galaxy-app 26.0.0

Galaxy application (backend)

Overview

The Galaxy application logic (backend).

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

History

26.0.0 (2026-04-08)

Bug fixes

• Fix workflow report time handling by @dannon in #19292

• Bump python-ldap from 3.4.0 to 3.4.5 in /lib/galaxy/dependencies by @dependabot[bot] in #21042

• Cross product tools: Fix typos in help section by @RZ9082 in #21061

• Bump urllib3 from 2.5.0 to 2.6.0 in /lib/galaxy/dependencies by @dependabot[bot] in #21399

• Don’t set OAUTHLIB_INSECURE_TRANSPORT setting in user_data by @nuwang in #21451

• Bump filelock from 3.20.0 to 3.20.1 in /lib/galaxy/dependencies by @dependabot[bot] in #21476

• Provide more accurate step hints for failing subworkflow steps by @mvdbeek in #21514

• Restrict collection of dynamic working dir output to specified directory in pulsar by @mvdbeek in #21515

• Fix input tags not being copied when using copy_inputs_to_history by @mvdbeek in #21529

• Bump aiohttp from 3.13.2 to 3.13.3 in /lib/galaxy/dependencies by @dependabot[bot] in #21538

• Bump urllib3 from 2.6.2 to 2.6.3 in /lib/galaxy/dependencies by @dependabot[bot] in #21546

• Bump werkzeug from 3.1.4 to 3.1.5 in /lib/galaxy/dependencies by @dependabot[bot] in #21549

• Overhaul ChatGXY Routing approach by @dannon in #21580

• Bump pyasn1 from 0.6.1 to 0.6.2 in /lib/galaxy/dependencies by @dependabot[bot] in #21605

• Fix toolshed tests on Python 3.14 by @mvdbeek in #21617

• Bump python-multipart from 0.0.21 to 0.0.22 in /lib/galaxy/dependencies by @dependabot[bot] in #21663

• Fix storing origin for workflow landing requests by @mvdbeek in #21696

• Handle TPV floating point memory values by @ksuderman in #21763

• Deserialize json string for export_metadata from old records by @mvdbeek in #21772

• Fix passing invalid job_destination dict to JobState constructor by @mvdbeek in #21798

• Update get_definitions() to FastAPI 0.128.8 by @nsoranzo in #21834

• Backport paired or unpaired mapping fix by @mvdbeek in #21936

• Fix dict leaking to process_dataset() during workflow execution by @mvdbeek in #21982

• Fix dataset collection tag duplication when copying a history by @mvdbeek in #21984

• Restore file doesn’t match sniffed datatype message by @mvdbeek in #21988

• Fix uncaught ImplicitConversionRequired by @mvdbeek in #22027

• Fix AttributeError when fetching citations for missing tools by @mvdbeek in #22029

• AttributeError when history is None during tool execution by @mvdbeek in #22031

• Fix AttributeError when export_metadata is a string instead of dict by @mvdbeek in #22033

• Fix TypeError when column_names metadata is None by @mvdbeek in #22057

• Fail job gracefully when output name exceeds 255 character DB limit by @mvdbeek in #22059

• Fix FileNotFoundError when workflow references purged HDA by @mvdbeek in #22060

• Add check_database_connection to workflow scheduling path by @mvdbeek in #22063

• Model hidden_data params as optional data in tool meta-models. by @jmchilton in #22116

• Fix unhandled exceptions in tool form model population by @guerler in #22129

• Backport transient CI fixes from #22102 to release_26.0 by @mvdbeek in #22135

• Do not queue paused jobs by @martenson in #22156

• Fix AmbiguousColumn error in job search for tools with long input names by @mvdbeek in #22167

• Fixes for gxformat2 by @jmchilton in #22179

• Add batch celery task for history dataset purging by @mvdbeek in #22180

• Include missing tools in stock_tool_paths. by @jmchilton in #22181

• Throw ParameterValueError instead of generic error by @guerler in #22188

• Fix event loop blocking in async API routes by @mvdbeek in #22202

• Update fastmcp requirement to 3.0.2 by @nsoranzo in #22221

• Add optional dataset collection mode to harmonize tool by @mvdbeek in #22236

• Fix batch history purge not updating user’s update_time by @mvdbeek in #22238

• Fix file source removal by @davelopez in #22246

• Validate replacement_params values are strings before storing by @mvdbeek in #22250

• Fix N+1 queries in fetch_job_states for jobs_summary endpoints by @mvdbeek in #22251

• Fix oauth2 template validation by @davelopez in #22253

• Drop stored workflow menu entries from user serialization by @mvdbeek in #22254

• Batch-prefetch HDCA job_state_summary in history contents listing by @mvdbeek in #22256

• Fix HDCA lost in tool form on rerun by @mvdbeek in #22258

• Fix purge for anon histories by @mvdbeek in #22275

• Raise error when API client sends invalid parameter keys by @mvdbeek in #22277

• Raise MessageException instead of generic Exception in rules_dsl by @mvdbeek in #22285

