| 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 |
| 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 |
| 9e4463e | Dannon Baker | 16 February 2022, 18:50:51 UTC | Merge remote-tracking branch 'upstream/release_20.05' into release_20.09 | 16 February 2022, 18:50:51 UTC |
| d4384ba | Dannon | 16 February 2022, 18:12:07 UTC | Merge pull request #13387 from mvdbeek/fix_history_export_include_hidden_handling [20.05] Fix history export include hidden handling | 16 February 2022, 18:12:07 UTC |
| c58f443 | Marius van den Beek | 16 February 2022, 15:00:06 UTC | Make test assertions more precise Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com> | 16 February 2022, 15:00:06 UTC |
| baed73d | mvdbeek | 16 February 2022, 10:38:36 UTC | Fix history_export include_hidden=False handling Fixes https://github.com/galaxyproject/galaxy/issues/13386 | 16 February 2022, 10:41:47 UTC |
| cea780c | mvdbeek | 16 February 2022, 10:36:06 UTC | Test that include_hidden is handled correctly | 16 February 2022, 10:41:44 UTC |
| b60e5ea | mvdbeek | 18 October 2021, 06:22:04 UTC | Merge branch 'release_20.05' into release_20.09 | 18 October 2021, 06:22:04 UTC |
| bf4dc3b | Marius van den Beek | 16 October 2021, 09:09:54 UTC | Merge pull request #12722 from mvdbeek/fix_recursively_deleting_hdcas [20.05] Continue deleting dataset collection if member HDA has no history | 16 October 2021, 09:09:54 UTC |
| 0aaef9c | mvdbeek | 15 October 2021, 16:25:39 UTC | Continue deleting dataset collection if member HDA has no history These can be cleaned up with pgcleanup. | 15 October 2021, 17:09:59 UTC |
| bb0da5f | Marius van den Beek | 28 September 2021, 07:33:46 UTC | Merge pull request #12572 from ic4f/release_20.09_12523 [20.09] Guard against instance of GenomeIndexToolData | 28 September 2021, 07:33:46 UTC |
| 256dd03 | mvdbeek | 23 September 2021, 14:53:32 UTC | Simplify and fix JobExportHistoryArchive / GenomeIndexToolData handling Output parameters must behave somewhat like a HDA, in that they need to have a dataset attribute that points to a Dataset instance. `GenomeIndexToolData` fits that requirement, `JobExportHistoryArchive` provides the fda property that behaves like a HDA. | 27 September 2021, 21:14:52 UTC |
| 5aa8ee8 | Sergey Golitsynskiy | 21 September 2021, 19:20:46 UTC | Guard against instance of GenomeIndexToolData | 27 September 2021, 21:14:46 UTC |
| 2f1af42 | Marius van den Beek | 12 May 2021, 13:12:38 UTC | Merge pull request #11965 from simonbray/patch-2 [20.09] Force galaxy_id to string in galactic_job_json | 12 May 2021, 13:12:38 UTC |
| f466edd | Simon Bray | 12 May 2021, 11:06:56 UTC | force galaxy_id to string in galactic_job_json | 12 May 2021, 11:06:56 UTC |
| f963b67 | Marius van den Beek | 11 May 2021, 15:59:47 UTC | Merge pull request #11955 from mvdbeek/fix_ipv6_port_parsing [20.09] Fix container port parsing if IPv6 hostname is ``::`` | 11 May 2021, 15:59:47 UTC |
| 01cdbd3 | mvdbeek | 11 May 2021, 14:38:27 UTC | Fix port_parse rsplit usage | 11 May 2021, 14:40:57 UTC |
| 8acf0d1 | Marius van den Beek | 11 May 2021, 12:57:21 UTC | Use different string formatting option Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com> | 11 May 2021, 12:57:21 UTC |
| d69a79f | Marius van den Beek | 11 May 2021, 12:56:50 UTC | Use generator expression instead of list comprehension Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com> | 11 May 2021, 12:56:50 UTC |
| 4db3af8 | Marius van den Beek | 11 May 2021, 12:54:56 UTC | Open container_monitor_exception.txt in write mode Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com> | 11 May 2021, 12:54:56 UTC |
| 7b9d2db | Marius van den Beek | 11 May 2021, 12:54:28 UTC | Skip :: hostname only Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com> | 11 May 2021, 12:54:28 UTC |
