opensource/galaxy
3
0
Fork 0
mirror of https://github.com/galaxyproject/galaxy.git synced 2026-10-24 12:13:33 +08:00
Code Issues Packages Projects Releases Wiki Activity
71,509 Commits 63 Branches 243 Tags
9d3d45a0e6bd8ed8434e1699f50ec3d141f528fb
Commit Graph
71509 Commits
This Branch
This Branch
All Branches
Author SHA1 Message Date
nuwang 9d3d45a0e6 Accept access token for api auth 2023-11-06 19:16:12 +05:30
nuwang d1aa6d1893 Add oidc logout tests and fix bug in server side logout 2023-11-06 19:16:12 +05:30
nuwang 6182222f0b Add test harness for oidc login against keycloak 2023-11-06 19:16:12 +05:30
Nicola Soranzo 83dfdcbc23 Merge pull request #16978 from galaxybot/dev_auto_update_dependencies 
Update Python dependencies
 2023-11-05 12:13:05 +00:00
galaxybot c208aac15e Update Python dependencies 2023-11-04 03:25:40 +00:00
Marius van den Beek abbb03c36d Merge pull request #16963 from common-workflow-lab/h5py_and_typos 
prep for updated h5py and typos
 2023-11-03 09:33:05 +01:00
Dannon 0db04441aa Merge pull request #16966 from nsoranzo/issue_16960 
Allow non-optional integer/float params without value attribute
 2023-11-02 21:22:13 -04:00
Martin Cech aa1702d845 Merge pull request #16672 from jmchilton/markdown 
Galaxy Markdown - add workflow image and license to Galaxy markdown.
 2023-11-03 02:20:50 +01:00
Nicola Soranzo 1e86672f83 Allow non-optional integer/float params without `value` attribute 
Previously a tool with such an input would fail to load.

Add test tool.
 2023-11-02 17:19:43 +00:00
Nicola Soranzo b3bdf058b5 Use `super()` 2023-11-02 17:08:20 +00:00
Nicola Soranzo 2720b0dc75 Add some type annotations to `ToolParameter` methods 2023-11-02 17:05:18 +00:00
John Chilton d3d812c57b Merge pull request #16340 from jmchilton/per_object_store_admin 
Augment pgcleanup to allow periodically deleting old datasets.
 2023-11-02 13:03:52 -04:00
John Chilton bbe0ee217b Merge pull request #16959 from jmchilton/typing_fixes_90 
Remove sentry.py from mypy exclusions.
 2023-11-02 11:05:42 -04:00
John Chilton 2baee6abbc Merge pull request #16964 from davelopez/invenio_external_storage_workaround 
Enhance Invenio RDM integration
 2023-11-02 11:04:35 -04:00
davelopez 85dbb929c6 Raise exception when trying to download from private record 2023-11-02 12:57:47 +01:00
davelopez 20c08b85b0 Use alternative download url for other storage classes 2023-11-02 10:09:39 +01:00
mvdbeek 707b31b059 Fix Anndata set_meta for updated h5py 2023-11-02 09:46:16 +01:00
Michael R. CrusoeandNicola Soranzo 4dafda64d1 typo fix 
Co-authored-by: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
 2023-11-02 09:46:15 +01:00
Michael R. Crusoe 2bc357c9b1 codespell: ignore "implementors" 2023-11-02 09:46:04 +01:00
davelopez ec01812051 Do not raise exception when serializing values 2023-11-02 09:36:30 +01:00
Marius van den Beek 8dad464ea4 Merge pull request #16955 from mvdbeek/unify_extra_files_path_persistence 
Move and re-use persist_extra_files
 2023-11-01 22:37:23 +01:00
Marius van den BeekandNicola Soranzo dbca4428d5 Add return type annotation for collect_extra_files 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2023-11-01 22:37:10 +01:00
John Chilton da213af8cf Remove sentry.py from mypy exclusions. 
Seems like typing has been fixed in it?
 2023-11-01 16:18:14 -04:00
mvdbeek 3f3e451fd4 Fix typo-ish bug with persisting collection element extra files 
I suppose we have no way to express in tools that we are discovering
collection elements with extra files, and that's why that hasn't caused
any problems ? Caught by 🦅👀!
