p">]</span>
+</span><span id="L-1153"><a href="#L-1153"><span class="linenos">1153</span></a> <span class="k">for</span> <span class="n">item</span> <span class="ow">in</span> <span class="n">config_data</span><span class="p">[</span><span class="s2">"phenotype"</span><span class="p">][</span><span class="s2">"concept_sets"</span><span class="p">]</span>
+</span><span id="L-1154"><a href="#L-1154"><span class="linenos">1154</span></a> <span class="p">}</span>
+</span><span id="L-1155"><a href="#L-1155"><span class="linenos">1155</span></a> <span class="n">name_set</span> <span class="o">=</span> <span class="nb">set</span><span class="p">(</span><span class="n">concepts_dict</span><span class="o">.</span><span class="n">keys</span><span class="p">())</span>
+</span><span id="L-1156"><a href="#L-1156"><span class="linenos">1156</span></a> <span class="k">return</span> <span class="n">concepts_dict</span><span class="p">,</span> <span class="n">name_set</span>
+</span><span id="L-1157"><a href="#L-1157"><span class="linenos">1157</span></a>
+</span><span id="L-1158"><a href="#L-1158"><span class="linenos">1158</span></a>
+</span><span id="L-1159"><a href="#L-1159"><span class="linenos">1159</span></a><span class="k">def</span><span class="w"> </span><span class="nf">extract_clean_deepdiff_keys</span><span class="p">(</span><span class="n">diff</span><span class="p">:</span> <span class="nb">dict</span><span class="p">,</span> <span class="n">key_type</span><span class="p">:</span> <span class="nb">str</span><span class="p">)</span> <span class="o">-></span> <span class="n">Set</span><span class="p">[</span><span class="n">Any</span><span class="p">]:</span>
+</span><span id="L-1160"><a href="#L-1160"><span class="linenos">1160</span></a><span class="w"> </span><span class="sd">"""</span>
+</span><span id="L-1161"><a href="#L-1161"><span class="linenos">1161</span></a><span class="sd"> Extracts clean keys from a DeepDiff dictionary.</span>
+</span><span id="L-1162"><a href="#L-1162"><span class="linenos">1162</span></a>
+</span><span id="L-1163"><a href="#L-1163"><span class="linenos">1163</span></a><span class="sd"> :param diff: DeepDiff result dictionary</span>
+</span><span id="L-1164"><a href="#L-1164"><span class="linenos">1164</span></a><span class="sd"> :param key_type: The type of change to extract (e.g., "dictionary_item_added", "dictionary_item_removed")</span>
+</span><span id="L-1165"><a href="#L-1165"><span class="linenos">1165</span></a><span class="sd"> :return: A set of clean key names</span>
+</span><span id="L-1166"><a href="#L-1166"><span class="linenos">1166</span></a><span class="sd"> """</span>
+</span><span id="L-1167"><a href="#L-1167"><span class="linenos">1167</span></a> <span class="k">return</span> <span class="p">{</span><span class="n">key</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s2">"root['"</span><span class="p">)[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s2">"']"</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span> <span class="k">for</span> <span class="n">key</span> <span class="ow">in</span> <span class="n">diff</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">key_type</span><span class="p">,</span> <span class="p">[])}</span>
+</span><span id="L-1168"><a href="#L-1168"><span class="linenos">1168</span></a>
+</span><span id="L-1169"><a href="#L-1169"><span class="linenos">1169</span></a>
+</span><span id="L-1170"><a href="#L-1170"><span class="linenos">1170</span></a><span class="k">def</span><span class="w"> </span><span class="nf">diff_config</span><span class="p">(</span><span class="n">old_config</span><span class="p">:</span> <span class="nb">dict</span><span class="p">,</span> <span class="n">new_config</span><span class="p">:</span> <span class="nb">dict</span><span class="p">)</span> <span class="o">-></span> <span class="nb">str</span><span class="p">:</span>
+</span><span id="L-1171"><a href="#L-1171"><span class="linenos">1171</span></a> <span class="n">report</span> <span class="o">=</span> <span class="sa">f</span><span class="s2">"</span><span class="se">\n</span><span class="s2"># Changes to phenotype configuration</span><span class="se">\n</span><span class="s2">"</span>
+</span><span id="L-1172"><a href="#L-1172"><span class="linenos">1172</span></a> <span class="n">report</span> <span class="o">+=</span> <span class="sa">f</span><span class="s2">"This compares changes in the phenotype configuration including added, removed and renamed concept sets and changes to concept set source concept code file paths</span><span class="se">\n\n</span><span class="s2">"</span>
+</span><span id="L-1173"><a href="#L-1173"><span class="linenos">1173</span></a>
+</span><span id="L-1174"><a href="#L-1174"><span class="linenos">1174</span></a> <span class="n">old_concepts</span><span class="p">,</span> <span class="n">old_names</span> <span class="o">=</span> <span class="n">extract_concepts</span><span class="p">(</span><span class="n">old_config</span><span class="p">)</span>
+</span><span id="L-1175"><a href="#L-1175"><span class="linenos">1175</span></a> <span class="n">new_concepts</span><span class="p">,</span> <span class="n">new_names</span> <span class="o">=</span> <span class="n">extract_concepts</span><span class="p">(</span><span class="n">new_config</span><span class="p">)</span>
+</span><span id="L-1176"><a href="#L-1176"><span class="linenos">1176</span></a>
+</span><span id="L-1177"><a href="#L-1177"><span class="linenos">1177</span></a> <span class="c1"># Check added and removed names</span>
+</span><span id="L-1178"><a href="#L-1178"><span class="linenos">1178</span></a> <span class="n">added_names</span> <span class="o">=</span> <span class="n">new_names</span> <span class="o">-</span> <span class="n">old_names</span> <span class="c1"># Names that appear in new but not in old</span>
+</span><span id="L-1179"><a href="#L-1179"><span class="linenos">1179</span></a> <span class="n">removed_names</span> <span class="o">=</span> <span class="n">old_names</span> <span class="o">-</span> <span class="n">new_names</span> <span class="c1"># Names that were in old but not in new</span>
+</span><span id="L-1180"><a href="#L-1180"><span class="linenos">1180</span></a>
+</span><span id="L-1181"><a href="#L-1181"><span class="linenos">1181</span></a> <span class="c1"># find file path changes for unchanged names</span>
+</span><span id="L-1182"><a href="#L-1182"><span class="linenos">1182</span></a> <span class="n">unchanged_names</span> <span class="o">=</span> <span class="n">old_names</span> <span class="o">&</span> <span class="n">new_names</span> <span class="c1"># Names that exist in both</span>
+</span><span id="L-1183"><a href="#L-1183"><span class="linenos">1183</span></a> <span class="n">file_diff</span> <span class="o">=</span> <span class="n">DeepDiff</span><span class="p">(</span>
+</span><span id="L-1184"><a href="#L-1184"><span class="linenos">1184</span></a> <span class="p">{</span><span class="n">name</span><span class="p">:</span> <span class="n">old_concepts</span><span class="p">[</span><span class="n">name</span><span class="p">]</span> <span class="k">for</span> <span class="n">name</span> <span class="ow">in</span> <span class="n">unchanged_names</span><span class="p">},</span>
+</span><span id="L-1185"><a href="#L-1185"><span class="linenos">1185</span></a> <span class="p">{</span><span class="n">name</span><span class="p">:</span> <span class="n">new_concepts</span><span class="p">[</span><span class="n">name</span><span class="p">]</span> <span class="k">for</span> <span class="n">name</span> <span class="ow">in</span> <span class="n">unchanged_names</span><span class="p">},</span>
+</span><span id="L-1186"><a href="#L-1186"><span class="linenos">1186</span></a> <span class="p">)</span>
+</span><span id="L-1187"><a href="#L-1187"><span class="linenos">1187</span></a>
+</span><span id="L-1188"><a href="#L-1188"><span class="linenos">1188</span></a> <span class="c1"># Find renamed concepts (same file, different name)</span>
+</span><span id="L-1189"><a href="#L-1189"><span class="linenos">1189</span></a> <span class="n">renamed_concepts</span> <span class="o">=</span> <span class="p">[]</span>
+</span><span id="L-1190"><a href="#L-1190"><span class="linenos">1190</span></a> <span class="k">for</span> <span class="n">removed</span> <span class="ow">in</span> <span class="n">removed_names</span><span class="p">:</span>
+</span><span id="L-1191"><a href="#L-1191"><span class="linenos">1191</span></a> <span class="n">old_path</span> <span class="o">=</span> <span class="n">old_concepts</span><span class="p">[</span><span class="n">removed</span><span class="p">]</span>
+</span><span id="L-1192"><a href="#L-1192"><span class="linenos">1192</span></a> <span class="k">for</span> <span class="n">added</span> <span class="ow">in</span> <span class="n">added_names</span><span class="p">:</span>
+</span><span id="L-1193"><a href="#L-1193"><span class="linenos">1193</span></a> <span class="n">new_path</span> <span class="o">=</span> <span class="n">new_concepts</span><span class="p">[</span><span class="n">added</span><span class="p">]</span>
+</span><span id="L-1194"><a href="#L-1194"><span class="linenos">1194</span></a> <span class="k">if</span> <span class="n">old_path</span> <span class="o">==</span> <span class="n">new_path</span><span class="p">:</span>
+</span><span id="L-1195"><a href="#L-1195"><span class="linenos">1195</span></a> <span class="n">renamed_concepts</span><span class="o">.</span><span class="n">append</span><span class="p">((</span><span class="n">removed</span><span class="p">,</span> <span class="n">added</span><span class="p">))</span>
+</span><span id="L-1196"><a href="#L-1196"><span class="linenos">1196</span></a>
+</span><span id="L-1197"><a href="#L-1197"><span class="linenos">1197</span></a> <span class="c1"># Remove renamed concepts from added and removed sets</span>
+</span><span id="L-1198"><a href="#L-1198"><span class="linenos">1198</span></a> <span class="k">for</span> <span class="n">old_name</span><span class="p">,</span> <span class="n">new_name</span> <span class="ow">in</span> <span class="n">renamed_concepts</span><span class="p">:</span>
+</span><span id="L-1199"><a href="#L-1199"><span class="linenos">1199</span></a> <span class="n">added_names</span><span class="o">.</span><span class="n">discard</span><span class="p">(</span><span class="n">new_name</span><span class="p">)</span>
+</span><span id="L-1200"><a href="#L-1200"><span class="linenos">1200</span></a> <span class="n">removed_names</span><span class="o">.</span><span class="n">discard</span><span class="p">(</span><span class="n">old_name</span><span class="p">)</span>
+</span><span id="L-1201"><a href="#L-1201"><span class="linenos">1201</span></a>
+</span><span id="L-1202"><a href="#L-1202"><span class="linenos">1202</span></a> <span class="c1"># generate config report</span>
+</span><span id="L-1203"><a href="#L-1203"><span class="linenos">1203</span></a> <span class="k">if</span> <span class="n">added_names</span><span class="p">:</span>
+</span><span id="L-1204"><a href="#L-1204"><span class="linenos">1204</span></a> <span class="n">report</span> <span class="o">+=</span> <span class="s2">"## Added Concepts</span><span class="se">\n</span><span class="s2">"</span>
+</span><span id="L-1205"><a href="#L-1205"><span class="linenos">1205</span></a> <span class="k">for</span> <span class="n">name</span> <span class="ow">in</span> <span class="n">added_names</span><span class="p">:</span>
+</span><span id="L-1206"><a href="#L-1206"><span class="linenos">1206</span></a> <span class="n">report</span> <span class="o">+=</span> <span class="sa">f</span><span class="s2">"- `</span><span class="si">{</span><span class="n">name</span><span class="si">}</span><span class="s2">` (File: `</span><span class="si">{</span><span class="n">new_concepts</span><span class="p">[</span><span class="n">name</span><span class="p">]</span><span class="si">}</span><span class="s2">`)</span><span class="se">\n</span><span class="s2">"</span>
+</span><span id="L-1207"><a href="#L-1207"><span class="linenos">1207</span></a> <span class="n">report</span> <span class="o">+=</span> <span class="s2">"</span><span class="se">\n</span><span class="s2">"</span>
+</span><span id="L-1208"><a href="#L-1208"><span class="linenos">1208</span></a>
+</span><span id="L-1209"><a href="#L-1209"><span class="linenos">1209</span></a> <span class="k">if</span> <span class="n">removed_names</span><span class="p">:</span>
+</span><span id="L-1210"><a href="#L-1210"><span class="linenos">1210</span></a> <span class="n">report</span> <span class="o">+=</span> <span class="s2">"## Removed Concepts</span><span class="se">\n</span><span class="s2">"</span>
+</span><span id="L-1211"><a href="#L-1211"><span class="linenos">1211</span></a> <span class="k">for</span> <span class="n">name</span> <span class="ow">in</span> <span class="n">removed_names</span><span class="p">:</span>
+</span><span id="L-1212"><a href="#L-1212"><span class="linenos">1212</span></a> <span class="n">report</span> <span class="o">+=</span> <span class="sa">f</span><span class="s2">"- `</span><span class="si">{</span><span class="n">name</span><span class="si">}</span><span class="s2">` (File: `</span><span class="si">{</span><span class="n">old_concepts</span><span class="p">[</span><span class="n">name</span><span class="p">]</span><span class="si">}</span><span class="s2">`)</span><span class="se">\n</span><span class="s2">"</span>
+</span><span id="L-1213"><a href="#L-1213"><span class="linenos">1213</span></a> <span class="n">report</span> <span class="o">+=</span> <span class="s2">"</span><span class="se">\n</span><span class="s2">"</span>
+</span><span id="L-1214"><a href="#L-1214"><span class="linenos">1214</span></a>
+</span><span id="L-1215"><a href="#L-1215"><span class="linenos">1215</span></a> <span class="k">if</span> <span class="n">renamed_concepts</span><span class="p">:</span>
+</span><span id="L-1216"><a href="#L-1216"><span class="linenos">1216</span></a> <span class="n">report</span> <span class="o">+=</span> <span class="s2">"## Renamed Concepts</span><span class="se">\n</span><span class="s2">"</span>
+</span><span id="L-1217"><a href="#L-1217"><span class="linenos">1217</span></a> <span class="k">for</span> <span class="n">old_name</span><span class="p">,</span> <span class="n">new_name</span> <span class="ow">in</span> <span class="n">renamed_concepts</span><span class="p">:</span>
+</span><span id="L-1218"><a href="#L-1218"><span class="linenos">1218</span></a> <span class="n">report</span> <span class="o">+=</span> <span class="p">(</span>
+</span><span id="L-1219"><a href="#L-1219"><span class="linenos">1219</span></a> <span class="sa">f</span><span class="s2">"- `</span><span class="si">{</span><span class="n">old_name</span><span class="si">}</span><span class="s2">` âž `</span><span class="si">{</span><span class="n">new_name</span><span class="si">}</span><span class="s2">` (File: `</span><span class="si">{</span><span class="n">old_concepts</span><span class="p">[</span><span class="n">old_name</span><span class="p">]</span><span class="si">}</span><span class="s2">`)</span><span class="se">\n</span><span class="s2">"</span>
+</span><span id="L-1220"><a href="#L-1220"><span class="linenos">1220</span></a> <span class="p">)</span>
+</span><span id="L-1221"><a href="#L-1221"><span class="linenos">1221</span></a> <span class="n">report</span> <span class="o">+=</span> <span class="s2">"</span><span class="se">\n</span><span class="s2">"</span>
+</span><span id="L-1222"><a href="#L-1222"><span class="linenos">1222</span></a>
+</span><span id="L-1223"><a href="#L-1223"><span class="linenos">1223</span></a> <span class="k">if</span> <span class="s2">"values_changed"</span> <span class="ow">in</span> <span class="n">file_diff</span><span class="p">:</span>
+</span><span id="L-1224"><a href="#L-1224"><span class="linenos">1224</span></a> <span class="n">report</span> <span class="o">+=</span> <span class="s2">"## Updated File Paths</span><span class="se">\n</span><span class="s2">"</span>
+</span><span id="L-1225"><a href="#L-1225"><span class="linenos">1225</span></a> <span class="k">for</span> <span class="n">name</span><span class="p">,</span> <span class="n">change</span> <span class="ow">in</span> <span class="n">file_diff</span><span class="p">[</span><span class="s2">"values_changed"</span><span class="p">]</span><span class="o">.</span><span class="n">items</span><span class="p">():</span>
+</span><span id="L-1226"><a href="#L-1226"><span class="linenos">1226</span></a> <span class="n">old_file</span> <span class="o">=</span> <span class="n">change</span><span class="p">[</span><span class="s2">"old_value"</span><span class="p">]</span>
+</span><span id="L-1227"><a href="#L-1227"><span class="linenos">1227</span></a> <span class="n">new_file</span> <span class="o">=</span> <span class="n">change</span><span class="p">[</span><span class="s2">"new_value"</span><span class="p">]</span>
+</span><span id="L-1228"><a href="#L-1228"><span class="linenos">1228</span></a> <span class="n">clean_name</span> <span class="o">=</span> <span class="n">name</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s2">"root['"</span><span class="p">)[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s2">"']"</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span>
+</span><span id="L-1229"><a href="#L-1229"><span class="linenos">1229</span></a> <span class="n">report</span> <span class="o">+=</span> <span class="p">(</span>
+</span><span id="L-1230"><a href="#L-1230"><span class="linenos">1230</span></a> <span class="sa">f</span><span class="s2">"- `</span><span class="si">{</span><span class="n">clean_name</span><span class="si">}</span><span class="s2">` changed file from `</span><span class="si">{</span><span class="n">old_file</span><span class="si">}</span><span class="s2">` âž `</span><span class="si">{</span><span class="n">new_file</span><span class="si">}</span><span class="s2">`</span><span class="se">\n</span><span class="s2">"</span>
+</span><span id="L-1231"><a href="#L-1231"><span class="linenos">1231</span></a> <span class="p">)</span>
+</span><span id="L-1232"><a href="#L-1232"><span class="linenos">1232</span></a> <span class="n">report</span> <span class="o">+=</span> <span class="s2">"</span><span class="se">\n</span><span class="s2">"</span>
+</span><span id="L-1233"><a href="#L-1233"><span class="linenos">1233</span></a>
+</span><span id="L-1234"><a href="#L-1234"><span class="linenos">1234</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="p">(</span>
+</span><span id="L-1235"><a href="#L-1235"><span class="linenos">1235</span></a> <span class="n">added_names</span>
+</span><span id="L-1236"><a href="#L-1236"><span class="linenos">1236</span></a> <span class="ow">or</span> <span class="n">removed_names</span>
+</span><span id="L-1237"><a href="#L-1237"><span class="linenos">1237</span></a> <span class="ow">or</span> <span class="n">renamed_concepts</span>
+</span><span id="L-1238"><a href="#L-1238"><span class="linenos">1238</span></a> <span class="ow">or</span> <span class="n">file_diff</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"values_changed"</span><span class="p">)</span>
+</span><span id="L-1239"><a href="#L-1239"><span class="linenos">1239</span></a> <span class="p">):</span>
+</span><span id="L-1240"><a href="#L-1240"><span class="linenos">1240</span></a> <span class="n">report</span> <span class="o">+=</span> <span class="s2">"No changes in concept sets.</span><span class="se">\n</span><span class="s2">"</span>
+</span><span id="L-1241"><a href="#L-1241"><span class="linenos">1241</span></a>
+</span><span id="L-1242"><a href="#L-1242"><span class="linenos">1242</span></a> <span class="k">return</span> <span class="n">report</span>
+</span><span id="L-1243"><a href="#L-1243"><span class="linenos">1243</span></a>
+</span><span id="L-1244"><a href="#L-1244"><span class="linenos">1244</span></a>
+</span><span id="L-1245"><a href="#L-1245"><span class="linenos">1245</span></a><span class="k">def</span><span class="w"> </span><span class="nf">diff_map_files</span><span class="p">(</span><span class="n">old_map_path</span><span class="p">:</span> <span class="n">Path</span><span class="p">,</span> <span class="n">new_map_path</span><span class="p">:</span> <span class="n">Path</span><span class="p">)</span> <span class="o">-></span> <span class="nb">str</span><span class="p">:</span>
+</span><span id="L-1246"><a href="#L-1246"><span class="linenos">1246</span></a> <span class="n">old_output_files</span> <span class="o">=</span> <span class="p">[</span>
+</span><span id="L-1247"><a href="#L-1247"><span class="linenos">1247</span></a> <span class="n">file</span><span class="o">.</span><span class="n">name</span>
+</span><span id="L-1248"><a href="#L-1248"><span class="linenos">1248</span></a> <span class="k">for</span> <span class="n">file</span> <span class="ow">in</span> <span class="n">old_map_path</span><span class="o">.</span><span class="n">iterdir</span><span class="p">()</span>
+</span><span id="L-1249"><a href="#L-1249"><span class="linenos">1249</span></a> <span class="k">if</span> <span class="n">file</span><span class="o">.</span><span class="n">is_file</span><span class="p">()</span> <span class="ow">and</span> <span class="ow">not</span> <span class="n">file</span><span class="o">.</span><span class="n">name</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s2">"."</span><span class="p">)</span>
+</span><span id="L-1250"><a href="#L-1250"><span class="linenos">1250</span></a> <span class="p">]</span>
+</span><span id="L-1251"><a href="#L-1251"><span class="linenos">1251</span></a> <span class="n">new_output_files</span> <span class="o">=</span> <span class="p">[</span>
+</span><span id="L-1252"><a href="#L-1252"><span class="linenos">1252</span></a> <span class="n">file</span><span class="o">.</span><span class="n">name</span>
+</span><span id="L-1253"><a href="#L-1253"><span class="linenos">1253</span></a> <span class="k">for</span> <span class="n">file</span> <span class="ow">in</span> <span class="n">new_map_path</span><span class="o">.</span><span class="n">iterdir</span><span class="p">()</span>
+</span><span id="L-1254"><a href="#L-1254"><span class="linenos">1254</span></a> <span class="k">if</span> <span class="n">file</span><span class="o">.</span><span class="n">is_file</span><span class="p">()</span> <span class="ow">and</span> <span class="ow">not</span> <span class="n">file</span><span class="o">.</span><span class="n">name</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s2">"."</span><span class="p">)</span>
+</span><span id="L-1255"><a href="#L-1255"><span class="linenos">1255</span></a> <span class="p">]</span>
+</span><span id="L-1256"><a href="#L-1256"><span class="linenos">1256</span></a>
+</span><span id="L-1257"><a href="#L-1257"><span class="linenos">1257</span></a> <span class="c1"># Convert the lists to sets for easy comparison</span>
+</span><span id="L-1258"><a href="#L-1258"><span class="linenos">1258</span></a> <span class="n">old_output_set</span> <span class="o">=</span> <span class="nb">set</span><span class="p">(</span><span class="n">old_output_files</span><span class="p">)</span>
+</span><span id="L-1259"><a href="#L-1259"><span class="linenos">1259</span></a> <span class="n">new_output_set</span> <span class="o">=</span> <span class="nb">set</span><span class="p">(</span><span class="n">new_output_files</span><span class="p">)</span>
+</span><span id="L-1260"><a href="#L-1260"><span class="linenos">1260</span></a>
+</span><span id="L-1261"><a href="#L-1261"><span class="linenos">1261</span></a> <span class="c1"># Outputs that are in old_output_set but not in new_output_set (removed files)</span>
+</span><span id="L-1262"><a href="#L-1262"><span class="linenos">1262</span></a> <span class="n">removed_outputs</span> <span class="o">=</span> <span class="n">old_output_set</span> <span class="o">-</span> <span class="n">new_output_set</span>
+</span><span id="L-1263"><a href="#L-1263"><span class="linenos">1263</span></a> <span class="c1"># Outputs that are in new_output_set but not in old_output_set (added files)</span>
+</span><span id="L-1264"><a href="#L-1264"><span class="linenos">1264</span></a> <span class="n">added_outputs</span> <span class="o">=</span> <span class="n">new_output_set</span> <span class="o">-</span> <span class="n">old_output_set</span>
+</span><span id="L-1265"><a href="#L-1265"><span class="linenos">1265</span></a> <span class="c1"># Outputs that are the intersection of old_output_set and new_output_set</span>
+</span><span id="L-1266"><a href="#L-1266"><span class="linenos">1266</span></a> <span class="n">common_outputs</span> <span class="o">=</span> <span class="n">old_output_set</span> <span class="o">&</span> <span class="n">new_output_set</span>
+</span><span id="L-1267"><a href="#L-1267"><span class="linenos">1267</span></a>
+</span><span id="L-1268"><a href="#L-1268"><span class="linenos">1268</span></a> <span class="n">report</span> <span class="o">=</span> <span class="sa">f</span><span class="s2">"</span><span class="se">\n</span><span class="s2"># Changes to available translations</span><span class="se">\n</span><span class="s2">"</span>
+</span><span id="L-1269"><a href="#L-1269"><span class="linenos">1269</span></a> <span class="n">report</span> <span class="o">+=</span> <span class="sa">f</span><span class="s2">"This compares the coding translations files available.</span><span class="se">\n\n</span><span class="s2">"</span>
+</span><span id="L-1270"><a href="#L-1270"><span class="linenos">1270</span></a> <span class="n">report</span> <span class="o">+=</span> <span class="sa">f</span><span class="s2">"- Removed outputs: </span><span class="si">{</span><span class="nb">sorted</span><span class="p">(</span><span class="nb">list</span><span class="p">(</span><span class="n">removed_outputs</span><span class="p">))</span><span class="si">}</span><span class="se">\n</span><span class="s2">"</span>
+</span><span id="L-1271"><a href="#L-1271"><span class="linenos">1271</span></a> <span class="n">report</span> <span class="o">+=</span> <span class="sa">f</span><span class="s2">"- Added outputs: </span><span class="si">{</span><span class="nb">sorted</span><span class="p">(</span><span class="nb">list</span><span class="p">(</span><span class="n">added_outputs</span><span class="p">))</span><span class="si">}</span><span class="se">\n</span><span class="s2">"</span>
+</span><span id="L-1272"><a href="#L-1272"><span class="linenos">1272</span></a> <span class="n">report</span> <span class="o">+=</span> <span class="sa">f</span><span class="s2">"- Common outputs: </span><span class="si">{</span><span class="nb">sorted</span><span class="p">(</span><span class="nb">list</span><span class="p">(</span><span class="n">common_outputs</span><span class="p">))</span><span class="si">}</span><span class="se">\n\n</span><span class="s2">"</span>
+</span><span id="L-1273"><a href="#L-1273"><span class="linenos">1273</span></a>
+</span><span id="L-1274"><a href="#L-1274"><span class="linenos">1274</span></a> <span class="c1"># Step N: Compare common outputs between versions</span>
+</span><span id="L-1275"><a href="#L-1275"><span class="linenos">1275</span></a> <span class="n">report</span> <span class="o">+=</span> <span class="sa">f</span><span class="s2">"# Changes to concepts in translation files</span><span class="se">\n\n</span><span class="s2">"</span>
+</span><span id="L-1276"><a href="#L-1276"><span class="linenos">1276</span></a> <span class="n">report</span> <span class="o">+=</span> <span class="sa">f</span><span class="s2">"This compares the added and removed concepts in each of the coding translation files. Note that this might be different to the config.yaml if the translations have not been run for the current config.</span><span class="se">\n\n</span><span class="s2">"</span>
+</span><span id="L-1277"><a href="#L-1277"><span class="linenos">1277</span></a> <span class="k">for</span> <span class="n">file</span> <span class="ow">in</span> <span class="n">common_outputs</span><span class="p">:</span>
+</span><span id="L-1278"><a href="#L-1278"><span class="linenos">1278</span></a> <span class="n">old_output</span> <span class="o">=</span> <span class="n">old_map_path</span> <span class="o">/</span> <span class="n">file</span>
+</span><span id="L-1279"><a href="#L-1279"><span class="linenos">1279</span></a> <span class="n">new_output</span> <span class="o">=</span> <span class="n">new_map_path</span> <span class="o">/</span> <span class="n">file</span>
+</span><span id="L-1280"><a href="#L-1280"><span class="linenos">1280</span></a>
+</span><span id="L-1281"><a href="#L-1281"><span class="linenos">1281</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Old ouptput: </span><span class="si">{</span><span class="nb">str</span><span class="p">(</span><span class="n">old_output</span><span class="o">.</span><span class="n">resolve</span><span class="p">())</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+</span><span id="L-1282"><a href="#L-1282"><span class="linenos">1282</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="sa">f</span><span class="s2">"New ouptput: </span><span class="si">{</span><span class="nb">str</span><span class="p">(</span><span class="n">new_output</span><span class="o">.</span><span class="n">resolve</span><span class="p">())</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+</span><span id="L-1283"><a href="#L-1283"><span class="linenos">1283</span></a>
+</span><span id="L-1284"><a href="#L-1284"><span class="linenos">1284</span></a> <span class="n">df1</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">read_csv</span><span class="p">(</span><span class="n">old_output</span><span class="p">)</span>
+</span><span id="L-1285"><a href="#L-1285"><span class="linenos">1285</span></a> <span class="n">df1</span> <span class="o">=</span> <span class="n">df1</span><span class="p">[[</span><span class="s2">"CONCEPT"</span><span class="p">,</span> <span class="s2">"CONCEPT_SET"</span><span class="p">]]</span><span class="o">.</span><span class="n">groupby</span><span class="p">(</span><span class="s2">"CONCEPT_SET"</span><span class="p">)</span><span class="o">.</span><span class="n">count</span><span class="p">()</span>
+</span><span id="L-1286"><a href="#L-1286"><span class="linenos">1286</span></a> <span class="n">df2</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">read_csv</span><span class="p">(</span><span class="n">new_output</span><span class="p">)</span>
+</span><span id="L-1287"><a href="#L-1287"><span class="linenos">1287</span></a> <span class="n">df2</span> <span class="o">=</span> <span class="n">df2</span><span class="p">[[</span><span class="s2">"CONCEPT"</span><span class="p">,</span> <span class="s2">"CONCEPT_SET"</span><span class="p">]]</span><span class="o">.</span><span class="n">groupby</span><span class="p">(</span><span class="s2">"CONCEPT_SET"</span><span class="p">)</span><span class="o">.</span><span class="n">count</span><span class="p">()</span>
+</span><span id="L-1288"><a href="#L-1288"><span class="linenos">1288</span></a>
+</span><span id="L-1289"><a href="#L-1289"><span class="linenos">1289</span></a> <span class="c1"># Check for added and removed concepts</span>
+</span><span id="L-1290"><a href="#L-1290"><span class="linenos">1290</span></a> <span class="n">report</span> <span class="o">+=</span> <span class="sa">f</span><span class="s2">"- File </span><span class="si">{</span><span class="n">file</span><span class="si">}</span><span class="se">\n</span><span class="s2">"</span>
+</span><span id="L-1291"><a href="#L-1291"><span class="linenos">1291</span></a> <span class="n">sorted_list</span> <span class="o">=</span> <span class="nb">sorted</span><span class="p">(</span><span class="nb">list</span><span class="p">(</span><span class="nb">set</span><span class="p">(</span><span class="n">df1</span><span class="o">.</span><span class="n">index</span><span class="p">)</span> <span class="o">-</span> <span class="nb">set</span><span class="p">(</span><span class="n">df2</span><span class="o">.</span><span class="n">index</span><span class="p">)))</span>
+</span><span id="L-1292"><a href="#L-1292"><span class="linenos">1292</span></a> <span class="n">report</span> <span class="o">+=</span> <span class="sa">f</span><span class="s2">"- Removed concepts </span><span class="si">{</span><span class="n">sorted_list</span><span class="si">}</span><span class="se">\n</span><span class="s2">"</span>
+</span><span id="L-1293"><a href="#L-1293"><span class="linenos">1293</span></a> <span class="n">sorted_list</span> <span class="o">=</span> <span class="nb">sorted</span><span class="p">(</span><span class="nb">list</span><span class="p">(</span><span class="nb">set</span><span class="p">(</span><span class="n">df2</span><span class="o">.</span><span class="n">index</span><span class="p">)</span> <span class="o">-</span> <span class="nb">set</span><span class="p">(</span><span class="n">df1</span><span class="o">.</span><span class="n">index</span><span class="p">)))</span>
+</span><span id="L-1294"><a href="#L-1294"><span class="linenos">1294</span></a> <span class="n">report</span> <span class="o">+=</span> <span class="sa">f</span><span class="s2">"- Added concepts </span><span class="si">{</span><span class="n">sorted_list</span><span class="si">}</span><span class="se">\n</span><span class="s2">"</span>
+</span><span id="L-1295"><a href="#L-1295"><span class="linenos">1295</span></a>
+</span><span id="L-1296"><a href="#L-1296"><span class="linenos">1296</span></a> <span class="c1"># Check for changed concepts</span>
+</span><span id="L-1297"><a href="#L-1297"><span class="linenos">1297</span></a> <span class="n">diff</span> <span class="o">=</span> <span class="n">df2</span> <span class="o">-</span> <span class="n">df1</span> <span class="c1"># diff in counts</span>
+</span><span id="L-1298"><a href="#L-1298"><span class="linenos">1298</span></a> <span class="n">diff</span> <span class="o">=</span> <span class="n">diff</span><span class="p">[</span>
+</span><span id="L-1299"><a href="#L-1299"><span class="linenos">1299</span></a> <span class="p">(</span><span class="o">~</span><span class="p">(</span><span class="n">diff</span><span class="p">[</span><span class="s2">"CONCEPT"</span><span class="p">]</span> <span class="o">==</span> <span class="mf">0.0</span><span class="p">))</span> <span class="o">&</span> <span class="n">diff</span><span class="p">[</span><span class="s2">"CONCEPT"</span><span class="p">]</span><span class="o">.</span><span class="n">notna</span><span class="p">()</span>
+</span><span id="L-1300"><a href="#L-1300"><span class="linenos">1300</span></a> <span class="p">]</span> <span class="c1"># get non-zero counts</span>
+</span><span id="L-1301"><a href="#L-1301"><span class="linenos">1301</span></a> <span class="n">s</span> <span class="o">=</span> <span class="s2">"</span><span class="se">\n</span><span class="s2">"</span>
+</span><span id="L-1302"><a href="#L-1302"><span class="linenos">1302</span></a> <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">diff</span><span class="o">.</span><span class="n">index</span><span class="p">)</span> <span class="o">></span> <span class="mi">0</span><span class="p">:</span>
+</span><span id="L-1303"><a href="#L-1303"><span class="linenos">1303</span></a> <span class="k">for</span> <span class="n">concept</span><span class="p">,</span> <span class="n">row</span> <span class="ow">in</span> <span class="n">diff</span><span class="o">.</span><span class="n">iterrows</span><span class="p">():</span>
+</span><span id="L-1304"><a href="#L-1304"><span class="linenos">1304</span></a> <span class="n">s</span> <span class="o">+=</span> <span class="s2">"</span><span class="se">\t</span><span class="s2"> - </span><span class="si">{}</span><span class="s2"> </span><span class="si">{}</span><span class="se">\n</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">concept</span><span class="p">,</span> <span class="n">row</span><span class="p">[</span><span class="s2">"CONCEPT"</span><span class="p">])</span>
+</span><span id="L-1305"><a href="#L-1305"><span class="linenos">1305</span></a> <span class="n">report</span> <span class="o">+=</span> <span class="sa">f</span><span class="s2">"- Changed concepts </span><span class="si">{</span><span class="n">s</span><span class="si">}</span><span class="se">\n\n</span><span class="s2">"</span>
+</span><span id="L-1306"><a href="#L-1306"><span class="linenos">1306</span></a> <span class="k">else</span><span class="p">:</span>
+</span><span id="L-1307"><a href="#L-1307"><span class="linenos">1307</span></a> <span class="n">report</span> <span class="o">+=</span> <span class="sa">f</span><span class="s2">"- Changed concepts []</span><span class="se">\n\n</span><span class="s2">"</span>
+</span><span id="L-1308"><a href="#L-1308"><span class="linenos">1308</span></a>
+</span><span id="L-1309"><a href="#L-1309"><span class="linenos">1309</span></a> <span class="k">return</span> <span class="n">report</span>
+</span><span id="L-1310"><a href="#L-1310"><span class="linenos">1310</span></a>
+</span><span id="L-1311"><a href="#L-1311"><span class="linenos">1311</span></a>
+</span><span id="L-1312"><a href="#L-1312"><span class="linenos">1312</span></a><span class="k">def</span><span class="w"> </span><span class="nf">diff_phen</span><span class="p">(</span>
+</span><span id="L-1313"><a href="#L-1313"><span class="linenos">1313</span></a> <span class="n">new_phen_path</span><span class="p">:</span> <span class="n">Path</span><span class="p">,</span>
+</span><span id="L-1314"><a href="#L-1314"><span class="linenos">1314</span></a> <span class="n">new_version</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+</span><span id="L-1315"><a href="#L-1315"><span class="linenos">1315</span></a> <span class="n">old_phen_path</span><span class="p">:</span> <span class="n">Path</span><span class="p">,</span>
+</span><span id="L-1316"><a href="#L-1316"><span class="linenos">1316</span></a> <span class="n">old_version</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+</span><span id="L-1317"><a href="#L-1317"><span class="linenos">1317</span></a> <span class="n">report_path</span><span class="p">:</span> <span class="n">Path</span><span class="p">,</span>
+</span><span id="L-1318"><a href="#L-1318"><span class="linenos">1318</span></a><span class="p">):</span>
+</span><span id="L-1319"><a href="#L-1319"><span class="linenos">1319</span></a><span class="w"> </span><span class="sd">"""Compare the differences between two versions of a phenotype"""</span>
+</span><span id="L-1320"><a href="#L-1320"><span class="linenos">1320</span></a>
+</span><span id="L-1321"><a href="#L-1321"><span class="linenos">1321</span></a> <span class="c1"># validate phenotypes</span>
+</span><span id="L-1322"><a href="#L-1322"><span class="linenos">1322</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Validating for diff old path: </span><span class="si">{</span><span class="nb">str</span><span class="p">(</span><span class="n">old_phen_path</span><span class="o">.</span><span class="n">resolve</span><span class="p">())</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+</span><span id="L-1323"><a href="#L-1323"><span class="linenos">1323</span></a> <span class="n">validate</span><span class="p">(</span><span class="nb">str</span><span class="p">(</span><span class="n">old_phen_path</span><span class="o">.</span><span class="n">resolve</span><span class="p">()))</span>
+</span><span id="L-1324"><a href="#L-1324"><span class="linenos">1324</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Validating for diff new path: </span><span class="si">{</span><span class="nb">str</span><span class="p">(</span><span class="n">new_phen_path</span><span class="o">.</span><span class="n">resolve</span><span class="p">())</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+</span><span id="L-1325"><a href="#L-1325"><span class="linenos">1325</span></a> <span class="n">validate</span><span class="p">(</span><span class="nb">str</span><span class="p">(</span><span class="n">new_phen_path</span><span class="o">.</span><span class="n">resolve</span><span class="p">()))</span>
+</span><span id="L-1326"><a href="#L-1326"><span class="linenos">1326</span></a>
+</span><span id="L-1327"><a href="#L-1327"><span class="linenos">1327</span></a> <span class="c1"># get old and new config</span>
+</span><span id="L-1328"><a href="#L-1328"><span class="linenos">1328</span></a> <span class="n">old_config_path</span> <span class="o">=</span> <span class="n">old_phen_path</span> <span class="o">/</span> <span class="n">CONFIG_FILE</span>
+</span><span id="L-1329"><a href="#L-1329"><span class="linenos">1329</span></a> <span class="k">with</span> <span class="n">old_config_path</span><span class="o">.</span><span class="n">open</span><span class="p">(</span><span class="s2">"r"</span><span class="p">)</span> <span class="k">as</span> <span class="n">file</span><span class="p">:</span>
+</span><span id="L-1330"><a href="#L-1330"><span class="linenos">1330</span></a> <span class="n">old_config</span> <span class="o">=</span> <span class="n">yaml</span><span class="o">.</span><span class="n">safe_load</span><span class="p">(</span><span class="n">file</span><span class="p">)</span>
+</span><span id="L-1331"><a href="#L-1331"><span class="linenos">1331</span></a> <span class="n">new_config_path</span> <span class="o">=</span> <span class="n">new_phen_path</span> <span class="o">/</span> <span class="n">CONFIG_FILE</span>
+</span><span id="L-1332"><a href="#L-1332"><span class="linenos">1332</span></a> <span class="k">with</span> <span class="n">new_config_path</span><span class="o">.</span><span class="n">open</span><span class="p">(</span><span class="s2">"r"</span><span class="p">)</span> <span class="k">as</span> <span class="n">file</span><span class="p">:</span>
+</span><span id="L-1333"><a href="#L-1333"><span class="linenos">1333</span></a> <span class="n">new_config</span> <span class="o">=</span> <span class="n">yaml</span><span class="o">.</span><span class="n">safe_load</span><span class="p">(</span><span class="n">file</span><span class="p">)</span>
+</span><span id="L-1334"><a href="#L-1334"><span class="linenos">1334</span></a>
+</span><span id="L-1335"><a href="#L-1335"><span class="linenos">1335</span></a> <span class="c1"># write report heading</span>
+</span><span id="L-1336"><a href="#L-1336"><span class="linenos">1336</span></a> <span class="n">report</span> <span class="o">=</span> <span class="sa">f</span><span class="s2">"# Phenotype Comparison Report</span><span class="se">\n</span><span class="s2">"</span>
+</span><span id="L-1337"><a href="#L-1337"><span class="linenos">1337</span></a> <span class="n">report</span> <span class="o">+=</span> <span class="sa">f</span><span class="s2">"## Original phenotype</span><span class="se">\n</span><span class="s2">"</span>
+</span><span id="L-1338"><a href="#L-1338"><span class="linenos">1338</span></a> <span class="n">report</span> <span class="o">+=</span> <span class="sa">f</span><span class="s2">" - </span><span class="si">{</span><span class="n">old_config</span><span class="p">[</span><span class="s1">'phenotype'</span><span class="p">][</span><span class="s1">'omop'</span><span class="p">][</span><span class="s1">'vocabulary_id'</span><span class="p">]</span><span class="si">}</span><span class="se">\n</span><span class="s2">"</span>
+</span><span id="L-1339"><a href="#L-1339"><span class="linenos">1339</span></a> <span class="n">report</span> <span class="o">+=</span> <span class="sa">f</span><span class="s2">" - </span><span class="si">{</span><span class="n">old_version</span><span class="si">}</span><span class="se">\n</span><span class="s2">"</span>
+</span><span id="L-1340"><a href="#L-1340"><span class="linenos">1340</span></a> <span class="n">report</span> <span class="o">+=</span> <span class="sa">f</span><span class="s2">" - </span><span class="si">{</span><span class="nb">str</span><span class="p">(</span><span class="n">old_phen_path</span><span class="o">.</span><span class="n">resolve</span><span class="p">())</span><span class="si">}</span><span class="se">\n</span><span class="s2">"</span>
+</span><span id="L-1341"><a href="#L-1341"><span class="linenos">1341</span></a> <span class="n">report</span> <span class="o">+=</span> <span class="sa">f</span><span class="s2">"## Changed phenotype:</span><span class="se">\n</span><span class="s2">"</span>
+</span><span id="L-1342"><a href="#L-1342"><span class="linenos">1342</span></a> <span class="n">report</span> <span class="o">+=</span> <span class="sa">f</span><span class="s2">" - </span><span class="si">{</span><span class="n">new_config</span><span class="p">[</span><span class="s1">'phenotype'</span><span class="p">][</span><span class="s1">'omop'</span><span class="p">][</span><span class="s1">'vocabulary_id'</span><span class="p">]</span><span class="si">}</span><span class="se">\n</span><span class="s2">"</span>
+</span><span id="L-1343"><a href="#L-1343"><span class="linenos">1343</span></a> <span class="n">report</span> <span class="o">+=</span> <span class="sa">f</span><span class="s2">" - </span><span class="si">{</span><span class="n">new_version</span><span class="si">}</span><span class="se">\n</span><span class="s2">"</span>
+</span><span id="L-1344"><a href="#L-1344"><span class="linenos">1344</span></a> <span class="n">report</span> <span class="o">+=</span> <span class="sa">f</span><span class="s2">" - </span><span class="si">{</span><span class="nb">str</span><span class="p">(</span><span class="n">new_phen_path</span><span class="o">.</span><span class="n">resolve</span><span class="p">())</span><span class="si">}</span><span class="se">\n</span><span class="s2">"</span>
+</span><span id="L-1345"><a href="#L-1345"><span class="linenos">1345</span></a>
+</span><span id="L-1346"><a href="#L-1346"><span class="linenos">1346</span></a> <span class="c1"># Step 1: check differences configuration files</span>
+</span><span id="L-1347"><a href="#L-1347"><span class="linenos">1347</span></a> <span class="c1"># Convert list of dicts into a dict: {name: file}</span>
+</span><span id="L-1348"><a href="#L-1348"><span class="linenos">1348</span></a> <span class="n">report</span> <span class="o">+=</span> <span class="n">diff_config</span><span class="p">(</span><span class="n">old_config</span><span class="p">,</span> <span class="n">new_config</span><span class="p">)</span>
+</span><span id="L-1349"><a href="#L-1349"><span class="linenos">1349</span></a>
+</span><span id="L-1350"><a href="#L-1350"><span class="linenos">1350</span></a> <span class="c1"># Step 2: check differences between map files</span>
+</span><span id="L-1351"><a href="#L-1351"><span class="linenos">1351</span></a> <span class="c1"># List files from output directories</span>
+</span><span id="L-1352"><a href="#L-1352"><span class="linenos">1352</span></a> <span class="n">old_map_path</span> <span class="o">=</span> <span class="n">old_phen_path</span> <span class="o">/</span> <span class="n">MAP_DIR</span>
+</span><span id="L-1353"><a href="#L-1353"><span class="linenos">1353</span></a> <span class="n">new_map_path</span> <span class="o">=</span> <span class="n">new_phen_path</span> <span class="o">/</span> <span class="n">MAP_DIR</span>
+</span><span id="L-1354"><a href="#L-1354"><span class="linenos">1354</span></a> <span class="n">report</span> <span class="o">+=</span> <span class="n">diff_map_files</span><span class="p">(</span><span class="n">old_map_path</span><span class="p">,</span> <span class="n">new_map_path</span><span class="p">)</span>
+</span><span id="L-1355"><a href="#L-1355"><span class="linenos">1355</span></a>
+</span><span id="L-1356"><a href="#L-1356"><span class="linenos">1356</span></a> <span class="c1"># initialise report file</span>
+</span><span id="L-1357"><a href="#L-1357"><span class="linenos">1357</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Writing to report file </span><span class="si">{</span><span class="nb">str</span><span class="p">(</span><span class="n">report_path</span><span class="o">.</span><span class="n">resolve</span><span class="p">())</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+</span><span id="L-1358"><a href="#L-1358"><span class="linenos">1358</span></a> <span class="n">report_file</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="n">report_path</span><span class="p">,</span> <span class="s2">"w"</span><span class="p">)</span>
+</span><span id="L-1359"><a href="#L-1359"><span class="linenos">1359</span></a> <span class="n">report_file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">report</span><span class="p">)</span>
+</span><span id="L-1360"><a href="#L-1360"><span class="linenos">1360</span></a> <span class="n">report_file</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
+</span><span id="L-1361"><a href="#L-1361"><span class="linenos">1361</span></a>
+</span><span id="L-1362"><a href="#L-1362"><span class="linenos">1362</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Phenotypes diff'd successfully"</span><span class="p">)</span>
+</span><span id="L-1363"><a href="#L-1363"><span class="linenos">1363</span></a>
+</span><span id="L-1364"><a href="#L-1364"><span class="linenos">1364</span></a>
+</span><span id="L-1365"><a href="#L-1365"><span class="linenos">1365</span></a><span class="k">def</span><span class="w"> </span><span class="nf">diff</span><span class="p">(</span><span class="n">phen_dir</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">version</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">old_phen_dir</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">old_version</span><span class="p">:</span> <span class="nb">str</span><span class="p">):</span>
+</span><span id="L-1366"><a href="#L-1366"><span class="linenos">1366</span></a> <span class="c1"># make tmp directory .acmc</span>
+</span><span id="L-1367"><a href="#L-1367"><span class="linenos">1367</span></a> <span class="n">timestamp</span> <span class="o">=</span> <span class="n">time</span><span class="o">.</span><span class="n">strftime</span><span class="p">(</span><span class="s2">"%Y%m</span><span class="si">%d</span><span class="s2">_%H%M%S"</span><span class="p">)</span>
+</span><span id="L-1368"><a href="#L-1368"><span class="linenos">1368</span></a> <span class="n">temp_dir</span> <span class="o">=</span> <span class="n">Path</span><span class="p">(</span><span class="sa">f</span><span class="s2">".acmc/diff_</span><span class="si">{</span><span class="n">timestamp</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+</span><span id="L-1369"><a href="#L-1369"><span class="linenos">1369</span></a>
+</span><span id="L-1370"><a href="#L-1370"><span class="linenos">1370</span></a> <span class="n">changed_phen_path</span> <span class="o">=</span> <span class="n">Path</span><span class="p">(</span><span class="n">phen_dir</span><span class="p">)</span>
+</span><span id="L-1371"><a href="#L-1371"><span class="linenos">1371</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="n">changed_phen_path</span><span class="o">.</span><span class="n">exists</span><span class="p">():</span>
+</span><span id="L-1372"><a href="#L-1372"><span class="linenos">1372</span></a> <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span>
+</span><span id="L-1373"><a href="#L-1373"><span class="linenos">1373</span></a> <span class="sa">f</span><span class="s2">"Changed phenotype directory does not exist: </span><span class="si">{</span><span class="nb">str</span><span class="p">(</span><span class="n">changed_phen_path</span><span class="o">.</span><span class="n">resolve</span><span class="p">())</span><span class="si">}</span><span class="s2">"</span>
+</span><span id="L-1374"><a href="#L-1374"><span class="linenos">1374</span></a> <span class="p">)</span>
+</span><span id="L-1375"><a href="#L-1375"><span class="linenos">1375</span></a>
+</span><span id="L-1376"><a href="#L-1376"><span class="linenos">1376</span></a> <span class="n">old_phen_path</span> <span class="o">=</span> <span class="n">Path</span><span class="p">(</span><span class="n">old_phen_dir</span><span class="p">)</span>
+</span><span id="L-1377"><a href="#L-1377"><span class="linenos">1377</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="n">old_phen_path</span><span class="o">.</span><span class="n">exists</span><span class="p">():</span>
+</span><span id="L-1378"><a href="#L-1378"><span class="linenos">1378</span></a> <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span>
+</span><span id="L-1379"><a href="#L-1379"><span class="linenos">1379</span></a> <span class="sa">f</span><span class="s2">"Old phenotype directory does not exist: </span><span class="si">{</span><span class="nb">str</span><span class="p">(</span><span class="n">old_phen_path</span><span class="o">.</span><span class="n">resolve</span><span class="p">())</span><span class="si">}</span><span class="s2">"</span>
+</span><span id="L-1380"><a href="#L-1380"><span class="linenos">1380</span></a> <span class="p">)</span>
+</span><span id="L-1381"><a href="#L-1381"><span class="linenos">1381</span></a>
+</span><span id="L-1382"><a href="#L-1382"><span class="linenos">1382</span></a> <span class="k">try</span><span class="p">:</span>
+</span><span id="L-1383"><a href="#L-1383"><span class="linenos">1383</span></a> <span class="c1"># Create the directory</span>
+</span><span id="L-1384"><a href="#L-1384"><span class="linenos">1384</span></a> <span class="n">temp_dir</span><span class="o">.</span><span class="n">mkdir</span><span class="p">(</span><span class="n">parents</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">exist_ok</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+</span><span id="L-1385"><a href="#L-1385"><span class="linenos">1385</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Temporary directory created: </span><span class="si">{</span><span class="n">temp_dir</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+</span><span id="L-1386"><a href="#L-1386"><span class="linenos">1386</span></a>
+</span><span id="L-1387"><a href="#L-1387"><span class="linenos">1387</span></a> <span class="c1"># Create temporary directories</span>
+</span><span id="L-1388"><a href="#L-1388"><span class="linenos">1388</span></a> <span class="n">changed_path</span> <span class="o">=</span> <span class="n">temp_dir</span> <span class="o">/</span> <span class="s2">"changed"</span>
+</span><span id="L-1389"><a href="#L-1389"><span class="linenos">1389</span></a> <span class="n">changed_path</span><span class="o">.</span><span class="n">mkdir</span><span class="p">(</span><span class="n">parents</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">exist_ok</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+</span><span id="L-1390"><a href="#L-1390"><span class="linenos">1390</span></a> <span class="n">old_path</span> <span class="o">=</span> <span class="n">temp_dir</span> <span class="o">/</span> <span class="s2">"old"</span>
+</span><span id="L-1391"><a href="#L-1391"><span class="linenos">1391</span></a> <span class="n">old_path</span><span class="o">.</span><span class="n">mkdir</span><span class="p">(</span><span class="n">parents</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">exist_ok</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+</span><span id="L-1392"><a href="#L-1392"><span class="linenos">1392</span></a>
+</span><span id="L-1393"><a href="#L-1393"><span class="linenos">1393</span></a> <span class="c1"># checkout changed</span>
+</span><span id="L-1394"><a href="#L-1394"><span class="linenos">1394</span></a> <span class="k">if</span> <span class="n">version</span> <span class="o">==</span> <span class="s2">"latest"</span><span class="p">:</span>
+</span><span id="L-1395"><a href="#L-1395"><span class="linenos">1395</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span>
+</span><span id="L-1396"><a href="#L-1396"><span class="linenos">1396</span></a> <span class="sa">f</span><span class="s2">"Copying changed repo from </span><span class="si">{</span><span class="n">phen_dir</span><span class="si">}</span><span class="s2"> into </span><span class="si">{</span><span class="n">changed_path</span><span class="si">}</span><span class="s2"> at version </span><span class="si">{</span><span class="n">version</span><span class="si">}</span><span class="s2">..."</span>
+</span><span id="L-1397"><a href="#L-1397"><span class="linenos">1397</span></a> <span class="p">)</span>
+</span><span id="L-1398"><a href="#L-1398"><span class="linenos">1398</span></a> <span class="n">shutil</span><span class="o">.</span><span class="n">copytree</span><span class="p">(</span><span class="n">changed_phen_path</span><span class="p">,</span> <span class="n">changed_path</span><span class="p">,</span> <span class="n">dirs_exist_ok</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+</span><span id="L-1399"><a href="#L-1399"><span class="linenos">1399</span></a> <span class="k">else</span><span class="p">:</span>
+</span><span id="L-1400"><a href="#L-1400"><span class="linenos">1400</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span>
+</span><span id="L-1401"><a href="#L-1401"><span class="linenos">1401</span></a> <span class="sa">f</span><span class="s2">"Cloning changed repo from </span><span class="si">{</span><span class="n">phen_dir</span><span class="si">}</span><span class="s2"> into </span><span class="si">{</span><span class="n">changed_path</span><span class="si">}</span><span class="s2"> at version </span><span class="si">{</span><span class="n">version</span><span class="si">}</span><span class="s2">..."</span>
+</span><span id="L-1402"><a href="#L-1402"><span class="linenos">1402</span></a> <span class="p">)</span>
+</span><span id="L-1403"><a href="#L-1403"><span class="linenos">1403</span></a> <span class="n">changed_repo</span> <span class="o">=</span> <span class="n">git</span><span class="o">.</span><span class="n">Repo</span><span class="o">.</span><span class="n">clone_from</span><span class="p">(</span><span class="n">changed_phen_path</span><span class="p">,</span> <span class="n">changed_path</span><span class="p">)</span>
+</span><span id="L-1404"><a href="#L-1404"><span class="linenos">1404</span></a> <span class="n">changed_repo</span><span class="o">.</span><span class="n">git</span><span class="o">.</span><span class="n">checkout</span><span class="p">(</span><span class="n">version</span><span class="p">)</span>
+</span><span id="L-1405"><a href="#L-1405"><span class="linenos">1405</span></a>
+</span><span id="L-1406"><a href="#L-1406"><span class="linenos">1406</span></a> <span class="c1"># checkout old</span>
+</span><span id="L-1407"><a href="#L-1407"><span class="linenos">1407</span></a> <span class="k">if</span> <span class="n">old_version</span> <span class="o">==</span> <span class="s2">"latest"</span><span class="p">:</span>
+</span><span id="L-1408"><a href="#L-1408"><span class="linenos">1408</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span>
+</span><span id="L-1409"><a href="#L-1409"><span class="linenos">1409</span></a> <span class="sa">f</span><span class="s2">"Copying old repo from </span><span class="si">{</span><span class="n">old_phen_dir</span><span class="si">}</span><span class="s2"> into </span><span class="si">{</span><span class="n">old_path</span><span class="si">}</span><span class="s2"> at version </span><span class="si">{</span><span class="n">old_version</span><span class="si">}</span><span class="s2">..."</span>
+</span><span id="L-1410"><a href="#L-1410"><span class="linenos">1410</span></a> <span class="p">)</span>
+</span><span id="L-1411"><a href="#L-1411"><span class="linenos">1411</span></a> <span class="n">shutil</span><span class="o">.</span><span class="n">copytree</span><span class="p">(</span><span class="n">old_phen_path</span><span class="p">,</span> <span class="n">old_path</span><span class="p">,</span> <span class="n">dirs_exist_ok</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+</span><span id="L-1412"><a href="#L-1412"><span class="linenos">1412</span></a> <span class="k">else</span><span class="p">:</span>
+</span><span id="L-1413"><a href="#L-1413"><span class="linenos">1413</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span>
+</span><span id="L-1414"><a href="#L-1414"><span class="linenos">1414</span></a> <span class="sa">f</span><span class="s2">"Cloning old repo from </span><span class="si">{</span><span class="n">old_phen_dir</span><span class="si">}</span><span class="s2"> into </span><span class="si">{</span><span class="n">old_path</span><span class="si">}</span><span class="s2"> at version </span><span class="si">{</span><span class="n">old_version</span><span class="si">}</span><span class="s2">..."</span>
+</span><span id="L-1415"><a href="#L-1415"><span class="linenos">1415</span></a> <span class="p">)</span>
+</span><span id="L-1416"><a href="#L-1416"><span class="linenos">1416</span></a> <span class="n">old_repo</span> <span class="o">=</span> <span class="n">git</span><span class="o">.</span><span class="n">Repo</span><span class="o">.</span><span class="n">clone_from</span><span class="p">(</span><span class="n">old_phen_dir</span><span class="p">,</span> <span class="n">old_path</span><span class="p">)</span>
+</span><span id="L-1417"><a href="#L-1417"><span class="linenos">1417</span></a> <span class="n">old_repo</span><span class="o">.</span><span class="n">git</span><span class="o">.</span><span class="n">checkout</span><span class="p">(</span><span class="n">old_version</span><span class="p">)</span>
+</span><span id="L-1418"><a href="#L-1418"><span class="linenos">1418</span></a>
+</span><span id="L-1419"><a href="#L-1419"><span class="linenos">1419</span></a> <span class="n">report_filename</span> <span class="o">=</span> <span class="sa">f</span><span class="s2">"</span><span class="si">{</span><span class="n">version</span><span class="si">}</span><span class="s2">_</span><span class="si">{</span><span class="n">old_version</span><span class="si">}</span><span class="s2">_diff.md"</span>
+</span><span id="L-1420"><a href="#L-1420"><span class="linenos">1420</span></a> <span class="n">report_path</span> <span class="o">=</span> <span class="n">changed_phen_path</span> <span class="o">/</span> <span class="n">report_filename</span>
+</span><span id="L-1421"><a href="#L-1421"><span class="linenos">1421</span></a> <span class="c1"># diff old with new</span>
+</span><span id="L-1422"><a href="#L-1422"><span class="linenos">1422</span></a> <span class="n">diff_phen</span><span class="p">(</span><span class="n">changed_path</span><span class="p">,</span> <span class="n">version</span><span class="p">,</span> <span class="n">old_path</span><span class="p">,</span> <span class="n">old_version</span><span class="p">,</span> <span class="n">report_path</span><span class="p">)</span>
+</span><span id="L-1423"><a href="#L-1423"><span class="linenos">1423</span></a>
+</span><span id="L-1424"><a href="#L-1424"><span class="linenos">1424</span></a> <span class="k">finally</span><span class="p">:</span>
+</span><span id="L-1425"><a href="#L-1425"><span class="linenos">1425</span></a> <span class="c1"># clean up tmp directory</span>
+</span><span id="L-1426"><a href="#L-1426"><span class="linenos">1426</span></a> <span class="k">if</span> <span class="n">temp_dir</span><span class="o">.</span><span class="n">exists</span><span class="p">():</span>
+</span><span id="L-1427"><a href="#L-1427"><span class="linenos">1427</span></a> <span class="n">shutil</span><span class="o">.</span><span class="n">rmtree</span><span class="p">(</span><span class="n">temp_dir</span><span class="p">)</span>
+</span><span id="L-1428"><a href="#L-1428"><span class="linenos">1428</span></a> <span class="nb">print</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Temporary directory removed: </span><span class="si">{</span><span class="n">temp_dir</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+</span></pre></div>
+
+
+ </section>
+ <section id="logger">
+ <div class="attr variable">
+ <span class="name">logger</span> =
+<span class="default_value"><Logger acmc_logger (INFO)></span>
+
+
+ </div>
+ <a class="headerlink" href="#logger"></a>
+
+
+
+ </section>
+ <section id="PHEN_DIR">
+ <div class="attr variable">
+ <span class="name">PHEN_DIR</span> =
+<span class="default_value">'phen'</span>
+
+
+ </div>
+ <a class="headerlink" href="#PHEN_DIR"></a>
+
+
+
+ </section>
+ <section id="DEFAULT_PHEN_PATH">
+ <div class="attr variable">
+ <span class="name">DEFAULT_PHEN_PATH</span> =
+<span class="default_value">PosixPath('workspace/phen')</span>
+
+
+ </div>
+ <a class="headerlink" href="#DEFAULT_PHEN_PATH"></a>
+
+
+
+ </section>
+ <section id="CONCEPTS_DIR">
+ <div class="attr variable">
+ <span class="name">CONCEPTS_DIR</span> =
+<span class="default_value">'concepts'</span>
+
+
+ </div>
+ <a class="headerlink" href="#CONCEPTS_DIR"></a>
+
+
+
+ </section>
+ <section id="MAP_DIR">
+ <div class="attr variable">
+ <span class="name">MAP_DIR</span> =
+<span class="default_value">'map'</span>
+
+
+ </div>
+ <a class="headerlink" href="#MAP_DIR"></a>
+
+
+
+ </section>
+ <section id="CONCEPT_SET_DIR">
+ <div class="attr variable">
+ <span class="name">CONCEPT_SET_DIR</span> =
+<span class="default_value">'concept-sets'</span>
+
+
+ </div>
+ <a class="headerlink" href="#CONCEPT_SET_DIR"></a>
+
+
+
+ </section>
+ <section id="CSV_PATH">
+ <div class="attr variable">
+ <span class="name">CSV_PATH</span> =
+<span class="default_value">PosixPath('concept-sets/csv')</span>
+
+
+ </div>
+ <a class="headerlink" href="#CSV_PATH"></a>
+
+
+
+ </section>
+ <section id="OMOP_PATH">
+ <div class="attr variable">
+ <span class="name">OMOP_PATH</span> =
+<span class="default_value">PosixPath('concept-sets/omop')</span>
+
+
+ </div>
+ <a class="headerlink" href="#OMOP_PATH"></a>
+
+
+
+ </section>
+ <section id="DEFAULT_PHEN_DIR_LIST">
+ <div class="attr variable">
+ <span class="name">DEFAULT_PHEN_DIR_LIST</span> =
+<span class="default_value">['concepts', 'map', 'concept-sets']</span>
+
+
+ </div>
+ <a class="headerlink" href="#DEFAULT_PHEN_DIR_LIST"></a>
+
+
+
+ </section>
+ <section id="CONFIG_FILE">
+ <div class="attr variable">
+ <span class="name">CONFIG_FILE</span> =
+<span class="default_value">'config.yaml'</span>
+
+
+ </div>
+ <a class="headerlink" href="#CONFIG_FILE"></a>
+
+
+
+ </section>
+ <section id="VOCAB_VERSION_FILE">
+ <div class="attr variable">
+ <span class="name">VOCAB_VERSION_FILE</span> =
+<span class="default_value">'vocab_version.yaml'</span>
+
+
+ </div>
+ <a class="headerlink" href="#VOCAB_VERSION_FILE"></a>
+
+
+
+ </section>
+ <section id="SEMANTIC_VERSION_TYPES">
+ <div class="attr variable">
+ <span class="name">SEMANTIC_VERSION_TYPES</span> =
+<span class="default_value">['major', 'minor', 'patch']</span>
+
+
+ </div>
+ <a class="headerlink" href="#SEMANTIC_VERSION_TYPES"></a>
+
+
+
+ </section>
+ <section id="DEFAULT_VERSION_INC">
+ <div class="attr variable">
+ <span class="name">DEFAULT_VERSION_INC</span> =
+<span class="default_value">'patch'</span>
+
+
+ </div>
+ <a class="headerlink" href="#DEFAULT_VERSION_INC"></a>
+
+
+
+ </section>
+ <section id="DEFAULT_GIT_BRANCH">
+ <div class="attr variable">
+ <span class="name">DEFAULT_GIT_BRANCH</span> =
+<span class="default_value">'main'</span>
+
+
+ </div>
+ <a class="headerlink" href="#DEFAULT_GIT_BRANCH"></a>
+
+
+
+ </section>
+ <section id="SPLIT_COL_ACTION">
+ <div class="attr variable">
+ <span class="name">SPLIT_COL_ACTION</span> =
+<span class="default_value">'split_col'</span>
+
+
+ </div>
+ <a class="headerlink" href="#SPLIT_COL_ACTION"></a>
+
+
+
+ </section>
+ <section id="CODES_COL_ACTION">
+ <div class="attr variable">
+ <span class="name">CODES_COL_ACTION</span> =
+<span class="default_value">'codes_col'</span>
+
+
+ </div>
+ <a class="headerlink" href="#CODES_COL_ACTION"></a>
+
+
+
+ </section>
+ <section id="DIVIDE_COL_ACTION">
+ <div class="attr variable">
+ <span class="name">DIVIDE_COL_ACTION</span> =
+<span class="default_value">'divide_col'</span>
+
+
+ </div>
+ <a class="headerlink" href="#DIVIDE_COL_ACTION"></a>
+
+
+
+ </section>
+ <section id="COL_ACTIONS">
+ <div class="attr variable">
+ <span class="name">COL_ACTIONS</span> =
+<span class="default_value">['split_col', 'codes_col', 'divide_col']</span>
+
+
+ </div>
+ <a class="headerlink" href="#COL_ACTIONS"></a>
+
+
+
+ </section>
+ <section id="CODE_FILE_TYPES">
+ <div class="attr variable">
+ <span class="name">CODE_FILE_TYPES</span> =
+<span class="default_value">['.xlsx', '.xls', '.csv']</span>
+
+
+ </div>
+ <a class="headerlink" href="#CODE_FILE_TYPES"></a>
+
+
+
+ </section>
+ <section id="SOURCE_COL_SUFFIX">
+ <div class="attr variable">
+ <span class="name">SOURCE_COL_SUFFIX</span> =
+<span class="default_value">'_acmc_source'</span>
+
+
+ </div>
+ <a class="headerlink" href="#SOURCE_COL_SUFFIX"></a>
+
+
+
+ </section>
+ <section id="TARGET_COL_SUFFIX">
+ <div class="attr variable">
+ <span class="name">TARGET_COL_SUFFIX</span> =
+<span class="default_value">'_acmc_target'</span>
+
+
+ </div>
+ <a class="headerlink" href="#TARGET_COL_SUFFIX"></a>
+
+
+
+ </section>
+ <section id="CONFIG_SCHEMA">
+ <div class="attr variable">
+ <span class="name">CONFIG_SCHEMA</span> =
+<input id="CONFIG_SCHEMA-view-value" class="view-value-toggle-state" type="checkbox" aria-hidden="true" tabindex="-1">
+ <label class="view-value-button pdoc-button" for="CONFIG_SCHEMA-view-value"></label><span class="default_value">{'phenotype': {'type': 'dict', 'required': True, 'schema': {'version': {'type': 'string', 'required': True, 'regex': '^\\d+\\.\\d+\\.\\d+$'}, 'omop': {'type': 'dict', 'required': True, 'schema': {'vocabulary_id': {'type': 'string', 'required': True}, 'vocabulary_name': {'type': 'string', 'required': True}, 'vocabulary_reference': {'type': 'string', 'required': True, 'regex': '^https?://.*'}}}, 'map': {'type': 'list', 'schema': {'type': 'string', 'allowed': ['opcs4', 'icd10', 'read3', 'snomed', 'read2', 'atc']}}, 'concept_sets': {'type': 'list', 'required': True, 'schema': {'type': 'dict', 'schema': {'name': {'type': 'string', 'required': True}, 'file': {'type': 'dict', 'required': False, 'schema': {'path': {'type': 'string', 'required': True}, 'columns': {'type': 'dict', 'required': True}, 'category': {'type': 'string'}, 'actions': {'type': 'dict', 'schema': {'divide_col': {'type': 'string'}}}}}, 'metadata': {'type': 'dict', 'required': True}}}}}}}</span>
+
+
+ </div>
+ <a class="headerlink" href="#CONFIG_SCHEMA"></a>
+
+
+
+ </section>
+ <section id="PhenValidationException">
+ <input id="PhenValidationException-view-source" class="view-source-toggle-state" type="checkbox" aria-hidden="true" tabindex="-1">
+<div class="attr class">
+
+ <span class="def">class</span>
+ <span class="name">PhenValidationException</span><wbr>(<span class="base">builtins.Exception</span>):
+
+ <label class="view-source-button" for="PhenValidationException-view-source"><span>View Source</span></label>
+
+ </div>
+ <a class="headerlink" href="#PhenValidationException"></a>
+ <div class="pdoc-code codehilite"><pre><span></span><span id="PhenValidationException-123"><a href="#PhenValidationException-123"><span class="linenos">123</span></a><span class="k">class</span><span class="w"> </span><span class="nc">PhenValidationException</span><span class="p">(</span><span class="ne">Exception</span><span class="p">):</span>
+</span><span id="PhenValidationException-124"><a href="#PhenValidationException-124"><span class="linenos">124</span></a><span class="w"> </span><span class="sd">"""Custom exception class raised when validation errors in phenotype configuration file"""</span>
+</span><span id="PhenValidationException-125"><a href="#PhenValidationException-125"><span class="linenos">125</span></a>
+</span><span id="PhenValidationException-126"><a href="#PhenValidationException-126"><span class="linenos">126</span></a> <span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">message</span><span class="p">,</span> <span class="n">validation_errors</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
+</span><span id="PhenValidationException-127"><a href="#PhenValidationException-127"><span class="linenos">127</span></a> <span class="nb">super</span><span class="p">()</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="n">message</span><span class="p">)</span>
+</span><span id="PhenValidationException-128"><a href="#PhenValidationException-128"><span class="linenos">128</span></a> <span class="bp">self</span><span class="o">.</span><span class="n">validation_errors</span> <span class="o">=</span> <span class="n">validation_errors</span>
+</span></pre></div>
+
+
+ <div class="docstring"><p>Custom exception class raised when validation errors in phenotype configuration file</p>
+</div>
+
+
+ <div id="PhenValidationException.__init__" class="classattr">
+ <input id="PhenValidationException.__init__-view-source" class="view-source-toggle-state" type="checkbox" aria-hidden="true" tabindex="-1">
+<div class="attr function">
+
+ <span class="name">PhenValidationException</span><span class="signature pdoc-code condensed">(<span class="param"><span class="n">message</span>, </span><span class="param"><span class="n">validation_errors</span><span class="o">=</span><span class="kc">None</span></span>)</span>
+
+ <label class="view-source-button" for="PhenValidationException.__init__-view-source"><span>View Source</span></label>
+
+ </div>
+ <a class="headerlink" href="#PhenValidationException.__init__"></a>
+ <div class="pdoc-code codehilite"><pre><span></span><span id="PhenValidationException.__init__-126"><a href="#PhenValidationException.__init__-126"><span class="linenos">126</span></a> <span class="k">def</span><span class="w"> </span><span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">message</span><span class="p">,</span> <span class="n">validation_errors</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
+</span><span id="PhenValidationException.__init__-127"><a href="#PhenValidationException.__init__-127"><span class="linenos">127</span></a> <span class="nb">super</span><span class="p">()</span><span class="o">.</span><span class="fm">__init__</span><span class="p">(</span><span class="n">message</span><span class="p">)</span>
+</span><span id="PhenValidationException.__init__-128"><a href="#PhenValidationException.__init__-128"><span class="linenos">128</span></a> <span class="bp">self</span><span class="o">.</span><span class="n">validation_errors</span> <span class="o">=</span> <span class="n">validation_errors</span>
+</span></pre></div>
+
+
+
+
+ </div>
+ <div id="PhenValidationException.validation_errors" class="classattr">
+ <div class="attr variable">
+ <span class="name">validation_errors</span>
+
+
+ </div>
+ <a class="headerlink" href="#PhenValidationException.validation_errors"></a>
+
+
+
+ </div>
+ </section>
+ <section id="construct_git_url">
+ <input id="construct_git_url-view-source" class="view-source-toggle-state" type="checkbox" aria-hidden="true" tabindex="-1">
+<div class="attr function">
+
+ <span class="def">def</span>
+ <span class="name">construct_git_url</span><span class="signature pdoc-code condensed">(<span class="param"><span class="n">remote_url</span><span class="p">:</span> <span class="nb">str</span></span><span class="return-annotation">):</span></span>
+
+ <label class="view-source-button" for="construct_git_url-view-source"><span>View Source</span></label>
+
+ </div>
+ <a class="headerlink" href="#construct_git_url"></a>
+ <div class="pdoc-code codehilite"><pre><span></span><span id="construct_git_url-131"><a href="#construct_git_url-131"><span class="linenos">131</span></a><span class="k">def</span><span class="w"> </span><span class="nf">construct_git_url</span><span class="p">(</span><span class="n">remote_url</span><span class="p">:</span> <span class="nb">str</span><span class="p">):</span>
+</span><span id="construct_git_url-132"><a href="#construct_git_url-132"><span class="linenos">132</span></a><span class="w"> </span><span class="sd">"""Constructs a git url for github or gitlab including a PAT token environment variable"""</span>
+</span><span id="construct_git_url-133"><a href="#construct_git_url-133"><span class="linenos">133</span></a> <span class="c1"># check the url</span>
+</span><span id="construct_git_url-134"><a href="#construct_git_url-134"><span class="linenos">134</span></a> <span class="n">parsed_url</span> <span class="o">=</span> <span class="n">urlparse</span><span class="p">(</span><span class="n">remote_url</span><span class="p">)</span>
+</span><span id="construct_git_url-135"><a href="#construct_git_url-135"><span class="linenos">135</span></a>
+</span><span id="construct_git_url-136"><a href="#construct_git_url-136"><span class="linenos">136</span></a> <span class="c1"># if github in the URL otherwise assume it's gitlab, if we want to use others such as codeberg we'd</span>
+</span><span id="construct_git_url-137"><a href="#construct_git_url-137"><span class="linenos">137</span></a> <span class="c1"># need to update this function if the URL scheme is different.</span>
+</span><span id="construct_git_url-138"><a href="#construct_git_url-138"><span class="linenos">138</span></a> <span class="k">if</span> <span class="s2">"github.com"</span> <span class="ow">in</span> <span class="n">parsed_url</span><span class="o">.</span><span class="n">netloc</span><span class="p">:</span>
+</span><span id="construct_git_url-139"><a href="#construct_git_url-139"><span class="linenos">139</span></a> <span class="c1"># get GitHub PAT from environment variable</span>
+</span><span id="construct_git_url-140"><a href="#construct_git_url-140"><span class="linenos">140</span></a> <span class="n">auth</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">getenv</span><span class="p">(</span><span class="s2">"ACMC_GITHUB_PAT"</span><span class="p">)</span>
+</span><span id="construct_git_url-141"><a href="#construct_git_url-141"><span class="linenos">141</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="n">auth</span><span class="p">:</span>
+</span><span id="construct_git_url-142"><a href="#construct_git_url-142"><span class="linenos">142</span></a> <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span>
+</span><span id="construct_git_url-143"><a href="#construct_git_url-143"><span class="linenos">143</span></a> <span class="s2">"GitHub PAT not found. Set the ACMC_GITHUB_PAT environment variable."</span>
+</span><span id="construct_git_url-144"><a href="#construct_git_url-144"><span class="linenos">144</span></a> <span class="p">)</span>
+</span><span id="construct_git_url-145"><a href="#construct_git_url-145"><span class="linenos">145</span></a> <span class="k">else</span><span class="p">:</span>
+</span><span id="construct_git_url-146"><a href="#construct_git_url-146"><span class="linenos">146</span></a> <span class="c1"># get GitLab PAT from environment variable</span>
+</span><span id="construct_git_url-147"><a href="#construct_git_url-147"><span class="linenos">147</span></a> <span class="n">auth</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">getenv</span><span class="p">(</span><span class="s2">"ACMC_GITLAB_PAT"</span><span class="p">)</span>
+</span><span id="construct_git_url-148"><a href="#construct_git_url-148"><span class="linenos">148</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="n">auth</span><span class="p">:</span>
+</span><span id="construct_git_url-149"><a href="#construct_git_url-149"><span class="linenos">149</span></a> <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span>
+</span><span id="construct_git_url-150"><a href="#construct_git_url-150"><span class="linenos">150</span></a> <span class="s2">"GitLab PAT not found. Set the ACMC_GITLAB_PAT environment variable."</span>
+</span><span id="construct_git_url-151"><a href="#construct_git_url-151"><span class="linenos">151</span></a> <span class="p">)</span>
+</span><span id="construct_git_url-152"><a href="#construct_git_url-152"><span class="linenos">152</span></a> <span class="n">auth</span> <span class="o">=</span> <span class="sa">f</span><span class="s2">"oauth2:</span><span class="si">{</span><span class="n">auth</span><span class="si">}</span><span class="s2">"</span>
+</span><span id="construct_git_url-153"><a href="#construct_git_url-153"><span class="linenos">153</span></a>
+</span><span id="construct_git_url-154"><a href="#construct_git_url-154"><span class="linenos">154</span></a> <span class="c1"># Construct the new URL with credentials</span>
+</span><span id="construct_git_url-155"><a href="#construct_git_url-155"><span class="linenos">155</span></a> <span class="n">new_netloc</span> <span class="o">=</span> <span class="sa">f</span><span class="s2">"</span><span class="si">{</span><span class="n">auth</span><span class="si">}</span><span class="s2">@</span><span class="si">{</span><span class="n">parsed_url</span><span class="o">.</span><span class="n">netloc</span><span class="si">}</span><span class="s2">"</span>
+</span><span id="construct_git_url-156"><a href="#construct_git_url-156"><span class="linenos">156</span></a> <span class="k">return</span> <span class="n">urlunparse</span><span class="p">(</span>
+</span><span id="construct_git_url-157"><a href="#construct_git_url-157"><span class="linenos">157</span></a> <span class="p">(</span>
+</span><span id="construct_git_url-158"><a href="#construct_git_url-158"><span class="linenos">158</span></a> <span class="n">parsed_url</span><span class="o">.</span><span class="n">scheme</span><span class="p">,</span>
+</span><span id="construct_git_url-159"><a href="#construct_git_url-159"><span class="linenos">159</span></a> <span class="n">new_netloc</span><span class="p">,</span>
+</span><span id="construct_git_url-160"><a href="#construct_git_url-160"><span class="linenos">160</span></a> <span class="n">parsed_url</span><span class="o">.</span><span class="n">path</span><span class="p">,</span>
+</span><span id="construct_git_url-161"><a href="#construct_git_url-161"><span class="linenos">161</span></a> <span class="n">parsed_url</span><span class="o">.</span><span class="n">params</span><span class="p">,</span>
+</span><span id="construct_git_url-162"><a href="#construct_git_url-162"><span class="linenos">162</span></a> <span class="n">parsed_url</span><span class="o">.</span><span class="n">query</span><span class="p">,</span>
+</span><span id="construct_git_url-163"><a href="#construct_git_url-163"><span class="linenos">163</span></a> <span class="n">parsed_url</span><span class="o">.</span><span class="n">fragment</span><span class="p">,</span>
+</span><span id="construct_git_url-164"><a href="#construct_git_url-164"><span class="linenos">164</span></a> <span class="p">)</span>
+</span><span id="construct_git_url-165"><a href="#construct_git_url-165"><span class="linenos">165</span></a> <span class="p">)</span>
+</span></pre></div>
+
+
+ <div class="docstring"><p>Constructs a git url for github or gitlab including a PAT token environment variable</p>
+</div>
+
+
+ </section>
+ <section id="create_empty_git_dir">
+ <input id="create_empty_git_dir-view-source" class="view-source-toggle-state" type="checkbox" aria-hidden="true" tabindex="-1">
+<div class="attr function">
+
+ <span class="def">def</span>
+ <span class="name">create_empty_git_dir</span><span class="signature pdoc-code condensed">(<span class="param"><span class="n">path</span><span class="p">:</span> <span class="n">pathlib</span><span class="o">.</span><span class="n">Path</span></span><span class="return-annotation">):</span></span>
+
+ <label class="view-source-button" for="create_empty_git_dir-view-source"><span>View Source</span></label>
+
+ </div>
+ <a class="headerlink" href="#create_empty_git_dir"></a>
+ <div class="pdoc-code codehilite"><pre><span></span><span id="create_empty_git_dir-168"><a href="#create_empty_git_dir-168"><span class="linenos">168</span></a><span class="k">def</span><span class="w"> </span><span class="nf">create_empty_git_dir</span><span class="p">(</span><span class="n">path</span><span class="p">:</span> <span class="n">Path</span><span class="p">):</span>
+</span><span id="create_empty_git_dir-169"><a href="#create_empty_git_dir-169"><span class="linenos">169</span></a><span class="w"> </span><span class="sd">"""Creates a directory with a .gitkeep file so that it's tracked in git"""</span>
+</span><span id="create_empty_git_dir-170"><a href="#create_empty_git_dir-170"><span class="linenos">170</span></a> <span class="n">path</span><span class="o">.</span><span class="n">mkdir</span><span class="p">(</span><span class="n">exist_ok</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+</span><span id="create_empty_git_dir-171"><a href="#create_empty_git_dir-171"><span class="linenos">171</span></a> <span class="n">keep_path</span> <span class="o">=</span> <span class="n">path</span> <span class="o">/</span> <span class="s2">".gitkeep"</span>
+</span><span id="create_empty_git_dir-172"><a href="#create_empty_git_dir-172"><span class="linenos">172</span></a> <span class="n">keep_path</span><span class="o">.</span><span class="n">touch</span><span class="p">(</span><span class="n">exist_ok</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+</span></pre></div>
+
+
+ <div class="docstring"><p>Creates a directory with a .gitkeep file so that it's tracked in git</p>
+</div>
+
+
+ </section>
+ <section id="check_delete_dir">
+ <input id="check_delete_dir-view-source" class="view-source-toggle-state" type="checkbox" aria-hidden="true" tabindex="-1">
+<div class="attr function">
+
+ <span class="def">def</span>
+ <span class="name">check_delete_dir</span><span class="signature pdoc-code condensed">(<span class="param"><span class="n">path</span><span class="p">:</span> <span class="n">pathlib</span><span class="o">.</span><span class="n">Path</span>, </span><span class="param"><span class="n">msg</span><span class="p">:</span> <span class="nb">str</span></span><span class="return-annotation">) -> <span class="nb">bool</span>:</span></span>
+
+ <label class="view-source-button" for="check_delete_dir-view-source"><span>View Source</span></label>
+
+ </div>
+ <a class="headerlink" href="#check_delete_dir"></a>
+ <div class="pdoc-code codehilite"><pre><span></span><span id="check_delete_dir-175"><a href="#check_delete_dir-175"><span class="linenos">175</span></a><span class="k">def</span><span class="w"> </span><span class="nf">check_delete_dir</span><span class="p">(</span><span class="n">path</span><span class="p">:</span> <span class="n">Path</span><span class="p">,</span> <span class="n">msg</span><span class="p">:</span> <span class="nb">str</span><span class="p">)</span> <span class="o">-></span> <span class="nb">bool</span><span class="p">:</span>
+</span><span id="check_delete_dir-176"><a href="#check_delete_dir-176"><span class="linenos">176</span></a><span class="w"> </span><span class="sd">"""Checks on the command line if a user wants to delete a directory</span>
+</span><span id="check_delete_dir-177"><a href="#check_delete_dir-177"><span class="linenos">177</span></a>
+</span><span id="check_delete_dir-178"><a href="#check_delete_dir-178"><span class="linenos">178</span></a><span class="sd"> Args:</span>
+</span><span id="check_delete_dir-179"><a href="#check_delete_dir-179"><span class="linenos">179</span></a><span class="sd"> path (Path): path of the directory to be deleted</span>
+</span><span id="check_delete_dir-180"><a href="#check_delete_dir-180"><span class="linenos">180</span></a><span class="sd"> msg (str): message to be displayed to the user</span>
+</span><span id="check_delete_dir-181"><a href="#check_delete_dir-181"><span class="linenos">181</span></a>
+</span><span id="check_delete_dir-182"><a href="#check_delete_dir-182"><span class="linenos">182</span></a><span class="sd"> Returns:</span>
+</span><span id="check_delete_dir-183"><a href="#check_delete_dir-183"><span class="linenos">183</span></a><span class="sd"> Boolean: True if deleted</span>
+</span><span id="check_delete_dir-184"><a href="#check_delete_dir-184"><span class="linenos">184</span></a><span class="sd"> """</span>
+</span><span id="check_delete_dir-185"><a href="#check_delete_dir-185"><span class="linenos">185</span></a> <span class="n">deleted</span> <span class="o">=</span> <span class="kc">False</span>
+</span><span id="check_delete_dir-186"><a href="#check_delete_dir-186"><span class="linenos">186</span></a>
+</span><span id="check_delete_dir-187"><a href="#check_delete_dir-187"><span class="linenos">187</span></a> <span class="n">user_input</span> <span class="o">=</span> <span class="nb">input</span><span class="p">(</span><span class="sa">f</span><span class="s2">"</span><span class="si">{</span><span class="n">msg</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span>
+</span><span id="check_delete_dir-188"><a href="#check_delete_dir-188"><span class="linenos">188</span></a> <span class="k">if</span> <span class="n">user_input</span> <span class="ow">in</span> <span class="p">[</span><span class="s2">"yes"</span><span class="p">,</span> <span class="s2">"y"</span><span class="p">]:</span>