• Fix toolshed static image url encoding by @mvdbeek in #22286

• Fix nested DatasetCollectionElement in dynamic options by @mvdbeek in #22287

• Fix flaky job search for HDCA inputs on PostgreSQL by @mvdbeek in #22290

• Fix HDCA shown as unavailable on tool form rerun by @mvdbeek in #22291

• Fix AttributeError when anonymous user searches workflows with is:bookmarked by @mvdbeek in #22296

• Downgrade authnz OAuth callback errors from ERROR/EXCEPTION to WARNING by @mvdbeek in #22300

• Delay workflow scheduling when collection has unresolved ‘auto’ extension by @mvdbeek in #22303

• Fix slow get_private_role_user_emails_dict query by @mvdbeek in #22307

• Mark dataset collections as deleted when purging a history by @mvdbeek in #22315

• Harden API parameter validation by @mvdbeek in #22351

• Remove broken serialize_urls from HDASerializer by @mvdbeek in #22358

• Fix HideDatasetAction not applied for cached workflow jobs by @mvdbeek in #22360

• Don’t retry JobNotReadyException in job destination mapping by @mvdbeek in #22377

• Fix workflow extract NoneType on LDDA leaf in implicit collection by @jmchilton in #22381

• Serialize data provider errors as MessageException subclasses by @mvdbeek in #22398

• Handle MaxDiscoveredFilesExceededError for dynamic collections by @mvdbeek in #22402

• Unwrap HDCAs/DCEs nested in multi data input lists by @mvdbeek in #22405

• Reject HDCA submitted to single data parameter by @mvdbeek in #22406

Enhancements

• Refactor display application handling by @guerler in #15076

• Replace Copy Dataset Mako with Vue Component by @guerler in #17507

• Add Support for HTTP Headers in URL Fetch Requests with Secure Storage for Landing Requests by @davelopez in #20924

• Tool Request API by @jmchilton in #20935

• Remove Trackster by @guerler in #20974

• Integrate ‘uv’ for enhanced package management by @arash77 in #21002

• Update Python dependencies by @galaxybot in #21043

• Improve type annotation of job runners by @nsoranzo in #21050

• Remove Job.params by @jdavcs in #21075

• Update Python dependencies by @galaxybot in #21104

• Pulsar relay implementation by @mvdbeek in #21118

• Remove legacy Visualization Mako and Controllers by @guerler in #21133

• Fix various bugs/hacks with tool_data_table handling. by @jmchilton in #21163

• Add type annotations to job handling code by @nsoranzo in #21171

• Replace tuswsgi with tuspyserver by @mvdbeek in #21201

• Update Python dependencies by @galaxybot in #21229

• Reimplement keycloak/cilogon as PSA providers and remove custos by @nuwang in #21234

• Allow filtering job searches by history ID by @nsoranzo in #21257

• Move js-client bootstrapping to FastAPI by @guerler in #21264

• Update Python dependencies by @galaxybot in #21301

• Implement GA4GH WES API by @jmchilton in #21335

• Update Python dependencies by @galaxybot in #21345

• Link to an external profile when user accounts are managed by a single OIDC provider by @marius-mather in #21356

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

• Update Python dependencies by @galaxybot in #21368

• Fix: tool execution typing improvements/fixes by @jmchilton in #21374

• Update fastapi to 0.123.4 and get_openapi() fork by @nsoranzo in #21384

• Add initial support for the DICOM format by @kostrykin in #21385

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

• Update Python dependencies by @galaxybot in #21400

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

• Add Google Batch job runner by @ksuderman in #21443

• Update Python dependencies by @galaxybot in #21449

• Add Jupyternaut adapter for JupyterLite integration by @guerler in #21463

• Add support for Python 3.14 by @nsoranzo in #21486

• Enable attaching sample sheet to landing requests by @mvdbeek in #21489

• Update Python dependencies by @galaxybot in #21500

• Raise ConfigurationError instead etree.ParseError by @mvdbeek in #21509

• Include subworkflow jobs in invocation metrics by @mvdbeek in #21511

• Update Python dependencies by @galaxybot in #21513

• Add support for workflow landing requests using simple URLs by @mvdbeek in #21525

• Update Python dependencies by @galaxybot in #21526

• Implement workflow completion monitoring with extensible hooks by @mvdbeek in #21532

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

• Update Python dependencies by @galaxybot in #21552

• Add discarded_data option to model store import API by @mvdbeek in #21582

• 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

• Update Python dependencies by @galaxybot in #21606

• Update to gravity 1.2.0 by @nsoranzo in #21608

• Move legacy Visualization Plugins API to FastAPI by @guerler in #21612

• Apply 2026 black style by @galaxybot in #21618

• Update Python dependencies by @galaxybot in #21653

• Add agent based AI tool recommendation by @dannon in #21661

• Type annotations and refactorings by @nsoranzo in #21673

• Check file source template config files for determining conditional dependencies + add constraint for zero-ice by @bernt-matthias in #21688

• Standardize agent API schemas and response metadata by @dannon in #21692

• Backport chat API improvements by @dannon in #21973

• Use ParameterValueError for dataset count validation to reduce Sentry noise by @mvdbeek in #22058

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

Other changes

• Merge 25.1 into dev, fix openapi schema generation for TypedDict by @mvdbeek in #21168

