@ottolab/shared 0.1.0 → 0.1.1

package/dist/constants/biomarker-ranges.d.ts

@@ -0,0 +1,20 @@
+export interface BiomarkerRange {
+    low: number;
+    high: number;
+    unit: string;
+    criticalLow?: number;
+    criticalHigh?: number;
+    optimalLow?: number;
+    optimalHigh?: number;
+    lowerIsBetter?: boolean;
+    bidirectional?: boolean;
+}
+/**
+ * Clinical reference ranges for all target biomarkers.
+ * Sources: AHA/ACC, ADA, AACE, KDIGO guidelines + prototype report thresholds.
+ *
+ * Convention: "low"/"high" = normal range. "optimalLow"/"optimalHigh" = tighter optimal range.
+ * "criticalLow"/"criticalHigh" = red-flag values requiring immediate attention.
+ */
+export declare const BIOMARKER_RANGES: Record<string, BiomarkerRange>;
+//# sourceMappingURL=biomarker-ranges.d.ts.map

package/dist/constants/biomarker-ranges.d.ts.map

@@ -0,0 +1 @@
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package/dist/constants/biomarker-ranges.js

@@ -0,0 +1,311 @@
+/**
+ * Clinical reference ranges for all target biomarkers.
+ * Sources: AHA/ACC, ADA, AACE, KDIGO guidelines + prototype report thresholds.
+ *
+ * Convention: "low"/"high" = normal range. "optimalLow"/"optimalHigh" = tighter optimal range.
+ * "criticalLow"/"criticalHigh" = red-flag values requiring immediate attention.
+ */
+export const BIOMARKER_RANGES = {
+    // ── Lipids (mg/dL) ───────────────────────────────────────
+    total_cholesterol: {
+        low: 125,
+        high: 200,
+        unit: 'mg/dL',
+        optimalHigh: 200,
+        criticalHigh: 240,
+        lowerIsBetter: true,
+    },
+    ldl_c: {
+        low: 0,
+        high: 100,
+        unit: 'mg/dL',
+        optimalHigh: 100,
+        criticalHigh: 160,
+        lowerIsBetter: true,
+    },
+    hdl: {
+        low: 40,
+        high: 100,
+        unit: 'mg/dL',
+        optimalLow: 60,
+        criticalLow: 40,
+    },
+    triglycerides: {
+        low: 0,
+        high: 150,
+        unit: 'mg/dL',
+        optimalHigh: 100,
+        criticalHigh: 500,
+        lowerIsBetter: true,
+    },
+    apoB: {
+        low: 0,
+        high: 90,
+        unit: 'mg/dL',
+        optimalHigh: 80,
+        criticalHigh: 120,
+        lowerIsBetter: true,
+    },
+    // ── Metabolic ─────────────────────────────────────────────
+    hba1c: {
+        low: 4.0,
+        high: 5.7,
+        unit: '%',
+        optimalHigh: 5.4,
+        criticalHigh: 6.5,
+        lowerIsBetter: true,
+    },
+    fasting_glucose: {
+        low: 65,
+        high: 100,
+        unit: 'mg/dL',
+        optimalLow: 65,
+        optimalHigh: 90,
+        criticalHigh: 126,
+        lowerIsBetter: true,
+    },
+    fasting_insulin: {
+        low: 2,
+        high: 25,
+        unit: 'uIU/mL',
+        optimalHigh: 6,
+        criticalHigh: 25,
+        lowerIsBetter: true,
+    },
+    homa_ir: {
+        low: 0,
+        high: 1.0,
+        unit: '',
+        criticalHigh: 2.5,
+        lowerIsBetter: true,
+    },
+    uric_acid: {
+        low: 2.5,
+        high: 7.0,
+        unit: 'mg/dL',
+        optimalHigh: 5.0,
+        criticalHigh: 9.0,
+        lowerIsBetter: true,
+    },
+    // ── Kidney ────────────────────────────────────────────────
+    creatinine: {
+        low: 0.5,
+        high: 1.1,
+        unit: 'mg/dL',
+        criticalHigh: 1.3,
+        lowerIsBetter: true,
+    },
+    bun: {
+        low: 7,
+        high: 20,
+        unit: 'mg/dL',
+        criticalHigh: 30,
+        lowerIsBetter: true,
+    },
+    egfr: {
+        low: 90,
+        high: 120,
+        unit: 'mL/min/1.73m2',
+        criticalLow: 60,
+    },
+    // ── Liver ─────────────────────────────────────────────────
+    alt: {
+        low: 7,
+        high: 35,
+        unit: 'U/L',
+        optimalHigh: 30,
+        criticalHigh: 50,
+        lowerIsBetter: true,
+    },
+    ast: {
+        low: 10,
+        high: 35,
+        unit: 'U/L',
+        optimalHigh: 30,
+        criticalHigh: 50,
+        lowerIsBetter: true,
+    },
+    alp: {
+        low: 44,
