mvdbeek
04441e503c
Fix encoded id unit test
2024-01-08 11:33:44 +01:00
mvdbeek
a13932c71c
Fix id field unit tests
2024-01-08 11:33:34 +01:00
mvdbeek
ed1c30a8b9
Fix fetch_data schema unit tests
2024-01-08 11:33:29 +01:00
mvdbeek
1593570e33
Replace DecodedDatabaseIdField.encode with Security.security.encode_id
2024-01-08 11:33:25 +01:00
mvdbeek
242f75ceec
Type fixes for starlette 0.34.0
...
Starlette removed some Any annotations in 0.34.0.
Issue tracked in https://github.com/abersheeran/a2wsgi/issues/44
2024-01-01 11:13:40 +02:00
John Davis
7d6a0eed19
Fix import in unit test
2023-12-18 15:03:10 -05:00
John Davis
c6dad0bce6
Fix linting, add attribution
2023-12-18 14:51:58 -05:00
John Davis
a8a2903a31
Copy fastapi-utils.cbv.py + unit tests, change import
2023-12-18 14:16:48 -05:00
Nicola Soranzo
ddbcb39fb3
Merge pull request #17058 from davelopez/remove_web_dependency_from_tools
...
Remove web framework dependency from tools
2023-12-01 12:29:26 +00:00
mvdbeek
e3d18005db
Merge branch 'release_23.1' into release_23.2
2023-12-01 11:52:34 +01:00
mvdbeek
e502863657
Add missing optional description field, fixes ephemeris data library example
2023-12-01 11:00:52 +01:00
davelopez
6f2b4ff559
Move short_term_storage related classes to its own path
...
The ShortTermStorageManager and related classes should live in their own package eventually and not within galaxy.web nor galaxy.managers as the short term storage microservices it's fairly independent and has way less dependencies than those other packages.
2023-11-30 17:01:29 +01:00
davelopez
d33bd688cd
Move short_term_storage related classes to managers
...
The ShortTermStorageManager is a manager and makes sense to have it live under galaxy.managers instead of galaxy.web.
It will also help reduce the dependency of the manager modules on web related stuff.
2023-11-30 16:42:04 +01:00
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 Davis
e90d9c204c
Fix mock: model arg required to cast Bunch as MinimalApp
2023-06-08 21:30:11 -04:00
Nicola Soranzo
d31a347547
Fix comparison-overlap mypy error
2023-04-05 13:54:05 +01:00
davelopez
0a043971af
Add unit test for model_store_storage_target
2023-04-04 17:31:32 +02:00
mvdbeek
29d7d14ae1
Update FastAPI
2023-02-10 18:40:00 +01:00
Nicola Soranzo
7fee81607c
Add linting with ruff
...
ruff (https://github.com/charliermarsh/ruff ) is a new and extremely fast
Python linter, written in Rust.
Ruff can be used to replace Flake8 (plus a variety of plugins), isort,
pydocstyle, yesqa, eradicate, pyupgrade, and autoflake.
Here ruff is added to our current linters (flake8, flake8-bugbear and isort)
while we assess its reliability.
I've not enabled the isort rules because many of the options we use are not
implemented yet. I have instead enabled the pyupgrade rules (a tool which I
run manually every few months).
Also:
- Fix new linting errors reported by ruff.
2023-01-16 14:34:56 +00:00
John Chilton
74491c2362
Migrate baseauth endpoint to FastAPI.
2022-12-17 10:16:27 -05:00
mvdbeek
792617d242
Drop unused contents_near api endpoint
...
It was added for the beta version of the new history, but it's unused
now.
2022-12-12 10:02:11 +01:00
John Davis and Nicola Soranzo
67c7e7d1ac
Use a simple cast instead of relying on dependency injection
...
