cdf2medmij-mapping-tool
Tool for transforming Cohort-study Data (CDF) into FHIR/MedMij compliant resource bundles
Science Score: 44.0%
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Low similarity (13.2%) to scientific vocabulary
Repository
Tool for transforming Cohort-study Data (CDF) into FHIR/MedMij compliant resource bundles
Basic Info
Statistics
- Stars: 1
- Watchers: 2
- Forks: 0
- Open Issues: 8
- Releases: 0
Metadata Files
README.md
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
- Clone the repository from GitHub:
bash
git clone https://github.com/your-username/fhir-cohort-data-transformer.git
- Navigate to the project directory:
bash
cd fhir-cohort-data-transformer
- Install the dependencies:
bash
npm install
- Compile
bash
tsc
Usage
- To create new pairing rules or JSON output-templates, refer to the developer manual.
- To run the unit tests :
bash
npm test
- To run the linter :
bash
npm run lint
* To transform the available input samples (./fhirvalidation/sampleinputs), and check the validity of their corresponding transformations against a FHIR profile:
bash
npm run validatesamples
- To preview a transformation of a given input
- Start the viewer server
npm run dev-viewer - Open editor at http://localhost:3000
- Tp generate FHIR-compliant data based on the rules already defined, and the mapping configuration:
```bash
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).
Owner
- Name: MyDigiTwinNL
- Login: MyDigiTwinNL
- Kind: organization
- Repositories: 1
- Profile: https://github.com/MyDigiTwinNL
Citation (CITATION.cff)
cff-version: 1.2.0
title: CDF2FHIR
message: >-
If you use this software, please cite it using the
metadata from this file.
type: software
authors:
- given-names: Héctor
family-names: Cadavid
email: h.cadavid@esciencecenter.nl
orcid: 'https://orcid.org/0000-0003-4965-4243'
url: "https://github.com/MyDigiTwinNL/CDF2Medmij-Mapping-tool"
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