opensource/galaxy
3
0
Fork 0
mirror of https://github.com/galaxyproject/galaxy.git synced 2026-09-24 16:30:27 +08:00
Code Issues Packages Projects Releases Wiki Activity
71,200 Commits 69 Branches 243 Tags
02b99b7478992c392bc9190c94de1dec49aef7bc
Commit Graph
83 Commits
Author SHA1 Message Date
Ahmed Awan a739f88aa6 Restore deprecated ToolsApi and create new api route for new panel structure 
- restore `api/tools` that had the older (list of tool sections
  with `.elems`) structure
- but use the new `api/tool_panel` structure in the client
 2023-10-17 13:58:43 -05:00
Ahmed Awan 5eb268ae83 fix api and integration tests (for removed panel_labels) 2023-10-13 19:31:09 -05:00
Ahmed Awan 8809476a17 fix all tests to work with the new GET 'api/tools' structure 2023-10-13 19:29:18 -05:00
mvdbeek 314f135330 Allow pending inputs in some collection operation tools 
For those tools where it makes sense. We can't of course do this for
tools that filter outputs based on dataset size or dataset state,
or tools that make decisions based on extra datasets (e.g text files
with new identifiers).
 2023-04-03 17:36:50 +02:00
Dannon Baker 5ac7306c91 Merge remote-tracking branch 'upstream/release_22.05' into release_23.0 2023-02-08 11:56:34 -05:00
mvdbeek 2d63389e72 Add test that verifies visible doesn't revert on job finish 
It isn't exactly a regression test, for that you'd have to time the test
so that we change the visible attribute while the job is finishing.  I
think this test here is worth running independently, and I don't think
we have an explicit test like that.
 2023-02-08 11:56:00 +01:00
Nicola Soranzo 30f60493c3 Format Python code with black 23.1.0 
with manual fixes to 3 files to make them compatible with black 22.12.0 .

We need to keep black pinned at `<23` until we vendorise `packaging`, since
the new version of black depends on `packaging >=22.0` which is the version
where `LegacyVersion` (which we use for tool lineages) was removed.
 2023-02-01 23:51:03 +00:00
Nicola Soranzo b9cf28d919 Remove unused `history_id` fixture requests 
Follow up on https://github.com/galaxyproject/galaxy/pull/15031 .
 2023-01-04 09:40:24 +00:00
Dannon 2b598e0125 Merge pull request #15203 from jmchilton/tool_test_typing_decompose_4 
A bit more typing in interactor.py.
 2023-01-03 11:23:10 -05:00
John Chilton 680b95ae0a A bit more typing in interactor.py. 
Again pulled from the tool state branch - trying to bisect these converter test failures.
 2022-12-13 19:45:48 -05:00
John Chilton bb9cf69ea1 Mark method parameter as meant to be used only for testing. 
Trying to figure out why converter tests are broken in tool state typing branch.
 2022-12-13 09:53:55 -05:00
John Chilton 958d403ce8 Type+PydanticModel more tool test code. 2022-12-12 17:54:02 -05:00
John Chilton 018d066e36 Useful test decorators and runtime support for annotating how tests will be used. 2022-11-26 11:28:36 -05:00
John Chilton aeac8c6060 Restore test framework features... 2022-11-26 11:28:36 -05:00
mvdbeek 304b12c143 Move things around 2022-11-16 17:01:28 +01:00
Nicola Soranzo 9610f1f0b7 Fix wrongly skipped test_test_data_null_boolean_inputs API test 
Introduced in commit a7a8754e24 .

Also simplify unnecessary f-strings.
 2022-11-15 13:22:00 +00:00
Nicola Soranzo b7e1f587cb Type annotations and refactorings of input staging 2022-11-10 14:35:13 +00:00
Nicola Soranzo 3a8997ccf2 Replace `unittest.TestCase` in API, framework, performance, Selenium and ToolShed tests 
In API tests, replace no more working `uses_test_history` decorator (because
the `history_id` method parameter is interpreted as a fixture) with a real
class-level pytest fixture.
As a consequence, replace use of `self.history_id` in API tests because it
interferes with the class-level `history_id` fixture.

Also:
- Some type annotations
 2022-11-07 15:44:01 +00:00
Nicola Soranzo 10802d35a9 Mark non-slow unit tests with more relevant `@skip_if_github_down` decorator 2022-11-03 18:47:31 +00:00
Nicola Soranzo 0391cd4b62 Rename FooBarTestCase test classes as TestFooBar in API, framework, performance, Selenium and ToolShed tests 
These are collected by pytest only because they are `unittest.TestCase` derived,
but normally pytest collects only test classes whose name starts with `Test`, see
https://docs.pytest.org/en/7.1.x/reference/reference.html#confval-python_classes

