@erosolaraijs/cure 1.0.2 → 1.0.3

package/src/bin/cure.ts

@@ -1,13 +1,15 @@
 #!/usr/bin/env node
 /**
  * Cure - AI Cancer Treatment Framework
- * Interactive CLI for precision oncology research and clinical decision support
+ * Interactive CLI powered by xAI Grok for precision oncology
  */
 
 import * as readline from 'readline';
+import * as https from 'https';
 import { CancerTreatmentCapabilityModule } from '../capabilities/cancerTreatmentCapability.js';
 
-const VERSION = '1.0.2';
+const VERSION = '1.0.3';
+const XAI_MODEL = 'grok-4-1-fast-reasoning';
 
 // ANSI color codes
 const colors = {
@@ -24,26 +26,126 @@ const colors = {
 };
 
 let cancerTreatment: CancerTreatmentCapabilityModule;
+let conversationHistory: Array<{role: string, content: string}> = [];
+
+const SYSTEM_PROMPT = `You are Cure, an advanced AI oncologist assistant powered by the Cure Cancer Treatment Framework. You help doctors, researchers, and patients with:
+
+1. Cancer diagnosis and staging analysis
+2. Personalized treatment planning (chemotherapy, immunotherapy, targeted therapy, CAR-T)
+3. Drug target discovery and mechanism analysis
+4. Clinical trial matching and eligibility
+5. Genomic biomarker interpretation (EGFR, KRAS, BRAF, HER2, PD-L1, etc.)
+6. Treatment response prediction and survival analysis
+7. Drug interaction and safety checks
+8. HIPAA-compliant patient data handling
+
+You have deep knowledge of:
+- NCCN, ESMO, ASCO treatment guidelines
+- FDA-approved cancer therapies and their mechanisms
+- Precision medicine and molecular oncology
+- Immunotherapy (checkpoint inhibitors, CAR-T, TILs)
+- Targeted therapies for driver mutations
+- Clinical trial design and interpretation
+
+Be concise, scientifically accurate, and clinically relevant. When discussing specific treatments, cite evidence levels and relevant trials. Always recommend consulting with treating oncologists for actual patient care decisions.
+
+Available commands the user can run:
+- /analyze [patient_id] - Analyze patient data
+- /plan [patient_id] - Design treatment plan
+- /discover [gene] [cancer] - Drug target discovery
+- /demo - Run framework demonstration
+- /help - Show available commands`;
+
+async function callXAI(userMessage: string): Promise<string> {
+  const apiKey = process.env.XAI_API_KEY;
+
+  if (!apiKey) {
+    return `${colors.yellow}Note: Set XAI_API_KEY environment variable for AI-powered responses.${colors.reset}\n\nI can help you with cancer treatment analysis. Try:\n  /analyze P001 - Analyze patient\n  /plan P001 - Design treatment plan\n  /discover EGFR Lung - Find drug targets\n  /demo - Run demonstration`;
+  }
+
+  conversationHistory.push({ role: 'user', content: userMessage });
+
+  const messages = [
+    { role: 'system', content: SYSTEM_PROMPT },
+    ...conversationHistory
+  ];
+
+  const requestBody = JSON.stringify({
+    model: XAI_MODEL,
+    messages: messages,
+    temperature: 0.7,
+    max_tokens: 2048
+  });
+
+  return new Promise((resolve, reject) => {
+    const options = {
+      hostname: 'api.x.ai',
+      port: 443,
+      path: '/v1/chat/completions',
+      method: 'POST',
+      headers: {
+        'Content-Type': 'application/json',
+        'Authorization': `Bearer ${apiKey}`,
+        'Content-Length': Buffer.byteLength(requestBody)
+      }
+    };
+
+    const req = https.request(options, (res) => {
+      let data = '';
+      res.on('data', (chunk) => { data += chunk; });
+      res.on('end', () => {
+        try {
+          const response = JSON.parse(data);
+          if (response.choices && response.choices[0]?.message?.content) {
+            const assistantMessage = response.choices[0].message.content;
+            conversationHistory.push({ role: 'assistant', content: assistantMessage });
+
+            // Keep conversation history manageable
+            if (conversationHistory.length > 20) {
+              conversationHistory = conversationHistory.slice(-16);
+            }
+
+            resolve(assistantMessage);
+          } else if (response.error) {
+            resolve(`${colors.red}API Error: ${response.error.message}${colors.reset}`);
+          } else {
+            resolve(`${colors.red}Unexpected response format${colors.reset}`);
+          }
+        } catch (e) {
+          resolve(`${colors.red}Failed to parse response${colors.reset}`);
+        }
+      });
+    });
+
+    req.on('error', (e) => {
+      resolve(`${colors.red}Connection error: ${e.message}${colors.reset}`);
+    });
+
+    req.setTimeout(30000, () => {
+      req.destroy();
+      resolve(`${colors.yellow}Request timed out. Try again.${colors.reset}`);
+    });
+
+    req.write(requestBody);
+    req.end();
+  });
+}
 
