Merge pull request #24 from Sudo-JHare/V4-Alpha

V4.1 - Merge release

.github/ct/chart-schema.yaml

@@ -0,0 +1,23 @@
+name: str()
+home: str()
+version: str()
+apiVersion: str()
+appVersion: any(str(), num(), required=False)
+type: str()
+dependencies: any(required=False)
+description: str()
+keywords: list(str(), required=False)
+sources: list(str(), required=False)
+maintainers: list(include('maintainer'), required=False)
+icon: str(required=False)
+engine: str(required=False)
+condition: str(required=False)
+tags: str(required=False)
+deprecated: bool(required=False)
+kubeVersion: str(required=False)
+annotations: map(str(), str(), required=False)
+---
+maintainer:
+  name: str()
+  email: str(required=False)
+  url: str(required=False)

.github/ct/config.yaml

@@ -0,0 +1,15 @@
+debug: true
+remote: origin
+chart-yaml-schema: .github/ct/chart-schema.yaml
+validate-maintainers: false
+validate-chart-schema: true
+validate-yaml: true
+check-version-increment: true
+chart-dirs:
+  - charts
+helm-extra-args: --timeout 300s
+upgrade: true
+skip-missing-values: true
+release-label: release
+release-name-template: "helm-v{{ .Version }}"
+target-branch: master

.github/workflows/build-images.yaml

@@ -0,0 +1,84 @@
+name: Build Container Images
+
+on:
+  push:
+    tags:
+      - "image/v*"
+    paths-ignore:
+      - "charts/**"
+  pull_request:
+    branches: [master]
+    paths-ignore:
+      - "charts/**"
+env:
+  IMAGES: docker.io/hapiproject/hapi
+  PLATFORMS: linux/amd64,linux/arm64/v8
+
+jobs:
+  build:
+    name: Build
+    runs-on: ubuntu-22.04
+    steps:
+      - name: Container meta for default (distroless) image
+        id: docker_meta
+        uses: docker/metadata-action@v5
+        with:
+          images: ${{ env.IMAGES }}
+          tags: |
+            type=match,pattern=image/(.*),group=1,enable=${{github.event_name != 'pull_request'}}
+           
+
+      - name: Container meta for tomcat image
+        id: docker_tomcat_meta
+        uses: docker/metadata-action@v5
+        with:
+          images: ${{ env.IMAGES }}
+          tags: |
+            type=match,pattern=image/(.*),group=1,enable=${{github.event_name != 'pull_request'}}
+          flavor: |
+            suffix=-tomcat,onlatest=true
+
+      - name: Set up QEMU
+        uses: docker/setup-qemu-action@v3
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3
+
+      - name: Login to DockerHub
+        uses: docker/login-action@v3
+        if: github.event_name != 'pull_request'
+        with:
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_TOKEN }}
+
+      - name: Cache Docker layers
+        uses: actions/cache@v3
+        with:
+          path: /tmp/.buildx-cache
+          key: ${{ runner.os }}-buildx-${{ github.sha }}
+          restore-keys: |
+            ${{ runner.os }}-buildx-
+
+      - name: Build and push default (distroless) image
+        id: docker_build
+        uses: docker/build-push-action@v5
+        with:
+          cache-from: type=local,src=/tmp/.buildx-cache
+          cache-to: type=local,dest=/tmp/.buildx-cache
+          push: ${{ github.event_name != 'pull_request' }}
+          tags: ${{ steps.docker_meta.outputs.tags }}
+          labels: ${{ steps.docker_meta.outputs.labels }}
+          platforms: ${{ env.PLATFORMS }}
+          target: default
+
+      - name: Build and push tomcat image
+        id: docker_build_tomcat
+        uses: docker/build-push-action@v5
+        with:
+          cache-from: type=local,src=/tmp/.buildx-cache
+          cache-to: type=local,dest=/tmp/.buildx-cache
+          push: ${{ github.event_name != 'pull_request' }}
+          tags: ${{ steps.docker_tomcat_meta.outputs.tags }}
+          labels: ${{ steps.docker_tomcat_meta.outputs.labels }}
+          platforms: ${{ env.PLATFORMS }}
+          target: tomcat

.github/workflows/chart-release.yaml

@@ -0,0 +1,41 @@
+name: Release Charts
+
+on:
+  push:
+    branches:
+      - main
+    paths:
+      - "charts/**"
+
+jobs:
+  release:
+    runs-on: ubuntu-22.04
+    steps:
+      - name: Add workspace as safe directory
+        run: |
+          git config --global --add safe.directory /__w/FHIRFLARE-IG-Toolkit/FHIRFLARE-IG-Toolkit
+
+      - name: Checkout
+        uses: actions/checkout@8e5e7e5ab8b370d6c329ec480221332ada57f0ab # v3.5.2
+        with:
+          fetch-depth: 0
+
+      - name: Configure Git
+        run: |
+          git config user.name "$GITHUB_ACTOR"
+          git config user.email "$GITHUB_ACTOR@users.noreply.github.com"
+
+      - name: Update dependencies
+        run: find charts/ ! -path charts/ -maxdepth 1 -type d -exec helm dependency update {} \;
+
+      - name: Add Helm Repositories
+        run: |
+          helm repo add hapifhir https://hapifhir.github.io/hapi-fhir-jpaserver-starter/
+          helm repo update
+
+      - name: Run chart-releaser
+        uses: helm/chart-releaser-action@be16258da8010256c6e82849661221415f031968 # v1.5.0
+        with:
+          config: .github/ct/config.yaml
+        env:
+          CR_TOKEN: "${{ secrets.GITHUB_TOKEN }}"

.github/workflows/chart-test.yaml

@@ -0,0 +1,73 @@
+name: Lint and Test Charts
+
+on:
+  pull_request:
+    branches:
+      - master
+    paths:
+      - "charts/**"
+
+jobs:
+  lint:
+    runs-on: ubuntu-22.04
+    container: quay.io/helmpack/chart-testing:v3.11.0@sha256:f2fd21d30b64411105c7eafb1862783236a219d29f2292219a09fe94ca78ad2a
+    steps:
+      - name: Install helm-docs
+        working-directory: /tmp
+        env:
+          HELM_DOCS_URL: https://github.com/norwoodj/helm-docs/releases/download/v1.14.2/helm-docs_1.14.2_Linux_x86_64.tar.gz
+        run: |
+          curl -LSs $HELM_DOCS_URL | tar xz && \
+          mv ./helm-docs /usr/local/bin/helm-docs && \
+          chmod +x /usr/local/bin/helm-docs && \
+          helm-docs --version
+
+      - name: Add workspace as safe directory
+        run: |
+          git config --global --add safe.directory /__w/hapi-fhir-jpaserver-starter/hapi-fhir-jpaserver-starter
+
+      - name: Checkout
+        uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4.1.1
+        with:
+          fetch-depth: 0
+
+      - name: Check if documentation is up-to-date
+        run: helm-docs && git diff --exit-code HEAD
+
+      - name: Run chart-testing (lint)
+        run: ct lint --config .github/ct/config.yaml
+
+  test:
+    runs-on: ubuntu-22.04
+    strategy:
+      matrix:
+        k8s-version: [1.30.8, 1.31.4, 1.32.0]
+    needs:
+      - lint
+    steps:
+      - name: Checkout
+        uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4.1.1
+        with:
+          fetch-depth: 0
+
+      - name: Set up chart-testing
+        uses: helm/chart-testing-action@e6669bcd63d7cb57cb4380c33043eebe5d111992 # v2.6.1
+
+      - name: Run chart-testing (list-changed)
+        id: list-changed
+        run: |
+          changed=$(ct list-changed --config .github/ct/config.yaml)
+          if [[ -n "$changed" ]]; then
+            echo "::set-output name=changed::true"
+          fi
+
+      - name: Create k8s Kind Cluster
+        uses: helm/kind-action@dda0770415bac9fc20092cacbc54aa298604d140 # v1.8.0
+        if: ${{ steps.list-changed.outputs.changed == 'true' }}
+        with:
+          cluster_name: kind-cluster-k8s-${{ matrix.k8s-version }}
+          node_image: kindest/node:v${{ matrix.k8s-version }}
+
+      - name: Run chart-testing (install)
+        run: ct install --config .github/ct/config.yaml
+        if: ${{ steps.list-changed.outputs.changed == 'true' }}

.github/workflows/docker-publish.yml

@@ -0,0 +1,58 @@
+# This workflow builds and pushes a multi-architecture Docker image to GitHub Container Registry (ghcr.io).
+#
+# The Docker meta step is required because GitHub repository names can contain uppercase letters, but Docker image tags must be lowercase.
+# The docker/metadata-action@v5 normalizes the repository name to lowercase, ensuring the build and push steps use a valid image tag.
+#
+# This workflow builds for both AMD64 and ARM64 architectures using Docker Buildx and QEMU emulation.
+
+name: Build and Push Docker image
+
+on:
+  push:
+    branches:
+      - main
+      - '*'  # This will run the workflow on any branch
+  workflow_dispatch:  # This enables manual triggering
+
+jobs:
+  build-and-push:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Set up QEMU
+        uses: docker/setup-qemu-action@v3
+        
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3
+
+      - name: Log in to GitHub Container Registry
+        uses: docker/login-action@v3
+        with:
+          registry: ghcr.io
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Docker meta
+        id: meta
+        uses: docker/metadata-action@v5
+        with:
+          images: ghcr.io/${{ github.repository }}
+
+      - name: Set normalized image name
+        run: |
+          if [[ "${{ github.ref_name }}" == "main" ]]; then
+            echo "IMAGE_NAME=$(echo ${{ steps.meta.outputs.tags }} | sed 's/:main/:latest/')" >> $GITHUB_ENV
+          else
+            echo "IMAGE_NAME=${{ steps.meta.outputs.tags }}" >> $GITHUB_ENV
+          fi
+
+      - name: Build and push multi-architecture Docker image
+        uses: docker/build-push-action@v5
+        with:
+          context: .
+          file: ./docker/Dockerfile
+          platforms: linux/amd64,linux/arm64
+          push: true
+          tags: ${{ env.IMAGE_NAME }}

.github/workflows/jekyll.yml

@@ -0,0 +1,40 @@
+name: Build and Deploy Jekyll site
+
+on:
+  push:
+    branches: [ main, master ]
+  pull_request:
+    branches: [ main, master ]
+  workflow_dispatch:
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        working-directory: website
+    
+    steps:
+    - uses: actions/checkout@v3
+    
+    - name: Setup Ruby
+      uses: ruby/setup-ruby@v1
+      with:
+        ruby-version: '3.2'
+        bundler-cache: true
+        working-directory: website
+    
+    - name: Install dependencies
+      run: |
+        bundle install
+    
+    - name: Build site
+      run: bundle exec jekyll build
+
+    - name: Deploy to gh_pages branch
+      uses: peaceiris/actions-gh-pages@v4
+      with:
+        github_token: ${{ secrets.GITHUB_TOKEN }}
+        publish_dir: ./website/_site
+        publish_branch: gh-pages
+        keep_files: true

.gitignore

@@ -0,0 +1,7 @@
+/logs/
+/.pydevproject
+/__pycache__/
+/myenv/
+/tmp/
+/Gemfile.lock
+/_site/

.project

@@ -0,0 +1,23 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<projectDescription>
+	<name>FHIRFLARE-IG-Toolkit</name>
+	<comment></comment>
+	<projects>
+	</projects>
+	<buildSpec>
+		<buildCommand>
+			<name>org.python.pydev.PyDevBuilder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+		<buildCommand>
+			<name>org.eclipse.wst.validation.validationbuilder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+	</buildSpec>
+	<natures>
+		<nature>org.eclipse.wst.jsdt.core.jsNature</nature>
+		<nature>org.python.pydev.pythonNature</nature>
+	</natures>
+</projectDescription>

.settings/.jsdtscope

@@ -0,0 +1,7 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<classpath>
+	<classpathentry kind="con" path="org.eclipse.wst.jsdt.launching.JRE_CONTAINER"/>
+	<classpathentry kind="con" path="org.eclipse.wst.jsdt.launching.baseBrowserLibrary"/>
+	<classpathentry kind="src" path=""/>
+	<classpathentry kind="output" path=""/>
+</classpath>

.settings/org.eclipse.wst.jsdt.ui.superType.container

@@ -0,0 +1 @@
+org.eclipse.wst.jsdt.launching.JRE_CONTAINER

.settings/org.eclipse.wst.jsdt.ui.superType.name

@@ -0,0 +1 @@
+Global

Build and Run for first time.bat

@@ -2,57 +2,130 @@
 setlocal enabledelayedexpansion
 
 REM --- Configuration ---
-set REPO_URL=https://github.com/hapifhir/hapi-fhir-jpaserver-starter.git
-set CLONE_DIR=hapi-fhir-jpaserver
+set REPO_URL_HAPI=https://github.com/hapifhir/hapi-fhir-jpaserver-starter.git
+set REPO_URL_CANDLE=https://github.com/FHIR/fhir-candle.git
+set CLONE_DIR_HAPI=hapi-fhir-jpaserver
+set CLONE_DIR_CANDLE=fhir-candle
 set SOURCE_CONFIG_DIR=hapi-fhir-setup
 set CONFIG_FILE=application.yaml
 
 REM --- Define Paths ---
 set SOURCE_CONFIG_PATH=..\%SOURCE_CONFIG_DIR%\target\classes\%CONFIG_FILE%
-set DEST_CONFIG_PATH=%CLONE_DIR%\target\classes\%CONFIG_FILE%
+set DEST_CONFIG_PATH=%CLONE_DIR_HAPI%\target\classes\%CONFIG_FILE%
 
-REM === CORRECTED: Prompt for Version ===
+REM --- NEW: Define a variable for the custom FHIR URL and server type ---
+set "CUSTOM_FHIR_URL_VAL="
+set "SERVER_TYPE="
+set "CANDLE_FHIR_VERSION="
+
+REM === MODIFIED: Prompt for Installation Mode ===
 :GetModeChoice
 SET "APP_MODE=" REM Clear the variable first
+echo.
 echo Select Installation Mode:
-echo 1. Standalone (Includes local HAPI FHIR Server - Requires Git & Maven)
-echo 2. Lite (Excludes local HAPI FHIR Server - No Git/Maven needed)
-CHOICE /C 12 /N /M "Enter your choice (1 or 2):"
+echo 1. Lite (Excludes local HAPI FHIR Server - No Git/Maven/Dotnet needed)
+echo 2. Custom URL (Uses a custom FHIR Server - No Git/Maven/Dotnet needed)
+echo 3. Hapi (Includes local HAPI FHIR Server - Requires Git & Maven)
+echo 4. Candle (Includes local FHIR Candle Server - Requires Git & Dotnet)
+CHOICE /C 1234 /N /M "Enter your choice (1, 2, 3, or 4):"
 
+IF ERRORLEVEL 4 (
+    SET APP_MODE=standalone
+    SET SERVER_TYPE=candle
+    goto :GetCandleFhirVersion
+)
+IF ERRORLEVEL 3 (
+    SET APP_MODE=standalone
+    SET SERVER_TYPE=hapi
+    goto :ModeSet
+)
 IF ERRORLEVEL 2 (
+    SET APP_MODE=standalone
+    goto :GetCustomUrl
+)
+IF ERRORLEVEL 1 (
     SET APP_MODE=lite
     goto :ModeSet
 )
-IF ERRORLEVEL 1 (
-    SET APP_MODE=standalone
-    goto :ModeSet
-)
+
 REM If somehow neither was chosen (e.g., Ctrl+C), loop back
 echo Invalid input. Please try again.
 goto :GetModeChoice
 
+:GetCustomUrl
+set "CONFIRMED_URL="
+:PromptUrlLoop
+echo.
+set /p "CUSTOM_URL_INPUT=Please enter the custom FHIR server URL: "
+echo.
+echo You entered: !CUSTOM_URL_INPUT!
+set /p "CONFIRM_URL=Is this URL correct? (Y/N): "
+if /i "!CONFIRM_URL!" EQU "Y" (
+    set "CONFIRMED_URL=!CUSTOM_URL_INPUT!"
+    goto :ConfirmUrlLoop
+) else (
+    goto :PromptUrlLoop
+)
+:ConfirmUrlLoop
+echo.
+echo Please re-enter the URL to confirm it is correct:
+set /p "CUSTOM_URL_INPUT=Re-enter URL: "
+if /i "!CUSTOM_URL_INPUT!" EQU "!CONFIRMED_URL!" (
+    set "CUSTOM_FHIR_URL_VAL=!CUSTOM_URL_INPUT!"
+    echo.
+    echo Custom URL confirmed: !CUSTOM_FHIR_URL_VAL!
+    goto :ModeSet
+) else (
+    echo.
+    echo URLs do not match. Please try again.
+    goto :PromptUrlLoop
+)
+
+:GetCandleFhirVersion
+echo.
+echo Select the FHIR version for the Candle server:
+echo 1. R4 (4.0)
+echo 2. R4B (4.3)
+echo 3. R5 (5.0)
+CHOICE /C 123 /N /M "Enter your choice (1, 2, or 3):"
+IF ERRORLEVEL 3 (
+    SET CANDLE_FHIR_VERSION=r5
+    goto :ModeSet
+)
+IF ERRORLEVEL 2 (
+    SET CANDLE_FHIR_VERSION=r4b
+    goto :ModeSet
+)
+IF ERRORLEVEL 1 (
+    SET CANDLE_FHIR_VERSION=r4
+    goto :ModeSet
+)
+echo Invalid input. Please try again.
+goto :GetCandleFhirVersion
+
 :ModeSet
 IF "%APP_MODE%"=="" (
     echo Invalid choice detected after checks. Exiting.
     goto :eof
 )
 echo Selected Mode: %APP_MODE%
+echo Server Type: %SERVER_TYPE%
 echo.
-REM === END CORRECTION ===
+REM === END MODIFICATION ===
 
 
-REM === Conditionally Execute HAPI Setup ===
-IF "%APP_MODE%"=="standalone" (
-    echo Running Standalone setup including HAPI FHIR...
+REM === Conditionally Execute Server Setup ===
+IF "%SERVER_TYPE%"=="hapi" (
+    echo Running Hapi server setup...
     echo.
     
     REM --- Step 0: Clean up previous clone (optional) ---
-    echo Checking for existing directory: %CLONE_DIR%
-    if exist "%CLONE_DIR%" (
+    echo Checking for existing directory: %CLONE_DIR_HAPI%
+    if exist "%CLONE_DIR_HAPI%" (
         echo Found existing directory, removing it...
-        rmdir /s /q "%CLONE_DIR%"
+        rmdir /s /q "%CLONE_DIR_HAPI%"
         if errorlevel 1 (
-            echo ERROR: Failed to remove existing directory: %CLONE_DIR%
+            echo ERROR: Failed to remove existing directory: %CLONE_DIR_HAPI%
             goto :error
         )
         echo Existing directory removed.
@@ -62,8 +135,8 @@ IF "%APP_MODE%"=="standalone" (
     echo.
 
     REM --- Step 1: Clone the HAPI FHIR server repository ---
-    echo Cloning repository: %REPO_URL% into %CLONE_DIR%...
-    git clone "%REPO_URL%" "%CLONE_DIR%"
+    echo Cloning repository: %REPO_URL_HAPI% into %CLONE_DIR_HAPI%...
+    git clone "%REPO_URL_HAPI%" "%CLONE_DIR_HAPI%"
     if errorlevel 1 (
         echo ERROR: Failed to clone repository. Check Git installation and network connection.
         goto :error
@@ -72,10 +145,10 @@ IF "%APP_MODE%"=="standalone" (
     echo.
 
     REM --- Step 2: Navigate into the cloned directory ---
-    echo Changing directory to %CLONE_DIR%...
-    cd "%CLONE_DIR%"
+    echo Changing directory to %CLONE_DIR_HAPI%...
+    cd "%CLONE_DIR_HAPI%"
     if errorlevel 1 (
-        echo ERROR: Failed to change directory to %CLONE_DIR%.
+        echo ERROR: Failed to change directory to %CLONE_DIR_HAPI%.
         goto :error
     )
     echo Current directory: %CD%
@@ -118,45 +191,141 @@ IF "%APP_MODE%"=="standalone" (
     echo Current directory: %CD%
     echo.
 
-) ELSE (
-    echo Running Lite setup, skipping HAPI FHIR build...
-    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%" (
-       echo Found existing HAPI directory in Lite mode. Removing it to avoid build issues...
-       rmdir /s /q "%CLONE_DIR%"
+) 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
         )
-    REM Create empty target directories expected by Dockerfile COPY, even if not used
-    mkdir "%CLONE_DIR%\target\classes" 2> nul
-    mkdir "%CLONE_DIR%\custom" 2> nul
-    REM Create a placeholder empty WAR file to satisfy Dockerfile COPY
-    echo. > "%CLONE_DIR%\target\ROOT.war"
-    echo. > "%CLONE_DIR%\target\classes\application.yaml"
+        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...
+    REM Ensure the server directories don't exist in Lite mode
+    if exist "%CLONE_DIR_HAPI%" (
+       echo Found existing HAPI directory in Lite mode. Removing it to avoid build issues...
+       rmdir /s /q "%CLONE_DIR_HAPI%"
+    )
+    if exist "%CLONE_DIR_CANDLE%" (
+       echo Found existing Candle directory in Lite mode. Removing it to avoid build issues...
+       rmdir /s /q "%CLONE_DIR_CANDLE%"
+    )
+    REM Create empty placeholder files to satisfy Dockerfile COPY commands in Lite mode.
+    mkdir "%CLONE_DIR_HAPI%\target\classes" 2> nul
+    mkdir "%CLONE_DIR_HAPI%\custom" 2> nul
+    echo. > "%CLONE_DIR_HAPI%\target\ROOT.war"
+    echo. > "%CLONE_DIR_HAPI%\target\classes\application.yaml"
+    mkdir "%CLONE_DIR_CANDLE%\publish" 2> nul
+    echo. > "%CLONE_DIR_CANDLE%\publish\fhir-candle.dll"
     echo Placeholder files created for Lite mode build.
     echo.
 )
 
-REM === Modify docker-compose.yml to set APP_MODE ===
-echo Updating docker-compose.yml with APP_MODE=%APP_MODE%...
+REM === MODIFIED: Update docker-compose.yml to set APP_MODE and HAPI_FHIR_URL ===
+echo Updating docker-compose.yml with APP_MODE=%APP_MODE% and HAPI_FHIR_URL...
 (
   echo version: '3.8'
   echo services:
   echo   fhirflare:
   echo     build:
   echo       context: .
-  echo       dockerfile: Dockerfile
+  IF "%SERVER_TYPE%"=="hapi" (
+        echo       dockerfile: Dockerfile.hapi
+    ) ELSE IF "%SERVER_TYPE%"=="candle" (
+        echo       dockerfile: Dockerfile.candle
+    ) ELSE (
+        echo       dockerfile: Dockerfile.lite
+  )
   echo     ports:
+  IF "%SERVER_TYPE%"=="candle" (
     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       - ./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=!CUSTOM_FHIR_URL_VAL!
+  ) ELSE (
+    IF "%SERVER_TYPE%"=="candle" (
+        echo       - HAPI_FHIR_URL=http://localhost:5826/fhir/%CANDLE_FHIR_VERSION%
+        echo       - ASPNETCORE_URLS=http://0.0.0.0:5826
+    ) ELSE (
+        echo       - HAPI_FHIR_URL=http://localhost:8080/fhir
+    )
+  )
   echo     command: supervisord -c /etc/supervisord.conf
 ) > docker-compose.yml.tmp
 

Dockerfile

@@ -3,17 +3,30 @@ FROM tomcat:10.1-jdk17
 
 # Install build dependencies, Node.js 18, and coreutils (for stdbuf)
 RUN apt-get update && apt-get install -y --no-install-recommends \
-    python3 python3-pip python3-venv curl coreutils \
+    python3 python3-pip python3-venv curl coreutils git \
     && curl -fsSL https://deb.nodesource.com/setup_18.x | bash - \
     && apt-get install -y --no-install-recommends nodejs \
     && rm -rf /var/lib/apt/lists/*
 
+# ADDED: Install the Dotnet SDK for the FHIR Candle server
+# This makes the image a universal base for either server type
+RUN apt-get update && apt-get install -y dotnet-sdk-6.0
+
 # Install specific versions of GoFSH and SUSHI
-# REMOVED pip install fhirpath from this line
 RUN npm install -g gofsh fsh-sushi
 
-# Set up Python environment
+# 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"
 
@@ -29,6 +42,7 @@ 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/
@@ -43,6 +57,9 @@ COPY hapi-fhir-jpaserver/target/classes/application.yaml /app/config/application
 COPY hapi-fhir-jpaserver/target/classes/application.yaml /usr/local/tomcat/webapps/app/config/application.yaml
 COPY hapi-fhir-jpaserver/custom/ /usr/local/tomcat/webapps/custom/
 
+# ADDED: Copy pre-built Candle DLL files
+COPY fhir-candle/publish/ /app/fhir-candle-publish/
+
 # Install supervisord
 RUN pip install supervisor
 
@@ -50,7 +67,7 @@ RUN pip install supervisor
 COPY supervisord.conf /etc/supervisord.conf
 
 # Expose ports
-EXPOSE 5000 8080
+EXPOSE 5000 8080 5001
 
 # Start supervisord
 CMD ["supervisord", "-c", "/etc/supervisord.conf"]

Dockerfile.candle

@@ -0,0 +1,64 @@
+# 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"]

Dockerfile.hapi

@@ -0,0 +1,66 @@
+# Base image with Python, Java, and Maven
+FROM tomcat:10.1-jdk17
+
+# Install build dependencies, Node.js 18, and coreutils (for stdbuf)
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    python3 python3-pip python3-venv curl coreutils git maven \
+    && curl -fsSL https://deb.nodesource.com/setup_18.x | bash - \
+    && apt-get install -y --no-install-recommends nodejs \
+    && rm -rf /var/lib/apt/lists/*
+
+# Install specific versions of GoFSH and SUSHI
+RUN npm install -g gofsh fsh-sushi
+
+# ADDED: Download the latest HL7 FHIR Validator CLI
+RUN mkdir -p /app/validator_cli
+WORKDIR /app/validator_cli
+# Download the validator JAR and a separate checksum file for verification
+RUN curl -L -o validator_cli.jar "https://github.com/hapifhir/org.hl7.fhir.core/releases/latest/download/validator_cli.jar"
+
+# Set permissions for the downloaded file
+RUN chmod 755 validator_cli.jar
+
+# Change back to the main app directory for the next steps
+WORKDIR /app
+# Set up Python environment
+RUN python3 -m venv /app/venv
+ENV PATH="/app/venv/bin:$PATH"
+
+# ADDED: Uninstall old fhirpath just in case it's in requirements.txt
+RUN pip uninstall -y fhirpath || true
+# ADDED: Install the new fhirpathpy library
+RUN pip install --no-cache-dir fhirpathpy
+
+# Copy Flask files
+COPY requirements.txt .
+# Install requirements (including Pydantic - check version compatibility if needed)
+RUN pip install --no-cache-dir -r requirements.txt
+COPY app.py .
+COPY services.py .
+COPY forms.py .
+COPY package.py .
+COPY templates/ templates/
+COPY static/ static/
+COPY tests/ tests/
+
+# Ensure /tmp, /app/h2-data, /app/static/uploads, and /app/logs are writable
+RUN mkdir -p /tmp /app/h2-data /app/static/uploads /app/logs && chmod 777 /tmp /app/h2-data /app/static/uploads /app/logs
+
+# Copy pre-built HAPI WAR and configuration
+COPY hapi-fhir-jpaserver/target/ROOT.war /usr/local/tomcat/webapps/
+COPY hapi-fhir-jpaserver/target/classes/application.yaml /usr/local/tomcat/conf/
+COPY hapi-fhir-jpaserver/target/classes/application.yaml /app/config/application.yaml
+COPY hapi-fhir-jpaserver/target/classes/application.yaml /usr/local/tomcat/webapps/app/config/application.yaml
+COPY hapi-fhir-jpaserver/custom/ /usr/local/tomcat/webapps/custom/
+
+# Install supervisord
+RUN pip install supervisor
+
+# Configure supervisord
+COPY supervisord.conf /etc/supervisord.conf
+
+# Expose ports
+EXPOSE 5000 8080
+
+# Start supervisord
+CMD ["supervisord", "-c", "/etc/supervisord.conf"]

Dockerfile.lite

@@ -0,0 +1,60 @@
+# 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"]

README.md

@@ -1,25 +1,69 @@
 # FHIRFLARE IG Toolkit
+![FHIRFLARE Logo](static/FHIRFLARE.png)
 
 ## Overview
 
-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), and uploading complex test data sets with dependency management. The toolkit includes live consoles for real-time feedback, making it an essential tool for FHIR developers and implementers.
+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 two modes:
+The application can run in four modes:
 
-* **Standalone:** Includes a Dockerized Flask frontend, SQLite database, and an embedded HAPI FHIR server for local validation and interaction.
-* **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.
+
+* Installation Modes (Lite, Custom URL, Hapi, and Candle)
+    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:**
+* **Standalone Version - Hapi / Candle:**
     * 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.
@@ -30,6 +74,12 @@ This toolkit offers two primary installation modes to suit different needs:
 ## Features
 
 * **Import IGs:** Download FHIR IG packages and dependencies from a package registry, supporting flexible version formats (e.g., `1.2.3`, `1.1.0-preview`, `current`) and dependency pulling modes (Recursive, Patch Canonical, Tree Shaking).
+* **Enhanced Package Search and Import:**
+    * Interactive page (`/search-and-import`) to search for FHIR IG packages from configured registries.
+    * Displays package details, version history, dependencies, and dependents.
+    * Utilizes a local database cache (`CachedPackage`) for faster subsequent searches.
+    * Background task to refresh the package cache from registries (`/api/refresh-cache-task`).
+    * Direct import from search results.
 * **Manage IGs:** View, process, unload, or delete downloaded IGs, with duplicate detection and resolution.
 * **Process IGs:** Extract resource types, profiles, must-support elements, examples, and profile relationships (`structuredefinition-compliesWithProfile` and `structuredefinition-imposeProfile`).
 * **Validate FHIR Resources/Bundles:** Validate single FHIR resources or bundles against selected IGs, with detailed error and warning reports (alpha feature). *Note: Lite version uses local SD checks only.*
@@ -55,9 +105,19 @@ This toolkit offers two primary installation modes to suit different needs:
     * Handles large numbers of files using a custom form parser.
 * **Profile Relationships:** Display and validate `compliesWithProfile` and `imposeProfile` extensions in the UI (configurable).
 * **FSH Converter:** Convert FHIR JSON/XML resources to FHIR Shorthand (FSH) using GoFSH, with advanced options (Package context, Output styles, Log levels, FHIR versions, Fishing Trip, Dependencies, Indentation, Meta Profile handling, Alias File, No Alias). Includes a waiting spinner.
+* **Retrieve and Split Bundles:**
+    * Retrieve specified resource types as bundles from a FHIR server.
+    * Optionally fetch referenced resources, either individually or as full bundles for each referenced type.
+    * Split uploaded ZIP files containing bundles into individual resource JSON files.
+    * Download retrieved/split resources as a ZIP archive.
+    * Streaming progress log via the UI for retrieval operations.
 * **FHIR Interaction UIs:** Explore FHIR server capabilities and interact with resources using the "FHIR API Explorer" (simple GET/POST/PUT/DELETE) and "FHIR UI Operations" (Swagger-like interface based on CapabilityStatement). *Note: Lite version requires custom server URLs.*
-* **API Support:** RESTful API endpoints for importing, pushing, retrieving metadata, validating, and uploading test data.
-* **Live Console:** Real-time logs for push, validation, upload test data, and FSH conversion operations.
+* **HAPI FHIR Configuration (Standalone Mode):**
+    * A dedicated page (`/config-hapi`) to view and edit the `application.yaml` configuration for the embedded HAPI FHIR server.
+    * Allows modification of HAPI FHIR properties directly from the UI.
+    * Option to restart the HAPI FHIR server (Tomcat) to apply changes.
+* **API Support:** RESTful API endpoints for importing, pushing, retrieving metadata, validating, uploading test data, and retrieving/splitting bundles.
+* **Live Console:** Real-time logs for push, validation, upload test data, FSH conversion, and bundle retrieval operations.
 * **Configurable Behavior:** Control validation modes, display options via `app.config`.
 * **Theming:** Supports light and dark modes.
 
@@ -101,9 +161,10 @@ docker run -d \
   -v ./logs:/app/logs \
   --name fhirflare-lite \
   ghcr.io/sudo-jhare/fhirflare-ig-toolkit-lite:latest
-
 Standalone Version (Includes local HAPI FHIR):
 
+Bash
+
 # Pull the latest Standalone image
 docker pull ghcr.io/sudo-jhare/fhirflare-ig-toolkit-standalone:latest
 
@@ -119,7 +180,6 @@ docker run -d \
   -v ./logs:/app/logs \
   --name fhirflare-standalone \
   ghcr.io/sudo-jhare/fhirflare-ig-toolkit-standalone:latest
-
 Building from Source (Developers)
 Using Windows .bat Scripts (Standalone Version Only):
 
@@ -127,258 +187,252 @@ First Time Setup:
 
 Run Build and Run for first time.bat:
 
+Code snippet
+
 cd "<project folder>"
 git clone [https://github.com/hapifhir/hapi-fhir-jpaserver-starter.git](https://github.com/hapifhir/hapi-fhir-jpaserver-starter.git) hapi-fhir-jpaserver
-copy .\hapi-fhir-Setup\target\classes\application.yaml .\hapi-fhir-jpaserver\target\classes\application.yaml
+copy .\\hapi-fhir-Setup\\target\\classes\\application.yaml .\\hapi-fhir-jpaserver\\target\\classes\\application.yaml
 mvn clean package -DskipTests=true -Pboot
 docker-compose build --no-cache
 docker-compose up -d
-
 This clones the HAPI FHIR server, copies configuration, builds the project, and starts the containers.
 
 Subsequent Runs:
 
 Run Run.bat:
 
+Code snippet
+
 cd "<project folder>"
 docker-compose up -d
-
 This starts the Flask app (port 5000) and HAPI FHIR server (port 8080).
 
 Access the Application:
 
 Flask UI: http://localhost:5000
-
 HAPI FHIR server: http://localhost:8080
-
 Manual Setup (Linux/MacOS/Windows):
 
 Preparation (Standalone Version Only):
 
+Bash
+
 cd <project folder>
 git clone [https://github.com/hapifhir/hapi-fhir-jpaserver-starter.git](https://github.com/hapifhir/hapi-fhir-jpaserver-starter.git) hapi-fhir-jpaserver
 cp ./hapi-fhir-Setup/target/classes/application.yaml ./hapi-fhir-jpaserver/target/classes/application.yaml
-
 Build:
 
+Bash
+
 # Build HAPI FHIR (Standalone Version Only)
 mvn clean package -DskipTests=true -Pboot
 
 # Build Docker Image (Specify APP_MODE=lite in docker-compose.yml for Lite version)
 docker-compose build --no-cache
-
 Run:
 
-docker-compose up -d
+Bash
 
+docker-compose up -d
 Access the Application:
 
 Flask UI: http://localhost:5000
-
 HAPI FHIR server (Standalone only): http://localhost:8080
-
 Local Development (Without Docker):
 
 Clone the Repository:
 
+Bash
+
 git clone [https://github.com/Sudo-JHare/FHIRFLARE-IG-Toolkit.git](https://github.com/Sudo-JHare/FHIRFLARE-IG-Toolkit.git)
 cd FHIRFLARE-IG-Toolkit
-
 Install Dependencies:
 
+Bash
+
 python -m venv venv
 source venv/bin/activate  # On Windows: venv\Scripts\activate
 pip install -r requirements.txt
-
 Install Node.js, GoFSH, and SUSHI (for FSH Converter):
 
+Bash
+
 # Example for Debian/Ubuntu
 curl -fsSL [https://deb.nodesource.com/setup_18.x](https://deb.nodesource.com/setup_18.x) | sudo bash -
 sudo apt-get install -y nodejs
 # Install globally
 npm install -g gofsh fsh-sushi
-
 Set Environment Variables:
 
+Bash
+
 export FLASK_SECRET_KEY='your-secure-secret-key'
 export API_KEY='your-api-key'
 # Optional: Set APP_MODE to 'lite' if desired
 # export APP_MODE='lite'
-
 Initialize Directories:
 
+Bash
+
 mkdir -p instance static/uploads logs
 # Ensure write permissions if needed
 # chmod -R 777 instance static/uploads logs
-
 Run the Application:
 
+Bash
+
 export FLASK_APP=app.py
 flask run
-
 Access at http://localhost:5000.
 
 Usage
 Import an IG
-Navigate to Import IG (/import-ig).
+### Search, View Details, and Import Packages
+Navigate to **Search and Import Packages** (`/search-and-import`).
+1.  The page will load a list of available FHIR Implementation Guide packages from a local cache or by fetching from configured registries.
+    * A loading animation and progress messages are shown if fetching from registries.
+    * The timestamp of the last cache update is displayed.
+2.  Use the search bar to filter packages by name or author.
+3.  Packages are paginated for easier Browse.
+4.  For each package, you can:
+    * View its latest official and absolute versions.
+    * Click on the package name to navigate to a **detailed view** (`/package-details/<name>`) showing:
+        * Comprehensive metadata (author, FHIR version, canonical URL, description).
+        * A full list of available versions with publication dates.
+        * Declared dependencies.
+        * Other packages that depend on it (dependents).
+        * Version history (logs).
+    * Directly import a specific version using the "Import" button on the search page or the details page.
+5.  **Cache Management:**
+    * A "Clear & Refresh Cache" button is available to trigger a background task (`/api/refresh-cache-task`) that clears the local database and in-memory cache and fetches the latest package information from all configured registries. Progress is shown via a live log.
 
 Enter a package name (e.g., hl7.fhir.au.core) and version (e.g., 1.1.0-preview).
-
 Choose a dependency mode:
-
 Current Recursive: Import all dependencies listed in package.json recursively.
-
 Patch Canonical Versions: Import only canonical FHIR packages (e.g., hl7.fhir.r4.core).
-
 Tree Shaking: Import only dependencies containing resources actually used by the main package.
-
 Click Import to download the package and dependencies.
-
 Manage IGs
 Go to Manage FHIR Packages (/view-igs) to view downloaded and processed IGs.
 
 Actions:
-
 Process: Extract metadata (resource types, profiles, must-support elements, examples).
-
 Unload: Remove processed IG data from the database.
-
 Delete: Remove package files from the filesystem.
-
 Duplicates are highlighted for resolution.
-
 View Processed IGs
 After processing, view IG details (/view-ig/<id>), including:
 
 Resource types and profiles.
-
 Must-support elements and examples.
-
 Profile relationships (compliesWithProfile, imposeProfile) if enabled (DISPLAY_PROFILE_RELATIONSHIPS).
-
 Interactive StructureDefinition viewer (Differential, Snapshot, Must Support, Key Elements, Constraints, Terminology, Search Params).
-
 Validate FHIR Resources/Bundles
 Navigate to Validate FHIR Sample (/validate-sample).
 
 Select a package (e.g., hl7.fhir.au.core#1.1.0-preview).
-
 Choose Single Resource or Bundle mode.
-
 Paste or upload FHIR JSON/XML (e.g., a Patient resource).
-
-Submit to view validation errors/warnings.
-
-Note: Alpha feature; report issues to GitHub (remove PHI).
-
+Submit to view validation errors/warnings. Note: Alpha feature; report issues to GitHub (remove PHI).
 Push IGs to a FHIR Server
 Go to Push IGs (/push-igs).
 
 Select a downloaded package.
-
 Enter the Target FHIR Server URL.
-
 Configure Authentication (None, Bearer Token).
-
 Choose options: Include Dependencies, Force Upload (skips comparison check), Dry Run, Verbose Log.
-
 Optionally filter by Resource Types (comma-separated) or Skip Specific Files (paths within package, comma/newline separated).
-
 Click Push to FHIR Server to upload resources. Canonical resources are checked before upload. Identical resources are skipped unless Force Upload is checked.
-
 Monitor progress in the live console.
-
 Upload Test Data
 Navigate to Upload Test Data (/upload-test-data).
 
 Enter the Target FHIR Server URL.
-
 Configure Authentication (None, Bearer Token).
-
 Select one or more .json, .xml files, or a single .zip file containing test resources.
-
 Optionally check Validate Resources Before Upload? and select a Validation Profile Package.
-
 Choose Upload Mode:
-
 Individual Resources: Uploads each resource one by one in dependency order.
-
 Transaction Bundle: Uploads all resources in a single transaction.
-
 Optionally check Use Conditional Upload (Individual Mode Only)? to use If-Match headers for updates.
-
 Choose Error Handling:
-
 Stop on First Error: Halts the process if any validation or upload fails.
-
 Continue on Error: Reports errors but attempts to process/upload remaining resources.
-
 Click Upload and Process. The tool parses files, optionally validates, analyzes dependencies, topologically sorts resources, and uploads them according to selected options.
-
 Monitor progress in the streaming log output.
-
 Convert FHIR to FSH
 Navigate to FSH Converter (/fsh-converter).
 
 Optionally select a package for context (e.g., hl7.fhir.au.core#1.1.0-preview).
-
 Choose input mode:
-
 Upload File: Upload a FHIR JSON/XML file.
-
 Paste Text: Paste FHIR JSON/XML content.
-
 Configure options:
-
 Output Style: file-per-definition, group-by-fsh-type, group-by-profile, single-file.
-
 Log Level: error, warn, info, debug.
-
 FHIR Version: R4, R4B, R5, or auto-detect.
-
 Fishing Trip: Enable round-trip validation with SUSHI, generating a comparison report.
-
 Dependencies: Specify additional packages (e.g., hl7.fhir.us.core@6.1.0, one per line).
-
 Indent Rules: Enable context path indentation for readable FSH.
-
 Meta Profile: Choose only-one, first, or none for meta.profile handling.
-
 Alias File: Upload an FSH file with aliases (e.g., $MyAlias = http://example.org).
-
 No Alias: Disable automatic alias generation.
-
 Click Convert to FSH to generate and display FSH output, with a waiting spinner (light/dark theme) during processing.
-
 If Fishing Trip is enabled, view the comparison report via the "Click here for SUSHI Validation" badge button.
-
 Download the result as a .fsh file.
+Retrieve and Split Bundles
+Navigate to Retrieve/Split Data (/retrieve-split-data).
 
