mirror of
https://github.com/MillironX/nf-configs.git
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75 lines
2.6 KiB
Python
75 lines
2.6 KiB
Python
#!/usr/bin/env python
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#######################################################################
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#######################################################################
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## Created on November 26 to check pipeline configs for nf-core/configs
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#######################################################################
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#######################################################################
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import os
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import sys
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import argparse
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import re
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import yaml
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############################################
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############################################
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## PARSE ARGUMENTS
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############################################
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############################################
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Description = 'Double check custom config file and github actions file to test all cases'
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Epilog = """Example usage: python cchecker.py <nfcore_custom.config> <github_actions_file>"""
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argParser = argparse.ArgumentParser(description=Description, epilog=Epilog)
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## REQUIRED PARAMETERS
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argParser.add_argument('CUSTOM_CONFIG', help="Input nfcore_custom.config.")
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argParser.add_argument('GITHUB_CONFIG', help="Input Github Actions YAML")
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args = argParser.parse_args()
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############################################
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############################################
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## MAIN FUNCTION
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############################################
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############################################
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def check_config(Config, Github):
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regex = 'includeConfig*'
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ERROR_STR = 'ERROR: Please check config file! Did you really update the profiles?'
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## CHECK Config First
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config_profiles = set()
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with open(Config, 'r') as cfg:
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for line in cfg:
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if re.search(regex, line):
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hit = line.split('/')[2].split('.')[0]
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config_profiles.add(hit.strip())
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### Check Github Config now
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tests = set()
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### Ignore these profiles
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ignore_me = ['czbiohub_aws']
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tests.update(ignore_me)
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# parse yaml GitHub actions file
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try:
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with open(Github, 'r') as ghfile:
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wf = yaml.safe_load(ghfile)
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profile_list = wf["jobs"]["profile_test"]["strategy"]["matrix"]["profile"]
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except Exception as e:
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print("Could not parse yaml file: {}, {}".format(Github, e))
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sys.exit(1)
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# Add profiles to test
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for profile in profile_list:
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tests.add(profile.strip())
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###Check if sets are equal
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try:
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assert tests == config_profiles
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except (AssertionError):
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print("Tests don't seem to test these profiles properly. Please check whether you added the profile to the Github Actions testing YAML.\n")
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print(config_profiles.symmetric_difference(tests))
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sys.exit(1)
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check_config(Config=args.CUSTOM_CONFIG,Github=args.GITHUB_CONFIG)
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