@erosolaraijs/cure 1.0.2 → 1.0.4

package/dist/index.js

@@ -0,0 +1,96 @@
+/**
+ * AGI Core - Cure Cancer
+ *
+ * ██████╗██╗   ██╗██████╗ ███████╗     ██████╗ █████╗ ███╗   ██╗ ██████╗███████╗██████╗
+ * ██╔════╝██║   ██║██╔══██╗██╔════╝    ██╔════╝██╔══██╗████╗  ██║██╔════╝██╔════╝██╔══██╗
+ * ██║     ██║   ██║██████╔╝█████╗      ██║     ███████║██╔██╗ ██║██║     █████╗  ██████╔╝
+ * ██║     ██║   ██║██╔══██╗██╔══╝      ██║     ██╔══██║██║╚██╗██║██║     ██╔══╝  ██╔══██╗
+ * ╚██████╗╚██████╔╝██║  ██║███████╗    ╚██████╗██║  ██║██║ ╚████║╚██████╗███████╗██║  ██║
+ *  ╚═════╝ ╚═════╝ ╚═╝  ╚═╝╚══════╝     ╚═════╝╚═╝  ╚═╝╚═╝  ╚═══╝ ╚═════╝╚══════╝╚═╝  ╚═╝
+ *
+ * Comprehensive AI-powered precision oncology platform connecting:
+ * - Real genomic sequencing data (Foundation Medicine, Guardant, Tempus)
+ * - Hospital EHR systems (Epic, Cerner via HL7 FHIR)
+ * - Clinical trial registries (ClinicalTrials.gov)
+ * - HIPAA-compliant data handling
+ * - ML-powered outcome prediction
+ * - Drug safety and interaction checking
+ * - Clinician decision support
+ * - Patient portal interfaces
+ *
+ * @packageDocumentation
+ */
+// ═══════════════════════════════════════════════════════════════════════════════
+// CORE CAPABILITIES
+// ═══════════════════════════════════════════════════════════════════════════════
+export { CancerTreatmentCapabilityModule } from './capabilities/cancerTreatmentCapability.js';
+// ═══════════════════════════════════════════════════════════════════════════════
+// REAL-WORLD ORCHESTRATION
+// ═══════════════════════════════════════════════════════════════════════════════
+import { RealWorldOncologyService as RWOService, createRealWorldOncologyService as createRWOService } from './orchestrator/realWorldOncology.js';
+export { RWOService as RealWorldOncologyService, createRWOService as createRealWorldOncologyService };
+// ═══════════════════════════════════════════════════════════════════════════════
+// INTEGRATIONS
+// ═══════════════════════════════════════════════════════════════════════════════
+// EHR Integration (HL7 FHIR)
+export { FHIRClient, EpicFHIRClient, CernerFHIRClient, createFHIRClient } from './integrations/ehr/index.js';
+// Genomic Platforms
+export { FoundationMedicineClient, GuardantHealthClient, TempusClient, UnifiedGenomicsService, createGenomicClient } from './integrations/genomics/index.js';
+// Clinical Trials
+export { ClinicalTrialsGovClient } from './integrations/clinicalTrials/index.js';
+// ═══════════════════════════════════════════════════════════════════════════════
+// COMPLIANCE
+// ═══════════════════════════════════════════════════════════════════════════════
+export { HIPAAComplianceService } from './compliance/index.js';
+// ═══════════════════════════════════════════════════════════════════════════════
+// MACHINE LEARNING
+// ═══════════════════════════════════════════════════════════════════════════════
+export { OutcomePredictorService } from './ml/index.js';
+// ═══════════════════════════════════════════════════════════════════════════════
+// SAFETY
+// ═══════════════════════════════════════════════════════════════════════════════
+export { DrugSafetyService } from './safety/index.js';
+// ═══════════════════════════════════════════════════════════════════════════════
+// VALIDATION
+// ═══════════════════════════════════════════════════════════════════════════════
+export { RetrospectiveValidationService } from './validation/index.js';
+// ═══════════════════════════════════════════════════════════════════════════════
+// CLINICIAN SUPPORT
+// ═══════════════════════════════════════════════════════════════════════════════
+export { ClinicalDecisionSupportService } from './clinician/index.js';
+// ═══════════════════════════════════════════════════════════════════════════════
+// PATIENT PORTAL
+// ═══════════════════════════════════════════════════════════════════════════════
+export { PatientPortalService } from './patient/index.js';
+// ═══════════════════════════════════════════════════════════════════════════════
+// QUICK START FACTORY
+// ═══════════════════════════════════════════════════════════════════════════════
+/**
+ * Quick start factory to create a fully configured oncology service
+ *
+ * @example
+ * ```typescript
+ * import { createOncologyPlatform } from 'agi-core-cure-cancer';
+ *
+ * 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']
+ *   }
+ * });
+ *
+ * const plan = await platform.generateComprehensivePlan(patient, 'DR001');
+ * ```
+ */
+export async function createOncologyPlatform(config) {
+    const service = createRWOService(config);
+    await service.initialize();
+    return service;
+}
+//# sourceMappingURL=index.js.map

