| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| b6836cb | Nicola Soranzo | 19 February 2021, 17:53:53 UTC | Merge branch 'release_20.01' into release_20.05 | 19 February 2021, 17:53:53 UTC |
| 320aae0 | Nicola Soranzo | 19 February 2021, 16:45:59 UTC | Merge pull request #11410 from bernt-matthias/topic/fix-configfile-20.05 | 19 February 2021, 16:45:59 UTC |
| db1618f | Marius van den Beek | 08 February 2021, 13:01:28 UTC | Use multiline yaml Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com> | 18 February 2021, 14:10:03 UTC |
| a8adab1 | mvdbeek | 08 February 2021, 12:08:45 UTC | Restore all integration subsets | 18 February 2021, 14:09:43 UTC |
| fc1d74d | mvdbeek | 08 February 2021, 10:19:41 UTC | Deploy postgresql and rabbitmq in kubernetes Setting up minikube stops the postgres and rabbitmq containers that are set up by the workflow. These are setup with custom docker networks, so it isn't trivial to restart them. Instead we just deploy them to minikube. | 18 February 2021, 14:09:34 UTC |
| 998f092 | Marius van den Beek | 18 February 2021, 13:55:42 UTC | Merge pull request #11396 from mvdbeek/workflow_versions [20.01] Backport Fix TypeError in WorkflowsAPIController.get_versions() | 18 February 2021, 13:55:42 UTC |
| cf50e90 | Nicola Soranzo | 15 January 2021, 19:06:56 UTC | Sync social-auth-core requirement in data package v4.0.2 dropped support for Python 3.5 | 18 February 2021, 13:48:52 UTC |
| bd5e8f3 | Matthias Bernt | 15 February 2021, 18:22:29 UTC | fix profile logic for configfile generation some follow up fixes to https://github.com/galaxyproject/galaxy/pull/9279/files https://github.com/galaxyproject/galaxy/pull/9776/files - wrong profile for the profile test tool (it used 20.01, but should have used 20.05) - the non-profile test tool used wrong assumptions. now fixed and also tested against 19.09 - in the profile version `value_wrapper.value` needs to be casted for `multiple==False` otherwise we gat `"None"` (which I do not understand 100%) | 18 February 2021, 11:33:07 UTC |
| e2076fb | Matthias Bernt | 15 February 2021, 17:08:31 UTC | fix genration of config files | 18 February 2021, 11:33:07 UTC |
| 9cc01de | rikeshi | 15 February 2021, 17:22:30 UTC | Apply suggestions from code review Co-authored-by: Simon Bray <32272674+simonbray@users.noreply.github.com> | 17 February 2021, 10:52:05 UTC |
| d69a6fc | rikeshi | 13 February 2021, 10:50:17 UTC | remove kwds arg from call to get_stored_accessible_workflow fix 'key' causing TypeError on GET request | 17 February 2021, 10:52:04 UTC |
| a11b994 | Dannon | 16 December 2020, 12:51:38 UTC | Merge pull request #10933 from mvdbeek/osx_fix [20.05] Fix OSX tests | 16 December 2020, 12:51:38 UTC |
| a3b7544 | mvdbeek | 16 December 2020, 11:20:22 UTC | Fix OSX tests | 16 December 2020, 11:20:22 UTC |
| 5f681b4 | Nicola Soranzo | 11 December 2020, 10:44:04 UTC | Merge branch 'release_20.01' into release_20.05 | 11 December 2020, 10:44:04 UTC |
| 3697c51 | Marius van den Beek | 10 December 2020, 09:05:34 UTC | Merge pull request #10882 from nsoranzo/release_20.01_update_lxml [20.01] Update lxml for CVE-2020-27783 | 10 December 2020, 09:05:34 UTC |
| 52c52c7 | Nicola Soranzo | 20 July 2020, 06:49:49 UTC | Update to sphinx-markdown-tables 0.0.14 0.0.13 seems buggy | 09 December 2020, 20:00:44 UTC |
| 26ea77b | Nicola Soranzo | 09 December 2020, 19:38:11 UTC | Update lxml for CVE-2020-27783 | 09 December 2020, 19:38:11 UTC |
