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AgeCommit message (Collapse)Author
2024-07-01Display error better.test-resumablejsFrederick 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.
2024-06-27Upload 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.
2024-06-14Add banner similar to GeneNetwork2Frederick Muriuki Muriithi
2024-06-14Fix minor UI bugsFrederick 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 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.
2024-04-12Consistently check for possibly non-existent dataFrederick Muriuki Muriithi
The "geno-dataset", "tissue", "pheno-study" and "pheno-dataset" data "objects" might not exist for a particular uploaded bundle, so we check in a consistent manner to ensure they are provided when needed.
2024-04-12Provide tissue-id details to probeset dataset templatesFrederick Muriuki Muriithi
2024-04-08Fix issues caught by integration tests.Frederick Muriuki Muriithi
2024-04-08bug: UI: Provide better error messaging.Frederick Muriuki Muriithi
2024-04-08bug: Handle IntegrityError: Studies cannot have same name.Frederick Muriuki Muriithi
2024-03-29Add UI to select/create tissue.Frederick Muriuki Muriithi
2024-03-20Use `url_for` to get icon.Frederick Muriuki Muriithi
2024-03-04Use `Id` rather than `ProbeFreezeId`.Frederick Muriuki Muriithi
2024-03-04Display flash messages correctly.Frederick Muriuki Muriithi
2024-02-15Provide only the file name, not full path.Frederick Muriuki Muriithi
There are 2 reasons to provide only the filename and not the full path: * Security: We do not want to inadvertently expose the paths to the outside world, or allow users to enter file system paths for this system. * The code does not assume a complete path, rather, it builds the path to the upload directory using the filename received from the user.
2024-02-14Provide endpoint to send data to.Frederick Muriuki Muriithi
2024-02-14Extract upload progress indication codeFrederick Muriuki Muriithi
* Extract the UI elements and code for indicating upload progress into separate, reusable "modules". * Fix bugs arising from changes.
2024-02-13Provide nice UI progress indicators.Frederick Muriuki Muriithi
2024-02-12Check for errors in the 'phenose' file.Frederick Muriuki Muriithi
2024-02-12Check for errors in the 'pheno' file.Frederick Muriuki Muriithi
2024-02-12Improve error display for generic errorsFrederick Muriuki Muriithi
2024-02-12Collect and display errors on 'geno' files in the bundle.Frederick Muriuki Muriithi
2024-02-12UI: Provide QC successful results pageFrederick Muriuki Muriithi
2024-02-12Retrive and display generic bundle errorsFrederick Muriuki Muriithi
Implement the first QC check for generic errors e.g. missing files in bundle, etc. Display retrieved errors on UI.
2024-02-12R/qtl2 QC: Set up scaffolding for QC UIFrederick Muriuki Muriithi
Set up the scaffolding for the flows and UI that will be used when running QC against the uploaded R/qtl2 bundle. This will be fleshed out later, and the UI is likely to change somewhat, down the line.
2024-02-07Fix error display: setup correct error classFrederick Muriuki Muriithi
2024-02-07Set up limits for inputs in UIFrederick Muriuki Muriithi
2024-02-06Bug: Fix routing issuesFrederick Muriuki Muriithi
Fix the routing issues that were redirecting the flow to the wrong endpoints.
2024-02-05Run QC on the 'geno' file in R/qtl2 bundle.Frederick Muriuki Muriithi
2024-02-05Do general bundle validation and show errorsFrederick Muriuki Muriithi
* Display any and all errors on the UI * Move `validate_bundle` to QC module and refactor to use `missing_files`
2024-02-05Update UI documentationFrederick Muriuki Muriithi
Improve the UI documentation by making it more explicit what each section deals with to help aleviate confusion of what the different features do.
2024-01-22UI: Fix some UI bugs.Frederick Muriuki Muriithi
2024-01-22scripts: Pass in logger to get detailed updates.Frederick Muriuki Muriithi
2024-01-22UI: Show progress of R/qtl2 bundle processing.Frederick Muriuki Muriithi
2024-01-20Fetch sample/case names from databaseFrederick Muriuki Muriithi
Fetch the sample/case names from the database rather than from a static file in the repository. Issue: https://issues.genenetwork.org/issues/quality-control/read-samples-from-database-by-species
2024-01-19UI: Present entry point for R/qtl2 bundles upload.Frederick Muriuki Muriithi
2024-01-18UI: Display summary information.Frederick Muriuki Muriithi