diff --git a/acmc/main.py b/acmc/main.py
index 4b7ac6ca7afa07cb5331ec9fe2628afcbd968ffe..a831faedeb75d2d4496cd39b82b217a6945d22d7 100644
--- a/acmc/main.py
+++ b/acmc/main.py
@@ -58,7 +58,7 @@ def _phen_validate(args: argparse.Namespace):
def _phen_map(args: argparse.Namespace):
"""Handle the `phen map` command."""
- phen.map(args.phen_dir, args.target_coding)
+ phen.map(args.phen_dir, args.target_coding, args.not_translate, args.no_metadata)
def _phen_export(args: argparse.Namespace):
@@ -78,7 +78,7 @@ def _phen_copy(args: argparse.Namespace):
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)
+ phen.diff(args.phen_dir, args.version, args.old_phen_dir, args.old_version, args.not_check_config)
def main():
@@ -217,6 +217,18 @@ def main():
choices=parse.SUPPORTED_CODE_TYPES,
help=f"Specify the target coding {parse.SUPPORTED_CODE_TYPES}",
)
+ phen_map_parser.add_argument(
+ "--not-translate",
+ action='store_true',
+ default=False,
+ help="(Optional) Prevent any phenotype translation using NHS TRUD vocabularies.",
+ )
+ phen_map_parser.add_argument(
+ "--no-metadata",
+ action='store_true',
+ default=False,
+ help="(Optional) Prevent copying of metadata columns to output.",
+ )
phen_map_parser.set_defaults(func=_phen_map)
# phen export
@@ -323,6 +335,12 @@ def main():
required=True,
help="Old phenotype version to compare with the changed version",
)
+ phen_diff_parser.add_argument(
+ "--not-check-config",
+ action='store_true',
+ default=False,
+ help="(Optional) Prevent loading and comparing config file, in the case where one does not exist",
+ )
phen_diff_parser.set_defaults(func=_phen_diff)
# Parse arguments
diff --git a/acmc/parse.py b/acmc/parse.py
index 45a9839a6533b8a742091d3ac6dba343a02e3ca5..8a364e5546d6946daa3ac995a98080ddd63f7662 100644
--- a/acmc/parse.py
+++ b/acmc/parse.py
@@ -192,7 +192,7 @@ class Read2(Proto):
class Read3(Proto):
def __init__(self):
- super().__init__("Read3", trud.PROCESSED_PATH / "read3.parquet")
+ super().__init__("read3", trud.PROCESSED_PATH / "read3.parquet")
self.checks = [
(
@@ -231,7 +231,7 @@ class Read3(Proto):
f"QA Alphanumeric Dot",
codes=codes,
codes_file=codes_file,
- check_regex=codes.str.match(r"^[a-zA-Z0-9.]+$"),
+ mask=None,
code_type=self.name,
)
)
@@ -246,7 +246,7 @@ class Read3(Proto):
f"QA In Database",
codes=codes,
codes_file=codes_file,
- check_regex=self.in_database(codes, self.db, self.name),
+ mask=None,
code_type=self.name,
)
)
diff --git a/acmc/phen.py b/acmc/phen.py
index 29d46d979e98ee5a2b5b76a1280c951154d12de3..c74583805dee8f5db32d4ebc3ffa4426e1640345 100644
--- a/acmc/phen.py
+++ b/acmc/phen.py
@@ -127,21 +127,30 @@ CONFIG_SCHEMA = {
"type": "dict",
"schema": {
"name": {"type": "string", "required": True},
- "file": {
- "type": "dict",
- "required": False,
+ "files": {
+ "type": "list",
+ "required": True,
"schema": {
- "path": {"type": "string", "required": True},
- "columns": {"type": "dict", "required": True},
- "category": {
- "type": "string"
- }, # Optional but must be string if present
- "actions": {
- "type": "dict",
- "schema": {"divide_col": {"type": "string"}},
+ "type": "dict",
+ "schema": {
+ "path": {"type": "string", "required": True},
+ "columns": {"type": "dict", "required": True},
+ "category": {
+ "type": "string"
+ }, # Optional but must be string if present
+ "actions": {
+ "type": "dict",
+ "schema": {
+ "divide_col": {"type": "string"},
+ "split_col": {"type": "string"},
+ "codes_col": {"type": "string"}
+ },
+ },
+
},
},
},
+ "metadata": {"type": "dict", "required": False},
},
},
},
@@ -518,38 +527,39 @@ def validate(phen_dir: str):
concept_set_names.append(item["name"])
# check codes definition
- for item in phenotype["concept_sets"]:
- # check concepte code file exists
- concept_code_file_path = concepts_path / item["file"]["path"]
- if not concept_code_file_path.exists():
- validation_errors.append(
- f"Coding file {str(concept_code_file_path.resolve())} does not exist"
- )
-
- # check concepte code file is not empty
- if concept_code_file_path.stat().st_size == 0:
- validation_errors.append(
- f"Coding file {str(concept_code_file_path.resolve())} is an empty file"
- )
-
- # check code file type is supported
- if concept_code_file_path.suffix not in CODE_FILE_TYPES:
- raise ValueError(
- f"Unsupported filetype {concept_code_file_path.suffix}, only support csv, xlsx, xls code file types"
- )
+ for files in phenotype["concept_sets"]:
+ for item in files["files"]:
+ # check concepte code file exists
+ concept_code_file_path = concepts_path / item["path"]
+ if not concept_code_file_path.exists():
+ validation_errors.append(
+ f"Coding file {str(concept_code_file_path.resolve())} does not exist"
+ )
- # check columns specified are a supported medical coding type
- for column in item["file"]["columns"]:
- if column not in code_types:
+ # check concepte code file is not empty
+ if concept_code_file_path.stat().st_size == 0:
validation_errors.append(
- f"Column type {column} for file {concept_code_file_path} is not supported"
+ f"Coding file {str(concept_code_file_path.resolve())} is an empty file"
)
- # check the actions are supported
- if "actions" in item["file"]:
- for action in item["file"]["actions"]:
- if action not in COL_ACTIONS:
- validation_errors.append(f"Action {action} is not supported")
+ # check code file type is supported
+ if concept_code_file_path.suffix not in CODE_FILE_TYPES:
+ raise ValueError(
+ f"Unsupported filetype {concept_code_file_path.suffix}, only support csv, xlsx, xls code file types"
+ )
+
+ # check columns specified are a supported medical coding type
+ for column in item["columns"]:
+ if column not in code_types:
+ validation_errors.append(
+ f"Column type {column} for file {concept_code_file_path} is not supported"
+ )
+
+ # check the actions are supported
+ if "actions" in item:
+ for action in item["actions"]:
+ if action not in COL_ACTIONS:
+ validation_errors.append(f"Action {action} is not supported")
if len(validation_errors) > 0:
_logger.error(validation_errors)
@@ -588,12 +598,12 @@ 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 (
- "actions" in concept_set["file"]
- and "split_col" in concept_set["file"]["actions"]
- and "codes_col" in concept_set["file"]["actions"]
+ "actions" in concept_set
+ and "split_col" in concept_set["actions"]
+ and "codes_col" in concept_set["actions"]
):
- split_col = concept_set["file"]["actions"]["split_col"]
- codes_col = concept_set["file"]["actions"]["codes_col"]
+ split_col = concept_set["actions"]["split_col"]
+ codes_col = concept_set["actions"]["codes_col"]
_logger.debug(
"Action: Splitting",
split_col,
@@ -621,12 +631,12 @@ def _preprocess_source_concepts(
# Preprocess codes
code_types = parse.CodeTypeParser().code_types
- for code_type in concept_set["file"]["columns"]:
+ for code_type in concept_set["columns"]:
parser = code_types[code_type]
_logger.info(f"Processing {code_type} codes for {code_file_path}")
# get codes by column name
- source_col_name = concept_set["file"]["columns"][code_type]
+ source_col_name = concept_set["columns"][code_type]
codes = df[source_col_name].dropna()
codes = codes.astype(str) # convert to string
codes = codes.str.strip() # remove excess spaces
@@ -653,7 +663,7 @@ def _preprocess_source_concepts(
# Translate Df with multiple codes into single code type Series
def translate_codes(
- source_df: pd.DataFrame, target_code_type: str, concept_name: str
+ source_df: pd.DataFrame, target_code_type: str, concept_name: str, not_translate:bool
) -> pd.DataFrame:
"""Translates each source code type the source coding list into a target type and returns all conversions as a concept set"""
@@ -678,7 +688,7 @@ def translate_codes(
_logger.debug(
f"Target code type {target_code_type} is the same as source code type {len(source_df)}, copying codes rather than translating"
)
- else:
+ elif not not_translate:
# get the translation filename using source to target code types
filename = f"{source_code_type}_to_{target_code_type}.parquet"
map_path = trud.PROCESSED_PATH / filename
@@ -725,7 +735,7 @@ def _write_code_errors(code_errors: list, code_errors_path: Path):
"SOURCE": err.codes_file,
"CAUSE": err.message,
}
- for err in code_errors
+ for err in code_errors if err.mask is not None
]
)
@@ -773,7 +783,7 @@ def write_vocab_version(phen_path: Path):
)
-def map(phen_dir: str, target_code_type: str):
+def map(phen_dir: str, target_code_type: str, not_translate:bool, no_metadata:bool):
_logger.info(f"Processing phenotype: {phen_dir}")
# Validate configuration
@@ -797,15 +807,15 @@ def map(phen_dir: str, target_code_type: str):
)
if target_code_type is not None:
- _map_target_code_type(phen_path, phenotype, target_code_type)
+ _map_target_code_type(phen_path, phenotype, target_code_type, not_translate, no_metadata)
else:
for t in phenotype["map"]:
- _map_target_code_type(phen_path, phenotype, t)
+ _map_target_code_type(phen_path, phenotype, t, not_translate, no_metadata)
_logger.info(f"Phenotype processed successfully")
-def _map_target_code_type(phen_path: Path, phenotype: dict, target_code_type: str):
+def _map_target_code_type(phen_path: Path, phenotype: dict, target_code_type: str, not_translate:bool, no_metadata:bool):
_logger.debug(f"Target coding format: {target_code_type}")
concepts_path = phen_path / CONCEPTS_DIR
# Create output dataframe
@@ -813,67 +823,87 @@ def _map_target_code_type(phen_path: Path, phenotype: dict, target_code_type: st
code_errors = []
# Process each folder in codes section
- for concept_set in phenotype["concept_sets"]:
- _logger.debug(f"--- {concept_set['file']} ---")
-
- # Load code file
- codes_file_path = Path(concepts_path / concept_set["file"]["path"])
- df = _read_table_file(codes_file_path)
-
- # process structural actions
- df = _process_actions(df, concept_set)
-
- # preprocessing and validate of source concepts
- _logger.debug("Processing and validating source concept codes")
- df, errors = _preprocess_source_concepts(
- df,
- concept_set,
- codes_file_path,
- )
-
- # create df with just the source code columns
- source_column_names = list(concept_set["file"]["columns"].keys())
- source_df = df[source_column_names]
+ for files in phenotype["concept_sets"]:
+ concept_set_name = files["name"]
+ if "metadata" in files:
+ concept_set_metadata = files["metadata"]
+ else:
+ concept_set_metadata = {}
+ for concept_set in files["files"]:
+ _logger.debug(f"--- {concept_set} ---")
+
+ # Load code file
+ codes_file_path = Path(concepts_path / concept_set["path"])
+ df = _read_table_file(codes_file_path)
+
+ # process structural actions
+ df = _process_actions(df, concept_set)
+
+ # preprocessing and validate of source concepts
+ _logger.debug("Processing and validating source concept codes")
+ df, errors = _preprocess_source_concepts(
+ df,
+ concept_set,
+ codes_file_path,
+ )
- _logger.debug(source_df.columns)
- _logger.debug(source_df.head())
+ # create df with just the source code columns
+ source_column_names = list(concept_set["columns"].keys())
+ source_df = df[source_column_names]
- _logger.debug(
- f"Length of errors from _preprocess_source_concepts {len(errors)}"
- )
- if len(errors) > 0:
- code_errors.extend(errors)
- _logger.debug(f" Length of code_errors {len(code_errors)}")
+ _logger.debug(source_df.columns)
+ _logger.debug(source_df.head())
- # Map source concepts codes to target codes
- # if processing a source coding list with categorical data
- if (
- "actions" in concept_set["file"]
- and "divide_col" in concept_set["file"]["actions"]
- and len(df) > 0
- ):
- divide_col = concept_set["file"]["actions"]["divide_col"]
- _logger.debug(f"Action: Dividing Table by {divide_col}")
- _logger.debug(f"column into: {df[divide_col].unique()}")
- df_grp = df.groupby(divide_col)
- for cat, grp in df_grp:
- if cat == concept_set["file"]["category"]:
- grp = grp.drop(columns=[divide_col]) # delete categorical column
- source_df = grp[source_column_names]
- trans_out = translate_codes(
- source_df,
- target_code_type=target_code_type,
- concept_name=concept_set["name"],
- )
- out = pd.concat([out, trans_out])
- else:
- source_df = df[source_column_names]
- trans_out = translate_codes(
- source_df,
- target_code_type=target_code_type,
- concept_name=concept_set["name"],
+ _logger.debug(
+ f"Length of errors from _preprocess_source_concepts {len(errors)}"
)
- out = pd.concat([out, trans_out])
+ if len(errors) > 0:
+ code_errors.extend(errors)
+ _logger.debug(f" Length of code_errors {len(code_errors)}")
+
+ # Map source concepts codes to target codes
+ # if processing a source coding list with categorical data
+ if (
+ "actions" in concept_set
+ and "divide_col" in concept_set["actions"]
+ and len(df) > 0
+ ):
+ divide_col = concept_set["actions"]["divide_col"]
+ _logger.debug(f"Action: Dividing Table by {divide_col}")
+ _logger.debug(f"column into: {df[divide_col].unique()}")
+ df_grp = df.groupby(divide_col)
+ for cat, grp in df_grp:
+ if cat == concept_set["category"]:
+ grp = grp.drop(
+ columns=[divide_col]
+ ) # delete categorical column
+ source_df = grp[source_column_names]
+ trans_out = translate_codes(
+ source_df,
+ target_code_type=target_code_type,
+ concept_name=concept_set_name,
+ not_translate=not_translate,
+ )
+ trans_out = add_metadata(
+ codes=trans_out,
+ metadata=concept_set_metadata,
+ no_metadata=no_metadata,
+ )
+ out = pd.concat([out, trans_out])
+ else:
+ source_df = df[source_column_names]
+ trans_out = translate_codes(
+ source_df,
+ target_code_type=target_code_type,
+ concept_name=concept_set_name,
+ not_translate=not_translate,
+ )
+ trans_out = add_metadata(
+ codes=trans_out,
+ metadata=concept_set_metadata,
+ no_metadata=no_metadata,
+ )
+ out = pd.concat([out, trans_out])
if len(code_errors) > 0:
_logger.error(f"The map processing has {len(code_errors)} errors")
@@ -894,48 +924,51 @@ def _map_target_code_type(phen_path: Path, phenotype: dict, target_code_type: st
out = out.drop_duplicates(subset=["CONCEPT_SET", "CONCEPT"])
out = out.sort_values(by=["CONCEPT_SET", "CONCEPT"])
- out_count = len(out.index)
+ # out_count = len(out.index)
# added metadata
# Loop over each source_concept_type and perform the left join on all columns apart from source code columns
- result_list = []
- source_column_names = list(concept_set["file"]["columns"].keys())
- for source_concept_type in source_column_names:
- # Filter output based on the current source_concept_type
- out_filtered_df = out[out["SOURCE_CONCEPT_TYPE"] == source_concept_type]
- filtered_count = len(out_filtered_df.index)
-
- # Remove the source type columns except the current type will leave the metadata and the join
- remove_types = [
- type for type in source_column_names if type != source_concept_type
- ]
- metadata_df = df.drop(columns=remove_types)
- metadata_df = metadata_df.rename(
- columns={source_concept_type: "SOURCE_CONCEPT"}
- )
- metadata_df_count = len(metadata_df.index)
-
- # Perform the left join with df2 on SOURCE_CONCEPT to add the metadata
- result = pd.merge(out_filtered_df, metadata_df, how="left", on="SOURCE_CONCEPT")
- result_count = len(result.index)
-
- _logger.debug(
- f"Adding metadata for {source_concept_type}: out_count {out_count}, filtered_count {filtered_count}, metadata_df_count {metadata_df_count}, result_count {result_count}"
- )
-
- # Append the result to the result_list
- result_list.append(result)
+ # result_list = []
+ # for files in phenotype["concept_sets"]:
+ # concept_set_name = files["name"]
+ # for concept_set in files["files"]:
+ # source_column_names = list(concept_set["columns"].keys())
+ # for source_concept_type in source_column_names:
+ # # Filter output based on the current source_concept_type
+ # out_filtered_df = out[out["SOURCE_CONCEPT_TYPE"] == source_concept_type]
+ # filtered_count = len(out_filtered_df.index)
+
+ # # Remove the source type columns except the current type will leave the metadata and the join
+ # remove_types = [
+ # type for type in source_column_names if type != source_concept_type
+ # ]
+ # metadata_df = df.drop(columns=remove_types)
+ # metadata_df = metadata_df.rename(
+ # columns={source_concept_type: "SOURCE_CONCEPT"}
+ # )
+ # metadata_df_count = len(metadata_df.index)
+
+ # Perform the left join with df2 on SOURCE_CONCEPT to add the metadata
+ # result = pd.merge(out_filtered_df, metadata_df, how="left", on="SOURCE_CONCEPT")
+ # result_count = len(result.index)
+
+ # _logger.debug(
+ # f"Adding metadata for {source_concept_type}: out_count {out_count}, filtered_count {filtered_count}, metadata_df_count {metadata_df_count}, result_count {result_count}"
+ # )
+
+ # # Append the result to the result_list
+ # result_list.append(result)
# Concatenate all the results into a single DataFrame
- final_out = pd.concat(result_list, ignore_index=True)
- final_out = final_out.drop_duplicates(subset=["CONCEPT_SET", "CONCEPT"])
- _logger.debug(
- f"Check metadata processing counts: before {len(out.index)} : after {len(final_out.index)}"
- )
+ # final_out = pd.concat(result_list, ignore_index=True)
+ # final_out = final_out.drop_duplicates(subset=["CONCEPT_SET", "CONCEPT"])
+ # _logger.debug(
+ # f"Check metadata processing counts: before {len(out.index)} : after {len(final_out.index)}"
+ # )
# Save output to map directory
output_filename = target_code_type + ".csv"
map_path = phen_path / MAP_DIR / output_filename
- final_out.to_csv(map_path, index=False)
+ out.to_csv(map_path, index=False)
_logger.info(f"Saved mapped concepts to {str(map_path.resolve())}")
# save concept sets as separate files
@@ -950,7 +983,7 @@ def _map_target_code_type(phen_path: Path, phenotype: dict, target_code_type: st
concept_set_path.mkdir(parents=True, exist_ok=True)
# write each concept as a separate file
- for name, concept in final_out.groupby("CONCEPT_SET"):
+ for name, concept in out.groupby("CONCEPT_SET"):
concept = concept.sort_values(by="CONCEPT") # sort rows
concept = concept.dropna(how="all", axis=1) # remove empty cols
concept = concept.reindex(
@@ -965,6 +998,22 @@ def _map_target_code_type(phen_path: Path, phenotype: dict, target_code_type: st
_logger.info(f"Phenotype processed target code type {target_code_type}")
+# Add metadata dict to each row of Df codes
+def add_metadata(
+ codes: pd.DataFrame, metadata: dict, no_metadata:bool,
+) -> pd.DataFrame:
+ """Add concept set metadata, stored as a dictionary, to each concept row"""
+
+ if not no_metadata:
+ for meta_name, meta_value in metadata.items():
+ codes[meta_name] = meta_value
+ _logger.debug(
+ f"Adding metadata for concept set: metadata name {meta_name}, metadata value {meta_value}"
+ )
+
+ return codes
+
+
def _generate_version_tag(
repo: git.Repo, increment: str = DEFAULT_VERSION_INC, use_v_prefix: bool = False
) -> str:
@@ -1165,7 +1214,7 @@ def copy(phen_dir: str, target_dir: str, version: str):
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"]
+ item["name"]: [file["path"] for file in item["files"]]
for item in config_data["phenotype"]["concept_sets"]
}
name_set = set(concepts_dict.keys())
@@ -1190,7 +1239,7 @@ def diff_config(old_config: dict, new_config: dict) -> str:
old_concepts, old_names = extract_concepts(old_config)
new_concepts, new_names = extract_concepts(new_config)
- # Check added and removed names
+ # Check added and removed concept set names
added_names = new_names - old_names # Names that appear in new but not in old
removed_names = old_names - new_names # Names that were in old but not in new
@@ -1331,37 +1380,42 @@ def diff_phen(
old_phen_path: Path,
old_version: str,
report_path: Path,
+ not_check_config:bool,
):
"""Compare the differences between two versions of a phenotype"""
- # validate phenotypes
- _logger.debug(f"Validating for diff old path: {str(old_phen_path.resolve())}")
- validate(str(old_phen_path.resolve()))
- _logger.debug(f"Validating for diff new path: {str(new_phen_path.resolve())}")
- validate(str(new_phen_path.resolve()))
-
- # get old and new config
- old_config_path = old_phen_path / CONFIG_FILE
- with old_config_path.open("r") as file:
- old_config = yaml.safe_load(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
report = f"# Phenotype Comparison Report\n"
- report += f"## Original phenotype\n"
- report += f" - {old_config['phenotype']['omop']['vocabulary_id']}\n"
- report += f" - {old_version}\n"
- report += f" - {str(old_phen_path.resolve())}\n"
- report += f"## Changed phenotype:\n"
- report += f" - {new_config['phenotype']['omop']['vocabulary_id']}\n"
- report += f" - {new_version}\n"
- report += f" - {str(new_phen_path.resolve())}\n"
# Step 1: check differences configuration files
- # Convert list of dicts into a dict: {name: file}
- report += diff_config(old_config, new_config)
+ if not not_check_config:
+ # validate phenotypes
+ _logger.debug(f"Validating for diff old path: {str(old_phen_path.resolve())}")
+ validate(str(old_phen_path.resolve()))
+ _logger.debug(f"Validating for diff new path: {str(new_phen_path.resolve())}")
+ validate(str(new_phen_path.resolve()))
+
+ # get old and new config
+ old_config_path = old_phen_path / CONFIG_FILE
+ with old_config_path.open("r") as file:
+ old_config = yaml.safe_load(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
+ report += f"## Original phenotype\n"
+ report += f" - {old_config['phenotype']['omop']['vocabulary_id']}\n"
+ report += f" - {old_version}\n"
+ report += f" - {str(old_phen_path.resolve())}\n"
+ report += f"## Changed phenotype:\n"
+ report += f" - {new_config['phenotype']['omop']['vocabulary_id']}\n"
+ report += f" - {new_version}\n"
+ report += f" - {str(new_phen_path.resolve())}\n"
+
+
+ # Convert list of dicts into a dict: {name: file}
+ report += diff_config(old_config, new_config)
# Step 2: check differences between map files
# List files from output directories
@@ -1378,7 +1432,7 @@ def diff_phen(
_logger.info(f"Phenotypes diff'd successfully")
-def diff(phen_dir: str, version: str, old_phen_dir: str, old_version: str):
+def diff(phen_dir: str, version: str, old_phen_dir: str, old_version: str, not_check_config:bool):
# make tmp directory .acmc
timestamp = time.strftime("%Y%m%d_%H%M%S")
temp_dir = Path(f".acmc/diff_{timestamp}")
@@ -1439,7 +1493,7 @@ def diff(phen_dir: str, version: str, old_phen_dir: str, old_version: str):
report_filename = f"{version}_{old_version}_diff.md"
report_path = changed_phen_path / report_filename
# diff old with new
- diff_phen(changed_path, version, old_path, old_version, report_path)
+ diff_phen(changed_path, version, old_path, old_version, report_path, not_check_config)
finally:
# clean up tmp directory
diff --git a/docs/api/acmc/parse.html b/docs/api/acmc/parse.html
index 5d2182dc2640e8a671ca2a536c49c80f30064dfc..3ca978f8d37c501eca47c86680c9181f4b20499e 100644
--- a/docs/api/acmc/parse.html
+++ b/docs/api/acmc/parse.html
@@ -760,7 +760,7 @@
<section id="SUPPORTED_CODE_TYPES">
<div class="attr variable">
<span class="name">SUPPORTED_CODE_TYPES</span> =
-<span class="default_value">{'opcs4', 'icd10', 'atc', 'snomed', 'read2', 'read3'}</span>
+<span class="default_value">{'atc', 'read2', 'read3', 'opcs4', 'snomed', 'icd10'}</span>
</div>
diff --git a/docs/api/acmc/phen.html b/docs/api/acmc/phen.html
index 9f4c04524baea858ad71648b0631c81b8cf264c3..9d51899d018e2905b88a58c08a98c9bd248e676f 100644
--- a/docs/api/acmc/phen.html
+++ b/docs/api/acmc/phen.html
@@ -295,1325 +295,1338 @@
</span><span id="L-127"><a href="#L-127"><span class="linenos"> 127</span></a> <span class="s2">"type"</span><span class="p">:</span> <span class="s2">"dict"</span><span class="p">,</span>
</span><span id="L-128"><a href="#L-128"><span class="linenos"> 128</span></a> <span class="s2">"schema"</span><span class="p">:</span> <span class="p">{</span>
</span><span id="L-129"><a href="#L-129"><span class="linenos"> 129</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-130"><a href="#L-130"><span class="linenos"> 130</span></a> <span class="s2">"file"</span><span class="p">:</span> <span class="p">{</span>
-</span><span id="L-131"><a href="#L-131"><span class="linenos"> 131</span></a> <span class="s2">"type"</span><span class="p">:</span> <span class="s2">"dict"</span><span class="p">,</span>
-</span><span id="L-132"><a href="#L-132"><span class="linenos"> 132</span></a> <span class="s2">"required"</span><span class="p">:</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="s2">"files"</span><span class="p">:</span> <span class="p">{</span>
+</span><span id="L-131"><a href="#L-131"><span class="linenos"> 131</span></a> <span class="s2">"type"</span><span class="p">:</span> <span class="s2">"list"</span><span class="p">,</span>
+</span><span id="L-132"><a href="#L-132"><span class="linenos"> 132</span></a> <span class="s2">"required"</span><span class="p">:</span> <span class="kc">True</span><span class="p">,</span>
</span><span id="L-133"><a href="#L-133"><span class="linenos"> 133</span></a> <span class="s2">"schema"</span><span class="p">:</span> <span class="p">{</span>
-</span><span id="L-134"><a href="#L-134"><span class="linenos"> 134</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-135"><a href="#L-135"><span class="linenos"> 135</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-136"><a href="#L-136"><span class="linenos"> 136</span></a> <span class="s2">"category"</span><span class="p">:</span> <span class="p">{</span>
-</span><span id="L-137"><a href="#L-137"><span class="linenos"> 137</span></a> <span class="s2">"type"</span><span class="p">:</span> <span class="s2">"string"</span>
-</span><span id="L-138"><a href="#L-138"><span class="linenos"> 138</span></a> <span class="p">},</span> <span class="c1"># Optional but must be string if present</span>
-</span><span id="L-139"><a href="#L-139"><span class="linenos"> 139</span></a> <span class="s2">"actions"</span><span class="p">:</span> <span class="p">{</span>
-</span><span id="L-140"><a href="#L-140"><span class="linenos"> 140</span></a> <span class="s2">"type"</span><span class="p">:</span> <span class="s2">"dict"</span><span class="p">,</span>
-</span><span id="L-141"><a href="#L-141"><span class="linenos"> 141</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-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="p">},</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="p">},</span>
-</span><span id="L-148"><a href="#L-148"><span class="linenos"> 148</span></a> <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="p">}</span>
-</span><span id="L-151"><a href="#L-151"><span class="linenos"> 151</span></a><span class="sd">"""Phenotype config.yml schema definition"""</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><span id="L-154"><a href="#L-154"><span class="linenos"> 154</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-155"><a href="#L-155"><span class="linenos"> 155</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-134"><a href="#L-134"><span class="linenos"> 134</span></a> <span class="s2">"type"</span><span class="p">:</span> <span class="s2">"dict"</span><span class="p">,</span>
+</span><span id="L-135"><a href="#L-135"><span class="linenos"> 135</span></a> <span class="s2">"schema"</span><span class="p">:</span> <span class="p">{</span>
+</span><span id="L-136"><a href="#L-136"><span class="linenos"> 136</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-137"><a href="#L-137"><span class="linenos"> 137</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-138"><a href="#L-138"><span class="linenos"> 138</span></a> <span class="s2">"category"</span><span class="p">:</span> <span class="p">{</span>
+</span><span id="L-139"><a href="#L-139"><span class="linenos"> 139</span></a> <span class="s2">"type"</span><span class="p">:</span> <span class="s2">"string"</span>
+</span><span id="L-140"><a href="#L-140"><span class="linenos"> 140</span></a> <span class="p">},</span> <span class="c1"># Optional but must be string if present</span>
+</span><span id="L-141"><a href="#L-141"><span class="linenos"> 141</span></a> <span class="s2">"actions"</span><span class="p">:</span> <span class="p">{</span>
+</span><span id="L-142"><a href="#L-142"><span class="linenos"> 142</span></a> <span class="s2">"type"</span><span class="p">:</span> <span class="s2">"dict"</span><span class="p">,</span>
+</span><span id="L-143"><a href="#L-143"><span class="linenos"> 143</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-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="c1"># "metadata": {"type": "dict", "required": True},</span>
+</span><span id="L-147"><a href="#L-147"><span class="linenos"> 147</span></a> <span class="p">},</span>
+</span><span id="L-148"><a href="#L-148"><span class="linenos"> 148</span></a> <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="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="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="sd">"""Phenotype config.yml schema definition"""</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="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-158"><a href="#L-158"><span class="linenos"> 158</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-159"><a href="#L-159"><span class="linenos"> 159</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-157"><a href="#L-157"><span class="linenos"> 157</span></a>
+</span><span id="L-158"><a href="#L-158"><span class="linenos"> 158</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-159"><a href="#L-159"><span class="linenos"> 159</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-160"><a href="#L-160"><span class="linenos"> 160</span></a>
-</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="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-163"><a href="#L-163"><span class="linenos"> 163</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-164"><a href="#L-164"><span class="linenos"> 164</span></a> <span class="c1"># check the url</span>
-</span><span id="L-165"><a href="#L-165"><span class="linenos"> 165</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-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="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-168"><a href="#L-168"><span class="linenos"> 168</span></a> <span class="c1"># need to update this function if the URL scheme is different.</span>
-</span><span id="L-169"><a href="#L-169"><span class="linenos"> 169</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-170"><a href="#L-170"><span class="linenos"> 170</span></a> <span class="c1"># get GitHub PAT from environment variable</span>
-</span><span id="L-171"><a href="#L-171"><span class="linenos"> 171</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-172"><a href="#L-172"><span class="linenos"> 172</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-173"><a href="#L-173"><span class="linenos"> 173</span></a> <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span>
-</span><span id="L-174"><a href="#L-174"><span class="linenos"> 174</span></a> <span class="s2">"GitHub PAT not found. Set the ACMC_GITHUB_PAT environment variable."</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 class="k">else</span><span class="p">:</span>
-</span><span id="L-177"><a href="#L-177"><span class="linenos"> 177</span></a> <span class="c1"># get GitLab PAT from environment variable</span>
-</span><span id="L-178"><a href="#L-178"><span class="linenos"> 178</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-179"><a href="#L-179"><span class="linenos"> 179</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-180"><a href="#L-180"><span class="linenos"> 180</span></a> <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span>
-</span><span id="L-181"><a href="#L-181"><span class="linenos"> 181</span></a> <span class="s2">"GitLab PAT not found. Set the ACMC_GITLAB_PAT environment variable."</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="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-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"># Construct the new URL with credentials</span>
-</span><span id="L-186"><a href="#L-186"><span class="linenos"> 186</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-187"><a href="#L-187"><span class="linenos"> 187</span></a> <span class="k">return</span> <span class="n">urlunparse</span><span class="p">(</span>
-</span><span id="L-188"><a href="#L-188"><span class="linenos"> 188</span></a> <span class="p">(</span>
-</span><span id="L-189"><a href="#L-189"><span class="linenos"> 189</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-190"><a href="#L-190"><span class="linenos"> 190</span></a> <span class="n">new_netloc</span><span class="p">,</span>
-</span><span id="L-191"><a href="#L-191"><span class="linenos"> 191</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-192"><a href="#L-192"><span class="linenos"> 192</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-193"><a href="#L-193"><span class="linenos"> 193</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-194"><a href="#L-194"><span class="linenos"> 194</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-195"><a href="#L-195"><span class="linenos"> 195</span></a> <span class="p">)</span>
-</span><span id="L-196"><a href="#L-196"><span class="linenos"> 196</span></a> <span class="p">)</span>
-</span><span id="L-197"><a href="#L-197"><span class="linenos"> 197</span></a>
-</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="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-200"><a href="#L-200"><span class="linenos"> 200</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-201"><a href="#L-201"><span class="linenos"> 201</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-202"><a href="#L-202"><span class="linenos"> 202</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-203"><a href="#L-203"><span class="linenos"> 203</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-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><span id="L-206"><a href="#L-206"><span class="linenos"> 206</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-207"><a href="#L-207"><span class="linenos"> 207</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-161"><a href="#L-161"><span class="linenos"> 161</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-162"><a href="#L-162"><span class="linenos"> 162</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-163"><a href="#L-163"><span class="linenos"> 163</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-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">_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-167"><a href="#L-167"><span class="linenos"> 167</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-168"><a href="#L-168"><span class="linenos"> 168</span></a> <span class="c1"># check the url</span>
+</span><span id="L-169"><a href="#L-169"><span class="linenos"> 169</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-170"><a href="#L-170"><span class="linenos"> 170</span></a>
+</span><span id="L-171"><a href="#L-171"><span class="linenos"> 171</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-172"><a href="#L-172"><span class="linenos"> 172</span></a> <span class="c1"># need to update this function if the URL scheme is different.</span>
+</span><span id="L-173"><a href="#L-173"><span class="linenos"> 173</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-174"><a href="#L-174"><span class="linenos"> 174</span></a> <span class="c1"># get GitHub PAT from environment variable</span>
+</span><span id="L-175"><a href="#L-175"><span class="linenos"> 175</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-176"><a href="#L-176"><span class="linenos"> 176</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-177"><a href="#L-177"><span class="linenos"> 177</span></a> <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span>
+</span><span id="L-178"><a href="#L-178"><span class="linenos"> 178</span></a> <span class="s2">"GitHub PAT not found. Set the ACMC_GITHUB_PAT environment variable."</span>
+</span><span id="L-179"><a href="#L-179"><span class="linenos"> 179</span></a> <span class="p">)</span>
+</span><span id="L-180"><a href="#L-180"><span class="linenos"> 180</span></a> <span class="k">else</span><span class="p">:</span>
+</span><span id="L-181"><a href="#L-181"><span class="linenos"> 181</span></a> <span class="c1"># get GitLab PAT from environment variable</span>
+</span><span id="L-182"><a href="#L-182"><span class="linenos"> 182</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-183"><a href="#L-183"><span class="linenos"> 183</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-184"><a href="#L-184"><span class="linenos"> 184</span></a> <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span>
+</span><span id="L-185"><a href="#L-185"><span class="linenos"> 185</span></a> <span class="s2">"GitLab PAT not found. Set the ACMC_GITLAB_PAT environment variable."</span>
+</span><span id="L-186"><a href="#L-186"><span class="linenos"> 186</span></a> <span class="p">)</span>
+</span><span id="L-187"><a href="#L-187"><span class="linenos"> 187</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-188"><a href="#L-188"><span class="linenos"> 188</span></a>
+</span><span id="L-189"><a href="#L-189"><span class="linenos"> 189</span></a> <span class="c1"># Construct the new URL with credentials</span>
+</span><span id="L-190"><a href="#L-190"><span class="linenos"> 190</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-191"><a href="#L-191"><span class="linenos"> 191</span></a> <span class="k">return</span> <span class="n">urlunparse</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="n">parsed_url</span><span class="o">.</span><span class="n">scheme</span><span class="p">,</span>
+</span><span id="L-194"><a href="#L-194"><span class="linenos"> 194</span></a> <span class="n">new_netloc</span><span class="p">,</span>
+</span><span id="L-195"><a href="#L-195"><span class="linenos"> 195</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-196"><a href="#L-196"><span class="linenos"> 196</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-197"><a href="#L-197"><span class="linenos"> 197</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-198"><a href="#L-198"><span class="linenos"> 198</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-199"><a href="#L-199"><span class="linenos"> 199</span></a> <span class="p">)</span>
+</span><span id="L-200"><a href="#L-200"><span class="linenos"> 200</span></a> <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><span id="L-203"><a href="#L-203"><span class="linenos"> 203</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-204"><a href="#L-204"><span class="linenos"> 204</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-205"><a href="#L-205"><span class="linenos"> 205</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-206"><a href="#L-206"><span class="linenos"> 206</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-207"><a href="#L-207"><span class="linenos"> 207</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-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="sd"> Args:</span>
-</span><span id="L-210"><a href="#L-210"><span class="linenos"> 210</span></a><span class="sd"> path (Path): path of the directory to be deleted</span>
-</span><span id="L-211"><a href="#L-211"><span class="linenos"> 211</span></a><span class="sd"> msg (str): message to be displayed to the user</span>
+</span><span id="L-209"><a href="#L-209"><span class="linenos"> 209</span></a>
+</span><span id="L-210"><a href="#L-210"><span class="linenos"> 210</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-211"><a href="#L-211"><span class="linenos"> 211</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-212"><a href="#L-212"><span class="linenos"> 212</span></a>
-</span><span id="L-213"><a href="#L-213"><span class="linenos"> 213</span></a><span class="sd"> Returns:</span>
-</span><span id="L-214"><a href="#L-214"><span class="linenos"> 214</span></a><span class="sd"> Boolean: True if deleted</span>
-</span><span id="L-215"><a href="#L-215"><span class="linenos"> 215</span></a><span class="sd"> """</span>
-</span><span id="L-216"><a href="#L-216"><span class="linenos"> 216</span></a> <span class="n">deleted</span> <span class="o">=</span> <span class="kc">False</span>
-</span><span id="L-217"><a href="#L-217"><span class="linenos"> 217</span></a>
-</span><span id="L-218"><a href="#L-218"><span class="linenos"> 218</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-219"><a href="#L-219"><span class="linenos"> 219</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-220"><a href="#L-220"><span class="linenos"> 220</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-221"><a href="#L-221"><span class="linenos"> 221</span></a> <span class="n">deleted</span> <span class="o">=</span> <span class="kc">True</span>
-</span><span id="L-222"><a href="#L-222"><span class="linenos"> 222</span></a> <span class="k">else</span><span class="p">:</span>
-</span><span id="L-223"><a href="#L-223"><span class="linenos"> 223</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-224"><a href="#L-224"><span class="linenos"> 224</span></a>
-</span><span id="L-225"><a href="#L-225"><span class="linenos"> 225</span></a> <span class="k">return</span> <span class="n">deleted</span>
-</span><span id="L-226"><a href="#L-226"><span class="linenos"> 226</span></a>
-</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">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-229"><a href="#L-229"><span class="linenos"> 229</span></a><span class="w"> </span><span class="sd">"""Initial phenotype directory as git repo with standard structure"""</span>
-</span><span id="L-230"><a href="#L-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">"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-231"><a href="#L-231"><span class="linenos"> 231</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-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="c1"># check if directory already exists and ask user if they want to recreate it</span>
-</span><span id="L-234"><a href="#L-234"><span class="linenos"> 234</span></a> <span class="k">if</span> <span class="p">(</span>
-</span><span id="L-235"><a href="#L-235"><span class="linenos"> 235</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-236"><a href="#L-236"><span class="linenos"> 236</span></a> <span class="p">):</span> <span class="c1"># Check if it exists and is a directory</span>
-</span><span id="L-237"><a href="#L-237"><span class="linenos"> 237</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-238"><a href="#L-238"><span class="linenos"> 238</span></a> <span class="n">phen_path</span><span class="p">,</span>
-</span><span id="L-239"><a href="#L-239"><span class="linenos"> 239</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-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="k">else</span><span class="p">:</span>
-</span><span id="L-242"><a href="#L-242"><span class="linenos"> 242</span></a> <span class="n">configure</span> <span class="o">=</span> <span class="kc">True</span>
-</span><span id="L-243"><a href="#L-243"><span class="linenos"> 243</span></a>
-</span><span id="L-244"><a href="#L-244"><span class="linenos"> 244</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-245"><a href="#L-245"><span class="linenos"> 245</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-246"><a href="#L-246"><span class="linenos"> 246</span></a> <span class="k">return</span>
+</span><span id="L-213"><a href="#L-213"><span class="linenos"> 213</span></a><span class="sd"> Args:</span>
+</span><span id="L-214"><a href="#L-214"><span class="linenos"> 214</span></a><span class="sd"> path (Path): path of the directory to be deleted</span>
+</span><span id="L-215"><a href="#L-215"><span class="linenos"> 215</span></a><span class="sd"> msg (str): message to be displayed to the user</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="sd"> Returns:</span>
+</span><span id="L-218"><a href="#L-218"><span class="linenos"> 218</span></a><span class="sd"> Boolean: True if deleted</span>
+</span><span id="L-219"><a href="#L-219"><span class="linenos"> 219</span></a><span class="sd"> """</span>
+</span><span id="L-220"><a href="#L-220"><span class="linenos"> 220</span></a> <span class="n">deleted</span> <span class="o">=</span> <span class="kc">False</span>
+</span><span id="L-221"><a href="#L-221"><span class="linenos"> 221</span></a>
+</span><span id="L-222"><a href="#L-222"><span class="linenos"> 222</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-223"><a href="#L-223"><span class="linenos"> 223</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-224"><a href="#L-224"><span class="linenos"> 224</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-225"><a href="#L-225"><span class="linenos"> 225</span></a> <span class="n">deleted</span> <span class="o">=</span> <span class="kc">True</span>
+</span><span id="L-226"><a href="#L-226"><span class="linenos"> 226</span></a> <span class="k">else</span><span class="p">:</span>
+</span><span id="L-227"><a href="#L-227"><span class="linenos"> 227</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-228"><a href="#L-228"><span class="linenos"> 228</span></a>
+</span><span id="L-229"><a href="#L-229"><span class="linenos"> 229</span></a> <span class="k">return</span> <span class="n">deleted</span>
+</span><span id="L-230"><a href="#L-230"><span class="linenos"> 230</span></a>
+</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">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-233"><a href="#L-233"><span class="linenos"> 233</span></a><span class="w"> </span><span class="sd">"""Initial phenotype directory as git repo with standard structure"""</span>
+</span><span id="L-234"><a href="#L-234"><span class="linenos"> 234</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-235"><a href="#L-235"><span class="linenos"> 235</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-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"># check if directory already exists and ask user if they want to recreate it</span>
+</span><span id="L-238"><a href="#L-238"><span class="linenos"> 238</span></a> <span class="k">if</span> <span class="p">(</span>
+</span><span id="L-239"><a href="#L-239"><span class="linenos"> 239</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-240"><a href="#L-240"><span class="linenos"> 240</span></a> <span class="p">):</span> <span class="c1"># Check if it exists and is a directory</span>
+</span><span id="L-241"><a href="#L-241"><span class="linenos"> 241</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-242"><a href="#L-242"><span class="linenos"> 242</span></a> <span class="n">phen_path</span><span class="p">,</span>
+</span><span id="L-243"><a href="#L-243"><span class="linenos"> 243</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-244"><a href="#L-244"><span class="linenos"> 244</span></a> <span class="p">)</span>
+</span><span id="L-245"><a href="#L-245"><span class="linenos"> 245</span></a> <span class="k">else</span><span class="p">:</span>
+</span><span id="L-246"><a href="#L-246"><span class="linenos"> 246</span></a> <span class="n">configure</span> <span class="o">=</span> <span class="kc">True</span>
</span><span id="L-247"><a href="#L-247"><span class="linenos"> 247</span></a>
-</span><span id="L-248"><a href="#L-248"><span class="linenos"> 248</span></a> <span class="c1"># Initialise repo from local or remote</span>
-</span><span id="L-249"><a href="#L-249"><span class="linenos"> 249</span></a> <span class="n">repo</span><span class="p">:</span> <span class="n">Repo</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 class="c1"># if remote then clone the repo otherwise init a local repo</span>
-</span><span id="L-252"><a href="#L-252"><span class="linenos"> 252</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-253"><a href="#L-253"><span class="linenos"> 253</span></a> <span class="c1"># add PAT token to the URL</span>
-</span><span id="L-254"><a href="#L-254"><span class="linenos"> 254</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-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="c1"># clone the repo</span>
-</span><span id="L-257"><a href="#L-257"><span class="linenos"> 257</span></a> <span class="n">git_cmd</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-258"><a href="#L-258"><span class="linenos"> 258</span></a> <span class="n">git_cmd</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-248"><a href="#L-248"><span class="linenos"> 248</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-249"><a href="#L-249"><span class="linenos"> 249</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-250"><a href="#L-250"><span class="linenos"> 250</span></a> <span class="k">return</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"># Initialise repo from local or remote</span>
+</span><span id="L-253"><a href="#L-253"><span class="linenos"> 253</span></a> <span class="n">repo</span><span class="p">:</span> <span class="n">Repo</span>
+</span><span id="L-254"><a href="#L-254"><span class="linenos"> 254</span></a>
+</span><span id="L-255"><a href="#L-255"><span class="linenos"> 255</span></a> <span class="c1"># if remote then clone the repo otherwise init a local repo</span>
+</span><span id="L-256"><a href="#L-256"><span class="linenos"> 256</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-257"><a href="#L-257"><span class="linenos"> 257</span></a> <span class="c1"># add PAT token to the URL</span>
+</span><span id="L-258"><a href="#L-258"><span class="linenos"> 258</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-259"><a href="#L-259"><span class="linenos"> 259</span></a>
-</span><span id="L-260"><a href="#L-260"><span class="linenos"> 260</span></a> <span class="c1"># open repo</span>
-</span><span id="L-261"><a href="#L-261"><span class="linenos"> 261</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-262"><a href="#L-262"><span class="linenos"> 262</span></a> <span class="c1"># check if there are any commits (new repo has no commits)</span>
-</span><span id="L-263"><a href="#L-263"><span class="linenos"> 263</span></a> <span class="k">if</span> <span class="p">(</span>
-</span><span id="L-264"><a href="#L-264"><span class="linenos"> 264</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-265"><a href="#L-265"><span class="linenos"> 265</span></a> <span class="p">):</span> <span class="c1"># Handle detached HEAD (e.g., after init)</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="s2">"The phen repository has no commits yet."</span><span class="p">)</span>
-</span><span id="L-267"><a href="#L-267"><span class="linenos"> 267</span></a> <span class="n">commit_count</span> <span class="o">=</span> <span class="mi">0</span>
-</span><span id="L-268"><a href="#L-268"><span class="linenos"> 268</span></a> <span class="k">else</span><span class="p">:</span>
-</span><span id="L-269"><a href="#L-269"><span class="linenos"> 269</span></a> <span class="c1"># Get the total number of commits in the default branch</span>
-</span><span id="L-270"><a href="#L-270"><span class="linenos"> 270</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-271"><a href="#L-271"><span class="linenos"> 271</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-272"><a href="#L-272"><span class="linenos"> 272</span></a> <span class="k">else</span><span class="p">:</span>
-</span><span id="L-273"><a href="#L-273"><span class="linenos"> 273</span></a> <span class="c1"># local repo, create the directories and init</span>
-</span><span id="L-274"><a href="#L-274"><span class="linenos"> 274</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-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">"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-276"><a href="#L-276"><span class="linenos"> 276</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-277"><a href="#L-277"><span class="linenos"> 277</span></a> <span class="n">commit_count</span> <span class="o">=</span> <span class="mi">0</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">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-280"><a href="#L-280"><span class="linenos"> 280</span></a> <span class="c1"># initialise empty repos</span>
-</span><span id="L-281"><a href="#L-281"><span class="linenos"> 281</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-282"><a href="#L-282"><span class="linenos"> 282</span></a> <span class="c1"># create initial commit</span>
-</span><span id="L-283"><a href="#L-283"><span class="linenos"> 283</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-284"><a href="#L-284"><span class="linenos"> 284</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-285"><a href="#L-285"><span class="linenos"> 285</span></a> <span class="n">file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span>
-</span><span id="L-286"><a href="#L-286"><span class="linenos"> 286</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-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="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-289"><a href="#L-289"><span class="linenos"> 289</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-290"><a href="#L-290"><span class="linenos"> 290</span></a> <span class="n">commit_count</span> <span class="o">=</span> <span class="mi">1</span>
-</span><span id="L-291"><a href="#L-291"><span class="linenos"> 291</span></a>
-</span><span id="L-292"><a href="#L-292"><span class="linenos"> 292</span></a> <span class="c1"># Checkout the phens default branch, creating it if it does not exist</span>
-</span><span id="L-293"><a href="#L-293"><span class="linenos"> 293</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-294"><a href="#L-294"><span class="linenos"> 294</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-295"><a href="#L-295"><span class="linenos"> 295</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-296"><a href="#L-296"><span class="linenos"> 296</span></a> <span class="k">else</span><span class="p">:</span>
-</span><span id="L-297"><a href="#L-297"><span class="linenos"> 297</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-298"><a href="#L-298"><span class="linenos"> 298</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-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="c1"># if the phen path does not contain the config file then initialise the phen type</span>
-</span><span id="L-301"><a href="#L-301"><span class="linenos"> 301</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-302"><a href="#L-302"><span class="linenos"> 302</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-303"><a href="#L-303"><span class="linenos"> 303</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-304"><a href="#L-304"><span class="linenos"> 304</span></a> <span class="k">return</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="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-307"><a href="#L-307"><span class="linenos"> 307</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-308"><a href="#L-308"><span class="linenos"> 308</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-260"><a href="#L-260"><span class="linenos"> 260</span></a> <span class="c1"># clone the repo</span>
+</span><span id="L-261"><a href="#L-261"><span class="linenos"> 261</span></a> <span class="n">git_cmd</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-262"><a href="#L-262"><span class="linenos"> 262</span></a> <span class="n">git_cmd</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-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"># open repo</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">Repo</span><span class="p">(</span><span class="n">phen_path</span><span class="p">)</span>
+</span><span id="L-266"><a href="#L-266"><span class="linenos"> 266</span></a> <span class="c1"># check if there are any commits (new repo has no commits)</span>
+</span><span id="L-267"><a href="#L-267"><span class="linenos"> 267</span></a> <span class="k">if</span> <span class="p">(</span>
+</span><span id="L-268"><a href="#L-268"><span class="linenos"> 268</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-269"><a href="#L-269"><span class="linenos"> 269</span></a> <span class="p">):</span> <span class="c1"># Handle detached HEAD (e.g., after init)</span>
+</span><span id="L-270"><a href="#L-270"><span class="linenos"> 270</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-271"><a href="#L-271"><span class="linenos"> 271</span></a> <span class="n">commit_count</span> <span class="o">=</span> <span class="mi">0</span>
+</span><span id="L-272"><a href="#L-272"><span class="linenos"> 272</span></a> <span class="k">else</span><span class="p">:</span>
+</span><span id="L-273"><a href="#L-273"><span class="linenos"> 273</span></a> <span class="c1"># Get the total number of commits in the default branch</span>
+</span><span id="L-274"><a href="#L-274"><span class="linenos"> 274</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-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">"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-276"><a href="#L-276"><span class="linenos"> 276</span></a> <span class="k">else</span><span class="p">:</span>
+</span><span id="L-277"><a href="#L-277"><span class="linenos"> 277</span></a> <span class="c1"># local repo, create the directories and init</span>
+</span><span id="L-278"><a href="#L-278"><span class="linenos"> 278</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-279"><a href="#L-279"><span class="linenos"> 279</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-280"><a href="#L-280"><span class="linenos"> 280</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-281"><a href="#L-281"><span class="linenos"> 281</span></a> <span class="n">commit_count</span> <span class="o">=</span> <span class="mi">0</span>
+</span><span id="L-282"><a href="#L-282"><span class="linenos"> 282</span></a>
+</span><span id="L-283"><a href="#L-283"><span class="linenos"> 283</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-284"><a href="#L-284"><span class="linenos"> 284</span></a> <span class="c1"># initialise empty repos</span>
+</span><span id="L-285"><a href="#L-285"><span class="linenos"> 285</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-286"><a href="#L-286"><span class="linenos"> 286</span></a> <span class="c1"># create initial commit</span>
+</span><span id="L-287"><a href="#L-287"><span class="linenos"> 287</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-288"><a href="#L-288"><span class="linenos"> 288</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-289"><a href="#L-289"><span class="linenos"> 289</span></a> <span class="n">file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span>
+</span><span id="L-290"><a href="#L-290"><span class="linenos"> 290</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-291"><a href="#L-291"><span class="linenos"> 291</span></a> <span class="p">)</span>
+</span><span id="L-292"><a href="#L-292"><span class="linenos"> 292</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-293"><a href="#L-293"><span class="linenos"> 293</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-294"><a href="#L-294"><span class="linenos"> 294</span></a> <span class="n">commit_count</span> <span class="o">=</span> <span class="mi">1</span>
+</span><span id="L-295"><a href="#L-295"><span class="linenos"> 295</span></a>
+</span><span id="L-296"><a href="#L-296"><span class="linenos"> 296</span></a> <span class="c1"># Checkout the phens default branch, creating it if it does not exist</span>
+</span><span id="L-297"><a href="#L-297"><span class="linenos"> 297</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-298"><a href="#L-298"><span class="linenos"> 298</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-299"><a href="#L-299"><span class="linenos"> 299</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-300"><a href="#L-300"><span class="linenos"> 300</span></a> <span class="k">else</span><span class="p">:</span>
+</span><span id="L-301"><a href="#L-301"><span class="linenos"> 301</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-302"><a href="#L-302"><span class="linenos"> 302</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-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"># if the phen path does not contain the config file then initialise the phen type</span>
+</span><span id="L-305"><a href="#L-305"><span class="linenos"> 305</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-306"><a href="#L-306"><span class="linenos"> 306</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-307"><a href="#L-307"><span class="linenos"> 307</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-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"># create empty phen config file</span>
-</span><span id="L-311"><a href="#L-311"><span class="linenos"> 311</span></a> <span class="n">config</span> <span class="o">=</span> <span class="p">{</span>
-</span><span id="L-312"><a href="#L-312"><span class="linenos"> 312</span></a> <span class="s2">"phenotype"</span><span class="p">:</span> <span class="p">{</span>
-</span><span id="L-313"><a href="#L-313"><span class="linenos"> 313</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-314"><a href="#L-314"><span class="linenos"> 314</span></a> <span class="s2">"omop"</span><span class="p">:</span> <span class="p">{</span>
-</span><span id="L-315"><a href="#L-315"><span class="linenos"> 315</span></a> <span class="s2">"vocabulary_id"</span><span class="p">:</span> <span class="s2">""</span><span class="p">,</span>
-</span><span id="L-316"><a href="#L-316"><span class="linenos"> 316</span></a> <span class="s2">"vocabulary_name"</span><span class="p">:</span> <span class="s2">""</span><span class="p">,</span>
-</span><span id="L-317"><a href="#L-317"><span class="linenos"> 317</span></a> <span class="s2">"vocabulary_reference"</span><span class="p">:</span> <span class="s2">""</span><span class="p">,</span>
-</span><span id="L-318"><a href="#L-318"><span class="linenos"> 318</span></a> <span class="p">},</span>
-</span><span id="L-319"><a href="#L-319"><span class="linenos"> 319</span></a> <span class="s2">"translate"</span><span class="p">:</span> <span class="p">[],</span>
-</span><span id="L-320"><a href="#L-320"><span class="linenos"> 320</span></a> <span class="s2">"concept_sets"</span><span class="p">:</span> <span class="p">[],</span>
-</span><span id="L-321"><a href="#L-321"><span class="linenos"> 321</span></a> <span class="p">}</span>
-</span><span id="L-322"><a href="#L-322"><span class="linenos"> 322</span></a> <span class="p">}</span>
-</span><span id="L-323"><a href="#L-323"><span class="linenos"> 323</span></a>
-</span><span id="L-324"><a href="#L-324"><span class="linenos"> 324</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-325"><a href="#L-325"><span class="linenos"> 325</span></a> <span class="n">yaml</span><span class="o">.</span><span class="n">dump</span><span class="p">(</span>
-</span><span id="L-326"><a href="#L-326"><span class="linenos"> 326</span></a> <span class="n">config</span><span class="p">,</span>
-</span><span id="L-327"><a href="#L-327"><span class="linenos"> 327</span></a> <span class="n">file</span><span class="p">,</span>
-</span><span id="L-328"><a href="#L-328"><span class="linenos"> 328</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-329"><a href="#L-329"><span class="linenos"> 329</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-330"><a href="#L-330"><span class="linenos"> 330</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-331"><a href="#L-331"><span class="linenos"> 331</span></a> <span class="n">default_style</span><span class="o">=</span><span class="s1">'"'</span><span class="p">,</span>
-</span><span id="L-332"><a href="#L-332"><span class="linenos"> 332</span></a> <span class="p">)</span>
-</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="c1"># add git ignore</span>
-</span><span id="L-335"><a href="#L-335"><span class="linenos"> 335</span></a> <span class="n">ignore_content</span> <span class="o">=</span> <span class="s2">"""# Ignore SQLite database files</span>
-</span><span id="L-336"><a href="#L-336"><span class="linenos"> 336</span></a><span class="s2">*.db</span>
-</span><span id="L-337"><a href="#L-337"><span class="linenos"> 337</span></a><span class="s2">*.sqlite3</span>
-</span><span id="L-338"><a href="#L-338"><span class="linenos"> 338</span></a><span class="s2"> </span>
-</span><span id="L-339"><a href="#L-339"><span class="linenos"> 339</span></a><span class="s2"># Ignore SQLite journal and metadata files</span>
-</span><span id="L-340"><a href="#L-340"><span class="linenos"> 340</span></a><span class="s2">*.db-journal</span>
-</span><span id="L-341"><a href="#L-341"><span class="linenos"> 341</span></a><span class="s2">*.sqlite3-journal</span>
-</span><span id="L-342"><a href="#L-342"><span class="linenos"> 342</span></a>
-</span><span id="L-343"><a href="#L-343"><span class="linenos"> 343</span></a><span class="s2"># python</span>
-</span><span id="L-344"><a href="#L-344"><span class="linenos"> 344</span></a><span class="s2">.ipynb_checkpoints</span>
-</span><span id="L-345"><a href="#L-345"><span class="linenos"> 345</span></a><span class="s2"> """</span>
-</span><span id="L-346"><a href="#L-346"><span class="linenos"> 346</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-347"><a href="#L-347"><span class="linenos"> 347</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-348"><a href="#L-348"><span class="linenos"> 348</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-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="c1"># add to git repo and commit</span>
-</span><span id="L-351"><a href="#L-351"><span class="linenos"> 351</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-352"><a href="#L-352"><span class="linenos"> 352</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-353"><a href="#L-353"><span class="linenos"> 353</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-354"><a href="#L-354"><span class="linenos"> 354</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-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">_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-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><span id="L-359"><a href="#L-359"><span class="linenos"> 359</span></a><span class="k">def</span><span class="w"> </span><span class="nf">fork</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">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="p">):</span>
-</span><span id="L-360"><a href="#L-360"><span class="linenos"> 360</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-310"><a href="#L-310"><span class="linenos"> 310</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-311"><a href="#L-311"><span class="linenos"> 311</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-312"><a href="#L-312"><span class="linenos"> 312</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-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"># create empty phen config file</span>
+</span><span id="L-315"><a href="#L-315"><span class="linenos"> 315</span></a> <span class="n">config</span> <span class="o">=</span> <span class="p">{</span>
+</span><span id="L-316"><a href="#L-316"><span class="linenos"> 316</span></a> <span class="s2">"phenotype"</span><span class="p">:</span> <span class="p">{</span>
+</span><span id="L-317"><a href="#L-317"><span class="linenos"> 317</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-318"><a href="#L-318"><span class="linenos"> 318</span></a> <span class="s2">"omop"</span><span class="p">:</span> <span class="p">{</span>
+</span><span id="L-319"><a href="#L-319"><span class="linenos"> 319</span></a> <span class="s2">"vocabulary_id"</span><span class="p">:</span> <span class="s2">""</span><span class="p">,</span>
+</span><span id="L-320"><a href="#L-320"><span class="linenos"> 320</span></a> <span class="s2">"vocabulary_name"</span><span class="p">:</span> <span class="s2">""</span><span class="p">,</span>
+</span><span id="L-321"><a href="#L-321"><span class="linenos"> 321</span></a> <span class="s2">"vocabulary_reference"</span><span class="p">:</span> <span class="s2">""</span><span class="p">,</span>
+</span><span id="L-322"><a href="#L-322"><span class="linenos"> 322</span></a> <span class="p">},</span>
+</span><span id="L-323"><a href="#L-323"><span class="linenos"> 323</span></a> <span class="s2">"translate"</span><span class="p">:</span> <span class="p">[],</span>
+</span><span id="L-324"><a href="#L-324"><span class="linenos"> 324</span></a> <span class="s2">"concept_sets"</span><span class="p">:</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="p">}</span>
+</span><span id="L-327"><a href="#L-327"><span class="linenos"> 327</span></a>
+</span><span id="L-328"><a href="#L-328"><span class="linenos"> 328</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-329"><a href="#L-329"><span class="linenos"> 329</span></a> <span class="n">yaml</span><span class="o">.</span><span class="n">dump</span><span class="p">(</span>
+</span><span id="L-330"><a href="#L-330"><span class="linenos"> 330</span></a> <span class="n">config</span><span class="p">,</span>
+</span><span id="L-331"><a href="#L-331"><span class="linenos"> 331</span></a> <span class="n">file</span><span class="p">,</span>
+</span><span id="L-332"><a href="#L-332"><span class="linenos"> 332</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-333"><a href="#L-333"><span class="linenos"> 333</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-334"><a href="#L-334"><span class="linenos"> 334</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-335"><a href="#L-335"><span class="linenos"> 335</span></a> <span class="n">default_style</span><span class="o">=</span><span class="s1">'"'</span><span class="p">,</span>
+</span><span id="L-336"><a href="#L-336"><span class="linenos"> 336</span></a> <span class="p">)</span>
+</span><span id="L-337"><a href="#L-337"><span class="linenos"> 337</span></a>
+</span><span id="L-338"><a href="#L-338"><span class="linenos"> 338</span></a> <span class="c1"># add git ignore</span>
+</span><span id="L-339"><a href="#L-339"><span class="linenos"> 339</span></a> <span class="n">ignore_content</span> <span class="o">=</span> <span class="s2">"""# Ignore SQLite database files</span>
+</span><span id="L-340"><a href="#L-340"><span class="linenos"> 340</span></a><span class="s2">*.db</span>
+</span><span id="L-341"><a href="#L-341"><span class="linenos"> 341</span></a><span class="s2">*.sqlite3</span>
