| 9503663 | Dannon Baker | 11 April 2023, 13:10:41 UTC | Update version to 23.0. | 11 April 2023, 13:10:41 UTC |
| 8469576 | Dannon | 11 April 2023, 12:36:29 UTC | Merge pull request #15922 from dannon/fix-release-version-parsing-kinda [23.0] Fix release script to be compatible with YY.X versions instead of YY.MM dates. | 11 April 2023, 12:36:29 UTC |
| a61dd93 | Dannon Baker | 11 April 2023, 11:46:14 UTC | Temporarily disable tests that rely on new style version numbers existing for the transition. | 11 April 2023, 11:46:14 UTC |
| 7279a22 | Dannon Baker | 10 April 2023, 20:55:06 UTC | Update release test script | 10 April 2023, 20:55:06 UTC |
| f94e552 | Dannon Baker | 10 April 2023, 20:43:15 UTC | Fix release script to be compatible with YY.X dates TODO: make this flexible enough to handle 24.X, but we need to discuss the rest of the process | 10 April 2023, 20:51:05 UTC |
| 629655d | Dannon | 10 April 2023, 19:55:38 UTC | Merge pull request #15915 from mvdbeek/another_pulsar_fix [23.0] Revert pulsar-side stdio redirection | 10 April 2023, 19:55:38 UTC |
| 90e32a2 | mvdbeek | 10 April 2023, 18:37:43 UTC | Run black on changed files | 10 April 2023, 18:37:43 UTC |
| c39b116 | mvdbeek | 10 April 2023, 18:37:13 UTC | Merge branch 'release_22.05' into HEAD | 10 April 2023, 18:37:13 UTC |
| 55c1dd8 | mvdbeek | 10 April 2023, 18:21:09 UTC | Fix black error caused by merging forward | 10 April 2023, 18:21:09 UTC |
| b84391d | Dannon | 10 April 2023, 18:15:17 UTC | Merge pull request #15921 from dannon/galaxy-client-release-23.0 [23.0] Pin client release version for 23.0 | 10 April 2023, 18:15:17 UTC |
| 7e46ad4 | mvdbeek | 10 April 2023, 17:58:47 UTC | Bump up pulsar-galaxy-lib version | 10 April 2023, 17:58:47 UTC |
| 5a0217a | mvdbeek | 07 April 2023, 06:02:44 UTC | Revert pulsar-side stdio redirection It just happened to pass tests in https://github.com/galaxyproject/galaxy/pull/15907 because the test framework looks at the stdio and stderr attributes, which are merged from tool_std{out,err} and job_std{out,err}. It however fails the tests for detect_errors that specifically checks tool_stdout and tool_stderr. I think it is a good idea to let pulsar handle the stdio redirection, but for this to work we'd have to ship parts of the command line to pulsar for final assembly, and that seems like a bigger change. | 10 April 2023, 17:58:20 UTC |
| 75f8e93 | mvdbeek | 10 April 2023, 14:43:16 UTC | Drop test tool that requires new pulsar release | 10 April 2023, 17:46:11 UTC |
| af86d2d | mvdbeek | 08 April 2023, 07:42:32 UTC | Automatically disable parallelism on pulsar job runner | 10 April 2023, 17:46:11 UTC |
| 1fbc33a | mvdbeek | 10 April 2023, 09:47:35 UTC | Write exit code file when when setting metadata outside of pulsar We need this to figure out the right stdout/stderr and job state with the `check_output` function. | 10 April 2023, 17:46:09 UTC |
| 97429c0 | mvdbeek | 10 April 2023, 10:32:27 UTC | Test tools for extra file handling in pulsar embedded test case | 10 April 2023, 17:45:08 UTC |
| 3a98d89 | mvdbeek | 09 April 2023, 17:13:16 UTC | Fix extra files path if metadata job runs in celery The job runner may have moved files to the object store already before calling `_handle_metadata_externally`, so the celery task needs to process files from the object store, not the job working directory. | 10 April 2023, 17:45:08 UTC |
