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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
2024-01-17Enable selecting from existing genotype datasets.Frederick Muriuki Muriithi
2024-01-16UI: Create UI for creating a new Genotype dataset.Frederick Muriuki Muriithi
2024-01-16UI: Create UI to select from existing genotype datasets.Frederick Muriuki Muriithi
2024-01-16Create intermediate stepFrederick Muriuki Muriithi
We do not have the option to modify the request and then redirect with the modification in place. To go around that, this commit creates an intermediate step that informs the user of their progress, while allowing us to store the filename for future steps.
2024-01-08Upload R/qtl2 zip bundle and check for errors.Frederick Muriuki Muriithi
2024-01-08Implement "POST" path for "select-population" route.Frederick Muriuki Muriithi
2024-01-05UI to select the population under which the data falls.Frederick Muriuki Muriithi
2024-01-05Initialise R/qtl2 bundle upload pathFrederick Muriuki Muriithi
Initialise the upload path for R/qtl2 bundles. This commit adds UI that allows the user to select from existing species, before proceeding to the next stage.
2023-12-20Add faviconFrederick Muriuki Muriithi
Add a favicon to reduce noise in the logs due to failed requests.
2023-12-19Commit missing templates.Frederick Muriuki Muriithi
2023-12-07Samples: Read an save data to db.Frederick Muriuki Muriithi