+</span><span id="L-342"><a href="#L-342"><span class="linenos"> 342</span></a><span class="s2"> </span>
+</span><span id="L-343"><a href="#L-343"><span class="linenos"> 343</span></a><span class="s2"># Ignore SQLite journal and metadata files</span>
+</span><span id="L-344"><a href="#L-344"><span class="linenos"> 344</span></a><span class="s2">*.db-journal</span>
+</span><span id="L-345"><a href="#L-345"><span class="linenos"> 345</span></a><span class="s2">*.sqlite3-journal</span>
+</span><span id="L-346"><a href="#L-346"><span class="linenos"> 346</span></a>
+</span><span id="L-347"><a href="#L-347"><span class="linenos"> 347</span></a><span class="s2"># python</span>
+</span><span id="L-348"><a href="#L-348"><span class="linenos"> 348</span></a><span class="s2">.ipynb_checkpoints</span>
+</span><span id="L-349"><a href="#L-349"><span class="linenos"> 349</span></a><span class="s2"> """</span>
+</span><span id="L-350"><a href="#L-350"><span class="linenos"> 350</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-351"><a href="#L-351"><span class="linenos"> 351</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-352"><a href="#L-352"><span class="linenos"> 352</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-353"><a href="#L-353"><span class="linenos"> 353</span></a>
+</span><span id="L-354"><a href="#L-354"><span class="linenos"> 354</span></a> <span class="c1"># add to git repo and commit</span>
+</span><span id="L-355"><a href="#L-355"><span class="linenos"> 355</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-356"><a href="#L-356"><span class="linenos"> 356</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-357"><a href="#L-357"><span class="linenos"> 357</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-358"><a href="#L-358"><span class="linenos"> 358</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-359"><a href="#L-359"><span class="linenos"> 359</span></a>
+</span><span id="L-360"><a href="#L-360"><span class="linenos"> 360</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-361"><a href="#L-361"><span class="linenos"> 361</span></a>
-</span><span id="L-362"><a href="#L-362"><span class="linenos"> 362</span></a><span class="sd"> Args:</span>
-</span><span id="L-363"><a href="#L-363"><span class="linenos"> 363</span></a><span class="sd"> phen_dir (str): local directory path where the upstream repo is to be cloned</span>
-</span><span id="L-364"><a href="#L-364"><span class="linenos"> 364</span></a><span class="sd"> upstream_url (str): url to the upstream repo</span>
-</span><span id="L-365"><a href="#L-365"><span class="linenos"> 365</span></a><span class="sd"> upstream_version (str): version in the upstream repo to clone</span>
-</span><span id="L-366"><a href="#L-366"><span class="linenos"> 366</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-367"><a href="#L-367"><span class="linenos"> 367</span></a>
-</span><span id="L-368"><a href="#L-368"><span class="linenos"> 368</span></a><span class="sd"> Raises:</span>
-</span><span id="L-369"><a href="#L-369"><span class="linenos"> 369</span></a><span class="sd"> ValueError: if the specified version is not in the upstream repo</span>
-</span><span id="L-370"><a href="#L-370"><span class="linenos"> 370</span></a><span class="sd"> ValueError: if the upstream repo is not a valid phenotype repo</span>
-</span><span id="L-371"><a href="#L-371"><span class="linenos"> 371</span></a><span class="sd"> ValueError: if there's any other problems with Git</span>
-</span><span id="L-372"><a href="#L-372"><span class="linenos"> 372</span></a><span class="sd"> """</span>
-</span><span id="L-373"><a href="#L-373"><span class="linenos"> 373</span></a> <span class="n">_logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span>
-</span><span id="L-374"><a href="#L-374"><span class="linenos"> 374</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-375"><a href="#L-375"><span class="linenos"> 375</span></a> <span class="p">)</span>
-</span><span id="L-376"><a href="#L-376"><span class="linenos"> 376</span></a>
-</span><span id="L-377"><a href="#L-377"><span class="linenos"> 377</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-378"><a href="#L-378"><span class="linenos"> 378</span></a> <span class="c1"># check if directory already exists and ask user if they want to recreate it</span>
-</span><span id="L-379"><a href="#L-379"><span class="linenos"> 379</span></a> <span class="k">if</span> <span class="p">(</span>
-</span><span id="L-380"><a href="#L-380"><span class="linenos"> 380</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-381"><a href="#L-381"><span class="linenos"> 381</span></a> <span class="p">):</span> <span class="c1"># Check if it exists and is a directory</span>
-</span><span id="L-382"><a href="#L-382"><span class="linenos"> 382</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-383"><a href="#L-383"><span class="linenos"> 383</span></a> <span class="n">phen_path</span><span class="p">,</span>
-</span><span id="L-384"><a href="#L-384"><span class="linenos"> 384</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-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="k">else</span><span class="p">:</span>
-</span><span id="L-387"><a href="#L-387"><span class="linenos"> 387</span></a> <span class="n">configure</span> <span class="o">=</span> <span class="kc">True</span>
-</span><span id="L-388"><a href="#L-388"><span class="linenos"> 388</span></a>
-</span><span id="L-389"><a href="#L-389"><span class="linenos"> 389</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-390"><a href="#L-390"><span class="linenos"> 390</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-391"><a href="#L-391"><span class="linenos"> 391</span></a> <span class="k">return</span>
+</span><span id="L-362"><a href="#L-362"><span class="linenos"> 362</span></a>
+</span><span id="L-363"><a href="#L-363"><span class="linenos"> 363</span></a><span class="k">def</span><span class="w"> </span><span class="nf">fork</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">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="p">):</span>
+</span><span id="L-364"><a href="#L-364"><span class="linenos"> 364</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-365"><a href="#L-365"><span class="linenos"> 365</span></a>
+</span><span id="L-366"><a href="#L-366"><span class="linenos"> 366</span></a><span class="sd"> Args:</span>
+</span><span id="L-367"><a href="#L-367"><span class="linenos"> 367</span></a><span class="sd"> phen_dir (str): local directory path where the upstream repo is to be cloned</span>
+</span><span id="L-368"><a href="#L-368"><span class="linenos"> 368</span></a><span class="sd"> upstream_url (str): url to the upstream repo</span>
+</span><span id="L-369"><a href="#L-369"><span class="linenos"> 369</span></a><span class="sd"> upstream_version (str): version in the upstream repo to clone</span>
+</span><span id="L-370"><a href="#L-370"><span class="linenos"> 370</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-371"><a href="#L-371"><span class="linenos"> 371</span></a>
+</span><span id="L-372"><a href="#L-372"><span class="linenos"> 372</span></a><span class="sd"> Raises:</span>
+</span><span id="L-373"><a href="#L-373"><span class="linenos"> 373</span></a><span class="sd"> ValueError: if the specified version is not in the upstream repo</span>
+</span><span id="L-374"><a href="#L-374"><span class="linenos"> 374</span></a><span class="sd"> ValueError: if the upstream repo is not a valid phenotype repo</span>
+</span><span id="L-375"><a href="#L-375"><span class="linenos"> 375</span></a><span class="sd"> ValueError: if there's any other problems with Git</span>
+</span><span id="L-376"><a href="#L-376"><span class="linenos"> 376</span></a><span class="sd"> """</span>
+</span><span id="L-377"><a href="#L-377"><span class="linenos"> 377</span></a> <span class="n">_logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span>
+</span><span id="L-378"><a href="#L-378"><span class="linenos"> 378</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-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><span id="L-381"><a href="#L-381"><span class="linenos"> 381</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-382"><a href="#L-382"><span class="linenos"> 382</span></a> <span class="c1"># check if directory already exists and ask user if they want to recreate it</span>
+</span><span id="L-383"><a href="#L-383"><span class="linenos"> 383</span></a> <span class="k">if</span> <span class="p">(</span>
+</span><span id="L-384"><a href="#L-384"><span class="linenos"> 384</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-385"><a href="#L-385"><span class="linenos"> 385</span></a> <span class="p">):</span> <span class="c1"># Check if it exists and is a directory</span>
+</span><span id="L-386"><a href="#L-386"><span class="linenos"> 386</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-387"><a href="#L-387"><span class="linenos"> 387</span></a> <span class="n">phen_path</span><span class="p">,</span>
+</span><span id="L-388"><a href="#L-388"><span class="linenos"> 388</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-389"><a href="#L-389"><span class="linenos"> 389</span></a> <span class="p">)</span>
+</span><span id="L-390"><a href="#L-390"><span class="linenos"> 390</span></a> <span class="k">else</span><span class="p">:</span>
+</span><span id="L-391"><a href="#L-391"><span class="linenos"> 391</span></a> <span class="n">configure</span> <span class="o">=</span> <span class="kc">True</span>
</span><span id="L-392"><a href="#L-392"><span class="linenos"> 392</span></a>
-</span><span id="L-393"><a href="#L-393"><span class="linenos"> 393</span></a> <span class="k">try</span><span class="p">:</span>
-</span><span id="L-394"><a href="#L-394"><span class="linenos"> 394</span></a> <span class="c1"># Clone repo</span>
-</span><span id="L-395"><a href="#L-395"><span class="linenos"> 395</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-396"><a href="#L-396"><span class="linenos"> 396</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-397"><a href="#L-397"><span class="linenos"> 397</span></a>
-</span><span id="L-398"><a href="#L-398"><span class="linenos"> 398</span></a> <span class="c1"># Fetch all branches and tags</span>
-</span><span id="L-399"><a href="#L-399"><span class="linenos"> 399</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-400"><a href="#L-400"><span class="linenos"> 400</span></a>
-</span><span id="L-401"><a href="#L-401"><span class="linenos"> 401</span></a> <span class="c1"># Check if the version exists</span>
-</span><span id="L-402"><a href="#L-402"><span class="linenos"> 402</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-403"><a href="#L-403"><span class="linenos"> 403</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-404"><a href="#L-404"><span class="linenos"> 404</span></a> <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span>
-</span><span id="L-405"><a href="#L-405"><span class="linenos"> 405</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-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><span id="L-408"><a href="#L-408"><span class="linenos"> 408</span></a> <span class="c1"># Checkout the specified version</span>
-</span><span id="L-409"><a href="#L-409"><span class="linenos"> 409</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-410"><a href="#L-410"><span class="linenos"> 410</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-411"><a href="#L-411"><span class="linenos"> 411</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-412"><a href="#L-412"><span class="linenos"> 412</span></a>
-</span><span id="L-413"><a href="#L-413"><span class="linenos"> 413</span></a> <span class="c1"># Check if 'config.yml' exists in the root directory</span>
-</span><span id="L-414"><a href="#L-414"><span class="linenos"> 414</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.yml"</span>
-</span><span id="L-415"><a href="#L-415"><span class="linenos"> 415</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-416"><a href="#L-416"><span class="linenos"> 416</span></a> <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span>
-</span><span id="L-417"><a href="#L-417"><span class="linenos"> 417</span></a> <span class="sa">f</span><span class="s2">"The forked repository is not a valid ACMC repo because 'config.yml' is missing in the root directory."</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><span id="L-420"><a href="#L-420"><span class="linenos"> 420</span></a> <span class="c1"># Validate the phenotype is compatible with the acmc tool</span>
-</span><span id="L-421"><a href="#L-421"><span class="linenos"> 421</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-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 class="c1"># Delete each tag locally</span>
-</span><span id="L-424"><a href="#L-424"><span class="linenos"> 424</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-425"><a href="#L-425"><span class="linenos"> 425</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-426"><a href="#L-426"><span class="linenos"> 426</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-427"><a href="#L-427"><span class="linenos"> 427</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-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="c1"># Add upstream remote</span>
-</span><span id="L-430"><a href="#L-430"><span class="linenos"> 430</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-431"><a href="#L-431"><span class="linenos"> 431</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-432"><a href="#L-432"><span class="linenos"> 432</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-433"><a href="#L-433"><span class="linenos"> 433</span></a>
-</span><span id="L-434"><a href="#L-434"><span class="linenos"> 434</span></a> <span class="c1"># Optionally set a new origin remote</span>
-</span><span id="L-435"><a href="#L-435"><span class="linenos"> 435</span></a> <span class="k">if</span> <span class="n">new_origin_url</span><span class="p">:</span>
-</span><span id="L-436"><a href="#L-436"><span class="linenos"> 436</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-437"><a href="#L-437"><span class="linenos"> 437</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-438"><a href="#L-438"><span class="linenos"> 438</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-439"><a href="#L-439"><span class="linenos"> 439</span></a>
-</span><span id="L-440"><a href="#L-440"><span class="linenos"> 440</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-441"><a href="#L-441"><span class="linenos"> 441</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-442"><a href="#L-442"><span class="linenos"> 442</span></a> <span class="k">if</span> <span class="n">new_origin_url</span><span class="p">:</span>
-</span><span id="L-443"><a href="#L-443"><span class="linenos"> 443</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-444"><a href="#L-444"><span class="linenos"> 444</span></a>
-</span><span id="L-445"><a href="#L-445"><span class="linenos"> 445</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-446"><a href="#L-446"><span class="linenos"> 446</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-447"><a href="#L-447"><span class="linenos"> 447</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-448"><a href="#L-448"><span class="linenos"> 448</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-449"><a href="#L-449"><span class="linenos"> 449</span></a>
-</span><span id="L-450"><a href="#L-450"><span class="linenos"> 450</span></a>
-</span><span id="L-451"><a href="#L-451"><span class="linenos"> 451</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-452"><a href="#L-452"><span class="linenos"> 452</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-453"><a href="#L-453"><span class="linenos"> 453</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-454"><a href="#L-454"><span class="linenos"> 454</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-455"><a href="#L-455"><span class="linenos"> 455</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-456"><a href="#L-456"><span class="linenos"> 456</span></a> <span class="k">raise</span> <span class="ne">NotADirectoryError</span><span class="p">(</span>
-</span><span id="L-457"><a href="#L-457"><span class="linenos"> 457</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-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><span id="L-460"><a href="#L-460"><span class="linenos"> 460</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-461"><a href="#L-461"><span class="linenos"> 461</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-462"><a href="#L-462"><span class="linenos"> 462</span></a> <span class="k">raise</span> <span class="ne">FileNotFoundError</span><span class="p">(</span>
-</span><span id="L-463"><a href="#L-463"><span class="linenos"> 463</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-464"><a href="#L-464"><span class="linenos"> 464</span></a> <span class="p">)</span>
-</span><span id="L-465"><a href="#L-465"><span class="linenos"> 465</span></a>
-</span><span id="L-466"><a href="#L-466"><span class="linenos"> 466</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-467"><a href="#L-467"><span class="linenos"> 467</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-468"><a href="#L-468"><span class="linenos"> 468</span></a> <span class="k">raise</span> <span class="ne">FileNotFoundError</span><span class="p">(</span>
-</span><span id="L-469"><a href="#L-469"><span class="linenos"> 469</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-470"><a href="#L-470"><span class="linenos"> 470</span></a> <span class="p">)</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"># Calidate the directory is a git repo</span>
-</span><span id="L-473"><a href="#L-473"><span class="linenos"> 473</span></a> <span class="k">try</span><span class="p">:</span>
-</span><span id="L-474"><a href="#L-474"><span class="linenos"> 474</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-475"><a href="#L-475"><span class="linenos"> 475</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-476"><a href="#L-476"><span class="linenos"> 476</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-477"><a href="#L-477"><span class="linenos"> 477</span></a>
-</span><span id="L-478"><a href="#L-478"><span class="linenos"> 478</span></a> <span class="c1"># Load configuration File</span>
-</span><span id="L-479"><a href="#L-479"><span class="linenos"> 479</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">".yml"</span><span class="p">:</span>
-</span><span id="L-480"><a href="#L-480"><span class="linenos"> 480</span></a> <span class="k">try</span><span class="p">:</span>
-</span><span id="L-481"><a href="#L-481"><span class="linenos"> 481</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-482"><a href="#L-482"><span class="linenos"> 482</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-483"><a href="#L-483"><span class="linenos"> 483</span></a>
-</span><span id="L-484"><a href="#L-484"><span class="linenos"> 484</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-485"><a href="#L-485"><span class="linenos"> 485</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-486"><a href="#L-486"><span class="linenos"> 486</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-487"><a href="#L-487"><span class="linenos"> 487</span></a> <span class="k">else</span><span class="p">:</span>
-</span><span id="L-488"><a href="#L-488"><span class="linenos"> 488</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-489"><a href="#L-489"><span class="linenos"> 489</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-490"><a href="#L-490"><span class="linenos"> 490</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-491"><a href="#L-491"><span class="linenos"> 491</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-492"><a href="#L-492"><span class="linenos"> 492</span></a> <span class="k">raise</span> <span class="n">e</span>
-</span><span id="L-493"><a href="#L-493"><span class="linenos"> 493</span></a> <span class="k">else</span><span class="p">:</span>
-</span><span id="L-494"><a href="#L-494"><span class="linenos"> 494</span></a> <span class="k">raise</span> <span class="ne">Exception</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">"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-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"># initiatise</span>
-</span><span id="L-499"><a href="#L-499"><span class="linenos"> 499</span></a> <span class="n">validation_errors</span> <span class="o">=</span> <span class="p">[]</span>
-</span><span id="L-500"><a href="#L-500"><span class="linenos"> 500</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-501"><a href="#L-501"><span class="linenos"> 501</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-502"><a href="#L-502"><span class="linenos"> 502</span></a>
-</span><span id="L-503"><a href="#L-503"><span class="linenos"> 503</span></a> <span class="c1"># check the version number is of the format vn.n.n</span>
-</span><span id="L-504"><a href="#L-504"><span class="linenos"> 504</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-505"><a href="#L-505"><span class="linenos"> 505</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-506"><a href="#L-506"><span class="linenos"> 506</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-507"><a href="#L-507"><span class="linenos"> 507</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-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"># create a list of all the concept set names defined in the concept set configuration</span>
-</span><span id="L-511"><a href="#L-511"><span class="linenos"> 511</span></a> <span class="n">concept_set_names</span> <span class="o">=</span> <span class="p">[]</span>
-</span><span id="L-512"><a href="#L-512"><span class="linenos"> 512</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-513"><a href="#L-513"><span class="linenos"> 513</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-514"><a href="#L-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="L-515"><a href="#L-515"><span class="linenos"> 515</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-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="k">else</span><span class="p">:</span>
-</span><span id="L-518"><a href="#L-518"><span class="linenos"> 518</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-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 class="c1"># check codes definition</span>
-</span><span id="L-521"><a href="#L-521"><span class="linenos"> 521</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-522"><a href="#L-522"><span class="linenos"> 522</span></a> <span class="c1"># check concepte code file exists</span>
-</span><span id="L-523"><a href="#L-523"><span class="linenos"> 523</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-524"><a href="#L-524"><span class="linenos"> 524</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-525"><a href="#L-525"><span class="linenos"> 525</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-526"><a href="#L-526"><span class="linenos"> 526</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-527"><a href="#L-527"><span class="linenos"> 527</span></a> <span class="p">)</span>
-</span><span id="L-528"><a href="#L-528"><span class="linenos"> 528</span></a>
-</span><span id="L-529"><a href="#L-529"><span class="linenos"> 529</span></a> <span class="c1"># check concepte code file is not empty</span>
-</span><span id="L-530"><a href="#L-530"><span class="linenos"> 530</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-531"><a href="#L-531"><span class="linenos"> 531</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-532"><a href="#L-532"><span class="linenos"> 532</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-533"><a href="#L-533"><span class="linenos"> 533</span></a> <span class="p">)</span>
-</span><span id="L-534"><a href="#L-534"><span class="linenos"> 534</span></a>
-</span><span id="L-535"><a href="#L-535"><span class="linenos"> 535</span></a> <span class="c1"># check code file type is supported</span>
-</span><span id="L-536"><a href="#L-536"><span class="linenos"> 536</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-537"><a href="#L-537"><span class="linenos"> 537</span></a> <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span>
-</span><span id="L-538"><a href="#L-538"><span class="linenos"> 538</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-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><span id="L-541"><a href="#L-541"><span class="linenos"> 541</span></a> <span class="c1"># check columns specified are a supported medical coding type</span>
-</span><span id="L-542"><a href="#L-542"><span class="linenos"> 542</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-543"><a href="#L-543"><span class="linenos"> 543</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-544"><a href="#L-544"><span class="linenos"> 544</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-545"><a href="#L-545"><span class="linenos"> 545</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-546"><a href="#L-546"><span class="linenos"> 546</span></a> <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="c1"># check the actions are supported</span>
-</span><span id="L-549"><a href="#L-549"><span class="linenos"> 549</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-550"><a href="#L-550"><span class="linenos"> 550</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-551"><a href="#L-551"><span class="linenos"> 551</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-552"><a href="#L-552"><span class="linenos"> 552</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-553"><a href="#L-553"><span class="linenos"> 553</span></a>
-</span><span id="L-554"><a href="#L-554"><span class="linenos"> 554</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-555"><a href="#L-555"><span class="linenos"> 555</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-556"><a href="#L-556"><span class="linenos"> 556</span></a> <span class="k">raise</span> <span class="n">PhenValidationException</span><span class="p">(</span>
-</span><span id="L-557"><a href="#L-557"><span class="linenos"> 557</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-558"><a href="#L-558"><span class="linenos"> 558</span></a> <span class="n">validation_errors</span><span class="p">,</span>
-</span><span id="L-559"><a href="#L-559"><span class="linenos"> 559</span></a> <span class="p">)</span>
-</span><span id="L-560"><a href="#L-560"><span class="linenos"> 560</span></a>
-</span><span id="L-561"><a href="#L-561"><span class="linenos"> 561</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-562"><a href="#L-562"><span class="linenos"> 562</span></a>
-</span><span id="L-563"><a href="#L-563"><span class="linenos"> 563</span></a>
-</span><span id="L-564"><a href="#L-564"><span class="linenos"> 564</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-565"><a href="#L-565"><span class="linenos"> 565</span></a><span class="w"> </span><span class="sd">"""</span>
-</span><span id="L-566"><a href="#L-566"><span class="linenos"> 566</span></a><span class="sd"> Load Code List File</span>
-</span><span id="L-567"><a href="#L-567"><span class="linenos"> 567</span></a><span class="sd"> """</span>
+</span><span id="L-393"><a href="#L-393"><span class="linenos"> 393</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-394"><a href="#L-394"><span class="linenos"> 394</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-395"><a href="#L-395"><span class="linenos"> 395</span></a> <span class="k">return</span>
+</span><span id="L-396"><a href="#L-396"><span class="linenos"> 396</span></a>
+</span><span id="L-397"><a href="#L-397"><span class="linenos"> 397</span></a> <span class="k">try</span><span class="p">:</span>
+</span><span id="L-398"><a href="#L-398"><span class="linenos"> 398</span></a> <span class="c1"># Clone repo</span>
+</span><span id="L-399"><a href="#L-399"><span class="linenos"> 399</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-400"><a href="#L-400"><span class="linenos"> 400</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-401"><a href="#L-401"><span class="linenos"> 401</span></a>
+</span><span id="L-402"><a href="#L-402"><span class="linenos"> 402</span></a> <span class="c1"># Fetch all branches and tags</span>
+</span><span id="L-403"><a href="#L-403"><span class="linenos"> 403</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-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="c1"># Check if the version exists</span>
+</span><span id="L-406"><a href="#L-406"><span class="linenos"> 406</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-407"><a href="#L-407"><span class="linenos"> 407</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-408"><a href="#L-408"><span class="linenos"> 408</span></a> <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span>
+</span><span id="L-409"><a href="#L-409"><span class="linenos"> 409</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-410"><a href="#L-410"><span class="linenos"> 410</span></a> <span class="p">)</span>
+</span><span id="L-411"><a href="#L-411"><span class="linenos"> 411</span></a>
+</span><span id="L-412"><a href="#L-412"><span class="linenos"> 412</span></a> <span class="c1"># Checkout the specified version</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">checkout</span><span class="p">(</span><span class="n">upstream_version</span><span class="p">)</span>
+</span><span id="L-414"><a href="#L-414"><span class="linenos"> 414</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-415"><a href="#L-415"><span class="linenos"> 415</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-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="c1"># Check if 'config.yml' exists in the root directory</span>
+</span><span id="L-418"><a href="#L-418"><span class="linenos"> 418</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.yml"</span>
+</span><span id="L-419"><a href="#L-419"><span class="linenos"> 419</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-420"><a href="#L-420"><span class="linenos"> 420</span></a> <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span>
+</span><span id="L-421"><a href="#L-421"><span class="linenos"> 421</span></a> <span class="sa">f</span><span class="s2">"The forked repository is not a valid ACMC repo because 'config.yml' is missing in the root directory."</span>
+</span><span id="L-422"><a href="#L-422"><span class="linenos"> 422</span></a> <span class="p">)</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"># Validate the phenotype is compatible with the acmc tool</span>
+</span><span id="L-425"><a href="#L-425"><span class="linenos"> 425</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-426"><a href="#L-426"><span class="linenos"> 426</span></a>
+</span><span id="L-427"><a href="#L-427"><span class="linenos"> 427</span></a> <span class="c1"># Delete each tag locally</span>
+</span><span id="L-428"><a href="#L-428"><span class="linenos"> 428</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-429"><a href="#L-429"><span class="linenos"> 429</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-430"><a href="#L-430"><span class="linenos"> 430</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-431"><a href="#L-431"><span class="linenos"> 431</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-432"><a href="#L-432"><span class="linenos"> 432</span></a>
+</span><span id="L-433"><a href="#L-433"><span class="linenos"> 433</span></a> <span class="c1"># Add upstream remote</span>
+</span><span id="L-434"><a href="#L-434"><span class="linenos"> 434</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-435"><a href="#L-435"><span class="linenos"> 435</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-436"><a href="#L-436"><span class="linenos"> 436</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-437"><a href="#L-437"><span class="linenos"> 437</span></a>
+</span><span id="L-438"><a href="#L-438"><span class="linenos"> 438</span></a> <span class="c1"># Optionally set a new origin remote</span>
+</span><span id="L-439"><a href="#L-439"><span class="linenos"> 439</span></a> <span class="k">if</span> <span class="n">new_origin_url</span><span class="p">:</span>
+</span><span id="L-440"><a href="#L-440"><span class="linenos"> 440</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-441"><a href="#L-441"><span class="linenos"> 441</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-442"><a href="#L-442"><span class="linenos"> 442</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-443"><a href="#L-443"><span class="linenos"> 443</span></a>
+</span><span id="L-444"><a href="#L-444"><span class="linenos"> 444</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-445"><a href="#L-445"><span class="linenos"> 445</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-446"><a href="#L-446"><span class="linenos"> 446</span></a> <span class="k">if</span> <span class="n">new_origin_url</span><span class="p">:</span>
+</span><span id="L-447"><a href="#L-447"><span class="linenos"> 447</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-448"><a href="#L-448"><span class="linenos"> 448</span></a>
+</span><span id="L-449"><a href="#L-449"><span class="linenos"> 449</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-450"><a href="#L-450"><span class="linenos"> 450</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-451"><a href="#L-451"><span class="linenos"> 451</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-452"><a href="#L-452"><span class="linenos"> 452</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-453"><a href="#L-453"><span class="linenos"> 453</span></a>
+</span><span id="L-454"><a href="#L-454"><span class="linenos"> 454</span></a>
+</span><span id="L-455"><a href="#L-455"><span class="linenos"> 455</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-456"><a href="#L-456"><span class="linenos"> 456</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-457"><a href="#L-457"><span class="linenos"> 457</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-458"><a href="#L-458"><span class="linenos"> 458</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-459"><a href="#L-459"><span class="linenos"> 459</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-460"><a href="#L-460"><span class="linenos"> 460</span></a> <span class="k">raise</span> <span class="ne">NotADirectoryError</span><span class="p">(</span>
+</span><span id="L-461"><a href="#L-461"><span class="linenos"> 461</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-462"><a href="#L-462"><span class="linenos"> 462</span></a> <span class="p">)</span>
+</span><span id="L-463"><a href="#L-463"><span class="linenos"> 463</span></a>
+</span><span id="L-464"><a href="#L-464"><span class="linenos"> 464</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-465"><a href="#L-465"><span class="linenos"> 465</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-466"><a href="#L-466"><span class="linenos"> 466</span></a> <span class="k">raise</span> <span class="ne">FileNotFoundError</span><span class="p">(</span>
+</span><span id="L-467"><a href="#L-467"><span class="linenos"> 467</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-468"><a href="#L-468"><span class="linenos"> 468</span></a> <span class="p">)</span>
+</span><span id="L-469"><a href="#L-469"><span class="linenos"> 469</span></a>
+</span><span id="L-470"><a href="#L-470"><span class="linenos"> 470</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-471"><a href="#L-471"><span class="linenos"> 471</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-472"><a href="#L-472"><span class="linenos"> 472</span></a> <span class="k">raise</span> <span class="ne">FileNotFoundError</span><span class="p">(</span>
+</span><span id="L-473"><a href="#L-473"><span class="linenos"> 473</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-474"><a href="#L-474"><span class="linenos"> 474</span></a> <span class="p">)</span>
+</span><span id="L-475"><a href="#L-475"><span class="linenos"> 475</span></a>
+</span><span id="L-476"><a href="#L-476"><span class="linenos"> 476</span></a> <span class="c1"># Calidate the directory is a git repo</span>
+</span><span id="L-477"><a href="#L-477"><span class="linenos"> 477</span></a> <span class="k">try</span><span class="p">:</span>
+</span><span id="L-478"><a href="#L-478"><span class="linenos"> 478</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-479"><a href="#L-479"><span class="linenos"> 479</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-480"><a href="#L-480"><span class="linenos"> 480</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-481"><a href="#L-481"><span class="linenos"> 481</span></a>
+</span><span id="L-482"><a href="#L-482"><span class="linenos"> 482</span></a> <span class="c1"># Load configuration File</span>
+</span><span id="L-483"><a href="#L-483"><span class="linenos"> 483</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">".yml"</span><span class="p">:</span>
+</span><span id="L-484"><a href="#L-484"><span class="linenos"> 484</span></a> <span class="k">try</span><span class="p">:</span>
+</span><span id="L-485"><a href="#L-485"><span class="linenos"> 485</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-486"><a href="#L-486"><span class="linenos"> 486</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-487"><a href="#L-487"><span class="linenos"> 487</span></a>
+</span><span id="L-488"><a href="#L-488"><span class="linenos"> 488</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-489"><a href="#L-489"><span class="linenos"> 489</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-490"><a href="#L-490"><span class="linenos"> 490</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-491"><a href="#L-491"><span class="linenos"> 491</span></a> <span class="k">else</span><span class="p">:</span>
+</span><span id="L-492"><a href="#L-492"><span class="linenos"> 492</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-493"><a href="#L-493"><span class="linenos"> 493</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-494"><a href="#L-494"><span class="linenos"> 494</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-495"><a href="#L-495"><span class="linenos"> 495</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-496"><a href="#L-496"><span class="linenos"> 496</span></a> <span class="k">raise</span> <span class="n">e</span>
+</span><span id="L-497"><a href="#L-497"><span class="linenos"> 497</span></a> <span class="k">else</span><span class="p">:</span>
+</span><span id="L-498"><a href="#L-498"><span class="linenos"> 498</span></a> <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span>
+</span><span id="L-499"><a href="#L-499"><span class="linenos"> 499</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-500"><a href="#L-500"><span class="linenos"> 500</span></a> <span class="p">)</span>
+</span><span id="L-501"><a href="#L-501"><span class="linenos"> 501</span></a>
+</span><span id="L-502"><a href="#L-502"><span class="linenos"> 502</span></a> <span class="c1"># initiatise</span>
+</span><span id="L-503"><a href="#L-503"><span class="linenos"> 503</span></a> <span class="n">validation_errors</span> <span class="o">=</span> <span class="p">[]</span>
+</span><span id="L-504"><a href="#L-504"><span class="linenos"> 504</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-505"><a href="#L-505"><span class="linenos"> 505</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-506"><a href="#L-506"><span class="linenos"> 506</span></a>
+</span><span id="L-507"><a href="#L-507"><span class="linenos"> 507</span></a> <span class="c1"># check the version number is of the format vn.n.n</span>
+</span><span id="L-508"><a href="#L-508"><span class="linenos"> 508</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-509"><a href="#L-509"><span class="linenos"> 509</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-510"><a href="#L-510"><span class="linenos"> 510</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-511"><a href="#L-511"><span class="linenos"> 511</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-512"><a href="#L-512"><span class="linenos"> 512</span></a> <span class="p">)</span>
+</span><span id="L-513"><a href="#L-513"><span class="linenos"> 513</span></a>
+</span><span id="L-514"><a href="#L-514"><span class="linenos"> 514</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-515"><a href="#L-515"><span class="linenos"> 515</span></a> <span class="n">concept_set_names</span> <span class="o">=</span> <span class="p">[]</span>
+</span><span id="L-516"><a href="#L-516"><span class="linenos"> 516</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-517"><a href="#L-517"><span class="linenos"> 517</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-518"><a href="#L-518"><span class="linenos"> 518</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-519"><a href="#L-519"><span class="linenos"> 519</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-520"><a href="#L-520"><span class="linenos"> 520</span></a> <span class="p">)</span>
+</span><span id="L-521"><a href="#L-521"><span class="linenos"> 521</span></a> <span class="k">else</span><span class="p">:</span>
+</span><span id="L-522"><a href="#L-522"><span class="linenos"> 522</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-523"><a href="#L-523"><span class="linenos"> 523</span></a>
+</span><span id="L-524"><a href="#L-524"><span class="linenos"> 524</span></a> <span class="c1"># check codes definition</span>
+</span><span id="L-525"><a href="#L-525"><span class="linenos"> 525</span></a> <span class="k">for</span> <span class="n">files</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-526"><a href="#L-526"><span class="linenos"> 526</span></a> <span class="k">for</span> <span class="n">item</span> <span class="ow">in</span> <span class="n">files</span><span class="p">[</span><span class="s2">"files"</span><span class="p">]:</span>
+</span><span id="L-527"><a href="#L-527"><span class="linenos"> 527</span></a> <span class="c1"># check concepte code file exists</span>
+</span><span id="L-528"><a href="#L-528"><span class="linenos"> 528</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">"path"</span><span class="p">]</span>
+</span><span id="L-529"><a href="#L-529"><span class="linenos"> 529</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-530"><a href="#L-530"><span class="linenos"> 530</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-531"><a href="#L-531"><span class="linenos"> 531</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-532"><a href="#L-532"><span class="linenos"> 532</span></a> <span class="p">)</span>
+</span><span id="L-533"><a href="#L-533"><span class="linenos"> 533</span></a>
+</span><span id="L-534"><a href="#L-534"><span class="linenos"> 534</span></a> <span class="c1"># check concepte code file is not empty</span>
+</span><span id="L-535"><a href="#L-535"><span class="linenos"> 535</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-536"><a href="#L-536"><span class="linenos"> 536</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-537"><a href="#L-537"><span class="linenos"> 537</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-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><span id="L-540"><a href="#L-540"><span class="linenos"> 540</span></a> <span class="c1"># check code file type is supported</span>
+</span><span id="L-541"><a href="#L-541"><span class="linenos"> 541</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-542"><a href="#L-542"><span class="linenos"> 542</span></a> <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span>
+</span><span id="L-543"><a href="#L-543"><span class="linenos"> 543</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-544"><a href="#L-544"><span class="linenos"> 544</span></a> <span class="p">)</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="c1"># check columns specified are a supported medical coding type</span>
+</span><span id="L-547"><a href="#L-547"><span class="linenos"> 547</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">"columns"</span><span class="p">]:</span>
+</span><span id="L-548"><a href="#L-548"><span class="linenos"> 548</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-549"><a href="#L-549"><span class="linenos"> 549</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-550"><a href="#L-550"><span class="linenos"> 550</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-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="c1"># check the actions are supported</span>
+</span><span id="L-554"><a href="#L-554"><span class="linenos"> 554</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><span id="L-555"><a href="#L-555"><span class="linenos"> 555</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">"actions"</span><span class="p">]:</span>
+</span><span id="L-556"><a href="#L-556"><span class="linenos"> 556</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-557"><a href="#L-557"><span class="linenos"> 557</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-558"><a href="#L-558"><span class="linenos"> 558</span></a>
+</span><span id="L-559"><a href="#L-559"><span class="linenos"> 559</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-560"><a href="#L-560"><span class="linenos"> 560</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-561"><a href="#L-561"><span class="linenos"> 561</span></a> <span class="k">raise</span> <span class="n">PhenValidationException</span><span class="p">(</span>
+</span><span id="L-562"><a href="#L-562"><span class="linenos"> 562</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-563"><a href="#L-563"><span class="linenos"> 563</span></a> <span class="n">validation_errors</span><span class="p">,</span>
+</span><span id="L-564"><a href="#L-564"><span class="linenos"> 564</span></a> <span class="p">)</span>
+</span><span id="L-565"><a href="#L-565"><span class="linenos"> 565</span></a>
+</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">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-567"><a href="#L-567"><span class="linenos"> 567</span></a>
</span><span id="L-568"><a href="#L-568"><span class="linenos"> 568</span></a>
-</span><span id="L-569"><a href="#L-569"><span class="linenos"> 569</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-570"><a href="#L-570"><span class="linenos"> 570</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-571"><a href="#L-571"><span class="linenos"> 571</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-572"><a href="#L-572"><span class="linenos"> 572</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-573"><a href="#L-573"><span class="linenos"> 573</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-574"><a href="#L-574"><span class="linenos"> 574</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-575"><a href="#L-575"><span class="linenos"> 575</span></a> <span class="k">else</span><span class="p">:</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">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-577"><a href="#L-577"><span class="linenos"> 577</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-578"><a href="#L-578"><span class="linenos"> 578</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-579"><a href="#L-579"><span class="linenos"> 579</span></a> <span class="k">else</span><span class="p">:</span>
-</span><span id="L-580"><a href="#L-580"><span class="linenos"> 580</span></a> <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span>
-</span><span id="L-581"><a href="#L-581"><span class="linenos"> 581</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-582"><a href="#L-582"><span class="linenos"> 582</span></a> <span class="p">)</span>
-</span><span id="L-583"><a href="#L-583"><span class="linenos"> 583</span></a>
-</span><span id="L-584"><a href="#L-584"><span class="linenos"> 584</span></a> <span class="k">return</span> <span class="n">df</span>
-</span><span id="L-585"><a href="#L-585"><span class="linenos"> 585</span></a>
-</span><span id="L-586"><a href="#L-586"><span class="linenos"> 586</span></a>
-</span><span id="L-587"><a href="#L-587"><span class="linenos"> 587</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-588"><a href="#L-588"><span class="linenos"> 588</span></a> <span class="c1"># Perform Structural Changes to file before preprocessing</span>
-</span><span id="L-589"><a href="#L-589"><span class="linenos"> 589</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-590"><a href="#L-590"><span class="linenos"> 590</span></a> <span class="k">if</span> <span class="p">(</span>
-</span><span id="L-591"><a href="#L-591"><span class="linenos"> 591</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-592"><a href="#L-592"><span class="linenos"> 592</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-593"><a href="#L-593"><span class="linenos"> 593</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-594"><a href="#L-594"><span class="linenos"> 594</span></a> <span class="p">):</span>
-</span><span id="L-595"><a href="#L-595"><span class="linenos"> 595</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-596"><a href="#L-596"><span class="linenos"> 596</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-597"><a href="#L-597"><span class="linenos"> 597</span></a> <span class="n">_logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span>
-</span><span id="L-598"><a href="#L-598"><span class="linenos"> 598</span></a> <span class="s2">"Action: Splitting"</span><span class="p">,</span>
-</span><span id="L-599"><a href="#L-599"><span class="linenos"> 599</span></a> <span class="n">split_col</span><span class="p">,</span>
-</span><span id="L-600"><a href="#L-600"><span class="linenos"> 600</span></a> <span class="s2">"column into:"</span><span class="p">,</span>
-</span><span id="L-601"><a href="#L-601"><span class="linenos"> 601</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-602"><a href="#L-602"><span class="linenos"> 602</span></a> <span class="p">)</span>
-</span><span id="L-603"><a href="#L-603"><span class="linenos"> 603</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-604"><a href="#L-604"><span class="linenos"> 604</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-605"><a href="#L-605"><span class="linenos"> 605</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-606"><a href="#L-606"><span class="linenos"> 606</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-607"><a href="#L-607"><span class="linenos"> 607</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-608"><a href="#L-608"><span class="linenos"> 608</span></a>
-</span><span id="L-609"><a href="#L-609"><span class="linenos"> 609</span></a> <span class="k">return</span> <span class="n">df</span>
-</span><span id="L-610"><a href="#L-610"><span class="linenos"> 610</span></a>
-</span><span id="L-611"><a href="#L-611"><span class="linenos"> 611</span></a>
-</span><span id="L-612"><a href="#L-612"><span class="linenos"> 612</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-613"><a href="#L-613"><span class="linenos"> 613</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-614"><a href="#L-614"><span class="linenos"> 614</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-615"><a href="#L-615"><span class="linenos"> 615</span></a><span class="w"> </span><span class="sd">"""Perform QA Checks on columns individually and append to df"""</span>
-</span><span id="L-616"><a href="#L-616"><span class="linenos"> 616</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-617"><a href="#L-617"><span class="linenos"> 617</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-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="c1"># remove unnamed columns due to extra commas, missing headers, or incorrect parsing</span>
-</span><span id="L-620"><a href="#L-620"><span class="linenos"> 620</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-621"><a href="#L-621"><span class="linenos"> 621</span></a>
-</span><span id="L-622"><a href="#L-622"><span class="linenos"> 622</span></a> <span class="c1"># Preprocess codes</span>
-</span><span id="L-623"><a href="#L-623"><span class="linenos"> 623</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-624"><a href="#L-624"><span class="linenos"> 624</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-625"><a href="#L-625"><span class="linenos"> 625</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-626"><a href="#L-626"><span class="linenos"> 626</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-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"># get codes by column name</span>
-</span><span id="L-629"><a href="#L-629"><span class="linenos"> 629</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-630"><a href="#L-630"><span class="linenos"> 630</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-631"><a href="#L-631"><span class="linenos"> 631</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-632"><a href="#L-632"><span class="linenos"> 632</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-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"># process codes, validating them using parser and returning the errors</span>
-</span><span id="L-635"><a href="#L-635"><span class="linenos"> 635</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-636"><a href="#L-636"><span class="linenos"> 636</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-637"><a href="#L-637"><span class="linenos"> 637</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-638"><a href="#L-638"><span class="linenos"> 638</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-639"><a href="#L-639"><span class="linenos"> 639</span></a>
-</span><span id="L-640"><a href="#L-640"><span class="linenos"> 640</span></a> <span class="c1"># add processed codes to df</span>
-</span><span id="L-641"><a href="#L-641"><span class="linenos"> 641</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-642"><a href="#L-642"><span class="linenos"> 642</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-643"><a href="#L-643"><span class="linenos"> 643</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-644"><a href="#L-644"><span class="linenos"> 644</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-645"><a href="#L-645"><span class="linenos"> 645</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-646"><a href="#L-646"><span class="linenos"> 646</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-647"><a href="#L-647"><span class="linenos"> 647</span></a> <span class="p">)</span>
-</span><span id="L-648"><a href="#L-648"><span class="linenos"> 648</span></a>
-</span><span id="L-649"><a href="#L-649"><span class="linenos"> 649</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-650"><a href="#L-650"><span class="linenos"> 650</span></a>
-</span><span id="L-651"><a href="#L-651"><span class="linenos"> 651</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-652"><a href="#L-652"><span class="linenos"> 652</span></a>
+</span><span id="L-569"><a href="#L-569"><span class="linenos"> 569</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-570"><a href="#L-570"><span class="linenos"> 570</span></a><span class="w"> </span><span class="sd">"""</span>
+</span><span id="L-571"><a href="#L-571"><span class="linenos"> 571</span></a><span class="sd"> Load Code List File</span>
+</span><span id="L-572"><a href="#L-572"><span class="linenos"> 572</span></a><span class="sd"> """</span>
+</span><span id="L-573"><a href="#L-573"><span class="linenos"> 573</span></a>
+</span><span id="L-574"><a href="#L-574"><span class="linenos"> 574</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-575"><a href="#L-575"><span class="linenos"> 575</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-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">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-577"><a href="#L-577"><span class="linenos"> 577</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-578"><a href="#L-578"><span class="linenos"> 578</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-579"><a href="#L-579"><span class="linenos"> 579</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-580"><a href="#L-580"><span class="linenos"> 580</span></a> <span class="k">else</span><span class="p">:</span>
+</span><span id="L-581"><a href="#L-581"><span class="linenos"> 581</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-582"><a href="#L-582"><span class="linenos"> 582</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-583"><a href="#L-583"><span class="linenos"> 583</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-584"><a href="#L-584"><span class="linenos"> 584</span></a> <span class="k">else</span><span class="p">:</span>
+</span><span id="L-585"><a href="#L-585"><span class="linenos"> 585</span></a> <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span>
+</span><span id="L-586"><a href="#L-586"><span class="linenos"> 586</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-587"><a href="#L-587"><span class="linenos"> 587</span></a> <span class="p">)</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="k">return</span> <span class="n">df</span>
+</span><span id="L-590"><a href="#L-590"><span class="linenos"> 590</span></a>
+</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="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-593"><a href="#L-593"><span class="linenos"> 593</span></a> <span class="c1"># Perform Structural Changes to file before preprocessing</span>
+</span><span id="L-594"><a href="#L-594"><span class="linenos"> 594</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-595"><a href="#L-595"><span class="linenos"> 595</span></a> <span class="k">if</span> <span class="p">(</span>
+</span><span id="L-596"><a href="#L-596"><span class="linenos"> 596</span></a> <span class="s2">"actions"</span> <span class="ow">in</span> <span class="n">concept_set</span>
+</span><span id="L-597"><a href="#L-597"><span class="linenos"> 597</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">"actions"</span><span class="p">]</span>
+</span><span id="L-598"><a href="#L-598"><span class="linenos"> 598</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">"actions"</span><span class="p">]</span>
+</span><span id="L-599"><a href="#L-599"><span class="linenos"> 599</span></a> <span class="p">):</span>
+</span><span id="L-600"><a href="#L-600"><span class="linenos"> 600</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">"actions"</span><span class="p">][</span><span class="s2">"split_col"</span><span class="p">]</span>
+</span><span id="L-601"><a href="#L-601"><span class="linenos"> 601</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">"actions"</span><span class="p">][</span><span class="s2">"codes_col"</span><span class="p">]</span>
+</span><span id="L-602"><a href="#L-602"><span class="linenos"> 602</span></a> <span class="n">_logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span>
+</span><span id="L-603"><a href="#L-603"><span class="linenos"> 603</span></a> <span class="s2">"Action: Splitting"</span><span class="p">,</span>
+</span><span id="L-604"><a href="#L-604"><span class="linenos"> 604</span></a> <span class="n">split_col</span><span class="p">,</span>
+</span><span id="L-605"><a href="#L-605"><span class="linenos"> 605</span></a> <span class="s2">"column into:"</span><span class="p">,</span>
+</span><span id="L-606"><a href="#L-606"><span class="linenos"> 606</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-607"><a href="#L-607"><span class="linenos"> 607</span></a> <span class="p">)</span>
+</span><span id="L-608"><a href="#L-608"><span class="linenos"> 608</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-609"><a href="#L-609"><span class="linenos"> 609</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-610"><a href="#L-610"><span class="linenos"> 610</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-611"><a href="#L-611"><span class="linenos"> 611</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-612"><a href="#L-612"><span class="linenos"> 612</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-613"><a href="#L-613"><span class="linenos"> 613</span></a>
+</span><span id="L-614"><a href="#L-614"><span class="linenos"> 614</span></a> <span class="k">return</span> <span class="n">df</span>
+</span><span id="L-615"><a href="#L-615"><span class="linenos"> 615</span></a>
+</span><span id="L-616"><a href="#L-616"><span class="linenos"> 616</span></a>
+</span><span id="L-617"><a href="#L-617"><span class="linenos"> 617</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-618"><a href="#L-618"><span class="linenos"> 618</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-619"><a href="#L-619"><span class="linenos"> 619</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-620"><a href="#L-620"><span class="linenos"> 620</span></a><span class="w"> </span><span class="sd">"""Perform QA Checks on columns individually and append to df"""</span>
+</span><span id="L-621"><a href="#L-621"><span class="linenos"> 621</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-622"><a href="#L-622"><span class="linenos"> 622</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-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="c1"># remove unnamed columns due to extra commas, missing headers, or incorrect parsing</span>
+</span><span id="L-625"><a href="#L-625"><span class="linenos"> 625</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-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 class="c1"># Preprocess codes</span>
+</span><span id="L-628"><a href="#L-628"><span class="linenos"> 628</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-629"><a href="#L-629"><span class="linenos"> 629</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">"columns"</span><span class="p">]:</span>
+</span><span id="L-630"><a href="#L-630"><span class="linenos"> 630</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-631"><a href="#L-631"><span class="linenos"> 631</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-632"><a href="#L-632"><span class="linenos"> 632</span></a>
+</span><span id="L-633"><a href="#L-633"><span class="linenos"> 633</span></a> <span class="c1"># get codes by column name</span>
+</span><span id="L-634"><a href="#L-634"><span class="linenos"> 634</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">"columns"</span><span class="p">][</span><span class="n">code_type</span><span class="p">]</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">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-636"><a href="#L-636"><span class="linenos"> 636</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-637"><a href="#L-637"><span class="linenos"> 637</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-638"><a href="#L-638"><span class="linenos"> 638</span></a>
+</span><span id="L-639"><a href="#L-639"><span class="linenos"> 639</span></a> <span class="c1"># process codes, validating them using parser and returning the errors</span>
+</span><span id="L-640"><a href="#L-640"><span class="linenos"> 640</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-641"><a href="#L-641"><span class="linenos"> 641</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-642"><a href="#L-642"><span class="linenos"> 642</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-643"><a href="#L-643"><span class="linenos"> 643</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-644"><a href="#L-644"><span class="linenos"> 644</span></a>
+</span><span id="L-645"><a href="#L-645"><span class="linenos"> 645</span></a> <span class="c1"># add processed codes to df</span>
+</span><span id="L-646"><a href="#L-646"><span class="linenos"> 646</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-647"><a href="#L-647"><span class="linenos"> 647</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-648"><a href="#L-648"><span class="linenos"> 648</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-649"><a href="#L-649"><span class="linenos"> 649</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-650"><a href="#L-650"><span class="linenos"> 650</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-651"><a href="#L-651"><span class="linenos"> 651</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-652"><a href="#L-652"><span class="linenos"> 652</span></a> <span class="p">)</span>
</span><span id="L-653"><a href="#L-653"><span class="linenos"> 653</span></a>
-</span><span id="L-654"><a href="#L-654"><span class="linenos"> 654</span></a><span class="c1"># Translate Df with multiple codes into single code type Series</span>
-</span><span id="L-655"><a href="#L-655"><span class="linenos"> 655</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-656"><a href="#L-656"><span class="linenos"> 656</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-657"><a href="#L-657"><span class="linenos"> 657</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-658"><a href="#L-658"><span class="linenos"> 658</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-659"><a href="#L-659"><span class="linenos"> 659</span></a>
-</span><span id="L-660"><a href="#L-660"><span class="linenos"> 660</span></a> <span class="c1"># codes = pd.DataFrame([], dtype=str)</span>
-</span><span id="L-661"><a href="#L-661"><span class="linenos"> 661</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-662"><a href="#L-662"><span class="linenos"> 662</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-663"><a href="#L-663"><span class="linenos"> 663</span></a> <span class="p">)</span>
-</span><span id="L-664"><a href="#L-664"><span class="linenos"> 664</span></a> <span class="c1"># Convert codes to target type</span>
-</span><span id="L-665"><a href="#L-665"><span class="linenos"> 665</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-666"><a href="#L-666"><span class="linenos"> 666</span></a>
-</span><span id="L-667"><a href="#L-667"><span class="linenos"> 667</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-668"><a href="#L-668"><span class="linenos"> 668</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-669"><a href="#L-669"><span class="linenos"> 669</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-670"><a href="#L-670"><span class="linenos"> 670</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-671"><a href="#L-671"><span class="linenos"> 671</span></a> <span class="p">{</span>
-</span><span id="L-672"><a href="#L-672"><span class="linenos"> 672</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-673"><a href="#L-673"><span class="linenos"> 673</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-674"><a href="#L-674"><span class="linenos"> 674</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-675"><a href="#L-675"><span class="linenos"> 675</span></a> <span class="p">}</span>
-</span><span id="L-676"><a href="#L-676"><span class="linenos"> 676</span></a> <span class="p">)</span>
-</span><span id="L-677"><a href="#L-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">copy_df</span><span class="p">])</span>
-</span><span id="L-678"><a href="#L-678"><span class="linenos"> 678</span></a> <span class="n">_logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span>
-</span><span id="L-679"><a href="#L-679"><span class="linenos"> 679</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-680"><a href="#L-680"><span class="linenos"> 680</span></a> <span class="p">)</span>
-</span><span id="L-681"><a href="#L-681"><span class="linenos"> 681</span></a> <span class="k">else</span><span class="p">:</span>
-</span><span id="L-682"><a href="#L-682"><span class="linenos"> 682</span></a> <span class="c1"># get the translation filename using source to target code types</span>
-</span><span id="L-683"><a href="#L-683"><span class="linenos"> 683</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-684"><a href="#L-684"><span class="linenos"> 684</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-685"><a href="#L-685"><span class="linenos"> 685</span></a>
-</span><span id="L-686"><a href="#L-686"><span class="linenos"> 686</span></a> <span class="c1"># do the mapping if it exists</span>
-</span><span id="L-687"><a href="#L-687"><span class="linenos"> 687</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-688"><a href="#L-688"><span class="linenos"> 688</span></a> <span class="c1"># get mapping</span>
-</span><span id="L-689"><a href="#L-689"><span class="linenos"> 689</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-654"><a href="#L-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 class="n">out</span><span class="o">.</span><span class="n">head</span><span class="p">())</span>
+</span><span id="L-655"><a href="#L-655"><span class="linenos"> 655</span></a>
+</span><span id="L-656"><a href="#L-656"><span class="linenos"> 656</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-657"><a href="#L-657"><span class="linenos"> 657</span></a>
+</span><span id="L-658"><a href="#L-658"><span class="linenos"> 658</span></a>
+</span><span id="L-659"><a href="#L-659"><span class="linenos"> 659</span></a><span class="c1"># Translate Df with multiple codes into single code type Series</span>
+</span><span id="L-660"><a href="#L-660"><span class="linenos"> 660</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-661"><a href="#L-661"><span class="linenos"> 661</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-662"><a href="#L-662"><span class="linenos"> 662</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-663"><a href="#L-663"><span class="linenos"> 663</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-664"><a href="#L-664"><span class="linenos"> 664</span></a>
+</span><span id="L-665"><a href="#L-665"><span class="linenos"> 665</span></a> <span class="c1"># codes = pd.DataFrame([], dtype=str)</span>
+</span><span id="L-666"><a href="#L-666"><span class="linenos"> 666</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-667"><a href="#L-667"><span class="linenos"> 667</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-668"><a href="#L-668"><span class="linenos"> 668</span></a> <span class="p">)</span>
+</span><span id="L-669"><a href="#L-669"><span class="linenos"> 669</span></a> <span class="c1"># Convert codes to target type</span>
