@precisa-saude/fhir-ocr-utils 0.20.2 → 0.20.3

package/dist/cli.js

@@ -147,6 +147,28 @@ var GENETIC_CONTEXT_PATTERNS = [
   /\bhomozigot/,
   /\bsequence change\b/
 ];
+var SKINFOLD_SITE_CODES = /* @__PURE__ */ new Set([
+  "SkinfoldAbdominal",
+  "SkinfoldChest",
+  "SkinfoldMidaxillary",
+  "SkinfoldSubscapular",
+  "SkinfoldSuprailiac",
+  "SkinfoldThigh",
+  "SkinfoldTriceps"
+]);
+var GIRTH_CONTEXT_PATTERNS = [
+  /\bcircumference\b/,
+  /\bcircunferencias?\b/,
+  /\bperimetros?\b/,
+  /\bgirth\b/
+];
+var SKINFOLD_CONTEXT_PATTERNS = [/\bdobras?\b/, /\bskin ?folds?\b/, /\bpregas?\b/];
+function hasGirthContext(line) {
+  if (SKINFOLD_CONTEXT_PATTERNS.some((re) => re.test(line))) {
+    return false;
+  }
+  return GIRTH_CONTEXT_PATTERNS.some((re) => re.test(line));
+}
 var DIGIT_PATTERN = /\d/;
 var cachedUnitTokens = null;
 function getUnitTokens() {
@@ -273,6 +295,7 @@ function findBiomarkersInText(ocrText) {
   const bestByCode = /* @__PURE__ */ new Map();
   const geneticLines = /* @__PURE__ */ new Map();
   const valueLines = /* @__PURE__ */ new Map();
+  const girthLines = /* @__PURE__ */ new Map();
   for (const candidate of resolveOverlaps(collectCandidates(normalizedText))) {
     const { end: lineEnd, start: lineStart } = getLineBounds(normalizedText, candidate.start);
     let genetic = geneticLines.get(lineStart);
@@ -288,10 +311,18 @@ function findBiomarkersInText(ocrText) {
       hasValue = hasValueEvidence(normalizedText.slice(lineStart, lineEnd));
       valueLines.set(lineStart, hasValue);
     }
+    let girth = girthLines.get(lineStart);
+    if (girth === void 0) {
+      girth = hasGirthContext(normalizedText.slice(lineStart, lineEnd));
+      girthLines.set(lineStart, girth);
+    }
     for (const entry of candidate.entries) {
       if (entry.ambiguous && !hasValue) {
         continue;
       }
+      if (girth && SKINFOLD_SITE_CODES.has(entry.code)) {
+        continue;
+      }
       let confidence = CONFIDENCE_NAME_ONLY;
       if (entry.ambiguous) {
         confidence = CONFIDENCE_AMBIGUOUS;
@@ -403,7 +434,7 @@ async function main() {
     strict: false
   });
   if (values.version) {
-    process.stdout.write(`${"0.20.2"}
+    process.stdout.write(`${"0.20.3"}
 `);
     return;
   }

package/dist/index.cjs

@@ -138,6 +138,28 @@ var GENETIC_CONTEXT_PATTERNS = [
   /\bhomozigot/,
   /\bsequence change\b/
 ];
+var SKINFOLD_SITE_CODES = /* @__PURE__ */ new Set([
+  "SkinfoldAbdominal",
+  "SkinfoldChest",
+  "SkinfoldMidaxillary",
+  "SkinfoldSubscapular",
+  "SkinfoldSuprailiac",
+  "SkinfoldThigh",
+  "SkinfoldTriceps"
+]);
+var GIRTH_CONTEXT_PATTERNS = [
+  /\bcircumference\b/,
+  /\bcircunferencias?\b/,
+  /\bperimetros?\b/,
+  /\bgirth\b/
+];
+var SKINFOLD_CONTEXT_PATTERNS = [/\bdobras?\b/, /\bskin ?folds?\b/, /\bpregas?\b/];
+function hasGirthContext(line) {
+  if (SKINFOLD_CONTEXT_PATTERNS.some((re) => re.test(line))) {
+    return false;
+  }
+  return GIRTH_CONTEXT_PATTERNS.some((re) => re.test(line));
+}
 var DIGIT_PATTERN = /\d/;
 var cachedUnitTokens = null;
 function getUnitTokens() {
@@ -264,6 +286,7 @@ function findBiomarkersInText(ocrText) {
   const bestByCode = /* @__PURE__ */ new Map();
