@erosolaraijs/cure 2.3.0 → 2.4.0

package/README.md

@@ -1,6 +1,15 @@
 # Cure
 
-AI-powered cancer treatment framework for precision oncology research and clinical decision support.
+AI-powered precision oncology platform for cancer treatment, clinical decision support, and research.
+
+```
+  ██████╗██╗   ██╗██████╗ ███████╗
+ ██╔════╝██║   ██║██╔══██╗██╔════╝
+ ██║     ██║   ██║██████╔╝█████╗
+ ██║     ██║   ██║██╔══██╗██╔══╝
+ ╚██████╗╚██████╔╝██║  ██║███████╗
+  ╚═════╝ ╚═════╝ ╚═╝  ╚═╝╚══════╝
+```
 
 ## Installation
 
@@ -8,61 +17,342 @@ AI-powered cancer treatment framework for precision oncology research and clinic
 npm install -g @erosolaraijs/cure
 ```
 
-## Usage
+## Quick Start
 
 ```bash
+# Launch interactive AI oncologist
 cure
+
+# Set your AI provider (xAI or OpenAI)
+/model openai
+/key YOUR_API_KEY
+
+# Generate a cure protocol
+/cure NSCLC IV KRAS_G12C
 ```
 
 ## Features
 
-### Patient Analysis
+### Interactive AI Oncologist
+
+Chat with an AI-powered oncology assistant for:
+- Treatment recommendations based on cancer type, stage, and biomarkers
+- Drug mechanism explanations
+- Clinical trial guidance
+- Biomarker interpretation
+
+**Multi-Provider Support:**
+- **xAI Grok** (`grok-4-1-fast-reasoning`) - Default
+- **OpenAI GPT-5.1** (`gpt-5.1`) - Alternative
+
+Switch providers at runtime with `/model xai` or `/model openai`.
+
+### Comprehensive Cancer Coverage
+
+| Category | Coverage |
+|----------|----------|
+| Cancer Types | 200+ types and histological subtypes |
+| Biomarkers | 500+ actionable targets |
+| Protocols | 100+ (NCCN, ESMO, ASCO, FDA) |
+| Patient Populations | Pediatric, AYA, adult, elderly, frail |
+| Special Circumstances | Pregnancy, transplant, autoimmune, HIV |
+| Stages | Localized, locally advanced, metastatic, recurrent |
+
+### Core Capabilities
+
+#### Patient Analysis (`/analyze`)
 - Genomic profiling and biomarker assessment
 - Risk stratification and survival prediction
 - Treatment response modeling
+- MSI/TMB/HRD status analysis
 
-### Treatment Planning
+#### Treatment Planning (`/plan`)
 - NCCN, ESMO, ASCO protocol integration
 - Personalized treatment recommendations
+- Multi-modality planning (surgery, radiation, systemic)
 - Timeline and monitoring schedules
 
-### Drug Discovery
+#### Cure Protocol Generation (`/cure`)
+- Comprehensive cure strategies by cancer type and stage
+- Drug target prioritization with evidence levels
+- Immunotherapy protocol matching
+- Projected outcomes (response rate, 5-year survival, cure confidence)
+
+#### Drug Target Discovery (`/discover`)
 - AI-driven target identification
-- Evidence-based prioritization
-- Research pathway planning
+- Evidence-based prioritization (FDA-approved, clinical trials, preclinical)
+- Pathway analysis
+- Approved drug matching
+
+#### Clinical Trial Matching (`/trials`)
+- ClinicalTrials.gov integration
+- Biomarker-based eligibility matching
+- Location-aware search
+- Phase and status filtering
+
+#### Drug Safety (`/safety`)
+- Drug-drug interaction checking
+- Black box warning alerts
+- QT prolongation risk assessment
+- Pharmacogenomic considerations (DPYD, UGT1A1, TPMT/NUDT15)
+
+#### ML Outcome Prediction (`/predict`)
+- Response prediction (CR, PR, SD, PD)
+- Survival estimates (PFS, OS with confidence intervals)
+- Toxicity risk assessment
+- Resistance prediction
+
+### EHR Integration
+
+Connect to hospital systems via HL7 FHIR R4:
+
+```bash
+/ehr connect epic
+/ehr connect cerner
+```
+
+**Supported Systems:**
+- Epic
+- Cerner
+
+**Data Exchange:**
+- Patient demographics
+- Cancer diagnoses (ICD-10)
+- Biomarker results
+- Treatment history
+- Medication records
+
+### Genomic Platform Integration
+
+```bash
+/genomics platforms
+```
+
+**Supported Platforms:**
+- **Foundation Medicine** (FoundationOne CDx)
+- **Guardant Health** (Guardant360, GuardantOMNI)
+- **Tempus** (xT, xF, xR)
+
+**Analysis Types:**
+- Somatic variant detection
+- Copy number alterations
+- Gene fusions
+- MSI/TMB analysis
+- Therapy matching
+
+### HIPAA Compliance
 
-### Clinical Trials
-- Patient eligibility matching
-- Protocol design support
-- Outcome tracking
+- End-to-end encryption
+- PHI masking and de-identification
+- Audit logging with 7-year retention
+- Role-based access control
+- Consent management
 
-### Integrations
-- **FHIR**: Electronic health record interoperability
-- **ClinicalTrials.gov**: Trial matching and enrollment
-- **Genomic Platforms**: Foundation Medicine, Tempus, Guardant integration
+## CLI Commands
 
-### Compliance
-- HIPAA-compliant data handling
-- Audit logging and access controls
-- PHI masking and encryption
+### AI Chat Commands
+| Command | Description |
+|---------|-------------|
+| `/key [provider] [key]` | Set API key (xai or openai) |
+| `/model [xai\|openai]` | Show/switch AI provider |
+| `/clear` | Clear conversation history |
 
-## API
+### Clinical Commands
+| Command | Description |
+|---------|-------------|
+| `/analyze [patient]` | Analyze patient data |
+| `/plan [patient]` | Design treatment plan |
+| `/cure [cancer] [stage] [mutations...]` | Generate cure protocol |
+| `/discover [gene] [cancer]` | Drug target discovery |
+| `/trials [cancer] [biomarkers...]` | Find clinical trials |
+| `/safety [drug1] [drug2...]` | Check drug interactions |
+| `/predict [patient]` | ML outcome predictions |
+
+### System Commands
+| Command | Description |
+|---------|-------------|
+| `/status` | System health check |
+| `/ehr [connect\|status]` | EHR integration |
+| `/genomics [platforms]` | Genomic platforms status |
+| `/demo` | Run framework demonstration |
+| `/version` | Show version |
+| `/update` | Check for updates |
+
+### Tool Commands
+| Command | Description |
+|---------|-------------|
+| `/tools` | List diagnostic tools |
+| `/tool <id>` | Run a tool (see `/tools`) |
+| `/tool all` | Run all tools |
+
+## Programmatic API
 
