genenetwork3 - GeneNetwork3 REST API for data science and machine learning

Age	Commit message (Collapse)	Author
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	auth: Define the `User` type	Frederick Muriuki Muriithi
	* gn3/auth/authentication.py -> gn3/auth/authentication/__init__.py: Convert module to package * gn3/auth/authentication/users.py: Define the `User` type
2022-11-16	auth: fix bugs in the code	Frederick Muriuki Muriithi
	* gn3/auth/authorisation/privileges.py: Set id to UUID type * gn3/auth/authorisation/roles.py: fix parameters to types that sqlite3 supports * gn3/auth/db.py: add logging for errors and re-raise the exception * tests/unit/auth/test_roles.py: fix test
2022-11-15	auth: Add `create_group_role` function.	Frederick Muriuki Muriithi

2022-11-15	auth: Return results of calling function directly	Frederick Muriuki Muriithi
	* gn3/auth/authorisation/checks.py: Return results of calling the function rather than a dict of values that include the results. * gn3/auth/authorisation/groups.py: Use the newer form of `authorised_p` decorator. * tests/unit/auth/test_groups.py: Update tests
2022-11-15	auth: Specify types for privileges, roles, groups	Frederick Muriuki Muriithi
	Use specified types for privileges, roles and types rather than using strings to help with limiting bugs. * gn3/auth/authorisation/groups.py: Specify and use the `Group` type * gn3/auth/authorisation/privileges.py: Specify and use the `Privilege` type * gn3/auth/authorisation/roles.py: Specify the `Role` type. Add the `create_role` function.
2022-11-15	auth: Add some typing information to the functions	Frederick Muriuki Muriithi

2022-11-15	auth: Reorganise package - move function to `checks` module	Frederick Muriuki Muriithi
	* gn3/auth/authorisation/__init__.py: delete function * gn3/auth/authorisation/checks.py: move function to `checks` module
2022-11-15	pylint: Fix linting errors.	Frederick Muriuki Muriithi

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`
2022-11-08	Tests: Tests the credentials check system	Frederick Muriuki Muriithi
	* gn3/auth/authentication.py: Fix issues caught by tests * tests/unit/auth/test_credentials.py: Add fixtures and tests for credentials checking
2022-11-03	Add credentials checking	Frederick Muriuki Muriithi
	* gn3/auth/authentication.py: new function `credentials_in_database` * gn3/auth/authentication/__init__.py: replace package with module * gn3/settings.py: new `AUTH_MIGRATIONS` configuration variable * migrations/auth/20221103_02_sGrIs-create-user-credentials-table.py: new migration * tests/unit/auth/test_credentials.py: test the `credentials_in_database` function * tests/unit/conftest.py: more test fixtures
2022-11-03	Initialise the Auth(entic\|oris)ation packages	Frederick Muriuki Muriithi
	Initialise the authentication/authorisation system packages and set up the initial database migrations to set up the system. * README.md: Add documentation on migrations * gn3/auth/__init__.py: init package * gn3/auth/authentication/__init__.py: init package * gn3/auth/authorisation/__init__.py: init package * gn3/migrations.py: provide migration utilities * migrations/auth/20221103_01_js9ub-initialise-the-auth-entic-oris-ation-database.py: new migration * tests/unit/auth/test_init_database.py: test new migration applies and rolls back as expected * tests/unit/conftest.py: fixtures for unit tests * yoyo.auth.ini: basic configuration for yoyo-migration for auth system migrations