+</span><span id="check_delete_dir-189"><a href="#check_delete_dir-189"><span class="linenos">189</span></a> <span class="n">shutil</span><span class="o">.</span><span class="n">rmtree</span><span class="p">(</span><span class="n">path</span><span class="p">)</span>
+</span><span id="check_delete_dir-190"><a href="#check_delete_dir-190"><span class="linenos">190</span></a> <span class="n">deleted</span> <span class="o">=</span> <span class="kc">True</span>
+</span><span id="check_delete_dir-191"><a href="#check_delete_dir-191"><span class="linenos">191</span></a> <span class="k">else</span><span class="p">:</span>
+</span><span id="check_delete_dir-192"><a href="#check_delete_dir-192"><span class="linenos">192</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">"Directory was not deleted."</span><span class="p">)</span>
+</span><span id="check_delete_dir-193"><a href="#check_delete_dir-193"><span class="linenos">193</span></a>
+</span><span id="check_delete_dir-194"><a href="#check_delete_dir-194"><span class="linenos">194</span></a> <span class="k">return</span> <span class="n">deleted</span>
+</span></pre></div>
+
+
+ <div class="docstring"><p>Checks on the command line if a user wants to delete a directory</p>
+
+<p>Args:
+ path (Path): path of the directory to be deleted
+ msg (str): message to be displayed to the user</p>
+
+<p>Returns:
+ Boolean: True if deleted</p>
+</div>
+
+
+ </section>
+ <section id="fork">
+ <input id="fork-view-source" class="view-source-toggle-state" type="checkbox" aria-hidden="true" tabindex="-1">
+<div class="attr function">
+
+ <span class="def">def</span>
+ <span class="name">fork</span><span class="signature pdoc-code multiline">(<span class="param"> <span class="n">phen_dir</span><span class="p">:</span> <span class="nb">str</span>,</span><span class="param"> <span class="n">upstream_url</span><span class="p">:</span> <span class="nb">str</span>,</span><span class="param"> <span class="n">upstream_version</span><span class="p">:</span> <span class="nb">str</span>,</span><span class="param"> <span class="n">new_origin_url</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="kc">None</span></span><span class="return-annotation">):</span></span>
+
+ <label class="view-source-button" for="fork-view-source"><span>View Source</span></label>
+
+ </div>
+ <a class="headerlink" href="#fork"></a>
+ <div class="pdoc-code codehilite"><pre><span></span><span id="fork-197"><a href="#fork-197"><span class="linenos">197</span></a><span class="k">def</span><span class="w"> </span><span class="nf">fork</span><span class="p">(</span>
+</span><span id="fork-198"><a href="#fork-198"><span class="linenos">198</span></a> <span class="n">phen_dir</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">upstream_url</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">upstream_version</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">new_origin_url</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="kc">None</span>
+</span><span id="fork-199"><a href="#fork-199"><span class="linenos">199</span></a><span class="p">):</span>
+</span><span id="fork-200"><a href="#fork-200"><span class="linenos">200</span></a><span class="w"> </span><span class="sd">"""Forks an upstream phenotype in a remote repo at a specific version to a local director, and optionally sets to a new remote origin"</span>
+</span><span id="fork-201"><a href="#fork-201"><span class="linenos">201</span></a>
+</span><span id="fork-202"><a href="#fork-202"><span class="linenos">202</span></a><span class="sd"> Args:</span>
+</span><span id="fork-203"><a href="#fork-203"><span class="linenos">203</span></a><span class="sd"> phen_dir (str): local directory path where the upstream repo is to be cloned</span>
+</span><span id="fork-204"><a href="#fork-204"><span class="linenos">204</span></a><span class="sd"> upstream_url (str): url to the upstream repo</span>
+</span><span id="fork-205"><a href="#fork-205"><span class="linenos">205</span></a><span class="sd"> upstream_version (str): version in the upstream repo to clone</span>
+</span><span id="fork-206"><a href="#fork-206"><span class="linenos">206</span></a><span class="sd"> new_origin_url (str, optional): url of the remote repo to set as the new origin. Defaults to None.</span>
+</span><span id="fork-207"><a href="#fork-207"><span class="linenos">207</span></a>
+</span><span id="fork-208"><a href="#fork-208"><span class="linenos">208</span></a><span class="sd"> Raises:</span>
+</span><span id="fork-209"><a href="#fork-209"><span class="linenos">209</span></a><span class="sd"> ValueError: if the specified version is not in the upstream repo</span>
+</span><span id="fork-210"><a href="#fork-210"><span class="linenos">210</span></a><span class="sd"> ValueError: if the upstream repo is not a valid phenotype repo</span>
+</span><span id="fork-211"><a href="#fork-211"><span class="linenos">211</span></a><span class="sd"> ValueError: if there's any other problems with Git</span>
+</span><span id="fork-212"><a href="#fork-212"><span class="linenos">212</span></a><span class="sd"> """</span>
+</span><span id="fork-213"><a href="#fork-213"><span class="linenos">213</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span>
+</span><span id="fork-214"><a href="#fork-214"><span class="linenos">214</span></a> <span class="sa">f</span><span class="s2">"Forking upstream repo </span><span class="si">{</span><span class="n">upstream_url</span><span class="si">}</span><span class="s2"> </span><span class="si">{</span><span class="n">upstream_version</span><span class="si">}</span><span class="s2"> into directory: </span><span class="si">{</span><span class="n">phen_dir</span><span class="si">}</span><span class="s2">"</span>
+</span><span id="fork-215"><a href="#fork-215"><span class="linenos">215</span></a> <span class="p">)</span>
+</span><span id="fork-216"><a href="#fork-216"><span class="linenos">216</span></a>
+</span><span id="fork-217"><a href="#fork-217"><span class="linenos">217</span></a> <span class="n">phen_path</span> <span class="o">=</span> <span class="n">Path</span><span class="p">(</span><span class="n">phen_dir</span><span class="p">)</span>
+</span><span id="fork-218"><a href="#fork-218"><span class="linenos">218</span></a> <span class="c1"># check if directory already exists and ask user if they want to recreate it</span>
+</span><span id="fork-219"><a href="#fork-219"><span class="linenos">219</span></a> <span class="k">if</span> <span class="p">(</span>
+</span><span id="fork-220"><a href="#fork-220"><span class="linenos">220</span></a> <span class="n">phen_path</span><span class="o">.</span><span class="n">exists</span><span class="p">()</span> <span class="ow">and</span> <span class="n">phen_path</span><span class="o">.</span><span class="n">is_dir</span><span class="p">()</span>
+</span><span id="fork-221"><a href="#fork-221"><span class="linenos">221</span></a> <span class="p">):</span> <span class="c1"># Check if it exists and is a directory</span>
+</span><span id="fork-222"><a href="#fork-222"><span class="linenos">222</span></a> <span class="n">configure</span> <span class="o">=</span> <span class="n">check_delete_dir</span><span class="p">(</span>
+</span><span id="fork-223"><a href="#fork-223"><span class="linenos">223</span></a> <span class="n">phen_path</span><span class="p">,</span>
+</span><span id="fork-224"><a href="#fork-224"><span class="linenos">224</span></a> <span class="sa">f</span><span class="s2">"The phen directory already exists. Do you want to reinitialise? (yes/no): "</span><span class="p">,</span>
+</span><span id="fork-225"><a href="#fork-225"><span class="linenos">225</span></a> <span class="p">)</span>
+</span><span id="fork-226"><a href="#fork-226"><span class="linenos">226</span></a> <span class="k">else</span><span class="p">:</span>
+</span><span id="fork-227"><a href="#fork-227"><span class="linenos">227</span></a> <span class="n">configure</span> <span class="o">=</span> <span class="kc">True</span>
+</span><span id="fork-228"><a href="#fork-228"><span class="linenos">228</span></a>
+</span><span id="fork-229"><a href="#fork-229"><span class="linenos">229</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="n">configure</span><span class="p">:</span>
+</span><span id="fork-230"><a href="#fork-230"><span class="linenos">230</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Exiting, phenotype not initiatised"</span><span class="p">)</span>
+</span><span id="fork-231"><a href="#fork-231"><span class="linenos">231</span></a> <span class="k">return</span>
+</span><span id="fork-232"><a href="#fork-232"><span class="linenos">232</span></a>
+</span><span id="fork-233"><a href="#fork-233"><span class="linenos">233</span></a> <span class="k">try</span><span class="p">:</span>
+</span><span id="fork-234"><a href="#fork-234"><span class="linenos">234</span></a> <span class="c1"># Clone repo</span>
+</span><span id="fork-235"><a href="#fork-235"><span class="linenos">235</span></a> <span class="n">git_url</span> <span class="o">=</span> <span class="n">construct_git_url</span><span class="p">(</span><span class="n">upstream_url</span><span class="p">)</span>
+</span><span id="fork-236"><a href="#fork-236"><span class="linenos">236</span></a> <span class="n">repo</span> <span class="o">=</span> <span class="n">git</span><span class="o">.</span><span class="n">Repo</span><span class="o">.</span><span class="n">clone_from</span><span class="p">(</span><span class="n">git_url</span><span class="p">,</span> <span class="n">phen_path</span><span class="p">)</span>
+</span><span id="fork-237"><a href="#fork-237"><span class="linenos">237</span></a>
+</span><span id="fork-238"><a href="#fork-238"><span class="linenos">238</span></a> <span class="c1"># Fetch all branches and tags</span>
+</span><span id="fork-239"><a href="#fork-239"><span class="linenos">239</span></a> <span class="n">repo</span><span class="o">.</span><span class="n">remotes</span><span class="o">.</span><span class="n">origin</span><span class="o">.</span><span class="n">fetch</span><span class="p">()</span>
+</span><span id="fork-240"><a href="#fork-240"><span class="linenos">240</span></a>
+</span><span id="fork-241"><a href="#fork-241"><span class="linenos">241</span></a> <span class="c1"># Check if the version exists</span>
+</span><span id="fork-242"><a href="#fork-242"><span class="linenos">242</span></a> <span class="n">available_refs</span> <span class="o">=</span> <span class="p">[</span><span class="n">ref</span><span class="o">.</span><span class="n">name</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s2">"/"</span><span class="p">)[</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span> <span class="k">for</span> <span class="n">ref</span> <span class="ow">in</span> <span class="n">repo</span><span class="o">.</span><span class="n">references</span><span class="p">]</span>
+</span><span id="fork-243"><a href="#fork-243"><span class="linenos">243</span></a> <span class="k">if</span> <span class="n">upstream_version</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">available_refs</span><span class="p">:</span>
+</span><span id="fork-244"><a href="#fork-244"><span class="linenos">244</span></a> <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span>
+</span><span id="fork-245"><a href="#fork-245"><span class="linenos">245</span></a> <span class="sa">f</span><span class="s2">"Version '</span><span class="si">{</span><span class="n">upstream_version</span><span class="si">}</span><span class="s2">' not found in the repository: </span><span class="si">{</span><span class="n">upstream_url</span><span class="si">}</span><span class="s2">."</span>
+</span><span id="fork-246"><a href="#fork-246"><span class="linenos">246</span></a> <span class="p">)</span>
+</span><span id="fork-247"><a href="#fork-247"><span class="linenos">247</span></a>
+</span><span id="fork-248"><a href="#fork-248"><span class="linenos">248</span></a> <span class="c1"># Checkout the specified version</span>
+</span><span id="fork-249"><a href="#fork-249"><span class="linenos">249</span></a> <span class="n">repo</span><span class="o">.</span><span class="n">git</span><span class="o">.</span><span class="n">checkout</span><span class="p">(</span><span class="n">upstream_version</span><span class="p">)</span>
+</span><span id="fork-250"><a href="#fork-250"><span class="linenos">250</span></a> <span class="n">main_branch</span> <span class="o">=</span> <span class="n">repo</span><span class="o">.</span><span class="n">heads</span><span class="p">[</span><span class="n">DEFAULT_GIT_BRANCH</span><span class="p">]</span>
+</span><span id="fork-251"><a href="#fork-251"><span class="linenos">251</span></a> <span class="n">main_branch</span><span class="o">.</span><span class="n">checkout</span><span class="p">()</span>
+</span><span id="fork-252"><a href="#fork-252"><span class="linenos">252</span></a>
+</span><span id="fork-253"><a href="#fork-253"><span class="linenos">253</span></a> <span class="c1"># Check if 'config.yaml' exists in the root directory</span>
+</span><span id="fork-254"><a href="#fork-254"><span class="linenos">254</span></a> <span class="n">config_path</span> <span class="o">=</span> <span class="n">phen_path</span> <span class="o">/</span> <span class="s2">"config.yaml"</span>
+</span><span id="fork-255"><a href="#fork-255"><span class="linenos">255</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">isfile</span><span class="p">(</span><span class="n">config_path</span><span class="p">):</span>
+</span><span id="fork-256"><a href="#fork-256"><span class="linenos">256</span></a> <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span>
+</span><span id="fork-257"><a href="#fork-257"><span class="linenos">257</span></a> <span class="sa">f</span><span class="s2">"The forked repository is not a valid ACMC repo because 'config.yaml' is missing in the root directory."</span>
+</span><span id="fork-258"><a href="#fork-258"><span class="linenos">258</span></a> <span class="p">)</span>
+</span><span id="fork-259"><a href="#fork-259"><span class="linenos">259</span></a>
+</span><span id="fork-260"><a href="#fork-260"><span class="linenos">260</span></a> <span class="c1"># Validate the phenotype is compatible with the acmc tool</span>
+</span><span id="fork-261"><a href="#fork-261"><span class="linenos">261</span></a> <span class="n">validate</span><span class="p">(</span><span class="nb">str</span><span class="p">(</span><span class="n">phen_path</span><span class="o">.</span><span class="n">resolve</span><span class="p">()))</span>
+</span><span id="fork-262"><a href="#fork-262"><span class="linenos">262</span></a>
+</span><span id="fork-263"><a href="#fork-263"><span class="linenos">263</span></a> <span class="c1"># Delete each tag locally</span>
+</span><span id="fork-264"><a href="#fork-264"><span class="linenos">264</span></a> <span class="n">tags</span> <span class="o">=</span> <span class="n">repo</span><span class="o">.</span><span class="n">tags</span>
+</span><span id="fork-265"><a href="#fork-265"><span class="linenos">265</span></a> <span class="k">for</span> <span class="n">tag</span> <span class="ow">in</span> <span class="n">tags</span><span class="p">:</span>
+</span><span id="fork-266"><a href="#fork-266"><span class="linenos">266</span></a> <span class="n">repo</span><span class="o">.</span><span class="n">delete_tag</span><span class="p">(</span><span class="n">tag</span><span class="p">)</span>
+</span><span id="fork-267"><a href="#fork-267"><span class="linenos">267</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Deleted tags from forked repo: </span><span class="si">{</span><span class="n">tag</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+</span><span id="fork-268"><a href="#fork-268"><span class="linenos">268</span></a>
+</span><span id="fork-269"><a href="#fork-269"><span class="linenos">269</span></a> <span class="c1"># Add upstream remote</span>
+</span><span id="fork-270"><a href="#fork-270"><span class="linenos">270</span></a> <span class="n">repo</span><span class="o">.</span><span class="n">create_remote</span><span class="p">(</span><span class="s2">"upstream"</span><span class="p">,</span> <span class="n">upstream_url</span><span class="p">)</span>
+</span><span id="fork-271"><a href="#fork-271"><span class="linenos">271</span></a> <span class="n">remote</span> <span class="o">=</span> <span class="n">repo</span><span class="o">.</span><span class="n">remotes</span><span class="p">[</span><span class="s2">"origin"</span><span class="p">]</span>
+</span><span id="fork-272"><a href="#fork-272"><span class="linenos">272</span></a> <span class="n">repo</span><span class="o">.</span><span class="n">delete_remote</span><span class="p">(</span><span class="n">remote</span><span class="p">)</span> <span class="c1"># Remove existing origin</span>
+</span><span id="fork-273"><a href="#fork-273"><span class="linenos">273</span></a>
+</span><span id="fork-274"><a href="#fork-274"><span class="linenos">274</span></a> <span class="c1"># Optionally set a new origin remote</span>
+</span><span id="fork-275"><a href="#fork-275"><span class="linenos">275</span></a> <span class="k">if</span> <span class="n">new_origin_url</span><span class="p">:</span>
+</span><span id="fork-276"><a href="#fork-276"><span class="linenos">276</span></a> <span class="n">git_url</span> <span class="o">=</span> <span class="n">construct_git_url</span><span class="p">(</span><span class="n">new_origin_url</span><span class="p">)</span>
+</span><span id="fork-277"><a href="#fork-277"><span class="linenos">277</span></a> <span class="n">repo</span><span class="o">.</span><span class="n">create_remote</span><span class="p">(</span><span class="s2">"origin"</span><span class="p">,</span> <span class="n">git_url</span><span class="p">)</span>
+</span><span id="fork-278"><a href="#fork-278"><span class="linenos">278</span></a> <span class="n">repo</span><span class="o">.</span><span class="n">git</span><span class="o">.</span><span class="n">push</span><span class="p">(</span><span class="s2">"--set-upstream"</span><span class="p">,</span> <span class="s2">"origin"</span><span class="p">,</span> <span class="s2">"main"</span><span class="p">)</span>
+</span><span id="fork-279"><a href="#fork-279"><span class="linenos">279</span></a>
+</span><span id="fork-280"><a href="#fork-280"><span class="linenos">280</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Repository forked successfully at </span><span class="si">{</span><span class="n">phen_path</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+</span><span id="fork-281"><a href="#fork-281"><span class="linenos">281</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Upstream set to </span><span class="si">{</span><span class="n">upstream_url</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+</span><span id="fork-282"><a href="#fork-282"><span class="linenos">282</span></a> <span class="k">if</span> <span class="n">new_origin_url</span><span class="p">:</span>
+</span><span id="fork-283"><a href="#fork-283"><span class="linenos">283</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Origin set to </span><span class="si">{</span><span class="n">new_origin_url</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+</span><span id="fork-284"><a href="#fork-284"><span class="linenos">284</span></a>
+</span><span id="fork-285"><a href="#fork-285"><span class="linenos">285</span></a> <span class="k">except</span> <span class="ne">Exception</span> <span class="k">as</span> <span class="n">e</span><span class="p">:</span>
+</span><span id="fork-286"><a href="#fork-286"><span class="linenos">286</span></a> <span class="k">if</span> <span class="n">phen_path</span><span class="o">.</span><span class="n">exists</span><span class="p">():</span>
+</span><span id="fork-287"><a href="#fork-287"><span class="linenos">287</span></a> <span class="n">shutil</span><span class="o">.</span><span class="n">rmtree</span><span class="p">(</span><span class="n">phen_path</span><span class="p">)</span>
+</span><span id="fork-288"><a href="#fork-288"><span class="linenos">288</span></a> <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Error occurred during repository fork: </span><span class="si">{</span><span class="nb">str</span><span class="p">(</span><span class="n">e</span><span class="p">)</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+</span></pre></div>
+
+
+ <div class="docstring"><p>Forks an upstream phenotype in a remote repo at a specific version to a local director, and optionally sets to a new remote origin"</p>
+
+<p>Args:
+ phen_dir (str): local directory path where the upstream repo is to be cloned
+ upstream_url (str): url to the upstream repo
+ upstream_version (str): version in the upstream repo to clone
+ new_origin_url (str, optional): url of the remote repo to set as the new origin. Defaults to None.</p>
+
+<p>Raises:
+ ValueError: if the specified version is not in the upstream repo
+ ValueError: if the upstream repo is not a valid phenotype repo
+ ValueError: if there's any other problems with Git</p>
+</div>
+
+
+ </section>
+ <section id="init">
+ <input id="init-view-source" class="view-source-toggle-state" type="checkbox" aria-hidden="true" tabindex="-1">
+<div class="attr function">
+
+ <span class="def">def</span>
+ <span class="name">init</span><span class="signature pdoc-code condensed">(<span class="param"><span class="n">phen_dir</span><span class="p">:</span> <span class="nb">str</span>, </span><span class="param"><span class="n">remote_url</span><span class="p">:</span> <span class="nb">str</span></span><span class="return-annotation">):</span></span>
+
+ <label class="view-source-button" for="init-view-source"><span>View Source</span></label>
+
+ </div>
+ <a class="headerlink" href="#init"></a>
+ <div class="pdoc-code codehilite"><pre><span></span><span id="init-291"><a href="#init-291"><span class="linenos">291</span></a><span class="k">def</span><span class="w"> </span><span class="nf">init</span><span class="p">(</span><span class="n">phen_dir</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">remote_url</span><span class="p">:</span> <span class="nb">str</span><span class="p">):</span>
+</span><span id="init-292"><a href="#init-292"><span class="linenos">292</span></a><span class="w"> </span><span class="sd">"""Initial phenotype directory as git repo with standard structure"""</span>
+</span><span id="init-293"><a href="#init-293"><span class="linenos">293</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Initialising Phenotype in directory: </span><span class="si">{</span><span class="n">phen_dir</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+</span><span id="init-294"><a href="#init-294"><span class="linenos">294</span></a> <span class="n">phen_path</span> <span class="o">=</span> <span class="n">Path</span><span class="p">(</span><span class="n">phen_dir</span><span class="p">)</span>
+</span><span id="init-295"><a href="#init-295"><span class="linenos">295</span></a>
+</span><span id="init-296"><a href="#init-296"><span class="linenos">296</span></a> <span class="c1"># check if directory already exists and ask user if they want to recreate it</span>
+</span><span id="init-297"><a href="#init-297"><span class="linenos">297</span></a> <span class="k">if</span> <span class="p">(</span>
+</span><span id="init-298"><a href="#init-298"><span class="linenos">298</span></a> <span class="n">phen_path</span><span class="o">.</span><span class="n">exists</span><span class="p">()</span> <span class="ow">and</span> <span class="n">phen_path</span><span class="o">.</span><span class="n">is_dir</span><span class="p">()</span>
+</span><span id="init-299"><a href="#init-299"><span class="linenos">299</span></a> <span class="p">):</span> <span class="c1"># Check if it exists and is a directory</span>
+</span><span id="init-300"><a href="#init-300"><span class="linenos">300</span></a> <span class="n">configure</span> <span class="o">=</span> <span class="n">check_delete_dir</span><span class="p">(</span>
+</span><span id="init-301"><a href="#init-301"><span class="linenos">301</span></a> <span class="n">phen_path</span><span class="p">,</span>
+</span><span id="init-302"><a href="#init-302"><span class="linenos">302</span></a> <span class="sa">f</span><span class="s2">"The phen directory already exists. Do you want to reinitialise? (yes/no): "</span><span class="p">,</span>
+</span><span id="init-303"><a href="#init-303"><span class="linenos">303</span></a> <span class="p">)</span>
+</span><span id="init-304"><a href="#init-304"><span class="linenos">304</span></a> <span class="k">else</span><span class="p">:</span>
+</span><span id="init-305"><a href="#init-305"><span class="linenos">305</span></a> <span class="n">configure</span> <span class="o">=</span> <span class="kc">True</span>
+</span><span id="init-306"><a href="#init-306"><span class="linenos">306</span></a>
+</span><span id="init-307"><a href="#init-307"><span class="linenos">307</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="n">configure</span><span class="p">:</span>
+</span><span id="init-308"><a href="#init-308"><span class="linenos">308</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Exiting, phenotype not initiatised"</span><span class="p">)</span>
+</span><span id="init-309"><a href="#init-309"><span class="linenos">309</span></a> <span class="k">return</span>
+</span><span id="init-310"><a href="#init-310"><span class="linenos">310</span></a>
+</span><span id="init-311"><a href="#init-311"><span class="linenos">311</span></a> <span class="c1"># Initialise repo from local or remote</span>
+</span><span id="init-312"><a href="#init-312"><span class="linenos">312</span></a> <span class="n">repo</span><span class="p">:</span> <span class="n">Repo</span>
+</span><span id="init-313"><a href="#init-313"><span class="linenos">313</span></a> <span class="c1"># if remote then clone the repo otherwise init a local repo</span>
+</span><span id="init-314"><a href="#init-314"><span class="linenos">314</span></a> <span class="k">if</span> <span class="n">remote_url</span> <span class="o">!=</span> <span class="kc">None</span><span class="p">:</span>
+</span><span id="init-315"><a href="#init-315"><span class="linenos">315</span></a> <span class="c1"># add PAT token to the URL</span>
+</span><span id="init-316"><a href="#init-316"><span class="linenos">316</span></a> <span class="n">git_url</span> <span class="o">=</span> <span class="n">construct_git_url</span><span class="p">(</span><span class="n">remote_url</span><span class="p">)</span>
+</span><span id="init-317"><a href="#init-317"><span class="linenos">317</span></a>
+</span><span id="init-318"><a href="#init-318"><span class="linenos">318</span></a> <span class="c1"># clone the repo</span>
+</span><span id="init-319"><a href="#init-319"><span class="linenos">319</span></a> <span class="n">repo</span> <span class="o">=</span> <span class="n">git</span><span class="o">.</span><span class="n">cmd</span><span class="o">.</span><span class="n">Git</span><span class="p">()</span>
+</span><span id="init-320"><a href="#init-320"><span class="linenos">320</span></a> <span class="n">repo</span><span class="o">.</span><span class="n">clone</span><span class="p">(</span><span class="n">git_url</span><span class="p">,</span> <span class="n">phen_path</span><span class="p">)</span>
+</span><span id="init-321"><a href="#init-321"><span class="linenos">321</span></a>
+</span><span id="init-322"><a href="#init-322"><span class="linenos">322</span></a> <span class="c1"># open repo</span>
+</span><span id="init-323"><a href="#init-323"><span class="linenos">323</span></a> <span class="n">repo</span> <span class="o">=</span> <span class="n">Repo</span><span class="p">(</span><span class="n">phen_path</span><span class="p">)</span>
+</span><span id="init-324"><a href="#init-324"><span class="linenos">324</span></a> <span class="c1"># check if there are any commits (new repo has no commits)</span>
+</span><span id="init-325"><a href="#init-325"><span class="linenos">325</span></a> <span class="k">if</span> <span class="p">(</span>
+</span><span id="init-326"><a href="#init-326"><span class="linenos">326</span></a> <span class="nb">len</span><span class="p">(</span><span class="n">repo</span><span class="o">.</span><span class="n">branches</span><span class="p">)</span> <span class="o">==</span> <span class="mi">0</span> <span class="ow">or</span> <span class="n">repo</span><span class="o">.</span><span class="n">head</span><span class="o">.</span><span class="n">is_detached</span>
+</span><span id="init-327"><a href="#init-327"><span class="linenos">327</span></a> <span class="p">):</span> <span class="c1"># Handle detached HEAD (e.g., after init)</span>
+</span><span id="init-328"><a href="#init-328"><span class="linenos">328</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="s2">"The phen repository has no commits yet."</span><span class="p">)</span>
+</span><span id="init-329"><a href="#init-329"><span class="linenos">329</span></a> <span class="n">commit_count</span> <span class="o">=</span> <span class="mi">0</span>
+</span><span id="init-330"><a href="#init-330"><span class="linenos">330</span></a> <span class="k">else</span><span class="p">:</span>
+</span><span id="init-331"><a href="#init-331"><span class="linenos">331</span></a> <span class="c1"># Get the total number of commits in the default branch</span>
+</span><span id="init-332"><a href="#init-332"><span class="linenos">332</span></a> <span class="n">commit_count</span> <span class="o">=</span> <span class="nb">sum</span><span class="p">(</span><span class="mi">1</span> <span class="k">for</span> <span class="n">_</span> <span class="ow">in</span> <span class="n">repo</span><span class="o">.</span><span class="n">iter_commits</span><span class="p">())</span>
+</span><span id="init-333"><a href="#init-333"><span class="linenos">333</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Repo has previous commits: </span><span class="si">{</span><span class="n">commit_count</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+</span><span id="init-334"><a href="#init-334"><span class="linenos">334</span></a> <span class="k">else</span><span class="p">:</span>
+</span><span id="init-335"><a href="#init-335"><span class="linenos">335</span></a> <span class="c1"># local repo, create the directories and init</span>
+</span><span id="init-336"><a href="#init-336"><span class="linenos">336</span></a> <span class="n">phen_path</span><span class="o">.</span><span class="n">mkdir</span><span class="p">(</span><span class="n">parents</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">exist_ok</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+</span><span id="init-337"><a href="#init-337"><span class="linenos">337</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Phen directory '</span><span class="si">{</span><span class="n">phen_path</span><span class="si">}</span><span class="s2">' has been created."</span><span class="p">)</span>
+</span><span id="init-338"><a href="#init-338"><span class="linenos">338</span></a> <span class="n">repo</span> <span class="o">=</span> <span class="n">git</span><span class="o">.</span><span class="n">Repo</span><span class="o">.</span><span class="n">init</span><span class="p">(</span><span class="n">phen_path</span><span class="p">)</span>
+</span><span id="init-339"><a href="#init-339"><span class="linenos">339</span></a> <span class="n">commit_count</span> <span class="o">=</span> <span class="mi">0</span>
+</span><span id="init-340"><a href="#init-340"><span class="linenos">340</span></a>
+</span><span id="init-341"><a href="#init-341"><span class="linenos">341</span></a> <span class="n">phen_path</span> <span class="o">=</span> <span class="n">phen_path</span><span class="o">.</span><span class="n">resolve</span><span class="p">()</span>
+</span><span id="init-342"><a href="#init-342"><span class="linenos">342</span></a> <span class="c1"># initialise empty repos</span>
+</span><span id="init-343"><a href="#init-343"><span class="linenos">343</span></a> <span class="k">if</span> <span class="n">commit_count</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
+</span><span id="init-344"><a href="#init-344"><span class="linenos">344</span></a> <span class="c1"># create initial commit</span>
+</span><span id="init-345"><a href="#init-345"><span class="linenos">345</span></a> <span class="n">initial_file_path</span> <span class="o">=</span> <span class="n">phen_path</span> <span class="o">/</span> <span class="s2">"README.md"</span>
+</span><span id="init-346"><a href="#init-346"><span class="linenos">346</span></a> <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">initial_file_path</span><span class="p">,</span> <span class="s2">"w"</span><span class="p">)</span> <span class="k">as</span> <span class="n">file</span><span class="p">:</span>
+</span><span id="init-347"><a href="#init-347"><span class="linenos">347</span></a> <span class="n">file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span>
+</span><span id="init-348"><a href="#init-348"><span class="linenos">348</span></a> <span class="s2">"# Initial commit</span><span class="se">\n</span><span class="s2">This is the first commit in the phen repository.</span><span class="se">\n</span><span class="s2">"</span>
+</span><span id="init-349"><a href="#init-349"><span class="linenos">349</span></a> <span class="p">)</span>
+</span><span id="init-350"><a href="#init-350"><span class="linenos">350</span></a> <span class="n">repo</span><span class="o">.</span><span class="n">index</span><span class="o">.</span><span class="n">add</span><span class="p">([</span><span class="n">initial_file_path</span><span class="p">])</span>
+</span><span id="init-351"><a href="#init-351"><span class="linenos">351</span></a> <span class="n">repo</span><span class="o">.</span><span class="n">index</span><span class="o">.</span><span class="n">commit</span><span class="p">(</span><span class="s2">"Initial commit"</span><span class="p">)</span>
+</span><span id="init-352"><a href="#init-352"><span class="linenos">352</span></a> <span class="n">commit_count</span> <span class="o">=</span> <span class="mi">1</span>
+</span><span id="init-353"><a href="#init-353"><span class="linenos">353</span></a>
+</span><span id="init-354"><a href="#init-354"><span class="linenos">354</span></a> <span class="c1"># Checkout the phens default branch, creating it if it does not exist</span>
+</span><span id="init-355"><a href="#init-355"><span class="linenos">355</span></a> <span class="k">if</span> <span class="n">DEFAULT_GIT_BRANCH</span> <span class="ow">in</span> <span class="n">repo</span><span class="o">.</span><span class="n">branches</span><span class="p">:</span>
+</span><span id="init-356"><a href="#init-356"><span class="linenos">356</span></a> <span class="n">main_branch</span> <span class="o">=</span> <span class="n">repo</span><span class="o">.</span><span class="n">heads</span><span class="p">[</span><span class="n">DEFAULT_GIT_BRANCH</span><span class="p">]</span>
+</span><span id="init-357"><a href="#init-357"><span class="linenos">357</span></a> <span class="n">main_branch</span><span class="o">.</span><span class="n">checkout</span><span class="p">()</span>
+</span><span id="init-358"><a href="#init-358"><span class="linenos">358</span></a> <span class="k">else</span><span class="p">:</span>
+</span><span id="init-359"><a href="#init-359"><span class="linenos">359</span></a> <span class="n">main_branch</span> <span class="o">=</span> <span class="n">repo</span><span class="o">.</span><span class="n">create_head</span><span class="p">(</span><span class="n">DEFAULT_GIT_BRANCH</span><span class="p">)</span>
+</span><span id="init-360"><a href="#init-360"><span class="linenos">360</span></a> <span class="n">main_branch</span><span class="o">.</span><span class="n">checkout</span><span class="p">()</span>
+</span><span id="init-361"><a href="#init-361"><span class="linenos">361</span></a>
+</span><span id="init-362"><a href="#init-362"><span class="linenos">362</span></a> <span class="c1"># if the phen path does not contain the config file then initialise the phen type</span>
+</span><span id="init-363"><a href="#init-363"><span class="linenos">363</span></a> <span class="n">config_path</span> <span class="o">=</span> <span class="n">phen_path</span> <span class="o">/</span> <span class="n">CONFIG_FILE</span>
+</span><span id="init-364"><a href="#init-364"><span class="linenos">364</span></a> <span class="k">if</span> <span class="n">config_path</span><span class="o">.</span><span class="n">exists</span><span class="p">():</span>
+</span><span id="init-365"><a href="#init-365"><span class="linenos">365</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Phenotype configuration files already exist"</span><span class="p">)</span>
+</span><span id="init-366"><a href="#init-366"><span class="linenos">366</span></a> <span class="k">return</span>
+</span><span id="init-367"><a href="#init-367"><span class="linenos">367</span></a>
+</span><span id="init-368"><a href="#init-368"><span class="linenos">368</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">"Creating phen directory structure and config files"</span><span class="p">)</span>
+</span><span id="init-369"><a href="#init-369"><span class="linenos">369</span></a> <span class="k">for</span> <span class="n">d</span> <span class="ow">in</span> <span class="n">DEFAULT_PHEN_DIR_LIST</span><span class="p">:</span>
+</span><span id="init-370"><a href="#init-370"><span class="linenos">370</span></a> <span class="n">create_empty_git_dir</span><span class="p">(</span><span class="n">phen_path</span> <span class="o">/</span> <span class="n">d</span><span class="p">)</span>
+</span><span id="init-371"><a href="#init-371"><span class="linenos">371</span></a>
+</span><span id="init-372"><a href="#init-372"><span class="linenos">372</span></a> <span class="c1"># create empty phen config file</span>
+</span><span id="init-373"><a href="#init-373"><span class="linenos">373</span></a> <span class="n">config</span> <span class="o">=</span> <span class="p">{</span>
+</span><span id="init-374"><a href="#init-374"><span class="linenos">374</span></a> <span class="s2">"phenotype"</span><span class="p">:</span> <span class="p">{</span>
+</span><span id="init-375"><a href="#init-375"><span class="linenos">375</span></a> <span class="s2">"version"</span><span class="p">:</span> <span class="s2">"0.0.0"</span><span class="p">,</span>
+</span><span id="init-376"><a href="#init-376"><span class="linenos">376</span></a> <span class="s2">"omop"</span><span class="p">:</span> <span class="p">{</span>
+</span><span id="init-377"><a href="#init-377"><span class="linenos">377</span></a> <span class="s2">"vocabulary_id"</span><span class="p">:</span> <span class="s2">""</span><span class="p">,</span>
+</span><span id="init-378"><a href="#init-378"><span class="linenos">378</span></a> <span class="s2">"vocabulary_name"</span><span class="p">:</span> <span class="s2">""</span><span class="p">,</span>
+</span><span id="init-379"><a href="#init-379"><span class="linenos">379</span></a> <span class="s2">"vocabulary_reference"</span><span class="p">:</span> <span class="s2">""</span><span class="p">,</span>
+</span><span id="init-380"><a href="#init-380"><span class="linenos">380</span></a> <span class="p">},</span>
+</span><span id="init-381"><a href="#init-381"><span class="linenos">381</span></a> <span class="s2">"translate"</span><span class="p">:</span> <span class="p">[],</span>
+</span><span id="init-382"><a href="#init-382"><span class="linenos">382</span></a> <span class="s2">"concept_sets"</span><span class="p">:</span> <span class="p">[],</span>
+</span><span id="init-383"><a href="#init-383"><span class="linenos">383</span></a> <span class="p">}</span>
+</span><span id="init-384"><a href="#init-384"><span class="linenos">384</span></a> <span class="p">}</span>
+</span><span id="init-385"><a href="#init-385"><span class="linenos">385</span></a>
+</span><span id="init-386"><a href="#init-386"><span class="linenos">386</span></a> <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">phen_path</span> <span class="o">/</span> <span class="n">CONFIG_FILE</span><span class="p">,</span> <span class="s2">"w"</span><span class="p">)</span> <span class="k">as</span> <span class="n">file</span><span class="p">:</span>
+</span><span id="init-387"><a href="#init-387"><span class="linenos">387</span></a> <span class="n">yaml</span><span class="o">.</span><span class="n">dump</span><span class="p">(</span>
+</span><span id="init-388"><a href="#init-388"><span class="linenos">388</span></a> <span class="n">config</span><span class="p">,</span>
+</span><span id="init-389"><a href="#init-389"><span class="linenos">389</span></a> <span class="n">file</span><span class="p">,</span>
+</span><span id="init-390"><a href="#init-390"><span class="linenos">390</span></a> <span class="n">Dumper</span><span class="o">=</span><span class="n">util</span><span class="o">.</span><span class="n">QuotedDumper</span><span class="p">,</span>
+</span><span id="init-391"><a href="#init-391"><span class="linenos">391</span></a> <span class="n">default_flow_style</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span>
+</span><span id="init-392"><a href="#init-392"><span class="linenos">392</span></a> <span class="n">sort_keys</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span>
+</span><span id="init-393"><a href="#init-393"><span class="linenos">393</span></a> <span class="n">default_style</span><span class="o">=</span><span class="s1">'"'</span><span class="p">,</span>
+</span><span id="init-394"><a href="#init-394"><span class="linenos">394</span></a> <span class="p">)</span>
+</span><span id="init-395"><a href="#init-395"><span class="linenos">395</span></a>
+</span><span id="init-396"><a href="#init-396"><span class="linenos">396</span></a> <span class="c1"># add git ignore</span>
+</span><span id="init-397"><a href="#init-397"><span class="linenos">397</span></a> <span class="n">ignore_content</span> <span class="o">=</span> <span class="s2">"""# Ignore SQLite database files</span>
+</span><span id="init-398"><a href="#init-398"><span class="linenos">398</span></a><span class="s2">*.db</span>
+</span><span id="init-399"><a href="#init-399"><span class="linenos">399</span></a><span class="s2">*.sqlite3</span>
+</span><span id="init-400"><a href="#init-400"><span class="linenos">400</span></a><span class="s2"> </span>
+</span><span id="init-401"><a href="#init-401"><span class="linenos">401</span></a><span class="s2"># Ignore SQLite journal and metadata files</span>
+</span><span id="init-402"><a href="#init-402"><span class="linenos">402</span></a><span class="s2">*.db-journal</span>
+</span><span id="init-403"><a href="#init-403"><span class="linenos">403</span></a><span class="s2">*.sqlite3-journal</span>
+</span><span id="init-404"><a href="#init-404"><span class="linenos">404</span></a>
+</span><span id="init-405"><a href="#init-405"><span class="linenos">405</span></a><span class="s2"># python</span>
+</span><span id="init-406"><a href="#init-406"><span class="linenos">406</span></a><span class="s2">.ipynb_checkpoints</span>
+</span><span id="init-407"><a href="#init-407"><span class="linenos">407</span></a><span class="s2"> """</span>
+</span><span id="init-408"><a href="#init-408"><span class="linenos">408</span></a> <span class="n">ignore_path</span> <span class="o">=</span> <span class="n">phen_path</span> <span class="o">/</span> <span class="s2">".gitignore"</span>
+</span><span id="init-409"><a href="#init-409"><span class="linenos">409</span></a> <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">ignore_path</span><span class="p">,</span> <span class="s2">"w"</span><span class="p">)</span> <span class="k">as</span> <span class="n">file</span><span class="p">:</span>
+</span><span id="init-410"><a href="#init-410"><span class="linenos">410</span></a> <span class="n">file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">ignore_content</span><span class="p">)</span>
+</span><span id="init-411"><a href="#init-411"><span class="linenos">411</span></a>
+</span><span id="init-412"><a href="#init-412"><span class="linenos">412</span></a> <span class="c1"># add to git repo and commit</span>
+</span><span id="init-413"><a href="#init-413"><span class="linenos">413</span></a> <span class="k">for</span> <span class="n">d</span> <span class="ow">in</span> <span class="n">DEFAULT_PHEN_DIR_LIST</span><span class="p">:</span>
+</span><span id="init-414"><a href="#init-414"><span class="linenos">414</span></a> <span class="n">repo</span><span class="o">.</span><span class="n">git</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="n">phen_path</span> <span class="o">/</span> <span class="n">d</span><span class="p">)</span>
+</span><span id="init-415"><a href="#init-415"><span class="linenos">415</span></a> <span class="n">repo</span><span class="o">.</span><span class="n">git</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="nb">all</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+</span><span id="init-416"><a href="#init-416"><span class="linenos">416</span></a> <span class="n">repo</span><span class="o">.</span><span class="n">index</span><span class="o">.</span><span class="n">commit</span><span class="p">(</span><span class="s2">"initialised the phen git repo."</span><span class="p">)</span>
+</span><span id="init-417"><a href="#init-417"><span class="linenos">417</span></a>
+</span><span id="init-418"><a href="#init-418"><span class="linenos">418</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Phenotype initialised successfully"</span><span class="p">)</span>
+</span></pre></div>
+
+
+ <div class="docstring"><p>Initial phenotype directory as git repo with standard structure</p>
+</div>
+
+
+ </section>
+ <section id="validate">
+ <input id="validate-view-source" class="view-source-toggle-state" type="checkbox" aria-hidden="true" tabindex="-1">
+<div class="attr function">
+
+ <span class="def">def</span>
+ <span class="name">validate</span><span class="signature pdoc-code condensed">(<span class="param"><span class="n">phen_dir</span><span class="p">:</span> <span class="nb">str</span></span><span class="return-annotation">):</span></span>
+
+ <label class="view-source-button" for="validate-view-source"><span>View Source</span></label>
+
+ </div>
+ <a class="headerlink" href="#validate"></a>
+ <div class="pdoc-code codehilite"><pre><span></span><span id="validate-421"><a href="#validate-421"><span class="linenos">421</span></a><span class="k">def</span><span class="w"> </span><span class="nf">validate</span><span class="p">(</span><span class="n">phen_dir</span><span class="p">:</span> <span class="nb">str</span><span class="p">):</span>
+</span><span id="validate-422"><a href="#validate-422"><span class="linenos">422</span></a><span class="w"> </span><span class="sd">"""Validates the phenotype directory is a git repo with standard structure"""</span>
+</span><span id="validate-423"><a href="#validate-423"><span class="linenos">423</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Validating phenotype: </span><span class="si">{</span><span class="n">phen_dir</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+</span><span id="validate-424"><a href="#validate-424"><span class="linenos">424</span></a> <span class="n">phen_path</span> <span class="o">=</span> <span class="n">Path</span><span class="p">(</span><span class="n">phen_dir</span><span class="p">)</span>
+</span><span id="validate-425"><a href="#validate-425"><span class="linenos">425</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="n">phen_path</span><span class="o">.</span><span class="n">is_dir</span><span class="p">():</span>
+</span><span id="validate-426"><a href="#validate-426"><span class="linenos">426</span></a> <span class="k">raise</span> <span class="ne">NotADirectoryError</span><span class="p">(</span>
+</span><span id="validate-427"><a href="#validate-427"><span class="linenos">427</span></a> <span class="sa">f</span><span class="s2">"Error: '</span><span class="si">{</span><span class="nb">str</span><span class="p">(</span><span class="n">phen_path</span><span class="o">.</span><span class="n">resolve</span><span class="p">())</span><span class="si">}</span><span class="s2">' is not a directory"</span>
+</span><span id="validate-428"><a href="#validate-428"><span class="linenos">428</span></a> <span class="p">)</span>
+</span><span id="validate-429"><a href="#validate-429"><span class="linenos">429</span></a>
+</span><span id="validate-430"><a href="#validate-430"><span class="linenos">430</span></a> <span class="n">config_path</span> <span class="o">=</span> <span class="n">phen_path</span> <span class="o">/</span> <span class="n">CONFIG_FILE</span>
+</span><span id="validate-431"><a href="#validate-431"><span class="linenos">431</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="n">config_path</span><span class="o">.</span><span class="n">is_file</span><span class="p">():</span>
+</span><span id="validate-432"><a href="#validate-432"><span class="linenos">432</span></a> <span class="k">raise</span> <span class="ne">FileNotFoundError</span><span class="p">(</span>
+</span><span id="validate-433"><a href="#validate-433"><span class="linenos">433</span></a> <span class="sa">f</span><span class="s2">"Error: phen configuration file '</span><span class="si">{</span><span class="n">config_path</span><span class="si">}</span><span class="s2">' does not exist."</span>
+</span><span id="validate-434"><a href="#validate-434"><span class="linenos">434</span></a> <span class="p">)</span>
+</span><span id="validate-435"><a href="#validate-435"><span class="linenos">435</span></a>
+</span><span id="validate-436"><a href="#validate-436"><span class="linenos">436</span></a> <span class="n">concepts_path</span> <span class="o">=</span> <span class="n">phen_path</span> <span class="o">/</span> <span class="n">CONCEPTS_DIR</span>
+</span><span id="validate-437"><a href="#validate-437"><span class="linenos">437</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="n">concepts_path</span><span class="o">.</span><span class="n">is_dir</span><span class="p">():</span>
+</span><span id="validate-438"><a href="#validate-438"><span class="linenos">438</span></a> <span class="k">raise</span> <span class="ne">FileNotFoundError</span><span class="p">(</span>
+</span><span id="validate-439"><a href="#validate-439"><span class="linenos">439</span></a> <span class="sa">f</span><span class="s2">"Error: source concepts directory </span><span class="si">{</span><span class="n">concepts_path</span><span class="si">}</span><span class="s2"> does not exist."</span>
+</span><span id="validate-440"><a href="#validate-440"><span class="linenos">440</span></a> <span class="p">)</span>
+</span><span id="validate-441"><a href="#validate-441"><span class="linenos">441</span></a>
+</span><span id="validate-442"><a href="#validate-442"><span class="linenos">442</span></a> <span class="c1"># Calidate the directory is a git repo</span>
+</span><span id="validate-443"><a href="#validate-443"><span class="linenos">443</span></a> <span class="k">try</span><span class="p">:</span>
+</span><span id="validate-444"><a href="#validate-444"><span class="linenos">444</span></a> <span class="n">git</span><span class="o">.</span><span class="n">Repo</span><span class="p">(</span><span class="n">phen_path</span><span class="p">)</span>
+</span><span id="validate-445"><a href="#validate-445"><span class="linenos">445</span></a> <span class="k">except</span> <span class="p">(</span><span class="n">git</span><span class="o">.</span><span class="n">exc</span><span class="o">.</span><span class="n">InvalidGitRepositoryError</span><span class="p">,</span> <span class="n">git</span><span class="o">.</span><span class="n">exc</span><span class="o">.</span><span class="n">NoSuchPathError</span><span class="p">):</span>
+</span><span id="validate-446"><a href="#validate-446"><span class="linenos">446</span></a> <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Phen directory </span><span class="si">{</span><span class="n">phen_path</span><span class="si">}</span><span class="s2"> is not a git repo"</span><span class="p">)</span>
+</span><span id="validate-447"><a href="#validate-447"><span class="linenos">447</span></a>
+</span><span id="validate-448"><a href="#validate-448"><span class="linenos">448</span></a> <span class="c1"># Load configuration File</span>
+</span><span id="validate-449"><a href="#validate-449"><span class="linenos">449</span></a> <span class="k">if</span> <span class="n">config_path</span><span class="o">.</span><span class="n">suffix</span> <span class="o">==</span> <span class="s2">".yaml"</span><span class="p">:</span>
+</span><span id="validate-450"><a href="#validate-450"><span class="linenos">450</span></a> <span class="k">try</span><span class="p">:</span>
+</span><span id="validate-451"><a href="#validate-451"><span class="linenos">451</span></a> <span class="k">with</span> <span class="n">config_path</span><span class="o">.</span><span class="n">open</span><span class="p">(</span><span class="s2">"r"</span><span class="p">)</span> <span class="k">as</span> <span class="n">file</span><span class="p">:</span>
+</span><span id="validate-452"><a href="#validate-452"><span class="linenos">452</span></a> <span class="n">phenotype</span> <span class="o">=</span> <span class="n">yaml</span><span class="o">.</span><span class="n">safe_load</span><span class="p">(</span><span class="n">file</span><span class="p">)</span>
+</span><span id="validate-453"><a href="#validate-453"><span class="linenos">453</span></a>
+</span><span id="validate-454"><a href="#validate-454"><span class="linenos">454</span></a> <span class="n">validator</span> <span class="o">=</span> <span class="n">Validator</span><span class="p">(</span><span class="n">CONFIG_SCHEMA</span><span class="p">)</span>
+</span><span id="validate-455"><a href="#validate-455"><span class="linenos">455</span></a> <span class="k">if</span> <span class="n">validator</span><span class="o">.</span><span class="n">validate</span><span class="p">(</span><span class="n">phenotype</span><span class="p">):</span>
+</span><span id="validate-456"><a href="#validate-456"><span class="linenos">456</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="s2">"YAML structure is valid."</span><span class="p">)</span>
+</span><span id="validate-457"><a href="#validate-457"><span class="linenos">457</span></a> <span class="k">else</span><span class="p">:</span>
+</span><span id="validate-458"><a href="#validate-458"><span class="linenos">458</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">error</span><span class="p">(</span><span class="sa">f</span><span class="s2">"YAML structure validation failed: </span><span class="si">{</span><span class="n">validator</span><span class="o">.</span><span class="n">errors</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+</span><span id="validate-459"><a href="#validate-459"><span class="linenos">459</span></a> <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="sa">f</span><span class="s2">"YAML structure validation failed: </span><span class="si">{</span><span class="n">validator</span><span class="o">.</span><span class="n">errors</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+</span><span id="validate-460"><a href="#validate-460"><span class="linenos">460</span></a> <span class="k">except</span> <span class="n">yaml</span><span class="o">.</span><span class="n">YAMLError</span> <span class="k">as</span> <span class="n">e</span><span class="p">:</span>
+</span><span id="validate-461"><a href="#validate-461"><span class="linenos">461</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">error</span><span class="p">(</span><span class="sa">f</span><span class="s2">"YAML syntax error: </span><span class="si">{</span><span class="n">e</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+</span><span id="validate-462"><a href="#validate-462"><span class="linenos">462</span></a> <span class="k">raise</span> <span class="n">e</span>
+</span><span id="validate-463"><a href="#validate-463"><span class="linenos">463</span></a> <span class="k">else</span><span class="p">:</span>
+</span><span id="validate-464"><a href="#validate-464"><span class="linenos">464</span></a> <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span>
+</span><span id="validate-465"><a href="#validate-465"><span class="linenos">465</span></a> <span class="sa">f</span><span class="s2">"Unsupported configuration filetype: </span><span class="si">{</span><span class="nb">str</span><span class="p">(</span><span class="n">config_path</span><span class="o">.</span><span class="n">resolve</span><span class="p">())</span><span class="si">}</span><span class="s2">"</span>
+</span><span id="validate-466"><a href="#validate-466"><span class="linenos">466</span></a> <span class="p">)</span>
+</span><span id="validate-467"><a href="#validate-467"><span class="linenos">467</span></a>
+</span><span id="validate-468"><a href="#validate-468"><span class="linenos">468</span></a> <span class="c1"># initiatise</span>
+</span><span id="validate-469"><a href="#validate-469"><span class="linenos">469</span></a> <span class="n">validation_errors</span> <span class="o">=</span> <span class="p">[]</span>
+</span><span id="validate-470"><a href="#validate-470"><span class="linenos">470</span></a> <span class="n">phenotype</span> <span class="o">=</span> <span class="n">phenotype</span><span class="p">[</span><span class="s2">"phenotype"</span><span class="p">]</span>
+</span><span id="validate-471"><a href="#validate-471"><span class="linenos">471</span></a> <span class="n">code_types</span> <span class="o">=</span> <span class="n">parse</span><span class="o">.</span><span class="n">CodeTypeParser</span><span class="p">()</span><span class="o">.</span><span class="n">code_types</span>
+</span><span id="validate-472"><a href="#validate-472"><span class="linenos">472</span></a>
+</span><span id="validate-473"><a href="#validate-473"><span class="linenos">473</span></a> <span class="c1"># check the version number is of the format vn.n.n</span>
+</span><span id="validate-474"><a href="#validate-474"><span class="linenos">474</span></a> <span class="n">match</span> <span class="o">=</span> <span class="n">re</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="sa">r</span><span class="s2">"(\d+\.\d+\.\d+)"</span><span class="p">,</span> <span class="n">phenotype</span><span class="p">[</span><span class="s2">"version"</span><span class="p">])</span>
+</span><span id="validate-475"><a href="#validate-475"><span class="linenos">475</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="n">match</span><span class="p">:</span>
+</span><span id="validate-476"><a href="#validate-476"><span class="linenos">476</span></a> <span class="n">validation_errors</span><span class="o">.</span><span class="n">append</span><span class="p">(</span>
+</span><span id="validate-477"><a href="#validate-477"><span class="linenos">477</span></a> <span class="sa">f</span><span class="s2">"Invalid version format in configuration file: </span><span class="si">{</span><span class="n">phenotype</span><span class="p">[</span><span class="s1">'version'</span><span class="p">]</span><span class="si">}</span><span class="s2">"</span>
+</span><span id="validate-478"><a href="#validate-478"><span class="linenos">478</span></a> <span class="p">)</span>
+</span><span id="validate-479"><a href="#validate-479"><span class="linenos">479</span></a>
+</span><span id="validate-480"><a href="#validate-480"><span class="linenos">480</span></a> <span class="c1"># create a list of all the concept set names defined in the concept set configuration</span>
+</span><span id="validate-481"><a href="#validate-481"><span class="linenos">481</span></a> <span class="n">concept_set_names</span> <span class="o">=</span> <span class="p">[]</span>
+</span><span id="validate-482"><a href="#validate-482"><span class="linenos">482</span></a> <span class="k">for</span> <span class="n">item</span> <span class="ow">in</span> <span class="n">phenotype</span><span class="p">[</span><span class="s2">"concept_sets"</span><span class="p">]:</span>
+</span><span id="validate-483"><a href="#validate-483"><span class="linenos">483</span></a> <span class="k">if</span> <span class="n">item</span><span class="p">[</span><span class="s2">"name"</span><span class="p">]</span> <span class="ow">in</span> <span class="n">concept_set_names</span><span class="p">:</span>
+</span><span id="validate-484"><a href="#validate-484"><span class="linenos">484</span></a> <span class="n">validation_errors</span><span class="o">.</span><span class="n">append</span><span class="p">(</span>
+</span><span id="validate-485"><a href="#validate-485"><span class="linenos">485</span></a> <span class="sa">f</span><span class="s2">"Duplicate concept set defined in concept sets </span><span class="si">{</span><span class="n">item</span><span class="p">[</span><span class="s1">'name'</span><span class="p">]</span><span class="w"> </span><span class="si">}</span><span class="s2">"</span>
+</span><span id="validate-486"><a href="#validate-486"><span class="linenos">486</span></a> <span class="p">)</span>
+</span><span id="validate-487"><a href="#validate-487"><span class="linenos">487</span></a> <span class="k">else</span><span class="p">:</span>
+</span><span id="validate-488"><a href="#validate-488"><span class="linenos">488</span></a> <span class="n">concept_set_names</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">item</span><span class="p">[</span><span class="s2">"name"</span><span class="p">])</span>
+</span><span id="validate-489"><a href="#validate-489"><span class="linenos">489</span></a>
+</span><span id="validate-490"><a href="#validate-490"><span class="linenos">490</span></a> <span class="c1"># check codes definition</span>
+</span><span id="validate-491"><a href="#validate-491"><span class="linenos">491</span></a> <span class="k">for</span> <span class="n">item</span> <span class="ow">in</span> <span class="n">phenotype</span><span class="p">[</span><span class="s2">"concept_sets"</span><span class="p">]:</span>
+</span><span id="validate-492"><a href="#validate-492"><span class="linenos">492</span></a> <span class="c1"># check concepte code file exists</span>
+</span><span id="validate-493"><a href="#validate-493"><span class="linenos">493</span></a> <span class="n">concept_code_file_path</span> <span class="o">=</span> <span class="n">concepts_path</span> <span class="o">/</span> <span class="n">item</span><span class="p">[</span><span class="s2">"file"</span><span class="p">][</span><span class="s2">"path"</span><span class="p">]</span>
+</span><span id="validate-494"><a href="#validate-494"><span class="linenos">494</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="n">concept_code_file_path</span><span class="o">.</span><span class="n">exists</span><span class="p">():</span>
+</span><span id="validate-495"><a href="#validate-495"><span class="linenos">495</span></a> <span class="n">validation_errors</span><span class="o">.</span><span class="n">append</span><span class="p">(</span>
+</span><span id="validate-496"><a href="#validate-496"><span class="linenos">496</span></a> <span class="sa">f</span><span class="s2">"Coding file </span><span class="si">{</span><span class="nb">str</span><span class="p">(</span><span class="n">concept_code_file_path</span><span class="o">.</span><span class="n">resolve</span><span class="p">())</span><span class="si">}</span><span class="s2"> does not exist"</span>
+</span><span id="validate-497"><a href="#validate-497"><span class="linenos">497</span></a> <span class="p">)</span>
+</span><span id="validate-498"><a href="#validate-498"><span class="linenos">498</span></a>
+</span><span id="validate-499"><a href="#validate-499"><span class="linenos">499</span></a> <span class="c1"># check concepte code file is not empty</span>
+</span><span id="validate-500"><a href="#validate-500"><span class="linenos">500</span></a> <span class="k">if</span> <span class="n">concept_code_file_path</span><span class="o">.</span><span class="n">stat</span><span class="p">()</span><span class="o">.</span><span class="n">st_size</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
+</span><span id="validate-501"><a href="#validate-501"><span class="linenos">501</span></a> <span class="n">validation_errors</span><span class="o">.</span><span class="n">append</span><span class="p">(</span>
+</span><span id="validate-502"><a href="#validate-502"><span class="linenos">502</span></a> <span class="sa">f</span><span class="s2">"Coding file </span><span class="si">{</span><span class="nb">str</span><span class="p">(</span><span class="n">concept_code_file_path</span><span class="o">.</span><span class="n">resolve</span><span class="p">())</span><span class="si">}</span><span class="s2"> is an empty file"</span>
+</span><span id="validate-503"><a href="#validate-503"><span class="linenos">503</span></a> <span class="p">)</span>
+</span><span id="validate-504"><a href="#validate-504"><span class="linenos">504</span></a>
+</span><span id="validate-505"><a href="#validate-505"><span class="linenos">505</span></a> <span class="c1"># check code file type is supported</span>
+</span><span id="validate-506"><a href="#validate-506"><span class="linenos">506</span></a> <span class="k">if</span> <span class="n">concept_code_file_path</span><span class="o">.</span><span class="n">suffix</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">CODE_FILE_TYPES</span><span class="p">:</span>
+</span><span id="validate-507"><a href="#validate-507"><span class="linenos">507</span></a> <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span>
+</span><span id="validate-508"><a href="#validate-508"><span class="linenos">508</span></a> <span class="sa">f</span><span class="s2">"Unsupported filetype </span><span class="si">{</span><span class="n">concept_code_file_path</span><span class="o">.</span><span class="n">suffix</span><span class="si">}</span><span class="s2">, only support csv, xlsx, xls code file types"</span>
+</span><span id="validate-509"><a href="#validate-509"><span class="linenos">509</span></a> <span class="p">)</span>
+</span><span id="validate-510"><a href="#validate-510"><span class="linenos">510</span></a>
+</span><span id="validate-511"><a href="#validate-511"><span class="linenos">511</span></a> <span class="c1"># check columns specified are a supported medical coding type</span>
+</span><span id="validate-512"><a href="#validate-512"><span class="linenos">512</span></a> <span class="k">for</span> <span class="n">column</span> <span class="ow">in</span> <span class="n">item</span><span class="p">[</span><span class="s2">"file"</span><span class="p">][</span><span class="s2">"columns"</span><span class="p">]:</span>
+</span><span id="validate-513"><a href="#validate-513"><span class="linenos">513</span></a> <span class="k">if</span> <span class="n">column</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">code_types</span><span class="p">:</span>
+</span><span id="validate-514"><a href="#validate-514"><span class="linenos">514</span></a> <span class="n">validation_errors</span><span class="o">.</span><span class="n">append</span><span class="p">(</span>
+</span><span id="validate-515"><a href="#validate-515"><span class="linenos">515</span></a> <span class="sa">f</span><span class="s2">"Column type </span><span class="si">{</span><span class="n">column</span><span class="si">}</span><span class="s2"> for file </span><span class="si">{</span><span class="n">concept_code_file_path</span><span class="si">}</span><span class="s2"> is not supported"</span>
+</span><span id="validate-516"><a href="#validate-516"><span class="linenos">516</span></a> <span class="p">)</span>
+</span><span id="validate-517"><a href="#validate-517"><span class="linenos">517</span></a>
+</span><span id="validate-518"><a href="#validate-518"><span class="linenos">518</span></a> <span class="c1"># check the actions are supported</span>
+</span><span id="validate-519"><a href="#validate-519"><span class="linenos">519</span></a> <span class="k">if</span> <span class="s2">"actions"</span> <span class="ow">in</span> <span class="n">item</span><span class="p">[</span><span class="s2">"file"</span><span class="p">]:</span>
+</span><span id="validate-520"><a href="#validate-520"><span class="linenos">520</span></a> <span class="k">for</span> <span class="n">action</span> <span class="ow">in</span> <span class="n">item</span><span class="p">[</span><span class="s2">"file"</span><span class="p">][</span><span class="s2">"actions"</span><span class="p">]:</span>
+</span><span id="validate-521"><a href="#validate-521"><span class="linenos">521</span></a> <span class="k">if</span> <span class="n">action</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">COL_ACTIONS</span><span class="p">:</span>
+</span><span id="validate-522"><a href="#validate-522"><span class="linenos">522</span></a> <span class="n">validation_errors</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Action </span><span class="si">{</span><span class="n">action</span><span class="si">}</span><span class="s2"> is not supported"</span><span class="p">)</span>
+</span><span id="validate-523"><a href="#validate-523"><span class="linenos">523</span></a>
+</span><span id="validate-524"><a href="#validate-524"><span class="linenos">524</span></a> <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">validation_errors</span><span class="p">)</span> <span class="o">></span> <span class="mi">0</span><span class="p">:</span>
+</span><span id="validate-525"><a href="#validate-525"><span class="linenos">525</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">error</span><span class="p">(</span><span class="n">validation_errors</span><span class="p">)</span>
+</span><span id="validate-526"><a href="#validate-526"><span class="linenos">526</span></a> <span class="k">raise</span> <span class="n">PhenValidationException</span><span class="p">(</span>
+</span><span id="validate-527"><a href="#validate-527"><span class="linenos">527</span></a> <span class="sa">f</span><span class="s2">"Configuration file </span><span class="si">{</span><span class="nb">str</span><span class="p">(</span><span class="n">config_path</span><span class="o">.</span><span class="n">resolve</span><span class="p">())</span><span class="si">}</span><span class="s2"> failed validation"</span><span class="p">,</span>
+</span><span id="validate-528"><a href="#validate-528"><span class="linenos">528</span></a> <span class="n">validation_errors</span><span class="p">,</span>
+</span><span id="validate-529"><a href="#validate-529"><span class="linenos">529</span></a> <span class="p">)</span>
+</span><span id="validate-530"><a href="#validate-530"><span class="linenos">530</span></a>
+</span><span id="validate-531"><a href="#validate-531"><span class="linenos">531</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Phenotype validated successfully"</span><span class="p">)</span>
+</span></pre></div>
+
+
+ <div class="docstring"><p>Validates the phenotype directory is a git repo with standard structure</p>
+</div>
+
+
+ </section>
+ <section id="read_table_file">
+ <input id="read_table_file-view-source" class="view-source-toggle-state" type="checkbox" aria-hidden="true" tabindex="-1">
+<div class="attr function">
+
+ <span class="def">def</span>
+ <span class="name">read_table_file</span><span class="signature pdoc-code condensed">(<span class="param"><span class="n">path</span><span class="p">:</span> <span class="n">pathlib</span><span class="o">.</span><span class="n">Path</span>, </span><span class="param"><span class="n">excel_sheet</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="s1">''</span></span><span class="return-annotation">):</span></span>
+
+ <label class="view-source-button" for="read_table_file-view-source"><span>View Source</span></label>
+
+ </div>
+ <a class="headerlink" href="#read_table_file"></a>
+ <div class="pdoc-code codehilite"><pre><span></span><span id="read_table_file-534"><a href="#read_table_file-534"><span class="linenos">534</span></a><span class="k">def</span><span class="w"> </span><span class="nf">read_table_file</span><span class="p">(</span><span class="n">path</span><span class="p">:</span> <span class="n">Path</span><span class="p">,</span> <span class="n">excel_sheet</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="s2">""</span><span class="p">):</span>
+</span><span id="read_table_file-535"><a href="#read_table_file-535"><span class="linenos">535</span></a><span class="w"> </span><span class="sd">"""</span>
+</span><span id="read_table_file-536"><a href="#read_table_file-536"><span class="linenos">536</span></a><span class="sd"> Load Code List File</span>
+</span><span id="read_table_file-537"><a href="#read_table_file-537"><span class="linenos">537</span></a><span class="sd"> """</span>
+</span><span id="read_table_file-538"><a href="#read_table_file-538"><span class="linenos">538</span></a>
+</span><span id="read_table_file-539"><a href="#read_table_file-539"><span class="linenos">539</span></a> <span class="n">path</span> <span class="o">=</span> <span class="n">path</span><span class="o">.</span><span class="n">resolve</span><span class="p">()</span>
+</span><span id="read_table_file-540"><a href="#read_table_file-540"><span class="linenos">540</span></a> <span class="k">if</span> <span class="n">path</span><span class="o">.</span><span class="n">suffix</span> <span class="o">==</span> <span class="s2">".csv"</span><span class="p">:</span>
+</span><span id="read_table_file-541"><a href="#read_table_file-541"><span class="linenos">541</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">read_csv</span><span class="p">(</span><span class="n">path</span><span class="p">,</span> <span class="n">dtype</span><span class="o">=</span><span class="nb">str</span><span class="p">)</span>
+</span><span id="read_table_file-542"><a href="#read_table_file-542"><span class="linenos">542</span></a> <span class="k">elif</span> <span class="n">path</span><span class="o">.</span><span class="n">suffix</span> <span class="o">==</span> <span class="s2">".xlsx"</span> <span class="ow">or</span> <span class="n">path</span><span class="o">.</span><span class="n">suffix</span> <span class="o">==</span> <span class="s2">".xls"</span><span class="p">:</span>
+</span><span id="read_table_file-543"><a href="#read_table_file-543"><span class="linenos">543</span></a> <span class="k">if</span> <span class="n">excel_sheet</span> <span class="o">!=</span> <span class="s2">""</span><span class="p">:</span>
+</span><span id="read_table_file-544"><a href="#read_table_file-544"><span class="linenos">544</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">read_excel</span><span class="p">(</span><span class="n">path</span><span class="p">,</span> <span class="n">sheet_name</span><span class="o">=</span><span class="n">excel_sheet</span><span class="p">,</span> <span class="n">dtype</span><span class="o">=</span><span class="nb">str</span><span class="p">)</span>
+</span><span id="read_table_file-545"><a href="#read_table_file-545"><span class="linenos">545</span></a> <span class="k">else</span><span class="p">:</span>
+</span><span id="read_table_file-546"><a href="#read_table_file-546"><span class="linenos">546</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">read_excel</span><span class="p">(</span><span class="n">path</span><span class="p">,</span> <span class="n">dtype</span><span class="o">=</span><span class="nb">str</span><span class="p">)</span>
+</span><span id="read_table_file-547"><a href="#read_table_file-547"><span class="linenos">547</span></a> <span class="k">elif</span> <span class="n">path</span><span class="o">.</span><span class="n">suffix</span> <span class="o">==</span> <span class="s2">".dta"</span><span class="p">:</span>
+</span><span id="read_table_file-548"><a href="#read_table_file-548"><span class="linenos">548</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">read_stata</span><span class="p">(</span><span class="n">path</span><span class="p">)</span>
+</span><span id="read_table_file-549"><a href="#read_table_file-549"><span class="linenos">549</span></a> <span class="k">else</span><span class="p">:</span>
+</span><span id="read_table_file-550"><a href="#read_table_file-550"><span class="linenos">550</span></a> <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span>
+</span><span id="read_table_file-551"><a href="#read_table_file-551"><span class="linenos">551</span></a> <span class="sa">f</span><span class="s2">"Unsupported filetype </span><span class="si">{</span><span class="n">path</span><span class="o">.</span><span class="n">suffix</span><span class="si">}</span><span class="s2">, only support</span><span class="si">{</span><span class="n">CODE_FILE_TYPES</span><span class="si">}</span><span class="s2"> code file types"</span>
+</span><span id="read_table_file-552"><a href="#read_table_file-552"><span class="linenos">552</span></a> <span class="p">)</span>
+</span><span id="read_table_file-553"><a href="#read_table_file-553"><span class="linenos">553</span></a>
+</span><span id="read_table_file-554"><a href="#read_table_file-554"><span class="linenos">554</span></a> <span class="k">return</span> <span class="n">df</span>
+</span></pre></div>
+
+
+ <div class="docstring"><p>Load Code List File</p>
+</div>
+
+
+ </section>
+ <section id="process_actions">
+ <input id="process_actions-view-source" class="view-source-toggle-state" type="checkbox" aria-hidden="true" tabindex="-1">
+<div class="attr function">
+
+ <span class="def">def</span>
+ <span class="name">process_actions</span><span class="signature pdoc-code multiline">(<span class="param"> <span class="n">df</span><span class="p">:</span> <span class="n">pandas</span><span class="o">.</span><span class="n">core</span><span class="o">.</span><span class="n">frame</span><span class="o">.</span><span class="n">DataFrame</span>,</span><span class="param"> <span class="n">concept_set</span><span class="p">:</span> <span class="nb">dict</span></span><span class="return-annotation">) -> <span class="n">pandas</span><span class="o">.</span><span class="n">core</span><span class="o">.</span><span class="n">frame</span><span class="o">.</span><span class="n">DataFrame</span>:</span></span>
+
+ <label class="view-source-button" for="process_actions-view-source"><span>View Source</span></label>
+
+ </div>
+ <a class="headerlink" href="#process_actions"></a>
+ <div class="pdoc-code codehilite"><pre><span></span><span id="process_actions-557"><a href="#process_actions-557"><span class="linenos">557</span></a><span class="k">def</span><span class="w"> </span><span class="nf">process_actions</span><span class="p">(</span><span class="n">df</span><span class="p">:</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">,</span> <span class="n">concept_set</span><span class="p">:</span> <span class="nb">dict</span><span class="p">)</span> <span class="o">-></span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">:</span>
+</span><span id="process_actions-558"><a href="#process_actions-558"><span class="linenos">558</span></a> <span class="c1"># Perform Structural Changes to file before preprocessing</span>
+</span><span id="process_actions-559"><a href="#process_actions-559"><span class="linenos">559</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="s2">"Processing file structural actions"</span><span class="p">)</span>
+</span><span id="process_actions-560"><a href="#process_actions-560"><span class="linenos">560</span></a> <span class="k">if</span> <span class="p">(</span>
+</span><span id="process_actions-561"><a href="#process_actions-561"><span class="linenos">561</span></a> <span class="s2">"actions"</span> <span class="ow">in</span> <span class="n">concept_set</span><span class="p">[</span><span class="s2">"file"</span><span class="p">]</span>
+</span><span id="process_actions-562"><a href="#process_actions-562"><span class="linenos">562</span></a> <span class="ow">and</span> <span class="s2">"split_col"</span> <span class="ow">in</span> <span class="n">concept_set</span><span class="p">[</span><span class="s2">"file"</span><span class="p">][</span><span class="s2">"actions"</span><span class="p">]</span>
+</span><span id="process_actions-563"><a href="#process_actions-563"><span class="linenos">563</span></a> <span class="ow">and</span> <span class="s2">"codes_col"</span> <span class="ow">in</span> <span class="n">concept_set</span><span class="p">[</span><span class="s2">"file"</span><span class="p">][</span><span class="s2">"actions"</span><span class="p">]</span>
+</span><span id="process_actions-564"><a href="#process_actions-564"><span class="linenos">564</span></a> <span class="p">):</span>
+</span><span id="process_actions-565"><a href="#process_actions-565"><span class="linenos">565</span></a> <span class="n">split_col</span> <span class="o">=</span> <span class="n">concept_set</span><span class="p">[</span><span class="s2">"file"</span><span class="p">][</span><span class="s2">"actions"</span><span class="p">][</span><span class="s2">"split_col"</span><span class="p">]</span>
+</span><span id="process_actions-566"><a href="#process_actions-566"><span class="linenos">566</span></a> <span class="n">codes_col</span> <span class="o">=</span> <span class="n">concept_set</span><span class="p">[</span><span class="s2">"file"</span><span class="p">][</span><span class="s2">"actions"</span><span class="p">][</span><span class="s2">"codes_col"</span><span class="p">]</span>
+</span><span id="process_actions-567"><a href="#process_actions-567"><span class="linenos">567</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span>
+</span><span id="process_actions-568"><a href="#process_actions-568"><span class="linenos">568</span></a> <span class="s2">"Action: Splitting"</span><span class="p">,</span>
+</span><span id="process_actions-569"><a href="#process_actions-569"><span class="linenos">569</span></a> <span class="n">split_col</span><span class="p">,</span>
+</span><span id="process_actions-570"><a href="#process_actions-570"><span class="linenos">570</span></a> <span class="s2">"column into:"</span><span class="p">,</span>
+</span><span id="process_actions-571"><a href="#process_actions-571"><span class="linenos">571</span></a> <span class="n">df</span><span class="p">[</span><span class="n">split_col</span><span class="p">]</span><span class="o">.</span><span class="n">unique</span><span class="p">(),</span>
+</span><span id="process_actions-572"><a href="#process_actions-572"><span class="linenos">572</span></a> <span class="p">)</span>
+</span><span id="process_actions-573"><a href="#process_actions-573"><span class="linenos">573</span></a> <span class="n">codes</span> <span class="o">=</span> <span class="n">df</span><span class="p">[</span><span class="n">codes_col</span><span class="p">]</span>
+</span><span id="process_actions-574"><a href="#process_actions-574"><span class="linenos">574</span></a> <span class="n">oh</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">get_dummies</span><span class="p">(</span><span class="n">df</span><span class="p">[</span><span class="n">split_col</span><span class="p">],</span> <span class="n">dtype</span><span class="o">=</span><span class="nb">bool</span><span class="p">)</span> <span class="c1"># one hot encode</span>
+</span><span id="process_actions-575"><a href="#process_actions-575"><span class="linenos">575</span></a> <span class="n">oh</span> <span class="o">=</span> <span class="n">oh</span><span class="o">.</span><span class="n">where</span><span class="p">((</span><span class="n">oh</span> <span class="o">!=</span> <span class="kc">True</span><span class="p">),</span> <span class="n">codes</span><span class="p">,</span> <span class="n">axis</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span> <span class="c1"># fill in 1s with codes</span>
+</span><span id="process_actions-576"><a href="#process_actions-576"><span class="linenos">576</span></a> <span class="n">oh</span><span class="p">[</span><span class="n">oh</span> <span class="o">==</span> <span class="kc">False</span><span class="p">]</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">nan</span> <span class="c1"># replace 0s with None</span>
+</span><span id="process_actions-577"><a href="#process_actions-577"><span class="linenos">577</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">concat</span><span class="p">([</span><span class="n">df</span><span class="p">,</span> <span class="n">oh</span><span class="p">],</span> <span class="n">axis</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span> <span class="c1"># merge in new columns</span>
+</span><span id="process_actions-578"><a href="#process_actions-578"><span class="linenos">578</span></a>
+</span><span id="process_actions-579"><a href="#process_actions-579"><span class="linenos">579</span></a> <span class="k">return</span> <span class="n">df</span>
+</span></pre></div>
+
+
+
+
+ </section>
+ <section id="preprocess_source_concepts">
+ <input id="preprocess_source_concepts-view-source" class="view-source-toggle-state" type="checkbox" aria-hidden="true" tabindex="-1">
+<div class="attr function">
+
+ <span class="def">def</span>
+ <span class="name">preprocess_source_concepts</span><span class="signature pdoc-code multiline">(<span class="param"> <span class="n">df</span><span class="p">:</span> <span class="n">pandas</span><span class="o">.</span><span class="n">core</span><span class="o">.</span><span class="n">frame</span><span class="o">.</span><span class="n">DataFrame</span>,</span><span class="param"> <span class="n">concept_set</span><span class="p">:</span> <span class="nb">dict</span>,</span><span class="param"> <span class="n">code_file_path</span><span class="p">:</span> <span class="n">pathlib</span><span class="o">.</span><span class="n">Path</span></span><span class="return-annotation">) -> <span class="n">Tuple</span><span class="p">[</span><span class="n">pandas</span><span class="o">.</span><span class="n">core</span><span class="o">.</span><span class="n">frame</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">,</span> <span class="nb">list</span><span class="p">]</span>:</span></span>
+
+ <label class="view-source-button" for="preprocess_source_concepts-view-source"><span>View Source</span></label>
+
+ </div>
+ <a class="headerlink" href="#preprocess_source_concepts"></a>
+ <div class="pdoc-code codehilite"><pre><span></span><span id="preprocess_source_concepts-583"><a href="#preprocess_source_concepts-583"><span class="linenos">583</span></a><span class="k">def</span><span class="w"> </span><span class="nf">preprocess_source_concepts</span><span class="p">(</span>
+</span><span id="preprocess_source_concepts-584"><a href="#preprocess_source_concepts-584"><span class="linenos">584</span></a> <span class="n">df</span><span class="p">:</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">,</span> <span class="n">concept_set</span><span class="p">:</span> <span class="nb">dict</span><span class="p">,</span> <span class="n">code_file_path</span><span class="p">:</span> <span class="n">Path</span>
+</span><span id="preprocess_source_concepts-585"><a href="#preprocess_source_concepts-585"><span class="linenos">585</span></a><span class="p">)</span> <span class="o">-></span> <span class="n">Tuple</span><span class="p">[</span><span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">,</span> <span class="nb">list</span><span class="p">]:</span>
+</span><span id="preprocess_source_concepts-586"><a href="#preprocess_source_concepts-586"><span class="linenos">586</span></a><span class="w"> </span><span class="sd">"""Parses each column individually - Order and length will not be preserved!"""</span>
+</span><span id="preprocess_source_concepts-587"><a href="#preprocess_source_concepts-587"><span class="linenos">587</span></a> <span class="n">out</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">([])</span> <span class="c1"># create output df to append to</span>
+</span><span id="preprocess_source_concepts-588"><a href="#preprocess_source_concepts-588"><span class="linenos">588</span></a> <span class="n">code_errors</span> <span class="o">=</span> <span class="p">[]</span> <span class="c1"># list of errors from processing</span>
+</span><span id="preprocess_source_concepts-589"><a href="#preprocess_source_concepts-589"><span class="linenos">589</span></a>
+</span><span id="preprocess_source_concepts-590"><a href="#preprocess_source_concepts-590"><span class="linenos">590</span></a> <span class="c1"># remove unnamed columns due to extra commas, missing headers, or incorrect parsing</span>
+</span><span id="preprocess_source_concepts-591"><a href="#preprocess_source_concepts-591"><span class="linenos">591</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">df</span><span class="o">.</span><span class="n">drop</span><span class="p">(</span><span class="n">columns</span><span class="o">=</span><span class="p">[</span><span class="n">col</span> <span class="k">for</span> <span class="n">col</span> <span class="ow">in</span> <span class="n">df</span><span class="o">.</span><span class="n">columns</span> <span class="k">if</span> <span class="s2">"Unnamed"</span> <span class="ow">in</span> <span class="n">col</span><span class="p">])</span>