 ```typescript
-import { CancerTreatmentCapability } from '@erosolaraijs/cure';
+import {
+  CancerTreatmentCapabilityModule,
+  createOncologyPlatform,
+  FHIRClient,
+  ClinicalTrialsGovClient,
+  OutcomePredictorService,
+  DrugSafetyService,
+  HIPAAComplianceService
+} from '@erosolaraijs/cure';
+
+// Quick start with full platform
+const platform = await createOncologyPlatform({
+  ehr: {
+    enabled: true,
+    vendor: 'epic',
+    baseUrl: 'https://epic.hospital.org/fhir',
+    clientId: 'your-client-id'
+  },
+  genomics: {
+    enabled: true,
+    platforms: ['foundation', 'guardant', 'tempus']
+  },
+  clinicalTrials: {
+    enabled: true,
+    maxDistance: 100
+  },
+  ml: {
+    enabled: true,
+    modelVersion: '1.0.0'
+  },
+  safety: {
+    enabled: true,
+    strictMode: true
+  },
+  compliance: {
+    enabled: true,
+    auditRetentionDays: 2555
+  }
+});
 
-const capability = new CancerTreatmentCapability();
+// Generate comprehensive treatment plan
+const plan = await platform.generateComprehensivePlan(patient, 'DR001');
+```
+
+### Core Module Usage
+
+```typescript
+// Cancer treatment capability
+const capability = new CancerTreatmentCapabilityModule();
 
