fcd9db1 | mvdbeek | 03 November 2021, 08:48:37 UTC | Version 21.9.1 of tool-util (tag galaxy-tool-util-21.9.1). | 03 November 2021, 08:48:37 UTC |
a5a4a0a | mvdbeek | 03 November 2021, 08:39:41 UTC | Version 21.9.0 of tool-util (tag galaxy-tool-util-21.9.0). | 03 November 2021, 08:39:41 UTC |
368a4b8 | Marius van den Beek | 03 November 2021, 08:19:23 UTC | Merge pull request #12839 from jmchilton/fix_requirement_linter [21.09] Backport #12527 - needed to fix the converter tests. | 03 November 2021, 08:19:23 UTC |
912f7d9 | John Chilton | 02 November 2021, 16:43:39 UTC | [21.09] Backport #12527 - needed to fix the converter tests. | 02 November 2021, 16:43:39 UTC |
b5ce46c | mvdbeek | 02 November 2021, 11:08:06 UTC | Update version to 21.09.1.dev0 | 02 November 2021, 11:08:06 UTC |
6b29202 | mvdbeek | 02 November 2021, 11:08:02 UTC | Update version to 21.09. | 02 November 2021, 11:08:02 UTC |
68d6d20 | mvdbeek | 02 November 2021, 10:33:01 UTC | Merge branch 'release_21.05' into release_21.09 | 02 November 2021, 10:33:01 UTC |
2b25c37 | Martin Cech | 02 November 2021, 10:20:09 UTC | Merge pull request #12832 from mvdbeek/disable_dockerhub_push [21.05] Disable dockerhub pushes | 02 November 2021, 10:20:09 UTC |
3a7324c | mvdbeek | 02 November 2021, 08:59:36 UTC | Disable dockerhub pushes | 02 November 2021, 08:59:36 UTC |
46c0a99 | Marius van den Beek | 02 November 2021, 08:55:44 UTC | Merge pull request #12821 from mvdbeek/release_21.09_release_notes_update [21.09] Finalize release notes | 02 November 2021, 08:55:44 UTC |
a6207d0 | mvdbeek | 02 November 2021, 07:57:42 UTC | Add last 2 PRs to release notes | 02 November 2021, 07:57:42 UTC |
0c28fc6 | Marius van den Beek | 02 November 2021, 07:43:32 UTC | Merge pull request #12827 from dannon/pin-around-uaparser [21.09] Pin a resolution for ua-parser-js to 0.7.30 | 02 November 2021, 07:43:32 UTC |
4257cd5 | mvdbeek | 02 November 2021, 07:42:19 UTC | Edits from Beatriz | 02 November 2021, 07:42:22 UTC |
80dd362 | Marius van den Beek | 02 November 2021, 06:40:37 UTC | Merge pull request #12830 from nsoranzo/release_21.09_followup_on_12795 [21.09] Allow sessionless access to some datasets API endpoints | 02 November 2021, 06:40:37 UTC |
eafca3f | Nicola Soranzo | 02 November 2021, 02:05:27 UTC | Allow sessionless access to some datasets API endpoints Commit c92fcb91d7f455d5c3d11febe3f5d028741e178f broke a BioBlend test where a public dataset is accessed anonymously via the API: https://github.com/galaxyproject/bioblend/blob/main/bioblend/_tests/TestGalaxyDatasets.py#L181-L190 See the GitHub workflow failed jobs: https://github.com/galaxyproject/bioblend/runs/4074342140?check_suite_focus=true N.B.: in terms of access control, `legacy_expose_api_anonymous` is equivalent to `expose_api_anonymous_and_sessionless` (not `expose_api_anonymous`). | 02 November 2021, 02:15:13 UTC |
ce2280b | Dannon Baker | 01 November 2021, 17:48:52 UTC | Pin a resolution for ua-parser-js to 0.7.30 xref: https://snyk.io/vuln/SNYK-JS-UAPARSERJS-1766952 | 01 November 2021, 17:51:22 UTC |
4145de7 | mvdbeek | 01 November 2021, 17:14:47 UTC | Merge branch 'release_21.05' into release_21.09 | 01 November 2021, 17:14:47 UTC |
48996b1 | Marius van den Beek | 01 November 2021, 17:14:10 UTC | Merge pull request #12816 from mvdbeek/fix_from_work_dir_glob_with_extended_metadata [21.09] Fix ``from_work_dir`` glob with extended metadata and pulsar | 01 November 2021, 17:14:10 UTC |
