galaxy-web-apps 26.0.1

Galaxy web apps

Overview

The Galaxy web apps (Galaxy, Reports, Tool Shed).

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

History

26.0.1 (2026-06-04)

Bug fixes

• Add debug middleware and regression tests for blocked main event loop by @mvdbeek in #22207

• Hide hidden tools in the tool form by @bgruening in #22215

• Fix data manager URL for managers with ‘+’ version suffix by @mvdbeek in #22525

• Handle list-valued tool_id in ToolRunner.__get_tool by @mvdbeek in #22545

• Fix admin resend-activation email missing hostname by @mvdbeek in #22568

• Fix error handling for Help Forum integration by @davelopez in #22604

• Fix data source tool redirect back to Galaxy SPA by @mvdbeek in #22720

• Backport FastAPI/Starlette upgrade for BadHost (CVE-2026-48710) by @mvdbeek in #22778

26.0.0 (2026-04-08)

Bug fixes

• Preserve assistant messages with tool calls by @guerler in #21545

• Fix incorrect router tag in plugins API by @dannon in #21669

• Fix redirect upon impersonation by @guerler in #21810

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

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

• Use inference_services config for plugin chat proxy by @dannon in #21986

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

• Fix invalid function schema error for tools with None parameters by @mvdbeek in #22030

• 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 AttributeError when dataset in inheritance chain has no user by @mvdbeek in #22062

• Fix make all histories private controller None id bug by @ahmedhamidawan in #22174

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

• Cache url path lookup by @mvdbeek in #22198

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

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

• Use /api/tool_data endpoints in DataTables.vue & DataManagerTable.vue by @mvdbeek in #22229

• Optimize dataset get_edit API by deferring expensive role queries by @mvdbeek in #22232

• Fix TypeError in ExternalIdentities by always including provider_label in authnz response by @guerler in #22234

• Delete dummy error controller, fix type error on invalid requests by @mvdbeek in #22245

• Make sure origins for data landings are persisted by @d-callan in #22248

• Replace BaseHTTPMiddleware with pure ASGI middleware for X-Frame-Options by @mvdbeek in #22255

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

• Improve timeout and error handling in /api/proxy endpoint by @mvdbeek in #22297

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

• Fix slow get_private_role_user_emails_dict query by @mvdbeek in #22307

• Pass tool_uuid as proper query parameter instead of reusing URL path id by @mvdbeek in #22309

• Strip content-length and accept-ranges headers from proxied streaming responses by @mvdbeek in #22314

• Fix tool “Copy Link” generating broken /root?tool_id= URLs by @mvdbeek in #22339

• Harden API parameter validation by @mvdbeek in #22351

• Show error message when display action not ready by @mvdbeek in #22383

• Fix invalid request error for get_metadata_file endpoint by @mvdbeek in #22389

• Offload AsyncClient construction to worker thread by @mvdbeek in #22392

Enhancements

• Refactor display application handling by @guerler in #15076

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

• Tool Request API by @jmchilton in #20935

• Remove Trackster by @guerler in #20974

• Update Python dependencies by @galaxybot in #21043

• Remove Reports Application by @guerler in #21076

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

• Replace tuswsgi with tuspyserver by @mvdbeek in #21201

• Consolidate Dataset State Display by @guerler in #21231

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

• Remove Tool Runner mako by @guerler in #21235

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

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

• Update error message handling for OIDC by @uwwint in #21297

• Implement GA4GH WES API by @jmchilton in #21335

• Add Beta Upload Activity - User Interface Redesign by @davelopez in #21338

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

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

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

• 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

• 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

• Drop support for Python 3.9 by @nsoranzo in #21583

• Sort data managers using case-insensitive order for display in admin UI by @jdavcs in #21587

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

• Apply 2026 black style by @galaxybot in #21618

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

• Backports: Return redirection instead of a JSON with the redirect URI by @davelopez in #21902

• Backport chat API improvements by @dannon in #21973

Other changes

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

25.1.2 (2026-03-09)

Bug fixes

• Make galaxy-web-apps package compatible with latest FastAPI by @nsoranzo in #21753

