galaxy-app 24.1.2

Galaxy application (backend)

Overview

The Galaxy application logic (backend).

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

History

24.1.2 (2024-09-25)

Bug fixes

• Return generic message for password reset email by @ahmedhamidawan in #18479

• Increase API robustness to invalid requests, improve compressed data serving by @mvdbeek in #18494

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

• Strip unicode null from tool stdio by @mvdbeek in #18527

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

• Fix for not-null in ‘column_list’ object by @hujambo-dunia in #18553

• Also fail ensure_dataset_on_disk if dataset is in new state by @mvdbeek in #18559

• Fix sqlalchemy statement in tooltagmanager reset output by @dannon in #18591

• Set minimum weasyprint version by @mvdbeek in #18606

• Improve relabel identifiers message when number of columns is not 2 by @mvdbeek in #18634

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

• Make sure we set file size also for purged outputs by @mvdbeek in #18681

• File source and object store instance api fixes by @mvdbeek in #18685

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

• Fill in missing help for cross product tools. by @jmchilton in #18698

• 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 directory get or create logic by @mvdbeek in #18752

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

• Allow to change only the description of a quota by @bernt-matthias in #18775

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

• Fix unspecified oidc_endpoint variable overwriting specified redirect_url by @bgruening in #18818

• Fix wrong celery_app config on job and workflow handlers by @mvdbeek in #18819

• Fix named cursor is not valid anymore by @mvdbeek in #18825

• Tighten TRS url check by @mvdbeek in #18841

• Fix Workflow index bookmark filter by @itisAliRH in #18842

• Skip metric collection if job working directory doesn’t exist by @mvdbeek in #18845

• Extend on disk checks to running, queued and error states by @mvdbeek in #18846

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

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

• Fix loading very old workflows with data inputs by @mvdbeek in #18876

Enhancements

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

• Implemented the generic OIDC backend from python-social-auth into Gal… by @Edmontosaurus in #18670

• Collect job metrics also when job failed by @mvdbeek in #18809

• prevent “missing refresh_token” errors by supporting <extra_scopes> also with Keycloak backend by @ljocha in #18826

24.1.1 (2024-07-02)

Bug fixes

• Unpin social-auth-core dependency by @nsoranzo in #17607

• Dynamic tool fixes by @dcore94 in #18085

• Fix for unexpected OIDC XML validation error by @Edmontosaurus in #18106

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

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

• Fix handler: access to result row items changed in SA2.0 by @jdavcs in #18274

• Fix various packages’ issues by @nsoranzo in #18301

• Adapt Tool prediction API to Transformer-based deep learning architecture by @anuprulez in #18305

• Fix empty usernames in database + bug in username generation by @jdavcs in #18379

• Add TypedDict for JobsSummary by @mvdbeek in #18418

• Pin pydantic to >=2.7.4 by @nsoranzo in #18423

• Update mercurial to non-yanked 6.7.4 by @nsoranzo in #18434

• Fix dropped when_expression on step upgrade by @mvdbeek in #18446

• Improve workflow-related exception reporting by @mvdbeek in #18447

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

• Disable password reset for deleted users [GCC2024_COFEST] by @laperlej in #18459