+</span><span id="preprocess_source_concepts-592"><a href="#preprocess_source_concepts-592"><span class="linenos">592</span></a>
+</span><span id="preprocess_source_concepts-593"><a href="#preprocess_source_concepts-593"><span class="linenos">593</span></a> <span class="c1"># Preprocess codes</span>
+</span><span id="preprocess_source_concepts-594"><a href="#preprocess_source_concepts-594"><span class="linenos">594</span></a> <span class="n">code_types</span> <span class="o">=</span> <span class="n">parse</span><span class="o">.</span><span class="n">CodeTypeParser</span><span class="p">()</span><span class="o">.</span><span class="n">code_types</span>
+</span><span id="preprocess_source_concepts-595"><a href="#preprocess_source_concepts-595"><span class="linenos">595</span></a> <span class="k">for</span> <span class="n">code_type</span> <span class="ow">in</span> <span class="n">concept_set</span><span class="p">[</span><span class="s2">"file"</span><span class="p">][</span><span class="s2">"columns"</span><span class="p">]:</span>
+</span><span id="preprocess_source_concepts-596"><a href="#preprocess_source_concepts-596"><span class="linenos">596</span></a> <span class="n">parser</span> <span class="o">=</span> <span class="n">code_types</span><span class="p">[</span><span class="n">code_type</span><span class="p">]</span>
+</span><span id="preprocess_source_concepts-597"><a href="#preprocess_source_concepts-597"><span class="linenos">597</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Processing </span><span class="si">{</span><span class="n">code_type</span><span class="si">}</span><span class="s2"> codes for </span><span class="si">{</span><span class="n">code_file_path</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+</span><span id="preprocess_source_concepts-598"><a href="#preprocess_source_concepts-598"><span class="linenos">598</span></a>
+</span><span id="preprocess_source_concepts-599"><a href="#preprocess_source_concepts-599"><span class="linenos">599</span></a> <span class="c1"># get codes by column name</span>
+</span><span id="preprocess_source_concepts-600"><a href="#preprocess_source_concepts-600"><span class="linenos">600</span></a> <span class="n">source_col_name</span> <span class="o">=</span> <span class="n">concept_set</span><span class="p">[</span><span class="s2">"file"</span><span class="p">][</span><span class="s2">"columns"</span><span class="p">][</span><span class="n">code_type</span><span class="p">]</span>
+</span><span id="preprocess_source_concepts-601"><a href="#preprocess_source_concepts-601"><span class="linenos">601</span></a> <span class="n">codes</span> <span class="o">=</span> <span class="n">df</span><span class="p">[</span><span class="n">source_col_name</span><span class="p">]</span><span class="o">.</span><span class="n">dropna</span><span class="p">()</span>
+</span><span id="preprocess_source_concepts-602"><a href="#preprocess_source_concepts-602"><span class="linenos">602</span></a> <span class="n">codes</span> <span class="o">=</span> <span class="n">codes</span><span class="o">.</span><span class="n">astype</span><span class="p">(</span><span class="nb">str</span><span class="p">)</span> <span class="c1"># convert to string</span>
+</span><span id="preprocess_source_concepts-603"><a href="#preprocess_source_concepts-603"><span class="linenos">603</span></a> <span class="n">codes</span> <span class="o">=</span> <span class="n">codes</span><span class="o">.</span><span class="n">str</span><span class="o">.</span><span class="n">strip</span><span class="p">()</span> <span class="c1"># remove excess spaces</span>
+</span><span id="preprocess_source_concepts-604"><a href="#preprocess_source_concepts-604"><span class="linenos">604</span></a>
+</span><span id="preprocess_source_concepts-605"><a href="#preprocess_source_concepts-605"><span class="linenos">605</span></a> <span class="c1"># process codes, validating them using parser and returning the errors</span>
+</span><span id="preprocess_source_concepts-606"><a href="#preprocess_source_concepts-606"><span class="linenos">606</span></a> <span class="n">codes</span><span class="p">,</span> <span class="n">errors</span> <span class="o">=</span> <span class="n">parser</span><span class="o">.</span><span class="n">process</span><span class="p">(</span><span class="n">codes</span><span class="p">,</span> <span class="n">code_file_path</span><span class="p">)</span>
+</span><span id="preprocess_source_concepts-607"><a href="#preprocess_source_concepts-607"><span class="linenos">607</span></a> <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">errors</span><span class="p">)</span> <span class="o">></span> <span class="mi">0</span><span class="p">:</span>
+</span><span id="preprocess_source_concepts-608"><a href="#preprocess_source_concepts-608"><span class="linenos">608</span></a> <span class="n">code_errors</span><span class="o">.</span><span class="n">extend</span><span class="p">(</span><span class="n">errors</span><span class="p">)</span>
+</span><span id="preprocess_source_concepts-609"><a href="#preprocess_source_concepts-609"><span class="linenos">609</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">warning</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Codes validation failed with </span><span class="si">{</span><span class="nb">len</span><span class="p">(</span><span class="n">errors</span><span class="p">)</span><span class="si">}</span><span class="s2"> errors"</span><span class="p">)</span>
+</span><span id="preprocess_source_concepts-610"><a href="#preprocess_source_concepts-610"><span class="linenos">610</span></a>
+</span><span id="preprocess_source_concepts-611"><a href="#preprocess_source_concepts-611"><span class="linenos">611</span></a> <span class="c1"># add processed codes to df</span>
+</span><span id="preprocess_source_concepts-612"><a href="#preprocess_source_concepts-612"><span class="linenos">612</span></a> <span class="n">new_col_name</span> <span class="o">=</span> <span class="sa">f</span><span class="s2">"</span><span class="si">{</span><span class="n">source_col_name</span><span class="si">}</span><span class="s2">_SOURCE"</span>
+</span><span id="preprocess_source_concepts-613"><a href="#preprocess_source_concepts-613"><span class="linenos">613</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">df</span><span class="o">.</span><span class="n">rename</span><span class="p">(</span><span class="n">columns</span><span class="o">=</span><span class="p">{</span><span class="n">source_col_name</span><span class="p">:</span> <span class="n">new_col_name</span><span class="p">})</span>
+</span><span id="preprocess_source_concepts-614"><a href="#preprocess_source_concepts-614"><span class="linenos">614</span></a> <span class="n">process_codes</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">({</span><span class="n">code_type</span><span class="p">:</span> <span class="n">codes</span><span class="p">})</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">df</span><span class="p">)</span>
+</span><span id="preprocess_source_concepts-615"><a href="#preprocess_source_concepts-615"><span class="linenos">615</span></a> <span class="n">out</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">concat</span><span class="p">(</span>
+</span><span id="preprocess_source_concepts-616"><a href="#preprocess_source_concepts-616"><span class="linenos">616</span></a> <span class="p">[</span><span class="n">out</span><span class="p">,</span> <span class="n">process_codes</span><span class="p">],</span>
+</span><span id="preprocess_source_concepts-617"><a href="#preprocess_source_concepts-617"><span class="linenos">617</span></a> <span class="n">ignore_index</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span>
+</span><span id="preprocess_source_concepts-618"><a href="#preprocess_source_concepts-618"><span class="linenos">618</span></a> <span class="p">)</span>
+</span><span id="preprocess_source_concepts-619"><a href="#preprocess_source_concepts-619"><span class="linenos">619</span></a>
+</span><span id="preprocess_source_concepts-620"><a href="#preprocess_source_concepts-620"><span class="linenos">620</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="n">out</span><span class="o">.</span><span class="n">head</span><span class="p">())</span>
+</span><span id="preprocess_source_concepts-621"><a href="#preprocess_source_concepts-621"><span class="linenos">621</span></a>
+</span><span id="preprocess_source_concepts-622"><a href="#preprocess_source_concepts-622"><span class="linenos">622</span></a> <span class="k">return</span> <span class="n">out</span><span class="p">,</span> <span class="n">code_errors</span>
+</span></pre></div>
+
+
+ <div class="docstring"><p>Parses each column individually - Order and length will not be preserved!</p>
+</div>
+
+
+ </section>
+ <section id="get_code_type_from_col_name">
+ <input id="get_code_type_from_col_name-view-source" class="view-source-toggle-state" type="checkbox" aria-hidden="true" tabindex="-1">
+<div class="attr function">
+
+ <span class="def">def</span>
+ <span class="name">get_code_type_from_col_name</span><span class="signature pdoc-code condensed">(<span class="param"><span class="n">col_name</span><span class="p">:</span> <span class="nb">str</span></span><span class="return-annotation">):</span></span>
+
+ <label class="view-source-button" for="get_code_type_from_col_name-view-source"><span>View Source</span></label>
+
+ </div>
+ <a class="headerlink" href="#get_code_type_from_col_name"></a>
+ <div class="pdoc-code codehilite"><pre><span></span><span id="get_code_type_from_col_name-625"><a href="#get_code_type_from_col_name-625"><span class="linenos">625</span></a><span class="k">def</span><span class="w"> </span><span class="nf">get_code_type_from_col_name</span><span class="p">(</span><span class="n">col_name</span><span class="p">:</span> <span class="nb">str</span><span class="p">):</span>
+</span><span id="get_code_type_from_col_name-626"><a href="#get_code_type_from_col_name-626"><span class="linenos">626</span></a> <span class="k">return</span> <span class="n">col_name</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s2">"_"</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span>
+</span></pre></div>
+
+
+
+
+ </section>
+ <section id="translate_codes">
+ <input id="translate_codes-view-source" class="view-source-toggle-state" type="checkbox" aria-hidden="true" tabindex="-1">
+<div class="attr function">
+
+ <span class="def">def</span>
+ <span class="name">translate_codes</span><span class="signature pdoc-code multiline">(<span class="param"> <span class="n">source_df</span><span class="p">:</span> <span class="n">pandas</span><span class="o">.</span><span class="n">core</span><span class="o">.</span><span class="n">frame</span><span class="o">.</span><span class="n">DataFrame</span>,</span><span class="param"> <span class="n">target_code_type</span><span class="p">:</span> <span class="nb">str</span>,</span><span class="param"> <span class="n">concept_name</span><span class="p">:</span> <span class="nb">str</span></span><span class="return-annotation">) -> <span class="n">pandas</span><span class="o">.</span><span class="n">core</span><span class="o">.</span><span class="n">frame</span><span class="o">.</span><span class="n">DataFrame</span>:</span></span>
+
+ <label class="view-source-button" for="translate_codes-view-source"><span>View Source</span></label>
+
+ </div>
+ <a class="headerlink" href="#translate_codes"></a>
+ <div class="pdoc-code codehilite"><pre><span></span><span id="translate_codes-630"><a href="#translate_codes-630"><span class="linenos">630</span></a><span class="k">def</span><span class="w"> </span><span class="nf">translate_codes</span><span class="p">(</span>
+</span><span id="translate_codes-631"><a href="#translate_codes-631"><span class="linenos">631</span></a> <span class="n">source_df</span><span class="p">:</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">,</span> <span class="n">target_code_type</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">concept_name</span><span class="p">:</span> <span class="nb">str</span>
+</span><span id="translate_codes-632"><a href="#translate_codes-632"><span class="linenos">632</span></a><span class="p">)</span> <span class="o">-></span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">:</span>
+</span><span id="translate_codes-633"><a href="#translate_codes-633"><span class="linenos">633</span></a><span class="w"> </span><span class="sd">"""Translates each source code type the source coding list into a target type and returns all conversions as a concept set"""</span>
+</span><span id="translate_codes-634"><a href="#translate_codes-634"><span class="linenos">634</span></a>
+</span><span id="translate_codes-635"><a href="#translate_codes-635"><span class="linenos">635</span></a> <span class="c1"># codes = pd.DataFrame([], dtype=str)</span>
+</span><span id="translate_codes-636"><a href="#translate_codes-636"><span class="linenos">636</span></a> <span class="n">codes</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">(</span>
+</span><span id="translate_codes-637"><a href="#translate_codes-637"><span class="linenos">637</span></a> <span class="n">columns</span><span class="o">=</span><span class="p">[</span><span class="s2">"SOURCE_CONCEPT"</span><span class="p">,</span> <span class="s2">"SOURCE_CONCEPT_TYPE"</span><span class="p">,</span> <span class="s2">"CONCEPT"</span><span class="p">],</span> <span class="n">dtype</span><span class="o">=</span><span class="s2">"string"</span>
+</span><span id="translate_codes-638"><a href="#translate_codes-638"><span class="linenos">638</span></a> <span class="p">)</span>
+</span><span id="translate_codes-639"><a href="#translate_codes-639"><span class="linenos">639</span></a> <span class="c1"># Convert codes to target type</span>
+</span><span id="translate_codes-640"><a href="#translate_codes-640"><span class="linenos">640</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Converting to target code type </span><span class="si">{</span><span class="n">target_code_type</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+</span><span id="translate_codes-641"><a href="#translate_codes-641"><span class="linenos">641</span></a>
+</span><span id="translate_codes-642"><a href="#translate_codes-642"><span class="linenos">642</span></a> <span class="k">for</span> <span class="n">source_code_type</span> <span class="ow">in</span> <span class="n">source_df</span><span class="o">.</span><span class="n">columns</span><span class="p">:</span>
+</span><span id="translate_codes-643"><a href="#translate_codes-643"><span class="linenos">643</span></a>
+</span><span id="translate_codes-644"><a href="#translate_codes-644"><span class="linenos">644</span></a> <span class="c1"># if target code type is the same as thet source code type, no translation, just appending source as target</span>
+</span><span id="translate_codes-645"><a href="#translate_codes-645"><span class="linenos">645</span></a> <span class="k">if</span> <span class="n">source_code_type</span> <span class="o">==</span> <span class="n">target_code_type</span><span class="p">:</span>
+</span><span id="translate_codes-646"><a href="#translate_codes-646"><span class="linenos">646</span></a> <span class="n">copy_df</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">(</span>
+</span><span id="translate_codes-647"><a href="#translate_codes-647"><span class="linenos">647</span></a> <span class="p">{</span>
+</span><span id="translate_codes-648"><a href="#translate_codes-648"><span class="linenos">648</span></a> <span class="s2">"SOURCE_CONCEPT"</span><span class="p">:</span> <span class="n">source_df</span><span class="p">[</span><span class="n">source_code_type</span><span class="p">],</span>
+</span><span id="translate_codes-649"><a href="#translate_codes-649"><span class="linenos">649</span></a> <span class="s2">"SOURCE_CONCEPT_TYPE"</span><span class="p">:</span> <span class="n">source_code_type</span><span class="p">,</span>
+</span><span id="translate_codes-650"><a href="#translate_codes-650"><span class="linenos">650</span></a> <span class="s2">"CONCEPT"</span><span class="p">:</span> <span class="n">source_df</span><span class="p">[</span><span class="n">source_code_type</span><span class="p">],</span>
+</span><span id="translate_codes-651"><a href="#translate_codes-651"><span class="linenos">651</span></a> <span class="p">}</span>
+</span><span id="translate_codes-652"><a href="#translate_codes-652"><span class="linenos">652</span></a> <span class="p">)</span>
+</span><span id="translate_codes-653"><a href="#translate_codes-653"><span class="linenos">653</span></a> <span class="n">codes</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">concat</span><span class="p">([</span><span class="n">codes</span><span class="p">,</span> <span class="n">copy_df</span><span class="p">])</span>
+</span><span id="translate_codes-654"><a href="#translate_codes-654"><span class="linenos">654</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span>
+</span><span id="translate_codes-655"><a href="#translate_codes-655"><span class="linenos">655</span></a> <span class="sa">f</span><span class="s2">"Target code type </span><span class="si">{</span><span class="n">target_code_type</span><span class="si">}</span><span class="s2"> is the same as source code type </span><span class="si">{</span><span class="nb">len</span><span class="p">(</span><span class="n">source_df</span><span class="p">)</span><span class="si">}</span><span class="s2">, copying codes rather than translating"</span>
+</span><span id="translate_codes-656"><a href="#translate_codes-656"><span class="linenos">656</span></a> <span class="p">)</span>
+</span><span id="translate_codes-657"><a href="#translate_codes-657"><span class="linenos">657</span></a> <span class="k">else</span><span class="p">:</span>
+</span><span id="translate_codes-658"><a href="#translate_codes-658"><span class="linenos">658</span></a> <span class="c1"># get the translation filename using source to target code types</span>
+</span><span id="translate_codes-659"><a href="#translate_codes-659"><span class="linenos">659</span></a> <span class="n">filename</span> <span class="o">=</span> <span class="sa">f</span><span class="s2">"</span><span class="si">{</span><span class="n">source_code_type</span><span class="si">}</span><span class="s2">_to_</span><span class="si">{</span><span class="n">target_code_type</span><span class="si">}</span><span class="s2">.parquet"</span>
+</span><span id="translate_codes-660"><a href="#translate_codes-660"><span class="linenos">660</span></a> <span class="n">map_path</span> <span class="o">=</span> <span class="n">trud</span><span class="o">.</span><span class="n">PROCESSED_PATH</span> <span class="o">/</span> <span class="n">filename</span>
+</span><span id="translate_codes-661"><a href="#translate_codes-661"><span class="linenos">661</span></a>
+</span><span id="translate_codes-662"><a href="#translate_codes-662"><span class="linenos">662</span></a> <span class="c1"># do the mapping if it exists</span>
+</span><span id="translate_codes-663"><a href="#translate_codes-663"><span class="linenos">663</span></a> <span class="k">if</span> <span class="n">map_path</span><span class="o">.</span><span class="n">exists</span><span class="p">():</span>
+</span><span id="translate_codes-664"><a href="#translate_codes-664"><span class="linenos">664</span></a> <span class="c1"># get mapping</span>
+</span><span id="translate_codes-665"><a href="#translate_codes-665"><span class="linenos">665</span></a> <span class="n">df_map</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">read_parquet</span><span class="p">(</span><span class="n">map_path</span><span class="p">)</span>
+</span><span id="translate_codes-666"><a href="#translate_codes-666"><span class="linenos">666</span></a>
+</span><span id="translate_codes-667"><a href="#translate_codes-667"><span class="linenos">667</span></a> <span class="c1"># do mapping</span>
+</span><span id="translate_codes-668"><a href="#translate_codes-668"><span class="linenos">668</span></a> <span class="n">translated_df</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">merge</span><span class="p">(</span>
+</span><span id="translate_codes-669"><a href="#translate_codes-669"><span class="linenos">669</span></a> <span class="n">source_df</span><span class="p">[</span><span class="n">source_code_type</span><span class="p">],</span> <span class="n">df_map</span><span class="p">,</span> <span class="n">how</span><span class="o">=</span><span class="s2">"left"</span>
+</span><span id="translate_codes-670"><a href="#translate_codes-670"><span class="linenos">670</span></a> <span class="p">)</span>
+</span><span id="translate_codes-671"><a href="#translate_codes-671"><span class="linenos">671</span></a>
+</span><span id="translate_codes-672"><a href="#translate_codes-672"><span class="linenos">672</span></a> <span class="c1"># normalise the output</span>
+</span><span id="translate_codes-673"><a href="#translate_codes-673"><span class="linenos">673</span></a> <span class="n">translated_df</span><span class="o">.</span><span class="n">columns</span> <span class="o">=</span> <span class="p">[</span><span class="s2">"SOURCE_CONCEPT"</span><span class="p">,</span> <span class="s2">"CONCEPT"</span><span class="p">]</span>
+</span><span id="translate_codes-674"><a href="#translate_codes-674"><span class="linenos">674</span></a> <span class="n">translated_df</span><span class="p">[</span><span class="s2">"SOURCE_CONCEPT_TYPE"</span><span class="p">]</span> <span class="o">=</span> <span class="n">source_code_type</span>
+</span><span id="translate_codes-675"><a href="#translate_codes-675"><span class="linenos">675</span></a>
+</span><span id="translate_codes-676"><a href="#translate_codes-676"><span class="linenos">676</span></a> <span class="c1"># add to list of codes</span>
+</span><span id="translate_codes-677"><a href="#translate_codes-677"><span class="linenos">677</span></a> <span class="n">codes</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">concat</span><span class="p">([</span><span class="n">codes</span><span class="p">,</span> <span class="n">translated_df</span><span class="p">])</span>
+</span><span id="translate_codes-678"><a href="#translate_codes-678"><span class="linenos">678</span></a>
+</span><span id="translate_codes-679"><a href="#translate_codes-679"><span class="linenos">679</span></a> <span class="k">else</span><span class="p">:</span>
+</span><span id="translate_codes-680"><a href="#translate_codes-680"><span class="linenos">680</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">warning</span><span class="p">(</span>
+</span><span id="translate_codes-681"><a href="#translate_codes-681"><span class="linenos">681</span></a> <span class="sa">f</span><span class="s2">"No mapping from </span><span class="si">{</span><span class="n">source_code_type</span><span class="si">}</span><span class="s2"> to </span><span class="si">{</span><span class="n">target_code_type</span><span class="si">}</span><span class="s2">, file </span><span class="si">{</span><span class="nb">str</span><span class="p">(</span><span class="n">map_path</span><span class="o">.</span><span class="n">resolve</span><span class="p">())</span><span class="si">}</span><span class="s2"> does not exist"</span>
+</span><span id="translate_codes-682"><a href="#translate_codes-682"><span class="linenos">682</span></a> <span class="p">)</span>
+</span><span id="translate_codes-683"><a href="#translate_codes-683"><span class="linenos">683</span></a>
+</span><span id="translate_codes-684"><a href="#translate_codes-684"><span class="linenos">684</span></a> <span class="n">codes</span> <span class="o">=</span> <span class="n">codes</span><span class="o">.</span><span class="n">dropna</span><span class="p">()</span> <span class="c1"># delete NaNs</span>
+</span><span id="translate_codes-685"><a href="#translate_codes-685"><span class="linenos">685</span></a>
+</span><span id="translate_codes-686"><a href="#translate_codes-686"><span class="linenos">686</span></a> <span class="c1"># added concept set type to output if any translations</span>
+</span><span id="translate_codes-687"><a href="#translate_codes-687"><span class="linenos">687</span></a> <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">codes</span><span class="o">.</span><span class="n">index</span><span class="p">)</span> <span class="o">></span> <span class="mi">0</span><span class="p">:</span>
+</span><span id="translate_codes-688"><a href="#translate_codes-688"><span class="linenos">688</span></a> <span class="n">codes</span><span class="p">[</span><span class="s2">"CONCEPT_SET"</span><span class="p">]</span> <span class="o">=</span> <span class="n">concept_name</span>
+</span><span id="translate_codes-689"><a href="#translate_codes-689"><span class="linenos">689</span></a> <span class="k">else</span><span class="p">:</span>
+</span><span id="translate_codes-690"><a href="#translate_codes-690"><span class="linenos">690</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="sa">f</span><span class="s2">"No codes converted with target code type </span><span class="si">{</span><span class="n">target_code_type</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+</span><span id="translate_codes-691"><a href="#translate_codes-691"><span class="linenos">691</span></a>
+</span><span id="translate_codes-692"><a href="#translate_codes-692"><span class="linenos">692</span></a> <span class="k">return</span> <span class="n">codes</span>
+</span></pre></div>
+
+
+ <div class="docstring"><p>Translates each source code type the source coding list into a target type and returns all conversions as a concept set</p>
+</div>
+
+
+ </section>
+ <section id="sql_row_exist">
+ <input id="sql_row_exist-view-source" class="view-source-toggle-state" type="checkbox" aria-hidden="true" tabindex="-1">
+<div class="attr function">
+
+ <span class="def">def</span>
+ <span class="name">sql_row_exist</span><span class="signature pdoc-code condensed">(<span class="param"><span class="n">conn</span><span class="p">:</span> <span class="n">sqlite3</span><span class="o">.</span><span class="n">Connection</span>, </span><span class="param"><span class="n">table</span><span class="p">:</span> <span class="nb">str</span>, </span><span class="param"><span class="n">column</span><span class="p">:</span> <span class="nb">str</span>, </span><span class="param"><span class="n">value</span><span class="p">:</span> <span class="nb">str</span></span><span class="return-annotation">) -> <span class="nb">bool</span>:</span></span>
+
+ <label class="view-source-button" for="sql_row_exist-view-source"><span>View Source</span></label>
+
+ </div>
+ <a class="headerlink" href="#sql_row_exist"></a>
+ <div class="pdoc-code codehilite"><pre><span></span><span id="sql_row_exist-695"><a href="#sql_row_exist-695"><span class="linenos">695</span></a><span class="k">def</span><span class="w"> </span><span class="nf">sql_row_exist</span><span class="p">(</span>
+</span><span id="sql_row_exist-696"><a href="#sql_row_exist-696"><span class="linenos">696</span></a> <span class="n">conn</span><span class="p">:</span> <span class="n">sqlite3</span><span class="o">.</span><span class="n">Connection</span><span class="p">,</span> <span class="n">table</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">column</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">value</span><span class="p">:</span> <span class="nb">str</span>
+</span><span id="sql_row_exist-697"><a href="#sql_row_exist-697"><span class="linenos">697</span></a><span class="p">)</span> <span class="o">-></span> <span class="nb">bool</span><span class="p">:</span>
+</span><span id="sql_row_exist-698"><a href="#sql_row_exist-698"><span class="linenos">698</span></a> <span class="c1"># Execute and check if a result exists</span>
+</span><span id="sql_row_exist-699"><a href="#sql_row_exist-699"><span class="linenos">699</span></a> <span class="n">cur</span> <span class="o">=</span> <span class="n">conn</span><span class="o">.</span><span class="n">cursor</span><span class="p">()</span>
+</span><span id="sql_row_exist-700"><a href="#sql_row_exist-700"><span class="linenos">700</span></a> <span class="n">query</span> <span class="o">=</span> <span class="sa">f</span><span class="s2">"SELECT 1 FROM </span><span class="si">{</span><span class="n">table</span><span class="si">}</span><span class="s2"> WHERE </span><span class="si">{</span><span class="n">column</span><span class="si">}</span><span class="s2"> = ? LIMIT 1;"</span>
+</span><span id="sql_row_exist-701"><a href="#sql_row_exist-701"><span class="linenos">701</span></a> <span class="n">cur</span><span class="o">.</span><span class="n">execute</span><span class="p">(</span><span class="n">query</span><span class="p">,</span> <span class="p">(</span><span class="n">value</span><span class="p">,))</span>
+</span><span id="sql_row_exist-702"><a href="#sql_row_exist-702"><span class="linenos">702</span></a> <span class="n">exists</span> <span class="o">=</span> <span class="n">cur</span><span class="o">.</span><span class="n">fetchone</span><span class="p">()</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span>
+</span><span id="sql_row_exist-703"><a href="#sql_row_exist-703"><span class="linenos">703</span></a>
+</span><span id="sql_row_exist-704"><a href="#sql_row_exist-704"><span class="linenos">704</span></a> <span class="k">return</span> <span class="n">exists</span>
+</span></pre></div>
+
+
+
+
+ </section>
+ <section id="write_code_errors">
+ <input id="write_code_errors-view-source" class="view-source-toggle-state" type="checkbox" aria-hidden="true" tabindex="-1">
+<div class="attr function">
+
+ <span class="def">def</span>
+ <span class="name">write_code_errors</span><span class="signature pdoc-code condensed">(<span class="param"><span class="n">code_errors</span><span class="p">:</span> <span class="nb">list</span>, </span><span class="param"><span class="n">code_errors_path</span><span class="p">:</span> <span class="n">pathlib</span><span class="o">.</span><span class="n">Path</span></span><span class="return-annotation">):</span></span>
+
+ <label class="view-source-button" for="write_code_errors-view-source"><span>View Source</span></label>
+
+ </div>
+ <a class="headerlink" href="#write_code_errors"></a>
+ <div class="pdoc-code codehilite"><pre><span></span><span id="write_code_errors-707"><a href="#write_code_errors-707"><span class="linenos">707</span></a><span class="k">def</span><span class="w"> </span><span class="nf">write_code_errors</span><span class="p">(</span><span class="n">code_errors</span><span class="p">:</span> <span class="nb">list</span><span class="p">,</span> <span class="n">code_errors_path</span><span class="p">:</span> <span class="n">Path</span><span class="p">):</span>
+</span><span id="write_code_errors-708"><a href="#write_code_errors-708"><span class="linenos">708</span></a> <span class="n">err_df</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">(</span>
+</span><span id="write_code_errors-709"><a href="#write_code_errors-709"><span class="linenos">709</span></a> <span class="p">[</span>
+</span><span id="write_code_errors-710"><a href="#write_code_errors-710"><span class="linenos">710</span></a> <span class="p">{</span>
+</span><span id="write_code_errors-711"><a href="#write_code_errors-711"><span class="linenos">711</span></a> <span class="s2">"CONCEPT"</span><span class="p">:</span> <span class="s2">", "</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">err</span><span class="o">.</span><span class="n">codes</span><span class="p">[</span><span class="o">~</span><span class="n">err</span><span class="o">.</span><span class="n">mask</span><span class="p">]</span><span class="o">.</span><span class="n">tolist</span><span class="p">()),</span>
+</span><span id="write_code_errors-712"><a href="#write_code_errors-712"><span class="linenos">712</span></a> <span class="s2">"VOCABULARY"</span><span class="p">:</span> <span class="n">err</span><span class="o">.</span><span class="n">code_type</span><span class="p">,</span>
+</span><span id="write_code_errors-713"><a href="#write_code_errors-713"><span class="linenos">713</span></a> <span class="s2">"SOURCE"</span><span class="p">:</span> <span class="n">err</span><span class="o">.</span><span class="n">codes_file</span><span class="p">,</span>
+</span><span id="write_code_errors-714"><a href="#write_code_errors-714"><span class="linenos">714</span></a> <span class="s2">"CAUSE"</span><span class="p">:</span> <span class="n">err</span><span class="o">.</span><span class="n">message</span><span class="p">,</span>
+</span><span id="write_code_errors-715"><a href="#write_code_errors-715"><span class="linenos">715</span></a> <span class="p">}</span>
+</span><span id="write_code_errors-716"><a href="#write_code_errors-716"><span class="linenos">716</span></a> <span class="k">for</span> <span class="n">err</span> <span class="ow">in</span> <span class="n">code_errors</span>
+</span><span id="write_code_errors-717"><a href="#write_code_errors-717"><span class="linenos">717</span></a> <span class="p">]</span>
+</span><span id="write_code_errors-718"><a href="#write_code_errors-718"><span class="linenos">718</span></a> <span class="p">)</span>
+</span><span id="write_code_errors-719"><a href="#write_code_errors-719"><span class="linenos">719</span></a>
+</span><span id="write_code_errors-720"><a href="#write_code_errors-720"><span class="linenos">720</span></a> <span class="n">err_df</span> <span class="o">=</span> <span class="n">err_df</span><span class="o">.</span><span class="n">drop_duplicates</span><span class="p">()</span> <span class="c1"># Remove Duplicates from Error file</span>
+</span><span id="write_code_errors-721"><a href="#write_code_errors-721"><span class="linenos">721</span></a> <span class="n">err_df</span> <span class="o">=</span> <span class="n">err_df</span><span class="o">.</span><span class="n">sort_values</span><span class="p">(</span><span class="n">by</span><span class="o">=</span><span class="p">[</span><span class="s2">"SOURCE"</span><span class="p">,</span> <span class="s2">"VOCABULARY"</span><span class="p">,</span> <span class="s2">"CONCEPT"</span><span class="p">])</span>
+</span><span id="write_code_errors-722"><a href="#write_code_errors-722"><span class="linenos">722</span></a> <span class="n">err_df</span><span class="o">.</span><span class="n">to_csv</span><span class="p">(</span><span class="n">code_errors_path</span><span class="p">,</span> <span class="n">index</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span> <span class="n">mode</span><span class="o">=</span><span class="s2">"w"</span><span class="p">)</span>
+</span></pre></div>
+
+
+
+
+ </section>
+ <section id="write_vocab_version">
+ <input id="write_vocab_version-view-source" class="view-source-toggle-state" type="checkbox" aria-hidden="true" tabindex="-1">
+<div class="attr function">
+
+ <span class="def">def</span>
+ <span class="name">write_vocab_version</span><span class="signature pdoc-code condensed">(<span class="param"><span class="n">phen_path</span><span class="p">:</span> <span class="n">pathlib</span><span class="o">.</span><span class="n">Path</span></span><span class="return-annotation">):</span></span>
+
+ <label class="view-source-button" for="write_vocab_version-view-source"><span>View Source</span></label>
+
+ </div>
+ <a class="headerlink" href="#write_vocab_version"></a>
+ <div class="pdoc-code codehilite"><pre><span></span><span id="write_vocab_version-725"><a href="#write_vocab_version-725"><span class="linenos">725</span></a><span class="k">def</span><span class="w"> </span><span class="nf">write_vocab_version</span><span class="p">(</span><span class="n">phen_path</span><span class="p">:</span> <span class="n">Path</span><span class="p">):</span>
+</span><span id="write_vocab_version-726"><a href="#write_vocab_version-726"><span class="linenos">726</span></a> <span class="c1"># write the vocab version files</span>
+</span><span id="write_vocab_version-727"><a href="#write_vocab_version-727"><span class="linenos">727</span></a>
+</span><span id="write_vocab_version-728"><a href="#write_vocab_version-728"><span class="linenos">728</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="n">trud</span><span class="o">.</span><span class="n">VERSION_PATH</span><span class="o">.</span><span class="n">exists</span><span class="p">():</span>
+</span><span id="write_vocab_version-729"><a href="#write_vocab_version-729"><span class="linenos">729</span></a> <span class="k">raise</span> <span class="ne">FileNotFoundError</span><span class="p">(</span>
+</span><span id="write_vocab_version-730"><a href="#write_vocab_version-730"><span class="linenos">730</span></a> <span class="sa">f</span><span class="s2">"TRUD version path </span><span class="si">{</span><span class="n">trud</span><span class="o">.</span><span class="n">VERSION_PATH</span><span class="si">}</span><span class="s2"> does not exist, please check TRUD is installed"</span>
+</span><span id="write_vocab_version-731"><a href="#write_vocab_version-731"><span class="linenos">731</span></a> <span class="p">)</span>
+</span><span id="write_vocab_version-732"><a href="#write_vocab_version-732"><span class="linenos">732</span></a>
+</span><span id="write_vocab_version-733"><a href="#write_vocab_version-733"><span class="linenos">733</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="n">omop</span><span class="o">.</span><span class="n">VERSION_PATH</span><span class="o">.</span><span class="n">exists</span><span class="p">():</span>
+</span><span id="write_vocab_version-734"><a href="#write_vocab_version-734"><span class="linenos">734</span></a> <span class="k">raise</span> <span class="ne">FileNotFoundError</span><span class="p">(</span>
+</span><span id="write_vocab_version-735"><a href="#write_vocab_version-735"><span class="linenos">735</span></a> <span class="sa">f</span><span class="s2">"OMOP version path </span><span class="si">{</span><span class="n">omop</span><span class="o">.</span><span class="n">VERSION_PATH</span><span class="si">}</span><span class="s2"> does not exist, please check OMOP is installed"</span>
+</span><span id="write_vocab_version-736"><a href="#write_vocab_version-736"><span class="linenos">736</span></a> <span class="p">)</span>
+</span><span id="write_vocab_version-737"><a href="#write_vocab_version-737"><span class="linenos">737</span></a>
+</span><span id="write_vocab_version-738"><a href="#write_vocab_version-738"><span class="linenos">738</span></a> <span class="k">with</span> <span class="n">trud</span><span class="o">.</span><span class="n">VERSION_PATH</span><span class="o">.</span><span class="n">open</span><span class="p">(</span><span class="s2">"r"</span><span class="p">)</span> <span class="k">as</span> <span class="n">file</span><span class="p">:</span>
+</span><span id="write_vocab_version-739"><a href="#write_vocab_version-739"><span class="linenos">739</span></a> <span class="n">trud_version</span> <span class="o">=</span> <span class="n">yaml</span><span class="o">.</span><span class="n">safe_load</span><span class="p">(</span><span class="n">file</span><span class="p">)</span>
+</span><span id="write_vocab_version-740"><a href="#write_vocab_version-740"><span class="linenos">740</span></a>
+</span><span id="write_vocab_version-741"><a href="#write_vocab_version-741"><span class="linenos">741</span></a> <span class="k">with</span> <span class="n">omop</span><span class="o">.</span><span class="n">VERSION_PATH</span><span class="o">.</span><span class="n">open</span><span class="p">(</span><span class="s2">"r"</span><span class="p">)</span> <span class="k">as</span> <span class="n">file</span><span class="p">:</span>
+</span><span id="write_vocab_version-742"><a href="#write_vocab_version-742"><span class="linenos">742</span></a> <span class="n">omop_version</span> <span class="o">=</span> <span class="n">yaml</span><span class="o">.</span><span class="n">safe_load</span><span class="p">(</span><span class="n">file</span><span class="p">)</span>
+</span><span id="write_vocab_version-743"><a href="#write_vocab_version-743"><span class="linenos">743</span></a>
+</span><span id="write_vocab_version-744"><a href="#write_vocab_version-744"><span class="linenos">744</span></a> <span class="c1"># Create the combined YAML structure</span>
+</span><span id="write_vocab_version-745"><a href="#write_vocab_version-745"><span class="linenos">745</span></a> <span class="n">version_data</span> <span class="o">=</span> <span class="p">{</span>
+</span><span id="write_vocab_version-746"><a href="#write_vocab_version-746"><span class="linenos">746</span></a> <span class="s2">"versions"</span><span class="p">:</span> <span class="p">{</span>
+</span><span id="write_vocab_version-747"><a href="#write_vocab_version-747"><span class="linenos">747</span></a> <span class="s2">"acmc"</span><span class="p">:</span> <span class="n">acmc</span><span class="o">.</span><span class="n">__version__</span><span class="p">,</span>
+</span><span id="write_vocab_version-748"><a href="#write_vocab_version-748"><span class="linenos">748</span></a> <span class="s2">"trud"</span><span class="p">:</span> <span class="n">trud_version</span><span class="p">,</span>
+</span><span id="write_vocab_version-749"><a href="#write_vocab_version-749"><span class="linenos">749</span></a> <span class="s2">"omop"</span><span class="p">:</span> <span class="n">omop_version</span><span class="p">,</span>
+</span><span id="write_vocab_version-750"><a href="#write_vocab_version-750"><span class="linenos">750</span></a> <span class="p">}</span>
+</span><span id="write_vocab_version-751"><a href="#write_vocab_version-751"><span class="linenos">751</span></a> <span class="p">}</span>
+</span><span id="write_vocab_version-752"><a href="#write_vocab_version-752"><span class="linenos">752</span></a>
+</span><span id="write_vocab_version-753"><a href="#write_vocab_version-753"><span class="linenos">753</span></a> <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">phen_path</span> <span class="o">/</span> <span class="n">VOCAB_VERSION_FILE</span><span class="p">,</span> <span class="s2">"w"</span><span class="p">)</span> <span class="k">as</span> <span class="n">file</span><span class="p">:</span>
+</span><span id="write_vocab_version-754"><a href="#write_vocab_version-754"><span class="linenos">754</span></a> <span class="n">yaml</span><span class="o">.</span><span class="n">dump</span><span class="p">(</span>
+</span><span id="write_vocab_version-755"><a href="#write_vocab_version-755"><span class="linenos">755</span></a> <span class="n">version_data</span><span class="p">,</span>
+</span><span id="write_vocab_version-756"><a href="#write_vocab_version-756"><span class="linenos">756</span></a> <span class="n">file</span><span class="p">,</span>
+</span><span id="write_vocab_version-757"><a href="#write_vocab_version-757"><span class="linenos">757</span></a> <span class="n">Dumper</span><span class="o">=</span><span class="n">util</span><span class="o">.</span><span class="n">QuotedDumper</span><span class="p">,</span>
+</span><span id="write_vocab_version-758"><a href="#write_vocab_version-758"><span class="linenos">758</span></a> <span class="n">default_flow_style</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span>
+</span><span id="write_vocab_version-759"><a href="#write_vocab_version-759"><span class="linenos">759</span></a> <span class="n">sort_keys</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span>
+</span><span id="write_vocab_version-760"><a href="#write_vocab_version-760"><span class="linenos">760</span></a> <span class="n">default_style</span><span class="o">=</span><span class="s1">'"'</span><span class="p">,</span>
+</span><span id="write_vocab_version-761"><a href="#write_vocab_version-761"><span class="linenos">761</span></a> <span class="p">)</span>
+</span></pre></div>
+
+
+
+
+ </section>
+ <section id="map">
+ <input id="map-view-source" class="view-source-toggle-state" type="checkbox" aria-hidden="true" tabindex="-1">
+<div class="attr function">
+
+ <span class="def">def</span>
+ <span class="name">map</span><span class="signature pdoc-code condensed">(<span class="param"><span class="n">phen_dir</span><span class="p">:</span> <span class="nb">str</span>, </span><span class="param"><span class="n">target_code_type</span><span class="p">:</span> <span class="nb">str</span></span><span class="return-annotation">):</span></span>
+
+ <label class="view-source-button" for="map-view-source"><span>View Source</span></label>
+
+ </div>
+ <a class="headerlink" href="#map"></a>
+ <div class="pdoc-code codehilite"><pre><span></span><span id="map-764"><a href="#map-764"><span class="linenos">764</span></a><span class="k">def</span><span class="w"> </span><span class="nf">map</span><span class="p">(</span><span class="n">phen_dir</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">target_code_type</span><span class="p">:</span> <span class="nb">str</span><span class="p">):</span>
+</span><span id="map-765"><a href="#map-765"><span class="linenos">765</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Processing phenotype: </span><span class="si">{</span><span class="n">phen_dir</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+</span><span id="map-766"><a href="#map-766"><span class="linenos">766</span></a>
+</span><span id="map-767"><a href="#map-767"><span class="linenos">767</span></a> <span class="c1"># Validate configuration</span>
+</span><span id="map-768"><a href="#map-768"><span class="linenos">768</span></a> <span class="n">validate</span><span class="p">(</span><span class="n">phen_dir</span><span class="p">)</span>
+</span><span id="map-769"><a href="#map-769"><span class="linenos">769</span></a>
+</span><span id="map-770"><a href="#map-770"><span class="linenos">770</span></a> <span class="c1"># initialise paths</span>
+</span><span id="map-771"><a href="#map-771"><span class="linenos">771</span></a> <span class="n">phen_path</span> <span class="o">=</span> <span class="n">Path</span><span class="p">(</span><span class="n">phen_dir</span><span class="p">)</span>
+</span><span id="map-772"><a href="#map-772"><span class="linenos">772</span></a> <span class="n">config_path</span> <span class="o">=</span> <span class="n">phen_path</span> <span class="o">/</span> <span class="n">CONFIG_FILE</span>
+</span><span id="map-773"><a href="#map-773"><span class="linenos">773</span></a>
+</span><span id="map-774"><a href="#map-774"><span class="linenos">774</span></a> <span class="c1"># load configuration</span>
+</span><span id="map-775"><a href="#map-775"><span class="linenos">775</span></a> <span class="k">with</span> <span class="n">config_path</span><span class="o">.</span><span class="n">open</span><span class="p">(</span><span class="s2">"r"</span><span class="p">)</span> <span class="k">as</span> <span class="n">file</span><span class="p">:</span>
+</span><span id="map-776"><a href="#map-776"><span class="linenos">776</span></a> <span class="n">config</span> <span class="o">=</span> <span class="n">yaml</span><span class="o">.</span><span class="n">safe_load</span><span class="p">(</span><span class="n">file</span><span class="p">)</span>
+</span><span id="map-777"><a href="#map-777"><span class="linenos">777</span></a> <span class="n">phenotype</span> <span class="o">=</span> <span class="n">config</span><span class="p">[</span><span class="s2">"phenotype"</span><span class="p">]</span>
+</span><span id="map-778"><a href="#map-778"><span class="linenos">778</span></a>
+</span><span id="map-779"><a href="#map-779"><span class="linenos">779</span></a> <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">phenotype</span><span class="p">[</span><span class="s2">"map"</span><span class="p">])</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
+</span><span id="map-780"><a href="#map-780"><span class="linenos">780</span></a> <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="sa">f</span><span class="s2">"No map codes defined in the phenotype configuration"</span><span class="p">)</span>
+</span><span id="map-781"><a href="#map-781"><span class="linenos">781</span></a>
+</span><span id="map-782"><a href="#map-782"><span class="linenos">782</span></a> <span class="k">if</span> <span class="n">target_code_type</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span> <span class="ow">and</span> <span class="n">target_code_type</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">phenotype</span><span class="p">[</span><span class="s2">"map"</span><span class="p">]:</span>
+</span><span id="map-783"><a href="#map-783"><span class="linenos">783</span></a> <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span>
+</span><span id="map-784"><a href="#map-784"><span class="linenos">784</span></a> <span class="sa">f</span><span class="s2">"Target code type </span><span class="si">{</span><span class="n">target_code_type</span><span class="si">}</span><span class="s2"> not in phenotype configuration map </span><span class="si">{</span><span class="n">phenotype</span><span class="p">[</span><span class="s1">'map'</span><span class="p">]</span><span class="si">}</span><span class="s2">"</span>
+</span><span id="map-785"><a href="#map-785"><span class="linenos">785</span></a> <span class="p">)</span>
+</span><span id="map-786"><a href="#map-786"><span class="linenos">786</span></a>
+</span><span id="map-787"><a href="#map-787"><span class="linenos">787</span></a> <span class="k">if</span> <span class="n">target_code_type</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+</span><span id="map-788"><a href="#map-788"><span class="linenos">788</span></a> <span class="n">map_target_code_type</span><span class="p">(</span><span class="n">phen_path</span><span class="p">,</span> <span class="n">phenotype</span><span class="p">,</span> <span class="n">target_code_type</span><span class="p">)</span>
+</span><span id="map-789"><a href="#map-789"><span class="linenos">789</span></a> <span class="k">else</span><span class="p">:</span>
+</span><span id="map-790"><a href="#map-790"><span class="linenos">790</span></a> <span class="k">for</span> <span class="n">t</span> <span class="ow">in</span> <span class="n">phenotype</span><span class="p">[</span><span class="s2">"map"</span><span class="p">]:</span>
+</span><span id="map-791"><a href="#map-791"><span class="linenos">791</span></a> <span class="n">map_target_code_type</span><span class="p">(</span><span class="n">phen_path</span><span class="p">,</span> <span class="n">phenotype</span><span class="p">,</span> <span class="n">t</span><span class="p">)</span>
+</span><span id="map-792"><a href="#map-792"><span class="linenos">792</span></a>
+</span><span id="map-793"><a href="#map-793"><span class="linenos">793</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Phenotype processed successfully"</span><span class="p">)</span>
+</span></pre></div>
+
+
+
+
+ </section>
+ <section id="map_target_code_type">
+ <input id="map_target_code_type-view-source" class="view-source-toggle-state" type="checkbox" aria-hidden="true" tabindex="-1">
+<div class="attr function">
+
+ <span class="def">def</span>
+ <span class="name">map_target_code_type</span><span class="signature pdoc-code condensed">(<span class="param"><span class="n">phen_path</span><span class="p">:</span> <span class="n">pathlib</span><span class="o">.</span><span class="n">Path</span>, </span><span class="param"><span class="n">phenotype</span><span class="p">:</span> <span class="nb">dict</span>, </span><span class="param"><span class="n">target_code_type</span><span class="p">:</span> <span class="nb">str</span></span><span class="return-annotation">):</span></span>
+
+ <label class="view-source-button" for="map_target_code_type-view-source"><span>View Source</span></label>
+
+ </div>
+ <a class="headerlink" href="#map_target_code_type"></a>
+ <div class="pdoc-code codehilite"><pre><span></span><span id="map_target_code_type-796"><a href="#map_target_code_type-796"><span class="linenos">796</span></a><span class="k">def</span><span class="w"> </span><span class="nf">map_target_code_type</span><span class="p">(</span><span class="n">phen_path</span><span class="p">:</span> <span class="n">Path</span><span class="p">,</span> <span class="n">phenotype</span><span class="p">:</span> <span class="nb">dict</span><span class="p">,</span> <span class="n">target_code_type</span><span class="p">:</span> <span class="nb">str</span><span class="p">):</span>
+</span><span id="map_target_code_type-797"><a href="#map_target_code_type-797"><span class="linenos">797</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Target coding format: </span><span class="si">{</span><span class="n">target_code_type</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+</span><span id="map_target_code_type-798"><a href="#map_target_code_type-798"><span class="linenos">798</span></a> <span class="n">concepts_path</span> <span class="o">=</span> <span class="n">phen_path</span> <span class="o">/</span> <span class="n">CONCEPTS_DIR</span>
+</span><span id="map_target_code_type-799"><a href="#map_target_code_type-799"><span class="linenos">799</span></a> <span class="c1"># Create output dataframe</span>
+</span><span id="map_target_code_type-800"><a href="#map_target_code_type-800"><span class="linenos">800</span></a> <span class="n">out</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">([])</span>
+</span><span id="map_target_code_type-801"><a href="#map_target_code_type-801"><span class="linenos">801</span></a> <span class="n">code_errors</span> <span class="o">=</span> <span class="p">[]</span>
+</span><span id="map_target_code_type-802"><a href="#map_target_code_type-802"><span class="linenos">802</span></a>
+</span><span id="map_target_code_type-803"><a href="#map_target_code_type-803"><span class="linenos">803</span></a> <span class="c1"># Process each folder in codes section</span>
+</span><span id="map_target_code_type-804"><a href="#map_target_code_type-804"><span class="linenos">804</span></a> <span class="k">for</span> <span class="n">concept_set</span> <span class="ow">in</span> <span class="n">phenotype</span><span class="p">[</span><span class="s2">"concept_sets"</span><span class="p">]:</span>
+</span><span id="map_target_code_type-805"><a href="#map_target_code_type-805"><span class="linenos">805</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="sa">f</span><span class="s2">"--- </span><span class="si">{</span><span class="n">concept_set</span><span class="p">[</span><span class="s1">'file'</span><span class="p">]</span><span class="si">}</span><span class="s2"> ---"</span><span class="p">)</span>
+</span><span id="map_target_code_type-806"><a href="#map_target_code_type-806"><span class="linenos">806</span></a>
+</span><span id="map_target_code_type-807"><a href="#map_target_code_type-807"><span class="linenos">807</span></a> <span class="c1"># Load code file</span>
+</span><span id="map_target_code_type-808"><a href="#map_target_code_type-808"><span class="linenos">808</span></a> <span class="n">codes_file_path</span> <span class="o">=</span> <span class="n">Path</span><span class="p">(</span><span class="n">concepts_path</span> <span class="o">/</span> <span class="n">concept_set</span><span class="p">[</span><span class="s2">"file"</span><span class="p">][</span><span class="s2">"path"</span><span class="p">])</span>
+</span><span id="map_target_code_type-809"><a href="#map_target_code_type-809"><span class="linenos">809</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">read_table_file</span><span class="p">(</span><span class="n">codes_file_path</span><span class="p">)</span>
+</span><span id="map_target_code_type-810"><a href="#map_target_code_type-810"><span class="linenos">810</span></a>
+</span><span id="map_target_code_type-811"><a href="#map_target_code_type-811"><span class="linenos">811</span></a> <span class="c1"># process structural actions</span>
+</span><span id="map_target_code_type-812"><a href="#map_target_code_type-812"><span class="linenos">812</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">process_actions</span><span class="p">(</span><span class="n">df</span><span class="p">,</span> <span class="n">concept_set</span><span class="p">)</span>
+</span><span id="map_target_code_type-813"><a href="#map_target_code_type-813"><span class="linenos">813</span></a>
+</span><span id="map_target_code_type-814"><a href="#map_target_code_type-814"><span class="linenos">814</span></a> <span class="c1"># preprocessing and validate of source concepts</span>
+</span><span id="map_target_code_type-815"><a href="#map_target_code_type-815"><span class="linenos">815</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="s2">"Processing and validating source concept codes"</span><span class="p">)</span>
+</span><span id="map_target_code_type-816"><a href="#map_target_code_type-816"><span class="linenos">816</span></a> <span class="n">df</span><span class="p">,</span> <span class="n">errors</span> <span class="o">=</span> <span class="n">preprocess_source_concepts</span><span class="p">(</span>
+</span><span id="map_target_code_type-817"><a href="#map_target_code_type-817"><span class="linenos">817</span></a> <span class="n">df</span><span class="p">,</span>
+</span><span id="map_target_code_type-818"><a href="#map_target_code_type-818"><span class="linenos">818</span></a> <span class="n">concept_set</span><span class="p">,</span>
+</span><span id="map_target_code_type-819"><a href="#map_target_code_type-819"><span class="linenos">819</span></a> <span class="n">codes_file_path</span><span class="p">,</span>
+</span><span id="map_target_code_type-820"><a href="#map_target_code_type-820"><span class="linenos">820</span></a> <span class="p">)</span>
+</span><span id="map_target_code_type-821"><a href="#map_target_code_type-821"><span class="linenos">821</span></a>
+</span><span id="map_target_code_type-822"><a href="#map_target_code_type-822"><span class="linenos">822</span></a> <span class="c1"># create df with just the source code columns</span>
+</span><span id="map_target_code_type-823"><a href="#map_target_code_type-823"><span class="linenos">823</span></a> <span class="n">source_column_names</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="n">concept_set</span><span class="p">[</span><span class="s2">"file"</span><span class="p">][</span><span class="s2">"columns"</span><span class="p">]</span><span class="o">.</span><span class="n">keys</span><span class="p">())</span>
+</span><span id="map_target_code_type-824"><a href="#map_target_code_type-824"><span class="linenos">824</span></a> <span class="n">source_df</span> <span class="o">=</span> <span class="n">df</span><span class="p">[</span><span class="n">source_column_names</span><span class="p">]</span>
+</span><span id="map_target_code_type-825"><a href="#map_target_code_type-825"><span class="linenos">825</span></a>
+</span><span id="map_target_code_type-826"><a href="#map_target_code_type-826"><span class="linenos">826</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="n">source_df</span><span class="o">.</span><span class="n">columns</span><span class="p">)</span>
+</span><span id="map_target_code_type-827"><a href="#map_target_code_type-827"><span class="linenos">827</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="n">source_df</span><span class="o">.</span><span class="n">head</span><span class="p">())</span>
+</span><span id="map_target_code_type-828"><a href="#map_target_code_type-828"><span class="linenos">828</span></a>
+</span><span id="map_target_code_type-829"><a href="#map_target_code_type-829"><span class="linenos">829</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Length of errors from preprocess_source_concepts </span><span class="si">{</span><span class="nb">len</span><span class="p">(</span><span class="n">errors</span><span class="p">)</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+</span><span id="map_target_code_type-830"><a href="#map_target_code_type-830"><span class="linenos">830</span></a> <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">errors</span><span class="p">)</span> <span class="o">></span> <span class="mi">0</span><span class="p">:</span>
+</span><span id="map_target_code_type-831"><a href="#map_target_code_type-831"><span class="linenos">831</span></a> <span class="n">code_errors</span><span class="o">.</span><span class="n">extend</span><span class="p">(</span><span class="n">errors</span><span class="p">)</span>
+</span><span id="map_target_code_type-832"><a href="#map_target_code_type-832"><span class="linenos">832</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="sa">f</span><span class="s2">" Length of code_errors </span><span class="si">{</span><span class="nb">len</span><span class="p">(</span><span class="n">code_errors</span><span class="p">)</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+</span><span id="map_target_code_type-833"><a href="#map_target_code_type-833"><span class="linenos">833</span></a>
+</span><span id="map_target_code_type-834"><a href="#map_target_code_type-834"><span class="linenos">834</span></a> <span class="c1"># Map source concepts codes to target codes</span>
+</span><span id="map_target_code_type-835"><a href="#map_target_code_type-835"><span class="linenos">835</span></a> <span class="c1"># if processing a source coding list with categorical data</span>
+</span><span id="map_target_code_type-836"><a href="#map_target_code_type-836"><span class="linenos">836</span></a> <span class="k">if</span> <span class="p">(</span>
+</span><span id="map_target_code_type-837"><a href="#map_target_code_type-837"><span class="linenos">837</span></a> <span class="s2">"actions"</span> <span class="ow">in</span> <span class="n">concept_set</span><span class="p">[</span><span class="s2">"file"</span><span class="p">]</span>
+</span><span id="map_target_code_type-838"><a href="#map_target_code_type-838"><span class="linenos">838</span></a> <span class="ow">and</span> <span class="s2">"divide_col"</span> <span class="ow">in</span> <span class="n">concept_set</span><span class="p">[</span><span class="s2">"file"</span><span class="p">][</span><span class="s2">"actions"</span><span class="p">]</span>
+</span><span id="map_target_code_type-839"><a href="#map_target_code_type-839"><span class="linenos">839</span></a> <span class="ow">and</span> <span class="nb">len</span><span class="p">(</span><span class="n">df</span><span class="p">)</span> <span class="o">></span> <span class="mi">0</span>
+</span><span id="map_target_code_type-840"><a href="#map_target_code_type-840"><span class="linenos">840</span></a> <span class="p">):</span>
+</span><span id="map_target_code_type-841"><a href="#map_target_code_type-841"><span class="linenos">841</span></a> <span class="n">divide_col</span> <span class="o">=</span> <span class="n">concept_set</span><span class="p">[</span><span class="s2">"file"</span><span class="p">][</span><span class="s2">"actions"</span><span class="p">][</span><span class="s2">"divide_col"</span><span class="p">]</span>
+</span><span id="map_target_code_type-842"><a href="#map_target_code_type-842"><span class="linenos">842</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Action: Dividing Table by </span><span class="si">{</span><span class="n">divide_col</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+</span><span id="map_target_code_type-843"><a href="#map_target_code_type-843"><span class="linenos">843</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="sa">f</span><span class="s2">"column into: </span><span class="si">{</span><span class="n">df</span><span class="p">[</span><span class="n">divide_col</span><span class="p">]</span><span class="o">.</span><span class="n">unique</span><span class="p">()</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+</span><span id="map_target_code_type-844"><a href="#map_target_code_type-844"><span class="linenos">844</span></a> <span class="n">df_grp</span> <span class="o">=</span> <span class="n">df</span><span class="o">.</span><span class="n">groupby</span><span class="p">(</span><span class="n">divide_col</span><span class="p">)</span>
+</span><span id="map_target_code_type-845"><a href="#map_target_code_type-845"><span class="linenos">845</span></a> <span class="k">for</span> <span class="n">cat</span><span class="p">,</span> <span class="n">grp</span> <span class="ow">in</span> <span class="n">df_grp</span><span class="p">:</span>
+</span><span id="map_target_code_type-846"><a href="#map_target_code_type-846"><span class="linenos">846</span></a> <span class="k">if</span> <span class="n">cat</span> <span class="o">==</span> <span class="n">concept_set</span><span class="p">[</span><span class="s2">"file"</span><span class="p">][</span><span class="s2">"category"</span><span class="p">]:</span>
+</span><span id="map_target_code_type-847"><a href="#map_target_code_type-847"><span class="linenos">847</span></a> <span class="n">grp</span> <span class="o">=</span> <span class="n">grp</span><span class="o">.</span><span class="n">drop</span><span class="p">(</span><span class="n">columns</span><span class="o">=</span><span class="p">[</span><span class="n">divide_col</span><span class="p">])</span> <span class="c1"># delete categorical column</span>
+</span><span id="map_target_code_type-848"><a href="#map_target_code_type-848"><span class="linenos">848</span></a> <span class="n">source_df</span> <span class="o">=</span> <span class="n">grp</span><span class="p">[</span><span class="n">source_column_names</span><span class="p">]</span>
+</span><span id="map_target_code_type-849"><a href="#map_target_code_type-849"><span class="linenos">849</span></a> <span class="n">trans_out</span> <span class="o">=</span> <span class="n">translate_codes</span><span class="p">(</span>
+</span><span id="map_target_code_type-850"><a href="#map_target_code_type-850"><span class="linenos">850</span></a> <span class="n">source_df</span><span class="p">,</span>
+</span><span id="map_target_code_type-851"><a href="#map_target_code_type-851"><span class="linenos">851</span></a> <span class="n">target_code_type</span><span class="o">=</span><span class="n">target_code_type</span><span class="p">,</span>
+</span><span id="map_target_code_type-852"><a href="#map_target_code_type-852"><span class="linenos">852</span></a> <span class="n">concept_name</span><span class="o">=</span><span class="n">concept_set</span><span class="p">[</span><span class="s2">"name"</span><span class="p">],</span>
+</span><span id="map_target_code_type-853"><a href="#map_target_code_type-853"><span class="linenos">853</span></a> <span class="p">)</span>
+</span><span id="map_target_code_type-854"><a href="#map_target_code_type-854"><span class="linenos">854</span></a> <span class="n">out</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">concat</span><span class="p">([</span><span class="n">out</span><span class="p">,</span> <span class="n">trans_out</span><span class="p">])</span>
+</span><span id="map_target_code_type-855"><a href="#map_target_code_type-855"><span class="linenos">855</span></a> <span class="k">else</span><span class="p">:</span>
+</span><span id="map_target_code_type-856"><a href="#map_target_code_type-856"><span class="linenos">856</span></a> <span class="n">source_df</span> <span class="o">=</span> <span class="n">df</span><span class="p">[</span><span class="n">source_column_names</span><span class="p">]</span>
+</span><span id="map_target_code_type-857"><a href="#map_target_code_type-857"><span class="linenos">857</span></a> <span class="n">trans_out</span> <span class="o">=</span> <span class="n">translate_codes</span><span class="p">(</span>
+</span><span id="map_target_code_type-858"><a href="#map_target_code_type-858"><span class="linenos">858</span></a> <span class="n">source_df</span><span class="p">,</span>
+</span><span id="map_target_code_type-859"><a href="#map_target_code_type-859"><span class="linenos">859</span></a> <span class="n">target_code_type</span><span class="o">=</span><span class="n">target_code_type</span><span class="p">,</span>
+</span><span id="map_target_code_type-860"><a href="#map_target_code_type-860"><span class="linenos">860</span></a> <span class="n">concept_name</span><span class="o">=</span><span class="n">concept_set</span><span class="p">[</span><span class="s2">"name"</span><span class="p">],</span>
+</span><span id="map_target_code_type-861"><a href="#map_target_code_type-861"><span class="linenos">861</span></a> <span class="p">)</span>
+</span><span id="map_target_code_type-862"><a href="#map_target_code_type-862"><span class="linenos">862</span></a> <span class="n">out</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">concat</span><span class="p">([</span><span class="n">out</span><span class="p">,</span> <span class="n">trans_out</span><span class="p">])</span>
+</span><span id="map_target_code_type-863"><a href="#map_target_code_type-863"><span class="linenos">863</span></a>
+</span><span id="map_target_code_type-864"><a href="#map_target_code_type-864"><span class="linenos">864</span></a> <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">code_errors</span><span class="p">)</span> <span class="o">></span> <span class="mi">0</span><span class="p">:</span>
+</span><span id="map_target_code_type-865"><a href="#map_target_code_type-865"><span class="linenos">865</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">error</span><span class="p">(</span><span class="sa">f</span><span class="s2">"The map processing has </span><span class="si">{</span><span class="nb">len</span><span class="p">(</span><span class="n">code_errors</span><span class="p">)</span><span class="si">}</span><span class="s2"> errors"</span><span class="p">)</span>
+</span><span id="map_target_code_type-866"><a href="#map_target_code_type-866"><span class="linenos">866</span></a> <span class="n">error_path</span> <span class="o">=</span> <span class="n">phen_path</span> <span class="o">/</span> <span class="n">MAP_DIR</span> <span class="o">/</span> <span class="s2">"errors"</span>
+</span><span id="map_target_code_type-867"><a href="#map_target_code_type-867"><span class="linenos">867</span></a> <span class="n">error_path</span><span class="o">.</span><span class="n">mkdir</span><span class="p">(</span><span class="n">parents</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">exist_ok</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+</span><span id="map_target_code_type-868"><a href="#map_target_code_type-868"><span class="linenos">868</span></a> <span class="n">error_filename</span> <span class="o">=</span> <span class="sa">f</span><span class="s2">"</span><span class="si">{</span><span class="n">target_code_type</span><span class="si">}</span><span class="s2">-code-errors.csv"</span>
+</span><span id="map_target_code_type-869"><a href="#map_target_code_type-869"><span class="linenos">869</span></a> <span class="n">write_code_errors</span><span class="p">(</span><span class="n">code_errors</span><span class="p">,</span> <span class="n">error_path</span> <span class="o">/</span> <span class="n">error_filename</span><span class="p">)</span>
+</span><span id="map_target_code_type-870"><a href="#map_target_code_type-870"><span class="linenos">870</span></a>
+</span><span id="map_target_code_type-871"><a href="#map_target_code_type-871"><span class="linenos">871</span></a> <span class="c1"># Check there is output from processing</span>
+</span><span id="map_target_code_type-872"><a href="#map_target_code_type-872"><span class="linenos">872</span></a> <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">out</span><span class="o">.</span><span class="n">index</span><span class="p">)</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
+</span><span id="map_target_code_type-873"><a href="#map_target_code_type-873"><span class="linenos">873</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">error</span><span class="p">(</span><span class="sa">f</span><span class="s2">"No output after map processing"</span><span class="p">)</span>
+</span><span id="map_target_code_type-874"><a href="#map_target_code_type-874"><span class="linenos">874</span></a> <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span>
+</span><span id="map_target_code_type-875"><a href="#map_target_code_type-875"><span class="linenos">875</span></a> <span class="sa">f</span><span class="s2">"No output after map processing, check config </span><span class="si">{</span><span class="nb">str</span><span class="p">(</span><span class="n">phen_path</span><span class="o">.</span><span class="n">resolve</span><span class="p">())</span><span class="si">}</span><span class="s2">"</span>
+</span><span id="map_target_code_type-876"><a href="#map_target_code_type-876"><span class="linenos">876</span></a> <span class="p">)</span>
+</span><span id="map_target_code_type-877"><a href="#map_target_code_type-877"><span class="linenos">877</span></a>
+</span><span id="map_target_code_type-878"><a href="#map_target_code_type-878"><span class="linenos">878</span></a> <span class="c1"># final processing</span>
+</span><span id="map_target_code_type-879"><a href="#map_target_code_type-879"><span class="linenos">879</span></a> <span class="n">out</span> <span class="o">=</span> <span class="n">out</span><span class="o">.</span><span class="n">reset_index</span><span class="p">(</span><span class="n">drop</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+</span><span id="map_target_code_type-880"><a href="#map_target_code_type-880"><span class="linenos">880</span></a> <span class="n">out</span> <span class="o">=</span> <span class="n">out</span><span class="o">.</span><span class="n">drop_duplicates</span><span class="p">(</span><span class="n">subset</span><span class="o">=</span><span class="p">[</span><span class="s2">"CONCEPT_SET"</span><span class="p">,</span> <span class="s2">"CONCEPT"</span><span class="p">])</span>
+</span><span id="map_target_code_type-881"><a href="#map_target_code_type-881"><span class="linenos">881</span></a> <span class="n">out</span> <span class="o">=</span> <span class="n">out</span><span class="o">.</span><span class="n">sort_values</span><span class="p">(</span><span class="n">by</span><span class="o">=</span><span class="p">[</span><span class="s2">"CONCEPT_SET"</span><span class="p">,</span> <span class="s2">"CONCEPT"</span><span class="p">])</span>
+</span><span id="map_target_code_type-882"><a href="#map_target_code_type-882"><span class="linenos">882</span></a>
+</span><span id="map_target_code_type-883"><a href="#map_target_code_type-883"><span class="linenos">883</span></a> <span class="n">out_count</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">out</span><span class="o">.</span><span class="n">index</span><span class="p">)</span>
+</span><span id="map_target_code_type-884"><a href="#map_target_code_type-884"><span class="linenos">884</span></a> <span class="c1"># added metadata</span>
+</span><span id="map_target_code_type-885"><a href="#map_target_code_type-885"><span class="linenos">885</span></a> <span class="c1"># Loop over each source_concept_type and perform the left join on all columns apart from source code columns</span>
+</span><span id="map_target_code_type-886"><a href="#map_target_code_type-886"><span class="linenos">886</span></a> <span class="n">result_list</span> <span class="o">=</span> <span class="p">[]</span>
+</span><span id="map_target_code_type-887"><a href="#map_target_code_type-887"><span class="linenos">887</span></a> <span class="n">source_column_names</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="n">concept_set</span><span class="p">[</span><span class="s2">"file"</span><span class="p">][</span><span class="s2">"columns"</span><span class="p">]</span><span class="o">.</span><span class="n">keys</span><span class="p">())</span>
+</span><span id="map_target_code_type-888"><a href="#map_target_code_type-888"><span class="linenos">888</span></a> <span class="k">for</span> <span class="n">source_concept_type</span> <span class="ow">in</span> <span class="n">source_column_names</span><span class="p">:</span>
+</span><span id="map_target_code_type-889"><a href="#map_target_code_type-889"><span class="linenos">889</span></a>
+</span><span id="map_target_code_type-890"><a href="#map_target_code_type-890"><span class="linenos">890</span></a> <span class="c1"># Filter output based on the current source_concept_type</span>
+</span><span id="map_target_code_type-891"><a href="#map_target_code_type-891"><span class="linenos">891</span></a> <span class="n">out_filtered_df</span> <span class="o">=</span> <span class="n">out</span><span class="p">[</span><span class="n">out</span><span class="p">[</span><span class="s2">"SOURCE_CONCEPT_TYPE"</span><span class="p">]</span> <span class="o">==</span> <span class="n">source_concept_type</span><span class="p">]</span>
+</span><span id="map_target_code_type-892"><a href="#map_target_code_type-892"><span class="linenos">892</span></a> <span class="n">filtered_count</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">out_filtered_df</span><span class="o">.</span><span class="n">index</span><span class="p">)</span>
+</span><span id="map_target_code_type-893"><a href="#map_target_code_type-893"><span class="linenos">893</span></a>
+</span><span id="map_target_code_type-894"><a href="#map_target_code_type-894"><span class="linenos">894</span></a> <span class="c1"># Remove the source type columns except the current type will leave the metadata and the join</span>
+</span><span id="map_target_code_type-895"><a href="#map_target_code_type-895"><span class="linenos">895</span></a> <span class="n">remove_types</span> <span class="o">=</span> <span class="p">[</span>
+</span><span id="map_target_code_type-896"><a href="#map_target_code_type-896"><span class="linenos">896</span></a> <span class="nb">type</span> <span class="k">for</span> <span class="nb">type</span> <span class="ow">in</span> <span class="n">source_column_names</span> <span class="k">if</span> <span class="nb">type</span> <span class="o">!=</span> <span class="n">source_concept_type</span>
+</span><span id="map_target_code_type-897"><a href="#map_target_code_type-897"><span class="linenos">897</span></a> <span class="p">]</span>
+</span><span id="map_target_code_type-898"><a href="#map_target_code_type-898"><span class="linenos">898</span></a> <span class="n">metadata_df</span> <span class="o">=</span> <span class="n">df</span><span class="o">.</span><span class="n">drop</span><span class="p">(</span><span class="n">columns</span><span class="o">=</span><span class="n">remove_types</span><span class="p">)</span>
+</span><span id="map_target_code_type-899"><a href="#map_target_code_type-899"><span class="linenos">899</span></a> <span class="n">metadata_df</span> <span class="o">=</span> <span class="n">metadata_df</span><span class="o">.</span><span class="n">rename</span><span class="p">(</span>
+</span><span id="map_target_code_type-900"><a href="#map_target_code_type-900"><span class="linenos">900</span></a> <span class="n">columns</span><span class="o">=</span><span class="p">{</span><span class="n">source_concept_type</span><span class="p">:</span> <span class="s2">"SOURCE_CONCEPT"</span><span class="p">}</span>
+</span><span id="map_target_code_type-901"><a href="#map_target_code_type-901"><span class="linenos">901</span></a> <span class="p">)</span>
+</span><span id="map_target_code_type-902"><a href="#map_target_code_type-902"><span class="linenos">902</span></a> <span class="n">metadata_df_count</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">metadata_df</span><span class="o">.</span><span class="n">index</span><span class="p">)</span>
+</span><span id="map_target_code_type-903"><a href="#map_target_code_type-903"><span class="linenos">903</span></a>
+</span><span id="map_target_code_type-904"><a href="#map_target_code_type-904"><span class="linenos">904</span></a> <span class="c1"># Perform the left join with df2 on SOURCE_CONCEPT to add the metadata</span>
+</span><span id="map_target_code_type-905"><a href="#map_target_code_type-905"><span class="linenos">905</span></a> <span class="n">result</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">merge</span><span class="p">(</span><span class="n">out_filtered_df</span><span class="p">,</span> <span class="n">metadata_df</span><span class="p">,</span> <span class="n">how</span><span class="o">=</span><span class="s2">"left"</span><span class="p">,</span> <span class="n">on</span><span class="o">=</span><span class="s2">"SOURCE_CONCEPT"</span><span class="p">)</span>
+</span><span id="map_target_code_type-906"><a href="#map_target_code_type-906"><span class="linenos">906</span></a> <span class="n">result_count</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">result</span><span class="o">.</span><span class="n">index</span><span class="p">)</span>
+</span><span id="map_target_code_type-907"><a href="#map_target_code_type-907"><span class="linenos">907</span></a>
+</span><span id="map_target_code_type-908"><a href="#map_target_code_type-908"><span class="linenos">908</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span>
+</span><span id="map_target_code_type-909"><a href="#map_target_code_type-909"><span class="linenos">909</span></a> <span class="sa">f</span><span class="s2">"Adding metadata for </span><span class="si">{</span><span class="n">source_concept_type</span><span class="si">}</span><span class="s2">: out_count </span><span class="si">{</span><span class="n">out_count</span><span class="si">}</span><span class="s2">, filtered_count </span><span class="si">{</span><span class="n">filtered_count</span><span class="si">}</span><span class="s2">, metadata_df_count </span><span class="si">{</span><span class="n">metadata_df_count</span><span class="si">}</span><span class="s2">, result_count </span><span class="si">{</span><span class="n">result_count</span><span class="si">}</span><span class="s2">"</span>
+</span><span id="map_target_code_type-910"><a href="#map_target_code_type-910"><span class="linenos">910</span></a> <span class="p">)</span>
+</span><span id="map_target_code_type-911"><a href="#map_target_code_type-911"><span class="linenos">911</span></a>
+</span><span id="map_target_code_type-912"><a href="#map_target_code_type-912"><span class="linenos">912</span></a> <span class="c1"># Append the result to the result_list</span>
+</span><span id="map_target_code_type-913"><a href="#map_target_code_type-913"><span class="linenos">913</span></a> <span class="n">result_list</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">result</span><span class="p">)</span>
+</span><span id="map_target_code_type-914"><a href="#map_target_code_type-914"><span class="linenos">914</span></a>
+</span><span id="map_target_code_type-915"><a href="#map_target_code_type-915"><span class="linenos">915</span></a> <span class="c1"># Concatenate all the results into a single DataFrame</span>
+</span><span id="map_target_code_type-916"><a href="#map_target_code_type-916"><span class="linenos">916</span></a> <span class="n">final_out</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">concat</span><span class="p">(</span><span class="n">result_list</span><span class="p">,</span> <span class="n">ignore_index</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+</span><span id="map_target_code_type-917"><a href="#map_target_code_type-917"><span class="linenos">917</span></a> <span class="n">final_out</span> <span class="o">=</span> <span class="n">final_out</span><span class="o">.</span><span class="n">drop_duplicates</span><span class="p">(</span><span class="n">subset</span><span class="o">=</span><span class="p">[</span><span class="s2">"CONCEPT_SET"</span><span class="p">,</span> <span class="s2">"CONCEPT"</span><span class="p">])</span>
+</span><span id="map_target_code_type-918"><a href="#map_target_code_type-918"><span class="linenos">918</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span>
+</span><span id="map_target_code_type-919"><a href="#map_target_code_type-919"><span class="linenos">919</span></a> <span class="sa">f</span><span class="s2">"Check metadata processing counts: before </span><span class="si">{</span><span class="nb">len</span><span class="p">(</span><span class="n">out</span><span class="o">.</span><span class="n">index</span><span class="p">)</span><span class="si">}</span><span class="s2"> : after </span><span class="si">{</span><span class="nb">len</span><span class="p">(</span><span class="n">final_out</span><span class="o">.</span><span class="n">index</span><span class="p">)</span><span class="si">}</span><span class="s2">"</span>
+</span><span id="map_target_code_type-920"><a href="#map_target_code_type-920"><span class="linenos">920</span></a> <span class="p">)</span>
+</span><span id="map_target_code_type-921"><a href="#map_target_code_type-921"><span class="linenos">921</span></a>
+</span><span id="map_target_code_type-922"><a href="#map_target_code_type-922"><span class="linenos">922</span></a> <span class="c1"># Save output to map directory</span>
+</span><span id="map_target_code_type-923"><a href="#map_target_code_type-923"><span class="linenos">923</span></a> <span class="n">output_filename</span> <span class="o">=</span> <span class="n">target_code_type</span> <span class="o">+</span> <span class="s2">".csv"</span>
+</span><span id="map_target_code_type-924"><a href="#map_target_code_type-924"><span class="linenos">924</span></a> <span class="n">map_path</span> <span class="o">=</span> <span class="n">phen_path</span> <span class="o">/</span> <span class="n">MAP_DIR</span> <span class="o">/</span> <span class="n">output_filename</span>
+</span><span id="map_target_code_type-925"><a href="#map_target_code_type-925"><span class="linenos">925</span></a> <span class="n">final_out</span><span class="o">.</span><span class="n">to_csv</span><span class="p">(</span><span class="n">map_path</span><span class="p">,</span> <span class="n">index</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span>
+</span><span id="map_target_code_type-926"><a href="#map_target_code_type-926"><span class="linenos">926</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Saved mapped concepts to </span><span class="si">{</span><span class="nb">str</span><span class="p">(</span><span class="n">map_path</span><span class="o">.</span><span class="n">resolve</span><span class="p">())</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+</span><span id="map_target_code_type-927"><a href="#map_target_code_type-927"><span class="linenos">927</span></a>
+</span><span id="map_target_code_type-928"><a href="#map_target_code_type-928"><span class="linenos">928</span></a> <span class="c1"># save concept sets as separate files</span>
+</span><span id="map_target_code_type-929"><a href="#map_target_code_type-929"><span class="linenos">929</span></a> <span class="n">concept_set_path</span> <span class="o">=</span> <span class="n">phen_path</span> <span class="o">/</span> <span class="n">CSV_PATH</span> <span class="o">/</span> <span class="n">target_code_type</span>
+</span><span id="map_target_code_type-930"><a href="#map_target_code_type-930"><span class="linenos">930</span></a>
+</span><span id="map_target_code_type-931"><a href="#map_target_code_type-931"><span class="linenos">931</span></a> <span class="c1"># empty the concept-set directory except for hiddle files, e.g. .git</span>
+</span><span id="map_target_code_type-932"><a href="#map_target_code_type-932"><span class="linenos">932</span></a> <span class="k">if</span> <span class="n">concept_set_path</span><span class="o">.</span><span class="n">exists</span><span class="p">():</span>
+</span><span id="map_target_code_type-933"><a href="#map_target_code_type-933"><span class="linenos">933</span></a> <span class="k">for</span> <span class="n">item</span> <span class="ow">in</span> <span class="n">concept_set_path</span><span class="o">.</span><span class="n">iterdir</span><span class="p">():</span>
+</span><span id="map_target_code_type-934"><a href="#map_target_code_type-934"><span class="linenos">934</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="n">item</span><span class="o">.</span><span class="n">name</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s2">"."</span><span class="p">):</span>
+</span><span id="map_target_code_type-935"><a href="#map_target_code_type-935"><span class="linenos">935</span></a> <span class="n">item</span><span class="o">.</span><span class="n">unlink</span><span class="p">()</span>
+</span><span id="map_target_code_type-936"><a href="#map_target_code_type-936"><span class="linenos">936</span></a> <span class="k">else</span><span class="p">:</span>
+</span><span id="map_target_code_type-937"><a href="#map_target_code_type-937"><span class="linenos">937</span></a> <span class="n">concept_set_path</span><span class="o">.</span><span class="n">mkdir</span><span class="p">(</span><span class="n">parents</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">exist_ok</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+</span><span id="map_target_code_type-938"><a href="#map_target_code_type-938"><span class="linenos">938</span></a>
