Input of array of enum is not recognized by the cwltool command line input object feature

[esanzgar]

If an input is defined as an array of enum, cwltool is unable to make a command line argument from it:

inputs:
  applications:
    type:
        - type: array
          items:
              type: enum
              symbols:
                  - a
                  - b
    inputBinding:
      itemSeparator: ","
      prefix: --applications

Expected Behavior

cwltool --debug https://raw.githubusercontent.com/esanzgar/webservice-cwl/master/docker_cwls/array_enum.cwl --application a --application b should feed --applications a,b to the tool.

Actual Behavior

cwltool --debug https://raw.githubusercontent.com/esanzgar/webservice-cwl/master/docker_cwls/array_enum.cwl --application a --application b

Can't make command line argument from [ordereddict([('type', 'array'), ('items', ordereddict([('type', 'enum'), ('symbols', [u'https://raw.githubusercontent.com/esanzgar/webservice-cwl/master/docker_cwls/array_enum.cwl#applications/a', u'https://raw.githubusercontent.com/esanzgar/webservice-cwl/master/docker_cwls/array_enum.cwl#applications/b']), ('name', u'applicationsbf7fee68-a1f1-410b-a430-39c74fc57643')]))])]
usage: https://raw.githubusercontent.com/esanzgar/webservice-cwl/master/docker_cwls/array_enum.cwl
       [-h] [job_order]
https://raw.githubusercontent.com/esanzgar/webservice-cwl/master/docker_cwls/array_enum.cwl: error: unrecognized arguments: --application --application b

Workflow Code

cwltool --debug https://raw.githubusercontent.com/esanzgar/webservice-cwl/master/docker_cwls/array_enum.cwl --application a --application b

Your Environment

• cwltool version: 1.0.20170928192020

[mr-c]

Thank you @esanzgar for your report

As a reminder, you can always create a YAML/JSON input file if the command line parser doesn't work. Though I find the command line interface to be very convenient!

[esanzgar]

As suggested here, I also tried this combination but it results in an exception:

inputs:
  applications:
    type:
        - "null"
        - type: array
          items:
              type: enum
              symbols:
                  - a
                  - b
    inputBinding:
      itemSeparator: ","
      prefix: --applications

Full Traceback

Traceback (most recent call last):
  File "/Users/eduardo/.config/virtualenvs/cwl/lib/python2.7/site-packages/cwltool/main.py", line 279, in single_job_executor
    for r in jobiter:
  File "/Users/eduardo/.config/virtualenvs/cwl/lib/python2.7/site-packages/cwltool/draft2tool.py", line 332, in job
    builder = self._init_job(job_order, **kwargs)
  File "/Users/eduardo/.config/virtualenvs/cwl/lib/python2.7/site-packages/cwltool/process.py", line 609, in _init_job
    builder.bindings.extend(builder.bind_input(self.inputs_record_schema, builder.job))
  File "/Users/eduardo/.config/virtualenvs/cwl/lib/python2.7/site-packages/cwltool/builder.py", line 120, in bind_input
    bindings.extend(self.bind_input(f, datum[f["name"]], lead_pos=lead_pos, tail_pos=f["name"]))
  File "/Users/eduardo/.config/virtualenvs/cwl/lib/python2.7/site-packages/cwltool/builder.py", line 99, in bind_input
    avsc = AvroSchemaFromJSONData(t, self.names)
  File "/Users/eduardo/.config/virtualenvs/cwl/lib/python2.7/site-packages/avro/schema.py", line 746, in make_avsc_object
    return ArraySchema(items, names, other_props)
  File "/Users/eduardo/.config/virtualenvs/cwl/lib/python2.7/site-packages/avro/schema.py", line 492, in __init__
    raise SchemaParseException(fail_msg)

SchemaParseException: Items schema (ordereddict([('type', 'enum'), ('symbols', [u'a', u'b']), ('name', u'applicationsba75a91b-31b9-41a1-8a12-42de373b7dec')])) not a valid Avro schema: The name "applicationsba75a91b-31b9-41a1-8a12-42de373b7dec" is already in use. (known names: ['outputs_record_schema', u'File_class', u'applicationsba75a91b-31b9-41a1-8a12-42de373b7dec', 'File', 'Directory', 'input_record_schema', u'Directory_class', 'Any'])
Workflow error, try again with --debug for more information:
Items schema (ordereddict([('type', 'enum'), ('symbols', [u'a', u'b']), ('name', u'applicationsba75a91b-31b9-41a1-8a12-42de373b7dec')])) not a valid Avro schema: The name "applicationsba75a91b-31b9-41a1-8a12-42de373b7dec" is already in use. (known names: ['outputs_record_schema', u'File_class', u'applicationsba75a91b-31b9-41a1-8a12-42de373b7dec', 'File', 'Directory', 'input_record_schema', u'Directory_class', 'Any'])
Traceback (most recent call last):
  File "/Users/eduardo/.config/virtualenvs/cwl/lib/python2.7/site-packages/cwltool/main.py", line 913, in main
    **vars(args))
  File "/Users/eduardo/.config/virtualenvs/cwl/lib/python2.7/site-packages/cwltool/main.py", line 294, in single_job_executor
    raise WorkflowException(Text(e))
WorkflowException: Items schema (ordereddict([('type', 'enum'), ('symbols', [u'a', u'b']), ('name', u'applicationsba75a91b-31b9-41a1-8a12-42de373b7dec')])) not a valid Avro schema: The name "applicationsba75a91b-31b9-41a1-8a12-42de373b7dec" is already in use. (known names: ['outputs_record_schema', u'File_class', u'applicationsba75a91b-31b9-41a1-8a12-42de373b7dec', 'File', 'Directory', 'input_record_schema', u'Directory_class', 'Any'])

[cwl-bot]

This issue has been mentioned on Common Workflow Language Discourse. There might be relevant details there:

https://cwl.discourse.group/t/set-tool-output-format-string-from-workflow-inputs/524/4