Galaxy application (backend)
Project description
Overview
The Galaxy application logic (backend).
History
25.1.1 (2026-02-03)
Bug fixes
Record input parameter invocation inputs by @mvdbeek in #21452
Maintain column definitions on map over by @mvdbeek in #21468
Do not update a user’s update_time when an admin archives (and purges) a history by @natefoo in #21484
Fix subworkflow runs for disconnected required inputs with defaults by @mvdbeek in #21488
Usability fixes for sample sheet selection. by @jmchilton in #21503
Fix type annotation for invocation report errors field by @mvdbeek in #21508
Filter out failed_metadata HDAs from job cache by @mvdbeek in #21544
Fix pulsar with rewrite_parameters: false by @mvdbeek in #21557
Fix Pulsar with default_file_action: none by @mvdbeek in #21578
Fix condor typo by @gsaudade99 in #21651
Fix HTCondor runner unwatching jobs when stopping containers by @kysrpex in #21656
Fix option propagation for workflow inputs connected to multiple subworkflows by @mvdbeek in #21712
Add missing filter_failed_collection_1.1.0.xml tool by @mvdbeek in #21719
Strip inline comments in conditional requirements by @mvdbeek in #21720
Enhancements
25.1.0 (2025-12-12)
Bug fixes
Workaround to numeric sorting in the local portion of tool versions if they are galaxy “build” numbers by @natefoo in #13570
Bump requests from 2.32.3 to 2.32.4 in /lib/galaxy/dependencies by @dependabot[bot] in #20422
Remove decoded ids from job/dataset error report email by @ahmedhamidawan in #20714
Fix multiple=”true” data collection map over for shell_command tools by @mvdbeek in #20859
Fix default conditional test parameters… by @jmchilton in #20942
Set minimum profile version for expression tools by @mvdbeek in #21151
Add Convert characters1 to workflow safe updates by @mvdbeek in #21160
Add missing more-itertools dependency by @nsoranzo in #21214
Fix downloading subworkflows without stored workflow by @mvdbeek in #21223
Fix optional subworkflow input scheduling bug by @mvdbeek in #21435
Maintain columns on sample sheet map over by @mvdbeek in #21436
Enhancements
Support credentials(secrets/variables) in tool requirements by @arash77 in #19084
Allow several Galaxy Markdown directives to be embedded. by @jmchilton in #19086
Add tags to output datasets from tool form by @PlushZ in #19225
Implement Sample Sheets by @jmchilton in #19305
Consider collections in on_strings for parameters accepting multiple datasets by @bernt-matthias in #19817
Update Python dependencies by @galaxybot in #20139
Split Login and Register, enable OIDC Registration. by @uwwint in #20287
Empower Users to More Pragmatically Import Datasets & Collections From Tables by @jmchilton in #20288
Switch Default Visualization Endpoint to script, migrate to YAML by @guerler in #20303
Add short term storage expiration indicator to history items by @davelopez in #20332
Update Python dependencies by @galaxybot in #20347
Install Visualization plugins as self-contained packages by @guerler in #20348
Prepare ToolBox.dynamic_tool_to_tool() for CWL formats by @nsoranzo in #20364
Install visualizations directly to static path, avoid duplication by @guerler in #20372
Update Python dependencies by @galaxybot in #20383
Type annotation fixes for mypy 1.16.0 by @nsoranzo in #20424
Implement dataset source requested transformations. by @jmchilton in #20435
Add username_key setting to configure python-social-auth OIDC by @marius-mather in #20497
Remove deprecated tool document cache by @nsoranzo in #20510
Fixes for invocation import. by @jmchilton in #20528
Update Python dependencies by @galaxybot in #20537
Decode OIDC access token as part of authentication pipeline by @marius-mather in #20547
Update Python dependencies by @galaxybot in #20577
Display the Galaxy Citation within the Export Tool References List by @mschatz in #20584
Implement Data Landing Requests by @jmchilton in #20592
Update Python dependencies by @galaxybot in #20601
Add a “Debug” (email report) tab to Workflow Invocations by @ahmedhamidawan in #20624
Update Python dependencies by @galaxybot in #20653
Update Python dependencies by @galaxybot in #20680
Update Python dependencies by @galaxybot in #20699
Improve cli and slurmcli runner traceability for job status and failure reasons by @selten in #20717
Refactor Files Sources Framework for stronger typing using pydantic models by @davelopez in #20728
Hierarchical display collection dataset states by @mvdbeek in #20731
Update Python dependencies by @galaxybot in #20732
Update Python dependencies by @galaxybot in #20753
Consolidate visualization mako, avoid user agent styles by @guerler in #20760
Add configfiles support and various enhancements for user defined tools by @mvdbeek in #20761
Drop old load_workflow controller method, use API by @mvdbeek in #20774
Update Python dependencies by @galaxybot in #20779
Add Hugging Face 🤗 file source and user-defined template by @davelopez in #20805
Update Python dependencies by @galaxybot in #20812
Update Python dependencies by @galaxybot in #20841
Allow adding extra steps to the default pipeline of the OIDC authentication by @marius-mather in #20845
Use a streaming based parser (ijson) when setting metadata for biom1 files. by @ksuderman in #20851
Various Container Execution Enhancements (including GCP Batch support) by @jmchilton in #20862
Replace tour_generator webhook with internal API and frontend by @ahmedhamidawan in #20868
Update Python dependencies by @galaxybot in #20869
Improve type annotation for job runners and InteractiveToolManager by @nsoranzo in #20871
Update Python dependencies by @galaxybot in #20905
Allow creation of visualizations without dataset by @guerler in #20914
Add support for picking from_work_dir directory by @mvdbeek in #20916
Add tool to add nesting level to collection by @bernt-matthias in #20926
Update Python dependencies by @galaxybot in #20930
Allow addressing user defined tools in job config by @mvdbeek in #20932
Wire up and test resource requirement via tpv by @mvdbeek in #20936
Limit admin requirement of selected tool data api endpoints by @guerler in #20949
Add resource docs and tweak tool source schema title generation by @mvdbeek in #20951
Allow sending and tracking landing request origin by @mvdbeek in #20957
Move tours schema to schema directory (to fix package structure) by @ahmedhamidawan in #20965
Update Python dependencies by @galaxybot in #20968
Log task execution errors with log.exception by @mvdbeek in #20970
Update Python dependencies by @galaxybot in #21005
Bump up total-perspective-vortex dependency by @mvdbeek in #21014
Tighter API for tool run tagging. by @jmchilton in #21210
Optimize /api/invocations/steps/{step_id} by @mvdbeek in #21249
Optionally include column headers in sample sheet file by @mvdbeek in #21439
Other changes
Merge release_25.0 into dev by @davelopez in #20484
Bump pillow from 11.2.1 to 11.3.0 in /lib/galaxy/dependencies by @dependabot[bot] in #20591
Sample Sheet Bug Fixes around Preserving Collection Metadata by @jmchilton in #20749
Validate sample sheet column definitions in workflow definitions on backend. by @jmchilton in #20880
Drop fastapi extra dep from sentry-sdk by @mvdbeek in #21156
Resolve possible symlink before establishing tool file location by @mvdbeek in #21175
25.0.4 (2025-11-18)
Bug fixes
Check for expiration in refresh token dictionary by @jdavcs in #20954
Deactivate user file source on unknown error by @mvdbeek in #20962
Don’t create workflow outputs to recover input parameter outputs by @mvdbeek in #20980
Fix PUT /api/workflows for user defined tools by @mvdbeek in #20987
Require OK datasets for filtering empty datasets by @bernt-matthias in #21023
