{"payload":{"feedbackUrl":"https://github.com/orgs/community/discussions/53140","repo":{"id":31211061,"defaultBranch":"dev","name":"galaxy","ownerLogin":"galaxyproject","currentUserCanPush":false,"isFork":false,"isEmpty":false,"createdAt":"2015-02-23T14:18:06.000Z","ownerAvatar":"https://avatars.githubusercontent.com/u/7937847?v=4","public":true,"private":false,"isOrgOwned":true},"refInfo":{"name":"","listCacheKey":"v0:1726667523.0","currentOid":""},"activityList":{"items":[{"before":"c61ad56a9cf31a9ad8ed338c02476359c0655902","after":null,"ref":"refs/heads/dependabot/npm_and_yarn/client/express-4.21.0","pushedAt":"2024-09-18T13:52:03.000Z","pushType":"branch_deletion","commitsCount":0,"pusher":{"login":"dependabot[bot]","name":null,"path":"/apps/dependabot","primaryAvatarUrl":"https://avatars.githubusercontent.com/in/29110?s=80&v=4"}},{"before":"5acc518b9607830916da85a05fb7ed7574ebd606","after":"aa2574343555f10294dc626f991d7b728dfccb5a","ref":"refs/heads/dev","pushedAt":"2024-09-18T13:51:54.000Z","pushType":"pr_merge","commitsCount":2,"pusher":{"login":"dannon","name":"Dannon","path":"/dannon","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/155398?s=80&v=4"},"commit":{"message":"Merge 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#18836 from guerler/workflow_labels\n\n[24.1] Fix alert handling in workflow label handler","shortMessageHtmlLink":"Merge pull request <a class=\"issue-link js-issue-link\" data-error-text=\"Failed to load title\" data-id=\"2531493015\" data-permission-text=\"Title is private\" data-url=\"https://github.com/galaxyproject/galaxy/issues/18836\" data-hovercard-type=\"pull_request\" data-hovercard-url=\"/galaxyproject/galaxy/pull/18836/hovercard\" href=\"https://github.com/galaxyproject/galaxy/pull/18836\">#18836</a> from guerler/workflow_labels"}},{"before":"5e42f10386e0657e0fdce807c39cb40f8a96ffc1","after":"07fa2e32d7bbaec497b49f74355edb2cd252f2b2","ref":"refs/heads/release_24.1","pushedAt":"2024-09-18T07:10:46.000Z","pushType":"pr_merge","commitsCount":4,"pusher":{"login":"mvdbeek","name":"Marius van den Beek","path":"/mvdbeek","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/6804901?s=80&v=4"},"commit":{"message":"Merge pull request #18826 from ljocha/release_24.1\n\n[24.1] prevent \"missing refresh_token\" errors by supporting <extra_scopes> also with Keycloak backend","shortMessageHtmlLink":"Merge pull request <a class=\"issue-link js-issue-link\" data-error-text=\"Failed to load title\" data-id=\"2531044208\" data-permission-text=\"Title is private\" data-url=\"https://github.com/galaxyproject/galaxy/issues/18826\" data-hovercard-type=\"pull_request\" data-hovercard-url=\"/galaxyproject/galaxy/pull/18826/hovercard\" href=\"https://github.com/galaxyproject/galaxy/pull/18826\">#18826</a> from ljocha/release_24.1"}},{"before":"43a2845609904e555367bbe78974548180330677","after":"5e42f10386e0657e0fdce807c39cb40f8a96ffc1","ref":"refs/heads/release_24.1","pushedAt":"2024-09-18T07:09:48.000Z","pushType":"pr_merge","commitsCount":2,"pusher":{"login":"mvdbeek","name":"Marius van den Beek","path":"/mvdbeek","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/6804901?s=80&v=4"},"commit":{"message":"Merge pull request #18839 from davelopez/24.1_fix_help_form_post_schema\n\n[24.1] Make all fields optional for HelpForumPost","shortMessageHtmlLink":"Merge pull request <a class=\"issue-link js-issue-link\" data-error-text=\"Failed to load title\" data-id=\"2531552004\" data-permission-text=\"Title is private\" data-url=\"https://github.com/galaxyproject/galaxy/issues/18839\" data-hovercard-type=\"pull_request\" data-hovercard-url=\"/galaxyproject/galaxy/pull/18839/hovercard\" href=\"https://github.com/galaxyproject/galaxy/pull/18839\">#18839</a> from