2025-11-05 17:45:14 +00:00
22 changed files with 1433 additions and 2691 deletions
--- a/time.bat
+++ b/time.bat
@ -2,130 +2,57 @@
 setlocal enabledelayedexpansion
 REM --- Configuration ---
-set REPO_URL_HAPI=https://github.com/hapifhir/hapi-fhir-jpaserver-starter.git
+set REPO_URL=https://github.com/hapifhir/hapi-fhir-jpaserver-starter.git
-set REPO_URL_CANDLE=https://github.com/FHIR/fhir-candle.git
+set CLONE_DIR=hapi-fhir-jpaserver
 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_HAPI%\target\classes\%CONFIG_FILE%
+set DEST_CONFIG_PATH=%CLONE_DIR%\target\classes\%CONFIG_FILE%
-REM --- NEW: Define a variable for the custom FHIR URL and server type ---
+REM === CORRECTED: Prompt for Version ===
 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. Lite (Excludes local HAPI FHIR Server - No Git/Maven/Dotnet needed)
+echo 1. Standalone (Includes local HAPI FHIR Server - Requires Git & Maven)
-echo 2. Custom URL (Uses a custom FHIR Server - No Git/Maven/Dotnet needed)
+echo 2. Lite (Excludes local HAPI FHIR Server - No Git/Maven needed)
-echo 3. Hapi (Includes local HAPI FHIR Server - Requires Git & Maven)
+CHOICE /C 12 /N /M "Enter your choice (1 or 2):"
 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 MODIFICATION ===
+REM === END CORRECTION ===
-REM === Conditionally Execute Server Setup ===
+REM === Conditionally Execute HAPI Setup ===
-IF "%SERVER_TYPE%"=="hapi" (
+IF "%APP_MODE%"=="standalone" (
-    echo Running Hapi server setup...
+    echo Running Standalone setup including HAPI FHIR...
    echo.
-    
+
    REM --- Step 0: Clean up previous clone (optional) ---
-    echo Checking for existing directory: %CLONE_DIR_HAPI%
+    echo Checking for existing directory: %CLONE_DIR%
-    if exist "%CLONE_DIR_HAPI%" (
+    if exist "%CLONE_DIR%" (
        echo Found existing directory, removing it...
-        rmdir /s /q "%CLONE_DIR_HAPI%"
+        rmdir /s /q "%CLONE_DIR%"
        if errorlevel 1 (
-            echo ERROR: Failed to remove existing directory: %CLONE_DIR_HAPI%
+            echo ERROR: Failed to remove existing directory: %CLONE_DIR%
            goto :error
        )
        echo Existing directory removed.
@ -135,8 +62,8 @@ IF "%SERVER_TYPE%"=="hapi" (
    echo.
    REM --- Step 1: Clone the HAPI FHIR server repository ---
-    echo Cloning repository: %REPO_URL_HAPI% into %CLONE_DIR_HAPI%...
+    echo Cloning repository: %REPO_URL% into %CLONE_DIR%...
-    git clone "%REPO_URL_HAPI%" "%CLONE_DIR_HAPI%"
+    git clone "%REPO_URL%" "%CLONE_DIR%"
    if errorlevel 1 (
        echo ERROR: Failed to clone repository. Check Git installation and network connection.
        goto :error
@ -145,10 +72,10 @@ IF "%SERVER_TYPE%"=="hapi" (
    echo.
    REM --- Step 2: Navigate into the cloned directory ---
-    echo Changing directory to %CLONE_DIR_HAPI%...
+    echo Changing directory to %CLONE_DIR%...
-    cd "%CLONE_DIR_HAPI%"
+    cd "%CLONE_DIR%"
    if errorlevel 1 (
-        echo ERROR: Failed to change directory to %CLONE_DIR_HAPI%.
+        echo ERROR: Failed to change directory to %CLONE_DIR%.
        goto :error
    )
    echo Current directory: %CD%
@ -165,7 +92,7 @@ IF "%SERVER_TYPE%"=="hapi" (
    )
    echo Maven build completed successfully. ErrorLevel: %errorlevel%
    echo.
-    
+
    REM --- Step 4: Copy the configuration file ---
    echo ===> "Starting file copy (Step 4)..."
    echo Copying configuration file...
@ -191,141 +118,47 @@ IF "%SERVER_TYPE%"=="hapi" (
    echo Current directory: %CD%
    echo.
 ) ELSE IF "%SERVER_TYPE%"=="candle" (
    echo Running FHIR Candle server setup...
    echo.
    REM --- Step 0: Clean up previous clone (optional) ---
    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.
    )
    echo.
    REM --- 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 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...
+    echo Running Lite setup, skipping HAPI FHIR build...
-    REM Ensure the server directories don't exist in Lite mode
+    REM Ensure the hapi-fhir-jpaserver directory doesn't exist or is empty if Lite mode is chosen after a standalone attempt
-    if exist "%CLONE_DIR_HAPI%" (
+    if exist "%CLONE_DIR%" (
       echo Found existing HAPI directory in Lite mode. Removing it to avoid build issues...
-       rmdir /s /q "%CLONE_DIR_HAPI%"
+       rmdir /s /q "%CLONE_DIR%"
    )
-    if exist "%CLONE_DIR_CANDLE%" (
+    REM Create empty target directories expected by Dockerfile COPY, even if not used
-       echo Found existing Candle directory in Lite mode. Removing it to avoid build issues...
+    mkdir "%CLONE_DIR%\target\classes" 2> nul
-       rmdir /s /q "%CLONE_DIR_CANDLE%"
+    mkdir "%CLONE_DIR%\custom" 2> nul
-    )
+    REM Create a placeholder empty WAR file to satisfy Dockerfile COPY
-    REM Create empty placeholder files to satisfy Dockerfile COPY commands in Lite mode.
+    echo. > "%CLONE_DIR%\target\ROOT.war"
-    mkdir "%CLONE_DIR_HAPI%\target\classes" 2> nul
+    echo. > "%CLONE_DIR%\target\classes\application.yaml"
    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 === MODIFIED: Update docker-compose.yml to set APP_MODE and HAPI_FHIR_URL ===
+REM === Modify docker-compose.yml to set APP_MODE ===
-echo Updating docker-compose.yml with APP_MODE=%APP_MODE% and HAPI_FHIR_URL...
+echo Updating docker-compose.yml with APP_MODE=%APP_MODE%...
 (
  echo version: '3.8'
  echo services:
  echo   fhirflare:
  echo     build:
  echo       context: .
-  IF "%SERVER_TYPE%"=="hapi" (
+  echo       dockerfile: Dockerfile
        echo       dockerfile: Dockerfile.hapi
    ) ELSE IF "%SERVER_TYPE%"=="candle" (
        echo       dockerfile: Dockerfile.candle
    ) ELSE (
        echo       dockerfile: Dockerfile.lite
  )
  echo     ports:
-  IF "%SERVER_TYPE%"=="candle" (
+  echo       - "5000:5000"
-    echo       - "5000:5000"
+  echo       - "8080:8080" # Keep port exposed, even if Tomcat isn't running useful stuff in Lite
    echo       - "5001:5826"
  ) ELSE (
    echo       - "5000:5000"
    echo       - "8080:8080"
  )
  echo     volumes:
  echo       - ./instance:/app/instance
  echo       - ./static/uploads:/app/static/uploads
-  IF "%SERVER_TYPE%"=="hapi" (
+  echo       - ./instance/hapi-h2-data/:/app/h2-data # Keep volume mounts consistent
    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
-  IF DEFINED CUSTOM_FHIR_URL_VAL (
+  echo       - HAPI_FHIR_URL=http://localhost:8080/fhir 
    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
@ -375,4 +208,4 @@ exit /b 1
 :eof
 echo Script execution finished.
-pause
+pause
--- a/26
+++ b/26
@ -3,30 +3,17 @@ 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 \
+    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/*
 # 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
 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
 WORKDIR /app
 RUN python3 -m venv /app/venv
 ENV PATH="/app/venv/bin:$PATH"
@ -57,9 +44,6 @@ COPY hapi-fhir-jpaserver/target/classes/application.yaml /app/config/application
 COPY hapi-fhir-jpaserver/target/classes/application.yaml /usr/local/tomcat/webapps/app/config/application.yaml
 COPY hapi-fhir-jpaserver/custom/ /usr/local/tomcat/webapps/custom/
 # ADDED: Copy pre-built Candle DLL files
 COPY fhir-candle/publish/ /app/fhir-candle-publish/
 # Install supervisord
 RUN pip install supervisor
@ -67,7 +51,7 @@ RUN pip install supervisor
 COPY supervisord.conf /etc/supervisord.conf
 # Expose ports
-EXPOSE 5000 8080 5001
+EXPOSE 5000 8080
 # Start supervisord
-CMD ["supervisord", "-c", "/etc/supervisord.conf"]
+CMD ["supervisord", "-c", "/etc/supervisord.conf"]
--- a/Dockerfile.candle
+++ b/Dockerfile.candle
@ -1,64 +0,0 @@
 # Base image with Python and Dotnet
 FROM mcr.microsoft.com/dotnet/sdk:9.0
 # Install build dependencies, Node.js 18, and coreutils (for stdbuf)
 RUN apt-get update && apt-get install -y --no-install-recommends \
    python3 python3-pip python3-venv \
    default-jre-headless \
    curl coreutils git \
    && curl -fsSL https://deb.nodesource.com/setup_18.x | bash - \
    && apt-get install -y --no-install-recommends nodejs \
    && rm -rf /var/lib/apt/lists/*
 # Install specific versions of GoFSH and SUSHI
 RUN npm install -g gofsh fsh-sushi
 # ADDED: Download the latest HL7 FHIR Validator CLI
 RUN mkdir -p /app/validator_cli
 WORKDIR /app/validator_cli
 # Download the validator JAR and a separate checksum file for verification
 RUN curl -L -o validator_cli.jar "https://github.com/hapifhir/org.hl7.fhir.core/releases/latest/download/validator_cli.jar"
 # Set permissions for the downloaded file
 RUN chmod 755 validator_cli.jar
 # Change back to the main app directory for the next steps
 WORKDIR /app
 # Set up Python environment
 RUN python3 -m venv /app/venv
 ENV PATH="/app/venv/bin:$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"]
--- a/Dockerfile.hapi
+++ b/Dockerfile.hapi
@ -1,66 +0,0 @@
 # 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"]
--- a/Dockerfile.lite
+++ b/Dockerfile.lite
@ -1,60 +0,0 @@
 # Base image with Python and Node.js
 FROM python:3.9-slim
 # Install JRE and other dependencies for the validator
 # We need to install `default-jre-headless` to get a minimal Java Runtime Environment
 RUN apt-get update && apt-get install -y --no-install-recommends \
    default-jre-headless \
    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"]
--- a/README.md
+++ b/README.md
@ -5,65 +5,22 @@
 The FHIRFLARE IG Toolkit is a Flask-based web application designed to streamline the management, processing, validation, and deployment of FHIR Implementation Guides (IGs) and test data. It offers a user-friendly interface for importing IG packages, extracting metadata, validating FHIR resources or bundles, pushing IGs to FHIR servers, converting FHIR resources to FHIR Shorthand (FSH), uploading complex test data sets with dependency management, and retrieving/splitting FHIR bundles. The toolkit includes live consoles for real-time feedback, making it an essential tool for FHIR developers and implementers.
-The application can run in four modes:
+The application can run in two modes:
-
+* **Standalone:** Includes a Dockerized Flask frontend, SQLite database, and an embedded HAPI FHIR server for local validation and interaction.
-* Installation Modes (Lite, Custom URL, Hapi, and Candle)
+* **Lite:** Includes only the Dockerized Flask frontend and SQLite database, excluding the local HAPI FHIR server. Requires connection to external FHIR servers for certain features.
    This toolkit now offers four primary installation modes, configured via a simple command-line prompt during setup:
    Lite Mode
    Includes the Flask frontend, SQLite database, and core tooling (GoFSH, SUSHI) without an embedded FHIR server.
    Requires you to provide a URL for an external FHIR server when using features like the FHIR API Explorer and validation.
    Does not require Git, Maven, or .NET for setup.
    Ideal for users who will always connect to an existing external FHIR server.
    Custom URL Mode
    Similar to Lite Mode, but prompts you for a specific external FHIR server URL to use as the default for the toolkit.
    The application will be pre-configured to use your custom URL for all FHIR-related operations.
    Does not require Git, Maven, or .NET for setup.
    Hapi Mode
    Includes the full FHIRFLARE toolkit and an embedded HAPI FHIR server.
    The docker-compose configuration will proxy requests to the internal HAPI server, which is accessible via http://localhost:8080/fhir.
    Requires Git and Maven during the initial build process to compile the HAPI FHIR server.
    Ideal for users who want a self-contained, offline development and testing environment.
    Candle Mode
    Includes the full FHIRFLARE toolkit and an embedded FHIR Candle server.
    The docker-compose configuration will proxy requests to the internal Candle server, which is accessible via http://localhost:5001/fhir/<version>.
    Requires Git and the .NET SDK during the initial build process.
    Ideal for users who want to use the .NET-based FHIR server for development and testing.
 ## Installation Modes (Lite vs. Standalone)
 This toolkit offers two primary installation modes to suit different needs:
-* **Standalone Version - Hapi / Candle:**
+* **Standalone Version:**
    * Includes the full FHIRFLARE Toolkit application **and** an embedded HAPI FHIR server running locally within the Docker environment.
    * Allows for local FHIR resource validation using HAPI FHIR's capabilities.
    * Enables the "Use Local HAPI" option in the FHIR API Explorer and FHIR UI Operations pages, proxying requests to the internal HAPI server (`http://localhost:8080/fhir`).
    * Requires Git and Maven during the initial build process (via the `.bat` script or manual steps) to prepare the HAPI FHIR server.
    * Ideal for users who want a self-contained environment for development and testing or who don't have readily available external FHIR servers.
