| e77b17d | mvdbeek | 23 October 2023, 19:35:24 UTC | Create version 23.1.1 | 23 October 2023, 19:35:24 UTC |
| 5aeff97 | mvdbeek | 23 October 2023, 16:01:52 UTC | Merge branch 'release_23.0' into release_23.1 # Conflicts: # lib/galaxy/version.py # packages/app/HISTORY.rst # packages/app/setup.cfg # packages/auth/HISTORY.rst # packages/auth/setup.cfg # packages/config/HISTORY.rst # packages/config/setup.cfg # packages/data/HISTORY.rst # packages/data/setup.cfg # packages/files/HISTORY.rst # packages/files/setup.cfg # packages/job_execution/HISTORY.rst # packages/job_execution/setup.cfg # packages/job_metrics/HISTORY.rst # packages/job_metrics/setup.cfg # packages/navigation/HISTORY.rst # packages/navigation/setup.cfg # packages/objectstore/HISTORY.rst # packages/objectstore/setup.cfg # packages/selenium/HISTORY.rst # packages/selenium/setup.cfg # packages/test_api/HISTORY.rst # packages/test_api/setup.cfg # packages/test_base/HISTORY.rst # packages/test_base/setup.cfg # packages/test_driver/HISTORY.rst # packages/test_driver/setup.cfg # packages/tool_util/HISTORY.rst # packages/tool_util/setup.cfg # packages/tours/HISTORY.rst # packages/tours/setup.cfg # packages/util/HISTORY.rst # packages/util/setup.cfg # packages/web_apps/HISTORY.rst # packages/web_apps/setup.cfg # packages/web_framework/HISTORY.rst # packages/web_framework/setup.cfg # packages/web_stack/HISTORY.rst # packages/web_stack/setup.cfg | 23 October 2023, 16:01:52 UTC |
| e88541e | mvdbeek | 23 October 2023, 16:01:40 UTC | Start work on 23.0.7.dev0 | 23 October 2023, 16:01:40 UTC |
| bce8be2 | mvdbeek | 23 October 2023, 16:01:36 UTC | Create version 23.0.6 | 23 October 2023, 16:01:36 UTC |
| 41e06d0 | Marius van den Beek | 23 October 2023, 15:27:46 UTC | Merge pull request #16879 from davelopez/23.1_fix_delete_collection [23.1] Fix delete collection + elements | 23 October 2023, 15:27:46 UTC |
| 905a85c | davelopez | 23 October 2023, 14:02:46 UTC | Remove unnecessary update if the element was already deleted in bulk | 23 October 2023, 14:02:46 UTC |
| b7eea2f | David López | 23 October 2023, 13:48:18 UTC | Fix typo Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com> | 23 October 2023, 13:48:18 UTC |
| 672518c | davelopez | 20 October 2023, 08:35:48 UTC | Unify bulk delete/purge behavior on collections Use the same default behavior as "bulk purge" and mark also elements as deleted. | 20 October 2023, 08:37:18 UTC |
| 4656698 | davelopez | 19 October 2023, 15:48:07 UTC | Add asserts on history contents in tests | 19 October 2023, 15:48:07 UTC |
| 74cbf83 | davelopez | 19 October 2023, 12:23:25 UTC | Refactor API tests | 19 October 2023, 12:23:25 UTC |
| 1ea7ee0 | davelopez | 19 October 2023, 12:23:07 UTC | Exclude from usage DCEs contained in deleted collections | 19 October 2023, 12:23:07 UTC |
| 3cfad7e | davelopez | 19 October 2023, 11:43:00 UTC | Add API tests for deleting collections in bulk | 19 October 2023, 11:43:00 UTC |
| 5173906 | davelopez | 19 October 2023, 11:42:29 UTC | Delete orphaned and hidden datasets in collection When deleting the collection via history bulk delete | 19 October 2023, 11:42:29 UTC |
| e4c4677 | Björn Grüning | 18 October 2023, 20:35:42 UTC | Merge pull request #16880 from mvdbeek/fix_nested_collection_query [23.1] Fix join condition for nested collection query | 18 October 2023, 20:35:42 UTC |
| e617099 | mvdbeek | 18 October 2023, 16:16:08 UTC | Fix join condition for nested collection query For a list:list:list collection this brings the query from 12.5 seconds (after the database cache is already hot ...) to 11 ms | 18 October 2023, 16:17:56 UTC |