• Fix AttributeError when requesting invalid metadata file by @mvdbeek in #21985

25.1.1 (2026-02-03)

Bug fixes

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

• Fix loading of credentials when associated tools are missing by @arash77 in #21599

25.1.0 (2025-12-12)

Bug fixes

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

• Require user for visualizations create endpoint by @guerler in #20615

• Allow cors on data and tool landing pages by @mvdbeek in #21078

• Test and fix CORS on exceptions by @mvdbeek in #21105

• Mark user creation API endpoint as admin-only by @mvdbeek in #21149

• Fix proxy endpoint encoding by @davelopez in #21169

Enhancements

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

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

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

• Implement Sample Sheets by @jmchilton in #19305

• 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

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

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

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

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

• Add recent downloads page for STS requests by @davelopez in #20585

• Implement Data Landing Requests by @jmchilton in #20592

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

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

• Update Python dependencies by @galaxybot in #20680

• Add more info to inheritance chain by @arash77 in #20701

• Make workflow invocation tabs routable by @ahmedhamidawan in #20719

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

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

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

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

• Add small improvements for running CWL tools by @nsoranzo in #20826

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

• 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

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

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

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

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

Other changes

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

• Implement bare-bones view of sample sheet collections as sheet. by @jmchilton in #20798

• Merge 25.0 into dev by @ahmedhamidawan in #20911

25.0.4 (2025-11-18)

Bug fixes

• Fix test_multiple_decorators unit test for FastAPI 0.118.0 by @nsoranzo in #20982

• Fix proxy url validation for non-printable characters by @davelopez in #21280

Enhancements

• Harden proxy redirect validation by @davelopez in #21185

Other changes

• Backport Fix proxy endpoint encoding by @davelopez in #21184

25.0.3 (2025-09-23)

Bug fixes

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

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

25.0.2 (2025-08-13)

Bug fixes

• Fix planemo serve, need user list by @mvdbeek in #20575

• Ignore webob http exceptions for logging purposes by @mvdbeek in #20630

Other changes

• Require user for visualizations create endpoint by @mvdbeek in #20629

25.0.1 (2025-06-20)

Bug fixes

• Do not expose user info to non authenticated users by @bernt-matthias in #20524

Other changes

• Fixes for static handling and the web_client package by @natefoo in #20516

25.0.0 (2025-06-18)

Bug fixes

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

• Display email activation help only if user activation is enabled by @jdavcs in #19402

• Fix wording of API doc string by @bernt-matthias in #19776

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

• Add hid to selection field in visualization creation form by @guerler in #20108

• Sort visualization datasets by hid by @guerler in #20123

• Move UnprivilegedToolResponse into api by @mvdbeek in #20207

• Increase proxy API robustness by validating URL before use by @davelopez in #20311

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

• Fix toolshed-installed tool icons by @dannon in #20399

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

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

Enhancements

• Workflow Editor Activity Bar by @ElectronicBlueberry in #18729

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

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

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

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

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

• Misc fixes 202412 by @nsoranzo in #19341

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

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

• Remove transaction helper by @jdavcs in #19407

• 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

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

• Remove tags used by @ElectronicBlueberry in #19576

• Enhance OpenAI Chat Integration by @uwwint in #19612

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

• Type annotation improvements by @nsoranzo in #19642

• More Vue Typescript Fixes by @jmchilton in #19663

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

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

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

• Update Python dependencies by @galaxybot in #19727

• Rename tool “Citations” to “References” by @nsoranzo in #19770

• Add history sharing and accessibility management view by @ahmedhamidawan in #19786

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

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

• Drop old galaxy_session records by @jdavcs in #19872

• Replace backend-based page creation controller endpoint by @guerler in #19914

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

• Allow resizing Visualizations in Markdown editor by @guerler in #19958

• 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

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

• Add rerun option for workflows by @ahmedhamidawan in #20032

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

• Add ZIP explorer to import individual files from local or remote ZIP archives by @davelopez in #20054

• Drop now unused controller method by @mvdbeek in #20129

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

• Add client package by @natefoo in #20171

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

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

• Enable visualizations for anonymous user by @guerler in #20210

• Touch up Dataset View by @guerler in #20290

• Enable retrieving contents from extra file paths when request contains leading / by @mvdbeek in #20336