 async function main(): Promise<void> {
   const args = process.argv.slice(2);
 
-  // Check for version flag
   if (args.includes('--version') || args.includes('-v')) {
     console.log(`cure v${VERSION}`);
     process.exit(0);
   }
 
-  // Check for help flag
   if (args.includes('--help') || args.includes('-h')) {
     printHelp();
     process.exit(0);
   }
 
-  // Initialize module
   cancerTreatment = new CancerTreatmentCapabilityModule();
 
-  // Handle direct commands or launch interactive mode
   if (args.length > 0) {
     await handleCommand(args);
   } else {
@@ -64,7 +166,12 @@ async function launchInteractiveMode(): Promise<void> {
     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`);
+  const modelInfo = process.env.XAI_API_KEY
+    ? `${colors.green}Connected to xAI ${XAI_MODEL}${colors.reset}`
+    : `${colors.yellow}Set XAI_API_KEY for AI responses${colors.reset}`;
+
+  console.log(`${colors.dim}${modelInfo}${colors.reset}`);
+  console.log(`${colors.dim}Type your question or /help for commands.${colors.reset}\n`);
   prompt();
 
   rl.on('line', async (input) => {
@@ -90,6 +197,8 @@ async function launchInteractiveMode(): Promise<void> {
     if (trimmed === '/clear') {
       console.clear();
       printBanner();
+      conversationHistory = [];
+      console.log(`${colors.dim}Conversation cleared.${colors.reset}`);
       prompt();
       return;
     }
@@ -104,8 +213,6 @@ async function launchInteractiveMode(): Promise<void> {
 }
 
 async function processInput(input: string): Promise<void> {
-  const lower = input.toLowerCase();
-
   // Slash commands
   if (input.startsWith('/')) {
     const parts = input.slice(1).split(' ');
@@ -115,71 +222,34 @@ async function processInput(input: string): Promise<void> {
     switch (cmd) {
       case 'analyze':
         await analyzePatient(args[0] || 'P001', args.includes('--genomics'));
-        break;
+        return;
       case 'plan':
         await designTreatmentPlan(args[0] || 'P001', args[1]);
-        break;
+        return;
       case 'discover':
         await discoverTargets(args[0] || 'EGFR', args[1] || 'Lung');
-        break;
+        return;
       case 'demo':
         await runDemo();
-        break;
+        return;
       case 'version':
-        console.log(`\n${colors.cyan}cure${colors.reset} v${VERSION}`);
-        break;
+        console.log(`\n${colors.cyan}cure${colors.reset} v${VERSION} (${XAI_MODEL})`);
+        return;
+      case 'model':
+        console.log(`\n${colors.cyan}Model:${colors.reset} ${XAI_MODEL}`);
+        console.log(`${colors.cyan}API:${colors.reset} ${process.env.XAI_API_KEY ? 'Connected' : 'Not configured'}`);
+        return;
       default:
         console.log(`\n${colors.red}Unknown command: /${cmd}${colors.reset}`);
         console.log(`${colors.dim}Type /help for available commands.${colors.reset}`);
+        return;
     }
-    return;
-  }
-
-  // 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 (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}`);
-  }
+  // AI-powered response for natural language
+  console.log(`\n${colors.dim}Thinking...${colors.reset}`);
+  const response = await callXAI(input);
+  console.log(`\n${response}`);
 }
 
