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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.
2024-02-07ShortName is optional, remove check and set defaultFrederick Muriuki Muriithi
The ShortName is optional, and can be set to the same value as Name. This commit removes the check that made it mandatory.
2024-02-07Prevent infinite redirect.Frederick Muriuki Muriithi
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
2024-02-05Fix linting and type errors.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.
2024-02-02Bug: Specify DictCursor class to return dict-like resultFrederick Muriuki Muriithi
Without specifying the `cursorclass`, the result is a tuple of the form: ((query_col01_val, query_col02_val, ...), ...) where the ellipsis specify the possibility of more than one of the previous form. We specify the DictCursor class instead so that the form changes to: ({query_col01_name: query_col01_val, ...}, ...) which allows us to pick the value we want with a string index.
2024-01-24Checks: Update code and tests to ensure all checks pass.Frederick Muriuki Muriithi
2024-01-24redis-prefix: update "upload samples" pathFrederick Muriuki Muriithi
2024-01-24redis-prefix: Update "insert data" path.Frederick Muriuki Muriithi
2024-01-24redis-prefix: Update file validation codeFrederick Muriuki Muriithi
Update the file validation script and routes to use the redis prefix for jobs.
2024-01-23Update scripts to use redis prefix.Frederick Muriuki Muriithi
2024-01-23Add prefix to redis keysFrederick Muriuki Muriithi
Since the GNQC application might find itself sharing the same redis server and/or database with other applications, add a prefix to its keys.
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
2024-01-19scripts: Process R/qtl2 bundleFrederick Muriuki Muriithi
Build script to start the processing of the R/qtl2 bundle.
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
2024-01-17Update flash-messages' categories.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.
2024-01-16Build a sha512 hash from the uploaded file's name and timestampFrederick Muriuki Muriithi
Build a sha512 message digest from the file's name and the timestamp of when the file was uploaded. This ensures that the filename is URL-safe, and reduces chances of name conflicts in the upload directory which could lead to data corruption when processing the files and saving the files into the database.
2024-01-15Update imports: `take` was moved to different package.Frederick Muriuki Muriithi
2024-01-08Fix errors with types.Frederick Muriuki Muriithi
2024-01-08Upload R/qtl2 zip bundle and check for errors.Frederick Muriuki Muriithi
2024-01-08Implement "create-population" route.Frederick Muriuki Muriithi
2024-01-08Implement "POST" path for "select-population" route.Frederick Muriuki Muriithi
2024-01-08Use extracted functions and fix bugsFrederick Muriuki Muriithi
2024-01-08Extract common database functions into a separate package.Frederick Muriuki Muriithi
2024-01-05Improve styling.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.
2023-12-20Reduce table columnsFrederick Muriuki Muriithi
Reduce the table columns displayed by javascript for the platforms.
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
2023-12-19Bug: Commit population before trying to upload data.Frederick Muriuki Muriithi