https://github.com/galaxyproject/galaxy

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Revision Author Date Message Commit Date
d6a76f7 Display record URL for verification 17 May 2024, 08:38:46 UTC
7c60446 Fix error message on access to restricted zenodo records 17 May 2024, 08:18:31 UTC
d638bf4 Merge pull request #18156 from mvdbeek/drop_redundant_error_message [24.0] Drop redundant error message 15 May 2024, 14:45:34 UTC
5280a79 Merge pull request #18155 from mvdbeek/raise_invalid_request_invalid_url [24.0] Raise ``RequestParameterInvalidException`` when url is invalid 15 May 2024, 13:09:00 UTC
34404bd Drop redundant error message There are only two places in the code where we set the job state to error (https://github.com/galaxyproject/galaxy/blob/ad9271cf6a33cb2e22bd7bed72f901e5215309da/lib/galaxy/jobs/handler.py#L722, https://github.com/galaxyproject/galaxy/blob/ad9271cf6a33cb2e22bd7bed72f901e5215309da/lib/galaxy/jobs/handler.py#L733) and both log more specific log messages. 15 May 2024, 12:20:17 UTC
6b06aac Merge pull request #18151 from mvdbeek/delay_tool_form_rendering_until_config_loaded [24.0] Delay tool form rendering until config is loaded 15 May 2024, 12:17:56 UTC
69e7940 Raise RequestParameterInvalidException when url is invalid Fixes https://github.com/galaxyproject/galaxy/issues/18154 15 May 2024, 11:56:48 UTC
7b509b6 Delay tool form rendering until config is loaded The config typically is already loaded once you hit the tool form, so this shouldn't cause a delay, and we already do the same effectively for the current user and current history id. Fixes https://github.com/galaxyproject/galaxy/issues/18139 ``` TypeError: e.config is null at $b (webpack://@galaxyproject/galaxy-client/./src/components/Tool/ToolForm.vue?5639:1:1709) at Vue.prototype._render (webpack://@galaxyproject/galaxy-client/./node_modules/vue/dist/vue.esm.js:2540:28) at updateComponent (webpack://@galaxyproject/galaxy-client/./node_modules/vue/dist/vue.esm.js:2980:27) at Watcher.prototype.get (webpack://@galaxyproject/galaxy-client/./node_modules/vue/dist/vue.esm.js:4164:33) at Watcher.prototype.run (webpack://@galaxyproject/galaxy-client/./node_modules/vue/dist/vue.esm.js:4240:30) ... (3 additional frame(s) were not displayed) ``` 15 May 2024, 08:36:21 UTC
ab56ee1 Merge pull request #18145 from mvdbeek/fix_legacy_page_view [24.0] Fix Legacy HTML page view 15 May 2024, 06:43:15 UTC
91f7bec Use Array.from instead of Object.values Co-authored-by: Dannon <dannon.baker@gmail.com> 15 May 2024, 06:42:50 UTC
6a60cc5 Merge pull request #18143 from dannon/fix-config-access-storagemanager [24.0] Fix config access in StorageManager 14 May 2024, 21:42:17 UTC
3180435 Fix Legacy HTML page view `.children` is a HTMLCollection object which doesn't have a forEach interface. I confirmed this renders a few old style pages successfully. Fixes https://github.com/galaxyproject/galaxy/issues/18144 14 May 2024, 19:02:35 UTC
62e78b7 Merge pull request #18141 from ahmedhamidawan/fix_tool_success_prop [24.0] Fix undefined `reading 'produces_entry_points'` TypeError 14 May 2024, 18:36:50 UTC
81abefe Fix accessing config prior to it potentially being populated. We don't need to gate this behind a loading span, it'll just show the alert when and if it needs to on load. 14 May 2024, 18:02:06 UTC
a20d163 add a `LoadingSpan` if there is no job response 14 May 2024, 17:14:39 UTC
48e1eda [24.0] Fix undefined `reading 'produces_entry_points'` TypeError Fixes https://github.com/galaxyproject/galaxy/issues/18138 14 May 2024, 17:01:13 UTC
e1815c3 Merge pull request #18132 from mvdbeek/fix_data_default_values_not_getting_added_to_history [24.0] Fix data default values not getting added to history 14 May 2024, 13:51:25 UTC
cd47ef6 Merge pull request #18131 from mvdbeek/no_commit_in_delete_pja [24.0] Don't commit in ``DeleteIntermediatesAction`` 14 May 2024, 12:52:30 UTC
25f8d7e Don't flush for inner elements 14 May 2024, 09:29:19 UTC