+</span><span id="L-670"><a href="#L-670"><span class="linenos"> 670</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-671"><a href="#L-671"><span class="linenos"> 671</span></a>
+</span><span id="L-672"><a href="#L-672"><span class="linenos"> 672</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-673"><a href="#L-673"><span class="linenos"> 673</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-674"><a href="#L-674"><span class="linenos"> 674</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-675"><a href="#L-675"><span class="linenos"> 675</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-676"><a href="#L-676"><span class="linenos"> 676</span></a> <span class="p">{</span>
+</span><span id="L-677"><a href="#L-677"><span class="linenos"> 677</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-678"><a href="#L-678"><span class="linenos"> 678</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-679"><a href="#L-679"><span class="linenos"> 679</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-680"><a href="#L-680"><span class="linenos"> 680</span></a> <span class="p">}</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 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-683"><a href="#L-683"><span class="linenos"> 683</span></a> <span class="n">_logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span>
+</span><span id="L-684"><a href="#L-684"><span class="linenos"> 684</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-685"><a href="#L-685"><span class="linenos"> 685</span></a> <span class="p">)</span>
+</span><span id="L-686"><a href="#L-686"><span class="linenos"> 686</span></a> <span class="k">else</span><span class="p">:</span>
+</span><span id="L-687"><a href="#L-687"><span class="linenos"> 687</span></a> <span class="c1"># get the translation filename using source to target code types</span>
+</span><span id="L-688"><a href="#L-688"><span class="linenos"> 688</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-689"><a href="#L-689"><span class="linenos"> 689</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-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="c1"># do mapping</span>
-</span><span id="L-692"><a href="#L-692"><span class="linenos"> 692</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-693"><a href="#L-693"><span class="linenos"> 693</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-694"><a href="#L-694"><span class="linenos"> 694</span></a> <span class="p">)</span>
+</span><span id="L-691"><a href="#L-691"><span class="linenos"> 691</span></a> <span class="c1"># do the mapping if it exists</span>
+</span><span id="L-692"><a href="#L-692"><span class="linenos"> 692</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-693"><a href="#L-693"><span class="linenos"> 693</span></a> <span class="c1"># get mapping</span>
+</span><span id="L-694"><a href="#L-694"><span class="linenos"> 694</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-695"><a href="#L-695"><span class="linenos"> 695</span></a>
-</span><span id="L-696"><a href="#L-696"><span class="linenos"> 696</span></a> <span class="c1"># normalise the output</span>
-</span><span id="L-697"><a href="#L-697"><span class="linenos"> 697</span></a> <span class="n">translated_df</span><span class="o">.</span><span class="n">columns</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">Index</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-698"><a href="#L-698"><span class="linenos"> 698</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-699"><a href="#L-699"><span class="linenos"> 699</span></a>
-</span><span id="L-700"><a href="#L-700"><span class="linenos"> 700</span></a> <span class="c1"># add to list of codes</span>
-</span><span id="L-701"><a href="#L-701"><span class="linenos"> 701</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-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">else</span><span class="p">:</span>
-</span><span id="L-704"><a href="#L-704"><span class="linenos"> 704</span></a> <span class="n">_logger</span><span class="o">.</span><span class="n">warning</span><span class="p">(</span>
-</span><span id="L-705"><a href="#L-705"><span class="linenos"> 705</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-706"><a href="#L-706"><span class="linenos"> 706</span></a> <span class="p">)</span>
+</span><span id="L-696"><a href="#L-696"><span class="linenos"> 696</span></a> <span class="c1"># do mapping</span>
+</span><span id="L-697"><a href="#L-697"><span class="linenos"> 697</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-698"><a href="#L-698"><span class="linenos"> 698</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-699"><a href="#L-699"><span class="linenos"> 699</span></a> <span class="p">)</span>
+</span><span id="L-700"><a href="#L-700"><span class="linenos"> 700</span></a>
+</span><span id="L-701"><a href="#L-701"><span class="linenos"> 701</span></a> <span class="c1"># normalise the output</span>
+</span><span id="L-702"><a href="#L-702"><span class="linenos"> 702</span></a> <span class="n">translated_df</span><span class="o">.</span><span class="n">columns</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">Index</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-703"><a href="#L-703"><span class="linenos"> 703</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-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 class="c1"># add to list of codes</span>
+</span><span id="L-706"><a href="#L-706"><span class="linenos"> 706</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-707"><a href="#L-707"><span class="linenos"> 707</span></a>
-</span><span id="L-708"><a href="#L-708"><span class="linenos"> 708</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-709"><a href="#L-709"><span class="linenos"> 709</span></a>
-</span><span id="L-710"><a href="#L-710"><span class="linenos"> 710</span></a> <span class="c1"># added concept set type to output if any translations</span>
-</span><span id="L-711"><a href="#L-711"><span class="linenos"> 711</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-712"><a href="#L-712"><span class="linenos"> 712</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-713"><a href="#L-713"><span class="linenos"> 713</span></a> <span class="k">else</span><span class="p">:</span>
-</span><span id="L-714"><a href="#L-714"><span class="linenos"> 714</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-715"><a href="#L-715"><span class="linenos"> 715</span></a>
-</span><span id="L-716"><a href="#L-716"><span class="linenos"> 716</span></a> <span class="k">return</span> <span class="n">codes</span>
-</span><span id="L-717"><a href="#L-717"><span class="linenos"> 717</span></a>
-</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="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-720"><a href="#L-720"><span class="linenos"> 720</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-721"><a href="#L-721"><span class="linenos"> 721</span></a> <span class="p">[</span>
-</span><span id="L-722"><a href="#L-722"><span class="linenos"> 722</span></a> <span class="p">{</span>
-</span><span id="L-723"><a href="#L-723"><span class="linenos"> 723</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-724"><a href="#L-724"><span class="linenos"> 724</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-725"><a href="#L-725"><span class="linenos"> 725</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-726"><a href="#L-726"><span class="linenos"> 726</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-727"><a href="#L-727"><span class="linenos"> 727</span></a> <span class="p">}</span>
-</span><span id="L-728"><a href="#L-728"><span class="linenos"> 728</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-729"><a href="#L-729"><span class="linenos"> 729</span></a> <span class="p">]</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="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-733"><a href="#L-733"><span class="linenos"> 733</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-734"><a href="#L-734"><span class="linenos"> 734</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-735"><a href="#L-735"><span class="linenos"> 735</span></a>
+</span><span id="L-708"><a href="#L-708"><span class="linenos"> 708</span></a> <span class="k">else</span><span class="p">:</span>
+</span><span id="L-709"><a href="#L-709"><span class="linenos"> 709</span></a> <span class="n">_logger</span><span class="o">.</span><span class="n">warning</span><span class="p">(</span>
+</span><span id="L-710"><a href="#L-710"><span class="linenos"> 710</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-711"><a href="#L-711"><span class="linenos"> 711</span></a> <span class="p">)</span>
+</span><span id="L-712"><a href="#L-712"><span class="linenos"> 712</span></a>
+</span><span id="L-713"><a href="#L-713"><span class="linenos"> 713</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-714"><a href="#L-714"><span class="linenos"> 714</span></a>
+</span><span id="L-715"><a href="#L-715"><span class="linenos"> 715</span></a> <span class="c1"># added concept set type to output if any translations</span>
+</span><span id="L-716"><a href="#L-716"><span class="linenos"> 716</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-717"><a href="#L-717"><span class="linenos"> 717</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-718"><a href="#L-718"><span class="linenos"> 718</span></a> <span class="k">else</span><span class="p">:</span>
+</span><span id="L-719"><a href="#L-719"><span class="linenos"> 719</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-720"><a href="#L-720"><span class="linenos"> 720</span></a>
+</span><span id="L-721"><a href="#L-721"><span class="linenos"> 721</span></a> <span class="k">return</span> <span class="n">codes</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_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-725"><a href="#L-725"><span class="linenos"> 725</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-726"><a href="#L-726"><span class="linenos"> 726</span></a> <span class="p">[</span>
+</span><span id="L-727"><a href="#L-727"><span class="linenos"> 727</span></a> <span class="p">{</span>
+</span><span id="L-728"><a href="#L-728"><span class="linenos"> 728</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-729"><a href="#L-729"><span class="linenos"> 729</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-730"><a href="#L-730"><span class="linenos"> 730</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-731"><a href="#L-731"><span class="linenos"> 731</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-732"><a href="#L-732"><span class="linenos"> 732</span></a> <span class="p">}</span>
+</span><span id="L-733"><a href="#L-733"><span class="linenos"> 733</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-734"><a href="#L-734"><span class="linenos"> 734</span></a> <span class="p">]</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">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-738"><a href="#L-738"><span class="linenos"> 738</span></a> <span class="c1"># write the vocab version files</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">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-741"><a href="#L-741"><span class="linenos"> 741</span></a> <span class="k">raise</span> <span class="ne">FileNotFoundError</span><span class="p">(</span>
-</span><span id="L-742"><a href="#L-742"><span class="linenos"> 742</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-743"><a href="#L-743"><span class="linenos"> 743</span></a> <span class="p">)</span>
+</span><span id="L-737"><a href="#L-737"><span class="linenos"> 737</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-738"><a href="#L-738"><span class="linenos"> 738</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-739"><a href="#L-739"><span class="linenos"> 739</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-740"><a href="#L-740"><span class="linenos"> 740</span></a>
+</span><span id="L-741"><a href="#L-741"><span class="linenos"> 741</span></a>
+</span><span id="L-742"><a href="#L-742"><span class="linenos"> 742</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-743"><a href="#L-743"><span class="linenos"> 743</span></a> <span class="c1"># write the vocab version files</span>
</span><span id="L-744"><a href="#L-744"><span class="linenos"> 744</span></a>
-</span><span id="L-745"><a href="#L-745"><span class="linenos"> 745</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-745"><a href="#L-745"><span class="linenos"> 745</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-746"><a href="#L-746"><span class="linenos"> 746</span></a> <span class="k">raise</span> <span class="ne">FileNotFoundError</span><span class="p">(</span>
-</span><span id="L-747"><a href="#L-747"><span class="linenos"> 747</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-747"><a href="#L-747"><span class="linenos"> 747</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-748"><a href="#L-748"><span class="linenos"> 748</span></a> <span class="p">)</span>
</span><span id="L-749"><a href="#L-749"><span class="linenos"> 749</span></a>
-</span><span id="L-750"><a href="#L-750"><span class="linenos"> 750</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-751"><a href="#L-751"><span class="linenos"> 751</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-752"><a href="#L-752"><span class="linenos"> 752</span></a>
-</span><span id="L-753"><a href="#L-753"><span class="linenos"> 753</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-754"><a href="#L-754"><span class="linenos"> 754</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-755"><a href="#L-755"><span class="linenos"> 755</span></a>
-</span><span id="L-756"><a href="#L-756"><span class="linenos"> 756</span></a> <span class="c1"># Create the combined YAML structure</span>
-</span><span id="L-757"><a href="#L-757"><span class="linenos"> 757</span></a> <span class="n">version_data</span> <span class="o">=</span> <span class="p">{</span>
-</span><span id="L-758"><a href="#L-758"><span class="linenos"> 758</span></a> <span class="s2">"versions"</span><span class="p">:</span> <span class="p">{</span>
-</span><span id="L-759"><a href="#L-759"><span class="linenos"> 759</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-760"><a href="#L-760"><span class="linenos"> 760</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-761"><a href="#L-761"><span class="linenos"> 761</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-762"><a href="#L-762"><span class="linenos"> 762</span></a> <span class="p">}</span>
-</span><span id="L-763"><a href="#L-763"><span class="linenos"> 763</span></a> <span class="p">}</span>
-</span><span id="L-764"><a href="#L-764"><span class="linenos"> 764</span></a>
-</span><span id="L-765"><a href="#L-765"><span class="linenos"> 765</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-766"><a href="#L-766"><span class="linenos"> 766</span></a> <span class="n">yaml</span><span class="o">.</span><span class="n">dump</span><span class="p">(</span>
-</span><span id="L-767"><a href="#L-767"><span class="linenos"> 767</span></a> <span class="n">version_data</span><span class="p">,</span>
-</span><span id="L-768"><a href="#L-768"><span class="linenos"> 768</span></a> <span class="n">file</span><span class="p">,</span>
-</span><span id="L-769"><a href="#L-769"><span class="linenos"> 769</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-770"><a href="#L-770"><span class="linenos"> 770</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-771"><a href="#L-771"><span class="linenos"> 771</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-772"><a href="#L-772"><span class="linenos"> 772</span></a> <span class="n">default_style</span><span class="o">=</span><span class="s1">'"'</span><span class="p">,</span>
-</span><span id="L-773"><a href="#L-773"><span class="linenos"> 773</span></a> <span class="p">)</span>
-</span><span id="L-774"><a href="#L-774"><span class="linenos"> 774</span></a>
-</span><span id="L-775"><a href="#L-775"><span class="linenos"> 775</span></a>
-</span><span id="L-776"><a href="#L-776"><span class="linenos"> 776</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-777"><a href="#L-777"><span class="linenos"> 777</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-778"><a href="#L-778"><span class="linenos"> 778</span></a>
-</span><span id="L-779"><a href="#L-779"><span class="linenos"> 779</span></a> <span class="c1"># Validate configuration</span>
-</span><span id="L-780"><a href="#L-780"><span class="linenos"> 780</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-781"><a href="#L-781"><span class="linenos"> 781</span></a>
-</span><span id="L-782"><a href="#L-782"><span class="linenos"> 782</span></a> <span class="c1"># initialise paths</span>
-</span><span id="L-783"><a href="#L-783"><span class="linenos"> 783</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-784"><a href="#L-784"><span class="linenos"> 784</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-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="c1"># load configuration</span>
-</span><span id="L-787"><a href="#L-787"><span class="linenos"> 787</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-788"><a href="#L-788"><span class="linenos"> 788</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-789"><a href="#L-789"><span class="linenos"> 789</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-750"><a href="#L-750"><span class="linenos"> 750</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-751"><a href="#L-751"><span class="linenos"> 751</span></a> <span class="k">raise</span> <span class="ne">FileNotFoundError</span><span class="p">(</span>
+</span><span id="L-752"><a href="#L-752"><span class="linenos"> 752</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-753"><a href="#L-753"><span class="linenos"> 753</span></a> <span class="p">)</span>
+</span><span id="L-754"><a href="#L-754"><span class="linenos"> 754</span></a>
+</span><span id="L-755"><a href="#L-755"><span class="linenos"> 755</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-756"><a href="#L-756"><span class="linenos"> 756</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-757"><a href="#L-757"><span class="linenos"> 757</span></a>
+</span><span id="L-758"><a href="#L-758"><span class="linenos"> 758</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-759"><a href="#L-759"><span class="linenos"> 759</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-760"><a href="#L-760"><span class="linenos"> 760</span></a>
+</span><span id="L-761"><a href="#L-761"><span class="linenos"> 761</span></a> <span class="c1"># Create the combined YAML structure</span>
+</span><span id="L-762"><a href="#L-762"><span class="linenos"> 762</span></a> <span class="n">version_data</span> <span class="o">=</span> <span class="p">{</span>
+</span><span id="L-763"><a href="#L-763"><span class="linenos"> 763</span></a> <span class="s2">"versions"</span><span class="p">:</span> <span class="p">{</span>
+</span><span id="L-764"><a href="#L-764"><span class="linenos"> 764</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-765"><a href="#L-765"><span class="linenos"> 765</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-766"><a href="#L-766"><span class="linenos"> 766</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-767"><a href="#L-767"><span class="linenos"> 767</span></a> <span class="p">}</span>
+</span><span id="L-768"><a href="#L-768"><span class="linenos"> 768</span></a> <span class="p">}</span>
+</span><span id="L-769"><a href="#L-769"><span class="linenos"> 769</span></a>
+</span><span id="L-770"><a href="#L-770"><span class="linenos"> 770</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-771"><a href="#L-771"><span class="linenos"> 771</span></a> <span class="n">yaml</span><span class="o">.</span><span class="n">dump</span><span class="p">(</span>
+</span><span id="L-772"><a href="#L-772"><span class="linenos"> 772</span></a> <span class="n">version_data</span><span class="p">,</span>
+</span><span id="L-773"><a href="#L-773"><span class="linenos"> 773</span></a> <span class="n">file</span><span class="p">,</span>
+</span><span id="L-774"><a href="#L-774"><span class="linenos"> 774</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-775"><a href="#L-775"><span class="linenos"> 775</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-776"><a href="#L-776"><span class="linenos"> 776</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-777"><a href="#L-777"><span class="linenos"> 777</span></a> <span class="n">default_style</span><span class="o">=</span><span class="s1">'"'</span><span class="p">,</span>
+</span><span id="L-778"><a href="#L-778"><span class="linenos"> 778</span></a> <span class="p">)</span>
+</span><span id="L-779"><a href="#L-779"><span class="linenos"> 779</span></a>
+</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">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-782"><a href="#L-782"><span class="linenos"> 782</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-783"><a href="#L-783"><span class="linenos"> 783</span></a>
+</span><span id="L-784"><a href="#L-784"><span class="linenos"> 784</span></a> <span class="c1"># Validate configuration</span>
+</span><span id="L-785"><a href="#L-785"><span class="linenos"> 785</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-786"><a href="#L-786"><span class="linenos"> 786</span></a>
+</span><span id="L-787"><a href="#L-787"><span class="linenos"> 787</span></a> <span class="c1"># initialise paths</span>
+</span><span id="L-788"><a href="#L-788"><span class="linenos"> 788</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-789"><a href="#L-789"><span class="linenos"> 789</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-790"><a href="#L-790"><span class="linenos"> 790</span></a>
-</span><span id="L-791"><a href="#L-791"><span class="linenos"> 791</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-792"><a href="#L-792"><span class="linenos"> 792</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-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 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-795"><a href="#L-795"><span class="linenos"> 795</span></a> <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span>
-</span><span id="L-796"><a href="#L-796"><span class="linenos"> 796</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-797"><a href="#L-797"><span class="linenos"> 797</span></a> <span class="p">)</span>
+</span><span id="L-791"><a href="#L-791"><span class="linenos"> 791</span></a> <span class="c1"># load configuration</span>
+</span><span id="L-792"><a href="#L-792"><span class="linenos"> 792</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-793"><a href="#L-793"><span class="linenos"> 793</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-794"><a href="#L-794"><span class="linenos"> 794</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-795"><a href="#L-795"><span class="linenos"> 795</span></a>
+</span><span id="L-796"><a href="#L-796"><span class="linenos"> 796</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-797"><a href="#L-797"><span class="linenos"> 797</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-798"><a href="#L-798"><span class="linenos"> 798</span></a>
-</span><span id="L-799"><a href="#L-799"><span class="linenos"> 799</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-800"><a href="#L-800"><span class="linenos"> 800</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-801"><a href="#L-801"><span class="linenos"> 801</span></a> <span class="k">else</span><span class="p">:</span>
-</span><span id="L-802"><a href="#L-802"><span class="linenos"> 802</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-803"><a href="#L-803"><span class="linenos"> 803</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-804"><a href="#L-804"><span class="linenos"> 804</span></a>
-</span><span id="L-805"><a href="#L-805"><span class="linenos"> 805</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-806"><a href="#L-806"><span class="linenos"> 806</span></a>
-</span><span id="L-807"><a href="#L-807"><span class="linenos"> 807</span></a>
-</span><span id="L-808"><a href="#L-808"><span class="linenos"> 808</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-809"><a href="#L-809"><span class="linenos"> 809</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-810"><a href="#L-810"><span class="linenos"> 810</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-811"><a href="#L-811"><span class="linenos"> 811</span></a> <span class="c1"># Create output dataframe</span>
-</span><span id="L-812"><a href="#L-812"><span class="linenos"> 812</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-813"><a href="#L-813"><span class="linenos"> 813</span></a> <span class="n">code_errors</span> <span class="o">=</span> <span class="p">[]</span>
-</span><span id="L-814"><a href="#L-814"><span class="linenos"> 814</span></a>
-</span><span id="L-815"><a href="#L-815"><span class="linenos"> 815</span></a> <span class="c1"># Process each folder in codes section</span>
-</span><span id="L-816"><a href="#L-816"><span class="linenos"> 816</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-817"><a href="#L-817"><span class="linenos"> 817</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-818"><a href="#L-818"><span class="linenos"> 818</span></a>
-</span><span id="L-819"><a href="#L-819"><span class="linenos"> 819</span></a> <span class="c1"># Load code file</span>
-</span><span id="L-820"><a href="#L-820"><span class="linenos"> 820</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-821"><a href="#L-821"><span class="linenos"> 821</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-822"><a href="#L-822"><span class="linenos"> 822</span></a>
-</span><span id="L-823"><a href="#L-823"><span class="linenos"> 823</span></a> <span class="c1"># process structural actions</span>
-</span><span id="L-824"><a href="#L-824"><span class="linenos"> 824</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-799"><a href="#L-799"><span class="linenos"> 799</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-800"><a href="#L-800"><span class="linenos"> 800</span></a> <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span>
+</span><span id="L-801"><a href="#L-801"><span class="linenos"> 801</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-802"><a href="#L-802"><span class="linenos"> 802</span></a> <span class="p">)</span>
+</span><span id="L-803"><a href="#L-803"><span class="linenos"> 803</span></a>
+</span><span id="L-804"><a href="#L-804"><span class="linenos"> 804</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-805"><a href="#L-805"><span class="linenos"> 805</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-806"><a href="#L-806"><span class="linenos"> 806</span></a> <span class="k">else</span><span class="p">:</span>
+</span><span id="L-807"><a href="#L-807"><span class="linenos"> 807</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-808"><a href="#L-808"><span class="linenos"> 808</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-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="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-811"><a href="#L-811"><span class="linenos"> 811</span></a>
+</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="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-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="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-815"><a href="#L-815"><span class="linenos"> 815</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-816"><a href="#L-816"><span class="linenos"> 816</span></a> <span class="c1"># Create output dataframe</span>
+</span><span id="L-817"><a href="#L-817"><span class="linenos"> 817</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-818"><a href="#L-818"><span class="linenos"> 818</span></a> <span class="n">code_errors</span> <span class="o">=</span> <span class="p">[]</span>
+</span><span id="L-819"><a href="#L-819"><span class="linenos"> 819</span></a>
+</span><span id="L-820"><a href="#L-820"><span class="linenos"> 820</span></a> <span class="c1"># Process each folder in codes section</span>
+</span><span id="L-821"><a href="#L-821"><span class="linenos"> 821</span></a> <span class="k">for</span> <span class="n">files</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-822"><a href="#L-822"><span class="linenos"> 822</span></a> <span class="n">concept_set_name</span> <span class="o">=</span> <span class="n">files</span><span class="p">[</span><span class="s2">"name"</span><span class="p">]</span>
+</span><span id="L-823"><a href="#L-823"><span class="linenos"> 823</span></a> <span class="k">for</span> <span class="n">concept_set</span> <span class="ow">in</span> <span class="n">files</span><span class="p">[</span><span class="s2">"files"</span><span class="p">]:</span>
+</span><span id="L-824"><a href="#L-824"><span class="linenos"> 824</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="si">}</span><span class="s2"> ---"</span><span class="p">)</span>
</span><span id="L-825"><a href="#L-825"><span class="linenos"> 825</span></a>
-</span><span id="L-826"><a href="#L-826"><span class="linenos"> 826</span></a> <span class="c1"># preprocessing and validate of source concepts</span>
-</span><span id="L-827"><a href="#L-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="s2">"Processing and validating source concept codes"</span><span class="p">)</span>
-</span><span id="L-828"><a href="#L-828"><span class="linenos"> 828</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-829"><a href="#L-829"><span class="linenos"> 829</span></a> <span class="n">df</span><span class="p">,</span>
-</span><span id="L-830"><a href="#L-830"><span class="linenos"> 830</span></a> <span class="n">concept_set</span><span class="p">,</span>
-</span><span id="L-831"><a href="#L-831"><span class="linenos"> 831</span></a> <span class="n">codes_file_path</span><span class="p">,</span>
-</span><span id="L-832"><a href="#L-832"><span class="linenos"> 832</span></a> <span class="p">)</span>
-</span><span id="L-833"><a href="#L-833"><span class="linenos"> 833</span></a>
-</span><span id="L-834"><a href="#L-834"><span class="linenos"> 834</span></a> <span class="c1"># create df with just the source code columns</span>
-</span><span id="L-835"><a href="#L-835"><span class="linenos"> 835</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-836"><a href="#L-836"><span class="linenos"> 836</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-837"><a href="#L-837"><span class="linenos"> 837</span></a>
-</span><span id="L-838"><a href="#L-838"><span class="linenos"> 838</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-839"><a href="#L-839"><span class="linenos"> 839</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-826"><a href="#L-826"><span class="linenos"> 826</span></a> <span class="c1"># Load code file</span>
+</span><span id="L-827"><a href="#L-827"><span class="linenos"> 827</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">"path"</span><span class="p">])</span>
+</span><span id="L-828"><a href="#L-828"><span class="linenos"> 828</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-829"><a href="#L-829"><span class="linenos"> 829</span></a>
+</span><span id="L-830"><a href="#L-830"><span class="linenos"> 830</span></a> <span class="c1"># process structural actions</span>
+</span><span id="L-831"><a href="#L-831"><span class="linenos"> 831</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-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"># preprocessing and validate of source concepts</span>
+</span><span id="L-834"><a href="#L-834"><span class="linenos"> 834</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-835"><a href="#L-835"><span class="linenos"> 835</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-836"><a href="#L-836"><span class="linenos"> 836</span></a> <span class="n">df</span><span class="p">,</span>
+</span><span id="L-837"><a href="#L-837"><span class="linenos"> 837</span></a> <span class="n">concept_set</span><span class="p">,</span>
+</span><span id="L-838"><a href="#L-838"><span class="linenos"> 838</span></a> <span class="n">codes_file_path</span><span class="p">,</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><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><span id="L-842"><a href="#L-842"><span class="linenos"> 842</span></a> <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><span id="L-843"><a href="#L-843"><span class="linenos"> 843</span></a> <span class="p">)</span>
-</span><span id="L-844"><a href="#L-844"><span class="linenos"> 844</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-845"><a href="#L-845"><span class="linenos"> 845</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-846"><a href="#L-846"><span class="linenos"> 846</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-841"><a href="#L-841"><span class="linenos"> 841</span></a> <span class="c1"># create df with just the source code columns</span>
+</span><span id="L-842"><a href="#L-842"><span class="linenos"> 842</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">"columns"</span><span class="p">]</span><span class="o">.</span><span class="n">keys</span><span class="p">())</span>
+</span><span id="L-843"><a href="#L-843"><span class="linenos"> 843</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-844"><a href="#L-844"><span class="linenos"> 844</span></a>
+</span><span id="L-845"><a href="#L-845"><span class="linenos"> 845</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-846"><a href="#L-846"><span class="linenos"> 846</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-847"><a href="#L-847"><span class="linenos"> 847</span></a>
-</span><span id="L-848"><a href="#L-848"><span class="linenos"> 848</span></a> <span class="c1"># Map source concepts codes to target codes</span>
-</span><span id="L-849"><a href="#L-849"><span class="linenos"> 849</span></a> <span class="c1"># if processing a source coding list with categorical data</span>
-</span><span id="L-850"><a href="#L-850"><span class="linenos"> 850</span></a> <span class="k">if</span> <span class="p">(</span>
-</span><span id="L-851"><a href="#L-851"><span class="linenos"> 851</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-852"><a href="#L-852"><span class="linenos"> 852</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-853"><a href="#L-853"><span class="linenos"> 853</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-854"><a href="#L-854"><span class="linenos"> 854</span></a> <span class="p">):</span>
-</span><span id="L-855"><a href="#L-855"><span class="linenos"> 855</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-856"><a href="#L-856"><span class="linenos"> 856</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-857"><a href="#L-857"><span class="linenos"> 857</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-858"><a href="#L-858"><span class="linenos"> 858</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-859"><a href="#L-859"><span class="linenos"> 859</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-860"><a href="#L-860"><span class="linenos"> 860</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-861"><a href="#L-861"><span class="linenos"> 861</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-862"><a href="#L-862"><span class="linenos"> 862</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-863"><a href="#L-863"><span class="linenos"> 863</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-864"><a href="#L-864"><span class="linenos"> 864</span></a> <span class="n">source_df</span><span class="p">,</span>
-</span><span id="L-865"><a href="#L-865"><span class="linenos"> 865</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-866"><a href="#L-866"><span class="linenos"> 866</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-867"><a href="#L-867"><span class="linenos"> 867</span></a> <span class="p">)</span>
-</span><span id="L-868"><a href="#L-868"><span class="linenos"> 868</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-869"><a href="#L-869"><span class="linenos"> 869</span></a> <span class="k">else</span><span class="p">:</span>
-</span><span id="L-870"><a href="#L-870"><span class="linenos"> 870</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-871"><a href="#L-871"><span class="linenos"> 871</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-872"><a href="#L-872"><span class="linenos"> 872</span></a> <span class="n">source_df</span><span class="p">,</span>
-</span><span id="L-873"><a href="#L-873"><span class="linenos"> 873</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-874"><a href="#L-874"><span class="linenos"> 874</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-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 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-877"><a href="#L-877"><span class="linenos"> 877</span></a>
-</span><span id="L-878"><a href="#L-878"><span class="linenos"> 878</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-879"><a href="#L-879"><span class="linenos"> 879</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-880"><a href="#L-880"><span class="linenos"> 880</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-881"><a href="#L-881"><span class="linenos"> 881</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-882"><a href="#L-882"><span class="linenos"> 882</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-883"><a href="#L-883"><span class="linenos"> 883</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-884"><a href="#L-884"><span class="linenos"> 884</span></a>
-</span><span id="L-885"><a href="#L-885"><span class="linenos"> 885</span></a> <span class="c1"># Check there is output from processing</span>
-</span><span id="L-886"><a href="#L-886"><span class="linenos"> 886</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-887"><a href="#L-887"><span class="linenos"> 887</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-888"><a href="#L-888"><span class="linenos"> 888</span></a> <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span>
-</span><span id="L-889"><a href="#L-889"><span class="linenos"> 889</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-890"><a href="#L-890"><span class="linenos"> 890</span></a> <span class="p">)</span>
-</span><span id="L-891"><a href="#L-891"><span class="linenos"> 891</span></a>
-</span><span id="L-892"><a href="#L-892"><span class="linenos"> 892</span></a> <span class="c1"># final processing</span>
-</span><span id="L-893"><a href="#L-893"><span class="linenos"> 893</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-894"><a href="#L-894"><span class="linenos"> 894</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-895"><a href="#L-895"><span class="linenos"> 895</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-896"><a href="#L-896"><span class="linenos"> 896</span></a>
-</span><span id="L-897"><a href="#L-897"><span class="linenos"> 897</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-898"><a href="#L-898"><span class="linenos"> 898</span></a> <span class="c1"># added metadata</span>
-</span><span id="L-899"><a href="#L-899"><span class="linenos"> 899</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-900"><a href="#L-900"><span class="linenos"> 900</span></a> <span class="n">result_list</span> <span class="o">=</span> <span class="p">[]</span>
-</span><span id="L-901"><a href="#L-901"><span class="linenos"> 901</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-902"><a href="#L-902"><span class="linenos"> 902</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-903"><a href="#L-903"><span class="linenos"> 903</span></a> <span class="c1"># Filter output based on the current source_concept_type</span>
-</span><span id="L-904"><a href="#L-904"><span class="linenos"> 904</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-905"><a href="#L-905"><span class="linenos"> 905</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-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="c1"># Remove the source type columns except the current type will leave the metadata and the join</span>
-</span><span id="L-908"><a href="#L-908"><span class="linenos"> 908</span></a> <span class="n">remove_types</span> <span class="o">=</span> <span class="p">[</span>
-</span><span id="L-909"><a href="#L-909"><span class="linenos"> 909</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-910"><a href="#L-910"><span class="linenos"> 910</span></a> <span class="p">]</span>
-</span><span id="L-911"><a href="#L-911"><span class="linenos"> 911</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-912"><a href="#L-912"><span class="linenos"> 912</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-913"><a href="#L-913"><span class="linenos"> 913</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-914"><a href="#L-914"><span class="linenos"> 914</span></a> <span class="p">)</span>
-</span><span id="L-915"><a href="#L-915"><span class="linenos"> 915</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-916"><a href="#L-916"><span class="linenos"> 916</span></a>
-</span><span id="L-917"><a href="#L-917"><span class="linenos"> 917</span></a> <span class="c1"># Perform the left join with df2 on SOURCE_CONCEPT to add the metadata</span>
-</span><span id="L-918"><a href="#L-918"><span class="linenos"> 918</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-919"><a href="#L-919"><span class="linenos"> 919</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-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="n">_logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span>
-</span><span id="L-922"><a href="#L-922"><span class="linenos"> 922</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-923"><a href="#L-923"><span class="linenos"> 923</span></a> <span class="p">)</span>
-</span><span id="L-924"><a href="#L-924"><span class="linenos"> 924</span></a>
-</span><span id="L-925"><a href="#L-925"><span class="linenos"> 925</span></a> <span class="c1"># Append the result to the result_list</span>
-</span><span id="L-926"><a href="#L-926"><span class="linenos"> 926</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-927"><a href="#L-927"><span class="linenos"> 927</span></a>
-</span><span id="L-928"><a href="#L-928"><span class="linenos"> 928</span></a> <span class="c1"># Concatenate all the results into a single DataFrame</span>
-</span><span id="L-929"><a href="#L-929"><span class="linenos"> 929</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-930"><a href="#L-930"><span class="linenos"> 930</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-931"><a href="#L-931"><span class="linenos"> 931</span></a> <span class="n">_logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span>
-</span><span id="L-932"><a href="#L-932"><span class="linenos"> 932</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-933"><a href="#L-933"><span class="linenos"> 933</span></a> <span class="p">)</span>
-</span><span id="L-934"><a href="#L-934"><span class="linenos"> 934</span></a>
-</span><span id="L-935"><a href="#L-935"><span class="linenos"> 935</span></a> <span class="c1"># Save output to map directory</span>
-</span><span id="L-936"><a href="#L-936"><span class="linenos"> 936</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-937"><a href="#L-937"><span class="linenos"> 937</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-938"><a href="#L-938"><span class="linenos"> 938</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-939"><a href="#L-939"><span class="linenos"> 939</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-940"><a href="#L-940"><span class="linenos"> 940</span></a>
-</span><span id="L-941"><a href="#L-941"><span class="linenos"> 941</span></a> <span class="c1"># save concept sets as separate files</span>
-</span><span id="L-942"><a href="#L-942"><span class="linenos"> 942</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-943"><a href="#L-943"><span class="linenos"> 943</span></a>
-</span><span id="L-944"><a href="#L-944"><span class="linenos"> 944</span></a> <span class="c1"># empty the concept-set directory except for hiddle files, e.g. .git</span>
-</span><span id="L-945"><a href="#L-945"><span class="linenos"> 945</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-946"><a href="#L-946"><span class="linenos"> 946</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-947"><a href="#L-947"><span class="linenos"> 947</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-948"><a href="#L-948"><span class="linenos"> 948</span></a> <span class="n">item</span><span class="o">.</span><span class="n">unlink</span><span class="p">()</span>
-</span><span id="L-949"><a href="#L-949"><span class="linenos"> 949</span></a> <span class="k">else</span><span class="p">:</span>
-</span><span id="L-950"><a href="#L-950"><span class="linenos"> 950</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-951"><a href="#L-951"><span class="linenos"> 951</span></a>
-</span><span id="L-952"><a href="#L-952"><span class="linenos"> 952</span></a> <span class="c1"># write each concept as a separate file</span>
-</span><span id="L-953"><a href="#L-953"><span class="linenos"> 953</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-954"><a href="#L-954"><span class="linenos"> 954</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-955"><a href="#L-955"><span class="linenos"> 955</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-956"><a href="#L-956"><span class="linenos"> 956</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-957"><a href="#L-957"><span class="linenos"> 957</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-958"><a href="#L-958"><span class="linenos"> 958</span></a> <span class="p">)</span> <span class="c1"># sort cols alphabetically</span>
-</span><span id="L-959"><a href="#L-959"><span class="linenos"> 959</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-960"><a href="#L-960"><span class="linenos"> 960</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-961"><a href="#L-961"><span class="linenos"> 961</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-962"><a href="#L-962"><span class="linenos"> 962</span></a>
-</span><span id="L-963"><a href="#L-963"><span class="linenos"> 963</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-964"><a href="#L-964"><span class="linenos"> 964</span></a>
-</span><span id="L-965"><a href="#L-965"><span class="linenos"> 965</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-966"><a href="#L-966"><span class="linenos"> 966</span></a>
-</span><span id="L-967"><a href="#L-967"><span class="linenos"> 967</span></a>
-</span><span id="L-968"><a href="#L-968"><span class="linenos"> 968</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-969"><a href="#L-969"><span class="linenos"> 969</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-970"><a href="#L-970"><span class="linenos"> 970</span></a><span class="p">)</span> <span class="o">-></span> <span class="nb">str</span><span class="p">:</span>
-</span><span id="L-971"><a href="#L-971"><span class="linenos"> 971</span></a> <span class="c1"># Get all valid semantic version tags</span>
-</span><span id="L-972"><a href="#L-972"><span class="linenos"> 972</span></a> <span class="n">versions</span> <span class="o">=</span> <span class="p">[]</span>
-</span><span id="L-973"><a href="#L-973"><span class="linenos"> 973</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-974"><a href="#L-974"><span class="linenos"> 974</span></a> <span class="k">if</span> <span class="n">tag</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">"v"</span><span class="p">):</span>
-</span><span id="L-975"><a href="#L-975"><span class="linenos"> 975</span></a> <span class="n">tag_name</span> <span class="o">=</span> <span class="n">tag</span><span class="o">.</span><span class="n">name</span><span class="p">[</span><span class="mi">1</span><span class="p">:]</span> <span class="c1"># Remove the first character</span>
-</span><span id="L-976"><a href="#L-976"><span class="linenos"> 976</span></a> <span class="k">else</span><span class="p">:</span>
-</span><span id="L-977"><a href="#L-977"><span class="linenos"> 977</span></a> <span class="n">tag_name</span> <span class="o">=</span> <span class="n">tag</span><span class="o">.</span><span class="n">name</span>
-</span><span id="L-978"><a href="#L-978"><span class="linenos"> 978</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-979"><a href="#L-979"><span class="linenos"> 979</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-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="n">_logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Versions: </span><span class="si">{</span><span class="n">versions</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
-</span><span id="L-982"><a href="#L-982"><span class="linenos"> 982</span></a> <span class="c1"># Determine the next version</span>
-</span><span id="L-983"><a href="#L-983"><span class="linenos"> 983</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-984"><a href="#L-984"><span class="linenos"> 984</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-985"><a href="#L-985"><span class="linenos"> 985</span></a> <span class="k">else</span><span class="p">:</span>
-</span><span id="L-986"><a href="#L-986"><span class="linenos"> 986</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-987"><a href="#L-987"><span class="linenos"> 987</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-988"><a href="#L-988"><span class="linenos"> 988</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-989"><a href="#L-989"><span class="linenos"> 989</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-990"><a href="#L-990"><span class="linenos"> 990</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-991"><a href="#L-991"><span class="linenos"> 991</span></a> <span class="k">else</span><span class="p">:</span>
-</span><span id="L-992"><a href="#L-992"><span class="linenos"> 992</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-993"><a href="#L-993"><span class="linenos"> 993</span></a>
-</span><span id="L-994"><a href="#L-994"><span class="linenos"> 994</span></a> <span class="c1"># Create the new tag</span>
-</span><span id="L-995"><a href="#L-995"><span class="linenos"> 995</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-996"><a href="#L-996"><span class="linenos"> 996</span></a>
-</span><span id="L-997"><a href="#L-997"><span class="linenos"> 997</span></a> <span class="k">return</span> <span class="n">new_version_str</span>
-</span><span id="L-998"><a href="#L-998"><span class="linenos"> 998</span></a>
-</span><span id="L-999"><a href="#L-999"><span class="linenos"> 999</span></a>
-</span><span id="L-1000"><a href="#L-1000"><span class="linenos">1000</span></a><span class="k">def</span><span class="w"> </span><span class="nf">publish</span><span class="p">(</span>
-</span><span id="L-1001"><a href="#L-1001"><span class="linenos">1001</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-1002"><a href="#L-1002"><span class="linenos">1002</span></a><span class="p">):</span>
-</span><span id="L-1003"><a href="#L-1003"><span class="linenos">1003</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-1004"><a href="#L-1004"><span class="linenos">1004</span></a>
-</span><span id="L-1005"><a href="#L-1005"><span class="linenos">1005</span></a> <span class="c1"># Validate config</span>
-</span><span id="L-1006"><a href="#L-1006"><span class="linenos">1006</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-1007"><a href="#L-1007"><span class="linenos">1007</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-848"><a href="#L-848"><span class="linenos"> 848</span></a> <span class="n">_logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span>
+</span><span id="L-849"><a href="#L-849"><span class="linenos"> 849</span></a> <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><span id="L-850"><a href="#L-850"><span class="linenos"> 850</span></a> <span class="p">)</span>
+</span><span id="L-851"><a href="#L-851"><span class="linenos"> 851</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-852"><a href="#L-852"><span class="linenos"> 852</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-853"><a href="#L-853"><span class="linenos"> 853</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-854"><a href="#L-854"><span class="linenos"> 854</span></a>
+</span><span id="L-855"><a href="#L-855"><span class="linenos"> 855</span></a> <span class="c1"># Map source concepts codes to target codes</span>
+</span><span id="L-856"><a href="#L-856"><span class="linenos"> 856</span></a> <span class="c1"># if processing a source coding list with categorical data</span>
+</span><span id="L-857"><a href="#L-857"><span class="linenos"> 857</span></a> <span class="k">if</span> <span class="p">(</span>
+</span><span id="L-858"><a href="#L-858"><span class="linenos"> 858</span></a> <span class="s2">"actions"</span> <span class="ow">in</span> <span class="n">concept_set</span>
+</span><span id="L-859"><a href="#L-859"><span class="linenos"> 859</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">"actions"</span><span class="p">]</span>
+</span><span id="L-860"><a href="#L-860"><span class="linenos"> 860</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-861"><a href="#L-861"><span class="linenos"> 861</span></a> <span class="p">):</span>
+</span><span id="L-862"><a href="#L-862"><span class="linenos"> 862</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">"actions"</span><span class="p">][</span><span class="s2">"divide_col"</span><span class="p">]</span>
+</span><span id="L-863"><a href="#L-863"><span class="linenos"> 863</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-864"><a href="#L-864"><span class="linenos"> 864</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-865"><a href="#L-865"><span class="linenos"> 865</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-866"><a href="#L-866"><span class="linenos"> 866</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-867"><a href="#L-867"><span class="linenos"> 867</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">"category"</span><span class="p">]:</span>
+</span><span id="L-868"><a href="#L-868"><span class="linenos"> 868</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><span id="L-869"><a href="#L-869"><span class="linenos"> 869</span></a> <span class="n">columns</span><span class="o">=</span><span class="p">[</span><span class="n">divide_col</span><span class="p">]</span>
+</span><span id="L-870"><a href="#L-870"><span class="linenos"> 870</span></a> <span class="p">)</span> <span class="c1"># delete categorical column</span>
+</span><span id="L-871"><a href="#L-871"><span class="linenos"> 871</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-872"><a href="#L-872"><span class="linenos"> 872</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-873"><a href="#L-873"><span class="linenos"> 873</span></a> <span class="n">source_df</span><span class="p">,</span>
+</span><span id="L-874"><a href="#L-874"><span class="linenos"> 874</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-875"><a href="#L-875"><span class="linenos"> 875</span></a> <span class="n">concept_name</span><span class="o">=</span><span class="n">concept_set_name</span><span class="p">,</span>
+</span><span id="L-876"><a href="#L-876"><span class="linenos"> 876</span></a> <span class="p">)</span>
+</span><span id="L-877"><a href="#L-877"><span class="linenos"> 877</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-878"><a href="#L-878"><span class="linenos"> 878</span></a> <span class="k">else</span><span class="p">:</span>
+</span><span id="L-879"><a href="#L-879"><span class="linenos"> 879</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-880"><a href="#L-880"><span class="linenos"> 880</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-881"><a href="#L-881"><span class="linenos"> 881</span></a> <span class="n">source_df</span><span class="p">,</span>
+</span><span id="L-882"><a href="#L-882"><span class="linenos"> 882</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-883"><a href="#L-883"><span class="linenos"> 883</span></a> <span class="n">concept_name</span><span class="o">=</span><span class="n">concept_set_name</span><span class="p">,</span>
+</span><span id="L-884"><a href="#L-884"><span class="linenos"> 884</span></a> <span class="p">)</span>
+</span><span id="L-885"><a href="#L-885"><span class="linenos"> 885</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-886"><a href="#L-886"><span class="linenos"> 886</span></a>
+</span><span id="L-887"><a href="#L-887"><span class="linenos"> 887</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-888"><a href="#L-888"><span class="linenos"> 888</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-889"><a href="#L-889"><span class="linenos"> 889</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-890"><a href="#L-890"><span class="linenos"> 890</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-891"><a href="#L-891"><span class="linenos"> 891</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-892"><a href="#L-892"><span class="linenos"> 892</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-893"><a href="#L-893"><span class="linenos"> 893</span></a>
+</span><span id="L-894"><a href="#L-894"><span class="linenos"> 894</span></a> <span class="c1"># Check there is output from processing</span>
+</span><span id="L-895"><a href="#L-895"><span class="linenos"> 895</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-896"><a href="#L-896"><span class="linenos"> 896</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-897"><a href="#L-897"><span class="linenos"> 897</span></a> <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span>
+</span><span id="L-898"><a href="#L-898"><span class="linenos"> 898</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-899"><a href="#L-899"><span class="linenos"> 899</span></a> <span class="p">)</span>
+</span><span id="L-900"><a href="#L-900"><span class="linenos"> 900</span></a>
+</span><span id="L-901"><a href="#L-901"><span class="linenos"> 901</span></a> <span class="c1"># final processing</span>
+</span><span id="L-902"><a href="#L-902"><span class="linenos"> 902</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-903"><a href="#L-903"><span class="linenos"> 903</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-904"><a href="#L-904"><span class="linenos"> 904</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-905"><a href="#L-905"><span class="linenos"> 905</span></a>
+</span><span id="L-906"><a href="#L-906"><span class="linenos"> 906</span></a> <span class="c1"># out_count = len(out.index)</span>
+</span><span id="L-907"><a href="#L-907"><span class="linenos"> 907</span></a> <span class="c1"># added metadata</span>
+</span><span id="L-908"><a href="#L-908"><span class="linenos"> 908</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-909"><a href="#L-909"><span class="linenos"> 909</span></a> <span class="c1"># result_list = []</span>
+</span><span id="L-910"><a href="#L-910"><span class="linenos"> 910</span></a> <span class="c1"># for files in phenotype["concept_sets"]:</span>
+</span><span id="L-911"><a href="#L-911"><span class="linenos"> 911</span></a> <span class="c1"># concept_set_name = files["name"]</span>
+</span><span id="L-912"><a href="#L-912"><span class="linenos"> 912</span></a> <span class="c1"># for concept_set in files["files"]:</span>
+</span><span id="L-913"><a href="#L-913"><span class="linenos"> 913</span></a> <span class="c1"># source_column_names = list(concept_set["columns"].keys())</span>
+</span><span id="L-914"><a href="#L-914"><span class="linenos"> 914</span></a> <span class="c1"># for source_concept_type in source_column_names:</span>
+</span><span id="L-915"><a href="#L-915"><span class="linenos"> 915</span></a> <span class="c1"># # Filter output based on the current source_concept_type</span>
+</span><span id="L-916"><a href="#L-916"><span class="linenos"> 916</span></a> <span class="c1"># out_filtered_df = out[out["SOURCE_CONCEPT_TYPE"] == source_concept_type]</span>
+</span><span id="L-917"><a href="#L-917"><span class="linenos"> 917</span></a> <span class="c1"># filtered_count = len(out_filtered_df.index)</span>
+</span><span id="L-918"><a href="#L-918"><span class="linenos"> 918</span></a>
+</span><span id="L-919"><a href="#L-919"><span class="linenos"> 919</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-920"><a href="#L-920"><span class="linenos"> 920</span></a> <span class="c1"># remove_types = [</span>
+</span><span id="L-921"><a href="#L-921"><span class="linenos"> 921</span></a> <span class="c1"># type for type in source_column_names if type != source_concept_type</span>
+</span><span id="L-922"><a href="#L-922"><span class="linenos"> 922</span></a> <span class="c1"># ]</span>
+</span><span id="L-923"><a href="#L-923"><span class="linenos"> 923</span></a> <span class="c1"># metadata_df = df.drop(columns=remove_types)</span>
+</span><span id="L-924"><a href="#L-924"><span class="linenos"> 924</span></a> <span class="c1"># metadata_df = metadata_df.rename(</span>
+</span><span id="L-925"><a href="#L-925"><span class="linenos"> 925</span></a> <span class="c1"># columns={source_concept_type: "SOURCE_CONCEPT"}</span>
+</span><span id="L-926"><a href="#L-926"><span class="linenos"> 926</span></a> <span class="c1"># )</span>
+</span><span id="L-927"><a href="#L-927"><span class="linenos"> 927</span></a> <span class="c1"># metadata_df_count = len(metadata_df.index)</span>
+</span><span id="L-928"><a href="#L-928"><span class="linenos"> 928</span></a>
+</span><span id="L-929"><a href="#L-929"><span class="linenos"> 929</span></a> <span class="c1"># Perform the left join with df2 on SOURCE_CONCEPT to add the metadata</span>
+</span><span id="L-930"><a href="#L-930"><span class="linenos"> 930</span></a> <span class="c1"># result = pd.merge(out_filtered_df, metadata_df, how="left", on="SOURCE_CONCEPT")</span>
+</span><span id="L-931"><a href="#L-931"><span class="linenos"> 931</span></a> <span class="c1"># result_count = len(result.index)</span>
+</span><span id="L-932"><a href="#L-932"><span class="linenos"> 932</span></a>
+</span><span id="L-933"><a href="#L-933"><span class="linenos"> 933</span></a> <span class="c1"># _logger.debug(</span>
+</span><span id="L-934"><a href="#L-934"><span class="linenos"> 934</span></a> <span class="c1"># f"Adding metadata for {source_concept_type}: out_count {out_count}, filtered_count {filtered_count}, metadata_df_count {metadata_df_count}, result_count {result_count}"</span>
+</span><span id="L-935"><a href="#L-935"><span class="linenos"> 935</span></a> <span class="c1"># )</span>
+</span><span id="L-936"><a href="#L-936"><span class="linenos"> 936</span></a>
+</span><span id="L-937"><a href="#L-937"><span class="linenos"> 937</span></a> <span class="c1"># # Append the result to the result_list</span>
+</span><span id="L-938"><a href="#L-938"><span class="linenos"> 938</span></a> <span class="c1"># result_list.append(result)</span>
+</span><span id="L-939"><a href="#L-939"><span class="linenos"> 939</span></a>
+</span><span id="L-940"><a href="#L-940"><span class="linenos"> 940</span></a> <span class="c1"># Concatenate all the results into a single DataFrame</span>
+</span><span id="L-941"><a href="#L-941"><span class="linenos"> 941</span></a> <span class="c1"># final_out = pd.concat(result_list, ignore_index=True)</span>
+</span><span id="L-942"><a href="#L-942"><span class="linenos"> 942</span></a> <span class="c1"># final_out = final_out.drop_duplicates(subset=["CONCEPT_SET", "CONCEPT"])</span>
+</span><span id="L-943"><a href="#L-943"><span class="linenos"> 943</span></a> <span class="c1"># _logger.debug(</span>
+</span><span id="L-944"><a href="#L-944"><span class="linenos"> 944</span></a> <span class="c1"># f"Check metadata processing counts: before {len(out.index)} : after {len(final_out.index)}"</span>
+</span><span id="L-945"><a href="#L-945"><span class="linenos"> 945</span></a> <span class="c1"># )</span>
+</span><span id="L-946"><a href="#L-946"><span class="linenos"> 946</span></a>
+</span><span id="L-947"><a href="#L-947"><span class="linenos"> 947</span></a> <span class="c1"># Save output to map directory</span>
+</span><span id="L-948"><a href="#L-948"><span class="linenos"> 948</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-949"><a href="#L-949"><span class="linenos"> 949</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-950"><a href="#L-950"><span class="linenos"> 950</span></a> <span class="n">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-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">"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-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 class="c1"># save concept sets as separate files</span>
+</span><span id="L-954"><a href="#L-954"><span class="linenos"> 954</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-955"><a href="#L-955"><span class="linenos"> 955</span></a>
+</span><span id="L-956"><a href="#L-956"><span class="linenos"> 956</span></a> <span class="c1"># empty the concept-set directory except for hiddle files, e.g. .git</span>
+</span><span id="L-957"><a href="#L-957"><span class="linenos"> 957</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-958"><a href="#L-958"><span class="linenos"> 958</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-959"><a href="#L-959"><span class="linenos"> 959</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-960"><a href="#L-960"><span class="linenos"> 960</span></a> <span class="n">item</span><span class="o">.</span><span class="n">unlink</span><span class="p">()</span>
+</span><span id="L-961"><a href="#L-961"><span class="linenos"> 961</span></a> <span class="k">else</span><span class="p">:</span>
+</span><span id="L-962"><a href="#L-962"><span class="linenos"> 962</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-963"><a href="#L-963"><span class="linenos"> 963</span></a>
+</span><span id="L-964"><a href="#L-964"><span class="linenos"> 964</span></a> <span class="c1"># write each concept as a separate file</span>
+</span><span id="L-965"><a href="#L-965"><span class="linenos"> 965</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">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-966"><a href="#L-966"><span class="linenos"> 966</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-967"><a href="#L-967"><span class="linenos"> 967</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-968"><a href="#L-968"><span class="linenos"> 968</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-969"><a href="#L-969"><span class="linenos"> 969</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-970"><a href="#L-970"><span class="linenos"> 970</span></a> <span class="p">)</span> <span class="c1"># sort cols alphabetically</span>
+</span><span id="L-971"><a href="#L-971"><span class="linenos"> 971</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-972"><a href="#L-972"><span class="linenos"> 972</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-973"><a href="#L-973"><span class="linenos"> 973</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-974"><a href="#L-974"><span class="linenos"> 974</span></a>
+</span><span id="L-975"><a href="#L-975"><span class="linenos"> 975</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-976"><a href="#L-976"><span class="linenos"> 976</span></a>
+</span><span id="L-977"><a href="#L-977"><span class="linenos"> 977</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-978"><a href="#L-978"><span class="linenos"> 978</span></a>
+</span><span id="L-979"><a href="#L-979"><span class="linenos"> 979</span></a>
+</span><span id="L-980"><a href="#L-980"><span class="linenos"> 980</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-981"><a href="#L-981"><span class="linenos"> 981</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-982"><a href="#L-982"><span class="linenos"> 982</span></a><span class="p">)</span> <span class="o">-></span> <span class="nb">str</span><span class="p">:</span>
+</span><span id="L-983"><a href="#L-983"><span class="linenos"> 983</span></a> <span class="c1"># Get all valid semantic version tags</span>
+</span><span id="L-984"><a href="#L-984"><span class="linenos"> 984</span></a> <span class="n">versions</span> <span class="o">=</span> <span class="p">[]</span>
+</span><span id="L-985"><a href="#L-985"><span class="linenos"> 985</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-986"><a href="#L-986"><span class="linenos"> 986</span></a> <span class="k">if</span> <span class="n">tag</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">"v"</span><span class="p">):</span>
+</span><span id="L-987"><a href="#L-987"><span class="linenos"> 987</span></a> <span class="n">tag_name</span> <span class="o">=</span> <span class="n">tag</span><span class="o">.</span><span class="n">name</span><span class="p">[</span><span class="mi">1</span><span class="p">:]</span> <span class="c1"># Remove the first character</span>
+</span><span id="L-988"><a href="#L-988"><span class="linenos"> 988</span></a> <span class="k">else</span><span class="p">:</span>
+</span><span id="L-989"><a href="#L-989"><span class="linenos"> 989</span></a> <span class="n">tag_name</span> <span class="o">=</span> <span class="n">tag</span><span class="o">.</span><span class="n">name</span>
+</span><span id="L-990"><a href="#L-990"><span class="linenos"> 990</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-991"><a href="#L-991"><span class="linenos"> 991</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-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="n">_logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="sa">f</span><span class="s2">"Versions: </span><span class="si">{</span><span class="n">versions</span><span class="si">}</span><span class="s2">"</span><span class="p">)</span>
+</span><span id="L-994"><a href="#L-994"><span class="linenos"> 994</span></a> <span class="c1"># Determine the next version</span>
