| 72bfa2b | Nicola Soranzo | 11 December 2022, 22:31:52 UTC | Merge branch 'release_21.05' into release_21.09 | 11 December 2022, 22:31:52 UTC |
| 6b9f090 | Nicola Soranzo | 11 December 2022, 21:54:23 UTC | Merge branch 'release_21.01' into release_21.05 | 11 December 2022, 21:54:23 UTC |
| 2b79cf2 | Dannon | 11 December 2022, 20:25:50 UTC | Merge pull request #15170 from nsoranzo/release_21.01_fix_passenv [21.01] Fix `passenv` option for tox 4.0 | 11 December 2022, 20:25:50 UTC |
| 653b415 | Nicola Soranzo | 11 December 2022, 18:29:54 UTC | Fix `passenv` option for tox 4.0 See https://tox.wiki/en/latest/faq.html#tox-4-changed-ini-rules | 11 December 2022, 18:35:04 UTC |
| 69ef571 | Nicola Soranzo | 08 December 2022, 12:52:58 UTC | Merge branch 'release_21.05' into release_21.09 | 08 December 2022, 12:52:58 UTC |
| a59d4d4 | Nicola Soranzo | 08 December 2022, 12:39:45 UTC | Merge branch 'release_21.01' into release_21.05 | 08 December 2022, 12:39:45 UTC |
| 7d21208 | Nicola Soranzo | 08 December 2022, 08:13:16 UTC | Merge pull request #15143 from martenson/release_21.01 [21.01] Rename removed tox configuration option | 08 December 2022, 08:13:16 UTC |
| 2887eb8 | Martin Cech | 07 December 2022, 20:47:41 UTC | rename removed tox configuration option | 07 December 2022, 20:47:41 UTC |
| ce40058 | Martin Cech | 05 November 2022, 16:17:37 UTC | Merge pull request #14908 from mvdbeek/backport_data_column_fix [21.09] Backport 14518: Always call strip() on data_column column values | 05 November 2022, 16:17:37 UTC |
| a01c8c5 | mvdbeek | 03 November 2022, 09:37:49 UTC | Use _run_jobs instead of _run_workflows | 03 November 2022, 09:37:49 UTC |
| e6aeb21 | mvdbeek | 26 August 2022, 15:49:50 UTC | Always call strip() on data_column column values Not just when they start with `c`. Should fix running workflows that were created by manually writing columns in the text area field and then hitting enter. | 02 November 2022, 16:51:20 UTC |
| e3d0561 | Nicola Soranzo | 02 November 2022, 15:40:57 UTC | Merge branch 'release_21.05' into release_21.09 | 02 November 2022, 15:40:57 UTC |
| d51d911 | Nicola Soranzo | 02 November 2022, 15:39:03 UTC | Merge branch 'release_21.01' into release_21.05 | 02 November 2022, 15:39:27 UTC |
| c8a514a | Nicola Soranzo | 02 November 2022, 15:32:58 UTC | Merge branch 'release_20.09' into release_21.01 | 02 November 2022, 15:37:59 UTC |
| 9d31330 | Nicola Soranzo | 02 November 2022, 15:32:02 UTC | Merge branch 'release_20.05' into release_20.09 | 02 November 2022, 15:32:02 UTC |
| 6df30d6 | Nicola Soranzo | 02 November 2022, 14:57:01 UTC | Merge branch 'release_20.01' into release_20.05 | 02 November 2022, 14:57:01 UTC |
| ae59839 | Nicola Soranzo | 02 November 2022, 14:55:38 UTC | Merge branch 'release_19.09' into release_20.01 | 02 November 2022, 14:55:38 UTC |
| f0a269c | Nicola Soranzo | 02 November 2022, 14:53:53 UTC | Merge branch 'release_19.05' into release_19.09 | 02 November 2022, 14:53:53 UTC |
| d48c4a4 | Nicola Soranzo | 02 November 2022, 14:48:21 UTC | Merge pull request #14900 from nsoranzo/release_19.05_backport_14882 [19.05] Backport fixes from #14882 | 02 November 2022, 14:48:21 UTC |
| 82a779e | Nicola Soranzo | 01 November 2022, 02:29:07 UTC | Force recomputation of conda properties after conda `install` conda version and conda-build availability may change after an `install` in the root environment. | 01 November 2022, 12:03:54 UTC |