| dc07e7a | mvdbeek | 08 April 2023, 07:08:38 UTC | Fix extra_files_path handling on pulsar without outputs_to_working_directory | 10 April 2023, 17:45:08 UTC |
| df3e18c | mvdbeek | 07 April 2023, 05:26:47 UTC | Fix pulsar error when when home_target is pwd Fixes: ``` ERROR galaxy.jobs.runners.pulsar:pulsar.py:531 failure running job 533 Traceback (most recent call last): File "/home/runner/work/pulsar/pulsar/galaxy/lib/galaxy/jobs/runners/pulsar.py", line 484, in __prepare_job job_wrapper.prepare(**prepare_kwds) File "/home/runner/work/pulsar/pulsar/galaxy/lib/galaxy/jobs/__init__.py", line 1253, in prepare ) = tool_evaluator.build() File "/home/runner/work/pulsar/pulsar/galaxy/lib/galaxy/tools/evaluation.py", line 560, in build global_tool_logs(self._build_environment_variables, config_file, "Building Environment Variables") File "/home/runner/work/pulsar/pulsar/galaxy/lib/galaxy/tools/evaluation.py", line 90, in global_tool_logs raise e File "/home/runner/work/pulsar/pulsar/galaxy/lib/galaxy/tools/evaluation.py", line 86, in global_tool_logs return func() File "/home/runner/work/pulsar/pulsar/galaxy/lib/galaxy/tools/evaluation.py", line 664, in _build_environment_variables home_dir = self.compute_environment.home_directory() File "/home/runner/work/pulsar/pulsar/galaxy/lib/galaxy/jobs/runners/pulsar.py", line 1163, in home_directory return self._target_to_directory(self.job_wrapper.home_target) File "/home/runner/work/pulsar/pulsar/galaxy/lib/galaxy/jobs/runners/pulsar.py", line 1179, in _target_to_directory raise Exception(f"Unknown target type [{target}]") Exception: Unknown target type [pwd] ``` | 10 April 2023, 17:45:07 UTC |
| 35e5097 | Dannon | 10 April 2023, 17:01:06 UTC | Merge pull request #15354 from dannon/23.0_release_notes [23.0] 23.0 Release notes | 10 April 2023, 17:01:06 UTC |
| 63a048e | Dannon Baker | 10 April 2023, 16:49:16 UTC | Pin client release version for 23.0 | 10 April 2023, 16:49:16 UTC |
| c09b875 | Dannon Baker | 10 April 2023, 16:19:25 UTC | Fix typo | 10 April 2023, 16:19:25 UTC |
| 5ba43c3 | Dannon Baker | 10 April 2023, 16:19:01 UTC | Highlights blurb | 10 April 2023, 16:19:01 UTC |
| 387660b | Marius van den Beek | 10 April 2023, 16:00:56 UTC | Merge pull request #15919 from mvdbeek/pulsar_fixes_22_05 [22.05] Various fixes for running pulsar jobs | 10 April 2023, 16:00:56 UTC |
| 8d117a8 | Dannon Baker | 10 April 2023, 15:36:29 UTC | Add administrative notes | 10 April 2023, 15:47:20 UTC |
| 39b5c2c | Dannon Baker | 10 April 2023, 15:24:51 UTC | Stable PRs regen | 10 April 2023, 15:26:54 UTC |
| 2e16486 | Dannon | 05 April 2023, 12:07:07 UTC | Apply suggestions from code review Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com> | 10 April 2023, 15:26:54 UTC |
| e59f1df | Dannon Baker | 05 April 2023, 04:14:25 UTC | Add configuration changes | 10 April 2023, 15:26:54 UTC |
| 6760fc3 | Dannon Baker | 05 April 2023, 04:00:31 UTC | Update freshly merged PRs for release notes | 10 April 2023, 15:26:54 UTC |
| f2d80a6 | Dannon Baker | 05 April 2023, 03:54:35 UTC | Update sample from config-rebuild | 10 April 2023, 15:26:54 UTC |
| 19489e8 | mvdbeek | 04 April 2023, 17:28:10 UTC | Add 23.0 to TOC | 10 April 2023, 15:26:54 UTC |
| 175a561 | mvdbeek | 04 April 2023, 13:55:44 UTC | Describe Conditional Workflow Steps | 10 April 2023, 15:26:54 UTC |