 * **Standalone Version - Custom Mode:**
    * Includes the full FHIRFLARE Toolkit application **and** point the Environmet variable at your chosen custom fhir url endpoint allowing for Custom setups
 * **Lite Version:**
    * Includes the FHIRFLARE Toolkit application **without** the embedded HAPI FHIR server.
    * Requires users to provide URLs for external FHIR servers when using features like the FHIR API Explorer and FHIR UI Operations pages. The "Use Local HAPI" option will be disabled in the UI.
--- a/app.py
+++ b/app.py
@ -29,7 +29,6 @@ import re
 import yaml
 import threading
 import time # Add time import
 import io
 import services
 from services import (
    services_bp,
@ -45,14 +44,9 @@ from services import (
    pkg_version,
    get_package_description,
    safe_parse_version,
-    import_manual_package_and_dependencies,
+    import_manual_package_and_dependencies
    parse_and_list_igs, 
    generate_ig_yaml,
    apply_and_validate,
    run_validator_cli,
    uuid
 )
-from forms import IgImportForm, ManualIgImportForm, ValidationForm, FSHConverterForm, TestDataUploadForm, RetrieveSplitDataForm, IgYamlForm
+from forms import IgImportForm, ManualIgImportForm, ValidationForm, FSHConverterForm, TestDataUploadForm, RetrieveSplitDataForm
 from wtforms import SubmitField
 from package import package_bp
 from flasgger import Swagger, swag_from # Import Flasgger
@ -72,16 +66,11 @@ app.config['FHIR_PACKAGES_DIR'] = os.path.join(instance_path, 'fhir_packages')
 app.config['API_KEY'] = os.environ.get('API_KEY', 'your-fallback-api-key-here')
 app.config['VALIDATE_IMPOSED_PROFILES'] = True
 app.config['DISPLAY_PROFILE_RELATIONSHIPS'] = True
 app.config['LATEST_BUILD_URL'] = "http://build.fhir.org/ig/qas.json"
 app.config['VALIDATION_LOG_DIR'] = os.path.join(app.instance_path, 'validation_logs')
 os.makedirs(app.config['VALIDATION_LOG_DIR'], exist_ok=True)
 app.config['UPLOAD_FOLDER'] = os.path.join(CURRENT_DIR, 'static', 'uploads')  # For GoFSH output
 app.config['APP_BASE_URL'] = os.environ.get('APP_BASE_URL', 'http://localhost:5000')
 app.config['HAPI_FHIR_URL'] = os.environ.get('HAPI_FHIR_URL', 'http://localhost:8080/fhir')
 CONFIG_PATH = os.environ.get('CONFIG_PATH', '/usr/local/tomcat/conf/application.yaml')
 # Basic Swagger configuration
 app.config['SWAGGER'] = {
    'title': 'FHIRFLARE IG Toolkit API',
@ -543,29 +532,6 @@ def restart_tomcat():
 def config_hapi():
    return render_template('config_hapi.html', site_name='FHIRFLARE IG Toolkit', now=datetime.datetime.now())
@app.route('/api/get-local-server-url', methods=['GET'])
@swag_from({
    'tags': ['FHIR Server Configuration'],
    'summary': 'Get the local FHIR server URL.',
    'description': 'Retrieves the base URL of the configured local FHIR server (HAPI). This is used by frontend components to make direct requests, bypassing the proxy.',
    'responses': {
        '200': {
            'description': 'The URL of the local FHIR server.',
            'schema': {
                'type': 'object',
                'properties': {
                    'url': {'type': 'string', 'example': 'http://localhost:8080/fhir'}
                }
            }
        }
    }
 })
 def get_local_server_url():
    """
    Expose the local HAPI FHIR server URL to the frontend.
    """
    return jsonify({'url': app.config.get('HAPI_FHIR_URL', 'http://localhost:8080/fhir')})
@app.route('/manual-import-ig', methods=['GET', 'POST'])
 def manual_import_ig():
    """
@ -1772,157 +1738,6 @@ csrf.exempt(api_push_ig)   # Add this line
 # Exempt the entire API blueprint (for routes defined IN services.py, like /api/validate-sample)
 csrf.exempt(services_bp) # Keep this line for routes defined in the blueprint
@app.route('/validate-sample', methods=['GET'])
 def validate_resource_page():
    """Renders the validation form page."""
    form = ValidationForm()
    # Fetch list of packages to populate the dropdown
    packages = current_app.config.get('MANUAL_PACKAGE_CACHE', [])
    return render_template('validate_sample.html', form=form, packages=packages)
@app.route('/api/validate', methods=['POST'])
@swag_from({
    'tags': ['Validation'],
    'summary': 'Starts a validation process for a FHIR resource or bundle.',
    'description': 'Starts a validation task and immediately returns a task ID for polling. The actual validation is run in a separate thread to prevent timeouts.',
    'security': [{'ApiKeyAuth': []}],
    'consumes': ['application/json'],
    'parameters': [
        {
            'name': 'validation_payload',
            'in': 'body',
            'required': True,
            'schema': {
                'type': 'object',
                'required': ['package_name', 'version', 'fhir_resource'],
                'properties': {
                    'package_name': {'type': 'string', 'example': 'hl7.fhir.us.core'},
                    'version': {'type': 'string', 'example': '6.1.0'},
                    'fhir_resource': {'type': 'string', 'description': 'A JSON string of the FHIR resource or Bundle to validate.'},
                    'fhir_version': {'type': 'string', 'example': '4.0.1'},
                    'do_native': {'type': 'boolean', 'default': False},
                    'hint_about_must_support': {'type': 'boolean', 'default': False},
                    'assume_valid_rest_references': {'type': 'boolean', 'default': False},
                    'no_extensible_binding_warnings': {'type': 'boolean', 'default': False},
                    'show_times': {'type': 'boolean', 'default': False},
                    'allow_example_urls': {'type': 'boolean', 'default': False},
                    'check_ips_codes': {'type': 'boolean', 'default': False},
                    'allow_any_extensions': {'type': 'boolean', 'default': False},
                    'tx_routing': {'type': 'boolean', 'default': False},
                    'snomed_ct_version': {'type': 'string', 'default': ''},
                    'profiles': {'type': 'string', 'description': 'Comma-separated list of profile URLs.'},
                    'extensions': {'type': 'string', 'description': 'Comma-separated list of extension URLs.'},
                    'terminology_server': {'type': 'string', 'description': 'URL of an alternate terminology server.'}
                }
            }
        }
    ],
    'responses': {
        '202': {'description': 'Validation process started successfully, returns a task_id.'},
        '400': {'description': 'Invalid request (e.g., missing fields, invalid JSON).'}
    }
 })
 def validate_resource():
    """API endpoint to run validation on a FHIR resource."""
    try:
        # Get data from the JSON payload
        data = request.get_json()
        if not data:
            return jsonify({'status': 'error', 'message': 'Invalid JSON: No data received.'}), 400
        fhir_resource_text = data.get('fhir_resource')
        fhir_version = data.get('fhir_version')
        package_name = data.get('package_name')
        version = data.get('version')
        profiles = data.get('profiles')
        extensions = data.get('extensions')
        terminology_server = data.get('terminology_server')
        snomed_ct_version = data.get('snomed_ct_version')
        # Build the list of IGs from the package name and version
        igs = [f"{package_name}#{version}"] if package_name and version else []
        flags = {
            'doNative': data.get('do_native'),
            'hintAboutMustSupport': data.get('hint_about_must_support'),
            'assumeValidRestReferences': data.get('assume_valid_rest_references'),
            'noExtensibleBindingWarnings': data.get('no_extensible_binding_warnings'),
            'showTimes': data.get('show_times'),
            'allowExampleUrls': data.get('allow_example_urls'),
            'checkIpsCodes': data.get('check_ips_codes'),
            'allowAnyExtensions': data.get('allow_any_extensions'),
            'txRouting': data.get('tx_routing'),
        }
        # Check for empty resource
        if not fhir_resource_text:
            return jsonify({'status': 'error', 'message': 'No FHIR resource provided.'}), 400
        try:
            # Generate a unique task ID
            task_id = str(uuid.uuid4())
            # Store a pending status in the global cache
            with services.cache_lock:
                services.validation_results_cache[task_id] = {"status": "pending"}
            # Start the validation process in a new thread
            app_context = app.app_context()
            thread = threading.Thread(
                target=services.validate_in_thread,
                args=(app_context, task_id, fhir_resource_text, fhir_version, igs, profiles, extensions, terminology_server, flags, snomed_ct_version),
                daemon=True
            )
            thread.start()
            logger.info(f"Validation task {task_id} started in background thread.")
            return jsonify({"status": "accepted", "message": "Validation started", "task_id": task_id}), 202
        except Exception as e:
            logger.error(f"Error starting validation thread: {e}", exc_info=True)
            return jsonify({'status': 'error', 'message': f'An internal server error occurred while starting the validation: {e}'}), 500
    except Exception as e:
        logger.error(f"Validation API error: {e}")
        return jsonify({'status': 'error', 'message': f'An internal server error occurred: {e}'}), 500
@app.route('/api/check-validation-status/<task_id>', methods=['GET'])
@swag_from({
    'tags': ['Validation'],
    'summary': 'Check the status of a validation task.',
    'description': 'Polls for the result of a validation task by its ID. Returns the full validation report when the task is complete.',
    'security': [{'ApiKeyAuth': []}],
    'parameters': [
        {'name': 'task_id', 'in': 'path', 'type': 'string', 'required': True, 'description': 'The unique ID of the validation task.'}
    ],
    'responses': {
        '200': {'description': 'Returns the full validation report if the task is complete.'},
        '202': {'description': 'The validation task is still in progress.'},
        '404': {'description': 'The specified task ID was not found.'}
    }
 })
 def check_validation_status(task_id):
    """
    This GET endpoint is polled by the frontend to check the status of a validation task.
    """
    with services.cache_lock:
        task_result = services.validation_results_cache.get(task_id)
    if task_result is None:
        return jsonify({"status": "error", "message": "Task not found."}), 404
    if task_result["status"] == "pending":
        return jsonify({"status": "pending", "message": "Validation is still in progress."}), 202
    # Remove the result from the cache after it has been retrieved to prevent a memory leak
    with services.cache_lock:
        del services.validation_results_cache[task_id]
    return jsonify({"status": "complete", "result": task_result["result"]}), 200
 def create_db():
    logger.debug(f"Attempting to create database tables for URI: {app.config['SQLALCHEMY_DATABASE_URI']}")
    try:
@ -3318,74 +3133,7 @@ def package_details_view(name):
                           package_name=actual_package_name,
                           latest_official_version=latest_official_version_str)
@app.route('/ig-configurator', methods=['GET', 'POST'])
 def ig_configurator():
    form = IgYamlForm()
    packages_dir = current_app.config['FHIR_PACKAGES_DIR']
    loaded_igs = services.parse_and_list_igs(packages_dir)
    form.igs.choices = [(name, f"{name} ({info['version']})") for name, info in loaded_igs.items()]
    yaml_output = None
    if form.validate_on_submit():
        selected_ig_names = form.igs.data
        try:
            yaml_output = generate_ig_yaml(selected_ig_names, loaded_igs)
            flash("YAML configuration generated successfully!", "success")
        except Exception as e:
            flash(f"Error generating YAML: {str(e)}", "error")
            logger.error(f"Error generating YAML: {str(e)}", exc_info=True)
    return render_template('ig_configurator.html', form=form, yaml_output=yaml_output)
@app.route('/download/<path:filename>')
 def download_file(filename):
    """
    Serves a file from the temporary directory created during validation.
    The filename includes the unique temporary directory name to prevent
    unauthorized file access and to correctly locate the file.
    """
    # Use the stored temporary directory path from app.config
    temp_dir = current_app.config.get('VALIDATION_TEMP_DIR')
    # If no temporary directory is set, or it's a security risk, return a 404.
    if not temp_dir or not os.path.exists(temp_dir):
        logger.error(f"Download request failed: Temporary directory not found or expired. Path: {temp_dir}")
        return jsonify({"error": "File not found or validation session expired."}), 404
    # Construct the full file path.
    file_path = os.path.join(temp_dir, filename)
    if not os.path.exists(file_path):
        logger.error(f"File not found for download: {file_path}")
        return jsonify({"error": "File not found."}), 404
    try:
        # Use send_file with as_attachment=True to trigger a download
        return send_file(file_path, as_attachment=True, download_name=filename)
    except Exception as e:
        logger.error(f"Error serving file {file_path}: {str(e)}")
        return jsonify({"error": "Error serving file.", "details": str(e)}), 500
@app.route('/api/clear-validation-results', methods=['POST'])
@csrf.exempt
 def clear_validation_results():
    """
    Clears the temporary directory containing the last validation run's results.
    """
    temp_dir = current_app.config.get('VALIDATION_TEMP_DIR')
    if temp_dir and os.path.exists(temp_dir):
        try:
            shutil.rmtree(temp_dir)
            current_app.config['VALIDATION_TEMP_DIR'] = None
            return jsonify({"status": "success", "message": f"Results cleared successfully."})
        except Exception as e:
            logger.error(f"Failed to clear validation results at {temp_dir}: {e}")
            return jsonify({"status": "error", "message": f"Failed to clear results: {e}"}), 500
    else:
        return jsonify({"status": "success", "message": "No results to clear."})
@app.route('/favicon.ico')
 def favicon():
--- a/docker-compose.yml
+++ b/docker-compose.yml
@ -3,13 +3,14 @@ services:
  fhirflare:
    build:
      context: .