| cdbbbbe | Marius van den Beek | 18 October 2023, 15:23:08 UTC | Merge pull request #16877 from mvdbeek/fix_tag_ownership_check [23.1] Fix tag ownership check | 18 October 2023, 15:23:08 UTC |
| b116321 | Marius van den Beek | 18 October 2023, 15:20:06 UTC | Merge pull request #16875 from mvdbeek/eliminate_more_flushes [23.1] Remove more flushes in database operation tools | 18 October 2023, 15:20:06 UTC |
| eed12c4 | davelopez | 18 October 2023, 15:03:59 UTC | Display menu when deleting a collection - Allow to delete only the top collection or also the items contained | 18 October 2023, 15:03:59 UTC |
| f979572 | mvdbeek | 18 October 2023, 09:30:58 UTC | Remove more flushes in database operation tools We sort of rely on the dataset not being flushed yet in order to bypass the security check for tagging post job actions, so this fixes: ``` ItemOwnershipException: User does not own item. File "galaxy/workflow/run.py", line 233, in invoke incomplete_or_none = self._invoke_step(workflow_invocation_step) File "galaxy/workflow/run.py", line 309, in _invoke_step incomplete_or_none = invocation_step.workflow_step.module.execute( File "galaxy/workflow/modules.py", line 2274, in execute workflow_invocation_uuid=invocation.uuid.hex, File "galaxy/tools/execute.py", line 169, in execute execute_single_job(execution_slice, completed_jobs[i], skip=skip) File "galaxy/tools/execute.py", line 116, in execute_single_job job, result = tool.handle_single_execution( File "galaxy/tools/__init__.py", line 1957, in handle_single_execution execution_cache=execution_cache, File "galaxy/tools/__init__.py", line 1937, in handle_single_execution execution_slice, File "galaxy/tools/__init__.py", line 2034, in execute args[key] = model.User.expand_user_properties(trans.user, param.value) File "galaxy/tools/actions/model_operations.py", line 102, in execute job_callback(job) File "galaxy/workflow/modules.py", line 2284, in <lambda> complete = True File "galaxy/workflow/modules.py", line 2351, in _handle_post_job_actions self.trans.sa_session.add(pjaa) File "galaxy/job_execution/actions/post.py", line 575, in execute ActionBox.actions[pja.action_type].execute( File "galaxy/job_execution/actions/post.py", line 473, in execute cls._execute(tag_handler, job.user, dataset_assoc.dataset, tags) File "galaxy/job_execution/actions/post.py", line 481, in _execute tag_handler.add_tags_from_list(user, output, tags, flush=False) File "galaxy/model/tags.py", line 74, in add_tags_from_list return self.set_tags_from_list(user, item, new_tags_set, flush=flush) File "galaxy/model/tags.py", line 92, in set_tags_from_list self.delete_item_tags(user, item) File "galaxy/model/tags.py", line 165, in delete_item_tags self._ensure_user_owns_item(user, item) File "galaxy/model/tags.py", line 193, in _ensure_user_owns_item raise ItemOwnershipException("User does not own item.") ``` (once again). From https://sentry.galaxyproject.org/share/issue/5b44d1ec20094a2ebe8331b1ef6e58a8/ | 18 October 2023, 11:47:25 UTC |
| cd9d132 | mvdbeek | 30 September 2023, 06:28:03 UTC | Fix tag ownership check I think that in the tool evaluation context we don't actually need the cached_id performance tweak: we batch flushes now on map over creation ... which in fact breaks the assumption that we're setting the user id here. | 18 October 2023, 11:42:39 UTC |
| 53f372a | mvdbeek | 30 September 2023, 06:54:02 UTC | Add test for PJA that tags output collection ... from database operation tool. | 18 October 2023, 11:42:39 UTC |
