opensource/galaxy
3
0
Fork 0
mirror of https://github.com/galaxyproject/galaxy.git synced 2026-11-05 07:52:07 +08:00
Code Issues Packages Projects Releases Wiki Activity
78,968 Commits 63 Branches 246 Tags
95c0950ba632cdfc94dea402c464df388704a77c
Commit Graph
456 Commits
Author SHA1 Message Date
Nicola Soranzo 95c0950ba6 Add type annotations to `JobRunnerMapper` and related code 2024-11-07 15:19:32 +00:00
Nicola Soranzo 1f223d0dc5 Test hash validation also for upload by path 2024-11-05 15:33:40 +00:00
davelopez 305dd2b181 Add has_deferred_data flag to MockDataset and FakeDatasetAssociation 2024-10-31 11:17:16 +01:00
davelopez b3a70863fc Add test for parsing allow_uri_if_protocol 2024-10-31 11:17:16 +01:00
Marius van den Beek 339724e0aa Merge pull request #19070 from mvdbeek/reuse_trs_import_in_workflow_contents_manager 
Move TRS import into WorkflowContentManager
 2024-10-30 15:27:21 -04:00
mvdbeek 48ed0682dc Move TRS import into WorkflowContentManager 
which fixes missing source metadata when importing a workflow through a
landing page.
 2024-10-30 17:32:23 +01:00
John Chilton 078ad6114b Fix param models for dynamic options and truevalue/falsevalue 2024-10-22 07:49:37 -04:00
John Chilton 730ea2ee03 Pydantic models for parameter validators. 2024-10-22 07:49:37 -04:00
John Chilton 8c10f36dd2 Refactor Tool._populate for reuse of hook checks. 2024-10-22 07:49:37 -04:00
John Chilton 639d3025b3 Merge pull request #18979 from mvdbeek/workflow_landing_improvements 
Workflow landing improvements
 2024-10-22 07:47:12 -04:00
mvdbeek f4a779e45f Fix unit tests 2024-10-20 18:34:57 -04:00
mvdbeek 67fff6ac73 Allow using TRS ids as workflow id in workflow landing requst 2024-10-15 15:25:38 +02:00
John Chilton edc5bc2a8f Allow oauth2 file sources with Dropbox initial implementation. 2024-10-14 15:16:41 +02:00
John Chilton 01c42c888b Expand pre-checking of file source/object store configuration. 
- UI for detailed display of errors.
- UI option to test configuration from management menu.
- API + UI for checking configuration before upgrading to new version of template.
- API + UI for checking configuration before updating current template's settings.
- Add an option during update/upgrade to allow forcing the update even if configuration doesn't validate - I don't allow creation of invalid things, but if there are problems with an existing thing - admins and power users should have recourse. It is their data.
 2024-10-14 14:27:05 +02:00
John Chilton 660f78fe37 Implement workflow landings. 
Includes a lot of plumbing for tools but not the APIs - they are not ready to go yet.
