@erosolaraijs/cure 1.0.1 → 1.0.2

package/src/bin/cure.ts

@@ -1,21 +1,36 @@
 #!/usr/bin/env node
 /**
- * 癌症治疗统一人工智能框架 - 核心医疗控制台
- * Unified Cancer Treatment Framework - Core Medical Console
- *
- * 全球首个人工通用智能驱动的癌症治疗统一指挥控制平台
- * 提供完整的癌症研究、药物发现、治疗规划、患者管理和医疗系统集成能力
+ * Cure - AI Cancer Treatment Framework
+ * Interactive CLI for precision oncology research and clinical decision support
  */
 
+import * as readline from 'readline';
 import { CancerTreatmentCapabilityModule } from '../capabilities/cancerTreatmentCapability.js';
 
+const VERSION = '1.0.2';
+
+// ANSI color codes
+const colors = {
+  reset: '\x1b[0m',
+  bold: '\x1b[1m',
+  dim: '\x1b[2m',
+  cyan: '\x1b[36m',
+  green: '\x1b[32m',
+  yellow: '\x1b[33m',
+  blue: '\x1b[34m',
+  magenta: '\x1b[35m',
+  red: '\x1b[31m',
+  white: '\x1b[37m',
+};
+
+let cancerTreatment: CancerTreatmentCapabilityModule;
+
 async function main(): Promise<void> {
   const args = process.argv.slice(2);
 
   // Check for version flag
   if (args.includes('--version') || args.includes('-v')) {
-    const pkg = JSON.parse(await import('fs').then(fs => fs.readFileSync(new URL('../../package.json', import.meta.url), 'utf-8')));
-    console.log(`agi-core-cancer-treatment v${pkg.version}`);
+    console.log(`cure v${VERSION}`);
     process.exit(0);
   }
 
@@ -26,157 +41,333 @@ async function main(): Promise<void> {
   }
 
   // Initialize module
-  const cancerTreatment = new CancerTreatmentCapabilityModule();
-
-  // Handle commands
-  if (args.includes('--cancer-treatment') || args.includes('--medical')) {
-    console.log('\n🏥 癌症治疗人工智能框架激活\n');
-    console.log('💊 最大能力癌症治疗框架 - 全面医疗与AI能力\n');
-    console.log('📊 框架提供以下核心能力:');
-    console.log('   • 个性化癌症治疗协议分析与规划');
-    console.log('   • AI驱动的药物靶点发现与设计');
-    console.log('   • 精准医疗与基因组分析管道');
-    console.log('   • 临床试验管理与优化');
-    console.log('   • 患者多维度评估与监测');
-    console.log('   • 医疗系统集成与数据协调');
-    console.log('   • 统一医疗指挥与协调系统');
-    console.log('   • 人工智能治疗决策支持\n');
-    
-    console.log('✅ 癌症治疗能力框架初始化完成');
-    console.log('🚀 使用 --help 查看可用命令');
-  }
-  else if (args.includes('--analyze-patient')) {
-    const patientId = args.find(arg => arg.startsWith('--patient='))?.split('=')[1] || 'P001';
-    const includeGenomics = args.includes('--genomics');
-    
-    console.log(`\n🔍 分析患者: ${patientId}`);
-    console.log('───────────────────────────');
-    
-    try {
-      const result = await cancerTreatment.analyzePatient(patientId, includeGenomics);
-      console.log('📊 分析结果:');
-      console.log(`   • 癌症类型: ${result.analysis.cancerType}`);
-      console.log(`   • 分期: ${result.analysis.stage}`);
-      console.log(`   • 生物标志物: ${result.analysis.biomarkers.join(', ')}`);
-      console.log(`   • 生存概率: ${(result.analysis.riskAssessment.survivalProbability * 100).toFixed(1)}%`);
-      console.log('✅ 分析完成');
-    } catch (error) {
-      console.error('❌ 分析失败:', error);
+  cancerTreatment = new CancerTreatmentCapabilityModule();
+
+  // Handle direct commands or launch interactive mode
+  if (args.length > 0) {
+    await handleCommand(args);
+  } else {
+    await launchInteractiveMode();
+  }
+}
+
+async function launchInteractiveMode(): Promise<void> {
+  console.clear();
+  printBanner();
+
+  const rl = readline.createInterface({
+    input: process.stdin,
