static/script.js

// Array to store problem history versions
const problemHistory = [];
let currentHistoryIndex = -1;
// Store all refined problem suggestions
let storedRefinedProblems = {};
document.getElementById("tab1").style.display = "block";

function openTab(evt, tabName) {
    var i, tabcontent, tablinks;
    tabcontent = document.getElementsByClassName("tabcontent");
    for (i = 0; i < tabcontent.length; i++) {
      tabcontent[i].style.display = "none";
    }
    tablinks = document.getElementsByClassName("tablinks");
    for (i = 0; i < tablinks.length; i++) {
      tablinks[i].className = tablinks[i].className.replace(" active", "");
    }
    document.getElementById(tabName).style.display = "block";
    evt.currentTarget.className += " active";
}

function navigateProblemHistory(direction) {
    const problemInput = document.getElementById('userProblemDescription');
    console.log("Current history index:", currentHistoryIndex, "Total history:", problemHistory.length);
    
    if (direction === 'prev' && currentHistoryIndex > 0) {
        currentHistoryIndex--;
        problemInput.value = problemHistory[currentHistoryIndex];
        console.log("Moving to previous version:", currentHistoryIndex);
    } else if (direction === 'next' && currentHistoryIndex < problemHistory.length - 1) {
        currentHistoryIndex++;
        problemInput.value = problemHistory[currentHistoryIndex];
        console.log("Moving to next version:", currentHistoryIndex);
    }
    
    updateHistoryNavigation();
}

function generateQueries(event) {
    event.preventDefault();
    
    const userInput = document.getElementById('userInput').value.trim();
    if (!userInput) {
        alert('Please enter a technical problem description');
        return;
    }
    
    // Show loading indicator
    document.querySelector(".progress-text").innerHTML = "Generating key issues ... Please wait."
    document.getElementById('globalLoadingOverlay').style.display = 'flex';
    
    // Send message to Flask backend
    fetch('/generate-key-issues', {
        method: 'POST',
        body: JSON.stringify({ 'query': userInput }),
        headers: { 'Content-Type': 'application/json' }
    })
    .then(response => response.json())
    .then(data => {
        // Hide loading indicator
        document.getElementById('globalLoadingOverlay').style.display = 'none';
        
        // Check if we have key issues in the response
        if (data.key_issues && data.key_issues.length > 0) {
            // Display the key issues
            displayKeyIssues(data.key_issues);
        } else if (data.error) {
            alert('Error: ' + data.error);
        } else {
            alert('No key issues found. Please try a different query.');
        }
    })
    .catch(error => {
        document.getElementById('globalLoadingOverlay').style.display = 'none';
        console.error('Error:', error);
        alert('There was an error communicating with the server. Please try again.');
    });
}

function performSearch(query, queryItemElement) {
    if (!query.trim()) {
        alert('Please enter a search query');
        return;
    }
    
    const loadingElement = queryItemElement.querySelector('.search-loading');
    const tableElement = queryItemElement.querySelector('.results-table');
    const tableBody = tableElement.querySelector('tbody');
    
    // Show loading and hide previous results
    loadingElement.style.display = 'block';
    tableElement.style.display = 'none';
    
    // Clear previous results
    tableBody.innerHTML = '';
    
    // Get checkbox values
    const pdfChecked = document.getElementById('pdfOption').checked;
    const patentChecked = document.getElementById('patentOption').checked;
    const webChecked = document.getElementById('webOption').checked;

    
    // Create form data with query and checkbox values
    const formData = new FormData();
    formData.append('query', query);
    formData.append('pdfOption', pdfChecked);
    formData.append('patentOption', patentChecked);
    formData.append('webOption', webChecked);

    
    // Send search request to backend
    fetch('/search', {
        method: 'POST',
        body: formData
    })
    .then(response => response.json())
    .then(data => {
        // Hide loading indicator
        loadingElement.style.display = 'none';
        
        if (data.results && data.results.length > 0) {
            // Populate table with results
            data.results.forEach(result => {
                const row = document.createElement('tr');

                const typeCell = document.createElement('td');
                typeCell.textContent = result.type;                        
                
                const titleCell = document.createElement('td');
                titleCell.textContent = result.title;
                
                const bodyCell = document.createElement('td');
                bodyCell.textContent = result.body;
                
                const urlCell = document.createElement('td');
                const urlLink = document.createElement('a');
                urlLink.href = result.url;
                urlLink.textContent = result.url;
                urlLink.className = 'url-link';
                urlLink.target = '_blank';
                urlCell.appendChild(urlLink);

                // Add "Analyze" button to the URL cell
                const analyzeButton = document.createElement('button');
                analyzeButton.textContent = 'Analyze';
                analyzeButton.className = 'action-button analyze-button';
                analyzeButton.onclick = function(e) {
                    e.preventDefault();
                    analyzePaper(result.url, queryItemElement);
                };
                urlCell.appendChild(document.createElement('br'));
                urlCell.appendChild(analyzeButton);
                
                row.appendChild(typeCell);
                row.appendChild(titleCell);
                row.appendChild(bodyCell);
                row.appendChild(urlCell);
                
                tableBody.appendChild(row);
            });
            
            // Show the table
            tableElement.style.display = 'table';
        } else {
            // No results
            const row = document.createElement('tr');
            const cell = document.createElement('td');
            cell.colSpan = 4; // Updated to 4 since we now have 4 columns with the type column
            cell.textContent = 'No results found.';
            cell.style.textAlign = 'center';
            row.appendChild(cell);
            tableBody.appendChild(row);
            tableElement.style.display = 'table';
        }
    })
    .catch(error => {
        loadingElement.style.display = 'none';
        console.error('Error:', error);
        
        // Show error in table
        const row = document.createElement('tr');
        const cell = document.createElement('td');
        cell.colSpan = 4; // Updated to 4 since we now have 4 columns with the type column
        cell.textContent = 'Error performing search. Please try again.';
        cell.style.textAlign = 'center';
        cell.style.color = 'red';
        row.appendChild(cell);
        tableBody.appendChild(row);
        tableElement.style.display = 'table';
    });
}

function analyzePaper(paperUrl, queryItemElement) {
    const patentBackground = document.getElementById('userProblemDescription').value.trim();
    if (!patentBackground) {
        alert('Please provide a patent background in the input field');
        return;
    }
    
    // Find the row containing this URL
    const rows = queryItemElement.querySelectorAll('tbody tr');
    let targetRow;
    let documentType = 'pdf'; // Default type
    
    for (const row of rows) {
        const urlLink = row.querySelector('.url-link');
        if (urlLink && urlLink.href === paperUrl) {
            targetRow = row;
            // Get the document type from the first cell of the row
            documentType = row.cells[0].textContent.toLowerCase();
            break;
        }
    }
    
    if (!targetRow) {
        alert('Could not find the paper in the results table');
        return;
    }
    
    // Check if we already have analysis columns
    let scoreCell, justificationCell;
    if (targetRow.cells.length <= 4) {
        // We need to create the cells
        scoreCell = document.createElement('td');
        scoreCell.className = 'score-cell';
        scoreCell.innerHTML = '<div class="loading-spinner"></div>';
        
        justificationCell = document.createElement('td');
        justificationCell.className = 'justification-cell';
        justificationCell.innerHTML = 'Analyzing...';
        
        targetRow.appendChild(scoreCell);
        targetRow.appendChild(justificationCell);
    } else {
        // Use existing cells
        scoreCell = targetRow.cells[4];
        justificationCell = targetRow.cells[5];
        scoreCell.innerHTML = '<div class="loading-spinner"></div>';
        justificationCell.innerHTML = 'Analyzing...';
    }
    
    // Send analysis request to backend
    fetch('/analyze', {
        method: 'POST',
        body: JSON.stringify({ 
            'patent_background': patentBackground, 
            'pdf_url': paperUrl,
            'data_type': documentType
        }),
        headers: { 'Content-Type': 'application/json' }
    })
    .then(response => response.json())
    .then(data => {
        if (data.error) {
            scoreCell.innerHTML = 'Error';
            justificationCell.innerHTML = data.error;
        } else if (data.result) {
            // Get score and justification from the result
            const result = data.result;
            const score = result.score !== undefined ? result.score : 'N/A';
            const justification = result.justification || 'No justification provided';
            
            // Update cells with results
            scoreCell.innerHTML = score;
            justificationCell.innerHTML = justification;
            
            // Color-code the score
            if (score >= 0 && score <= 5) {
                const redComponent = Math.floor((score / 5) * 255);
                const greenComponent = Math.floor(((5 - score) / 5) * 255);
                scoreCell.style.backgroundColor = `rgb(${redComponent}, ${greenComponent}, 0)`;
                scoreCell.style.color = 'white';
                scoreCell.style.fontWeight = 'bold';
                scoreCell.style.textAlign = 'center';
            }
            