 async function analyzePatient(patientId: string, includeGenomics: boolean = false): Promise<void> {
@@ -270,6 +340,8 @@ async function runDemo(): Promise<void> {
 }
 
 async function handleCommand(args: string[]): Promise<void> {
+  cancerTreatment = new CancerTreatmentCapabilityModule();
+
   if (args.includes('--analyze-patient')) {
     const patientId = args.find(a => a.startsWith('--patient='))?.split('=')[1] || 'P001';
     await analyzePatient(patientId, args.includes('--genomics'));
@@ -305,7 +377,7 @@ ${colors.cyan}${colors.bold}  ╔═══════════════
   ║   ╚═════╝ ╚═════╝ ╚═╝  ╚═╝╚══════╝                         ║
   ║                                                             ║
   ║   AI Cancer Treatment Framework                             ║
-  ║   Precision Oncology Research & Clinical Decision Support   ║
+  ║   Powered by xAI Grok ${XAI_MODEL}              ║
   ║                                                             ║
   ╚═══════════════════════════════════════════════════════════╝${colors.reset}
 
@@ -321,25 +393,29 @@ ${colors.dim}──────────────────────
   ${colors.cyan}/plan${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
+  ${colors.cyan}/model${colors.reset}                 Show AI model info
+  ${colors.cyan}/clear${colors.reset}                 Clear conversation
   ${colors.cyan}/help${colors.reset}                  Show this help
   ${colors.cyan}/exit${colors.reset}                  Exit
 
-${colors.bold}Natural Language${colors.reset}
+${colors.bold}AI Chat${colors.reset}
 ${colors.dim}─────────────────────────────${colors.reset}
-  "analyze patient P001"
-  "create treatment plan for P002"
-  "find EGFR targets in lung cancer"
-  "run demo"
+  Just type naturally to chat with the AI oncologist:
+
+  "What are the treatment options for EGFR+ lung cancer?"
+  "Explain pembrolizumab mechanism of action"
+  "What biomarkers predict response to immunotherapy?"
+  "Compare osimertinib vs erlotinib for EGFR mutations"
 `);
 }
 
 function printHelp(): void {
   console.log(`
 ${colors.bold}Cure - AI Cancer Treatment Framework${colors.reset}
+Powered by xAI ${XAI_MODEL}
 
 ${colors.bold}Usage:${colors.reset}
-  cure                    Launch interactive mode
+  cure                    Launch interactive AI chat
   cure [command]          Run a specific command
 
 ${colors.bold}Commands:${colors.reset}
@@ -357,10 +433,12 @@ ${colors.bold}Options:${colors.reset}
   --target=<gene>         Target gene (default: EGFR)
   --cancer=<type>         Cancer type (default: Lung)
 
+${colors.bold}Environment:${colors.reset}
+  XAI_API_KEY             xAI API key for AI-powered responses
+
 ${colors.bold}Examples:${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}

package/src/clinician/index.ts

@@ -0,0 +1,11 @@
+/**
+ * Clinician Decision Support Module Exports
+ */
+export {
+  ClinicalDecisionSupportService,
+  type ClinicalRecommendation,
+  type ClinicianOverride,
+  type OverrideCategory,
+  type TumorBoardCase,
+  type AlertAcknowledgment
+} from './decisionSupport.js';

