aboutsummaryrefslogtreecommitdiff
AgeCommit message (Collapse)Author
2023-03-09auth: introspection: Protect introspection endpointFrederick Muriuki Muriithi
The introspection endpoint could contain privileged information, thus requires that the endpoint be protected. This commit ensures that a user has authenticated to the system and that the client they are using be one of the allowed clients.
2023-03-08auth: users: Use the same basic functions for password hashingFrederick Muriuki Muriithi
To avoid repeating the same thing in multiple places, leading to errors and breakages, reuse the same basic functions for password hashing.
2023-03-08Replace Bcrypt with Argon2 for better security.Frederick Muriuki Muriithi
Bcrypt is now somewhat vulnerable to offline cracking, so we move our password hashing over to Argon2.
2023-03-07auth: group_roles: Enable addition/deletion of privilegesFrederick Muriuki Muriithi
2023-03-07auth: resources: unassign roles on resource from a user.Frederick Muriuki Muriithi
2023-03-07auth: user_by_id: Return a user or raise an exceptionFrederick 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.
2023-03-06auth: privileges/roles: fix issues caught by tests.Frederick Muriuki Muriithi
2023-03-06auth: resources: Enable assigning a user roles on resourcesFrederick Muriuki Muriithi
2023-03-06auth: resources: Link role's group to the resource's groupFrederick Muriuki Muriithi
2023-03-06auth: resources: Get all users with access to a particular resource.Frederick Muriuki Muriithi
2023-03-03auth: Enable viewing group role details.Frederick Muriuki Muriithi
2023-03-03auth: group roles: enable creation and listing of group roles.Frederick Muriuki Muriithi
2023-03-02auth: user registration: Rework error checking. Add email validationFrederick Muriuki Muriithi
2023-03-01Fetch sampledataMunyoki Kilyungi
* gn3/api/sampledata.py (get_sampledata): New end-point. * gn3/app.py: Register above end-point. * gn3/settings.py: Add new conf variable for LMDB. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-03-01Open lmdb path in readonly modeMunyoki Kilyungi
* gn3/db/matrix.py (get_total_versions, get_nth_matrix, get_current_matrix): Open lmdb in readonly mode. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-03-01Create API endpoint for fetching trait metadataMunyoki Kilyungi
* gn3/api/metadata.py (dataset_metadata): New function and endpoint. (jsonify_dataset_metadata): Rename to dataset_metadata. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-03-01Fetch trait metadata from RDFMunyoki Kilyungi
* gn3/db/rdf.py (get_dataset_metadata): New function. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-02-28auth: Unlink data from resourcesdata-access-levels-endpointFrederick Muriuki Muriithi
Enable the data editor to unlink data from a particular resource.
2023-02-28auth: Unlink data from resourcesFrederick 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.
2023-02-24auth: resources: Fix query for data not linked to resourcesFrederick Muriuki Muriithi
2023-02-24auth: resources: Fix queries loading resources data.Frederick Muriuki Muriithi
2023-02-24auth: resources: Link data to resources.Frederick Muriuki Muriithi
2023-02-23auth: Link data in MySQL to the groups (in SQLite)Frederick Muriuki Muriithi
In order for the group leaders (and other resource creators) to be able to link data to the resources, the data needs to be first linked to the relevant group. This commit enables the system admin to link the data in MySQL to the groups.
2023-02-22auth: List data not linked to any group.Frederick Muriuki Muriithi
2023-02-21auth: db: DEBUG: Output quer(y|ies) that were run.Frederick Muriuki Muriithi
2023-02-21auth: resources: Attach resource data and list unlinked data.Frederick Muriuki Muriithi
Load the data that is attached to a particular resource together with the resource. List any unlinked data: useful when linking data to resources.
2023-02-21auth: migrations: Link to data in main dbFrederick Muriuki Muriithi
Provide the `linked_group_data` table to be used to link to data in the main database. Update the `mrna_resources`, `genotype_resources` and `phenotype_resources` tables to rely on the `linked_group_data` table.
2023-02-13scripts: Fallback to 1 worker when indexing.Arun Isaac
* scripts/index-genenetwork (worker_queue): Set default number of workers to 1 if the number of CPUs cannot be determined.
2023-02-13scripts: Type hint xapian indexing script.Arun Isaac
* scripts/index-genenetwork: Import Callable, Generator, Iterable and List from typing. Type hint all functions.
2023-02-10Return empty tuple rather than NothingFrederick Muriuki Muriithi
When user has no roles assigned, return an empty tuple rather than pymonad.maybe.Nothing to ease maintenance.
2023-02-10Fix linting errors.Frederick Muriuki Muriithi
2023-02-10Add example utility script to run development serverFrederick Muriuki Muriithi
2023-02-10auth: CLI: Provide a way to set an existing user as a system adminFrederick Muriuki Muriithi
Provide a way to set a user as a system administrator via CLI. This method was chosen rather that using the WebUI since most users will not have access to the CLI. It also means that assigning system administration privileges will not be an accident, since one has to actually run the command manually on the CLI.
2023-02-10auth: migrations: new privilege and roleFrederick Muriuki Muriithi
Add a new data distribution privilege Add a new system-administrator role
2023-02-09auth: 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.
2023-02-09auth: users: Check whether a user has an active join request.Frederick Muriuki Muriithi
2023-02-08auth: groups: handle join requests.Frederick Muriuki Muriithi
2023-02-07auth: groups: Enable users to request to join group.Frederick Muriuki Muriithi
2023-02-06Get the N-th matrix given N, an index valueMunyoki Kilyungi
* gn3/db/matrix.py (get_nth_matrix): New function. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-02-06Get total number of versions that a database hasMunyoki Kilyungi
* gn3/db/matrix.py (get_total_versions): New function. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-02-06Add method to fetch the current matrixMunyoki Kilyungi
* gn3/db/matrix.py: New file. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-02-06auth: resource: Enable viewing the details of a resource.Frederick Muriuki Muriithi
2023-02-03auth: commit missing module.Frederick Muriuki Muriithi
2023-02-03oauth: enable resource creationFrederick Muriuki Muriithi
2023-02-03auth: tests: mock token acquisition. Fix minor bugs.Frederick Muriuki Muriithi
2023-02-02auth: Improve authorisationFrederick Muriuki Muriithi
Retrieve the token, and user in the authorisation decorator to enable checking of privileges.
2023-02-02auth: Reorganise modules/packages for easier dev and maintenanceFrederick 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.
2023-01-31auth: Retrieve group members.Frederick Muriuki Muriithi
2023-01-31auth: Remove the @authenticated_p decoratorFrederick Muriuki Muriithi
The @authenticated_p decorator (and function), is an artifact of the original development ideas and should be removed from use.
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-23 01:36:50 +0000