V4.1 Prep

Build Path options

added Candle
Added Custom

Build and Run for first time.bat

@@ -2,57 +2,130 @@
 setlocal enabledelayedexpansion
 
 REM --- Configuration ---
-set REPO_URL=https://github.com/hapifhir/hapi-fhir-jpaserver-starter.git
+set REPO_URL_HAPI=https://github.com/hapifhir/hapi-fhir-jpaserver-starter.git
-set CLONE_DIR=hapi-fhir-jpaserver
+set REPO_URL_CANDLE=https://github.com/FHIR/fhir-candle.git
+set CLONE_DIR_HAPI=hapi-fhir-jpaserver
+set CLONE_DIR_CANDLE=fhir-candle
 set SOURCE_CONFIG_DIR=hapi-fhir-setup
 set CONFIG_FILE=application.yaml
 
 REM --- Define Paths ---
 set SOURCE_CONFIG_PATH=..\%SOURCE_CONFIG_DIR%\target\classes\%CONFIG_FILE%
-set DEST_CONFIG_PATH=%CLONE_DIR%\target\classes\%CONFIG_FILE%
+set DEST_CONFIG_PATH=%CLONE_DIR_HAPI%\target\classes\%CONFIG_FILE%
 
-REM === CORRECTED: Prompt for Version ===
+REM --- NEW: Define a variable for the custom FHIR URL and server type ---
+set "CUSTOM_FHIR_URL_VAL="
+set "SERVER_TYPE="
+set "CANDLE_FHIR_VERSION="
+
+REM === MODIFIED: Prompt for Installation Mode ===
 :GetModeChoice
 SET "APP_MODE=" REM Clear the variable first
+echo.
 echo Select Installation Mode:
-echo 1. Standalone (Includes local HAPI FHIR Server - Requires Git & Maven)
+echo 1. Lite (Excludes local HAPI FHIR Server - No Git/Maven/Dotnet needed)
-echo 2. Lite (Excludes local HAPI FHIR Server - No Git/Maven needed)
+echo 2. Custom URL (Uses a custom FHIR Server - No Git/Maven/Dotnet needed)
-CHOICE /C 12 /N /M "Enter your choice (1 or 2):"
+echo 3. Hapi (Includes local HAPI FHIR Server - Requires Git & Maven)
+echo 4. Candle (Includes local FHIR Candle Server - Requires Git & Dotnet)
+CHOICE /C 1234 /N /M "Enter your choice (1, 2, 3, or 4):"
 
+IF ERRORLEVEL 4 (
+    SET APP_MODE=standalone
+    SET SERVER_TYPE=candle
+    goto :GetCandleFhirVersion
+)
+IF ERRORLEVEL 3 (
+    SET APP_MODE=standalone
+    SET SERVER_TYPE=hapi
+    goto :ModeSet
+)
 IF ERRORLEVEL 2 (
+    SET APP_MODE=standalone
+    goto :GetCustomUrl
+)
+IF ERRORLEVEL 1 (
     SET APP_MODE=lite
     goto :ModeSet
 )
-IF ERRORLEVEL 1 (
+
-    SET APP_MODE=standalone
-    goto :ModeSet
-)
 REM If somehow neither was chosen (e.g., Ctrl+C), loop back
 echo Invalid input. Please try again.
 goto :GetModeChoice
 
