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22 July 2024, 14:10:58 UTC
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af730bc mvdbeek 29 July 2023, 10:28:32 UTC Create version 23.0.5 29 July 2023, 10:28:32 UTC
d9b3ede Dannon 28 July 2023, 19:02:06 UTC Merge pull request #16480 from bernt-matthias/fix/profile-regex [23.0] Linter: fix regex for profile version 28 July 2023, 19:02:06 UTC
4f3b8da Matthias Bernt 28 July 2023, 16:57:41 UTC make pattern even more flexible since in the past releases were quite irregular 28 July 2023, 16:57:41 UTC
0205f9b Marius van den Beek 28 July 2023, 16:39:26 UTC Merge pull request #16482 from simonbray/patch-3 [23.0] Adjust test_data_download method in GalaxyInteractorApi so an admin user is not required 28 July 2023, 16:39:26 UTC
77c0e91 Matthias Bernt 28 July 2023, 08:28:04 UTC fix regex for profile version - did not allow for new style profile versions (that may have only a single digit after the dot) - fix: do not allow `,` in profile version 28 July 2023, 15:32:20 UTC
34dcced Simon Bray 28 July 2023, 15:11:04 UTC adjust test_data_download method in GalaxyInteractorApi so an admin user is not required 28 July 2023, 15:11:04 UTC
3269758 Marius van den Beek 26 July 2023, 14:35:19 UTC Merge pull request #16449 from kysrpex/biotools [23.0] Fix parsing tool metadata from bio.tools 26 July 2023, 14:35:19 UTC
47b99ae Marius van den Beek 26 July 2023, 14:34:33 UTC Merge pull request #16464 from davelopez/23.0_fix_user_preferences_disabled_condition [23.0] Fix filtering of disabled user preferences in UI 26 July 2023, 14:34:33 UTC
a12ca8f Marius van den Beek 26 July 2023, 12:30:30 UTC Merge pull request #16424 from bernt-matthias/23.0-fix-gitlab-error-report [23.0] Fixes for (gitlab) error reporting 26 July 2023, 12:30:30 UTC
ff7565d mvdbeek 26 July 2023, 12:13:32 UTC Merge branch 'release_22.05' into release_23.0 26 July 2023, 12:16:34 UTC
075e630 Marius van den Beek 26 July 2023, 12:03:58 UTC Merge pull request #16461 from mvdbeek/chromedriver_bump [22.05] Bump version of chromedriver setup action 26 July 2023, 12:03:58 UTC
b9c07a7 mvdbeek 26 July 2023, 10:29:36 UTC Use reusable workflow in all selenium workflows 26 July 2023, 10:29:36 UTC
989551d mvdbeek 26 July 2023, 10:06:15 UTC Externalize selenium setup with reusable workflow 26 July 2023, 10:25:04 UTC
b56d785 mvdbeek 26 July 2023, 09:46:13 UTC Use action 26 July 2023, 10:25:00 UTC
eee8632 mvdbeek 26 July 2023, 08:42:30 UTC Use upstream command to install chrome and chromedriver 26 July 2023, 09:17:24 UTC
9dc2ca8 Marius van den Beek 26 July 2023, 08:32:26 UTC Merge pull request #16459 from mira-miracoli/fix-urlparser Fix urlparser 26 July 2023, 08:32:26 UTC
65c2037 davelopez 26 July 2023, 08:10:26 UTC Fix filtering of disabled user preferences 26 July 2023, 08:10:26 UTC
9d2b386 M Bernt 25 July 2023, 13:54:56 UTC Update lib/galaxy/tools/error_reports/plugins/github.py Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com> 25 July 2023, 13:54:56 UTC
b66f941 Marius van den Beek 25 July 2023, 13:11:59 UTC Merge pull request #16443 from bdwheele/media_player_fix_issue_16415 [23.0] Media player fix issue 16415 25 July 2023, 13:11:59 UTC
89b063f Marius van den Beek 25 July 2023, 12:31:19 UTC Merge pull request #15933 from bernt-matthias/topic/fix-output-label-linter [23.0] fix linter: duplicated label check 25 July 2023, 12:31:19 UTC
37977eb mvdbeek 25 July 2023, 12:11:04 UTC Bump version of chromedriver setup action 25 July 2023, 12:11:04 UTC
da8fc06 M Bernt 25 July 2023, 11:28:36 UTC more black 25 July 2023, 11:28:36 UTC
c684e0b Matthias Bernt 09 May 2023, 14:13:12 UTC also warn in case of a filter 25 July 2023, 11:14:20 UTC
