How to Access Live FHIR Data in Visual Studio Code via Cline

Cline is an autonomous coding agent right in your IDE, capable of creating/editing files, running commands, using the browser, and more with your permission every step of the way. When paired with CData Code Assist MCP for FHIR, you get live access to CRM data within your IDE, enabling you to build, test, and validate data-driven features using real-time schema and records without ever leaving your development environment.

CData Code Assist MCP provides schema-aware context to AI tools — whether you're using it for AI-assisted code generation in IDEs like Cursor and Cline, or for querying live data through chat interfaces like Claude Desktop.

This article outlines how to run CData Code Assist MCP for FHIR on WSL (Windows Subsystem for Linux) and connect to it from the Cline extension in Visual Studio Code on Windows.

Background

Code Assist MCP is typically designed for clients like Claude Desktop. However, when attempting to use it via the Cline extension in Windows VS Code, the following error occurred:

MCP error -32000: Connection closed

This issue is suspected to be caused by I/O handling problems in the stdio transport implementation on the Windows version of the Cline extension.

• Related GitHub Issue: https://github.com/cline/cline/issues/3464
• Additionally, environment variables such as PATH may not be inherited correctly when launching processes like Java or Node.

Prerequisites

• Visual Studio Code installed on Windows
• Cline extension installed and configured in VS Code
• Windows Subsystem for Linux (WSL) installed with a working Linux distribution (e.g., Ubuntu)
• Java 21+ JRE installed in WSL
• CData Code Assist MCP for FHIR installed on Windows

Step 1: Authenticate with FHIR (on Windows)

Before running Code Assist MCP in WSL, you must complete authentication flow in a Windows environment. This ensures all necessary credentials are generated and stored properly. Find and run "CData Code Assist MCP for FHIR" or execute the JAR file to open the configuration wizard.

java -jar "C:\Program Files\CData\CData Code Assist MCP for FHIR 20XX\lib\cdata.mcp.fhir.jar"

Connecting to FHIR

Set URL to the Service Base URL of the FHIR server. This is the address where the resources are defined in the FHIR server you would like to connect to. Set ConnectionType to a supported connection type. Set ContentType to the format of your documents. Set AuthScheme based on the authentication requirements for your FHIR server.

Generic, Azure-based, AWS-based, and Google-based FHIR server implementations are supported.

Sample Service Base URLs

• Generic: http://my_fhir_server/r4b/
• Azure: https://MY_AZURE_FHIR.azurehealthcareapis.com/
• AWS: https://healthlake.REGION.amazonaws.com/datastore/DATASTORE_ID/r4/
• Google: https://healthcare.googleapis.com/v1/projects/PROJECT_ID/locations/LOCATION/datasets/DATASET_ID/fhirStores/FHIR_STORE_ID/fhir/

Generic FHIR Instances

The product supports connections to custom instances of FHIR. Authentication to custom FHIR servers is handled via OAuth (read more about OAuth in the Help documentation. Before you can connect to custom FHIR instances, you must set ConnectionType to Generic.

Configuring Code Assist MCP

Name your configuration (e.g. cdatafhir), enter the required connection properties, and click "Connect."

👁 The Code Assist MCP configuration wizard (Google Sheets is shown).

Upon successful connection, the following directory and files will be created:

C:\Users\<username>\AppData\Roaming\CData\fhir Provider\
 |-- cdatafhir.mcp
 |-- (other supporting config files)

Step 2: Copy the Code Assist MCP Configuration into WSL

Next, copy the entire configuration folder from Windows into your WSL environment.

mkdir -p ~/.config/CData/
cp -r /mnt/c/Users/<username>/AppData/Roaming/CData/"fhir Provider" ~/.config/CData/

Ensure the destination path matches exactly: ~/.config/CData/fhir Provider/.

Step 3: Install Code Assist MCP on WSL

Install Java and place the Code Assist MCP JAR in the desired location within WSL:

sudo apt update
sudo apt install openjdk-21-jre-headless
sudo mkdir -p /opt/cdata/mcp_fhir/lib
sudo cp /mnt/c/Program\ Files/CData/CData\ Code\ Assist\ MCP\ for\ FHIR\ 20XX/lib/cdata.mcp.fhir.jar /opt/cdata/mcp_fhir/lib/

Step 4: Configure Cline

Now, configure the Cline extension to launch Code Assist MCP inside WSL using the wsl command.

Create or update cline_mcp_settings.json with the following content:

{
 "mcpServers": {
 "cdatafhir": {
 "autoApprove": ["*"],
 "disabled": false,
 "timeout": 60,
 "type": "stdio",
 "command": "wsl",
 "args": [
 "-d",
 "Ubuntu", // Replace with your installed WSL distro name
 "--",
 "/usr/bin/java",
 "-jar",
 "/opt/cdata/mcp_fhir/lib/cdata.mcp.fhir.jar",
 "cdatafhir"
 ],
 "env": {
 "JAVA_TOOL_OPTIONS": "-Xmx2g"
 }
 }
 }
}

Note: Replace Ubuntu with your actual WSL distribution name (e.g., Ubuntu-22.04). Run wsl -l in PowerShell or CMD to confirm.

Step 5: Interact with Live Data in Cline

From within Visual Studio Code, you can now run MCP commands through the Cline extension.

cdatafhir_get_tables
cdatafhir_get_columns Patient

If configured correctly, these commands will return a list of available FHIR objects and metadata, allowing you to interact with your CRM schema in real time.

Try natural language prompts like:

• "Generate a React form to create a new FHIR Lead."
• "Write a Python function to pull Opportunities closed this quarter."

Build with Code Assist MCP. Deploy with CData Drivers.

Download Code Assist MCP for free and give your AI tools schema-aware access to live FHIR data during development. When you're ready to move to production, CData FHIR Drivers deliver the same SQL-based access with enterprise-grade performance, security, and reliability.

Visit the CData Community to share insights, ask questions, and explore what's possible with MCP-powered AI workflows.