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AgeCommit message (Expand)Author
2023-08-02Integrate Temp traits to Auth...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. Frederick Muriuki Muriithi
2023-07-31Fix typing issueFrederick Muriuki Muriithi
2023-07-31Fix linting and typing issues.Frederick Muriuki Muriithi
2023-07-31Fix bugs. Return resource without data items....* Fix bugs introduced while attempting pagination. * Return resource object without attached data items. Frederick Muriuki Muriithi
2023-07-31Paginate the resource data items.Frederick Muriuki Muriithi
2023-07-12Move documentation comment to beginning of functionFrederick Muriuki Muriithi
2023-07-06Provide the client_id as part of the post request.Frederick Muriuki Muriithi
2023-07-03Spruce up UI...Make UI somewhat consistent with the GN2 UI. Frederick Muriuki Muriithi
2023-07-03Enable deletion of OAuth2 clients.Frederick Muriuki Muriithi
2023-06-30Edit some of the details of OAuth2 clientsFrederick Muriuki Muriithi
2023-06-30List all OAuth2 clients.Frederick Muriuki Muriithi
2023-06-23Fetch all collections, rename variables...Fetch from `__REDIS_COLLECTION_KEY__` not `"collections"` to ensure all collections are retrieved correctly. Rename from `__*_DOC__` to `__REDIS_*_KEY__` to more clearly express what the variables are about. Frederick Muriuki Muriithi
2023-06-20Fix conflictszsloan
2023-06-20Bug: Don't overwrite/delete old collectionsFrederick Muriuki Muriithi
2023-06-13Namespace session variable...Extract the functions acting on the session into a separate module and namespace the session variable to prevent conflicts. Frederick Muriuki Muriithi
2023-06-08Fix bugs with accessing/creating collectionszsloan
2023-06-05Logging: Don't allow getting user info to stop application starting...In certain scenarios (probably due to host contamination) the effective UID of the running application is not the expected "genenetwork" user, rather, it is a user on the host system, which leads to the error: KeyError: 'getpwuid(): uid not found: 1000' This commit prevents the application from failing in such a case, but still logs out such weirdness. Frederick Muriuki Muriithi
2023-06-05Logging: Get user information.Frederick Muriuki Muriithi
2023-06-05Handle unhandled SQLite3 errors.Frederick Muriuki Muriithi
2023-05-30auth: Change check for client secret...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. Frederick Muriuki Muriithi
2023-05-29auth: Enable registration of OAuth2 clients...Add UI and code to enable the administrative user to register new OAuth2 clients that can access the API server. Frederick Muriuki Muriithi
2023-05-29Enable Administrator login on GN3...* gn3/auth/authentication/oauth2/views.py: Remove endpoint * gn3/auth/authorisation/users/admin/__init__.py: New admin module * gn3/auth/authorisation/users/admin/ui.py: New admin module * gn3/auth/authorisation/users/admin/views.py: New admin module * gn3/auth/views.py: Use new admin module * gn3/errors.py: Fix linting errors * gn3/templates/login.html: New html template * main.py: Fix linting errors Frederick Muriuki Muriithi
2023-05-27Document Use of OAuth2 Clients...* docs/authentication_and_authorisation/oauth2_clients.md: New documentation * gn3/auth/authentication/oauth2/server.py: Raise appropriate error if no client is found. * gn3/auth/authentication/oauth2/views.py: Handle exception in the case where a UI should be presented to the user, rather than presenting the raw JSON response to the user. * gn3/errors.py: Handle any authlib OAuth2Error at the application's top-level * gn3/templates/oauth2/oauth2_error.html: Handle any authlib OAuth2Error at the application's top-level Frederick Muriuki Muriithi
2023-05-25Script to assign existing data to publicly-visible resources...A script to assign existing data not assigned to any group to publicly-visible resources. Frederick Muriuki Muriithi
2023-05-25Set whether resource is publicly viewable on creationFrederick Muriuki Muriithi
2023-05-23auth: Enable user masquerade...Enable users with the appropriate privileges to masquerade as other users by providing an endpoint that provides a new token for the "masqueradee" Frederick Muriuki Muriithi
2023-05-19auth: Provide user and resource info in the trait data...Provide the user and resource_id information in each trait's authorisation details to help with linking on the UI end. Frederick Muriuki Muriithi
2023-05-19auth: Check for json on authorisation endpoint. Add user data....Ensure the authorisation endpoint expects only JSON. Add the user data to the response from the endpoint. Frederick Muriuki Muriithi
2023-05-18auth: Rename collections...Enable renaming collections. Frederick Muriuki Muriithi
2023-05-18auth: user collections: Add and/or remove traits.Frederick Muriuki Muriithi
2023-05-17auth: Delete collections by ID.Frederick Muriuki Muriithi
2023-05-17auth: Import/Delete Anonymous Collections...Add code to enable the importation/deletion of anonymous collections in the active session to the authenticated user's collections. Frederick Muriuki Muriithi
2023-05-16auth: View a collection by its ID.Frederick Muriuki Muriithi
2023-05-15collections: Move code to new package. Create new collections....Move the code to a new package. Enable the creation of new collection by both authenticated and anonymous users. Frederick Muriuki Muriithi
2023-05-12auth: Provide separate endpoint for anonymous collections.Frederick Muriuki Muriithi
2023-05-11auth: Fix bug with migration of user collections...The code, as written previously had a subtle bug - if the user created a new collection before they had tried accessing their list of collections, the older code would not have migrated the older collections. This commit fixes that by enabling the migration of older collections, whether or not the user has created a collection with their new accounts. Frederick Muriuki Muriithi
2023-05-10auth: Add the /oauth2/user/collections/list endpoint...Add an endpoint to list a user's collections. This only works for logged in users. Frederick Muriuki Muriithi
2023-05-10auth: Only check deliverability of emails at registration....Check only that the email format is correct, but don't bother with the deliverability check during authentication. The deliverability check is done at registration. Frederick Muriuki Muriithi
2023-05-09auth: Implement "Authorization Code Flow"...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. auth/implement-authorization-code-flowFrederick Muriuki Muriithi
2023-04-27auth: Retrieve `system:*` privileges from resource roles...With the assignment of `system:*` privileges to roles, we need to check for their existence when doing authorisation. This commit provides a hack for that, seeing as user groups (and the system itself) are not treated as resources, and therefore the way to fetch the privileges is not entirely consistent. Frederick Muriuki Muriithi
2023-04-27auth: List also the non-resource privileges the user has...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. Frederick Muriuki Muriithi
2023-04-27auth: Add authorisation checks for role editting.Frederick Muriuki Muriithi
2023-04-27oauth2: Provide missing `user_editable` argument.Frederick Muriuki Muriithi
2023-04-25auth: bug: Provide missing `user_editable` argument.Frederick Muriuki Muriithi
2023-04-25auth: provide `user_editable` flag in dictified outputFrederick Muriuki Muriithi
2023-04-25auth: Roles: Check for editability...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. Frederick Muriuki Muriithi
2023-04-24auth: Return the actual privileges for the user...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. Frederick Muriuki Muriithi
2023-04-21auth: Attach linked data to specific resources.Frederick Muriuki Muriithi
2023-04-21auth: Fetch user group phenotypes not attached to a resource.Frederick Muriuki Muriithi
2023-04-19oauth2: Link the phenotype traits to user groups.Frederick Muriuki Muriithi