clinical-reasoning: Instructions file for Codex

AGENTS.md

Project Overview

This is the CQF Clinical Reasoning on FHIR repository, which provides JVM-based, FHIR-enabled clinical reasoning components. The project implements FHIR Clinical Reasoning operations like Measure evaluation ($evaluate-measure), PlanDefinition application ($apply), and CQL evaluation capabilities.

See the ARCHITECTURE.md document for a detailed overview of the vision, architecture, design patterns, and coding standards used in this project.

Build and Test Commands

Building the Project

# Full build with tests
./gradlew build

# Build without tests
./gradlew assemble

# Compile only
./gradlew compileJava

# Parallel build (enabled by default via gradle.properties)
./gradlew build

Running Tests

# Run all tests
./gradlew test

# Run tests in a specific module
./gradlew :cqf-fhir-cr:test

# Run a single test class
./gradlew :MODULE:test --tests ClassName

# Run a single test method
./gradlew :MODULE:test --tests "ClassName.methodName"

# Run integration tests
./gradlew integrationTest

# Skip tests
./gradlew assemble

Code Formatting and Quality

# Check code formatting (runs in CI on PRs)
./gradlew spotlessCheck

# Apply code formatting fixes
./gradlew spotlessApply

# This project uses Palantir Java Format (configured in buildSrc convention plugins)
# Checkstyle runs automatically as part of the build

Linked Builds (Cross-Repo Development)

To build against a local checkout of a dependency (e.g., CQL Engine) instead of Maven Central:

# Copy the template and set paths to your local checkouts
cp local.properties.example local.properties

# Edit local.properties — uncomment and set the path:
# cql.engine.path=../clinical_quality_language

# Build as normal — the settings plugin detects local.properties and includes the linked build
./gradlew build

Available linked builds are listed in local.properties.example. The registry is defined in build-logic/src/main/kotlin/cqf/LinkedBuild.kt.