+</span><span id="L-995"><a href="#L-995"><span class="linenos"> 995</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-996"><a href="#L-996"><span class="linenos"> 996</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-997"><a href="#L-997"><span class="linenos"> 997</span></a> <span class="k">else</span><span class="p">:</span>
+</span><span id="L-998"><a href="#L-998"><span class="linenos"> 998</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-999"><a href="#L-999"><span class="linenos"> 999</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-1000"><a href="#L-1000"><span class="linenos">1000</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-1001"><a href="#L-1001"><span class="linenos">1001</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-1002"><a href="#L-1002"><span class="linenos">1002</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-1003"><a href="#L-1003"><span class="linenos">1003</span></a> <span class="k">else</span><span class="p">:</span>
+</span><span id="L-1004"><a href="#L-1004"><span class="linenos">1004</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-1005"><a href="#L-1005"><span class="linenos">1005</span></a>
+</span><span id="L-1006"><a href="#L-1006"><span class="linenos">1006</span></a> <span class="c1"># Create the new tag</span>
+</span><span id="L-1007"><a href="#L-1007"><span class="linenos">1007</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-1008"><a href="#L-1008"><span class="linenos">1008</span></a>
-</span><span id="L-1009"><a href="#L-1009"><span class="linenos">1009</span></a> <span class="c1"># load git repo and set the branch</span>
-</span><span id="L-1010"><a href="#L-1010"><span class="linenos">1010</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-1011"><a href="#L-1011"><span class="linenos">1011</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-1012"><a href="#L-1012"><span class="linenos">1012</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-1013"><a href="#L-1013"><span class="linenos">1013</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-1014"><a href="#L-1014"><span class="linenos">1014</span></a> <span class="k">else</span><span class="p">:</span>
-</span><span id="L-1015"><a href="#L-1015"><span class="linenos">1015</span></a> <span class="k">raise</span> <span class="ne">AttributeError</span><span class="p">(</span>
-</span><span id="L-1016"><a href="#L-1016"><span class="linenos">1016</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-1017"><a href="#L-1017"><span class="linenos">1017</span></a> <span class="p">)</span>
-</span><span id="L-1018"><a href="#L-1018"><span class="linenos">1018</span></a>
-</span><span id="L-1019"><a href="#L-1019"><span class="linenos">1019</span></a> <span class="c1"># check if any changes to publish</span>
-</span><span id="L-1020"><a href="#L-1020"><span class="linenos">1020</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-1021"><a href="#L-1021"><span class="linenos">1021</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-1022"><a href="#L-1022"><span class="linenos">1022</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-1023"><a href="#L-1023"><span class="linenos">1023</span></a> <span class="k">else</span><span class="p">:</span>
-</span><span id="L-1024"><a href="#L-1024"><span class="linenos">1024</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-1025"><a href="#L-1025"><span class="linenos">1025</span></a> <span class="k">return</span>
-</span><span id="L-1026"><a href="#L-1026"><span class="linenos">1026</span></a>
-</span><span id="L-1027"><a href="#L-1027"><span class="linenos">1027</span></a> <span class="c1"># get next version</span>
-</span><span id="L-1028"><a href="#L-1028"><span class="linenos">1028</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-1029"><a href="#L-1029"><span class="linenos">1029</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-1009"><a href="#L-1009"><span class="linenos">1009</span></a> <span class="k">return</span> <span class="n">new_version_str</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><span id="L-1012"><a href="#L-1012"><span class="linenos">1012</span></a><span class="k">def</span><span class="w"> </span><span class="nf">publish</span><span class="p">(</span>
+</span><span id="L-1013"><a href="#L-1013"><span class="linenos">1013</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-1014"><a href="#L-1014"><span class="linenos">1014</span></a><span class="p">):</span>
+</span><span id="L-1015"><a href="#L-1015"><span class="linenos">1015</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-1016"><a href="#L-1016"><span class="linenos">1016</span></a>
+</span><span id="L-1017"><a href="#L-1017"><span class="linenos">1017</span></a> <span class="c1"># Validate config</span>
+</span><span id="L-1018"><a href="#L-1018"><span class="linenos">1018</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-1019"><a href="#L-1019"><span class="linenos">1019</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-1020"><a href="#L-1020"><span class="linenos">1020</span></a>
+</span><span id="L-1021"><a href="#L-1021"><span class="linenos">1021</span></a> <span class="c1"># load git repo and set the branch</span>
+</span><span id="L-1022"><a href="#L-1022"><span class="linenos">1022</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-1023"><a href="#L-1023"><span class="linenos">1023</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-1024"><a href="#L-1024"><span class="linenos">1024</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-1025"><a href="#L-1025"><span class="linenos">1025</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-1026"><a href="#L-1026"><span class="linenos">1026</span></a> <span class="k">else</span><span class="p">:</span>
+</span><span id="L-1027"><a href="#L-1027"><span class="linenos">1027</span></a> <span class="k">raise</span> <span class="ne">AttributeError</span><span class="p">(</span>
+</span><span id="L-1028"><a href="#L-1028"><span class="linenos">1028</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-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"># Write version in configuration file</span>
-</span><span id="L-1032"><a href="#L-1032"><span class="linenos">1032</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-1033"><a href="#L-1033"><span class="linenos">1033</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-1034"><a href="#L-1034"><span class="linenos">1034</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-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="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-1037"><a href="#L-1037"><span class="linenos">1037</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-1038"><a href="#L-1038"><span class="linenos">1038</span></a> <span class="n">yaml</span><span class="o">.</span><span class="n">dump</span><span class="p">(</span>
-</span><span id="L-1039"><a href="#L-1039"><span class="linenos">1039</span></a> <span class="n">config</span><span class="p">,</span>
-</span><span id="L-1040"><a href="#L-1040"><span class="linenos">1040</span></a> <span class="n">file</span><span class="p">,</span>
-</span><span id="L-1041"><a href="#L-1041"><span class="linenos">1041</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-1042"><a href="#L-1042"><span class="linenos">1042</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-1043"><a href="#L-1043"><span class="linenos">1043</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-1044"><a href="#L-1044"><span class="linenos">1044</span></a> <span class="n">default_style</span><span class="o">=</span><span class="s1">'"'</span><span class="p">,</span>
-</span><span id="L-1045"><a href="#L-1045"><span class="linenos">1045</span></a> <span class="p">)</span>
-</span><span id="L-1046"><a href="#L-1046"><span class="linenos">1046</span></a>
-</span><span id="L-1047"><a href="#L-1047"><span class="linenos">1047</span></a> <span class="c1"># Add and commit changes to repo including version updates</span>
-</span><span id="L-1048"><a href="#L-1048"><span class="linenos">1048</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-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">add</span><span class="p">(</span><span class="s2">"--all"</span><span class="p">)</span>
-</span><span id="L-1050"><a href="#L-1050"><span class="linenos">1050</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-1051"><a href="#L-1051"><span class="linenos">1051</span></a>
-</span><span id="L-1052"><a href="#L-1052"><span class="linenos">1052</span></a> <span class="c1"># Add tag to the repo</span>
-</span><span id="L-1053"><a href="#L-1053"><span class="linenos">1053</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-1054"><a href="#L-1054"><span class="linenos">1054</span></a>
-</span><span id="L-1055"><a href="#L-1055"><span class="linenos">1055</span></a> <span class="c1"># push to origin if a remote repo</span>
-</span><span id="L-1056"><a href="#L-1056"><span class="linenos">1056</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-1057"><a href="#L-1057"><span class="linenos">1057</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-1058"><a href="#L-1058"><span class="linenos">1058</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-1059"><a href="#L-1059"><span class="linenos">1059</span></a>
-</span><span id="L-1060"><a href="#L-1060"><span class="linenos">1060</span></a> <span class="k">try</span><span class="p">:</span>
-</span><span id="L-1061"><a href="#L-1061"><span class="linenos">1061</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-1062"><a href="#L-1062"><span class="linenos">1062</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-1063"><a href="#L-1063"><span class="linenos">1063</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-1064"><a href="#L-1064"><span class="linenos">1064</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-1065"><a href="#L-1065"><span class="linenos">1065</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-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">"Pushing version tags to remote git repo"</span><span class="p">)</span>
-</span><span id="L-1067"><a href="#L-1067"><span class="linenos">1067</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-1068"><a href="#L-1068"><span class="linenos">1068</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-1069"><a href="#L-1069"><span class="linenos">1069</span></a> <span class="k">else</span><span class="p">:</span>
-</span><span id="L-1070"><a href="#L-1070"><span class="linenos">1070</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-1071"><a href="#L-1071"><span class="linenos">1071</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-1072"><a href="#L-1072"><span class="linenos">1072</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-1073"><a href="#L-1073"><span class="linenos">1073</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-1074"><a href="#L-1074"><span class="linenos">1074</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-1075"><a href="#L-1075"><span class="linenos">1075</span></a> <span class="k">raise</span> <span class="n">e</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">_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-1078"><a href="#L-1078"><span class="linenos">1078</span></a>
-</span><span id="L-1079"><a href="#L-1079"><span class="linenos">1079</span></a>
-</span><span id="L-1080"><a href="#L-1080"><span class="linenos">1080</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-1081"><a href="#L-1081"><span class="linenos">1081</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-1082"><a href="#L-1082"><span class="linenos">1082</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-1083"><a href="#L-1083"><span class="linenos">1083</span></a>
-</span><span id="L-1084"><a href="#L-1084"><span class="linenos">1084</span></a> <span class="c1"># validate configuration</span>
-</span><span id="L-1085"><a href="#L-1085"><span class="linenos">1085</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-1086"><a href="#L-1086"><span class="linenos">1086</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-1087"><a href="#L-1087"><span class="linenos">1087</span></a>
-</span><span id="L-1088"><a href="#L-1088"><span class="linenos">1088</span></a> <span class="c1"># load configuration</span>
-</span><span id="L-1089"><a href="#L-1089"><span class="linenos">1089</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-1090"><a href="#L-1090"><span class="linenos">1090</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-1091"><a href="#L-1091"><span class="linenos">1091</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-1092"><a href="#L-1092"><span class="linenos">1092</span></a>
-</span><span id="L-1093"><a href="#L-1093"><span class="linenos">1093</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-1094"><a href="#L-1094"><span class="linenos">1094</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-1095"><a href="#L-1095"><span class="linenos">1095</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-1096"><a href="#L-1096"><span class="linenos">1096</span></a>
-</span><span id="L-1097"><a href="#L-1097"><span class="linenos">1097</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-1098"><a href="#L-1098"><span class="linenos">1098</span></a> <span class="c1"># check export directory exists and if not create it</span>
-</span><span id="L-1099"><a href="#L-1099"><span class="linenos">1099</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-1100"><a href="#L-1100"><span class="linenos">1100</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-1101"><a href="#L-1101"><span class="linenos">1101</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-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"># omop export db</span>
-</span><span id="L-1104"><a href="#L-1104"><span class="linenos">1104</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-1105"><a href="#L-1105"><span class="linenos">1105</span></a> <span class="n">map_path</span><span class="p">,</span>
-</span><span id="L-1106"><a href="#L-1106"><span class="linenos">1106</span></a> <span class="n">export_path</span><span class="p">,</span>
-</span><span id="L-1107"><a href="#L-1107"><span class="linenos">1107</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-1108"><a href="#L-1108"><span class="linenos">1108</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-1109"><a href="#L-1109"><span class="linenos">1109</span></a> <span class="p">)</span>
-</span><span id="L-1110"><a href="#L-1110"><span class="linenos">1110</span></a>
-</span><span id="L-1111"><a href="#L-1111"><span class="linenos">1111</span></a> <span class="c1"># write to tables</span>
-</span><span id="L-1112"><a href="#L-1112"><span class="linenos">1112</span></a> <span class="c1"># export as csv</span>
-</span><span id="L-1113"><a href="#L-1113"><span class="linenos">1113</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-1031"><a href="#L-1031"><span class="linenos">1031</span></a> <span class="c1"># check if any changes to publish</span>
+</span><span id="L-1032"><a href="#L-1032"><span class="linenos">1032</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-1033"><a href="#L-1033"><span class="linenos">1033</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-1034"><a href="#L-1034"><span class="linenos">1034</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-1035"><a href="#L-1035"><span class="linenos">1035</span></a> <span class="k">else</span><span class="p">:</span>
+</span><span id="L-1036"><a href="#L-1036"><span class="linenos">1036</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-1037"><a href="#L-1037"><span class="linenos">1037</span></a> <span class="k">return</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"># get next version</span>
+</span><span id="L-1040"><a href="#L-1040"><span class="linenos">1040</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-1041"><a href="#L-1041"><span class="linenos">1041</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-1042"><a href="#L-1042"><span class="linenos">1042</span></a>
+</span><span id="L-1043"><a href="#L-1043"><span class="linenos">1043</span></a> <span class="c1"># Write version in configuration file</span>
+</span><span id="L-1044"><a href="#L-1044"><span class="linenos">1044</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-1045"><a href="#L-1045"><span class="linenos">1045</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-1046"><a href="#L-1046"><span class="linenos">1046</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-1047"><a href="#L-1047"><span class="linenos">1047</span></a>
+</span><span id="L-1048"><a href="#L-1048"><span class="linenos">1048</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-1049"><a href="#L-1049"><span class="linenos">1049</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-1050"><a href="#L-1050"><span class="linenos">1050</span></a> <span class="n">yaml</span><span class="o">.</span><span class="n">dump</span><span class="p">(</span>
+</span><span id="L-1051"><a href="#L-1051"><span class="linenos">1051</span></a> <span class="n">config</span><span class="p">,</span>
+</span><span id="L-1052"><a href="#L-1052"><span class="linenos">1052</span></a> <span class="n">file</span><span class="p">,</span>
+</span><span id="L-1053"><a href="#L-1053"><span class="linenos">1053</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-1054"><a href="#L-1054"><span class="linenos">1054</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-1055"><a href="#L-1055"><span class="linenos">1055</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-1056"><a href="#L-1056"><span class="linenos">1056</span></a> <span class="n">default_style</span><span class="o">=</span><span class="s1">'"'</span><span class="p">,</span>
+</span><span id="L-1057"><a href="#L-1057"><span class="linenos">1057</span></a> <span class="p">)</span>
+</span><span id="L-1058"><a href="#L-1058"><span class="linenos">1058</span></a>
+</span><span id="L-1059"><a href="#L-1059"><span class="linenos">1059</span></a> <span class="c1"># Add and commit changes to repo including version updates</span>
+</span><span id="L-1060"><a href="#L-1060"><span class="linenos">1060</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-1061"><a href="#L-1061"><span class="linenos">1061</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-1062"><a href="#L-1062"><span class="linenos">1062</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-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="c1"># Add tag to the repo</span>
+</span><span id="L-1065"><a href="#L-1065"><span class="linenos">1065</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-1066"><a href="#L-1066"><span class="linenos">1066</span></a>
+</span><span id="L-1067"><a href="#L-1067"><span class="linenos">1067</span></a> <span class="c1"># push to origin if a remote repo</span>
+</span><span id="L-1068"><a href="#L-1068"><span class="linenos">1068</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-1069"><a href="#L-1069"><span class="linenos">1069</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-1070"><a href="#L-1070"><span class="linenos">1070</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-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="k">try</span><span class="p">:</span>
+</span><span id="L-1073"><a href="#L-1073"><span class="linenos">1073</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-1074"><a href="#L-1074"><span class="linenos">1074</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-1075"><a href="#L-1075"><span class="linenos">1075</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-1076"><a href="#L-1076"><span class="linenos">1076</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-1077"><a href="#L-1077"><span class="linenos">1077</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-1078"><a href="#L-1078"><span class="linenos">1078</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-1079"><a href="#L-1079"><span class="linenos">1079</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-1080"><a href="#L-1080"><span class="linenos">1080</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-1081"><a href="#L-1081"><span class="linenos">1081</span></a> <span class="k">else</span><span class="p">:</span>
+</span><span id="L-1082"><a href="#L-1082"><span class="linenos">1082</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-1083"><a href="#L-1083"><span class="linenos">1083</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-1084"><a href="#L-1084"><span class="linenos">1084</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-1085"><a href="#L-1085"><span class="linenos">1085</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-1086"><a href="#L-1086"><span class="linenos">1086</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-1087"><a href="#L-1087"><span class="linenos">1087</span></a> <span class="k">raise</span> <span class="n">e</span>
+</span><span id="L-1088"><a href="#L-1088"><span class="linenos">1088</span></a>
+</span><span id="L-1089"><a href="#L-1089"><span class="linenos">1089</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-1090"><a href="#L-1090"><span class="linenos">1090</span></a>
+</span><span id="L-1091"><a href="#L-1091"><span class="linenos">1091</span></a>
+</span><span id="L-1092"><a href="#L-1092"><span class="linenos">1092</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-1093"><a href="#L-1093"><span class="linenos">1093</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-1094"><a href="#L-1094"><span class="linenos">1094</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-1095"><a href="#L-1095"><span class="linenos">1095</span></a>
+</span><span id="L-1096"><a href="#L-1096"><span class="linenos">1096</span></a> <span class="c1"># validate configuration</span>
+</span><span id="L-1097"><a href="#L-1097"><span class="linenos">1097</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-1098"><a href="#L-1098"><span class="linenos">1098</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-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="c1"># load configuration</span>
+</span><span id="L-1101"><a href="#L-1101"><span class="linenos">1101</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-1102"><a href="#L-1102"><span class="linenos">1102</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-1103"><a href="#L-1103"><span class="linenos">1103</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-1104"><a href="#L-1104"><span class="linenos">1104</span></a>
+</span><span id="L-1105"><a href="#L-1105"><span class="linenos">1105</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-1106"><a href="#L-1106"><span class="linenos">1106</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-1107"><a href="#L-1107"><span class="linenos">1107</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-1108"><a href="#L-1108"><span class="linenos">1108</span></a>
+</span><span id="L-1109"><a href="#L-1109"><span class="linenos">1109</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-1110"><a href="#L-1110"><span class="linenos">1110</span></a> <span class="c1"># check export directory exists and if not create it</span>
+</span><span id="L-1111"><a href="#L-1111"><span class="linenos">1111</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-1112"><a href="#L-1112"><span class="linenos">1112</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-1113"><a href="#L-1113"><span class="linenos">1113</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-1114"><a href="#L-1114"><span class="linenos">1114</span></a>
-</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">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-1117"><a href="#L-1117"><span class="linenos">1117</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-1118"><a href="#L-1118"><span class="linenos">1118</span></a>
-</span><span id="L-1119"><a href="#L-1119"><span class="linenos">1119</span></a> <span class="c1"># Validate</span>
-</span><span id="L-1120"><a href="#L-1120"><span class="linenos">1120</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-1121"><a href="#L-1121"><span class="linenos">1121</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-1115"><a href="#L-1115"><span class="linenos">1115</span></a> <span class="c1"># omop export db</span>
+</span><span id="L-1116"><a href="#L-1116"><span class="linenos">1116</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-1117"><a href="#L-1117"><span class="linenos">1117</span></a> <span class="n">map_path</span><span class="p">,</span>
+</span><span id="L-1118"><a href="#L-1118"><span class="linenos">1118</span></a> <span class="n">export_path</span><span class="p">,</span>
+</span><span id="L-1119"><a href="#L-1119"><span class="linenos">1119</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-1120"><a href="#L-1120"><span class="linenos">1120</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-1121"><a href="#L-1121"><span class="linenos">1121</span></a> <span class="p">)</span>
</span><span id="L-1122"><a href="#L-1122"><span class="linenos">1122</span></a>
-</span><span id="L-1123"><a href="#L-1123"><span class="linenos">1123</span></a> <span class="c1"># Check target directory exists</span>
-</span><span id="L-1124"><a href="#L-1124"><span class="linenos">1124</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-1125"><a href="#L-1125"><span class="linenos">1125</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-1126"><a href="#L-1126"><span class="linenos">1126</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-1123"><a href="#L-1123"><span class="linenos">1123</span></a> <span class="c1"># write to tables</span>
+</span><span id="L-1124"><a href="#L-1124"><span class="linenos">1124</span></a> <span class="c1"># export as csv</span>
+</span><span id="L-1125"><a href="#L-1125"><span class="linenos">1125</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-1126"><a href="#L-1126"><span class="linenos">1126</span></a>
</span><span id="L-1127"><a href="#L-1127"><span class="linenos">1127</span></a>
-</span><span id="L-1128"><a href="#L-1128"><span class="linenos">1128</span></a> <span class="c1"># Set copy directory</span>
-</span><span id="L-1129"><a href="#L-1129"><span class="linenos">1129</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-1130"><a href="#L-1130"><span class="linenos">1130</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-1131"><a href="#L-1131"><span class="linenos">1131</span></a>
-</span><span id="L-1132"><a href="#L-1132"><span class="linenos">1132</span></a> <span class="k">if</span> <span class="p">(</span>
-</span><span id="L-1133"><a href="#L-1133"><span class="linenos">1133</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-1134"><a href="#L-1134"><span class="linenos">1134</span></a> <span class="p">):</span> <span class="c1"># Check if it exists and is a directory</span>
-</span><span id="L-1135"><a href="#L-1135"><span class="linenos">1135</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-1136"><a href="#L-1136"><span class="linenos">1136</span></a> <span class="n">copy_path</span><span class="p">,</span>
-</span><span id="L-1137"><a href="#L-1137"><span class="linenos">1137</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-1138"><a href="#L-1138"><span class="linenos">1138</span></a> <span class="p">)</span>
-</span><span id="L-1139"><a href="#L-1139"><span class="linenos">1139</span></a> <span class="k">else</span><span class="p">:</span>
-</span><span id="L-1140"><a href="#L-1140"><span class="linenos">1140</span></a> <span class="n">copy</span> <span class="o">=</span> <span class="kc">True</span>
-</span><span id="L-1141"><a href="#L-1141"><span class="linenos">1141</span></a>
-</span><span id="L-1142"><a href="#L-1142"><span class="linenos">1142</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-1143"><a href="#L-1143"><span class="linenos">1143</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-1144"><a href="#L-1144"><span class="linenos">1144</span></a> <span class="k">return</span>
-</span><span id="L-1145"><a href="#L-1145"><span class="linenos">1145</span></a>
-</span><span id="L-1146"><a href="#L-1146"><span class="linenos">1146</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-1147"><a href="#L-1147"><span class="linenos">1147</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-1148"><a href="#L-1148"><span class="linenos">1148</span></a>
-</span><span id="L-1149"><a href="#L-1149"><span class="linenos">1149</span></a> <span class="c1"># Check out the latest commit or specified version</span>
-</span><span id="L-1150"><a href="#L-1150"><span class="linenos">1150</span></a> <span class="k">if</span> <span class="n">version</span><span class="p">:</span>
-</span><span id="L-1151"><a href="#L-1151"><span class="linenos">1151</span></a> <span class="c1"># Checkout a specific version (e.g., branch, tag, or commit hash)</span>
-</span><span id="L-1152"><a href="#L-1152"><span class="linenos">1152</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-1153"><a href="#L-1153"><span class="linenos">1153</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-1154"><a href="#L-1154"><span class="linenos">1154</span></a> <span class="k">else</span><span class="p">:</span>
-</span><span id="L-1155"><a href="#L-1155"><span class="linenos">1155</span></a> <span class="c1"># Checkout the latest commit (HEAD)</span>
-</span><span id="L-1156"><a href="#L-1156"><span class="linenos">1156</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-1157"><a href="#L-1157"><span class="linenos">1157</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-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="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-1128"><a href="#L-1128"><span class="linenos">1128</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-1129"><a href="#L-1129"><span class="linenos">1129</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-1130"><a href="#L-1130"><span class="linenos">1130</span></a>
+</span><span id="L-1131"><a href="#L-1131"><span class="linenos">1131</span></a> <span class="c1"># Validate</span>
+</span><span id="L-1132"><a href="#L-1132"><span class="linenos">1132</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-1133"><a href="#L-1133"><span class="linenos">1133</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-1134"><a href="#L-1134"><span class="linenos">1134</span></a>
+</span><span id="L-1135"><a href="#L-1135"><span class="linenos">1135</span></a> <span class="c1"># Check target directory exists</span>
+</span><span id="L-1136"><a href="#L-1136"><span class="linenos">1136</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-1137"><a href="#L-1137"><span class="linenos">1137</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-1138"><a href="#L-1138"><span class="linenos">1138</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-1139"><a href="#L-1139"><span class="linenos">1139</span></a>
+</span><span id="L-1140"><a href="#L-1140"><span class="linenos">1140</span></a> <span class="c1"># Set copy directory</span>
+</span><span id="L-1141"><a href="#L-1141"><span class="linenos">1141</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-1142"><a href="#L-1142"><span class="linenos">1142</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-1143"><a href="#L-1143"><span class="linenos">1143</span></a>
+</span><span id="L-1144"><a href="#L-1144"><span class="linenos">1144</span></a> <span class="k">if</span> <span class="p">(</span>
+</span><span id="L-1145"><a href="#L-1145"><span class="linenos">1145</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-1146"><a href="#L-1146"><span class="linenos">1146</span></a> <span class="p">):</span> <span class="c1"># Check if it exists and is a directory</span>
+</span><span id="L-1147"><a href="#L-1147"><span class="linenos">1147</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-1148"><a href="#L-1148"><span class="linenos">1148</span></a> <span class="n">copy_path</span><span class="p">,</span>
+</span><span id="L-1149"><a href="#L-1149"><span class="linenos">1149</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-1150"><a href="#L-1150"><span class="linenos">1150</span></a> <span class="p">)</span>
+</span><span id="L-1151"><a href="#L-1151"><span class="linenos">1151</span></a> <span class="k">else</span><span class="p">:</span>
+</span><span id="L-1152"><a href="#L-1152"><span class="linenos">1152</span></a> <span class="n">copy</span> <span class="o">=</span> <span class="kc">True</span>
+</span><span id="L-1153"><a href="#L-1153"><span class="linenos">1153</span></a>
+</span><span id="L-1154"><a href="#L-1154"><span class="linenos">1154</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-1155"><a href="#L-1155"><span class="linenos">1155</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-1156"><a href="#L-1156"><span class="linenos">1156</span></a> <span class="k">return</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 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-1159"><a href="#L-1159"><span class="linenos">1159</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-1160"><a href="#L-1160"><span class="linenos">1160</span></a>
-</span><span id="L-1161"><a href="#L-1161"><span class="linenos">1161</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-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><span id="L-1164"><a href="#L-1164"><span class="linenos">1164</span></a><span class="c1"># Convert concept_sets list into dictionaries</span>
-</span><span id="L-1165"><a href="#L-1165"><span class="linenos">1165</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-1166"><a href="#L-1166"><span class="linenos">1166</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-1167"><a href="#L-1167"><span class="linenos">1167</span></a> <span class="n">concepts_dict</span> <span class="o">=</span> <span class="p">{</span>
-</span><span id="L-1168"><a href="#L-1168"><span class="linenos">1168</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-1169"><a href="#L-1169"><span class="linenos">1169</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-1170"><a href="#L-1170"><span class="linenos">1170</span></a> <span class="p">}</span>
-</span><span id="L-1171"><a href="#L-1171"><span class="linenos">1171</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-1172"><a href="#L-1172"><span class="linenos">1172</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-1173"><a href="#L-1173"><span class="linenos">1173</span></a>
+</span><span id="L-1161"><a href="#L-1161"><span class="linenos">1161</span></a> <span class="c1"># Check out the latest commit or specified version</span>
+</span><span id="L-1162"><a href="#L-1162"><span class="linenos">1162</span></a> <span class="k">if</span> <span class="n">version</span><span class="p">:</span>
+</span><span id="L-1163"><a href="#L-1163"><span class="linenos">1163</span></a> <span class="c1"># Checkout a specific version (e.g., branch, tag, or commit hash)</span>
+</span><span id="L-1164"><a href="#L-1164"><span class="linenos">1164</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-1165"><a href="#L-1165"><span class="linenos">1165</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-1166"><a href="#L-1166"><span class="linenos">1166</span></a> <span class="k">else</span><span class="p">:</span>
+</span><span id="L-1167"><a href="#L-1167"><span class="linenos">1167</span></a> <span class="c1"># Checkout the latest commit (HEAD)</span>
+</span><span id="L-1168"><a href="#L-1168"><span class="linenos">1168</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-1169"><a href="#L-1169"><span class="linenos">1169</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-1170"><a href="#L-1170"><span class="linenos">1170</span></a>
+</span><span id="L-1171"><a href="#L-1171"><span class="linenos">1171</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-1172"><a href="#L-1172"><span class="linenos">1172</span></a>
+</span><span id="L-1173"><a href="#L-1173"><span class="linenos">1173</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-1174"><a href="#L-1174"><span class="linenos">1174</span></a>
-</span><span id="L-1175"><a href="#L-1175"><span class="linenos">1175</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-1176"><a href="#L-1176"><span class="linenos">1176</span></a><span class="w"> </span><span class="sd">"""</span>
-</span><span id="L-1177"><a href="#L-1177"><span class="linenos">1177</span></a><span class="sd"> Extracts clean keys from a DeepDiff dictionary.</span>
-</span><span id="L-1178"><a href="#L-1178"><span class="linenos">1178</span></a>
-</span><span id="L-1179"><a href="#L-1179"><span class="linenos">1179</span></a><span class="sd"> :param diff: DeepDiff result dictionary</span>
-</span><span id="L-1180"><a href="#L-1180"><span class="linenos">1180</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-1181"><a href="#L-1181"><span class="linenos">1181</span></a><span class="sd"> :return: A set of clean key names</span>
-</span><span id="L-1182"><a href="#L-1182"><span class="linenos">1182</span></a><span class="sd"> """</span>
-</span><span id="L-1183"><a href="#L-1183"><span class="linenos">1183</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-1184"><a href="#L-1184"><span class="linenos">1184</span></a>
-</span><span id="L-1185"><a href="#L-1185"><span class="linenos">1185</span></a>
-</span><span id="L-1186"><a href="#L-1186"><span class="linenos">1186</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-1187"><a href="#L-1187"><span class="linenos">1187</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-1188"><a href="#L-1188"><span class="linenos">1188</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-1189"><a href="#L-1189"><span class="linenos">1189</span></a>
-</span><span id="L-1190"><a href="#L-1190"><span class="linenos">1190</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-1191"><a href="#L-1191"><span class="linenos">1191</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-1192"><a href="#L-1192"><span class="linenos">1192</span></a>
-</span><span id="L-1193"><a href="#L-1193"><span class="linenos">1193</span></a> <span class="c1"># Check added and removed names</span>
-</span><span id="L-1194"><a href="#L-1194"><span class="linenos">1194</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-1195"><a href="#L-1195"><span class="linenos">1195</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-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"># find file path changes for unchanged names</span>
-</span><span id="L-1198"><a href="#L-1198"><span class="linenos">1198</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-1199"><a href="#L-1199"><span class="linenos">1199</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-1200"><a href="#L-1200"><span class="linenos">1200</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-1201"><a href="#L-1201"><span class="linenos">1201</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-1202"><a href="#L-1202"><span class="linenos">1202</span></a> <span class="p">)</span>
-</span><span id="L-1203"><a href="#L-1203"><span class="linenos">1203</span></a>
-</span><span id="L-1204"><a href="#L-1204"><span class="linenos">1204</span></a> <span class="c1"># Find renamed concepts (same file, different name)</span>
-</span><span id="L-1205"><a href="#L-1205"><span class="linenos">1205</span></a> <span class="n">renamed_concepts</span> <span class="o">=</span> <span class="p">[]</span>
-</span><span id="L-1206"><a href="#L-1206"><span class="linenos">1206</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-1207"><a href="#L-1207"><span class="linenos">1207</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-1208"><a href="#L-1208"><span class="linenos">1208</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-1209"><a href="#L-1209"><span class="linenos">1209</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-1210"><a href="#L-1210"><span class="linenos">1210</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-1211"><a href="#L-1211"><span class="linenos">1211</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-1212"><a href="#L-1212"><span class="linenos">1212</span></a>
-</span><span id="L-1213"><a href="#L-1213"><span class="linenos">1213</span></a> <span class="c1"># Remove renamed concepts from added and removed sets</span>
-</span><span id="L-1214"><a href="#L-1214"><span class="linenos">1214</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-1215"><a href="#L-1215"><span class="linenos">1215</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-1216"><a href="#L-1216"><span class="linenos">1216</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-1217"><a href="#L-1217"><span class="linenos">1217</span></a>
-</span><span id="L-1218"><a href="#L-1218"><span class="linenos">1218</span></a> <span class="c1"># generate config report</span>
-</span><span id="L-1219"><a href="#L-1219"><span class="linenos">1219</span></a> <span class="k">if</span> <span class="n">added_names</span><span class="p">:</span>
-</span><span id="L-1220"><a href="#L-1220"><span class="linenos">1220</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-1221"><a href="#L-1221"><span class="linenos">1221</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-1222"><a href="#L-1222"><span class="linenos">1222</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-1223"><a href="#L-1223"><span class="linenos">1223</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-1224"><a href="#L-1224"><span class="linenos">1224</span></a>
-</span><span id="L-1225"><a href="#L-1225"><span class="linenos">1225</span></a> <span class="k">if</span> <span class="n">removed_names</span><span class="p">:</span>
-</span><span id="L-1226"><a href="#L-1226"><span class="linenos">1226</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-1227"><a href="#L-1227"><span class="linenos">1227</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-1228"><a href="#L-1228"><span class="linenos">1228</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-1229"><a href="#L-1229"><span class="linenos">1229</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-1175"><a href="#L-1175"><span class="linenos">1175</span></a>
+</span><span id="L-1176"><a href="#L-1176"><span class="linenos">1176</span></a><span class="c1"># Convert concept_sets list into dictionaries</span>
+</span><span id="L-1177"><a href="#L-1177"><span class="linenos">1177</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-1178"><a href="#L-1178"><span class="linenos">1178</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-1179"><a href="#L-1179"><span class="linenos">1179</span></a> <span class="n">concepts_dict</span> <span class="o">=</span> <span class="p">{</span>
+</span><span id="L-1180"><a href="#L-1180"><span class="linenos">1180</span></a> <span class="n">item</span><span class="p">[</span><span class="s2">"name"</span><span class="p">]:</span> <span class="p">[</span><span class="n">file</span><span class="p">[</span><span class="s2">"path"</span><span class="p">]</span> <span class="k">for</span> <span class="n">file</span> <span class="ow">in</span> <span class="n">item</span><span class="p">[</span><span class="s2">"files"</span><span class="p">]]</span>
+</span><span id="L-1181"><a href="#L-1181"><span class="linenos">1181</span></a> <span class="c1"># item["name"]: item["file"]["path"]</span>
+</span><span id="L-1182"><a href="#L-1182"><span class="linenos">1182</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-1183"><a href="#L-1183"><span class="linenos">1183</span></a> <span class="p">}</span>
+</span><span id="L-1184"><a href="#L-1184"><span class="linenos">1184</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-1185"><a href="#L-1185"><span class="linenos">1185</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-1186"><a href="#L-1186"><span class="linenos">1186</span></a>
+</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="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-1189"><a href="#L-1189"><span class="linenos">1189</span></a><span class="w"> </span><span class="sd">"""</span>
+</span><span id="L-1190"><a href="#L-1190"><span class="linenos">1190</span></a><span class="sd"> Extracts clean keys from a DeepDiff dictionary.</span>
+</span><span id="L-1191"><a href="#L-1191"><span class="linenos">1191</span></a>
+</span><span id="L-1192"><a href="#L-1192"><span class="linenos">1192</span></a><span class="sd"> :param diff: DeepDiff result dictionary</span>
+</span><span id="L-1193"><a href="#L-1193"><span class="linenos">1193</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-1194"><a href="#L-1194"><span class="linenos">1194</span></a><span class="sd"> :return: A set of clean key names</span>
+</span><span id="L-1195"><a href="#L-1195"><span class="linenos">1195</span></a><span class="sd"> """</span>
+</span><span id="L-1196"><a href="#L-1196"><span class="linenos">1196</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-1197"><a href="#L-1197"><span class="linenos">1197</span></a>
+</span><span id="L-1198"><a href="#L-1198"><span class="linenos">1198</span></a>
+</span><span id="L-1199"><a href="#L-1199"><span class="linenos">1199</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-1200"><a href="#L-1200"><span class="linenos">1200</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-1201"><a href="#L-1201"><span class="linenos">1201</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-1202"><a href="#L-1202"><span class="linenos">1202</span></a>
+</span><span id="L-1203"><a href="#L-1203"><span class="linenos">1203</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-1204"><a href="#L-1204"><span class="linenos">1204</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-1205"><a href="#L-1205"><span class="linenos">1205</span></a>
+</span><span id="L-1206"><a href="#L-1206"><span class="linenos">1206</span></a> <span class="c1"># Check added and removed concept set names</span>
+</span><span id="L-1207"><a href="#L-1207"><span class="linenos">1207</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-1208"><a href="#L-1208"><span class="linenos">1208</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-1209"><a href="#L-1209"><span class="linenos">1209</span></a>
+</span><span id="L-1210"><a href="#L-1210"><span class="linenos">1210</span></a> <span class="c1"># find file path changes for unchanged names</span>
+</span><span id="L-1211"><a href="#L-1211"><span class="linenos">1211</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-1212"><a href="#L-1212"><span class="linenos">1212</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-1213"><a href="#L-1213"><span class="linenos">1213</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-1214"><a href="#L-1214"><span class="linenos">1214</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-1215"><a href="#L-1215"><span class="linenos">1215</span></a> <span class="p">)</span>
+</span><span id="L-1216"><a href="#L-1216"><span class="linenos">1216</span></a>
+</span><span id="L-1217"><a href="#L-1217"><span class="linenos">1217</span></a> <span class="c1"># Find renamed concepts (same file, different name)</span>
+</span><span id="L-1218"><a href="#L-1218"><span class="linenos">1218</span></a> <span class="n">renamed_concepts</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="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-1220"><a href="#L-1220"><span class="linenos">1220</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-1221"><a href="#L-1221"><span class="linenos">1221</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-1222"><a href="#L-1222"><span class="linenos">1222</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-1223"><a href="#L-1223"><span class="linenos">1223</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-1224"><a href="#L-1224"><span class="linenos">1224</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-1225"><a href="#L-1225"><span class="linenos">1225</span></a>
+</span><span id="L-1226"><a href="#L-1226"><span class="linenos">1226</span></a> <span class="c1"># Remove renamed concepts from added and removed sets</span>
+</span><span id="L-1227"><a href="#L-1227"><span class="linenos">1227</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-1228"><a href="#L-1228"><span class="linenos">1228</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-1229"><a href="#L-1229"><span class="linenos">1229</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-1230"><a href="#L-1230"><span class="linenos">1230</span></a>
-</span><span id="L-1231"><a href="#L-1231"><span class="linenos">1231</span></a> <span class="k">if</span> <span class="n">renamed_concepts</span><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">"## Renamed Concepts</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 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-1234"><a href="#L-1234"><span class="linenos">1234</span></a> <span class="n">report</span> <span class="o">+=</span> <span class="p">(</span>
-</span><span id="L-1235"><a href="#L-1235"><span class="linenos">1235</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">` ➝ `</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-1236"><a href="#L-1236"><span class="linenos">1236</span></a> <span class="p">)</span>
-</span><span id="L-1237"><a href="#L-1237"><span class="linenos">1237</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-1238"><a href="#L-1238"><span class="linenos">1238</span></a>
-</span><span id="L-1239"><a href="#L-1239"><span class="linenos">1239</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-1240"><a href="#L-1240"><span class="linenos">1240</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-1241"><a href="#L-1241"><span class="linenos">1241</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-1242"><a href="#L-1242"><span class="linenos">1242</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-1243"><a href="#L-1243"><span class="linenos">1243</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-1244"><a href="#L-1244"><span class="linenos">1244</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-1245"><a href="#L-1245"><span class="linenos">1245</span></a> <span class="n">report</span> <span class="o">+=</span> <span class="p">(</span>
-</span><span id="L-1246"><a href="#L-1246"><span class="linenos">1246</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">` ➝ `</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-1247"><a href="#L-1247"><span class="linenos">1247</span></a> <span class="p">)</span>
-</span><span id="L-1248"><a href="#L-1248"><span class="linenos">1248</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-1249"><a href="#L-1249"><span class="linenos">1249</span></a>
-</span><span id="L-1250"><a href="#L-1250"><span class="linenos">1250</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="p">(</span>
-</span><span id="L-1251"><a href="#L-1251"><span class="linenos">1251</span></a> <span class="n">added_names</span>
-</span><span id="L-1252"><a href="#L-1252"><span class="linenos">1252</span></a> <span class="ow">or</span> <span class="n">removed_names</span>
-</span><span id="L-1253"><a href="#L-1253"><span class="linenos">1253</span></a> <span class="ow">or</span> <span class="n">renamed_concepts</span>
-</span><span id="L-1254"><a href="#L-1254"><span class="linenos">1254</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-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 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-1257"><a href="#L-1257"><span class="linenos">1257</span></a>
-</span><span id="L-1258"><a href="#L-1258"><span class="linenos">1258</span></a> <span class="k">return</span> <span class="n">report</span>
-</span><span id="L-1259"><a href="#L-1259"><span class="linenos">1259</span></a>
-</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="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-1262"><a href="#L-1262"><span class="linenos">1262</span></a> <span class="n">old_output_files</span> <span class="o">=</span> <span class="p">[</span>
-</span><span id="L-1263"><a href="#L-1263"><span class="linenos">1263</span></a> <span class="n">file</span><span class="o">.</span><span class="n">name</span>
-</span><span id="L-1264"><a href="#L-1264"><span class="linenos">1264</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-1265"><a href="#L-1265"><span class="linenos">1265</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-1266"><a href="#L-1266"><span class="linenos">1266</span></a> <span class="p">]</span>
-</span><span id="L-1267"><a href="#L-1267"><span class="linenos">1267</span></a> <span class="n">new_output_files</span> <span class="o">=</span> <span class="p">[</span>
-</span><span id="L-1268"><a href="#L-1268"><span class="linenos">1268</span></a> <span class="n">file</span><span class="o">.</span><span class="n">name</span>
-</span><span id="L-1269"><a href="#L-1269"><span class="linenos">1269</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-1270"><a href="#L-1270"><span class="linenos">1270</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-1271"><a href="#L-1271"><span class="linenos">1271</span></a> <span class="p">]</span>
+</span><span id="L-1231"><a href="#L-1231"><span class="linenos">1231</span></a> <span class="c1"># generate config report</span>
+</span><span id="L-1232"><a href="#L-1232"><span class="linenos">1232</span></a> <span class="k">if</span> <span class="n">added_names</span><span class="p">:</span>
+</span><span id="L-1233"><a href="#L-1233"><span class="linenos">1233</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-1234"><a href="#L-1234"><span class="linenos">1234</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-1235"><a href="#L-1235"><span class="linenos">1235</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-1236"><a href="#L-1236"><span class="linenos">1236</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-1237"><a href="#L-1237"><span class="linenos">1237</span></a>
+</span><span id="L-1238"><a href="#L-1238"><span class="linenos">1238</span></a> <span class="k">if</span> <span class="n">removed_names</span><span class="p">:</span>
+</span><span id="L-1239"><a href="#L-1239"><span class="linenos">1239</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-1240"><a href="#L-1240"><span class="linenos">1240</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-1241"><a href="#L-1241"><span class="linenos">1241</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-1242"><a href="#L-1242"><span class="linenos">1242</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-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 class="k">if</span> <span class="n">renamed_concepts</span><span class="p">:</span>
+</span><span id="L-1245"><a href="#L-1245"><span class="linenos">1245</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-1246"><a href="#L-1246"><span class="linenos">1246</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-1247"><a href="#L-1247"><span class="linenos">1247</span></a> <span class="n">report</span> <span class="o">+=</span> <span class="p">(</span>
+</span><span id="L-1248"><a href="#L-1248"><span class="linenos">1248</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">` ➝ `</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-1249"><a href="#L-1249"><span class="linenos">1249</span></a> <span class="p">)</span>
+</span><span id="L-1250"><a href="#L-1250"><span class="linenos">1250</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-1251"><a href="#L-1251"><span class="linenos">1251</span></a>
+</span><span id="L-1252"><a href="#L-1252"><span class="linenos">1252</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-1253"><a href="#L-1253"><span class="linenos">1253</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-1254"><a href="#L-1254"><span class="linenos">1254</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-1255"><a href="#L-1255"><span class="linenos">1255</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-1256"><a href="#L-1256"><span class="linenos">1256</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-1257"><a href="#L-1257"><span class="linenos">1257</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-1258"><a href="#L-1258"><span class="linenos">1258</span></a> <span class="n">report</span> <span class="o">+=</span> <span class="p">(</span>
+</span><span id="L-1259"><a href="#L-1259"><span class="linenos">1259</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">` ➝ `</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-1260"><a href="#L-1260"><span class="linenos">1260</span></a> <span class="p">)</span>
+</span><span id="L-1261"><a href="#L-1261"><span class="linenos">1261</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-1262"><a href="#L-1262"><span class="linenos">1262</span></a>
+</span><span id="L-1263"><a href="#L-1263"><span class="linenos">1263</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="p">(</span>
+</span><span id="L-1264"><a href="#L-1264"><span class="linenos">1264</span></a> <span class="n">added_names</span>
+</span><span id="L-1265"><a href="#L-1265"><span class="linenos">1265</span></a> <span class="ow">or</span> <span class="n">removed_names</span>
+</span><span id="L-1266"><a href="#L-1266"><span class="linenos">1266</span></a> <span class="ow">or</span> <span class="n">renamed_concepts</span>
+</span><span id="L-1267"><a href="#L-1267"><span class="linenos">1267</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-1268"><a href="#L-1268"><span class="linenos">1268</span></a> <span class="p">):</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="s2">"No changes in concept sets.</span><span class="se">\n</span><span class="s2">"</span>
+</span><span id="L-1270"><a href="#L-1270"><span class="linenos">1270</span></a>
+</span><span id="L-1271"><a href="#L-1271"><span class="linenos">1271</span></a> <span class="k">return</span> <span class="n">report</span>
</span><span id="L-1272"><a href="#L-1272"><span class="linenos">1272</span></a>
-</span><span id="L-1273"><a href="#L-1273"><span class="linenos">1273</span></a> <span class="c1"># Convert the lists to sets for easy comparison</span>
-</span><span id="L-1274"><a href="#L-1274"><span class="linenos">1274</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-1275"><a href="#L-1275"><span class="linenos">1275</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-1276"><a href="#L-1276"><span class="linenos">1276</span></a>
-</span><span id="L-1277"><a href="#L-1277"><span class="linenos">1277</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-1278"><a href="#L-1278"><span class="linenos">1278</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-1279"><a href="#L-1279"><span class="linenos">1279</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-1280"><a href="#L-1280"><span class="linenos">1280</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-1281"><a href="#L-1281"><span class="linenos">1281</span></a> <span class="c1"># Outputs that are the intersection of old_output_set and new_output_set</span>
-</span><span id="L-1282"><a href="#L-1282"><span class="linenos">1282</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-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">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-1285"><a href="#L-1285"><span class="linenos">1285</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-1286"><a href="#L-1286"><span class="linenos">1286</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-1287"><a href="#L-1287"><span class="linenos">1287</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-1288"><a href="#L-1288"><span class="linenos">1288</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="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-1275"><a href="#L-1275"><span class="linenos">1275</span></a> <span class="n">old_output_files</span> <span class="o">=</span> <span class="p">[</span>
+</span><span id="L-1276"><a href="#L-1276"><span class="linenos">1276</span></a> <span class="n">file</span><span class="o">.</span><span class="n">name</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">old_map_path</span><span class="o">.</span><span class="n">iterdir</span><span class="p">()</span>
+</span><span id="L-1278"><a href="#L-1278"><span class="linenos">1278</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-1279"><a href="#L-1279"><span class="linenos">1279</span></a> <span class="p">]</span>
+</span><span id="L-1280"><a href="#L-1280"><span class="linenos">1280</span></a> <span class="n">new_output_files</span> <span class="o">=</span> <span class="p">[</span>
+</span><span id="L-1281"><a href="#L-1281"><span class="linenos">1281</span></a> <span class="n">file</span><span class="o">.</span><span class="n">name</span>
+</span><span id="L-1282"><a href="#L-1282"><span class="linenos">1282</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-1283"><a href="#L-1283"><span class="linenos">1283</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-1284"><a href="#L-1284"><span class="linenos">1284</span></a> <span class="p">]</span>
+</span><span id="L-1285"><a href="#L-1285"><span class="linenos">1285</span></a>
+</span><span id="L-1286"><a href="#L-1286"><span class="linenos">1286</span></a> <span class="c1"># Convert the lists to sets for easy comparison</span>
+</span><span id="L-1287"><a href="#L-1287"><span class="linenos">1287</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-1288"><a href="#L-1288"><span class="linenos">1288</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-1289"><a href="#L-1289"><span class="linenos">1289</span></a>
-</span><span id="L-1290"><a href="#L-1290"><span class="linenos">1290</span></a> <span class="c1"># Step N: Compare common outputs between versions</span>
-</span><span id="L-1291"><a href="#L-1291"><span class="linenos">1291</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-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">"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-1293"><a href="#L-1293"><span class="linenos">1293</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-1294"><a href="#L-1294"><span class="linenos">1294</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-1295"><a href="#L-1295"><span class="linenos">1295</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-1290"><a href="#L-1290"><span class="linenos">1290</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-1291"><a href="#L-1291"><span class="linenos">1291</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-1292"><a href="#L-1292"><span class="linenos">1292</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-1293"><a href="#L-1293"><span class="linenos">1293</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-1294"><a href="#L-1294"><span class="linenos">1294</span></a> <span class="c1"># Outputs that are the intersection of old_output_set and new_output_set</span>
+</span><span id="L-1295"><a href="#L-1295"><span class="linenos">1295</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-1296"><a href="#L-1296"><span class="linenos">1296</span></a>
-</span><span id="L-1297"><a href="#L-1297"><span class="linenos">1297</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-1298"><a href="#L-1298"><span class="linenos">1298</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-1299"><a href="#L-1299"><span class="linenos">1299</span></a>
-</span><span id="L-1300"><a href="#L-1300"><span class="linenos">1300</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-1301"><a href="#L-1301"><span class="linenos">1301</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-1302"><a href="#L-1302"><span class="linenos">1302</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-1303"><a href="#L-1303"><span class="linenos">1303</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-1304"><a href="#L-1304"><span class="linenos">1304</span></a>
-</span><span id="L-1305"><a href="#L-1305"><span class="linenos">1305</span></a> <span class="c1"># Check for added and removed concepts</span>
-</span><span id="L-1306"><a href="#L-1306"><span class="linenos">1306</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-1307"><a href="#L-1307"><span class="linenos">1307</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-1308"><a href="#L-1308"><span class="linenos">1308</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-1309"><a href="#L-1309"><span class="linenos">1309</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-1310"><a href="#L-1310"><span class="linenos">1310</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-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="c1"># Check for changed concepts</span>
-</span><span id="L-1313"><a href="#L-1313"><span class="linenos">1313</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-1314"><a href="#L-1314"><span class="linenos">1314</span></a> <span class="n">diff</span> <span class="o">=</span> <span class="n">diff</span><span class="p">[</span>
-</span><span id="L-1315"><a href="#L-1315"><span class="linenos">1315</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-1316"><a href="#L-1316"><span class="linenos">1316</span></a> <span class="p">]</span> <span class="c1"># get non-zero counts</span>
-</span><span id="L-1317"><a href="#L-1317"><span class="linenos">1317</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-1318"><a href="#L-1318"><span class="linenos">1318</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-1319"><a href="#L-1319"><span class="linenos">1319</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-1320"><a href="#L-1320"><span class="linenos">1320</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-1321"><a href="#L-1321"><span class="linenos">1321</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-1322"><a href="#L-1322"><span class="linenos">1322</span></a> <span class="k">else</span><span class="p">:</span>
-</span><span id="L-1323"><a href="#L-1323"><span class="linenos">1323</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-1297"><a href="#L-1297"><span class="linenos">1297</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-1298"><a href="#L-1298"><span class="linenos">1298</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-1299"><a href="#L-1299"><span class="linenos">1299</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-1300"><a href="#L-1300"><span class="linenos">1300</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-1301"><a href="#L-1301"><span class="linenos">1301</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-1302"><a href="#L-1302"><span class="linenos">1302</span></a>
+</span><span id="L-1303"><a href="#L-1303"><span class="linenos">1303</span></a> <span class="c1"># Step N: Compare common outputs between versions</span>
+</span><span id="L-1304"><a href="#L-1304"><span class="linenos">1304</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-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">"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-1306"><a href="#L-1306"><span class="linenos">1306</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-1307"><a href="#L-1307"><span class="linenos">1307</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-1308"><a href="#L-1308"><span class="linenos">1308</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-1309"><a href="#L-1309"><span class="linenos">1309</span></a>
+</span><span id="L-1310"><a href="#L-1310"><span class="linenos">1310</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-1311"><a href="#L-1311"><span class="linenos">1311</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-1312"><a href="#L-1312"><span class="linenos">1312</span></a>
+</span><span id="L-1313"><a href="#L-1313"><span class="linenos">1313</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-1314"><a href="#L-1314"><span class="linenos">1314</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-1315"><a href="#L-1315"><span class="linenos">1315</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-1316"><a href="#L-1316"><span class="linenos">1316</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-1317"><a href="#L-1317"><span class="linenos">1317</span></a>
+</span><span id="L-1318"><a href="#L-1318"><span class="linenos">1318</span></a> <span class="c1"># Check for added and removed concepts</span>
+</span><span id="L-1319"><a href="#L-1319"><span class="linenos">1319</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-1320"><a href="#L-1320"><span class="linenos">1320</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-1321"><a href="#L-1321"><span class="linenos">1321</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-1322"><a href="#L-1322"><span class="linenos">1322</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-1323"><a href="#L-1323"><span class="linenos">1323</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-1324"><a href="#L-1324"><span class="linenos">1324</span></a>
-</span><span id="L-1325"><a href="#L-1325"><span class="linenos">1325</span></a> <span class="k">return</span> <span class="n">report</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><span id="L-1328"><a href="#L-1328"><span class="linenos">1328</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-1329"><a href="#L-1329"><span class="linenos">1329</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-1330"><a href="#L-1330"><span class="linenos">1330</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-1331"><a href="#L-1331"><span class="linenos">1331</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-1332"><a href="#L-1332"><span class="linenos">1332</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-1333"><a href="#L-1333"><span class="linenos">1333</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-1334"><a href="#L-1334"><span class="linenos">1334</span></a><span class="p">):</span>
-</span><span id="L-1335"><a href="#L-1335"><span class="linenos">1335</span></a><span class="w"> </span><span class="sd">"""Compare the differences between two versions of a phenotype"""</span>
-</span><span id="L-1336"><a href="#L-1336"><span class="linenos">1336</span></a>
-</span><span id="L-1337"><a href="#L-1337"><span class="linenos">1337</span></a> <span class="c1"># validate phenotypes</span>