Fix InvalidRequestError when saving workflow step with dynamic tool by @mvdbeek in #21056
Run landing request state through validator by @mvdbeek in #21087
Create new datasets when creating skipped database operation tool outputs by @mvdbeek in #21142
Fix refresh token expiration retrieval logic by @nuwang in #21213
Enhancements
25.0.3 (2025-09-23)
Bug fixes
Ensure that workflow invocations are persisted with state by @mvdbeek in #20784
Fix password reset functionality for lowercase emails by @jdavcs in #20801
Drop eager argument from invocation related methods by @mvdbeek in #20863
Make check for existing user in custos_authnz.py case insensitive by @cat-bro in #20893
Avoid potential race condition in replacement_for_connection by @mvdbeek in #20909
25.0.2 (2025-08-13)
Bug fixes
Fix restricting user defined tool input datasets extensions by @mvdbeek in #20545
Don’t assume cwd = job directory when running prepare dirs by @natefoo in #20571
Prevent importing workflows with invalid step UUID by @davelopez in #20596
Constraint conditional redis version to allow only minor updates by @davelopez in #20603
Fix optional unspecified input to conditional step by @mvdbeek in #20647
Avoid postgres truncation of aliases and labels by @mvdbeek in #20649
Fix deferred datasets in multiple dataset parameters. by @jmchilton in #20650
Fix dataset serializers and response models by @arash77 in #20694
Fix maximum workflow invocation duration test by @mvdbeek in #20729
Enhancements
Add redis conditional dependency by @davelopez in #20502
25.0.1 (2025-06-20)
Bug fixes
Enhancements
Other changes
25.0.0 (2025-06-18)
Bug fixes
Bump tornado from 6.4.1 to 6.4.2 in /lib/galaxy/dependencies by @dependabot[bot] in #19189
Don’t calculate dataset hash for datasets in non-OK state by @nsoranzo in #19191
Bump python-multipart from 0.0.17 to 0.0.18 in /lib/galaxy/dependencies by @dependabot[bot] in #19233
Use resource_path() to access datatypes_conf.xml.sample as a package resource by @nsoranzo in #19331
Require importlib-resources also for Python 3.9-3.11 by @nsoranzo in #19358
Bump jinja2 from 3.1.4 to 3.1.5 in /lib/galaxy/dependencies by @dependabot[bot] in #19369
Better handling of public pages and workflows authored by deleted users by @jdavcs in #19394
Avoid using custos refresh tokens which are expired by @martenson in #19411
Use fissix also when python3-lib2to3 is not installed by @nsoranzo in #19749
Fix setting env and tags on resubmission by @bernt-matthias in #19753
Fix Galaxy ignoring job object_store_id for quota check by @bernt-matthias in #19854
Fix broken optimisation introduced in #19852 by @nsoranzo in #19871
Fix various mypy issues around mapped attributes by @mvdbeek in #19883
More fixes to FormData drag and drop and typing by @ahmedhamidawan in #19900
Fix ownership check in history contents update route by @mvdbeek in #19969
Allow deferred and ok state datasets for vis by @guerler in #20143
Fix certain cases of collection parameter handling during workflow execution. by @jmchilton in #20152
Fix NFDI auth by @bgruening in #20217
Rerun workflows for the correct version/instance by @ahmedhamidawan in #20313
Fix workflow bookmark filtering by @davelopez in #20325
Generate a tenant-unique UID for tapis. by @dannon in #20370
Fix job rerun with tool version change by @mvdbeek in #20417
Upgrade tensorflow conditional dependency version to 2.15.1 by @cat-bro in #20434
Dataset Display and Preferred Viz fixes by @dannon in #20439
Enhancements
Dynamic options: add data table filter by @bernt-matthias in #12941
Run the tool working dir backup/restore on Pulsar by @natefoo in #16696
Implement tool markdown reports. by @jmchilton in #19054
Let file sources choose a path for uploaded files by @kysrpex in #19154
Calculate hash for new non-deferred datasets when finishing a job by @nsoranzo in #19181
Update Python dependencies by @galaxybot in #19190
Refactor for better reuse of workflow parameter type constants by @nsoranzo in #19260
Migrate WF Collection Input Form Definition to Client Side by @jmchilton in #19313
Hide outdated visualizations from visualizations activity panel by @guerler in #19353
Update Python dependencies by @galaxybot in #19366
Add Dataverse RDM repository integration by @KaiOnGitHub in #19367
Type annotation fixes for mypy 1.14.0 by @nsoranzo in #19372
Empower Users to Build More Kinds of Collections, More Intelligently by @jmchilton in #19377
Set safe default extraction filter for tar archives by @nsoranzo in #19406
Prevent users from reusing a banned email after account is purged by @jdavcs in #19413
Update Python dependencies by @galaxybot in #19418
Improve asynchronous tasks error handling and reporting by @davelopez in #19448
Update Python dependencies by @galaxybot in #19464
Update Python dependencies by @galaxybot in #19510
Add config options for tool dependency installs by @afgane in #19565
Update Python dependencies by @galaxybot in #19567
Remove tags used by @ElectronicBlueberry in #19576
Expand workflow metadata for readme. by @jmchilton in #19591
Add failed jobs working directory cleanup as a celery periodic task by @sanjaysrikakulam in #19594
Use correct plugin_kind in user file sources by @davelopez in #19622
Update Python dependencies by @galaxybot in #19623
Refactor dependencies for tool output actions. by @jmchilton in #19662
Add webdavclient3 to conditional-requirements.txt by @bgruening in #19671
Update Python dependencies by @galaxybot in #19682
Define simple models for job messages. by @jmchilton in #19688
Move RequiredAppT back into galaxy packages. by @jmchilton in #19704
Use model classes from galaxy.model instead of app.model object - Part 1 by @nsoranzo in #19706
Preserve workflow labels in final invocation reports by @guerler in #19721
ToolShed 2.1 - Various bugfixes and enhancements. by @jmchilton in #19722
Use model classes from galaxy.model instead of app.model object - Part 2 by @nsoranzo in #19726
Update Python dependencies by @galaxybot in #19727
Show workflow help (and readme?) in run form by @ahmedhamidawan in #19736
Improvements to package decomposition. by @jmchilton in #19759
Update Python dependencies by @galaxybot in #19772
Add visualization framework interface to cell-based markdown editor by @guerler in #19775
Update Python dependencies by @galaxybot in #19816
Populate image metadata without allocating memory for the entire image content by @kostrykin in #19830
Syntactic sugar to ease TPV configuration. by @jmchilton in #19834
Improve markdown editor modularity and structure by @guerler in #19835
Add mandatory RO-Crate metadata when exporting by @elichad in #19846
Add basic support for icons in tools by @davelopez in #19850
Improve type annotations of ModelPersistenceContext and derived classes by @nsoranzo in #19852
Update Python dependencies by @galaxybot in #19874
Migrate Page editing controller endpoint to API by @guerler in #19923
Update Python dependencies by @galaxybot in #19929
Add type hints around collection copying and job things by @mvdbeek in #19961
Job cache allow different names when possible by @mvdbeek in #19962
Update Python dependencies by @galaxybot in #19964
Allow different AI providers (as long as they are openai compatible) by @uwwint in #19989
Improve type annotation of tool parameter wrapping by @nsoranzo in #19991
Update Python dependencies by @galaxybot in #19998
Implement dataset collection support in workflow landing requests by @mvdbeek in #20004
Enable warn_redundant_casts mypy option and drop redundant casts by @nsoranzo in #20008
Add support for Markdown help text in visualizations by @guerler in #20043