+    output: process.stdout,
+  });
+
+  const prompt = () => {
+    process.stdout.write(`\n${colors.cyan}cure${colors.reset} ${colors.dim}>${colors.reset} `);
+  };
+
+  console.log(`${colors.dim}Type a command or describe what you need. Type /help for commands.${colors.reset}\n`);
+  prompt();
+
+  rl.on('line', async (input) => {
+    const trimmed = input.trim();
+
+    if (!trimmed) {
+      prompt();
+      return;
+    }
+
+    if (trimmed === '/exit' || trimmed === '/quit' || trimmed === 'exit' || trimmed === 'quit') {
+      console.log(`\n${colors.dim}Goodbye.${colors.reset}\n`);
+      rl.close();
+      process.exit(0);
     }
+
+    if (trimmed === '/help' || trimmed === 'help') {
+      printInteractiveHelp();
+      prompt();
+      return;
+    }
+
+    if (trimmed === '/clear') {
+      console.clear();
+      printBanner();
+      prompt();
+      return;
+    }
+
+    await processInput(trimmed);
+    prompt();
+  });
+
+  rl.on('close', () => {
+    process.exit(0);
+  });
+}
+
+async function processInput(input: string): Promise<void> {
+  const lower = input.toLowerCase();
+
+  // Slash commands
+  if (input.startsWith('/')) {
+    const parts = input.slice(1).split(' ');
+    const cmd = parts[0];
+    const args = parts.slice(1);
+
+    switch (cmd) {
+      case 'analyze':
+        await analyzePatient(args[0] || 'P001', args.includes('--genomics'));
+        break;
+      case 'plan':
+        await designTreatmentPlan(args[0] || 'P001', args[1]);
+        break;
+      case 'discover':
+        await discoverTargets(args[0] || 'EGFR', args[1] || 'Lung');
+        break;
+      case 'demo':
+        await runDemo();
+        break;
+      case 'version':
+        console.log(`\n${colors.cyan}cure${colors.reset} v${VERSION}`);
+        break;
+      default:
+        console.log(`\n${colors.red}Unknown command: /${cmd}${colors.reset}`);
+        console.log(`${colors.dim}Type /help for available commands.${colors.reset}`);
+    }
+    return;
   }
-  else if (args.includes('--treatment-plan')) {
-    const patientId = args.find(arg => arg.startsWith('--patient='))?.split('=')[1] || 'P001';
-    const protocolId = args.find(arg => arg.startsWith('--protocol='))?.split('=')[1];
-    
-    console.log(`\n💊 设计治疗计划: ${patientId}`);
-    console.log('─────────────────────────────');
-    
-    try {
-      const result = await cancerTreatment.designTreatmentPlan(patientId, protocolId);
-      console.log('📋 治疗计划:');
-      console.log(`   • 协议: ${result.plan.protocol.name}`);
-      console.log(`   • 治疗方式: ${result.plan.protocol.treatmentModalities.join(', ')}`);
-      console.log(`   • 预计疗效: ${(result.estimatedEfficacy * 100).toFixed(1)}%`);
-      console.log(`   • 时间线: ${result.plan.treatmentTimeline.length} 周`);
-      console.log('✅ 治疗计划设计完成');
-    } catch (error) {
-      console.error('❌ 治疗计划设计失败:', error);
+
+  // Natural language processing
+  if (lower.includes('analyze') && lower.includes('patient')) {
+    const match = input.match(/patient\s+(\w+)/i) || input.match(/P\d+/i);
+    const patientId = match ? match[0].replace(/patient\s+/i, '') : 'P001';
+    await analyzePatient(patientId, lower.includes('genom'));
+  }
+  else if (lower.includes('treatment') || lower.includes('plan')) {
+    const match = input.match(/patient\s+(\w+)/i) || input.match(/P\d+/i);
