| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 2024-06-14 | Remove unused template imports | Frederick Muriuki Muriithi | |
| 2024-06-14 | Use bootstrap for displaying progress widget | Frederick 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. | |||
| 2024-06-14 | jquery, bootstrap: update page dependencies | Frederick Muriuki Muriithi | |
| * Add jquery which is needed for bootstrap plugins. * Add the default bootstrap theme. * Provide route to serve up jquery libraries. | |||
| 2024-06-14 | Move the modal to top of page to avoid display issues | Frederick 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. | |||
| 2024-06-13 | Fix tests and issues caught by tests.update-templates-for-bootstrap | Frederick Muriuki Muriithi | |
| 2024-06-13 | Handle HTTP errors gracefully. | Frederick Muriuki Muriithi | |
| 2024-06-13 | Update the help text. | Frederick Muriuki Muriithi | |
| 2024-06-13 | Clean up landing page | Frederick Muriuki Muriithi | |
| Leave only data upload type selection on landing page. | |||
| 2024-06-13 | Update html templates to use bootstrap for styling | Frederick Muriuki Muriithi | |
| 2024-06-12 | Update templates to use bootstrap classes. | Frederick Muriuki Muriithi | |
| 2024-06-12 | Use bundled bootstrap for styling the UI | Frederick Muriuki Muriithi | |
| Use bootstrap to eliminate a myriad of UI styling headaches. | |||
| 2024-06-12 | Make 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. | |||
| 2024-04-12 | Consistently check for possibly non-existent data | Frederick 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. | |||
| 2024-04-12 | Provide tissue-id details to probeset dataset templates | Frederick Muriuki Muriithi | |
| 2024-04-08 | Fix issues caught by integration tests. | Frederick Muriuki Muriithi | |
| 2024-04-08 | bug: UI: Provide better error messaging. | Frederick Muriuki Muriithi | |
| 2024-04-08 | bug: Handle IntegrityError: Studies cannot have same name. | Frederick Muriuki Muriithi | |
| 2024-03-29 | Add UI to select/create tissue. | Frederick Muriuki Muriithi | |
| 2024-03-20 | Use `url_for` to get icon. | Frederick Muriuki Muriithi | |
| 2024-03-04 | Use `Id` rather than `ProbeFreezeId`. | Frederick Muriuki Muriithi | |
| 2024-03-04 | Display flash messages correctly. | Frederick Muriuki Muriithi | |
| 2024-02-15 | Provide 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. | |||
| 2024-02-14 | Provide endpoint to send data to. | Frederick Muriuki Muriithi | |
| 2024-02-14 | Extract upload progress indication code | Frederick Muriuki Muriithi | |
| * Extract the UI elements and code for indicating upload progress into separate, reusable "modules". * Fix bugs arising from changes. | |||
| 2024-02-13 | Provide nice UI progress indicators. | Frederick Muriuki Muriithi | |
| 2024-02-12 | Check for errors in the 'phenose' file. | Frederick Muriuki Muriithi | |
| 2024-02-12 | Check for errors in the 'pheno' file. | Frederick Muriuki Muriithi | |
| 2024-02-12 | Improve error display for generic errors | Frederick Muriuki Muriithi | |
| 2024-02-12 | Collect and display errors on 'geno' files in the bundle. | Frederick Muriuki Muriithi | |
| 2024-02-12 | UI: Provide QC successful results page | Frederick Muriuki Muriithi | |
| 2024-02-12 | Retrive and display generic bundle errors | Frederick Muriuki Muriithi | |
| Implement the first QC check for generic errors e.g. missing files in bundle, etc. Display retrieved errors on UI. | |||
| 2024-02-12 | R/qtl2 QC: Set up scaffolding for QC UI | Frederick 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. | |||
| 2024-02-07 | Fix error display: setup correct error class | Frederick Muriuki Muriithi | |
| 2024-02-07 | Set up limits for inputs in UI | Frederick Muriuki Muriithi | |
| 2024-02-06 | Bug: Fix routing issues | Frederick Muriuki Muriithi | |
| Fix the routing issues that were redirecting the flow to the wrong endpoints. | |||
| 2024-02-05 | Run QC on the 'geno' file in R/qtl2 bundle. | Frederick Muriuki Muriithi | |
| 2024-02-05 | Do general bundle validation and show errors | Frederick Muriuki Muriithi | |
| * Display any and all errors on the UI * Move `validate_bundle` to QC module and refactor to use `missing_files` | |||
| 2024-02-05 | Update UI documentation | Frederick 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. | |||
| 2024-01-22 | UI: Fix some UI bugs. | Frederick Muriuki Muriithi | |
| 2024-01-22 | scripts: Pass in logger to get detailed updates. | Frederick Muriuki Muriithi | |
| 2024-01-22 | UI: Show progress of R/qtl2 bundle processing. | Frederick Muriuki Muriithi | |
| 2024-01-20 | Fetch sample/case names from database | Frederick 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 | |||
| 2024-01-19 | UI: Present entry point for R/qtl2 bundles upload. | Frederick Muriuki Muriithi | |
| 2024-01-18 | UI: Display summary information. | Frederick Muriuki Muriithi | |
| 2024-01-18 | UI: Create new ProbeSet dataset. | Frederick Muriuki Muriithi | |
| 2024-01-18 | UI: Select from existing ProbeSet datasets. | Frederick Muriuki Muriithi | |
| 2024-01-18 | Create new ProbeSet study. | Frederick Muriuki Muriithi | |
| 2024-01-17 | UI: Select ProbeSet study. | Frederick Muriuki Muriithi | |
| 2024-01-17 | UI: Implement creating new genotype datasets. | Frederick Muriuki Muriithi | |
| 2024-01-17 | UI: Initialise summary page. | Frederick Muriuki Muriithi | |
 |
index : gn-uploader | |
| gn-uploader: Data uploader for GeneNetwork |
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