diff --git a/acmc.py b/acmc.py
index ae4b051122bcf45cc4331b1f91f3394b1f29386d..40a3d78b2a432e7f32d700ac8ba19005e2145362 100644
--- a/acmc.py
+++ b/acmc.py
@@ -97,7 +97,7 @@ def main():
map_process_parser = map_subparsers.add_parser("process", help="Process map configuration file")
map_process_parser.add_argument("-c", "--config-file", required=True, help="Phenotype configuration file")
map_process_parser.add_argument("-s", "--source-codes-dir", required=True, help="Source codes root directory")
- map_process_parser.add_argument("-t", "--target-coding", required=True, choices=['read2', 'read3', 'icd10', 'snomed', 'opcs4'], help="Specify the target coding (read2, read3, icd10, snomed, opcs4)")
+ map_process_parser.add_argument("-t", "--target-coding", required=True, choices=['read2_code', 'read3_code', 'icd10_code', 'snomed_code', 'opcs4_code'], help="Specify the target coding (read2, read3, icd10, snomed, opcs4)")
map_process_parser.add_argument("-o", "--output-file", type=str, default=str(map.OUTPUT_PATH.resolve()), help="Output directory for CSV or OMOP database")
# Flags
diff --git a/example/phenotype_config.json b/example/phenotype_config.json
index af73d026dde455c0e54ae60f422ed93217ee2d82..c99ffcc76dfcae38c488d72067e5cdd18c78c3e2 100644
--- a/example/phenotype_config.json
+++ b/example/phenotype_config.json
@@ -22,25 +22,7 @@
"CODING LIST": "https://git.soton.ac.uk/meld/meldb-external/phenotype/-/tree/main/codes/ClinicalCodes.org%20from%20the%20University%20of%20Manchester/Symptom%20code%20lists/Abdominal%20pain/res176-abdominal-pain.csv ",
"NOTES": "2023-09-08: Clinical SF confirmed that the clinical view would be that this would need to be recurrent or persistent."
}
- },
- {
- "concept_set_name": "CVD_EVENTS",
- "concept_set_status": "AGREED",
- "metadata": {
- "#": "9",
- "CONCEPT DESCRIPTION": "Cardiovascular events",
- "CONCEPT TYPE": "Outcome event",
- "CONCEPT ONTOLOGY CLASS": "nan",
- "DATE ADDED ": "2023-08-25",
- "REQUEST REASON ": "SF - requested by email - to explore an examplar 'outcome measure'",
- "SOURCE INFO": "YES",
- "FUNCTION": "QUERY BY CODING LIST",
- "FUNCTION.1": "https://clinicalcodes.rss.mhs.man.ac.uk/",
- "CODING LIST": "https://git.soton.ac.uk/meld/meldb-external/phenotype/-/tree/main/codes/ClinicalCodes.org%20from%20the%20University%20of%20Manchester/Cardiovascular%20events%20(ICD10)/res52-cardiovascular-events-icd10.csv",
- "NOTES": "2023-11-17 - Code cannot currently be PROCESSED = COMPLETE as no mappings from ICD10 to Read v2 exist, pending confirmation from clinical team on next steps.",
- "Relation to Ontology": "YES WITH ISSUES"
- }
- }
+ }
]
},
"codes": [
@@ -51,7 +33,7 @@
{
"file": "Symptom code lists/Abdominal pain/res176-abdominal-pain.csv",
"columns": {
- "read2": "code",
+ "read2_code": "code",
"metadata": [
"description"
]
@@ -59,20 +41,7 @@
"concept_set": [
"ABDO_PAIN"
]
- },
- {
- "file": "Cardiovascular events (ICD10)/res52-cardiovascular-events-icd10.csv",
- "columns": {
- "icd10_code": "code",
- "metadata": [
- "description"
- ]
- },
- "concept_set": [
- "CVD_EVENTS"
- ]
- }
-
+ }
]
}
]
diff --git a/map.py b/map.py
index 5456de729fe0c3a07f25af60b575d711f7370f69..05239c88da45c1fa89e7da709a8012e1156b9071 100644
--- a/map.py
+++ b/map.py
@@ -203,6 +203,7 @@ def process(config_file, source_codes_dir, target_code_type, translate=True, ver
# Perform Structural Changes to file before preprocessing
# split column with multiple code types
+ print("Processing actions")
if ("actions" in file and "split_col" in file["actions"] and "codes_col" in file["actions"]):
split_col = file["actions"]["split_col"]
codes_col = file["actions"]["codes_col"]
@@ -213,7 +214,7 @@ def process(config_file, source_codes_dir, target_code_type, translate=True, ver
oh[oh == False] = np.nan # replace 0s with None
df = pd.concat([df, oh], axis=1) # merge in new columns
- # Preprocessing & Validation Checks
+ # Preprocessing & Validation Checks
if "columns" in file:
meta_columns = [] # meta columns to keep with codes
if "actions" in file and "divide_col" in file["actions"]:
@@ -225,17 +226,17 @@ def process(config_file, source_codes_dir, target_code_type, translate=True, ver
else:
raise Exception("No column format provided")
- # partition table by categorical column
+ # partition table by categorical column
if ("actions" in file and "divide_col" in file["actions"] and len(df) > 0):
divide_col = file["actions"]["divide_col"]
print("Action: Dividing Table by", divide_col, "column into: ", df[divide_col].unique(),)
df = df.groupby(divide_col)
-
- # Map to MELDB Concept/Phenotype
- if len(df) == 0:
+
+ # Map to MELDB Concept/Phenotype
+ if len(df) == 0:
pass
# out = df
- elif ("concept_set" in file) and isinstance(df, pd.core.frame.DataFrame):
+ elif ("concept_set" in file) and isinstance(df, pd.core.frame.DataFrame):
out = map_file(df, target_code_type, out, concepts=file["concept_set"], meta_columns=meta_columns, translate=translate,)
elif ("concept_set_categories" in file) and isinstance(df, pd.core.groupby.generic.DataFrameGroupBy):
meta_columns.remove(divide_col) # delete categorical column
diff --git a/parse.py b/parse.py
index ddf07484c68deb7100268de9c551ec71d31bc38d..8d66f305db0dbb1fb11d0e50d9f4405649b966b1 100644
--- a/parse.py
+++ b/parse.py
@@ -344,14 +344,14 @@ class Cprd_code(Proto_code):
]
code_types = {
- "read2": Read2_code,
- "read3": Read3_code,
- "icd10": Icd10_code,
- "snomed": Snomed_code,
- "opcs4": Opcs4_code,
- "atc": Atc_code,
- "med": Med_code,
- "cprd": Cprd_code,
+ "read2_code": Read2_code,
+ "read3_code": Read3_code,
+ "icd10_code": Icd10_code,
+ "snomed_code": Snomed_code,
+ "opcs4_code": Opcs4_code,
+ "atc_code": Atc_code,
+ "med_code": Med_code,
+ "cprd_code": Cprd_code,
}
vocab_types = {