| Age | Commit message (Expand) | Author |
|---|
| 2024-11-22 | Use code in gn_libs for MySQL/MariaDB connection....Update the application to use the gn_libs code for connecting to the
database, rather than using a local module.
| Frederick Muriuki Muriithi |
| 2024-10-09 | Linting: Fix minor linting errors | Frederick Muriuki Muriithi |
| 2024-10-09 | Fix masquerading logic...Update the code to actually use JWT bearer tokens that the older plain
authorisation tokens that were previously used.
| Frederick Muriuki Muriithi |
| 2024-10-09 | Update Configs: Change `OAUTH2_SCOPE` => `OAUTH2_SCOPES_SUPPORTED`...Use the OAUTH2_SCOPES_SUPPORTED application configuration variable,
that is used by the flask integration for the Authlib library to set
up the supported scopes.
| Frederick Muriuki Muriithi |
| 2024-10-09 | Pass on all GET parameters when redirecting. | Frederick Muriuki Muriithi |
| 2024-10-09 | Put routes behind auth. | Frederick Muriuki Muriithi |
| 2024-10-03 | BugFix: Fetch also roles assigned to user...When fetching the resource roles, fetch also any roles that are
assigned to the user for that resource.
| Frederick Muriuki Muriithi |
| 2024-10-03 | BugFix: Remove duplicates from resources list...Issue:
https://issues.genenetwork.org/issues/gn-auth/resources-duplicates-in-resources-list
The query was returning multiple instances of the same resource in
situations where a user had more than one role of a particular resource.
| Frederick Muriuki Muriithi |
| 2024-10-03 | Provide a way to change OAuth2 client secrets. | Frederick Muriuki Muriithi |
| 2024-09-30 | Refactor: Initialise phenotype package...* Move code into a new phenotypes package and update references.
* Add new functions to fetch linked resources from GN3 data
identifiers — this is useful for auth
* Provide endpoint to fetch authorisation details for a specific
phenotype.
| Frederick Muriuki Muriithi |
| 2024-09-30 | Create a better named function, with less data in the args....The new name serves better to reflect what the function does.
We then pass only the data that the function needs to perform its
operation rather than full objects with extra data — this has
implications for security.
| Frederick Muriuki Muriithi |
| 2024-09-30 | Extract function to prevent circular dependencies. | Frederick Muriuki Muriithi |
| 2024-09-26 | Add type annotation to variable. | Frederick Muriuki Muriithi |
| 2024-09-26 | Bugfix: Fix bugs that were preventing creation of geno resource...Fix the bugs that were causing the creation of a genotype resource via
API to fail.
| Frederick Muriuki Muriithi |
| 2024-09-25 | Implement genotype resource creation via API with resource data...Create the resource, assign the resource-owner role and link the
resource's data in a single API call.
| Frederick Muriuki Muriithi |
| 2024-09-25 | Extract common role assignment to its own module | Frederick Muriuki Muriithi |
| 2024-09-16 | Create population resource and assign appropriate roles...Provide an endpoint to create a new population
resource (inbredset-group) and assign the active user with the
appropriate privileges against the new resource.
| Frederick Muriuki Muriithi |
| 2024-09-16 | Rename blueprint and register it one level lower...Register the populations/inbredset blueprint with the "resources"
blueprint rather than at the higher level "auth" blueprint to retain
the hierarchy of the blueprints and make maintenance arguably easier.
| Frederick Muriuki Muriithi |
| 2024-09-16 | Pass cursor rather than connection to create_resource function...In order to decouple the `create_resource` function from the related
functions that assign roles to users, this commit changes the code to
pass in a cursor rather than a connection.
