bioinformatics-mcp-server
Version:
🧬 生物信息学MCP服务器 - 专为ModelScope设计的智能生物数据分析工具
612 lines (544 loc) • 19.6 kB
JavaScript
import * as fs from 'fs';
import * as path from 'path';
import { exec } from 'child_process';
import { promisify } from 'util';
const execAsync = promisify(exec);
/**
* 生成HTML执行报告
*/
export function generateHtmlReport(result, scripts, executionDir) {
const reportPath = path.join(executionDir, 'execution_report.html');
console.error(`生成HTML报告: ${reportPath}`);
console.error(`执行目录: ${executionDir}`);
// 检测生成的图像文件
const imageFiles = detectImageFiles(executionDir);
console.error(`检测到图像文件: ${imageFiles.length} 个`);
if (imageFiles.length > 0) {
console.error(`图像文件列表: ${imageFiles.join(', ')}`);
}
const html = createHtmlContent(result, scripts, imageFiles, executionDir);
try {
fs.writeFileSync(reportPath, html, 'utf8');
console.error(`HTML报告文件写入成功，大小: ${html.length} 字符`);
}
catch (writeError) {
console.error(`HTML报告写入失败: ${writeError instanceof Error ? writeError.message : writeError}`);
throw writeError;
}
return reportPath;
}
/**
* 检测执行目录中的图像文件
*/
function detectImageFiles(executionDir) {
const imageExtensions = ['.png', '.jpg', '.jpeg', '.svg', '.pdf'];
const imageFiles = [];
try {
const files = fs.readdirSync(executionDir);
for (const file of files) {
const ext = path.extname(file).toLowerCase();
if (imageExtensions.includes(ext)) {
imageFiles.push(file);
}
}
}
catch (error) {
console.error('Error detecting image files:', error);
}
return imageFiles;
}
/**
* 自动在浏览器中打开HTML报告
*/
export async function openHtmlReport(reportPath) {
try {
// Windows下使用start命令打开默认浏览器
// 使用cmd /c 确保命令正确执行
const command = `cmd /c start "" "${reportPath}"`;
console.error(`尝试打开HTML报告: ${command}`);
await execAsync(command, {
timeout: 10000,
encoding: 'utf8',
env: { ...process.env, PYTHONIOENCODING: 'utf-8' }
});
console.error(`HTML报告已在浏览器中打开: ${reportPath}`);
}
catch (error) {
console.error(`无法自动打开浏览器: ${error instanceof Error ? error.message : error}`);
console.error(`请手动打开报告文件: ${reportPath}`);
// 尝试备用方法
try {
console.error('尝试备用打开方法...');
await execAsync(`explorer "${reportPath}"`, {
timeout: 5000,
encoding: 'utf8'
});
console.error('使用资源管理器打开文件');
}
catch (explorerError) {
console.error(`备用方法也失败: ${explorerError instanceof Error ? explorerError.message : explorerError}`);
}
}
}
/**
* 创建HTML内容
*/
function createHtmlContent(result, scripts, imageFiles, executionDir) {
const successCount = result.execution_results.filter(r => r.status === 'success').length;
const errorCount = result.execution_results.filter(r => r.status === 'error').length;
const totalScripts = result.execution_results.length;
// 计算脚本统计信息
const totalLines = scripts.reduce((sum, s) => sum + (s.lineCount || 0), 0);
return `
<html lang="zh-CN">
<head>
<meta charset="UTF-8">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>生物信息学脚本执行报告 - ${result.workflow_id}</title>
<style>
* {
margin: 0;
padding: 0;
box-sizing: border-box;
}
body {
font-family: 'Segoe UI', Tahoma, Geneva, Verdana, sans-serif;
line-height: 1.6;
color: #333;
background: linear-gradient(135deg, #667eea 0%, #764ba2 100%);
min-height: 100vh;
padding: 20px;
}
.container {
max-width: 1200px;
margin: 0 auto;
background: white;
border-radius: 15px;
box-shadow: 0 20px 40px rgba(0,0,0,0.1);
overflow: hidden;
}
.header {
background: linear-gradient(135deg, #4CAF50 0%, #45a049 100%);
color: white;
padding: 30px;
text-align: center;
}
.header h1 {
font-size: 2.5em;
margin-bottom: 10px;
text-shadow: 2px 2px 4px rgba(0,0,0,0.3);
}
.header .subtitle {
font-size: 1.2em;
opacity: 0.9;
}
.summary {
padding: 30px;
background: #f8f9fa;
border-bottom: 1px solid #e9ecef;
}
.stats {
display: grid;
grid-template-columns: repeat(auto-fit, minmax(200px, 1fr));
gap: 20px;
margin-bottom: 20px;
}
.stat-card {
background: white;
padding: 20px;
border-radius: 10px;
text-align: center;
box-shadow: 0 4px 6px rgba(0,0,0,0.1);
transition: transform 0.3s ease;
}
.stat-card:hover {
transform: translateY(-5px);
}
.stat-number {
font-size: 2.5em;
font-weight: bold;
margin-bottom: 5px;
}
.stat-label {
color: #666;
font-size: 0.9em;
}
.success { color: #28a745; }
.error { color: #dc3545; }