package/dist/index.js.map

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package/dist/integrations/clinicalTrials/index.d.ts

@@ -1,5 +1,5 @@
 /**
  * Clinical Trials Integration Module Exports
  */
-export { ClinicalTrialsGovClient, PatientTrialMatcher, type ClinicalTrial, type TrialLocation, type TrialEligibility, type PatientTrialMatch, type TrialSearchCriteria, type ClinicalTrialsConfig } from './clinicalTrialsGov.js';
+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';
 //# sourceMappingURL=index.d.ts.map

package/dist/integrations/clinicalTrials/index.d.ts.map

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package/dist/integrations/clinicalTrials/index.js

@@ -1,5 +1,5 @@
 /**
  * Clinical Trials Integration Module Exports
  */
-export { ClinicalTrialsGovClient, PatientTrialMatcher } from './clinicalTrialsGov.js';
+export { ClinicalTrialsGovClient } from './clinicalTrialsGov.js';
 //# sourceMappingURL=index.js.map

package/dist/integrations/clinicalTrials/index.js.map

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package/dist/integrations/ehr/index.d.ts

@@ -1,5 +1,5 @@
 /**
  * EHR Integration Module Exports
  */
-export { FHIRClient, EpicAdapter, CernerAdapter, FHIRPatientSummary, CancerDiagnosis, CancerBiomarkers, TreatmentHistory, type FHIRConfig, type FHIRResource, type FHIRPatient, type FHIRObservation, type FHIRCondition, type FHIRMedicationRequest, type FHIRProcedure, type FHIRDiagnosticReport } from './fhir.js';
+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';
 //# sourceMappingURL=index.d.ts.map

package/dist/integrations/ehr/index.d.ts.map

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package/dist/integrations/ehr/index.js

@@ -1,5 +1,5 @@
 /**
  * EHR Integration Module Exports
  */
-export { FHIRClient, EpicAdapter, CernerAdapter, FHIRPatientSummary } from './fhir.js';
+export { FHIRClient, EpicFHIRClient, CernerFHIRClient, createFHIRClient } from './fhir.js';
 //# sourceMappingURL=index.js.map

package/dist/integrations/ehr/index.js.map

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package/dist/integrations/genomics/index.d.ts

@@ -1,5 +1,5 @@
 /**
  * Genomic Platform Integration Module Exports
  */
-export { FoundationMedicineClient, GuardantHealthClient, TempusClient, UnifiedGenomicsService, type GenomicVariant, type CopyNumberAlteration, type GeneFusion, type GenomicReport, type TherapyMatch, type GenomicPlatformConfig } from './genomicPlatforms.js';
+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';
 //# sourceMappingURL=index.d.ts.map

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package/dist/integrations/genomics/index.js

@@ -1,5 +1,5 @@
 /**
  * Genomic Platform Integration Module Exports
  */
-export { FoundationMedicineClient, GuardantHealthClient, TempusClient, UnifiedGenomicsService } from './genomicPlatforms.js';
+export { FoundationMedicineClient, GuardantHealthClient, TempusClient, UnifiedGenomicsService, createGenomicClient } from './genomicPlatforms.js';
 //# sourceMappingURL=index.js.map

package/dist/integrations/genomics/index.js.map

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package/dist/ml/index.d.ts

@@ -1,5 +1,5 @@
 /**
  * Machine Learning Module Exports
  */
-export { OutcomePredictionService, ResponsePredictor, SurvivalPredictor, ToxicityPredictor, ResistancePredictor, TherapyRanker, type PredictionInput, type ResponsePrediction, type SurvivalPrediction, type ToxicityPrediction, type ResistancePrediction, type TherapyRanking, type ModelMetadata, type MLConfig } from './outcomePredictor.js';
+export { OutcomePredictorService, type PatientFeatures, type TreatmentFeatures, type ResponsePrediction, type SurvivalPrediction, type ToxicityPrediction, type ResistancePrediction, type TherapyRanking, type MLModel, type ModelRegistry } from './outcomePredictor.js';
 //# sourceMappingURL=index.d.ts.map