| 75f5877 | mvdbeek | 10 May 2021, 15:22:54 UTC | Log exceptions IT port monitor fails and stop job That should make it significantly easier to debug issues when the container monitor dies unexpectedly (which I sort of expect in the future given that we parse output from the docker CLI). | 10 May 2021, 15:43:46 UTC |
| a1ececd | mvdbeek | 10 May 2021, 11:51:50 UTC | Fix contianer port parsing if ::: in port line :: is an unspecified ipv6 address and just recently appeared in the docker port output. | 10 May 2021, 15:37:29 UTC |
| 306e774 | Nicola Soranzo | 10 May 2021, 09:57:10 UTC | Merge pull request #11951 from mvdbeek/fix_anonymous_user_job_walltime_query | 10 May 2021, 09:57:10 UTC |
| bdc366c | mvdbeek | 07 May 2021, 11:09:41 UTC | Fix pause message when over walltime | 07 May 2021, 11:20:59 UTC |
| 958e526 | Maiken Pedersen | 04 May 2021, 11:12:18 UTC | Fix job query filter in walltime check | 07 May 2021, 11:19:29 UTC |
| 2586104 | John Chilton | 21 April 2021, 18:21:59 UTC | Merge pull request #11876 from natefoo/total-walltime-fix [20.09] Fix user total walltime calculation when jobs are missing states in job state history | 21 April 2021, 18:21:59 UTC |
| e015db0 | Nate Coraor | 21 April 2021, 15:07:48 UTC | No f-strings in 3.5. | 21 April 2021, 15:07:48 UTC |
| 55f4d5f | Nate Coraor | 21 April 2021, 14:50:17 UTC | Fix user total walltime calculation when jobs are missing states in job state history. | 21 April 2021, 14:50:17 UTC |
| 69b65ac | Nate Coraor | 21 April 2021, 14:39:33 UTC | Merge remote-tracking branch 'upstream/release_20.09' into release_20.09 | 21 April 2021, 14:39:33 UTC |
| 9169f6c | mvdbeek | 20 April 2021, 09:10:25 UTC | Merge branch 'release_20.05' into release_20.09 | 20 April 2021, 09:10:25 UTC |
| 9e62d11 | Marius van den Beek | 20 April 2021, 09:09:09 UTC | Merge pull request #11867 from rhpvorderman/fixwatchdog20.05 Backport to 20.05: watchdog dependency check bugfix. | 20 April 2021, 09:09:09 UTC |
| 8f324ec | Ruben Vorderman | 19 April 2021, 12:12:02 UTC | Also check for boolean True, not just string 'True' when evaluating conditional dependencies. When people know how actual yaml works they might have galaxy: watch_tools: true as their config. Which signifies an actual Boolean value. This should be considered by the script as well. | 20 April 2021, 06:45:28 UTC |
| 84e1d54 | mvdbeek | 07 April 2021, 12:30:48 UTC | Merge branch 'release_20.05' into release_20.09 | 07 April 2021, 12:30:48 UTC |
| b71a4c5 | mvdbeek | 07 April 2021, 12:30:03 UTC | Merge branch 'release_20.01' into release_20.05 | 07 April 2021, 12:30:03 UTC |
| 93d19df | Marius van den Beek | 07 April 2021, 12:29:27 UTC | Merge pull request #11793 from eancelet/release_20.01 [21.01] Lower tool id case while populating resource params | 07 April 2021, 12:29:27 UTC |
| d5cb3c3 | Estelle Ancelet | 06 April 2021, 16:08:22 UTC | Lower tool id case while populating resource params | 06 April 2021, 16:08:22 UTC |
| 4bc8b9a | John Chilton | 23 March 2021, 13:05:05 UTC | Merge pull request #11708 from mvdbeek/make_all_extra_user_preferences_behave_like_defaultdict [20.09] Make extra user preferences behave like defaultdict | 23 March 2021, 13:05:05 UTC |
| 27b7d57 | mvdbeek | 23 March 2021, 11:03:33 UTC | Make extra user preferences behave like defaultdict This was the intention in https://github.com/galaxyproject/galaxy/pull/10747 and is an alternative to https://github.com/galaxyproject/galaxy/pull/11707 To test this, enable the file sources, and make sure you add a plugin you haven't configured in your user preferences. | 23 March 2021, 11:04:49 UTC |
