From 305237d500d0727eba18e2331ecbb3ab2044fe4b Mon Sep 17 00:00:00 2001
From: Michael Boniface <m.j.boniface@soton.ac.uk>
Date: Thu, 20 Feb 2025 09:02:38 +0000
Subject: [PATCH] standardised code_type import in phen
---
acmc/parse.py | 16 ++++++++--------
acmc/phen.py | 12 ++++++------
2 files changed, 14 insertions(+), 14 deletions(-)
diff --git a/acmc/parse.py b/acmc/parse.py
index 790cad6..2a04067 100644
--- a/acmc/parse.py
+++ b/acmc/parse.py
@@ -397,14 +397,14 @@ class Cprd(Proto):
]
code_types = {
- "read2": Read2,
- "read3": Read3,
- "icd10": Icd10,
- "snomed": Snomed,
- "opcs4": Opcs4,
- "atc": Atc,
- "med": Med,
- "cprd": Cprd,
+ "read2": Read2(),
+ "read3": Read3(),
+ "icd10": Icd10(),
+ "snomed": Snomed(),
+ "opcs4": Opcs4(),
+ "atc": Atc(),
+ "med": Med(),
+ "cprd": Cprd(),
}
vocab_types = {
diff --git a/acmc/phen.py b/acmc/phen.py
index bc0d7e5..90884db 100644
--- a/acmc/phen.py
+++ b/acmc/phen.py
@@ -384,21 +384,21 @@ def preprocess(df, file, target_code_type=None, codes_file=None, translate=True,
out = preprocess_code(out=out,
codes=df[file[columns][target_code_type]].dropna(),
codes_file=codes_file,
- checker=parse.code_types[target_code_type](),
+ checker=parse.code_types[target_code_type],
output_col=target_code_type,
metadata_df=df[meta_columns])
else:
logger.warning(f"No {target_code_type} Codes to process")
else:
# QA for every code type in df run preprocess_code()
- for k, v in parse.code_types.items():
- if k in file['columns']:
+ for code_type_name, code_type in parse.code_types.items():
+ if code_type_name in file['columns']:
logger.info(f"Processing {k} Codes...")
out = preprocess_code(out=out,
- codes=df[file['columns'][k]].dropna(),
+ codes=df[file['columns'][code_type_name]].dropna(),
codes_file=codes_file,
- checker=v(),
- output_col=k,
+ checker=code_type,
+ output_col=code_type_name,
metadata_df=df[meta_columns])
return out, meta_columns
--
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