| d947481 | Matthias Bernt | 28 June 2024, 09:08:00 UTC | Create version 24.0.3 | 28 June 2024, 09:08:00 UTC |
| 8a52443 | Marius van den Beek | 28 June 2024, 07:22:30 UTC | Merge pull request #18428 from mvdbeek/replace_busybox [24.0] Replace busybox:ubuntu-14.04 image with busybox:1.36.1-glibc | 28 June 2024, 07:22:30 UTC |
| 2257c22 | Marius van den Beek | 24 June 2024, 12:03:26 UTC | Merge pull request #18430 from dannon/fix-chargs-24.0 [24.0] Fix mounting utility usage of pinia (fixes charts form components) | 24 June 2024, 12:03:26 UTC |
| 6f5aeeb | Marius van den Beek | 24 June 2024, 12:02:21 UTC | Merge pull request #18435 from nsoranzo/release_24.0_openapi_setup-node [24.0] Install node from setup-node action | 24 June 2024, 12:02:21 UTC |
| 7ceef4b | Marius van den Beek | 24 June 2024, 12:02:02 UTC | Drop extra quote Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com> | 24 June 2024, 12:02:02 UTC |
| 2fd90d1 | Nicola Soranzo | 24 June 2024, 09:02:08 UTC | Install node from setup-node action | 24 June 2024, 09:02:10 UTC |
| 98690d9 | Dannon Baker | 21 June 2024, 17:17:14 UTC | Pinia plugin fixes when using component mounting utilities. This has changed multiple times in descendant branches so this is a flattened, cleaned up version for application against 24.0. | 21 June 2024, 17:17:14 UTC |
| bcca24b | Nicola Soranzo | 19 June 2024, 11:19:14 UTC | Prepare for NumPy 2.0 | 21 June 2024, 14:58:21 UTC |
| 7c6fc18 | mvdbeek | 21 June 2024, 13:03:28 UTC | Replace busybox:ubuntu-14.04 image with busybox:1.36.1-glibc | 21 June 2024, 14:58:21 UTC |
| d2aea97 | Nicola Soranzo | 19 June 2024, 10:57:01 UTC | Merge pull request #18421 from mvdbeek/fix_linting_error [24.0] Minor linting cleanup | 19 June 2024, 10:57:01 UTC |
| 111d563 | mvdbeek | 19 June 2024, 08:24:55 UTC | Run make format | 19 June 2024, 08:24:55 UTC |
| 2891489 | Martin Cech | 18 June 2024, 15:21:20 UTC | Merge pull request #18389 from mvdbeek/ensure_data_extension_if_no_extension_specified [24.0] Assign default ``data`` extension on discovered collection output | 18 June 2024, 15:21:20 UTC |
| f5610e7 | Marius van den Beek | 18 June 2024, 14:59:32 UTC | Merge pull request #18411 from bernt-matthias/topic/in-range-txt [24.0] Really allow in-range validator for txt | 18 June 2024, 14:59:32 UTC |
| b82e4bf | Marius van den Beek | 18 June 2024, 14:56:08 UTC | Merge pull request #18420 from davelopez/24.0_fix_purged_dataset_not_reflected_in_collections [24.0] Serialize purged flag for datasets in collections | 18 June 2024, 14:56:08 UTC |
| c4d124b | davelopez | 18 June 2024, 09:46:43 UTC | Adapt unit test to include purged flag | 18 June 2024, 09:46:43 UTC |
| f090fbf | davelopez | 18 June 2024, 08:27:53 UTC | Serialize purged flag for DCEObjects | 18 June 2024, 09:31:59 UTC |
| 5297fa3 | M Bernt | 18 June 2024, 07:59:33 UTC | Apply suggestions from code review | 18 June 2024, 07:59:33 UTC |
| 4b17f1b | Marius van den Beek | 17 June 2024, 20:21:42 UTC | Merge pull request #18416 from mvdbeek/fix_collection_type_batch_status_drag [24.0] Fix collection map over status for dragged collections | 17 June 2024, 20:21:42 UTC |