2775005 Matthias Bernt 09 May 2023, 13:26:03 UTC make duplicated label a warning 25 July 2023, 11:14:20 UTC
af797d9 Matthias Bernt 13 April 2023, 11:43:05 UTC fix linter: duplicated label check duplicated labels may be OK if there are filters 25 July 2023, 11:14:20 UTC
2831f62 M Bernt 25 July 2023, 11:08:26 UTC black 25 July 2023, 11:08:26 UTC
fd26e7c Mira Kuntz 25 July 2023, 07:39:13 UTC fix hostname matching 25 July 2023, 07:39:13 UTC
f74de07 Mira Kuntz 25 July 2023, 07:38:51 UTC fix robots.txt and favicon.ico 25 July 2023, 07:38:51 UTC
b1f7c47 José Manuel Domínguez 24 July 2023, 14:00:56 UTC Use an empty list as topic and function when they are missing from bio.tools metadata Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com> 24 July 2023, 14:00:56 UTC
dc88496 mvdbeek 24 July 2023, 13:44:11 UTC Fix linting 24 July 2023, 13:44:11 UTC
963d2f6 Brian Wheeler 24 July 2023, 13:13:53 UTC Fix send_file so media player works Make sure there's a valid start/end time when generating headers 24 July 2023, 13:42:49 UTC
b4d3611 José Manuel Domínguez 24 July 2023, 12:37:09 UTC Fix parsing tool metadata from bio.tools The keys "topic" and "function" do not exist any longer for many tools. Thus, such tools fail to load. 24 July 2023, 12:54:40 UTC
f97c6a7 Matthias Bernt 20 July 2023, 22:06:42 UTC do not quote messages from error reporters so far users have seen e.g. `<p>Your error report has been sent</p>` from the email reporter. Another example is the link to the created issue of the gitlab error reporter. 24 July 2023, 11:05:17 UTC
77fe9e8 Matthias Bernt 20 July 2023, 22:04:00 UTC fixes to gitlab error reporting plugin - URLs for low level gitlab functions (self.gitlab.http_post) need to be quoted - closed issues need to be cached if a comment should be added to existing (potentially closed) issues 24 July 2023, 11:05:17 UTC
07f942e Dannon 23 July 2023, 13:40:36 UTC Merge pull request #16403 from bernt-matthias/topic/startup-conda [23.0] fixes to common startup 23 July 2023, 13:40:36 UTC
c7db0bb Nicola Soranzo 20 July 2023, 15:54:49 UTC Do not install npm/yarn via conda if they already available at the correct version 20 July 2023, 23:58:36 UTC
a9b2a4f Nicola Soranzo 20 July 2023, 15:23:00 UTC Code refactoring Simplification allowed by commit 39c0000c1bbf6c96f55f0143bc788f82107745a9 . 20 July 2023, 23:58:36 UTC
1b2ac2a Matthias Bernt 19 July 2023, 16:21:38 UTC also set galaxy config file variable in common startup otherwise GALAXY_CONDITIONAL_DEPENDENCIES can not be determined. in run.sh set_galaxy_config_file_var is called only after common_startup is called. 20 July 2023, 23:58:35 UTC
bb90e3b Matthias Bernt 19 July 2023, 16:14:14 UTC activate the conda env before the python venv and install node and yarn via conda if a conda env is used 20 July 2023, 23:58:35 UTC
e1e99b5 Matthias Bernt 19 July 2023, 15:40:30 UTC fix job config parsing for getting conditional requirements noticed that I did not get `drmaa` installed automatically. reason is that self.config.get("job_config_file") only gets the name of the config file relative to the path containing the galaxy config. 20 July 2023, 23:58:34 UTC
961e2d9 Nicola Soranzo 12 May 2023, 17:01:22 UTC Split matplotlib requirement to support Python 3.11 on macOS matplotlib 3.5.3 (the latest version supporting Python 3.7) fails to build a wheel for Python 3.11 on macOS. Although it can be still be installed via the `setup.py install` fallback, this has been removed in pip 23.1 . 20 July 2023, 23:58:34 UTC
741ecf6 Nicola Soranzo 12 May 2023, 14:48:09 UTC Pin pysam to >=0.21.0 This reverts commit 353c08cbb942a766e1c1a5e96060d2032bf2a1a0 . pysam 0.20.0 doesn't build for Python 3.11 on macOS, so we need to temporarily add the unnecessary Cython runtime dependency that pysam 0.21 brings in. 20 July 2023, 23:58:33 UTC