+        high: 147,
+        unit: 'U/L',
+        criticalHigh: 200,
+    },
+    ggt: {
+        low: 9,
+        high: 48,
+        unit: 'U/L',
+        criticalHigh: 80,
+        lowerIsBetter: true,
+    },
+    bilirubin_total: {
+        low: 0.1,
+        high: 1.2,
+        unit: 'mg/dL',
+        criticalHigh: 2.0,
+    },
+    albumin: {
+        low: 3.5,
+        high: 5.5,
+        unit: 'g/dL',
+        criticalLow: 3.0,
+    },
+    // ── Inflammatory ──────────────────────────────────────────
+    hs_crp: {
+        low: 0,
+        high: 1.0,
+        unit: 'mg/L',
+        optimalHigh: 1.0,
+        criticalHigh: 3.0,
+        lowerIsBetter: true,
+    },
+    esr: {
+        low: 0,
+        high: 20,
+        unit: 'mm/hr',
+        criticalHigh: 40,
+        lowerIsBetter: true,
+    },
+    // ── Hormones ──────────────────────────────────────────────
+    cortisol: {
+        low: 6,
+        high: 18,
+        unit: 'ug/dL',
+        criticalHigh: 23,
+        lowerIsBetter: true,
+    },
+    testosterone: {
+        low: 300,
+        high: 1000,
+        unit: 'ng/dL',
+        optimalLow: 500,
+        criticalLow: 300,
+    },
+    estradiol: {
+        low: 15,
+        high: 350,
+        unit: 'pg/mL',
+        bidirectional: true,
+    },
+    tsh: {
+        low: 0.5,
+        high: 4.5,
+        unit: 'mIU/L',
+        optimalLow: 0.5,
+        optimalHigh: 2.5,
+        criticalLow: 0.3,
+        criticalHigh: 10,
+        bidirectional: true,
+    },
+    // ── Hematology ────────────────────────────────────────────
+    wbc: {
+        low: 4.5,
+        high: 11.0,
+        unit: '10^3/uL',
+        criticalLow: 3.0,
+        criticalHigh: 15.0,
+        bidirectional: true,
+    },
+    rbc: {
+        low: 4.0,
+        high: 5.5,
+        unit: '10^6/uL',
+        criticalLow: 3.5,
+        criticalHigh: 6.0,
+        bidirectional: true,
+    },
+    hemoglobin: {
+        low: 12.0,
+        high: 17.5,
+        unit: 'g/dL',
+        criticalLow: 10.0,
+        bidirectional: true,
+    },
+    hematocrit: {
+        low: 36,
+        high: 52,
+        unit: '%',
+        criticalLow: 30,
+        bidirectional: true,
+    },
+    platelets: {
+        low: 150,
+        high: 400,
+        unit: '10^3/uL',
+        criticalLow: 100,
+        criticalHigh: 500,
+        bidirectional: true,
+    },
+    mcv: {
+        low: 80,
+        high: 100,
+        unit: 'fL',
+        criticalLow: 70,
+        criticalHigh: 110,
+        bidirectional: true,
+    },
+    rdw: {
+        low: 11.5,
+        high: 14.5,
+        unit: '%',
+        criticalHigh: 17.0,
+        lowerIsBetter: true,
+    },
+    lymphocyte_percent: {
+        low: 20,
+        high: 40,
+        unit: '%',
+        criticalLow: 15,
+        criticalHigh: 50,
+        bidirectional: true,
+    },
+    // ── Vitamins ──────────────────────────────────────────────
+    vitamin_d: {
+        low: 30,
+        high: 100,
+        unit: 'ng/mL',
+        optimalLow: 40,
+        optimalHigh: 80,
+        criticalLow: 20,
+    },
+    // ── Vitals ────────────────────────────────────────────────
+    weight: { low: 40, high: 150, unit: 'kg' },
+    height: { low: 140, high: 210, unit: 'cm' },
+    bmi: {
+        low: 18.5,
+        high: 24.9,
+        unit: 'kg/m2',
+        criticalHigh: 30,
+        lowerIsBetter: true,
+    },
+    body_fat_percent: {
+        low: 8,
+        high: 25,
+        unit: '%',
+        criticalHigh: 35,
+        lowerIsBetter: true,
+    },
+    systolic_bp: {
+        low: 90,
+        high: 120,
+        unit: 'mmHg',
+        criticalHigh: 140,
+        lowerIsBetter: true,
+    },
+    diastolic_bp: {
+        low: 60,
+        high: 80,
+        unit: 'mmHg',
+        criticalHigh: 90,
+        lowerIsBetter: true,
+    },
+    heart_rate: {
+        low: 50,
+        high: 100,
+        unit: 'bpm',
+        optimalLow: 50,
+        optimalHigh: 70,
+        bidirectional: true,
+    },
+};
+//# sourceMappingURL=biomarker-ranges.js.map

