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Add openBIS file source - #23458

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PlushZ wants to merge 2 commits into
galaxyproject:devfrom
PlushZ:add-openbis-fs
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Add openBIS file source#23458
PlushZ wants to merge 2 commits into
galaxyproject:devfrom
PlushZ:add-openbis-fs

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@PlushZ

@PlushZ PlushZ commented Sep 4, 2026

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This PR adds an openBIS Galaxy file source using pyBIS.
Users can:

  • Browse Spaces, Projects, Collections, Objects and existing DataSets.
  • Import files from read-only DataSets.
  • Import and export files through openBIS AFS.
  • Create AFS folders for Collections and Objects.
  • Authenticate with a Personal Access Token and configure TLS verification.
    New uploads use AFS exclusively because openBIS recommends it for mutable file storage and legacy DataSets are immutable.
    The PR also adds clearer export errors.

How to test the changes?

(Select all options that apply)

  • I've included appropriate automated tests.
  • This is a refactoring of components with existing test coverage.
  • Instructions for manual testing are as follows:
    1. [add testing steps and prerequisites here if you didn't write automated tests covering all your changes]

License

  • I agree to license these and all my past contributions to the core galaxy codebase under the MIT license.

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