| ff47050 | Helena | 04 April 2023, 13:24:55 UTC | Update doc/source/releases/23.0_announce_user.rst Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com> | 10 April 2023, 15:26:54 UTC |
| 21e68c7 | David López | 08 March 2023, 14:31:51 UTC | Apply suggestions from code review Co-authored-by: Helena <hexylena@galaxians.org> | 10 April 2023, 15:26:54 UTC |
| a967f8d | davelopez | 08 March 2023, 14:06:06 UTC | Update user facing release notes - Update the WF Invocations Export section - Add the History Export Tracking section | 10 April 2023, 15:26:54 UTC |
| 2f16a98 | Martin Cech | 08 March 2023, 02:38:03 UTC | update 23.1 tag and estimates | 10 April 2023, 15:26:54 UTC |
| 6455001 | Dannon Baker | 07 March 2023, 17:53:23 UTC | Regenerate PRs | 10 April 2023, 15:26:54 UTC |
| ad0520e | Dannon Baker | 22 February 2023, 02:23:32 UTC | Cleanup in user announce post-regen | 10 April 2023, 15:26:54 UTC |
| 6171b9b | Dannon Baker | 22 February 2023, 02:16:08 UTC | Regenerate notes to include new PRs. | 10 April 2023, 15:26:54 UTC |
| 3fd382a | Helena Rasche | 17 February 2023, 09:51:13 UTC | add video thanks to @delphine-l | 10 April 2023, 15:26:54 UTC |
| 8c388c6 | Dannon Baker | 14 February 2023, 15:49:22 UTC | Deprecation notice for myexperiment.org workflow exports | 10 April 2023, 15:26:54 UTC |
| 4dfccd6 | Dannon Baker | 14 February 2023, 13:07:23 UTC | Note trackster deprecation | 10 April 2023, 15:26:54 UTC |
| e1bf303 | Helena Rasche | 10 February 2023, 16:51:59 UTC | Add separators, labels Per @electronicblueberry's suggestion | 10 April 2023, 15:26:54 UTC |
| ab5da86 | Helena Rasche | 10 February 2023, 16:31:11 UTC | fix links, make list | 10 April 2023, 15:26:54 UTC |
| 8649598 | Helena Rasche | 10 February 2023, 15:38:47 UTC | Write user facing release notes | 10 April 2023, 15:26:54 UTC |
| abb7d7f | Helena Rasche | 10 February 2023, 14:12:16 UTC | Use semantic headings | 10 April 2023, 15:26:54 UTC |
| 46f2a72 | Helena Rasche | 10 February 2023, 11:45:25 UTC | credit | 10 April 2023, 15:26:54 UTC |
| 0c6d57f | Helena Rasche | 10 February 2023, 11:45:22 UTC | More non-relevant refactorings | 10 April 2023, 15:26:54 UTC |
| a13e53e | Helena Rasche | 10 February 2023, 11:44:07 UTC | Cleanup non-relevant items and refactorings | 10 April 2023, 15:26:54 UTC |
| 793f112 | Helena Rasche | 10 February 2023, 11:42:39 UTC | Add link to admin highlights | 10 April 2023, 15:26:54 UTC |
| 0ebd5a1 | Dannon | 26 January 2023, 18:04:13 UTC | Update doc/source/releases/23.0_announce_user.rst Co-authored-by: John Davis <jdavcs@gmail.com> | 10 April 2023, 15:26:54 UTC |
| d5d5515 | Dannon Baker | 23 January 2023, 02:32:30 UTC | More date tweaks | 10 April 2023, 15:26:54 UTC |
| 6a7bd15 | Dannon Baker | 23 January 2023, 02:27:19 UTC | Initial 23.0 release notes | 10 April 2023, 15:26:54 UTC |
| 2f9b721 | mvdbeek | 10 April 2023, 14:43:16 UTC | Drop test tool that requires new pulsar release | 10 April 2023, 14:43:16 UTC |
| 31b0321 | Dannon | 10 April 2023, 14:40:10 UTC | Merge pull request #15913 from ahmedhamidawan/history_page_view_add_statistics [23.0] Show `HistoryCounter` in `HistoryView` | 10 April 2023, 14:40:10 UTC |
| ef6812d | mvdbeek | 08 April 2023, 07:42:32 UTC | Automatically disable parallelism on pulsar job runner | 10 April 2023, 12:17:52 UTC |