package/dist/constants/biomarker-ranges.js.map

@@ -0,0 +1 @@
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package/dist/constants/drug-data.d.ts

@@ -0,0 +1,5 @@
+export declare const DRUG_DATA: Record<string, {
+    name: string;
+    category: string;
+}>;
+//# sourceMappingURL=drug-data.d.ts.map

package/dist/constants/drug-data.d.ts.map

@@ -0,0 +1 @@
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package/dist/constants/drug-data.js

@@ -0,0 +1,3 @@
+// Drug interaction and protocol data — populated in Phase 5
+export const DRUG_DATA = {};
+//# sourceMappingURL=drug-data.js.map

package/dist/constants/drug-data.js.map

@@ -0,0 +1 @@
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package/dist/constants/unit-conversions.d.ts

@@ -0,0 +1,6 @@
+export declare const UNIT_CONVERSIONS: Record<string, {
+    fromUnit: string;
+    toUnit: string;
+    factor: number;
+}>;
+//# sourceMappingURL=unit-conversions.d.ts.map

package/dist/constants/unit-conversions.d.ts.map

@@ -0,0 +1 @@
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package/dist/constants/unit-conversions.js

@@ -0,0 +1,15 @@
+export const UNIT_CONVERSIONS = {
+    total_cholesterol: { fromUnit: 'mmol/L', toUnit: 'mg/dL', factor: 38.67 },
+    ldl_c: { fromUnit: 'mmol/L', toUnit: 'mg/dL', factor: 38.67 },
+    hdl: { fromUnit: 'mmol/L', toUnit: 'mg/dL', factor: 38.67 },
+    triglycerides: { fromUnit: 'mmol/L', toUnit: 'mg/dL', factor: 88.57 },
+    fasting_glucose: { fromUnit: 'mmol/L', toUnit: 'mg/dL', factor: 18.016 },
+    creatinine: { fromUnit: 'umol/L', toUnit: 'mg/dL', factor: 1 / 88.401 },
+    uric_acid: { fromUnit: 'umol/L', toUnit: 'mg/dL', factor: 1 / 59.48 },
+    albumin: { fromUnit: 'g/L', toUnit: 'g/dL', factor: 0.1 },
+    hs_crp: { fromUnit: 'mg/dL', toUnit: 'mg/L', factor: 10 },
+    bilirubin_total: { fromUnit: 'umol/L', toUnit: 'mg/dL', factor: 1 / 17.1 },
+    bun: { fromUnit: 'mmol/L', toUnit: 'mg/dL', factor: 2.801 },
+    vitamin_d: { fromUnit: 'nmol/L', toUnit: 'ng/mL', factor: 1 / 2.496 },
+};
+//# sourceMappingURL=unit-conversions.js.map

package/dist/constants/unit-conversions.js.map

@@ -0,0 +1 @@
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package/dist/index.d.ts

