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06 April 2024, 09:42:01 UTC
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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
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