 // Analyze patient
-const analysis = await capability.analyzePatient(patientData);
+const analysis = await capability.analyzePatient('P001', true);
 
-// Generate treatment plan
-const plan = await capability.generateTreatmentPlan(patientId, options);
+// Generate cure protocol
+const cure = await capability.cureCancer('P001', 'Lung', 'IV', {
+  mutations: ['EGFR', 'TP53'],
+  biomarkers: ['PD-L1'],
+  msiStatus: 'MSS',
+  tmbLevel: 'High'
+});
 
 // Discover drug targets
-const targets = await capability.discoverDrugTargets(cancerType, genomicData);
+const targets = await capability.discoverDrugTargets('Melanoma', 'BRAF');
 ```
 
+### Individual Services
+
+```typescript
+// EHR Integration
+const fhir = new FHIRClient(config);
+const patient = await fhir.getPatient('12345');
+const conditions = await fhir.getConditions('12345');
+
+// Clinical Trials
+const trials = new ClinicalTrialsGovClient();
+const matches = await trials.searchTrials({
+  condition: 'Non-Small Cell Lung Cancer',
+  intervention: 'pembrolizumab',
+  status: 'RECRUITING'
+});
+
+// ML Predictions
+const predictor = new OutcomePredictorService();
+const response = await predictor.predictResponse(patientFeatures, treatmentFeatures);
+
+// Drug Safety
+const safety = new DrugSafetyService();
+const interactions = await safety.checkInteractions(['pembrolizumab', 'ipilimumab']);
+
+// HIPAA Compliance
+const hipaa = new HIPAAComplianceService();
+await hipaa.logAccess(userId, patientId, 'VIEW', 'Clinical review');
+```
+
+## Environment Variables
+
+| Variable | Description |
+|----------|-------------|
+| `AI_PROVIDER` | AI provider: `xai` or `openai` (default: xai) |
+| `XAI_API_KEY` | xAI API key |
+| `OPENAI_API_KEY` | OpenAI API key |
+| `FHIR_BASE_URL` | FHIR server URL |
+| `FHIR_CLIENT_ID` | FHIR OAuth client ID |
+| `FHIR_CLIENT_SECRET` | FHIR OAuth client secret |
+
+## Supported Cancer Types
+
+<details>
+<summary>Click to expand full list</summary>
+
+**Solid Tumors:**
+- Lung (NSCLC, SCLC, mesothelioma)
+- Breast (HR+, HER2+, TNBC)
+- Colorectal
+- Prostate
+- Melanoma
+- Pancreatic
+- Hepatocellular
+- Gastric/Esophageal
+- Ovarian
+- Endometrial
+- Cervical
+- Bladder/Urothelial
+- Renal Cell
+- Head and Neck
+- Thyroid
+- Sarcomas
+- Brain (GBM, meningioma)
+- And 150+ more subtypes
+
+**Hematologic Malignancies:**
+- Acute Myeloid Leukemia (AML)
+- Acute Lymphoblastic Leukemia (ALL)
+- Chronic Myeloid Leukemia (CML)
+- Chronic Lymphocytic Leukemia (CLL)
+- Diffuse Large B-Cell Lymphoma
+- Follicular Lymphoma
+- Hodgkin Lymphoma
+- Multiple Myeloma
+- Myelodysplastic Syndromes
+- Myeloproliferative Neoplasms
+
+**Rare Cancers:**
+- Cholangiocarcinoma
+- Neuroendocrine Tumors
+- GIST
+- Adrenocortical Carcinoma
+- Thymoma
+- And more
+
+</details>
+
+## Emerging Therapeutics
+
+The platform includes cutting-edge treatment modalities:
+
+- **Antibody-Drug Conjugates (ADCs):** T-DXd, sacituzumab govitecan
+- **Bispecific Antibodies:** teclistamab, glofitamab
+- **CAR-T Therapies:** axi-cel, liso-cel, ide-cel
+- **Tumor-Infiltrating Lymphocytes (TILs):** lifileucel
+- **KRAS Inhibitors:** sotorasib, adagrasib
+- **Protein Degraders:** PROTACs, molecular glues
+- **Radiopharmaceuticals:** Lu-177 PSMA, I-131 MIBG
+- **Cancer Vaccines:** mRNA-4157, personalized neoantigen vaccines
+
 ## Requirements
 
 - Node.js >= 18.0.0
@@ -70,3 +360,8 @@ const targets = await capability.discoverDrugTargets(cancerType, genomicData);
 ## License
 
 MIT
+
+## Links
+
+- [npm Package](https://www.npmjs.com/package/@erosolaraijs/cure)
+- [Report Issues](https://github.com/anthropics/claude-code/issues)

package/dist/bin/cure.js

@@ -19,7 +19,8 @@ import * as path from 'path';
 import * as os from 'os';
