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Create setup_linux.sh
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setup_linux.sh
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231
setup_linux.sh
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#!/bin/bash
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# --- Configuration ---
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REPO_URL="https://github.com/hapifhir/hapi-fhir-jpaserver-starter.git"
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CLONE_DIR="hapi-fhir-jpaserver"
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SOURCE_CONFIG_DIR="hapi-fhir-setup" # Assuming this is relative to the script's parent
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CONFIG_FILE="application.yaml"
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# --- Define Paths ---
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# Note: Adjust SOURCE_CONFIG_PATH if SOURCE_CONFIG_DIR is not a sibling directory
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# This assumes the script is run from a directory, and hapi-fhir-setup is at the same level
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SOURCE_CONFIG_PATH="../${SOURCE_CONFIG_DIR}/target/classes/${CONFIG_FILE}"
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DEST_CONFIG_PATH="${CLONE_DIR}/target/classes/${CONFIG_FILE}"
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APP_MODE=""
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# --- Error Handling Function ---
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handle_error() {
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echo "------------------------------------"
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echo "An error occurred: $1"
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echo "Script aborted."
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echo "------------------------------------"
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# Removed 'read -p "Press Enter to exit..."' as it's not typical for non-interactive CI/CD
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exit 1
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}
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# === Prompt for Installation Mode ===
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get_mode_choice() {
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echo "Select Installation Mode:"
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echo "1. Standalone (Includes local HAPI FHIR Server - Requires Git & Maven)"
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echo "2. Lite (Excludes local HAPI FHIR Server - No Git/Maven needed)"
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while true; do
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read -r -p "Enter your choice (1 or 2): " choice
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case "$choice" in
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1)
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APP_MODE="standalone"
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break
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;;
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2)
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APP_MODE="lite"
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break
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;;
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*)
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echo "Invalid input. Please try again."
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;;
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esac
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done
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echo "Selected Mode: $APP_MODE"
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echo
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}
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# Call the function to get mode choice
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get_mode_choice
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# === Conditionally Execute HAPI Setup ===
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if [ "$APP_MODE" = "standalone" ]; then
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echo "Running Standalone setup including HAPI FHIR..."
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echo
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# --- Step 0: Clean up previous clone (optional) ---
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echo "Checking for existing directory: $CLONE_DIR"
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if [ -d "$CLONE_DIR" ]; then
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echo "Found existing directory, removing it..."
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rm -rf "$CLONE_DIR"
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if [ $? -ne 0 ]; then
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handle_error "Failed to remove existing directory: $CLONE_DIR"
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fi
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echo "Existing directory removed."
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else
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echo "Directory does not exist, proceeding with clone."
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fi
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echo
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# --- Step 1: Clone the HAPI FHIR server repository ---
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echo "Cloning repository: $REPO_URL into $CLONE_DIR..."
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git clone "$REPO_URL" "$CLONE_DIR"
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if [ $? -ne 0 ]; then
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handle_error "Failed to clone repository. Check Git installation and network connection."
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fi
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echo "Repository cloned successfully."
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echo
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# --- Step 2: Navigate into the cloned directory ---
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echo "Changing directory to $CLONE_DIR..."
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cd "$CLONE_DIR" || handle_error "Failed to change directory to $CLONE_DIR."
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echo "Current directory: $(pwd)"
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echo
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# --- Step 3: Build the HAPI server using Maven ---
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echo "===> Starting Maven build (Step 3)..."
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mvn clean package -DskipTests=true -Pboot
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if [ $? -ne 0 ]; then
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echo "ERROR: Maven build failed."
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cd ..
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handle_error "Maven build process resulted in an error."
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fi
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echo "Maven build completed successfully."
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echo
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# --- Step 4: Copy the configuration file ---
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echo "===> Starting file copy (Step 4)..."
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echo "Copying configuration file..."
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# Corrected SOURCE_CONFIG_PATH to be relative to the new current directory ($CLONE_DIR)
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# This assumes the original script's SOURCE_CONFIG_PATH was relative to its execution location
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# If SOURCE_CONFIG_DIR is ../hapi-fhir-setup relative to script's original location:
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# Then from within CLONE_DIR, it becomes ../../hapi-fhir-setup
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# We defined SOURCE_CONFIG_PATH earlier relative to the script start.
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# So, when inside CLONE_DIR, the path from original script location should be used.
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# The original script had: set SOURCE_CONFIG_PATH=..\%SOURCE_CONFIG_DIR%\target\classes\%CONFIG_FILE%
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# And then: xcopy "%SOURCE_CONFIG_PATH%" "target\classes\"
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# This implies SOURCE_CONFIG_PATH is relative to the original script's location, not the $CLONE_DIR
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# Therefore, we need to construct the correct relative path from *within* $CLONE_DIR back to the source.
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# Assuming the script is in dir X, and SOURCE_CONFIG_DIR is ../hapi-fhir-setup from X.
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# So, hapi-fhir-setup is a sibling of X's parent.
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# If CLONE_DIR is also in X, then from within CLONE_DIR, the path is ../ + original SOURCE_CONFIG_PATH
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# For simplicity and robustness, let's use an absolute path or a more clearly defined relative path from the start.
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# The original `SOURCE_CONFIG_PATH=..\%SOURCE_CONFIG_DIR%\target\classes\%CONFIG_FILE%` implies
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# that `hapi-fhir-setup` is a sibling of the directory where the script *is being run from*.
