From c5bbb8ac8f8271b631331f2546111f273ed2e57c Mon Sep 17 00:00:00 2001
From: Jakub Dylag <jjd1c23@soton.ac.uk>
Date: Wed, 23 Apr 2025 09:37:22 +0100
Subject: [PATCH] (feat) flag do not translate in phen map
---
acmc/main.py | 8 +++++++-
acmc/phen.py | 14 ++++++++------
docs/cli.md | 2 ++
3 files changed, 17 insertions(+), 7 deletions(-)
diff --git a/acmc/main.py b/acmc/main.py
index 5f796b0..91a40bc 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)
def _phen_export(args: argparse.Namespace):
@@ -217,6 +217,12 @@ 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.set_defaults(func=_phen_map)
# phen export
diff --git a/acmc/phen.py b/acmc/phen.py
index 052e1a0..8d6cb82 100644
--- a/acmc/phen.py
+++ b/acmc/phen.py
@@ -663,7 +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"""
@@ -688,7 +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
@@ -783,7 +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):
_logger.info(f"Processing phenotype: {phen_dir}")
# Validate configuration
@@ -807,15 +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)
else:
for t in phenotype["map"]:
- _map_target_code_type(phen_path, phenotype, t)
+ _map_target_code_type(phen_path, phenotype, t, not_translate)
_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):
_logger.debug(f"Target coding format: {target_code_type}")
concepts_path = phen_path / CONCEPTS_DIR
# Create output dataframe
@@ -882,6 +882,7 @@ def _map_target_code_type(phen_path: Path, phenotype: dict, target_code_type: st
source_df,
target_code_type=target_code_type,
concept_name=concept_set_name,
+ not_translate=not_translate,
)
trans_out = add_metadata(
codes=trans_out,
@@ -894,6 +895,7 @@ def _map_target_code_type(phen_path: Path, phenotype: dict, target_code_type: st
source_df,
target_code_type=target_code_type,
concept_name=concept_set_name,
+ not_translate=not_translate,
)
trans_out = add_metadata(
codes=trans_out,
diff --git a/docs/cli.md b/docs/cli.md
index 4b756dc..0a1cf39 100644
--- a/docs/cli.md
+++ b/docs/cli.md
@@ -111,6 +111,8 @@ 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.
+
- **Publish Phenotype Configuration**
--
GitLab