galaxyproject/galaxy v24.0.3

on GitHub

What's Changed

• [24.0] Backport OIDC schema fix by @mvdbeek in #18111
• [23.2] Allow purge query param, deprecate purge body param by @mvdbeek in #18105
• [24.0] Fix switching between nested collection elements by @mvdbeek in #18115
• [24.0] Fix deprecated deprecated argument by @mvdbeek in #18119
• [24.0] Ignore AdminRequired and RegisteredUserRequired Sentry events by @mvdbeek in #18118
• [24.0] Include traceback when logging email PJA exception by @mvdbeek in #18122
• [24.0] Downgrade missing output file in working directory to warning for failed jobs by @mvdbeek in #18123
• [24.0] Don't log exception if cancelled slurm job doesn't have stderr file by @mvdbeek in #18121
• [24.0] Raise exception if collection elements missing during download by @jdavcs in #18094
• [24.0] Fix and unify axios error handling by @mvdbeek in #18112
• [24.0] Fix activity bar touch events on iOS devices by @mvdbeek in #18109
• [24.0] Fix vanishing connections on workflow upgrade by @ElectronicBlueberry in #18107
• [24.0] Fix listing possibly untitled records in Invenio Plugin by @davelopez in #18130
• [24.0] Don't commit in DeleteIntermediatesAction by @mvdbeek in #18131
• [24.0] Fix data default values not getting added to history by @mvdbeek in #18132
• [24.0] Fix undefined reading 'produces_entry_points' TypeError by @ahmedhamidawan in #18141
• [24.0] Fix config access in StorageManager by @dannon in #18143
• [24.0] Fix Legacy HTML page view by @mvdbeek in #18145
• [24.0] Delay tool form rendering until config is loaded by @mvdbeek in #18151
• [24.0] Raise RequestParameterInvalidException when url is invalid by @mvdbeek in #18155
• [24.0] Drop redundant error message by @mvdbeek in #18156
• [24.0] Fix error message when accessing restricted Zenodo records by @davelopez in #18169
• [24.0] Downgrade count lines error to warning by @mvdbeek in #18175
• [24.0] Emit warning when user-cancelled job already complete by @mvdbeek in #18178
• [24.0] Fix typos in create release documentation page by @jdavcs in #18181
• [24.0] Fix on success redirect by @mvdbeek in #18187
• [24.0] Fix Edit Dataset UI when there is an error retrieving the dataset by @davelopez in #18188
• [24.0] Avoid object store path lookup when constructing JobState object by @mvdbeek in #18190
• [24.0] Fix make all histories private with immutable histories by @davelopez in #18200
• [24.0] Remove legacy code, reference to sqlalchemy migrate by @jdavcs in #18202
• [24.0] Fix submitted value in workflow run form if data is constrained by tag filter by @mvdbeek in #18193
• [24.0] Add string cast for dbkey / genome_build by @mvdbeek in #18207
• [24.0] Include stack when reporting delete error by @mvdbeek in #18208
• [24.0] Replace Multiselect selectLabel with icons in FormSelect by @ahmedhamidawan in #18194
• [24.0] Fix pca 3d rendering of tabular files and visualization error handling in general by @mvdbeek in #18211
• [24.0] Don't fail metadata if we only have an extra output files dir by @mvdbeek in #18179
• [24.0] Add GenericItem error handling by @ahmedhamidawan in #18203
• [24.0] Backport #18197 by @nsoranzo in #18212
• [24.0] Use config_section to distinguish between galaxy and ts or other apps by @jdavcs in #18215
• [24.0] Prevent anonymous and inactive users from running workflows by @ahmedhamidawan in #18192
• [24.0] Restrict job_files access to jobs that are not terminal by @mvdbeek in #18217
• [24.0] Check dataset state when attempting to acces dataset contents by @mvdbeek in #18214
• [24.0] do not expand datasets that are known to be inaccessible by @martenson in #17818
• [24.0] Raise RequestParameterInvalidException if url can't be verified by @mvdbeek in #18230
• [24.0] Don't set dataset peek for errored jobs by @mvdbeek in #18231
• [24.0] Decrease log level for expected visualization errors by @mvdbeek in #18229
• [24.0] Raise appropriate exception if accessing deleted input file by @mvdbeek in #18223
• [24.0] Reset content-length for unhandled exceptions by @mvdbeek in #18233
• [24.0] Fix element serialization for collections that aren't populated yet by @mvdbeek in #18235
