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2024-08-16Ignore comment lines.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
2024-07-25Add session module: handles session management.Frederick Muriuki Muriithi
2024-07-25Fix typing and linting errors.Frederick Muriuki Muriithi
2024-07-25Rename module: qc_app --> uploaderFrederick Muriuki Muriithi
2024-07-22Handle generic errors for chunked uploads better.Frederick Muriuki Muriithi
2024-07-05bug: Return a hashable key, not a dict.Frederick Muriuki Muriithi
2024-07-02Call correct method.Frederick Muriuki Muriithi
2024-07-02Add URL information to debug informationFrederick Muriuki Muriithi
To help with error reporting, as the user to also provide the URL of the error page to help with debugging issues that the user encounters.
2024-07-02Ensure no duplicated values for the query.Frederick Muriuki Muriithi
2024-07-01Respond with JSON. Handle error messages on UI.Frederick Muriuki Muriithi
2024-07-01Display error better.test-resumablejsFrederick Muriuki Muriithi
2024-07-01Check for genotype samples in the databaseFrederick Muriuki Muriithi
Check for genotype samples in both the R/qtl2 file and in the database.
2024-06-27Remove unnecessary debugging statements.Frederick Muriuki Muriithi