+</span><span id="map_target_code_type-939"><a href="#map_target_code_type-939"><span class="linenos">939</span></a> <span class="c1"># write each concept as a separate file</span>
+</span><span id="map_target_code_type-940"><a href="#map_target_code_type-940"><span class="linenos">940</span></a> <span class="k">for</span> <span class="n">name</span><span class="p">,</span> <span class="n">concept</span> <span class="ow">in</span> <span class="n">final_out</span><span class="o">.</span><span class="n">groupby</span><span class="p">(</span><span class="s2">"CONCEPT_SET"</span><span class="p">):</span>
+</span><span id="map_target_code_type-941"><a href="#map_target_code_type-941"><span class="linenos">941</span></a> <span class="n">concept</span> <span class="o">=</span> <span class="n">concept</span><span class="o">.</span><span class="n">sort_values</span><span class="p">(</span><span class="n">by</span><span class="o">=</span><span class="s2">"CONCEPT"</span><span class="p">)</span> <span class="c1"># sort rows</span>
+</span><span id="map_target_code_type-942"><a href="#map_target_code_type-942"><span class="linenos">942</span></a> <span class="n">concept</span> <span class="o">=</span> <span class="n">concept</span><span class="o">.</span><span class="n">dropna</span><span class="p">(</span><span class="n">how</span><span class="o">=</span><span class="s2">"all"</span><span class="p">,</span> <span class="n">axis</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span> <span class="c1"># remove empty cols</span>
+</span><span id="map_target_code_type-943"><a href="#map_target_code_type-943"><span class="linenos">943</span></a> <span class="n">concept</span> <span class="o">=</span> <span class="n">concept</span><span class="o">.</span><span class="n">reindex</span><span class="p">(</span>
+</span><span id="map_target_code_type-944"><a href="#map_target_code_type-944"><span class="linenos">944</span></a> <span class="nb">sorted</span><span class="p">(</span><span class="n">concept</span><span class="o">.</span><span class="n">columns</span><span class="p">),</span> <span class="n">axis</span><span class="o">=</span><span class="mi">1</span>
+</span><span id="map_target_code_type-945"><a href="#map_target_code_type-945"><span class="linenos">945</span></a> <span class="p">)</span> <span class="c1"># sort cols alphabetically</span>
+</span><span id="map_target_code_type-946"><a href="#map_target_code_type-946"><span class="linenos">946</span></a> <span class="n">filename</span> <span class="o">=</span> <span class="sa">f</span><span class="s2">"</span><span class="si">{</span><span class="n">name</span><span class="si">}</span><span class="s2">.csv"</span>
+</span><span id="map_target_code_type-947"><a href="#map_target_code_type-947"><span class="linenos">947</span></a> <span class="n">concept_path</span> <span class="o">=</span> <span class="n">concept_set_path</span> <span class="o">/</span> <span class="n">filename</span>
+</span><span id="map_target_code_type-948"><a href="#map_target_code_type-948"><span class="linenos">948</span></a> <span class="n">concept</span><span class="o">.</span><span class="n">to_csv</span><span class="p">(</span><span class="n">concept_path</span><span class="p">,</span> <span class="n">index</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span>
+</span><span id="map_target_code_type-949"><a href="#map_target_code_type-949"><span class="linenos">949</span></a>
+</span><span id="map_target_code_type-950"><a href="#map_target_code_type-950"><span class="linenos">950</span></a> <span class="n">write_vocab_version</span><span class="p">(</span><span class="n">phen_path</span><span class="p">)</span>
+</span><span id="map_target_code_type-951"><a href="#map_target_code_type-951"><span class="linenos">951</span></a>
+</span><span id="map_target_code_type-952"><a href="#map_target_code_type-952"><span class="linenos">952</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Phenotype processed target code type </span><span class="si">{</span><span class="n">target_code_type</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+</span></pre></div>
+
+
+
+
+ </section>
+ <section id="generate_version_tag">
+ <input id="generate_version_tag-view-source" class="view-source-toggle-state" type="checkbox" aria-hidden="true" tabindex="-1">
+<div class="attr function">
+
+ <span class="def">def</span>
+ <span class="name">generate_version_tag</span><span class="signature pdoc-code multiline">(<span class="param"> <span class="n">repo</span><span class="p">:</span> <span class="n">git</span><span class="o">.</span><span class="n">repo</span><span class="o">.</span><span class="n">base</span><span class="o">.</span><span class="n">Repo</span>,</span><span class="param"> <span class="n">increment</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="s1">'patch'</span>,</span><span class="param"> <span class="n">use_v_prefix</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">False</span></span><span class="return-annotation">) -> <span class="nb">str</span>:</span></span>
+
+ <label class="view-source-button" for="generate_version_tag-view-source"><span>View Source</span></label>
+
+ </div>
+ <a class="headerlink" href="#generate_version_tag"></a>
+ <div class="pdoc-code codehilite"><pre><span></span><span id="generate_version_tag-955"><a href="#generate_version_tag-955"><span class="linenos">955</span></a><span class="k">def</span><span class="w"> </span><span class="nf">generate_version_tag</span><span class="p">(</span>
+</span><span id="generate_version_tag-956"><a href="#generate_version_tag-956"><span class="linenos">956</span></a> <span class="n">repo</span><span class="p">:</span> <span class="n">git</span><span class="o">.</span><span class="n">Repo</span><span class="p">,</span> <span class="n">increment</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="n">DEFAULT_VERSION_INC</span><span class="p">,</span> <span class="n">use_v_prefix</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">False</span>
+</span><span id="generate_version_tag-957"><a href="#generate_version_tag-957"><span class="linenos">957</span></a><span class="p">)</span> <span class="o">-></span> <span class="nb">str</span><span class="p">:</span>
+</span><span id="generate_version_tag-958"><a href="#generate_version_tag-958"><span class="linenos">958</span></a> <span class="c1"># Get all valid semantic version tags</span>
+</span><span id="generate_version_tag-959"><a href="#generate_version_tag-959"><span class="linenos">959</span></a> <span class="n">versions</span> <span class="o">=</span> <span class="p">[]</span>
+</span><span id="generate_version_tag-960"><a href="#generate_version_tag-960"><span class="linenos">960</span></a> <span class="k">for</span> <span class="n">tag</span> <span class="ow">in</span> <span class="n">repo</span><span class="o">.</span><span class="n">tags</span><span class="p">:</span>
+</span><span id="generate_version_tag-961"><a href="#generate_version_tag-961"><span class="linenos">961</span></a> <span class="n">tag_name</span> <span class="o">=</span> <span class="p">(</span>
+</span><span id="generate_version_tag-962"><a href="#generate_version_tag-962"><span class="linenos">962</span></a> <span class="n">tag</span><span class="o">.</span><span class="n">name</span><span class="o">.</span><span class="n">lstrip</span><span class="p">(</span><span class="s2">"v"</span><span class="p">)</span> <span class="k">if</span> <span class="n">use_v_prefix</span> <span class="k">else</span> <span class="n">tag</span><span class="o">.</span><span class="n">name</span>
+</span><span id="generate_version_tag-963"><a href="#generate_version_tag-963"><span class="linenos">963</span></a> <span class="p">)</span> <span class="c1"># Remove 'v' if needed</span>
+</span><span id="generate_version_tag-964"><a href="#generate_version_tag-964"><span class="linenos">964</span></a> <span class="k">if</span> <span class="n">semver</span><span class="o">.</span><span class="n">Version</span><span class="o">.</span><span class="n">is_valid</span><span class="p">(</span><span class="n">tag_name</span><span class="p">):</span>
+</span><span id="generate_version_tag-965"><a href="#generate_version_tag-965"><span class="linenos">965</span></a> <span class="n">versions</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">semver</span><span class="o">.</span><span class="n">Version</span><span class="o">.</span><span class="n">parse</span><span class="p">(</span><span class="n">tag_name</span><span class="p">))</span>
+</span><span id="generate_version_tag-966"><a href="#generate_version_tag-966"><span class="linenos">966</span></a>
+</span><span id="generate_version_tag-967"><a href="#generate_version_tag-967"><span class="linenos">967</span></a> <span class="c1"># Determine the next version</span>
+</span><span id="generate_version_tag-968"><a href="#generate_version_tag-968"><span class="linenos">968</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="n">versions</span><span class="p">:</span>
+</span><span id="generate_version_tag-969"><a href="#generate_version_tag-969"><span class="linenos">969</span></a> <span class="n">new_version</span> <span class="o">=</span> <span class="n">semver</span><span class="o">.</span><span class="n">Version</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">1</span><span class="p">)</span>
+</span><span id="generate_version_tag-970"><a href="#generate_version_tag-970"><span class="linenos">970</span></a> <span class="k">else</span><span class="p">:</span>
+</span><span id="generate_version_tag-971"><a href="#generate_version_tag-971"><span class="linenos">971</span></a> <span class="n">latest_version</span> <span class="o">=</span> <span class="nb">max</span><span class="p">(</span><span class="n">versions</span><span class="p">)</span>
+</span><span id="generate_version_tag-972"><a href="#generate_version_tag-972"><span class="linenos">972</span></a> <span class="k">if</span> <span class="n">increment</span> <span class="o">==</span> <span class="s2">"major"</span><span class="p">:</span>
+</span><span id="generate_version_tag-973"><a href="#generate_version_tag-973"><span class="linenos">973</span></a> <span class="n">new_version</span> <span class="o">=</span> <span class="n">latest_version</span><span class="o">.</span><span class="n">bump_major</span><span class="p">()</span>
+</span><span id="generate_version_tag-974"><a href="#generate_version_tag-974"><span class="linenos">974</span></a> <span class="k">elif</span> <span class="n">increment</span> <span class="o">==</span> <span class="s2">"minor"</span><span class="p">:</span>
+</span><span id="generate_version_tag-975"><a href="#generate_version_tag-975"><span class="linenos">975</span></a> <span class="n">new_version</span> <span class="o">=</span> <span class="n">latest_version</span><span class="o">.</span><span class="n">bump_minor</span><span class="p">()</span>
+</span><span id="generate_version_tag-976"><a href="#generate_version_tag-976"><span class="linenos">976</span></a> <span class="k">else</span><span class="p">:</span>
+</span><span id="generate_version_tag-977"><a href="#generate_version_tag-977"><span class="linenos">977</span></a> <span class="n">new_version</span> <span class="o">=</span> <span class="n">latest_version</span><span class="o">.</span><span class="n">bump_patch</span><span class="p">()</span>
+</span><span id="generate_version_tag-978"><a href="#generate_version_tag-978"><span class="linenos">978</span></a>
+</span><span id="generate_version_tag-979"><a href="#generate_version_tag-979"><span class="linenos">979</span></a> <span class="c1"># Create the new tag</span>
+</span><span id="generate_version_tag-980"><a href="#generate_version_tag-980"><span class="linenos">980</span></a> <span class="n">new_version_str</span> <span class="o">=</span> <span class="sa">f</span><span class="s2">"v</span><span class="si">{</span><span class="n">new_version</span><span class="si">}</span><span class="s2">"</span> <span class="k">if</span> <span class="n">use_v_prefix</span> <span class="k">else</span> <span class="nb">str</span><span class="p">(</span><span class="n">new_version</span><span class="p">)</span>
+</span><span id="generate_version_tag-981"><a href="#generate_version_tag-981"><span class="linenos">981</span></a>
+</span><span id="generate_version_tag-982"><a href="#generate_version_tag-982"><span class="linenos">982</span></a> <span class="k">return</span> <span class="n">new_version_str</span>
+</span></pre></div>
+
+
+
+
+ </section>
+ <section id="publish">
+ <input id="publish-view-source" class="view-source-toggle-state" type="checkbox" aria-hidden="true" tabindex="-1">
+<div class="attr function">
+
+ <span class="def">def</span>
+ <span class="name">publish</span><span class="signature pdoc-code condensed">(<span class="param"><span class="n">phen_dir</span><span class="p">:</span> <span class="nb">str</span>, </span><span class="param"><span class="n">msg</span><span class="p">:</span> <span class="nb">str</span>, </span><span class="param"><span class="n">remote_url</span><span class="p">:</span> <span class="nb">str</span>, </span><span class="param"><span class="n">increment</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="s1">'patch'</span></span><span class="return-annotation">):</span></span>
+
+ <label class="view-source-button" for="publish-view-source"><span>View Source</span></label>
+
+ </div>
+ <a class="headerlink" href="#publish"></a>
+ <div class="pdoc-code codehilite"><pre><span></span><span id="publish-985"><a href="#publish-985"><span class="linenos"> 985</span></a><span class="k">def</span><span class="w"> </span><span class="nf">publish</span><span class="p">(</span>
+</span><span id="publish-986"><a href="#publish-986"><span class="linenos"> 986</span></a> <span class="n">phen_dir</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">msg</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">remote_url</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">increment</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="n">DEFAULT_VERSION_INC</span>
+</span><span id="publish-987"><a href="#publish-987"><span class="linenos"> 987</span></a><span class="p">):</span>
+</span><span id="publish-988"><a href="#publish-988"><span class="linenos"> 988</span></a><span class="w"> </span><span class="sd">"""Publishes updates to the phenotype by commiting all changes to the repo directory"""</span>
+</span><span id="publish-989"><a href="#publish-989"><span class="linenos"> 989</span></a>
+</span><span id="publish-990"><a href="#publish-990"><span class="linenos"> 990</span></a> <span class="c1"># Validate config</span>
+</span><span id="publish-991"><a href="#publish-991"><span class="linenos"> 991</span></a> <span class="n">validate</span><span class="p">(</span><span class="n">phen_dir</span><span class="p">)</span>
+</span><span id="publish-992"><a href="#publish-992"><span class="linenos"> 992</span></a> <span class="n">phen_path</span> <span class="o">=</span> <span class="n">Path</span><span class="p">(</span><span class="n">phen_dir</span><span class="p">)</span>
+</span><span id="publish-993"><a href="#publish-993"><span class="linenos"> 993</span></a>
+</span><span id="publish-994"><a href="#publish-994"><span class="linenos"> 994</span></a> <span class="c1"># load git repo and set the branch</span>
+</span><span id="publish-995"><a href="#publish-995"><span class="linenos"> 995</span></a> <span class="n">repo</span> <span class="o">=</span> <span class="n">git</span><span class="o">.</span><span class="n">Repo</span><span class="p">(</span><span class="n">phen_path</span><span class="p">)</span>
+</span><span id="publish-996"><a href="#publish-996"><span class="linenos"> 996</span></a> <span class="k">if</span> <span class="n">DEFAULT_GIT_BRANCH</span> <span class="ow">in</span> <span class="n">repo</span><span class="o">.</span><span class="n">branches</span><span class="p">:</span>
+</span><span id="publish-997"><a href="#publish-997"><span class="linenos"> 997</span></a> <span class="n">main_branch</span> <span class="o">=</span> <span class="n">repo</span><span class="o">.</span><span class="n">heads</span><span class="p">[</span><span class="n">DEFAULT_GIT_BRANCH</span><span class="p">]</span>
+</span><span id="publish-998"><a href="#publish-998"><span class="linenos"> 998</span></a> <span class="n">main_branch</span><span class="o">.</span><span class="n">checkout</span><span class="p">()</span>
+</span><span id="publish-999"><a href="#publish-999"><span class="linenos"> 999</span></a> <span class="k">else</span><span class="p">:</span>
+</span><span id="publish-1000"><a href="#publish-1000"><span class="linenos">1000</span></a> <span class="k">raise</span> <span class="ne">AttributeError</span><span class="p">(</span>
+</span><span id="publish-1001"><a href="#publish-1001"><span class="linenos">1001</span></a> <span class="sa">f</span><span class="s2">"Phen repo does not contain the default branch </span><span class="si">{</span><span class="n">DEFAULT_GIT_BRANCH</span><span class="si">}</span><span class="s2">"</span>
+</span><span id="publish-1002"><a href="#publish-1002"><span class="linenos">1002</span></a> <span class="p">)</span>
+</span><span id="publish-1003"><a href="#publish-1003"><span class="linenos">1003</span></a>
+</span><span id="publish-1004"><a href="#publish-1004"><span class="linenos">1004</span></a> <span class="c1"># check if any changes to publish</span>
+</span><span id="publish-1005"><a href="#publish-1005"><span class="linenos">1005</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="n">repo</span><span class="o">.</span><span class="n">is_dirty</span><span class="p">()</span> <span class="ow">and</span> <span class="ow">not</span> <span class="n">repo</span><span class="o">.</span><span class="n">untracked_files</span><span class="p">:</span>
+</span><span id="publish-1006"><a href="#publish-1006"><span class="linenos">1006</span></a> <span class="k">if</span> <span class="n">remote_url</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span> <span class="ow">and</span> <span class="s2">"origin"</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">repo</span><span class="o">.</span><span class="n">remotes</span><span class="p">:</span>
+</span><span id="publish-1007"><a href="#publish-1007"><span class="linenos">1007</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"First publish to remote url </span><span class="si">{</span><span class="n">remote_url</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+</span><span id="publish-1008"><a href="#publish-1008"><span class="linenos">1008</span></a> <span class="k">else</span><span class="p">:</span>
+</span><span id="publish-1009"><a href="#publish-1009"><span class="linenos">1009</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">"Nothing to publish, no changes to the repo"</span><span class="p">)</span>
+</span><span id="publish-1010"><a href="#publish-1010"><span class="linenos">1010</span></a> <span class="k">return</span>
+</span><span id="publish-1011"><a href="#publish-1011"><span class="linenos">1011</span></a>
+</span><span id="publish-1012"><a href="#publish-1012"><span class="linenos">1012</span></a> <span class="c1"># get next version</span>
+</span><span id="publish-1013"><a href="#publish-1013"><span class="linenos">1013</span></a> <span class="n">new_version_str</span> <span class="o">=</span> <span class="n">generate_version_tag</span><span class="p">(</span><span class="n">repo</span><span class="p">,</span> <span class="n">increment</span><span class="p">)</span>
+</span><span id="publish-1014"><a href="#publish-1014"><span class="linenos">1014</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"New version: </span><span class="si">{</span><span class="n">new_version_str</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+</span><span id="publish-1015"><a href="#publish-1015"><span class="linenos">1015</span></a>
+</span><span id="publish-1016"><a href="#publish-1016"><span class="linenos">1016</span></a> <span class="c1"># Write version in configuration file</span>
+</span><span id="publish-1017"><a href="#publish-1017"><span class="linenos">1017</span></a> <span class="n">config_path</span> <span class="o">=</span> <span class="n">phen_path</span> <span class="o">/</span> <span class="n">CONFIG_FILE</span>
+</span><span id="publish-1018"><a href="#publish-1018"><span class="linenos">1018</span></a> <span class="k">with</span> <span class="n">config_path</span><span class="o">.</span><span class="n">open</span><span class="p">(</span><span class="s2">"r"</span><span class="p">)</span> <span class="k">as</span> <span class="n">file</span><span class="p">:</span>
+</span><span id="publish-1019"><a href="#publish-1019"><span class="linenos">1019</span></a> <span class="n">config</span> <span class="o">=</span> <span class="n">yaml</span><span class="o">.</span><span class="n">safe_load</span><span class="p">(</span><span class="n">file</span><span class="p">)</span>
+</span><span id="publish-1020"><a href="#publish-1020"><span class="linenos">1020</span></a>
+</span><span id="publish-1021"><a href="#publish-1021"><span class="linenos">1021</span></a> <span class="n">config</span><span class="p">[</span><span class="s2">"phenotype"</span><span class="p">][</span><span class="s2">"version"</span><span class="p">]</span> <span class="o">=</span> <span class="n">new_version_str</span>
+</span><span id="publish-1022"><a href="#publish-1022"><span class="linenos">1022</span></a> <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">config_path</span><span class="p">,</span> <span class="s2">"w"</span><span class="p">)</span> <span class="k">as</span> <span class="n">file</span><span class="p">:</span>
+</span><span id="publish-1023"><a href="#publish-1023"><span class="linenos">1023</span></a> <span class="n">yaml</span><span class="o">.</span><span class="n">dump</span><span class="p">(</span>
+</span><span id="publish-1024"><a href="#publish-1024"><span class="linenos">1024</span></a> <span class="n">config</span><span class="p">,</span>
+</span><span id="publish-1025"><a href="#publish-1025"><span class="linenos">1025</span></a> <span class="n">file</span><span class="p">,</span>
+</span><span id="publish-1026"><a href="#publish-1026"><span class="linenos">1026</span></a> <span class="n">Dumper</span><span class="o">=</span><span class="n">util</span><span class="o">.</span><span class="n">QuotedDumper</span><span class="p">,</span>
+</span><span id="publish-1027"><a href="#publish-1027"><span class="linenos">1027</span></a> <span class="n">default_flow_style</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span>
+</span><span id="publish-1028"><a href="#publish-1028"><span class="linenos">1028</span></a> <span class="n">sort_keys</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span>
+</span><span id="publish-1029"><a href="#publish-1029"><span class="linenos">1029</span></a> <span class="n">default_style</span><span class="o">=</span><span class="s1">'"'</span><span class="p">,</span>
+</span><span id="publish-1030"><a href="#publish-1030"><span class="linenos">1030</span></a> <span class="p">)</span>
+</span><span id="publish-1031"><a href="#publish-1031"><span class="linenos">1031</span></a>
+</span><span id="publish-1032"><a href="#publish-1032"><span class="linenos">1032</span></a> <span class="c1"># Add and commit changes to repo including version updates</span>
+</span><span id="publish-1033"><a href="#publish-1033"><span class="linenos">1033</span></a> <span class="n">commit_message</span> <span class="o">=</span> <span class="sa">f</span><span class="s2">"Committing updates to phenotype </span><span class="si">{</span><span class="n">phen_path</span><span class="si">}</span><span class="s2">"</span>
+</span><span id="publish-1034"><a href="#publish-1034"><span class="linenos">1034</span></a> <span class="n">repo</span><span class="o">.</span><span class="n">git</span><span class="o">.</span><span class="n">add</span><span class="p">(</span><span class="s2">"--all"</span><span class="p">)</span>
+</span><span id="publish-1035"><a href="#publish-1035"><span class="linenos">1035</span></a> <span class="n">repo</span><span class="o">.</span><span class="n">index</span><span class="o">.</span><span class="n">commit</span><span class="p">(</span><span class="n">commit_message</span><span class="p">)</span>
+</span><span id="publish-1036"><a href="#publish-1036"><span class="linenos">1036</span></a>
+</span><span id="publish-1037"><a href="#publish-1037"><span class="linenos">1037</span></a> <span class="c1"># Add tag to the repo</span>
+</span><span id="publish-1038"><a href="#publish-1038"><span class="linenos">1038</span></a> <span class="n">repo</span><span class="o">.</span><span class="n">create_tag</span><span class="p">(</span><span class="n">new_version_str</span><span class="p">)</span>
+</span><span id="publish-1039"><a href="#publish-1039"><span class="linenos">1039</span></a>
+</span><span id="publish-1040"><a href="#publish-1040"><span class="linenos">1040</span></a> <span class="c1"># push to origin if a remote repo</span>
+</span><span id="publish-1041"><a href="#publish-1041"><span class="linenos">1041</span></a> <span class="k">if</span> <span class="n">remote_url</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span> <span class="ow">and</span> <span class="s2">"origin"</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">repo</span><span class="o">.</span><span class="n">remotes</span><span class="p">:</span>
+</span><span id="publish-1042"><a href="#publish-1042"><span class="linenos">1042</span></a> <span class="n">git_url</span> <span class="o">=</span> <span class="n">construct_git_url</span><span class="p">(</span><span class="n">remote_url</span><span class="p">)</span>
+</span><span id="publish-1043"><a href="#publish-1043"><span class="linenos">1043</span></a> <span class="n">repo</span><span class="o">.</span><span class="n">create_remote</span><span class="p">(</span><span class="s2">"origin"</span><span class="p">,</span> <span class="n">git_url</span><span class="p">)</span>
+</span><span id="publish-1044"><a href="#publish-1044"><span class="linenos">1044</span></a>
+</span><span id="publish-1045"><a href="#publish-1045"><span class="linenos">1045</span></a> <span class="k">try</span><span class="p">:</span>
+</span><span id="publish-1046"><a href="#publish-1046"><span class="linenos">1046</span></a> <span class="k">if</span> <span class="s2">"origin"</span> <span class="ow">in</span> <span class="n">repo</span><span class="o">.</span><span class="n">remotes</span><span class="p">:</span>
+</span><span id="publish-1047"><a href="#publish-1047"><span class="linenos">1047</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Remote 'origin' is set </span><span class="si">{</span><span class="n">repo</span><span class="o">.</span><span class="n">remotes</span><span class="o">.</span><span class="n">origin</span><span class="o">.</span><span class="n">url</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+</span><span id="publish-1048"><a href="#publish-1048"><span class="linenos">1048</span></a> <span class="n">origin</span> <span class="o">=</span> <span class="n">repo</span><span class="o">.</span><span class="n">remotes</span><span class="o">.</span><span class="n">origin</span>
+</span><span id="publish-1049"><a href="#publish-1049"><span class="linenos">1049</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Pushing main branch to remote repo"</span><span class="p">)</span>
+</span><span id="publish-1050"><a href="#publish-1050"><span class="linenos">1050</span></a> <span class="n">repo</span><span class="o">.</span><span class="n">git</span><span class="o">.</span><span class="n">push</span><span class="p">(</span><span class="s2">"--set-upstream"</span><span class="p">,</span> <span class="s2">"origin"</span><span class="p">,</span> <span class="s2">"main"</span><span class="p">)</span>
+</span><span id="publish-1051"><a href="#publish-1051"><span class="linenos">1051</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Pushing version tags to remote git repo"</span><span class="p">)</span>
+</span><span id="publish-1052"><a href="#publish-1052"><span class="linenos">1052</span></a> <span class="n">origin</span><span class="o">.</span><span class="n">push</span><span class="p">(</span><span class="n">tags</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+</span><span id="publish-1053"><a href="#publish-1053"><span class="linenos">1053</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="s2">"Changes pushed to 'origin'"</span><span class="p">)</span>
+</span><span id="publish-1054"><a href="#publish-1054"><span class="linenos">1054</span></a> <span class="k">else</span><span class="p">:</span>
+</span><span id="publish-1055"><a href="#publish-1055"><span class="linenos">1055</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="s2">"Remote 'origin' is not set"</span><span class="p">)</span>
+</span><span id="publish-1056"><a href="#publish-1056"><span class="linenos">1056</span></a> <span class="k">except</span> <span class="ne">Exception</span> <span class="k">as</span> <span class="n">e</span><span class="p">:</span>
+</span><span id="publish-1057"><a href="#publish-1057"><span class="linenos">1057</span></a> <span class="n">tag_ref</span> <span class="o">=</span> <span class="n">repo</span><span class="o">.</span><span class="n">tags</span><span class="p">[</span><span class="n">new_version_str</span><span class="p">]</span>
+</span><span id="publish-1058"><a href="#publish-1058"><span class="linenos">1058</span></a> <span class="n">repo</span><span class="o">.</span><span class="n">delete_tag</span><span class="p">(</span><span class="n">tag_ref</span><span class="p">)</span>
+</span><span id="publish-1059"><a href="#publish-1059"><span class="linenos">1059</span></a> <span class="n">repo</span><span class="o">.</span><span class="n">git</span><span class="o">.</span><span class="n">reset</span><span class="p">(</span><span class="s2">"--soft"</span><span class="p">,</span> <span class="s2">"HEAD~1"</span><span class="p">)</span>
+</span><span id="publish-1060"><a href="#publish-1060"><span class="linenos">1060</span></a> <span class="k">raise</span> <span class="n">e</span>
+</span><span id="publish-1061"><a href="#publish-1061"><span class="linenos">1061</span></a>
+</span><span id="publish-1062"><a href="#publish-1062"><span class="linenos">1062</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Phenotype published successfully"</span><span class="p">)</span>
+</span></pre></div>
+
+
+ <div class="docstring"><p>Publishes updates to the phenotype by commiting all changes to the repo directory</p>
+</div>
+
+
+ </section>
+ <section id="export">
+ <input id="export-view-source" class="view-source-toggle-state" type="checkbox" aria-hidden="true" tabindex="-1">
+<div class="attr function">
+
+ <span class="def">def</span>
+ <span class="name">export</span><span class="signature pdoc-code condensed">(<span class="param"><span class="n">phen_dir</span><span class="p">:</span> <span class="nb">str</span>, </span><span class="param"><span class="n">version</span><span class="p">:</span> <span class="nb">str</span></span><span class="return-annotation">):</span></span>
+
+ <label class="view-source-button" for="export-view-source"><span>View Source</span></label>
+
+ </div>
+ <a class="headerlink" href="#export"></a>
+ <div class="pdoc-code codehilite"><pre><span></span><span id="export-1065"><a href="#export-1065"><span class="linenos">1065</span></a><span class="k">def</span><span class="w"> </span><span class="nf">export</span><span class="p">(</span><span class="n">phen_dir</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">version</span><span class="p">:</span> <span class="nb">str</span><span class="p">):</span>
+</span><span id="export-1066"><a href="#export-1066"><span class="linenos">1066</span></a><span class="w"> </span><span class="sd">"""Exports a phen repo at a specific tagged version into a target directory"""</span>
+</span><span id="export-1067"><a href="#export-1067"><span class="linenos">1067</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Exporting phenotype </span><span class="si">{</span><span class="n">phen_dir</span><span class="si">}</span><span class="s2"> at version </span><span class="si">{</span><span class="n">version</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+</span><span id="export-1068"><a href="#export-1068"><span class="linenos">1068</span></a>
+</span><span id="export-1069"><a href="#export-1069"><span class="linenos">1069</span></a> <span class="c1"># validate configuration</span>
+</span><span id="export-1070"><a href="#export-1070"><span class="linenos">1070</span></a> <span class="n">validate</span><span class="p">(</span><span class="n">phen_dir</span><span class="p">)</span>
+</span><span id="export-1071"><a href="#export-1071"><span class="linenos">1071</span></a> <span class="n">phen_path</span> <span class="o">=</span> <span class="n">Path</span><span class="p">(</span><span class="n">phen_dir</span><span class="p">)</span>
+</span><span id="export-1072"><a href="#export-1072"><span class="linenos">1072</span></a>
+</span><span id="export-1073"><a href="#export-1073"><span class="linenos">1073</span></a> <span class="c1"># load configuration</span>
+</span><span id="export-1074"><a href="#export-1074"><span class="linenos">1074</span></a> <span class="n">config_path</span> <span class="o">=</span> <span class="n">phen_path</span> <span class="o">/</span> <span class="n">CONFIG_FILE</span>
+</span><span id="export-1075"><a href="#export-1075"><span class="linenos">1075</span></a> <span class="k">with</span> <span class="n">config_path</span><span class="o">.</span><span class="n">open</span><span class="p">(</span><span class="s2">"r"</span><span class="p">)</span> <span class="k">as</span> <span class="n">file</span><span class="p">:</span>
+</span><span id="export-1076"><a href="#export-1076"><span class="linenos">1076</span></a> <span class="n">config</span> <span class="o">=</span> <span class="n">yaml</span><span class="o">.</span><span class="n">safe_load</span><span class="p">(</span><span class="n">file</span><span class="p">)</span>
+</span><span id="export-1077"><a href="#export-1077"><span class="linenos">1077</span></a>
+</span><span id="export-1078"><a href="#export-1078"><span class="linenos">1078</span></a> <span class="n">map_path</span> <span class="o">=</span> <span class="n">phen_path</span> <span class="o">/</span> <span class="n">MAP_DIR</span>
+</span><span id="export-1079"><a href="#export-1079"><span class="linenos">1079</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="n">map_path</span><span class="o">.</span><span class="n">exists</span><span class="p">():</span>
+</span><span id="export-1080"><a href="#export-1080"><span class="linenos">1080</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">warning</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Map path does not exist '</span><span class="si">{</span><span class="n">map_path</span><span class="si">}</span><span class="s2">'"</span><span class="p">)</span>
+</span><span id="export-1081"><a href="#export-1081"><span class="linenos">1081</span></a>
+</span><span id="export-1082"><a href="#export-1082"><span class="linenos">1082</span></a> <span class="n">export_path</span> <span class="o">=</span> <span class="n">phen_path</span> <span class="o">/</span> <span class="n">OMOP_PATH</span>
+</span><span id="export-1083"><a href="#export-1083"><span class="linenos">1083</span></a> <span class="c1"># check export directory exists and if not create it</span>
+</span><span id="export-1084"><a href="#export-1084"><span class="linenos">1084</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="n">export_path</span><span class="o">.</span><span class="n">exists</span><span class="p">():</span>
+</span><span id="export-1085"><a href="#export-1085"><span class="linenos">1085</span></a> <span class="n">export_path</span><span class="o">.</span><span class="n">mkdir</span><span class="p">(</span><span class="n">parents</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+</span><span id="export-1086"><a href="#export-1086"><span class="linenos">1086</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="sa">f</span><span class="s2">"OMOP export directory '</span><span class="si">{</span><span class="n">export_path</span><span class="si">}</span><span class="s2">' created."</span><span class="p">)</span>
+</span><span id="export-1087"><a href="#export-1087"><span class="linenos">1087</span></a>
+</span><span id="export-1088"><a href="#export-1088"><span class="linenos">1088</span></a> <span class="c1"># omop export db</span>
+</span><span id="export-1089"><a href="#export-1089"><span class="linenos">1089</span></a> <span class="n">export_db_path</span> <span class="o">=</span> <span class="n">omop</span><span class="o">.</span><span class="n">export</span><span class="p">(</span>
+</span><span id="export-1090"><a href="#export-1090"><span class="linenos">1090</span></a> <span class="n">map_path</span><span class="p">,</span>
+</span><span id="export-1091"><a href="#export-1091"><span class="linenos">1091</span></a> <span class="n">export_path</span><span class="p">,</span>
+</span><span id="export-1092"><a href="#export-1092"><span class="linenos">1092</span></a> <span class="n">config</span><span class="p">[</span><span class="s2">"phenotype"</span><span class="p">][</span><span class="s2">"version"</span><span class="p">],</span>
+</span><span id="export-1093"><a href="#export-1093"><span class="linenos">1093</span></a> <span class="n">config</span><span class="p">[</span><span class="s2">"phenotype"</span><span class="p">][</span><span class="s2">"omop"</span><span class="p">],</span>
+</span><span id="export-1094"><a href="#export-1094"><span class="linenos">1094</span></a> <span class="p">)</span>
+</span><span id="export-1095"><a href="#export-1095"><span class="linenos">1095</span></a>
+</span><span id="export-1096"><a href="#export-1096"><span class="linenos">1096</span></a> <span class="c1"># write to tables</span>
+</span><span id="export-1097"><a href="#export-1097"><span class="linenos">1097</span></a> <span class="c1"># export as csv</span>
+</span><span id="export-1098"><a href="#export-1098"><span class="linenos">1098</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Phenotype exported successfully"</span><span class="p">)</span>
+</span></pre></div>
+
+
+ <div class="docstring"><p>Exports a phen repo at a specific tagged version into a target directory</p>
+</div>
+
+
+ </section>
+ <section id="copy">
+ <input id="copy-view-source" class="view-source-toggle-state" type="checkbox" aria-hidden="true" tabindex="-1">
+<div class="attr function">
+
+ <span class="def">def</span>
+ <span class="name">copy</span><span class="signature pdoc-code condensed">(<span class="param"><span class="n">phen_dir</span><span class="p">:</span> <span class="nb">str</span>, </span><span class="param"><span class="n">target_dir</span><span class="p">:</span> <span class="nb">str</span>, </span><span class="param"><span class="n">version</span><span class="p">:</span> <span class="nb">str</span></span><span class="return-annotation">):</span></span>
+
+ <label class="view-source-button" for="copy-view-source"><span>View Source</span></label>
+
+ </div>
+ <a class="headerlink" href="#copy"></a>
+ <div class="pdoc-code codehilite"><pre><span></span><span id="copy-1101"><a href="#copy-1101"><span class="linenos">1101</span></a><span class="k">def</span><span class="w"> </span><span class="nf">copy</span><span class="p">(</span><span class="n">phen_dir</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">target_dir</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">version</span><span class="p">:</span> <span class="nb">str</span><span class="p">):</span>
+</span><span id="copy-1102"><a href="#copy-1102"><span class="linenos">1102</span></a><span class="w"> </span><span class="sd">"""Copys a phen repo at a specific tagged version into a target directory"""</span>
+</span><span id="copy-1103"><a href="#copy-1103"><span class="linenos">1103</span></a>
+</span><span id="copy-1104"><a href="#copy-1104"><span class="linenos">1104</span></a> <span class="c1"># Validate</span>
+</span><span id="copy-1105"><a href="#copy-1105"><span class="linenos">1105</span></a> <span class="n">validate</span><span class="p">(</span><span class="n">phen_dir</span><span class="p">)</span>
+</span><span id="copy-1106"><a href="#copy-1106"><span class="linenos">1106</span></a> <span class="n">phen_path</span> <span class="o">=</span> <span class="n">Path</span><span class="p">(</span><span class="n">phen_dir</span><span class="p">)</span>
+</span><span id="copy-1107"><a href="#copy-1107"><span class="linenos">1107</span></a>
+</span><span id="copy-1108"><a href="#copy-1108"><span class="linenos">1108</span></a> <span class="c1"># Check target directory exists</span>
+</span><span id="copy-1109"><a href="#copy-1109"><span class="linenos">1109</span></a> <span class="n">target_path</span> <span class="o">=</span> <span class="n">Path</span><span class="p">(</span><span class="n">target_dir</span><span class="p">)</span>
+</span><span id="copy-1110"><a href="#copy-1110"><span class="linenos">1110</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="n">target_path</span><span class="o">.</span><span class="n">exists</span><span class="p">():</span>
+</span><span id="copy-1111"><a href="#copy-1111"><span class="linenos">1111</span></a> <span class="k">raise</span> <span class="ne">FileNotFoundError</span><span class="p">(</span><span class="sa">f</span><span class="s2">"The target directory </span><span class="si">{</span><span class="n">target_path</span><span class="si">}</span><span class="s2"> does not exist"</span><span class="p">)</span>
+</span><span id="copy-1112"><a href="#copy-1112"><span class="linenos">1112</span></a>
+</span><span id="copy-1113"><a href="#copy-1113"><span class="linenos">1113</span></a> <span class="c1"># Set copy directory</span>
+</span><span id="copy-1114"><a href="#copy-1114"><span class="linenos">1114</span></a> <span class="n">copy_path</span> <span class="o">=</span> <span class="n">target_path</span> <span class="o">/</span> <span class="n">version</span>
+</span><span id="copy-1115"><a href="#copy-1115"><span class="linenos">1115</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Copying repo </span><span class="si">{</span><span class="n">phen_path</span><span class="si">}</span><span class="s2"> to </span><span class="si">{</span><span class="n">copy_path</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+</span><span id="copy-1116"><a href="#copy-1116"><span class="linenos">1116</span></a>
+</span><span id="copy-1117"><a href="#copy-1117"><span class="linenos">1117</span></a> <span class="k">if</span> <span class="p">(</span>
+</span><span id="copy-1118"><a href="#copy-1118"><span class="linenos">1118</span></a> <span class="n">copy_path</span><span class="o">.</span><span class="n">exists</span><span class="p">()</span> <span class="ow">and</span> <span class="n">copy_path</span><span class="o">.</span><span class="n">is_dir</span><span class="p">()</span>
+</span><span id="copy-1119"><a href="#copy-1119"><span class="linenos">1119</span></a> <span class="p">):</span> <span class="c1"># Check if it exists and is a directory</span>
+</span><span id="copy-1120"><a href="#copy-1120"><span class="linenos">1120</span></a> <span class="n">copy</span> <span class="o">=</span> <span class="n">check_delete_dir</span><span class="p">(</span>
+</span><span id="copy-1121"><a href="#copy-1121"><span class="linenos">1121</span></a> <span class="n">copy_path</span><span class="p">,</span>
+</span><span id="copy-1122"><a href="#copy-1122"><span class="linenos">1122</span></a> <span class="sa">f</span><span class="s2">"The directory </span><span class="si">{</span><span class="nb">str</span><span class="p">(</span><span class="n">copy_path</span><span class="o">.</span><span class="n">resolve</span><span class="p">())</span><span class="si">}</span><span class="s2"> already exists. Do you want to overwrite? (yes/no): "</span><span class="p">,</span>
+</span><span id="copy-1123"><a href="#copy-1123"><span class="linenos">1123</span></a> <span class="p">)</span>
+</span><span id="copy-1124"><a href="#copy-1124"><span class="linenos">1124</span></a> <span class="k">else</span><span class="p">:</span>
+</span><span id="copy-1125"><a href="#copy-1125"><span class="linenos">1125</span></a> <span class="n">copy</span> <span class="o">=</span> <span class="kc">True</span>
+</span><span id="copy-1126"><a href="#copy-1126"><span class="linenos">1126</span></a>
+</span><span id="copy-1127"><a href="#copy-1127"><span class="linenos">1127</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="n">copy</span><span class="p">:</span>
+</span><span id="copy-1128"><a href="#copy-1128"><span class="linenos">1128</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Not copying the version </span><span class="si">{</span><span class="n">version</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+</span><span id="copy-1129"><a href="#copy-1129"><span class="linenos">1129</span></a> <span class="k">return</span>
+</span><span id="copy-1130"><a href="#copy-1130"><span class="linenos">1130</span></a>
+</span><span id="copy-1131"><a href="#copy-1131"><span class="linenos">1131</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Cloning repo from </span><span class="si">{</span><span class="n">phen_path</span><span class="si">}</span><span class="s2"> into </span><span class="si">{</span><span class="n">copy_path</span><span class="si">}</span><span class="s2">..."</span><span class="p">)</span>
+</span><span id="copy-1132"><a href="#copy-1132"><span class="linenos">1132</span></a> <span class="n">repo</span> <span class="o">=</span> <span class="n">git</span><span class="o">.</span><span class="n">Repo</span><span class="o">.</span><span class="n">clone_from</span><span class="p">(</span><span class="n">phen_path</span><span class="p">,</span> <span class="n">copy_path</span><span class="p">)</span>
+</span><span id="copy-1133"><a href="#copy-1133"><span class="linenos">1133</span></a>
+</span><span id="copy-1134"><a href="#copy-1134"><span class="linenos">1134</span></a> <span class="c1"># Check out the latest commit or specified version</span>
+</span><span id="copy-1135"><a href="#copy-1135"><span class="linenos">1135</span></a> <span class="k">if</span> <span class="n">version</span><span class="p">:</span>
+</span><span id="copy-1136"><a href="#copy-1136"><span class="linenos">1136</span></a> <span class="c1"># Checkout a specific version (e.g., branch, tag, or commit hash)</span>
+</span><span id="copy-1137"><a href="#copy-1137"><span class="linenos">1137</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Checking out version </span><span class="si">{</span><span class="n">version</span><span class="si">}</span><span class="s2">..."</span><span class="p">)</span>
+</span><span id="copy-1138"><a href="#copy-1138"><span class="linenos">1138</span></a> <span class="n">repo</span><span class="o">.</span><span class="n">git</span><span class="o">.</span><span class="n">checkout</span><span class="p">(</span><span class="n">version</span><span class="p">)</span>
+</span><span id="copy-1139"><a href="#copy-1139"><span class="linenos">1139</span></a> <span class="k">else</span><span class="p">:</span>
+</span><span id="copy-1140"><a href="#copy-1140"><span class="linenos">1140</span></a> <span class="c1"># Checkout the latest commit (HEAD)</span>
+</span><span id="copy-1141"><a href="#copy-1141"><span class="linenos">1141</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Checking out the latest commit..."</span><span class="p">)</span>
+</span><span id="copy-1142"><a href="#copy-1142"><span class="linenos">1142</span></a> <span class="n">repo</span><span class="o">.</span><span class="n">git</span><span class="o">.</span><span class="n">checkout</span><span class="p">(</span><span class="s2">"HEAD"</span><span class="p">)</span>
+</span><span id="copy-1143"><a href="#copy-1143"><span class="linenos">1143</span></a>
+</span><span id="copy-1144"><a href="#copy-1144"><span class="linenos">1144</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Copied </span><span class="si">{</span><span class="n">phen_path</span><span class="si">}</span><span class="s2"> </span><span class="si">{</span><span class="n">repo</span><span class="o">.</span><span class="n">head</span><span class="o">.</span><span class="n">commit</span><span class="o">.</span><span class="n">hexsha</span><span class="p">[:</span><span class="mi">7</span><span class="p">]</span><span class="si">}</span><span class="s2"> in </span><span class="si">{</span><span class="n">copy_path</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+</span><span id="copy-1145"><a href="#copy-1145"><span class="linenos">1145</span></a>
+</span><span id="copy-1146"><a href="#copy-1146"><span class="linenos">1146</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Phenotype copied successfully"</span><span class="p">)</span>
+</span></pre></div>
+
+
+ <div class="docstring"><p>Copys a phen repo at a specific tagged version into a target directory</p>
+</div>
+
+
+ </section>
+ <section id="extract_concepts">
+ <input id="extract_concepts-view-source" class="view-source-toggle-state" type="checkbox" aria-hidden="true" tabindex="-1">
+<div class="attr function">
+
+ <span class="def">def</span>
+ <span class="name">extract_concepts</span><span class="signature pdoc-code condensed">(<span class="param"><span class="n">config_data</span><span class="p">:</span> <span class="nb">dict</span></span><span class="return-annotation">) -> <span class="n">Tuple</span><span class="p">[</span><span class="nb">dict</span><span class="p">,</span> <span class="n">Set</span><span class="p">[</span><span class="nb">str</span><span class="p">]]</span>:</span></span>
+
+ <label class="view-source-button" for="extract_concepts-view-source"><span>View Source</span></label>
+
+ </div>
+ <a class="headerlink" href="#extract_concepts"></a>
+ <div class="pdoc-code codehilite"><pre><span></span><span id="extract_concepts-1150"><a href="#extract_concepts-1150"><span class="linenos">1150</span></a><span class="k">def</span><span class="w"> </span><span class="nf">extract_concepts</span><span class="p">(</span><span class="n">config_data</span><span class="p">:</span> <span class="nb">dict</span><span class="p">)</span> <span class="o">-></span> <span class="n">Tuple</span><span class="p">[</span><span class="nb">dict</span><span class="p">,</span> <span class="n">Set</span><span class="p">[</span><span class="nb">str</span><span class="p">]]:</span>
+</span><span id="extract_concepts-1151"><a href="#extract_concepts-1151"><span class="linenos">1151</span></a><span class="w"> </span><span class="sd">"""Extracts concepts as {name: file_path} dictionary and a name set."""</span>
+</span><span id="extract_concepts-1152"><a href="#extract_concepts-1152"><span class="linenos">1152</span></a> <span class="n">concepts_dict</span> <span class="o">=</span> <span class="p">{</span>
+</span><span id="extract_concepts-1153"><a href="#extract_concepts-1153"><span class="linenos">1153</span></a> <span class="n">item</span><span class="p">[</span><span class="s2">"name"</span><span class="p">]:</span> <span class="n">item</span><span class="p">[</span><span class="s2">"file"</span><span class="p">][</span><span class="s2">"path"</span><span class="p">]</span>
+</span><span id="extract_concepts-1154"><a href="#extract_concepts-1154"><span class="linenos">1154</span></a> <span class="k">for</span> <span class="n">item</span> <span class="ow">in</span> <span class="n">config_data</span><span class="p">[</span><span class="s2">"phenotype"</span><span class="p">][</span><span class="s2">"concept_sets"</span><span class="p">]</span>
+</span><span id="extract_concepts-1155"><a href="#extract_concepts-1155"><span class="linenos">1155</span></a> <span class="p">}</span>
+</span><span id="extract_concepts-1156"><a href="#extract_concepts-1156"><span class="linenos">1156</span></a> <span class="n">name_set</span> <span class="o">=</span> <span class="nb">set</span><span class="p">(</span><span class="n">concepts_dict</span><span class="o">.</span><span class="n">keys</span><span class="p">())</span>
+</span><span id="extract_concepts-1157"><a href="#extract_concepts-1157"><span class="linenos">1157</span></a> <span class="k">return</span> <span class="n">concepts_dict</span><span class="p">,</span> <span class="n">name_set</span>
+</span></pre></div>
+
+
+ <div class="docstring"><p>Extracts concepts as {name: file_path} dictionary and a name set.</p>
+</div>
+
+
+ </section>
+ <section id="extract_clean_deepdiff_keys">
+ <input id="extract_clean_deepdiff_keys-view-source" class="view-source-toggle-state" type="checkbox" aria-hidden="true" tabindex="-1">
+<div class="attr function">
+
+ <span class="def">def</span>
+ <span class="name">extract_clean_deepdiff_keys</span><span class="signature pdoc-code condensed">(<span class="param"><span class="n">diff</span><span class="p">:</span> <span class="nb">dict</span>, </span><span class="param"><span class="n">key_type</span><span class="p">:</span> <span class="nb">str</span></span><span class="return-annotation">) -> <span class="n">Set</span><span class="p">[</span><span class="n">Any</span><span class="p">]</span>:</span></span>
+
+ <label class="view-source-button" for="extract_clean_deepdiff_keys-view-source"><span>View Source</span></label>
+
+ </div>
+ <a class="headerlink" href="#extract_clean_deepdiff_keys"></a>
+ <div class="pdoc-code codehilite"><pre><span></span><span id="extract_clean_deepdiff_keys-1160"><a href="#extract_clean_deepdiff_keys-1160"><span class="linenos">1160</span></a><span class="k">def</span><span class="w"> </span><span class="nf">extract_clean_deepdiff_keys</span><span class="p">(</span><span class="n">diff</span><span class="p">:</span> <span class="nb">dict</span><span class="p">,</span> <span class="n">key_type</span><span class="p">:</span> <span class="nb">str</span><span class="p">)</span> <span class="o">-></span> <span class="n">Set</span><span class="p">[</span><span class="n">Any</span><span class="p">]:</span>
+</span><span id="extract_clean_deepdiff_keys-1161"><a href="#extract_clean_deepdiff_keys-1161"><span class="linenos">1161</span></a><span class="w"> </span><span class="sd">"""</span>
+</span><span id="extract_clean_deepdiff_keys-1162"><a href="#extract_clean_deepdiff_keys-1162"><span class="linenos">1162</span></a><span class="sd"> Extracts clean keys from a DeepDiff dictionary.</span>
+</span><span id="extract_clean_deepdiff_keys-1163"><a href="#extract_clean_deepdiff_keys-1163"><span class="linenos">1163</span></a>
+</span><span id="extract_clean_deepdiff_keys-1164"><a href="#extract_clean_deepdiff_keys-1164"><span class="linenos">1164</span></a><span class="sd"> :param diff: DeepDiff result dictionary</span>
+</span><span id="extract_clean_deepdiff_keys-1165"><a href="#extract_clean_deepdiff_keys-1165"><span class="linenos">1165</span></a><span class="sd"> :param key_type: The type of change to extract (e.g., "dictionary_item_added", "dictionary_item_removed")</span>
+</span><span id="extract_clean_deepdiff_keys-1166"><a href="#extract_clean_deepdiff_keys-1166"><span class="linenos">1166</span></a><span class="sd"> :return: A set of clean key names</span>
+</span><span id="extract_clean_deepdiff_keys-1167"><a href="#extract_clean_deepdiff_keys-1167"><span class="linenos">1167</span></a><span class="sd"> """</span>
+</span><span id="extract_clean_deepdiff_keys-1168"><a href="#extract_clean_deepdiff_keys-1168"><span class="linenos">1168</span></a> <span class="k">return</span> <span class="p">{</span><span class="n">key</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s2">"root['"</span><span class="p">)[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s2">"']"</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span> <span class="k">for</span> <span class="n">key</span> <span class="ow">in</span> <span class="n">diff</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">key_type</span><span class="p">,</span> <span class="p">[])}</span>
+</span></pre></div>
+
+
+ <div class="docstring"><p>Extracts clean keys from a DeepDiff dictionary.</p>
+
+<p>:param diff: DeepDiff result dictionary
+:param key_type: The type of change to extract (e.g., "dictionary_item_added", "dictionary_item_removed")
+:return: A set of clean key names</p>
+</div>
+
+
+ </section>
+ <section id="diff_config">
+ <input id="diff_config-view-source" class="view-source-toggle-state" type="checkbox" aria-hidden="true" tabindex="-1">
+<div class="attr function">
+
+ <span class="def">def</span>
+ <span class="name">diff_config</span><span class="signature pdoc-code condensed">(<span class="param"><span class="n">old_config</span><span class="p">:</span> <span class="nb">dict</span>, </span><span class="param"><span class="n">new_config</span><span class="p">:</span> <span class="nb">dict</span></span><span class="return-annotation">) -> <span class="nb">str</span>:</span></span>
+
+ <label class="view-source-button" for="diff_config-view-source"><span>View Source</span></label>
+
+ </div>
+ <a class="headerlink" href="#diff_config"></a>
+ <div class="pdoc-code codehilite"><pre><span></span><span id="diff_config-1171"><a href="#diff_config-1171"><span class="linenos">1171</span></a><span class="k">def</span><span class="w"> </span><span class="nf">diff_config</span><span class="p">(</span><span class="n">old_config</span><span class="p">:</span> <span class="nb">dict</span><span class="p">,</span> <span class="n">new_config</span><span class="p">:</span> <span class="nb">dict</span><span class="p">)</span> <span class="o">-></span> <span class="nb">str</span><span class="p">:</span>
+</span><span id="diff_config-1172"><a href="#diff_config-1172"><span class="linenos">1172</span></a> <span class="n">report</span> <span class="o">=</span> <span class="sa">f</span><span class="s2">"</span><span class="se">\n</span><span class="s2"># Changes to phenotype configuration</span><span class="se">\n</span><span class="s2">"</span>
+</span><span id="diff_config-1173"><a href="#diff_config-1173"><span class="linenos">1173</span></a> <span class="n">report</span> <span class="o">+=</span> <span class="sa">f</span><span class="s2">"This compares changes in the phenotype configuration including added, removed and renamed concept sets and changes to concept set source concept code file paths</span><span class="se">\n\n</span><span class="s2">"</span>
+</span><span id="diff_config-1174"><a href="#diff_config-1174"><span class="linenos">1174</span></a>
+</span><span id="diff_config-1175"><a href="#diff_config-1175"><span class="linenos">1175</span></a> <span class="n">old_concepts</span><span class="p">,</span> <span class="n">old_names</span> <span class="o">=</span> <span class="n">extract_concepts</span><span class="p">(</span><span class="n">old_config</span><span class="p">)</span>
+</span><span id="diff_config-1176"><a href="#diff_config-1176"><span class="linenos">1176</span></a> <span class="n">new_concepts</span><span class="p">,</span> <span class="n">new_names</span> <span class="o">=</span> <span class="n">extract_concepts</span><span class="p">(</span><span class="n">new_config</span><span class="p">)</span>
+</span><span id="diff_config-1177"><a href="#diff_config-1177"><span class="linenos">1177</span></a>
+</span><span id="diff_config-1178"><a href="#diff_config-1178"><span class="linenos">1178</span></a> <span class="c1"># Check added and removed names</span>
+</span><span id="diff_config-1179"><a href="#diff_config-1179"><span class="linenos">1179</span></a> <span class="n">added_names</span> <span class="o">=</span> <span class="n">new_names</span> <span class="o">-</span> <span class="n">old_names</span> <span class="c1"># Names that appear in new but not in old</span>
+</span><span id="diff_config-1180"><a href="#diff_config-1180"><span class="linenos">1180</span></a> <span class="n">removed_names</span> <span class="o">=</span> <span class="n">old_names</span> <span class="o">-</span> <span class="n">new_names</span> <span class="c1"># Names that were in old but not in new</span>
+</span><span id="diff_config-1181"><a href="#diff_config-1181"><span class="linenos">1181</span></a>
+</span><span id="diff_config-1182"><a href="#diff_config-1182"><span class="linenos">1182</span></a> <span class="c1"># find file path changes for unchanged names</span>
+</span><span id="diff_config-1183"><a href="#diff_config-1183"><span class="linenos">1183</span></a> <span class="n">unchanged_names</span> <span class="o">=</span> <span class="n">old_names</span> <span class="o">&</span> <span class="n">new_names</span> <span class="c1"># Names that exist in both</span>
+</span><span id="diff_config-1184"><a href="#diff_config-1184"><span class="linenos">1184</span></a> <span class="n">file_diff</span> <span class="o">=</span> <span class="n">DeepDiff</span><span class="p">(</span>
+</span><span id="diff_config-1185"><a href="#diff_config-1185"><span class="linenos">1185</span></a> <span class="p">{</span><span class="n">name</span><span class="p">:</span> <span class="n">old_concepts</span><span class="p">[</span><span class="n">name</span><span class="p">]</span> <span class="k">for</span> <span class="n">name</span> <span class="ow">in</span> <span class="n">unchanged_names</span><span class="p">},</span>
+</span><span id="diff_config-1186"><a href="#diff_config-1186"><span class="linenos">1186</span></a> <span class="p">{</span><span class="n">name</span><span class="p">:</span> <span class="n">new_concepts</span><span class="p">[</span><span class="n">name</span><span class="p">]</span> <span class="k">for</span> <span class="n">name</span> <span class="ow">in</span> <span class="n">unchanged_names</span><span class="p">},</span>
+</span><span id="diff_config-1187"><a href="#diff_config-1187"><span class="linenos">1187</span></a> <span class="p">)</span>
+</span><span id="diff_config-1188"><a href="#diff_config-1188"><span class="linenos">1188</span></a>
+</span><span id="diff_config-1189"><a href="#diff_config-1189"><span class="linenos">1189</span></a> <span class="c1"># Find renamed concepts (same file, different name)</span>
+</span><span id="diff_config-1190"><a href="#diff_config-1190"><span class="linenos">1190</span></a> <span class="n">renamed_concepts</span> <span class="o">=</span> <span class="p">[]</span>
+</span><span id="diff_config-1191"><a href="#diff_config-1191"><span class="linenos">1191</span></a> <span class="k">for</span> <span class="n">removed</span> <span class="ow">in</span> <span class="n">removed_names</span><span class="p">:</span>
+</span><span id="diff_config-1192"><a href="#diff_config-1192"><span class="linenos">1192</span></a> <span class="n">old_path</span> <span class="o">=</span> <span class="n">old_concepts</span><span class="p">[</span><span class="n">removed</span><span class="p">]</span>
+</span><span id="diff_config-1193"><a href="#diff_config-1193"><span class="linenos">1193</span></a> <span class="k">for</span> <span class="n">added</span> <span class="ow">in</span> <span class="n">added_names</span><span class="p">:</span>
+</span><span id="diff_config-1194"><a href="#diff_config-1194"><span class="linenos">1194</span></a> <span class="n">new_path</span> <span class="o">=</span> <span class="n">new_concepts</span><span class="p">[</span><span class="n">added</span><span class="p">]</span>
+</span><span id="diff_config-1195"><a href="#diff_config-1195"><span class="linenos">1195</span></a> <span class="k">if</span> <span class="n">old_path</span> <span class="o">==</span> <span class="n">new_path</span><span class="p">:</span>
+</span><span id="diff_config-1196"><a href="#diff_config-1196"><span class="linenos">1196</span></a> <span class="n">renamed_concepts</span><span class="o">.</span><span class="n">append</span><span class="p">((</span><span class="n">removed</span><span class="p">,</span> <span class="n">added</span><span class="p">))</span>
+</span><span id="diff_config-1197"><a href="#diff_config-1197"><span class="linenos">1197</span></a>
+</span><span id="diff_config-1198"><a href="#diff_config-1198"><span class="linenos">1198</span></a> <span class="c1"># Remove renamed concepts from added and removed sets</span>
+</span><span id="diff_config-1199"><a href="#diff_config-1199"><span class="linenos">1199</span></a> <span class="k">for</span> <span class="n">old_name</span><span class="p">,</span> <span class="n">new_name</span> <span class="ow">in</span> <span class="n">renamed_concepts</span><span class="p">:</span>
+</span><span id="diff_config-1200"><a href="#diff_config-1200"><span class="linenos">1200</span></a> <span class="n">added_names</span><span class="o">.</span><span class="n">discard</span><span class="p">(</span><span class="n">new_name</span><span class="p">)</span>
+</span><span id="diff_config-1201"><a href="#diff_config-1201"><span class="linenos">1201</span></a> <span class="n">removed_names</span><span class="o">.</span><span class="n">discard</span><span class="p">(</span><span class="n">old_name</span><span class="p">)</span>
+</span><span id="diff_config-1202"><a href="#diff_config-1202"><span class="linenos">1202</span></a>
+</span><span id="diff_config-1203"><a href="#diff_config-1203"><span class="linenos">1203</span></a> <span class="c1"># generate config report</span>
+</span><span id="diff_config-1204"><a href="#diff_config-1204"><span class="linenos">1204</span></a> <span class="k">if</span> <span class="n">added_names</span><span class="p">:</span>
+</span><span id="diff_config-1205"><a href="#diff_config-1205"><span class="linenos">1205</span></a> <span class="n">report</span> <span class="o">+=</span> <span class="s2">"## Added Concepts</span><span class="se">\n</span><span class="s2">"</span>
+</span><span id="diff_config-1206"><a href="#diff_config-1206"><span class="linenos">1206</span></a> <span class="k">for</span> <span class="n">name</span> <span class="ow">in</span> <span class="n">added_names</span><span class="p">:</span>
+</span><span id="diff_config-1207"><a href="#diff_config-1207"><span class="linenos">1207</span></a> <span class="n">report</span> <span class="o">+=</span> <span class="sa">f</span><span class="s2">"- `</span><span class="si">{</span><span class="n">name</span><span class="si">}</span><span class="s2">` (File: `</span><span class="si">{</span><span class="n">new_concepts</span><span class="p">[</span><span class="n">name</span><span class="p">]</span><span class="si">}</span><span class="s2">`)</span><span class="se">\n</span><span class="s2">"</span>
+</span><span id="diff_config-1208"><a href="#diff_config-1208"><span class="linenos">1208</span></a> <span class="n">report</span> <span class="o">+=</span> <span class="s2">"</span><span class="se">\n</span><span class="s2">"</span>
+</span><span id="diff_config-1209"><a href="#diff_config-1209"><span class="linenos">1209</span></a>
+</span><span id="diff_config-1210"><a href="#diff_config-1210"><span class="linenos">1210</span></a> <span class="k">if</span> <span class="n">removed_names</span><span class="p">:</span>
+</span><span id="diff_config-1211"><a href="#diff_config-1211"><span class="linenos">1211</span></a> <span class="n">report</span> <span class="o">+=</span> <span class="s2">"## Removed Concepts</span><span class="se">\n</span><span class="s2">"</span>
+</span><span id="diff_config-1212"><a href="#diff_config-1212"><span class="linenos">1212</span></a> <span class="k">for</span> <span class="n">name</span> <span class="ow">in</span> <span class="n">removed_names</span><span class="p">:</span>
+</span><span id="diff_config-1213"><a href="#diff_config-1213"><span class="linenos">1213</span></a> <span class="n">report</span> <span class="o">+=</span> <span class="sa">f</span><span class="s2">"- `</span><span class="si">{</span><span class="n">name</span><span class="si">}</span><span class="s2">` (File: `</span><span class="si">{</span><span class="n">old_concepts</span><span class="p">[</span><span class="n">name</span><span class="p">]</span><span class="si">}</span><span class="s2">`)</span><span class="se">\n</span><span class="s2">"</span>
+</span><span id="diff_config-1214"><a href="#diff_config-1214"><span class="linenos">1214</span></a> <span class="n">report</span> <span class="o">+=</span> <span class="s2">"</span><span class="se">\n</span><span class="s2">"</span>
+</span><span id="diff_config-1215"><a href="#diff_config-1215"><span class="linenos">1215</span></a>
+</span><span id="diff_config-1216"><a href="#diff_config-1216"><span class="linenos">1216</span></a> <span class="k">if</span> <span class="n">renamed_concepts</span><span class="p">:</span>
+</span><span id="diff_config-1217"><a href="#diff_config-1217"><span class="linenos">1217</span></a> <span class="n">report</span> <span class="o">+=</span> <span class="s2">"## Renamed Concepts</span><span class="se">\n</span><span class="s2">"</span>
+</span><span id="diff_config-1218"><a href="#diff_config-1218"><span class="linenos">1218</span></a> <span class="k">for</span> <span class="n">old_name</span><span class="p">,</span> <span class="n">new_name</span> <span class="ow">in</span> <span class="n">renamed_concepts</span><span class="p">:</span>
+</span><span id="diff_config-1219"><a href="#diff_config-1219"><span class="linenos">1219</span></a> <span class="n">report</span> <span class="o">+=</span> <span class="p">(</span>
+</span><span id="diff_config-1220"><a href="#diff_config-1220"><span class="linenos">1220</span></a> <span class="sa">f</span><span class="s2">"- `</span><span class="si">{</span><span class="n">old_name</span><span class="si">}</span><span class="s2">` âž `</span><span class="si">{</span><span class="n">new_name</span><span class="si">}</span><span class="s2">` (File: `</span><span class="si">{</span><span class="n">old_concepts</span><span class="p">[</span><span class="n">old_name</span><span class="p">]</span><span class="si">}</span><span class="s2">`)</span><span class="se">\n</span><span class="s2">"</span>
+</span><span id="diff_config-1221"><a href="#diff_config-1221"><span class="linenos">1221</span></a> <span class="p">)</span>
+</span><span id="diff_config-1222"><a href="#diff_config-1222"><span class="linenos">1222</span></a> <span class="n">report</span> <span class="o">+=</span> <span class="s2">"</span><span class="se">\n</span><span class="s2">"</span>
+</span><span id="diff_config-1223"><a href="#diff_config-1223"><span class="linenos">1223</span></a>
+</span><span id="diff_config-1224"><a href="#diff_config-1224"><span class="linenos">1224</span></a> <span class="k">if</span> <span class="s2">"values_changed"</span> <span class="ow">in</span> <span class="n">file_diff</span><span class="p">:</span>
+</span><span id="diff_config-1225"><a href="#diff_config-1225"><span class="linenos">1225</span></a> <span class="n">report</span> <span class="o">+=</span> <span class="s2">"## Updated File Paths</span><span class="se">\n</span><span class="s2">"</span>
+</span><span id="diff_config-1226"><a href="#diff_config-1226"><span class="linenos">1226</span></a> <span class="k">for</span> <span class="n">name</span><span class="p">,</span> <span class="n">change</span> <span class="ow">in</span> <span class="n">file_diff</span><span class="p">[</span><span class="s2">"values_changed"</span><span class="p">]</span><span class="o">.</span><span class="n">items</span><span class="p">():</span>
+</span><span id="diff_config-1227"><a href="#diff_config-1227"><span class="linenos">1227</span></a> <span class="n">old_file</span> <span class="o">=</span> <span class="n">change</span><span class="p">[</span><span class="s2">"old_value"</span><span class="p">]</span>
+</span><span id="diff_config-1228"><a href="#diff_config-1228"><span class="linenos">1228</span></a> <span class="n">new_file</span> <span class="o">=</span> <span class="n">change</span><span class="p">[</span><span class="s2">"new_value"</span><span class="p">]</span>
+</span><span id="diff_config-1229"><a href="#diff_config-1229"><span class="linenos">1229</span></a> <span class="n">clean_name</span> <span class="o">=</span> <span class="n">name</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s2">"root['"</span><span class="p">)[</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s2">"']"</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span>
+</span><span id="diff_config-1230"><a href="#diff_config-1230"><span class="linenos">1230</span></a> <span class="n">report</span> <span class="o">+=</span> <span class="p">(</span>
+</span><span id="diff_config-1231"><a href="#diff_config-1231"><span class="linenos">1231</span></a> <span class="sa">f</span><span class="s2">"- `</span><span class="si">{</span><span class="n">clean_name</span><span class="si">}</span><span class="s2">` changed file from `</span><span class="si">{</span><span class="n">old_file</span><span class="si">}</span><span class="s2">` âž `</span><span class="si">{</span><span class="n">new_file</span><span class="si">}</span><span class="s2">`</span><span class="se">\n</span><span class="s2">"</span>
+</span><span id="diff_config-1232"><a href="#diff_config-1232"><span class="linenos">1232</span></a> <span class="p">)</span>
+</span><span id="diff_config-1233"><a href="#diff_config-1233"><span class="linenos">1233</span></a> <span class="n">report</span> <span class="o">+=</span> <span class="s2">"</span><span class="se">\n</span><span class="s2">"</span>
+</span><span id="diff_config-1234"><a href="#diff_config-1234"><span class="linenos">1234</span></a>
+</span><span id="diff_config-1235"><a href="#diff_config-1235"><span class="linenos">1235</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="p">(</span>
+</span><span id="diff_config-1236"><a href="#diff_config-1236"><span class="linenos">1236</span></a> <span class="n">added_names</span>
+</span><span id="diff_config-1237"><a href="#diff_config-1237"><span class="linenos">1237</span></a> <span class="ow">or</span> <span class="n">removed_names</span>
+</span><span id="diff_config-1238"><a href="#diff_config-1238"><span class="linenos">1238</span></a> <span class="ow">or</span> <span class="n">renamed_concepts</span>
+</span><span id="diff_config-1239"><a href="#diff_config-1239"><span class="linenos">1239</span></a> <span class="ow">or</span> <span class="n">file_diff</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"values_changed"</span><span class="p">)</span>
+</span><span id="diff_config-1240"><a href="#diff_config-1240"><span class="linenos">1240</span></a> <span class="p">):</span>
+</span><span id="diff_config-1241"><a href="#diff_config-1241"><span class="linenos">1241</span></a> <span class="n">report</span> <span class="o">+=</span> <span class="s2">"No changes in concept sets.</span><span class="se">\n</span><span class="s2">"</span>
+</span><span id="diff_config-1242"><a href="#diff_config-1242"><span class="linenos">1242</span></a>
+</span><span id="diff_config-1243"><a href="#diff_config-1243"><span class="linenos">1243</span></a> <span class="k">return</span> <span class="n">report</span>
+</span></pre></div>
+
+
+
+
+ </section>
+ <section id="diff_map_files">
+ <input id="diff_map_files-view-source" class="view-source-toggle-state" type="checkbox" aria-hidden="true" tabindex="-1">
+<div class="attr function">
+
+ <span class="def">def</span>
+ <span class="name">diff_map_files</span><span class="signature pdoc-code condensed">(<span class="param"><span class="n">old_map_path</span><span class="p">:</span> <span class="n">pathlib</span><span class="o">.</span><span class="n">Path</span>, </span><span class="param"><span class="n">new_map_path</span><span class="p">:</span> <span class="n">pathlib</span><span class="o">.</span><span class="n">Path</span></span><span class="return-annotation">) -> <span class="nb">str</span>:</span></span>
+
+ <label class="view-source-button" for="diff_map_files-view-source"><span>View Source</span></label>
+
+ </div>
+ <a class="headerlink" href="#diff_map_files"></a>
+ <div class="pdoc-code codehilite"><pre><span></span><span id="diff_map_files-1246"><a href="#diff_map_files-1246"><span class="linenos">1246</span></a><span class="k">def</span><span class="w"> </span><span class="nf">diff_map_files</span><span class="p">(</span><span class="n">old_map_path</span><span class="p">:</span> <span class="n">Path</span><span class="p">,</span> <span class="n">new_map_path</span><span class="p">:</span> <span class="n">Path</span><span class="p">)</span> <span class="o">-></span> <span class="nb">str</span><span class="p">:</span>
+</span><span id="diff_map_files-1247"><a href="#diff_map_files-1247"><span class="linenos">1247</span></a> <span class="n">old_output_files</span> <span class="o">=</span> <span class="p">[</span>
+</span><span id="diff_map_files-1248"><a href="#diff_map_files-1248"><span class="linenos">1248</span></a> <span class="n">file</span><span class="o">.</span><span class="n">name</span>
+</span><span id="diff_map_files-1249"><a href="#diff_map_files-1249"><span class="linenos">1249</span></a> <span class="k">for</span> <span class="n">file</span> <span class="ow">in</span> <span class="n">old_map_path</span><span class="o">.</span><span class="n">iterdir</span><span class="p">()</span>
+</span><span id="diff_map_files-1250"><a href="#diff_map_files-1250"><span class="linenos">1250</span></a> <span class="k">if</span> <span class="n">file</span><span class="o">.</span><span class="n">is_file</span><span class="p">()</span> <span class="ow">and</span> <span class="ow">not</span> <span class="n">file</span><span class="o">.</span><span class="n">name</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s2">"."</span><span class="p">)</span>
+</span><span id="diff_map_files-1251"><a href="#diff_map_files-1251"><span class="linenos">1251</span></a> <span class="p">]</span>
+</span><span id="diff_map_files-1252"><a href="#diff_map_files-1252"><span class="linenos">1252</span></a> <span class="n">new_output_files</span> <span class="o">=</span> <span class="p">[</span>
+</span><span id="diff_map_files-1253"><a href="#diff_map_files-1253"><span class="linenos">1253</span></a> <span class="n">file</span><span class="o">.</span><span class="n">name</span>
+</span><span id="diff_map_files-1254"><a href="#diff_map_files-1254"><span class="linenos">1254</span></a> <span class="k">for</span> <span class="n">file</span> <span class="ow">in</span> <span class="n">new_map_path</span><span class="o">.</span><span class="n">iterdir</span><span class="p">()</span>
+</span><span id="diff_map_files-1255"><a href="#diff_map_files-1255"><span class="linenos">1255</span></a> <span class="k">if</span> <span class="n">file</span><span class="o">.</span><span class="n">is_file</span><span class="p">()</span> <span class="ow">and</span> <span class="ow">not</span> <span class="n">file</span><span class="o">.</span><span class="n">name</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s2">"."</span><span class="p">)</span>
+</span><span id="diff_map_files-1256"><a href="#diff_map_files-1256"><span class="linenos">1256</span></a> <span class="p">]</span>
+</span><span id="diff_map_files-1257"><a href="#diff_map_files-1257"><span class="linenos">1257</span></a>
+</span><span id="diff_map_files-1258"><a href="#diff_map_files-1258"><span class="linenos">1258</span></a> <span class="c1"># Convert the lists to sets for easy comparison</span>
+</span><span id="diff_map_files-1259"><a href="#diff_map_files-1259"><span class="linenos">1259</span></a> <span class="n">old_output_set</span> <span class="o">=</span> <span class="nb">set</span><span class="p">(</span><span class="n">old_output_files</span><span class="p">)</span>
+</span><span id="diff_map_files-1260"><a href="#diff_map_files-1260"><span class="linenos">1260</span></a> <span class="n">new_output_set</span> <span class="o">=</span> <span class="nb">set</span><span class="p">(</span><span class="n">new_output_files</span><span class="p">)</span>
+</span><span id="diff_map_files-1261"><a href="#diff_map_files-1261"><span class="linenos">1261</span></a>
+</span><span id="diff_map_files-1262"><a href="#diff_map_files-1262"><span class="linenos">1262</span></a> <span class="c1"># Outputs that are in old_output_set but not in new_output_set (removed files)</span>
+</span><span id="diff_map_files-1263"><a href="#diff_map_files-1263"><span class="linenos">1263</span></a> <span class="n">removed_outputs</span> <span class="o">=</span> <span class="n">old_output_set</span> <span class="o">-</span> <span class="n">new_output_set</span>
+</span><span id="diff_map_files-1264"><a href="#diff_map_files-1264"><span class="linenos">1264</span></a> <span class="c1"># Outputs that are in new_output_set but not in old_output_set (added files)</span>
+</span><span id="diff_map_files-1265"><a href="#diff_map_files-1265"><span class="linenos">1265</span></a> <span class="n">added_outputs</span> <span class="o">=</span> <span class="n">new_output_set</span> <span class="o">-</span> <span class="n">old_output_set</span>
+</span><span id="diff_map_files-1266"><a href="#diff_map_files-1266"><span class="linenos">1266</span></a> <span class="c1"># Outputs that are the intersection of old_output_set and new_output_set</span>
+</span><span id="diff_map_files-1267"><a href="#diff_map_files-1267"><span class="linenos">1267</span></a> <span class="n">common_outputs</span> <span class="o">=</span> <span class="n">old_output_set</span> <span class="o">&</span> <span class="n">new_output_set</span>
+</span><span id="diff_map_files-1268"><a href="#diff_map_files-1268"><span class="linenos">1268</span></a>
+</span><span id="diff_map_files-1269"><a href="#diff_map_files-1269"><span class="linenos">1269</span></a> <span class="n">report</span> <span class="o">=</span> <span class="sa">f</span><span class="s2">"</span><span class="se">\n</span><span class="s2"># Changes to available translations</span><span class="se">\n</span><span class="s2">"</span>
+</span><span id="diff_map_files-1270"><a href="#diff_map_files-1270"><span class="linenos">1270</span></a> <span class="n">report</span> <span class="o">+=</span> <span class="sa">f</span><span class="s2">"This compares the coding translations files available.</span><span class="se">\n\n</span><span class="s2">"</span>
+</span><span id="diff_map_files-1271"><a href="#diff_map_files-1271"><span class="linenos">1271</span></a> <span class="n">report</span> <span class="o">+=</span> <span class="sa">f</span><span class="s2">"- Removed outputs: </span><span class="si">{</span><span class="nb">sorted</span><span class="p">(</span><span class="nb">list</span><span class="p">(</span><span class="n">removed_outputs</span><span class="p">))</span><span class="si">}</span><span class="se">\n</span><span class="s2">"</span>
+</span><span id="diff_map_files-1272"><a href="#diff_map_files-1272"><span class="linenos">1272</span></a> <span class="n">report</span> <span class="o">+=</span> <span class="sa">f</span><span class="s2">"- Added outputs: </span><span class="si">{</span><span class="nb">sorted</span><span class="p">(</span><span class="nb">list</span><span class="p">(</span><span class="n">added_outputs</span><span class="p">))</span><span class="si">}</span><span class="se">\n</span><span class="s2">"</span>
+</span><span id="diff_map_files-1273"><a href="#diff_map_files-1273"><span class="linenos">1273</span></a> <span class="n">report</span> <span class="o">+=</span> <span class="sa">f</span><span class="s2">"- Common outputs: </span><span class="si">{</span><span class="nb">sorted</span><span class="p">(</span><span class="nb">list</span><span class="p">(</span><span class="n">common_outputs</span><span class="p">))</span><span class="si">}</span><span class="se">\n\n</span><span class="s2">"</span>
+</span><span id="diff_map_files-1274"><a href="#diff_map_files-1274"><span class="linenos">1274</span></a>
+</span><span id="diff_map_files-1275"><a href="#diff_map_files-1275"><span class="linenos">1275</span></a> <span class="c1"># Step N: Compare common outputs between versions</span>
+</span><span id="diff_map_files-1276"><a href="#diff_map_files-1276"><span class="linenos">1276</span></a> <span class="n">report</span> <span class="o">+=</span> <span class="sa">f</span><span class="s2">"# Changes to concepts in translation files</span><span class="se">\n\n</span><span class="s2">"</span>
+</span><span id="diff_map_files-1277"><a href="#diff_map_files-1277"><span class="linenos">1277</span></a> <span class="n">report</span> <span class="o">+=</span> <span class="sa">f</span><span class="s2">"This compares the added and removed concepts in each of the coding translation files. Note that this might be different to the config.yaml if the translations have not been run for the current config.</span><span class="se">\n\n</span><span class="s2">"</span>
+</span><span id="diff_map_files-1278"><a href="#diff_map_files-1278"><span class="linenos">1278</span></a> <span class="k">for</span> <span class="n">file</span> <span class="ow">in</span> <span class="n">common_outputs</span><span class="p">:</span>
+</span><span id="diff_map_files-1279"><a href="#diff_map_files-1279"><span class="linenos">1279</span></a> <span class="n">old_output</span> <span class="o">=</span> <span class="n">old_map_path</span> <span class="o">/</span> <span class="n">file</span>
+</span><span id="diff_map_files-1280"><a href="#diff_map_files-1280"><span class="linenos">1280</span></a> <span class="n">new_output</span> <span class="o">=</span> <span class="n">new_map_path</span> <span class="o">/</span> <span class="n">file</span>
+</span><span id="diff_map_files-1281"><a href="#diff_map_files-1281"><span class="linenos">1281</span></a>
+</span><span id="diff_map_files-1282"><a href="#diff_map_files-1282"><span class="linenos">1282</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Old ouptput: </span><span class="si">{</span><span class="nb">str</span><span class="p">(</span><span class="n">old_output</span><span class="o">.</span><span class="n">resolve</span><span class="p">())</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+</span><span id="diff_map_files-1283"><a href="#diff_map_files-1283"><span class="linenos">1283</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="sa">f</span><span class="s2">"New ouptput: </span><span class="si">{</span><span class="nb">str</span><span class="p">(</span><span class="n">new_output</span><span class="o">.</span><span class="n">resolve</span><span class="p">())</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+</span><span id="diff_map_files-1284"><a href="#diff_map_files-1284"><span class="linenos">1284</span></a>
+</span><span id="diff_map_files-1285"><a href="#diff_map_files-1285"><span class="linenos">1285</span></a> <span class="n">df1</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">read_csv</span><span class="p">(</span><span class="n">old_output</span><span class="p">)</span>
+</span><span id="diff_map_files-1286"><a href="#diff_map_files-1286"><span class="linenos">1286</span></a> <span class="n">df1</span> <span class="o">=</span> <span class="n">df1</span><span class="p">[[</span><span class="s2">"CONCEPT"</span><span class="p">,</span> <span class="s2">"CONCEPT_SET"</span><span class="p">]]</span><span class="o">.</span><span class="n">groupby</span><span class="p">(</span><span class="s2">"CONCEPT_SET"</span><span class="p">)</span><span class="o">.</span><span class="n">count</span><span class="p">()</span>
+</span><span id="diff_map_files-1287"><a href="#diff_map_files-1287"><span class="linenos">1287</span></a> <span class="n">df2</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">read_csv</span><span class="p">(</span><span class="n">new_output</span><span class="p">)</span>
+</span><span id="diff_map_files-1288"><a href="#diff_map_files-1288"><span class="linenos">1288</span></a> <span class="n">df2</span> <span class="o">=</span> <span class="n">df2</span><span class="p">[[</span><span class="s2">"CONCEPT"</span><span class="p">,</span> <span class="s2">"CONCEPT_SET"</span><span class="p">]]</span><span class="o">.</span><span class="n">groupby</span><span class="p">(</span><span class="s2">"CONCEPT_SET"</span><span class="p">)</span><span class="o">.</span><span class="n">count</span><span class="p">()</span>
+</span><span id="diff_map_files-1289"><a href="#diff_map_files-1289"><span class="linenos">1289</span></a>
+</span><span id="diff_map_files-1290"><a href="#diff_map_files-1290"><span class="linenos">1290</span></a> <span class="c1"># Check for added and removed concepts</span>
