https://github.com/galaxyproject/galaxy

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Revision Author Date Message Commit Date
887f1ec Update version to 23.1. 25 September 2023, 22:06:55 UTC
c99bde3 Merge pull request #16329 from dannon/release_notes_23.1 [23.1] 23.1 Release Notes 25 September 2023, 21:58:29 UTC
6352f42 Merge remote-tracking branch 'upstream/release_23.0' into release_23.1 25 September 2023, 21:19:21 UTC
11fac15 User facing release notes updates, images. 25 September 2023, 19:52:31 UTC
65cbe51 Final release note PR update. 25 September 2023, 16:53:25 UTC
48101bf Merge pull request #16717 from mvdbeek/copy_elements [23.1] Copy the collection contents by default when copying a collection 25 September 2023, 15:52:40 UTC
b9a6d17 Run and include release-diff output for 23.1 25 September 2023, 15:51:48 UTC
ab8a645 Remaining PRs reconciled. 25 September 2023, 14:21:25 UTC
0677336 Fix milestones for several PRs, regenerate. 25 September 2023, 14:21:25 UTC
d6a8aca Apply suggestions from code review Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com> 25 September 2023, 14:21:25 UTC
9e8624f Add deprecation of Python 3.7 for v24.0 25 September 2023, 14:21:25 UTC
1e30917 Regenerate PRs post-release-util fix. 25 September 2023, 14:21:25 UTC
75dbea8 Deduplicate announce PRs 25 September 2023, 14:21:25 UTC
ded80cb Add user facing doc stub from NatalieW -- needs screenshots, org, and text updates. 25 September 2023, 14:21:25 UTC
a62edd1 Update release note PRs 25 September 2023, 14:21:25 UTC
28a0565 Apply suggestions from code review Co-authored-by: John Davis <jdavcs@gmail.com> 25 September 2023, 14:21:25 UTC
5c59a0e Regenerate base docs 25 September 2023, 14:21:25 UTC
2eb4e8c Add 23.1 notes to toc 25 September 2023, 14:21:25 UTC
95078e1 Bootstrap 23.1 release notes 25 September 2023, 14:21:25 UTC
73be5f3 Fix test_extract_copied_mapping_from_history ... by copying the history instead of its contents. With the change of copying hdca contents by default we'd otherwise have find the right hids, which isn't really what this test is about. 25 September 2023, 13:56:37 UTC
05f6cae Update API test case for new collection copy default 25 September 2023, 13:56:37 UTC
9860ebe Also copy contents to history when send to new history is active 25 September 2023, 13:56:37 UTC
70a1ca2 Copy the collection contents by default when copying a collection That got left out when creating the new multi history view. Fixes https://github.com/galaxyproject/galaxy/issues/16716 and https://github.com/galaxyproject/galaxy/issues/16619. 25 September 2023, 13:56:36 UTC
53790d0 Merge pull request #16734 from martenson/toolbox-scrollbar [23.1] prevent toolbox scrollbar 25 September 2023, 13:36:34 UTC
cf1bc2f Merge pull request #16732 from martenson/23-param-over [23.1] force wrap long parameter names in the workflow form 25 September 2023, 13:25:13 UTC
602cdd4 Merge pull request #16728 from kysrpex/job_resource_parameters_child_elements_missing [23.1] Workaround for XML nodes of job resource parameters losing their children 25 September 2023, 08:22:45 UTC
4bb1d56 Fix imports order 25 September 2023, 07:37:41 UTC
ff3ad41 Import `etree` from `galaxy.util` Import `etree` from `galaxy.util` as suggested in the code review. Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com> 25 September 2023, 07:00:36 UTC
73ad4f4 Merge pull request #16729 from mvdbeek/fix_allowlist_deserialization [23.1] Fix allowlist deserialization in file sources 24 September 2023, 17:38:10 UTC
6341c7c Pass fetch_url_allowlist from DRS to HTTP source 24 September 2023, 15:07:10 UTC
7a02769 break also mid-words for tool panel prevent long tool names, descriptions and workflow names to create scrollbar in tool panel 22 September 2023, 21:11:40 UTC
319e492 force wrap long output names winse wf box is fixed width 22 September 2023, 20:02:22 UTC
bb2daaf Move config parsing to util package 22 September 2023, 19:18:02 UTC
3087717 Add missing attribute in unit test config 22 September 2023, 18:50:18 UTC
cac5495 Fix allowlist deserialization in file sources 22 September 2023, 17:37:41 UTC
54f3769 Merge pull request #16726 from dannon/fix-unittest-mocks [23.1] Fix unittest mocks to support us checking geturl() 22 September 2023, 17:24:04 UTC
ff96f26 Merge branch 'release_23.1' into job_resource_parameters_child_elements_missing 22 September 2023, 16:18:41 UTC
