Add scripts to extract workflows from WorkflowHub and UseGalaxy servers #158

bebatut · 2024-08-01T15:39:01Z

No description provided.

…extractor into add_workflows

nsoranzo · 2024-08-02T10:50:30Z

Fixed the linting, don't have time to look at the rest at the moment, sorry!

bebatut · 2024-08-02T14:09:12Z

Fixed the linting, don't have time to look at the rest at the moment, sorry!

Thanks already for fixing the linting!!

…extractor into add_workflows

- Add matrix strategy for test tutorial and test workflows - Replace pull_request_target by pull_request

paulzierep

Could you add the output of a test run ? That would make the review simpler. Will try to check tomorrow.

paulzierep · 2024-10-13T18:55:01Z

sources/bin/shared.py

+    Shorten tool id
+    """
+    if "toolshed" in tool:
+        return tool.split("/")[-2]


are you sure it's not [-1] ?

If we want to have the suite id it is [-2] and it is what we used there: https://github.com/galaxyproject/galaxy_codex/pull/158/files#diff-fded0df90a63fa85d73a79a61797665ed61e1b1a921558f0d3b301d877a54dc4L38

True, I just remembered we do it different for the tool stats (but there we compare wrapper ids - so all good !)

paulzierep

Looks good and I like the OO approach, could you provide the test output, still ?

paulzierep · 2024-10-14T09:54:16Z

sources/bin/shared.py

+    Shorten tool id
+    """
+    if "toolshed" in tool:
+        return tool.split("/")[-2]


True, I just remembered we do it different for the tool stats (but there we compare wrapper ids - so all good !)

CI fails

paulzierep · 2024-10-14T11:41:55Z

workflow CI fails, with

        wfhub_wfs = shared.get_request_json(
            "https://workflowhub.eu/workflows?filter[workflow_type]=galaxy",
            header,
        )

locally it worked for me, maybe we need to retry this a few times ... ?

paulzierep

Really nice ! Thanks @bebatut !

bebatut added 6 commits July 31, 2024 16:27

Add workflow extraction

22ea1fc

Merge branch 'main' of github.com:galaxyproject/galaxy_tool_metadata_…

14db8c2

…extractor into add_workflows

Add functional tests for workflows

8ca261e

Add mkdir for community result folder

fff676f

Fix linting

ad54245

Fix microgalaxy wf tags

5cd4039

bebatut temporarily deployed to fetch-tools August 1, 2024 15:39 — with GitHub Actions Inactive

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bebatut force-pushed the add_workflows branch from 1908d66 to 101891e Compare August 1, 2024 15:47

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bebatut force-pushed the add_workflows branch from 101891e to d208d81 Compare August 1, 2024 15:48

bebatut had a problem deploying to fetch-tools August 1, 2024 15:48 — with GitHub Actions Failure

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bebatut force-pushed the add_workflows branch from d208d81 to 44f70dd Compare August 1, 2024 15:53

bebatut had a problem deploying to fetch-tools August 1, 2024 15:53 — with GitHub Actions Failure

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bebatut force-pushed the add_workflows branch from 44f70dd to ce413d6 Compare August 1, 2024 15:58

bebatut had a problem deploying to fetch-tools August 1, 2024 15:58 — with GitHub Actions Failure

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Try to fix CI linting

32436b8

bebatut force-pushed the add_workflows branch from ce413d6 to 32436b8 Compare August 2, 2024 05:44

bebatut had a problem deploying to fetch-tools August 2, 2024 05:44 — with GitHub Actions Failure

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bebatut had a problem deploying to fetch-tools August 2, 2024 05:47 — with GitHub Actions Failure

bebatut temporarily deployed to fetch-tools August 2, 2024 05:47 — with GitHub Actions Inactive

Remove linting for Python 3.8

9cb366b

bebatut force-pushed the add_workflows branch from c40f65d to 9cb366b Compare August 2, 2024 05:49

bebatut had a problem deploying to fetch-tools August 2, 2024 05:49 — with GitHub Actions Failure

nsoranzo had a problem deploying to fetch-tools August 2, 2024 10:48 — with GitHub Actions Failure

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bebatut added 3 commits October 11, 2024 10:44

Merge branch 'main' of github.com:galaxyproject/galaxy_tool_metadata_…

a5c95d3

…extractor into add_workflows

Add microgalaxy wf tag and fix scripts

d37af5e

Fix linting on Python 3.8 - @nsoranzo commit

d00ddcb

bebatut force-pushed the add_workflows branch from 4dcc114 to d00ddcb Compare October 11, 2024 12:20

bebatut temporarily deployed to fetch-tools October 11, 2024 12:20 — with GitHub Actions Inactive

Remove Python 3.8 from the tests

66baf7e

bebatut temporarily deployed to fetch-tools October 11, 2024 12:23 — with GitHub Actions Inactive

Fix GitHub workflow

9755079

- Add matrix strategy for test tutorial and test workflows - Replace pull_request_target by pull_request

bebatut temporarily deployed to fetch-tools October 11, 2024 12:32 — with GitHub Actions Inactive

paulzierep reviewed Oct 13, 2024

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paulzierep previously approved these changes Oct 14, 2024

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paulzierep self-requested a review October 14, 2024 11:26

Add tests

5731241

bebatut temporarily deployed to fetch-tools October 14, 2024 12:04 — with GitHub Actions Inactive

paulzierep approved these changes Oct 16, 2024

View reviewed changes

paulzierep merged commit e0d9747 into main Oct 16, 2024
10 checks passed

paulzierep deleted the add_workflows branch October 16, 2024 11:37

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Add scripts to extract workflows from WorkflowHub and UseGalaxy servers #158

Add scripts to extract workflows from WorkflowHub and UseGalaxy servers #158

bebatut commented Aug 1, 2024

nsoranzo commented Aug 2, 2024

bebatut commented Aug 2, 2024

paulzierep left a comment

paulzierep Oct 13, 2024

bebatut Oct 14, 2024

paulzierep Oct 14, 2024

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paulzierep Oct 14, 2024

paulzierep commented Oct 14, 2024

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Add scripts to extract workflows from WorkflowHub and UseGalaxy servers #158

Add scripts to extract workflows from WorkflowHub and UseGalaxy servers #158

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bebatut commented Aug 1, 2024

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