cwltool does not support the specification in 3.7

[tom-tan]

In my understanding, Section 3.7 says that the platforms must look in several directories such as ~/.local/share/commonwl to search for CWL documents.
However, cwltool does not look in these directories.

How to reproduce

$ git clone [email protected]:common-workflow-language/common-workflow-language.git
$ cd common-workflow-language/v1.0/v1.0
$ mkdir -p ~/.local/share/commonwl
$ mv echo-tool-default.cwl ~/.local/share/commonwl
$ cwltool echo-wf-default.cwl

Expected Behavior

cwltool can find echo-tool-default.cwl for step step1 in echo-wf-default.cwl.

$ cwltool echo-wf-default.cwl
...
[workflow echo-wf-default.cwl] completed success
{
    "default_output": "workflow_default"
}
Final process status is success

Actual Behavior

cwltool failed to find echo-tool-default.cwl. It seems not to look in ~/.local/share/commonwl.

$ cwltool --debug echo-wf-default.cwl
/Users/tom-tan/.pyenv/versions/3.6.5/bin/cwltool 1.0.20180403145700
Resolved 'echo-wf-default.cwl' to 'file:///Users/tom-tan/common-workflow-language/v1.0/v1.0/echo-wf-default.cwl'
Tool definition failed validation:
echo-wf-default.cwl:7:1: checking field `steps`
echo-wf-default.cwl:8:3:   checking object `echo-wf-default.cwl#step1`
echo-wf-default.cwl:9:5:     Field `run` contains undefined reference to `file:///Users/tom-tan/common-workflow-language/v1.0/v1.0/echo-tool-default.cwl`
Traceback (most recent call last):
  File "/Users/tom-tan/.pyenv/versions/3.6.5/lib/python3.6/site-packages/cwltool/main.py", line 483, in main
    do_validate=args.do_validate)
  File "/Users/tom-tan/.pyenv/versions/3.6.5/lib/python3.6/site-packages/cwltool/load_tool.py", line 266, in validate_document
    processobj, new_metadata = document_loader.resolve_all(workflowobj, fileuri, checklinks=do_validate)
  File "/Users/tom-tan/.pyenv/versions/3.6.5/lib/python3.6/site-packages/schema_salad/ref_resolver.py", line 913, in resolve_all
    self.validate_links(document, u"", all_doc_ids)
  File "/Users/tom-tan/.pyenv/versions/3.6.5/lib/python3.6/site-packages/schema_salad/ref_resolver.py", line 1081, in validate_links
    raise errors[0]
schema_salad.validate.ValidationException: echo-wf-default.cwl:7:1: checking field `steps`
echo-wf-default.cwl:8:3:   checking object `echo-wf-default.cwl#step1`
echo-wf-default.cwl:9:5:     Field `run` contains undefined reference to `file:///Users/tom-tan/common-workflow-language/v1.0/v1.0/echo-tool-default.cwl`

Workflow Code

echo-wf-default.cwl

class: Workflow
cwlVersion: v1.0

inputs: []

steps:
  step1:
    run: echo-tool-default.cwl
    in:
      in: 
        default: workflow_default
    out: [out]
    
outputs:
    default_output:
      type: string
      outputSource: step1/out

echo-tool-default.cwl

#!/usr/bin/env cwl-runner

class: CommandLineTool
cwlVersion: v1.0
inputs:
  in:
    type: string
    default: tool_default
    inputBinding:
      position: 1
outputs:
  out:
    type: string
    outputBinding:
      glob: out.txt
      loadContents: true
      outputEval: $(self[0].contents)
baseCommand: [echo, -n]
stdout: out.txt

Full Traceback

Traceback (most recent call last):
  File "/Users/tom-tan/.pyenv/versions/3.6.5/lib/python3.6/site-packages/cwltool/main.py", line 483, in main
    do_validate=args.do_validate)
  File "/Users/tom-tan/.pyenv/versions/3.6.5/lib/python3.6/site-packages/cwltool/load_tool.py", line 266, in validate_document
    processobj, new_metadata = document_loader.resolve_all(workflowobj, fileuri, checklinks=do_validate)
  File "/Users/tom-tan/.pyenv/versions/3.6.5/lib/python3.6/site-packages/schema_salad/ref_resolver.py", line 913, in resolve_all
    self.validate_links(document, u"", all_doc_ids)
  File "/Users/tom-tan/.pyenv/versions/3.6.5/lib/python3.6/site-packages/schema_salad/ref_resolver.py", line 1081, in validate_links
    raise errors[0]
schema_salad.validate.ValidationException: echo-wf-default.cwl:7:1: checking field `steps`
echo-wf-default.cwl:8:3:   checking object `echo-wf-default.cwl#step1`
echo-wf-default.cwl:9:5:     Field `run` contains undefined reference to `file:///Users/tom-tan/common-workflow-language/v1.0/v1.0/echo-tool-default.cwl`

Your Environment

• cwltool version:

$ cwltool --version
/Users/tom-tan/.pyenv/versions/3.6.5/bin/cwltool 1.0.20180403145700