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<!DOCTYPE html>
<html lang="en">
<head>
    <meta charset="UTF-8">
    <meta name="viewport" content="width=device-width, initial-scale=1.0">
    <title>R&D DocMap Catalog - Document Dependency Mapper</title>
    <!-- Load Tailwind CSS -->
    <script src="https://cdn.tailwindcss.com"></script>
    <!-- Load Lucide Icons -->
    <link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/lucide-static@latest/font/Lucide.css">
    <!-- Load Mermaid properly with specific version -->
    <script src="https://cdn.jsdelivr.net/npm/mermaid@10.6.1/dist/mermaid.min.js"></script>
    <link href="https://fonts.googleapis.com/css2?family=Inter:wght@400;500;600;700&display=swap" rel="stylesheet">
    <style>
        /* Base styles */
        body {
            font-family: 'Inter', sans-serif;
            background-color: #f9fafb;
        }
        .doc-link, .flow-link { cursor: pointer; color: #2563eb; text-decoration: underline; font-weight: 500; }
        .doc-link:hover, .flow-link:hover { color: #1d4ed8; }
        .custom-scroll::-webkit-scrollbar { width: 6px; height: 6px; }
        .custom-scroll::-webkit-scrollbar-track { background: #e5e7eb; border-radius: 3px; }
        .custom-scroll::-webkit-scrollbar-thumb { background: #9ca3af; border-radius: 3px; }
        .custom-scroll::-webkit-scrollbar-thumb:hover { background: #6b7280; }
        .lucide { vertical-align: -0.125em; display: inline-block; margin-right: 0.35rem; }
        .main-tab { transition: all 0.2s ease-in-out; border-bottom-width: 3px; border-color: transparent; }
        .main-tab.active { border-color: #2563eb; color: #1e40af; font-weight: 600; }
        #documentGraphContainerInModal, #flowsContainer { min-height: 200px; }
        .modal { display: none; position: fixed; z-index: 1000; left: 0; top: 0; width: 100%; height: 100%; overflow: hidden; background-color: rgba(0,0,0,0.5); align-items: center; justify-content: center; }
        .modal-content { background-color: #fefefe; padding: 0; border: 1px solid #888; width: 90%; max-width: 1000px; border-radius: 8px; position: relative; max-height: 90vh; display: flex; flex-direction: column; overflow: hidden; }
        .modal-header { padding: 1rem 1.5rem; border-bottom: 1px solid #e5e7eb; display: flex; justify-content: space-between; align-items: center; flex-shrink: 0; }
        .modal-title { font-size: 1.25rem; font-weight: 600; color: #374151; }
        .modal-close { color: #9ca3af; background: none; border: none; font-size: 1.75rem; font-weight: bold; cursor: pointer; padding: 0; line-height: 1; }
        .modal-close:hover, .modal-close:focus { color: #1f2937; text-decoration: none; }
        .modal-body { padding: 1.5rem; overflow-y: auto; flex-grow: 1; }
        .modal-footer { padding: 1rem 1.5rem; border-top: 1px solid #e5e7eb; display: flex; justify-content: space-between; align-items: center; flex-shrink: 0; }
        .nav-button { background-color: #e5e7eb; color: #374151; padding: 0.5rem 1rem; border: none; border-radius: 0.375rem; font-weight: 500; cursor: pointer; transition: background-color 0.2s; }
        .nav-button:hover:not(:disabled) { background-color: #d1d5db; }
        .nav-button:disabled { opacity: 0.5; cursor: not-allowed; }
        .mermaid text, .mermaid tspan { user-select: text !important; -webkit-user-select: text !important; -moz-user-select: text !important; -ms-user-select: text !important; }
        .mermaid .node { cursor: pointer; }
        .hidden-container { display: none !important; }
        
        /* Dashboard Card Specific Styles */
        .dashboard-card { transition: all 0.3s ease; }
        .dashboard-card:hover { transform: translateY(-5px); box-shadow: 0 10px 15px -3px rgba(0, 0, 0, 0.1), 0 4px 6px -2px rgba(0, 0, 0, 0.05); }
        
