FHIR Cohort Data Transformer

The FHIR Cohort Data Transformer is a TypeScript tool designed to transform cohort-study data into FHIR-compliant data. This tool allows you to specify and test the pairing rules between the cohort-study data and the properties of a given FHIR resource. Once you have defined these rules, you can link them to one or more FHIR-compliant templates.

Features

• Transform cohort-study data into FHIR-compliant data
• Allows the definition of pairing rules between cohort-study data and FHIR resource properties
• Paring rules are specified in independent modules to make them testeable

Prerequisites

To use this tool, ensure you have the following installed:

• Node.js (version 12 or higher)
• npm (Node Package Manager)
• TypeScript (installed globally)

Installation

1. Clone the repository from GitHub:

git clone https://github.com/your-username/fhir-cohort-data-transformer.git

2. Navigate to the project directory:

cd fhir-cohort-data-transformer

3. Install the dependencies:

npm install

4. Compile

tsc

Usage

1. To create new pairing rules or JSON output-templates, refer to the developer manual.

• To run the unit tests :

  npm test

• To run the linter :

  npm run lint

• To transform the available input samples (./fhirvalidation/sampleinputs), and check the validity of their corresponding transformations against a FHIR profile:

  npm run validatesamples

2. To preview a transformation of a given input

   • Start the viewer server

   npm run dev-viewer
   

   • Open editor at http://localhost:3000

3. Tp generate FHIR-compliant data based on the rules already defined, and the mapping configuration:

#Transform a single file, print the ouput to STDOUT
npm run transform -- ./fhirvalidation/sampleinputs/input-p1234.json
#Transform a single file, save the output on the given folder
npm run transform -- ./fhirvalidation/sampleinputs/input-p1234.json -o /tmp/out
#Transform all the .json files in a given folder, save the output on the given folder
npm run transform -- ./fhirvalidation/sampleinputs -o /tmp/out

End-user and Developer documentation

The developer documentation with the description of the tool design, and further details for creating new templates/pairing rules can be found here (still under development).