https://github.com/galaxyproject/galaxy

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Revision Author Date Message Commit Date
df98405 Always discard session after __handle_waiting_jobs is done 05 April 2024, 11:54:02 UTC
aa0a85d Make sure step removal also resets mapOver state Fixes https://github.com/galaxyproject/galaxy/issues/17906 05 April 2024, 11:39:30 UTC
f3377c4 Merge pull request #17904 from mvdbeek/fix_losing_markdown [24.0] Fix lost reports when switching workflow versions 05 April 2024, 11:00:30 UTC
b887bf3 Merge pull request #17911 from davelopez/update_config_samples 05 April 2024, 10:36:09 UTC
a6ddaac Run make config-rebuild 05 April 2024, 09:31:11 UTC
e72ae49 Merge pull request #17907 from ahmedhamidawan/dont_save_wf_without_informing [24.0] Do not save workflow on Run without user confirmation 05 April 2024, 07:27:36 UTC
1cd9752 Merge pull request #17895 from martenson/backp [24.0] do not show copy button when editing 04 April 2024, 22:00:08 UTC
ad6af8d [24.0] Do not save workflow on Run without user confirmation This adds a modal when the user runs a workflow with changes, that asks for user confirmation on whether to proceed without saving changes or to save changes and then proceed. Currently, we _always_ save the workflow when it is run (even if there are no changes at all). Fixes https://github.com/galaxyproject/galaxy/issues/17903 04 April 2024, 20:33:55 UTC
d308444 Merge branch 'release_23.2' into release_24.0 04 April 2024, 16:47:22 UTC
173b326 Merge pull request #17901 from mvdbeek/fix_workflow_saving [23.2] Fix saving workflows with freehand_comments only 04 April 2024, 16:45:40 UTC
8630e3b Fix lost reports when switching workflow versions We serialize workflow.reports, but we were only setting it on the workflow instance if the markdown editor emits it. Fixes a part of https://github.com/galaxyproject/galaxy/issues/17903 04 April 2024, 16:41:34 UTC
cd7de55 disable instead of hiding 04 April 2024, 16:39:23 UTC
661d93a Merge pull request #17869 from mvdbeek/drop_dummy_replacement [24.0] Fix workflow run form failing on certain histories 04 April 2024, 15:06:54 UTC
46c20cd Merge pull request #17899 from mvdbeek/fix_basic_tool_util [24.0] Fix conditional Image imports 04 April 2024, 14:44:30 UTC
b825f79 Reduce for loop nesting 04 April 2024, 14:14:55 UTC
023178d Fix saving workflows with freehand_comments only 04 April 2024, 13:53:33 UTC
d331cc2 Fix conditional Image imports 04 April 2024, 13:06:18 UTC
e970ae5 Merge pull request #17898 from nsoranzo/release_24.0_sphinx_rtd_theme_conf_fixes [24.0] Fix search and version menu in docs 04 April 2024, 03:54:25 UTC
ed5b002 Fix search and version menu in docs The `html_theme_path` option should not be used any more with sphinx-rtd-theme since it switches off the theme's ability to automatically enable the sphinxcontrib-jquery extension, i.e. jQuery is not loaded in the web pages when building the docs with Sphinx >=6. xref: https://github.com/readthedocs/sphinx_rtd_theme/issues/1434#issuecomment-1472671651 Also replace the deprecated `canonical_url` theme option with Sphinx's `html_baseurl`. xref: https://sphinx-rtd-theme.readthedocs.io/en/stable/configuring.html#confval-canonical_url 04 April 2024, 01:39:52 UTC
4827ff8 Merge pull request #17896 from mvdbeek/shorten_transaction [24.0] Fix deadlock that can occur when changing job state 03 April 2024, 22:17:49 UTC
2594276 Update comments Co-authored-by: John Davis <jdavcs@gmail.com> 03 April 2024, 17:39:50 UTC
061d4c3 Commit after changing job state 03 April 2024, 17:19:40 UTC
16e0e4b Only update job if state really changed 03 April 2024, 17:19:40 UTC
4f331e4 do not show copy button when editing 03 April 2024, 17:16:53 UTC
ab2aa7d Merge pull request #17892 from mvdbeek/fix_assert_ok [24.0] Make `wait_for_history_jobs` look at jobs, not datasets 03 April 2024, 15:20:57 UTC
4bb7dd0 Merge pull request #17894 from jdavcs/24.0_notesfix2 [24.0] Fix release notes 03 April 2024, 13:34:56 UTC
