app.py

#!/usr/bin/env python3
"""
BibGuard Gradio Web Application

A web interface for checking bibliography and LaTeX quality.
"""
import gradio as gr
import tempfile
import shutil
from pathlib import Path
from typing import Optional, Tuple
import base64

from src.parsers import BibParser, TexParser
from src.fetchers import ArxivFetcher, CrossRefFetcher, SemanticScholarFetcher, OpenAlexFetcher, DBLPFetcher
from src.analyzers import MetadataComparator, UsageChecker, DuplicateDetector
from src.report.generator import ReportGenerator, EntryReport
from src.config.yaml_config import BibGuardConfig, FilesConfig, BibliographyConfig, SubmissionConfig, OutputConfig, WorkflowStep
from src.config.workflow import WorkflowConfig, WorkflowStep as WFStep, get_default_workflow
from src.checkers import CHECKER_REGISTRY
from src.report.line_report import LineByLineReportGenerator
from app_helper import fetch_and_compare_with_workflow


# Custom CSS for better Markdown rendering
CUSTOM_CSS = """
@import url('https://fonts.googleapis.com/css2?family=Inter:wght@400;500;600;700&display=swap');

* {
    font-family: 'Inter', -apple-system, BlinkMacSystemFont, sans-serif;
}
"""

WELCOME_HTML = """
<div class="scrollable-report-area">
    <div class="report-card" style="max-width: 800px; margin: 0 auto;">
        <div class="card-header">
            <h3 class="card-title" style="font-size: 1.5em;">👋 Welcome to BibGuard</h3>
        </div>
        <div class="card-content" style="line-height: 1.6; color: #374151;">
            <p style="font-size: 1.1em; margin-bottom: 24px;">
                Ensure your academic paper is flawless. Upload your <code>.bib</code> and <code>.tex</code> files on the left and click <strong>"Check Now"</strong>.
            </p>
            
            <div style="display: grid; gap: 20px; grid-template-columns: repeat(auto-fit, minmax(300px, 1fr));">
                <div style="background: #fefce8; padding: 16px; border-radius: 8px; border: 1px solid #fde047;">
                    <strong style="color: #854d0e; display: block; margin-bottom: 8px;">⚠️ Metadata Check Defaults</strong> 
                    "🔍 Metadata" is <strong>disabled by default</strong>. It verifies your entries against ArXiv/DBLP/Crossref but takes time (1-3 mins) to fetch data. Enable it if you want strict verification.
                </div>
                
                <div style="background: #eff6ff; padding: 16px; border-radius: 8px; border: 1px solid #bfdbfe;">
                    <strong style="color: #1e40af; display: block; margin-bottom: 8px;">🚀 Go Pro with Local Version</strong> 
                    LLM-based context relevance checking (is this citation actually relevant?) is excluded here. Clone the <a href="https://github.com/thinkwee/BibGuard" target="_blank" style="color: #2563eb; text-decoration: underline; font-weight: 600;">GitHub repo</a> to use the full power with your API key.
                </div>
            </div>
            
            <h4 style="margin: 24px 0 12px 0; color: #111827; font-size: 1.1em;">📊 Understanding Your Reports</h4>
            <div style="display: grid; gap: 12px;">
                <div style="display: flex; gap: 12px; align-items: baseline;">
                    <span style="background: #e0e7ff; color: #3730a3; padding: 2px 8px; border-radius: 4px; font-size: 0.9em; font-weight: 600; white-space: nowrap;">📚 Bibliography</span>
                    <span>Validates metadata fields, detects duplicates, and checks citation counts.</span>
                </div>
                <div style="display: flex; gap: 12px; align-items: baseline;">
                    <span style="background: #dcfce7; color: #166534; padding: 2px 8px; border-radius: 4px; font-size: 0.9em; font-weight: 600; white-space: nowrap;">📝 LaTeX Quality</span>
                    <span>Syntax check, caption validation, acronym consistency, and style suggestions.</span>
                </div>
                <div style="display: flex; gap: 12px; align-items: baseline;">
                    <span style="background: #f3f4f6; color: #4b5563; padding: 2px 8px; border-radius: 4px; font-size: 0.9em; font-weight: 600; white-space: nowrap;">📋 Line-by-Line</span>
                    <span>Maps every issue found directly to the line number in your source file.</span>
                </div>
            </div>
        </div>
    </div>
</div>
"""

