From efa866595c1aec6a089a8f1e2efd57e142de3da4 Mon Sep 17 00:00:00 2001
From: burri0000 <dominik.burri@unibas.ch>
Date: Wed, 14 Jul 2021 09:59:24 +0200
Subject: [PATCH] Report missing required keys, restructure rule config
handling.
---
workflow/Snakefile | 37 +++++++++++++++++++------------------
1 file changed, 19 insertions(+), 18 deletions(-)
diff --git a/workflow/Snakefile b/workflow/Snakefile
index e5d270b..346f081 100644
--- a/workflow/Snakefile
+++ b/workflow/Snakefile
@@ -28,36 +28,37 @@ try:
with open(template_config_path) as _file:
template_config = yaml.safe_load(_file)
logger.info(f"Loaded template config from {template_config_path}.")
- # Check if config contains required fields in example config
- for key in template_config:
- if key != 'optional':
- assert key in config
except FileNotFoundError:
logger.error(f"No config file found at {template_config_path}! ")
raise
-except AssertionError:
- logger.error(f"Required config fields from {template_config_path} do not match {config.keys()}")
- raise
+# Check if config contains required fields in example config
+missing = [key for key in template_config if key not in config and key != 'optional']
+if missing:
+ err_msg = f"Required keys missing: {missing}"
+ logger.error(err_msg)
+ raise ValueError(err_msg)
# Check if optional field available
-if 'optional' not in config:
+if 'optional' not in config or config['optional'] != dict:
+ logger.info(f'No "optional" field found or no valid configuration for config.yaml.')
config['optional'] = {}
# Check optional fields and include in config if not present
for optkey, value in template_config['optional'].items():
if optkey not in config['optional']:
config['optional'][optkey] = value
- logger.info(f"Added optional field: \"{optkey}\" with value: \"{value}\" to config.")
+ logger.info(f'Set default value for optional parameter "{optkey}" to : "{value}"')
# Parse YAML rule config file
-if 'rule_config' in config['optional'] and config['optional']['rule_config']:
- try:
- with open(config['optional']['rule_config']) as _file:
- rule_config = yaml.safe_load(_file)
- logger.info(f"Loaded rule_config from {config['optional']['rule_config']}.")
- except FileNotFoundError:
- logger.error(f"No rule config file found at {config['optional']['rule_config']}. Either provide file or remove rule_config parameter from config.yaml! ")
- raise
-else:
+try:
+ with open(config['optional']['rule_config']) as _file:
+ rule_config = yaml.safe_load(_file)
+ logger.info(f"Loaded rule_config from {config['optional']['rule_config']}.")
+except TypeError:
+ logger.error(f'No string supplied at field "rule_config", but: {config["optional"]["rule_config"]}')
+except FileNotFoundError:
+ logger.error(f"No rule config file found at {config['optional']['rule_config']}. Either provide file or remove rule_config parameter from config.yaml! ")
+ raise
+except KeyError:
rule_config = {}
logger.warning(f"No rule config specified: using default values for all tools.")
--
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