• Don’t return 404 when file name can’t be serialized by @mvdbeek in #21577

• Reduce completion monitor logging by @mvdbeek in #21674

• Backport: Fix dbkey filter returning no options when dbkey unset by @bernt-matthias in #21945

• Show invalid tool error reasons in Tool Shed UI by @mvdbeek in #22040

• Backport of 21939 by @jdavcs in #22265

25.1.2 (2026-03-09)

Bug fixes

• Add selenium test and fix inline images in workflow report tables by @mvdbeek in #21698

• Allow workflow download with missing file source references by @mvdbeek in #21814

• Fix AWS Batch monitor crash, delete copied monitor method by @mvdbeek in #21818

• Fix tool credentials on containerized (Singularity/Docker) destinations by @arash77 in #21821

• Add builtin_converters section to integrated tool panel by @ahmedhamidawan in #21838

• Fix output dataset permission guessing by @mvdbeek in #21862

• Enforce storage quota for Celery-based data fetch jobs by @mvdbeek in #21941

• Fix optional parameter persisting NO_REPLACEMENT sentinel when not provided by @mvdbeek in #21964

• Fix recording duplicate workflow_request_input_step_parameter rows by @mvdbeek in #21980

• Fix NoReplacement handling in workflow callback_helper by @mvdbeek in #21994

• Fix pick_value output inheriting hidden state from input datasets by @mvdbeek in #21995

25.1.1 (2026-02-03)

Bug fixes

• Record input parameter invocation inputs by @mvdbeek in #21452

• Maintain column definitions on map over by @mvdbeek in #21468

• Do not update a user’s update_time when an admin archives (and purges) a history by @natefoo in #21484

• Fix subworkflow runs for disconnected required inputs with defaults by @mvdbeek in #21488

• Usability fixes for sample sheet selection. by @jmchilton in #21503

• Fix type annotation for invocation report errors field by @mvdbeek in #21508

• Filter out failed_metadata HDAs from job cache by @mvdbeek in #21544

• Fix pulsar with rewrite_parameters: false by @mvdbeek in #21557

• Fix Pulsar with default_file_action: none by @mvdbeek in #21578

• Fix condor typo by @gsaudade99 in #21651

• Fix HTCondor runner unwatching jobs when stopping containers by @kysrpex in #21656

• Fix option propagation for workflow inputs connected to multiple subworkflows by @mvdbeek in #21712

• Add missing filter_failed_collection_1.1.0.xml tool by @mvdbeek in #21719

• Strip inline comments in conditional requirements by @mvdbeek in #21720

Enhancements

• Add sample sheet support to many database operation tools by @mvdbeek in #21465

• Add database operation tool to convert sample sheets to list collections by @mvdbeek in #21625

25.1.0 (2025-12-12)

Bug fixes

• Workaround to numeric sorting in the local portion of tool versions if they are galaxy “build” numbers by @natefoo in #13570

• Bump requests from 2.32.3 to 2.32.4 in /lib/galaxy/dependencies by @dependabot[bot] in #20422

• Remove decoded ids from job/dataset error report email by @ahmedhamidawan in #20714

• Fix multiple=”true” data collection map over for shell_command tools by @mvdbeek in #20859

• Fix default conditional test parameters… by @jmchilton in #20942

• Set minimum profile version for expression tools by @mvdbeek in #21151

• Add Convert characters1 to workflow safe updates by @mvdbeek in #21160

• Bump up minimal tpv version by @mvdbeek in #21166

• Add missing more-itertools dependency by @nsoranzo in #21214

• Fix downloading subworkflows without stored workflow by @mvdbeek in #21223

• Fix fastapi package conflict by @mvdbeek in #21349

• Skip mako for rendering tool help by @mvdbeek in #21428

• Fix optional subworkflow input scheduling bug by @mvdbeek in #21435

• Maintain columns on sample sheet map over by @mvdbeek in #21436

Enhancements

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

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

• Add tags to output datasets from tool form by @PlushZ in #19225

• Implement Sample Sheets by @jmchilton in #19305

• Consider collections in on_strings for parameters accepting multiple datasets by @bernt-matthias in #19817

• Remove backbone-based charts modules by @guerler in #19892

• Update Python dependencies by @galaxybot in #20139

• Remove legacy visualizations by @guerler in #20173

• Split Login and Register, enable OIDC Registration. by @uwwint in #20287

• Empower Users to More Pragmatically Import Datasets & Collections From Tables by @jmchilton in #20288

• Switch Default Visualization Endpoint to script, migrate to YAML by @guerler in #20303

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

• Update Python dependencies by @galaxybot in #20347

• Install Visualization plugins as self-contained packages by @guerler in #20348

• Prepare ToolBox.dynamic_tool_to_tool() for CWL formats by @nsoranzo in #20364

• Install visualizations directly to static path, avoid duplication by @guerler in #20372

• Update Python dependencies by @galaxybot in #20383

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

• Implement dataset source requested transformations. by @jmchilton in #20435

• Add username_key setting to configure python-social-auth OIDC by @marius-mather in #20497