| 3cbf332 | Nicola Soranzo | 01 November 2022, 01:31:08 UTC | Retry conda `install` and `create` commands without strict channel priority Restore the possibility to solve environments with packages present in multiple channels but whose requested version is not available in the highest priority one. The issue applies only when using conda >=4.7.5. Fix the following error for the `test/integration/test_resolvers.py::TestCondaResolutionIntegration::test_dependency_install` integration test: ``` ____________ TestCondaResolutionIntegration.test_dependency_install ____________ self = <integration.test_resolvers.TestCondaResolutionIntegration object at 0x7f7009682950> def test_dependency_install(self): """ Test installation of GNUPLOT dependency. """ data = GNUPLOT create_response = self._post("dependency_resolvers/dependency", data=data, admin=True) self._assert_status_code_is(create_response, 200) response = create_response.json() > self._assert_dependency_type(response) test/integration/test_resolvers.py:46: _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ self = <integration.test_resolvers.TestCondaResolutionIntegration object at 0x7f7009682950> response = {'cacheable': False, 'dependency_resolver': {'auto_init': True, 'auto_install': False, 'can_uninstall_dependencies': T...nda,defaults', ...}, 'dependency_type': 'conda', 'environment_path': '/tmp/tmp5f_37kj2/conda/envs/__gnuplot@_uv_', ...} type = 'conda', exact = True def _assert_dependency_type(self, response, type="conda", exact=True): if "dependency_type" not in response: raise Exception(f"Response [{response}] did not contain key 'dependency_type'") dependency_type = response["dependency_type"] assert dependency_type == type, f"Dependency type [{dependency_type}] not the expected value [{type}]" if "exact" not in response: raise Exception(f"Response [{response}] did not contain key 'exact'") > assert response["exact"] is exact E assert False is True test/integration/test_resolvers.py:150: AssertionError ``` due to the fact that this test tries to install version 4.6 of gnuplot, while in the highest priority conda-forge channel the oldest version available is 5.0.5. When trying to create the environment, conda fails to resolve it, so Galaxy falls back to create an environment with an unversioned gnuplot, which fails the exact version test. Introduced in commit bb000b2403e51b2ecf2a4dfe9d2ac560b333a437 . | 01 November 2022, 11:57:29 UTC |
| c262156 | Nicola Soranzo | 31 October 2022, 22:28:16 UTC | Fix mistakenly overwriting ``self._conda_version`` with conda-build version. Introduced in commit 0ed66646e1234a93193edbd4b5577c535ed32f99 . | 01 November 2022, 11:57:07 UTC |
| 3bc34bf | Nicola Soranzo | 26 October 2022, 17:43:18 UTC | Merge branch 'release_21.05' into release_21.09 | 26 October 2022, 17:43:18 UTC |
| 85ad2a0 | Nicola Soranzo | 26 October 2022, 15:57:32 UTC | Merge branch 'release_21.01' into release_21.05 | 26 October 2022, 15:57:32 UTC |
| cc0d811 | Nicola Soranzo | 26 October 2022, 15:55:05 UTC | Merge branch 'release_20.09' into release_21.01 | 26 October 2022, 15:55:05 UTC |
| 14f3fc2 | Nicola Soranzo | 26 October 2022, 13:18:20 UTC | Merge branch 'release_20.05' into release_20.09 | 26 October 2022, 13:18:20 UTC |
| a99bea6 | Nicola Soranzo | 26 October 2022, 10:44:37 UTC | Merge branch 'release_20.01' into release_20.05 | 26 October 2022, 10:44:37 UTC |
| 68ba6fd | Nicola Soranzo | 26 October 2022, 10:30:22 UTC | Merge branch 'release_19.09' into release_20.01 | 26 October 2022, 10:30:22 UTC |
| 563b9e7 | Nicola Soranzo | 26 October 2022, 09:07:50 UTC | Merge branch 'release_19.05' into release_19.09 | 26 October 2022, 09:07:50 UTC |
| e8eb248 | Nicola Soranzo | 26 October 2022, 09:03:07 UTC | Merge pull request #14856 from nsoranzo/release_19.05_fix_14848 [19.05] Require also a recent pyOpenSSL package when installing conda | 26 October 2022, 09:03:07 UTC |
