This is the code repository for www.iddynamics.jhsph.edu/covid/dashboard, an interactive tool for visualizing COVID-19 intervention scenario models produced by the Johns Hopkins University's Infectious Disease Dynamics Working Group (IDD Working Group) in support of the COVID-19 operational response of federal and state agencies.

Public health decision makers look to epidemiological models for decision support in allocating resources, developing non-pharmaceutical interventions, and characterizing the dynamics of COVID-19 in their jurisdictions. In response, the IDD Working Group developed a flexible scenario modeling pipeline that could quickly tailor models for decision makers seeking to compare projections of epidemic trajectories and healthcare impacts from multiple intervention scenarios in different locations. This interactive tool visualizes those models to expedite data exploration and decision making for municipal emergency response.

Summary

• Getting Started
• Deployment
• Bugs and Feature Requests
• Troubleshooting
• Future Work
• License

Getting Started

Prerequisites

npm >= 10.22.0

Development

If you would like to contribute to this project, set up your local development environment like so:

# install node dependencies
$ npm init

# spin up local dev server
$ npm start

Testing with local data files

Currently the data files are being fetched from the IDD Working Group's s3 bucket idd-dashboard-runs. However, if you would like to test your own data files or change the data format for testing, drop the new data files into the store directory and indicate in store/config.tsx which data files should use the local copy. For example, if you would like to use a local countyBoundaries files for testing, indicate like so:

export const CONFIGS = {
    'outcomes': {
        'use_local': false,
        'file_name': ''
    },
    'statsForMap': {
        'use_local': false,
        'file_name': ''
    },
    'countyBoundaries': {
        'use_local': true,
        'file_name': 'countyBoundaries_to_test.json'
    }
}

Deployment

Currently, on each merge into master, the GitHub Actions workflow defined in s3.yml gets kicked off.

1. This workflow builds the website static artifacts
2. The workflow also syncs the build files into the staging s3 bucket
3. The data files listed in the table below are expected to be present in the json-files key prefix of the staging s3 bucket
4. The IDD Working Group will run the validator (the source of truth lives in scripts/validate.py) to ensure all JSON files abide by the expected data format. Once validation is complete, these JSON files will be pushed into the staging bucket json_output key.
5. Once the staging website has been user tested and QA-ed, the IDD Working Group will push the contents of the staging bucket into the production bucket via aws s3 cp --recursive s3://idd-dashboard-runs-staging s3://idd-dashboard-runs

Data Files Expected in S3 Bucket

The IDD Working Group will produce new model runs ~1/week. After running the validator (scripts/validate.py) to confirm expected data format, the data files will be pushed to the staging s3 bucket. If any of the data files below are missing from the bucket, contact the IDD Working Group.

A working copy of each JSON file is provided in /store as an example of the expected structure.

Staging and Production Buckets

Bugs and Feature Requests

Feel free to submit an issue or feature request on the GitHub repository.

For issues, please be sure to include a summary of the issue and the steps to reproduce the issue. For feature requests, please add as much detail as you can when doing so. If you wish, you are more than welcome to suggest a patch and open a PR to address an issue or feature request!

Troubleshooting

403 Access Denied

If you are trying to reach the endpoint iddynamics.jhsph.edu/covid/dashboard and Amazon S3 returns a 403 Access Denied error, check the following:

• Block Public Access is turned off
• Static website hosting has been enabled
• Ensure the account that owns the bucket also owns all objects in bucket aws s3api get-object-acl --bucket idd-dashboard-runs --key index.html The AWS secret keys stored in this repo should belong to the owner of the s3 bucket
• Bucket policy allows s3:GetObject for all

  {
  "Sid": "Stmt..",
  "Effect": "Allow",
  "Principal": "*",
  "Action": "s3:GetObject",
  "Resource": "arn:aws:s3:::idd-dashboard-runs/*"
  }

Additional information can be found in the aws docs.

Data Unavailable Error Message

This message will occur if the selected county does not exists or if the file isn't formatted in a structure that the web app exists.

1. Confirm that 060852.json does exist in s3 bucket idd-dashboard-runs-staging
2. Try to select a different county or state from the dropdown. It's possible the one county selected is unavailable while other counties are available.
3. If all counties you are interested in are unavailable, contact the Hopkins IDD Working Group to ensure your county files exist in the s3 bucket and that the data files have all been run through the validator script.

Fetch was Problematic

If you suspect that a specific data file being fetched from the s3 bucket is preventing the web app from compiling, you can debug by making changes to the config.tsx:

1. On localhost, substitute out the idd-dashboard-runs-staging bucket for the covid-scenario-dashboard bucket which contains previous data that should compile completely. If localhost compiles successfully, you've confirmed that the problem is a data issue.

   export const s3BucketUrl = process.env.NODE_ENV === 'development' ?
           'https://idd-dashboard-runs-staging.s3.amazonaws.com/json-files/'
           //'https://covid-scenario-dashboard.s3.amazonaws.com/json-files/'
           : 'json-files/'; 

2. You can dig in deeper by isolating which data file is problematic. In the store/ directory, a working copy of all required data files for testing have been provided. You can substitute each one out to figure out which is the culprit. For example, if I suspect the geoid file, I will set USE_LOCAL_GEOID to true and LOCAL_GEOID to 06085.json, which has been provided in store/. If localhost compiles successfully, I know that there is a problem with the 06085.json file in the staging s3 bucket idd-dashboard-runs-staging.

   
   export const USE_LOCAL_GEOID = true
   export const LOCAL_GEOID = '06085.json'

export const USE_LOCAL_ACTUALS = false export const LOCAL_ACTUALS = '' // '06085_actuals.json'

// static files export const CONFIGS = { 'outcomes': { 'use_local': false, 'file_name': '' // 'outcomes.json' }, 'statsForMap': { 'use_local': false, 'file_name': '' // 'statsForMap.json' }, 'countyBoundaries': { 'use_local': false, 'file_name': '' // 'countyBoundaries.json' } }

## Future Work
- Add Testing Framework
- Finish TypeScript Migration
- Add Redux

## License

GNU GENERAL PUBLIC LICENSE Version 3, 29 June 2007

Copyright (C) 2007 Free Software Foundation, Inc. https://fsf.org/

Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed.