| 124ee9c | John Davis | 02 April 2024, 19:01:43 UTC | Update version to 24.0. | 02 April 2024, 19:01:43 UTC |
| feeb74a | John Davis | 02 April 2024, 18:49:22 UTC | Merge pull request #17887 from jdavcs/24.0_release_notes [24.0] Add more last minute PRs to release notes | 02 April 2024, 18:49:22 UTC |
| a129b65 | John Davis | 02 April 2024, 18:40:57 UTC | Add more last min PRs | 02 April 2024, 18:40:57 UTC |
| 098ec92 | John Davis | 02 April 2024, 18:32:49 UTC | Merge pull request #17856 from davelopez/24.0_fix_archived_histories_mixing_with_active [24.0] Fix archived histories mixing with active in histories list | 02 April 2024, 18:32:49 UTC |
| 7284e3e | John Davis | 02 April 2024, 18:06:46 UTC | Merge pull request #17610 from jdavcs/24.0_release_notes [24.0] 24.0 release notes | 02 April 2024, 18:06:46 UTC |
| 99f31df | John Davis | 02 April 2024, 18:06:12 UTC | Add latest PRs | 02 April 2024, 18:06:12 UTC |
| 76895fb | Nicola Soranzo | 02 April 2024, 17:26:28 UTC | Merge pull request #17880 from mvdbeek/ignore_user_data_table_errors [24.0] Ignore user data table errors for now | 02 April 2024, 17:26:28 UTC |
| e17e0c0 | Laila Los | 02 April 2024, 17:03:55 UTC | add details to column select feature highlight | 02 April 2024, 17:03:55 UTC |
| 5bf204a | Marius van den Beek | 02 April 2024, 15:46:09 UTC | Split up into part that actually fails Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com> | 02 April 2024, 15:46:09 UTC |
| dee8278 | mvdbeek | 02 April 2024, 15:02:34 UTC | Ignore user data table errors for now Fixes https://github.com/galaxyproject/galaxy/issues/17822 | 02 April 2024, 15:02:41 UTC |
| e331ccb | Marius van den Beek | 02 April 2024, 12:00:13 UTC | Merge pull request #17874 from bernt-matthias/assert-empty-output_24.0 [24.0] Missing outputs should be recorded as test errors | 02 April 2024, 12:00:13 UTC |
| 8612c35 | Matthias Bernt | 26 March 2024, 07:50:38 UTC | black | 02 April 2024, 07:46:55 UTC |
| 1a545ae | Matthias Bernt | 26 March 2024, 07:44:54 UTC | move registering the exception then it might be clearer what's going on here | 02 April 2024, 07:46:55 UTC |
| e1ec2c8 | M Bernt | 25 March 2024, 14:44:11 UTC | Update test/functional/tools/output_filter.xml | 02 April 2024, 07:46:55 UTC |
| ae594c1 | M Bernt | 25 March 2024, 14:34:57 UTC | Add back test output | 02 April 2024, 07:46:55 UTC |
| e0fee40 | Matthias Bernt | 25 March 2024, 14:31:20 UTC | check only presence of outputs mentioned in the tests | 02 April 2024, 07:46:55 UTC |
| 0b082d2 | M Bernt | 25 March 2024, 12:40:35 UTC | Just use the suggestion Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com> | 02 April 2024, 07:46:55 UTC |
| b05bfc3 | Matthias Bernt | 25 March 2024, 12:35:05 UTC | move assertion instead of removing it otherwise the tool test will just return a list out of bounds exception which is unclear to the user | 02 April 2024, 07:46:55 UTC |
| fb01590 | Matthias Bernt | 20 July 2023, 12:02:38 UTC | register later | 02 April 2024, 07:46:55 UTC |
| 6da8719 | Matthias Bernt | 20 July 2023, 07:53:22 UTC | register failure to produce output thereby we implicitly make the assumption that a test needs to produce an output also make message more specific | 02 April 2024, 07:46:55 UTC |
| 46abd27 | Matthias Bernt | 20 July 2023, 07:38:22 UTC | make test a bit more specific | 02 April 2024, 07:46:55 UTC |