   const geneticLines = /* @__PURE__ */ new Map();
   const valueLines = /* @__PURE__ */ new Map();
+  const girthLines = /* @__PURE__ */ new Map();
   for (const candidate of resolveOverlaps(collectCandidates(normalizedText))) {
     const { end: lineEnd, start: lineStart } = getLineBounds(normalizedText, candidate.start);
     let genetic = geneticLines.get(lineStart);
@@ -279,10 +302,18 @@ function findBiomarkersInText(ocrText) {
       hasValue = hasValueEvidence(normalizedText.slice(lineStart, lineEnd));
       valueLines.set(lineStart, hasValue);
     }
+    let girth = girthLines.get(lineStart);
+    if (girth === void 0) {
+      girth = hasGirthContext(normalizedText.slice(lineStart, lineEnd));
+      girthLines.set(lineStart, girth);
+    }
     for (const entry of candidate.entries) {
       if (entry.ambiguous && !hasValue) {
         continue;
       }
+      if (girth && SKINFOLD_SITE_CODES.has(entry.code)) {
+        continue;
+      }
       let confidence = CONFIDENCE_NAME_ONLY;
       if (entry.ambiguous) {
         confidence = CONFIDENCE_AMBIGUOUS;

package/dist/index.cjs.map

@@ -1 +1 @@
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* OCR Anchor — Biomarker text anchoring\n *\n * Scans OCR text for biomarker names BEFORE sending to LLM.\n * This prevents hallucination by constraining what biomarkers\n * the LLM is allowed to extract.\n *\n * Matching is deliberately conservative: a name only anchors when it appears\n * as a whole token, is not swallowed by a longer biomarker name, is not inside\n * a genetic report line, and — for generic single-word names — sits on a line\n * that actually carries a value.\n */\n\nimport {\n  type BiomarkerSearchPattern,\n  generateFilteredLLMReference,\n  getAllSearchPatterns,\n  UNIT_TO_UCUM,\n} from '@precisa-saude/fhir';\n\nexport interface AnchorMatch {\n  code: string;\n  confidence: number;\n  loinc?: string;\n  matchedName: string;\n  position: number;\n}\n\nexport interface AnchorResult {\n  filteredReference: string;\n  matches: AnchorMatch[];\n  stats: {\n    totalPatterns: number;\n    matchedCount: number;\n    scanTimeMs: number;\n  };\n}\n\n/**\n * Confidence 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string): string {\n  return text\n    .normalize('NFD')\n    .replace(/[\\u0300-\\u036f]/g, '')\n    .toLowerCase()\n    .replace(/[^\\S\\n]+/g, ' ');\n}\n\nconst UNAMBIGUOUS_SHORT_NAMES = new Set([\n  'hdl',\n  'ldl',\n  'lh',\n  'tsh',\n  'crp',\n  'pcr',\n  'ggt',\n  'alt',\n  'ast',\n  'bun',\n  'wbc',\n  'rbc',\n  'mcv',\n  'mch',\n  'rdw',\n  'mpv',\n  'psa',\n  'fsh',\n  'hba1c',\n  'egfr',\n  'acr',\n  'esr',\n  'vhs',\n  'bmc',\n  'bmd',\n  'vat',\n  'dxa',\n  'dmo',\n  'cmo',\n  'ffm',\n  'lbm',\n  'mlg',\n  'tav',\n]);\n\n/**\n * Single-word catalog names that are ordinary words in EN/PT, so seeing them\n * proves nothing on its own. They only anchor when the line also carries a\n * value. Qualitative urine markers (`Color`, `Protein`, `Blood`, …) are\n * detected automatically — see `isQualitativeUrine` — and don't belong here.