CUSTOM_CSS += """
/* Global Reset */
body, gradio-app {
    overflow: hidden !important; /* Prevent double scrollbars on the page */
}

.gradio-container {
    max-width: none !important;
    width: 100% !important;
    /* height: 100vh !important;  <-- Removed to prevent iframe infinite loop */
    padding: 0 !important;
    margin: 0 !important;
}

/* Header Styling */
.app-header {
    padding: 20px;
    background: white;
    border-bottom: 1px solid #e5e7eb;
}

/* Sidebar Styling */
.app-sidebar {
    height: auto !important;
    max-height: calc(100vh - 100px) !important;
    overflow-y: auto !important;
    padding: 20px !important;
    border-right: 1px solid #e5e7eb;
}

/* Main Content Area */
.app-content {
    height: auto !important;
    max-height: calc(100vh - 100px) !important;
    padding: 0 !important;
}

/* The Magic Scroll Container - Clean and Explicit */
.scrollable-report-area {
    /* Fixed height relative to viewport can cause loops in Spaces */
    max-height: 800px !important; 
    height: auto !important;
    min-height: 500px !important;
    overflow-y: auto !important;
    padding: 24px;
    background-color: #f9fafb;
    border: 1px solid #e5e7eb;
    border-radius: 8px;
    margin-top: 10px;
}

/* Report Card Styling */
.report-card {
    background: white;
    border-radius: 12px;
    padding: 24px;
    margin-bottom: 16px; /* Spacing between cards */
    box-shadow: 0 1px 3px rgba(0,0,0,0.1);
    border: 1px solid #e5e7eb;
    transition: transform 0.2s, box-shadow 0.2s;
}

.report-card:hover {
    box-shadow: 0 4px 6px -1px rgba(0, 0, 0, 0.1), 0 2px 4px -1px rgba(0, 0, 0, 0.06);
    transform: translateY(-2px);
}

/* Card Internals */
.card-header {
    display: flex;
    justify-content: space-between;
    align-items: flex-start;
    margin-bottom: 16px;
    padding-bottom: 16px;
    border-bottom: 1px solid #f3f4f6;
}

.card-title {
    font-size: 1.1em;
    font-weight: 600;
    color: #111827;
    margin: 0 0 4px 0;
}

.card-subtitle {
    font-size: 0.9em;
    color: #6b7280;
    font-family: monospace;
}

.card-content {
    font-size: 0.95em;
    color: #374151;
    line-height: 1.5;
}

/* Badges */
.badge {
    display: inline-flex;
    align-items: center;
    padding: 4px 10px;
    border-radius: 9999px;
    font-size: 0.8em;
    font-weight: 500;
}

.badge-success { background-color: #dcfce7; color: #166534; }
.badge-warning { background-color: #fef9c3; color: #854d0e; }
.badge-error { background-color: #fee2e2; color: #991b1b; }
.badge-info { background-color: #dbeafe; color: #1e40af; }
.badge-neutral { background-color: #f3f4f6; color: #4b5563; }

/* Stats Grid */
.stats-container {
    display: grid;
    grid-template-columns: repeat(auto-fit, minmax(140px, 1fr));
    gap: 16px;
    margin-bottom: 24px;
}

.stat-card {
    padding: 16px;
    border-radius: 12px;
    color: white;
    text-align: center;
    box-shadow: 0 4px 6px -1px rgba(0, 0, 0, 0.1);
}

.stat-value { font-size: 1.8em; font-weight: 700; }
.stat-label { font-size: 0.9em; opacity: 0.9; }

/* Detail Grid - Flexbox for better filling */
.detail-grid {
    display: flex;
    flex-wrap: wrap;
    gap: 12px;
    margin-bottom: 16px;
    width: 100%;
}

.detail-item {
    background: #f9fafb;
    padding: 10px 12px;
    border-radius: 8px;
    border: 1px solid #f3f4f6;
    
