genenetwork3 - GeneNetwork3 REST API for data science and machine learning

Age	Commit message (Collapse)	Author
2023-01-31	auth: Remove the @authenticated_p decorator	Frederick Muriuki Muriithi
	The @authenticated_p decorator (and function), is an artifact of the original development ideas and should be removed from use.
2023-01-30	auth: Do not treat not finding a group as an error	Frederick Muriuki Muriithi
	Stop treating not finding a group for a user as an error, since that is an actual expected state in the system at some point. Rather, restore the use of Maybe rather than using Either. We can raise the NotFoundError at the API level rather than at database retrival level.
2023-01-30	auth: API: Retrieve a user's group	Frederick Muriuki Muriithi
	Add endpoint to retrieve the group in which the user is a member.
2023-01-28	auth: Enable retrieval of a role by id.	Frederick Muriuki Muriithi

2023-01-28	auth: rework dictify	Frederick Muriuki Muriithi
	Define a Protocol type to use with the `dictify` function and implement the `dictify` methods for the various classes.
2023-01-23	auth: create group: Fix group creation.	Frederick Muriuki Muriithi
	* gn3/auth/authorisation/checks.py: Enable passing user to authorisation checking function. Raise error on authorisation failure for consistent error handling. * gn3/auth/authorisation/groups.py: Add user to group, updating the privileges as appropriate. * gn3/auth/authorisation/resources.py: Fix resources querying * gn3/auth/authorisation/roles.py: Assign/revoke roles by name * gn3/auth/authorisation/views.py: Create group * migrations/auth/20221108_01_CoxYh-create-the-groups-table.py: Add group_metadata field * tests/unit/auth/fixtures/group_fixtures.py: fix tests * tests/unit/auth/test_groups.py: fix tests * tests/unit/auth/test_resources.py: fix tests * tests/unit/auth/test_roles.py: fix tests
2023-01-21	auth: Roles - Fix bug with role retrieval.	Frederick Muriuki Muriithi

2023-01-19	auth: Fix user registration	Frederick Muriuki Muriithi
	The code checking for errors was buggy and would let empty values through. The sqlite3.IntegrityError exception was not being handled correctly, and would cause a failure in the application. This commit fixes the issues noted above. * gn3/auth/authorisation/roles.py: fix bug in generating query params * gn3/auth/authorisation/views.py: fix error checking code. Raise exception if email is already registered.
2023-01-16	auth: update privileges format	Frederick Muriuki Muriithi
	Save privileges with ids of the form <top-level>:<sub-level>:<privilege-name> rather than using a UUID, to reduce indirection levels. * migrations/auth/20230116_01_KwuJ3-rework-privileges-schema.py: new migration to change the schema and IDs for the privileges. * Update code to use new privileges format * gn3/auth/authorisation/checks.py * gn3/auth/authorisation/groups.py * gn3/auth/authorisation/privileges.py * gn3/auth/authorisation/resources.py * gn3/auth/authorisation/roles.py * migrations/auth/20230116_01_KwuJ3-rework-privileges-schema.py * tests/unit/auth/fixtures/role_fixtures.py * tests/unit/auth/test_groups.py * tests/unit/auth/test_privileges.py * tests/unit/auth/test_roles.py
2023-01-11	auth: assign default role. separate group creation from group admin	Frederick Muriuki Muriithi
	A newly registered user will have the ability to create a group. Once a user is a member of a group, either by creating a new group, or being added to a group, they should not be able to create any more groups, i.e. they lose the 'create-group' (and/or equivalent) privileges. This means that the group-administration privileges should be separated from the group-creation privilege. * gn3/auth/authorisation/roles.py: assign default roles to user on registration * gn3/auth/authorisation/views.py: assign default roles to user on registration * migrations/auth/20230111_01_Wd6IZ-remove-create-group-privilege-from-group-leader.py: separate group-creation role from group-administration role. * tests/unit/auth/fixtures/user_fixtures.py: Add group-creation role to test user * tests/unit/auth/test_roles.py: Add the group-creation role explicitly in the expected results for the test
2023-01-04	auth: Return only non-resource roles on `/user-roles` endpoint	Frederick Muriuki Muriithi
	Resource roles will be returned as part of the resources request. * gn3/auth/authorisation/roles.py: Simplify query - only get non-resource roles * gn3/auth/authorisation/views.py: update docstring
2023-01-03	auth: Fetch all of a user's roles.	Frederick Muriuki Muriithi
	* gn3/auth/authorisation/roles.py: Fetch roles from DB * gn3/auth/authorisation/views.py: Provide API endpoint for user roles * tests/unit/auth/test_roles.py: Tests to check fetching roles works correctly Fix linting and typing issues in the following files: * gn3/auth/authentication/oauth2/resource_server.py * gn3/auth/authentication/oauth2/views.py * tests/unit/auth/fixtures/oauth2_client_fixtures.py
2022-11-24	auth: Check for authentication and fix errors	Frederick Muriuki Muriithi
	* gn3/auth/authorisation/groups.py: base `MembershipError` on new `AuthorisationError` base exception. Use new authentication checking decorator. * gn3/auth/authorisation/privileges.py: Change argument to User object rather than UUID object * gn3/auth/authorisation/roles.py: Use new authentication checking decorator. * tests/unit/auth/test_groups.py: use `conftest.TEST_USER` * tests/unit/auth/test_privileges.py: use `conftest.TEST_USER` * tests/unit/auth/test_roles.py: use `conftest.TEST_USER`
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: 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.