• Remove deprecated tool document cache by @nsoranzo in #20510

• Fixes for invocation import. by @jmchilton in #20528

• Update Python dependencies by @galaxybot in #20537

• Decode OIDC access token as part of authentication pipeline by @marius-mather in #20547

• Update Python dependencies by @galaxybot in #20577

• Display the Galaxy Citation within the Export Tool References List by @mschatz in #20584

• Implement Data Landing Requests by @jmchilton in #20592

• Update Python dependencies by @galaxybot in #20601

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

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

• Update Python dependencies by @galaxybot in #20653

• Update Python dependencies by @galaxybot in #20680

• Update Python dependencies by @galaxybot in #20699

• Improve cli and slurmcli runner traceability for job status and failure reasons by @selten in #20717

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

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

• Update Python dependencies by @galaxybot in #20732

• Update Python dependencies by @galaxybot in #20753

• Consolidate visualization mako, avoid user agent styles by @guerler in #20760

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

• Drop old load_workflow controller method, use API by @mvdbeek in #20774

• Update Python dependencies by @galaxybot in #20779

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

• Update Python dependencies by @galaxybot in #20812

• Update pytest to v8 by @nsoranzo in #20838

• Update Python dependencies by @galaxybot in #20841

• Allow adding extra steps to the default pipeline of the OIDC authentication by @marius-mather in #20845

• Use a streaming based parser (ijson) when setting metadata for biom1 files. by @ksuderman in #20851

• Various Container Execution Enhancements (including GCP Batch support) by @jmchilton in #20862

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

• Update Python dependencies by @galaxybot in #20869

• Improve type annotation for job runners and InteractiveToolManager by @nsoranzo in #20871

• Replace deprecated codecs.open() by @nsoranzo in #20891

• Update Python dependencies by @galaxybot in #20905

• Allow creation of visualizations without dataset by @guerler in #20914

• Add support for picking from_work_dir directory by @mvdbeek in #20916

• Add tool to add nesting level to collection by @bernt-matthias in #20926

• Update Python dependencies by @galaxybot in #20930

• Allow addressing user defined tools in job config by @mvdbeek in #20932

• Wire up and test resource requirement via tpv by @mvdbeek in #20936

• Limit admin requirement of selected tool data api endpoints by @guerler in #20949

• 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

• Use nodejs-wheel to install node by @mvdbeek in #20963

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

• Update Python dependencies by @galaxybot in #20968

• Log task execution errors with log.exception by @mvdbeek in #20970

• Update Python dependencies by @galaxybot in #21005

• Bump up total-perspective-vortex dependency by @mvdbeek in #21014

• Tighter API for tool run tagging. by @jmchilton in #21210

• Optimize /api/invocations/steps/{step_id} by @mvdbeek in #21249

• Optionally include column headers in sample sheet file by @mvdbeek in #21439

Other changes

• Merge release_25.0 into dev by @davelopez in #20484

• Bump pillow from 11.2.1 to 11.3.0 in /lib/galaxy/dependencies by @dependabot[bot] in #20591

• Sample Sheet Bug Fixes around Preserving Collection Metadata by @jmchilton in #20749

• Validate sample sheet column definitions in workflow definitions on backend. by @jmchilton in #20880

• Drop fastapi extra dep from sentry-sdk by @mvdbeek in #21156

• Resolve possible symlink before establishing tool file location by @mvdbeek in #21175

25.0.4 (2025-11-18)

Bug fixes

• Check for expiration in refresh token dictionary by @jdavcs in #20954

• Deactivate user file source on unknown error by @mvdbeek in #20962

• Don’t create workflow outputs to recover input parameter outputs by @mvdbeek in #20980

• Fix PUT /api/workflows for user defined tools by @mvdbeek in #20987

• Store pulsar job prep error messages by @mvdbeek in #21013

• Require OK datasets for filtering empty datasets by @bernt-matthias in #21023

• Fix InvalidRequestError when saving workflow step with dynamic tool by @mvdbeek in #21056

• Run landing request state through validator by @mvdbeek in #21087

• Create new datasets when creating skipped database operation tool outputs by @mvdbeek in #21142

• Fix refresh token expiration retrieval logic by @nuwang in #21213

Enhancements

• Use job cache also for implicit conversions by @mvdbeek in #21021

25.0.3 (2025-09-23)

Bug fixes

• Ensure that workflow invocations are persisted with state by @mvdbeek in #20784

• Fix password reset functionality for lowercase emails by @jdavcs in #20801

• Fix token refresh bug (cilogon) by @jdavcs in #20821

• Drop eager argument from invocation related methods by @mvdbeek in #20863

• Fix role.description bug by @jdavcs in #20883

• Make check for existing user in custos_authnz.py case insensitive by @cat-bro in #20893

• Avoid potential race condition in replacement_for_connection by @mvdbeek in #20909

25.0.2 (2025-08-13)

Bug fixes

• Fix restricting user defined tool input datasets extensions by @mvdbeek in #20545

• Don’t assume cwd = job directory when running prepare dirs by @natefoo in #20571

• Fix apply rules ownership check by @mvdbeek in #20582

• Prevent importing workflows with invalid step UUID by @davelopez in #20596

• Constraint conditional redis version to allow only minor updates by @davelopez in #20603