+:GetCustomUrl
+set "CONFIRMED_URL="
+:PromptUrlLoop
+echo.
+set /p "CUSTOM_URL_INPUT=Please enter the custom FHIR server URL: "
+echo.
+echo You entered: !CUSTOM_URL_INPUT!
+set /p "CONFIRM_URL=Is this URL correct? (Y/N): "
+if /i "!CONFIRM_URL!" EQU "Y" (
+    set "CONFIRMED_URL=!CUSTOM_URL_INPUT!"
+    goto :ConfirmUrlLoop
+) else (
+    goto :PromptUrlLoop
+)
+:ConfirmUrlLoop
+echo.
+echo Please re-enter the URL to confirm it is correct:
+set /p "CUSTOM_URL_INPUT=Re-enter URL: "
+if /i "!CUSTOM_URL_INPUT!" EQU "!CONFIRMED_URL!" (
+    set "CUSTOM_FHIR_URL_VAL=!CUSTOM_URL_INPUT!"
+    echo.
+    echo Custom URL confirmed: !CUSTOM_FHIR_URL_VAL!
+    goto :ModeSet
+) else (
+    echo.
+    echo URLs do not match. Please try again.
+    goto :PromptUrlLoop
+)
+
+:GetCandleFhirVersion
+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)
+CHOICE /C 123 /N /M "Enter your choice (1, 2, or 3):"
+IF ERRORLEVEL 3 (
+    SET CANDLE_FHIR_VERSION=r5
+    goto :ModeSet
+)
+IF ERRORLEVEL 2 (
+    SET CANDLE_FHIR_VERSION=r4b
+    goto :ModeSet
+)
+IF ERRORLEVEL 1 (
+    SET CANDLE_FHIR_VERSION=r4
+    goto :ModeSet
+)
+echo Invalid input. Please try again.
+goto :GetCandleFhirVersion
+
 :ModeSet
 IF "%APP_MODE%"=="" (
     echo Invalid choice detected after checks. Exiting.
     goto :eof
 )
 echo Selected Mode: %APP_MODE%
+echo Server Type: %SERVER_TYPE%
 echo.
-REM === END CORRECTION ===
+REM === END MODIFICATION ===
 
 
-REM === Conditionally Execute HAPI Setup ===
+REM === Conditionally Execute Server Setup ===
-IF "%APP_MODE%"=="standalone" (
+IF "%SERVER_TYPE%"=="hapi" (
-    echo Running Standalone setup including HAPI FHIR...
+    echo Running Hapi server setup...
     echo.
     
     REM --- Step 0: Clean up previous clone (optional) ---
-    echo Checking for existing directory: %CLONE_DIR%
+    echo Checking for existing directory: %CLONE_DIR_HAPI%
-    if exist "%CLONE_DIR%" (
+    if exist "%CLONE_DIR_HAPI%" (
         echo Found existing directory, removing it...
-        rmdir /s /q "%CLONE_DIR%"
+        rmdir /s /q "%CLONE_DIR_HAPI%"
         if errorlevel 1 (
-            echo ERROR: Failed to remove existing directory: %CLONE_DIR%
+            echo ERROR: Failed to remove existing directory: %CLONE_DIR_HAPI%
             goto :error
         )
         echo Existing directory removed.
@@ -62,8 +135,8 @@ IF "%APP_MODE%"=="standalone" (
     echo.
 
     REM --- Step 1: Clone the HAPI FHIR server repository ---
-    echo Cloning repository: %REPO_URL% into %CLONE_DIR%...
+    echo Cloning repository: %REPO_URL_HAPI% into %CLONE_DIR_HAPI%...
-    git clone "%REPO_URL%" "%CLONE_DIR%"
+    git clone "%REPO_URL_HAPI%" "%CLONE_DIR_HAPI%"
     if errorlevel 1 (
         echo ERROR: Failed to clone repository. Check Git installation and network connection.
         goto :error
@@ -72,10 +145,10 @@ IF "%APP_MODE%"=="standalone" (
     echo.
 
     REM --- Step 2: Navigate into the cloned directory ---
-    echo Changing directory to %CLONE_DIR%...
+    echo Changing directory to %CLONE_DIR_HAPI%...
-    cd "%CLONE_DIR%"
+    cd "%CLONE_DIR_HAPI%"
     if errorlevel 1 (
-        echo ERROR: Failed to change directory to %CLONE_DIR%.
+        echo ERROR: Failed to change directory to %CLONE_DIR_HAPI%.
         goto :error
     )
     echo Current directory: %CD%
@@ -118,47 +191,141 @@ IF "%APP_MODE%"=="standalone" (
     echo Current directory: %CD%
     echo.
 
