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Commit Graph
1396 Commits
Author SHA1 Message Date
mvdbeek 9f919eb5e1 Track landing request with invocation 
Contains stub for tool request tracking, once that is merged we could
start using it.
 2025-09-27 09:19:33 +02:00
mvdbeek 77f28029e5 Allow sending and tracking landing request origin 2025-09-26 16:07:24 +02:00
Aysam Guerler 8ec885eda0 Merge pull request #20868 from ahmedhamidawan/move_tour_generator_webhook_to_core 
Replace tour_generator webhook with internal API and frontend
 2025-09-26 07:45:08 +03:00
mvdbeek a1ecabdfbc Adjust API tests 
Most of the time we just want an OK status code. 202, 204, 200 should
all be OK and some of this depends on the Galaxy instance config,
so this should be more robust to future changes.
 2025-09-23 22:16:20 +02:00
Ahmed Hamid Awan 8ca7075df5 Merge pull request #19225 from PlushZ/execute-tags 
Add tags to output datasets from tool form
 2025-09-23 09:46:02 -05:00
Ahmed Awan 355cce56f6 change tool generated tour API test's tool from cat1 to random lines 
I did this because `cat1` does not have supported input types for TGTs.
 2025-09-23 08:41:28 -05:00
Ahmed Awan 850d344e5a add API tests for tool generated tours 
These utilize the `performs_upload` parameter which was added for this purpose; since we do not have a valid history available to upload the datasets to.
 2025-09-23 08:41:28 -05:00
John Chilton 28e6e2c6f8 Fix default conditional test parameters... 
... for tools using 21.01 input format.
 2025-09-22 17:04:38 -04:00
Polina Polunina 9c0cde8d34 Merge branch 'dev' into execute-tags 2025-09-22 17:05:09 +02:00
mvdbeek 0c09aa9e5c Add test for proposed prod-like deployment 2025-09-21 17:03:17 +02:00
John Chilton a8df2c8ea7 Validate column definitions. 2025-09-09 12:32:47 -04:00
mvdbeek 5ccf97752b Verify collection is correctly consumed 2025-09-04 14:48:44 +02:00
mvdbeek 2c19e16994 Assert dynamic tool error message specificity 2025-09-01 17:36:10 +02:00
PlushZ b821de248d fix import sorting 2025-08-30 14:39:42 +02:00
PlushZ d7696974bd move test from unit to api, remove mocking behavior 2025-08-30 12:19:29 +02:00
Marius van den Beek 41a72b2ab9 Merge pull request #20592 from jmchilton/tool_landing 
Implement Data Landing Requests
 2025-08-19 14:55:55 +02:00
John Chilton a252af81b9 Tool Landing API... 2025-08-18 11:08:06 -04:00
John Chilton ebd48c7516 Tests for preserving column definitions in different metadata collection strategies. 2025-08-14 09:57:45 -04:00
John Chilton 7f71bf5a57 More sample sheet testing. 2025-08-14 09:57:45 -04:00
John Chilton 502ee7cb4c Merge pull request #20718 from mvdbeek/deduplicate_materialization 
Attempt to reuse previously materialized datasets
 2025-08-13 08:03:03 -04:00
Arash 411aabca6c Refactor dataset user identification: replace 'same_user' boolean with 'user_id' string in schema and update related logic in DatasetInheritanceChainEntry and tests. 2025-08-12 12:34:20 +02:00
mvdbeek 4ecc99a6dc Verify cached workflow input datasets are used 
if url and hash are provided.
 2025-08-11 18:30:54 +02:00
mvdbeek 8b2bf6f413 Test that dematerilization works in combination with job cache 2025-08-11 18:30:51 +02:00
Nicola Soranzo 1d9d93ea50 Merge branch 'release_25.0' into dev 2025-08-07 15:54:38 +01:00
Marius van den Beek 1e2737a4bc Merge pull request #20650 from jmchilton/deferred_multiple_25_0 
[25.0] Fix deferred datasets in multiple dataset parameters.
