galaxy-files 26.0.1.dev0

Galaxy file source framework and default plugins

Overview

The Galaxy file sources framework and default plugins.

• Code: https://github.com/galaxyproject/galaxy

History

26.0.1.dev0

26.0.0 (2026-04-08)

Bug fixes

• Various fixes around ascp file source by @mvdbeek in #21372

• Better error message for unencoded/unresolvable filesource uri by @dannon in #21562

• Fix OMERO file source download multi channel TIFF by @davelopez in #21856

• Fix ascp download retries by @mvdbeek in #21857

• Fixes some more optional fields in templates by @davelopez in #21891

• Fix Pydantic UnsupportedFieldAttributeWarning for Field defaults in Annotated by @mvdbeek in #21923

• Fix OMERO temp directory handling by @davelopez in #22262

• Harden API parameter validation by @mvdbeek in #22351

Enhancements

• Add DRS compact identifier support by @dannon in #20410

• Add service account support for Google Cloud Storage client initialization by @dannon in #21027

• Update Python dependencies by @galaxybot in #21043

• Add Custom Validation for User-Configured Templates by @davelopez in #21155

• Ascp plugin by @d-callan in #21357

• Add OMERO File Source Plugin by @davelopez in #21367

• Add new Azure Flat object store file source by @guerler in #21398

• Add AI Agent Framework and ChatGXY 2.0 by @dannon in #21434

• Clean up code with pyupgrade by @nsoranzo in #21540

• Drop support for Python 3.9 by @nsoranzo in #21583

• Switch Google Cloud Storage file source from fs-gcsfs to gcsfs (fsspec) by @mvdbeek in #21590

• Unify extensions of file source templates by @bernt-matthias in #21594

• Various fixes to file source template’s validation system by @davelopez in #21704

• Adds ImageJ metadata support to TIFF export by @davelopez in #21882

• Use mock test server when tests don’t target external galaxy server by @mvdbeek in #22103

25.1.2 (2026-03-09)

No recorded changes since last release

25.1.1 (2026-02-03)

Bug fixes

• Add missing dependencies to galaxy-files package by @nsoranzo in #21518

• Supports Dataverse file access via both persistent and database IDs by @davelopez in #21569

• Harden Dataverse integration by @davelopez in #21624

25.1.0 (2025-12-12)

Bug fixes

• Change wording of the client side storage handling by @bgruening in #19815

• Fix GCS file source to handle virtual directories without marker objects by @dannon in #21051

• Fix Huggingface timestamp parsing when last_commit is missing by @davelopez in #21072

• Fixes download for restricted Zenodo records by @davelopez in #21274

Enhancements

• Type annotation fixes for mypy 1.16.0 by @nsoranzo in #20424

• Add Dataverse template by @davelopez in #20551

• Clean up code from pyupgrade by @nsoranzo in #20642

• Add fsspec base implementation for File Source plugins by @davelopez in #20698

• Refactor Files Sources Framework for stronger typing using pydantic models by @davelopez in #20728

• Adapt S3 file source to fsspec by @davelopez in #20794

• Fix fsspec fs path handling by @davelopez in #20799

• Add Hugging Face 🤗 file source and user-defined template by @davelopez in #20805

• Support remote file source hashes by @davelopez in #20853

25.0.4 (2025-11-18)

No recorded changes since last release

25.0.3 (2025-09-23)

No recorded changes since last release

25.0.2 (2025-08-13)

Bug fixes

• Fix Invenio file downloads for published records with draft by @davelopez in #20685

25.0.1 (2025-06-20)

No recorded changes since last release

25.0.0 (2025-06-18)

Bug fixes

• Use resource_path() to access datatypes_conf.xml.sample as a package resource by @nsoranzo in #19331

• Fix wrong URI written to ExportObjectResultMetadata when exporting histories to eLabFTW by @kysrpex in #19541

• Update webdav user file source template help text by @sanjaysrikakulam in #19784

• Change wording in the google drive user file source template by @sanjaysrikakulam in #19927

Enhancements

• Let file sources choose a path for uploaded files by @kysrpex in #19154

• eLabFTW integration via Galaxy file source by @kysrpex in #19319

• Add Dataverse RDM repository integration by @KaiOnGitHub in #19367

• Type annotation fixes for mypy 1.14.0 by @nsoranzo in #19372

• Handles S3 listing errors by @itisAliRH in #19446

• Add eLabFTW file source from file source templates by @kysrpex in #19493

• Add InvenioRDM file source template by @davelopez in #19619

• Use discriminated unions in object stores and file source template configs by @davelopez in #19621

• Add Zenodo file source template by @davelopez in #19638

• Drop support for Python 3.8 by @nsoranzo in #19685

• Enable warn_redundant_casts mypy option and drop redundant casts by @nsoranzo in #20008

• Add ZIP explorer to import individual files from local or remote ZIP archives by @davelopez in #20054

• Implement file source to integrate Galaxy with RSpace by @kysrpex in #20167

24.2.4 (2025-06-17)

Enhancements

• Fix Invenio file source downloads not working with some Invenio instances by @davelopez in #19930

24.2.3 (2025-03-16)

Bug fixes

• Fix private role name performance issue by @jdavcs in #19679

24.2.2 (2025-03-08)

Bug fixes

• Fix RDM token access for user-defined file sources by @davelopez in #19768

24.2.1 (2025-02-28)