-) ELSE (
+) ELSE IF "%SERVER_TYPE%"=="candle" (
-    echo Running Lite setup, skipping HAPI FHIR build...
+    echo Running FHIR Candle server setup...
-    REM Ensure the hapi-fhir-jpaserver directory doesn't exist or is empty if Lite mode is chosen after a standalone attempt
+    echo.
-    if exist "%CLONE_DIR%" (
+
-       echo Found existing HAPI directory in Lite mode. Removing it to avoid build issues...
+    REM --- Step 0: Clean up previous clone (optional) ---
-       rmdir /s /q "%CLONE_DIR%"
+    echo Checking for existing directory: %CLONE_DIR_CANDLE%
+    if exist "%CLONE_DIR_CANDLE%" (
+        echo Found existing directory, removing it...
+        rmdir /s /q "%CLONE_DIR_CANDLE%"
+        if errorlevel 1 (
+            echo ERROR: Failed to remove existing directory: %CLONE_DIR_CANDLE%
+            goto :error
+        )
+        echo Existing directory removed.
+    ) else (
+        echo Directory does not exist, proceeding with clone.
     )
-    REM Create empty target directories expected by Dockerfile COPY, even if not used
+    echo.
-    mkdir "%CLONE_DIR%\target\classes" 2> nul
+
-    mkdir "%CLONE_DIR%\custom" 2> nul
+    REM --- Step 1: Clone the FHIR Candle server repository ---
-    REM Create a placeholder empty WAR file to satisfy Dockerfile COPY
+    echo Cloning repository: %REPO_URL_CANDLE% into %CLONE_DIR_CANDLE%...
-    echo. > "%CLONE_DIR%\target\ROOT.war"
+    git clone "%REPO_URL_CANDLE%" "%CLONE_DIR_CANDLE%"
-    echo. > "%CLONE_DIR%\target\classes\application.yaml"
+    if errorlevel 1 (
+        echo ERROR: Failed to clone repository. Check Git and Dotnet installation and network connection.
+        goto :error
+    )
+    echo Repository cloned successfully.
+    echo.
+    
+    REM --- Step 2: Navigate into the cloned directory ---
+    echo Changing directory to %CLONE_DIR_CANDLE%...
+    cd "%CLONE_DIR_CANDLE%"
+    if errorlevel 1 (
+        echo ERROR: Failed to change directory to %CLONE_DIR_CANDLE%.
+        goto :error
+    )
+    echo Current directory: %CD%
+    echo.
+
+    REM --- Step 3: Build the FHIR Candle server using Dotnet ---
+    echo ===> "Starting Dotnet build (Step 3)...""
+    dotnet publish -c Release -f net9.0 -o publish
+    echo ===> Dotnet command finished. Checking error level...
+    if errorlevel 1 (
+        echo ERROR: Dotnet build failed. Check Dotnet SDK installation.
+        cd ..
+        goto :error
+    )
+    echo Dotnet build completed successfully. ErrorLevel: %errorlevel%
+    echo.
+    
+    REM --- Step 4: Navigate back to the parent directory ---
+    echo ===> "Changing directory back (Step 4)..."
+    cd ..
+    if errorlevel 1 (
+        echo ERROR: Failed to change back to the parent directory. ErrorLevel: %errorlevel%
+        goto :error
+    )
+    echo Current directory: %CD%
+    echo.
+
+) ELSE (
+    echo Running Lite setup, skipping server build...
+    REM Ensure the server directories don't exist in Lite mode
+    if exist "%CLONE_DIR_HAPI%" (
+       echo Found existing HAPI directory in Lite mode. Removing it to avoid build issues...
+       rmdir /s /q "%CLONE_DIR_HAPI%"
+    )
+    if exist "%CLONE_DIR_CANDLE%" (
+       echo Found existing Candle directory in Lite mode. Removing it to avoid build issues...
+       rmdir /s /q "%CLONE_DIR_CANDLE%"
+    )
+    REM Create empty placeholder files to satisfy Dockerfile COPY commands in Lite mode.
+    mkdir "%CLONE_DIR_HAPI%\target\classes" 2> nul
+    mkdir "%CLONE_DIR_HAPI%\custom" 2> nul
+    echo. > "%CLONE_DIR_HAPI%\target\ROOT.war"
+    echo. > "%CLONE_DIR_HAPI%\target\classes\application.yaml"
+    mkdir "%CLONE_DIR_CANDLE%\publish" 2> nul
+    echo. > "%CLONE_DIR_CANDLE%\publish\fhir-candle.dll"
     echo Placeholder files created for Lite mode build.
     echo.
 )
 