        /* Document item enhancements */
        .document-item {
          transition: all 0.3s ease;
          border-left: 4px solid transparent;
        }
        
        .document-item:hover {
          transform: translateX(5px);
          background-color: #f8fafc;
        }
        
        /* Phase-specific colors */
        .document-item[data-phase="Discovery"] { border-left-color: #3b82f6; }
        .document-item[data-phase="Preclinical"] { border-left-color: #10b981; }
        .document-item[data-phase="Clinical Phase 1"] { border-left-color: #6366f1; }
        .document-item[data-phase="Clinical Phase 2"] { border-left-color: #8b5cf6; }
        .document-item[data-phase="Clinical Phase 3"] { border-left-color: #a855f7; }
        .document-item[data-phase="Clinical (All Phases)"] { border-left-color: #7c3aed; }
        .document-item[data-phase="Regulatory Submission"] { border-left-color: #ec4899; }
        .document-item[data-phase="Post-Marketing"] { border-left-color: #f59e0b; }
        .document-item[data-phase="Pre/Post-Approval"] { border-left-color: #f97316; }
        
        /* Tab styles for document detail modal */
        .details-tabs {
          display: flex;
          border-bottom: 1px solid #e5e7eb;
          margin-bottom: 1rem;
        }
        
        .details-tab {
          padding: 0.5rem 1rem;
          cursor: pointer;
          border-bottom: 3px solid transparent;
          font-weight: 500;
          transition: all 0.2s ease;
        }
        
        .details-tab.active {
          border-bottom-color: #3b82f6;
          color: #1e40af;
        }
        
        .details-tab:hover:not(.active) {
          border-bottom-color: #e5e7eb;
        }
        
        .details-content {
          display: none;
        }
        
        .details-content.active {
          display: block;
          animation: fadeIn 0.3s ease;
        }
        
        @keyframes fadeIn {
          from { opacity: 0; }
          to { opacity: 1; }
        }
        
        /* Dependency graph styles */
        .dependency-graph {
          width: 100%;
          height: 400px;
          border: 1px solid #e5e7eb;
          border-radius: 0.375rem;
          overflow: hidden;
        }
        
        /* Flow card styles */
        .flow-card {
          cursor: pointer;
          transition: all 0.3s ease;
          border: 1px solid #e5e7eb;
          border-radius: 0.375rem;
          padding: 1rem;
          margin-bottom: 1rem;
          background-color: white;
        }
        
        .flow-card:hover {
          transform: translateY(-3px);
          box-shadow: 0 4px 6px -1px rgba(0, 0, 0, 0.1), 0 2px 4px -1px rgba(0, 0, 0, 0.06);
          border-color: #3b82f6;
        }
        
        .flow-card.active {
          border-color: #3b82f6;
          background-color: #eff6ff;
        }
        
        /* Loading spinner */
        .loading-spinner {
          width: 40px;
          height: 40px;
          margin: 2rem auto;
          border-radius: 50%;
          border: 4px solid #e5e7eb;
          border-top-color: #3b82f6;
          animation: spin 1s linear infinite;
        }
        
        @keyframes spin {
          to { transform: rotate(360deg); }
        }
        
        /* Text truncation utility */
        .line-clamp-2 {
            display: -webkit-box;
            -webkit-line-clamp: 2;
            -webkit-box-orient: vertical;
            overflow: hidden;
        }

        /* Enhanced detail card styles for better readability */
        .detail-card {
            background-color: white;
            border-radius: 0.5rem;
            box-shadow: 0 4px 6px -1px rgba(0, 0, 0, 0.1);
            padding: 1.25rem;
            margin-bottom: 1rem;
            border-left: 4px solid #3b82f6;
        }

        .detail-card-header {
            display: flex;
            justify-content: space-between;
            margin-bottom: 0.75rem;
            border-bottom: 1px solid #e5e7eb;
            padding-bottom: 0.75rem;
        }

        .detail-card-title {
            font-size: 1.125rem;
            font-weight: 600;
            color: #1e40af;
        }

        .detail-card-badge {
            background-color: #eff6ff;
            color: #1e40af;
            padding: 0.25rem 0.5rem;
            border-radius: 9999px;
            font-size: 0.75rem;
            font-weight: 500;
        }

