@ottolab/shared 0.1.0

package/package.json

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+{
+  "name": "@ottolab/shared",
+  "version": "0.1.0",
+  "license": "MIT",
+  "repository": "https://github.com/hokev/Otto",
+  "publishConfig": { "access": "public" },
+  "type": "module",
+  "exports": {
+    ".": {
+      "import": {
+        "types": "./dist/index.d.ts",
+        "default": "./dist/index.js"
+      },
+      "source": "./src/index.ts"
+    }
+  },
+  "scripts": {
+    "build": "tsc --build",
+    "lint": "eslint src/",
+    "test": "echo 'No tests yet'"
+  }
+}

package/src/constants/biomarker-ranges.ts

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+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 const BIOMARKER_RANGES: Record<string, BiomarkerRange> = {
+  // ── 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,
+  },
+};

package/src/constants/drug-data.ts

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+// Drug interaction and protocol data — populated in Phase 5
+export const DRUG_DATA: Record<string, { name: string; category: string }> = {};

package/src/constants/unit-conversions.ts

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+export const UNIT_CONVERSIONS: Record<
+  string,
+  { fromUnit: string; toUnit: string; factor: number }
+> = {
+  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 },
+};

package/src/index.ts

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+// Types
+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';
+
+// Constants
+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';

package/src/types/biomarkers.ts

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+export interface BiomarkerValue {
+  name: string;
+  value: number;
+  unit: string;
+  referenceRange?: { low: number; high: number };
+  flag?: 'low' | 'normal' | 'high' | 'critical';
+}
+
+export interface BiomarkerSet {
+  // Vitals
+  weight?: BiomarkerValue;
+  height?: BiomarkerValue;
+  bmi?: BiomarkerValue;
+  bodyFatPercent?: BiomarkerValue;
+  bloodPressureSystolic?: BiomarkerValue;
+  bloodPressureDiastolic?: BiomarkerValue;
+  heartRate?: BiomarkerValue;
+
+  // Lipids
+  totalCholesterol?: BiomarkerValue;
+  ldlC?: BiomarkerValue;
+  hdl?: BiomarkerValue;
+  triglycerides?: BiomarkerValue;
+  apoB?: BiomarkerValue;
+
+  // Metabolic
+  hba1c?: BiomarkerValue;
+  fastingGlucose?: BiomarkerValue;
+  fastingInsulin?: BiomarkerValue;
+  homaIr?: BiomarkerValue;
+  uricAcid?: BiomarkerValue;
+
+  // Kidney
+  creatinine?: BiomarkerValue;
+  bun?: BiomarkerValue;
+  egfr?: BiomarkerValue;
+
+  // Liver
+  alt?: BiomarkerValue;
+  ast?: BiomarkerValue;
+  alp?: BiomarkerValue;
+  ggt?: BiomarkerValue;
+  bilirubinTotal?: BiomarkerValue;
+  albumin?: BiomarkerValue;
+
+  // Inflammatory
+  hsCrp?: BiomarkerValue;
+  esr?: BiomarkerValue;
+
+  // Hormones
+  cortisol?: BiomarkerValue;
+  testosterone?: BiomarkerValue;
+  estradiol?: BiomarkerValue;
+  tsh?: BiomarkerValue;
+
+  // Hematology
+  wbc?: BiomarkerValue;
+  rbc?: BiomarkerValue;
+  hemoglobin?: BiomarkerValue;
+  hematocrit?: BiomarkerValue;
+  platelets?: BiomarkerValue;
+  mcv?: BiomarkerValue;
+  rdw?: BiomarkerValue;
+  lymphocytePercent?: BiomarkerValue;
+
+  // Vitamins
+  vitaminD?: BiomarkerValue;
+}

package/src/types/lab-report.ts

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+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;
+}

package/src/types/llm.ts

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+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; // base64
+  mimeType: string;
+}
+
+export interface ImagePart {
+  type: 'image';
+  data: string; // base64
+  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>;
+}