896bd88 | mvdbeek | 01 November 2021, 17:03:56 UTC | More punctuation fixes! | 01 November 2021, 17:10:44 UTC |
1c75d43 | mvdbeek | 01 November 2021, 16:42:47 UTC | Capitalize Backbone | 01 November 2021, 16:42:47 UTC |
317a8b5 | mvdbeek | 01 November 2021, 16:27:00 UTC | More whitespace and punctuation fixes | 01 November 2021, 16:27:26 UTC |
4a1e102 | Marius van den Beek | 01 November 2021, 15:05:48 UTC | Remove David from release testers for 21.09 Co-authored-by: David López <46503462+davelopez@users.noreply.github.com> | 01 November 2021, 15:05:48 UTC |
fa8c1a5 | John Chilton | 01 November 2021, 13:56:22 UTC | Merge pull request #12815 from mvdbeek/fix_object_store_datasets_not_purged [21.09] Fix remote object store datasets not purged | 01 November 2021, 13:56:22 UTC |
483631e | John Chilton | 01 November 2021, 13:53:44 UTC | Merge pull request #12817 from mvdbeek/allow_anon_delete [21.09] Allow dataset and dataset collection deletion for anonymous users | 01 November 2021, 13:53:44 UTC |
84ff152 | John Chilton | 01 November 2021, 13:29:29 UTC | Merge pull request #12823 from simonbray/workflow-missing-tools-fix [21.09] Add missing tool_ids to workflow invocation failure message | 01 November 2021, 13:29:29 UTC |
5583141 | mvdbeek | 01 November 2021, 12:23:17 UTC | One more PR | 01 November 2021, 12:24:13 UTC |
fae99b9 | Marius van den Beek | 01 November 2021, 12:19:54 UTC | Merge pull request #12520 from almahmoud/2105-imagebuild [21.05] Add image auto-building through GA | 01 November 2021, 12:19:54 UTC |
aa7b10e | mvdbeek | 01 November 2021, 12:11:29 UTC | Only build docker image for galaxyproject repo limit concurrency and only build for release and anvil branches. | 01 November 2021, 12:16:22 UTC |
c657675 | mvdbeek | 01 November 2021, 12:01:02 UTC | Adjust check_blocking_issues to PyGithub usage | 01 November 2021, 12:01:02 UTC |
3b4cd15 | mvdbeek | 01 November 2021, 11:47:02 UTC | Add remaining open PRs | 01 November 2021, 11:47:02 UTC |
c378d08 | mvdbeek | 01 November 2021, 11:30:36 UTC | Add release-diff.py to process | 01 November 2021, 11:37:53 UTC |
a9058c5 | mvdbeek | 01 November 2021, 11:26:39 UTC | Produce Literal Blocks for config value changes These scroll correctly and don't fail when config description changes includes newlines or long text. | 01 November 2021, 11:37:53 UTC |
1a96895 | Simon Bray | 01 November 2021, 10:57:48 UTC | add missing tool_ids to workflow invocation failure message | 01 November 2021, 11:04:02 UTC |
ef2ace8 | mvdbeek | 01 November 2021, 10:33:20 UTC | Write full release notes | 01 November 2021, 10:43:03 UTC |
696a99b | mvdbeek | 01 November 2021, 10:31:40 UTC | More PR fixes | 01 November 2021, 10:31:40 UTC |
11f1296 | mvdbeek | 01 November 2021, 09:10:13 UTC | More fixes to PR titles | 01 November 2021, 09:10:13 UTC |
46be208 | mvdbeek | 31 October 2021, 19:39:10 UTC | Capitalize PR | 31 October 2021, 19:39:10 UTC |
2aebc4f | mvdbeek | 31 October 2021, 19:32:27 UTC | Add release testing team credits | 31 October 2021, 19:32:27 UTC |
696331e | mvdbeek | 31 October 2021, 19:14:50 UTC | Drop anchors | 31 October 2021, 19:18:01 UTC |
380b15b | Marius van den Beek | 31 October 2021, 18:41:10 UTC | Merge pull request #12818 from mvdbeek/backport_list_builder_pairing_fix [21.09] Backport list builder pairing fix | 31 October 2021, 18:41:10 UTC |
