genenetwork3 - GeneNetwork3 REST API for data science and machine learning

Age	Commit message (Collapse)	Author
2023-02-03	auth: tests: mock token acquisition. Fix minor bugs.	Frederick Muriuki Muriithi

2022-12-12	tests: Reorganise fixtures	Frederick Muriuki Muriithi
	Split the fixtures into separate modules for easier management * tests/unit/auth/conftest.py: Import all from the `fixtures` package. Delete all fixtures from the file * tests/unit/auth/fixtures/__init__.py: new `fixtures` package * tests/unit/auth/fixtures/group_fixtures.py: new groups fixtures module * tests/unit/auth/fixtures/migration_fixtures.py: new migrations fixtures module * tests/unit/auth/fixtures/resource_fixtures.py: new resources fixtures module * tests/unit/auth/fixtures/role_fixtures.py: new roles fixtures module * tests/unit/auth/fixtures/user_fixtures.py: new users fixtures module
2022-12-08	auth: test for `user_resources` function (incomplete)	Frederick Muriuki Muriithi
	* gn3/auth/authorisation/resources.py: dummy `user_resources` function * tests/unit/auth/conftest.py: (incomplete): Add some fixtures for testing the `user_resources` function * tests/unit/auth/test_resources.py: test the `user_resources` function
2022-11-24	auth: Implement `create_resource` function	Frederick Muriuki Muriithi
	* gn3/auth/authentication/checks.py: new `authenticated_p` decorator to apply on any function that requires the user to be authenticated before it runs. * gn3/auth/authorisation/checks.py: use a `auth.authentication.users.User` object rather than a UUID object in the global `g`. * gn3/auth/authorisation/groups.py: Implement the `authenticated_user_group` function to get the group(s) in which the currently authenticated user belongs. * gn3/auth/authorisation/resources.py: Implement the `create_resource` function correctly. * tests/unit/auth/conftest.py: extract the User objects into a global variable for reusability with the tests. * tests/unit/auth/test_resources.py: Use global user objects from conftest in the tests. Set a User object (rather than UUID) in the global `g` variable.
2022-11-17	auth: Finish implementation of `create_group_role`	Frederick Muriuki Muriithi
	* gn3/auth/authorisation/groups.py: Add `GroupRole` type. Fix typing annotations. Fix bugs. * tests/unit/auth/conftest.py: Fix bugs. * tests/unit/auth/test_groups.py: Fix test to run.
2022-11-17	tests: Add test to check creation of roles attached to groups	Frederick Muriuki Muriithi
	* tests/unit/auth/conftest.py: Add fixtures to help with testing * tests/unit/auth/test_groups.py: Add incomplete and failing test
2022-11-15	pylint: Fix a myriad of linting errors	Frederick Muriuki Muriithi

2022-11-15	tests: Use `gn3.auth.db` functions for db connection and cursor	Frederick Muriuki Muriithi
	* tests/unit/auth/conftest.py: use the functions in `gn3.auth.db` to acquire the database connection and cursor since they handle some of the basic issues like rollback and commit, meaning we do not have to explicitly handle said issues in the fixtures.
2022-11-14	auth: Implement `create_group`	Frederick Muriuki Muriithi

2022-11-14	auth: Add test for `create_group`	Frederick Muriuki Muriithi
	* gn3/auth/authorisation/__init__.py: Add `authorised_p` decorator to be used for all function requiring authorisation. * gn3/auth/authorisation/groups.py: Add `create_group` function stub * tests/unit/auth/conftest.py: Add fixture for test users * tests/unit/auth/test_groups.py: Add tests for `create_group`
2022-11-09	Tests: Provide backend fixture to (apply\|rollback)_single_migration	Frederick Muriuki Muriithi

2022-11-08	Tests: Separate ALL unit test fixtures from auth-specific ones	Frederick Muriuki Muriithi
	* tests/unit/auth/conftest.py: add fixtures specific to auth * tests/unit/auth/test_migration_create_users_table.py: import from new fixtures module * tests/unit/conftest.py: remove auth-specific fixtures from ALL unit tests fixture module.