| f19f4ae | Matthias Bernt | 15 May 2023, 16:53:36 UTC | tool verification: move no output assertion from planemo the verify_tool function is called from [within an try-except block](https://github.com/galaxyproject/planemo/blob/1aa3eb05a97ad20c0be6f6560ab5cec090e76612/planemo/engine/galaxy.py#L109) which silently catches any exception. Thus any exception raised from within verify_tool will not be detected, i.e. the assertion needs to be moved into `_verify_outputs` (which also seems to make sense by name) in order to make verify_tool record the problem properly. | 02 April 2024, 07:46:55 UTC |
| 6687cdc | Matthias Bernt | 15 May 2023, 18:57:24 UTC | adapt output filter test - remove the output that is always present - add a test that has no outputs | 02 April 2024, 07:46:22 UTC |
| 4857324 | John Davis | 01 April 2024, 19:24:46 UTC | Add links to published videos | 01 April 2024, 19:24:46 UTC |
| b9c94ce | John Davis | 01 April 2024, 18:05:42 UTC | Add alt text to figures | 01 April 2024, 18:05:42 UTC |
| 86b4345 | John Davis | 01 April 2024, 14:47:51 UTC | Move image_diff section to main announcement | 01 April 2024, 14:47:51 UTC |
| b828a16 | David López | 30 March 2024, 17:39:40 UTC | Apply suggestions from code review Co-authored-by: John Davis <jdavcs@gmail.com> | 30 March 2024, 17:39:40 UTC |
| e10ed2e | mvdbeek | 29 March 2024, 23:22:52 UTC | Merge branch 'release_23.2' into release_24.0 | 29 March 2024, 23:22:52 UTC |
| c88d285 | mvdbeek | 29 March 2024, 23:22:24 UTC | Merge branch 'release_23.1' into release_23.2 | 29 March 2024, 23:22:24 UTC |
| 95a3797 | Marius van den Beek | 29 March 2024, 23:21:58 UTC | Merge pull request #17868 from mvdbeek/parse_extensions_as_lowercase_and_stripped [23.1] Normalize extensions when loading tool | 29 March 2024, 23:21:58 UTC |
| 91b93eb | Marius van den Beek | 29 March 2024, 21:24:25 UTC | Merge pull request #17865 from martenson/config-type [24.0] wait for config to load with user prefs options | 29 March 2024, 21:24:25 UTC |
| 45c4675 | mvdbeek | 29 March 2024, 21:11:47 UTC | Normalize extensions when loading tool Fixes https://github.com/galaxyproject/galaxy/issues/17864 | 29 March 2024, 21:15:34 UTC |
| d957695 | davelopez | 29 March 2024, 12:16:21 UTC | Add more test coverage and adjust for other user's histories | 29 March 2024, 12:16:21 UTC |
| 2bba32d | Dannon | 29 March 2024, 00:54:19 UTC | Merge pull request #17861 from ElectronicBlueberry/embed-download-fix [24.0] Embed download fix | 29 March 2024, 00:54:19 UTC |
| aa00cb8 | Martin Cech | 28 March 2024, 21:02:50 UTC | config is not defined yet on load | 28 March 2024, 21:02:50 UTC |
| 30bf8eb | Marius van den Beek | 28 March 2024, 20:13:58 UTC | Merge pull request #17847 from ahmedhamidawan/tool_panel_slow_computed | 28 March 2024, 20:13:58 UTC |
| d34f758 | davelopez | 28 March 2024, 18:52:11 UTC | Add `show_archived` per code review | 28 March 2024, 18:52:11 UTC |
| 4f0f753 | Ahmed Awan | 28 March 2024, 18:40:59 UTC | set tool search worker to `null` to remove references while unmounted | 28 March 2024, 18:40:59 UTC |
| 7155ad7 | Martin Cech | 28 March 2024, 17:34:37 UTC | Merge pull request #17860 from davelopez/24.0_fix_activity_bar_unreachable [24.0] Fix activity bar unreachable in some pages | 28 March 2024, 17:34:37 UTC |
| 3439265 | Laila Los | 28 March 2024, 16:21:31 UTC | replace to with href | 28 March 2024, 16:21:31 UTC |