2800070 | mvdbeek | 31 October 2021, 14:41:40 UTC | Allow dataset / collection deletion for anonymous users Fixes https://github.com/galaxyproject/galaxy/issues/12442 | 31 October 2021, 18:40:17 UTC |
45ef46c | Marius van den Beek | 31 October 2021, 17:36:36 UTC | Merge pull request #12819 from mvdbeek/ncbi_datasets_containerized [21.09] Set profile version of ncbi_datasets so it can run containerized | 31 October 2021, 17:36:36 UTC |
63e25b2 | mvdbeek | 31 October 2021, 15:27:51 UTC | Set profile version of ncbi_datasets so it can run containerized | 31 October 2021, 15:28:38 UTC |
9bfaf66 | mvdbeek | 31 October 2021, 15:25:03 UTC | Add release_21.09 to release toc | 31 October 2021, 15:25:03 UTC |
3b0c86f | mvdbeek | 31 October 2021, 15:24:38 UTC | Fix and update bootstrap_history | 31 October 2021, 15:24:38 UTC |
b3163b1 | mvdbeek | 31 October 2021, 15:10:04 UTC | Update and finalize release notes | 31 October 2021, 15:10:04 UTC |
0d93169 | Assunta DeSanto | 15 October 2021, 21:36:58 UTC | increased matchPercentage used for autopairing | 31 October 2021, 14:57:15 UTC |
c27c86d | mvdbeek | 31 October 2021, 13:19:38 UTC | Disable created_from_basename test, doesn't work with default setup | 31 October 2021, 13:19:38 UTC |
1a531cd | mvdbeek | 31 October 2021, 11:19:58 UTC | Fix from work dir glob with extended metadata I also have a commit coming for pulsar that fixes this if pulsar stages out from_work_dir outputs. | 31 October 2021, 12:06:41 UTC |
1cde925 | Marius van den Beek | 31 October 2021, 07:32:04 UTC | Merge pull request #12805 from mvdbeek/fix_wrong_dataset_details_link [21.09] Fix wrong dataset details link | 31 October 2021, 07:32:04 UTC |
12a4b2e | mvdbeek | 31 October 2021, 06:18:20 UTC | Ignore SameFileError | 31 October 2021, 06:18:43 UTC |
ca4a2d7 | mvdbeek | 30 October 2021, 14:32:51 UTC | Drop heuristic that was supposed to prevent moving empty working directory outputs This broke updating remote object stores from their cache directory, as evidenced by a broken test_cache_repopulated test. | 30 October 2021, 19:26:26 UTC |
4902589 | mvdbeek | 30 October 2021, 14:26:05 UTC | Never fail to delete remote object store files if cache path doesn't exist We correctly realized this is a problem in the irods object store, but never applied this to the other object stores. Fixes https://github.com/galaxyproject/galaxy/issues/11940 | 30 October 2021, 14:42:07 UTC |
673e068 | mvdbeek | 30 October 2021, 14:24:36 UTC | Add test case that verifies various object store cache operations | 30 October 2021, 14:41:41 UTC |
8507756 | mvdbeek | 30 October 2021, 14:24:01 UTC | Refactor SiwftObjectStore test so it can be re-used more easily | 30 October 2021, 14:36:50 UTC |
9ecfcc9 | Marius van den Beek | 30 October 2021, 10:38:06 UTC | Merge pull request #12814 from mvdbeek/restore_tool_entry_point [21.09] Restore ToolEntryPoints component | 30 October 2021, 10:38:06 UTC |
513f694 | mvdbeek | 30 October 2021, 07:36:04 UTC | Restore ToolEntryPoints component Fixes https://github.com/galaxyproject/galaxy/issues/12692 | 30 October 2021, 07:36:51 UTC |
d41bb73 | Oleg Zharkov | 29 October 2021, 17:25:59 UTC | Merge pull request #12807 from mvdbeek/display_unknown_datatype [21.05] If datatype is unknown display warning when trying to connect nodes | 29 October 2021, 17:25:59 UTC |