+    const patientId = match ? match[0].replace(/patient\s+/i, '') : 'P001';
+    await designTreatmentPlan(patientId);
+  }
+  else if (lower.includes('drug') || lower.includes('target') || lower.includes('discover')) {
+    const genes = ['EGFR', 'KRAS', 'BRAF', 'HER2', 'ALK', 'ROS1', 'PIK3CA', 'TP53'];
+    const cancers = ['lung', 'breast', 'colon', 'melanoma', 'pancreatic'];
+
+    let gene = 'EGFR';
+    let cancer = 'Lung';
+
+    for (const g of genes) {
+      if (lower.includes(g.toLowerCase())) {
+        gene = g;
+        break;
+      }
+    }
+    for (const c of cancers) {
+      if (lower.includes(c)) {
+        cancer = c.charAt(0).toUpperCase() + c.slice(1);
+        break;
+      }
     }
+
+    await discoverTargets(gene, cancer);
   }
-  else if (args.includes('--drug-discovery')) {
-    const targetGene = args.find(arg => arg.startsWith('--target='))?.split('=')[1] || 'EGFR';
-    const cancerType = args.find(arg => arg.startsWith('--cancer='))?.split('=')[1] || 'Lung';
-    
-    console.log(`\n🧬 药物靶点发现: ${targetGene} (${cancerType} 癌症)`);
-    console.log('──────────────────────────────');
-    
-    try {
-      const result = await cancerTreatment.discoverDrugTargets(cancerType, targetGene);
-      console.log('🔬 发现结果:');
-      console.log(`   • 癌症类型: ${result.cancerType}`);
-      console.log(`   • 目标基因: ${result.targetGene || '所有'}`);
-      console.log(`   • 发现靶点: ${result.discoveredTargets.length} 个`);
-      
-      result.discoveredTargets.slice(0, 3).forEach((target: any, index: number) => {
-        console.log(`   ${index + 1}. ${target.gene} - ${target.evidenceLevel} 证据等级`);
-        console.log(`      相关癌症: ${target.cancerTypes.join(', ')}`);
-      });
-      
-      console.log('✅ 药物靶点发现完成');
-    } catch (error) {
-      console.error('❌ 药物发现失败:', error);
+  else if (lower.includes('demo')) {
+    await runDemo();
+  }
+  else {
+    // Default response
+    console.log(`\n${colors.cyan}I can help you with:${colors.reset}`);
+    console.log(`  ${colors.dim}•${colors.reset} Analyzing patient data`);
+    console.log(`  ${colors.dim}•${colors.reset} Designing treatment plans`);
+    console.log(`  ${colors.dim}•${colors.reset} Discovering drug targets`);
+    console.log(`  ${colors.dim}•${colors.reset} Running clinical demos`);
+    console.log(`\n${colors.dim}Try: "analyze patient P001" or type /help${colors.reset}`);
+  }
+}
+
+async function analyzePatient(patientId: string, includeGenomics: boolean = false): Promise<void> {
+  console.log(`\n${colors.cyan}Analyzing patient ${patientId}...${colors.reset}\n`);
+
+  try {
+    const result = await cancerTreatment.analyzePatient(patientId, includeGenomics);
+
+    console.log(`${colors.bold}Patient Analysis${colors.reset}`);
+    console.log(`${colors.dim}─────────────────────────────${colors.reset}`);
+    console.log(`  Cancer Type:    ${colors.yellow}${result.analysis.cancerType}${colors.reset}`);
+    console.log(`  Stage:          ${colors.yellow}${result.analysis.stage}${colors.reset}`);
+    console.log(`  Biomarkers:     ${result.analysis.biomarkers.join(', ')}`);
+    console.log(`  Survival Prob:  ${colors.green}${(result.analysis.riskAssessment.survivalProbability * 100).toFixed(1)}%${colors.reset}`);