+</span><span id="diff_map_files-1291"><a href="#diff_map_files-1291"><span class="linenos">1291</span></a> <span class="n">report</span> <span class="o">+=</span> <span class="sa">f</span><span class="s2">"- File </span><span class="si">{</span><span class="n">file</span><span class="si">}</span><span class="se">\n</span><span class="s2">"</span>
+</span><span id="diff_map_files-1292"><a href="#diff_map_files-1292"><span class="linenos">1292</span></a> <span class="n">sorted_list</span> <span class="o">=</span> <span class="nb">sorted</span><span class="p">(</span><span class="nb">list</span><span class="p">(</span><span class="nb">set</span><span class="p">(</span><span class="n">df1</span><span class="o">.</span><span class="n">index</span><span class="p">)</span> <span class="o">-</span> <span class="nb">set</span><span class="p">(</span><span class="n">df2</span><span class="o">.</span><span class="n">index</span><span class="p">)))</span>
+</span><span id="diff_map_files-1293"><a href="#diff_map_files-1293"><span class="linenos">1293</span></a> <span class="n">report</span> <span class="o">+=</span> <span class="sa">f</span><span class="s2">"- Removed concepts </span><span class="si">{</span><span class="n">sorted_list</span><span class="si">}</span><span class="se">\n</span><span class="s2">"</span>
+</span><span id="diff_map_files-1294"><a href="#diff_map_files-1294"><span class="linenos">1294</span></a> <span class="n">sorted_list</span> <span class="o">=</span> <span class="nb">sorted</span><span class="p">(</span><span class="nb">list</span><span class="p">(</span><span class="nb">set</span><span class="p">(</span><span class="n">df2</span><span class="o">.</span><span class="n">index</span><span class="p">)</span> <span class="o">-</span> <span class="nb">set</span><span class="p">(</span><span class="n">df1</span><span class="o">.</span><span class="n">index</span><span class="p">)))</span>
+</span><span id="diff_map_files-1295"><a href="#diff_map_files-1295"><span class="linenos">1295</span></a> <span class="n">report</span> <span class="o">+=</span> <span class="sa">f</span><span class="s2">"- Added concepts </span><span class="si">{</span><span class="n">sorted_list</span><span class="si">}</span><span class="se">\n</span><span class="s2">"</span>
+</span><span id="diff_map_files-1296"><a href="#diff_map_files-1296"><span class="linenos">1296</span></a>
+</span><span id="diff_map_files-1297"><a href="#diff_map_files-1297"><span class="linenos">1297</span></a> <span class="c1"># Check for changed concepts</span>
+</span><span id="diff_map_files-1298"><a href="#diff_map_files-1298"><span class="linenos">1298</span></a> <span class="n">diff</span> <span class="o">=</span> <span class="n">df2</span> <span class="o">-</span> <span class="n">df1</span> <span class="c1"># diff in counts</span>
+</span><span id="diff_map_files-1299"><a href="#diff_map_files-1299"><span class="linenos">1299</span></a> <span class="n">diff</span> <span class="o">=</span> <span class="n">diff</span><span class="p">[</span>
+</span><span id="diff_map_files-1300"><a href="#diff_map_files-1300"><span class="linenos">1300</span></a> <span class="p">(</span><span class="o">~</span><span class="p">(</span><span class="n">diff</span><span class="p">[</span><span class="s2">"CONCEPT"</span><span class="p">]</span> <span class="o">==</span> <span class="mf">0.0</span><span class="p">))</span> <span class="o">&</span> <span class="n">diff</span><span class="p">[</span><span class="s2">"CONCEPT"</span><span class="p">]</span><span class="o">.</span><span class="n">notna</span><span class="p">()</span>
+</span><span id="diff_map_files-1301"><a href="#diff_map_files-1301"><span class="linenos">1301</span></a> <span class="p">]</span> <span class="c1"># get non-zero counts</span>
+</span><span id="diff_map_files-1302"><a href="#diff_map_files-1302"><span class="linenos">1302</span></a> <span class="n">s</span> <span class="o">=</span> <span class="s2">"</span><span class="se">\n</span><span class="s2">"</span>
+</span><span id="diff_map_files-1303"><a href="#diff_map_files-1303"><span class="linenos">1303</span></a> <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">diff</span><span class="o">.</span><span class="n">index</span><span class="p">)</span> <span class="o">></span> <span class="mi">0</span><span class="p">:</span>
+</span><span id="diff_map_files-1304"><a href="#diff_map_files-1304"><span class="linenos">1304</span></a> <span class="k">for</span> <span class="n">concept</span><span class="p">,</span> <span class="n">row</span> <span class="ow">in</span> <span class="n">diff</span><span class="o">.</span><span class="n">iterrows</span><span class="p">():</span>
+</span><span id="diff_map_files-1305"><a href="#diff_map_files-1305"><span class="linenos">1305</span></a> <span class="n">s</span> <span class="o">+=</span> <span class="s2">"</span><span class="se">\t</span><span class="s2"> - </span><span class="si">{}</span><span class="s2"> </span><span class="si">{}</span><span class="se">\n</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">concept</span><span class="p">,</span> <span class="n">row</span><span class="p">[</span><span class="s2">"CONCEPT"</span><span class="p">])</span>
+</span><span id="diff_map_files-1306"><a href="#diff_map_files-1306"><span class="linenos">1306</span></a> <span class="n">report</span> <span class="o">+=</span> <span class="sa">f</span><span class="s2">"- Changed concepts </span><span class="si">{</span><span class="n">s</span><span class="si">}</span><span class="se">\n\n</span><span class="s2">"</span>
+</span><span id="diff_map_files-1307"><a href="#diff_map_files-1307"><span class="linenos">1307</span></a> <span class="k">else</span><span class="p">:</span>
+</span><span id="diff_map_files-1308"><a href="#diff_map_files-1308"><span class="linenos">1308</span></a> <span class="n">report</span> <span class="o">+=</span> <span class="sa">f</span><span class="s2">"- Changed concepts []</span><span class="se">\n\n</span><span class="s2">"</span>
+</span><span id="diff_map_files-1309"><a href="#diff_map_files-1309"><span class="linenos">1309</span></a>
+</span><span id="diff_map_files-1310"><a href="#diff_map_files-1310"><span class="linenos">1310</span></a> <span class="k">return</span> <span class="n">report</span>
+</span></pre></div>
+
+
+
+
+ </section>
+ <section id="diff_phen">
+ <input id="diff_phen-view-source" class="view-source-toggle-state" type="checkbox" aria-hidden="true" tabindex="-1">
+<div class="attr function">
+
+ <span class="def">def</span>
+ <span class="name">diff_phen</span><span class="signature pdoc-code multiline">(<span class="param"> <span class="n">new_phen_path</span><span class="p">:</span> <span class="n">pathlib</span><span class="o">.</span><span class="n">Path</span>,</span><span class="param"> <span class="n">new_version</span><span class="p">:</span> <span class="nb">str</span>,</span><span class="param"> <span class="n">old_phen_path</span><span class="p">:</span> <span class="n">pathlib</span><span class="o">.</span><span class="n">Path</span>,</span><span class="param"> <span class="n">old_version</span><span class="p">:</span> <span class="nb">str</span>,</span><span class="param"> <span class="n">report_path</span><span class="p">:</span> <span class="n">pathlib</span><span class="o">.</span><span class="n">Path</span></span><span class="return-annotation">):</span></span>
+
+ <label class="view-source-button" for="diff_phen-view-source"><span>View Source</span></label>
+
+ </div>
+ <a class="headerlink" href="#diff_phen"></a>
+ <div class="pdoc-code codehilite"><pre><span></span><span id="diff_phen-1313"><a href="#diff_phen-1313"><span class="linenos">1313</span></a><span class="k">def</span><span class="w"> </span><span class="nf">diff_phen</span><span class="p">(</span>
+</span><span id="diff_phen-1314"><a href="#diff_phen-1314"><span class="linenos">1314</span></a> <span class="n">new_phen_path</span><span class="p">:</span> <span class="n">Path</span><span class="p">,</span>
+</span><span id="diff_phen-1315"><a href="#diff_phen-1315"><span class="linenos">1315</span></a> <span class="n">new_version</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+</span><span id="diff_phen-1316"><a href="#diff_phen-1316"><span class="linenos">1316</span></a> <span class="n">old_phen_path</span><span class="p">:</span> <span class="n">Path</span><span class="p">,</span>
+</span><span id="diff_phen-1317"><a href="#diff_phen-1317"><span class="linenos">1317</span></a> <span class="n">old_version</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+</span><span id="diff_phen-1318"><a href="#diff_phen-1318"><span class="linenos">1318</span></a> <span class="n">report_path</span><span class="p">:</span> <span class="n">Path</span><span class="p">,</span>
+</span><span id="diff_phen-1319"><a href="#diff_phen-1319"><span class="linenos">1319</span></a><span class="p">):</span>
+</span><span id="diff_phen-1320"><a href="#diff_phen-1320"><span class="linenos">1320</span></a><span class="w"> </span><span class="sd">"""Compare the differences between two versions of a phenotype"""</span>
+</span><span id="diff_phen-1321"><a href="#diff_phen-1321"><span class="linenos">1321</span></a>
+</span><span id="diff_phen-1322"><a href="#diff_phen-1322"><span class="linenos">1322</span></a> <span class="c1"># validate phenotypes</span>
+</span><span id="diff_phen-1323"><a href="#diff_phen-1323"><span class="linenos">1323</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Validating for diff old path: </span><span class="si">{</span><span class="nb">str</span><span class="p">(</span><span class="n">old_phen_path</span><span class="o">.</span><span class="n">resolve</span><span class="p">())</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+</span><span id="diff_phen-1324"><a href="#diff_phen-1324"><span class="linenos">1324</span></a> <span class="n">validate</span><span class="p">(</span><span class="nb">str</span><span class="p">(</span><span class="n">old_phen_path</span><span class="o">.</span><span class="n">resolve</span><span class="p">()))</span>
+</span><span id="diff_phen-1325"><a href="#diff_phen-1325"><span class="linenos">1325</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Validating for diff new path: </span><span class="si">{</span><span class="nb">str</span><span class="p">(</span><span class="n">new_phen_path</span><span class="o">.</span><span class="n">resolve</span><span class="p">())</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+</span><span id="diff_phen-1326"><a href="#diff_phen-1326"><span class="linenos">1326</span></a> <span class="n">validate</span><span class="p">(</span><span class="nb">str</span><span class="p">(</span><span class="n">new_phen_path</span><span class="o">.</span><span class="n">resolve</span><span class="p">()))</span>
+</span><span id="diff_phen-1327"><a href="#diff_phen-1327"><span class="linenos">1327</span></a>
+</span><span id="diff_phen-1328"><a href="#diff_phen-1328"><span class="linenos">1328</span></a> <span class="c1"># get old and new config</span>
+</span><span id="diff_phen-1329"><a href="#diff_phen-1329"><span class="linenos">1329</span></a> <span class="n">old_config_path</span> <span class="o">=</span> <span class="n">old_phen_path</span> <span class="o">/</span> <span class="n">CONFIG_FILE</span>
+</span><span id="diff_phen-1330"><a href="#diff_phen-1330"><span class="linenos">1330</span></a> <span class="k">with</span> <span class="n">old_config_path</span><span class="o">.</span><span class="n">open</span><span class="p">(</span><span class="s2">"r"</span><span class="p">)</span> <span class="k">as</span> <span class="n">file</span><span class="p">:</span>
+</span><span id="diff_phen-1331"><a href="#diff_phen-1331"><span class="linenos">1331</span></a> <span class="n">old_config</span> <span class="o">=</span> <span class="n">yaml</span><span class="o">.</span><span class="n">safe_load</span><span class="p">(</span><span class="n">file</span><span class="p">)</span>
+</span><span id="diff_phen-1332"><a href="#diff_phen-1332"><span class="linenos">1332</span></a> <span class="n">new_config_path</span> <span class="o">=</span> <span class="n">new_phen_path</span> <span class="o">/</span> <span class="n">CONFIG_FILE</span>
+</span><span id="diff_phen-1333"><a href="#diff_phen-1333"><span class="linenos">1333</span></a> <span class="k">with</span> <span class="n">new_config_path</span><span class="o">.</span><span class="n">open</span><span class="p">(</span><span class="s2">"r"</span><span class="p">)</span> <span class="k">as</span> <span class="n">file</span><span class="p">:</span>
+</span><span id="diff_phen-1334"><a href="#diff_phen-1334"><span class="linenos">1334</span></a> <span class="n">new_config</span> <span class="o">=</span> <span class="n">yaml</span><span class="o">.</span><span class="n">safe_load</span><span class="p">(</span><span class="n">file</span><span class="p">)</span>
+</span><span id="diff_phen-1335"><a href="#diff_phen-1335"><span class="linenos">1335</span></a>
+</span><span id="diff_phen-1336"><a href="#diff_phen-1336"><span class="linenos">1336</span></a> <span class="c1"># write report heading</span>
+</span><span id="diff_phen-1337"><a href="#diff_phen-1337"><span class="linenos">1337</span></a> <span class="n">report</span> <span class="o">=</span> <span class="sa">f</span><span class="s2">"# Phenotype Comparison Report</span><span class="se">\n</span><span class="s2">"</span>
+</span><span id="diff_phen-1338"><a href="#diff_phen-1338"><span class="linenos">1338</span></a> <span class="n">report</span> <span class="o">+=</span> <span class="sa">f</span><span class="s2">"## Original phenotype</span><span class="se">\n</span><span class="s2">"</span>
+</span><span id="diff_phen-1339"><a href="#diff_phen-1339"><span class="linenos">1339</span></a> <span class="n">report</span> <span class="o">+=</span> <span class="sa">f</span><span class="s2">" - </span><span class="si">{</span><span class="n">old_config</span><span class="p">[</span><span class="s1">'phenotype'</span><span class="p">][</span><span class="s1">'omop'</span><span class="p">][</span><span class="s1">'vocabulary_id'</span><span class="p">]</span><span class="si">}</span><span class="se">\n</span><span class="s2">"</span>
+</span><span id="diff_phen-1340"><a href="#diff_phen-1340"><span class="linenos">1340</span></a> <span class="n">report</span> <span class="o">+=</span> <span class="sa">f</span><span class="s2">" - </span><span class="si">{</span><span class="n">old_version</span><span class="si">}</span><span class="se">\n</span><span class="s2">"</span>
+</span><span id="diff_phen-1341"><a href="#diff_phen-1341"><span class="linenos">1341</span></a> <span class="n">report</span> <span class="o">+=</span> <span class="sa">f</span><span class="s2">" - </span><span class="si">{</span><span class="nb">str</span><span class="p">(</span><span class="n">old_phen_path</span><span class="o">.</span><span class="n">resolve</span><span class="p">())</span><span class="si">}</span><span class="se">\n</span><span class="s2">"</span>
+</span><span id="diff_phen-1342"><a href="#diff_phen-1342"><span class="linenos">1342</span></a> <span class="n">report</span> <span class="o">+=</span> <span class="sa">f</span><span class="s2">"## Changed phenotype:</span><span class="se">\n</span><span class="s2">"</span>
+</span><span id="diff_phen-1343"><a href="#diff_phen-1343"><span class="linenos">1343</span></a> <span class="n">report</span> <span class="o">+=</span> <span class="sa">f</span><span class="s2">" - </span><span class="si">{</span><span class="n">new_config</span><span class="p">[</span><span class="s1">'phenotype'</span><span class="p">][</span><span class="s1">'omop'</span><span class="p">][</span><span class="s1">'vocabulary_id'</span><span class="p">]</span><span class="si">}</span><span class="se">\n</span><span class="s2">"</span>
+</span><span id="diff_phen-1344"><a href="#diff_phen-1344"><span class="linenos">1344</span></a> <span class="n">report</span> <span class="o">+=</span> <span class="sa">f</span><span class="s2">" - </span><span class="si">{</span><span class="n">new_version</span><span class="si">}</span><span class="se">\n</span><span class="s2">"</span>
+</span><span id="diff_phen-1345"><a href="#diff_phen-1345"><span class="linenos">1345</span></a> <span class="n">report</span> <span class="o">+=</span> <span class="sa">f</span><span class="s2">" - </span><span class="si">{</span><span class="nb">str</span><span class="p">(</span><span class="n">new_phen_path</span><span class="o">.</span><span class="n">resolve</span><span class="p">())</span><span class="si">}</span><span class="se">\n</span><span class="s2">"</span>
+</span><span id="diff_phen-1346"><a href="#diff_phen-1346"><span class="linenos">1346</span></a>
+</span><span id="diff_phen-1347"><a href="#diff_phen-1347"><span class="linenos">1347</span></a> <span class="c1"># Step 1: check differences configuration files</span>
+</span><span id="diff_phen-1348"><a href="#diff_phen-1348"><span class="linenos">1348</span></a> <span class="c1"># Convert list of dicts into a dict: {name: file}</span>
+</span><span id="diff_phen-1349"><a href="#diff_phen-1349"><span class="linenos">1349</span></a> <span class="n">report</span> <span class="o">+=</span> <span class="n">diff_config</span><span class="p">(</span><span class="n">old_config</span><span class="p">,</span> <span class="n">new_config</span><span class="p">)</span>
+</span><span id="diff_phen-1350"><a href="#diff_phen-1350"><span class="linenos">1350</span></a>
+</span><span id="diff_phen-1351"><a href="#diff_phen-1351"><span class="linenos">1351</span></a> <span class="c1"># Step 2: check differences between map files</span>
+</span><span id="diff_phen-1352"><a href="#diff_phen-1352"><span class="linenos">1352</span></a> <span class="c1"># List files from output directories</span>
+</span><span id="diff_phen-1353"><a href="#diff_phen-1353"><span class="linenos">1353</span></a> <span class="n">old_map_path</span> <span class="o">=</span> <span class="n">old_phen_path</span> <span class="o">/</span> <span class="n">MAP_DIR</span>
+</span><span id="diff_phen-1354"><a href="#diff_phen-1354"><span class="linenos">1354</span></a> <span class="n">new_map_path</span> <span class="o">=</span> <span class="n">new_phen_path</span> <span class="o">/</span> <span class="n">MAP_DIR</span>
+</span><span id="diff_phen-1355"><a href="#diff_phen-1355"><span class="linenos">1355</span></a> <span class="n">report</span> <span class="o">+=</span> <span class="n">diff_map_files</span><span class="p">(</span><span class="n">old_map_path</span><span class="p">,</span> <span class="n">new_map_path</span><span class="p">)</span>
+</span><span id="diff_phen-1356"><a href="#diff_phen-1356"><span class="linenos">1356</span></a>
+</span><span id="diff_phen-1357"><a href="#diff_phen-1357"><span class="linenos">1357</span></a> <span class="c1"># initialise report file</span>
+</span><span id="diff_phen-1358"><a href="#diff_phen-1358"><span class="linenos">1358</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Writing to report file </span><span class="si">{</span><span class="nb">str</span><span class="p">(</span><span class="n">report_path</span><span class="o">.</span><span class="n">resolve</span><span class="p">())</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+</span><span id="diff_phen-1359"><a href="#diff_phen-1359"><span class="linenos">1359</span></a> <span class="n">report_file</span> <span class="o">=</span> <span class="nb">open</span><span class="p">(</span><span class="n">report_path</span><span class="p">,</span> <span class="s2">"w"</span><span class="p">)</span>
+</span><span id="diff_phen-1360"><a href="#diff_phen-1360"><span class="linenos">1360</span></a> <span class="n">report_file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">report</span><span class="p">)</span>
+</span><span id="diff_phen-1361"><a href="#diff_phen-1361"><span class="linenos">1361</span></a> <span class="n">report_file</span><span class="o">.</span><span class="n">close</span><span class="p">()</span>
+</span><span id="diff_phen-1362"><a href="#diff_phen-1362"><span class="linenos">1362</span></a>
+</span><span id="diff_phen-1363"><a href="#diff_phen-1363"><span class="linenos">1363</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Phenotypes diff'd successfully"</span><span class="p">)</span>
+</span></pre></div>
+
+
+ <div class="docstring"><p>Compare the differences between two versions of a phenotype</p>
+</div>
+
+
+ </section>
+ <section id="diff">
+ <input id="diff-view-source" class="view-source-toggle-state" type="checkbox" aria-hidden="true" tabindex="-1">
+<div class="attr function">
+
+ <span class="def">def</span>
+ <span class="name">diff</span><span class="signature pdoc-code condensed">(<span class="param"><span class="n">phen_dir</span><span class="p">:</span> <span class="nb">str</span>, </span><span class="param"><span class="n">version</span><span class="p">:</span> <span class="nb">str</span>, </span><span class="param"><span class="n">old_phen_dir</span><span class="p">:</span> <span class="nb">str</span>, </span><span class="param"><span class="n">old_version</span><span class="p">:</span> <span class="nb">str</span></span><span class="return-annotation">):</span></span>
+
+ <label class="view-source-button" for="diff-view-source"><span>View Source</span></label>
+
+ </div>
+ <a class="headerlink" href="#diff"></a>
+ <div class="pdoc-code codehilite"><pre><span></span><span id="diff-1366"><a href="#diff-1366"><span class="linenos">1366</span></a><span class="k">def</span><span class="w"> </span><span class="nf">diff</span><span class="p">(</span><span class="n">phen_dir</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">version</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">old_phen_dir</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">old_version</span><span class="p">:</span> <span class="nb">str</span><span class="p">):</span>
+</span><span id="diff-1367"><a href="#diff-1367"><span class="linenos">1367</span></a> <span class="c1"># make tmp directory .acmc</span>
+</span><span id="diff-1368"><a href="#diff-1368"><span class="linenos">1368</span></a> <span class="n">timestamp</span> <span class="o">=</span> <span class="n">time</span><span class="o">.</span><span class="n">strftime</span><span class="p">(</span><span class="s2">"%Y%m</span><span class="si">%d</span><span class="s2">_%H%M%S"</span><span class="p">)</span>
+</span><span id="diff-1369"><a href="#diff-1369"><span class="linenos">1369</span></a> <span class="n">temp_dir</span> <span class="o">=</span> <span class="n">Path</span><span class="p">(</span><span class="sa">f</span><span class="s2">".acmc/diff_</span><span class="si">{</span><span class="n">timestamp</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+</span><span id="diff-1370"><a href="#diff-1370"><span class="linenos">1370</span></a>
+</span><span id="diff-1371"><a href="#diff-1371"><span class="linenos">1371</span></a> <span class="n">changed_phen_path</span> <span class="o">=</span> <span class="n">Path</span><span class="p">(</span><span class="n">phen_dir</span><span class="p">)</span>
+</span><span id="diff-1372"><a href="#diff-1372"><span class="linenos">1372</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="n">changed_phen_path</span><span class="o">.</span><span class="n">exists</span><span class="p">():</span>
+</span><span id="diff-1373"><a href="#diff-1373"><span class="linenos">1373</span></a> <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span>
+</span><span id="diff-1374"><a href="#diff-1374"><span class="linenos">1374</span></a> <span class="sa">f</span><span class="s2">"Changed phenotype directory does not exist: </span><span class="si">{</span><span class="nb">str</span><span class="p">(</span><span class="n">changed_phen_path</span><span class="o">.</span><span class="n">resolve</span><span class="p">())</span><span class="si">}</span><span class="s2">"</span>
+</span><span id="diff-1375"><a href="#diff-1375"><span class="linenos">1375</span></a> <span class="p">)</span>
+</span><span id="diff-1376"><a href="#diff-1376"><span class="linenos">1376</span></a>
+</span><span id="diff-1377"><a href="#diff-1377"><span class="linenos">1377</span></a> <span class="n">old_phen_path</span> <span class="o">=</span> <span class="n">Path</span><span class="p">(</span><span class="n">old_phen_dir</span><span class="p">)</span>
+</span><span id="diff-1378"><a href="#diff-1378"><span class="linenos">1378</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="n">old_phen_path</span><span class="o">.</span><span class="n">exists</span><span class="p">():</span>
+</span><span id="diff-1379"><a href="#diff-1379"><span class="linenos">1379</span></a> <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span>
+</span><span id="diff-1380"><a href="#diff-1380"><span class="linenos">1380</span></a> <span class="sa">f</span><span class="s2">"Old phenotype directory does not exist: </span><span class="si">{</span><span class="nb">str</span><span class="p">(</span><span class="n">old_phen_path</span><span class="o">.</span><span class="n">resolve</span><span class="p">())</span><span class="si">}</span><span class="s2">"</span>
+</span><span id="diff-1381"><a href="#diff-1381"><span class="linenos">1381</span></a> <span class="p">)</span>
+</span><span id="diff-1382"><a href="#diff-1382"><span class="linenos">1382</span></a>
+</span><span id="diff-1383"><a href="#diff-1383"><span class="linenos">1383</span></a> <span class="k">try</span><span class="p">:</span>
+</span><span id="diff-1384"><a href="#diff-1384"><span class="linenos">1384</span></a> <span class="c1"># Create the directory</span>
+</span><span id="diff-1385"><a href="#diff-1385"><span class="linenos">1385</span></a> <span class="n">temp_dir</span><span class="o">.</span><span class="n">mkdir</span><span class="p">(</span><span class="n">parents</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">exist_ok</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+</span><span id="diff-1386"><a href="#diff-1386"><span class="linenos">1386</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Temporary directory created: </span><span class="si">{</span><span class="n">temp_dir</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+</span><span id="diff-1387"><a href="#diff-1387"><span class="linenos">1387</span></a>
+</span><span id="diff-1388"><a href="#diff-1388"><span class="linenos">1388</span></a> <span class="c1"># Create temporary directories</span>
+</span><span id="diff-1389"><a href="#diff-1389"><span class="linenos">1389</span></a> <span class="n">changed_path</span> <span class="o">=</span> <span class="n">temp_dir</span> <span class="o">/</span> <span class="s2">"changed"</span>
+</span><span id="diff-1390"><a href="#diff-1390"><span class="linenos">1390</span></a> <span class="n">changed_path</span><span class="o">.</span><span class="n">mkdir</span><span class="p">(</span><span class="n">parents</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">exist_ok</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+</span><span id="diff-1391"><a href="#diff-1391"><span class="linenos">1391</span></a> <span class="n">old_path</span> <span class="o">=</span> <span class="n">temp_dir</span> <span class="o">/</span> <span class="s2">"old"</span>
+</span><span id="diff-1392"><a href="#diff-1392"><span class="linenos">1392</span></a> <span class="n">old_path</span><span class="o">.</span><span class="n">mkdir</span><span class="p">(</span><span class="n">parents</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">exist_ok</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+</span><span id="diff-1393"><a href="#diff-1393"><span class="linenos">1393</span></a>
+</span><span id="diff-1394"><a href="#diff-1394"><span class="linenos">1394</span></a> <span class="c1"># checkout changed</span>
+</span><span id="diff-1395"><a href="#diff-1395"><span class="linenos">1395</span></a> <span class="k">if</span> <span class="n">version</span> <span class="o">==</span> <span class="s2">"latest"</span><span class="p">:</span>
+</span><span id="diff-1396"><a href="#diff-1396"><span class="linenos">1396</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span>
+</span><span id="diff-1397"><a href="#diff-1397"><span class="linenos">1397</span></a> <span class="sa">f</span><span class="s2">"Copying changed repo from </span><span class="si">{</span><span class="n">phen_dir</span><span class="si">}</span><span class="s2"> into </span><span class="si">{</span><span class="n">changed_path</span><span class="si">}</span><span class="s2"> at version </span><span class="si">{</span><span class="n">version</span><span class="si">}</span><span class="s2">..."</span>
+</span><span id="diff-1398"><a href="#diff-1398"><span class="linenos">1398</span></a> <span class="p">)</span>
+</span><span id="diff-1399"><a href="#diff-1399"><span class="linenos">1399</span></a> <span class="n">shutil</span><span class="o">.</span><span class="n">copytree</span><span class="p">(</span><span class="n">changed_phen_path</span><span class="p">,</span> <span class="n">changed_path</span><span class="p">,</span> <span class="n">dirs_exist_ok</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+</span><span id="diff-1400"><a href="#diff-1400"><span class="linenos">1400</span></a> <span class="k">else</span><span class="p">:</span>
+</span><span id="diff-1401"><a href="#diff-1401"><span class="linenos">1401</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span>
+</span><span id="diff-1402"><a href="#diff-1402"><span class="linenos">1402</span></a> <span class="sa">f</span><span class="s2">"Cloning changed repo from </span><span class="si">{</span><span class="n">phen_dir</span><span class="si">}</span><span class="s2"> into </span><span class="si">{</span><span class="n">changed_path</span><span class="si">}</span><span class="s2"> at version </span><span class="si">{</span><span class="n">version</span><span class="si">}</span><span class="s2">..."</span>
+</span><span id="diff-1403"><a href="#diff-1403"><span class="linenos">1403</span></a> <span class="p">)</span>
+</span><span id="diff-1404"><a href="#diff-1404"><span class="linenos">1404</span></a> <span class="n">changed_repo</span> <span class="o">=</span> <span class="n">git</span><span class="o">.</span><span class="n">Repo</span><span class="o">.</span><span class="n">clone_from</span><span class="p">(</span><span class="n">changed_phen_path</span><span class="p">,</span> <span class="n">changed_path</span><span class="p">)</span>
+</span><span id="diff-1405"><a href="#diff-1405"><span class="linenos">1405</span></a> <span class="n">changed_repo</span><span class="o">.</span><span class="n">git</span><span class="o">.</span><span class="n">checkout</span><span class="p">(</span><span class="n">version</span><span class="p">)</span>
+</span><span id="diff-1406"><a href="#diff-1406"><span class="linenos">1406</span></a>
+</span><span id="diff-1407"><a href="#diff-1407"><span class="linenos">1407</span></a> <span class="c1"># checkout old</span>
+</span><span id="diff-1408"><a href="#diff-1408"><span class="linenos">1408</span></a> <span class="k">if</span> <span class="n">old_version</span> <span class="o">==</span> <span class="s2">"latest"</span><span class="p">:</span>
+</span><span id="diff-1409"><a href="#diff-1409"><span class="linenos">1409</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span>
+</span><span id="diff-1410"><a href="#diff-1410"><span class="linenos">1410</span></a> <span class="sa">f</span><span class="s2">"Copying old repo from </span><span class="si">{</span><span class="n">old_phen_dir</span><span class="si">}</span><span class="s2"> into </span><span class="si">{</span><span class="n">old_path</span><span class="si">}</span><span class="s2"> at version </span><span class="si">{</span><span class="n">old_version</span><span class="si">}</span><span class="s2">..."</span>
+</span><span id="diff-1411"><a href="#diff-1411"><span class="linenos">1411</span></a> <span class="p">)</span>
+</span><span id="diff-1412"><a href="#diff-1412"><span class="linenos">1412</span></a> <span class="n">shutil</span><span class="o">.</span><span class="n">copytree</span><span class="p">(</span><span class="n">old_phen_path</span><span class="p">,</span> <span class="n">old_path</span><span class="p">,</span> <span class="n">dirs_exist_ok</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+</span><span id="diff-1413"><a href="#diff-1413"><span class="linenos">1413</span></a> <span class="k">else</span><span class="p">:</span>
+</span><span id="diff-1414"><a href="#diff-1414"><span class="linenos">1414</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span>
+</span><span id="diff-1415"><a href="#diff-1415"><span class="linenos">1415</span></a> <span class="sa">f</span><span class="s2">"Cloning old repo from </span><span class="si">{</span><span class="n">old_phen_dir</span><span class="si">}</span><span class="s2"> into </span><span class="si">{</span><span class="n">old_path</span><span class="si">}</span><span class="s2"> at version </span><span class="si">{</span><span class="n">old_version</span><span class="si">}</span><span class="s2">..."</span>
+</span><span id="diff-1416"><a href="#diff-1416"><span class="linenos">1416</span></a> <span class="p">)</span>
+</span><span id="diff-1417"><a href="#diff-1417"><span class="linenos">1417</span></a> <span class="n">old_repo</span> <span class="o">=</span> <span class="n">git</span><span class="o">.</span><span class="n">Repo</span><span class="o">.</span><span class="n">clone_from</span><span class="p">(</span><span class="n">old_phen_dir</span><span class="p">,</span> <span class="n">old_path</span><span class="p">)</span>
+</span><span id="diff-1418"><a href="#diff-1418"><span class="linenos">1418</span></a> <span class="n">old_repo</span><span class="o">.</span><span class="n">git</span><span class="o">.</span><span class="n">checkout</span><span class="p">(</span><span class="n">old_version</span><span class="p">)</span>
+</span><span id="diff-1419"><a href="#diff-1419"><span class="linenos">1419</span></a>
+</span><span id="diff-1420"><a href="#diff-1420"><span class="linenos">1420</span></a> <span class="n">report_filename</span> <span class="o">=</span> <span class="sa">f</span><span class="s2">"</span><span class="si">{</span><span class="n">version</span><span class="si">}</span><span class="s2">_</span><span class="si">{</span><span class="n">old_version</span><span class="si">}</span><span class="s2">_diff.md"</span>
+</span><span id="diff-1421"><a href="#diff-1421"><span class="linenos">1421</span></a> <span class="n">report_path</span> <span class="o">=</span> <span class="n">changed_phen_path</span> <span class="o">/</span> <span class="n">report_filename</span>
+</span><span id="diff-1422"><a href="#diff-1422"><span class="linenos">1422</span></a> <span class="c1"># diff old with new</span>
+</span><span id="diff-1423"><a href="#diff-1423"><span class="linenos">1423</span></a> <span class="n">diff_phen</span><span class="p">(</span><span class="n">changed_path</span><span class="p">,</span> <span class="n">version</span><span class="p">,</span> <span class="n">old_path</span><span class="p">,</span> <span class="n">old_version</span><span class="p">,</span> <span class="n">report_path</span><span class="p">)</span>
+</span><span id="diff-1424"><a href="#diff-1424"><span class="linenos">1424</span></a>
+</span><span id="diff-1425"><a href="#diff-1425"><span class="linenos">1425</span></a> <span class="k">finally</span><span class="p">:</span>
+</span><span id="diff-1426"><a href="#diff-1426"><span class="linenos">1426</span></a> <span class="c1"># clean up tmp directory</span>
+</span><span id="diff-1427"><a href="#diff-1427"><span class="linenos">1427</span></a> <span class="k">if</span> <span class="n">temp_dir</span><span class="o">.</span><span class="n">exists</span><span class="p">():</span>
+</span><span id="diff-1428"><a href="#diff-1428"><span class="linenos">1428</span></a> <span class="n">shutil</span><span class="o">.</span><span class="n">rmtree</span><span class="p">(</span><span class="n">temp_dir</span><span class="p">)</span>
+</span><span id="diff-1429"><a href="#diff-1429"><span class="linenos">1429</span></a> <span class="nb">print</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Temporary directory removed: </span><span class="si">{</span><span class="n">temp_dir</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+</span></pre></div>
+
+
+
+
+ </section>
+ </main>
+<script>
+ function escapeHTML(html) {
+ return document.createElement('div').appendChild(document.createTextNode(html)).parentNode.innerHTML;
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+ }
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+ window.scrollTo({top: 0, left: 0, behavior: 'auto'});
+
+ const results = search(term);
+
+ let html;
+ if (results.length === 0) {
+ html = `No search results for '${escapeHTML(term)}'.`
+ } else {
+ html = `<h4>${results.length} search result${results.length > 1 ? "s" : ""} for '${escapeHTML(term)}'.</h4>`;
+ }
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+ let doc = result.doc;
+ let url = `../${doc.modulename.replaceAll(".", "/")}.html`;
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+ }
+ break;
+ case "class":
+ heading = `<span class="def">class</span> <span class="name">${doc.fullname}</span>`;
+ if (doc.bases)
+ heading += `<wbr>(<span class="base">${doc.bases}</span>)`;
+ heading += `:`;
+ break;
+ case "variable":
+ heading = `<span class="name">${doc.fullname}</span>`;
+ if (doc.annotation)
+ heading += `<span class="annotation">${doc.annotation}</span>`;
+ if (doc.default_value)
+ heading += `<span class="default_value"> = ${doc.default_value}</span>`;
+ break;
+ default:
+ heading = `<span class="name">${doc.fullname}</span>`;
+ break;
+ }
+ html += `
+ <section class="search-result">
+ <a href="${url}" class="attr ${doc.kind}">${heading}</a>
+ <div class="docstring">${doc.doc}</div>
+ </section>
+ `;
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+ return html;
+ })());
+ }
+
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+ if (["ArrowDown", "ArrowUp", "Enter"].includes(e.key)) {
+ let focused = currentContent.querySelector(".search-result.focused");
+ if (!focused) {
+ currentContent.querySelector(".search-result").classList.add("focused");
+ } else if (
+ e.key === "ArrowDown"
+ && focused.nextElementSibling
+ && focused.nextElementSibling.classList.contains("search-result")
+ ) {
+ focused.classList.remove("focused");
+ focused.nextElementSibling.classList.add("focused");
+ focused.nextElementSibling.scrollIntoView({
+ behavior: "smooth",
+ block: "nearest",
+ inline: "nearest"
+ });
+ } else if (
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+ && focused.previousElementSibling
+ && focused.previousElementSibling.classList.contains("search-result")
+ ) {
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+ focused.previousElementSibling.scrollIntoView({
+ behavior: "smooth",
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+</script></body>
+</html>
\ No newline at end of file
diff --git a/docs/api/acmc/trud.html b/docs/api/acmc/trud.html
new file mode 100644
index 0000000000000000000000000000000000000000..fdfb631c1f9f2d6a450caebfcfa5914bdcdfc827
--- /dev/null
+++ b/docs/api/acmc/trud.html
@@ -0,0 +1,1382 @@
+<!doctype html>
+<html lang="en">
+<head>
+ <meta charset="utf-8">
+ <meta name="viewport" content="width=device-width, initial-scale=1">
+ <meta name="generator" content="pdoc 15.0.1"/>
+ <title>acmc.trud API documentation</title>
+
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+ <div> <a class="pdoc-button module-list-button" href="../acmc.html">
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+ pattern=".+" required>
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+
+
+ <h2>API Documentation</h2>
+ <ul class="memberlist">
+ <li>
+ <a class="variable" href="#logger">logger</a>
+ </li>
+ <li>
+ <a class="variable" href="#FQDN">FQDN</a>
+ </li>
+ <li>
+ <a class="variable" href="#VOCAB_PATH">VOCAB_PATH</a>
+ </li>
+ <li>
+ <a class="variable" href="#VERSION_FILE">VERSION_FILE</a>
+ </li>
+ <li>
+ <a class="variable" href="#VERSION_PATH">VERSION_PATH</a>
+ </li>
+ <li>
+ <a class="variable" href="#DOWNLOADS_PATH">DOWNLOADS_PATH</a>
+ </li>
+ <li>
+ <a class="variable" href="#PROCESSED_PATH">PROCESSED_PATH</a>
+ </li>
+ <li>
+ <a class="function" href="#get_releases">get_releases</a>
+ </li>
+ <li>
+ <a class="function" href="#download_release_file">download_release_file</a>
+ </li>
+ <li>
+ <a class="function" href="#validate_download_hash">validate_download_hash</a>
+ </li>
+ <li>
+ <a class="function" href="#unzip_download">unzip_download</a>
+ </li>
+ <li>
+ <a class="function" href="#extract_icd10">extract_icd10</a>
+ </li>
+ <li>
+ <a class="function" href="#extract_opsc4">extract_opsc4</a>
+ </li>
+ <li>
+ <a class="function" href="#extract_nhs_data_migrations">extract_nhs_data_migrations</a>
+ </li>
+ <li>
+ <a class="function" href="#extract_nhs_read_browser">extract_nhs_read_browser</a>
+ </li>
+ <li>
+ <a class="function" href="#create_map_directories">create_map_directories</a>
+ </li>
+ <li>
+ <a class="function" href="#install">install</a>
+ </li>
+ </ul>
+
+
+
+ <a class="attribution" title="pdoc: Python API documentation generator" href="https://pdoc.dev" target="_blank">
+ built with <span class="visually-hidden">pdoc</span><img
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+ src="data:image/svg+xml,%3Csvg%20xmlns%3D%22http%3A//www.w3.org/2000/svg%22%20role%3D%22img%22%20aria-label%3D%22pdoc%20logo%22%20width%3D%22300%22%20height%3D%22150%22%20viewBox%3D%22-1%200%2060%2030%22%3E%3Ctitle%3Epdoc%3C/title%3E%3Cpath%20d%3D%22M29.621%2021.293c-.011-.273-.214-.475-.511-.481a.5.5%200%200%200-.489.503l-.044%201.393c-.097.551-.695%201.215-1.566%201.704-.577.428-1.306.486-2.193.182-1.426-.617-2.467-1.654-3.304-2.487l-.173-.172a3.43%203.43%200%200%200-.365-.306.49.49%200%200%200-.286-.196c-1.718-1.06-4.931-1.47-7.353.191l-.219.15c-1.707%201.187-3.413%202.131-4.328%201.03-.02-.027-.49-.685-.141-1.763.233-.721.546-2.408.772-4.076.042-.09.067-.187.046-.288.166-1.347.277-2.625.241-3.351%201.378-1.008%202.271-2.586%202.271-4.362%200-.976-.272-1.935-.788-2.774-.057-.094-.122-.18-.184-.268.033-.167.052-.339.052-.516%200-1.477-1.202-2.679-2.679-2.679-.791%200-1.496.352-1.987.9a6.3%206.3%200%200%200-1.001.029c-.492-.564-1.207-.929-2.012-.929-1.477%200-2.679%201.202-2.679%202.679A2.65%202.65%200%200%200%20.97%206.554c-.383.747-.595%201.572-.595%202.41%200%202.311%201.507%204.29%203.635%205.107-.037.699-.147%202.27-.423%203.294l-.137.461c-.622%202.042-2.515%208.257%201.727%2010.643%201.614.908%203.06%201.248%204.317%201.248%202.665%200%204.492-1.524%205.322-2.401%201.476-1.559%202.886-1.854%206.491.82%201.877%201.393%203.514%201.753%204.861%201.068%202.223-1.713%202.811-3.867%203.399-6.374.077-.846.056-1.469.054-1.537zm-4.835%204.313c-.054.305-.156.586-.242.629-.034-.007-.131-.022-.307-.157-.145-.111-.314-.478-.456-.908.221.121.432.25.675.355.115.039.219.051.33.081zm-2.251-1.238c-.05.33-.158.648-.252.694-.022.001-.125-.018-.307-.157-.217-.166-.488-.906-.639-1.573.358.344.754.693%201.198%201.036zm-3.887-2.337c-.006-.116-.018-.231-.041-.342.635.145%201.189.368%201.599.625.097.231.166.481.174.642-.03.049-.055.101-.067.158-.046.013-.128.026-.298.004-.278-.037-.901-.57-1.367-1.087zm-1.127-.497c.116.306.176.625.12.71-.019.014-.117.045-.345.016-.206-.027-.604-.332-.986-.695.41-.051.816-.056%201.211-.031zm-4.535%201.535c.209.22.379.47.358.598-.006.041-.088.138-.351.234-.144.055-.539-.063-.979-.259a11.66%2011.66%200%200%200%20.972-.573zm.983-.664c.359-.237.738-.418%201.126-.554.25.237.479.548.457.694-.006.042-.087.138-.351.235-.174.064-.694-.105-1.232-.375zm-3.381%201.794c-.022.145-.061.29-.149.401-.133.166-.358.248-.69.251h-.002c-.133%200-.306-.26-.45-.621.417.091.854.07%201.291-.031zm-2.066-8.077a4.78%204.78%200%200%201-.775-.584c.172-.115.505-.254.88-.378l-.105.962zm-.331%202.302a10.32%2010.32%200%200%201-.828-.502c.202-.143.576-.328.984-.49l-.156.992zm-.45%202.157l-.701-.403c.214-.115.536-.249.891-.376a11.57%2011.57%200%200%201-.19.779zm-.181%201.716c.064.398.194.702.298.893-.194-.051-.435-.162-.736-.398.061-.119.224-.3.438-.495zM8.87%204.141c0%20.152-.123.276-.276.276s-.275-.124-.275-.276.123-.276.276-.276.275.124.275.276zm-.735-.389a1.15%201.15%200%200%200-.314.783%201.16%201.16%200%200%200%201.162%201.162c.457%200%20.842-.27%201.032-.653.026.117.042.238.042.362a1.68%201.68%200%200%201-1.679%201.679%201.68%201.68%200%200%201-1.679-1.679c0-.843.626-1.535%201.436-1.654zM5.059%205.406A1.68%201.68%200%200%201%203.38%207.085a1.68%201.68%200%200%201-1.679-1.679c0-.037.009-.072.011-.109.21.3.541.508.935.508a1.16%201.16%200%200%200%201.162-1.162%201.14%201.14%200%200%200-.474-.912c.015%200%20.03-.005.045-.005.926.001%201.679.754%201.679%201.68zM3.198%204.141c0%20.152-.123.276-.276.276s-.275-.124-.275-.276.123-.276.276-.276.275.124.275.276zM1.375%208.964c0-.52.103-1.035.288-1.52.466.394%201.06.64%201.717.64%201.144%200%202.116-.725%202.499-1.738.383%201.012%201.355%201.738%202.499%201.738.867%200%201.631-.421%202.121-1.062.307.605.478%201.267.478%201.942%200%202.486-2.153%204.51-4.801%204.51s-4.801-2.023-4.801-4.51zm24.342%2019.349c-.985.498-2.267.168-3.813-.979-3.073-2.281-5.453-3.199-7.813-.705-1.315%201.391-4.163%203.365-8.423.97-3.174-1.786-2.239-6.266-1.261-9.479l.146-.492c.276-1.02.395-2.457.444-3.268a6.11%206.11%200%200%200%201.18.115%206.01%206.01%200%200%200%202.536-.562l-.006.175c-.802.215-1.848.612-2.021%201.25-.079.295.021.601.274.837.219.203.415.364.598.501-.667.304-1.243.698-1.311%201.179-.02.144-.022.507.393.787.213.144.395.26.564.365-1.285.521-1.361.96-1.381%201.126-.018.142-.011.496.427.746l.854.489c-.473.389-.971.914-.999%201.429-.018.278.095.532.316.713.675.556%201.231.721%201.653.721.059%200%20.104-.014.158-.02.207.707.641%201.64%201.513%201.64h.013c.8-.008%201.236-.345%201.462-.626.173-.216.268-.457.325-.692.424.195.93.374%201.372.374.151%200%20.294-.021.423-.068.732-.27.944-.704.993-1.021.009-.061.003-.119.002-.179.266.086.538.147.789.147.15%200%20.294-.021.423-.069.542-.2.797-.489.914-.754.237.147.478.258.704.288.106.014.205.021.296.021.356%200%20.595-.101.767-.229.438.435%201.094.992%201.656%201.067.106.014.205.021.296.021a1.56%201.56%200%200%200%20.323-.035c.17.575.453%201.289.866%201.605.358.273.665.362.914.362a.99.99%200%200%200%20.421-.093%201.03%201.03%200%200%200%20.245-.164c.168.42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+ </a>
+</div>
+ </nav>
+ <main class="pdoc">
+ <section class="module-info">
+ <h1 class="modulename">
+<a href="./../acmc.html">acmc</a><wbr>.trud </h1>
+
+
+ <input id="mod-trud-view-source" class="view-source-toggle-state" type="checkbox" aria-hidden="true" tabindex="-1">
+
+ <label class="view-source-button" for="mod-trud-view-source"><span>View Source</span></label>
+
+ <div class="pdoc-code codehilite"><pre><span></span><span id="L-1"><a href="#L-1"><span class="linenos"> 1</span></a><span class="kn">import</span><span class="w"> </span><span class="nn">os</span>
+</span><span id="L-2"><a href="#L-2"><span class="linenos"> 2</span></a><span class="kn">import</span><span class="w"> </span><span class="nn">sys</span>
+</span><span id="L-3"><a href="#L-3"><span class="linenos"> 3</span></a><span class="kn">import</span><span class="w"> </span><span class="nn">requests</span>
+</span><span id="L-4"><a href="#L-4"><span class="linenos"> 4</span></a><span class="kn">import</span><span class="w"> </span><span class="nn">argparse</span>
+</span><span id="L-5"><a href="#L-5"><span class="linenos"> 5</span></a><span class="kn">import</span><span class="w"> </span><span class="nn">shutil</span>
+</span><span id="L-6"><a href="#L-6"><span class="linenos"> 6</span></a><span class="kn">import</span><span class="w"> </span><span class="nn">hashlib</span>
+</span><span id="L-7"><a href="#L-7"><span class="linenos"> 7</span></a><span class="kn">import</span><span class="w"> </span><span class="nn">zipfile</span>
+</span><span id="L-8"><a href="#L-8"><span class="linenos"> 8</span></a><span class="kn">import</span><span class="w"> </span><span class="nn">pandas</span><span class="w"> </span><span class="k">as</span><span class="w"> </span><span class="nn">pd</span>
+</span><span id="L-9"><a href="#L-9"><span class="linenos"> 9</span></a><span class="kn">import</span><span class="w"> </span><span class="nn">simpledbf</span> <span class="c1"># type: ignore</span>
+</span><span id="L-10"><a href="#L-10"><span class="linenos"> 10</span></a><span class="kn">import</span><span class="w"> </span><span class="nn">yaml</span>
+</span><span id="L-11"><a href="#L-11"><span class="linenos"> 11</span></a><span class="kn">from</span><span class="w"> </span><span class="nn">pathlib</span><span class="w"> </span><span class="kn">import</span> <span class="n">Path</span>
+</span><span id="L-12"><a href="#L-12"><span class="linenos"> 12</span></a>
+</span><span id="L-13"><a href="#L-13"><span class="linenos"> 13</span></a><span class="c1"># setup logging</span>
+</span><span id="L-14"><a href="#L-14"><span class="linenos"> 14</span></a><span class="kn">from</span><span class="w"> </span><span class="nn">acmc</span><span class="w"> </span><span class="kn">import</span> <span class="n">util</span><span class="p">,</span> <span class="n">logging_config</span> <span class="k">as</span> <span class="n">lc</span>
+</span><span id="L-15"><a href="#L-15"><span class="linenos"> 15</span></a>
+</span><span id="L-16"><a href="#L-16"><span class="linenos"> 16</span></a><span class="n">logger</span> <span class="o">=</span> <span class="n">lc</span><span class="o">.</span><span class="n">setup_logger</span><span class="p">()</span>
+</span><span id="L-17"><a href="#L-17"><span class="linenos"> 17</span></a>
+</span><span id="L-18"><a href="#L-18"><span class="linenos"> 18</span></a><span class="c1"># Constants</span>
+</span><span id="L-19"><a href="#L-19"><span class="linenos"> 19</span></a><span class="n">FQDN</span> <span class="o">=</span> <span class="s2">"isd.digital.nhs.uk"</span>
+</span><span id="L-20"><a href="#L-20"><span class="linenos"> 20</span></a><span class="n">VOCAB_PATH</span> <span class="o">=</span> <span class="n">Path</span><span class="p">(</span><span class="s2">"./vocab/trud"</span><span class="p">)</span>
+</span><span id="L-21"><a href="#L-21"><span class="linenos"> 21</span></a><span class="n">VERSION_FILE</span> <span class="o">=</span> <span class="s2">"trud_version.yaml"</span>
+</span><span id="L-22"><a href="#L-22"><span class="linenos"> 22</span></a><span class="n">VERSION_PATH</span> <span class="o">=</span> <span class="n">VOCAB_PATH</span> <span class="o">/</span> <span class="n">VERSION_FILE</span>
+</span><span id="L-23"><a href="#L-23"><span class="linenos"> 23</span></a><span class="n">DOWNLOADS_PATH</span> <span class="o">=</span> <span class="n">VOCAB_PATH</span> <span class="o">/</span> <span class="s2">"downloads"</span>
+</span><span id="L-24"><a href="#L-24"><span class="linenos"> 24</span></a><span class="n">PROCESSED_PATH</span> <span class="o">=</span> <span class="n">VOCAB_PATH</span> <span class="o">/</span> <span class="s2">"processed"</span>
+</span><span id="L-25"><a href="#L-25"><span class="linenos"> 25</span></a>
+</span><span id="L-26"><a href="#L-26"><span class="linenos"> 26</span></a>
+</span><span id="L-27"><a href="#L-27"><span class="linenos"> 27</span></a><span class="k">def</span><span class="w"> </span><span class="nf">get_releases</span><span class="p">(</span><span class="n">item_id</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">API_KEY</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">latest</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span> <span class="o">-></span> <span class="nb">list</span><span class="p">:</span>
+</span><span id="L-28"><a href="#L-28"><span class="linenos"> 28</span></a><span class="w"> </span><span class="sd">"""Retrieve release information for an item from the TRUD API."""</span>
+</span><span id="L-29"><a href="#L-29"><span class="linenos"> 29</span></a> <span class="n">url</span> <span class="o">=</span> <span class="sa">f</span><span class="s2">"https://</span><span class="si">{</span><span class="n">FQDN</span><span class="si">}</span><span class="s2">/trud/api/v1/keys/</span><span class="si">{</span><span class="n">API_KEY</span><span class="si">}</span><span class="s2">/items/</span><span class="si">{</span><span class="n">item_id</span><span class="si">}</span><span class="s2">/releases"</span>
+</span><span id="L-30"><a href="#L-30"><span class="linenos"> 30</span></a> <span class="k">if</span> <span class="n">latest</span><span class="p">:</span>
+</span><span id="L-31"><a href="#L-31"><span class="linenos"> 31</span></a> <span class="n">url</span> <span class="o">+=</span> <span class="s2">"?latest"</span>
+</span><span id="L-32"><a href="#L-32"><span class="linenos"> 32</span></a>
+</span><span id="L-33"><a href="#L-33"><span class="linenos"> 33</span></a> <span class="n">response</span> <span class="o">=</span> <span class="n">requests</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">url</span><span class="p">)</span>
+</span><span id="L-34"><a href="#L-34"><span class="linenos"> 34</span></a> <span class="k">if</span> <span class="n">response</span><span class="o">.</span><span class="n">status_code</span> <span class="o">!=</span> <span class="mi">200</span><span class="p">:</span>
+</span><span id="L-35"><a href="#L-35"><span class="linenos"> 35</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">error</span><span class="p">(</span>
+</span><span id="L-36"><a href="#L-36"><span class="linenos"> 36</span></a> <span class="sa">f</span><span class="s2">"Failed to fetch releases for item </span><span class="si">{</span><span class="n">item_id</span><span class="si">}</span><span class="s2">. Status code: </span><span class="si">{</span><span class="n">response</span><span class="o">.</span><span class="n">status_code</span><span class="si">}</span><span class="s2">, error </span><span class="si">{</span><span class="n">response</span><span class="o">.</span><span class="n">json</span><span class="p">()[</span><span class="s1">'message'</span><span class="p">]</span><span class="si">}</span><span class="s2">. If no releases found for API key, please ensure you are subscribed to the data release and that it is not pending approval"</span>
+</span><span id="L-37"><a href="#L-37"><span class="linenos"> 37</span></a> <span class="p">)</span>
+</span><span id="L-38"><a href="#L-38"><span class="linenos"> 38</span></a> <span class="n">response</span><span class="o">.</span><span class="n">raise_for_status</span><span class="p">()</span>
+</span><span id="L-39"><a href="#L-39"><span class="linenos"> 39</span></a>
+</span><span id="L-40"><a href="#L-40"><span class="linenos"> 40</span></a> <span class="n">data</span> <span class="o">=</span> <span class="n">response</span><span class="o">.</span><span class="n">json</span><span class="p">()</span>
+</span><span id="L-41"><a href="#L-41"><span class="linenos"> 41</span></a> <span class="k">if</span> <span class="n">data</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"message"</span><span class="p">)</span> <span class="o">!=</span> <span class="s2">"OK"</span><span class="p">:</span>
+</span><span id="L-42"><a href="#L-42"><span class="linenos"> 42</span></a> <span class="n">msg</span> <span class="o">=</span> <span class="sa">f</span><span class="s2">"Unknown error occurred </span><span class="si">{</span><span class="n">data</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">'message'</span><span class="p">)</span><span class="si">}</span><span class="s2">"</span>
+</span><span id="L-43"><a href="#L-43"><span class="linenos"> 43</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">error</span><span class="p">(</span><span class="n">msg</span><span class="p">)</span>
+</span><span id="L-44"><a href="#L-44"><span class="linenos"> 44</span></a> <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="n">msg</span><span class="p">)</span>
+</span><span id="L-45"><a href="#L-45"><span class="linenos"> 45</span></a>
+</span><span id="L-46"><a href="#L-46"><span class="linenos"> 46</span></a> <span class="k">return</span> <span class="n">data</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"releases"</span><span class="p">,</span> <span class="p">[])</span>
+</span><span id="L-47"><a href="#L-47"><span class="linenos"> 47</span></a>
+</span><span id="L-48"><a href="#L-48"><span class="linenos"> 48</span></a>
+</span><span id="L-49"><a href="#L-49"><span class="linenos"> 49</span></a><span class="k">def</span><span class="w"> </span><span class="nf">download_release_file</span><span class="p">(</span>
+</span><span id="L-50"><a href="#L-50"><span class="linenos"> 50</span></a> <span class="n">item_id</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+</span><span id="L-51"><a href="#L-51"><span class="linenos"> 51</span></a> <span class="n">release_ordinal</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+</span><span id="L-52"><a href="#L-52"><span class="linenos"> 52</span></a> <span class="n">release</span><span class="p">:</span> <span class="nb">dict</span><span class="p">,</span>
+</span><span id="L-53"><a href="#L-53"><span class="linenos"> 53</span></a> <span class="n">file_json_prefix</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+</span><span id="L-54"><a href="#L-54"><span class="linenos"> 54</span></a> <span class="n">file_type</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
+</span><span id="L-55"><a href="#L-55"><span class="linenos"> 55</span></a><span class="p">)</span> <span class="o">-></span> <span class="n">Path</span><span class="p">:</span>
+</span><span id="L-56"><a href="#L-56"><span class="linenos"> 56</span></a><span class="w"> </span><span class="sd">"""Download specified file type for a given release of an item."""</span>
+</span><span id="L-57"><a href="#L-57"><span class="linenos"> 57</span></a>
+</span><span id="L-58"><a href="#L-58"><span class="linenos"> 58</span></a> <span class="c1"># check folder is a directory</span>
+</span><span id="L-59"><a href="#L-59"><span class="linenos"> 59</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="n">DOWNLOADS_PATH</span><span class="o">.</span><span class="n">is_dir</span><span class="p">():</span>
+</span><span id="L-60"><a href="#L-60"><span class="linenos"> 60</span></a> <span class="k">raise</span> <span class="ne">NotADirectoryError</span><span class="p">(</span>
+</span><span id="L-61"><a href="#L-61"><span class="linenos"> 61</span></a> <span class="sa">f</span><span class="s2">"Error: '</span><span class="si">{</span><span class="n">DOWNLOADS_PATH</span><span class="si">}</span><span class="s2">' for TRUD resources is not a directory"</span>
+</span><span id="L-62"><a href="#L-62"><span class="linenos"> 62</span></a> <span class="p">)</span>
+</span><span id="L-63"><a href="#L-63"><span class="linenos"> 63</span></a>
+</span><span id="L-64"><a href="#L-64"><span class="linenos"> 64</span></a> <span class="n">file_type</span> <span class="o">=</span> <span class="n">file_type</span> <span class="ow">or</span> <span class="n">file_json_prefix</span>
+</span><span id="L-65"><a href="#L-65"><span class="linenos"> 65</span></a> <span class="n">file_url</span> <span class="o">=</span> <span class="n">release</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="sa">f</span><span class="s2">"</span><span class="si">{</span><span class="n">file_json_prefix</span><span class="si">}</span><span class="s2">FileUrl"</span><span class="p">)</span>
+</span><span id="L-66"><a href="#L-66"><span class="linenos"> 66</span></a> <span class="n">file_name</span> <span class="o">=</span> <span class="n">release</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="sa">f</span><span class="s2">"</span><span class="si">{</span><span class="n">file_json_prefix</span><span class="si">}</span><span class="s2">FileName"</span><span class="p">)</span>
+</span><span id="L-67"><a href="#L-67"><span class="linenos"> 67</span></a> <span class="n">file_destination</span> <span class="o">=</span> <span class="n">DOWNLOADS_PATH</span> <span class="o">/</span> <span class="n">file_name</span>
+</span><span id="L-68"><a href="#L-68"><span class="linenos"> 68</span></a>
+</span><span id="L-69"><a href="#L-69"><span class="linenos"> 69</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="n">file_url</span> <span class="ow">or</span> <span class="ow">not</span> <span class="n">file_name</span><span class="p">:</span>
+</span><span id="L-70"><a href="#L-70"><span class="linenos"> 70</span></a> <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span>
+</span><span id="L-71"><a href="#L-71"><span class="linenos"> 71</span></a> <span class="sa">f</span><span class="s2">"Missing </span><span class="si">{</span><span class="n">file_type</span><span class="si">}</span><span class="s2"> file information for release </span><span class="si">{</span><span class="n">release_ordinal</span><span class="si">}</span><span class="s2"> of item </span><span class="si">{</span><span class="n">item_id</span><span class="si">}</span><span class="s2">."</span>
+</span><span id="L-72"><a href="#L-72"><span class="linenos"> 72</span></a> <span class="p">)</span>
+</span><span id="L-73"><a href="#L-73"><span class="linenos"> 73</span></a>
+</span><span id="L-74"><a href="#L-74"><span class="linenos"> 74</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span>
+</span><span id="L-75"><a href="#L-75"><span class="linenos"> 75</span></a> <span class="sa">f</span><span class="s2">"Downloading item </span><span class="si">{</span><span class="n">item_id</span><span class="si">}</span><span class="s2"> </span><span class="si">{</span><span class="n">file_type</span><span class="si">}</span><span class="s2"> file: </span><span class="si">{</span><span class="n">file_name</span><span class="si">}</span><span class="s2"> from </span><span class="si">{</span><span class="n">file_url</span><span class="si">}</span><span class="s2"> to </span><span class="si">{</span><span class="n">file_destination</span><span class="si">}</span><span class="s2">"</span>
+</span><span id="L-76"><a href="#L-76"><span class="linenos"> 76</span></a> <span class="p">)</span>
+</span><span id="L-77"><a href="#L-77"><span class="linenos"> 77</span></a> <span class="n">response</span> <span class="o">=</span> <span class="n">requests</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">file_url</span><span class="p">,</span> <span class="n">stream</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+</span><span id="L-78"><a href="#L-78"><span class="linenos"> 78</span></a>
+</span><span id="L-79"><a href="#L-79"><span class="linenos"> 79</span></a> <span class="k">if</span> <span class="n">response</span><span class="o">.</span><span class="n">status_code</span> <span class="o">==</span> <span class="mi">200</span><span class="p">:</span>
+</span><span id="L-80"><a href="#L-80"><span class="linenos"> 80</span></a> <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">file_destination</span><span class="p">,</span> <span class="s2">"wb"</span><span class="p">)</span> <span class="k">as</span> <span class="n">f</span><span class="p">:</span>
+</span><span id="L-81"><a href="#L-81"><span class="linenos"> 81</span></a> <span class="n">f</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">response</span><span class="o">.</span><span class="n">content</span><span class="p">)</span>
+</span><span id="L-82"><a href="#L-82"><span class="linenos"> 82</span></a> <span class="k">else</span><span class="p">:</span>
+</span><span id="L-83"><a href="#L-83"><span class="linenos"> 83</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">error</span><span class="p">(</span>
+</span><span id="L-84"><a href="#L-84"><span class="linenos"> 84</span></a> <span class="sa">f</span><span class="s2">"Failed to download </span><span class="si">{</span><span class="n">file_type</span><span class="si">}</span><span class="s2"> file for item </span><span class="si">{</span><span class="n">item_id</span><span class="si">}</span><span class="s2">. Status code: </span><span class="si">{</span><span class="n">response</span><span class="o">.</span><span class="n">status_code</span><span class="si">}</span><span class="s2">"</span>
+</span><span id="L-85"><a href="#L-85"><span class="linenos"> 85</span></a> <span class="p">)</span>
+</span><span id="L-86"><a href="#L-86"><span class="linenos"> 86</span></a> <span class="n">response</span><span class="o">.</span><span class="n">raise_for_status</span><span class="p">()</span>
+</span><span id="L-87"><a href="#L-87"><span class="linenos"> 87</span></a>
+</span><span id="L-88"><a href="#L-88"><span class="linenos"> 88</span></a> <span class="k">return</span> <span class="n">file_destination</span>
+</span><span id="L-89"><a href="#L-89"><span class="linenos"> 89</span></a>
+</span><span id="L-90"><a href="#L-90"><span class="linenos"> 90</span></a>
+</span><span id="L-91"><a href="#L-91"><span class="linenos"> 91</span></a><span class="k">def</span><span class="w"> </span><span class="nf">validate_download_hash</span><span class="p">(</span><span class="n">file_destination</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">item_hash</span><span class="p">:</span> <span class="nb">str</span><span class="p">):</span>
+</span><span id="L-92"><a href="#L-92"><span class="linenos"> 92</span></a> <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">file_destination</span><span class="p">,</span> <span class="s2">"rb"</span><span class="p">)</span> <span class="k">as</span> <span class="n">f</span><span class="p">:</span>
+</span><span id="L-93"><a href="#L-93"><span class="linenos"> 93</span></a> <span class="nb">hash</span> <span class="o">=</span> <span class="n">hashlib</span><span class="o">.</span><span class="n">sha256</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">read</span><span class="p">())</span><span class="o">.</span><span class="n">hexdigest</span><span class="p">()</span>
+</span><span id="L-94"><a href="#L-94"><span class="linenos"> 94</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="nb">hash</span><span class="p">)</span>
+</span><span id="L-95"><a href="#L-95"><span class="linenos"> 95</span></a> <span class="k">if</span> <span class="nb">hash</span><span class="o">.</span><span class="n">upper</span><span class="p">()</span> <span class="o">==</span> <span class="n">item_hash</span><span class="o">.</span><span class="n">upper</span><span class="p">():</span>
+</span><span id="L-96"><a href="#L-96"><span class="linenos"> 96</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Verified hash of </span><span class="si">{</span><span class="n">file_destination</span><span class="si">}</span><span class="s2"> </span><span class="si">{</span><span class="nb">hash</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+</span><span id="L-97"><a href="#L-97"><span class="linenos"> 97</span></a> <span class="k">else</span><span class="p">:</span>
+</span><span id="L-98"><a href="#L-98"><span class="linenos"> 98</span></a> <span class="n">msg</span> <span class="o">=</span> <span class="sa">f</span><span class="s2">"Could not validate origin of </span><span class="si">{</span><span class="n">file_destination</span><span class="si">}</span><span class="s2">. The SHA-256 hash should be: </span><span class="si">{</span><span class="n">item_hash</span><span class="si">}</span><span class="s2">, but got </span><span class="si">{</span><span class="nb">hash</span><span class="si">}</span><span class="s2"> instead"</span>
+</span><span id="L-99"><a href="#L-99"><span class="linenos"> 99</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">error</span><span class="p">(</span><span class="n">msg</span><span class="p">)</span>
+</span><span id="L-100"><a href="#L-100"><span class="linenos">100</span></a> <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="n">msg</span><span class="p">)</span>
+</span><span id="L-101"><a href="#L-101"><span class="linenos">101</span></a>
+</span><span id="L-102"><a href="#L-102"><span class="linenos">102</span></a>
+</span><span id="L-103"><a href="#L-103"><span class="linenos">103</span></a><span class="k">def</span><span class="w"> </span><span class="nf">unzip_download</span><span class="p">(</span><span class="n">file_destination</span><span class="p">:</span> <span class="nb">str</span><span class="p">):</span>
+</span><span id="L-104"><a href="#L-104"><span class="linenos">104</span></a>
+</span><span id="L-105"><a href="#L-105"><span class="linenos">105</span></a> <span class="c1"># check folder is a directory</span>
+</span><span id="L-106"><a href="#L-106"><span class="linenos">106</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="n">DOWNLOADS_PATH</span><span class="o">.</span><span class="n">is_dir</span><span class="p">():</span>
+</span><span id="L-107"><a href="#L-107"><span class="linenos">107</span></a> <span class="k">raise</span> <span class="ne">NotADirectoryError</span><span class="p">(</span>
+</span><span id="L-108"><a href="#L-108"><span class="linenos">108</span></a> <span class="sa">f</span><span class="s2">"Error: '</span><span class="si">{</span><span class="n">DOWNLOADS_PATH</span><span class="si">}</span><span class="s2">' for TRUD resoruces is not a directory"</span>
+</span><span id="L-109"><a href="#L-109"><span class="linenos">109</span></a> <span class="p">)</span>
+</span><span id="L-110"><a href="#L-110"><span class="linenos">110</span></a>
+</span><span id="L-111"><a href="#L-111"><span class="linenos">111</span></a> <span class="k">with</span> <span class="n">zipfile</span><span class="o">.</span><span class="n">ZipFile</span><span class="p">(</span><span class="n">file_destination</span><span class="p">,</span> <span class="s2">"r"</span><span class="p">)</span> <span class="k">as</span> <span class="n">zip_ref</span><span class="p">:</span>
+</span><span id="L-112"><a href="#L-112"><span class="linenos">112</span></a> <span class="n">zip_ref</span><span class="o">.</span><span class="n">extractall</span><span class="p">(</span><span class="n">DOWNLOADS_PATH</span><span class="p">)</span>
+</span><span id="L-113"><a href="#L-113"><span class="linenos">113</span></a>
+</span><span id="L-114"><a href="#L-114"><span class="linenos">114</span></a>
+</span><span id="L-115"><a href="#L-115"><span class="linenos">115</span></a><span class="k">def</span><span class="w"> </span><span class="nf">extract_icd10</span><span class="p">():</span>
+</span><span id="L-116"><a href="#L-116"><span class="linenos">116</span></a> <span class="c1"># ICD10_edition5</span>
+</span><span id="L-117"><a href="#L-117"><span class="linenos">117</span></a> <span class="n">file_path</span> <span class="o">=</span> <span class="p">(</span>
+</span><span id="L-118"><a href="#L-118"><span class="linenos">118</span></a> <span class="n">DOWNLOADS_PATH</span>
+</span><span id="L-119"><a href="#L-119"><span class="linenos">119</span></a> <span class="o">/</span> <span class="s2">"ICD10_Edition5_XML_20160401"</span>
+</span><span id="L-120"><a href="#L-120"><span class="linenos">120</span></a> <span class="o">/</span> <span class="s2">"Content"</span>
+</span><span id="L-121"><a href="#L-121"><span class="linenos">121</span></a> <span class="o">/</span> <span class="s2">"ICD10_Edition5_CodesAndTitlesAndMetadata_GB_20160401.xml"</span>
+</span><span id="L-122"><a href="#L-122"><span class="linenos">122</span></a> <span class="p">)</span>
+</span><span id="L-123"><a href="#L-123"><span class="linenos">123</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">read_xml</span><span class="p">(</span><span class="n">file_path</span><span class="p">)</span>
+</span><span id="L-124"><a href="#L-124"><span class="linenos">124</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">df</span><span class="p">[[</span><span class="s2">"CODE"</span><span class="p">,</span> <span class="s2">"ALT_CODE"</span><span class="p">,</span> <span class="s2">"DESCRIPTION"</span><span class="p">]]</span>
+</span><span id="L-125"><a href="#L-125"><span class="linenos">125</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">df</span><span class="o">.</span><span class="n">rename</span><span class="p">(</span>
+</span><span id="L-126"><a href="#L-126"><span class="linenos">126</span></a> <span class="n">columns</span><span class="o">=</span><span class="p">{</span><span class="s2">"CODE"</span><span class="p">:</span> <span class="s2">"icd10"</span><span class="p">,</span> <span class="s2">"ALT_CODE"</span><span class="p">:</span> <span class="s2">"icd10_alt"</span><span class="p">,</span> <span class="s2">"DESCRIPTION"</span><span class="p">:</span> <span class="s2">"description"</span><span class="p">}</span>
+</span><span id="L-127"><a href="#L-127"><span class="linenos">127</span></a> <span class="p">)</span>
+</span><span id="L-128"><a href="#L-128"><span class="linenos">128</span></a> <span class="n">output_path</span> <span class="o">=</span> <span class="n">PROCESSED_PATH</span> <span class="o">/</span> <span class="s2">"icd10.parquet"</span>
+</span><span id="L-129"><a href="#L-129"><span class="linenos">129</span></a> <span class="n">df</span><span class="o">.</span><span class="n">to_parquet</span><span class="p">(</span><span class="n">output_path</span><span class="p">,</span> <span class="n">index</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span>
+</span><span id="L-130"><a href="#L-130"><span class="linenos">130</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Extracted: </span><span class="si">{</span><span class="n">output_path</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+</span><span id="L-131"><a href="#L-131"><span class="linenos">131</span></a>
+</span><span id="L-132"><a href="#L-132"><span class="linenos">132</span></a>
+</span><span id="L-133"><a href="#L-133"><span class="linenos">133</span></a><span class="k">def</span><span class="w"> </span><span class="nf">extract_opsc4</span><span class="p">():</span>
+</span><span id="L-134"><a href="#L-134"><span class="linenos">134</span></a> <span class="n">file_path</span> <span class="o">=</span> <span class="p">(</span>
+</span><span id="L-135"><a href="#L-135"><span class="linenos">135</span></a> <span class="n">DOWNLOADS_PATH</span>
+</span><span id="L-136"><a href="#L-136"><span class="linenos">136</span></a> <span class="o">/</span> <span class="s2">"OPCS410 Data files txt"</span>
+</span><span id="L-137"><a href="#L-137"><span class="linenos">137</span></a> <span class="o">/</span> <span class="s2">"OPCS410 CodesAndTitles Nov 2022 V1.0.txt"</span>
+</span><span id="L-138"><a href="#L-138"><span class="linenos">138</span></a> <span class="p">)</span>
+</span><span id="L-139"><a href="#L-139"><span class="linenos">139</span></a>
+</span><span id="L-140"><a href="#L-140"><span class="linenos">140</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">read_csv</span><span class="p">(</span><span class="n">file_path</span><span class="p">,</span> <span class="n">sep</span><span class="o">=</span><span class="s2">"</span><span class="se">\t</span><span class="s2">"</span><span class="p">,</span> <span class="n">dtype</span><span class="o">=</span><span class="nb">str</span><span class="p">,</span> <span class="n">header</span><span class="o">=</span><span class="kc">None</span><span class="p">)</span>
+</span><span id="L-141"><a href="#L-141"><span class="linenos">141</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">df</span><span class="o">.</span><span class="n">rename</span><span class="p">(</span><span class="n">columns</span><span class="o">=</span><span class="p">{</span><span class="mi">0</span><span class="p">:</span> <span class="s2">"opcs4"</span><span class="p">,</span> <span class="mi">1</span><span class="p">:</span> <span class="s2">"description"</span><span class="p">})</span>
+</span><span id="L-142"><a href="#L-142"><span class="linenos">142</span></a>
+</span><span id="L-143"><a href="#L-143"><span class="linenos">143</span></a> <span class="n">output_path</span> <span class="o">=</span> <span class="n">PROCESSED_PATH</span> <span class="o">/</span> <span class="s2">"opcs4.parquet"</span>
+</span><span id="L-144"><a href="#L-144"><span class="linenos">144</span></a> <span class="n">df</span><span class="o">.</span><span class="n">to_parquet</span><span class="p">(</span><span class="n">output_path</span><span class="p">,</span> <span class="n">index</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span>
+</span><span id="L-145"><a href="#L-145"><span class="linenos">145</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Extracted: </span><span class="si">{</span><span class="n">output_path</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+</span><span id="L-146"><a href="#L-146"><span class="linenos">146</span></a>
+</span><span id="L-147"><a href="#L-147"><span class="linenos">147</span></a>
+</span><span id="L-148"><a href="#L-148"><span class="linenos">148</span></a><span class="k">def</span><span class="w"> </span><span class="nf">extract_nhs_data_migrations</span><span class="p">():</span>
+</span><span id="L-149"><a href="#L-149"><span class="linenos">149</span></a> <span class="c1"># NHS Data Migrations</span>
+</span><span id="L-150"><a href="#L-150"><span class="linenos">150</span></a>
+</span><span id="L-151"><a href="#L-151"><span class="linenos">151</span></a> <span class="c1"># snomed only</span>
+</span><span id="L-152"><a href="#L-152"><span class="linenos">152</span></a> <span class="n">file_path</span> <span class="o">=</span> <span class="p">(</span>
+</span><span id="L-153"><a href="#L-153"><span class="linenos">153</span></a> <span class="n">DOWNLOADS_PATH</span>
+</span><span id="L-154"><a href="#L-154"><span class="linenos">154</span></a> <span class="o">/</span> <span class="s2">"Mapping Tables"</span>
+</span><span id="L-155"><a href="#L-155"><span class="linenos">155</span></a> <span class="o">/</span> <span class="s2">"Updated"</span>
+</span><span id="L-156"><a href="#L-156"><span class="linenos">156</span></a> <span class="o">/</span> <span class="s2">"Clinically Assured"</span>
+</span><span id="L-157"><a href="#L-157"><span class="linenos">157</span></a> <span class="o">/</span> <span class="s2">"sctcremap_uk_20200401000001.txt"</span>
+</span><span id="L-158"><a href="#L-158"><span class="linenos">158</span></a> <span class="p">)</span>
+</span><span id="L-159"><a href="#L-159"><span class="linenos">159</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">read_csv</span><span class="p">(</span><span class="n">file_path</span><span class="p">,</span> <span class="n">sep</span><span class="o">=</span><span class="s2">"</span><span class="se">\t</span><span class="s2">"</span><span class="p">)</span>
+</span><span id="L-160"><a href="#L-160"><span class="linenos">160</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">df</span><span class="p">[[</span><span class="s2">"SCT_CONCEPTID"</span><span class="p">]]</span>
+</span><span id="L-161"><a href="#L-161"><span class="linenos">161</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">df</span><span class="o">.</span><span class="n">rename</span><span class="p">(</span><span class="n">columns</span><span class="o">=</span><span class="p">{</span><span class="s2">"SCT_CONCEPTID"</span><span class="p">:</span> <span class="s2">"snomed"</span><span class="p">})</span>
+</span><span id="L-162"><a href="#L-162"><span class="linenos">162</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">df</span><span class="o">.</span><span class="n">drop_duplicates</span><span class="p">()</span>
+</span><span id="L-163"><a href="#L-163"><span class="linenos">163</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">df</span><span class="o">.</span><span class="n">astype</span><span class="p">(</span><span class="nb">str</span><span class="p">)</span>
+</span><span id="L-164"><a href="#L-164"><span class="linenos">164</span></a>
+</span><span id="L-165"><a href="#L-165"><span class="linenos">165</span></a> <span class="n">output_path</span> <span class="o">=</span> <span class="n">PROCESSED_PATH</span> <span class="o">/</span> <span class="s2">"snomed.parquet"</span>
+</span><span id="L-166"><a href="#L-166"><span class="linenos">166</span></a> <span class="n">df</span><span class="o">.</span><span class="n">to_parquet</span><span class="p">(</span><span class="n">output_path</span><span class="p">,</span> <span class="n">index</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span>
+</span><span id="L-167"><a href="#L-167"><span class="linenos">167</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Extracted: </span><span class="si">{</span><span class="n">output_path</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+</span><span id="L-168"><a href="#L-168"><span class="linenos">168</span></a>
+</span><span id="L-169"><a href="#L-169"><span class="linenos">169</span></a> <span class="c1"># r2 -> r3</span>
+</span><span id="L-170"><a href="#L-170"><span class="linenos">170</span></a> <span class="n">file_path</span> <span class="o">=</span> <span class="p">(</span>
+</span><span id="L-171"><a href="#L-171"><span class="linenos">171</span></a> <span class="n">DOWNLOADS_PATH</span>
+</span><span id="L-172"><a href="#L-172"><span class="linenos">172</span></a> <span class="o">/</span> <span class="s2">"Mapping Tables"</span>
+</span><span id="L-173"><a href="#L-173"><span class="linenos">173</span></a> <span class="o">/</span> <span class="s2">"Updated"</span>
+</span><span id="L-174"><a href="#L-174"><span class="linenos">174</span></a> <span class="o">/</span> <span class="s2">"Clinically Assured"</span>
+</span><span id="L-175"><a href="#L-175"><span class="linenos">175</span></a> <span class="o">/</span> <span class="s2">"rctctv3map_uk_20200401000001.txt"</span>
+</span><span id="L-176"><a href="#L-176"><span class="linenos">176</span></a> <span class="p">)</span>
+</span><span id="L-177"><a href="#L-177"><span class="linenos">177</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">read_csv</span><span class="p">(</span><span class="n">file_path</span><span class="p">,</span> <span class="n">sep</span><span class="o">=</span><span class="s2">"</span><span class="se">\t</span><span class="s2">"</span><span class="p">)</span>
+</span><span id="L-178"><a href="#L-178"><span class="linenos">178</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">df</span><span class="p">[[</span><span class="s2">"V2_CONCEPTID"</span><span class="p">,</span> <span class="s2">"CTV3_CONCEPTID"</span><span class="p">]]</span>
+</span><span id="L-179"><a href="#L-179"><span class="linenos">179</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">df</span><span class="o">.</span><span class="n">rename</span><span class="p">(</span><span class="n">columns</span><span class="o">=</span><span class="p">{</span><span class="s2">"V2_CONCEPTID"</span><span class="p">:</span> <span class="s2">"read2"</span><span class="p">,</span> <span class="s2">"CTV3_CONCEPTID"</span><span class="p">:</span> <span class="s2">"read3"</span><span class="p">})</span>
+</span><span id="L-180"><a href="#L-180"><span class="linenos">180</span></a>
+</span><span id="L-181"><a href="#L-181"><span class="linenos">181</span></a> <span class="n">output_path</span> <span class="o">=</span> <span class="n">PROCESSED_PATH</span> <span class="o">/</span> <span class="s2">"read2_to_read3.parquet"</span>
+</span><span id="L-182"><a href="#L-182"><span class="linenos">182</span></a> <span class="n">df</span><span class="o">.</span><span class="n">to_parquet</span><span class="p">(</span><span class="n">output_path</span><span class="p">,</span> <span class="n">index</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span>
+</span><span id="L-183"><a href="#L-183"><span class="linenos">183</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Extracted: </span><span class="si">{</span><span class="n">output_path</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+</span><span id="L-184"><a href="#L-184"><span class="linenos">184</span></a>
+</span><span id="L-185"><a href="#L-185"><span class="linenos">185</span></a> <span class="c1"># r3->r2</span>
+</span><span id="L-186"><a href="#L-186"><span class="linenos">186</span></a> <span class="n">file_path</span> <span class="o">=</span> <span class="p">(</span>
+</span><span id="L-187"><a href="#L-187"><span class="linenos">187</span></a> <span class="n">DOWNLOADS_PATH</span>
+</span><span id="L-188"><a href="#L-188"><span class="linenos">188</span></a> <span class="o">/</span> <span class="s2">"Mapping Tables"</span>
+</span><span id="L-189"><a href="#L-189"><span class="linenos">189</span></a> <span class="o">/</span> <span class="s2">"Updated"</span>
+</span><span id="L-190"><a href="#L-190"><span class="linenos">190</span></a> <span class="o">/</span> <span class="s2">"Clinically Assured"</span>
+</span><span id="L-191"><a href="#L-191"><span class="linenos">191</span></a> <span class="o">/</span> <span class="s2">"ctv3rctmap_uk_20200401000002.txt"</span>
+</span><span id="L-192"><a href="#L-192"><span class="linenos">192</span></a> <span class="p">)</span>
+</span><span id="L-193"><a href="#L-193"><span class="linenos">193</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">read_csv</span><span class="p">(</span><span class="n">file_path</span><span class="p">,</span> <span class="n">sep</span><span class="o">=</span><span class="s2">"</span><span class="se">\t</span><span class="s2">"</span><span class="p">)</span>
+</span><span id="L-194"><a href="#L-194"><span class="linenos">194</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">df</span><span class="p">[[</span><span class="s2">"CTV3_CONCEPTID"</span><span class="p">,</span> <span class="s2">"V2_CONCEPTID"</span><span class="p">]]</span>
+</span><span id="L-195"><a href="#L-195"><span class="linenos">195</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">df</span><span class="o">.</span><span class="n">rename</span><span class="p">(</span><span class="n">columns</span><span class="o">=</span><span class="p">{</span><span class="s2">"CTV3_CONCEPTID"</span><span class="p">:</span> <span class="s2">"read3"</span><span class="p">,</span> <span class="s2">"V2_CONCEPTID"</span><span class="p">:</span> <span class="s2">"read2"</span><span class="p">})</span>
+</span><span id="L-196"><a href="#L-196"><span class="linenos">196</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">df</span><span class="o">.</span><span class="n">drop_duplicates</span><span class="p">()</span>
+</span><span id="L-197"><a href="#L-197"><span class="linenos">197</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">df</span><span class="p">[</span><span class="o">~</span><span class="n">df</span><span class="p">[</span><span class="s2">"read2"</span><span class="p">]</span><span class="o">.</span><span class="n">str</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="s2">"^.*_.*$"</span><span class="p">)]</span> <span class="c1"># remove r2 codes with '_'</span>
+</span><span id="L-198"><a href="#L-198"><span class="linenos">198</span></a>
+</span><span id="L-199"><a href="#L-199"><span class="linenos">199</span></a> <span class="n">output_path</span> <span class="o">=</span> <span class="n">PROCESSED_PATH</span> <span class="o">/</span> <span class="s2">"read3_to_read2.parquet"</span>
+</span><span id="L-200"><a href="#L-200"><span class="linenos">200</span></a> <span class="n">df</span><span class="o">.</span><span class="n">to_parquet</span><span class="p">(</span><span class="n">output_path</span><span class="p">,</span> <span class="n">index</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span>
+</span><span id="L-201"><a href="#L-201"><span class="linenos">201</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Extracted: </span><span class="si">{</span><span class="n">output_path</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+</span><span id="L-202"><a href="#L-202"><span class="linenos">202</span></a>
+</span><span id="L-203"><a href="#L-203"><span class="linenos">203</span></a> <span class="c1"># r2 -> snomed</span>
+</span><span id="L-204"><a href="#L-204"><span class="linenos">204</span></a> <span class="n">file_path</span> <span class="o">=</span> <span class="p">(</span>
+</span><span id="L-205"><a href="#L-205"><span class="linenos">205</span></a> <span class="n">DOWNLOADS_PATH</span>
+</span><span id="L-206"><a href="#L-206"><span class="linenos">206</span></a> <span class="o">/</span> <span class="s2">"Mapping Tables"</span>
+</span><span id="L-207"><a href="#L-207"><span class="linenos">207</span></a> <span class="o">/</span> <span class="s2">"Updated"</span>
+</span><span id="L-208"><a href="#L-208"><span class="linenos">208</span></a> <span class="o">/</span> <span class="s2">"Clinically Assured"</span>
+</span><span id="L-209"><a href="#L-209"><span class="linenos">209</span></a> <span class="o">/</span> <span class="s2">"rcsctmap2_uk_20200401000001.txt"</span>
+</span><span id="L-210"><a href="#L-210"><span class="linenos">210</span></a> <span class="p">)</span>