-      dockerfile: Dockerfile.lite
+      dockerfile: Dockerfile
    ports:
      - "5000:5000"
-      - "8080:8080"
+      - "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
@ -17,5 +18,5 @@ services:
      - NODE_PATH=/usr/lib/node_modules
      - APP_MODE=standalone
      - APP_BASE_URL=http://localhost:5000
-      - HAPI_FHIR_URL=https://smile.sparked-fhir.com/aucore/fhir/DEFAULT/
+      - HAPI_FHIR_URL=http://localhost:8080/fhir 
    command: supervisord -c /etc/supervisord.conf
--- a/forms.py
+++ b/forms.py
@ -1,6 +1,6 @@
 # forms.py
 from flask_wtf import FlaskForm
-from wtforms import StringField, SelectField, TextAreaField, BooleanField, SubmitField, FileField, PasswordField, SelectMultipleField
+from wtforms import StringField, SelectField, TextAreaField, BooleanField, SubmitField, FileField, PasswordField
 from wtforms.validators import DataRequired, Regexp, ValidationError, URL, Optional, InputRequired
 from flask import request
 import json
@ -306,64 +306,4 @@ class FhirRequestForm(FlaskForm):
                if not self.basic_auth_password.data:
                    self.basic_auth_password.errors.append('Password is required for Basic Authentication with a custom URL.')
                    return False
-        return True
+        return True
 class IgYamlForm(FlaskForm):
    """Form to select IGs for YAML generation."""
    igs = SelectMultipleField('Select IGs to include', validators=[DataRequired()])
    generate_yaml = SubmitField('Generate YAML')
 # --- New ValidationForm class for the new page ---
 class ValidationForm(FlaskForm):
    """Form for validating a single FHIR resource with various options."""
    # Added fields to match the HTML template
    package_name = StringField('Package Name', validators=[Optional()])
    version = StringField('Package Version', validators=[Optional()])
    # Main content fields
    fhir_resource = TextAreaField('FHIR Resource (JSON or XML)', validators=[InputRequired()],
                                  render_kw={'placeholder': 'Paste your FHIR JSON here...'})
    fhir_version = SelectField('FHIR Version', choices=[
        ('4.0.1', 'R4 (4.0.1)'),
        ('3.0.2', 'STU3 (3.0.2)'),
        ('5.0.0', 'R5 (5.0.0)')
    ], default='4.0.1', validators=[DataRequired()])
    # Flags and options from validator settings.pdf
    do_native = BooleanField('Native Validation (doNative)')
    hint_about_must_support = BooleanField('Must Support (hintAboutMustSupport)')
    assume_valid_rest_references = BooleanField('Assume Valid Rest References (assumeValidRestReferences)')
    no_extensible_binding_warnings = BooleanField('Extensible Binding Warnings (noExtensibleBindingWarnings)')
    show_times = BooleanField('Show Times (-show-times)')
    allow_example_urls = BooleanField('Allow Example URLs (-allow-example-urls)')
    check_ips_codes = BooleanField('Check IPS Codes (-check-ips-codes)')
    allow_any_extensions = BooleanField('Allow Any Extensions (-allow-any-extensions)')
    tx_routing = BooleanField('Show Terminology Routing (-tx-routing)')
    # SNOMED CT options
    snomed_ct_version = SelectField('Select SNOMED Version', choices=[
        ('', '-- No selection --'),
        ('intl', 'International edition (900000000000207008)'),
        ('us', 'US edition (731000124108)'),
        ('uk', 'United Kingdom Edition (999000041000000102)'),
        ('es', 'Spanish Language Edition (449081005)'),
        ('nl', 'Netherlands Edition (11000146104)'),
        ('ca', 'Canadian Edition (20611000087101)'),
        ('dk', 'Danish Edition (554471000005108)'),
        ('se', 'Swedish Edition (45991000052106)'),
        ('au', 'Australian Edition (32506021000036107)'),
        ('be', 'Belgium Edition (11000172109)')
    ], validators=[Optional()])
    # Text input fields
    profiles = StringField('Profiles',
                           validators=[Optional()],
                           render_kw={'placeholder': 'e.g. http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient'})
    extensions = StringField('Extensions',
                             validators=[Optional()],
                             render_kw={'placeholder': 'e.g. http://hl7.org/fhir/StructureDefinition/elementdefinition-namespace'})
    terminology_server = StringField('Terminology Server',
                                     validators=[Optional()],
                                     render_kw={'placeholder': 'e.g. http://tx.fhir.org'})
    submit = SubmitField('Validate')
--- a/requirements.txt
+++ b/requirements.txt
@ -11,4 +11,4 @@ Flask-Migrate==4.1.0
 cachetools
 beautifulsoup4
 feedparser==6.0.11
-flasgger
+flasgger
--- a/services.py
+++ b/services.py
--- a/setup_linux.sh
+++ b/setup_linux.sh
@ -1,21 +1,18 @@
 #!/bin/bash
 # --- Configuration ---
-REPO_URL_HAPI="https://github.com/hapifhir/hapi-fhir-jpaserver-starter.git"
+REPO_URL="https://github.com/hapifhir/hapi-fhir-jpaserver-starter.git"
-REPO_URL_CANDLE="https://github.com/FHIR/fhir-candle.git"
+CLONE_DIR="hapi-fhir-jpaserver"
-CLONE_DIR_HAPI="hapi-fhir-jpaserver"
+SOURCE_CONFIG_DIR="hapi-fhir-Setup" # Assuming this is relative to the script's parent
 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="${CLONE_DIR_HAPI}/target/classes/${CONFIG_FILE}"
+DEST_CONFIG_PATH="${CLONE_DIR}/target/classes/${CONFIG_FILE}"
 APP_MODE=""
 CUSTOM_FHIR_URL_VAL=""
 SERVER_TYPE=""
 CANDLE_FHIR_VERSION=""
 # --- Error Handling Function ---
 handle_error() {
@ -23,39 +20,25 @@ handle_error() {
    echo "An error occurred: $1"
    echo "Script aborted."
    echo "------------------------------------"
    # Removed 'read -p "Press Enter to exit..."' as it's not typical for non-interactive CI/CD
    exit 1
 }
-# === MODIFIED: Prompt for Installation Mode ===
+# === Prompt for Installation Mode ===
 get_mode_choice() {
    echo ""
    echo "Select Installation Mode:"
-    echo "1. Lite (Excludes local HAPI FHIR Server - No Git/Maven/Dotnet needed)"
+    echo "1. Standalone (Includes local HAPI FHIR Server - Requires Git & Maven)"
-    echo "2. Custom URL (Uses a custom FHIR Server - No Git/Maven/Dotnet needed)"
+    echo "2. Lite (Excludes local HAPI FHIR Server - No Git/Maven needed)"
    echo "3. Hapi (Includes local HAPI FHIR Server - Requires Git & Maven)"
    echo "4. Candle (Includes local FHIR Candle Server - Requires Git & Dotnet)"
    while true; do
-        read -r -p "Enter your choice (1, 2, 3, or 4): " choice
+        read -r -p "Enter your choice (1 or 2): " choice
        case "$choice" in
            1)
-                APP_MODE="lite"
+                APP_MODE="standalone"
                break
                ;;
            2)
-                APP_MODE="standalone"
+                APP_MODE="lite"
                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
                ;;
            *)
@ -64,301 +47,156 @@ 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 "$choice" in
            1)
                CANDLE_FHIR_VERSION=r4
                break
                ;;
            2)
                CANDLE_FHIR_VERSION=r4b
                break
                ;;
            3)
                CANDLE_FHIR_VERSION=r5
                break
                ;;
            *)
                echo "Invalid input. Please try again."
                ;;
        esac
    done
 }
 # Call the function to get mode choice
 get_mode_choice
-# === Conditionally Execute Server Setup ===
+# === Conditionally Execute HAPI Setup ===
-case "$SERVER_TYPE" in
+if [ "$APP_MODE" = "standalone" ]; then
-    "hapi")
+    echo "Running Standalone setup including HAPI FHIR..."
-        echo "Running Hapi server setup..."
+    echo
        echo
-        # --- Step 0: Clean up previous clone (optional) ---
+    # --- Step 0: Clean up previous clone (optional) ---
-        echo "Checking for existing directory: $CLONE_DIR_HAPI"
+    echo "Checking for existing directory: $CLONE_DIR"
-        if [ -d "$CLONE_DIR_HAPI" ]; then
+    if [ -d "$CLONE_DIR" ]; then
-            echo "Found existing directory, removing it..."
+        echo "Found existing directory, removing it..."
-            rm -rf "$CLONE_DIR_HAPI"
+        rm -rf "$CLONE_DIR"
            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."
+            handle_error "Failed to remove existing directory: $CLONE_DIR"
        fi
-        echo "Repository cloned successfully."
+        echo "Existing directory removed."
-        echo
+    else
        echo "Directory does not exist, proceeding with clone."
    fi
    echo
-        # --- Step 2: Navigate into the cloned directory ---
+    # --- Step 1: Clone the HAPI FHIR server repository ---
-        echo "Changing directory to $CLONE_DIR_HAPI..."
+    echo "Cloning repository: $REPO_URL into $CLONE_DIR..."
-        cd "$CLONE_DIR_HAPI" || handle_error "Failed to change directory to $CLONE_DIR_HAPI."
+    git clone "$REPO_URL" "$CLONE_DIR"
-        echo "Current directory: $(pwd)"
+    if [ $? -ne 0 ]; then
-        echo
+        handle_error "Failed to clone repository. Check Git installation and network connection."
    fi
    echo "Repository cloned successfully."
    echo
-        # --- Step 3: Build the HAPI server using Maven ---
+    # --- Step 2: Navigate into the cloned directory ---
-        echo "===> Starting Maven build (Step 3)..."
+    echo "Changing directory to $CLONE_DIR..."
-        mvn clean package -DskipTests=true -Pboot
+    cd "$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 [ $? -ne 0 ]; then
-            echo "ERROR: Maven build failed."
+            echo "WARNING: Failed to copy configuration file. Check if the source file exists and permissions."
            cd ..
            handle_error "Maven build process resulted in an error."
        fi
        echo "Maven build completed successfully."
        echo
        # --- Step 4: Copy the configuration file ---
        echo "===> Starting file copy (Step 4)..."
        echo "Copying configuration file..."
        INITIAL_SCRIPT_DIR=$(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/"
+            echo "Configuration file copied successfully."
            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
+    fi
    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: $(pwd)"
-        echo
+    echo
        ;;
-    "candle")
+else # APP_MODE is "lite"
-        echo "Running FHIR Candle server setup..."
+    echo "Running Lite setup, skipping HAPI FHIR build..."
-        echo
+    # Ensure the hapi-fhir-jpaserver directory doesn't exist or is empty if Lite mode is chosen
-        
+    if [ -d "$CLONE_DIR" ]; then
-        # --- Step 0: Clean up previous clone (optional) ---
+        echo "Found existing HAPI directory ($CLONE_DIR) in Lite mode. Removing it..."
-        echo "Checking for existing directory: $CLONE_DIR_CANDLE"
+        rm -rf "$CLONE_DIR"
-        if [ -d "$CLONE_DIR_CANDLE" ]; then
+    fi
-            echo "Found existing directory, removing it..."
+    # Create empty target directories expected by Dockerfile COPY, even if not used
-            rm -rf "$CLONE_DIR_CANDLE"
+    mkdir -p "${CLONE_DIR}/target/classes"
-            if [ $? -ne 0 ]; then
+    mkdir -p "${CLONE_DIR}/custom" # This was in the original batch, ensure it's here
-                handle_error "Failed to remove existing directory: $CLONE_DIR_CANDLE"
+    # Create a placeholder empty WAR file and application.yaml to satisfy Dockerfile COPY
-            fi
+    touch "${CLONE_DIR}/target/ROOT.war"
-            echo "Existing directory removed."
+    touch "${CLONE_DIR}/target/classes/application.yaml"
-        else
+    echo "Placeholder files and directories created for Lite mode build in $CLONE_DIR."
-            echo "Directory does not exist, proceeding with clone."
+    echo
-        fi
+fi
        echo
-        # --- Step 1: Clone the FHIR Candle server repository ---
+# === Modify docker-compose.yml to set APP_MODE ===
-        echo "Cloning repository: $REPO_URL_CANDLE into $CLONE_DIR_CANDLE..."
+echo "Updating docker-compose.yml with APP_MODE=$APP_MODE..."
        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: ${DOCKERFILE_TO_USE}
+      dockerfile: Dockerfile
    ports:
 EOF
 if [ "$SERVER_TYPE" = "candle" ]; then
    cat << EOF >> "$DOCKER_COMPOSE_TMP"
      - "5000:5000"
-      - "5001:5826"
+      - "8080:8080" # Keep port exposed, even if Tomcat isn't running useful stuff in Lite
 EOF
 else
    cat << EOF >> "$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 >> "$DOCKER_COMPOSE_TMP"
      - ./instance/hapi-h2-data/:/app/h2-data # Keep volume mounts consistent
-      - ./hapi-fhir-jpaserver/target/ROOT.war:/usr/local/tomcat/webapps/ROOT.war
+      - ./logs:/app/logs
      - ./hapi-fhir-jpaserver/target/classes/application.yaml:/usr/local/tomcat/conf/application.yaml
 EOF
 elif [ "$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}
+      - HAPI_FHIR_URL=http://localhost:8080/fhir
 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
--- a/static/animations/Validation
+++ b/static/animations/Validation
--- a/supervisord.conf
+++ b/supervisord.conf
@ -33,18 +33,4 @@ stdout_logfile_maxbytes=10MB
 stdout_logfile_backups=5 
 stderr_logfile=/app/logs/tomcat_err.log 
 stderr_logfile_maxbytes=10MB 
-stderr_logfile_backups=5
+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
--- a/templates/about.html
+++ b/templates/about.html
@ -19,11 +19,11 @@
            <p>Whether you're downloading the latest IG versions, checking compliance, converting resources to FHIR Shorthand (FSH), or pushing guides to a test server, this toolkit aims to be an essential companion.</p>
             {% if app_mode == 'lite' %}
                <div class="alert alert-info" role="alert">
-                    <i class="bi bi-info-circle-fill me-2"></i>You are currently running the <strong>Lite Version</strong> of the toolkit. This version excludes the built-in FHIR server depending and relies on external FHIR servers for functionalities like the API Explorer and Operations UI. Validation uses local StructureDefinition checks.
