genenetwork3 - GeneNetwork3 REST API for data science and machine learning

Age	Commit message (Collapse)	Author
2023-10-10	Remove authentication from GN3	Frederick Muriuki Muriithi
	Authentication should be handled by the auth server (gn-auth) and thus, this commit removes code handling user authentication from the GN3 system.
2023-05-25	Script to assign existing data to publicly-visible resources	Frederick Muriuki Muriithi
	A script to assign existing data not assigned to any group to publicly-visible resources.
2023-04-27	auth: List also the non-resource privileges the user has	Frederick Muriuki Muriithi
	While creating new group roles, enable the listing of non-resource privileges, e.g. `system:group:` and `system:user:` that the user has to allow for them to be used in role creation.
2023-04-27	auth: Add authorisation checks for role editting.	Frederick Muriuki Muriithi

2023-04-25	auth: Roles: Check for editability	Frederick Muriuki Muriithi
	Some roles should not be user-editable, and as such, we need to check before allowing any edits on such roles. This commit makes that possible.
2023-04-21	auth: Attach linked data to specific resources.	Frederick Muriuki Muriithi

2023-04-21	auth: Fetch user group phenotypes not attached to a resource.	Frederick Muriuki Muriithi

2023-04-17	Hook up code to use external search script for phenotypes	Frederick Muriuki Muriithi

2023-04-17	auth: Delete code that is no longer used	Frederick Muriuki Muriithi

2023-04-15	Decouple `gn3.db_utils` from `flask.current_app`.	Frederick Muriuki Muriithi
	Decouple the `gn3.db_utils` module from the global `flask.current_app` object, ensuring that the database uri value is passed in as a required argument to the `gn3.db_utils.database_connection` function.
2023-04-12	auth: Enable listing of unlinked genotype/mRNA group data.	Frederick Muriuki Muriithi

2023-03-22	auth: Enable linking multiple datasets to the group at once.	Frederick Muriuki Muriithi

2023-03-20	auth: data: Enable offset in queries	Frederick Muriuki Muriithi
	Enable the 'OFFSET' clause in the queries to allow for progressive fetching of data from the database using the 'Previous' and 'Next' buttons.
2023-03-20	auth: data: List Phenotypes at the trait level	Frederick Muriuki Muriithi
	For Phenotypes, list the Phenotype traits rather than the dataset(s).
2023-03-09	auth: redis data: migrate data in redis	Frederick Muriuki Muriithi
	Implement the code to migrate the data from redis to SQLite.
2023-03-07	auth: group_roles: Enable addition/deletion of privileges	Frederick Muriuki Muriithi

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.
2023-03-03	auth: Enable viewing group role details.	Frederick Muriuki Muriithi

2023-03-03	auth: group roles: enable creation and listing of group roles.	Frederick Muriuki Muriithi

2023-02-24	auth: resources: Fix query for data not linked to resources	Frederick Muriuki Muriithi

2023-02-24	auth: resources: Link data to resources.	Frederick Muriuki Muriithi

2023-02-09	auth: Reject request to join a group.	Frederick Muriuki Muriithi
	* gn3/auth/authorisation/groups/models.py: Modify function to either accept or reject join requests. * gn3/auth/authorisation/groups/views.py: Provide endpoint to reject join requests. * migrations/auth/20230207_01_r0bkZ-create-group-join-requests-table.py: Prevent user from applying to join the same group more than once.
2023-02-08	auth: groups: handle join requests.	Frederick Muriuki Muriithi

2023-02-07	auth: groups: Enable users to request to join group.	Frederick Muriuki Muriithi

2023-02-06	auth: resource: Enable viewing the details of a resource.	Frederick Muriuki Muriithi

2023-02-02	auth: Improve authorisation	Frederick Muriuki Muriithi
	Retrieve the token, and user in the authorisation decorator to enable checking of privileges.
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.