| b301e01 | davelopez | 28 March 2024, 13:46:17 UTC | Remove style from Base component for visual consistency | 28 March 2024, 13:46:17 UTC |
| 801eb24 | davelopez | 28 March 2024, 13:24:00 UTC | Avoid page reload for data libraries and admin pages | 28 March 2024, 13:24:00 UTC |
| 3968449 | davelopez | 28 March 2024, 13:23:31 UTC | Move Admin, Libraries and Storage Dashboard panels To the center panel instead of their own full page. This will keep the activity bar always visible. | 28 March 2024, 13:23:31 UTC |
| c32b87d | davelopez | 28 March 2024, 10:26:42 UTC | Fix filtering archived histories | 28 March 2024, 10:26:42 UTC |
| cd9c84d | davelopez | 28 March 2024, 10:14:25 UTC | Add test coverage for history advanced filters When dealing with archived histories. | 28 March 2024, 10:14:25 UTC |
| f4115bb | Marius van den Beek | 28 March 2024, 09:29:42 UTC | Merge pull request #17852 from ElectronicBlueberry/embed-fix [24.0] Embed fix | 28 March 2024, 09:29:42 UTC |
| 75a809e | Marius van den Beek | 28 March 2024, 09:29:28 UTC | Merge pull request #17812 from davelopez/24.0_fix_multi_history_counts [24.0] Fix Multi-History status bar reactivity | 28 March 2024, 09:29:28 UTC |
| 3669cae | mvdbeek | 28 March 2024, 08:29:33 UTC | Merge branch 'release_23.2' into release_24.0 | 28 March 2024, 08:29:33 UTC |
| ea3025d | Marius van den Beek | 28 March 2024, 08:29:07 UTC | Merge pull request #17854 from mvdbeek/fix_role_query [23.2] Fix user login when duplicate UserRoleAssociation exists | 28 March 2024, 08:29:07 UTC |
| 50d9d1f | mvdbeek | 27 March 2024, 18:15:37 UTC | Fix user login when duplicate UserRoleAssociation exists In https://github.com/galaxyproject/galaxy/commit/3fd5b0252f840dbb92aaebf31b9d21034b21c578 we changed the sqlalchemy query construct `one_or_none` method to use the core statement `.scalar_one_or_none`, which bypasses the identity map. Since there are a handful of legacy accounts with duplicate UserRoleAssociation rows on usegalaxy.{org,eu} the deduplication that occured via the entity map meant that no exception was raised, while for the core level construct this happened. Fortunately it's easy enough to simply add a distinct statement to return to the old behavior. Here's an ipython session to prove this: """ In [4]: ura = sa_session.query(UserRoleAssociation).filter_by(user_id=1, role_id=1).all() In [5]: ura Out[5]: [<galaxy.model.UserRoleAssociation(1) at 0x165809190>] In [6]: new_ura = UserRoleAssociation(sa_session.get(User, 1), sa_session.get(Role, 1)) In [7]: sa_session.add(new_ura) In [8]: sa_session.flush() In [9]: role = ( ...: sa_session.query(Role) ...: .filter( ...: and_( ...: UserRoleAssociation.table.c.user_id == 1, ...: Role.id == UserRoleAssociation.table.c.role_id, ...: Role.type == Role.types.PRIVATE, ...: ) ...: ) ...: .one_or_none() ...: ) In [10]: stmt = select(Role).where( ...: and_( ...: UserRoleAssociation.user_id == 1, ...: Role.id == UserRoleAssociation.role_id, ...: Role.type == Role.types.PRIVATE, ...: ) ...: ) ...: role = sa_session.execute(stmt).scalar_one_or_none() --------------------------------------------------------------------------- MultipleResultsFound Traceback (most recent call last) Cell In[10], line 8 1 stmt = select(Role).where( 2 and_( 3 UserRoleAssociation.user_id == 1, (...) 