Commit Graph
34 Commits
Author SHA1 Message Date
mvdbeek 76823c5b67 Fix optional unspecified input to conditional step
Fixes https://github.com/galaxyproject/galaxy/issues/20182
2025-07-11 15:59:36 +02:00
John Chilton 9b0fb38a76 More workflow mapping test cases. 2025-05-03 10:21:17 -04:00
John Chilton f9e1022360 Test case for bug where workflow collection mapping interprets collection at wrong rank. 2025-05-03 10:21:17 -04:00
John Chilton f91012244b New packages galaxy-tool-util-models, galaxy-tool-shed-schema.
The galaxy-tool-shed-schema package is basically pydantic models for the whole tool shed API. It is used by both the backend code for the new tool shed and the testing code that runs on both the old and new tool shed.

The creation of galaxy-tool-util-models package is something I've wanted to do for a while - it should solve some TODOs I've left in the base. I think beyond enabling galaxy-tool-shed-schema package - the other nice thing is that galaxy-schema code can now rely on various tool stuff without requiring dependency on any of the parser or runtime code.

This should also fix things for the new record types in #19377. I've introduced a type that can be used tools and is included schema for collection creation. The galaxy-tool-util-models packages can now be dependended on by galaxy-schema and galaxy-tool-util and these two packages do not need to depend on each other - either direction of that dependency would make me uncomfortable. xref
https://github.com/galaxyproject/galaxy/actions/runs/13704893929/job/38327692654?pr=19377
2025-04-16 12:47:37 +02:00
mvdbeek 4c7ab9f898 Support directory uploads in workflow framework tests 2025-02-25 18:10:12 +01:00
mvdbeek ff3a7efe61 Return string, not TemporaryFileNameWrapper 2025-02-25 18:10:11 +01:00
mvdbeek 07a4a7c058 Fix directory uploads, use `__FETCH_DATA__` api
for tool tests, which were still using upload1.
2025-02-25 18:10:10 +01:00
mvdbeek 6512b4c366 Add bwa_mem2_index datatype 2025-02-19 17:26:09 +01:00
mvdbeek f4ee34f507 Record NO_REPLACEMENT as step output for unspecified value 2024-12-19 12:51:09 +01:00
mvdbeek c9832dd88c Add test case for optional unspecified text parameter
which is accessed after scheduling. Caused the failure in
https://github.com/galaxyproject/galaxy/issues/19328.
2024-12-18 10:54:16 +01:00
mvdbeek 59dc2a4b57 Add test for default value with optional input 2024-11-29 16:43:02 +01:00
mvdbeek 5d4e34134e Replace explicit null with default value 2024-11-29 16:43:02 +01:00
mvdbeek 8aa986f60b Extend tests 2024-11-29 16:43:02 +01:00
mvdbeek 70a74c2186 Fix and add test for required workflow parameters with a default value
The SimpleTextParameter change might have larger implications
(https://github.com/galaxyproject/galaxy/pull/13523), but it allows us
to detect if we need to use the provided default value.
2024-11-29 16:43:01 +01:00
John Chilton 7f7710d392 Implement recovering normalized workflow request from invocation. 2024-10-15 09:12:05 -04:00
mvdbeek 1c2bfb9459 Test filter null tool in workflow 2024-10-02 20:05:39 +02:00
mvdbeek 0139a6f001 Allow testing only element_count 2024-10-02 20:03:05 +02:00
mvdbeek bdbd38fbeb Rename framework workflow test script for easier test collection
If you want to run or collect workflow tests now you've got to indicate
the full path currently (i.e. `pytest --collect-only
lib/galaxy_test/workflow/tests.py`). With this change `pytest
--collect-only lib/galaxy_test/workflow/` or just `pytest --collect-only
lib/galaxy_test/` will also discover the workflow tests.
2024-10-02 16:24:16 +02:00
John Chilton 389f3989a0 Improvements to test format.
- Allow class: File and class: Collection on file and collection test descriptions.
- Allow collection_type: <type> in collection test descriptions. Implement this.
- Update test workflows to reflect these two things as best practices.
2024-09-25 11:35:20 -04:00
John Chilton 2d8bb3d913 Workflow test with literal test outputs. 2024-09-24 14:00:08 -04:00
John Chilton b07750554d Migrate mapover expression test to wf test framework. 2024-09-24 14:00:08 -04:00
John Chilton 675c9670e2 Models for YAML test format. 2024-09-24 12:47:07 -04:00
mvdbeek a73139d1d9 Add workflow tests for multiple="true" workflow parameter 2024-08-19 17:06:45 +02:00
mvdbeek dc632c3a34 Allow connecting integer param into data column parameter
Closes https://github.com/galaxyproject/galaxy/issues/16491
2024-08-09 19:41:14 +02:00
John ChiltonandMarius van den Beek 419f538adb Update lib/galaxy_test/workflow/__init__.py
Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com>
2024-07-29 11:11:32 -04:00
John Chilton ad0ad8561b Migrate another collection flatten workflow test to workflow test framework. 2024-07-29 09:19:10 -04:00
John Chilton efedd7c89f Migrate workflow flatten test to workflow test framework. 2024-07-29 09:19:10 -04:00
John Chilton eeafa488ab Move zip collection workflow test into workflow framework tests 2024-07-29 09:19:10 -04:00
John Chilton dc14564b38 Replace API tests with workflow tests for various parameter replacement. 2024-07-29 09:19:09 -04:00
John Chilton a7ce90d168 Rework and improve workflow tests for tools with different versions. 2024-07-29 09:19:09 -04:00
John Chilton 4a7d75071d Migrate a workflow test case for output renaming to workflow test framework. 2024-07-29 09:19:09 -04:00
John Chilton 8697b61d45 Move empty sort workflow test into workflow test framework. 2024-07-29 09:19:09 -04:00
John Chilton ece5025f84 Test to verify/document behavior of mapping over multi-selects. 2024-07-29 09:19:09 -04:00
John Chilton f6fcc95099 Setup workflow test framework. 2024-07-29 09:19:09 -04:00