            // Add "Extract Insights" button to the justify cell
            const insightsButton = document.createElement('button');
            insightsButton.textContent = 'Extract Insights';
            insightsButton.className = 'action-button insights-button';
            insightsButton.style.marginTop = '5px';
            insightsButton.style.fontSize = '0.8em';
            insightsButton.onclick = function(e) {
                e.preventDefault();
                extractInsights(paperUrl, targetRow);
            };
            justificationCell.appendChild(document.createElement('br'));
            justificationCell.appendChild(insightsButton);
        } else {
            scoreCell.innerHTML = 'No data';
            justificationCell.innerHTML = 'Analysis failed';
        }
    })
    .catch(error => {
        console.error('Error:', error);
        scoreCell.innerHTML = 'Error';
        justificationCell.innerHTML = 'Failed to analyze paper';
    });
}

function extractInsights(paperUrl, row) {
    const patentBackground = document.getElementById('userProblemDescription').value.trim();
    if (!patentBackground) {
        alert('Please provide a patent background in the input field');
        return;
    }
    
    const documentType = row.cells[0].textContent.toLowerCase();
    
    // Check if there's already an insights row for this document
    let insightsRow = row.nextElementSibling;
    if (insightsRow && insightsRow.className === 'insights-row') {
        // Insights row already exists, get the container
        insightsContainer = insightsRow.querySelector('.insights-container');
        insightsContainer.innerHTML = '<div class="loading-spinner"></div><div>Extracting insights...</div>';
    } else {
        // Create insights row that spans across all columns
        insightsRow = document.createElement('tr');
        insightsRow.className = 'insights-row';
        
        const insightsTd = document.createElement('td');
        insightsTd.colSpan = row.cells.length;
        
        insightsContainer = document.createElement('div');
        insightsContainer.className = 'insights-container';
        insightsContainer.innerHTML = '<div class="loading-spinner"></div><div>Extracting insights...</div>';
        
        insightsTd.appendChild(insightsContainer);
        insightsRow.appendChild(insightsTd);
        
        // Insert after the current row
        row.parentNode.insertBefore(insightsRow, row.nextSibling);
    }
    
    // Store the row reference as a data attribute on the container for later access
    insightsContainer.dataset.parentRow = row.rowIndex;
    
    // Send request to extract insights
    fetch('/post_insights', {
        method: 'POST',
        body: JSON.stringify({ 
            'patent_background': patentBackground, 
            'pdf_url': paperUrl,
            'data_type': documentType
        }),
        headers: { 'Content-Type': 'application/json' }
    })
    .then(response => response.json())
    .then(data => {
        if (data.error) {
            insightsContainer.innerHTML = `<div class="error">Error: ${data.error}</div>`;
        } else if (data.result && data.result.insights) {
            // Create header with title and actions
            const insightsHeader = document.createElement('div');
            insightsHeader.className = 'insights-header';
            
            const insightsTitle = document.createElement('div');
            insightsTitle.className = 'insights-title';
            insightsTitle.textContent = 'Document Insights';
            
            const insightsActions = document.createElement('div');
            insightsActions.className = 'insights-actions';
            
            // Store the insights for this specific container
            const containerInsights = [...data.result.insights];
            insightsContainer.dataset.allInsights = JSON.stringify(containerInsights);
            
            const selectAllBtn = document.createElement('button');
            selectAllBtn.className = 'insights-button select-all-btn';
            selectAllBtn.textContent = 'Select All';
            // Use a closure to ensure the button has access to the correct container and row
            selectAllBtn.addEventListener('click', function() {
                const container = this.closest('.insights-container');
                const parentRow = row;
                const allInsights = JSON.parse(container.dataset.allInsights || '[]');
                
                const tags = container.querySelectorAll('.insight-tag');
                tags.forEach(tag => tag.classList.add('selected'));
                
                parentRow.dataset.selectedInsights = JSON.stringify(allInsights);
                parentRow.dataset.unselectedInsights = JSON.stringify([]);
                
                // Trigger check for enabling/disabling enhance button
                checkSelectedInsights();
            });
            
            const clearAllBtn = document.createElement('button');
            clearAllBtn.className = 'insights-button clear-all-btn';
            clearAllBtn.textContent = 'Clear All';
            // Use a closure to ensure the button has access to the correct container and row
            clearAllBtn.addEventListener('click', function() {
                const container = this.closest('.insights-container');
                const parentRow = row;
                const allInsights = JSON.parse(container.dataset.allInsights || '[]');
                
                const tags = container.querySelectorAll('.insight-tag');
                tags.forEach(tag => tag.classList.remove('selected'));
                
                parentRow.dataset.selectedInsights = JSON.stringify([]);
                parentRow.dataset.unselectedInsights = JSON.stringify(allInsights);
                
                // Trigger check for enabling/disabling enhance button
                checkSelectedInsights();
            });
            
            insightsActions.appendChild(selectAllBtn);
            insightsActions.appendChild(clearAllBtn);
            
            insightsHeader.appendChild(insightsTitle);
            insightsHeader.appendChild(insightsActions);
            
            // Create insight tags
            const insightsList = document.createElement('div');
            insightsList.className = 'insights-list';
            
            // Clear the container and add the new elements
            insightsContainer.innerHTML = '';
            insightsContainer.appendChild(insightsHeader);
            insightsContainer.appendChild(insightsList);
            
            // Initialize selected insights
            const selectedInsights = [];
            const unselectedInsights = [];
            
            // Add insight tags
            data.result.insights.forEach(insight => {
                const tagElement = document.createElement('div');
                tagElement.className = 'insight-tag';
                tagElement.textContent = insight;
                tagElement.addEventListener('click', function() {
                    this.classList.toggle('selected');
                    
                    // Update selected insights
                    updateSelectedInsights(row, insightsContainer);
                    
                    // Trigger check for enabling/disabling enhance button
                    checkSelectedInsights();
                });
                
                // Add to unselected by default
                // tagElement.classList.add('selected');
                unselectedInsights.push(insight);
                
                insightsList.appendChild(tagElement);
            });
            
            // Store initial selections
            row.dataset.selectedInsights = JSON.stringify(selectedInsights);
            row.dataset.unselectedInsights = JSON.stringify(unselectedInsights);
            
            // Trigger check for enabling/disabling enhance button immediately
            checkSelectedInsights();
            
        } else {
            insightsContainer.innerHTML = '<div class="error">No insights found</div>';
        }
    })
    .catch(error => {
        console.error('Error:', error);
        insightsContainer.innerHTML = `<div class="error">Error extracting insights: ${error.message}</div>`;
    });
}

function updateSelectedInsights(row, insightsContainer) {
    const selectedInsights = [];
    const unselectedInsights = [];
    
    const tags = insightsContainer.querySelectorAll('.insight-tag');
    tags.forEach(tag => {
        if (tag.classList.contains('selected')) {
            selectedInsights.push(tag.textContent);
        } else {
            unselectedInsights.push(tag.textContent);
        }
    });
    
    row.dataset.selectedInsights = JSON.stringify(selectedInsights);
    row.dataset.unselectedInsights = JSON.stringify(unselectedInsights);
}

function checkSelectedInsights() {
    const selectedInsights = collectAllSelectedInsights();
    const enhanceButton = document.getElementById('enhanceProblemButton');
    
    if (selectedInsights.length > 0) {
        enhanceButton.classList.remove('disabled');
        enhanceButton.disabled = false;
    } else {
        enhanceButton.classList.add('disabled');
        enhanceButton.disabled = true;
    }
}

function collectAllSelectedInsights() {
    const allSelectedInsights = [];
    const queryItems = document.querySelectorAll('.query-item');
    
    queryItems.forEach(queryItem => {
        const rows = queryItem.querySelectorAll('tbody tr:not(.insights-row)');
        rows.forEach(row => {
            if (row.dataset.selectedInsights) {
                try {
                    const selectedInsights = JSON.parse(row.dataset.selectedInsights);
                    selectedInsights.forEach(insight => {
                        if (!allSelectedInsights.includes(insight)) {
                            allSelectedInsights.push(insight);
                        }
                    });
                } catch (e) {
                    console.error('Error parsing selected insights:', e);
                }
            }
        });
    });
    
    return allSelectedInsights;
}

function exportToExcel() {
    // Show loading overlay
    const loadingOverlay = document.getElementById('globalLoadingOverlay');
    if (loadingOverlay) {
        loadingOverlay.style.display = 'flex';
        loadingOverlay.querySelector('.progress-text').textContent = 'Generating Excel file...';
    }
    
    try {
        // Collect all data from all tables
        const allData = [];
        const queryItems = document.querySelectorAll('.query-item');
        
        queryItems.forEach(queryItem => {
            // Get the search query text for this table
            const queryText = queryItem.querySelector('.query-field').value;
            
