https://github.com/galaxyproject/galaxy

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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
69fb6ce fix comments used before assigned 26 April 2024, 12:41:42 UTC
f9b2a68 use dict instead of relying on list order 26 April 2024, 12:25:50 UTC
061d5a4 copy comments when copying workflow 25 April 2024, 13:29:05 UTC
e0bc13c [23.2] Updated the datatypes name for FASTK tool 25 April 2024, 12:09:06 UTC
b7eda89 Add test to verify export dataset without hid works 25 April 2024, 10:06:28 UTC
6748d0e Remove unused parameters in get_export_dataset_extra_files_dir_name 25 April 2024, 09:24:56 UTC
b20f4a0 Use dataset's encoded_id instead of hid for export filenames 25 April 2024, 09:23:26 UTC
21a57d2 Merge pull request #18046 from mvdbeek/access_logging_middleware [24.0] Add middleware for logging start and end of request 24 April 2024, 16:54:21 UTC
ab08738 Update setup-miniconda@v3 action 24 April 2024, 15:38:58 UTC
64be33e Update k8s-version 24 April 2024, 15:11:53 UTC
f26e90f Log start and end of request Configurable via `use_access_logging_middleware`. Looks like this: ``` galaxy.webapps.base.api DEBUG 2024-04-23 17:14:43,776 [pN:main,p:73562,tN:MainThread] GET /history/current_history_json?since=2024-04-22T17:24:13.936493 f8c75e2c-30eb-4fcb-9b96-25bd4b2df435 galaxy.webapps.base.api DEBUG 2024-04-23 17:14:48,719 [pN:main,p:73562,tN:MainThread] GET /history/current_history_json?since=2024-04-22T17:24:13.936493 f8c75e2c-30eb-4fcb-9b96-25bd4b2df435 200 galaxy.webapps.base.api DEBUG 2024-04-23 17:14:51,767 [pN:main,p:73562,tN:MainThread] GET /history/current_history_json?since=2024-04-22T17:24:13.936493 2fe6094c-67bb-4144-a19f-cbb4a1b18fb4 galaxy.webapps.base.api DEBUG 2024-04-23 17:14:51,786 [pN:main,p:73562,tN:MainThread] GET /history/current_history_json?since=2024-04-22T17:24:13.936493 2fe6094c-67bb-4144-a19f-cbb4a1b18fb4 200 galaxy.webapps.base.api DEBUG 2024-04-23 17:14:53,139 [pN:main,p:73562,tN:MainThread] GET /api/entry_points?running=true 763693e9-4fd3-4a97-a100-a3c259b4b4c8 ``` 24 April 2024, 15:08:06 UTC
625cd8a Merge pull request #18033 from martenson/storage-details [24.0] clarify the object store relocate functionality 23 April 2024, 15:50:16 UTC
4582704 Merge pull request #18044 from mvdbeek/ensure_offset_and_limit_not_negative [24.0] Ensure that offset and limit are never negative 23 April 2024, 15:49:04 UTC
b97825b Merge pull request #18036 from mvdbeek/implicit_conversion_no_hid_fix [24.0] Fix History Dataset Association creation so that hid is always set 23 April 2024, 13:32:11 UTC
5545dcd Adjust and enhance job filtering test 23 April 2024, 12:00:13 UTC
4bc09c0 Ensure that offset and limit are never negative And set minimum limit consistently to 1 ... 0 doesn't seem to have much utility but would also be an option. Fixes part of https://github.com/galaxyproject/galaxy/issues/18043. 23 April 2024, 09:56:36 UTC
7722cf0 Merge pull request #18040 from mvdbeek/show_error_on_wrong_quota_source_fitler [24.0] Change wrong quota_source value from KeyError to ValueError 22 April 2024, 19:13:57 UTC
857a14e Change wrong quota_source value from KeyError to ValueError Which is caught in https://github.com/galaxyproject/galaxy/blob/44782a44c14885df2d9d1bcb91698245bfb3aed8/lib/galaxy/managers/base.py#L1121-L1124 Fixes https://sentry.galaxyproject.org/share/issue/16a3342631224d8292ef792298175dea/: ``` KeyError: "Could not find key nul in object store keys [None, 'scratch']" File "starlette/applications.py", line 123, in __call__ await self.middleware_stack(scope, receive, send) File "starlette/middleware/errors.py", line 186, in __call__ raise exc File "starlette/middleware/errors.py", line 164, in __call__ await self.app(scope, receive, _send) File "starlette_context/middleware/raw_middleware.py", line 92, in __call__ await self.app(scope, receive, send_wrapper) File "starlette/middleware/base.py", line 189, in __call__ with collapse_excgroups(): File "contextlib.py", line 