\n */\nconst CONTEXT_REQUIRED_NAMES = new Set([\n  'bacteria', // Bacteria_Urine — tem unidade, escapa da regra automática\n  'bacterias', // Bacteria_Urine\n  'lead', // Lead — verbo/substantivo comuníssimo em inglês\n  'peso', // TotalMass\n  'saturation', // TransferrinSaturation — \"oxygen saturation\", \"saturation index\"\n  'tap', // ProthrombinTime — \"tap\" em inglês\n  'volume', // VATVolume\n  'weight', // TotalMass\n]);\n\n/**\n * Qualitative results expected next to a non-numeric biomarker\n * (urine dipstick, sediment, appearance). Normalized, single tokens —\n * \"não reagente\" is covered by `reagente`, \"não detectado\" by `detectado`.\n */\nconst QUALITATIVE_VALUE_TERMS = new Set([\n  'absent',\n  'alguns',\n  'amarela',\n  'amarelo',\n  'anormal',\n  'ausencia',\n  'ausente',\n  'ausentes',\n  'citrino',\n  'claro',\n  'clear',\n  'cloudy',\n  'colorless',\n  'detectado',\n  'detected',\n  'escuro',\n  'incolor',\n  'indetectavel',\n  'limpido',\n  'moderada',\n  'moderado',\n  'negativa',\n  'negative',\n  'negativo',\n  'normais',\n  'normal',\n  'numerosos',\n  'ocasional',\n  'positiva',\n  'positive',\n  'positivo',\n  'present',\n  'presente',\n  'presentes',\n  'raras',\n  'raro',\n  'raros',\n  'reagente',\n  'trace',\n  'traces',\n  'tracos',\n  'turvo',\n  'undetectable',\n  'yellow',\n]);\n\n/**\n * Signals that a line comes from a genetic/molecular report rather than from a\n * panel of measured values. Gene symbols collide with biomarker names (`APOB`\n * the gene vs. `ApoB` the lipoprotein), so the context — not a static HGNC\n * blocklist — is what tells them apart. 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string): string {\n  return text\n    .normalize('NFD')\n    .replace(/[\\u0300-\\u036f]/g, '')\n    .toLowerCase()\n    .replace(/[^\\S\\n]+/g, ' ');\n}\n\nconst UNAMBIGUOUS_SHORT_NAMES = new Set([\n  'hdl',\n  'ldl',\n  'lh',\n  'tsh',\n  'crp',\n  'pcr',\n  'ggt',\n  'alt',\n  'ast',\n  'bun',\n  'wbc',\n  'rbc',\n  'mcv',\n  'mch',\n  'rdw',\n  'mpv',\n  'psa',\n  'fsh',\n  'hba1c',\n  'egfr',\n  'acr',\n  'esr',\n  'vhs',\n  'bmc',\n  'bmd',\n  'vat',\n  'dxa',\n  'dmo',\n  'cmo',\n  'ffm',\n  'lbm',\n  'mlg',\n  'tav',\n]);\n\n/**\n * Single-word catalog names that are ordinary words in EN/PT, so seeing them\n * proves nothing on its own. They only anchor when the line also carries a\n * value. Qualitative urine markers (`Color`, `Protein`, `Blood`, …) are\n * detected automatically — see `isQualitativeUrine` — and don't belong here.\n */\nconst CONTEXT_REQUIRED_NAMES = new Set([\n  'bacteria', // Bacteria_Urine — tem unidade, escapa da regra automática\n  'bacterias', // Bacteria_Urine\n  'lead', // Lead — verbo/substantivo comuníssimo em inglês\n  'peso', // TotalMass\n  'saturation', // TransferrinSaturation — \"oxygen saturation\", \"saturation index\"\n  'tap', // ProthrombinTime — \"tap\" em inglês\n  'volume', // VATVolume\n  'weight', // TotalMass\n]);\n\n/**\n * Qualitative results expected next to a non-numeric biomarker\n * (urine dipstick, sediment, appearance). Normalized, single tokens —\n * \"não reagente\" is covered by `reagente`, \"não detectado\" by `detectado`.