| 74ae354 | mvdbeek | 17 June 2024, 15:23:52 UTC | Fix collection map over status for dragged collections Fixes https://github.com/galaxyproject/galaxy/issues/12614, which is the source of many templating errors such as https://sentry.galaxyproject.org/share/issue/008a129bf7e44b3086491789f4bfb07e/: ``` NotFound: cannot find 'forward' File "galaxy/util/template.py", line 87, in fill_template return unicodify(t, log_exception=False) File "galaxy/util/__init__.py", line 1183, in unicodify value = str(value) File "Cheetah/Template.py", line 1053, in __unicode__ return getattr(self, mainMethName)() File "cheetah_DynamicallyCompiledCheetahTemplate_1718305116_116218_60583.py", line 206, in respond ``` If we don't set `batch` and `map_over_type` (this is correctly done by the backend when building the parameter options from the history) we pass in the whole collection, which likely won't have a `forward` element. | 17 June 2024, 16:54:58 UTC |
| a2d1a5d | Matthias Bernt | 17 June 2024, 11:58:36 UTC | really allow in-range validator for txt just enabling the linter https://github.com/galaxyproject/galaxy/pull/18403 was not sufficient | 17 June 2024, 12:57:56 UTC |
| 86b6eba | Marius van den Beek | 17 June 2024, 06:07:46 UTC | Merge pull request #18400 from mvdbeek/fix_get_accessible_job_without_session [24.0] Fix ``get_accessible_job`` if called without session | 17 June 2024, 06:07:46 UTC |
| cedc325 | Marius van den Beek | 17 June 2024, 06:06:56 UTC | Merge pull request #18402 from mvdbeek/fix_invocation_state_serialization [24.0] Fix invocation step_job_summary for new collections | 17 June 2024, 06:06:56 UTC |
| fb60cfc | Marius van den Beek | 16 June 2024, 18:19:02 UTC | Merge pull request #18403 from bernt-matthias/lint-inrange-select [24.0] Allow in_range validator for selects | 16 June 2024, 18:19:02 UTC |
| a2fa98d | Matthias Bernt | 14 June 2024, 20:25:27 UTC | Allow in_range validator for selects this is for instance needed if we have a data table with version information and we want to restrict the chosen options by the version column. | 14 June 2024, 20:25:27 UTC |
| a245bd9 | mvdbeek | 14 June 2024, 16:21:23 UTC | Fix invocation step_job_summary for new collections Fixes https://github.com/galaxyproject/galaxy/issues/18401 | 14 June 2024, 16:21:29 UTC |
| 5e6afdd | mvdbeek | 14 June 2024, 16:01:42 UTC | Fix ``get_accessible_job`` if called without session Fixes https://github.com/galaxyproject/galaxy/issues/18399: ``` ExceptionGroup: unhandled errors in a TaskGroup File "starlette/_utils.py", line 87, in collapse_excgroups yield File "starlette/middleware/base.py", line 190, in __call__ async with anyio.create_task_group() as task_group: File "anyio/_backends/_asyncio.py", line 678, in __aexit__ raise BaseExceptionGroup( AttributeError: 'NoneType' object has no attribute 'id' (25 additional frame(s) were not displayed) ... File "galaxy/webapps/galaxy/fast_app.py", line 109, in add_x_frame_options response = await call_next(request) File "galaxy/webapps/galaxy/api/jobs.py", line 261, in common_problems job = self.service.get_job(trans=trans, job_id=job_id) File "galaxy/webapps/galaxy/services/jobs.py", line 121, in get_job return self.job_manager.get_accessible_job(trans, decoded_job_id=job_id) File "galaxy/managers/jobs.py", line 271, in get_accessible_job else (job.session_id == trans.get_galaxy_session().id) ``` | 14 June 2024, 16:01:48 UTC |
| 3e403e0 | Marius van den Beek | 14 June 2024, 08:05:07 UTC | Merge pull request #18374 from davelopez/24.0_fix_update_group_api_endpoint [24.0] Fix update group API payload model | 14 June 2024, 08:05:07 UTC |
