galaxyproject/galaxy v24.1.2

on GitHub

What's Changed

• [24.1] fix no-op workflow "relabel" shouldn't result in a notification by @ElectronicBlueberry in #18473
• [24.1] Make default_panel_view a _by_host option by @natefoo in #18471
• [24.1] Stabilize test_purge_while_job_running test by @mvdbeek in #18498
• [24.1] Increase API robustness to invalid requests, improve compressed data serving by @mvdbeek in #18494
• [24.0] Return generic message for password reset email by @ahmedhamidawan in #18479
• [24.1] Backport pod5 datatype by @TomHarrop in #18507
• [23.2] Handle all requests error in ApiBiotoolsMetadataSource._raw_get_metadata by @nsoranzo in #18510
• [24.0] Follow-up on #18212 by @nsoranzo in #18516
• [24.0] Fix view parameter type in Job index API by @davelopez in #18521
• [24.1] Prevent job submission if input collection element is deleted by @mvdbeek in #18517
• [24.1] Use name instead of ID for displaying object stores + revise user-facing language in UI by @davelopez in #18525
• [24.1] Check if dataset has any data before running provider checks by @mvdbeek in #18526
• [24.1] Strip unicode null from tool stdio by @mvdbeek in #18527
• [24.1] Simplify and fix useDatatypesMapper by @mvdbeek in #18550
• [24.1] Also check dataset.deleted when determining if data can be displayed by @mvdbeek in #18547
• [24.1] Fix map over calculation for runtime inputs by @mvdbeek in #18535
• [24.1] Fix shared caches with extended metadata collection. by @jmchilton in #18520
• [24.1] Fix undo removing all freehand comments by @ElectronicBlueberry in #18557
• [24.1] Also fail ensure_dataset_on_disk if dataset is in new state by @mvdbeek in #18559
• [24.1] Apply statsd arg sanitization to all pages by @mvdbeek in #18509
• [24.1] Raise appropriate exception if ldda not found by @mvdbeek in #18569
• [24.1] Fix history changes switch to simple form by @ElectronicBlueberry in #18574
• [24.0] Fix Archive header encoding by @arash77 in #18583
• [24.0] Fix for not-null in 'column_list' object by @hujambo-dunia in #18553
• [23.0] Fix API key reveals on mouse hover by @itisAliRH in #18593
• [24.0] Fix sqlalchemy statement in tooltagmanager reset output by @dannon in #18591
• [24.0] Set minimum weasyprint version by @mvdbeek in #18606
• [24.1] Adjust sentry default config -- drop replay by @dannon in #18622
• [24.1] More datatype deprecation warnings by @mvdbeek in #18612
• [23.0] Fix for Numeric form field to allow Null min/max values in validation methods by @hujambo-dunia in #18585
• [24.1] xsd: allow change_format and actions also in statically defined collection elements, and break recursion by @bernt-matthias in #18605
• [24.1] Improve relabel identifiers message when number of columns is not 2 by @mvdbeek in #18634
• [24.1] Include workflow invocation id in exception logs by @mvdbeek in #18594
• [24.1] Fix invocation view steps scroll bug by @ahmedhamidawan in #18614
• [24.1] Fix resume_paused_jobs if no session provided by @mvdbeek in #18640
• [24.0] Close install model session when request ends by @mvdbeek in #18629
• [24.1] Update h5web by @dannon in #18552
• [24.0] Don't set file size to zero by @mvdbeek in #18653
• [23.2] Strip whitespace when listifying admin users by @jdavcs in #18656
• [24.1] Fix extract workflow from history when implicit collection has no jobs by @mvdbeek in #18661
• [24.1] Optimize useInvocationGraph for Invocation view by @ahmedhamidawan in #18663
• [24.0] Improve workflow creating/saving UX by @ahmedhamidawan in #18657
• [24.1] Fix export_remote include/exclude metadata flag by @davelopez in #18659
• [24.0] Remove unnecessary assert for file_size by @davelopez in #18669
• [24.1] Fix h5ad metadata by @nilchia in #18635
• [24.1] Return error when following a link to a non-ready display application by @mvdbeek in #18672
• [24.1] Only load authnz routes when oidc enabled by @mvdbeek in #18683
• [24.1] File source and object store instance api fixes by @mvdbeek in #18685
• [24.0] Fix import all datasets from library folder by @davelopez in #18687
• [24.0] Make sure we set file size also for purged outputs by @mvdbeek in #18681
• [24.1] Fix sorting users in admin by last login by @jdavcs in #18694
• [24.1] Fix change datatype PJA on expression tool data outputs by @mvdbeek in #18691
• [24.1] Fix upload when current history changes by @davelopez in #18703
• [24.1] Fix output hover for workflow parameter outputs by @mvdbeek in #18720
