diff --git a/.gitignore b/.gitignore
index 2424433f464d54ba4b0b92d79bfcdc2c346d6161..ab0c2dcfa60a17d7b771e35b4a4cd373ae6e3bbd 100644
--- a/.gitignore
+++ b/.gitignore
@@ -14,12 +14,7 @@ __pycache__
# Build
build/*
-output/
-concepts-output/
-archive/
-maps/*
-concepts-new/
-codes/
+*output*
# temporary
script
diff --git a/acmc.py b/acmc.py
index 40a3d78b2a432e7f32d700ac8ba19005e2145362..9318e9b159b8cbfece3a2d4333f8d56a7e58b0ac 100644
--- a/acmc.py
+++ b/acmc.py
@@ -2,61 +2,36 @@ import argparse
import trud
import omop
-import map
+import phen
from pathlib import Path
def trud_install(args):
"""Handle the `trud install` command."""
- print(f"Installing TRUD")
trud.install(args.api_key)
- print(f"TRUD installation completed")
def omop_install(args):
"""Handle the `omop install` command."""
- print(f"Installing OMOP database")
omop.install(omop.OMOP_DB_PATH, args.omop_folder)
- print(f"OMOP installation completed")
def omop_clear(args):
"""Handle the `omop clear` command."""
- print(f"Clearing OMOP data from database")
- omop.clear(omop.OMOP_DB_PATH)
- print(f"OMOP database cleared")
+ omop.clear(omop.OMOP_DB_PATH)
def omop_delete(args):
"""Handle the `omop delete` command."""
- print(f"Deleting OMOP database")
omop.delete(omop.OMOP_DB_PATH)
- print(f"OMOP database deleted")
-def map_process(args):
- """Handle the `map process` command."""
- print(f"Processing map with phenotype config file: {args.config_file}")
- print(f"Output directory: {args.output_file}")
- print(f"Target coding format: {args.target_coding}")
- if args.translate:
- print("Translating code types.")
- else:
- print("Not translating codes")
- if args.verify:
- print("Verifying codes.")
- else:
- print("Not verifying codes.")
- if args.error_log:
- print(f"Saving errors to: {args.error_log}")
- else:
- args.error_log = 'errors.csv'
-
- map.process(args.config_file,
- args.source_codes_dir,
- args.target_coding,
- args.translate,
- args.verify,
- error_path=Path(args.error_log),
- output_path=Path(args.output_file))
+def phen_init(args):
+ """Handle the `phen init` command."""
+ phen.init(args.phen_dir)
- print(f"Phenotype processing completed")
+def phen_map(args):
+ """Handle the `phen map` command."""
+ phen.map(args.phen_dir,
+ args.target_coding,
+ args.translate,
+ args.verify)
def main():
parser = argparse.ArgumentParser(description="ACMC command-line tool")
@@ -85,30 +60,31 @@ def main():
# omop clear
omop_clear_parser = omop_subparsers.add_parser("clear", help="Clear OMOP data from database")
omop_clear_parser.set_defaults(func=omop_clear)
+
# omop delete
omop_delete_parser = omop_subparsers.add_parser("delete", help="Delete OMOP database")
omop_delete_parser.set_defaults(func=omop_delete)
- ### MAP Command ###
- map_parser = subparsers.add_parser("map", help="Map commands")
- map_subparsers = map_parser.add_subparsers(dest="subcommand", required=True, help="Map subcommands")
+ ### PHEN Command ###
+ phen_parser = subparsers.add_parser("phen", help="Phen commands")
+ phen_subparsers = phen_parser.add_subparsers(dest="subcommand", required=True, help="Phen subcommands")
+
+ # phen init
+ phen_init_parser = phen_subparsers.add_parser("init", help="Initiatise phenotype configuration")
+ phen_init_parser.add_argument("-d", "--phen-dir", type=str, default=phen.DEFAULT_PHEN_PATH.resolve, help="Phenotype directory")
+ phen_init_parser.set_defaults(func=phen_init)
- # map process
- map_process_parser = map_subparsers.add_parser("process", help="Process map configuration file")
- map_process_parser.add_argument("-c", "--config-file", required=True, help="Phenotype configuration file")
- map_process_parser.add_argument("-s", "--source-codes-dir", required=True, help="Source codes root directory")
- map_process_parser.add_argument("-t", "--target-coding", required=True, choices=['read2_code', 'read3_code', 'icd10_code', 'snomed_code', 'opcs4_code'], help="Specify the target coding (read2, read3, icd10, snomed, opcs4)")
- map_process_parser.add_argument("-o", "--output-file", type=str, default=str(map.OUTPUT_PATH.resolve()), help="Output directory for CSV or OMOP database")
+ # phen map
+ phen_map_parser = phen_subparsers.add_parser("map", help="Process phen configuration file")
+ phen_map_parser.add_argument("-d", "--phen-dir", type=str, default=phen.DEFAULT_PHEN_PATH.resolve, help="Phenotype directory")
+ phen_map_parser.add_argument("-t", "--target-coding", required=True, choices=['read2_code', 'read3_code', 'icd10_code', 'snomed_code', 'opcs4_code'], help="Specify the target coding (read2, read3, icd10, snomed, opcs4)")