+Retrieve Bundles from Server:
+
+Enter the FHIR Server URL (defaults to the proxy if empty).
+Select one or more Resource Types to retrieve (e.g., Patient, Observation).
+Optionally check Fetch Referenced Resources.
+If checked, further optionally check Fetch Full Reference Bundles to retrieve entire bundles for each referenced type (e.g., all Patients if a Patient is referenced) instead of individual resources by ID.
+Click Retrieve Bundles.
+Monitor progress in the streaming log. A ZIP file containing the retrieved bundles/resources will be prepared for download.
+Split Uploaded Bundles:
+
+Upload a ZIP file containing FHIR bundles (JSON format).
+Click Split Bundles.
+A ZIP file containing individual resources extracted from the bundles will be prepared for download.
 Explore FHIR Operations
 Navigate to FHIR UI Operations (/fhir-ui-operations).
 
 Toggle between local HAPI (/fhir) or a custom FHIR server.
-
 Click Fetch Metadata to load the server’s CapabilityStatement.
-
 Select a resource type (e.g., Patient, Observation) or System to view operations:
-
 System operations: GET /metadata, POST /, GET /_history, GET/POST /$diff, POST /$reindex, POST /$expunge, etc.
-
 Resource operations: GET Patient/:id, POST Observation/_search, etc.
-
 Use Try it out to input parameters or request bodies, then Execute to view results in JSON, XML, or narrative formats.
 
+### Configure Embedded HAPI FHIR Server (Standalone Mode)
+For users running the **Standalone version**, which includes an embedded HAPI FHIR server.
+1.  Navigate to **Configure HAPI FHIR** (`/config-hapi`).
+2.  The page displays the content of the HAPI FHIR server's `application.yaml` file.
+3.  You can edit the configuration directly in the text area.
+    * *Caution: Incorrect modifications can break the HAPI FHIR server.*
+4.  Click **Save Configuration** to apply your changes to the `application.yaml` file.
+5.  Click **Restart Tomcat** to restart the HAPI FHIR server and load the new configuration. The restart process may take a few moments.
+
 API Usage
 Import IG
+Bash
+
 curl -X POST http://localhost:5000/api/import-ig \
 -H "Content-Type: application/json" \
 -H "X-API-Key: your-api-key" \
 -d '{"package_name": "hl7.fhir.au.core", "version": "1.1.0-preview", "dependency_mode": "recursive"}'
-
 Returns complies_with_profiles, imposed_profiles, and duplicate_packages_present info.
 
+### Refresh Package Cache (Background Task)
+```bash
+curl -X POST http://localhost:5000/api/refresh-cache-task \
+-H "X-API-Key: your-api-key"
+
 Push IG
+Bash
+
 curl -X POST http://localhost:5000/api/push-ig \
 -H "Content-Type: application/json" \
 -H "Accept: application/x-ndjson" \
@@ -393,10 +447,11 @@ curl -X POST http://localhost:5000/api/push-ig \
       "verbose": false,
       "auth_type": "none"
     }'
-
 Returns a streaming NDJSON response with progress and final summary.
 
 Upload Test Data
+Bash
+
 curl -X POST http://localhost:5000/api/upload-test-data \
 -H "X-API-Key: your-api-key" \
 -H "Accept: application/x-ndjson" \
@@ -410,10 +465,29 @@ curl -X POST http://localhost:5000/api/upload-test-data \
 -F "use_conditional_uploads=true" \
 -F "test_data_files=@/path/to/your/patient.json" \
 -F "test_data_files=@/path/to/your/observations.zip"
+Returns a streaming NDJSON response with progress and final summary. Uses multipart/form-data for file uploads.
 
-Returns a streaming NDJSON response with progress and final summary.
+Retrieve Bundles
+Bash
 
-Uses multipart/form-data for file uploads.
+curl -X POST http://localhost:5000/api/retrieve-bundles \
+-H "X-API-Key: your-api-key" \
+-H "Accept: application/x-ndjson" \
+-F "fhir_server_url=http://your-fhir-server/fhir" \
+-F "resources=Patient" \
+-F "resources=Observation" \
+-F "validate_references=true" \
+-F "fetch_reference_bundles=false"
+Returns a streaming NDJSON response with progress. The X-Zip-Path header in the final response part will contain the path to download the ZIP archive (e.g., /tmp/retrieved_bundles_datetime.zip).
+
+Split Bundles
+Bash
+
+curl -X POST http://localhost:5000/api/split-bundles \
+-H "X-API-Key: your-api-key" \
+-H "Accept: application/x-ndjson" \
+-F "split_bundle_zip_path=@/path/to/your/bundles.zip"
+Returns a streaming NDJSON response. The X-Zip-Path header in the final response part will contain the path to download the ZIP archive of split resources.
 
 Validate Resource/Bundle
 Not yet exposed via API; use the UI at /validate-sample.
@@ -422,181 +496,132 @@ Configuration Options
 Located in app.py:
 
 VALIDATE_IMPOSED_PROFILES: (Default: True) Validates resources against imposed profiles during push.
-
 DISPLAY_PROFILE_RELATIONSHIPS: (Default: True) Shows compliesWithProfile and imposeProfile in the UI.
-
 FHIR_PACKAGES_DIR: (Default: /app/instance/fhir_packages) Stores .tgz packages and metadata.
-
 UPLOAD_FOLDER: (Default: /app/static/uploads) Stores GoFSH output files and FSH comparison reports.
-
 SECRET_KEY: Required for CSRF protection and sessions. Set via environment variable or directly.
-
 API_KEY: Required for API authentication. Set via environment variable or directly.
-
 MAX_CONTENT_LENGTH: (Default: Flask default) Max size for HTTP request body (e.g., 16 * 1024 * 1024 for 16MB). Important for large uploads.
-
 MAX_FORM_PARTS: (Default: Werkzeug default, often 1000) Default max number of form parts. Overridden for /api/upload-test-data by CustomFormDataParser.
 
+### Get HAPI FHIR Configuration (Standalone Mode)
+```bash
+curl -X GET http://localhost:5000/api/config \
+-H "X-API-Key: your-api-key"
+
+Save HAPI FHIR Configuration:
+curl -X POST http://localhost:5000/api/config \
+-H "Content-Type: application/json" \
+-H "X-API-Key: your-api-key" \
+-d '{"your_yaml_key": "your_value", ...}' # Send the full YAML content as JSON
+
+Restart HAPI FHIR Server:
+curl -X POST http://localhost:5000/api/restart-tomcat \
+-H "X-API-Key: your-api-key"
+
 Testing
 The project includes a test suite covering UI, API, database, file operations, and security.
 
 Test Prerequisites:
 
 pytest: For running tests.
-
-pytest-mock: For mocking dependencies.
-
-Install: pip install pytest pytest-mock
-
+pytest-mock: For mocking dependencies. Install: pip install pytest pytest-mock
 Running Tests:
 
+Bash
+
 cd <project folder>
 pytest tests/test_app.py -v
-
 Test Coverage:
 
-UI Pages: Homepage, Import IG, Manage IGs, Push IGs, Validate Sample, View Processed IG, FSH Converter, Upload Test Data.
-
-API Endpoints: POST /api/import-ig, POST /api/push-ig, GET /get-structure, GET /get-example, POST /api/upload-test-data.
-
+UI Pages: Homepage, Import IG, Manage IGs, Push IGs, Validate Sample, View Processed IG, FSH Converter, Upload Test Data, Retrieve/Split Data.
+API Endpoints: POST /api/import-ig, POST /api/push-ig, GET /get-structure, GET /get-example, POST /api/upload-test-data, POST /api/retrieve-bundles, POST /api/split-bundles.
 Database: IG processing, unloading, viewing.
-
-File Operations: Package processing, deletion, FSH output.
-
+File Operations: Package processing, deletion, FSH output, ZIP handling.
 Security: CSRF protection, flash messages, secret key.
-
 FSH Converter: Form submission, file/text input, GoFSH execution, Fishing Trip comparison.
-
 Upload Test Data: Parsing, dependency graph, sorting, upload modes, validation, conditional uploads.
-
 Development Notes
 Background
-The toolkit addresses the need for a comprehensive FHIR IG management tool, with recent enhancements for resource validation, FSH conversion with advanced GoFSH features, flexible versioning, improved IG pushing, and dependency-aware test data uploading, making it a versatile platform for FHIR developers.
+The toolkit addresses the need for a comprehensive FHIR IG management tool, with recent enhancements for resource validation, FSH conversion with advanced GoFSH features, flexible versioning, improved IG pushing, dependency-aware test data uploading, and bundle retrieval/splitting, making it a versatile platform for FHIR developers.
 
 Technical Decisions
 Flask: Lightweight and flexible for web development.
-
 SQLite: Simple for development; consider PostgreSQL for production.
-
 Bootstrap 5.3.3: Responsive UI with custom styling.
-
 Lottie-Web: Renders themed animations for FSH conversion waiting spinner.
-
 GoFSH/SUSHI: Integrated via Node.js for advanced FSH conversion and round-trip validation.
-
 Docker: Ensures consistent deployment with Flask and HAPI FHIR.
-
 Flexible Versioning: Supports non-standard IG versions (e.g., -preview, -ballot).
-
-Live Console/Streaming: Real-time feedback for complex operations (Push, Upload Test Data, FSH).
-
+Live Console/Streaming: Real-time feedback for complex operations (Push, Upload Test Data, FSH, Retrieve Bundles).
 Validation: Alpha feature with ongoing FHIRPath improvements.
-
 Dependency Management: Uses topological sort for Upload Test Data feature.
-
 Form Parsing: Uses custom Werkzeug parser for Upload Test Data to handle large numbers of files.
-
 Recent Updates
+* Enhanced package search page with caching, detailed views (dependencies, dependents, version history), and background cache refresh.
 Upload Test Data Enhancements (April 2025):
-
 Added optional Pre-Upload Validation against selected IG profiles.
-
 Added optional Conditional Uploads (GET + POST/PUT w/ If-Match) for individual mode.
-
 Implemented robust XML parsing using fhir.resources library (when available).
-
 Fixed 413 Request Entity Too Large errors for large file counts using a custom Werkzeug FormDataParser.
-
 Path: templates/upload_test_data.html, app.py, services.py, forms.py.
-
 Push IG Enhancements (April 2025):
-
 Added semantic comparison to skip uploading identical resources.
-
 Added "Force Upload" option to bypass comparison.
-
 Improved handling of canonical resources (search before PUT/POST).
-
 Added filtering by specific files to skip during push.
-
 More detailed summary report in stream response.
-
 Path: templates/cp_push_igs.html, app.py, services.py.
-
 Waiting Spinner for FSH Converter (April 2025):
-
 Added a themed (light/dark) Lottie animation spinner during FSH execution.
-
 Path: templates/fsh_converter.html, static/animations/, static/js/lottie-web.min.js.
-
 Advanced FSH Converter (April 2025):
-
 Added support for GoFSH advanced options: --fshing-trip, --dependency, --indent, --meta-profile, --alias-file, --no-alias.
-
 Displays Fishing Trip comparison reports.
-
 Path: templates/fsh_converter.html, app.py, services.py, forms.py.
-
-(Keep older updates listed here if desired)
-
+(New) Retrieve and Split Data (May 2025):
+Added UI and API for retrieving bundles from a FHIR server by resource type.
+Added options to fetch referenced resources (individually or as full type bundles).
+Added functionality to split uploaded ZIP files of bundles into individual resources.
+Streaming log for retrieval and ZIP download for results.
+Paths: templates/retrieve_split_data.html, app.py, services.py, forms.py.
 Known Issues and Workarounds
 Favicon 404: Clear browser cache or verify /app/static/favicon.ico.
-
 CSRF Errors: Set FLASK_SECRET_KEY and ensure {{ form.hidden_tag() }} in forms.
-
 Import Fails: Check package name/version and connectivity.
-
 Validation Accuracy: Alpha feature; report issues to GitHub (remove PHI).
-
 Package Parsing: Non-standard .tgz filenames may parse incorrectly. Fallback uses name-only parsing.
-
 Permissions: Ensure instance/ and static/uploads/ are writable.
-
 GoFSH/SUSHI Errors: Check ./logs/flask_err.log for ERROR:services:GoFSH failed. Ensure valid FHIR inputs and SUSHI installation.
-
 Upload Test Data XML Parsing: Relies on fhir.resources library for full validation; basic parsing used as fallback. Complex XML structures might not be fully analyzed for dependencies with basic parsing. Prefer JSON for reliable dependency analysis.
-
 413 Request Entity Too Large: Primarily handled by CustomFormDataParser for /api/upload-test-data. Check the parser's max_form_parts limit if still occurring. MAX_CONTENT_LENGTH in app.py controls overall size. Reverse proxy limits (client_max_body_size in Nginx) might also apply.
 
+
 Future Improvements
 Upload Test Data: Improve XML parsing further (direct XML->fhir.resource object if possible), add visual progress bar, add upload order preview, implement transaction bundle size splitting, add 'Clear Target Server' option (with confirmation).
-
 Validation: Enhance FHIRPath for complex constraints; add API endpoint.
-
 Sorting: Sort IG versions in /view-igs (e.g., ascending).
-
 Duplicate Resolution: Options to keep latest version or merge resources.
-
 Production Database: Support PostgreSQL.
-
 Error Reporting: Detailed validation error paths in the UI.
-
 FSH Enhancements: Add API endpoint for FSH conversion; support inline instance construction.
-
 FHIR Operations: Add complex parameter support (e.g., /$diff with left/right).
-
+Retrieve/Split Data: Add option to filter resources during retrieval (e.g., by date, specific IDs).
 Completed Items
 Testing suite with basic coverage.
-
 API endpoints for POST /api/import-ig and POST /api/push-ig.
-
 Flexible versioning (-preview, -ballot).
-
 CSRF fixes for forms.
-
 Resource validation UI (alpha).
-
 FSH Converter with advanced GoFSH features and waiting spinner.
-
 Push IG enhancements (force upload, semantic comparison, canonical handling, skip files).
-
 Upload Test Data feature with dependency sorting, multiple upload modes, pre-upload validation, conditional uploads, robust XML parsing, and fix for large file counts.
-
+Retrieve and Split Data functionality with reference fetching and ZIP download.
 Far-Distant Improvements
 Cache Service: Use Redis for IG metadata caching.
-
 Database Optimization: Composite index on ProcessedIg.package_name and ProcessedIg.version.
 
+
 Directory Structure
 FHIRFLARE-IG-Toolkit/
 ├── app.py                              # Main Flask application
@@ -608,7 +633,7 @@ FHIRFLARE-IG-Toolkit/
 ├── README.md                           # Project documentation
 ├── requirements.txt                    # Python dependencies
 ├── Run.bat                             # Windows script for running Docker
-├── services.py                         # Logic for IG import, processing, validation, pushing, FSH conversion, test data upload
+├── services.py                         # Logic for IG import, processing, validation, pushing, FSH conversion, test data upload, retrieve/split
 ├── supervisord.conf                    # Supervisor configuration
 ├── hapi-fhir-Setup/
 │   ├── README.md                       # HAPI FHIR setup instructions
@@ -649,38 +674,31 @@ FHIRFLARE-IG-Toolkit/
 │   ├── fsh_converter.html              # UI for FSH conversion
 │   ├── import_ig.html                  # UI for importing IGs
 │   ├── index.html                      # Homepage
+│   ├── retrieve_split_data.html        # UI for Retrieve and Split Data
 │   ├── upload_test_data.html           # UI for Uploading Test Data
 │   ├── validate_sample.html            # UI for validating resources/bundles
+│   ├── config_hapi.html                # UI for HAPI FHIR Configuration
 │   └── _form_helpers.html              # Form helper macros
 ├── tests/
 │   └── test_app.py                     # Test suite
 └── hapi-fhir-jpaserver/                # HAPI FHIR server resources (if Standalone)
 
+Contributing
+Fork the repository.
+Create a feature branch (git checkout -b feature/your-feature).
+Commit changes (git commit -m "Add your feature").
+Push to your branch (git push origin feature/your-feature).
+Open a Pull Request.
+Ensure code follows PEP 8 and includes tests in tests/test_app.py.
 
-## Contributing
-
-* Fork the repository.
-* Create a feature branch (`git checkout -b feature/your-feature`).
-* Commit changes (`git commit -m "Add your feature"`).
-* Push to your branch (`git push origin feature/your-feature`).
-* Open a Pull Request.
-
-Ensure code follows PEP 8 and includes tests in `tests/test_app.py`.
-
-## Troubleshooting
-
-* **Favicon 404:** Clear browser cache or verify `/app/static/favicon.ico`:
-    `docker exec -it <container_name> curl http://localhost:5000/static/favicon.ico`
-* **CSRF Errors:** Set `FLASK_SECRET_KEY` and ensure `{{ form.hidden_tag() }}` in forms.
-* **Import Fails:** Check package name/version and connectivity.
-* **Validation Accuracy:** Alpha feature; report issues to GitHub (remove PHI).
-* **Package Parsing:** Non-standard `.tgz` filenames may parse incorrectly. Fallback uses name-only parsing.
-* **Permissions:** Ensure `instance/` and `static/uploads/` are writable:
-    `chmod -R 777 instance static/uploads logs`
-* **GoFSH/SUSHI Errors:** Check `./logs/flask_err.log` for `ERROR:services:GoFSH failed`. Ensure valid FHIR inputs and SUSHI installation:
-    `docker exec -it <container_name> sushi --version`
-* **413 Request Entity Too Large:** Increase `MAX_CONTENT_LENGTH` and `MAX_FORM_PARTS` in `app.py`. If using a reverse proxy (e.g., Nginx), increase its `client_max_body_size` setting as well. Ensure the application/container is fully restarted/rebuilt.
-
-## License
-
-Licensed under the Apache 2.0 License. See `LICENSE.md` for details.
+Troubleshooting
+Favicon 404: Clear browser cache or verify /app/static/favicon.ico: docker exec -it <container_name> curl http://localhost:5000/static/favicon.ico
+CSRF Errors: Set FLASK_SECRET_KEY and ensure {{ form.hidden_tag() }} in forms.
+Import Fails: Check package name/version and connectivity.
+Validation Accuracy: Alpha feature; report issues to GitHub (remove PHI).
+Package Parsing: Non-standard .tgz filenames may parse incorrectly. Fallback uses name-only parsing.
+Permissions: Ensure instance/ and static/uploads/ are writable: chmod -R 777 instance static/uploads logs
+GoFSH/SUSHI Errors: Check ./logs/flask_err.log for ERROR:services:GoFSH failed. Ensure valid FHIR inputs and SUSHI installation: docker exec -it <container_name> sushi --version
+413 Request Entity Too Large: Increase MAX_CONTENT_LENGTH and MAX_FORM_PARTS in app.py. If using a reverse proxy (e.g., Nginx), increase its client_max_body_size setting as well. Ensure the application/container is fully restarted/rebuilt.
+License
+Licensed under the Apache 2.0 License. See LICENSE.md for details.

charts/.gitignore

@@ -0,0 +1 @@
+/hapi-fhir-jpaserver-0.20.0.tgz

charts/fhirflare-ig-toolkit/.gitignore

@@ -0,0 +1 @@
+/rendered/

charts/fhirflare-ig-toolkit/Chart.yaml

@@ -0,0 +1,16 @@
+apiVersion: v2
+name: fhirflare-ig-toolkit
+version: 0.5.0
+description: Helm chart for deploying the fhirflare-ig-toolkit application
+type: application
+appVersion: "latest"
+icon: https://github.com/jgsuess/FHIRFLARE-IG-Toolkit/raw/main/static/FHIRFLARE.png
+keywords:
+  - fhir
+  - healthcare
+  - ig-toolkit
+  - implementation-guide
+home: https://github.com/jgsuess/FHIRFLARE-IG-Toolkit
+maintainers:
+  - name: Jörn Guy Süß
+    email: jgsuess@gmail.com

charts/fhirflare-ig-toolkit/templates/_helpers.tpl

@@ -0,0 +1,152 @@
+{{/*
+Expand the name of the chart.
+*/}}
+{{- define "fhirflare-ig-toolkit.name" -}}
+{{- default .Chart.Name .Values.nameOverride | trunc 63 | trimSuffix "-" }}
+{{- end }}
+
+{{/*
+Create a default fully qualified app name.
+We truncate at 63 chars because some Kubernetes name fields are limited to this (by the DNS naming spec).
+If release name contains chart name it will be used as a full name.
+*/}}
+{{- define "fhirflare-ig-toolkit.fullname" -}}
+{{- if .Values.fullnameOverride }}
+{{- .Values.fullnameOverride | trunc 63 | trimSuffix "-" }}
+{{- else }}
+{{- $name := default .Chart.Name .Values.nameOverride }}
+{{- if contains $name .Release.Name }}
+{{- .Release.Name | trunc 63 | trimSuffix "-" }}
+{{- else }}
+{{- printf "%s-%s" .Release.Name $name | trunc 63 | trimSuffix "-" }}
+{{- end }}
+{{- end }}
+{{- end }}
+
+{{/*
+Create chart name and version as used by the chart label.
+*/}}
+{{- define "fhirflare-ig-toolkit.chart" -}}
+{{- printf "%s-%s" .Chart.Name .Chart.Version | replace "+" "_" | trunc 63 | trimSuffix "-" }}
+{{- end }}
+
+{{/*
+Common labels
+*/}}
+{{- define "fhirflare-ig-toolkit.labels" -}}
+helm.sh/chart: {{ include "fhirflare-ig-toolkit.chart" . }}
+{{ include "fhirflare-ig-toolkit.selectorLabels" . }}
+{{- if .Chart.AppVersion }}
+app.kubernetes.io/version: {{ .Chart.AppVersion | quote }}
+{{- end }}
+app.kubernetes.io/managed-by: {{ .Release.Service }}
+{{- end }}
+
+{{/*
+Selector labels
+*/}}
+{{- define "fhirflare-ig-toolkit.selectorLabels" -}}
+app.kubernetes.io/name: {{ include "fhirflare-ig-toolkit.name" . }}
+app.kubernetes.io/instance: {{ .Release.Name }}
+{{- end }}
+
+{{/*
+Create the name of the service account to use
+*/}}
+{{- define "hapi-fhir-jpaserver.serviceAccountName" -}}
+{{- if .Values.serviceAccount.create }}
+{{- default (include "hapi-fhir-jpaserver.fullname" .) .Values.serviceAccount.name }}
+{{- else }}
+{{- default "default" .Values.serviceAccount.name }}
+{{- end }}
+{{- end }}
+
+{{/*
+Create a default fully qualified postgresql name.
+We truncate at 63 chars because some Kubernetes name fields are limited to this (by the DNS naming spec).
+*/}}
+{{- define "hapi-fhir-jpaserver.postgresql.fullname" -}}
+{{- $name := default "postgresql" .Values.postgresql.nameOverride -}}
+{{- printf "%s-%s" .Release.Name $name | trunc 63 | trimSuffix "-" -}}
+{{- end -}}
+
+{{/*
+Get the Postgresql credentials secret name.
+*/}}
+{{- define "hapi-fhir-jpaserver.postgresql.secretName" -}}
+{{- if .Values.postgresql.enabled -}}
+    {{- if .Values.postgresql.auth.existingSecret -}}
+        {{- printf "%s" .Values.postgresql.auth.existingSecret -}}
+    {{- else -}}
+        {{- printf "%s" (include "hapi-fhir-jpaserver.postgresql.fullname" .) -}}
+    {{- end -}}
+{{- else }}
+    {{- if .Values.externalDatabase.existingSecret -}}
+        {{- printf "%s" .Values.externalDatabase.existingSecret -}}
+    {{- else -}}
+        {{ printf "%s-%s" (include "hapi-fhir-jpaserver.fullname" .) "external-db" }}
+    {{- end -}}
+{{- end -}}
+{{- end -}}
+
+{{/*
+Get the Postgresql credentials secret key.
+*/}}
+{{- define "hapi-fhir-jpaserver.postgresql.secretKey" -}}
+{{- if .Values.postgresql.enabled -}}
+    {{- if .Values.postgresql.auth.username -}}
+        {{- printf "%s" .Values.postgresql.auth.secretKeys.userPasswordKey -}}
+    {{- else -}}
+        {{- printf "%s" .Values.postgresql.auth.secretKeys.adminPasswordKey -}}
+    {{- end -}}
+{{- else }}
+    {{- if .Values.externalDatabase.existingSecret -}}
+        {{- printf "%s" .Values.externalDatabase.existingSecretKey -}}
+    {{- else -}}
+        {{- printf "postgres-password" -}}
+    {{- end -}}
+{{- end -}}
+{{- end -}}
+
+{{/*
+Add environment variables to configure database values
+*/}}
+{{- define "hapi-fhir-jpaserver.database.host" -}}
+{{- ternary (include "hapi-fhir-jpaserver.postgresql.fullname" .) .Values.externalDatabase.host .Values.postgresql.enabled -}}
+{{- end -}}
+
+{{/*
+Add environment variables to configure database values
+*/}}
+{{- define "hapi-fhir-jpaserver.database.user" -}}
+{{- if .Values.postgresql.enabled -}}
+    {{- printf "%s" .Values.postgresql.auth.username | default "postgres" -}}
+{{- else -}}
+    {{- printf "%s" .Values.externalDatabase.user -}}
+{{- end -}}
+{{- end -}}
+
+{{/*
+Add environment variables to configure database values
+*/}}
+{{- define "hapi-fhir-jpaserver.database.name" -}}
+{{- ternary .Values.postgresql.auth.database .Values.externalDatabase.database .Values.postgresql.enabled -}}
+{{- end -}}
+
+{{/*
+Add environment variables to configure database values
+*/}}
+{{- define "hapi-fhir-jpaserver.database.port" -}}
+{{- ternary "5432" .Values.externalDatabase.port .Values.postgresql.enabled -}}
+{{- end -}}
+
+{{/*
+Create the JDBC URL from the host, port and database name.
+*/}}
+{{- define "hapi-fhir-jpaserver.database.jdbcUrl" -}}
+{{- $host := (include "hapi-fhir-jpaserver.database.host" .) -}}
+{{- $port := (include "hapi-fhir-jpaserver.database.port" .) -}}
+{{- $name := (include "hapi-fhir-jpaserver.database.name" .) -}}
+{{- $appName := .Release.Name -}}
+{{ printf "jdbc:postgresql://%s:%d/%s?ApplicationName=%s" $host (int $port) $name $appName }}
+{{- end -}}

charts/fhirflare-ig-toolkit/templates/deployment.yaml

@@ -0,0 +1,91 @@
+apiVersion: apps/v1
+kind: Deployment
+metadata:
+  name: {{ include "fhirflare-ig-toolkit.fullname" . }}
+  labels:
+    {{- include "fhirflare-ig-toolkit.labels" . | nindent 4 }}
+spec:
+  replicas: {{ .Values.replicaCount | default 1 }}
+  selector:
+    matchLabels:
+      {{- include "fhirflare-ig-toolkit.selectorLabels" . | nindent 6 }}
+  strategy:
+    type: Recreate
+  template:
+    metadata:
+      labels:
+        {{- include "fhirflare-ig-toolkit.selectorLabels" . | nindent 8 }}
+      {{- with .Values.podAnnotations }}
+      annotations:
+        {{- toYaml . | nindent 8 }}
+      {{- end }}
+    spec:
+      {{- with .Values.imagePullSecrets }}
+      imagePullSecrets:
+        {{- toYaml . | nindent 8 }}
+      {{- end }}
+      securityContext:
+        {{- toYaml .Values.podSecurityContext | nindent 8 }}
+      containers:
+        - name: {{ .Chart.Name }}
+          securityContext:
+            {{- toYaml .Values.securityContext | nindent 12 }}
+          image: "{{ .Values.image.repository }}:{{ .Values.image.tag | default .Chart.AppVersion }}"
+          imagePullPolicy: {{ .Values.image.pullPolicy }}
+          args: ["supervisord", "-c", "/etc/supervisord.conf"]
+          env:
+            - name: APP_BASE_URL
+              value: {{ .Values.config.appBaseUrl | default "http://localhost:5000" | quote }}
+            - name: APP_MODE
+              value: {{ .Values.config.appMode | default "lite" | quote }}
+            - name: FLASK_APP
+              value: {{ .Values.config.flaskApp | default "app.py" | quote }}
+            - name: FLASK_ENV
+              value: {{ .Values.config.flaskEnv | default "development" | quote }}
+            - name: HAPI_FHIR_URL
+              value: {{ .Values.config.externalHapiServerUrl | default "http://external-hapi-fhir:8080/fhir" | quote }}
+            - name: NODE_PATH
+              value: {{ .Values.config.nodePath | default "/usr/lib/node_modules" | quote }}
+            - name: TMPDIR
+              value: "/tmp-dir"
+          ports:
+            - name: http
+              containerPort: {{ .Values.service.port | default 5000 }}
+              protocol: TCP
+          volumeMounts:
+            - name: logs
+              mountPath: /app/logs
+            - name: tmp-dir
+              mountPath: /tmp-dir
+          {{- with .Values.resources }}
+          resources:
+            {{- toYaml . | nindent 12 }}
+          {{- end }}
+          {{- with .Values.livenessProbe }}
+          livenessProbe:
+            {{- toYaml . | nindent 12 }}
+          {{- end }}
+          {{- with .Values.readinessProbe }}
+          readinessProbe:
+            {{- toYaml . | nindent 12 }}
+          {{- end }}
+      volumes:
+        - name: logs
+          emptyDir: {}
+        - name: tmp-dir
+          emptyDir: {}
+      # Always require Intel 64-bit architecture nodes
+      nodeSelector:
+        kubernetes.io/arch: amd64
+      {{- with .Values.nodeSelector }}
+      # Merge with user-defined nodeSelectors if any
+        {{- toYaml . | nindent 8 }}
+      {{- end }}
+      {{- with .Values.affinity }}
+      affinity:
+        {{- toYaml . | nindent 8 }}
+      {{- end }}
+      {{- with .Values.tolerations }}
+      tolerations:
+        {{- toYaml . | nindent 8 }}
+      {{- end }}

charts/fhirflare-ig-toolkit/templates/ingress.yaml

@@ -0,0 +1,36 @@
+{{- if .Values.ingress.enabled -}}
+{{- $fullName := include "fhirflare-ig-toolkit.fullname" . -}}
+{{- if semverCompare ">=1.19-0" .Capabilities.KubeVersion.GitVersion }}
+apiVersion: networking.k8s.io/v1
+{{- else if semverCompare ">=1.14-0" .Capabilities.KubeVersion.GitVersion }}
+apiVersion: networking.k8s.io/v1beta1
+{{- else }}
+apiVersion: extensions/v1beta1
+{{- end }}
+kind: Ingress
+metadata:
+  name: {{ $fullName }}
+  labels:
+    {{- include "fhirflare-ig-toolkit.labels" . | nindent 4 }}
+  {{- with .Values.ingress.annotations }}
+  annotations:
+    {{- toYaml . | nindent 4 }}
+  {{- end }}
+spec:
+  rules:
+  - http:
+      paths:
+      - path: /
+        {{- if semverCompare ">=1.19-0" .Capabilities.KubeVersion.GitVersion }}
+        pathType: Prefix
+        backend:
+          service:
+            name: {{ $fullName }}
+            port:
+              number: {{ .Values.service.port | default 5000 }}
+        {{- else }}
+        backend:
+          serviceName: {{ $fullName }}
+          servicePort: {{ .Values.service.port | default 5000 }}
+        {{- end }}
+{{- end }}

charts/fhirflare-ig-toolkit/templates/service.yaml

@@ -0,0 +1,18 @@
+apiVersion: v1
+kind: Service
+metadata:
+  name: {{ include "fhirflare-ig-toolkit.fullname" . }}
+  labels:
+    {{- include "fhirflare-ig-toolkit.labels" . | nindent 4 }}
+spec:
+  type: {{ .Values.service.type | default "ClusterIP" }}
+  ports:
+    - name: http
+      port: {{ .Values.service.port | default 5000 }}
+      targetPort: {{ .Values.service.port | default 5000 }}
+      protocol: TCP
+      {{- if and (eq .Values.service.type "NodePort") .Values.service.nodePort }}
+      nodePort: {{ .Values.service.nodePort }}
+      {{- end }}
+  selector:
+    {{- include "fhirflare-ig-toolkit.selectorLabels" . | nindent 4 }}

charts/fhirflare-ig-toolkit/templates/tests/test-endpoints.yaml

@@ -0,0 +1,41 @@
+apiVersion: v1
+kind: Pod
+metadata:
+  name: "{{ .Release.Name }}-fhirflare-test-endpoint"
+  labels:
+    helm.sh/chart: "{{ .Chart.Name }}-{{ .Chart.Version }}"
+    app.kubernetes.io/name: {{ .Chart.Name }}
+    app.kubernetes.io/instance: {{ .Release.Name }}
+    app.kubernetes.io/version: {{ .Chart.AppVersion | quote }}
+    app.kubernetes.io/managed-by: {{ .Release.Service }}
+    app.kubernetes.io/component: tests
+  annotations:
+    "helm.sh/hook": test
+spec:
+  restartPolicy: Never
+  containers:
+    - name: test-fhirflare-endpoint
+      image: curlimages/curl:8.12.1
+      command: ["curl", "--fail-with-body", "--retry", "5", "--retry-delay", "10"]
+      args: ["http://fhirflare:5000"]
+      securityContext:
+        allowPrivilegeEscalation: false
+        capabilities:
+          drop:
+          - ALL
+        privileged: false
+        readOnlyRootFilesystem: true
+        runAsGroup: 65534
+        runAsNonRoot: true
+        runAsUser: 65534
+        seccompProfile:
+          type: RuntimeDefault
+      resources:
+        limits:
+          cpu: 150m
+          ephemeral-storage: 2Gi
+          memory: 192Mi
+        requests:
+          cpu: 100m
+          ephemeral-storage: 50Mi
+          memory: 128Mi

charts/fhirflare-ig-toolkit/values.yaml

@@ -0,0 +1,89 @@
+# Default values for fhirflare-ig-toolkit
+replicaCount: 1
+
+image:
+  repository: ghcr.io/jgsuess/fhirflare-ig-toolkit
+  pullPolicy: Always
+  tag: "latest"
+
+imagePullSecrets: []
+nameOverride: ""
+fullnameOverride: ""
+
+# FHIRflare specific configuration
+config:
+  # Application mode: "lite" means using external HAPI server, "standalone" means running with embedded HAPI server
+  appMode: "lite"
+  # URL for the external HAPI FHIR server when in lite mode
+  externalHapiServerUrl: "http://external-hapi-fhir:8080/fhir"
+  appBaseUrl: "http://localhost:5000"
+  flaskApp: "app.py"
+  flaskEnv: "development"
+  nodePath: "/usr/lib/node_modules"
+
+service:
+  type: ClusterIP
+  port: 5000
+  nodePort: null
+
+podAnnotations: {}
+
+# podSecurityContext:
+#   fsGroup: 65532
+#   fsGroupChangePolicy: OnRootMismatch
+#   runAsNonRoot: true
+#   runAsGroup: 65532
+#   runAsUser: 65532
+#   seccompProfile:
+#     type: RuntimeDefault
+
+# securityContext:
+#   allowPrivilegeEscalation: false
+#   capabilities:
+#     drop:
+#       - ALL
+#   privileged: false
+#   readOnlyRootFilesystem: true
+#   runAsGroup: 65532
+#   runAsNonRoot: true
+#   runAsUser: 65532
+#   seccompProfile:
+#     type: RuntimeDefault
+
+resources:
+  limits:
+    cpu: 500m
+    memory: 512Mi
+    ephemeral-storage: 1Gi
+  requests:
+    cpu: 100m
+    memory: 128Mi
+    ephemeral-storage: 100Mi
+
+livenessProbe:
+  httpGet:
+    path: /
+    port: http
+  initialDelaySeconds: 30
+  periodSeconds: 10
+  timeoutSeconds: 5
+  failureThreshold: 6
+  successThreshold: 1
+
+readinessProbe:
+  httpGet:
+    path: /
+    port: http
+  initialDelaySeconds: 5
+  periodSeconds: 10
+  timeoutSeconds: 5
+  failureThreshold: 6
+  successThreshold: 1
+
+nodeSelector: {}
+tolerations: []
+affinity: {}
+
+ingress:
+  # -- whether to create a primitive Ingress to expose the FHIR server HTTP endpoint
+  enabled: false

charts/install.sh

@@ -0,0 +1,23 @@
+#!/bin/bash
+#
+# FHIRFLARE-IG-Toolkit Installation Script
+# 
+# Description:
+#   This script installs the FHIRFLARE-IG-Toolkit Helm chart into a Kubernetes cluster.
+#   It adds the FHIRFLARE-IG-Toolkit Helm repository and then installs the chart
+#   in the 'flare' namespace, creating the namespace if it doesn't exist.
+#
+# Usage:
+#   ./install.sh
+#
+# Requirements:
+#   - Helm (v3+)
+#   - kubectl configured with access to your Kubernetes cluster
+#
+
+# Add the FHIRFLARE-IG-Toolkit Helm repository
+helm repo add flare https://jgsuess.github.io/FHIRFLARE-IG-Toolkit/
+
+# Install the FHIRFLARE-IG-Toolkit chart in the 'flare' namespace
+
+helm install flare/fhirflare-ig-toolkit --namespace flare --create-namespace --generate-name --set hapi-fhir-jpaserver.postgresql.primary.persistence.storageClass=gp2 --atomic

docker-compose.yml

@@ -3,18 +3,19 @@ services:
   fhirflare:
     build:
       context: .
-      dockerfile: Dockerfile
+      dockerfile: Dockerfile.lite
     ports:
       - "5000:5000"
-      - "8080:8080" # Keep port exposed, even if Tomcat isn't running useful stuff in Lite
+      - "8080:8080"
     volumes:
       - ./instance:/app/instance
       - ./static/uploads:/app/static/uploads
-      - ./instance/hapi-h2-data/:/app/h2-data # Keep volume mounts consistent
       - ./logs:/app/logs
     environment:
       - FLASK_APP=app.py
       - FLASK_ENV=development
       - 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/
     command: supervisord -c /etc/supervisord.conf

docker-compose/all-in-one/docker-compose.yml

@@ -0,0 +1,22 @@
+# This docker-compose file uses ephemeral Docker named volumes for all data storage.
+# These volumes persist only as long as the Docker volumes exist and are deleted if you run `docker-compose down -v`.
+# No data is stored on the host filesystem. If you want persistent storage, replace these with host mounts.
+services:
+  fhirflare-standalone:
+    image: ${FHIRFLARE_IMAGE:-ghcr.io/sudo-jhare/fhirflare-ig-toolkit-standalone:latest}
+    container_name: fhirflare-standalone
+    ports:
+      - "5000:5000"
+      - "8080:8080"
+    volumes:
+      - fhirflare-instance:/app/instance
+      - fhirflare-uploads:/app/static/uploads
+      - fhirflare-h2-data:/app/h2-data
+      - fhirflare-logs:/app/logs
+    restart: unless-stopped
+
+volumes:
+  fhirflare-instance:
+  fhirflare-uploads:
+  fhirflare-h2-data:
+  fhirflare-logs:

docker-compose/all-in-one/down.sh

@@ -0,0 +1,5 @@
+#!/bin/bash
+
+# Stop and remove all containers defined in the Docker Compose file,
+# along with any anonymous volumes attached to them.
+docker compose down --volumes

docker-compose/all-in-one/up.sh

@@ -0,0 +1,5 @@
+#!/bin/bash
+
+# Run Docker Compose
+
+docker compose up --detach --force-recreate --renew-anon-volumes --always-recreate-deps

docker-compose/lite/local/application.yaml

@@ -0,0 +1,18 @@
+hapi.fhir:
+  ig_runtime_upload_enabled: false
+  narrative_enabled: true
+  logical_urls:
+    - http://terminology.hl7.org/*
+    - https://terminology.hl7.org/*
+    - http://snomed.info/*
+    - https://snomed.info/*
+    - http://unitsofmeasure.org/*
+    - https://unitsofmeasure.org/*
+    - http://loinc.org/*
+    - https://loinc.org/*
+  cors:
+    allow_Credentials: true
+    allowed_origin:
+      - '*'
+  tester.home.name: FHIRFLARE Tester
+  inline_resource_storage_below_size: 4000

docker-compose/lite/local/docker-compose.yml

@@ -0,0 +1,50 @@
+services:
+  fhirflare:
+    image: ${FHIRFLARE_IMAGE:-ghcr.io/sudo-jhare/fhirflare-ig-toolkit-lite:latest}
+    ports:
+      - "5000:5000"
+    # Ephemeral Docker named volumes for all data storage. No data is stored on the host filesystem.
+    volumes:
+      - fhirflare-instance:/app/instance
+      - fhirflare-uploads:/app/static/uploads
+      - fhirflare-h2-data:/app/h2-data
+      - fhirflare-logs:/app/logs
+    environment:
+      - FLASK_APP=app.py
+      - FLASK_ENV=development
+      - NODE_PATH=/usr/lib/node_modules
+      - APP_MODE=lite
+      - APP_BASE_URL=http://localhost:5000
+      - HAPI_FHIR_URL=http://fhir:8080/fhir
+    command: supervisord -c /etc/supervisord.conf
+
+  fhir:
+    container_name: hapi
+    image: "hapiproject/hapi:v8.2.0-1"
+    ports:
+      - "8080:8080"
+    configs:
+      - source: hapi
+        target: /app/config/application.yaml
+    depends_on:
+      - db
+
+  db:
+    image: "postgres:17.2-bookworm"
+    restart: always
+    environment:
+      POSTGRES_PASSWORD: admin
+      POSTGRES_USER: admin
+      POSTGRES_DB: hapi
+    volumes:
+      - ./hapi.postgress.data:/var/lib/postgresql/data
+
+configs:
+  hapi:
+     file: ./application.yaml
+
+volumes:
+  fhirflare-instance:
+  fhirflare-uploads:
+  fhirflare-h2-data:
+  fhirflare-logs:

docker-compose/lite/local/down.sh

@@ -0,0 +1,5 @@
+#!/bin/bash
+
+# Stop and remove all containers defined in the Docker Compose file,
+# along with any anonymous volumes attached to them.
+docker compose down --volumes

docker-compose/lite/local/readme.md

@@ -0,0 +1,19 @@
+# FHIRFLARE IG Toolkit
+
+This directory provides scripts and configuration to start and stop a FHIRFLARE instance with an attached HAPI FHIR server using Docker Compose.
+
+## Usage
+
+- To start the FHIRFLARE toolkit and HAPI server:
+  ```sh
+  ./docker-compose/up.sh
+  ```
+
+- To stop and remove the containers and volumes:
+  ```sh
+  ./docker-compose/down.sh
+  ```
+
+The web interface will be available at [http://localhost:5000](http://localhost:5000) and the HAPI FHIR server at [http://localhost:8080/fhir](http://localhost:8080/fhir).
+
+For more details, see the configuration files in this directory.

