Validation error... could not validate field secondaryFiles

[jeremiahsavage]

With

$ cwl-runner --version
/home/ubuntu/.virtualenvs/p2/bin/cwl-runner 1.0.20151124040259

using input:
https://github.com/jeremiahsavage/workflows/blob/587d3fba885f27289643280d11ad0e09ff2a1f32/tools/remove_qcfail.cwl.yaml
I get error below.

Version cwltool-1.0.20151110030107 does not give this error, while cwltool-1.0.20151121032923 does. I could bisect further on other versions if that would be useful, using https://pypi.python.org/simple/cwltool/

$ cwl-runner /mnt/SCRATCH/tools/workflows/tools/remove_qcfail.cwl.yaml --first_input_bam ~/SCRATCH/47b42e81-2500-4ebc-a0c2-acd3187cc2f0/C440.TCGA-IN-8462-01A-11D-2340-08.1.bam --second_input_bam ~/SCRATCH/47b42e81-2500-4ebc-a0c2-acd3187cc2f0/realn/md/C440.TCGA-IN-8462-01A-11D-2340-08.1.bam --uuid test
/home/ubuntu/.virtualenvs/p2/bin/cwl-runner 1.0.20151124040259
Tool definition failed validation:
Validation error in object file:///mnt/SCRATCH/tools/workflows/tools/remove_qcfail.cwl.yaml
  Could not validate as `CommandLineTool` because
    could not validate field `inputs` because
      At position 0
        could not validate field `inputBinding` because
          the value `{'prefix': '--first_bam',
           'secondaryFiles': [{'engine': 'node-engine.cwl',
                               'script': '{\n  return {"path": $job[\'first_input_bam\'].path.[...]`
           is not a valid type in the union, expected one of:
          - null, but
             the value `{'prefix': '--first_bam',
             'secondaryFiles': [{'engine': 'node-engine.cwl',
                                 'script': '{\n  return {"path": $job[\'first_input_bam\'].path.[...]` is not null
          - CommandLineBinding, but
             could not validate field `secondaryFiles` because
              the value `[{'engine': 'node-engine.cwl',
                'script': '{\n  return {"path": $job[\'first_input_bam\'].path.slice(0,-4)+".bai", "class": "File"};\n}\n'}]`
               is not a valid type in the union, expected one of:
              - null, but
                 the value `[{'engine': 'node-engine.cwl',
                  'script': '{\n  return {"path": $job[\'first_input_bam\'].path.slice(0,-4)+".bai", "class": "File"};\n}\n'}]` is not null
              - string, but
                 the value `[{'engine': 'node-engine.cwl',
                  'script': '{\n  return {"path": $job[\'first_input_bam\'].path.slice(0,-4)+".bai", "class": "File"};\n}\n'}]` is not string
              - Expression, but
                 the value `[{'engine': 'node-engine.cwl',
                  'script': '{\n  return {"path": $job[\'first_input_bam\'].path.slice(0,-4)+".bai", "class": "File"};\n}\n'}]`
                 is not a valid symbol in enum Expression, expected one of 'ExpressionPlaceholder'
              - array of <string or Expression>, but
                 At position 0
                  the value `{'engine': 'node-engine.cwl',
                   'script': '{\n  return {"path": $job[\'first_input_bam\'].path.slice(0,-4)+".bai", "class": "File"};\n}\n'}`
                   is not a valid type in the union, expected one of:
                  - string, but
                     the value `{'engine': 'node-engine.cwl',
                     'script': '{\n  return {"path": $job[\'first_input_bam\'].path.slice(0,-4)+".bai", "class": "File"};\n}\n'}` is not string
                  - Expression, but
                     the value `{'engine': 'node-engine.cwl',
                     'script': '{\n  return {"path": $job[\'first_input_bam\'].path.slice(0,-4)+".bai", "class": "File"};\n}\n'}`
                     is not a valid symbol in enum Expression, expected one of 'ExpressionPlaceholder'

  Could not validate as `Workflow` because
    could not validate field `inputs` because
      At position 0
        could not validate field `inputBinding` because
          the value `{'prefix': '--first_bam',
           'secondaryFiles': [{'engine': 'node-engine.cwl',
                               'script': '{\n  return {"path": $job[\'first_input_bam\'].path.[...]`
           is not a valid type in the union, expected one of:
          - null, but
             the value `{'prefix': '--first_bam',
             'secondaryFiles': [{'engine': 'node-engine.cwl',
                                 'script': '{\n  return {"path": $job[\'first_input_bam\'].path.[...]` is not null
          - Binding, but
             could not validate field `secondaryFiles` because
              the value `[{'engine': 'node-engine.cwl',
                'script': '{\n  return {"path": $job[\'first_input_bam\'].path.slice(0,-4)+".bai", "class": "File"};\n}\n'}]`
               is not a valid type in the union, expected one of:
              - null, but
                 the value `[{'engine': 'node-engine.cwl',
                  'script': '{\n  return {"path": $job[\'first_input_bam\'].path.slice(0,-4)+".bai", "class": "File"};\n}\n'}]` is not null
              - string, but
                 the value `[{'engine': 'node-engine.cwl',
                  'script': '{\n  return {"path": $job[\'first_input_bam\'].path.slice(0,-4)+".bai", "class": "File"};\n}\n'}]` is not string
              - Expression, but
                 the value `[{'engine': 'node-engine.cwl',
                  'script': '{\n  return {"path": $job[\'first_input_bam\'].path.slice(0,-4)+".bai", "class": "File"};\n}\n'}]`
                 is not a valid symbol in enum Expression, expected one of 'ExpressionPlaceholder'
              - array of <string or Expression>, but
                 At position 0
                  the value `{'engine': 'node-engine.cwl',
                   'script': '{\n  return {"path": $job[\'first_input_bam\'].path.slice(0,-4)+".bai", "class": "File"};\n}\n'}`
                   is not a valid type in the union, expected one of:
                  - string, but
                     the value `{'engine': 'node-engine.cwl',
                     'script': '{\n  return {"path": $job[\'first_input_bam\'].path.slice(0,-4)+".bai", "class": "File"};\n}\n'}` is not string
                  - Expression, but
                     the value `{'engine': 'node-engine.cwl',
                     'script': '{\n  return {"path": $job[\'first_input_bam\'].path.slice(0,-4)+".bai", "class": "File"};\n}\n'}`
                     is not a valid symbol in enum Expression, expected one of 'ExpressionPlaceholder'