• [24.0] Fix userOwnsHistory conditions by @davelopez in #18243
• [23.1] Minor fix to enable external hgweb process by @mvdbeek in #18256
• [24.0] Skip tests if toolshed, dx.doi not responding by @mvdbeek in #18250
• [23.1] Add missing TS migration by @jdavcs in #18267
• [23.2] Add hgweb_repo_prefix attribute to TestToolShedConfig by @nsoranzo in #18268
• [24.0] Format with black by @nsoranzo in #18273
• [24.0] Transparently open compressed files in DatasetDataProvider by @mvdbeek in #18248
• [24.0] Raise exception when extracting dataset from collection without datasets by @mvdbeek in #18249
• [24.0] Fix Invenio credentials handling by @davelopez in #18255
• [23.1] Add revision tags for TS migration in 23.1 by @jdavcs in #18271
• [24.0] Only log error if deleting directory really failed by @mvdbeek in #18236
• [24.0] Don't attempt to download purged datasets by @mvdbeek in #18278
• [24.0] Set page importable to false when serializing by @mvdbeek in #18263
• [24.0] Fix first_dataset_element type hint by @mvdbeek in #18284
• [23.2] Add toolshed database revision tags for 23.2 by @jdavcs in #18293
• [24.0] Add TS db revision tags for 24.0 by @jdavcs in #18294
• [24.0] Use correct link for log in or register in Copy Modal by @davelopez in #18289
• [24.0] Redirect anonymous users to home when importing public histories by @davelopez in #18286
• [24.0] Check various preconditions in FeatureLocationIndexDataProvider by @davelopez in #18283
• [24.0] Move tool shed specific driver function to tool_shed.test by @mvdbeek in #18296
• [24.0] Don't serialize display application links for deleted datasets by @mvdbeek in #18307
• [23.1] More fixes for running the TS with external hgweb by @mvdbeek in #18279
• Merge 23.1 into 23.2 by @mvdbeek in #18320
• [23.2] Fix integration tests by @mvdbeek in #18326
• [23.2] Fix tool_shed package unit tests by @mvdbeek in #18327
• [23.2] Fix one more tool shed unit test by @mvdbeek in #18328
• [23.1] Make toolshed repo permissions world-readable by @mvdbeek in #18332
• [24.0] Downgrade doi fetch error to debug by @mvdbeek in #18330
• [24.0] Fix users API serialization when listing users by @davelopez in #18329
• [23.2] Skip new history creation if user is anonymous and login is required by @mvdbeek in #18319
• [24.0] Fix seek in slurm memory check by @mvdbeek in #18338
• [24.0] Fix authentication error for anonymous users querying jobs by @davelopez in #18333
• [23.2] Allow DCE as outer input to to_cwl by @mvdbeek in #18349
• [24.0] Fix anonymous user job retrieval logic by @davelopez in #18358
• [24.0] Do not copy purged outputs to object store by @mvdbeek in #18342
• [24.0] Sanitize FormElement error messages by @mvdbeek in #18377
• [24.0] Drop unnecessary escaping for workflow name and annotation by @mvdbeek in #18376
• [24.0] Fix user's private role can be missing by @davelopez in #18381
• [24.0] Make sure that all Linter subclasses are imported for listing them by @bernt-matthias in #18339
• [24.0] Kill pulsar job if job stopped on galaxy side by @mvdbeek in #18348
• [24.0] Fix null inputs in database operation tools by @mvdbeek in #18385
• [24.0] Fix workflow editor tool form scroll memory by @ElectronicBlueberry in #18390
• [24.0] Fix update group API payload model by @davelopez in #18374
• [24.0] Allow in_range validator for selects by @bernt-matthias in #18403
• [24.0] Fix invocation step_job_summary for new collections by @mvdbeek in #18402
• [24.0] Fix get_accessible_job if called without session by @mvdbeek in #18400
• [24.0] Fix collection map over status for dragged collections by @mvdbeek in #18416
• [24.0] Serialize purged flag for datasets in collections by @davelopez in #18420
• [24.0] Really allow in-range validator for txt by @bernt-matthias in #18411
• [24.0] Assign default data extension on discovered collection output by @mvdbeek in #18389
• [24.0] Minor linting cleanup by @mvdbeek in #18421
• [24.0] Install node from setup-node action by @nsoranzo in #18435
• [24.0] Fix mounting utility usage of pinia (fixes charts form components) by @dannon in #18430
• [24.0] Replace busybox:ubuntu-14.04 image with busybox:1.36.1-glibc by @mvdbeek in #18428

Full Changelog: v24.0.2...v24.0.3