docker-compose/lite/local/up.sh

@@ -0,0 +1,5 @@
+#!/bin/bash
+
+# Run Docker Compose
+
+docker compose up --detach --force-recreate --renew-anon-volumes --always-recreate-deps

docker-compose/lite/remote/docker-compose.yml

@@ -0,0 +1,25 @@
+services:
+  fhirflare:
+    image: ${FHIRFLARE_IMAGE:-ghcr.io/sudo-jhare/fhirflare-ig-toolkit-lite:latest}
+    ports:
+      - "5000:5000"
+    # Ephemeral Docker named volumes for all data storage. No data is stored on the host filesystem.
+    volumes:
+      - fhirflare-instance:/app/instance
+      - fhirflare-uploads:/app/static/uploads
+      - fhirflare-h2-data:/app/h2-data
+      - fhirflare-logs:/app/logs
+    environment:
+      - FLASK_APP=app.py
+      - FLASK_ENV=development
+      - NODE_PATH=/usr/lib/node_modules
+      - APP_MODE=lite
+      - APP_BASE_URL=http://localhost:5000
+      - HAPI_FHIR_URL=https://cdr.fhirlab.net/fhir
+    command: supervisord -c /etc/supervisord.conf
+
+volumes:
+  fhirflare-instance:
+  fhirflare-uploads:
+  fhirflare-h2-data:
+  fhirflare-logs:

docker-compose/lite/remote/down.sh

@@ -0,0 +1,5 @@
+#!/bin/bash
+
+# Stop and remove all containers defined in the Docker Compose file,
+# along with any anonymous volumes attached to them.
+docker compose down --volumes

docker-compose/lite/remote/readme.md

@@ -0,0 +1,19 @@
+# FHIRFLARE IG Toolkit
+
+This directory provides scripts and configuration to start and stop a FHIRFLARE instance with an attached HAPI FHIR server using Docker Compose.
+
+## Usage
+
+- To start the FHIRFLARE toolkit and HAPI server:
+  ```sh
+  ./docker-compose/up.sh
+  ```
+
+- To stop and remove the containers and volumes:
+  ```sh
+  ./docker-compose/down.sh
+  ```
+
+The web interface will be available at [http://localhost:5000](http://localhost:5000) and the HAPI FHIR server at [http://localhost:8080/fhir](http://localhost:8080/fhir).
+
+For more details, see the configuration files in this directory.

docker-compose/lite/remote/up.sh

@@ -0,0 +1,5 @@
+#!/bin/bash
+
+# Run Docker Compose
+
+docker compose up --detach --force-recreate --renew-anon-volumes --always-recreate-deps

docker/Dockerfile

@@ -0,0 +1,66 @@
+# ------------------------------------------------------------------------------
+# Dockerfile for FHIRFLARE-IG-Toolkit (Optimized for Python/Flask)
+#
+# This Dockerfile builds a container for the FHIRFLARE-IG-Toolkit application.
+#
+# Key Features:
+# - Uses python:3.11-slim as the base image for a minimal, secure Python runtime.
+# - Installs Node.js and global NPM packages (gofsh, fsh-sushi) for FHIR IG tooling.
+# - Sets up a Python virtual environment and installs all Python dependencies.
+# - Installs and configures Supervisor to manage the Flask app and related processes.
+# - Copies all necessary application code, templates, static files, and configuration.
+# - Exposes ports 5000 (Flask) and 8080 (optional, for compatibility).
+# - Entrypoint runs Supervisor for process management.
+#
+# Notes:
+# - The Dockerfile is optimized for Python. Tomcat/Java is not included.
+# - Node.js is only installed if needed for FHIR IG tooling.
+# - The image is suitable for development and production with minimal changes.
+# ------------------------------------------------------------------------------
+
+# Optimized Dockerfile for Python (Flask)
+FROM python:3.11-slim AS base
+
+# Install system dependencies
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    curl \
+    coreutils \
+    && rm -rf /var/lib/apt/lists/*
+
+# Optional: Install Node.js if needed for GoFSH/SUSHI
+RUN curl -fsSL https://deb.nodesource.com/setup_18.x | bash - \
+    && apt-get install -y --no-install-recommends nodejs \
+    && npm install -g gofsh fsh-sushi \
+    && rm -rf /var/lib/apt/lists/*
+
+# Set workdir
+WORKDIR /app
+
+# Copy requirements and install Python dependencies
+COPY requirements.txt .
+RUN python -m venv /app/venv \
+    && . /app/venv/bin/activate \
+    && pip install --upgrade pip \
+    && pip install --no-cache-dir -r requirements.txt \
+    && pip uninstall -y fhirpath || true \
+    && pip install --no-cache-dir fhirpathpy \
+    && pip install supervisor
+
+# Copy application files
+COPY app.py .
+COPY services.py .
+COPY forms.py .
+COPY package.py .
+COPY templates/ templates/
+COPY static/ static/
+COPY tests/ tests/
+COPY supervisord.conf /etc/supervisord.conf
+
+# Expose ports
+EXPOSE 5000 8080
+
+# Set environment
+ENV PATH="/app/venv/bin:$PATH"
+
+# Start supervisord
+CMD ["supervisord", "-c", "/etc/supervisord.conf"]

docker/build-docker.sh

@@ -0,0 +1,7 @@
+#!/bin/bash
+# Build FHIRFLARE-IG-Toolkit Docker image
+
+# Build the image using the Dockerfile in the docker directory
+docker build -f Dockerfile -t fhirflare-ig-toolkit:latest ..
+
+echo "Docker image built successfully"

forms.py

@@ -1,16 +1,63 @@
 # forms.py
 from flask_wtf import FlaskForm
-from wtforms import StringField, SelectField, TextAreaField, BooleanField, SubmitField, FileField
+from wtforms import StringField, SelectField, TextAreaField, BooleanField, SubmitField, FileField, PasswordField, SelectMultipleField
 from wtforms.validators import DataRequired, Regexp, ValidationError, URL, Optional, InputRequired
-from flask import request # Import request for file validation in FSHConverterForm
+from flask import request
 import json
 import xml.etree.ElementTree as ET
 import re
-import logging # Import logging
+import logging
+import os
 
-logger = logging.getLogger(__name__) # Setup logger if needed elsewhere
+logger = logging.getLogger(__name__)
+
+class RetrieveSplitDataForm(FlaskForm):
+    """Form for retrieving FHIR bundles and splitting them into individual resources."""
+    fhir_server_url = StringField('FHIR Server URL', validators=[URL(), Optional()],
+                                 render_kw={'placeholder': 'e.g., https://hapi.fhir.org/baseR4'})
+    auth_type = SelectField('Authentication Type (for Custom URL)', choices=[
+        ('none', 'None'),
+        ('bearerToken', 'Bearer Token'),
+        ('basicAuth', 'Basic Authentication')
+    ], default='none', validators=[Optional()])
+    auth_token = StringField('Bearer Token', validators=[Optional()],
+                             render_kw={'placeholder': 'Enter Bearer Token', 'type': 'password'})
+    basic_auth_username = StringField('Username', validators=[Optional()],
+                                   render_kw={'placeholder': 'Enter Basic Auth Username'})
+    basic_auth_password = PasswordField('Password', validators=[Optional()],
+                                     render_kw={'placeholder': 'Enter Basic Auth Password'})
+    validate_references = BooleanField('Fetch Referenced Resources', default=False,
+                                      description="If checked, fetches resources referenced by the initial bundles.")
+    fetch_reference_bundles = BooleanField('Fetch Full Reference Bundles (instead of individual resources)', default=False,
+                                           description="Requires 'Fetch Referenced Resources'. Fetches e.g. /Patient instead of Patient/id for each reference.",
+                                           render_kw={'data-dependency': 'validate_references'})
+    split_bundle_zip = FileField('Upload Bundles to Split (ZIP)', validators=[Optional()],
+                                render_kw={'accept': '.zip'})
+    submit_retrieve = SubmitField('Retrieve Bundles')
+    submit_split = SubmitField('Split Bundles')
+
+    def validate(self, extra_validators=None):
+        if not super().validate(extra_validators):
+            return False
+        if self.fetch_reference_bundles.data and not self.validate_references.data:
+            self.fetch_reference_bundles.errors.append('Cannot fetch full reference bundles unless "Fetch Referenced Resources" is also checked.')
+            return False
+        if self.auth_type.data == 'bearerToken' and self.submit_retrieve.data and not self.auth_token.data:
+            self.auth_token.errors.append('Bearer Token is required when Bearer Token authentication is selected.')
+            return False
+        if self.auth_type.data == 'basicAuth' and self.submit_retrieve.data:
+            if not self.basic_auth_username.data:
+                self.basic_auth_username.errors.append('Username is required for Basic Authentication.')
+                return False
+            if not self.basic_auth_password.data:
+                self.basic_auth_password.errors.append('Password is required for Basic Authentication.')
+                return False
+        if self.split_bundle_zip.data:
+            if not self.split_bundle_zip.data.filename.lower().endswith('.zip'):
+                self.split_bundle_zip.errors.append('File must be a ZIP file.')
+                return False
+        return True
 
-# Existing forms (IgImportForm, ValidationForm) remain unchanged
 class IgImportForm(FlaskForm):
     """Form for importing Implementation Guides."""
     package_name = StringField('Package Name', validators=[
@@ -28,6 +75,62 @@ class IgImportForm(FlaskForm):
     ], default='recursive')
     submit = SubmitField('Import')
 
+class ManualIgImportForm(FlaskForm):
+    """Form for manual importing Implementation Guides via file or URL."""
+    import_mode = SelectField('Import Mode', choices=[
+        ('file', 'Upload File'),
+        ('url', 'From URL')
+    ], default='file', validators=[DataRequired()])
+    tgz_file = FileField('IG Package File (.tgz)', validators=[Optional()],
+                         render_kw={'accept': '.tgz'})
+    tgz_url = StringField('IG Package URL', validators=[Optional(), URL()],
+                          render_kw={'placeholder': 'e.g., https://example.com/hl7.fhir.au.core-1.1.0-preview.tgz'})
+    dependency_mode = SelectField('Dependency Mode', choices=[
+        ('recursive', 'Current Recursive'),
+        ('patch-canonical', 'Patch Canonical Versions'),
+        ('tree-shaking', 'Tree Shaking (Only Used Dependencies)')
+    ], default='recursive')
+    resolve_dependencies = BooleanField('Resolve Dependencies', default=True,
+                                       render_kw={'class': 'form-check-input'})
+    submit = SubmitField('Import')
+
+    def validate(self, extra_validators=None):
+        if not super().validate(extra_validators):
+            return False
+        mode = self.import_mode.data
+        has_file = request and request.files and self.tgz_file.name in request.files and request.files[self.tgz_file.name].filename != ''
+        has_url = bool(self.tgz_url.data)  # Convert to boolean: True if non-empty string
+
+        # Ensure exactly one input method is used
+        inputs_provided = sum([has_file, has_url])
+        if inputs_provided != 1:
+            if inputs_provided == 0:
+                self.import_mode.errors.append('Please provide input for one import method (File or URL).')
+            else:
+                self.import_mode.errors.append('Please use only one import method at a time.')
+            return False
+
+        # Validate based on import mode
+        if mode == 'file':
+            if not has_file:
+                self.tgz_file.errors.append('A .tgz file is required for File import.')
+                return False
+            if not self.tgz_file.data.filename.lower().endswith('.tgz'):
+                self.tgz_file.errors.append('File must be a .tgz file.')
+                return False
+        elif mode == 'url':
+            if not has_url:
+                self.tgz_url.errors.append('A valid URL is required for URL import.')
+                return False
+            if not self.tgz_url.data.lower().endswith('.tgz'):
+                self.tgz_url.errors.append('URL must point to a .tgz file.')
+                return False
+        else:
+            self.import_mode.errors.append('Invalid import mode selected.')
+            return False
+
+        return True
+
 class ValidationForm(FlaskForm):
     """Form for validating FHIR samples."""
     package_name = StringField('Package Name', validators=[DataRequired()])
@@ -39,7 +142,6 @@ class ValidationForm(FlaskForm):
     ], default='single')
     sample_input = TextAreaField('Sample Input', validators=[
         DataRequired(),
-        # Removed lambda validator for simplicity, can be added back if needed
     ])
     submit = SubmitField('Validate')
 
@@ -64,7 +166,7 @@ class FSHConverterForm(FlaskForm):
         ('info', 'Info'),
         ('debug', 'Debug')
     ], validators=[DataRequired()])
-    fhir_version = SelectField('FHIR Version', choices=[ # Corrected label
+    fhir_version = SelectField('FHIR Version', choices=[
         ('', 'Auto-detect'),
         ('4.0.1', 'R4'),
         ('4.3.0', 'R4B'),
@@ -83,116 +185,185 @@ class FSHConverterForm(FlaskForm):
     submit = SubmitField('Convert to FSH')
 
     def validate(self, extra_validators=None):
-        """Custom validation for FSH Converter Form."""
-        # Run default validators first
         if not super().validate(extra_validators):
             return False
-
-        # Check file/text input based on mode
-        # Need to check request.files for file uploads as self.fhir_file.data might be None during initial POST validation
         has_file_in_request = request and request.files and self.fhir_file.name in request.files and request.files[self.fhir_file.name].filename != ''
         if self.input_mode.data == 'file' and not has_file_in_request:
-            # If it's not in request.files, check if data is already populated (e.g., on re-render after error)
             if not self.fhir_file.data:
                  self.fhir_file.errors.append('File is required when input mode is Upload File.')
                  return False
         if self.input_mode.data == 'text' and not self.fhir_text.data:
             self.fhir_text.errors.append('Text input is required when input mode is Paste Text.')
             return False
-
-        # Validate text input format
         if self.input_mode.data == 'text' and self.fhir_text.data:
             try:
                 content = self.fhir_text.data.strip()
-                if not content: # Empty text is technically valid but maybe not useful
-                     pass # Allow empty text for now
-                elif content.startswith('{'):
-                    json.loads(content)
-                elif content.startswith('<'):
-                    ET.fromstring(content) # Basic XML check
+                if not content: pass
+                elif content.startswith('{'): json.loads(content)
+                elif content.startswith('<'): ET.fromstring(content)
                 else:
-                    # If content exists but isn't JSON or XML, it's an error
                     self.fhir_text.errors.append('Text input must be valid JSON or XML.')
                     return False
             except (json.JSONDecodeError, ET.ParseError):
                 self.fhir_text.errors.append('Invalid JSON or XML format.')
                 return False
-
-        # Validate dependency format
         if self.dependencies.data:
             for dep in self.dependencies.data.splitlines():
                 dep = dep.strip()
-                # Allow versions like 'current', 'dev', etc. but require package@version format
                 if dep and not re.match(r'^[a-zA-Z0-9\-\.]+@[a-zA-Z0-9\.\-]+$', dep):
                     self.dependencies.errors.append(f'Invalid dependency format: "{dep}". Use package@version (e.g., hl7.fhir.us.core@6.1.0).')
                     return False
-
-        # Validate alias file extension (optional, basic check)
-        # Check request.files for alias file as well
         has_alias_file_in_request = request and request.files and self.alias_file.name in request.files and request.files[self.alias_file.name].filename != ''
         alias_file_data = self.alias_file.data or (request.files.get(self.alias_file.name) if request else None)
-
         if alias_file_data and alias_file_data.filename:
              if not alias_file_data.filename.lower().endswith('.fsh'):
                   self.alias_file.errors.append('Alias file should have a .fsh extension.')
-                  # return False # Might be too strict, maybe just warn?
-
         return True
 
-
 class TestDataUploadForm(FlaskForm):
     """Form for uploading FHIR test data."""
     fhir_server_url = StringField('Target FHIR Server URL', validators=[DataRequired(), URL()],
                                   render_kw={'placeholder': 'e.g., http://localhost:8080/fhir'})
-
     auth_type = SelectField('Authentication Type', choices=[
         ('none', 'None'),
-        ('bearerToken', 'Bearer Token')
+        ('bearerToken', 'Bearer Token'),
+        ('basic', 'Basic Authentication')
     ], default='none')
-
     auth_token = StringField('Bearer Token', validators=[Optional()],
                              render_kw={'placeholder': 'Enter Bearer Token', 'type': 'password'})
-
+    username = StringField('Username', validators=[Optional()],
+                          render_kw={'placeholder': 'Enter Basic Auth Username'})
+    password = PasswordField('Password', validators=[Optional()],
+                            render_kw={'placeholder': 'Enter Basic Auth Password'})
     test_data_file = FileField('Select Test Data File(s)', validators=[InputRequired("Please select at least one file.")],
                               render_kw={'multiple': True, 'accept': '.json,.xml,.zip'})
-
     validate_before_upload = BooleanField('Validate Resources Before Upload?', default=False,
                                           description="Validate resources against selected package profile before uploading.")
     validation_package_id = SelectField('Validation Profile Package (Optional)',
                                         choices=[('', '-- Select Package for Validation --')],
                                         validators=[Optional()],
                                         description="Select the processed IG package to use for validation.")
-
     upload_mode = SelectField('Upload Mode', choices=[
-        ('individual', 'Individual Resources'), # Simplified label
-        ('transaction', 'Transaction Bundle') # Simplified label
+        ('individual', 'Individual Resources'),
+        ('transaction', 'Transaction Bundle')
     ], default='individual')
-
-    # --- NEW FIELD for Conditional Upload ---
     use_conditional_uploads = BooleanField('Use Conditional Upload (Individual Mode Only)?', default=True,
                                            description="If checked, checks resource existence (GET) and uses If-Match (PUT) or creates (PUT). If unchecked, uses simple PUT for all.")
-    # --- END NEW FIELD ---
-
     error_handling = SelectField('Error Handling', choices=[
         ('stop', 'Stop on First Error'),
         ('continue', 'Continue on Error')
     ], default='stop')
-
     submit = SubmitField('Upload and Process')
 
     def validate(self, extra_validators=None):
-        """Custom validation for Test Data Upload Form."""
-        if not super().validate(extra_validators): return False
+        if not super().validate(extra_validators):
+            return False
         if self.validate_before_upload.data and not self.validation_package_id.data:
             self.validation_package_id.errors.append('Please select a package to validate against when pre-upload validation is enabled.')
             return False
-        # Add check: Conditional uploads only make sense for individual mode
         if self.use_conditional_uploads.data and self.upload_mode.data == 'transaction':
             self.use_conditional_uploads.errors.append('Conditional Uploads only apply to the "Individual Resources" mode.')
-             # We might allow this combination but warn the user it has no effect,
-             # or enforce it here. Let's enforce for clarity.
-             # return False # Optional: Make this a hard validation failure
-             # Or just let it pass and ignore the flag in the backend for transaction mode.
-             pass # Let it pass for now, backend will ignore if mode is transaction
-
+            return False
+        if self.auth_type.data == 'bearerToken' and not self.auth_token.data:
+            self.auth_token.errors.append('Bearer Token is required when Bearer Token authentication is selected.')
+            return False
+        if self.auth_type.data == 'basic':
+            if not self.username.data:
+                self.username.errors.append('Username is required for Basic Authentication.')
+                return False
+            if not self.password.data:
+                self.password.errors.append('Password is required for Basic Authentication.')
+                return False
         return True
+
+class FhirRequestForm(FlaskForm):
+    fhir_server_url = StringField('FHIR Server URL', validators=[URL(), Optional()],
+                                 render_kw={'placeholder': 'e.g., https://hapi.fhir.org/baseR4'})
+    auth_type = SelectField('Authentication Type (for Custom URL)', choices=[
+        ('none', 'None'),
+        ('bearerToken', 'Bearer Token'),
+        ('basicAuth', 'Basic Authentication')
+    ], default='none', validators=[Optional()])
+    auth_token = StringField('Bearer Token', validators=[Optional()],
+                             render_kw={'placeholder': 'Enter Bearer Token', 'type': 'password'})
+    basic_auth_username = StringField('Username', validators=[Optional()],
+                                   render_kw={'placeholder': 'Enter Basic Auth Username'})
+    basic_auth_password = PasswordField('Password', validators=[Optional()],
+                                     render_kw={'placeholder': 'Enter Basic Auth Password'})
+    submit = SubmitField('Send Request')
+
+    def validate(self, extra_validators=None):
+        if not super().validate(extra_validators):
+            return False
+        if self.fhir_server_url.data:
+            if self.auth_type.data == 'bearerToken' and not self.auth_token.data:
+                self.auth_token.errors.append('Bearer Token is required when Bearer Token authentication is selected for a custom URL.')
+                return False
+            if self.auth_type.data == 'basicAuth':
+                if not self.basic_auth_username.data:
+                    self.basic_auth_username.errors.append('Username is required for Basic Authentication with a custom URL.')
+                return False
+                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
+
+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')

instance/fhir_packages/hl7.fhir.au.base-5.1.0-preview.metadata.json

@@ -1,22 +0,0 @@
-{
-  "package_name": "hl7.fhir.au.base",
-  "version": "5.1.0-preview",
-  "dependency_mode": "recursive",
-  "imported_dependencies": [
-    {
-      "name": "hl7.fhir.r4.core",
-      "version": "4.0.1"
-    },
-    {
-      "name": "hl7.terminology.r4",
-      "version": "6.2.0"
-    },
-    {
-      "name": "hl7.fhir.uv.extensions.r4",
-      "version": "5.2.0"
-    }
-  ],
-  "complies_with_profiles": [],
-  "imposed_profiles": [],
-  "timestamp": "2025-04-17T04:04:45.070781+00:00"
-}

instance/fhir_packages/hl7.fhir.au.core-1.1.0-preview.metadata.json

@@ -1,34 +0,0 @@
-{
-  "package_name": "hl7.fhir.au.core",
-  "version": "1.1.0-preview",
-  "dependency_mode": "recursive",
-  "imported_dependencies": [
-    {
-      "name": "hl7.fhir.r4.core",
-      "version": "4.0.1"
-    },
-    {
-      "name": "hl7.terminology.r4",
-      "version": "6.2.0"
-    },
-    {
-      "name": "hl7.fhir.uv.extensions.r4",
-      "version": "5.2.0"
-    },
-    {
-      "name": "hl7.fhir.au.base",
-      "version": "5.1.0-preview"
-    },
-    {
-      "name": "hl7.fhir.uv.smart-app-launch",
-      "version": "2.1.0"
-    },
-    {
-      "name": "hl7.fhir.uv.ipa",
-      "version": "1.0.0"
-    }
-  ],
-  "complies_with_profiles": [],
-  "imposed_profiles": [],
-  "timestamp": "2025-04-17T04:04:20.523471+00:00"
-}

instance/fhir_packages/hl7.fhir.r4.core-4.0.1.metadata.json

@@ -1,9 +0,0 @@
-{
-  "package_name": "hl7.fhir.r4.core",
-  "version": "4.0.1",
-  "dependency_mode": "recursive",
-  "imported_dependencies": [],
-  "complies_with_profiles": [],
-  "imposed_profiles": [],
-  "timestamp": "2025-04-17T04:04:29.230227+00:00"
-}

instance/fhir_packages/hl7.fhir.uv.extensions.r4-5.2.0.metadata.json

@@ -1,14 +0,0 @@
-{
-  "package_name": "hl7.fhir.uv.extensions.r4",
-  "version": "5.2.0",
-  "dependency_mode": "recursive",
-  "imported_dependencies": [
-    {
-      "name": "hl7.fhir.r4.core",
-      "version": "4.0.1"
-    }
-  ],
-  "complies_with_profiles": [],
-  "imposed_profiles": [],
-  "timestamp": "2025-04-17T04:04:41.588025+00:00"
-}

instance/fhir_packages/hl7.fhir.uv.ipa-1.0.0.metadata.json

@@ -1,22 +0,0 @@
-{
-  "package_name": "hl7.fhir.uv.ipa",
-  "version": "1.0.0",
-  "dependency_mode": "recursive",
-  "imported_dependencies": [
-    {
-      "name": "hl7.fhir.r4.core",
-      "version": "4.0.1"
-    },
-    {
-      "name": "hl7.terminology.r4",
-      "version": "5.0.0"
-    },
-    {
-      "name": "hl7.fhir.uv.smart-app-launch",
-      "version": "2.0.0"
-    }
-  ],
-  "complies_with_profiles": [],
-  "imposed_profiles": [],
-  "timestamp": "2025-04-17T04:04:49.395594+00:00"
-}

instance/fhir_packages/hl7.fhir.uv.smart-app-launch-2.0.0.metadata.json

@@ -1,14 +0,0 @@
-{
-  "package_name": "hl7.fhir.uv.smart-app-launch",
-  "version": "2.0.0",
-  "dependency_mode": "recursive",
-  "imported_dependencies": [
-    {
-      "name": "hl7.fhir.r4.core",
-      "version": "4.0.1"
-    }
-  ],
-  "complies_with_profiles": [],
-  "imposed_profiles": [],
-  "timestamp": "2025-04-17T04:04:56.492512+00:00"
-}

instance/fhir_packages/hl7.fhir.uv.smart-app-launch-2.1.0.metadata.json

@@ -1,18 +0,0 @@
-{
-  "package_name": "hl7.fhir.uv.smart-app-launch",
-  "version": "2.1.0",
-  "dependency_mode": "recursive",
-  "imported_dependencies": [
-    {
-      "name": "hl7.fhir.r4.core",
-      "version": "4.0.1"
-    },
-    {
-      "name": "hl7.terminology.r4",
-      "version": "5.0.0"
-    }
-  ],
-  "complies_with_profiles": [],
-  "imposed_profiles": [],
-  "timestamp": "2025-04-17T04:04:46.943079+00:00"
-}

instance/fhir_packages/hl7.terminology.r4-5.0.0.metadata.json

@@ -1,14 +0,0 @@
-{
-  "package_name": "hl7.terminology.r4",
-  "version": "5.0.0",
-  "dependency_mode": "recursive",
-  "imported_dependencies": [
-    {
-      "name": "hl7.fhir.r4.core",
-      "version": "4.0.1"
-    }
-  ],
-  "complies_with_profiles": [],
-  "imposed_profiles": [],
-  "timestamp": "2025-04-17T04:04:54.857273+00:00"
-}

instance/fhir_packages/hl7.terminology.r4-6.2.0.metadata.json

@@ -1,14 +0,0 @@
-{
-  "package_name": "hl7.terminology.r4",
-  "version": "6.2.0",
-  "dependency_mode": "recursive",
-  "imported_dependencies": [
-    {
-      "name": "hl7.fhir.r4.core",
-      "version": "4.0.1"
-    }
-  ],
-  "complies_with_profiles": [],
-  "imposed_profiles": [],
-  "timestamp": "2025-04-17T04:04:37.703082+00:00"
-}

instance/hapi-h2-data/fhir.lock.db

@@ -1,6 +0,0 @@
-#FileLock
-#Fri Apr 25 13:11:59 UTC 2025
-server=172.19.0.2\:35493
-hostName=499bb2429005
-method=file
-id=1966d138790b0be6a4873c639ee5ac2e23787fd766d

package.py

@@ -0,0 +1,123 @@
+from flask import Blueprint, jsonify, current_app, render_template
+import os
+import tarfile
+import json
+from datetime import datetime
+import time
+from services import pkg_version, safe_parse_version
+
+package_bp = Blueprint('package', __name__)
+
+@package_bp.route('/logs/<name>')
+def logs(name):
+    """
+    Fetch logs for a package, listing each version with its publication date.
+    
+    Args:
+        name (str): The name of the package.
+    
+    Returns:
+        Rendered template with logs or an error message.
+    """
+    try:
+        in_memory_cache = current_app.config.get('MANUAL_PACKAGE_CACHE', [])
+        if not in_memory_cache:
+            current_app.logger.error(f"No in-memory cache found for package logs: {name}")
+            return "<p class='text-muted'>Package cache not found.</p>"
+
+        package_data = next((pkg for pkg in in_memory_cache if isinstance(pkg, dict) and pkg.get('name', '').lower() == name.lower()), None)
+        if not package_data:
+            current_app.logger.error(f"Package not found in cache: {name}")
+            return "<p class='text-muted'>Package not found.</p>"
+
+        # Get the versions list with pubDate
+        versions = package_data.get('all_versions', [])
+        if not versions:
+            current_app.logger.warning(f"No versions found for package: {name}. Package data: {package_data}")
+            return "<p class='text-muted'>No version history found for this package.</p>"
+
+        current_app.logger.debug(f"Found {len(versions)} versions for package {name}: {versions[:5]}...")
+
+        logs = []
+        now = time.time()
+        for version_info in versions:
+            if not isinstance(version_info, dict):
+                current_app.logger.warning(f"Invalid version info for {name}: {version_info}")
+                continue
+            version = version_info.get('version', '')
+            pub_date_str = version_info.get('pubDate', '')
+            if not version or not pub_date_str:
+                current_app.logger.warning(f"Skipping version info with missing version or pubDate: {version_info}")
+                continue
+
+            # Parse pubDate and calculate "when"
+            when = "Unknown"
+            try:
+                pub_date = datetime.strptime(pub_date_str, "%a, %d %b %Y %H:%M:%S %Z")
+                pub_time = pub_date.timestamp()
+                time_diff = now - pub_time
+                days_ago = int(time_diff / 86400)
+                if days_ago < 1:
+                    hours_ago = int(time_diff / 3600)
+                    if hours_ago < 1:
+                        minutes_ago = int(time_diff / 60)
+                        when = f"{minutes_ago} minute{'s' if minutes_ago != 1 else ''} ago"
+                    else:
+                        when = f"{hours_ago} hour{'s' if hours_ago != 1 else ''} ago"
+                else:
+                    when = f"{days_ago} day{'s' if days_ago != 1 else ''} ago"
+            except ValueError as e:
+                current_app.logger.warning(f"Failed to parse pubDate '{pub_date_str}' for version {version}: {e}")
+
+            logs.append({
+                "version": version,
+                "pubDate": pub_date_str,
+                "when": when
+            })
+
+        if not logs:
+            current_app.logger.warning(f"No valid version entries with pubDate for package: {name}")
+            return "<p class='text-muted'>No version history found for this package.</p>"
+
+        # Sort logs by version number (newest first)
+        logs.sort(key=lambda x: safe_parse_version(x.get('version', '0.0.0a0')), reverse=True)
+
+        current_app.logger.debug(f"Rendering logs for {name} with {len(logs)} entries")
+        return render_template('package.logs.html', logs=logs)
+
+    except Exception as e:
+        current_app.logger.error(f"Error in logs endpoint for {name}: {str(e)}", exc_info=True)
+        return "<p class='text-danger'>Error loading version history.</p>", 500
+
+@package_bp.route('/dependents/<name>')
+def dependents(name):
+    """
+    HTMX endpoint to fetch packages that depend on the current package.
+    Returns an HTML fragment with a table of dependent packages.
+    """
+    in_memory_cache = current_app.config.get('MANUAL_PACKAGE_CACHE', [])
+    package_data = next((pkg for pkg in in_memory_cache if isinstance(pkg, dict) and pkg.get('name', '').lower() == name.lower()), None)
+
+    if not package_data:
+        return "<p class='text-danger'>Package not found.</p>"
+
+    # Find dependents: packages whose dependencies include the current package
+    dependents = []
+    for pkg in in_memory_cache:
+        if not isinstance(pkg, dict):
+            continue
+        dependencies = pkg.get('dependencies', [])
+        for dep in dependencies:
+            dep_name = dep.get('name', '')
+            if dep_name.lower() == name.lower():
+                dependents.append({
+                    "name": pkg.get('name', 'Unknown'),
+                    "version": pkg.get('latest_absolute_version', 'N/A'),
+                    "author": pkg.get('author', 'N/A'),
+                    "fhir_version": pkg.get('fhir_version', 'N/A'),
+                    "version_count": pkg.get('version_count', 0),
+                    "canonical": pkg.get('canonical', 'N/A')
+                })
+                break
+
+    return render_template('package.dependents.html', dependents=dependents)

requirements.txt

@@ -5,5 +5,10 @@ requests==2.31.0
 Flask-WTF==1.2.1
 WTForms==3.1.2
 Pytest
+pyyaml==6.0.1
 fhir.resources==8.0.0
 Flask-Migrate==4.1.0
+cachetools
+beautifulsoup4
+feedparser==6.0.11
+flasgger

setup_linux.sh

@@ -0,0 +1,395 @@
+#!/bin/bash
+
+# --- Configuration ---
+REPO_URL_HAPI="https://github.com/hapifhir/hapi-fhir-jpaserver-starter.git"
+REPO_URL_CANDLE="https://github.com/FHIR/fhir-candle.git"
+CLONE_DIR_HAPI="hapi-fhir-jpaserver"
+CLONE_DIR_CANDLE="fhir-candle"
+SOURCE_CONFIG_DIR="hapi-fhir-Setup"
+CONFIG_FILE="application.yaml"
+
+# --- Define Paths ---
+SOURCE_CONFIG_PATH="../${SOURCE_CONFIG_DIR}/target/classes/${CONFIG_FILE}"
+DEST_CONFIG_PATH="${CLONE_DIR_HAPI}/target/classes/${CONFIG_FILE}"
+
+APP_MODE=""
+CUSTOM_FHIR_URL_VAL=""
+SERVER_TYPE=""
+CANDLE_FHIR_VERSION=""
+
+# --- Error Handling Function ---
+handle_error() {
+    echo "------------------------------------"
+    echo "An error occurred: $1"
+    echo "Script aborted."
+    echo "------------------------------------"
+    exit 1
+}
+
+# === MODIFIED: Prompt for Installation Mode ===
+get_mode_choice() {
+    echo ""
+    echo "Select Installation Mode:"
+    echo "1. Lite (Excludes local HAPI FHIR Server - No Git/Maven/Dotnet needed)"
+    echo "2. Custom URL (Uses a custom FHIR Server - No Git/Maven/Dotnet needed)"
+    echo "3. Hapi (Includes local HAPI FHIR Server - Requires Git & Maven)"
+    echo "4. Candle (Includes local FHIR Candle Server - Requires Git & Dotnet)"
+
+    while true; do
+        read -r -p "Enter your choice (1, 2, 3, or 4): " choice
+        case "$choice" in
+            1)
+                APP_MODE="lite"
+                break
+                ;;
+            2)
+                APP_MODE="standalone"
+                get_custom_url_prompt
+                break
+                ;;
+            3)
+                APP_MODE="standalone"
+                SERVER_TYPE="hapi"
+                break
+                ;;
+            4)
+                APP_MODE="standalone"
+                SERVER_TYPE="candle"
+                get_candle_fhir_version
+                break
+                ;;
+            *)
+                echo "Invalid input. Please try again."
+                ;;
+        esac
+    done
+    echo "Selected Mode: $APP_MODE"
+    echo "Server Type: $SERVER_TYPE"
+    echo
+}
+
+# === NEW: Prompt for Custom URL ===
+get_custom_url_prompt() {
+    local confirmed_url=""
+    while true; do
+        echo
+        read -r -p "Please enter the custom FHIR server URL: " custom_url_input
+        echo
+        echo "You entered: $custom_url_input"
+        read -r -p "Is this URL correct? (Y/N): " confirm_url
+        if [[ "$confirm_url" =~ ^[Yy]$ ]]; then
+            confirmed_url="$custom_url_input"
+            break
+        else
+            echo "URL not confirmed. Please re-enter."
+        fi
+    done
+
+    while true; do
+        echo
+        read -r -p "Please re-enter the URL to confirm it is correct: " custom_url_input
+        if [ "$custom_url_input" = "$confirmed_url" ]; then
+            CUSTOM_FHIR_URL_VAL="$custom_url_input"
+            echo
+            echo "Custom URL confirmed: $CUSTOM_FHIR_URL_VAL"
+            break
+        else
+            echo
+            echo "URLs do not match. Please try again."
+            confirmed_url="$custom_url_input"
+        fi
+    done
+}
+
+# === NEW: Prompt for Candle FHIR version ===
+get_candle_fhir_version() {
+    echo ""
+    echo "Select the FHIR version for the Candle server:"
+    echo "1. R4 (4.0)"
+    echo "2. R4B (4.3)"
+    echo "3. R5 (5.0)"
+    while true; do
+        read -r -p "Enter your choice (1, 2, or 3): " choice
+        case "$choice" in
+            1)
+                CANDLE_FHIR_VERSION=r4
+                break
+                ;;
+            2)
+                CANDLE_FHIR_VERSION=r4b
+                break
+                ;;
+            3)
+                CANDLE_FHIR_VERSION=r5
+                break
+                ;;
+            *)
+                echo "Invalid input. Please try again."
+                ;;
+        esac
+    done
+}
+
+
+# Call the function to get mode choice
+get_mode_choice
+
+# === Conditionally Execute Server Setup ===
+case "$SERVER_TYPE" in
+    "hapi")
+        echo "Running Hapi server setup..."
+        echo
+
+        # --- Step 0: Clean up previous clone (optional) ---
+        echo "Checking for existing directory: $CLONE_DIR_HAPI"
+        if [ -d "$CLONE_DIR_HAPI" ]; then
+            echo "Found existing directory, removing it..."
+            rm -rf "$CLONE_DIR_HAPI"
+            if [ $? -ne 0 ]; then
+                handle_error "Failed to remove existing directory: $CLONE_DIR_HAPI"
+            fi
+            echo "Existing directory removed."
+        else
+            echo "Directory does not exist, proceeding with clone."
+        fi
+        echo
+
+        # --- Step 1: Clone the HAPI FHIR server repository ---
+        echo "Cloning repository: $REPO_URL_HAPI into $CLONE_DIR_HAPI..."
+        git clone "$REPO_URL_HAPI" "$CLONE_DIR_HAPI"
+        if [ $? -ne 0 ]; then
+            handle_error "Failed to clone repository. Check Git installation and network connection."
+        fi
+        echo "Repository cloned successfully."
+        echo
+
+        # --- Step 2: Navigate into the cloned directory ---
+        echo "Changing directory to $CLONE_DIR_HAPI..."
+        cd "$CLONE_DIR_HAPI" || handle_error "Failed to change directory to $CLONE_DIR_HAPI."
+        echo "Current directory: $(pwd)"
+        echo
+
+        # --- Step 3: Build the HAPI server using Maven ---
+        echo "===> Starting Maven build (Step 3)..."
+        mvn clean package -DskipTests=true -Pboot
+        if [ $? -ne 0 ]; then
+            echo "ERROR: Maven build failed."
+            cd ..
+            handle_error "Maven build process resulted in an error."
+        fi
+        echo "Maven build completed successfully."
+        echo
+
+        # --- Step 4: Copy the configuration file ---
+        echo "===> Starting file copy (Step 4)..."
+        echo "Copying configuration file..."
+        INITIAL_SCRIPT_DIR=$(pwd)
+        ABSOLUTE_SOURCE_CONFIG_PATH="${INITIAL_SCRIPT_DIR}/../${SOURCE_CONFIG_DIR}/target/classes/${CONFIG_FILE}"
+
+        echo "Source: $ABSOLUTE_SOURCE_CONFIG_PATH"
+        echo "Destination: target/classes/$CONFIG_FILE"
+
+        if [ ! -f "$ABSOLUTE_SOURCE_CONFIG_PATH" ]; then
+            echo "WARNING: Source configuration file not found at $ABSOLUTE_SOURCE_CONFIG_PATH."
+            echo "The script will continue, but the server might use default configuration."
+        else
+            cp "$ABSOLUTE_SOURCE_CONFIG_PATH" "target/classes/"
+            if [ $? -ne 0 ]; then
+                echo "WARNING: Failed to copy configuration file. Check if the source file exists and permissions."
+                echo "The script will continue, but the server might use default configuration."
+            else
+                echo "Configuration file copied successfully."
+            fi
+        fi
+        echo
+
+        # --- Step 5: Navigate back to the parent directory ---
+        echo "===> Changing directory back (Step 5)..."
+        cd .. || handle_error "Failed to change back to the parent directory."
+        echo "Current directory: $(pwd)"
+        echo
+        ;;
+
+    "candle")
+        echo "Running FHIR Candle server setup..."
+        echo
+        
+        # --- Step 0: Clean up previous clone (optional) ---
+        echo "Checking for existing directory: $CLONE_DIR_CANDLE"
+        if [ -d "$CLONE_DIR_CANDLE" ]; then
+            echo "Found existing directory, removing it..."
+            rm -rf "$CLONE_DIR_CANDLE"
+            if [ $? -ne 0 ]; then
+                handle_error "Failed to remove existing directory: $CLONE_DIR_CANDLE"
+            fi
+            echo "Existing directory removed."
+        else
+            echo "Directory does not exist, proceeding with clone."
+        fi
+        echo
+
+        # --- Step 1: Clone the FHIR Candle server repository ---
+        echo "Cloning repository: $REPO_URL_CANDLE into $CLONE_DIR_CANDLE..."
+        git clone "$REPO_URL_CANDLE" "$CLONE_DIR_CANDLE"
+        if [ $? -ne 0 ]; then
+            handle_error "Failed to clone repository. Check Git and Dotnet SDK installation and network connection."
+        fi
+        echo "Repository cloned successfully."
+        echo
+        
+        # --- Step 2: Navigate into the cloned directory ---
+        echo "Changing directory to $CLONE_DIR_CANDLE..."
+        cd "$CLONE_DIR_CANDLE" || handle_error "Failed to change directory to $CLONE_DIR_CANDLE."
+        echo "Current directory: $(pwd)"
+        echo
+
+        # --- Step 3: Build the FHIR Candle server using Dotnet ---
+        echo "===> Starting Dotnet build (Step 3)..."
+        dotnet publish -c Release -f net9.0 -o publish
+        if [ $? -ne 0 ]; then
+            handle_error "Dotnet build failed. Check Dotnet SDK installation."
+        fi
+        echo "Dotnet build completed successfully."
+        echo
+        
+        # --- Step 4: Navigate back to the parent directory ---
+        echo "===> Changing directory back (Step 4)..."
+        cd .. || handle_error "Failed to change back to the parent directory."
+        echo "Current directory: $(pwd)"
+        echo
+        ;;
+
+    *) # APP_MODE is Lite, no SERVER_TYPE
+        echo "Running Lite setup, skipping server build..."
+        if [ -d "$CLONE_DIR_HAPI" ]; then
+            echo "Found existing HAPI directory in Lite mode. Removing it to avoid build issues..."
+            rm -rf "$CLONE_DIR_HAPI"
+        fi
+        if [ -d "$CLONE_DIR_CANDLE" ]; then
+            echo "Found existing Candle directory in Lite mode. Removing it to avoid build issues..."
+            rm -rf "$CLONE_DIR_CANDLE"
+        fi
+        mkdir -p "${CLONE_DIR_HAPI}/target/classes"
+        mkdir -p "${CLONE_DIR_HAPI}/custom"
+        touch "${CLONE_DIR_HAPI}/target/ROOT.war"
+        touch "${CLONE_DIR_HAPI}/target/classes/application.yaml"
+        mkdir -p "${CLONE_DIR_CANDLE}/publish"
+        touch "${CLONE_DIR_CANDLE}/publish/fhir-candle.dll"
+        echo "Placeholder files and directories created for Lite mode build."
+        echo
+        ;;
+esac
+
+# === MODIFIED: Update docker-compose.yml to set APP_MODE and HAPI_FHIR_URL and DOCKERFILE ===
+echo "Updating docker-compose.yml with APP_MODE=$APP_MODE and HAPI_FHIR_URL..."
+DOCKER_COMPOSE_TMP="docker-compose.yml.tmp"
+DOCKER_COMPOSE_ORIG="docker-compose.yml"
+
+HAPI_URL_TO_USE="https://fhir.hl7.org.au/aucore/fhir/DEFAULT/"
+if [ -n "$CUSTOM_FHIR_URL_VAL" ]; then
+    HAPI_URL_TO_USE="$CUSTOM_FHIR_URL_VAL"
+elif [ "$SERVER_TYPE" = "candle" ]; then
+    HAPI_URL_TO_USE="http://localhost:5826/fhir/${CANDLE_FHIR_VERSION}"
+else
+    HAPI_URL_TO_USE="http://localhost:8080/fhir"
+fi
+
+DOCKERFILE_TO_USE="Dockerfile.lite"
+if [ "$SERVER_TYPE" = "hapi" ]; then
+    DOCKERFILE_TO_USE="Dockerfile.hapi"
+elif [ "$SERVER_TYPE" = "candle" ]; then
+    DOCKERFILE_TO_USE="Dockerfile.candle"
+fi
+
+cat << EOF > "$DOCKER_COMPOSE_TMP"
+version: '3.8'
+services:
+  fhirflare:
+    build:
+      context: .
+      dockerfile: ${DOCKERFILE_TO_USE}
+    ports:
+EOF
+
+if [ "$SERVER_TYPE" = "candle" ]; then
+    cat << EOF >> "$DOCKER_COMPOSE_TMP"
+      - "5000:5000"
+      - "5001:5826"
+EOF
+else
+    cat << EOF >> "$DOCKER_COMPOSE_TMP"
+      - "5000:5000"
+      - "8080:8080"
+EOF
+fi
+
+cat << EOF >> "$DOCKER_COMPOSE_TMP"
+    volumes:
+      - ./instance:/app/instance
+      - ./static/uploads:/app/static/uploads
+      - ./logs:/app/logs
+EOF
+
+if [ "$SERVER_TYPE" = "hapi" ]; then
+    cat << EOF >> "$DOCKER_COMPOSE_TMP"
+      - ./instance/hapi-h2-data/:/app/h2-data # Keep volume mounts consistent
+      - ./hapi-fhir-jpaserver/target/ROOT.war:/usr/local/tomcat/webapps/ROOT.war
+      - ./hapi-fhir-jpaserver/target/classes/application.yaml:/usr/local/tomcat/conf/application.yaml
+EOF
+elif [ "$SERVER_TYPE" = "candle" ]; then
+    cat << EOF >> "$DOCKER_COMPOSE_TMP"
+      - ./fhir-candle/publish/:/app/fhir-candle-publish/
+EOF
+fi
+
+cat << EOF >> "$DOCKER_COMPOSE_TMP"
+    environment:
+      - FLASK_APP=app.py
+      - FLASK_ENV=development
+      - NODE_PATH=/usr/lib/node_modules
+      - APP_MODE=${APP_MODE}
+      - APP_BASE_URL=http://localhost:5000
+      - HAPI_FHIR_URL=${HAPI_URL_TO_USE}
+EOF
+
+if [ "$SERVER_TYPE" = "candle" ]; then
+    cat << EOF >> "$DOCKER_COMPOSE_TMP"
+      - ASPNETCORE_URLS=http://0.0.0.0:5826
+EOF
+fi
+
+cat << EOF >> "$DOCKER_COMPOSE_TMP"
+    command: supervisord -c /etc/supervisord.conf
+EOF
+
+if [ ! -f "$DOCKER_COMPOSE_TMP" ]; then
+    handle_error "Failed to create temporary docker-compose file ($DOCKER_COMPOSE_TMP)."
+fi
+
+# Replace the original docker-compose.yml
+mv "$DOCKER_COMPOSE_TMP" "$DOCKER_COMPOSE_ORIG"
+echo "docker-compose.yml updated successfully."
+echo
+
+# --- Step 6: Build Docker images ---
+echo "===> Starting Docker build (Step 6)..."
+docker-compose build --no-cache
+if [ $? -ne 0 ]; then
+    handle_error "Docker Compose build failed. Check Docker installation and docker-compose.yml file."
+fi
+echo "Docker images built successfully."
+echo
+
+# --- Step 7: Start Docker containers ---
+echo "===> Starting Docker containers (Step 7)..."
+docker-compose up -d
+if [ $? -ne 0 ]; then
+    handle_error "Docker Compose up failed. Check Docker installation and container configurations."
+fi
+echo "Docker containers started successfully."
+echo
+
+echo "===================================="
+echo "Script finished successfully! (Mode: $APP_MODE)"
+echo "===================================="
+exit 0

