galaxy-app 23.1.1

Galaxy application (backend)

Overview

The Galaxy application logic (backend).

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

History

23.1.1 (2023-10-23)

Bug fixes

• read job_conf directly from config_dir instead of computing it again from config_file by @bernt-matthias in #15596

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

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

• Fix revision scripts, run migrations in CI, add repair option, improve migrations utils by @jdavcs in #15811

• Change confusing pulsar logs message by @kysrpex in #16038

• Fix and test startup with Python 3.11 on macOS by @nsoranzo in #16082

• Fix : Ignore error messages for admin created accounts by @jvanbraekel in #16132

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

• Fix “database is locked” error (occurring in the context of workflow testing under SQLite) by @jdavcs in #16208

• Fix ordering of data libraries from API by @martenson in #16300

• 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 select statement syntax for SQLAlchemy 2.0 by @jdavcs in #16421

• Fix up unit tests for local use by @mvdbeek in #16483

• Run through tmp_dir_creation_statement only once by @mvdbeek in #16529

• Fix double-encoding notification content by @mvdbeek in #16530

• Limit tool document cache to tool configs with explicit cache path by @mvdbeek in #16537

• Fix multiple remote test data by @davelopez in #16542

• Ignore errors with user-set job resources by @mvdbeek in #16579

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

• make sure that TMP, TEMP, and TMPDIR are set by @bernt-matthias in #16594

• Bump minimum tpv version to 2.3.2 by @mvdbeek in #16597

• Backport tool mem fixes by @mvdbeek in #16601

• Reload toolbox after forking when using –preload by @mvdbeek in #16620

• Account for expires/expires_in when refreshing token by @mvdbeek in #16621

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

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

• Ensure Job belongs to current SA session by @mvdbeek in #16655

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

• Make sort_collection tool require terminal datasets by @mvdbeek in #16661

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

• Fix metadata setting in extended metadata + outputs_to_working_directory mode by @mvdbeek in #16678

• Fix regex validation for global inline flags by @mvdbeek in #16683

• Fix closed transaction error on galaxy startup/check jobs by @jdavcs in #16687

• Add missing join condition in job search by @mvdbeek in #16710

• Fix job search query by @mvdbeek in #16714

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

• Fix collection id encoding by @davelopez in #16718

• Workaround for XML nodes of job resource parameters losing their children by @kysrpex in #16728

• move the email and username redacting from the role loop by @martenson in #16820

• Fix parameter display in job info page for tools with sections by @mvdbeek in #16821

• Fix workflow preview display if tool state does not contain all parameter values by @mvdbeek in #16829

• Fix up local tool version handling by @mvdbeek in #16836

• Fix and prevent persisting null file_size by @mvdbeek in #16855

• Allow referring to steps by label only in markdown editor by @mvdbeek in #16861

• Fix safe update version handling in run form by @mvdbeek in #16865

• Remove more flushes in database operation tools by @mvdbeek in #16875

• Fix tag ownership check by @mvdbeek in #16877

Enhancements

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

• External Login Flow: Redirect users if account already exists by @ahmedhamidawan in #15019

• Add slack error reporting plugin by @hexylena in #15025

• Various Tool Shed Cleanup by @jmchilton in #15247

• Add Storage Management API by @davelopez in #15295

• OIDC tokens by @SergeyYakubov in #15300

• Expose additional beaker caching backends by @claudiofr in #15349

• Add support for visualizing HDF5 datasets. by @jarrah42 in #15394

• Towards SQLAlchemy 2.0: drop session autocommit setting by @jdavcs in #15421

• Update Python dependencies by @galaxybot in #15435

• Fix for new style conda packages by @bernt-matthias in #15446

• Move database access code out of tool_util by @jdavcs in #15467

• Protection against problematic boolean parameters. by @jmchilton in #15493

• Use connection instead of session for ItemGrabber by @jdavcs in #15496

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

• Move TS to Alembic by @jdavcs in #15509

• Explore tool remote test data by @davelopez in #15510

• Handle “email_from” config option consistently, as per schema description by @jdavcs in #15557

• Update Python dependencies by @galaxybot in #15564

• Drop workflow exports to myexperiment.org by @dannon in #15576

• Update database_heartbeat for SA 2.0 compatibility by @jdavcs in #15611

• Add suggested Training material to Tool Form by @ElectronicBlueberry in #15628

• Wrap check_jobs_at_startup operation in a transaction (SA 2.0 compatibility) by @jdavcs in #15643

• Add Galaxy Notification System by @davelopez in #15663

• Unpin Beaker requirement by @nsoranzo in #15665

• Add transactional state to JobHandlerStopQueue by @jdavcs in #15671

• Verify that activation and reset emails are properly generated by @guerler in #15681

