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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`auth_server_jwks()` to use for fetching the keys from the session if present, or from the server when absent or out-of-date.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
2024-08-16Log out correct parameters.Frederick Muriuki Muriithi
2024-08-13Bug: cross reference with NULL cM when "gmap" file is absentFrederick Muriuki Muriithi
The "gmap" file might not exist in some bundles. In those instances, cross-reference the data without including the genotypes' physical positions (cM).
2024-08-12Bug: Ensure file type values are lists.Frederick Muriuki Muriithi
2024-08-12Update check for missing files: Check from directory.Frederick Muriuki Muriithi
Enable the check for missing files to act upon a directory where the R/qtl2 bundle has been extracted into.
2024-08-12Add utility to transpose CSVs, renaming the original file.Frederick Muriuki Muriithi
2024-08-12Define new InvalidValue error type.Frederick Muriuki Muriithi
Redesign the InvalidValue error type for the R/qtl2 bundles to list the errors according to the row and column titles rather than line numbers. This makes the error-reporting independent on whether or not the file is transposed. This will replace the use of the older `quality_control.errors.InvalidValue` error type that depends on the line and column numbers, and thus cannot work with transposable files.
2024-08-12Rename module: Module contains exceptions classes.Frederick Muriuki Muriithi
2024-08-09Read R/qtl2 control data from a directory with extracted files.Frederick Muriuki Muriithi
2024-08-08Function to transpose CSV files.Frederick Muriuki Muriithi
Some files come in a transposed form, so we need to transpose them again in order to use the same processing code for all files.
2024-08-08Add utility function to extract R/qtl2 zip bundlesFrederick Muriuki Muriithi
2024-08-08Fix linting issues.Frederick Muriuki Muriithi
2024-08-08Fix bugs and pass in logger to functions.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.
2024-08-07Update installer manifest.Frederick Muriuki Muriithi
2024-08-07Make passing SQL_URI to `database_connection` mandatory.Frederick Muriuki Muriithi
2024-08-06Pass logger on to inner functionsFrederick Muriuki Muriithi
Pass the logger forward to inner functions to help with debugging things.
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