# Flags
- map_process_parser.add_argument("-tr", "--translate", action="store_true", default=False, help="Do not translate code types")
- map_process_parser.add_argument("-v", "--verify", action="store_true", default=False, help="Do not verify codes")
-
- # Error log file
- map_process_parser.add_argument("-l", "--error-log", type=str, default=str(map.ERROR_PATH.resolve()), help="Filepath to save error log to")
+ phen_map_parser.add_argument("-tr", "--translate", action="store_true", default=False, help="Do not translate code types")
+ phen_map_parser.add_argument("-v", "--verify", action="store_true", default=False, help="Do not verify codes")
# Set the function to call when 'process' subcommand is used
- map_process_parser.set_defaults(func=map_process)
+ phen_map_parser.set_defaults(func=phen_map)
# Parse arguments
args = parser.parse_args()
diff --git a/example/clinical-codes-org/About the source.docx b/example/codes/clinical-codes-org/About the source.docx
similarity index 100%
rename from example/clinical-codes-org/About the source.docx
rename to example/codes/clinical-codes-org/About the source.docx
diff --git a/example/clinical-codes-org/Behaviours code lists/Alcohol intake/Where this code list comes from .docx b/example/codes/clinical-codes-org/Behaviours code lists/Alcohol intake/Where this code list comes from .docx
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rename from example/clinical-codes-org/Behaviours code lists/Alcohol intake/Where this code list comes from .docx
rename to example/codes/clinical-codes-org/Behaviours code lists/Alcohol intake/Where this code list comes from .docx
diff --git a/example/clinical-codes-org/Behaviours code lists/Alcohol intake/res47-alcohol-intake.csv b/example/codes/clinical-codes-org/Behaviours code lists/Alcohol intake/res47-alcohol-intake.csv
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rename from example/clinical-codes-org/Behaviours code lists/Alcohol intake/res47-alcohol-intake.csv
rename to example/codes/clinical-codes-org/Behaviours code lists/Alcohol intake/res47-alcohol-intake.csv
diff --git a/example/clinical-codes-org/Behaviours code lists/Physical activity/Where this code list comes from .docx b/example/codes/clinical-codes-org/Behaviours code lists/Physical activity/Where this code list comes from .docx
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rename to example/codes/clinical-codes-org/Behaviours code lists/Physical activity/Where this code list comes from .docx
diff --git a/example/clinical-codes-org/Behaviours code lists/Physical activity/res47-physical-activity.csv b/example/codes/clinical-codes-org/Behaviours code lists/Physical activity/res47-physical-activity.csv
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rename from example/clinical-codes-org/Behaviours code lists/Physical activity/res47-physical-activity.csv
rename to example/codes/clinical-codes-org/Behaviours code lists/Physical activity/res47-physical-activity.csv
diff --git a/example/clinical-codes-org/Behaviours code lists/Smoking status/Where this code list comes from .docx b/example/codes/clinical-codes-org/Behaviours code lists/Smoking status/Where this code list comes from .docx
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rename to example/codes/clinical-codes-org/Behaviours code lists/Smoking status/Where this code list comes from .docx
diff --git a/example/clinical-codes-org/Behaviours code lists/Smoking status/res56-smoking-status.csv b/example/codes/clinical-codes-org/Behaviours code lists/Smoking status/res56-smoking-status.csv
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rename from example/clinical-codes-org/Behaviours code lists/Smoking status/res56-smoking-status.csv
rename to example/codes/clinical-codes-org/Behaviours code lists/Smoking status/res56-smoking-status.csv
diff --git a/example/clinical-codes-org/Cardiovascular events (ICD10)/Where this code list comes from .docx b/example/codes/clinical-codes-org/Cardiovascular events (ICD10)/Where this code list comes from .docx
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rename from example/clinical-codes-org/Cardiovascular events (ICD10)/Where this code list comes from .docx
rename to example/codes/clinical-codes-org/Cardiovascular events (ICD10)/Where this code list comes from .docx
