common-workflow-language / cwltool

Common Workflow Language reference implementation
https://cwltool.readthedocs.io/
Apache License 2.0
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cwltool --update behaves unexpectedly #31

Closed denis-yuen closed 8 years ago

denis-yuen commented 8 years ago

cwltool --update does not seem to accept draft-3 as a valid version (and it only updates as far as dev4) which is odd because it seems like it should https://github.com/common-workflow-language/cwltool/blob/master/cwltool/schemas/draft-3/Process.yml#L31

ex:

dyuen@orz:~/dockstore/dockstore-launcher$ cat test.cwl 
#!/usr/bin/env cwl-runner

class: CommandLineTool
description: "Markdown description text here"
id: "HelloWorld"
label: "HelloWorld Tool"

cwlVersion: "cwl:draft-3.dev1"
dyuen@orz:~/dockstore/dockstore-launcher$ cwltool --non-strict --update test.cwl
/usr/local/bin/cwltool 1.0.20160108200940
{
    "cwlVersion": "https://w3id.org/cwl/cwl#draft-3.dev4", 
    "requirements": [
        {
            "class": "InlineJavascriptRequirement"
        }
    ], 
    "description": "Markdown description text here", 
    "id": "HelloWorld", 
    "label": "HelloWorld Tool", 
    "class": "CommandLineTool", 
    "name": "file:///home/dyuen/dockstore/dockstore-launcher/test.cwl"
}
dyuen@orz:~/dockstore/dockstore-launcher$ vim test.cwl 
dyuen@orz:~/dockstore/dockstore-launcher$ cat test.cwl 
#!/usr/bin/env cwl-runner

class: CommandLineTool
description: "Markdown description text here"
id: "HelloWorld"
label: "HelloWorld Tool"

cwlVersion: "cwl:draft-3"
dyuen@orz:~/dockstore/dockstore-launcher$ cwltool --non-strict --update test.cwl
/usr/local/bin/cwltool 1.0.20160108200940
I'm sorry, I couldn't load this CWL file.
Unrecognized version https://w3id.org/cwl/cwl#draft-3
dyuen@orz:~/dockstore/dockstore-launcher$ 

Versions of stuff:

dyuen@orz:~/dockstore/dockstore-launcher$ pip list | grep cwl
cwl-runner (1.0)
cwltool (1.0.20160108200940)
dyuen@orz:~/dockstore/dockstore-launcher$ sudo pip install cwltool --upgrade
...
Requirement already up-to-date: cwltool in /usr/local/lib/python2.7/dist-packages

This is related to https://github.com/common-workflow-language/schema_salad/issues/7 (sorry)

mr-c commented 8 years ago

Looks like this works now so I'm going to close this issue.