@ottolab/extraction 0.1.0 → 0.1.1

package/src/llm-extractor.ts

@@ -1,157 +0,0 @@
-import type { SourceLab, ExtendedLLMProvider } from '@ottolab/shared';
-import { BASE_EXTRACTION_PROMPT } from './prompts/base.js';
-import { QUEST_EXTRACTION_PROMPT } from './prompts/quest.js';
-import { LABCORP_EXTRACTION_PROMPT } from './prompts/labcorp.js';
-
-/** Raw extraction output — flat key/value from LLM. */
-export type RawBiomarkers = Record<string, number | string | null>;
-
-/**
- * Select the appropriate extraction prompt based on detected lab.
- */
-function getPromptForLab(lab: SourceLab): string {
-  switch (lab) {
-    case 'quest':
-      return QUEST_EXTRACTION_PROMPT;
-    case 'labcorp':
-      return LABCORP_EXTRACTION_PROMPT;
-    default:
-      return BASE_EXTRACTION_PROMPT;
-  }
-}
-
-/**
- * Extract biomarkers from a PDF using multimodal LLM.
- *
- * Sends the full PDF as base64 inline data with a lab-specific prompt.
- * Returns raw key/value pairs (not yet validated or normalized).
- */
-export async function extractFromPdf(
-  pdfBase64: string,
-  lab: SourceLab,
-  provider: ExtendedLLMProvider,
-): Promise<RawBiomarkers> {
-  const prompt = getPromptForLab(lab);
-
-  const response = await provider.chatMultimodal(
-    [
-      { type: 'document', data: pdfBase64, mimeType: 'application/pdf' },
-      { type: 'text', text: prompt },
-    ],
-    { temperature: 0, maxTokens: 4096, responseFormat: 'json' },
-  );
-
-  return parseExtractionResponse(response);
-}
-
-/**
- * Extract biomarkers from CSV text.
- *
- * Expects a simple CSV with header row containing biomarker names
- * and a single data row with values.
- */
-export function extractFromCsv(csvText: string): RawBiomarkers {
-  const lines = csvText.trim().split('\n');
-  if (lines.length < 2) {
-    throw new Error('CSV must have at least a header row and a data row');
-  }
-
-  const headers = lines[0].split(',').map((h) => h.trim().toLowerCase());
-  const values = lines[1].split(',').map((v) => v.trim());
-
-  const result: RawBiomarkers = {};
-  for (let i = 0; i < headers.length; i++) {
-    const key = normalizeHeaderName(headers[i]);
-    const raw = values[i];
-    if (!key || !raw || raw === '') continue;
-
-    const num = parseFloat(raw);
-    result[key] = Number.isNaN(num) ? raw : num;
-  }
-
-  return result;
-}
-
-/**
- * Normalize CSV header names to our canonical biomarker keys.
- */
-function normalizeHeaderName(header: string): string {
-  const mappings: Record<string, string> = {
-    'total cholesterol': 'total_cholesterol',
-    cholesterol: 'total_cholesterol',
-    'ldl-c': 'ldl_c',
-    ldl: 'ldl_c',
-    'hdl-c': 'hdl',
-    hdl: 'hdl',
-    triglycerides: 'triglycerides',
-    tg: 'triglycerides',
-    hba1c: 'hba1c',
-    a1c: 'hba1c',
-    glucose: 'fasting_glucose',
-    'fasting glucose': 'fasting_glucose',
-    insulin: 'fasting_insulin',
-    'fasting insulin': 'fasting_insulin',
-    'uric acid': 'uric_acid',
-    creatinine: 'creatinine',
-    bun: 'bun',
-    egfr: 'egfr',
-    alt: 'alt',
-    sgpt: 'alt',
-    ast: 'ast',
-    sgot: 'ast',
-    alp: 'alp',
-    ggt: 'ggt',
-    bilirubin: 'bilirubin_total',
-    albumin: 'albumin',
-    'hs-crp': 'hs_crp',
-    crp: 'hs_crp',
-    esr: 'esr',
-    cortisol: 'cortisol',
-    testosterone: 'testosterone',
-    estradiol: 'estradiol',
-    tsh: 'tsh',
-    wbc: 'wbc',
-    rbc: 'rbc',
-    hemoglobin: 'hemoglobin',
-    hgb: 'hemoglobin',
-    hematocrit: 'hematocrit',
-    hct: 'hematocrit',
-    platelets: 'platelets',
-    plt: 'platelets',
-    mcv: 'mcv',
-    rdw: 'rdw',
-    'lymphocyte %': 'lymphocyte_percent',
-    lymphocytes: 'lymphocyte_percent',
-    'vitamin d': 'vitamin_d',
-    '25-oh vitamin d': 'vitamin_d',
-    weight: 'weight_kg',
-    height: 'height_cm',
-    bmi: 'bmi',
-    'body fat': 'body_fat_percent',
-    'systolic bp': 'systolic_bp',
-    'diastolic bp': 'diastolic_bp',
-    'heart rate': 'heart_rate',
-    apob: 'apoB',
-    'apo b': 'apoB',
-  };
-
-  return mappings[header] ?? header.replace(/[\s-]+/g, '_').toLowerCase();
-}
-
-function parseExtractionResponse(text: string): RawBiomarkers {
-  let cleaned = text.trim();
-
-  // Strip markdown code fences
-  if (cleaned.startsWith('```')) {
-    cleaned = cleaned.replace(/^```(?:json)?\s*/, '').replace(/\s*```$/, '');
-  }
-
-  // Find JSON object
-  const start = cleaned.indexOf('{');
-  const end = cleaned.lastIndexOf('}');
-  if (start === -1 || end === -1) {
-    throw new Error('No JSON object found in LLM extraction response');
-  }
-
-  return JSON.parse(cleaned.slice(start, end + 1)) as RawBiomarkers;
-}