| dffacde | Marius van den Beek | 16 March 2021, 15:30:33 UTC | Merge pull request #11624 from ic4f/2009_team [20.09] Add release testing team to 20.09 release notes | 16 March 2021, 15:30:33 UTC |
| 057e06c | Dannon | 16 March 2021, 15:17:24 UTC | Merge pull request #11623 from OlegZharkov/collection-fix [20.09] fix exporting datasets from library as collection | 16 March 2021, 15:17:24 UTC |
| 7e0c298 | Oleg Zharkov | 15 March 2021, 17:05:04 UTC | fix collection history export in libraries | 15 March 2021, 17:05:04 UTC |
| a1ecf0f | Sergey Golitsynskiy | 15 March 2021, 16:33:03 UTC | Add release testing teaam to release notes | 15 March 2021, 16:36:58 UTC |
| 256474c | Marius van den Beek | 15 March 2021, 09:06:35 UTC | Merge pull request #11605 from OlegZharkov/fix-saving [20.09] fix saving FileSource parameter in a workflow | 15 March 2021, 09:06:35 UTC |
| 57d66b9 | Marius van den Beek | 12 March 2021, 16:48:11 UTC | Merge pull request #11603 from nsoranzo/release_20.09_fix_metadata_bcf_framework_test [20.09] Fix ``metadata_bcf`` framework test | 12 March 2021, 16:48:11 UTC |
| 734b081 | Nicola Soranzo | 11 March 2021, 22:39:29 UTC | Use latest pip in package testing Fix the following error when running `tox -e test_galaxy_packages` on Python 3.5: ``` ERROR: Could not find a version that satisfies the requirement networkx==2.5 (from isa-rwval->galaxy-data==20.9.1.dev0) (from versions: 0.34, 0.35, 0.35.1, 0.36, 0.37, 0.99, 1.0rc1, 1.0, 1.0.1, 1.1, 1.2rc1, 1.2, 1.3rc1, 1.3, 1.4rc1, 1.4, 1.5rc1, 1.5, 1.6rc1, 1.6, 1.7rc1, 1.7, 1.8rc1, 1.8, 1.8.1, 1.9rc1, 1.9, 1.9.1, 1.10rc2, 1.10, 1.11rc1, 1.11rc2, 1.11, 2.0, 2.1, 2.2rc1, 2.2, 2.3rc3, 2.3rc4, 2.3, 2.4rc1, 2.4rc2, 2.4) ERROR: No matching distribution found for networkx==2.5 (from isa-rwval->galaxy-data==20.9.1.dev0) WARNING: You are using pip version 20.2.2; however, version 20.3.4 is available. You should consider upgrading via the '/tmp/gxpkgtestenviQxuK1/bin/python -m pip install --upgrade pip' command. ERROR: InvocationError for command /bin/bash packages/test.sh (exited with code 1) ___________________________________ summary ____________________________________ ERROR: test_galaxy_packages: commands failed ``` | 11 March 2021, 22:41:10 UTC |
| 3a36bed | Oleg Zharkov | 11 March 2021, 21:48:08 UTC | fix saving fieldDirectoryUri in workflow | 11 March 2021, 21:48:08 UTC |
| 3506abc | Nicola Soranzo | 11 March 2021, 20:11:28 UTC | Fix ``metadata_bcf`` framework test Somewhere between file/libmagic 5.36 and 5.39, the output of `file` on a `.csi` file changed, breaking the ``metadata_bcf`` framework test with the following error: ``` if found_exceptions: > raise JobOutputsError(found_exceptions, job_stdio) E galaxy.tool_util.verify.interactor.JobOutputsError: Output output_of_input_metadata: different than expected, difference (using contains): E ( /tmp/tmpu1a3dgjcbcf_index_metadata_test.txt v. /tmp/tmpkt78tzggbcf_index_metadata_test.txt ) E Failed to find 'gzip compressed data, extra field' in history data. (lines_diff=0): lib/galaxy/tool_util/verify/interactor.py:1222: JobOutputsError ``` So add a requirement for the latest `file` version and update the test accordingly. | 11 March 2021, 20:21:00 UTC |
| f2d294a | Dannon | 10 March 2021, 15:00:19 UTC | Merge pull request #11586 from OlegZharkov/20.09-fix-ui-file-source [20.09] fix undefined error in ui-file-source | 10 March 2021, 15:00:19 UTC |
| 27ba8ed | Oleg Zharkov | 10 March 2021, 13:39:03 UTC | Update client/src/mvc/ui/ui-file-source.js Co-authored-by: Dannon <dannon.baker@gmail.com> | 10 March 2021, 13:39:03 UTC |
| 5e8985c | Oleg Zharkov | 10 March 2021, 13:17:24 UTC | add _value check | 10 March 2021, 13:17:24 UTC |
| 81ddf7e | Dannon | 09 March 2021, 12:38:13 UTC | Merge pull request #11574 from mvdbeek/anndata_select2_fix [20.09] Don't display obs_names in select list | 09 March 2021, 12:38:13 UTC |