 2023-11-01 19:24:41 +01:00
mvdbeek 3776f9c9a1 Fix wrong relpath calculation if object store cache is used 2023-11-01 19:24:41 +01:00
mvdbeek f0dd85cab0 Move and re-use persist_extra_files 2023-11-01 19:24:41 +01:00
Marius van den Beek af386d2e7e Merge pull request #16953 from common-workflow-lab/src_id_to_item 
Add helper to get dataset or collection via ``src`` and ``id``
 2023-11-01 15:06:03 +01:00
Michael R. CrusoeandMarius van den Beek 1959e7920e new sqlalchemy 2.0 compatible syntax 
Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com>
 2023-11-01 12:40:10 +01:00
mvdbeekandMichael R. Crusoe 78d44158eb add src_id_to_item helper 
Co-authored-by: Michael R. Crusoe <michael.crusoe@gmail.com>
 2023-11-01 11:59:36 +01:00
Martin Cech 50d6e8105b Merge pull request #16944 from davelopez/allow_delete_from_dashboard_viz 
Allow to permanently delete non-deleted items in Storage Dashboard Visualizations
 2023-10-31 19:42:33 +01:00
Dannon 3943f1a449 Merge pull request #16924 from jmchilton/toolshedpackage 
Publish tool shed frontend to npm.
 2023-10-31 13:06:03 -04:00
Marius van den Beek a5b88e0624 Merge pull request #16949 from dannon/color 
Standardize to W3C naming for color.
 2023-10-31 17:51:41 +01:00
Dannon Baker 140a65c146 Update 'color' spelling in workflow editor comment testing 2023-10-31 10:13:22 -04:00
Dannon 5b44e848af Merge pull request #16945 from davelopez/storage_dashboard_set_current_history 
Allow switching histories from Storage Dashboard Visualizations
 2023-10-31 08:22:35 -04:00
Dannon Baker c70ecf6bf0 Standardize to W3C naming for color. 2023-10-31 08:06:37 -04:00
Dannon 67cf270c79 Merge pull request #16612 from ElectronicBlueberry/workflow-annotations 
Workflow Comments 💬
 2023-10-31 07:54:07 -04:00
davelopez 1a3e0a1c4e Fix typing issue with possible null slot value 
Type 'null' is not assignable to type 'DataValuePoint'.
 2023-10-31 10:01:02 +01:00
davelopez 1e4d8232bc Allow to set current history from Storage Dashboard 2023-10-31 09:41:02 +01:00
Dannon a8b32e9d09 Merge pull request #16900 from davelopez/remove_invenio_record_access_handling 
Remove record access handling for Invenio RDM plugin
 2023-10-30 16:47:50 -04:00
Dannon f70df518e7 Merge pull request #16928 from ahmedhamidawan/change_api_tool_panel_route 
Change `api/tool_panel` to `api/tool_panels/...`
 2023-10-30 16:45:42 -04:00
davelopez dafb2e415d Allow to permanently delete non-deleted items 
In Storage Dashboard Visualizations
 2023-10-30 20:47:50 +01:00
Martin Cech 082c9009eb Merge pull request #16942 from ElectronicBlueberry/fix-select-header-not-showing 
Fix select parameter doesn't show parameter name in UI
 2023-10-30 19:48:39 +01:00
John Chilton aea795769a Publish tool shed frontend to npm. 2023-10-30 11:43:46 -04:00
Laila Los a3e7eed970 fallback to test_param.name 2023-10-30 15:55:01 +01:00
Dannon 1a999e88b4 Merge pull request #16939 from galaxybot/dev_auto_update_dependencies 
Update Python dependencies
 2023-10-29 14:32:02 -04:00
Marius van den Beek eaea64209d Merge pull request #16940 from mvdbeek/dev 
Merge 23.1 into dev
 2023-10-29 10:58:44 +01:00
mvdbeek 3f4b9a78c8 Merge branch 'release_23.1' into dev 2023-10-29 09:05:09 +01:00
Nicola Soranzo 45fb60c530 Ignore UP036 ruff check in check_python.py 2023-10-28 17:35:12 +01:00
galaxybot 077e35a540 Update Python dependencies 2023-10-28 03:17:24 +00:00
Martin Cech 12b20c69d4 Merge pull request #16929 from davelopez/23.1_fix_discarded_dataset_ordering 
[23.1] Fix discarded dataset ordering in Storage Dashboard
 2023-10-27 22:45:34 +02:00