.info { color: #17a2b8; }
.warning { color: #ffc107; }
.content {
padding: 30px;
}
.section {
margin-bottom: 40px;
}
.section h2 {
color: #2c3e50;
border-bottom: 3px solid #3498db;
padding-bottom: 10px;
margin-bottom: 20px;
font-size: 1.8em;
}
.script-card {
background: #f8f9fa;
border-left: 5px solid #3498db;
padding: 20px;
margin-bottom: 20px;
border-radius: 0 10px 10px 0;
transition: all 0.3s ease;
}
.script-card:hover {
box-shadow: 0 5px 15px rgba(0,0,0,0.1);
}
.script-card.success {
border-left-color: #28a745;
}
.script-card.error {
border-left-color: #dc3545;
}
.script-header {
display: flex;
justify-content: space-between;
align-items: center;
margin-bottom: 15px;
}
.script-title {
font-size: 1.3em;
font-weight: bold;
color: #2c3e50;
}
.status-badge {
padding: 5px 15px;
border-radius: 20px;
font-size: 0.9em;
font-weight: bold;
text-transform: uppercase;
}
.status-success {
background: #d4edda;
color: #155724;
}
.status-error {
background: #f8d7da;
color: #721c24;
}
.script-info {
margin-bottom: 15px;
}
.info-item {
margin-bottom: 5px;
color: #666;
}
.code-block {
background: #2d3748;
color: #e2e8f0;
padding: 15px;
border-radius: 8px;
font-family: 'Courier New', monospace;
font-size: 0.9em;
overflow-x: auto;
margin: 10px 0;
}
.dependencies {
display: flex;
flex-wrap: wrap;
gap: 5px;
margin-top: 10px;
}
.dependency-tag {
background: #e3f2fd;
color: #1976d2;
padding: 3px 8px;
border-radius: 15px;
font-size: 0.8em;
}
.alert {
padding: 15px;
border-radius: 8px;
margin-bottom: 20px;
}
.alert-warning {
background: #fff3cd;
border: 1px solid #ffeaa7;
color: #856404;
}
.alert-info {
background: #d1ecf1;
border: 1px solid #bee5eb;
color: #0c5460;
}
.footer {
background: #2c3e50;
color: white;
padding: 20px;
text-align: center;
}
.collapsible {
cursor: pointer;
user-select: none;
}
.collapsible:after {
content: ' ▼';
font-size: 0.8em;
}
.collapsible.collapsed:after {
content: ' ▶';
}
.collapsible-content {
max-height: 1000px;
overflow: hidden;
transition: max-height 0.3s ease;
}
.collapsible-content.collapsed {
max-height: 0;
}
.visualization-gallery {
display: grid;
grid-template-columns: repeat(auto-fit, minmax(300px, 1fr));
gap: 20px;
margin-top: 20px;
}
.visualization-item {
background: white;
border-radius: 10px;
padding: 15px;
box-shadow: 0 4px 6px rgba(0,0,0,0.1);
text-align: center;
}
.visualization-item h4 {
margin-bottom: 10px;
color: #2c3e50;
font-size: 1.1em;
}
.visualization-image {
max-width: 100%;
height: auto;
border-radius: 8px;
cursor: pointer;
transition: transform 0.3s ease;
}
.visualization-image:hover {
transform: scale(1.05);
}
.pdf-placeholder {
background: #f8f9fa;
border: 2px dashed #dee2e6;
border-radius: 8px;
padding: 20px;
color: #6c757d;
}
.modal {
display: none;
position: fixed;
z-index: 1000;
left: 0;
top: 0;
width: 100%;
height: 100%;
background-color: rgba(0,0,0,0.9);
}
.modal-content {
margin: auto;
display: block;
width: 90%;
max-width: 1200px;
max-height: 90%;
object-fit: contain;
}
.close {
position: absolute;
top: 15px;
right: 35px;
color: #f1f1f1;
font-size: 40px;
font-weight: bold;
cursor: pointer;
}
.close:hover,
.close:focus {
color: #bbb;
text-decoration: none;
}
</style>
</head>
<body>
<div class="container">
<div class="header">
<h1>🧬 生物信息学脚本执行报告</h1>
<div class="subtitle">工作流ID: ${result.workflow_id}</div>
<div class="subtitle">执行时间: ${new Date(result.executed_at).toLocaleString('zh-CN')}</div>
</div>
<div class="summary">
<div class="stats">
<div class="stat-card">
<div class="stat-number info">${totalScripts}</div>
<div class="stat-label">总脚本数</div>
</div>
<div class="stat-card">
<div class="stat-number success">${successCount}</div>
<div class="stat-label">成功执行</div>
</div>
<div class="stat-card">
<div class="stat-number error">${errorCount}</div>
<div class="stat-label">执行失败</div>
</div>
<div class="stat-card">
<div class="stat-number warning">${result.dependencies_detected.length}</div>
<div class="stat-label">依赖包数</div>
</div>
<div class="stat-card">
<div class="stat-number info">${totalLines}</div>
<div class="stat-label">总代码行数</div>
</div>
</div>
<div class="alert alert-info">
<strong>📊 执行概况:</strong>
${errorCount === 0 ?