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com >
2022-11-30 13:33:42 -05:00
John Davis
cbabba8f49
Fix typing error in unit test
2022-11-29 14:59:17 -05:00
Nicola Soranzo
de5e9c0e71
Add some type annotations to `WebApplication and GalaxyWebTransaction`
2022-11-28 04:50:03 +00:00
Nicola Soranzo
2b362fbd1d
Merge branch 'release_22.05' into dev
2022-11-17 22:50:45 +00:00
mvdbeek
7254dc9fef
Also support byte-range in legacy send_file method
2022-11-16 18:33:46 +01:00
mvdbeek
7f0754eef7
Upgrade FastAPI to 0.87.0, drop old workarounds
2022-11-16 14:31:49 +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
f3b04b8f26
Remove `unittest.main()` calls
2022-09-21 23:50:05 +01:00
Nicola Soranzo
b5c7e2c86a
Replace `self.assert* method calls with plain asserts in test/`
...
using https://github.com/pytest-dev/unittest2pytest with the following command:
```
unittest2pytest -f self_assert -w -n test/
```
(excluding ``self.assertRaises*`` method calls).
2022-09-21 23:50:05 +01:00
davelopez
a7303e219e
Fix API unit tests with ID encodings
2022-08-24 12:05:47 +02:00
davelopez
8355d5e12d
Add more unit tests for ID fields
2022-08-24 12:00:26 +02:00
davelopez
1d59487365
Add unit tests for query_parameter_as_list
2022-08-19 08:59:02 +02:00
Marius van den Beek and Nicola Soranzo
973d0779b6
Include timezone testing
...
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com >
2022-08-17 18:43:57 +02:00
mvdbeek
b0d9cff6c4
Add unit test
...
That was meant to go into the first commit ...
2022-08-16 13:12:28 +02:00
davelopez
af949c2fd3
Revert adding __hash__ to BaseDatabaseIdField
2022-08-04 11:23:31 +02:00
davelopez
e5b11bb25b
Add unit tests for DabaseIdFields hashing
2022-08-02 11:10:35 +02:00
mvdbeek
22f761aa10
Fix validation of nested element fetch data payloads
...
Fixes https://github.com/galaxyproject/galaxy/issues/14242
2022-07-01 13:52:06 +02:00
mvdbeek
84ea10767a
Unit test for No response returned error
2022-06-27 18:11:49 +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
Nicola Soranzo
15ba0f8747
Fix warning in pytest collection
...
Fix:
```
test/unit/web_framework/framework/test_framework_base.py:4
/home/runner/work/galaxy/galaxy/galaxy root/test/unit/web_framework/framework/test_framework_base.py:4: PytestCollectionWarning: cannot collect test class 'TestWebapp' because it has a __init__ constructor
class TestWebapp(WebApplication):
```
Also:
- Use f-string.
- Simplify code using assert.
2022-05-12 16:38:15 +01:00
mvdbeek
55e22ca8a9
Use separate model for fetch data form payload
2022-04-25 18:28:01 +02:00
mvdbeek
02ac5b3c9e
Add FastAPI route for tools/fetch
2022-04-23 12:01:32 +02:00
mvdbeek
1d5a52ec05
Schema for fetch_data
2022-04-22 17:08:41 +02:00
mvdbeek
3bc7d7c867
Drop legacy mapping unit tests for FastAPI routes
2022-03-21 13:14:43 +01:00
John Chilton
427847bcc4
Fix up some import "issues".
2022-03-16 14:22:50 -04:00
John Chilton
4dae7c6f21
Disable implicit re-imports across the projects.
...
Exclude galaxy.util for now, but the exclusion is tracked in setup.cfg. Elimiantes a bunch of flake exception markers.
2022-03-15 19:58:42 -04:00
Nicola Soranzo
a62e86fc2e
Merge branch 'release_22.01' into dev
2022-03-04 17:02:22 +00:00
mvdbeek
873d43eac2
Move tool shed and reports config schema to config package
...
And restore unit tests to proper place.
2022-03-03 16:57:39 +01:00
Nicola Soranzo
7f04b5d698
Merge branch 'release_22.01' into dev
2022-03-02 20:08:55 +00:00
mvdbeek