52dedfa | mvdbeek | 29 October 2021, 14:34:02 UTC | Fix unit tests for iterating only over valid folder datasets | 29 October 2021, 14:34:02 UTC |
f42dd7f | mvdbeek | 29 October 2021, 14:11:34 UTC | Fix performance test workflow | 29 October 2021, 14:11:34 UTC |
6d1edce | mvdbeek | 29 October 2021, 12:23:35 UTC | If datatype is unknown display warning when trying to connect nodes | 29 October 2021, 14:04:14 UTC |
0736e8f | mvdbeek | 29 October 2021, 14:02:53 UTC | Merge branch 'release_21.05' into release_21.09 | 29 October 2021, 14:02:53 UTC |
69ca27e | Marius van den Beek | 29 October 2021, 12:37:31 UTC | Merge pull request #12806 from mvdbeek/diable_library_uploads_using_master_api_key [21.05] Disable library uploads using master API key | 29 October 2021, 12:37:31 UTC |
3925c17 | mvdbeek | 29 October 2021, 06:53:16 UTC | Fix wrong dataset details link Fixes https://github.com/galaxyproject/galaxy/issues/12804. This is not the ideal fix, the client should ideally contruct the link ... but it's the old history, it's an easy fix and it's consistent with what the new history does (for now). There is some backbone manipulation of the model id (which is not HistoryDatasetAssociation, but a DatasetCollectionElement in a collection context) which is supposed to set the id to the HistoryDatasetAssociation id. I guess it may not have run on time ? I also don't know where it is and how to find it, might have been deleted ? I think it was related to https://github.com/galaxyproject/galaxy/blob/dev/client/src/mvc/collection/collection-model.js#L86. | 29 October 2021, 12:30:48 UTC |
2f89e55 | Marius van den Beek | 29 October 2021, 10:20:23 UTC | Fix typo Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com> | 29 October 2021, 10:20:23 UTC |
c151af0 | mvdbeek | 29 October 2021, 09:02:52 UTC | Exclude invalid LibraryDataset items from folder | 29 October 2021, 09:03:26 UTC |
629abab | mvdbeek | 29 October 2021, 08:00:51 UTC | Disable library uploads using master API key and cleanup some of the parameter validation. | 29 October 2021, 08:42:04 UTC |
42ffa7f | Marius van den Beek | 28 October 2021, 14:53:37 UTC | Merge pull request #12757 from bernt-matthias/topic/output_ext_linting [21.09] Two fixes for linting | 28 October 2021, 14:53:37 UTC |
0bd899a | Marius van den Beek | 28 October 2021, 14:49:34 UTC | Merge pull request #12712 from bernt-matthias/topic/rds [21.05] Add support for RDS files and improvements for RData | 28 October 2021, 14:49:34 UTC |
ea2d8d7 | mvdbeek | 28 October 2021, 11:01:58 UTC | Use build_sniff_from_prefix for rds and rdata | 28 October 2021, 11:01:58 UTC |
511d52f | Nicola Soranzo | 28 October 2021, 10:09:20 UTC | Merge branch 'release_21.05' into release_21.09 | 28 October 2021, 10:09:20 UTC |
d0dbd99 | mvdbeek | 28 October 2021, 10:01:49 UTC | Fetch pattern from NAMED_PATTERNS | 28 October 2021, 10:01:49 UTC |
80595eb | mvdbeek | 28 October 2021, 09:25:12 UTC | Merge branch 'release_21.05' into release_21.09 | 28 October 2021, 09:25:12 UTC |
a48b2c3 | Marius van den Beek | 28 October 2021, 09:18:58 UTC | Merge pull request #12796 from mvdbeek/move_collection_update_put_to_post_copy [21.09] Use post instead of put to create copy of dataset collection | 28 October 2021, 09:18:58 UTC |
5d83ea6 | Marius van den Beek | 28 October 2021, 09:18:31 UTC | Merge pull request #12799 from nsoranzo/release_21.05_genomes_api_allow_sessionless [21.05] Allow sessionless access to genomes API | 28 October 2021, 09:18:31 UTC |