            // Get all rows in this table
            const rows = queryItem.querySelectorAll('tbody tr:not(.insights-row)');
            
            rows.forEach(row => {
                // Skip empty rows or error rows
                if (row.cells.length === 1 && row.cells[0].colSpan > 1) {
                    return; // Skip "No results found" rows
                }
                
                // Prepare object for this row
                const rowData = {
                    'Topic': queryText,
                    'Type': row.cells[0].textContent,
                    'Title': row.cells[1].textContent,
                    'Description': row.cells[2].textContent,
                    'URL': row.querySelector('.url-link')?.href || ''
                };
                
                // Add score and justification if they exist
                if (row.cells.length > 4) {
                    rowData['Score'] = row.cells[4].textContent;
                    rowData['Justification'] = row.cells[5].textContent.split('\n')[0]; // Only get the justification text
                } else {
                    rowData['Score'] = '';
                    rowData['Justification'] = '';
                }
                
                // Add selected and unselected insights if they exist
                if (row.dataset.selectedInsights) {
                    try {
                        const selectedInsights = JSON.parse(row.dataset.selectedInsights);
                        rowData['Selected Insights'] = selectedInsights.join('; ');
                    } catch (e) {
                        rowData['Selected Insights'] = '';
                    }
                } else {
                    rowData['Selected Insights'] = '';
                }
                
                if (row.dataset.unselectedInsights) {
                    try {
                        const unselectedInsights = JSON.parse(row.dataset.unselectedInsights);
                        rowData['Unselected Insights'] = unselectedInsights.join('; ');
                    } catch (e) {
                        rowData['Unselected Insights'] = '';
                    }
                } else {
                    rowData['Unselected Insights'] = '';
                }
                
                allData.push(rowData);
            });
        });
        
        // Check if we have any data
        if (allData.length === 0) {
            if (loadingOverlay) loadingOverlay.style.display = 'none';
            alert('No data to export. Please perform a search first.');
            return;
        }
        
        // Get all problem versions
        const problemVersions = {};
        if (problemHistory.length > 0) {
            problemHistory.forEach((problem, index) => {
                problemVersions[`Problem Version ${index + 1}`] = problem;
            });
        } else {
            // If no history, just use the current problem
            const currentProblem = document.getElementById('userProblemDescription').value.trim();
            if (currentProblem) {
                problemVersions['Problem Version 1'] = currentProblem;
            }
        }
        
        // Send to server for Excel generation
        fetch('/export-excel', {
            method: 'POST',
            body: JSON.stringify({
                'tableData': allData,
                'userQuery': document.getElementById('userProblemDescription').value,
                'problemVersions': problemVersions
            }),
            headers: { 'Content-Type': 'application/json' }
        })
        .then(response => {
            if (!response.ok) {
                throw new Error(`Server error: ${response.status}`);
            }
            return response.blob();
        })
        .then(blob => {
            // Hide loading overlay
            if (loadingOverlay) loadingOverlay.style.display = 'none';
            
            // Create URL for the blob
            const url = window.URL.createObjectURL(new Blob([blob], {
                type: 'application/vnd.openxmlformats-officedocument.spreadsheetml.sheet'
            }));
            
            // Create a link and trigger download
            const a = document.createElement('a');
            a.href = url;
            a.download = 'patent_search_results.xlsx';
            document.body.appendChild(a);
            a.click();
            
            // Clean up
            window.URL.revokeObjectURL(url);
            document.body.removeChild(a);
        })
        .catch(error => {
            console.error('Error exporting to Excel:', error);
            if (loadingOverlay) loadingOverlay.style.display = 'none';
            alert(`Error exporting to Excel: ${error.message}`);
        });
    } catch (error) {
        console.error('Error preparing Excel data:', error);
        if (loadingOverlay) loadingOverlay.style.display = 'none';
        alert(`Error preparing data for export: ${error.message}`);
    }
}

function hasSearchResults() {
    const resultsContainer = document.getElementById('resultsContainer');
    const hasResults = resultsContainer && resultsContainer.style.display !== 'none';
    const hasTables = document.querySelectorAll('.results-table[style*="display: table"]').length > 0;
    return hasResults && hasTables;
}


function analyzeAllPapers() {
    // Show loading overlay
    const loadingOverlay = document.getElementById('globalLoadingOverlay');
    if (loadingOverlay) loadingOverlay.style.display = 'flex';
    if (loadingOverlay) loadingOverlay.querySelector('.progress-text').textContent = 'Analyzing all papers...';
    
    // Get all query items
    const queryItems = document.querySelectorAll('.query-item');
    let totalToAnalyze = 0;
    let completedAnalyses = 0;
    
    // Count total papers that need analysis
    queryItems.forEach(queryItem => {
        const rows = queryItem.querySelectorAll('tbody tr');
        rows.forEach(row => {
            if (row.cells.length <= 4 || row.cells[4].textContent.trim() === 'Error' || 
                row.cells[4].textContent.trim() === 'N/A' || row.cells[4].textContent.trim() === '') {
                totalToAnalyze++;
            }
        });
    });
    
    if (totalToAnalyze === 0) {
        alert('No papers need analysis');
        if (loadingOverlay) loadingOverlay.style.display = 'none';
        return;
    }
    
    // Function to update progress
    function updateProgress() {
        completedAnalyses++;
        if (loadingOverlay) {
            const progressElement = loadingOverlay.querySelector('.progress-text');
            if (progressElement) {
                progressElement.textContent = `Analyzing papers: ${completedAnalyses}/${totalToAnalyze}`;
            }
        }
        
        if (completedAnalyses >= totalToAnalyze) {
            if (loadingOverlay) loadingOverlay.style.display = 'none';
        }
    }
    
    // Analyze each paper that needs it
    queryItems.forEach(queryItem => {
        const rows = queryItem.querySelectorAll('tbody tr');
        rows.forEach(row => {
            // Check if this row needs analysis
            if (row.cells.length <= 4 || row.cells[4].textContent.trim() === 'Error' || 
                row.cells[4].textContent.trim() === 'N/A' || row.cells[4].textContent.trim() === '') {
                
                // Get the URL
                const urlLink = row.querySelector('.url-link');
                const documentType = row.cells[0].textContent.toLowerCase();
                if (urlLink && urlLink.href) {
                    // Create a promise for this analysis
                    const promise = new Promise((resolve) => {
                        // Prepare for analysis
                        const patentBackground = document.getElementById('userProblemDescription').value.trim();
                        
                        // Create score and justification cells if needed
                        let scoreCell, justificationCell;
                        if (row.cells.length <= 4) {
                            scoreCell = document.createElement('td');
                            scoreCell.className = 'score-cell';
                            scoreCell.innerHTML = '<div class="loading-spinner"></div>';
                            
                            justificationCell = document.createElement('td');
                            justificationCell.className = 'justification-cell';
                            justificationCell.innerHTML = 'Analyzing...';
                            
                            row.appendChild(scoreCell);
                            row.appendChild(justificationCell);
                        } else {
                            scoreCell = row.cells[4];
                            justificationCell = row.cells[5];
                            scoreCell.innerHTML = '<div class="loading-spinner"></div>';
                            justificationCell.innerHTML = 'Analyzing...';
                        }
                        
                        // Send analysis request
                        fetch('/analyze', {
                            method: 'POST',
                            body: JSON.stringify({ 
                                'patent_background': patentBackground, 
                                'pdf_url': urlLink.href,
                                'data_type': documentType
                            }),
                            headers: { 'Content-Type': 'application/json' }
                        })
                        .then(response => response.json())
                        .then(data => {
                            if (data.error) {
                                scoreCell.innerHTML = 'Error';
                                justificationCell.innerHTML = data.error;
                            } else if (data.result) {
                                // Get score and justification
                                const result = data.result;
                                const score = result.score !== undefined ? result.score : 'N/A';
                                const justification = result.justification || 'No justification provided';
                                
                                // Update cells
                                scoreCell.innerHTML = score;
                                justificationCell.innerHTML = justification;
                                
                                // Color-code score
                                if (score >= 0 && score <= 5) {
                                    const redComponent = Math.floor((score / 5) * 255);
                                    const greenComponent = Math.floor(((5 - score) / 5) * 255);
                                    scoreCell.style.backgroundColor = `rgb(${redComponent}, ${greenComponent}, 0)`;
                                    scoreCell.style.color = 'white';
                                    scoreCell.style.fontWeight = 'bold';
                                    scoreCell.style.textAlign = 'center';
                                }
                                
