Did you include a $schemas section?

[evan-wehi]

Hello,

I'm building a workflow and using CommandLineTool examples from this repository (which are great!). Many have metadata but including them in a workflow produces:

$ ../src/pdx-pl.cwl pdx-inp.yml 
/home/thomas.e/.local/bin/cwl-runner 1.0.20170622090721
Resolved '../src/pdx-pl.cwl' to 'file:///stornext/Home/data/allstaff/t/thomas.e/dev/pdx-genome/src/pdx-pl.cwl'
No handlers could be found for logger "rdflib.term"
../src/tools/samtools-sort.cwl:66:1: unrecognized extension field `s:downloadUrl`.  Did you include a $schemas section?
../src/tools/samtools-sort.cwl:68:1: unrecognized extension field `s:license`.  Did you include a $schemas section?
../src/tools/samtools-sort.cwl:75:1: unrecognized extension field `s:author`.  Did you include a $schemas section?

This example uses the samtools-sort.cwl directly from the repository (other than commenting out the imports for envvar-global.ylm and samtools-docker.yml)

[michael-kotliar]

It's not the best solution, but you may try to run it with --non-strict flag. It will allow to ignore these warnings

[mr-c]

Hello @evan-wehi

Thank you for reporting your issue. This is a regression in cwltool -- I thought we had documented it already, but evidently not. I'm moving the issue to common-workflow-language/cwltool#455

[evan-wehi]

Thanks for looking at it @mr-c Evan. From: Michael R. Crusoe [mailto:notifications@github.com] Sent: 06 July 2017 20:57 To: common-workflow-language/workflows <workflows@noreply.github.com> Cc: Evan Thomas <thomas.e@wehi.edu.au>; Mention <mention@noreply.github.com> Subject: Re: [common-workflow-language/workflows] Did you include a $schemas section? (#137) Hello @evan-wehi<https://github.com/evan-wehi> Thank you for reporting your issue. This is a regression in cwltool -- I thought we had documented it already, but evidently not. I'm moving the issue to common-workflow-language/cwltool#455<common-workflow-language/cwltool#455> — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub<#137 (comment)>, or mute the thread<https://github.com/notifications/unsubscribe-auth/AVADDe4DbsHHQjYwgvuqvUy-iARJVFDPks5sLL2BgaJpZM4OPKHk>.