| e29f927 | mvdbeek | 10 April 2023, 09:47:35 UTC | Write exit code file when when setting metadata outside of pulsar We need this to figure out the right stdout/stderr and job state with the `check_output` function. | 10 April 2023, 12:17:52 UTC |
| 8019207 | mvdbeek | 10 April 2023, 10:32:27 UTC | Test tools for extra file handling in pulsar embedded test case | 10 April 2023, 12:17:52 UTC |
| 33f9edf | mvdbeek | 09 April 2023, 17:13:16 UTC | Fix extra files path if metadata job runs in celery The job runner may have moved files to the object store already before calling `_handle_metadata_externally`, so the celery task needs to process files from the object store, not the job working directory. | 10 April 2023, 12:17:52 UTC |
| f487d80 | mvdbeek | 08 April 2023, 07:08:38 UTC | Fix extra_files_path handling on pulsar without outputs_to_working_directory | 10 April 2023, 10:25:33 UTC |
| 356d33b | John Chilton | 08 April 2023, 20:20:34 UTC | Merge pull request #15914 from mvdbeek/fix_unknown_target_type [22.05] Fix pulsar error when when home_target is pwd | 08 April 2023, 20:20:34 UTC |
| 2959bcf | Ahmed Awan | 07 April 2023, 17:56:34 UTC | Show HistoryCounter in HistoryView | 07 April 2023, 17:56:34 UTC |
| ad1c87a | Björn Grüning | 07 April 2023, 14:17:23 UTC | Merge pull request #15916 from davelopez/23.0_fix_history_rocrate_export_with_discarded [23.0] Fix history RO-crate export with discarded datasets | 07 April 2023, 14:17:23 UTC |
| 8e29924 | davelopez | 07 April 2023, 10:12:28 UTC | Skip discarded datasets on export to RO-crate The RO-crate needs the file name as reference, but discarded datasets don't have a file on disk. Skipping those datasets for now to avoid crashes. This probably can be registered as special case in the RO-crate when the full history metadata profile is implemented. | 07 April 2023, 10:12:28 UTC |
| cc0f96b | davelopez | 07 April 2023, 10:07:48 UTC | Add integration test To export rocrate with discarded dataset. The test will fail without the fix. | 07 April 2023, 10:07:48 UTC |
| 24a2df1 | David López | 07 April 2023, 09:16:55 UTC | Merge pull request #15911 from dannon/backport-webpack-changes [23.0] Client build performance tweak backport | 07 April 2023, 09:16:55 UTC |
| e7c5543 | mvdbeek | 07 April 2023, 05:26:47 UTC | Fix pulsar error when when home_target is pwd Fixes: ``` ERROR galaxy.jobs.runners.pulsar:pulsar.py:531 failure running job 533 Traceback (most recent call last): File "/home/runner/work/pulsar/pulsar/galaxy/lib/galaxy/jobs/runners/pulsar.py", line 484, in __prepare_job job_wrapper.prepare(**prepare_kwds) File "/home/runner/work/pulsar/pulsar/galaxy/lib/galaxy/jobs/__init__.py", line 1253, in prepare ) = tool_evaluator.build() File "/home/runner/work/pulsar/pulsar/galaxy/lib/galaxy/tools/evaluation.py", line 560, in build global_tool_logs(self._build_environment_variables, config_file, "Building Environment Variables") File "/home/runner/work/pulsar/pulsar/galaxy/lib/galaxy/tools/evaluation.py", line 90, in global_tool_logs raise e File "/home/runner/work/pulsar/pulsar/galaxy/lib/galaxy/tools/evaluation.py", line 86, in global_tool_logs return func() File "/home/runner/work/pulsar/pulsar/galaxy/lib/galaxy/tools/evaluation.py", line 664, in _build_environment_variables home_dir = self.compute_environment.home_directory() File "/home/runner/work/pulsar/pulsar/galaxy/lib/galaxy/jobs/runners/pulsar.py", line 1163, in home_directory return self._target_to_directory(self.job_wrapper.home_target) File "/home/runner/work/pulsar/pulsar/galaxy/lib/galaxy/jobs/runners/pulsar.py", line 1179, in _target_to_directory raise Exception(f"Unknown target type [{target}]") Exception: Unknown target type [pwd] ``` | 07 April 2023, 05:28:01 UTC |