                                // Add "Extract Insights" button to the justify cell - for Analyze All function
                                const insightsButton = document.createElement('button');
                                insightsButton.textContent = 'Extract Insights';
                                insightsButton.className = 'action-button insights-button';
                                insightsButton.style.marginTop = '5px';
                                insightsButton.style.fontSize = '0.8em';
                                insightsButton.onclick = function(e) {
                                    e.preventDefault();
                                    extractInsights(urlLink.href, row);
                                };
                                justificationCell.appendChild(document.createElement('br'));
                                justificationCell.appendChild(insightsButton);
                            } else {
                                scoreCell.innerHTML = 'No data';
                                justificationCell.innerHTML = 'Analysis failed';
                            }
                            resolve();
                        })
                        .catch(error => {
                            console.error('Error:', error);
                            scoreCell.innerHTML = 'Error';
                            justificationCell.innerHTML = 'Failed to analyze paper';
                            resolve();
                        });
                    });
                    
                    // When this analysis is done, update the progress
                    promise.then(() => {
                        updateProgress();
                    });
                } else {
                    // No URL found, count as completed
                    updateProgress();
                }
            }
        });
    });
}

function removeFailedAnalyses() {
    const queryItems = document.querySelectorAll('.query-item');
    let removedCount = 0;
    
    queryItems.forEach(queryItem => {
        const tbody = queryItem.querySelector('tbody');
        const rows = Array.from(tbody.querySelectorAll('tr'));
        
        rows.forEach(row => {
            if (row.cells.length > 4) {
                const scoreText = row.cells[4].textContent.trim();
                if (scoreText === 'Error' || scoreText === 'N/A' || scoreText === 'No data') {
                    tbody.removeChild(row);
                    removedCount++;
                }
            }
        });
    });
    
    // Create and display a simple notification instead of alert
    const notification = document.createElement('div');
    notification.className = 'simple-notification';
    notification.textContent = `Removed ${removedCount} papers with failed analyses`;
    notification.style.position = 'fixed';
    notification.style.top = '20px';
    notification.style.right = '20px';
    notification.style.background = '#4CAF50';
    notification.style.color = 'white';
    notification.style.padding = '15px';
    notification.style.borderRadius = '5px';
    notification.style.boxShadow = '0 2px 5px rgba(0,0,0,0.2)';
    notification.style.zIndex = '10000';
    
    // Add notification to the body
    document.body.appendChild(notification);
    
    // Remove notification after 3 seconds
    setTimeout(() => {
        if (notification.parentNode) {
            notification.parentNode.removeChild(notification);
        }
    }, 3000);
}

function extractAllInsights() {
    const patentBackground = document.getElementById('userProblemDescription').value.trim();
    if (!patentBackground) {
        alert('Please provide a patent background in the input field');
        return;
    }
    
    // Show loading overlay
    const loadingOverlay = document.getElementById('globalLoadingOverlay');
    if (loadingOverlay) {
        loadingOverlay.style.display = 'flex';
        loadingOverlay.querySelector('.progress-text').textContent = 'Extracting insights from all documents...';
    }
    
    // Get all query items
    const queryItems = document.querySelectorAll('.query-item');
    let totalDocuments = 0;
    let completedDocuments = 0;
    
    // Count total analyzed documents that need insights extraction
    const analyzedRows = [];
    queryItems.forEach(queryItem => {
        const rows = queryItem.querySelectorAll('tbody tr:not(.insights-row)');
        rows.forEach(row => {
            // Only include rows that have been analyzed (have score and justification cells)
            if (row.cells.length > 4 && row.cells[4].textContent.trim() !== 'Error' && 
                row.cells[4].textContent.trim() !== 'N/A' && row.cells[4].textContent.trim() !== '') {
                analyzedRows.push(row);
                totalDocuments++;
            }
        });
    });
    
    if (totalDocuments === 0) {
        if (loadingOverlay) loadingOverlay.style.display = 'none';
        alert('No analyzed documents found. Please analyze documents first.');
        return;
    }
    
    // Function to update progress
    function updateProgress() {
        completedDocuments++;
        if (loadingOverlay) {
            const progressElement = loadingOverlay.querySelector('.progress-text');
            if (progressElement) {
                progressElement.textContent = `Extracting insights: ${completedDocuments}/${totalDocuments}`;
            }
        }
        
        if (completedDocuments >= totalDocuments) {
            if (loadingOverlay) loadingOverlay.style.display = 'none';
            checkSelectedInsights(); // Update enhance button state based on selected insights
        }
    }
    
    // Process each analyzed document sequentially to avoid overwhelming the server
    function processNextDocument(index) {
        if (index >= analyzedRows.length) {
            return; // All documents processed
        }
        
        const row = analyzedRows[index];
        const urlLink = row.querySelector('.url-link');
        const documentType = row.cells[0].textContent.toLowerCase();
        
        if (!urlLink || !urlLink.href) {
            updateProgress();
            processNextDocument(index + 1);
            return;
        }
        
        // Check if there's already an insights row for this document
        let insightsRow = row.nextElementSibling;
        if (insightsRow && insightsRow.className === 'insights-row') {
            // Insights row already exists, get the container
            insightsContainer = insightsRow.querySelector('.insights-container');
            insightsContainer.innerHTML = '<div class="loading-spinner"></div><div>Extracting insights...</div>';
        } else {
            // Create insights row that spans across all columns
            insightsRow = document.createElement('tr');
            insightsRow.className = 'insights-row';
            
            const insightsTd = document.createElement('td');
            insightsTd.colSpan = row.cells.length;
            
            insightsContainer = document.createElement('div');
            insightsContainer.className = 'insights-container';
            insightsContainer.innerHTML = '<div class="loading-spinner"></div><div>Extracting insights...</div>';
            
            insightsTd.appendChild(insightsContainer);
            insightsRow.appendChild(insightsTd);
            
            // Insert after the current row
            row.parentNode.insertBefore(insightsRow, row.nextSibling);
        }
        
        // Store the row reference as a data attribute on the container for later access
        insightsContainer.dataset.parentRow = row.rowIndex;
        
        // Send request to extract insights
        fetch('/post_insights', {
            method: 'POST',
            body: JSON.stringify({ 
                'patent_background': patentBackground, 
                'pdf_url': urlLink.href,
                'data_type': documentType
            }),
            headers: { 'Content-Type': 'application/json' }
        })
        .then(response => response.json())
        .then(data => {
            if (data.error) {
                insightsContainer.innerHTML = `<div class="error">Error: ${data.error}</div>`;
            } else if (data.result && data.result.insights) {
                // Create header with title and actions
                const insightsHeader = document.createElement('div');
                insightsHeader.className = 'insights-header';
                
                const insightsTitle = document.createElement('div');
                insightsTitle.className = 'insights-title';
                insightsTitle.textContent = 'Document Insights';
                
                const insightsActions = document.createElement('div');
                insightsActions.className = 'insights-actions';
                
                // Store the insights for this specific container
                const containerInsights = [...data.result.insights];
                insightsContainer.dataset.allInsights = JSON.stringify(containerInsights);
                
                const selectAllBtn = document.createElement('button');
                selectAllBtn.className = 'insights-button select-all-btn';
                selectAllBtn.textContent = 'Select All';
                selectAllBtn.addEventListener('click', function() {
                    const container = this.closest('.insights-container');
                    const parentRow = row;
                    const allInsights = JSON.parse(container.dataset.allInsights || '[]');
                    
                    const tags = container.querySelectorAll('.insight-tag');
                    tags.forEach(tag => tag.classList.add('selected'));
                    
                    parentRow.dataset.selectedInsights = JSON.stringify(allInsights);
                    parentRow.dataset.unselectedInsights = JSON.stringify([]);
                    
                    checkSelectedInsights();
                });
                
                const clearAllBtn = document.createElement('button');
                clearAllBtn.className = 'insights-button clear-all-btn';
                clearAllBtn.textContent = 'Clear All';
                clearAllBtn.addEventListener('click', function() {
                    const container = this.closest('.insights-container');
                    const parentRow = row;
                    const allInsights = JSON.parse(container.dataset.allInsights || '[]');
                    
                    const tags = container.querySelectorAll('.insight-tag');
                    tags.forEach(tag => tag.classList.remove('selected'));
                    
                    parentRow.dataset.selectedInsights = JSON.stringify([]);
                    parentRow.dataset.unselectedInsights = JSON.stringify(allInsights);
                    
                    checkSelectedInsights();
                });
                
                insightsActions.appendChild(selectAllBtn);
                insightsActions.appendChild(clearAllBtn);
                
                insightsHeader.appendChild(insightsTitle);
                insightsHeader.appendChild(insightsActions);
                
                // Create insight tags
                const insightsList = document.createElement('div');
                insightsList.className = 'insights-list';
                