+                    <i class="bi bi-info-circle-fill me-2"></i>You are currently running the <strong>Lite Version</strong> of the toolkit. This version excludes the built-in HAPI FHIR server and relies on external FHIR servers for functionalities like the API Explorer and Operations UI. Validation uses local StructureDefinition checks.
                </div>
             {% else %}
                 <div class="alert alert-success" role="alert">
-                     <i class="bi bi-check-circle-fill me-2"></i>You are currently running the <strong>Standalone Version</strong> of the toolkit, which includes a built-in FHIR server based on your build choice (accessible via the `/fhir` proxy) for local validation and exploration, if you configured the Server ENV variable this could also be whatever customer server you have pointed the local ENV variable at allowing you to use any fhir server of your choice.
+                     <i class="bi bi-check-circle-fill me-2"></i>You are currently running the <strong>Standalone Version</strong> of the toolkit, which includes a built-in HAPI FHIR server (accessible via the `/fhir` proxy) for local validation and exploration.
                 </div>
             {% endif %}
@ -36,7 +36,7 @@
                <li><strong>FHIR Server Interaction:</strong>
                    <ul>
                        <li>Push processed IGs (including dependencies) to a target FHIR server with real-time console feedback.</li>
-                        <li>Explore FHIR server capabilities and interact with resources using the "FHIR API Explorer" (GET/POST/PUT/DELETE) and "FHIR UI Operations" pages, supporting both the local server (in Standalone mode) and external servers.</li>
+                        <li>Explore FHIR server capabilities and interact with resources using the "FHIR API Explorer" (GET/POST/PUT/DELETE) and "FHIR UI Operations" pages, supporting both the local HAPI server (in Standalone mode) and external servers.</li>
                    </ul>
                </li>
                <li><strong>FHIR Shorthand (FSH) Conversion:</strong> Convert FHIR JSON or XML resources to FSH using the integrated GoFSH tool. Offers advanced options like context package selection, various output styles, FHIR version selection, dependency loading, alias file usage, and round-trip validation ("Fishing Trip") with SUSHI. Includes a loading indicator during conversion.</li>
@ -48,7 +48,7 @@
            <ul>
                <li><strong>Backend:</strong> Python with the Flask web framework and SQLAlchemy for database interaction (SQLite).</li>
                <li><strong>Frontend:</strong> HTML, Bootstrap 5 for styling, and JavaScript for interactivity and dynamic content loading. Uses Lottie-Web for animations.</li>
-                <li><strong>FHIR Tooling:</strong> Integrates GoFSH and SUSHI (via Node.js) for FSH conversion and validation. Utilizes the Local FHIR server (in Standalone mode) for robust FHIR validation and operations.</li>
+                <li><strong>FHIR Tooling:</strong> Integrates GoFSH and SUSHI (via Node.js) for FSH conversion and validation. Utilizes the HAPI FHIR server (in Standalone mode) for robust FHIR validation and operations.</li>
                <li><strong>Deployment:</strong> Runs within a Docker container managed by Docker Compose and Supervisor, ensuring a consistent environment.</li>
            </ul>
--- a/templates/base.html
+++ b/templates/base.html
@ -796,14 +796,11 @@
                    <li class="nav-item">
                        <a class="nav-link {{ 'active' if request.endpoint == 'fsh_converter' else '' }}" href="{{ url_for('fsh_converter') }}"><i class="fas fa-file-code me-1"></i> FSH Converter</a>
                    </li>
-                    <!-- <li class="nav-item">
+                    {% if app_mode != 'lite' %}
                        <a class="nav-link {{ 'active' if request.endpoint == 'ig_configurator' else '' }}" href="{{ url_for('ig_configurator') }}"><i class="fas fa-wrench me-1"></i> IG Valid-Conf Gen</a>
                    </li> -->
                    <!-- {% if app_mode != 'lite' %}
                    <li class="nav-item">
                        <a class="nav-link {{ 'active' if request.endpoint == 'config_hapi' else '' }}" href="{{ url_for('config_hapi') }}"><i class="fas fa-cog me-1"></i> Configure HAPI</a>
                    </li>
-                    {% endif %} -->
+                    {% endif %}
                    </ul>
                <div class="navbar-controls d-flex align-items-center">
                    <div class="form-check form-switch">
--- a/templates/cp_downloaded_igs.html
+++ b/templates/cp_downloaded_igs.html
@ -40,7 +40,7 @@
    <div class="row g-4">
        <!-- LEFT: Downloaded Packages -->
-        <div class="col-md-5">
+        <div class="col-md-6">
            <div class="card h-100">
                <div class="card-header"><i class="bi bi-folder-symlink me-1"></i> Downloaded Packages ({{ packages|length }})</div>
                <div class="card-body">
@ -65,20 +65,20 @@
                                            </td>
                                            <td>{{ pkg.version }}</td>
                                            <td>
-                                                <div class="btn-group-vertical btn-group-sm w-80">
+                                                <div class="btn-group btn-group-sm">
                                                    {% if is_processed %}
                                                        <span class="btn btn-success disabled"><i class="bi bi-check-lg"></i> Processed</span>
                                                    {% else %}
                                                        <form method="POST" action="{{ url_for('process_ig') }}" style="display:inline;">
                                                            {{ form.csrf_token }}
                                                            <input type="hidden" name="filename" value="{{ pkg.filename }}">
-                                                            <button type="submit" class="btn btn-outline-primary w-80"><i class="bi bi-gear"></i> Process</button>
+                                                            <button type="submit" class="btn btn-outline-primary"><i class="bi bi-gear"></i> Process</button>
                                                        </form>
                                                    {% endif %}
                                                    <form method="POST" action="{{ url_for('delete_ig') }}" style="display:inline;">
                                                        {{ form.csrf_token }}
                                                        <input type="hidden" name="filename" value="{{ pkg.filename }}">
-                                                        <button type="submit" class="btn btn-outline-danger w-80" onclick="return confirm('Are you sure you want to delete {{ pkg.name }}#{{ pkg.version }}?');"><i class="bi bi-trash"></i> Delete</button>
+                                                        <button type="submit" class="btn btn-outline-danger" onclick="return confirm('Are you sure you want to delete {{ pkg.name }}#{{ pkg.version }}?');"><i class="bi bi-trash"></i> Delete</button>
                                                    </form>
                                                </div>
                                            </td>
@ -105,7 +105,7 @@
        </div>
        <!-- RIGHT: Processed Packages -->
-        <div class="col-md-7">
+        <div class="col-md-6">
            <div class="card h-100">
                <div class="card-header"><i class="bi bi-check-circle me-1"></i> Processed Packages ({{ processed_list|length }})</div>
                <div class="card-body">
@ -139,12 +139,12 @@
                                                {% endif %}
                                            </td>
                                            <td>
-                                                <div class="btn-group-vertical btn-group-sm w-80">
+                                                <div class="btn-group-vertical btn-group-sm w-100">
-                                                    <a href="{{ url_for('view_ig', processed_ig_id=processed_ig.id) }}" class="btn btn-outline-info w-80" title="View Details"><i class="bi bi-search"></i> View</a>
+                                                    <a href="{{ url_for('view_ig', processed_ig_id=processed_ig.id) }}" class="btn btn-outline-info w-100" title="View Details"><i class="bi bi-search"></i> View</a>
                                                    <form method="POST" action="{{ url_for('unload_ig') }}" style="display:inline;">
                                                        {{ form.csrf_token }}
                                                        <input type="hidden" name="ig_id" value="{{ processed_ig.id }}">
-                                                        <button type="submit" class="btn btn-outline-warning w-80 mt-1" onclick="return confirm('Are you sure you want to unload {{ processed_ig.package_name }}#{{ processed_ig.version }}?');"><i class="bi bi-x-lg"></i> Unload</button>
+                                                        <button type="submit" class="btn btn-outline-warning w-100 mt-1" onclick="return confirm('Are you sure you want to unload {{ processed_ig.package_name }}#{{ processed_ig.version }}?');"><i class="bi bi-x-lg"></i> Unload</button>
                                                    </form>
                                                </div>
                                            </td>
--- a/templates/fhir_ui.html
+++ b/templates/fhir_ui.html
@ -21,7 +21,7 @@
                    <label class="form-label">FHIR Server</label>
                    <div class="input-group">
                        <button type="button" class="btn btn-outline-primary" id="toggleServer">
-                            <span id="toggleLabel">Use Local Server</span>
+                            <span id="toggleLabel">Use Local HAPI</span>
                        </button>
                        <input type="text" class="form-control" id="fhirServerUrl" name="fhir_server_url" placeholder="e.g., https://hapi.fhir.org/baseR4" style="display: none;" aria-describedby="fhirServerHelp">
                    </div>
@ -126,7 +126,7 @@ document.addEventListener('DOMContentLoaded', function() {
    const authSection = document.getElementById('authSection');
    const authTypeSelect = document.getElementById('authType');
    const authInputsGroup = document.getElementById('authInputsGroup');
-    const bearerTokenInput = document.getElementById('bearerTokenInput');
+    const bearerTokenInput = document.getElementById('bearerToken');
    const basicAuthInputs = document.getElementById('basicAuthInputs');
    const usernameInput = document.getElementById('username');
    const passwordInput = document.getElementById('password');
@ -212,7 +212,7 @@ document.addEventListener('DOMContentLoaded', function() {
            toggleServerButton.style.pointerEvents = 'auto';
            toggleServerButton.removeAttribute('aria-disabled');
            toggleServerButton.title = "Toggle between Local HAPI and Custom URL";
-            toggleLabel.textContent = useLocalHapi ? 'Using Local Server' : 'Using Custom URL';
+            toggleLabel.textContent = useLocalHapi ? 'Using Local HAPI' : 'Using Custom URL';
            fhirServerUrlInput.style.display = useLocalHapi ? 'none' : 'block';
            fhirServerUrlInput.placeholder = "e.g., https://hapi.fhir.org/baseR4";
            fhirServerUrlInput.required = !useLocalHapi;
@ -244,8 +244,7 @@ document.addEventListener('DOMContentLoaded', function() {
            fhirServerUrlInput.value = '';
        }
        updateServerToggleUI();
-        updateAuthInputsUI();
+        console.log(`Server toggled: Now using ${useLocalHapi ? 'Local HAPI' : 'Custom URL'}`);
        console.log(`Server toggled: Now using ${useLocalHapi ? 'Local Server' : 'Custom URL'}`);
    }
    function updateRequestBodyVisibility() {
@ -296,7 +295,7 @@ document.addEventListener('DOMContentLoaded', function() {
        const customUrl = fhirServerUrlInput.value.trim();
        let body = undefined;
        const authType = authTypeSelect ? authTypeSelect.value : 'none';
-        const bearerToken = document.getElementById('bearerToken').value.trim();
+        const bearerToken = bearerTokenInput ? bearerTokenInput.value.trim() : '';
        const username = usernameInput ? usernameInput.value.trim() : '';
        const password = passwordInput ? passwordInput.value : '';
@ -335,7 +334,7 @@ document.addEventListener('DOMContentLoaded', function() {
        if (!useLocalHapi) {
            if (authType === 'bearer' && !bearerToken) {
                alert('Please enter a Bearer Token.');
-                document.getElementById('bearerToken').classList.add('is-invalid');
+                bearerTokenInput.classList.add('is-invalid');
                sendButton.disabled = false;
                sendButton.textContent = 'Send Request';
                return;
@ -454,7 +453,7 @@ document.addEventListener('DOMContentLoaded', function() {
        } catch (error) {
            console.error('Fetch error:', error);
            responseCard.style.display = 'block';
-            responseStatus.textContent = 'Network Error';
+            responseStatus.textContent = `Network Error`;
            responseStatus.className = 'badge bg-danger';
            responseHeaders.textContent = 'N/A';
            let errorDetail = `Error: ${error.message}\n\n`;
--- a/templates/fhir_ui_operations.html
+++ b/templates/fhir_ui_operations.html
--- a/templates/ig_configurator.html
+++ b/templates/ig_configurator.html
@ -1,40 +0,0 @@
 {% extends "base.html" %}
 {% block content %}
 <div class="container mt-4">
    <h2>IG Configuration Generator</h2>
    <p>Select the Implementation Guides you want to load into Local FHIR for validation. This will generate the YAML configuration required for the <code>application.yaml</code> file.</p>
    <div class="card mb-4">
        <div class="card-header">Select IGs</div>
        <div class="card-body">
            <form method="POST">
                {{ form.hidden_tag() }}
                <div class="mb-3">
                    <label class="form-label">IGs and their dependencies</label>
                    {% for choice in form.igs.choices %}
                    <div class="form-check">
                        <input class="form-check-input" type="checkbox" name="igs" value="{{ choice[0] }}" id="ig-{{ choice[0] }}">
                        <label class="form-check-label" for="ig-{{ choice[0] }}">{{ choice[1] }}</label>
                    </div>
                    {% endfor %}
                </div>
                {{ form.generate_yaml(class="btn btn-primary") }}
            </form>
        </div>
    </div>
    {% if yaml_output %}
    <div class="card mt-4">
        <div class="card-header">Generated <code>application.yaml</code> Excerpt</div>
        <div class="card-body">
            <p>Copy the following configuration block and paste it into the `hapi.fhir` section of your HAPI server's <code>application.yaml</code> file.</p>
            <pre><code class="language-yaml">{{ yaml_output }}</code></pre>
            <div class="alert alert-warning mt-3">
                <strong>Important:</strong> After updating the <code>application.yaml</code> file, you must **restart your HAPI server** for the changes to take effect.
