From 47dcd2ebb11d4c5497cf1a9d01e64e7eae3a2ccb Mon Sep 17 00:00:00 2001
From: Jakub Dylag <jjd1c23@soton.ac.uk>
Date: Wed, 23 Apr 2025 11:06:42 +0100
Subject: [PATCH] (feat) flag no metadata in phen map output
---
acmc/main.py | 8 +++++++-
acmc/phen.py | 27 +++++++++++++++------------
docs/cli.md | 1 +
3 files changed, 23 insertions(+), 13 deletions(-)
diff --git a/acmc/main.py b/acmc/main.py
index 91a40bc..a831fae 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, args.not_translate)
+ phen.map(args.phen_dir, args.target_coding, args.not_translate, args.no_metadata)
def _phen_export(args: argparse.Namespace):
@@ -223,6 +223,12 @@ def main():
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
diff --git a/acmc/phen.py b/acmc/phen.py
index 8d6cb82..c745838 100644
--- a/acmc/phen.py
+++ b/acmc/phen.py
@@ -783,7 +783,7 @@ def write_vocab_version(phen_path: Path):
)
-def map(phen_dir: str, target_code_type: str, not_translate:bool):
+def map(phen_dir: str, target_code_type: str, not_translate:bool, no_metadata:bool):
_logger.info(f"Processing phenotype: {phen_dir}")
# Validate configuration
@@ -807,15 +807,15 @@ def map(phen_dir: str, target_code_type: str, not_translate:bool):
)
if target_code_type is not None:
- _map_target_code_type(phen_path, phenotype, target_code_type, not_translate)
+ _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, not_translate)
+ _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, not_translate:bool):
+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
@@ -886,7 +886,8 @@ def _map_target_code_type(phen_path: Path, phenotype: dict, target_code_type: st
)
trans_out = add_metadata(
codes=trans_out,
- metadata=concept_set_metadata
+ metadata=concept_set_metadata,
+ no_metadata=no_metadata,
)
out = pd.concat([out, trans_out])
else:
@@ -899,7 +900,8 @@ def _map_target_code_type(phen_path: Path, phenotype: dict, target_code_type: st
)
trans_out = add_metadata(
codes=trans_out,
- metadata=concept_set_metadata
+ metadata=concept_set_metadata,
+ no_metadata=no_metadata,
)
out = pd.concat([out, trans_out])
@@ -998,15 +1000,16 @@ def _map_target_code_type(phen_path: Path, phenotype: dict, target_code_type: st
# Add metadata dict to each row of Df codes
def add_metadata(
- codes: pd.DataFrame, metadata: dict
+ codes: pd.DataFrame, metadata: dict, no_metadata:bool,
) -> pd.DataFrame:
"""Add concept set metadata, stored as a dictionary, to each concept row"""
- 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}"
- )
+ 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
diff --git a/docs/cli.md b/docs/cli.md
index 0a1cf39..396f529 100644
--- a/docs/cli.md
+++ b/docs/cli.md
@@ -112,6 +112,7 @@ 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**
--
GitLab