@papaemmelab/isabl-report

Isabl Reports

Frontend to visualize results for MSK Kids Reports and RNA Data Expression at cohort level.

How to use

nvm use v18.16.1     # Use a node working version
npm install -g yarn  # Install yarn

yarn install     # Install dependencies
yarn dev         # Run web server

You might need to add your isabl auth token to the the browser local storage for development purposes:

// Run in your browser console
localStorage.setItem('user-token', <your-isabl-auth-token>)

Setup backend

You need an isabl backend to run the dashboard.

# Clone Repo and checkout to the proper branch
git clone https://github.com/papaemmelab/isabl_msk
cd isabl_msk
git checkout isabl_dashboard # or `master` or the branch you want to use

# Build containers and run (uses -f local.yml by default)
docker-compose build
docker-compose up -d

# See the logs
docker-compose logs -f

Create Test Data for development

• For the RNA Dashboard:

You might need to get these 3 files from production, which you can find in a SALMON_GENCODE Project-level Application (gene_level.feather), and in a WGTS_REPORT Project-level Application (tsne_blood.feather and tsne_solid.feather)

isabl_msk
└── isabl_dashboard
  └──  tests
    └── data
      ├── gene_level.feather
      ├── tsne_blood.feather
      └── tsne_solid.feather

• For the PTMP Reports:

You need to create both new Inviduals and WGTS_REPORT (3.0.0) Individual-level Analyses with json results for report, where you link it to a real report file from production.

For example:

1. Copy real json results from WGTS_REPORT in production:

   isabl_msk
   └── isabl_dashboard
     └──  tests
       └── data
         ├── DEV_000001.json
         ├── DEV_000002.json
         └── DEV_000003.json
   

2. Create a new Application with name WGTS_REPORT and version 3.0.0

3. Create a new Individual. i.e Individual(DEV_000001).

4. Create a new Analysis, whose Project-level key is the new Individual and the new Application you just created. Set its status to SUCCEEDED, and finally link the json file to its results:

   {
       "json": "/app/isabl_dashboard/tests/data/DEV_000001.json"
   }

   Note: The /app location is where the isabl_msk code its located inside the docker compose container.

You should be now ready to go! 🚀

📦 Deploy to NPM

yarn deploy