            </div>
        </div>
    </div>
    {% endif %}
 </div>
 {% endblock %}
--- a/templates/retrieve_split_data.html
+++ b/templates/retrieve_split_data.html
@ -10,6 +10,7 @@
        </p>
    </div>
 </div>
 <div class="container mt-4">
    <div class="card shadow-sm mb-4">
        <div class="card-header">
@ -27,17 +28,18 @@
                </div>
            {% endif %}
            <form id="retrieveForm" method="POST">
-                {{ form.csrf_token(id='retrieve_csrf_token') }}
+                {{ form.hidden_tag() }}
                <div class="mb-3">
                    <label class="form-label fw-bold">FHIR Server</label>
                    <div class="input-group">
                        <button type="button" class="btn btn-outline-primary" id="toggleServer">
-                            <span id="toggleLabel">Use Local Server</span>
+                            <span id="toggleLabel">Use Local HAPI</span>
                        </button>
                        {{ form.fhir_server_url(class="form-control", id="fhirServerUrl", style="display: none;", placeholder="e.g., https://fhir.hl7.org.au/aucore/fhir/DEFAULT", **{'aria-describedby': 'fhirServerHelp'}) }}
                    </div>
-                    <small id="fhirServerHelp" class="form-text text-muted">Toggle to use local Fhir Server(/fhir proxy) or enter a custom FHIR server URL.</small>
+                    <small id="fhirServerHelp" class="form-text text-muted">Toggle to use local HAPI (/fhir proxy) or enter a custom FHIR server URL.</small>
                </div>
                {# Authentication Section (Shown for Custom URL) #}
                <div class="mb-3" id="authSection" style="display: none;">
                    <label class="form-label fw-bold">Authentication</label>
@ -66,6 +68,7 @@
                    </div>
                    <small class="form-text text-muted">Select authentication method for the custom FHIR server.</small>
                </div>
                {# Checkbox Row #}
                <div class="row g-3 mb-3 align-items-center">
                    <div class="col-md-6">
@ -75,6 +78,7 @@
                        {{ render_field(form.fetch_reference_bundles, id='fetch_reference_bundles_checkbox') }}
                    </div>
                </div>
                <button type="button" class="btn btn-primary mb-3" id="fetchMetadata">Fetch Metadata</button>
                <div class="banner3 mt-3" id="resourceTypes" style="display: none;">
                    <h5>Resource Types</h5>
@ -98,13 +102,14 @@
            </div>
        </div>
    </div>
    <div class="card shadow-sm">
        <div class="card-header">
            <h4 class="my-0 fw-normal"><i class="bi bi-scissors me-2"></i>Split Bundles</h4>
        </div>
        <div class="card-body">
            <form id="splitForm" method="POST" enctype="multipart/form-data">
-                {{ form.csrf_token(id='split_csrf_token') }}
+                {{ form.hidden_tag() }}
                <div class="mb-3">
                    <label class="form-label fw-bold">Bundle Source</label>
                    <div class="form-check">
@ -136,6 +141,7 @@
        </div>
    </div>
 </div>
 <script>
 document.addEventListener('DOMContentLoaded', () => {
    // --- DOM Element References ---
@ -162,10 +168,11 @@ document.addEventListener('DOMContentLoaded', () => {
    const authSection = document.getElementById('authSection');
    const authTypeSelect = document.getElementById('authType');
    const authInputsGroup = document.getElementById('authInputsGroup');
-    const bearerTokenInput = document.getElementById('bearerTokenInput');
+    const bearerTokenInput = document.getElementById('bearerToken');
    const basicAuthInputs = document.getElementById('basicAuthInputs');
    const usernameInput = document.getElementById('username');
    const passwordInput = document.getElementById('password');
    // --- State & Config Variables ---
    const appMode = '{{ app_mode | default("standalone") | lower }}';
    const apiKey = '{{ api_key }}';
@ -174,9 +181,10 @@ document.addEventListener('DOMContentLoaded', () => {
    let retrieveZipPath = null;
    let splitZipPath = null;
    let fetchedMetadataCache = null;
-    let localHapiBaseUrl = ''; // To store the fetched URL
+
    // --- Helper Functions ---
    const sanitizeText = (str) => str ? String(str).replace(/</g, "&lt;").replace(/>/g, "&gt;") : "";
    // --- UI Update Functions ---
    function updateBundleSourceUI() {
        const selectedSource = Array.from(bundleSourceRadios).find(radio => radio.checked)?.value;
@ -187,23 +195,10 @@ document.addEventListener('DOMContentLoaded', () => {
            splitBundleZipInput.required = selectedSource === 'upload';
        }
    }
-    async function fetchLocalUrlAndSetUI() {
+
        try {
            const response = await fetch('/api/get-local-server-url');
            if (!response.ok) throw new Error('Failed to fetch local server URL.');
            const data = await response.json();
            localHapiBaseUrl = data.url.replace(/\/+$/, ''); // Normalize by removing trailing slashes
            console.log(`Local HAPI URL fetched: ${localHapiBaseUrl}`);
        } catch (error) {
            console.error(error);
            localHapiBaseUrl = '/fhir'; // Fallback to proxy
            alert('Could not fetch local HAPI server URL. Falling back to proxy.');
        } finally {
            updateServerToggleUI();
        }
    }
    function updateServerToggleUI() {
        if (!toggleLabel || !fhirServerUrlInput || !toggleServerButton || !authSection) return;
        if (appMode === 'lite') {
            useLocalHapi = false;
            toggleServerButton.disabled = true;
@ -221,7 +216,7 @@ document.addEventListener('DOMContentLoaded', () => {
            toggleServerButton.classList.remove('disabled');
            toggleServerButton.style.pointerEvents = 'auto';
            toggleServerButton.removeAttribute('aria-disabled');
-            toggleLabel.textContent = useLocalHapi ? 'Use Local Server' : 'Use Custom URL';
+            toggleLabel.textContent = useLocalHapi ? 'Using Local HAPI' : 'Using Custom URL';
            fhirServerUrlInput.style.display = useLocalHapi ? 'none' : 'block';
            fhirServerUrlInput.placeholder = "e.g., https://hapi.fhir.org/baseR4";
            fhirServerUrlInput.required = !useLocalHapi;
@ -231,22 +226,18 @@ document.addEventListener('DOMContentLoaded', () => {
        updateAuthInputsUI();
        console.log(`Server toggle UI updated: useLocalHapi=${useLocalHapi}, customUrl=${fhirServerUrlInput.value}`);
    }
    function updateAuthInputsUI() {
        if (!authTypeSelect || !authInputsGroup || !bearerTokenInput || !basicAuthInputs) return;
        const authType = authTypeSelect.value;
        authInputsGroup.style.display = (authType === 'bearer' || authType === 'basic') ? 'block' : 'none';
        bearerTokenInput.style.display = authType === 'bearer' ? 'block' : 'none';
        basicAuthInputs.style.display = authType === 'basic' ? 'block' : 'none';
-        if (authType !== 'bearer') {
+        if (authType !== 'bearer' && bearerTokenInput) bearerTokenInput.value = '';
-            // Correctly reference the input element by its ID
+        if (authType !== 'basic' && usernameInput) usernameInput.value = '';
-            const tokenInput = document.getElementById('bearerToken');
+        if (authType !== 'basic' && passwordInput) passwordInput.value = '';
            if (tokenInput) tokenInput.value = '';
        }
        if (authType !== 'basic') {
            if (usernameInput) usernameInput.value = '';
            if (passwordInput) passwordInput.value = '';
        }
    }
    function toggleFetchReferenceBundles() {
        if (validateReferencesCheckbox && fetchReferenceBundlesGroup) {
            fetchReferenceBundlesGroup.style.display = validateReferencesCheckbox.checked ? 'block' : 'none';
@ -257,40 +248,44 @@ document.addEventListener('DOMContentLoaded', () => {
            console.warn("Could not find checkbox elements needed for toggling.");
        }
    }
    // --- Event Listeners ---
    bundleSourceRadios.forEach(radio => {
        radio.addEventListener('change', updateBundleSourceUI);
    });
    toggleServerButton.addEventListener('click', () => {
        if (appMode === 'lite') return;
        useLocalHapi = !useLocalHapi;
        if (useLocalHapi) fhirServerUrlInput.value = '';
        updateServerToggleUI();
        updateAuthInputsUI();
        resourceTypesDiv.style.display = 'none';
        fetchedMetadataCache = null;
        console.log(`Server toggled: useLocalHapi=${useLocalHapi}`);
    });
    if (authTypeSelect) {
        authTypeSelect.addEventListener('change', updateAuthInputsUI);
    }
    if (validateReferencesCheckbox) {
        validateReferencesCheckbox.addEventListener('change', toggleFetchReferenceBundles);
    } else {
        console.warn("Validate references checkbox not found.");
    }
    fetchMetadataButton.addEventListener('click', async () => {
        resourceButtonsContainer.innerHTML = '<span class="text-muted">Fetching...</span>';
        resourceTypesDiv.style.display = 'block';
-        let customUrl = null;
+        const customUrl = useLocalHapi ? null : fhirServerUrlInput.value.trim().replace(/\/+$/, '');
        if (!useLocalHapi && !customUrl) {
            fhirServerUrlInput.classList.add('is-invalid');
            alert('Please enter a valid FHIR server URL.');
            resourceButtonsContainer.innerHTML = '<span class="text-danger">Error: Custom URL required.</span>';
            return;
        }
        if (!useLocalHapi) {
            customUrl = fhirServerUrlInput.value.trim().replace(/\/+$/, ''); // Normalize custom URL
            if (!customUrl) {
                fhirServerUrlInput.classList.add('is-invalid');
                alert('Please enter a valid FHIR server URL.');
                resourceButtonsContainer.innerHTML = '<span class="text-danger">Error: Custom URL required.</span>';
                return;
            }
            try { new URL(customUrl); } catch (_) {
                fhirServerUrlInput.classList.add('is-invalid');
                alert('Invalid custom URL format.');
@ -299,32 +294,32 @@ document.addEventListener('DOMContentLoaded', () => {
            }
        }
        fhirServerUrlInput.classList.remove('is-invalid');
        fetchMetadataButton.disabled = true;
        fetchMetadataButton.textContent = 'Fetching...';
        try {
-            // Build URL and headers based on the toggle state
+            const fetchUrl = useLocalHapi ? '/fhir/metadata' : `${customUrl}/metadata`;
            let fetchUrl;
            const headers = { 'Accept': 'application/fhir+json' };
-            if (useLocalHapi) {
+            if (!useLocalHapi && customUrl) {
-                if (!localHapiBaseUrl) {
+                if (authTypeSelect && authTypeSelect.value !== 'none') {
-                    throw new Error("Local HAPI URL not available. Please refresh.");
+                    const authType = authTypeSelect.value;
                    if (authType === 'bearer' && bearerTokenInput && bearerTokenInput.value) {
                        headers['Authorization'] = `Bearer ${bearerTokenInput.value}`;
                    } else if (authType === 'basic' && usernameInput && passwordInput && usernameInput.value && passwordInput.value) {
                        const credentials = btoa(`${usernameInput.value}:${passwordInput.value}`);
                        headers['Authorization'] = `Basic ${credentials}`;
                    }
                }
-                fetchUrl = `${localHapiBaseUrl}/metadata`; // localHapiBaseUrl is already normalized
+                console.log(`Fetching metadata directly from: ${customUrl}`);
                console.log(`Fetching metadata directly from local URL: ${fetchUrl}`);
            } else {
-                fetchUrl = `${customUrl}/metadata`;
+                console.log("Fetching metadata from local HAPI server via proxy");
                // Add authentication headers for the direct request to the custom server
                const authType = authTypeSelect.value;
                if (authType === 'bearer' && document.getElementById('bearerToken') && document.getElementById('bearerToken').value) {
                    headers['Authorization'] = `Bearer ${document.getElementById('bearerToken').value}`;
                } else if (authType === 'basic' && usernameInput && passwordInput && usernameInput.value && passwordInput.value) {
                    const credentials = btoa(`${usernameInput.value}:${passwordInput.value}`);
                    headers['Authorization'] = `Basic ${credentials}`;
                }
                console.log(`Fetching metadata directly from custom URL: ${fetchUrl}`);
            }
            console.log(`Fetch URL: ${fetchUrl}`);
            console.log(`Request Headers sent: ${JSON.stringify(headers)}`);
            const response = await fetch(fetchUrl, { method: 'GET', headers: headers });
            if (!response.ok) {
                let errorText = `Request failed with status ${response.status} ${response.statusText}`;