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# Let's assume the script is run from the root of FHIRFLARE-IG-Toolkit.
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# And hapi-fhir-setup is also in the root, next to this script.
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# Then SOURCE_CONFIG_PATH would be ./hapi-fhir-setup/target/classes/application.yaml
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# And from within ./hapi-fhir-jpaserver/, the path would be ../hapi-fhir-setup/target/classes/application.yaml
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# The original batch file sets SOURCE_CONFIG_PATH as "..\%SOURCE_CONFIG_DIR%\target\classes\%CONFIG_FILE%"
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# And COPIES it to "target\classes\" *while inside CLONE_DIR*.
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# This means the source path is relative to where the *cd %CLONE_DIR%* happened from.
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# Let's make it relative to the script's initial execution directory.
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INITIAL_SCRIPT_DIR=$(pwd)
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ABSOLUTE_SOURCE_CONFIG_PATH="${INITIAL_SCRIPT_DIR}/../${SOURCE_CONFIG_DIR}/target/classes/${CONFIG_FILE}" # This matches the ..\ logic
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echo "Source: $ABSOLUTE_SOURCE_CONFIG_PATH"
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echo "Destination: target/classes/$CONFIG_FILE"
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if [ ! -f "$ABSOLUTE_SOURCE_CONFIG_PATH" ]; then
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echo "WARNING: Source configuration file not found at $ABSOLUTE_SOURCE_CONFIG_PATH."
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echo "The script will continue, but the server might use default configuration."
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else
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cp "$ABSOLUTE_SOURCE_CONFIG_PATH" "target/classes/"
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if [ $? -ne 0 ]; then
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echo "WARNING: Failed to copy configuration file. Check if the source file exists and permissions."
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echo "The script will continue, but the server might use default configuration."
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else
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echo "Configuration file copied successfully."
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fi
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fi
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echo
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# --- Step 5: Navigate back to the parent directory ---
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echo "===> Changing directory back (Step 5)..."
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cd .. || handle_error "Failed to change back to the parent directory."
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echo "Current directory: $(pwd)"
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echo
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else # APP_MODE is "lite"
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echo "Running Lite setup, skipping HAPI FHIR build..."
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# Ensure the hapi-fhir-jpaserver directory doesn't exist or is empty if Lite mode is chosen
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if [ -d "$CLONE_DIR" ]; then
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echo "Found existing HAPI directory ($CLONE_DIR) in Lite mode. Removing it..."
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rm -rf "$CLONE_DIR"
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fi
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# Create empty target directories expected by Dockerfile COPY, even if not used
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mkdir -p "${CLONE_DIR}/target/classes"
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mkdir -p "${CLONE_DIR}/custom" # This was in the original batch, ensure it's here
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# Create a placeholder empty WAR file and application.yaml to satisfy Dockerfile COPY
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touch "${CLONE_DIR}/target/ROOT.war"
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touch "${CLONE_DIR}/target/classes/application.yaml"
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echo "Placeholder files and directories created for Lite mode build in $CLONE_DIR."
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echo
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fi
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# === Modify docker-compose.yml to set APP_MODE ===
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echo "Updating docker-compose.yml with APP_MODE=$APP_MODE..."
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DOCKER_COMPOSE_TMP="docker-compose.yml.tmp"
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DOCKER_COMPOSE_ORIG="docker-compose.yml"
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cat << EOF > "$DOCKER_COMPOSE_TMP"
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version: '3.8'
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services:
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fhirflare:
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build:
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context: .
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dockerfile: Dockerfile
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ports:
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- "5000:5000"
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- "8080:8080" # Keep port exposed, even if Tomcat isn't running useful stuff in Lite
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volumes:
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- ./instance:/app/instance
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- ./static/uploads:/app/static/uploads
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- ./instance/hapi-h2-data/:/app/h2-data # Keep volume mounts consistent
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- ./logs:/app/logs
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environment:
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- FLASK_APP=app.py
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- FLASK_ENV=development
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- NODE_PATH=/usr/lib/node_modules
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- APP_MODE=${APP_MODE}
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command: supervisord -c /etc/supervisord.conf
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EOF
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if [ ! -f "$DOCKER_COMPOSE_TMP" ]; then
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handle_error "Failed to create temporary docker-compose file ($DOCKER_COMPOSE_TMP)."
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fi
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# Replace the original docker-compose.yml
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mv "$DOCKER_COMPOSE_TMP" "$DOCKER_COMPOSE_ORIG"
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echo "docker-compose.yml updated successfully."
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echo
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# --- Step 6: Build Docker images ---
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echo "===> Starting Docker build (Step 6)..."
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docker-compose build --no-cache
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if [ $? -ne 0 ]; then
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handle_error "Docker Compose build failed. Check Docker installation and docker-compose.yml file."
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fi
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echo "Docker images built successfully."
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echo
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# --- Step 7: Start Docker containers ---
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echo "===> Starting Docker containers (Step 7)..."
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docker-compose up -d
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if [ $? -ne 0 ]; then
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handle_error "Docker Compose up failed. Check Docker installation and container configurations."
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fi
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echo "Docker containers started successfully."
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echo
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echo "===================================="
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echo "Script finished successfully! (Mode: $APP_MODE)"
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echo "===================================="
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exit 0
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