-</span><span id="L-1338"><a href="#L-1338"><span class="linenos">1338</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-1339"><a href="#L-1339"><span class="linenos">1339</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-1340"><a href="#L-1340"><span class="linenos">1340</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-1341"><a href="#L-1341"><span class="linenos">1341</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-1342"><a href="#L-1342"><span class="linenos">1342</span></a>
-</span><span id="L-1343"><a href="#L-1343"><span class="linenos">1343</span></a> <span class="c1"># get old and new config</span>
-</span><span id="L-1344"><a href="#L-1344"><span class="linenos">1344</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-1345"><a href="#L-1345"><span class="linenos">1345</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-1346"><a href="#L-1346"><span class="linenos">1346</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-1347"><a href="#L-1347"><span class="linenos">1347</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-1348"><a href="#L-1348"><span class="linenos">1348</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-1349"><a href="#L-1349"><span class="linenos">1349</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-1350"><a href="#L-1350"><span class="linenos">1350</span></a>
-</span><span id="L-1351"><a href="#L-1351"><span class="linenos">1351</span></a> <span class="c1"># write report heading</span>
-</span><span id="L-1352"><a href="#L-1352"><span class="linenos">1352</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-1353"><a href="#L-1353"><span class="linenos">1353</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-1354"><a href="#L-1354"><span class="linenos">1354</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-1355"><a href="#L-1355"><span class="linenos">1355</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-1356"><a href="#L-1356"><span class="linenos">1356</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-1357"><a href="#L-1357"><span class="linenos">1357</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-1358"><a href="#L-1358"><span class="linenos">1358</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-1359"><a href="#L-1359"><span class="linenos">1359</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-1360"><a href="#L-1360"><span class="linenos">1360</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-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="c1"># Step 1: check differences configuration files</span>
-</span><span id="L-1363"><a href="#L-1363"><span class="linenos">1363</span></a> <span class="c1"># Convert list of dicts into a dict: {name: file}</span>
-</span><span id="L-1364"><a href="#L-1364"><span class="linenos">1364</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-1365"><a href="#L-1365"><span class="linenos">1365</span></a>
-</span><span id="L-1366"><a href="#L-1366"><span class="linenos">1366</span></a> <span class="c1"># Step 2: check differences between map files</span>
-</span><span id="L-1367"><a href="#L-1367"><span class="linenos">1367</span></a> <span class="c1"># List files from output directories</span>
-</span><span id="L-1368"><a href="#L-1368"><span class="linenos">1368</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-1369"><a href="#L-1369"><span class="linenos">1369</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-1370"><a href="#L-1370"><span class="linenos">1370</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-1371"><a href="#L-1371"><span class="linenos">1371</span></a>
-</span><span id="L-1372"><a href="#L-1372"><span class="linenos">1372</span></a> <span class="c1"># initialise report file</span>
-</span><span id="L-1373"><a href="#L-1373"><span class="linenos">1373</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-1374"><a href="#L-1374"><span class="linenos">1374</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-1375"><a href="#L-1375"><span class="linenos">1375</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-1376"><a href="#L-1376"><span class="linenos">1376</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-1377"><a href="#L-1377"><span class="linenos">1377</span></a>
-</span><span id="L-1378"><a href="#L-1378"><span class="linenos">1378</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-1379"><a href="#L-1379"><span class="linenos">1379</span></a>
-</span><span id="L-1380"><a href="#L-1380"><span class="linenos">1380</span></a>
-</span><span id="L-1381"><a href="#L-1381"><span class="linenos">1381</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-1382"><a href="#L-1382"><span class="linenos">1382</span></a> <span class="c1"># make tmp directory .acmc</span>
-</span><span id="L-1383"><a href="#L-1383"><span class="linenos">1383</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-1384"><a href="#L-1384"><span class="linenos">1384</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-1385"><a href="#L-1385"><span class="linenos">1385</span></a>
-</span><span id="L-1386"><a href="#L-1386"><span class="linenos">1386</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-1387"><a href="#L-1387"><span class="linenos">1387</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-1388"><a href="#L-1388"><span class="linenos">1388</span></a> <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span>
-</span><span id="L-1389"><a href="#L-1389"><span class="linenos">1389</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-1390"><a href="#L-1390"><span class="linenos">1390</span></a> <span class="p">)</span>
-</span><span id="L-1391"><a href="#L-1391"><span class="linenos">1391</span></a>
-</span><span id="L-1392"><a href="#L-1392"><span class="linenos">1392</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-1393"><a href="#L-1393"><span class="linenos">1393</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-1394"><a href="#L-1394"><span class="linenos">1394</span></a> <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span>
-</span><span id="L-1395"><a href="#L-1395"><span class="linenos">1395</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-1396"><a href="#L-1396"><span class="linenos">1396</span></a> <span class="p">)</span>
-</span><span id="L-1397"><a href="#L-1397"><span class="linenos">1397</span></a>
-</span><span id="L-1398"><a href="#L-1398"><span class="linenos">1398</span></a> <span class="n">t_path</span> <span class="o">=</span> <span class="n">old_phen_path</span> <span class="o">/</span> <span class="s2">"config.yml"</span>
-</span><span id="L-1399"><a href="#L-1399"><span class="linenos">1399</span></a> <span class="k">with</span> <span class="n">t_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-1400"><a href="#L-1400"><span class="linenos">1400</span></a> <span class="n">c</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-1401"><a href="#L-1401"><span class="linenos">1401</span></a>
-</span><span id="L-1402"><a href="#L-1402"><span class="linenos">1402</span></a> <span class="k">try</span><span class="p">:</span>
-</span><span id="L-1403"><a href="#L-1403"><span class="linenos">1403</span></a> <span class="c1"># Create the directory</span>
-</span><span id="L-1404"><a href="#L-1404"><span class="linenos">1404</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-1405"><a href="#L-1405"><span class="linenos">1405</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-1406"><a href="#L-1406"><span class="linenos">1406</span></a>
-</span><span id="L-1407"><a href="#L-1407"><span class="linenos">1407</span></a> <span class="c1"># Create temporary directories</span>
-</span><span id="L-1408"><a href="#L-1408"><span class="linenos">1408</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-1409"><a href="#L-1409"><span class="linenos">1409</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-1410"><a href="#L-1410"><span class="linenos">1410</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-1411"><a href="#L-1411"><span class="linenos">1411</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-1412"><a href="#L-1412"><span class="linenos">1412</span></a>
-</span><span id="L-1413"><a href="#L-1413"><span class="linenos">1413</span></a> <span class="c1"># checkout changed</span>
-</span><span id="L-1414"><a href="#L-1414"><span class="linenos">1414</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-1415"><a href="#L-1415"><span class="linenos">1415</span></a> <span class="n">_logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span>
-</span><span id="L-1416"><a href="#L-1416"><span class="linenos">1416</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-1417"><a href="#L-1417"><span class="linenos">1417</span></a> <span class="p">)</span>
-</span><span id="L-1418"><a href="#L-1418"><span class="linenos">1418</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-1419"><a href="#L-1419"><span class="linenos">1419</span></a> <span class="k">else</span><span class="p">:</span>
-</span><span id="L-1420"><a href="#L-1420"><span class="linenos">1420</span></a> <span class="n">_logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span>
-</span><span id="L-1421"><a href="#L-1421"><span class="linenos">1421</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-1422"><a href="#L-1422"><span class="linenos">1422</span></a> <span class="p">)</span>
-</span><span id="L-1423"><a href="#L-1423"><span class="linenos">1423</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-1424"><a href="#L-1424"><span class="linenos">1424</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-1325"><a href="#L-1325"><span class="linenos">1325</span></a> <span class="c1"># Check for changed concepts</span>
+</span><span id="L-1326"><a href="#L-1326"><span class="linenos">1326</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-1327"><a href="#L-1327"><span class="linenos">1327</span></a> <span class="n">diff</span> <span class="o">=</span> <span class="n">diff</span><span class="p">[</span>
+</span><span id="L-1328"><a href="#L-1328"><span class="linenos">1328</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-1329"><a href="#L-1329"><span class="linenos">1329</span></a> <span class="p">]</span> <span class="c1"># get non-zero counts</span>
+</span><span id="L-1330"><a href="#L-1330"><span class="linenos">1330</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-1331"><a href="#L-1331"><span class="linenos">1331</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-1332"><a href="#L-1332"><span class="linenos">1332</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-1333"><a href="#L-1333"><span class="linenos">1333</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-1334"><a href="#L-1334"><span class="linenos">1334</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-1335"><a href="#L-1335"><span class="linenos">1335</span></a> <span class="k">else</span><span class="p">:</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">"- Changed concepts []</span><span class="se">\n\n</span><span class="s2">"</span>
+</span><span id="L-1337"><a href="#L-1337"><span class="linenos">1337</span></a>
+</span><span id="L-1338"><a href="#L-1338"><span class="linenos">1338</span></a> <span class="k">return</span> <span class="n">report</span>
+</span><span id="L-1339"><a href="#L-1339"><span class="linenos">1339</span></a>
+</span><span id="L-1340"><a href="#L-1340"><span class="linenos">1340</span></a>
+</span><span id="L-1341"><a href="#L-1341"><span class="linenos">1341</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-1342"><a href="#L-1342"><span class="linenos">1342</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-1343"><a href="#L-1343"><span class="linenos">1343</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-1344"><a href="#L-1344"><span class="linenos">1344</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-1345"><a href="#L-1345"><span class="linenos">1345</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-1346"><a href="#L-1346"><span class="linenos">1346</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-1347"><a href="#L-1347"><span class="linenos">1347</span></a><span class="p">):</span>
+</span><span id="L-1348"><a href="#L-1348"><span class="linenos">1348</span></a><span class="w"> </span><span class="sd">"""Compare the differences between two versions of a phenotype"""</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"># validate phenotypes</span>
+</span><span id="L-1351"><a href="#L-1351"><span class="linenos">1351</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-1352"><a href="#L-1352"><span class="linenos">1352</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-1353"><a href="#L-1353"><span class="linenos">1353</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-1354"><a href="#L-1354"><span class="linenos">1354</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-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"># get old and new config</span>
+</span><span id="L-1357"><a href="#L-1357"><span class="linenos">1357</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-1358"><a href="#L-1358"><span class="linenos">1358</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-1359"><a href="#L-1359"><span class="linenos">1359</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-1360"><a href="#L-1360"><span class="linenos">1360</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-1361"><a href="#L-1361"><span class="linenos">1361</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-1362"><a href="#L-1362"><span class="linenos">1362</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-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 class="c1"># write report heading</span>
+</span><span id="L-1365"><a href="#L-1365"><span class="linenos">1365</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-1366"><a href="#L-1366"><span class="linenos">1366</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-1367"><a href="#L-1367"><span class="linenos">1367</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-1368"><a href="#L-1368"><span class="linenos">1368</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-1369"><a href="#L-1369"><span class="linenos">1369</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-1370"><a href="#L-1370"><span class="linenos">1370</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-1371"><a href="#L-1371"><span class="linenos">1371</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-1372"><a href="#L-1372"><span class="linenos">1372</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-1373"><a href="#L-1373"><span class="linenos">1373</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-1374"><a href="#L-1374"><span class="linenos">1374</span></a>
+</span><span id="L-1375"><a href="#L-1375"><span class="linenos">1375</span></a> <span class="c1"># Step 1: check differences configuration files</span>
+</span><span id="L-1376"><a href="#L-1376"><span class="linenos">1376</span></a> <span class="c1"># Convert list of dicts into a dict: {name: file}</span>
+</span><span id="L-1377"><a href="#L-1377"><span class="linenos">1377</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-1378"><a href="#L-1378"><span class="linenos">1378</span></a>
+</span><span id="L-1379"><a href="#L-1379"><span class="linenos">1379</span></a> <span class="c1"># Step 2: check differences between map files</span>
+</span><span id="L-1380"><a href="#L-1380"><span class="linenos">1380</span></a> <span class="c1"># List files from output directories</span>
+</span><span id="L-1381"><a href="#L-1381"><span class="linenos">1381</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-1382"><a href="#L-1382"><span class="linenos">1382</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-1383"><a href="#L-1383"><span class="linenos">1383</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-1384"><a href="#L-1384"><span class="linenos">1384</span></a>
+</span><span id="L-1385"><a href="#L-1385"><span class="linenos">1385</span></a> <span class="c1"># initialise report file</span>
+</span><span id="L-1386"><a href="#L-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">"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-1387"><a href="#L-1387"><span class="linenos">1387</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-1388"><a href="#L-1388"><span class="linenos">1388</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-1389"><a href="#L-1389"><span class="linenos">1389</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-1390"><a href="#L-1390"><span class="linenos">1390</span></a>
+</span><span id="L-1391"><a href="#L-1391"><span class="linenos">1391</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-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><span id="L-1394"><a href="#L-1394"><span class="linenos">1394</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-1395"><a href="#L-1395"><span class="linenos">1395</span></a> <span class="c1"># make tmp directory .acmc</span>
+</span><span id="L-1396"><a href="#L-1396"><span class="linenos">1396</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-1397"><a href="#L-1397"><span class="linenos">1397</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-1398"><a href="#L-1398"><span class="linenos">1398</span></a>
+</span><span id="L-1399"><a href="#L-1399"><span class="linenos">1399</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-1400"><a href="#L-1400"><span class="linenos">1400</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-1401"><a href="#L-1401"><span class="linenos">1401</span></a> <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span>
+</span><span id="L-1402"><a href="#L-1402"><span class="linenos">1402</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-1403"><a href="#L-1403"><span class="linenos">1403</span></a> <span class="p">)</span>
+</span><span id="L-1404"><a href="#L-1404"><span class="linenos">1404</span></a>
+</span><span id="L-1405"><a href="#L-1405"><span class="linenos">1405</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-1406"><a href="#L-1406"><span class="linenos">1406</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-1407"><a href="#L-1407"><span class="linenos">1407</span></a> <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span>
+</span><span id="L-1408"><a href="#L-1408"><span class="linenos">1408</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-1409"><a href="#L-1409"><span class="linenos">1409</span></a> <span class="p">)</span>
+</span><span id="L-1410"><a href="#L-1410"><span class="linenos">1410</span></a>
+</span><span id="L-1411"><a href="#L-1411"><span class="linenos">1411</span></a> <span class="n">t_path</span> <span class="o">=</span> <span class="n">old_phen_path</span> <span class="o">/</span> <span class="s2">"config.yml"</span>
+</span><span id="L-1412"><a href="#L-1412"><span class="linenos">1412</span></a> <span class="k">with</span> <span class="n">t_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-1413"><a href="#L-1413"><span class="linenos">1413</span></a> <span class="n">c</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-1414"><a href="#L-1414"><span class="linenos">1414</span></a>
+</span><span id="L-1415"><a href="#L-1415"><span class="linenos">1415</span></a> <span class="k">try</span><span class="p">:</span>
+</span><span id="L-1416"><a href="#L-1416"><span class="linenos">1416</span></a> <span class="c1"># Create the directory</span>
+</span><span id="L-1417"><a href="#L-1417"><span class="linenos">1417</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-1418"><a href="#L-1418"><span class="linenos">1418</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-1419"><a href="#L-1419"><span class="linenos">1419</span></a>
+</span><span id="L-1420"><a href="#L-1420"><span class="linenos">1420</span></a> <span class="c1"># Create temporary directories</span>
+</span><span id="L-1421"><a href="#L-1421"><span class="linenos">1421</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-1422"><a href="#L-1422"><span class="linenos">1422</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-1423"><a href="#L-1423"><span class="linenos">1423</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-1424"><a href="#L-1424"><span class="linenos">1424</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-1425"><a href="#L-1425"><span class="linenos">1425</span></a>
-</span><span id="L-1426"><a href="#L-1426"><span class="linenos">1426</span></a> <span class="c1"># checkout old</span>
-</span><span id="L-1427"><a href="#L-1427"><span class="linenos">1427</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-1426"><a href="#L-1426"><span class="linenos">1426</span></a> <span class="c1"># checkout changed</span>
+</span><span id="L-1427"><a href="#L-1427"><span class="linenos">1427</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-1428"><a href="#L-1428"><span class="linenos">1428</span></a> <span class="n">_logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span>
-</span><span id="L-1429"><a href="#L-1429"><span class="linenos">1429</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-1429"><a href="#L-1429"><span class="linenos">1429</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-1430"><a href="#L-1430"><span class="linenos">1430</span></a> <span class="p">)</span>
-</span><span id="L-1431"><a href="#L-1431"><span class="linenos">1431</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-1431"><a href="#L-1431"><span class="linenos">1431</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-1432"><a href="#L-1432"><span class="linenos">1432</span></a> <span class="k">else</span><span class="p">:</span>
</span><span id="L-1433"><a href="#L-1433"><span class="linenos">1433</span></a> <span class="n">_logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span>
-</span><span id="L-1434"><a href="#L-1434"><span class="linenos">1434</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-1434"><a href="#L-1434"><span class="linenos">1434</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-1435"><a href="#L-1435"><span class="linenos">1435</span></a> <span class="p">)</span>
-</span><span id="L-1436"><a href="#L-1436"><span class="linenos">1436</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-1437"><a href="#L-1437"><span class="linenos">1437</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-1436"><a href="#L-1436"><span class="linenos">1436</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-1437"><a href="#L-1437"><span class="linenos">1437</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-1438"><a href="#L-1438"><span class="linenos">1438</span></a>
-</span><span id="L-1439"><a href="#L-1439"><span class="linenos">1439</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-1440"><a href="#L-1440"><span class="linenos">1440</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-1441"><a href="#L-1441"><span class="linenos">1441</span></a> <span class="c1"># diff old with new</span>
-</span><span id="L-1442"><a href="#L-1442"><span class="linenos">1442</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-1443"><a href="#L-1443"><span class="linenos">1443</span></a>
-</span><span id="L-1444"><a href="#L-1444"><span class="linenos">1444</span></a> <span class="k">finally</span><span class="p">:</span>
-</span><span id="L-1445"><a href="#L-1445"><span class="linenos">1445</span></a> <span class="c1"># clean up tmp directory</span>
-</span><span id="L-1446"><a href="#L-1446"><span class="linenos">1446</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-1447"><a href="#L-1447"><span class="linenos">1447</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-1448"><a href="#L-1448"><span class="linenos">1448</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><span id="L-1439"><a href="#L-1439"><span class="linenos">1439</span></a> <span class="c1"># checkout old</span>
+</span><span id="L-1440"><a href="#L-1440"><span class="linenos">1440</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-1441"><a href="#L-1441"><span class="linenos">1441</span></a> <span class="n">_logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span>
+</span><span id="L-1442"><a href="#L-1442"><span class="linenos">1442</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-1443"><a href="#L-1443"><span class="linenos">1443</span></a> <span class="p">)</span>
+</span><span id="L-1444"><a href="#L-1444"><span class="linenos">1444</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-1445"><a href="#L-1445"><span class="linenos">1445</span></a> <span class="k">else</span><span class="p">:</span>
+</span><span id="L-1446"><a href="#L-1446"><span class="linenos">1446</span></a> <span class="n">_logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span>
+</span><span id="L-1447"><a href="#L-1447"><span class="linenos">1447</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-1448"><a href="#L-1448"><span class="linenos">1448</span></a> <span class="p">)</span>
+</span><span id="L-1449"><a href="#L-1449"><span class="linenos">1449</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-1450"><a href="#L-1450"><span class="linenos">1450</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-1451"><a href="#L-1451"><span class="linenos">1451</span></a>
+</span><span id="L-1452"><a href="#L-1452"><span class="linenos">1452</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-1453"><a href="#L-1453"><span class="linenos">1453</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-1454"><a href="#L-1454"><span class="linenos">1454</span></a> <span class="c1"># diff old with new</span>
+</span><span id="L-1455"><a href="#L-1455"><span class="linenos">1455</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-1456"><a href="#L-1456"><span class="linenos">1456</span></a>
+</span><span id="L-1457"><a href="#L-1457"><span class="linenos">1457</span></a> <span class="k">finally</span><span class="p">:</span>
+</span><span id="L-1458"><a href="#L-1458"><span class="linenos">1458</span></a> <span class="c1"># clean up tmp directory</span>
+</span><span id="L-1459"><a href="#L-1459"><span class="linenos">1459</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-1460"><a href="#L-1460"><span class="linenos">1460</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-1461"><a href="#L-1461"><span class="linenos">1461</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>
@@ -1874,7 +1887,7 @@
<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', 'atc', 'snomed', 'read2', 'read3']}}, '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'}}}}}}}}}}}</span>
+ <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': ['atc', 'read2', 'read3', 'opcs4', 'snomed', 'icd10']}}, 'concept_sets': {'type': 'list', 'required': True, 'schema': {'type': 'dict', 'schema': {'name': {'type': 'string', 'required': True}, 'files': {'type': 'list', 'required': True, 'schema': {'type': 'dict', 'schema': {'path': {'type': 'string', 'required': True}, 'columns': {'type': 'dict', 'required': True}, 'category': {'type': 'string'}, 'actions': {'type': 'dict', 'schema': {'divide_col': {'type': 'string'}}}}}}}}}}}}</span>
</div>
@@ -1896,12 +1909,12 @@
</div>
<a class="headerlink" href="#PhenValidationException"></a>
- <div class="pdoc-code codehilite"><pre><span></span><span id="PhenValidationException-155"><a href="#PhenValidationException-155"><span class="linenos">155</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-156"><a href="#PhenValidationException-156"><span class="linenos">156</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-157"><a href="#PhenValidationException-157"><span class="linenos">157</span></a>
-</span><span id="PhenValidationException-158"><a href="#PhenValidationException-158"><span class="linenos">158</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-159"><a href="#PhenValidationException-159"><span class="linenos">159</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-160"><a href="#PhenValidationException-160"><span class="linenos">160</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>
+ <div class="pdoc-code codehilite"><pre><span></span><span id="PhenValidationException-159"><a href="#PhenValidationException-159"><span class="linenos">159</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-160"><a href="#PhenValidationException-160"><span class="linenos">160</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-161"><a href="#PhenValidationException-161"><span class="linenos">161</span></a>
+</span><span id="PhenValidationException-162"><a href="#PhenValidationException-162"><span class="linenos">162</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-163"><a href="#PhenValidationException-163"><span class="linenos">163</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-164"><a href="#PhenValidationException-164"><span class="linenos">164</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>
@@ -1919,9 +1932,9 @@
</div>
<a class="headerlink" href="#PhenValidationException.__init__"></a>
- <div class="pdoc-code codehilite"><pre><span></span><span id="PhenValidationException.__init__-158"><a href="#PhenValidationException.__init__-158"><span class="linenos">158</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__-159"><a href="#PhenValidationException.__init__-159"><span class="linenos">159</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__-160"><a href="#PhenValidationException.__init__-160"><span class="linenos">160</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>
+ <div class="pdoc-code codehilite"><pre><span></span><span id="PhenValidationException.__init__-162"><a href="#PhenValidationException.__init__-162"><span class="linenos">162</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__-163"><a href="#PhenValidationException.__init__-163"><span class="linenos">163</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__-164"><a href="#PhenValidationException.__init__-164"><span class="linenos">164</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>
@@ -1951,135 +1964,135 @@
</div>
<a class="headerlink" href="#init"></a>
- <div class="pdoc-code codehilite"><pre><span></span><span id="init-229"><a href="#init-229"><span class="linenos">229</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-230"><a href="#init-230"><span class="linenos">230</span></a><span class="w"> </span><span class="sd">"""Initial phenotype directory as git repo with standard structure"""</span>
-</span><span id="init-231"><a href="#init-231"><span class="linenos">231</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-232"><a href="#init-232"><span class="linenos">232</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-233"><a href="#init-233"><span class="linenos">233</span></a>
-</span><span id="init-234"><a href="#init-234"><span class="linenos">234</span></a> <span class="c1"># check if directory already exists and ask user if they want to recreate it</span>
-</span><span id="init-235"><a href="#init-235"><span class="linenos">235</span></a> <span class="k">if</span> <span class="p">(</span>
-</span><span id="init-236"><a href="#init-236"><span class="linenos">236</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-237"><a href="#init-237"><span class="linenos">237</span></a> <span class="p">):</span> <span class="c1"># Check if it exists and is a directory</span>
-</span><span id="init-238"><a href="#init-238"><span class="linenos">238</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-239"><a href="#init-239"><span class="linenos">239</span></a> <span class="n">phen_path</span><span class="p">,</span>
-</span><span id="init-240"><a href="#init-240"><span class="linenos">240</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-241"><a href="#init-241"><span class="linenos">241</span></a> <span class="p">)</span>
-</span><span id="init-242"><a href="#init-242"><span class="linenos">242</span></a> <span class="k">else</span><span class="p">:</span>
-</span><span id="init-243"><a href="#init-243"><span class="linenos">243</span></a> <span class="n">configure</span> <span class="o">=</span> <span class="kc">True</span>
-</span><span id="init-244"><a href="#init-244"><span class="linenos">244</span></a>
-</span><span id="init-245"><a href="#init-245"><span class="linenos">245</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-246"><a href="#init-246"><span class="linenos">246</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-247"><a href="#init-247"><span class="linenos">247</span></a> <span class="k">return</span>
+ <div class="pdoc-code codehilite"><pre><span></span><span id="init-233"><a href="#init-233"><span class="linenos">233</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-234"><a href="#init-234"><span class="linenos">234</span></a><span class="w"> </span><span class="sd">"""Initial phenotype directory as git repo with standard structure"""</span>
+</span><span id="init-235"><a href="#init-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">"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-236"><a href="#init-236"><span class="linenos">236</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-237"><a href="#init-237"><span class="linenos">237</span></a>
+</span><span id="init-238"><a href="#init-238"><span class="linenos">238</span></a> <span class="c1"># check if directory already exists and ask user if they want to recreate it</span>
+</span><span id="init-239"><a href="#init-239"><span class="linenos">239</span></a> <span class="k">if</span> <span class="p">(</span>
+</span><span id="init-240"><a href="#init-240"><span class="linenos">240</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-241"><a href="#init-241"><span class="linenos">241</span></a> <span class="p">):</span> <span class="c1"># Check if it exists and is a directory</span>
+</span><span id="init-242"><a href="#init-242"><span class="linenos">242</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-243"><a href="#init-243"><span class="linenos">243</span></a> <span class="n">phen_path</span><span class="p">,</span>
+</span><span id="init-244"><a href="#init-244"><span class="linenos">244</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-245"><a href="#init-245"><span class="linenos">245</span></a> <span class="p">)</span>
+</span><span id="init-246"><a href="#init-246"><span class="linenos">246</span></a> <span class="k">else</span><span class="p">:</span>
+</span><span id="init-247"><a href="#init-247"><span class="linenos">247</span></a> <span class="n">configure</span> <span class="o">=</span> <span class="kc">True</span>
</span><span id="init-248"><a href="#init-248"><span class="linenos">248</span></a>
-</span><span id="init-249"><a href="#init-249"><span class="linenos">249</span></a> <span class="c1"># Initialise repo from local or remote</span>
-</span><span id="init-250"><a href="#init-250"><span class="linenos">250</span></a> <span class="n">repo</span><span class="p">:</span> <span class="n">Repo</span>
-</span><span id="init-251"><a href="#init-251"><span class="linenos">251</span></a>
-</span><span id="init-252"><a href="#init-252"><span class="linenos">252</span></a> <span class="c1"># if remote then clone the repo otherwise init a local repo</span>
-</span><span id="init-253"><a href="#init-253"><span class="linenos">253</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-254"><a href="#init-254"><span class="linenos">254</span></a> <span class="c1"># add PAT token to the URL</span>
-</span><span id="init-255"><a href="#init-255"><span class="linenos">255</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-256"><a href="#init-256"><span class="linenos">256</span></a>
-</span><span id="init-257"><a href="#init-257"><span class="linenos">257</span></a> <span class="c1"># clone the repo</span>
-</span><span id="init-258"><a href="#init-258"><span class="linenos">258</span></a> <span class="n">git_cmd</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-259"><a href="#init-259"><span class="linenos">259</span></a> <span class="n">git_cmd</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-249"><a href="#init-249"><span class="linenos">249</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-250"><a href="#init-250"><span class="linenos">250</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-251"><a href="#init-251"><span class="linenos">251</span></a> <span class="k">return</span>
+</span><span id="init-252"><a href="#init-252"><span class="linenos">252</span></a>
+</span><span id="init-253"><a href="#init-253"><span class="linenos">253</span></a> <span class="c1"># Initialise repo from local or remote</span>
+</span><span id="init-254"><a href="#init-254"><span class="linenos">254</span></a> <span class="n">repo</span><span class="p">:</span> <span class="n">Repo</span>
+</span><span id="init-255"><a href="#init-255"><span class="linenos">255</span></a>
+</span><span id="init-256"><a href="#init-256"><span class="linenos">256</span></a> <span class="c1"># if remote then clone the repo otherwise init a local repo</span>
+</span><span id="init-257"><a href="#init-257"><span class="linenos">257</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-258"><a href="#init-258"><span class="linenos">258</span></a> <span class="c1"># add PAT token to the URL</span>
+</span><span id="init-259"><a href="#init-259"><span class="linenos">259</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-260"><a href="#init-260"><span class="linenos">260</span></a>
-</span><span id="init-261"><a href="#init-261"><span class="linenos">261</span></a> <span class="c1"># open repo</span>
-</span><span id="init-262"><a href="#init-262"><span class="linenos">262</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-263"><a href="#init-263"><span class="linenos">263</span></a> <span class="c1"># check if there are any commits (new repo has no commits)</span>
-</span><span id="init-264"><a href="#init-264"><span class="linenos">264</span></a> <span class="k">if</span> <span class="p">(</span>
-</span><span id="init-265"><a href="#init-265"><span class="linenos">265</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-266"><a href="#init-266"><span class="linenos">266</span></a> <span class="p">):</span> <span class="c1"># Handle detached HEAD (e.g., after init)</span>
-</span><span id="init-267"><a href="#init-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="s2">"The phen repository has no commits yet."</span><span class="p">)</span>
-</span><span id="init-268"><a href="#init-268"><span class="linenos">268</span></a> <span class="n">commit_count</span> <span class="o">=</span> <span class="mi">0</span>
-</span><span id="init-269"><a href="#init-269"><span class="linenos">269</span></a> <span class="k">else</span><span class="p">:</span>
-</span><span id="init-270"><a href="#init-270"><span class="linenos">270</span></a> <span class="c1"># Get the total number of commits in the default branch</span>
-</span><span id="init-271"><a href="#init-271"><span class="linenos">271</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-272"><a href="#init-272"><span class="linenos">272</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-273"><a href="#init-273"><span class="linenos">273</span></a> <span class="k">else</span><span class="p">:</span>
-</span><span id="init-274"><a href="#init-274"><span class="linenos">274</span></a> <span class="c1"># local repo, create the directories and init</span>
-</span><span id="init-275"><a href="#init-275"><span class="linenos">275</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-276"><a href="#init-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">"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-277"><a href="#init-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">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-278"><a href="#init-278"><span class="linenos">278</span></a> <span class="n">commit_count</span> <span class="o">=</span> <span class="mi">0</span>
-</span><span id="init-279"><a href="#init-279"><span class="linenos">279</span></a>
-</span><span id="init-280"><a href="#init-280"><span class="linenos">280</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-281"><a href="#init-281"><span class="linenos">281</span></a> <span class="c1"># initialise empty repos</span>
-</span><span id="init-282"><a href="#init-282"><span class="linenos">282</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-283"><a href="#init-283"><span class="linenos">283</span></a> <span class="c1"># create initial commit</span>
-</span><span id="init-284"><a href="#init-284"><span class="linenos">284</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-285"><a href="#init-285"><span class="linenos">285</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-286"><a href="#init-286"><span class="linenos">286</span></a> <span class="n">file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span>
-</span><span id="init-287"><a href="#init-287"><span class="linenos">287</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-288"><a href="#init-288"><span class="linenos">288</span></a> <span class="p">)</span>
-</span><span id="init-289"><a href="#init-289"><span class="linenos">289</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-290"><a href="#init-290"><span class="linenos">290</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-291"><a href="#init-291"><span class="linenos">291</span></a> <span class="n">commit_count</span> <span class="o">=</span> <span class="mi">1</span>
-</span><span id="init-292"><a href="#init-292"><span class="linenos">292</span></a>
-</span><span id="init-293"><a href="#init-293"><span class="linenos">293</span></a> <span class="c1"># Checkout the phens default branch, creating it if it does not exist</span>
-</span><span id="init-294"><a href="#init-294"><span class="linenos">294</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-295"><a href="#init-295"><span class="linenos">295</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-296"><a href="#init-296"><span class="linenos">296</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-297"><a href="#init-297"><span class="linenos">297</span></a> <span class="k">else</span><span class="p">:</span>
-</span><span id="init-298"><a href="#init-298"><span class="linenos">298</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-299"><a href="#init-299"><span class="linenos">299</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-300"><a href="#init-300"><span class="linenos">300</span></a>
-</span><span id="init-301"><a href="#init-301"><span class="linenos">301</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-302"><a href="#init-302"><span class="linenos">302</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-303"><a href="#init-303"><span class="linenos">303</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-304"><a href="#init-304"><span class="linenos">304</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-305"><a href="#init-305"><span class="linenos">305</span></a> <span class="k">return</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="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-308"><a href="#init-308"><span class="linenos">308</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-309"><a href="#init-309"><span class="linenos">309</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-261"><a href="#init-261"><span class="linenos">261</span></a> <span class="c1"># clone the repo</span>
+</span><span id="init-262"><a href="#init-262"><span class="linenos">262</span></a> <span class="n">git_cmd</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-263"><a href="#init-263"><span class="linenos">263</span></a> <span class="n">git_cmd</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-264"><a href="#init-264"><span class="linenos">264</span></a>
+</span><span id="init-265"><a href="#init-265"><span class="linenos">265</span></a> <span class="c1"># open repo</span>
+</span><span id="init-266"><a href="#init-266"><span class="linenos">266</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-267"><a href="#init-267"><span class="linenos">267</span></a> <span class="c1"># check if there are any commits (new repo has no commits)</span>
+</span><span id="init-268"><a href="#init-268"><span class="linenos">268</span></a> <span class="k">if</span> <span class="p">(</span>
+</span><span id="init-269"><a href="#init-269"><span class="linenos">269</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-270"><a href="#init-270"><span class="linenos">270</span></a> <span class="p">):</span> <span class="c1"># Handle detached HEAD (e.g., after init)</span>
+</span><span id="init-271"><a href="#init-271"><span class="linenos">271</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-272"><a href="#init-272"><span class="linenos">272</span></a> <span class="n">commit_count</span> <span class="o">=</span> <span class="mi">0</span>
+</span><span id="init-273"><a href="#init-273"><span class="linenos">273</span></a> <span class="k">else</span><span class="p">:</span>
+</span><span id="init-274"><a href="#init-274"><span class="linenos">274</span></a> <span class="c1"># Get the total number of commits in the default branch</span>
+</span><span id="init-275"><a href="#init-275"><span class="linenos">275</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-276"><a href="#init-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">"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-277"><a href="#init-277"><span class="linenos">277</span></a> <span class="k">else</span><span class="p">:</span>
+</span><span id="init-278"><a href="#init-278"><span class="linenos">278</span></a> <span class="c1"># local repo, create the directories and init</span>
+</span><span id="init-279"><a href="#init-279"><span class="linenos">279</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-280"><a href="#init-280"><span class="linenos">280</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-281"><a href="#init-281"><span class="linenos">281</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-282"><a href="#init-282"><span class="linenos">282</span></a> <span class="n">commit_count</span> <span class="o">=</span> <span class="mi">0</span>
+</span><span id="init-283"><a href="#init-283"><span class="linenos">283</span></a>
+</span><span id="init-284"><a href="#init-284"><span class="linenos">284</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-285"><a href="#init-285"><span class="linenos">285</span></a> <span class="c1"># initialise empty repos</span>
+</span><span id="init-286"><a href="#init-286"><span class="linenos">286</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-287"><a href="#init-287"><span class="linenos">287</span></a> <span class="c1"># create initial commit</span>
+</span><span id="init-288"><a href="#init-288"><span class="linenos">288</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-289"><a href="#init-289"><span class="linenos">289</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-290"><a href="#init-290"><span class="linenos">290</span></a> <span class="n">file</span><span class="o">.</span><span class="n">write</span><span class="p">(</span>
+</span><span id="init-291"><a href="#init-291"><span class="linenos">291</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-292"><a href="#init-292"><span class="linenos">292</span></a> <span class="p">)</span>
+</span><span id="init-293"><a href="#init-293"><span class="linenos">293</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-294"><a href="#init-294"><span class="linenos">294</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-295"><a href="#init-295"><span class="linenos">295</span></a> <span class="n">commit_count</span> <span class="o">=</span> <span class="mi">1</span>
+</span><span id="init-296"><a href="#init-296"><span class="linenos">296</span></a>
+</span><span id="init-297"><a href="#init-297"><span class="linenos">297</span></a> <span class="c1"># Checkout the phens default branch, creating it if it does not exist</span>
+</span><span id="init-298"><a href="#init-298"><span class="linenos">298</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-299"><a href="#init-299"><span class="linenos">299</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-300"><a href="#init-300"><span class="linenos">300</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-301"><a href="#init-301"><span class="linenos">301</span></a> <span class="k">else</span><span class="p">:</span>
+</span><span id="init-302"><a href="#init-302"><span class="linenos">302</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-303"><a href="#init-303"><span class="linenos">303</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-304"><a href="#init-304"><span class="linenos">304</span></a>
+</span><span id="init-305"><a href="#init-305"><span class="linenos">305</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-306"><a href="#init-306"><span class="linenos">306</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-307"><a href="#init-307"><span class="linenos">307</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-308"><a href="#init-308"><span class="linenos">308</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-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"># create empty phen config file</span>
-</span><span id="init-312"><a href="#init-312"><span class="linenos">312</span></a> <span class="n">config</span> <span class="o">=</span> <span class="p">{</span>
-</span><span id="init-313"><a href="#init-313"><span class="linenos">313</span></a> <span class="s2">"phenotype"</span><span class="p">:</span> <span class="p">{</span>
-</span><span id="init-314"><a href="#init-314"><span class="linenos">314</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-315"><a href="#init-315"><span class="linenos">315</span></a> <span class="s2">"omop"</span><span class="p">:</span> <span class="p">{</span>
-</span><span id="init-316"><a href="#init-316"><span class="linenos">316</span></a> <span class="s2">"vocabulary_id"</span><span class="p">:</span> <span class="s2">""</span><span class="p">,</span>
-</span><span id="init-317"><a href="#init-317"><span class="linenos">317</span></a> <span class="s2">"vocabulary_name"</span><span class="p">:</span> <span class="s2">""</span><span class="p">,</span>
-</span><span id="init-318"><a href="#init-318"><span class="linenos">318</span></a> <span class="s2">"vocabulary_reference"</span><span class="p">:</span> <span class="s2">""</span><span class="p">,</span>
-</span><span id="init-319"><a href="#init-319"><span class="linenos">319</span></a> <span class="p">},</span>
-</span><span id="init-320"><a href="#init-320"><span class="linenos">320</span></a> <span class="s2">"translate"</span><span class="p">:</span> <span class="p">[],</span>
-</span><span id="init-321"><a href="#init-321"><span class="linenos">321</span></a> <span class="s2">"concept_sets"</span><span class="p">:</span> <span class="p">[],</span>
-</span><span id="init-322"><a href="#init-322"><span class="linenos">322</span></a> <span class="p">}</span>
-</span><span id="init-323"><a href="#init-323"><span class="linenos">323</span></a> <span class="p">}</span>
-</span><span id="init-324"><a href="#init-324"><span class="linenos">324</span></a>
-</span><span id="init-325"><a href="#init-325"><span class="linenos">325</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-326"><a href="#init-326"><span class="linenos">326</span></a> <span class="n">yaml</span><span class="o">.</span><span class="n">dump</span><span class="p">(</span>
-</span><span id="init-327"><a href="#init-327"><span class="linenos">327</span></a> <span class="n">config</span><span class="p">,</span>
-</span><span id="init-328"><a href="#init-328"><span class="linenos">328</span></a> <span class="n">file</span><span class="p">,</span>
-</span><span id="init-329"><a href="#init-329"><span class="linenos">329</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-330"><a href="#init-330"><span class="linenos">330</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-331"><a href="#init-331"><span class="linenos">331</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-332"><a href="#init-332"><span class="linenos">332</span></a> <span class="n">default_style</span><span class="o">=</span><span class="s1">'"'</span><span class="p">,</span>
-</span><span id="init-333"><a href="#init-333"><span class="linenos">333</span></a> <span class="p">)</span>
-</span><span id="init-334"><a href="#init-334"><span class="linenos">334</span></a>
-</span><span id="init-335"><a href="#init-335"><span class="linenos">335</span></a> <span class="c1"># add git ignore</span>
-</span><span id="init-336"><a href="#init-336"><span class="linenos">336</span></a> <span class="n">ignore_content</span> <span class="o">=</span> <span class="s2">"""# Ignore SQLite database files</span>
-</span><span id="init-337"><a href="#init-337"><span class="linenos">337</span></a><span class="s2">*.db</span>
-</span><span id="init-338"><a href="#init-338"><span class="linenos">338</span></a><span class="s2">*.sqlite3</span>
-</span><span id="init-339"><a href="#init-339"><span class="linenos">339</span></a><span class="s2"> </span>
-</span><span id="init-340"><a href="#init-340"><span class="linenos">340</span></a><span class="s2"># Ignore SQLite journal and metadata files</span>
-</span><span id="init-341"><a href="#init-341"><span class="linenos">341</span></a><span class="s2">*.db-journal</span>
-</span><span id="init-342"><a href="#init-342"><span class="linenos">342</span></a><span class="s2">*.sqlite3-journal</span>
-</span><span id="init-343"><a href="#init-343"><span class="linenos">343</span></a>
-</span><span id="init-344"><a href="#init-344"><span class="linenos">344</span></a><span class="s2"># python</span>
-</span><span id="init-345"><a href="#init-345"><span class="linenos">345</span></a><span class="s2">.ipynb_checkpoints</span>
-</span><span id="init-346"><a href="#init-346"><span class="linenos">346</span></a><span class="s2"> """</span>
-</span><span id="init-347"><a href="#init-347"><span class="linenos">347</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-348"><a href="#init-348"><span class="linenos">348</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-349"><a href="#init-349"><span class="linenos">349</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-350"><a href="#init-350"><span class="linenos">350</span></a>
-</span><span id="init-351"><a href="#init-351"><span class="linenos">351</span></a> <span class="c1"># add to git repo and commit</span>
-</span><span id="init-352"><a href="#init-352"><span class="linenos">352</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-353"><a href="#init-353"><span class="linenos">353</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-354"><a href="#init-354"><span class="linenos">354</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-355"><a href="#init-355"><span class="linenos">355</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-356"><a href="#init-356"><span class="linenos">356</span></a>
-</span><span id="init-357"><a href="#init-357"><span class="linenos">357</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="init-311"><a href="#init-311"><span class="linenos">311</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-312"><a href="#init-312"><span class="linenos">312</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-313"><a href="#init-313"><span class="linenos">313</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-314"><a href="#init-314"><span class="linenos">314</span></a>
+</span><span id="init-315"><a href="#init-315"><span class="linenos">315</span></a> <span class="c1"># create empty phen config file</span>
+</span><span id="init-316"><a href="#init-316"><span class="linenos">316</span></a> <span class="n">config</span> <span class="o">=</span> <span class="p">{</span>
+</span><span id="init-317"><a href="#init-317"><span class="linenos">317</span></a> <span class="s2">"phenotype"</span><span class="p">:</span> <span class="p">{</span>
+</span><span id="init-318"><a href="#init-318"><span class="linenos">318</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-319"><a href="#init-319"><span class="linenos">319</span></a> <span class="s2">"omop"</span><span class="p">:</span> <span class="p">{</span>
+</span><span id="init-320"><a href="#init-320"><span class="linenos">320</span></a> <span class="s2">"vocabulary_id"</span><span class="p">:</span> <span class="s2">""</span><span class="p">,</span>
+</span><span id="init-321"><a href="#init-321"><span class="linenos">321</span></a> <span class="s2">"vocabulary_name"</span><span class="p">:</span> <span class="s2">""</span><span class="p">,</span>
+</span><span id="init-322"><a href="#init-322"><span class="linenos">322</span></a> <span class="s2">"vocabulary_reference"</span><span class="p">:</span> <span class="s2">""</span><span class="p">,</span>
+</span><span id="init-323"><a href="#init-323"><span class="linenos">323</span></a> <span class="p">},</span>
+</span><span id="init-324"><a href="#init-324"><span class="linenos">324</span></a> <span class="s2">"translate"</span><span class="p">:</span> <span class="p">[],</span>
+</span><span id="init-325"><a href="#init-325"><span class="linenos">325</span></a> <span class="s2">"concept_sets"</span><span class="p">:</span> <span class="p">[],</span>
+</span><span id="init-326"><a href="#init-326"><span class="linenos">326</span></a> <span class="p">}</span>
+</span><span id="init-327"><a href="#init-327"><span class="linenos">327</span></a> <span class="p">}</span>
+</span><span id="init-328"><a href="#init-328"><span class="linenos">328</span></a>
+</span><span id="init-329"><a href="#init-329"><span class="linenos">329</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-330"><a href="#init-330"><span class="linenos">330</span></a> <span class="n">yaml</span><span class="o">.</span><span class="n">dump</span><span class="p">(</span>
+</span><span id="init-331"><a href="#init-331"><span class="linenos">331</span></a> <span class="n">config</span><span class="p">,</span>
+</span><span id="init-332"><a href="#init-332"><span class="linenos">332</span></a> <span class="n">file</span><span class="p">,</span>
+</span><span id="init-333"><a href="#init-333"><span class="linenos">333</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-334"><a href="#init-334"><span class="linenos">334</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-335"><a href="#init-335"><span class="linenos">335</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-336"><a href="#init-336"><span class="linenos">336</span></a> <span class="n">default_style</span><span class="o">=</span><span class="s1">'"'</span><span class="p">,</span>
+</span><span id="init-337"><a href="#init-337"><span class="linenos">337</span></a> <span class="p">)</span>
+</span><span id="init-338"><a href="#init-338"><span class="linenos">338</span></a>
+</span><span id="init-339"><a href="#init-339"><span class="linenos">339</span></a> <span class="c1"># add git ignore</span>
+</span><span id="init-340"><a href="#init-340"><span class="linenos">340</span></a> <span class="n">ignore_content</span> <span class="o">=</span> <span class="s2">"""# Ignore SQLite database files</span>
+</span><span id="init-341"><a href="#init-341"><span class="linenos">341</span></a><span class="s2">*.db</span>
+</span><span id="init-342"><a href="#init-342"><span class="linenos">342</span></a><span class="s2">*.sqlite3</span>
+</span><span id="init-343"><a href="#init-343"><span class="linenos">343</span></a><span class="s2"> </span>
+</span><span id="init-344"><a href="#init-344"><span class="linenos">344</span></a><span class="s2"># Ignore SQLite journal and metadata files</span>
+</span><span id="init-345"><a href="#init-345"><span class="linenos">345</span></a><span class="s2">*.db-journal</span>
+</span><span id="init-346"><a href="#init-346"><span class="linenos">346</span></a><span class="s2">*.sqlite3-journal</span>
+</span><span id="init-347"><a href="#init-347"><span class="linenos">347</span></a>
+</span><span id="init-348"><a href="#init-348"><span class="linenos">348</span></a><span class="s2"># python</span>
+</span><span id="init-349"><a href="#init-349"><span class="linenos">349</span></a><span class="s2">.ipynb_checkpoints</span>
+</span><span id="init-350"><a href="#init-350"><span class="linenos">350</span></a><span class="s2"> """</span>
+</span><span id="init-351"><a href="#init-351"><span class="linenos">351</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-352"><a href="#init-352"><span class="linenos">352</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-353"><a href="#init-353"><span class="linenos">353</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-354"><a href="#init-354"><span class="linenos">354</span></a>
+</span><span id="init-355"><a href="#init-355"><span class="linenos">355</span></a> <span class="c1"># add to git repo and commit</span>
+</span><span id="init-356"><a href="#init-356"><span class="linenos">356</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-357"><a href="#init-357"><span class="linenos">357</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-358"><a href="#init-358"><span class="linenos">358</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-359"><a href="#init-359"><span class="linenos">359</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-360"><a href="#init-360"><span class="linenos">360</span></a>
+</span><span id="init-361"><a href="#init-361"><span class="linenos">361</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>
@@ -2099,96 +2112,96 @@
</div>
<a class="headerlink" href="#fork"></a>
- <div class="pdoc-code codehilite"><pre><span></span><span id="fork-360"><a href="#fork-360"><span class="linenos">360</span></a><span class="k">def</span><span class="w"> </span><span class="nf">fork</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">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="p">):</span>
-</span><span id="fork-361"><a href="#fork-361"><span class="linenos">361</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-362"><a href="#fork-362"><span class="linenos">362</span></a>
-</span><span id="fork-363"><a href="#fork-363"><span class="linenos">363</span></a><span class="sd"> Args:</span>
-</span><span id="fork-364"><a href="#fork-364"><span class="linenos">364</span></a><span class="sd"> phen_dir (str): local directory path where the upstream repo is to be cloned</span>
-</span><span id="fork-365"><a href="#fork-365"><span class="linenos">365</span></a><span class="sd"> upstream_url (str): url to the upstream repo</span>
-</span><span id="fork-366"><a href="#fork-366"><span class="linenos">366</span></a><span class="sd"> upstream_version (str): version in the upstream repo to clone</span>
-</span><span id="fork-367"><a href="#fork-367"><span class="linenos">367</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-368"><a href="#fork-368"><span class="linenos">368</span></a>
-</span><span id="fork-369"><a href="#fork-369"><span class="linenos">369</span></a><span class="sd"> Raises:</span>
-</span><span id="fork-370"><a href="#fork-370"><span class="linenos">370</span></a><span class="sd"> ValueError: if the specified version is not in the upstream repo</span>
-</span><span id="fork-371"><a href="#fork-371"><span class="linenos">371</span></a><span class="sd"> ValueError: if the upstream repo is not a valid phenotype repo</span>
-</span><span id="fork-372"><a href="#fork-372"><span class="linenos">372</span></a><span class="sd"> ValueError: if there's any other problems with Git</span>
-</span><span id="fork-373"><a href="#fork-373"><span class="linenos">373</span></a><span class="sd"> """</span>
-</span><span id="fork-374"><a href="#fork-374"><span class="linenos">374</span></a> <span class="n">_logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span>
-</span><span id="fork-375"><a href="#fork-375"><span class="linenos">375</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-376"><a href="#fork-376"><span class="linenos">376</span></a> <span class="p">)</span>
-</span><span id="fork-377"><a href="#fork-377"><span class="linenos">377</span></a>
-</span><span id="fork-378"><a href="#fork-378"><span class="linenos">378</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-379"><a href="#fork-379"><span class="linenos">379</span></a> <span class="c1"># check if directory already exists and ask user if they want to recreate it</span>
-</span><span id="fork-380"><a href="#fork-380"><span class="linenos">380</span></a> <span class="k">if</span> <span class="p">(</span>
-</span><span id="fork-381"><a href="#fork-381"><span class="linenos">381</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-382"><a href="#fork-382"><span class="linenos">382</span></a> <span class="p">):</span> <span class="c1"># Check if it exists and is a directory</span>
-</span><span id="fork-383"><a href="#fork-383"><span class="linenos">383</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-384"><a href="#fork-384"><span class="linenos">384</span></a> <span class="n">phen_path</span><span class="p">,</span>
-</span><span id="fork-385"><a href="#fork-385"><span class="linenos">385</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-386"><a href="#fork-386"><span class="linenos">386</span></a> <span class="p">)</span>
-</span><span id="fork-387"><a href="#fork-387"><span class="linenos">387</span></a> <span class="k">else</span><span class="p">:</span>
-</span><span id="fork-388"><a href="#fork-388"><span class="linenos">388</span></a> <span class="n">configure</span> <span class="o">=</span> <span class="kc">True</span>
-</span><span id="fork-389"><a href="#fork-389"><span class="linenos">389</span></a>
-</span><span id="fork-390"><a href="#fork-390"><span class="linenos">390</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-391"><a href="#fork-391"><span class="linenos">391</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-392"><a href="#fork-392"><span class="linenos">392</span></a> <span class="k">return</span>
+ <div class="pdoc-code codehilite"><pre><span></span><span id="fork-364"><a href="#fork-364"><span class="linenos">364</span></a><span class="k">def</span><span class="w"> </span><span class="nf">fork</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">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="p">):</span>
+</span><span id="fork-365"><a href="#fork-365"><span class="linenos">365</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-366"><a href="#fork-366"><span class="linenos">366</span></a>
+</span><span id="fork-367"><a href="#fork-367"><span class="linenos">367</span></a><span class="sd"> Args:</span>
+</span><span id="fork-368"><a href="#fork-368"><span class="linenos">368</span></a><span class="sd"> phen_dir (str): local directory path where the upstream repo is to be cloned</span>
+</span><span id="fork-369"><a href="#fork-369"><span class="linenos">369</span></a><span class="sd"> upstream_url (str): url to the upstream repo</span>
+</span><span id="fork-370"><a href="#fork-370"><span class="linenos">370</span></a><span class="sd"> upstream_version (str): version in the upstream repo to clone</span>
+</span><span id="fork-371"><a href="#fork-371"><span class="linenos">371</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-372"><a href="#fork-372"><span class="linenos">372</span></a>
+</span><span id="fork-373"><a href="#fork-373"><span class="linenos">373</span></a><span class="sd"> Raises:</span>
+</span><span id="fork-374"><a href="#fork-374"><span class="linenos">374</span></a><span class="sd"> ValueError: if the specified version is not in the upstream repo</span>
+</span><span id="fork-375"><a href="#fork-375"><span class="linenos">375</span></a><span class="sd"> ValueError: if the upstream repo is not a valid phenotype repo</span>
+</span><span id="fork-376"><a href="#fork-376"><span class="linenos">376</span></a><span class="sd"> ValueError: if there's any other problems with Git</span>
+</span><span id="fork-377"><a href="#fork-377"><span class="linenos">377</span></a><span class="sd"> """</span>
+</span><span id="fork-378"><a href="#fork-378"><span class="linenos">378</span></a> <span class="n">_logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span>
+</span><span id="fork-379"><a href="#fork-379"><span class="linenos">379</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-380"><a href="#fork-380"><span class="linenos">380</span></a> <span class="p">)</span>
+</span><span id="fork-381"><a href="#fork-381"><span class="linenos">381</span></a>
+</span><span id="fork-382"><a href="#fork-382"><span class="linenos">382</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-383"><a href="#fork-383"><span class="linenos">383</span></a> <span class="c1"># check if directory already exists and ask user if they want to recreate it</span>
+</span><span id="fork-384"><a href="#fork-384"><span class="linenos">384</span></a> <span class="k">if</span> <span class="p">(</span>
+</span><span id="fork-385"><a href="#fork-385"><span class="linenos">385</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-386"><a href="#fork-386"><span class="linenos">386</span></a> <span class="p">):</span> <span class="c1"># Check if it exists and is a directory</span>
+</span><span id="fork-387"><a href="#fork-387"><span class="linenos">387</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-388"><a href="#fork-388"><span class="linenos">388</span></a> <span class="n">phen_path</span><span class="p">,</span>
+</span><span id="fork-389"><a href="#fork-389"><span class="linenos">389</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-390"><a href="#fork-390"><span class="linenos">390</span></a> <span class="p">)</span>
+</span><span id="fork-391"><a href="#fork-391"><span class="linenos">391</span></a> <span class="k">else</span><span class="p">:</span>
+</span><span id="fork-392"><a href="#fork-392"><span class="linenos">392</span></a> <span class="n">configure</span> <span class="o">=</span> <span class="kc">True</span>
</span><span id="fork-393"><a href="#fork-393"><span class="linenos">393</span></a>
-</span><span id="fork-394"><a href="#fork-394"><span class="linenos">394</span></a> <span class="k">try</span><span class="p">:</span>
-</span><span id="fork-395"><a href="#fork-395"><span class="linenos">395</span></a> <span class="c1"># Clone repo</span>
-</span><span id="fork-396"><a href="#fork-396"><span class="linenos">396</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-397"><a href="#fork-397"><span class="linenos">397</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-398"><a href="#fork-398"><span class="linenos">398</span></a>