'🎉 所有脚本都成功执行！' :
`${successCount}/${totalScripts} 个脚本成功执行，${errorCount} 个脚本执行失败。`}
</div>
</div>
<div class="content">
${result.execution_context ? `
<div class="section">
<h2>📝 执行上下文</h2>
<p>${result.execution_context}</p>
</div>
` : ''}
<div class="section">
<h2>📦 依赖包安装</h2>
${result.package_installation.logs.map(log => `<div class="info-item">${log}</div>`).join('')}
</div>
${imageFiles.length > 0 ? `
<div class="section">
<h2>📊 生成的可视化结果</h2>
<div class="visualization-gallery">
${imageFiles.map(imageFile => `
<div class="visualization-item">
<h4>${imageFile}</h4>
${path.extname(imageFile).toLowerCase() === '.pdf' ?
`<div class="pdf-placeholder">
<p>📄 PDF文件: ${imageFile}</p>
<p>请在执行目录中查看此PDF文件</p>
</div>` :
`<img src="${imageFile}" alt="${imageFile}" class="visualization-image" onclick="openImageModal(this)">`}
</div>
`).join('')}
</div>
</div>
` : ''}
<div class="section">
<h2>🐍 脚本执行详情</h2>
${result.execution_results.map((execResult, index) => {
const script = scripts[index];
const isSuccess = execResult.status === 'success';
return `
<div class="script-card ${isSuccess ? 'success' : 'error'}">
<div class="script-header">
<div class="script-title">${execResult.script_name}</div>
<div class="status-badge ${isSuccess ? 'status-success' : 'status-error'}">
${isSuccess ? '✅ 成功' : '❌ 失败'}
</div>
</div>
<div class="script-info">
<div class="info-item"><strong>描述:</strong> ${execResult.description}</div>
<div class="info-item"><strong>执行时间:</strong> ${new Date(execResult.execution_time).toLocaleString('zh-CN')}</div>
${script?.lineCount ? `<div class="info-item"><strong>代码行数:</strong> ${script.lineCount} 行</div>` : ''}
${execResult.dependencies.length > 0 ? `
<div class="info-item">
<strong>依赖包:</strong>
<div class="dependencies">
${execResult.dependencies.map(dep => `<span class="dependency-tag">${dep}</span>`).join('')}
</div>
</div>
` : ''}
</div>
${execResult.stdout ? `
<div>
<h4 class="collapsible" onclick="toggleCollapse(this)">标准输出</h4>
<div class="collapsible-content">
<div class="code-block">${escapeHtml(execResult.stdout)}</div>
</div>
</div>
` : ''}
${execResult.stderr ? `
<div>
<h4 class="collapsible" onclick="toggleCollapse(this)">错误输出</h4>
<div class="collapsible-content">
<div class="code-block">${escapeHtml(execResult.stderr)}</div>
</div>
</div>
` : ''}
</div>
`;
}).join('')}
</div>
</div>
<div class="footer">
<p>🧬 BioNext-MCP 生物信息学分析助手</p>
<p>报告生成时间: ${new Date().toLocaleString('zh-CN')}</p>
</div>
</div>
<!-- 图片模态框 -->
<div id="imageModal" class="modal">
<span class="close" onclick="closeImageModal()">×</span>
<img class="modal-content" id="modalImage">
</div>
<script>
function toggleCollapse(element) {
const content = element.nextElementSibling;
const isCollapsed = content.classList.contains('collapsed');
if (isCollapsed) {
content.classList.remove('collapsed');
element.classList.remove('collapsed');
} else {
content.classList.add('collapsed');
element.classList.add('collapsed');
}
}
// 图片模态框功能
function openImageModal(img) {
const modal = document.getElementById('imageModal');
const modalImg = document.getElementById('modalImage');
modal.style.display = 'block';
modalImg.src = img.src;
}
function closeImageModal() {
const modal = document.getElementById('imageModal');
modal.style.display = 'none';
}
// 点击模态框外部关闭
window.onclick = function(event) {
const modal = document.getElementById('imageModal');
if (event.target == modal) {
modal.style.display = 'none';
}
}
// 默认折叠长输出
document.addEventListener('DOMContentLoaded', function() {
const codeBlocks = document.querySelectorAll('.code-block');
codeBlocks.forEach(block => {
if (block.textContent.length > 1000) {
const header = block.previousElementSibling;
if (header && header.classList.contains('collapsible')) {
toggleCollapse(header);
}
}
});
});
</script>
</body>
</html>`;
}
/**
* HTML转义
*/
function escapeHtml(text) {
return text
.replace(/&/g, '&')
.replace(/</g, '<')
.replace(/>/g, '>')
.replace(/"/g, '"')
.replace(/'/g, ''');
}