387aa1d Nicola Soranzo 10 May 2023, 12:07:35 UTC Test first startup on macOS also with Python 3.11 - Allow passing GALAXY_CONDA_PYTHON_VERSION environment variable to the startup script to specify the Python version to use when creating the `_galaxy_` conda environment. - Some Shellcheck fixes. 20 July 2023, 23:58:33 UTC
92806a9 Matthias Bernt 14 July 2023, 07:18:55 UTC Improve log message wording 20 July 2023, 17:32:00 UTC
2eb6888 John Chilton 17 July 2023, 13:01:25 UTC Merge pull request #16413 from mvdbeek/mockssh_import_fix [23.0] Fix test discovery in vscode 17 July 2023, 13:01:25 UTC
a5275e6 mvdbeek 16 July 2023, 02:08:23 UTC Fix test discovery in vscode The vscode extension doesn't like the skip being raised during discovery anymore. 16 July 2023, 02:17:06 UTC
8d26b5c Marius van den Beek 13 July 2023, 01:55:40 UTC Merge pull request #16395 from nsoranzo/dont_always_install_node_in_venv 13 July 2023, 01:55:40 UTC
6249746 Nicola Soranzo 12 July 2023, 18:25:15 UTC Don't always install node in the virtualenv if it's already installed system-wide at the correct version. Prevent node installation issues during CI builds where we install node with the setup-node action but it was ignored because it was not inside the virtualenv, e.g.: https://github.com/galaxyproject/galaxy/actions/runs/5530959878/jobs/10091018774 12 July 2023, 18:26:02 UTC
eb36c37 Marius van den Beek 11 July 2023, 23:19:08 UTC Merge pull request #16390 from nsoranzo/release_23.0_pin_black [23.0] Pin black version to 23.3.0 in workflow action 11 July 2023, 23:19:08 UTC
e7500ae Nicola Soranzo 11 July 2023, 11:25:38 UTC Pin black version to 23.3.0 in workflow action black 23.7.0 has dropped support for Python 3.7 . 11 July 2023, 11:25:41 UTC
c93a718 Marius van den Beek 07 July 2023, 02:41:18 UTC Merge pull request #16377 from mvdbeek/copy_when_expression_when_copying_step [23.0] Copy when_expression when copying workflow step 07 July 2023, 02:41:18 UTC
6a2b0e4 mvdbeek 07 July 2023, 01:54:29 UTC Copy when_expression for when copying workflow step 07 July 2023, 01:54:29 UTC
61a6a0b David López 05 July 2023, 08:17:06 UTC Merge pull request #16364 from mvdbeek/fix_active_node_in_sidepanel_23.0 [23.0] Fix active step display in workflow editor side panel 05 July 2023, 08:17:06 UTC
f704c64 mvdbeek 03 July 2023, 17:09:52 UTC Fix active node display in side panel The minimal fix is the switch from `toRefs` to the computed property for configForm. I think that is because when we inserted a minimal new step we didn't include the `config_form` key, and so the later addition wasn't reactive ? Not exactly sure that is the right explanation. In any case the extended fix creates valid object that satisfies the `NewStep` interface, and drop the label and annotation handling, which does not happen in the tool state inputs. 04 July 2023, 19:04:53 UTC
6774c5a Marius van den Beek 04 July 2023, 15:26:32 UTC Merge pull request #16368 from davelopez/23.0_fix_named_tags_in_mako [23.0] Fix display of named tags in mako 04 July 2023, 15:26:32 UTC
a644d1d davelopez 04 July 2023, 08:06:38 UTC Fix display of named tags in mako 04 July 2023, 08:06:38 UTC
ffaf991 John Davis 03 July 2023, 13:37:08 UTC Merge pull request #16362 from neoformit/23.0-mail-template-fix [23.0] Minor bug fix for default mail templates 03 July 2023, 13:37:08 UTC
da6d77c Cameron Hyde 02 July 2023, 21:17:30 UTC Fix typo 02 July 2023, 21:17:30 UTC
dc2d286 Cameron Hyde 02 July 2023, 21:03:05 UTC Update default mail templates 02 July 2023, 21:03:05 UTC