4984523 Change test with no outputs to not fail ``out_3`` has been removed in https://github.com/galaxyproject/galaxy/pull/17874 . 03 April 2024, 12:11:36 UTC
1332eb1 Fix ``test_workflow_optional_input_filtering`` API test to produce one output again 03 April 2024, 12:10:53 UTC
8ab16a9 Make wait_for_history_jobs look at jobs, not datasets That fixes test_optional_workflow_output, which started failing after https://github.com/galaxyproject/galaxy/pull/17874, which removed the last static output of `output_filter`, and so there would never be any active datasets to wait on. 03 April 2024, 11:23:42 UTC
8139b76 Merge pull request #17890 from mvdbeek/fix_empty_nested_collection_element_count [24.0] Always serialize element_count and populated when listing contents 03 April 2024, 11:13:59 UTC
3920f21 Merge branch 'release_23.2' into release_24.0 03 April 2024, 09:21:14 UTC
a7398df Merge pull request #17875 from SaimMomin12/release_23.2 Added 4dn_pairs and 4dn_pairsam datatypes 03 April 2024, 09:20:36 UTC
5548b11 Merge pull request #17886 from ahmedhamidawan/fix_history_has_owner_function [24.0] Fix hasOwner function for histories in client 03 April 2024, 09:15:52 UTC
f21cbda Always serialize element_count and populated when listing collection contents Fixes https://github.com/galaxyproject/galaxy/issues/17883 03 April 2024, 09:06:47 UTC
9501826 Fix release notes correct links to videos better images 03 April 2024, 02:28:15 UTC
a7f310c Start work on 24.0.1.dev0 02 April 2024, 23:07:02 UTC
119aaa0 Create version 24.0.0 02 April 2024, 23:06:58 UTC
33505f7 Update version to 24.0.0.dev0 02 April 2024, 19:01:44 UTC
124ee9c Update version to 24.0. 02 April 2024, 19:01:43 UTC
feeb74a 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 Add more last min PRs 02 April 2024, 18:40:57 UTC
098ec92 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 Merge pull request #17610 from jdavcs/24.0_release_notes [24.0] 24.0 release notes 02 April 2024, 18:06:46 UTC
99f31df Add latest PRs 02 April 2024, 18:06:12 UTC
76895fb 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
09f77f4 [24.0] Fix hasOwner function for histories in client The `hasOwner` function in `api/index.ts` was checking: ``` return "user_id" in history; ``` whereas, it also needed to check: ``` return "user_id" in history && history.user_id !== null; ``` because we assume histories (summaries) initally fetched for the `historyStore` without user_id are owned by the current user, but the key is still present in the backend return. This was causing a really troublesome bug in the `HistoryScrollList` found in the history selector modal, where we could constantly keep fetching `api/histories/count` since we didn't have the expected no. of histories loaded in the component; because `historiesProxy` (which only contains owned histories) would end up being empty. 02 April 2024, 17:19:50 UTC
3d1ef1e Add type hints to process_key 02 April 2024, 17:10:21 UTC
8158772 Build nested tool state only once 02 April 2024, 17:10:21 UTC
626baad Refactor RuntimeValue utils for re-use Moving this to tools.parameters.workflow_utils avoids a circular dependency when importing is_runtime_value in tools.parameters.dynamic_options. 02 April 2024, 17:10:20 UTC
6eb5ed6 Less intrusive fix maybe? 02 April 2024, 17:10:20 UTC
ee901d5 Never fail dynamic option generation Just move on, so we can build the tool form even if you have e.g. misassigned datatypes in your history. 02 April 2024, 17:10:20 UTC
55029be Avoid get_initial_value when we have a tool state It's not guaranteed this will always work, and it's unnecessary if we have e.g. `ConnectedValue` in a workflow context. 02 April 2024, 17:10:20 UTC
98ed998 Don't fill in concrete values for connected values 02 April 2024, 17:10:20 UTC
969e995 Add test tool w/ dynamic select in conditional Include this in a workflow, and notice that the run form breaks if the history contains a dataset that trips up the dynamic parameter. 02 April 2024, 17:10:20 UTC