| 84d6971 | davelopez | 13 June 2024, 17:15:40 UTC | Use random user in test Since we cannot remove the user from the group to restore its previous state we need to use a user that will not be part of other tests to avoid unwanted interactions. | 13 June 2024, 17:15:40 UTC |
| fbf903d | davelopez | 13 June 2024, 16:24:18 UTC | Refactor API test for updating a group | 13 June 2024, 16:24:18 UTC |
| a04942f | davelopez | 13 June 2024, 16:05:16 UTC | Keep old API behavior for now Do not allow to remove or replace, only add users and roles. | 13 June 2024, 16:05:16 UTC |
| 1e2348e | davelopez | 13 June 2024, 15:44:09 UTC | Fix typing | 13 June 2024, 15:44:09 UTC |
| 480358c | davelopez | 13 June 2024, 14:54:35 UTC | Fix update group API endpoint Allow to replace or remove users and roles from the group | 13 June 2024, 14:54:35 UTC |
| d0ebd5a | Dannon | 13 June 2024, 14:53:52 UTC | Merge pull request #18390 from ElectronicBlueberry/fix-node-scroll-memory [24.0] Fix workflow editor tool form scroll memory | 13 June 2024, 14:53:52 UTC |
| a8cb547 | davelopez | 13 June 2024, 14:53:41 UTC | Add tests for replacing and removing group users and roles | 13 June 2024, 14:53:41 UTC |
| e438b2d | Laila Los | 13 June 2024, 12:27:13 UTC | scroll to top on node change | 13 June 2024, 12:31:19 UTC |
| 6551f31 | mvdbeek | 13 June 2024, 10:52:48 UTC | Implement default format on collection level | 13 June 2024, 11:02:51 UTC |
| e5fca08 | mvdbeek | 13 June 2024, 10:15:00 UTC | Assign default `data` extension on discovered collection output They used to be persisted as null in the database prior to this change. | 13 June 2024, 11:01:48 UTC |
| dd171fe | mvdbeek | 13 June 2024, 09:50:37 UTC | Add test tool for default ext handling in discovered collections | 13 June 2024, 10:53:28 UTC |
| 4fd73fc | John Davis | 12 June 2024, 14:47:34 UTC | Merge pull request #18385 from mvdbeek/fix_inputs_ready_check [24.0] Fix null inputs in database operation tools | 12 June 2024, 14:47:34 UTC |
| 4ba1ee5 | John Davis | 12 June 2024, 14:31:51 UTC | Merge pull request #18348 from mvdbeek/kill_pulsar_job_if_still_running [24.0] Kill pulsar job if job stopped on galaxy side | 12 June 2024, 14:31:51 UTC |
| d295669 | Marius van den Beek | 12 June 2024, 12:22:11 UTC | Merge pull request #18339 from bernt-matthias/topic/linter_list_import [24.0] Make sure that all Linter subclasses are imported for listing them | 12 June 2024, 12:22:11 UTC |
| cb7357a | Marius van den Beek | 12 June 2024, 12:19:51 UTC | Merge pull request #18381 from davelopez/24.0_fix_private_role_can_be_none [24.0] Fix user's private role can be missing | 12 June 2024, 12:19:51 UTC |
| b2d52ac | mvdbeek | 12 June 2024, 11:59:15 UTC | Fix null inputs in database operation tools And fix test that was supposed to cover this. Fixes https://github.com/galaxyproject/galaxy/issues/18384 | 12 June 2024, 12:06:22 UTC |
| c69e54a | davelopez | 11 June 2024, 15:50:52 UTC | Update client API schema | 12 June 2024, 10:40:50 UTC |
| 0b504cf | davelopez | 11 June 2024, 15:36:46 UTC | Fix update group payload model All fields in the payload should be optional when updating. | 12 June 2024, 10:40:49 UTC |
| d73a820 | davelopez | 11 June 2024, 15:35:13 UTC | Increase API test coverage for group update The second update does not provide a group_name as we are not changing it. This will fail with the current code as the update payload model is the same as the create one. | 12 June 2024, 10:40:48 UTC |
