Olamide Isreal
a871107728
Make .gradle, output, build, and modules directories writable (chmod 777) so the container works when K8s runs it as a non-root user.
61 lines
1.9 KiB
Docker
61 lines
1.9 KiB
Docker
FROM eclipse-temurin:17-jdk
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WORKDIR /app
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# Install Python and dependencies
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RUN apt-get update && apt-get install -y \
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python3 \
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python3-pip \
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python3-venv \
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git \
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&& rm -rf /var/lib/apt/lists/*
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# Set up Python virtual environment
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RUN python3 -m venv /opt/venv
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ENV PATH="/opt/venv/bin:$PATH"
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# Install Anthropic and tqdm in the virtual environment
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RUN pip3 install --no-cache-dir "anthropic>=0.8.1,<0.9.0" tqdm==4.66.2 python-dotenv==1.0.1
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# Clone the official Synthea repository directly into /app
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RUN git clone https://github.com/synthetichealth/synthea.git /app-temp && \
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cp -r /app-temp/* /app/ && \
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rm -rf /app-temp
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# Create directory structure for our custom modules and python scripts
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RUN mkdir -p /app/module_generator \
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/app/output \
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/app/src/main/resources/modules
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# First build the project with the official modules - this will compile the Java code
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RUN ./gradlew build -x test
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# Make the run_synthea script executable
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RUN chmod +x /app/run_synthea
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# Copy our Python scripts and module generators
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COPY module_generator/*.py /app/module_generator/
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COPY src/main/resources/modules/* /app/src/main/resources/modules/
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COPY src/main/resources/disease/* /app/src/main/resources/
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COPY scripts/* /app/scripts/
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# Make scripts executable
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RUN chmod +x /app/module_generator/*.py /app/scripts/*
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# Verify and fix module JSON structures
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RUN python3 /app/scripts/check_condition_structure.py --modules_dir /app/src/main/resources/modules --verbose
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# Create a directory for modules that will be mounted from the host
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RUN mkdir -p /app/modules
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# Test a simple module generation to ensure Synthea works
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RUN ./run_synthea -p 1 -m hypertension
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# Make directories writable for K8s (may run as non-root)
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RUN chmod -R 777 /app/.gradle /app/output /app/build /app/modules \
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/app/src/main/resources/modules
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# Set PYTHONPATH to ensure modules can be found
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ENV PYTHONPATH="/app"
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# Default command when container runs
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CMD ["tail", "-f", "/dev/null"] |