@@ -0,0 +1,12 @@
+export type { User, UserStatus, Channel, ChannelIdentity } from './types/user.js';
+export type { BiomarkerValue, BiomarkerSet } from './types/biomarkers.js';
+export type { SourceLab, ExtractionResult, BioAgeResult, ReportCard, ReportHighlight, FlaggedBiomarker, LabReport, } from './types/lab-report.js';
+export type { ProtocolCategory, EvidenceLevel, Protocol, EvidenceReference, Recommendation, } from './types/recommendation.js';
+export type { SimulationInput, DailySnapshot, ModuleSummary, ModuleResult, BiomarkerDelta, SimulationResult, } from './types/simulation.js';
+export type { MessageRole, ConversationStatus, InboundMessage, OutboundMessage, Conversation, Message, } from './types/messaging.js';
+export type { ChatMessage, ContentPart, LLMOptions, LLMProvider, DocumentPart, ImagePart, TextPart, MultimodalPart, ExtendedLLMProvider, } from './types/llm.js';
+export { UNIT_CONVERSIONS } from './constants/unit-conversions.js';
+export { BIOMARKER_RANGES } from './constants/biomarker-ranges.js';
+export type { BiomarkerRange } from './constants/biomarker-ranges.js';
+export { DRUG_DATA } from './constants/drug-data.js';
+//# sourceMappingURL=index.d.ts.map

package/dist/index.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AACA,YAAY,EAAE,IAAI,EAAE,UAAU,EAAE,OAAO,EAAE,eAAe,EAAE,MAAM,iBAAiB,CAAC;AAClF,YAAY,EAAE,cAAc,EAAE,YAAY,EAAE,MAAM,uBAAuB,CAAC;AAC1E,YAAY,EACV,SAAS,EACT,gBAAgB,EAChB,YAAY,EACZ,UAAU,EACV,eAAe,EACf,gBAAgB,EAChB,SAAS,GACV,MAAM,uBAAuB,CAAC;AAC/B,YAAY,EACV,gBAAgB,EAChB,aAAa,EACb,QAAQ,EACR,iBAAiB,EACjB,cAAc,GACf,MAAM,2BAA2B,CAAC;AACnC,YAAY,EACV,eAAe,EACf,aAAa,EACb,aAAa,EACb,YAAY,EACZ,cAAc,EACd,gBAAgB,GACjB,MAAM,uBAAuB,CAAC;AAC/B,YAAY,EACV,WAAW,EACX,kBAAkB,EAClB,cAAc,EACd,eAAe,EACf,YAAY,EACZ,OAAO,GACR,MAAM,sBAAsB,CAAC;AAC9B,YAAY,EACV,WAAW,EACX,WAAW,EACX,UAAU,EACV,WAAW,EACX,YAAY,EACZ,SAAS,EACT,QAAQ,EACR,cAAc,EACd,mBAAmB,GACpB,MAAM,gBAAgB,CAAC;AAGxB,OAAO,EAAE,gBAAgB,EAAE,MAAM,iCAAiC,CAAC;AACnE,OAAO,EAAE,gBAAgB,EAAE,MAAM,iCAAiC,CAAC;AACnE,YAAY,EAAE,cAAc,EAAE,MAAM,iCAAiC,CAAC;AACtE,OAAO,EAAE,SAAS,EAAE,MAAM,0BAA0B,CAAC"}

package/dist/index.js

@@ -0,0 +1,5 @@
+// Constants
+export { UNIT_CONVERSIONS } from './constants/unit-conversions.js';
+export { BIOMARKER_RANGES } from './constants/biomarker-ranges.js';
+export { DRUG_DATA } from './constants/drug-data.js';
+//# sourceMappingURL=index.js.map