• Fix optional unspecified input to conditional step by @mvdbeek in #20647

• Avoid postgres truncation of aliases and labels by @mvdbeek in #20649

• Fix deferred datasets in multiple dataset parameters. by @jmchilton in #20650

• Bump up pulsar dependency to 0.15.9 by @mvdbeek in #20672

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

• Update galaxy-release-util by @mvdbeek in #20727

• Fix maximum workflow invocation duration test by @mvdbeek in #20729

Enhancements

• Add redis conditional dependency by @davelopez in #20502

• Improve workflow monitor loop times by @mvdbeek in #20522

25.0.1 (2025-06-20)

Bug fixes

• Fix single data element identifier to be a regular string by @mvdbeek in #20438

• Pin isa-rwval 0.10.11, drop conditional import handling by @natefoo in #20527

• Fix galaxy-config script, move install to galaxy-dependencies in app package by @natefoo in #20531

Enhancements

• Bump gravity dependency to 1.1.0 by @mvdbeek in #20520

Other changes

• Bump Gravity to 1.1.1 by @natefoo in #20533

25.0.0 (2025-06-18)

Bug fixes

• Bump tornado from 6.4.1 to 6.4.2 in /lib/galaxy/dependencies by @dependabot[bot] in #19189

• Don’t calculate dataset hash for datasets in non-OK state by @nsoranzo in #19191

• Bump python-multipart from 0.0.17 to 0.0.18 in /lib/galaxy/dependencies by @dependabot[bot] in #19233

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

• Require importlib-resources also for Python 3.9-3.11 by @nsoranzo in #19358

• Bump jinja2 from 3.1.4 to 3.1.5 in /lib/galaxy/dependencies by @dependabot[bot] in #19369

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

• Alternative format_source fix by @mvdbeek in #19395

• Avoid using custos refresh tokens which are expired by @martenson in #19411

• Use fissix also when python3-lib2to3 is not installed by @nsoranzo in #19749

• Fix setting env and tags on resubmission by @bernt-matthias in #19753

• Fix Galaxy ignoring job object_store_id for quota check by @bernt-matthias in #19854

• Fix broken optimisation introduced in #19852 by @nsoranzo in #19871

• Fix various mypy issues around mapped attributes by @mvdbeek in #19883

• More fixes to FormData drag and drop and typing by @ahmedhamidawan in #19900

• Fix ownership check in history contents update route by @mvdbeek in #19969

• Pass host url to visualizations by @guerler in #20022

• Allow deferred and ok state datasets for vis by @guerler in #20143

• Fix certain cases of collection parameter handling during workflow execution. by @jmchilton in #20152

• Fix tapis module typing errors by @jdavcs in #20175

• Fix NFDI auth by @bgruening in #20217

• Add non-dev httpx dependency by @mvdbeek in #20281

• Rerun workflows for the correct version/instance by @ahmedhamidawan in #20313

• Fix workflow bookmark filtering by @davelopez in #20325

• Generate a tenant-unique UID for tapis. by @dannon in #20370

• Fix job rerun with tool version change by @mvdbeek in #20417

• Update pulsar-galaxy-lib to 0.15.8 by @mvdbeek in #20419

• Upgrade tensorflow conditional dependency version to 2.15.1 by @cat-bro in #20434

• Dataset Display and Preferred Viz fixes by @dannon in #20439

Enhancements

• Dynamic options: add data table filter by @bernt-matthias in #12941

• Run the tool working dir backup/restore on Pulsar by @natefoo in #16696

• 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

• Update Python dependencies by @galaxybot in #19190

• Fix UP031 errors - Part 1 by @nsoranzo in #19194

• Fix UP031 errors - Part 3 by @nsoranzo in #19218

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

• Refactor for better reuse of workflow parameter type constants by @nsoranzo in #19260

• Fix UP031 errors - Part 5 by @nsoranzo in #19282

• Migrate WF Collection Input Form Definition to Client Side by @jmchilton in #19313

• Fix UP031 errors - Part 6 by @nsoranzo in #19314

• Update pydantic to 2.10.3 by @nsoranzo in #19326

• Misc fixes 202412 by @nsoranzo in #19341

• Hide outdated visualizations from visualizations activity panel by @guerler in #19353

• Update Python dependencies by @galaxybot in #19366

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

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

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

• Set safe default extraction filter for tar archives by @nsoranzo in #19406

• Remove transaction helper by @jdavcs in #19407

• Prevent users from reusing a banned email after account is purged by @jdavcs in #19413

• Update Python dependencies by @galaxybot in #19418

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

• Type annotations improvements by @nsoranzo in #19442

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

• Update Python dependencies by @galaxybot in #19464

• Type annotation improvements by @nsoranzo in #19485

• Update Python dependencies by @galaxybot in #19510

• Add config options for tool dependency installs by @afgane in #19565

• Update Python dependencies by @galaxybot in #19567

• Remove tags used by @ElectronicBlueberry in #19576

• Expand workflow metadata for readme. by @jmchilton in #19591

• Add failed jobs working directory cleanup as a celery periodic task by @sanjaysrikakulam in #19594

