| Age | Commit message (Expand) | Author |
|---|
| 2024-06-27 | Handle chunks on backend and update UI with progress...Handle the uploaded chunks, enabling resumption of the upload if
incomplete.
Update the UI with the progress of the upload.
| Frederick Muriuki Muriithi |
| 2024-06-27 | Upload chunking: Provide UI and code for drag&drop and chunking...* 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.
| Frederick Muriuki Muriithi |
| 2024-06-14 | Add banner similar to GeneNetwork2 | Frederick Muriuki Muriithi |
| 2024-06-14 | Fix minor UI bugs | Frederick Muriuki Muriithi |
| 2024-06-14 | Update page headings | Frederick Muriuki Muriithi |
| 2024-06-14 | Remove unused template imports | Frederick Muriuki Muriithi |
| 2024-06-14 | Use bootstrap for displaying progress widget...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.
| Frederick Muriuki Muriithi |
| 2024-06-14 | jquery, bootstrap: update page dependencies...* Add jquery which is needed for bootstrap plugins.
* Add the default bootstrap theme.
* Provide route to serve up jquery libraries.
| Frederick Muriuki Muriithi |
| 2024-06-14 | Move the modal to top of page to avoid display issues...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.
| Frederick Muriuki Muriithi |
| 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...Leave only data upload type selection on landing page.
| Frederick Muriuki Muriithi |
| 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...Use bootstrap to eliminate a myriad of UI styling headaches.
| Frederick Muriuki Muriithi |
| 2024-06-12 | Make URI and UI correspond to each other....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.
| Frederick Muriuki Muriithi |
| 2024-04-12 | Consistently check for possibly non-existent data...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.
| Frederick Muriuki Muriithi |
| 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....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.
| Frederick Muriuki Muriithi |
| 2024-02-14 | Provide endpoint to send data to. | Frederick Muriuki Muriithi |
| 2024-02-14 | Extract upload progress indication code...* Extract the UI elements and code for indicating upload progress into
separate, reusable "modules".
* Fix bugs arising from changes.
| Frederick Muriuki Muriithi |
| 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...Implement the first QC check for generic errors e.g. missing files in
bundle, etc. Display retrieved errors on UI.
| Frederick Muriuki Muriithi |
| 2024-02-12 | R/qtl2 QC: Set up scaffolding for QC UI...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.
| Frederick Muriuki Muriithi |
| 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...Fix the routing issues that were redirecting the flow to the wrong
endpoints.
| Frederick Muriuki Muriithi |
| 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...* Display any and all errors on the UI
* Move `validate_bundle` to QC module and refactor to use
`missing_files`
| Frederick Muriuki Muriithi |
| 2024-02-05 | Update UI documentation...Improve the UI documentation by making it more explicit what each
section deals with to help aleviate confusion of what the different
features do.
| Frederick Muriuki Muriithi |
| 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...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
| Frederick Muriuki Muriithi |
| 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 |
