galaxy-schema 25.1.0

Pydantic models for Galaxy

Overview

The Galaxy API schema objects.

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

History

25.1.0 (2025-12-12)

Bug fixes

• Collection API related spelling fix. by @jmchilton in #20470

Enhancements

• Don’t serialize view of item in delete/purge request by @mvdbeek in #18732

• Support credentials(secrets/variables) in tool requirements by @arash77 in #19084

• Allow several Galaxy Markdown directives to be embedded. by @jmchilton in #19086

• Implement Sample Sheets by @jmchilton in #19305

• Add short term storage expiration indicator to history items by @davelopez in #20332

• Update create_time field to be required in history content items by @davelopez in #20357

• Implement Data Landing Requests by @jmchilton in #20592

• Add a “Debug” (email report) tab to Workflow Invocations by @ahmedhamidawan in #20624

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

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

• Hierarchical display collection dataset states by @mvdbeek in #20731

• Change Advanced Tool Search to a Tool Discovery View by @ahmedhamidawan in #20747

• Add configfiles support and various enhancements for user defined tools by @mvdbeek in #20761

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

• Replace tour_generator webhook with internal API and frontend by @ahmedhamidawan in #20868

• Update Python dependencies by @galaxybot in #20905

• Add resource docs and tweak tool source schema title generation by @mvdbeek in #20951

• Allow sending and tracking landing request origin by @mvdbeek in #20957

• Track landing request with invocation by @mvdbeek in #20960

• Move tours schema to schema directory (to fix package structure) by @ahmedhamidawan in #20965

• Use workflow-style payload in data landing request by @mvdbeek in #21107

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

• Correct visualization response schema by @guerler in #20627

• Fix dataset serializers and response models by @arash77 in #20694

Other changes

• Merge 24.2 into 25.0 by @ahmedhamidawan in #20681

25.0.1 (2025-06-20)

No recorded changes since last release

25.0.0 (2025-06-18)

Bug fixes

• Better handling of public pages and workflows authored by deleted users by @jdavcs in #19394

Enhancements

• Implement tool markdown reports. by @jmchilton in #19054

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

• Calculate hash for new non-deferred datasets when finishing a job by @nsoranzo in #19181

• Fix UP031 errors - Part 4 by @nsoranzo in #19235

• Update pydantic to 2.10.3 by @nsoranzo in #19326

• Empower Users to Build More Kinds of Collections, More Intelligently by @jmchilton in #19377

• Add User-Defined Tools by @mvdbeek in #19434

• Improve asynchronous tasks error handling and reporting by @davelopez in #19448

• Allow to send notifications when Admins cancel jobs by @davelopez in #19547

• Remove tags used by @ElectronicBlueberry in #19576

• Generate correct types for Dataset source transformations on backend. by @jmchilton in #19666

• Define simple models for job messages. by @jmchilton in #19688

• Show workflow help (and readme?) in run form by @ahmedhamidawan in #19736

• Migrate Page editing controller endpoint to API by @guerler in #19923

• Update Python dependencies by @galaxybot in #19929

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

• Add DOI to workflow metadata by @jdavcs in #20033

24.2.4 (2025-06-17)

Bug fixes

• ChatGXY Error Handling by @dannon in #19987

24.2.3 (2025-03-16)

No recorded changes since last release

24.2.2 (2025-03-08)

Enhancements

• Add bwa_mem2_index directory datatype, framework enhancements for testing directories by @mvdbeek in #19694

24.2.1 (2025-02-28)

No recorded changes since last release

24.2.0 (2025-02-11)

Bug fixes

• Drop “Send to cloud” tool and associated cloudauthz code by @jdavcs in #18196

• Fix issue with generating slug for sharing by @arash77 in #18986

• Fix invocation metrics usability by providing job context. by @jmchilton in #19279

Enhancements

• Experimental galactic wizard by @dannon in #15860

• Feature - stdout live reporting by @gecage952 in #16975

• Add errors fast api by @arash77 in #18093

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

• Improve datasets permissions API schema typing by @davelopez in #18563

• Improve typing for archived histories API schema by @davelopez in #18586

• Tighten user notification API response types by @davelopez in #18599

• Improve update user API payload schema by @davelopez in #18602

• Improve update history payload schema by @davelopez in #18618

• Improve types around User in schema and client by @davelopez in #18645

• Improve accept header API schema by @davelopez in #18668

• Migrate Visualizations API to FastAPI by @arash77 in #18721

• Backend handling of setting user-role, user-group, and group-role associations by @jdavcs in #18777

• Update Visualization FastAPI by @arash77 in #18792

• Workflow Landing Requests by @jmchilton in #18807

• Migrate Library Contents API to FastAPI by @arash77 in #18838

• Enable ignore-without-code mypy error code by @nsoranzo in #18898

• Decouple user email from role name by @jdavcs in #18966

• Workflow landing improvements by @mvdbeek in #18979

• Allow recovering a normalized version of workflow request state from API by @jmchilton in #18985