| 71cf555 | Nate Coraor | 06 April 2023, 21:18:22 UTC | Merge pull request #15912 from dannon/messagebox-tweak [23.0] Allow messagebox rich contents | 06 April 2023, 21:18:22 UTC |
| 42c587d | Dannon Baker | 06 April 2023, 20:01:28 UTC | Messagebox should accept html; this is only delivered by administrators via config and is trusted content | 06 April 2023, 20:01:28 UTC |
| cbced46 | Marius van den Beek | 06 April 2023, 19:18:54 UTC | Merge pull request #15909 from mvdbeek/fix_parallelism_hang_in_pulsar_tests [23.0] Fail linked job if task fails | 06 April 2023, 19:18:54 UTC |
| eb1a2ff | mvdbeek | 06 April 2023, 17:52:30 UTC | Fail linked job if task fails | 06 April 2023, 18:01:55 UTC |
| 9a283fc | Nate Coraor | 06 April 2023, 17:03:58 UTC | Merge pull request #15907 from mvdbeek/fix_stdout_stderr_puslar [23.0] Fix tool stdio on pulsar and implement job stdio | 06 April 2023, 17:03:58 UTC |
| 04de938 | Dannon Baker | 06 April 2023, 16:45:12 UTC | Backport of webpack improvements. Build highest quality sourcemaps when requested, but drop minimzation completely for dev. Drop console statements in production build. | 06 April 2023, 16:45:12 UTC |
| decc966 | mvdbeek | 06 April 2023, 11:55:29 UTC | Fix tool stdio on pulsar and implement job stdio Depends on https://github.com/galaxyproject/pulsar/pull/318 | 06 April 2023, 15:07:00 UTC |
| 95156cb | David López | 06 April 2023, 13:48:34 UTC | Merge pull request #15906 from dannon/admin-deny-route [23.0] Admin interface navguard | 06 April 2023, 13:48:34 UTC |
| ae7049e | Dannon Baker | 06 April 2023, 01:59:08 UTC | Add router onError handling and simple component that doesn't require any context for presenting an error. | 06 April 2023, 02:35:20 UTC |
| 9481922 | Dannon Baker | 05 April 2023, 19:34:35 UTC | Basic navigation guard for admin routes; todo: notification of some sort. | 05 April 2023, 19:34:38 UTC |
| 5464443 | Marius van den Beek | 05 April 2023, 13:05:28 UTC | Merge pull request #15897 from davelopez/23.0_fix_public_histories_annotation_search [23.0] Fix history annotation filtering: make it case insensitive | 05 April 2023, 13:05:28 UTC |
| 7452b2e | Nicola Soranzo | 05 April 2023, 10:48:36 UTC | Merge branch 'release_22.05' into release_23.0 | 05 April 2023, 10:51:03 UTC |
| f420a61 | Marius van den Beek | 05 April 2023, 08:29:56 UTC | Merge pull request #15896 from bernt-matthias/merge/22.01_22.05 [22.05] merge 22.01 | 05 April 2023, 08:29:56 UTC |
| 0698979 | John Chilton | 04 April 2023, 17:04:36 UTC | Merge pull request #15894 from davelopez/23.0_fix_export_archive_extension [23.0] Fix short term storage archive export extension on download | 04 April 2023, 17:04:36 UTC |
| b6c4668 | davelopez | 04 April 2023, 16:28:37 UTC | Make annotation filtering case insensitive | 04 April 2023, 16:28:37 UTC |
| 0a04397 | davelopez | 04 April 2023, 13:10:05 UTC | Add unit test for model_store_storage_target | 04 April 2023, 15:31:32 UTC |