davelopez/24.1_fix_help_form_post_schema"}},{"before":"a5679440b5d3758144fb0744cc9b83d8495d50c3","after":"43a2845609904e555367bbe78974548180330677","ref":"refs/heads/release_24.1","pushedAt":"2024-09-18T07:07:37.000Z","pushType":"pr_merge","commitsCount":2,"pusher":{"login":"mvdbeek","name":"Marius van den Beek","path":"/mvdbeek","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/6804901?s=80&v=4"},"commit":{"message":"Merge pull request #18833 from mvdbeek/maybe_fix_flaky_navigation_v2_ts_tests\n\n[24.1] Maybe fix flaky navigation v2 ts tests","shortMessageHtmlLink":"Merge pull request <a class=\"issue-link js-issue-link\" data-error-text=\"Failed to load title\" data-id=\"2531451610\" data-permission-text=\"Title is private\" data-url=\"https://github.com/galaxyproject/galaxy/issues/18833\" data-hovercard-type=\"pull_request\" data-hovercard-url=\"/galaxyproject/galaxy/pull/18833/hovercard\" href=\"https://github.com/galaxyproject/galaxy/pull/18833\">#18833</a> from mvdbeek/maybe_fix_flaky_navigation_v2_…"}},{"before":"236f1b3b73ae033d792f16803291494b02f682a9","after":"5acc518b9607830916da85a05fb7ed7574ebd606","ref":"refs/heads/dev","pushedAt":"2024-09-17T15:28:52.000Z","pushType":"pr_merge","commitsCount":4,"pusher":{"login":"jmchilton","name":"John Chilton","path":"/jmchilton","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/216771?s=80&v=4"},"commit":{"message":"Merge pull request #18787 from jmchilton/assertion_overhaul\n\nModelling for Test Assertions","shortMessageHtmlLink":"Merge pull request <a class=\"issue-link js-issue-link\" data-error-text=\"Failed to load title\" data-id=\"2510695979\" data-permission-text=\"Title is private\" data-url=\"https://github.com/galaxyproject/galaxy/issues/18787\" data-hovercard-type=\"pull_request\" data-hovercard-url=\"/galaxyproject/galaxy/pull/18787/hovercard\" href=\"https://github.com/galaxyproject/galaxy/pull/18787\">#18787</a> from jmchilton/assertion_overhaul"}},{"before":"b24e8e11a9ed3447b60b2586ff219b7b71b91690","after":"f9703e1d4aca18a4a4462dd4a7a2c05596dd8358","ref":"refs/heads/usegalaxy","pushedAt":"2024-09-17T14:55:58.000Z","pushType":"force_push","commitsCount":0,"pusher":{"login":"mvdbeek","name":"Marius van den Beek","path":"/mvdbeek","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/6804901?s=80&v=4"},"commit":{"message":"Remove stray `h`","shortMessageHtmlLink":"Remove stray <code>h</code>"}},{"before":"d17d7425d0536992ab225e90d693318a58de0b6a","after":"a5679440b5d3758144fb0744cc9b83d8495d50c3","ref":"refs/heads/release_24.1","pushedAt":"2024-09-17T14:55:13.000Z","pushType":"pr_merge","commitsCount":2,"pusher":{"login":"mvdbeek","name":"Marius van den Beek","path":"/mvdbeek","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/6804901?s=80&v=4"},"commit":{"message":"Merge pull request #18819 from mvdbeek/fix_celery_config_when_galaxy_started_via_main_py\n\n[24.1] Fix wrong celery_app config on job and workflow handlers","shortMessageHtmlLink":"Merge pull request <a class=\"issue-link js-issue-link\" data-error-text=\"Failed to load title\" data-id=\"2528899231\" data-permission-text=\"Title is private\" data-url=\"https://github.com/galaxyproject/galaxy/issues/18819\" data-hovercard-type=\"pull_request\" data-hovercard-url=\"/galaxyproject/galaxy/pull/18819/hovercard\" href=\"https://github.com/galaxyproject/galaxy/pull/18819\">#18819</a> from mvdbeek/fix_celery_config_when_galaxy_…"}},{"before":"3e17d8e75df7744c30d07d189ec64fd7ba6e48d4","after":"d17d7425d0536992ab225e90d693318a58de0b6a","ref":"refs/heads/release_24.1","pushedAt":"2024-09-17T14:53:29.000Z","pushType":"pr_merge","commitsCount":2,"pusher":{"login":"mvdbeek","name":"Marius van den Beek","path":"/mvdbeek","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/6804901?s=80&v=4"},"commit":{"message":"Merge