| bb000b2 | Nicola Soranzo | 25 October 2022, 18:28:57 UTC | Add `--strict-channel-priority` to conda create/install commands Fix https://github.com/galaxyproject/galaxy/issues/12790 . This is added only if using conda >=4.7.5 , which includes this bug fix: https://github.com/conda/conda/pull/8819 | 25 October 2022, 18:29:14 UTC |
| 32e3287 | Nicola Soranzo | 25 October 2022, 18:21:41 UTC | Require also a recent pyOpenSSL package when installing conda Fix https://github.com/galaxyproject/galaxy/issues/14848 . | 25 October 2022, 18:26:59 UTC |
| 0ed6664 | Nicola Soranzo | 25 October 2022, 18:18:11 UTC | Rewrite `CondaContext._guess_conda_properties()` to use `conda info` | 25 October 2022, 18:18:11 UTC |
| cf036f1 | Marius van den Beek | 17 October 2022, 10:13:56 UTC | Merge pull request #14530 from bernt-matthias/correct-fail [21.09] JobWrapper: use correct fail method | 17 October 2022, 10:13:56 UTC |
| cd4ae46 | Matthias Bernt | 28 June 2022, 10:04:38 UTC | JobWrapper: use correct fail method if the JobWrapper.fail method is called directly exit code (etc) are lost. fixes https://github.com/galaxyproject/galaxy/issues/14206 not sure why this error popped up now, probably a change in tool verification ..? | 16 September 2022, 11:05:23 UTC |
| 06baa27 | Nicola Soranzo | 06 September 2022, 10:24:20 UTC | Merge branch 'release_21.05' into release_21.09 | 06 September 2022, 10:24:20 UTC |
| 8069584 | Nicola Soranzo | 06 September 2022, 10:12:59 UTC | Merge branch 'release_21.01' into release_21.05 | 06 September 2022, 10:12:59 UTC |
| 50bdd35 | Marius van den Beek | 05 September 2022, 17:18:56 UTC | Merge pull request #14513 from bernt-matthias/topic/bed-metadata [21.01] fix metadata setting for bed and interval | 05 September 2022, 17:18:56 UTC |
| f3eb503 | Dannon | 31 August 2022, 12:11:58 UTC | Merge pull request #14497 from mvdbeek/fix_finding_repository_directory [21.05] Fix finding repository directory if repository is repeated in path | 31 August 2022, 12:11:58 UTC |
| 9b66e46 | Matthias Bernt | 26 August 2022, 15:04:01 UTC | always use default=0 for strandCol just for consistency | 26 August 2022, 15:04:01 UTC |
| fe30308 | Matthias Bernt | 26 August 2022, 10:55:08 UTC | bed, interval: set default for strandCol bed and interval datatypes `check element_is_set` before overwriting metadata. since the having `default=None` and `no_value=0` makes `element_is_set` return True (since `None!=0`). Therefore metadata values are never set | 26 August 2022, 13:53:40 UTC |
| 4e23fbb | Matthias Bernt | 26 August 2022, 10:01:54 UTC | Revert "set metadata default to no_value if default is None" This reverts commit dff9d4087bdcd500912eb4a7e5512b9b26ab9879. | 26 August 2022, 10:01:54 UTC |
| dff9d40 | Matthias Bernt | 25 August 2022, 15:30:13 UTC | set metadata default to no_value if default is None | 25 August 2022, 15:30:13 UTC |
| 59f7704 | Matthias Bernt | 25 August 2022, 14:43:31 UTC | test case showing failing set_meta broke in https://github.com/galaxyproject/galaxy/commit/7d0ec29fa06ae6f04c0ae6fc193a390bc11cddcd | 25 August 2022, 14:45:26 UTC |
| 05cad6d | mvdbeek | 23 August 2022, 13:47:56 UTC | Fix finding repository directory if repository directory is repeated in path As happens for instance for toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/0e3cf9594bb7/ncbi_blast_plus/tools/ncbi_blast_plus | 23 August 2022, 13:49:48 UTC |
| 52de57b | Nicola Soranzo | 23 June 2022, 13:43:21 UTC | Merge branch 'release_21.05' into release_21.09 | 23 June 2022, 13:43:21 UTC |
| 00ba0a9 | Marius van den Beek | 23 June 2022, 13:35:52 UTC | Merge pull request #13907 from davelopez/21.05_fix_anonymous_import_histories [21.05] Fix condition importing histories anonymously | 23 June 2022, 13:35:52 UTC |
