Sudo-JHare/FHIRFLARE-IG-Toolkit
Sudo-JHare/FHIRFLARE-IG-Toolkit
1
0
Fork 0
mirror of https://github.com/Sudo-JHare/FHIRFLARE-IG-Toolkit.git synced 2025-09-17 18:35:02 +00:00
Code Issues Packages Projects Releases 6 Wiki Activity
FHIRFLARE-IG-Toolkit/setup_linux.sh
Sudo-JHare 6ae0e56118 V4.1 Prep 
Build Path options

added Candle
Added Custom
2025-08-27 12:47:16 +10:00

396 lines
13 KiB
Bash
Raw Blame History

#!/bin/bash
# --- Configuration ---
REPO_URL_HAPI="https://github.com/hapifhir/hapi-fhir-jpaserver-starter.git"
REPO_URL_CANDLE="https://github.com/FHIR/fhir-candle.git"
CLONE_DIR_HAPI="hapi-fhir-jpaserver"
CLONE_DIR_CANDLE="fhir-candle"
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="${CLONE_DIR_HAPI}/target/classes/${CONFIG_FILE}"
APP_MODE=""
CUSTOM_FHIR_URL_VAL=""
SERVER_TYPE=""
CANDLE_FHIR_VERSION=""
# --- Error Handling Function ---
handle_error() {
echo "------------------------------------"
echo "An error occurred: $1"
echo "Script aborted."
echo "------------------------------------"
exit 1
}
# === MODIFIED: Prompt for Installation Mode ===
get_mode_choice() {
echo ""
echo "Select Installation Mode:"
echo "1. Lite (Excludes local HAPI FHIR Server - No Git/Maven/Dotnet needed)"
echo "2. Custom URL (Uses a custom FHIR Server - No Git/Maven/Dotnet needed)"
echo "3. Hapi (Includes local HAPI FHIR Server - Requires Git & Maven)"
echo "4. Candle (Includes local FHIR Candle Server - Requires Git & Dotnet)"
while true; do
read -r -p "Enter your choice (1, 2, 3, or 4): " choice
case "$choice" in
1)
APP_MODE="lite"
break
;;
2)
APP_MODE="standalone"
get_custom_url_prompt
break
;;
3)
APP_MODE="standalone"
SERVER_TYPE="hapi"
break
;;
4)
APP_MODE="standalone"
SERVER_TYPE="candle"
get_candle_fhir_version
break
;;
*)
echo "Invalid input. Please try again."
;;
esac
done
echo "Selected Mode: $APP_MODE"
echo "Server Type: $SERVER_TYPE"
echo
}
# === NEW: Prompt for Custom URL ===
get_custom_url_prompt() {
local confirmed_url=""
while true; do
echo
read -r -p "Please enter the custom FHIR server URL: " custom_url_input
echo
echo "You entered: $custom_url_input"
read -r -p "Is this URL correct? (Y/N): " confirm_url
if [[ "$confirm_url" =~ ^[Yy]$ ]]; then
confirmed_url="$custom_url_input"
break
else
echo "URL not confirmed. Please re-enter."
fi
done
while true; do
echo
read -r -p "Please re-enter the URL to confirm it is correct: " custom_url_input
if [ "$custom_url_input" = "$confirmed_url" ]; then
CUSTOM_FHIR_URL_VAL="$custom_url_input"
echo
echo "Custom URL confirmed: $CUSTOM_FHIR_URL_VAL"
break
else
echo
echo "URLs do not match. Please try again."
confirmed_url="$custom_url_input"
fi
done
}
# === NEW: Prompt for Candle FHIR version ===
get_candle_fhir_version() {
echo ""
echo "Select the FHIR version for the Candle server:"
echo "1. R4 (4.0)"
echo "2. R4B (4.3)"
echo "3. R5 (5.0)"
while true; do
read -r -p "Enter your choice (1, 2, or 3): " choice
case "$choice" in
1)
CANDLE_FHIR_VERSION=r4
break
;;
2)
CANDLE_FHIR_VERSION=r4b
break
;;
3)
CANDLE_FHIR_VERSION=r5
break
;;
*)
echo "Invalid input. Please try again."
;;
esac
done
}
# Call the function to get mode choice
get_mode_choice
# === Conditionally Execute Server Setup ===
case "$SERVER_TYPE" in
"hapi")
echo "Running Hapi server setup..."
echo
# --- Step 0: Clean up previous clone (optional) ---
echo "Checking for existing directory: $CLONE_DIR_HAPI"
if [ -d "$CLONE_DIR_HAPI" ]; then
echo "Found existing directory, removing it..."
rm -rf "$CLONE_DIR_HAPI"
if [ $? -ne 0 ]; then
handle_error "Failed to remove existing directory: $CLONE_DIR_HAPI"
fi
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_HAPI into $CLONE_DIR_HAPI..."
git clone "$REPO_URL_HAPI" "$CLONE_DIR_HAPI"
if [ $? -ne 0 ]; then
handle_error "Failed to clone repository. Check Git installation and network connection."
fi
echo "Repository cloned successfully."
echo
# --- Step 2: Navigate into the cloned directory ---
echo "Changing directory to $CLONE_DIR_HAPI..."
cd "$CLONE_DIR_HAPI" || handle_error "Failed to change directory to $CLONE_DIR_HAPI."
