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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
2024-08-05Provide a generalised way to handle errors and exceptions.Frederick Muriuki Muriithi
2024-08-05Put endpoints behind an authorisation checkFrederick Muriuki Muriithi
Put all endpoints that cause data changes behind authorisation.
2024-08-05mypy and pylint fixes.Frederick Muriuki Muriithi
2024-08-05Enable logout.Frederick Muriuki Muriithi
2024-08-05Differentiate python's requests library from our monadic wrappers.Frederick Muriuki Muriithi
2024-08-05Fix bugs in POST wrapper for OAuth2 clientFrederick Muriuki Muriithi
* Call the correct __post__ function * Set up the headers appropriately
2024-08-05Add OAuth2/JWK-related endpoints.Frederick Muriuki Muriithi
2024-07-26Add module to handle the JSON Web Keys.Frederick Muriuki Muriithi
2024-07-26Add wrappers for OAuth2Session's `get` and `post` methods. Fix bugs.Frederick Muriuki Muriithi