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d62f688221af6c3f63d180952154b13fc79bedcf
Commit Graph
29157 Commits
Author SHA1 Message Date
mvdbeek d62f688221 Tweak docs for container_resolver_* options 2021-11-12 14:47:28 +01:00
davelopez b678b1dd97 Temporary downgrade FastAPI to v0.68.2 2021-11-04 19:00:15 +01:00
Nicola Soranzo dc715ef2d7 Merge branch 'release_21.09' into dev 2021-11-04 11:48:46 +00:00
Nicola Soranzo 75196db5cd Downgrade bowtie requirement for CONVERTER_fasta_to_bowtie_color_index 2021-11-04 09:56:55 +00:00
Dannon 542b1cd5fb Merge pull request #12802 from dannon/beta-history-menus 
Beta history menu reorg, display fixes.
 2021-11-03 14:08:46 -04:00
mvdbeek f04632e0f1 Merge branch 'release_21.09' into dev 2021-11-03 16:16:42 +01:00
Marius van den Beek 1a3f4aeaf4 Merge pull request #12836 from davelopez/upgrade_fastapi_dependencies 
Upgrade FastAPI to v0.70.0
 2021-11-03 16:15:00 +01:00
mvdbeek 8e035ffbdf Add version to fasta_to_index builders 2021-11-03 15:30:49 +01:00
Dannon 38bbc4f206 Merge pull request #12840 from OlegZharkov/check-wf-bookmark 
Fix bookmarking workflow twice
 2021-11-03 08:11:38 -04:00
davelopez af4ef0cedf Upgrade FastAPI to v0.70.0 
https://github.com/tiangolo/fastapi/releases/tag/0.70.0
 2021-11-03 10:48:53 +01:00
davelopez 8788b8c513 Upgrade FastAPI to v0.69.0 
https://github.com/tiangolo/fastapi/releases/tag/0.69.0
 2021-11-03 10:46:32 +01:00
davelopez a9714da2c6 Upgrade FastAPI to v0.68.2 
https://github.com/tiangolo/fastapi/releases/tag/0.68.2
 2021-11-03 10:46:32 +01:00
Marius van den Beek f99510f3aa Merge pull request #12833 from abretaud/patch-9 
GxITs: don't always add trailing slash to entry point url
 2021-11-03 09:06:19 +01:00
Oleg ZharkovandAuthor: davelopez ef075621ce don't add bookmarked wf to menu_entries if it's already there 
Co-authored-by: Author: davelopez <46503462+davelopez@users.noreply.github.com>
 2021-11-02 18:59:42 +01:00
John Chilton 912f7d99c7 [21.09] Backport #12527 - needed to fix the converter tests. 2021-11-02 12:43:39 -04:00
mvdbeek b5ce46c929 Update version to 21.09.1.dev0 2021-11-02 12:08:06 +01:00
mvdbeek 6b29202be6 Update version to 21.09. 2021-11-02 12:08:02 +01:00
mvdbeek bc329c7b84 Merge branch 'release_21.09' into dev 2021-11-02 11:54:42 +01:00
Anthony Bretaudeau d896908395 Don't always add trailing slash 2021-11-02 10:33:12 +01:00
Nicola Soranzo eafca3f68c Allow sessionless access to some datasets API endpoints 
Commit c92fcb91d7 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`).
 2021-11-02 02:15:13 +00:00
mvdbeek 54cc6b68e4 Create new history for anonymous API users via history/current_history_json 2021-11-01 21:39:42 +01:00
mvdbeek 58b2837c7c Merge branch 'release_21.09' into dev 2021-11-01 18:17:54 +01:00
Marius van den Beek 48996b1aaa 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
 2021-11-01 18:14:10 +01:00
John Chilton fa8c1a5fdc Merge pull request #12815 from mvdbeek/fix_object_store_datasets_not_purged 
[21.09] Fix remote object store datasets not purged
 2021-11-01 09:56:22 -04:00
John Chilton 483631ec31 Merge pull request #12817 from mvdbeek/allow_anon_delete 
[21.09] Allow dataset and dataset collection deletion for anonymous users
 2021-11-01 09:53:44 -04:00
Dannon Baker ab650b2596 Update selenium tests for history reorg 2021-11-01 08:53:48 -04:00
Simon Bray 1a968952cc add missing tool_ids to workflow invocation failure message 2021-11-01 12:04:02 +01:00
mvdbeek 28000701d7 Allow dataset / collection deletion for anonymous users 
Fixes https://github.com/galaxyproject/galaxy/issues/12442
 2021-10-31 19:40:17 +01:00
mvdbeek 1a531cd1a0 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.
 2021-10-31 13:06:41 +01:00
mvdbeek 12a4b2e9d1 Ignore SameFileError 2021-10-31 07:18:43 +01:00
mvdbeek ca4a2d728d 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.
 2021-10-30 21:26:26 +02:00
mvdbeek 49025893db 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
 2021-10-30 16:42:07 +02:00
mvdbeek 673e068358 Add test case that verifies various object store cache operations 2021-10-30 16:41:41 +02:00
Marius van den Beek 7856c4d784 Merge pull request #12813 from jmchilton/pdf_cleanup_2 
Fixes and test for PDF generation.
 2021-10-30 09:03:35 +02:00
John Chilton ebcedbaf09 Test case for PDF generation of pages. 2021-10-29 15:10:26 -04:00
John Chilton f5670ec1cd Cleanup/refactor markdown_util ahead of async task based version. 2021-10-29 15:10:26 -04:00
John Chilton 9a994a9770 Generics to improve typing of managers. 2021-10-29 12:05:27 -04:00
John Chilton 65a09634ff Improved typing for annotatable manager. 2021-10-29 12:05:27 -04:00
John Chilton f87c83b619 Progress toward strong typing in deletable manager helper. 2021-10-29 12:05:27 -04:00
John Chilton 026e3f93a4 Progress on strong typing for workflows manager. 2021-10-29 12:05:27 -04:00
John Chilton 2a9b0dcbe5 Improved typing of histories. 2021-10-29 12:05:27 -04:00
John Chilton 5310960e8a Types fixes for jobs manager. 2021-10-29 12:05:27 -04:00
mvdbeek b244c5ec93 Merge branch 'release_21.09' into dev 2021-10-29 16:57:13 +02:00
mvdbeek 0736e8f834 Merge branch 'release_21.05' into release_21.09 2021-10-29 16:02:53 +02:00
Marius van den Beek 69ca27ee5f Merge pull request #12806 from mvdbeek/diable_library_uploads_using_master_api_key 
[21.05] Disable library uploads using master API key
 2021-10-29 14:37:31 +02:00
Marius van den BeekandNicola Soranzo 2f89e55b77 Fix typo 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2021-10-29 12:20:23 +02:00
mvdbeek c151af0d1f Exclude invalid LibraryDataset items from folder 2021-10-29 11:03:26 +02:00
davelopez 51569be1dd Change update operation to copy 2021-10-29 11:01:10 +02:00
mvdbeek 629ababe42 Disable library uploads using master API key 
and cleanup some of the parameter validation.
 2021-10-29 10:42:04 +02:00
davelopez 888f8300fc Fix type parameter in create endpoint in history contents API 
The type may be specified in the path or query parameter
 2021-10-29 10:31:59 +02:00