• Use correct plugin_kind in user file sources by @davelopez in #19622

• Update Python dependencies by @galaxybot in #19623

• Format code with black 25.1.0 by @nsoranzo in #19625

• Type annotation improvements by @nsoranzo in #19642

• Refactor dependencies for tool output actions. by @jmchilton in #19662

• Add webdavclient3 to conditional-requirements.txt by @bgruening in #19671

• Update Python dependencies by @galaxybot in #19682

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

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

• Move RequiredAppT back into galaxy packages. by @jmchilton in #19704

• Use model classes from galaxy.model instead of app.model object - Part 1 by @nsoranzo in #19706

• Preserve workflow labels in final invocation reports by @guerler in #19721

• ToolShed 2.1 - Various bugfixes and enhancements. by @jmchilton in #19722

• Use model classes from galaxy.model instead of app.model object - Part 2 by @nsoranzo in #19726

• Update Python dependencies by @galaxybot in #19727

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

• Improvements to package decomposition. by @jmchilton in #19759

• Update Python dependencies by @galaxybot in #19772

• Add visualization framework interface to cell-based markdown editor by @guerler in #19775

• Update Python dependencies by @galaxybot in #19816

• Populate image metadata without allocating memory for the entire image content by @kostrykin in #19830

• Syntactic sugar to ease TPV configuration. by @jmchilton in #19834

• Improve markdown editor modularity and structure by @guerler in #19835

• Add mandatory RO-Crate metadata when exporting by @elichad in #19846

• Add basic support for icons in tools by @davelopez in #19850

• Improve type annotations of ModelPersistenceContext and derived classes by @nsoranzo in #19852

• Drop old galaxy_session records by @jdavcs in #19872

• Update Python dependencies by @galaxybot in #19874

• Add Tapis auth support by @dannon in #19887

• Remove unnecessary code duplications by @nsoranzo in #19921

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

• Update Python dependencies by @galaxybot in #19929

• Add type hints around collection copying and job things by @mvdbeek in #19961

• Job cache allow different names when possible by @mvdbeek in #19962

• Update Python dependencies by @galaxybot in #19964

• Allow different AI providers (as long as they are openai compatible) by @uwwint in #19989

• Improve type annotation of tool parameter wrapping by @nsoranzo in #19991

• IT Activity Panel by @dannon in #19996

• Update Python dependencies by @galaxybot in #19998

• Implement dataset collection support in workflow landing requests by @mvdbeek in #20004

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

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

• Add support for Markdown help text in visualizations by @guerler in #20043

• Add sample datasets for visualizations by @guerler in #20046

• Use visualization dropdown solely for examples by @guerler in #20094

• Update Python dependencies by @galaxybot in #20096

• Adds Example Datasets and Help Text for Visualizations by @guerler in #20097

• Additional type hints for toolbox.get_tool / toolbox.has_tool by @mvdbeek in #20150

• Create working dir output outside of tool evaluator by @mvdbeek in #20153

• Add three AAI providers by @martenson in #20165

• Add replacement_dataset option to collection filter tools by @simonbray in #20166

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

• Visualization-First Display functionality by @dannon in #20190

• Improve type annotation of galaxy.model.dataset_collections by @nsoranzo in #20194

• Improve performance of job cache query by @mvdbeek in #20319

Other changes

• Merge 24.2 into dev by @jdavcs in #19590

• Fix import and update_page type signature by @mvdbeek in #19932

• Fix copying job output from discovered outputs by @mvdbeek in #19999

• Bump h11 from 0.14.0 to 0.16.0 in /lib/galaxy/dependencies by @dependabot[bot] in #20088

• Fix job rerun for dynamic tools by @mvdbeek in #20259

24.2.4 (2025-06-17)

Bug fixes

• Reduce default framework tool test timeout to 60 seconds by @mvdbeek in #19819

• Fix various job concurrency limit issues by @mvdbeek in #19824

• Handle directories with percents directories with export_remote.xml. by @jmchilton in #19865

• Fix tabular metadata setting on pulsar with remote metadata by @mvdbeek in #19891

• Skip data_meta filter in run form by @mvdbeek in #19895

• Fix duplicate extensions for data inputs by @ahmedhamidawan in #19903

• Skip implicit HDA conversions in DataToolParameter options by @davelopez in #19911

• Better interactive tool entry point query by @mvdbeek in #19942

• Drop unnecessary job cache job subquery by @mvdbeek in #19945

• Fix attempt restriction on multiple connections by @mvdbeek in #19948

• Fix various parameter validation issues. by @jmchilton in #19949

• Sort intersected options by @mvdbeek in #19953

• Do not print OIDC access tokens to the logs by @kysrpex in #19966

• Renew OIDC access tokens using valid refresh tokens by @kysrpex in #19967

• Add missing job state history entry for queued state by @mvdbeek in #19977

• Restrict job cache to terminal jobs (and other fixes) by @mvdbeek in #19978

• Fix dynamic filter option access when building command line by @mvdbeek in #19982