Add sample datasets for visualizations by @guerler in #20046
Use visualization dropdown solely for examples by @guerler in #20094
Update Python dependencies by @galaxybot in #20096
Adds Example Datasets and Help Text for Visualizations by @guerler in #20097
Additional type hints for toolbox.get_tool / toolbox.has_tool by @mvdbeek in #20150
Create working dir output outside of tool evaluator by @mvdbeek in #20153
Add three AAI providers by @martenson in #20165
Add replacement_dataset option to collection filter tools by @simonbray in #20166
Implement file source to integrate Galaxy with RSpace by @kysrpex in #20167
Visualization-First Display functionality by @dannon in #20190
Improve type annotation of galaxy.model.dataset_collections by @nsoranzo in #20194
Improve performance of job cache query by @mvdbeek in #20319
Other changes
24.2.4 (2025-06-17)
Bug fixes
Reduce default framework tool test timeout to 60 seconds by @mvdbeek in #19819
Fix various job concurrency limit issues by @mvdbeek in #19824
Handle directories with percents directories with export_remote.xml. by @jmchilton in #19865
Fix tabular metadata setting on pulsar with remote metadata by @mvdbeek in #19891
Fix duplicate extensions for data inputs by @ahmedhamidawan in #19903
Skip implicit HDA conversions in DataToolParameter options by @davelopez in #19911
Better interactive tool entry point query by @mvdbeek in #19942
Drop unnecessary job cache job subquery by @mvdbeek in #19945
Fix attempt restriction on multiple connections by @mvdbeek in #19948
Fix various parameter validation issues. by @jmchilton in #19949
Do not print OIDC access tokens to the logs by @kysrpex in #19966
Renew OIDC access tokens using valid refresh tokens by @kysrpex in #19967
Add missing job state history entry for queued state by @mvdbeek in #19977
Restrict job cache to terminal jobs (and other fixes) by @mvdbeek in #19978
Fix dynamic filter option access when building command line by @mvdbeek in #19982
Renew access tokens from PSA using valid refresh tokens by @kysrpex in #20040
Skip param_value filter if ref value is runtime value by @mvdbeek in #20144
Fix invocation failure dataset reference by @mvdbeek in #20200
Fall back to name in job summary if no input label given by @mvdbeek in #20258
Skip validation of expression.json input in workflow parameter validator by @mvdbeek in #20412
24.2.3 (2025-03-16)
Bug fixes
24.2.2 (2025-03-08)
Bug fixes
Fix conditional dependency path resolution by @mvdbeek in #19723
Allow tool state changes in refactor actions by @mvdbeek in #19730
Update fs.dropboxfs conditional dependency version to 1.0.3 by @davelopez in #19741
Follow-up to #19651: Do not reassign: method modifies object in-place by @jdavcs in #19746
Enhancements
Other changes
24.2.1 (2025-02-28)
Bug fixes
Raise RequestParameterInvalidException on invalid input_format parameter by @mvdbeek in #19631
Raise serializable exception on invalid workflow connection by @mvdbeek in #19636
Raise MessageException when using data provider on incompatible data by @mvdbeek in #19639
Initialize dictionary used to set connection execution options by @jdavcs in #19653
Fix various bugs around tool data table bundles by @mvdbeek in #19659
24.2.0 (2025-02-11)
Bug fixes
Drop “Send to cloud” tool and associated cloudauthz code by @jdavcs in #18196
Fixes for errors reported by mypy 1.11.0 by @nsoranzo in #18608
Replace types-pkg-resources with types-setuptools by @nsoranzo in #18708
Fix tag processing in library upload by @davelopez in #18714
Fix new flake8-bugbear B039 and mypy type-var errors by @nsoranzo in #18755
Fixes and tests for data fetch models. by @jmchilton in #18834
data_column params: offer same columns with and without use_header_names by @wm75 in #18879
Fix issue with generating slug for sharing by @arash77 in #18986
Fix job directory not being cleaned up by @davelopez in #18997
Fixes random job failures in kubernetes by @mapk-amazon in #19001
Fix numerous issues with tool input format “21.01” by @jmchilton in #19030
quota: do not complain on no-change of default by @bernt-matthias in #19045
Normalize usernames to lowercase in OIDC authentication by @arash77 in #19131
Fix invocation metrics usability by providing job context. by @jmchilton in #19279
Fix import of previously-deleted TRS workflow by @mvdbeek in #19311
Fix quota usage with user object stores by @davelopez in #19323
Fix workflows with optional non-default parameter input by @mvdbeek in #19332
Backport #19001 kubernetes api client fix by @mvdbeek in #19338
Use select_from_url test data from github, not usegalaxy.org by @mvdbeek in #19352
Fix to only show ChatGXY when available. by @dannon in #19389
Fix job parameter summary for inputs without label by @mvdbeek in #19427
Show Keycloak provider label in UI by @ahmedhamidawan in #19447
Expression tool format source backport by @mvdbeek in #19466
backport of defensive refresh tokens by @martenson in #19471
Improve relabel from file error if file doesn’t contain enough lines by @mvdbeek in #19480
Serialize message exceptions on execution error by @mvdbeek in #19483
Fail with error message when submitting invalid request by @mvdbeek in #19489
Fix deleting lddas in batch by @davelopez in #19506
Skip token refresh without refresh token in psa by @mvdbeek in #19514
Downgrade ‘InteractiveTools are not enabled’ to warning by @mvdbeek in #19518
Fix extracting workflows from purged and deleted histories by @mvdbeek in #19525
Fix error message when subworkflow input connection missing by @mvdbeek in #19526
Fix admin cancel job message not being displayed to the user by @davelopez in #19537
Use instance wide default real_system_username if not defined on destination by @bernt-matthias in #19544
Fix job paused on user defined object store by @davelopez in #19578
Enhancements
Add clean up job working directory as celery task by @sanjaysrikakulam in #15816
Feature - stdout live reporting by @gecage952 in #16975
Update Python dependencies by @galaxybot in #18226
Allow OAuth 2.0 user defined file sources (w/Dropbox integration) by @jmchilton in #18272
More data access tests, some refactoring and cleanup by @jdavcs in #18312
Update Python dependencies by @galaxybot in #18406
Support high-availability setups for the interactive tools proxy by @kysrpex in #18481
Add unique constraints to the email and username fields in the galaxy_user table by @jdavcs in #18493
Update Python dependencies by @galaxybot in #18505
Improvements for K8S deployment (especially ITs) by @almahmoud in #18514
Add Tool-Centric APIs to the Tool Shed 2.0 by @jmchilton in #18524
Improvements to Tool Test Parsing by @jmchilton in #18560
Group tool templating exceptions in sentry by @mvdbeek in #18570
Update Python dependencies by @galaxybot in #18578
Record container id and type in core job metrics by @mvdbeek in #18579
Rev pinned gxformat2. by @jmchilton in #18624
Better Typing for Tool Execution Plumbing by @jmchilton in #18626
Remove unused functions in dataset managers by @jmchilton in #18631
Parameter Model Improvements by @jmchilton in #18641
Parse stored config details to script-based visualizations by @guerler in #18651
Another round of parameter model improvements. by @jmchilton in #18673
Allow access to invocation via shared or published history by @mvdbeek in #18707
Allow specifying multi-select workflow parameters by @mvdbeek in #18715
Improvements to help terms & tool help. by @jmchilton in #18722
More typing, docs, and decomposition around tool execution by @jmchilton in #18758
Add Workflow Title and Annotation sections by @hujambo-dunia in #18762
Refactor LibraryDatasetsManager and fix type annotation issue by @nsoranzo in #18773