• Add input extra files to get_input_fnames by @mvdbeek in #18462

Enhancements

• Only include tool stdout/stderr in HDA info by @natefoo in #16730

• Adding object store plugin for Rucio by @SergeyYakubov in #17156

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

• Add onedata objectstore by @bwalkowi in #17540

• Type annotation improvements by @nsoranzo in #17601

• Type annotation and CWL-related improvements by @nsoranzo in #17630

• Update Python dependencies by @galaxybot in #17653

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

• Update Python dependencies by @galaxybot in #17764

• SQLAlchemy 2.0 by @jdavcs in #17778

• Update Python dependencies by @galaxybot in #17819

• Update Python dependencies by @galaxybot in #17870

• Add email notifications channel by @davelopez in #17914

• Model edits and bug fixes by @jdavcs in #17922

• Update Python dependencies by @galaxybot in #17923

• Model typing and SA2.0 follow-up by @jdavcs in #17958

• Error reporting unit tests by @jmchilton in #17968

• Make urgent notifications mandatory by @davelopez in #17975

• Update Python dependencies by @galaxybot in #17982

• 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

• Update Python dependencies by @galaxybot in #18035

• 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

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

• Ensure history update_time is set when exporting by @davelopez in #18086

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

• Update Python dependencies by @galaxybot in #18095

• Update Python dependencies by @galaxybot in #18125

• Revises handling of warnings in the workflow run form by @guerler in #18126

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

• Update s3fs dependency. by @jmchilton in #18135

• More unit testing for object store stuff. by @jmchilton in #18136

• Harden User Object Store and File Source Creation by @jmchilton in #18172

• Fix boto3-stubs typecheck dependency by @nsoranzo in #18173

• More structured indexing for user data objects. by @jmchilton in #18291

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

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

Other changes

• Chore: remove repetitive words by @tianzedavid in #18076

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

• Merge 24.0 into 24.1 by @jdavcs in #18353

• Merge 24.0 into 24.1 by @jdavcs in #18365

24.0.3 (2024-06-28)

Bug fixes

• Raise exception if collection elements missing during download by @jdavcs in #18094

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

• Backport OIDC schema fix by @mvdbeek in #18111

• Don’t log exception if cancelled slurm job doesn’t have stderr file by @mvdbeek in #18121

• Downgrade missing output file in working directory to warning for failed jobs by @mvdbeek in #18123

• Fix data default values not getting added to history by @mvdbeek in #18132

• Drop redundant error message by @mvdbeek in #18156

• Emit warning when user-cancelled job already complete by @mvdbeek in #18178

• Avoid object store path lookup when constructing JobState object by @mvdbeek in #18190

• Add string cast for dbkey / genome_build by @mvdbeek in #18207

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

• Don’t set dataset peek for errored jobs by @mvdbeek in #18231

• Raise exception when extracting dataset from collection without datasets by @mvdbeek in #18249

• Skip tests if toolshed, dx.doi not responding by @mvdbeek in #18250

• Don’t attempt to download purged datasets by @mvdbeek in #18278

• Check various preconditions in FeatureLocationIndexDataProvider by @davelopez in #18283

• Don’t serialize display application links for deleted datasets by @mvdbeek in #18307

• Downgrade doi fetch error to debug by @mvdbeek in #18330

• Fix authentication error for anonymous users querying jobs by @davelopez in #18333

• Fix seek in slurm memory check by @mvdbeek in #18338

• Do not copy purged outputs to object store by @mvdbeek in #18342

• Kill pulsar job if job stopped on galaxy side by @mvdbeek in #18348

• Allow DCE as outer input to to_cwl by @mvdbeek in #18349

• Fix anonymous user job retrieval logic by @davelopez in #18358

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

• Fix user’s private role can be missing by @davelopez in #18381

• Fix null inputs in database operation tools by @mvdbeek in #18385

• Assign default data extension on discovered collection output by @mvdbeek in #18389

• Fix get_accessible_job if called without session by @mvdbeek in #18400

• Fix invocation step_job_summary for new collections by @mvdbeek in #18402

• Really allow in-range validator for txt by @bernt-matthias in #18411

• Fix collection map over status for dragged collections by @mvdbeek in #18416

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

Other changes

• Minor linting cleanup by @mvdbeek in #18421

• Replace busybox:ubuntu-14.04 image with busybox:1.36.1-glibc by @mvdbeek in #18428

24.0.2 (2024-05-07)

Bug fixes

• Adds logging of messageExceptions in the fastapi exception handler. by @dannon in #18041

• 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

• Fix saving workflows with freehand_comments only by @mvdbeek in #17901

• Always discard session after __handle_waiting_jobs is done by @mvdbeek in #17913

• Fix workflow run form for workflows with null rename PJA by @mvdbeek in #17929

• Revert unnecessary error change by @mvdbeek in #17948

• 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

• Backport: Fix bug: call unique() on result, not select stmt by @jdavcs in #17981

• Fix LengthValidator if no value passed by @mvdbeek in #17983

• Raise RequestParameterInvalidException if collection element has unknown extension by @mvdbeek in #17985

• Don’t attempt to commit in dry_run mode by @mvdbeek in #17987

• Don’t fail if reporting invalid parameter values by @mvdbeek in #18002

• Include exception info when something goes wrong while refreshing tokens by @mvdbeek in #18008