dde02a8 Dannon 02 July 2023, 18:48:07 UTC Merge pull request #15329 from itisAliRH/fix-dataset-create-time-convert [23.0] Fix dataset create time convert 02 July 2023, 18:48:07 UTC
ba4517a Nate Coraor 01 July 2023, 00:21:59 UTC Merge pull request #16359 from natefoo/fix-mem-self-flush [23.0] Don't attempt to call a bool when using mem-self handler assignment. 01 July 2023, 00:21:59 UTC
fc33d6b Nate Coraor 30 June 2023, 22:55:08 UTC Don't attempt to call a bool when using mem-self handler assignment. 30 June 2023, 22:55:08 UTC
25b52a9 Nate Coraor 30 June 2023, 21:14:00 UTC Start work on 23.0.5.dev0 30 June 2023, 21:14:00 UTC
03d9eb6 Nate Coraor 30 June 2023, 21:13:57 UTC Create version 23.0.4 30 June 2023, 21:13:57 UTC
34e7580 Marius van den Beek 30 June 2023, 19:52:20 UTC Merge pull request #16354 from natefoo/packages-pin-pydantic [23.0] Pin pydantic in packages to <2 30 June 2023, 19:52:20 UTC
492b2ee Nate Coraor 30 June 2023, 19:20:22 UTC Pin fastapi to <0.99 30 June 2023, 19:20:22 UTC
10fe1c8 Nate Coraor 30 June 2023, 18:55:58 UTC Also pin pydantic in pyproject.toml 30 June 2023, 18:55:58 UTC
ab1e048 Nate Coraor 30 June 2023, 18:51:18 UTC Pin pydantic in packages to <2 30 June 2023, 18:51:18 UTC
9893cb3 Marius van den Beek 30 June 2023, 12:46:53 UTC Merge pull request #16349 from mvdbeek/redact_name_in_private_user_role [23.0] Redact private role name and description when purging user 30 June 2023, 12:46:53 UTC
9106772 mvdbeek 30 June 2023, 10:23:10 UTC Redact private role name when purging user Fixes ``` UniqueViolation: duplicate key value violates unique constraint "ix_role_name" DETAIL: Key (name)=(email@example.com) already exists. File "sqlalchemy/engine/base.py", line 1905, in _execute_context self.dialect.do_execute( File "sqlalchemy/engine/default.py", line 736, in do_execute cursor.execute(statement, parameters) IntegrityError: (psycopg2.errors.UniqueViolation) duplicate key value violates unique constraint "ix_role_name" DETAIL: Key (name)=(email@example.com) already exists. [SQL: INSERT INTO role (create_time, update_time, name, description, type, deleted) VALUES (%(create_time)s, %(update_time)s, %(name)s, %(description)s, %(type)s, %(deleted)s) RETURNING role.id] [parameters: {'create_time': datetime.datetime(2023, 6, 28, 22, 15, 51, 947910), 'update_time': datetime.datetime(2023, 6, 28, 22, 15, 51, 947918), 'name': 'email@example.com', 'description': 'Private Role for email@example.com', 'type': <types.PRIVATE: 'private'>, 'deleted': False}] (Background on this error at: https://sqlalche.me/e/14/gkpj) File "galaxy/web/framework/decorators.py", line 337, in decorator rval = func(self, trans, *args, **kwargs) File "galaxy/webapps/galaxy/controllers/user.py", line 142, in login return self.__validate_login(trans, payload, **kwd) File "galaxy/webapps/galaxy/controllers/user.py", line 199, in __validate_login trans.handle_user_login(user) File "galaxy/webapps/base/webapp.py", line 891, in handle_user_login self.app.security_agent.create_user_role(user, self.app) File "galaxy/model/security.py", line 738, in create_user_role self.get_private_user_role(user, auto_create=True) File "galaxy/model/security.py", line 765, in get_private_user_role return self.create_private_user_role(user) File "galaxy/model/security.py", line 748, in create_private_user_role user.attempt_create_private_role() File "galaxy/model/__init__.py", line 1105, in attempt_create_private_role with transaction(session): File "contextlib.py", line 113, in __enter__ return next(self.gen) File "galaxy/model/base.py", line 52, in transaction with session.begin(): File "<string>", line 2, in begin File "sqlalchemy/util/deprecations.py", line 375, in warned return fn(*args, **kwargs) File "sqlalchemy/orm/session.py", line 