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2023-10-26case-attribute: Fix linting errors.Frederick Muriuki Muriithi
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.
2023-09-05Fix C3001: Lambda expression assigned to a variableMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-09-05Remove un-necessary ellipsisMunyoki Kilyungi
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
2023-09-05Remove pylint skipMunyoki Kilyungi
* gn3/auth/authentication/oauth2/models/oauth2token.py (introspect_token, check_permission): Delete "pylint: disable=[no-self-use]". R0022: Useless option value for 'disable', 'no-self-use' was moved to an optional extension, see https://pylint.pycqa.org/en/latest/whatsnew/2/2.14/summary.html#removed-checkers. * gn3/auth/authentication/oauth2/grants/authorisation_code_grant.py (delete_authorization_code): Ditto. * tests/unit/test_heatmaps.py (test_cluster_traits): Delete "pylint: disable=R0201". R0022: Useless option value for 'disable', 'no-self-use' was moved to an optional extension, see https://pylint.pycqa.org/en/latest/whatsnew/2/2.14/summary.html#removed-checkers. * tests/unit/computations/test_partial_correlations.py (test_tissue_correlation): Ditto. Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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.
2023-07-31Fix typing issueFrederick Muriuki Muriithi
2023-07-31Fix linting and typing issues.Frederick Muriuki Muriithi
2023-07-31Fix bugs. Return resource without data items.Frederick Muriuki Muriithi
* Fix bugs introduced while attempting pagination. * Return resource object without attached data items.
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 UIFrederick Muriuki Muriithi
Make UI somewhat consistent with the GN2 UI.
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 variablesFrederick Muriuki Muriithi
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.
2023-06-20Fix conflictszsloan
2023-06-20Bug: Don't overwrite/delete old collectionsFrederick Muriuki Muriithi
2023-06-13Namespace session variableFrederick Muriuki Muriithi
Extract the functions acting on the session into a separate module and namespace the session variable to prevent conflicts.
2023-06-08Fix bugs with accessing/creating collectionszsloan
2023-06-05Logging: Don't allow getting user info to stop application startingFrederick Muriuki Muriithi
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.
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 secretFrederick 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.
2023-05-29auth: Enable registration of OAuth2 clientsFrederick Muriuki Muriithi
Add UI and code to enable the administrative user to register new OAuth2 clients that can access the API server.
2023-05-29Enable Administrator login on GN3Frederick Muriuki Muriithi
* 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
2023-05-27Document Use of OAuth2 ClientsFrederick Muriuki Muriithi
* 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
2023-05-25Script to assign existing data to publicly-visible resourcesFrederick Muriuki Muriithi
A script to assign existing data not assigned to any group to publicly-visible resources.
2023-05-25Set whether resource is publicly viewable on creationFrederick Muriuki Muriithi
2023-05-23auth: Enable user masqueradeFrederick Muriuki Muriithi
Enable users with the appropriate privileges to masquerade as other users by providing an endpoint that provides a new token for the "masqueradee"
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.
2023-05-18auth: Rename collectionsFrederick Muriuki Muriithi
Enable renaming collections.
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 CollectionsFrederick Muriuki Muriithi
Add code to enable the importation/deletion of anonymous collections in the active session to the authenticated user's collections.
2023-05-16auth: View a collection by its ID.Frederick Muriuki Muriithi
2023-05-15collections: Move code to new package. Create new collections.Frederick Muriuki Muriithi
Move the code to a new package. Enable the creation of new collection by both authenticated and anonymous users.
2023-05-12auth: Provide separate endpoint for anonymous collections.Frederick Muriuki Muriithi
2023-05-11auth: Fix bug with migration of user collectionsFrederick Muriuki Muriithi
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.
2023-05-10auth: Add the /oauth2/user/collections/list endpointFrederick Muriuki Muriithi
Add an endpoint to list a user's collections. This only works for logged in users.
2023-05-10auth: Only check deliverability of emails at registration.Frederick Muriuki Muriithi
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.
2023-05-09auth: Implement "Authorization Code Flow"auth/implement-authorization-code-flowFrederick 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.
2023-04-27auth: Retrieve `system:*` privileges from resource rolesFrederick Muriuki Muriithi
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.
2023-04-27auth: List also the non-resource privileges the user hasFrederick 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.
2023-04-27auth: 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
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-22 08:41:54 +0000