| 634d04f | Marius van den Beek | 17 October 2023, 17:06:13 UTC | Merge pull request #16861 from mvdbeek/label_only_markdown_report [23.1] Allow referring to steps by label only in markdown editor | 17 October 2023, 17:06:13 UTC |
| bf1df29 | John Davis | 17 October 2023, 16:42:11 UTC | Merge pull request #16869 from mvdbeek/fix_step_copy [23.1] Fix workflow import losing tool_version | 17 October 2023, 16:42:11 UTC |
| fef87ab | Nicola Soranzo | 17 October 2023, 15:23:16 UTC | Merge pull request #16865 from mvdbeek/add_filter1_bump_to_workflow_safe_update_versions [23.1] Fix safe update version handling in run form | 17 October 2023, 15:23:16 UTC |
| 94a12ee | mvdbeek | 17 October 2023, 14:32:58 UTC | Copy ``tool_version`` on workflow steps when copying workflows This is a problem when importing a shared workflow. | 17 October 2023, 15:01:28 UTC |
| 13b0696 | Marius van den Beek | 17 October 2023, 11:55:16 UTC | Drop unnecessary checks Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com> | 17 October 2023, 12:34:33 UTC |
| a2b7c86 | mvdbeek | 17 October 2023, 09:50:09 UTC | Skip run form warning if we know upgrade is safe Should fix warning for built-in tools in run form. Also makes the check more strict by checking that the version requested in the module is actually in the safe range. | 17 October 2023, 12:34:33 UTC |
| 2e502a7 | mvdbeek | 17 October 2023, 12:33:23 UTC | Add test for version handling in run form | 17 October 2023, 12:34:33 UTC |
| 5fb9ac4 | mvdbeek | 17 October 2023, 09:15:43 UTC | Fail gracefully if step reference not found | 17 October 2023, 09:15:43 UTC |
| 6d8cbee | mvdbeek | 17 October 2023, 08:38:25 UTC | Allow referring to steps by label only in markdown editor | 17 October 2023, 08:38:25 UTC |
| d01a21a | Marius van den Beek | 16 October 2023, 13:53:31 UTC | Merge pull request #16855 from mvdbeek/file_size_debug [23.1] Fix and prevent persisting null file_size | 16 October 2023, 13:53:31 UTC |
| 7e41cce | mvdbeek | 15 October 2023, 21:25:24 UTC | Set size for null datasets | 15 October 2023, 21:25:24 UTC |
| 23d938f | mvdbeek | 15 October 2023, 20:10:44 UTC | Fix dataset collection unit tests | 15 October 2023, 20:10:44 UTC |
| 6d68b78 | mvdbeek | 15 October 2023, 20:06:47 UTC | Set dataset size also when failing jobs | 15 October 2023, 20:06:47 UTC |
| 1003351 | mvdbeek | 15 October 2023, 14:50:27 UTC | Skip unnecessary flush when applying permissions | 15 October 2023, 20:00:52 UTC |
| 7a06271 | mvdbeek | 15 October 2023, 12:37:38 UTC | Fix and prevent persisting null file_size | 15 October 2023, 20:00:50 UTC |
| c62b2d9 | mvdbeek | 15 October 2023, 11:00:42 UTC | Raise exception if persisting HDA will null file_size | 15 October 2023, 20:00:25 UTC |
| 8082c2d | John Chilton | 13 October 2023, 14:40:10 UTC | Merge pull request #16844 from afgane/23.1_img_fix Specify uid for the k8s image | 13 October 2023, 14:40:10 UTC |
| 6659840 | Marius van den Beek | 13 October 2023, 14:03:24 UTC | Merge pull request #16850 from mvdbeek/limit_watch_events [23.1] Exclude on_opened and on_closed from watcher events | 13 October 2023, 14:03:24 UTC |
| e9bc593 | mvdbeek | 13 October 2023, 10:13:42 UTC | Exclude on_opened and on_closed from watcher events We're not interested in these. `on_opened` in particular was introduced in https://github.com/gorakhargosh/watchdog/pull/941 and then partially reverted in https://github.com/gorakhargosh/watchdog/commit/25a2d1fec55fc32f97055ba827c8ce7b959acb34, but that doesn't work for us. Should fix https://github.com/galaxyproject/galaxy/issues/16840 | 13 October 2023, 10:18:38 UTC |
