From d4b8f3b47bcb879f8cb9c9d80d5ed0cb5ccf368f Mon Sep 17 00:00:00 2001
From: Amandine PERRIN <amandine.perrin@pasteur.fr>
Date: Wed, 10 Feb 2021 11:21:16 +0100
Subject: [PATCH] Raise error if duplication in parameters in config file
---
PanACoTA/utils_argparse.py | 8 ++++++--
1 file changed, 6 insertions(+), 2 deletions(-)
diff --git a/PanACoTA/utils_argparse.py b/PanACoTA/utils_argparse.py
index 27b816af..363cf317 100644
--- a/PanACoTA/utils_argparse.py
+++ b/PanACoTA/utils_argparse.py
@@ -196,11 +196,15 @@ class Conf_all_parser(configparser.ConfigParser):
"""
def __init__(self, conffile, readsec=[]):
super().__init__()
- if not os.path.isfile(conffile):
+ if conffile != "" and not os.path.isfile(conffile):
print(f"Error: config file {conffile} not found.")
sys.exit(1)
self.conffile = conffile
- self.read(conffile)
+ try:
+ self.read(conffile)
+ except configparser.DuplicateOptionError as err:
+ print(err)
+ sys.exit(1)
self.sec_dicts = {}
for sec in readsec:
# If section in configfile, put its arguments and values to a dict
--
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