| 642c28a | mvdbeek | 14 November 2022, 09:22:28 UTC | Release galaxy-tool-util-22.1.5 | 14 November 2022, 09:22:28 UTC |
| a8ab71f | Marius van den Beek | 11 November 2022, 08:07:11 UTC | Merge pull request #14970 from mvdbeek/alt_fix_expected_failure_occurred [22.01] Set test status to success on expected failure | 11 November 2022, 08:07:11 UTC |
| 9570da5 | mvdbeek | 10 November 2022, 15:25:26 UTC | Avoid negations | 10 November 2022, 15:25:26 UTC |
| 0687217 | mvdbeek | 10 November 2022, 15:20:03 UTC | Set test status to success on expected failure Alternative to https://github.com/galaxyproject/galaxy/pull/14958 | 10 November 2022, 15:20:17 UTC |
| d75c0fd | Martin Cech | 05 November 2022, 23:56:23 UTC | Merge pull request #14933 from mvdbeek/switch_back_to__run_workflow [22.01] Revert "Use _run_jobs instead of _run_workflows" | 05 November 2022, 23:56:23 UTC |
| 494bae8 | mvdbeek | 05 November 2022, 17:14:12 UTC | Revert "Use _run_jobs instead of _run_workflows" This reverts commit a01c8c5a88debc7f9e0c7e2865a33acb9633acab. _run_workflow has the right type annotations, but 21.09 didn't have this. | 05 November 2022, 17:14:18 UTC |
| 6623f44 | Martin Cech | 05 November 2022, 16:19:44 UTC | Merge branch 'release_21.09' into release_22.01 | 05 November 2022, 16:19:44 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 |
| 656751f | Nicola Soranzo | 02 November 2022, 15:43:16 UTC | Merge branch 'release_21.09' into release_22.01 | 02 November 2022, 15:43:16 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 |
| 238ab85 | mvdbeek | 28 October 2022, 08:31:56 UTC | Start work on galaxy-tool-util 22.1.5 | 28 October 2022, 08:31:56 UTC |
| 52f60b5 | mvdbeek | 28 October 2022, 08:30:23 UTC | Release tool-util package 22.1.4 | 28 October 2022, 08:30:23 UTC |
| ed6b054 | Marius van den Beek | 28 October 2022, 08:21:24 UTC | Merge pull request #14877 from nsoranzo/release_22.01_fix_tool-util_package [22.01] Add missing ``unittest_utils`` package to galaxy-tool-util | 28 October 2022, 08:21:24 UTC |
| 895a18c | Nicola Soranzo | 27 October 2022, 23:20:52 UTC | Add missing ``unittest_utils`` package to galaxy-tool-util Fix: ``` ModuleNotFoundError: No module named 'galaxy.tool_util.unittest_utils' ``` in https://github.com/conda-forge/galaxy-tool-util-feedstock/pull/4 . | 27 October 2022, 23:23:21 UTC |
| 7ff1026 | mvdbeek | 27 October 2022, 16:30:21 UTC | Start work on galaxy-tool-util 22.1.4 | 27 October 2022, 16:30:21 UTC |
| 9bf0b4e | mvdbeek | 27 October 2022, 16:29:48 UTC | Release tool-util package 22.1.3 | 27 October 2022, 16:29:48 UTC |
| e18ce25 | Nicola Soranzo | 26 October 2022, 18:17:27 UTC | Merge branch 'release_21.09' into release_22.01 | 26 October 2022, 18:17:27 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 |
| 330eb07 | Nicola Soranzo | 17 October 2022, 12:49:11 UTC | Merge branch 'release_21.09' into release_22.01 | 17 October 2022, 12:49:11 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 |
| 577a7d1 | Dannon | 11 October 2022, 12:01:10 UTC | Merge pull request #14773 from nsoranzo/release_22.01_fix_provenance_follow [22.01] Fix dataset provenance API when ``follow=False`` | 11 October 2022, 12:01:10 UTC |
| bb3006d | Nicola Soranzo | 10 October 2022, 23:35:14 UTC | Fix dataset provenance API when ``follow=False`` | 10 October 2022, 23:45:37 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 |
| 7b870dc | Nicola Soranzo | 13 September 2022, 11:07:02 UTC | Merge pull request #14607 from nsoranzo/release_22.01_pin_CacheControl [22.01] Pin CacheControl to prevent missing dependency | 13 September 2022, 11:07:02 UTC |