• Avoid exception when opening apply rules tool and no collection in history by @mvdbeek in #18011

• Don’t commit without having set a hid by @mvdbeek in #18014

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

• Fix tag regex pattern by @jdavcs in #18025

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

• Change wrong quota_source value from KeyError to ValueError by @mvdbeek in #18040

• Check database connection to issue a rollback if no connection by @jdavcs in #18070

Enhancements

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

Other changes

• Drop left-over debug statement by @mvdbeek in #17939

24.0.0 (2024-04-02)

Bug fixes

• Reload built-in converters on toolbox reload by @bernt-matthias in #17209

• Optional Reply-to SMTP header in tool error reports by @neoformit in #17243

• Package tests fixes by @nsoranzo in #17301

• Follow-up on #17274 and #17262 by @nsoranzo in #17302

• Rollback invalidated transaction: catch them earlier by @jdavcs in #17312

• Fixes for flake8-bugbear 24.1.17 by @nsoranzo in #17340

• Fix data_source and data_source_async bugs by @wm75 in #17422

• More efficient change_state queries, maybe fix deadlock by @mvdbeek in #17632

• Don’t index tasks without task_uuid by @mvdbeek in #17646

• Separate ConnectedValue from RuntimeValue by @mvdbeek in #17678

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

• Fix usage of DISTINCT by @jdavcs in #17759

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

• Use hg clone --stream to clone repos by @mvdbeek in #17786

• Defer job attributes that are usually not needed by @mvdbeek in #17795

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

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

• Normalize extensions when loading tool by @mvdbeek in #17868

• Ignore user data table errors for now by @mvdbeek in #17880

Enhancements

• Add harmonize collections tool (or whatever other name) by @lldelisle in #16662

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

• SQLAlchemy 2.0 upgrades (part 5) by @jdavcs in #16932

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

• Support for OIDC API Auth and OIDC integration tests by @nuwang in #16977

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

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

• Vueify Admin User Grid by @guerler in #17030

• Remove web framework dependency from tools by @davelopez in #17058

• Add select parameter with options from remote resources by @mvdbeek in #17087

• Expose more tool information / navigability in UI. by @jmchilton in #17105

• Vueify Admin Roles Grid by @guerler in #17118

• SA2.0 updates: handling “object is being merged into a Session along the backref cascade path” by @jdavcs in #17122

• Update Python dependencies by @galaxybot in #17123

• Vueify Admin Groups Grid by @guerler in #17126

• Towards SQLAlchemy 2.0: fix last cases of RemovedIn20Warning by @jdavcs in #17132

• Vueify Admin Forms and Quota grids by @guerler in #17141

• Update Python dependencies by @galaxybot in #17157

• Update Python dependencies by @galaxybot in #17201

• Vendorize fastapi-utls.cbv by @jdavcs in #17205

• Fix usage of graphene-sqlalchemy, bump to 3.0.0rc1 by @jdavcs in #17216

• Vueifiy History Grids by @guerler in #17219

• Update Python dependencies by @galaxybot in #17230

• Update Python dependencies by @galaxybot in #17235

• Allow job files to consume TUS uploads by @jmchilton in #17242

• Update Python dependencies by @galaxybot in #17247

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

• Consider Null inputs by @bernt-matthias in #17271

• Add OIDC backend configuration schema and validation by @uwwint in #17274

• Adds delete, purge and undelete batch operations to History Grid by @guerler in #17282

• Add __KEEP_SUCCESS_DATASETS__ by @lldelisle in #17294

• Improve ModelManager type hints by @mvdbeek in #17299

• API endpoint that allows “changing” the objectstore for “safe” scenarios. by @jmchilton in #17329

• Update Python dependencies by @galaxybot in #17333

• Add element_identifier and ext to inputs config file export by @bernt-matthias in #17357

• Remove unused statements in job search function by @mvdbeek in #17361

• Enable warn_unreachable mypy option by @mvdbeek in #17365

• Fix type annotation of code using XML etree by @nsoranzo in #17367

• More specific type annotation for BaseJobExec.parse_status() by @nsoranzo in #17381

• 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

• Update Python dependencies by @galaxybot in #17420

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

• Adds published histories to grid list by @guerler in #17449

• Allow filtering history datasets by object store ID and quota source. by @jmchilton in #17460

