| Age | Commit message (Expand) | Author |
|---|
| 2024-08-12 | Update check for missing files: Check from directory....Enable the check for missing files to act upon a directory where the
R/qtl2 bundle has been extracted into.
| Frederick Muriuki Muriithi |
| 2024-08-12 | Add utility to transpose CSVs, renaming the original file. | Frederick Muriuki Muriithi |
| 2024-08-12 | Define new InvalidValue error type....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.
| Frederick Muriuki Muriithi |
| 2024-08-12 | Rename module: Module contains exceptions classes. | Frederick Muriuki Muriithi |
| 2024-08-09 | Read R/qtl2 control data from a directory with extracted files. | Frederick Muriuki Muriithi |
| 2024-08-08 | Function to transpose CSV files....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.
| Frederick Muriuki Muriithi |
| 2024-08-08 | Add utility function to extract R/qtl2 zip bundles | Frederick Muriuki Muriithi |
| 2024-08-08 | Fix linting issues. | Frederick Muriuki Muriithi |
| 2024-08-08 | Fix bugs and pass in logger to functions. | Frederick Muriuki Muriithi |
| 2024-08-08 | Set up logging for the application....Set up logging for the application to help with debugging issues.
| Frederick Muriuki Muriithi |
| 2024-08-07 | Update installer manifest. | Frederick Muriuki Muriithi |
| 2024-08-07 | Make passing SQL_URI to `database_connection` mandatory. | Frederick Muriuki Muriithi |
| 2024-08-06 | Pass logger on to inner functions...Pass the logger forward to inner functions to help with debugging things.
| Frederick Muriuki Muriithi |
| 2024-08-06 | Override `client_secret_post`: use JSON...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.
| Frederick Muriuki Muriithi |
| 2024-08-06 | Avoid hitting auth server to check for token...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.
| Frederick Muriuki Muriithi |
| 2024-08-05 | Fix token revocation...Token revocation was failing due to missing hint.
| Frederick Muriuki Muriithi |
| 2024-08-05 | Display the stack trace correctly on the template. | Frederick Muriuki Muriithi |
| 2024-08-05 | If no user is logged in, notify and redirect appropriately. | Frederick Muriuki Muriithi |
| 2024-08-05 | Provide a generalised way to handle errors and exceptions. | Frederick Muriuki Muriithi |
| 2024-08-05 | Put endpoints behind an authorisation check...Put all endpoints that cause data changes behind authorisation.
| Frederick Muriuki Muriithi |
| 2024-08-05 | mypy and pylint fixes. | Frederick Muriuki Muriithi |
| 2024-08-05 | Enable logout. | Frederick Muriuki Muriithi |
| 2024-08-05 | Differentiate python's requests library from our monadic wrappers. | Frederick Muriuki Muriithi |
| 2024-08-05 | Fix bugs in POST wrapper for OAuth2 client...* Call the correct __post__ function
* Set up the headers appropriately
| Frederick Muriuki Muriithi |
| 2024-08-05 | Add OAuth2/JWK-related endpoints. | Frederick Muriuki Muriithi |
| 2024-07-26 | Add module to handle the JSON Web Keys. | Frederick Muriuki Muriithi |
| 2024-07-26 | Add wrappers for OAuth2Session's `get` and `post` methods. Fix bugs. | Frederick Muriuki Muriithi |
| 2024-07-26 | Provide UI for enabling login to the application. | Frederick Muriuki Muriithi |
| 2024-07-26 | Initialise sessions for the application. | Frederick Muriuki Muriithi |
| 2024-07-26 | Rename configuration variable...QCAPP_CONF --> UPLOADER_CONF
| Frederick Muriuki Muriithi |
| 2024-07-26 | Setup secrets from config file. | Frederick Muriuki Muriithi |
| 2024-07-26 | authorisation module: utilities for basic authorisation. | Frederick Muriuki Muriithi |
| 2024-07-26 | OAuth2 package: Handle OAuth2 related issues...Adds utilities to handle talking to the authentication/authorisation
server.
| Frederick Muriuki Muriithi |
| 2024-07-26 | Add monadic wrapper for requests library. | Frederick Muriuki Muriithi |
| 2024-07-25 | Add session module: handles session management. | Frederick Muriuki Muriithi |
| 2024-07-25 | Fix typing and linting errors. | Frederick Muriuki Muriithi |
| 2024-07-25 | Rename module: qc_app --> uploader | Frederick Muriuki Muriithi |
| 2024-07-22 | Handle generic errors for chunked uploads better. | Frederick Muriuki Muriithi |
| 2024-07-05 | bug: Return a hashable key, not a dict. | Frederick Muriuki Muriithi |
| 2024-07-02 | Call correct method. | Frederick Muriuki Muriithi |
| 2024-07-02 | Add URL information to debug information...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.
| Frederick Muriuki Muriithi |
| 2024-07-02 | Ensure no duplicated values for the query. | Frederick Muriuki Muriithi |
| 2024-07-01 | Respond with JSON. Handle error messages on UI. | Frederick Muriuki Muriithi |
| 2024-07-01 | Display error better.test-resumablejs | Frederick Muriuki Muriithi |
| 2024-07-01 | Check for genotype samples in the database...Check for genotype samples in both the R/qtl2 file and in the
database.
| Frederick Muriuki Muriithi |
| 2024-06-27 | Remove unnecessary debugging statements. | Frederick Muriuki Muriithi |
| 2024-06-27 | Handle chunks on backend and update UI with progress...Handle the uploaded chunks, enabling resumption of the upload if
incomplete.
Update the UI with the progress of the upload.
| Frederick Muriuki Muriithi |
| 2024-06-27 | Fix bug with the logging setup. | Frederick Muriuki Muriithi |
| 2024-06-27 | Fix bugs in error-reporting. | Frederick Muriuki Muriithi |
| 2024-06-27 | Upload chunking: Provide UI and code for drag&drop and chunking...* Use resumable.js to handle the drag-and-drop feature, and chunking.
* Add styling for the drag-and-drop area, and provide visual
indication when a file is successfully dropped and added to the
upload list.
| Frederick Muriuki Muriithi |