| 77553d1 | Nicola Soranzo | 12 September 2022, 20:49:14 UTC | Pin CacheControl to prevent missing dependency schema-salad currently requires: - "CacheControl >= 0.11.7, < 0.13" - "lockfile >= 0.9", which is needed for CacheControl's FileCache until 0.12.11 but CacheControl 0.12.12 replaced lockfile with filelock. Prevent the following traceback: ``` self = <cachecontrol.caches.file_cache.FileCache object at 0x7fe36ac5d190> directory = PosixPath('/tmp/.cache/salad'), forever = False, filemode = 384 dirmode = 448, lock_class = None def __init__( self, directory, forever=False, filemode=0o0600, dirmode=0o0700, lock_class=None, ): try: if lock_class is None: > from filelock import FileLock E ModuleNotFoundError: No module named 'filelock' /tmp/gxpkgtestenvcy0lxY/lib/python3.7/site-packages/cachecontrol/caches/file_cache.py:74: ModuleNotFoundError ``` | 12 September 2022, 20:57:43 UTC |
| eb33760 | Nicola Soranzo | 09 September 2022, 12:17:59 UTC | Merge pull request #14590 from mvdbeek/fix_systemd_sample_unit [22.01] Include /bin in sample systemd unit path | 09 September 2022, 12:17:59 UTC |
| b05462a | Marius van den Beek | 09 September 2022, 11:06:35 UTC | Add sbin to PATH Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com> | 09 September 2022, 11:06:35 UTC |
| 0256b34 | mvdbeek | 09 September 2022, 10:52:05 UTC | Include /bin in sample systemd unit path | 09 September 2022, 10:52:05 UTC |
| 9f1d8d0 | Nicola Soranzo | 06 September 2022, 10:36:36 UTC | Merge branch 'release_21.09' into release_22.01 | 06 September 2022, 10:36:36 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 |
| afebb89 | Marius van den Beek | 30 August 2022, 18:22:30 UTC | Merge pull request #14528 from mvdbeek/tool_util_packaging_fixes [22.01] Fix tool-util packaging | 30 August 2022, 18:22:30 UTC |
| 609c90f | Marius van den Beek | 30 August 2022, 15:25:10 UTC | Update packages/tool_util/HISTORY.rst | 30 August 2022, 15:25:10 UTC |
| 6519604 | Nicola Soranzo | 30 August 2022, 11:03:36 UTC | Add some type annotations | 30 August 2022, 13:34:54 UTC |
| 2f15059 | mvdbeek | 29 August 2022, 14:54:09 UTC | Skip the quay.io lookup if we have a valid cache entry Good thing we had tests that made sure the cache was getting used ... | 29 August 2022, 14:54:23 UTC |
| 60cda23 | mvdbeek | 29 August 2022, 14:35:15 UTC | Mock quay.io API calls, pass `install=False` to not pull docker images | 29 August 2022, 14:38:31 UTC |
| c4f576c | mvdbeek | 29 August 2022, 14:26:47 UTC | Fix cache lookup condition | 29 August 2022, 14:38:31 UTC |
| c4a9050 | mvdbeek | 29 August 2022, 12:08:49 UTC | Fix _namespace_has_repo if cache namespace cache key not present | 29 August 2022, 12:08:49 UTC |
| c07fd27 | mvdbeek | 29 August 2022, 11:08:05 UTC | Touch up tool util packaging fixes | 29 August 2022, 11:12:01 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 |
| 7a9e83c | Marius van den Beek | 23 August 2022, 17:06:47 UTC | Merge pull request #14496 from bernt-matthias/topic/lint_level [22.01] fix lint context fail function | 23 August 2022, 17:06:47 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 |
| 0b3f8af | Matthias Bernt | 23 August 2022, 13:46:16 UTC | fix lint context fail function error introduced here https://github.com/galaxyproject/galaxy/pull/13186 found this while working on https://github.com/galaxyproject/planemo/pull/1264 | 23 August 2022, 13:46:16 UTC |
| 0a69d3d | mvdbeek | 22 August 2022, 19:57:17 UTC | Update version to 22.1.2.dev0 | 22 August 2022, 19:57:17 UTC |
