From 1e8776a8b2dbcd74b5f43ceeffe91a44d2d0e399 Mon Sep 17 00:00:00 2001
From: Michael Boniface <m.j.boniface@soton.ac.uk>
Date: Thu, 20 Feb 2025 10:37:49 +0000
Subject: [PATCH] added exceptions in phen
---
acmc/phen.py | 14 ++++++++------
1 file changed, 8 insertions(+), 6 deletions(-)
diff --git a/acmc/phen.py b/acmc/phen.py
index 25ab3d4..c232421 100644
--- a/acmc/phen.py
+++ b/acmc/phen.py
@@ -404,10 +404,6 @@ def translate_codes(df, target_code_type):
# merge on corresponding codes and take target column
translated = pd.merge(col, df_map, how="left")[target_code_type]
# TODO: BUG mask does not match column
- # log_invalid_code(col,
- # ~translated.isna(),
- # code_type=col_name,
- # cause=f"Translation to {target}") #log codes with no translation
codes = pd.concat([codes, translated]) # merge to output
else:
logger.warning(f"No mapping from {col_name} to {target_code_type}, file {str(map_path.resolve())} does not exist")
@@ -419,10 +415,12 @@ def map_file(df, target_code_type, out, concepts, meta_columns=[]):
# seperate out meta_columns
metadata_df = df[meta_columns]
df = df.drop(columns=meta_columns)
+
+ # translate codes
codes = translate_codes(df, target_code_type)
codes = codes.dropna() # delete NaNs
- # Append to out df
+ # Append to output if translated
if len(codes) > 0:
codes = pd.DataFrame({"CONCEPT": codes})
codes = codes.join(metadata_df)
@@ -509,10 +507,14 @@ def map(phen_dir, target_code_type):
out,
concepts=file["concept_set_categories"][cat],
meta_columns=meta_columns,)
+ else:
+ raise AttributeError(f"File {file} has either no concept_set or conceot_set_categories or the instance of dataframe objectives associated is incorrect, concept_set must be a DataFrame, conceot_set_categories must be pd.core.groupby.generic.DataFrameGroupBy")
+ else:
+ logger.warning(f"File {file} has no output after preprocessing in config {str(config_path.resolve())}")
# Check there is output from processing
if len(out.index) == 0:
- raise Exception(f"No output after map processing, check configuration {str(config_path.resolve())}")
+ raise Exception(f"No output after map processing, check config {str(config_path.resolve())}")
# Final processing
out = out.reset_index(drop=True)
--
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