| fda88e4 | David López | 23 June 2022, 13:17:05 UTC | Merge pull request #14057 from mvdbeek/backport_session_fix [21.09][Backport] Add sessioncookie with ``SameSite=None; secure`` for tool_runner path | 23 June 2022, 13:17:05 UTC |
| 8361240 | Marius van den Beek | 23 June 2022, 12:15:52 UTC | Merge pull request #14161 from mvdbeek/fix_dataset_controller_actions [21.09] Fix dataset controller actions (delete, purge, unhide) | 23 June 2022, 12:15:52 UTC |
| 3700be2 | mvdbeek | 22 June 2022, 18:28:15 UTC | Fix dataset controller actions We don't have a parent property anymore. That's been broken since 21.09. Fixes https://sentry.galaxyproject.org/organizations/galaxy/issues/4971/?project=3&query=is%3Aunresolved&statsPeriod=14d: ``` AttributeError: 'HistoryDatasetAssociation' object has no attribute 'parent' File "galaxy/webapps/galaxy/controllers/dataset.py", line 897, in _undelete while topmost_parent.parent: ``` | 22 June 2022, 18:34:18 UTC |
| b08fe47 | John Chilton | 18 June 2022, 13:46:20 UTC | Merge pull request #14086 from mvdbeek/fix_rule_builder_integer_dataset [21.09] Fix rule builder input with integer values | 18 June 2022, 13:46:20 UTC |
| a314bcb | mvdbeek | 17 June 2022, 10:08:29 UTC | Fix rule builder input with integer values Upload a dataset with the only content being `123`. Go to the upload module, select the `Rule-based` tab. Select `Load tabular data from: `History Dataset` and select the dataset you just uploaded. Without this fix you'd see ``` vue.runtime.esm.js?2b0e:1897 TypeError: selection.content.split is not a function at createCollectionViaRules (RuleBasedCollectionCreatorModal.js?46f9:63:1) at child.buildCollection (history-view-edit.js?0c85:387:1) at VueComponent._buildSelection (RulesInput.vue?5e16:199:1) at VueComponent._eventBuild (RulesInput.vue?5e16:164:1) at invokeWithErrorHandling (vue.runtime.esm.js?2b0e:1863:1) at HTMLButtonElement.invoker (vue.runtime.esm.js?2b0e:2184:1) at original._wrapper (vue.runtime.esm.js?2b0e:6961:1) ``` That because `selection.content` is an integer value. | 17 June 2022, 10:30:55 UTC |
| 6679571 | mvdbeek | 13 June 2022, 13:49:37 UTC | Improve tool_runner path construction That'll work without galaxy_url_prefix and seems a little more robust. | 13 June 2022, 16:56:21 UTC |
| 55ecc38 | mvdbeek | 09 June 2022, 10:18:42 UTC | Add selenium test for ucsc table browser data source | 13 June 2022, 09:03:13 UTC |
| eec196b | mvdbeek | 09 June 2022, 09:12:00 UTC | Api test to verify tool runner session handling | 13 June 2022, 08:58:58 UTC |
| 7fd52cb | mvdbeek | 08 June 2022, 18:17:36 UTC | Add sessioncookie with SameSite=None; secure for tool_runner path That should fix https://github.com/galaxyproject/galaxy/issues/11066 / https://github.com/galaxyproject/galaxy/issues/11374. | 13 June 2022, 08:58:42 UTC |
| c5527ed | Nicola Soranzo | 06 June 2022, 09:22:29 UTC | Merge pull request #14020 from nuwang/fix_missing_biotools | 06 June 2022, 09:22:29 UTC |
| 16d9981 | Nuwan Goonasekera | 06 June 2022, 06:15:55 UTC | Fix missing biotools package | 06 June 2022, 06:15:55 UTC |
| 6159fe2 | Nicola Soranzo | 06 June 2022, 01:04:09 UTC | Merge pull request #14018 from nuwang/fix_missing_webapp_packages | 06 June 2022, 01:04:09 UTC |
| 4a779c4 | Björn Grüning | 03 June 2022, 09:04:59 UTC | try fixing the integration tests | 05 June 2022, 22:35:22 UTC |
| 9fdb5f2 | David López | 12 April 2022, 11:42:57 UTC | Add type hint suggestion Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com> | 05 June 2022, 18:28:50 UTC |
| 44bf638 | davelopez | 12 April 2022, 11:24:55 UTC | Fix mypy error | 05 June 2022, 18:28:38 UTC |
| 6e43464 | Nuwan Goonasekera | 05 June 2022, 18:08:05 UTC | Update packages/app/requirements.txt Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com> | 05 June 2022, 18:08:05 UTC |
