| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 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 | Lint: Add documentation strings. Fix import order. | 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 | |
| 2024-09-25 | feat: add base implementation for hooks system | John Nduli | |
| 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 | |
| 2024-08-30 | Commit missing template. | 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 | |
| 2024-08-21 | Use username and password, when present, during sending emails | Frederick Muriuki Muriithi | |
| If the username and password are provided, make use of them to send emails out. | |||
| 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 | Add notification to outgoing emails. | 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 | Improve the messaging in the UI. | 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: cast args to str | 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. | |||
| 2024-08-14 | docs: update documentation to reflect new secrets handling | John Nduli | |
| 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 | Fix bug with sending e-mails | zsloan | |
| We changed the from address from genenetwork.org to uthsc.edu, which seems to have fixed the issue with e-mails not being properly sent. We also stopped activating tls | |||
| 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 | |
| 2024-08-07 | Log out exceptions at the `ERROR` log level | Frederick Muriuki Muriithi | |
| Log out any unhandled exceptions at the `ERROR` log level to ensure that any and all unhandled errors show up in the logs under normal running of the application. | |||
| 2024-08-05 | Fix linting errors. | Frederick Muriuki Muriithi | |
| 2024-08-02 | feat: improve local set up utility functions | John Nduli | |
| Ensures running `init_dev_users` and `init_dev_clients` multiple times succeeds and updates the local database entry. Also provide a custom flag to set the gn2's client url and add jwt-bearer to list of accepted grants. | |||
| 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 | |||
| 2024-08-01 | Handle generic exception and return a value.enable-key-rotation | Frederick Muriuki Muriithi | |
| 2024-07-31 | Add missing image for favicon.ico | Frederick Muriuki Muriithi | |
| 2024-07-31 | Update all endpoints to use the `client_secret_post` auth method. | Frederick Muriuki Muriithi | |
 |
index : gn-auth | |
| GN authentication and authorization service |
| aboutsummaryrefslogtreecommitdiff |