                // Clear the container and add the new elements
                insightsContainer.innerHTML = '';
                insightsContainer.appendChild(insightsHeader);
                insightsContainer.appendChild(insightsList);
                
                // Initialize selected insights
                const selectedInsights = [];
                const unselectedInsights = [];
                
                // Add insight tags
                data.result.insights.forEach(insight => {
                    const tagElement = document.createElement('div');
                    tagElement.className = 'insight-tag';
                    tagElement.textContent = insight;
                    tagElement.addEventListener('click', function() {
                        this.classList.toggle('selected');
                        updateSelectedInsights(row, insightsContainer);
                        checkSelectedInsights();
                    });
                    
                    // Add to unselected by default
                    // tagElement.classList.add('selected');
                    unselectedInsights.push(insight);
                    
                    insightsList.appendChild(tagElement);
                });
                
                // Store initial selections
                row.dataset.selectedInsights = JSON.stringify(selectedInsights);
                row.dataset.unselectedInsights = JSON.stringify(unselectedInsights);
                
            } else {
                insightsContainer.innerHTML = '<div class="error">No insights found</div>';
            }
            
            // Process next document
            updateProgress();
            processNextDocument(index + 1);
        })
        .catch(error => {
            console.error('Error:', error);
            insightsContainer.innerHTML = `<div class="error">Error extracting insights: ${error.message}</div>`;
            
            // Continue with next document even if this one failed
            updateProgress();
            processNextDocument(index + 1);
        });
    }
    
    // Start processing documents
    processNextDocument(0);
}


function groupInsightsByScore() {
    // Get all query items
    const queryItems = document.querySelectorAll('.query-item');
    let hasInsights = false;
    
    // Create structure to hold insights grouped by score
    const insightsByScore = {
        5: { insights: [], sources: [] },
        4: { insights: [], sources: [] },
        3: { insights: [], sources: [] },
        2: { insights: [], sources: [] },
        1: { insights: [], sources: [] },
        0: { insights: [], sources: [] }
    };
    
    // Collect all insights from all documents and group by score
    queryItems.forEach(queryItem => {
        const rows = queryItem.querySelectorAll('tbody tr:not(.insights-row)');
        rows.forEach(row => {
            // Skip if no score or insights
            if (row.cells.length <= 4 || !row.dataset.selectedInsights) {
                return;
            }
            
            // Get the score
            const scoreText = row.cells[4].textContent.trim();
            if (scoreText === 'Error' || scoreText === 'N/A' || isNaN(parseFloat(scoreText))) {
                return;
            }
            
            const score = Math.round(parseFloat(scoreText));
            const urlLink = row.querySelector('.url-link');
            
            if (!urlLink) return;
            
            // Get insights from this document
            try {
                const selectedInsights = JSON.parse(row.dataset.selectedInsights || '[]');
                const unselectedInsights = JSON.parse(row.dataset.unselectedInsights || '[]');
                const allInsights = [...selectedInsights, ...unselectedInsights];
                
                // Add insights to the appropriate score group
                if (score >= 0 && score <= 5 && allInsights.length > 0) {
                    hasInsights = true;
                    
                    // For all insights in this document
                    allInsights.forEach(insight => {
                        // Check if this insight is already in the group
                        const existingIndex = insightsByScore[score].insights.findIndex(i => i === insight);
                        
                        if (existingIndex === -1) {
                            // New insight
                            insightsByScore[score].insights.push(insight);
                            insightsByScore[score].sources.push({
                                url: urlLink.href,
                                title: row.cells[1].textContent.trim().substring(0, 30) + '...',
                                selected: selectedInsights.includes(insight)
                            });
                        }
                    });
                }
            } catch (e) {
                console.error('Error parsing insights:', e);
            }
        });
    });
    
    if (!hasInsights) {
        alert('No insights found. Please analyze documents and extract insights first.');
        return;
    }
    
    // Create or get the grouped insights container
    let container = document.getElementById('groupedInsightsContainer');
    if (!container) {
        container = document.createElement('div');
        container.id = 'groupedInsightsContainer';
        container.className = 'grouped-insights-container';
        
        // Insert after the problem input card
        const card = document.querySelector("#tab2 .card");
        card.parentNode.insertBefore(container, card.nextSibling);
    }
    
    // Create header
    const header = document.createElement('div');
    header.className = 'grouped-insights-header';
    header.innerHTML = `
        <div>Insights Grouped by Score</div>
        <div class="grouped-insights-actions">
            <button class="ai-select-btn pulse" id="aiSelectButton" onclick="aiSelectInsights()">AI Select Insights</button>
            <div class="grouped-insights-close" onclick="closeGroupedInsights()">&times;</div>
        </div>
    `;
    
    // Create content area
    const content = document.createElement('div');
    content.className = 'grouped-insights-content';
    
    // Create score groups
    for (let score = 5; score >= 0; score--) {
        const insights = insightsByScore[score].insights;
        const sources = insightsByScore[score].sources;
        
        if (insights.length === 0) continue;
        
        const scoreGroup = document.createElement('div');
        scoreGroup.className = 'score-group';
        scoreGroup.dataset.score = score;
        
        // Create score header
        const scoreHeader = document.createElement('div');
        scoreHeader.className = 'score-group-header';
        
        let scoreColor = '';
        if (score >= 0 && score <= 5) {
            const redComponent = Math.floor((score / 5) * 255);
            const greenComponent = Math.floor(((5 - score) / 5) * 255);
            scoreColor = `background-color: rgb(${redComponent}, ${greenComponent}, 0); color: white;`;
        }
        
        scoreHeader.innerHTML = `
            <div>
                <span style="display: inline-block; width: 25px; height: 25px; text-align: center; border-radius: 50%; ${scoreColor} font-weight: bold;">${score}</span>
                <span style="margin-left: 8px;">Score ${score} Insights (${insights.length})</span>
            </div>
            <div class="score-group-actions">
                <button class="insights-button select-score-all-btn" onclick="selectAllInScore(${score})">Select All</button>
                <button class="insights-button clear-score-all-btn" onclick="clearAllInScore(${score})">Clear All</button>
            </div>
        `;
        
        // Create insights list
        const insightsList = document.createElement('div');
        insightsList.className = 'score-insights-list';
        
        // Add each insight
        insights.forEach((insight, index) => {
            const source = sources[index];
            const tagElement = document.createElement('div');
            tagElement.className = `grouped-insight-tag${source.selected ? ' selected' : ''}`;
            tagElement.dataset.score = score;
            tagElement.dataset.index = index;
            tagElement.dataset.source = source.url;
            
            // Create insight text with source link
            tagElement.innerHTML = `
                ${insight}
                <a href="${source.url}" target="_blank" class="insight-source" title="${source.title}">${score}</a>
            `;
            
            // Add click event to toggle selection
            tagElement.addEventListener('click', function(e) {
                // Prevent clicking on the source link from toggling selection
                if (e.target.classList.contains('insight-source')) return;
                
                this.classList.toggle('selected');
                updateGroupedInsightSelections();
            });
            
            insightsList.appendChild(tagElement);
        });
        
        // Add header and list to score group
        scoreGroup.appendChild(scoreHeader);
        scoreGroup.appendChild(insightsList);
        
        // Add score group to content
        content.appendChild(scoreGroup);
    }
    
    // Clear the container and add new content
    container.innerHTML = '';
    container.appendChild(header);
    container.appendChild(content);
    
    // Show the container
    container.style.display = 'block';
    
    // Collapse all accordions
    const accordions = document.querySelectorAll('.accordion-section');
    accordions.forEach(accordion => {
        const header = accordion.querySelector('.accordion-header');
        const body = accordion.querySelector('.accordion-body');
        if (header && body && !header.classList.contains('collapsed')) {
            header.classList.add('collapsed');
            body.classList.add('collapsed');
            
            // Update the toggle icon
            const toggleIcon = header.querySelector('.toggle-icon');
            if (toggleIcon) toggleIcon.textContent = '▶';
        }
    });
    
    // Scroll to the insights container
    container.scrollIntoView({ behavior: 'smooth' });
    
    // Remove the pulse animation after a few seconds
    setTimeout(() => {
        const aiSelectBtn = document.getElementById('aiSelectButton');
        if (aiSelectBtn) {
            aiSelectBtn.classList.remove('pulse');
        }
    }, 5000);
}

function enhanceProblem() {
    const problemInput = document.getElementById('userProblemDescription');
    const originalProblem = problemInput.value.trim();
    
    if (!originalProblem) {
        alert('Please provide a technical problem description first');
        return;
    }
    
    const selectedInsights = collectAllSelectedInsights();
    if (selectedInsights.length === 0) {
        alert('Please select at least one insight to enhance the problem');
        return;
    }
    
    // Get user comments if any
    const userComments = document.getElementById('insightCommentArea')?.value || '';
    
