If a workflow step input has a type of `[File, Directory]`, spurious warnings are emitted

[ThomasHickman]

If you define a CommandLineTool which has an input of type [File, Directory], using this parameter in a wofkflow results in a spurious warning of:

Warning: invalid field `nameroot`, expected one of: 'class', 'location', 'path', 'basename', 'listing'
Warning: invalid field `nameext`, expected one of: 'class', 'location', 'path', 'basename', 'listing'

​

Expected Behavior

The warnings do not appear. ​

Actual Behavior

The warnings do appear. ​

Workflow Code

workflow.cwl

cwlVersion: v1.2
class: Workflow
​
inputs: []
​
steps:
  - id: step1
    in: []
    run: cmd1.cwl
    out: [directory]
​
  - id: step2
    in:
      directory: step1/directory
    run: cmd2.cwl
    out: []
​
outputs: []
​

​ cmd1.cwl

cwlVersion: v1.2
class: CommandLineTool
id: cmd1
​
baseCommand:
    - mkdir
    - directory
​
inputs: []
​
outputs:
  directory:
    type: Directory
    outputBinding:
        glob: directory
​

​ cmd2.cwl

cwlVersion: v1.2
class: CommandLineTool
id: cmd2
​
baseCommand:
    - ls
inputs:
  directory:
    type:
        - Directory
        - File
    inputBinding:
      position: 1
​
outputs: []
​

​

Full Traceback

$ cwltool --debug workflow.cwl 
INFO /home/user/Documents/checkouts/cwltool/venv/bin/cwltool 3.1.20221115160822
INFO Resolved 'workflow.cwl' to 'file:///home/user/Documents/checkouts/cwltool/my/workflow.cwl'
DEBUG Parsed job order from command line: {
    "id": "workflow.cwl"
}
DEBUG [workflow ] initialized from file:///home/user/Documents/checkouts/cwltool/my/workflow.cwl
INFO [workflow ] start
DEBUG [workflow ] inputs {}
DEBUG [workflow ] job step file:///home/user/Documents/checkouts/cwltool/my/workflow.cwl#step2 not ready
INFO [workflow ] starting step step1
DEBUG [step step1] job input {}
DEBUG [step step1] evaluated job input to {}
INFO [step step1] start
DEBUG [job step1] initializing from file:///home/user/Documents/checkouts/cwltool/my/cmd1.cwl#cmd1 as part of step step1
DEBUG [job step1] {}
DEBUG [job step1] path mappings is {}
DEBUG [job step1] command line bindings is [
    {
        "position": [
            -1000000,
            0
        ],
        "datum": "mkdir"
    },
    {
        "position": [
            -1000000,
            1
        ],
        "datum": "directory"
    }
]
DEBUG [job step1] initial work dir {}
INFO [job step1] /tmp/72ugel1k$ mkdir \
    directory
DEBUG Could not collect memory usage, job ended before monitoring began.
INFO [job step1] completed success
DEBUG [job step1] outputs {
    "directory": {
        "location": "file:///tmp/72ugel1k/directory",
        "basename": "directory",
        "nameroot": "directory",
        "nameext": "",
        "class": "Directory"
    }
}
DEBUG [step step1] produced output {
    "file:///home/user/Documents/checkouts/cwltool/my/workflow.cwl#step1/directory": {
        "location": "file:///tmp/72ugel1k/directory",
        "basename": "directory",
        "nameroot": "directory",
        "nameext": "",
        "class": "Directory"
    }
}
INFO [step step1] completed success
DEBUG [job step1] Removing input staging directory /tmp/arn5kz29
DEBUG [job step1] Removing temporary directory /tmp/xpc1uscj
INFO [workflow ] starting step step2
DEBUG [step step2] job input {
    "file:///home/user/Documents/checkouts/cwltool/my/workflow.cwl#step2/directory": {
        "location": "file:///tmp/72ugel1k/directory",
        "basename": "directory",
        "nameroot": "directory",
        "nameext": "",
        "class": "Directory"
    }
}
DEBUG [step step2] evaluated job input to {
    "file:///home/user/Documents/checkouts/cwltool/my/workflow.cwl#step2/directory": {
        "location": "file:///tmp/72ugel1k/directory",
        "basename": "directory",
        "nameroot": "directory",
        "nameext": "",
        "class": "Directory"
    }
}
INFO [step step2] start
Warning: invalid field `nameroot`, expected one of: 'class', 'location', 'path', 'basename', 'listing'
Warning: invalid field `nameext`, expected one of: 'class', 'location', 'path', 'basename', 'listing'
DEBUG [job step2] initializing from file:///home/user/Documents/checkouts/cwltool/my/cmd2.cwl#cmd2 as part of step step2
DEBUG [job step2] {
    "directory": {
        "location": "file:///tmp/72ugel1k/directory",
        "basename": "directory",
        "nameroot": "directory",
        "nameext": "",
        "class": "Directory"
    }
}
DEBUG [job step2] path mappings is {
    "file:///tmp/72ugel1k/directory": [
        "/tmp/72ugel1k/directory",
        "/tmp/zmdmhchf/stgf8ab6da1-48e3-42b8-9d9b-988a3b5abfa1/directory",
        "Directory",
        true
    ]
}
DEBUG [job step2] command line bindings is [
    {
        "position": [
            -1000000,
            0
        ],
        "datum": "ls"
    },
    {
        "position": [
            1,
            "directory"
        ],
        "datum": {
            "location": "file:///tmp/72ugel1k/directory",
            "basename": "directory",
            "nameroot": "directory",
            "nameext": "",
            "class": "Directory",
            "path": "/tmp/zmdmhchf/stgf8ab6da1-48e3-42b8-9d9b-988a3b5abfa1/directory",
            "dirname": "/tmp/zmdmhchf/stgf8ab6da1-48e3-42b8-9d9b-988a3b5abfa1"
        }
    }
]
DEBUG [job step2] initial work dir {}
INFO [job step2] /tmp/357pyxc8$ ls \
    /tmp/zmdmhchf/stgf8ab6da1-48e3-42b8-9d9b-988a3b5abfa1/directory
DEBUG Could not collect memory usage, job ended before monitoring began.
INFO [job step2] completed success
DEBUG [job step2] outputs {}
DEBUG [step step2] produced output {}
INFO [step step2] completed success
INFO [workflow ] completed success
DEBUG [workflow ] outputs {}
DEBUG [job step2] Removing input staging directory /tmp/zmdmhchf
DEBUG [job step2] Removing temporary directory /tmp/ht2_s5q8
DEBUG Removing intermediate output directory /tmp/357pyxc8
DEBUG Removing intermediate output directory /tmp/72ugel1k
DEBUG Removing intermediate output directory /tmp/5zhy_b_g
{}INFO Final process status is success

​

Your Environment

• cwltool version:

$ cwltool --version
/home/user/Documents/checkouts/cwltool/venv/bin/cwltool 3.1.20221115160822

(using the tip of main)