 2025-08-01 08:26:09 +02:00
Nicola Soranzo 7f89e0eab9 Code cleanups from pyupgrade 
Found by running:

```
make pyupgrade
ruff check --fix .
ruff check --preview --unsafe-fixes --select=F401 --fix .
make format
make update-client-api-schema
```

The bulk of the changes are replacements of typing deprecated aliases
such as `Dict` and `List` with the standard library classes. These
aliases became redundant in Python 3.9 when the corresponding
pre-existing classes were enhanced to support `[]`, see
https://docs.python.org/3/library/typing.html#deprecated-aliases

Also:
- Update the `pyupgrade` Makefile target to use `--py38-plus` for the
  packages needed by Pulsar, including the new galaxy-tool-util-models
  package.
 2025-07-31 11:17:22 +01:00
Nicola Soranzo e2777065eb Merge branch 'release_25.0' into dev 2025-07-30 17:45:20 +01:00
John Chilton 7769f6379d Merge pull request #20553 from mvdbeek/live_fix_cry_emoji 
[25.0] Propagate cached job output replacement to copies of outputs
 2025-07-29 10:26:42 -04:00
John Chilton d26605517e Implement sample sheets. 2025-07-25 11:46:59 -04:00
John Chilton 316d9817a8 Validate workflow inputs more directly on the backend. 2025-07-25 11:46:24 -04:00
Arash b5d27075fb Add tests for copying datasets with copied_from fields in history and library 2025-07-25 15:28:27 +02:00
mvdbeek d1543b7be3 Assert output copies are correctly replaced 2025-07-21 18:37:51 +02:00
John Chilton da575fe2d0 Fix deferred datasets in multi-data parameters. 2025-07-11 13:44:27 -04:00
John Chilton 505ac8d8d5 Migrate some tool-on-deferred tests to newer style execute tests. 2025-07-11 13:44:26 -04:00
mvdbeek 306374f394 Merge branch 'release_25.0' into dev 2025-07-08 15:45:04 +02:00
David LópezandNicola Soranzo 1708721eab Refactor test to simplify assertion 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2025-07-03 14:07:42 +02:00
davelopez 7318b85469 Add test for invalid UUID v4 format in workflow steps 2025-07-03 13:33:06 +02:00
Nate Coraor 96523d4570 Merge remote-tracking branch 'upstream/release_25.0' into dev 2025-06-20 16:18:47 -04:00
Nicola Soranzo cc26ab7834 Merge branch 'release_24.2' into release_25.0 2025-06-20 13:00:45 +01:00
John Chilton 85d634ae9f Implement fetch workbooks. 2025-06-19 22:54:56 -04:00
John Chilton 7efe923b4c Sharper exception handling in apply rules test. 2025-06-19 22:54:55 -04:00
John Chilton 05ecc12d96 Test case for rule builder backend errors. 2025-06-19 22:54:55 -04:00
John Chilton a776836dba Update rule builder to allow list:paired_or_unpaired creation. 2025-06-19 22:54:55 -04:00
Nicola Soranzo fdf931b954 Fix new `test_index_anon` API test 2025-06-19 20:01:47 +01:00
Matthias Bernt 98ddca1e11 fixup 2025-06-19 19:34:52 +02:00
Matthias Bernt b71eaaf437 try to add test 2025-06-19 18:58:01 +02:00
John Chilton 3190de2a07 Test case for using workflow inputs with implicit conversions. 2025-06-18 11:46:37 -04:00
davelopez fdac8820a6 Merge release_25.0 into dev 2025-06-16 14:12:30 +02:00
Marius van den Beek 1d8b6247e7 Merge pull request #19900 from ahmedhamidawan/form_data_various_fixes 
[25.0] More fixes to `FormData` drag and drop and typing
 2025-06-16 13:47:57 +02:00
mvdbeek f928b08fa7 Add `/api/datasets/{dataset_id}/extra_files/raw/{filename:path}` 
We need this for the vitessce visualization, that will build urls based
on the path of the current url. In practice, to get the file expected at `obs/.zattrs` the
visualization will build
https://usegalaxy.org/api/datasets/f9cad7b01a4721358531a44ecfb1aff6/display/obs/.zattrs?filename=A/1/bdbd683b-1870-4c11-ae29-b35ff0be59b2.adata.zarr,
because it reasonably assumes the query parameter is independent of the
path.
With this change we can access the file in question via
https://usegalaxy.org/api/datasets/f9cad7b01a4721358531a44ecfb1aff6/extra_files/raw/A/1/bdbd683b-1870-4c11-ae29-b35ff0be59b2.adata.zarr/obs/.zattrs.
 2025-06-15 16:10:49 +02:00