+</span><span id="L-211"><a href="#L-211"><span class="linenos">211</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">read_csv</span><span class="p">(</span><span class="n">file_path</span><span class="p">,</span> <span class="n">sep</span><span class="o">=</span><span class="s2">"</span><span class="se">\t</span><span class="s2">"</span><span class="p">,</span> <span class="n">dtype</span><span class="o">=</span><span class="nb">str</span><span class="p">)</span>
+</span><span id="L-212"><a href="#L-212"><span class="linenos">212</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">df</span><span class="p">[[</span><span class="s2">"ReadCode"</span><span class="p">,</span> <span class="s2">"ConceptId"</span><span class="p">]]</span>
+</span><span id="L-213"><a href="#L-213"><span class="linenos">213</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">df</span><span class="o">.</span><span class="n">rename</span><span class="p">(</span><span class="n">columns</span><span class="o">=</span><span class="p">{</span><span class="s2">"ReadCode"</span><span class="p">:</span> <span class="s2">"read2"</span><span class="p">,</span> <span class="s2">"ConceptId"</span><span class="p">:</span> <span class="s2">"snomed"</span><span class="p">})</span>
+</span><span id="L-214"><a href="#L-214"><span class="linenos">214</span></a>
+</span><span id="L-215"><a href="#L-215"><span class="linenos">215</span></a> <span class="n">output_path</span> <span class="o">=</span> <span class="n">PROCESSED_PATH</span> <span class="o">/</span> <span class="s2">"read2_to_snomed.parquet"</span>
+</span><span id="L-216"><a href="#L-216"><span class="linenos">216</span></a> <span class="n">df</span><span class="o">.</span><span class="n">to_parquet</span><span class="p">(</span><span class="n">output_path</span><span class="p">,</span> <span class="n">index</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span>
+</span><span id="L-217"><a href="#L-217"><span class="linenos">217</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Extracted: </span><span class="si">{</span><span class="n">output_path</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+</span><span id="L-218"><a href="#L-218"><span class="linenos">218</span></a>
+</span><span id="L-219"><a href="#L-219"><span class="linenos">219</span></a> <span class="c1"># r3->snomed</span>
+</span><span id="L-220"><a href="#L-220"><span class="linenos">220</span></a> <span class="n">file_path</span> <span class="o">=</span> <span class="p">(</span>
+</span><span id="L-221"><a href="#L-221"><span class="linenos">221</span></a> <span class="n">DOWNLOADS_PATH</span>
+</span><span id="L-222"><a href="#L-222"><span class="linenos">222</span></a> <span class="o">/</span> <span class="s2">"Mapping Tables"</span>
+</span><span id="L-223"><a href="#L-223"><span class="linenos">223</span></a> <span class="o">/</span> <span class="s2">"Updated"</span>
+</span><span id="L-224"><a href="#L-224"><span class="linenos">224</span></a> <span class="o">/</span> <span class="s2">"Clinically Assured"</span>
+</span><span id="L-225"><a href="#L-225"><span class="linenos">225</span></a> <span class="o">/</span> <span class="s2">"ctv3sctmap2_uk_20200401000001.txt"</span>
+</span><span id="L-226"><a href="#L-226"><span class="linenos">226</span></a> <span class="p">)</span>
+</span><span id="L-227"><a href="#L-227"><span class="linenos">227</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">read_csv</span><span class="p">(</span><span class="n">file_path</span><span class="p">,</span> <span class="n">sep</span><span class="o">=</span><span class="s2">"</span><span class="se">\t</span><span class="s2">"</span><span class="p">,</span> <span class="n">dtype</span><span class="o">=</span><span class="nb">str</span><span class="p">)</span>
+</span><span id="L-228"><a href="#L-228"><span class="linenos">228</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">df</span><span class="p">[[</span><span class="s2">"CTV3_TERMID"</span><span class="p">,</span> <span class="s2">"SCT_CONCEPTID"</span><span class="p">]]</span>
+</span><span id="L-229"><a href="#L-229"><span class="linenos">229</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">df</span><span class="o">.</span><span class="n">rename</span><span class="p">(</span><span class="n">columns</span><span class="o">=</span><span class="p">{</span><span class="s2">"CTV3_TERMID"</span><span class="p">:</span> <span class="s2">"read3"</span><span class="p">,</span> <span class="s2">"SCT_CONCEPTID"</span><span class="p">:</span> <span class="s2">"snomed"</span><span class="p">})</span>
+</span><span id="L-230"><a href="#L-230"><span class="linenos">230</span></a> <span class="n">df</span><span class="p">[</span><span class="s2">"snomed"</span><span class="p">]</span> <span class="o">=</span> <span class="n">df</span><span class="p">[</span><span class="s2">"snomed"</span><span class="p">]</span><span class="o">.</span><span class="n">astype</span><span class="p">(</span><span class="nb">str</span><span class="p">)</span>
+</span><span id="L-231"><a href="#L-231"><span class="linenos">231</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">df</span><span class="p">[</span><span class="o">~</span><span class="n">df</span><span class="p">[</span><span class="s2">"snomed"</span><span class="p">]</span><span class="o">.</span><span class="n">str</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="s2">"^.*_.*$"</span><span class="p">)]</span> <span class="c1"># remove snomed codes with '_'</span>
+</span><span id="L-232"><a href="#L-232"><span class="linenos">232</span></a>
+</span><span id="L-233"><a href="#L-233"><span class="linenos">233</span></a> <span class="n">output_path</span> <span class="o">=</span> <span class="n">PROCESSED_PATH</span> <span class="o">/</span> <span class="s2">"read3_to_snomed.parquet"</span>
+</span><span id="L-234"><a href="#L-234"><span class="linenos">234</span></a> <span class="n">df</span><span class="o">.</span><span class="n">to_parquet</span><span class="p">(</span><span class="n">output_path</span><span class="p">,</span> <span class="n">index</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span>
+</span><span id="L-235"><a href="#L-235"><span class="linenos">235</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Extracted: </span><span class="si">{</span><span class="n">output_path</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+</span><span id="L-236"><a href="#L-236"><span class="linenos">236</span></a>
+</span><span id="L-237"><a href="#L-237"><span class="linenos">237</span></a>
+</span><span id="L-238"><a href="#L-238"><span class="linenos">238</span></a><span class="k">def</span><span class="w"> </span><span class="nf">extract_nhs_read_browser</span><span class="p">():</span>
+</span><span id="L-239"><a href="#L-239"><span class="linenos">239</span></a> <span class="c1"># r2 only</span>
+</span><span id="L-240"><a href="#L-240"><span class="linenos">240</span></a> <span class="n">input_path</span> <span class="o">=</span> <span class="n">DOWNLOADS_PATH</span> <span class="o">/</span> <span class="s2">"Standard"</span> <span class="o">/</span> <span class="s2">"V2"</span> <span class="o">/</span> <span class="s2">"ANCESTOR.DBF"</span>
+</span><span id="L-241"><a href="#L-241"><span class="linenos">241</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">simpledbf</span><span class="o">.</span><span class="n">Dbf5</span><span class="p">(</span><span class="n">input_path</span><span class="p">)</span><span class="o">.</span><span class="n">to_dataframe</span><span class="p">()</span>
+</span><span id="L-242"><a href="#L-242"><span class="linenos">242</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">concat</span><span class="p">([</span><span class="n">df</span><span class="p">[</span><span class="s2">"READCODE"</span><span class="p">],</span> <span class="n">df</span><span class="p">[</span><span class="s2">"DESCENDANT"</span><span class="p">]])</span>
+</span><span id="L-243"><a href="#L-243"><span class="linenos">243</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">(</span><span class="n">df</span><span class="o">.</span><span class="n">drop_duplicates</span><span class="p">())</span>
+</span><span id="L-244"><a href="#L-244"><span class="linenos">244</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">df</span><span class="o">.</span><span class="n">rename</span><span class="p">(</span><span class="n">columns</span><span class="o">=</span><span class="p">{</span><span class="mi">0</span><span class="p">:</span> <span class="s2">"read2"</span><span class="p">})</span>
+</span><span id="L-245"><a href="#L-245"><span class="linenos">245</span></a> <span class="n">output_path</span> <span class="o">=</span> <span class="n">PROCESSED_PATH</span> <span class="o">/</span> <span class="s2">"read2.parquet"</span>
+</span><span id="L-246"><a href="#L-246"><span class="linenos">246</span></a> <span class="n">df</span><span class="o">.</span><span class="n">to_parquet</span><span class="p">(</span><span class="n">output_path</span><span class="p">,</span> <span class="n">index</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span>
+</span><span id="L-247"><a href="#L-247"><span class="linenos">247</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Extracted: </span><span class="si">{</span><span class="n">output_path</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+</span><span id="L-248"><a href="#L-248"><span class="linenos">248</span></a>
+</span><span id="L-249"><a href="#L-249"><span class="linenos">249</span></a> <span class="c1"># r2 -> atc</span>
+</span><span id="L-250"><a href="#L-250"><span class="linenos">250</span></a> <span class="n">input_path</span> <span class="o">=</span> <span class="n">DOWNLOADS_PATH</span> <span class="o">/</span> <span class="s2">"Standard"</span> <span class="o">/</span> <span class="s2">"V2"</span> <span class="o">/</span> <span class="s2">"ATC.DBF"</span>
+</span><span id="L-251"><a href="#L-251"><span class="linenos">251</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">simpledbf</span><span class="o">.</span><span class="n">Dbf5</span><span class="p">(</span><span class="n">input_path</span><span class="p">)</span><span class="o">.</span><span class="n">to_dataframe</span><span class="p">()</span>
+</span><span id="L-252"><a href="#L-252"><span class="linenos">252</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">df</span><span class="p">[[</span><span class="s2">"READCODE"</span><span class="p">,</span> <span class="s2">"ATC"</span><span class="p">]]</span>
+</span><span id="L-253"><a href="#L-253"><span class="linenos">253</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">df</span><span class="o">.</span><span class="n">rename</span><span class="p">(</span><span class="n">columns</span><span class="o">=</span><span class="p">{</span><span class="s2">"READCODE"</span><span class="p">:</span> <span class="s2">"read2"</span><span class="p">,</span> <span class="s2">"ATC"</span><span class="p">:</span> <span class="s2">"atc"</span><span class="p">})</span>
+</span><span id="L-254"><a href="#L-254"><span class="linenos">254</span></a> <span class="n">output_path</span> <span class="o">=</span> <span class="n">PROCESSED_PATH</span> <span class="o">/</span> <span class="s2">"read2_to_atc.parquet"</span>
+</span><span id="L-255"><a href="#L-255"><span class="linenos">255</span></a> <span class="n">df</span><span class="o">.</span><span class="n">to_parquet</span><span class="p">(</span><span class="n">output_path</span><span class="p">,</span> <span class="n">index</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span>
+</span><span id="L-256"><a href="#L-256"><span class="linenos">256</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Extracted: </span><span class="si">{</span><span class="n">output_path</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+</span><span id="L-257"><a href="#L-257"><span class="linenos">257</span></a>
+</span><span id="L-258"><a href="#L-258"><span class="linenos">258</span></a> <span class="c1"># r2 -> icd10</span>
+</span><span id="L-259"><a href="#L-259"><span class="linenos">259</span></a> <span class="n">input_path</span> <span class="o">=</span> <span class="n">DOWNLOADS_PATH</span> <span class="o">/</span> <span class="s2">"Standard"</span> <span class="o">/</span> <span class="s2">"V2"</span> <span class="o">/</span> <span class="s2">"ICD10.DBF"</span>
+</span><span id="L-260"><a href="#L-260"><span class="linenos">260</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">simpledbf</span><span class="o">.</span><span class="n">Dbf5</span><span class="p">(</span><span class="n">input_path</span><span class="p">)</span><span class="o">.</span><span class="n">to_dataframe</span><span class="p">()</span>
+</span><span id="L-261"><a href="#L-261"><span class="linenos">261</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">df</span><span class="p">[[</span><span class="s2">"READ_CODE"</span><span class="p">,</span> <span class="s2">"TARG_CODE"</span><span class="p">]]</span>
+</span><span id="L-262"><a href="#L-262"><span class="linenos">262</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">df</span><span class="o">.</span><span class="n">rename</span><span class="p">(</span><span class="n">columns</span><span class="o">=</span><span class="p">{</span><span class="s2">"READ_CODE"</span><span class="p">:</span> <span class="s2">"read2"</span><span class="p">,</span> <span class="s2">"TARG_CODE"</span><span class="p">:</span> <span class="s2">"icd10"</span><span class="p">})</span>
+</span><span id="L-263"><a href="#L-263"><span class="linenos">263</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">df</span><span class="p">[</span><span class="o">~</span><span class="n">df</span><span class="p">[</span><span class="s2">"icd10"</span><span class="p">]</span><span class="o">.</span><span class="n">str</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="s2">"^.*-.*$"</span><span class="p">)]</span> <span class="c1"># remove codes with '-'</span>
+</span><span id="L-264"><a href="#L-264"><span class="linenos">264</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">df</span><span class="p">[</span><span class="o">~</span><span class="n">df</span><span class="p">[</span><span class="s2">"read2"</span><span class="p">]</span><span class="o">.</span><span class="n">str</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="s2">"^.*-.*$"</span><span class="p">)]</span> <span class="c1"># remove codes with '-'</span>
+</span><span id="L-265"><a href="#L-265"><span class="linenos">265</span></a> <span class="n">output_path</span> <span class="o">=</span> <span class="n">PROCESSED_PATH</span> <span class="o">/</span> <span class="s2">"read2_to_icd10.parquet"</span>
+</span><span id="L-266"><a href="#L-266"><span class="linenos">266</span></a> <span class="n">df</span><span class="o">.</span><span class="n">to_parquet</span><span class="p">(</span><span class="n">output_path</span><span class="p">,</span> <span class="n">index</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span>
+</span><span id="L-267"><a href="#L-267"><span class="linenos">267</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Extracted: </span><span class="si">{</span><span class="n">output_path</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+</span><span id="L-268"><a href="#L-268"><span class="linenos">268</span></a>
+</span><span id="L-269"><a href="#L-269"><span class="linenos">269</span></a> <span class="c1"># r2 -> opcs4</span>
+</span><span id="L-270"><a href="#L-270"><span class="linenos">270</span></a> <span class="n">input_path</span> <span class="o">=</span> <span class="n">DOWNLOADS_PATH</span> <span class="o">/</span> <span class="s2">"Standard"</span> <span class="o">/</span> <span class="s2">"V2"</span> <span class="o">/</span> <span class="s2">"OPCS4V3.DBF"</span>
+</span><span id="L-271"><a href="#L-271"><span class="linenos">271</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">simpledbf</span><span class="o">.</span><span class="n">Dbf5</span><span class="p">(</span><span class="n">input_path</span><span class="p">)</span><span class="o">.</span><span class="n">to_dataframe</span><span class="p">()</span>
+</span><span id="L-272"><a href="#L-272"><span class="linenos">272</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">df</span><span class="p">[[</span><span class="s2">"READ_CODE"</span><span class="p">,</span> <span class="s2">"TARG_CODE"</span><span class="p">]]</span>
+</span><span id="L-273"><a href="#L-273"><span class="linenos">273</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">df</span><span class="o">.</span><span class="n">rename</span><span class="p">(</span><span class="n">columns</span><span class="o">=</span><span class="p">{</span><span class="s2">"READ_CODE"</span><span class="p">:</span> <span class="s2">"read2"</span><span class="p">,</span> <span class="s2">"TARG_CODE"</span><span class="p">:</span> <span class="s2">"opcs4"</span><span class="p">})</span>
+</span><span id="L-274"><a href="#L-274"><span class="linenos">274</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">df</span><span class="p">[</span><span class="o">~</span><span class="n">df</span><span class="p">[</span><span class="s2">"opcs4"</span><span class="p">]</span><span class="o">.</span><span class="n">str</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="s2">"^.*-.*$"</span><span class="p">)]</span> <span class="c1"># remove codes with '-'</span>
+</span><span id="L-275"><a href="#L-275"><span class="linenos">275</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">df</span><span class="p">[</span><span class="o">~</span><span class="n">df</span><span class="p">[</span><span class="s2">"read2"</span><span class="p">]</span><span class="o">.</span><span class="n">str</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="s2">"^.*-.*$"</span><span class="p">)]</span> <span class="c1"># remove codes with '-'</span>
+</span><span id="L-276"><a href="#L-276"><span class="linenos">276</span></a> <span class="n">output_path</span> <span class="o">=</span> <span class="n">PROCESSED_PATH</span> <span class="o">/</span> <span class="s2">"read2_to_opcs4.parquet"</span>
+</span><span id="L-277"><a href="#L-277"><span class="linenos">277</span></a> <span class="n">df</span><span class="o">.</span><span class="n">to_parquet</span><span class="p">(</span><span class="n">output_path</span><span class="p">,</span> <span class="n">index</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span>
+</span><span id="L-278"><a href="#L-278"><span class="linenos">278</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Extracted: </span><span class="si">{</span><span class="n">output_path</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+</span><span id="L-279"><a href="#L-279"><span class="linenos">279</span></a>
+</span><span id="L-280"><a href="#L-280"><span class="linenos">280</span></a> <span class="c1"># r3 only</span>
+</span><span id="L-281"><a href="#L-281"><span class="linenos">281</span></a> <span class="n">input_path</span> <span class="o">=</span> <span class="n">DOWNLOADS_PATH</span> <span class="o">/</span> <span class="s2">"Standard"</span> <span class="o">/</span> <span class="s2">"V3"</span> <span class="o">/</span> <span class="s2">"ANCESTOR.DBF"</span>
+</span><span id="L-282"><a href="#L-282"><span class="linenos">282</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">simpledbf</span><span class="o">.</span><span class="n">Dbf5</span><span class="p">(</span><span class="n">input_path</span><span class="p">)</span><span class="o">.</span><span class="n">to_dataframe</span><span class="p">()</span>
+</span><span id="L-283"><a href="#L-283"><span class="linenos">283</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">concat</span><span class="p">([</span><span class="n">df</span><span class="p">[</span><span class="s2">"READCODE"</span><span class="p">],</span> <span class="n">df</span><span class="p">[</span><span class="s2">"DESCENDANT"</span><span class="p">]])</span>
+</span><span id="L-284"><a href="#L-284"><span class="linenos">284</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">(</span><span class="n">df</span><span class="o">.</span><span class="n">drop_duplicates</span><span class="p">())</span>
+</span><span id="L-285"><a href="#L-285"><span class="linenos">285</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">df</span><span class="o">.</span><span class="n">rename</span><span class="p">(</span><span class="n">columns</span><span class="o">=</span><span class="p">{</span><span class="mi">0</span><span class="p">:</span> <span class="s2">"read3"</span><span class="p">})</span>
+</span><span id="L-286"><a href="#L-286"><span class="linenos">286</span></a> <span class="n">output_path</span> <span class="o">=</span> <span class="n">PROCESSED_PATH</span> <span class="o">/</span> <span class="s2">"read3.parquet"</span>
+</span><span id="L-287"><a href="#L-287"><span class="linenos">287</span></a> <span class="n">df</span><span class="o">.</span><span class="n">to_parquet</span><span class="p">(</span><span class="n">output_path</span><span class="p">,</span> <span class="n">index</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span>
+</span><span id="L-288"><a href="#L-288"><span class="linenos">288</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Extracted: </span><span class="si">{</span><span class="n">output_path</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+</span><span id="L-289"><a href="#L-289"><span class="linenos">289</span></a>
+</span><span id="L-290"><a href="#L-290"><span class="linenos">290</span></a> <span class="c1"># r3 -> icd10</span>
+</span><span id="L-291"><a href="#L-291"><span class="linenos">291</span></a> <span class="n">input_path</span> <span class="o">=</span> <span class="n">DOWNLOADS_PATH</span> <span class="o">/</span> <span class="s2">"Standard"</span> <span class="o">/</span> <span class="s2">"V3"</span> <span class="o">/</span> <span class="s2">"ICD10.DBF"</span>
+</span><span id="L-292"><a href="#L-292"><span class="linenos">292</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">simpledbf</span><span class="o">.</span><span class="n">Dbf5</span><span class="p">(</span><span class="n">input_path</span><span class="p">)</span><span class="o">.</span><span class="n">to_dataframe</span><span class="p">()</span>
+</span><span id="L-293"><a href="#L-293"><span class="linenos">293</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">df</span><span class="p">[[</span><span class="s2">"READ_CODE"</span><span class="p">,</span> <span class="s2">"TARG_CODE"</span><span class="p">]]</span>
+</span><span id="L-294"><a href="#L-294"><span class="linenos">294</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">df</span><span class="o">.</span><span class="n">rename</span><span class="p">(</span><span class="n">columns</span><span class="o">=</span><span class="p">{</span><span class="s2">"READ_CODE"</span><span class="p">:</span> <span class="s2">"read3"</span><span class="p">,</span> <span class="s2">"TARG_CODE"</span><span class="p">:</span> <span class="s2">"icd10"</span><span class="p">})</span>
+</span><span id="L-295"><a href="#L-295"><span class="linenos">295</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">df</span><span class="p">[</span><span class="o">~</span><span class="n">df</span><span class="p">[</span><span class="s2">"icd10"</span><span class="p">]</span><span class="o">.</span><span class="n">str</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="s2">"^.*-.*$"</span><span class="p">)]</span> <span class="c1"># remove codes with '-'</span>
+</span><span id="L-296"><a href="#L-296"><span class="linenos">296</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">df</span><span class="p">[</span><span class="o">~</span><span class="n">df</span><span class="p">[</span><span class="s2">"read3"</span><span class="p">]</span><span class="o">.</span><span class="n">str</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="s2">"^.*-.*$"</span><span class="p">)]</span> <span class="c1"># remove codes with '-'</span>
+</span><span id="L-297"><a href="#L-297"><span class="linenos">297</span></a> <span class="n">output_path</span> <span class="o">=</span> <span class="n">PROCESSED_PATH</span> <span class="o">/</span> <span class="s2">"read3_to_icd10.parquet"</span>
+</span><span id="L-298"><a href="#L-298"><span class="linenos">298</span></a> <span class="n">df</span><span class="o">.</span><span class="n">to_parquet</span><span class="p">(</span><span class="n">output_path</span><span class="p">,</span> <span class="n">index</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span>
+</span><span id="L-299"><a href="#L-299"><span class="linenos">299</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Extracted: </span><span class="si">{</span><span class="n">output_path</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+</span><span id="L-300"><a href="#L-300"><span class="linenos">300</span></a>
+</span><span id="L-301"><a href="#L-301"><span class="linenos">301</span></a> <span class="c1"># r3 -> icd9</span>
+</span><span id="L-302"><a href="#L-302"><span class="linenos">302</span></a> <span class="c1"># dbf = simpledbf.Dbf5('build/maps/downloads/Standard/V3/ICD9V3.DBF')</span>
+</span><span id="L-303"><a href="#L-303"><span class="linenos">303</span></a>
+</span><span id="L-304"><a href="#L-304"><span class="linenos">304</span></a> <span class="c1"># r3 -> opcs4</span>
+</span><span id="L-305"><a href="#L-305"><span class="linenos">305</span></a> <span class="n">input_path</span> <span class="o">=</span> <span class="n">DOWNLOADS_PATH</span> <span class="o">/</span> <span class="s2">"Standard"</span> <span class="o">/</span> <span class="s2">"V3"</span> <span class="o">/</span> <span class="s2">"OPCS4V3.DBF"</span>
+</span><span id="L-306"><a href="#L-306"><span class="linenos">306</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">simpledbf</span><span class="o">.</span><span class="n">Dbf5</span><span class="p">(</span><span class="n">input_path</span><span class="p">)</span><span class="o">.</span><span class="n">to_dataframe</span><span class="p">()</span>
+</span><span id="L-307"><a href="#L-307"><span class="linenos">307</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">df</span><span class="p">[[</span><span class="s2">"READ_CODE"</span><span class="p">,</span> <span class="s2">"TARG_CODE"</span><span class="p">]]</span>
+</span><span id="L-308"><a href="#L-308"><span class="linenos">308</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">df</span><span class="o">.</span><span class="n">rename</span><span class="p">(</span><span class="n">columns</span><span class="o">=</span><span class="p">{</span><span class="s2">"READ_CODE"</span><span class="p">:</span> <span class="s2">"read3"</span><span class="p">,</span> <span class="s2">"TARG_CODE"</span><span class="p">:</span> <span class="s2">"opcs4"</span><span class="p">})</span>
+</span><span id="L-309"><a href="#L-309"><span class="linenos">309</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">df</span><span class="p">[</span><span class="o">~</span><span class="n">df</span><span class="p">[</span><span class="s2">"opcs4"</span><span class="p">]</span><span class="o">.</span><span class="n">str</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="s2">"^.*-.*$"</span><span class="p">)]</span> <span class="c1"># remove codes with '-'</span>
+</span><span id="L-310"><a href="#L-310"><span class="linenos">310</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">df</span><span class="p">[</span><span class="o">~</span><span class="n">df</span><span class="p">[</span><span class="s2">"read3"</span><span class="p">]</span><span class="o">.</span><span class="n">str</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="s2">"^.*-.*$"</span><span class="p">)]</span> <span class="c1"># remove codes with '-'</span>
+</span><span id="L-311"><a href="#L-311"><span class="linenos">311</span></a> <span class="n">output_path</span> <span class="o">=</span> <span class="n">PROCESSED_PATH</span> <span class="o">/</span> <span class="s2">"read3_to_opcs4.parquet"</span>
+</span><span id="L-312"><a href="#L-312"><span class="linenos">312</span></a> <span class="n">df</span><span class="o">.</span><span class="n">to_parquet</span><span class="p">(</span><span class="n">output_path</span><span class="p">,</span> <span class="n">index</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span>
+</span><span id="L-313"><a href="#L-313"><span class="linenos">313</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Extracted: </span><span class="si">{</span><span class="n">output_path</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+</span><span id="L-314"><a href="#L-314"><span class="linenos">314</span></a>
+</span><span id="L-315"><a href="#L-315"><span class="linenos">315</span></a>
+</span><span id="L-316"><a href="#L-316"><span class="linenos">316</span></a><span class="k">def</span><span class="w"> </span><span class="nf">create_map_directories</span><span class="p">():</span>
+</span><span id="L-317"><a href="#L-317"><span class="linenos">317</span></a><span class="w"> </span><span class="sd">"""Create map directories."""</span>
+</span><span id="L-318"><a href="#L-318"><span class="linenos">318</span></a>
+</span><span id="L-319"><a href="#L-319"><span class="linenos">319</span></a> <span class="c1"># Check if build directory exists</span>
+</span><span id="L-320"><a href="#L-320"><span class="linenos">320</span></a> <span class="n">create_map_dirs</span> <span class="o">=</span> <span class="kc">False</span>
+</span><span id="L-321"><a href="#L-321"><span class="linenos">321</span></a> <span class="k">if</span> <span class="n">VOCAB_PATH</span><span class="o">.</span><span class="n">exists</span><span class="p">():</span>
+</span><span id="L-322"><a href="#L-322"><span class="linenos">322</span></a> <span class="n">user_input</span> <span class="o">=</span> <span class="p">(</span>
+</span><span id="L-323"><a href="#L-323"><span class="linenos">323</span></a> <span class="nb">input</span><span class="p">(</span>
+</span><span id="L-324"><a href="#L-324"><span class="linenos">324</span></a> <span class="sa">f</span><span class="s2">"The map directory </span><span class="si">{</span><span class="n">VOCAB_PATH</span><span class="si">}</span><span class="s2"> already exists. Do you want to download and process trud data again? (y/n): "</span>
+</span><span id="L-325"><a href="#L-325"><span class="linenos">325</span></a> <span class="p">)</span>
+</span><span id="L-326"><a href="#L-326"><span class="linenos">326</span></a> <span class="o">.</span><span class="n">strip</span><span class="p">()</span>
+</span><span id="L-327"><a href="#L-327"><span class="linenos">327</span></a> <span class="o">.</span><span class="n">lower</span><span class="p">()</span>
+</span><span id="L-328"><a href="#L-328"><span class="linenos">328</span></a> <span class="p">)</span>
+</span><span id="L-329"><a href="#L-329"><span class="linenos">329</span></a> <span class="k">if</span> <span class="n">user_input</span> <span class="o">==</span> <span class="s2">"y"</span><span class="p">:</span>
+</span><span id="L-330"><a href="#L-330"><span class="linenos">330</span></a> <span class="c1"># delete all build files</span>
+</span><span id="L-331"><a href="#L-331"><span class="linenos">331</span></a> <span class="n">shutil</span><span class="o">.</span><span class="n">rmtree</span><span class="p">(</span><span class="n">VOCAB_PATH</span><span class="p">)</span>
+</span><span id="L-332"><a href="#L-332"><span class="linenos">332</span></a> <span class="n">create_map_dirs</span> <span class="o">=</span> <span class="kc">True</span>
+</span><span id="L-333"><a href="#L-333"><span class="linenos">333</span></a> <span class="k">elif</span> <span class="n">user_input</span> <span class="o">==</span> <span class="s2">"n"</span><span class="p">:</span>
+</span><span id="L-334"><a href="#L-334"><span class="linenos">334</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">"Exiting TRUD installation"</span><span class="p">)</span>
+</span><span id="L-335"><a href="#L-335"><span class="linenos">335</span></a> <span class="n">sys</span><span class="o">.</span><span class="n">exit</span><span class="p">(</span><span class="mi">0</span><span class="p">)</span>
+</span><span id="L-336"><a href="#L-336"><span class="linenos">336</span></a> <span class="k">else</span><span class="p">:</span>
+</span><span id="L-337"><a href="#L-337"><span class="linenos">337</span></a> <span class="n">create_map_dirs</span> <span class="o">=</span> <span class="kc">True</span>
+</span><span id="L-338"><a href="#L-338"><span class="linenos">338</span></a>
+</span><span id="L-339"><a href="#L-339"><span class="linenos">339</span></a> <span class="k">if</span> <span class="n">create_map_dirs</span><span class="p">:</span>
+</span><span id="L-340"><a href="#L-340"><span class="linenos">340</span></a> <span class="c1"># create maps directories</span>
+</span><span id="L-341"><a href="#L-341"><span class="linenos">341</span></a> <span class="n">VOCAB_PATH</span><span class="o">.</span><span class="n">mkdir</span><span class="p">(</span><span class="n">parents</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">exist_ok</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+</span><span id="L-342"><a href="#L-342"><span class="linenos">342</span></a> <span class="n">DOWNLOADS_PATH</span><span class="o">.</span><span class="n">mkdir</span><span class="p">(</span><span class="n">parents</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">exist_ok</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+</span><span id="L-343"><a href="#L-343"><span class="linenos">343</span></a> <span class="n">PROCESSED_PATH</span><span class="o">.</span><span class="n">mkdir</span><span class="p">(</span><span class="n">parents</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">exist_ok</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+</span><span id="L-344"><a href="#L-344"><span class="linenos">344</span></a>
+</span><span id="L-345"><a href="#L-345"><span class="linenos">345</span></a>
+</span><span id="L-346"><a href="#L-346"><span class="linenos">346</span></a><span class="k">def</span><span class="w"> </span><span class="nf">install</span><span class="p">():</span>
+</span><span id="L-347"><a href="#L-347"><span class="linenos">347</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Installing TRUD"</span><span class="p">)</span>
+</span><span id="L-348"><a href="#L-348"><span class="linenos">348</span></a>
+</span><span id="L-349"><a href="#L-349"><span class="linenos">349</span></a> <span class="c1"># get TRUD api key from environment variable</span>
+</span><span id="L-350"><a href="#L-350"><span class="linenos">350</span></a> <span class="n">api_key</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">getenv</span><span class="p">(</span><span class="s2">"ACMC_TRUD_API_KEY"</span><span class="p">)</span>
+</span><span id="L-351"><a href="#L-351"><span class="linenos">351</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="n">api_key</span><span class="p">:</span>
+</span><span id="L-352"><a href="#L-352"><span class="linenos">352</span></a> <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span>
+</span><span id="L-353"><a href="#L-353"><span class="linenos">353</span></a> <span class="s2">"TRUD API KEY not found. Set the ACMC_TRUD_API_KEY environment variable."</span>
+</span><span id="L-354"><a href="#L-354"><span class="linenos">354</span></a> <span class="p">)</span>
+</span><span id="L-355"><a href="#L-355"><span class="linenos">355</span></a>
+</span><span id="L-356"><a href="#L-356"><span class="linenos">356</span></a> <span class="n">create_map_directories</span><span class="p">()</span>
+</span><span id="L-357"><a href="#L-357"><span class="linenos">357</span></a>
+</span><span id="L-358"><a href="#L-358"><span class="linenos">358</span></a> <span class="n">items_latest</span> <span class="o">=</span> <span class="kc">True</span>
+</span><span id="L-359"><a href="#L-359"><span class="linenos">359</span></a> <span class="n">items</span> <span class="o">=</span> <span class="p">[</span>
+</span><span id="L-360"><a href="#L-360"><span class="linenos">360</span></a> <span class="p">{</span>
+</span><span id="L-361"><a href="#L-361"><span class="linenos">361</span></a> <span class="s2">"id"</span><span class="p">:</span> <span class="mi">259</span><span class="p">,</span>
+</span><span id="L-362"><a href="#L-362"><span class="linenos">362</span></a> <span class="s2">"name"</span><span class="p">:</span> <span class="s2">"NHS ICD-10 5th Edition XML data files"</span><span class="p">,</span>
+</span><span id="L-363"><a href="#L-363"><span class="linenos">363</span></a> <span class="s2">"hash"</span><span class="p">:</span> <span class="s2">"A4F7BBA6E86349AADD0F4696C5E91152EB99CC06121427FC359160439B9F883F"</span><span class="p">,</span>
+</span><span id="L-364"><a href="#L-364"><span class="linenos">364</span></a> <span class="s2">"extract"</span><span class="p">:</span> <span class="n">extract_icd10</span><span class="p">,</span>
+</span><span id="L-365"><a href="#L-365"><span class="linenos">365</span></a> <span class="p">},</span>
+</span><span id="L-366"><a href="#L-366"><span class="linenos">366</span></a> <span class="p">{</span>
+</span><span id="L-367"><a href="#L-367"><span class="linenos">367</span></a> <span class="s2">"id"</span><span class="p">:</span> <span class="mi">119</span><span class="p">,</span>
+</span><span id="L-368"><a href="#L-368"><span class="linenos">368</span></a> <span class="s2">"name"</span><span class="p">:</span> <span class="s2">"OPCS-4 data files"</span><span class="p">,</span>
+</span><span id="L-369"><a href="#L-369"><span class="linenos">369</span></a> <span class="s2">"hash"</span><span class="p">:</span> <span class="s2">"0615A2BF43FFEF94517F1D1E0C05493B627839F323F22C52CBCD8B40BF767CD3"</span><span class="p">,</span>
+</span><span id="L-370"><a href="#L-370"><span class="linenos">370</span></a> <span class="s2">"extract"</span><span class="p">:</span> <span class="n">extract_opsc4</span><span class="p">,</span>
+</span><span id="L-371"><a href="#L-371"><span class="linenos">371</span></a> <span class="p">},</span>
+</span><span id="L-372"><a href="#L-372"><span class="linenos">372</span></a> <span class="p">{</span>
+</span><span id="L-373"><a href="#L-373"><span class="linenos">373</span></a> <span class="s2">"id"</span><span class="p">:</span> <span class="mi">9</span><span class="p">,</span>
+</span><span id="L-374"><a href="#L-374"><span class="linenos">374</span></a> <span class="s2">"name"</span><span class="p">:</span> <span class="s2">"NHS Data Migration"</span><span class="p">,</span>
+</span><span id="L-375"><a href="#L-375"><span class="linenos">375</span></a> <span class="s2">"hash"</span><span class="p">:</span> <span class="s2">"D4317B3ADBA6E1247CF17F0B7CD2B8850FD36C0EA2923BF684EA6159F3A54765"</span><span class="p">,</span>
+</span><span id="L-376"><a href="#L-376"><span class="linenos">376</span></a> <span class="s2">"extract"</span><span class="p">:</span> <span class="n">extract_nhs_data_migrations</span><span class="p">,</span>
+</span><span id="L-377"><a href="#L-377"><span class="linenos">377</span></a> <span class="p">},</span>
+</span><span id="L-378"><a href="#L-378"><span class="linenos">378</span></a> <span class="p">{</span>
+</span><span id="L-379"><a href="#L-379"><span class="linenos">379</span></a> <span class="s2">"id"</span><span class="p">:</span> <span class="mi">8</span><span class="p">,</span>
+</span><span id="L-380"><a href="#L-380"><span class="linenos">380</span></a> <span class="s2">"name"</span><span class="p">:</span> <span class="s2">"NHS Read Browser"</span><span class="p">,</span>
+</span><span id="L-381"><a href="#L-381"><span class="linenos">381</span></a> <span class="s2">"hash"</span><span class="p">:</span> <span class="s2">"1FFF2CBF11D0E6D7FC6CC6F13DD52D2F459095C3D83A3F754E6C359F16913C5E"</span><span class="p">,</span>
+</span><span id="L-382"><a href="#L-382"><span class="linenos">382</span></a> <span class="s2">"extract"</span><span class="p">:</span> <span class="n">extract_nhs_read_browser</span><span class="p">,</span>
+</span><span id="L-383"><a href="#L-383"><span class="linenos">383</span></a> <span class="p">},</span>
+</span><span id="L-384"><a href="#L-384"><span class="linenos">384</span></a> <span class="c1"># TODO: Download BNF from separate site? https://www.nhsbsa.nhs.uk/sites/default/files/2024-10/BNF%20Snomed%20Mapping%20data%2020241016.zip</span>
+</span><span id="L-385"><a href="#L-385"><span class="linenos">385</span></a> <span class="p">]</span>
+</span><span id="L-386"><a href="#L-386"><span class="linenos">386</span></a>
+</span><span id="L-387"><a href="#L-387"><span class="linenos">387</span></a> <span class="c1"># remove function from items to save versions</span>
+</span><span id="L-388"><a href="#L-388"><span class="linenos">388</span></a> <span class="n">data</span> <span class="o">=</span> <span class="p">[{</span><span class="n">k</span><span class="p">:</span> <span class="n">v</span> <span class="k">for</span> <span class="n">k</span><span class="p">,</span> <span class="n">v</span> <span class="ow">in</span> <span class="n">d</span><span class="o">.</span><span class="n">items</span><span class="p">()</span> <span class="k">if</span> <span class="n">k</span> <span class="o">!=</span> <span class="s2">"extract"</span><span class="p">}</span> <span class="k">for</span> <span class="n">d</span> <span class="ow">in</span> <span class="n">items</span><span class="p">]</span>
+</span><span id="L-389"><a href="#L-389"><span class="linenos">389</span></a> <span class="c1"># save TRUD versions to file to main record of what was downloaded</span>
+</span><span id="L-390"><a href="#L-390"><span class="linenos">390</span></a> <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">VERSION_PATH</span><span class="p">,</span> <span class="s2">"w"</span><span class="p">)</span> <span class="k">as</span> <span class="n">file</span><span class="p">:</span>
+</span><span id="L-391"><a href="#L-391"><span class="linenos">391</span></a> <span class="n">yaml</span><span class="o">.</span><span class="n">dump</span><span class="p">(</span>
+</span><span id="L-392"><a href="#L-392"><span class="linenos">392</span></a> <span class="n">data</span><span class="p">,</span>
+</span><span id="L-393"><a href="#L-393"><span class="linenos">393</span></a> <span class="n">file</span><span class="p">,</span>
+</span><span id="L-394"><a href="#L-394"><span class="linenos">394</span></a> <span class="n">Dumper</span><span class="o">=</span><span class="n">util</span><span class="o">.</span><span class="n">QuotedDumper</span><span class="p">,</span>
+</span><span id="L-395"><a href="#L-395"><span class="linenos">395</span></a> <span class="n">default_flow_style</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span>
+</span><span id="L-396"><a href="#L-396"><span class="linenos">396</span></a> <span class="n">sort_keys</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span>
+</span><span id="L-397"><a href="#L-397"><span class="linenos">397</span></a> <span class="n">default_style</span><span class="o">=</span><span class="s1">'"'</span><span class="p">,</span>
+</span><span id="L-398"><a href="#L-398"><span class="linenos">398</span></a> <span class="p">)</span>
+</span><span id="L-399"><a href="#L-399"><span class="linenos">399</span></a>
+</span><span id="L-400"><a href="#L-400"><span class="linenos">400</span></a> <span class="c1"># Validate and process each item ID</span>
+</span><span id="L-401"><a href="#L-401"><span class="linenos">401</span></a> <span class="k">for</span> <span class="n">item</span> <span class="ow">in</span> <span class="n">items</span><span class="p">:</span>
+</span><span id="L-402"><a href="#L-402"><span class="linenos">402</span></a> <span class="n">item_id</span> <span class="o">=</span> <span class="n">item</span><span class="p">[</span><span class="s2">"id"</span><span class="p">]</span>
+</span><span id="L-403"><a href="#L-403"><span class="linenos">403</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"--- </span><span class="si">{</span><span class="n">item</span><span class="p">[</span><span class="s1">'name'</span><span class="p">]</span><span class="si">}</span><span class="s2"> ---"</span><span class="p">)</span>
+</span><span id="L-404"><a href="#L-404"><span class="linenos">404</span></a>
+</span><span id="L-405"><a href="#L-405"><span class="linenos">405</span></a> <span class="n">releases</span> <span class="o">=</span> <span class="n">get_releases</span><span class="p">(</span><span class="n">item_id</span><span class="p">,</span> <span class="n">API_KEY</span><span class="o">=</span><span class="n">api_key</span><span class="p">,</span> <span class="n">latest</span><span class="o">=</span><span class="n">items_latest</span><span class="p">)</span>
+</span><span id="L-406"><a href="#L-406"><span class="linenos">406</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="n">releases</span><span class="p">:</span>
+</span><span id="L-407"><a href="#L-407"><span class="linenos">407</span></a> <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="sa">f</span><span class="s2">"No releases found for item </span><span class="si">{</span><span class="n">item_id</span><span class="si">}</span><span class="s2">."</span><span class="p">)</span>
+</span><span id="L-408"><a href="#L-408"><span class="linenos">408</span></a>
+</span><span id="L-409"><a href="#L-409"><span class="linenos">409</span></a> <span class="c1"># Process each release in reverse order</span>
+</span><span id="L-410"><a href="#L-410"><span class="linenos">410</span></a> <span class="k">for</span> <span class="n">release_ordinal</span><span class="p">,</span> <span class="n">release</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">releases</span><span class="p">[::</span><span class="o">-</span><span class="mi">1</span><span class="p">],</span> <span class="mi">1</span><span class="p">):</span>
+</span><span id="L-411"><a href="#L-411"><span class="linenos">411</span></a> <span class="c1"># Download archive file</span>
+</span><span id="L-412"><a href="#L-412"><span class="linenos">412</span></a> <span class="n">file_destination</span> <span class="o">=</span> <span class="n">download_release_file</span><span class="p">(</span>
+</span><span id="L-413"><a href="#L-413"><span class="linenos">413</span></a> <span class="n">item_id</span><span class="p">,</span> <span class="n">release_ordinal</span><span class="p">,</span> <span class="n">release</span><span class="p">,</span> <span class="s2">"archive"</span>
+</span><span id="L-414"><a href="#L-414"><span class="linenos">414</span></a> <span class="p">)</span>
+</span><span id="L-415"><a href="#L-415"><span class="linenos">415</span></a>
+</span><span id="L-416"><a href="#L-416"><span class="linenos">416</span></a> <span class="c1"># Optional files</span>
+</span><span id="L-417"><a href="#L-417"><span class="linenos">417</span></a> <span class="c1"># if items.checksum:</span>
+</span><span id="L-418"><a href="#L-418"><span class="linenos">418</span></a> <span class="c1"># download_release_file(item["id"], release_ordinal, release, "checksum")</span>
+</span><span id="L-419"><a href="#L-419"><span class="linenos">419</span></a> <span class="c1"># if items.signature:</span>
+</span><span id="L-420"><a href="#L-420"><span class="linenos">420</span></a> <span class="c1"># download_release_file(item["id"], release_ordinal, release, "signature")</span>
+</span><span id="L-421"><a href="#L-421"><span class="linenos">421</span></a> <span class="c1"># if items.public_key:</span>
+</span><span id="L-422"><a href="#L-422"><span class="linenos">422</span></a> <span class="c1"># download_release_file(item["id"], release_ordinal, release, "publicKey", "public key")</span>
+</span><span id="L-423"><a href="#L-423"><span class="linenos">423</span></a>
+</span><span id="L-424"><a href="#L-424"><span class="linenos">424</span></a> <span class="c1"># Verify Hash if available</span>
+</span><span id="L-425"><a href="#L-425"><span class="linenos">425</span></a> <span class="k">if</span> <span class="s2">"hash"</span> <span class="ow">in</span> <span class="n">item</span><span class="p">:</span>
+</span><span id="L-426"><a href="#L-426"><span class="linenos">426</span></a> <span class="n">validate_download_hash</span><span class="p">(</span><span class="n">file_destination</span><span class="p">,</span> <span class="n">item</span><span class="p">[</span><span class="s2">"hash"</span><span class="p">])</span>
+</span><span id="L-427"><a href="#L-427"><span class="linenos">427</span></a>
+</span><span id="L-428"><a href="#L-428"><span class="linenos">428</span></a> <span class="c1"># Unzip downloaded .zip</span>
+</span><span id="L-429"><a href="#L-429"><span class="linenos">429</span></a> <span class="n">unzip_download</span><span class="p">(</span><span class="n">file_destination</span><span class="p">)</span>
+</span><span id="L-430"><a href="#L-430"><span class="linenos">430</span></a>
+</span><span id="L-431"><a href="#L-431"><span class="linenos">431</span></a> <span class="c1"># Extract Tables to parquet</span>
+</span><span id="L-432"><a href="#L-432"><span class="linenos">432</span></a> <span class="k">if</span> <span class="s2">"extract"</span> <span class="ow">in</span> <span class="n">item</span><span class="p">:</span>
+</span><span id="L-433"><a href="#L-433"><span class="linenos">433</span></a> <span class="n">item</span><span class="p">[</span><span class="s2">"extract"</span><span class="p">]()</span>
+</span><span id="L-434"><a href="#L-434"><span class="linenos">434</span></a>
+</span><span id="L-435"><a href="#L-435"><span class="linenos">435</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Downloaded </span><span class="si">{</span><span class="n">release_ordinal</span><span class="si">}</span><span class="s2"> release(s) for item </span><span class="si">{</span><span class="n">item_id</span><span class="si">}</span><span class="s2">."</span><span class="p">)</span>
+</span><span id="L-436"><a href="#L-436"><span class="linenos">436</span></a>
+</span><span id="L-437"><a href="#L-437"><span class="linenos">437</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"TRUD installation completed"</span><span class="p">)</span>
+</span></pre></div>
+
+
+ </section>
+ <section id="logger">
+ <div class="attr variable">
+ <span class="name">logger</span> =
+<span class="default_value"><Logger acmc_logger (INFO)></span>
+
+
+ </div>
+ <a class="headerlink" href="#logger"></a>
+
+
+
+ </section>
+ <section id="FQDN">
+ <div class="attr variable">
+ <span class="name">FQDN</span> =
+<span class="default_value">'isd.digital.nhs.uk'</span>
+
+
+ </div>
+ <a class="headerlink" href="#FQDN"></a>
+
+
+
+ </section>
+ <section id="VOCAB_PATH">
+ <div class="attr variable">
+ <span class="name">VOCAB_PATH</span> =
+<span class="default_value">PosixPath('vocab/trud')</span>
+
+
+ </div>
+ <a class="headerlink" href="#VOCAB_PATH"></a>
+
+
+
+ </section>
+ <section id="VERSION_FILE">
+ <div class="attr variable">
+ <span class="name">VERSION_FILE</span> =
+<span class="default_value">'trud_version.yaml'</span>
+
+
+ </div>
+ <a class="headerlink" href="#VERSION_FILE"></a>
+
+
+
+ </section>
+ <section id="VERSION_PATH">
+ <div class="attr variable">
+ <span class="name">VERSION_PATH</span> =
+<span class="default_value">PosixPath('vocab/trud/trud_version.yaml')</span>
+
+
+ </div>
+ <a class="headerlink" href="#VERSION_PATH"></a>
+
+
+
+ </section>
+ <section id="DOWNLOADS_PATH">
+ <div class="attr variable">
+ <span class="name">DOWNLOADS_PATH</span> =
+<span class="default_value">PosixPath('vocab/trud/downloads')</span>
+
+
+ </div>
+ <a class="headerlink" href="#DOWNLOADS_PATH"></a>
+
+
+
+ </section>
+ <section id="PROCESSED_PATH">
+ <div class="attr variable">
+ <span class="name">PROCESSED_PATH</span> =
+<span class="default_value">PosixPath('vocab/trud/processed')</span>
+
+
+ </div>
+ <a class="headerlink" href="#PROCESSED_PATH"></a>
+
+
+
+ </section>
+ <section id="get_releases">
+ <input id="get_releases-view-source" class="view-source-toggle-state" type="checkbox" aria-hidden="true" tabindex="-1">
+<div class="attr function">
+
+ <span class="def">def</span>
+ <span class="name">get_releases</span><span class="signature pdoc-code condensed">(<span class="param"><span class="n">item_id</span><span class="p">:</span> <span class="nb">str</span>, </span><span class="param"><span class="n">API_KEY</span><span class="p">:</span> <span class="nb">str</span>, </span><span class="param"><span class="n">latest</span><span class="o">=</span><span class="kc">False</span></span><span class="return-annotation">) -> <span class="nb">list</span>:</span></span>
+
+ <label class="view-source-button" for="get_releases-view-source"><span>View Source</span></label>
+
+ </div>
+ <a class="headerlink" href="#get_releases"></a>
+ <div class="pdoc-code codehilite"><pre><span></span><span id="get_releases-28"><a href="#get_releases-28"><span class="linenos">28</span></a><span class="k">def</span><span class="w"> </span><span class="nf">get_releases</span><span class="p">(</span><span class="n">item_id</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">API_KEY</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">latest</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span> <span class="o">-></span> <span class="nb">list</span><span class="p">:</span>
+</span><span id="get_releases-29"><a href="#get_releases-29"><span class="linenos">29</span></a><span class="w"> </span><span class="sd">"""Retrieve release information for an item from the TRUD API."""</span>
+</span><span id="get_releases-30"><a href="#get_releases-30"><span class="linenos">30</span></a> <span class="n">url</span> <span class="o">=</span> <span class="sa">f</span><span class="s2">"https://</span><span class="si">{</span><span class="n">FQDN</span><span class="si">}</span><span class="s2">/trud/api/v1/keys/</span><span class="si">{</span><span class="n">API_KEY</span><span class="si">}</span><span class="s2">/items/</span><span class="si">{</span><span class="n">item_id</span><span class="si">}</span><span class="s2">/releases"</span>
+</span><span id="get_releases-31"><a href="#get_releases-31"><span class="linenos">31</span></a> <span class="k">if</span> <span class="n">latest</span><span class="p">:</span>
+</span><span id="get_releases-32"><a href="#get_releases-32"><span class="linenos">32</span></a> <span class="n">url</span> <span class="o">+=</span> <span class="s2">"?latest"</span>
+</span><span id="get_releases-33"><a href="#get_releases-33"><span class="linenos">33</span></a>
+</span><span id="get_releases-34"><a href="#get_releases-34"><span class="linenos">34</span></a> <span class="n">response</span> <span class="o">=</span> <span class="n">requests</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">url</span><span class="p">)</span>
+</span><span id="get_releases-35"><a href="#get_releases-35"><span class="linenos">35</span></a> <span class="k">if</span> <span class="n">response</span><span class="o">.</span><span class="n">status_code</span> <span class="o">!=</span> <span class="mi">200</span><span class="p">:</span>
+</span><span id="get_releases-36"><a href="#get_releases-36"><span class="linenos">36</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">error</span><span class="p">(</span>
+</span><span id="get_releases-37"><a href="#get_releases-37"><span class="linenos">37</span></a> <span class="sa">f</span><span class="s2">"Failed to fetch releases for item </span><span class="si">{</span><span class="n">item_id</span><span class="si">}</span><span class="s2">. Status code: </span><span class="si">{</span><span class="n">response</span><span class="o">.</span><span class="n">status_code</span><span class="si">}</span><span class="s2">, error </span><span class="si">{</span><span class="n">response</span><span class="o">.</span><span class="n">json</span><span class="p">()[</span><span class="s1">'message'</span><span class="p">]</span><span class="si">}</span><span class="s2">. If no releases found for API key, please ensure you are subscribed to the data release and that it is not pending approval"</span>
+</span><span id="get_releases-38"><a href="#get_releases-38"><span class="linenos">38</span></a> <span class="p">)</span>
+</span><span id="get_releases-39"><a href="#get_releases-39"><span class="linenos">39</span></a> <span class="n">response</span><span class="o">.</span><span class="n">raise_for_status</span><span class="p">()</span>
+</span><span id="get_releases-40"><a href="#get_releases-40"><span class="linenos">40</span></a>
+</span><span id="get_releases-41"><a href="#get_releases-41"><span class="linenos">41</span></a> <span class="n">data</span> <span class="o">=</span> <span class="n">response</span><span class="o">.</span><span class="n">json</span><span class="p">()</span>
+</span><span id="get_releases-42"><a href="#get_releases-42"><span class="linenos">42</span></a> <span class="k">if</span> <span class="n">data</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"message"</span><span class="p">)</span> <span class="o">!=</span> <span class="s2">"OK"</span><span class="p">:</span>
+</span><span id="get_releases-43"><a href="#get_releases-43"><span class="linenos">43</span></a> <span class="n">msg</span> <span class="o">=</span> <span class="sa">f</span><span class="s2">"Unknown error occurred </span><span class="si">{</span><span class="n">data</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">'message'</span><span class="p">)</span><span class="si">}</span><span class="s2">"</span>
+</span><span id="get_releases-44"><a href="#get_releases-44"><span class="linenos">44</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">error</span><span class="p">(</span><span class="n">msg</span><span class="p">)</span>
+</span><span id="get_releases-45"><a href="#get_releases-45"><span class="linenos">45</span></a> <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="n">msg</span><span class="p">)</span>
+</span><span id="get_releases-46"><a href="#get_releases-46"><span class="linenos">46</span></a>
+</span><span id="get_releases-47"><a href="#get_releases-47"><span class="linenos">47</span></a> <span class="k">return</span> <span class="n">data</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">"releases"</span><span class="p">,</span> <span class="p">[])</span>
+</span></pre></div>
+
+
+ <div class="docstring"><p>Retrieve release information for an item from the TRUD API.</p>
+</div>
+
+
+ </section>
+ <section id="download_release_file">
+ <input id="download_release_file-view-source" class="view-source-toggle-state" type="checkbox" aria-hidden="true" tabindex="-1">
+<div class="attr function">
+
+ <span class="def">def</span>
+ <span class="name">download_release_file</span><span class="signature pdoc-code multiline">(<span class="param"> <span class="n">item_id</span><span class="p">:</span> <span class="nb">str</span>,</span><span class="param"> <span class="n">release_ordinal</span><span class="p">:</span> <span class="nb">str</span>,</span><span class="param"> <span class="n">release</span><span class="p">:</span> <span class="nb">dict</span>,</span><span class="param"> <span class="n">file_json_prefix</span><span class="p">:</span> <span class="nb">str</span>,</span><span class="param"> <span class="n">file_type</span><span class="o">=</span><span class="kc">None</span></span><span class="return-annotation">) -> <span class="n">pathlib</span><span class="o">.</span><span class="n">Path</span>:</span></span>
+
+ <label class="view-source-button" for="download_release_file-view-source"><span>View Source</span></label>
+
+ </div>
+ <a class="headerlink" href="#download_release_file"></a>
+ <div class="pdoc-code codehilite"><pre><span></span><span id="download_release_file-50"><a href="#download_release_file-50"><span class="linenos">50</span></a><span class="k">def</span><span class="w"> </span><span class="nf">download_release_file</span><span class="p">(</span>
+</span><span id="download_release_file-51"><a href="#download_release_file-51"><span class="linenos">51</span></a> <span class="n">item_id</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+</span><span id="download_release_file-52"><a href="#download_release_file-52"><span class="linenos">52</span></a> <span class="n">release_ordinal</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+</span><span id="download_release_file-53"><a href="#download_release_file-53"><span class="linenos">53</span></a> <span class="n">release</span><span class="p">:</span> <span class="nb">dict</span><span class="p">,</span>
+</span><span id="download_release_file-54"><a href="#download_release_file-54"><span class="linenos">54</span></a> <span class="n">file_json_prefix</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+</span><span id="download_release_file-55"><a href="#download_release_file-55"><span class="linenos">55</span></a> <span class="n">file_type</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span>
+</span><span id="download_release_file-56"><a href="#download_release_file-56"><span class="linenos">56</span></a><span class="p">)</span> <span class="o">-></span> <span class="n">Path</span><span class="p">:</span>
+</span><span id="download_release_file-57"><a href="#download_release_file-57"><span class="linenos">57</span></a><span class="w"> </span><span class="sd">"""Download specified file type for a given release of an item."""</span>
+</span><span id="download_release_file-58"><a href="#download_release_file-58"><span class="linenos">58</span></a>
+</span><span id="download_release_file-59"><a href="#download_release_file-59"><span class="linenos">59</span></a> <span class="c1"># check folder is a directory</span>
+</span><span id="download_release_file-60"><a href="#download_release_file-60"><span class="linenos">60</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="n">DOWNLOADS_PATH</span><span class="o">.</span><span class="n">is_dir</span><span class="p">():</span>
+</span><span id="download_release_file-61"><a href="#download_release_file-61"><span class="linenos">61</span></a> <span class="k">raise</span> <span class="ne">NotADirectoryError</span><span class="p">(</span>
+</span><span id="download_release_file-62"><a href="#download_release_file-62"><span class="linenos">62</span></a> <span class="sa">f</span><span class="s2">"Error: '</span><span class="si">{</span><span class="n">DOWNLOADS_PATH</span><span class="si">}</span><span class="s2">' for TRUD resources is not a directory"</span>
+</span><span id="download_release_file-63"><a href="#download_release_file-63"><span class="linenos">63</span></a> <span class="p">)</span>
+</span><span id="download_release_file-64"><a href="#download_release_file-64"><span class="linenos">64</span></a>
+</span><span id="download_release_file-65"><a href="#download_release_file-65"><span class="linenos">65</span></a> <span class="n">file_type</span> <span class="o">=</span> <span class="n">file_type</span> <span class="ow">or</span> <span class="n">file_json_prefix</span>
+</span><span id="download_release_file-66"><a href="#download_release_file-66"><span class="linenos">66</span></a> <span class="n">file_url</span> <span class="o">=</span> <span class="n">release</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="sa">f</span><span class="s2">"</span><span class="si">{</span><span class="n">file_json_prefix</span><span class="si">}</span><span class="s2">FileUrl"</span><span class="p">)</span>
+</span><span id="download_release_file-67"><a href="#download_release_file-67"><span class="linenos">67</span></a> <span class="n">file_name</span> <span class="o">=</span> <span class="n">release</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="sa">f</span><span class="s2">"</span><span class="si">{</span><span class="n">file_json_prefix</span><span class="si">}</span><span class="s2">FileName"</span><span class="p">)</span>
+</span><span id="download_release_file-68"><a href="#download_release_file-68"><span class="linenos">68</span></a> <span class="n">file_destination</span> <span class="o">=</span> <span class="n">DOWNLOADS_PATH</span> <span class="o">/</span> <span class="n">file_name</span>
+</span><span id="download_release_file-69"><a href="#download_release_file-69"><span class="linenos">69</span></a>
+</span><span id="download_release_file-70"><a href="#download_release_file-70"><span class="linenos">70</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="n">file_url</span> <span class="ow">or</span> <span class="ow">not</span> <span class="n">file_name</span><span class="p">:</span>
+</span><span id="download_release_file-71"><a href="#download_release_file-71"><span class="linenos">71</span></a> <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span>
+</span><span id="download_release_file-72"><a href="#download_release_file-72"><span class="linenos">72</span></a> <span class="sa">f</span><span class="s2">"Missing </span><span class="si">{</span><span class="n">file_type</span><span class="si">}</span><span class="s2"> file information for release </span><span class="si">{</span><span class="n">release_ordinal</span><span class="si">}</span><span class="s2"> of item </span><span class="si">{</span><span class="n">item_id</span><span class="si">}</span><span class="s2">."</span>
+</span><span id="download_release_file-73"><a href="#download_release_file-73"><span class="linenos">73</span></a> <span class="p">)</span>
+</span><span id="download_release_file-74"><a href="#download_release_file-74"><span class="linenos">74</span></a>
+</span><span id="download_release_file-75"><a href="#download_release_file-75"><span class="linenos">75</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span>
+</span><span id="download_release_file-76"><a href="#download_release_file-76"><span class="linenos">76</span></a> <span class="sa">f</span><span class="s2">"Downloading item </span><span class="si">{</span><span class="n">item_id</span><span class="si">}</span><span class="s2"> </span><span class="si">{</span><span class="n">file_type</span><span class="si">}</span><span class="s2"> file: </span><span class="si">{</span><span class="n">file_name</span><span class="si">}</span><span class="s2"> from </span><span class="si">{</span><span class="n">file_url</span><span class="si">}</span><span class="s2"> to </span><span class="si">{</span><span class="n">file_destination</span><span class="si">}</span><span class="s2">"</span>
+</span><span id="download_release_file-77"><a href="#download_release_file-77"><span class="linenos">77</span></a> <span class="p">)</span>
+</span><span id="download_release_file-78"><a href="#download_release_file-78"><span class="linenos">78</span></a> <span class="n">response</span> <span class="o">=</span> <span class="n">requests</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">file_url</span><span class="p">,</span> <span class="n">stream</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+</span><span id="download_release_file-79"><a href="#download_release_file-79"><span class="linenos">79</span></a>
+</span><span id="download_release_file-80"><a href="#download_release_file-80"><span class="linenos">80</span></a> <span class="k">if</span> <span class="n">response</span><span class="o">.</span><span class="n">status_code</span> <span class="o">==</span> <span class="mi">200</span><span class="p">:</span>
+</span><span id="download_release_file-81"><a href="#download_release_file-81"><span class="linenos">81</span></a> <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">file_destination</span><span class="p">,</span> <span class="s2">"wb"</span><span class="p">)</span> <span class="k">as</span> <span class="n">f</span><span class="p">:</span>
+</span><span id="download_release_file-82"><a href="#download_release_file-82"><span class="linenos">82</span></a> <span class="n">f</span><span class="o">.</span><span class="n">write</span><span class="p">(</span><span class="n">response</span><span class="o">.</span><span class="n">content</span><span class="p">)</span>
+</span><span id="download_release_file-83"><a href="#download_release_file-83"><span class="linenos">83</span></a> <span class="k">else</span><span class="p">:</span>
+</span><span id="download_release_file-84"><a href="#download_release_file-84"><span class="linenos">84</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">error</span><span class="p">(</span>
+</span><span id="download_release_file-85"><a href="#download_release_file-85"><span class="linenos">85</span></a> <span class="sa">f</span><span class="s2">"Failed to download </span><span class="si">{</span><span class="n">file_type</span><span class="si">}</span><span class="s2"> file for item </span><span class="si">{</span><span class="n">item_id</span><span class="si">}</span><span class="s2">. Status code: </span><span class="si">{</span><span class="n">response</span><span class="o">.</span><span class="n">status_code</span><span class="si">}</span><span class="s2">"</span>
+</span><span id="download_release_file-86"><a href="#download_release_file-86"><span class="linenos">86</span></a> <span class="p">)</span>
+</span><span id="download_release_file-87"><a href="#download_release_file-87"><span class="linenos">87</span></a> <span class="n">response</span><span class="o">.</span><span class="n">raise_for_status</span><span class="p">()</span>
+</span><span id="download_release_file-88"><a href="#download_release_file-88"><span class="linenos">88</span></a>
+</span><span id="download_release_file-89"><a href="#download_release_file-89"><span class="linenos">89</span></a> <span class="k">return</span> <span class="n">file_destination</span>
+</span></pre></div>
+
+
+ <div class="docstring"><p>Download specified file type for a given release of an item.</p>
+</div>
+
+
+ </section>
+ <section id="validate_download_hash">
+ <input id="validate_download_hash-view-source" class="view-source-toggle-state" type="checkbox" aria-hidden="true" tabindex="-1">
+<div class="attr function">
+
+ <span class="def">def</span>
+ <span class="name">validate_download_hash</span><span class="signature pdoc-code condensed">(<span class="param"><span class="n">file_destination</span><span class="p">:</span> <span class="nb">str</span>, </span><span class="param"><span class="n">item_hash</span><span class="p">:</span> <span class="nb">str</span></span><span class="return-annotation">):</span></span>
+
+ <label class="view-source-button" for="validate_download_hash-view-source"><span>View Source</span></label>
+
+ </div>
+ <a class="headerlink" href="#validate_download_hash"></a>
+ <div class="pdoc-code codehilite"><pre><span></span><span id="validate_download_hash-92"><a href="#validate_download_hash-92"><span class="linenos"> 92</span></a><span class="k">def</span><span class="w"> </span><span class="nf">validate_download_hash</span><span class="p">(</span><span class="n">file_destination</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">item_hash</span><span class="p">:</span> <span class="nb">str</span><span class="p">):</span>
+</span><span id="validate_download_hash-93"><a href="#validate_download_hash-93"><span class="linenos"> 93</span></a> <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">file_destination</span><span class="p">,</span> <span class="s2">"rb"</span><span class="p">)</span> <span class="k">as</span> <span class="n">f</span><span class="p">:</span>
+</span><span id="validate_download_hash-94"><a href="#validate_download_hash-94"><span class="linenos"> 94</span></a> <span class="nb">hash</span> <span class="o">=</span> <span class="n">hashlib</span><span class="o">.</span><span class="n">sha256</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">read</span><span class="p">())</span><span class="o">.</span><span class="n">hexdigest</span><span class="p">()</span>
+</span><span id="validate_download_hash-95"><a href="#validate_download_hash-95"><span class="linenos"> 95</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="nb">hash</span><span class="p">)</span>
+</span><span id="validate_download_hash-96"><a href="#validate_download_hash-96"><span class="linenos"> 96</span></a> <span class="k">if</span> <span class="nb">hash</span><span class="o">.</span><span class="n">upper</span><span class="p">()</span> <span class="o">==</span> <span class="n">item_hash</span><span class="o">.</span><span class="n">upper</span><span class="p">():</span>
+</span><span id="validate_download_hash-97"><a href="#validate_download_hash-97"><span class="linenos"> 97</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Verified hash of </span><span class="si">{</span><span class="n">file_destination</span><span class="si">}</span><span class="s2"> </span><span class="si">{</span><span class="nb">hash</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+</span><span id="validate_download_hash-98"><a href="#validate_download_hash-98"><span class="linenos"> 98</span></a> <span class="k">else</span><span class="p">:</span>
+</span><span id="validate_download_hash-99"><a href="#validate_download_hash-99"><span class="linenos"> 99</span></a> <span class="n">msg</span> <span class="o">=</span> <span class="sa">f</span><span class="s2">"Could not validate origin of </span><span class="si">{</span><span class="n">file_destination</span><span class="si">}</span><span class="s2">. The SHA-256 hash should be: </span><span class="si">{</span><span class="n">item_hash</span><span class="si">}</span><span class="s2">, but got </span><span class="si">{</span><span class="nb">hash</span><span class="si">}</span><span class="s2"> instead"</span>
+</span><span id="validate_download_hash-100"><a href="#validate_download_hash-100"><span class="linenos">100</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">error</span><span class="p">(</span><span class="n">msg</span><span class="p">)</span>
+</span><span id="validate_download_hash-101"><a href="#validate_download_hash-101"><span class="linenos">101</span></a> <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="n">msg</span><span class="p">)</span>
+</span></pre></div>
+
+
+
+
+ </section>
+ <section id="unzip_download">
+ <input id="unzip_download-view-source" class="view-source-toggle-state" type="checkbox" aria-hidden="true" tabindex="-1">
+<div class="attr function">
+
+ <span class="def">def</span>
+ <span class="name">unzip_download</span><span class="signature pdoc-code condensed">(<span class="param"><span class="n">file_destination</span><span class="p">:</span> <span class="nb">str</span></span><span class="return-annotation">):</span></span>
+
+ <label class="view-source-button" for="unzip_download-view-source"><span>View Source</span></label>
+
+ </div>
+ <a class="headerlink" href="#unzip_download"></a>
+ <div class="pdoc-code codehilite"><pre><span></span><span id="unzip_download-104"><a href="#unzip_download-104"><span class="linenos">104</span></a><span class="k">def</span><span class="w"> </span><span class="nf">unzip_download</span><span class="p">(</span><span class="n">file_destination</span><span class="p">:</span> <span class="nb">str</span><span class="p">):</span>
+</span><span id="unzip_download-105"><a href="#unzip_download-105"><span class="linenos">105</span></a>
+</span><span id="unzip_download-106"><a href="#unzip_download-106"><span class="linenos">106</span></a> <span class="c1"># check folder is a directory</span>
+</span><span id="unzip_download-107"><a href="#unzip_download-107"><span class="linenos">107</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="n">DOWNLOADS_PATH</span><span class="o">.</span><span class="n">is_dir</span><span class="p">():</span>
+</span><span id="unzip_download-108"><a href="#unzip_download-108"><span class="linenos">108</span></a> <span class="k">raise</span> <span class="ne">NotADirectoryError</span><span class="p">(</span>
+</span><span id="unzip_download-109"><a href="#unzip_download-109"><span class="linenos">109</span></a> <span class="sa">f</span><span class="s2">"Error: '</span><span class="si">{</span><span class="n">DOWNLOADS_PATH</span><span class="si">}</span><span class="s2">' for TRUD resoruces is not a directory"</span>
+</span><span id="unzip_download-110"><a href="#unzip_download-110"><span class="linenos">110</span></a> <span class="p">)</span>
+</span><span id="unzip_download-111"><a href="#unzip_download-111"><span class="linenos">111</span></a>
+</span><span id="unzip_download-112"><a href="#unzip_download-112"><span class="linenos">112</span></a> <span class="k">with</span> <span class="n">zipfile</span><span class="o">.</span><span class="n">ZipFile</span><span class="p">(</span><span class="n">file_destination</span><span class="p">,</span> <span class="s2">"r"</span><span class="p">)</span> <span class="k">as</span> <span class="n">zip_ref</span><span class="p">:</span>
+</span><span id="unzip_download-113"><a href="#unzip_download-113"><span class="linenos">113</span></a> <span class="n">zip_ref</span><span class="o">.</span><span class="n">extractall</span><span class="p">(</span><span class="n">DOWNLOADS_PATH</span><span class="p">)</span>
+</span></pre></div>
+
+
+
+
+ </section>
+ <section id="extract_icd10">
+ <input id="extract_icd10-view-source" class="view-source-toggle-state" type="checkbox" aria-hidden="true" tabindex="-1">
+<div class="attr function">
+
+ <span class="def">def</span>
+ <span class="name">extract_icd10</span><span class="signature pdoc-code condensed">(<span class="return-annotation">):</span></span>
+
+ <label class="view-source-button" for="extract_icd10-view-source"><span>View Source</span></label>
+
+ </div>
+ <a class="headerlink" href="#extract_icd10"></a>
+ <div class="pdoc-code codehilite"><pre><span></span><span id="extract_icd10-116"><a href="#extract_icd10-116"><span class="linenos">116</span></a><span class="k">def</span><span class="w"> </span><span class="nf">extract_icd10</span><span class="p">():</span>
+</span><span id="extract_icd10-117"><a href="#extract_icd10-117"><span class="linenos">117</span></a> <span class="c1"># ICD10_edition5</span>
+</span><span id="extract_icd10-118"><a href="#extract_icd10-118"><span class="linenos">118</span></a> <span class="n">file_path</span> <span class="o">=</span> <span class="p">(</span>
+</span><span id="extract_icd10-119"><a href="#extract_icd10-119"><span class="linenos">119</span></a> <span class="n">DOWNLOADS_PATH</span>
+</span><span id="extract_icd10-120"><a href="#extract_icd10-120"><span class="linenos">120</span></a> <span class="o">/</span> <span class="s2">"ICD10_Edition5_XML_20160401"</span>
+</span><span id="extract_icd10-121"><a href="#extract_icd10-121"><span class="linenos">121</span></a> <span class="o">/</span> <span class="s2">"Content"</span>
+</span><span id="extract_icd10-122"><a href="#extract_icd10-122"><span class="linenos">122</span></a> <span class="o">/</span> <span class="s2">"ICD10_Edition5_CodesAndTitlesAndMetadata_GB_20160401.xml"</span>
+</span><span id="extract_icd10-123"><a href="#extract_icd10-123"><span class="linenos">123</span></a> <span class="p">)</span>
+</span><span id="extract_icd10-124"><a href="#extract_icd10-124"><span class="linenos">124</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">read_xml</span><span class="p">(</span><span class="n">file_path</span><span class="p">)</span>
+</span><span id="extract_icd10-125"><a href="#extract_icd10-125"><span class="linenos">125</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">df</span><span class="p">[[</span><span class="s2">"CODE"</span><span class="p">,</span> <span class="s2">"ALT_CODE"</span><span class="p">,</span> <span class="s2">"DESCRIPTION"</span><span class="p">]]</span>
+</span><span id="extract_icd10-126"><a href="#extract_icd10-126"><span class="linenos">126</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">df</span><span class="o">.</span><span class="n">rename</span><span class="p">(</span>
+</span><span id="extract_icd10-127"><a href="#extract_icd10-127"><span class="linenos">127</span></a> <span class="n">columns</span><span class="o">=</span><span class="p">{</span><span class="s2">"CODE"</span><span class="p">:</span> <span class="s2">"icd10"</span><span class="p">,</span> <span class="s2">"ALT_CODE"</span><span class="p">:</span> <span class="s2">"icd10_alt"</span><span class="p">,</span> <span class="s2">"DESCRIPTION"</span><span class="p">:</span> <span class="s2">"description"</span><span class="p">}</span>
+</span><span id="extract_icd10-128"><a href="#extract_icd10-128"><span class="linenos">128</span></a> <span class="p">)</span>
+</span><span id="extract_icd10-129"><a href="#extract_icd10-129"><span class="linenos">129</span></a> <span class="n">output_path</span> <span class="o">=</span> <span class="n">PROCESSED_PATH</span> <span class="o">/</span> <span class="s2">"icd10.parquet"</span>
+</span><span id="extract_icd10-130"><a href="#extract_icd10-130"><span class="linenos">130</span></a> <span class="n">df</span><span class="o">.</span><span class="n">to_parquet</span><span class="p">(</span><span class="n">output_path</span><span class="p">,</span> <span class="n">index</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span>
+</span><span id="extract_icd10-131"><a href="#extract_icd10-131"><span class="linenos">131</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Extracted: </span><span class="si">{</span><span class="n">output_path</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+</span></pre></div>
+
+
+
+
+ </section>
+ <section id="extract_opsc4">
+ <input id="extract_opsc4-view-source" class="view-source-toggle-state" type="checkbox" aria-hidden="true" tabindex="-1">
+<div class="attr function">
+
+ <span class="def">def</span>
+ <span class="name">extract_opsc4</span><span class="signature pdoc-code condensed">(<span class="return-annotation">):</span></span>
+
+ <label class="view-source-button" for="extract_opsc4-view-source"><span>View Source</span></label>
+
+ </div>
+ <a class="headerlink" href="#extract_opsc4"></a>
+ <div class="pdoc-code codehilite"><pre><span></span><span id="extract_opsc4-134"><a href="#extract_opsc4-134"><span class="linenos">134</span></a><span class="k">def</span><span class="w"> </span><span class="nf">extract_opsc4</span><span class="p">():</span>
+</span><span id="extract_opsc4-135"><a href="#extract_opsc4-135"><span class="linenos">135</span></a> <span class="n">file_path</span> <span class="o">=</span> <span class="p">(</span>
+</span><span id="extract_opsc4-136"><a href="#extract_opsc4-136"><span class="linenos">136</span></a> <span class="n">DOWNLOADS_PATH</span>
+</span><span id="extract_opsc4-137"><a href="#extract_opsc4-137"><span class="linenos">137</span></a> <span class="o">/</span> <span class="s2">"OPCS410 Data files txt"</span>
+</span><span id="extract_opsc4-138"><a href="#extract_opsc4-138"><span class="linenos">138</span></a> <span class="o">/</span> <span class="s2">"OPCS410 CodesAndTitles Nov 2022 V1.0.txt"</span>
+</span><span id="extract_opsc4-139"><a href="#extract_opsc4-139"><span class="linenos">139</span></a> <span class="p">)</span>
+</span><span id="extract_opsc4-140"><a href="#extract_opsc4-140"><span class="linenos">140</span></a>
+</span><span id="extract_opsc4-141"><a href="#extract_opsc4-141"><span class="linenos">141</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">read_csv</span><span class="p">(</span><span class="n">file_path</span><span class="p">,</span> <span class="n">sep</span><span class="o">=</span><span class="s2">"</span><span class="se">\t</span><span class="s2">"</span><span class="p">,</span> <span class="n">dtype</span><span class="o">=</span><span class="nb">str</span><span class="p">,</span> <span class="n">header</span><span class="o">=</span><span class="kc">None</span><span class="p">)</span>
+</span><span id="extract_opsc4-142"><a href="#extract_opsc4-142"><span class="linenos">142</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">df</span><span class="o">.</span><span class="n">rename</span><span class="p">(</span><span class="n">columns</span><span class="o">=</span><span class="p">{</span><span class="mi">0</span><span class="p">:</span> <span class="s2">"opcs4"</span><span class="p">,</span> <span class="mi">1</span><span class="p">:</span> <span class="s2">"description"</span><span class="p">})</span>
+</span><span id="extract_opsc4-143"><a href="#extract_opsc4-143"><span class="linenos">143</span></a>
+</span><span id="extract_opsc4-144"><a href="#extract_opsc4-144"><span class="linenos">144</span></a> <span class="n">output_path</span> <span class="o">=</span> <span class="n">PROCESSED_PATH</span> <span class="o">/</span> <span class="s2">"opcs4.parquet"</span>
+</span><span id="extract_opsc4-145"><a href="#extract_opsc4-145"><span class="linenos">145</span></a> <span class="n">df</span><span class="o">.</span><span class="n">to_parquet</span><span class="p">(</span><span class="n">output_path</span><span class="p">,</span> <span class="n">index</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span>
+</span><span id="extract_opsc4-146"><a href="#extract_opsc4-146"><span class="linenos">146</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Extracted: </span><span class="si">{</span><span class="n">output_path</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+</span></pre></div>
+
+
+
+
+ </section>
+ <section id="extract_nhs_data_migrations">
+ <input id="extract_nhs_data_migrations-view-source" class="view-source-toggle-state" type="checkbox" aria-hidden="true" tabindex="-1">
+<div class="attr function">
+
+ <span class="def">def</span>
+ <span class="name">extract_nhs_data_migrations</span><span class="signature pdoc-code condensed">(<span class="return-annotation">):</span></span>
+
+ <label class="view-source-button" for="extract_nhs_data_migrations-view-source"><span>View Source</span></label>
+
+ </div>
+ <a class="headerlink" href="#extract_nhs_data_migrations"></a>
+ <div class="pdoc-code codehilite"><pre><span></span><span id="extract_nhs_data_migrations-149"><a href="#extract_nhs_data_migrations-149"><span class="linenos">149</span></a><span class="k">def</span><span class="w"> </span><span class="nf">extract_nhs_data_migrations</span><span class="p">():</span>
+</span><span id="extract_nhs_data_migrations-150"><a href="#extract_nhs_data_migrations-150"><span class="linenos">150</span></a> <span class="c1"># NHS Data Migrations</span>
+</span><span id="extract_nhs_data_migrations-151"><a href="#extract_nhs_data_migrations-151"><span class="linenos">151</span></a>
+</span><span id="extract_nhs_data_migrations-152"><a href="#extract_nhs_data_migrations-152"><span class="linenos">152</span></a> <span class="c1"># snomed only</span>
+</span><span id="extract_nhs_data_migrations-153"><a href="#extract_nhs_data_migrations-153"><span class="linenos">153</span></a> <span class="n">file_path</span> <span class="o">=</span> <span class="p">(</span>
+</span><span id="extract_nhs_data_migrations-154"><a href="#extract_nhs_data_migrations-154"><span class="linenos">154</span></a> <span class="n">DOWNLOADS_PATH</span>
+</span><span id="extract_nhs_data_migrations-155"><a href="#extract_nhs_data_migrations-155"><span class="linenos">155</span></a> <span class="o">/</span> <span class="s2">"Mapping Tables"</span>
+</span><span id="extract_nhs_data_migrations-156"><a href="#extract_nhs_data_migrations-156"><span class="linenos">156</span></a> <span class="o">/</span> <span class="s2">"Updated"</span>
+</span><span id="extract_nhs_data_migrations-157"><a href="#extract_nhs_data_migrations-157"><span class="linenos">157</span></a> <span class="o">/</span> <span class="s2">"Clinically Assured"</span>
+</span><span id="extract_nhs_data_migrations-158"><a href="#extract_nhs_data_migrations-158"><span class="linenos">158</span></a> <span class="o">/</span> <span class="s2">"sctcremap_uk_20200401000001.txt"</span>
+</span><span id="extract_nhs_data_migrations-159"><a href="#extract_nhs_data_migrations-159"><span class="linenos">159</span></a> <span class="p">)</span>
+</span><span id="extract_nhs_data_migrations-160"><a href="#extract_nhs_data_migrations-160"><span class="linenos">160</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">read_csv</span><span class="p">(</span><span class="n">file_path</span><span class="p">,</span> <span class="n">sep</span><span class="o">=</span><span class="s2">"</span><span class="se">\t</span><span class="s2">"</span><span class="p">)</span>
+</span><span id="extract_nhs_data_migrations-161"><a href="#extract_nhs_data_migrations-161"><span class="linenos">161</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">df</span><span class="p">[[</span><span class="s2">"SCT_CONCEPTID"</span><span class="p">]]</span>