1347, in begin trans = SessionTransaction(self, nested=nested) File "sqlalchemy/orm/session.py", line 545, in __init__ self._take_snapshot(autobegin=autobegin) File "sqlalchemy/orm/session.py", line 662, in _take_snapshot self.session.flush() File "sqlalchemy/orm/session.py", line 3449, in flush self._flush(objects) File "sqlalchemy/orm/session.py", line 3589, in _flush transaction.rollback(_capture_exception=True) File "sqlalchemy/util/langhelpers.py", line 70, in __exit__ compat.raise_( File "sqlalchemy/util/compat.py", line 211, in raise_ raise exception File "sqlalchemy/orm/session.py", line 3549, in _flush flush_context.execute() File "sqlalchemy/orm/unitofwork.py", line 456, in execute rec.execute(self) File "sqlalchemy/orm/unitofwork.py", line 630, in execute util.preloaded.orm_persistence.save_obj( File "sqlalchemy/orm/persistence.py", line 245, in save_obj _emit_insert_statements( File "sqlalchemy/orm/persistence.py", line 1238, in _emit_insert_statements result = connection._execute_20( File "sqlalchemy/engine/base.py", line 1710, in _execute_20 return meth(self, args_10style, kwargs_10style, execution_options) File "sqlalchemy/sql/elements.py", line 334, in _execute_on_connection return connection._execute_clauseelement( File "sqlalchemy/engine/base.py", line 1577, in _execute_clauseelement ret = self._execute_context( File "sqlalchemy/engine/base.py", line 1948, in _execute_context self._handle_dbapi_exception( File "sqlalchemy/engine/base.py", line 2129, in _handle_dbapi_exception util.raise_( File "sqlalchemy/util/compat.py", line 211, in raise_ raise exception File "sqlalchemy/engine/base.py", line 1905, in _execute_context self.dialect.do_execute( File "sqlalchemy/engine/default.py", line 736, in do_execute cursor.execute(statement, parameters) ``` when a user attempts to login after they previously purged their account. 30 June 2023, 10:46:35 UTC
fe21c1a Marius van den Beek 28 June 2023, 13:20:36 UTC Merge pull request #16332 from mvdbeek/fix_for_default_when_statement [23.0] Fix default when statement evaluation 28 June 2023, 13:20:36 UTC
96bc25e Marius van den Beek 28 June 2023, 13:04:20 UTC Merge pull request #16330 from mvdbeek/fix_folder_access_anonymous_user [23.0] Fix folder access for anonymous user 28 June 2023, 13:04:20 UTC
84a053d mvdbeek 28 June 2023, 11:33:09 UTC Fix default when statement evaluation One can either do `${return inputs.when}` or the shorter `$(inputs.when)`, not `${inputs.when}`. Fixes https://github.com/galaxyproject/galaxy/issues/16331 28 June 2023, 11:47:21 UTC
6a2b095 mvdbeek 28 June 2023, 10:24:02 UTC Fix folder access for anonymous user if trans.user is None the value passed on to the model is None, and that leads to ``` 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 ValidationError: 1 validation error for FileLibraryFolderItem can_manage none is not an allowed value (type=type_error.none.not_allowed) 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/folder_contents.py", line 114, in index return self.service.index(trans, folder_id, payload) File "galaxy/webapps/galaxy/services/library_folder_contents.py", line 83, in index self._serialize_library_dataset(trans, current_user_roles, tag_manager, content_item) File "galaxy/webapps/galaxy/services/library_folder_contents.py", line 168, in _serialize_library_dataset dataset_item = FileLibraryFolderItem( File "pydantic/main.py", line 341, in pydantic.main.BaseModel.__init__ raise validation_error ``` as seen in https://sentry.galaxyproject.org/share/issue/3eec9cfa26744415b0c8d9885de9d273/ 28 June 2023, 10:24:06 UTC
1019ea4 Alireza Heidari 27 June 2023, 10:08:08 UTC Update client/src/co mponents/UtcDate.vue 27 June 2023, 10:08:08 UTC