static/css/animation.css

@@ -0,0 +1,390 @@
+body {
+    width: 100%;
+    font-family: 'Inter', -apple-system, BlinkMacSystemFont, 'Segoe UI', Roboto, sans-serif;
+}
+
+/* Apply overflow and height constraints only for fire animation page
+body.fire-animation-page {
+    overflow: hidden;
+    height: 100vh;
+}
+*/
+/* Fire animation overlay */
+.fire-on {
+    position: absolute;
+    top: 0;
+    left: 0;
+    width: 100%;
+    height: 100%;
+    background: linear-gradient(#1d4456, #112630);
+    opacity: 1;
+    z-index: 1;
+    transition: all 1200ms linear;
+}
+
+.section-center {
+    position: relative;
+    width: 300px; /* Reduced size for landing page */
+    height: 300px;
+    margin: 0 auto;
+    display: block;
+    overflow: hidden;
+    border: 8px solid rgba(0,0,0,.2);
+    border-radius: 50%;
+    z-index: 5;
+    background-color: #1d4456;
+    box-shadow: 0 0 50px 5px rgba(255,148,0,.1);
+    transition: all 500ms linear;
+}
+
+/* Wood and star using local images */
+.wood {
+    position: absolute;
+    z-index: 21;
+    left: 50%;
+    bottom: 12%;
+    width: 80px;
+    margin-left: -40px;
+    height: 30px;
+    background-image: url('{{ url_for('static', filename='img/wood.png') }}');
+    background-size: 80px 30px;
+    border-radius: 5px;
+}
+
+.star {
+    z-index: 2;
+    position: absolute;
+    top: 138px;
+    left: 18px;
+    background-image: url('{{ url_for('static', filename='img/star.png') }}');
+    background-size: 11px 11px;
+    width: 11px;
+    height: 11px;
+    opacity: 0.4;
+    animation: starShine 3.5s linear infinite;
+    transition: all 1200ms linear;
+}
+
+.wood-circle {
+    position: absolute;
+    z-index: 20;
+    left: 50%;
+    bottom: 11%;
+    width: 100px;
+    margin-left: -50px;
+    height: 20px;
+    border-radius: 100%;
+    background-color: #0a171d;
+}
+
+.circle {
+    position: absolute;
+    z-index: 6;
+    right: -225px;
+    bottom: -337px;
+    width: 562px;
+    height: 525px;
+    border-radius: 100%;
+    background-color: #112630;
+}
+
+/* Moon */
+.moon {
+    position: absolute;
+    top: 37px;
+    left: 86px;
+    width: 60px;
+    height: 60px;
+    background-color: #b2b7bc;
+    border-radius: 50%;
+    box-shadow: inset -15px 1.5px 0 0px #c0c3c9, 0 0 7px 3px rgba(228,228,222,.4);
+    z-index: 1;
+    animation: brilla-moon 4s alternate infinite;
+    transition: all 2000ms linear;
+}
+
+.moon div:nth-child(1) {
+    position: absolute;
+    top: 50%;
+    left: 10%;
+    width: 12%;
+    height: 12%;
+    border-radius: 50%;
+    border: 1px solid #adaca2;
+    box-shadow: inset 1.5px -0.75px 0 0px #85868b;
+    opacity: 0.4;
+}
+
+.moon div:nth-child(2) {
+    position: absolute;
+    top: 20%;
+    left: 38%;
+    width: 16%;
+    height: 16%;
+    border-radius: 50%;
+    border: 1px solid #adaca2;
+    box-shadow: inset 1.5px -0.75px 0 0px #85868b;
+    opacity: 0.4;
+}
+
+.moon div:nth-child(3) {
+    position: absolute;
+    top: 60%;
+    left: 45%;
+    width: 20%;
+    height: 20%;
+    border-radius: 50%;
+    border: 1px solid #adaca2;
+    box-shadow: inset 1.5px -0.75px 0 0px #85868b;
+    opacity: 0.4;
+}
+
+@keyframes brilla-moon {
+    0% { box-shadow: inset -15px 1.5px 0 0px #c0c3c9, 0 0 7px 3px rgba(228,228,222,.4); }
+    50% { box-shadow: inset -15px 1.5px 0 0px #c0c3c9, 0 0 11px 6px rgba(228,228,222,.4); }
+}
+
+/* Shooting stars */
+.shooting-star {
+    z-index: 2;
+    width: 1px;
+    height: 37px;
+    border-bottom-left-radius: 50%;
+    border-bottom-right-radius: 50%;
+    position: absolute;
+    top: 0;
+    left: -52px;
+    background: linear-gradient(to bottom, rgba(255, 255, 255, 0), white);
+    animation: animShootingStar 6s linear infinite;
+    transition: all 2000ms linear;
+}
+
+@keyframes animShootingStar {
+    from { transform: translateY(0px) translateX(0px) rotate(-45deg); opacity: 1; height: 3px; }
+    to { transform: translateY(960px) translateX(960px) rotate(-45deg); opacity: 1; height: 600px; }
+}
+
+.shooting-star-2 {
+    z-index: 2;
+    width: 1px;
+    height: 37px;
+    border-bottom-left-radius: 50%;
+    border-bottom-right-radius: 50%;
+    position: absolute;
+    top: 0;
+    left: 150px;
+    background: linear-gradient(to bottom, rgba(255, 255, 255, 0), white);
+    animation: animShootingStar-2 9s linear infinite;
+    transition: all 2000ms linear;
+}
+
+@keyframes animShootingStar-2 {
+    from { transform: translateY(0px) translateX(0px) rotate(-45deg); opacity: 1; height: 3px; }
+    to { transform: translateY(1440px) translateX(1440px) rotate(-45deg); opacity: 1; height: 600px; }
+}
+
+/* Stars */
+.star.snd { top: 75px; left: 232px; animation-delay: 1s; }
+.star.trd { top: 97px; left: 75px; animation-delay: 1.4s; }
+.star.fth { top: 15px; left: 150px; animation-delay: 1.8s; }
+.star.fith { top: 63px; left: 165px; animation-delay: 2.2s; }
+
+@keyframes starShine {
+    0% { transform: scale(0.3) rotate(0deg); opacity: 0.4; }
+    25% { transform: scale(1) rotate(360deg); opacity: 1; }
+    50% { transform: scale(0.3) rotate(720deg); opacity: 0.4; }
+    100% { transform: scale(0.3) rotate(0deg); opacity: 0.4; }
+}
+
+/* Trees */
+.tree-1 {
+    position: relative;
+    top: 112px;
+    left: 37px;
+    width: 0;
+    height: 0;
+    z-index: 8;
+    border-bottom: 67px solid #0a171d;
+    border-left: 22px solid transparent;
+    border-right: 22px solid transparent;
+}
+
+.tree-1:before {
+    position: absolute;
+    bottom: -82px;
+    left: 50%;
+    margin-left: -3px;
+    width: 6px;
+    height: 22px;
+    z-index: 7;
+    content: '';
+    background-color: #000;
+}
+
+.tree-2 {
+    position: relative;
+    top: 0;
+    left: 187px;
+    width: 0;
+    height: 0;
+    z-index: 8;
+    border-bottom: 67px solid #0a171d;
+    border-left: 22px solid transparent;
+    border-right: 22px solid transparent;
+}
+
+.tree-2:before {
+    position: absolute;
+    bottom: -82px;
+    left: 50%;
+    margin-left: -3px;
+    width: 6px;
+    height: 22px;
+    z-index: 7;
+    content: '';
+    background-color: #000;
+}
+
+/* Fire */
+.fire {
+    position: absolute;
+    z-index: 39;
+    width: 2px;
+    margin-left: -1px;
+    left: 50%;
+    bottom: 60px;
+    transition: all 1200ms linear;
+}
+
+.fire span {
+    display: block;
+    position: absolute;
+    bottom: -11px;
+    margin-left: -15px;
+    height: 0;
+    width: 0;
+    border: 22px solid #febd08; /* Main flame: yellow-orange */
+    border-radius: 50%;
+    border-top-left-radius: 0;
+    left: -6px;
+    box-shadow: 0 0 7px 3px rgba(244,110,28,0.8), 0 0 15px 7px rgba(244,110,28,0.6), 0 0 22px 11px rgba(244,110,28,0.3);
+    transform: scale(0.45, 0.75) rotate(45deg);
+    animation: brilla-fire 2.5s alternate infinite;
+    z-index: 9;
+    transition: all 1200ms linear;
+}
+
+.fire span:nth-child(2) {
+    left: -16px;
+    border: 22px solid #e63946; /* Outside flame: red */
+    box-shadow: 0 0 7px 3px rgba(230,57,70,0.8), 0 0 15px 7px rgba(230,57,70,0.6), 0 0 22px 11px rgba(230,57,70,0.3);
+    transform: scale(0.3, 0.55) rotate(15deg);
+    z-index: 8;
+    animation: brilla-fire-red 1.5s alternate infinite;
+}
+
+.fire span:nth-child(3) {
+    left: 3px;
+    border: 22px solid #e63946; /* Outside flame: red */
+    box-shadow: 0 0 7px 3px rgba(230,57,70,0.8), 0 0 15px 7px rgba(230,57,70,0.6), 0 0 22px 11px rgba(230,57,70,0.3);
+    transform: scale(0.3, 0.55) rotate(80deg);
+    z-index: 8;
+    animation: brilla-fire-red 2s alternate infinite;
+}
+
+.fire span:after {
+    display: block;
+    position: absolute;
+    bottom: -22px;
+    content: '';
+    margin-left: -3px;
+    height: 22px;
+    width: 9px;
+    background-color: rgba(244,110,28,0.7);
+    border-radius: 80px;
+    border-top-right-radius: 0;
+    border-bottom-right-radius: 0;
+    box-shadow: 0 0 15px 7px rgba(244,110,28,0.7);
+    left: -6px;
+    opacity: 0.8;
+    transform: rotate(-50deg);
+}
+
+.fire span:nth-child(2):after {
+    background-color: rgba(230,57,70,0.7); /* Match red flame */
+    box-shadow: 0 0 15px 7px rgba(230,57,70,0.7);
+}
+
+.fire span:nth-child(3):after {
+    background-color: rgba(230,57,70,0.7); /* Match red flame */
+    box-shadow: 0 0 15px 7px rgba(230,57,70,0.7);
+}
+
+@keyframes brilla-fire {
+    0%, 100% { box-shadow: 0 0 7px 3px rgba(244,110,28,0.8), 0 0 15px 7px rgba(244,110,28,0.6), 0 0 22px 11px rgba(244,110,28,0.3); }
+    50% { box-shadow: 0 0 10px 5px rgba(244,110,28,0.8), 0 0 21px 10px rgba(244,110,28,0.6), 0 0 31px 15px rgba(244,110,28,0.3); }
+}
+
+@keyframes brilla-fire-red {
+    0%, 100% { box-shadow: 0 0 7px 3px rgba(230,57,70,0.8), 0 0 15px 7px rgba(230,57,70,0.6), 0 0 22px 11px rgba(230,57,70,0.3); }
+    50% { box-shadow: 0 0 10px 5px rgba(230,57,70,0.8), 0 0 21px 10px rgba(230,57,70,0.6), 0 0 31px 15px rgba(230,57,70,0.3); }
+}
+
+/* Smoke */
+.smoke {
+    position: absolute;
+    z-index: 40;
+    width: 2px;
+    margin-left: -1px;
+    left: 50%;
+    bottom: 79px;
+    opacity: 0;
+    transition: all 800ms linear;
+}
+
+.smoke span {
+    display: block;
+    position: absolute;
+    bottom: -26px;
+    left: 50%;
+    margin-left: -15px;
+    height: 0;
+    width: 0;
+    border: 22px solid rgba(0, 0, 0, .6);
+    border-radius: 16px;
+    border-bottom-left-radius: 0;
+    border-top-right-radius: 0;
+    left: -6px;
+    opacity: 0;
+    transform: scale(0.2, 0.2) rotate(-45deg);
+}
+
+@keyframes smokeLeft {
+    0% { transform: scale(0.2, 0.2) translate(0, 0) rotate(-45deg); }
+    10% { opacity: 1; transform: scale(0.2, 0.3) translate(0, -3px) rotate(-45deg); }
+    60% { opacity: 0.6; transform: scale(0.3, 0.5) translate(-7px, -60px) rotate(-45deg); }
+    100% { opacity: 0; transform: scale(0.4, 0.8) translate(-15px, -90px) rotate(-45deg); }
+}
+
+@keyframes smokeRight {
+    0% { transform: scale(0.2, 0.2) translate(0, 0) rotate(-45deg); }
+    10% { opacity: 1; transform: scale(0.2, 0.3) translate(0, -3px) rotate(-45deg); }
+    60% { opacity: 0.6; transform: scale(0.3, 0.5) translate(7px, -60px) rotate(-45deg); }
+    100% { opacity: 0; transform: scale(0.4, 0.8) translate(15px, -90px) rotate(-45deg); }
+}
+
+.smoke .s-0 { animation: smokeLeft 7s 0s infinite; }
+.smoke .s-1 { animation: smokeRight 7s 0.7s infinite; }
+.smoke .s-2 { animation: smokeLeft 7s 1.4s infinite; }
+.smoke .s-3 { animation: smokeRight 7s 2.1s infinite; }
+.smoke .s-4 { animation: smokeLeft 7s 2.8s infinite; }
+.smoke .s-5 { animation: smokeRight 7s 3.5s infinite; }
+.smoke .s-6 { animation: smokeLeft 7s 4.2s infinite; }
+.smoke .s-7 { animation: smokeRight 7s 4.9s infinite; }
+.smoke .s-8 { animation: smokeLeft 7s 5.6s infinite; }
+.smoke .s-9 { animation: smokeRight 7s 6.3s infinite; }
+
+/* Fire-off state (light theme) */
+body:not(.fire-on) .section-center { box-shadow: 0 0 50px 5px rgba(200,200,200,.2); }
+body:not(.fire-on) .smoke { opacity: 1; transition-delay: 0.8s; }
+body:not(.fire-on) .fire span { bottom: -26px; transform: scale(0.15, 0.15) rotate(45deg); }

static/css/fire-animation.css

@@ -0,0 +1,223 @@
+/* /app/static/css/fire-animation.css */
+
+/* Removed html, body, stage styles */
+
+.minifire-container { /* Add a wrapper for positioning/sizing */
+  display: flex;
+  align-items: center;
+  justify-content: center;
+  position: relative;
+  height: 130px; /* Overall height of the animation area */
+  overflow: hidden; /* Hide parts extending beyond the container */
+  background-color: #270537; /* Optional: Add a background */
+  border-radius: 4px;
+  border: 1px solid #444;
+  margin-top: 0.5rem; /* Space above animation */
+}
+
+.minifire-campfire {
+  position: relative;
+  /* Base size significantly reduced (original was 600px) */
+  width: 150px;
+  height: 150px;
+  transform-origin: bottom center;
+  /* Scale down slightly more if needed, adjusted positioning based on origin */
+  transform: scale(0.8) translateY(15px); /* Pushes it down slightly */
+}
+
+/* --- Scaled Down Logs --- */
+.minifire-log {
+  position: absolute;
+  width: 60px; /* 238/4 */
+  height: 18px; /* 70/4 */
+  border-radius: 8px; /* 32/4 */
+  background: #781e20;
+  overflow: hidden;
+  opacity: 0.99;
+  transform-origin: center center;
+  box-shadow: 0 0 1px 0.5px rgba(0,0,0,0.15); /* Scaled shadow */
+}
+
+.minifire-log:before {
+  content: '';
+  display: block;
+  position: absolute;
+  top: 50%;
+  left: 9px; /* 35/4 */
+  width: 2px; /* 8/4 */
+  height: 2px; /* 8/4 */
+  border-radius: 8px; /* 32/4 */
+  background: #b35050;
+  transform: translate(-50%, -50%);
+  z-index: 3;
+  /* Scaled box-shadows */
+  box-shadow: 0 0 0 0.5px #781e20, /* 2.5/4 -> 0.6 -> 0.5 */
+              0 0 0 2.5px #b35050, /* 10.5/4 -> 2.6 -> 2.5 */
+              0 0 0 3.5px #781e20, /* 13/4 -> 3.25 -> 3.5 */
+              0 0 0 5.5px #b35050, /* 21/4 -> 5.25 -> 5.5 */
+              0 0 0 6px #781e20,   /* 23.5/4 -> 5.9 -> 6 */
+              0 0 0 8px #b35050;   /* 31.5/4 -> 7.9 -> 8 */
+}
+
+.minifire-streak {
+  position: absolute;
+  height: 1px; /* Min height */
+  border-radius: 5px; /* 20/4 */
+  background: #b35050;
+}
+/* Scaled streaks */
+.minifire-streak:nth-child(1) { top: 3px; width: 23px; } /* 10/4, 90/4 */
+.minifire-streak:nth-child(2) { top: 3px; left: 25px; width: 20px; } /* 10/4, 100/4, 80/4 */
+.minifire-streak:nth-child(3) { top: 3px; left: 48px; width: 8px; } /* 10/4, 190/4, 30/4 */
+.minifire-streak:nth-child(4) { top: 6px; width: 33px; } /* 22/4, 132/4 */
+.minifire-streak:nth-child(5) { top: 6px; left: 36px; width: 12px; } /* 22/4, 142/4, 48/4 */
+.minifire-streak:nth-child(6) { top: 6px; left: 50px; width: 7px; } /* 22/4, 200/4, 28/4 */
+.minifire-streak:nth-child(7) { top: 9px; left: 19px; width: 40px; } /* 34/4, 74/4, 160/4 */
+.minifire-streak:nth-child(8) { top: 12px; left: 28px; width: 10px; } /* 46/4, 110/4, 40/4 */
+.minifire-streak:nth-child(9) { top: 12px; left: 43px; width: 14px; } /* 46/4, 170/4, 54/4 */
+.minifire-streak:nth-child(10) { top: 15px; left: 23px; width: 28px; } /* 58/4, 90/4, 110/4 */
+
+/* Scaled Log Positions (Relative to 150px campfire) */
+.minifire-log:nth-child(1) { bottom: 25px; left: 25px; transform: rotate(150deg) scaleX(0.75); z-index: 20; } /* 100/4, 100/4 */
+.minifire-log:nth-child(2) { bottom: 30px; left: 35px; transform: rotate(110deg) scaleX(0.75); z-index: 10; } /* 120/4, 140/4 */
+.minifire-log:nth-child(3) { bottom: 25px; left: 17px; transform: rotate(-10deg) scaleX(0.75); } /* 98/4, 68/4 */
+.minifire-log:nth-child(4) { bottom: 20px; left: 55px; transform: rotate(-120deg) scaleX(0.75); z-index: 26; } /* 80/4, 220/4 */
+.minifire-log:nth-child(5) { bottom: 19px; left: 53px; transform: rotate(-30deg) scaleX(0.75); z-index: 25; } /* 75/4, 210/4 */
+.minifire-log:nth-child(6) { bottom: 23px; left: 70px; transform: rotate(35deg) scaleX(0.85); z-index: 30; } /* 92/4, 280/4 */
+.minifire-log:nth-child(7) { bottom: 18px; left: 75px; transform: rotate(-30deg) scaleX(0.75); z-index: 20; } /* 70/4, 300/4 */
+
+/* --- Scaled Down Sticks --- */
+.minifire-stick {
+  position: absolute;
+  width: 17px; /* 68/4 */
+  height: 5px; /* 20/4 */
+  border-radius: 3px; /* 10/4 */
+  box-shadow: 0 0 1px 0.5px rgba(0,0,0,0.1);
+  background: #781e20;
+  transform-origin: center center;
+}
+.minifire-stick:before {
+  content: '';
+  display: block;
+  position: absolute;
+  bottom: 100%;
+  left: 7px; /* 30/4 -> 7.5 */
+  width: 1.5px; /* 6/4 */
+  height: 5px; /* 20/4 */
+  background: #781e20;
+  border-radius: 3px; /* 10/4 */
+  transform: translateY(50%) rotate(32deg);
+}
+.minifire-stick:after {
+  content: '';
+  display: block;
+  position: absolute;
+  top: 0;
+  right: 0;
+  width: 5px; /* 20/4 */
+  height: 5px; /* 20/4 */
+  background: #b35050;
+  border-radius: 3px; /* 10/4 */
+}
+/* Scaled Stick Positions */
+.minifire-stick:nth-child(1) { left: 40px; bottom: 41px; transform: rotate(-152deg) scaleX(0.8); z-index: 12; } /* 158/4, 164/4 */
+.minifire-stick:nth-child(2) { left: 45px; bottom: 8px; transform: rotate(20deg) scaleX(0.9); } /* 180/4, 30/4 */
+.minifire-stick:nth-child(3) { left: 100px; bottom: 10px; transform: rotate(170deg) scaleX(0.9); } /* 400/4, 38/4 */
+.minifire-stick:nth-child(3):before { display: none; }
+.minifire-stick:nth-child(4) { left: 93px; bottom: 38px; transform: rotate(80deg) scaleX(0.9); z-index: 20; } /* 370/4, 150/4 */
+.minifire-stick:nth-child(4):before { display: none; }
+
+/* --- Scaled Down Fire --- */
+.minifire-fire .minifire-flame {
+  position: absolute;
+  transform-origin: bottom center;
+  opacity: 0.9;
+}
+
+/* Red Flames */
+.minifire-fire__red .minifire-flame {
+  width: 12px; /* 48/4 */
+  border-radius: 12px; /* 48/4 */
+  background: #e20f00;
+  box-shadow: 0 0 20px 5px rgba(226,15,0,0.4); /* Scaled shadow */
+}
+/* Scaled positions/heights */
+.minifire-fire__red .minifire-flame:nth-child(1) { left: 35px; height: 40px; bottom: 25px; animation: minifire-fire 2s 0.15s ease-in-out infinite alternate; } /* 138/4, 160/4, 100/4 */
+.minifire-fire__red .minifire-flame:nth-child(2) { left: 47px; height: 60px; bottom: 25px; animation: minifire-fire 2s 0.35s ease-in-out infinite alternate; } /* 186/4, 240/4, 100/4 */
+.minifire-fire__red .minifire-flame:nth-child(3) { left: 59px; height: 75px; bottom: 25px; animation: minifire-fire 2s 0.1s ease-in-out infinite alternate; } /* 234/4, 300/4, 100/4 */
+.minifire-fire__red .minifire-flame:nth-child(4) { left: 71px; height: 90px; bottom: 25px; animation: minifire-fire 2s 0s ease-in-out infinite alternate; } /* 282/4, 360/4, 100/4 */
+.minifire-fire__red .minifire-flame:nth-child(5) { left: 83px; height: 78px; bottom: 25px; animation: minifire-fire 2s 0.45s ease-in-out infinite alternate; } /* 330/4, 310/4, 100/4 */
+.minifire-fire__red .minifire-flame:nth-child(6) { left: 95px; height: 58px; bottom: 25px; animation: minifire-fire 2s 0.3s ease-in-out infinite alternate; } /* 378/4, 232/4, 100/4 */
+.minifire-fire__red .minifire-flame:nth-child(7) { left: 107px; height: 35px; bottom: 25px; animation: minifire-fire 2s 0.1s ease-in-out infinite alternate; } /* 426/4, 140/4, 100/4 */
+
+/* Orange Flames */
+.minifire-fire__orange .minifire-flame {
+  width: 12px; border-radius: 12px; background: #ff9c00;
+  box-shadow: 0 0 20px 5px rgba(255,156,0,0.4);
+}
+.minifire-fire__orange .minifire-flame:nth-child(1) { left: 35px; height: 35px; bottom: 25px; animation: minifire-fire 2s 0.05s ease-in-out infinite alternate; }
+.minifire-fire__orange .minifire-flame:nth-child(2) { left: 47px; height: 53px; bottom: 25px; animation: minifire-fire 2s 0.1s ease-in-out infinite alternate; }
+.minifire-fire__orange .minifire-flame:nth-child(3) { left: 59px; height: 63px; bottom: 25px; animation: minifire-fire 2s 0.35s ease-in-out infinite alternate; }
+.minifire-fire__orange .minifire-flame:nth-child(4) { left: 71px; height: 75px; bottom: 25px; animation: minifire-fire 2s 0.4s ease-in-out infinite alternate; }
+.minifire-fire__orange .minifire-flame:nth-child(5) { left: 83px; height: 65px; bottom: 25px; animation: minifire-fire 2s 0.5s ease-in-out infinite alternate; }
+.minifire-fire__orange .minifire-flame:nth-child(6) { left: 95px; height: 51px; bottom: 25px; animation: minifire-fire 2s 0.35s ease-in-out infinite alternate; }
+.minifire-fire__orange .minifire-flame:nth-child(7) { left: 107px; height: 28px; bottom: 25px; animation: minifire-fire 2s 0.1s ease-in-out infinite alternate; }
+
+/* Yellow Flames */
+.minifire-fire__yellow .minifire-flame {
+  width: 12px; border-radius: 12px; background: #ffeb6e;
+  box-shadow: 0 0 20px 5px rgba(255,235,110,0.4);
+}
+.minifire-fire__yellow .minifire-flame:nth-child(1) { left: 47px; height: 35px; bottom: 25px; animation: minifire-fire 2s 0.6s ease-in-out infinite alternate; }
+.minifire-fire__yellow .minifire-flame:nth-child(2) { left: 59px; height: 43px; bottom: 30px; animation: minifire-fire 2s 0.4s ease-in-out infinite alternate; } /* Adjusted bottom slightly */
+.minifire-fire__yellow .minifire-flame:nth-child(3) { left: 71px; height: 60px; bottom: 25px; animation: minifire-fire 2s 0.38s ease-in-out infinite alternate; }
+.minifire-fire__yellow .minifire-flame:nth-child(4) { left: 83px; height: 50px; bottom: 25px; animation: minifire-fire 2s 0.22s ease-in-out infinite alternate; }
+.minifire-fire__yellow .minifire-flame:nth-child(5) { left: 95px; height: 36px; bottom: 25px; animation: minifire-fire 2s 0.18s ease-in-out infinite alternate; }
+
+/* White Flames */
+.minifire-fire__white .minifire-flame {
+  width: 12px; border-radius: 12px; background: #fef1d9;
+  box-shadow: 0 0 20px 5px rgba(254,241,217,0.4);
+}
+.minifire-fire__white .minifire-flame:nth-child(1) { left: 39px; width: 8px; height: 25px; bottom: 25px; animation: minifire-fire 2s 0.22s ease-in-out infinite alternate; } /* Scaled width too */
+.minifire-fire__white .minifire-flame:nth-child(2) { left: 45px; width: 8px; height: 30px; bottom: 25px; animation: minifire-fire 2s 0.42s ease-in-out infinite alternate; }
+.minifire-fire__white .minifire-flame:nth-child(3) { left: 59px; height: 43px; bottom: 25px; animation: minifire-fire 2s 0.32s ease-in-out infinite alternate; }
+.minifire-fire__white .minifire-flame:nth-child(4) { left: 71px; height: 53px; bottom: 25px; animation: minifire-fire 2s 0.8s ease-in-out infinite alternate; }
+.minifire-fire__white .minifire-flame:nth-child(5) { left: 83px; height: 43px; bottom: 25px; animation: minifire-fire 2s 0.85s ease-in-out infinite alternate; }
+.minifire-fire__white .minifire-flame:nth-child(6) { left: 95px; width: 8px; height: 28px; bottom: 25px; animation: minifire-fire 2s 0.64s ease-in-out infinite alternate; }
+.minifire-fire__white .minifire-flame:nth-child(7) { left: 102px; width: 8px; height: 25px; bottom: 25px; animation: minifire-fire 2s 0.32s ease-in-out infinite alternate; }
+
+/* --- Scaled Down Sparks --- */
+.minifire-spark {
+  position: absolute;
+  width: 1.5px; /* 6/4 */
+  height: 5px; /* 20/4 */
+  background: #fef1d9;
+  border-radius: 5px; /* 18/4 -> 4.5 */
+  z-index: 50;
+  transform-origin: bottom center;
+  transform: scaleY(0);
+}
+/* Scaled spark positions/animations */
+.minifire-spark:nth-child(1) { left: 40px; bottom: 53px; animation: minifire-spark 1s 0.4s linear infinite; } /* 160/4, 212/4 */
+.minifire-spark:nth-child(2) { left: 45px; bottom: 60px; animation: minifire-spark 1s 1s linear infinite; } /* 180/4, 240/4 */
+.minifire-spark:nth-child(3) { left: 52px; bottom: 80px; animation: minifire-spark 1s 0.8s linear infinite; } /* 208/4, 320/4 */
+.minifire-spark:nth-child(4) { left: 78px; bottom: 100px; animation: minifire-spark 1s 2s linear infinite; } /* 310/4, 400/4 */
+.minifire-spark:nth-child(5) { left: 90px; bottom: 95px; animation: minifire-spark 1s 0.75s linear infinite; } /* 360/4, 380/4 */
+.minifire-spark:nth-child(6) { left: 98px; bottom: 80px; animation: minifire-spark 1s 0.65s linear infinite; } /* 390/4, 320/4 */
+.minifire-spark:nth-child(7) { left: 100px; bottom: 70px; animation: minifire-spark 1s 1s linear infinite; } /* 400/4, 280/4 */
+.minifire-spark:nth-child(8) { left: 108px; bottom: 53px; animation: minifire-spark 1s 1.4s linear infinite; } /* 430/4, 210/4 */
+
+/* --- Keyframes (Rename to avoid conflicts) --- */
+/* Use the same keyframe logic, just rename them */
+@keyframes minifire-fire {
+  0% { transform: scaleY(1); } 28% { transform: scaleY(0.7); } 38% { transform: scaleY(0.8); } 50% { transform: scaleY(0.6); } 70% { transform: scaleY(0.95); } 82% { transform: scaleY(0.58); } 100% { transform: scaleY(1); }
+}
+@keyframes minifire-spark {
+  0%, 35% { transform: scaleY(0) translateY(0); opacity: 0; }
+  50% { transform: scaleY(1) translateY(0); opacity: 1; }
+  /* Adjusted translateY for smaller scale */
+  70% { transform: scaleY(1) translateY(-3px); opacity: 1; } /* 10/4 -> 2.5 -> 3 */
+  75% { transform: scaleY(1) translateY(-3px); opacity: 0; }
+  100% { transform: scaleY(0) translateY(0); opacity: 0; }
+}

supervisord.conf

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

templates/_flash_messages.html

@@ -0,0 +1,24 @@
+{# templates/_flash_messages.html #}
+
+{# Check if there are any flashed messages #}
+{% with messages = get_flashed_messages(with_categories=true) %}
+  {% if messages %}
+    {# Loop through messages and display them as Bootstrap alerts #}
+    {% for category, message in messages %}
+      {# Map Flask message categories (e.g., 'error', 'success', 'warning') to Bootstrap alert classes #}
+      {% set alert_class = 'alert-info' %} {# Default class #}
+      {% if category == 'error' or category == 'danger' %}
+        {% set alert_class = 'alert-danger' %}
+      {% elif category == 'success' %}
+        {% set alert_class = 'alert-success' %}
+      {% elif category == 'warning' %}
+        {% set alert_class = 'alert-warning' %}
+      {% endif %}
+
+      <div class="alert {{ alert_class }} alert-dismissible fade show" role="alert">
+        {{ message }}
+        <button type="button" class="btn-close" data-bs-dismiss="alert" aria-label="Close"></button>
+      </div>
+    {% endfor %}
+  {% endif %}
+{% endwith %}

templates/_search_results_table.html

@@ -0,0 +1,113 @@
+{# templates/_search_results_table.html #}
+{# This partial template renders the search results table and pagination #}
+
+{% if packages %}
+    <table class="table table-striped table-hover">
+        <thead>
+            <tr>
+                <th scope="col">Package</th>
+                <th scope="col">Latest</th>
+                <th scope="col">Author</th>
+                <th scope="col">FHIR</th>
+                <th scope="col">Versions</th>
+                <!-- <th scope="col">Canonical</th> -->
+                {# Add Dependencies header if needed based on your data #}
+                {# <th scope="col">Dependencies</th> #}
+            </tr>
+        </thead>
+        <tbody>
+            {% for pkg in packages %}
+            <tr>
+                <td>
+                    <i class="bi bi-box-seam me-2"></i>
+                    {# Link to package details page - adjust if endpoint name is different #}
+                    <a class="text-primary"
+                       href="{{ url_for('package_details_view', name=pkg.name) }}"
+                       {# Optional: Add HTMX GET for inline details if desired #}
+                       {# hx-get="{{ url_for('package_details', name=pkg.name) }}" #}
+                       {# hx-target="#search-results" #}
+                       >
+                       {{ pkg.name }}
+                    </a>
+                </td>
+                <td>{{ pkg.display_version }}</td>
+                <td>{{ pkg.author or '' }}</td>
+                <td>{{ pkg.fhir_version or '' }}</td>
+                <td>{{ pkg.version_count }}</td>
+                <!-- <td>{{ pkg.canonical or '' }}</td> -->
+                {# Add Dependencies data if needed #}
+                {# <td>{{ pkg.dependencies | join(', ') if pkg.dependencies else '' }}</td> #}
+            </tr>
+            {% endfor %}
+        </tbody>
+    </table>
+
+    {# Pagination Controls - Ensure 'pagination' object is passed from the route #}
+    {% if pagination and pagination.pages > 1 %}
+    <nav aria-label="Page navigation">
+        <ul class="pagination justify-content-center">
+            {# Previous Page Link #}
+            {% if pagination.has_prev %}
+            <li class="page-item">
+                {# Use hx-get for HTMX-powered pagination within the results area #}
+                <a class="page-link"
+                   href="{{ url_for('search_and_import', page=pagination.prev_num, search=request.args.get('search', '')) }}" {# Keep standard link for non-JS fallback #}
+                   hx-get="{{ url_for('api_search_packages', page=pagination.prev_num, search=request.args.get('search', '')) }}" {# HTMX target #}
+                   hx-target="#search-results"
+                   hx-indicator=".htmx-indicator"
+                   aria-label="Previous">
+                    <span aria-hidden="true">&laquo;</span>
+                </a>
+            </li>
+            {% else %}
+            <li class="page-item disabled">
+                <span class="page-link">&laquo;</span>
+            </li>
+            {% endif %}
+
+            {# Page Number Links #}
+            {% for p in pagination.iter_pages %} {# Iterate over the pre-computed list #}
+                {% if p %}
+                    <li class="page-item {% if p == pagination.page %}active{% endif %}">
+                         <a class="page-link"
+                            href="{{ url_for('search_and_import', page=p, search=request.args.get('search', '')) }}"
+                            hx-get="{{ url_for('api_search_packages', page=p, search=request.args.get('search', '')) }}"
+                            hx-target="#search-results"
+                            hx-indicator=".htmx-indicator">
+                            {{ p }}
+                         </a>
+                    </li>
+                {% else %}
+                    {# Ellipsis for skipped pages #}
+                    <li class="page-item disabled"><span class="page-link">...</span></li>
+                {% endif %}
+            {% endfor %}
+
+            {# Next Page Link #}
+            {% if pagination.has_next %}
+            <li class="page-item">
+                 <a class="page-link"
+                    href="{{ url_for('search_and_import', page=pagination.next_num, search=request.args.get('search', '')) }}"
+                    hx-get="{{ url_for('api_search_packages', page=pagination.next_num, search=request.args.get('search', '')) }}"
+                    hx-target="#search-results"
+                    hx-indicator=".htmx-indicator"
+                    aria-label="Next">
+                    <span aria-hidden="true">&raquo;</span>
+                </a>
+            </li>
+             {% else %}
+            <li class="page-item disabled">
+                <span class="page-link">&raquo;</span>
+            </li>
+            {% endif %}
+        </ul>
+    </nav>
+    {% endif %} {# End pagination nav #}
+
+{% elif request and request.args.get('search') %}
+    {# Message when search term is present but no results found #}
+     <p class="text-muted text-center mt-3">No packages found matching your search term.</p>
+{% else %}
+    {# Initial message before any search #}
+    <p class="text-muted text-center mt-3">Start typing in the search box above to find packages.</p>
+{% endif %}

