FHIR to OMOP Conversion

Created a modular Node.js/TypeScript program that converts FHIR data to OMOP CDM format.

User Registration:

• Email and password registration

• Password confirmation

• Error handling

• Navigation to converter after successful registration

Forgot Password:

• Email input for password reset

• Success/error messages

• Link back to login

Reset Password:

• New password and confirmation inputs

• Handles reset token from URL

• Redirects to login after successful reset

Enhanced Login:

• Added links to registration and forgot password

• Improved error handling

• Better UI/UX with Material-UI components

Updated Auth Context:

• Added password reset functions

• Improved type safety

• Better error handling

The application now has a complete authentication flow with proper validation and error handling. Users can register, login, reset their password, and securely access the converter.

Here's what each file does:

• src/index.ts: Main entry point that sets up the database and runs the converter
• src/database.ts: Database setup using SQLite (in-memory for demo) with OMOP schema
• src/converter.ts: Core conversion logic with type validation using Zod
• src/sample-data.ts: Sample FHIR data for testing
• src/tests/converter.test.ts: Unit tests for the converter

Key features:

• Type safety with TypeScript

• Data validation using Zod

• SQLite database with Knex.js ORM

• Unit testing with Vitest

• Modular design for easy expansion

• Currently implements Patient → Person conversion. To extend:

• Add more OMOP tables in database.ts

• Create new conversion methods in converter.ts

• Add schemas for other FHIR resources

• Implement vocabulary mapping service

Added a modern React-based UI with Material-UI components that includes:

Split-pane view with FHIR input and OMOP output
JSON formatting for better readability
Error handling and loading states
Sample data reset button
Clean, responsive design
Syntax-highlighted text areas
Real-time conversion
The UI allows you to:

Edit FHIR patient data in JSON format Convert it to OMOP format with a single click View the conversion results Reset to sample data if needed See any validation errors or conversion issues To run:

Tests: npm test
Program: npm start

To run the docker immage

npm install
npm run dev
docker-compose up -d
docker run -p 3000:3000 fhir_omop

Example FHIR buddles are given to check the installation.

AMedicationDispenseBundle.json
CompleteDischageSummary.json
DiagnosticreportBudle.json
EncounterMultipleDiagnosis.json
ImmunizationBudle.json
MinimalPatientandObservationBundle.json
SearchsetBundle.json
TransactionBundle.json
simpleCollectionBundle.json

To learn Typescript follow https://basarat.gitbook.io/typescript/getting-started