+    console.log(`  Recurrence:     ${colors.yellow}${(result.analysis.riskAssessment.recurrenceRisk * 100).toFixed(1)}%${colors.reset}`);
+
+    if (result.analysis.genomicProfile) {
+      console.log(`\n${colors.bold}Genomic Profile${colors.reset}`);
+      console.log(`  Mutations:      ${result.analysis.genomicProfile.mutations?.length || 0} detected`);
     }
+
+    console.log(`\n${colors.green}✓ Analysis complete${colors.reset}`);
+  } catch (error) {
+    console.error(`${colors.red}✗ Analysis failed:${colors.reset}`, error);
   }
-  else if (args.includes('--demo')) {
-    console.log('\n🏥 癌症治疗框架演示');
-    console.log('────────────────────');
-    
-    try {
-      const { demonstrateCancerTreatmentFramework } = await import('../examples/cancerTreatmentDemo.js');
-      await demonstrateCancerTreatmentFramework();
-    } catch (error) {
-      console.error('❌ 演示失败:', error);
+}
+
+async function designTreatmentPlan(patientId: string, protocolId?: string): Promise<void> {
+  console.log(`\n${colors.cyan}Designing treatment plan for ${patientId}...${colors.reset}\n`);
+
+  try {
+    const result = await cancerTreatment.designTreatmentPlan(patientId, protocolId);
+
+    console.log(`${colors.bold}Treatment Plan${colors.reset}`);
+    console.log(`${colors.dim}─────────────────────────────${colors.reset}`);
+    console.log(`  Protocol:       ${colors.yellow}${result.plan.protocol.name}${colors.reset}`);
+    console.log(`  Modalities:     ${result.plan.protocol.treatmentModalities.join(', ')}`);
+    console.log(`  Est. Efficacy:  ${colors.green}${(result.estimatedEfficacy * 100).toFixed(1)}%${colors.reset}`);
+    console.log(`  Duration:       ${result.plan.treatmentTimeline.length} weeks`);
+
+    console.log(`\n${colors.bold}Timeline${colors.reset}`);
+    result.plan.treatmentTimeline.slice(0, 4).forEach((week: any, i: number) => {
+      console.log(`  Week ${i + 1}: ${week.phase} - ${week.activities.join(', ')}`);
+    });
+    if (result.plan.treatmentTimeline.length > 4) {
+      console.log(`  ${colors.dim}... and ${result.plan.treatmentTimeline.length - 4} more weeks${colors.reset}`);
     }
+
+    console.log(`\n${colors.green}✓ Plan generated${colors.reset}`);
+  } catch (error) {
+    console.error(`${colors.red}✗ Plan generation failed:${colors.reset}`, error);
+  }
+}
+
+async function discoverTargets(gene: string, cancerType: string): Promise<void> {
+  console.log(`\n${colors.cyan}Discovering drug targets for ${gene} in ${cancerType} cancer...${colors.reset}\n`);
+
+  try {
+    const result = await cancerTreatment.discoverDrugTargets(cancerType, gene);
+
+    console.log(`${colors.bold}Drug Target Discovery${colors.reset}`);
+    console.log(`${colors.dim}─────────────────────────────${colors.reset}`);
+    console.log(`  Cancer Type:    ${colors.yellow}${result.cancerType}${colors.reset}`);
+    console.log(`  Target Gene:    ${colors.yellow}${result.targetGene || 'All'}${colors.reset}`);
+    console.log(`  Targets Found:  ${result.discoveredTargets.length}`);
+
+    console.log(`\n${colors.bold}Top Targets${colors.reset}`);
+    result.discoveredTargets.slice(0, 5).forEach((target: any, i: number) => {
+      console.log(`  ${i + 1}. ${colors.cyan}${target.gene}${colors.reset} - ${target.evidenceLevel} evidence`);
+      console.log(`     ${colors.dim}Cancers: ${target.cancerTypes.slice(0, 3).join(', ')}${colors.reset}`);