    // If we have stored refined problems for this exact problem, just show them
    const currentProblemKey = JSON.stringify({
        problem: originalProblem,
        insights: selectedInsights.sort(),
        comments: userComments
    });
    
    if (storedRefinedProblems[currentProblemKey]) {
        showRefinedProblems(storedRefinedProblems[currentProblemKey]);
        return;
    }
    
    // Show loading overlay
    const loadingOverlay = document.getElementById('globalLoadingOverlay');
    if (loadingOverlay) {
        loadingOverlay.style.display = 'flex';
        loadingOverlay.querySelector('.progress-text').textContent = 'Enhancing problem statement...';
    }
    
    // Send request to backend to refine the problem
    fetch('/refine-problem', {
        method: 'POST',
        body: JSON.stringify({
            'original_problem': originalProblem,
            'insights': selectedInsights,
            'user_comments': userComments
        }),
        headers: { 'Content-Type': 'application/json' }
    })
    .then(response => response.json())
    .then(data => {
        // Hide loading overlay
        if (loadingOverlay) loadingOverlay.style.display = 'none';
        
        if (data.error) {
            alert(`Error: ${data.error}`);
            return;
        }
        
        if (data.result) {
            // Add current problem to history if not already there
            if (currentHistoryIndex === -1) {
                problemHistory.push(originalProblem);
                currentHistoryIndex = 0;
            }
            
            // Store the refined problems for future use
            storedRefinedProblems[currentProblemKey] = data.result;
            
            // Show refined problem options
            showRefinedProblems(data.result);
        }
    })
    .catch(error => {
        console.error('Error:', error);
        if (loadingOverlay) loadingOverlay.style.display = 'none';
        alert(`Error enhancing problem: ${error.message}`);
    });
}

function closeGroupedInsights() {
    const container = document.getElementById('groupedInsightsContainer');
    if (container) {
        container.style.display = 'none';
    }
}

// Select all insights for a specific score
function selectAllInScore(score) {
    const container = document.getElementById('groupedInsightsContainer');
    const tags = container.querySelectorAll(`.grouped-insight-tag[data-score="${score}"]`);
    
    tags.forEach(tag => {
        tag.classList.add('selected');
    });
    
    updateGroupedInsightSelections();
}

// Clear all insights for a specific score
function clearAllInScore(score) {
    const container = document.getElementById('groupedInsightsContainer');
    const tags = container.querySelectorAll(`.grouped-insight-tag[data-score="${score}"]`);
    
    tags.forEach(tag => {
        tag.classList.remove('selected');
    });
    
    updateGroupedInsightSelections();
}

function updateGroupedInsightSelections() {
    // Get all selected insights from the grouped view
    const container = document.getElementById('groupedInsightsContainer');
    const selectedTags = container.querySelectorAll('.grouped-insight-tag.selected');
    
    // Create a mapping of URL to selected insights
    const selectionsBySource = {};
    
    // Process each selected tag
    selectedTags.forEach(tag => {
        const insight = tag.textContent.trim().replace(/\d+$/, '').trim(); // Remove the score number at the end
        const sourceUrl = tag.dataset.source;
        
        if (!selectionsBySource[sourceUrl]) {
            selectionsBySource[sourceUrl] = [];
        }
        
        selectionsBySource[sourceUrl].push(insight);
    });
    
    // Now update the original document rows
    const queryItems = document.querySelectorAll('.query-item');
    queryItems.forEach(queryItem => {
        const rows = queryItem.querySelectorAll('tbody tr:not(.insights-row)');
        rows.forEach(row => {
            const urlLink = row.querySelector('.url-link');
            if (!urlLink) return;
            
            const sourceUrl = urlLink.href;
            
            // If we have selections for this source
            if (selectionsBySource[sourceUrl]) {
                // Get all insights for this row
                try {
                    // Combine selected and unselected to get all insights
                    const currentSelected = JSON.parse(row.dataset.selectedInsights || '[]');
                    const currentUnselected = JSON.parse(row.dataset.unselectedInsights || '[]');
                    const allInsights = [...currentSelected, ...currentUnselected];
                    
                    // New selected and unselected based on grouped view
                    const newSelected = [];
                    const newUnselected = [];
                    
                    // Process each insight
                    allInsights.forEach(insight => {
                        if (selectionsBySource[sourceUrl].includes(insight)) {
                            newSelected.push(insight);
                        } else {
                            newUnselected.push(insight);
                        }
                    });
                    
                    // Update the dataset
                    row.dataset.selectedInsights = JSON.stringify(newSelected);
                    row.dataset.unselectedInsights = JSON.stringify(newUnselected);
                } catch (e) {
                    console.error('Error updating insights selections:', e);
                }
            }
        });
    });
    
    // Update enhance button state
    checkSelectedInsights();
}

function showRefinedProblems(result) {
    const refinedContainer = document.getElementById('refinedProblemContainer');
    const tabs = document.getElementById('refinedProblemTabs');
    const content = document.getElementById('refinedProblemContent');
    
    // Clear previous content
    tabs.innerHTML = '';
    content.innerHTML = '';
    
    // Add tabs and content for each refined problem
    let isFirst = true;
    for (const key in result) {
        if (result.hasOwnProperty(key)) {
            const problem = result[key];
            
            // Create tab
            const tab = document.createElement('div');
            tab.className = `refined-problem-tab ${isFirst ? 'active' : ''}`;
            tab.dataset.target = key;
            tab.textContent = `Option ${key.split('_')[1]}`;
            tab.onclick = function() {
                document.querySelectorAll('.refined-problem-tab').forEach(t => t.classList.remove('active'));
                document.querySelectorAll('.refined-problem').forEach(p => p.classList.remove('active'));
                tab.classList.add('active');
                document.getElementById(key).classList.add('active');
            };
            tabs.appendChild(tab);
            
            // Create content
            const problemDiv = document.createElement('div');
            problemDiv.className = `refined-problem ${isFirst ? 'active' : ''}`;
            problemDiv.id = key;
            
            const title = document.createElement('div');
            title.className = 'refined-problem-title';
            title.textContent = problem.title;
            
            const description = document.createElement('div');
            description.className = 'refined-problem-description';
            description.textContent = problem.description;
            
            const applyButton = document.createElement('button');
            applyButton.className = 'apply-problem-btn';
            applyButton.textContent = 'Apply This Problem';
            applyButton.onclick = function() {
                applyRefinedProblem(problem.description);
            };
            
            problemDiv.appendChild(title);
            problemDiv.appendChild(description);
            problemDiv.appendChild(applyButton);
            
            content.appendChild(problemDiv);
            
            isFirst = false;
        }
    }
    
    // Show the container
    refinedContainer.style.display = 'block';
    
    // Scroll to the container
    refinedContainer.scrollIntoView({ behavior: 'smooth' });
}

function applyRefinedProblem(problemText) {
    const problemInput = document.getElementById('userProblemDescription');
    
    // Add current problem to history
    problemHistory.push(problemInput.value);
    currentHistoryIndex = problemHistory.length - 1; // Set to latest version
    
    // Update problem text with the new version
    problemInput.value = problemText;
    
    // Now add the new version to history
    problemHistory.push(problemText);
    currentHistoryIndex = problemHistory.length - 1; // Update index to point to the newly added version
    
    // Update history navigation display
    updateHistoryNavigation();
    
    // Display is kept visible, removed: document.getElementById('refinedProblemContainer').style.display = 'none';
    
    // Focus on the problem input
    problemInput.focus();
    
    console.log("Problem history after applying:", problemHistory, "Current index:", currentHistoryIndex);
}

function updateHistoryNavigation() {
    const historyNav = document.getElementById('problemHistoryNav');
    const prevBtn = historyNav.querySelector('.history-prev');
    const nextBtn = historyNav.querySelector('.history-next');
    const status = historyNav.querySelector('.history-status');
    
    // Update buttons state
    prevBtn.classList.toggle('disabled', currentHistoryIndex <= 0);
    nextBtn.classList.toggle('disabled', currentHistoryIndex >= problemHistory.length - 1);
    
    // Update status text
    if (problemHistory.length > 0) {
        status.textContent = `Version ${currentHistoryIndex + 1} of ${problemHistory.length}`;
        historyNav.style.display = 'flex';
    } else {
        historyNav.style.display = 'none';
    }
}

function aiSelectInsights() {
    const patentBackground = document.getElementById('userProblemDescription').value.trim();
    if (!patentBackground) {
        alert('Please provide a patent background in the input field');
        return;
    }
    
    // Change button appearance to show it's working
    const aiSelectBtn = document.getElementById('aiSelectButton');
    if (aiSelectBtn) {
        aiSelectBtn.disabled = true;
        aiSelectBtn.textContent = 'AI Selecting...';
        aiSelectBtn.style.opacity = '0.7';
    }
    
