genenetwork3 - GeneNetwork3 REST API for data science and machine learning

Age	Commit message (Collapse)	Author
2023-02-02	auth: Reorganise modules/packages for easier dev and maintenance	Frederick Muriuki Muriithi
	Split the views/routes into separate modules each dealing with a narrower scope of the application to aid in maintenance, and help with making the development easier.
2023-01-31	auth: Set the token scope as a string, not a list	Frederick Muriuki Muriithi
	Setting the scope as a list of strings was leading to errors when attempting to logout. This commit leaves the scope as a string to avoid the errors.
2023-01-21	auth: Fix saving of scope values. Add scope items.	Frederick Muriuki Muriithi

2023-01-20	mypy: minor fixes to typing errors	Frederick Muriuki Muriithi

2023-01-20	auth: rename revocation endpoint	Frederick Muriuki Muriithi

2023-01-20	auth: Save token with update	Frederick Muriuki Muriithi
	If the token already exists, then update the details rather than trying to insert.
2023-01-20	auth: Setup the user correctly	Frederick Muriuki Muriithi
	* gn3/auth/authentication/oauth2/grants/password_grant.py: Return user rather than boolean * gn3/auth/authentication/oauth2/models/oauth2client.py: provide optional `user` argument to allow flexibility in setting up the client's user * gn3/auth/authentication/oauth2/models/oauth2token.py: Set token and client user correctly * gn3/auth/authentication/oauth2/server.py: Set token user from the request
2023-01-20	auth: Add development utils/tools	Frederick Muriuki Muriithi
	To avoid having to manually rebuild some default data for exploration of concepts while developing the system, add a way to build up the test users and oauth2 clients to use for testing.
2023-01-04	auth: Add `/register-user` endpoint	Frederick Muriuki Muriithi
	* gn3/app.py: register top-level error handlers. reorganise oauth2 blueprint. * gn3/auth/__init__.py: reorganise oaut2 blueprint. * gn3/auth/authentication/oauth2/views.py: reorganise oauth2 blueprint. * gn3/auth/authorisation/exceptions.py -> gn3/auth/authorisation/errors.py * gn3/auth/authorisation/groups.py: rename file/module * gn3/auth/authorisation/resources.py: rename file/module * gn3/auth/authorisation/views.py: Add `/register-user` endpoint * gn3/auth/blueprint.py: reorganise oauth2 blueprint. * gn3/errors.py: register top-level error handlers.
2023-01-04	auth: return group info as part of user details	Frederick Muriuki Muriithi
	* gn3/app.py: import blueprint from authorisation views inorder to get all endpoints * gn3/auth/authentication/oauth2/views.py: remove the `/user` endpoint * gn3/auth/authorisation/views.py: add the `/user` endpoint and add the group information to the user details.
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
2022-12-28	auth: Add resource server and /user endpoint	Frederick Muriuki Muriithi
	Add a resource server with the validator for the bearer token to protect the resources endpoints. Add a protected `/user` endpoint that returns the user details for valid tokens. * gn3/auth/authentication/oauth2/resource_server.py: new file * gn3/auth/authentication/oauth2/views.py: add /user endpoint
2022-12-22	auth: implement OAuth2 flow.oauth2_auth_flow	Frederick Muriuki Muriithi
	Add code to implement the OAuth2 flow. * Add test fixtures for setting up users and OAuth2 clients * Add tests for token generation with the "Password Grant" flow * Fix some issues with test due to changes in the database connection's row_factory