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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
2024-07-26Provide UI for enabling login to the application.Frederick Muriuki Muriithi
2024-07-26Initialise sessions for the application.Frederick Muriuki Muriithi
2024-07-26Rename configuration variableFrederick Muriuki Muriithi
QCAPP_CONF --> UPLOADER_CONF
2024-07-26Setup secrets from config file.Frederick Muriuki Muriithi
2024-07-26authorisation module: utilities for basic authorisation.Frederick Muriuki Muriithi
2024-07-26OAuth2 package: Handle OAuth2 related issuesFrederick Muriuki Muriithi
Adds utilities to handle talking to the authentication/authorisation server.
2024-07-26Add monadic wrapper for requests library.Frederick Muriuki Muriithi