diff --git a/example/clinical-codes-org/Cardiovascular events (ICD10)/res52-cardiovascular-events-icd10.csv b/example/codes/clinical-codes-org/Cardiovascular events (ICD10)/res52-cardiovascular-events-icd10.csv
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rename from example/clinical-codes-org/Cardiovascular events (ICD10)/res52-cardiovascular-events-icd10.csv
rename to example/codes/clinical-codes-org/Cardiovascular events (ICD10)/res52-cardiovascular-events-icd10.csv
diff --git a/example/clinical-codes-org/Motor neurone disease/Where this code list comes from .docx b/example/codes/clinical-codes-org/Motor neurone disease/Where this code list comes from .docx
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diff --git a/example/clinical-codes-org/Motor neurone disease/phenotype_PH62_ver_124_concepts_20230719T112819.csv b/example/codes/clinical-codes-org/Motor neurone disease/phenotype_PH62_ver_124_concepts_20230719T112819.csv
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diff --git a/example/clinical-codes-org/Non-attendance codes/Where this code list comes from .docx b/example/codes/clinical-codes-org/Non-attendance codes/Where this code list comes from .docx
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diff --git a/example/clinical-codes-org/Non-attendance codes/res201-did-not-attend-appointment.csv b/example/codes/clinical-codes-org/Non-attendance codes/res201-did-not-attend-appointment.csv
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diff --git a/example/clinical-codes-org/Obsessive Compulsive Disorder/Where this code list comes from .docx b/example/codes/clinical-codes-org/Obsessive Compulsive Disorder/Where this code list comes from .docx
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diff --git a/example/clinical-codes-org/Obsessive Compulsive Disorder/phenotype_PH223_ver_446_concepts_20230719T114228.csv b/example/codes/clinical-codes-org/Obsessive Compulsive Disorder/phenotype_PH223_ver_446_concepts_20230719T114228.csv
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diff --git a/example/clinical-codes-org/Palliative care codes/Where this code list comes from .docx b/example/codes/clinical-codes-org/Palliative care codes/Where this code list comes from .docx
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diff --git a/example/clinical-codes-org/Palliative care codes/res176-palliative-and-end-of-life-care.csv b/example/codes/clinical-codes-org/Palliative care codes/res176-palliative-and-end-of-life-care.csv
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diff --git a/example/clinical-codes-org/Peptic ulcer/Where this code list comes from .docx b/example/codes/clinical-codes-org/Peptic ulcer/Where this code list comes from .docx
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diff --git a/example/clinical-codes-org/Peptic ulcer/phenotype_PH1091_ver_2385_concepts_20230719T122902.csv b/example/codes/clinical-codes-org/Peptic ulcer/phenotype_PH1091_ver_2385_concepts_20230719T122902.csv
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diff --git a/example/clinical-codes-org/Personality disorders/Where this code list comes from .docx b/example/codes/clinical-codes-org/Personality disorders/Where this code list comes from .docx
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rename to example/codes/clinical-codes-org/Personality disorders/res38-personality-disorder.csv
diff --git a/example/clinical-codes-org/Self harm/Where this code list comes from .docx b/example/codes/clinical-codes-org/Self harm/Where this code list comes from .docx
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rename to example/codes/clinical-codes-org/Self harm/res41-self-harm.csv
diff --git a/example/clinical-codes-org/Symptom code lists/Abdominal pain/Where this code list comes from .docx b/example/codes/clinical-codes-org/Symptom code lists/Abdominal pain/Where this code list comes from .docx
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diff --git a/example/clinical-codes-org/Symptom code lists/Falls/Where this code list comes from .docx b/example/codes/clinical-codes-org/Symptom code lists/Falls/Where this code list comes from .docx
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diff --git a/example/clinical-codes-org/Symptom code lists/Falls/res202-falls-outcome.csv b/example/codes/clinical-codes-org/Symptom code lists/Falls/res202-falls-outcome.csv
