static_checker mistakenly fails with source -> sink

[michael-kotliar]

Expected Behavior

Workflow inputs

inputs:
    file1:
      - type: array
        items: File
    file2:
      - type: array
        items: File

should be exactly the same as

inputs:
    file1:
      type: File[]
    file2:
      type: File[]

Actual Behavior

static_checker mistakenly fails with source -> sink mismatch

Tool definition failed validation:
count-lines11-wf.cwl:9:5: Source 'file1' of type [{"type": "array", "items": "File"}] is incompatible
count-lines11-wf.cwl:25:7:   with sink 'file1' of type {"type": "array", "items": "File"}
count-lines11-wf.cwl:25:7:   sink has linkMerge method merge_flattened
count-lines11-wf.cwl:12:5: Source 'file2' of type [{"type": "array", "items": "File"}] is incompatible
count-lines11-wf.cwl:25:7:   with sink 'file1' of type {"type": "array", "items": "File"}
count-lines11-wf.cwl:25:7:   sink has linkMerge method merge_flattened

Workflow Code

Workflow count-lines11-wf.cwl

#!/usr/bin/env cwl-runner
class: Workflow
cwlVersion: v1.0

requirements:
  - class: MultipleInputFeatureRequirement

inputs:
    file1:
      - type: array
        items: File
    file2:
      - type: array
        items: File

outputs:
    count_output:
      type: int
      outputSource: step1/output

steps:
  step1:
    run: wc3-tool.cwl
    in:
      file1:
        source: [file1, file2]
        linkMerge: merge_flattened
    out: [output]

tool wc3-tool.cwl

#!/usr/bin/env cwl-runner
class: CommandLineTool
cwlVersion: v1.0

requirements:
  - class: InlineJavascriptRequirement

inputs:
    file1:
      type: File[]
      inputBinding: {}
outputs:
    output:
      type: int
      outputBinding:
        glob: output.txt
        loadContents: true
        outputEval: |
              ${
                var s = self[0].contents.split(/\r?\n/);
                return parseInt(s[s.length-2]);
              }
stdout: output.txt
baseCommand: wc

job count-lines6-job.json

{
    "file1": [
        {
            "class": "File",
            "location": "whale.txt"
        },
        {
            "class": "File",
            "location": "whale.txt"
        }
    ],
    "file2": [
        {
            "class": "File",
            "location": "hello.txt"
        },
        {
            "class": "File",
            "location": "hello.txt"
        }
    ]
}

Full Traceback

cwltool --debug count-lines11-wf.cwl count-lines6-job.json
/Users/kot4or/venv/cwl_latest/bin/cwltool 1.0.20170622090721
Resolved 'count-lines11-wf.cwl' to 'file:///Users/kot4or/workspaces/python_ws/common-workflow-language/v1.0/v1.0/count-lines11-wf.cwl'
Tool definition failed validation:
count-lines11-wf.cwl:9:5: Source 'file1' of type [{"type": "array", "items": "File"}] is incompatible
count-lines11-wf.cwl:25:7:   with sink 'file1' of type {"type": "array", "items": "File"}
count-lines11-wf.cwl:25:7:   sink has linkMerge method merge_flattened
count-lines11-wf.cwl:12:5: Source 'file2' of type [{"type": "array", "items": "File"}] is incompatible
count-lines11-wf.cwl:25:7:   with sink 'file1' of type {"type": "array", "items": "File"}
count-lines11-wf.cwl:25:7:   sink has linkMerge method merge_flattened
Traceback (most recent call last):
  File "/Users/kot4or/venv/cwl_latest/lib/python2.7/site-packages/cwltool/main.py", line 715, in main
    makeTool, vars(args))
  File "/Users/kot4or/venv/cwl_latest/lib/python2.7/site-packages/cwltool/load_tool.py", line 251, in make_tool
    tool = makeTool(processobj, **kwargs)
  File "/Users/kot4or/venv/cwl_latest/lib/python2.7/site-packages/cwltool/workflow.py", line 37, in defaultMakeTool
    return Workflow(toolpath_object, **kwargs)
  File "/Users/kot4or/venv/cwl_latest/lib/python2.7/site-packages/cwltool/workflow.py", line 524, in __init__
    static_checker(workflow_inputs, workflow_outputs, step_inputs, step_outputs)
  File "/Users/kot4or/venv/cwl_latest/lib/python2.7/site-packages/cwltool/workflow.py", line 612, in static_checker
    raise validate.ValidationException(all_exception_msg)
ValidationException: count-lines11-wf.cwl:9:5: Source 'file1' of type [{"type": "array", "items": "File"}] is incompatible
count-lines11-wf.cwl:25:7:   with sink 'file1' of type {"type": "array", "items": "File"}
count-lines11-wf.cwl:25:7:   sink has linkMerge method merge_flattened
count-lines11-wf.cwl:12:5: Source 'file2' of type [{"type": "array", "items": "File"}] is incompatible
count-lines11-wf.cwl:25:7:   with sink 'file1' of type {"type": "array", "items": "File"}
count-lines11-wf.cwl:25:7:   sink has linkMerge method merge_flattened

Your Environment

• cwltool version: 1.0.20170622090721

Link to reproduce test

count-lines11-wf.cwl
count-lines6-job.json
wc3-tool.cwl
whale.txt
hello.txt