• DatasetView and Card Polish by @dannon in #20342

• Add /api/datasets/{dataset_id}/extra_files/raw/{filename:path} by @mvdbeek in #20468

Other changes

• Log controller exceptions by @natefoo in #19974

• Fix formatting in webapp and client/install.py by @dannon in #20185

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

24.2.4 (2025-06-17)

Bug fixes

• Try to recover from recurring activation link error by @jdavcs in #19844

• Fix bug in psa-authnz redirect handling by @dannon in #19968

• ChatGXY Error Handling by @dannon in #19987

• Job cache backports by @mvdbeek in #20078

• Fix searching roles in admin UI by @jdavcs in #20394

• Fix legacy get_metadata_file controller route by @mvdbeek in #20477

• Prevent running datatype autodetect on purged datasets by @mvdbeek in #20479

Other changes

• Remove unused client route for standalone wizard interface by @dannon in #19836

24.2.3 (2025-03-16)

Bug fixes

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

24.2.2 (2025-03-08)

No recorded changes since last release

24.2.1 (2025-02-28)

Bug fixes

• Fix user preferences secret (without vault) lost on save by @davelopez in #19610

• Disable chatgxy wizard for anon users by @mvdbeek in #19628

24.2.0 (2025-02-11)

Bug fixes

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

• Fix some deprecations by @nsoranzo in #18433

• Fix MessageException handling in get_edit by @mvdbeek in #18529

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

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

• Fix response if dataset requested by display application is deleted by @mvdbeek in #18803

• Ignore preflight options in API schema by @jmchilton in #18983

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

• Fix auto-detect metadata from Edit Dataset Attributes panel by @davelopez in #19025

• Prevent purged users from logging in by @jdavcs in #19094

• Restore access to saved visualizations by @guerler in #19136

• Fix PSA Redirect by @dannon in #19247

• Login redirect followup by @dannon in #19251

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

• Fix importing shared workflows with deeply nested subworkflows by @mvdbeek in #19335

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

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

• Use visualizations api in trackster by @mvdbeek in #19495

• Set a hard limit of 100 invocations per request in api/invocations by @mvdbeek in #19497

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

• Fix WSGI response status handling in controller methods by @mvdbeek in #19520

• Fix saved visualization (non-trackster ones) not displaying by @davelopez in #19561

• Allow unused query params in workflows/export_to_file by @mvdbeek in #19574

Enhancements

• Experimental galactic wizard by @dannon in #15860

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

• Add errors fast api by @arash77 in #18093

• 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

• Replace History Dataset Picker in Library Folder by @itisAliRH in #18518

• Update openapi-typescript dependency to version 6.7.6 by @davelopez in #18519

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

• Drop unused datasets controller methods by @mvdbeek in #18568

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

• More tool test typing. by @jmchilton in #18590

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

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

• Parameter Model Improvements by @jmchilton in #18641

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

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

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

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

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

• 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

• Update Visualization FastAPI by @arash77 in #18792

• Workflow Landing Requests by @jmchilton in #18807

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

• Enable extra user preferences for remotely authorized users by @maartenschermer in #18887

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

• Type annotations and fixes by @nsoranzo in #18911

• Allow CORS requests to /api/workflow_landings by @mvdbeek in #18963

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

• Optimize to_history_dataset_association in create_datasets_from_library_folder by @arash77 in #18970

• Workflow landing improvements by @mvdbeek in #18979

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

• 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

• Run installed Galaxy with no config and a simplified entry point by @natefoo in #19050

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

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

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

• Backport of Workflow Editor Activity Bar by @dannon in #19212

• Workflow Inputs Activity by @ElectronicBlueberry in #19252

Other changes

• Format dev to fix linting. by @jmchilton in #18860

24.1.4 (2024-12-11)

Bug fixes

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

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

• Check if dataset has any data before running provider checks by @mvdbeek in #18526