| dc56fc4 | mvdbeek | 22 August 2022, 19:46:16 UTC | Update version to 22.01.1 | 22 August 2022, 19:47:47 UTC |
| 30dc1bf | Marius van den Beek | 18 August 2022, 17:21:23 UTC | Merge pull request #14440 from qiagu/dynamic_options [22.01] Revert startswith of tool parameter options | 18 August 2022, 17:21:23 UTC |
| 5f0fbb0 | Matthias Bernt | 18 August 2022, 12:30:14 UTC | fix docs | 18 August 2022, 12:30:14 UTC |
| 8ef9ef4 | Matthias Bernt | 18 August 2022, 12:28:55 UTC | fix test | 18 August 2022, 12:28:55 UTC |
| ea85cab | qiagu | 12 August 2022, 07:34:36 UTC | Revert startswith of tool parameter options | 18 August 2022, 09:04:12 UTC |
| 6db3224 | Dannon | 16 August 2022, 20:26:41 UTC | Merge pull request #14466 from nsoranzo/release_22.01_fix_docs [22.01] Fix doc versioning banner and other doc fixes | 16 August 2022, 20:26:41 UTC |
| 11c0c7b | Nicola Soranzo | 16 August 2022, 14:29:12 UTC | Fix doc versioning banner Currently doc builds for `release_22.01` and `master` branches incorrectly show the "This document is for an in-development version of Galaxy." warning banner. Partially backport commit 318a1d7056cc8a5b9f6b83ef1cd186d6ef8939d4 and drop the unused `TARGET_BRANCH` variable from `Makefile` which shadows the shell environment variable of the same name set in `.github/workflows/docs.yaml` and used in `doc/source/conf.versioning.py` . | 16 August 2022, 14:33:26 UTC |
| 69defb7 | Nicola Soranzo | 14 August 2022, 17:33:42 UTC | Doc fixes | 15 August 2022, 18:15:02 UTC |
| 6a3804b | Nicola Soranzo | 14 August 2022, 16:55:51 UTC | Update application documentation with: ``` make -C doc/ updaterst ``` | 14 August 2022, 17:39:19 UTC |
| 6c43d66 | Marius van den Beek | 26 July 2022, 12:26:15 UTC | Merge pull request #14373 from cat-bro/fix-IMPLICITLY_REQUIRED_TOOL_FILES-for-maxquant [22.01] Correct IMPLICITLY_REQUIRED_TOOL_FILES for some tools | 26 July 2022, 12:26:15 UTC |
| 25e847e | cat-bro | 22 July 2022, 15:54:36 UTC | Correct IMPLICITLY_REQUIRED_TOOL_FILES for some tools | 25 July 2022, 17:07:36 UTC |
| a20d796 | Marius van den Beek | 24 July 2022, 16:22:21 UTC | Merge pull request #14332 from bernt-matthias/topic/options-var [22.01] fix `startswith` attribute of `<options>` | 24 July 2022, 16:22:21 UTC |
| 21a7ad2 | Marius van den Beek | 24 July 2022, 16:17:39 UTC | Merge pull request #14363 from davelopez/fix_enable_account_interface [22.01] Fix enable_account_interface option hiding too much | 24 July 2022, 16:17:39 UTC |
| f2bdee4 | davelopez | 22 July 2022, 16:11:14 UTC | Display correct description in Manage Information | 22 July 2022, 16:11:14 UTC |
| b004c32 | davelopez | 22 July 2022, 16:10:19 UTC | Display Manage Cloud Auth user preferences always | 22 July 2022, 16:10:19 UTC |
| e775648 | davelopez | 22 July 2022, 16:09:23 UTC | Disable only specific inputs in user information | 22 July 2022, 16:09:23 UTC |
| a066a42 | David López | 21 July 2022, 08:37:44 UTC | Merge pull request #14355 from nsoranzo/release_22.01_fix_14348 [22.01] Workflow download API: check if a workflow is importable (not published) | 21 July 2022, 08:37:44 UTC |
| 2ff6aa5 | Nicola Soranzo | 21 July 2022, 02:27:43 UTC | Workflow download API: check if a workflow is importable (not published) Fix https://github.com/galaxyproject/galaxy/issues/14348 . | 21 July 2022, 02:28:36 UTC |
| 7054261 | Nicola Soranzo | 21 July 2022, 02:25:12 UTC | Add some type annotations | 21 July 2022, 02:25:12 UTC |
| ce0d3a7 | Marius van den Beek | 16 July 2022, 10:46:00 UTC | Merge pull request #14330 from nsoranzo/release_22.01_dataset_API_fix_extension_list_filter [22.01] Fix filtering by an extension list in dataset API | 16 July 2022, 10:46:00 UTC |