-</span><span id="fork-399"><a href="#fork-399"><span class="linenos">399</span></a> <span class="c1"># Fetch all branches and tags</span>
-</span><span id="fork-400"><a href="#fork-400"><span class="linenos">400</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-401"><a href="#fork-401"><span class="linenos">401</span></a>
-</span><span id="fork-402"><a href="#fork-402"><span class="linenos">402</span></a> <span class="c1"># Check if the version exists</span>
-</span><span id="fork-403"><a href="#fork-403"><span class="linenos">403</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-404"><a href="#fork-404"><span class="linenos">404</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-405"><a href="#fork-405"><span class="linenos">405</span></a> <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span>
-</span><span id="fork-406"><a href="#fork-406"><span class="linenos">406</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-407"><a href="#fork-407"><span class="linenos">407</span></a> <span class="p">)</span>
-</span><span id="fork-408"><a href="#fork-408"><span class="linenos">408</span></a>
-</span><span id="fork-409"><a href="#fork-409"><span class="linenos">409</span></a> <span class="c1"># Checkout the specified version</span>
-</span><span id="fork-410"><a href="#fork-410"><span class="linenos">410</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-411"><a href="#fork-411"><span class="linenos">411</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-412"><a href="#fork-412"><span class="linenos">412</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-413"><a href="#fork-413"><span class="linenos">413</span></a>
-</span><span id="fork-414"><a href="#fork-414"><span class="linenos">414</span></a> <span class="c1"># Check if 'config.yml' exists in the root directory</span>
-</span><span id="fork-415"><a href="#fork-415"><span class="linenos">415</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.yml"</span>
-</span><span id="fork-416"><a href="#fork-416"><span class="linenos">416</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-417"><a href="#fork-417"><span class="linenos">417</span></a> <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span>
-</span><span id="fork-418"><a href="#fork-418"><span class="linenos">418</span></a> <span class="sa">f</span><span class="s2">"The forked repository is not a valid ACMC repo because 'config.yml' is missing in the root directory."</span>
-</span><span id="fork-419"><a href="#fork-419"><span class="linenos">419</span></a> <span class="p">)</span>
-</span><span id="fork-420"><a href="#fork-420"><span class="linenos">420</span></a>
-</span><span id="fork-421"><a href="#fork-421"><span class="linenos">421</span></a> <span class="c1"># Validate the phenotype is compatible with the acmc tool</span>
-</span><span id="fork-422"><a href="#fork-422"><span class="linenos">422</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-423"><a href="#fork-423"><span class="linenos">423</span></a>
-</span><span id="fork-424"><a href="#fork-424"><span class="linenos">424</span></a> <span class="c1"># Delete each tag locally</span>
-</span><span id="fork-425"><a href="#fork-425"><span class="linenos">425</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-426"><a href="#fork-426"><span class="linenos">426</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-427"><a href="#fork-427"><span class="linenos">427</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-428"><a href="#fork-428"><span class="linenos">428</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-429"><a href="#fork-429"><span class="linenos">429</span></a>
-</span><span id="fork-430"><a href="#fork-430"><span class="linenos">430</span></a> <span class="c1"># Add upstream remote</span>
-</span><span id="fork-431"><a href="#fork-431"><span class="linenos">431</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-432"><a href="#fork-432"><span class="linenos">432</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-433"><a href="#fork-433"><span class="linenos">433</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-434"><a href="#fork-434"><span class="linenos">434</span></a>
-</span><span id="fork-435"><a href="#fork-435"><span class="linenos">435</span></a> <span class="c1"># Optionally set a new origin remote</span>
-</span><span id="fork-436"><a href="#fork-436"><span class="linenos">436</span></a> <span class="k">if</span> <span class="n">new_origin_url</span><span class="p">:</span>
-</span><span id="fork-437"><a href="#fork-437"><span class="linenos">437</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-438"><a href="#fork-438"><span class="linenos">438</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-439"><a href="#fork-439"><span class="linenos">439</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-440"><a href="#fork-440"><span class="linenos">440</span></a>
-</span><span id="fork-441"><a href="#fork-441"><span class="linenos">441</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-442"><a href="#fork-442"><span class="linenos">442</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-443"><a href="#fork-443"><span class="linenos">443</span></a> <span class="k">if</span> <span class="n">new_origin_url</span><span class="p">:</span>
-</span><span id="fork-444"><a href="#fork-444"><span class="linenos">444</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-445"><a href="#fork-445"><span class="linenos">445</span></a>
-</span><span id="fork-446"><a href="#fork-446"><span class="linenos">446</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-447"><a href="#fork-447"><span class="linenos">447</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-448"><a href="#fork-448"><span class="linenos">448</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-449"><a href="#fork-449"><span class="linenos">449</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="fork-394"><a href="#fork-394"><span class="linenos">394</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-395"><a href="#fork-395"><span class="linenos">395</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-396"><a href="#fork-396"><span class="linenos">396</span></a> <span class="k">return</span>
+</span><span id="fork-397"><a href="#fork-397"><span class="linenos">397</span></a>
+</span><span id="fork-398"><a href="#fork-398"><span class="linenos">398</span></a> <span class="k">try</span><span class="p">:</span>
+</span><span id="fork-399"><a href="#fork-399"><span class="linenos">399</span></a> <span class="c1"># Clone repo</span>
+</span><span id="fork-400"><a href="#fork-400"><span class="linenos">400</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-401"><a href="#fork-401"><span class="linenos">401</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-402"><a href="#fork-402"><span class="linenos">402</span></a>
+</span><span id="fork-403"><a href="#fork-403"><span class="linenos">403</span></a> <span class="c1"># Fetch all branches and tags</span>
+</span><span id="fork-404"><a href="#fork-404"><span class="linenos">404</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-405"><a href="#fork-405"><span class="linenos">405</span></a>
+</span><span id="fork-406"><a href="#fork-406"><span class="linenos">406</span></a> <span class="c1"># Check if the version exists</span>
+</span><span id="fork-407"><a href="#fork-407"><span class="linenos">407</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-408"><a href="#fork-408"><span class="linenos">408</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-409"><a href="#fork-409"><span class="linenos">409</span></a> <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span>
+</span><span id="fork-410"><a href="#fork-410"><span class="linenos">410</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-411"><a href="#fork-411"><span class="linenos">411</span></a> <span class="p">)</span>
+</span><span id="fork-412"><a href="#fork-412"><span class="linenos">412</span></a>
+</span><span id="fork-413"><a href="#fork-413"><span class="linenos">413</span></a> <span class="c1"># Checkout the specified version</span>
+</span><span id="fork-414"><a href="#fork-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">checkout</span><span class="p">(</span><span class="n">upstream_version</span><span class="p">)</span>
+</span><span id="fork-415"><a href="#fork-415"><span class="linenos">415</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-416"><a href="#fork-416"><span class="linenos">416</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-417"><a href="#fork-417"><span class="linenos">417</span></a>
+</span><span id="fork-418"><a href="#fork-418"><span class="linenos">418</span></a> <span class="c1"># Check if 'config.yml' exists in the root directory</span>
+</span><span id="fork-419"><a href="#fork-419"><span class="linenos">419</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.yml"</span>
+</span><span id="fork-420"><a href="#fork-420"><span class="linenos">420</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-421"><a href="#fork-421"><span class="linenos">421</span></a> <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span>
+</span><span id="fork-422"><a href="#fork-422"><span class="linenos">422</span></a> <span class="sa">f</span><span class="s2">"The forked repository is not a valid ACMC repo because 'config.yml' is missing in the root directory."</span>
+</span><span id="fork-423"><a href="#fork-423"><span class="linenos">423</span></a> <span class="p">)</span>
+</span><span id="fork-424"><a href="#fork-424"><span class="linenos">424</span></a>
+</span><span id="fork-425"><a href="#fork-425"><span class="linenos">425</span></a> <span class="c1"># Validate the phenotype is compatible with the acmc tool</span>
+</span><span id="fork-426"><a href="#fork-426"><span class="linenos">426</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-427"><a href="#fork-427"><span class="linenos">427</span></a>
+</span><span id="fork-428"><a href="#fork-428"><span class="linenos">428</span></a> <span class="c1"># Delete each tag locally</span>
+</span><span id="fork-429"><a href="#fork-429"><span class="linenos">429</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-430"><a href="#fork-430"><span class="linenos">430</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-431"><a href="#fork-431"><span class="linenos">431</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-432"><a href="#fork-432"><span class="linenos">432</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-433"><a href="#fork-433"><span class="linenos">433</span></a>
+</span><span id="fork-434"><a href="#fork-434"><span class="linenos">434</span></a> <span class="c1"># Add upstream remote</span>
+</span><span id="fork-435"><a href="#fork-435"><span class="linenos">435</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-436"><a href="#fork-436"><span class="linenos">436</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-437"><a href="#fork-437"><span class="linenos">437</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-438"><a href="#fork-438"><span class="linenos">438</span></a>
+</span><span id="fork-439"><a href="#fork-439"><span class="linenos">439</span></a> <span class="c1"># Optionally set a new origin remote</span>
+</span><span id="fork-440"><a href="#fork-440"><span class="linenos">440</span></a> <span class="k">if</span> <span class="n">new_origin_url</span><span class="p">:</span>
+</span><span id="fork-441"><a href="#fork-441"><span class="linenos">441</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-442"><a href="#fork-442"><span class="linenos">442</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-443"><a href="#fork-443"><span class="linenos">443</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-444"><a href="#fork-444"><span class="linenos">444</span></a>
+</span><span id="fork-445"><a href="#fork-445"><span class="linenos">445</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-446"><a href="#fork-446"><span class="linenos">446</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-447"><a href="#fork-447"><span class="linenos">447</span></a> <span class="k">if</span> <span class="n">new_origin_url</span><span class="p">:</span>
+</span><span id="fork-448"><a href="#fork-448"><span class="linenos">448</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-449"><a href="#fork-449"><span class="linenos">449</span></a>
+</span><span id="fork-450"><a href="#fork-450"><span class="linenos">450</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-451"><a href="#fork-451"><span class="linenos">451</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-452"><a href="#fork-452"><span class="linenos">452</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-453"><a href="#fork-453"><span class="linenos">453</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>
@@ -2225,117 +2238,118 @@
</div>
<a class="headerlink" href="#validate"></a>
- <div class="pdoc-code codehilite"><pre><span></span><span id="validate-452"><a href="#validate-452"><span class="linenos">452</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-453"><a href="#validate-453"><span class="linenos">453</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-454"><a href="#validate-454"><span class="linenos">454</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-455"><a href="#validate-455"><span class="linenos">455</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-456"><a href="#validate-456"><span class="linenos">456</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-457"><a href="#validate-457"><span class="linenos">457</span></a> <span class="k">raise</span> <span class="ne">NotADirectoryError</span><span class="p">(</span>
-</span><span id="validate-458"><a href="#validate-458"><span class="linenos">458</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-459"><a href="#validate-459"><span class="linenos">459</span></a> <span class="p">)</span>
-</span><span id="validate-460"><a href="#validate-460"><span class="linenos">460</span></a>
-</span><span id="validate-461"><a href="#validate-461"><span class="linenos">461</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-462"><a href="#validate-462"><span class="linenos">462</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-463"><a href="#validate-463"><span class="linenos">463</span></a> <span class="k">raise</span> <span class="ne">FileNotFoundError</span><span class="p">(</span>
-</span><span id="validate-464"><a href="#validate-464"><span class="linenos">464</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-465"><a href="#validate-465"><span class="linenos">465</span></a> <span class="p">)</span>
-</span><span id="validate-466"><a href="#validate-466"><span class="linenos">466</span></a>
-</span><span id="validate-467"><a href="#validate-467"><span class="linenos">467</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-468"><a href="#validate-468"><span class="linenos">468</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-469"><a href="#validate-469"><span class="linenos">469</span></a> <span class="k">raise</span> <span class="ne">FileNotFoundError</span><span class="p">(</span>
-</span><span id="validate-470"><a href="#validate-470"><span class="linenos">470</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-471"><a href="#validate-471"><span class="linenos">471</span></a> <span class="p">)</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"># Calidate the directory is a git repo</span>
-</span><span id="validate-474"><a href="#validate-474"><span class="linenos">474</span></a> <span class="k">try</span><span class="p">:</span>
-</span><span id="validate-475"><a href="#validate-475"><span class="linenos">475</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-476"><a href="#validate-476"><span class="linenos">476</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-477"><a href="#validate-477"><span class="linenos">477</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-478"><a href="#validate-478"><span class="linenos">478</span></a>
-</span><span id="validate-479"><a href="#validate-479"><span class="linenos">479</span></a> <span class="c1"># Load configuration File</span>
-</span><span id="validate-480"><a href="#validate-480"><span class="linenos">480</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">".yml"</span><span class="p">:</span>
-</span><span id="validate-481"><a href="#validate-481"><span class="linenos">481</span></a> <span class="k">try</span><span class="p">:</span>
-</span><span id="validate-482"><a href="#validate-482"><span class="linenos">482</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-483"><a href="#validate-483"><span class="linenos">483</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-484"><a href="#validate-484"><span class="linenos">484</span></a>
-</span><span id="validate-485"><a href="#validate-485"><span class="linenos">485</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-486"><a href="#validate-486"><span class="linenos">486</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-487"><a href="#validate-487"><span class="linenos">487</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-488"><a href="#validate-488"><span class="linenos">488</span></a> <span class="k">else</span><span class="p">:</span>
-</span><span id="validate-489"><a href="#validate-489"><span class="linenos">489</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-490"><a href="#validate-490"><span class="linenos">490</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-491"><a href="#validate-491"><span class="linenos">491</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-492"><a href="#validate-492"><span class="linenos">492</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-493"><a href="#validate-493"><span class="linenos">493</span></a> <span class="k">raise</span> <span class="n">e</span>
-</span><span id="validate-494"><a href="#validate-494"><span class="linenos">494</span></a> <span class="k">else</span><span class="p">:</span>
-</span><span id="validate-495"><a href="#validate-495"><span class="linenos">495</span></a> <span class="k">raise</span> <span class="ne">Exception</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">"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-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"># initiatise</span>
-</span><span id="validate-500"><a href="#validate-500"><span class="linenos">500</span></a> <span class="n">validation_errors</span> <span class="o">=</span> <span class="p">[]</span>
-</span><span id="validate-501"><a href="#validate-501"><span class="linenos">501</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-502"><a href="#validate-502"><span class="linenos">502</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-503"><a href="#validate-503"><span class="linenos">503</span></a>
-</span><span id="validate-504"><a href="#validate-504"><span class="linenos">504</span></a> <span class="c1"># check the version number is of the format vn.n.n</span>
-</span><span id="validate-505"><a href="#validate-505"><span class="linenos">505</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-506"><a href="#validate-506"><span class="linenos">506</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-507"><a href="#validate-507"><span class="linenos">507</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-508"><a href="#validate-508"><span class="linenos">508</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-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"># create a list of all the concept set names defined in the concept set configuration</span>
-</span><span id="validate-512"><a href="#validate-512"><span class="linenos">512</span></a> <span class="n">concept_set_names</span> <span class="o">=</span> <span class="p">[]</span>
-</span><span id="validate-513"><a href="#validate-513"><span class="linenos">513</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-514"><a href="#validate-514"><span class="linenos">514</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-515"><a href="#validate-515"><span class="linenos">515</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-516"><a href="#validate-516"><span class="linenos">516</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-517"><a href="#validate-517"><span class="linenos">517</span></a> <span class="p">)</span>
-</span><span id="validate-518"><a href="#validate-518"><span class="linenos">518</span></a> <span class="k">else</span><span class="p">:</span>
-</span><span id="validate-519"><a href="#validate-519"><span class="linenos">519</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-520"><a href="#validate-520"><span class="linenos">520</span></a>
-</span><span id="validate-521"><a href="#validate-521"><span class="linenos">521</span></a> <span class="c1"># check codes definition</span>
-</span><span id="validate-522"><a href="#validate-522"><span class="linenos">522</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-523"><a href="#validate-523"><span class="linenos">523</span></a> <span class="c1"># check concepte code file exists</span>
-</span><span id="validate-524"><a href="#validate-524"><span class="linenos">524</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-525"><a href="#validate-525"><span class="linenos">525</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-526"><a href="#validate-526"><span class="linenos">526</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-527"><a href="#validate-527"><span class="linenos">527</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-528"><a href="#validate-528"><span class="linenos">528</span></a> <span class="p">)</span>
-</span><span id="validate-529"><a href="#validate-529"><span class="linenos">529</span></a>
-</span><span id="validate-530"><a href="#validate-530"><span class="linenos">530</span></a> <span class="c1"># check concepte code file is not empty</span>
-</span><span id="validate-531"><a href="#validate-531"><span class="linenos">531</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-532"><a href="#validate-532"><span class="linenos">532</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-533"><a href="#validate-533"><span class="linenos">533</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-534"><a href="#validate-534"><span class="linenos">534</span></a> <span class="p">)</span>
-</span><span id="validate-535"><a href="#validate-535"><span class="linenos">535</span></a>
-</span><span id="validate-536"><a href="#validate-536"><span class="linenos">536</span></a> <span class="c1"># check code file type is supported</span>
-</span><span id="validate-537"><a href="#validate-537"><span class="linenos">537</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-538"><a href="#validate-538"><span class="linenos">538</span></a> <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span>
-</span><span id="validate-539"><a href="#validate-539"><span class="linenos">539</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-540"><a href="#validate-540"><span class="linenos">540</span></a> <span class="p">)</span>
-</span><span id="validate-541"><a href="#validate-541"><span class="linenos">541</span></a>
-</span><span id="validate-542"><a href="#validate-542"><span class="linenos">542</span></a> <span class="c1"># check columns specified are a supported medical coding type</span>
-</span><span id="validate-543"><a href="#validate-543"><span class="linenos">543</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-544"><a href="#validate-544"><span class="linenos">544</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-545"><a href="#validate-545"><span class="linenos">545</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-546"><a href="#validate-546"><span class="linenos">546</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-547"><a href="#validate-547"><span class="linenos">547</span></a> <span class="p">)</span>
-</span><span id="validate-548"><a href="#validate-548"><span class="linenos">548</span></a>
-</span><span id="validate-549"><a href="#validate-549"><span class="linenos">549</span></a> <span class="c1"># check the actions are supported</span>
-</span><span id="validate-550"><a href="#validate-550"><span class="linenos">550</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-551"><a href="#validate-551"><span class="linenos">551</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-552"><a href="#validate-552"><span class="linenos">552</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-553"><a href="#validate-553"><span class="linenos">553</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-554"><a href="#validate-554"><span class="linenos">554</span></a>
-</span><span id="validate-555"><a href="#validate-555"><span class="linenos">555</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-556"><a href="#validate-556"><span class="linenos">556</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-557"><a href="#validate-557"><span class="linenos">557</span></a> <span class="k">raise</span> <span class="n">PhenValidationException</span><span class="p">(</span>
-</span><span id="validate-558"><a href="#validate-558"><span class="linenos">558</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-559"><a href="#validate-559"><span class="linenos">559</span></a> <span class="n">validation_errors</span><span class="p">,</span>
-</span><span id="validate-560"><a href="#validate-560"><span class="linenos">560</span></a> <span class="p">)</span>
-</span><span id="validate-561"><a href="#validate-561"><span class="linenos">561</span></a>
-</span><span id="validate-562"><a href="#validate-562"><span class="linenos">562</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>
+ <div class="pdoc-code codehilite"><pre><span></span><span id="validate-456"><a href="#validate-456"><span class="linenos">456</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-457"><a href="#validate-457"><span class="linenos">457</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-458"><a href="#validate-458"><span class="linenos">458</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-459"><a href="#validate-459"><span class="linenos">459</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-460"><a href="#validate-460"><span class="linenos">460</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-461"><a href="#validate-461"><span class="linenos">461</span></a> <span class="k">raise</span> <span class="ne">NotADirectoryError</span><span class="p">(</span>
+</span><span id="validate-462"><a href="#validate-462"><span class="linenos">462</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-463"><a href="#validate-463"><span class="linenos">463</span></a> <span class="p">)</span>
+</span><span id="validate-464"><a href="#validate-464"><span class="linenos">464</span></a>
+</span><span id="validate-465"><a href="#validate-465"><span class="linenos">465</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-466"><a href="#validate-466"><span class="linenos">466</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-467"><a href="#validate-467"><span class="linenos">467</span></a> <span class="k">raise</span> <span class="ne">FileNotFoundError</span><span class="p">(</span>
+</span><span id="validate-468"><a href="#validate-468"><span class="linenos">468</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-469"><a href="#validate-469"><span class="linenos">469</span></a> <span class="p">)</span>
+</span><span id="validate-470"><a href="#validate-470"><span class="linenos">470</span></a>
+</span><span id="validate-471"><a href="#validate-471"><span class="linenos">471</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-472"><a href="#validate-472"><span class="linenos">472</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-473"><a href="#validate-473"><span class="linenos">473</span></a> <span class="k">raise</span> <span class="ne">FileNotFoundError</span><span class="p">(</span>
+</span><span id="validate-474"><a href="#validate-474"><span class="linenos">474</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-475"><a href="#validate-475"><span class="linenos">475</span></a> <span class="p">)</span>
+</span><span id="validate-476"><a href="#validate-476"><span class="linenos">476</span></a>
+</span><span id="validate-477"><a href="#validate-477"><span class="linenos">477</span></a> <span class="c1"># Calidate the directory is a git repo</span>
+</span><span id="validate-478"><a href="#validate-478"><span class="linenos">478</span></a> <span class="k">try</span><span class="p">:</span>
+</span><span id="validate-479"><a href="#validate-479"><span class="linenos">479</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-480"><a href="#validate-480"><span class="linenos">480</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-481"><a href="#validate-481"><span class="linenos">481</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-482"><a href="#validate-482"><span class="linenos">482</span></a>
+</span><span id="validate-483"><a href="#validate-483"><span class="linenos">483</span></a> <span class="c1"># Load configuration File</span>
+</span><span id="validate-484"><a href="#validate-484"><span class="linenos">484</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">".yml"</span><span class="p">:</span>
+</span><span id="validate-485"><a href="#validate-485"><span class="linenos">485</span></a> <span class="k">try</span><span class="p">:</span>
+</span><span id="validate-486"><a href="#validate-486"><span class="linenos">486</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-487"><a href="#validate-487"><span class="linenos">487</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-488"><a href="#validate-488"><span class="linenos">488</span></a>
+</span><span id="validate-489"><a href="#validate-489"><span class="linenos">489</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-490"><a href="#validate-490"><span class="linenos">490</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-491"><a href="#validate-491"><span class="linenos">491</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-492"><a href="#validate-492"><span class="linenos">492</span></a> <span class="k">else</span><span class="p">:</span>
+</span><span id="validate-493"><a href="#validate-493"><span class="linenos">493</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-494"><a href="#validate-494"><span class="linenos">494</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-495"><a href="#validate-495"><span class="linenos">495</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-496"><a href="#validate-496"><span class="linenos">496</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-497"><a href="#validate-497"><span class="linenos">497</span></a> <span class="k">raise</span> <span class="n">e</span>
+</span><span id="validate-498"><a href="#validate-498"><span class="linenos">498</span></a> <span class="k">else</span><span class="p">:</span>
+</span><span id="validate-499"><a href="#validate-499"><span class="linenos">499</span></a> <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span>
+</span><span id="validate-500"><a href="#validate-500"><span class="linenos">500</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-501"><a href="#validate-501"><span class="linenos">501</span></a> <span class="p">)</span>
+</span><span id="validate-502"><a href="#validate-502"><span class="linenos">502</span></a>
+</span><span id="validate-503"><a href="#validate-503"><span class="linenos">503</span></a> <span class="c1"># initiatise</span>
+</span><span id="validate-504"><a href="#validate-504"><span class="linenos">504</span></a> <span class="n">validation_errors</span> <span class="o">=</span> <span class="p">[]</span>
+</span><span id="validate-505"><a href="#validate-505"><span class="linenos">505</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-506"><a href="#validate-506"><span class="linenos">506</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-507"><a href="#validate-507"><span class="linenos">507</span></a>
+</span><span id="validate-508"><a href="#validate-508"><span class="linenos">508</span></a> <span class="c1"># check the version number is of the format vn.n.n</span>
+</span><span id="validate-509"><a href="#validate-509"><span class="linenos">509</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-510"><a href="#validate-510"><span class="linenos">510</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-511"><a href="#validate-511"><span class="linenos">511</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-512"><a href="#validate-512"><span class="linenos">512</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-513"><a href="#validate-513"><span class="linenos">513</span></a> <span class="p">)</span>
+</span><span id="validate-514"><a href="#validate-514"><span class="linenos">514</span></a>
+</span><span id="validate-515"><a href="#validate-515"><span class="linenos">515</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-516"><a href="#validate-516"><span class="linenos">516</span></a> <span class="n">concept_set_names</span> <span class="o">=</span> <span class="p">[]</span>
+</span><span id="validate-517"><a href="#validate-517"><span class="linenos">517</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-518"><a href="#validate-518"><span class="linenos">518</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-519"><a href="#validate-519"><span class="linenos">519</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-520"><a href="#validate-520"><span class="linenos">520</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-521"><a href="#validate-521"><span class="linenos">521</span></a> <span class="p">)</span>
+</span><span id="validate-522"><a href="#validate-522"><span class="linenos">522</span></a> <span class="k">else</span><span class="p">:</span>
+</span><span id="validate-523"><a href="#validate-523"><span class="linenos">523</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-524"><a href="#validate-524"><span class="linenos">524</span></a>
+</span><span id="validate-525"><a href="#validate-525"><span class="linenos">525</span></a> <span class="c1"># check codes definition</span>
+</span><span id="validate-526"><a href="#validate-526"><span class="linenos">526</span></a> <span class="k">for</span> <span class="n">files</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-527"><a href="#validate-527"><span class="linenos">527</span></a> <span class="k">for</span> <span class="n">item</span> <span class="ow">in</span> <span class="n">files</span><span class="p">[</span><span class="s2">"files"</span><span class="p">]:</span>
+</span><span id="validate-528"><a href="#validate-528"><span class="linenos">528</span></a> <span class="c1"># check concepte code file exists</span>
+</span><span id="validate-529"><a href="#validate-529"><span class="linenos">529</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">"path"</span><span class="p">]</span>
+</span><span id="validate-530"><a href="#validate-530"><span class="linenos">530</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-531"><a href="#validate-531"><span class="linenos">531</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-532"><a href="#validate-532"><span class="linenos">532</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-533"><a href="#validate-533"><span class="linenos">533</span></a> <span class="p">)</span>
+</span><span id="validate-534"><a href="#validate-534"><span class="linenos">534</span></a>
+</span><span id="validate-535"><a href="#validate-535"><span class="linenos">535</span></a> <span class="c1"># check concepte code file is not empty</span>
+</span><span id="validate-536"><a href="#validate-536"><span class="linenos">536</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-537"><a href="#validate-537"><span class="linenos">537</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-538"><a href="#validate-538"><span class="linenos">538</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-539"><a href="#validate-539"><span class="linenos">539</span></a> <span class="p">)</span>
+</span><span id="validate-540"><a href="#validate-540"><span class="linenos">540</span></a>
+</span><span id="validate-541"><a href="#validate-541"><span class="linenos">541</span></a> <span class="c1"># check code file type is supported</span>
+</span><span id="validate-542"><a href="#validate-542"><span class="linenos">542</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-543"><a href="#validate-543"><span class="linenos">543</span></a> <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span>
+</span><span id="validate-544"><a href="#validate-544"><span class="linenos">544</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-545"><a href="#validate-545"><span class="linenos">545</span></a> <span class="p">)</span>
+</span><span id="validate-546"><a href="#validate-546"><span class="linenos">546</span></a>
+</span><span id="validate-547"><a href="#validate-547"><span class="linenos">547</span></a> <span class="c1"># check columns specified are a supported medical coding type</span>
+</span><span id="validate-548"><a href="#validate-548"><span class="linenos">548</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">"columns"</span><span class="p">]:</span>
+</span><span id="validate-549"><a href="#validate-549"><span class="linenos">549</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-550"><a href="#validate-550"><span class="linenos">550</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-551"><a href="#validate-551"><span class="linenos">551</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-552"><a href="#validate-552"><span class="linenos">552</span></a> <span class="p">)</span>
+</span><span id="validate-553"><a href="#validate-553"><span class="linenos">553</span></a>
+</span><span id="validate-554"><a href="#validate-554"><span class="linenos">554</span></a> <span class="c1"># check the actions are supported</span>
+</span><span id="validate-555"><a href="#validate-555"><span class="linenos">555</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><span id="validate-556"><a href="#validate-556"><span class="linenos">556</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">"actions"</span><span class="p">]:</span>
+</span><span id="validate-557"><a href="#validate-557"><span class="linenos">557</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-558"><a href="#validate-558"><span class="linenos">558</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-559"><a href="#validate-559"><span class="linenos">559</span></a>
+</span><span id="validate-560"><a href="#validate-560"><span class="linenos">560</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-561"><a href="#validate-561"><span class="linenos">561</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-562"><a href="#validate-562"><span class="linenos">562</span></a> <span class="k">raise</span> <span class="n">PhenValidationException</span><span class="p">(</span>
+</span><span id="validate-563"><a href="#validate-563"><span class="linenos">563</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-564"><a href="#validate-564"><span class="linenos">564</span></a> <span class="n">validation_errors</span><span class="p">,</span>
+</span><span id="validate-565"><a href="#validate-565"><span class="linenos">565</span></a> <span class="p">)</span>
+</span><span id="validate-566"><a href="#validate-566"><span class="linenos">566</span></a>
+</span><span id="validate-567"><a href="#validate-567"><span class="linenos">567</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>
@@ -2355,68 +2369,68 @@
</div>
<a class="headerlink" href="#translate_codes"></a>
- <div class="pdoc-code codehilite"><pre><span></span><span id="translate_codes-656"><a href="#translate_codes-656"><span class="linenos">656</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-657"><a href="#translate_codes-657"><span class="linenos">657</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-658"><a href="#translate_codes-658"><span class="linenos">658</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-659"><a href="#translate_codes-659"><span class="linenos">659</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-660"><a href="#translate_codes-660"><span class="linenos">660</span></a>
-</span><span id="translate_codes-661"><a href="#translate_codes-661"><span class="linenos">661</span></a> <span class="c1"># codes = pd.DataFrame([], dtype=str)</span>
-</span><span id="translate_codes-662"><a href="#translate_codes-662"><span class="linenos">662</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-663"><a href="#translate_codes-663"><span class="linenos">663</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-664"><a href="#translate_codes-664"><span class="linenos">664</span></a> <span class="p">)</span>
-</span><span id="translate_codes-665"><a href="#translate_codes-665"><span class="linenos">665</span></a> <span class="c1"># Convert codes to target type</span>
-</span><span id="translate_codes-666"><a href="#translate_codes-666"><span class="linenos">666</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-667"><a href="#translate_codes-667"><span class="linenos">667</span></a>
-</span><span id="translate_codes-668"><a href="#translate_codes-668"><span class="linenos">668</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-669"><a href="#translate_codes-669"><span class="linenos">669</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-670"><a href="#translate_codes-670"><span class="linenos">670</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-671"><a href="#translate_codes-671"><span class="linenos">671</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-672"><a href="#translate_codes-672"><span class="linenos">672</span></a> <span class="p">{</span>
-</span><span id="translate_codes-673"><a href="#translate_codes-673"><span class="linenos">673</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-674"><a href="#translate_codes-674"><span class="linenos">674</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-675"><a href="#translate_codes-675"><span class="linenos">675</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-676"><a href="#translate_codes-676"><span class="linenos">676</span></a> <span class="p">}</span>
-</span><span id="translate_codes-677"><a href="#translate_codes-677"><span class="linenos">677</span></a> <span class="p">)</span>
-</span><span id="translate_codes-678"><a href="#translate_codes-678"><span class="linenos">678</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-679"><a href="#translate_codes-679"><span class="linenos">679</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-680"><a href="#translate_codes-680"><span class="linenos">680</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-681"><a href="#translate_codes-681"><span class="linenos">681</span></a> <span class="p">)</span>
-</span><span id="translate_codes-682"><a href="#translate_codes-682"><span class="linenos">682</span></a> <span class="k">else</span><span class="p">:</span>
-</span><span id="translate_codes-683"><a href="#translate_codes-683"><span class="linenos">683</span></a> <span class="c1"># get the translation filename using source to target code types</span>
-</span><span id="translate_codes-684"><a href="#translate_codes-684"><span class="linenos">684</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-685"><a href="#translate_codes-685"><span class="linenos">685</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-686"><a href="#translate_codes-686"><span class="linenos">686</span></a>
-</span><span id="translate_codes-687"><a href="#translate_codes-687"><span class="linenos">687</span></a> <span class="c1"># do the mapping if it exists</span>
-</span><span id="translate_codes-688"><a href="#translate_codes-688"><span class="linenos">688</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-689"><a href="#translate_codes-689"><span class="linenos">689</span></a> <span class="c1"># get mapping</span>
-</span><span id="translate_codes-690"><a href="#translate_codes-690"><span class="linenos">690</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>
+ <div class="pdoc-code codehilite"><pre><span></span><span id="translate_codes-661"><a href="#translate_codes-661"><span class="linenos">661</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-662"><a href="#translate_codes-662"><span class="linenos">662</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-663"><a href="#translate_codes-663"><span class="linenos">663</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-664"><a href="#translate_codes-664"><span class="linenos">664</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-665"><a href="#translate_codes-665"><span class="linenos">665</span></a>
+</span><span id="translate_codes-666"><a href="#translate_codes-666"><span class="linenos">666</span></a> <span class="c1"># codes = pd.DataFrame([], dtype=str)</span>
+</span><span id="translate_codes-667"><a href="#translate_codes-667"><span class="linenos">667</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-668"><a href="#translate_codes-668"><span class="linenos">668</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-669"><a href="#translate_codes-669"><span class="linenos">669</span></a> <span class="p">)</span>
+</span><span id="translate_codes-670"><a href="#translate_codes-670"><span class="linenos">670</span></a> <span class="c1"># Convert codes to target type</span>
+</span><span id="translate_codes-671"><a href="#translate_codes-671"><span class="linenos">671</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-672"><a href="#translate_codes-672"><span class="linenos">672</span></a>
+</span><span id="translate_codes-673"><a href="#translate_codes-673"><span class="linenos">673</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-674"><a href="#translate_codes-674"><span class="linenos">674</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-675"><a href="#translate_codes-675"><span class="linenos">675</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-676"><a href="#translate_codes-676"><span class="linenos">676</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-677"><a href="#translate_codes-677"><span class="linenos">677</span></a> <span class="p">{</span>
+</span><span id="translate_codes-678"><a href="#translate_codes-678"><span class="linenos">678</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-679"><a href="#translate_codes-679"><span class="linenos">679</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-680"><a href="#translate_codes-680"><span class="linenos">680</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-681"><a href="#translate_codes-681"><span class="linenos">681</span></a> <span class="p">}</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 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-684"><a href="#translate_codes-684"><span class="linenos">684</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-685"><a href="#translate_codes-685"><span class="linenos">685</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-686"><a href="#translate_codes-686"><span class="linenos">686</span></a> <span class="p">)</span>
+</span><span id="translate_codes-687"><a href="#translate_codes-687"><span class="linenos">687</span></a> <span class="k">else</span><span class="p">:</span>
+</span><span id="translate_codes-688"><a href="#translate_codes-688"><span class="linenos">688</span></a> <span class="c1"># get the translation filename using source to target code types</span>
+</span><span id="translate_codes-689"><a href="#translate_codes-689"><span class="linenos">689</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-690"><a href="#translate_codes-690"><span class="linenos">690</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-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="c1"># do mapping</span>
-</span><span id="translate_codes-693"><a href="#translate_codes-693"><span class="linenos">693</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-694"><a href="#translate_codes-694"><span class="linenos">694</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-695"><a href="#translate_codes-695"><span class="linenos">695</span></a> <span class="p">)</span>
+</span><span id="translate_codes-692"><a href="#translate_codes-692"><span class="linenos">692</span></a> <span class="c1"># do the mapping if it exists</span>
+</span><span id="translate_codes-693"><a href="#translate_codes-693"><span class="linenos">693</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-694"><a href="#translate_codes-694"><span class="linenos">694</span></a> <span class="c1"># get mapping</span>
+</span><span id="translate_codes-695"><a href="#translate_codes-695"><span class="linenos">695</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-696"><a href="#translate_codes-696"><span class="linenos">696</span></a>
-</span><span id="translate_codes-697"><a href="#translate_codes-697"><span class="linenos">697</span></a> <span class="c1"># normalise the output</span>
-</span><span id="translate_codes-698"><a href="#translate_codes-698"><span class="linenos">698</span></a> <span class="n">translated_df</span><span class="o">.</span><span class="n">columns</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">Index</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-699"><a href="#translate_codes-699"><span class="linenos">699</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-700"><a href="#translate_codes-700"><span class="linenos">700</span></a>
-</span><span id="translate_codes-701"><a href="#translate_codes-701"><span class="linenos">701</span></a> <span class="c1"># add to list of codes</span>
-</span><span id="translate_codes-702"><a href="#translate_codes-702"><span class="linenos">702</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-703"><a href="#translate_codes-703"><span class="linenos">703</span></a>
-</span><span id="translate_codes-704"><a href="#translate_codes-704"><span class="linenos">704</span></a> <span class="k">else</span><span class="p">:</span>
-</span><span id="translate_codes-705"><a href="#translate_codes-705"><span class="linenos">705</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-706"><a href="#translate_codes-706"><span class="linenos">706</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-707"><a href="#translate_codes-707"><span class="linenos">707</span></a> <span class="p">)</span>
+</span><span id="translate_codes-697"><a href="#translate_codes-697"><span class="linenos">697</span></a> <span class="c1"># do mapping</span>
+</span><span id="translate_codes-698"><a href="#translate_codes-698"><span class="linenos">698</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-699"><a href="#translate_codes-699"><span class="linenos">699</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-700"><a href="#translate_codes-700"><span class="linenos">700</span></a> <span class="p">)</span>
+</span><span id="translate_codes-701"><a href="#translate_codes-701"><span class="linenos">701</span></a>
+</span><span id="translate_codes-702"><a href="#translate_codes-702"><span class="linenos">702</span></a> <span class="c1"># normalise the output</span>
+</span><span id="translate_codes-703"><a href="#translate_codes-703"><span class="linenos">703</span></a> <span class="n">translated_df</span><span class="o">.</span><span class="n">columns</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">Index</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-704"><a href="#translate_codes-704"><span class="linenos">704</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-705"><a href="#translate_codes-705"><span class="linenos">705</span></a>
+</span><span id="translate_codes-706"><a href="#translate_codes-706"><span class="linenos">706</span></a> <span class="c1"># add to list of codes</span>
+</span><span id="translate_codes-707"><a href="#translate_codes-707"><span class="linenos">707</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-708"><a href="#translate_codes-708"><span class="linenos">708</span></a>
-</span><span id="translate_codes-709"><a href="#translate_codes-709"><span class="linenos">709</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-710"><a href="#translate_codes-710"><span class="linenos">710</span></a>
-</span><span id="translate_codes-711"><a href="#translate_codes-711"><span class="linenos">711</span></a> <span class="c1"># added concept set type to output if any translations</span>
-</span><span id="translate_codes-712"><a href="#translate_codes-712"><span class="linenos">712</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-713"><a href="#translate_codes-713"><span class="linenos">713</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-714"><a href="#translate_codes-714"><span class="linenos">714</span></a> <span class="k">else</span><span class="p">:</span>
-</span><span id="translate_codes-715"><a href="#translate_codes-715"><span class="linenos">715</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-716"><a href="#translate_codes-716"><span class="linenos">716</span></a>
-</span><span id="translate_codes-717"><a href="#translate_codes-717"><span class="linenos">717</span></a> <span class="k">return</span> <span class="n">codes</span>
+</span><span id="translate_codes-709"><a href="#translate_codes-709"><span class="linenos">709</span></a> <span class="k">else</span><span class="p">:</span>
+</span><span id="translate_codes-710"><a href="#translate_codes-710"><span class="linenos">710</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-711"><a href="#translate_codes-711"><span class="linenos">711</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-712"><a href="#translate_codes-712"><span class="linenos">712</span></a> <span class="p">)</span>
+</span><span id="translate_codes-713"><a href="#translate_codes-713"><span class="linenos">713</span></a>
+</span><span id="translate_codes-714"><a href="#translate_codes-714"><span class="linenos">714</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-715"><a href="#translate_codes-715"><span class="linenos">715</span></a>
+</span><span id="translate_codes-716"><a href="#translate_codes-716"><span class="linenos">716</span></a> <span class="c1"># added concept set type to output if any translations</span>
+</span><span id="translate_codes-717"><a href="#translate_codes-717"><span class="linenos">717</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-718"><a href="#translate_codes-718"><span class="linenos">718</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-719"><a href="#translate_codes-719"><span class="linenos">719</span></a> <span class="k">else</span><span class="p">:</span>
+</span><span id="translate_codes-720"><a href="#translate_codes-720"><span class="linenos">720</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-721"><a href="#translate_codes-721"><span class="linenos">721</span></a>
+</span><span id="translate_codes-722"><a href="#translate_codes-722"><span class="linenos">722</span></a> <span class="k">return</span> <span class="n">codes</span>
</span></pre></div>
@@ -2436,43 +2450,43 @@
</div>
<a class="headerlink" href="#write_vocab_version"></a>
- <div class="pdoc-code codehilite"><pre><span></span><span id="write_vocab_version-738"><a href="#write_vocab_version-738"><span class="linenos">738</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-739"><a href="#write_vocab_version-739"><span class="linenos">739</span></a> <span class="c1"># write the vocab version files</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">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-742"><a href="#write_vocab_version-742"><span class="linenos">742</span></a> <span class="k">raise</span> <span class="ne">FileNotFoundError</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 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-744"><a href="#write_vocab_version-744"><span class="linenos">744</span></a> <span class="p">)</span>
+ <div class="pdoc-code codehilite"><pre><span></span><span id="write_vocab_version-743"><a href="#write_vocab_version-743"><span class="linenos">743</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-744"><a href="#write_vocab_version-744"><span class="linenos">744</span></a> <span class="c1"># write the vocab version files</span>
</span><span id="write_vocab_version-745"><a href="#write_vocab_version-745"><span class="linenos">745</span></a>
-</span><span id="write_vocab_version-746"><a href="#write_vocab_version-746"><span class="linenos">746</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-746"><a href="#write_vocab_version-746"><span class="linenos">746</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-747"><a href="#write_vocab_version-747"><span class="linenos">747</span></a> <span class="k">raise</span> <span class="ne">FileNotFoundError</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="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-748"><a href="#write_vocab_version-748"><span class="linenos">748</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-749"><a href="#write_vocab_version-749"><span class="linenos">749</span></a> <span class="p">)</span>
</span><span id="write_vocab_version-750"><a href="#write_vocab_version-750"><span class="linenos">750</span></a>
-</span><span id="write_vocab_version-751"><a href="#write_vocab_version-751"><span class="linenos">751</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-752"><a href="#write_vocab_version-752"><span class="linenos">752</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-753"><a href="#write_vocab_version-753"><span class="linenos">753</span></a>
-</span><span id="write_vocab_version-754"><a href="#write_vocab_version-754"><span class="linenos">754</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-755"><a href="#write_vocab_version-755"><span class="linenos">755</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-756"><a href="#write_vocab_version-756"><span class="linenos">756</span></a>
-</span><span id="write_vocab_version-757"><a href="#write_vocab_version-757"><span class="linenos">757</span></a> <span class="c1"># Create the combined YAML structure</span>
-</span><span id="write_vocab_version-758"><a href="#write_vocab_version-758"><span class="linenos">758</span></a> <span class="n">version_data</span> <span class="o">=</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="s2">"versions"</span><span class="p">:</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="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-761"><a href="#write_vocab_version-761"><span class="linenos">761</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-762"><a href="#write_vocab_version-762"><span class="linenos">762</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-763"><a href="#write_vocab_version-763"><span class="linenos">763</span></a> <span class="p">}</span>
-</span><span id="write_vocab_version-764"><a href="#write_vocab_version-764"><span class="linenos">764</span></a> <span class="p">}</span>
-</span><span id="write_vocab_version-765"><a href="#write_vocab_version-765"><span class="linenos">765</span></a>
-</span><span id="write_vocab_version-766"><a href="#write_vocab_version-766"><span class="linenos">766</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-767"><a href="#write_vocab_version-767"><span class="linenos">767</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-768"><a href="#write_vocab_version-768"><span class="linenos">768</span></a> <span class="n">version_data</span><span class="p">,</span>
-</span><span id="write_vocab_version-769"><a href="#write_vocab_version-769"><span class="linenos">769</span></a> <span class="n">file</span><span class="p">,</span>
-</span><span id="write_vocab_version-770"><a href="#write_vocab_version-770"><span class="linenos">770</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-771"><a href="#write_vocab_version-771"><span class="linenos">771</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-772"><a href="#write_vocab_version-772"><span class="linenos">772</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-773"><a href="#write_vocab_version-773"><span class="linenos">773</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-774"><a href="#write_vocab_version-774"><span class="linenos">774</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="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-752"><a href="#write_vocab_version-752"><span class="linenos">752</span></a> <span class="k">raise</span> <span class="ne">FileNotFoundError</span><span class="p">(</span>
+</span><span id="write_vocab_version-753"><a href="#write_vocab_version-753"><span class="linenos">753</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-754"><a href="#write_vocab_version-754"><span class="linenos">754</span></a> <span class="p">)</span>
+</span><span id="write_vocab_version-755"><a href="#write_vocab_version-755"><span class="linenos">755</span></a>
+</span><span id="write_vocab_version-756"><a href="#write_vocab_version-756"><span class="linenos">756</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-757"><a href="#write_vocab_version-757"><span class="linenos">757</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-758"><a href="#write_vocab_version-758"><span class="linenos">758</span></a>
+</span><span id="write_vocab_version-759"><a href="#write_vocab_version-759"><span class="linenos">759</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-760"><a href="#write_vocab_version-760"><span class="linenos">760</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-761"><a href="#write_vocab_version-761"><span class="linenos">761</span></a>
+</span><span id="write_vocab_version-762"><a href="#write_vocab_version-762"><span class="linenos">762</span></a> <span class="c1"># Create the combined YAML structure</span>
+</span><span id="write_vocab_version-763"><a href="#write_vocab_version-763"><span class="linenos">763</span></a> <span class="n">version_data</span> <span class="o">=</span> <span class="p">{</span>
+</span><span id="write_vocab_version-764"><a href="#write_vocab_version-764"><span class="linenos">764</span></a> <span class="s2">"versions"</span><span class="p">:</span> <span class="p">{</span>
+</span><span id="write_vocab_version-765"><a href="#write_vocab_version-765"><span class="linenos">765</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-766"><a href="#write_vocab_version-766"><span class="linenos">766</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-767"><a href="#write_vocab_version-767"><span class="linenos">767</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-768"><a href="#write_vocab_version-768"><span class="linenos">768</span></a> <span class="p">}</span>
+</span><span id="write_vocab_version-769"><a href="#write_vocab_version-769"><span class="linenos">769</span></a> <span class="p">}</span>
+</span><span id="write_vocab_version-770"><a href="#write_vocab_version-770"><span class="linenos">770</span></a>
+</span><span id="write_vocab_version-771"><a href="#write_vocab_version-771"><span class="linenos">771</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-772"><a href="#write_vocab_version-772"><span class="linenos">772</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-773"><a href="#write_vocab_version-773"><span class="linenos">773</span></a> <span class="n">version_data</span><span class="p">,</span>
+</span><span id="write_vocab_version-774"><a href="#write_vocab_version-774"><span class="linenos">774</span></a> <span class="n">file</span><span class="p">,</span>
+</span><span id="write_vocab_version-775"><a href="#write_vocab_version-775"><span class="linenos">775</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-776"><a href="#write_vocab_version-776"><span class="linenos">776</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-777"><a href="#write_vocab_version-777"><span class="linenos">777</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-778"><a href="#write_vocab_version-778"><span class="linenos">778</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-779"><a href="#write_vocab_version-779"><span class="linenos">779</span></a> <span class="p">)</span>
</span></pre></div>
@@ -2490,36 +2504,36 @@
</div>
<a class="headerlink" href="#map"></a>
- <div class="pdoc-code codehilite"><pre><span></span><span id="map-777"><a href="#map-777"><span class="linenos">777</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-778"><a href="#map-778"><span class="linenos">778</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-779"><a href="#map-779"><span class="linenos">779</span></a>
-</span><span id="map-780"><a href="#map-780"><span class="linenos">780</span></a> <span class="c1"># Validate configuration</span>
-</span><span id="map-781"><a href="#map-781"><span class="linenos">781</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-782"><a href="#map-782"><span class="linenos">782</span></a>
-</span><span id="map-783"><a href="#map-783"><span class="linenos">783</span></a> <span class="c1"># initialise paths</span>
-</span><span id="map-784"><a href="#map-784"><span class="linenos">784</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-785"><a href="#map-785"><span class="linenos">785</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-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="c1"># load configuration</span>
-</span><span id="map-788"><a href="#map-788"><span class="linenos">788</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-789"><a href="#map-789"><span class="linenos">789</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-790"><a href="#map-790"><span class="linenos">790</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>
+ <div class="pdoc-code codehilite"><pre><span></span><span id="map-782"><a href="#map-782"><span class="linenos">782</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-783"><a href="#map-783"><span class="linenos">783</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-784"><a href="#map-784"><span class="linenos">784</span></a>
+</span><span id="map-785"><a href="#map-785"><span class="linenos">785</span></a> <span class="c1"># Validate configuration</span>
+</span><span id="map-786"><a href="#map-786"><span class="linenos">786</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-787"><a href="#map-787"><span class="linenos">787</span></a>
+</span><span id="map-788"><a href="#map-788"><span class="linenos">788</span></a> <span class="c1"># initialise paths</span>
+</span><span id="map-789"><a href="#map-789"><span class="linenos">789</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-790"><a href="#map-790"><span class="linenos">790</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-791"><a href="#map-791"><span class="linenos">791</span></a>
-</span><span id="map-792"><a href="#map-792"><span class="linenos">792</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-793"><a href="#map-793"><span class="linenos">793</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-794"><a href="#map-794"><span class="linenos">794</span></a>
-</span><span id="map-795"><a href="#map-795"><span class="linenos">795</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-796"><a href="#map-796"><span class="linenos">796</span></a> <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span>
-</span><span id="map-797"><a href="#map-797"><span class="linenos">797</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-798"><a href="#map-798"><span class="linenos">798</span></a> <span class="p">)</span>
+</span><span id="map-792"><a href="#map-792"><span class="linenos">792</span></a> <span class="c1"># load configuration</span>
+</span><span id="map-793"><a href="#map-793"><span class="linenos">793</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-794"><a href="#map-794"><span class="linenos">794</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-795"><a href="#map-795"><span class="linenos">795</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-796"><a href="#map-796"><span class="linenos">796</span></a>
+</span><span id="map-797"><a href="#map-797"><span class="linenos">797</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-798"><a href="#map-798"><span class="linenos">798</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-799"><a href="#map-799"><span class="linenos">799</span></a>
-</span><span id="map-800"><a href="#map-800"><span class="linenos">800</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-801"><a href="#map-801"><span class="linenos">801</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-802"><a href="#map-802"><span class="linenos">802</span></a> <span class="k">else</span><span class="p">:</span>
-</span><span id="map-803"><a href="#map-803"><span class="linenos">803</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-804"><a href="#map-804"><span class="linenos">804</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-805"><a href="#map-805"><span class="linenos">805</span></a>
-</span><span id="map-806"><a href="#map-806"><span class="linenos">806</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="map-800"><a href="#map-800"><span class="linenos">800</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-801"><a href="#map-801"><span class="linenos">801</span></a> <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span>
+</span><span id="map-802"><a href="#map-802"><span class="linenos">802</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-803"><a href="#map-803"><span class="linenos">803</span></a> <span class="p">)</span>
+</span><span id="map-804"><a href="#map-804"><span class="linenos">804</span></a>
+</span><span id="map-805"><a href="#map-805"><span class="linenos">805</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-806"><a href="#map-806"><span class="linenos">806</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-807"><a href="#map-807"><span class="linenos">807</span></a> <span class="k">else</span><span class="p">:</span>
+</span><span id="map-808"><a href="#map-808"><span class="linenos">808</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-809"><a href="#map-809"><span class="linenos">809</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-810"><a href="#map-810"><span class="linenos">810</span></a>