155, in __exit__ self.gen.throw(typ, value, traceback) File "starlette/_utils.py", line 93, in collapse_excgroups raise exc File "starlette/middleware/base.py", line 191, in __call__ response = await self.dispatch_func(request, call_next) File "galaxy/webapps/galaxy/fast_app.py", line 108, in add_x_frame_options response = await call_next(request) File "starlette/middleware/base.py", line 165, in call_next raise app_exc File "starlette/middleware/base.py", line 151, in coro await self.app(scope, receive_or_disconnect, send_no_error) File "starlette/middleware/exceptions.py", line 62, in __call__ await wrap_app_handling_exceptions(self.app, conn)(scope, receive, send) File "starlette/_exception_handler.py", line 64, in wrapped_app raise exc File "starlette/_exception_handler.py", line 53, in wrapped_app await app(scope, receive, sender) File "starlette/routing.py", line 758, in __call__ await self.middleware_stack(scope, receive, send) File "starlette/routing.py", line 778, in app await route.handle(scope, receive, send) File "starlette/routing.py", line 299, in handle await self.app(scope, receive, send) File "starlette/routing.py", line 79, in app await wrap_app_handling_exceptions(app, request)(scope, receive, send) File "starlette/_exception_handler.py", line 64, in wrapped_app raise exc File "starlette/_exception_handler.py", line 53, in wrapped_app await app(scope, receive, sender) File "starlette/routing.py", line 74, in app response = await func(request) File "fastapi/routing.py", line 278, in app raw_response = await run_endpoint_function( File "fastapi/routing.py", line 193, in run_endpoint_function return await run_in_threadpool(dependant.call, **values) File "starlette/concurrency.py", line 42, in run_in_threadpool return await anyio.to_thread.run_sync(func, *args) File "anyio/to_thread.py", line 56, in run_sync return await get_async_backend().run_sync_in_worker_thread( File "anyio/_backends/_asyncio.py", line 2144, in run_sync_in_worker_thread return await future File "anyio/_backends/_asyncio.py", line 851, in run result = context.run(func, *args) File "galaxy/webapps/galaxy/api/history_contents.py", line 465, in index items = self.service.index( File "galaxy/webapps/galaxy/services/history_contents.py", line 312, in index return self.__index_v2(trans, history_id, params, serialization_params, filter_query_params, accept) File "galaxy/webapps/galaxy/services/history_contents.py", line 972, in __index_v2 filters = self.history_contents_filters.parse_query_filters_with_relations(filter_query_params, history_id) File "galaxy/managers/history_contents.py", line 525, in parse_query_filters_with_relations return super().parse_query_filters(query_filters) File "galaxy/managers/base.py", line 1087, in parse_query_filters return self.parse_filters(filter_params) File "galaxy/managers/base.py", line 1096, in parse_filters filter_ = self.parse_filter(attr, op, val) File "galaxy/managers/base.py", line 1116, in parse_filter orm_filter = self._parse_orm_filter(attr, op, val) File "galaxy/managers/history_contents.py", line 601, in _parse_orm_filter if (column_filter := get_filter(attr, op, val)) is not None: File "galaxy/managers/history_contents.py", line 595, in get_filter raise KeyError(f"Could not find key {val} in object store keys {list(ids.keys())}") ``` 22 April 2024, 17:44:31 UTC
b8c39a5 change language to relocate 22 April 2024, 16:58:02 UTC
121f27e Default HID to -1 if for whatever reason we didn't record a HID 22 April 2024, 15:20:42 UTC
44782a4 Merge pull request #18023 from mvdbeek/fix_non_ready_collection_submission [24.0] Raise appropriate exception if user forces a collection that is not populated with elements as input 22 April 2024, 14:13:36 UTC
c2140bd Avoid flush in set_meta by using MetadataFile.uuid 22 April 2024, 11:32:09 UTC
badbd3a Fix premature flush in hda_manager.copy 22 April 2024, 09:52:19 UTC
a56f642 Drop unused method 22 April 2024, 09:52:19 UTC