+    });
+
+    console.log(`\n${colors.green}✓ Discovery complete${colors.reset}`);
+  } catch (error) {
+    console.error(`${colors.red}✗ Discovery failed:${colors.reset}`, error);
+  }
+}
+
+async function runDemo(): Promise<void> {
+  console.log(`\n${colors.cyan}Running framework demo...${colors.reset}\n`);
+
+  try {
+    const { demonstrateCancerTreatmentFramework } = await import('../examples/cancerTreatmentDemo.js');
+    await demonstrateCancerTreatmentFramework();
+  } catch (error) {
+    console.error(`${colors.red}✗ Demo failed:${colors.reset}`, error);
+  }
+}
+
+async function handleCommand(args: string[]): Promise<void> {
+  if (args.includes('--analyze-patient')) {
+    const patientId = args.find(a => a.startsWith('--patient='))?.split('=')[1] || 'P001';
+    await analyzePatient(patientId, args.includes('--genomics'));
+  }
+  else if (args.includes('--treatment-plan')) {
+    const patientId = args.find(a => a.startsWith('--patient='))?.split('=')[1] || 'P001';
+    const protocolId = args.find(a => a.startsWith('--protocol='))?.split('=')[1];
+    await designTreatmentPlan(patientId, protocolId);
   }
-  else if (args.length === 0) {
-    // Interactive mode
-    console.log('\n🏥 AGI 癌症治疗框架');
-    console.log('══════════════════════════════════════');
-    console.log('\n🔧 可用命令:');
-    console.log('  agi --cancer-treatment             激活癌症治疗框架');
-    console.log('  agi --analyze-patient --patient=P001 分析患者数据');
-    console.log('  agi --treatment-plan --patient=P001 设计治疗计划');
-    console.log('  agi --drug-discovery --target=EGFR 药物靶点发现');
-    console.log('  agi --clinical-trial               临床试验演示');
-    console.log('  agi --demo                        完整框架演示');
-    console.log('  agi --help                        显示帮助信息');
-    console.log('  agi --version                     显示版本信息');
-    console.log('\n📚 了解更多:');
-    console.log('  查看 README.md 获取完整文档和使用指南');
+  else if (args.includes('--drug-discovery')) {
+    const gene = args.find(a => a.startsWith('--target='))?.split('=')[1] || 'EGFR';
+    const cancer = args.find(a => a.startsWith('--cancer='))?.split('=')[1] || 'Lung';
+    await discoverTargets(gene, cancer);
+  }
+  else if (args.includes('--demo')) {
+    await runDemo();
   }
   else {
-    console.log('❌ 未知命令。使用 agi --help 查看可用命令。');
+    console.log(`${colors.red}Unknown command.${colors.reset} Use cure --help for usage.`);
     process.exit(1);
   }
 }
 
+function printBanner(): void {
+  console.log(`
+${colors.cyan}${colors.bold}  ╔═══════════════════════════════════════════════════════════╗
+  ║                                                             ║
+  ║   ██████╗██╗   ██╗██████╗ ███████╗                         ║
+  ║  ██╔════╝██║   ██║██╔══██╗██╔════╝                         ║
+  ║  ██║     ██║   ██║██████╔╝█████╗                           ║
+  ║  ██║     ██║   ██║██╔══██╗██╔══╝                           ║
+  ║  ╚██████╗╚██████╔╝██║  ██║███████╗                         ║
+  ║   ╚═════╝ ╚═════╝ ╚═╝  ╚═╝╚══════╝                         ║
+  ║                                                             ║
+  ║   AI Cancer Treatment Framework                             ║
+  ║   Precision Oncology Research & Clinical Decision Support   ║