-REM === Modify docker-compose.yml to set APP_MODE ===
+REM === MODIFIED: Update docker-compose.yml to set APP_MODE and HAPI_FHIR_URL ===
-echo Updating docker-compose.yml with APP_MODE=%APP_MODE%...
+echo Updating docker-compose.yml with APP_MODE=%APP_MODE% and HAPI_FHIR_URL...
 (
   echo version: '3.8'
   echo services:
   echo   fhirflare:
   echo     build:
   echo       context: .
-  echo       dockerfile: Dockerfile
+  IF "%SERVER_TYPE%"=="hapi" (
+        echo       dockerfile: Dockerfile.hapi
+    ) ELSE IF "%SERVER_TYPE%"=="candle" (
+        echo       dockerfile: Dockerfile.candle
+    ) ELSE (
+        echo       dockerfile: Dockerfile.lite
+  )
   echo     ports:
-  echo       - "5000:5000"
+  IF "%SERVER_TYPE%"=="candle" (
-  echo       - "8080:8080" # Keep port exposed, even if Tomcat isn't running useful stuff in Lite
+    echo       - "5000:5000"
+    echo       - "5001:5826"
+  ) ELSE (
+    echo       - "5000:5000"
+    echo       - "8080:8080"
+  )
   echo     volumes:
   echo       - ./instance:/app/instance
   echo       - ./static/uploads:/app/static/uploads
-  echo       - ./instance/hapi-h2-data/:/app/h2-data # Keep volume mounts consistent
+  IF "%SERVER_TYPE%"=="hapi" (
+    echo       - ./instance/hapi-h2-data/:/app/h2-data # Keep volume mounts consistent
+  )
   echo       - ./logs:/app/logs
+  IF "%SERVER_TYPE%"=="hapi" (
+    echo       - ./hapi-fhir-jpaserver/target/ROOT.war:/usr/local/tomcat/webapps/ROOT.war
+    echo       - ./hapi-fhir-jpaserver/target/classes/application.yaml:/usr/local/tomcat/conf/application.yaml
+  ) ELSE IF "%SERVER_TYPE%"=="candle" (
+    echo       - ./fhir-candle/publish/:/app/fhir-candle-publish/
+  )
   echo     environment:
   echo       - FLASK_APP=app.py
   echo       - FLASK_ENV=development
   echo       - NODE_PATH=/usr/lib/node_modules
   echo       - APP_MODE=%APP_MODE%
   echo       - APP_BASE_URL=http://localhost:5000
-  echo       - HAPI_FHIR_URL=http://localhost:8080/fhir 
+  IF DEFINED CUSTOM_FHIR_URL_VAL (
+    echo       - HAPI_FHIR_URL=!CUSTOM_FHIR_URL_VAL!
+  ) ELSE (
+    IF "%SERVER_TYPE%"=="candle" (
+        echo       - HAPI_FHIR_URL=http://localhost:5826/fhir/%CANDLE_FHIR_VERSION%
+        echo       - ASPNETCORE_URLS=http://0.0.0.0:5826
+    ) ELSE (
+        echo       - HAPI_FHIR_URL=http://localhost:8080/fhir
+    )
+  )
   echo     command: supervisord -c /etc/supervisord.conf
 ) > docker-compose.yml.tmp
 

Dockerfile

@@ -3,13 +3,16 @@ 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 \
+    python3 python3-pip python3-venv curl coreutils git \
     && curl -fsSL https://deb.nodesource.com/setup_18.x | bash - \
     && apt-get install -y --no-install-recommends nodejs \
     && rm -rf /var/lib/apt/lists/*
 