    // Show loading overlay
    const loadingOverlay = document.getElementById('globalLoadingOverlay');
    if (loadingOverlay) {
        loadingOverlay.style.display = 'flex';
        loadingOverlay.querySelector('.progress-text').textContent = 'AI selecting the most relevant insights...';
    }
    
    // Get all insights from all score groups
    const container = document.getElementById('groupedInsightsContainer');
    const insightTags = container.querySelectorAll('.grouped-insight-tag');
    const insights = Array.from(insightTags).map(tag => {
        return tag.textContent.trim().replace(/\d+$/, '').trim(); // Remove the score number
    });
    
    if (insights.length === 0) {
        if (loadingOverlay) loadingOverlay.style.display = 'none';
        alert('No insights found');
        return;
    }
    
    // Send request to backend to get AI selection
    fetch('/ai-select-insights', {
        method: 'POST',
        body: JSON.stringify({
            'patent_background': patentBackground,
            'insights': insights
        }),
        headers: { 'Content-Type': 'application/json' }
    })
    .then(response => response.json())
    .then(data => {
        // Reset button appearance
        if (aiSelectBtn) {
            aiSelectBtn.disabled = false;
            aiSelectBtn.textContent = 'AI Select Insights';
            aiSelectBtn.style.opacity = '1';
        }
        
        if (loadingOverlay) loadingOverlay.style.display = 'none';
        
        if (data.error) {
            alert(`Error: ${data.error}`);
            return;
        }
        
        if (data.selected_insights && data.selected_insights.length > 0) {
            // First clear all selections
            insightTags.forEach(tag => {
                tag.classList.remove('selected');
            });
            
            // Then select the recommended insights
            insightTags.forEach(tag => {
                const insightText = tag.textContent.trim().replace(/\d+$/, '').trim();
                if (data.selected_insights.includes(insightText)) {
                    tag.classList.add('selected');
                }
            });
            
            // Update the original document rows
            updateGroupedInsightSelections();
            
            // Remove alert notification - user can see the selected insights visually
            // alert(`AI selected ${data.selected_insights.length} insights from ${insights.length} available insights`);
        } else {
            alert('AI could not identify any relevant insights to select');
        }
    })
    .catch(error => {
        console.error('Error:', error);
        
        // Reset button appearance
        if (aiSelectBtn) {
            aiSelectBtn.disabled = false;
            aiSelectBtn.textContent = 'AI Select Insights';
            aiSelectBtn.style.opacity = '1';
        }
        
        if (loadingOverlay) loadingOverlay.style.display = 'none';
        alert(`Error using AI to select insights: ${error.message}`);
    });
}

function generateSearchQueries() {
    function addQueryField(queryText = '', container = null) {
        const queriesContainer = container || document.getElementById('queriesContainer');
        
        // Count existing query items in this container for indexing
        const queryItems = container ? 
            container.querySelectorAll('.query-item') : 
            document.getElementById('queriesContainer').querySelectorAll('.query-item');
        
        const queryIndex = queryItems.length + 1;
        
        // Create main container for this query item
        const queryItem = document.createElement('div');
        queryItem.className = 'query-item';
        
        // Create container for query field and buttons
        const queryContainer = document.createElement('div');
        queryContainer.className = 'query-container';
        
        // Input field
        const queryField = document.createElement('input');
        queryField.type = 'text';
        queryField.className = 'query-field';
        queryField.value = queryText;
        queryField.placeholder = `Search Query ${queryIndex}`;
        
        // Delete button
        const deleteButton = document.createElement('button');
        deleteButton.type = 'button';
        deleteButton.className = 'action-button delete-button';
        deleteButton.textContent = 'Delete';
        deleteButton.onclick = function() {
            queryItem.parentNode.removeChild(queryItem);
            
            // Update the placeholder numbers for remaining queries within this container
            const parent = container || document.getElementById('queriesContainer');
            const items = parent.querySelectorAll('.query-item');
            items.forEach((item, idx) => {
                const field = item.querySelector('.query-field');
                if (field) field.placeholder = `Search Query ${idx + 1}`;
            });
        };
        
        // Search button
        const searchButton = document.createElement('button');
        searchButton.type = 'button';
        searchButton.className = 'action-button search-button';
        searchButton.textContent = 'Search';
        searchButton.onclick = function() {
            performSearch(queryField.value, queryItem);
        };
        
        // Add elements to container
        queryContainer.appendChild(queryField);
        queryContainer.appendChild(searchButton);
        queryContainer.appendChild(deleteButton);
        
        // Create loading indicator for this search
        const searchLoading = document.createElement('div');
        searchLoading.className = 'search-loading';
        searchLoading.textContent = 'Searching... Please wait.';
        
        // Create table for results
        const resultsTable = document.createElement('table');
        resultsTable.className = 'results-table';
        
        // Add table header
        const tableHeader = document.createElement('thead');
        const headerRow = document.createElement('tr');
    
        const typeHeader = document.createElement('th');
        typeHeader.textContent = 'Type';
    
        const titleHeader = document.createElement('th');
        titleHeader.textContent = 'Title';
    
        const bodyHeader = document.createElement('th');
        bodyHeader.textContent = 'Description';
    
        const urlHeader = document.createElement('th');
        urlHeader.textContent = 'URL';
    
        const scoreHeader = document.createElement('th');
        scoreHeader.textContent = 'Score';
    
        const justificationHeader = document.createElement('th');
        justificationHeader.textContent = 'Justification';
    
        headerRow.appendChild(typeHeader);
        headerRow.appendChild(titleHeader);
        headerRow.appendChild(bodyHeader);
        headerRow.appendChild(urlHeader);
        headerRow.appendChild(scoreHeader);
        headerRow.appendChild(justificationHeader);
        tableHeader.appendChild(headerRow);
        
        // Add table body
        const tableBody = document.createElement('tbody');
        
        resultsTable.appendChild(tableHeader);
        resultsTable.appendChild(tableBody);
        
        // Add all elements to the query item
        queryItem.appendChild(queryContainer);
        queryItem.appendChild(searchLoading);
        queryItem.appendChild(resultsTable);
        
        // Add container to the queries list
        queriesContainer.appendChild(queryItem);
    }
    
    function createAccordionSection(timestamp) {
        const accordionSection = document.createElement('div');
        accordionSection.className = 'accordion-section';
        
        const accordionHeader = document.createElement('div');
        accordionHeader.className = 'accordion-header';
        accordionHeader.innerHTML = `
            <span>Search Results <span class="query-timestamp">${timestamp}</span></span>
            <span class="toggle-icon">▼</span>
        `;
        accordionHeader.onclick = function() {
            this.classList.toggle('collapsed');
            const body = this.nextElementSibling;
            body.classList.toggle('collapsed');
            
            // Update the toggle icon
            const toggleIcon = this.querySelector('.toggle-icon');
            if (body.classList.contains('collapsed')) {
                toggleIcon.textContent = '▶';
            } else {
                toggleIcon.textContent = '▼';
            }
        };
        
        const accordionBody = document.createElement('div');
        accordionBody.className = 'accordion-body';
        
        const accordionContent = document.createElement('div');
        accordionContent.className = 'accordion-content';
        accordionBody.appendChild(accordionContent);
        
        accordionSection.appendChild(accordionHeader);
        accordionSection.appendChild(accordionBody);
        
        return accordionSection;
    }

    const userInput = document.getElementById('userProblemDescription').value.trim();
    if (!userInput) {
        alert('Please enter a technical problem description');
        return;
    }
    
    // Show loading indicator
    document.getElementById('loadingIndicator').style.display = 'block';
    
    // Collapse all existing query sections
    const existingAccordions = document.querySelectorAll('.accordion-section');
    existingAccordions.forEach(accordion => {
        const header = accordion.querySelector('.accordion-header');
        const body = accordion.querySelector('.accordion-body');
        if (header && body && !header.classList.contains('collapsed')) {
            header.classList.add('collapsed');
            body.classList.add('collapsed');
        }
    });
    
    // Send message to Flask backend
    fetch('/chat', {
        method: 'POST',
        body: new URLSearchParams({ 'message': userInput }),
        headers: { 'Content-Type': 'application/x-www-form-urlencoded' }
    })
    .then(response => response.json())
    .then(data => {
        // Hide loading indicator
        document.getElementById('loadingIndicator').style.display = 'none';
        
        try {
            // Parse the JSON string from the LLM response
            let jsonData;
            // First check if data.reply is already an object
            if (typeof data.reply === 'object') {
                jsonData = data.reply;
            } else {
                // Try to extract JSON if it's a string possibly with markdown code blocks
                const jsonString = data.reply.replace(/```json|```/g, '').trim();
                jsonData = JSON.parse(jsonString);
            }
            