6 ) 7 ) ----> 8 role = sa_session.execute(stmt).scalar_one_or_none() File ~/src/galaxy/.venv/lib/python3.11/site-packages/sqlalchemy/engine/result.py:1225, in Result.scalar_one_or_none(self) 1212 def scalar_one_or_none(self): 1213 """Return exactly one scalar result or ``None``. 1214 1215 This is equivalent to calling :meth:`_engine.Result.scalars` and (...) 1223 1224 """ -> 1225 return self._only_one_row( 1226 raise_for_second_row=True, raise_for_none=False, scalar=True 1227 ) File ~/src/galaxy/.venv/lib/python3.11/site-packages/sqlalchemy/engine/result.py:614, in ResultInternal._only_one_row(self, raise_for_second_row, raise_for_none, scalar) 612 if next_row is not _NO_ROW: 613 self._soft_close(hard=True) --> 614 raise exc.MultipleResultsFound( 615 "Multiple rows were found when exactly one was required" 616 if raise_for_none 617 else "Multiple rows were found when one or none " 618 "was required" 619 ) 620 else: 621 next_row = _NO_ROW MultipleResultsFound: Multiple rows were found when one or none was required In [11]: stmt = select(Role).where( ...: and_( ...: UserRoleAssociation.user_id == 1, ...: Role.id == UserRoleAssociation.role_id, ...: Role.type == Role.types.PRIVATE, ...: ) ...: ).distinct() ...: role = sa_session.execute(stmt).scalar_one_or_none() """ I think that's what the sqlalchemy docs for [Query.one_or_none](https://docs.sqlalchemy.org/en/14/orm/query.html#sqlalchemy.orm.Query.one_or_none) mean to communicate with > Returns None if the query selects no rows. Raises sqlalchemy.orm.exc.MultipleResultsFound if multiple object identities are returned, or if multiple rows are returned for a query that returns only scalar values as opposed to full identity-mapped entities. Fixes https://github.com/galaxyproject/galaxy/issues/17848 | 27 March 2024, 18:22:38 UTC |
| 0d75267 | Ahmed Awan | 27 March 2024, 17:39:53 UTC | keep tool search worker in `toolStore` to prevent multiple bundle fetches | 27 March 2024, 17:39:53 UTC |
| d8e4f9d | Martin Cech | 27 March 2024, 16:45:29 UTC | Merge pull request #17851 from dannon/fix-miscinfo-fixthis [24.0] Fix incorrect miscinfo 'fix this' display | 27 March 2024, 16:45:29 UTC |
| 540be69 | Laila Los | 27 March 2024, 15:01:30 UTC | fix iframe tag and style | 27 March 2024, 15:01:30 UTC |
| 572a7b5 | Dannon Baker | 27 March 2024, 14:10:34 UTC | Walk all (just the one) knownErrors | 27 March 2024, 14:10:34 UTC |
| 248bf22 | Dannon Baker | 27 March 2024, 13:57:44 UTC | Fix miscinfo 'how to fix this' always showing | 27 March 2024, 13:57:44 UTC |
| 9b91fa5 | Dannon Baker | 27 March 2024, 12:59:06 UTC | Address reactivity bug; ensure newly added properties are reactive -- this is much cleaner in vue3... | 27 March 2024, 12:59:06 UTC |
| c6be941 | davelopez | 27 March 2024, 12:45:27 UTC | Adapt client API schemas for histories To accurately reflect what the server is serializing for each different view or usual request from the client. | 27 March 2024, 12:45:27 UTC |
| d3e9c3b | davelopez | 27 March 2024, 12:27:23 UTC | Revert schema changes in backend Let's do this on dev, after we evaluate what to improve. | 27 March 2024, 12:27:23 UTC |
| f719222 | mvdbeek | 27 March 2024, 09:20:10 UTC | Make toolsById a shallowRef A given tool never changes attributes (currently), so no need to track reactivity for the whole object. | 27 March 2024, 09:21:26 UTC |
