galaxy-test-api 24.1.3

Galaxy API tests

Overview

The Galaxy API tests.

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

History

24.1.3 (2024-10-25)

Bug fixes

• Fix subwofklow tags serialization type by @arash77 in #18456

• Prevent job submission if input collection element is deleted by @mvdbeek in #18517

• Fix view parameter type in Job index API by @davelopez in #18521

• Fix map over calculation for runtime inputs by @mvdbeek in #18535

• Fix Archive header encoding by @arash77 in #18583

• Don’t set file size to zero by @mvdbeek in #18653

• Fix extract workflow from history when implicit collection has no jobs by @mvdbeek in #18661

• Fix change datatype PJA on expression tool data outputs by @mvdbeek in #18691

• Fix subworkflow scheduling for delayed subworkflow steps connected to data inputs by @mvdbeek in #18731

• Catch and display exceptions when importing malformatted yaml workflows by @mvdbeek in #18734

• Fix infinitely delayed workflow scheduling if skipped step creates HDCA by @mvdbeek in #18751

• Fix copying workflow with subworkflow step for step that you own by @mvdbeek in #18802

• Raise MessageException instead of assertions on rerun problems by @mvdbeek in #18858

• Fix data_column ref to nested collection by @mvdbeek in #18875

• Access tool data table filters in workflow building mode by @mvdbeek in #18900

24.1.2 (2024-09-25)

Bug fixes

• Prevent job submission if input collection element is deleted by @mvdbeek in #18517

• Fix view parameter type in Job index API by @davelopez in #18521

• Fix map over calculation for runtime inputs by @mvdbeek in #18535

• Fix Archive header encoding by @arash77 in #18583

• Don’t set file size to zero by @mvdbeek in #18653

• Fix extract workflow from history when implicit collection has no jobs by @mvdbeek in #18661

• Fix change datatype PJA on expression tool data outputs by @mvdbeek in #18691

• Fix subworkflow scheduling for delayed subworkflow steps connected to data inputs by @mvdbeek in #18731

• Catch and display exceptions when importing malformatted yaml workflows by @mvdbeek in #18734

• Fix infinitely delayed workflow scheduling if skipped step creates HDCA by @mvdbeek in #18751

• Fix copying workflow with subworkflow step for step that you own by @mvdbeek in #18802

• Raise MessageException instead of assertions on rerun problems by @mvdbeek in #18858

• Fix data_column ref to nested collection by @mvdbeek in #18875

24.1.1 (2024-07-02)

Bug fixes

• Revert some requests import changes by @nsoranzo in #18199

• Fix subwofklow tags serialization type by @arash77 in #18456

Enhancements

• Remove deprecated BCO export endpoint by @martenson in #16645

• Enable all-vs-all collection analysis patterns. by @jmchilton in #17366

• 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

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

• Update Python dependencies by @galaxybot in #18063

24.0.3 (2024-06-28)

Bug fixes

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

• Prevent anonymous and inactive users from running workflows by @ahmedhamidawan in #18192

• Check dataset state when attempting to acces dataset contents by @mvdbeek in #18214

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

24.0.2 (2024-05-07)

Bug fixes

• Improve error message for Extract dataset tool by @mvdbeek in #18078

24.0.1 (2024-05-02)

Bug fixes

• Fix tool version switch in editor by @mvdbeek in #17858

• Fix workflow run form failing on certain histories by @mvdbeek in #17869

• Always serialize element_count and populated when listing contents by @mvdbeek in #17890

• Make wait_for_history_jobs look at jobs, not datasets by @mvdbeek in #17892

• Fix missing implicit conversion for mapped over jobs by @mvdbeek in #17952

• Fix get_content_as_text for compressed text datatypes by @mvdbeek in #17976

• Raise appropriate exception if user forces a collection that is not populated with elements as input by @mvdbeek in #18023

• Fix test_get_tags_histories_content test by @mvdbeek in #18026

• Ensure that offset and limit are never negative by @mvdbeek in #18044

• Fix history update time after bulk operation by @davelopez in #18068

24.0.0 (2024-04-02)

Bug fixes

• Only check access permissions in /api/{history_dataset_collection_id}/contents/{dataset_collection_id} by @ahmedhamidawan in #17444

• Fix test_index_advanced_filter API test re-running by @nsoranzo in #17547

• Limit new anon histories by @mvdbeek in #17657

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

• Fix histories API index_query serialization by @davelopez in #17726

• Fix source history update_time being updated when importing a public history by @jmchilton in #17728

• Also set extension and metadata on copies of job outputs when finishing job by @mvdbeek in #17777