| b83dbeb | Nicola Soranzo | 09 December 2020, 19:15:15 UTC | Merge branch 'release_20.01' into release_20.05 | 09 December 2020, 19:15:15 UTC |
| f6e48ee | John Chilton | 08 December 2020, 13:57:43 UTC | Merge pull request #10870 from mvdbeek/backport_unittest_fix [20.01] Backport mulled unit test | 08 December 2020, 13:57:43 UTC |
| 7ffd929 | mvdbeek | 07 December 2020, 14:16:50 UTC | Fix mulled unit test Recipe probably doesn't use build.sh anymore. | 08 December 2020, 09:19:12 UTC |
| 5ac0c39 | mvdbeek | 07 December 2020, 17:30:12 UTC | Merge branch 'release_20.01' into release_20.05 | 07 December 2020, 17:30:12 UTC |
| 3221677 | John Chilton | 06 December 2020, 14:08:58 UTC | Merge pull request #10851 from mvdbeek/add_title_fallback [20.01] Fix workflow preview for repeats without title | 06 December 2020, 14:08:58 UTC |
| e353165 | Nicola Soranzo | 04 December 2020, 18:59:55 UTC | Merge branch 'release_20.01' into release_20.05 | 04 December 2020, 18:59:55 UTC |
| f1311e8 | mvdbeek | 04 December 2020, 16:12:57 UTC | Fix workflow preview for repeats without title These would fail with ``` URL: http://127.0.0.1:8000/u/mvdbeek/w/covid-19-variation-analysis-reporting-imported-from-uploaded-file File '/Users/mvandenb/src/galaxy/lib/galaxy/web/framework/middleware/error.py', line 153 in __call__ app_iter = self.application(environ, sr_checker) File '/Users/mvandenb/src/galaxy/.venv/lib/python3.8/site-packages/paste/recursive.py', line 85 in __call__ return self.application(environ, start_response) File '/Users/mvandenb/src/galaxy/.venv/lib/python3.8/site-packages/paste/httpexceptions.py', line 640 in __call__ return self.application(environ, start_response) File '/Users/mvandenb/src/galaxy/lib/galaxy/web/framework/base.py', line 136 in __call__ return self.handle_request(environ, start_response) File '/Users/mvandenb/src/galaxy/lib/galaxy/web/framework/base.py', line 215 in handle_request body = method(trans, **kwargs) File '/Users/mvandenb/src/galaxy/lib/galaxy/webapps/galaxy/controllers/workflow.py', line 230 in display_by_username_and_slug return self._display(trans, stored_workflow) File '/Users/mvandenb/src/galaxy/lib/galaxy/webapps/galaxy/controllers/workflow.py', line 266 in _display return trans.fill_template_mako("workflow/display.mako", File '/Users/mvandenb/src/galaxy/lib/galaxy/webapps/base/webapp.py', line 971 in fill_template_mako return template.render(**data) File '/Users/mvandenb/src/galaxy/.venv/lib/python3.8/site-packages/mako/template.py', line 476 in render return runtime._render(self, self.callable_, args, data) File '/Users/mvandenb/src/galaxy/.venv/lib/python3.8/site-packages/mako/runtime.py', line 878 in _render _render_context( File '/Users/mvandenb/src/galaxy/.venv/lib/python3.8/site-packages/mako/runtime.py', line 920 in _render_context _exec_template(inherit, lclcontext, args=args, kwargs=kwargs) File '/Users/mvandenb/src/galaxy/.venv/lib/python3.8/site-packages/mako/runtime.py', line 947 in _exec_template callable_(context, *args, **kwargs) File '/Users/mvandenb/src/galaxy/database/compiled_templates/base/base_panels.mako.py', line 124 in render_body __M_writer(str(self.center_panel())) File '/Users/mvandenb/src/galaxy/database/compiled_templates/display_base.mako.py', line 234 in render_center_panel __M_writer(str(self.render_content())) File '/Users/mvandenb/src/galaxy/database/compiled_templates/display_base.mako.py', line 269 in render_render_content __M_writer(str(self.render_item( item, item_data ))) File '/Users/mvandenb/src/galaxy/database/compiled_templates/workflow/display.mako.py', line 256 in render_render_item __M_writer(str(do_inputs( tool.inputs, step.state.inputs, "", step ))) File '/Users/mvandenb/src/galaxy/database/compiled_templates/workflow/display.mako.py', line 229 in do_inputs return render_do_inputs(context,inputs,values,prefix,step,other_values) File '/Users/mvandenb/src/galaxy/database/compiled_templates/workflow/display.mako.py', line 88 in render_do_inputs __M_writer(str(input.title_plural)) File '/Users/mvandenb/src/galaxy/lib/galaxy/tools/parameters/grouping.py', line 80 in title_plural return inflector.pluralize(self.title) File '/Users/mvandenb/src/galaxy/lib/galaxy/util/inflection.py', line 86 in pluralize return self._transform(self.PLURALIZE_RULES, word) File '/Users/mvandenb/src/galaxy/lib/galaxy/util/inflection.py', line 99 in _transform return self._handle_nonchanging(word) or self._handle_irregular(word, pluralize=pluralize) or self._apply_rules(rules, word) or word File '/Users/mvandenb/src/galaxy/lib/galaxy/util/inflection.py', line 102 in _handle_nonchanging lower_cased_word = word.lower() AttributeError: 'NoneType' object has no attribute 'lower' ``` `title` is a mandatory attribute of repeats, but repeats without title work fine otherwise. The tool in question is https://github.com/galaxyproject/tools-iuc/blob/master/tools/compose_text_param/compose_text_param.xml#L13 which has passed planemo linting. | 04 December 2020, 16:19:19 UTC |
| 83e57ff | Marius van den Beek | 04 December 2020, 16:18:52 UTC | Merge pull request #10826 from nsoranzo/release_20.01_fix_dep_for_pip_20.3 [20.01] Update `sphinx-markdown-tables` to fix conflict | 04 December 2020, 16:18:52 UTC |
| 7d1569e | Nicola Soranzo | 30 November 2020, 16:48:42 UTC | Update `sphinx-markdown-tables` to fix conflict `sphinx-markdown-tables` 0.0.12 had a strict pin which is causing a conflict error with the new pip 20.3: ``` ERROR: Cannot install -r ./lib/galaxy/dependencies/dev-requirements.txt (line 55) and markdown==3.1.1 because these package versions have conflicting dependencies. ERROR: ResolutionImpossible: for help visit https://pip.pypa.io/en/latest/user_guide/#fixing-conflicting-dependencies The conflict is caused by: The user requested markdown==3.1.1 The user requested markdown==3.1.1 sphinx-markdown-tables 0.0.12 depends on markdown==3.0.1 To fix this you could try to: 1. loosen the range of package versions you've specified 2. remove package versions to allow pip attempt to solve the dependency conflict ``` See https://github.com/galaxyproject/galaxy/pull/10825/checks?check_run_id=1474883413 | 30 November 2020, 16:51:22 UTC |
| 2c0401b | Dannon | 30 November 2020, 16:40:09 UTC | Merge pull request #10825 from nsoranzo/release_20.01_fix_10824 [20.01] Cast `ncores` to str for `subprocess.call()` | 30 November 2020, 16:40:09 UTC |
| 5fe9c91 | Nicola Soranzo | 30 November 2020, 13:49:09 UTC | Cast ``ncores`` to str for ``subprocess.call()`` Fix https://github.com/galaxyproject/galaxy/issues/10824 . | 30 November 2020, 13:55:34 UTC |
| 587e5b0 | Marius van den Beek | 17 November 2020, 15:47:06 UTC | Merge pull request #10731 from mvdbeek/osx_startup_test_fix [20.05] Use newer setup-miniconda action | 17 November 2020, 15:47:06 UTC |
| 2696b78 | mvdbeek | 17 November 2020, 15:12:55 UTC | Use newer setup-miniconda action | 17 November 2020, 15:25:36 UTC |