| 6b46650 | davelopez | 26 March 2024, 13:48:36 UTC | Disable history operations conditional if multi-view I don't like this at all, but we don't have a way to deal with those operations in a multi-view scenario. This should be a temporary fix util we work on enabling real multi-history support both in backend and client. | 27 March 2024, 09:16:03 UTC |
| 7f95bf8 | davelopez | 26 March 2024, 12:16:28 UTC | Add updateContentStats action to histories store This allows to request only those fields that might have changed after an operation in the history contents. | 27 March 2024, 09:16:02 UTC |
| 7b7ee0a | davelopez | 26 March 2024, 12:05:44 UTC | Refactor useExtendedHistory composable | 27 March 2024, 09:16:02 UTC |
| fd02efd | davelopez | 26 March 2024, 11:46:58 UTC | Drop history placeholder as it doesn't really help | 27 March 2024, 09:16:01 UTC |
| 45e0539 | davelopez | 22 March 2024, 15:44:50 UTC | Refactor MultipleView.test.js to improve test setup | 27 March 2024, 09:16:01 UTC |
| dc5a172 | davelopez | 22 March 2024, 14:33:32 UTC | Refactor HistoryScrollList To use AnyHistory type and userOwnsHistory function | 27 March 2024, 09:16:00 UTC |
| 23b2da3 | davelopez | 22 March 2024, 14:16:52 UTC | Fix multi-history view stats Add composables to deal with "extended" versions of histories when needed. Use proper types for history references in components. | 27 March 2024, 09:15:49 UTC |
| 33cca2e | davelopez | 22 March 2024, 13:18:43 UTC | Add history placeholder to prevent multiple requests And avoid reactivity issues with lost references | 27 March 2024, 09:14:39 UTC |
| 841a281 | davelopez | 22 March 2024, 13:17:11 UTC | Use proper types for history requests in the store This should give us an idea of what information is being stored and retrieved each time. | 27 March 2024, 09:14:38 UTC |
| 1361af8 | davelopez | 22 March 2024, 12:41:54 UTC | Load current history through the historyStore in watcher This will make the history data available for all the app and reduce duplicated requests. | 27 March 2024, 09:14:38 UTC |
| 7387286 | davelopez | 22 March 2024, 12:30:09 UTC | Add HistoryDevDetailed schema model Technically this model is used by the "client API" in the old controllers so the current API is not using it, but it is useful to have the schema in the client to know what we are getting when requesting something from the server. | 27 March 2024, 09:14:37 UTC |
| 4a466f9 | davelopez | 22 March 2024, 10:43:09 UTC | Reduce redundant detailed history load The current history details will be loaded by the history watcher anyway. | 27 March 2024, 09:14:37 UTC |
| a132651 | davelopez | 22 March 2024, 10:07:15 UTC | Refactor async calls to avoid mixing `await` and `then` | 27 March 2024, 09:14:36 UTC |
| 575806a | mvdbeek | 27 March 2024, 08:32:14 UTC | Optimize getValidToolsInEachSection | 27 March 2024, 08:33:11 UTC |
| a7bff17 | mvdbeek | 27 March 2024, 08:31:50 UTC | Optimize getValidToolsInCurrentView | 27 March 2024, 08:33:11 UTC |
| 6bb34b9 | Ahmed Awan | 26 March 2024, 23:08:15 UTC | Improve panel speed Co-authored-by: mvdbeek <m.vandenbeek@gmail.com> | 27 March 2024, 08:33:11 UTC |
| a8727a3 | Martin Cech | 26 March 2024, 18:32:26 UTC | Merge pull request #17842 from mvdbeek/docs_x_accel_redirect [23.2] Proxy Access-Control-* headers when using x-accel-redirect | 26 March 2024, 18:32:26 UTC |
| f5e07b1 | Dannon | 26 March 2024, 18:05:50 UTC | Merge pull request #17844 from ElectronicBlueberry/help-forum-short-id [24.0] Fix Help Forum Integration uses Long ID | 26 March 2024, 18:05:50 UTC |
