Trying to fix basic functionality again.

Dockerfile

@@ -0,0 +1,70 @@
+FROM eclipse-temurin:17-jdk
+
+WORKDIR /app
+
+# Install Python and dependencies
+RUN apt-get update && apt-get install -y \
+    python3 \
+    python3-pip \
+    python3-venv \
+    git \
+    && rm -rf /var/lib/apt/lists/*
+
+# Set up Python virtual environment
+RUN python3 -m venv /opt/venv
+ENV PATH="/opt/venv/bin:$PATH"
+
+# Install Anthropic and tqdm in the virtual environment
+RUN pip3 install --no-cache-dir "anthropic>=0.8.1,<0.9.0" tqdm==4.66.2 python-dotenv==1.0.1
+
+# Clone the official Synthea repository directly into /app
+RUN git clone https://github.com/synthetichealth/synthea.git /app-temp && \
+    cp -r /app-temp/* /app/ && \
+    rm -rf /app-temp
+
+# Create directory structure for our custom modules and python scripts
+RUN mkdir -p /app/module_generator \
+    /app/output \
+    /app/src/main/resources/modules 
+
+# First build the project with the official modules - this will compile the Java code
+RUN ./gradlew build -x test
+
+# Make the run_synthea script executable
+RUN chmod +x /app/run_synthea
+
+# Copy our Python scripts and module generators
+COPY module_generator/*.py /app/module_generator/
+COPY src/main/resources/modules/* /app/src/main/resources/modules/
+COPY src/main/resources/disease/* /app/src/main/resources/
+COPY scripts/* /app/scripts/
+
+# Make scripts executable
+RUN chmod +x /app/module_generator/*.py /app/scripts/*
+
+# Verify and fix module JSON structures
+RUN python3 /app/scripts/check_condition_structure.py --modules_dir /app/src/main/resources/modules --verbose
+# Create a directory for modules that will be mounted from the host
+RUN mkdir -p /app/modules
+
+# Test a simple module generation to ensure Synthea works
+RUN ./run_synthea -p 1 -m hypertension
+
+# Set up a symlink from mounted modules to Synthea modules directory
+RUN echo '#!/bin/sh\n\
+# Update modules symlinks\n\
+# Load environment variables\n\
+if [ -f /app/.env ]; then\n\
+  export $(grep -v "^#" /app/.env | xargs)\n\
+fi\n\
+\n\
+exec "$@"' > /app/entrypoint.sh && chmod +x /app/entrypoint.sh
+
+# Set PYTHONPATH to ensure modules can be found
+ENV PYTHONPATH="/app"
+
+# Set entrypoint to use our script
+ENTRYPOINT ["/app/entrypoint.sh"]
+
+# Default command when container runs
+CMD ["tail", "-f", "/dev/null"]