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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
2024-06-27Handle chunks on backend and update UI with progressFrederick Muriuki Muriithi
Handle the uploaded chunks, enabling resumption of the upload if incomplete. Update the UI with the progress of the upload.
2024-06-27Fix bug with the logging setup.Frederick Muriuki Muriithi
2024-06-27Fix bugs in error-reporting.Frederick Muriuki Muriithi
2024-06-27Upload chunking: Provide UI and code for drag&drop and chunkingFrederick Muriuki Muriithi
* 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.
2024-06-25Add route to fetch node-js modules.Frederick Muriuki Muriithi
2024-06-20Check for special files that might share names/extensionsFrederick Muriuki Muriithi
Check for special files and hidden files that might be inadvertently added to the zip bundle by the operating system in use that might share names and/or extensions with the main bundle files.
2024-06-14Add banner similar to GeneNetwork2Frederick Muriuki Muriithi
2024-06-14Fix minor UI bugsFrederick Muriuki Muriithi
2024-06-14Commit missing test.Frederick Muriuki Muriithi
2024-06-14Update page headingsFrederick Muriuki Muriithi
2024-06-14Remove unused template importsFrederick Muriuki Muriithi
2024-06-14Use bootstrap for displaying progress widgetFrederick Muriuki Muriithi
This commit converts the progress indication widget into a bootstrap modal dialog, and updates the javascript to prevent the code from interacting with bootstrap in unpredictable ways.
2024-06-14jquery, bootstrap: update page dependenciesFrederick Muriuki Muriithi
* Add jquery which is needed for bootstrap plugins. * Add the default bootstrap theme. * Provide route to serve up jquery libraries.
2024-06-14Move the modal to top of page to avoid display issuesFrederick Muriuki Muriithi
According to https://getbootstrap.com/docs/3.3/javascript/#callout-modal-markup-placement the bootstrap modal dialogs should be placed at the top of the page to avoid other components affecting their display and/or functionality.
2024-06-13Fix tests and issues caught by tests.update-templates-for-bootstrapFrederick Muriuki Muriithi
2024-06-13Handle HTTP errors gracefully.Frederick Muriuki Muriithi
2024-06-13Update the help text.Frederick Muriuki Muriithi
2024-06-13Clean up landing pageFrederick Muriuki Muriithi
Leave only data upload type selection on landing page.
2024-06-13Update html templates to use bootstrap for stylingFrederick Muriuki Muriithi
2024-06-12Update documentationFrederick Muriuki Muriithi
2024-06-12Update templates to use bootstrap classes.Frederick Muriuki Muriithi
2024-06-12Use bundled bootstrap for styling the UIFrederick Muriuki Muriithi
Use bootstrap to eliminate a myriad of UI styling headaches.
2024-06-12Make URI and UI correspond to each other.Frederick Muriuki Muriithi
Formerly, the URI and UI were not corresponding to each other, e.g. the URI /upload/samples/select_species would display the UI for selecting/creating the population. This was very confusing. This commit fixes that. The commit also adds in user input validation to catch input errors.
2024-06-12Bug: Provide missing argument. Remove unused verr variable.Frederick Muriuki Muriithi
2024-06-12Validate input before attempting to use it.Frederick Muriuki Muriithi
2024-06-12Provide an input validation module.Frederick Muriuki Muriithi
2024-05-05Fix indentation.Frederick Muriuki Muriithi
2024-05-05Provide default for InbredSetIdFrederick Muriuki Muriithi
The `InbredSetId` field in the `InbredSet` table in MariaDB is in some instances a required field, so we need to provide a value. This value should be the same as that for the `Id` field, that we do not previously know. This commit provides a value of zero (0) as the default. This value is subsequently updated to be same as that of the `Id` field.
2024-04-17Use `cursor.lastrowid` to get row identifierFrederick Muriuki Muriithi
Use the more robust `cursor.lastrowid` to get the row identifier value, rather than using the `SELECT MAX(Id) …` form. With the `cursor.lastrowid` form, we do not have to remember to add 1 to the value to avoid conflict.