• Raise appropriate exception if ldda not found by @mvdbeek in #18569

• Close install model session when request ends by @mvdbeek in #18629

• Fix resume_paused_jobs if no session provided by @mvdbeek in #18640

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

• Return error when following a link to a non-ready display application by @mvdbeek in #18672

• Only load authnz routes when oidc enabled by @mvdbeek in #18683

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

• Fix sorting users in admin by last login by @jdavcs in #18694

• Fix resume paused jobs response handling by @dannon in #18733

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

• Tighten TRS url check by @mvdbeek in #18841

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

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

• Limit max number of items in dataproviders by @mvdbeek in #18881

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

• Don’t use async def where not appropriate by @mvdbeek in #18944

• Fix very slow workflow editor loading by @mvdbeek in #19068

Enhancements

• Make default_panel_view a _by_host option by @natefoo in #18471

Other changes

• Fix check dataset check by @mvdbeek in #18856

24.1.3 (2024-10-25)

Bug fixes

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

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

• Check if dataset has any data before running provider checks by @mvdbeek in #18526

• Raise appropriate exception if ldda not found by @mvdbeek in #18569

• Close install model session when request ends by @mvdbeek in #18629

• Fix resume_paused_jobs if no session provided by @mvdbeek in #18640

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

• Return error when following a link to a non-ready display application by @mvdbeek in #18672

• Only load authnz routes when oidc enabled by @mvdbeek in #18683

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

• Fix sorting users in admin by last login by @jdavcs in #18694

• Fix resume paused jobs response handling by @dannon in #18733

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

• Tighten TRS url check by @mvdbeek in #18841

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

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

• Limit max number of items in dataproviders by @mvdbeek in #18881

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

• Don’t use async def where not appropriate by @mvdbeek in #18944

Enhancements

• Make default_panel_view a _by_host option by @natefoo in #18471

Other changes

• Fix check dataset check by @mvdbeek in #18856

24.1.2 (2024-09-25)

Bug fixes

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

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

• Check if dataset has any data before running provider checks by @mvdbeek in #18526

• Raise appropriate exception if ldda not found by @mvdbeek in #18569

• Close install model session when request ends by @mvdbeek in #18629

• Fix resume_paused_jobs if no session provided by @mvdbeek in #18640

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

• Return error when following a link to a non-ready display application by @mvdbeek in #18672

• Only load authnz routes when oidc enabled by @mvdbeek in #18683

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

• Fix sorting users in admin by last login by @jdavcs in #18694

• Fix resume paused jobs response handling by @dannon in #18733

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

• Tighten TRS url check by @mvdbeek in #18841

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

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

Enhancements

• Make default_panel_view a _by_host option by @natefoo in #18471

Other changes

• Fix check dataset check by @mvdbeek in #18856

24.1.1 (2024-07-02)

Bug fixes

• Fix permissions for temporary upload file for API uploads by @bernt-matthias in #17850

• Dynamic tool fixes by @dcore94 in #18085

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

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

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

Enhancements

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

• Implement a page object accessibility dialog by @jmchilton in #17225

• Enable storage management by object store by @jmchilton in #17500

• 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

• SQLAlchemy 2.0 by @jdavcs in #17778

• Add email notifications channel by @davelopez in #17914

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

• Drop unused workflow controller methods by @mvdbeek in #17974

• Enable warn_unused_ignores mypy option by @nsoranzo in #17991

• Add galaxy to user agent by @mvdbeek in #18003

• Consolidate Visualization container, avoid using default iframe by @guerler in #18016

• 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

• Change InvocationsList into a grid using GridList by @ahmedhamidawan in #18088

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

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

• Drop restriction to switch to immutable histories by @davelopez in #18234

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

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

Other changes

• Fix typing issue in reused variable by @davelopez in #18344

24.0.3 (2024-06-28)

Bug fixes

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

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

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

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

• Fix make all histories private with immutable histories by @davelopez in #18200

• Fix pca 3d rendering of tabular files and visualization error handling in general by @mvdbeek in #18211

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

• Restrict job_files access to jobs that are not terminal by @mvdbeek in #18217

• Raise appropriate exception if accessing deleted input file by @mvdbeek in #18223

• Fix element serialization for collections that aren’t populated yet by @mvdbeek in #18235

