Warnings printed to stderr, --no-warning partially ignored

[poshul]

Expected Behavior

Warnings should be printed to stdout not stderr. --no-warning should silence warnings

Actual Behavior

warnings are printed to stderr. passing --no-warning does not silence warnings.

Example output:

with --no-warning

py_venv) samuel@Wald2:~/git/OpenMS$ cwltool --no-warning --validate --non-strict share/OpenMS/commonwl/NucleicAcidSearchEngine.cwl
share/OpenMS/commonwl/NucleicAcidSearchEngine.cwl:21:3: object id 'share/OpenMS/commonwl/NucleicAcidSearchEngine.cwl#db_out' previously defined
share/OpenMS/commonwl/NucleicAcidSearchEngine.cwl:24:3: object id 'share/OpenMS/commonwl/NucleicAcidSearchEngine.cwl#digest_out' previously defined
share/OpenMS/commonwl/NucleicAcidSearchEngine.cwl:33:3: object id 'share/OpenMS/commonwl/NucleicAcidSearchEngine.cwl#exp_ms2_out' previously defined
share/OpenMS/commonwl/NucleicAcidSearchEngine.cwl:18:3: object id 'share/OpenMS/commonwl/NucleicAcidSearchEngine.cwl#id_out' previously defined
share/OpenMS/commonwl/NucleicAcidSearchEngine.cwl:27:3: object id 'share/OpenMS/commonwl/NucleicAcidSearchEngine.cwl#lfq_out' previously defined
share/OpenMS/commonwl/NucleicAcidSearchEngine.cwl:15:3: object id 'share/OpenMS/commonwl/NucleicAcidSearchEngine.cwl#out' previously defined
share/OpenMS/commonwl/NucleicAcidSearchEngine.cwl:30:3: object id 'share/OpenMS/commonwl/NucleicAcidSearchEngine.cwl#theo_ms2_out' previously defined
share/OpenMS/commonwl/NucleicAcidSearchEngine.cwl is valid CWL.

without --no-warning:

(py_venv) samuel@Wald2:~/git/OpenMS$ cwltool --validate --non-strict share/OpenMS/commonwl/NucleicAcidSearchEngine.cwl 1>/dev/null
INFO /home/samuel/Downloads/py_venv/bin/cwltool 3.1.20241112140730
INFO Resolved 'share/OpenMS/commonwl/NucleicAcidSearchEngine.cwl' to 'file:///home/samuel/git/OpenMS/share/OpenMS/commonwl/NucleicAcidSearchEngine.cwl'
share/OpenMS/commonwl/NucleicAcidSearchEngine.cwl:21:3: object id 'share/OpenMS/commonwl/NucleicAcidSearchEngine.cwl#db_out' previously defined
WARNING share/OpenMS/commonwl/NucleicAcidSearchEngine.cwl:21:3: object id 'share/OpenMS/commonwl/NucleicAcidSearchEngine.cwl#db_out' previously defined
share/OpenMS/commonwl/NucleicAcidSearchEngine.cwl:24:3: object id 'share/OpenMS/commonwl/NucleicAcidSearchEngine.cwl#digest_out' previously defined
WARNING share/OpenMS/commonwl/NucleicAcidSearchEngine.cwl:24:3: object id 'share/OpenMS/commonwl/NucleicAcidSearchEngine.cwl#digest_out' previously defined
share/OpenMS/commonwl/NucleicAcidSearchEngine.cwl:33:3: object id 'share/OpenMS/commonwl/NucleicAcidSearchEngine.cwl#exp_ms2_out' previously defined
WARNING share/OpenMS/commonwl/NucleicAcidSearchEngine.cwl:33:3: object id 'share/OpenMS/commonwl/NucleicAcidSearchEngine.cwl#exp_ms2_out' previously defined
share/OpenMS/commonwl/NucleicAcidSearchEngine.cwl:18:3: object id 'share/OpenMS/commonwl/NucleicAcidSearchEngine.cwl#id_out' previously defined
WARNING share/OpenMS/commonwl/NucleicAcidSearchEngine.cwl:18:3: object id 'share/OpenMS/commonwl/NucleicAcidSearchEngine.cwl#id_out' previously defined
share/OpenMS/commonwl/NucleicAcidSearchEngine.cwl:27:3: object id 'share/OpenMS/commonwl/NucleicAcidSearchEngine.cwl#lfq_out' previously defined
WARNING share/OpenMS/commonwl/NucleicAcidSearchEngine.cwl:27:3: object id 'share/OpenMS/commonwl/NucleicAcidSearchEngine.cwl#lfq_out' previously defined
share/OpenMS/commonwl/NucleicAcidSearchEngine.cwl:15:3: object id 'share/OpenMS/commonwl/NucleicAcidSearchEngine.cwl#out' previously defined
WARNING share/OpenMS/commonwl/NucleicAcidSearchEngine.cwl:15:3: object id 'share/OpenMS/commonwl/NucleicAcidSearchEngine.cwl#out' previously defined
share/OpenMS/commonwl/NucleicAcidSearchEngine.cwl:30:3: object id 'share/OpenMS/commonwl/NucleicAcidSearchEngine.cwl#theo_ms2_out' previously defined
WARNING share/OpenMS/commonwl/NucleicAcidSearchEngine.cwl:30:3: object id 'share/OpenMS/commonwl/NucleicAcidSearchEngine.cwl#theo_ms2_out' previously defined

[mr-c]

Warnings should be printed to stdout

For cwltool --validate that could be okay, but for the normal use of cwltool to execute a CWL document, we can't print warnings to stdout as the output of cwltool is the JSON CWL output object representing the results of the execution.

I agree that --no-warning should silence the previously defined messages (which come from Schema Salad)

[poshul]

For our CI purposes, as long as --no-warning silences the warnings we don't care too much where they'd get printed otherwise, so if changing that (even for --validate only) is problematic I'm okay just not doing it.

[mr-c]

@poshul a fix for --no-warnings to not print warnings is incoming. But maybe more interesting is that --validate will have all warnings and errors in stdout, so maybe you won't need --no-warnings.