                try { const errorBody = await response.text(); errorText += ` - Body: ${errorBody.substring(0, 200)}...`; } catch (e) {}
@ -334,6 +329,7 @@ document.addEventListener('DOMContentLoaded', () => {
            const data = await response.json();
            console.log("Metadata received:", JSON.stringify(data, null, 2).substring(0, 500));
            fetchedMetadataCache = data;
            const resourceTypes = data.rest?.[0]?.resource?.map(r => r.type)?.filter(Boolean) || [];
            resourceButtonsContainer.innerHTML = '';
            if (!resourceTypes.length) {
@ -364,6 +360,7 @@ document.addEventListener('DOMContentLoaded', () => {
            fetchMetadataButton.textContent = 'Fetch Metadata';
        }
    });
    retrieveForm.addEventListener('submit', async (e) => {
        e.preventDefault();
        const spinner = retrieveButton.querySelector('.spinner-border');
@ -374,6 +371,7 @@ document.addEventListener('DOMContentLoaded', () => {
        downloadRetrieveButton.style.display = 'none';
        retrieveZipPath = null;
        retrieveConsole.innerHTML = `<div>${new Date().toLocaleTimeString()} [INFO] Starting bundle retrieval...</div>`;
        const selectedResources = Array.from(resourceButtonsContainer.querySelectorAll('.btn.active')).map(btn => btn.dataset.resource);
        if (!selectedResources.length) {
            alert('Please select at least one resource type.');
@ -382,20 +380,31 @@ document.addEventListener('DOMContentLoaded', () => {
            if (icon) icon.style.display = 'inline-block';
            return;
        }
-        const currentFhirServerUrl = useLocalHapi ? localHapiBaseUrl : fhirServerUrlInput.value.trim().replace(/\/+$/, '');
+
-        if (!currentFhirServerUrl) {
+        const currentFhirServerUrl = useLocalHapi ? null : fhirServerUrlInput.value.trim();
-            alert('FHIR Server URL is required.');
+        if (!useLocalHapi && !currentFhirServerUrl) {
            alert('Custom FHIR Server URL is required.');
            fhirServerUrlInput.classList.add('is-invalid');
            retrieveButton.disabled = false;
            if (spinner) spinner.style.display = 'none';
            if (icon) icon.style.display = 'inline-block';
            return;
        }
        const formData = new FormData();
        const csrfTokenInput = retrieveForm.querySelector('input[name="csrf_token"]');
        if (csrfTokenInput) formData.append('csrf_token', csrfTokenInput.value);
        selectedResources.forEach(res => formData.append('resources', res));
-        formData.append('fhir_server_url', currentFhirServerUrl);
+
        // --- FIX APPLIED HERE ---
        if (!useLocalHapi && currentFhirServerUrl) {
            formData.append('fhir_server_url', currentFhirServerUrl);
        } else {
            // Explicitly use the proxy URL if local HAPI is selected
            formData.append('fhir_server_url', '/fhir');
        }
        // --- END FIX ---
        if (validateReferencesCheckbox) {
            formData.append('validate_references', validateReferencesCheckbox.checked ? 'true' : 'false');
        }
@ -408,19 +417,19 @@ document.addEventListener('DOMContentLoaded', () => {
        } else {
            formData.append('fetch_reference_bundles', 'false');
        }
        if (!useLocalHapi && authTypeSelect) {
            const authType = authTypeSelect.value;
            formData.append('auth_type', authType);
-            if (authType === 'bearer') {
+            if (authType === 'bearer' && bearerTokenInput) {
-                const bearerToken = document.getElementById('bearerToken').value.trim();
+                if (!bearerTokenInput.value) {
                if (!bearerToken) {
                    alert('Please enter a Bearer Token.');
                    retrieveButton.disabled = false;
                    if (spinner) spinner.style.display = 'none';
                    if (icon) icon.style.display = 'inline-block';
                    return;
                }
-                formData.append('bearer_token', bearerToken);
+                formData.append('bearer_token', bearerTokenInput.value);
            } else if (authType === 'basic' && usernameInput && passwordInput) {
                if (!usernameInput.value || !passwordInput.value) {
                    alert('Please enter both Username and Password for Basic Authentication.');
@ -433,20 +442,24 @@ document.addEventListener('DOMContentLoaded', () => {
                formData.append('password', passwordInput.value);
            }
        }
        const headers = {
            'Accept': 'application/x-ndjson',
            'X-CSRFToken': csrfTokenInput ? csrfTokenInput.value : '',
            'X-API-Key': apiKey
        };
        console.log(`Submitting retrieve request. Server: ${currentFhirServerUrl}, ValidateRefs: ${formData.get('validate_references')}, FetchRefBundles: ${formData.get('fetch_reference_bundles')}, AuthType: ${formData.get('auth_type')}`);
        try {
            const response = await fetch('/api/retrieve-bundles', { method: 'POST', headers: headers, body: formData });
            if (!response.ok) {
                const errorData = await response.json().catch(() => ({ message: 'Failed to parse error response.' }));
                throw new Error(`HTTP ${response.status}: ${errorData.message || 'Unknown error during retrieval'}`);
            }
            retrieveZipPath = response.headers.get('X-Zip-Path');
            console.log(`Received X-Zip-Path: ${retrieveZipPath}`);
            const reader = response.body.getReader();
            const decoder = new TextDecoder();
            let buffer = '';
@ -468,11 +481,13 @@ document.addEventListener('DOMContentLoaded', () => {
                        else if (data.type === 'success') { prefix = '[SUCCESS]'; messageClass = 'text-success'; }
                        else if (data.type === 'progress') { prefix = '[PROGRESS]'; messageClass = 'text-light'; }
                        else if (data.type === 'complete') { prefix = '[COMPLETE]'; messageClass = 'text-primary'; }
                        const messageDiv = document.createElement('div');
                        messageDiv.className = messageClass;
                        messageDiv.innerHTML = `${timestamp} ${prefix} ${sanitizeText(data.message)}`;
                        retrieveConsole.appendChild(messageDiv);
                        retrieveConsole.scrollTop = retrieveConsole.scrollHeight;
                        if (data.type === 'complete' && retrieveZipPath) {
                            const completeData = data.data || {};
                            const bundlesFound = (completeData.total_initial_bundles > 0) || (completeData.fetched_individual_references > 0) || (completeData.fetched_type_bundles > 0);
@ -490,6 +505,7 @@ document.addEventListener('DOMContentLoaded', () => {
                }
            }
            if (buffer.trim()) { /* Handle final buffer */ }
        } catch (e) {
            console.error('Retrieval error:', e);
            const ts = new Date().toLocaleTimeString();
@ -501,17 +517,20 @@ document.addEventListener('DOMContentLoaded', () => {
            if (icon) icon.style.display = 'inline-block';
        }
    });
    downloadRetrieveButton.addEventListener('click', () => {
        if (retrieveZipPath) {
            const filename = retrieveZipPath.split('/').pop() || 'retrieved_bundles.zip';
            const downloadUrl = `/tmp/${filename}`;
            console.log(`Attempting to download ZIP from Flask endpoint: ${downloadUrl}`);
            const link = document.createElement('a');
            link.href = downloadUrl;
            link.download = 'retrieved_bundles.zip';
            document.body.appendChild(link);
            link.click();
            document.body.removeChild(link);
            setTimeout(() => {
                const csrfToken = retrieveForm.querySelector('input[name="csrf_token"]')?.value || '';
                fetch('/clear-session', { method: 'POST', headers: { 'X-CSRFToken': csrfToken }})
@ -529,6 +548,7 @@ document.addEventListener('DOMContentLoaded', () => {
            alert("Download error: No file path available.");
        }
    });
    splitForm.addEventListener('submit', async (e) => {
        e.preventDefault();
        const spinner = splitButton.querySelector('.spinner-border');
@ -539,10 +559,13 @@ document.addEventListener('DOMContentLoaded', () => {
        downloadSplitButton.style.display = 'none';
        splitZipPath = null;
        splitConsole.innerHTML = `<div>${new Date().toLocaleTimeString()} [INFO] Starting bundle splitting...</div>`;
        const formData = new FormData();
        const csrfTokenInput = splitForm.querySelector('input[name="csrf_token"]');
        if (csrfTokenInput) formData.append('csrf_token', csrfTokenInput.value);
        const bundleSource = Array.from(bundleSourceRadios).find(radio => radio.checked)?.value;
        if (bundleSource === 'upload') {
            if (!splitBundleZipInput || splitBundleZipInput.files.length === 0) {
                alert('Please select a ZIP file to upload for splitting.');
@ -574,13 +597,16 @@ document.addEventListener('DOMContentLoaded', () => {
            if (icon) icon.style.display = 'inline-block';
            return;
        }
        const headers = {
            'Accept': 'application/x-ndjson',
            'X-CSRFToken': csrfTokenInput ? csrfTokenInput.value : '',
            'X-API-Key': apiKey
        };
        try {
            const response = await fetch('/api/split-bundles', { method: 'POST', headers: headers, body: formData });
            if (!response.ok) {
                const errorMsg = await response.text();
                let detail = errorMsg;
@ -589,6 +615,7 @@ document.addEventListener('DOMContentLoaded', () => {
            }
            splitZipPath = response.headers.get('X-Zip-Path');
            console.log(`Received X-Zip-Path for split: ${splitZipPath}`);
            const reader = response.body.getReader();
            const decoder = new TextDecoder();
            let buffer = '';
@ -621,6 +648,7 @@ document.addEventListener('DOMContentLoaded', () => {
                }
            }
            if (buffer.trim()) { /* Handle final buffer */ }
        } catch (e) {
            console.error('Splitting error:', e);
            const ts = new Date().toLocaleTimeString();
@ -632,6 +660,7 @@ document.addEventListener('DOMContentLoaded', () => {
            if (icon) icon.style.display = 'inline-block';
        }
    });
    downloadSplitButton.addEventListener('click', () => {
        if (splitZipPath) {
            const filename = splitZipPath.split('/').pop() || 'split_resources.zip';
@ -656,9 +685,10 @@ document.addEventListener('DOMContentLoaded', () => {
            alert("Download error: No file path available.");
        }
    });
    // --- Initial Setup Calls ---
    updateBundleSourceUI();
-    fetchLocalUrlAndSetUI();
+    updateServerToggleUI();
    toggleFetchReferenceBundles();
 });
 </script>
--- a/templates/validate_sample.html
+++ b/templates/validate_sample.html
@ -1,3 +1,4 @@
 <!-- templates/validate_sample.html -->
 {% extends "base.html" %}
 {% block content %}
@ -6,15 +7,14 @@
    <h1 class="display-5 fw-bold text-body-emphasis">Validate FHIR Sample</h1>
    <div class="col-lg-6 mx-auto">
        <p class="lead mb-4">
-            Validate a FHIR resource or bundle against a selected Implementation Guide.
+            Validate a FHIR resource or bundle against a selected Implementation Guide. (ALPHA - TEST Fhir pathing is complex and the logic is WIP, please report anomalies you find in Github issues alongside your sample json REMOVE PHI)
        </p>
-    </div>
+          <!-----------------------------------------------------------------remove the buttons-----------------------------------------------------
-</div>
+        <div class="d-grid gap-2 d-sm-flex justify-content-sm-center">
-
+            <a href="{{ url_for('index') }}" class="btn btn-primary btn-lg px-4 gap-3">Back to Home</a>
-<div id="spinner-overlay" class="d-none position-fixed top-0 start-0 w-100 h-100 bg-dark bg-opacity-50 d-flex align-items-center justify-content-center" style="z-index: 1050;">
+            <a href="{{ url_for('view_igs') }}" class="btn btn-outline-secondary btn-lg px-4">Manage FHIR Packages</a>
-    <div class="text-center text-white">
+        </div>
-        <div id="spinner-animation" style="width: 200px; height: 200px;"></div>
+          ----------------------------------------------------------------remove the buttons----------------------------------------------------->
        <p class="mt-3" id="spinner-message">Waiting, don't leave this page...</p>
    </div>
 </div>
@ -22,9 +22,8 @@
    <div class="card">
        <div class="card-header">Validation Form</div>
        <div class="card-body">
-            <form id="validationForm" method="POST" action="/api/validate">
+            <form id="validationForm">
-                {{ form.csrf_token }}
+                {{ form.hidden_tag() }}
                <div class="mb-3">
                    <small class="form-text text-muted">
                        Select a package from the list below or enter a new one (e.g., <code>hl7.fhir.us.core</code>).