• Renew access tokens from PSA using valid refresh tokens by @kysrpex in #20040

• Job cache backports by @mvdbeek in #20078

• Skip param_value filter if ref value is runtime value by @mvdbeek in #20144

• Fix invocation failure dataset reference by @mvdbeek in #20200

• Fall back to name in job summary if no input label given by @mvdbeek in #20258

• Skip validation of expression.json input in workflow parameter validator by @mvdbeek in #20412

24.2.3 (2025-03-16)

Bug fixes

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

• Fix tool directory pulsar transfer by @mvdbeek in #19799

• Use materialized datasets in pulsar job runner by @mvdbeek in #19807

24.2.2 (2025-03-08)

Bug fixes

• Fix conditional dependency path resolution by @mvdbeek in #19723

• Allow tool state changes in refactor actions by @mvdbeek in #19730

• Update fs.dropboxfs conditional dependency version to 1.0.3 by @davelopez in #19741

• Follow-up to #19651: Do not reassign: method modifies object in-place by @jdavcs in #19746

Enhancements

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

• Skip slow tests for manage_db, db_dev scripts by @jdavcs in #19744

Other changes

• Make k8s user and group ids overriddable per job by @nuwang in #19568

24.2.1 (2025-02-28)

Bug fixes

• Remove unused and broken methods by @nsoranzo in #19614

• Raise RequestParameterInvalidException on invalid input_format parameter by @mvdbeek in #19631

• Raise serializable exception on invalid workflow connection by @mvdbeek in #19636

• Raise MessageException when using data provider on incompatible data by @mvdbeek in #19639

• Apply exec options to connection by @jdavcs in #19651

• Initialize dictionary used to set connection execution options by @jdavcs in #19653

• Fix various bugs around tool data table bundles by @mvdbeek in #19659

24.2.0 (2025-02-11)

Bug fixes

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

• Dynamics options add library dataset by @gagayuan in #18198

• Fix some deprecations by @nsoranzo in #18433

• Fixes for errors reported by mypy 1.11.0 by @nsoranzo in #18608

• Update mercurial by @mvdbeek in #18686

• Replace types-pkg-resources with types-setuptools by @nsoranzo in #18708

• Fix tag processing in library upload by @davelopez in #18714

• Update ruff to 0.6.1 by @nsoranzo in #18716

• Fix new flake8-bugbear B039 and mypy type-var errors by @nsoranzo in #18755

• Fixes and tests for data fetch models. by @jmchilton in #18834

• data_column params: offer same columns with and without use_header_names by @wm75 in #18879

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

• Fix the bioblend test failures by @arash77 in #18991

• Fix job directory not being cleaned up by @davelopez in #18997

• Fixes random job failures in kubernetes by @mapk-amazon in #19001

• Fix numerous issues with tool input format “21.01” by @jmchilton in #19030

• Fix test_stock.py unit test by @mvdbeek in #19037

• quota: do not complain on no-change of default by @bernt-matthias in #19045

• Normalize usernames to lowercase in OIDC authentication by @arash77 in #19131

• 2 small uv config fixes by @nsoranzo in #19146

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

• Fix import of previously-deleted TRS workflow by @mvdbeek in #19311

• Fix quota usage with user object stores by @davelopez in #19323

• Fix workflows with optional non-default parameter input by @mvdbeek in #19332

• Backport #19001 kubernetes api client fix by @mvdbeek in #19338

• Partial backport of #19331 by @nsoranzo in #19342

• Use select_from_url test data from github, not usegalaxy.org by @mvdbeek in #19352

• Fix to only show ChatGXY when available. by @dannon in #19389

• Fix job parameter summary for inputs without label by @mvdbeek in #19427

• Show Keycloak provider label in UI by @ahmedhamidawan in #19447

• Expression tool format source backport by @mvdbeek in #19466

• backport of defensive refresh tokens by @martenson in #19471

• Improve relabel from file error if file doesn’t contain enough lines by @mvdbeek in #19480

• Serialize message exceptions on execution error by @mvdbeek in #19483

• Fail with error message when submitting invalid request by @mvdbeek in #19489

• Fix deleting lddas in batch by @davelopez in #19506

• Skip token refresh without refresh token in psa by @mvdbeek in #19514

• Downgrade ‘InteractiveTools are not enabled’ to warning by @mvdbeek in #19518

• Fix extracting workflows from purged and deleted histories by @mvdbeek in #19525

• Fix error message when subworkflow input connection missing by @mvdbeek in #19526

• Fix remap for parameter called id by @mvdbeek in #19532

• Fix admin cancel job message not being displayed to the user by @davelopez in #19537

• Use instance wide default real_system_username if not defined on destination by @bernt-matthias in #19544

• Fix job paused on user defined object store by @davelopez in #19578

Enhancements

• Add clean up job working directory as celery task by @sanjaysrikakulam in #15816

• Experimental galactic wizard by @dannon in #15860

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

• Update Python dependencies by @galaxybot in #18226

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

• More data access tests, some refactoring and cleanup by @jdavcs in #18312

• Update Python dependencies by @galaxybot in #18406

• Add Python 3.13 support by @nsoranzo in #18449

• Add onedata templates by @bwalkowi in #18457

• Support high-availability setups for the interactive tools proxy by @kysrpex in #18481