• Skip new history creation if user is anonymous and login is required by @mvdbeek in #18319

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

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

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

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

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

• Drop unnecessary escaping for workflow name and annotation by @mvdbeek in #18376

Other changes

• Decrease log level for expected visualization errors by @mvdbeek in #18229

24.0.2 (2024-05-07)

Bug fixes

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

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

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

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

Enhancements

• Add middleware for logging start and end of request by @mvdbeek in #18046

24.0.0 (2024-04-02)

Bug fixes

• tus wants a json response from v2.0.0 by @mira-miracoli in #17246

• Fix quotas ID encoding by @davelopez in #17335

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

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

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

• Associate default history with session when creating a new session by @mvdbeek in #17557

• Fix tool shed webapp by @mvdbeek in #17597

• Don’t call get_or_create_default_history() twice for invalidated sessions by @nsoranzo in #17613

• Fix tool panel workflow and favorites button bugs by @ahmedhamidawan in #17634

• Fix DataResult type by @mvdbeek in #17639

• Prevent 500 for anon /api/invocations by @mvdbeek in #17640

• Don’t fail for anon /api/users request by @mvdbeek in #17645

• Limit new anon histories by @mvdbeek in #17657

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

• Handle missing indexer for a dataset by @ahmedhamidawan in #17736

• Don’t require history to calculate anon disk usage by @mvdbeek in #17765

• Fix anon user values again by @mvdbeek in #17772

• Fix new default history creation when in remote or single user mode by @dannon in #17796

• Return published histories first in display_by_username_and_slug by @mvdbeek in #17808

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

Enhancements

• New Workflow List and Card View by @itisAliRH in #16607

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

• 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

• Vueify Admin User Grid by @guerler in #17030

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

• 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

• 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

• Migrate dataset extra files store to Pinia by @davelopez in #17145

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

• Remove legacy tool versions list from admin panel by @guerler in #17155

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

• Drop fastapi-utils.InferringRouter in favor of fastapi.APIRouter by @jdavcs in #17184

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

• Vueifiy History Grids by @guerler in #17219

• Update Python dependencies by @galaxybot in #17235

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

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

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

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

• Fix any type for tool_data_file_path by @mvdbeek in #17293

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

• Update Python dependencies by @galaxybot in #17333

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

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

• Replaces Trackster Grids with Data Dialog, Removes Phyloviz, Circster and Sweepster by @guerler in #17415

• Removes outdated Grid controller and backbone modules by @guerler in #17434

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

• Modernize bits and pieces of storage display by @jmchilton in #17436

• UI for “relocating” a dataset to a new object store (when safe) by @jmchilton in #17437

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

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

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

• Removes legacy history xml makos by @guerler in #17505

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

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

• Filter out subworkflow invocations by @mvdbeek in #17558

• Links to individual invocations. by @jmchilton in #17566

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

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

23.2.1 (2024-02-21)

Bug fixes

• Rename to_dict to populate in FormDefintion to fix bug by @jdavcs in #16553

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

• chore: fix typos by @afuetterer in #16851

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

• Ruff and flake8 fixes by @nsoranzo in #16884

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

• Fix Display Application link generation by @mvdbeek in #17227

• Display application fixes and tests by @mvdbeek in #17233

• Respect upstream_gzip setting when streaming dataset collection archive by @mvdbeek in #17400

• Fix history bulk operations menu conditions by @davelopez in #17433

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

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

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

Enhancements

• Tool Shed 2.0 by @jmchilton in #15639

• 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

• Notifications admin panel by @itisAliRH in #16278

• Migrate cloud API to Fast API by @heisner-tillman in #16296

• Drop (admin only) userskeys controller by @dannon in #16318

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

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

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

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

• Update Python dependencies by @galaxybot in #16436

• Published Workflow Sharing Page Overhaul by @ElectronicBlueberry in #16510

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

• Update Python dependencies by @galaxybot in #16577

• Workflow Comments 💬 by @ElectronicBlueberry in #16612

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

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

• Enhance task monitor composable by @davelopez in #16695

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

• Migrate collection elements store to Pinia by @davelopez in #16725

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

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

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

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

• 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

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

• Vueify Visualizations Grid by @guerler in #16892

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

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

• Update API tool_panels route conditions by @dannon in #16991

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

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

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

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

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

Other changes

• Merge 23.1 into dev by @mvdbeek in #16534

• Fix succces typo by @mvdbeek in #17481

23.1.4 (2024-01-04)

