galaxyproject / galaxy

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Saving a workflow with missing tools not guiding sufficiently #13524

Closed afgane closed 2 years ago

afgane commented 2 years ago

Trying to save an edited workflow that continues to have issues does not work with an error saying the issues need to be corrected first. However, as a user, I have no idea what issues remain and meanwhile I cannot save progress that I've made thus far on fixing the workflow. It'd be nice to show the actual list of issues in the modal.

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mvdbeek commented 2 years ago

There are red boxes with the missing tools, right ? Otherwise something was wrong with the Galaxy instance.

afgane commented 2 years ago

This is on usegalaxy.org with the rna-seq-reads-to-counts.ga training workflow. A (white) box shows up when you try to load a workflow but nothing when you try to save it.

mvdbeek commented 2 years ago

Oh, that message is wrong. There's no missing tool (just a tool version mismatch), this is weird.

mvdbeek commented 2 years ago

@guerler do you have some time to check this out ? Looks like a problem with the state inside the editor. If you flip the versions in the workflow @afgane posted for featureCounts and Samtools indxstats you can actually save the workflow.

mvdbeek commented 2 years ago

In particular it's the content_id that doesn't get updated. This is from the PUT payload:

annotation: ""
content_id: "toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.2"
errors: null
id: "8"
input_connections: {input: [{id: "5", output_name: "output_alignments"}]}
label: null
position: {x: 2307.5086189038825, y: 1481.5416740648673, width: 66, height: 44.22002029418945,…}
post_job_actions: {}
tool_state: {input: "{"__class__": "ConnectedValue"}", __page__: null, __rerun_remap_job_id__: null}
tool_version: "2.0.3"
type: "tool"
uuid: "f645b890-43fc-4f67-ae9f-bb63622a035e"
workflow_outputs: [{output_name: "output", label: null}]

The tool_version is correct, the content_id is not

mvdbeek commented 2 years ago

Alright, that is actually a backend problem, we return the specified tool id, and not the actual tool id. I'll have a fix