        .detail-card-section {
            margin-bottom: 0.75rem;
        }

        .detail-card-label {
            font-weight: 500;
            color: #4b5563;
            margin-bottom: 0.25rem;
            display: block;
        }

        .detail-card-value {
            background-color: #f9fafb;
            padding: 0.5rem;
            border-radius: 0.25rem;
            font-size: 0.875rem;
            color: #1f2937;
        }

        /* Data lineage view styles */
        .lineage-container {
            padding: 1.5rem;
            background-color: white;
            border-radius: 0.5rem;
            box-shadow: 0 1px 3px rgba(0, 0, 0, 0.1);
        }

        .lineage-filters {
            display: flex;
            gap: 1rem;
            margin-bottom: 1.5rem;
            flex-wrap: wrap;
        }

        .lineage-filters select {
            padding: 0.5rem;
            border-radius: 0.25rem;
            border: 1px solid #d1d5db;
            background-color: white;
            min-width: 200px;
        }

        .lineage-graph {
            height: 600px;
            border: 1px solid #e5e7eb;
            border-radius: 0.375rem;
            overflow: hidden;
        }
    </style>
    <link rel="icon" href="data:image/svg+xml,<svg xmlns=%22http://www.w3.org/2000/svg%22 viewBox=%220 0 100 100%22><text y=%22.9em%22 font-size=%2290%22>🗺️</text></svg>">
</head>
<body class="flex flex-col h-screen">

    <header class="bg-gradient-to-r from-blue-600 to-indigo-700 text-white shadow-md p-4 flex items-center justify-between flex-shrink-0">
        <div class="flex items-center space-x-3">
            <span id="logo-placeholder" class="inline-block bg-white rounded-full p-1 leading-none">
                <i class="lucide lucide-map text-blue-700 text-2xl"></i>
            </span>
            <h1 class="text-2xl font-bold">R&D DocMap Catalog</h1>
        </div>
        <div class="flex items-center space-x-4">
            <button id="homeButton" class="text-white hover:text-blue-200 flex items-center text-sm">
                <i class="lucide lucide-home"></i> Home
            </button>
            <div class="relative hidden md:block">
                <input type="text" id="headerSearchInput" placeholder="Search all docs..." class="bg-blue-500 placeholder-blue-200 text-white rounded-full py-1.5 px-4 pl-10 text-sm focus:outline-none focus:ring-2 focus:ring-white">
                <i class="lucide lucide-search absolute left-3 top-1/2 transform -translate-y-1/2 text-blue-200"></i>
            </div>
            <button id="showExampleFlowBtn" class="bg-white text-blue-700 hover:bg-blue-50 font-semibold py-2 px-4 rounded-md shadow text-sm flex items-center">
                <i class="lucide lucide-git-fork"></i> Show Example Flow
            </button>
        </div>
    </header>

    <div class="bg-gray-100 border-b border-gray-200 px-4 py-2 text-sm flex-shrink-0">
        <nav id="breadcrumbNav" aria-label="Breadcrumb">
            <span class="text-gray-500">Home</span>
        </nav>
    </div>

    <main id="mainContentArea" class="flex-1 overflow-y-auto p-4 md:p-6">

        <section id="home" class="space-y-6">
            <div class="bg-white rounded-lg shadow p-6 text-center">
                <h2 class="text-2xl font-semibold text-gray-800 mb-2">Welcome to R&D DocMap Catalog</h2>
                <p class="text-gray-600">A comprehensive R&D document catalog and authoring dependency mapper</p>
            </div>