+# ADDED: Install the Dotnet SDK for the FHIR Candle server
+# This makes the image a universal base for either server type
+RUN apt-get update && apt-get install -y dotnet-sdk-6.0
+
 # Install specific versions of GoFSH and SUSHI
-# REMOVED pip install fhirpath from this line
 RUN npm install -g gofsh fsh-sushi
 
 # ADDED: Download the latest HL7 FHIR Validator CLI
@@ -24,7 +27,6 @@ RUN chmod 755 validator_cli.jar
 # Change back to the main app directory for the next steps
 WORKDIR /app
 # Set up Python environment
-WORKDIR /app
 RUN python3 -m venv /app/venv
 ENV PATH="/app/venv/bin:$PATH"
 
@@ -55,6 +57,9 @@ COPY hapi-fhir-jpaserver/target/classes/application.yaml /app/config/application
 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/
 
+# ADDED: Copy pre-built Candle DLL files
+COPY fhir-candle/publish/ /app/fhir-candle-publish/
+
 # Install supervisord
 RUN pip install supervisor
 
@@ -62,7 +67,7 @@ RUN pip install supervisor
 COPY supervisord.conf /etc/supervisord.conf
 
 # Expose ports
-EXPOSE 5000 8080
+EXPOSE 5000 8080 5001
 
 # Start supervisord
 CMD ["supervisord", "-c", "/etc/supervisord.conf"]

Dockerfile.candle

@@ -0,0 +1,62 @@
+# Base image with Python and Dotnet
+FROM mcr.microsoft.com/dotnet/sdk:9.0
+
+# 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 git \
+    && 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
+RUN npm install -g gofsh fsh-sushi
+
+# ADDED: Download the latest HL7 FHIR Validator CLI
+RUN mkdir -p /app/validator_cli
+WORKDIR /app/validator_cli
+# Download the validator JAR and a separate checksum file for verification
+RUN curl -L -o validator_cli.jar "https://github.com/hapifhir/org.hl7.fhir.core/releases/latest/download/validator_cli.jar"
+
+# Set permissions for the downloaded file
+RUN chmod 755 validator_cli.jar
+
+# Change back to the main app directory for the next steps
+WORKDIR /app
+# Set up Python environment
+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 Candle DLL files
+COPY fhir-candle/publish/ /app/fhir-candle-publish/
+
+# Install supervisord
+RUN pip install supervisor
+
+# Configure supervisord
+COPY supervisord.conf /etc/supervisord.conf
+
+# Expose ports
+EXPOSE 5000 5001
+
+# Start supervisord
+CMD ["supervisord", "-c", "/etc/supervisord.conf"]

Dockerfile.hapi

@@ -0,0 +1,66 @@
+# Base image with Python, Java, and Maven
+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 git maven \
+    && 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
+RUN npm install -g gofsh fsh-sushi
+
+# ADDED: Download the latest HL7 FHIR Validator CLI
+RUN mkdir -p /app/validator_cli
+WORKDIR /app/validator_cli
+# Download the validator JAR and a separate checksum file for verification
+RUN curl -L -o validator_cli.jar "https://github.com/hapifhir/org.hl7.fhir.core/releases/latest/download/validator_cli.jar"
+
+# Set permissions for the downloaded file
+RUN chmod 755 validator_cli.jar
+
+# Change back to the main app directory for the next steps
+WORKDIR /app
+# Set up Python environment
+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"]