Backend handling of setting user-role, user-group, and group-role associations by @jdavcs in #18777
Allow using tracks and groups in visualization xml by @guerler in #18779
Workflow Landing Requests by @jmchilton in #18807
Update Mypy to 1.11.2 and fix new signature override errors by @nsoranzo in #18811
Migrate Library Contents API to FastAPI by @arash77 in #18838
Update Python dependencies by @galaxybot in #18864
Implement Pydantic model for workflow test format. by @jmchilton in #18884
Remove some unused dynamic drill down options. by @jmchilton in #18892
Enable ignore-without-code mypy error code by @nsoranzo in #18898
Update Python dependencies by @galaxybot in #18904
Add filter null collection operation tool by @mvdbeek in #18928
Remove outdated fimo wrapper and galaxy-sequence-utils dependency by @nsoranzo in #18937
Update Python dependencies by @galaxybot in #18943
Allow to overwrite real_system_username per destination by @bernt-matthias in #18945
Assert that data_column parameters have a valid data_ref by @bernt-matthias in #18949
Update Python dependencies by @galaxybot in #18982
Allow recovering a normalized version of workflow request state from API by @jmchilton in #18985
Enhance relabel_from_file to work with any column pair in mapping file by @wm75 in #19022
A variety of improvements around tool parameter modeling (second try) by @jmchilton in #19027
Better logging around tool loading by @jmchilton in #19029
Update Python dependencies by @galaxybot in #19031
Silence the quota manager for updates by @bernt-matthias in #19046
Update Python dependencies by @galaxybot in #19062
Annotate DatasetAssociationManager as generic type by @nsoranzo in #19063
Move TRS import into WorkflowContentManager by @mvdbeek in #19070
Allow deferred datasets to behave as URIs by @davelopez in #19077
Implement workflow parameter validators. by @jmchilton in #19092
Allow directory_uri workflow parameters. by @jmchilton in #19093
Better cleanup of sharing roles on user purge by @jdavcs in #19096
Support deferred datasets in visualizations by @davelopez in #19097
uv: Do not recalculate dependencies when exporting by @nsoranzo in #19099
Access public history in job cache / job search by @mvdbeek in #19108
Test hash validation also for upload by path by @nsoranzo in #19109
Add type annotations to JobRunnerMapper and related code by @nsoranzo in #19115
Update Python dependencies by @galaxybot in #19123
Allow a posix file source to prefer linking. by @jmchilton in #19132
Remove OpenLayers legacy files and add SVG logo by @guerler in #19135
Update Python dependencies by @galaxybot in #19149
Fix default value handling for parameters connected to required parameters by @mvdbeek in #19219
Workflow Inputs Activity by @ElectronicBlueberry in #19252
Other changes
24.1.4 (2024-12-11)
Bug fixes
Replace busybox:ubuntu-14.04 image with busybox:1.36.1-glibc by @mvdbeek in #18428
Fix dropped when_expression on step upgrade by @mvdbeek in #18446
Improve workflow-related exception reporting by @mvdbeek in #18447
Fix subwofklow tags serialization type by @arash77 in #18456
Add input extra files to get_input_fnames by @mvdbeek in #18462
Return generic message for password reset email by @ahmedhamidawan in #18479
Increase API robustness to invalid requests, improve compressed data serving by @mvdbeek in #18494
Don’t call job_runner.stop_job on jobs in new state by @mvdbeek in #18495
Prevent job submission if input collection element is deleted by @mvdbeek in #18517
Fix map over calculation for runtime inputs by @mvdbeek in #18535
Fix for not-null in ‘column_list’ object by @hujambo-dunia in #18553
Also fail ensure_dataset_on_disk if dataset is in new state by @mvdbeek in #18559
Fix sqlalchemy statement in tooltagmanager reset output by @dannon in #18591
Improve relabel identifiers message when number of columns is not 2 by @mvdbeek in #18634
Fix extract workflow from history when implicit collection has no jobs by @mvdbeek in #18661
Make sure we set file size also for purged outputs by @mvdbeek in #18681
File source and object store instance api fixes by @mvdbeek in #18685
Fix change datatype PJA on expression tool data outputs by @mvdbeek in #18691
Fill in missing help for cross product tools. by @jmchilton in #18698
Fix subworkflow scheduling for delayed subworkflow steps connected to data inputs by @mvdbeek in #18731
Catch and display exceptions when importing malformatted yaml workflows by @mvdbeek in #18734
Fix infinitely delayed workflow scheduling if skipped step creates HDCA by @mvdbeek in #18751
Fix job summary for optional unset job data inputs by @mvdbeek in #18754
Allow to change only the description of a quota by @bernt-matthias in #18775
Fix wrong extension on pick data output by @mvdbeek in #18798
Fix unspecified oidc_endpoint variable overwriting specified redirect_url by @bgruening in #18818
Fix wrong celery_app config on job and workflow handlers by @mvdbeek in #18819
Fix Workflow index bookmark filter by @itisAliRH in #18842
Skip metric collection if job working directory doesn’t exist by @mvdbeek in #18845
Extend on disk checks to running, queued and error states by @mvdbeek in #18846
Raise MessageException instead of assertions on rerun problems by @mvdbeek in #18858
Fix data_column ref to nested collection by @mvdbeek in #18875
Fix loading very old workflows with data inputs by @mvdbeek in #18876
Access tool data table filters in workflow building mode by @mvdbeek in #18900
Fix username used in invocation report by @mvdbeek in #18932
Disable locking when opening h5 files, add missing with by @mvdbeek in #18976
Put cached jobs back into queue on handler restart by @mvdbeek in #19012
Create harmonized collections from correct tool outputs by @wm75 in #19222
Enhancements
Include workflow invocation id in exception logs by @mvdbeek in #18594
Implemented the generic OIDC backend from python-social-auth into Gal… by @Edmontosaurus in #18670
Collect job metrics also when job failed by @mvdbeek in #18809
prevent “missing refresh_token” errors by supporting <extra_scopes> also with Keycloak backend by @ljocha in #18826
24.1.3 (2024-10-25)
Bug fixes
Replace busybox:ubuntu-14.04 image with busybox:1.36.1-glibc by @mvdbeek in #18428
Fix dropped when_expression on step upgrade by @mvdbeek in #18446
Improve workflow-related exception reporting by @mvdbeek in #18447
Fix subwofklow tags serialization type by @arash77 in #18456
Add input extra files to get_input_fnames by @mvdbeek in #18462
Return generic message for password reset email by @ahmedhamidawan in #18479
Increase API robustness to invalid requests, improve compressed data serving by @mvdbeek in #18494
Prevent job submission if input collection element is deleted by @mvdbeek in #18517
Fix map over calculation for runtime inputs by @mvdbeek in #18535
Fix for not-null in ‘column_list’ object by @hujambo-dunia in #18553
Also fail ensure_dataset_on_disk if dataset is in new state by @mvdbeek in #18559
Fix sqlalchemy statement in tooltagmanager reset output by @dannon in #18591
Improve relabel identifiers message when number of columns is not 2 by @mvdbeek in #18634
Fix extract workflow from history when implicit collection has no jobs by @mvdbeek in #18661
Make sure we set file size also for purged outputs by @mvdbeek in #18681
File source and object store instance api fixes by @mvdbeek in #18685
Fix change datatype PJA on expression tool data outputs by @mvdbeek in #18691
Fill in missing help for cross product tools. by @jmchilton in #18698
Fix subworkflow scheduling for delayed subworkflow steps connected to data inputs by @mvdbeek in #18731