            <div class="grid grid-cols-1 sm:grid-cols-2 lg:grid-cols-4 gap-6">
                <div data-target-view="documentViewWrapper" data-initial-tab="All" class="dashboard-card bg-white rounded-lg shadow p-6 text-center cursor-pointer flex flex-col items-center">
                    <i class="lucide lucide-book-open text-4xl text-blue-500 mb-4"></i>
                    <h3 class="text-lg font-semibold text-gray-700 mb-2">Document Catalog</h3>
                    <p class="text-sm text-gray-500 mb-4 flex-grow">Browse and search all document types across R&D phases.</p>
                    <button class="bg-blue-500 hover:bg-blue-600 text-white font-medium py-2 px-4 rounded-md text-sm w-full">Explore</button>
                </div>
                <div data-target-view="flowsViewWrapper" data-initial-tab="Flows" class="dashboard-card bg-white rounded-lg shadow p-6 text-center cursor-pointer flex flex-col items-center">
                    <i class="lucide lucide-git-fork text-4xl text-purple-500 mb-4"></i>
                    <h3 class="text-lg font-semibold text-gray-700 mb-2">Process Visualization</h3>
                    <p class="text-sm text-gray-500 mb-4 flex-grow">Visualize document workflows and dependencies.</p>
                    <button class="bg-purple-500 hover:bg-purple-600 text-white font-medium py-2 px-4 rounded-md text-sm w-full">Explore</button>
                </div>
                <div data-target-view="dataLineageViewWrapper" data-initial-tab="Lineage" class="dashboard-card bg-white rounded-lg shadow p-6 text-center cursor-pointer flex flex-col items-center">
                    <i class="lucide lucide-git-branch text-4xl text-green-500 mb-4"></i>
                    <h3 class="text-lg font-semibold text-gray-700 mb-2">Section Lineage</h3>
                    <p class="text-sm text-gray-500 mb-4 flex-grow">Explore section-level document dependencies and data lineage.</p>
                    <button class="bg-green-500 hover:bg-green-600 text-white font-medium py-2 px-4 rounded-md text-sm w-full">Explore</button>
                </div>
                <div data-target-view="uberDepViewWrapper" data-initial-tab="UberDep" class="dashboard-card bg-white rounded-lg shadow p-6 text-center cursor-pointer flex flex-col items-center">
                    <i class="lucide lucide-network text-4xl text-amber-500 mb-4"></i>
                    <h3 class="text-lg font-semibold text-gray-700 mb-2">DocGen Dependencies</h3>
                    <p class="text-sm text-gray-500 mb-4 flex-grow">Visualize uber interdependencies across document generation.</p>
                    <button class="bg-amber-500 hover:bg-amber-600 text-white font-medium py-2 px-4 rounded-md text-sm w-full">Explore</button>
                </div>
            </div>

            <div class="bg-white rounded-lg shadow p-4 mt-6">
                <h3 class="font-semibold text-gray-700 mb-3">Recent Updates</h3>
                <ul class="text-sm text-gray-600 space-y-1">
                    <li><span class="text-gray-400 mr-2">[April 7, 2025]</span>Added section-level lineage visualization capabilities.</li>
                    <li><span class="text-gray-400 mr-2">[April 6, 2025]</span>Enhanced document visualization system launched.</li>
                    <li><span class="text-gray-400 mr-2">[April 5, 2025]</span>Added IND pathway and clinical program flows.</li>
                </ul>
            </div>
        </section>

        <section id="documentViewWrapper" class="hidden-container flex flex-col flex-1 gap-4 overflow-hidden">
            <div class="bg-white rounded-lg shadow p-3 flex-shrink-0">
                <div id="mainTabsDocView" class="flex space-x-4 border-b border-gray-200 overflow-x-auto custom-scroll pb-1">
                    <span class="text-gray-500">Loading phases...</span>
                </div>
            </div>
            <div class="relative flex-shrink-0 bg-white rounded-lg shadow p-4">
                <input type="text" id="searchInputDocView" placeholder="Search documents in selected phase (or all)..." class="w-full pl-10 pr-4 py-2 border border-gray-300 rounded-md focus:outline-none focus:ring-2 focus:ring-blue-500 focus:border-transparent text-sm">
                <i class="lucide lucide-search absolute left-3 top-1/2 transform -translate-y-1/2 text-gray-400 ml-4"></i>
            </div>
            <div id="documentListDocView" class="bg-white rounded-lg shadow flex-1 overflow-y-auto custom-scroll p-4">
                <p class="text-gray-500 text-center py-4">Select a phase tab above.</p>
            </div>
        </section>