| cc931e1 | davelopez | 12 June 2024, 08:54:01 UTC | Fix auto-creation of private role for new users | 12 June 2024, 08:54:01 UTC |
| 0258be8 | davelopez | 12 June 2024, 08:46:55 UTC | Restore model_class for creating user as this code is shared with Toolshed | 12 June 2024, 08:46:55 UTC |
| b89cb42 | davelopez | 12 June 2024, 07:25:49 UTC | Commit user and private role in a single DB transaction | 12 June 2024, 07:25:49 UTC |
| 4c9e6cf | davelopez | 12 June 2024, 07:24:38 UTC | Raise appropriate error message when user's private role is missing on purge | 12 June 2024, 07:24:38 UTC |
| 62b60bd | Marius van den Beek | 12 June 2024, 07:20:49 UTC | Merge pull request #18376 from mvdbeek/drop_unnecessary_workflow_name_and_annotation_escaping [24.0] Drop unnecessary escaping for workflow name and annotation | 12 June 2024, 07:20:49 UTC |
| 794c8ab | Dannon | 11 June 2024, 20:00:46 UTC | Merge pull request #18377 from mvdbeek/sanitize_form_element_form_error_v_html [24.0] Sanitize FormElement error messages | 11 June 2024, 20:00:46 UTC |
| 4f5d813 | mvdbeek | 11 June 2024, 17:35:20 UTC | Sanitize FormElement error messages v-html was introduced in https://github.com/galaxyproject/galaxy/commit/6682ca60fe64087a15d3e69c68a2054ca950d538 to show bold items. `FormElement` however is used so widely that it's hard to keep track on whether or not user-modifiable fields are shown, so better safe than sorry. | 11 June 2024, 17:35:26 UTC |
| 0a2d50a | mvdbeek | 11 June 2024, 16:25:48 UTC | Drop unnecessary escaping for workflow name and annotation These shouldn't ever have been escaped before storing in the database, this should've always just been applied on the way out. We also don't need to do that anymore since we don't use `v-html` for these fields. Fixes https://github.com/galaxyproject/galaxy/issues/18354 | 11 June 2024, 17:31:43 UTC |
| 96c9be3 | Marius van den Beek | 11 June 2024, 11:35:10 UTC | Merge pull request #18342 from mvdbeek/fix_copying_purged_files [24.0] Do not copy purged outputs to object store | 11 June 2024, 11:35:10 UTC |
| f0e09cc | mvdbeek | 10 June 2024, 13:46:32 UTC | Fix up tests | 11 June 2024, 06:18:14 UTC |
| d7dad3a | Martin Cech | 11 June 2024, 00:28:44 UTC | Merge pull request #18358 from davelopez/24.0_fix_condition_anonymous_jobs [24.0] Fix anonymous user job retrieval logic | 11 June 2024, 00:28:44 UTC |
| 9df23a6 | davelopez | 10 June 2024, 14:21:44 UTC | Require session to list jobs instead of returning empty job list for anonymous Co-authored-by: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> | 10 June 2024, 14:33:47 UTC |
| 3c7730c | mvdbeek | 10 June 2024, 13:45:49 UTC | Delete purged outputs from object store when importing dataset for purged output | 10 June 2024, 14:21:22 UTC |
| 50b7f8f | mvdbeek | 10 June 2024, 13:44:04 UTC | Do not overwrite purged or deleted states when importing datasets from job | 10 June 2024, 14:21:22 UTC |
| 5ab3120 | mvdbeek | 10 June 2024, 13:42:20 UTC | Purge dataset if finishing job for purged output | 10 June 2024, 14:21:21 UTC |
| a6b45e5 | davelopez | 10 June 2024, 11:31:36 UTC | Filter jobs by session instead of using the session current history for anonymous Co-authored-by: mvdbeek <m.vandenbeek@gmail.com> | 10 June 2024, 11:34:27 UTC |
| af923d6 | davelopez | 10 June 2024, 10:29:46 UTC | Fix anonymous user job retrieval logic For anonymous users, if a history_id is provided, do not override with the current session history and instead rely on the history accessibility | 10 June 2024, 10:33:11 UTC |
