Integrating GitHub Copilot CLI with FHIR data via CData CLI

GitHub Copilot CLI is the terminal interface for GitHub Copilot, giving developers direct access to an AI agent without leaving the command line. It can autonomously complete multi-step tasks driven by natural language instructions, including reading and modifying files, running shell commands, managing pull requests on GitHub, and delegating work to specialized custom agents. Its support for agent skills and custom instructions makes it well-suited for structured, tool-driven workflows, making it a natural fit for connecting to external data sources through CData CLI.

By describing your data goals in plain language, GitHub Copilot CLI can handle the full setup process, from driver configuration and license activation to connection creation and query execution, without manual intervention at each step.

This article details step-by-step directions for how to connect FHIR data to GitHub Copilot CLI through CData CLI.

Prerequisites

1. GitHub Copilot CLI installed
2. CData CLI installed
3. Access to FHIR

Step 1: Download the skill (one-time setup)

Always use CData CLI with the official skill.

1. The official CData CLI Skill is available on GitHub and installs through npx skills in the terminal:

   npx skills add CDataSoftware/cli-skills

2. Follow the prompts in the terminal to install for GitHub Copilot. 👁 Install for GitHub Copilot
   

Step 2: Set up the project directory

Create a project directory to contain all project files.

1. Navigate to the directory within the terminal and start a session with the copilot command: 👁 Start a session
   👁 GitHub Copilot CLI UI
   

Step 3: Establish the driver and connection

Describe what you want to accomplish in this session with the CLI and FHIR data.

I would like to build a command line app that connects to FHIR data and checks for updates from Patient. Make sure to include data from important columns like Id and [name-use].

This prompt automatically loads the skill and kicks off the following process. You can always manually prompt the agent for each of the following steps.

1. Driver setup: GitHub Copilot CLI checks for an existing CData FHIR driver, or searches and downloads a new one:

• cdatacli drivers list

• cdatacli drivers search --driver "FHIR"

• cdatacli drivers download --artifact-id <artifact-id>

2. Activation: Activate the FHIR driver with a single command for a trial or full license:

• cdatacli drivers activate "FHIR" --name "<name>" --email "<email>" --trial

• cdatacli drivers activate "FHIR" --name "<name>" --email "<email>" --key "<product-key>"

3. Establish the FHIR connection: Check for existing FHIR connections or create a new one:

• cdatacli connection list

• cdatacli connection create --driver FHIR --name my_fhir_connection --connectionstring "Prop1=value1;Prop2=value2;..."

4. Create a FHIR skill (if applicable): CData provides driver instructions for popular sources. You can use these to generate a source-specific skill file that guides the agent through best practices for the driver.
• Run the following command and save the output to your skills directory, either at the project level or globally. (Note: If you receive a "No instructions available for FHIR" message, no driver instructions exist for this source. You can continue using the main driver skill.)

  cdatacli drivers skill "FHIR" > ~/skills/cdata-fhir/SKILL.md

Step 4: Query FHIR data

With the CData driver fully configured, your agent can now execute queries and write code against live FHIR data:

cdatacli query sql --connection my_fhir_connection --sql "SELECT * FROM Patient"

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Query FHIR data directly from your terminal with CData CLI

GitHub Copilot CLI and CData CLI together give your AI coding agent a direct path to live FHIR data without custom middleware, scheduled syncs, or manual setup at each step. Describe your goal in plain language, and the agent handles driver configuration, connection setup, and query execution from start to finish in the terminal.

Download the free CData CLI and start a free, 30-day trial of the CData JDBC Driver for FHIR today.