27320b6 Workaround for XML nodes of job resource parameters losing their children This bug was spotted because the job resource parameters selector broke on usegalaxy.eu. For the tool keras_train_and_eval, the option "Use GPU resources" shows up, but no drop-down menu is available and no items can be selected. The options are available as children of the XML nodes tagged with "param" within the scope of `galaxy.jobs.parse_resource_parameters`. They are then returned and later retrieved within the scope of `galaxy.util.parse_resource_parameters`, but by then, the children of the XML node (the options) are gone. See https://github.com/galaxyproject/galaxy/issues/16727 for more details. 22 September 2023, 16:06:51 UTC
d01b039 Fix unittest mocks to support us checking geturl() after opening connections. 22 September 2023, 15:05:24 UTC
5ff729d Constrain http filesource by fetch_url_allowlist while still following redirects 21 September 2023, 22:21:23 UTC
fead133 Merge branch 'release_22.05' into release_23.0 21 September 2023, 21:48:06 UTC
5003134 Backport re-checking local ip exclusion from fetching after connection is open 21 September 2023, 18:44:09 UTC
9d79596 Merge pull request #16718 from davelopez/fix_collection_id_encoding [23.1] Fix collection id encoding 21 September 2023, 16:02:01 UTC
1f068f3 Update json test samples 21 September 2023, 12:03:02 UTC
7321492 Makes sure collection_id is encoded 21 September 2023, 11:57:29 UTC
551fabd Merge pull request #16714 from mvdbeek/fix_unbalanced_query [23.1] Fix job search query 20 September 2023, 21:06:50 UTC
1eabd67 Fix job search query We need to add the dataset_id to the select here (just like in the cases below) ... just calling query.add_columns() doesn't change the query in place. Fixes the new error @bwlang ran into in https://help.galaxyproject.org/t/i-tried-to-run-a-new-workflow-but-it-stopped-scheduling-at-some-point-seems-like-a-better-error-message-is-in-order/10719 20 September 2023, 19:00:30 UTC
f3f1d7b Merge pull request #16710 from mvdbeek/job_cache_fix_missing_join [23.1] Add missing join condition in job search 19 September 2023, 14:33:51 UTC
635ec57 Add missing join condition in job search Fixes https://help.galaxyproject.org/t/i-tried-to-run-a-new-workflow-but-it-stopped-scheduling-at-some-point-seems-like-a-better-error-message-is-in-order/10719 19 September 2023, 12:54:50 UTC
4bfd5b4 Merge pull request #16703 from davelopez/fix_dashboard_chart_legend [23.1] Fix legend not scrollable in storage overview charts 18 September 2023, 15:53:48 UTC
4bc24b5 Merge pull request #16701 from mvdbeek/update_pulsar_client_library [23.0] Update pulsar client library to 0.15.5 17 September 2023, 17:28:25 UTC
60b7d65 Merge pull request #16705 from mvdbeek/no_extra_files_for_pending [23.1] List extra files only for terminal datasets 17 September 2023, 08:02:12 UTC
3e991f1 Merge pull request #16704 from bgruening/universial_newline [23.1] FileInput no longer accept 'U' in the file mode 17 September 2023, 07:17:36 UTC
d699486 List extra files only for terminal datasets Fixes: ``` WouldBlock: null File "anyio/streams/memory.py", line 98, in receive return self.receive_nowait() File "anyio/streams/memory.py", line 93, in receive_nowait raise WouldBlock EndOfStream: null File "starlette/middleware/base.py", line 78, in call_next message = await recv_stream.receive() File "anyio/streams/memory.py", line 118, in receive raise EndOfStream KeyError: None File "starlette/applications.py", line 122, in __call__ await self.middleware_stack(scope, receive, send) File "starlette/middleware/errors.py", line 184, in __call__ raise exc File "starlette/middleware/errors.py", line 162, in __call__ await self.app(scope, receive, _send) File "starlette_context/middleware/raw_middleware.py", line 93, in __call__ await self.app(scope, receive, send_wrapper) File "starlette/middleware/base.py", line 108, in __call__ response = await self.dispatch_func(request, call_next) File "galaxy/webapps/galaxy/fast_app.py", line 103, in add_x_frame_options response = await call_next(request) File "starlette/middleware/base.py", line 84, in call_next raise app_exc File "starlette/middleware/base.py", line 70, in coro await self.app(scope, receive_or_disconnect, send_no_error) File "starlette/middleware/exceptions.py", line 