No recorded changes since last release

24.2.0 (2025-02-11)

Enhancements

• Allow OAuth 2.0 user defined file sources (w/Dropbox integration) by @jmchilton in #18272

• Add onedata templates by @bwalkowi in #18457

• Add missing version in the file sources and object store templates by @sanjaysrikakulam in #18497

• Add a new version of the production s3fs file source template with the writable configuration variable added by @sanjaysrikakulam in #18575

• Bring your own file sources: Add the WebDAV template and configuration by @sanjaysrikakulam in #18598

• Allow setting a few global defaults for file source plugin types. by @jmchilton in #18909

• Type annotations and fixes by @nsoranzo in #18911

• Allow a posix file source to prefer linking. by @jmchilton in #19132

24.1.4 (2024-12-11)

Bug fixes

• Fix production_aws_private_bucket.yml by @mvdbeek in #19155

24.1.3 (2024-10-25)

No recorded changes since last release

24.1.2 (2024-09-25)

No recorded changes since last release

24.1.1 (2024-07-02)

Bug fixes

• Fix file source search query with empty string value by @davelopez in #18191

• Small bug fixes for user data plugins by @jmchilton in #18246

• Fix check for anonymous by @jdavcs in #18364

Enhancements

• Add onedata objectstore by @bwalkowi in #17540

• Update Python dependencies by @galaxybot in #17653

• Code cleanups from ruff and pyupgrade by @nsoranzo in #17654

• Enable warn_unused_ignores mypy option by @nsoranzo in #17991

• Add galaxy to user agent by @mvdbeek in #18003

• Add Zenodo integration by @davelopez in #18022

• More typing in galaxy.files. by @jmchilton in #18037

• Refactor galaxy.files plugin loading + config handling. by @jmchilton in #18049

• Add stronger type annotations in file sources + refactoring by @davelopez in #18050

• Add pagination support to Files Source plugins by @davelopez in #18059

• Update Python dependencies by @galaxybot in #18063

• Overhaul Azure storage infrastructure. by @jmchilton in #18087

• Empower users to bring their own storage and file sources by @jmchilton in #18127

• Display DOIs in Archived Histories by @davelopez in #18134

• Update s3fs dependency. by @jmchilton in #18135

• Onedada object store and files source stability fixes by @bwalkowi in #18372

Other changes

• Fix #18316 (anonymous file sources) by @jmchilton in #18352

24.0.3 (2024-06-28)

Bug fixes

• Fix listing possibly untitled records in Invenio Plugin by @davelopez in #18130

• Raise RequestParameterInvalidException when url is invalid by @mvdbeek in #18155

• Fix error message when accessing restricted Zenodo records by @davelopez in #18169

• Raise RequestParameterInvalidException if url can’t be verified by @mvdbeek in #18230

• Fix Invenio credentials handling by @davelopez in #18255

24.0.2 (2024-05-07)

No recorded changes since last release

24.0.1 (2024-05-02)

Bug fixes

• Invenio plugin fixes by @davelopez in #17997

Enhancements

• Fix remote files sources error handling by @davelopez in #18027

24.0.0 (2024-04-02)

Enhancements

• Add support for Python 3.12 by @tuncK in #16796

• Python 3.8 as minimum by @mr-c in #16954

• Update Python dependencies by @galaxybot in #17235

• fix s3fs templating by @bgruening in #17311

• Update to black 2024 stable style by @nsoranzo in #17391

23.2.1 (2024-02-21)

Bug fixes

• pin fs.dropboxfs to >=1 by @bernt-matthias in #16451

• Write to a temp filename in posix file source plugin by @natefoo in #17350

• Set webdav file source to use temp files by default by @davelopez in #17388

• More defensive access of extra props in filesources by @nuwang in #17445

Enhancements

• Add Invenio RDM repository integration by @davelopez in #16381

• Refactor FilesDialog + Remote Files API schema improvements by @davelopez in #16420

• Use fs.onedatarestfs for Onedata files source plugin implementation by @lopiola in #16690

• Remove record access handling for Invenio RDM plugin by @davelopez in #16900

• Enhance Invenio RDM integration by @davelopez in #16964

23.1.4 (2024-01-04)

Bug fixes

• Separate collection and non-collection data element by @mvdbeek in #17236

23.1.3 (2023-12-01)

No recorded changes since last release

23.1.2 (2023-11-29)

Bug fixes

• Implement missing upload for S3 file sources by @davelopez in #17100

23.1.1 (2023-10-23)

Bug fixes

• Fix some drs handling issues by @nuwang in #15777

• Fix filesource file url support by @nuwang in #15794

• Fix unittest mocks to support us checking geturl() by @dannon in #16726

• Fix allowlist deserialization in file sources by @mvdbeek in #16729

Enhancements

• Unify url handling with filesources by @nuwang in #15497

23.0.6 (2023-10-23)

No recorded changes since last release

23.0.5 (2023-07-29)

No recorded changes since last release

23.0.4 (2023-06-30)

No recorded changes since last release

23.0.3 (2023-06-26)

No recorded changes since last release

23.0.2 (2023-06-13)

Bug fixes

• Fix dropbox import to support newer versions by @nuwang in #16239

23.0.1 (2023-06-08)

No recorded changes since last release

22.1.1 (2022-08-22)

• Initial standalone release of this package.