galaxy-test-api 26.1.1

Avoid missing field value failure in data tables by @guerler in #21008

Fix dbkey filter returning no options when dbkey unset by @jmchilton in #21916

Fix workflow implicit mapping of flat collections over paired_or_unpaired by @jmchilton in #21933

Fix test that transiently fails if GitHub rejects a request by @jmchilton in #22005

Skip X-Frame-Options header for published embed views by @dannon in #22107

Fix tag duplication when copying datasets/collections between histories by @dannon in #22109

Fix transient failure in test_workflow_with_deleted_dataset_step_parameter by @jmchilton in #22138

Fix more paired_or_unpaired collection issues by @jmchilton in #22170

Honor group-derived roles in unprivileged tool access check by @mvdbeek in #22623

Update test workflows to respect gxformat2 0.26.0 syntax by @nsoranzo in #22642

Fix workflow extraction not including user-defined tool steps by @ahmedhamidawan in #22694

Harden access control for user-defined tools by @mvdbeek in #22704

Fix WES workflow completion and add missing WES docs by @jmchilton in #22857

Create notebooks from invocation reports instead of a new page/report by @ahmedhamidawan in #22872

Fix input mangling when conditional parameter name ends in `_N` by @mvdbeek in #22891

Always attempt to build tool request for new API endpoint by @mvdbeek in #22894

Make unowned but accessible pages uneditable by @ahmedhamidawan in #22911

Keep collection-operation outputs as workflow steps in extraction by @jmchilton in #22912

Accept dce collection references in the tool request model by @mvdbeek in #22926

Include hidden intermediates in workflow extraction summary (#22967) by @jmchilton in #22970

Resolve user-defined tools in by-ids workflow extraction by @mvdbeek in #22992

Fix Workflow.copy() dropping readme, help, logo_url and doi by @mvdbeek in #23117

Fix `set_history` committing None `galaxy_session` by @ahmedhamidawan in #23156

Fix fasta preview rendering for sequences larger than 100 KB by @mvdbeek in #23163

Fix webhooks broken by the Backbone/underscore removal by @itisAliRH in #23173

Show persistent best practice results in workflow editor by @mvdbeek in #19546

Skip test_abort_fetch_job if httpstat.us is down by @jmchilton in #21718

Add Selenium tests for workflow extraction UI by @jmchilton in #21805

Various YAML Tool Hardening and Progress toward Tool State Goals by @jmchilton in #21828

Migrate tool execution request from api/tools to api/jobs by @guerler in #21842

Support URL and TRS references for subworkflows in workflow import by @mvdbeek in #21887

Add the History Graph API by @guerler in #21932

Convert workflow extraction interface to Vue by @ahmedhamidawan in #21935

Update Python dependencies by @galaxybot in #21951

Migrate Python packages to `src` layout and pure namespace packages by @mr-c in #21977

Model subcollection mapping (map_over_type) and DCE in tool parameter schema by @jmchilton in #21991

Update Python dependencies by @galaxybot in #22003

Enrich tool parameter JSON Schema with Galaxy metadata via model methods by @mvdbeek in #22020

Replace mocked agent tests with static YAML backend for deterministic API/E2E testing by @jmchilton in #22070

Add API tests proving __current_case__ is redundant at execution time by @jmchilton in #22134

Extend the favorite tool panel concept by @bgruening in #22212

Add `pick_value` Workflow Module by @jmchilton in #22222

Simplify gxformat2 contract - drop ImporterGalaxyInterface, convert_and_import_workflow by @jmchilton in #22241

Search and paginate user and roles api by @mvdbeek in #22311

Galaxy Notebooks: Persistent Narrative for Human-AI Collaborative Science in Galaxy by @jmchilton in #22361

Clean up various pytest warnings by @mvdbeek in #22472

Narrow YAML schema by @jmchilton in #22507

Use now() wrapper instead of datetime.now() by @bgruening in #22579

Improve type annotation of workflow management methods by @nsoranzo in #22637

Paginate /api/tools/{tool_id}/build history options by @mvdbeek in #22643

Enhance workflow extraction by IDs with deduplication and UI improvements by @jmchilton in #22706

More structured HistoryGraph API references by @jmchilton in #22732

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

Fix IndexError in SplitPairedAndUnpairedTool for unpaired elements by @ernestprovo23 in #22282

Fix `get_structure` when it is passed a DCE with nested elements by @mvdbeek in #22453

Treat paused inputs as not-ready in DatabaseOperationTool by @mvdbeek in #22529

Fix crash merging structurally invalid nested collections by @mvdbeek in #22546

Raise ToolInputsNotReady for unpopulated structured_like target by @mvdbeek in #22552