| 5ebd1e7 | Enis Afgan | 12 October 2023, 21:16:43 UTC | Specify uid for the k8s image | 12 October 2023, 21:16:43 UTC |
| 4a397b1 | Dannon | 12 October 2023, 19:25:11 UTC | Merge pull request #16836 from mvdbeek/fix_up_tool_version_handling [23.1] Fix up local tool version handling | 12 October 2023, 19:25:11 UTC |
| b34e378 | Nicola Soranzo | 12 October 2023, 09:52:59 UTC | Merge branch 'release_23.0' into release_23.1 | 12 October 2023, 09:52:59 UTC |
| 2b15183 | mvdbeek | 12 October 2023, 09:43:07 UTC | Extend selenium test for downgrading a tool | 12 October 2023, 09:43:07 UTC |
| 519066a | mvdbeek | 12 October 2023, 04:57:30 UTC | Fix tool version switching for local tools They don't have the version in the tool id, so we need to explicitly include tool_version. | 12 October 2023, 07:58:51 UTC |
| 5f1471e | mvdbeek | 12 October 2023, 04:55:02 UTC | Get correct tool version in workflow preview And remove the step.type is None condition, which I don't think can happen and even if it can, would have already failed at the module inection in module_factory.from_workflow_step. | 12 October 2023, 04:55:10 UTC |
| b54e7a7 | Marius van den Beek | 11 October 2023, 14:29:36 UTC | Merge pull request #16831 from nsoranzo/release_23.0_conda_23.9 [23.0] Fix create/install commands for conda 23.9.0 | 11 October 2023, 14:29:36 UTC |
| c38dd5f | Dannon | 11 October 2023, 13:22:57 UTC | Merge pull request #16829 from mvdbeek/fix_workflow_displau [23.1] Fix workflow preview display if tool state does not contain all parameter values | 11 October 2023, 13:22:57 UTC |
| 4f4526d | John Davis | 11 October 2023, 13:04:28 UTC | Merge pull request #16818 from davelopez/23.1_increase_external_user_id_db_size [23.1] Increase `CustosAuthnzToken.external_user_id` column size | 11 October 2023, 13:04:28 UTC |
| 7fc4142 | Nicola Soranzo | 11 October 2023, 12:08:59 UTC | Fix create/install commands for conda 23.9.0 The `--experimental-solver` option was removed. | 11 October 2023, 12:09:12 UTC |
| d989ec3 | mvdbeek | 11 October 2023, 00:37:56 UTC | Fix display of tools where parameter values have been added | 11 October 2023, 00:40:19 UTC |
| 9735633 | davelopez | 08 October 2023, 10:54:07 UTC | Update db revision tags for 23.1 | 10 October 2023, 14:50:39 UTC |
| 239fd39 | davelopez | 08 October 2023, 10:43:22 UTC | Add DB migration to increase external_user_id length | 10 October 2023, 14:50:28 UTC |
| af7d63b | davelopez | 08 October 2023, 10:07:05 UTC | Increase length of CustosAuthnzToken.external_user_id | 10 October 2023, 14:46:54 UTC |
| fba2605 | Marius van den Beek | 09 October 2023, 19:08:08 UTC | Merge pull request #16822 from martenson/231-tostring [23.1] backport of pysam tostring | 09 October 2023, 19:08:08 UTC |
| f3fdd8b | Martin Cech | 09 October 2023, 18:54:24 UTC | Merge pull request #16820 from martenson/231-purge-unampass [23.1] move the email and username redacting from the role loop | 09 October 2023, 18:54:24 UTC |
| f15c4c4 | Martin Cech | 07 October 2023, 19:49:17 UTC | fix the call arguments https://pysam.readthedocs.io/en/v0.21.0/api.html?highlight=AlignedSegment#pysam.AlignedSegment.tostring | 09 October 2023, 18:28:15 UTC |
| 14fc85c | Marius van den Beek | 06 October 2023, 18:06:56 UTC | Update outdated comment Co-authored-by: Dannon <dannon.baker@gmail.com> | 09 October 2023, 18:28:03 UTC |