pull request #18825 from mvdbeek/fix_named_cursor_issue\n\n[24.1] Fix ``named cursor is not valid anymore``","shortMessageHtmlLink":"Merge pull request <a class=\"issue-link js-issue-link\" data-error-text=\"Failed to load title\" data-id=\"2530864885\" data-permission-text=\"Title is private\" data-url=\"https://github.com/galaxyproject/galaxy/issues/18825\" data-hovercard-type=\"pull_request\" data-hovercard-url=\"/galaxyproject/galaxy/pull/18825/hovercard\" href=\"https://github.com/galaxyproject/galaxy/pull/18825\">#18825</a> from mvdbeek/fix_named_cursor_issue"}},{"before":"5b4d8a1688de8ce530018c548096f8824b7cd8a1","after":"3e17d8e75df7744c30d07d189ec64fd7ba6e48d4","ref":"refs/heads/master","pushedAt":"2024-09-17T13:39:03.000Z","pushType":"push","commitsCount":46,"pusher":{"login":"nsoranzo","name":"Nicola Soranzo","path":"/nsoranzo","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/4924623?s=80&v=4"},"commit":{"message":"Merge pull request #18824 from mvdbeek/fix_job_handler_startup_order\n\n[24.1] Start job handler only after building InteractiveToolManager","shortMessageHtmlLink":"Merge pull request <a class=\"issue-link js-issue-link\" data-error-text=\"Failed to load title\" data-id=\"2530842500\" data-permission-text=\"Title is private\" data-url=\"https://github.com/galaxyproject/galaxy/issues/18824\" data-hovercard-type=\"pull_request\" data-hovercard-url=\"/galaxyproject/galaxy/pull/18824/hovercard\" href=\"https://github.com/galaxyproject/galaxy/pull/18824\">#18824</a> from mvdbeek/fix_job_handler_startup_order"}},{"before":"106b0383aebba28d1e642022bc9e0bf19e50d5d6","after":"3e17d8e75df7744c30d07d189ec64fd7ba6e48d4","ref":"refs/heads/release_24.1","pushedAt":"2024-09-17T13:09:20.000Z","pushType":"pr_merge","commitsCount":2,"pusher":{"login":"mvdbeek","name":"Marius van den Beek","path":"/mvdbeek","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/6804901?s=80&v=4"},"commit":{"message":"Merge pull request #18824 from mvdbeek/fix_job_handler_startup_order\n\n[24.1] Start job handler only after building InteractiveToolManager","shortMessageHtmlLink":"Merge pull request <a class=\"issue-link js-issue-link\" data-error-text=\"Failed to load title\" data-id=\"2530842500\" data-permission-text=\"Title is private\" data-url=\"https://github.com/galaxyproject/galaxy/issues/18824\" data-hovercard-type=\"pull_request\" data-hovercard-url=\"/galaxyproject/galaxy/pull/18824/hovercard\" href=\"https://github.com/galaxyproject/galaxy/pull/18824\">#18824</a> from mvdbeek/fix_job_handler_startup_order"}},{"before":null,"after":"28bf05ffcbff81db58f3b8963af1a600c4fe5afb","ref":"refs/heads/dependabot/npm_and_yarn/client/dompurify-3.1.3","pushedAt":"2024-09-16T20:49:35.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"dependabot[bot]","name":null,"path":"/apps/dependabot","primaryAvatarUrl":"https://avatars.githubusercontent.com/in/29110?s=80&v=4"},"commit":{"message":"Bump dompurify from 3.0.6 to 3.1.3 in /client\n\nBumps [dompurify](https://github.com/cure53/DOMPurify) from 3.0.6 to 3.1.3.\n- [Release notes](https://github.com/cure53/DOMPurify/releases)\n- [Commits](https://github.com/cure53/DOMPurify/compare/3.0.6...3.1.3)\n\n---\nupdated-dependencies:\n- dependency-name: dompurify\n  dependency-type: direct:production\n...