 2024-09-30 13:25:02 -04:00
John Chilton dc4b59d6f5 Fixes and tests for data fetch models. 2024-09-30 13:25:02 -04:00
John DavisandMarius van den Beek 99afd7b5a5 Refactor setting user/group/role associations 
Fix typo

Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com>
 2024-09-23 16:11:00 -04:00
John Davis d8abcadd26 Fix bug in test_rule_helper 2024-09-20 17:24:20 -04:00
mvdbeek ac71c06854 Merge branch 'release_24.1' into dev 2024-09-13 16:59:22 +02:00
Dannon bd54d465fc Merge pull request #18651 from guerler/parse_missing_viz_config 
Parse stored config details to script-based visualizations
 2024-09-12 20:39:58 -04:00
mvdbeek ee63214516 Fix wrong extension on pick data output 
This fixes https://github.com/galaxyproject/galaxy/issues/18795
 2024-09-11 12:21:33 +02:00
guerler 5441399860 Add new minimal example plugin 2024-09-04 15:59:50 +03:00
guerler db22b485c6 Add additional test conditions for script based plugins 2024-09-04 15:05:41 +03:00
guerler 1a1e8a9e92 Adjust script viz unit tests, fix typo 2024-09-04 09:58:11 +03:00
guerler 0fbb153ed5 Fix default visualization name test 2024-09-04 09:56:11 +03:00
John Chilton 27dcee1a9f Typing around tool state. 2024-09-03 17:01:19 -04:00
Marius van den Beek 94611cba14 Merge pull request #18626 from jmchilton/tool_execution_typing 
Better Typing for Tool Execution Plumbing
 2024-08-06 15:28:28 +02:00
Nicola Soranzo 0c8666f328 Rework otherwise unused dataset create 2024-08-02 22:18:45 +01:00
John Chilton 578199237e remove history manager copy 2024-08-02 19:16:51 +01:00
John Chilton 0cdce52b40 Fixup the type signatures of authnz backends. 2024-08-01 18:25:56 +01:00
Nicola Soranzo bc250177c3 Fixes for errors reported by mypy 1.11.0 in `BaseObjectStore` 2024-08-01 18:24:13 +01:00
John Chilton 3345de12f6 Typing for much of the tool execution and action plumbing. 2024-07-31 20:37:56 -04:00
mvdbeek 864bec4739 Merge branch 'release_24.1' into dev 2024-07-18 09:57:36 +02:00
John Chilton 6dec2f482e Stock tools. 2024-07-15 09:46:13 -04:00
John Chilton 32a968f01c More tool parsing abstractions, for greater reuse outside main app. 2024-07-15 09:46:13 -04:00
mvdbeek a5960ee262 Fix map over calculation for runtime inputs 
Fixes https://github.com/galaxyproject/galaxy/issues/18506
 2024-07-14 20:53:52 +02:00
Nicola Soranzo 49f820da8b Merge branch 'release_24.0' into release_24.1 2024-07-08 20:11:56 +01:00
Ahmed Hamid AwanandJohn Davis 077832bc29 Update test/unit/app/managers/test_UserManager.py 
Co-authored-by: John Davis <jdavcs@gmail.com>
 2024-07-01 13:56:50 -05:00
Ahmed Awan a6e70816f3 adjust test_reset_email_user_deleted for None instead of str 2024-07-01 13:42:44 -05:00
mvdbeek 33f27d5456 Merge branch 'release_24.0' into release_24.1 2024-07-01 18:23:55 +02:00
Jonathan Laperle beb705428a fix indentation 2024-06-28 12:50:32 -04:00
Jonathan Laperle e69d7b2f8b Prevent deleted users from reseting password 2024-06-28 08:01:25 -04:00
Dannon Baker 6ec7521e1a Merge remote-tracking branch 'upstream/release_24.0' into release_24.1 2024-06-28 09:48:27 +02:00
Marius van den Beek 8a52443a0a Merge pull request #18428 from mvdbeek/replace_busybox 
[24.0] Replace busybox:ubuntu-14.04 image with busybox:1.36.1-glibc
 2024-06-28 09:22:30 +02:00
mvdbeek 7c6fc1800f Replace busybox:ubuntu-14.04 image with busybox:1.36.1-glibc 2024-06-21 16:58:21 +02:00
Nicola Soranzo 08d42ea24f Merge branch 'release_24.0' into release_24.1 2024-06-19 13:14:15 +01:00
mvdbeek 111d5632ff Run make format 2024-06-19 10:24:55 +02:00
Martin Cech 2891489cad Merge pull request #18389 from mvdbeek/ensure_data_extension_if_no_extension_specified 
[24.0] Assign default ``data`` extension on discovered collection output
 2024-06-18 17:21:20 +02:00
mvdbeek ed2369f9a0 Merge branch 'release_24.0' into release_24.1 2024-06-18 17:19:55 +02:00
M Bernt 5297fa3137 Apply suggestions from code review 2024-06-18 09:59:33 +02:00