| a25f98d | mvdbeek | 06 October 2023, 17:57:39 UTC | Use AlignedSegment.to_string | 09 October 2023, 18:27:52 UTC |
| c83d549 | Martin Cech | 09 October 2023, 17:50:50 UTC | Merge pull request #16821 from mvdbeek/fix_parameter_summary_for_section [23.1] Fix parameter display in job info page for tools with sections | 09 October 2023, 17:50:50 UTC |
| 455d9e6 | Martin Cech | 06 October 2023, 18:44:00 UTC | remove the email and username redacting frmo the role loop I guess this worked because user is guaranteed to have a role? | 09 October 2023, 16:09:43 UTC |
| 4df4901 | mvdbeek | 09 October 2023, 16:07:34 UTC | Fix parameter display for tools with sections Fixes: ``` Message Uncaught exception in exposed API method: Stack Trace(most recent call first) TypeError: Object of type method is not JSON serializable File "galaxy/util/json.py", line 74, in safe_dumps dumped = json.dumps(obj, allow_nan=False, **kwargs) File "__init__.py", line 234, in dumps return cls( File "json/encoder.py", line 199, in encode chunks = self.iterencode(o, _one_shot=True) File "json/encoder.py", line 257, in iterencode return _iterencode(o, 0) File "json/encoder.py", line 179, in default raise TypeError(f'Object of type {o.__class__.__name__} ' TypeError: Object of type method is not JSON serializable File "galaxy/web/framework/decorators.py", line 341, in decorator rval = format_return_as_json(rval, jsonp_callback, pretty=trans.debug) File "galaxy/web/framework/decorators.py", line 378, in format_return_as_json json = safe_dumps(rval, **dumps_kwargs) File "galaxy/util/json.py", line 77, in safe_dumps dumped = json.dumps(obj, allow_nan=False, **kwargs) File "__init__.py", line 234, in dumps return cls( File "json/encoder.py", line 199, in encode chunks = self.iterencode(o, _one_shot=True) File "json/encoder.py", line 257, in iterencode return _iterencode(o, 0) File "json/encoder.py", line 179, in default raise TypeError(f'Object of type {o.__class__.__name__} ' ``` from https://sentry.galaxyproject.org/share/issue/665556bc240f4a04978f7c81c2be629c/ | 09 October 2023, 16:07:41 UTC |
| 7b978a0 | Martin Cech | 09 October 2023, 14:02:12 UTC | Merge pull request #16809 from mvdbeek/versionless_tool_id_in_tool_panel [23.1] Fix tool panel views for versionless tool ids | 09 October 2023, 14:02:12 UTC |
| d2e1b56 | Martin Cech | 09 October 2023, 14:01:18 UTC | Merge pull request #16808 from martenson/tooltips-outofway-231 [23.1] move history and tool panel tooltips out of the way | 09 October 2023, 14:01:18 UTC |
| 4490331 | mvdbeek | 08 October 2023, 13:35:44 UTC | Avoid AttributeError when accessing toolbox Fixes: ``` Traceback (most recent call last): File "/cvmfs/test.galaxyproject.org/galaxy/lib/galaxy/webapps/galaxy/buildapp.py", line 59, in app_pair app = galaxy.app.UniverseApplication(global_conf=global_conf, is_webapp=True, **kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/cvmfs/test.galaxyproject.org/galaxy/lib/galaxy/app.py", line 691, in __init__ self._configure_toolbox() File "/cvmfs/test.galaxyproject.org/galaxy/lib/galaxy/app.py", line 309, in _configure_toolbox self._toolbox = tools.ToolBox(self.config.tool_configs, self.config.tool_path, self) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/cvmfs/test.galaxyproject.org/galaxy/lib/galaxy/tools/__init__.py", line 420, in __init__ super().