Inputs containing both directories and files within directories fail to get mounted to correct places for CWL >= 1.1 workflows

[ThomasHickman]

If you pass in a directory and a file contained within this directory to a CWL tool using cwl>=1.1, the file contained within this directory does not get put into the correct location for the tool to run.

Expected Behavior

The file contained within the directory should get put in the correct location.

Actual Behavior

The file contained within the directory does not get put in the correct location when you use cwl >= 1.1.

Workflow Code

tool.cwl

cwlVersion: v1.1
class: CommandLineTool
id: tool

baseCommand:
  - ls

inputs:
  file:
    type: File
    inputBinding:
      position: 1
  directory:
    type: Directory
    inputBinding:
      position: 2

outputs: []

inputs.yaml

directory:
  class: Directory
  path: directory
file:
  class: File
  path: directory/file

Full Traceback

$ cwltool --debug tool.cwl inputs.yaml
INFO /home/user/Documents/checkouts/cwltool/venv/bin/cwltool 3.1.20221115160822
INFO Resolved 'tool.cwl' to 'file:///home/user/Documents/checkouts/cwltool/my/issue2/tool.cwl'
DEBUG [job tool] initializing from file:///home/user/Documents/checkouts/cwltool/my/issue2/tool.cwl#tool
DEBUG [job tool] {
    "directory": {
        "class": "Directory",
        "location": "file:///home/user/Documents/checkouts/cwltool/my/issue2/directory",
        "basename": "directory"
    },
    "file": {
        "class": "File",
        "location": "file:///home/user/Documents/checkouts/cwltool/my/issue2/directory/file",
        "size": 0,
        "basename": "file",
        "nameroot": "file",
        "nameext": ""
    }
}
DEBUG [job tool] path mappings is {
    "file:///home/user/Documents/checkouts/cwltool/my/issue2/directory": [
        "/home/user/Documents/checkouts/cwltool/my/issue2/directory",
        "/tmp/qu6q87wp/stgdcb1db8c-5f78-4354-b36e-915ec91ebab8/directory",
        "Directory",
        true
    ],
    "file:///home/user/Documents/checkouts/cwltool/my/issue2/directory/file": [
        "/home/user/Documents/checkouts/cwltool/my/issue2/directory/file",
        "/tmp/qu6q87wp/stg0fec546f-112c-4c2c-afa0-17256f9bd17a/file",
        "File",
        true
    ]
}
DEBUG [job tool] command line bindings is [
    {
        "position": [
            -1000000,
            0
        ],
        "datum": "ls"
    },
    {
        "position": [
            1,
            "file"
        ],
        "datum": {
            "class": "File",
            "location": "file:///home/user/Documents/checkouts/cwltool/my/issue2/directory/file",
            "size": 0,
            "basename": "file",
            "nameroot": "file",
            "nameext": "",
            "path": "/tmp/qu6q87wp/stg0fec546f-112c-4c2c-afa0-17256f9bd17a/file",
            "dirname": "/tmp/qu6q87wp/stg0fec546f-112c-4c2c-afa0-17256f9bd17a"
        }
    },
    {
        "position": [
            2,
            "directory"
        ],
        "datum": {
            "class": "Directory",
            "location": "file:///home/user/Documents/checkouts/cwltool/my/issue2/directory",
            "basename": "directory",
            "path": "/tmp/qu6q87wp/stgdcb1db8c-5f78-4354-b36e-915ec91ebab8/directory",
            "dirname": "/tmp/qu6q87wp/stgdcb1db8c-5f78-4354-b36e-915ec91ebab8"
        }
    }
]
DEBUG [job tool] initial work dir {}
INFO [job tool] /tmp/89n9yj5o$ ls \
    /tmp/qu6q87wp/stg0fec546f-112c-4c2c-afa0-17256f9bd17a/file \
    /tmp/qu6q87wp/stgdcb1db8c-5f78-4354-b36e-915ec91ebab8/directory
ls: cannot access '/tmp/qu6q87wp/stg0fec546f-112c-4c2c-afa0-17256f9bd17a/file': No such file or directory
/tmp/qu6q87wp/stgdcb1db8c-5f78-4354-b36e-915ec91ebab8/directory:
file
DEBUG Could not collect memory usage, job ended before monitoring began.
WARNING [job tool] exited with status: 2
WARNING [job tool] completed permanentFail
DEBUG [job tool] outputs {}
DEBUG [job tool] Removing input staging directory /tmp/qu6q87wp
DEBUG [job tool] Removing temporary directory /tmp/pk_1qhky
DEBUG Removing intermediate output directory /tmp/89n9yj5o
{}WARNING Final process status is permanentFail