| c489eb2 | mvdbeek | 10 June 2024, 10:10:53 UTC | Set file_size and total_size to 0 for discovered but purged datasets | 10 June 2024, 10:10:53 UTC |
| a35033d | mvdbeek | 10 June 2024, 09:56:03 UTC | Extend test to make sure disk path remains purged | 10 June 2024, 09:58:46 UTC |
| fc42b61 | mvdbeek | 10 June 2024, 09:55:36 UTC | Fix metadata setting on purged outputs | 10 June 2024, 09:55:36 UTC |
| eb2e318 | mvdbeek | 10 June 2024, 09:52:08 UTC | Elevate external metadata setting to warning This is a tricky one. There could be systematic issues here that an admin would want to fix, but it could also just be the case that a user forced a wrong datatype. Ideally we'd probably tag this as job execution issue ? It's not very different from a job error IMO. | 10 June 2024, 09:53:41 UTC |
| 03eca7c | mvdbeek | 09 June 2024, 06:50:19 UTC | Fix handling of collecting discovered but purged outputs | 10 June 2024, 08:34:15 UTC |
| 435a8cd | mvdbeek | 09 June 2024, 06:48:20 UTC | Fix up test cases Add a sleep so we can delay output purging until command line is templated. If we don't sleep we generate a command line where the output path is just `''`. That needs another fix! | 10 June 2024, 08:34:15 UTC |
| 65e9605 | mvdbeek | 08 June 2024, 18:02:32 UTC | Don't fail _finish_or_resubmit if tool_stdout / tool_stderr not written These are only written if the command actually ran, so we'd fail here for instance if the outputs are deleted before the job had a chance to run. | 08 June 2024, 18:09:18 UTC |
| 8bc3f21 | mvdbeek | 08 June 2024, 14:27:49 UTC | Add tool that produces all types of outputs | 08 June 2024, 14:27:49 UTC |
| c6930ff | mvdbeek | 08 June 2024, 13:53:41 UTC | Merge branch 'release_23.2' into release_24.0 | 08 June 2024, 13:53:41 UTC |
| 18d9bbb | Marius van den Beek | 08 June 2024, 13:43:01 UTC | Merge pull request #18349 from mvdbeek/fix_dce_to_cwl [23.2] Allow DCE as outer input to to_cwl | 08 June 2024, 13:43:01 UTC |
| f38461b | Marius van den Beek | 07 June 2024, 15:45:54 UTC | Merge pull request #18333 from davelopez/24.0_fix_500_for_anonymous_job_listing [24.0] Fix authentication error for anonymous users querying jobs | 07 June 2024, 15:45:54 UTC |
| dff6307 | mvdbeek | 07 June 2024, 15:26:20 UTC | Allow DCE as outer input to to_cwl | 07 June 2024, 15:29:07 UTC |
| 62eadc8 | Nicola Soranzo | 07 June 2024, 15:26:04 UTC | Merge branch 'release_23.2' into release_24.0 | 07 June 2024, 15:26:04 UTC |
| 3817559 | Nicola Soranzo | 07 June 2024, 15:24:43 UTC | Merge branch 'release_23.1' into release_23.2 | 07 June 2024, 15:24:43 UTC |
| 8beef0b | Nicola Soranzo | 07 June 2024, 15:17:18 UTC | Fix ``list_listers`` alias definition to appease mypy | 07 June 2024, 15:17:18 UTC |
| e29cb1d | mvdbeek | 07 June 2024, 14:29:24 UTC | Kill pulsar job if job stopped on galaxy side This seems like it would also help with https://github.com/galaxyproject/pulsar/issues/364. It probably fixes https://github.com/galaxyproject/galaxy/issues/18347. | 07 June 2024, 14:44:46 UTC |
| 8e6e25d | mvdbeek | 07 June 2024, 07:36:43 UTC | Don't push purged dataset contents to object store This in particular needs a lot of new tests. We will also need to actively purge datasets in the model store import code, since users might have purged datasets while the job ran. Again, more tests needed. | 07 June 2024, 13:20:45 UTC |