• data_column parameter: use column_names metadata if present by @bernt-matthias in #17478

• Update Python dependencies by @galaxybot in #17486

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

• Update k8s docker python to 3.12 by @nuwang in #17494

• add encode ID API endpoint by @mira-miracoli in #17510

• Fixing data_source tools and incrementing tool profile by @wm75 in #17515

• Update Python dependencies by @galaxybot in #17541

• Add image_diff comparison method for test output verification using images by @kostrykin in #17556

• Filter out subworkflow invocations by @mvdbeek in #17558

• Update Python dependencies by @galaxybot in #17580

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

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

• Improved error messages for runtime sharing problems. by @jmchilton in #17794

• Allow admin to sharpen language about selected object stores. by @jmchilton in #17806

Other changes

• consistently compare profile versions by @bernt-matthias in #16492

23.2.1 (2024-02-21)

Bug fixes

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

• Remove unnecessary check: item cannot be None by @jdavcs in #16550

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

• Fix dependency update GitHub workflow by @nsoranzo in #16639

• Ensure Job belongs to current SA session by @jdavcs in #16647

• Account for shared usage between TS and galaxy apps by @jdavcs in #16746

• move the email and username redacting from the role loop by @martenson in #16805

• Fix shed unit test by @mvdbeek in #16811

• chore: fix typos by @afuetterer in #16851

• Fix bug in SQLAlchemy statement by @jdavcs in #16881

• Ruff and flake8 fixes by @nsoranzo in #16884

• Update help in relabel_from_file.xml by @lldelisle in #16891

• Fix subtle bug in listify function + simplify list munging by @jdavcs in #16904

• prep for updated h5py and typos by @mr-c in #16963

• Enhancement to Tool Form page, Repeating form fields implement parameter instructions by @hujambo-dunia in #17018

• Expose file_name property in DatasetFilenameWrapper by @jdavcs in #17107

• Fix to_cwl for nested collections by @mvdbeek in #17276

• Rollback invalidated transaction by @jdavcs in #17280

• Install newer celery on python 3.8+ by @mvdbeek in #17309

• Backport Rollback invalidated transaction: catch them earlier by @mvdbeek in #17315

• Discard sqlalchemy session after task completion by @mvdbeek in #17317

• Scope session for job runner monitor loop by @mvdbeek in #17319

• Fix History contents genome_build filter postgresql bug by @ahmedhamidawan in #17384

• Update python-multipart to 0.0.7 by @nsoranzo in #17429

• Build param dict before creating entrypoint by @mvdbeek in #17440

• Fix bug: true >> True by @jdavcs in #17446

• Set metadata states on dataset association, not dataset by @mvdbeek in #17474

• Remove two print statements by @bernt-matthias in #17480

• Provide working routes.url_for every ASGI request by @mvdbeek in #17497

Enhancements

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

• Enable job resubmissions in k8s runner by @pcm32 in #15238

• Add parameter name to validation errors by @bernt-matthias in #15440

• Tool Shed 2.0 by @jmchilton in #15639

• Add ability to assert metadata properties on input dataset parameters by @bernt-matthias in #15825

• Limit number of celery task executions per second per user by @claudiofr in #16232

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

• Towards SQLAlchemy 2.0 (upgrades to SA Core usage) by @jdavcs in #16264

• Update Python dependencies by @galaxybot in #16305

• Add carbon emissions admin configuration options by @Renni771 in #16307

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

• Update Python dependencies by @galaxybot in #16360

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

• Update Python dependencies by @galaxybot in #16389

• Update Python dependencies by @galaxybot in #16409

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

• Towards SQLAlchemy 2.0 (upgrades to SA ORM usage in /test) by @jdavcs in #16431

• SQLAlchemy 2.0 upgrades to ORM usage in /lib by @jdavcs in #16434

• Update Python dependencies by @galaxybot in #16436

• Update Python dependencies by @galaxybot in #16485

• Rename MetadataEqualsValidator by @bernt-matthias in #16489

• Add support for CILogon deployments in different regions than the US by @uwwint in #16490

• Refactor/OIDC custos by @uwwint in #16497

• Update Python dependencies by @galaxybot in #16521

• Move database access code out of galaxy.util by @jdavcs in #16526

• Tweak tool memory use and optimize shared memory when using preload by @mvdbeek in #16536