• Add unique constraints to the email and username fields in the galaxy_user table by @jdavcs in #18493

• Update Python dependencies by @galaxybot in #18505

• Improvements for K8S deployment (especially ITs) by @almahmoud in #18514

• Add Tool-Centric APIs to the Tool Shed 2.0 by @jmchilton in #18524

• Improvements to Tool Test Parsing by @jmchilton in #18560

• Group tool templating exceptions in sentry by @mvdbeek in #18570

• Update Python dependencies by @galaxybot in #18578

• Record container id and type in core job metrics by @mvdbeek in #18579

• Rev pinned gxformat2. by @jmchilton in #18624

• Better Typing for Tool Execution Plumbing by @jmchilton in #18626

• Remove unused functions in dataset managers by @jmchilton in #18631

• Parameter Model Improvements by @jmchilton in #18641

• Parse stored config details to script-based visualizations by @guerler in #18651

• Another round of parameter model improvements. by @jmchilton in #18673

• Allow access to invocation via shared or published history by @mvdbeek in #18707

• Allow specifying multi-select workflow parameters by @mvdbeek in #18715

• Improvements to help terms & tool help. by @jmchilton in #18722

• Add a retry when deleting a k8s job by @afgane in #18744

• More typing, docs, and decomposition around tool execution by @jmchilton in #18758

• Add Workflow Title and Annotation sections by @hujambo-dunia in #18762

• Refactor LibraryDatasetsManager and fix type annotation issue by @nsoranzo in #18773

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

• Allow using tracks and groups in visualization xml by @guerler in #18779

• Workflow Landing Requests by @jmchilton in #18807

• Update Mypy to 1.11.2 and fix new signature override errors by @nsoranzo in #18811

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

• Update Python dependencies by @galaxybot in #18864

• Implement Pydantic model for workflow test format. by @jmchilton in #18884

• Remove some unused dynamic drill down options. by @jmchilton in #18892

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

• Update Python dependencies by @galaxybot in #18904

• Type annotations and fixes by @nsoranzo in #18911

• Add filter null collection operation tool by @mvdbeek in #18928

• Remove outdated fimo wrapper and galaxy-sequence-utils dependency by @nsoranzo in #18937

• Update Python dependencies by @galaxybot in #18943

• Allow to overwrite real_system_username per destination by @bernt-matthias in #18945

• Assert that data_column parameters have a valid data_ref by @bernt-matthias in #18949

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

• Workflow landing improvements by @mvdbeek in #18979

• Update Python dependencies by @galaxybot in #18982

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

• Enhance relabel_from_file to work with any column pair in mapping file by @wm75 in #19022

• A variety of improvements around tool parameter modeling (second try) by @jmchilton in #19027

• Better logging around tool loading by @jmchilton in #19029

• Update Python dependencies by @galaxybot in #19031

• Silence the quota manager for updates by @bernt-matthias in #19046

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

• Update Python dependencies by @galaxybot in #19062

• Annotate DatasetAssociationManager as generic type by @nsoranzo in #19063

• Move TRS import into WorkflowContentManager by @mvdbeek in #19070

• Replace poetry with uv by @nsoranzo in #19075

• Allow deferred datasets to behave as URIs by @davelopez in #19077

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

• Allow directory_uri workflow parameters. by @jmchilton in #19093

• Better cleanup of sharing roles on user purge by @jdavcs in #19096

• Support deferred datasets in visualizations by @davelopez in #19097

• uv: Do not recalculate dependencies when exporting by @nsoranzo in #19099

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

• Test hash validation also for upload by path by @nsoranzo in #19109

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

• Add type annotations to JobRunnerMapper and related code by @nsoranzo in #19115

• Update Python dependencies by @galaxybot in #19123

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

• Remove OpenLayers legacy files and add SVG logo by @guerler in #19135

• Update Python dependencies by @galaxybot in #19149

• Fix default value handling for parameters connected to required parameters by @mvdbeek in #19219

• Workflow Inputs Activity by @ElectronicBlueberry in #19252

Other changes

• Fix workflow invocation accessibility check by @mvdbeek in #18746

• Fix destentation typo by @mvdbeek in #19140

24.1.4 (2024-12-11)

Bug fixes

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

• 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

• by @laperlej in #18459

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

• 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

• Don’t call job_runner.stop_job on jobs in new state by @mvdbeek in #18495

• 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

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

• Fix username used in invocation report by @mvdbeek in #18932

• Disable locking when opening h5 files, add missing with by @mvdbeek in #18976

• Fix job search statement building by @mvdbeek in #19010

• Put cached jobs back into queue on handler restart by @mvdbeek in #19012

• Fix various invocation export issues by @mvdbeek in #19215

• Create harmonized collections from correct tool outputs by @wm75 in #19222

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

24.1.3 (2024-10-25)

Bug fixes

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

• 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

• by @laperlej in #18459

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

• 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

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

• Fix username used in invocation report by @mvdbeek in #18932

• Disable locking when opening h5 files, add missing with by @mvdbeek in #18976

• Fix job search statement building by @mvdbeek in #19010

• Put cached jobs back into queue on handler restart by @mvdbeek in #19012

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

24.1.2 (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.