From 8ab33d12a167fa612d6eec76ddf033171e3ca905 Mon Sep 17 00:00:00 2001
From: Michael Boniface <m.j.boniface@soton.ac.uk>
Date: Thu, 20 Feb 2025 09:11:16 +0000
Subject: [PATCH] fixed empty output exception as it did not print the config
file path
---
acmc/phen.py | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/acmc/phen.py b/acmc/phen.py
index ad3b9f2..15c2e49 100644
--- a/acmc/phen.py
+++ b/acmc/phen.py
@@ -380,10 +380,10 @@ def preprocess(df, file, target_code_type=None, codes_file=None, translate=True,
if target_code_type and not translate:
# QA only on target codes
- if target_code_type in file[columns]:
+ if target_code_type in file['columns']:
logger.info(f"Processing {target_code_type} Codes...")
out = preprocess_code(out=out,
- codes=df[file[columns][target_code_type]].dropna(),
+ codes=df[file['columns'][target_code_type]].dropna(),
codes_file=codes_file,
checker=parse.code_types[target_code_type],
output_col=target_code_type,
@@ -534,7 +534,7 @@ def map(phen_dir, target_code_type, translate=True):
# test if there's any output from processing
if len(out.index) == 0:
- raise Exception("The output after map processing has no output, check configuration file {str(config_path.resolve())} is not empty")
+ raise Exception(f"No output after map processing, check configuration {str(config_path.resolve())}")
# Final processing
out = out.reset_index(drop=True)
--
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