Catch and display exceptions when importing malformatted yaml workflows by @mvdbeek in #18734
Fix infinitely delayed workflow scheduling if skipped step creates HDCA by @mvdbeek in #18751
Fix job summary for optional unset job data inputs by @mvdbeek in #18754
Allow to change only the description of a quota by @bernt-matthias in #18775
Fix wrong extension on pick data output by @mvdbeek in #18798
Fix unspecified oidc_endpoint variable overwriting specified redirect_url by @bgruening in #18818
Fix wrong celery_app config on job and workflow handlers by @mvdbeek in #18819
Fix Workflow index bookmark filter by @itisAliRH in #18842
Skip metric collection if job working directory doesn’t exist by @mvdbeek in #18845
Extend on disk checks to running, queued and error states by @mvdbeek in #18846
Raise MessageException instead of assertions on rerun problems by @mvdbeek in #18858
Fix data_column ref to nested collection by @mvdbeek in #18875
Fix loading very old workflows with data inputs by @mvdbeek in #18876
Access tool data table filters in workflow building mode by @mvdbeek in #18900
Fix username used in invocation report by @mvdbeek in #18932
Disable locking when opening h5 files, add missing with by @mvdbeek in #18976
Put cached jobs back into queue on handler restart by @mvdbeek in #19012
Enhancements
Include workflow invocation id in exception logs by @mvdbeek in #18594
Implemented the generic OIDC backend from python-social-auth into Gal… by @Edmontosaurus in #18670
Collect job metrics also when job failed by @mvdbeek in #18809
prevent “missing refresh_token” errors by supporting <extra_scopes> also with Keycloak backend by @ljocha in #18826
24.1.2 (2024-09-25)
Bug fixes
Return generic message for password reset email by @ahmedhamidawan in #18479
Increase API robustness to invalid requests, improve compressed data serving by @mvdbeek in #18494
Prevent job submission if input collection element is deleted by @mvdbeek in #18517
Fix map over calculation for runtime inputs by @mvdbeek in #18535
Fix for not-null in ‘column_list’ object by @hujambo-dunia in #18553
Also fail ensure_dataset_on_disk if dataset is in new state by @mvdbeek in #18559
Fix sqlalchemy statement in tooltagmanager reset output by @dannon in #18591
Improve relabel identifiers message when number of columns is not 2 by @mvdbeek in #18634
Fix extract workflow from history when implicit collection has no jobs by @mvdbeek in #18661
Make sure we set file size also for purged outputs by @mvdbeek in #18681
File source and object store instance api fixes by @mvdbeek in #18685
Fix change datatype PJA on expression tool data outputs by @mvdbeek in #18691
Fill in missing help for cross product tools. by @jmchilton in #18698
Fix subworkflow scheduling for delayed subworkflow steps connected to data inputs by @mvdbeek in #18731
Catch and display exceptions when importing malformatted yaml workflows by @mvdbeek in #18734
Fix infinitely delayed workflow scheduling if skipped step creates HDCA by @mvdbeek in #18751
Fix job summary for optional unset job data inputs by @mvdbeek in #18754
Allow to change only the description of a quota by @bernt-matthias in #18775
Fix wrong extension on pick data output by @mvdbeek in #18798
Fix unspecified oidc_endpoint variable overwriting specified redirect_url by @bgruening in #18818
Fix wrong celery_app config on job and workflow handlers by @mvdbeek in #18819
Fix Workflow index bookmark filter by @itisAliRH in #18842
Skip metric collection if job working directory doesn’t exist by @mvdbeek in #18845
Extend on disk checks to running, queued and error states by @mvdbeek in #18846
Raise MessageException instead of assertions on rerun problems by @mvdbeek in #18858
Fix data_column ref to nested collection by @mvdbeek in #18875
Fix loading very old workflows with data inputs by @mvdbeek in #18876
Enhancements
Include workflow invocation id in exception logs by @mvdbeek in #18594
Implemented the generic OIDC backend from python-social-auth into Gal… by @Edmontosaurus in #18670
Collect job metrics also when job failed by @mvdbeek in #18809
prevent “missing refresh_token” errors by supporting <extra_scopes> also with Keycloak backend by @ljocha in #18826
24.1.1 (2024-07-02)
Bug fixes
Fix for unexpected OIDC XML validation error by @Edmontosaurus in #18106
Small bug fixes for user data plugins by @jmchilton in #18246
Fix handler: access to result row items changed in SA2.0 by @jdavcs in #18274
Adapt Tool prediction API to Transformer-based deep learning architecture by @anuprulez in #18305
Fix empty usernames in database + bug in username generation by @jdavcs in #18379
Fix dropped when_expression on step upgrade by @mvdbeek in #18446
Improve workflow-related exception reporting by @mvdbeek in #18447
Fix subwofklow tags serialization type by @arash77 in #18456
Disable password reset for deleted users [GCC2024_COFEST] by @laperlej in #18459
Add input extra files to get_input_fnames by @mvdbeek in #18462
Enhancements
Only include tool stdout/stderr in HDA info by @natefoo in #16730
Adding object store plugin for Rucio by @SergeyYakubov in #17156
Enable all-vs-all collection analysis patterns. by @jmchilton in #17366
Type annotation and CWL-related improvements by @nsoranzo in #17630
Update Python dependencies by @galaxybot in #17653
Code cleanups from ruff and pyupgrade by @nsoranzo in #17654
Update Python dependencies by @galaxybot in #17764
Update Python dependencies by @galaxybot in #17819
Update Python dependencies by @galaxybot in #17870
Add email notifications channel by @davelopez in #17914
Update Python dependencies by @galaxybot in #17923
Error reporting unit tests by @jmchilton in #17968
Make urgent notifications mandatory by @davelopez in #17975
Update Python dependencies by @galaxybot in #17982
Enable warn_unused_ignores mypy option by @nsoranzo in #17991
Add Zenodo integration by @davelopez in #18022
Update Python dependencies by @galaxybot in #18035
Add stronger type annotations in file sources + refactoring by @davelopez in #18050
Add pagination support to Files Source plugins by @davelopez in #18059
Update Python dependencies by @galaxybot in #18063
Enable flake8-implicit-str-concat ruff rules by @nsoranzo in #18067
Ensure history update_time is set when exporting by @davelopez in #18086
Overhaul Azure storage infrastructure. by @jmchilton in #18087
Update Python dependencies by @galaxybot in #18095
Update Python dependencies by @galaxybot in #18125
Revises handling of warnings in the workflow run form by @guerler in #18126
Empower users to bring their own storage and file sources by @jmchilton in #18127
Update s3fs dependency. by @jmchilton in #18135
More unit testing for object store stuff. by @jmchilton in #18136
Harden User Object Store and File Source Creation by @jmchilton in #18172
More structured indexing for user data objects. by @jmchilton in #18291
Onedada object store and files source stability fixes by @bwalkowi in #18372
Allow running and editing workflows for specific versions by @ahmedhamidawan in #18378
Other changes
Chore: remove repetitive words by @tianzedavid in #18076
Fix #18316 (anonymous file sources) by @jmchilton in #18352
24.0.3 (2024-06-28)
Bug fixes
Raise exception if collection elements missing during download by @jdavcs in #18094
Allow purge query param, deprecate purge body param by @mvdbeek in #18105
Don’t log exception if cancelled slurm job doesn’t have stderr file by @mvdbeek in #18121
Downgrade missing output file in working directory to warning for failed jobs by @mvdbeek in #18123
Fix data default values not getting added to history by @mvdbeek in #18132