| c61e391 | Nuwan Goonasekera | 05 June 2022, 07:51:38 UTC | Add missing whoosh package to galaxy-app package requirements | 05 June 2022, 07:51:38 UTC |
| 635944a | Nuwan Goonasekera | 05 June 2022, 06:47:47 UTC | Also add missing error_reports.plugins | 05 June 2022, 06:47:47 UTC |
| dd0702e | Nuwan Goonasekera | 04 June 2022, 21:00:37 UTC | Add root webapp to webapp package | 04 June 2022, 21:11:58 UTC |
| 42b3c6e | davelopez | 11 May 2022, 14:31:46 UTC | Fix condition importing histories anonymously | 11 May 2022, 14:31:46 UTC |
| b924a86 | Marius van den Beek | 15 April 2022, 09:10:42 UTC | Merge pull request #13728 from davelopez/21.09_fix_collection_error_handling [21.09] Fix collection population error handling | 15 April 2022, 09:10:42 UTC |
| d33b563 | davelopez | 14 April 2022, 18:10:37 UTC | Simulate errored datasets when collection population fails This is a temporal hack for the legacy history panel. It needs to be correctly handled in the new history. | 14 April 2022, 18:10:37 UTC |
| 1b36d16 | davelopez | 14 April 2022, 18:08:32 UTC | Display population error in collection panel | 14 April 2022, 18:08:32 UTC |
| f5d96e8 | davelopez | 14 April 2022, 14:55:31 UTC | Fix collection error message rendering - Display `populated_state_message` as description when the populated_state is `failed` | 14 April 2022, 18:05:31 UTC |
| 52167a7 | davelopez | 14 April 2022, 14:11:07 UTC | Fix collection `populated_state` error check The backend returns `failed` and not `error` as `populated_state` | 14 April 2022, 14:11:07 UTC |
| 3403972 | Björn Grüning | 13 April 2022, 18:20:31 UTC | Merge pull request #13720 from davelopez/21.09_backport_job_error_message_fix [21.09] Backport job error message fix | 13 April 2022, 18:20:31 UTC |
| 8ffa4d4 | davelopez | 28 March 2022, 13:44:38 UTC | Display response error message if job fails To make the real error more obvious: - If there is an err_msg in the response, it is displayed in `danger` alert style - The fixed message indicating the request cannot be completed and pointing to the submitted data appears now in `warning` alert style | 13 April 2022, 16:18:17 UTC |
| 27f9fcc | davelopez | 28 March 2022, 13:40:08 UTC | Fix job definition object not displayed on error `this.jobDef` was always empty in case of an error | 13 April 2022, 16:17:48 UTC |
| 3356ef6 | John Chilton | 11 April 2022, 15:16:25 UTC | Merge pull request #13697 from bernt-matthias/topic/backport13688pt2 [21.09] backport of #13688 part 2 (Fix sorting of recursively discovered datasets) | 11 April 2022, 15:16:25 UTC |
| 4bc5603 | Matthias Bernt | 07 April 2022, 12:09:12 UTC | add test for correct sorting on recursive discovery | 08 April 2022, 17:38:50 UTC |
| 98b324a | Matthias Bernt | 07 April 2022, 12:07:43 UTC | refactor: do not store intermediate lists | 08 April 2022, 17:38:39 UTC |
| c01f9d4 | Matthias Bernt | 07 April 2022, 10:17:13 UTC | fix sorting for recursively discovered datasets files in subdirectories were not subject to sort | 08 April 2022, 17:38:23 UTC |
| 7275b2f | Nicola Soranzo | 04 April 2022, 16:58:51 UTC | Merge pull request #13667 from nsoranzo/release_21.09_add_rich_requirement | 04 April 2022, 16:58:51 UTC |