            // Create a new accordion section for these search results
            const timestamp = new Date().toLocaleString();
            const accordionSection = createAccordionSection(timestamp);
            
            // Add each query from the response to this accordion
            Object.keys(jsonData).forEach(key => {
                addQueryField(jsonData[key], accordionSection.querySelector('.accordion-content'));
            });
            
            // Add the accordion to the container
            const queriesContainer = document.getElementById('queriesContainer');
            queriesContainer.insertBefore(accordionSection, queriesContainer.firstChild);
            
            // Show results container
            document.getElementById('resultsContainer').style.display = 'block';
        } catch (error) {
            console.error('Error parsing JSON:', error);
            alert('There was an error processing the response. Please try again.');
        }
    })
    .catch(error => {
        document.getElementById('loadingIndicator').style.display = 'none';
        console.error('Error:', error);
        alert('There was an error communicating with the server. Please try again.');
    });
}

function displayKeyIssues(keyIssues) {
    // Get or create the key issues container
    let keyIssuesContainer = document.getElementById('keyIssuesContainer');
    if (!keyIssuesContainer) {
        keyIssuesContainer = document.createElement('div');
        keyIssuesContainer.id = 'keyIssuesContainer';
        keyIssuesContainer.className = 'key-issues-container';
        document.getElementById('resultsContainer').appendChild(keyIssuesContainer);
    }
    
    // Clear previous content
    keyIssuesContainer.innerHTML = '';
    
    // Create header
    const header = document.createElement('h3');
    header.textContent = 'Key Issues';
    keyIssuesContainer.appendChild(header);
    
    // Create issues list
    const issuesList = document.createElement('div');
    issuesList.className = 'key-issues-list';

    const KIsubmitButton = document.createElement('button');
    KIsubmitButton.className = "btn btn-primary";
    KIsubmitButton.id = "key-issues-submit-btn";
    KIsubmitButton.textContent = "Generate problem descriptions";
    KIsubmitButton.style.marginTop = "10px";
    KIsubmitButton.onclick = generateProblemDescriptions;

    const centerButton = document.createElement("center");
    centerButton.appendChild(KIsubmitButton);

    
    // Add each key issue
    keyIssues.forEach(issue => {
        const issueCard = document.createElement('div');
        issueCard.className = 'key-issue-card';
        issueCard.dataset.id = issue.id;
        
        const issueTitle = document.createElement('div');
        issueTitle.className = 'key-issue-title';
        issueTitle.textContent = issue.title;
        
        const issueDescription = document.createElement('div');
        issueDescription.className = 'key-issue-description';
        issueDescription.textContent = issue.description;
        
        const challengesTitle = document.createElement('div');
        challengesTitle.style.fontWeight = 'bold';
        challengesTitle.style.marginTop = '10px';
        challengesTitle.textContent = 'Challenges:';
        
        const challengesList = document.createElement('ul');
        challengesList.className = 'key-issue-challenges';
        
        issue.challenges.forEach(challenge => {
            const challengeItem = document.createElement('li');
            challengeItem.textContent = challenge;
            challengesList.appendChild(challengeItem);
        });
        
        const impactTitle = document.createElement('div');
        impactTitle.style.fontWeight = 'bold';
        impactTitle.style.marginTop = '10px';
        impactTitle.textContent = 'Potential Impact:';
        
        const issueImpact = document.createElement('div');
        issueImpact.className = 'key-issue-impact';
        issueImpact.textContent = issue.potential_impact;
        
        // Add click handler to toggle selection
        issueCard.addEventListener('click', function() {
            this.classList.toggle('selected');
        });
        
        // Append all elements
        issueCard.appendChild(issueTitle);
        issueCard.appendChild(issueDescription);
        issueCard.appendChild(challengesTitle);
        issueCard.appendChild(challengesList);
        issueCard.appendChild(impactTitle);
        issueCard.appendChild(issueImpact);
        
        issuesList.appendChild(issueCard);
    });
    
    keyIssuesContainer.appendChild(issuesList);
    keyIssuesContainer.appendChild(centerButton);
    keyIssuesContainer.style.display = "block";
}

function generateProblemDescriptions(){
    let result = {
        descriptions: {},
        challenges: {}
    };

    const selectedCards = document.querySelectorAll(".key-issue-card.selected");

    selectedCards.forEach(card => {
        const userInput = document.getElementById('userInput').value.trim();
        const id = card.getAttribute("data-id");
        const description = card.querySelector('.key-issue-description').textContent.trim();
        const challenges = Array.from(card.querySelectorAll(".key-issue-challenges li")).map(challenge => challenge.textContent.trim());

        result.descriptions[id] = description;
        result.challenges[id] = challenges;
        result["technical_topic"] = userInput;
    })

    document.querySelector('.progress-text').innerHTML = "Generating problem descriptions ... This may take a while."
    document.getElementById('globalLoadingOverlay').style.display = 'flex';
    
    // Send message to Flask backend
    fetch('/create-several-probdesc', {
        method: 'POST',
        body: JSON.stringify(result),
        headers: { 'Content-Type': 'application/json' }
    })
    .then(response => response.json())
    .then(data => {
        // Hide loading indicator
        document.getElementById('globalLoadingOverlay').style.display = 'none';
        
        // Check if we have key issues in the response
        if (data.problem_descriptions && data.problem_descriptions.length > 0) {
            // Display the key issues
            displayProblemDescriptions(data.problem_descriptions);
        } else if (data.error) {
            alert('Error: ' + data.error);
        } else {
            alert('No problem descriptions found/generated. Please try again with another or the same query.');
        }
    })
    .catch(error => {
        document.getElementById('globalLoadingOverlay').style.display = 'none';
        console.error('Error:', error);
        alert('There was an error communicating with the server. Please try again.');
    });
}

function displayProblemDescriptions(probDescs) {
    // Get or create the key issues container
    let probDescCards = document.getElementById("probDescCards");
    let probDescContainer = document.getElementById('probDescContainer');
    // Clear previous content
    probDescContainer.innerHTML = '';
    
    // Create header
    const header = document.createElement('h3');
    header.textContent = 'Problem Descriptions';
    probDescContainer.appendChild(header);
    
    // Create issues list
    const descriptionList = document.createElement('div');
    descriptionList.className = 'prob-desc-list';
    
    // Add each key issue
    probDescs.forEach((desc, index) => {
        const descCard = document.createElement('div');
        descCard.className = 'prob-desc-card';
        descCard.dataset.id = index+1;
        
        const descTitle = document.createElement('div');
        descTitle.className = 'prob-desc-title';
        descTitle.textContent = `Problem Description n°${index+1}`;
        
        const descDescription = document.createElement('div');
        descDescription.className = 'prob-desc-description';
        descDescription.textContent = desc;
        
        // Add click handler to toggle selection
        descCard.addEventListener('click', function() {
            document.getElementById("userProblemDescription").textContent = desc;
            document.getElementsByClassName("tablinks")[1].click();
        });
        
        // Append all elements
        descCard.appendChild(descTitle);
        descCard.appendChild(descDescription);
        
        descriptionList.appendChild(descCard);
    });
    
    probDescContainer.appendChild(descriptionList);
    probDescCards.style.display = "block";
}

function initRibbonAccordion() {
    const ribbon = document.querySelector('.ribbon-accordion');
    const ribbonHeader = ribbon.querySelector('.ribbon-header');
    
    ribbonHeader.addEventListener('click', function() {
        ribbon.classList.toggle('collapsed');
    });
}

function setupRibbonButtons() {
    // Generate Queries
    document.getElementById('ribbonGenerateQueriesButton').addEventListener('click', function() {
        generateSearchQueries();
    });
    
    // Analyze All
    document.getElementById('ribbonAnalyzeAllButton').addEventListener('click', function() {
        if(hasSearchResults()) {
            analyzeAllPapers();
        }
    });
    
    // Remove Failed
    document.getElementById('ribbonRemoveFailedButton').addEventListener('click', function() {
        if(hasSearchResults()) {
            removeFailedAnalyses();
        }
    });
    
    // Extract All Insights
    document.getElementById('ribbonExtractAllInsightsButton').addEventListener('click', function() {
        extractAllInsights();
    });
    
    // Group Insights
    document.getElementById('ribbonGroupInsightsButton').addEventListener('click', function() {
        groupInsightsByScore();
    });
    
    // Enhance Problem
    document.getElementById('ribbonEnhanceProblemButton').addEventListener('click', function() {
        enhanceProblem();
    });
    
    // Export to Excel
    document.getElementById('ribbonExportExcelButton').addEventListener('click', function() {
        if(hasSearchResults()) {
            exportToExcel();
        }
    });
}

initRibbonAccordion();
setupRibbonButtons();