| Age | Commit message (Expand) | Author |
|---|
| 2023-10-26 | case-attribute: Fix linting errors. | Frederick Muriuki Muriithi |
| 2023-10-10 | Remove authentication from GN3...Authentication should be handled by the auth server (gn-auth) and thus, this
commit removes code handling user authentication from the GN3 system.
| Frederick Muriuki Muriithi |
| 2023-09-05 | Fix C3001: Lambda expression assigned to a variable...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-09-05 | Remove un-necessary ellipsis...Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
| Munyoki Kilyungi |
| 2023-09-05 | Remove pylint skip...* 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>
| Munyoki Kilyungi |
| 2023-08-02 | Integrate 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 |
| 2023-07-31 | Fix typing issue | Frederick Muriuki Muriithi |
| 2023-07-31 | Fix linting and typing issues. | Frederick Muriuki Muriithi |
| 2023-07-31 | Fix bugs. Return resource without data items....* Fix bugs introduced while attempting pagination.
* Return resource object without attached data items.
| Frederick Muriuki Muriithi |
| 2023-07-31 | Paginate the resource data items. | Frederick Muriuki Muriithi |
| 2023-07-12 | Move documentation comment to beginning of function | Frederick Muriuki Muriithi |
| 2023-07-06 | Provide the client_id as part of the post request. | Frederick Muriuki Muriithi |
| 2023-07-03 | Spruce up UI...Make UI somewhat consistent with the GN2 UI.
| Frederick Muriuki Muriithi |
| 2023-07-03 | Enable deletion of OAuth2 clients. | Frederick Muriuki Muriithi |
| 2023-06-30 | Edit some of the details of OAuth2 clients | Frederick Muriuki Muriithi |
| 2023-06-30 | List all OAuth2 clients. | Frederick Muriuki Muriithi |
| 2023-06-23 | Fetch 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 |
| 2023-06-20 | Fix conflicts | zsloan |
| 2023-06-20 | Bug: Don't overwrite/delete old collections | Frederick Muriuki Muriithi |
| 2023-06-13 | Namespace session variable...Extract the functions acting on the session into a separate module and
namespace the session variable to prevent conflicts.
| Frederick Muriuki Muriithi |
| 2023-06-08 | Fix bugs with accessing/creating collections | zsloan |
| 2023-06-05 | Logging: 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 |
| 2023-06-05 | Logging: Get user information. | Frederick Muriuki Muriithi |
| 2023-06-05 | Handle unhandled SQLite3 errors. | Frederick Muriuki Muriithi |
| 2023-05-30 | auth: 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 |
| 2023-05-29 | auth: 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 |
| 2023-05-29 | Enable 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 |
| 2023-05-27 | Document 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 |
| 2023-05-25 | Script 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 |
| 2023-05-25 | Set whether resource is publicly viewable on creation | Frederick Muriuki Muriithi |
| 2023-05-23 | auth: 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 |
| 2023-05-19 | auth: 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 |
| 2023-05-19 | auth: 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 |
| 2023-05-18 | auth: Rename collections...Enable renaming collections.
| Frederick Muriuki Muriithi |
| 2023-05-18 | auth: user collections: Add and/or remove traits. | Frederick Muriuki Muriithi |
| 2023-05-17 | auth: Delete collections by ID. | Frederick Muriuki Muriithi |
| 2023-05-17 | auth: 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 |
| 2023-05-16 | auth: View a collection by its ID. | Frederick Muriuki Muriithi |
| 2023-05-15 | collections: 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 |
| 2023-05-12 | auth: Provide separate endpoint for anonymous collections. | Frederick Muriuki Muriithi |
| 2023-05-11 | auth: 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 |
| 2023-05-10 | auth: 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 |
| 2023-05-10 | auth: 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 |
| 2023-05-09 | auth: 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-flow | Frederick Muriuki Muriithi |
| 2023-04-27 | auth: 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 |
| 2023-04-27 | auth: 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 |
| 2023-04-27 | auth: Add authorisation checks for role editting. | Frederick Muriuki Muriithi |
| 2023-04-27 | oauth2: Provide missing `user_editable` argument. | Frederick Muriuki Muriithi |
| 2023-04-25 | auth: bug: Provide missing `user_editable` argument. | Frederick Muriuki Muriithi |
| 2023-04-25 | auth: provide `user_editable` flag in dictified output | Frederick Muriuki Muriithi |