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diff --git a/example/clinical-codes-org/Symptom code lists/Fatigue/Where this code list comes from .docx b/example/codes/clinical-codes-org/Symptom code lists/Fatigue/Where this code list comes from .docx
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diff --git a/example/clinical-codes-org/Symptom code lists/Headache/Where this code list comes from .docx b/example/codes/clinical-codes-org/Symptom code lists/Headache/Where this code list comes from .docx
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diff --git a/example/clinical-codes-org/Symptom code lists/Headache/res175-headache.csv b/example/codes/clinical-codes-org/Symptom code lists/Headache/res175-headache.csv
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diff --git a/example/clinical-codes-org/Symptom code lists/Incontinence/Where this code list comes from .docx b/example/codes/clinical-codes-org/Symptom code lists/Incontinence/Where this code list comes from .docx
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diff --git a/example/clinical-codes-org/Symptom code lists/Incontinence/res11-incontinence.csv b/example/codes/clinical-codes-org/Symptom code lists/Incontinence/res11-incontinence.csv
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diff --git a/example/clinical-codes-org/Symptom code lists/Musculoskeletal pain/Where this code list comes from .docx b/example/codes/clinical-codes-org/Symptom code lists/Musculoskeletal pain/Where this code list comes from .docx
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diff --git a/example/clinical-codes-org/Symptom code lists/Musculoskeletal pain/res175-msk-pain.csv b/example/codes/clinical-codes-org/Symptom code lists/Musculoskeletal pain/res175-msk-pain.csv
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diff --git a/example/clinical-codes-org/Symptom code lists/Neuropathic pain/Where this code list comes from .docx b/example/codes/clinical-codes-org/Symptom code lists/Neuropathic pain/Where this code list comes from .docx
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diff --git a/example/clinical-codes-org/Symptom code lists/Neuropathic pain/res55-neuropathic_pain.csv b/example/codes/clinical-codes-org/Symptom code lists/Neuropathic pain/res55-neuropathic_pain.csv
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diff --git a/example/clinical-codes-org/Symptom code lists/Sleep problems/Where this code list comes from .docx b/example/codes/clinical-codes-org/Symptom code lists/Sleep problems/Where this code list comes from .docx
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diff --git a/example/clinical-codes-org/Symptom code lists/Sleep problems/res175-sleep-problems.csv b/example/codes/clinical-codes-org/Symptom code lists/Sleep problems/res175-sleep-problems.csv
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diff --git a/example/clinical-codes-org/Tuberculosis/phenotype_PH87_ver_174_concepts_20230719T113229.csv b/example/codes/clinical-codes-org/Tuberculosis/phenotype_PH87_ver_174_concepts_20230719T113229.csv
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diff --git a/example/clinical-codes-org/Urinary tract stones/phenotype_PH331_ver_662_concepts_20230719T121545.csv b/example/codes/clinical-codes-org/Urinary tract stones/phenotype_PH331_ver_662_concepts_20230719T121545.csv
similarity index 100%
rename from example/clinical-codes-org/Urinary tract stones/phenotype_PH331_ver_662_concepts_20230719T121545.csv
rename to example/codes/clinical-codes-org/Urinary tract stones/phenotype_PH331_ver_662_concepts_20230719T121545.csv
diff --git a/example/phenotype_config.json b/example/config.json
similarity index 100%
rename from example/phenotype_config.json
rename to example/config.json
diff --git a/omop.py b/omop.py
index 6a9ecde0613d2e26977387d40da6ba61aa9bcc09..e7ec110f43607c49b81f0208de11fa0a29fb88b7 100644
--- a/omop.py
+++ b/omop.py
@@ -10,8 +10,7 @@ OMOP_DB_PATH = OMOP_DB_DIR / 'omop_54.sqlite'
#Populate SQLite3 Database with default OMOP CONCEPTS
def install (db_path, omop_install_folder):
-
- print(f"Installing OMOP files from {omop_install_folder}")
+ print(f"Installing OMOP database from {omop_install_folder}")
# check folder for omop install files is a directory
omop_install_path = Path(omop_install_folder)
@@ -42,8 +41,10 @@ def install (db_path, omop_install_folder):
raise Exception(f"Error reading file {file_path}: {e}")
conn.close()
+ print(f"OMOP installation completed")
def clear(db_path):
+ print(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.")
@@ -61,13 +62,16 @@ def clear(db_path):
#cur.execute("DROP TABLE CONCEPT_SET_ITEM;")
conn.close()
-
+ print(f"OMOP database cleared")
+
def delete(db_path):
+ print(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.")
omop_db_path.unlink()
+ print(f"OMOP database deleted")
def table_exists(cursor, table_name):
# Query to check if the table exists
diff --git a/map.py b/phen.py
similarity index 82%
rename from map.py
rename to phen.py
index a4262d63eefa3753aea9a88ad27760de2eb944a8..6e8b2901983f55a87386ab90444ffda1c7c828bf 100644
--- a/map.py
+++ b/phen.py
@@ -5,9 +5,10 @@ import json
import os
import sqlite3
import sys
-import trud
+import shutil
from pathlib import Path
+import trud
from base import log_invalid_code
from base import bcolors
from base import raise_
@@ -26,14 +27,76 @@ from omop import setup
pd.set_option("mode.chained_assignment", None)
-OUTPUT_PATH = Path('build') / 'phenotype_mapping.csv'
-ERROR_PATH = Path('build') / 'errors.csv'
+DEFAULT_PHEN_PATH = Path('build') / 'phen'
+CODES_DIR = 'codes'
+CONFIG_FILE = 'config.json'
+OUTPUT_FILE = 'phen_output.csv'
+ERROR_FILE = 'errors.csv'
SPLIT_COL_ACTION = "split_col"
CODES_COL_ACTION = "codes_col"
DIVIDE_COL_ACTION = "divide_col"
COL_ACTIONS = [SPLIT_COL_ACTION, CODES_COL_ACTION, DIVIDE_COL_ACTION]
+def init(phen_dir):
+ print(f"Initialising Phenotype in directory: {phen_dir}")
+
+ configure = False
+ phen_path = Path(phen_dir)
+ if phen_path.exists() and phen_path.is_dir(): # Check if it exists and is a directory
+ user_input = input(f"The phen directory '{phen_path}' already exists. Do you want to reinitialise phenotype, deleting all current configuration in this directory? (yes/no): ").strip().lower()
+ if user_input in ['yes', 'y']:
+ shutil.rmtree(phen_path) # Remove directory and all contents
+ configure = True;
+ else:
+ print("Phen directory was not recreated.")
+ else:
+ configure=True
+
+ if configure:
+ # create root phen directory
+ phen_path.mkdir(parents=True, exist_ok=True) # Recreate directory
+ print(f"Phen directory '{phen_path}' has been created.")
+ # create codes directory
+ codes_path = phen_path / CODES_DIR
+ codes_path.mkdir()
+ # create config file
+ config = {
+ "concept_sets": {
+ "version": "0.0.1",
+ "omop": {
+ "vocabulary_id": "",
+ "vocabulary_name": "",
+ "vocabulary_reference": ""
+ },
+ "concept_set": [
+ {
+ "concept_set_name": "",
+ "concept_set_status": "",
+ "metadata": {
+
+ }
+ }
+ ]
+ },
+ "codes": [
+ {
+ "folder": "",
+ "description": "",
+ "files": [
+
+ ]
+ }
+ ]
+ }
+
+ config_path = phen_path / "phen_config.json"
+ # Write the JSON data to a file
+ with open(config_path, "w", encoding="utf-8") as f:
+ json.dump(config, f, indent=4) # Pretty-printing with indentation
+
+ print(f"Phenotype initialised")
+
def read_table_file(path, excel_sheet=None):
"""
Load Code List File
@@ -212,12 +275,30 @@ def sql_row_exist(conn, table, column, value):
return exists
-def process(config_file, source_codes_dir, target_code_type, translate=True, verify=True, error_path=ERROR_PATH, output_path=OUTPUT_PATH):
- config_path = Path(config_file)
+def map(phen_dir,
+ target_code_type,
+ translate=True,
+ verify=True):
+ print(f"Processing phenotype directory: {phen_dir}")
+ print(f"Target coding format: {target_code_type}")
+ if translate:
+ print("Translating code types.")