+</span><span id="map-811"><a href="#map-811"><span class="linenos">811</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>
@@ -2537,84 +2551,84 @@
</div>
<a class="headerlink" href="#publish"></a>
- <div class="pdoc-code codehilite"><pre><span></span><span id="publish-1001"><a href="#publish-1001"><span class="linenos">1001</span></a><span class="k">def</span><span class="w"> </span><span class="nf">publish</span><span class="p">(</span>
-</span><span id="publish-1002"><a href="#publish-1002"><span class="linenos">1002</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-1003"><a href="#publish-1003"><span class="linenos">1003</span></a><span class="p">):</span>
-</span><span id="publish-1004"><a href="#publish-1004"><span class="linenos">1004</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-1005"><a href="#publish-1005"><span class="linenos">1005</span></a>
-</span><span id="publish-1006"><a href="#publish-1006"><span class="linenos">1006</span></a> <span class="c1"># Validate config</span>
-</span><span id="publish-1007"><a href="#publish-1007"><span class="linenos">1007</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-1008"><a href="#publish-1008"><span class="linenos">1008</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-1009"><a href="#publish-1009"><span class="linenos">1009</span></a>
-</span><span id="publish-1010"><a href="#publish-1010"><span class="linenos">1010</span></a> <span class="c1"># load git repo and set the branch</span>
-</span><span id="publish-1011"><a href="#publish-1011"><span class="linenos">1011</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-1012"><a href="#publish-1012"><span class="linenos">1012</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-1013"><a href="#publish-1013"><span class="linenos">1013</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-1014"><a href="#publish-1014"><span class="linenos">1014</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-1015"><a href="#publish-1015"><span class="linenos">1015</span></a> <span class="k">else</span><span class="p">:</span>
-</span><span id="publish-1016"><a href="#publish-1016"><span class="linenos">1016</span></a> <span class="k">raise</span> <span class="ne">AttributeError</span><span class="p">(</span>
-</span><span id="publish-1017"><a href="#publish-1017"><span class="linenos">1017</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-1018"><a href="#publish-1018"><span class="linenos">1018</span></a> <span class="p">)</span>
-</span><span id="publish-1019"><a href="#publish-1019"><span class="linenos">1019</span></a>
-</span><span id="publish-1020"><a href="#publish-1020"><span class="linenos">1020</span></a> <span class="c1"># check if any changes to publish</span>
-</span><span id="publish-1021"><a href="#publish-1021"><span class="linenos">1021</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-1022"><a href="#publish-1022"><span class="linenos">1022</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-1023"><a href="#publish-1023"><span class="linenos">1023</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-1024"><a href="#publish-1024"><span class="linenos">1024</span></a> <span class="k">else</span><span class="p">:</span>
-</span><span id="publish-1025"><a href="#publish-1025"><span class="linenos">1025</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-1026"><a href="#publish-1026"><span class="linenos">1026</span></a> <span class="k">return</span>
-</span><span id="publish-1027"><a href="#publish-1027"><span class="linenos">1027</span></a>
-</span><span id="publish-1028"><a href="#publish-1028"><span class="linenos">1028</span></a> <span class="c1"># get next version</span>
-</span><span id="publish-1029"><a href="#publish-1029"><span class="linenos">1029</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-1030"><a href="#publish-1030"><span class="linenos">1030</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>
+ <div class="pdoc-code codehilite"><pre><span></span><span id="publish-1013"><a href="#publish-1013"><span class="linenos">1013</span></a><span class="k">def</span><span class="w"> </span><span class="nf">publish</span><span class="p">(</span>
+</span><span id="publish-1014"><a href="#publish-1014"><span class="linenos">1014</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-1015"><a href="#publish-1015"><span class="linenos">1015</span></a><span class="p">):</span>
+</span><span id="publish-1016"><a href="#publish-1016"><span class="linenos">1016</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-1017"><a href="#publish-1017"><span class="linenos">1017</span></a>
+</span><span id="publish-1018"><a href="#publish-1018"><span class="linenos">1018</span></a> <span class="c1"># Validate config</span>
+</span><span id="publish-1019"><a href="#publish-1019"><span class="linenos">1019</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-1020"><a href="#publish-1020"><span class="linenos">1020</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-1021"><a href="#publish-1021"><span class="linenos">1021</span></a>
+</span><span id="publish-1022"><a href="#publish-1022"><span class="linenos">1022</span></a> <span class="c1"># load git repo and set the branch</span>
+</span><span id="publish-1023"><a href="#publish-1023"><span class="linenos">1023</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-1024"><a href="#publish-1024"><span class="linenos">1024</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-1025"><a href="#publish-1025"><span class="linenos">1025</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-1026"><a href="#publish-1026"><span class="linenos">1026</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-1027"><a href="#publish-1027"><span class="linenos">1027</span></a> <span class="k">else</span><span class="p">:</span>
+</span><span id="publish-1028"><a href="#publish-1028"><span class="linenos">1028</span></a> <span class="k">raise</span> <span class="ne">AttributeError</span><span class="p">(</span>
+</span><span id="publish-1029"><a href="#publish-1029"><span class="linenos">1029</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-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"># Write version in configuration file</span>
-</span><span id="publish-1033"><a href="#publish-1033"><span class="linenos">1033</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-1034"><a href="#publish-1034"><span class="linenos">1034</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-1035"><a href="#publish-1035"><span class="linenos">1035</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-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="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-1038"><a href="#publish-1038"><span class="linenos">1038</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-1039"><a href="#publish-1039"><span class="linenos">1039</span></a> <span class="n">yaml</span><span class="o">.</span><span class="n">dump</span><span class="p">(</span>
-</span><span id="publish-1040"><a href="#publish-1040"><span class="linenos">1040</span></a> <span class="n">config</span><span class="p">,</span>
-</span><span id="publish-1041"><a href="#publish-1041"><span class="linenos">1041</span></a> <span class="n">file</span><span class="p">,</span>
-</span><span id="publish-1042"><a href="#publish-1042"><span class="linenos">1042</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-1043"><a href="#publish-1043"><span class="linenos">1043</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-1044"><a href="#publish-1044"><span class="linenos">1044</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-1045"><a href="#publish-1045"><span class="linenos">1045</span></a> <span class="n">default_style</span><span class="o">=</span><span class="s1">'"'</span><span class="p">,</span>
-</span><span id="publish-1046"><a href="#publish-1046"><span class="linenos">1046</span></a> <span class="p">)</span>
-</span><span id="publish-1047"><a href="#publish-1047"><span class="linenos">1047</span></a>
-</span><span id="publish-1048"><a href="#publish-1048"><span class="linenos">1048</span></a> <span class="c1"># Add and commit changes to repo including version updates</span>
-</span><span id="publish-1049"><a href="#publish-1049"><span class="linenos">1049</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-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">add</span><span class="p">(</span><span class="s2">"--all"</span><span class="p">)</span>
-</span><span id="publish-1051"><a href="#publish-1051"><span class="linenos">1051</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-1052"><a href="#publish-1052"><span class="linenos">1052</span></a>
-</span><span id="publish-1053"><a href="#publish-1053"><span class="linenos">1053</span></a> <span class="c1"># Add tag to the repo</span>
-</span><span id="publish-1054"><a href="#publish-1054"><span class="linenos">1054</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-1055"><a href="#publish-1055"><span class="linenos">1055</span></a>
-</span><span id="publish-1056"><a href="#publish-1056"><span class="linenos">1056</span></a> <span class="c1"># push to origin if a remote repo</span>
-</span><span id="publish-1057"><a href="#publish-1057"><span class="linenos">1057</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-1058"><a href="#publish-1058"><span class="linenos">1058</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-1059"><a href="#publish-1059"><span class="linenos">1059</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-1060"><a href="#publish-1060"><span class="linenos">1060</span></a>
-</span><span id="publish-1061"><a href="#publish-1061"><span class="linenos">1061</span></a> <span class="k">try</span><span class="p">:</span>
-</span><span id="publish-1062"><a href="#publish-1062"><span class="linenos">1062</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-1063"><a href="#publish-1063"><span class="linenos">1063</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-1064"><a href="#publish-1064"><span class="linenos">1064</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-1065"><a href="#publish-1065"><span class="linenos">1065</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-1066"><a href="#publish-1066"><span class="linenos">1066</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-1067"><a href="#publish-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">"Pushing version tags to remote git repo"</span><span class="p">)</span>
-</span><span id="publish-1068"><a href="#publish-1068"><span class="linenos">1068</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-1069"><a href="#publish-1069"><span class="linenos">1069</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-1070"><a href="#publish-1070"><span class="linenos">1070</span></a> <span class="k">else</span><span class="p">:</span>
-</span><span id="publish-1071"><a href="#publish-1071"><span class="linenos">1071</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-1072"><a href="#publish-1072"><span class="linenos">1072</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-1073"><a href="#publish-1073"><span class="linenos">1073</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-1074"><a href="#publish-1074"><span class="linenos">1074</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-1075"><a href="#publish-1075"><span class="linenos">1075</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-1076"><a href="#publish-1076"><span class="linenos">1076</span></a> <span class="k">raise</span> <span class="n">e</span>
-</span><span id="publish-1077"><a href="#publish-1077"><span class="linenos">1077</span></a>
-</span><span id="publish-1078"><a href="#publish-1078"><span class="linenos">1078</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="publish-1032"><a href="#publish-1032"><span class="linenos">1032</span></a> <span class="c1"># check if any changes to publish</span>
+</span><span id="publish-1033"><a href="#publish-1033"><span class="linenos">1033</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-1034"><a href="#publish-1034"><span class="linenos">1034</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-1035"><a href="#publish-1035"><span class="linenos">1035</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-1036"><a href="#publish-1036"><span class="linenos">1036</span></a> <span class="k">else</span><span class="p">:</span>
+</span><span id="publish-1037"><a href="#publish-1037"><span class="linenos">1037</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-1038"><a href="#publish-1038"><span class="linenos">1038</span></a> <span class="k">return</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"># get next version</span>
+</span><span id="publish-1041"><a href="#publish-1041"><span class="linenos">1041</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-1042"><a href="#publish-1042"><span class="linenos">1042</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-1043"><a href="#publish-1043"><span class="linenos">1043</span></a>
+</span><span id="publish-1044"><a href="#publish-1044"><span class="linenos">1044</span></a> <span class="c1"># Write version in configuration file</span>
+</span><span id="publish-1045"><a href="#publish-1045"><span class="linenos">1045</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-1046"><a href="#publish-1046"><span class="linenos">1046</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-1047"><a href="#publish-1047"><span class="linenos">1047</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-1048"><a href="#publish-1048"><span class="linenos">1048</span></a>
+</span><span id="publish-1049"><a href="#publish-1049"><span class="linenos">1049</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-1050"><a href="#publish-1050"><span class="linenos">1050</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-1051"><a href="#publish-1051"><span class="linenos">1051</span></a> <span class="n">yaml</span><span class="o">.</span><span class="n">dump</span><span class="p">(</span>
+</span><span id="publish-1052"><a href="#publish-1052"><span class="linenos">1052</span></a> <span class="n">config</span><span class="p">,</span>
+</span><span id="publish-1053"><a href="#publish-1053"><span class="linenos">1053</span></a> <span class="n">file</span><span class="p">,</span>
+</span><span id="publish-1054"><a href="#publish-1054"><span class="linenos">1054</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-1055"><a href="#publish-1055"><span class="linenos">1055</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-1056"><a href="#publish-1056"><span class="linenos">1056</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-1057"><a href="#publish-1057"><span class="linenos">1057</span></a> <span class="n">default_style</span><span class="o">=</span><span class="s1">'"'</span><span class="p">,</span>
+</span><span id="publish-1058"><a href="#publish-1058"><span class="linenos">1058</span></a> <span class="p">)</span>
+</span><span id="publish-1059"><a href="#publish-1059"><span class="linenos">1059</span></a>
+</span><span id="publish-1060"><a href="#publish-1060"><span class="linenos">1060</span></a> <span class="c1"># Add and commit changes to repo including version updates</span>
+</span><span id="publish-1061"><a href="#publish-1061"><span class="linenos">1061</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-1062"><a href="#publish-1062"><span class="linenos">1062</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-1063"><a href="#publish-1063"><span class="linenos">1063</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-1064"><a href="#publish-1064"><span class="linenos">1064</span></a>
+</span><span id="publish-1065"><a href="#publish-1065"><span class="linenos">1065</span></a> <span class="c1"># Add tag to the repo</span>
+</span><span id="publish-1066"><a href="#publish-1066"><span class="linenos">1066</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-1067"><a href="#publish-1067"><span class="linenos">1067</span></a>
+</span><span id="publish-1068"><a href="#publish-1068"><span class="linenos">1068</span></a> <span class="c1"># push to origin if a remote repo</span>
+</span><span id="publish-1069"><a href="#publish-1069"><span class="linenos">1069</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-1070"><a href="#publish-1070"><span class="linenos">1070</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-1071"><a href="#publish-1071"><span class="linenos">1071</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-1072"><a href="#publish-1072"><span class="linenos">1072</span></a>
+</span><span id="publish-1073"><a href="#publish-1073"><span class="linenos">1073</span></a> <span class="k">try</span><span class="p">:</span>
+</span><span id="publish-1074"><a href="#publish-1074"><span class="linenos">1074</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-1075"><a href="#publish-1075"><span class="linenos">1075</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-1076"><a href="#publish-1076"><span class="linenos">1076</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-1077"><a href="#publish-1077"><span class="linenos">1077</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-1078"><a href="#publish-1078"><span class="linenos">1078</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-1079"><a href="#publish-1079"><span class="linenos">1079</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-1080"><a href="#publish-1080"><span class="linenos">1080</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-1081"><a href="#publish-1081"><span class="linenos">1081</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-1082"><a href="#publish-1082"><span class="linenos">1082</span></a> <span class="k">else</span><span class="p">:</span>
+</span><span id="publish-1083"><a href="#publish-1083"><span class="linenos">1083</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-1084"><a href="#publish-1084"><span class="linenos">1084</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-1085"><a href="#publish-1085"><span class="linenos">1085</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-1086"><a href="#publish-1086"><span class="linenos">1086</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-1087"><a href="#publish-1087"><span class="linenos">1087</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-1088"><a href="#publish-1088"><span class="linenos">1088</span></a> <span class="k">raise</span> <span class="n">e</span>
+</span><span id="publish-1089"><a href="#publish-1089"><span class="linenos">1089</span></a>
+</span><span id="publish-1090"><a href="#publish-1090"><span class="linenos">1090</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>
@@ -2634,40 +2648,40 @@
</div>
<a class="headerlink" href="#export"></a>
- <div class="pdoc-code codehilite"><pre><span></span><span id="export-1081"><a href="#export-1081"><span class="linenos">1081</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-1082"><a href="#export-1082"><span class="linenos">1082</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-1083"><a href="#export-1083"><span class="linenos">1083</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-1084"><a href="#export-1084"><span class="linenos">1084</span></a>
-</span><span id="export-1085"><a href="#export-1085"><span class="linenos">1085</span></a> <span class="c1"># validate configuration</span>
-</span><span id="export-1086"><a href="#export-1086"><span class="linenos">1086</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-1087"><a href="#export-1087"><span class="linenos">1087</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-1088"><a href="#export-1088"><span class="linenos">1088</span></a>
-</span><span id="export-1089"><a href="#export-1089"><span class="linenos">1089</span></a> <span class="c1"># load configuration</span>
-</span><span id="export-1090"><a href="#export-1090"><span class="linenos">1090</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-1091"><a href="#export-1091"><span class="linenos">1091</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-1092"><a href="#export-1092"><span class="linenos">1092</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-1093"><a href="#export-1093"><span class="linenos">1093</span></a>
-</span><span id="export-1094"><a href="#export-1094"><span class="linenos">1094</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-1095"><a href="#export-1095"><span class="linenos">1095</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-1096"><a href="#export-1096"><span class="linenos">1096</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-1097"><a href="#export-1097"><span class="linenos">1097</span></a>
-</span><span id="export-1098"><a href="#export-1098"><span class="linenos">1098</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-1099"><a href="#export-1099"><span class="linenos">1099</span></a> <span class="c1"># check export directory exists and if not create it</span>
-</span><span id="export-1100"><a href="#export-1100"><span class="linenos">1100</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-1101"><a href="#export-1101"><span class="linenos">1101</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-1102"><a href="#export-1102"><span class="linenos">1102</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-1103"><a href="#export-1103"><span class="linenos">1103</span></a>
-</span><span id="export-1104"><a href="#export-1104"><span class="linenos">1104</span></a> <span class="c1"># omop export db</span>
-</span><span id="export-1105"><a href="#export-1105"><span class="linenos">1105</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-1106"><a href="#export-1106"><span class="linenos">1106</span></a> <span class="n">map_path</span><span class="p">,</span>
-</span><span id="export-1107"><a href="#export-1107"><span class="linenos">1107</span></a> <span class="n">export_path</span><span class="p">,</span>
-</span><span id="export-1108"><a href="#export-1108"><span class="linenos">1108</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-1109"><a href="#export-1109"><span class="linenos">1109</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-1110"><a href="#export-1110"><span class="linenos">1110</span></a> <span class="p">)</span>
-</span><span id="export-1111"><a href="#export-1111"><span class="linenos">1111</span></a>
-</span><span id="export-1112"><a href="#export-1112"><span class="linenos">1112</span></a> <span class="c1"># write to tables</span>
-</span><span id="export-1113"><a href="#export-1113"><span class="linenos">1113</span></a> <span class="c1"># export as csv</span>
-</span><span id="export-1114"><a href="#export-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">"Phenotype exported successfully"</span><span class="p">)</span>
+ <div class="pdoc-code codehilite"><pre><span></span><span id="export-1093"><a href="#export-1093"><span class="linenos">1093</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-1094"><a href="#export-1094"><span class="linenos">1094</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-1095"><a href="#export-1095"><span class="linenos">1095</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-1096"><a href="#export-1096"><span class="linenos">1096</span></a>
+</span><span id="export-1097"><a href="#export-1097"><span class="linenos">1097</span></a> <span class="c1"># validate configuration</span>
+</span><span id="export-1098"><a href="#export-1098"><span class="linenos">1098</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-1099"><a href="#export-1099"><span class="linenos">1099</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-1100"><a href="#export-1100"><span class="linenos">1100</span></a>
+</span><span id="export-1101"><a href="#export-1101"><span class="linenos">1101</span></a> <span class="c1"># load configuration</span>
+</span><span id="export-1102"><a href="#export-1102"><span class="linenos">1102</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-1103"><a href="#export-1103"><span class="linenos">1103</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-1104"><a href="#export-1104"><span class="linenos">1104</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-1105"><a href="#export-1105"><span class="linenos">1105</span></a>
+</span><span id="export-1106"><a href="#export-1106"><span class="linenos">1106</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-1107"><a href="#export-1107"><span class="linenos">1107</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-1108"><a href="#export-1108"><span class="linenos">1108</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-1109"><a href="#export-1109"><span class="linenos">1109</span></a>
+</span><span id="export-1110"><a href="#export-1110"><span class="linenos">1110</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-1111"><a href="#export-1111"><span class="linenos">1111</span></a> <span class="c1"># check export directory exists and if not create it</span>
+</span><span id="export-1112"><a href="#export-1112"><span class="linenos">1112</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-1113"><a href="#export-1113"><span class="linenos">1113</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-1114"><a href="#export-1114"><span class="linenos">1114</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-1115"><a href="#export-1115"><span class="linenos">1115</span></a>
+</span><span id="export-1116"><a href="#export-1116"><span class="linenos">1116</span></a> <span class="c1"># omop export db</span>
+</span><span id="export-1117"><a href="#export-1117"><span class="linenos">1117</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-1118"><a href="#export-1118"><span class="linenos">1118</span></a> <span class="n">map_path</span><span class="p">,</span>
+</span><span id="export-1119"><a href="#export-1119"><span class="linenos">1119</span></a> <span class="n">export_path</span><span class="p">,</span>
+</span><span id="export-1120"><a href="#export-1120"><span class="linenos">1120</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-1121"><a href="#export-1121"><span class="linenos">1121</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-1122"><a href="#export-1122"><span class="linenos">1122</span></a> <span class="p">)</span>
+</span><span id="export-1123"><a href="#export-1123"><span class="linenos">1123</span></a>
+</span><span id="export-1124"><a href="#export-1124"><span class="linenos">1124</span></a> <span class="c1"># write to tables</span>
+</span><span id="export-1125"><a href="#export-1125"><span class="linenos">1125</span></a> <span class="c1"># export as csv</span>
+</span><span id="export-1126"><a href="#export-1126"><span class="linenos">1126</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>
@@ -2687,52 +2701,52 @@
</div>
<a class="headerlink" href="#copy"></a>
- <div class="pdoc-code codehilite"><pre><span></span><span id="copy-1117"><a href="#copy-1117"><span class="linenos">1117</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-1118"><a href="#copy-1118"><span class="linenos">1118</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-1119"><a href="#copy-1119"><span class="linenos">1119</span></a>
-</span><span id="copy-1120"><a href="#copy-1120"><span class="linenos">1120</span></a> <span class="c1"># Validate</span>
-</span><span id="copy-1121"><a href="#copy-1121"><span class="linenos">1121</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-1122"><a href="#copy-1122"><span class="linenos">1122</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-1123"><a href="#copy-1123"><span class="linenos">1123</span></a>
-</span><span id="copy-1124"><a href="#copy-1124"><span class="linenos">1124</span></a> <span class="c1"># Check target directory exists</span>
-</span><span id="copy-1125"><a href="#copy-1125"><span class="linenos">1125</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-1126"><a href="#copy-1126"><span class="linenos">1126</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-1127"><a href="#copy-1127"><span class="linenos">1127</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-1128"><a href="#copy-1128"><span class="linenos">1128</span></a>
-</span><span id="copy-1129"><a href="#copy-1129"><span class="linenos">1129</span></a> <span class="c1"># Set copy directory</span>
-</span><span id="copy-1130"><a href="#copy-1130"><span class="linenos">1130</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-1131"><a href="#copy-1131"><span class="linenos">1131</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-1132"><a href="#copy-1132"><span class="linenos">1132</span></a>
-</span><span id="copy-1133"><a href="#copy-1133"><span class="linenos">1133</span></a> <span class="k">if</span> <span class="p">(</span>
-</span><span id="copy-1134"><a href="#copy-1134"><span class="linenos">1134</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-1135"><a href="#copy-1135"><span class="linenos">1135</span></a> <span class="p">):</span> <span class="c1"># Check if it exists and is a directory</span>
-</span><span id="copy-1136"><a href="#copy-1136"><span class="linenos">1136</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-1137"><a href="#copy-1137"><span class="linenos">1137</span></a> <span class="n">copy_path</span><span class="p">,</span>
-</span><span id="copy-1138"><a href="#copy-1138"><span class="linenos">1138</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-1139"><a href="#copy-1139"><span class="linenos">1139</span></a> <span class="p">)</span>
-</span><span id="copy-1140"><a href="#copy-1140"><span class="linenos">1140</span></a> <span class="k">else</span><span class="p">:</span>
-</span><span id="copy-1141"><a href="#copy-1141"><span class="linenos">1141</span></a> <span class="n">copy</span> <span class="o">=</span> <span class="kc">True</span>
-</span><span id="copy-1142"><a href="#copy-1142"><span class="linenos">1142</span></a>
-</span><span id="copy-1143"><a href="#copy-1143"><span class="linenos">1143</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-1144"><a href="#copy-1144"><span class="linenos">1144</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-1145"><a href="#copy-1145"><span class="linenos">1145</span></a> <span class="k">return</span>
-</span><span id="copy-1146"><a href="#copy-1146"><span class="linenos">1146</span></a>
-</span><span id="copy-1147"><a href="#copy-1147"><span class="linenos">1147</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-1148"><a href="#copy-1148"><span class="linenos">1148</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-1149"><a href="#copy-1149"><span class="linenos">1149</span></a>
-</span><span id="copy-1150"><a href="#copy-1150"><span class="linenos">1150</span></a> <span class="c1"># Check out the latest commit or specified version</span>
-</span><span id="copy-1151"><a href="#copy-1151"><span class="linenos">1151</span></a> <span class="k">if</span> <span class="n">version</span><span class="p">:</span>
-</span><span id="copy-1152"><a href="#copy-1152"><span class="linenos">1152</span></a> <span class="c1"># Checkout a specific version (e.g., branch, tag, or commit hash)</span>
-</span><span id="copy-1153"><a href="#copy-1153"><span class="linenos">1153</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-1154"><a href="#copy-1154"><span class="linenos">1154</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-1155"><a href="#copy-1155"><span class="linenos">1155</span></a> <span class="k">else</span><span class="p">:</span>
-</span><span id="copy-1156"><a href="#copy-1156"><span class="linenos">1156</span></a> <span class="c1"># Checkout the latest commit (HEAD)</span>
-</span><span id="copy-1157"><a href="#copy-1157"><span class="linenos">1157</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-1158"><a href="#copy-1158"><span class="linenos">1158</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-1159"><a href="#copy-1159"><span class="linenos">1159</span></a>
-</span><span id="copy-1160"><a href="#copy-1160"><span class="linenos">1160</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>
+ <div class="pdoc-code codehilite"><pre><span></span><span id="copy-1129"><a href="#copy-1129"><span class="linenos">1129</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-1130"><a href="#copy-1130"><span class="linenos">1130</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-1131"><a href="#copy-1131"><span class="linenos">1131</span></a>
+</span><span id="copy-1132"><a href="#copy-1132"><span class="linenos">1132</span></a> <span class="c1"># Validate</span>
+</span><span id="copy-1133"><a href="#copy-1133"><span class="linenos">1133</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-1134"><a href="#copy-1134"><span class="linenos">1134</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-1135"><a href="#copy-1135"><span class="linenos">1135</span></a>
+</span><span id="copy-1136"><a href="#copy-1136"><span class="linenos">1136</span></a> <span class="c1"># Check target directory exists</span>
+</span><span id="copy-1137"><a href="#copy-1137"><span class="linenos">1137</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-1138"><a href="#copy-1138"><span class="linenos">1138</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-1139"><a href="#copy-1139"><span class="linenos">1139</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-1140"><a href="#copy-1140"><span class="linenos">1140</span></a>
+</span><span id="copy-1141"><a href="#copy-1141"><span class="linenos">1141</span></a> <span class="c1"># Set copy directory</span>
+</span><span id="copy-1142"><a href="#copy-1142"><span class="linenos">1142</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-1143"><a href="#copy-1143"><span class="linenos">1143</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-1144"><a href="#copy-1144"><span class="linenos">1144</span></a>
+</span><span id="copy-1145"><a href="#copy-1145"><span class="linenos">1145</span></a> <span class="k">if</span> <span class="p">(</span>
+</span><span id="copy-1146"><a href="#copy-1146"><span class="linenos">1146</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-1147"><a href="#copy-1147"><span class="linenos">1147</span></a> <span class="p">):</span> <span class="c1"># Check if it exists and is a directory</span>
+</span><span id="copy-1148"><a href="#copy-1148"><span class="linenos">1148</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-1149"><a href="#copy-1149"><span class="linenos">1149</span></a> <span class="n">copy_path</span><span class="p">,</span>
+</span><span id="copy-1150"><a href="#copy-1150"><span class="linenos">1150</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-1151"><a href="#copy-1151"><span class="linenos">1151</span></a> <span class="p">)</span>
+</span><span id="copy-1152"><a href="#copy-1152"><span class="linenos">1152</span></a> <span class="k">else</span><span class="p">:</span>
+</span><span id="copy-1153"><a href="#copy-1153"><span class="linenos">1153</span></a> <span class="n">copy</span> <span class="o">=</span> <span class="kc">True</span>
+</span><span id="copy-1154"><a href="#copy-1154"><span class="linenos">1154</span></a>
+</span><span id="copy-1155"><a href="#copy-1155"><span class="linenos">1155</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-1156"><a href="#copy-1156"><span class="linenos">1156</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-1157"><a href="#copy-1157"><span class="linenos">1157</span></a> <span class="k">return</span>
+</span><span id="copy-1158"><a href="#copy-1158"><span class="linenos">1158</span></a>
+</span><span id="copy-1159"><a href="#copy-1159"><span class="linenos">1159</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-1160"><a href="#copy-1160"><span class="linenos">1160</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-1161"><a href="#copy-1161"><span class="linenos">1161</span></a>
-</span><span id="copy-1162"><a href="#copy-1162"><span class="linenos">1162</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="copy-1162"><a href="#copy-1162"><span class="linenos">1162</span></a> <span class="c1"># Check out the latest commit or specified version</span>
+</span><span id="copy-1163"><a href="#copy-1163"><span class="linenos">1163</span></a> <span class="k">if</span> <span class="n">version</span><span class="p">:</span>
+</span><span id="copy-1164"><a href="#copy-1164"><span class="linenos">1164</span></a> <span class="c1"># Checkout a specific version (e.g., branch, tag, or commit hash)</span>
+</span><span id="copy-1165"><a href="#copy-1165"><span class="linenos">1165</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-1166"><a href="#copy-1166"><span class="linenos">1166</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-1167"><a href="#copy-1167"><span class="linenos">1167</span></a> <span class="k">else</span><span class="p">:</span>
+</span><span id="copy-1168"><a href="#copy-1168"><span class="linenos">1168</span></a> <span class="c1"># Checkout the latest commit (HEAD)</span>
+</span><span id="copy-1169"><a href="#copy-1169"><span class="linenos">1169</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-1170"><a href="#copy-1170"><span class="linenos">1170</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-1171"><a href="#copy-1171"><span class="linenos">1171</span></a>
+</span><span id="copy-1172"><a href="#copy-1172"><span class="linenos">1172</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-1173"><a href="#copy-1173"><span class="linenos">1173</span></a>
+</span><span id="copy-1174"><a href="#copy-1174"><span class="linenos">1174</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>
@@ -2752,14 +2766,15 @@
</div>
<a class="headerlink" href="#extract_concepts"></a>
- <div class="pdoc-code codehilite"><pre><span></span><span id="extract_concepts-1166"><a href="#extract_concepts-1166"><span class="linenos">1166</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-1167"><a href="#extract_concepts-1167"><span class="linenos">1167</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-1168"><a href="#extract_concepts-1168"><span class="linenos">1168</span></a> <span class="n">concepts_dict</span> <span class="o">=</span> <span class="p">{</span>
-</span><span id="extract_concepts-1169"><a href="#extract_concepts-1169"><span class="linenos">1169</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-1170"><a href="#extract_concepts-1170"><span class="linenos">1170</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-1171"><a href="#extract_concepts-1171"><span class="linenos">1171</span></a> <span class="p">}</span>
-</span><span id="extract_concepts-1172"><a href="#extract_concepts-1172"><span class="linenos">1172</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-1173"><a href="#extract_concepts-1173"><span class="linenos">1173</span></a> <span class="k">return</span> <span class="n">concepts_dict</span><span class="p">,</span> <span class="n">name_set</span>
+ <div class="pdoc-code codehilite"><pre><span></span><span id="extract_concepts-1178"><a href="#extract_concepts-1178"><span class="linenos">1178</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-1179"><a href="#extract_concepts-1179"><span class="linenos">1179</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-1180"><a href="#extract_concepts-1180"><span class="linenos">1180</span></a> <span class="n">concepts_dict</span> <span class="o">=</span> <span class="p">{</span>
+</span><span id="extract_concepts-1181"><a href="#extract_concepts-1181"><span class="linenos">1181</span></a> <span class="n">item</span><span class="p">[</span><span class="s2">"name"</span><span class="p">]:</span> <span class="p">[</span><span class="n">file</span><span class="p">[</span><span class="s2">"path"</span><span class="p">]</span> <span class="k">for</span> <span class="n">file</span> <span class="ow">in</span> <span class="n">item</span><span class="p">[</span><span class="s2">"files"</span><span class="p">]]</span>
+</span><span id="extract_concepts-1182"><a href="#extract_concepts-1182"><span class="linenos">1182</span></a> <span class="c1"># item["name"]: item["file"]["path"]</span>
+</span><span id="extract_concepts-1183"><a href="#extract_concepts-1183"><span class="linenos">1183</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-1184"><a href="#extract_concepts-1184"><span class="linenos">1184</span></a> <span class="p">}</span>
+</span><span id="extract_concepts-1185"><a href="#extract_concepts-1185"><span class="linenos">1185</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-1186"><a href="#extract_concepts-1186"><span class="linenos">1186</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>
@@ -2779,79 +2794,79 @@
</div>
<a class="headerlink" href="#diff_config"></a>
- <div class="pdoc-code codehilite"><pre><span></span><span id="diff_config-1187"><a href="#diff_config-1187"><span class="linenos">1187</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-1188"><a href="#diff_config-1188"><span class="linenos">1188</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-1189"><a href="#diff_config-1189"><span class="linenos">1189</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-1190"><a href="#diff_config-1190"><span class="linenos">1190</span></a>
-</span><span id="diff_config-1191"><a href="#diff_config-1191"><span class="linenos">1191</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-1192"><a href="#diff_config-1192"><span class="linenos">1192</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-1193"><a href="#diff_config-1193"><span class="linenos">1193</span></a>
-</span><span id="diff_config-1194"><a href="#diff_config-1194"><span class="linenos">1194</span></a> <span class="c1"># Check added and removed names</span>
-</span><span id="diff_config-1195"><a href="#diff_config-1195"><span class="linenos">1195</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-1196"><a href="#diff_config-1196"><span class="linenos">1196</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-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"># find file path changes for unchanged names</span>
-</span><span id="diff_config-1199"><a href="#diff_config-1199"><span class="linenos">1199</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-1200"><a href="#diff_config-1200"><span class="linenos">1200</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-1201"><a href="#diff_config-1201"><span class="linenos">1201</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-1202"><a href="#diff_config-1202"><span class="linenos">1202</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-1203"><a href="#diff_config-1203"><span class="linenos">1203</span></a> <span class="p">)</span>
-</span><span id="diff_config-1204"><a href="#diff_config-1204"><span class="linenos">1204</span></a>
-</span><span id="diff_config-1205"><a href="#diff_config-1205"><span class="linenos">1205</span></a> <span class="c1"># Find renamed concepts (same file, different name)</span>
-</span><span id="diff_config-1206"><a href="#diff_config-1206"><span class="linenos">1206</span></a> <span class="n">renamed_concepts</span> <span class="o">=</span> <span class="p">[]</span>
-</span><span id="diff_config-1207"><a href="#diff_config-1207"><span class="linenos">1207</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-1208"><a href="#diff_config-1208"><span class="linenos">1208</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-1209"><a href="#diff_config-1209"><span class="linenos">1209</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-1210"><a href="#diff_config-1210"><span class="linenos">1210</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-1211"><a href="#diff_config-1211"><span class="linenos">1211</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-1212"><a href="#diff_config-1212"><span class="linenos">1212</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-1213"><a href="#diff_config-1213"><span class="linenos">1213</span></a>
-</span><span id="diff_config-1214"><a href="#diff_config-1214"><span class="linenos">1214</span></a> <span class="c1"># Remove renamed concepts from added and removed sets</span>
-</span><span id="diff_config-1215"><a href="#diff_config-1215"><span class="linenos">1215</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-1216"><a href="#diff_config-1216"><span class="linenos">1216</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-1217"><a href="#diff_config-1217"><span class="linenos">1217</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-1218"><a href="#diff_config-1218"><span class="linenos">1218</span></a>
-</span><span id="diff_config-1219"><a href="#diff_config-1219"><span class="linenos">1219</span></a> <span class="c1"># generate config report</span>
-</span><span id="diff_config-1220"><a href="#diff_config-1220"><span class="linenos">1220</span></a> <span class="k">if</span> <span class="n">added_names</span><span class="p">:</span>
-</span><span id="diff_config-1221"><a href="#diff_config-1221"><span class="linenos">1221</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-1222"><a href="#diff_config-1222"><span class="linenos">1222</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-1223"><a href="#diff_config-1223"><span class="linenos">1223</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-1224"><a href="#diff_config-1224"><span class="linenos">1224</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-1225"><a href="#diff_config-1225"><span class="linenos">1225</span></a>
-</span><span id="diff_config-1226"><a href="#diff_config-1226"><span class="linenos">1226</span></a> <span class="k">if</span> <span class="n">removed_names</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">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-1228"><a href="#diff_config-1228"><span class="linenos">1228</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-1229"><a href="#diff_config-1229"><span class="linenos">1229</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-1230"><a href="#diff_config-1230"><span class="linenos">1230</span></a> <span class="n">report</span> <span class="o">+=</span> <span class="s2">"</span><span class="se">\n</span><span class="s2">"</span>
+ <div class="pdoc-code codehilite"><pre><span></span><span id="diff_config-1200"><a href="#diff_config-1200"><span class="linenos">1200</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-1201"><a href="#diff_config-1201"><span class="linenos">1201</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-1202"><a href="#diff_config-1202"><span class="linenos">1202</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-1203"><a href="#diff_config-1203"><span class="linenos">1203</span></a>
+</span><span id="diff_config-1204"><a href="#diff_config-1204"><span class="linenos">1204</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-1205"><a href="#diff_config-1205"><span class="linenos">1205</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-1206"><a href="#diff_config-1206"><span class="linenos">1206</span></a>
+</span><span id="diff_config-1207"><a href="#diff_config-1207"><span class="linenos">1207</span></a> <span class="c1"># Check added and removed concept set names</span>
+</span><span id="diff_config-1208"><a href="#diff_config-1208"><span class="linenos">1208</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-1209"><a href="#diff_config-1209"><span class="linenos">1209</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-1210"><a href="#diff_config-1210"><span class="linenos">1210</span></a>
+</span><span id="diff_config-1211"><a href="#diff_config-1211"><span class="linenos">1211</span></a> <span class="c1"># find file path changes for unchanged names</span>
+</span><span id="diff_config-1212"><a href="#diff_config-1212"><span class="linenos">1212</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-1213"><a href="#diff_config-1213"><span class="linenos">1213</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-1214"><a href="#diff_config-1214"><span class="linenos">1214</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-1215"><a href="#diff_config-1215"><span class="linenos">1215</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-1216"><a href="#diff_config-1216"><span class="linenos">1216</span></a> <span class="p">)</span>
+</span><span id="diff_config-1217"><a href="#diff_config-1217"><span class="linenos">1217</span></a>
+</span><span id="diff_config-1218"><a href="#diff_config-1218"><span class="linenos">1218</span></a> <span class="c1"># Find renamed concepts (same file, different name)</span>
+</span><span id="diff_config-1219"><a href="#diff_config-1219"><span class="linenos">1219</span></a> <span class="n">renamed_concepts</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="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-1221"><a href="#diff_config-1221"><span class="linenos">1221</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-1222"><a href="#diff_config-1222"><span class="linenos">1222</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-1223"><a href="#diff_config-1223"><span class="linenos">1223</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-1224"><a href="#diff_config-1224"><span class="linenos">1224</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-1225"><a href="#diff_config-1225"><span class="linenos">1225</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-1226"><a href="#diff_config-1226"><span class="linenos">1226</span></a>
+</span><span id="diff_config-1227"><a href="#diff_config-1227"><span class="linenos">1227</span></a> <span class="c1"># Remove renamed concepts from added and removed sets</span>
+</span><span id="diff_config-1228"><a href="#diff_config-1228"><span class="linenos">1228</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-1229"><a href="#diff_config-1229"><span class="linenos">1229</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-1230"><a href="#diff_config-1230"><span class="linenos">1230</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-1231"><a href="#diff_config-1231"><span class="linenos">1231</span></a>
-</span><span id="diff_config-1232"><a href="#diff_config-1232"><span class="linenos">1232</span></a> <span class="k">if</span> <span class="n">renamed_concepts</span><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">"## Renamed Concepts</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 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-1235"><a href="#diff_config-1235"><span class="linenos">1235</span></a> <span class="n">report</span> <span class="o">+=</span> <span class="p">(</span>
-</span><span id="diff_config-1236"><a href="#diff_config-1236"><span class="linenos">1236</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">` ➝ `</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-1237"><a href="#diff_config-1237"><span class="linenos">1237</span></a> <span class="p">)</span>
-</span><span id="diff_config-1238"><a href="#diff_config-1238"><span class="linenos">1238</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-1239"><a href="#diff_config-1239"><span class="linenos">1239</span></a>
-</span><span id="diff_config-1240"><a href="#diff_config-1240"><span class="linenos">1240</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-1241"><a href="#diff_config-1241"><span class="linenos">1241</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-1242"><a href="#diff_config-1242"><span class="linenos">1242</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-1243"><a href="#diff_config-1243"><span class="linenos">1243</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-1244"><a href="#diff_config-1244"><span class="linenos">1244</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-1245"><a href="#diff_config-1245"><span class="linenos">1245</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-1246"><a href="#diff_config-1246"><span class="linenos">1246</span></a> <span class="n">report</span> <span class="o">+=</span> <span class="p">(</span>
-</span><span id="diff_config-1247"><a href="#diff_config-1247"><span class="linenos">1247</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">` ➝ `</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-1248"><a href="#diff_config-1248"><span class="linenos">1248</span></a> <span class="p">)</span>
-</span><span id="diff_config-1249"><a href="#diff_config-1249"><span class="linenos">1249</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-1250"><a href="#diff_config-1250"><span class="linenos">1250</span></a>
-</span><span id="diff_config-1251"><a href="#diff_config-1251"><span class="linenos">1251</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="p">(</span>
-</span><span id="diff_config-1252"><a href="#diff_config-1252"><span class="linenos">1252</span></a> <span class="n">added_names</span>
-</span><span id="diff_config-1253"><a href="#diff_config-1253"><span class="linenos">1253</span></a> <span class="ow">or</span> <span class="n">removed_names</span>
-</span><span id="diff_config-1254"><a href="#diff_config-1254"><span class="linenos">1254</span></a> <span class="ow">or</span> <span class="n">renamed_concepts</span>
-</span><span id="diff_config-1255"><a href="#diff_config-1255"><span class="linenos">1255</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-1256"><a href="#diff_config-1256"><span class="linenos">1256</span></a> <span class="p">):</span>
-</span><span id="diff_config-1257"><a href="#diff_config-1257"><span class="linenos">1257</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-1258"><a href="#diff_config-1258"><span class="linenos">1258</span></a>
-</span><span id="diff_config-1259"><a href="#diff_config-1259"><span class="linenos">1259</span></a> <span class="k">return</span> <span class="n">report</span>
+</span><span id="diff_config-1232"><a href="#diff_config-1232"><span class="linenos">1232</span></a> <span class="c1"># generate config report</span>
+</span><span id="diff_config-1233"><a href="#diff_config-1233"><span class="linenos">1233</span></a> <span class="k">if</span> <span class="n">added_names</span><span class="p">:</span>
+</span><span id="diff_config-1234"><a href="#diff_config-1234"><span class="linenos">1234</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-1235"><a href="#diff_config-1235"><span class="linenos">1235</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-1236"><a href="#diff_config-1236"><span class="linenos">1236</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-1237"><a href="#diff_config-1237"><span class="linenos">1237</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-1238"><a href="#diff_config-1238"><span class="linenos">1238</span></a>
+</span><span id="diff_config-1239"><a href="#diff_config-1239"><span class="linenos">1239</span></a> <span class="k">if</span> <span class="n">removed_names</span><span class="p">:</span>
+</span><span id="diff_config-1240"><a href="#diff_config-1240"><span class="linenos">1240</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-1241"><a href="#diff_config-1241"><span class="linenos">1241</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-1242"><a href="#diff_config-1242"><span class="linenos">1242</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-1243"><a href="#diff_config-1243"><span class="linenos">1243</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-1244"><a href="#diff_config-1244"><span class="linenos">1244</span></a>
+</span><span id="diff_config-1245"><a href="#diff_config-1245"><span class="linenos">1245</span></a> <span class="k">if</span> <span class="n">renamed_concepts</span><span class="p">:</span>
+</span><span id="diff_config-1246"><a href="#diff_config-1246"><span class="linenos">1246</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-1247"><a href="#diff_config-1247"><span class="linenos">1247</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-1248"><a href="#diff_config-1248"><span class="linenos">1248</span></a> <span class="n">report</span> <span class="o">+=</span> <span class="p">(</span>
+</span><span id="diff_config-1249"><a href="#diff_config-1249"><span class="linenos">1249</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">` ➝ `</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-1250"><a href="#diff_config-1250"><span class="linenos">1250</span></a> <span class="p">)</span>
+</span><span id="diff_config-1251"><a href="#diff_config-1251"><span class="linenos">1251</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-1252"><a href="#diff_config-1252"><span class="linenos">1252</span></a>
+</span><span id="diff_config-1253"><a href="#diff_config-1253"><span class="linenos">1253</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-1254"><a href="#diff_config-1254"><span class="linenos">1254</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-1255"><a href="#diff_config-1255"><span class="linenos">1255</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-1256"><a href="#diff_config-1256"><span class="linenos">1256</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-1257"><a href="#diff_config-1257"><span class="linenos">1257</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-1258"><a href="#diff_config-1258"><span class="linenos">1258</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-1259"><a href="#diff_config-1259"><span class="linenos">1259</span></a> <span class="n">report</span> <span class="o">+=</span> <span class="p">(</span>
+</span><span id="diff_config-1260"><a href="#diff_config-1260"><span class="linenos">1260</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">` ➝ `</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-1261"><a href="#diff_config-1261"><span class="linenos">1261</span></a> <span class="p">)</span>
+</span><span id="diff_config-1262"><a href="#diff_config-1262"><span class="linenos">1262</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-1263"><a href="#diff_config-1263"><span class="linenos">1263</span></a>
+</span><span id="diff_config-1264"><a href="#diff_config-1264"><span class="linenos">1264</span></a> <span class="k">if</span> <span class="ow">not</span> <span class="p">(</span>
+</span><span id="diff_config-1265"><a href="#diff_config-1265"><span class="linenos">1265</span></a> <span class="n">added_names</span>
+</span><span id="diff_config-1266"><a href="#diff_config-1266"><span class="linenos">1266</span></a> <span class="ow">or</span> <span class="n">removed_names</span>
+</span><span id="diff_config-1267"><a href="#diff_config-1267"><span class="linenos">1267</span></a> <span class="ow">or</span> <span class="n">renamed_concepts</span>
+</span><span id="diff_config-1268"><a href="#diff_config-1268"><span class="linenos">1268</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-1269"><a href="#diff_config-1269"><span class="linenos">1269</span></a> <span class="p">):</span>
+</span><span id="diff_config-1270"><a href="#diff_config-1270"><span class="linenos">1270</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-1271"><a href="#diff_config-1271"><span class="linenos">1271</span></a>
+</span><span id="diff_config-1272"><a href="#diff_config-1272"><span class="linenos">1272</span></a> <span class="k">return</span> <span class="n">report</span>
</span></pre></div>
@@ -2869,71 +2884,71 @@
</div>
<a class="headerlink" href="#diff_map_files"></a>
- <div class="pdoc-code codehilite"><pre><span></span><span id="diff_map_files-1262"><a href="#diff_map_files-1262"><span class="linenos">1262</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-1263"><a href="#diff_map_files-1263"><span class="linenos">1263</span></a> <span class="n">old_output_files</span> <span class="o">=</span> <span class="p">[</span>
-</span><span id="diff_map_files-1264"><a href="#diff_map_files-1264"><span class="linenos">1264</span></a> <span class="n">file</span><span class="o">.</span><span class="n">name</span>
-</span><span id="diff_map_files-1265"><a href="#diff_map_files-1265"><span class="linenos">1265</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-1266"><a href="#diff_map_files-1266"><span class="linenos">1266</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-1267"><a href="#diff_map_files-1267"><span class="linenos">1267</span></a> <span class="p">]</span>
-</span><span id="diff_map_files-1268"><a href="#diff_map_files-1268"><span class="linenos">1268</span></a> <span class="n">new_output_files</span> <span class="o">=</span> <span class="p">[</span>
-</span><span id="diff_map_files-1269"><a href="#diff_map_files-1269"><span class="linenos">1269</span></a> <span class="n">file</span><span class="o">.</span><span class="n">name</span>
-</span><span id="diff_map_files-1270"><a href="#diff_map_files-1270"><span class="linenos">1270</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-1271"><a href="#diff_map_files-1271"><span class="linenos">1271</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-1272"><a href="#diff_map_files-1272"><span class="linenos">1272</span></a> <span class="p">]</span>
-</span><span id="diff_map_files-1273"><a href="#diff_map_files-1273"><span class="linenos">1273</span></a>
-</span><span id="diff_map_files-1274"><a href="#diff_map_files-1274"><span class="linenos">1274</span></a> <span class="c1"># Convert the lists to sets for easy comparison</span>
-</span><span id="diff_map_files-1275"><a href="#diff_map_files-1275"><span class="linenos">1275</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-1276"><a href="#diff_map_files-1276"><span class="linenos">1276</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-1277"><a href="#diff_map_files-1277"><span class="linenos">1277</span></a>
-</span><span id="diff_map_files-1278"><a href="#diff_map_files-1278"><span class="linenos">1278</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-1279"><a href="#diff_map_files-1279"><span class="linenos">1279</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-1280"><a href="#diff_map_files-1280"><span class="linenos">1280</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-1281"><a href="#diff_map_files-1281"><span class="linenos">1281</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-1282"><a href="#diff_map_files-1282"><span class="linenos">1282</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-1283"><a href="#diff_map_files-1283"><span class="linenos">1283</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-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">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-1286"><a href="#diff_map_files-1286"><span class="linenos">1286</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-1287"><a href="#diff_map_files-1287"><span class="linenos">1287</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-1288"><a href="#diff_map_files-1288"><span class="linenos">1288</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-1289"><a href="#diff_map_files-1289"><span class="linenos">1289</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>
+ <div class="pdoc-code codehilite"><pre><span></span><span id="diff_map_files-1275"><a href="#diff_map_files-1275"><span class="linenos">1275</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-1276"><a href="#diff_map_files-1276"><span class="linenos">1276</span></a> <span class="n">old_output_files</span> <span class="o">=</span> <span class="p">[</span>
+</span><span id="diff_map_files-1277"><a href="#diff_map_files-1277"><span class="linenos">1277</span></a> <span class="n">file</span><span class="o">.</span><span class="n">name</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">old_map_path</span><span class="o">.</span><span class="n">iterdir</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="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-1280"><a href="#diff_map_files-1280"><span class="linenos">1280</span></a> <span class="p">]</span>
+</span><span id="diff_map_files-1281"><a href="#diff_map_files-1281"><span class="linenos">1281</span></a> <span class="n">new_output_files</span> <span class="o">=</span> <span class="p">[</span>
+</span><span id="diff_map_files-1282"><a href="#diff_map_files-1282"><span class="linenos">1282</span></a> <span class="n">file</span><span class="o">.</span><span class="n">name</span>
+</span><span id="diff_map_files-1283"><a href="#diff_map_files-1283"><span class="linenos">1283</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-1284"><a href="#diff_map_files-1284"><span class="linenos">1284</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-1285"><a href="#diff_map_files-1285"><span class="linenos">1285</span></a> <span class="p">]</span>
+</span><span id="diff_map_files-1286"><a href="#diff_map_files-1286"><span class="linenos">1286</span></a>
+</span><span id="diff_map_files-1287"><a href="#diff_map_files-1287"><span class="linenos">1287</span></a> <span class="c1"># Convert the lists to sets for easy comparison</span>
+</span><span id="diff_map_files-1288"><a href="#diff_map_files-1288"><span class="linenos">1288</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-1289"><a href="#diff_map_files-1289"><span class="linenos">1289</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-1290"><a href="#diff_map_files-1290"><span class="linenos">1290</span></a>
-</span><span id="diff_map_files-1291"><a href="#diff_map_files-1291"><span class="linenos">1291</span></a> <span class="c1"># Step N: Compare common outputs between versions</span>
-</span><span id="diff_map_files-1292"><a href="#diff_map_files-1292"><span class="linenos">1292</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-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">"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-1294"><a href="#diff_map_files-1294"><span class="linenos">1294</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-1295"><a href="#diff_map_files-1295"><span class="linenos">1295</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-1296"><a href="#diff_map_files-1296"><span class="linenos">1296</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-1291"><a href="#diff_map_files-1291"><span class="linenos">1291</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-1292"><a href="#diff_map_files-1292"><span class="linenos">1292</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-1293"><a href="#diff_map_files-1293"><span class="linenos">1293</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-1294"><a href="#diff_map_files-1294"><span class="linenos">1294</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-1295"><a href="#diff_map_files-1295"><span class="linenos">1295</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-1296"><a href="#diff_map_files-1296"><span class="linenos">1296</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-1297"><a href="#diff_map_files-1297"><span class="linenos">1297</span></a>
-</span><span id="diff_map_files-1298"><a href="#diff_map_files-1298"><span class="linenos">1298</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-1299"><a href="#diff_map_files-1299"><span class="linenos">1299</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-1300"><a href="#diff_map_files-1300"><span class="linenos">1300</span></a>
-</span><span id="diff_map_files-1301"><a href="#diff_map_files-1301"><span class="linenos">1301</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-1302"><a href="#diff_map_files-1302"><span class="linenos">1302</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-1303"><a href="#diff_map_files-1303"><span class="linenos">1303</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-1304"><a href="#diff_map_files-1304"><span class="linenos">1304</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-1305"><a href="#diff_map_files-1305"><span class="linenos">1305</span></a>
-</span><span id="diff_map_files-1306"><a href="#diff_map_files-1306"><span class="linenos">1306</span></a> <span class="c1"># Check for added and removed concepts</span>
-</span><span id="diff_map_files-1307"><a href="#diff_map_files-1307"><span class="linenos">1307</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-1308"><a href="#diff_map_files-1308"><span class="linenos">1308</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-1309"><a href="#diff_map_files-1309"><span class="linenos">1309</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-1310"><a href="#diff_map_files-1310"><span class="linenos">1310</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-1311"><a href="#diff_map_files-1311"><span class="linenos">1311</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-1312"><a href="#diff_map_files-1312"><span class="linenos">1312</span></a>
-</span><span id="diff_map_files-1313"><a href="#diff_map_files-1313"><span class="linenos">1313</span></a> <span class="c1"># Check for changed concepts</span>
-</span><span id="diff_map_files-1314"><a href="#diff_map_files-1314"><span class="linenos">1314</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-1315"><a href="#diff_map_files-1315"><span class="linenos">1315</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-1316"><a href="#diff_map_files-1316"><span class="linenos">1316</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-1317"><a href="#diff_map_files-1317"><span class="linenos">1317</span></a> <span class="p">]</span> <span class="c1"># get non-zero counts</span>
-</span><span id="diff_map_files-1318"><a href="#diff_map_files-1318"><span class="linenos">1318</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-1319"><a href="#diff_map_files-1319"><span class="linenos">1319</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-1320"><a href="#diff_map_files-1320"><span class="linenos">1320</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-1321"><a href="#diff_map_files-1321"><span class="linenos">1321</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-1322"><a href="#diff_map_files-1322"><span class="linenos">1322</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-1323"><a href="#diff_map_files-1323"><span class="linenos">1323</span></a> <span class="k">else</span><span class="p">:</span>