package/src/validator.ts

@@ -1,218 +0,0 @@
-import type { BiomarkerValue, BiomarkerSet } from '@ottolab/shared';
-import type { RawBiomarkers } from './llm-extractor.js';
-
-/**
- * Clinical ranges for validation — generous bounds to avoid false rejections.
- * Values outside these ranges are likely extraction errors.
- */
-const CLINICAL_RANGES: Record<string, [number, number]> = {
-  weight_kg: [20, 300],
-  height_cm: [100, 250],
-  bmi: [10, 60],
-  body_fat_percent: [2, 60],
-  systolic_bp: [60, 250],
-  diastolic_bp: [30, 150],
-  heart_rate: [30, 220],
-  total_cholesterol: [50, 500],
-  ldl_c: [10, 400],
-  hdl: [5, 150],
-  triglycerides: [10, 2000],
-  apoB: [10, 300],
-  hba1c: [3, 15],
-  fasting_glucose: [30, 500],
-  fasting_insulin: [0.5, 300],
-  uric_acid: [0.5, 20],
-  creatinine: [0.1, 15],
-  bun: [2, 100],
-  egfr: [5, 150],
-  alt: [1, 2000],
-  ast: [1, 2000],
-  alp: [10, 1000],
-  ggt: [1, 2000],
-  bilirubin_total: [0.05, 30],
-  albumin: [1, 6],
-  hs_crp: [0.01, 300],
-  esr: [0, 140],
-  cortisol: [0.5, 60],
-  testosterone: [1, 2000],
-  estradiol: [1, 5000],
-  tsh: [0.01, 100],
-  wbc: [1, 50],
-  rbc: [1, 10],
-  hemoglobin: [3, 25],
-  hematocrit: [15, 65],
-  platelets: [10, 1000],
-  mcv: [50, 130],
-  rdw: [9, 25],
-  lymphocyte_percent: [2, 70],
-  vitamin_d: [3, 200],
-};
-
-/**
- * Map from raw extraction keys to BiomarkerSet field names and display metadata.
- */
-const BIOMARKER_MAP: Record<string, { field: keyof BiomarkerSet; name: string; unit: string }> = {
-  weight_kg: { field: 'weight', name: 'Weight', unit: 'kg' },
-  height_cm: { field: 'height', name: 'Height', unit: 'cm' },
-  bmi: { field: 'bmi', name: 'BMI', unit: 'kg/m2' },
-  body_fat_percent: { field: 'bodyFatPercent', name: 'Body Fat', unit: '%' },
-  systolic_bp: { field: 'bloodPressureSystolic', name: 'Systolic BP', unit: 'mmHg' },
-  diastolic_bp: { field: 'bloodPressureDiastolic', name: 'Diastolic BP', unit: 'mmHg' },
-  heart_rate: { field: 'heartRate', name: 'Heart Rate', unit: 'bpm' },
-  total_cholesterol: { field: 'totalCholesterol', name: 'Total Cholesterol', unit: 'mg/dL' },
-  ldl_c: { field: 'ldlC', name: 'LDL-C', unit: 'mg/dL' },
-  hdl: { field: 'hdl', name: 'HDL', unit: 'mg/dL' },
-  triglycerides: { field: 'triglycerides', name: 'Triglycerides', unit: 'mg/dL' },
-  apoB: { field: 'apoB', name: 'ApoB', unit: 'mg/dL' },
-  hba1c: { field: 'hba1c', name: 'HbA1c', unit: '%' },
-  fasting_glucose: { field: 'fastingGlucose', name: 'Fasting Glucose', unit: 'mg/dL' },
-  fasting_insulin: { field: 'fastingInsulin', name: 'Fasting Insulin', unit: 'uIU/mL' },
-  uric_acid: { field: 'uricAcid', name: 'Uric Acid', unit: 'mg/dL' },
-  creatinine: { field: 'creatinine', name: 'Creatinine', unit: 'mg/dL' },
