/multi-param-query-builder-cellular-assays

Primary LanguageJavaScript

Compound Comparison Tool

This React app uses the following technologies:

  • ReactJS
  • fastapi (backend)

Summary

The React app is a web application that is built using ReactJS, a popular JavaScript library for building user interfaces. The app is designed to fetch and display data related to various types of assays performed on FT/KIN compounds, and export as a .csv file. The app allows users to select various parameters for the assay, including the compound ID, the CRO, the cell incubation hour, the cell assay type, and the percentage serum. The backend generates a dynamic SQL string that joins multiple compound ids together based on the selected parameters. The output allows scientists to quickly compare what assays have been performed on what compounds and their respective geomean values.

Technical

This is only the frontend UI. The geomean fastapi python backend https://github.com/Kinnate/geomean-ic50-flagger.git is used to generate the SQL and run it against the connected Oracle database. The application was deployed using Jenkins CI/CD pipline. The Jenkinsfile can be inspected to understand what is performed. Basically, the docker image is built, then pushed to ECR, then deployed using helm. The app lives in the main apps namespace within helm as well as kubectl. Run kubectl get all -n apps -l app=compound-comparison-tool to get the kubernetes resources. Currently, the app can be visited by navigating to: http://compound.comparison.kinnate. The only parts that this frontend relies on is the backend's compound_id, cros, cell_incubation_hr, cell_line, cell_assay_type, pct_serum, variant and the main sql function: gen_multi_cmpId_sql_template_cell(). There are several scheduled tasks that run in the background every couple hours to refresh new parameters such as: FT numbers or cell lines, etc.

Additional notes

Once jenkins deploys the app and the pods and services are running the next step is to expose the application through a kubernetes nginx ingress. Just as in any other app, one must add a new ingress rule to the ingress yaml file. This can be obtained by running: kubectl get ingress -o yaml and applyling it locally, or editing the yaml on the fly (expert user) like so: kubectl edit ingress -n apps. The ingress rule block should resemble something like:

    - host: $APP_NAME.kinnate
      http:
        paths:
          - path: /
            pathType: Prefix
            backend:
              service:
                name: $APP_NAME-svc
                port:
                  name: http

Then ensure this A-record is added to Route 53 with the appropriate LoadBalancer name as the Route traffic to value.