From 3fe12a80303e563dbb14f615299d6f1945972be8 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?J=C3=B6rn=20Guy=20S=C3=BC=C3=9F?= <joernguy.suess@csiro.au>
Date: Tue, 15 Jul 2025 11:01:27 +1000
Subject: [PATCH] feat: Add a shell script for Linux users

---
 build_and_run.sh | 147 +++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 147 insertions(+)
 create mode 100644 build_and_run.sh

diff --git a/build_and_run.sh b/build_and_run.sh
new file mode 100644
index 0000000..faa259c
--- /dev/null
+++ b/build_and_run.sh
@@ -0,0 +1,147 @@
+#!/bin/bash
+set -e
+
+# --- Configuration ---
+REPO_URL="https://github.com/hapifhir/hapi-fhir-jpaserver-starter.git"
+CLONE_DIR="hapi-fhir-jpaserver"
+SOURCE_CONFIG_DIR="hapi-fhir-setup"
+CONFIG_FILE="application.yaml"
+
+# --- Define Paths ---
+SOURCE_CONFIG_PATH="../$SOURCE_CONFIG_DIR/target/classes/$CONFIG_FILE"
+DEST_CONFIG_PATH="$CLONE_DIR/target/classes/$CONFIG_FILE"
+
+# === Prompt for Version ===
+while true; do
+    echo "Select Installation Mode:"
+    echo "1. Standalone (Includes local HAPI FHIR Server - Requires Git & Maven)"
+    echo "2. Lite (Excludes local HAPI FHIR Server - No Git/Maven needed)"
+    read -p "Enter your choice (1 or 2): " choice
+    case $choice in
+        1)
+            APP_MODE="standalone"
+            break
+            ;;
+        2)
+            APP_MODE="lite"
+            break
+            ;;
+        *)
+            echo "Invalid input. Please try again."
+            ;;
+    esac
+done
+
+echo "Selected Mode: $APP_MODE"
+echo
+
+# === Conditionally Execute HAPI Setup ===
+if [ "$APP_MODE" = "standalone" ]; then
+    echo "Running Standalone setup including HAPI FHIR..."
+    echo
+
+    # Step 0: Clean up previous clone (optional)
+    if [ -d "$CLONE_DIR" ]; then
+        echo "Found existing directory, removing it..."
+        rm -rf "$CLONE_DIR"
+        echo "Existing directory removed."
+    else
+        echo "Directory does not exist, proceeding with clone."
+    fi
+    echo
+
+    # Step 1: Clone the HAPI FHIR server repository
+    echo "Cloning repository: $REPO_URL into $CLONE_DIR..."
+    git clone "$REPO_URL" "$CLONE_DIR"
+    echo "Repository cloned successfully."
+    echo
+
+    # Step 2: Navigate into the cloned directory
+    cd "$CLONE_DIR"
+    echo "Current directory: $(pwd)"
+    echo
+
+    # Step 3: Build the HAPI server using Maven
+    echo "===> Starting Maven build (Step 3)..."
+    mvn clean package -DskipTests=true -Pboot
+    echo "Maven build completed successfully."
+    echo
+
+    # Step 4: Copy the configuration file
+    echo "===> Starting file copy (Step 4)..."
+    echo "Copying configuration file..."
+    echo "Source: $SOURCE_CONFIG_PATH"
+    echo "Destination: target/classes/$CONFIG_FILE"
+    cp "$SOURCE_CONFIG_PATH" "target/classes/" || echo "WARNING: Failed to copy configuration file. The server might use default configuration."
+    echo "Configuration file copy step finished."
+    echo
+
+    # Step 5: Navigate back to the parent directory
+    cd ..
+    echo "Current directory: $(pwd)"
+    echo
+else
+    echo "Running Lite setup, skipping HAPI FHIR build..."
+    # Ensure the hapi-fhir-jpaserver directory doesn't exist or is empty if Lite mode is chosen after a standalone attempt
+    if [ -d "$CLONE_DIR" ]; then
+        echo "Found existing HAPI directory in Lite mode. Removing it to avoid build issues..."
+        rm -rf "$CLONE_DIR"
+    fi
+    # Create empty target directories expected by Dockerfile COPY, even if not used
+    mkdir -p "$CLONE_DIR/target/classes"
+    mkdir -p "$CLONE_DIR/custom"
+    # Create a placeholder empty WAR file to satisfy Dockerfile COPY
+    touch "$CLONE_DIR/target/ROOT.war"
+    touch "$CLONE_DIR/target/classes/application.yaml"
+    echo "Placeholder files created for Lite mode build."
+    echo
+fi
+
+# === Modify docker-compose.yml to set APP_MODE ===
+echo "Updating docker-compose.yml with APP_MODE=$APP_MODE..."
+cat <<EOF > docker-compose.yml.tmp
+version: '3.8'
+services:
+  fhirflare:
+    build:
+      context: .
+      dockerfile: Dockerfile
+    ports:
+      - "5000:5000"
+      - "8080:8080"
+    volumes:
+      - ./instance:/app/instance
+      - ./static/uploads:/app/static/uploads
+      - ./instance/hapi-h2-data/:/app/h2-data
+      - ./logs:/app/logs
+    environment:
+      - FLASK_APP=app.py
+      - FLASK_ENV=development
+      - NODE_PATH=/usr/lib/node_modules
+      - APP_MODE=$APP_MODE
+      - APP_BASE_URL=http://localhost:5000
+      - HAPI_FHIR_URL=http://localhost:8080/fhir
+    command: supervisord -c /etc/supervisord.conf
+EOF
+
+# Replace the original docker-compose.yml
+mv docker-compose.yml.tmp docker-compose.yml
+
+echo "docker-compose.yml updated successfully."
+echo
+
+# --- Step 6: Build Docker images ---
+echo "===> Starting Docker build (Step 6)..."
+docker compose build --no-cache
+echo "Docker images built successfully."
+echo
+
+# --- Step 7: Start Docker containers ---
+echo "===> Starting Docker containers (Step 7)..."
+docker compose up -d
+echo "Docker containers started successfully."
+echo
+
+echo "===================================="
+echo "Script finished successfully! (Mode: $APP_MODE)"
+echo "===================================="