+  ║                                                             ║
+  ╚═══════════════════════════════════════════════════════════╝${colors.reset}
+
+  ${colors.dim}v${VERSION}${colors.reset}
+`);
+}
+
+function printInteractiveHelp(): void {
+  console.log(`
+${colors.bold}Commands${colors.reset}
+${colors.dim}─────────────────────────────${colors.reset}
+  ${colors.cyan}/analyze${colors.reset} [patient]     Analyze patient data
+  ${colors.cyan}/plan${colors.reset} [patient]        Design treatment plan
+  ${colors.cyan}/discover${colors.reset} [gene]       Drug target discovery
+  ${colors.cyan}/demo${colors.reset}                  Run framework demo
+  ${colors.cyan}/clear${colors.reset}                 Clear screen
+  ${colors.cyan}/help${colors.reset}                  Show this help
+  ${colors.cyan}/exit${colors.reset}                  Exit
+
+${colors.bold}Natural Language${colors.reset}
+${colors.dim}─────────────────────────────${colors.reset}
+  "analyze patient P001"
+  "create treatment plan for P002"
+  "find EGFR targets in lung cancer"
+  "run demo"
+`);
+}
+
 function printHelp(): void {
   console.log(`
-🏥 AGI 癌症治疗框架 - 命令行工具
-
-使用方法:
-  agi [命令] [选项]
-
-	命令:
-	  --cancer-treatment, --medical     激活癌症治疗框架
-	  --analyze-patient                 分析患者数据
-	  --treatment-plan                  设计个性化治疗计划
-	  --drug-discovery                  AI驱动的药物靶点发现
-	  --demo                           完整框架演示
-	  --help, -h                       显示此帮助信息
-	  --version, -v                    显示版本信息
-
-选项:
-  --patient=<id>                   患者ID (默认: P001)
-  --protocol=<id>                  治疗协议ID
-  --genomics                       包含基因组数据分析
-  --target=<gene>                  目标基因 (默认: EGFR)
-  --cancer=<type>                  癌症类型 (默认: Lung)
-
-示例:
-  agi --cancer-treatment
-  agi --analyze-patient --patient=P001 --genomics
-  agi --treatment-plan --patient=P001 --protocol=nccn-breast-early
-  agi --drug-discovery --target=EGFR --cancer=Lung
-  agi --demo
-
-📞 技术支持: medical-support@agi-cancer-treatment.org
-📚 文档: 查看项目目录中的 README.md
+${colors.bold}Cure - AI Cancer Treatment Framework${colors.reset}
+
+${colors.bold}Usage:${colors.reset}
+  cure                    Launch interactive mode
+  cure [command]          Run a specific command
+
+${colors.bold}Commands:${colors.reset}
+  --analyze-patient       Analyze patient data
+  --treatment-plan        Design treatment plan
+  --drug-discovery        Drug target discovery
+  --demo                  Run framework demo
+  --help, -h              Show this help
+  --version, -v           Show version
+
+${colors.bold}Options:${colors.reset}
+  --patient=<id>          Patient ID (default: P001)
+  --protocol=<id>         Treatment protocol
+  --genomics              Include genomic analysis
+  --target=<gene>         Target gene (default: EGFR)
+  --cancer=<type>         Cancer type (default: Lung)
+
+${colors.bold}Examples:${colors.reset}
+  cure
+  cure --analyze-patient --patient=P001 --genomics
+  cure --treatment-plan --patient=P001
+  cure --drug-discovery --target=BRAF --cancer=Melanoma
+
+${colors.dim}https://npmjs.com/package/@erosolaraijs/cure${colors.reset}
 `);
 }
 
-// Run main function
 main().catch((error) => {
-  console.error('应用程序错误:', error);
+  console.error(`${colors.red}Error:${colors.reset}`, error);
   process.exit(1);
-});
+});