 import { CancerTreatmentCapabilityModule } from '../capabilities/cancerTreatmentCapability.js';
 import { createRealWorldOncologyService } from '../orchestrator/realWorldOncology.js';
-const VERSION = '2.3.0';
+import { getCliTool, listCliTools } from '../tools/index.js';
+const VERSION = '2.4.0';
 const PACKAGE_NAME = '@erosolaraijs/cure';
 const UPDATE_CHECK_INTERVAL = 24 * 60 * 60 * 1000; // 24 hours
 let currentProvider = process.env.AI_PROVIDER || 'xai';
@@ -498,6 +499,23 @@ async function processInput(input) {
             case 'predict':
                 await predictOutcomes(args[0] || 'P001');
                 return;
+            case 'tools':
+                printToolList();
+                return;
+            case 'tool':
+                if (!args[0]) {
+                    console.log(`\n${colors.yellow}Usage: /tool <selftest|validate>${colors.reset}`);
+                    printToolList();
+                    return;
+                }
+                await runTool(args[0], args.slice(1));
+                return;
+            case 'selftest':
+                await runTool('selftest', args);
+                return;
+            case 'validate':
+                await runTool('validate', args);
+                return;
             case 'status':
                 await showSystemStatus();
                 return;
@@ -966,6 +984,69 @@ async function manageGenomics(args) {
             break;
     }
 }
+function printToolList() {
+    const tools = listCliTools();
+    console.log(`\n${colors.bold}Tools${colors.reset}`);
+    console.log(`${colors.dim}─────────────────────────────${colors.reset}`);
+    tools.forEach(tool => {
+        console.log(`  ${colors.cyan}${tool.id}${colors.reset}  ${tool.description}`);
+    });
+    console.log(`  ${colors.cyan}all${colors.reset}  Run all tools`);
+    console.log(`${colors.dim}Use /tool <id> to run a tool.${colors.reset}`);
+}
+async function runTool(toolId, args) {
+    if (toolId === 'all') {
+        await runAllTools(args);
+        return;
+    }
+    const tool = getCliTool(toolId);
+    if (!tool) {
+        console.log(`\n${colors.red}Unknown tool: ${toolId}${colors.reset}`);
+        printToolList();
+        return;
+    }
+    console.log(`\n${colors.cyan}Running tool: ${tool.id}${colors.reset}`);
+    const context = { cancerTreatment, oncologyService, serviceConfig };
+    const report = await tool.run(context, args);
+    printToolReport(report);
+}
+async function runAllTools(args) {
+    const tools = listCliTools();
+    const context = { cancerTreatment, oncologyService, serviceConfig };
+    const results = [];
+    for (const tool of tools) {
+        console.log(`\n${colors.cyan}Running tool: ${tool.id}${colors.reset}`);
+        const report = await tool.run(context, args);
+        results.push(report);
+        printToolReport(report);
+    }
+    const failures = results.filter(result => !result.ok).length;
+    const statusColor = failures === 0 ? colors.green : colors.yellow;
+    console.log(`\n${statusColor}All tools complete: ${results.length} run, ${failures} failed.${colors.reset}`);
+}
+function printToolReport(report) {
+    const statusLabel = report.ok ? `${colors.green}OK${colors.reset}` : `${colors.red}FAIL${colors.reset}`;
+    console.log(`\n${colors.bold}Tool Report${colors.reset}`);
+    console.log(`${colors.dim}─────────────────────────────${colors.reset}`);
+    console.log(`  Tool:      ${report.toolId}`);
+    console.log(`  Status:    ${statusLabel}`);
+    console.log(`  Summary:   ${report.summary}`);
+    console.log(`  Duration:  ${report.durationMs}ms`);
+    if (report.checks && report.checks.length > 0) {
+        console.log(`\n${colors.bold}Checks${colors.reset}`);
+        report.checks.forEach(check => {