| a1d41ab | mvdbeek | 07 June 2024, 07:35:58 UTC | Raise appropriate exception if require path parameter is missing | 07 June 2024, 13:20:45 UTC |
| c3a5d61 | mvdbeek | 07 June 2024, 07:35:19 UTC | Don't include purged outputs in from_work_dir outputs | 07 June 2024, 13:20:44 UTC |
| 87124a3 | mvdbeek | 07 June 2024, 07:34:34 UTC | Don't copy from_work_dir outputs to purged path in shell fragment | 07 June 2024, 13:20:44 UTC |
| 6453707 | Matthias Bernt | 07 June 2024, 08:55:04 UTC | make alias work | 07 June 2024, 08:55:04 UTC |
| 089cc1f | M Bernt | 07 June 2024, 07:57:48 UTC | Alias needs to be a classmethod | 07 June 2024, 07:57:48 UTC |
| 0f5bbc0 | M Bernt | 06 June 2024, 17:05:49 UTC | Add alias Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com> | 06 June 2024, 17:05:49 UTC |
| c052463 | M Bernt | 06 June 2024, 16:25:09 UTC | Fix typo | 06 June 2024, 16:25:09 UTC |
| 35a758b | John Davis | 06 June 2024, 14:52:55 UTC | Merge pull request #18338 from mvdbeek/fix_memory_limit_check [24.0] Fix seek in slurm memory check | 06 June 2024, 14:52:55 UTC |
| 7caee0b | davelopez | 06 June 2024, 14:03:35 UTC | Import from typing in preparation for more type annotations Co-authored-by: Nicola Soranzo <nicola.soranzo@earlham.ac.uk> | 06 June 2024, 14:03:35 UTC |
| 497ca2f | davelopez | 06 June 2024, 13:04:30 UTC | Fix mypy: now it catches this error thanks to the ProvidesUserContext type hint | 06 June 2024, 13:04:30 UTC |
| 2e91272 | davelopez | 06 June 2024, 12:59:36 UTC | Fix error for anonymous user listing jobs | 06 June 2024, 12:59:36 UTC |
| 1f9a2fa | Matthias Bernt | 06 June 2024, 10:49:35 UTC | make sure that all Linter subclasses are imported for listing them needed in planemo | 06 June 2024, 10:49:35 UTC |
| cf322eb | Marius van den Beek | 06 June 2024, 10:47:34 UTC | restore line.strip() Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com> | 06 June 2024, 10:47:34 UTC |
| c49a9ef | mvdbeek | 06 June 2024, 09:20:02 UTC | Fix seek in slurm memory check Fixes https://sentry.galaxyproject.org/share/issue/e196a12836fe40da83c5e9e24c4c8329/: ``` UnsupportedOperation: can't do nonzero end-relative seeks File "galaxy/jobs/runners/slurm.py", line 217, in __check_memory_limit f.seek(-2048, os.SEEK_END) ``` which has probably been broken since we moved to python 3. | 06 June 2024, 09:20:05 UTC |
| dc145ed | mvdbeek | 06 June 2024, 08:17:56 UTC | Merge branch 'release_23.2' into release_24.0 | 06 June 2024, 08:17:56 UTC |
| bd4a529 | Marius van den Beek | 06 June 2024, 08:14:07 UTC | Merge pull request #18319 from mvdbeek/skip_history_creation_with_require_login_true [23.2] Skip new history creation if user is anonymous and login is required | 06 June 2024, 08:14:07 UTC |
| 7867b69 | Marius van den Beek | 06 June 2024, 08:12:27 UTC | Merge pull request #18329 from davelopez/24.0_fix_users_api_serialization [24.0] Fix users API serialization when listing users | 06 June 2024, 08:12:27 UTC |
| b208eac | Martin Cech | 05 June 2024, 17:12:08 UTC | Merge pull request #18330 from mvdbeek/downgrade_doi_fetch_error [24.0] Downgrade doi fetch error to debug | 05 June 2024, 17:12:08 UTC |
| 9b60a8c | Martin Cech | 05 June 2024, 17:10:30 UTC | Merge pull request #18332 from mvdbeek/permission_fix [23.1] Make toolshed repo permissions world-readable | 05 June 2024, 17:10:30 UTC |
| 8ee3b90 | mvdbeek | 05 June 2024, 15:59:13 UTC | Make repo permissions world-readable | 05 June 2024, 15:59:13 UTC |