The cursor will be the same cursor passed into the role assignment
functions ensuring that the resource creation and role assignment
happen in a single transaction.
| Frederick Muriuki Muriithi |
| 2024-09-13 | Notes: Add note on some items that could go into hooks. | Frederick Muriuki Muriithi |
| 2024-08-30 | If config variables are not set, return empty string. | Frederick Muriuki Muriithi |
| 2024-08-21 | Only import anonymous collections if they contain traits | zsloan |
| 2024-08-21 | Update 'changed' field when traits are added or removed from collections | zsloan |
| 2024-08-21 | Do actual password change. | Frederick Muriuki Muriithi |
| 2024-08-21 | Provide email and improve UI text/notification. | Frederick Muriuki Muriithi |
| 2024-08-20 | Save to DB then send email...Separate the saving of the token from its sending.
| Frederick Muriuki Muriithi |
| 2024-08-20 | Handle the "GET" part of the change-password request...- Delete any expired tokens
- Display the UI if token is valid, else redirect with error notification.
| Frederick Muriuki Muriithi |
| 2024-08-20 | Pass GET parameters for correct redirection. | Frederick Muriuki Muriithi |
| 2024-08-20 | Fix query: Replace any existing token. | Frederick Muriuki Muriithi |
| 2024-08-19 | Generate token and send out "Forgot Password" email...* Generate token to use for verifying the password-change request
* Send out email with token
| Frederick Muriuki Muriithi |
| 2024-08-15 | Fix a bunch of linting errors. | Frederick Muriuki Muriithi |
| 2024-08-15 | Reduce UI complexity...Providing both the "Enter Verification Token" and the "Send
Verification Email" elements of the same user interface seems to
confuse users.
This commit ensures that the system will provide one or the other, but
not both, depending on whether or not there is a pending verification
token present for the user.
| Frederick Muriuki Muriithi |
| 2024-08-15 | Import specific classes from the datetime module. | Frederick Muriuki Muriithi |
| 2024-08-15 | fix: bugs with generating auth tokens | John Nduli |
| 2024-08-15 | fix: bugs in masquerade api | John Nduli |
| 2024-08-13 | Emails: Make "From" address configurable...We are running GeneNetwork in different environments. Each environment
could have it's own separate domain, and need a different sender email
to allow the underlying services to allow the emails through.
| Frederick Muriuki Muriithi |
| 2024-08-08 | Bug: Prevent fall-through to verification if code is expired. | Frederick Muriuki Muriithi |
| 2024-08-08 | Forward email to email verification page. | Frederick Muriuki Muriithi |
| 2024-08-07 | Log out user registration errors at the `ERROR` log-level. | Frederick Muriuki Muriithi |
| 2024-08-05 | Fix linting errors. | Frederick Muriuki Muriithi |
| 2024-08-01 | Handle generic exception and return a value.enable-key-rotation | Frederick Muriuki Muriithi |
| 2024-07-31 | Enable registration of a public-jwks-uri for every client | Frederick Muriuki Muriithi |
| 2024-07-31 | Enable external configuration of session expiry period...Enable passing in the number of minutes that a session can be valid
for. This enables the length of time that the session can last to be
configurable rather than hard-coded.
| Frederick Muriuki Muriithi |
| 2024-07-31 | Ignore warning from mypy. | Frederick Muriuki Muriithi |
| 2024-07-31 | Remove obsoleted SSL_PRIVATE_KEY configuration...With the key rotation in place, eliminate the use of the
SSL_PRIVATE_KEY configuration which pointed to a specific non-changing
JWK.
| Frederick Muriuki Muriithi |
| 2024-07-17 | Add non-interactive script to assign make data public by default. | Frederick Muriuki Muriithi |
| 2024-06-25 | Roles: Get rid of use of GroupRole; use Role directly for resources...The GroupRole idea was flawed, and led to a critical bug that would
have allowed privilege escalation. This uses the Role directly acting
on a specific resource when assigning said role to a user.
| Frederick Muriuki Muriithi |
| 2024-06-20 | Reorganise test fixtures. Fix tests and issues caught....Reorganise test fixtures to more closely follow the design of the auth
system.
Fix the broken tests due to refactors and fix all issues caught by the
running tests.
| Frederick Muriuki Muriithi |
| 2024-06-18 | fix mypy errors | Frederick Muriuki Muriithi |
| 2024-06-17 | Fix mypy errors | Frederick Muriuki Muriithi |