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
if [ $? -ne 0 ]; then
echo "ERROR: Maven build failed."
cd ..
handle_error "Maven build process resulted in an error."
fi
echo "Maven build completed successfully."
echo
# --- Step 4: Copy the configuration file ---
echo "===> Starting file copy (Step 4)..."
echo "Copying configuration file..."
INITIAL_SCRIPT_DIR=$(pwd)
ABSOLUTE_SOURCE_CONFIG_PATH="${INITIAL_SCRIPT_DIR}/../${SOURCE_CONFIG_DIR}/target/classes/${CONFIG_FILE}"
echo "Source: $ABSOLUTE_SOURCE_CONFIG_PATH"
echo "Destination: target/classes/$CONFIG_FILE"
if [ ! -f "$ABSOLUTE_SOURCE_CONFIG_PATH" ]; then
echo "WARNING: Source configuration file not found at $ABSOLUTE_SOURCE_CONFIG_PATH."
echo "The script will continue, but the server might use default configuration."
else
cp "$ABSOLUTE_SOURCE_CONFIG_PATH" "target/classes/"
if [ $? -ne 0 ]; then
echo "WARNING: Failed to copy configuration file. Check if the source file exists and permissions."
echo "The script will continue, but the server might use default configuration."
else
echo "Configuration file copied successfully."
fi
fi
echo
# --- Step 5: Navigate back to the parent directory ---
echo "===> Changing directory back (Step 5)..."
cd .. || handle_error "Failed to change back to the parent directory."
echo "Current directory: $(pwd)"
echo
;;
"candle")
echo "Running FHIR Candle server setup..."
echo
# --- Step 0: Clean up previous clone (optional) ---
echo "Checking for existing directory: $CLONE_DIR_CANDLE"
if [ -d "$CLONE_DIR_CANDLE" ]; then
echo "Found existing directory, removing it..."
rm -rf "$CLONE_DIR_CANDLE"
if [ $? -ne 0 ]; then
handle_error "Failed to remove existing directory: $CLONE_DIR_CANDLE"
fi
echo "Existing directory removed."
else
echo "Directory does not exist, proceeding with clone."
fi
echo
# --- Step 1: Clone the FHIR Candle server repository ---
echo "Cloning repository: $REPO_URL_CANDLE into $CLONE_DIR_CANDLE..."
git clone "$REPO_URL_CANDLE" "$CLONE_DIR_CANDLE"
if [ $? -ne 0 ]; then
handle_error "Failed to clone repository. Check Git and Dotnet SDK installation and network connection."
fi
echo "Repository cloned successfully."
echo
# --- Step 2: Navigate into the cloned directory ---
echo "Changing directory to $CLONE_DIR_CANDLE..."
cd "$CLONE_DIR_CANDLE" || handle_error "Failed to change directory to $CLONE_DIR_CANDLE."
echo "Current directory: $(pwd)"
echo
# --- Step 3: Build the FHIR Candle server using Dotnet ---
echo "===> Starting Dotnet build (Step 3)..."
dotnet publish -c Release -f net9.0 -o publish
if [ $? -ne 0 ]; then
handle_error "Dotnet build failed. Check Dotnet SDK installation."
fi
echo "Dotnet build completed successfully."
echo
# --- Step 4: Navigate back to the parent directory ---
echo "===> Changing directory back (Step 4)..."
cd .. || handle_error "Failed to change back to the parent directory."
echo "Current directory: $(pwd)"
echo
;;
*) # APP_MODE is Lite, no SERVER_TYPE
echo "Running Lite setup, skipping server build..."
if [ -d "$CLONE_DIR_HAPI" ]; then
echo "Found existing HAPI directory in Lite mode. Removing it to avoid build issues..."
rm -rf "$CLONE_DIR_HAPI"
fi
if [ -d "$CLONE_DIR_CANDLE" ]; then
echo "Found existing Candle directory in Lite mode. Removing it to avoid build issues..."
rm -rf "$CLONE_DIR_CANDLE"
fi
mkdir -p "${CLONE_DIR_HAPI}/target/classes"
mkdir -p "${CLONE_DIR_HAPI}/custom"
touch "${CLONE_DIR_HAPI}/target/ROOT.war"
touch "${CLONE_DIR_HAPI}/target/classes/application.yaml"
mkdir -p "${CLONE_DIR_CANDLE}/publish"
touch "${CLONE_DIR_CANDLE}/publish/fhir-candle.dll"
echo "Placeholder files and directories created for Lite mode build."
echo
;;
esac
# === MODIFIED: Update docker-compose.yml to set APP_MODE and HAPI_FHIR_URL and DOCKERFILE ===
echo "Updating docker-compose.yml with APP_MODE=$APP_MODE and HAPI_FHIR_URL..."