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 HAPI FHIR server 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 FHIR server depending 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 HAPI FHIR server (accessible via the `/fhir` proxy) for local validation and exploration.
+                     <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.
                  </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 HAPI 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 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 HAPI 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 Local 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>
 

templates/base.html

@@ -1,15 +1,22 @@
 <!DOCTYPE html>
-<html lang="en">
+<html lang="en" data-theme="{% if request.cookies.get('theme') == 'dark' %}dark{% else %}light{% endif %}">
 <head>
     <meta charset="utf-8">
     <meta name="viewport" content="width=device-width, initial-scale=1">
     <link href="https://cdn.jsdelivr.net/npm/bootstrap@5.3.3/dist/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-QWTKZyjpPEjISv5WaRU9OFeRpok6YctnYmDr5pNlyT2bRjXh0JMhjY6hW+ALEwIH" crossorigin="anonymous">
     <link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/bootstrap-icons@1.11.3/font/bootstrap-icons.min.css">
-    <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.4.2/css/all.min.css" integrity="sha512-z3gLpd7yknf1YoNbCzqRKc4qyor8gaKU1qmn+CShxbuBusANI9QpRohGBreCFkKxLhei6S9CQXFEbbKuqLg0DA==" crossorigin="anonymous" referrerpolicy="no-referrer" />
+    <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.4.2/css/all.min.css" xintegrity="sha512-z3gLpd7yknf1YoNbCzqRKc4qyor8gaKU1qmn+CShxbuBusANI9QpRohGBreCFkKxLhei6S9CQXFEbbKuqLg0DA==" crossorigin="anonymous" referrerpolicy="no-referrer" />
     <link href="https://cdnjs.cloudflare.com/ajax/libs/prism/1.29.0/themes/prism-okaidia.min.css" rel="stylesheet" />
     <link rel="icon" type="image/x-icon" href="{{ url_for('static', filename='favicon.ico') }}">
+    <link rel="stylesheet" href="{{ url_for('static', filename='css/fire-animation.css') }}">
+    <link rel="stylesheet" href="{{ url_for('static', filename='css/animation.css') }}">
+    <script src="{{ url_for('static', filename='js/htmx.min.js') }}"></script>
     <title>{% if app_mode == 'lite' %}(Lite Version) {% endif %}{% if title %}{{ title }} - {% endif %}{{ site_name }}</title>
     <style>
+        /* Prevent flash of unstyled content */
+        :root { visibility: hidden; }
+        [data-theme="dark"], [data-theme="light"] { visibility: visible; }
+
         /* Default (Light Theme) Styles */
         body {
             font-family: 'Inter', -apple-system, BlinkMacSystemFont, 'Segoe UI', Roboto, sans-serif;
@@ -177,44 +184,44 @@
              background: inherit; /* Ensure background comes from pre or theme */
         }
 
-/* General Button Theme (Primary, Secondary) */
-.btn-primary {
+        /* General Button Theme (Primary, Secondary) */
+        .btn-primary {
             background-color: #007bff;
             border-color: #007bff;
             color: white;
-}
-.btn-primary:hover {
+        }
+        .btn-primary:hover {
             background-color: #0056b3;
             border-color: #004085;
-}
-.btn-outline-primary {
+        }
+        .btn-outline-primary {
             color: #007bff;
             border-color: #007bff;
-}
-.btn-outline-primary:hover {
+        }
+        .btn-outline-primary:hover {
             background-color: #007bff;
             color: white;
-}
+        }
 
-.btn-secondary {
+        .btn-secondary {
             background-color: #6c757d;
             border-color: #6c757d;
             color: white;
-}
-.btn-secondary:hover {
+        }
+        .btn-secondary:hover {
             background-color: #5a6268;
             border-color: #545b62;
-}
-.btn-outline-secondary {
+        }
+        .btn-outline-secondary {
             color: #6c757d;
             border-color: #6c757d;
-}
-.btn-outline-secondary:hover {
+        }
+        .btn-outline-secondary:hover {
             background-color: #6c757d;
             color: white;
-}
+        }
 
-/* --- Prism.js Theme Overrides for Light Mode --- */
+        /* --- Prism.js Theme Overrides for Light Mode --- */
 
         /* Target code blocks only when NOT in dark theme */
         html:not([data-theme="dark"]) .token.punctuation,
@@ -256,19 +263,19 @@
 
         /* --- End Prism.js Overrides --- */
 
-/* --- Theme Styles for FSH Code Blocks --- */
-pre, pre code {
+        /* --- Theme Styles for FSH Code Blocks --- */
+        pre, pre code {
             font-family: SFMono-Regular, Menlo, Monaco, Consolas, "Liberation Mono", "Courier New", monospace;
             font-size: 0.875em;
             white-space: pre-wrap; /* Allow wrapping */
             word-break: break-all; /* Break long lines */
-}
+        }
 
-/* Target pre blocks specifically used for FSH output if needed */
-/* If the pre block has a specific class or ID, use that */
-#fsh-output pre, /* Targets any pre within the output container */
-._fsh_output pre /* Targets any pre within the partial template content */
-{
+        /* Target pre blocks specifically used for FSH output if needed */
+        /* If the pre block has a specific class or ID, use that */
+        #fsh-output pre, /* Targets any pre within the output container */
+        ._fsh_output pre /* Targets any pre within the partial template content */
+        {
             background-color: #e9ecef; /* Light theme background */
             color: #212529; /* Light theme text */
             border: 1px solid #dee2e6;
@@ -276,297 +283,294 @@ pre, pre code {
             padding: 10px;
             max-height: 600px; /* Adjust as needed */
             overflow: auto;
-}
+        }
 
-#fsh-output pre code,
-._fsh_output pre code {
+        #fsh-output pre code,
+        ._fsh_output pre code {
              background-color: transparent !important; /* Ensure code tag doesn't override pre bg */
              padding: 0;
              color: inherit; /* Inherit text color from pre */
              font-size: inherit; /* Inherit font size from pre */
              display: block; /* Make code fill pre */
-}
+        }
 
-
-/* Dark Theme Override */
-html[data-theme="dark"] #fsh-output pre,
-html[data-theme="dark"] ._fsh_output pre
- {
+        /* Dark Theme Override */
+        html[data-theme="dark"] #fsh-output pre,
+        html[data-theme="dark"] ._fsh_output pre {
             background-color: #495057; /* Dark theme background */
             color: #f8f9fa; /* Dark theme text */
             border-color: #6c757d;
-}
+        }
 
         html[data-theme="dark"] #fsh-output pre code,
         html[data-theme="dark"] ._fsh_output pre code {
             color: inherit;
         }
 
-/* --- Theme Styles for FHIR UI Operations (fhir_ui_operations.html) --- */
+        /* --- Theme Styles for FHIR UI Operations (fhir_ui_operations.html) --- */
 
-/* Operation Block Container */
-.opblock {
+        /* Operation Block Container */
+        .opblock {
             border: 1px solid #dee2e6; /* Light theme border */
             background: #ffffff; /* Light theme background */
             color: #212529; /* Light theme text */
-}
-html[data-theme="dark"] .opblock {
+        }
+        html[data-theme="dark"] .opblock {
             border-color: #495057; /* Dark theme border */
             background: #343a40; /* Dark theme background (card bg) */
             color: #f8f9fa; /* Dark theme text */
-}
+        }
 
-/* Operation Summary (Header) */
-.opblock-summary {
+        /* Operation Summary (Header) */
+        .opblock-summary {
             background: #f8f9fa; /* Light theme summary bg */
             border-bottom: 1px solid #dee2e6;
             color: #212529; /* Default text color for summary */
-}
-.opblock-summary:hover {
+        }
+        .opblock-summary:hover {
             background: #e9ecef;
-}
-html[data-theme="dark"] .opblock-summary {
+        }
+        html[data-theme="dark"] .opblock-summary {
             background: #40464c; /* Darker summary bg */
             border-bottom-color: #495057;
             color: #f8f9fa;
-}
-html[data-theme="dark"] .opblock-summary:hover {
+        }
+        html[data-theme="dark"] .opblock-summary:hover {
             background: #495057;
-}
-/* Keep method badge colors fixed - DO NOT override .opblock-summary-method */
-.opblock-summary-description {
+        }
+        /* Keep method badge colors fixed - DO NOT override .opblock-summary-method */
+        .opblock-summary-description {
             color: #495057; /* Slightly muted description text */
-}
-html[data-theme="dark"] .opblock-summary-description {
+        }
+        html[data-theme="dark"] .opblock-summary-description {
             color: #adb5bd; /* Lighter muted text for dark */
-}
+        }
 
-/* Operation Body (Expanded Section) */
-.opblock-body {
+        /* Operation Body (Expanded Section) */
+        .opblock-body {
             border-top: 1px solid #dee2e6;
-}
-html[data-theme="dark"] .opblock-body {
+        }
+        html[data-theme="dark"] .opblock-body {
             border-top-color: #495057;
-}
+        }
 
-/* Section Headers within Body */
-.opblock-section-header {
+        /* Section Headers within Body */
+        .opblock-section-header {
             border-bottom: 1px solid #eee;
             color: inherit; /* Inherit from .opblock */
-}
-html[data-theme="dark"] .opblock-section-header {
+        }
+        html[data-theme="dark"] .opblock-section-header {
             border-bottom-color: #495057;
-}
-.opblock-title {
+        }
+        .opblock-title {
              color: inherit; /* Inherit from .opblock */
-}
+        }
 
-/* Parameters Table */
-.parameters-table th,
-.parameters-table td {
+        /* Parameters Table */
+        .parameters-table th,
+        .parameters-table td {
             border: 1px solid #dee2e6;
             color: inherit; /* Inherit from .opblock */
-}
-html[data-theme="dark"] .parameters-table th,
-html[data-theme="dark"] .parameters-table td {
+        }
+        html[data-theme="dark"] .parameters-table th,
+        html[data-theme="dark"] .parameters-table td {
             border-color: #495057;
-}
-.parameter__type,
-.parameter__in {
+        }
+        .parameter__type,
+        .parameter__in {
             color: #6c757d; /* Use standard muted color */
-}
-html[data-theme="dark"] .parameter__type,
-html[data-theme="dark"] .parameter__in {
+        }
+        html[data-theme="dark"] .parameter__type,
+        html[data-theme="dark"] .parameter__in {
             color: #adb5bd; /* Use standard dark muted color */
-}
-.parameters-col_description input[type="text"],
-.parameters-col_description input[type="number"] {
+        }
+        .parameters-col_description input[type="text"],
+        .parameters-col_description input[type="number"] {
             background-color: #fff; /* Match light form controls */
             border: 1px solid #ced4da;
             color: #212529;
-}
-html[data-theme="dark"] .parameters-col_description input[type="text"],
-html[data-theme="dark"] .parameters-col_description input[type="number"] {
+        }
+        html[data-theme="dark"] .parameters-col_description input[type="text"],
+        html[data-theme="dark"] .parameters-col_description input[type="number"] {
             background-color: #495057; /* Match dark form controls */
             border-color: #6c757d;
             color: #f8f9fa;
-}
+        }
 
-/* Request Body Textarea */
-.request-body-textarea {
+        /* Request Body Textarea */
+        .request-body-textarea {
             background-color: #fff; /* Match light form controls */
             border: 1px solid #ced4da;
             color: #212529;
-}
-html[data-theme="dark"] .request-body-textarea {
+        }
+        html[data-theme="dark"] .request-body-textarea {
             background-color: #495057; /* Match dark form controls */
             border-color: #6c757d;
             color: #f8f9fa;
-}
+        }
 
-/* Responses Table */
-.responses-table th,
-.responses-table td {
+        /* Responses Table */
+        .responses-table th,
+        .responses-table td {
             border: 1px solid #dee2e6;
             color: inherit;
-}
-html[data-theme="dark"] .responses-table th,
-html[data-theme="dark"] .responses-table td {
+        }
+        html[data-theme="dark"] .responses-table th,
+        html[data-theme="dark"] .responses-table td {
             border-color: #495057;
-}
+        }
 
-/* Example/Schema Tabs & Controls */
-.response-control-media-type {
+        /* Example/Schema Tabs & Controls */
+        .response-control-media-type {
             background-color: #f8f9fa;
-}
-html[data-theme="dark"] .response-control-media-type {
+        }
+        html[data-theme="dark"] .response-control-media-type {
             background-color: #40464c; /* Match summary header bg */
-}
-.tablinks.badge { /* Default inactive tab */
+        }
+        .tablinks.badge { /* Default inactive tab */
             background: #dee2e6 !important; /* Light grey inactive */
             color: #333 !important;
-}
-.tablinks.badge.active { /* Default active tab */
+        }
+        .tablinks.badge.active { /* Default active tab */
             background: #007bff !important; /* Use primary color */
             color: white !important;
-}
-html[data-theme="dark"] .tablinks.badge { /* Dark inactive tab */
+        }
+        html[data-theme="dark"] .tablinks.badge { /* Dark inactive tab */
             background: #6c757d !important; /* Dark grey inactive */
             color: white !important;
-}
-html[data-theme="dark"] .tablinks.badge.active { /* Dark active tab */
+        }
+        html[data-theme="dark"] .tablinks.badge.active { /* Dark active tab */
             background: #4dabf7 !important; /* Use dark primary color */
             color: #000 !important;
-}
+        }
 
-/* Code/Output Blocks */
-.highlight-code,
-.request-url-output,
-.curl-output,
-.execute-wrapper pre.response-output-content {
+        /* Code/Output Blocks */
+        .highlight-code,
+        .request-url-output,
+        .curl-output,
+        .execute-wrapper pre.response-output-content {
             background: #e9ecef; /* Light theme pre background */
             color: #212529;
             border: 1px solid #dee2e6;
-}
-html[data-theme="dark"] .highlight-code,
-html[data-theme="dark"] .request-url-output,
-html[data-theme="dark"] .curl-output,
-html[data-theme="dark"] .execute-wrapper pre.response-output-content {
+        }
+        html[data-theme="dark"] .highlight-code,
+        html[data-theme="dark"] .request-url-output,
+        html[data-theme="dark"] .curl-output,
+        html[data-theme="dark"] .execute-wrapper pre.response-output-content {
             background: #495057; /* Dark theme pre background */
             color: #f8f9fa;
             border-color: #6c757d;
-}
+        }
 
-/* Narrative Response Box */
-.execute-wrapper div.response-output-narrative {
+        /* Narrative Response Box */
+        .execute-wrapper div.response-output-narrative {
              background: #ffffff;
              color: #212529;
              border: 1px solid #dee2e6;
-}
-html[data-theme="dark"] .execute-wrapper div.response-output-narrative {
+        }
+        html[data-theme="dark"] .execute-wrapper div.response-output-narrative {
              background: #343a40; /* Match card body */
              color: #f8f9fa;
              border: 1px solid #495057;
-}
+        }
 
-/* Response Status Text */
-.execute-wrapper .response-status[style*="color: green"] { color: #198754 !important; }
-.execute-wrapper .response-status[style*="color: red"] { color: #dc3545 !important; }
-html[data-theme="dark"] .execute-wrapper .response-status[style*="color: green"] { color: #20c997 !important; }
-html[data-theme="dark"] .execute-wrapper .response-status[style*="color: red"] { color: #e63946 !important; }
+        /* Response Status Text */
+        .execute-wrapper .response-status[style*="color: green"] { color: #198754 !important; }
+        .execute-wrapper .response-status[style*="color: red"] { color: #dc3545 !important; }
+        html[data-theme="dark"] .execute-wrapper .response-status[style*="color: green"] { color: #20c997 !important; }
+        html[data-theme="dark"] .execute-wrapper .response-status[style*="color: red"] { color: #e63946 !important; }
 
+        /* Specific Action Buttons (Success, Danger, Warning, Info) */
+        .btn-success { background-color: #198754; border-color: #198754; color: white; }
+        .btn-success:hover { background-color: #157347; border-color: #146c43; }
+        .btn-outline-success { color: #198754; border-color: #198754; }
+        .btn-outline-success:hover { background-color: #198754; color: white; }
 
-/* Specific Action Buttons (Success, Danger, Warning, Info) */
-.btn-success { background-color: #198754; border-color: #198754; color: white; }
-.btn-success:hover { background-color: #157347; border-color: #146c43; }
-.btn-outline-success { color: #198754; border-color: #198754; }
-.btn-outline-success:hover { background-color: #198754; color: white; }
+        .btn-danger { background-color: #dc3545; border-color: #dc3545; color: white; }
+        .btn-danger:hover { background-color: #bb2d3b; border-color: #b02a37; }
+        .btn-outline-danger { color: #dc3545; border-color: #dc3545; }
+        .btn-outline-danger:hover { background-color: #dc3545; color: white; }
 
-.btn-danger { background-color: #dc3545; border-color: #dc3545; color: white; }
-.btn-danger:hover { background-color: #bb2d3b; border-color: #b02a37; }
-.btn-outline-danger { color: #dc3545; border-color: #dc3545; }
-.btn-outline-danger:hover { background-color: #dc3545; color: white; }
+        .btn-warning { background-color: #ffc107; border-color: #ffc107; color: #000; }
+        .btn-warning:hover { background-color: #ffca2c; border-color: #ffc720; }
+        .btn-outline-warning { color: #ffc107; border-color: #ffc107; }
+        .btn-outline-warning:hover { background-color: #ffc107; color: #000; }
 
-.btn-warning { background-color: #ffc107; border-color: #ffc107; color: #000; }
-.btn-warning:hover { background-color: #ffca2c; border-color: #ffc720; }
-.btn-outline-warning { color: #ffc107; border-color: #ffc107; }
-.btn-outline-warning:hover { background-color: #ffc107; color: #000; }
+        .btn-info { background-color: #0dcaf0; border-color: #0dcaf0; color: #000; }
+        .btn-info:hover { background-color: #31d2f2; border-color: #25cff2; }
+        .btn-outline-info { color: #0dcaf0; border-color: #0dcaf0; }
+        .btn-outline-info:hover { background-color: #0dcaf0; color: #000; }
 
-.btn-info { background-color: #0dcaf0; border-color: #0dcaf0; color: #000; }
-.btn-info:hover { background-color: #31d2f2; border-color: #25cff2; }
-.btn-outline-info { color: #0dcaf0; border-color: #0dcaf0; }
-.btn-outline-info:hover { background-color: #0dcaf0; color: #000; }
-
-/* General Badge Theme */
-.badge {
+        /* General Badge Theme */
+        .badge {
             padding: 0.4em 0.6em; /* Slightly larger padding */
             font-size: 0.85em;
             font-weight: 600;
-}
-/* Specific Badge Backgrounds (Add more as needed) */
-.badge.bg-primary { background-color: #007bff !important; color: white !important; }
-.badge.bg-secondary { background-color: #6c757d !important; color: white !important; }
-.badge.bg-success { background-color: #198754 !important; color: white !important; }
-.badge.bg-danger { background-color: #dc3545 !important; color: white !important; }
-.badge.bg-warning { background-color: #ffc107 !important; color: #000 !important; }
-.badge.bg-info { background-color: #0dcaf0 !important; color: #000 !important; }
-.badge.bg-light { background-color: #f8f9fa !important; color: #000 !important; border: 1px solid #dee2e6; }
-.badge.bg-dark { background-color: #343a40 !important; color: white !important; }
+        }
+        /* Specific Badge Backgrounds (Add more as needed) */
+        .badge.bg-primary { background-color: #007bff !important; color: white !important; }
+        .badge.bg-secondary { background-color: #6c757d !important; color: white !important; }
+        .badge.bg-success { background-color: #198754 !important; color: white !important; }
+        .badge.bg-danger { background-color: #dc3545 !important; color: white !important; }
+        .badge.bg-warning { background-color: #ffc107 !important; color: #000 !important; }
+        .badge.bg-info { background-color: #0dcaf0 !important; color: #000 !important; }
+        .badge.bg-light { background-color: #f8f9fa !important; color: #000 !important; border: 1px solid #dee2e6; }
+        .badge.bg-dark { background-color: #343a40 !important; color: white !important; }
 
-/* Copy Button Specific Style */
-.btn-copy { /* Optional: Add a specific class if needed, or style .btn-outline-secondary directly */
+        /* Copy Button Specific Style */
+        .btn-copy { /* Optional: Add a specific class if needed, or style .btn-outline-secondary directly */
             padding: 0.25rem 0.5rem;
             font-size: 0.875rem;
             line-height: 1.5;
-}
+        }
 
-/* --- Dark Theme Overrides --- */
-html[data-theme="dark"] .btn-primary { background-color: #4dabf7; border-color: #4dabf7; color: #000; }
-html[data-theme="dark"] .btn-primary:hover { background-color: #68bcef; border-color: #5fb7ea; }
-html[data-theme="dark"] .btn-outline-primary { color: #4dabf7; border-color: #4dabf7; }
-html[data-theme="dark"] .btn-outline-primary:hover { background-color: #4dabf7; color: #000; }
+        /* --- Dark Theme Overrides --- */
+        html[data-theme="dark"] .btn-primary { background-color: #4dabf7; border-color: #4dabf7; color: #000; }
+        html[data-theme="dark"] .btn-primary:hover { background-color: #68bcef; border-color: #5fb7ea; }
+        html[data-theme="dark"] .btn-outline-primary { color: #4dabf7; border-color: #4dabf7; }
+        html[data-theme="dark"] .btn-outline-primary:hover { background-color: #4dabf7; color: #000; }
 
-html[data-theme="dark"] .btn-secondary { background-color: #6c757d; border-color: #6c757d; color: white; }
-html[data-theme="dark"] .btn-secondary:hover { background-color: #5a6268; border-color: #545b62; }
-html[data-theme="dark"] .btn-outline-secondary { color: #adb5bd; border-color: #6c757d; } /* Lighter text/border */
-html[data-theme="dark"] .btn-outline-secondary:hover { background-color: #6c757d; color: white; }
+        html[data-theme="dark"] .btn-secondary { background-color: #6c757d; border-color: #6c757d; color: white; }
+        html[data-theme="dark"] .btn-secondary:hover { background-color: #5a6268; border-color: #545b62; }
+        html[data-theme="dark"] .btn-outline-secondary { color: #adb5bd; border-color: #6c757d; } /* Lighter text/border */
+        html[data-theme="dark"] .btn-outline-secondary:hover { background-color: #6c757d; color: white; }
 
-html[data-theme="dark"] .btn-success { background-color: #20c997; border-color: #20c997; color: #000; }
-html[data-theme="dark"] .btn-success:hover { background-color: #3ce0ac; border-color: #36d8a3; }
-html[data-theme="dark"] .btn-outline-success { color: #20c997; border-color: #20c997; }
-html[data-theme="dark"] .btn-outline-success:hover { background-color: #20c997; color: #000; }
+        html[data-theme="dark"] .btn-success { background-color: #20c997; border-color: #20c997; color: #000; }
+        html[data-theme="dark"] .btn-success:hover { background-color: #3ce0ac; border-color: #36d8a3; }
+        html[data-theme="dark"] .btn-outline-success { color: #20c997; border-color: #20c997; }
+        html[data-theme="dark"] .btn-outline-success:hover { background-color: #20c997; color: #000; }
 
-/* Keep danger as is */
-html[data-theme="dark"] .btn-danger { background-color: #e63946; border-color: #e63946; color: white; }
-html[data-theme="dark"] .btn-danger:hover { background-color: #c82b39; border-color: #bd2130; }
-html[data-theme="dark"] .btn-outline-danger { color: #e63946; border-color: #e63946; }
-html[data-theme="dark"] .btn-outline-danger:hover { background-color: #e63946; color: white; }
+        /* Keep danger as is */
+        html[data-theme="dark"] .btn-danger { background-color: #e63946; border-color: #e63946; color: white; }
+        html[data-theme="dark"] .btn-danger:hover { background-color: #c82b39; border-color: #bd2130; }
+        html[data-theme="dark"] .btn-outline-danger { color: #e63946; border-color: #e63946; }
+        html[data-theme="dark"] .btn-outline-danger:hover { background-color: #e63946; color: white; }
 
-html[data-theme="dark"] .btn-warning { background-color: #ffca2c; border-color: #ffca2c; color: #000; }
-html[data-theme="dark"] .btn-warning:hover { background-color: #ffd24a; border-color: #ffce3d; }
-html[data-theme="dark"] .btn-outline-warning { color: #ffca2c; border-color: #ffca2c; }
-html[data-theme="dark"] .btn-outline-warning:hover { background-color: #ffca2c; color: #000; }
+        html[data-theme="dark"] .btn-warning { background-color: #ffca2c; border-color: #ffca2c; color: #000; }
+        html[data-theme="dark"] .btn-warning:hover { background-color: #ffd24a; border-color: #ffce3d; }
+        html[data-theme="dark"] .btn-outline-warning { color: #ffca2c; border-color: #ffca2c; }
+        html[data-theme="dark"] .btn-outline-warning:hover { background-color: #ffca2c; color: #000; }
 
-html[data-theme="dark"] .btn-info { background-color: #22b8cf; border-color: #22b8cf; color: #000; }
-html[data-theme="dark"] .btn-info:hover { background-color: #44cee3; border-color: #38cae0; }
-html[data-theme="dark"] .btn-outline-info { color: #22b8cf; border-color: #22b8cf; }
-html[data-theme="dark"] .btn-outline-info:hover { background-color: #22b8cf; color: #000; }
+        html[data-theme="dark"] .btn-info { background-color: #22b8cf; border-color: #22b8cf; color: #000; }
+        html[data-theme="dark"] .btn-info:hover { background-color: #44cee3; border-color: #38cae0; }
+        html[data-theme="dark"] .btn-outline-info { color: #22b8cf; border-color: #22b8cf; }
+        html[data-theme="dark"] .btn-outline-info:hover { background-color: #22b8cf; color: #000; }
 
-/* Dark Theme Badges */
-html[data-theme="dark"] .badge.bg-primary { background-color: #4dabf7 !important; color: #000 !important; }
-html[data-theme="dark"] .badge.bg-secondary { background-color: #6c757d !important; color: white !important; }
-html[data-theme="dark"] .badge.bg-success { background-color: #20c997 !important; color: #000 !important; }
-html[data-theme="dark"] .badge.bg-danger { background-color: #e63946 !important; color: white !important; }
-html[data-theme="dark"] .badge.bg-warning { background-color: #ffca2c !important; color: #000 !important; }
-html[data-theme="dark"] .badge.bg-info { background-color: #22b8cf !important; color: #000 !important; }
-html[data-theme="dark"] .badge.bg-light { background-color: #495057 !important; color: #f8f9fa !important; border: 1px solid #6c757d; }
-html[data-theme="dark"] .badge.bg-dark { background-color: #adb5bd !important; color: #000 !important; }
+        /* Dark Theme Badges */
+        html[data-theme="dark"] .badge.bg-primary { background-color: #4dabf7 !important; color: #000 !important; }
+        html[data-theme="dark"] .badge.bg-secondary { background-color: #6c757d !important; color: white !important; }
+        html[data-theme="dark"] .badge.bg-success { background-color: #20c997 !important; color: #000 !important; }
+        html[data-theme="dark"] .badge.bg-danger { background-color: #e63946 !important; color: white !important; }
+        html[data-theme="dark"] .badge.bg-warning { background-color: #ffca2c !important; color: #000 !important; }
+        html[data-theme="dark"] .badge.bg-info { background-color: #22b8cf !important; color: #000 !important; }
+        html[data-theme="dark"] .badge.bg-light { background-color: #495057 !important; color: #f8f9fa !important; border: 1px solid #6c757d; }
+        html[data-theme="dark"] .badge.bg-dark { background-color: #adb5bd !important; color: #000 !important; }
 
-/* --- Themed Backgrounds for Code/Structure View (cp_view_processed_ig.html) --- */
+        /* --- Themed Backgrounds for Code/Structure View (cp_view_processed_ig.html) --- */
 
-/* Styling for <pre> blocks containing code */
-#raw-structure-wrapper pre,
-#example-content-wrapper pre {
+        /* Styling for <pre> blocks containing code */
+        #raw-structure-wrapper pre,
+        #example-content-wrapper pre {
             background-color: #e9ecef; /* Light theme background */
             color: #212529; /* Light theme text */
             border: 1px solid #dee2e6;
@@ -576,11 +580,11 @@ html[data-theme="dark"] .badge.bg-dark { background-color: #adb5bd !important; c
             overflow-y: auto; /* Keep existing overflow */
             white-space: pre-wrap; /* Ensure wrapping */
             word-break: break-all; /* Break long strings */
-}
+        }
 
-/* Ensure code tag inside inherits background and has appropriate font */
-#raw-structure-wrapper pre code,
-#example-content-wrapper pre code {
+        /* Ensure code tag inside inherits background and has appropriate font */
+        #raw-structure-wrapper pre code,
+        #example-content-wrapper pre code {
             background-color: transparent !important; /* Let pre handle background */
             padding: 0;
             font-family: SFMono-Regular, Menlo, Monaco, Consolas, "Liberation Mono", "Courier New", monospace;
@@ -589,47 +593,47 @@ html[data-theme="dark"] .badge.bg-dark { background-color: #adb5bd !important; c
             display: block; /* Make code block fill pre */
             white-space: pre-wrap;
             word-break: break-all;
-}
+        }
 
-/* Styling for the Structure Definition tree list items */
-.structure-tree-root .list-group-item {
+        /* Styling for the Structure Definition tree list items */
+        .structure-tree-root .list-group-item {
             background-color: #ffffff; /* Light theme default background */
             border-color: #dee2e6;
             color: #212529;
-}
+        }
 
-.structure-tree-root .list-group-item-warning {
+        .structure-tree-root .list-group-item-warning {
             background-color: #fff3cd; /* Bootstrap light theme warning */
             border-color: #ffeeba;
             /*color: #856404;  Ensure text is readable */
-}
+        }
 
-/* --- Dark Theme Overrides for Code/Structure View --- */
-html[data-theme="dark"] #raw-structure-wrapper pre,
-html[data-theme="dark"] #example-content-wrapper pre {
+        /* --- Dark Theme Overrides for Code/Structure View --- */
+        html[data-theme="dark"] #raw-structure-wrapper pre,
+        html[data-theme="dark"] #example-content-wrapper pre {
             background-color: #495057; /* Dark theme background */
             color: #f8f9fa; /* Dark theme text */
             border-color: #6c757d;
-}
+        }
 
-/* Dark theme code text color already inherited, but explicit doesn't hurt */
-html[data-theme="dark"] #raw-structure-wrapper pre code,
-html[data-theme="dark"] #example-content-wrapper pre code {
+        /* Dark theme code text color already inherited, but explicit doesn't hurt */
+        html[data-theme="dark"] #raw-structure-wrapper pre code,
+        html[data-theme="dark"] #example-content-wrapper pre code {
              color: #f8f9fa;
-}
+        }
 
-/* Dark theme structure list items */
-html[data-theme="dark"] .structure-tree-root .list-group-item {
+        /* Dark theme structure list items */
+        html[data-theme="dark"] .structure-tree-root .list-group-item {
             background-color: #343a40; /* Dark theme card background */
             border-color: #495057;
             color: #f8f9fa;
-}
+        }
 
-html[data-theme="dark"] .structure-tree-root .list-group-item-warning {
+        html[data-theme="dark"] .structure-tree-root .list-group-item-warning {
             background-color: #664d03; /* Darker warning background */
             border-color: #997404;
             /*color: #ffecb5; Lighter text for contrast */
-}
+        }
 
         /* Dark Theme Styles */
         html[data-theme="dark"] body {
@@ -750,7 +754,7 @@ html[data-theme="dark"] .structure-tree-root .list-group-item-warning {
         }
     </style>
 </head>
-<body class="d-flex flex-column min-vh-100">
+<body class="d-flex flex-column min-vh-100 {% block body_class %}{% endblock %}">
     <nav class="navbar navbar-expand-lg navbar-light">
         <div class="container-fluid">
             <a class="navbar-brand" href="{{ url_for('index') }}">{{ site_name }}{% if app_mode == 'lite' %} (Lite){% endif %}</a>
@@ -763,10 +767,13 @@ html[data-theme="dark"] .structure-tree-root .list-group-item-warning {
                         <a class="nav-link {{ 'active' if request.endpoint == 'index' else '' }}" aria-current="page" href="{{ url_for('index') }}"><i class="fas fa-house me-1"></i> Home</a>
                     </li>
                     <li class="nav-item">
-                        <a class="nav-link {{ 'active' if request.endpoint == 'view_igs' else '' }}" href="{{ url_for('view_igs') }}"><i class="fas fa-folder-open me-1"></i> Manage FHIR Packages</a>
+                        <a class="nav-link {% if request.path == '/search-and-import' %}active{% endif %}" href="{{ url_for('search_and_import') }}"><i class="fas fa-download me-1"></i> Search and Import</a>
                     </li>
                     <li class="nav-item">
-                        <a class="nav-link {{ 'active' if request.endpoint == 'import_ig' else '' }}" href="{{ url_for('import_ig') }}"><i class="fas fa-download me-1"></i> Import IGs</a>
+                        <a class="nav-link {{ 'active' if request.endpoint == 'manual_import_ig' else '' }}" href="{{ url_for('manual_import_ig') }}"><i class="fas fa-folder-open me-1"></i> Manual Import</a>
+                    </li>
+                    <li class="nav-item">                        
+                        <a class="nav-link {{ 'active' if request.endpoint == 'view_igs' else '' }}" href="{{ url_for('view_igs') }}"><i class="fas fa-folder-open me-1"></i> Manage FHIR Packages</a>
                     </li>
                     <li class="nav-item">
                         <a class="nav-link {{ 'active' if request.endpoint == 'push_igs' else '' }}" href="{{ url_for('push_igs') }}"><i class="fas fa-upload me-1"></i> Push IGs</a>
@@ -777,6 +784,9 @@ html[data-theme="dark"] .structure-tree-root .list-group-item-warning {
                     <li class="nav-item">
                         <a class="nav-link {{ 'active' if request.endpoint == 'validate_sample' else '' }}" href="{{ url_for('validate_sample') }}"><i class="fas fa-check-circle me-1"></i> Validate FHIR Sample</a>
                     </li>
+                    <li class="nav-item">
+                        <a class="nav-link {{ 'active' if request.endpoint == 'retrieve_split_data' else '' }}" href="{{ url_for('retrieve_split_data') }}"><i class="fas bi-cloud-download me-1"></i> Retrieve & Split Data</a>
+                    </li>
                     <li class="nav-item">
                         <a class="nav-link {{ 'active' if request.endpoint == 'fhir_ui' else '' }}" href="{{ url_for('fhir_ui') }}"><i class="fas fa-cloud-download-alt me-1"></i> FHIR API Explorer</a>
                     </li>
@@ -786,6 +796,14 @@ html[data-theme="dark"] .structure-tree-root .list-group-item-warning {
                     <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">
+                        <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 %} -->
                     </ul>
                 <div class="navbar-controls d-flex align-items-center">
                     <div class="form-check form-switch">
@@ -802,7 +820,6 @@ html[data-theme="dark"] .structure-tree-root .list-group-item-warning {
 
     <main class="flex-grow-1">
         <div class="container mt-4">
-            <!-- Flashed Messages Section -->
             {% with messages = get_flashed_messages(with_categories=true) %}
                 {% if messages %}
                     <div class="mt-3">
@@ -837,6 +854,7 @@ html[data-theme="dark"] .structure-tree-root .list-group-item-warning {
                     <a href="https://github.com/Sudo-JHare/FHIRFLARE-IG-Toolkit/issues/new/choose" class="text-danger text-decoration-none" aria-label="FHIRFLARE support"><i class="fas fa-exclamation-circle me-1"></i> Raise an Issue</a>
                 </div>
                 <div class="footer-right">
+                    <a class="nav-link {{ 'active' if request.endpoint == 'flasgger.apidocs' else '' }}" href="{{ url_for('flasgger.apidocs') }}" aria-label="API Documentation"><i class="fas fa-book-open me-1"></i> API Docs</a>
                     <a href="https://github.com/Sudo-JHare/FHIRFLARE-IG-Toolkit/discussions" target="_blank" rel="noreferrer" aria-label="Project Discussion">Project Discussions</a>
                     <a href="https://github.com/Sudo-JHare" aria-label="Developer">Developer</a>
                     <a href="https://github.com/Sudo-JHare/FHIRFLARE-IG-Toolkit/blob/main/LICENSE.md" aria-label="License">License</a>
@@ -847,41 +865,38 @@ html[data-theme="dark"] .structure-tree-root .list-group-item-warning {
 
     <script src="https://cdn.jsdelivr.net/npm/bootstrap@5.3.3/dist/js/bootstrap.bundle.min.js" integrity="sha384-YvpcrYf0tY3lHB60NNkmXc5s9fDVZLESaAA55NDzOxhy9GkcIdslK1eN7N6jIeHz" crossorigin="anonymous"></script>
     <script>
+        function getCookie(name) {
+            const value = `; ${document.cookie}`;
+            const parts = value.split(`; ${name}=`);
+            if (parts.length === 2) return parts.pop().split(';').shift();
+            return null;
+        }
+
         function toggleTheme() {
             const html = document.documentElement;
             const toggle = document.getElementById('themeToggle');
             const sunIcon = document.querySelector('.fa-sun');
             const moonIcon = document.querySelector('.fa-moon');
-            if (toggle.checked) {
-                html.setAttribute('data-theme', 'dark');
-                localStorage.setItem('theme', 'dark');
-                sunIcon.classList.add('d-none');
-                moonIcon.classList.remove('d-none');
-            } else {
-                html.removeAttribute('data-theme');
-                localStorage.setItem('theme', 'light');
-                sunIcon.classList.remove('d-none');
-                moonIcon.classList.add('d-none');
-            }
-            if (typeof loadLottieAnimation === 'function') {
             const newTheme = toggle.checked ? 'dark' : 'light';
+            html.setAttribute('data-theme', newTheme);
+            localStorage.setItem('theme', newTheme);
+            sunIcon.classList.toggle('d-none', toggle.checked);
+            moonIcon.classList.toggle('d-none', !toggle.checked);
+            document.cookie = `theme=${newTheme}; path=/; max-age=31536000`;
+            if (typeof loadLottieAnimation === 'function') {
                 loadLottieAnimation(newTheme);
             }
-            // Set cookie to persist theme
-            document.cookie = `theme=${toggle.checked ? 'dark' : 'light'}; path=/; max-age=31536000`;
         }
 
         document.addEventListener('DOMContentLoaded', () => {
-            const savedTheme = localStorage.getItem('theme') || (document.cookie.includes('theme=dark') ? 'dark' : 'light');
+            const savedTheme = localStorage.getItem('theme') || getCookie('theme') || 'light';
             const themeToggle = document.getElementById('themeToggle');
             const sunIcon = document.querySelector('.fa-sun');
             const moonIcon = document.querySelector('.fa-moon');
-            if (savedTheme === 'dark' && themeToggle) {
-                document.documentElement.setAttribute('data-theme', 'dark');
-                themeToggle.checked = true;
-                sunIcon.classList.add('d-none');
-                moonIcon.classList.remove('d-none');
-            }
+            document.documentElement.setAttribute('data-theme', savedTheme);
+            themeToggle.checked = savedTheme === 'dark';
+            sunIcon.classList.toggle('d-none', savedTheme === 'dark');
+            moonIcon.classList.toggle('d-none', savedTheme !== 'dark');
             const tooltips = document.querySelectorAll('[data-bs-toggle="tooltip"]');
             tooltips.forEach(t => new bootstrap.Tooltip(t));
         });