2950ae6 Fix addition of default collection to history 14 May 2024, 09:09:59 UTC
b388b81 Drop unnecessary commit() call 14 May 2024, 09:05:34 UTC
fa3ef46 Merge pull request #18130 from davelopez/24.0_fix_invenio_record_missing_title [24.0] Fix listing possibly untitled records in Invenio Plugin 13 May 2024, 20:22:50 UTC
1552e06 Merge pull request #18107 from ElectronicBlueberry/fix-upgrade-removes-connections [24.0] Fix Vanishing Connections on Workflow Upgrade 13 May 2024, 19:01:58 UTC
299b607 Fix listing possibly untitled records in Invenio Plugin Ensure the record title is always available and provide a default `No title` otherwise. Even if the title is a required attribute, users can save draft records without title until they are published. 13 May 2024, 15:36:12 UTC
9a93800 move next tick to reset stores function 13 May 2024, 13:20:03 UTC
4129a9b wait for store reset to propagate 13 May 2024, 13:16:40 UTC
43d79fd Merge pull request #18109 from mvdbeek/fix_activity_bar_touch_iphone [24.0] Fix activity bar touch events on iOS devices 13 May 2024, 09:46:05 UTC
2c1208d Merge pull request #18112 from mvdbeek/fix_axios_error_handling [24.0] Fix and unify axios error handling 13 May 2024, 09:45:03 UTC
8ff7e2f Merge pull request #18094 from jdavcs/240_emptycolldownload [24.0] Raise exception if collection elements missing during download 12 May 2024, 19:26:24 UTC
f218a39 Disable download link if collection not populated 10 May 2024, 20:08:44 UTC
375268c Merge pull request #18121 from mvdbeek/dont_report_exception_for_file_not_found [24.0] Don't log exception if cancelled slurm job doesn't have stderr file 10 May 2024, 14:40:01 UTC
880f3ef Fix bug (populated_optimized is property, not method) 10 May 2024, 14:05:55 UTC
0045692 Access `populated_optimized` on DatasetCollection, not instance. Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com> 10 May 2024, 14:05:55 UTC
48771a9 Raise appropriate error; check collection populated state 10 May 2024, 14:05:55 UTC
f70d556 Raise exception if collection elements missing during download 10 May 2024, 14:05:55 UTC
1f2c86d Merge pull request #18123 from mvdbeek/downgrade_moving_file_for_failed_job_to_warning [24.0] Downgrade missing output file in working directory to warning for failed jobs 10 May 2024, 13:23:36 UTC
4fd8ad0 Merge pull request #18122 from mvdbeek/log_exception_instead_of_error [24.0] Include traceback when logging email PJA exception 10 May 2024, 12:15:47 UTC
d5e5f7d Downgrade missing output file in working directory for failed jobs That seems perfectly normal, since jobs might die before they're actually even sent to the DRM, for instance when this happens: ``` parameter 'input1': the previously selected dataset has been deleted. ``` Might even set this to debug ... 10 May 2024, 05:30:37 UTC
c2d6986 Include traceback when logging email PJA exception The exception that is logged currently is: ``` EmailAction PJA Failed, exception: 'NoneType' object has no attribute 'name' ``` The unepxected NoneType is probably job.history, but hard to know. 10 May 2024, 05:09:05 UTC
036d4fa Don't log exception if cancelled slurm job doesn't have stderr file This seems entirely expected and not worth reporting at an ERROR level. Fixes https://sentry.galaxyproject.org/share/issue/c7332e0cf1554c33b2cf56283acfcd1d/: ``` FileNotFoundError [Errno 2] No such file or directory: '/corral4/main/jobs/057/797/57797989/galaxy_57797989.e' ``` 10 May 2024, 05:01:14 UTC
5a88e40 Merge pull request #18118 from mvdbeek/ignore_admin_required_registered_user_required_events [24.0] Ignore AdminRequired and RegisteredUserRequired Sentry events 09 May 2024, 20:30:14 UTC
f2ddaa4 Merge pull request #18119 from mvdbeek/fix_deprecated_argument [24.0] Fix deprecated `deprecated` argument 09 May 2024, 17:27:26 UTC
421c524 Fix deprecated `deprecated` argument I broke that while merging forward https://github.com/galaxyproject/galaxy/pull/18105 09 May 2024, 16:50:54 UTC