    /* Flex sizing: grow, shrink, min-basis */
    flex: 1 1 160px;
    min-width: 0; /* Important for word-break to work in flex children */
    
    /* Layout control */
    display: flex;
    flex-direction: column;
    
    /* Height constraint to prevent one huge card from stretching the row */
    max-height: 100px; 
    overflow-y: auto;
}

/* Custom scrollbar for detail items */
.detail-item::-webkit-scrollbar {
    width: 4px;
}
.detail-item::-webkit-scrollbar-thumb {
    background-color: #d1d5db;
    border-radius: 4px;
}

.detail-label {
    font-size: 0.75em;
    color: #6b7280;
    text-transform: uppercase;
    letter-spacing: 0.05em;
    margin-bottom: 2px;
    position: sticky;
    top: 0;
    background: #f9fafb; /* Maintain bg on scroll */
    z-index: 1;
}

.detail-value {
    font-weight: 500;
    color: #1f2937;
    font-size: 0.9em;
    line-height: 1.4;
    word-break: break-word; /* Fix overflow */
    overflow-wrap: break-word;
}    border: 1px solid #e5e7eb;
    transition: all 0.2s;
}

.report-card:hover {
    box-shadow: 0 10px 15px -3px rgba(0, 0, 0, 0.1), 0 4px 6px -2px rgba(0, 0, 0, 0.05);
}

/* Card Header */
.card-header {
    display: flex;
    justify-content: space-between;
    align-items: flex-start;
    margin-bottom: 12px;
    border-bottom: 1px solid #f3f4f6;
    padding-bottom: 12px;
}

.card-title {
    font-size: 1.1em;
    font-weight: 600;
    color: #1f2937;
    margin: 0;
}

.card-subtitle {
    font-size: 0.9em;
    color: #6b7280;
    margin-top: 4px;
}

/* Status Badges */
.badge {
    display: inline-flex;
    align-items: center;
    padding: 4px 10px;
    border-radius: 9999px;
    font-size: 0.8em;
    font-weight: 500;
}

.badge-success { background-color: #dcfce7; color: #166534; }
.badge-warning { background-color: #fef9c3; color: #854d0e; }
.badge-error { background-color: #fee2e2; color: #991b1b; }
.badge-info { background-color: #dbeafe; color: #1e40af; }
.badge-neutral { background-color: #f3f4f6; color: #374151; }

/* Content Styling */
.card-content {
    font-size: 15px;
    color: #374151;
    line-height: 1.6;
}

.card-content code {
    background-color: #f3f4f6;
    padding: 2px 6px;
    border-radius: 4px;
    font-family: monospace;
    font-size: 0.9em;
    color: #c2410c;
}

/* Grid for details */
.detail-grid {
    display: grid;
    grid-template-columns: repeat(auto-fill, minmax(200px, 1fr));
    gap: 12px;
    margin-top: 12px;
}

.detail-item {
    background: #f9fafb;
    padding: 10px;
    border-radius: 6px;
}

.detail-label {
    font-size: 0.8em;
    color: #6b7280;
    text-transform: uppercase;
    letter-spacing: 0.05em;
}

.detail-value {
    font-weight: 500;
    color: #111827;
}

/* Summary Stats */
.stats-container {
    display: grid;
    grid-template-columns: repeat(3, 1fr);
    gap: 16px;
    margin-bottom: 24px;
}

.stat-card {
    background: linear-gradient(135deg, #667eea 0%, #764ba2 100%);
    color: white;
    padding: 20px;
    border-radius: 12px;
    text-align: center;
    box-shadow: 0 4px 6px rgba(102, 126, 234, 0.25);
}

.stat-value {
    font-size: 2em;
    font-weight: 700;
}

.stat-label {
    font-size: 0.9em;
    opacity: 0.9;
    margin-top: 4px;
}

/* Button styling */
.primary-btn {
    background: linear-gradient(135deg, #667eea 0%, #764ba2 100%) !important;
    border: none !important;
    font-weight: 600 !important;
}

