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2024-09-13Leave notes on things that need to be handled in code and UIFrederick Muriuki Muriithi
2024-09-13Increase default number of items displayed per page.Frederick Muriuki Muriithi
2024-09-13Samples: provide more informative page content.Frederick Muriuki Muriithi
2024-09-13Put views behind authorisation.Frederick Muriuki Muriithi
2024-09-13Initialise genotypes' UIFrederick Muriuki Muriithi
2024-09-12Add "Family" to the UIFrederick Muriuki Muriithi
2024-09-12Save the updated species details.Frederick Muriuki Muriithi
2024-09-10Improve "Edit species" UI.Frederick Muriuki Muriithi
2024-09-10Require that user selects the family.Frederick Muriuki Muriithi
2024-09-09Enable samples uploads.Frederick Muriuki Muriithi
2024-09-09Initialise samples uploadsFrederick 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.
2024-09-09Display species details in populations views.Frederick Muriuki Muriithi
2024-09-06Add more fields when creating a populationFrederick Muriuki Muriithi
Add more of the missing fields when creating a population, to ensure that the created population works as expected.
2024-09-05Provide basic UI for editing the Species details.Frederick Muriuki Muriithi
2024-09-05Improve error messaging for "Create Population" feature.Frederick Muriuki Muriithi
2024-09-05Synchronise 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.
2024-09-04Provide 'edit species' endpointFrederick Muriuki Muriithi
* Verify new authorisation wrapper works as expected.
2024-09-04Provide top-level navigation placeholder link.Frederick Muriuki Muriithi
2024-09-04Introduce wrapper that validates tokensFrederick Muriuki Muriithi
Validate token and pass it on to functions that require more fine-grained authorisation checks.
2024-09-04Update retrival of JSON Web KeysFrederick 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`auth_server_jwks()` to use for fetching the keys from the session if present, or from the server when absent or out-of-date.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.
2024-09-04Add function to update the JSON Web Keys in the sessionFrederick 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.
2024-09-04Improve styling.Frederick Muriuki Muriithi
2024-09-04Create populations (InbredSet groups) under Species.Frederick Muriuki Muriithi
2024-09-03Improve UI copy.Frederick Muriuki Muriithi
2024-09-03Display any error messages.Frederick Muriuki Muriithi
2024-09-03View a specific population's details.Frederick Muriuki Muriithi
2024-09-03Improve UI styling.Frederick Muriuki Muriithi
2024-09-03Provide means to debug actual query run and params used.Frederick Muriuki Muriithi
2024-09-03Update 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.
2024-09-03Put 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.
2024-09-03Initialise the populations package and update references.Frederick Muriuki Muriithi
2024-09-03Extract common UI pattern to separate module for reusability.Frederick Muriuki Muriithi
2024-09-03Provide generic way to select species.Frederick Muriuki Muriithi
2024-09-03Provide UI for viewing species details.Frederick Muriuki Muriithi
2024-09-03Enable third level of breadcrumbs.Frederick Muriuki Muriithi
2024-09-03Update species queriesFrederick Muriuki Muriithi
* Use the more reliable 'Species.Id' field * Provide more of a species' details
2024-09-03Save a species to the database.Frederick Muriuki Muriithi
2024-09-03Put active pages behind auth. Flash all error messages.Frederick Muriuki Muriithi
2024-08-30Initialise package for dealing with Species.Frederick Muriuki Muriithi
2024-08-28Fix imports, and minor bugs.Frederick Muriuki Muriithi
2024-08-28Move code handling expression data upload into new module.Frederick Muriuki Muriithi
2024-08-28Rework UI: present menus on the left, content on the right.Frederick Muriuki Muriithi
2024-08-08Fix linting issues.Frederick Muriuki Muriithi
2024-08-08Set up logging for the application.Frederick Muriuki Muriithi
Set up logging for the application to help with debugging issues.
2024-08-07Make passing SQL_URI to `database_connection` mandatory.Frederick Muriuki Muriithi
2024-08-06Override `client_secret_post`: use JSONFrederick 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.
2024-08-06Avoid hitting auth server to check for tokenFrederick 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.
2024-08-05Fix token revocationFrederick Muriuki Muriithi
Token revocation was failing due to missing hint.
2024-08-05Display the stack trace correctly on the template.Frederick Muriuki Muriithi
2024-08-05If no user is logged in, notify and redirect appropriately.Frederick Muriuki Muriithi