galaxy-web-apps 24.1.1

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

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

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

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

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

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

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

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

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

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

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

Merge 23.1 into dev by @mvdbeek in #16534

Fix succces typo by @mvdbeek in #17481

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

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

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

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

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

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

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

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