+ else:
+ print("Not translating codes")
+ if verify:
+ print("Verifying codes.")
+ else:
+ print("Not verifying codes.")
+
+ phen_path = Path(phen_dir)
+ if not phen_path.is_dir():
+ raise NotADirectoryError(f"Error: '{phen_path}' is not a directory")
+
+ config_path = phen_path / CONFIG_FILE
if not config_path.is_file():
- raise FileNotFoundError(f"Error: phenotype configuration file '{config_path}' does not exist.")
+ raise FileNotFoundError(f"Error: phen configuration file '{config_path}' does not exist.")
- codes_path = Path(source_codes_dir)
+ codes_path = phen_path / CODES_DIR
if not codes_path.is_dir():
raise FileNotFoundError(f"Error: source codes directory {source_codes_dir} does not exist.")
@@ -233,7 +314,7 @@ def process(config_file, source_codes_dir, target_code_type, translate=True, ver
summary_config = mapping["concept_sets"]
folders = mapping["codes"]
- out = pd.DataFrame([]) # Create Output File to append to
+ out = pd.DataFrame([]) # Create Output dataframe to append to
# Iterate JSON mapping file (OBJECT FORMAT)
for folder in folders:
@@ -280,7 +361,7 @@ def process(config_file, source_codes_dir, target_code_type, translate=True, ver
print("Action: Dividing Table by", divide_col, "column into: ", df[divide_col].unique(),)
df = df.groupby(divide_col)
- # Map to MELDB Concept/Phenotype
+ # Map to Concept/Phenotype
if len(df) == 0:
pass
# out = df
@@ -326,8 +407,9 @@ def process(config_file, source_codes_dir, target_code_type, translate=True, ver
# Save Output File
print(bcolors.HEADER, "---" * 5, "OUTPUT", "---" * 5, bcolors.ENDC)
print(out)
- if output_path == "atlas":
+ output_path = phen_path / OUTPUT_FILE
+ if output_path == "atlas":
vocab_id = summary_config["omop"]["vocabulary_id"]
vocab_version = summary_config["version"]
vocab_name = summary_config["omop"]["vocabulary_name"]
@@ -348,8 +430,11 @@ def process(config_file, source_codes_dir, target_code_type, translate=True, ver
print("Saved to", output_path)
# Save Error File
+ error_path = phen_path / ERROR_FILE
if error_path.exists():
error_df = pd.read_csv(error_path)
error_df = error_df.drop_duplicates() # Remove Duplicates from Error file
error_df = error_df.sort_values(by=["SOURCE", "VOCABULARY", "CONCEPT"])
error_df.to_csv(error_path, index=False)
+
+ print(f"Phenotype processing completed")
\ No newline at end of file
diff --git a/trud.py b/trud.py
index 0d36c26a7b345bbab226585bbfe4e4080275ff79..869aa09b3bb6b85d9a6a3f2f3d25accca8e0cbbc 100644
--- a/trud.py
+++ b/trud.py
@@ -273,7 +273,8 @@ def create_map_directories():
MAPS_DOWNLOADS_DIR.mkdir(parents=True, exist_ok=True)
MAPS_PROCESSED_DIR.mkdir(parents=True,exist_ok=True)
-def install(api_key):
+def install(api_key):
+ print(f"Installing TRUD")
create_map_directories()
items_latest = True
@@ -340,3 +341,4 @@ def install(api_key):
print(f"Downloaded {release_ordinal} release(s) for item {item_id}.")
+ print(f"TRUD installation completed")
\ No newline at end of file