        <section id="flowsViewWrapper" class="hidden-container flex-1 bg-white rounded-lg shadow p-4 overflow-hidden flex flex-col gap-4">
            <h2 class="text-xl font-semibold text-gray-700 mb-2 flex items-center flex-shrink-0">
                <i class="lucide lucide-git-fork mr-2 text-purple-600"></i> Process Flows
            </h2>
            <div class="flex flex-1 gap-4 overflow-hidden">
                <div class="w-full md:w-1/4 border-r pr-4 border-gray-200 overflow-y-auto custom-scroll">
                    <div id="flowsList" class="space-y-3">
                        <p class="text-gray-500">Loading flows...</p>
                    </div>
                    <button id="showExampleFlowBtnFlowView" class="mt-4 bg-gray-100 text-gray-700 hover:bg-gray-200 font-medium py-1.5 px-3 rounded-md shadow-sm text-xs flex items-center w-full text-left">
                        <i class="lucide lucide-presentation"></i> Show Example P1 Flow
                    </button>
                </div>
                <div id="flowsContainer" class="w-full md:w-3/4 overflow-auto custom-scroll bg-gray-50 rounded">
                    <p id="flowPlaceholder" class="text-gray-500 text-center py-10 px-4">Select a flow from the list to view the process graph.</p>
                    <div id="mermaidFlowGraph" class="mermaid w-full h-full p-4">
                    </div>
                </div>
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            <h2 class="text-xl font-semibold text-gray-700 mb-2 flex items-center flex-shrink-0">
                <i class="lucide lucide-git-branch mr-2 text-green-600"></i> Section-Level Lineage
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                <div>
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                    <select id="lineageSectionSelect" class="w-full" disabled>
                        <option value="">Select a section...</option>
                        <!-- Sections will be populated after selecting a document -->
                    </select>
                </div>
            </div>
            <div class="lineage-container flex-1 flex flex-col">
                <div id="lineageGraphContainer" class="lineage-graph flex-1">
                    <p id="lineagePlaceholder" class="text-gray-500 text-center py-10 px-4">Select a document and section to visualize data lineage.</p>
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                </div>
            </div>
        </section>

        <!-- New Uber Dependencies View Section -->
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            <h2 class="text-xl font-semibold text-gray-700 mb-2 flex items-center flex-shrink-0">
                <i class="lucide lucide-network mr-2 text-amber-600"></i> DocGen Dependencies
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                <div class="w-full md:w-1/4 border-r pr-4 border-gray-200 overflow-y-auto custom-scroll">
                    <div>
                        <h3 class="font-medium text-gray-700 mb-2">Filter By:</h3>
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                                <select id="uberDepDocTypeSelect" class="w-full border border-gray-300 rounded-md p-2">
                                    <option value="all">All Document Types</option>
                                    <!-- Document types will be populated by JavaScript -->
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                            <div>
                                <label class="block text-sm font-medium text-gray-700 mb-1">Phase</label>
                                <select id="uberDepPhaseSelect" class="w-full border border-gray-300 rounded-md p-2">
                                    <option value="all">All Phases</option>
                                    <!-- Phases will be populated by JavaScript -->
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                        <h3 class="font-medium text-gray-700 mb-2">Legend</h3>
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        </section>

    </main>

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                <h2 class="modal-title">Example Flow: Phase 1 SAD Study Documents</h2>
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                <button id="prevDocBtn" class="nav-button" disabled><i class="lucide lucide-arrow-left"></i> Previous</button>
                <button id="nextDocBtn" class="nav-button" disabled>Next <i class="lucide lucide-arrow-right"></i></button>
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            <div class="w-16 h-16 border-4 border-blue-500 border-t-transparent rounded-full animate-spin mb-4"></div>
            <p class="text-gray-700 font-medium">Loading R&D DocMap Catalog...</p>
        </div>
    </div>

    <script>
        // Initialize Mermaid with proper configuration
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            // Initialize Mermaid properly
            mermaid.initialize({ 
                startOnLoad: false, 
                theme: 'base', 
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                themeVariables: {
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        // More JavaScript functionality will be added in a separate script file
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    <script src="docmap.js"></script>
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