| 48a0145 | Nicola Soranzo | 04 April 2022, 14:42:27 UTC | Add missing pin for `rich`, dependency of refgenconf 0.12.0 Pinning to the version that was current when https://github.com/galaxyproject/galaxy/pull/12435 was merged to fix the following traceback with rich 12.1.0: ``` 2022-04-04T14:16:19.5073158Z File "/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy/tools/data/__init__.py", line 21, in <module> 2022-04-04T14:16:19.5073535Z import refgenconf 2022-04-04T14:16:19.5074393Z File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/refgenconf/__init__.py", line 6, in <module> 2022-04-04T14:16:19.5074853Z from .populator import looper_refgenie_populate 2022-04-04T14:16:19.5075535Z File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/refgenconf/populator.py", line 9, in <module> 2022-04-04T14:16:19.5075970Z from . import refgenconf 2022-04-04T14:16:19.5076607Z File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/refgenconf/refgenconf.py", line 27, in <module> 2022-04-04T14:16:19.5077091Z from rich.progress import BarColumn, Progress, TextColumn 2022-04-04T14:16:19.5077768Z File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/rich/progress.py", line 43, in <module> 2022-04-04T14:16:19.5078272Z from .console import Console, JustifyMethod, RenderableType, Group 2022-04-04T14:16:19.5078956Z File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/rich/console.py", line 46, in <module> 2022-04-04T14:16:19.5079437Z from ._log_render import FormatTimeCallable, LogRender 2022-04-04T14:16:19.5080105Z File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/rich/_log_render.py", line 5, in <module> 2022-04-04T14:16:19.5124479Z from .text import Text, TextType 2022-04-04T14:16:19.5130069Z File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/rich/text.py", line 5, in <module> 2022-04-04T14:16:19.5134858Z from rich.emoji import EmojiVariant 2022-04-04T14:16:19.5139847Z File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/rich/emoji.py", line 4, in <module> 2022-04-04T14:16:19.5144648Z from .jupyter import JupyterMixin 2022-04-04T14:16:19.5147478Z File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/rich/jupyter.py", line 4, in <module> 2022-04-04T14:16:19.5150060Z from .segment import Segment 2022-04-04T14:16:19.5152862Z File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/rich/segment.py", line 19, in <module> 2022-04-04T14:16:19.5155442Z from .cells import ( 2022-04-04T14:16:19.5158112Z File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/rich/cells.py", line 6, in <module> 2022-04-04T14:16:19.5159612Z from ._lru_cache import LRUCache 2022-04-04T14:16:19.5161691Z File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/rich/_lru_cache.py", line 8, in <module> 2022-04-04T14:16:19.5163233Z from typing_extensions import OrderedDict 2022-04-04T14:16:19.5165289Z ImportError: cannot import name 'OrderedDict' from 'typing_extensions' (/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/typing_extensions.py) ``` | 04 April 2022, 14:43:43 UTC |
| c7ce60a | Nicola Soranzo | 04 April 2022, 14:11:17 UTC | Merge branch 'release_21.05' into release_21.09 | 04 April 2022, 14:11:17 UTC |
| 06d37d9 | Marius van den Beek | 04 April 2022, 13:52:53 UTC | Merge pull request #13664 from nsoranzo/release_21.05_backport_dbf7ac364a20835acf16ccdffea3018a58023e2d [21.05] Partially backport #13532 to fix `test_github_search` mulled unit test | 04 April 2022, 13:52:53 UTC |
| 2cbbf1e | Nicola Soranzo | 10 March 2022, 19:42:10 UTC | Check GitHub API rate limit in GitHubSearch. Deprecate `get_json()` search Follow-up on https://github.com/galaxyproject/galaxy/pull/13509 . | 04 April 2022, 11:56:07 UTC |
| 58d7e3c | Nicola Soranzo | 20 July 2021, 14:26:30 UTC | Raise exception if GET request returned an unsuccessful status code | 04 April 2022, 11:40:16 UTC |
| 8e4bdb5 | Nicola Soranzo | 18 March 2022, 18:08:10 UTC | Merge branch 'release_21.05' into release_21.09 | 18 March 2022, 18:08:10 UTC |
| 74a51d9 | Marius van den Beek | 18 March 2022, 14:42:43 UTC | Merge pull request #13552 from mvdbeek/fix_tag_creation_metadata_strategy_extended [21.09] Fix creating tags within sessionless context | 18 March 2022, 14:42:43 UTC |
