From 315be70939dae5d7aebc91adb833ff1149033be8 Mon Sep 17 00:00:00 2001
From: Michael Boniface <m.j.boniface@soton.ac.uk>
Date: Thu, 20 Feb 2025 09:07:12 +0000
Subject: [PATCH] changed code types to objectives not classes so don't need to
instantiate them when used. This is possible as there's no state specific to
instances
---
acmc/phen.py | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
diff --git a/acmc/phen.py b/acmc/phen.py
index 90884db..ad3b9f2 100644
--- a/acmc/phen.py
+++ b/acmc/phen.py
@@ -233,6 +233,7 @@ def validate(phen_dir):
# check codes definition
concept_set_mapping_names = []
for item in concept_codes:
+
required_keys = {"folder", "files"}
if required_keys.issubset(item.keys()):
# check concept codes path is a directory
@@ -393,7 +394,7 @@ def preprocess(df, file, target_code_type=None, codes_file=None, translate=True,
# QA for every code type in df run preprocess_code()
for code_type_name, code_type in parse.code_types.items():
if code_type_name in file['columns']:
- logger.info(f"Processing {k} Codes...")
+ logger.info(f"Processing {code_type_name} Codes...")
out = preprocess_code(out=out,
codes=df[file['columns'][code_type_name]].dropna(),
codes_file=codes_file,
--
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