templates/config_hapi.html

@@ -0,0 +1,234 @@
+{% extends "base.html" %}
+{% block content %}
+<div class="container mt-4">
+  <h1 class="mb-4">HAPI FHIR Configuration Manager</h1>
+  {% with messages = get_flashed_messages(with_categories=true) %}
+    {% if messages %}
+      {% for category, message in messages %}
+        <div class="alert alert-{{ category }} alert-dismissible fade show" role="alert">
+          {{ message }}
+          <button type="button" class="btn-close" data-bs-dismiss="alert" aria-label="Close"></button>
+        </div>
+      {% endfor %}
+    {% endif %}
+  {% endwith %}
+  <div id="loading" class="text-center my-4">
+    <p>Loading configuration...</p>
+    <div class="spinner-border" role="status">
+      <span class="visually-hidden">Loading...</span>
+    </div>
+  </div>
+  <div id="error" class="alert alert-danger d-none" role="alert"></div>
+  <div id="config-form" class="d-none">
+    <div class="mb-3">
+      <button id="save-btn" class="btn btn-primary me-2">Save Configuration</button>
+      <button id="restart-btn" class="btn btn-success">Restart HAPI Server</button>
+      <span id="restart-status" class="ms-3 text-success d-none"></span>
+    </div>
+    <div id="config-sections"></div>
+  </div>
+</div>
+
+<script>
+  // Configuration descriptions from HAPI FHIR JPA documentation
+  const CONFIG_DESCRIPTIONS = {
+    'hapi.fhir.narrative_enabled': 'Enables or disables the generation of FHIR resource narratives (human-readable summaries). Set to false to reduce processing overhead. Default: false.',
+    'hapi.fhir.mdm_enabled': 'Enables Master Data Management (MDM) features for linking and matching resources (e.g., Patient records). Requires mdm_rules_json_location to be set. Default: false.',
+    'hapi.fhir.mdm_rules_json_location': 'Path to the JSON file defining MDM rules for resource matching. Example: "mdm-rules.json".',
+    'hapi.fhir.cors.allow_Credentials': 'Allows credentials (e.g., cookies, authorization headers) in CORS requests. Set to true to support authenticated cross-origin requests. Default: true.',
+    'hapi.fhir.cors.allowed_origin': 'List of allowed origins for CORS requests. Use ["*"] to allow all origins or specify domains (e.g., ["https://example.com"]). Default: ["*"].',
+    'hapi.fhir.tester.home.name': 'Name of the local tester configuration for HAPI FHIR testing UI. Example: "Local Tester".',
+    'hapi.fhir.tester.home.server_address': 'URL of the local FHIR server for testing. Example: "http://localhost:8080/fhir".',
+    'hapi.fhir.tester.home.refuse_to_fetch_third_party_urls': 'Prevents the tester from fetching third-party URLs. Set to true for security. Default: false.',
+    'hapi.fhir.tester.home.fhir_version': 'FHIR version for the local tester (e.g., "R4", "R5"). Default: R4.',
+    'hapi.fhir.tester.global.name': 'Name of the global tester configuration for HAPI FHIR testing UI. Example: "Global Tester".',
+    'hapi.fhir.tester.global.server_address': 'URL of the global FHIR server for testing. Example: "http://hapi.fhir.org/baseR4".',
+    'hapi.fhir.tester.global.refuse_to_fetch_third_party_urls': 'Prevents the global tester from fetching third-party URLs. Default: false.',
+    'hapi.fhir.tester.global.fhir_version': 'FHIR version for the global tester (e.g., "R4"). Default: R4.',
+    'hapi.fhir.cr.enabled': 'Enables Clinical Reasoning (CR) module for operations like evaluate-measure. Default: false.',
+    'hapi.fhir.cr.caregaps.reporter': 'Reporter mode for care gaps in the CR module. Default: "default".',
+    'hapi.fhir.cr.caregaps.section_author': 'Author identifier for care gap sections. Default: "default".',
+    'hapi.fhir.cr.cql.use_embedded_libraries': 'Uses embedded CQL libraries for Clinical Quality Language processing. Default: true.',
+    'hapi.fhir.inline_resource_storage_below_size': 'Maximum size (in bytes) for storing FHIR resources inline in the database. Default: 4000.',
+    'hapi.fhir.advanced_lucene_indexing': 'Enables experimental advanced Lucene/Elasticsearch indexing for enhanced search capabilities. Default: false. Note: May not support all FHIR features like _total=accurate.',
+    'hapi.fhir.enable_index_of_type': 'Enables indexing of resource types for faster searches. Default: true.',
+    // Add more descriptions as needed based on your application.yaml
+  };
+
+  document.addEventListener('DOMContentLoaded', () => {
+    const configForm = document.getElementById('config-form');
+    const loading = document.getElementById('loading');
+    const errorDiv = document.getElementById('error');
+    const configSections = document.getElementById('config-sections');
+    const saveBtn = document.getElementById('save-btn');
+    const restartBtn = document.getElementById('restart-btn');
+    const restartStatus = document.getElementById('restart-status');
+    let configData = {};
+
+    // Fetch initial configuration
+    fetch('/api/config')
+      .then(res => res.json())
+      .then(data => {
+        configData = data;
+        renderConfigSections();
+        loading.classList.add('d-none');
+        configForm.classList.remove('d-none');
+        // Initialize Bootstrap tooltips
+        document.querySelectorAll('[data-bs-toggle="tooltip"]').forEach(el => {
+          new bootstrap.Tooltip(el);
+        });
+      })
+      .catch(err => {
+        showError('Failed to load configuration');
+        loading.classList.add('d-none');
+      });
+
+    // Render configuration sections
+    function renderConfigSections() {
+      configSections.innerHTML = '';
+      Object.entries(configData).forEach(([section, values]) => {
+        const sectionDiv = document.createElement('div');
+        sectionDiv.className = 'card mb-3';
+        sectionDiv.innerHTML = `
+          <div class="card-header">
+            <h3 class="card-title">${section.charAt(0).toUpperCase() + section.slice(1)}</h3>
+          </div>
+          <div class="card-body">
+            ${renderInputs(values, [section])}
+          </div>
+        `;
+        configSections.appendChild(sectionDiv);
+      });
+    }
+
+    // Render inputs recursively with descriptions
+    function renderInputs(obj, path) {
+      let html = '';
+      Object.entries(obj).forEach(([key, value]) => {
+        const inputId = path.concat(key).join('-');
+        const configPath = path.concat(key).join('.');
+        const description = CONFIG_DESCRIPTIONS[configPath] || 'No description available.';
+        if (typeof value === 'boolean') {
+          html += `
+            <div class="form-check mb-2">
+              <input class="form-check-input" type="checkbox" id="${inputId}" ${value ? 'checked' : ''}>
+              <label class="form-check-label" for="${inputId}">
+                ${key}
+                <i class="fas fa-info-circle ms-1" data-bs-toggle="tooltip" data-bs-placement="top" title="${description}"></i>
+              </label>
+            </div>
+          `;
+        } else if (typeof value === 'string' || typeof value === 'number') {
+          html += `
+            <div class="mb-2">
+              <label for="${inputId}" class="form-label">
+                ${key}
+                <i class="fas fa-info-circle ms-1" data-bs-toggle="tooltip" data-bs-placement="top" title="${description}"></i>
+              </label>
+              <input type="text" class="form-control" id="${inputId}" value="${value}">
+            </div>
+          `;
+        } else if (Array.isArray(value)) {
+          html += `
+            <div class="mb-2">
+              <label for="${inputId}" class="form-label">
+                ${key} (comma-separated)
+                <i class="fas fa-info-circle ms-1" data-bs-toggle="tooltip" data-bs-placement="top" title="${description}"></i>
+              </label>
+              <input type="text" class="form-control" id="${inputId}" value="${value.join(',')}">
+            </div>
+          `;
+        } else if (typeof value === 'object' && value !== null) {
+          html += `
+            <div class="border-start ps-3 ms-3">
+              <h4>${key}</h4>
+              ${renderInputs(value, path.concat(key))}
+            </div>
+          `;
+        }
+      });
+      return html;
+    }
+
+    // Update config data on input change
+    configSections.addEventListener('change', (e) => {
+      const path = e.target.id.split('-');
+      let value = e.target.type === 'checkbox' ? e.target.checked : e.target.value;
+      if (e.target.type === 'text' && e.target.value.includes(',')) {
+        value = e.target.value.split(',').map(v => v.trim());
+      }
+      updateConfig(path, value);
+    });
+
+    // Update config object
+    function updateConfig(path, value) {
+      let current = configData;
+      for (let i = 0; i < path.length - 1; i++) {
+        current = current[path[i]];
+      }
+      current[path[path.length - 1]] = value;
+    }
+
+    // Save configuration
+    saveBtn.addEventListener('click', () => {
+      fetch('/api/config', {
+        method: 'POST',
+        headers: { 'Content-Type': 'application/json' },
+        body: JSON.stringify(configData)
+      })
+        .then(res => res.json())
+        .then(data => {
+          if (data.error) {
+            showError(data.error);
+          } else {
+            showSuccess('Configuration saved successfully');
+          }
+        })
+        .catch(() => showError('Failed to save configuration'));
+    });
+
+    // Restart HAPI server
+    restartBtn.addEventListener('click', () => {
+      restartStatus.textContent = 'Restarting...';
+      restartStatus.classList.remove('d-none');
+      fetch('/api/restart-tomcat', { method: 'POST' })
+        .then(res => res.json())
+        .then(data => {
+          if (data.error) {
+            showError(data.error);
+            restartStatus.classList.add('d-none');
+          } else {
+            restartStatus.textContent = 'HAPI server restarted successfully';
+            setTimeout(() => {
+              restartStatus.classList.add('d-none');
+              restartStatus.textContent = '';
+            }, 3000);
+          }
+        })
+        .catch(() => {
+          showError('Failed to restart HAPI server');
+          restartStatus.classList.add('d-none');
+        });
+    });
+
+    // Show error message
+    function showError(message) {
+      errorDiv.textContent = message;
+      errorDiv.classList.remove('d-none');
+      setTimeout(() => errorDiv.classList.add('d-none'), 5000);
+    }
+
+    // Show success message
+    function showSuccess(message) {
+      const alert = document.createElement('div');
+      alert.className = 'alert alert-success alert-dismissible fade show';
+      alert.innerHTML = `
+        ${message}
+        <button type="button" class="btn-close" data-bs-dismiss="alert" aria-label="Close"></button>
+      `;
+      document.querySelector('.container').insertBefore(alert, configForm);
+      setTimeout(() => alert.remove(), 5000);
+    }
+  });
+</script>
+{% endblock %}

templates/cp_downloaded_igs.html

@@ -10,7 +10,7 @@
         </p>
           <!-----------------------------------------------------------------remove the buttons-----------------------------------------------------
         <div class="d-grid gap-2 d-sm-flex justify-content-sm-center">
-            <a href="{{ url_for('import_ig') }}" class="btn btn-primary btn-lg px-4 gap-3">Import IGs</a>
+            <a href="{{ url_for('search_and_import') }}" class="btn btn-primary btn-lg px-4 gap-3">Import IGs</a>
             <a href="{{ url_for('view_igs') }}" class="btn btn-outline-secondary btn-lg px-4 disabled">Manage FHIR Packages</a>
             <a href="{{ url_for('push_igs') }}" class="btn btn-outline-secondary btn-lg px-4">Upload IG's</a>
         </div>
@@ -34,13 +34,13 @@
     <div class="d-flex justify-content-between align-items-center mb-4">
         <h2><i class="bi bi-journal-arrow-down me-2"></i>Manage FHIR Packages</h2>
         <div>
-            <a href="{{ url_for('import_ig') }}" class="btn btn-success"><i class="bi bi-download me-1"></i> Import More IGs</a>
+            <a href="{{ url_for('search_and_import') }}" class="btn btn-success"><i class="bi bi-download me-1"></i> Import More IGs</a>
         </div>
     </div>
 
     <div class="row g-4">
         <!-- LEFT: Downloaded Packages -->
-        <div class="col-md-6">
+        <div class="col-md-5">
             <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 btn-group-sm">
+                                                <div class="btn-group-vertical btn-group-sm w-80">
                                                     {% 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"><i class="bi bi-gear"></i> Process</button>
+                                                            <button type="submit" class="btn btn-outline-primary w-80"><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" 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 w-80" 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-6">
+        <div class="col-md-7">
             <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-100">
-                                                    <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>
+                                                <div class="btn-group-vertical btn-group-sm w-80">
+                                                    <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>
                                                     <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-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>
+                                                        <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>
                                                     </form>
                                                 </div>
                                             </td>

templates/cp_push_igs.html

@@ -1,6 +1,6 @@
 {% extends "base.html" %}
 
-{# Import form helpers if needed, e.g., for CSRF token #}
+{# Import form helpers for CSRF token and field rendering #}
 {% from "_form_helpers.html" import render_field %}
 
 {% block content %}
@@ -48,11 +48,10 @@
                 <p class="text-muted">No packages downloaded yet. Use the "Import IG" tab.</p>
             {% endif %}
 
-            {# --- MOVED: Push Response Area --- #}
+            {# Push Response Area #}
             <div class="mt-4">
                 <div class="d-flex justify-content-between align-items-center mb-2">
                     <h4><i class="bi bi-file-earmark-text me-2"></i>Push Report</h4>
-                     {# --- NEW: Report Action Buttons --- #}
                     <div id="reportActions" style="display: none;">
                         <button id="copyReportBtn" class="btn btn-sm btn-outline-secondary me-2" title="Copy Report Text">
                             <i class="bi bi-clipboard"></i> Copy
@@ -61,11 +60,9 @@
                             <i class="bi bi-download"></i> Download
                         </button>
                     </div>
-                     {# --- END NEW --- #}
                 </div>
                 <div id="pushResponse" class="border p-3 rounded bg-light" style="min-height: 100px;">
                     <span class="text-muted">Report summary will appear here after pushing...</span>
-                     {# Flash messages can still appear here if needed #}
                     {% with messages = get_flashed_messages(with_categories=true) %}
                         {% if messages %}
                             {% for category, message in messages %}
@@ -78,15 +75,13 @@
                     {% endwith %}
                 </div>
             </div>
-             {# --- END MOVED --- #}
-
         </div>{# End Left Column #}
 
         {# Right Column: Push IGs Form and Console #}
         <div class="col-md-6">
             <h2><i class="bi bi-upload me-2"></i>Push IGs to FHIR Server</h2>
             <form id="pushIgForm">
-                 {{ form.csrf_token if form else '' }} {# Use form passed from route #}
+                {{ form.csrf_token if form else '' }}
 
                 {# Package Selection #}
                 <div class="mb-3">
@@ -111,21 +106,31 @@
                     <input type="url" class="form-control" id="fhirServerUrl" name="fhir_server_url" placeholder="e.g., http://localhost:8080/fhir" required>
                 </div>
 
-                 {# --- RESTRUCTURED: Auth and Checkboxes --- #}
+                {# Authentication Section #}
                 <div class="row g-3 mb-3 align-items-end">
-                     {# Authentication Dropdown & Token Input #}
                     <div class="col-md-5">
                         <label for="authType" class="form-label">Authentication</label>
                         <select class="form-select" id="authType" name="auth_type">
                             <option value="none" selected>None</option>
                             <option value="apiKey">Toolkit API Key (Internal)</option>
                             <option value="bearerToken">Bearer Token</option>
+                            <option value="basic">Basic Authentication</option>
                         </select>
                     </div>
-                     <div class="col-md-7" id="authTokenGroup" style="display: none;">
+                    <div class="col-md-7" id="authInputsGroup" style="display: none;">
+                        {# Bearer Token Input #}
+                        <div id="bearerTokenInput" style="display: none;">
                             <label for="authToken" class="form-label">Bearer Token</label>
                             <input type="password" class="form-control" id="authToken" name="auth_token" placeholder="Enter Bearer Token">
                         </div>
+                        {# Basic Auth Inputs #}
+                        <div id="basicAuthInputs" style="display: none;">
+                            <label for="username" class="form-label">Username</label>
+                            <input type="text" class="form-control mb-2" id="username" name="username" placeholder="Enter Basic Auth Username">
+                            <label for="password" class="form-label">Password</label>
+                            <input type="password" class="form-control" id="password" name="password" placeholder="Enter Basic Auth Password">
+                        </div>
+                    </div>
                 </div>
 
                 {# Checkboxes Row #}
@@ -154,12 +159,10 @@
                         <div class="form-check">
                             <input type="checkbox" class="form-check-input" id="verbose" name="verbose">
                             <label class="form-check-label" for="verbose">Verbose Log</label>
-                             <small class="form-text text-muted d-block">Show detailed Log.</small>
+                            <small class="form-text text-muted d-block">Show detailed log.</small>
                         </div>
                     </div>
                 </div>
-                 {# --- END RESTRUCTURED --- #}
-
 
                 {# Resource Type Filter #}
                 <div class="mb-3">
@@ -185,7 +188,6 @@
                     <span class="text-muted">Console output will appear here...</span>
                 </div>
             </div>
-
         </div> {# End Right Column #}
     </div> {# End row #}
 </div> {# End container-fluid #}
@@ -198,13 +200,17 @@ document.addEventListener('DOMContentLoaded', function() {
     const pushIgForm = document.getElementById('pushIgForm');
     const pushButton = document.getElementById('pushButton');
     const liveConsole = document.getElementById('liveConsole');
-    const responseDiv = document.getElementById('pushResponse'); // Area for final report
-    const reportActions = document.getElementById('reportActions'); // Container for report buttons
-    const copyReportBtn = document.getElementById('copyReportBtn'); // New copy button
-    const downloadReportBtn = document.getElementById('downloadReportBtn'); // New download button
+    const responseDiv = document.getElementById('pushResponse');
+    const reportActions = document.getElementById('reportActions');
+    const copyReportBtn = document.getElementById('copyReportBtn');
+    const downloadReportBtn = document.getElementById('downloadReportBtn');
     const authTypeSelect = document.getElementById('authType');
-    const authTokenGroup = document.getElementById('authTokenGroup');
+    const authInputsGroup = document.getElementById('authInputsGroup');
+    const bearerTokenInput = document.getElementById('bearerTokenInput');
+    const basicAuthInputs = document.getElementById('basicAuthInputs');
     const authTokenInput = document.getElementById('authToken');
+    const usernameInput = document.getElementById('username');
+    const passwordInput = document.getElementById('password');
     const resourceTypesFilterInput = document.getElementById('resourceTypesFilter');
     const skipFilesFilterInput = document.getElementById('skipFilesFilter');
     const dryRunCheckbox = document.getElementById('dryRun');
@@ -226,7 +232,7 @@ document.addEventListener('DOMContentLoaded', function() {
     if (packageSelect && dependencyModeField) {
         packageSelect.addEventListener('change', function() {
             const packageId = this.value;
-            dependencyModeField.value = ''; // Clear on change
+            dependencyModeField.value = '';
             if (packageId) {
                 const [packageName, version] = packageId.split('#');
                 fetch(`/get-package-metadata?package_name=${packageName}&version=${version}`)
@@ -240,24 +246,32 @@ document.addEventListener('DOMContentLoaded', function() {
         if (packageSelect.value) { packageSelect.dispatchEvent(new Event('change')); }
     }
 
-    // Show/Hide Bearer Token Input
-    if (authTypeSelect && authTokenGroup) {
+    // Show/Hide Auth Inputs
+    if (authTypeSelect && authInputsGroup && bearerTokenInput && basicAuthInputs) {
         authTypeSelect.addEventListener('change', function() {
-            authTokenGroup.style.display = this.value === 'bearerToken' ? 'block' : 'none';
+            authInputsGroup.style.display = (this.value === 'bearerToken' || this.value === 'basic') ? 'block' : 'none';
+            bearerTokenInput.style.display = this.value === 'bearerToken' ? 'block' : 'none';
+            basicAuthInputs.style.display = this.value === 'basic' ? 'block' : 'none';
+            // Clear inputs when switching
             if (this.value !== 'bearerToken' && authTokenInput) authTokenInput.value = '';
+            if (this.value !== 'basic' && usernameInput) usernameInput.value = '';
+            if (this.value !== 'basic' && passwordInput) passwordInput.value = '';
         });
-        authTokenGroup.style.display = authTypeSelect.value === 'bearerToken' ? 'block' : 'none';
+        authInputsGroup.style.display = (authTypeSelect.value === 'bearerToken' || authTypeSelect.value === 'basic') ? 'block' : 'none';
+        bearerTokenInput.style.display = authTypeSelect.value === 'bearerToken' ? 'block' : 'none';
+        basicAuthInputs.style.display = authTypeSelect.value === 'basic' ? 'block' : 'none';
+    } else {
+        console.error("Auth elements not found.");
     }
 
-    // --- NEW: Report Action Button Listeners ---
+    // Report Action Button Listeners
     if (copyReportBtn && responseDiv) {
         copyReportBtn.addEventListener('click', () => {
-            const reportAlert = responseDiv.querySelector('.alert'); // Get the alert div inside
-            const reportText = reportAlert ? reportAlert.innerText || reportAlert.textContent : ''; // Get text content
+            const reportAlert = responseDiv.querySelector('.alert');
+            const reportText = reportAlert ? reportAlert.innerText || reportAlert.textContent : '';
             if (reportText && navigator.clipboard) {
                 navigator.clipboard.writeText(reportText)
                     .then(() => {
-                        // Optional: Provide feedback (e.g., change button text/icon)
                         const originalIcon = copyReportBtn.innerHTML;
                         copyReportBtn.innerHTML = '<i class="bi bi-check-lg"></i> Copied!';
                         setTimeout(() => { copyReportBtn.innerHTML = originalIcon; }, 2000);
@@ -292,27 +306,27 @@ document.addEventListener('DOMContentLoaded', function() {
                 document.body.appendChild(link);
                 link.click();
                 document.body.removeChild(link);
-                URL.revokeObjectURL(url); // Clean up
+                URL.revokeObjectURL(url);
             } else {
                 alert('No report content found to download.');
             }
         });
     }
-    // --- END NEW ---
 
-
-    // --- Form Submission ---
+    // Form Submission
     if (pushIgForm) {
         pushIgForm.addEventListener('submit', async function(event) {
             event.preventDefault();
 
-            // Get form values (with null checks for elements)
+            // Get form values
             const packageId = packageSelect ? packageSelect.value : null;
             const fhirServerUrl = fhirServerUrlInput ? fhirServerUrlInput.value.trim() : null;
             if (!packageId || !fhirServerUrl) { alert('Please select package and enter FHIR Server URL.'); return; }
             const [packageName, version] = packageId.split('#');
             const auth_type = authTypeSelect ? authTypeSelect.value : 'none';
             const auth_token = (auth_type === 'bearerToken' && authTokenInput) ? authTokenInput.value : null;
+            const username = (auth_type === 'basic' && usernameInput) ? usernameInput.value.trim() : null;
+            const password = (auth_type === 'basic' && passwordInput) ? passwordInput.value : null;
             const resource_types_filter_raw = resourceTypesFilterInput ? resourceTypesFilterInput.value.trim() : '';
             const resource_types_filter = resource_types_filter_raw ? resource_types_filter_raw.split(',').map(s => s.trim()).filter(s => s) : null;
             const skip_files_raw = skipFilesFilterInput ? skipFilesFilterInput.value.trim() : '';
@@ -322,12 +336,23 @@ document.addEventListener('DOMContentLoaded', function() {
             const include_dependencies = includeDependenciesCheckbox ? includeDependenciesCheckbox.checked : true;
             const force_upload = forceUploadCheckbox ? forceUploadCheckbox.checked : false;
 
-            // UI Updates & API Key
-            if (pushButton) { pushButton.disabled = true; pushButton.textContent = 'Processing...'; }
-            if (liveConsole) { liveConsole.innerHTML = `<div>${new Date().toLocaleTimeString()} [INFO] Starting ${dry_run ? 'DRY RUN ' : ''}${force_upload ? 'FORCE ' : ''}push for ${packageName}#${version}...</div>`; }
-            if (responseDiv) { responseDiv.innerHTML = '<span class="text-muted">Processing...</span>'; } // Clear previous report
-            if (reportActions) { reportActions.style.display = 'none'; } // Hide report buttons initially
-            const internalApiKey = {{ api_key | default("") | tojson }}; // Use tojson filter
+            // Validate Basic Auth inputs
+            if (auth_type === 'basic') {
+                if (!username) { alert('Please enter a username for Basic Authentication.'); return; }
+                if (!password) { alert('Please enter a password for Basic Authentication.'); return; }
+            }
+
+            // UI Updates
+            if (pushButton) {
+                pushButton.disabled = true;
+                pushButton.innerHTML = '<span class="spinner-border spinner-border-sm" role="status" aria-hidden="true"></span> Processing...';
+            }
+            if (liveConsole) {
+                liveConsole.innerHTML = `<div>${new Date().toLocaleTimeString()} [INFO] Starting ${dry_run ? 'DRY RUN ' : ''}${force_upload ? 'FORCE ' : ''}push for ${packageName}#${version}...</div>`;
+            }
+            if (responseDiv) { responseDiv.innerHTML = '<span class="text-muted">Processing...</span>'; }
+            if (reportActions) { reportActions.style.display = 'none'; }
+            const internalApiKey = {{ api_key | default("") | tojson }};
 
             try {
                 // API Fetch
@@ -335,10 +360,19 @@ document.addEventListener('DOMContentLoaded', function() {
                     method: 'POST',
                     headers: { 'Content-Type': 'application/json', 'Accept': 'application/x-ndjson', 'X-CSRFToken': csrfToken, 'X-API-Key': internalApiKey },
                     body: JSON.stringify({
-                        package_name: packageName, version: version, fhir_server_url: fhirServerUrl,
-                        include_dependencies: include_dependencies, auth_type: auth_type, auth_token: auth_token,
-                        resource_types_filter: resource_types_filter, skip_files: skip_files,
-                        dry_run: dry_run, verbose: isVerboseChecked, force_upload: force_upload
+                        package_name: packageName,
+                        version: version,
+                        fhir_server_url: fhirServerUrl,
+                        include_dependencies: include_dependencies,
+                        auth_type: auth_type,
+                        auth_token: auth_token,
+                        username: username,
+                        password: password,
+                        resource_types_filter: resource_types_filter,
+                        skip_files: skip_files,
+                        dry_run: dry_run,
+                        verbose: isVerboseChecked,
+                        force_upload: force_upload
                     })
                 });
 
@@ -361,25 +395,28 @@ document.addEventListener('DOMContentLoaded', function() {
                             const data = JSON.parse(line); const timestamp = new Date().toLocaleTimeString();
                             let messageClass = 'text-light'; let prefix = '[INFO]'; let shouldDisplay = false;
 
-                            switch (data.type) { // Determine if message should display based on verbose
+                            switch (data.type) {
                                 case 'start': case 'error': case 'complete': shouldDisplay = true; break;
                                 case 'success': case 'warning': case 'info': case 'progress': if (isVerboseChecked) { shouldDisplay = true; } break;
                                 default: if (isVerboseChecked) { shouldDisplay = true; console.warn("Unknown type:", data.type); prefix = '[UNKNOWN]'; } break;
                             }
 
-                            if (shouldDisplay && liveConsole) { // Set prefix/class and append to console
+                            if (shouldDisplay && liveConsole) {
                                 if(data.type==='error'){prefix='[ERROR]';messageClass='text-danger';}
                                 else if(data.type==='complete'){const s=data.data?.status||'info';if(s==='success'){prefix='[SUCCESS]';messageClass='text-success';}else if(s==='partial'){prefix='[PARTIAL]';messageClass='text-warning';}else{prefix='[ERROR]';messageClass='text-danger';}}
                                 else if(data.type==='start'){prefix='[START]';messageClass='text-info';}
-                                else if(data.type==='success'){prefix='[SUCCESS]';messageClass='text-success';}else if(data.type==='warning'){prefix='[WARNING]';messageClass='text-warning';}else if(data.type==='info'){prefix='[INFO]';messageClass='text-info';}else{prefix='[PROGRESS]';messageClass='text-light';}
+                                else if(data.type==='success'){prefix='[SUCCESS]';messageClass='text-success';}
+                                else if(data.type==='warning'){prefix='[WARNING]';messageClass='text-warning';}
+                                else if(data.type==='info'){prefix='[INFO]';messageClass='text-info';}
+                                else{prefix='[PROGRESS]';messageClass='text-light';}
 
                                 const messageDiv = document.createElement('div'); messageDiv.className = messageClass;
                                 const messageText = (data.type === 'complete' && data.data) ? data.data.message : data.message;
-                                messageDiv.textContent = `${timestamp} ${prefix} ${sanitizeText(messageText) || 'Empty message.'}`;
+                                messageDiv.innerHTML = `${timestamp} ${prefix} ${sanitizeText(messageText) || 'Empty message.'}`;
                                 liveConsole.appendChild(messageDiv); liveConsole.scrollTop = liveConsole.scrollHeight;
                             }
 
-                            if (data.type === 'complete' && responseDiv) { // Update final summary box
+                            if (data.type === 'complete' && responseDiv) {
                                 const summaryData = data.data || {}; let alertClass = 'alert-info'; let statusText = 'Info'; let pushedPkgs = 'None'; let failHtml = ''; let skipHtml = '';
                                 const isDryRun = summaryData.dry_run || false; const isForceUpload = summaryData.force_upload || false;
                                 const typeFilterUsed = summaryData.resource_types_filter ? summaryData.resource_types_filter.join(', ') : 'All';
@@ -391,28 +428,74 @@ document.addEventListener('DOMContentLoaded', function() {
                                 if (summaryData.skipped_details?.length > 0) { skipHtml = '<hr><strong>Skipped:</strong><ul class="list-unstyled" style="font-size: 0.9em; max-height: 150px; overflow-y: auto; padding-left: 1em;">'; summaryData.skipped_details.forEach(s => {skipHtml += `<li><strong>${sanitizeText(s.resource)}:</strong> ${sanitizeText(s.reason)}</li>`;}); skipHtml += '</ul>';}
 
                                 responseDiv.innerHTML = `<div class="alert ${alertClass} mt-0"><strong>${isDryRun?'[DRY RUN] ':''}${isForceUpload?'[FORCE] ':''}${statusText}:</strong> ${sanitizeText(summaryData.message)||'Complete.'}<hr><strong>Target:</strong> ${sanitizeText(summaryData.target_server)}<br><strong>Package:</strong> ${sanitizeText(summaryData.package_name)}#${sanitizeText(summaryData.version)}<br><strong>Config:</strong> Deps=${summaryData.included_dependencies?'Yes':'No'}, Types=${sanitizeText(typeFilterUsed)}, SkipFiles=${sanitizeText(fileFilterUsed)}, DryRun=${isDryRun?'Yes':'No'}, Force=${isForceUpload?'Yes':'No'}, Verbose=${isVerboseChecked?'Yes':'No'}<br><strong>Stats:</strong> Attempt=${sanitizeText(summaryData.resources_attempted)}, Success=${sanitizeText(summaryData.success_count)}, Fail=${sanitizeText(summaryData.failure_count)}, Skip=${sanitizeText(summaryData.skipped_count)}<br><strong>Pushed Pkgs:</strong><br><div style="padding-left:15px;">${pushedPkgs}</div>${failHtml}${skipHtml}</div>`;
-                                if (reportActions) { reportActions.style.display = 'block'; } // Show report buttons
+                                if (reportActions) { reportActions.style.display = 'block'; }
+                            }
+                        } catch (parseError) {
+                            console.error('Stream parse error:', parseError);
+                            if (liveConsole) {
+                                const errDiv = document.createElement('div');
+                                errDiv.className = 'text-danger';
+                                errDiv.textContent = `${new Date().toLocaleTimeString()} [ERROR] Stream parse error: ${sanitizeText(parseError.message)}`;
+                                liveConsole.appendChild(errDiv);
+                                liveConsole.scrollTop = liveConsole.scrollHeight;
+                            }
+                        }
+                    }
                 }
-                        } catch (parseError) { /* (Handle JSON parse errors) */ console.error('Stream parse error:', parseError); if(liveConsole){/*...add error to console...*/} }
-                    } // end for loop
-                } // end while loop
 
-                // Process Final Buffer (if any)
+                // Process Final Buffer
                 if (buffer.trim()) {
-                     try { /* (Parsing logic for final buffer, similar to above) */ }
-                     catch (parseError) { /* (Handle final buffer parse error) */ }
+                    try {
+                        const data = JSON.parse(buffer.trim());
+                        if (data.type === 'complete' && responseDiv) {
+                            // Same summary rendering as above
+                            const summaryData = data.data || {};
+                            let alertClass = 'alert-info'; let statusText = 'Info'; let pushedPkgs = 'None'; let failHtml = ''; let skipHtml = '';
+                            const isDryRun = summaryData.dry_run || false; const isForceUpload = summaryData.force_upload || false;
+                            const typeFilterUsed = summaryData.resource_types_filter ? summaryData.resource_types_filter.join(', ') : 'All';
+                            const fileFilterUsed = summaryData.skip_files_filter ? summaryData.skip_files_filter.join(', ') : 'None';
+
+                            if (summaryData.pushed_packages_summary?.length > 0) { pushedPkgs = summaryData.pushed_packages_summary.map(p => `${sanitizeText(p.id)} (${sanitizeText(p.resource_count)} resources)`).join('<br>'); }
+                            if (summaryData.status === 'success') { alertClass = 'alert-success'; statusText = 'Success';} else if (summaryData.status === 'partial') { alertClass = 'alert-warning'; statusText = 'Partial Success'; } else { alertClass = 'alert-danger'; statusText = 'Error'; }
+                            if (summaryData.failed_details?.length > 0) { failHtml = '<hr><strong>Failures:</strong><ul class="list-unstyled" style="font-size: 0.9em; max-height: 150px; overflow-y: auto; padding-left: 1em;">'; summaryData.failed_details.forEach(f => {failHtml += `<li><strong>${sanitizeText(f.resource)}:</strong> ${sanitizeText(f.error)}</li>`;}); failHtml += '</ul>';}
+                            if (summaryData.skipped_details?.length > 0) { skipHtml = '<hr><strong>Skipped:</strong><ul class="list-unstyled" style="font-size: 0.9em; max-height: 150px; overflow-y: auto; padding-left: 1em;">'; summaryData.skipped_details.forEach(s => {skipHtml += `<li><strong>${sanitizeText(s.resource)}:</strong> ${sanitizeText(s.reason)}</li>`;}); skipHtml += '</ul>';}
+
+                            responseDiv.innerHTML = `<div class="alert ${alertClass} mt-0"><strong>${isDryRun?'[DRY RUN] ':''}${isForceUpload?'[FORCE] ':''}${statusText}:</strong> ${sanitizeText(summaryData.message)||'Complete.'}<hr><strong>Target:</strong> ${sanitizeText(summaryData.target_server)}<br><strong>Package:</strong> ${sanitizeText(summaryData.package_name)}#${sanitizeText(summaryData.version)}<br><strong>Config:</strong> Deps=${summaryData.included_dependencies?'Yes':'No'}, Types=${sanitizeText(typeFilterUsed)}, SkipFiles=${sanitizeText(fileFilterUsed)}, DryRun=${isDryRun?'Yes':'No'}, Force=${isForceUpload?'Yes':'No'}, Verbose=${isVerboseChecked?'Yes':'No'}<br><strong>Stats:</strong> Attempt=${sanitizeText(summaryData.resources_attempted)}, Success=${sanitizeText(summaryData.success_count)}, Fail=${sanitizeText(summaryData.failure_count)}, Skip=${sanitizeText(summaryData.skipped_count)}<br><strong>Pushed Pkgs:</strong><br><div style="padding-left:15px;">${pushedPkgs}</div>${failHtml}${skipHtml}</div>`;
+                            if (reportActions) { reportActions.style.display = 'block'; }
+                        }
+                    } catch (parseError) {
+                        console.error('Final buffer parse error:', parseError);
+                        if (liveConsole) {
+                            const errDiv = document.createElement('div');
+                            errDiv.className = 'text-danger';
+                            errDiv.textContent = `${new Date().toLocaleTimeString()} [ERROR] Final buffer parse error: ${sanitizeText(parseError.message)}`;
+                            liveConsole.appendChild(errDiv);
+                            liveConsole.scrollTop = liveConsole.scrollHeight;
+                        }
+                    }
                 }
 
-            } catch (error) { // Handle overall fetch/network errors
+            } catch (error) {
                 console.error("Push operation failed:", error);
-                if (liveConsole) { /* ... add error to console ... */ }
-                if (responseDiv) { responseDiv.innerHTML = `<div class="alert alert-danger mt-3"><strong>Error:</strong> ${sanitizeText(error.message || error)}</div>`; }
-                if (reportActions) { reportActions.style.display = 'none'; } // Hide buttons on error
-            } finally { // Re-enable button
-                if (pushButton) { pushButton.disabled = false; pushButton.textContent = 'Push to FHIR Server'; }
+                if (liveConsole) {
+                    const errDiv = document.createElement('div');
+                    errDiv.className = 'text-danger';
+                    errDiv.textContent = `${new Date().toLocaleTimeString()} [ERROR] ${sanitizeText(error.message || error)}`;
+                    liveConsole.appendChild(errDiv);
+                    liveConsole.scrollTop = liveConsole.scrollHeight;
                 }
-        }); // End form submit listener
+                if (responseDiv) {
+                    responseDiv.innerHTML = `<div class="alert alert-danger mt-3"><strong>Error:</strong> ${sanitizeText(error.message || error)}</div>`;
+                }
+                if (reportActions) { reportActions.style.display = 'none'; }
+            } finally {
+                if (pushButton) {
+                    pushButton.disabled = false;
+                    pushButton.innerHTML = '<i class="bi bi-cloud-upload me-2"></i>Push to FHIR Server';
+                }
+            }
+        });
     } else { console.error("Push IG Form element not found."); }
-}); // End DOMContentLoaded listener
+});
 </script>
 {% endblock %}

templates/cp_view_processed_ig.html

@@ -8,13 +8,6 @@
         <p class="lead mb-4">
             View details of the processed FHIR Implementation Guide.
         </p>
-          <!-----------------------------------------------------------------remove the buttons-----------------------------------------------------
-        <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>
-            <a href="{{ url_for('view_igs') }}" class="btn btn-outline-secondary btn-lg px-4">Manage FHIR Packages</a>
-            <a href="{{ url_for('push_igs') }}" class="btn btn-outline-secondary btn-lg px-4">Upload IG's</a>
-        </div>
-          ----------------------------------------------------------------remove the buttons----------------------------------------------------------------------------->
     </div>
 </div>
 
@@ -269,7 +262,7 @@
 
         <div id="raw-structure-wrapper" class="mt-4" style="display: none;">
             <div class="card">
-                 <div class="card-header d-flex justify-content-between align-items-center">
+                <div class="card-header d-flex justify-content-between align-itemsitum-center">
                     <span>Raw Structure Definition for <code id="raw-structure-title"></code></span>
                     <button type="button" class="btn btn-sm btn-outline-secondary btn-copy" id="copy-raw-def-button"
                             data-bs-toggle="tooltip" data-bs-placement="top" title="Copy Raw Definition JSON">
@@ -285,7 +278,6 @@
                 </div>
             </div>
         </div>
-
         <div id="example-display-wrapper" class="mt-4" style="display: none;">
             <div class="card">
                 <div class="card-header">Examples for <code id="example-resource-type-title"></code></div>
@@ -298,6 +290,10 @@
                         <div class="spinner-border spinner-border-sm text-secondary" role="status"><span class="visually-hidden">Loading...</span></div>
                     </div>
                     <div id="example-content-wrapper" style="display: none;">
+                        <div class="form-check mb-2">
+                            <input type="checkbox" class="form-check-input" id="includeNarrative" checked>
+                            <label class="form-check-label" for="includeNarrative">Include Narrative</label>
+                        </div>
                         <h6 id="example-filename" class="mt-2 small text-muted"></h6>
                         <div class="row">
                             <div class="col-md-6">
@@ -352,6 +348,7 @@ let copyRawDefTooltipInstance = null;
 let copyRawExTooltipInstance = null;
 let copyPrettyJsonTooltipInstance = null;
 let structureDataCache = {}; // Cache for fetched structure data
+let includeNarrativeCheckbox; // New global for narrative toggle
 
 // --- Global Helper Functions ---
 function parseFhirPath(path) {
@@ -379,14 +376,12 @@ function getNodeKey(element) {
     const baseKey = (element.id && element.id.includes('.')) ? element.id : element.path;
     if (!baseKey) {
         console.warn("Cannot generate key: element missing structured id and path", element);
-        // Provide a fallback key if absolutely necessary, though this indicates data issues
         return `no-key-${Math.random()}`;
     }
     // Append sliceName if present to ensure uniqueness for slices
     return element.sliceName ? `${baseKey}::slice::${element.sliceName}` : baseKey;
 }
 
-
 // Helper function to initialize a node
 function createNode(path, name, parentPathKey, element = null) {
     // Determine flags based on element data passed from backend
@@ -458,9 +453,6 @@ function flagSlicingEntriesWithMSSlices(node) {
     // Flag THIS node if it defines slicing AND (a direct child is an MS slice OR a deeper descendant is an MS slice)
     if (node.element?.slicing && (directChildIsMSSlice || containedMSSliceInChildren)) {
         node.containsMustSupportSlice = true;
-        // --- DEBUG LOG ---
-        // console.log(`>>> Flagged Slicing Entry ${node.path} as containsMustSupportSlice = true (DirectChild: ${directChildIsMSSlice}, Descendant: ${containedMSSliceInChildren})`);
-        // --- END DEBUG LOG ---
     }
 
     // Return true if THIS node is an MS slice OR if it was flagged as containing one below it
@@ -468,7 +460,6 @@ function flagSlicingEntriesWithMSSlices(node) {
     return isMustSupportSlice || node.containsMustSupportSlice === true;
 } // End flagSlicingEntriesWithMSSlices V2
 
-
 // --- Build Tree Data - V13 (Correct Parent Finding for Nested Slices) ---
 function buildTreeData(elements, view, mustSupportPaths) {
     const treeData = [];
@@ -524,13 +515,6 @@ function buildTreeData(elements, view, mustSupportPaths) {
         const nodeKey = getNodeKey(element);
         const isSlice = !!element.sliceName;
 
-        // Optional Debug Log
-        const debugPaths = ['Observation.component', 'Observation.component.code', 'Observation.component.code.coding'];
-        const shouldDebug = debugPaths.some(p => path?.startsWith(p));
-        // if (shouldDebug) { // Keep this commented out unless actively debugging parent finding
-        //    console.log(`[Debug] Processing element ${index}: Path='${path}', SliceName='${element.sliceName}', ID='${id}', Key='${nodeKey}'`);
-        // }
-
         if (!path || !nodeKey) { console.warn(`Skipping element ${index} with missing path/key`, element); return; }
 
         // Root element handling (Keep V12 logic)
@@ -558,12 +542,9 @@ function buildTreeData(elements, view, mustSupportPaths) {
             // Derive the expected parent ID/Path from the slice's ID or Path
             if (id && id.includes('.')) {
                 // Try deriving from ID first (more specific)
-                // Example: id = Observation.component:DiastolicBP.code.coding:DBPCode
-                // We want the parent ID = Observation.component:DiastolicBP.code.coding
                 const idParts = id.split(':');
                 if (idParts.length > 1) {
                     const parentIdGuess = idParts.slice(0, -1).join(':');
-                     // Check if the parent ID ends with a path segment (contains '.')
                     if (parentIdGuess.includes('.')) {
                         expectedParentId = parentIdGuess;
                     }
@@ -572,7 +553,6 @@ function buildTreeData(elements, view, mustSupportPaths) {
                 if (!expectedParentId && path && path.includes('.')) {
                     expectedParentPath = path; // The base path is the parent slicing entry path
                 }
-
             } else if (path && path.includes('.')) {
                 // If no complex ID, use the path
                 expectedParentPath = path;
@@ -593,7 +573,6 @@ function buildTreeData(elements, view, mustSupportPaths) {
                 parentElement = slicingEntryElement;
                 parentNodeKey = getNodeKey(parentElement);
                 parentFound = true;
-                 // console.log(`[Debug] Parent Check 1 (Slice V13): ${nodeKey} -> ${parentNodeKey} (ParentID: ${expectedParentId}, ParentPath: ${expectedParentPath})`);
             } else {
                 console.warn(`Slicing entry element NOT FOUND for expected parent (ID: ${expectedParentId}, Path: ${expectedParentPath}) needed by slice '${nodeKey}'. Assigning root.`);
                 parentElement = rootElementData;
@@ -601,7 +580,7 @@ function buildTreeData(elements, view, mustSupportPaths) {
                 parentFound = true; // Consider parent determined (fallback)
             }
         }
-        // Check 2: Descendant of a Slice (using ID structure) (Keep V12 logic - seems okay from logs)
+        // Check 2: Descendant of a Slice (using ID structure) (Keep V12 logic)
         else if (id && id.includes(':') && id.includes('.')) {
             const idParts = id.split('.');
             let potentialSliceParentId = null;
@@ -615,13 +594,11 @@ function buildTreeData(elements, view, mustSupportPaths) {
                     const potentialParentNode = nodeMap.get(potentialParentKey);
                     if (potentialParentNode?.element) {
                         parentNodeKey = potentialParentKey; parentElement = potentialParentNode.element; parentFound = true;
-                         // console.log(`[Debug] Parent Check 2 (Slice Descendant ID V13): ${nodeKey} -> ${parentNodeKey} (via Map Key ${potentialParentKey})`);
                     } else { console.warn(`Node found in map for key ${potentialParentKey} but its element was missing. Falling back.`); }
                 } else {
                     const sliceParentElement = elements.find(el => el.id === potentialSliceParentId);
                     if (sliceParentElement) {
                         parentNodeKey = getNodeKey(sliceParentElement); parentElement = sliceParentElement; parentFound = true;
-                          // console.log(`[Debug] Parent Check 2 (Slice Descendant ID V13): ${nodeKey} -> ${parentNodeKey} (via Element ID ${potentialSliceParentId})`);
                     } else { console.warn(`Slice parent element ID '${potentialSliceParentId}' not found for descendant '${id}'. Falling back.`); }
                 }
             }
@@ -642,16 +619,13 @@ function buildTreeData(elements, view, mustSupportPaths) {
                     parentElement = potentialParentNode.element;
                     parentNodeKey = getNodeKey(parentElement);
                     parentFound = true;
-                    // console.log(`[Debug] Parent Check 3/4 (Path V13): ${nodeKey} -> ${parentNodeKey}`);
                 } else {
                     parentElement = rootElementData; parentNodeKey = getNodeKey(parentElement);
                     parentFound = true;
-                    // console.warn(`[Debug] Parent Check 3/4 (Path V13): Parent node NOT FOUND for path '${parentPathString}' needed by '${nodeKey}'. Assigning root.`);
                 }
             } else {
                 parentElement = rootElementData; parentNodeKey = getNodeKey(parentElement);
                 parentFound = true;
-                // console.log(`[Debug] Parent Check 3/4 (Path V13): Parent is root for ${nodeKey}`);
             }
         }
         // --- End Parent Finding Logic ---
@@ -683,7 +657,6 @@ function buildTreeData(elements, view, mustSupportPaths) {
             if (parentNode) {
                 if (!parentNode.children) parentNode.children = [];
                 parentNode.children.push(newNode);
-                 // console.log(`[Debug] Attaching new node ${nodeKey} to parent ${parentNodeKey}`);
             } else {
                 console.error(`Cannot add child ${nodeKey} as parent node object is unexpectedly null.`);
             }
@@ -727,12 +700,8 @@ function buildTreeData(elements, view, mustSupportPaths) {
     return treeData;
 } // End buildTreeData V13
 