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package/dist/ml/index.js

@@ -1,5 +1,5 @@
 /**
  * Machine Learning Module Exports
  */
-export { OutcomePredictionService, ResponsePredictor, SurvivalPredictor, ToxicityPredictor, ResistancePredictor, TherapyRanker } from './outcomePredictor.js';
+export { OutcomePredictorService } from './outcomePredictor.js';
 //# sourceMappingURL=index.js.map

package/dist/ml/index.js.map

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package/dist/orchestrator/index.d.ts

@@ -0,0 +1,5 @@
+/**
+ * Orchestrator Module - Real-World Oncology Service
+ */
+export { RealWorldOncologyService, createRealWorldOncologyService, type RealWorldConfig, type RealWorldPatient, type ComprehensiveTreatmentPlan, type TreatmentOutcome } from './realWorldOncology.js';
+//# sourceMappingURL=index.d.ts.map

package/dist/orchestrator/index.d.ts.map

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package/dist/orchestrator/index.js

@@ -0,0 +1,5 @@
+/**
+ * Orchestrator Module - Real-World Oncology Service
+ */
+export { RealWorldOncologyService, createRealWorldOncologyService } from './realWorldOncology.js';
+//# sourceMappingURL=index.js.map

package/dist/orchestrator/index.js.map

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package/dist/orchestrator/realWorldOncology.d.ts