+</span><span id="extract_nhs_data_migrations-162"><a href="#extract_nhs_data_migrations-162"><span class="linenos">162</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">df</span><span class="o">.</span><span class="n">rename</span><span class="p">(</span><span class="n">columns</span><span class="o">=</span><span class="p">{</span><span class="s2">"SCT_CONCEPTID"</span><span class="p">:</span> <span class="s2">"snomed"</span><span class="p">})</span>
+</span><span id="extract_nhs_data_migrations-163"><a href="#extract_nhs_data_migrations-163"><span class="linenos">163</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">df</span><span class="o">.</span><span class="n">drop_duplicates</span><span class="p">()</span>
+</span><span id="extract_nhs_data_migrations-164"><a href="#extract_nhs_data_migrations-164"><span class="linenos">164</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">df</span><span class="o">.</span><span class="n">astype</span><span class="p">(</span><span class="nb">str</span><span class="p">)</span>
+</span><span id="extract_nhs_data_migrations-165"><a href="#extract_nhs_data_migrations-165"><span class="linenos">165</span></a>
+</span><span id="extract_nhs_data_migrations-166"><a href="#extract_nhs_data_migrations-166"><span class="linenos">166</span></a> <span class="n">output_path</span> <span class="o">=</span> <span class="n">PROCESSED_PATH</span> <span class="o">/</span> <span class="s2">"snomed.parquet"</span>
+</span><span id="extract_nhs_data_migrations-167"><a href="#extract_nhs_data_migrations-167"><span class="linenos">167</span></a> <span class="n">df</span><span class="o">.</span><span class="n">to_parquet</span><span class="p">(</span><span class="n">output_path</span><span class="p">,</span> <span class="n">index</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span>
+</span><span id="extract_nhs_data_migrations-168"><a href="#extract_nhs_data_migrations-168"><span class="linenos">168</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Extracted: </span><span class="si">{</span><span class="n">output_path</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+</span><span id="extract_nhs_data_migrations-169"><a href="#extract_nhs_data_migrations-169"><span class="linenos">169</span></a>
+</span><span id="extract_nhs_data_migrations-170"><a href="#extract_nhs_data_migrations-170"><span class="linenos">170</span></a> <span class="c1"># r2 -> r3</span>
+</span><span id="extract_nhs_data_migrations-171"><a href="#extract_nhs_data_migrations-171"><span class="linenos">171</span></a> <span class="n">file_path</span> <span class="o">=</span> <span class="p">(</span>
+</span><span id="extract_nhs_data_migrations-172"><a href="#extract_nhs_data_migrations-172"><span class="linenos">172</span></a> <span class="n">DOWNLOADS_PATH</span>
+</span><span id="extract_nhs_data_migrations-173"><a href="#extract_nhs_data_migrations-173"><span class="linenos">173</span></a> <span class="o">/</span> <span class="s2">"Mapping Tables"</span>
+</span><span id="extract_nhs_data_migrations-174"><a href="#extract_nhs_data_migrations-174"><span class="linenos">174</span></a> <span class="o">/</span> <span class="s2">"Updated"</span>
+</span><span id="extract_nhs_data_migrations-175"><a href="#extract_nhs_data_migrations-175"><span class="linenos">175</span></a> <span class="o">/</span> <span class="s2">"Clinically Assured"</span>
+</span><span id="extract_nhs_data_migrations-176"><a href="#extract_nhs_data_migrations-176"><span class="linenos">176</span></a> <span class="o">/</span> <span class="s2">"rctctv3map_uk_20200401000001.txt"</span>
+</span><span id="extract_nhs_data_migrations-177"><a href="#extract_nhs_data_migrations-177"><span class="linenos">177</span></a> <span class="p">)</span>
+</span><span id="extract_nhs_data_migrations-178"><a href="#extract_nhs_data_migrations-178"><span class="linenos">178</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">read_csv</span><span class="p">(</span><span class="n">file_path</span><span class="p">,</span> <span class="n">sep</span><span class="o">=</span><span class="s2">"</span><span class="se">\t</span><span class="s2">"</span><span class="p">)</span>
+</span><span id="extract_nhs_data_migrations-179"><a href="#extract_nhs_data_migrations-179"><span class="linenos">179</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">df</span><span class="p">[[</span><span class="s2">"V2_CONCEPTID"</span><span class="p">,</span> <span class="s2">"CTV3_CONCEPTID"</span><span class="p">]]</span>
+</span><span id="extract_nhs_data_migrations-180"><a href="#extract_nhs_data_migrations-180"><span class="linenos">180</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">df</span><span class="o">.</span><span class="n">rename</span><span class="p">(</span><span class="n">columns</span><span class="o">=</span><span class="p">{</span><span class="s2">"V2_CONCEPTID"</span><span class="p">:</span> <span class="s2">"read2"</span><span class="p">,</span> <span class="s2">"CTV3_CONCEPTID"</span><span class="p">:</span> <span class="s2">"read3"</span><span class="p">})</span>
+</span><span id="extract_nhs_data_migrations-181"><a href="#extract_nhs_data_migrations-181"><span class="linenos">181</span></a>
+</span><span id="extract_nhs_data_migrations-182"><a href="#extract_nhs_data_migrations-182"><span class="linenos">182</span></a> <span class="n">output_path</span> <span class="o">=</span> <span class="n">PROCESSED_PATH</span> <span class="o">/</span> <span class="s2">"read2_to_read3.parquet"</span>
+</span><span id="extract_nhs_data_migrations-183"><a href="#extract_nhs_data_migrations-183"><span class="linenos">183</span></a> <span class="n">df</span><span class="o">.</span><span class="n">to_parquet</span><span class="p">(</span><span class="n">output_path</span><span class="p">,</span> <span class="n">index</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span>
+</span><span id="extract_nhs_data_migrations-184"><a href="#extract_nhs_data_migrations-184"><span class="linenos">184</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Extracted: </span><span class="si">{</span><span class="n">output_path</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+</span><span id="extract_nhs_data_migrations-185"><a href="#extract_nhs_data_migrations-185"><span class="linenos">185</span></a>
+</span><span id="extract_nhs_data_migrations-186"><a href="#extract_nhs_data_migrations-186"><span class="linenos">186</span></a> <span class="c1"># r3->r2</span>
+</span><span id="extract_nhs_data_migrations-187"><a href="#extract_nhs_data_migrations-187"><span class="linenos">187</span></a> <span class="n">file_path</span> <span class="o">=</span> <span class="p">(</span>
+</span><span id="extract_nhs_data_migrations-188"><a href="#extract_nhs_data_migrations-188"><span class="linenos">188</span></a> <span class="n">DOWNLOADS_PATH</span>
+</span><span id="extract_nhs_data_migrations-189"><a href="#extract_nhs_data_migrations-189"><span class="linenos">189</span></a> <span class="o">/</span> <span class="s2">"Mapping Tables"</span>
+</span><span id="extract_nhs_data_migrations-190"><a href="#extract_nhs_data_migrations-190"><span class="linenos">190</span></a> <span class="o">/</span> <span class="s2">"Updated"</span>
+</span><span id="extract_nhs_data_migrations-191"><a href="#extract_nhs_data_migrations-191"><span class="linenos">191</span></a> <span class="o">/</span> <span class="s2">"Clinically Assured"</span>
+</span><span id="extract_nhs_data_migrations-192"><a href="#extract_nhs_data_migrations-192"><span class="linenos">192</span></a> <span class="o">/</span> <span class="s2">"ctv3rctmap_uk_20200401000002.txt"</span>
+</span><span id="extract_nhs_data_migrations-193"><a href="#extract_nhs_data_migrations-193"><span class="linenos">193</span></a> <span class="p">)</span>
+</span><span id="extract_nhs_data_migrations-194"><a href="#extract_nhs_data_migrations-194"><span class="linenos">194</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">read_csv</span><span class="p">(</span><span class="n">file_path</span><span class="p">,</span> <span class="n">sep</span><span class="o">=</span><span class="s2">"</span><span class="se">\t</span><span class="s2">"</span><span class="p">)</span>
+</span><span id="extract_nhs_data_migrations-195"><a href="#extract_nhs_data_migrations-195"><span class="linenos">195</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">df</span><span class="p">[[</span><span class="s2">"CTV3_CONCEPTID"</span><span class="p">,</span> <span class="s2">"V2_CONCEPTID"</span><span class="p">]]</span>
+</span><span id="extract_nhs_data_migrations-196"><a href="#extract_nhs_data_migrations-196"><span class="linenos">196</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">df</span><span class="o">.</span><span class="n">rename</span><span class="p">(</span><span class="n">columns</span><span class="o">=</span><span class="p">{</span><span class="s2">"CTV3_CONCEPTID"</span><span class="p">:</span> <span class="s2">"read3"</span><span class="p">,</span> <span class="s2">"V2_CONCEPTID"</span><span class="p">:</span> <span class="s2">"read2"</span><span class="p">})</span>
+</span><span id="extract_nhs_data_migrations-197"><a href="#extract_nhs_data_migrations-197"><span class="linenos">197</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">df</span><span class="o">.</span><span class="n">drop_duplicates</span><span class="p">()</span>
+</span><span id="extract_nhs_data_migrations-198"><a href="#extract_nhs_data_migrations-198"><span class="linenos">198</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">df</span><span class="p">[</span><span class="o">~</span><span class="n">df</span><span class="p">[</span><span class="s2">"read2"</span><span class="p">]</span><span class="o">.</span><span class="n">str</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="s2">"^.*_.*$"</span><span class="p">)]</span> <span class="c1"># remove r2 codes with '_'</span>
+</span><span id="extract_nhs_data_migrations-199"><a href="#extract_nhs_data_migrations-199"><span class="linenos">199</span></a>
+</span><span id="extract_nhs_data_migrations-200"><a href="#extract_nhs_data_migrations-200"><span class="linenos">200</span></a> <span class="n">output_path</span> <span class="o">=</span> <span class="n">PROCESSED_PATH</span> <span class="o">/</span> <span class="s2">"read3_to_read2.parquet"</span>
+</span><span id="extract_nhs_data_migrations-201"><a href="#extract_nhs_data_migrations-201"><span class="linenos">201</span></a> <span class="n">df</span><span class="o">.</span><span class="n">to_parquet</span><span class="p">(</span><span class="n">output_path</span><span class="p">,</span> <span class="n">index</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span>
+</span><span id="extract_nhs_data_migrations-202"><a href="#extract_nhs_data_migrations-202"><span class="linenos">202</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Extracted: </span><span class="si">{</span><span class="n">output_path</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+</span><span id="extract_nhs_data_migrations-203"><a href="#extract_nhs_data_migrations-203"><span class="linenos">203</span></a>
+</span><span id="extract_nhs_data_migrations-204"><a href="#extract_nhs_data_migrations-204"><span class="linenos">204</span></a> <span class="c1"># r2 -> snomed</span>
+</span><span id="extract_nhs_data_migrations-205"><a href="#extract_nhs_data_migrations-205"><span class="linenos">205</span></a> <span class="n">file_path</span> <span class="o">=</span> <span class="p">(</span>
+</span><span id="extract_nhs_data_migrations-206"><a href="#extract_nhs_data_migrations-206"><span class="linenos">206</span></a> <span class="n">DOWNLOADS_PATH</span>
+</span><span id="extract_nhs_data_migrations-207"><a href="#extract_nhs_data_migrations-207"><span class="linenos">207</span></a> <span class="o">/</span> <span class="s2">"Mapping Tables"</span>
+</span><span id="extract_nhs_data_migrations-208"><a href="#extract_nhs_data_migrations-208"><span class="linenos">208</span></a> <span class="o">/</span> <span class="s2">"Updated"</span>
+</span><span id="extract_nhs_data_migrations-209"><a href="#extract_nhs_data_migrations-209"><span class="linenos">209</span></a> <span class="o">/</span> <span class="s2">"Clinically Assured"</span>
+</span><span id="extract_nhs_data_migrations-210"><a href="#extract_nhs_data_migrations-210"><span class="linenos">210</span></a> <span class="o">/</span> <span class="s2">"rcsctmap2_uk_20200401000001.txt"</span>
+</span><span id="extract_nhs_data_migrations-211"><a href="#extract_nhs_data_migrations-211"><span class="linenos">211</span></a> <span class="p">)</span>
+</span><span id="extract_nhs_data_migrations-212"><a href="#extract_nhs_data_migrations-212"><span class="linenos">212</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">read_csv</span><span class="p">(</span><span class="n">file_path</span><span class="p">,</span> <span class="n">sep</span><span class="o">=</span><span class="s2">"</span><span class="se">\t</span><span class="s2">"</span><span class="p">,</span> <span class="n">dtype</span><span class="o">=</span><span class="nb">str</span><span class="p">)</span>
+</span><span id="extract_nhs_data_migrations-213"><a href="#extract_nhs_data_migrations-213"><span class="linenos">213</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">df</span><span class="p">[[</span><span class="s2">"ReadCode"</span><span class="p">,</span> <span class="s2">"ConceptId"</span><span class="p">]]</span>
+</span><span id="extract_nhs_data_migrations-214"><a href="#extract_nhs_data_migrations-214"><span class="linenos">214</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">df</span><span class="o">.</span><span class="n">rename</span><span class="p">(</span><span class="n">columns</span><span class="o">=</span><span class="p">{</span><span class="s2">"ReadCode"</span><span class="p">:</span> <span class="s2">"read2"</span><span class="p">,</span> <span class="s2">"ConceptId"</span><span class="p">:</span> <span class="s2">"snomed"</span><span class="p">})</span>
+</span><span id="extract_nhs_data_migrations-215"><a href="#extract_nhs_data_migrations-215"><span class="linenos">215</span></a>
+</span><span id="extract_nhs_data_migrations-216"><a href="#extract_nhs_data_migrations-216"><span class="linenos">216</span></a> <span class="n">output_path</span> <span class="o">=</span> <span class="n">PROCESSED_PATH</span> <span class="o">/</span> <span class="s2">"read2_to_snomed.parquet"</span>
+</span><span id="extract_nhs_data_migrations-217"><a href="#extract_nhs_data_migrations-217"><span class="linenos">217</span></a> <span class="n">df</span><span class="o">.</span><span class="n">to_parquet</span><span class="p">(</span><span class="n">output_path</span><span class="p">,</span> <span class="n">index</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span>
+</span><span id="extract_nhs_data_migrations-218"><a href="#extract_nhs_data_migrations-218"><span class="linenos">218</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Extracted: </span><span class="si">{</span><span class="n">output_path</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+</span><span id="extract_nhs_data_migrations-219"><a href="#extract_nhs_data_migrations-219"><span class="linenos">219</span></a>
+</span><span id="extract_nhs_data_migrations-220"><a href="#extract_nhs_data_migrations-220"><span class="linenos">220</span></a> <span class="c1"># r3->snomed</span>
+</span><span id="extract_nhs_data_migrations-221"><a href="#extract_nhs_data_migrations-221"><span class="linenos">221</span></a> <span class="n">file_path</span> <span class="o">=</span> <span class="p">(</span>
+</span><span id="extract_nhs_data_migrations-222"><a href="#extract_nhs_data_migrations-222"><span class="linenos">222</span></a> <span class="n">DOWNLOADS_PATH</span>
+</span><span id="extract_nhs_data_migrations-223"><a href="#extract_nhs_data_migrations-223"><span class="linenos">223</span></a> <span class="o">/</span> <span class="s2">"Mapping Tables"</span>
+</span><span id="extract_nhs_data_migrations-224"><a href="#extract_nhs_data_migrations-224"><span class="linenos">224</span></a> <span class="o">/</span> <span class="s2">"Updated"</span>
+</span><span id="extract_nhs_data_migrations-225"><a href="#extract_nhs_data_migrations-225"><span class="linenos">225</span></a> <span class="o">/</span> <span class="s2">"Clinically Assured"</span>
+</span><span id="extract_nhs_data_migrations-226"><a href="#extract_nhs_data_migrations-226"><span class="linenos">226</span></a> <span class="o">/</span> <span class="s2">"ctv3sctmap2_uk_20200401000001.txt"</span>
+</span><span id="extract_nhs_data_migrations-227"><a href="#extract_nhs_data_migrations-227"><span class="linenos">227</span></a> <span class="p">)</span>
+</span><span id="extract_nhs_data_migrations-228"><a href="#extract_nhs_data_migrations-228"><span class="linenos">228</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">read_csv</span><span class="p">(</span><span class="n">file_path</span><span class="p">,</span> <span class="n">sep</span><span class="o">=</span><span class="s2">"</span><span class="se">\t</span><span class="s2">"</span><span class="p">,</span> <span class="n">dtype</span><span class="o">=</span><span class="nb">str</span><span class="p">)</span>
+</span><span id="extract_nhs_data_migrations-229"><a href="#extract_nhs_data_migrations-229"><span class="linenos">229</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">df</span><span class="p">[[</span><span class="s2">"CTV3_TERMID"</span><span class="p">,</span> <span class="s2">"SCT_CONCEPTID"</span><span class="p">]]</span>
+</span><span id="extract_nhs_data_migrations-230"><a href="#extract_nhs_data_migrations-230"><span class="linenos">230</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">df</span><span class="o">.</span><span class="n">rename</span><span class="p">(</span><span class="n">columns</span><span class="o">=</span><span class="p">{</span><span class="s2">"CTV3_TERMID"</span><span class="p">:</span> <span class="s2">"read3"</span><span class="p">,</span> <span class="s2">"SCT_CONCEPTID"</span><span class="p">:</span> <span class="s2">"snomed"</span><span class="p">})</span>
+</span><span id="extract_nhs_data_migrations-231"><a href="#extract_nhs_data_migrations-231"><span class="linenos">231</span></a> <span class="n">df</span><span class="p">[</span><span class="s2">"snomed"</span><span class="p">]</span> <span class="o">=</span> <span class="n">df</span><span class="p">[</span><span class="s2">"snomed"</span><span class="p">]</span><span class="o">.</span><span class="n">astype</span><span class="p">(</span><span class="nb">str</span><span class="p">)</span>
+</span><span id="extract_nhs_data_migrations-232"><a href="#extract_nhs_data_migrations-232"><span class="linenos">232</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">df</span><span class="p">[</span><span class="o">~</span><span class="n">df</span><span class="p">[</span><span class="s2">"snomed"</span><span class="p">]</span><span class="o">.</span><span class="n">str</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="s2">"^.*_.*$"</span><span class="p">)]</span> <span class="c1"># remove snomed codes with '_'</span>
+</span><span id="extract_nhs_data_migrations-233"><a href="#extract_nhs_data_migrations-233"><span class="linenos">233</span></a>
+</span><span id="extract_nhs_data_migrations-234"><a href="#extract_nhs_data_migrations-234"><span class="linenos">234</span></a> <span class="n">output_path</span> <span class="o">=</span> <span class="n">PROCESSED_PATH</span> <span class="o">/</span> <span class="s2">"read3_to_snomed.parquet"</span>
+</span><span id="extract_nhs_data_migrations-235"><a href="#extract_nhs_data_migrations-235"><span class="linenos">235</span></a> <span class="n">df</span><span class="o">.</span><span class="n">to_parquet</span><span class="p">(</span><span class="n">output_path</span><span class="p">,</span> <span class="n">index</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span>
+</span><span id="extract_nhs_data_migrations-236"><a href="#extract_nhs_data_migrations-236"><span class="linenos">236</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Extracted: </span><span class="si">{</span><span class="n">output_path</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+</span></pre></div>
+
+
+
+
+ </section>
+ <section id="extract_nhs_read_browser">
+ <input id="extract_nhs_read_browser-view-source" class="view-source-toggle-state" type="checkbox" aria-hidden="true" tabindex="-1">
+<div class="attr function">
+
+ <span class="def">def</span>
+ <span class="name">extract_nhs_read_browser</span><span class="signature pdoc-code condensed">(<span class="return-annotation">):</span></span>
+
+ <label class="view-source-button" for="extract_nhs_read_browser-view-source"><span>View Source</span></label>
+
+ </div>
+ <a class="headerlink" href="#extract_nhs_read_browser"></a>
+ <div class="pdoc-code codehilite"><pre><span></span><span id="extract_nhs_read_browser-239"><a href="#extract_nhs_read_browser-239"><span class="linenos">239</span></a><span class="k">def</span><span class="w"> </span><span class="nf">extract_nhs_read_browser</span><span class="p">():</span>
+</span><span id="extract_nhs_read_browser-240"><a href="#extract_nhs_read_browser-240"><span class="linenos">240</span></a> <span class="c1"># r2 only</span>
+</span><span id="extract_nhs_read_browser-241"><a href="#extract_nhs_read_browser-241"><span class="linenos">241</span></a> <span class="n">input_path</span> <span class="o">=</span> <span class="n">DOWNLOADS_PATH</span> <span class="o">/</span> <span class="s2">"Standard"</span> <span class="o">/</span> <span class="s2">"V2"</span> <span class="o">/</span> <span class="s2">"ANCESTOR.DBF"</span>
+</span><span id="extract_nhs_read_browser-242"><a href="#extract_nhs_read_browser-242"><span class="linenos">242</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">simpledbf</span><span class="o">.</span><span class="n">Dbf5</span><span class="p">(</span><span class="n">input_path</span><span class="p">)</span><span class="o">.</span><span class="n">to_dataframe</span><span class="p">()</span>
+</span><span id="extract_nhs_read_browser-243"><a href="#extract_nhs_read_browser-243"><span class="linenos">243</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">concat</span><span class="p">([</span><span class="n">df</span><span class="p">[</span><span class="s2">"READCODE"</span><span class="p">],</span> <span class="n">df</span><span class="p">[</span><span class="s2">"DESCENDANT"</span><span class="p">]])</span>
+</span><span id="extract_nhs_read_browser-244"><a href="#extract_nhs_read_browser-244"><span class="linenos">244</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">(</span><span class="n">df</span><span class="o">.</span><span class="n">drop_duplicates</span><span class="p">())</span>
+</span><span id="extract_nhs_read_browser-245"><a href="#extract_nhs_read_browser-245"><span class="linenos">245</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">df</span><span class="o">.</span><span class="n">rename</span><span class="p">(</span><span class="n">columns</span><span class="o">=</span><span class="p">{</span><span class="mi">0</span><span class="p">:</span> <span class="s2">"read2"</span><span class="p">})</span>
+</span><span id="extract_nhs_read_browser-246"><a href="#extract_nhs_read_browser-246"><span class="linenos">246</span></a> <span class="n">output_path</span> <span class="o">=</span> <span class="n">PROCESSED_PATH</span> <span class="o">/</span> <span class="s2">"read2.parquet"</span>
+</span><span id="extract_nhs_read_browser-247"><a href="#extract_nhs_read_browser-247"><span class="linenos">247</span></a> <span class="n">df</span><span class="o">.</span><span class="n">to_parquet</span><span class="p">(</span><span class="n">output_path</span><span class="p">,</span> <span class="n">index</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span>
+</span><span id="extract_nhs_read_browser-248"><a href="#extract_nhs_read_browser-248"><span class="linenos">248</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Extracted: </span><span class="si">{</span><span class="n">output_path</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+</span><span id="extract_nhs_read_browser-249"><a href="#extract_nhs_read_browser-249"><span class="linenos">249</span></a>
+</span><span id="extract_nhs_read_browser-250"><a href="#extract_nhs_read_browser-250"><span class="linenos">250</span></a> <span class="c1"># r2 -> atc</span>
+</span><span id="extract_nhs_read_browser-251"><a href="#extract_nhs_read_browser-251"><span class="linenos">251</span></a> <span class="n">input_path</span> <span class="o">=</span> <span class="n">DOWNLOADS_PATH</span> <span class="o">/</span> <span class="s2">"Standard"</span> <span class="o">/</span> <span class="s2">"V2"</span> <span class="o">/</span> <span class="s2">"ATC.DBF"</span>
+</span><span id="extract_nhs_read_browser-252"><a href="#extract_nhs_read_browser-252"><span class="linenos">252</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">simpledbf</span><span class="o">.</span><span class="n">Dbf5</span><span class="p">(</span><span class="n">input_path</span><span class="p">)</span><span class="o">.</span><span class="n">to_dataframe</span><span class="p">()</span>
+</span><span id="extract_nhs_read_browser-253"><a href="#extract_nhs_read_browser-253"><span class="linenos">253</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">df</span><span class="p">[[</span><span class="s2">"READCODE"</span><span class="p">,</span> <span class="s2">"ATC"</span><span class="p">]]</span>
+</span><span id="extract_nhs_read_browser-254"><a href="#extract_nhs_read_browser-254"><span class="linenos">254</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">df</span><span class="o">.</span><span class="n">rename</span><span class="p">(</span><span class="n">columns</span><span class="o">=</span><span class="p">{</span><span class="s2">"READCODE"</span><span class="p">:</span> <span class="s2">"read2"</span><span class="p">,</span> <span class="s2">"ATC"</span><span class="p">:</span> <span class="s2">"atc"</span><span class="p">})</span>
+</span><span id="extract_nhs_read_browser-255"><a href="#extract_nhs_read_browser-255"><span class="linenos">255</span></a> <span class="n">output_path</span> <span class="o">=</span> <span class="n">PROCESSED_PATH</span> <span class="o">/</span> <span class="s2">"read2_to_atc.parquet"</span>
+</span><span id="extract_nhs_read_browser-256"><a href="#extract_nhs_read_browser-256"><span class="linenos">256</span></a> <span class="n">df</span><span class="o">.</span><span class="n">to_parquet</span><span class="p">(</span><span class="n">output_path</span><span class="p">,</span> <span class="n">index</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span>
+</span><span id="extract_nhs_read_browser-257"><a href="#extract_nhs_read_browser-257"><span class="linenos">257</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Extracted: </span><span class="si">{</span><span class="n">output_path</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+</span><span id="extract_nhs_read_browser-258"><a href="#extract_nhs_read_browser-258"><span class="linenos">258</span></a>
+</span><span id="extract_nhs_read_browser-259"><a href="#extract_nhs_read_browser-259"><span class="linenos">259</span></a> <span class="c1"># r2 -> icd10</span>
+</span><span id="extract_nhs_read_browser-260"><a href="#extract_nhs_read_browser-260"><span class="linenos">260</span></a> <span class="n">input_path</span> <span class="o">=</span> <span class="n">DOWNLOADS_PATH</span> <span class="o">/</span> <span class="s2">"Standard"</span> <span class="o">/</span> <span class="s2">"V2"</span> <span class="o">/</span> <span class="s2">"ICD10.DBF"</span>
+</span><span id="extract_nhs_read_browser-261"><a href="#extract_nhs_read_browser-261"><span class="linenos">261</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">simpledbf</span><span class="o">.</span><span class="n">Dbf5</span><span class="p">(</span><span class="n">input_path</span><span class="p">)</span><span class="o">.</span><span class="n">to_dataframe</span><span class="p">()</span>
+</span><span id="extract_nhs_read_browser-262"><a href="#extract_nhs_read_browser-262"><span class="linenos">262</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">df</span><span class="p">[[</span><span class="s2">"READ_CODE"</span><span class="p">,</span> <span class="s2">"TARG_CODE"</span><span class="p">]]</span>
+</span><span id="extract_nhs_read_browser-263"><a href="#extract_nhs_read_browser-263"><span class="linenos">263</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">df</span><span class="o">.</span><span class="n">rename</span><span class="p">(</span><span class="n">columns</span><span class="o">=</span><span class="p">{</span><span class="s2">"READ_CODE"</span><span class="p">:</span> <span class="s2">"read2"</span><span class="p">,</span> <span class="s2">"TARG_CODE"</span><span class="p">:</span> <span class="s2">"icd10"</span><span class="p">})</span>
+</span><span id="extract_nhs_read_browser-264"><a href="#extract_nhs_read_browser-264"><span class="linenos">264</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">df</span><span class="p">[</span><span class="o">~</span><span class="n">df</span><span class="p">[</span><span class="s2">"icd10"</span><span class="p">]</span><span class="o">.</span><span class="n">str</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="s2">"^.*-.*$"</span><span class="p">)]</span> <span class="c1"># remove codes with '-'</span>
+</span><span id="extract_nhs_read_browser-265"><a href="#extract_nhs_read_browser-265"><span class="linenos">265</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">df</span><span class="p">[</span><span class="o">~</span><span class="n">df</span><span class="p">[</span><span class="s2">"read2"</span><span class="p">]</span><span class="o">.</span><span class="n">str</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="s2">"^.*-.*$"</span><span class="p">)]</span> <span class="c1"># remove codes with '-'</span>
+</span><span id="extract_nhs_read_browser-266"><a href="#extract_nhs_read_browser-266"><span class="linenos">266</span></a> <span class="n">output_path</span> <span class="o">=</span> <span class="n">PROCESSED_PATH</span> <span class="o">/</span> <span class="s2">"read2_to_icd10.parquet"</span>
+</span><span id="extract_nhs_read_browser-267"><a href="#extract_nhs_read_browser-267"><span class="linenos">267</span></a> <span class="n">df</span><span class="o">.</span><span class="n">to_parquet</span><span class="p">(</span><span class="n">output_path</span><span class="p">,</span> <span class="n">index</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span>
+</span><span id="extract_nhs_read_browser-268"><a href="#extract_nhs_read_browser-268"><span class="linenos">268</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Extracted: </span><span class="si">{</span><span class="n">output_path</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+</span><span id="extract_nhs_read_browser-269"><a href="#extract_nhs_read_browser-269"><span class="linenos">269</span></a>
+</span><span id="extract_nhs_read_browser-270"><a href="#extract_nhs_read_browser-270"><span class="linenos">270</span></a> <span class="c1"># r2 -> opcs4</span>
+</span><span id="extract_nhs_read_browser-271"><a href="#extract_nhs_read_browser-271"><span class="linenos">271</span></a> <span class="n">input_path</span> <span class="o">=</span> <span class="n">DOWNLOADS_PATH</span> <span class="o">/</span> <span class="s2">"Standard"</span> <span class="o">/</span> <span class="s2">"V2"</span> <span class="o">/</span> <span class="s2">"OPCS4V3.DBF"</span>
+</span><span id="extract_nhs_read_browser-272"><a href="#extract_nhs_read_browser-272"><span class="linenos">272</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">simpledbf</span><span class="o">.</span><span class="n">Dbf5</span><span class="p">(</span><span class="n">input_path</span><span class="p">)</span><span class="o">.</span><span class="n">to_dataframe</span><span class="p">()</span>
+</span><span id="extract_nhs_read_browser-273"><a href="#extract_nhs_read_browser-273"><span class="linenos">273</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">df</span><span class="p">[[</span><span class="s2">"READ_CODE"</span><span class="p">,</span> <span class="s2">"TARG_CODE"</span><span class="p">]]</span>
+</span><span id="extract_nhs_read_browser-274"><a href="#extract_nhs_read_browser-274"><span class="linenos">274</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">df</span><span class="o">.</span><span class="n">rename</span><span class="p">(</span><span class="n">columns</span><span class="o">=</span><span class="p">{</span><span class="s2">"READ_CODE"</span><span class="p">:</span> <span class="s2">"read2"</span><span class="p">,</span> <span class="s2">"TARG_CODE"</span><span class="p">:</span> <span class="s2">"opcs4"</span><span class="p">})</span>
+</span><span id="extract_nhs_read_browser-275"><a href="#extract_nhs_read_browser-275"><span class="linenos">275</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">df</span><span class="p">[</span><span class="o">~</span><span class="n">df</span><span class="p">[</span><span class="s2">"opcs4"</span><span class="p">]</span><span class="o">.</span><span class="n">str</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="s2">"^.*-.*$"</span><span class="p">)]</span> <span class="c1"># remove codes with '-'</span>
+</span><span id="extract_nhs_read_browser-276"><a href="#extract_nhs_read_browser-276"><span class="linenos">276</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">df</span><span class="p">[</span><span class="o">~</span><span class="n">df</span><span class="p">[</span><span class="s2">"read2"</span><span class="p">]</span><span class="o">.</span><span class="n">str</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="s2">"^.*-.*$"</span><span class="p">)]</span> <span class="c1"># remove codes with '-'</span>
+</span><span id="extract_nhs_read_browser-277"><a href="#extract_nhs_read_browser-277"><span class="linenos">277</span></a> <span class="n">output_path</span> <span class="o">=</span> <span class="n">PROCESSED_PATH</span> <span class="o">/</span> <span class="s2">"read2_to_opcs4.parquet"</span>
+</span><span id="extract_nhs_read_browser-278"><a href="#extract_nhs_read_browser-278"><span class="linenos">278</span></a> <span class="n">df</span><span class="o">.</span><span class="n">to_parquet</span><span class="p">(</span><span class="n">output_path</span><span class="p">,</span> <span class="n">index</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span>
+</span><span id="extract_nhs_read_browser-279"><a href="#extract_nhs_read_browser-279"><span class="linenos">279</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Extracted: </span><span class="si">{</span><span class="n">output_path</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+</span><span id="extract_nhs_read_browser-280"><a href="#extract_nhs_read_browser-280"><span class="linenos">280</span></a>
+</span><span id="extract_nhs_read_browser-281"><a href="#extract_nhs_read_browser-281"><span class="linenos">281</span></a> <span class="c1"># r3 only</span>
+</span><span id="extract_nhs_read_browser-282"><a href="#extract_nhs_read_browser-282"><span class="linenos">282</span></a> <span class="n">input_path</span> <span class="o">=</span> <span class="n">DOWNLOADS_PATH</span> <span class="o">/</span> <span class="s2">"Standard"</span> <span class="o">/</span> <span class="s2">"V3"</span> <span class="o">/</span> <span class="s2">"ANCESTOR.DBF"</span>
+</span><span id="extract_nhs_read_browser-283"><a href="#extract_nhs_read_browser-283"><span class="linenos">283</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">simpledbf</span><span class="o">.</span><span class="n">Dbf5</span><span class="p">(</span><span class="n">input_path</span><span class="p">)</span><span class="o">.</span><span class="n">to_dataframe</span><span class="p">()</span>
+</span><span id="extract_nhs_read_browser-284"><a href="#extract_nhs_read_browser-284"><span class="linenos">284</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">concat</span><span class="p">([</span><span class="n">df</span><span class="p">[</span><span class="s2">"READCODE"</span><span class="p">],</span> <span class="n">df</span><span class="p">[</span><span class="s2">"DESCENDANT"</span><span class="p">]])</span>
+</span><span id="extract_nhs_read_browser-285"><a href="#extract_nhs_read_browser-285"><span class="linenos">285</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">(</span><span class="n">df</span><span class="o">.</span><span class="n">drop_duplicates</span><span class="p">())</span>
+</span><span id="extract_nhs_read_browser-286"><a href="#extract_nhs_read_browser-286"><span class="linenos">286</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">df</span><span class="o">.</span><span class="n">rename</span><span class="p">(</span><span class="n">columns</span><span class="o">=</span><span class="p">{</span><span class="mi">0</span><span class="p">:</span> <span class="s2">"read3"</span><span class="p">})</span>
+</span><span id="extract_nhs_read_browser-287"><a href="#extract_nhs_read_browser-287"><span class="linenos">287</span></a> <span class="n">output_path</span> <span class="o">=</span> <span class="n">PROCESSED_PATH</span> <span class="o">/</span> <span class="s2">"read3.parquet"</span>
+</span><span id="extract_nhs_read_browser-288"><a href="#extract_nhs_read_browser-288"><span class="linenos">288</span></a> <span class="n">df</span><span class="o">.</span><span class="n">to_parquet</span><span class="p">(</span><span class="n">output_path</span><span class="p">,</span> <span class="n">index</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span>
+</span><span id="extract_nhs_read_browser-289"><a href="#extract_nhs_read_browser-289"><span class="linenos">289</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Extracted: </span><span class="si">{</span><span class="n">output_path</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+</span><span id="extract_nhs_read_browser-290"><a href="#extract_nhs_read_browser-290"><span class="linenos">290</span></a>
+</span><span id="extract_nhs_read_browser-291"><a href="#extract_nhs_read_browser-291"><span class="linenos">291</span></a> <span class="c1"># r3 -> icd10</span>
+</span><span id="extract_nhs_read_browser-292"><a href="#extract_nhs_read_browser-292"><span class="linenos">292</span></a> <span class="n">input_path</span> <span class="o">=</span> <span class="n">DOWNLOADS_PATH</span> <span class="o">/</span> <span class="s2">"Standard"</span> <span class="o">/</span> <span class="s2">"V3"</span> <span class="o">/</span> <span class="s2">"ICD10.DBF"</span>
+</span><span id="extract_nhs_read_browser-293"><a href="#extract_nhs_read_browser-293"><span class="linenos">293</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">simpledbf</span><span class="o">.</span><span class="n">Dbf5</span><span class="p">(</span><span class="n">input_path</span><span class="p">)</span><span class="o">.</span><span class="n">to_dataframe</span><span class="p">()</span>
+</span><span id="extract_nhs_read_browser-294"><a href="#extract_nhs_read_browser-294"><span class="linenos">294</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">df</span><span class="p">[[</span><span class="s2">"READ_CODE"</span><span class="p">,</span> <span class="s2">"TARG_CODE"</span><span class="p">]]</span>
+</span><span id="extract_nhs_read_browser-295"><a href="#extract_nhs_read_browser-295"><span class="linenos">295</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">df</span><span class="o">.</span><span class="n">rename</span><span class="p">(</span><span class="n">columns</span><span class="o">=</span><span class="p">{</span><span class="s2">"READ_CODE"</span><span class="p">:</span> <span class="s2">"read3"</span><span class="p">,</span> <span class="s2">"TARG_CODE"</span><span class="p">:</span> <span class="s2">"icd10"</span><span class="p">})</span>
+</span><span id="extract_nhs_read_browser-296"><a href="#extract_nhs_read_browser-296"><span class="linenos">296</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">df</span><span class="p">[</span><span class="o">~</span><span class="n">df</span><span class="p">[</span><span class="s2">"icd10"</span><span class="p">]</span><span class="o">.</span><span class="n">str</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="s2">"^.*-.*$"</span><span class="p">)]</span> <span class="c1"># remove codes with '-'</span>
+</span><span id="extract_nhs_read_browser-297"><a href="#extract_nhs_read_browser-297"><span class="linenos">297</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">df</span><span class="p">[</span><span class="o">~</span><span class="n">df</span><span class="p">[</span><span class="s2">"read3"</span><span class="p">]</span><span class="o">.</span><span class="n">str</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="s2">"^.*-.*$"</span><span class="p">)]</span> <span class="c1"># remove codes with '-'</span>
+</span><span id="extract_nhs_read_browser-298"><a href="#extract_nhs_read_browser-298"><span class="linenos">298</span></a> <span class="n">output_path</span> <span class="o">=</span> <span class="n">PROCESSED_PATH</span> <span class="o">/</span> <span class="s2">"read3_to_icd10.parquet"</span>
+</span><span id="extract_nhs_read_browser-299"><a href="#extract_nhs_read_browser-299"><span class="linenos">299</span></a> <span class="n">df</span><span class="o">.</span><span class="n">to_parquet</span><span class="p">(</span><span class="n">output_path</span><span class="p">,</span> <span class="n">index</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span>
+</span><span id="extract_nhs_read_browser-300"><a href="#extract_nhs_read_browser-300"><span class="linenos">300</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Extracted: </span><span class="si">{</span><span class="n">output_path</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+</span><span id="extract_nhs_read_browser-301"><a href="#extract_nhs_read_browser-301"><span class="linenos">301</span></a>
+</span><span id="extract_nhs_read_browser-302"><a href="#extract_nhs_read_browser-302"><span class="linenos">302</span></a> <span class="c1"># r3 -> icd9</span>
+</span><span id="extract_nhs_read_browser-303"><a href="#extract_nhs_read_browser-303"><span class="linenos">303</span></a> <span class="c1"># dbf = simpledbf.Dbf5('build/maps/downloads/Standard/V3/ICD9V3.DBF')</span>
+</span><span id="extract_nhs_read_browser-304"><a href="#extract_nhs_read_browser-304"><span class="linenos">304</span></a>
+</span><span id="extract_nhs_read_browser-305"><a href="#extract_nhs_read_browser-305"><span class="linenos">305</span></a> <span class="c1"># r3 -> opcs4</span>
+</span><span id="extract_nhs_read_browser-306"><a href="#extract_nhs_read_browser-306"><span class="linenos">306</span></a> <span class="n">input_path</span> <span class="o">=</span> <span class="n">DOWNLOADS_PATH</span> <span class="o">/</span> <span class="s2">"Standard"</span> <span class="o">/</span> <span class="s2">"V3"</span> <span class="o">/</span> <span class="s2">"OPCS4V3.DBF"</span>
+</span><span id="extract_nhs_read_browser-307"><a href="#extract_nhs_read_browser-307"><span class="linenos">307</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">simpledbf</span><span class="o">.</span><span class="n">Dbf5</span><span class="p">(</span><span class="n">input_path</span><span class="p">)</span><span class="o">.</span><span class="n">to_dataframe</span><span class="p">()</span>
+</span><span id="extract_nhs_read_browser-308"><a href="#extract_nhs_read_browser-308"><span class="linenos">308</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">df</span><span class="p">[[</span><span class="s2">"READ_CODE"</span><span class="p">,</span> <span class="s2">"TARG_CODE"</span><span class="p">]]</span>
+</span><span id="extract_nhs_read_browser-309"><a href="#extract_nhs_read_browser-309"><span class="linenos">309</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">df</span><span class="o">.</span><span class="n">rename</span><span class="p">(</span><span class="n">columns</span><span class="o">=</span><span class="p">{</span><span class="s2">"READ_CODE"</span><span class="p">:</span> <span class="s2">"read3"</span><span class="p">,</span> <span class="s2">"TARG_CODE"</span><span class="p">:</span> <span class="s2">"opcs4"</span><span class="p">})</span>
+</span><span id="extract_nhs_read_browser-310"><a href="#extract_nhs_read_browser-310"><span class="linenos">310</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">df</span><span class="p">[</span><span class="o">~</span><span class="n">df</span><span class="p">[</span><span class="s2">"opcs4"</span><span class="p">]</span><span class="o">.</span><span class="n">str</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="s2">"^.*-.*$"</span><span class="p">)]</span> <span class="c1"># remove codes with '-'</span>
+</span><span id="extract_nhs_read_browser-311"><a href="#extract_nhs_read_browser-311"><span class="linenos">311</span></a> <span class="n">df</span> <span class="o">=</span> <span class="n">df</span><span class="p">[</span><span class="o">~</span><span class="n">df</span><span class="p">[</span><span class="s2">"read3"</span><span class="p">]</span><span class="o">.</span><span class="n">str</span><span class="o">.</span><span class="n">match</span><span class="p">(</span><span class="s2">"^.*-.*$"</span><span class="p">)]</span> <span class="c1"># remove codes with '-'</span>
+</span><span id="extract_nhs_read_browser-312"><a href="#extract_nhs_read_browser-312"><span class="linenos">312</span></a> <span class="n">output_path</span> <span class="o">=</span> <span class="n">PROCESSED_PATH</span> <span class="o">/</span> <span class="s2">"read3_to_opcs4.parquet"</span>
+</span><span id="extract_nhs_read_browser-313"><a href="#extract_nhs_read_browser-313"><span class="linenos">313</span></a> <span class="n">df</span><span class="o">.</span><span class="n">to_parquet</span><span class="p">(</span><span class="n">output_path</span><span class="p">,</span> <span class="n">index</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span>
+</span><span id="extract_nhs_read_browser-314"><a href="#extract_nhs_read_browser-314"><span class="linenos">314</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Extracted: </span><span class="si">{</span><span class="n">output_path</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+</span></pre></div>
+
+
+
+
+ </section>
+ <section id="create_map_directories">
+ <input id="create_map_directories-view-source" class="view-source-toggle-state" type="checkbox" aria-hidden="true" tabindex="-1">
+<div class="attr function">
+
+ <span class="def">def</span>
+ <span class="name">create_map_directories</span><span class="signature pdoc-code condensed">(<span class="return-annotation">):</span></span>
+
+ <label class="view-source-button" for="create_map_directories-view-source"><span>View Source</span></label>
+
+ </div>
+ <a class="headerlink" href="#create_map_directories"></a>
+ <div class="pdoc-code codehilite"><pre><span></span><span id="create_map_directories-317"><a href="#create_map_directories-317"><span class="linenos">317</span></a><span class="k">def</span><span class="w"> </span><span class="nf">create_map_directories</span><span class="p">():</span>
+</span><span id="create_map_directories-318"><a href="#create_map_directories-318"><span class="linenos">318</span></a><span class="w"> </span><span class="sd">"""Create map directories."""</span>
+</span><span id="create_map_directories-319"><a href="#create_map_directories-319"><span class="linenos">319</span></a>
+</span><span id="create_map_directories-320"><a href="#create_map_directories-320"><span class="linenos">320</span></a> <span class="c1"># Check if build directory exists</span>
+</span><span id="create_map_directories-321"><a href="#create_map_directories-321"><span class="linenos">321</span></a> <span class="n">create_map_dirs</span> <span class="o">=</span> <span class="kc">False</span>
+</span><span id="create_map_directories-322"><a href="#create_map_directories-322"><span class="linenos">322</span></a> <span class="k">if</span> <span class="n">VOCAB_PATH</span><span class="o">.</span><span class="n">exists</span><span class="p">():</span>
+</span><span id="create_map_directories-323"><a href="#create_map_directories-323"><span class="linenos">323</span></a> <span class="n">user_input</span> <span class="o">=</span> <span class="p">(</span>
+</span><span id="create_map_directories-324"><a href="#create_map_directories-324"><span class="linenos">324</span></a> <span class="nb">input</span><span class="p">(</span>
+</span><span id="create_map_directories-325"><a href="#create_map_directories-325"><span class="linenos">325</span></a> <span class="sa">f</span><span class="s2">"The map directory </span><span class="si">{</span><span class="n">VOCAB_PATH</span><span class="si">}</span><span class="s2"> already exists. Do you want to download and process trud data again? (y/n): "</span>
+</span><span id="create_map_directories-326"><a href="#create_map_directories-326"><span class="linenos">326</span></a> <span class="p">)</span>
+</span><span id="create_map_directories-327"><a href="#create_map_directories-327"><span class="linenos">327</span></a> <span class="o">.</span><span class="n">strip</span><span class="p">()</span>
+</span><span id="create_map_directories-328"><a href="#create_map_directories-328"><span class="linenos">328</span></a> <span class="o">.</span><span class="n">lower</span><span class="p">()</span>
+</span><span id="create_map_directories-329"><a href="#create_map_directories-329"><span class="linenos">329</span></a> <span class="p">)</span>
+</span><span id="create_map_directories-330"><a href="#create_map_directories-330"><span class="linenos">330</span></a> <span class="k">if</span> <span class="n">user_input</span> <span class="o">==</span> <span class="s2">"y"</span><span class="p">:</span>
+</span><span id="create_map_directories-331"><a href="#create_map_directories-331"><span class="linenos">331</span></a> <span class="c1"># delete all build files</span>
+</span><span id="create_map_directories-332"><a href="#create_map_directories-332"><span class="linenos">332</span></a> <span class="n">shutil</span><span class="o">.</span><span class="n">rmtree</span><span class="p">(</span><span class="n">VOCAB_PATH</span><span class="p">)</span>
+</span><span id="create_map_directories-333"><a href="#create_map_directories-333"><span class="linenos">333</span></a> <span class="n">create_map_dirs</span> <span class="o">=</span> <span class="kc">True</span>
+</span><span id="create_map_directories-334"><a href="#create_map_directories-334"><span class="linenos">334</span></a> <span class="k">elif</span> <span class="n">user_input</span> <span class="o">==</span> <span class="s2">"n"</span><span class="p">:</span>
+</span><span id="create_map_directories-335"><a href="#create_map_directories-335"><span class="linenos">335</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">"Exiting TRUD installation"</span><span class="p">)</span>
+</span><span id="create_map_directories-336"><a href="#create_map_directories-336"><span class="linenos">336</span></a> <span class="n">sys</span><span class="o">.</span><span class="n">exit</span><span class="p">(</span><span class="mi">0</span><span class="p">)</span>
+</span><span id="create_map_directories-337"><a href="#create_map_directories-337"><span class="linenos">337</span></a> <span class="k">else</span><span class="p">:</span>
+</span><span id="create_map_directories-338"><a href="#create_map_directories-338"><span class="linenos">338</span></a> <span class="n">create_map_dirs</span> <span class="o">=</span> <span class="kc">True</span>
+</span><span id="create_map_directories-339"><a href="#create_map_directories-339"><span class="linenos">339</span></a>
+</span><span id="create_map_directories-340"><a href="#create_map_directories-340"><span class="linenos">340</span></a> <span class="k">if</span> <span class="n">create_map_dirs</span><span class="p">:</span>
+</span><span id="create_map_directories-341"><a href="#create_map_directories-341"><span class="linenos">341</span></a> <span class="c1"># create maps directories</span>
+</span><span id="create_map_directories-342"><a href="#create_map_directories-342"><span class="linenos">342</span></a> <span class="n">VOCAB_PATH</span><span class="o">.</span><span class="n">mkdir</span><span class="p">(</span><span class="n">parents</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">exist_ok</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+</span><span id="create_map_directories-343"><a href="#create_map_directories-343"><span class="linenos">343</span></a> <span class="n">DOWNLOADS_PATH</span><span class="o">.</span><span class="n">mkdir</span><span class="p">(</span><span class="n">parents</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">exist_ok</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+</span><span id="create_map_directories-344"><a href="#create_map_directories-344"><span class="linenos">344</span></a> <span class="n">PROCESSED_PATH</span><span class="o">.</span><span class="n">mkdir</span><span class="p">(</span><span class="n">parents</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">exist_ok</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+</span></pre></div>
+
+
+ <div class="docstring"><p>Create map directories.</p>
+</div>
+
+
+ </section>
+ <section id="install">
+ <input id="install-view-source" class="view-source-toggle-state" type="checkbox" aria-hidden="true" tabindex="-1">
+<div class="attr function">
+
+ <span class="def">def</span>
+ <span class="name">install</span><span class="signature pdoc-code condensed">(<span class="return-annotation">):</span></span>
+
+ <label class="view-source-button" for="install-view-source"><span>View Source</span></label>
+
+ </div>
+ <a class="headerlink" href="#install"></a>
+ <div class="pdoc-code codehilite"><pre><span></span><span id="install-347"><a href="#install-347"><span class="linenos">347</span></a><span class="k">def</span><span class="w"> </span><span class="nf">install</span><span class="p">():</span>
+</span><span id="install-348"><a href="#install-348"><span class="linenos">348</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Installing TRUD"</span><span class="p">)</span>
+</span><span id="install-349"><a href="#install-349"><span class="linenos">349</span></a>
+</span><span id="install-350"><a href="#install-350"><span class="linenos">350</span></a> <span class="c1"># get TRUD api key from environment variable</span>
+</span><span id="install-351"><a href="#install-351"><span class="linenos">351</span></a> <span class="n">api_key</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">getenv</span><span class="p">(</span><span class="s2">"ACMC_TRUD_API_KEY"</span><span class="p">)</span>
+</span><span id="install-352"><a href="#install-352"><span class="linenos">352</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="n">api_key</span><span class="p">:</span>
+</span><span id="install-353"><a href="#install-353"><span class="linenos">353</span></a> <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span>
+</span><span id="install-354"><a href="#install-354"><span class="linenos">354</span></a> <span class="s2">"TRUD API KEY not found. Set the ACMC_TRUD_API_KEY environment variable."</span>
+</span><span id="install-355"><a href="#install-355"><span class="linenos">355</span></a> <span class="p">)</span>
+</span><span id="install-356"><a href="#install-356"><span class="linenos">356</span></a>
+</span><span id="install-357"><a href="#install-357"><span class="linenos">357</span></a> <span class="n">create_map_directories</span><span class="p">()</span>
+</span><span id="install-358"><a href="#install-358"><span class="linenos">358</span></a>
+</span><span id="install-359"><a href="#install-359"><span class="linenos">359</span></a> <span class="n">items_latest</span> <span class="o">=</span> <span class="kc">True</span>
+</span><span id="install-360"><a href="#install-360"><span class="linenos">360</span></a> <span class="n">items</span> <span class="o">=</span> <span class="p">[</span>
+</span><span id="install-361"><a href="#install-361"><span class="linenos">361</span></a> <span class="p">{</span>
+</span><span id="install-362"><a href="#install-362"><span class="linenos">362</span></a> <span class="s2">"id"</span><span class="p">:</span> <span class="mi">259</span><span class="p">,</span>
+</span><span id="install-363"><a href="#install-363"><span class="linenos">363</span></a> <span class="s2">"name"</span><span class="p">:</span> <span class="s2">"NHS ICD-10 5th Edition XML data files"</span><span class="p">,</span>
+</span><span id="install-364"><a href="#install-364"><span class="linenos">364</span></a> <span class="s2">"hash"</span><span class="p">:</span> <span class="s2">"A4F7BBA6E86349AADD0F4696C5E91152EB99CC06121427FC359160439B9F883F"</span><span class="p">,</span>
+</span><span id="install-365"><a href="#install-365"><span class="linenos">365</span></a> <span class="s2">"extract"</span><span class="p">:</span> <span class="n">extract_icd10</span><span class="p">,</span>
+</span><span id="install-366"><a href="#install-366"><span class="linenos">366</span></a> <span class="p">},</span>
+</span><span id="install-367"><a href="#install-367"><span class="linenos">367</span></a> <span class="p">{</span>
+</span><span id="install-368"><a href="#install-368"><span class="linenos">368</span></a> <span class="s2">"id"</span><span class="p">:</span> <span class="mi">119</span><span class="p">,</span>
+</span><span id="install-369"><a href="#install-369"><span class="linenos">369</span></a> <span class="s2">"name"</span><span class="p">:</span> <span class="s2">"OPCS-4 data files"</span><span class="p">,</span>
+</span><span id="install-370"><a href="#install-370"><span class="linenos">370</span></a> <span class="s2">"hash"</span><span class="p">:</span> <span class="s2">"0615A2BF43FFEF94517F1D1E0C05493B627839F323F22C52CBCD8B40BF767CD3"</span><span class="p">,</span>
+</span><span id="install-371"><a href="#install-371"><span class="linenos">371</span></a> <span class="s2">"extract"</span><span class="p">:</span> <span class="n">extract_opsc4</span><span class="p">,</span>
+</span><span id="install-372"><a href="#install-372"><span class="linenos">372</span></a> <span class="p">},</span>
+</span><span id="install-373"><a href="#install-373"><span class="linenos">373</span></a> <span class="p">{</span>
+</span><span id="install-374"><a href="#install-374"><span class="linenos">374</span></a> <span class="s2">"id"</span><span class="p">:</span> <span class="mi">9</span><span class="p">,</span>
+</span><span id="install-375"><a href="#install-375"><span class="linenos">375</span></a> <span class="s2">"name"</span><span class="p">:</span> <span class="s2">"NHS Data Migration"</span><span class="p">,</span>
+</span><span id="install-376"><a href="#install-376"><span class="linenos">376</span></a> <span class="s2">"hash"</span><span class="p">:</span> <span class="s2">"D4317B3ADBA6E1247CF17F0B7CD2B8850FD36C0EA2923BF684EA6159F3A54765"</span><span class="p">,</span>
+</span><span id="install-377"><a href="#install-377"><span class="linenos">377</span></a> <span class="s2">"extract"</span><span class="p">:</span> <span class="n">extract_nhs_data_migrations</span><span class="p">,</span>
+</span><span id="install-378"><a href="#install-378"><span class="linenos">378</span></a> <span class="p">},</span>
+</span><span id="install-379"><a href="#install-379"><span class="linenos">379</span></a> <span class="p">{</span>
+</span><span id="install-380"><a href="#install-380"><span class="linenos">380</span></a> <span class="s2">"id"</span><span class="p">:</span> <span class="mi">8</span><span class="p">,</span>
+</span><span id="install-381"><a href="#install-381"><span class="linenos">381</span></a> <span class="s2">"name"</span><span class="p">:</span> <span class="s2">"NHS Read Browser"</span><span class="p">,</span>
+</span><span id="install-382"><a href="#install-382"><span class="linenos">382</span></a> <span class="s2">"hash"</span><span class="p">:</span> <span class="s2">"1FFF2CBF11D0E6D7FC6CC6F13DD52D2F459095C3D83A3F754E6C359F16913C5E"</span><span class="p">,</span>
+</span><span id="install-383"><a href="#install-383"><span class="linenos">383</span></a> <span class="s2">"extract"</span><span class="p">:</span> <span class="n">extract_nhs_read_browser</span><span class="p">,</span>
+</span><span id="install-384"><a href="#install-384"><span class="linenos">384</span></a> <span class="p">},</span>
+</span><span id="install-385"><a href="#install-385"><span class="linenos">385</span></a> <span class="c1"># TODO: Download BNF from separate site? https://www.nhsbsa.nhs.uk/sites/default/files/2024-10/BNF%20Snomed%20Mapping%20data%2020241016.zip</span>
+</span><span id="install-386"><a href="#install-386"><span class="linenos">386</span></a> <span class="p">]</span>
+</span><span id="install-387"><a href="#install-387"><span class="linenos">387</span></a>
+</span><span id="install-388"><a href="#install-388"><span class="linenos">388</span></a> <span class="c1"># remove function from items to save versions</span>
+</span><span id="install-389"><a href="#install-389"><span class="linenos">389</span></a> <span class="n">data</span> <span class="o">=</span> <span class="p">[{</span><span class="n">k</span><span class="p">:</span> <span class="n">v</span> <span class="k">for</span> <span class="n">k</span><span class="p">,</span> <span class="n">v</span> <span class="ow">in</span> <span class="n">d</span><span class="o">.</span><span class="n">items</span><span class="p">()</span> <span class="k">if</span> <span class="n">k</span> <span class="o">!=</span> <span class="s2">"extract"</span><span class="p">}</span> <span class="k">for</span> <span class="n">d</span> <span class="ow">in</span> <span class="n">items</span><span class="p">]</span>
+</span><span id="install-390"><a href="#install-390"><span class="linenos">390</span></a> <span class="c1"># save TRUD versions to file to main record of what was downloaded</span>
+</span><span id="install-391"><a href="#install-391"><span class="linenos">391</span></a> <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">VERSION_PATH</span><span class="p">,</span> <span class="s2">"w"</span><span class="p">)</span> <span class="k">as</span> <span class="n">file</span><span class="p">:</span>
+</span><span id="install-392"><a href="#install-392"><span class="linenos">392</span></a> <span class="n">yaml</span><span class="o">.</span><span class="n">dump</span><span class="p">(</span>
+</span><span id="install-393"><a href="#install-393"><span class="linenos">393</span></a> <span class="n">data</span><span class="p">,</span>
+</span><span id="install-394"><a href="#install-394"><span class="linenos">394</span></a> <span class="n">file</span><span class="p">,</span>
+</span><span id="install-395"><a href="#install-395"><span class="linenos">395</span></a> <span class="n">Dumper</span><span class="o">=</span><span class="n">util</span><span class="o">.</span><span class="n">QuotedDumper</span><span class="p">,</span>
+</span><span id="install-396"><a href="#install-396"><span class="linenos">396</span></a> <span class="n">default_flow_style</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span>
+</span><span id="install-397"><a href="#install-397"><span class="linenos">397</span></a> <span class="n">sort_keys</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span>
+</span><span id="install-398"><a href="#install-398"><span class="linenos">398</span></a> <span class="n">default_style</span><span class="o">=</span><span class="s1">'"'</span><span class="p">,</span>
+</span><span id="install-399"><a href="#install-399"><span class="linenos">399</span></a> <span class="p">)</span>
+</span><span id="install-400"><a href="#install-400"><span class="linenos">400</span></a>
+</span><span id="install-401"><a href="#install-401"><span class="linenos">401</span></a> <span class="c1"># Validate and process each item ID</span>
+</span><span id="install-402"><a href="#install-402"><span class="linenos">402</span></a> <span class="k">for</span> <span class="n">item</span> <span class="ow">in</span> <span class="n">items</span><span class="p">:</span>
+</span><span id="install-403"><a href="#install-403"><span class="linenos">403</span></a> <span class="n">item_id</span> <span class="o">=</span> <span class="n">item</span><span class="p">[</span><span class="s2">"id"</span><span class="p">]</span>
+</span><span id="install-404"><a href="#install-404"><span class="linenos">404</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"--- </span><span class="si">{</span><span class="n">item</span><span class="p">[</span><span class="s1">'name'</span><span class="p">]</span><span class="si">}</span><span class="s2"> ---"</span><span class="p">)</span>
+</span><span id="install-405"><a href="#install-405"><span class="linenos">405</span></a>
+</span><span id="install-406"><a href="#install-406"><span class="linenos">406</span></a> <span class="n">releases</span> <span class="o">=</span> <span class="n">get_releases</span><span class="p">(</span><span class="n">item_id</span><span class="p">,</span> <span class="n">API_KEY</span><span class="o">=</span><span class="n">api_key</span><span class="p">,</span> <span class="n">latest</span><span class="o">=</span><span class="n">items_latest</span><span class="p">)</span>
+</span><span id="install-407"><a href="#install-407"><span class="linenos">407</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="n">releases</span><span class="p">:</span>
+</span><span id="install-408"><a href="#install-408"><span class="linenos">408</span></a> <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="sa">f</span><span class="s2">"No releases found for item </span><span class="si">{</span><span class="n">item_id</span><span class="si">}</span><span class="s2">."</span><span class="p">)</span>
+</span><span id="install-409"><a href="#install-409"><span class="linenos">409</span></a>
+</span><span id="install-410"><a href="#install-410"><span class="linenos">410</span></a> <span class="c1"># Process each release in reverse order</span>
+</span><span id="install-411"><a href="#install-411"><span class="linenos">411</span></a> <span class="k">for</span> <span class="n">release_ordinal</span><span class="p">,</span> <span class="n">release</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">releases</span><span class="p">[::</span><span class="o">-</span><span class="mi">1</span><span class="p">],</span> <span class="mi">1</span><span class="p">):</span>
+</span><span id="install-412"><a href="#install-412"><span class="linenos">412</span></a> <span class="c1"># Download archive file</span>
+</span><span id="install-413"><a href="#install-413"><span class="linenos">413</span></a> <span class="n">file_destination</span> <span class="o">=</span> <span class="n">download_release_file</span><span class="p">(</span>
+</span><span id="install-414"><a href="#install-414"><span class="linenos">414</span></a> <span class="n">item_id</span><span class="p">,</span> <span class="n">release_ordinal</span><span class="p">,</span> <span class="n">release</span><span class="p">,</span> <span class="s2">"archive"</span>
+</span><span id="install-415"><a href="#install-415"><span class="linenos">415</span></a> <span class="p">)</span>
+</span><span id="install-416"><a href="#install-416"><span class="linenos">416</span></a>
+</span><span id="install-417"><a href="#install-417"><span class="linenos">417</span></a> <span class="c1"># Optional files</span>
+</span><span id="install-418"><a href="#install-418"><span class="linenos">418</span></a> <span class="c1"># if items.checksum:</span>
+</span><span id="install-419"><a href="#install-419"><span class="linenos">419</span></a> <span class="c1"># download_release_file(item["id"], release_ordinal, release, "checksum")</span>
+</span><span id="install-420"><a href="#install-420"><span class="linenos">420</span></a> <span class="c1"># if items.signature:</span>
+</span><span id="install-421"><a href="#install-421"><span class="linenos">421</span></a> <span class="c1"># download_release_file(item["id"], release_ordinal, release, "signature")</span>
+</span><span id="install-422"><a href="#install-422"><span class="linenos">422</span></a> <span class="c1"># if items.public_key:</span>
+</span><span id="install-423"><a href="#install-423"><span class="linenos">423</span></a> <span class="c1"># download_release_file(item["id"], release_ordinal, release, "publicKey", "public key")</span>
+</span><span id="install-424"><a href="#install-424"><span class="linenos">424</span></a>
+</span><span id="install-425"><a href="#install-425"><span class="linenos">425</span></a> <span class="c1"># Verify Hash if available</span>
+</span><span id="install-426"><a href="#install-426"><span class="linenos">426</span></a> <span class="k">if</span> <span class="s2">"hash"</span> <span class="ow">in</span> <span class="n">item</span><span class="p">:</span>
+</span><span id="install-427"><a href="#install-427"><span class="linenos">427</span></a> <span class="n">validate_download_hash</span><span class="p">(</span><span class="n">file_destination</span><span class="p">,</span> <span class="n">item</span><span class="p">[</span><span class="s2">"hash"</span><span class="p">])</span>
+</span><span id="install-428"><a href="#install-428"><span class="linenos">428</span></a>
+</span><span id="install-429"><a href="#install-429"><span class="linenos">429</span></a> <span class="c1"># Unzip downloaded .zip</span>
+</span><span id="install-430"><a href="#install-430"><span class="linenos">430</span></a> <span class="n">unzip_download</span><span class="p">(</span><span class="n">file_destination</span><span class="p">)</span>
+</span><span id="install-431"><a href="#install-431"><span class="linenos">431</span></a>
+</span><span id="install-432"><a href="#install-432"><span class="linenos">432</span></a> <span class="c1"># Extract Tables to parquet</span>
+</span><span id="install-433"><a href="#install-433"><span class="linenos">433</span></a> <span class="k">if</span> <span class="s2">"extract"</span> <span class="ow">in</span> <span class="n">item</span><span class="p">:</span>
+</span><span id="install-434"><a href="#install-434"><span class="linenos">434</span></a> <span class="n">item</span><span class="p">[</span><span class="s2">"extract"</span><span class="p">]()</span>
+</span><span id="install-435"><a href="#install-435"><span class="linenos">435</span></a>
+</span><span id="install-436"><a href="#install-436"><span class="linenos">436</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Downloaded </span><span class="si">{</span><span class="n">release_ordinal</span><span class="si">}</span><span class="s2"> release(s) for item </span><span class="si">{</span><span class="n">item_id</span><span class="si">}</span><span class="s2">."</span><span class="p">)</span>
+</span><span id="install-437"><a href="#install-437"><span class="linenos">437</span></a>
+</span><span id="install-438"><a href="#install-438"><span class="linenos">438</span></a> <span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">"TRUD installation completed"</span><span class="p">)</span>
+</span></pre></div>
+
+
+
+
+ </section>
+ </main>
+<script>
+ function escapeHTML(html) {
+ return document.createElement('div').appendChild(document.createTextNode(html)).parentNode.innerHTML;
+ }
+
+ const originalContent = document.querySelector("main.pdoc");
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+
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+ elem.innerHTML = innerHTML;
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+ }
+
+ window.scrollTo({top: 0, left: 0, behavior: 'auto'});
+
+ const results = search(term);
+
+ let html;
+ if (results.length === 0) {
+ html = `No search results for '${escapeHTML(term)}'.`
+ } else {
+ html = `<h4>${results.length} search result${results.length > 1 ? "s" : ""} for '${escapeHTML(term)}'.</h4>`;
+ }
+ for (let result of results.slice(0, 10)) {
+ let doc = result.doc;
+ let url = `../${doc.modulename.replaceAll(".", "/")}.html`;
+ if (doc.qualname) {
+ url += `#${doc.qualname}`;
+ }
+
+ let heading;
+ switch (result.doc.kind) {
+ case "function":
+ if (doc.fullname.endsWith(".__init__")) {
+ heading = `<span class="name">${doc.fullname.replace(/\.__init__$/, "")}</span>${doc.signature}`;
+ } else {
+ heading = `<span class="def">${doc.funcdef}</span> <span class="name">${doc.fullname}</span>${doc.signature}`;
+ }
+ break;
+ case "class":
+ heading = `<span class="def">class</span> <span class="name">${doc.fullname}</span>`;
+ if (doc.bases)
+ heading += `<wbr>(<span class="base">${doc.bases}</span>)`;
+ heading += `:`;
+ break;
+ case "variable":
+ heading = `<span class="name">${doc.fullname}</span>`;
+ if (doc.annotation)
+ heading += `<span class="annotation">${doc.annotation}</span>`;
+ if (doc.default_value)
+ heading += `<span class="default_value"> = ${doc.default_value}</span>`;
+ break;
+ default:
+ heading = `<span class="name">${doc.fullname}</span>`;
+ break;
+ }
+ html += `
+ <section class="search-result">
+ <a href="${url}" class="attr ${doc.kind}">${heading}</a>
+ <div class="docstring">${doc.doc}</div>
+ </section>
+ `;
+
+ }
+ return html;
+ })());
+ }
+
+ if (getSearchTerm()) {
+ initialize();
+ searchBox.value = getSearchTerm();
+ onInput();
+ } else {
+ searchBox.addEventListener("focus", initialize, {once: true});
+ }
+
+ searchBox.addEventListener("keydown", e => {
+ if (["ArrowDown", "ArrowUp", "Enter"].includes(e.key)) {
+ let focused = currentContent.querySelector(".search-result.focused");
+ if (!focused) {
+ currentContent.querySelector(".search-result").classList.add("focused");
+ } else if (
+ e.key === "ArrowDown"
+ && focused.nextElementSibling
+ && focused.nextElementSibling.classList.contains("search-result")
+ ) {
+ focused.classList.remove("focused");
+ focused.nextElementSibling.classList.add("focused");
+ focused.nextElementSibling.scrollIntoView({
+ behavior: "smooth",
+ block: "nearest",
+ inline: "nearest"
+ });
+ } else if (
+ e.key === "ArrowUp"
+ && focused.previousElementSibling
+ && focused.previousElementSibling.classList.contains("search-result")
+ ) {
+ focused.classList.remove("focused");
+ focused.previousElementSibling.classList.add("focused");
+ focused.previousElementSibling.scrollIntoView({
+ behavior: "smooth",
+ block: "nearest",
+ inline: "nearest"
+ });
+ } else if (
+ e.key === "Enter"
+ ) {
+ focused.querySelector("a").click();
+ }
+ }
+ });
+</script></body>
+</html>
\ No newline at end of file
diff --git a/docs/api/acmc/util.html b/docs/api/acmc/util.html
new file mode 100644
index 0000000000000000000000000000000000000000..ade18c037e30f0b9e2a941d675b14a44ca14b009
--- /dev/null
+++ b/docs/api/acmc/util.html
@@ -0,0 +1,296 @@
+<!doctype html>
+<html lang="en">
+<head>
+ <meta charset="utf-8">
+ <meta name="viewport" content="width=device-width, initial-scale=1">
+ <meta name="generator" content="pdoc 15.0.1"/>
+ <title>acmc.util API documentation</title>
+
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+ </a>
+</div>
+ </nav>
+ <main class="pdoc">
+ <section class="module-info">
+ <h1 class="modulename">
+<a href="./../acmc.html">acmc</a><wbr>.util </h1>
+
+
+ <input id="mod-util-view-source" class="view-source-toggle-state" type="checkbox" aria-hidden="true" tabindex="-1">
+
+ <label class="view-source-button" for="mod-util-view-source"><span>View Source</span></label>
+
+ <div class="pdoc-code codehilite"><pre><span></span><span id="L-1"><a href="#L-1"><span class="linenos">1</span></a><span class="kn">import</span><span class="w"> </span><span class="nn">yaml</span>
+</span><span id="L-2"><a href="#L-2"><span class="linenos">2</span></a>
+</span><span id="L-3"><a href="#L-3"><span class="linenos">3</span></a>
+</span><span id="L-4"><a href="#L-4"><span class="linenos">4</span></a><span class="c1"># Custom Dumper to retain quotes on strings in yaml library</span>
+</span><span id="L-5"><a href="#L-5"><span class="linenos">5</span></a><span class="k">class</span><span class="w"> </span><span class="nc">QuotedDumper</span><span class="p">(</span><span class="n">yaml</span><span class="o">.</span><span class="n">Dumper</span><span class="p">):</span>
+</span><span id="L-6"><a href="#L-6"><span class="linenos">6</span></a> <span class="k">def</span><span class="w"> </span><span class="nf">increase_indent</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">flow</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span> <span class="n">indentless</span><span class="o">=</span><span class="kc">False</span><span class="p">):</span>
+</span><span id="L-7"><a href="#L-7"><span class="linenos">7</span></a> <span class="k">return</span> <span class="nb">super</span><span class="p">(</span><span class="n">QuotedDumper</span><span class="p">,</span> <span class="bp">self</span><span class="p">)</span><span class="o">.</span><span class="n">increase_indent</span><span class="p">(</span><span class="n">flow</span><span class="p">,</span> <span class="n">indentless</span><span class="p">)</span>
+</span></pre></div>
+
+
+ </section>
+ <section id="QuotedDumper">
+ <input id="QuotedDumper-view-source" class="view-source-toggle-state" type="checkbox" aria-hidden="true" tabindex="-1">
+<div class="attr class">
+
+ <span class="def">class</span>
+ <span class="name">QuotedDumper</span><wbr>(<span class="base">yaml.dumper.Dumper</span>):
+
+ <label class="view-source-button" for="QuotedDumper-view-source"><span>View Source</span></label>
+
+ </div>
+ <a class="headerlink" href="#QuotedDumper"></a>
+ <div class="pdoc-code codehilite"><pre><span></span><span id="QuotedDumper-6"><a href="#QuotedDumper-6"><span class="linenos">6</span></a><span class="k">class</span><span class="w"> </span><span class="nc">QuotedDumper</span><span class="p">(</span><span class="n">yaml</span><span class="o">.</span><span class="n">Dumper</span><span class="p">):</span>
+</span><span id="QuotedDumper-7"><a href="#QuotedDumper-7"><span class="linenos">7</span></a> <span class="k">def</span><span class="w"> </span><span class="nf">increase_indent</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">flow</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span> <span class="n">indentless</span><span class="o">=</span><span class="kc">False</span><span class="p">):</span>
+</span><span id="QuotedDumper-8"><a href="#QuotedDumper-8"><span class="linenos">8</span></a> <span class="k">return</span> <span class="nb">super</span><span class="p">(</span><span class="n">QuotedDumper</span><span class="p">,</span> <span class="bp">self</span><span class="p">)</span><span class="o">.</span><span class="n">increase_indent</span><span class="p">(</span><span class="n">flow</span><span class="p">,</span> <span class="n">indentless</span><span class="p">)</span>
+</span></pre></div>
+
+
+
+
+ <div id="QuotedDumper.increase_indent" class="classattr">
+ <input id="QuotedDumper.increase_indent-view-source" class="view-source-toggle-state" type="checkbox" aria-hidden="true" tabindex="-1">
+<div class="attr function">
+
+ <span class="def">def</span>
+ <span class="name">increase_indent</span><span class="signature pdoc-code condensed">(<span class="param"><span class="bp">self</span>, </span><span class="param"><span class="n">flow</span><span class="o">=</span><span class="kc">False</span>, </span><span class="param"><span class="n">indentless</span><span class="o">=</span><span class="kc">False</span></span><span class="return-annotation">):</span></span>
+
+ <label class="view-source-button" for="QuotedDumper.increase_indent-view-source"><span>View Source</span></label>
+
+ </div>
+ <a class="headerlink" href="#QuotedDumper.increase_indent"></a>
+ <div class="pdoc-code codehilite"><pre><span></span><span id="QuotedDumper.increase_indent-7"><a href="#QuotedDumper.increase_indent-7"><span class="linenos">7</span></a> <span class="k">def</span><span class="w"> </span><span class="nf">increase_indent</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">flow</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span> <span class="n">indentless</span><span class="o">=</span><span class="kc">False</span><span class="p">):</span>
+</span><span id="QuotedDumper.increase_indent-8"><a href="#QuotedDumper.increase_indent-8"><span class="linenos">8</span></a> <span class="k">return</span> <span class="nb">super</span><span class="p">(</span><span class="n">QuotedDumper</span><span class="p">,</span> <span class="bp">self</span><span class="p">)</span><span class="o">.</span><span class="n">increase_indent</span><span class="p">(</span><span class="n">flow</span><span class="p">,</span> <span class="n">indentless</span><span class="p">)</span>
+</span></pre></div>
+
+
+
+
+ </div>
+ </section>
+ </main>
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+ function escapeHTML(html) {
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+ const results = search(term);
+
+ let html;
+ if (results.length === 0) {
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+ html = `<h4>${results.length} search result${results.length > 1 ? "s" : ""} for '${escapeHTML(term)}'.</h4>`;
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+ heading += `<wbr>(<span class="base">${doc.bases}</span>)`;
+ heading += `:`;
+ break;
+ case "variable":
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+ if (doc.annotation)
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+ break;
+ default:
+ heading = `<span class="name">${doc.fullname}</span>`;
+ break;
+ }
+ html += `
+ <section class="search-result">
+ <a href="${url}" class="attr ${doc.kind}">${heading}</a>
+ <div class="docstring">${doc.doc}</div>
+ </section>
+ `;
+
+ }
+ return html;
+ })());
+ }
+
+ if (getSearchTerm()) {
+ initialize();
+ searchBox.value = getSearchTerm();
+ onInput();
+ } else {
+ searchBox.addEventListener("focus", initialize, {once: true});
+ }
+
+ searchBox.addEventListener("keydown", e => {
+ if (["ArrowDown", "ArrowUp", "Enter"].includes(e.key)) {
+ let focused = currentContent.querySelector(".search-result.focused");
+ if (!focused) {
+ currentContent.querySelector(".search-result").classList.add("focused");
+ } else if (
+ e.key === "ArrowDown"
+ && focused.nextElementSibling
+ && focused.nextElementSibling.classList.contains("search-result")
+ ) {
+ focused.classList.remove("focused");
+ focused.nextElementSibling.classList.add("focused");
+ focused.nextElementSibling.scrollIntoView({
+ behavior: "smooth",
+ block: "nearest",
+ inline: "nearest"
+ });
+ } else if (
+ e.key === "ArrowUp"
+ && focused.previousElementSibling
+ && focused.previousElementSibling.classList.contains("search-result")
+ ) {
+ focused.classList.remove("focused");
+ focused.previousElementSibling.classList.add("focused");
+ focused.previousElementSibling.scrollIntoView({
+ behavior: "smooth",
+ block: "nearest",
+ inline: "nearest"
+ });
+ } else if (
+ e.key === "Enter"
+ ) {
+ focused.querySelector("a").click();
+ }
+ }
+ });
+</script></body>
+</html>
\ No newline at end of file
diff --git a/docs/api/index.html b/docs/api/index.html
new file mode 100644
index 0000000000000000000000000000000000000000..566bd088aee2d892b13758267a4a298b7b6da730
--- /dev/null
+++ b/docs/api/index.html
@@ -0,0 +1,7 @@
+<!doctype html>
+<html>
+<head>
+ <meta charset="utf-8">
+ <meta http-equiv="refresh" content="0; url=./acmc.html"/>
+</head>
+</html>
diff --git a/docs/api/search.js b/docs/api/search.js
new file mode 100644
index 0000000000000000000000000000000000000000..cf931d57eb8f0fc27bc13bf332d9b5ac4e601bb8
--- /dev/null
+++ b/docs/api/search.js
@@ -0,0 +1,46 @@
+window.pdocSearch = (function(){