| 358a1e5 | mvdbeek | 09 March 2021, 10:34:42 UTC | Don't display obs_names in select list This would result in thousands of select items, which breaks Select2 atm. Fixes https://github.com/galaxyproject/galaxy/issues/11406 while we replace select2 hopefully soon. | 09 March 2021, 10:37:46 UTC |
| ad18ff0 | Dannon | 03 March 2021, 22:41:41 UTC | Merge pull request #11520 from dannon/oidc-logout-fix [20.09] OIDC Logout+Redirect fix. | 03 March 2021, 22:41:41 UTC |
| dcb48bd | John Chilton | 02 March 2021, 16:18:34 UTC | Merge pull request #11513 from mvdbeek/variation_report_fix [20.09] Fix random-ish workflow error with maximum_workflow_jobs_per_scheduling_iteration | 02 March 2021, 16:18:34 UTC |
| 52089b2 | John Chilton | 02 March 2021, 15:15:25 UTC | Merge pull request #11517 from mvdbeek/subworkflow_fixes [20.09] Fix embedding subworkflow | 02 March 2021, 15:15:25 UTC |
| 3f9fa34 | John Chilton | 02 March 2021, 15:14:53 UTC | Merge pull request #11515 from mvdbeek/improve_logging_if_shed_tool_config_file_not_found [20.09] Add logging if installable tool config file not found | 02 March 2021, 15:14:53 UTC |
| 84affcf | Dannon Baker | 26 February 2021, 18:24:46 UTC | OIDC Logout+Redirect fix. This was a nightmare to track down so I'm going to add extra logging for when we toss cookies. | 02 March 2021, 14:36:41 UTC |
| d443151 | Nate Coraor | 02 March 2021, 14:03:22 UTC | Version 20.9.1 of data (tag galaxy-data-20.9.1). | 02 March 2021, 14:03:22 UTC |
| ae79ed6 | mvdbeek | 02 March 2021, 13:09:25 UTC | Test test workflow embedding in workflow editor | 02 March 2021, 13:09:25 UTC |
| 6cfd858 | mvdbeek | 02 March 2021, 10:21:31 UTC | Fix embedding subworkflow This broke in 88d7c4bb798d884b410213738f1bf21ae219070b. | 02 March 2021, 10:32:27 UTC |
| 6f0de08 | mvdbeek | 02 March 2021, 09:33:22 UTC | Add logging if installable tool config file not found Should make it easier to debug failing installations like this: ``` Mar 02 09:39:41 svvm0085 uwsgi[2626501]: galaxy.tool_shed.galaxy_install.install_manager ERROR 2021-03-02 09:39:41,329 [p:2626501,w:1,m:0] [uWSGIWorker1Core0] Error installing repository 'data_manager_fetch_genome_dbkeys_all_fasta' Mar 02 09:39:41 svvm0085 uwsgi[2626501]: Traceback (most recent call last): Mar 02 09:39:41 svvm0085 uwsgi[2626501]: File "/data/galaxy/galaxy//server/lib/galaxy/tool_shed/galaxy_install/install_manager.py", line 848, in install_repositories Mar 02 09:39:41 svvm0085 uwsgi[2626501]: self.install_tool_shed_repository(tool_shed_repository, Mar 02 09:39:41 svvm0085 uwsgi[2626501]: File "/data/galaxy/galaxy//server/lib/galaxy/tool_shed/galaxy_install/install_manager.py", line 926, in install_tool_shed_repository Mar 02 09:39:41 svvm0085 uwsgi[2626501]: self.__handle_repository_contents(tool_shed_repository=tool_shed_repository, Mar 02 09:39:41 svvm0085 uwsgi[2626501]: File "/data/galaxy/galaxy//server/lib/galaxy/tool_shed/galaxy_install/install_manager.py", line 574, in __handle_repository_contents Mar 02 09:39:41 svvm0085 uwsgi[2626501]: dmh.install_data_managers(self.app.config.shed_data_manager_config_file, Mar 02 09:39:41 svvm0085 uwsgi[2626501]: File "/data/galaxy/galaxy//server/lib/galaxy/tool_shed/galaxy_install/tools/data_manager.py", line 81, in install_data_managers Mar 02 09:39:41 svvm0085 uwsgi[2626501]: relative_repo_data_manager_dir = os.path.join(shed_config_dict.get('tool_path', ''), relative_install_dir) Mar 02 09:39:41 svvm0085 uwsgi[2626501]: AttributeError: 'NoneType' object has no attribute 'get' ``` In this case there was an extra slash in the tool_path section in the tool_path attribute of the shed_tool_config_file. Includes a small fix where we check both paths to be compared using the abspath value. | 02 March 2021, 09:39:14 UTC |