@@ -0,0 +1,351 @@
+/**
+ * Real-World Oncology Orchestration Service
+ *
+ * ██████╗ ███████╗ █████╗ ██╗         ██╗    ██╗ ██████╗ ██████╗ ██╗     ██████╗
+ * ██╔══██╗██╔════╝██╔══██╗██║         ██║    ██║██╔═══██╗██╔══██╗██║     ██╔══██╗
+ * ██████╔╝█████╗  ███████║██║         ██║ █╗ ██║██║   ██║██████╔╝██║     ██║  ██║
+ * ██╔══██╗██╔══╝  ██╔══██║██║         ██║███╗██║██║   ██║██╔══██╗██║     ██║  ██║
+ * ██║  ██║███████╗██║  ██║███████╗    ╚███╔███╔╝╚██████╔╝██║  ██║███████╗██████╔╝
+ * ╚═╝  ╚═╝╚══════╝╚═╝  ╚═╝╚══════╝     ╚══╝╚══╝  ╚═════╝ ╚═╝  ╚═╝╚══════╝╚═════╝
+ *  ██████╗ ███╗   ██╗ ██████╗ ██████╗ ██╗      ██████╗  ██████╗██╗   ██╗
+ * ██╔═══██╗████╗  ██║██╔════╝██╔═══██╗██║     ██╔═══██╗██╔════╝╚██╗ ██╔╝
+ * ██║   ██║██╔██╗ ██║██║     ██║   ██║██║     ██║   ██║██║  ███╗╚████╔╝
+ * ██║   ██║██║╚██╗██║██║     ██║   ██║██║     ██║   ██║██║   ██║ ╚██╔╝
+ * ╚██████╔╝██║ ╚████║╚██████╗╚██████╔╝███████╗╚██████╔╝╚██████╔╝  ██║
+ *  ╚═════╝ ╚═╝  ╚═══╝ ╚═════╝ ╚═════╝ ╚══════╝ ╚═════╝  ╚═════╝   ╚═╝
+ *
+ * This service orchestrates all components of the real-world precision oncology system:
+ * - EHR Integration (Epic, Cerner via HL7 FHIR)
+ * - Genomic Platforms (Foundation Medicine, Guardant Health, Tempus)
+ * - Clinical Trials (ClinicalTrials.gov)
+ * - HIPAA Compliance (Audit, Consent, Encryption, Access Control)
+ * - ML Outcome Prediction (Response, Survival, Toxicity, Resistance)
+ * - Drug Safety (Interactions, Contraindications, Pharmacogenomics)
+ * - Validation Framework (Retrospective validation, Concordance analysis)
+ * - Clinician Decision Support (Recommendations, Overrides, Tumor Board)
+ * - Patient Portal (Symptoms, Adherence, QoL, Messaging)
+ */
+import { CancerCureResult } from '../capabilities/cancerTreatmentCapability.js';
+export interface RealWorldConfig {
+    ehr: {
+        enabled: boolean;
+        vendor: 'epic' | 'cerner' | 'other';
+        baseUrl: string;
+        clientId: string;
+        clientSecret?: string;
+    };
+    genomics: {
+        enabled: boolean;
+        platforms: ('foundation' | 'guardant' | 'tempus')[];
+    };
+    clinicalTrials: {
+        enabled: boolean;
+        maxDistance?: number;
+    };
+    compliance: {
+        enabled: boolean;
+        encryptionKey?: string;
+        auditRetentionDays: number;
+    };
+    ml: {
+        enabled: boolean;
+        modelVersion: string;
+    };
+    safety: {
+        enabled: boolean;
+        strictMode: boolean;
+    };
+}
+export interface RealWorldPatient {
+    id: string;
+    mrn?: string;
+    demographics: {
+        firstName: string;
+        lastName: string;
+        dateOfBirth: Date;
+        gender: 'male' | 'female' | 'other';
+        ethnicity?: string;
+        address?: {
+            city: string;
+            state: string;
+            zipCode: string;
+            country: string;
+        };
+    };
+    diagnosis: {
+        cancerType: string;
+        stage: string;
+        diagnosisDate: Date;
+        histology?: string;
+        grade?: string;
+        primarySite?: string;
+        metastaticSites?: string[];
+    };
+    genomics?: {
+        testDate?: Date;
+        platform?: string;
+        mutations: string[];
+        biomarkers: Record<string, any>;
+        msiStatus?: 'MSI-H' | 'MSS';
+        tmbLevel?: 'High' | 'Low';
+        tmbValue?: number;
+        pdl1Expression?: number;
+        hrdStatus?: boolean;
+        hrdScore?: number;
+    };
+    treatments?: {
+        treatmentId: string;
+        regimen: string;
+        startDate: Date;
+        endDate?: Date;
+        response?: 'CR' | 'PR' | 'SD' | 'PD';
+        discontinuationReason?: string;
+    }[];
+    medications?: {
+        name: string;
+        dose: string;
+        frequency: string;
+        startDate: Date;
+    }[];
+    comorbidities?: string[];
+    allergies?: string[];
+    performanceStatus?: 0 | 1 | 2 | 3 | 4;
+    labValues?: {
+        testName: string;
+        value: number;
+        unit: string;
+        date: Date;
+        isAbnormal: boolean;
+    }[];
+}
+export interface ComprehensiveTreatmentPlan {
+    patientId: string;
+    planId: string;
+    createdAt: Date;
+    createdBy: string;
+    coreRecommendation: CancerCureResult;
+    ehrData?: {
+        source: string;
+        lastSync: Date;
+        patientSummary: any;
+    };
+    genomicData?: {
+        platforms: string[];
+        lastUpdated: Date;
+        unifiedReport: any;
+        therapyMatches: any[];
+    };
+    clinicalTrials?: {
+        matchingTrials: {
+            nctId: string;
+            title: string;
+            phase: string;
+            eligibilityScore: number;
+            distance?: number;
+        }[];
+        searchDate: Date;
+    };
+    predictions?: {
+        responseProb: {
+            CR: number;
+            PR: number;
+            SD: number;
+            PD: number;
+        };
+        survivalEstimates: {
+            pfs: {
+                median: number;
+                ci95: [number, number];
+            };
+            os: {
+                median: number;
+                ci95: [number, number];
+            };
+        };
+        toxicityRisks: {
+            toxicity: string;
+            grade34Risk: number;
+            mitigationStrategy: string;
+        }[];
+        resistancePrediction: {
+            mechanism: string;
+            probability: number;
+            timeToResistance?: number;
+        }[];
+    };
