History ------- .. to_doc --------- 26.1.dev0 --------- ------------------- 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.