| 1fa50dc | Martin Cech | 26 March 2024, 16:47:32 UTC | Merge pull request #17806 from jmchilton/respect_user_os_selection [24.0] Allow admin to sharpen language about selected object stores. | 26 March 2024, 16:47:32 UTC |
| aa715e4 | John Davis | 26 March 2024, 12:18:32 UTC | Update doc/source/releases/24.0_announce_user.rst Co-authored-by: Helena <hexylena@galaxians.org> | 26 March 2024, 12:18:32 UTC |
| 89d4f9c | John Davis | 26 March 2024, 12:17:57 UTC | Update doc/source/releases/24.0_announce_user.rst Co-authored-by: Helena <hexylena@galaxians.org> | 26 March 2024, 12:17:57 UTC |
| 96d1dc2 | John Davis | 26 March 2024, 12:17:30 UTC | Update doc/source/releases/24.0_announce_user.rst Co-authored-by: Helena <hexylena@galaxians.org> | 26 March 2024, 12:17:30 UTC |
| 2b321ef | Laila Los | 26 March 2024, 11:14:25 UTC | use short tool id as help forum tag | 26 March 2024, 11:14:25 UTC |
| 92bfdb2 | Laila Los | 26 March 2024, 11:14:08 UTC | consolidate tool id shortening methods | 26 March 2024, 11:14:08 UTC |
| 17b6fb3 | Laila Los | 26 March 2024, 11:13:29 UTC | add getShortToolId util | 26 March 2024, 11:13:29 UTC |
| 2ce2686 | mvdbeek | 26 March 2024, 09:54:29 UTC | Proxy Access-Control-* headers when using x-accel-redirect | 26 March 2024, 09:54:29 UTC |
| a941f40 | John Davis | 26 March 2024, 03:17:25 UTC | Add main announcement highlights | 26 March 2024, 03:17:41 UTC |
| 65a860b | John Davis | 26 March 2024, 03:07:34 UTC | Add user release notes and images | 26 March 2024, 03:07:34 UTC |
| 0d70005 | John Davis | 25 March 2024, 22:51:53 UTC | Merge pull request #17837 from jdavcs/23.2_releasenotesfix [23.2] Fix error in release notes | 25 March 2024, 22:51:53 UTC |
| 98b3636 | John Davis | 25 March 2024, 22:37:21 UTC | Add config notes | 25 March 2024, 22:37:21 UTC |
| b36372d | John Davis | 25 March 2024, 22:10:27 UTC | Add admin notes | 25 March 2024, 22:10:27 UTC |
| 93ff028 | John Davis | 25 March 2024, 21:38:27 UTC | Fix error in notes | 25 March 2024, 21:38:27 UTC |
| 6a34031 | John Davis | 25 March 2024, 20:22:26 UTC | More PR title fixes | 25 March 2024, 20:22:26 UTC |
| 6352742 | Björn Grüning | 25 March 2024, 19:24:41 UTC | Merge pull request #17835 from jdavcs/24.0_query_refactor [24.0] Minor refactor of query building logic for readability | 25 March 2024, 19:24:41 UTC |
| 480ec69 | John Davis | 25 March 2024, 18:56:46 UTC | Add 24.0 to releases/index.rst | 25 March 2024, 18:56:46 UTC |
| 9e6382c | John Davis | 25 March 2024, 18:45:42 UTC | Add PRs merged since the freeze | 25 March 2024, 18:45:42 UTC |
| dfe7508 | John Davis | 13 March 2024, 04:43:34 UTC | Add Amirhossein to testing team | 25 March 2024, 18:28:29 UTC |
| 0550e76 | John Davis | 05 March 2024, 23:57:03 UTC | Add more boilerplate to main announcement TODO: add all this to galaxy-release-util script | 25 March 2024, 18:28:29 UTC |
| ccb3043 | John Davis | 05 March 2024, 23:35:28 UTC | Edit dates, titles Make title in user release notes consistent with main announcement. Change "February", "Early" to "March". Dates: 2/26 was the freeze; 3/25 gives us sufficient time to releaase. | 25 March 2024, 18:28:29 UTC |
| 446e012 | John Davis | 05 March 2024, 23:42:36 UTC | Add release testing team | 25 March 2024, 18:28:29 UTC |
| 03b6c39 | John Davis | 05 March 2024, 23:33:15 UTC | Change dates for 24.1 We need more time before GCC | 25 March 2024, 18:28:29 UTC |