e2bdabf Alireza Heidari 27 June 2023, 09:29:29 UTC Update client/src/components/DatasetInformation/DatasetInformation.test.js Co-authored-by: Laila Los <44241786+ElectronicBlueberry@users.noreply.github.com> 27 June 2023, 09:41:51 UTC
abd7f9e Alireza Heidari 18 January 2023, 13:35:16 UTC fix UtcDate unit test 27 June 2023, 09:41:50 UTC
4cc45a7 Alireza Heidari 18 January 2023, 11:55:40 UTC remove unused package `date-fns-tz` 27 June 2023, 09:41:50 UTC
a53d01e Alireza Heidari 18 January 2023, 11:55:01 UTC display time in the user's local time for pretty mode 27 June 2023, 09:41:49 UTC
1d4460a Martin Cech 27 June 2023, 02:53:22 UTC Merge pull request #15852 from anuprulez/patch-4 [23.0] Fix tool recommendations shown in a d3 js tree 27 June 2023, 02:53:22 UTC
1ef440e mvdbeek 26 June 2023, 07:32:37 UTC Start work on 23.0.4.dev0 26 June 2023, 07:32:37 UTC
b4adbb4 mvdbeek 26 June 2023, 07:32:32 UTC Create version 23.0.3 26 June 2023, 07:32:32 UTC
5c4fa2e Marius van den Beek 26 June 2023, 05:27:29 UTC Merge pull request #16308 from nuwang/add_missing_init [23.0] Missing init prevents models.py being bundled into tool_util 26 June 2023, 05:27:29 UTC
4a66240 nuwang 25 June 2023, 15:16:20 UTC Missing init prevents models.py being bundled into tool_util 25 June 2023, 15:16:20 UTC
353359f Martin Cech 21 June 2023, 22:16:24 UTC Merge pull request #16271 from nuwang/forward_port_oidc_username_fix [23.0] Forward port of slugify username received from oidc 21 June 2023, 22:16:24 UTC
bd6b2e8 Marius van den Beek 21 June 2023, 17:55:51 UTC Merge pull request #16284 from nsoranzo/release_23.0_fix_python3.11 [23.0] Fix converting Enum value to str for Python 3.11 21 June 2023, 17:55:51 UTC
25398bf Nicola Soranzo 21 June 2023, 15:42:02 UTC Fix converting Enum value to str for Python 3.11 Fix the following traceback: ``` Traceback (most recent call last): File "/tmp/tmpiustglxt/galaxy-dev/lib/galaxy/util/dictifiable.py", line 57, in to_dict visible_keys = self.__getattribute__(f"dict_{view}_visible_keys") ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ AttributeError: 'WorkflowInvocation' object has no attribute 'dict_InvocationSerializationView.element_visible_keys' During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/tmp/tmpiustglxt/galaxy-dev/lib/galaxy/web/framework/decorators.py", line 337, in decorator rval = func(self, trans, *args, **kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/tmp/tmpiustglxt/galaxy-dev/lib/galaxy/webapps/galaxy/api/workflows.py", line 891, in show_invocation return self.__encode_invocation(workflow_invocation, **kwd) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/tmp/tmpiustglxt/galaxy-dev/lib/galaxy/webapps/galaxy/api/workflows.py", line 1108, in __encode_invocation return self.invocations_service.serialize_workflow_invocation(invocation, params) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/tmp/tmpiustglxt/galaxy-dev/lib/galaxy/webapps/galaxy/services/invocations.py", line 202, in serialize_workflow_invocation as_dict = invocation.to_dict(view, step_details=step_details, legacy_job_state=legacy_job_state) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/tmp/tmpiustglxt/galaxy-dev/lib/galaxy/model/__init__.py", line 7814, in to_dict rval = super().to_dict(view=view, value_mapper=value_mapper) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/tmp/tmpiustglxt/galaxy-dev/lib/galaxy/util/dictifiable.py", line 59, in to_dict raise Exception(f"Unknown Dictifiable view: {view}") Exception: Unknown Dictifiable view: InvocationSerializationView.element ``` Broken in https://github.com/galaxyproject/galaxy/pull/13875 . 21 June 2023, 16:33:45 UTC