\n\nSigned-off-by: dependabot[bot] <support@github.com>","shortMessageHtmlLink":"Bump dompurify from 3.0.6 to 3.1.3 in /client"}},{"before":"8faed8fc93b6eca290fa3aa390e581651455e35f","after":"b24e8e11a9ed3447b60b2586ff219b7b71b91690","ref":"refs/heads/usegalaxy","pushedAt":"2024-09-16T17:19:47.000Z","pushType":"force_push","commitsCount":0,"pusher":{"login":"mvdbeek","name":"Marius van den Beek","path":"/mvdbeek","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/6804901?s=80&v=4"},"commit":{"message":"Fix wrong celery_app config on job and workflow handlers\n\nFixes https://github.com/galaxyproject/galaxy/issues/18727 /\nhttps://sentry.galaxyproject.org/share/issue/8091a452f32645b89b37976362779532/:\n```\nMessage\n(59965185/49195886) Job wrapper finish method failed\nStack Trace\n\nNewest\n\nOperationalError: unable to open database file\n  File \"sqlalchemy/engine/base.py\", line 146, in __init__\n    self._dbapi_connection = engine.raw_connection()\n  File \"sqlalchemy/engine/base.py\", line 3300, in raw_connection\n    return self.pool.connect()\n  File \"sqlalchemy/pool/base.py\", line 449, in connect\n    return _ConnectionFairy._checkout(self)\n  File \"sqlalchemy/pool/base.py\", line 1263, in _checkout\n    fairy = _ConnectionRecord.checkout(pool)\n  File \"sqlalchemy/pool/base.py\", line 712, in checkout\n    rec = pool._do_get()\n  File \"sqlalchemy/pool/impl.py\", line 179, in _do_get\n    with util.safe_reraise():\n  File \"sqlalchemy/util/langhelpers.py\", line 146, in __exit__\n    raise exc_value.with_traceback(exc_tb)\n  File \"sqlalchemy/pool/impl.py\", line 177, in _do_get\n    return self._create_connection()\n  File \"sqlalchemy/pool/base.py\", line 390, in _create_connection\n    return _ConnectionRecord(self)\n  File \"sqlalchemy/pool/base.py\", line 674, in __init__\n    self.__connect()\n  File \"sqlalchemy/pool/base.py\", line 900, in __connect\n    with util.safe_reraise():\n  File \"sqlalchemy/util/langhelpers.py\", line 146, in __exit__\n    raise exc_value.with_traceback(exc_tb)\n  File \"sqlalchemy/pool/base.py\", line 896, in __connect\n    self.dbapi_connection = connection = pool._invoke_creator(self)\n  File \"sqlalchemy/engine/create.py\", line 643, in connect\n    return dialect.connect(*cargs, **cparams)\n  File \"sqlalchemy/engine/default.py\", line 620, in connect\n    return self.loaded_dbapi.connect(*cargs, **cparams)\nOperationalError: (sqlite3.OperationalError) unable to open database file\n(Background on this error at: https://sqlalche.me/e/20/e3q8)\n  File \"kombu/connection.py\", line 472, in _reraise_as_library_errors\n    yield\n  File \"kombu/connection.py\", line 556, in _ensured\n    return fun(*args, **kwargs)\n  File \"kombu/messaging.py\", line 202, in _publish\n    [maybe_declare(entity) for entity in declare]\n  File \"kombu/messaging.py\", line 202, in <listcomp>\n    [maybe_declare(entity) for entity in declare]\n  File \"kombu/messaging.py\", line 107, in maybe_declare\n    return maybe_declare(entity, self.channel, retry, **retry_policy)\n  File \"kombu/common.py\", line 113, in maybe_declare\n    return _maybe_declare(entity, channel)\n  File \"kombu/common.py\", line 153, in _maybe_declare\n    entity.declare(channel=channel)\n  File \"kombu/entity.py\", line 617, in declare\n    self._create_queue(nowait=nowait, channel=channel)\n  File \"kombu/entity.py\", line 626, in _create_queue\n    self.queue_declare(nowait=nowait, passive=False, channel=channel)\n  File \"kombu/entity.py\", line 655, in queue_declare\n    ret = channel.queue_declare(\n  File \"kombu/transport/virtual/base.py\", line 537, in queue_declare\n    self._new_queue(queue, **kwargs)\n  File \"kombu/transport/sqlalchemy/__init__.py\", line 159, in _new_queue\n    self._get_or_create(queue)\n  File \"kombu/transport/sqlalchemy/__init__.py\", line 138, in _get_or_create\n    obj = self.session.query(self.queue_cls) \\\n  File \"kombu/transport/sqlalchemy/__init__.py\", line 133, in session\n    _, Session = self._open()\n  File \"kombu/transport/sqlalchemy/__init__.py\", line 125, in _open\n    metadata.create_all(engine)\n  File \"sqlalchemy/sql/schema.py\", line 5857, in