genenetwork3 - GeneNetwork3 REST API for data science and machine learning

Age	Commit message (Collapse)	Author
2023-07-10	Fix linting errors caused by bump to Python 3.10migrate-to-python3.10	Frederick Muriuki Muriithi

2023-07-03	Enable deletion of OAuth2 clients.	Frederick Muriuki Muriithi

2023-06-30	List all OAuth2 clients.	Frederick Muriuki Muriithi

2023-05-30	auth: Change check for client secret	Frederick Muriuki Muriithi
	We are saving the client secret in an encrypted form, meaning we have to verify that the CLIENT_SECRET that is provided is the same one as was generated at registration in a different way. Initially, I was doing a direct comparison, having saved the CLIENT_SECRET value as unencrypted plain-text.
2023-05-29	auth: Enable registration of OAuth2 clients	Frederick Muriuki Muriithi
	Add UI and code to enable the administrative user to register new OAuth2 clients that can access the API server.
2023-05-09	auth: Implement "Authorization Code Flow"auth/implement-authorization-code-flow	Frederick Muriuki Muriithi
	Implement the "Authorization Code Flow" for the authentication of users. * gn3/auth/authentication/oauth2/grants/authorisation_code_grant.py: query and save the authorisation code. * gn3/auth/authentication/oauth2/models/authorization_code.py: Implement the `AuthorisationCode` model * gn3/auth/authentication/oauth2/models/oauth2client.py: Fix typo * gn3/auth/authentication/oauth2/server.py: Register the `AuthorisationCodeGrant` grant with the server. * gn3/auth/authentication/oauth2/views.py: Implement `/authorise` endpoint * gn3/templates/base.html: New HTML Templates of authorisation UI * gn3/templates/common-macros.html: New HTML Templates of authorisation UI * gn3/templates/oauth2/authorise-user.html: New HTML Templates of authorisation UI * main.py: Allow both "code" and "token" response types.
2023-03-23	auth: Don't try loading the user if no client is found	Frederick Muriuki Muriithi
	Fix the bug where the system was trying to load a user from a non-existing OAuth2 client, leading to an exception.
2023-03-13	auth: separate user detail migration from data migration	Frederick Muriuki Muriithi
	Due to the fact that the data migration requires higher privileges than the user details, separate the user details migration endpoint from the data migrations endpoint.
2023-03-07	auth: user_by_id: Return a user or raise an exception	Frederick Muriuki Muriithi
	Fetching the user by id should return the user, or raise an exception. We get rid of the Maybe monad here since it is leading to some weird code flows - probably the wrong monad to use here.
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: 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.
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