            could not validate field `prefix` because it is not recognized and strict is True ([u'name', u'id'])

    could not validate field `outputs` because
      At position 0
        could not validate field `outputBinding` because
          the value `{'glob': '${\n  return "remove_qcfail/"+inputs[\'second_input_bam\'].path.split(\'/\').slice(-1)[0];\n}\n'}` is not a valid type in the union, expected one of:
          - null, but
             the value `{'glob': '${\n  return "remove_qcfail/"+inputs[\'second_input_bam\'].path.split(\'/\').slice(-1)[0];\n}\n'}` is not null
          - Binding, but
             could not validate field `glob` because it is not recognized and strict is True ([u'name', u'id'])

    missing required field `steps`
    could not validate field `baseCommand` because it is not recognized and strict is True ([u'name', u'id'])
  Could not validate as `ExpressionTool` because
    could not validate field `inputs` because
      At position 0
        could not validate field `inputBinding` because
          the value `{'prefix': '--first_bam',
           'secondaryFiles': [{'engine': 'node-engine.cwl',
                               'script': '{\n  return {"path": $job[\'first_input_bam\'].path.[...]`
           is not a valid type in the union, expected one of:
          - null, but
             the value `{'prefix': '--first_bam',
             'secondaryFiles': [{'engine': 'node-engine.cwl',
                                 'script': '{\n  return {"path": $job[\'first_input_bam\'].path.[...]` is not null
          - Binding, but
             could not validate field `secondaryFiles` because
              the value `[{'engine': 'node-engine.cwl',
                'script': '{\n  return {"path": $job[\'first_input_bam\'].path.slice(0,-4)+".bai", "class": "File"};\n}\n'}]`
               is not a valid type in the union, expected one of:
              - null, but
                 the value `[{'engine': 'node-engine.cwl',
                  'script': '{\n  return {"path": $job[\'first_input_bam\'].path.slice(0,-4)+".bai", "class": "File"};\n}\n'}]` is not null
              - string, but
                 the value `[{'engine': 'node-engine.cwl',
                  'script': '{\n  return {"path": $job[\'first_input_bam\'].path.slice(0,-4)+".bai", "class": "File"};\n}\n'}]` is not string
              - Expression, but
                 the value `[{'engine': 'node-engine.cwl',
                  'script': '{\n  return {"path": $job[\'first_input_bam\'].path.slice(0,-4)+".bai", "class": "File"};\n}\n'}]`
                 is not a valid symbol in enum Expression, expected one of 'ExpressionPlaceholder'
              - array of <string or Expression>, but
                 At position 0
                  the value `{'engine': 'node-engine.cwl',
                   'script': '{\n  return {"path": $job[\'first_input_bam\'].path.slice(0,-4)+".bai", "class": "File"};\n}\n'}`
                   is not a valid type in the union, expected one of:
                  - string, but
                     the value `{'engine': 'node-engine.cwl',
                     'script': '{\n  return {"path": $job[\'first_input_bam\'].path.slice(0,-4)+".bai", "class": "File"};\n}\n'}` is not string
                  - Expression, but
                     the value `{'engine': 'node-engine.cwl',
                     'script': '{\n  return {"path": $job[\'first_input_bam\'].path.slice(0,-4)+".bai", "class": "File"};\n}\n'}`
                     is not a valid symbol in enum Expression, expected one of 'ExpressionPlaceholder'

            could not validate field `prefix` because it is not recognized and strict is True ([u'name', u'id'])

    could not validate field `outputs` because
      At position 0
        could not validate field `outputBinding` because
          the value `{'glob': '${\n  return "remove_qcfail/"+inputs[\'second_input_bam\'].path.split(\'/\').slice(-1)[0];\n}\n'}` is not a valid type in the union, expected one of:
          - null, but
             the value `{'glob': '${\n  return "remove_qcfail/"+inputs[\'second_input_bam\'].path.split(\'/\').slice(-1)[0];\n}\n'}` is not null
          - Binding, but
             could not validate field `glob` because it is not recognized and strict is True ([u'name', u'id'])

    missing required field `expression`
    could not validate field `baseCommand` because it is not recognized and strict is True ([u'name', u'id'])
$