Step input with multiple sources adds extra value to array

[michael-kotliar]

Expected Behavior

When using MultipleInputFeatureRequirement with merge_nested the input must be an array consisting of exactly one entry for each input link. It should be the same even if the type for the source is a list of two or more items.

Actual Behavior

If the source has a type set as a list of two or more items, it will be added to the result array exactly the same number of times as the length of its type list.

Workflow Code

cwlVersion: v1.0
class: Workflow

requirements:
  - class: SubworkflowFeatureRequirement
  - class: ScatterFeatureRequirement
  - class: StepInputExpressionRequirement
  - class: InlineJavascriptRequirement
  - class: MultipleInputFeatureRequirement

inputs:
  input_1:
    type: int
  input_2:
    type:
    - File
    - int

outputs:
  resut:
    type: int
    outputSource: echo/result

steps:
  echo:
    run: echo.cwl
    in:
      data:
        source: [input_1, input_2]
        valueFrom: |
          ${
              return self[0] + self[1];
          }
    out: [result]

Short Traceback

"file:///Users/kot4or/workspaces/cwl_ws/cwl_sandbox/multiple_input_source/workflow.cwl#echo/data": [
        1, 
        2, 
        2
    ]
}

Full Traceback

cwltool --debug workflow.cwl job.yml 
/usr/local/bin/cwltool 1.0.20170525215327
Resolved 'workflow.cwl' to 'file:///Users/kot4or/workspaces/cwl_ws/cwl_sandbox/multiple_input_source/workflow.cwl'
[workflow workflow.cwl] initialized from file:///Users/kot4or/workspaces/cwl_ws/cwl_sandbox/multiple_input_source/workflow.cwl
[workflow workflow.cwl] start
[workflow workflow.cwl] starting step echo
[job step echo] job input {
    "file:///Users/kot4or/workspaces/cwl_ws/cwl_sandbox/multiple_input_source/workflow.cwl#echo/data": [
        1, 
        2, 
        2
    ]
}
[job step echo] evaluated job input to {
    "file:///Users/kot4or/workspaces/cwl_ws/cwl_sandbox/multiple_input_source/workflow.cwl#echo/data": 3
}
[step echo] start
[job echo] initializing from file:///Users/kot4or/workspaces/cwl_ws/cwl_sandbox/multiple_input_source/echo.cwl as part of step echo
[job echo] {
    "data": 3
}
[job echo] path mappings is {}
[job echo] command line bindings is [
    {
        "position": [
            -1000000, 
            0
        ], 
        "datum": "echo"
    }, 
    {
        "position": [
            1, 
            "data"
        ], 
        "datum": 3
    }
]
[job echo] /var/folders/sd/41rg42_16q72_2yzl_vvgsbw0000gn/T/tmpzDqvrt$ docker \
    run \
    -i \
    --volume=/private/var/folders/sd/41rg42_16q72_2yzl_vvgsbw0000gn/T/tmpzDqvrt:/private/var/spool/cwl:rw \
    --volume=/private/var/folders/sd/41rg42_16q72_2yzl_vvgsbw0000gn/T/tmpnYvOeu:/tmp:rw \
    --workdir=/private/var/spool/cwl \
    --read-only=true \
    --log-driver=none \
    --user=501 \
    --rm \
    --env=TMPDIR=/tmp \
    --env=HOME=/private/var/spool/cwl \
    ubuntu \
    echo \
    3 > /var/folders/sd/41rg42_16q72_2yzl_vvgsbw0000gn/T/tmpzDqvrt/output.txt
[job echo] completed success
[job echo] {
    "result": 3
}
[step echo] produced output {
    "file:///Users/kot4or/workspaces/cwl_ws/cwl_sandbox/multiple_input_source/workflow.cwl#echo/result": 3
}
[step echo] completed success
[workflow workflow.cwl] completed success
[job echo] Removing input staging directory /var/folders/sd/41rg42_16q72_2yzl_vvgsbw0000gn/T/tmp1Q0eyL
[job echo] Removing temporary directory /var/folders/sd/41rg42_16q72_2yzl_vvgsbw0000gn/T/tmpnYvOeu
Removing intermediate output directory /var/folders/sd/41rg42_16q72_2yzl_vvgsbw0000gn/T/tmp2OqTZa
{
    "resut": 3
}
Final process status is success

Link to reproduce test

https://github.com/michael-kotliar/cwl_sandbox/tree/master/multiple_input_source

Your Environment

• cwltool version: 1.0.20170525215327