Emit warning when user-cancelled job already complete by @mvdbeek in #18178
Avoid object store path lookup when constructing JobState object by @mvdbeek in #18190
Add string cast for dbkey / genome_build by @mvdbeek in #18207
Check dataset state when attempting to acces dataset contents by @mvdbeek in #18214
Don’t set dataset peek for errored jobs by @mvdbeek in #18231
Raise exception when extracting dataset from collection without datasets by @mvdbeek in #18249
Skip tests if toolshed, dx.doi not responding by @mvdbeek in #18250
Don’t attempt to download purged datasets by @mvdbeek in #18278
Check various preconditions in FeatureLocationIndexDataProvider by @davelopez in #18283
Don’t serialize display application links for deleted datasets by @mvdbeek in #18307
Fix authentication error for anonymous users querying jobs by @davelopez in #18333
Do not copy purged outputs to object store by @mvdbeek in #18342
Kill pulsar job if job stopped on galaxy side by @mvdbeek in #18348
Fix anonymous user job retrieval logic by @davelopez in #18358
Fix update group API payload model by @davelopez in #18374
Fix user’s private role can be missing by @davelopez in #18381
Fix null inputs in database operation tools by @mvdbeek in #18385
Assign default data extension on discovered collection output by @mvdbeek in #18389
Fix get_accessible_job if called without session by @mvdbeek in #18400
Fix invocation step_job_summary for new collections by @mvdbeek in #18402
Really allow in-range validator for txt by @bernt-matthias in #18411
Fix collection map over status for dragged collections by @mvdbeek in #18416
Serialize purged flag for datasets in collections by @davelopez in #18420
Other changes
24.0.2 (2024-05-07)
Bug fixes
24.0.1 (2024-05-02)
Bug fixes
Fix workflow run form failing on certain histories by @mvdbeek in #17869
Always serialize element_count and populated when listing contents by @mvdbeek in #17890
Fix saving workflows with freehand_comments only by @mvdbeek in #17901
Always discard session after __handle_waiting_jobs is done by @mvdbeek in #17913
Fix workflow run form for workflows with null rename PJA by @mvdbeek in #17929
Fix missing implicit conversion for mapped over jobs by @mvdbeek in #17952
Fix get_content_as_text for compressed text datatypes by @mvdbeek in #17976
Backport: Fix bug: call unique() on result, not select stmt by @jdavcs in #17981
Fix LengthValidator if no value passed by @mvdbeek in #17983
Raise RequestParameterInvalidException if collection element has unknown extension by @mvdbeek in #17985
Don’t attempt to commit in dry_run mode by @mvdbeek in #17987
Don’t fail if reporting invalid parameter values by @mvdbeek in #18002
Include exception info when something goes wrong while refreshing tokens by @mvdbeek in #18008
Avoid exception when opening apply rules tool and no collection in history by @mvdbeek in #18011
Raise appropriate exception if user forces a collection that is not populated with elements as input by @mvdbeek in #18023
Fix History Dataset Association creation so that hid is always set by @mvdbeek in #18036
Change wrong quota_source value from KeyError to ValueError by @mvdbeek in #18040
Check database connection to issue a rollback if no connection by @jdavcs in #18070
Enhancements
Fix remote files sources error handling by @davelopez in #18027
Other changes
24.0.0 (2024-04-02)
Bug fixes
Reload built-in converters on toolbox reload by @bernt-matthias in #17209
Optional Reply-to SMTP header in tool error reports by @neoformit in #17243
Rollback invalidated transaction: catch them earlier by @jdavcs in #17312
Fix data_source and data_source_async bugs by @wm75 in #17422
More efficient change_state queries, maybe fix deadlock by @mvdbeek in #17632
Separate ConnectedValue from RuntimeValue by @mvdbeek in #17678
Fix step type serialization for StoredWorkflowDetailed models by @mvdbeek in #17716
Also set extension and metadata on copies of job outputs when finishing job by @mvdbeek in #17777
Defer job attributes that are usually not needed by @mvdbeek in #17795
Fix change_datatype PJA for dynamic collections by @mvdbeek in #17803
Fix archived histories mixing with active in histories list by @davelopez in #17856
Normalize extensions when loading tool by @mvdbeek in #17868
Enhancements
Add harmonize collections tool (or whatever other name) by @lldelisle in #16662
Support for OIDC API Auth and OIDC integration tests by @nuwang in #16977
Toward declarative help for Galaxy markdown directives. by @jmchilton in #16979
Extend regex groups in stdio regex matches by @bernt-matthias in #17016
Remove web framework dependency from tools by @davelopez in #17058
Add select parameter with options from remote resources by @mvdbeek in #17087
Expose more tool information / navigability in UI. by @jmchilton in #17105
SA2.0 updates: handling “object is being merged into a Session along the backref cascade path” by @jdavcs in #17122
Update Python dependencies by @galaxybot in #17123
Towards SQLAlchemy 2.0: fix last cases of RemovedIn20Warning by @jdavcs in #17132
Update Python dependencies by @galaxybot in #17157
Update Python dependencies by @galaxybot in #17201
Fix usage of graphene-sqlalchemy, bump to 3.0.0rc1 by @jdavcs in #17216
Update Python dependencies by @galaxybot in #17230
Update Python dependencies by @galaxybot in #17235
Allow job files to consume TUS uploads by @jmchilton in #17242
Update Python dependencies by @galaxybot in #17247
Consider Null inputs by @bernt-matthias in #17271
Add OIDC backend configuration schema and validation by @uwwint in #17274
Adds delete, purge and undelete batch operations to History Grid by @guerler in #17282
Add __KEEP_SUCCESS_DATASETS__ by @lldelisle in #17294
API endpoint that allows “changing” the objectstore for “safe” scenarios. by @jmchilton in #17329
Update Python dependencies by @galaxybot in #17333
Add element_identifier and ext to inputs config file export by @bernt-matthias in #17357
Remove unused statements in job search function by @mvdbeek in #17361
Fix type annotation of code using XML etree by @nsoranzo in #17367
More specific type annotation for BaseJobExec.parse_status() by @nsoranzo in #17381
Cancel all active jobs when the user is deleted by @davelopez in #17390
Purge groups and roles from DB (for real) by @davelopez in #17411
Update Python dependencies by @galaxybot in #17420
Allow using tool data bundles as inputs to reference data select parameters by @mvdbeek in #17435
Allow filtering history datasets by object store ID and quota source. by @jmchilton in #17460
data_column parameter: use column_names metadata if present by @bernt-matthias in #17478
Update Python dependencies by @galaxybot in #17486
Consolidate resource grids into tab views by @guerler in #17487
add encode ID API endpoint by @mira-miracoli in #17510
Fixing data_source tools and incrementing tool profile by @wm75 in #17515
Update Python dependencies by @galaxybot in #17541
Add image_diff comparison method for test output verification using images by @kostrykin in #17556
Update Python dependencies by @galaxybot in #17580
Restore histories API behavior for keys query parameter by @davelopez in #17779
Fix datasets API custom keys encoding by @davelopez in #17793
Improved error messages for runtime sharing problems. by @jmchilton in #17794
Allow admin to sharpen language about selected object stores. by @jmchilton in #17806
Other changes
consistently compare profile versions by @bernt-matthias in #16492
23.2.1 (2024-02-21)
Bug fixes
pin fs.dropboxfs to >=1 by @bernt-matthias in #16451
Remove unnecessary check: item cannot be None by @jdavcs in #16550
Fix: serialize tool_shed_urls directly from the API by @davelopez in #16561