79, in __call__ raise exc File "starlette/middleware/exceptions.py", line 68, in __call__ await self.app(scope, receive, sender) File "fastapi/middleware/asyncexitstack.py", line 20, in __call__ raise e File "fastapi/middleware/asyncexitstack.py", line 17, in __call__ await self.app(scope, receive, send) File "starlette/routing.py", line 718, in __call__ await route.handle(scope, receive, send) File "starlette/routing.py", line 276, in handle await self.app(scope, receive, send) File "starlette/routing.py", line 66, in app response = await func(request) File "fastapi/routing.py", line 241, in app raw_response = await run_endpoint_function( File "fastapi/routing.py", line 169, in run_endpoint_function return await run_in_threadpool(dependant.call, **values) File "starlette/concurrency.py", line 41, in run_in_threadpool return await anyio.to_thread.run_sync(func, *args) File "anyio/to_thread.py", line 33, in run_sync return await get_asynclib().run_sync_in_worker_thread( File "anyio/_backends/_asyncio.py", line 877, in run_sync_in_worker_thread return await future File "anyio/_backends/_asyncio.py", line 807, in run result = context.run(func, *args) File "galaxy/webapps/galaxy/api/datasets.py", line 253, in extra_files return self.service.extra_files(trans, history_content_id) File "galaxy/webapps/galaxy/services/datasets.py", line 548, in extra_files extra_files_path = hda.extra_files_path File "galaxy/model/__init__.py", line 4421, in extra_files_path return self.dataset.extra_files_path File "galaxy/model/__init__.py", line 3989, in get_extra_files_path return self.object_store.construct_path( File "galaxy/objectstore/__init__.py", line 419, in construct_path return self._invoke("construct_path", obj, **kwargs) File "galaxy/objectstore/__init__.py", line 413, in _invoke return self.__getattribute__(f"_{delegate}")(obj=obj, **kwargs) File "galaxy/objectstore/__init__.py", line 1157, in _construct_path return self.backends[obj.object_store_id].construct_path(obj, **kwargs) ``` 16 September 2023, 17:23:08 UTC
a9f5400 FileInput no longer accept 'U' in the file mode 16 September 2023, 16:33:07 UTC
8093dc0 Fix Chart legend not scrollable 15 September 2023, 20:09:29 UTC
0d280f2 Update pulsar client library to 0.15.5 15 September 2023, 11:27:17 UTC
2eeddee Merge pull request #16687 from jdavcs/23.1_closed_transaction_on_check_jobs [23.1] Fix closed transaction error on galaxy startup/check jobs 14 September 2023, 14:44:28 UTC
aedbb39 Fix closed transaction error 13 September 2023, 19:56:07 UTC
944a610 Merge pull request #16674 from dannon/galaxy-charts-version-bump [23.1] Update galaxyproject/charts utilizing visualizations 13 September 2023, 12:03:31 UTC
5f4107d Merge pull request #16680 from dannon/page-owner-edit-restrict [23.1] Only show 'edit' on published pages when viewer is the owner. 13 September 2023, 11:56:12 UTC
a7caa73 Merge pull request #16678 from mvdbeek/fix_metadata_setting [23.1] Fix metadata setting in extended metadata + outputs_to_working_directory mode 13 September 2023, 11:52:21 UTC
5d6a11a Merge pull request #16683 from mvdbeek/use_more_lenient_regex_library_to_allow_inline_global_regex_flags [23.1] Fix regex validation for global inline flags 13 September 2023, 11:31:27 UTC
ed94b91 Use --biocontainers in converter tests 13 September 2023, 10:18:25 UTC
63442d1 Fix regex validation for global inline flags Fixes https://github.com/galaxyproject/galaxy/issues/16676 13 September 2023, 10:00:57 UTC
3930c6a Fix empty file check timing 12 September 2023, 21:46:34 UTC
4a46073 Fix test_pulsar_embedded_remote_metadata.py::test_tools[job_properties] 12 September 2023, 21:11:26 UTC
7fe197b Fix file discovery 12 September 2023, 21:11:26 UTC
01d4d43 Drop unnecessary getsize guard 12 September 2023, 17:53:13 UTC
9961ec3 Fix pulsar path rewrite for set_metadata This looks quite weird, can we just get the outputs from the tool run maybe ? 12 September 2023, 17:53:13 UTC
8ae0b92 Always reset external filename 12 September 2023, 15:22:05 UTC
c26e5b6 Only show 'edit' on published pages when viewer is the owner. Shared pages don't grant edit permissions, so this is good enough. All actual security is enforced in the API, so this just displays (or not) the UI. 12 September 2023, 14:35:30 UTC
af9a0f3 Merge pull request #16652 from dannon/login-fixes [23.1] Login/Register fixes 12 September 2023, 14:06:17 UTC