4797285 Ignore AdminRequired and RegisteredUserRequired Sentry events 09 May 2024, 16:37:16 UTC
bec08c3 Fix and unify axios error handling Fixes https://sentry.galaxyproject.org/organizations/galaxy/issues/151896/?project=3&query=is%3Aunresolved&referrer=issue-stream&statsPeriod=24h&stream_index=8: ``` TypeError: undefined is not an object (evaluating 'e.response.data') at <anonymous>(webpack://@galaxyproject/galaxy-client/src/components/Login/RegisterForm.vue:201:43) ``` 09 May 2024, 15:24:21 UTC
3c79a2d Merge pull request #18115 from mvdbeek/fix_nested_collection_switching [24.0] Fix switching between nested collection elements 09 May 2024, 13:50:02 UTC
1e4f406 Merge branch 'release_23.2' into release_24.0 09 May 2024, 11:08:39 UTC
2dc7ecc Merge pull request #18105 from mvdbeek/make_purge_query_parameter [23.2] Allow purge query param, deprecate purge body param 09 May 2024, 11:04:41 UTC
ff49010 Fix switching between nested collection elements Fixes https://github.com/galaxyproject/galaxy/issues/18114 09 May 2024, 10:45:56 UTC
40b3151 Update ``test_purge_user`` test to use request parameter 09 May 2024, 10:21:04 UTC
127e461 Use ``Annotated`` and actual default value as recommended in https://fastapi.tiangolo.com/tutorial/query-params-str-validations/#alternative-old-query-as-the-default-value 09 May 2024, 10:16:45 UTC
788c870 Redact private role only once 09 May 2024, 10:14:24 UTC
c994951 Fix activity bar touch events on iphone I'm not sure what the issue is here, the minimal fix is this: ``` diff --git a/client/src/components/Popper/usePopper.ts b/client/src/components/Popper/usePopper.ts index ad18847d8d..183d2e49be 100644 --- a/client/src/components/Popper/usePopper.ts +++ b/client/src/components/Popper/usePopper.ts @@ -190,7 +190,7 @@ export function usePopperjs( on(referenceRef.value!, "mouseout", doMouseout); on(popperRef.value!, "mouseout", doMouseout); on(referenceRef.value!, "mousedown", doMouseout); - on(popperRef.value!, "mousedown", doMouseout); + // on(popperRef.value!, "mousedown", doMouseout); break; } ``` but I think we can probably just rely on events happening on referenceRef. 09 May 2024, 10:12:44 UTC
777b18d Merge pull request #18111 from mvdbeek/oidc_schema_fix_backport [24.0] Backport OIDC schema fix 09 May 2024, 09:40:42 UTC
f7b1f5e Fix for OIDC XML validation error despite valid configuration & updated OIDC backend example file. * Since Galaxy 23.1 using the api_url configuration parameter in the "oidc_backend_config.xml" file for authenticating with Azure will return an error when a user tries to log in. This bug has been documented before and can be seen here: https://github.com/galaxyproject/galaxy/issues/16373 * This problem can be solved by replacing the "api_url" parameter with the "tenant_id" parameter. However, this change of parameter name and expected value has not been documented in either the galaxy docs or in the oidc_backends_config.xml.sample example file since changes to the OIDC code have been made. This pull request attempts to solve that by updating the example file. * In addition, since release_24.0, an XML validation is performed on the oidc_backends_config.xml file which causes the Galaxy process to return an error and exit on startup because it fails to acknowledge "tenant_id" as a legitimate parameter in the XML file. Even though this parameter is required since the OIDC changes in Galaxy 23.1. The changes to the oidc_backends_config.xsd file in this commit can fix that problem. 09 May 2024, 06:58:42 UTC
25825e3 Allow purge query param, deprecate purge body param Fixes https://github.com/galaxyproject/galaxy/issues/18104 08 May 2024, 07:13:03 UTC
b9808b3 Start work on 24.0.3.dev0 07 May 2024, 13:55:40 UTC
439bb62 Create version 24.0.2 07 May 2024, 13:55:37 UTC
03d1f66 Merge pull request #18096 from bernt-matthias/topic/output-filter-fp [24.0] tool linters: output filters should only consider child filter nodes 06 May 2024, 08:15:30 UTC