• Add transactional state to workflow scheduling manager by @jdavcs in #15683

• Remove DELETED_NEW job state from code base by @jdavcs in #15690

• Fix/Enhance recalculate disk usage API endpoint by @davelopez in #15739

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

• Migrate to MyST-Parser for Markdown docs by @nsoranzo in #15844

• Drop use_legacy_history from config by @dannon in #15861

• Drop database views by @jdavcs in #15876

• Update Python dependencies by @galaxybot in #15890

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

• Updated doc and tests for attribute value filter by @tuncK in #15929

• Update Python dependencies by @galaxybot in #15942

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

• Export tool citations configurable message by @minh-biocommons in #15998

• Add History Archival feature by @davelopez in #16003

• Code cleanups from ruff and pyupgrade by @nsoranzo in #16035

• Add missing fields to HistorySummary schema model by @davelopez in #16041

• Vendorise packaging.versions.LegacyVersion by @nsoranzo in #16058

• Add Repository owner field to ToolSearch by @ahmedhamidawan in #16061

• Add count support for listing filters by @davelopez in #16075

• Update Python dependencies by @galaxybot in #16086

• Improved Cache Monitoring for Object Stores by @jmchilton in #16110

• Integrate accessibility testing into Selenium testing by @jmchilton in #16122

• Update Python dependencies by @galaxybot in #16123

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

• Update Python dependencies by @galaxybot in #16153

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

• adjust grid sharing indicators by @martenson in #16163

• Update Python dependencies by @galaxybot in #16182

• Drop workarounds for old ro-crate-py and docutils versions by @mvdbeek in #16198

• Remove various fallback behaviors by @mvdbeek in #16199

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

• Update Python dependencies by @galaxybot in #16227

• Update Python dependencies by @galaxybot in #16267

• Fix tool remote test data by @davelopez in #16311

• Hide conditionally skipped output by @mvdbeek in #16356

• Fix Storage Dashboard missing archived histories by @davelopez in #16473

• Bump bx-python to 0.10.0 by @mvdbeek in #16484

• Drop expunge_all() call in WebTransactionRequest by @mvdbeek in #16606

Other changes

• Follow up on object store selection PR. by @jmchilton in #15654

• merge release_23.0 into dev by @martenson in #15830

• Move axe-selenium-python to dev dependencies by @nsoranzo in #16162

• Bump msal version by @mvdbeek in #16285

• Fix error_reports linting by @mvdbeek in #16465

23.0.6 (2023-10-23)

Bug fixes

• Fix upload paramfile handling (for real user setups) by @bernt-matthias in #16504

• Fix extra files path handling by @mvdbeek in #16541

• Make sure job_wrapper uses a consistent metadata strategy by @mvdbeek in #16569

• Fix conditional step evaluation with datasets in repeats by @mvdbeek in #16584

• Don’t read request body into memory by @mvdbeek in #16585

• Fixes for extra files handling and cached object stores by @mvdbeek in #16595

• Lazy load tool data tables in celery worker by @mvdbeek in #16640

• Force __DUPLICATE_FILE_TO_COLLECTION__ ‘size’ param to integer by @simonbray in #16659

Enhancements

• Update pulsar client library to 0.15.5 by @mvdbeek in #16701

23.0.5 (2023-07-29)

Bug fixes

• Skip installing npm/yarn if available, fix conditional dependency parsing, create virtualenv via conda when conda active by @bernt-matthias in #16403

• Fix test discovery in vscode by @mvdbeek in #16413

• Fixes for (gitlab) error reporting by @bernt-matthias in #16424

23.0.4 (2023-06-30)

Bug fixes

• Fix default when statement evaluation by @mvdbeek in #16332

• Redact private role name and description when purging user by @mvdbeek in #16349

23.0.3 (2023-06-26)

Bug fixes

• Bump galaxy-release-util version to 0.1.2 by @mvdbeek in #16241

Enhancements

• When importing tool data bundles, use the first loc file for the matching table by @natefoo in #16247

Other changes

• Forward port of slugify username received from oidc by @nuwang in #16271

23.0.2 (2023-06-13)

Bug fixes

• Fix Text File Busy errors at the source by @mvdbeek in #16212

Enhancements

• Point release deps fixes and docs by @mvdbeek in #16214

• Use galaxy-release-util to upload python packages by @mvdbeek in #16240

23.0.1 (2023-06-08)

Bug fixes

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

• Fix mixed outputs_to_working_directory pulsar destinations by @mvdbeek in #15927

• Update Gravity to 1.0.3 by @natefoo in #15939

• Various fixes to path prefix handling by @mvdbeek in #16033

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

• Fix gcsfs test discovery by @mvdbeek in #16039

• Replace httpbin service with pytest-httpserver by @mvdbeek in #16042

• Update pulsar to 0.15.2 by @mvdbeek in #16050

• Anonymous User tool link bug fix by @ahmedhamidawan in #16065

• Fix BCO export by updating gxformat2 by @mvdbeek in #16081

• Fix job failure handling when condor indicates job failure by @mvdbeek in #16096

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

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

• Fix sort error when re-running job with DCE collection input by @mvdbeek in #16126

• Fix related-hid in bulk contents API by @mvdbeek in #16128

• Fix rank calculation for jobs waiting to be run by anonymous users by @jdavcs in #16137

• Tool warnings can either be None or a Dictionary but not a String by @guerler in #16183

• Pin minimum tpv version by @mvdbeek in #16201

Other changes

• Startup fix when tool removed between reboot by @mvdbeek in #16175

20.9.0 (2020-10-15)

• First release from the 20.09 branch of Galaxy.

20.5.0 (2020-07-04)

• First release from the 20.05 branch of Galaxy.