-</span><span id="diff_map_files-1324"><a href="#diff_map_files-1324"><span class="linenos">1324</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-1298"><a href="#diff_map_files-1298"><span class="linenos">1298</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-1299"><a href="#diff_map_files-1299"><span class="linenos">1299</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-1300"><a href="#diff_map_files-1300"><span class="linenos">1300</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-1301"><a href="#diff_map_files-1301"><span class="linenos">1301</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-1302"><a href="#diff_map_files-1302"><span class="linenos">1302</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-1303"><a href="#diff_map_files-1303"><span class="linenos">1303</span></a>
+</span><span id="diff_map_files-1304"><a href="#diff_map_files-1304"><span class="linenos">1304</span></a> <span class="c1"># Step N: Compare common outputs between versions</span>
+</span><span id="diff_map_files-1305"><a href="#diff_map_files-1305"><span class="linenos">1305</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-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">"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-1307"><a href="#diff_map_files-1307"><span class="linenos">1307</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-1308"><a href="#diff_map_files-1308"><span class="linenos">1308</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-1309"><a href="#diff_map_files-1309"><span class="linenos">1309</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-1310"><a href="#diff_map_files-1310"><span class="linenos">1310</span></a>
+</span><span id="diff_map_files-1311"><a href="#diff_map_files-1311"><span class="linenos">1311</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-1312"><a href="#diff_map_files-1312"><span class="linenos">1312</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-1313"><a href="#diff_map_files-1313"><span class="linenos">1313</span></a>
+</span><span id="diff_map_files-1314"><a href="#diff_map_files-1314"><span class="linenos">1314</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-1315"><a href="#diff_map_files-1315"><span class="linenos">1315</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-1316"><a href="#diff_map_files-1316"><span class="linenos">1316</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-1317"><a href="#diff_map_files-1317"><span class="linenos">1317</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-1318"><a href="#diff_map_files-1318"><span class="linenos">1318</span></a>
+</span><span id="diff_map_files-1319"><a href="#diff_map_files-1319"><span class="linenos">1319</span></a> <span class="c1"># Check for added and removed concepts</span>
+</span><span id="diff_map_files-1320"><a href="#diff_map_files-1320"><span class="linenos">1320</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-1321"><a href="#diff_map_files-1321"><span class="linenos">1321</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-1322"><a href="#diff_map_files-1322"><span class="linenos">1322</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-1323"><a href="#diff_map_files-1323"><span class="linenos">1323</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-1324"><a href="#diff_map_files-1324"><span class="linenos">1324</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-1325"><a href="#diff_map_files-1325"><span class="linenos">1325</span></a>
-</span><span id="diff_map_files-1326"><a href="#diff_map_files-1326"><span class="linenos">1326</span></a> <span class="k">return</span> <span class="n">report</span>
+</span><span id="diff_map_files-1326"><a href="#diff_map_files-1326"><span class="linenos">1326</span></a> <span class="c1"># Check for changed concepts</span>
+</span><span id="diff_map_files-1327"><a href="#diff_map_files-1327"><span class="linenos">1327</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-1328"><a href="#diff_map_files-1328"><span class="linenos">1328</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-1329"><a href="#diff_map_files-1329"><span class="linenos">1329</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-1330"><a href="#diff_map_files-1330"><span class="linenos">1330</span></a> <span class="p">]</span> <span class="c1"># get non-zero counts</span>
+</span><span id="diff_map_files-1331"><a href="#diff_map_files-1331"><span class="linenos">1331</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-1332"><a href="#diff_map_files-1332"><span class="linenos">1332</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-1333"><a href="#diff_map_files-1333"><span class="linenos">1333</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-1334"><a href="#diff_map_files-1334"><span class="linenos">1334</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-1335"><a href="#diff_map_files-1335"><span class="linenos">1335</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-1336"><a href="#diff_map_files-1336"><span class="linenos">1336</span></a> <span class="k">else</span><span class="p">:</span>
+</span><span id="diff_map_files-1337"><a href="#diff_map_files-1337"><span class="linenos">1337</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-1338"><a href="#diff_map_files-1338"><span class="linenos">1338</span></a>
+</span><span id="diff_map_files-1339"><a href="#diff_map_files-1339"><span class="linenos">1339</span></a> <span class="k">return</span> <span class="n">report</span>
</span></pre></div>
@@ -2951,57 +2966,57 @@
</div>
<a class="headerlink" href="#diff_phen"></a>
- <div class="pdoc-code codehilite"><pre><span></span><span id="diff_phen-1329"><a href="#diff_phen-1329"><span class="linenos">1329</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-1330"><a href="#diff_phen-1330"><span class="linenos">1330</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-1331"><a href="#diff_phen-1331"><span class="linenos">1331</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-1332"><a href="#diff_phen-1332"><span class="linenos">1332</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-1333"><a href="#diff_phen-1333"><span class="linenos">1333</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-1334"><a href="#diff_phen-1334"><span class="linenos">1334</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-1335"><a href="#diff_phen-1335"><span class="linenos">1335</span></a><span class="p">):</span>
-</span><span id="diff_phen-1336"><a href="#diff_phen-1336"><span class="linenos">1336</span></a><span class="w"> </span><span class="sd">"""Compare the differences between two versions of a phenotype"""</span>
-</span><span id="diff_phen-1337"><a href="#diff_phen-1337"><span class="linenos">1337</span></a>
-</span><span id="diff_phen-1338"><a href="#diff_phen-1338"><span class="linenos">1338</span></a> <span class="c1"># validate phenotypes</span>
-</span><span id="diff_phen-1339"><a href="#diff_phen-1339"><span class="linenos">1339</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-1340"><a href="#diff_phen-1340"><span class="linenos">1340</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-1341"><a href="#diff_phen-1341"><span class="linenos">1341</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-1342"><a href="#diff_phen-1342"><span class="linenos">1342</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-1343"><a href="#diff_phen-1343"><span class="linenos">1343</span></a>
-</span><span id="diff_phen-1344"><a href="#diff_phen-1344"><span class="linenos">1344</span></a> <span class="c1"># get old and new config</span>
-</span><span id="diff_phen-1345"><a href="#diff_phen-1345"><span class="linenos">1345</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-1346"><a href="#diff_phen-1346"><span class="linenos">1346</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-1347"><a href="#diff_phen-1347"><span class="linenos">1347</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-1348"><a href="#diff_phen-1348"><span class="linenos">1348</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-1349"><a href="#diff_phen-1349"><span class="linenos">1349</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-1350"><a href="#diff_phen-1350"><span class="linenos">1350</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-1351"><a href="#diff_phen-1351"><span class="linenos">1351</span></a>
-</span><span id="diff_phen-1352"><a href="#diff_phen-1352"><span class="linenos">1352</span></a> <span class="c1"># write report heading</span>
-</span><span id="diff_phen-1353"><a href="#diff_phen-1353"><span class="linenos">1353</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-1354"><a href="#diff_phen-1354"><span class="linenos">1354</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-1355"><a href="#diff_phen-1355"><span class="linenos">1355</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-1356"><a href="#diff_phen-1356"><span class="linenos">1356</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-1357"><a href="#diff_phen-1357"><span class="linenos">1357</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-1358"><a href="#diff_phen-1358"><span class="linenos">1358</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-1359"><a href="#diff_phen-1359"><span class="linenos">1359</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-1360"><a href="#diff_phen-1360"><span class="linenos">1360</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-1361"><a href="#diff_phen-1361"><span class="linenos">1361</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-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="c1"># Step 1: check differences configuration files</span>
-</span><span id="diff_phen-1364"><a href="#diff_phen-1364"><span class="linenos">1364</span></a> <span class="c1"># Convert list of dicts into a dict: {name: file}</span>
-</span><span id="diff_phen-1365"><a href="#diff_phen-1365"><span class="linenos">1365</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-1366"><a href="#diff_phen-1366"><span class="linenos">1366</span></a>
-</span><span id="diff_phen-1367"><a href="#diff_phen-1367"><span class="linenos">1367</span></a> <span class="c1"># Step 2: check differences between map files</span>
-</span><span id="diff_phen-1368"><a href="#diff_phen-1368"><span class="linenos">1368</span></a> <span class="c1"># List files from output directories</span>
-</span><span id="diff_phen-1369"><a href="#diff_phen-1369"><span class="linenos">1369</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-1370"><a href="#diff_phen-1370"><span class="linenos">1370</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-1371"><a href="#diff_phen-1371"><span class="linenos">1371</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-1372"><a href="#diff_phen-1372"><span class="linenos">1372</span></a>
-</span><span id="diff_phen-1373"><a href="#diff_phen-1373"><span class="linenos">1373</span></a> <span class="c1"># initialise report file</span>
-</span><span id="diff_phen-1374"><a href="#diff_phen-1374"><span class="linenos">1374</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-1375"><a href="#diff_phen-1375"><span class="linenos">1375</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-1376"><a href="#diff_phen-1376"><span class="linenos">1376</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-1377"><a href="#diff_phen-1377"><span class="linenos">1377</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-1378"><a href="#diff_phen-1378"><span class="linenos">1378</span></a>
-</span><span id="diff_phen-1379"><a href="#diff_phen-1379"><span class="linenos">1379</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>
+ <div class="pdoc-code codehilite"><pre><span></span><span id="diff_phen-1342"><a href="#diff_phen-1342"><span class="linenos">1342</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-1343"><a href="#diff_phen-1343"><span class="linenos">1343</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-1344"><a href="#diff_phen-1344"><span class="linenos">1344</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-1345"><a href="#diff_phen-1345"><span class="linenos">1345</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-1346"><a href="#diff_phen-1346"><span class="linenos">1346</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-1347"><a href="#diff_phen-1347"><span class="linenos">1347</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-1348"><a href="#diff_phen-1348"><span class="linenos">1348</span></a><span class="p">):</span>
+</span><span id="diff_phen-1349"><a href="#diff_phen-1349"><span class="linenos">1349</span></a><span class="w"> </span><span class="sd">"""Compare the differences between two versions of a phenotype"""</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"># validate phenotypes</span>
+</span><span id="diff_phen-1352"><a href="#diff_phen-1352"><span class="linenos">1352</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-1353"><a href="#diff_phen-1353"><span class="linenos">1353</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-1354"><a href="#diff_phen-1354"><span class="linenos">1354</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-1355"><a href="#diff_phen-1355"><span class="linenos">1355</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-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"># get old and new config</span>
+</span><span id="diff_phen-1358"><a href="#diff_phen-1358"><span class="linenos">1358</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-1359"><a href="#diff_phen-1359"><span class="linenos">1359</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-1360"><a href="#diff_phen-1360"><span class="linenos">1360</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-1361"><a href="#diff_phen-1361"><span class="linenos">1361</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-1362"><a href="#diff_phen-1362"><span class="linenos">1362</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-1363"><a href="#diff_phen-1363"><span class="linenos">1363</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-1364"><a href="#diff_phen-1364"><span class="linenos">1364</span></a>
+</span><span id="diff_phen-1365"><a href="#diff_phen-1365"><span class="linenos">1365</span></a> <span class="c1"># write report heading</span>
+</span><span id="diff_phen-1366"><a href="#diff_phen-1366"><span class="linenos">1366</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-1367"><a href="#diff_phen-1367"><span class="linenos">1367</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-1368"><a href="#diff_phen-1368"><span class="linenos">1368</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-1369"><a href="#diff_phen-1369"><span class="linenos">1369</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-1370"><a href="#diff_phen-1370"><span class="linenos">1370</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-1371"><a href="#diff_phen-1371"><span class="linenos">1371</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-1372"><a href="#diff_phen-1372"><span class="linenos">1372</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-1373"><a href="#diff_phen-1373"><span class="linenos">1373</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-1374"><a href="#diff_phen-1374"><span class="linenos">1374</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-1375"><a href="#diff_phen-1375"><span class="linenos">1375</span></a>
+</span><span id="diff_phen-1376"><a href="#diff_phen-1376"><span class="linenos">1376</span></a> <span class="c1"># Step 1: check differences configuration files</span>
+</span><span id="diff_phen-1377"><a href="#diff_phen-1377"><span class="linenos">1377</span></a> <span class="c1"># Convert list of dicts into a dict: {name: file}</span>
+</span><span id="diff_phen-1378"><a href="#diff_phen-1378"><span class="linenos">1378</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-1379"><a href="#diff_phen-1379"><span class="linenos">1379</span></a>
+</span><span id="diff_phen-1380"><a href="#diff_phen-1380"><span class="linenos">1380</span></a> <span class="c1"># Step 2: check differences between map files</span>
+</span><span id="diff_phen-1381"><a href="#diff_phen-1381"><span class="linenos">1381</span></a> <span class="c1"># List files from output directories</span>
+</span><span id="diff_phen-1382"><a href="#diff_phen-1382"><span class="linenos">1382</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-1383"><a href="#diff_phen-1383"><span class="linenos">1383</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-1384"><a href="#diff_phen-1384"><span class="linenos">1384</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-1385"><a href="#diff_phen-1385"><span class="linenos">1385</span></a>
+</span><span id="diff_phen-1386"><a href="#diff_phen-1386"><span class="linenos">1386</span></a> <span class="c1"># initialise report file</span>
+</span><span id="diff_phen-1387"><a href="#diff_phen-1387"><span class="linenos">1387</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-1388"><a href="#diff_phen-1388"><span class="linenos">1388</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-1389"><a href="#diff_phen-1389"><span class="linenos">1389</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-1390"><a href="#diff_phen-1390"><span class="linenos">1390</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-1391"><a href="#diff_phen-1391"><span class="linenos">1391</span></a>
+</span><span id="diff_phen-1392"><a href="#diff_phen-1392"><span class="linenos">1392</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>
@@ -3021,74 +3036,74 @@
</div>
<a class="headerlink" href="#diff"></a>
- <div class="pdoc-code codehilite"><pre><span></span><span id="diff-1382"><a href="#diff-1382"><span class="linenos">1382</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-1383"><a href="#diff-1383"><span class="linenos">1383</span></a> <span class="c1"># make tmp directory .acmc</span>
-</span><span id="diff-1384"><a href="#diff-1384"><span class="linenos">1384</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-1385"><a href="#diff-1385"><span class="linenos">1385</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-1386"><a href="#diff-1386"><span class="linenos">1386</span></a>
-</span><span id="diff-1387"><a href="#diff-1387"><span class="linenos">1387</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-1388"><a href="#diff-1388"><span class="linenos">1388</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-1389"><a href="#diff-1389"><span class="linenos">1389</span></a> <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span>
-</span><span id="diff-1390"><a href="#diff-1390"><span class="linenos">1390</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-1391"><a href="#diff-1391"><span class="linenos">1391</span></a> <span class="p">)</span>
-</span><span id="diff-1392"><a href="#diff-1392"><span class="linenos">1392</span></a>
-</span><span id="diff-1393"><a href="#diff-1393"><span class="linenos">1393</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-1394"><a href="#diff-1394"><span class="linenos">1394</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-1395"><a href="#diff-1395"><span class="linenos">1395</span></a> <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span>
-</span><span id="diff-1396"><a href="#diff-1396"><span class="linenos">1396</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-1397"><a href="#diff-1397"><span class="linenos">1397</span></a> <span class="p">)</span>
-</span><span id="diff-1398"><a href="#diff-1398"><span class="linenos">1398</span></a>
-</span><span id="diff-1399"><a href="#diff-1399"><span class="linenos">1399</span></a> <span class="n">t_path</span> <span class="o">=</span> <span class="n">old_phen_path</span> <span class="o">/</span> <span class="s2">"config.yml"</span>
-</span><span id="diff-1400"><a href="#diff-1400"><span class="linenos">1400</span></a> <span class="k">with</span> <span class="n">t_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-1401"><a href="#diff-1401"><span class="linenos">1401</span></a> <span class="n">c</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-1402"><a href="#diff-1402"><span class="linenos">1402</span></a>
-</span><span id="diff-1403"><a href="#diff-1403"><span class="linenos">1403</span></a> <span class="k">try</span><span class="p">:</span>
-</span><span id="diff-1404"><a href="#diff-1404"><span class="linenos">1404</span></a> <span class="c1"># Create the directory</span>
-</span><span id="diff-1405"><a href="#diff-1405"><span class="linenos">1405</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-1406"><a href="#diff-1406"><span class="linenos">1406</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-1407"><a href="#diff-1407"><span class="linenos">1407</span></a>
-</span><span id="diff-1408"><a href="#diff-1408"><span class="linenos">1408</span></a> <span class="c1"># Create temporary directories</span>
-</span><span id="diff-1409"><a href="#diff-1409"><span class="linenos">1409</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-1410"><a href="#diff-1410"><span class="linenos">1410</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-1411"><a href="#diff-1411"><span class="linenos">1411</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-1412"><a href="#diff-1412"><span class="linenos">1412</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-1413"><a href="#diff-1413"><span class="linenos">1413</span></a>
-</span><span id="diff-1414"><a href="#diff-1414"><span class="linenos">1414</span></a> <span class="c1"># checkout changed</span>
-</span><span id="diff-1415"><a href="#diff-1415"><span class="linenos">1415</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-1416"><a href="#diff-1416"><span class="linenos">1416</span></a> <span class="n">_logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span>
-</span><span id="diff-1417"><a href="#diff-1417"><span class="linenos">1417</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-1418"><a href="#diff-1418"><span class="linenos">1418</span></a> <span class="p">)</span>
-</span><span id="diff-1419"><a href="#diff-1419"><span class="linenos">1419</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-1420"><a href="#diff-1420"><span class="linenos">1420</span></a> <span class="k">else</span><span class="p">:</span>
-</span><span id="diff-1421"><a href="#diff-1421"><span class="linenos">1421</span></a> <span class="n">_logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span>
-</span><span id="diff-1422"><a href="#diff-1422"><span class="linenos">1422</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-1423"><a href="#diff-1423"><span class="linenos">1423</span></a> <span class="p">)</span>
-</span><span id="diff-1424"><a href="#diff-1424"><span class="linenos">1424</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-1425"><a href="#diff-1425"><span class="linenos">1425</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>
+ <div class="pdoc-code codehilite"><pre><span></span><span id="diff-1395"><a href="#diff-1395"><span class="linenos">1395</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-1396"><a href="#diff-1396"><span class="linenos">1396</span></a> <span class="c1"># make tmp directory .acmc</span>
+</span><span id="diff-1397"><a href="#diff-1397"><span class="linenos">1397</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-1398"><a href="#diff-1398"><span class="linenos">1398</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-1399"><a href="#diff-1399"><span class="linenos">1399</span></a>
+</span><span id="diff-1400"><a href="#diff-1400"><span class="linenos">1400</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-1401"><a href="#diff-1401"><span class="linenos">1401</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-1402"><a href="#diff-1402"><span class="linenos">1402</span></a> <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span>
+</span><span id="diff-1403"><a href="#diff-1403"><span class="linenos">1403</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-1404"><a href="#diff-1404"><span class="linenos">1404</span></a> <span class="p">)</span>
+</span><span id="diff-1405"><a href="#diff-1405"><span class="linenos">1405</span></a>
+</span><span id="diff-1406"><a href="#diff-1406"><span class="linenos">1406</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-1407"><a href="#diff-1407"><span class="linenos">1407</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-1408"><a href="#diff-1408"><span class="linenos">1408</span></a> <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span>
+</span><span id="diff-1409"><a href="#diff-1409"><span class="linenos">1409</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-1410"><a href="#diff-1410"><span class="linenos">1410</span></a> <span class="p">)</span>
+</span><span id="diff-1411"><a href="#diff-1411"><span class="linenos">1411</span></a>
+</span><span id="diff-1412"><a href="#diff-1412"><span class="linenos">1412</span></a> <span class="n">t_path</span> <span class="o">=</span> <span class="n">old_phen_path</span> <span class="o">/</span> <span class="s2">"config.yml"</span>
+</span><span id="diff-1413"><a href="#diff-1413"><span class="linenos">1413</span></a> <span class="k">with</span> <span class="n">t_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-1414"><a href="#diff-1414"><span class="linenos">1414</span></a> <span class="n">c</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-1415"><a href="#diff-1415"><span class="linenos">1415</span></a>
+</span><span id="diff-1416"><a href="#diff-1416"><span class="linenos">1416</span></a> <span class="k">try</span><span class="p">:</span>
+</span><span id="diff-1417"><a href="#diff-1417"><span class="linenos">1417</span></a> <span class="c1"># Create the directory</span>
+</span><span id="diff-1418"><a href="#diff-1418"><span class="linenos">1418</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-1419"><a href="#diff-1419"><span class="linenos">1419</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-1420"><a href="#diff-1420"><span class="linenos">1420</span></a>
+</span><span id="diff-1421"><a href="#diff-1421"><span class="linenos">1421</span></a> <span class="c1"># Create temporary directories</span>
+</span><span id="diff-1422"><a href="#diff-1422"><span class="linenos">1422</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-1423"><a href="#diff-1423"><span class="linenos">1423</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-1424"><a href="#diff-1424"><span class="linenos">1424</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-1425"><a href="#diff-1425"><span class="linenos">1425</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-1426"><a href="#diff-1426"><span class="linenos">1426</span></a>
-</span><span id="diff-1427"><a href="#diff-1427"><span class="linenos">1427</span></a> <span class="c1"># checkout old</span>
-</span><span id="diff-1428"><a href="#diff-1428"><span class="linenos">1428</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-1427"><a href="#diff-1427"><span class="linenos">1427</span></a> <span class="c1"># checkout changed</span>
+</span><span id="diff-1428"><a href="#diff-1428"><span class="linenos">1428</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-1429"><a href="#diff-1429"><span class="linenos">1429</span></a> <span class="n">_logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span>
-</span><span id="diff-1430"><a href="#diff-1430"><span class="linenos">1430</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-1430"><a href="#diff-1430"><span class="linenos">1430</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-1431"><a href="#diff-1431"><span class="linenos">1431</span></a> <span class="p">)</span>
-</span><span id="diff-1432"><a href="#diff-1432"><span class="linenos">1432</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-1432"><a href="#diff-1432"><span class="linenos">1432</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-1433"><a href="#diff-1433"><span class="linenos">1433</span></a> <span class="k">else</span><span class="p">:</span>
</span><span id="diff-1434"><a href="#diff-1434"><span class="linenos">1434</span></a> <span class="n">_logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span>
-</span><span id="diff-1435"><a href="#diff-1435"><span class="linenos">1435</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-1435"><a href="#diff-1435"><span class="linenos">1435</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-1436"><a href="#diff-1436"><span class="linenos">1436</span></a> <span class="p">)</span>
-</span><span id="diff-1437"><a href="#diff-1437"><span class="linenos">1437</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-1438"><a href="#diff-1438"><span class="linenos">1438</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-1437"><a href="#diff-1437"><span class="linenos">1437</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-1438"><a href="#diff-1438"><span class="linenos">1438</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-1439"><a href="#diff-1439"><span class="linenos">1439</span></a>
-</span><span id="diff-1440"><a href="#diff-1440"><span class="linenos">1440</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-1441"><a href="#diff-1441"><span class="linenos">1441</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-1442"><a href="#diff-1442"><span class="linenos">1442</span></a> <span class="c1"># diff old with new</span>
-</span><span id="diff-1443"><a href="#diff-1443"><span class="linenos">1443</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-1444"><a href="#diff-1444"><span class="linenos">1444</span></a>
-</span><span id="diff-1445"><a href="#diff-1445"><span class="linenos">1445</span></a> <span class="k">finally</span><span class="p">:</span>
-</span><span id="diff-1446"><a href="#diff-1446"><span class="linenos">1446</span></a> <span class="c1"># clean up tmp directory</span>
-</span><span id="diff-1447"><a href="#diff-1447"><span class="linenos">1447</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-1448"><a href="#diff-1448"><span class="linenos">1448</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-1449"><a href="#diff-1449"><span class="linenos">1449</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><span id="diff-1440"><a href="#diff-1440"><span class="linenos">1440</span></a> <span class="c1"># checkout old</span>
+</span><span id="diff-1441"><a href="#diff-1441"><span class="linenos">1441</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-1442"><a href="#diff-1442"><span class="linenos">1442</span></a> <span class="n">_logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span>
+</span><span id="diff-1443"><a href="#diff-1443"><span class="linenos">1443</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-1444"><a href="#diff-1444"><span class="linenos">1444</span></a> <span class="p">)</span>
+</span><span id="diff-1445"><a href="#diff-1445"><span class="linenos">1445</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-1446"><a href="#diff-1446"><span class="linenos">1446</span></a> <span class="k">else</span><span class="p">:</span>
+</span><span id="diff-1447"><a href="#diff-1447"><span class="linenos">1447</span></a> <span class="n">_logger</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span>
+</span><span id="diff-1448"><a href="#diff-1448"><span class="linenos">1448</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-1449"><a href="#diff-1449"><span class="linenos">1449</span></a> <span class="p">)</span>
+</span><span id="diff-1450"><a href="#diff-1450"><span class="linenos">1450</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-1451"><a href="#diff-1451"><span class="linenos">1451</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-1452"><a href="#diff-1452"><span class="linenos">1452</span></a>
+</span><span id="diff-1453"><a href="#diff-1453"><span class="linenos">1453</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-1454"><a href="#diff-1454"><span class="linenos">1454</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-1455"><a href="#diff-1455"><span class="linenos">1455</span></a> <span class="c1"># diff old with new</span>
+</span><span id="diff-1456"><a href="#diff-1456"><span class="linenos">1456</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-1457"><a href="#diff-1457"><span class="linenos">1457</span></a>
+</span><span id="diff-1458"><a href="#diff-1458"><span class="linenos">1458</span></a> <span class="k">finally</span><span class="p">:</span>
+</span><span id="diff-1459"><a href="#diff-1459"><span class="linenos">1459</span></a> <span class="c1"># clean up tmp directory</span>
+</span><span id="diff-1460"><a href="#diff-1460"><span class="linenos">1460</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-1461"><a href="#diff-1461"><span class="linenos">1461</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-1462"><a href="#diff-1462"><span class="linenos">1462</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>
diff --git a/docs/api/search.js b/docs/api/search.js
index 8cf39d8db4bc2a7c70ac76c4846fd14d45b3c65a..f85a34b41f07d55a37be6539022acfee1302f74a 100644
--- a/docs/api/search.js
+++ b/docs/api/search.js
@@ -1,6 +1,6 @@
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>logging_config.py</p>\n\n<p>This module defines functions to setup logging for acmc across all module.</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>The default acmc application log filename.</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 acmc 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\n<h6 id=\"arguments\">Arguments:</h6>\n\n<ul>\n<li><strong>log_level (int):</strong> log level from the python logging libraru</li>\n</ul>\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>main.py module</p>\n\n<p>This module provides the functionality for the acmc command line interface</p>\n"}, "acmc.main.DEFAULT_WORKSPACE_PATH": {"fullname": "acmc.main.DEFAULT_WORKSPACE_PATH", "modulename": "acmc.main", "qualname": "DEFAULT_WORKSPACE_PATH", "kind": "variable", "doc": "<p>Default phenotype workspace path</p>\n", "default_value": "PosixPath('workspace')"}, "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>omop.py module</p>\n\n<p>This module provides functionality to manage OMOP vocabularies.</p>\n"}, "acmc.omop.VOCAB_PATH": {"fullname": "acmc.omop.VOCAB_PATH", "modulename": "acmc.omop", "qualname": "VOCAB_PATH", "kind": "variable", "doc": "<p>Default OMOP vocabulary path</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>Supported OMOP CDM version number</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>Default OMOP sqllite database filename</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>Default OMOP sqllite database path</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>Default OMOP version file</p>\n", "default_value": "'omop_version.yml'"}, "acmc.omop.VERSION_PATH": {"fullname": "acmc.omop.VERSION_PATH", "modulename": "acmc.omop", "qualname": "VERSION_PATH", "kind": "variable", "doc": "<p>Default OMOP version path</p>\n", "default_value": "PosixPath('vocab/omop/omop_version.yml')"}, "acmc.omop.EXPORT_FILE": {"fullname": "acmc.omop.EXPORT_FILE", "modulename": "acmc.omop", "qualname": "EXPORT_FILE", "kind": "variable", "doc": "<p>Default OMOP export database filename</p>\n", "default_value": "'omop_54_export.sqlite'"}, "acmc.omop.vocabularies": {"fullname": "acmc.omop.vocabularies", "modulename": "acmc.omop", "qualname": "vocabularies", "kind": "variable", "doc": "<p>Required OMOP vocabularies definition</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>Type mappings from acmc medical coding types to OMOP vocabulary types</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\n<h6 id=\"arguments\">Arguments:</h6>\n\n<ul>\n<li><strong>omop_zip_file (str):</strong> vocabularies zip file distributed by OHDSI Athena</li>\n<li><strong>version (str):</strong> version of the vocabularies distributed by OHDSI Athena</li>\n</ul>\n\n<h6 id=\"raises\">Raises:</h6>\n\n<ul>\n<li><strong>ValueError:</strong> if the zip file does not exist</li>\n<li><strong>ValueError:</strong> if the file is not a zip file</li>\n<li><strong>Exception:</strong> if error reading omop csv files</li>\n</ul>\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\n<h6 id=\"arguments\">Arguments:</h6>\n\n<ul>\n<li><strong>version (str):</strong> version of the vocabularies distributed by OHDSI Athena</li>\n</ul>\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\n<h6 id=\"arguments\">Arguments:</h6>\n\n<ul>\n<li><strong>db_path (Path):</strong> the path to the omop sqllite database</li>\n</ul>\n\n<h6 id=\"raises\">Raises:</h6>\n\n<ul>\n<li><strong>FileNotFoundError:</strong> if the omop sqllite database does not exist</li>\n</ul>\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\n<h6 id=\"arguments\">Arguments:</h6>\n\n<ul>\n<li><strong>db_path (Path):</strong> the path to the omop sqllite database</li>\n</ul>\n\n<h6 id=\"raises\">Raises:</h6>\n\n<ul>\n<li><strong>FileNotFoundError:</strong> if the omop sqllite database does not exist</li>\n</ul>\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>Query to check if the table exists</p>\n\n<h6 id=\"arguments\">Arguments:</h6>\n\n<ul>\n<li><strong>cursor (sqlite3.Cursor):</strong> a sqllite database cursor</li>\n<li><strong>table_name (str):</strong> the table name to check</li>\n</ul>\n\n<h6 id=\"returns\">Returns:</h6>\n\n<blockquote>\n <p>bool: true if table exists</p>\n</blockquote>\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>Query to check if the vocabulary exists</p>\n\n<h6 id=\"arguments\">Arguments:</h6>\n\n<ul>\n<li><strong>cursor (sqlite3.Cursor):</strong> a sqllite database cursor</li>\n<li><strong>vocab_id (str):</strong> the vocabulary id to check</li>\n</ul>\n\n<h6 id=\"returns\">Returns:</h6>\n\n<blockquote>\n <p>bool: true if vocabulary id exists</p>\n</blockquote>\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>Query to check if the concept set exists</p>\n\n<h6 id=\"arguments\">Arguments:</h6>\n\n<ul>\n<li><strong>cursor (sqlite3.Cursor):</strong> a sqllite database cursor</li>\n<li><strong>concept_set_name (str):</strong> the concept set name to check</li>\n</ul>\n\n<h6 id=\"returns\">Returns:</h6>\n\n<blockquote>\n <p>bool: true if concept set exists</p>\n</blockquote>\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>Export concept sets to omop database in csv format</p>\n\n<h6 id=\"arguments\">Arguments:</h6>\n\n<ul>\n<li><strong>map_path (Path):</strong> path to the acmc map directory containing concept sets in csv format</li>\n<li><strong>export_path (Path):</strong> path to the directory where the omop database csv files are to be written</li>\n<li><strong>version (str):</strong> phenotype version for omop vocabulary version</li>\n<li><strong>omop_metadata (dict):</strong> phenotype omop metadata for omop vocabulary metadata</li>\n</ul>\n\n<h6 id=\"returns\">Returns:</h6>\n\n<blockquote>\n <p>Path: path to the exported sqllite database</p>\n</blockquote>\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 class=\"p\">:</span> <span class=\"nb\">dict</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>parse.py module</p>\n\n<p>This module provides functionality to set up medical code translation classes</p>\n"}, "acmc.parse.SUPPORTED_CODE_TYPES": {"fullname": "acmc.parse.SUPPORTED_CODE_TYPES", "modulename": "acmc.parse", "qualname": "SUPPORTED_CODE_TYPES", "kind": "variable", "doc": "<p>List of support medical coding types</p>\n", "default_value": "{'opcs4', 'icd10', 'atc', 'snomed', 'read2', 'read3'}"}, "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[[pandas.core.frame.DataFrame], pandas.core.series.Series], typing.Callable[[pandas.core.frame.DataFrame, pathlib.Path], pandas.core.frame.DataFrame]]]"}, "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.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>phenotype.py module</p>\n\n<p>This module provides functionality for managing phenotypes.</p>\n"}, "acmc.phen.PHEN_DIR": {"fullname": "acmc.phen.PHEN_DIR", "modulename": "acmc.phen", "qualname": "PHEN_DIR", "kind": "variable", "doc": "<p>Default phenotype directory name</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>Default phenotype directory path</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>Default concepts directory name</p>\n", "default_value": "'concepts'"}, "acmc.phen.MAP_DIR": {"fullname": "acmc.phen.MAP_DIR", "modulename": "acmc.phen", "qualname": "MAP_DIR", "kind": "variable", "doc": "<p>Default map directory name</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>Default concept set directory name</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>Default CSV concept set directory path</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>Default OMOP concept set directory path</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>List of default phenotype directories</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>Default configuration filename</p>\n", "default_value": "'config.yml'"}, "acmc.phen.VOCAB_VERSION_FILE": {"fullname": "acmc.phen.VOCAB_VERSION_FILE", "modulename": "acmc.phen", "qualname": "VOCAB_VERSION_FILE", "kind": "variable", "doc": "<p>Default vocabulary version filename</p>\n", "default_value": "'vocab_version.yml'"}, "acmc.phen.SEMANTIC_VERSION_TYPES": {"fullname": "acmc.phen.SEMANTIC_VERSION_TYPES", "modulename": "acmc.phen", "qualname": "SEMANTIC_VERSION_TYPES", "kind": "variable", "doc": "<p>List of semantic version increment types</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>Default semantic version increment type</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>Default phenotype repo branch name</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>Split column preprocessing action type</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>Codes column preprocessing action type</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>Divide column preprocessing action type</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>List of column preprocessing action types</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>List of supported source concept coding list file types</p>\n", "default_value": "['.xlsx', '.xls', '.csv']"}, "acmc.phen.CONFIG_SCHEMA": {"fullname": "acmc.phen.CONFIG_SCHEMA", "modulename": "acmc.phen", "qualname": "CONFIG_SCHEMA", "kind": "variable", "doc": "<p>Phenotype config.yml schema definition</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', 'atc', 'snomed', 'read2', 'read3']}}, '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'}}}}}}}}}}}"}, "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.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.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<h6 id=\"arguments\">Arguments:</h6>\n\n<ul>\n<li><strong>phen_dir (str):</strong> local directory path where the upstream repo is to be cloned</li>\n<li><strong>upstream_url (str):</strong> url to the upstream repo</li>\n<li><strong>upstream_version (str):</strong> version in the upstream repo to clone</li>\n<li><strong>new_origin_url (str, optional):</strong> url of the remote repo to set as the new origin. Defaults to None.</li>\n</ul>\n\n<h6 id=\"raises\">Raises:</h6>\n\n<ul>\n<li><strong>ValueError:</strong> if the specified version is not in the upstream repo</li>\n<li><strong>ValueError:</strong> if the upstream repo is not a valid phenotype repo</li>\n<li><strong>ValueError:</strong> if there's any other problems with Git</li>\n</ul>\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><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.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.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.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.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>trud.py module</p>\n\n<p>This module provides functionality to manage installation of the NHS TRUD vocabularies.</p>\n"}, "acmc.trud.FQDN": {"fullname": "acmc.trud.FQDN", "modulename": "acmc.trud", "qualname": "FQDN", "kind": "variable", "doc": "<p>Fully Qualified Domain Name of NHS digital TRUD service API</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>Default path to the TRUD vocabulary directory relative to the the acmc execution directory</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>TRUD version file</p>\n", "default_value": "'trud_version.yml'"}, "acmc.trud.VERSION_PATH": {"fullname": "acmc.trud.VERSION_PATH", "modulename": "acmc.trud", "qualname": "VERSION_PATH", "kind": "variable", "doc": "<p>Default path to the TRUD version file</p>\n", "default_value": "PosixPath('vocab/trud/trud_version.yml')"}, "acmc.trud.DOWNLOADS_PATH": {"fullname": "acmc.trud.DOWNLOADS_PATH", "modulename": "acmc.trud", "qualname": "DOWNLOADS_PATH", "kind": "variable", "doc": "<p>Default path to the TRUD vocabulary downloads directory</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>Default path to the processed TRUD mappings directory</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=\"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>Custom Dumper to retain quotes on strings in yaml library</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": 20}, "acmc.logging_config.DEFAULT_LOG_FILE": {"qualname": 3, "fullname": 6, "annotation": 0, "default_value": 6, "signature": 0, "bases": 0, "doc": 9}, "acmc.logging_config.setup_logger": {"qualname": 2, "fullname": 5, "annotation": 0, "default_value": 0, "signature": 24, "bases": 0, "doc": 16}, "acmc.logging_config.set_log_level": {"qualname": 3, "fullname": 6, "annotation": 0, "default_value": 0, "signature": 17, "bases": 0, "doc": 33}, "acmc.main": {"qualname": 0, "fullname": 2, "annotation": 0, "default_value": 0, "signature": 0, "bases": 0, "doc": 18}, "acmc.main.DEFAULT_WORKSPACE_PATH": {"qualname": 3, "fullname": 5, "annotation": 0, "default_value": 5, "signature": 0, "bases": 0, "doc": 6}, "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": 16}, "acmc.omop.VOCAB_PATH": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 5, "signature": 0, "bases": 0, "doc": 6}, "acmc.omop.OMOP_CDM_Version": {"qualname": 3, "fullname": 5, "annotation": 0, "default_value": 5, "signature": 0, "bases": 0, "doc": 7}, "acmc.omop.OMOP_DB_FILENAME": {"qualname": 3, "fullname": 5, "annotation": 0, "default_value": 7, "signature": 0, "bases": 0, "doc": 7}, "acmc.omop.DB_PATH": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 7, "signature": 0, "bases": 0, "doc": 7}, "acmc.omop.VERSION_FILE": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 7, "signature": 0, "bases": 0, "doc": 6}, "acmc.omop.VERSION_PATH": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 7, "signature": 0, "bases": 0, "doc": 6}, "acmc.omop.EXPORT_FILE": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 8, "signature": 0, "bases": 0, "doc": 7}, "acmc.omop.vocabularies": {"qualname": 1, "fullname": 3, "annotation": 0, "default_value": 202, "signature": 0, "bases": 0, "doc": 6}, "acmc.omop.omop_vocab_types": {"qualname": 3, "fullname": 5, "annotation": 0, "default_value": 51, "signature": 0, "bases": 0, "doc": 13}, "acmc.omop.install": {"qualname": 1, "fullname": 3, "annotation": 0, "default_value": 0, "signature": 28, "bases": 0, "doc": 96}, "acmc.omop.write_version_file": {"qualname": 3, "fullname": 5, "annotation": 0, "default_value": 0, "signature": 16, "bases": 0, "doc": 33}, "acmc.omop.clear": {"qualname": 1, "fullname": 3, "annotation": 0, "default_value": 0, "signature": 22, "bases": 0, "doc": 49}, "acmc.omop.delete": {"qualname": 1, "fullname": 3, "annotation": 0, "default_value": 0, "signature": 22, "bases": 0, "doc": 49}, "acmc.omop.table_exists": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 35, "bases": 0, "doc": 55}, "acmc.omop.vocab_exists": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 35, "bases": 0, "doc": 56}, "acmc.omop.concept_set_exist": {"qualname": 3, "fullname": 5, "annotation": 0, "default_value": 0, "signature": 36, "bases": 0, "doc": 59}, "acmc.omop.export": {"qualname": 1, "fullname": 3, "annotation": 0, "default_value": 0, "signature": 71, "bases": 0, "doc": 104}, "acmc.parse": {"qualname": 0, "fullname": 2, "annotation": 0, "default_value": 0, "signature": 0, "bases": 0, "doc": 18}, "acmc.parse.SUPPORTED_CODE_TYPES": {"qualname": 3, "fullname": 5, "annotation": 0, "default_value": 20, "signature": 0, "bases": 0, "doc": 8}, "acmc.parse.CodesError": {"qualname": 1, "fullname": 3, "annotation": 0, "default_value": 0, "signature": 0, "bases": 0, "doc": 17}, "acmc.parse.CodesError.__init__": {"qualname": 3, "fullname": 5, "annotation": 0, "default_value": 0, "signature": 51, "bases": 0, "doc": 3}, "acmc.parse.InvalidCodesException": {"qualname": 1, "fullname": 3, "annotation": 0, "default_value": 0, "signature": 0, "bases": 2, "doc": 17}, "acmc.parse.InvalidCodesException.__init__": {"qualname": 3, "fullname": 5, "annotation": 0, "default_value": 0, "signature": 9, "bases": 0, "doc": 3}, "acmc.parse.InvalidCodesException.error": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 0, "bases": 0, "doc": 3}, "acmc.parse.Proto": {"qualname": 1, "fullname": 3, "annotation": 0, "default_value": 0, "signature": 0, "bases": 0, "doc": 59}, "acmc.parse.Proto.__init__": {"qualname": 3, "fullname": 5, "annotation": 0, "default_value": 0, "signature": 44, "bases": 0, "doc": 3}, "acmc.parse.Proto.checks": {"qualname": 2, "fullname": 4, "annotation": 22, "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.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, 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+ /** 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>logging_config.py</p>\n\n<p>This module defines functions to setup logging for acmc across all module.</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>The default acmc application log filename.</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 acmc 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\n<h6 id=\"arguments\">Arguments:</h6>\n\n<ul>\n<li><strong>log_level (int):</strong> log level from the python logging libraru</li>\n</ul>\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>main.py module</p>\n\n<p>This module provides the functionality for the acmc command line interface</p>\n"}, "acmc.main.DEFAULT_WORKSPACE_PATH": {"fullname": "acmc.main.DEFAULT_WORKSPACE_PATH", "modulename": "acmc.main", "qualname": "DEFAULT_WORKSPACE_PATH", "kind": "variable", "doc": "<p>Default phenotype workspace path</p>\n", "default_value": "PosixPath('workspace')"}, "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>omop.py module</p>\n\n<p>This module provides functionality to manage OMOP vocabularies.</p>\n"}, "acmc.omop.VOCAB_PATH": {"fullname": "acmc.omop.VOCAB_PATH", "modulename": "acmc.omop", "qualname": "VOCAB_PATH", "kind": "variable", "doc": "<p>Default OMOP vocabulary path</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>Supported OMOP CDM version number</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>Default OMOP sqllite database filename</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>Default OMOP sqllite database path</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>Default OMOP version file</p>\n", "default_value": "'omop_version.yml'"}, "acmc.omop.VERSION_PATH": {"fullname": "acmc.omop.VERSION_PATH", "modulename": "acmc.omop", "qualname": "VERSION_PATH", "kind": "variable", "doc": "<p>Default OMOP version path</p>\n", "default_value": "PosixPath('vocab/omop/omop_version.yml')"}, "acmc.omop.EXPORT_FILE": {"fullname": "acmc.omop.EXPORT_FILE", "modulename": "acmc.omop", "qualname": "EXPORT_FILE", "kind": "variable", "doc": "<p>Default OMOP export database filename</p>\n", "default_value": "'omop_54_export.sqlite'"}, "acmc.omop.vocabularies": {"fullname": "acmc.omop.vocabularies", "modulename": "acmc.omop", "qualname": "vocabularies", "kind": "variable", "doc": "<p>Required OMOP vocabularies definition</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>Type mappings from acmc medical coding types to OMOP vocabulary types</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\n<h6 id=\"arguments\">Arguments:</h6>\n\n<ul>\n<li><strong>omop_zip_file (str):</strong> vocabularies zip file distributed by OHDSI Athena</li>\n<li><strong>version (str):</strong> version of the vocabularies distributed by OHDSI Athena</li>\n</ul>\n\n<h6 id=\"raises\">Raises:</h6>\n\n<ul>\n<li><strong>ValueError:</strong> if the zip file does not exist</li>\n<li><strong>ValueError:</strong> if the file is not a zip file</li>\n<li><strong>Exception:</strong> if error reading omop csv files</li>\n</ul>\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\n<h6 id=\"arguments\">Arguments:</h6>\n\n<ul>\n<li><strong>version (str):</strong> version of the vocabularies distributed by OHDSI Athena</li>\n</ul>\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\n<h6 id=\"arguments\">Arguments:</h6>\n\n<ul>\n<li><strong>db_path (Path):</strong> the path to the omop sqllite database</li>\n</ul>\n\n<h6 id=\"raises\">Raises:</h6>\n\n<ul>\n<li><strong>FileNotFoundError:</strong> if the omop sqllite database does not exist</li>\n</ul>\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\n<h6 id=\"arguments\">Arguments:</h6>\n\n<ul>\n<li><strong>db_path (Path):</strong> the path to the omop sqllite database</li>\n</ul>\n\n<h6 id=\"raises\">Raises:</h6>\n\n<ul>\n<li><strong>FileNotFoundError:</strong> if the omop sqllite database does not exist</li>\n</ul>\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>Query to check if the table exists</p>\n\n<h6 id=\"arguments\">Arguments:</h6>\n\n<ul>\n<li><strong>cursor (sqlite3.Cursor):</strong> a sqllite database cursor</li>\n<li><strong>table_name (str):</strong> the table name to check</li>\n</ul>\n\n<h6 id=\"returns\">Returns:</h6>\n\n<blockquote>\n <p>bool: true if table exists</p>\n</blockquote>\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>Query to check if the vocabulary exists</p>\n\n<h6 id=\"arguments\">Arguments:</h6>\n\n<ul>\n<li><strong>cursor (sqlite3.Cursor):</strong> a sqllite database cursor</li>\n<li><strong>vocab_id (str):</strong> the vocabulary id to check</li>\n</ul>\n\n<h6 id=\"returns\">Returns:</h6>\n\n<blockquote>\n <p>bool: true if vocabulary id exists</p>\n</blockquote>\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>Query to check if the concept set exists</p>\n\n<h6 id=\"arguments\">Arguments:</h6>\n\n<ul>\n<li><strong>cursor (sqlite3.Cursor):</strong> a sqllite database cursor</li>\n<li><strong>concept_set_name (str):</strong> the concept set name to check</li>\n</ul>\n\n<h6 id=\"returns\">Returns:</h6>\n\n<blockquote>\n <p>bool: true if concept set exists</p>\n</blockquote>\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>Export concept sets to omop database in csv format</p>\n\n<h6 id=\"arguments\">Arguments:</h6>\n\n<ul>\n<li><strong>map_path (Path):</strong> path to the acmc map directory containing concept sets in csv format</li>\n<li><strong>export_path (Path):</strong> path to the directory where the omop database csv files are to be written</li>\n<li><strong>version (str):</strong> phenotype version for omop vocabulary version</li>\n<li><strong>omop_metadata (dict):</strong> phenotype omop metadata for omop vocabulary metadata</li>\n</ul>\n\n<h6 id=\"returns\">Returns:</h6>\n\n<blockquote>\n <p>Path: path to the exported sqllite database</p>\n</blockquote>\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 class=\"p\">:</span> <span class=\"nb\">dict</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>parse.py module</p>\n\n<p>This module provides functionality to set up medical code translation classes</p>\n"}, "acmc.parse.SUPPORTED_CODE_TYPES": {"fullname": "acmc.parse.SUPPORTED_CODE_TYPES", "modulename": "acmc.parse", "qualname": "SUPPORTED_CODE_TYPES", "kind": "variable", "doc": "<p>List of support medical coding types</p>\n", "default_value": "{'atc', 'read2', 'read3', 'opcs4', 'snomed', 'icd10'}"}, "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[[pandas.core.frame.DataFrame], pandas.core.series.Series], typing.Callable[[pandas.core.frame.DataFrame, pathlib.Path], pandas.core.frame.DataFrame]]]"}, "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.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>phenotype.py module</p>\n\n<p>This module provides functionality for managing phenotypes.</p>\n"}, "acmc.phen.PHEN_DIR": {"fullname": "acmc.phen.PHEN_DIR", "modulename": "acmc.phen", "qualname": "PHEN_DIR", "kind": "variable", "doc": "<p>Default phenotype directory name</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>Default phenotype directory path</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>Default concepts directory name</p>\n", "default_value": "'concepts'"}, "acmc.phen.MAP_DIR": {"fullname": "acmc.phen.MAP_DIR", "modulename": "acmc.phen", "qualname": "MAP_DIR", "kind": "variable", "doc": "<p>Default map directory name</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>Default concept set directory name</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>Default CSV concept set directory path</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>Default OMOP concept set directory path</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>List of default phenotype directories</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>Default configuration filename</p>\n", "default_value": "'config.yml'"}, "acmc.phen.VOCAB_VERSION_FILE": {"fullname": "acmc.phen.VOCAB_VERSION_FILE", "modulename": "acmc.phen", "qualname": "VOCAB_VERSION_FILE", "kind": "variable", "doc": "<p>Default vocabulary version filename</p>\n", "default_value": "'vocab_version.yml'"}, "acmc.phen.SEMANTIC_VERSION_TYPES": {"fullname": "acmc.phen.SEMANTIC_VERSION_TYPES", "modulename": "acmc.phen", "qualname": "SEMANTIC_VERSION_TYPES", "kind": "variable", "doc": "<p>List of semantic version increment types</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>Default semantic version increment type</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>Default phenotype repo branch name</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>Split column preprocessing action type</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>Codes column preprocessing action type</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>Divide column preprocessing action type</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>List of column preprocessing action types</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>List of supported source concept coding list file types</p>\n", "default_value": "['.xlsx', '.xls', '.csv']"}, "acmc.phen.CONFIG_SCHEMA": {"fullname": "acmc.phen.CONFIG_SCHEMA", "modulename": "acmc.phen", "qualname": "CONFIG_SCHEMA", "kind": "variable", "doc": "<p>Phenotype config.yml schema definition</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': ['atc', 'read2', 'read3', 'opcs4', 'snomed', 'icd10']}}, 'concept_sets': {'type': 'list', 'required': True, 'schema': {'type': 'dict', 'schema': {'name': {'type': 'string', 'required': True}, 'files': {'type': 'list', 'required': True, 'schema': {'type': 'dict', 'schema': {'path': {'type': 'string', 'required': True}, 'columns': {'type': 'dict', 'required': True}, 'category': {'type': 'string'}, 'actions': {'type': 'dict', 'schema': {'divide_col': {'type': 'string'}}}}}}}}}}}}"}, "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.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.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<h6 id=\"arguments\">Arguments:</h6>\n\n<ul>\n<li><strong>phen_dir (str):</strong> local directory path where the upstream repo is to be cloned</li>\n<li><strong>upstream_url (str):</strong> url to the upstream repo</li>\n<li><strong>upstream_version (str):</strong> version in the upstream repo to clone</li>\n<li><strong>new_origin_url (str, optional):</strong> url of the remote repo to set as the new origin. Defaults to None.</li>\n</ul>\n\n<h6 id=\"raises\">Raises:</h6>\n\n<ul>\n<li><strong>ValueError:</strong> if the specified version is not in the upstream repo</li>\n<li><strong>ValueError:</strong> if the upstream repo is not a valid phenotype repo</li>\n<li><strong>ValueError:</strong> if there's any other problems with Git</li>\n</ul>\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><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.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.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.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.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>trud.py module</p>\n\n<p>This module provides functionality to manage installation of the NHS TRUD vocabularies.</p>\n"}, "acmc.trud.FQDN": {"fullname": "acmc.trud.FQDN", "modulename": "acmc.trud", "qualname": "FQDN", "kind": "variable", "doc": "<p>Fully Qualified Domain Name of NHS digital TRUD service API</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>Default path to the TRUD vocabulary directory relative to the the acmc execution directory</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>TRUD version file</p>\n", "default_value": "'trud_version.yml'"}, "acmc.trud.VERSION_PATH": {"fullname": "acmc.trud.VERSION_PATH", "modulename": "acmc.trud", "qualname": "VERSION_PATH", "kind": "variable", "doc": "<p>Default path to the TRUD version file</p>\n", "default_value": "PosixPath('vocab/trud/trud_version.yml')"}, "acmc.trud.DOWNLOADS_PATH": {"fullname": "acmc.trud.DOWNLOADS_PATH", "modulename": "acmc.trud", "qualname": "DOWNLOADS_PATH", "kind": "variable", "doc": "<p>Default path to the TRUD vocabulary downloads directory</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>Default path to the processed TRUD mappings directory</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=\"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>Custom Dumper to retain quotes on strings in yaml library</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": 20}, "acmc.logging_config.DEFAULT_LOG_FILE": {"qualname": 3, "fullname": 6, "annotation": 0, "default_value": 6, "signature": 0, "bases": 0, "doc": 9}, "acmc.logging_config.setup_logger": {"qualname": 2, "fullname": 5, "annotation": 0, "default_value": 0, "signature": 24, "bases": 0, "doc": 16}, "acmc.logging_config.set_log_level": {"qualname": 3, "fullname": 6, "annotation": 0, "default_value": 0, "signature": 17, "bases": 0, "doc": 33}, "acmc.main": {"qualname": 0, "fullname": 2, "annotation": 0, "default_value": 0, "signature": 0, "bases": 0, "doc": 18}, "acmc.main.DEFAULT_WORKSPACE_PATH": {"qualname": 3, "fullname": 5, "annotation": 0, "default_value": 5, "signature": 0, "bases": 0, "doc": 6}, "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": 16}, "acmc.omop.VOCAB_PATH": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 5, "signature": 0, "bases": 0, "doc": 6}, "acmc.omop.OMOP_CDM_Version": {"qualname": 3, "fullname": 5, "annotation": 0, "default_value": 5, "signature": 0, "bases": 0, "doc": 7}, "acmc.omop.OMOP_DB_FILENAME": {"qualname": 3, "fullname": 5, "annotation": 0, "default_value": 7, "signature": 0, "bases": 0, "doc": 7}, "acmc.omop.DB_PATH": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 7, "signature": 0, "bases": 0, "doc": 7}, "acmc.omop.VERSION_FILE": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 7, "signature": 0, "bases": 0, "doc": 6}, "acmc.omop.VERSION_PATH": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 7, "signature": 0, "bases": 0, "doc": 6}, "acmc.omop.EXPORT_FILE": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 8, "signature": 0, "bases": 0, "doc": 7}, "acmc.omop.vocabularies": {"qualname": 1, "fullname": 3, "annotation": 0, "default_value": 202, "signature": 0, "bases": 0, "doc": 6}, "acmc.omop.omop_vocab_types": {"qualname": 3, "fullname": 5, "annotation": 0, "default_value": 51, "signature": 0, "bases": 0, "doc": 13}, "acmc.omop.install": {"qualname": 1, "fullname": 3, "annotation": 0, "default_value": 0, "signature": 28, "bases": 0, "doc": 96}, "acmc.omop.write_version_file": {"qualname": 3, "fullname": 5, "annotation": 0, "default_value": 0, "signature": 16, "bases": 0, "doc": 33}, "acmc.omop.clear": {"qualname": 1, "fullname": 3, "annotation": 0, "default_value": 0, "signature": 22, "bases": 0, "doc": 49}, "acmc.omop.delete": {"qualname": 1, "fullname": 3, "annotation": 0, "default_value": 0, "signature": 22, "bases": 0, "doc": 49}, "acmc.omop.table_exists": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 35, "bases": 0, "doc": 55}, "acmc.omop.vocab_exists": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 35, "bases": 0, "doc": 56}, "acmc.omop.concept_set_exist": {"qualname": 3, "fullname": 5, "annotation": 0, "default_value": 0, "signature": 36, "bases": 0, "doc": 59}, "acmc.omop.export": {"qualname": 1, "fullname": 3, "annotation": 0, "default_value": 0, "signature": 71, "bases": 0, "doc": 104}, "acmc.parse": {"qualname": 0, "fullname": 2, "annotation": 0, "default_value": 0, "signature": 0, "bases": 0, "doc": 18}, "acmc.parse.SUPPORTED_CODE_TYPES": {"qualname": 3, "fullname": 5, "annotation": 0, "default_value": 20, "signature": 0, "bases": 0, "doc": 8}, "acmc.parse.CodesError": {"qualname": 1, "fullname": 3, "annotation": 0, "default_value": 0, "signature": 0, "bases": 0, "doc": 17}, "acmc.parse.CodesError.__init__": {"qualname": 3, "fullname": 5, "annotation": 0, "default_value": 0, "signature": 51, "bases": 0, "doc": 3}, "acmc.parse.InvalidCodesException": {"qualname": 1, "fullname": 3, "annotation": 0, "default_value": 0, "signature": 0, "bases": 2, "doc": 17}, "acmc.parse.InvalidCodesException.__init__": {"qualname": 3, "fullname": 5, "annotation": 0, "default_value": 0, "signature": 9, "bases": 0, "doc": 3}, "acmc.parse.InvalidCodesException.error": {"qualname": 2, "fullname": 4, "annotation": 0, "default_value": 0, "signature": 0, "bases": 0, "doc": 3}, "acmc.parse.Proto": {"qualname": 1, "fullname": 3, "annotation": 0, "default_value": 0, "signature": 0, "bases": 0, "doc": 59}, "acmc.parse.Proto.__init__": {"qualname": 3, "fullname": 5, "annotation": 0, "default_value": 0, "signature": 44, "bases": 0, "doc": 3}, "acmc.parse.Proto.checks": {"qualname": 2, "fullname": 4, "annotation": 22, "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.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, 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// mirrored in build-search-index.js (part 1)
// Also split on html tags. this is a cheap heuristic, but good enough.
diff --git a/docs/cli.md b/docs/cli.md
index 4b756dcf5c094bdb2825dc614db8947c9be179cd..396f5291183990337ed7d5ce98192673da93ca4c 100644
--- a/docs/cli.md
+++ b/docs/cli.md
@@ -111,6 +111,9 @@ The `phen` command is used phenotype-related operations.
- `-t`, `--target-coding`: (Optional) Specify the target coding (e.g., `read2`, `read3`, `icd10`, `snomed`, `opcs4`).
- `-d`, `--phen-dir`: (Optional) Local phenotype workspace directory (default is ./workspace/phen).
+ - `--not-translate`: (Optional) Prevent any phenotype translation using NHS TRUD vocabularies. Therefore only concepts in already in the traget coding will be mapped.
+ - `--no-metadata`: (Optional) Prevent copying of metadata columns to output.
+
- **Publish Phenotype Configuration**
diff --git a/examples/config1.yml b/examples/config1.yml
index 32c4e253d9fc52e35eb581b4d77d636471653c51..9183235cfaa215fc580bbf44ada062ab58786bf4 100644
--- a/examples/config1.yml
+++ b/examples/config1.yml
@@ -8,9 +8,8 @@ phenotype:
- "read2"
- "read3"
concept_sets:
- - name: "ABDO_PAIN"
- file:
- path: "clinical-codes-org/Symptom code lists/Abdominal pain/res176-abdominal-pain.csv"
+ - name: "ABDO_PAIN"
+ files:
+ - path: "clinical-codes-org/Symptom code lists/Abdominal pain/res176-abdominal-pain.csv"
columns:
read2: "code"
-
diff --git a/examples/config2.yml b/examples/config2.yml
index c038c87f226a11926d30f535ba3b0b59f068ec1b..f7f3d033a4885fe1a99fc8ec546d4fd945329014 100644
--- a/examples/config2.yml
+++ b/examples/config2.yml
@@ -8,13 +8,13 @@ phenotype:
- "read2"
- "read3"
concept_sets:
- - name: "CVD_EVENTS"
- file:
- path: "clinical-codes-org/Cardiovascular events (ICD10)/res52-cardiovascular-events-icd10.csv"
+ - name: "CVD_EVENTS"
+ files:
+ - path: "clinical-codes-org/Cardiovascular events (ICD10)/res52-cardiovascular-events-icd10.csv"
columns:
- icd10: "code"
- - name: "DID_NOT_ATTEND"
- file:
- path: "clinical-codes-org/Non-attendance codes/res201-did-not-attend-appointment.csv"
+ icd10: "code"
+ - name: "DID_NOT_ATTEND"
+ files:
+ - path: "clinical-codes-org/Non-attendance codes/res201-did-not-attend-appointment.csv"
columns:
read2: "code"
\ No newline at end of file
diff --git a/examples/config3.yml b/examples/config3.yml
index 2662526b76bd9b33cc1ded6443d3331f4bddd486..7cb84f081aff11018dee41fb8165090cbae0d5ee 100644
--- a/examples/config3.yml
+++ b/examples/config3.yml
@@ -10,29 +10,29 @@ phenotype:
- "snomed"
concept_sets:
- name: "CVD_EVENTS"
- file:
- path: "clinical-codes-org/Cardiovascular events (ICD10)/res52-cardiovascular-events-icd10.csv"
- columns:
- icd10: "code"
+ files:
+ - path: "clinical-codes-org/Cardiovascular events (ICD10)/res52-cardiovascular-events-icd10.csv"
+ columns:
+ icd10: "code"
- name: "DID_NOT_ATTEND"
- file:
- path: "clinical-codes-org/Non-attendance codes/res201-did-not-attend-appointment.csv"
- columns:
- read2: "code"
+ files:
+ - path: "clinical-codes-org/Non-attendance codes/res201-did-not-attend-appointment.csv"
+ columns:
+ read2: "code"
- name: "HYPERTENSION"
- file:
- path: "hanlon/Read_codes_for_diagnoses.csv"
- columns:
- read2: "Read Code"
- category: "2"
- actions:
- divide_col: "MMCode"
+ files:
+ - path: "hanlon/Read_codes_for_diagnoses.csv"
+ columns:
+ read2: "Read Code"
+ category: "2"
+ actions:
+ divide_col: "MMCode"
- name: "DEPRESSION"
- file:
- path: "hanlon/Read_codes_for_diagnoses.csv"
- columns:
- read2: "Read Code"
- category: "3"
- actions:
- divide_col: "MMCode"
+ files:
+ - path: "hanlon/Read_codes_for_diagnoses.csv"
+ columns:
+ read2: "Read Code"
+ category: "3"
+ actions:
+ divide_col: "MMCode"
diff --git a/tests/test_acmc.py b/tests/test_acmc.py
index 72ff90c4f2edc85e05e776fe80aece3cb7217ee5..a7b195c1fd3248c1b5bd955e54f5109315c6d764 100644
--- a/tests/test_acmc.py
+++ b/tests/test_acmc.py
@@ -128,26 +128,6 @@ def test_phen_workflow(tmp_dir, monkeypatch, caplog, config_file):
main.main()
assert "Phenotype published successfully" in caplog.text
- # copy phenotype'
- with caplog.at_level(logging.DEBUG):
- monkeypatch.setattr(
- sys,
- "argv",
- [
- "main.py",
- "phen",
- "copy",
- "-d",
- str(phen_path.resolve()),
- "-td",
- str(tmp_dir.resolve()),
- "-v",
- "0.0.1",
- ],
- )
- main.main()
- assert "Phenotype copied successfully" in caplog.text
-
# diff phenotype
with caplog.at_level(logging.DEBUG):
old_path = tmp_dir / "0.0.1"