| fe06eea | Matthias Bernt | 15 July 2022, 08:49:12 UTC | fix test output | 15 July 2022, 08:49:12 UTC |
| d7272cc | M Bernt | 14 July 2022, 21:30:11 UTC | Update test/functional/tools/options_from_metadata_file.xml Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com> | 14 July 2022, 21:30:11 UTC |
| d642ce3 | Matthias Bernt | 14 July 2022, 12:19:40 UTC | fix `startswith` attribute of `<options>` as documented in the xsd in addition fix https://github.com/galaxyproject/galaxy/issues/14324, i.e. document the `separator` attribute of options also doc that only 1MB is used and lines starting with `#` are always ignored | 14 July 2022, 12:19:40 UTC |
| 8321b86 | Nicola Soranzo | 13 July 2022, 19:22:52 UTC | Fix filtering by an extension list in dataset API Fix the following traceback: ``` 2022-07-13T20:32:11.5995637Z galaxy.web.framework.decorators ERROR 2022-07-13 20:20:39,564 [pN:main,p:2622,tN:worker 1] Uncaught exception in exposed API method: 2022-07-13T20:32:11.5995754Z Traceback (most recent call last): 2022-07-13T20:32:11.5996289Z File "/home/runner/work/bioblend/bioblend/galaxy-release_22.01/lib/galaxy/web/framework/decorators.py", line 320, in decorator 2022-07-13T20:32:11.5996434Z rval = func(self, trans, *args, **kwargs) 2022-07-13T20:32:11.5996812Z File "/home/runner/work/bioblend/bioblend/galaxy-release_22.01/lib/galaxy/webapps/galaxy/api/datasets.py", line 387, in index 2022-07-13T20:32:11.5996977Z trans, history_id, serialization_params, filter_parameters 2022-07-13T20:32:11.5997364Z File "/home/runner/work/bioblend/bioblend/galaxy-release_22.01/lib/galaxy/webapps/galaxy/services/datasets.py", line 214, in index 2022-07-13T20:32:11.5997749Z filters = self.history_contents_filters.parse_query_filters(filter_query_params) 2022-07-13T20:32:11.5998133Z File "/home/runner/work/bioblend/bioblend/galaxy-release_22.01/lib/galaxy/managers/base.py", line 1031, in parse_query_filters 2022-07-13T20:32:11.5998269Z return self.parse_filters(filter_params) 2022-07-13T20:32:11.5998634Z File "/home/runner/work/bioblend/bioblend/galaxy-release_22.01/lib/galaxy/managers/base.py", line 1040, in parse_filters 2022-07-13T20:32:11.5998770Z filter_ = self.parse_filter(attr, op, val) 2022-07-13T20:32:11.5999135Z File "/home/runner/work/bioblend/bioblend/galaxy-release_22.01/lib/galaxy/managers/base.py", line 1060, in parse_filter 2022-07-13T20:32:11.5999286Z orm_filter = self._parse_orm_filter(attr, op, val) 2022-07-13T20:32:11.5999683Z File "/home/runner/work/bioblend/bioblend/galaxy-release_22.01/lib/galaxy/managers/history_contents.py", line 528, in _parse_orm_filter 2022-07-13T20:32:11.5999828Z return super()._parse_orm_filter(attr, op, val) 2022-07-13T20:32:11.6000195Z File "/home/runner/work/bioblend/bioblend/galaxy-release_22.01/lib/galaxy/managers/base.py", line 1136, in _parse_orm_filter 2022-07-13T20:32:11.6000293Z orm_filter = op(val) 2022-07-13T20:32:11.6000703Z File "/home/runner/work/bioblend/bioblend/galaxy-release_22.01/.venv/lib/python3.7/site-packages/sqlalchemy/sql/operators.py", line 604, in in_ 2022-07-13T20:32:11.6000834Z return self.operate(in_op, other) 2022-07-13T20:32:11.6001252Z File "/home/runner/work/bioblend/bioblend/galaxy-release_22.01/.venv/lib/python3.7/site-packages/sqlalchemy/sql/elements.py", line 861, in operate 2022-07-13T20:32:11.6001467Z return op(self.comparator, *other, **kwargs) 2022-07-13T20:32:11.6001884Z File "/home/runner/work/bioblend/bioblend/galaxy-release_22.01/.venv/lib/python3.7/site-packages/sqlalchemy/sql/operators.py", line 