__init__( File "/cvmfs/test.galaxyproject.org/galaxy/lib/galaxy/tool_util/toolbox/base.py", line 237, in __init__ self._load_tool_panel_views() File "/cvmfs/test.galaxyproject.org/galaxy/lib/galaxy/tool_util/toolbox/base.py", line 600, in _load_tool_panel_views self._tool_panel_view_rendered[key] = view.apply_view(self._integrated_tool_panel, registry) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/cvmfs/test.galaxyproject.org/galaxy/lib/galaxy/tool_util/toolbox/views/static.py", line 195, in apply_view return definition_with_items_to_panel(root_defintion, items=root_items) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/cvmfs/test.galaxyproject.org/galaxy/lib/galaxy/tool_util/toolbox/views/static.py", line 87, in definition_with_items_to_panel panel = definition_with_items_to_panel(section_def, allow_sections=False) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/cvmfs/test.galaxyproject.org/galaxy/lib/galaxy/tool_util/toolbox/views/static.py", line 142, in definition_with_items_to_panel tool = toolbox_registry.get_tool(tool_id) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/cvmfs/test.galaxyproject.org/galaxy/lib/galaxy/tool_util/toolbox/base.py", line 107, in get_tool return self.__toolbox.get_tool(tool_id) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/cvmfs/test.galaxyproject.org/galaxy/lib/galaxy/tool_util/toolbox/base.py", line 719, in get_tool tool_lineage = self._lineage_map.get(tool_id) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/cvmfs/test.galaxyproject.org/galaxy/lib/galaxy/tool_util/toolbox/lineages/factory.py", line 47, in get tool = self.app.toolbox._tools_by_id.get(tool_id) ^^^^^^^^^^^^^^^^ File "/cvmfs/test.galaxyproject.org/galaxy/lib/galaxy/app.py", line 351, in toolbox return self._toolbox ^^^^^^^^^^^^^ AttributeError: 'UniverseApplication' object has no attribute '_toolbox' ``` when attempting to apply a panel view that contains tools that aren't installed on a server. | 08 October 2023, 13:37:07 UTC |
| 612f1d6 | mvdbeek | 07 October 2023, 20:06:22 UTC | Fix tool panel views for versionless tool ids | 07 October 2023, 20:06:22 UTC |
| df8642f | Björn Grüning | 07 October 2023, 19:32:55 UTC | Merge pull request #16793 from ahmedhamidawan/copy_history_mult_times [23.1] Disable button in `CopyModal` for histories when copying history | 07 October 2023, 19:32:55 UTC |
| 911460d | Martin Cech | 07 October 2023, 18:28:09 UTC | move history and tool panel tooltips out of the way also make them noninteractive so they don't stay in way | 07 October 2023, 18:31:15 UTC |
| 11110c2 | Marius van den Beek | 06 October 2023, 19:07:22 UTC | Merge pull request #16800 from jmchilton/fix_old_ids [23.1] Fix short ids in tool panel views. | 06 October 2023, 19:07:22 UTC |
| 3773a56 | John Chilton | 07 September 2023, 19:34:54 UTC | Fix short ids in tool panel views. Use new data structure to optimize get_tool(exact=False) as well - should speed up certain kinds of toolbox related operations. | 06 October 2023, 16:38:06 UTC |
| 35f77af | Ahmed Awan | 05 October 2023, 18:57:08 UTC | Disable button in `CopyModal` for histories when copying history | 05 October 2023, 18:57:08 UTC |
| b40f108 | mvdbeek | 05 October 2023, 15:37:54 UTC | Merge branch 'release_23.0' into release_23.1 | 05 October 2023, 15:37:54 UTC |
| 84f08b2 | Dannon | 04 October 2023, 15:11:55 UTC | Merge pull request #16741 from ahmedhamidawan/import_history_same_name [23.1] Allow importing history with same name as original history | 04 October 2023, 15:11:55 UTC |
| 054be47 | Ahmed Awan | 02 October 2023, 19:56:08 UTC | Allow importing history with same name as original history | 02 October 2023, 19:56:08 UTC |