DOCKER_COMPOSE_TMP="docker-compose.yml.tmp"
DOCKER_COMPOSE_ORIG="docker-compose.yml"
HAPI_URL_TO_USE="https://fhir.hl7.org.au/aucore/fhir/DEFAULT/"
if [ -n "$CUSTOM_FHIR_URL_VAL" ]; then
HAPI_URL_TO_USE="$CUSTOM_FHIR_URL_VAL"
elif [ "$SERVER_TYPE" = "candle" ]; then
HAPI_URL_TO_USE="http://localhost:5826/fhir/${CANDLE_FHIR_VERSION}"
else
HAPI_URL_TO_USE="http://localhost:8080/fhir"
fi
DOCKERFILE_TO_USE="Dockerfile.lite"
if [ "$SERVER_TYPE" = "hapi" ]; then
DOCKERFILE_TO_USE="Dockerfile.hapi"
elif [ "$SERVER_TYPE" = "candle" ]; then
DOCKERFILE_TO_USE="Dockerfile.candle"
fi
cat << EOF > "$DOCKER_COMPOSE_TMP"
version: '3.8'
services:
fhirflare:
build:
context: .
dockerfile: ${DOCKERFILE_TO_USE}
ports:
EOF
if [ "$SERVER_TYPE" = "candle" ]; then
cat << EOF >> "$DOCKER_COMPOSE_TMP"
- "5000:5000"
- "5001:5826"
EOF
else
cat << EOF >> "$DOCKER_COMPOSE_TMP"
- "5000:5000"
- "8080:8080"
EOF
fi
cat << EOF >> "$DOCKER_COMPOSE_TMP"
volumes:
- ./instance:/app/instance
- ./static/uploads:/app/static/uploads
- ./logs:/app/logs
EOF
if [ "$SERVER_TYPE" = "hapi" ]; then
cat << EOF >> "$DOCKER_COMPOSE_TMP"
- ./instance/hapi-h2-data/:/app/h2-data # Keep volume mounts consistent
- ./hapi-fhir-jpaserver/target/ROOT.war:/usr/local/tomcat/webapps/ROOT.war
- ./hapi-fhir-jpaserver/target/classes/application.yaml:/usr/local/tomcat/conf/application.yaml
EOF
elif [ "$SERVER_TYPE" = "candle" ]; then
cat << EOF >> "$DOCKER_COMPOSE_TMP"
- ./fhir-candle/publish/:/app/fhir-candle-publish/
EOF
fi
cat << EOF >> "$DOCKER_COMPOSE_TMP"
environment:
- FLASK_APP=app.py
- FLASK_ENV=development
- NODE_PATH=/usr/lib/node_modules
- APP_MODE=${APP_MODE}
- APP_BASE_URL=http://localhost:5000
- HAPI_FHIR_URL=${HAPI_URL_TO_USE}
EOF
if [ "$SERVER_TYPE" = "candle" ]; then
cat << EOF >> "$DOCKER_COMPOSE_TMP"
- ASPNETCORE_URLS=http://0.0.0.0:5826
EOF
fi
cat << EOF >> "$DOCKER_COMPOSE_TMP"
command: supervisord -c /etc/supervisord.conf
EOF
if [ ! -f "$DOCKER_COMPOSE_TMP" ]; then
handle_error "Failed to create temporary docker-compose file ($DOCKER_COMPOSE_TMP)."
fi
# Replace the original docker-compose.yml
mv "$DOCKER_COMPOSE_TMP" "$DOCKER_COMPOSE_ORIG"
echo "docker-compose.yml updated successfully."
echo
# --- Step 6: Build Docker images ---
echo "===> Starting Docker build (Step 6)..."
docker-compose build --no-cache
if [ $? -ne 0 ]; then
handle_error "Docker Compose build failed. Check Docker installation and docker-compose.yml file."
fi
echo "Docker images built successfully."
echo
# --- Step 7: Start Docker containers ---
echo "===> Starting Docker containers (Step 7)..."
docker-compose up -d
if [ $? -ne 0 ]; then
handle_error "Docker Compose up failed. Check Docker installation and container configurations."
fi
echo "Docker containers started successfully."
echo
echo "===================================="
echo "Script finished successfully! (Mode: $APP_MODE)"
echo "===================================="
exit 0
Reference in New Issue View Git Blame Copy Permalink