Bug fixes

• Properly clear session on OIDC logout by @guerler in #17120

23.1.3 (2023-12-01)

Bug fixes

• Add missing optional description field, fixes ephemeris data library example by @mvdbeek in #17116

23.1.2 (2023-11-29)

Bug fixes

• Provide error message instead of internal server error by @mvdbeek in #16905

• Fix input dates in notifications: consider timezone offset by @davelopez in #17088

Enhancements

• Add HEAD route to job_files endpoint by @mvdbeek in #17072

23.1.1 (2023-10-23)

Bug fixes

• Create ToolSuccess route and refactor component by @ahmedhamidawan in #15484

• fix premature return in user API by @martenson in #15781

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

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

• Fix form builder value handling by @guerler in #16304

• Fix tags ownership by @davelopez in #16339

• Fix histories count by @davelopez in #16400

• Make datatype edit default value a string instead of list of strings by @mvdbeek in #16591

• Backport tool mem fixes by @mvdbeek in #16601

• Optimize getting current user session by @mvdbeek in #16604

• Drop RecursiveMiddleware by @mvdbeek in #16605

• List extra files only for terminal datasets by @mvdbeek in #16705

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

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

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

Enhancements

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

• Add Storage Dashboard visualizations for histories by @davelopez in #14820

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

• Various Tool Shed Cleanup by @jmchilton in #15247

• Add Storage Management API by @davelopez in #15295

• OIDC tokens by @SergeyYakubov in #15300

• 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

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

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

• Update Python dependencies by @galaxybot in #15564

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

• Add Galaxy Notification System by @davelopez in #15663

• Mention OpenAPI docs in Galaxy API Documentation by @bernt-matthias in #15713

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

• Update Python dependencies by @galaxybot in #15890

• Add History Archival feature by @davelopez in #16003

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

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

• Paginate History Store by @ahmedhamidawan in #16084

• Allow HEAD request for requesting metadata files by @martenson in #16113

• Add option to see invocations related to a history by @martenson in #16136

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

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

• adjust grid sharing indicators by @martenson in #16163

• Remove various fallback behaviors by @mvdbeek in #16199

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

• Small test decorator improvements. by @jmchilton in #16220

• Don’t error on missing parameters or unused parameters in UI controllers by @mvdbeek in #16246

• Update Python dependencies by @galaxybot in #16267

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

• Add missing archived filter in saved histories by @davelopez in #16475

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

Other changes

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

• Tweaks to new object store and quota APIs by @jmchilton in #15709

• Fix Enums in API docs by @davelopez in #15740

• Quota source labelling bug fixes and improvements by @jmchilton in #15795

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

• merge release_23.0 into dev by @martenson in #15854

• Merge 23.0 into dev by @nsoranzo in #15902

• Fix recalculate_quota throug kombu message by @mvdbeek in #16299

23.0.6 (2023-10-23)

Bug fixes

• Fix incorrect ASGI request host by @davelopez in #16574

• Allow the legacy DELETE dataset endpoint to accept any string for the history_id by @assuntad23 in #16593

23.0.5 (2023-07-29)

Bug fixes

• Fix active step display in workflow editor side panel by @mvdbeek in #16364

23.0.4 (2023-06-30)

Bug fixes

• Fix folder access for anonymous user by @mvdbeek in #16330

23.0.3 (2023-06-26)

Bug fixes

• Fix converting Enum value to str for Python 3.11 by @nsoranzo in #16284

Enhancements

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

23.0.2 (2023-06-13)

No recorded changes since last release

23.0.1 (2023-06-08)

Bug fixes

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

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

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

• Ignore invalid query params in display_by_username_and_slug by @mvdbeek in #16117

20.5.0 (2020-07-04)

• First release from the 20.05 branch of Galaxy.