| bb8d4b0 | Björn Grüning | 30 September 2023, 13:54:20 UTC | Merge pull request #16773 from mvdbeek/flush_optimization [23.1] Fix ItemOwnerShipException in tag removal | 30 September 2023, 13:54:20 UTC |
| ea2be33 | Marius van den Beek | 30 September 2023, 12:00:53 UTC | Merge pull request #16772 from mvdbeek/message_exception_in_ui [23.0] Show MessageException in invocation UI | 30 September 2023, 12:00:53 UTC |
| 50d144f | mvdbeek | 30 September 2023, 10:13:33 UTC | Fix ItemOwnerShipException in tag removal This is another way to fix https://sentry.galaxyproject.org/share/issue/8308250826df4554aa456a94b45bbe6a/: ``` ItemOwnershipException: User does not own item. File "galaxy/workflow/run.py", line 233, in invoke incomplete_or_none = self._invoke_step(workflow_invocation_step) File "galaxy/workflow/run.py", line 309, in _invoke_step incomplete_or_none = invocation_step.workflow_step.module.execute( File "galaxy/workflow/modules.py", line 2274, in execute execution_tracker = execute( File "galaxy/tools/execute.py", line 169, in execute execute_single_job(execution_slice, completed_jobs[i], skip=skip) File "galaxy/tools/execute.py", line 116, in execute_single_job job, result = tool.handle_single_execution( File "galaxy/tools/__init__.py", line 1957, in handle_single_execution raise e File "galaxy/tools/__init__.py", line 1937, in handle_single_execution rval = self.execute( File "galaxy/tools/__init__.py", line 2034, in execute return self.tool_action.execute( File "galaxy/tools/actions/__init__.py", line 683, in execute job_callback(job) File "galaxy/workflow/modules.py", line 2284, in <lambda> job_callback=lambda job: self._handle_post_job_actions( File "galaxy/workflow/modules.py", line 2351, in _handle_post_job_actions ActionBox.execute(self.trans.app, self.trans.sa_session, pja, job, replacement_dict) File "galaxy/job_execution/actions/post.py", line 575, in execute ActionBox.actions[pja.action_type].execute( File "galaxy/job_execution/actions/post.py", line 477, in execute cls._execute(tag_handler, job.user, dataset_collection_assoc.dataset_collection_instance, tags) File "galaxy/job_execution/actions/post.py", line 501, in _execute tag_handler.remove_tags_from_list(user, output, tags) File "galaxy/model/tags.py", line 81, in remove_tags_from_list return self.set_tags_from_list(user, item, tags_set, flush=flush) File "galaxy/model/tags.py", line 94, in set_tags_from_list self.apply_item_tags(user, item, unicodify(new_tags_str, "utf-8"), flush=flush) File "galaxy/model/tags.py", line 270, in apply_item_tags self.apply_item_tag(user, item, name, value, flush=flush) File "galaxy/model/tags.py", line 222, in apply_item_tag self._ensure_user_owns_item(user, item) File "galaxy/model/tags.py", line 193, in _ensure_user_owns_item raise ItemOwnershipException("User does not own item.") ``` By not flushing on tag removal the item for which tag ownership is being checked will not have a primary id, so we know we can skip the ownership check. | 30 September 2023, 10:15:53 UTC |
| bce7bdd | mvdbeek | 30 September 2023, 09:59:55 UTC | Show MessageException in invocation UI | 30 September 2023, 10:03:47 UTC |
| 79cb585 | Björn Grüning | 29 September 2023, 18:43:05 UTC | Merge pull request #16766 from davelopez/23.1_fix_archived_history_not_importable [23.1] Fix public archived histories not importable | 29 September 2023, 18:43:05 UTC |
| 395a043 | Marius van den Beek | 29 September 2023, 18:12:35 UTC | Merge pull request #16759 from mvdbeek/fix_required_select_field [23.1] Don't allow empty selection on required select field | 29 September 2023, 18:12:35 UTC |
