| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 2024-09-09 | Initialise samples uploads | Frederick Muriuki Muriithi | |
| * Move existing code to new module * Rework the UI: create new templates * Rework the routes: Select species and populations before attempting an upload. | |||
| 2024-09-09 | Display species details in populations views. | Frederick Muriuki Muriithi | |
| 2024-09-06 | Add more fields when creating a population | Frederick Muriuki Muriithi | |
| Add more of the missing fields when creating a population, to ensure that the created population works as expected. | |||
| 2024-09-05 | Provide basic UI for editing the Species details. | Frederick Muriuki Muriithi | |
| 2024-09-05 | Improve error messaging for "Create Population" feature. | Frederick Muriuki Muriithi | |
| 2024-09-05 | Synchronise token refreshing. | Frederick Muriuki Muriithi | |
| When running flask with multiple threads/workers, as happens when using gunicorn, there is a potential for more than one thread running with an expired token, leading to multiple uncoordinated token refreshes. This commit coordinates the threads in the case there is need to refresh a token, ensuring only one thread does the token refresh. | |||
| 2024-09-04 | Provide 'edit species' endpoint | Frederick Muriuki Muriithi | |
| * Verify new authorisation wrapper works as expected. | |||
| 2024-09-04 | Provide top-level navigation placeholder link. | Frederick Muriuki Muriithi | |
| 2024-09-04 | Introduce wrapper that validates tokens | Frederick Muriuki Muriithi | |
| Validate token and pass it on to functions that require more fine-grained authorisation checks. | |||
| 2024-09-04 | Update retrival of JSON Web Keys | Frederick Muriuki Muriithi | |
| * Introduce the function `auth_server_jwks()` to use for fetching the keys from the session if present, or from the server when absent or out-of-date. It also handles updating the keys in the session. * Remove the unnecessary verification of JWKs until the point where that is needed, i.e. at the point(s) where there is need to verify authorisation. | |||
| 2024-09-04 | Add function to update the JSON Web Keys in the session | Frederick Muriuki Muriithi | |
| When new JSON Web Keys (JWKs) are fetched from the server, the function added in this commit will help with updating them in the session for subsequent uses, validating the tokens when needed. | |||
| 2024-09-04 | Improve styling. | Frederick Muriuki Muriithi | |
| 2024-09-04 | Create populations (InbredSet groups) under Species. | Frederick Muriuki Muriithi | |
| 2024-09-03 | Improve UI copy. | Frederick Muriuki Muriithi | |
| 2024-09-03 | Display any error messages. | Frederick Muriuki Muriithi | |
| 2024-09-03 | View a specific population's details. | Frederick Muriuki Muriithi | |
| 2024-09-03 | Improve UI styling. | Frederick Muriuki Muriithi | |
| 2024-09-03 | Provide means to debug actual query run and params used. | Frederick Muriuki Muriithi | |
| 2024-09-03 | Update navigation scaffolding. | Frederick Muriuki Muriithi | |
| Provide the navigation to the features we expect to provide with the system, even though, at this point, the features have not been implemented yet. | |||
| 2024-09-03 | Put populations under species: improve hierarchy. | Frederick Muriuki Muriithi | |
| Populations cannot exist without the species they are related to. This commit updates the URI hierarchy to reflect that expectation. | |||
| 2024-09-03 | Initialise the populations package and update references. | Frederick Muriuki Muriithi | |
| 2024-09-03 | Extract common UI pattern to separate module for reusability. | Frederick Muriuki Muriithi | |
| 2024-09-03 | Provide generic way to select species. | Frederick Muriuki Muriithi | |
| 2024-09-03 | Provide UI for viewing species details. | Frederick Muriuki Muriithi | |
| 2024-09-03 | Enable third level of breadcrumbs. | Frederick Muriuki Muriithi | |
| 2024-09-03 | Update species queries | Frederick Muriuki Muriithi | |
| * Use the more reliable 'Species.Id' field * Provide more of a species' details | |||
| 2024-09-03 | Save a species to the database. | Frederick Muriuki Muriithi | |
| 2024-09-03 | Put active pages behind auth. Flash all error messages. | Frederick Muriuki Muriithi | |
| 2024-08-30 | Initialise package for dealing with Species. | Frederick Muriuki Muriithi | |
| 2024-08-28 | Fix imports, and minor bugs. | Frederick Muriuki Muriithi | |
| 2024-08-28 | Move code handling expression data upload into new module. | Frederick Muriuki Muriithi | |
| 2024-08-28 | Rework UI: present menus on the left, content on the right. | Frederick Muriuki Muriithi | |
| 2024-08-08 | Fix linting issues. | Frederick Muriuki Muriithi | |
| 2024-08-08 | Set up logging for the application. | Frederick Muriuki Muriithi | |
| Set up logging for the application to help with debugging issues. | |||
| 2024-08-07 | Make passing SQL_URI to `database_connection` mandatory. | Frederick Muriuki Muriithi | |
| 2024-08-06 | Override `client_secret_post`: use JSON | Frederick Muriuki Muriithi | |
| Override the `client_secret_post` auth method to use JSON rather than FORMDATA in order to gain some consistency while communicating with the auth server. | |||
| 2024-08-06 | Avoid hitting auth server to check for token | Frederick Muriuki Muriithi | |
| If the user is already logged in, they will have a token. Whether a token is valid or not should be handled elsewhere, not with every single request to gn-uploader, whether or not it requires to access the auth server. | |||
| 2024-08-05 | Fix token revocation | Frederick Muriuki Muriithi | |
| Token revocation was failing due to missing hint. | |||
| 2024-08-05 | Display the stack trace correctly on the template. | Frederick Muriuki Muriithi | |
| 2024-08-05 | If no user is logged in, notify and redirect appropriately. | Frederick Muriuki Muriithi | |
| 2024-08-05 | Provide a generalised way to handle errors and exceptions. | Frederick Muriuki Muriithi | |
| 2024-08-05 | Put endpoints behind an authorisation check | Frederick Muriuki Muriithi | |
| Put all endpoints that cause data changes behind authorisation. | |||
| 2024-08-05 | mypy and pylint fixes. | Frederick Muriuki Muriithi | |
| 2024-08-05 | Enable logout. | Frederick Muriuki Muriithi | |
| 2024-08-05 | Differentiate python's requests library from our monadic wrappers. | Frederick Muriuki Muriithi | |
| 2024-08-05 | Fix bugs in POST wrapper for OAuth2 client | Frederick Muriuki Muriithi | |
| * Call the correct __post__ function * Set up the headers appropriately | |||
| 2024-08-05 | Add OAuth2/JWK-related endpoints. | Frederick Muriuki Muriithi | |
| 2024-07-26 | Add module to handle the JSON Web Keys. | Frederick Muriuki Muriithi | |
| 2024-07-26 | Add wrappers for OAuth2Session's `get` and `post` methods. Fix bugs. | Frederick Muriuki Muriithi | |
| 2024-07-26 | Provide UI for enabling login to the application. | Frederick Muriuki Muriithi | |
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index : gn-uploader | |
| gn-uploader: Data uploader for GeneNetwork |
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