6210267 Set up output_fnames also with ``use_metadata_binary`` We'll surely need that too, as well as a datatypes config file. I'd assume this probably didn't fully work before and that we have no tests ? It does seem a little hard to test and I found no traces of tests. 12 September 2023, 11:27:32 UTC
90c8438 Fix and extend extended metadata outputs to working directory tests 12 September 2023, 11:07:10 UTC
8c5ac57 Fix incorrect ``output_fnames`` calculation in pulsar job runner ``` outputs = [ Bunch(false_path=os.path.join(outputs_directory, os.path.basename(path)), real_path=path) for path in self.get_output_files(job_wrapper) ] ``` would always set the false_path attribute, even if that is not correct because outputs_to_working_directory isn't activated and pulsar doesn't need to do any staging (e.g. with ``` default_file_action: copy # don't copy outputs, not needed. file_actions: paths: - path_types: output action: none ``` as done in embedded_pulsar_metadata_extended_job_conf.xml. Fixing this allows us to eliminate the `if object_store:` guard to setting the external filename, which in turn fixes the metadata value setting if `outputs_to_working_directory: true` and `metadata_strategy: extended` is used. 12 September 2023, 10:39:29 UTC
0cd7a0c Update galaxyproject/charts utilizing visualizations to match the latest version which uses the modern api for deleting. 11 September 2023, 17:45:02 UTC
cd50265 Merge pull request #16655 from mvdbeek/detached_instance_fix [23.1] Ensure Job belongs to current SA session 10 September 2023, 08:25:52 UTC
7b98816 Merge pull request #16667 from mvdbeek/object_store_push_fix [23.1] Push to object store even if ``set_meta`` fails 10 September 2023, 08:17:59 UTC
3f76e1d Fix pulsar_embedded_metadata_extended_metadata tests 09 September 2023, 21:26:09 UTC
e657893 Simplify ``if not metadata_set_successfully:`` branch 09 September 2023, 12:53:56 UTC
5e26987 Ignore failed metadata for expression.json outputs 09 September 2023, 12:53:56 UTC
d35414e Add test case for expression tool data output with bam pja 09 September 2023, 12:53:56 UTC
df54cb6 Try to always push outputs back to object store 09 September 2023, 12:53:55 UTC
5b4179e Merge branch 'release_23.0' into release_23.1 08 September 2023, 12:41:13 UTC
98da565 Merge branch 'release_22.05' into release_23.0 08 September 2023, 12:40:36 UTC
591eff4 Merge pull request #16669 from mvdbeek/chromedriver_upstream [22.05] Switch to upstream setup-chromedriver action 08 September 2023, 12:39:48 UTC
7c11227 Switch to upstream setup-chromedriver action 08 September 2023, 11:45:26 UTC
ea148f3 Merge pull request #16659 from simonbray/patch-3 [23.0] Force `__DUPLICATE_FILE_TO_COLLECTION__` 'size' param to integer 08 September 2023, 11:23:09 UTC
b0230bf Merge pull request #16656 from mvdbeek/fix_nested_tool_state_when_eval [23.1] Fix expression evaluation for nested state 08 September 2023, 11:22:13 UTC
ab87587 Merge pull request #16663 from bernt-matthias/topic/xsd_test_collection_name [23.1] xsd: allow name attribute of test collections 08 September 2023, 10:19:10 UTC
eecfc02 Fix expression evaluation for nested state 08 September 2023, 09:43:25 UTC
3199134 Apply suggestions from code review Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com> 07 September 2023, 20:02:15 UTC
85124d8 xsd: allow name attrbute of test collections already supported by the framework fixes: https://github.com/galaxyproject/galaxy/issues/16654 07 September 2023, 18:16:26 UTC
c77636b Merge pull request #16661 from mvdbeek/terminal_state_in_sort_collection_tool [23.1] Make sort_collection tool require terminal datasets 07 September 2023, 16:52:38 UTC
076b825 force __DUPLICATE_FILE_TO_COLLECTION__ 'size' param to integer 07 September 2023, 15:10:44 UTC
3c07df1 Minor login -> Log in tweaks 07 September 2023, 14:55:43 UTC
21d3b93 Make sort_collection tool require terminal datasets It would be nice if we could limit this just to the dataset that we're reading the element identifiers from, but this will do as a bugfix. 07 September 2023, 14:52:07 UTC
0d3a399 Add test for conditional step with nested tool state 07 September 2023, 07:40:26 UTC
87a588d Treat RuntimeValue as None for now 07 September 2023, 07:40:26 UTC
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