-  bun: { field: 'bun', name: 'BUN', unit: 'mg/dL' },
-  egfr: { field: 'egfr', name: 'eGFR', unit: 'mL/min/1.73m2' },
-  alt: { field: 'alt', name: 'ALT', unit: 'U/L' },
-  ast: { field: 'ast', name: 'AST', unit: 'U/L' },
-  alp: { field: 'alp', name: 'ALP', unit: 'U/L' },
-  ggt: { field: 'ggt', name: 'GGT', unit: 'U/L' },
-  bilirubin_total: { field: 'bilirubinTotal', name: 'Bilirubin (Total)', unit: 'mg/dL' },
-  albumin: { field: 'albumin', name: 'Albumin', unit: 'g/dL' },
-  hs_crp: { field: 'hsCrp', name: 'hs-CRP', unit: 'mg/L' },
-  esr: { field: 'esr', name: 'ESR', unit: 'mm/hr' },
-  cortisol: { field: 'cortisol', name: 'Cortisol', unit: 'ug/dL' },
-  testosterone: { field: 'testosterone', name: 'Testosterone', unit: 'ng/dL' },
-  estradiol: { field: 'estradiol', name: 'Estradiol', unit: 'pg/mL' },
-  tsh: { field: 'tsh', name: 'TSH', unit: 'mIU/L' },
-  wbc: { field: 'wbc', name: 'WBC', unit: '10^3/uL' },
-  rbc: { field: 'rbc', name: 'RBC', unit: '10^6/uL' },
-  hemoglobin: { field: 'hemoglobin', name: 'Hemoglobin', unit: 'g/dL' },
-  hematocrit: { field: 'hematocrit', name: 'Hematocrit', unit: '%' },
-  platelets: { field: 'platelets', name: 'Platelets', unit: '10^3/uL' },
-  mcv: { field: 'mcv', name: 'MCV', unit: 'fL' },
-  rdw: { field: 'rdw', name: 'RDW', unit: '%' },
-  lymphocyte_percent: { field: 'lymphocytePercent', name: 'Lymphocyte %', unit: '%' },
-  vitamin_d: { field: 'vitaminD', name: 'Vitamin D', unit: 'ng/mL' },
-};
-
-export interface ValidationResult {
-  biomarkers: BiomarkerSet;
-  accepted: number;
-  rejected: number;
-  confidence: number;
-  rejections: { key: string; value: unknown; reason: string }[];
-}
-
-/**
- * Validate and transform raw LLM extraction output to typed BiomarkerSet.
- *
- * Steps:
- * 1. Filter nulls/undefined
- * 2. Type-check numeric values
- * 3. Range-check against generous clinical bounds
- * 4. Map to BiomarkerSet fields
- * 5. Compute extraction confidence score
- */
-export function validateExtraction(raw: RawBiomarkers): ValidationResult {
-  const biomarkers: BiomarkerSet = {};
-  const rejections: { key: string; value: unknown; reason: string }[] = [];
-  let accepted = 0;
-  let rejected = 0;
-
-  for (const [key, value] of Object.entries(raw)) {
-    // Skip gender and non-biomarker fields
-    if (key === 'gender') continue;
-
-    // Skip null/undefined
-    if (value === null || value === undefined) continue;
-
-    // Skip string values (qualitative results like "Negative")
-    if (typeof value === 'string') continue;
-
-    // Must be a number at this point
-    if (typeof value !== 'number' || !Number.isFinite(value)) {
-      rejections.push({ key, value, reason: 'not a finite number' });
-      rejected++;
-      continue;
-    }
-
-    // Check clinical ranges
-    const range = CLINICAL_RANGES[key];