If we use CWL v1.0, this runs successfully:

$ cwltool --debug tool.cwl inputs.yaml
INFO /home/user/Documents/checkouts/cwltool/venv/bin/cwltool 3.1.20221115160822
INFO Resolved 'tool.cwl' to 'file:///home/user/Documents/checkouts/cwltool/my/issue2/tool.cwl'
DEBUG [job tool] initializing from file:///home/user/Documents/checkouts/cwltool/my/issue2/tool.cwl#tool
DEBUG [job tool] {
    "directory": {
        "class": "Directory",
        "location": "file:///home/user/Documents/checkouts/cwltool/my/issue2/directory",
        "basename": "directory",
        "listing": [
            {
                "class": "File",
                "location": "file:///home/user/Documents/checkouts/cwltool/my/issue2/directory/file",
                "basename": "file",
                "size": 0
            }
        ]
    },
    "file": {
        "class": "File",
        "location": "file:///home/user/Documents/checkouts/cwltool/my/issue2/directory/file",
        "size": 0,
        "basename": "file",
        "nameroot": "file",
        "nameext": ""
    }
}
DEBUG [job tool] path mappings is {
    "file:///home/user/Documents/checkouts/cwltool/my/issue2/directory": [
        "/home/user/Documents/checkouts/cwltool/my/issue2/directory",
        "/tmp/4k4zjduc/stg81d0fed8-0aa8-498c-b9c2-54a06ad10208/directory",
        "Directory",
        true
    ],
    "file:///home/user/Documents/checkouts/cwltool/my/issue2/directory/file": [
        "/home/user/Documents/checkouts/cwltool/my/issue2/directory/file",
        "/tmp/4k4zjduc/stg81d0fed8-0aa8-498c-b9c2-54a06ad10208/directory/file",
        "File",
        false
    ]
}
DEBUG [job tool] command line bindings is [
    {
        "position": [
            -1000000,
            0
        ],
        "datum": "ls"
    },
    {
        "position": [
            1,
            "file"
        ],
        "datum": {
            "class": "File",
            "location": "file:///home/user/Documents/checkouts/cwltool/my/issue2/directory/file",
            "size": 0,
            "basename": "file",
            "nameroot": "file",
            "nameext": "",
            "path": "/tmp/4k4zjduc/stg81d0fed8-0aa8-498c-b9c2-54a06ad10208/directory/file",
            "dirname": "/tmp/4k4zjduc/stg81d0fed8-0aa8-498c-b9c2-54a06ad10208/directory"
        }
    },
    {
        "position": [
            2,
            "directory"
        ],
        "datum": {
            "class": "Directory",
            "location": "file:///home/user/Documents/checkouts/cwltool/my/issue2/directory",
            "basename": "directory",
            "listing": [
                {
                    "class": "File",
                    "location": "file:///home/user/Documents/checkouts/cwltool/my/issue2/directory/file",
                    "basename": "file",
                    "size": 0,
                    "path": "/tmp/4k4zjduc/stg81d0fed8-0aa8-498c-b9c2-54a06ad10208/directory/file",
                    "dirname": "/tmp/4k4zjduc/stg81d0fed8-0aa8-498c-b9c2-54a06ad10208/directory",
                    "nameroot": "file",
                    "nameext": ""
                }
            ],
            "path": "/tmp/4k4zjduc/stg81d0fed8-0aa8-498c-b9c2-54a06ad10208/directory",
            "dirname": "/tmp/4k4zjduc/stg81d0fed8-0aa8-498c-b9c2-54a06ad10208"
        }
    }
]
DEBUG [job tool] initial work dir {}
INFO [job tool] /tmp/0aycvk8u$ ls \
    /tmp/4k4zjduc/stg81d0fed8-0aa8-498c-b9c2-54a06ad10208/directory/file \
    /tmp/4k4zjduc/stg81d0fed8-0aa8-498c-b9c2-54a06ad10208/directory
/tmp/4k4zjduc/stg81d0fed8-0aa8-498c-b9c2-54a06ad10208/directory/file

/tmp/4k4zjduc/stg81d0fed8-0aa8-498c-b9c2-54a06ad10208/directory:
file
DEBUG Could not collect memory usage, job ended before monitoring began.
INFO [job tool] completed success
DEBUG [job tool] outputs {}
DEBUG [job tool] Removing input staging directory /tmp/4k4zjduc
DEBUG [job tool] Removing temporary directory /tmp/mt4vd3cg
DEBUG Removing intermediate output directory /tmp/0aycvk8u
{}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)