• Update Python dependencies by @galaxybot in #16577

• Vueify Tool Form Data Selector by @guerler in #16578

• Workflow Comments 💬 by @ElectronicBlueberry in #16612

• Switch out conditional requirement parser by @mvdbeek in #16636

• Add scroll pagination and username filter to HistoryPublishedList by @ahmedhamidawan in #16642

• Bump samtools converters by @bernt-matthias in #16668

• Galaxy Markdown - add workflow image and license to Galaxy markdown. by @jmchilton in #16672

• Implement instance URLs in Galaxy markdown. by @jmchilton in #16675

• Change Sentry error reporting plug-in by @kysrpex in #16686

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

• Enhance task monitor composable by @davelopez in #16695

• Misc. edits/refactorings to session handling by @jdavcs in #16712

• SQLAlchemy 2.0 upgrades (part 2) by @jdavcs in #16724

• Update Python dependencies by @galaxybot in #16735

• Convert ISO to UTC for Date/Time in workflow reports by @assuntad23 in #16758

• Replace ELIXIR AAI button with Life Science login by @sebastian-schaaf in #16762

• Update Python dependencies by @galaxybot in #16770

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

• Add EGI Check-in as OIDC authentication option by @enolfc in #16782

• Replace file_name property with get_file_name function by @SergeyYakubov in #16783

• Updated path-based interactive tools with entry point path injection, support for ITs with relative links, shortened URLs, doc and config updates including Podman job_conf by @sveinugu in #16795

• Galaxy help forum integration by @ElectronicBlueberry in #16798

• Update Python dependencies by @galaxybot in #16807

• Another batch of SA2.0 edits in TS2.0 (part 3) by @jdavcs in #16833

• Remove remaining legacy backbone form input elements by @guerler in #16834

• SQLAlchemy 2.0 upgrades (part 4) by @jdavcs in #16852

• Update Python dependencies by @galaxybot in #16853

• Drop unused HistoryContentManager code and related tests by @jdavcs in #16882

• Vueify Visualizations Grid by @guerler in #16892

• Update Python dependencies by @galaxybot in #16896

• Enable some flake8-logging-format rules in ruff by @nsoranzo in #16915

• Remove “Create Workflow” form and allow workflow creation in editor by @ahmedhamidawan in #16938

• Update Python dependencies by @galaxybot in #16939

• Add helper to get dataset or collection via src and id by @mr-c in #16953

• Allow non-optional integer/float params without value attribute by @nsoranzo in #16966

• Update Python dependencies by @galaxybot in #16978

• Fix invocation report to target correct workflow version. by @jmchilton in #17008

• Update Python dependencies by @galaxybot in #17011

• Upgrade job manager’s index_query method to SA2.0 by @jdavcs in #17020

• optimize object store cache operations by @SergeyYakubov in #17025

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

• Update Python dependencies by @galaxybot in #17050

• Migrate groups API to fastAPI by @arash77 in #17051

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

• Update Python dependencies by @galaxybot in #17084

• Use python-isal for fast zip deflate compression in rocrate export by @mvdbeek in #17342

Other changes

• Merge 23.1 into dev by @mvdbeek in #16534

• Revert “[23.1] Enable job resubmissions in k8s runner” by @nuwang in #17323

• Fix succces typo by @mvdbeek in #17481

23.1.4 (2024-01-04)

Bug fixes

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

• Fix url_for in tool error reports by @davelopez in #17210

23.1.3 (2023-12-01)

No recorded changes since last release

23.1.2 (2023-11-29)

Bug fixes

• Fix unbound runner variable when there is an error in the job config by @mvdbeek in #16906

• Fix discarded dataset ordering in Storage Dashboard by @davelopez in #16929

• Include owner’s annotation when exporting workflow by @dannon in #16930

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

• Prevent Singular external auth users from disconnecting identity by @ahmedhamidawan in #16961

• Prevent workflow submission with missing input values by @mvdbeek in #17048

• Fix extra files collection if using store_by="id" and outputs_to_working_directory by @mvdbeek in #17067

• Remove rollback from __check_jobs_at_startup by @mvdbeek in #17085

Enhancements

• Improve invocation error reporting by @mvdbeek in #16917

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.