/* Tab styling */
.tab-nav button {
    font-weight: 500 !important;
    font-size: 15px !important;
}
"""


def create_config_from_ui(
    check_metadata: bool,
    check_usage: bool, 
    check_duplicates: bool,
    check_preprint_ratio: bool,
    caption: bool,
    reference: bool,
    formatting: bool,
    equation: bool,
    ai_artifacts: bool,
    sentence: bool,
    consistency: bool,
    acronym: bool,
    number: bool,
    citation_quality: bool,
    anonymization: bool
) -> BibGuardConfig:
    """Create a BibGuardConfig from UI settings."""
    config = BibGuardConfig()
    
    config.bibliography = BibliographyConfig(
        check_metadata=check_metadata,
        check_usage=check_usage,
        check_duplicates=check_duplicates,
        check_preprint_ratio=check_preprint_ratio,
        check_relevance=False  # Disabled for web
    )
    
    config.submission = SubmissionConfig(
        caption=caption,
        reference=reference,
        formatting=formatting,
        equation=equation,
        ai_artifacts=ai_artifacts,
        sentence=sentence,
        consistency=consistency,
        acronym=acronym,
        number=number,
        citation_quality=citation_quality,
        anonymization=anonymization
    )
    
    config.output = OutputConfig(quiet=True, minimal_verified=False)
    
    return config


def generate_bibliography_html(report_gen: ReportGenerator, entries: list) -> str:
    """Generate HTML content for bibliography report."""
    html = ['<div class="scrollable-report-area">']
    
    # 1. Summary Stats
    total = len(entries)
    verified = sum(1 for e in report_gen.entries if e.comparison and e.comparison.is_match)
    used = sum(1 for e in report_gen.entries if e.usage and e.usage.is_used)
    
    html.append('<div class="stats-container">')
    html.append(f'<div class="stat-card"><div class="stat-value">{total}</div><div class="stat-label">Total Entries</div></div>')
    html.append(f'<div class="stat-card"><div class="stat-value">{verified}</div><div class="stat-label">Verified</div></div>')
    html.append(f'<div class="stat-card"><div class="stat-value">{used}</div><div class="stat-label">Used in Text</div></div>')
    html.append('</div>')
    
    # 2. Entries
    for report in report_gen.entries:
        entry = report.entry
        status_badges = []
        
        # Metadata Status
        if report.comparison:
            if report.comparison.is_match:
                status_badges.append('<span class="badge badge-success">✓ Verified</span>')
                if report.comparison.source:
                    status_badges.append(f'<span class="badge badge-info">{report.comparison.source.upper()}</span>')
            else:
                status_badges.append('<span class="badge badge-error">⚠ Metadata Mismatch</span>')
        else:
             status_badges.append('<span class="badge badge-neutral">No Metadata Check</span>')
            
        # Usage Status
        if report.usage:
            if report.usage.is_used:
                status_badges.append(f'<span class="badge badge-success">Used: {report.usage.usage_count}x</span>')
            else:
                status_badges.append('<span class="badge badge-warning">Unused</span>')
        
        # Build Card
        html.append(f'''
        <div class="report-card">
            <div class="card-header">
                <div>
                    <h3 class="card-title">{entry.title or "No Title"}</h3>
                    <div class="card-subtitle">{entry.key} • {entry.year} • {entry.entry_type}</div>
                </div>
                <div style="display: flex; gap: 8px;">
                    {" ".join(status_badges)}
                </div>
            </div>
            
            <div class="card-content">
                <div class="detail-grid">
                    {
                        (lambda e: "".join([
                            f'<div class="detail-item"><div class="detail-label">{k}</div><div class="detail-value">{v}</div></div>'
                            for k, v in filter(None, [
                                ("Authors", e.author or "N/A"),
                                ("Venue", e.journal or e.booktitle or e.publisher or "N/A"),
                                ("DOI", e.doi) if e.doi else None,
                                ("ArXiv", e.arxiv_id) if e.arxiv_id and not e.doi else None,
                                ("Volume/Pages", f"{'Vol.'+e.volume if e.volume else ''} {'pp.'+e.pages if e.pages else ''}".strip()) if e.volume or e.pages else None,
                                ("URL", f'<a href="{e.url}" target="_blank" style="text-decoration:underline;">Link</a>') if e.url else None
                            ])
                        ]))(entry)
                    }
                </div>
        ''')
        