Raises error if decoding fails during relabeling from file by @guerler in #22595

Fix job access check for collection-only outputs by @mvdbeek in #22603

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

Fix HDA leak in tool form for data managers (#22674) by @mvdbeek in #22724

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

Replace per-term joins in workflow search with EXISTS subqueries by @mvdbeek in #22548

Attempt to fix transient API test failure for jobs search. by @jmchilton in #20898

Drop down revision for drop_job_params migration by @mvdbeek in #21122

Plumbing for tracking potential fixes for transient failures (and a fix demonstrating it) by @jmchilton in #21243

Attempt to fix transient failure in list_list_copy by @jmchilton in #21381

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

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

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

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

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

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

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

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

Use base64 URL instead of GitHub URL in test_stage_fetch_decompress_true by @mvdbeek in #22069

Fixes for gxformat2 by @jmchilton in #22179

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

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

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

Fix purge for anon histories by @mvdbeek in #22275

Fix validation of certain classes of text validators in tools. by @jmchilton in #22280

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

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

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

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

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

Validate workflow invocation parameters values are dicts by @mvdbeek in #22388

Fix dataset preview rendering to preserve newlines by @mvdbeek in #22397

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

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

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

Refactor display application handling by @guerler in #15076

Tool Request API by @jmchilton in #20935

Selenium test exercising workflow debug, failed jobs, etc… (20912) by @jmchilton in #21058

Richer tracking of transient failures. by @jmchilton in #21227

Remove Tool Runner mako by @guerler in #21235

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

Implement GA4GH WES API by @jmchilton in #21335

More use of base64 to improve test stability. by @jmchilton in #21383

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

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

Implement subworkflow invocation export by @mvdbeek in #21512

Add workflow API test for use_cached_job with sample sheet collections by @mvdbeek in #21522

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

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

Clean up code with pyupgrade by @nsoranzo in #21540

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

Drop support for Python 3.9 by @nsoranzo in #21583

Apply 2026 black style by @galaxybot in #21618

Type annotations and refactorings by @nsoranzo in #21673

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

Fix tool request API for multiple select parameters with defaults. by @jmchilton in #21416

Reduce completion monitor logging by @mvdbeek in #21674

Fix test_value_restriction_with_select_from_multiple_subworkflow_inputs formatting by @mvdbeek in #21723

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

Sample sheet column fix by @mvdbeek in #21446

Record input parameter invocation inputs by @mvdbeek in #21452

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

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

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

Fix job cache collection copy by @mvdbeek in #21558

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

Fix collection job state not preserved during history export/import by @mvdbeek in #21716

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

Fix a transiently failing API test. by @jmchilton in #20278

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

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

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

Fix type annotation in test_run_workflow_use_cached_job_implicit_conv… by @mvdbeek in #21138

Fix proxy endpoint encoding by @davelopez in #21169

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

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

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

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

Implement Sample Sheets by @jmchilton in #19305

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

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

Test case for using URL-based workflow inputs with implicit conversions. by @jmchilton in #20509

Implement Data Landing Requests by @jmchilton in #20592

Clean up code from pyupgrade by @nsoranzo in #20642

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

Attempt to reuse previously materialized datasets by @mvdbeek in #20718

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

Modernize tools in the filters/ dir by @natefoo in #20840

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

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

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

Allow sending and tracking landing request origin by @mvdbeek in #20957

Track landing request with invocation by @mvdbeek in #20960

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

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

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

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

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

Fix TOOL_WITH_SHELL_COMMAND import source by @mvdbeek in #21070

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

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

Fix workflow run form input restrictions by @mvdbeek in #21095

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

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

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

Harden proxy redirect validation by @davelopez in #21185

Backport Fix proxy endpoint encoding by @davelopez in #21184

Alternative format_source fix by @mvdbeek in #19395

Fix wrong id in test_combined_mapping_and_subcollection_mapping by @mvdbeek in #19481

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

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

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

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

Add test for workflow instance download fix by @ahmedhamidawan in #20326

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

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

Fix copying of job metrics for cached jobs by @mvdbeek in #20436

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

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

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

Add User-Defined Tools by @mvdbeek in #19434

Add test that verifies workflow source_metadata is preserved on landing claim by @mvdbeek in #19454

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

Update test_create_dataset_in_subfolder to check for the dataset presence by @davelopez in #19660

Relax job status check in test_delete_user_cancel_all_jobs by @davelopez in #19661

Drop support for Python 3.8 by @nsoranzo in #19685

Improved simplicity and isolation in transiently failing test. by @jmchilton in #19709