| 5c56704 | mvdbeek | 01 March 2021, 20:53:44 UTC | use if max_num_job is not None | 01 March 2021, 21:51:55 UTC |
| e79a5df | Nicola Soranzo | 10 February 2021, 18:33:07 UTC | Fix command line building when using interpreter Partially revert commit efa9e0fdd1d11d58f4a504a3e8242cc59f3f1416 which broke tools which use `interpreter` and `&&` or environment variables in the `<command />`. xref.: https://github.com/galaxyproject/galaxy/pull/10674/commits/efa9e0fdd1d11d58f4a504a3e8242cc59f3f1416#r573844945 | 01 March 2021, 21:51:55 UTC |
| 373489e | Nate Coraor | 01 March 2021, 21:37:33 UTC | Starting work on objectstore 20.9.2 | 01 March 2021, 21:37:33 UTC |
| 7c8a5c1 | Nicola Soranzo | 10 November 2020, 17:17:15 UTC | Fix command line for tools using `interpreter` when galaxy root contains spaces | 01 March 2021, 20:50:04 UTC |
| 0fbbf73 | Nate Coraor | 01 March 2021, 20:29:38 UTC | Version 20.9.1 of objectstore (tag galaxy-objectstore-20.9.1). | 01 March 2021, 20:29:38 UTC |
| 1f82927 | mvdbeek | 01 March 2021, 19:02:11 UTC | Don't set empty step output if no job was created Fixes ``` Traceback (most recent call last): File "/Users/mvandenb/src/galaxy/lib/galaxy/workflow/run.py", line 82, in __invoke outputs = invoker.invoke() File "/Users/mvandenb/src/galaxy/lib/galaxy/workflow/run.py", line 190, in invoke incomplete_or_none = self._invoke_step(workflow_invocation_step) File "/Users/mvandenb/src/galaxy/lib/galaxy/workflow/run.py", line 263, in _invoke_step incomplete_or_none = invocation_step.workflow_step.module.execute(self.trans, File "/Users/mvandenb/src/galaxy/lib/galaxy/workflow/modules.py", line 1659, in execute collection_info = self.compute_collection_info(progress, step, all_inputs) File "/Users/mvandenb/src/galaxy/lib/galaxy/workflow/modules.py", line 335, in compute_collection_info collections_to_match = self._find_collections_to_match( File "/Users/mvandenb/src/galaxy/lib/galaxy/workflow/modules.py", line 354, in _find_collections_to_match data = progress.replacement_for_input(step, input_dict) File "/Users/mvandenb/src/galaxy/lib/galaxy/workflow/run.py", line 328, in replacement_for_input replacement = [self.replacement_for_connection(c) for c in connection] File "/Users/mvandenb/src/galaxy/lib/galaxy/workflow/run.py", line 328, in <listcomp> replacement = [self.replacement_for_connection(c) for c in connection] File "/Users/mvandenb/src/galaxy/lib/galaxy/workflow/run.py", line 358, in replacement_for_connection raise Exception(message) Exception: Workflow evaluation problem - failed to find output_name list_output in step_outputs {} galaxy.workflow.scheduling_manager DEBUG 2021-03-01 19:58:59,493 Workflow invocation [1] scheduled ``` | 01 March 2021, 19:09:03 UTC |
| 15cf05a | mvdbeek | 01 March 2021, 14:56:48 UTC | Add testcase for explicit output collection step_outputs when reaching max_num_jobs This should recapitulate the error seen when running workflow tests against https://github.com/galaxyproject/iwc/pull/23. | 01 March 2021, 19:09:03 UTC |
| fbf1639 | Marius van den Beek | 25 February 2021, 14:09:33 UTC | Merge pull request #11448 from bernt-matthias/topic/container_tmp_rw_20.09 [20.09] always mount a job tmp rw | 25 February 2021, 14:09:33 UTC |
| 2419778 | Matthias Bernt | 25 February 2021, 12:49:58 UTC | Fix another integration test TmpDirAsShellCommandJobEnvironmentIntegrationTestCase.test_default_environment_1801 - actually create a dir - create the dir in the job working dir | 25 February 2021, 12:49:58 UTC |
| 5c2ef80 | Matthias Bernt | 25 February 2021, 10:45:02 UTC | fix chained dynamic destinations integration test - create a tmp dir as absolute path - actually create a dir in the dyndest test | 25 February 2021, 12:49:19 UTC |