Fix dependency update GitHub workflow by @nsoranzo in #16639
Ensure Job belongs to current SA session by @jdavcs in #16647
Account for shared usage between TS and galaxy apps by @jdavcs in #16746
move the email and username redacting from the role loop by @martenson in #16805
chore: fix typos by @afuetterer in #16851
Update help in relabel_from_file.xml by @lldelisle in #16891
Fix subtle bug in listify function + simplify list munging by @jdavcs in #16904
Enhancement to Tool Form page, Repeating form fields implement parameter instructions by @hujambo-dunia in #17018
Expose file_name property in DatasetFilenameWrapper by @jdavcs in #17107
Backport Rollback invalidated transaction: catch them earlier by @mvdbeek in #17315
Discard sqlalchemy session after task completion by @mvdbeek in #17317
Scope session for job runner monitor loop by @mvdbeek in #17319
Fix History contents genome_build filter postgresql bug by @ahmedhamidawan in #17384
Build param dict before creating entrypoint by @mvdbeek in #17440
Set metadata states on dataset association, not dataset by @mvdbeek in #17474
Remove two print statements by @bernt-matthias in #17480
Provide working routes.url_for every ASGI request by @mvdbeek in #17497
Enhancements
Implement default locations for data and collection parameters. by @jmchilton in #14955
Add parameter name to validation errors by @bernt-matthias in #15440
Tool Shed 2.0 by @jmchilton in #15639
Add ability to assert metadata properties on input dataset parameters by @bernt-matthias in #15825
Limit number of celery task executions per second per user by @claudiofr in #16232
Delete non-terminal jobs and subworkflow invocations when cancelling invocation by @mvdbeek in #16252
Towards SQLAlchemy 2.0 (upgrades to SA Core usage) by @jdavcs in #16264
Update Python dependencies by @galaxybot in #16305
Add carbon emissions admin configuration options by @Renni771 in #16307
Migrate a part of the users API to Fast API by @heisner-tillman in #16341
Update Python dependencies by @galaxybot in #16360
Add Invenio RDM repository integration by @davelopez in #16381
Update Python dependencies by @galaxybot in #16389
Update Python dependencies by @galaxybot in #16409
Refactor FilesDialog + Remote Files API schema improvements by @davelopez in #16420
Towards SQLAlchemy 2.0 (upgrades to SA ORM usage in /test) by @jdavcs in #16431
SQLAlchemy 2.0 upgrades to ORM usage in /lib by @jdavcs in #16434
Update Python dependencies by @galaxybot in #16436
Update Python dependencies by @galaxybot in #16485
Rename MetadataEqualsValidator by @bernt-matthias in #16489
Add support for CILogon deployments in different regions than the US by @uwwint in #16490
Update Python dependencies by @galaxybot in #16521
Move database access code out of galaxy.util by @jdavcs in #16526
Tweak tool memory use and optimize shared memory when using preload by @mvdbeek in #16536
Update Python dependencies by @galaxybot in #16577
Workflow Comments 💬 by @ElectronicBlueberry in #16612
Switch out conditional requirement parser by @mvdbeek in #16636
Add scroll pagination and username filter to HistoryPublishedList by @ahmedhamidawan in #16642
Bump samtools converters by @bernt-matthias in #16668
Galaxy Markdown - add workflow image and license to Galaxy markdown. by @jmchilton in #16672
Implement instance URLs in Galaxy markdown. by @jmchilton in #16675
Use fs.onedatarestfs for Onedata files source plugin implementation by @lopiola in #16690
Enhance task monitor composable by @davelopez in #16695
Misc. edits/refactorings to session handling by @jdavcs in #16712
Update Python dependencies by @galaxybot in #16735
Convert ISO to UTC for Date/Time in workflow reports by @assuntad23 in #16758
Replace ELIXIR AAI button with Life Science login by @sebastian-schaaf in #16762
Update Python dependencies by @galaxybot in #16770
Migrate a part of the jobs API to Fast API by @heisner-tillman in #16778
Add EGI Check-in as OIDC authentication option by @enolfc in #16782
Replace file_name property with get_file_name function by @SergeyYakubov in #16783
Updated path-based interactive tools with entry point path injection, support for ITs with relative links, shortened URLs, doc and config updates including Podman job_conf by @sveinugu in #16795
Galaxy help forum integration by @ElectronicBlueberry in #16798
Update Python dependencies by @galaxybot in #16807
Another batch of SA2.0 edits in TS2.0 (part 3) by @jdavcs in #16833
Remove remaining legacy backbone form input elements by @guerler in #16834
Update Python dependencies by @galaxybot in #16853
Drop unused HistoryContentManager code and related tests by @jdavcs in #16882
Update Python dependencies by @galaxybot in #16896
Enable some flake8-logging-format rules in ruff by @nsoranzo in #16915
Remove “Create Workflow” form and allow workflow creation in editor by @ahmedhamidawan in #16938
Update Python dependencies by @galaxybot in #16939
Add helper to get dataset or collection via src and id by @mr-c in #16953
Allow non-optional integer/float params without value attribute by @nsoranzo in #16966
Update Python dependencies by @galaxybot in #16978
Fix invocation report to target correct workflow version. by @jmchilton in #17008
Update Python dependencies by @galaxybot in #17011
Upgrade job manager’s index_query method to SA2.0 by @jdavcs in #17020
optimize object store cache operations by @SergeyYakubov in #17025
Require name for workflows on save, set default to Unnamed Workflow by @ahmedhamidawan in #17038
Update Python dependencies by @galaxybot in #17050
Update Python dependencies by @galaxybot in #17084
Use python-isal for fast zip deflate compression in rocrate export by @mvdbeek in #17342
Other changes
23.1.4 (2024-01-04)
Bug fixes
Fix workflow index total matches counting by @davelopez in #17176
Fix url_for in tool error reports by @davelopez in #17210
23.1.3 (2023-12-01)
No recorded changes since last release
23.1.2 (2023-11-29)
Bug fixes
Fix unbound runner variable when there is an error in the job config by @mvdbeek in #16906
Fix discarded dataset ordering in Storage Dashboard by @davelopez in #16929
Include owner’s annotation when exporting workflow by @dannon in #16930
Skip state filtering in __MERGE_COLLECTION__ tool by @mvdbeek in #16937
Prevent Singular external auth users from disconnecting identity by @ahmedhamidawan in #16961
Prevent workflow submission with missing input values by @mvdbeek in #17048
Fix extra files collection if using store_by="id" and outputs_to_working_directory by @mvdbeek in #17067
Remove rollback from __check_jobs_at_startup by @mvdbeek in #17085
Enhancements
23.1.1 (2023-10-23)
Bug fixes
read job_conf directly from config_dir instead of computing it again from config_file by @bernt-matthias in #15596
Fix revision scripts, run migrations in CI, add repair option, improve migrations utils by @jdavcs in #15811
Fix and test startup with Python 3.11 on macOS by @nsoranzo in #16082
Fix : Ignore error messages for admin created accounts by @jvanbraekel in #16132
Ensure session is request-scoped for legacy endpoints by @jdavcs in #16207
Fix “database is locked” error (occurring in the context of workflow testing under SQLite) by @jdavcs in #16208
Fix ordering of data libraries from API by @martenson in #16300
qualify querying for an api-key by @martenson in #16320
Fix tags ownership by @davelopez in #16339
Fix histories count by @davelopez in #16400
Fix select statement syntax for SQLAlchemy 2.0 by @jdavcs in #16421
Run through tmp_dir_creation_statement only once by @mvdbeek in #16529
Fix double-encoding notification content by @mvdbeek in #16530