-    if (range && (value < range[0] || value > range[1])) {
-      rejections.push({
-        key,
-        value,
-        reason: `outside clinical range [${range[0]}, ${range[1]}]`,
-      });
-      rejected++;
-      continue;
-    }
-
-    // Map to BiomarkerSet
-    const mapping = BIOMARKER_MAP[key];
-    if (!mapping) continue; // skip unknown keys
-
-    const biomarkerValue: BiomarkerValue = {
-      name: mapping.name,
-      value,
-      unit: mapping.unit,
-    };
-
-    (biomarkers as Record<string, BiomarkerValue>)[mapping.field] = biomarkerValue;
-    accepted++;
-  }
-
-  // Confidence based on yield ratio and cross-checks
-  const confidence = computeConfidence(biomarkers, accepted, rejected);
-
-  return { biomarkers, accepted, rejected, confidence, rejections };
-}
-
-/**
- * Compute extraction confidence score (0-1).
- *
- * Factors:
- * - Yield: how many biomarkers were successfully extracted
- * - Rejection rate: high rejections lower confidence
- * - Cross-biomarker consistency checks
- */
-function computeConfidence(biomarkers: BiomarkerSet, accepted: number, rejected: number): number {
-  if (accepted === 0) return 0;
-
-  // Base confidence from yield (diminishing returns above 15 markers)
-  const yieldScore = Math.min(accepted / 15, 1.0);
-
-  // Penalty for rejections
-  const total = accepted + rejected;
-  const rejectionPenalty = total > 0 ? rejected / total : 0;
-
-  // Cross-biomarker consistency checks
-  let consistencyScore = 1.0;
-
-  // Check: if both ALT and AST exist, AST should generally be ≤ 2×ALT in healthy
-  if (biomarkers.alt && biomarkers.ast) {
-    if (biomarkers.ast.value > biomarkers.alt.value * 5) {
-      consistencyScore -= 0.1;
-    }
-  }
-
-  // Check: HDL should be less than total cholesterol
-  if (biomarkers.hdl && biomarkers.totalCholesterol) {
-    if (biomarkers.hdl.value > biomarkers.totalCholesterol.value) {
-      consistencyScore -= 0.15;
-    }
-  }
-
-  // Check: LDL should be less than total cholesterol
-  if (biomarkers.ldlC && biomarkers.totalCholesterol) {
-    if (biomarkers.ldlC.value > biomarkers.totalCholesterol.value) {
-      consistencyScore -= 0.15;
-    }
-  }
-
-  const raw =
-    yieldScore * 0.5 + (1 - rejectionPenalty) * 0.25 + Math.max(consistencyScore, 0) * 0.25;
-  return Math.round(Math.min(Math.max(raw, 0), 1) * 100) / 100;
-}
-
-// Export for testing
-export { CLINICAL_RANGES, BIOMARKER_MAP };

package/tsconfig.json

@@ -1,10 +0,0 @@
-{
-  "extends": "../../tsconfig.json",
-  "compilerOptions": {
-    "composite": true,
-    "outDir": "dist",
-    "rootDir": "src"
-  },
-  "include": ["src"],
-  "references": [{ "path": "../shared" }]
-}

package/tsconfig.tsbuildinfo

@@ -1 +0,0 @@
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