f57b68c linters: output filters should only consider child filter nodes otherwise these option filters (which we should document) produce false positives https://github.com/galaxyproject/tools-iuc/blob/57fa4dcee2aaa115df4a5b7173a3a8fb889bc5a3/tools/bwa/bwa_macros.xml#L83 04 May 2024, 14:16:35 UTC
9c43535 Merge pull request #18092 from ahmedhamidawan/pinned_histories_on_top_multiview [24.0] History Multiview panel shows pinned histories on top 03 May 2024, 21:16:43 UTC
2866345 remove a couple tooltips that render incorrectly 03 May 2024, 15:40:08 UTC
bb24c23 [24.0] History Multiview panel shows pinned histories on top Fixes https://github.com/galaxyproject/galaxy/issues/18082 03 May 2024, 15:32:31 UTC
dcf8207 Merge pull request #18091 from bernt-matthias/skip-name-restore [24.0] Tool linters: allow to skip by old linter names (by allowing to skip linter modules) 03 May 2024, 14:44:47 UTC
8a15165 Merge pull request #18061 from dannon/citations-list-default-prop-fix [24.0] CitationsList - fix prop spec and config access. 03 May 2024, 14:27:56 UTC
ca6b91d Merge branch 'release_23.2' into release_24.0 03 May 2024, 11:47:13 UTC
a7af352 Merge pull request #18083 from davelopez/23.2_backport_18052 [23.2] Fix history export with missing dataset hids 03 May 2024, 11:44:23 UTC
2bb61ea Merge pull request #18078 from mvdbeek/better_exception_extract_dataset [24.0] Improve error message for ``Extract dataset`` tool 03 May 2024, 11:40:51 UTC
07aa429 linting: restore possibiity to skip old linter function names until 23.2 we had linter functions lint_xyz in linter modules xyz. with 24.0 we splited the functions linter classes. lint contexts allow to skip linters by name (xyz for the old functions now the class name), i.e. we can not skip by the old names anymore. this may break planemo command lines xref https://github.com/galaxyproject/planemo/pull/1441#discussion_r1587995463. here I suggest to add a check for the module name against the names listed in the skip list. this restores the possibility to skip by old linter names and adds the possibility to skip whole linter modules (which might be handy anyway). tried to add some tests that hopefully help to maintain this functionality. 03 May 2024, 11:05:15 UTC
0a784e4 Merge pull request #18041 from dannon/extra-exception-logging [24.0] Adds logging of messageExceptions in the fastapi exception handler. 03 May 2024, 07:20:24 UTC
1bea8a7 Cancel ProcessPoolFuture when aborting job Fixes the occasional timeout error in jobs that follow the `test_abort_fetch_job` test. 02 May 2024, 15:31:26 UTC
419e495 Add test to verify export dataset without hid works 02 May 2024, 11:21:27 UTC
78bf048 Remove unused parameters in get_export_dataset_extra_files_dir_name 02 May 2024, 11:21:16 UTC
ab868b3 Use dataset's encoded_id instead of hid for export filenames 02 May 2024, 11:21:07 UTC
acec4f6 Improve error message for __EXTRACT_DATASETS__ tool Provides a reasonable error message to users, instead of the internal error https://sentry.galaxyproject.org/share/issue/a197159192b64b9db065a762ee5dbbfc/: ``` KeyError: 'Dataset collection has no element_identifier with key 2.' File "galaxy/tools/__init__.py", line 1972, in handle_single_execution rval = self.execute( File "galaxy/tools/__init__.py", line 2069, in execute return self.tool_action.execute( File "galaxy/tools/actions/model_operations.py", line 88, in execute self._produce_outputs( File "galaxy/tools/actions/model_operations.py", line 119, in _produce_outputs tool.produce_outputs( File "galaxy/tools/__init__.py", line 3351, in produce_outputs extracted_element = collection[incoming["which"]["identifier"]] File "galaxy/model/__init__.py", line 6434, in __getitem__ raise KeyError(error_message) ``` Also makes the `identifier` parameter explicitly required (it is now inferred to be optional because text parameters are by default optional if no validator raises an exception upon validating an empty string). That prevents ``` KeyError: 'Dataset collection has no element_identifier with key None.' File "galaxy/tools/__init__.py", line 1972, in handle_single_execution rval = self.execute( File "galaxy/tools/__init__.py", line 2069, in execute return self.tool_action.execute( File "galaxy/tools/actions/model_operations.py", line 88, in execute self._produce_outputs( File "galaxy/tools/actions/model_operations.py", line 119, in _produce_outputs tool.produce_outputs( File "galaxy/tools/__init__.py", line 3351, in produce_outputs extracted_element = collection[incoming["which"]["identifier"]] File "galaxy/model/__init__.py", line 6434, in __getitem__ raise KeyError(error_message) ``` 02 May 2024, 10:40:52 UTC
7408ebb Start work on 24.0.2.dev0 02 May 2024, 10:27:06 UTC
592cf1e Create version 24.0.1 02 May 2024, 10:27:00 UTC
e5c59e1 Fix imports after suggestions from code review. 01 May 2024, 15:01:30 UTC
e2798c9 Apply suggestions from code review Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com> 01 May 2024, 15:01:30 UTC
1c1317b Only log if it's a 500 01 May 2024, 15:01:29 UTC
52a7a14 Downgrade message to log.info to avoid sending redundantly to sentry 01 May 2024, 15:01:29 UTC
28f0fc8 Chage MessageException typing to only accept str as err_msg. 01 May 2024, 15:01:29 UTC
114803b Force MessageExceptions used in workflow modules to have a string error message. 01 May 2024, 15:01:22 UTC
2a083fa Adds logging of messageExceptions in the fastapi exception handler. We're intentionally not doing a full log.exception with the traceback here, though we could. This exception will also be dispatched to Sentry if configured, this just makes logs less opaque when one sees a 500. 01 May 2024, 15:00:05 UTC
49ca43c Merge pull request #18068 from davelopez/24.0_fix_history_update_time_after_bulk_op [24.0] Fix history update time after bulk operation 30 April 2024, 15:02:29 UTC
6ed6843 Merge pull request #18070 from jdavcs/24.0_pendingrollback_rsrepo [24.0] Check database connection to issue a rollback if no connection 30 April 2024, 13:58:46 UTC
f237455 Merge branch 'release_23.2' into release_24.0 30 April 2024, 13:47:24 UTC
51d8743 Update models to include UsesCreateAndUpdateTime mixin For the sake of consistency, those models that have `create_time`, `update_time` and `tags` should share the same interface to update the `update_time` when tags are added or removed. 30 April 2024, 08:43:48 UTC
dbdfcb4 Only call update if it exists 30 April 2024, 08:43:47 UTC
407708f Move update to tag handler 30 April 2024, 08:43:47 UTC
a1fc936 Mark item as updated when undelete had no effect Usually if the dataset was not deleted or if it was purged and un-deleting does not do anything 30 April 2024, 08:43:46 UTC
7329257 Mark the item as updated after altering the associated tags 30 April 2024, 08:43:46 UTC
c6f776d Add tests to ensure history update_time gets updated We need this after a bulk operation to ensure the client will catch-up with the results (even if no-op) so it knows the operation ended. 30 April 2024, 08:43:45 UTC
7d1da18 Merge pull request #18052 from davelopez/24.0_fix_missing_hid_history_export [24.0] Fix history export with missing dataset hids 29 April 2024, 18:29:08 UTC
724e795 Check db connection to issue a rollback if no connection 29 April 2024, 18:18:16 UTC
984c53e Merge pull request #18060 from ElectronicBlueberry/fix-comments-lost-on-import [24.0] Fix comments lost on import 29 April 2024, 13:59:20 UTC
ecef3ef Merge pull request #18053 from SaimMomin12/release_23.2 [23.2] Updated the datatypes name for FASTK tool 29 April 2024, 13:57:47 UTC
97efcea Explicitly specify that outputFormat is a string -- this fixes tsc getting confused below when reassigning 26 April 2024, 15:25:55 UTC
fe8ecb1 Fix usage of citations_export_message when config is not loaded yet 26 April 2024, 13:42:58 UTC
d3c7638 Fix CitationsList default prop. 26 April 2024, 13:17:37 UTC
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