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

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

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

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

Add DOI to workflow metadata by @jdavcs in #20033

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

Add specific datatypes for Cytoscape and Kepler.gl by @guerler in #20117

Yaml parser fixes and improvements (part 1) by @mvdbeek in #20158

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

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

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

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

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

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

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

Record implicitly converted dataset as input dataset by @mvdbeek in #19301

Expression tool format source backport by @mvdbeek in #19466

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

Fix deleting lddas in batch by @davelopez in #19506

Fix test_storage_show API test by @nsoranzo in #19522

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

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

Improve usability of Directory datatype by @wm75 in #17614

Implement Declarative Testing for Workflow Behaviors by @jmchilton in #18542

More tool test typing. by @jmchilton in #18590

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

Parameter Model Improvements by @jmchilton in #18641

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

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

Migrate Visualizations API to FastAPI by @arash77 in #18721

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

Workflow Landing Requests by @jmchilton in #18807

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

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

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

More concise, readable tool execution testing. by @jmchilton in #18977

Workflow landing improvements by @mvdbeek in #18979

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

Do not skip CI tests on missing tools. by @jmchilton in #19002

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

Add job metrics per invocation by @mvdbeek in #19048

Move TRS import into WorkflowContentManager by @mvdbeek in #19070

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

Implement workflow parameter validators. by @jmchilton in #19092

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

Always validate hashes when provided by @nsoranzo in #19110

Enable specifying dataset hash in test jobs by @mvdbeek in #19113

Enhance UTF-8 support for filename handling in downloads by @arash77 in #19161

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

Fix workflow invocation accessibility check by @mvdbeek in #18746

Revert some requests import changes by @nsoranzo in #18199

Fix subwofklow tags serialization type by @arash77 in #18456

Remove deprecated BCO export endpoint by @martenson in #16645

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

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

Enable warn_unused_ignores mypy option by @nsoranzo in #17991

Add galaxy to user agent by @mvdbeek in #18003

Refactor galaxy.files plugin loading + config handling. by @jmchilton in #18049

Update Python dependencies by @galaxybot in #18063

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

Fix test_index_advanced_filter API test re-running by @nsoranzo in #17547

Limit new anon histories by @mvdbeek in #17657

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

Fix histories API index_query serialization by @davelopez in #17726

Fix source history update_time being updated when importing a public history by @jmchilton in #17728

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

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

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

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

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

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

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

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

Vueifiy History Grids by @guerler in #17219

Reuse test instance during non-integration tests by @mvdbeek in #17234

Migrate models to pydantic 2 by @mvdbeek in #17262

Add __KEEP_SUCCESS_DATASETS__ by @lldelisle in #17294

Enable warn_unreachable mypy option by @mvdbeek in #17365

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

Cancel all active jobs when the user is deleted by @davelopez in #17390

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

Purge groups and roles from DB (for real) by @davelopez in #17411

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

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

Filter out subworkflow invocations by @mvdbeek in #17558

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

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

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

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

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

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

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

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

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

Vueify Visualizations Grid by @guerler in #16892

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

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

Migrate ItemTags API to FastAPI by @arash77 in #17064

Merge 23.1 into dev by @mvdbeek in #16534

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

Fix duplicated tools in tool panel view section copying by @jmchilton in #17036

Improve invocation error reporting by @mvdbeek in #16917

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

qualify querying for an api-key by @martenson in #16320

Fix tags ownership by @davelopez in #16339

Job cache fixes for DCEs by @mvdbeek in #16384

Fix histories count by @davelopez in #16400

Fix replacement parameters for subworkflows. by @jmchilton in #16592

Fixes for conditional subworkflow steps by @mvdbeek in #16632

Fix nested conditional workflow steps by @mvdbeek in #16641

Fix expression evaluation for nested state by @mvdbeek in #16656

Push to object store even if set_meta fails by @mvdbeek in #16667

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

Fix allowlist deserialization in file sources by @mvdbeek in #16729

Fix workflow import losing tool_version by @mvdbeek in #16869

Fix tag ownership check by @mvdbeek in #16877

Fix delete collection + elements by @davelopez in #16879

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

Outline Deployment Tests by @jmchilton in #15420

Unify url handling with filesources by @nuwang in #15497

Update Python dependencies by @galaxybot in #15564

Add API test and refactor code for related:hid history filter by @ahmedhamidawan in #15786

Allow pending inputs in some collection operation tools by @mvdbeek in #15892

Record input datasets and collections at full parameter path by @mvdbeek in #15978

Add History Archival feature by @davelopez in #16003

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

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

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

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

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

Fix folder listing via file browser by @mvdbeek in #15950

Fix case sensitive filtering by name in histories by @davelopez in #16036

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

Extract HDA for code_file validate_input hook by @mvdbeek in #16120

Add support for launching workflows via Tutorial Mode by @hexylena in #15684

Allow setting auto_decompress property in staging interface by @mvdbeek in #16014