| 3498fcf | mvdbeek | 16 November 2020, 20:05:27 UTC | Merge branch 'release_20.01' into release_20.05 | 16 November 2020, 20:05:27 UTC |
| 693191b | John Chilton | 16 November 2020, 19:49:15 UTC | Merge pull request #10723 from mvdbeek/backport_step_output_value_recovery [20.01] Backport invocation step output value recovery | 16 November 2020, 19:49:15 UTC |
| ac74bfa | John Chilton | 16 November 2020, 19:49:00 UTC | Merge pull request #10704 from mvdbeek/cryptography_backport [20.01] Bump cryptography dependency to 3.2.1 | 16 November 2020, 19:49:00 UTC |
| f730e8b | mvdbeek | 13 November 2020, 08:53:51 UTC | Silence DeprecationWarning for all job scripts Once we hit the job script we really don't want this to bleed through to the stderr, since there's nothing a user can do to fix it. It's a bit harsh, but I don't think this would hide dependency issues. | 16 November 2020, 10:44:38 UTC |
| 63a7cc1 | mvdbeek | 15 November 2020, 09:55:13 UTC | Add test for input parameter in nested workflow | 16 November 2020, 09:47:38 UTC |
| 907b928 | mvdbeek | 14 November 2020, 22:15:40 UTC | Recover step output value in WorkflowProgress instance. Fixes running subworkflows with parameter_input steps. Fixes https://github.com/galaxyproject/galaxy/issues/8390 and allows us to get rid of one FIXME I added when working around https://github.com/galaxyproject/galaxy/issues/8248. | 16 November 2020, 09:47:38 UTC |
| 84f0ad4 | mvdbeek | 12 November 2020, 15:00:57 UTC | Bump cryptography dependency to 3.2.1 | 12 November 2020, 15:00:57 UTC |
| 76cb40d | John Chilton | 03 November 2020, 15:58:10 UTC | Merge pull request #10560 from mvdbeek/fix_extracting_workflow_from_history_with_netsed_collection_input [20.05] Fix workflow extraction if nested collection in input step | 03 November 2020, 15:58:10 UTC |
| cffa939 | mvdbeek | 03 November 2020, 14:57:02 UTC | Merge branch 'release_20.01' into release_20.05 | 03 November 2020, 14:57:02 UTC |
| 1e393a0 | Nicola Soranzo | 02 November 2020, 19:26:35 UTC | Merge pull request #10609 from mvdbeek/response_body_fix [20.01] Change response body from str to bytes | 02 November 2020, 19:26:35 UTC |
| 33df9c1 | Qiang Gu | 16 October 2020, 19:36:45 UTC | Change response body from str to bytes | 02 November 2020, 15:27:02 UTC |
| bca4203 | mvdbeek | 26 October 2020, 16:12:47 UTC | Fix workflow extraction if nested collection in history Fixes https://github.com/galaxyproject/galaxy/issues/10452. | 29 October 2020, 18:55:53 UTC |
| 24db43a | Nicola Soranzo | 27 October 2020, 16:46:40 UTC | Merge branch 'release_20.01' into release_20.05 | 27 October 2020, 16:46:40 UTC |
| 06ef6b3 | Marius van den Beek | 27 October 2020, 07:35:02 UTC | Merge pull request #10552 from mvdbeek/compare_by_id [20.01] Fix get_output_path when HDA identity changes | 27 October 2020, 07:35:02 UTC |
| 6500e32 | mvdbeek | 26 October 2020, 13:46:27 UTC | Fix get_output_path when HDA identity changes @RJMW reported this on gitter: ``` galaxy.jobs.runners ERROR 2020-10-13 09:34:24,937 [p:23472,w:1,m:0] [SlurmRunner.monitor_thread] (442471) Failure preparing job Traceback (most recent call last): File "lib/galaxy/jobs/runners/__init__.py", line 236, in prepare_job job_wrapper.prepare() File "lib/galaxy/jobs/__init__.py", line 1077, in prepare tool_evaluator.set_compute_environment(compute_environment, get_special=get_special) File "lib/galaxy/tools/evaluation.py", line 110, in set_compute_environment output_collections=out_collections, File "lib/galaxy/tools/evaluation.py", line 149, in build_param_dict self.