Dockerfile.lite

@@ -0,0 +1,58 @@
+# Base image with Python and Node.js
+FROM python:3.9-slim
+
+# Install Node.js 18 and npm
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    curl coreutils git \
+    && 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
+RUN npm install -g gofsh fsh-sushi
+
+# ADDED: Download the latest HL7 FHIR Validator CLI
+RUN mkdir -p /app/validator_cli
+WORKDIR /app/validator_cli
+# Download the validator JAR and a separate checksum file for verification
+RUN curl -L -o validator_cli.jar "https://github.com/hapifhir/org.hl7.fhir.core/releases/latest/download/validator_cli.jar"
+
+# Set permissions for the downloaded file
+RUN chmod 755 validator_cli.jar
+
+# Change back to the main app directory for the next steps
+WORKDIR /app
+# Set up Python environment
+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 .
+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 necessary directories are writable
+RUN mkdir -p /app/static/uploads /app/logs && chmod 777 /app/static/uploads /app/logs
+
+# Install supervisord
+RUN pip install supervisor
+
+# Configure supervisord
+COPY supervisord.conf /etc/supervisord.conf
+
+# Expose ports
+EXPOSE 5000
+
+# Start supervisord
+CMD ["supervisord", "-c", "/etc/supervisord.conf"]

docker-compose.yml

@@ -3,14 +3,13 @@ services:
   fhirflare:
     build:
       context: .
-      dockerfile: Dockerfile
+      dockerfile: Dockerfile.lite
     ports:
       - "5000:5000"
-      - "8080:8080" # Keep port exposed, even if Tomcat isn't running useful stuff in Lite
+      - "8080:8080"
     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

setup_linux.sh

@@ -1,18 +1,21 @@
 #!/bin/bash
 
 # --- Configuration ---
-REPO_URL="https://github.com/hapifhir/hapi-fhir-jpaserver-starter.git"
+REPO_URL_HAPI="https://github.com/hapifhir/hapi-fhir-jpaserver-starter.git"
-CLONE_DIR="hapi-fhir-jpaserver"
+REPO_URL_CANDLE="https://github.com/FHIR/fhir-candle.git"
-SOURCE_CONFIG_DIR="hapi-fhir-Setup" # Assuming this is relative to the script's parent
+CLONE_DIR_HAPI="hapi-fhir-jpaserver"
+CLONE_DIR_CANDLE="fhir-candle"
+SOURCE_CONFIG_DIR="hapi-fhir-Setup"
 CONFIG_FILE="application.yaml"
 
 # --- Define Paths ---
-# Note: Adjust SOURCE_CONFIG_PATH if SOURCE_CONFIG_DIR is not a sibling directory
-# This assumes the script is run from a directory, and hapi-fhir-setup is at the same level
 SOURCE_CONFIG_PATH="../${SOURCE_CONFIG_DIR}/target/classes/${CONFIG_FILE}"
-DEST_CONFIG_PATH="${CLONE_DIR}/target/classes/${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() {
@@ -20,25 +23,39 @@ handle_error() {
     echo "An error occurred: $1"
     echo "Script aborted."
     echo "------------------------------------"
-    # Removed 'read -p "Press Enter to exit..."' as it's not typical for non-interactive CI/CD
     exit 1
 }
 
-# === Prompt for Installation Mode ===
+# === MODIFIED: Prompt for Installation Mode ===
 get_mode_choice() {
+    echo ""
     echo "Select Installation Mode:"
-    echo "1. Standalone (Includes local HAPI FHIR Server - Requires Git & Maven)"
+    echo "1. Lite (Excludes local HAPI FHIR Server - No Git/Maven/Dotnet needed)"
-    echo "2. Lite (Excludes local HAPI FHIR Server - No Git/Maven 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 or 2): " choice
+        read -r -p "Enter your choice (1, 2, 3, or 4): " choice
         case "$choice" in
             1)
-                APP_MODE="standalone"
+                APP_MODE="lite"
                 break
                 ;;
             2)
-                APP_MODE="lite"
+                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
                 ;;
             *)
@@ -47,156 +64,301 @@ get_mode_choice() {
         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 HAPI Setup ===
+# === Conditionally Execute Server Setup ===
-if [ "$APP_MODE" = "standalone" ]; then
+case "$SERVER_TYPE" in
-    echo "Running Standalone setup including HAPI FHIR..."
+    "hapi")
-    echo
+        echo "Running Hapi server setup..."
+        echo
 