Limit tool document cache to tool configs with explicit cache path by @mvdbeek in #16537
Fix multiple remote test data by @davelopez in #16542
Ignore errors with user-set job resources by @mvdbeek in #16579
Fix replacement parameters for subworkflows. by @jmchilton in #16592
make sure that TMP, TEMP, and TMPDIR are set by @bernt-matthias in #16594
Reload toolbox after forking when using –preload by @mvdbeek in #16620
Account for expires/expires_in when refreshing token by @mvdbeek in #16621
Fixes for conditional subworkflow steps by @mvdbeek in #16632
Ensure Job belongs to current SA session by @mvdbeek in #16655
Fix expression evaluation for nested state by @mvdbeek in #16656
Make sort_collection tool require terminal datasets by @mvdbeek in #16661
Push to object store even if set_meta fails by @mvdbeek in #16667
Fix metadata setting in extended metadata + outputs_to_working_directory mode by @mvdbeek in #16678
Fix regex validation for global inline flags by @mvdbeek in #16683
Fix closed transaction error on galaxy startup/check jobs by @jdavcs in #16687
Add missing join condition in job search by @mvdbeek in #16710
Copy the collection contents by default when copying a collection by @mvdbeek in #16717
Fix collection id encoding by @davelopez in #16718
Workaround for XML nodes of job resource parameters losing their children by @kysrpex in #16728
move the email and username redacting from the role loop by @martenson in #16820
Fix parameter display in job info page for tools with sections by @mvdbeek in #16821
Fix workflow preview display if tool state does not contain all parameter values by @mvdbeek in #16829
Fix and prevent persisting null file_size by @mvdbeek in #16855
Allow referring to steps by label only in markdown editor by @mvdbeek in #16861
Fix safe update version handling in run form by @mvdbeek in #16865
Remove more flushes in database operation tools by @mvdbeek in #16875
Enhancements
Empower Users to Select Storage Destination by @jmchilton in #14073
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
Expose additional beaker caching backends by @claudiofr in #15349
Add support for visualizing HDF5 datasets. by @jarrah42 in #15394
Towards SQLAlchemy 2.0: drop session autocommit setting by @jdavcs in #15421
Update Python dependencies by @galaxybot in #15435
Fix for new style conda packages by @bernt-matthias in #15446
Move database access code out of tool_util by @jdavcs in #15467
Protection against problematic boolean parameters. by @jmchilton in #15493
Use connection instead of session for ItemGrabber by @jdavcs in #15496
Explore tool remote test data by @davelopez in #15510
Handle “email_from” config option consistently, as per schema description by @jdavcs in #15557
Update Python dependencies by @galaxybot in #15564
Drop workflow exports to myexperiment.org by @dannon in #15576
Update database_heartbeat for SA 2.0 compatibility by @jdavcs in #15611
Add suggested Training material to Tool Form by @ElectronicBlueberry in #15628
Wrap check_jobs_at_startup operation in a transaction (SA 2.0 compatibility) by @jdavcs in #15643
Add Galaxy Notification System by @davelopez in #15663
Add transactional state to JobHandlerStopQueue by @jdavcs in #15671
Verify that activation and reset emails are properly generated by @guerler in #15681
Add transactional state to workflow scheduling manager by @jdavcs in #15683
Remove DELETED_NEW job state from code base by @jdavcs in #15690
Fix/Enhance recalculate disk usage API endpoint by @davelopez in #15739
Add API test and refactor code for related:hid history filter by @ahmedhamidawan in #15786
Migrate to MyST-Parser for Markdown docs by @nsoranzo in #15844
Update Python dependencies by @galaxybot in #15890
Allow pending inputs in some collection operation tools by @mvdbeek in #15892
Updated doc and tests for attribute value filter by @tuncK in #15929
Update Python dependencies by @galaxybot in #15942
Record input datasets and collections at full parameter path by @mvdbeek in #15978
Export tool citations configurable message by @minh-biocommons in #15998
Add History Archival feature by @davelopez in #16003
Code cleanups from ruff and pyupgrade by @nsoranzo in #16035
Add missing fields to HistorySummary schema model by @davelopez in #16041
Vendorise packaging.versions.LegacyVersion by @nsoranzo in #16058
Add Repository owner field to ToolSearch by @ahmedhamidawan in #16061
Add count support for listing filters by @davelopez in #16075
Update Python dependencies by @galaxybot in #16086
Improved Cache Monitoring for Object Stores by @jmchilton in #16110
Integrate accessibility testing into Selenium testing by @jmchilton in #16122
Update Python dependencies by @galaxybot in #16123
Improve histories and datasets immutability checks by @davelopez in #16143
Update Python dependencies by @galaxybot in #16153
Migrate display applications API to Fast API by @heisner-tillman in #16156
adjust grid sharing indicators by @martenson in #16163
Update Python dependencies by @galaxybot in #16182
Drop workarounds for old ro-crate-py and docutils versions by @mvdbeek in #16198
bring grids for (published) pages on par with workflows by @martenson in #16209
Update Python dependencies by @galaxybot in #16227
Update Python dependencies by @galaxybot in #16267
Fix tool remote test data by @davelopez in #16311
Fix Storage Dashboard missing archived histories by @davelopez in #16473
Drop expunge_all() call in WebTransactionRequest by @mvdbeek in #16606
Other changes
Follow up on object store selection PR. by @jmchilton in #15654
merge release_23.0 into dev by @martenson in #15830
Move axe-selenium-python to dev dependencies by @nsoranzo in #16162
23.0.6 (2023-10-23)
Bug fixes
Fix upload paramfile handling (for real user setups) by @bernt-matthias in #16504
Make sure job_wrapper uses a consistent metadata strategy by @mvdbeek in #16569
Fix conditional step evaluation with datasets in repeats by @mvdbeek in #16584
Fixes for extra files handling and cached object stores by @mvdbeek in #16595
Lazy load tool data tables in celery worker by @mvdbeek in #16640
Force __DUPLICATE_FILE_TO_COLLECTION__ ‘size’ param to integer by @simonbray in #16659
Enhancements
23.0.5 (2023-07-29)
Bug fixes
Skip installing npm/yarn if available, fix conditional dependency parsing, create virtualenv via conda when conda active by @bernt-matthias in #16403
Fixes for (gitlab) error reporting by @bernt-matthias in #16424
23.0.4 (2023-06-30)
Bug fixes
23.0.3 (2023-06-26)
Bug fixes
Enhancements
Other changes
23.0.2 (2023-06-13)
Bug fixes
Enhancements
23.0.1 (2023-06-08)
Bug fixes
Display DCE in job parameter component, allow rerunning with DCE input by @mvdbeek in #15744
Fix mixed outputs_to_working_directory pulsar destinations by @mvdbeek in #15927
Fix case sensitive filtering by name in histories by @davelopez in #16036
Replace httpbin service with pytest-httpserver by @mvdbeek in #16042
Anonymous User tool link bug fix by @ahmedhamidawan in #16065
Fix job failure handling when condor indicates job failure by @mvdbeek in #16096
Fix dataype_change not updating HDCA update_time by @mvdbeek in #16099
Extract HDA for code_file validate_input hook by @mvdbeek in #16120
Fix sort error when re-running job with DCE collection input by @mvdbeek in #16126
Fix rank calculation for jobs waiting to be run by anonymous users by @jdavcs in #16137
Tool warnings can either be None or a Dictionary but not a String by @guerler in #16183
Other changes
20.9.0 (2020-10-15)
First release from the 20.09 branch of Galaxy.
20.5.0 (2020-07-04)
First release from the 20.05 branch of Galaxy.
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