| 8708e01 | Matthias Bernt | 25 February 2021, 10:46:08 UTC | create a test file in $HOME | 25 February 2021, 11:28:21 UTC |
| 03b7ca0 | Matthias Bernt | 24 February 2021, 20:46:20 UTC | fix unit test the export of GALAXY_SLOTS is now part of the slots_statement | 25 February 2021, 11:27:48 UTC |
| 4ce12fd | Matthias Bernt | 24 February 2021, 20:27:59 UTC | Revert "Remove superficial export of _GALAXY_JOB_HOME_DIR" This reverts commit 365fb066b0d8c86f4d45a3e626969756506c315a. | 25 February 2021, 11:27:40 UTC |
| 11b7b36 | Matthias Bernt | 24 February 2021, 12:09:59 UTC | simplify debugging | 25 February 2021, 11:27:26 UTC |
| 7aa833d | M Bernt | 23 February 2021, 12:19:06 UTC | Remove superficial export of _GALAXY_JOB_HOME_DIR Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com> | 25 February 2021, 11:25:53 UTC |
| 22e7b98 | M Bernt | 23 February 2021, 12:18:34 UTC | Remove doc of _GALAXY_JOB_HOME_DIR Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com> | 25 February 2021, 11:25:46 UTC |
| a2a8328 | Matthias Bernt | 27 November 2020, 18:12:42 UTC | add docs to xsd | 25 February 2021, 11:25:40 UTC |
| 95f7383 | Matthias Bernt | 27 November 2020, 16:10:19 UTC | export _GALAXY_JOB_HOME_DIR and _GALAXY_JOB_TMP_DIR these two variables are available in containers because of `docker run ...-e "_GALAXY_JOB_HOME_DIR=$_GALAXY_JOB_HOME_DIR" -e "_GALAXY_JOB_TMP_DIR=$_GALAXY_JOB_TMP_DIR"` but since they are not exported the same does not hold for non containerised jobs. Also moved `export GALAXY_SLOTS` to CLUSTER_SLOTS_STATEMENT.sh. Unsure if this export should be changed to something more complex as in MEMORY_STATEMENT.sh. | 25 February 2021, 11:25:34 UTC |
| 21a5837 | M Bernt | 23 February 2021, 17:28:55 UTC | fix quoting Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com> | 25 February 2021, 11:25:21 UTC |
| 742bae0 | Matthias Bernt | 23 February 2021, 10:23:30 UTC | test writing to job home and tmp | 25 February 2021, 11:24:42 UTC |
| e9f2b3a | Matthias Bernt | 23 February 2021, 09:52:43 UTC | always mount a job tmp rw | 25 February 2021, 11:23:27 UTC |
| 61e25db | Marius van den Beek | 23 February 2021, 07:57:41 UTC | Merge pull request #11434 from mvdbeek/recover_workflow_handler_from_database_hiccup [20.09] Wrap core of workflow monitor thread in try/except | 23 February 2021, 07:57:41 UTC |
| dc961c8 | mvdbeek | 22 February 2021, 17:41:35 UTC | Wrap core of workflow monitor thread in try/except Should prevent an exception like this: ``` galaxy.workflow.scheduling_manager DEBUG 2021-02-21 15:59:11,789 Attempting to schedule workflow invocation [(535353,)] Exception in thread WorkflowRequestMonitor.monitor_thread: Traceback (most recent call last): File "/cvmfs/main.galaxyproject.org/venv/lib/python3.6/site-packages/sqlalchemy/engine/base.py", line 2336, in _wrap_pool_connect return fn() File "/cvmfs/main.galaxyproject.org/venv/lib/python3.6/site-packages/sqlalchemy/pool/base.py", line 364, in conne ct return _ConnectionFairy._checkout(self) File "/cvmfs/main.galaxyproject.org/venv/lib/python3.6/site-packages/sqlalchemy/pool/base.py", line 778, in _checkout fairy = _ConnectionRecord.checkout(pool) File "/cvmfs/main.galaxyproject.org/venv/lib/python3.6/site-packages/sqlalchemy/pool/base.py", line 500, in checkout rec._checkin_failed(err) File "/cvmfs/main.galaxyproject.org/venv/lib/python3.6/site-packages/sqlalchemy/util/langhelpers.py", line 70, in __exit__ with_traceback=exc_tb, File "/cvmfs/main.galaxyproject.org/venv/lib/python3.6/site-packages/sqlalchemy/util/compat.py", line 182, in raise_ raise exception File "/cvmfs/main.galaxyproject.org/venv/lib/python3.6/site-packages/sqlalchemy/pool/base.py", line 497, in checkout dbapi_connection = rec.get_connection() File "/cvmfs/main.galaxyproject.org/venv/lib/python3.6/site-packages/sqlalchemy/pool/base.py", line 610, in get_connection self.