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downloads remote inputs via HTTP(S)

See original GitHub issue

Expected Behavior

a URI should be accepted for inputs with type: File

http://www.commonwl.org/v1.0/CommandLineTool.html#File

Actual Behavior

No such file or directory: ‘/home/michael/src/2017-cloud-workflows-misc/http://github.com/CancerCollaboratory/dockstore-tool-bamstats/raw/develop/rna.SRR948778.bam’

Workflow Code

cwltool https://github.com/CancerCollaboratory/dockstore-tool-bamstats/raw/develop/Dockstore.cwl \
 --bam_input https://github.com/CancerCollaboratory/dockstore-tool-bamstats/raw/develop/rna.SRR948778.bam

Full Traceback

/home/michael/src/2017-cloud-workflows-misc/env/bin/cwltool 1.0.20170712193248
https://github.com/CancerCollaboratory/dockstore-tool-bamstats/raw/develop/Dockstore.cwl:3:1: unrecognized extension field `http://purl.org/dc/terms/creator`.  Did you include a $schemas section?
[job Dockstore.cwl] initializing from https://github.com/CancerCollaboratory/dockstore-tool-bamstats/raw/develop/Dockstore.cwl
[job Dockstore.cwl] {
    "bam_input": {
        "class": "File", 
        "location": "https://github.com/CancerCollaboratory/dockstore-tool-bamstats/raw/develop/rna.SRR948778.bam", 
        "basename": "rna.SRR948778.bam", 
        "nameroot": "rna.SRR948778", 
        "nameext": ".bam"
    }, 
    "mem_gb": 0
}
Got workflow error
Traceback (most recent call last):
  File "/home/michael/src/2017-cloud-workflows-misc/env/local/lib/python2.7/site-packages/cwltool/main.py", line 270, in single_job_executor
    for r in jobiter:
  File "/home/michael/src/2017-cloud-workflows-misc/env/local/lib/python2.7/site-packages/cwltool/draft2tool.py", line 323, in job
    builder.pathmapper = self.makePathMapper(reffiles, builder.stagedir, **make_path_mapper_kwargs)
  File "/home/michael/src/2017-cloud-workflows-misc/env/local/lib/python2.7/site-packages/cwltool/draft2tool.py", line 204, in makePathMapper
    return PathMapper(reffiles, kwargs["basedir"], stagedir)
  File "/home/michael/src/2017-cloud-workflows-misc/env/local/lib/python2.7/site-packages/cwltool/pathmapper.py", line 180, in __init__
    self.setup(dedup(referenced_files), basedir)
  File "/home/michael/src/2017-cloud-workflows-misc/env/local/lib/python2.7/site-packages/cwltool/pathmapper.py", line 228, in setup
    self.visit(fob, stagedir, basedir, copy=fob.get("writable"), staged=True)
  File "/home/michael/src/2017-cloud-workflows-misc/env/local/lib/python2.7/site-packages/cwltool/pathmapper.py", line 217, in visit
    self.visitlisting(obj.get("secondaryFiles", []), stagedir, basedir, copy=copy, staged=staged)
  File "/home/michael/src/2017-cloud-workflows-misc/env/local/lib/python2.7/site-packages/schema_salad/sourceline.py", line 152, in __exit__
    raise self.makeError(six.text_type(exc_value))
ValidationException: params.yaml:3:5: [Errno 2] No such file or directory: '/home/michael/src/2017-cloud-workflows-misc/http://github.com/CancerCollaboratory/dockstore-tool-bamstats/raw/develop/rna.SRR948778.bam'
Workflow error, try again with --debug for more information:
params.yaml:3:5: [Errno 2] No such file or directory:
                 '/home/michael/src/2017-cloud-workflows-misc/http://github.com/CancerCollaboratory/dockstore-tool-bamstats/raw/develop/rna.SRR948778.bam'
Traceback (most recent call last):
  File "/home/michael/src/2017-cloud-workflows-misc/env/local/lib/python2.7/site-packages/cwltool/main.py", line 886, in main
    **vars(args))
  File "/home/michael/src/2017-cloud-workflows-misc/env/local/lib/python2.7/site-packages/cwltool/main.py", line 285, in single_job_executor
    raise WorkflowException(Text(e))
WorkflowException: params.yaml:3:5: [Errno 2] No such file or directory: '/home/michael/src/2017-cloud-workflows-misc/http://github.com/CancerCollaboratory/dockstore-tool-bamstats/raw/develop/rna.SRR948778.bam'