-
 // --- Render Node as List Item - V19 (Fixes isSlice error, keeps V18 logic) ---
 function renderNodeAsLi(node, mustSupportPathsSet, resourceType, level = 0, view = 'snapshot') {
-    // --- Constants for Primitive Types ---
-    // REMOVED PRIMITIVE_TYPES check to align with reference rendering
-
     if (!node || !node.path || !node.name) { console.warn(`Skipping render for invalid node:`, node); return ''; }
     const el = node.element || {};
     const path = el.path || node.path || `node-${level}-${Math.random()}`;
@@ -758,8 +727,6 @@ function renderNodeAsLi(node, mustSupportPathsSet, resourceType, level = 0, view
         mustSupportTitle = `Must Support (Slice: ${sliceName})`;
         fhirPathExpression = `${path}[sliceName='${sliceName}']`;
     }
-    // Optional Debug Log for highlighting
-    // if (node.path === 'Patient.extension' || node.path === 'Patient.identifier') { console.log(...) }
     const msIconClass = (isMustSupport || node.containsMustSupportSlice) ? 'text-warning' : '';
     const mustSupportDisplay = (isMustSupport || node.containsMustSupportSlice) ? `<i class="bi bi-check-circle-fill ${msIconClass} ms-1" title="${escapeHtmlAttr(mustSupportTitle)}" data-bs-toggle="tooltip" data-fhirpath="${escapeHtmlAttr(fhirPathExpression)}"></i>` : '';
 
@@ -798,7 +765,6 @@ function renderNodeAsLi(node, mustSupportPathsSet, resourceType, level = 0, view
     } else if (el.contentReference) { typeString = `<span class="text-info" title="Content Reference">Ref: ${escapeHtmlAttr(el.contentReference)}</span>`; }
     else if (el.sliceName && path.endsWith('extension')) { typeString = '<span class="text-muted">Extension</span>'; }
 
-
     // Children HTML / Choice Type Display (V18 logic - reverted primitive filtering)
     let childrenOrChoiceHtml = '';
     if (showToggle) {
@@ -863,7 +829,6 @@ function renderNodeAsLi(node, mustSupportPathsSet, resourceType, level = 0, view
     return itemHtml;
 } // End renderNodeAsLi (V19)
 
-
 // --- Function to Initialize Collapse Icon Listeners (Bootstrap Events) V3 - Explicit Cleanup ---
 function initializeBootstrapCollapseListeners(containerElement) {
     if (!containerElement) { return; }
@@ -876,8 +841,8 @@ function initializeBootstrapCollapseListeners(containerElement) {
         if (!triggerEl) { console.warn(`Trigger not found for #${collapseId}`); }
         if (collapseEl._handleShow && typeof collapseEl._handleShow === 'function') { collapseEl.removeEventListener('show.bs.collapse', collapseEl._handleShow); }
         if (collapseEl._handleHide && typeof collapseEl._handleHide === 'function') { collapseEl.removeEventListener('hide.bs.collapse', collapseEl._handleHide); }
-        const handleShow = (event) => { if (event.target === collapseEl && icon) { icon.classList.replace('bi-chevron-right', 'bi-chevron-down'); } /* console.log(...) */ };
-        const handleHide = (event) => { if (event.target === collapseEl && icon) { icon.classList.replace('bi-chevron-down', 'bi-chevron-right'); } /* console.log(...) */ };
+        const handleShow = (event) => { if (event.target === collapseEl && icon) { icon.classList.replace('bi-chevron-right', 'bi-chevron-down'); } };
+        const handleHide = (event) => { if (event.target === collapseEl && icon) { icon.classList.replace('bi-chevron-down', 'bi-chevron-right'); } };
         collapseEl._handleShow = handleShow; collapseEl._handleHide = handleHide;
         collapseEl.addEventListener('show.bs.collapse', handleShow);
         collapseEl.addEventListener('hide.bs.collapse', handleHide);
@@ -885,15 +850,14 @@ function initializeBootstrapCollapseListeners(containerElement) {
     });
 } // End initializeBootstrapCollapseListeners V3
 
-
-// --- Render Structure Tree (Calls V11 buildTreeData, V19 renderNode, V3 initBSCollapse) ---
+// --- Render Structure Tree (Calls V13 buildTreeData, V19 renderNode, V3 initBSCollapse) ---
 async function renderStructureTree(resourceType, view, snapshotElements, mustSupportPaths) { // Accepts snapshot elements
     const treeContainer = document.getElementById(`structure-tree-${view}`);
     if (!treeContainer) { console.error(`Tree container missing: ${view}`); return; }
     treeContainer.innerHTML = '';
 
     try {
-        // Build tree using V11 buildTreeData and snapshot data
+        // Build tree using V13 buildTreeData and snapshot data
         const treeData = buildTreeData(snapshotElements, view, mustSupportPaths);
 
         // Render HTML using V19 renderNodeAsLi
@@ -908,7 +872,13 @@ async function renderStructureTree(resourceType, view, snapshotElements, mustSup
         // Init listeners/tooltips
         initializeBootstrapCollapseListeners(treeContainer); // V3
         const tooltipTriggerList = treeContainer.querySelectorAll('[data-bs-toggle="tooltip"]');
-         tooltipTriggerList.forEach(tooltipTriggerEl => { const e=bootstrap.Tooltip.getInstance(tooltipTriggerEl); if(e){e.dispose();} if(tooltipTriggerEl.getAttribute('title')||tooltipTriggerEl.getAttribute('data-bs-original-title')){new bootstrap.Tooltip(tooltipTriggerEl);} });
+        tooltipTriggerList.forEach(tooltipTriggerEl => { 
+            const e = bootstrap.Tooltip.getInstance(tooltipTriggerEl); 
+            if (e) { e.dispose(); }
+            if (tooltipTriggerEl.getAttribute('title') || tooltipTriggerEl.getAttribute('data-bs-original-title')) {
+                new bootstrap.Tooltip(tooltipTriggerEl);
+            }
+        });
 
     } catch (error) {
         console.error(`Error rendering ${view} tree:`, error);
@@ -916,15 +886,21 @@ async function renderStructureTree(resourceType, view, snapshotElements, mustSup
     }
 } // End renderStructureTree
 
-
 // --- Fetch Structure Definition for Specific View ---
-async function fetchStructure(resourceType, view) {
-    const cacheKey = `${resourceType}-${view}`;
+async function fetchStructure(resourceType, view, includeNarrative, raw = false) {
+    const cacheKey = `${resourceType}-${view}-${includeNarrative}-${raw}`;
     if (structureDataCache[cacheKey]) {
         try { return JSON.parse(JSON.stringify(structureDataCache[cacheKey])); } catch (e) { return structureDataCache[cacheKey]; }
     }
     const structureBaseUrl = "{{ url_for('get_structure') }}";
-    const params = new URLSearchParams({ package_name: "{{ processed_ig.package_name }}", package_version: "{{ processed_ig.version }}", resource_type: resourceType, view: view });
+    const params = new URLSearchParams({ 
+        package_name: "{{ processed_ig.package_name }}", 
+        version: "{{ processed_ig.version }}",
+        resource_type: resourceType, 
+        view: view,
+        include_narrative: includeNarrative,
+        raw: raw
+    });
     const fetchUrl = `${structureBaseUrl}?${params.toString()}`;
     try {
         const response = await fetch(fetchUrl);
@@ -932,13 +908,11 @@ async function fetchStructure(resourceType, view) {
         const data = await response.json();
         try { structureDataCache[cacheKey] = JSON.parse(JSON.stringify(data)); } catch(e) { structureDataCache[cacheKey] = data; }
         return JSON.parse(JSON.stringify(data));
-    } catch (error) { console.error(`Error fetching ${view} structure:`, error); throw error; }
+    } catch (error) { console.error(`Error fetching ${raw ? 'raw' : view} structure:`, error); throw error; }
 }
 
-
-// --- Populate Structure for All Views - V4 (Add Search Param Logging) ---
+// --- Populate Structure for All Views - V5 (Add Search Param Logging, Include Narrative) ---
 async function populateStructure(resourceType) {
-    // ... (keep existing variable assignments and UI resets at the beginning) ...
     if (structureTitle) structureTitle.textContent = `${resourceType} ({{ processed_ig.package_name }}#{{ processed_ig.version }})`;
     if (rawStructureTitle) rawStructureTitle.textContent = `${resourceType} ({{ processed_ig.package_name }}#{{ processed_ig.version }})`;
     if (structureLoading) structureLoading.style.display = 'block';
@@ -955,70 +929,51 @@ async function populateStructure(resourceType) {
     if (bindingsTableBody) bindingsTableBody.innerHTML = '<tr><td colspan="4" class="text-center text-muted fst-italic">Loading...</td></tr>';
     if (searchParamsTableBody) searchParamsTableBody.innerHTML = '<tr><td colspan="4" class="text-center text-muted fst-italic">Loading...</td></tr>';
     if (rawStructureContent) rawStructureContent.textContent = 'Loading...';
-
     try {
         console.log(`PopulateStructure V4: Fetching structure and search params for ${resourceType}`);
-        const structureBaseUrl = "{{ url_for('get_structure') }}";
-        const params = new URLSearchParams({ package_name: "{{ processed_ig.package_name }}", package_version: "{{ processed_ig.version }}", resource_type: resourceType });
-        const fetchUrl = `${structureBaseUrl}?${params.toString()}`;
-        const response = await fetch(fetchUrl);
-        if (!response.ok) {
-            const errorText = await response.text();
-            throw new Error(`HTTP error ${response.status}: ${errorText}`);
-        }
-        const data = await response.json();
-
-        if (!data || !data.elements) { throw new Error(`Structure data or elements missing for ${resourceType}.`); }
-
-        const snapshotElementsCopy = JSON.parse(JSON.stringify(data.elements));
-        const mustSupportPaths = new Set(data.must_support_paths || []);
-        const searchParams = data.search_parameters || []; // Get search params
-        const fallbackUsed = data.fallback_used || false;
-        const fallbackSource = data.source_package || 'FHIR core';
-
-        // *** ADDED LOG: Check received search parameters ***
+        const includeNarrative = includeNarrativeCheckbox ? includeNarrativeCheckbox.checked : true;
+        // Fetch processed data for UI tabs
+        const processedData = await fetchStructure(resourceType, 'snapshot', includeNarrative, false);
+        if (!processedData || !processedData.elements) { throw new Error(`Structure data or elements missing for ${resourceType}.`); }
+        const snapshotElementsCopy = JSON.parse(JSON.stringify(processedData.elements));
+        const mustSupportPaths = new Set(processedData.must_support_paths || []);
+        const searchParams = processedData.search_parameters || [];
+        const fallbackUsed = processedData.fallback_used || false;
+        const sourcePackage = processedData.source_package || 'FHIR core';
         console.log('[populateStructure] Received search_parameters:', searchParams);
-        // *************************************************
-
-        // Update Raw JSON View
+        // Fetch raw StructureDefinition for raw view
+        const rawData = await fetchStructure(resourceType, 'snapshot', includeNarrative, true);
         if (rawStructureContent) {
-            rawStructureContent.textContent = JSON.stringify(data, null, 4);
+            rawStructureContent.textContent = JSON.stringify(rawData, null, 4);
             if (rawStructureContent.classList.contains('hljs')) { rawStructureContent.classList.remove('hljs'); }
+            rawStructureContent.dataset.highlighted = '';
             hljs.highlightElement(rawStructureContent);
             if (fallbackUsed && structureFallbackMessage) {
-                 structureFallbackMessage.textContent = `Note: Displaying structure from fallback package: ${fallbackSource}`;
+                structureFallbackMessage.textContent = `Note: Displaying structure from fallback package: ${sourcePackage}`;
                 structureFallbackMessage.style.display = 'block';
             }
-        } else { if (rawStructureContent) rawStructureContent.textContent = '(Raw content display element not found)';}
-
-        // Render the Tree Views
+        } else { if (rawStructureContent) rawStructureContent.textContent = '(Raw content display element not found)'; }
         for (const view of views) {
             console.log(`PopulateStructure V4: Rendering view '${view}' for ${resourceType}`);
             const treeContainer = document.getElementById(`structure-tree-${view}`);
             if (!treeContainer) { console.error(`Container missing for ${view}`); continue; }
             await renderStructureTree(resourceType, view, JSON.parse(JSON.stringify(snapshotElementsCopy)), mustSupportPaths);
         }
-
-        // Render Constraints & Bindings tables
-        renderConstraintsTable(data.elements);
-        renderBindingsTable(data.elements);
-        // Render Search Params table (passing potentially empty array)
-        renderSearchParametersTable(searchParams); // Pass the retrieved data
-
+        renderConstraintsTable(processedData.elements);
+        renderBindingsTable(processedData.elements);
+        renderSearchParametersTable(searchParams);
     } catch (error) {
         console.error("Error populating structure:", error);
-        // ... existing error handling ...
         views.forEach(v => { const tc = document.getElementById(`structure-tree-${v}`); if(tc) tc.innerHTML = `<div class="alert alert-danger m-2">Error loading structure: ${error.message}</div>`; });
         if (constraintsTableBody) constraintsTableBody.innerHTML = `<tr><td colspan="5" class="text-danger text-center">Error loading constraints: ${error.message}</td></tr>`;
         if (bindingsTableBody) bindingsTableBody.innerHTML = `<tr><td colspan="4" class="text-danger text-center">Error loading bindings: ${error.message}</td></tr>`;
-        if (searchParamsTableBody) searchParamsTableBody.innerHTML = `<tr><td colspan="4" class="text-danger text-center">Error loading search params: ${error.message}</td></tr>`; // Show error here too
+        if (searchParamsTableBody) searchParamsTableBody.innerHTML = `<tr><td colspan="4" class="text-danger text-center">Error loading search params: ${error.message}</td></tr>`;
         if (rawStructureContent) { rawStructureContent.textContent = `Error: ${error.message}`; }
     } finally {
         if (structureLoading) structureLoading.style.display = 'none';
         if (rawStructureLoading) rawStructureLoading.style.display = 'none';
     }
-} // End populateStructure V4
-
+}// End populateStructure V5
 
 // --- Populate Example Selector Dropdown ---
 function populateExampleSelector(resourceOrProfileIdentifier) {
@@ -1040,24 +995,73 @@ async function fetchAndDisplayExample(selectedFilePath) {
     const resetCopyButton = (button, tooltipInstance, originalTitle) => { if (tooltipInstance && button?.isConnected) { tooltipInstance.hide(); button.setAttribute('data-bs-original-title', originalTitle); button.querySelector('i')?.classList.replace('bi-check-lg', 'bi-clipboard'); } };
     resetCopyButton(copyRawExButton, copyRawExTooltipInstance, 'Copy Raw Content'); resetCopyButton(copyPrettyJsonButton, copyPrettyJsonTooltipInstance, 'Copy JSON');
     if (!selectedFilePath) { exampleLoading.style.display = 'none'; return; }
-    const exampleBaseUrl = "{{ url_for('get_example') }}"; const exampleParams = new URLSearchParams({ package_name: "{{ processed_ig.package_name }}", package_version: "{{ processed_ig.version }}", filename: selectedFilePath }); const exampleFetchUrl = `${exampleBaseUrl}?${exampleParams.toString()}`;
+    const exampleBaseUrl = "{{ url_for('get_example') }}";
+    const includeNarrative = includeNarrativeCheckbox ? includeNarrativeCheckbox.checked : true;
+    const exampleParams = new URLSearchParams({ 
+        package_name: "{{ processed_ig.package_name }}", 
+        version: "{{ processed_ig.version }}",  // Changed from package_version to version
+        filename: selectedFilePath,
+        include_narrative: includeNarrative
+    });
+    const exampleFetchUrl = `${exampleBaseUrl}?${exampleParams.toString()}`;
     try {
-        const response = await fetch(exampleFetchUrl); if (!response.ok) { throw new Error(`HTTP error ${response.status}`); } const rawData = await response.text();
-        if(exampleFilename) exampleFilename.textContent = `Source: ${selectedFilePath.split('/').pop()}`; if(exampleContentRaw) exampleContentRaw.textContent = rawData; let prettyJson = '(Not valid JSON)';
-        try { prettyJson = JSON.stringify(JSON.parse(rawData), null, 4); } catch (e) { prettyJson = rawData.startsWith('<') ? '(Content is XML, not JSON)' : `(Error parsing JSON: ${e.message})`; } if(exampleContentJson) exampleContentJson.textContent = prettyJson;
-        if (exampleContentRaw) hljs.highlightElement(exampleContentRaw); if (exampleContentJson) hljs.highlightElement(exampleContentJson); if(exampleContentWrapper) exampleContentWrapper.style.display = 'block';
-    } catch (error) { console.error("Error fetching or displaying example:", error); if (exampleFilename) exampleFilename.textContent = 'Error loading example'; if (exampleContentRaw) exampleContentRaw.textContent = `Error: ${error.message}`; if (exampleContentJson) exampleContentJson.textContent = `Error: ${error.message}`; if (exampleContentWrapper) exampleContentWrapper.style.display = 'block'; }
-    finally { if (exampleLoading) exampleLoading.style.display = 'none'; }
+        const response = await fetch(exampleFetchUrl); 
+        if (!response.ok) { throw new Error(`HTTP error ${response.status}`); } 
+        const rawData = await response.text();
+        if(exampleFilename) exampleFilename.textContent = `Source: ${selectedFilePath.split('/').pop()}`; 
+        if(exampleContentRaw) exampleContentRaw.textContent = rawData; 
+        let prettyJson = '(Not valid JSON)';
+        try { prettyJson = JSON.stringify(JSON.parse(rawData), null, 4); } catch (e) { prettyJson = rawData.startsWith('<') ? '(Content is XML, not JSON)' : `(Error parsing JSON: ${e.message})`; } 
+        if(exampleContentJson) exampleContentJson.textContent = prettyJson;
+        if (exampleContentRaw) hljs.highlightElement(exampleContentRaw); 
+        if (exampleContentJson) hljs.highlightElement(exampleContentJson); 
+        if(exampleContentWrapper) exampleContentWrapper.style.display = 'block';
+    } catch (error) { 
+        console.error("Error fetching or displaying example:", error); 
+        if (exampleFilename) exampleFilename.textContent = 'Error loading example'; 
+        if (exampleContentRaw) exampleContentRaw.textContent = `Error: ${error.message}`; 
+        if (exampleContentJson) exampleContentJson.textContent = `Error: ${error.message}`; 
+        if (exampleContentWrapper) exampleContentWrapper.style.display = 'block'; 
+    } finally { 
+        if (exampleLoading) exampleLoading.style.display = 'none'; 
+    }
 }
 
-
 // --- Generic Copy Logic Function ---
 function setupCopyButton(buttonElement, sourceElement, tooltipInstance, successTitle, originalTitle, errorTitle, nothingTitle) {
     if (!buttonElement || !sourceElement) { return null; }
     bootstrap.Tooltip.getInstance(buttonElement)?.dispose();
     tooltipInstance = new bootstrap.Tooltip(buttonElement, { title: originalTitle });
-    const clickHandler = () => { const textToCopy = sourceElement.textContent; const copyIcon = buttonElement.querySelector('i'); const updateTooltip = (newTitle, iconClass) => { buttonElement.setAttribute('data-bs-original-title', newTitle); tooltipInstance?.setContent({ '.tooltip-inner': newTitle }); tooltipInstance?.show(); if (copyIcon) copyIcon.className = `bi ${iconClass}`; setTimeout(() => { if (buttonElement.isConnected) { tooltipInstance?.hide(); buttonElement.setAttribute('data-bs-original-title', originalTitle); if (copyIcon) copyIcon.className = 'bi bi-clipboard'; } }, 1500); }; if (textToCopy && textToCopy.trim() && !textToCopy.startsWith('(Could not') && !textToCopy.startsWith('(Not valid') && !textToCopy.startsWith('Error:')) { navigator.clipboard.writeText(textToCopy).then(() => { updateTooltip(successTitle, 'bi-check-lg'); }).catch(err => { console.error(`Copy failed:`, err); updateTooltip(errorTitle, 'bi-exclamation-triangle'); }); } else { updateTooltip(nothingTitle, 'bi-clipboard'); } };
-    buttonElement.removeEventListener('click', clickHandler); buttonElement.addEventListener('click', clickHandler); return tooltipInstance;
+    const clickHandler = () => { 
+        const textToCopy = sourceElement.textContent; 
+        const copyIcon = buttonElement.querySelector('i'); 
+        const updateTooltip = (newTitle, iconClass) => { 
+            buttonElement.setAttribute('data-bs-original-title', newTitle); 
+            tooltipInstance?.setContent({ '.tooltip-inner': newTitle }); 
+            tooltipInstance?.show(); 
+            if (copyIcon) copyIcon.className = `bi ${iconClass}`; 
+            setTimeout(() => { 
+                if (buttonElement.isConnected) { 
+                    tooltipInstance?.hide(); 
+                    buttonElement.setAttribute('data-bs-original-title', originalTitle); 
+                    if (copyIcon) copyIcon.className = 'bi bi-clipboard'; 
+                } 
+            }, 1500); 
+        }; 
+        if (textToCopy && textToCopy.trim() && !textToCopy.startsWith('(Could not') && !textToCopy.startsWith('(Not valid') && !textToCopy.startsWith('Error:')) { 
+            navigator.clipboard.writeText(textToCopy).then(() => { 
+                updateTooltip(successTitle, 'bi-check-lg'); 
+            }).catch(err => { 
+                console.error(`Copy failed:`, err); 
+                updateTooltip(errorTitle, 'bi-exclamation-triangle'); 
+            }); 
+        } else { 
+            updateTooltip(nothingTitle, 'bi-clipboard'); 
+        } 
+    };
+    buttonElement.removeEventListener('click', clickHandler); 
+    buttonElement.addEventListener('click', clickHandler); 
+    return tooltipInstance;
 }
 
 // --- Function to Render Constraints Table ---
@@ -1075,9 +1079,7 @@ function renderConstraintsTable(elements) {
         elements = []; // Prevent errors later
     }
 
-
     elements.forEach(element => {
-        // Check if element exists and has a constraint property which is an array
         if (element && element.constraint && Array.isArray(element.constraint) && element.constraint.length > 0) {
             element.constraint.forEach(constraint => {
                 if (constraint) { // Ensure constraint object itself exists
@@ -1106,10 +1108,8 @@ function renderConstraintsTable(elements) {
     }
 
     // Re-run highlight.js for the new code blocks
-    // Use setTimeout to allow the DOM to update before highlighting
     setTimeout(() => {
         document.querySelectorAll('#constraints-table code.language-fhirpath').forEach((block) => {
-             // Remove existing highlight classes if any, before re-highlighting
             block.classList.remove('hljs');
             hljs.highlightElement(block);
         });
@@ -1132,7 +1132,6 @@ function renderBindingsTable(elements) {
     }
 
     elements.forEach(element => {
-        // Check if element exists and has a binding property which is an object
         if (element && element.binding && typeof element.binding === 'object') {
             bindingsFound = true;
             const binding = element.binding;
@@ -1143,7 +1142,6 @@ function renderBindingsTable(elements) {
             if (binding.valueSet) {
                 const valueSetLink = document.createElement('a');
                 valueSetLink.href = binding.valueSet; // Ideally, resolve canonical to actual URL if possible
-                // Try to show last part of URL as name, or full URL if no '/'
                 const urlParts = binding.valueSet.split('/');
                 valueSetLink.textContent = urlParts.length > 1 ? urlParts[urlParts.length - 1] : binding.valueSet;
                 valueSetLink.target = '_blank'; // Open in new tab
@@ -1170,110 +1168,71 @@ function renderBindingsTable(elements) {
 
 // --- Function to Render Search Parameters Table (Includes Conformance Badges & Tooltips) ---
 function renderSearchParametersTable(searchParamsData) {
-    // Find the table body element using its ID
     const tableBody = document.getElementById('searchparams-table')?.querySelector('tbody');
-
-    // Check if the table body element exists
     if (!tableBody) {
         console.error('Search Params table body element (#searchparams-table > tbody) not found');
-        return; // Exit if the table body isn't found
+        return;
     }
 
-    tableBody.innerHTML = ''; // Clear any existing rows (like loading indicators)
-
-    // Log the data received for debugging
+    tableBody.innerHTML = '';
     console.log('[renderSearchParametersTable] Received data:', searchParamsData);
 
-    // Check if the received data is valid and is an array with items
     if (!searchParamsData || !Array.isArray(searchParamsData) || searchParamsData.length === 0) {
         console.log('[renderSearchParametersTable] No valid search parameter data found, displaying message.');
-        // Display a message indicating no parameters were found
         const row = tableBody.insertRow();
         const cell = row.insertCell();
-        cell.colSpan = 4; // Span across all columns
+        cell.colSpan = 4;
         cell.textContent = 'No relevant search parameters found for this resource type.';
         cell.style.textAlign = 'center';
-        cell.classList.add('text-muted', 'fst-italic'); // Style the message
-        return; // Exit the function
+        cell.classList.add('text-muted', 'fst-italic');
+        return;
     }
 
-    // Sort parameters alphabetically by their 'code' before rendering
     searchParamsData.sort((a, b) => (a.code || '').localeCompare(b.code || ''));
 
-    // Iterate through each search parameter object in the sorted array
     searchParamsData.forEach((param, index) => {
-        console.log(`[renderSearchParametersTable] Processing param ${index + 1}:`, param); // Log each parameter
-
-        const row = tableBody.insertRow(); // Create a new table row
-
-        // --- Column 1: Parameter Code ---
+        console.log(`[renderSearchParametersTable] Processing param ${index + 1}:`, param);
+        const row = tableBody.insertRow();
         const nameCell = row.insertCell();
-        // Use escapeHtmlAttr (ensure this helper function exists in your scope)
-        // Display the parameter code within a <code> tag
         nameCell.innerHTML = `<code>${escapeHtmlAttr(param.code || 'N/A')}</code>`;
-
-        // --- Column 2: Parameter Type ---
-        row.insertCell().textContent = param.type || 'N/A'; // Display the parameter type
-
-        // --- Column 3: Conformance Level (with Badges and Tooltip) ---
+        row.insertCell().textContent = param.type || 'N/A';
         const conformanceCell = row.insertCell();
-        // Default to 'Optional' if conformance isn't specified in the data
         const conformanceValue = param.conformance || 'Optional';
-        let badgeClass = 'bg-secondary'; // Default badge style
-        let titleText = 'Conformance level not specified in CapabilityStatement.'; // Default tooltip text
-
-        // Determine badge style and tooltip text based on the conformance value
+        let badgeClass = 'bg-secondary';
+        let titleText = 'Conformance level not specified in CapabilityStatement.';
         if (conformanceValue === 'SHALL') {
-            badgeClass = 'bg-danger'; // Red for SHALL (Mandatory)
+            badgeClass = 'bg-danger';
             titleText = 'Server SHALL support this parameter.';
         } else if (conformanceValue === 'SHOULD') {
-            badgeClass = 'bg-warning text-dark'; // Yellow for SHOULD (Recommended)
+            badgeClass = 'bg-warning text-dark';
             titleText = 'Server SHOULD support this parameter.';
         } else if (conformanceValue === 'MAY') {
-            badgeClass = 'bg-info text-dark'; // Blue for MAY (Optional but defined)
+            badgeClass = 'bg-info text-dark';
             titleText = 'Server MAY support this parameter.';
         } else if (conformanceValue === 'Optional') {
-             badgeClass = 'bg-light text-dark border'; // Light grey for Optional (Not explicitly mentioned in Caps)
+            badgeClass = 'bg-light text-dark border';
             titleText = 'Server support for this parameter is optional.';
         }
-        // Add handling for other potential values like 'SHALL-NOT', 'SHOULD-NOT' if needed
-
-        // Set the tooltip attributes
         conformanceCell.setAttribute('title', titleText);
         conformanceCell.setAttribute('data-bs-toggle', 'tooltip');
         conformanceCell.setAttribute('data-bs-placement', 'top');
-        // Set the cell content with the styled badge
         conformanceCell.innerHTML = `<span class="badge ${badgeClass}">${escapeHtmlAttr(conformanceValue)}</span>`;
-
-        // Initialize or re-initialize the Bootstrap tooltip for this specific cell
-        // This is important because the table rows are added dynamically
         const existingTooltip = bootstrap.Tooltip.getInstance(conformanceCell);
-        if (existingTooltip) {
-            existingTooltip.dispose(); // Remove any previous tooltip instance to avoid conflicts
-        }
-        new bootstrap.Tooltip(conformanceCell); // Create and initialize the new tooltip
-
-        // --- Column 4: Description (with FHIRPath Tooltip if available) ---
+        if (existingTooltip) { existingTooltip.dispose(); }
+        new bootstrap.Tooltip(conformanceCell);
         const descriptionCell = row.insertCell();
-        // Use escapeHtmlAttr for the description text
         descriptionCell.innerHTML = `<small>${escapeHtmlAttr(param.description || 'No description available.')}</small>`;
-        // If a FHIRPath expression exists, add it as a tooltip
         if (param.expression) {
             descriptionCell.setAttribute('title', `FHIRPath: ${param.expression}`);
             descriptionCell.setAttribute('data-bs-toggle', 'tooltip');
             descriptionCell.setAttribute('data-bs-placement', 'top');
-             // Initialize or re-initialize the tooltip
             const existingDescTooltip = bootstrap.Tooltip.getInstance(descriptionCell);
-             if (existingDescTooltip) {
-                 existingDescTooltip.dispose();
-             }
+            if (existingDescTooltip) { existingDescTooltip.dispose(); }
             new bootstrap.Tooltip(descriptionCell);
         }
-    }); // End forEach loop over searchParamsData
-
+    });
     console.log('[renderSearchParametersTable] Finished rendering parameters.');
-} // End renderSearchParametersTable function
-
+} // End renderSearchParametersTable
 
 // --- DOMContentLoaded Listener ---
 document.addEventListener('DOMContentLoaded', function() {
@@ -1303,6 +1262,7 @@ document.addEventListener('DOMContentLoaded', function() {
         copyRawDefButton = document.getElementById('copy-raw-def-button');
         copyRawExButton = document.getElementById('copy-raw-ex-button');
         copyPrettyJsonButton = document.getElementById('copy-pretty-json-button');
+        includeNarrativeCheckbox = document.getElementById('includeNarrative');
 
         // --- Initialize Highlight.js ---
         hljs.configure({ languages: ['json'] });
@@ -1325,7 +1285,7 @@ document.addEventListener('DOMContentLoaded', function() {
                 const resourceType = link.dataset.resourceType;
                 if (!resourceType) { console.error("Missing data-resource-type"); return; }
                 console.log("Resource type link clicked:", resourceType);
-                await populateStructure(resourceType); // Uses V9 buildTreeData, V2 populateStructure
+                await populateStructure(resourceType);
                 populateExampleSelector(resourceType);
                 if (structureDisplayWrapper) { structureDisplayWrapper.scrollIntoView({ behavior: 'smooth', block: 'start' }); }
             });
@@ -1336,7 +1296,21 @@ document.addEventListener('DOMContentLoaded', function() {
             exampleSelect.addEventListener('change', function(event) { fetchAndDisplayExample(this.value); });
         } else { console.warn("Example select dropdown not found."); }
 
-        // --- No Collapse Listeners Here ---
+        // Narrative Toggle Checkbox Handler
+        if (includeNarrativeCheckbox) {
+            includeNarrativeCheckbox.addEventListener('change', async function() {
+                const selectedFilePath = exampleSelect?.value;
+                const resourceType = exampleResourceTypeTitle?.textContent;
+                if (selectedFilePath) {
+                    await fetchAndDisplayExample(selectedFilePath);
+                }
+                if (resourceType && resourceType !== '(unknown)') {
+                    await populateStructure(resourceType);
+                }
+            });
+        } else {
+            console.warn("Narrative checkbox not found.");
+        }
 
         // --- Initial UI State ---
         if(structureDisplayWrapper) structureDisplayWrapper.style.display = 'none';

templates/fhir_ui.html

@@ -8,13 +8,6 @@
         <p class="lead mb-4">
             Interact with FHIR servers using GET, POST, PUT, or DELETE requests. Toggle between local HAPI or a custom server to explore resources or perform searches.
         </p>
-        <!-----------------------------------------------------------------remove the buttons-----------------------------------------------------
-        <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>
-            <a href="{{ url_for('validate_sample') }}" class="btn btn-outline-secondary btn-lg px-4">Validate FHIR Sample</a>
-            <a href="{{ url_for('fhir_ui_operations') }}" class="btn btn-outline-secondary btn-lg px-4">FHIR UI Operations</a>
-        </div>
-        -------------------------------------------------------------------------------------------------------------------------------------------->
     </div>
 </div>
 
@@ -28,12 +21,37 @@
                     <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 HAPI</span>
+                            <span id="toggleLabel">Use Local Server</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>
                     <small id="fhirServerHelp" class="form-text text-muted">Toggle to use local HAPI (http://localhost:8080/fhir) or enter a custom FHIR server URL.</small>
                 </div>
+                <div class="mb-3" id="authSection" style="display: none;">
+                    <label class="form-label">Authentication</label>
+                    <div class="row g-3 align-items-end">
+                        <div class="col-md-5">
+                            <select class="form-select" id="authType" name="auth_type">
+                                <option value="none" selected>None</option>
+                                <option value="bearer">Bearer Token</option>
+                                <option value="basic">Basic Authentication</option>
+                            </select>
+                        </div>
+                        <div class="col-md-7" id="authInputsGroup" style="display: none;">
+                            <div id="bearerTokenInput" style="display: none;">
+                                <label for="bearerToken" class="form-label">Bearer Token</label>
+                                <input type="password" class="form-control" id="bearerToken" name="bearer_token" placeholder="Enter Bearer Token">
+                            </div>
+                            <div id="basicAuthInputs" style="display: none;">
+                                <label for="username" class="form-label">Username</label>
+                                <input type="text" class="form-control mb-2" id="username" name="username" placeholder="Enter Username">
+                                <label for="password" class="form-label">Password</label>
+                                <input type="password" class="form-control" id="password" name="password" placeholder="Enter Password">
+                            </div>
+                        </div>
+                    </div>
+                    <small class="form-text text-muted">Select authentication method for the custom FHIR server.</small>
+                </div>
                 <div class="mb-3">
                     <label for="fhirPath" class="form-label">FHIR Path</label>
                     <input type="text" class="form-control" id="fhirPath" name="fhir_path" placeholder="e.g., Patient/wang-li" required aria-describedby="fhirPathHelp">
@@ -44,13 +62,10 @@
                     <div class="d-flex gap-2 flex-wrap">
                         <input type="radio" class="btn-check" name="method" id="get" value="GET" checked>
                         <label class="btn btn-outline-success" for="get"><span class="badge bg-success">GET</span></label>
-
                         <input type="radio" class="btn-check" name="method" id="post" value="POST">
                         <label class="btn btn-outline-primary" for="post"><span class="badge bg-primary">POST</span></label>
-
                         <input type="radio" class="btn-check" name="method" id="put" value="PUT">
                         <label class="btn btn-outline-warning" for="put"><span class="badge bg-warning text-dark">PUT</span></label>
-
                         <input type="radio" class="btn-check" name="method" id="delete" value="DELETE">
                         <label class="btn btn-outline-danger" for="delete"><span class="badge bg-danger">DELETE</span></label>
                     </div>
@@ -108,209 +123,272 @@ document.addEventListener('DOMContentLoaded', function() {
     const copyRequestBodyButton = document.getElementById('copyRequestBody');
     const copyResponseHeadersButton = document.getElementById('copyResponseHeaders');
     const copyResponseBodyButton = document.getElementById('copyResponseBody');
+    const authSection = document.getElementById('authSection');
+    const authTypeSelect = document.getElementById('authType');
+    const authInputsGroup = document.getElementById('authInputsGroup');
+    const bearerTokenInput = document.getElementById('bearerTokenInput');
+    const basicAuthInputs = document.getElementById('basicAuthInputs');
+    const usernameInput = document.getElementById('username');
+    const passwordInput = document.getElementById('password');
 
     // Basic check for critical elements
     if (!form || !sendButton || !fhirPathInput || !responseCard || !toggleServerButton || !fhirServerUrlInput || !responseStatus || !responseHeaders || !responseBody || !toggleLabel) {
         console.error("One or more critical UI elements could not be found. Script execution halted.");
         alert("Error initializing UI components. Please check the console.");
-        return; // Stop script execution
+        return;
     }
     console.log("All critical elements checked/found.");
 
     // --- State Variable ---
-    // Default assumes standalone, will be forced otherwise by appMode check below
     let useLocalHapi = true;
 
     // --- Get App Mode from Flask Context ---
-    // Ensure this variable is correctly passed from Flask using the context_processor
     const appMode = '{{ app_mode | default("standalone") | lower }}';
     console.log('App Mode Detected:', appMode);
 
-    // --- DEFINE HELPER FUNCTIONS ---
-
-    // Validates request body, returns null on error, otherwise returns body string or empty string
+    // --- Helper Functions ---
     function validateRequestBody(method, path) {
         if (!requestBodyInput || !jsonError) return (method === 'POST' || method === 'PUT') ? '' : undefined;
         const bodyValue = requestBodyInput.value.trim();
-        requestBodyInput.classList.remove('is-invalid'); // Reset validation
+        requestBodyInput.classList.remove('is-invalid');
         jsonError.style.display = 'none';
 
-        if (!bodyValue) return ''; // Empty body is valid for POST/PUT
+        if (!bodyValue) return '';
 
         const isSearch = path && path.endsWith('_search');
         const isJson = bodyValue.startsWith('{') || bodyValue.startsWith('[');
         const isXml = bodyValue.startsWith('<');
         const isForm = !isJson && !isXml;
 
-        if (method === 'POST' && isSearch && isForm) { // POST Search with form params
+        if (method === 'POST' && isSearch && isForm) {
             return bodyValue;
-        } else if (method === 'POST' || method === 'PUT') { // Other POST/PUT expect JSON/XML
+        } else if (method === 'POST' || method === 'PUT') {
             if (isJson) {
                 try { JSON.parse(bodyValue); return bodyValue; }
                 catch (e) { jsonError.textContent = `Invalid JSON: ${e.message}`; }
             } else if (isXml) {
-                // Basic XML check is difficult in JS, accept it for now
-                // Backend or target server will validate fully
                 return bodyValue;
-            } else { // Neither JSON nor XML, and not a POST search form
+            } else {
                 jsonError.textContent = 'Request body must be valid JSON or XML for PUT/POST (unless using POST _search with form parameters).';
             }
             requestBodyInput.classList.add('is-invalid');
             jsonError.style.display = 'block';
-            return null; // Indicate validation error
+            return null;
         }
-        return undefined; // Indicate no body should be sent for GET/DELETE
+        return undefined;
     }
 
-    // Cleans path for proxying
     function cleanFhirPath(path) {
         if (!path) return '';
-        // Remove optional leading 'r4/' or 'fhir/', then trim slashes
         return path.replace(/^(r4\/|fhir\/)*/i, '').replace(/^\/+|\/+$/g, '');
     }
 
-    // Copies text to clipboard
     async function copyToClipboard(text, button) {
         if (text === null || text === undefined || !button || !navigator.clipboard) return;
         try {
             await navigator.clipboard.writeText(String(text));
             const originalIcon = button.innerHTML;
             button.innerHTML = '<i class="bi bi-check-lg"></i> Copied!';
-            setTimeout(() => { if(button.isConnected) button.innerHTML = originalIcon; }, 1500);
-        } catch (err) { console.error('Copy failed:', err); /* Optionally alert user */ }
+            setTimeout(() => { if (button.isConnected) button.innerHTML = originalIcon; }, 1500);
+        } catch (err) { console.error('Copy failed:', err); }
     }
 