• [24.1] Fill in missing help for cross product tools. by @jmchilton in #18698
• [24.1] Add error handling in WorkflowInvocationState by @ahmedhamidawan in #18726
• [24.1] Fix subworkflow scheduling for delayed subworkflow steps connected to data inputs by @mvdbeek in #18731
• [24.1] Fix invocation grid selenium that fails intermittently by @ahmedhamidawan in #18735
• [24.1] Fix resume paused jobs response handling by @dannon in #18733
• [24.1] Catch and display exceptions when importing malformatted yaml workflows by @mvdbeek in #18734
• [24.1] Fix datatype validation of newly built collection by @mvdbeek in #18738
• [24.1] Handle error when workflow is unowned in Invocation view by @ahmedhamidawan in #18730
• [24.1] Show items with same hid but different id in history by @ahmedhamidawan in #18689
• [24.0] Fix rules runtime editable by @ElectronicBlueberry in #18741
• [24.1] Fix directory get or create logic by @mvdbeek in #18752
• [24.1] Fix scratch storage modal title by @mvdbeek in #18753
• [24.1] Fix job summary for optional unset job data inputs by @mvdbeek in #18754
• [24.1] Fix infinitely delayed workflow scheduling if skipped step creates HDCA by @mvdbeek in #18751
• [24.1] Fix infinite rapid polling in useKeyedCache by @mvdbeek in #18756
• [24.0] Fix TypeError from Pydantic 2.9.0 by @nsoranzo in #18788
• Implemented the generic OIDC backend from python-social-auth into Gal… by @Edmontosaurus in #18670
• [24.1] Fixing RegisterForm.vue not appending prefix when set. by @mcuaya1 in #18786
• [24.0] Update ENA url in ebi_sra tool by @mvdbeek in #18771
• [24.1] Fix wrong extension on pick data output by @mvdbeek in #18798
• [24.1] Backport PR 18630 "Add BlobToolkit to the list of interactive tools" to release_24.1 by @cat-bro in #18784
• [24.1] Fix copying workflow with subworkflow step for step that you own by @mvdbeek in #18802
• [24.1] Use smtplib send_message to support utf-8 chars in to and from by @mvdbeek in #18805
• [24.1] Collect job metrics also when job failed by @mvdbeek in #18809
• [24.1] Fix optional text handling in LibraryEditField by @mvdbeek in #18814
• [24.1] Make pylibmagic import optional by @mvdbeek in #18813
• [24.1] Add error handling for SwitchToHistoryLink by @ahmedhamidawan in #18765
• [24.1] Allow drag and drop for collection elements by @ahmedhamidawan in #18699
• [24.1] Prevent optional output to required input connection in editor by @mvdbeek in #18810
• [24.1] Fix unspecified oidc_endpoint variable overwriting specified redirect_url by @bgruening in #18818
• [24.1] Start job handler only after building InteractiveToolManager by @mvdbeek in #18824
• [24.1] Fix named cursor is not valid anymore by @mvdbeek in #18825
• [24.1] Fix wrong celery_app config on job and workflow handlers by @mvdbeek in #18819
• [24.1] Maybe fix flaky navigation v2 ts tests by @mvdbeek in #18833
• [24.1] Make all fields optional for HelpForumPost by @davelopez in #18839
• [24.1] prevent "missing refresh_token" errors by supporting <extra_scopes> also with Keycloak backend by @ljocha in #18826
• [24.1] Fix alert handling in workflow label handler by @guerler in #18836
• [24.1] Extend on disk checks to running, queued and error states by @mvdbeek in #18846
• [24.1] Skip metric collection if job working directory doesn't exist by @mvdbeek in #18845
• [24.1] Tighten TRS url check by @mvdbeek in #18841
• [24.0] Ignore converted datasets in invalid input states by @mvdbeek in #18850
• [24.1] Allow to change only the description of a quota by @bernt-matthias in #18775
• [24.1] Fix Workflow index bookmark filter by @itisAliRH in #18842
• [24.0] Fix discovered outputs with directory metadata and distributed object by @mvdbeek in #18855
• [24.1] Fix check dataset check by @mvdbeek in #18856
• [24.1] Retry container monitor POST if it fails (don't assume it succeeded) by @natefoo in #18863
• [24.0] Fix wrong final state when init_from is used by @mvdbeek in #18871
• [24.1] Raise MessageException instead of assertions on rerun problems by @mvdbeek in #18858
• [24.1] Fix history import when parent_hda not serialized by @mvdbeek in #18873
• [24.1] Fix loading very old workflows with data inputs by @mvdbeek in #18876
• [24.1] Fix data_column ref to nested collection by @mvdbeek in #18875

New Contributors

• @nilchia made their first contribution in #18635
• @mcuaya1 made their first contribution in #18786
• @ljocha made their first contribution in #18826

Full Changelog: v24.1.1...v24.1.2