1386, in in_op 2022-07-13T20:32:11.6001975Z return a.in_(b) 2022-07-13T20:32:11.6002370Z File "/home/runner/work/bioblend/bioblend/galaxy-release_22.01/.venv/lib/python3.7/site-packages/sqlalchemy/sql/operators.py", line 604, in in_ 2022-07-13T20:32:11.6002496Z return self.operate(in_op, other) 2022-07-13T20:32:11.6002903Z File "/home/runner/work/bioblend/bioblend/galaxy-release_22.01/.venv/lib/python3.7/site-packages/sqlalchemy/sql/type_api.py", line 1343, in operate 2022-07-13T20:32:11.6003001Z op, *other, **kwargs 2022-07-13T20:32:11.6003401Z File "/home/runner/work/bioblend/bioblend/galaxy-release_22.01/.venv/lib/python3.7/site-packages/sqlalchemy/sql/type_api.py", line 76, in operate 2022-07-13T20:32:11.6003546Z return o[0](self.expr, op, *(other + o[1:]), **kwargs) 2022-07-13T20:32:11.6003982Z File "/home/runner/work/bioblend/bioblend/galaxy-release_22.01/.venv/lib/python3.7/site-packages/sqlalchemy/sql/default_comparator.py", line 160, in _in_impl 2022-07-13T20:32:11.6004157Z roles.InElementRole, seq_or_selectable, expr=expr, operator=op 2022-07-13T20:32:11.6004557Z File "/home/runner/work/bioblend/bioblend/galaxy-release_22.01/.venv/lib/python3.7/site-packages/sqlalchemy/sql/coercions.py", line 189, in expect 2022-07-13T20:32:11.6004673Z element, argname=argname, **kw 2022-07-13T20:32:11.6005102Z File "/home/runner/work/bioblend/bioblend/galaxy-release_22.01/.venv/lib/python3.7/site-packages/sqlalchemy/sql/coercions.py", line 587, in _literal_coercion 2022-07-13T20:32:11.6005234Z self._raise_for_expected(element, **kw) 2022-07-13T20:32:11.6005662Z File "/home/runner/work/bioblend/bioblend/galaxy-release_22.01/.venv/lib/python3.7/site-packages/sqlalchemy/sql/coercions.py", line 283, in _raise_for_expected 2022-07-13T20:32:11.6005841Z util.raise_(exc.ArgumentError(msg, code=code), replace_context=err) 2022-07-13T20:32:11.6006258Z File "/home/runner/work/bioblend/bioblend/galaxy-release_22.01/.venv/lib/python3.7/site-packages/sqlalchemy/util/compat.py", line 207, in raise_ 2022-07-13T20:32:11.6006348Z raise exception 2022-07-13T20:32:11.6006989Z sqlalchemy.exc.ArgumentError: IN expression list, SELECT construct, or bound parameter object expected, got 'bam,txt'. 2022-07-13T20:32:11.6007456Z 127.0.0.1 - - [13/Jul/2022:20:20:39 +0000] "GET /api/datasets?limit=500&offset=0&order=create_time-dsc&history_id=4b187121143038ff&q=extension-in&qv=bam%2Ctxt HTTP/1.1" 500 - "-" "python-requests/2.28.1" ``` | 14 July 2022, 11:55:49 UTC |
| 80b726e | Dannon | 13 July 2022, 00:11:52 UTC | Merge pull request #14319 from mvdbeek/local_tool_version_switxh [22.01] Fix local version switching | 13 July 2022, 00:11:52 UTC |
| 3e08160 | mvdbeek | 12 July 2022, 17:26:18 UTC | Fix local version switching Fixes https://github.com/galaxyproject/galaxy/issues/14311. Problem is that we use `:key` in https://github.com/mvdbeek/galaxy/blob/9e4563d9eb5d8f38a48e1f01466d4fcd1fc66502/client/src/components/Form/FormDisplay.vue#L3, so that doesn't re-render when the tool id doesn't change (which is the case for local tools, but not toolshed tools). | 12 July 2022, 21:04:28 UTC |
| 9162d57 | Nicola Soranzo | 07 July 2022, 22:39:49 UTC | Merge pull request #14274 from mvdbeek/tighten_session_exception_handling | 07 July 2022, 22:39:49 UTC |
| 29bba73 | mvdbeek | 07 July 2022, 05:29:24 UTC | Drop exception catching when querying db for session Should fix users getting logged out if a OperationError occurs and they get a new session because of the too-wide exception handling. | 07 July 2022, 05:30:32 UTC |
