cwltool --print-dot fails with python 3.8 (or newer) due pydot version 3.0.0 (or newer)

[jmfernandez]

I have found a reproducibility issue with cwltool --print-dot command line, which depends on the python version used.

Expected Behavior

If you install cwltool 3.1.20230906142556 with python 3.7, cwltool --print-dot works as expected, as it generates the dot representation of the graph.

Actual Behavior

But, if you install cwltool 3.1.20230906142556 (or newer) with python 3.8 (or newer), then an execution of cwltool --print-dot gives an error similar to next:

INFO /home/jmfernandez/projects/WfExS/WfExS-backend_full_circle/wfexs-backend-test/CWLWorkflowEngine/truñi3d/bin/cwltool 3.1.20230906142556
INFO Resolved '/home/jmfernandez/projects/WfExS/WfExS-backend_full_circle/wfexs-backend-test_WorkDir/dd0988dd-d37d-471b-8ecd-7f109b1ab6ce/consolidated-workflow/dd0988dd-d37d-471b-8ecd-7f109b1ab6ce_workflow.cwl' to 'file:///home/jmfernandez/projects/WfExS/WfExS-backend_full_circle/wfexs-backend-test_WorkDir/dd0988dd-d37d-471b-8ecd-7f109b1ab6ce/consolidated-workflow/dd0988dd-d37d-471b-8ecd-7f109b1ab6ce_workflow.cwl'
ERROR I'm sorry, I couldn't load this CWL file, try again with --debug for more information.
The error was: 'Subgraph' object has no attribute 'create_attribute_methods'

I have been able to get the expected behaviour in all the cwltool versions I have tested just downgrading pydot to 2.0.0.

Workflow Code

{
    "$graph": [
        {
            "class": "CommandLineTool",
            "id": "#hello-tool.cwl",
            "label": "hello",
            "requirements": [
                {
                    "class": "DockerRequirement",
                    "dockerPull": "bash:5.2.15"
                },
                {
                    "class": "InitialWorkDirRequirement",
                    "listing": [
                        {
                            "entryname": "hello-world.bash",
                            "entry": "echo \"Hello world!!!!!!!\"\necho\necho \"Computing the md5 of $(inputs.an_input)\"\nmd5sum $(inputs.an_input.path)\necho\necho \"Showing the inherited environment\"\nenv"
                        }
                    ]
                }
            ],
            "baseCommand": [
                "bash",
                "hello-world.bash"
            ],
            "inputs": [
                {
                    "type": "File",
                    "id": "#hello-tool.cwl/hello/an_input"
                }
            ],
            "stdout": "hello_output.txt",
            "outputs": [
                {
                    "type": "File",
                    "id": "#hello-tool.cwl/hello/hello_output",
                    "outputBinding": {
                        "glob": "hello_output.txt"
                    }
                }
            ]
        },
        {
            "class": "Workflow",
            "id": "#main",
            "label": "cosifer-workflow",
            "inputs": [
                {
                    "type": "File",
                    "doc": "Input file to compute the MD5",
                    "id": "#main/an_input"
                }
            ],
            "outputs": [
                {
                    "type": "File",
                    "outputSource": "#main/hello/hello_output",
                    "id": "#main/hello_output"
                }
            ],
            "steps": [
                {
                    "run": "#hello-tool.cwl",
                    "in": [
                        {
                            "source": "#main/an_input",
                            "id": "#main/hello/an_input"
                        }
                    ],
                    "out": [
                        "#main/hello/hello_output"
                    ],
                    "id": "#main/hello"
                }
            ]
        }
    ],
    "cwlVersion": "v1.0"
}

Full Traceback

INFO /home/jmfernandez/projects/WfExS/WfExS-backend_full_circle/wfexs-backend-test/CWLWorkflowEngine/truñi3d/bin/cwltool 3.1.20230906142556
INFO Resolved '/home/jmfernandez/projects/WfExS/WfExS-backend_full_circle/wfexs-backend-test_WorkDir/dd0988dd-d37d-471b-8ecd-7f109b1ab6ce/consolidated-workflow/dd0988dd-d37d-471b-8ecd-7f109b1ab6ce_workflow.cwl' to 'file:///home/jmfernandez/projects/WfExS/WfExS-backend_full_circle/wfexs-backend-test_WorkDir/dd0988dd-d37d-471b-8ecd-7f109b1ab6ce/consolidated-workflow/dd0988dd-d37d-471b-8ecd-7f109b1ab6ce_workflow.cwl'
ERROR I'm sorry, I couldn't load this CWL file.
The error was: 
Traceback (most recent call last):
  File "/home/jmfernandez/projects/WfExS/WfExS-backend_full_circle/wfexs-backend-test/CWLWorkflowEngine/truñi3d/lib/python3.8/site-packages/cwltool/main.py", line 1149, in main
    printdot(tool, loadingContext.loader.ctx, stdout)
  File "/home/jmfernandez/projects/WfExS/WfExS-backend_full_circle/wfexs-backend-test/CWLWorkflowEngine/truñi3d/lib/python3.8/site-packages/cwltool/cwlrdf.py", line 211, in printdot
    cwl_viewer: CWLViewer = CWLViewer(printrdf(wf, ctx, "n3"))
  File "/home/jmfernandez/projects/WfExS/WfExS-backend_full_circle/wfexs-backend-test/CWLWorkflowEngine/truñi3d/lib/python3.8/site-packages/cwltool/cwlviewer.py", line 25, in __init__
    self._set_input_edges()
  File "/home/jmfernandez/projects/WfExS/WfExS-backend_full_circle/wfexs-backend-test/CWLWorkflowEngine/truñi3d/lib/python3.8/site-packages/cwltool/cwlviewer.py", line 102, in _set_input_edges
    inputs_subgraph.create_attribute_methods(["style"])
AttributeError: 'Subgraph' object has no attribute 'create_attribute_methods'

Your Environment

I have reproduced this issue with several cwltool (3.1.20230906142556, 3.1.20240708091337, 3.1.20240508115724, 3.1.20240404144621, 3.1.20240112164112)
and python (3.8, 3.9, ...., 3.12) releases. Downgrading pydot to 2.0.0 the issue disappears.