| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 2024-09-05 | Provide basic UI for editing the Species details. | Frederick Muriuki Muriithi | |
| 2024-09-05 | Improve error messaging for "Create Population" feature. | Frederick Muriuki Muriithi | |
| 2024-09-05 | Synchronise token refreshing. | Frederick Muriuki Muriithi | |
| When running flask with multiple threads/workers, as happens when using gunicorn, there is a potential for more than one thread running with an expired token, leading to multiple uncoordinated token refreshes. This commit coordinates the threads in the case there is need to refresh a token, ensuring only one thread does the token refresh. | |||
| 2024-09-04 | Provide 'edit species' endpoint | Frederick Muriuki Muriithi | |
| * Verify new authorisation wrapper works as expected. | |||
| 2024-09-04 | Provide top-level navigation placeholder link. | Frederick Muriuki Muriithi | |
| 2024-09-04 | Introduce wrapper that validates tokens | Frederick Muriuki Muriithi | |
| Validate token and pass it on to functions that require more fine-grained authorisation checks. | |||
| 2024-09-04 | Update retrival of JSON Web Keys | Frederick Muriuki Muriithi | |
| * Introduce the function `auth_server_jwks()` to use for fetching the keys from the session if present, or from the server when absent or out-of-date. It also handles updating the keys in the session. * Remove the unnecessary verification of JWKs until the point where that is needed, i.e. at the point(s) where there is need to verify authorisation. | |||
| 2024-09-04 | Add function to update the JSON Web Keys in the session | Frederick Muriuki Muriithi | |
| When new JSON Web Keys (JWKs) are fetched from the server, the function added in this commit will help with updating them in the session for subsequent uses, validating the tokens when needed. | |||
| 2024-09-04 | Improve styling. | Frederick Muriuki Muriithi | |
| 2024-09-04 | Create populations (InbredSet groups) under Species. | Frederick Muriuki Muriithi | |
| 2024-09-03 | Improve UI copy. | Frederick Muriuki Muriithi | |
| 2024-09-03 | Display any error messages. | Frederick Muriuki Muriithi | |
| 2024-09-03 | View a specific population's details. | Frederick Muriuki Muriithi | |
| 2024-09-03 | Improve UI styling. | Frederick Muriuki Muriithi | |
| 2024-09-03 | Provide means to debug actual query run and params used. | Frederick Muriuki Muriithi | |
| 2024-09-03 | Update 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. | |||
| 2024-09-03 | Put 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. | |||
| 2024-09-03 | Initialise the populations package and update references. | Frederick Muriuki Muriithi | |
| 2024-09-03 | Extract common UI pattern to separate module for reusability. | Frederick Muriuki Muriithi | |
| 2024-09-03 | Provide generic way to select species. | Frederick Muriuki Muriithi | |
| 2024-09-03 | Provide UI for viewing species details. | Frederick Muriuki Muriithi | |
| 2024-09-03 | Enable third level of breadcrumbs. | Frederick Muriuki Muriithi | |
| 2024-09-03 | Update species queries | Frederick Muriuki Muriithi | |
| * Use the more reliable 'Species.Id' field * Provide more of a species' details | |||
| 2024-09-03 | Save a species to the database. | Frederick Muriuki Muriithi | |
| 2024-09-03 | Put active pages behind auth. Flash all error messages. | Frederick Muriuki Muriithi | |
| 2024-08-30 | Initialise package for dealing with Species. | Frederick Muriuki Muriithi | |
| 2024-08-28 | Fix imports, and minor bugs. | Frederick Muriuki Muriithi | |
| 2024-08-28 | Move code handling expression data upload into new module. | Frederick Muriuki Muriithi | |
| 2024-08-28 | Rework UI: present menus on the left, content on the right. | 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 | |
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index : gn-uploader | |
| gn-uploader: Data uploader for GeneNetwork |
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