        # Add issues if any
        issues = []
        if report.comparison and not report.comparison.is_match:
             # Add main message derived from match status
             if report.comparison.issues:
                 for issue in report.comparison.issues:
                     issues.append(f'<div style="margin-left: 20px; font-size: 0.9em; color: #b91c1c;">• {issue}</div>')
             else:
                  issues.append(f'<div style="margin-left: 20px; font-size: 0.9em; color: #b91c1c;">• Verification failed</div>')
        
        if issues:
            html.append('<div style="margin-top: 16px; padding-top: 12px; border-top: 1px solid #eee;">')
            html.append("".join(issues))
            html.append('</div>')
            
        html.append('</div></div>') # Close card-content and report-card
        
    html.append('</div>') # Close container
    return "".join(html)

def generate_latex_html(results: list) -> str:
    """Generate HTML for LaTeX quality check."""
    from src.checkers import CheckSeverity

    html = ['<div class="scrollable-report-area">']
    
    # Stats
    errors = sum(1 for r in results if r.severity == CheckSeverity.ERROR)
    warnings = sum(1 for r in results if r.severity == CheckSeverity.WARNING)
    infos = sum(1 for r in results if r.severity == CheckSeverity.INFO)
    
    html.append('<div class="stats-container">')
    html.append(f'<div class="stat-card" style="background: linear-gradient(135deg, #ef4444 0%, #b91c1c 100%);"><div class="stat-value">{errors}</div><div class="stat-label">Errors</div></div>')
    html.append(f'<div class="stat-card" style="background: linear-gradient(135deg, #f59e0b 0%, #d97706 100%);"><div class="stat-value">{warnings}</div><div class="stat-label">Warnings</div></div>')
    html.append(f'<div class="stat-card" style="background: linear-gradient(135deg, #3b82f6 0%, #1d4ed8 100%);"><div class="stat-value">{infos}</div><div class="stat-label">Suggestions</div></div>')
    html.append('</div>')
    
    if not results:
        html.append('<div class="report-card"><div class="card-content" style="text-align: center; padding: 40px; color: #166534; font-size: 1.2em;">✅ No issues found in LaTeX code!</div></div>')
    else:
        # Group by Checker
        results.sort(key=lambda x: x.checker_name)
        current_checker = None
        
        for result in results:
            badge_class = "badge-neutral"
            if result.severity == CheckSeverity.ERROR: badge_class = "badge-error"
            elif result.severity == CheckSeverity.WARNING: badge_class = "badge-warning"
            elif result.severity == CheckSeverity.INFO: badge_class = "badge-info"
            
            html.append(f'''
            <div class="report-card">
                <div class="card-header">
                    <div>
                        <h3 class="card-title">{result.checker_name}</h3>
                        <div class="card-subtitle">Line {result.line_number}</div>
                    </div>
                     <span class="badge {badge_class}">{result.severity.name}</span>
                </div>
                <div class="card-content">
                    {result.message}
                    {f'<div style="margin-top: 8px; background: #f3f4f6; padding: 8px; border-radius: 4px; font-family: monospace;">{result.line_content}</div>' if result.line_content else ''}
                    {f'<div style="margin-top: 8px; color: #166534;">💡 Suggestion: {result.suggestion}</div>' if result.suggestion else ''}
                </div>
            </div>
            ''')
            
    html.append('</div>')
    return "".join(html)

def generate_line_html(content: str, results: list) -> str:
    """Generate HTML for Line-by-Line report."""
    # Build a dictionary of line_number -> list of issues
    issues_by_line = {}
    for r in results:
        if r.line_number not in issues_by_line:
            issues_by_line[r.line_number] = []
        issues_by_line[r.line_number].append(r)
        
    lines = content.split('\n')
    
    html = ['<div class="scrollable-report-area">']
    
    html.append('<div class="report-card"><div class="card-content">Issues are mapped to specific lines below.</div></div>')
    
    for i, line in enumerate(lines, 1):
        if i in issues_by_line:
            # Highlight this line
            line_issues = issues_by_line[i]
            