37c75a4 | Marius van den Beek | 28 October 2021, 09:17:09 UTC | Merge pull request #12793 from davelopez/fix_bootstrap_admin_run_jobs [21.05] Raise Bad Request when bootstrap admins (master key) try to run jobs/tools | 28 October 2021, 09:17:09 UTC |
3941659 | Nicola Soranzo | 27 October 2021, 18:17:00 UTC | Fix broken f-strings | 27 October 2021, 18:17:00 UTC |
4467a27 | Nicola Soranzo | 27 October 2021, 18:15:09 UTC | Allow sessionless access to genomes API Broken in commit 47e37cddda77a053b9283574ae444cb54834fcff Reported by @innovate-invent | 27 October 2021, 18:16:16 UTC |
269c0d5 | Marius van den Beek | 27 October 2021, 18:04:19 UTC | Merge pull request #12798 from mvdbeek/fix_datasets_details_page [21.09] Add error state to dataset provider, show error in dataset details page | 27 October 2021, 18:04:19 UTC |
b676249 | Marius van den Beek | 27 October 2021, 17:56:50 UTC | Merge pull request #12795 from mvdbeek/fix_api_dataset_permission_error_handling [21.09] Drop legacy_expose_api from api/datasets | 27 October 2021, 17:56:50 UTC |
35e029a | Marius van den Beek | 27 October 2021, 17:21:39 UTC | Merge pull request #12792 from nuwang/fix_container_cgroup_metrics [21.09] Use correct path for cgroup metrics when running within containers | 27 October 2021, 17:21:39 UTC |
6cd2467 | mvdbeek | 27 October 2021, 17:07:09 UTC | Add error state to dataset provider, show error in dataset details page | 27 October 2021, 17:07:44 UTC |
d779b61 | davelopez | 27 October 2021, 16:42:58 UTC | Raise Bad Request when bootstrap admin try to run/create workflows | 27 October 2021, 16:42:58 UTC |
0dd2180 | Marius van den Beek | 27 October 2021, 16:18:06 UTC | Merge pull request #12785 from mvdbeek/extended_metadata_fixes_21_09 [21.09] Various fixes and enhancements for metadata_strategy: extended | 27 October 2021, 16:18:06 UTC |
ff319fa | mvdbeek | 27 October 2021, 16:17:07 UTC | Clarify intention to allow changing other attributes in the future | 27 October 2021, 16:17:07 UTC |
b9f7a61 | davelopez | 27 October 2021, 14:10:21 UTC | Raise Bad Request when bootstrap admins try to run jobs/tools | 27 October 2021, 15:57:49 UTC |
d3e7c47 | mvdbeek | 27 October 2021, 15:44:57 UTC | PUT /api/dataset_collections/{id} to POST /api/dataset_collections/{id}/copy to reflect creation of new collection | 27 October 2021, 15:44:57 UTC |
c92fcb9 | mvdbeek | 27 October 2021, 15:08:30 UTC | Drop legacy_expose_api from api/datasets We raise MessageException inside the security checks, and these are not handled in legacy_expose_api. Fixes ``` MessageException: You are not allowed to access this dataset File "galaxy/web/framework/decorators.py", line 184, in decorator rval = func(self, trans, *args, **kwargs) File "galaxy/webapps/galaxy/api/datasets.py", line 134, in show dataset = self.get_hda_or_ldda(trans, hda_ldda=hda_ldda, dataset_id=id) File "galaxy/webapps/base/controller.py", line 987, in get_hda_or_ldda return self.get_hda(trans, dataset_id, check_ownership=False, check_accessible=True) File "galaxy/webapps/base/controller.py", line 1023, in get_hda error("You are not allowed to access this dataset") File "galaxy/web/framework/decorators.py", line 32, in error raise MessageException(message, type='error') ``` (https://sentry.galaxyproject.org/organizations/galaxy/issues/6012/?project=3&query=is%3Aunresolved). | 27 October 2021, 15:29:37 UTC |