@ -47,7 +46,6 @@
                        <div class="text-danger">{{ error }}</div>
                    {% endfor %}
                </div>
                <div class="mb-3">
                    <label for="{{ form.version.id }}" class="form-label">Package Version</label>
                    {{ form.version(class="form-control", id=form.version.id) }}
@ -55,404 +53,145 @@
                        <div class="text-danger">{{ error }}</div>
                    {% endfor %}
                </div>
                <hr class="my-4">
                <!-- New Fields from ValidationForm -->
                <div class="mb-3">
-                    <label for="fhir_resource" class="form-label">FHIR Resource (JSON or XML)</label>
+                    <label for="{{ form.include_dependencies.id }}" class="form-label">Include Dependencies</label>
-                    {{ form.fhir_resource(class="form-control", rows=10, placeholder="Paste your FHIR JSON here...") }}
+                    <div class="form-check">
-                </div>
+                        {{ form.include_dependencies(class="form-check-input") }}
-
+                        {{ form.include_dependencies.label(class="form-check-label") }}
                <div class="row g-3">
                    <div class="col-md-6">
                        <label for="fhir_version" class="form-label">FHIR Version</label>
                        {{ form.fhir_version(class="form-select") }}
                    </div>
                </div>
-
+                <div class="mb-3">
-                <hr class="my-4">
+                    <label for="{{ form.mode.id }}" class="form-label">Validation Mode</label>
-
+                    {{ form.mode(class="form-select") }}
                <h5>Validation Flags</h5>
                <div class="row g-3">
                    <div class="col-md-6">
                        <div class="form-check">
                            {{ form.do_native(class="form-check-input") }}
                            <label class="form-check-label" for="do_native">{{ form.do_native.label }}</label>
                        </div>
                        <div class="form-check">
                            {{ form.hint_about_must_support(class="form-check-input") }}
                            <label class="form-check-label" for="hint_about_must_support">{{ form.hint_about_must_support.label }}</label>
                        </div>
                        <div class="form-check">
                            {{ form.assume_valid_rest_references(class="form-check-input") }}
                            <label class="form-check-label" for="assume_valid_rest_references">{{ form.assume_valid_rest_references.label }}</label>
                        </div>
                        <div class="form-check">
                            {{ form.no_extensible_binding_warnings(class="form-check-input") }}
                            <label class="form-check-label" for="no_extensible_binding_warnings">{{ form.no_extensible_binding_warnings.label }}</label>
                        </div>
                    </div>
                    <div class="col-md-6">
                        <div class="form-check">
                            {{ form.show_times(class="form-check-input") }}
                            <label class="form-check-label" for="show_times">{{ form.show_times.label }}</label>
                        </div>
                        <div class="form-check">
                            {{ form.allow_example_urls(class="form-check-input") }}
                            <label class="form-check-label" for="allow_example_urls">{{ form.allow_example_urls.label }}</label>
                        </div>
                        <div class="form-check">
                            {{ form.check_ips_codes(class="form-check-input") }}
                            <label class="form-check-label" for="check_ips_codes">{{ form.check_ips_codes.label }}</label>
                        </div>
                        <div class="form-check">
                            {{ form.allow_any_extensions(class="form-check-input") }}
                            <label class="form-check-label" for="allow_any_extensions">{{ form.allow_any_extensions.label }}</label>
                        </div>
                        <div class="form-check">
                            {{ form.tx_routing(class="form-check-input") }}
                            <label class="form-check-label" for="tx_routing">{{ form.tx_routing.label }}</label>
                        </div>
                    </div>
                </div>
-
+                <div class="mb-3">
-                <hr class="my-4">
+                    <label for="{{ form.sample_input.id }}" class="form-label">Sample FHIR Resource/Bundle (JSON)</label>
-
+                    {{ form.sample_input(class="form-control", rows=10, placeholder="Paste your FHIR JSON here...") }}
-                <h5>Other Settings</h5>
+                    {% for error in form.sample_input.errors %}
-                <div class="row g-3">
+                        <div class="text-danger">{{ error }}</div>
-                    <div class="col-md-6">
+                    {% endfor %}
                        <label for="profiles" class="form-label">{{ form.profiles.label }}</label>
                        {{ form.profiles(class="form-control") }}
                        <small class="form-text text-muted">Comma-separated URLs, e.g., url1,url2</small>
                    </div>
                    <div class="col-md-6">
                        <label for="extensions" class="form-label">{{ form.extensions.label }}</label>
                        {{ form.extensions(class="form-control") }}
                        <small class="form-text text-muted">Comma-separated URLs, e.g., url1,url2</small>
                    </div>
                    <div class="col-md-6">
                        <label for="terminology_server" class="form-label">{{ form.terminology_server.label }}</label>
                        {{ form.terminology_server(class="form-control") }}
                        <small class="form-text text-muted">e.g., http://tx.fhir.org</small>
                    </div>
                    <div class="col-md-6">
                        <label for="snomed_ct_version" class="form-label">{{ form.snomed_ct_version.label }}</label>
                        {{ form.snomed_ct_version(class="form-select") }}
                        <small class="form-text text-muted">Select a SNOMED CT edition.</small>
                    </div>
                </div>
                <div class="mt-4 text-center">
                    <button type="submit" id="validateButton" class="btn btn-primary btn-lg">
                        Validate Resource
                    </button>
                    <button type="button" id="clearResultsButton" class="btn btn-secondary btn-lg d-none">
                        Clear Results
                    </button>
                </div>
                <button type="button" class="btn btn-primary" id="validateButton">Validate</button>
            </form>
        </div>
    </div>
-    
+
-    <div id="validationResult" class="card mt-4" style="display: none;">
+    <div class="card mt-4" id="validationResult" style="display: none;">
-        <div class="card-header">Validation Results</div>
+        <div class="card-header">Validation Report</div>
        <div class="card-body" id="validationContent">
-            <!-- Results will be displayed here -->
+            <!-- Results will be populated dynamically -->
        </div>
    </div>
 </div>
 <script src="{{ url_for('static', filename='js/lottie.min.js') }}"></script>
 <script>
-    // --- Global Variables and Helper Functions ---
+document.addEventListener('DOMContentLoaded', function() {
-    let currentLottieAnimation = null;
+    const packageSelect = document.getElementById('packageSelect');
-    let pollInterval = null;
+    const packageNameInput = document.getElementById('{{ form.package_name.id }}');
-    const spinnerOverlay = document.getElementById('spinner-overlay');
+    const versionInput = document.getElementById('{{ form.version.id }}');
-    const spinnerMessage = document.getElementById('spinner-message');
+    const validateButton = document.getElementById('validateButton');
-    const spinnerContainer = document.getElementById('spinner-animation');
+    const sampleInput = document.getElementById('{{ form.sample_input.id }}');
-    const perPage = 10;
+    const validationResult = document.getElementById('validationResult');
-    
+    const validationContent = document.getElementById('validationContent');
    // Function to load the Lottie animation based on theme
    function loadLottieAnimation(theme) {
        if (currentLottieAnimation) {
            currentLottieAnimation.destroy();
            currentLottieAnimation = null;
        }
        const animationPath = (theme === 'dark')
            ? '{{ url_for('static', filename='animations/Validation abstract.json') }}'
            : '{{ url_for('static', filename='animations/Validation abstract.json') }}';
        try {
            currentLottieAnimation = lottie.loadAnimation({
                container: spinnerContainer,
                renderer: 'svg',
                loop: true,
                autoplay: true,
                path: animationPath
            });
        } catch(lottieError) {
            console.error("Error loading Lottie animation:", lottieError);
        }
    }
-    // Function to show/hide the spinner with a custom message
+    // Debug DOM elements
-    function toggleSpinner(show, message = "Running validator...") {
+    console.log('Package Select:', packageSelect ? 'Found' : 'Missing');
-        if (show) {
+    console.log('Package Name Input:', packageNameInput ? 'Found' : 'Missing');
-            spinnerMessage.textContent = message;
+    console.log('Version Input:', versionInput ? 'Found' : 'Missing');
            spinnerOverlay.classList.remove('d-none');
            const currentTheme = document.documentElement.getAttribute('data-theme') === 'dark' ? 'dark' : 'light';
            loadLottieAnimation(currentTheme);
        } else {
            spinnerOverlay.classList.add('d-none');
            if (currentLottieAnimation) {
                currentLottieAnimation.destroy();
                currentLottieAnimation = null;
            }
        }
    }
-    // --- Frontend logic starts here
+    // Update package_name and version fields from dropdown
-    document.addEventListener('DOMContentLoaded', function() {
+    function updatePackageFields(select) {
-        const form = document.getElementById('validationForm');
+        const value = select.value;
-        const validateButton = document.getElementById('validateButton');
+        console.log('Selected package:', value);
-        const clearResultsButton = document.getElementById('clearResultsButton');
+        if (!packageNameInput || !versionInput) {
-        const validationResult = document.getElementById('validationResult');
+            console.error('Input fields not found');
-        const validationContent = document.getElementById('validationContent');
+            return;
-        const csrfToken = document.querySelector('input[name="csrf_token"]').value;
+        }
-        const packageSelect = document.getElementById('packageSelect');
+        if (value) {
-        const packageNameInput = document.getElementById('{{ form.package_name.id }}');
+            const [name, version] = value.split('#');
-        const versionInput = document.getElementById('{{ form.version.id }}');
+            if (name && version) {
-        const fhirResourceInput = document.getElementById('fhir_resource');
+                packageNameInput.value = name;
-        
+                versionInput.value = version;
-        // Function to update package fields when a package is selected from the dropdown
+                console.log('Updated fields:', { packageName: name, version });
        function updatePackageFields(select) {
            const value = select.value;
            if (!packageNameInput || !versionInput) return;
            if (value) {
                const [name, version] = value.split('#');
                if (name && version) {
                    packageNameInput.value = name;
                    versionInput.value = version;
                } else {
                    packageNameInput.value = '';
                    versionInput.value = '';
                }
            } else {
                console.warn('Invalid package format:', value);
                packageNameInput.value = '';
                versionInput.value = '';
            }
        } else {
            packageNameInput.value = '';
            versionInput.value = '';
            console.log('Cleared fields: no package selected');
        }
-        
+    }
-        // Sanitize text to prevent XSS
+
-        function sanitizeText(text) {
+    // Initialize dropdown based on form values
-            const div = document.createElement('div');
+    if (packageNameInput && versionInput && packageNameInput.value && versionInput.value) {
-            div.textContent = text;
+        const currentValue = `${packageNameInput.value}#${versionInput.value}`;
-            return div.innerHTML;
+        if (packageSelect.querySelector(`option[value="${currentValue}"]`)) {
            packageSelect.value = currentValue;
            console.log('Initialized dropdown with:', currentValue);
        }
    }
-        // Tidy up the display by paginating results
+    // Debug dropdown options
-        function renderResultList(container, items, title, isWarnings = false) {
+    console.log('Dropdown options:', Array.from(packageSelect.options).map(opt => opt.value));
            container.innerHTML = '';
            if (items.length === 0) {
                return;
            }
-            const wrapper = document.createElement('div');
+    // Attach event listener for package selection
-            const listId = `list-${title.toLowerCase()}`;
+    if (packageSelect) {
        packageSelect.addEventListener('change', function() {
            updatePackageFields(this);
        });
    }
-            let initialItems = items.slice(0, perPage);
+    // Client-side JSON validation preview
-            let remainingItems = items.slice(perPage);
+    if (sampleInput) {
-
+        sampleInput.addEventListener('input', function() {
-            const titleElement = document.createElement('h5');
+            try {
-            titleElement.textContent = title;
+                if (this.value.trim()) {
-            wrapper.appendChild(titleElement);
+                    JSON.parse(this.value);
-            
+                    this.classList.remove('is-invalid');
-            const ul = document.createElement('ul');
+                    this.classList.add('is-valid');
-            ul.className = 'list-unstyled';
+                } else {
-            initialItems.forEach(item => {
+                    this.classList.remove('is-valid', 'is-invalid');
                const li = document.createElement('li');
                li.innerHTML = `
                    <div class="alert alert-${isWarnings ? 'warning' : 'danger'}">
                        ${sanitizeText(typeof item === 'string' ? item : item.message || item.issue)}
                        ${isWarnings && (item.issue && item.issue.includes('Must Support')) ? ' <i class="bi bi-info-circle" title="This element is marked as Must Support in the profile."></i>' : ''}
                    </div>
                `;
                ul.appendChild(li);
            });
            wrapper.appendChild(ul);
            if (remainingItems.length > 0) {
                const toggleButton = document.createElement('a');
                toggleButton.href = '#';
                toggleButton.className = 'btn btn-sm btn-link text-decoration-none';
                toggleButton.textContent = `Show More (${remainingItems.length} more)`;
                const remainingUl = document.createElement('ul');
                remainingUl.className = 'list-unstyled d-none';
                remainingItems.forEach(item => {
                    const li = document.createElement('li');
                    li.innerHTML = `
                        <div class="alert alert-${isWarnings ? 'warning' : 'danger'}">
                            ${sanitizeText(typeof item === 'string' ? item : item.message || item.issue)}
                            ${isWarnings && (item.issue && item.issue.includes('Must Support')) ? ' <i class="bi bi-info-circle" title="This element is marked as Must Support in the profile."></i>' : ''}
                        </div>
                    `;
                    remainingUl.appendChild(li);
                });
                toggleButton.addEventListener('click', (e) => {
                    e.preventDefault();
                    if (remainingUl.classList.contains('d-none')) {
                        remainingUl.classList.remove('d-none');
                        toggleButton.textContent = 'Show Less';
                    } else {
                        remainingUl.classList.add('d-none');
                        toggleButton.textContent = `Show More (${remainingItems.length} more)`;
                    }
                });
                wrapper.appendChild(toggleButton);
                wrapper.appendChild(remainingUl);
            }
            container.appendChild(wrapper);
        }
        function displayFinalReport(data) {
            validationContent.innerHTML = '';
            let hasContent = false;
            clearResultsButton.classList.remove('d-none');
            if (data.file_paths) {
                // Use the paths returned from the server to create download links
                const jsonFileName = data.file_paths.json.split('/').pop();
                const htmlFileName = data.file_paths.html.split('/').pop();
                const downloadDiv = document.createElement('div');
                downloadDiv.className = 'alert alert-info d-flex justify-content-between align-items-center';
                downloadDiv.innerHTML = `
                    <span>Download Raw Reports:</span>
                    <div>
                        <a href="/download/${jsonFileName}" class="btn btn-sm btn-secondary me-2" download>Download JSON</a>
                        <a href="/download/${htmlFileName}" class="btn btn-sm btn-secondary" download>Download HTML</a>
                    </div>
                `;
                validationContent.appendChild(downloadDiv);
                hasContent = true;
            }
            if (data.errors && data.errors.length > 0) {
                hasContent = true;
                const errorContainer = document.createElement('div');
                renderResultList(errorContainer, data.errors, 'Errors');
                validationContent.appendChild(errorContainer);
            }
            if (data.warnings && data.warnings.length > 0) {
                hasContent = true;
                const warningContainer = document.createElement('div');
                renderResultList(warningContainer, data.warnings, 'Warnings', true);
                validationContent.appendChild(warningContainer);
            }
            if (data.results) {
                hasContent = true;
                const resultsDiv = document.createElement('div');
                resultsDiv.innerHTML = '<h5>Detailed Results</h5>';
                let index = 0;
                for (const [resourceId, result] of Object.entries(data.results)) {
                    const collapseId = `result-collapse-${index++}`;
                    resultsDiv.innerHTML += `
                        <div class="card mb-2">
                            <div class="card-header" role="button" data-bs-toggle="collapse" data-bs-target="#${collapseId}" aria-expanded="false" aria-controls="${collapseId}">
                                <h6 class="mb-0">${sanitizeText(resourceId)}</h6>
                                <p class="mb-0"><strong>Valid:</strong> ${result.valid ? 'Yes' : 'No'}</p>
                            </div>
                            <div id="${collapseId}" class="collapse">
                                <div class="card-body">
                                    ${result.details && result.details.length > 0 ? `
                                        <ul>