e17e0c0 add details to column select feature highlight 02 April 2024, 17:03:55 UTC
5bf204a Split up into part that actually fails Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com> 02 April 2024, 15:46:09 UTC
dee8278 Ignore user data table errors for now Fixes https://github.com/galaxyproject/galaxy/issues/17822 02 April 2024, 15:02:41 UTC
e331ccb 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
2b42faf Added 4dn_pairs and 4dn_pairsam datatypes 02 April 2024, 09:07:44 UTC
8612c35 black 02 April 2024, 07:46:55 UTC
1a545ae move registering the exception then it might be clearer what's going on here 02 April 2024, 07:46:55 UTC
e1ec2c8 Update test/functional/tools/output_filter.xml 02 April 2024, 07:46:55 UTC
ae594c1 Add back test output 02 April 2024, 07:46:55 UTC
e0fee40 check only presence of outputs mentioned in the tests 02 April 2024, 07:46:55 UTC
0b082d2 Just use the suggestion Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com> 02 April 2024, 07:46:55 UTC
b05bfc3 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 register later 02 April 2024, 07:46:55 UTC
6da8719 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 make test a bit more specific 02 April 2024, 07:46:55 UTC
f19f4ae 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 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 Add links to published videos 01 April 2024, 19:24:46 UTC
b9c94ce Add alt text to figures 01 April 2024, 18:05:42 UTC
86b4345 Move image_diff section to main announcement 01 April 2024, 14:47:51 UTC
b828a16 Apply suggestions from code review Co-authored-by: John Davis <jdavcs@gmail.com> 30 March 2024, 17:39:40 UTC
e10ed2e Merge branch 'release_23.2' into release_24.0 29 March 2024, 23:22:52 UTC
c88d285 Merge branch 'release_23.1' into release_23.2 29 March 2024, 23:22:24 UTC
95a3797 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 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 Normalize extensions when loading tool Fixes https://github.com/galaxyproject/galaxy/issues/17864 29 March 2024, 21:15:34 UTC
d957695 Add more test coverage and adjust for other user's histories 29 March 2024, 12:16:21 UTC
2bba32d Merge pull request #17861 from ElectronicBlueberry/embed-download-fix [24.0] Embed download fix 29 March 2024, 00:54:19 UTC
aa00cb8 config is not defined yet on load 28 March 2024, 21:02:50 UTC
30bf8eb Merge pull request #17847 from ahmedhamidawan/tool_panel_slow_computed 28 March 2024, 20:13:58 UTC
d34f758 Add `show_archived` per code review 28 March 2024, 18:52:11 UTC
4f0f753 set tool search worker to `null` to remove references while unmounted 28 March 2024, 18:40:59 UTC
7155ad7 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 replace to with href 28 March 2024, 16:21:31 UTC
b301e01 Remove style from Base component for visual consistency 28 March 2024, 13:46:17 UTC
801eb24 Avoid page reload for data libraries and admin pages 28 March 2024, 13:24:00 UTC
3968449 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 Fix filtering archived histories 28 March 2024, 10:26:42 UTC
cd9c84d Add test coverage for history advanced filters When dealing with archived histories. 28 March 2024, 10:14:25 UTC
f4115bb Merge pull request #17852 from ElectronicBlueberry/embed-fix [24.0] Embed fix 28 March 2024, 09:29:42 UTC
75a809e 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 Merge branch 'release_23.2' into release_24.0 28 March 2024, 08:29:33 UTC
ea3025d 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 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 keep tool search worker in `toolStore` to prevent multiple bundle fetches 27 March 2024, 17:39:53 UTC
d8e4f9d Merge pull request #17851 from dannon/fix-miscinfo-fixthis [24.0] Fix incorrect miscinfo 'fix this' display 27 March 2024, 16:45:29 UTC
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