__populate_output_dataset_wrappers(param_dict, output_datasets, job_working_directory) File "lib/galaxy/tools/evaluation.py", line 341, in __populate_output_dataset_wrappers param_dict[name] = DatasetFilenameWrapper(hda, compute_environment=self.compute_environment, io_type="output") File "lib/galaxy/tools/wrappers.py", line 289, in __init__ path_rewrite = compute_environment and compute_environment.output_path_rewrite(dataset) File "lib/galaxy/jobs/__init__.py", line 2546, in output_path_rewrite dataset_path = self.job_wrapper.get_output_path(dataset) File "lib/galaxy/jobs/__init__.py", line 1912, in get_output_path raise KeyError("Couldn't find job output for [%s] in [%s]" % (dataset, self.output_hdas_and_paths.values())) KeyError: "Couldn't find job output for [<galaxy.model.HistoryDatasetAssociation(714739) at 0x7f59c5d269b0>] in [dict_values([(<galaxy.model.HistoryDatasetAssociation(714739) at 0x7f5976dd5be0>, <galaxy.job_execution.datasets.DatasetPath object at 0x7f59783efc18>)])]" ``` The HDA with the id 714739 is present in the outputs, but the identity is not the same. I don't know why that happened (maybe a flush?) but in this case it should be safe to compare HDAs by database id. | 26 October 2020, 17:11:26 UTC |
| 535c236 | Marius van den Beek | 22 October 2020, 16:12:33 UTC | Merge pull request #10528 from dannon/backport-vizfix [20.05] (backport) Bugfix: include an index link in visualization base to allow the app … | 22 October 2020, 16:12:33 UTC |
| b21bab7 | Dannon Baker | 09 October 2020, 03:19:11 UTC | Bugfix: include an index link in visualization base to allow the app to derive baseUrl | 22 October 2020, 15:28:16 UTC |
| 916afa3 | Marius van den Beek | 21 October 2020, 15:22:50 UTC | Merge pull request #10484 from abretaud/patch-6 [20.05] Update amqp, needed by kombu 4.6.11 | 21 October 2020, 15:22:50 UTC |
| 77efb7c | Anthony Bretaudeau | 21 October 2020, 11:04:07 UTC | Update amqp, needed by kombu 4.6.11 | 21 October 2020, 11:04:07 UTC |
| 9cd0468 | John Chilton | 19 October 2020, 20:07:49 UTC | Merge pull request #10431 from mvdbeek/collection_identifier_handling [20.01] Backport #10427: Fix handling of collection element identifiers in history panel | 19 October 2020, 20:07:49 UTC |
| f56815a | mvdbeek | 17 October 2020, 08:22:36 UTC | Merge branch 'release_20.01' into release_20.05 | 17 October 2020, 08:22:36 UTC |
| a7765ba | mvdbeek | 17 October 2020, 08:21:07 UTC | Merge branch 'release_19.09' into release_20.01 | 17 October 2020, 08:21:07 UTC |
| 82b06aa | Marius van den Beek | 17 October 2020, 08:18:49 UTC | Merge pull request #10444 from almahmoud/patch-5 [19.09] Fixing bug in k8s runner's k8s_pod_retrials | 17 October 2020, 08:18:49 UTC |
| cf97ffc | Alexandru Mahmoud | 16 October 2020, 22:41:53 UTC | [19.09] Fixing bug in k8s runner's k8s_pod_retrials | 16 October 2020, 22:41:53 UTC |
| 4588977 | guerler | 14 October 2020, 16:07:23 UTC | Fix handling of collection element identifiers in history panel | 15 October 2020, 11:23:06 UTC |
| e3c5df3 | mvdbeek | 14 October 2020, 08:10:01 UTC | Merge branch 'release_20.01' into release_20.05 | 14 October 2020, 08:10:01 UTC |
| 999a2c3 | Marius van den Beek | 14 October 2020, 08:08:37 UTC | Merge pull request #10416 from nuwang/patch_k8s_job_name_length Restrict k8s max job name length to 63 and shorten prefix | 14 October 2020, 08:08:37 UTC |