package/src/types/messaging.ts

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+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;
+}

package/src/types/recommendation.ts

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+export type ProtocolCategory =
+  | 'medication'
+  | 'supplement'
+  | 'diet'
+  | 'exercise'
+  | 'lifestyle'
+  | 'monitoring';
+
+export type EvidenceLevel = 'A' | 'B' | 'C' | 'D' | 'expert_opinion';
+
+export interface Protocol {
+  id: string;
+  name: string;
+  category: ProtocolCategory;
+  description: string;
+  dosage?: string;
+  frequency?: string;
+  duration?: string;
+  evidenceLevel: EvidenceLevel;
+  guidelineSource: string;
+  targetBiomarkers: string[];
+}
+
+export interface EvidenceReference {
+  pmid?: string;
+  doi?: string;
+  title: string;
+  authors: string;
+  journal: string;
+  year: number;
+  summary: string;
+}
+
+export interface Recommendation {
+  id: string;
+  labReportId: string;
+  userId: string;
+  protocols: Protocol[];
+  simulationSummary: Record<string, unknown> | null;
+  evidenceRefs: EvidenceReference[];
+  createdAt: Date;
+}

package/src/types/simulation.ts

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+import type { BiomarkerSet } from './biomarkers.js';
+
+// ── Input ────────────────────────────────────────────
+
+export interface SimulationInput {
+  biomarkers: BiomarkerSet;
+  protocols: string[];
+  durationDays?: number;
+  gender?: 'm' | 'f';
+  age?: number;
+}
+
+// ── Timeline ─────────────────────────────────────────
+
+export interface DailySnapshot {
+  day: number;
+  weight?: number;
+  fatMass?: number;
+  leanMass?: number;
+  ldlC?: number;
+  hdl?: number;
+  triglycerides?: number;
+  apoB?: number;
+  hba1c?: number;
+  fastingGlucose?: number;
+  fastingInsulin?: number;
+  homaIr?: number;
+  hsCrp?: number;
+  testosterone?: number;
+  cortisol?: number;
+  uricAcid?: number;
+}
+
+// ── Module outputs ───────────────────────────────────
+
+export interface ModuleSummary {
+  [key: string]: number | string | boolean | null | undefined;
+}
+
+export interface ModuleResult {
+  id: string;
+  name: string;
+  summary: ModuleSummary;
+  finalValues: Record<string, number>;
+}
+
+// ── Result ───────────────────────────────────────────
+
+export interface BiomarkerDelta {
+  start: number;
+  end: number;
+  change: number;
+  changePercent: number;
+}
+
+export interface SimulationResult {
+  timeline: DailySnapshot[];
+  moduleResults: ModuleResult[];
+  biomarkerDeltas: Record<string, BiomarkerDelta>;
+  durationDays: number;
+  activeModules: string[];
+}

package/src/types/user.ts

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+export type UserStatus = 'active' | 'suspended' | 'deleted';
+
+export type Channel = 'whatsapp' | 'telegram' | 'line' | 'sms' | 'app';
+
+export interface User {
+  id: string;
+  createdAt: Date;
+  updatedAt: Date;
+  status: UserStatus;
+  displayName: string | null;
+  timezone: string;
+  onboardedAt: Date | null;
+}
+
+export interface ChannelIdentity {
+  id: string;
+  userId: string;
+  channel: Channel;
+  channelUserId: string;
+  isPrimary: boolean;
+  linkedAt: Date;
+  metadata: Record<string, unknown>;
+}

package/tsconfig.json

@@ -0,0 +1,9 @@
+{
+  "extends": "../../tsconfig.json",
+  "compilerOptions": {
+    "composite": true,
+    "outDir": "dist",
+    "rootDir": "src"
+  },
+  "include": ["src"]
+}

package/tsconfig.tsbuildinfo

@@ -0,0 +1 @@
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