__connect() File "/cvmfs/main.galaxyproject.org/venv/lib/python3.6/site-packages/sqlalchemy/pool/base.py", line 661, in __connect pool.logger.debug("Error on connect(): %s", e) File "/cvmfs/main.galaxyproject.org/venv/lib/python3.6/site-packages/sqlalchemy/util/langhelpers.py", line 70, in __exit__ with_traceback=exc_tb, File "/cvmfs/main.galaxyproject.org/venv/lib/python3.6/site-packages/sqlalchemy/util/compat.py", line 182, in raise_ raise exception File "/cvmfs/main.galaxyproject.org/venv/lib/python3.6/site-packages/sqlalchemy/pool/base.py", line 656, in __connect connection = pool._invoke_creator(self) File "/cvmfs/main.galaxyproject.org/venv/lib/python3.6/site-packages/sqlalchemy/engine/strategies.py", line 114, in connect return dialect.connect(*cargs, **cparams) File "/cvmfs/main.galaxyproject.org/venv/lib/python3.6/site-packages/sqlalchemy/engine/default.py", line 493, in connect return self.dbapi.connect(*cargs, **cparams) File "/cvmfs/main.galaxyproject.org/venv/lib/python3.6/site-packages/psycopg2/__init__.py", line 126, in connect conn = _connect(dsn, connection_factory=connection_factory, **kwasync) psycopg2.OperationalError: FATAL: the database system is in recovery mode The above exception was the direct cause of the following exception: Traceback (most recent call last): File "/cvmfs/main.galaxyproject.org/deps/_conda/envs/_galaxy_/lib/python3.6/threading.py", line 916, in _bootstrap_inner self.run() File "/cvmfs/main.galaxyproject.org/deps/_conda/envs/_galaxy_/lib/python3.6/threading.py", line 864, in run self._target(*self._args, **self._kwargs) File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/workflow/scheduling_manager.py", line 297, in __monitor self.__schedule(workflow_scheduler_id, workflow_scheduler) File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/workflow/scheduling_manager.py", line 305, in __schedule self.__attempt_schedule(invocation_id, workflow_scheduler) File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/workflow/scheduling_manager.py", line 311, in __attempt_schedule workflow_invocation = sa_session.query(model.WorkflowInvocation).get(invocation_id) File "/cvmfs/main.galaxyproject.org/venv/lib/python3.6/site-packages/sqlalchemy/orm/query.py", line 1018, in get return self._get_impl(ident, loading.load_on_pk_identity) File "/cvmfs/main.galaxyproject.org/venv/lib/python3.6/site-packages/sqlalchemy/orm/query.py", line 1135, in _get_impl return db_load_fn(self, primary_key_identity) File "/cvmfs/main.galaxyproject.org/venv/lib/python3.6/site-packages/sqlalchemy/orm/loading.py", line 286, in load_on_pk_identity return q.one() File "/cvmfs/main.galaxyproject.org/venv/lib/python3.6/site-packages/sqlalchemy/orm/query.py", line 3490, in one ret = self.one_or_none() File "/cvmfs/main.galaxyproject.org/venv/lib/python3.6/site-packages/sqlalchemy/orm/query.py", line 3459, in one_or_none ret = list(self) File "/cvmfs/main.galaxyproject.org/venv/lib/python3.6/site-packages/sqlalchemy/orm/query.py", line 3535, in __it er__ return self._execute_and_instances(context) File "/cvmfs/main.galaxyproject.org/venv/lib/python3.6/site-packages/sqlalchemy/orm/query.py", line 3557, in _execute_and_instances querycontext, self._connection_from_session, close_with_result=True File "/cvmfs/main.galaxyproject.org/venv/lib/python3.6/site-packages/sqlalchemy/orm/query.py", line 3572, in _get_bind_args mapper=self._bind_mapper(), clause=querycontext.statement, **kw File "/cvmfs/main.galaxyproject.org/venv/lib/python3.6/site-packages/sqlalchemy/orm/query.py", line 