-    # --- Step 0: Clean up previous clone (optional) ---
+        # --- Step 0: Clean up previous clone (optional) ---
-    echo "Checking for existing directory: $CLONE_DIR"
+        echo "Checking for existing directory: $CLONE_DIR_HAPI"
-    if [ -d "$CLONE_DIR" ]; then
+        if [ -d "$CLONE_DIR_HAPI" ]; then
-        echo "Found existing directory, removing it..."
+            echo "Found existing directory, removing it..."
-        rm -rf "$CLONE_DIR"
+            rm -rf "$CLONE_DIR_HAPI"
-        if [ $? -ne 0 ]; then
+            if [ $? -ne 0 ]; then
-            handle_error "Failed to remove existing directory: $CLONE_DIR"
+                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 "Existing directory removed."
+        echo
-    else
-        echo "Directory does not exist, proceeding with clone."
-    fi
-    echo
 
-    # --- Step 1: Clone the HAPI FHIR server repository ---
+        # --- Step 1: Clone the HAPI FHIR server repository ---
-    echo "Cloning repository: $REPO_URL into $CLONE_DIR..."
+        echo "Cloning repository: $REPO_URL_HAPI into $CLONE_DIR_HAPI..."
-    git clone "$REPO_URL" "$CLONE_DIR"
+        git clone "$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 $CLONE_DIR..."
-    cd "$CLONE_DIR" || handle_error "Failed to change directory to $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
-    if [ $? -ne 0 ]; then
-        echo "ERROR: Maven build failed."
-        cd ..
-        handle_error "Maven build process resulted in an error."
-    fi
-    echo "Maven build completed successfully."
-    echo
-
-    # --- Step 4: Copy the configuration file ---
-    echo "===> Starting file copy (Step 4)..."
-    echo "Copying configuration file..."
-    # Corrected SOURCE_CONFIG_PATH to be relative to the new current directory ($CLONE_DIR)
-    # This assumes the original script's SOURCE_CONFIG_PATH was relative to its execution location
-    # If SOURCE_CONFIG_DIR is ../hapi-fhir-setup relative to script's original location:
-    # Then from within CLONE_DIR, it becomes ../../hapi-fhir-setup
-    # We defined SOURCE_CONFIG_PATH earlier relative to the script start.
-    # So, when inside CLONE_DIR, the path from original script location should be used.
-    # The original script had: set SOURCE_CONFIG_PATH=..\%SOURCE_CONFIG_DIR%\target\classes\%CONFIG_FILE%
-    # And then: xcopy "%SOURCE_CONFIG_PATH%" "target\classes\"
-    # This implies SOURCE_CONFIG_PATH is relative to the original script's location, not the $CLONE_DIR
-    # Therefore, we need to construct the correct relative path from *within* $CLONE_DIR back to the source.
-    # Assuming the script is in dir X, and SOURCE_CONFIG_DIR is ../hapi-fhir-setup from X.
-    # So, hapi-fhir-setup is a sibling of X's parent.
-    # If CLONE_DIR is also in X, then from within CLONE_DIR, the path is ../ + original SOURCE_CONFIG_PATH
-    # For simplicity and robustness, let's use an absolute path or a more clearly defined relative path from the start.
-    # The original `SOURCE_CONFIG_PATH=..\%SOURCE_CONFIG_DIR%\target\classes\%CONFIG_FILE%` implies
-    # that `hapi-fhir-setup` is a sibling of the directory where the script *is being run from*.
-
-    # Let's assume the script is run from the root of FHIRFLARE-IG-Toolkit.
-    # And hapi-fhir-setup is also in the root, next to this script.
-    # Then SOURCE_CONFIG_PATH would be ./hapi-fhir-setup/target/classes/application.yaml
-    # And from within ./hapi-fhir-jpaserver/, the path would be ../hapi-fhir-setup/target/classes/application.yaml
-
-    # The original batch file sets SOURCE_CONFIG_PATH as "..\%SOURCE_CONFIG_DIR%\target\classes\%CONFIG_FILE%"
-    # And COPIES it to "target\classes\" *while inside CLONE_DIR*.
-    # This means the source path is relative to where the *cd %CLONE_DIR%* happened from.
-    # Let's make it relative to the script's initial execution directory.
-    INITIAL_SCRIPT_DIR=$(pwd)
-    ABSOLUTE_SOURCE_CONFIG_PATH="${INITIAL_SCRIPT_DIR}/../${SOURCE_CONFIG_DIR}/target/classes/${CONFIG_FILE}" # This matches the ..\ logic
-
-    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."
+            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 $ABSOLUTE_SOURCE_CONFIG_PATH."
             echo "The script will continue, but the server might use default configuration."
         else
-            echo "Configuration file copied successfully."
+            cp "$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
-    fi
+        echo
-    echo
 