package/src/compliance/index.ts

@@ -0,0 +1,19 @@
+/**
+ * HIPAA Compliance Module Exports
+ */
+export {
+  HIPAAComplianceService,
+  type AuditLogEntry,
+  type AuditEventType,
+  type AuditAction,
+  type PatientConsent,
+  type ConsentType,
+  type DataCategory,
+  type ConsentPurpose,
+  type AccessPolicy,
+  type AccessCondition,
+  type AccessDecision,
+  type EncryptionConfig,
+  type EncryptedData,
+  type DataMaskingConfig
+} from './hipaa.js';

package/src/integrations/clinicalTrials/index.ts

@@ -0,0 +1,21 @@
+/**
+ * Clinical Trials Integration Module Exports
+ */
+export {
+  ClinicalTrialsGovClient,
+  type ClinicalTrial,
+  type TrialStatus,
+  type TrialPhase,
+  type TrialIntervention,
+  type TrialEligibility,
+  type TrialLocation,
+  type TrialSponsor,
+  type TrialContact,
+  type TrialArm,
+  type TrialOutcome,
+  type BiomarkerRequirement,
+  type TrialSearchParams,
+  type TrialSearchResult,
+  type PatientProfile,
+  type TrialMatch
+} from './clinicalTrialsGov.js';

package/src/integrations/ehr/index.ts

@@ -0,0 +1,32 @@
+/**
+ * EHR Integration Module Exports
+ */
+export {
+  FHIRClient,
+  EpicFHIRClient,
+  CernerFHIRClient,
+  createFHIRClient,
+  type FHIRConfig,
+  type FHIRPatient,
+  type FHIRIdentifier,
+  type FHIRHumanName,
+  type FHIRAddress,
+  type FHIRContactPoint,
+  type FHIRCodeableConcept,
+  type FHIRCoding,
+  type FHIRExtension,
+  type FHIRCondition,
+  type FHIRObservation,
+  type FHIRQuantity,
+  type FHIRReference,
+  type FHIRMedicationRequest,
+  type FHIRDosage,
+  type FHIRDiagnosticReport,
+  type FHIRProcedure,
+  type FHIRBundle,
+  type FHIRResource,
+  type CancerDiagnosis,
+  type CancerBiomarkers,
+  type TreatmentHistory,
+  type AuditEvent
+} from './fhir.js';

package/src/integrations/genomics/index.ts

@@ -0,0 +1,23 @@
+/**
+ * Genomic Platform Integration Module Exports
+ */
+export {
+  FoundationMedicineClient,
+  GuardantHealthClient,
+  TempusClient,
+  UnifiedGenomicsService,
+  createGenomicClient,
+  type GenomicTestOrder,
+  type GenomicTestResult,
+  type GenomicVariant,
+  type CopyNumberAlteration,
+  type GeneFusion,
+  type GenomicBiomarker,
+  type MSIResult,
+  type TMBResult,
+  type HRDResult,
+  type LOHResult,
+  type TherapyMatch,
+  type ClinicalTrialMatch,
+  type GenomicPlatformConfig
+} from './genomicPlatforms.js';

package/src/ml/index.ts

@@ -0,0 +1,15 @@
+/**
+ * Machine Learning Module Exports
+ */
+export {
+  OutcomePredictorService,
+  type PatientFeatures,
+  type TreatmentFeatures,
+  type ResponsePrediction,
+  type SurvivalPrediction,
+  type ToxicityPrediction,
+  type ResistancePrediction,
+  type TherapyRanking,
+  type MLModel,
+  type ModelRegistry
+} from './outcomePredictor.js';

package/src/orchestrator/index.ts

@@ -0,0 +1,11 @@
+/**
+ * Orchestrator Module - Real-World Oncology Service
+ */
+export {
+  RealWorldOncologyService,
+  createRealWorldOncologyService,
+  type RealWorldConfig,
+  type RealWorldPatient,
+  type ComprehensiveTreatmentPlan,
+  type TreatmentOutcome
+} from './realWorldOncology.js';