            html.append(f'''
            <div class="report-card" style="border-left: 4px solid #ef4444; padding: 12px;">
                <div style="font-family: monospace; color: #6b7280; font-size: 0.9em; margin-bottom: 4px;">Line {i}</div>
                <div style="font-family: monospace; background: #fee2e2; padding: 4px; border-radius: 4px; overflow-x: auto; white-space: pre;">{line}</div>
                <div style="margin-top: 8px;">
            ''')
            
            for issue in line_issues:
                html.append(f'<div style="color: #991b1b; font-size: 0.95em; margin-top: 4px;">• {issue.message}</div>')
                
            html.append('</div></div>')
            
    html.append('</div>')
    return "".join(html)




def run_check(
    bib_file,
    tex_file,
    check_metadata: bool,
    check_usage: bool,
    check_duplicates: bool,
    check_preprint_ratio: bool,
    caption: bool,
    reference: bool,
    formatting: bool,
    equation: bool,
    ai_artifacts: bool,
    sentence: bool,
    consistency: bool,
    acronym: bool,
    number: bool,
    citation_quality: bool,
    anonymization: bool,
    progress=gr.Progress()
) -> Tuple[str, str, str]:
    """Run BibGuard checks and return three reports."""
    
    if bib_file is None or tex_file is None:
        return (
            "⚠️ Please upload both `.bib` and `.tex` files.",
            "⚠️ Please upload both `.bib` and `.tex` files.",
            "⚠️ Please upload both `.bib` and `.tex` files."
        )
    
    try:
        # Create config from UI
        config = create_config_from_ui(
            check_metadata, check_usage, check_duplicates, check_preprint_ratio,
            caption, reference, formatting, equation, ai_artifacts,
            sentence, consistency, acronym, number, citation_quality, anonymization
        )
        
        # Get file paths from uploaded files
        bib_path = bib_file.name
        tex_path = tex_file.name
        
        # Read tex content for checkers
        tex_content = Path(tex_path).read_text(encoding='utf-8', errors='replace')
        
        # Parse files
        bib_parser = BibParser()
        entries = bib_parser.parse_file(bib_path)
        
        tex_parser = TexParser()
        tex_parser.parse_file(tex_path)
        
        bib_config = config.bibliography
        
        # Initialize components
        arxiv_fetcher = None
        crossref_fetcher = None
        semantic_scholar_fetcher = None
        openalex_fetcher = None
        dblp_fetcher = None
        comparator = None
        usage_checker = None
        duplicate_detector = None
        
        if bib_config.check_metadata:
            arxiv_fetcher = ArxivFetcher()
            semantic_scholar_fetcher = SemanticScholarFetcher()
            openalex_fetcher = OpenAlexFetcher()
            dblp_fetcher = DBLPFetcher()
            crossref_fetcher = CrossRefFetcher()
            comparator = MetadataComparator()
        
        if bib_config.check_usage:
            usage_checker = UsageChecker(tex_parser)
        
        if bib_config.check_duplicates:
            duplicate_detector = DuplicateDetector()
        
        # Initialize report generator
        report_gen = ReportGenerator(
            minimal_verified=False,
            check_preprint_ratio=bib_config.check_preprint_ratio,
            preprint_warning_threshold=bib_config.preprint_warning_threshold
        )
        report_gen.set_metadata([bib_file.name], [tex_file.name])
        
        # Run submission quality checks
        progress(0.2, desc="Running LaTeX quality checks...")
        submission_results = []
        enabled_checkers = config.submission.get_enabled_checkers()
        
        for checker_name in enabled_checkers:
            if checker_name in CHECKER_REGISTRY:
                checker = CHECKER_REGISTRY[checker_name]()
                results = checker.check(tex_content, {})
                for r in results:
                    r.file_path = tex_file.name
                submission_results.extend(results)
        
        report_gen.set_submission_results(submission_results, None)
        
        # Check for duplicates
        if bib_config.check_duplicates and duplicate_detector:
            duplicate_groups = duplicate_detector.find_duplicates(entries)
            report_gen.set_duplicate_groups(duplicate_groups)
        
