Galaxy application (backend)
Project description
Overview
The Galaxy application logic (backend).
History
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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