e1a45a2 Drop unused copy_from_ldda method 22 April 2024, 09:52:19 UTC
d889002 Commit only after copying library item to history 22 April 2024, 09:52:19 UTC
5aecc08 Fall back to populated method if collection not committed yet 22 April 2024, 09:52:19 UTC
bf34997 Fix unitialize typo 22 April 2024, 09:52:19 UTC
5648478 Adjust schema for collection elements of collections that aren't populated 22 April 2024, 09:52:18 UTC
e3aba2d Relax requirement for DCEs of collections that are not populated 21 April 2024, 20:51:00 UTC
1b1094b Set (copied) output hid before queuing job Otherwise we may end up with a history item that either temporarily or permanently lacks a hid. This could currently be encountered via implicit conversion that set `visible=False` in the when calling `datatype.convert_dataset`. 21 April 2024, 19:10:51 UTC
b1333e0 Also perform strict checks for new database objects I think that's the missing piece to find all the instances where we might still be committing HDAs without HIDs, and I think we might have a similar bug for DatasetCollectionElements. 21 April 2024, 19:10:51 UTC
a671090 Fix test_map_over_empty_collection test It was using the wrong id type, and since we don't prepopulate the collection we need to wait until discovery happens. It actually nicely illustrates the bug. 21 April 2024, 07:58:22 UTC
cff711f Raise appropriate exception if user forces non-ready collection as input 21 April 2024, 07:58:21 UTC
8f4968f Merge pull request #18027 from davelopez/24.0_fix_files_sources_error_handling [24.0] Fix remote files sources error handling 21 April 2024, 07:57:19 UTC
03111fa move the link from heading to the body and change to a button - add minor text adjustments - close the modal when clicking on the currently selected storage 19 April 2024, 20:23:10 UTC
97371f1 add relocation docs to the object store samples 19 April 2024, 19:37:25 UTC
9d715ce Merge pull request #18029 from mvdbeek/colabfold_backport [24.0] Backport colabfold tar file datatype 19 April 2024, 16:28:45 UTC
47f2ca6 add colabfold tar file datatype 19 April 2024, 16:26:23 UTC
0d1c41f Prefer AuthenticationRequired for credential issues 19 April 2024, 14:36:51 UTC
f98f6f7 Merge pull request #18025 from jdavcs/24.0_tag_regex [24.0] Fix tag regex pattern 19 April 2024, 14:35:09 UTC
ac8338f Update test/unit/schema/test_schema.py Co-authored-by: Dannon <dannon.baker@gmail.com> 19 April 2024, 13:47:38 UTC
90bb4c9 Update test/unit/schema/test_schema.py Co-authored-by: Dannon <dannon.baker@gmail.com> 19 April 2024, 13:47:31 UTC
b798109 Update lib/galaxy/model/tags.py Co-authored-by: Dannon <dannon.baker@gmail.com> 19 April 2024, 13:47:18 UTC
b5a93f0 Update lib/galaxy/model/tags.py Co-authored-by: Dannon <dannon.baker@gmail.com> 19 April 2024, 13:47:11 UTC
645ff00 Update lib/galaxy/model/tags.py Co-authored-by: Dannon <dannon.baker@gmail.com> 19 April 2024, 13:47:00 UTC
b32480c Update lib/galaxy/model/tags.py Co-authored-by: Dannon <dannon.baker@gmail.com> 19 April 2024, 13:46:48 UTC
53f5b5f Use less cryptic error when unexpected error 19 April 2024, 11:44:08 UTC
91bf0c6 Handle Dropbox special case 19 April 2024, 11:32:24 UTC
0bbb982 Handle errors creating new entries more gracefully 19 April 2024, 11:31:30 UTC
e765e66 Handle PyFilesystem2 errors more gracefully 19 April 2024, 11:29:02 UTC
9c26321 Merge pull request #18026 from mvdbeek/fix_test_get_tags_histories_content [24.0] Fix ``test_get_tags_histories_content`` test 19 April 2024, 09:57:18 UTC
e32b9aa Fix test_get_tags_histories_content test The calling code expects that this creates a dataset, but instead this used to create dataset collection. 19 April 2024, 08:22:45 UTC
ee64fc4 Update client valid tag regex 19 April 2024, 02:40:18 UTC
c31bccf Fix regex pattern 19 April 2024, 02:40:13 UTC
7ec1311 Add unit test to verify spllitting tag string into name/value 19 April 2024, 02:40:08 UTC
972f918 Add unit test (failing) for tag string regex 19 April 2024, 02:40:04 UTC
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