        # Check missing citations
        if bib_config.check_usage and usage_checker:
            missing = usage_checker.get_missing_entries(entries)
            report_gen.set_missing_citations(missing)
        
        # Build workflow
        workflow_config = get_default_workflow()
        
        # Process entries
        progress(0.3, desc="Processing bibliography entries...")
        total_entries = len(entries)
        
        for i, entry in enumerate(entries):
            progress(0.3 + 0.5 * (i / total_entries), desc=f"Checking: {entry.key}")
            
            # Check usage
            usage_result = None
            if usage_checker:
                usage_result = usage_checker.check_usage(entry)
            
            # Fetch and compare metadata
            comparison_result = None
            if bib_config.check_metadata and comparator:
                comparison_result = fetch_and_compare_with_workflow(
                    entry, workflow_config, arxiv_fetcher, crossref_fetcher,
                    semantic_scholar_fetcher, openalex_fetcher, dblp_fetcher, comparator
                )
            
            # Create entry report
            entry_report = EntryReport(
                entry=entry,
                comparison=comparison_result,
                usage=usage_result,
                evaluations=[]
            )
            report_gen.add_entry_report(entry_report)
        
        progress(0.85, desc="Generating structured reports...")
        
        # Generate Bibliography HTML Report
        bib_report = generate_bibliography_html(report_gen, entries)
        
        # Generate LaTeX Quality HTML Report
        latex_report = generate_latex_html(submission_results)
        
        # Generate Line-by-Line HTML Report
        line_report = ""
        if submission_results:
            line_report = generate_line_html(tex_content, submission_results)
        else:
             line_report = '<div class="report-container"><div class="report-card"><div class="card-content">No issues to display line-by-line.</div></div></div>'
        
        progress(1.0, desc="Done!")
        
        return bib_report, latex_report, line_report
        
    except Exception as e:
        error_msg = f"❌ Error: {str(e)}"
        import traceback
        error_msg += f"\n\n```\n{traceback.format_exc()}\n```"
        return error_msg, error_msg, error_msg



def create_app():
    """Create and configure the Gradio app."""
    
    # Load icon as base64
    icon_html = ""
    try:
        icon_path = Path("assets/icon-192.png")
        if icon_path.exists():
            with open(icon_path, "rb") as f:
                encoding = base64.b64encode(f.read()).decode()
            icon_html = f'<img src="data:image/png;base64,{encoding}" style="width: 48px; height: 48px; border-radius: 8px;" alt="BibGuard">'
        else:
            icon_html = '<span style="font-size: 48px;">📚</span>'
    except Exception:
        icon_html = '<span style="font-size: 48px;">📚</span>'

    with gr.Blocks(title="BibGuard - Bibliography & LaTeX Quality Checker") as app:
        
        # Header with icon
        with gr.Row(elem_classes=["app-header"]):
            gr.HTML(f"""
            <div style="display: flex; align-items: center; gap: 12px; margin-bottom: 16px;">
                {icon_html}
                <div>
                    <h1 style="margin: 0; font-size: 1.8em;">BibGuard</h1>
                    <p style="margin: 0; color: #666; font-size: 14px;">Bibliography & LaTeX Quality Checker</p>
                </div>
            </div>
            """)
        
        with gr.Row(elem_classes=["app-body"]):
            # Left column: Upload & Settings
            with gr.Column(scale=1, min_width=280, elem_classes=["app-sidebar"]):
                gr.Markdown("### 📁 Upload Files")
                
                bib_file = gr.File(
                    label="Bibliography (.bib)",
                    file_types=[".bib"],
                    file_count="single"
                )
                
                tex_file = gr.File(
                    label="LaTeX Source (.tex)", 
                    file_types=[".tex"],
                    file_count="single"
                )
                