324bc05 | mvdbeek | 27 October 2021, 10:46:13 UTC | Move output discovery before changing and flushing dataset state For discovered outputs that prevents a brief period during which the HDA extension is not yet set (and so defaults to `data`), leading to ``` _______ ToolsUploadTestCase.test_fetch_compressed_auto_decompress_target _______ self = <galaxy_test.api.test_tools_upload.ToolsUploadTestCase testMethod=test_fetch_compressed_auto_decompress_target> history_id = 'cc474525c8fa3aba' @uses_test_history(require_new=True) def test_fetch_compressed_auto_decompress_target(self, history_id): # TODO: this should definitely be fixed to allow auto decompression via that API. fastqgz_path = TestDataResolver().get_filename("1.fastqsanger.gz") with open(fastqgz_path, "rb") as fh: details = self._upload_and_get_details(fh, api="fetch", history_id=history_id, assert_ok=False, auto_decompress=True) assert details["state"] == "ok" > assert details["file_ext"] == "fastqsanger.gz", details E AssertionError: {'accessible': True, 'annotation': None, 'api_type': 'file', 'copied_from_ldda_id': None, ...} E assert 'data' == 'fastqsanger.gz' E - fastqsanger.gz E + data ``` You can simulate this (reliably) by reverting this commit and placing a time.sleep(2) before self.discover_outputs(job, inp_data, out_data, out_collections, final_job_state=final_job_state). | 27 October 2021, 14:04:50 UTC |
babc82d | Nuwan Goonasekera | 26 October 2021, 21:16:45 UTC | Use correct path for cgroup metrics when running within containers | 27 October 2021, 12:53:15 UTC |
b3a6149 | mvdbeek | 27 October 2021, 08:11:27 UTC | Add various include/exclude patterns for github workflows | 27 October 2021, 08:11:27 UTC |
5b8a0e2 | mvdbeek | 27 October 2021, 07:23:53 UTC | Fix test_fetch_nested_elements_from test The order within which datasets and dataset collection are added to the history is different between extended metadata and directory/legacy metadata collection. To fix the test we just check for the last dataset collection in the history. | 27 October 2021, 07:23:55 UTC |
daffe7d | mvdbeek | 26 October 2021, 20:06:14 UTC | Fix access to self.job.implicit_collection_jobs_association.id | 26 October 2021, 20:06:14 UTC |
fb1f197 | mvdbeek | 26 October 2021, 15:06:29 UTC | Run interactive tool finish with internal metadata | 26 October 2021, 15:59:09 UTC |
2a95a3d | mvdbeek | 25 October 2021, 07:57:23 UTC | Don't transfer work_dir_outputs in extended metadata mode | 26 October 2021, 15:59:08 UTC |
71cad3d | mvdbeek | 24 October 2021, 18:48:28 UTC | Fix task splitting jobs for extended metadata | 26 October 2021, 15:59:08 UTC |
e075fa1 | mvdbeek | 24 October 2021, 17:13:00 UTC | Don't send output_files into ClientOutputs in extended metadata mode If we don't do this then staging back the output file will overwrite the file in the object store. | 26 October 2021, 15:59:08 UTC |
0f2e601 | mvdbeek | 24 October 2021, 14:54:32 UTC | Add tsv to test datatype config | 26 October 2021, 15:59:07 UTC |
dfea4e8 | mvdbeek | 24 October 2021, 14:30:33 UTC | Use remote_metadata in pulsar_embedded_mq test | 26 October 2021, 15:59:07 UTC |
9ecbe0f | mvdbeek | 24 October 2021, 14:13:06 UTC | Relax test, get latest HDCA I think the external metadata addition of HDAs first makes more sense ? | 26 October 2021, 15:59:07 UTC |