| a99c137 | Matthias Bernt | 04 April 2023, 14:15:45 UTC | Merge branch 'release_22.01' into merge/22.01_22.05 | 04 April 2023, 14:15:45 UTC |
| 2acf212 | Dannon | 04 April 2023, 13:08:49 UTC | Merge pull request #15891 from ElectronicBlueberry/webhook-z-index [23.0] Fix tool bar on top of pop-ups | 04 April 2023, 13:08:49 UTC |
| f76d894 | Marius van den Beek | 04 April 2023, 12:35:04 UTC | Merge pull request #15893 from bernt-matthias/fix/cached_explicit_singularity_container_description [22.01] cached_explicit_singularity: needs to copy container description | 04 April 2023, 12:35:04 UTC |
| d5bc7ff | davelopez | 04 April 2023, 12:18:17 UTC | Guess mime type for short term storage files | 04 April 2023, 12:18:17 UTC |
| 8b715de | davelopez | 04 April 2023, 12:15:20 UTC | Fix extension lost after cleaning filename | 04 April 2023, 12:15:20 UTC |
| e81fc67 | Matthias Bernt | 04 April 2023, 09:26:07 UTC | cached_explicit_singularity: copy container description otherwise `container_description.identifier = cache_path` (at the end of the function) will modify the original (i.e. the tools) container description which influences i.e. (may break) successive container resolutions. | 04 April 2023, 10:09:36 UTC |
| bee3d2e | Nicola Soranzo | 03 April 2023, 15:31:48 UTC | Merge branch 'release_22.05' into release_23.0 | 03 April 2023, 15:31:48 UTC |
| b855a81 | Laila Los | 03 April 2023, 10:24:27 UTC | increase webhook z-index | 03 April 2023, 10:24:27 UTC |
| 42c9aff | Marius van den Beek | 03 April 2023, 08:35:26 UTC | Merge pull request #15882 from davelopez/22.05_fix_ids_on_errors [22.05] Remove some IDs from error messages | 03 April 2023, 08:35:26 UTC |
| 905e89f | Martin Cech | 31 March 2023, 23:03:02 UTC | Merge pull request #15883 from mvdbeek/tags_in_collection_view [23.0] List tags in ``/api/dataset_collections/{hdca_id}/contents/{parent_id}`` | 31 March 2023, 23:03:02 UTC |
| 7f425d1 | mvdbeek | 31 March 2023, 15:30:03 UTC | List tags in /api/dataset_collections/{hdca_id}/contents/{parent_id} Fixes https://github.com/galaxyproject/galaxy/issues/15878. I don't love it, but the endpoint is paginated, and if we want to show tags in the summary view I think we have to do this. | 31 March 2023, 15:41:37 UTC |
| 7d9cbc7 | Marius van den Beek | 31 March 2023, 14:45:49 UTC | Merge pull request #15841 from pauldg/fix_rocrate_metadata [23.0] Fix Invocation RO-Crate metadata | 31 March 2023, 14:45:49 UTC |
| 051c922 | Dannon | 31 March 2023, 12:01:06 UTC | Merge pull request #15593 from mvdbeek/make_drag_icon_transparent [23.0] Make dragImage transparent in workflow editor | 31 March 2023, 12:01:06 UTC |
| 682da9f | davelopez | 31 March 2023, 10:23:20 UTC | Remove IDs from error messages Simplifies encoding/decoding of IDs and prevents exposure issues | 31 March 2023, 10:35:00 UTC |
| d22dc4a | mvdbeek | 16 February 2023, 11:37:41 UTC | Make dragImage transparent Fixes https://github.com/galaxyproject/galaxy/issues/15512 | 30 March 2023, 15:57:50 UTC |
| d0551dd | Marius van den Beek | 30 March 2023, 13:08:54 UTC | Merge pull request #15856 from cat-bro/cherry-pick-job-files-api-fix-for-22.05 [22.05] Backport cast job_key to string #15578 | 30 March 2023, 13:08:54 UTC |
| e7b70f5 | pauldg | 30 March 2023, 11:52:10 UTC | removed unnecessary str casting | 30 March 2023, 11:52:10 UTC |