• Add job metrics per invocation by @mvdbeek in #19048

• Implement workflow parameter validators. by @jmchilton in #19092

• Access public history in job cache / job search by @mvdbeek in #19108

• Always validate hashes when provided by @nsoranzo in #19110

24.1.4 (2024-12-11)

Bug fixes

• Handle error when workflow is unowned in Invocation view by @ahmedhamidawan in #18730

• Fix datatype validation of newly built collection by @mvdbeek in #18738

• Fix job summary for optional unset job data inputs by @mvdbeek in #18754

• Fix TypeError from Pydantic 2.9.0 by @nsoranzo in #18788

• Fix wrong extension on pick data output by @mvdbeek in #18798

• Make all fields optional for HelpForumPost by @davelopez in #18839

• Remove the default Incoming suffix in GenericModel class by @davelopez in #19174

Enhancements

• Include workflow invocation id in exception logs by @mvdbeek in #18594

24.1.3 (2024-10-25)

Bug fixes

• Handle error when workflow is unowned in Invocation view by @ahmedhamidawan in #18730

• Fix datatype validation of newly built collection by @mvdbeek in #18738

• Fix job summary for optional unset job data inputs by @mvdbeek in #18754

• Fix TypeError from Pydantic 2.9.0 by @nsoranzo in #18788

• Fix wrong extension on pick data output by @mvdbeek in #18798

• Make all fields optional for HelpForumPost by @davelopez in #18839

Enhancements

• Include workflow invocation id in exception logs by @mvdbeek in #18594

24.1.2 (2024-09-25)

Bug fixes

• Handle error when workflow is unowned in Invocation view by @ahmedhamidawan in #18730

• Fix datatype validation of newly built collection by @mvdbeek in #18738

• Fix job summary for optional unset job data inputs by @mvdbeek in #18754

• Fix TypeError from Pydantic 2.9.0 by @nsoranzo in #18788

• Fix wrong extension on pick data output by @mvdbeek in #18798

• Make all fields optional for HelpForumPost by @davelopez in #18839

Enhancements

• Include workflow invocation id in exception logs by @mvdbeek in #18594

24.1.1 (2024-07-02)

Enhancements

• Visualizing workflow runs with an invocation graph view by @ahmedhamidawan in #17413

• Add email notifications channel by @davelopez in #17914

• Enable warn_unused_ignores mypy option by @nsoranzo in #17991

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

• Enable flake8-implicit-str-concat ruff rules by @nsoranzo in #18067

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

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

• Allow running and editing workflows for specific versions by @ahmedhamidawan in #18378

24.0.3 (2024-06-28)

Bug fixes

• do not expand datasets that are known to be inaccessible by @martenson in #17818

• Allow purge query param, deprecate purge body param by @mvdbeek in #18105

• Fix deprecated deprecated argument by @mvdbeek in #18119

• Fix users API serialization when listing users by @davelopez in #18329

• Fix update group API payload model by @davelopez in #18374

• Serialize purged flag for datasets in collections by @davelopez in #18420

24.0.2 (2024-05-07)

No recorded changes since last release

24.0.1 (2024-05-02)

Bug fixes

• Fix tag regex pattern by @jdavcs in #18025

• Fix History Dataset Association creation so that hid is always set by @mvdbeek in #18036

24.0.0 (2024-04-02)

Bug fixes

• Fix Workflow Comment Model for Pydantic 2 by @ElectronicBlueberry in #17296

• Add basic model import attribute validation by @mvdbeek in #17628

• Make latest_workflow_uuid optional by @mvdbeek in #17629

• Fix workflow person validation by @dannon in #17636

• Make WorkflowInput label, value and uuid optional by @mvdbeek in #17638

• Fix step type serialization for StoredWorkflowDetailed models by @mvdbeek in #17716

• Fix input parameter step type by @mvdbeek in #17767

• Fix optional types in Help Forum API by @davelopez in #17832

• Fix archived histories mixing with active in histories list by @davelopez in #17856

Enhancements

• port invocation API to fastapi by @martenson in #16707

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

• Toward declarative help for Galaxy markdown directives. by @jmchilton in #16979

• Create pydantic model for the return of show operation - get: /api/jobs/{job_id} by @heisner-tillman in #17153

• Vueifiy History Grids by @guerler in #17219

• Refactor two of the missing invocation routes to FastAPI by @heisner-tillman in #17237

• Migrate models to pydantic 2 by @mvdbeek in #17262

• Combines legacy qv-pattern and advanced filter pattern in history index endpoint by @guerler in #17368

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

• Allow using tool data bundles as inputs to reference data select parameters by @mvdbeek in #17435

• Refactor Workflow API routes - Part 1 by @heisner-tillman in #17463

• Consolidate resource grids into tab views by @guerler in #17487

• Display workflow invocation counts. by @jmchilton in #17488

• Filter out subworkflow invocations by @mvdbeek in #17558

• Restore histories API behavior for keys query parameter by @davelopez in #17779

• Fix datasets API custom keys encoding by @davelopez in #17793

23.2.1 (2024-02-21)

First release