package/dist/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AA+CA,YAAY;AACZ,OAAO,EAAE,gBAAgB,EAAE,MAAM,iCAAiC,CAAC;AACnE,OAAO,EAAE,gBAAgB,EAAE,MAAM,iCAAiC,CAAC;AAEnE,OAAO,EAAE,SAAS,EAAE,MAAM,0BAA0B,CAAC"}

package/dist/types/biomarkers.d.ts

@@ -0,0 +1,54 @@
+export interface BiomarkerValue {
+    name: string;
+    value: number;
+    unit: string;
+    referenceRange?: {
+        low: number;
+        high: number;
+    };
+    flag?: 'low' | 'normal' | 'high' | 'critical';
+}
+export interface BiomarkerSet {
+    weight?: BiomarkerValue;
+    height?: BiomarkerValue;
+    bmi?: BiomarkerValue;
+    bodyFatPercent?: BiomarkerValue;
+    bloodPressureSystolic?: BiomarkerValue;
+    bloodPressureDiastolic?: BiomarkerValue;
+    heartRate?: BiomarkerValue;
+    totalCholesterol?: BiomarkerValue;
+    ldlC?: BiomarkerValue;
+    hdl?: BiomarkerValue;
+    triglycerides?: BiomarkerValue;
+    apoB?: BiomarkerValue;
+    hba1c?: BiomarkerValue;
+    fastingGlucose?: BiomarkerValue;
+    fastingInsulin?: BiomarkerValue;
+    homaIr?: BiomarkerValue;
+    uricAcid?: BiomarkerValue;
+    creatinine?: BiomarkerValue;
+    bun?: BiomarkerValue;
+    egfr?: BiomarkerValue;
+    alt?: BiomarkerValue;
+    ast?: BiomarkerValue;
+    alp?: BiomarkerValue;
+    ggt?: BiomarkerValue;
+    bilirubinTotal?: BiomarkerValue;
+    albumin?: BiomarkerValue;
+    hsCrp?: BiomarkerValue;
+    esr?: BiomarkerValue;
+    cortisol?: BiomarkerValue;
+    testosterone?: BiomarkerValue;
+    estradiol?: BiomarkerValue;
+    tsh?: BiomarkerValue;
+    wbc?: BiomarkerValue;
+    rbc?: BiomarkerValue;
+    hemoglobin?: BiomarkerValue;
+    hematocrit?: BiomarkerValue;
+    platelets?: BiomarkerValue;
+    mcv?: BiomarkerValue;
+    rdw?: BiomarkerValue;
+    lymphocytePercent?: BiomarkerValue;
+    vitaminD?: BiomarkerValue;
+}
+//# sourceMappingURL=biomarkers.d.ts.map

package/dist/types/biomarkers.d.ts.map

@@ -0,0 +1 @@
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package/dist/types/biomarkers.js

@@ -0,0 +1,2 @@
+export {};
+//# sourceMappingURL=biomarkers.js.map

package/dist/types/biomarkers.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"biomarkers.js","sourceRoot":"","sources":["../../src/types/biomarkers.ts"],"names":[],"mappings":""}

package/dist/types/lab-report.d.ts

@@ -0,0 +1,48 @@
+import type { BiomarkerSet } from './biomarkers.js';
+export type SourceLab = 'quest' | 'labcorp' | 'international' | 'unknown';
+export interface ExtractionResult {
+    biomarkers: BiomarkerSet;
+    sourceLab: SourceLab;
+    sourceLanguage: string;
+    confidence: number;
+}
+export interface BioAgeResult {
+    phenoAge: number;
+    delta: number;
+    mortalityScore: number;
+    isProxy: boolean;
+    kdmAge?: number;
+    kdmDelta?: number;
+}
+export interface ReportCard {
+    bioAge: BioAgeResult;
+    summary: string;
+    highlights: ReportHighlight[];
+    flaggedBiomarkers: FlaggedBiomarker[];
+}
+export interface ReportHighlight {
+    category: string;
+    status: 'good' | 'warning' | 'critical';
+    message: string;
+}
+export interface FlaggedBiomarker {
+    name: string;
+    value: number;
+    unit: string;
+    flag: 'low' | 'high' | 'critical';
+    message: string;
+}
+export interface LabReport {
+    id: string;
+    userId: string;
+    uploadedAt: Date;
+    sourceLab: SourceLab | null;
+    sourceLanguage: string;
+    rawFileUrl: string | null;
+    biomarkers: BiomarkerSet;
+    extractionConfidence: number | null;
+    bioAgeResult: BioAgeResult | null;
+    reportCard: ReportCard | null;
+    createdAt: Date;
+}
+//# sourceMappingURL=lab-report.d.ts.map

