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Upgrade workflow with 'when' disconnect #18441

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lldelisle opened this issue Jun 25, 2024 · 1 comment · Fixed by #18446
Closed

Upgrade workflow with 'when' disconnect #18441

lldelisle opened this issue Jun 25, 2024 · 1 comment · Fixed by #18446

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@lldelisle
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Describe the bug
If you upgrade a workflow in UI or with planemo, if the tool you are upgrading has a 'when' then the 'when' input is disconnected

Galaxy Version and/or server at which you observed the bug
Galaxy Version: 24.1, 24.0 etc...
On usegalaxy.org, usegalaxy.eu, planemo etc...

Browser and Operating System
Operating System: Linux
Browser: Firefox

To Reproduce
Steps to reproduce the behavior:
1.Make a minimal workflow like with a tool with a not last version tool with a when:

{
    "a_galaxy_workflow": "true",
    "annotation": "",
    "comments": [],
    "format-version": "0.1",
    "name": "Minimal workflow",
    "steps": {
        "0": {
            "annotation": "",
            "content_id": null,
            "errors": null,
            "id": 0,
            "input_connections": {},
            "inputs": [
                {
                    "description": "",
                    "name": "run head"
                }
            ],
            "label": "run head",
            "name": "Input parameter",
            "outputs": [],
            "position": {
                "left": 0.0,
                "top": 0.0
            },
            "tool_id": null,
            "tool_state": "{\"parameter_type\": \"boolean\", \"optional\": false}",
            "tool_version": null,
            "type": "parameter_input",
            "uuid": "920c0880-4f35-4fe1-b1d3-e5da3502e51b",
            "when": null,
            "workflow_outputs": []
        },
        "1": {
            "annotation": "",
            "content_id": null,
            "errors": null,
            "id": 1,
            "input_connections": {},
            "inputs": [
                {
                    "description": "",
                    "name": "input text"
                }
            ],
            "label": "input text",
            "name": "Input dataset",
            "outputs": [],
            "position": {
                "left": 113.00000000000006,
                "top": 96.04206350578201
            },
            "tool_id": null,
            "tool_state": "{\"optional\": false, \"tag\": null}",
            "tool_version": null,
            "type": "data_input",
            "uuid": "b5346c7e-3d1c-45ab-a65f-cc1a2a44e3dc",
            "when": null,
            "workflow_outputs": []
        },
        "2": {
            "annotation": "",
            "content_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_head_tool/1.1.0",
            "errors": null,
            "id": 2,
            "input_connections": {
                "infile": {
                    "id": 1,
                    "output_name": "output"
                },
                "when": {
                    "id": 0,
                    "output_name": "output"
                }
            },
            "inputs": [
                {
                    "description": "runtime parameter for tool Select first",
                    "name": "infile"
                }
            ],
            "label": "get first 10 lines",
            "name": "Select first",
            "outputs": [
                {
                    "name": "outfile",
                    "type": "input"
                }
            ],
            "position": {
                "left": 484.56665039062534,
                "top": 143.74846045400975
            },
            "post_job_actions": {},
            "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_head_tool/1.1.0",
            "tool_shed_repository": {
                "changeset_revision": "ddf54b12c295",
                "name": "text_processing",
                "owner": "bgruening",
                "tool_shed": "toolshed.g2.bx.psu.edu"
            },
            "tool_state": "{\"complement\": \"\", \"count\": \"10\", \"infile\": {\"__class__\": \"RuntimeValue\"}, \"__page__\": null, \"__rerun_remap_job_id__\": null}",
            "tool_version": "1.1.0",
            "type": "tool",
            "uuid": "fc693bb3-7e0c-4e9f-8a4d-4fbdb5ffdd16",
            "when": "$(inputs.when)",
            "workflow_outputs": [
                {
                    "label": "outfile",
                    "output_name": "outfile",
                    "uuid": "0401547e-1c8f-4dbe-924d-7eba864a13ff"
                }
            ]
        }
    },
    "tags": [],
    "uuid": "5e4c9d3c-69f2-45bf-89ce-1e0a37ffd99f",
    "version": 3
}
  1. Click on Upgrade workflow
  2. See warning

Expected behavior
An upgrade of the tool keeping the when.

Screenshots
Peek 2024-06-25 13-51

@lldelisle
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Thanks @mvdbeek

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2 participants