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path: root/gn3/auth/authorisation/data
AgeCommit message (Collapse)Author
2023-10-10Remove authentication from GN3Frederick 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.
2023-08-02Integrate Temp traits to AuthFrederick Muriuki Muriithi
Temporary traits are not saved to the database, and have no attached resource (at this time). As such, make them all simply public-read to enable access for users. This might change after more information on usage of temporary traits is collected and considered.
2023-07-12Move documentation comment to beginning of functionFrederick Muriuki Muriithi
2023-05-19auth: Provide user and resource info in the trait dataFrederick Muriuki Muriithi
Provide the user and resource_id information in each trait's authorisation details to help with linking on the UI end.
2023-05-19auth: Check for json on authorisation endpoint. Add user data.Frederick Muriuki Muriithi
Ensure the authorisation endpoint expects only JSON. Add the user data to the response from the endpoint.
2023-04-24auth: Return the actual privileges for the userFrederick Muriuki Muriithi
Previously, the `oauth2/data/authorisation` endpoint was returning hard-coded values for the privileges assigned to the user for each resource. In this change, we rework to return the actual privileges for the user.
2023-04-19oauth2: Link the phenotype traits to user groups.Frederick Muriuki Muriithi
2023-04-19Fix minor linting and typing issuesFrederick Muriuki Muriithi
2023-04-19auth: Setup selected traits correctlyFrederick Muriuki Muriithi
Fix bugs with setting up of the selected traits for use while filtering the search results.
2023-04-19auth: phenotypes - provide default empty list for selected traits.Frederick Muriuki Muriithi
2023-04-18auth: Pass `--per-page` and `--selected` options.Frederick Muriuki Muriithi
2023-04-17Hook up code to use external search script for phenotypesFrederick Muriuki Muriithi
2023-04-17auth: Delete code that is no longer usedFrederick Muriuki Muriithi
2023-04-15Decouple `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.
2023-04-14auth: Add external script to search for phenotypesFrederick Muriuki Muriithi
We need a search through the available phenotype traits in the database when linking the traits to user groups. Unfortunately, the Xapian Search indexes do not (and should not) include the internal identifiers we use to disambiguate the traits. On the other hand, we do not want to present the user with traits that have already been linked to any user group within the search results. The script in this commit, together with the modified queries for fetching the phenotype data form a "hack" of sorts to wrap around the way the search works while ensuring we do not present the user with "non-actionable" (linked) traits in the search results.
2023-04-10Add search and link for mRNA Assay datasets.Frederick Muriuki Muriithi
2023-04-10Update expected request key.Frederick Muriuki Muriithi
2023-04-10Enable search, filtering out selected, but not linked dataFrederick Muriuki Muriithi
When a user selects some datasets and does a new search, we filter out the selected datasets too, even though they are yet to be linked.
2023-04-08auth: Link genotype datasets to groups.Frederick Muriuki Muriithi
2023-04-04auth: Search for linking genotype datasets.Frederick Muriuki Muriithi
2023-03-23auth: list the species in the database.Frederick Muriuki Muriithi
2023-03-22auth: data linking: build functions to fetch unlinked phenotypesFrederick Muriuki Muriithi
This is an initial attempt: it does not allow a search to be carried out across the data available in the database. I will need to rework this, probably start from the UI and work backward.
2023-03-15auth: Data Migrations: Rework migration triggerFrederick Muriuki Muriithi
Rework the migration trigger endpoint such that it does a bulk import of all the resources in the redis store. It also expects that the user that triggers the migration have the appropriate privileges.
2023-03-14auth: Fix some linting and typing issues.Frederick Muriuki Muriithi
2023-03-13oauth2: data: Temporarily escalate privileges to enable migrationFrederick Muriuki Muriithi
The functions that fetch the unlinked data have checks to ensure they are called by users with the appropriate privileges. This commit enables a temporary escalation of privileges to enable fetching the data, so as to allow successful data migration.
2023-03-13auth: separate user detail migration from data migrationFrederick 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.
2023-03-10auth: data-migration: Fix minor bugsFrederick Muriuki Muriithi
2023-03-09auth: redis data: migrate data in redisFrederick Muriuki Muriithi
Implement the code to migrate the data from redis to SQLite.
2023-03-09auth: data migration: Data migration outlineFrederick Muriuki Muriithi
Provide an outline of the data migration steps to be taken from some results of the experiments with the data in redis.
2023-02-28auth: Unlink data from resourcesdata-access-levels-endpointFrederick Muriuki Muriithi
Enable the data editor to unlink data from a particular resource.
2023-02-27auth: Endpoint to get access levels for dataFrederick Muriuki Muriithi
When the endpoint is accessed with a list of traits, it should/will respond with the access privileges for each of the traits attached for the active user.