• Fix change_datatype PJA for dynamic collections by @mvdbeek in #17803

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

Enhancements

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

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

• Extend regex groups in stdio regex matches by @bernt-matthias in #17016

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

• Don’t require admin user to list /api/tool_data by @jozh2008 in #17161

• Vueifiy History Grids by @guerler in #17219

• Reuse test instance during non-integration tests by @mvdbeek in #17234

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

• Add __KEEP_SUCCESS_DATASETS__ by @lldelisle in #17294

• Enable warn_unreachable mypy option by @mvdbeek in #17365

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

• Cancel all active jobs when the user is deleted by @davelopez in #17390

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

• Purge groups and roles from DB (for real) by @davelopez in #17411

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

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

• 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)

Bug fixes

• Fix: serialize tool_shed_urls directly from the API by @davelopez in #16561

• Restore ToolsApi and create new api route for new panel structure by @ahmedhamidawan in #16872

• Ruff and flake8 fixes by @nsoranzo in #16884

• Make payload optional again for create tag API by @nsoranzo in #17144

• Only check access permissions in /api/{history_dataset_collection_id}/contents/{dataset_collection_id} by @mvdbeek in #17459

Enhancements

• Implement default locations for data and collection parameters. by @jmchilton in #14955

• Delete non-terminal jobs and subworkflow invocations when cancelling invocation by @mvdbeek in #16252

• Migrate a part of the users API to Fast API by @heisner-tillman in #16341

• Refactor Tool Panel views structures and combine ToolBox and ToolBoxWorkflow into one component by @ahmedhamidawan in #16739

• Don’t copy collection elements in test_dataset_collection_hide_originals by @nsoranzo in #16747

• Drop legacy server-side search by @jdavcs in #16755

• Migrate a part of the jobs API to Fast API by @heisner-tillman in #16778

• Vueify Visualizations Grid by @guerler in #16892

• Change api/tool_panel to api/tool_panels/… by @ahmedhamidawan in #16928

• Require name for workflows on save, set default to Unnamed Workflow by @ahmedhamidawan in #17038

• Migrate ItemTags API to FastAPI by @arash77 in #17064

Other changes

• Merge 23.1 into dev by @mvdbeek in #16534

23.1.4 (2024-01-04)

Bug fixes

• Assert that tus uploader instance has URL by @mvdbeek in #17133

• Fix workflow index total matches counting by @davelopez in #17176

23.1.3 (2023-12-01)

No recorded changes since last release

23.1.2 (2023-11-29)

Bug fixes

• Skip state filtering in __MERGE_COLLECTION__ tool by @mvdbeek in #16937

• Fix duplicated tools in tool panel view section copying by @jmchilton in #17036

Enhancements

• Improve invocation error reporting by @mvdbeek in #16917

23.1.1 (2023-10-23)

Bug fixes

• Ensure session is request-scoped for legacy endpoints by @jdavcs in #16207

• allow anon access for api/datasets/get_content_as_text by @martenson in #16226

• qualify querying for an api-key by @martenson in #16320

• Fix tags ownership by @davelopez in #16339

• Job cache fixes for DCEs by @mvdbeek in #16384

• Fix histories count by @davelopez in #16400

• Fix replacement parameters for subworkflows. by @jmchilton in #16592

• Fixes for conditional subworkflow steps by @mvdbeek in #16632

• Fix nested conditional workflow steps by @mvdbeek in #16641

• Fix expression evaluation for nested state by @mvdbeek in #16656

• Push to object store even if set_meta fails by @mvdbeek in #16667

• Copy the collection contents by default when copying a collection by @mvdbeek in #16717

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

• Fix workflow import losing tool_version by @mvdbeek in #16869

• Fix tag ownership check by @mvdbeek in #16877

• Fix delete collection + elements by @davelopez in #16879

Enhancements

• Empower Users to Select Storage Destination by @jmchilton in #14073

• Outline Deployment Tests by @jmchilton in #15420

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

• Update Python dependencies by @galaxybot in #15564

• Add API test and refactor code for related:hid history filter by @ahmedhamidawan in #15786

• Allow pending inputs in some collection operation tools by @mvdbeek in #15892

• Record input datasets and collections at full parameter path by @mvdbeek in #15978

• Add History Archival feature by @davelopez in #16003

• Dataset chunking tests (and small fixes) by @jmchilton in #16069

• Improve histories and datasets immutability checks by @davelopez in #16143

• Migrate display applications API to Fast API by @heisner-tillman in #16156

• bring grids for (published) pages on par with workflows by @martenson in #16209

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)

No recorded changes since last release

23.0.1 (2023-06-08)

Bug fixes

• Display DCE in job parameter component, allow rerunning with DCE input by @mvdbeek in #15744

• Fix folder listing via file browser by @mvdbeek in #15950

• Fix case sensitive filtering by name in histories by @davelopez in #16036

• Fix dataype_change not updating HDCA update_time by @mvdbeek in #16099

• Extract HDA for code_file validate_input hook by @mvdbeek in #16120

Enhancements

• Add support for launching workflows via Tutorial Mode by @hexylena in #15684

• Allow setting auto_decompress property in staging interface by @mvdbeek in #16014

20.9.0 (2020-10-15)

• Initial import from dev branch of Galaxy during 20.09 branch of Galaxy.