| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 2024-08-21 | Save errors for each file in lists. Parallelise error checking.rewrite-rqtl2-qc | Frederick Muriuki Muriithi | |
| * Save the errors for each file in a redis list for that file. * Make error checking parallel, i.e. ensure every file of a particular type is checked completely independent of other files of the same type. | |||
| 2024-08-16 | Rewrite the QC code for R/qtl2 | Frederick Muriuki Muriithi | |
| 2024-08-16 | Ignore comment lines. | Frederick Muriuki Muriithi | |
| 2024-08-16 | Log out correct parameters. | Frederick Muriuki Muriithi | |
| 2024-08-13 | Bug: cross reference with NULL cM when "gmap" file is absent | Frederick 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). | |||
| 2024-08-12 | Bug: Ensure file type values are lists. | Frederick Muriuki Muriithi | |
| 2024-08-12 | Update 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. | |||
| 2024-08-12 | Add utility to transpose CSVs, renaming the original file. | Frederick Muriuki Muriithi | |
| 2024-08-12 | Define 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. | |||
| 2024-08-12 | 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. | 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. | |||
| 2024-08-08 | 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. | Frederick Muriuki Muriithi | |
| Set up logging for the application to help with debugging issues. | |||
| 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 | Frederick Muriuki Muriithi | |
| Pass the logger forward to inner functions to help with debugging things. | |||
| 2024-08-06 | Override `client_secret_post`: use JSON | Frederick 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. | |||
| 2024-08-06 | Avoid hitting auth server to check for token | Frederick 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. | |||
| 2024-08-05 | Fix token revocation | Frederick Muriuki Muriithi | |
| Token revocation was failing due to missing hint. | |||
| 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 | Frederick Muriuki Muriithi | |
| Put all endpoints that cause data changes behind authorisation. | |||
| 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 | Frederick Muriuki Muriithi | |
| * Call the correct __post__ function * Set up the headers appropriately | |||
| 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 | Frederick Muriuki Muriithi | |
| QCAPP_CONF --> UPLOADER_CONF | |||
| 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 | Frederick Muriuki Muriithi | |
| Adds utilities to handle talking to the authentication/authorisation server. | |||
| 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 | Frederick 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. | |||
| 2024-07-02 | 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 | |
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| gn-uploader: Data uploader for GeneNetwork |
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