SQL on FHIR analytics example project

Installation

docker compose up -d

docker compose log -f

This will start the following services:

• PostgreSQL
• Aidbox
• Grafana
• Jupyter

Open http://localhost:8080 and login into aidbox.

Open notebook

load data and install views

node init.js

Open grafana at http://localhost:3000 and login with admin/admin.

Create your view

Go to http://localhost:8080/ui/console#/sof

{
  "resource": "MedicationRequest",
  "id": "medreq",
  "name": "medreq",
  "status": "active",
  "select": [
    {
      "column": [
        {
          "name": "id",
          "path": "id",
          "type": "id"
        },
        {
          "name": "patient_id",
          "path": "subject.id",
          "type": "id"
        },
        {
          "name": "rxnorm_display",
          "path": "medication.ofType(CodeableConcept).coding.where(system='http://www.nlm.nih.gov/research/umls/rxnorm').display"
        },
        {
          "name": "rxnorm_code",
          "path": "medication.ofType(CodeableConcept).coding.where(system='http://www.nlm.nih.gov/research/umls/rxnorm').code"
        },
        {
          "name": "rest",
          "path": "$this"
        }
      ]
    }
  ]
}

Jupyter

Open http://localhost:8888 and open sql-on-fhir notebook.

Run mini app

node run dev
open http://localhost:7777