create_all\n    bind._run_ddl_visitor(\n  File \"sqlalchemy/engine/base.py\", line 3250, in _run_ddl_visitor\n    with self.begin() as conn:\n  File \"contextlib.py\", line 137, in __enter__\n    return next(self.gen)\n  File \"sqlalchemy/engine/base.py\", line 3240, in begin\n    with self.connect() as conn:\n  File \"sqlalchemy/engine/base.py\", line 3276, in connect\n    return self._connection_cls(self)\n  File \"sqlalchemy/engine/base.py\", line 148, in __init__\n    Connection._handle_dbapi_exception_noconnection(\n  File \"sqlalchemy/engine/base.py\", line 2440, in _handle_dbapi_exception_noconnection\n    raise sqlalchemy_exception.with_traceback(exc_info[2]) from e\n  File \"sqlalchemy/engine/base.py\", line 146, in __init__\n    self._dbapi_connection = engine.raw_connection()\n  File \"sqlalchemy/engine/base.py\", line 3300, in raw_connection\n    return self.pool.connect()\n  File \"sqlalchemy/pool/base.py\", line 449, in connect\n    return _ConnectionFairy._checkout(self)\n  File \"sqlalchemy/pool/base.py\", line 1263, in _checkout\n    fairy = _ConnectionRecord.checkout(pool)\n  File \"sqlalchemy/pool/base.py\", line 712, in checkout\n    rec = pool._do_get()\n  File \"sqlalchemy/pool/impl.py\", line 179, in _do_get\n    with util.safe_reraise():\n  File \"sqlalchemy/util/langhelpers.py\", line 146, in __exit__\n    raise exc_value.with_traceback(exc_tb)\n  File \"sqlalchemy/pool/impl.py\", line 177, in _do_get\n    return self._create_connection()\n  File \"sqlalchemy/pool/base.py\", line 390, in _create_connection\n    return _ConnectionRecord(self)\n  File \"sqlalchemy/pool/base.py\", line 674, in __init__\n    self.__connect()\n  File \"sqlalchemy/pool/base.py\", line 900, in __connect\n    with util.safe_reraise():\n  File \"sqlalchemy/util/langhelpers.py\", line 146, in __exit__\n    raise exc_value.with_traceback(exc_tb)\n  File \"sqlalchemy/pool/base.py\", line 896, in __connect\n    self.dbapi_connection = connection = pool._invoke_creator(self)\n  File \"sqlalchemy/engine/create.py\", line 643, in connect\n    return dialect.connect(*cargs, **cparams)\n  File \"sqlalchemy/engine/default.py\", line 620, in connect\n    return self.loaded_dbapi.connect(*cargs, **cparams)\nOperationalError: (sqlite3.OperationalError) unable to open database file\n(Background on this error at: https://sqlalche.me/e/20/e3q8)\n  File \"galaxy/jobs/runners/__init__.py\", line 677, in _finish_or_resubmit_job\n    job_wrapper.finish(\n  File \"galaxy/jobs/__init__.py\", line 2070, in finish\n    task_wrapper.delay()\n  File \"celery/canvas.py\", line 353, in delay\n    return self.apply_async(partial_args, partial_kwargs)\n  File \"celery/canvas.py\", line 400, in apply_async\n    return _apply(args, kwargs, **options)\n  File \"celery/app/task.py\", line 594, in apply_async\n    return app.send_task(\n  File \"celery/app/base.py\", line 801, in send_task\n    amqp.send_task_message(P, name, message, **options)\n  File \"celery/app/amqp.py\", line 518, in send_task_message\n    ret = producer.publish(\n  File \"kombu/messaging.py\", line 186, in publish\n    return _publish(\n  File \"kombu/connection.py\", line 553, in _ensured\n    with self._reraise_as_library_errors():\n  File \"contextlib.py\", line 155, in __exit__\n    self.gen.throw(typ, value, traceback)\n  File \"kombu/connection.py\", line 476, in _reraise_as_library_errors\n    raise ConnectionError(str(exc)) from exc\n```\nThe issue was that we aren't setting `GALAXY_CONFIG_FILE` if the job and\nworkflow handlers are started with `-c path/to/galaxy.yml`, and the\ncelery config heuristic isn't looking at sys.argv.","shortMessageHtmlLink":"Fix wrong celery_app config on job and workflow 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