-    // Updates the UI elements related to the server toggle button/input
     function updateServerToggleUI() {
         if (appMode === 'lite') {
-            // LITE MODE: Force Custom URL, disable toggle
-            useLocalHapi = false; // Force state
+            useLocalHapi = false;
             toggleServerButton.disabled = true;
             toggleServerButton.classList.add('disabled');
-            toggleServerButton.style.pointerEvents = 'none'; // Make unclickable
+            toggleServerButton.style.pointerEvents = 'none';
             toggleServerButton.setAttribute('aria-disabled', 'true');
             toggleServerButton.title = "Local HAPI server is unavailable in Lite mode";
-            toggleLabel.textContent = 'Use Custom URL'; // Always show this label
-            fhirServerUrlInput.style.display = 'block'; // Always show input
+            toggleLabel.textContent = 'Use Custom URL';
+            fhirServerUrlInput.style.display = 'block';
             fhirServerUrlInput.placeholder = "Enter FHIR Base URL (Local HAPI unavailable)";
-            fhirServerUrlInput.required = true; // Make required in lite mode
+            fhirServerUrlInput.required = true;
+            authSection.style.display = 'block';
         } else {
-            // STANDALONE MODE: Allow toggle
             toggleServerButton.disabled = false;
             toggleServerButton.classList.remove('disabled');
             toggleServerButton.style.pointerEvents = 'auto';
             toggleServerButton.removeAttribute('aria-disabled');
             toggleServerButton.title = "Toggle between Local HAPI and Custom URL";
-            toggleLabel.textContent = useLocalHapi ? 'Using Local HAPI' : 'Using Custom URL';
+            toggleLabel.textContent = useLocalHapi ? 'Using Local Server' : 'Using Custom URL';
             fhirServerUrlInput.style.display = useLocalHapi ? 'none' : 'block';
             fhirServerUrlInput.placeholder = "e.g., https://hapi.fhir.org/baseR4";
-            fhirServerUrlInput.required = !useLocalHapi; // Required only if custom is selected
+            fhirServerUrlInput.required = !useLocalHapi;
+            authSection.style.display = useLocalHapi ? 'none' : 'block';
         }
-        fhirServerUrlInput.classList.remove('is-invalid'); // Clear validation state on toggle
+        fhirServerUrlInput.classList.remove('is-invalid');
+        updateAuthInputsUI();
         console.log(`UI Updated: useLocalHapi=${useLocalHapi}, Button Disabled=${toggleServerButton.disabled}, Input Visible=${fhirServerUrlInput.style.display !== 'none'}, Input Required=${fhirServerUrlInput.required}`);
     }
 
-    // Toggles the server selection state (only effective in Standalone mode)
+    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' && bearerTokenInput) bearerTokenInput.value = '';
+        if (authType !== 'basic' && usernameInput) usernameInput.value = '';
+        if (authType !== 'basic' && passwordInput) passwordInput.value = '';
+    }
+
     function toggleServer() {
         if (appMode === 'lite') {
             console.log("Toggle ignored: Lite mode active.");
-            return; // Do nothing in lite mode
+            return;
         }
         useLocalHapi = !useLocalHapi;
         if (useLocalHapi && fhirServerUrlInput) {
-            fhirServerUrlInput.value = ''; // Clear custom URL when switching to local
+            fhirServerUrlInput.value = '';
         }
-        updateServerToggleUI(); // Update UI based on new state
-        console.log(`Server toggled: Now using ${useLocalHapi ? 'Local HAPI' : 'Custom URL'}`);
+        updateServerToggleUI();
+        updateAuthInputsUI();
+        console.log(`Server toggled: Now using ${useLocalHapi ? 'Local Server' : 'Custom URL'}`);
     }
 
-    // Updates visibility of the Request Body textarea based on selected HTTP method
     function updateRequestBodyVisibility() {
         const selectedMethod = document.querySelector('input[name="method"]:checked')?.value;
         if (!requestBodyGroup || !selectedMethod) return;
         const showBody = (selectedMethod === 'POST' || selectedMethod === 'PUT');
         requestBodyGroup.style.display = showBody ? 'block' : 'none';
-        if (!showBody) { // Clear body and errors if body not needed
+        if (!showBody) {
             if (requestBodyInput) requestBodyInput.value = '';
             if (jsonError) jsonError.style.display = 'none';
             if (requestBodyInput) requestBodyInput.classList.remove('is-invalid');
         }
     }
 
-    // --- INITIAL SETUP & MODE CHECK ---
-    updateServerToggleUI(); // Set initial UI based on detected mode and default state
-    updateRequestBodyVisibility(); // Set initial visibility based on default method (GET)
+    // --- Initial Setup ---
+    updateServerToggleUI();
+    updateRequestBodyVisibility();
 
-    // --- ATTACH EVENT LISTENERS ---
+    // --- Event Listeners ---
     toggleServerButton.addEventListener('click', toggleServer);
     if (methodRadios) { methodRadios.forEach(radio => { radio.addEventListener('change', updateRequestBodyVisibility); }); }
-    if (requestBodyInput && fhirPathInput) { requestBodyInput.addEventListener('input', () => validateRequestBody( document.querySelector('input[name="method"]:checked')?.value, fhirPathInput.value )); }
+    if (requestBodyInput && fhirPathInput) { requestBodyInput.addEventListener('input', () => validateRequestBody(document.querySelector('input[name="method"]:checked')?.value, fhirPathInput.value)); }
     if (copyRequestBodyButton && requestBodyInput) { copyRequestBodyButton.addEventListener('click', () => copyToClipboard(requestBodyInput.value, copyRequestBodyButton)); }
     if (copyResponseHeadersButton && responseHeaders) { copyResponseHeadersButton.addEventListener('click', () => copyToClipboard(responseHeaders.textContent, copyResponseHeadersButton)); }
     if (copyResponseBodyButton && responseBody) { copyResponseBodyButton.addEventListener('click', () => copyToClipboard(responseBody.textContent, copyResponseBodyButton)); }
+    if (authTypeSelect) { authTypeSelect.addEventListener('change', updateAuthInputsUI); }
 
     // --- Send Request Button Listener ---
     sendButton.addEventListener('click', async function() {
         console.log("Send Request button clicked.");
-        // --- UI Reset ---
-        sendButton.disabled = true; sendButton.textContent = 'Sending...';
+        sendButton.disabled = true;
+        sendButton.textContent = 'Sending...';
         responseCard.style.display = 'none';
-        responseStatus.textContent = ''; responseHeaders.textContent = ''; responseBody.textContent = '';
-        responseStatus.className = 'badge'; // Reset badge class
-        fhirServerUrlInput.classList.remove('is-invalid'); // Reset validation
-        if(requestBodyInput) requestBodyInput.classList.remove('is-invalid');
-        if(jsonError) jsonError.style.display = 'none';
+        responseStatus.textContent = '';
+        responseHeaders.textContent = '';
+        responseBody.textContent = '';
+        responseStatus.className = 'badge';
+        fhirServerUrlInput.classList.remove('is-invalid');
+        if (requestBodyInput) requestBodyInput.classList.remove('is-invalid');
+        if (jsonError) jsonError.style.display = 'none';
+        if (bearerTokenInput) bearerTokenInput.classList.remove('is-invalid');
+        if (usernameInput) usernameInput.classList.remove('is-invalid');
+        if (passwordInput) passwordInput.classList.remove('is-invalid');
 
         // --- Get Values ---
         const path = fhirPathInput.value.trim();
         const method = document.querySelector('input[name="method"]:checked')?.value;
         const customUrl = fhirServerUrlInput.value.trim();
         let body = undefined;
+        const authType = authTypeSelect ? authTypeSelect.value : 'none';
+        const bearerToken = document.getElementById('bearerToken').value.trim();
+        const username = usernameInput ? usernameInput.value.trim() : '';
+        const password = passwordInput ? passwordInput.value : '';
 
         // --- Basic Input Validation ---
-        if (!path) { alert('Please enter a FHIR Path.'); sendButton.disabled = false; sendButton.textContent = 'Send Request'; return; }
-        if (!method) { alert('Please select a Request Type.'); sendButton.disabled = false; sendButton.textContent = 'Send Request'; return; }
-        if (!useLocalHapi && !customUrl) { // Custom URL mode needs a URL
-            alert('Please enter a custom FHIR Server URL.'); fhirServerUrlInput.classList.add('is-invalid'); sendButton.disabled = false; sendButton.textContent = 'Send Request'; return;
+        if (!path) {
+            alert('Please enter a FHIR Path.');
+            sendButton.disabled = false;
+            sendButton.textContent = 'Send Request';
+            return;
         }
-        if (!useLocalHapi && customUrl) { // Validate custom URL format
+        if (!method) {
+            alert('Please select a Request Type.');
+            sendButton.disabled = false;
+            sendButton.textContent = 'Send Request';
+            return;
+        }
+        if (!useLocalHapi && !customUrl) {
+            alert('Please enter a custom FHIR Server URL.');
+            fhirServerUrlInput.classList.add('is-invalid');
+            sendButton.disabled = false;
+            sendButton.textContent = 'Send Request';
+            return;
+        }
+        if (!useLocalHapi && customUrl) {
             try { new URL(customUrl); }
-             catch (_) { alert('Invalid custom FHIR Server URL format.'); fhirServerUrlInput.classList.add('is-invalid'); sendButton.disabled = false; sendButton.textContent = 'Send Request'; return; }
+            catch (_) {
+                alert('Invalid custom FHIR Server URL format.');
+                fhirServerUrlInput.classList.add('is-invalid');
+                sendButton.disabled = false;
+                sendButton.textContent = 'Send Request';
+                return;
+            }
         }
 
-        // --- Validate & Get Body (if needed) ---
+        // --- Validate Authentication ---
+        if (!useLocalHapi) {
+            if (authType === 'bearer' && !bearerToken) {
+                alert('Please enter a Bearer Token.');
+                document.getElementById('bearerToken').classList.add('is-invalid');
+                sendButton.disabled = false;
+                sendButton.textContent = 'Send Request';
+                return;
+            }
+            if (authType === 'basic' && (!username || !password)) {
+                alert('Please enter both Username and Password for Basic Authentication.');
+                if (!username) usernameInput.classList.add('is-invalid');
+                if (!password) passwordInput.classList.add('is-invalid');
+                sendButton.disabled = false;
+                sendButton.textContent = 'Send Request';
+                return;
+            }
+        }
+
+        // --- Validate & Get Body ---
         if (method === 'POST' || method === 'PUT') {
             body = validateRequestBody(method, path);
-             if (body === null) { // null indicates validation error
-                 alert('Request body contains invalid JSON/Format.'); sendButton.disabled = false; sendButton.textContent = 'Send Request'; return;
+            if (body === null) {
+                alert('Request body contains invalid JSON/Format.');
+                sendButton.disabled = false;
+                sendButton.textContent = 'Send Request';
+                return;
             }
-             // If body is empty string, ensure it's treated as such for fetch
             if (body === '') body = '';
         }
 
         // --- Determine Fetch URL and Headers ---
         const cleanedPath = cleanFhirPath(path);
-        const finalFetchUrl = '/fhir/' + cleanedPath; // Always send to the backend proxy endpoint
+        const finalFetchUrl = '/fhir/' + cleanedPath;
         const headers = { 'Accept': 'application/fhir+json, application/fhir+xml;q=0.9, */*;q=0.8' };
 
-        // Determine Content-Type if body exists
         if (body !== undefined) {
             if (body.trim().startsWith('{')) { headers['Content-Type'] = 'application/fhir+json'; }
             else if (body.trim().startsWith('<')) { headers['Content-Type'] = 'application/fhir+xml'; }
             else if (method === 'POST' && path.endsWith('_search') && body && !body.trim().startsWith('{') && !body.trim().startsWith('<')) { headers['Content-Type'] = 'application/x-www-form-urlencoded'; }
-             else if (body) { headers['Content-Type'] = 'application/fhir+json'; } // Default if unknown but present
+            else if (body) { headers['Content-Type'] = 'application/fhir+json'; }
         }
 
-        // Add Custom Target Header if needed
         if (!useLocalHapi && customUrl) {
-            headers['X-Target-FHIR-Server'] = customUrl.replace(/\/+$/, ''); // Send custom URL without trailing slash
+            headers['X-Target-FHIR-Server'] = customUrl.replace(/\/+$/, '');
             console.log("Adding header X-Target-FHIR-Server:", headers['X-Target-FHIR-Server']);
+            if (authType === 'bearer') {
+                headers['Authorization'] = `Bearer ${bearerToken}`;
+                console.log("Adding header Authorization: Bearer <truncated>");
+            } else if (authType === 'basic') {
+                const credentials = btoa(`${username}:${password}`);
+                headers['Authorization'] = `Basic ${credentials}`;
+                console.log("Adding header Authorization: Basic <redacted>");
+            }
         }
 
-        // Add CSRF token ONLY if sending to local proxy (for modifying methods)
         const csrfTokenInput = form.querySelector('input[name="csrf_token"]');
         const csrfToken = csrfTokenInput ? csrfTokenInput.value : null;
-        // Include DELETE method for CSRF check
         if (useLocalHapi && ['POST', 'PUT', 'DELETE', 'PATCH'].includes(method) && csrfToken) {
             headers['X-CSRFToken'] = csrfToken;
             console.log("CSRF Token added for local request.");
@@ -319,7 +397,7 @@ document.addEventListener('DOMContentLoaded', function() {
         }
 
         console.log(`Executing Fetch: Method=${method}, URL=${finalFetchUrl}, LocalHAPI=${useLocalHapi}`);
-        console.log("Request Headers:", headers);
+        console.log("Request Headers:", { ...headers, Authorization: headers.Authorization ? '<redacted>' : undefined });
         if (body !== undefined) console.log("Request Body (first 300 chars):", (body || '').substring(0, 300) + ((body?.length ?? 0) > 300 ? "..." : ""));
 
         // --- Make the Fetch Request ---
@@ -327,10 +405,9 @@ document.addEventListener('DOMContentLoaded', function() {
             const response = await fetch(finalFetchUrl, {
                 method: method,
                 headers: headers,
-                body: body // Will be undefined for GET/DELETE
+                body: body
             });
 
-            // --- Process Response ---
             responseCard.style.display = 'block';
             responseStatus.textContent = `${response.status} ${response.statusText}`;
             responseStatus.className = `badge ${response.ok ? 'bg-success' : 'bg-danger'}`;
@@ -343,13 +420,10 @@ document.addEventListener('DOMContentLoaded', function() {
             let responseBodyText = await response.text();
             let displayBody = responseBodyText;
 
-            // Attempt to pretty-print JSON
             if (responseContentType.includes('json') && responseBodyText.trim()) {
                 try { displayBody = JSON.stringify(JSON.parse(responseBodyText), null, 2); }
-                catch (e) { console.warn("Failed to pretty-print JSON response:", e); /* Show raw text */ }
-            }
-            // Attempt to pretty-print XML (basic indentation)
-            else if (responseContentType.includes('xml') && responseBodyText.trim()) {
+                catch (e) { console.warn("Failed to pretty-print JSON response:", e); }
+            } else if (responseContentType.includes('xml') && responseBodyText.trim()) {
                 try {
                     let formattedXml = '';
                     let indent = 0;
@@ -357,34 +431,32 @@ document.addEventListener('DOMContentLoaded', function() {
                     for (let i = 0; i < xmlLines.length; i++) {
                         const node = xmlLines[i];
                         if (!node || node.trim().length === 0) continue;
-                           if (node.match(/^<\/\w/)) indent--; // Closing tag
+                        if (node.match(/^<\/\w/)) indent--;
                         formattedXml += '  '.repeat(Math.max(0, indent)) + node.trim() + '\n';
-                           if (node.match(/^<\w/) && !node.match(/\/>$/) && !node.match(/^<\?/)) indent++; // Opening tag
+                        if (node.match(/^<\w/) && !node.match(/\/>$/) && !node.match(/^<\?/)) indent++;
                     }
                     displayBody = formattedXml.trim();
-                 } catch(e) { console.warn("Basic XML formatting failed:", e); /* Show raw text */ }
+                } catch (e) { console.warn("Basic XML formatting failed:", e); }
             }
 
             responseBody.textContent = displayBody;
 
-             // Highlight response body if Prism.js is available
             if (typeof Prism !== 'undefined') {
-                 responseBody.className = 'border p-2 bg-light'; // Reset base classes
+                responseBody.className = 'border p-2 bg-light';
                 if (responseContentType.includes('json')) {
                     responseBody.classList.add('language-json');
                 } else if (responseContentType.includes('xml')) {
                     responseBody.classList.add('language-xml');
-                 } // Add other languages if needed
+                }
                 Prism.highlightElement(responseBody);
             }
 
         } 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';
-            // Provide a more informative error message
             let errorDetail = `Error: ${error.message}\n\n`;
             if (useLocalHapi) {
                 errorDetail += `Could not connect to the FHIRFLARE proxy at ${finalFetchUrl}. Ensure the toolkit server and the local HAPI FHIR server (at http://localhost:8080/fhir) are running.`;
@@ -393,10 +465,10 @@ document.addEventListener('DOMContentLoaded', function() {
             }
             responseBody.textContent = errorDetail;
         } finally {
-            sendButton.disabled = false; sendButton.textContent = 'Send Request';
+            sendButton.disabled = false;
+            sendButton.textContent = 'Send Request';
         }
-    }); // End sendButton listener
-
-}); // End DOMContentLoaded Listener
+    });
+});
 </script>
 {% endblock %}

templates/ig_configurator.html

@@ -0,0 +1,40 @@
+{% 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 %}

templates/import_ig.html

@@ -1,22 +1,45 @@
 {% extends "base.html" %}
-
 {% from "_form_helpers.html" import render_field %}
 
 {% block content %}
 <div class="px-4 py-5 my-5 text-center">
-    <img class="d-block mx-auto mb-4" src="{{ url_for('static', filename='FHIRFLARE.png') }}" alt="FHIRFLARE Ig Toolkit" width="192" height="192">
+    <img class="d-block mx-auto mb-4" src="{{ url_for('static', filename='FHIRFLARE.png') }}" alt="FHIRFLARE IG Toolkit" width="192" height="192">
     <h1 class="display-5 fw-bold text-body-emphasis">Import FHIR Implementation Guides</h1>
     <div class="col-lg-6 mx-auto">
         <p class="lead mb-4">
             Import new FHIR Implementation Guides to the system for viewing.
         </p>
-          <!-----------------------------------------------------------------remove the buttons-----------------------------------------------------
-        <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>
-            <a href="{{ url_for('view_igs') }}" class="btn btn-outline-secondary btn-lg px-4">View Downloaded IGs</a>
-            <a href="{{ url_for('push_igs') }}" class="btn btn-outline-secondary btn-lg px-4">Upload IG's</a>
     </div>
-          -----------------------------------------------------------------remove the buttons----------------------------------------------------->
+</div>
+
+<div id="fire-loading-overlay" class="fire-loading-overlay d-none">
+    <div class="campfire">
+        <div class="campfire-scaler">
+            <div class="sparks">
+                <div class="spark"></div> <div class="spark"></div> <div class="spark"></div> <div class="spark"></div>
+                <div class="spark"></div> <div class="spark"></div> <div class="spark"></div> <div class="spark"></div>
+            </div>
+            <div class="logs">
+                <div class="log"><div class="streak"></div><div class="streak"></div><div class="streak"></div><div class="streak"></div><div class="streak"></div><div class="streak"></div><div class="streak"></div><div class="streak"></div><div class="streak"></div><div class="streak"></div></div>
+                <div class="log"><div class="streak"></div><div class="streak"></div><div class="streak"></div><div class="streak"></div><div class="streak"></div><div class="streak"></div><div class="streak"></div><div class="streak"></div><div class="streak"></div><div class="streak"></div></div>
+                <div class="log"><div class="streak"></div><div class="streak"></div><div class="streak"></div><div class="streak"></div><div class="streak"></div><div class="streak"></div><div class="streak"></div><div class="streak"></div><div class="streak"></div><div class="streak"></div></div>
+                <div class="log"><div class="streak"></div><div class="streak"></div><div class="streak"></div><div class="streak"></div><div class="streak"></div><div class="streak"></div><div class="streak"></div><div class="streak"></div><div class="streak"></div><div class="streak"></div></div>
+                <div class="log"><div class="streak"></div><div class="streak"></div><div class="streak"></div><div class="streak"></div><div class="streak"></div><div class="streak"></div><div class="streak"></div><div class="streak"></div><div class="streak"></div><div class="streak"></div></div>
+                <div class="log"><div class="streak"></div><div class="streak"></div><div class="streak"></div><div class="streak"></div><div class="streak"></div><div class="streak"></div><div class="streak"></div><div class="streak"></div><div class="streak"></div><div class="streak"></div></div>
+                <div class="log"><div class="streak"></div><div class="streak"></div><div class="streak"></div><div class="streak"></div><div class="streak"></div><div class="streak"></div><div class="streak"></div><div class="streak"></div><div class="streak"></div><div class="streak"></div></div>
+            </div>
+            <div class="sticks">
+                <div class="stick"></div><div class="stick"></div><div class="stick"></div><div class="stick"></div>
+            </div>
+            <div class="fire">
+                <div class="fire__red"><div class="flame"></div><div class="flame"></div><div class="flame"></div><div class="flame"></div><div class="flame"></div><div class="flame"></div><div class="flame"></div></div>
+                <div class="fire__orange"><div class="flame"></div><div class="flame"></div><div class="flame"></div><div class="flame"></div><div class="flame"></div><div class="flame"></div><div class="flame"></div></div>
+                <div class="fire__yellow"><div class="flame"></div><div class="flame"></div><div class="flame"></div><div class="flame"></div><div class="flame"></div></div>
+                <div class="fire__white"><div class="flame"></div><div class="flame"></div><div class="flame"></div><div class="flame"></div><div class="flame"></div><div class="flame"></div><div class="flame"></div></div>
+            </div>
+        </div> </div> <div class="loading-text text-center">
+        <p class="text-white mt-3">Importing Implementation Guide... Please wait.</p>
+        <p id="log-display" class="text-white mb-0"></p>
     </div>
 </div>
 
@@ -26,21 +49,13 @@
         <div class="col-md-6">
             <div class="card">
                 <div class="card-body">
-                    <form method="POST" class="form">
+                    <form id="import-ig-form" method="POST" class="form">
                         {{ form.hidden_tag() }}
                         {{ render_field(form.package_name) }}
                         {{ render_field(form.package_version) }}
-                        <!-- Dependency Pulling Mode Toggle -->
-                        <div class="mb-3">
-                            <label for="dependency_mode" class="form-label">Dependency Pulling Mode:</label>
-                            <select class="form-select" id="dependency_mode" name="dependency_mode">
-                                <option value="recursive" selected>Current Recursive</option>
-                                <option value="patch-canonical">Patch Canonical Versions</option>
-                                <option value="tree-shaking">Tree Shaking (Only Used Dependencies)</option>
-                            </select>
-                        </div>
+                        {{ render_field(form.dependency_mode) }}
                         <div class="d-grid gap-2 d-sm-flex">
-                            {{ form.submit(class="btn btn-success") }}
+                            {{ form.submit(class="btn btn-success", id="submit-btn") }}
                             <a href="{{ url_for('index') }}" class="btn btn-secondary">Back</a>
                         </div>
                     </form>
@@ -49,4 +64,82 @@
         </div>
     </div>
 </div>
+
+<script>
+    // Your existing JS here (exactly as provided before)
+    document.addEventListener('DOMContentLoaded', function() {
+        const form = document.getElementById('import-ig-form');
+        const submitBtn = document.getElementById('submit-btn');
+        const loadingOverlay = document.getElementById('fire-loading-overlay');
+        const logDisplay = document.getElementById('log-display');
+
+        if (form && submitBtn && loadingOverlay && logDisplay) {
+            form.addEventListener('submit', async function(event) {
+                event.preventDefault();
+                submitBtn.disabled = true;
+                logDisplay.textContent = 'Starting import...';
+                loadingOverlay.classList.remove('d-none'); // Show the overlay
+
+                let eventSource;
+                try {
+                    eventSource = new EventSource('{{ url_for('stream_import_logs') }}');
+                    eventSource.onmessage = function(event) {
+                        if (event.data === '[DONE]') {
+                            eventSource.close();
+                            return;
+                        }
+                        logDisplay.textContent = event.data;
+                    };
+                    eventSource.onerror = function() {
+                        console.error('SSE connection error');
+                        if(eventSource) eventSource.close();
+                        logDisplay.textContent = 'Log streaming interrupted.';
+                    };
+                } catch (e) {
+                    console.error('Failed to initialize SSE:', e);
+                    logDisplay.textContent = 'Unable to stream logs: ' + e.message;
+                }
+
+                const formData = new FormData(form);
+                try {
+                    const response = await fetch('{{ url_for('import_ig') }}', {
+                        method: 'POST',
+                        headers: { 'X-Requested-With': 'XMLHttpRequest' },
+                        body: formData
+                    });
+
+                    if (eventSource && eventSource.readyState !== EventSource.CLOSED) {
+                        eventSource.close();
+                    }
+
+                    if (!response.ok) {
+                        const errorData = await response.json().catch(() => ({ message: `HTTP error: ${response.status}` }));
+                        throw new Error(errorData.message || `HTTP error: ${response.status}`);
+                    }
+
+                    const data = await response.json();
+                    if (data.redirect) {
+                        window.location.href = data.redirect;
+                    } else {
+                        // Optional: display success message
+                    }
+                } catch (error) {
+                    console.error('Import error:', error);
+                    if (eventSource && eventSource.readyState !== EventSource.CLOSED) {
+                        eventSource.close();
+                    }
+                    const alertDiv = document.createElement('div');
+                    alertDiv.className = 'alert alert-danger mt-3';
+                    alertDiv.textContent = `Import failed: ${error.message}`;
+                    form.closest('.card-body').appendChild(alertDiv);
+                } finally {
+                    loadingOverlay.classList.add('d-none'); // Hide overlay when done
+                    submitBtn.disabled = false;
+                }
+            });
+        } else {
+            console.error('Required elements missing for import script.');
+        }
+    });
+</script>
 {% endblock %}

templates/index.html

@@ -1,24 +1,168 @@
 {% extends "base.html" %}
 
+{% block body_class %}fire-animation-page{% endblock %}
+
 {% block content %}
 <div class="px-4 py-5 my-5 text-center">
-    <img class="d-block mx-auto mb-4" src="{{ url_for('static', filename='FHIRFLARE.png') }}" alt="FHIRFLARE Ig Toolkit" width="512" height="512">
+    <div id="logo-container" class="mb-4">
+        <img class="d-block mx-auto" src="{{ url_for('static', filename='FHIRFLARE.png') }}" alt="FHIRFLARE IG Toolkit" width="256" height="256">
+    </div>
+    <div id="animation-container" class="mb-4 d-none">
+        <div class="section-center">
+            <div class="moon">
+                <div></div>
+                <div></div>
+                <div></div>
+            </div>
+            <div class="shooting-star"></div>
+            <div class="shooting-star-2"></div>
+            <div class="star"></div>
+            <div class="star snd"></div>
+            <div class="star trd"></div>
+            <div class="star fth"></div>
+            <div class="star fith"></div>
+            <div class="circle"></div>
+            <div class="wood-circle"></div>
+            <div class="wood"></div>
+            <div class="tree-1"></div>
+            <div class="tree-2"></div>
+            <div class="fire">
+                <span></span>
+                <span></span>
+                <span></span>
+            </div>
+            <div class="smoke">
+                <span class="s-0"></span>
+                <span class="s-1"></span>
+                <span class="s-2"></span>
+                <span class="s-3"></span>
+                <span class="s-4"></span>
+                <span class="s-5"></span>
+                <span class="s-6"></span>
+                <span class="s-7"></span>
+                <span class="s-8"></span>
+                <span class="s-9"></span>
+            </div>
+        </div>
+    </div>
     <h1 class="display-5 fw-bold text-body-emphasis">Welcome to {{ site_name }}</h1>
     <div class="col-lg-6 mx-auto">
-        <p class="lead mb-4">
-            Simple tool for importing, viewing, and validating FHIR Implementation Guides.
-        </p>
-        <div class="d-grid gap-2 d-sm-flex justify-content-sm-center flex-wrap"> 
-            <a href="{{ url_for('import_ig') }}" class="btn btn-primary btn-lg px-4 gap-3 mb-2">Import FHIR IG</a>
-            <a href="{{ url_for('view_igs') }}" class="btn btn-outline-secondary btn-lg px-4 mb-2">Manage FHIR Packages</a> 
-            <a href="{{ url_for('push_igs') }}" class="btn btn-outline-secondary btn-lg px-4 mb-2">Push IGs</a> 
-            <a href="{{ url_for('upload_test_data') }}" class="btn btn-outline-secondary btn-lg px-4 mb-2">Upload Test Data</a>
-            <a href="{{ url_for('validate_sample') }}" class="btn btn-outline-secondary btn-lg px-4 mb-2">Validate FHIR Sample</a>
-            <a href="{{ url_for('fhir_ui') }}" class="btn btn-outline-secondary btn-lg px-4 mb-2">FHIR API Explorer</a>
-            <a href="{{ url_for('fhir_ui_operations') }}" class="btn btn-outline-secondary btn-lg px-4 mb-2">FHIR UI Operations</a>
-            <a href="{{ url_for('fsh_converter') }}" class="btn btn-outline-secondary btn-lg px-4 mb-2">FSH Converter</a>
-            <a href="{{ url_for('about') }}" class="btn btn-outline-info btn-lg px-4 mb-2">About</a>
-        </div>
+        <p class="lead mb-2">Simple tool for importing, viewing, and validating FHIR Implementation Guides.</p>
+        <p class="text-muted">Streamline Your FHIR Workflow</p>
     </div>
 </div>
+
+<div class="container">
+    <div class="row g-4">
+        <!-- IG Management -->
+        <div class="col-md-4">
+            <div class="card h-100">
+                <div class="card-body text-center">
+                    <h5 class="card-title">IG Management</h5>
+                    <p class="card-text">Import and manage FHIR Implementation Guides.</p>
+                    <div class="d-grid gap-2">
+                        <!-- <a href="{{ url_for('import_ig') }}" class="btn btn-primary">Import FHIR IG</a> -->
+                        <a href="{{ url_for('search_and_import') }}" class="btn btn-primary">Search & Import IGs</a>
+                        <a href="{{ url_for('view_igs') }}" class="btn btn-outline-secondary">Manage FHIR Packages</a>
+                        <a href="{{ url_for('push_igs') }}" class="btn btn-outline-secondary">Push IGs</a>
+                    </div>
+                </div>
+            </div>
+        </div>
+        <!-- Validation & Testing -->
+        <div class="col-md-4">
+            <div class="card h-100">
+                <div class="card-body text-center">
+                    <h5 class="card-title">Validation & Testing</h5>
+                    <p class="card-text">Validate and test FHIR resources.</p>
+                    <div class="d-grid gap-2">
+                        <a href="{{ url_for('upload_test_data') }}" class="btn btn-outline-secondary">Upload Test Data</a>
+                        <a href="{{ url_for('validate_sample') }}" class="btn btn-outline-secondary">Validate FHIR Sample</a>
+                        <a href="{{ url_for('retrieve_split_data') }}" class="btn btn-outline-secondary">Retrieve & Split Data</a>
+                    </div>
+                </div>
+            </div>
+        </div>
+        <!-- API & Tools -->
+        <div class="col-md-4">
+            <div class="card h-100">
+                <div class="card-body text-center">
+                    <h5 class="card-title">API & Tools</h5>
+                    <p class="card-text">Explore FHIR APIs and convert resources.</p>
+                    <div class="d-grid gap-2">
+                        <a href="{{ url_for('fhir_ui') }}" class="btn btn-outline-secondary">FHIR API Explorer</a>
+                        <a href="{{ url_for('fhir_ui_operations') }}" class="btn btn-outline-secondary">FHIR UI Operations</a>
+                        <a href="{{ url_for('fsh_converter') }}" class="btn btn-outline-secondary">FSH Converter</a>
+                    </div>
+                </div>
+            </div>
+        </div>
+    </div>
+    <div class="text-center mt-4">
+        <a href="{{ url_for('about') }}" class="btn btn-outline-info">About FHIRFLARE</a>
+    </div>
+</div>
+
+<style>
+    #logo-container {
+        animation: fadeOut 30s forwards;
+    }
+
+    @keyframes fadeOut {
+        0% { opacity: 1; }
+        95% { opacity: 1; }
+        100% { opacity: 0; display: none; }
+    }
+
+    #animation-container {
+        transition: opacity 1s ease;
+    }
+</style>
+
+<script>
+document.addEventListener('DOMContentLoaded', () => {
+    const logoContainer = document.getElementById('logo-container');
+    const animationContainer = document.getElementById('animation-container');
+    const htmlElement = document.documentElement;
+
+    // After 30 seconds, fade out logo and show animation
+    setTimeout(() => {
+        logoContainer.style.display = 'none';
+        animationContainer.classList.remove('d-none');
+        animationContainer.style.opacity = '1';
+    }, 30000);
+
+    // Sync animation with theme (reversed: dark = fire-on, light = fire-off)
+    const updateAnimationState = () => {
+        const savedTheme = localStorage.getItem('theme') || (document.cookie.includes('theme=dark') ? 'dark' : 'light');
+        const isDark = savedTheme === 'dark';
+        document.body.classList.toggle('fire-on', isDark); // Dark theme: fire-on, Light theme: fire-off
+    };
+
+    // Initial state
+    updateAnimationState();
+
+    // Override toggleTheme to ensure animation updates
+    const originalToggleTheme = window.toggleTheme || function() {};
+    window.toggleTheme = function() {
+        originalToggleTheme();
+        updateAnimationState();
+    };
+
+    // Observe changes to data-theme attribute
+    const observer = new MutationObserver((mutations) => {
+        mutations.forEach((mutation) => {
+            if (mutation.attributeName === 'data-theme') {
+                updateAnimationState();
+            }
+        });
+    });
+    observer.observe(htmlElement, { attributes: true });
+
+    // Clean up observer on page unload
+    window.addEventListener('unload', () => {
+        observer.disconnect();
+    });
+});
+</script>
 {% endblock %}

templates/manual_import_ig.html

@@ -0,0 +1,194 @@
+{% extends "base.html" %}
+{% from "_form_helpers.html" import render_field %}
+
+{% block content %}
+<div class="container">
+    {% include "_flash_messages.html" %}
+
+    <h1 class="mt-4 mb-3">Import FHIR Implementation Guides</h1>
+    <div class="row">
+        <div class="col-md-12">
+            <p class="lead">Import new FHIR Implementation Guides to the system via file or URL.</p>
+        </div>
+    </div>
+
+    <div class="row">
+        <div class="col-md-6">
+            <h2>Import a New IG</h2>
+            <form id="manual-import-ig-form" method="POST" action="{{ url_for('manual_import_ig') }}" enctype="multipart/form-data">
+                {{ form.hidden_tag() }}
+                <div class="mb-3">
+                    {{ render_field(form.import_mode, class="form-select") }}
+                </div>
+                <div id="file-field" class="{% if form.import_mode.data != 'file' %}d-none{% endif %}">
+                    <div class="mb-3">
+                        <label for="tgz_file" class="form-label">IG Package File (.tgz)</label>
+                        <div class="input-group">
+                            <input type="file" name="tgz_file" id="tgz_file" accept=".tgz" class="form-control custom-file-input">
+                            <span id="file-label" class="custom-file-label">No file selected</span>
+                        </div>
+                        {% if form.tgz_file.errors %}
+                            <div class="form-error">
+                                {% for error in form.tgz_file.errors %}
+                                    <p>{{ error }}</p>
+                                {% endfor %}
+                            </div>
+                        {% endif %}
+                    </div>
+                </div>
+                <div id="url-field" class="{% if form.import_mode.data != 'url' %}d-none{% endif %}">
+                    <div class="mb-3">
+                        {{ render_field(form.tgz_url, class="form-control url-input") }}
+                    </div>
+                </div>
+                <div class="mb-3">
+                    {{ render_field(form.dependency_mode, class="form-select") }}
+                </div>
+                <div class="form-check mb-3">
+                    {{ form.resolve_dependencies(type="checkbox", class="form-check-input") }}
+                    <label class="form-check-label" for="resolve_dependencies">Resolve Dependencies</label>
+                    {% if form.resolve_dependencies.errors %}
+                        <div class="form-error">
+                            {% for error in form.resolve_dependencies.errors %}
+                                <p>{{ error }}</p>
+                            {% endfor %}
+                        </div>
+                    {% endif %}
+                </div>
+                <div class="d-grid gap-2 d-sm-flex mt-3">
+                    {{ form.submit(class="btn btn-success", id="submit-btn") }}
+                    <a href="{{ url_for('index') }}" class="btn btn-secondary">Back</a>
+                </div>
+            </form>
+        </div>
+    </div>
+</div>
+
+<style>
+    .form-error {
+        color: #dc3545;
+        font-size: 0.875rem;
+        margin-top: 0.25rem;
+    }
+    .custom-file-input {
+        width: 100%;
+        padding: 0.375rem 0.75rem;
+        font-size: 1rem;
+        line-height: 1.5;
+        color: #495057;
+        background-color: #fff;
+        border: 1px solid #ced4da;
+        border-radius: 0.25rem;
+        cursor: pointer;
+    }
+    .custom-file-input::-webkit-file-upload-button {
+        display: none;
+    }
+    .custom-file-input::before {
+        content: 'Choose File';
+        display: inline-block;
+        background: #007bff;
+        color: #fff;
+        padding: 0.375rem 0.75rem;
+        border-radius: 0.25rem;
+        margin-right: 0.5rem;
+    }
+    .custom-file-input:hover::before {
+        background: #0056b3;
+    }
+    .custom-file-label {
+        display: inline-block;
+        overflow: hidden;
+        text-overflow: ellipsis;
+        white-space: nowrap;
+        vertical-align: middle;
+        max-width: 60%;
+    }
+    #file-field, #url-field {
+        display: none;
+    }
+    #file-field:not(.d-none), #url-field:not(.d-none) {
+        display: block;
+    }
+</style>
+
+<script>
+document.addEventListener('DOMContentLoaded', function() {
+    console.debug('DOMContentLoaded fired for manual_import_ig.html');
+
+    const importForm = document.getElementById('manual-import-ig-form');
+    const importModeSelect = document.querySelector('#import_mode');
+    const fileField = document.querySelector('#file-field');
+    const urlField = document.querySelector('#url-field');
+    const fileInput = document.querySelector('#tgz_file');
+    const fileLabel = document.querySelector('#file-label');
+    const urlInput = document.querySelector('#tgz_url');
+
+    // Debug DOM elements
+    console.debug('importForm:', !!importForm);
+    console.debug('importModeSelect:', !!importModeSelect);
+    console.debug('fileField:', !!fileField);
+    console.debug('urlField:', !!urlField);
+    console.debug('fileInput:', !!fileInput);
+    console.debug('fileLabel:', !!fileLabel);
+    console.debug('urlInput:', !!urlInput);
+
+    function toggleFields() {
+        if (!importModeSelect || !fileField || !urlField) {
+            console.error('Required elements for toggling not found');
+            return;
+        }
+        const mode = importModeSelect.value;
+        console.debug(`Toggling fields for mode: ${mode}`);
+        fileField.classList.toggle('d-none', mode !== 'file');
+        urlField.classList.toggle('d-none', mode !== 'url');
+        console.debug(`file-field d-none: ${fileField.classList.contains('d-none')}, url-field d-none: ${urlField.classList.contains('d-none')}`);
+    }
+
+    function updateFileLabel() {
+        if (fileInput && fileLabel) {
+            const fileName = fileInput.files.length > 0 ? fileInput.files[0].name : 'No file selected';
+            fileLabel.textContent = fileName;
+            console.debug(`Updated file label to: ${fileName}`);
+        } else {
+            console.warn('File input or label not found');
+        }
+    }
+
+    if (importModeSelect) {
+        importModeSelect.addEventListener('change', function() {
+            console.debug('Import mode changed to:', importModeSelect.value);
+            toggleFields();
+        });
+        toggleFields();
+    } else {
+        console.error('Import mode select not found');
+    }
+
+    if (fileInput) {
+        fileInput.addEventListener('change', function() {
+            console.debug('File input changed');
+            updateFileLabel();
+        });
+        updateFileLabel();
+    }
+
+    if (urlInput) {
+        urlInput.addEventListener('input', function() {
+            console.debug(`URL input value: ${urlInput.value}`);
+        });
+    }
+
+    if (importForm) {
+        importForm.addEventListener('submit', function(evt) {
+            console.debug('Form submission triggered');
+            if (!importForm.checkValidity()) {
+                evt.preventDefault();
+                console.error('Form validation failed');
+                importForm.reportValidity();
+            }
+        });
+    }
+});
+</script>
+{% endblock %}

templates/package.canonicals.html

@@ -0,0 +1,7 @@
+<ul class="list-group">
+    {% for canonical in canonicals %}
+    <li class="list-group-item">
+        <a href="{{ canonical }}" target="_blank">{{ canonical }}</a>
+    </li>
+    {% endfor %}
+</ul>

templates/package.dependents.html

@@ -0,0 +1,31 @@
+{% if dependents %}
+    <table class="table table-striped table-hover">
+        <thead>
+            <tr>
+                <th scope="col">Package</th>
+                <th scope="col">Latest</th>
+                <th scope="col">Author</th>
+                <th scope="col">FHIR</th>
+                <th scope="col">Versions</th>
+                <th scope="col">Canonical</th>
+            </tr>
+        </thead>
+        <tbody>
+            {% for dep in dependents %}
+            <tr>
+                <td>
+                    <i class="bi bi-box-seam me-2"></i>
+                    <a class="text-primary" href="{{ url_for('package_details_view', name=dep.name) }}">{{ dep.name }}</a>
+                </td>
+                <td>{{ dep.version }}</td>
+                <td>{{ dep.author }}</td>
+                <td>{{ dep.fhir_version }}</td>
+                <td>{{ dep.version_count }}</td>
+                <td>{{ dep.canonical }}</td>
+            </tr>
+            {% endfor %}
+        </tbody>
+    </table>
+{% else %}
+    <p class="text-muted">No dependent packages found for this package.</p>
+{% endif %}

templates/package.logs.html

@@ -0,0 +1,22 @@
+{% if logs %}
+    <table class="table table-striped table-hover">
+        <thead>
+            <tr>
+                <th scope="col">Version</th>
+                <th scope="col">Publication Date</th>
+                <th scope="col">When</th>
+            </tr>
+        </thead>
+        <tbody>
+            {% for log in logs %}
+            <tr>
+                <td>{{ log.version }}</td>
+                <td>{{ log.pubDate }}</td>
+                <td>{{ log.when }}</td>
+            </tr>
+            {% endfor %}
+        </tbody>
+    </table>
+{% else %}
+    <p class="text-muted">No version history found for this package.</p>
+{% endif %}

templates/package.problems.html

@@ -0,0 +1,16 @@
+<table class="table table-striped">
+    <thead>
+        <tr>
+            <th>Package</th>
+            <th>Dependency</th>
+        </tr>
+    </thead>
+    <tbody>
+        {% for problem in problems %}
+        <tr>
+            <td>{{ problem.package }}</td>
+            <td class="text-danger">{{ problem.dependency }}</td>
+        </tr>
+        {% endfor %}
+    </tbody>
+</table>