+/** elasticlunr - http://weixsong.github.io * Copyright (C) 2017 Oliver Nightingale * Copyright (C) 2017 Wei Song * MIT Licensed */!function(){function e(e){if(null===e||"object"!=typeof e)return e;var t=e.constructor();for(var n in e)e.hasOwnProperty(n)&&(t[n]=e[n]);return t}var t=function(e){var n=new t.Index;return n.pipeline.add(t.trimmer,t.stopWordFilter,t.stemmer),e&&e.call(n,n),n};t.version="0.9.5",lunr=t,t.utils={},t.utils.warn=function(e){return function(t){e.console&&console.warn&&console.warn(t)}}(this),t.utils.toString=function(e){return void 0===e||null===e?"":e.toString()},t.EventEmitter=function(){this.events={}},t.EventEmitter.prototype.addListener=function(){var e=Array.prototype.slice.call(arguments),t=e.pop(),n=e;if("function"!=typeof t)throw new TypeError("last argument must be a function");n.forEach(function(e){this.hasHandler(e)||(this.events[e]=[]),this.events[e].push(t)},this)},t.EventEmitter.prototype.removeListener=function(e,t){if(this.hasHandler(e)){var n=this.events[e].indexOf(t);-1!==n&&(this.events[e].splice(n,1),0==this.events[e].length&&delete this.events[e])}},t.EventEmitter.prototype.emit=function(e){if(this.hasHandler(e)){var t=Array.prototype.slice.call(arguments,1);this.events[e].forEach(function(e){e.apply(void 0,t)},this)}},t.EventEmitter.prototype.hasHandler=function(e){return e in this.events},t.tokenizer=function(e){if(!arguments.length||null===e||void 0===e)return[];if(Array.isArray(e)){var n=e.filter(function(e){return null===e||void 0===e?!1:!0});n=n.map(function(e){return t.utils.toString(e).toLowerCase()});var i=[];return n.forEach(function(e){var n=e.split(t.tokenizer.seperator);i=i.concat(n)},this),i}return e.toString().trim().toLowerCase().split(t.tokenizer.seperator)},t.tokenizer.defaultSeperator=/[\s\-]+/,t.tokenizer.seperator=t.tokenizer.defaultSeperator,t.tokenizer.setSeperator=function(e){null!==e&&void 0!==e&&"object"==typeof e&&(t.tokenizer.seperator=e)},t.tokenizer.resetSeperator=function(){t.tokenizer.seperator=t.tokenizer.defaultSeperator},t.tokenizer.getSeperator=function(){return t.tokenizer.seperator},t.Pipeline=function(){this._queue=[]},t.Pipeline.registeredFunctions={},t.Pipeline.registerFunction=function(e,n){n in t.Pipeline.registeredFunctions&&t.utils.warn("Overwriting existing registered function: "+n),e.label=n,t.Pipeline.registeredFunctions[n]=e},t.Pipeline.getRegisteredFunction=function(e){return e in t.Pipeline.registeredFunctions!=!0?null:t.Pipeline.registeredFunctions[e]},t.Pipeline.warnIfFunctionNotRegistered=function(e){var n=e.label&&e.label in this.registeredFunctions;n||t.utils.warn("Function is not registered with pipeline. This may cause problems when serialising the index.\n",e)},t.Pipeline.load=function(e){var n=new t.Pipeline;return e.forEach(function(e){var i=t.Pipeline.getRegisteredFunction(e);if(!i)throw new Error("Cannot load un-registered function: "+e);n.add(i)}),n},t.Pipeline.prototype.add=function(){var e=Array.prototype.slice.call(arguments);e.forEach(function(e){t.Pipeline.warnIfFunctionNotRegistered(e),this._queue.push(e)},this)},t.Pipeline.prototype.after=function(e,n){t.Pipeline.warnIfFunctionNotRegistered(n);var i=this._queue.indexOf(e);if(-1===i)throw new Error("Cannot find existingFn");this._queue.splice(i+1,0,n)},t.Pipeline.prototype.before=function(e,n){t.Pipeline.warnIfFunctionNotRegistered(n);var i=this._queue.indexOf(e);if(-1===i)throw new Error("Cannot find existingFn");this._queue.splice(i,0,n)},t.Pipeline.prototype.remove=function(e){var t=this._queue.indexOf(e);-1!==t&&this._queue.splice(t,1)},t.Pipeline.prototype.run=function(e){for(var t=[],n=e.length,i=this._queue.length,o=0;n>o;o++){for(var r=e[o],s=0;i>s&&(r=this._queue[s](r,o,e),void 0!==r&&null!==r);s++);void 0!==r&&null!==r&&t.push(r)}return t},t.Pipeline.prototype.reset=function(){this._queue=[]},t.Pipeline.prototype.get=function(){return this._queue},t.Pipeline.prototype.toJSON=function(){return this._queue.map(function(e){return t.Pipeline.warnIfFunctionNotRegistered(e),e.label})},t.Index=function(){this._fields=[],this._ref="id",this.pipeline=new t.Pipeline,this.documentStore=new t.DocumentStore,this.index={},this.eventEmitter=new t.EventEmitter,this._idfCache={},this.on("add","remove","update",function(){this._idfCache={}}.bind(this))},t.Index.prototype.on=function(){var e=Array.prototype.slice.call(arguments);return this.eventEmitter.addListener.apply(this.eventEmitter,e)},t.Index.prototype.off=function(e,t){return this.eventEmitter.removeListener(e,t)},t.Index.load=function(e){e.version!==t.version&&t.utils.warn("version mismatch: current "+t.version+" importing "+e.version);var n=new this;n._fields=e.fields,n._ref=e.ref,n.documentStore=t.DocumentStore.load(e.documentStore),n.pipeline=t.Pipeline.load(e.pipeline),n.index={};for(var i in e.index)n.index[i]=t.InvertedIndex.load(e.index[i]);return n},t.Index.prototype.addField=function(e){return this._fields.push(e),this.index[e]=new t.InvertedIndex,this},t.Index.prototype.setRef=function(e){return this._ref=e,this},t.Index.prototype.saveDocument=function(e){return this.documentStore=new t.DocumentStore(e),this},t.Index.prototype.addDoc=function(e,n){if(e){var n=void 0===n?!0:n,i=e[this._ref];this.documentStore.addDoc(i,e),this._fields.forEach(function(n){var o=this.pipeline.run(t.tokenizer(e[n]));this.documentStore.addFieldLength(i,n,o.length);var r={};o.forEach(function(e){e in r?r[e]+=1:r[e]=1},this);for(var s in r){var u=r[s];u=Math.sqrt(u),this.index[n].addToken(s,{ref:i,tf:u})}},this),n&&this.eventEmitter.emit("add",e,this)}},t.Index.prototype.removeDocByRef=function(e){if(e&&this.documentStore.isDocStored()!==!1&&this.documentStore.hasDoc(e)){var t=this.documentStore.getDoc(e);this.removeDoc(t,!1)}},t.Index.prototype.removeDoc=function(e,n){if(e){var n=void 0===n?!0:n,i=e[this._ref];this.documentStore.hasDoc(i)&&(this.documentStore.removeDoc(i),this._fields.forEach(function(n){var o=this.pipeline.run(t.tokenizer(e[n]));o.forEach(function(e){this.index[n].removeToken(e,i)},this)},this),n&&this.eventEmitter.emit("remove",e,this))}},t.Index.prototype.updateDoc=function(e,t){var t=void 0===t?!0:t;this.removeDocByRef(e[this._ref],!1),this.addDoc(e,!1),t&&this.eventEmitter.emit("update",e,this)},t.Index.prototype.idf=function(e,t){var n="@"+t+"/"+e;if(Object.prototype.hasOwnProperty.call(this._idfCache,n))return this._idfCache[n];var i=this.index[t].getDocFreq(e),o=1+Math.log(this.documentStore.length/(i+1));return this._idfCache[n]=o,o},t.Index.prototype.getFields=function(){return this._fields.slice()},t.Index.prototype.search=function(e,n){if(!e)return[];e="string"==typeof e?{any:e}:JSON.parse(JSON.stringify(e));var i=null;null!=n&&(i=JSON.stringify(n));for(var o=new t.Configuration(i,this.getFields()).get(),r={},s=Object.keys(e),u=0;u<s.length;u++){var a=s[u];r[a]=this.pipeline.run(t.tokenizer(e[a]))}var l={};for(var c in o){var d=r[c]||r.any;if(d){var f=this.fieldSearch(d,c,o),h=o[c].boost;for(var p in f)f[p]=f[p]*h;for(var p in f)p in l?l[p]+=f[p]:l[p]=f[p]}}var v,g=[];for(var p in l)v={ref:p,score:l[p]},this.documentStore.hasDoc(p)&&(v.doc=this.documentStore.getDoc(p)),g.push(v);return g.sort(function(e,t){return t.score-e.score}),g},t.Index.prototype.fieldSearch=function(e,t,n){var i=n[t].bool,o=n[t].expand,r=n[t].boost,s=null,u={};return 0!==r?(e.forEach(function(e){var n=[e];1==o&&(n=this.index[t].expandToken(e));var r={};n.forEach(function(n){var o=this.index[t].getDocs(n),a=this.idf(n,t);if(s&&"AND"==i){var l={};for(var c in s)c in o&&(l[c]=o[c]);o=l}n==e&&this.fieldSearchStats(u,n,o);for(var c in o){var d=this.index[t].getTermFrequency(n,c),f=this.documentStore.getFieldLength(c,t),h=1;0!=f&&(h=1/Math.sqrt(f));var p=1;n!=e&&(p=.15*(1-(n.length-e.length)/n.length));var v=d*a*h*p;c in r?r[c]+=v:r[c]=v}},this),s=this.mergeScores(s,r,i)},this),s=this.coordNorm(s,u,e.length)):void 0},t.Index.prototype.mergeScores=function(e,t,n){if(!e)return t;if("AND"==n){var i={};for(var o in t)o in e&&(i[o]=e[o]+t[o]);return i}for(var o in t)o in e?e[o]+=t[o]:e[o]=t[o];return e},t.Index.prototype.fieldSearchStats=function(e,t,n){for(var i in n)i in e?e[i].push(t):e[i]=[t]},t.Index.prototype.coordNorm=function(e,t,n){for(var i in e)if(i in t){var o=t[i].length;e[i]=e[i]*o/n}return e},t.Index.prototype.toJSON=function(){var e={};return this._fields.forEach(function(t){e[t]=this.index[t].toJSON()},this),{version:t.version,fields:this._fields,ref:this._ref,documentStore:this.documentStore.toJSON(),index:e,pipeline:this.pipeline.toJSON()}},t.Index.prototype.use=function(e){var t=Array.prototype.slice.call(arguments,1);t.unshift(this),e.apply(this,t)},t.DocumentStore=function(e){this._save=null===e||void 0===e?!0:e,this.docs={},this.docInfo={},this.length=0},t.DocumentStore.load=function(e){var t=new this;return t.length=e.length,t.docs=e.docs,t.docInfo=e.docInfo,t._save=e.save,t},t.DocumentStore.prototype.isDocStored=function(){return this._save},t.DocumentStore.prototype.addDoc=function(t,n){this.hasDoc(t)||this.length++,this.docs[t]=this._save===!0?e(n):null},t.DocumentStore.prototype.getDoc=function(e){return this.hasDoc(e)===!1?null:this.docs[e]},t.DocumentStore.prototype.hasDoc=function(e){return e in this.docs},t.DocumentStore.prototype.removeDoc=function(e){this.hasDoc(e)&&(delete this.docs[e],delete this.docInfo[e],this.length--)},t.DocumentStore.prototype.addFieldLength=function(e,t,n){null!==e&&void 0!==e&&0!=this.hasDoc(e)&&(this.docInfo[e]||(this.docInfo[e]={}),this.docInfo[e][t]=n)},t.DocumentStore.prototype.updateFieldLength=function(e,t,n){null!==e&&void 0!==e&&0!=this.hasDoc(e)&&this.addFieldLength(e,t,n)},t.DocumentStore.prototype.getFieldLength=function(e,t){return null===e||void 0===e?0:e in this.docs&&t in this.docInfo[e]?this.docInfo[e][t]:0},t.DocumentStore.prototype.toJSON=function(){return{docs:this.docs,docInfo:this.docInfo,length:this.length,save:this._save}},t.stemmer=function(){var e={ational:"ate",tional:"tion",enci:"ence",anci:"ance",izer:"ize",bli:"ble",alli:"al",entli:"ent",eli:"e",ousli:"ous",ization:"ize",ation:"ate",ator:"ate",alism:"al",iveness:"ive",fulness:"ful",ousness:"ous",aliti:"al",iviti:"ive",biliti:"ble",logi:"log"},t={icate:"ic",ative:"",alize:"al",iciti:"ic",ical:"ic",ful:"",ness:""},n="[^aeiou]",i="[aeiouy]",o=n+"[^aeiouy]*",r=i+"[aeiou]*",s="^("+o+")?"+r+o,u="^("+o+")?"+r+o+"("+r+")?$",a="^("+o+")?"+r+o+r+o,l="^("+o+")?"+i,c=new RegExp(s),d=new RegExp(a),f=new RegExp(u),h=new RegExp(l),p=/^(.+?)(ss|i)es$/,v=/^(.+?)([^s])s$/,g=/^(.+?)eed$/,m=/^(.+?)(ed|ing)$/,y=/.$/,S=/(at|bl|iz)$/,x=new RegExp("([^aeiouylsz])\\1$"),w=new RegExp("^"+o+i+"[^aeiouwxy]$"),I=/^(.+?[^aeiou])y$/,b=/^(.+?)(ational|tional|enci|anci|izer|bli|alli|entli|eli|ousli|ization|ation|ator|alism|iveness|fulness|ousness|aliti|iviti|biliti|logi)$/,E=/^(.+?)(icate|ative|alize|iciti|ical|ful|ness)$/,D=/^(.+?)(al|ance|ence|er|ic|able|ible|ant|ement|ment|ent|ou|ism|ate|iti|ous|ive|ize)$/,F=/^(.+?)(s|t)(ion)$/,_=/^(.+?)e$/,P=/ll$/,k=new RegExp("^"+o+i+"[^aeiouwxy]$"),z=function(n){var i,o,r,s,u,a,l;if(n.length<3)return n;if(r=n.substr(0,1),"y"==r&&(n=r.toUpperCase()+n.substr(1)),s=p,u=v,s.test(n)?n=n.replace(s,"$1$2"):u.test(n)&&(n=n.replace(u,"$1$2")),s=g,u=m,s.test(n)){var z=s.exec(n);s=c,s.test(z[1])&&(s=y,n=n.replace(s,""))}else if(u.test(n)){var z=u.exec(n);i=z[1],u=h,u.test(i)&&(n=i,u=S,a=x,l=w,u.test(n)?n+="e":a.test(n)?(s=y,n=n.replace(s,"")):l.test(n)&&(n+="e"))}if(s=I,s.test(n)){var z=s.exec(n);i=z[1],n=i+"i"}if(s=b,s.test(n)){var z=s.exec(n);i=z[1],o=z[2],s=c,s.test(i)&&(n=i+e[o])}if(s=E,s.test(n)){var z=s.exec(n);i=z[1],o=z[2],s=c,s.test(i)&&(n=i+t[o])}if(s=D,u=F,s.test(n)){var z=s.exec(n);i=z[1],s=d,s.test(i)&&(n=i)}else if(u.test(n)){var z=u.exec(n);i=z[1]+z[2],u=d,u.test(i)&&(n=i)}if(s=_,s.test(n)){var z=s.exec(n);i=z[1],s=d,u=f,a=k,(s.test(i)||u.test(i)&&!a.test(i))&&(n=i)}return s=P,u=d,s.test(n)&&u.test(n)&&(s=y,n=n.replace(s,"")),"y"==r&&(n=r.toLowerCase()+n.substr(1)),n};return z}(),t.Pipeline.registerFunction(t.stemmer,"stemmer"),t.stopWordFilter=function(e){return e&&t.stopWordFilter.stopWords[e]!==!0?e:void 0},t.clearStopWords=function(){t.stopWordFilter.stopWords={}},t.addStopWords=function(e){null!=e&&Array.isArray(e)!==!1&&e.forEach(function(e){t.stopWordFilter.stopWords[e]=!0},this)},t.resetStopWords=function(){t.stopWordFilter.stopWords=t.defaultStopWords},t.defaultStopWords={"":!0,a:!0,able:!0,about:!0,across:!0,after:!0,all:!0,almost:!0,also:!0,am:!0,among:!0,an:!0,and:!0,any:!0,are:!0,as:!0,at:!0,be:!0,because:!0,been:!0,but:!0,by:!0,can:!0,cannot:!0,could:!0,dear:!0,did:!0,"do":!0,does:!0,either:!0,"else":!0,ever:!0,every:!0,"for":!0,from:!0,get:!0,got:!0,had:!0,has:!0,have:!0,he:!0,her:!0,hers:!0,him:!0,his:!0,how:!0,however:!0,i:!0,"if":!0,"in":!0,into:!0,is:!0,it:!0,its:!0,just:!0,least:!0,let:!0,like:!0,likely:!0,may:!0,me:!0,might:!0,most:!0,must:!0,my:!0,neither:!0,no:!0,nor:!0,not:!0,of:!0,off:!0,often:!0,on:!0,only:!0,or:!0,other:!0,our:!0,own:!0,rather:!0,said:!0,say:!0,says:!0,she:!0,should:!0,since:!0,so:!0,some:!0,than:!0,that:!0,the:!0,their:!0,them:!0,then:!0,there:!0,these:!0,they:!0,"this":!0,tis:!0,to:!0,too:!0,twas:!0,us:!0,wants:!0,was:!0,we:!0,were:!0,what:!0,when:!0,where:!0,which:!0,"while":!0,who:!0,whom:!0,why:!0,will:!0,"with":!0,would:!0,yet:!0,you:!0,your:!0},t.stopWordFilter.stopWords=t.defaultStopWords,t.Pipeline.registerFunction(t.stopWordFilter,"stopWordFilter"),t.trimmer=function(e){if(null===e||void 0===e)throw new Error("token should not be undefined");return e.replace(/^\W+/,"").replace(/\W+$/,"")},t.Pipeline.registerFunction(t.trimmer,"trimmer"),t.InvertedIndex=function(){this.root={docs:{},df:0}},t.InvertedIndex.load=function(e){var t=new this;return t.root=e.root,t},t.InvertedIndex.prototype.addToken=function(e,t,n){for(var n=n||this.root,i=0;i<=e.length-1;){var o=e[i];o in n||(n[o]={docs:{},df:0}),i+=1,n=n[o]}var r=t.ref;n.docs[r]?n.docs[r]={tf:t.tf}:(n.docs[r]={tf:t.tf},n.df+=1)},t.InvertedIndex.prototype.hasToken=function(e){if(!e)return!1;for(var t=this.root,n=0;n<e.length;n++){if(!t[e[n]])return!1;t=t[e[n]]}return!0},t.InvertedIndex.prototype.getNode=function(e){if(!e)return null;for(var t=this.root,n=0;n<e.length;n++){if(!t[e[n]])return null;t=t[e[n]]}return t},t.InvertedIndex.prototype.getDocs=function(e){var t=this.getNode(e);return null==t?{}:t.docs},t.InvertedIndex.prototype.getTermFrequency=function(e,t){var n=this.getNode(e);return null==n?0:t in n.docs?n.docs[t].tf:0},t.InvertedIndex.prototype.getDocFreq=function(e){var t=this.getNode(e);return null==t?0:t.df},t.InvertedIndex.prototype.removeToken=function(e,t){if(e){var n=this.getNode(e);null!=n&&t in n.docs&&(delete n.docs[t],n.df-=1)}},t.InvertedIndex.prototype.expandToken=function(e,t,n){if(null==e||""==e)return[];var t=t||[];if(void 0==n&&(n=this.getNode(e),null==n))return t;n.df>0&&t.push(e);for(var i in n)"docs"!==i&&"df"!==i&&this.expandToken(e+i,t,n[i]);return t},t.InvertedIndex.prototype.toJSON=function(){return{root:this.root}},t.Configuration=function(e,n){var e=e||"";if(void 0==n||null==n)throw new Error("fields should not be null");this.config={};var i;try{i=JSON.parse(e),this.buildUserConfig(i,n)}catch(o){t.utils.warn("user configuration parse failed, will use default configuration"),this.buildDefaultConfig(n)}},t.Configuration.prototype.buildDefaultConfig=function(e){this.reset(),e.forEach(function(e){this.config[e]={boost:1,bool:"OR",expand:!1}},this)},t.Configuration.prototype.buildUserConfig=function(e,n){var i="OR",o=!1;if(this.reset(),"bool"in e&&(i=e.bool||i),"expand"in e&&(o=e.expand||o),"fields"in e)for(var r in e.fields)if(n.indexOf(r)>-1){var s=e.fields[r],u=o;void 0!=s.expand&&(u=s.expand),this.config[r]={boost:s.boost||0===s.boost?s.boost:1,bool:s.bool||i,expand:u}}else t.utils.warn("field name in user configuration not found in index instance fields");else this.addAllFields2UserConfig(i,o,n)},t.Configuration.prototype.addAllFields2UserConfig=function(e,t,n){n.forEach(function(n){this.config[n]={boost:1,bool:e,expand:t}},this)},t.Configuration.prototype.get=function(){return this.config},t.Configuration.prototype.reset=function(){this.config={}},lunr.SortedSet=function(){this.length=0,this.elements=[]},lunr.SortedSet.load=function(e){var t=new this;return t.elements=e,t.length=e.length,t},lunr.SortedSet.prototype.add=function(){var e,t;for(e=0;e<arguments.length;e++)t=arguments[e],~this.indexOf(t)||this.elements.splice(this.locationFor(t),0,t);this.length=this.elements.length},lunr.SortedSet.prototype.toArray=function(){return this.elements.slice()},lunr.SortedSet.prototype.map=function(e,t){return this.elements.map(e,t)},lunr.SortedSet.prototype.forEach=function(e,t){return this.elements.forEach(e,t)},lunr.SortedSet.prototype.indexOf=function(e){for(var t=0,n=this.elements.length,i=n-t,o=t+Math.floor(i/2),r=this.elements[o];i>1;){if(r===e)return o;e>r&&(t=o),r>e&&(n=o),i=n-t,o=t+Math.floor(i/2),r=this.elements[o]}return r===e?o:-1},lunr.SortedSet.prototype.locationFor=function(e){for(var t=0,n=this.elements.length,i=n-t,o=t+Math.floor(i/2),r=this.elements[o];i>1;)e>r&&(t=o),r>e&&(n=o),i=n-t,o=t+Math.floor(i/2),r=this.elements[o];return r>e?o:e>r?o+1:void 0},lunr.SortedSet.prototype.intersect=function(e){for(var t=new lunr.SortedSet,n=0,i=0,o=this.length,r=e.length,s=this.elements,u=e.elements;;){if(n>o-1||i>r-1)break;s[n]!==u[i]?s[n]<u[i]?n++:s[n]>u[i]&&i++:(t.add(s[n]),n++,i++)}return t},lunr.SortedSet.prototype.clone=function(){var e=new lunr.SortedSet;return e.elements=this.toArray(),e.length=e.elements.length,e},lunr.SortedSet.prototype.union=function(e){var t,n,i;this.length>=e.length?(t=this,n=e):(t=e,n=this),i=t.clone();for(var o=0,r=n.toArray();o<r.length;o++)i.add(r[o]);return i},lunr.SortedSet.prototype.toJSON=function(){return this.toArray()},function(e,t){"function"==typeof define&&define.amd?define(t):"object"==typeof exports?module.exports=t():e.elasticlunr=t()}(this,function(){return t})}();
+ /** pdoc search index */const docs = {"version": "0.9.5", "fields": ["qualname", "fullname", "annotation", "default_value", "signature", "bases", "doc"], "ref": "fullname", "documentStore": {"docs": {"acmc": {"fullname": "acmc", "modulename": "acmc", "kind": "module", "doc": "<p></p>\n"}, "acmc.logging_config": {"fullname": "acmc.logging_config", "modulename": "acmc.logging_config", "kind": "module", "doc": "<p></p>\n"}, "acmc.logging_config.DEFAULT_LOG_FILE": {"fullname": "acmc.logging_config.DEFAULT_LOG_FILE", "modulename": "acmc.logging_config", "qualname": "DEFAULT_LOG_FILE", "kind": "variable", "doc": "<p></p>\n", "default_value": "'acmc.log'"}, "acmc.logging_config.setup_logger": {"fullname": "acmc.logging_config.setup_logger", "modulename": "acmc.logging_config", "qualname": "setup_logger", "kind": "function", "doc": "<p>Sets up logger as a singleton outputing to file and sysout syserr</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">log_level</span><span class=\"p\">:</span> <span class=\"nb\">int</span> <span class=\"o\">=</span> <span class=\"mi\">20</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.logging_config.set_log_level": {"fullname": "acmc.logging_config.set_log_level", "modulename": "acmc.logging_config", "qualname": "set_log_level", "kind": "function", "doc": "<p>Sets the log level for the acmc logger</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">log_level</span><span class=\"p\">:</span> <span class=\"nb\">int</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.main": {"fullname": "acmc.main", "modulename": "acmc.main", "kind": "module", "doc": "<p></p>\n"}, "acmc.main.logger": {"fullname": "acmc.main.logger", "modulename": "acmc.main", "qualname": "logger", "kind": "variable", "doc": "<p></p>\n", "default_value": "<Logger acmc_logger (INFO)>"}, "acmc.main.DEFAULT_WORKSPACE_PATH": {"fullname": "acmc.main.DEFAULT_WORKSPACE_PATH", "modulename": "acmc.main", "qualname": "DEFAULT_WORKSPACE_PATH", "kind": "variable", "doc": "<p></p>\n", "default_value": "PosixPath('workspace')"}, "acmc.main.trud_install": {"fullname": "acmc.main.trud_install", "modulename": "acmc.main", "qualname": "trud_install", "kind": "function", "doc": "<p>Handle the <code>trud install</code> command.</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">args</span><span class=\"p\">:</span> <span class=\"n\">argparse</span><span class=\"o\">.</span><span class=\"n\">Namespace</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.main.omop_install": {"fullname": "acmc.main.omop_install", "modulename": "acmc.main", "qualname": "omop_install", "kind": "function", "doc": "<p>Handle the <code>omop install</code> command.</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">args</span><span class=\"p\">:</span> <span class=\"n\">argparse</span><span class=\"o\">.</span><span class=\"n\">Namespace</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.main.omop_clear": {"fullname": "acmc.main.omop_clear", "modulename": "acmc.main", "qualname": "omop_clear", "kind": "function", "doc": "<p>Handle the <code>omop clear</code> command.</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">args</span><span class=\"p\">:</span> <span class=\"n\">argparse</span><span class=\"o\">.</span><span class=\"n\">Namespace</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.main.omop_delete": {"fullname": "acmc.main.omop_delete", "modulename": "acmc.main", "qualname": "omop_delete", "kind": "function", "doc": "<p>Handle the <code>omop delete</code> command.</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">args</span><span class=\"p\">:</span> <span class=\"n\">argparse</span><span class=\"o\">.</span><span class=\"n\">Namespace</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.main.phen_init": {"fullname": "acmc.main.phen_init", "modulename": "acmc.main", "qualname": "phen_init", "kind": "function", "doc": "<p>Handle the <code>phen init</code> command.</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">args</span><span class=\"p\">:</span> <span class=\"n\">argparse</span><span class=\"o\">.</span><span class=\"n\">Namespace</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.main.phen_fork": {"fullname": "acmc.main.phen_fork", "modulename": "acmc.main", "qualname": "phen_fork", "kind": "function", "doc": "<p>Handle the <code>phen fork</code> command.</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">args</span><span class=\"p\">:</span> <span class=\"n\">argparse</span><span class=\"o\">.</span><span class=\"n\">Namespace</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.main.phen_validate": {"fullname": "acmc.main.phen_validate", "modulename": "acmc.main", "qualname": "phen_validate", "kind": "function", "doc": "<p>Handle the <code>phen validate</code> command.</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">args</span><span class=\"p\">:</span> <span class=\"n\">argparse</span><span class=\"o\">.</span><span class=\"n\">Namespace</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.main.phen_map": {"fullname": "acmc.main.phen_map", "modulename": "acmc.main", "qualname": "phen_map", "kind": "function", "doc": "<p>Handle the <code>phen map</code> command.</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">args</span><span class=\"p\">:</span> <span class=\"n\">argparse</span><span class=\"o\">.</span><span class=\"n\">Namespace</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.main.phen_export": {"fullname": "acmc.main.phen_export", "modulename": "acmc.main", "qualname": "phen_export", "kind": "function", "doc": "<p>Handle the <code>phen copy</code> command.</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">args</span><span class=\"p\">:</span> <span class=\"n\">argparse</span><span class=\"o\">.</span><span class=\"n\">Namespace</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.main.phen_publish": {"fullname": "acmc.main.phen_publish", "modulename": "acmc.main", "qualname": "phen_publish", "kind": "function", "doc": "<p>Handle the <code>phen publish</code> command.</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">args</span><span class=\"p\">:</span> <span class=\"n\">argparse</span><span class=\"o\">.</span><span class=\"n\">Namespace</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.main.phen_copy": {"fullname": "acmc.main.phen_copy", "modulename": "acmc.main", "qualname": "phen_copy", "kind": "function", "doc": "<p>Handle the <code>phen copy</code> command.</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">args</span><span class=\"p\">:</span> <span class=\"n\">argparse</span><span class=\"o\">.</span><span class=\"n\">Namespace</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.main.phen_diff": {"fullname": "acmc.main.phen_diff", "modulename": "acmc.main", "qualname": "phen_diff", "kind": "function", "doc": "<p>Handle the <code>phen diff</code> command.</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">args</span><span class=\"p\">:</span> <span class=\"n\">argparse</span><span class=\"o\">.</span><span class=\"n\">Namespace</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.main.main": {"fullname": "acmc.main.main", "modulename": "acmc.main", "qualname": "main", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.omop": {"fullname": "acmc.omop", "modulename": "acmc.omop", "kind": "module", "doc": "<p></p>\n"}, "acmc.omop.logger": {"fullname": "acmc.omop.logger", "modulename": "acmc.omop", "qualname": "logger", "kind": "variable", "doc": "<p></p>\n", "default_value": "<Logger acmc_logger (INFO)>"}, "acmc.omop.VOCAB_PATH": {"fullname": "acmc.omop.VOCAB_PATH", "modulename": "acmc.omop", "qualname": "VOCAB_PATH", "kind": "variable", "doc": "<p></p>\n", "default_value": "PosixPath('vocab/omop')"}, "acmc.omop.OMOP_CDM_Version": {"fullname": "acmc.omop.OMOP_CDM_Version", "modulename": "acmc.omop", "qualname": "OMOP_CDM_Version", "kind": "variable", "doc": "<p></p>\n", "default_value": "'54'"}, "acmc.omop.OMOP_DB_FILENAME": {"fullname": "acmc.omop.OMOP_DB_FILENAME", "modulename": "acmc.omop", "qualname": "OMOP_DB_FILENAME", "kind": "variable", "doc": "<p></p>\n", "default_value": "'omop_54.sqlite'"}, "acmc.omop.DB_PATH": {"fullname": "acmc.omop.DB_PATH", "modulename": "acmc.omop", "qualname": "DB_PATH", "kind": "variable", "doc": "<p></p>\n", "default_value": "PosixPath('vocab/omop/omop_54.sqlite')"}, "acmc.omop.VERSION_FILE": {"fullname": "acmc.omop.VERSION_FILE", "modulename": "acmc.omop", "qualname": "VERSION_FILE", "kind": "variable", "doc": "<p></p>\n", "default_value": "'omop_version.yaml'"}, "acmc.omop.VERSION_PATH": {"fullname": "acmc.omop.VERSION_PATH", "modulename": "acmc.omop", "qualname": "VERSION_PATH", "kind": "variable", "doc": "<p></p>\n", "default_value": "PosixPath('vocab/omop/omop_version.yaml')"}, "acmc.omop.EXPORT_FILE": {"fullname": "acmc.omop.EXPORT_FILE", "modulename": "acmc.omop", "qualname": "EXPORT_FILE", "kind": "variable", "doc": "<p></p>\n", "default_value": "'omop_54_export.sqlite'"}, "acmc.omop.vocabularies": {"fullname": "acmc.omop.vocabularies", "modulename": "acmc.omop", "qualname": "vocabularies", "kind": "variable", "doc": "<p></p>\n", "default_value": "{'source': 'OHDSI Athena', 'url': 'https://athena.ohdsi.org/vocabulary/list', 'cdm_version': '54', 'version': '', 'vocabularies': [{'id': 1, 'name': 'SNOMED'}, {'id': 2, 'name': 'ICD9CM'}, {'id': 17, 'name': 'Readv2'}, {'id': 21, 'name': 'ATC'}, {'id': 55, 'name': 'OPCS4'}, {'id': 57, 'name': 'HES Specialty'}, {'id': 70, 'name': 'ICD10CM'}, {'id': 75, 'name': 'dm+d'}, {'id': 144, 'name': 'UK Biobank'}, {'id': 154, 'name': 'NHS Ethnic Category'}, {'id': 155, 'name': 'NHS Place of Service'}], 'tables': []}"}, "acmc.omop.omop_vocab_types": {"fullname": "acmc.omop.omop_vocab_types", "modulename": "acmc.omop", "qualname": "omop_vocab_types", "kind": "variable", "doc": "<p></p>\n", "default_value": "{'read2': 'Read', 'read3': None, 'icd10': 'ICD10CM', 'snomed': 'SNOMED', 'opcs4': 'OPCS4', 'atc': 'ATC', 'med': None, 'cprd': None}"}, "acmc.omop.install": {"fullname": "acmc.omop.install", "modulename": "acmc.omop", "qualname": "install", "kind": "function", "doc": "<p>Installs the OMOP release csv files in a file-based sql database</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">omop_zip_file</span><span class=\"p\">:</span> <span class=\"nb\">str</span>, </span><span class=\"param\"><span class=\"n\">version</span><span class=\"p\">:</span> <span class=\"nb\">str</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.omop.write_version_file": {"fullname": "acmc.omop.write_version_file", "modulename": "acmc.omop", "qualname": "write_version_file", "kind": "function", "doc": "<p>Writes the OMOP vocaburaries and version to a file</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">version</span><span class=\"p\">:</span> <span class=\"nb\">str</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.omop.clear": {"fullname": "acmc.omop.clear", "modulename": "acmc.omop", "qualname": "clear", "kind": "function", "doc": "<p>Clears the OMOP sql database</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">db_path</span><span class=\"p\">:</span> <span class=\"n\">pathlib</span><span class=\"o\">.</span><span class=\"n\">Path</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.omop.delete": {"fullname": "acmc.omop.delete", "modulename": "acmc.omop", "qualname": "delete", "kind": "function", "doc": "<p>Deletes the OMOP sql database</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">db_path</span><span class=\"p\">:</span> <span class=\"n\">pathlib</span><span class=\"o\">.</span><span class=\"n\">Path</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.omop.table_exists": {"fullname": "acmc.omop.table_exists", "modulename": "acmc.omop", "qualname": "table_exists", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">cursor</span><span class=\"p\">:</span> <span class=\"n\">sqlite3</span><span class=\"o\">.</span><span class=\"n\">Cursor</span>, </span><span class=\"param\"><span class=\"n\">table_name</span><span class=\"p\">:</span> <span class=\"nb\">str</span></span><span class=\"return-annotation\">) -> <span class=\"nb\">bool</span>:</span></span>", "funcdef": "def"}, "acmc.omop.vocab_exists": {"fullname": "acmc.omop.vocab_exists", "modulename": "acmc.omop", "qualname": "vocab_exists", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">cursor</span><span class=\"p\">:</span> <span class=\"n\">sqlite3</span><span class=\"o\">.</span><span class=\"n\">Cursor</span>, </span><span class=\"param\"><span class=\"n\">vocab_id</span><span class=\"p\">:</span> <span class=\"nb\">str</span></span><span class=\"return-annotation\">) -> <span class=\"nb\">bool</span>:</span></span>", "funcdef": "def"}, "acmc.omop.concept_set_exist": {"fullname": "acmc.omop.concept_set_exist", "modulename": "acmc.omop", "qualname": "concept_set_exist", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">cursor</span><span class=\"p\">:</span> <span class=\"n\">sqlite3</span><span class=\"o\">.</span><span class=\"n\">Cursor</span>, </span><span class=\"param\"><span class=\"n\">concept_set_name</span><span class=\"p\">:</span> <span class=\"nb\">str</span></span><span class=\"return-annotation\">) -> <span class=\"nb\">bool</span>:</span></span>", "funcdef": "def"}, "acmc.omop.export": {"fullname": "acmc.omop.export", "modulename": "acmc.omop", "qualname": "export", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code multiline\">(<span class=\"param\">\t<span class=\"n\">map_path</span><span class=\"p\">:</span> <span class=\"n\">pathlib</span><span class=\"o\">.</span><span class=\"n\">Path</span>,</span><span class=\"param\">\t<span class=\"n\">export_path</span><span class=\"p\">:</span> <span class=\"n\">pathlib</span><span class=\"o\">.</span><span class=\"n\">Path</span>,</span><span class=\"param\">\t<span class=\"n\">version</span><span class=\"p\">:</span> <span class=\"nb\">str</span>,</span><span class=\"param\">\t<span class=\"n\">omop_metadata</span></span><span class=\"return-annotation\">) -> <span class=\"n\">pathlib</span><span class=\"o\">.</span><span class=\"n\">Path</span>:</span></span>", "funcdef": "def"}, "acmc.parse": {"fullname": "acmc.parse", "modulename": "acmc.parse", "kind": "module", "doc": "<p></p>\n"}, "acmc.parse.logger": {"fullname": "acmc.parse.logger", "modulename": "acmc.parse", "qualname": "logger", "kind": "variable", "doc": "<p></p>\n", "default_value": "<Logger acmc_logger (INFO)>"}, "acmc.parse.SUPPORTED_CODE_TYPES": {"fullname": "acmc.parse.SUPPORTED_CODE_TYPES", "modulename": "acmc.parse", "qualname": "SUPPORTED_CODE_TYPES", "kind": "variable", "doc": "<p></p>\n", "default_value": "{'opcs4', 'icd10', 'read3', 'snomed', 'read2', 'atc'}"}, "acmc.parse.CodesError": {"fullname": "acmc.parse.CodesError", "modulename": "acmc.parse", "qualname": "CodesError", "kind": "class", "doc": "<p>A class used in InvalidCodesException to report an error if a code parser check fails</p>\n"}, "acmc.parse.CodesError.__init__": {"fullname": "acmc.parse.CodesError.__init__", "modulename": "acmc.parse", "qualname": "CodesError.__init__", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">message</span>, </span><span class=\"param\"><span class=\"n\">codes</span><span class=\"o\">=</span><span class=\"kc\">None</span>, </span><span class=\"param\"><span class=\"n\">codes_file</span><span class=\"o\">=</span><span class=\"kc\">None</span>, </span><span class=\"param\"><span class=\"n\">mask</span><span class=\"o\">=</span><span class=\"kc\">None</span>, </span><span class=\"param\"><span class=\"n\">code_type</span><span class=\"o\">=</span><span class=\"kc\">None</span></span>)</span>"}, "acmc.parse.InvalidCodesException": {"fullname": "acmc.parse.InvalidCodesException", "modulename": "acmc.parse", "qualname": "InvalidCodesException", "kind": "class", "doc": "<p>Custom exception class raised when invalid codes are found that cannot be resolved by processing</p>\n", "bases": "builtins.Exception"}, "acmc.parse.InvalidCodesException.__init__": {"fullname": "acmc.parse.InvalidCodesException.__init__", "modulename": "acmc.parse", "qualname": "InvalidCodesException.__init__", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">error</span></span>)</span>"}, "acmc.parse.InvalidCodesException.error": {"fullname": "acmc.parse.InvalidCodesException.error", "modulename": "acmc.parse", "qualname": "InvalidCodesException.error", "kind": "variable", "doc": "<p></p>\n"}, "acmc.parse.Proto": {"fullname": "acmc.parse.Proto", "modulename": "acmc.parse", "qualname": "Proto", "kind": "class", "doc": "<p>Define checks as list of 3 tuple: (Message, Condition, Process)</p>\n\n<ul>\n<li>Message = The name of the condition (what is printed and logged)</li>\n<li>Condition = True if Passed, and False if Failed</li>\n<li>Process = Aims to resolve all issues that stop condition from passing (Do not change index!)</li>\n</ul>\n"}, "acmc.parse.Proto.__init__": {"fullname": "acmc.parse.Proto.__init__", "modulename": "acmc.parse", "qualname": "Proto.__init__", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">name</span><span class=\"p\">:</span> <span class=\"nb\">str</span>, </span><span class=\"param\"><span class=\"n\">trud_codes_path</span><span class=\"p\">:</span> <span class=\"n\">Optional</span><span class=\"p\">[</span><span class=\"n\">pathlib</span><span class=\"o\">.</span><span class=\"n\">Path</span><span class=\"p\">]</span> <span class=\"o\">=</span> <span class=\"kc\">None</span></span>)</span>"}, "acmc.parse.Proto.checks": {"fullname": "acmc.parse.Proto.checks", "modulename": "acmc.parse", "qualname": "Proto.checks", "kind": "variable", "doc": "<p></p>\n", "annotation": ": list[tuple[str, typing.Callable[[list], pandas.core.series.Series], typing.Callable[[list, pathlib.Path], NoneType]]]"}, "acmc.parse.Proto.name": {"fullname": "acmc.parse.Proto.name", "modulename": "acmc.parse", "qualname": "Proto.name", "kind": "variable", "doc": "<p></p>\n", "annotation": ": str"}, "acmc.parse.Proto.raise_exception": {"fullname": "acmc.parse.Proto.raise_exception", "modulename": "acmc.parse", "qualname": "Proto.raise_exception", "kind": "function", "doc": "<p>Raises an exception inside a lambda function. Python does not allow using raise statement inside lambda because lambda can only contain expressions, not statements. Using raise_exception not raise_ as it's more explict</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"bp\">self</span>, </span><span class=\"param\"><span class=\"n\">ex</span><span class=\"p\">:</span> <span class=\"ne\">Exception</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.parse.Proto.in_database": {"fullname": "acmc.parse.Proto.in_database", "modulename": "acmc.parse", "qualname": "Proto.in_database", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code multiline\">(<span class=\"param\">\t<span class=\"bp\">self</span>,</span><span class=\"param\">\t<span class=\"n\">codes</span><span class=\"p\">:</span> <span class=\"n\">pandas</span><span class=\"o\">.</span><span class=\"n\">core</span><span class=\"o\">.</span><span class=\"n\">frame</span><span class=\"o\">.</span><span class=\"n\">DataFrame</span>,</span><span class=\"param\">\t<span class=\"n\">db</span><span class=\"p\">:</span> <span class=\"n\">pandas</span><span class=\"o\">.</span><span class=\"n\">core</span><span class=\"o\">.</span><span class=\"n\">frame</span><span class=\"o\">.</span><span class=\"n\">DataFrame</span>,</span><span class=\"param\">\t<span class=\"n\">col</span><span class=\"p\">:</span> <span class=\"nb\">str</span></span><span class=\"return-annotation\">) -> <span class=\"n\">pandas</span><span class=\"o\">.</span><span class=\"n\">core</span><span class=\"o\">.</span><span class=\"n\">frame</span><span class=\"o\">.</span><span class=\"n\">DataFrame</span>:</span></span>", "funcdef": "def"}, "acmc.parse.Proto.process": {"fullname": "acmc.parse.Proto.process", "modulename": "acmc.parse", "qualname": "Proto.process", "kind": "function", "doc": "<p>identify issues that do not pass and fix them with define/d process</p>\n", "signature": "<span class=\"signature pdoc-code multiline\">(<span class=\"param\">\t<span class=\"bp\">self</span>,</span><span class=\"param\">\t<span class=\"n\">codes</span><span class=\"p\">:</span> <span class=\"n\">pandas</span><span class=\"o\">.</span><span class=\"n\">core</span><span class=\"o\">.</span><span class=\"n\">frame</span><span class=\"o\">.</span><span class=\"n\">DataFrame</span>,</span><span class=\"param\">\t<span class=\"n\">codes_file</span><span class=\"p\">:</span> <span class=\"n\">pathlib</span><span class=\"o\">.</span><span class=\"n\">Path</span></span><span class=\"return-annotation\">) -> <span class=\"n\">Tuple</span><span class=\"p\">[</span><span class=\"n\">pandas</span><span class=\"o\">.</span><span class=\"n\">core</span><span class=\"o\">.</span><span class=\"n\">frame</span><span class=\"o\">.</span><span class=\"n\">DataFrame</span><span class=\"p\">,</span> <span class=\"nb\">list</span><span class=\"p\">]</span>:</span></span>", "funcdef": "def"}, "acmc.parse.Proto.verify": {"fullname": "acmc.parse.Proto.verify", "modulename": "acmc.parse", "qualname": "Proto.verify", "kind": "function", "doc": "<p>verify codes in codes file</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"bp\">self</span>, </span><span class=\"param\"><span class=\"n\">codes</span><span class=\"p\">:</span> <span class=\"n\">pandas</span><span class=\"o\">.</span><span class=\"n\">core</span><span class=\"o\">.</span><span class=\"n\">frame</span><span class=\"o\">.</span><span class=\"n\">DataFrame</span>, </span><span class=\"param\"><span class=\"n\">codes_file</span><span class=\"p\">:</span> <span class=\"n\">pathlib</span><span class=\"o\">.</span><span class=\"n\">Path</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.parse.Read2": {"fullname": "acmc.parse.Read2", "modulename": "acmc.parse", "qualname": "Read2", "kind": "class", "doc": "<p>This Read2 class extends Proto, adding custom validation checks for a dataset of \"Read2\" codes. It ensures that the dataset is loaded, validates the codes based on several rules, and applies corrections or logs errors when necessary.</p>\n", "bases": "Proto"}, "acmc.parse.Read2.checks": {"fullname": "acmc.parse.Read2.checks", "modulename": "acmc.parse", "qualname": "Read2.checks", "kind": "variable", "doc": "<p></p>\n"}, "acmc.parse.Read3": {"fullname": "acmc.parse.Read3", "modulename": "acmc.parse", "qualname": "Read3", "kind": "class", "doc": "<p>Define checks as list of 3 tuple: (Message, Condition, Process)</p>\n\n<ul>\n<li>Message = The name of the condition (what is printed and logged)</li>\n<li>Condition = True if Passed, and False if Failed</li>\n<li>Process = Aims to resolve all issues that stop condition from passing (Do not change index!)</li>\n</ul>\n", "bases": "Proto"}, "acmc.parse.Read3.checks": {"fullname": "acmc.parse.Read3.checks", "modulename": "acmc.parse", "qualname": "Read3.checks", "kind": "variable", "doc": "<p></p>\n"}, "acmc.parse.Icd10": {"fullname": "acmc.parse.Icd10", "modulename": "acmc.parse", "qualname": "Icd10", "kind": "class", "doc": "<p>Define checks as list of 3 tuple: (Message, Condition, Process)</p>\n\n<ul>\n<li>Message = The name of the condition (what is printed and logged)</li>\n<li>Condition = True if Passed, and False if Failed</li>\n<li>Process = Aims to resolve all issues that stop condition from passing (Do not change index!)</li>\n</ul>\n", "bases": "Proto"}, "acmc.parse.Icd10.checks": {"fullname": "acmc.parse.Icd10.checks", "modulename": "acmc.parse", "qualname": "Icd10.checks", "kind": "variable", "doc": "<p></p>\n"}, "acmc.parse.Icd10.trim_icd10": {"fullname": "acmc.parse.Icd10.trim_icd10", "modulename": "acmc.parse", "qualname": "Icd10.trim_icd10", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">codes</span><span class=\"p\">:</span> <span class=\"n\">pandas</span><span class=\"o\">.</span><span class=\"n\">core</span><span class=\"o\">.</span><span class=\"n\">frame</span><span class=\"o\">.</span><span class=\"n\">DataFrame</span></span><span class=\"return-annotation\">) -> <span class=\"n\">pandas</span><span class=\"o\">.</span><span class=\"n\">core</span><span class=\"o\">.</span><span class=\"n\">frame</span><span class=\"o\">.</span><span class=\"n\">DataFrame</span>:</span></span>", "funcdef": "def"}, "acmc.parse.Snomed": {"fullname": "acmc.parse.Snomed", "modulename": "acmc.parse", "qualname": "Snomed", "kind": "class", "doc": "<p>Define checks as list of 3 tuple: (Message, Condition, Process)</p>\n\n<ul>\n<li>Message = The name of the condition (what is printed and logged)</li>\n<li>Condition = True if Passed, and False if Failed</li>\n<li>Process = Aims to resolve all issues that stop condition from passing (Do not change index!)</li>\n</ul>\n", "bases": "Proto"}, "acmc.parse.Snomed.checks": {"fullname": "acmc.parse.Snomed.checks", "modulename": "acmc.parse", "qualname": "Snomed.checks", "kind": "variable", "doc": "<p></p>\n"}, "acmc.parse.Opcs4": {"fullname": "acmc.parse.Opcs4", "modulename": "acmc.parse", "qualname": "Opcs4", "kind": "class", "doc": "<p>Define checks as list of 3 tuple: (Message, Condition, Process)</p>\n\n<ul>\n<li>Message = The name of the condition (what is printed and logged)</li>\n<li>Condition = True if Passed, and False if Failed</li>\n<li>Process = Aims to resolve all issues that stop condition from passing (Do not change index!)</li>\n</ul>\n", "bases": "Proto"}, "acmc.parse.Opcs4.checks": {"fullname": "acmc.parse.Opcs4.checks", "modulename": "acmc.parse", "qualname": "Opcs4.checks", "kind": "variable", "doc": "<p></p>\n"}, "acmc.parse.Atc": {"fullname": "acmc.parse.Atc", "modulename": "acmc.parse", "qualname": "Atc", "kind": "class", "doc": "<p>Define checks as list of 3 tuple: (Message, Condition, Process)</p>\n\n<ul>\n<li>Message = The name of the condition (what is printed and logged)</li>\n<li>Condition = True if Passed, and False if Failed</li>\n<li>Process = Aims to resolve all issues that stop condition from passing (Do not change index!)</li>\n</ul>\n", "bases": "Proto"}, "acmc.parse.Atc.checks": {"fullname": "acmc.parse.Atc.checks", "modulename": "acmc.parse", "qualname": "Atc.checks", "kind": "variable", "doc": "<p></p>\n"}, "acmc.parse.Med": {"fullname": "acmc.parse.Med", "modulename": "acmc.parse", "qualname": "Med", "kind": "class", "doc": "<p>Define checks as list of 3 tuple: (Message, Condition, Process)</p>\n\n<ul>\n<li>Message = The name of the condition (what is printed and logged)</li>\n<li>Condition = True if Passed, and False if Failed</li>\n<li>Process = Aims to resolve all issues that stop condition from passing (Do not change index!)</li>\n</ul>\n", "bases": "Proto"}, "acmc.parse.Med.checks": {"fullname": "acmc.parse.Med.checks", "modulename": "acmc.parse", "qualname": "Med.checks", "kind": "variable", "doc": "<p></p>\n"}, "acmc.parse.Cprd": {"fullname": "acmc.parse.Cprd", "modulename": "acmc.parse", "qualname": "Cprd", "kind": "class", "doc": "<p>Define checks as list of 3 tuple: (Message, Condition, Process)</p>\n\n<ul>\n<li>Message = The name of the condition (what is printed and logged)</li>\n<li>Condition = True if Passed, and False if Failed</li>\n<li>Process = Aims to resolve all issues that stop condition from passing (Do not change index!)</li>\n</ul>\n", "bases": "Proto"}, "acmc.parse.Cprd.checks": {"fullname": "acmc.parse.Cprd.checks", "modulename": "acmc.parse", "qualname": "Cprd.checks", "kind": "variable", "doc": "<p></p>\n"}, "acmc.parse.CodeTypeParser": {"fullname": "acmc.parse.CodeTypeParser", "modulename": "acmc.parse", "qualname": "CodeTypeParser", "kind": "class", "doc": "<p>A class used in InvalidCodesException to report an error if a code parser check fails</p>\n"}, "acmc.parse.CodeTypeParser.__init__": {"fullname": "acmc.parse.CodeTypeParser.__init__", "modulename": "acmc.parse", "qualname": "CodeTypeParser.__init__", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">trud_processed_dir</span><span class=\"p\">:</span> <span class=\"n\">pathlib</span><span class=\"o\">.</span><span class=\"n\">Path</span> <span class=\"o\">=</span> <span class=\"n\">PosixPath</span><span class=\"p\">(</span><span class=\"s1\">'vocab/trud/processed'</span><span class=\"p\">)</span></span>)</span>"}, "acmc.parse.CodeTypeParser.code_types": {"fullname": "acmc.parse.CodeTypeParser.code_types", "modulename": "acmc.parse", "qualname": "CodeTypeParser.code_types", "kind": "variable", "doc": "<p></p>\n"}, "acmc.phen": {"fullname": "acmc.phen", "modulename": "acmc.phen", "kind": "module", "doc": "<p></p>\n"}, "acmc.phen.logger": {"fullname": "acmc.phen.logger", "modulename": "acmc.phen", "qualname": "logger", "kind": "variable", "doc": "<p></p>\n", "default_value": "<Logger acmc_logger (INFO)>"}, "acmc.phen.PHEN_DIR": {"fullname": "acmc.phen.PHEN_DIR", "modulename": "acmc.phen", "qualname": "PHEN_DIR", "kind": "variable", "doc": "<p></p>\n", "default_value": "'phen'"}, "acmc.phen.DEFAULT_PHEN_PATH": {"fullname": "acmc.phen.DEFAULT_PHEN_PATH", "modulename": "acmc.phen", "qualname": "DEFAULT_PHEN_PATH", "kind": "variable", "doc": "<p></p>\n", "default_value": "PosixPath('workspace/phen')"}, "acmc.phen.CONCEPTS_DIR": {"fullname": "acmc.phen.CONCEPTS_DIR", "modulename": "acmc.phen", "qualname": "CONCEPTS_DIR", "kind": "variable", "doc": "<p></p>\n", "default_value": "'concepts'"}, "acmc.phen.MAP_DIR": {"fullname": "acmc.phen.MAP_DIR", "modulename": "acmc.phen", "qualname": "MAP_DIR", "kind": "variable", "doc": "<p></p>\n", "default_value": "'map'"}, "acmc.phen.CONCEPT_SET_DIR": {"fullname": "acmc.phen.CONCEPT_SET_DIR", "modulename": "acmc.phen", "qualname": "CONCEPT_SET_DIR", "kind": "variable", "doc": "<p></p>\n", "default_value": "'concept-sets'"}, "acmc.phen.CSV_PATH": {"fullname": "acmc.phen.CSV_PATH", "modulename": "acmc.phen", "qualname": "CSV_PATH", "kind": "variable", "doc": "<p></p>\n", "default_value": "PosixPath('concept-sets/csv')"}, "acmc.phen.OMOP_PATH": {"fullname": "acmc.phen.OMOP_PATH", "modulename": "acmc.phen", "qualname": "OMOP_PATH", "kind": "variable", "doc": "<p></p>\n", "default_value": "PosixPath('concept-sets/omop')"}, "acmc.phen.DEFAULT_PHEN_DIR_LIST": {"fullname": "acmc.phen.DEFAULT_PHEN_DIR_LIST", "modulename": "acmc.phen", "qualname": "DEFAULT_PHEN_DIR_LIST", "kind": "variable", "doc": "<p></p>\n", "default_value": "['concepts', 'map', 'concept-sets']"}, "acmc.phen.CONFIG_FILE": {"fullname": "acmc.phen.CONFIG_FILE", "modulename": "acmc.phen", "qualname": "CONFIG_FILE", "kind": "variable", "doc": "<p></p>\n", "default_value": "'config.yaml'"}, "acmc.phen.VOCAB_VERSION_FILE": {"fullname": "acmc.phen.VOCAB_VERSION_FILE", "modulename": "acmc.phen", "qualname": "VOCAB_VERSION_FILE", "kind": "variable", "doc": "<p></p>\n", "default_value": "'vocab_version.yaml'"}, "acmc.phen.SEMANTIC_VERSION_TYPES": {"fullname": "acmc.phen.SEMANTIC_VERSION_TYPES", "modulename": "acmc.phen", "qualname": "SEMANTIC_VERSION_TYPES", "kind": "variable", "doc": "<p></p>\n", "default_value": "['major', 'minor', 'patch']"}, "acmc.phen.DEFAULT_VERSION_INC": {"fullname": "acmc.phen.DEFAULT_VERSION_INC", "modulename": "acmc.phen", "qualname": "DEFAULT_VERSION_INC", "kind": "variable", "doc": "<p></p>\n", "default_value": "'patch'"}, "acmc.phen.DEFAULT_GIT_BRANCH": {"fullname": "acmc.phen.DEFAULT_GIT_BRANCH", "modulename": "acmc.phen", "qualname": "DEFAULT_GIT_BRANCH", "kind": "variable", "doc": "<p></p>\n", "default_value": "'main'"}, "acmc.phen.SPLIT_COL_ACTION": {"fullname": "acmc.phen.SPLIT_COL_ACTION", "modulename": "acmc.phen", "qualname": "SPLIT_COL_ACTION", "kind": "variable", "doc": "<p></p>\n", "default_value": "'split_col'"}, "acmc.phen.CODES_COL_ACTION": {"fullname": "acmc.phen.CODES_COL_ACTION", "modulename": "acmc.phen", "qualname": "CODES_COL_ACTION", "kind": "variable", "doc": "<p></p>\n", "default_value": "'codes_col'"}, "acmc.phen.DIVIDE_COL_ACTION": {"fullname": "acmc.phen.DIVIDE_COL_ACTION", "modulename": "acmc.phen", "qualname": "DIVIDE_COL_ACTION", "kind": "variable", "doc": "<p></p>\n", "default_value": "'divide_col'"}, "acmc.phen.COL_ACTIONS": {"fullname": "acmc.phen.COL_ACTIONS", "modulename": "acmc.phen", "qualname": "COL_ACTIONS", "kind": "variable", "doc": "<p></p>\n", "default_value": "['split_col', 'codes_col', 'divide_col']"}, "acmc.phen.CODE_FILE_TYPES": {"fullname": "acmc.phen.CODE_FILE_TYPES", "modulename": "acmc.phen", "qualname": "CODE_FILE_TYPES", "kind": "variable", "doc": "<p></p>\n", "default_value": "['.xlsx', '.xls', '.csv']"}, "acmc.phen.SOURCE_COL_SUFFIX": {"fullname": "acmc.phen.SOURCE_COL_SUFFIX", "modulename": "acmc.phen", "qualname": "SOURCE_COL_SUFFIX", "kind": "variable", "doc": "<p></p>\n", "default_value": "'_acmc_source'"}, "acmc.phen.TARGET_COL_SUFFIX": {"fullname": "acmc.phen.TARGET_COL_SUFFIX", "modulename": "acmc.phen", "qualname": "TARGET_COL_SUFFIX", "kind": "variable", "doc": "<p></p>\n", "default_value": "'_acmc_target'"}, "acmc.phen.CONFIG_SCHEMA": {"fullname": "acmc.phen.CONFIG_SCHEMA", "modulename": "acmc.phen", "qualname": "CONFIG_SCHEMA", "kind": "variable", "doc": "<p></p>\n", "default_value": "{'phenotype': {'type': 'dict', 'required': True, 'schema': {'version': {'type': 'string', 'required': True, 'regex': '^\\\\d+\\\\.\\\\d+\\\\.\\\\d+$'}, 'omop': {'type': 'dict', 'required': True, 'schema': {'vocabulary_id': {'type': 'string', 'required': True}, 'vocabulary_name': {'type': 'string', 'required': True}, 'vocabulary_reference': {'type': 'string', 'required': True, 'regex': '^https?://.*'}}}, 'map': {'type': 'list', 'schema': {'type': 'string', 'allowed': ['opcs4', 'icd10', 'read3', 'snomed', 'read2', 'atc']}}, 'concept_sets': {'type': 'list', 'required': True, 'schema': {'type': 'dict', 'schema': {'name': {'type': 'string', 'required': True}, 'file': {'type': 'dict', 'required': False, 'schema': {'path': {'type': 'string', 'required': True}, 'columns': {'type': 'dict', 'required': True}, 'category': {'type': 'string'}, 'actions': {'type': 'dict', 'schema': {'divide_col': {'type': 'string'}}}}}, 'metadata': {'type': 'dict', 'required': True}}}}}}}"}, "acmc.phen.PhenValidationException": {"fullname": "acmc.phen.PhenValidationException", "modulename": "acmc.phen", "qualname": "PhenValidationException", "kind": "class", "doc": "<p>Custom exception class raised when validation errors in phenotype configuration file</p>\n", "bases": "builtins.Exception"}, "acmc.phen.PhenValidationException.__init__": {"fullname": "acmc.phen.PhenValidationException.__init__", "modulename": "acmc.phen", "qualname": "PhenValidationException.__init__", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">message</span>, </span><span class=\"param\"><span class=\"n\">validation_errors</span><span class=\"o\">=</span><span class=\"kc\">None</span></span>)</span>"}, "acmc.phen.PhenValidationException.validation_errors": {"fullname": "acmc.phen.PhenValidationException.validation_errors", "modulename": "acmc.phen", "qualname": "PhenValidationException.validation_errors", "kind": "variable", "doc": "<p></p>\n"}, "acmc.phen.construct_git_url": {"fullname": "acmc.phen.construct_git_url", "modulename": "acmc.phen", "qualname": "construct_git_url", "kind": "function", "doc": "<p>Constructs a git url for github or gitlab including a PAT token environment variable</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">remote_url</span><span class=\"p\">:</span> <span class=\"nb\">str</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.phen.create_empty_git_dir": {"fullname": "acmc.phen.create_empty_git_dir", "modulename": "acmc.phen", "qualname": "create_empty_git_dir", "kind": "function", "doc": "<p>Creates a directory with a .gitkeep file so that it's tracked in git</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">path</span><span class=\"p\">:</span> <span class=\"n\">pathlib</span><span class=\"o\">.</span><span class=\"n\">Path</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.phen.check_delete_dir": {"fullname": "acmc.phen.check_delete_dir", "modulename": "acmc.phen", "qualname": "check_delete_dir", "kind": "function", "doc": "<p>Checks on the command line if a user wants to delete a directory</p>\n\n<p>Args:\n path (Path): path of the directory to be deleted\n msg (str): message to be displayed to the user</p>\n\n<p>Returns:\n Boolean: True if deleted</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">path</span><span class=\"p\">:</span> <span class=\"n\">pathlib</span><span class=\"o\">.</span><span class=\"n\">Path</span>, </span><span class=\"param\"><span class=\"n\">msg</span><span class=\"p\">:</span> <span class=\"nb\">str</span></span><span class=\"return-annotation\">) -> <span class=\"nb\">bool</span>:</span></span>", "funcdef": "def"}, "acmc.phen.fork": {"fullname": "acmc.phen.fork", "modulename": "acmc.phen", "qualname": "fork", "kind": "function", "doc": "<p>Forks an upstream phenotype in a remote repo at a specific version to a local director, and optionally sets to a new remote origin\"</p>\n\n<p>Args:\n phen_dir (str): local directory path where the upstream repo is to be cloned\n upstream_url (str): url to the upstream repo\n upstream_version (str): version in the upstream repo to clone\n new_origin_url (str, optional): url of the remote repo to set as the new origin. Defaults to None.</p>\n\n<p>Raises:\n ValueError: if the specified version is not in the upstream repo\n ValueError: if the upstream repo is not a valid phenotype repo\n ValueError: if there's any other problems with Git</p>\n", "signature": "<span class=\"signature pdoc-code multiline\">(<span class=\"param\">\t<span class=\"n\">phen_dir</span><span class=\"p\">:</span> <span class=\"nb\">str</span>,</span><span class=\"param\">\t<span class=\"n\">upstream_url</span><span class=\"p\">:</span> <span class=\"nb\">str</span>,</span><span class=\"param\">\t<span class=\"n\">upstream_version</span><span class=\"p\">:</span> <span class=\"nb\">str</span>,</span><span class=\"param\">\t<span class=\"n\">new_origin_url</span><span class=\"p\">:</span> <span class=\"nb\">str</span> <span class=\"o\">=</span> <span class=\"kc\">None</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.phen.init": {"fullname": "acmc.phen.init", "modulename": "acmc.phen", "qualname": "init", "kind": "function", "doc": "<p>Initial phenotype directory as git repo with standard structure</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">phen_dir</span><span class=\"p\">:</span> <span class=\"nb\">str</span>, </span><span class=\"param\"><span class=\"n\">remote_url</span><span class=\"p\">:</span> <span class=\"nb\">str</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.phen.validate": {"fullname": "acmc.phen.validate", "modulename": "acmc.phen", "qualname": "validate", "kind": "function", "doc": "<p>Validates the phenotype directory is a git repo with standard structure</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">phen_dir</span><span class=\"p\">:</span> <span class=\"nb\">str</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.phen.read_table_file": {"fullname": "acmc.phen.read_table_file", "modulename": "acmc.phen", "qualname": "read_table_file", "kind": "function", "doc": "<p>Load Code List File</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">path</span><span class=\"p\">:</span> <span class=\"n\">pathlib</span><span class=\"o\">.</span><span class=\"n\">Path</span>, </span><span class=\"param\"><span class=\"n\">excel_sheet</span><span class=\"p\">:</span> <span class=\"nb\">str</span> <span class=\"o\">=</span> <span class=\"s1\">''</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.phen.process_actions": {"fullname": "acmc.phen.process_actions", "modulename": "acmc.phen", "qualname": "process_actions", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code multiline\">(<span class=\"param\">\t<span class=\"n\">df</span><span class=\"p\">:</span> <span class=\"n\">pandas</span><span class=\"o\">.</span><span class=\"n\">core</span><span class=\"o\">.</span><span class=\"n\">frame</span><span class=\"o\">.</span><span class=\"n\">DataFrame</span>,</span><span class=\"param\">\t<span class=\"n\">concept_set</span><span class=\"p\">:</span> <span class=\"nb\">dict</span></span><span class=\"return-annotation\">) -> <span class=\"n\">pandas</span><span class=\"o\">.</span><span class=\"n\">core</span><span class=\"o\">.</span><span class=\"n\">frame</span><span class=\"o\">.</span><span class=\"n\">DataFrame</span>:</span></span>", "funcdef": "def"}, "acmc.phen.preprocess_source_concepts": {"fullname": "acmc.phen.preprocess_source_concepts", "modulename": "acmc.phen", "qualname": "preprocess_source_concepts", "kind": "function", "doc": "<p>Parses each column individually - Order and length will not be preserved!</p>\n", "signature": "<span class=\"signature pdoc-code multiline\">(<span class=\"param\">\t<span class=\"n\">df</span><span class=\"p\">:</span> <span class=\"n\">pandas</span><span class=\"o\">.</span><span class=\"n\">core</span><span class=\"o\">.</span><span class=\"n\">frame</span><span class=\"o\">.</span><span class=\"n\">DataFrame</span>,</span><span class=\"param\">\t<span class=\"n\">concept_set</span><span class=\"p\">:</span> <span class=\"nb\">dict</span>,</span><span class=\"param\">\t<span class=\"n\">code_file_path</span><span class=\"p\">:</span> <span class=\"n\">pathlib</span><span class=\"o\">.</span><span class=\"n\">Path</span></span><span class=\"return-annotation\">) -> <span class=\"n\">Tuple</span><span class=\"p\">[</span><span class=\"n\">pandas</span><span class=\"o\">.</span><span class=\"n\">core</span><span class=\"o\">.</span><span class=\"n\">frame</span><span class=\"o\">.</span><span class=\"n\">DataFrame</span><span class=\"p\">,</span> <span class=\"nb\">list</span><span class=\"p\">]</span>:</span></span>", "funcdef": "def"}, "acmc.phen.get_code_type_from_col_name": {"fullname": "acmc.phen.get_code_type_from_col_name", "modulename": "acmc.phen", "qualname": "get_code_type_from_col_name", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">col_name</span><span class=\"p\">:</span> <span class=\"nb\">str</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.phen.translate_codes": {"fullname": "acmc.phen.translate_codes", "modulename": "acmc.phen", "qualname": "translate_codes", "kind": "function", "doc": "<p>Translates each source code type the source coding list into a target type and returns all conversions as a concept set</p>\n", "signature": "<span class=\"signature pdoc-code multiline\">(<span class=\"param\">\t<span class=\"n\">source_df</span><span class=\"p\">:</span> <span class=\"n\">pandas</span><span class=\"o\">.</span><span class=\"n\">core</span><span class=\"o\">.</span><span class=\"n\">frame</span><span class=\"o\">.</span><span class=\"n\">DataFrame</span>,</span><span class=\"param\">\t<span class=\"n\">target_code_type</span><span class=\"p\">:</span> <span class=\"nb\">str</span>,</span><span class=\"param\">\t<span class=\"n\">concept_name</span><span class=\"p\">:</span> <span class=\"nb\">str</span></span><span class=\"return-annotation\">) -> <span class=\"n\">pandas</span><span class=\"o\">.</span><span class=\"n\">core</span><span class=\"o\">.</span><span class=\"n\">frame</span><span class=\"o\">.</span><span class=\"n\">DataFrame</span>:</span></span>", "funcdef": "def"}, "acmc.phen.sql_row_exist": {"fullname": "acmc.phen.sql_row_exist", "modulename": "acmc.phen", "qualname": "sql_row_exist", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">conn</span><span class=\"p\">:</span> <span class=\"n\">sqlite3</span><span class=\"o\">.</span><span class=\"n\">Connection</span>, </span><span class=\"param\"><span class=\"n\">table</span><span class=\"p\">:</span> <span class=\"nb\">str</span>, </span><span class=\"param\"><span class=\"n\">column</span><span class=\"p\">:</span> <span class=\"nb\">str</span>, </span><span class=\"param\"><span class=\"n\">value</span><span class=\"p\">:</span> <span class=\"nb\">str</span></span><span class=\"return-annotation\">) -> <span class=\"nb\">bool</span>:</span></span>", "funcdef": "def"}, "acmc.phen.write_code_errors": {"fullname": "acmc.phen.write_code_errors", "modulename": "acmc.phen", "qualname": "write_code_errors", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">code_errors</span><span class=\"p\">:</span> <span class=\"nb\">list</span>, </span><span class=\"param\"><span class=\"n\">code_errors_path</span><span class=\"p\">:</span> <span class=\"n\">pathlib</span><span class=\"o\">.</span><span class=\"n\">Path</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.phen.write_vocab_version": {"fullname": "acmc.phen.write_vocab_version", "modulename": "acmc.phen", "qualname": "write_vocab_version", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">phen_path</span><span class=\"p\">:</span> <span class=\"n\">pathlib</span><span class=\"o\">.</span><span class=\"n\">Path</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.phen.map": {"fullname": "acmc.phen.map", "modulename": "acmc.phen", "qualname": "map", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">phen_dir</span><span class=\"p\">:</span> <span class=\"nb\">str</span>, </span><span class=\"param\"><span class=\"n\">target_code_type</span><span class=\"p\">:</span> <span class=\"nb\">str</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.phen.map_target_code_type": {"fullname": "acmc.phen.map_target_code_type", "modulename": "acmc.phen", "qualname": "map_target_code_type", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">phen_path</span><span class=\"p\">:</span> <span class=\"n\">pathlib</span><span class=\"o\">.</span><span class=\"n\">Path</span>, </span><span class=\"param\"><span class=\"n\">phenotype</span><span class=\"p\">:</span> <span class=\"nb\">dict</span>, </span><span class=\"param\"><span class=\"n\">target_code_type</span><span class=\"p\">:</span> <span class=\"nb\">str</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.phen.generate_version_tag": {"fullname": "acmc.phen.generate_version_tag", "modulename": "acmc.phen", "qualname": "generate_version_tag", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code multiline\">(<span class=\"param\">\t<span class=\"n\">repo</span><span class=\"p\">:</span> <span class=\"n\">git</span><span class=\"o\">.</span><span class=\"n\">repo</span><span class=\"o\">.</span><span class=\"n\">base</span><span class=\"o\">.</span><span class=\"n\">Repo</span>,</span><span class=\"param\">\t<span class=\"n\">increment</span><span class=\"p\">:</span> <span class=\"nb\">str</span> <span class=\"o\">=</span> <span class=\"s1\">'patch'</span>,</span><span class=\"param\">\t<span class=\"n\">use_v_prefix</span><span class=\"p\">:</span> <span class=\"nb\">bool</span> <span class=\"o\">=</span> <span class=\"kc\">False</span></span><span class=\"return-annotation\">) -> <span class=\"nb\">str</span>:</span></span>", "funcdef": "def"}, "acmc.phen.publish": {"fullname": "acmc.phen.publish", "modulename": "acmc.phen", "qualname": "publish", "kind": "function", "doc": "<p>Publishes updates to the phenotype by commiting all changes to the repo directory</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">phen_dir</span><span class=\"p\">:</span> <span class=\"nb\">str</span>, </span><span class=\"param\"><span class=\"n\">msg</span><span class=\"p\">:</span> <span class=\"nb\">str</span>, </span><span class=\"param\"><span class=\"n\">remote_url</span><span class=\"p\">:</span> <span class=\"nb\">str</span>, </span><span class=\"param\"><span class=\"n\">increment</span><span class=\"p\">:</span> <span class=\"nb\">str</span> <span class=\"o\">=</span> <span class=\"s1\">'patch'</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.phen.export": {"fullname": "acmc.phen.export", "modulename": "acmc.phen", "qualname": "export", "kind": "function", "doc": "<p>Exports a phen repo at a specific tagged version into a target directory</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">phen_dir</span><span class=\"p\">:</span> <span class=\"nb\">str</span>, </span><span class=\"param\"><span class=\"n\">version</span><span class=\"p\">:</span> <span class=\"nb\">str</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.phen.copy": {"fullname": "acmc.phen.copy", "modulename": "acmc.phen", "qualname": "copy", "kind": "function", "doc": "<p>Copys a phen repo at a specific tagged version into a target directory</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">phen_dir</span><span class=\"p\">:</span> <span class=\"nb\">str</span>, </span><span class=\"param\"><span class=\"n\">target_dir</span><span class=\"p\">:</span> <span class=\"nb\">str</span>, </span><span class=\"param\"><span class=\"n\">version</span><span class=\"p\">:</span> <span class=\"nb\">str</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.phen.extract_concepts": {"fullname": "acmc.phen.extract_concepts", "modulename": "acmc.phen", "qualname": "extract_concepts", "kind": "function", "doc": "<p>Extracts concepts as {name: file_path} dictionary and a name set.</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">config_data</span><span class=\"p\">:</span> <span class=\"nb\">dict</span></span><span class=\"return-annotation\">) -> <span class=\"n\">Tuple</span><span class=\"p\">[</span><span class=\"nb\">dict</span><span class=\"p\">,</span> <span class=\"n\">Set</span><span class=\"p\">[</span><span class=\"nb\">str</span><span class=\"p\">]]</span>:</span></span>", "funcdef": "def"}, "acmc.phen.extract_clean_deepdiff_keys": {"fullname": "acmc.phen.extract_clean_deepdiff_keys", "modulename": "acmc.phen", "qualname": "extract_clean_deepdiff_keys", "kind": "function", "doc": "<p>Extracts clean keys from a DeepDiff dictionary.</p>\n\n<p>:param diff: DeepDiff result dictionary\n:param key_type: The type of change to extract (e.g., \"dictionary_item_added\", \"dictionary_item_removed\")\n:return: A set of clean key names</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">diff</span><span class=\"p\">:</span> <span class=\"nb\">dict</span>, </span><span class=\"param\"><span class=\"n\">key_type</span><span class=\"p\">:</span> <span class=\"nb\">str</span></span><span class=\"return-annotation\">) -> <span class=\"n\">Set</span><span class=\"p\">[</span><span class=\"n\">Any</span><span class=\"p\">]</span>:</span></span>", "funcdef": "def"}, "acmc.phen.diff_config": {"fullname": "acmc.phen.diff_config", "modulename": "acmc.phen", "qualname": "diff_config", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">old_config</span><span class=\"p\">:</span> <span class=\"nb\">dict</span>, </span><span class=\"param\"><span class=\"n\">new_config</span><span class=\"p\">:</span> <span class=\"nb\">dict</span></span><span class=\"return-annotation\">) -> <span class=\"nb\">str</span>:</span></span>", "funcdef": "def"}, "acmc.phen.diff_map_files": {"fullname": "acmc.phen.diff_map_files", "modulename": "acmc.phen", "qualname": "diff_map_files", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">old_map_path</span><span class=\"p\">:</span> <span class=\"n\">pathlib</span><span class=\"o\">.</span><span class=\"n\">Path</span>, </span><span class=\"param\"><span class=\"n\">new_map_path</span><span class=\"p\">:</span> <span class=\"n\">pathlib</span><span class=\"o\">.</span><span class=\"n\">Path</span></span><span class=\"return-annotation\">) -> <span class=\"nb\">str</span>:</span></span>", "funcdef": "def"}, "acmc.phen.diff_phen": {"fullname": "acmc.phen.diff_phen", "modulename": "acmc.phen", "qualname": "diff_phen", "kind": "function", "doc": "<p>Compare the differences between two versions of a phenotype</p>\n", "signature": "<span class=\"signature pdoc-code multiline\">(<span class=\"param\">\t<span class=\"n\">new_phen_path</span><span class=\"p\">:</span> <span class=\"n\">pathlib</span><span class=\"o\">.</span><span class=\"n\">Path</span>,</span><span class=\"param\">\t<span class=\"n\">new_version</span><span class=\"p\">:</span> <span class=\"nb\">str</span>,</span><span class=\"param\">\t<span class=\"n\">old_phen_path</span><span class=\"p\">:</span> <span class=\"n\">pathlib</span><span class=\"o\">.</span><span class=\"n\">Path</span>,</span><span class=\"param\">\t<span class=\"n\">old_version</span><span class=\"p\">:</span> <span class=\"nb\">str</span>,</span><span class=\"param\">\t<span class=\"n\">report_path</span><span class=\"p\">:</span> <span class=\"n\">pathlib</span><span class=\"o\">.</span><span class=\"n\">Path</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.phen.diff": {"fullname": "acmc.phen.diff", "modulename": "acmc.phen", "qualname": "diff", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">phen_dir</span><span class=\"p\">:</span> <span class=\"nb\">str</span>, </span><span class=\"param\"><span class=\"n\">version</span><span class=\"p\">:</span> <span class=\"nb\">str</span>, </span><span class=\"param\"><span class=\"n\">old_phen_dir</span><span class=\"p\">:</span> <span class=\"nb\">str</span>, </span><span class=\"param\"><span class=\"n\">old_version</span><span class=\"p\">:</span> <span class=\"nb\">str</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.trud": {"fullname": "acmc.trud", "modulename": "acmc.trud", "kind": "module", "doc": "<p></p>\n"}, "acmc.trud.logger": {"fullname": "acmc.trud.logger", "modulename": "acmc.trud", "qualname": "logger", "kind": "variable", "doc": "<p></p>\n", "default_value": "<Logger acmc_logger (INFO)>"}, "acmc.trud.FQDN": {"fullname": "acmc.trud.FQDN", "modulename": "acmc.trud", "qualname": "FQDN", "kind": "variable", "doc": "<p></p>\n", "default_value": "'isd.digital.nhs.uk'"}, "acmc.trud.VOCAB_PATH": {"fullname": "acmc.trud.VOCAB_PATH", "modulename": "acmc.trud", "qualname": "VOCAB_PATH", "kind": "variable", "doc": "<p></p>\n", "default_value": "PosixPath('vocab/trud')"}, "acmc.trud.VERSION_FILE": {"fullname": "acmc.trud.VERSION_FILE", "modulename": "acmc.trud", "qualname": "VERSION_FILE", "kind": "variable", "doc": "<p></p>\n", "default_value": "'trud_version.yaml'"}, "acmc.trud.VERSION_PATH": {"fullname": "acmc.trud.VERSION_PATH", "modulename": "acmc.trud", "qualname": "VERSION_PATH", "kind": "variable", "doc": "<p></p>\n", "default_value": "PosixPath('vocab/trud/trud_version.yaml')"}, "acmc.trud.DOWNLOADS_PATH": {"fullname": "acmc.trud.DOWNLOADS_PATH", "modulename": "acmc.trud", "qualname": "DOWNLOADS_PATH", "kind": "variable", "doc": "<p></p>\n", "default_value": "PosixPath('vocab/trud/downloads')"}, "acmc.trud.PROCESSED_PATH": {"fullname": "acmc.trud.PROCESSED_PATH", "modulename": "acmc.trud", "qualname": "PROCESSED_PATH", "kind": "variable", "doc": "<p></p>\n", "default_value": "PosixPath('vocab/trud/processed')"}, "acmc.trud.get_releases": {"fullname": "acmc.trud.get_releases", "modulename": "acmc.trud", "qualname": "get_releases", "kind": "function", "doc": "<p>Retrieve release information for an item from the TRUD API.</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">item_id</span><span class=\"p\">:</span> <span class=\"nb\">str</span>, </span><span class=\"param\"><span class=\"n\">API_KEY</span><span class=\"p\">:</span> <span class=\"nb\">str</span>, </span><span class=\"param\"><span class=\"n\">latest</span><span class=\"o\">=</span><span class=\"kc\">False</span></span><span class=\"return-annotation\">) -> <span class=\"nb\">list</span>:</span></span>", "funcdef": "def"}, "acmc.trud.download_release_file": {"fullname": "acmc.trud.download_release_file", "modulename": "acmc.trud", "qualname": "download_release_file", "kind": "function", "doc": "<p>Download specified file type for a given release of an item.</p>\n", "signature": "<span class=\"signature pdoc-code multiline\">(<span class=\"param\">\t<span class=\"n\">item_id</span><span class=\"p\">:</span> <span class=\"nb\">str</span>,</span><span class=\"param\">\t<span class=\"n\">release_ordinal</span><span class=\"p\">:</span> <span class=\"nb\">str</span>,</span><span class=\"param\">\t<span class=\"n\">release</span><span class=\"p\">:</span> <span class=\"nb\">dict</span>,</span><span class=\"param\">\t<span class=\"n\">file_json_prefix</span><span class=\"p\">:</span> <span class=\"nb\">str</span>,</span><span class=\"param\">\t<span class=\"n\">file_type</span><span class=\"o\">=</span><span class=\"kc\">None</span></span><span class=\"return-annotation\">) -> <span class=\"n\">pathlib</span><span class=\"o\">.</span><span class=\"n\">Path</span>:</span></span>", "funcdef": "def"}, "acmc.trud.validate_download_hash": {"fullname": "acmc.trud.validate_download_hash", "modulename": "acmc.trud", "qualname": "validate_download_hash", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">file_destination</span><span class=\"p\">:</span> <span class=\"nb\">str</span>, </span><span class=\"param\"><span class=\"n\">item_hash</span><span class=\"p\">:</span> <span class=\"nb\">str</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.trud.unzip_download": {"fullname": "acmc.trud.unzip_download", "modulename": "acmc.trud", "qualname": "unzip_download", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"n\">file_destination</span><span class=\"p\">:</span> <span class=\"nb\">str</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.trud.extract_icd10": {"fullname": "acmc.trud.extract_icd10", "modulename": "acmc.trud", "qualname": "extract_icd10", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.trud.extract_opsc4": {"fullname": "acmc.trud.extract_opsc4", "modulename": "acmc.trud", "qualname": "extract_opsc4", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.trud.extract_nhs_data_migrations": {"fullname": "acmc.trud.extract_nhs_data_migrations", "modulename": "acmc.trud", "qualname": "extract_nhs_data_migrations", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.trud.extract_nhs_read_browser": {"fullname": "acmc.trud.extract_nhs_read_browser", "modulename": "acmc.trud", "qualname": "extract_nhs_read_browser", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.trud.create_map_directories": {"fullname": "acmc.trud.create_map_directories", "modulename": "acmc.trud", "qualname": "create_map_directories", "kind": "function", "doc": "<p>Create map directories.</p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.trud.install": {"fullname": "acmc.trud.install", "modulename": "acmc.trud", "qualname": "install", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"return-annotation\">):</span></span>", "funcdef": "def"}, "acmc.util": {"fullname": "acmc.util", "modulename": "acmc.util", "kind": "module", "doc": "<p></p>\n"}, "acmc.util.QuotedDumper": {"fullname": "acmc.util.QuotedDumper", "modulename": "acmc.util", "qualname": "QuotedDumper", "kind": "class", "doc": "<p></p>\n", "bases": "yaml.dumper.Dumper"}, "acmc.util.QuotedDumper.increase_indent": {"fullname": "acmc.util.QuotedDumper.increase_indent", "modulename": "acmc.util", "qualname": "QuotedDumper.increase_indent", "kind": "function", "doc": "<p></p>\n", "signature": "<span class=\"signature pdoc-code condensed\">(<span class=\"param\"><span class=\"bp\">self</span>, </span><span class=\"param\"><span class=\"n\">flow</span><span class=\"o\">=</span><span class=\"kc\">False</span>, </span><span class=\"param\"><span class=\"n\">indentless</span><span class=\"o\">=</span><span class=\"kc\">False</span></span><span class=\"return-annotation\">):</span></span>", "funcdef": "def"}}, "docInfo": {"acmc": {"qualname": 0, "fullname": 1, "annotation": 0, "default_value": 0, "signature": 0, "bases": 0, "doc": 3}, "acmc.logging_config": {"qualname": 0, "fullname": 3, "annotation": 0, "default_value": 0, "signature": 0, "bases": 0, "doc": 3}, "acmc.logging_config.DEFAULT_LOG_FILE": {"qualname": 3, "fullname": 6, "annotation": 0, "default_value": 6, "signature": 0, "bases": 0, "doc": 3}, "acmc.logging_config.setup_logger": {"qualname": 2, "fullname": 5, "annotation": 0, "default_value": 0, "signature": 24, "bases": 0, "doc": 14}, "acmc.logging_config.set_log_level": {"qualname": 3, "fullname": 6, "annotation": 0, "default_value": 0, "signature": 17, "bases": 0, "doc": 10}, "acmc.main": {"qualname": 0, "fullname": 2, "annotation": 0, "default_value": 0, "signature": 0, "bases": 0, "doc": 3}, "acmc.main.logger": {"qualname": 1, "fullname": 3, "annotation": 0, "default_value": 8, "signature": 0, "bases": 0, "doc": 3}, "acmc.main.DEFAULT_WORKSPACE_PATH": {"qualname": 3, "fullname": 5, "annotation": 0, "default_value": 5, "signature": 0, "bases": 0, "doc": 3}, "acmc.main.trud_install": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 21, "bases": 0, "doc": 10}, "acmc.main.omop_install": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 21, "bases": 0, "doc": 10}, "acmc.main.omop_clear": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 21, "bases": 0, "doc": 10}, "acmc.main.omop_delete": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 21, "bases": 0, "doc": 10}, "acmc.main.phen_init": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 21, "bases": 0, "doc": 10}, "acmc.main.phen_fork": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 21, "bases": 0, "doc": 10}, "acmc.main.phen_validate": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 21, "bases": 0, "doc": 10}, "acmc.main.phen_map": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 21, "bases": 0, "doc": 10}, "acmc.main.phen_export": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 21, "bases": 0, "doc": 10}, "acmc.main.phen_publish": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 21, "bases": 0, "doc": 10}, "acmc.main.phen_copy": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 21, "bases": 0, "doc": 10}, "acmc.main.phen_diff": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 21, "bases": 0, "doc": 10}, "acmc.main.main": {"qualname": 1, "fullname": 3, "annotation": 0, "default_value": 0, "signature": 7, "bases": 0, "doc": 3}, "acmc.omop": {"qualname": 0, "fullname": 2, "annotation": 0, "default_value": 0, "signature": 0, "bases": 0, "doc": 3}, "acmc.omop.logger": {"qualname": 1, "fullname": 3, "annotation": 0, "default_value": 8, "signature": 0, "bases": 0, "doc": 3}, "acmc.omop.VOCAB_PATH": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 5, "signature": 0, "bases": 0, "doc": 3}, "acmc.omop.OMOP_CDM_Version": {"qualname": 3, "fullname": 5, "annotation": 0, "default_value": 5, "signature": 0, "bases": 0, "doc": 3}, "acmc.omop.OMOP_DB_FILENAME": {"qualname": 3, "fullname": 5, "annotation": 0, "default_value": 7, "signature": 0, "bases": 0, "doc": 3}, "acmc.omop.DB_PATH": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 7, "signature": 0, "bases": 0, "doc": 3}, "acmc.omop.VERSION_FILE": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 7, "signature": 0, "bases": 0, "doc": 3}, "acmc.omop.VERSION_PATH": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 7, "signature": 0, "bases": 0, "doc": 3}, "acmc.omop.EXPORT_FILE": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 8, "signature": 0, "bases": 0, "doc": 3}, "acmc.omop.vocabularies": {"qualname": 1, "fullname": 3, "annotation": 0, "default_value": 202, "signature": 0, "bases": 0, "doc": 3}, "acmc.omop.omop_vocab_types": {"qualname": 3, "fullname": 5, "annotation": 0, "default_value": 51, "signature": 0, "bases": 0, "doc": 3}, "acmc.omop.install": {"qualname": 1, "fullname": 3, "annotation": 0, "default_value": 0, "signature": 28, "bases": 0, "doc": 14}, "acmc.omop.write_version_file": {"qualname": 3, "fullname": 5, "annotation": 0, "default_value": 0, "signature": 16, "bases": 0, "doc": 11}, "acmc.omop.clear": {"qualname": 1, "fullname": 3, "annotation": 0, "default_value": 0, "signature": 22, "bases": 0, "doc": 7}, "acmc.omop.delete": {"qualname": 1, "fullname": 3, "annotation": 0, "default_value": 0, "signature": 22, "bases": 0, "doc": 7}, "acmc.omop.table_exists": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 35, "bases": 0, "doc": 3}, "acmc.omop.vocab_exists": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 35, "bases": 0, "doc": 3}, "acmc.omop.concept_set_exist": {"qualname": 3, "fullname": 5, "annotation": 0, "default_value": 0, "signature": 36, "bases": 0, "doc": 3}, "acmc.omop.export": {"qualname": 1, "fullname": 3, "annotation": 0, "default_value": 0, "signature": 66, "bases": 0, "doc": 3}, "acmc.parse": {"qualname": 0, "fullname": 2, "annotation": 0, "default_value": 0, "signature": 0, "bases": 0, "doc": 3}, "acmc.parse.logger": {"qualname": 1, "fullname": 3, "annotation": 0, "default_value": 8, "signature": 0, "bases": 0, "doc": 3}, "acmc.parse.SUPPORTED_CODE_TYPES": {"qualname": 3, "fullname": 5, "annotation": 0, "default_value": 20, "signature": 0, "bases": 0, "doc": 3}, "acmc.parse.CodesError": {"qualname": 1, "fullname": 3, "annotation": 0, 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"default_value": 0, "signature": 0, "bases": 0, "doc": 3}, "acmc.parse.Proto.name": {"qualname": 2, "fullname": 4, "annotation": 2, "default_value": 0, "signature": 0, "bases": 0, "doc": 3}, "acmc.parse.Proto.raise_exception": {"qualname": 3, "fullname": 5, "annotation": 0, "default_value": 0, "signature": 21, "bases": 0, "doc": 36}, "acmc.parse.Proto.in_database": {"qualname": 3, "fullname": 5, "annotation": 0, "default_value": 0, "signature": 93, "bases": 0, "doc": 3}, "acmc.parse.Proto.process": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 85, "bases": 0, "doc": 14}, "acmc.parse.Proto.verify": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 52, "bases": 0, "doc": 7}, "acmc.parse.Read2": {"qualname": 1, "fullname": 3, "annotation": 0, "default_value": 0, "signature": 0, "bases": 1, "doc": 40}, "acmc.parse.Read2.checks": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 0, "bases": 0, "doc": 3}, "acmc.parse.Read3": {"qualname": 1, "fullname": 3, "annotation": 0, "default_value": 0, "signature": 0, "bases": 1, "doc": 59}, "acmc.parse.Read3.checks": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 0, "bases": 0, "doc": 3}, "acmc.parse.Icd10": {"qualname": 1, "fullname": 3, "annotation": 0, "default_value": 0, "signature": 0, "bases": 1, "doc": 59}, "acmc.parse.Icd10.checks": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 0, "bases": 0, "doc": 3}, "acmc.parse.Icd10.trim_icd10": {"qualname": 3, "fullname": 5, "annotation": 0, "default_value": 0, "signature": 49, "bases": 0, "doc": 3}, "acmc.parse.Snomed": {"qualname": 1, "fullname": 3, "annotation": 0, "default_value": 0, "signature": 0, "bases": 1, "doc": 59}, "acmc.parse.Snomed.checks": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 0, "bases": 0, "doc": 3}, "acmc.parse.Opcs4": {"qualname": 1, "fullname": 3, "annotation": 0, "default_value": 0, "signature": 0, "bases": 1, "doc": 59}, "acmc.parse.Opcs4.checks": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 0, "bases": 0, "doc": 3}, "acmc.parse.Atc": {"qualname": 1, "fullname": 3, "annotation": 0, "default_value": 0, "signature": 0, "bases": 1, "doc": 59}, "acmc.parse.Atc.checks": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 0, "bases": 0, "doc": 3}, "acmc.parse.Med": {"qualname": 1, "fullname": 3, "annotation": 0, "default_value": 0, "signature": 0, "bases": 1, "doc": 59}, "acmc.parse.Med.checks": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 0, "bases": 0, "doc": 3}, "acmc.parse.Cprd": {"qualname": 1, "fullname": 3, "annotation": 0, "default_value": 0, "signature": 0, "bases": 1, "doc": 59}, "acmc.parse.Cprd.checks": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 0, "bases": 0, "doc": 3}, "acmc.parse.CodeTypeParser": {"qualname": 1, "fullname": 3, "annotation": 0, "default_value": 0, "signature": 0, "bases": 0, "doc": 17}, "acmc.parse.CodeTypeParser.__init__": {"qualname": 3, "fullname": 5, "annotation": 0, "default_value": 0, "signature": 40, "bases": 0, "doc": 3}, "acmc.parse.CodeTypeParser.code_types": {"qualname": 3, "fullname": 5, "annotation": 0, "default_value": 0, "signature": 0, "bases": 0, "doc": 3}, "acmc.phen": {"qualname": 0, "fullname": 2, "annotation": 0, "default_value": 0, "signature": 0, "bases": 0, "doc": 3}, "acmc.phen.logger": {"qualname": 1, "fullname": 3, "annotation": 0, "default_value": 8, "signature": 0, "bases": 0, "doc": 3}, "acmc.phen.PHEN_DIR": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 5, "signature": 0, "bases": 0, "doc": 3}, "acmc.phen.DEFAULT_PHEN_PATH": {"qualname": 3, "fullname": 5, "annotation": 0, "default_value": 5, "signature": 0, "bases": 0, "doc": 3}, "acmc.phen.CONCEPTS_DIR": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 5, "signature": 0, "bases": 0, "doc": 3}, "acmc.phen.MAP_DIR": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 5, "signature": 0, "bases": 0, "doc": 3}, "acmc.phen.CONCEPT_SET_DIR": {"qualname": 3, "fullname": 5, "annotation": 0, "default_value": 6, "signature": 0, "bases": 0, "doc": 3}, "acmc.phen.CSV_PATH": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 6, "signature": 0, "bases": 0, "doc": 3}, "acmc.phen.OMOP_PATH": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 6, "signature": 0, "bases": 0, "doc": 3}, "acmc.phen.DEFAULT_PHEN_DIR_LIST": {"qualname": 4, "fullname": 6, "annotation": 0, "default_value": 12, "signature": 0, "bases": 0, "doc": 3}, "acmc.phen.CONFIG_FILE": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 6, "signature": 0, "bases": 0, "doc": 3}, "acmc.phen.VOCAB_VERSION_FILE": {"qualname": 3, "fullname": 5, "annotation": 0, "default_value": 7, "signature": 0, "bases": 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1}, "acmc.phen.extract_clean_deepdiff_keys": {"tf": 1}}, "df": 2}}}}}}}, "n": {"docs": {}, "df": 0, "s": {"docs": {}, "df": 0, "u": {"docs": {}, "df": 0, "r": {"docs": {}, "df": 0, "e": {"docs": {}, "df": 0, "s": {"docs": {"acmc.parse.Read2": {"tf": 1}}, "df": 1}}}}}, "v": {"docs": {}, "df": 0, "i": {"docs": {}, "df": 0, "r": {"docs": {}, "df": 0, "o": {"docs": {}, "df": 0, "n": {"docs": {}, "df": 0, "m": {"docs": {}, "df": 0, "e": {"docs": {}, "df": 0, "n": {"docs": {}, "df": 0, "t": {"docs": {"acmc.phen.construct_git_url": {"tf": 1}}, "df": 1}}}}}}}}}}, "a": {"docs": {}, "df": 0, "c": {"docs": {}, "df": 0, "h": {"docs": {"acmc.phen.preprocess_source_concepts": {"tf": 1}, "acmc.phen.translate_codes": {"tf": 1}}, "df": 2}}}}, "n": {"docs": {}, "df": 0, "a": {"docs": {}, "df": 0, "m": {"docs": {}, "df": 0, "e": {"docs": {"acmc.parse.Proto": {"tf": 1}, "acmc.parse.Read3": {"tf": 1}, "acmc.parse.Icd10": {"tf": 1}, "acmc.parse.Snomed": {"tf": 1}, "acmc.parse.Opcs4": {"tf": 1}, "acmc.parse.Atc": {"tf": 1}, "acmc.parse.Med": {"tf": 1}, "acmc.parse.Cprd": {"tf": 1}, "acmc.phen.extract_concepts": {"tf": 1.4142135623730951}}, "df": 9, "s": {"docs": {"acmc.phen.extract_clean_deepdiff_keys": {"tf": 1}}, "df": 1}}}}, "o": {"docs": {}, "df": 0, "t": {"docs": {"acmc.parse.Proto": {"tf": 1}, "acmc.parse.Proto.raise_exception": {"tf": 1.7320508075688772}, "acmc.parse.Proto.process": {"tf": 1}, "acmc.parse.Read3": {"tf": 1}, "acmc.parse.Icd10": {"tf": 1}, "acmc.parse.Snomed": {"tf": 1}, "acmc.parse.Opcs4": {"tf": 1}, "acmc.parse.Atc": {"tf": 1}, "acmc.parse.Med": {"tf": 1}, "acmc.parse.Cprd": {"tf": 1}, "acmc.phen.fork": {"tf": 1.4142135623730951}, "acmc.phen.preprocess_source_concepts": {"tf": 1}}, "df": 12}, "n": {"docs": {}, "df": 0, "e": {"docs": {"acmc.phen.fork": {"tf": 1}}, "df": 1}}}, "e": {"docs": {}, "df": 0, "c": {"docs": {}, "df": 0, "e": {"docs": {}, "df": 0, "s": {"docs": {}, "df": 0, "s": {"docs": {}, "df": 0, "a": {"docs": {}, "df": 0, "r": {"docs": {}, "df": 0, "y": {"docs": {"acmc.parse.Read2": {"tf": 1}}, "df": 1}}}}}}}, "w": {"docs": {"acmc.phen.fork": {"tf": 1.7320508075688772}}, "df": 1}}}, "g": {"docs": {"acmc.phen.extract_clean_deepdiff_keys": {"tf": 1}}, "df": 1, "i": {"docs": {}, "df": 0, "t": {"docs": {"acmc.phen.construct_git_url": {"tf": 1}, "acmc.phen.create_empty_git_dir": {"tf": 1}, "acmc.phen.fork": {"tf": 1}, "acmc.phen.init": {"tf": 1}, "acmc.phen.validate": {"tf": 1}}, "df": 5, "h": {"docs": {}, "df": 0, "u": {"docs": {}, "df": 0, "b": {"docs": {"acmc.phen.construct_git_url": {"tf": 1}}, "df": 1}}}, "l": {"docs": {}, "df": 0, "a": {"docs": {}, "df": 0, "b": {"docs": {"acmc.phen.construct_git_url": {"tf": 1}}, "df": 1}}}, "k": {"docs": {}, "df": 0, "e": {"docs": {}, "df": 0, "e": {"docs": {}, "df": 0, "p": {"docs": {"acmc.phen.create_empty_git_dir": {"tf": 1}}, "df": 1}}}}}, "v": {"docs": {}, "df": 0, "e": {"docs": {}, "df": 0, "n": {"docs": {"acmc.trud.download_release_file": {"tf": 1}}, "df": 1}}}}}, "k": {"docs": {}, "df": 0, "e": {"docs": {}, "df": 0, "y": {"docs": {"acmc.phen.extract_clean_deepdiff_keys": {"tf": 1.4142135623730951}}, "df": 1, "s": {"docs": {"acmc.phen.extract_clean_deepdiff_keys": {"tf": 1}}, "df": 1}}}}}}}, "pipeline": ["trimmer"], "_isPrebuiltIndex": true};
+
+ // mirrored in build-search-index.js (part 1)
+ // Also split on html tags. this is a cheap heuristic, but good enough.
+ elasticlunr.tokenizer.setSeperator(/[\s\-.;&_'"=,()]+|<[^>]*>/);
+
+ let searchIndex;
+ if (docs._isPrebuiltIndex) {
+ console.info("using precompiled search index");
+ searchIndex = elasticlunr.Index.load(docs);
+ } else {
+ console.time("building search index");
+ // mirrored in build-search-index.js (part 2)
+ searchIndex = elasticlunr(function () {
+ this.pipeline.remove(elasticlunr.stemmer);
+ this.pipeline.remove(elasticlunr.stopWordFilter);
+ this.addField("qualname");
+ this.addField("fullname");
+ this.addField("annotation");
+ this.addField("default_value");
+ this.addField("signature");
+ this.addField("bases");
+ this.addField("doc");
+ this.setRef("fullname");
+ });
+ for (let doc of docs) {
+ searchIndex.addDoc(doc);
+ }
+ console.timeEnd("building search index");
+ }
+
+ return (term) => searchIndex.search(term, {
+ fields: {
+ qualname: {boost: 4},
+ fullname: {boost: 2},
+ annotation: {boost: 2},
+ default_value: {boost: 2},
+ signature: {boost: 2},
+ bases: {boost: 2},
+ doc: {boost: 1},
+ },
+ expand: true
+ });
+})();
\ No newline at end of file
diff --git a/docs/index.md b/docs/index.md
index ef5cc82be542d91f863ef52eb116feabbcc34cbe..0a6d9d81730213ad065f456c75642fe484cbceed 100644
--- a/docs/index.md
+++ b/docs/index.md
@@ -9,7 +9,7 @@
- [Example 1 - Basic local phenotype](./tutorials/example1.md)
- [Example 2 - More complex local phenotype](./tutorials/example2.md)
- [Example 3 - Using a remote git repository](./tutorials/example3.md)
- - [API Reference](./api.md)
+ - [API Reference](./api/acmc.html)
- [Change Log](./changelog.md)
- [Troubleshooting](./troubleshooting.md)
diff --git a/mkdocs.yml b/mkdocs.yml
deleted file mode 100644
index 493e64b2ffdedb7f2b1a5b81d691881533811644..0000000000000000000000000000000000000000
--- a/mkdocs.yml
+++ /dev/null
@@ -1,19 +0,0 @@
-site_name: ACMC Documentation
-theme:
- name: material
- features:
- - navigation.tabs
- - navigation.expand
- - content.code.copy
-nav:
- - Home: index.md
- - Installation: installation.md
- - Usage: usage.md
- - API Reference: api.md
- - Tutorials:
- - Example 1 - Basic local phenotype: ./tutorials/example1.md
- - Example 2 - More complex local phenotype: ./tutorials/example2.md
- - Example 3 - Using a remote git repository: ./tutorials/example3.md
- - Change Log: changelog.md
- - Troubleshooting: troubleshooting.md
-repo_url: https://git.soton.ac.uk/meldb/concepts-processing/
diff --git a/pyproject.toml b/pyproject.toml
index 39f046a78c4a754df4293a128cec7dc64fb2ff1a..60b3698d6e78f21e64b5a494cfd0feb4c756c71c 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -54,6 +54,7 @@ Repository = "https://git.soton.ac.uk/meldb/concepts-processing"
Documentation = "https://git.soton.ac.uk/meldb/concepts-processing/docs"
Issues = "https://git.soton.ac.uk/meldb/concepts-processing/-/issues"
+
[tool.hatch.build.targets.wheel]
packages = ["acmc"]
@@ -65,17 +66,17 @@ dependencies = [
[tool.hatch.envs.dev]
dependencies = [
- "pydocstyle",
"pytest",
"black",
"mypy",
- "mkdocs",
- "mkdocs-material",
- "mkdocstrings"
+ "pdoc",
]
[tool.hatch.envs.dev.scripts]
-check = "black . && mypy ."
+format = "black ."
+type = "mypy ."
+docs = "pdoc -o docs/api -d markdown --docformat markdown --include-undocumented acmc"
+precommit = "hatch format && type mypy && hatch docs"
[tool.hatch.build]
include = ["acmc/**"] # Ensure only the acmc package is included
diff --git a/readthedocs.yaml b/readthedocs.yaml
deleted file mode 100644
index 802fc26c54c43ae8e09148da8367ab4e205c3577..0000000000000000000000000000000000000000
--- a/readthedocs.yaml
+++ /dev/null
@@ -1,23 +0,0 @@
-# Read the Docs configuration file
-# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
-
-# Required
-version: 2
-
-# Set the OS, Python version, and other tools you might need
-build:
- os: ubuntu-24.04
- tools:
- python: "3.13"
-
-# Build documentation with Mkdocs
-mkdocs:
- configuration: mkdocs.yml
-
-# Optionally, but recommended,
-# declare the Python requirements required to build your documentation
-# See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
-# python:
-# install:
-# - requirements: docs/requirements.txt
-
\ No newline at end of file