Avoid parse already parsed Workflows in update.py

[alexbarrera]

When cwltool tries to update a workflow that includes more than once the
same subworkflow an exception is raised. This is a product of the updating
procedure where workflows are passed by reference in the document. Once
a workflow has been updated, it should not be processed again -otherwise
expected keys will be missed.

This is a hacky fix that I do not expect to be merged because it does not cover all use cases of the update.py script, but I thought it would be a good way to draft a possible solution. To test the problem, try running cwltool/cwl-runner with any DukeGCB top level pipelines with-control like this one.

Try:

cwl-runner --debug https://raw.githubusercontent.com/Duke-GCB/GGR-cwl/master/ChIP-seq_pipeline/pipeline-se-narrow-with-control.cwl

Which produces the following error:

/Users/abarrera/miniconda2/envs/cwl10/bin/cwltool 1.0.20160726135535
I'm sorry, I couldn't load this CWL file.  The error was:
Traceback (most recent call last):
  File "/Users/abarrera/miniconda2/envs/cwl10/lib/python2.7/site-packages/cwltool/main.py", line 638, in main
    preprocess_only=args.print_pre or args.pack)
  File "/Users/abarrera/miniconda2/envs/cwl10/lib/python2.7/site-packages/cwltool/load_tool.py", line 130, in validate_document
    processobj, document_loader, fileuri, enable_dev, metadata)
  File "/Users/abarrera/miniconda2/envs/cwl10/lib/python2.7/site-packages/cwltool/update.py", line 503, in update
    (cdoc, version) = nextupdate(cdoc, loader, baseuri)
  File "/Users/abarrera/miniconda2/envs/cwl10/lib/python2.7/site-packages/cwltool/update.py", line 358, in draft3toDraft4dev1
    return (_draft3toDraft4dev1(doc, loader, baseuri), "draft-4.dev1")
  File "/Users/abarrera/miniconda2/envs/cwl10/lib/python2.7/site-packages/cwltool/update.py", line 349, in _draft3toDraft4dev1
    doc[key] = _draft3toDraft4dev1(value, loader, baseuri)
  File "/Users/abarrera/miniconda2/envs/cwl10/lib/python2.7/site-packages/cwltool/update.py", line 351, in _draft3toDraft4dev1
    doc = [_draft3toDraft4dev1(item, loader, baseuri) for item in doc]
  File "/Users/abarrera/miniconda2/envs/cwl10/lib/python2.7/site-packages/cwltool/update.py", line 349, in _draft3toDraft4dev1
    doc[key] = _draft3toDraft4dev1(value, loader, baseuri)
  File "/Users/abarrera/miniconda2/envs/cwl10/lib/python2.7/site-packages/cwltool/update.py", line 333, in _draft3toDraft4dev1
    step["in"] = step["inputs"]
KeyError: 'inputs'

[cwl-bot]

Can one of the admins verify this patch?

[mr-c]

Jenkins, add to testlist

[mr-c]

Hey @alexbarrera can you give me ("the maintainers)" permission to update your PR?

[alexbarrera]

@mr-c done. Thanks for looking into this!

[mr-c]

@alexbarrera You are very welcome. FYI: I've rebased the branch and I'm likely to merge it