| 2409326 | Nuwan Goonasekera | 13 October 2020, 19:05:03 UTC | Restrict k8s max job name length to 63 and shorten prefix | 13 October 2020, 19:09:35 UTC |
| 3395d72 | Nicola Soranzo | 13 October 2020, 01:47:57 UTC | Merge branch 'release_20.01' into release_20.05 | 13 October 2020, 01:47:57 UTC |
| 05aa4c2 | Dannon | 13 October 2020, 01:45:55 UTC | Merge pull request #10401 from nsoranzo/release_20.01_retry_also_when_email_is_lowercase [20.01] Try case-insensitive match on email also when it's lowercase | 13 October 2020, 01:45:55 UTC |
| 150ab0d | Nicola Soranzo | 09 October 2020, 16:06:35 UTC | Try case-insensitive match on email also when it's lowercase Fix login for a user whose registered email is mixed case which tries to login with lowercase. | 10 October 2020, 19:54:01 UTC |
| d942952 | mvdbeek | 09 October 2020, 16:45:58 UTC | Merge branch 'release_20.01' into release_20.05 | 09 October 2020, 16:45:58 UTC |
| 53b6003 | John Chilton | 09 October 2020, 16:43:42 UTC | Merge pull request #10390 from mvdbeek/rule_builder_fix_20.01 [20.01] Fix regex replacement wrongly appearing in rule builder | 09 October 2020, 16:43:42 UTC |
| 715b370 | mvdbeek | 09 October 2020, 09:08:41 UTC | Fix regex replacement wrongly appearing in rule builder Fixes https://github.com/galaxyproject/galaxy/issues/10389 | 09 October 2020, 09:11:19 UTC |
| 85e0edb | Dannon Baker | 08 October 2020, 15:16:27 UTC | Merge remote-tracking branch 'upstream/release_20.01' into release_20.05 | 08 October 2020, 15:16:27 UTC |
| 11ea2cb | Marius van den Beek | 08 October 2020, 14:28:07 UTC | Merge pull request #10307 from nuwang/fix_k8s_job_id_clash [20.01] Ensure that k8s job ids are unique | 08 October 2020, 14:28:07 UTC |
| 488baee | Nuwan Goonasekera | 02 October 2020, 11:43:42 UTC | Use generated uuid instead of galaxy job id for k8s job name Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com> | 06 October 2020, 13:32:54 UTC |
| 3b42717 | Nuwan Goonasekera | 27 September 2020, 20:04:58 UTC | Ensure that k8s job ids are unique | 06 October 2020, 13:32:43 UTC |
| 076e640 | John Chilton | 02 October 2020, 14:57:38 UTC | Merge pull request #10321 from nsoranzo/release_20.05_fix_use_shared_home_with_docker [20.05] Respect ``use_shared_home="false"`` when running tools in container | 02 October 2020, 14:57:38 UTC |
| 71e01da | mvdbeek | 02 October 2020, 13:32:35 UTC | Merge branch 'release_20.01' into release_20.05 | 02 October 2020, 13:32:35 UTC |
| 535e4c5 | Marius van den Beek | 02 October 2020, 10:28:31 UTC | Merge pull request #10308 from nuwang/fix_k8s_job_cleanup_loop [20.01] Prevent endless cleanup loops when duplicate job or k8s job not found | 02 October 2020, 10:28:31 UTC |
| 1a8e271 | Marius van den Beek | 02 October 2020, 10:25:35 UTC | Merge pull request #10342 from dannon/fix-toolbox-wrap-20.05 [20.05] Use block elements for labels to handle wrapping indentation | 02 October 2020, 10:25:35 UTC |
| e0d221a | Nuwan Goonasekera | 15 May 2020, 13:47:57 UTC | Also check for expected output in k8s delete test | 01 October 2020, 18:41:50 UTC |
| ada9ee6 | Nuwan Goonasekera | 15 May 2020, 13:32:19 UTC | Minor refactoring of k8s tests | 01 October 2020, 18:16:18 UTC |
| 5d1b54c | Nuwan Goonasekera | 15 May 2020, 12:47:26 UTC | Added test to check that jobs fail when deleted directly via k8s api | 01 October 2020, 18:16:18 UTC |