Also:
- Some type annotations
 2022-10-15 17:54:31 +01:00
Nicola Soranzo c35d8f2a06 Replace `unittest.TestCase` with pytest-based partial re-implementation 
Also:
- Rename `FooBarTestCase` test classes as `TestFooBar`. These were collected
  by pytest only because they were `unittest.TestCase` derived, but normally
  pytest collects only test classes whose name starts with `Test`, see
  https://docs.pytest.org/en/7.1.x/reference/reference.html#confval-python_classes
 2022-09-27 03:34:58 +01:00
Nicola Soranzo 3091737ab9 Misc test fixes 2022-09-27 03:34:55 +01:00
Nicola Soranzo a69103dd2c Replace `self.assert* method calls with plain asserts in lib/galaxy_test/` 
using https://github.com/pytest-dev/unittest2pytest with the following command:

```
unittest2pytest -f self_assert -w -n lib/galaxy_test/
```
 2022-09-21 23:50:04 +01:00
mvdbeek df6551da78 Test that metadata validators work 2022-06-25 12:55:51 +02:00
mvdbeek 8178178736 Test deferred data with extended metadata and metadata files 
And also test that option filters work correctly.
 2022-06-25 12:55:51 +02:00
John Chilton c5bf63bc91 Add DEFERRED datasets to Galaxy 
- Improves options and display around discarded datasets.
- Adds new APIs for importing model stores.
- Adds support to model store layer for importing/exporting workflow invocations and APIs and tests to support this.
- Add new DEFERRED dataset state - with APIs for materializing them or the option to defer them on the worker node if using tool_evaluation_strategy=remote on the job destination.
- UI and API options for uploading deferred datasets individually or into collections.
 2022-05-23 19:48:47 -04:00
mvdbeek 9abbac0180 Switch most tests to use `__DATA_FETCH__ instead of upload1` 2022-04-23 12:05:54 +02:00
Dannon Baker 623a5e165a Apply black formatting. 
Apply isort.
 2022-02-03 07:42:20 -05:00
mvdbeek d56dff1769 Add API tests for raw_tool_source endpoint 2021-11-15 11:33:13 +01:00
davelopez fb02841b7e Adapt API tests to use JSON payload 
See https://github.com/galaxyproject/galaxy/pull/12152 for details.
 2021-10-29 10:31:59 +02:00
John Chilton fa2d2092f8 Type fixes: galaxy_test.api.test_tools. 2021-10-11 16:32:29 -04:00
John Chilton 9ccdc7e852 Annotate more tests as requiring Github to be online. 2021-10-05 21:51:06 -04:00
Assunta DeSanto 93103f1cb5 formatting python 2021-09-13 23:49:28 -04:00
Assunta DeSanto e4723082b6 fixes to conversion api test 2021-09-13 19:29:01 -04:00
Assunta DeSanto baecb07fc7 Resolving some test tools PR comments and small issues in collections 2021-09-08 23:28:33 -04:00
Assunta DeSanto f55dd2b1bc Linting errors 2021-08-27 00:02:04 -04:00
Assunta DeSanto 7a7bb69819 Added API tests for conversion endpoint 2021-08-26 23:46:07 -04:00
John Chilton 38ed01ba35 Improvements to new conversion API. 2021-08-25 00:05:40 -04:00
John Chilton 853d7e978d API test case to ensure dataset names get escaped during tool evaluation. 
I think other sanitization properties aren't testing that model properties are escaped.
 2021-08-18 13:41:06 -04:00
John Chilton e6de9b7496 Allow bio.tools mappings for legacy tools. 
Assigning these in the tools for new tool installs is great (https://github.com/galaxyproject/tools-iuc/pull/3411/files) but there will be thousands of old tools that are missing these and we should have a way to fill in this information as "missing info" bug fixes.
 2021-07-26 11:09:42 -04:00
Nicola Soranzo e6e2e367a9 Merge branch 'release_21.05' into dev 2021-07-05 10:44:03 +01:00
Nicola Soranzo 0adc8d3066 Merge branch 'release_21.01' into release_21.05 2021-07-05 10:40:17 +01:00
mvdbeek a87405cbb4 Fix test_identifier_map_over_input_in_conditional 
So it acts as a regression test for
https://github.com/galaxyproject/galaxy/issues/6182.
 2021-07-02 11:00:10 +02:00
Dannon Baker f1ff658cb7 Concatenation pass, fstring conversion 2021-05-11 13:53:20 -04:00
Dannon Baker 22e7601653 First pass fstring conversion 2021-05-11 13:47:00 -04:00
John Chilton 556a0e843d API tests for tool parameter baseurl handling. 2021-05-03 11:36:44 -04:00
cat-bro 0e88054792 fix other test that fails because of the the extra version of multiple_versions tool 2021-04-30 01:57:05 +10:00
John Chilton d983fc72e8 Exhibit bug when unzipping collections with nametags. 2021-03-26 15:43:12 -04:00
John Chilton 8f9bdd6eb5 Failing test case for output problem. 2021-03-14 19:58:31 -04:00
Matthias Bernt d512049a4a more specific functional tool tests involving fasta_indexes.loc 
rename entries such that they are suffixed by the column name
(execpt for dbkey).
this makes tests more specific, because this ensures that always
the correct column is used.
 2021-01-12 13:44:58 +01:00