+    safetyAssessment?: {
+        interactions: {
+            drug1: string;
+            drug2: string;
+            severity: 'major' | 'moderate' | 'minor';
+            description: string;
+        }[];
+        contraindications: {
+            drug: string;
+            reason: string;
+            severity: 'absolute' | 'relative';
+        }[];
+        pharmacogenomics: {
+            gene: string;
+            variant: string;
+            implication: string;
+            recommendation: string;
+        }[];
+        overallSafetyScore: number;
+    };
+    decisionSupport?: {
+        evidenceLevel: 'Category 1' | 'Category 2A' | 'Category 2B' | 'Category 3';
+        guidelines: string[];
+        alternativeOptions: {
+            regimen: string;
+            rationale: string;
+            tradeoffs: string;
+        }[];
+        tumorBoardRequired: boolean;
+    };
+    patientSummary?: {
+        treatmentGoal: string;
+        whatToExpect: string;
+        sideEffectsToWatch: string[];
+        questionsForDoctor: string[];
+        supportResources: string[];
+    };
+    compliance?: {
+        consentStatus: 'obtained' | 'pending' | 'declined';
+        consentDate?: Date;
+        auditLogId: string;
+        accessLog: {
+            userId: string;
+            action: string;
+            timestamp: Date;
+        }[];
+    };
+    status: 'draft' | 'pending_review' | 'approved' | 'active' | 'completed' | 'discontinued';
+    approvedBy?: string;
+    approvedAt?: Date;
+}
+export interface TreatmentOutcome {
+    patientId: string;
+    planId: string;
+    response: {
+        assessmentDate: Date;
+        recistResponse: 'CR' | 'PR' | 'SD' | 'PD';
+        targetLesions: {
+            lesionId: string;
+            baselineSize: number;
+            currentSize: number;
+            percentChange: number;
+        }[];
+        newLesions: boolean;
+    };
+    survival: {
+        progressionDate?: Date;
+        deathDate?: Date;
+        lastFollowUpDate: Date;
+        pfsMonths?: number;
+        osMonths?: number;
+    };
+    toxicities: {
+        toxicityType: string;
+        grade: 1 | 2 | 3 | 4 | 5;
+        onsetDate: Date;
+        resolvedDate?: Date;
+        interventionRequired: boolean;
+        doseModification: 'none' | 'reduction' | 'delay' | 'discontinuation';
+    }[];
+    qualityOfLife: {
+        assessmentDate: Date;
+        instrument: 'FACT-G' | 'EORTC-QLQ-C30' | 'PRO-CTCAE' | 'other';
+        totalScore: number;
+        domainScores: Record<string, number>;
+    }[];
+    adherence: {
+        overallAdherence: number;
+        missedDoses: number;
+        reasonsForMissing: string[];
+    };
+}
+export declare class RealWorldOncologyService {
+    private config;
+    private cancerCapability;
+    private ehrService;
+    private genomicsService;
+    private trialsService;
+    private complianceService;
+    private mlService;
+    private safetyService;
+    private validationService;
+    private decisionSupportService;
+    private patientPortalService;
+    constructor(config?: Partial<RealWorldConfig>);
+    private mergeDefaultConfig;
+    /**
+     * Initialize all enabled services
+     */
+    initialize(): Promise<void>;
+    private initializeEHR;
+    private initializeGenomics;
+    private initializeClinicalTrials;
+    private initializeCompliance;
+    private initializeML;
+    private initializeSafety;
+    /**
+     * Generate a comprehensive treatment plan for a patient
+     */
+    generateComprehensivePlan(patient: RealWorldPatient, clinicianId: string, options?: {
+        includeTrials?: boolean;
+        includePredictions?: boolean;
+        includeSafetyCheck?: boolean;
+        requireTumorBoard?: boolean;
+    }): Promise<ComprehensiveTreatmentPlan>;
+    /**
+     * Record treatment outcome for validation
+     */
+    recordOutcome(outcome: TreatmentOutcome): Promise<void>;
+    /**
+     * Validate system predictions against actual outcomes
+     */
+    runValidation(cohortCriteria: {
+        cancerTypes?: string[];
+        stages?: string[];
+        dateRange?: {
+            start: Date;
+            end: Date;
+        };
+        minPatients?: number;
+    }): Promise<{
+        cohortSize: number;
+        concordanceRate: number;
+        responseAUC: number;
+        survivalCIndex: number;
+        calibrationError: number;
+        subgroupResults: Record<string, any>;
+    }>;
+    private logAccess;
+    private fetchEHRData;
+    private aggregateGenomicData;
+    private findMatchingTrials;
+    private generatePredictions;
+    private performSafetyAssessment;
+    private generateDecisionSupport;
+    private createPatientSummary;
+    /**
+     * Convert internal patient type to CancerPatient for the capability module
+     */
+    private toCancerPatient;
+    private calculateAge;
+    /**
+     * Get system status and health check
+     */
+    getSystemStatus(): Promise<{
+        status: 'healthy' | 'degraded' | 'unhealthy';
+        services: Record<string, {
+            status: string;
+            latency?: number;
+        }>;
+        lastValidation?: Date;
+        modelVersion: string;
+    }>;
+}
+export declare function createRealWorldOncologyService(config?: Partial<RealWorldConfig>): RealWorldOncologyService;
+//# sourceMappingURL=realWorldOncology.d.ts.map

package/dist/orchestrator/realWorldOncology.d.ts.map

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