-    # --- Step 5: Navigate back to the parent directory ---
+        # --- Step 5: Navigate back to the parent directory ---
-    echo "===> Changing directory back (Step 5)..."
+        echo "===> Changing directory back (Step 5)..."
-    cd .. || handle_error "Failed to change back to the parent directory."
+        cd .. || handle_error "Failed to change back to the parent directory."
-    echo "Current directory: $(pwd)"
+        echo "Current directory: $(pwd)"
-    echo
+        echo
+        ;;
 
-else # APP_MODE is "lite"
+    "candle")
-    echo "Running Lite setup, skipping HAPI FHIR build..."
+        echo "Running FHIR Candle server setup..."
-    # Ensure the hapi-fhir-jpaserver directory doesn't exist or is empty if Lite mode is chosen
+        echo
-    if [ -d "$CLONE_DIR" ]; then
-        echo "Found existing HAPI directory ($CLONE_DIR) in Lite mode. Removing it..."
-        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 "${CLONE_DIR}/custom" # This was in the original batch, ensure it's here
-    # Create a placeholder empty WAR file and application.yaml to satisfy Dockerfile COPY
-    touch "${CLONE_DIR}/target/ROOT.war"
-    touch "${CLONE_DIR}/target/classes/application.yaml"
-    echo "Placeholder files and directories created for Lite mode build in $CLONE_DIR."
-    echo
-fi
         
-# === Modify docker-compose.yml to set APP_MODE ===
+        # --- Step 0: Clean up previous clone (optional) ---
-echo "Updating docker-compose.yml with APP_MODE=$APP_MODE..."
+        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
+      dockerfile: ${DOCKERFILE_TO_USE}
     ports:
+EOF
+
+if [ "$SERVER_TYPE" = "candle" ]; then
+    cat << EOF >> "$DOCKER_COMPOSE_TMP"
       - "5000:5000"
-      - "8080:8080" # Keep port exposed, even if Tomcat isn't running useful stuff in Lite
+      - "5001:5826"
+EOF
+else
+    cat << EOF >> "$DOCKER_COMPOSE_TMP"
+      - "5000:5000"
+      - "8080:8080"
+EOF
+fi
+
+cat << EOF >> "$DOCKER_COMPOSE_TMP"
     volumes:
       - ./instance:/app/instance
       - ./static/uploads:/app/static/uploads
-      - ./instance/hapi-h2-data/:/app/h2-data # Keep volume mounts consistent
       - ./logs:/app/logs
+EOF
+
+if [ "$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=${APP_MODE}
       - APP_BASE_URL=http://localhost:5000
-      - HAPI_FHIR_URL=http://localhost:8080/fhir
+      - HAPI_FHIR_URL=${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
 

supervisord.conf

@@ -34,3 +34,17 @@ stdout_logfile_backups=5
 stderr_logfile=/app/logs/tomcat_err.log 
 stderr_logfile_maxbytes=10MB 
 stderr_logfile_backups=5
+
+[program:candle]
+command=dotnet /app/fhir-candle-publish/fhir-candle.dll
+directory=/app/fhir-candle-publish
+autostart=true
+autorestart=true
+startsecs=10
+stopwaitsecs=10
+stdout_logfile=/app/logs/candle.log
+stdout_logfile_maxbytes=10MB
+stdout_logfile_backups=5
+stderr_logfile=/app/logs/candle_err.log
+stderr_logfile_maxbytes=10MB
+stderr_logfile_backups=5