| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 10 days | Delete local mariadb connections module. | Frederick Muriuki Muriithi | |
| We no longer need this module after moving the code to use gn-libs. | |||
| 10 days | Use code in gn_libs for MySQL/MariaDB connection. | Frederick Muriuki Muriithi | |
| Update the application to use the gn_libs code for connecting to the database, rather than using a local module. | |||
| 2024-11-08 | Revert "Debug: Add debug logging to trace JWK fetching." | Frederick Muriuki Muriithi | |
| This reverts commit 5a6dc1fb81bf223750f42f4697f3cd7d86b39e71. Remove debugging statements and restore original code. | |||
| 2024-11-05 | Debug: Add debug logging to trace JWK fetching. | Frederick Muriuki Muriithi | |
| 2024-11-04 | Output KeySet retrieved from the client. | Frederick Muriuki Muriithi | |
| 2024-10-09 | Linting: Fix minor linting errors | Frederick Muriuki Muriithi | |
| 2024-10-09 | Fix masquerading logic | Frederick Muriuki Muriithi | |
| Update the code to actually use JWT bearer tokens that the older plain authorisation tokens that were previously used. | |||
| 2024-10-09 | Add a client to the JWTBearerToken objects. | Frederick Muriuki Muriithi | |
| 2024-10-09 | Update Configs: Change `OAUTH2_SCOPE` => `OAUTH2_SCOPES_SUPPORTED` | Frederick Muriuki Muriithi | |
| 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. | |||
| 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 | Frederick Muriuki Muriithi | |
| When fetching the resource roles, fetch also any roles that are assigned to the user for that resource. | |||
| 2024-10-03 | BugFix: Remove duplicates from resources list | Frederick Muriuki Muriithi | |
| 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. | |||
| 2024-10-03 | Provide a way to change OAuth2 client secrets. | Frederick Muriuki Muriithi | |
| 2024-09-30 | Refactor: Initialise phenotype package | Frederick Muriuki Muriithi | |
| * 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. | |||
| 2024-09-30 | Create a better named function, with less data in the args. | Frederick Muriuki Muriithi | |
| 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. | |||
| 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 | Frederick Muriuki Muriithi | |
| Fix the bugs that were causing the creation of a genotype resource via API to fail. | |||
| 2024-09-25 | Implement genotype resource creation via API with resource data | Frederick Muriuki Muriithi | |
| Create the resource, assign the resource-owner role and link the resource's data in a single API call. | |||
| 2024-09-25 | Extract common role assignment to its own module | Frederick Muriuki Muriithi | |
| 2024-09-16 | Create population resource and assign appropriate roles | Frederick Muriuki Muriithi | |
| Provide an endpoint to create a new population resource (inbredset-group) and assign the active user with the appropriate privileges against the new resource. | |||
| 2024-09-16 | Rename blueprint and register it one level lower | Frederick Muriuki Muriithi | |
| 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. | |||
| 2024-09-16 | Pass cursor rather than connection to create_resource function | Frederick Muriuki Muriithi | |
| 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. | |||
| 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 | Frederick Muriuki Muriithi | |
| Separate the saving of the token from its sending. | |||
| 2024-08-20 | Handle the "GET" part of the change-password request | Frederick Muriuki Muriithi | |
| - Delete any expired tokens - Display the UI if token is valid, else redirect with error notification. | |||
| 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 | Frederick Muriuki Muriithi | |
| * Generate token to use for verifying the password-change request * Send out email with token | |||
| 2024-08-19 | Show "Forgot Password" link. | Frederick Muriuki Muriithi | |
| Provide the user with the "Forgot Password" link, if the backend supports it. | |||
| 2024-08-15 | Fix a bunch of linting errors. | Frederick Muriuki Muriithi | |
| 2024-08-15 | Reduce UI complexity | Frederick Muriuki Muriithi | |
| 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. | |||
| 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 | |
| 2024-08-14 | fix: import timedelta in jwks | John Nduli | |
| 2024-08-14 | refactor: move newest_jwk_with_rotation function to jwks.py | John Nduli | |
| We have a similar jwk module in gn2 that does similar functionality. Moving the newest_jwk_with_rotation function to the module ensures that there's some consistency between both modules so that when we ever want to remove the duplication (e.g. by creating some python pip package) it's easier. | |||
| 2024-08-13 | Emails: Make "From" address configurable | Frederick Muriuki Muriithi | |
| 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. | |||
| 2024-08-08 | Bug: Prevent fall-through to verification if code is expired. | Frederick Muriuki Muriithi | |
| 2024-08-08 | Get data from form too. | 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 | |
| 2024-08-02 | fix: use json to support parsing oauth2 requests | John Nduli | |
| The local sign in request used by gn2 uses json. However, the default parsing assumes form data, see: - https://github.com/lepture/authlib/blob/v1.2.0/authlib/integrations/flask_oauth2/authorization_server.py#L72 - https://github.com/lepture/authlib/blob/v1.2.0/authlib/integrations/flask_helpers.py#L5 We create a custom Authorization server that defaults to `use_json=True` when creating the oauth request object | |||
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index : gn-auth | |
| GN authentication and authorization service |
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