| Age | Commit message (Expand) | Author |
|---|
| 2024-09-03 | Update navigation scaffolding....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.
| Frederick Muriuki Muriithi |
| 2024-09-03 | Put populations under species: improve hierarchy....Populations cannot exist without the species they are related to. This
commit updates the URI hierarchy to reflect that expectation.
| Frederick Muriuki Muriithi |
| 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...* Use the more reliable 'Species.Id' field
* Provide more of a species' details
| Frederick Muriuki Muriithi |
| 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...The "gmap" file might not exist in some bundles. In those instances,
cross-reference the data without including the genotypes' physical
positions (cM).
| Frederick Muriuki Muriithi |
| 2024-08-12 | Bug: Ensure file type values are lists. | Frederick Muriuki Muriithi |
| 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 |
