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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
2024-01-18UI: Create new ProbeSet dataset.Frederick Muriuki Muriithi
2024-01-18UI: Select from existing ProbeSet datasets.Frederick Muriuki Muriithi
2024-01-18Create new ProbeSet study.Frederick Muriuki Muriithi
2024-01-17UI: Select ProbeSet study.Frederick Muriuki Muriithi
2024-01-17UI: Implement creating new genotype datasets.Frederick Muriuki Muriithi
2024-01-17UI: Initialise summary page.Frederick Muriuki Muriithi