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7736 Commits
Author SHA1 Message Date
mvdbeek 0bb93e562e Merge branch 'release_23.1' into dev 2023-10-06 16:17:22 -04:00
John Chilton 3773a56107 Fix short ids in tool panel views. 
Use new data structure to optimize get_tool(exact=False) as well - should speed up certain kinds of toolbox related operations.
 2023-10-06 12:38:06 -04:00
John Chilton 7dc0b1378b WIP: modern tool shed frontend 2023-09-27 14:30:42 -04:00
John Chilton 04e75635f5 Option config_hg_for_dev... 2023-09-26 13:47:00 -04:00
John Chilton dd58bfcfe6 Implement the GA4GH TRS API in the new tool shed. 2023-09-26 13:46:59 -04:00
John Chilton d1d629074b ToolShed API 2.0 2023-09-26 13:46:58 -04:00
John Chilton 698d58eed4 WIP: Implement dry_run in upload API. 2023-09-26 13:46:58 -04:00
John Chilton cdfdaaf017 Bug fix: data manager changes misaligned... 
- Data manager changes force a new installable changeset on reset but not when updating repositories.
 2023-09-26 13:46:56 -04:00
John Chilton b66a0bc175 More integration-y unit tests for tool shed... 2023-09-26 13:46:56 -04:00
John Chilton 8852f0733b Progress toward exercising less of the tool shed upload API. 
So we can kill it.
 2023-09-26 13:46:56 -04:00
John Chilton 2c5f63a054 Integration-y unit tests for the core tool shed code. 2023-09-26 13:46:55 -04:00
John Chilton 59cff45fb1 Decompose tool shed + schema package. 
This commit creates two new packages - below a description of these packages and why they are being created.

galaxy-schema: This package contains the pydantic models that power the API. The purpose of packaging them is to ensure they can be reused by clients with minimal external dependencies. Reusing the schema in client code would very quickly provide rapid documentation and validation and static checking for Python clients using the Galaxy API.

galaxy-tool-shed: This package contains the tool shed server code. This has been a long term project to allow the tool shed to be spun out but maintain real galaxy dependencies and maintain testing. More discussions around this project can be found as part of https://github.com/galaxyproject/galaxy/pull/8830.
 2023-09-26 13:46:55 -04:00
John Chilton 179f59217e Preparation for creating galaxy tool shed client package... 2023-09-26 13:46:54 -04:00
John Chilton ca1e7e53b9 Standalone app for installing tools... 2023-09-26 13:46:54 -04:00
John Chilton f1c2dde09f Protocol to try to break up app for cleaner tool shed install typing. 2023-09-26 13:46:53 -04:00
John Davis 7a06b006c6 Refactor get_user_by_username, get_user_by_email; use across code base 2023-09-25 09:23:08 -04:00
mvdbeek 09ff121dd9 Merge branch 'release_23.1' into dev 2023-09-25 10:23:14 +02:00
Dannon Baker d01b039415 Fix unittest mocks to support us checking geturl() after opening connections. 2023-09-22 11:05:24 -04:00
John Davis cf5cf5921b Merge pull request #16712 from jdavcs/dev_sa20_101 
Misc. edits/refactorings to session handling
 2023-09-20 12:51:33 -04:00
John Davis 3379174406 Resuse MockQuery and MockContext in other unit tests 2023-09-20 11:33:31 -04:00
davelopez a47abb9a3b TMP: testing the tab element should be there... 2023-09-20 14:39:45 +02:00
mvdbeek 0f2ef4dc0c Merge branch 'release_23.1' into dev 2023-09-14 13:43:50 +02:00
davelopez c96b9a4efc Relax lint message string comparison 
This will allow to check that certain reasonable parts of the message are present without expecting an exact match.

This is useful, when the warning or error messages slightly differ from version to version.
 2023-09-13 17:20:39 +02:00
davelopez 7b8c1767a9 Add valid test expression 2023-09-13 16:38:23 +02:00
davelopez fafe2f1ce2 Validate the syntax of the expressions 2023-09-13 16:37:25 +02:00
davelopez 8d636ef5f1 Consider only regex as regular expression 
`expression` is just a Python (eval) expression.
 2023-09-13 14:29:14 +02:00
davelopez 5866764993 Add test for regex validator must contain text 2023-09-13 14:17:52 +02:00
Marius van den Beek a7caa73dd3 Merge pull request #16678 from mvdbeek/fix_metadata_setting 
[23.1] Fix metadata setting in extended metadata + outputs_to_working_directory mode
 2023-09-13 13:52:21 +02:00
mvdbeek 63442d1d72 Fix regex validation for global inline flags 
Fixes https://github.com/galaxyproject/galaxy/issues/16676
 2023-09-13 12:00:57 +02:00
mvdbeek 90c8438a83 Fix and extend extended metadata outputs to working directory tests 2023-09-12 13:07:10 +02:00
Marius van den Beek f43f350982 Merge pull request #16668 from bernt-matthias/topic/samtools-bump 
Bump samtools converters
 2023-09-10 10:17:26 +02:00
Matthias Bernt 8841408406 fix functional test 2023-09-09 13:19:47 +02:00
Martin Cech 174257d88a Merge pull request #16642 from ahmedhamidawan/published_history_pagination 
Add scroll pagination and username filter to `HistoryPublishedList`
 2023-09-08 23:40:49 +02:00
mvdbeek 33aab28217 Merge branch 'release_23.1' into dev 2023-09-08 14:43:01 +02:00
Matthias Bernt 2117385d13 fix framework test 
by allowing lines_diff
 2023-09-08 13:16:52 +02:00
M BerntandNicola Soranzo 3199134aa8 Apply suggestions from code review 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2023-09-07 22:02:15 +02:00
Matthias Bernt 85124d8500 xsd: allow name attrbute of test collections 
already supported by the framework

fixes: https://github.com/galaxyproject/galaxy/issues/16654
 2023-09-07 20:16:26 +02:00
Ahmed Awan c6f19988de add selenium and unit test for published histories username filter 2023-09-06 17:41:58 -05:00
Nicola Soranzo 82c30f6c69 Merge branch 'release_23.1' into dev 2023-09-05 15:26:22 +01:00
mvdbeek 5c38cae7c2 Merge branch 'release_23.0' into release_23.1 2023-09-05 14:12:28 +02:00
mvdbeek 5684562f37 Send reload message after data bundle import is complete 2023-09-03 18:24:28 +02:00
mvdbeek 09b8d54f19 Use parse_change_format in unit test 2023-08-26 10:08:15 +02:00
mvdbeek 00a64d734f Unit test fix for is_webapp 2023-08-26 10:08:14 +02:00
mvdbeek eb8a49d805 Drop delayed_tool_init config setting 2023-08-26 10:08:13 +02:00
mvdbeek b9ae7a16ba Merge branch 'release_23.1' into dev 2023-08-26 10:02:33 +02:00
mvdbeek 8d5feb4fa1 Merge branch 'release_23.0' into release_23.1 2023-08-26 10:01:32 +02:00
mvdbeek 0477581217 Push extra files from object store cache to object store 2023-08-26 08:30:16 +02:00
mvdbeek ff504d9d3d Extend data bundle integration test to use S3 object store, check that cache can be repopulated 2023-08-26 08:30:16 +02:00
mvdbeek effd5e8ade Merge branch 'release_23.1' into dev 2023-08-24 17:03:44 +02:00
mvdbeek 3af41be3eb Merge branch 'release_23.0' into release_23.1 2023-08-24 17:03:02 +02:00