                                            ${result.details.map(d => `
                                                <li class="${d.severity === 'error' ? 'text-danger' : d.severity === 'warning' ? 'text-warning' : 'text-info'}">
                                                    ${sanitizeText(d.issue)}
                                                    ${d.description && d.description !== d.issue ? `<br><small class="text-muted">${sanitizeText(d.description)}</small>` : ''}
                                                </li>
                                            `).join('')}
                                        </ul>
                                    ` : '<p>No additional details.</p>'}
                                </div>
                            </div>
                        </div>
                    `;
                }
-                validationContent.appendChild(resultsDiv);
+            } catch (e) {
                this.classList.remove('is-valid');
                this.classList.add('is-invalid');
            }
        });
    }
-            if (data.summary) {
+    // Check HAPI server status
-                const summaryDiv = document.createElement('div');
+    function checkHapiStatus() {
-                summaryDiv.className = 'alert alert-info';
+        return fetch('/fhir/metadata', { method: 'GET' })
-                summaryDiv.innerHTML = `
+            .then(response => {
-                    <h5>Summary</h5>
+                if (!response.ok) {
-                    <p>Valid: ${data.valid ? 'Yes' : 'No'}</p>
+                    throw new Error('HAPI server unavailable');
-                    <p>Errors: ${data.summary.error_count || 0}, Warnings: ${data.summary.warning_count || 0}</p>
+                }
-                `;
+                return true;
-                validationContent.appendChild(summaryDiv);
+            })
-                hasContent = true;
+            .catch(error => {
-            }
+                console.warn('HAPI status check failed:', error.message);
-
+                validationContent.innerHTML = '<div class="alert alert-warning">HAPI server unavailable; using local validation.</div>';
-            if (!hasContent && data.valid) {
+                return false;
                validationContent.innerHTML = '<div class="alert alert-success">Validation passed with no errors or warnings.</div>';
            }
            document.querySelectorAll('[data-bs-toggle="collapse"]').forEach(el => {
                el.addEventListener('click', () => {
                    const target = document.querySelector(el.getAttribute('data-bs-target'));
                    target.classList.toggle('show');
                });
            });
-            document.querySelectorAll('[data-bs-toggle="tooltip"]').forEach(el => {
+    }
-                new bootstrap.Tooltip(el);
+
-            });
+    // Sanitize text to prevent XSS
-        }
+    function sanitizeText(text) {
-        
+        const div = document.createElement('div');
-        function checkValidationStatus(taskId) {
+        div.textContent = text;
-            fetch(`/api/check-validation-status/${taskId}`)
+        return div.innerHTML;
-                .then(response => {
+    }
-                    if (response.status === 202) {
+
-                        console.log('Validation still in progress...');
+    // Validate button handler
-                        return null; 
+    if (validateButton) {
-                    } else if (response.status === 200) {
+        validateButton.addEventListener('click', function() {
-                        clearInterval(pollInterval);
+            const packageName = packageNameInput.value;
-                        toggleSpinner(false);
+            const version = versionInput.value;
-                        return response.json();
+            const sampleData = sampleInput.value.trim();
-                    } else {
+            const includeDependencies = document.getElementById('{{ form.include_dependencies.id }}').checked;
                        clearInterval(pollInterval);
                        toggleSpinner(false);
                        return response.json().then(errorData => {
                            throw new Error(errorData.message);
                        });
                    }
                })
                .then(data => {
                    if (data && data.status === 'complete') {
                        validationResult.style.display = 'block';
                        displayFinalReport(data.result);
                    }
                })
                .catch(error => {
                    clearInterval(pollInterval);
                    toggleSpinner(false);
                    console.error('Validation failed during polling:', error);
                    validationResult.style.display = 'block';
                    validationContent.innerHTML = `<div class="alert alert-danger">An unexpected error occurred during validation: ${sanitizeText(error.message)}</div>`;
                });
        }
        function runBlockingValidation(e) {
            e.preventDefault(); // This is the crucial line to prevent default form submission
            const packageName = document.getElementById('{{ form.package_name.id }}').value;
            const version = document.getElementById('{{ form.version.id }}').value;
            const sampleData = document.getElementById('fhir_resource').value.trim();
            const csrfToken = document.querySelector('input[name="csrf_token"]').value;
            if (!packageName || !version) {
                validationResult.style.display = 'block';
@ -462,126 +201,176 @@
            if (!sampleData) {
                validationResult.style.display = 'block';
-                validationContent.innerHTML = '<div class="alert alert-danger">Please provide FHIR sample JSON or XML.</div>';
+                validationContent.innerHTML = '<div class="alert alert-danger">Please provide FHIR sample JSON.</div>';
                return;
            }
            toggleSpinner(true, "Running FHIR Validator (This may take up to 5 minutes on the first run).");
            // Collect all form data including the new fields
            const data = {
                package_name: packageName,
                version: version,
                fhir_resource: sampleData,
                fhir_version: document.getElementById('fhir_version').value,
                do_native: document.getElementById('do_native').checked,
                hint_about_must_support: document.getElementById('hint_about_must_support').checked,
                assume_valid_rest_references: document.getElementById('assume_valid_rest_references').checked,
                no_extensible_binding_warnings: document.getElementById('no_extensible_binding_warnings').checked,
                show_times: document.getElementById('show_times').checked,
                allow_example_urls: document.getElementById('allow_example_urls').checked,
                check_ips_codes: document.getElementById('check_ips_codes').checked,
                allow_any_extensions: document.getElementById('allow_any_extensions').checked,
                tx_routing: document.getElementById('tx_routing').checked,
                snomed_ct_version: document.getElementById('snomed_ct_version').value,
                profiles: document.getElementById('profiles').value,
                extensions: document.getElementById('extensions').value,
                terminology_server: document.getElementById('terminology_server').value
            };
-            fetch('/api/validate', {
+            try {
-                method: 'POST',
+                JSON.parse(sampleData);
-                headers: {
+            } catch (e) {
                    'Content-Type': 'application/json',
                    'X-CSRFToken': csrfToken
                },
                body: JSON.stringify(data)
            })
            .then(response => {
                if (response.status === 202) {
                    return response.json();
                } else {
                    toggleSpinner(false);
                    return response.json().then(errorData => {
                        throw new Error(errorData.message);
                    });
                }
            })
            .then(data => {
                if (data.status === 'accepted' && data.task_id) {
                    pollInterval = setInterval(() => checkValidationStatus(data.task_id), 3000);
                } else {
                    toggleSpinner(false);
                    validationResult.style.display = 'block';
                    validationContent.innerHTML = `<div class="alert alert-danger">Server response format unexpected.</div>`;
                }
            })
            .catch(error => {
                clearInterval(pollInterval);
                toggleSpinner(false);
                console.error('Validation failed:', error);
                validationResult.style.display = 'block';
-                validationContent.innerHTML = `<div class="alert alert-danger">An unexpected error occurred during validation: ${sanitizeText(error.message)}</div>`;
+                validationContent.innerHTML = '<div class="alert alert-danger">Invalid JSON: ' + sanitizeText(e.message) + '</div>';
-            });
+                return;
-        };
+            }
-        
+
-        clearResultsButton.addEventListener('click', function() {
+            validationResult.style.display = 'block';
-            fetch('/api/clear-validation-results', {
+            validationContent.innerHTML = '<div class="text-center py-3"><div class="spinner-border text-primary" role="status"><span class="visually-hidden">Validating...</span></div></div>';
-                method: 'POST',
+
-                headers: {
+            // Check HAPI status before validation
-                    'X-CSRFToken': csrfToken
+            checkHapiStatus().then(() => {
-                }
+                console.log('Sending request to /api/validate-sample with:', {
-            })
+                    package_name: packageName,
-            .then(response => response.json())
+                    version: version,
-            .then(data => {
+                    include_dependencies: includeDependencies,
-                if (data.status === 'success') {
+                    sample_data_length: sampleData.length
-                    validationResult.style.display = 'none';
+                });
-                    clearResultsButton.classList.add('d-none');
+
-                } else {
+                fetch('/api/validate-sample', {
-                    console.error('Failed to clear results:', data.message);
+                    method: 'POST',
-                }
+                    headers: {
-            })
+                        'Content-Type': 'application/json',
-            .catch(error => {
+                        'X-CSRFToken': '{{ form.csrf_token._value() }}'
-                console.error('Network error while clearing results:', error);
+                    },
                    body: JSON.stringify({
                        package_name: packageName,
                        version: version,
                        include_dependencies: includeDependencies,
                        sample_data: sampleData
                    })
                })
                .then(response => {
                    console.log('Server response status:', response.status, response.statusText);
                    if (!response.ok) {
                        return response.text().then(text => {
                            console.error('Server response text:', text.substring(0, 200) + (text.length > 200 ? '...' : ''));
                            throw new Error(`HTTP error ${response.status}: ${text.substring(0, 100)}...`);
                        });
                    }
                    return response.json();
                })
                .then(data => {
                    console.log('Validation response:', data);
                    validationContent.innerHTML = '';
                    let hasContent = false;
                    // Display profile information
                    if (data.results) {
                        const profileDiv = document.createElement('div');
                        profileDiv.className = 'mb-3';
                        const profiles = new Set();
                        Object.values(data.results).forEach(result => {
                            if (result.profile) profiles.add(result.profile);
                        });
                        if (profiles.size > 0) {
                            profileDiv.innerHTML = `
                                <h5>Validated Against Profile${profiles.size > 1 ? 's' : ''}</h5>
                                <ul>
                                    ${Array.from(profiles).map(p => `<li><a href="${sanitizeText(p)}" target="_blank">${sanitizeText(p.split('/').pop())}</a></li>`).join('')}
                                </ul>
                            `;
                            validationContent.appendChild(profileDiv);
                            hasContent = true;
                        }
                    }
                    // Display errors
                    if (data.errors && data.errors.length > 0) {
                        hasContent = true;
                        const errorDiv = document.createElement('div');
                        errorDiv.className = 'alert alert-danger';
                        errorDiv.innerHTML = `
                            <h5>Errors</h5>
                            <ul>
                                ${data.errors.map(e => `<li>${sanitizeText(typeof e === 'string' ? e : e.message)}</li>`).join('')}
                            </ul>
                        `;
                        validationContent.appendChild(errorDiv);
                    }
                    // Display warnings
                    if (data.warnings && data.warnings.length > 0) {
                        hasContent = true;
                        const warningDiv = document.createElement('div');
                        warningDiv.className = 'alert alert-warning';
                        warningDiv.innerHTML = `
                            <h5>Warnings</h5>
                            <ul>
                                ${data.warnings.map(w => {
                                    const isMustSupport = w.includes('Must Support');
                                    return `<li>${sanitizeText(typeof w === 'string' ? w : w.message)}${isMustSupport ? ' <i class="bi bi-info-circle" title="This element is marked as Must Support in the profile."></i>' : ''}</li>`;
                                }).join('')}
                            </ul>
                        `;
                        validationContent.appendChild(warningDiv);
                    }
                    // Detailed results with collapsible sections
                    if (data.results) {
                        hasContent = true;
                        const resultsDiv = document.createElement('div');
                        resultsDiv.innerHTML = '<h5>Detailed Results</h5>';
                        let index = 0;
                        for (const [resourceId, result] of Object.entries(data.results)) {
                            const collapseId = `result-collapse-${index++}`;
                            resultsDiv.innerHTML += `
                                <div class="card mb-2">
                                    <div class="card-header" role="button" data-bs-toggle="collapse" data-bs-target="#${collapseId}" aria-expanded="false" aria-controls="${collapseId}">
                                        <h6 class="mb-0">${sanitizeText(resourceId)}</h6>
                                        <p class="mb-0"><strong>Valid:</strong> ${result.valid ? 'Yes' : 'No'}</p>
                                    </div>
                                    <div id="${collapseId}" class="collapse">
                                        <div class="card-body">
                                            ${result.details && result.details.length > 0 ? `
                                                <ul>
                                                    ${result.details.map(d => `
                                                        <li class="${d.severity === 'error' ? 'text-danger' : d.severity === 'warning' ? 'text-warning' : 'text-info'}">
                                                            ${sanitizeText(d.issue)}
                                                            ${d.description && d.description !== d.issue ? `<br><small class="text-muted">${sanitizeText(d.description)}</small>` : ''}
                                                        </li>
                                                    `).join('')}
                                                </ul>
                                            ` : '<p>No additional details.</p>'}
                                        </div>
                                    </div>
                                </div>
                            `;
                        }
                        validationContent.appendChild(resultsDiv);
                    }
                    // Summary
                    const summaryDiv = document.createElement('div');
                    summaryDiv.className = 'alert alert-info';
                    summaryDiv.innerHTML = `
                        <h5>Summary</h5>
                        <p>Valid: ${data.valid ? 'Yes' : 'No'}</p>
                        <p>Errors: ${data.summary.error_count || 0}, Warnings: ${data.summary.warning_count || 0}</p>
                    `;
                    validationContent.appendChild(summaryDiv);
                    hasContent = true;
                    if (!hasContent && data.valid) {
                        validationContent.innerHTML = '<div class="alert alert-success">Validation passed with no errors or warnings.</div>';
                    }
                    // Initialize Bootstrap collapse and tooltips
                    document.querySelectorAll('[data-bs-toggle="collapse"]').forEach(el => {
                        el.addEventListener('click', () => {
                            const target = document.querySelector(el.getAttribute('data-bs-target'));
                            target.classList.toggle('show');
                        });
                    });
                    document.querySelectorAll('[data-bs-toggle="tooltip"]').forEach(el => {
                        new bootstrap.Tooltip(el);
                    });
                })
                .catch(error => {
                    console.error('Validation error:', error);
                    validationContent.innerHTML = `<div class="alert alert-danger">Error during validation: ${sanitizeText(error.message)}</div>`;
                });
            });
        });
-
+    }
-        if (packageSelect) {
+});
            packageSelect.addEventListener('change', function() {
                updatePackageFields(this);
            });
        }
        if (validateButton) {
            validateButton.addEventListener('click', function(e) {
                runBlockingValidation(e);
            });
        }
        if (packageNameInput.value && versionInput.value) {
            const currentValue = `${packageNameInput.value}#${versionInput.value}`;
            const optionExists = Array.from(packageSelect.options).some(opt => opt.value === currentValue);
            if (optionExists) {
                packageSelect.value = currentValue;
            }
        }
        if (fhirResourceInput) {
            fhirResourceInput.addEventListener('input', function() {
                try {
                    if (this.value.trim()) {
                        JSON.parse(this.value);
                        this.classList.remove('is-invalid');
                        this.classList.add('is-valid');
                    } else {
                        this.classList.remove('is-valid', 'is-invalid');
                    }
                } catch (e) {
                    this.classList.remove('is-valid');
                    this.classList.add('is-invalid');
                }
            });
        }
    });
 </script>
-{% endblock %}
+{% endblock %}