(feat) flag do not translate in phen map

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

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,

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**