6544f0d nuwang 15 June 2023, 14:07:20 UTC Slugify username received from oidc 20 June 2023, 05:15:11 UTC
d3f9a33 Dannon 16 June 2023, 15:14:31 UTC Merge pull request #16251 from nuwang/fix_escape_of_preferred_username [22.05] Slugify username received from oidc 16 June 2023, 15:14:31 UTC
0f4db94 John Chilton 16 June 2023, 13:18:28 UTC Merge pull request #16262 from bernt-matthias/xsd/sep [23.0] xsd: add missing `sep` attribute for `has_n_columns` 16 June 2023, 13:18:28 UTC
0f65705 Matthias Bernt 16 June 2023, 09:07:04 UTC add missing sep attribute for has_n_columns forgotten here https://github.com/galaxyproject/galaxy/pull/12528 but I guess we do not need to backport further since it only affects the tool linting xsd check 16 June 2023, 09:24:18 UTC
4a4e5ab Nate Coraor 15 June 2023, 20:46:24 UTC Merge pull request #16244 from mvdbeek/load_data_tables_in_celery_worker [23.0] Load data tables in Celery worker 15 June 2023, 20:46:24 UTC
6cde078 Nate Coraor 15 June 2023, 14:14:41 UTC Merge pull request #16247 from natefoo/tool-data-bundle-file-path [23.0] When importing tool data bundles, use the first loc file for the matching table 15 June 2023, 14:14:41 UTC
791add0 nuwang 15 June 2023, 14:07:20 UTC Slugify username received from oidc 15 June 2023, 14:07:20 UTC
7f4dc26 Dannon Baker 14 June 2023, 18:59:35 UTC Amend schema to fix lint 14 June 2023, 18:59:35 UTC
0dfe8b4 Nate Coraor 14 June 2023, 17:40:40 UTC When importing tool data bundles, use the first loc file for the matching table, unless an explicit file path is passed via the API. 14 June 2023, 18:41:43 UTC
362bf76 mvdbeek 14 June 2023, 06:06:22 UTC Load data tables in Celery worker This is needed so that data bundle imports will work. The test case covering this will just receive the full integration app and thus didn't have this problem. Should fix: ``` [2023-06-13 21:33:38,899: ERROR/main] Task galaxy.import_data_bundle[0853f72f-c8ce-4e59-b6e8-25e208ce79f7] raised unexpected: AttributeError("'GalaxyManagerApplication' object has no attribute 'tool_data_tables'") Traceback (most recent call last): File "/cvmfs/main.galaxyproject.org/venv/lib/python3.8/site-packages/celery/app/trace.py", line 451, in trace_task R = retval = fun(*args, **kwargs) File "/cvmfs/main.galaxyproject.org/venv/lib/python3.8/site-packages/celery/app/trace.py", line 734, in __protected_call__ return self.run(*args, **kwargs) File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/celery/__init__.py", line 163, in wrapper rval = app.magic_partial(func)(*args, **kwds) File "/cvmfs/main.galaxyproject.org/venv/lib/python3.8/site-packages/lagom/wrapping.py", line 27, in _bound_func bound_args, bound_kwargs = argument_updater(args, kwargs) File "lagom/container.py", line 350, in _update_args File "lagom/container.py", line 425, in _infer_dependencies File "lagom/container.py", line 265, in resolve File "lagom/container.py", line 392, in _reflection_build_with_err_handling File "lagom/container.py", line 408, in _reflection_build File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/managers/tool_data.py", line 114, in __init__ self.tool_data_tables = app.tool_data_tables AttributeError: 'GalaxyManagerApplication' object has no attribute 'tool_data_tables' ``` 14 June 2023, 06:06:24 UTC
8d1f9f8 Marius van den Beek 13 June 2023, 17:32:57 UTC Merge pull request #16241 from mvdbeek/bump_galaxy_release_util_dep [23.0] Bump galaxy-release-util version to 0.1.2 13 June 2023, 17:32:57 UTC
cf7c012 mvdbeek 13 June 2023, 16:59:57 UTC Bump galaxy-release-util version to 0.1.2 13 June 2023, 16:59:57 UTC
414abff mvdbeek 13 June 2023, 15:58:19 UTC Start work on 23.0.3.dev0 13 June 2023, 15:58:19 UTC
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