+            const icon = check.ok ? `${colors.green}✓${colors.reset}` : `${colors.red}✗${colors.reset}`;
+            const detail = check.detail ? ` ${colors.dim}${check.detail}${colors.reset}` : '';
+            console.log(`  ${icon} ${check.name}${detail}`);
+        });
+    }
+    if (report.metrics && Object.keys(report.metrics).length > 0) {
+        console.log(`\n${colors.bold}Metrics${colors.reset}`);
+        Object.entries(report.metrics).forEach(([key, value]) => {
+            console.log(`  ${colors.cyan}${key}${colors.reset}: ${value}`);
+        });
+    }
+}
 async function runDemo() {
     console.log(`\n${colors.cyan}Running framework demo...${colors.reset}\n`);
     try {
@@ -1013,6 +1094,23 @@ async function handleCommand(args) {
     else if (args.includes('--status')) {
         await showSystemStatus();
     }
+    else if (args.includes('--tools')) {
+        printToolList();
+    }
+    else if (args.some(arg => arg.startsWith('--tool='))) {
+        const toolId = args.find(arg => arg.startsWith('--tool='))?.split('=')[1];
+        if (!toolId) {
+            console.log(`${colors.red}Missing tool id.${colors.reset} Use --tool=<id>.`);
+            process.exit(1);
+        }
+        await runTool(toolId, []);
+    }
+    else if (args.includes('--selftest')) {
+        await runTool('selftest', []);
+    }
+    else if (args.includes('--validate')) {
+        await runTool('validate', []);
+    }
     else if (args.includes('--demo')) {
         await runDemo();
     }
@@ -1054,6 +1152,14 @@ ${colors.dim}──────────────────────
   ${colors.cyan}/predict${colors.reset} [patient]       ML outcome predictions
   ${colors.cyan}/status${colors.reset}                  System health check
 
+${colors.bold}Tools${colors.reset}
+${colors.dim}─────────────────────────────────────${colors.reset}
+  ${colors.cyan}/tools${colors.reset}                   List diagnostic tools
+  ${colors.cyan}/tool${colors.reset} <id>               Run a tool (see /tools)
+  ${colors.cyan}/tool${colors.reset} all                Run all tools
+  ${colors.cyan}/selftest${colors.reset}                Run core capability checks
+  ${colors.cyan}/validate${colors.reset}                Run retrospective validation
+
 ${colors.bold}Integrations${colors.reset}
 ${colors.dim}─────────────────────────────────────${colors.reset}
   ${colors.cyan}/ehr${colors.reset} [connect|status]    EHR integration (Epic/Cerner)
@@ -1113,6 +1219,10 @@ ${colors.bold}Commands:${colors.reset}
   --safety                Check drug interactions
   --predict               ML outcome predictions
   --status                System health check
+  --tools                 List diagnostic tools
+  --tool=<id>             Run a tool (use --tools to list, or --tool=all)
+  --selftest              Run core capability checks
+  --validate              Run retrospective validation
   --demo                  Run framework demo
   --help, -h              Show this help
   --version, -v           Show version
@@ -1127,6 +1237,7 @@ ${colors.bold}Options:${colors.reset}
   --mutations=<list>      Comma-separated mutations
   --biomarkers=<list>     Comma-separated biomarkers
   --drugs=<list>          Comma-separated drug names
+  --tool=<id>             Tool ID (use --tool=all to run all tools)
 
 ${colors.bold}Environment:${colors.reset}
   AI_PROVIDER             AI provider: 'xai' or 'openai' (default: xai)
@@ -1143,6 +1254,8 @@ ${colors.bold}Examples:${colors.reset}
   cure --safety --drugs=pembrolizumab,ipilimumab
   cure --analyze-patient --patient=P001 --genomics
   cure --drug-discovery --target=BRAF --cancer=Melanoma
+  cure --selftest
+  cure --tool=all
 
 ${colors.bold}Integrated Systems:${colors.reset}
   • EHR: Epic, Cerner (HL7 FHIR R4)