conformance test gives "TypeError: __init__() got an unexpected keyword argument 'type'"

[samuell]

I tend to get these errors with cwltool --conformance-test, white a bit.

One example is for the samtools-view tool, but I suddenly got a similar error for my work on bwa-aln.cwl, after adding a trailing slash to a namespace (s: http://schema.org/ instead of s: http://schema.org).

Any hints?

[samuel tools]$ cwltool --conformance-test samtools-view.cwl 
/home/samuel/.pyenv/versions/2.7.11/bin/cwltool 1.0.20160427142240
Traceback (most recent call last):
  File "/home/samuel/.pyenv/versions/2.7.11/bin/cwltool", line 9, in <module>
    load_entry_point('cwltool==1.0.20160427142240', 'console_scripts', 'cwltool')()
  File "/home/samuel/.pyenv/versions/2.7.11/lib/python2.7/site-packages/cwltool/main.py", line 590, in main
    stdout=stdout)
  File "/home/samuel/.pyenv/versions/2.7.11/lib/python2.7/site-packages/cwltool/main.py", line 429, in load_job_order
    toolparser = generate_parser(argparse.ArgumentParser(prog=args.workflow), t, namemap)
  File "/home/samuel/.pyenv/versions/2.7.11/lib/python2.7/site-packages/cwltool/main.py", line 283, in generate_parser
    help=ahelp, action=action, type=atype, default=default)
  File "/home/samuel/.pyenv/versions/2.7.11/lib/python2.7/argparse.py", line 1294, in add_argument
    action = action_class(**kwargs)
TypeError: __init__() got an unexpected keyword argument 'type'

[samuell]

Yeah, well, removing the trailing slash from http://schema.org/ on line 238 in samtools-view.cwl actually avoids the error message for samtools view as well.

[samuell]

... and so does escaping / putting a backslash, before the last slash, also:

$namespaces:
  s: http://schema.org\/  # <-- like so

... so I guess it might be a yaml parsing issue?

[samuell]

The only way to get past this error, without messing up the schema url, seems to be to use the > char and a newline:

$namespaces:
  s: >
    http://schema.org/

So, then this seems like an issue with the samtools tool config rather than with cwltool ...

[mr-c]

Hello @samuell, thank you for reporting this.

cwltool --conformance-test is meant to be used with a tool definition and a job file, as part of the testing infrastructure. See https://github.com/common-workflow-language/cwltool/blob/master/cwltool/cwltest.py#L81 https://github.com/common-workflow-language/workflows/blob/master/test/test.sh and https://github.com/common-workflow-language/workflows/blob/master/test/samtools-view-test.yaml

(env) mcrusoe@mrcdev:~/workflows$ cwltool --conformance-test tools/samtools-view.cwl  test/samtools-view-job.json 
/home/mcrusoe/workflows/env/bin/cwltool 1.0.20160504183010
('file:///home/mcrusoe/workflows/tools/samtools-view.cwl', 'https://sparql-test.commonwl.org/schema.rdf')
{
    "args": [
        "samtools", 
        "view", 
        "-@", 
        "4", 
        "-b", 
        "-o", 
        "./test-files/SRR1031972.sorted.bam", 
        "/var/lib/cwl/job468835025_test-files/SRR1031972.Aligned.sortedByCoord.out.bam"
    ]
}

[samuell]

@mr-c Ah, IC!

[samuell]

So, maybe just a more sensible error message would help?

[manu-chroma]

Looks like --conformance-test option is removed now. Found this related commit: e84b359

[mr-c]

Thank you for finding this :-)