                # Check options in grid layout
                gr.Markdown("#### ⚙️ Options")
                
                with gr.Row():
                    check_metadata = gr.Checkbox(label="🔍 Metadata", value=False)
                    check_usage = gr.Checkbox(label="📊 Usage", value=True)
                
                with gr.Row():
                    check_duplicates = gr.Checkbox(label="👯 Duplicates", value=True)
                    check_preprint_ratio = gr.Checkbox(label="📄 Preprints", value=True)
                
                with gr.Row():
                    caption = gr.Checkbox(label="🖼️ Captions", value=True)
                    reference = gr.Checkbox(label="🔗 References", value=True)
                
                with gr.Row():
                    formatting = gr.Checkbox(label="✨ Formatting", value=True)
                    equation = gr.Checkbox(label="🔢 Equations", value=True)
                
                with gr.Row():
                    ai_artifacts = gr.Checkbox(label="🤖 AI Artifacts", value=True)
                    sentence = gr.Checkbox(label="📝 Sentences", value=True)
                
                with gr.Row():
                    consistency = gr.Checkbox(label="🔄 Consistency", value=True)
                    acronym = gr.Checkbox(label="🔤 Acronyms", value=True)
                
                with gr.Row():
                    number = gr.Checkbox(label="🔢 Numbers", value=True)
                    citation_quality = gr.Checkbox(label="📚 Citations", value=True)
                
                with gr.Row():
                    anonymization = gr.Checkbox(label="🎭 Anonymization", value=True)
                
                run_btn = gr.Button("🔍 Check Now", variant="primary", size="lg")
                
                gr.HTML("""
                <div style="text-align: center; margin-top: 16px;">
                <a href="https://github.com/thinkwee/BibGuard" target="_blank" style="text-decoration: none; color: #666; display: inline-flex; align-items: center; gap: 6px;">
                <svg height="20" width="20" viewBox="0 0 16 16"><path fill="currentColor" d="M8 0C3.58 0 0 3.58 0 8c0 3.54 2.29 6.53 5.47 7.59.4.07.55-.17.55-.38 0-.19-.01-.82-.01-1.49-2.01.37-2.53-.49-2.69-.94-.09-.23-.48-.94-.82-1.13-.28-.15-.68-.52-.01-.53.63-.01 1.08.58 1.23.82.72 1.21 1.87.87 2.33.66.07-.52.28-.87.51-1.07-1.78-.2-3.64-.89-3.64-3.95 0-.87.31-1.59.82-2.15-.08-.2-.36-1.02.08-2.12 0 0 .67-.21 2.2.82.64-.18 1.32-.27 2-.27.68 0 1.36.09 2 .27 1.53-1.04 2.2-.82 2.2-.82.44 1.1.16 1.92.08 2.12.51.56.82 1.27.82 2.15 0 3.07-1.87 3.75-3.65 3.95.29.25.54.73.54 1.48 0 1.07-.01 1.93-.01 2.2 0 .21.15.46.55.38A8.013 8.013 0 0016 8c0-4.42-3.58-8-8-8z"></path></svg>
                GitHub
                </a>
                <p style="margin: 8px 0 0 0; color: #999; font-size: 12px;">Developed with ❤️ for researchers</p>
                </div>
                """)
            
            # Right column: Reports
            with gr.Column(scale=4, elem_classes=["app-content"]):
                with gr.Tabs():
                    with gr.Tab("📚 Bibliography Report"):
                        bib_report = gr.HTML(
                            value=WELCOME_HTML,
                            elem_classes=["report-panel"]
                        )
                    
                    with gr.Tab("📝 LaTeX Quality"):
                        latex_report = gr.HTML(
                            value=WELCOME_HTML,
                            elem_classes=["report-panel"]
                        )
                    
                    with gr.Tab("📋 Line-by-Line"):
                        line_report = gr.HTML(
                            value=WELCOME_HTML,
                            elem_classes=["report-panel"]
                        )
        
        # Event handling
        run_btn.click(
            fn=run_check,
            inputs=[
                bib_file, tex_file,
                check_metadata, check_usage, check_duplicates, check_preprint_ratio,
                caption, reference, formatting, equation, ai_artifacts,
                sentence, consistency, acronym, number, citation_quality, anonymization
            ],
            outputs=[bib_report, latex_report, line_report]
        )
    
    return app


# Create the app
app = create_app()

if __name__ == "__main__":
    app.launch(
        favicon_path="assets/icon-192.png",
        show_error=True,
        css=CUSTOM_CSS,
        theme=gr.themes.Soft()
    )