| 7aae40d | mvdbeek | 18 March 2022, 11:01:29 UTC | Include unit test for sessionless export/import with tags Seems like the only way you could previously include tags was if you included them in the data fetch tool. | 18 March 2022, 11:16:17 UTC |
| 558cad2 | mvdbeek | 18 March 2022, 10:12:06 UTC | Return tag in get_tag_by_name function | 18 March 2022, 10:12:06 UTC |
| bad8ecb | Nicola Soranzo | 16 March 2022, 18:00:25 UTC | Merge pull request #13554 from mvdbeek/fix_sff_extractor_tool | 16 March 2022, 18:00:25 UTC |
| e2d4380 | mvdbeek | 16 March 2022, 14:13:40 UTC | Fix ``sff_extract`` tool, drop type annotation I don't think this tool is really used much, but it is loaded in `tool_conf.xml`. https://github.com/galaxyproject/galaxy/pull/11877 added type annotations, and that's a syntax error on 2.7 The alternative would be to fix the rest of the tool for 3.x, but I think we're just wasting our time there and we shouldn't touch this again. | 16 March 2022, 14:24:55 UTC |
| 880c129 | mvdbeek | 16 March 2022, 10:32:01 UTC | Fix creating tags within sessionless context xref: https://github.com/galaxyproject/galaxy/issues/13551, fixes ``` galaxy.jobs ERROR 2022-03-15 00:21:29,515 [pN:main,p:2180,tN:LocalRunner.work_thread-3] problem importing job outputs. stdout [] stderr [ Traceback (most recent call last): File "metadata/set.py", line 1, in <module> from galaxy_ext.metadata.set_metadata import set_metadata; set_metadata() File "/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy/metadata/set_metadata.py", line 121, in set_metadata set_metadata_portable() File "/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy/metadata/set_metadata.py", line 291, in set_metadata_portable collect_dynamic_outputs(job_context, output_collections) File "/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy/job_execution/output_collect.py", line 147, in collect_dynamic_outputs persist_elements_to_hdca(job_context, elements, hdca, collector=DEFAULT_DATASET_COLLECTOR) File "/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy/model/store/discover.py", line 719, in persist_elements_to_hdca filenames, File "/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy/model/store/discover.py", line 292, in populate_collection_elements final_job_state=final_job_state, File "/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy/model/store/discover.py", line 354, in _populate_elements self.add_tags_to_datasets(datasets=element_datasets["datasets"], tag_lists=element_datasets["tag_lists"]) File "/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy/model/store/discover.py", line 576, in add_tags_to_datasets self.tag_handler.add_tags_from_list(user, dataset, tags, flush=False) File "/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy/model/tags.py", line 61, in add_tags_from_list return self.set_tags_from_list(user, item, new_tags_set, flush=flush) File "/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy/model/tags.py", line 75, in set_tags_from_list self.apply_item_tags(user, item, unicodify(new_tags_str, "utf-8"), flush=flush) File "/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy/model/tags.py", line 207, in apply_item_tags self.apply_item_tag(user, item, name, value, flush=flush) File "/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy/model/tags.py", line 179, in apply_item_tag tag = self._get_or_create_tag(lc_name) File "/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy/model/tags.py", line 281, in _get_or_create_tag tag = self._create_tag(scrubbed_tag_str) File "/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy/model/tags.py", line 246, in _create_tag tag = self._create_tag_instance(tag_name) File "/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy/model/tags.py", line 428, in _create_tag_instance tag = super()._create_tag_instance(tag_name) File "/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy/model/tags.py", line 259, in _create_tag_instance Session = sessionmaker(self.sa_session.bind) AttributeError: 'NoneType' object has no attribute 'bind' ] Traceback (most recent call last): File "/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy/jobs/__init__.py", line 1828, in finish import_model_store.perform_import(history=job.history, job=job) File "/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy/model/store/__init__.py", line 209, in perform_import datasets_attrs = self.datasets_properties() File "/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy/model/store/__init__.py", line 930, in datasets_properties datasets_attrs = load(open(datasets_attrs_file_name)) FileNotFoundError: [Errno 2] No such file or directory: '/tmp/tmp19s6x278/tmpt0rr8vmw/tmp2mjq6ysx/database/job_working_directory1/000/7/metadata/outputs_populated/datasets_attrs.txt' galaxy.jobs.runners ERROR 2022-03-15 00:21:29,516 [pN:main,p:2180,tN:LocalRunner.work_thread-3] (7/) Job wrapper finish method failed Traceback (most recent call last): File "/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy/jobs/runners/__init__.py", line 594, in _finish_or_resubmit_job job_stderr=job_stderr, File "/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy/jobs/__init__.py", line 1828, in finish import_model_store.perform_import(history=job.history, job=job) File "/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy/model/store/__init__.py", line 209, in perform_import datasets_attrs = self.datasets_properties() File "/home/runner/work/galaxy/galaxy/galaxy root/lib/galaxy/model/store/__init__.py", line 930, in datasets_properties datasets_attrs = load(open(datasets_attrs_file_name)) FileNotFoundError: [Errno 2] No such file or directory: '/tmp/tmp19s6x278/tmpt0rr8vmw/tmp2mjq6ysx/database/job_working_directory1/000/7/metadata/outputs_populated/datasets_attrs.txt' ``` | 16 March 2022, 10:32:06 UTC |
| 525f443 | mvdbeek | 15 March 2022, 14:11:26 UTC | Merge branch 'release_21.05' into release_21.09 | 15 March 2022, 14:11:26 UTC |
| 99835a8 | Björn Grüning | 14 March 2022, 20:30:26 UTC | Merge pull request #13537 from davelopez/patch_21.05_allow_admins_access_datasets [21.05] Allow admin access to datasets API (before refactoring) | 14 March 2022, 20:30:26 UTC |
| 7bc55b9 | Björn Grüning | 14 March 2022, 20:29:37 UTC | Merge pull request #13538 from davelopez/patch_21.09_allow_admin_access_private_datasets [21.09] Allow admin access to datasets API (before refactoring) | 14 March 2022, 20:29:37 UTC |
| ffd916f | John Chilton | 25 October 2021, 15:48:05 UTC | Fixes for LDDA manager - clearly that didn't work at all. | 14 March 2022, 17:23:15 UTC |
| 1330da2 | John Chilton | 25 October 2021, 15:48:05 UTC | Fixes for LDDA manager - clearly that didn't work at all. | 14 March 2022, 17:21:03 UTC |
| 248ec4e | davelopez | 14 March 2022, 14:05:17 UTC | Allow admin access to datasets API (before refactoring) This patch contains the changes in #13060 and it is meant to be applied only to 21.09 do not merge forward this commit into 22.01 since it is already fixed there | 14 March 2022, 14:05:17 UTC |
| 71742ac | davelopez | 14 March 2022, 13:50:22 UTC | Allow admin access to datasets API (before refactoring) This patch contains the changes in #13060 and it is meant to be applied only to 21.05 do not merge forward this commit into 22.01 since it is already fixed there | 14 March 2022, 13:50:22 UTC |
| 6bbf5f6 | Marius van den Beek | 09 March 2022, 14:49:24 UTC | Merge pull request #13497 from nuwang/pin_docker_playbook [21.09] Pin corresponding playbook repo to sync with Galaxy release | 09 March 2022, 14:49:24 UTC |