package/dist/types/lab-report.d.ts.map

@@ -0,0 +1 @@
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package/dist/types/lab-report.js

@@ -0,0 +1,2 @@
+export {};
+//# sourceMappingURL=lab-report.js.map

package/dist/types/lab-report.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"lab-report.js","sourceRoot":"","sources":["../../src/types/lab-report.ts"],"names":[],"mappings":""}

package/dist/types/llm.d.ts

@@ -0,0 +1,46 @@
+export interface ChatMessage {
+    role: 'system' | 'user' | 'assistant';
+    content: string | ContentPart[];
+}
+export interface ContentPart {
+    type: 'text' | 'image';
+    text?: string;
+    image?: {
+        data: string;
+        mediaType: string;
+    };
+}
+export interface LLMOptions {
+    temperature?: number;
+    maxTokens?: number;
+    responseFormat?: 'text' | 'json';
+}
+export interface LLMProvider {
+    chat(messages: ChatMessage[], options?: LLMOptions): Promise<string>;
+    chatStream(messages: ChatMessage[], options?: LLMOptions): AsyncIterable<string>;
+}
+/**
+ * Content part types for multimodal messages (PDF, images).
+ */
+export interface DocumentPart {
+    type: 'document';
+    data: string;
+    mimeType: string;
+}
+export interface ImagePart {
+    type: 'image';
+    data: string;
+    mediaType: string;
+}
+export interface TextPart {
+    type: 'text';
+    text: string;
+}
+export type MultimodalPart = TextPart | ImagePart | DocumentPart;
+/**
+ * Extended provider interface with multimodal support.
+ */
+export interface ExtendedLLMProvider extends LLMProvider {
+    chatMultimodal(parts: MultimodalPart[], options?: LLMOptions): Promise<string>;
+}
+//# sourceMappingURL=llm.d.ts.map

package/dist/types/llm.d.ts.map

@@ -0,0 +1 @@
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package/dist/types/llm.js

@@ -0,0 +1,2 @@
+export {};
+//# sourceMappingURL=llm.js.map

package/dist/types/llm.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"llm.js","sourceRoot":"","sources":["../../src/types/llm.ts"],"names":[],"mappings":""}

package/dist/types/messaging.d.ts

@@ -0,0 +1,45 @@
+import type { Channel } from './user.js';
+export type MessageRole = 'user' | 'assistant' | 'system';
+export type ConversationStatus = 'active' | 'paused' | 'closed';
+export interface InboundMessage {
+    channel: Channel;
+    channelUserId: string;
+    text?: string;
+    media?: {
+        type: string;
+        url: string;
+        mimeType?: string;
+    };
+    referral?: string;
+    messageId?: string;
+}
+export interface OutboundMessage {
+    text: string;
+    buttons?: {
+        id: string;
+        label: string;
+    }[];
+    media?: {
+        type: string;
+        url: string;
+    };
+}
+export interface Conversation {
+    id: string;
+    userId: string;
+    channel: string;
+    channelUserId: string;
+    startedAt: Date;
+    lastMessageAt: Date;
+    status: ConversationStatus;
+    planDelivered: boolean;
+}
+export interface Message {
+    id: string;
+    conversationId: string;
+    role: MessageRole;
+    content: string;
+    skillUsed: string | null;
+    createdAt: Date;
+}
+//# sourceMappingURL=messaging.d.ts.map