3550, in _connection_from_session conn = self.session.connection(**kw) File "/cvmfs/main.galaxyproject.org/venv/lib/python3.6/site-packages/sqlalchemy/orm/session.py", line 1141, in connection execution_options=execution_options, File "/cvmfs/main.galaxyproject.org/venv/lib/python3.6/site-packages/sqlalchemy/orm/session.py", line 1150, in _connection_for_bind conn = engine._contextual_connect(**kw) File "/cvmfs/main.galaxyproject.org/venv/lib/python3.6/site-packages/sqlalchemy/engine/base.py", line 2302, in _contextual_connect self._wrap_pool_connect(self.pool.connect, None), File "/cvmfs/main.galaxyproject.org/venv/lib/python3.6/site-packages/sqlalchemy/engine/base.py", line 2340, in _wrap_pool_connect e, dialect, self File "/cvmfs/main.galaxyproject.org/venv/lib/python3.6/site-packages/sqlalchemy/engine/base.py", line 1584, in _h andle_dbapi_exception_noconnection sqlalchemy_exception, with_traceback=exc_info[2], from_=e File "/cvmfs/main.galaxyproject.org/venv/lib/python3.6/site-packages/sqlalchemy/util/compat.py", line 182, in raise_ raise exception File "/cvmfs/main.galaxyproject.org/venv/lib/python3.6/site-packages/sqlalchemy/engine/base.py", line 2336, in _wrap_pool_connect return fn() File "/cvmfs/main.galaxyproject.org/venv/lib/python3.6/site-packages/sqlalchemy/pool/base.py", line 364, in connect return _ConnectionFairy._checkout(self) File "/cvmfs/main.galaxyproject.org/venv/lib/python3.6/site-packages/sqlalchemy/pool/base.py", line 778, in _checkout fairy = _ConnectionRecord.checkout(pool) File "/cvmfs/main.galaxyproject.org/venv/lib/python3.6/site-packages/sqlalchemy/pool/base.py", line 500, in checkout rec._checkin_failed(err) File "/cvmfs/main.galaxyproject.org/venv/lib/python3.6/site-packages/sqlalchemy/util/langhelpers.py", line 70, in __exit__ with_traceback=exc_tb, File "/cvmfs/main.galaxyproject.org/venv/lib/python3.6/site-packages/sqlalchemy/util/compat.py", line 182, in raise_ raise exception File "/cvmfs/main.galaxyproject.org/venv/lib/python3.6/site-packages/sqlalchemy/pool/base.py", line 497, in check out dbapi_connection = rec.get_connection() File "/cvmfs/main.galaxyproject.org/venv/lib/python3.6/site-packages/sqlalchemy/pool/base.py", line 610, in get_connection self.__connect() File "/cvmfs/main.galaxyproject.org/venv/lib/python3.6/site-packages/sqlalchemy/pool/base.py", line 661, in __connect pool.logger.debug("Error on connect(): %s", e) File "/cvmfs/main.galaxyproject.org/venv/lib/python3.6/site-packages/sqlalchemy/util/langhelpers.py", line 70, in __exit__ with_traceback=exc_tb, File "/cvmfs/main.galaxyproject.org/venv/lib/python3.6/site-packages/sqlalchemy/util/compat.py", line 182, in raise_ raise exception File "/cvmfs/main.galaxyproject.org/venv/lib/python3.6/site-packages/sqlalchemy/pool/base.py", line 656, in __connect connection = pool._invoke_creator(self) File "/cvmfs/main.galaxyproject.org/venv/lib/python3.6/site-packages/sqlalchemy/engine/strategies.py", line 114, in connect return dialect.connect(*cargs, **cparams) File "/cvmfs/main.galaxyproject.org/venv/lib/python3.6/site-packages/sqlalchemy/engine/default.py", line 493, in connect return self.dbapi.connect(*cargs, **cparams) File "/cvmfs/main.galaxyproject.org/venv/lib/python3.6/site-packages/psycopg2/__init__.py", line 126, in connect conn = _connect(dsn, connection_factory=connection_factory, **kwasync) sqlalchemy.exc.OperationalError: (psycopg2.OperationalError) FATAL: the database system is in recovery mode ``` to stop the monitor thread. | 22 February 2021, 17:44:23 UTC |
| 8906491 | Nicola Soranzo | 22 February 2021, 14:16:18 UTC | Merge pull request #11427 from mvdbeek/secure_hash [20.09] Make hash selection mandatory | 22 February 2021, 14:16:18 UTC |
