Don't configure the root logger when importing image_puller - #471
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mr-c merged 1 commit intoSep 26, 2026
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cwl_utils.image_puller called logging.basicConfig(level=logging.INFO) at import time. Since cwltool 3.3 imports it from cwltool.singularity, any program that imports cwltool gets its root logger set to INFO with a stderr handler, so INFO messages from unrelated libraries start going to stderr. Configure logging in docker-extract's main() instead, so the CLI output is unchanged.
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cwl_utils.image_puller calls logging.basicConfig(level=logging.INFO) at import time, and cwltool 3.3 imports it. Any Galaxy process that imports cwltool then logs INFO messages to stderr, which fails jobs whose tools treat stderr as an error, such as history export to a URI (gcsfs logs an INFO line when imported). With cwl-utils 0.44 excluded the resolver falls back to cwltool 3.2.20260720092025 and cwl-utils 0.43, as on dev. Upstream fix: common-workflow-language/cwl-utils#471
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Coverage 38.85% 38.86%
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mr-c
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Thank you @mvdbeek ! |
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Thanks for the quick merge! |
mvdbeek
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cwl-utils 0.45 includes the fix for the import-time logging.basicConfig() (common-workflow-language/cwl-utils#471), so the cwltool update can go ahead. The cwl-utils!=0.44 exclusion stays.
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cwl_utils.image_pullercallslogging.basicConfig(level=logging.INFO)at import time. cwltool 3.3.20260925135507 now imports it fromcwltool/singularity.py, so any program that imports cwltool has its root logger set to INFO with a stderr handler. INFO messages from unrelated libraries then go to stderr.In Galaxy this broke history exports. The export job imports cwltool indirectly, gcsfs then logs an INFO line at import, and Galaxy treats unexpected stderr from that job as a failure (galaxyproject/galaxy#23736).
This moves the
basicConfigcall intodocker-extract'smain(), so the CLI still prints the puller's INFO messages, and adds a test that importingcwl_utils.image_pullerleaves the root logger unconfigured. I checked that the test fails without the change.