Commit Graph
1135 Commits
Author SHA1 Message Date
John Chilton 6d7842e66f Numerous fixes for tool input format "21.01" parameters. 2024-10-30 10:52:08 -04:00
John Chilton 7f7710d392 Implement recovering normalized workflow request from invocation. 2024-10-15 09:12:05 -04:00
davelopez 946bded098 Use UUID instead of ID in user object store test 2024-10-15 11:33:13 +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
mvdbeek 46ba18cbc8 Allow CORS requests to api/workflow_landings 2024-10-10 09:40:28 +02:00
John Chilton 93f2af6a44 Allow dataset and source checksum validation during materialization. 2024-09-30 13:25:02 -04:00
John Davis 527b371104 Fix integration test that violated db integrity constraint 2024-09-20 17:24:20 -04:00
mvdbeek 7572e5c41f Merge branch 'release_24.1' into dev 2024-09-20 08:54:14 +02:00
mvdbeek 2bbae08220 Merge branch 'release_24.0' into release_24.1 2024-09-20 08:27:18 +02:00
mvdbeek e1d6c93a21 Fix discovered outputs with directory metadata and distributed object
stores

The problem is that `object_store.is_private` would check in which
object store the dataset is stored, and that fails if we haven't written
to the object store yet (which is why extended metadata is a
workaround).

Fixes https://github.com/galaxyproject/galaxy/issues/17208
2024-09-19 19:51:51 +02:00
mvdbeek a608f9fa55 Merge branch 'release_24.1' into dev 2024-09-19 16:52:48 +02:00
M BerntandMarius van den Beek fc9d2f1dc7 remove assert
Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com>
2024-09-19 09:39:08 +02:00
Matthias Bernt 1d9a61132c add test for updating quota description 2024-09-19 09:39:08 +02:00
mvdbeek 236f1b3b73 Merge branch 'release_24.1' into dev 2024-09-16 16:35:29 +02:00
Marius van den Beek 310cbd976c Merge pull request #18809 from mvdbeek/collect_job_metrics_also_when_job_failed
[24.1] Collect job metrics also when job failed
2024-09-13 17:40:18 +02:00
mvdbeek ac71c06854 Merge branch 'release_24.1' into dev 2024-09-13 16:59:22 +02:00
mvdbeek 4a5b3dd0bb Fix job metric collection when job fails 2024-09-13 14:36:12 +02:00
mvdbeek 14909829f7 Test metric collection when runner fails 2024-09-13 12:37:14 +02:00
mvdbeek 1dce8cf75b Add test for keeping picked dataset's extension in place 2024-09-10 18:50:12 +02:00
Arash b73333a74a Fix TestVisualizationTags and NotificationsIntegrationBase to send data as json to Visualization api 2024-08-20 17:27:58 +02:00
mvdbeek 03a7fda6a3 Merge branch 'release_24.1' into dev 2024-08-09 15:57:48 +02:00
mvdbeek 302328f05f Merge branch 'release_24.0' into release_24.1 2024-08-09 15:57:24 +02:00
davelopez d9051005bc Remove unnecessary assert for file_size
The file_size should be preserved in the database for traceability and other uses.
2024-08-09 14:03:53 +02:00
mvdbeek d4ae33ad97 Add missing test case attribute 2024-07-28 12:15:28 +02:00
mvdbeek 9b772f1ff5 Fix container recording for pulsar
And re-use abstractions for determining file path.
2024-07-26 18:51:24 +02:00
mvdbeek 5a27e70000 Add test case for recording container id and type 2024-07-26 18:51:11 +02:00
Anthony Bretaudeau 41741041e0 Fix worklfow typo here and there 2024-07-10 15:18:31 +02:00
Nicola Soranzo 3216bc09b5 Merge branch 'release_24.1' into dev 2024-07-08 20:16:01 +01:00
mvdbeek e395ea7d6d Stabilize test_purge_while_job_running test
In the extended_metadata + remote tool_evaluation_strategy the
commandline is templated as part of the job, so we need to give the test
more time to start running before we delete outputs (as then we can't
template the command line anymore).
2024-07-04 17:35:57 +02:00
mvdbeek 9110349227 Merge branch 'release_24.1' into dev 2024-07-01 18:25:02 +02:00
mvdbeek 33f27d5456 Merge branch 'release_24.0' into release_24.1 2024-07-01 18:23:55 +02:00
Marius van den Beek 444ae58736 Merge pull request #18446 from mvdbeek/when_upgrade_fix
[24.0] Fix dropped when_expression on step upgrade
2024-07-01 18:19:18 +02:00
Dannon Baker fbaac02e69 Merge remote-tracking branch 'upstream/release_24.1' into dev 2024-06-28 09:55:22 +02:00
Dannon Baker 6ec7521e1a Merge remote-tracking branch 'upstream/release_24.0' into release_24.1 2024-06-28 09:48:27 +02:00
mvdbeek ed8dc4b8e2 Fix dropped when_expression on workflow/tool_upgrade
Fixes https://github.com/galaxyproject/galaxy/issues/18441
2024-06-27 15:31:30 +02:00
mvdbeek 5050ccde3d Add test to make sure when_expression is not lost on refactoring 2024-06-27 15:31:29 +02:00
mvdbeek 7c6fc1800f Replace busybox:ubuntu-14.04 image with busybox:1.36.1-glibc 2024-06-21 16:58:21 +02:00
mvdbeek 4d35888ca0 Merge branch 'release_24.1' into dev 2024-06-11 14:00:31 +02:00
mvdbeek b8e2bfc9c7 Merge branch 'release_24.0' into release_24.1 2024-06-11 13:42:48 +02:00
mvdbeek f0e09cc8bd Fix up tests 2024-06-11 08:18:14 +02:00
John Davis 0c840d025f Add first user data access tests 2024-06-10 15:48:10 -04:00
John Chilton 659d5059e8 Merge remote-tracking branch 'origin/release_24.1' into merge_to_dev_0 2024-06-10 10:39:10 -04:00
mvdbeek a35033d821 Extend test to make sure disk path remains purged 2024-06-10 11:58:46 +02:00
mvdbeek 435a8cd37f Fix up test cases
Add a sleep so we can delay output purging until command line is
templated. If we don't sleep we generate a command line where the
output path is just `''`. That needs another fix!
2024-06-10 10:34:15 +02:00
John Chilton 821b31c3b2 More structured indexing for user data objects.
I think I clung to the idea of having two ways to do this too long. I did a bunch of testing with the old way (exposing integer references based on numeric database primary keys). Having a config option that if changed would break everything exisiting is also a symptom of maybe me clinging too hard for too long.

The result of dropping this option is a much cleaner API schema, simpler API objects, and better typing throughout. We can also be more certain of how things entering the Vault are stored - I think being more strucutured about this is good.

Ultimately, the future facing stuff (e.g. OAuth 2.0) is going to require UUIDs so that I can store things like refresh tokens in the store before the object has been fully created.
2024-06-07 19:20:11 -04:00
Nicola Soranzo df19283caf Merge branch 'release_24.1' into dev 2024-06-07 16:29:10 +01:00
davelopez 28e0a5b77e Fix linting unnecessary list literal 2024-06-07 11:51:26 +02:00
mvdbeek 1865c43be8 Merge branch 'release_24.1' into dev 2024-06-06 10:19:12 +02:00
mvdbeek 49660628bb Merge branch 'release_24.0' into release_24.1 2024-06-06 10:18:25 +02:00
davelopez 62049e3803 Rename integration test base class
To make the `check_test_class_names` linter happy
2024-06-05 15:30:26 +02:00