| 1888eb7 | Nicola Soranzo | 29 September 2023, 17:01:56 UTC | Merge pull request #16765 from mvdbeek/fix_doc_building [23.0] Fix RE for new version scheme in doc/source/conf.versioning.py | 29 September 2023, 17:01:56 UTC |
| 488c082 | Dannon | 29 September 2023, 15:47:22 UTC | Merge pull request #16763 from mvdbeek/add_missing_requirements [23.1] Add missing requirements to perl tools | 29 September 2023, 15:47:22 UTC |
| f2ad0a7 | davelopez | 29 September 2023, 15:46:15 UTC | Add tooltip with disabled reason | 29 September 2023, 15:46:15 UTC |
| a4c60dc | davelopez | 29 September 2023, 14:42:54 UTC | Display Import button when public history is archived | 29 September 2023, 14:42:54 UTC |
| 5bfb6fb | davelopez | 29 September 2023, 14:42:16 UTC | Add unit tests for HistoryView when archived | 29 September 2023, 14:42:16 UTC |
| 2920429 | mvdbeek | 29 September 2023, 14:29:18 UTC | Accomodate new version scheme in doc/source/conf.versioning.py | 29 September 2023, 14:29:18 UTC |
| 626c86e | mvdbeek | 29 September 2023, 11:32:44 UTC | Add missing requirements to perl tools | 29 September 2023, 13:22:09 UTC |
| 7e2d717 | John Davis | 28 September 2023, 18:12:12 UTC | Merge pull request #16756 from jdavcs/23.1_search_deprecation [23.1] Add deprecation notice for api/search | 28 September 2023, 18:12:12 UTC |
| ac3cd58 | mvdbeek | 28 September 2023, 15:59:05 UTC | Don't allow empty selection on required select field | 28 September 2023, 16:48:24 UTC |
| 61cb77e | Björn Grüning | 28 September 2023, 15:24:45 UTC | Merge pull request #16749 from mvdbeek/fix_output_display_without_label [23.1] Fix workflow output display without label | 28 September 2023, 15:24:45 UTC |
| 0496021 | John Davis | 28 September 2023, 15:05:15 UTC | Add deprecation notice for api/search | 28 September 2023, 15:05:15 UTC |
| 2292142 | Marius van den Beek | 28 September 2023, 13:09:17 UTC | Use classes instead of style, add rounded, drop unnecessary gapx Co-authored-by: Laila Los <44241786+ElectronicBlueberry@users.noreply.github.com> | 28 September 2023, 13:09:17 UTC |
| a7ab719 | mvdbeek | 27 September 2023, 11:01:52 UTC | List invocation outputs without explicit label using a unique label that we compute on the fly. Should hopefully not happen often now that we set a default label when we make an output a workflow output. | 28 September 2023, 07:58:00 UTC |
| a72a9c1 | mvdbeek | 27 September 2023, 11:00:19 UTC | Set workflow output label to output name in checkbox And since that makes it considerably easier to have duplicate output labels we now highlight duplicate output labels. | 28 September 2023, 07:58:00 UTC |
| fc7e0a7 | Dannon Baker | 25 September 2023, 22:06:56 UTC | Update version to 23.1.1.dev0 | 25 September 2023, 22:06:56 UTC |
| 887f1ec | Dannon Baker | 25 September 2023, 22:06:55 UTC | Update version to 23.1. | 25 September 2023, 22:06:55 UTC |
| c99bde3 | Dannon | 25 September 2023, 21:58:29 UTC | Merge pull request #16329 from dannon/release_notes_23.1 [23.1] 23.1 Release Notes | 25 September 2023, 21:58:29 UTC |
| 6352f42 | Dannon Baker | 25 September 2023, 21:19:21 UTC | Merge remote-tracking branch 'upstream/release_23.0' into release_23.1 | 25 September 2023, 21:19:21 UTC |
| 11fac15 | Dannon Baker | 25 September 2023, 19:52:31 UTC | User facing release notes updates, images. | 25 September 2023, 19:52:31 UTC |
| 65cbe51 | Dannon Baker | 25 September 2023, 16:53:25 UTC | Final release note PR update. | 25 September 2023, 16:53:25 UTC |
