adding in build files

DockerCommands.MD

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+Docker Commands.MD
+
+
+<HAPI-server.>
+to pull and clone:
+git clone https://github.com/hapifhir/hapi-fhir-jpaserver-starter.git hapi-fhir-jpaserver
+ 
+to build:
+mvn clean package -DskipTests=true -Pboot
+ 
+to run:
+java -jar target/ROOT.war
+
+
+<rest-of-the-app:>
+
+docker-compose build --no-cache
+docker-compose  up -d
+
+
+
+<useful-stuff:>
+
+cp <CONTAINERID>:/app/PATH/Filename.ext .     - . copies to the root folder you ran it from
+
+docker exec -it <CONTAINERID> bash - to get a bash - session in the container  - 

Dockerfile

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+# Base image with Python and Java
+FROM tomcat:10.1-jdk17
+
+# Install build dependencies, Node.js 18, and coreutils (for stdbuf)
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    python3 python3-pip python3-venv curl coreutils \
+    && curl -fsSL https://deb.nodesource.com/setup_18.x | bash - \
+    && apt-get install -y --no-install-recommends nodejs \
+    && rm -rf /var/lib/apt/lists/*
+
+# Install specific versions of GoFSH and SUSHI
+# REMOVED pip install fhirpath from this line
+RUN npm install -g gofsh fsh-sushi
+
+# Set up Python environment
+WORKDIR /app
+RUN python3 -m venv /app/venv
+ENV PATH="/app/venv/bin:$PATH"
+
+# ADDED: Uninstall old fhirpath just in case it's in requirements.txt
+RUN pip uninstall -y fhirpath || true
+# ADDED: Install the new fhirpathpy library
+RUN pip install --no-cache-dir fhirpathpy
+
+# Copy Flask files
+COPY requirements.txt .
+# Install requirements (including Pydantic - check version compatibility if needed)
+RUN pip install --no-cache-dir -r requirements.txt
+COPY app.py .
+COPY services.py .
+COPY forms.py .
+COPY package.py .
+COPY templates/ templates/
+COPY static/ static/
+COPY tests/ tests/
+
+# Ensure /tmp, /app/h2-data, /app/static/uploads, and /app/logs are writable
+RUN mkdir -p /tmp /app/h2-data /app/static/uploads /app/logs && chmod 777 /tmp /app/h2-data /app/static/uploads /app/logs
+
+# Copy pre-built HAPI WAR and configuration
+COPY hapi-fhir-jpaserver/target/ROOT.war /usr/local/tomcat/webapps/
+COPY hapi-fhir-jpaserver/target/classes/application.yaml /usr/local/tomcat/conf/
+COPY hapi-fhir-jpaserver/target/classes/application.yaml /app/config/application.yaml
+COPY hapi-fhir-jpaserver/target/classes/application.yaml /usr/local/tomcat/webapps/app/config/application.yaml
+COPY hapi-fhir-jpaserver/custom/ /usr/local/tomcat/webapps/custom/
+
+# Install supervisord
+RUN pip install supervisor
+
+# Configure supervisord
+COPY supervisord.conf /etc/supervisord.conf
+
+# Expose ports
+EXPOSE 5000 8080
+
+# Start supervisord
+CMD ["supervisord", "-c", "/etc/supervisord.conf"]

docker-compose.yml

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+version: '3.8'
+services:
+  fhirflare:
+    build:
+      context: .
+      dockerfile: Dockerfile
+    ports:
+      - "5000:5000"
+      - "8080:8080" # Keep port exposed, even if Tomcat isn't running useful stuff in Lite
+    volumes:
+      - ./instance:/app/instance
+      - ./static/uploads:/app/static/uploads
+      - ./instance/hapi-h2-data/:/app/h2-data # Keep volume mounts consistent
+      - ./logs:/app/logs
+    environment:
+      - FLASK_APP=app.py
+      - FLASK_ENV=development
+      - NODE_PATH=/usr/lib/node_modules
+      - APP_MODE=standalone
+      - APP_BASE_URL=http://localhost:5000
+      - HAPI_FHIR_URL=http://localhost:8080/fhir 
+    command: supervisord -c /etc/supervisord.conf