\n */\nconst QUALITATIVE_VALUE_TERMS = new Set([\n  'absent',\n  'alguns',\n  'amarela',\n  'amarelo',\n  'anormal',\n  'ausencia',\n  'ausente',\n  'ausentes',\n  'citrino',\n  'claro',\n  'clear',\n  'cloudy',\n  'colorless',\n  'detectado',\n  'detected',\n  'escuro',\n  'incolor',\n  'indetectavel',\n  'limpido',\n  'moderada',\n  'moderado',\n  'negativa',\n  'negative',\n  'negativo',\n  'normais',\n  'normal',\n  'numerosos',\n  'ocasional',\n  'positiva',\n  'positive',\n  'positivo',\n  'present',\n  'presente',\n  'presentes',\n  'raras',\n  'raro',\n  'raros',\n  'reagente',\n  'trace',\n  'traces',\n  'tracos',\n  'turvo',\n  'undetectable',\n  'yellow',\n]);\n\n/**\n * Signals that a line comes from a genetic/molecular report rather than from a\n * panel of measured values. Gene symbols collide with biomarker names (`APOB`\n * the gene vs. `ApoB` the lipoprotein), so the context — not a static HGNC\n * blocklist — is what tells them apart. Blocking the token itself would break\n * real lipid panels.\n */\nconst GENETIC_CONTEXT_PATTERNS: RegExp[] = [\n  /\\b[nx][mrpc]_\\d{6,}/, // RefSeq: NM_000384.2, NP_, NR_, XM_\n  /\\bens[gtp]\\d{6,}/, // Ensembl: ENSG00000084674\n  /\\bp\\.[a-z]{3}\\d/, // HGVS proteína: p.Trp448*\n  /\\bc\\.\\d+[acgt]?[>_+-]/, // HGVS codificante: c.1234A>G, c.76_78del\n  /\\brs\\d{4,}\\b/, // dbSNP\n  /\\bgenes?\\b/,\n  /\\bvariante?s?\\b/,\n  /\\bexons?\\b/,\n  /\\bzygosity\\b/,\n  /\\bzigosidade\\b/,\n  /\\balleles?\\b/,\n  /\\balelos?\\b/,\n  /\\bmutations?\\b/,\n  /\\bmutac(ao|oes)\\b/,\n  /\\bpathogenic/,\n  /\\bpatogenic/,\n  /\\bheterozyg/,\n  /\\bhomozyg/,\n  /\\bheterozigot/,\n  /\\bhomozigot/,\n  /\\bsequence change\\b/,\n];\n\n/**\n * Sítios de dobra cutânea cujo nome nu também nomeia uma circunferência:\n * \"Coxa\" aparece tanto em \"Dobra Cutânea Coxa\" quanto em \"Circunferência da\n * Coxa\". O termo nu precisa existir como alias, porque há laudo que imprime\n * só o sítio na coluna, então a desambiguação tem que vir do contexto da\n * linha, como já se faz com laudo genético.\n */\nconst SKINFOLD_SITE_CODES = new Set([\n  'SkinfoldAbdominal',\n  'SkinfoldChest',\n  'SkinfoldMidaxillary',\n  'SkinfoldSubscapular',\n  'SkinfoldSuprailiac',\n  'SkinfoldThigh',\n  'SkinfoldTriceps',\n]);\n\n/** Uma linha de circunferência ou perímetro não mede dobra. */\nconst GIRTH_CONTEXT_PATTERNS: RegExp[] = [\n  /\\bcircumference\\b/,\n  /\\bcircunferencias?\\b/,\n  /\\bperimetros?\\b/,\n  /\\bgirth\\b/,\n];\n\n/**\n * Só bloqueia quando a linha fala de circunferência e não fala de dobra:\n * \"Dobra Cutânea Coxa\" e \"Thigh Skinfold\" continuam ancorando normalmente,\n * e uma linha que traga as duas palavras é ambígua demais para descartar.\n */\nconst SKINFOLD_CONTEXT_PATTERNS: RegExp[] = [/\\bdobras?\\b/, /\\bskin ?folds?\\b/, /\\bpregas?\\b/];\n\nfunction hasGirthContext(line: string): boolean {\n  if (SKINFOLD_CONTEXT_PATTERNS.some((re) => re.test(line))) {\n    return false;\n  }\n  return GIRTH_CONTEXT_PATTERNS.some((re) => re.test(line));\n}\n\nconst DIGIT_PATTERN = /\\d/;\n\n/** Unit tokens reused from the core catalog instead of a parallel list. */\nlet cachedUnitTokens: Set<string> | null = null;\n\nfunction getUnitTokens(): Set<string> {\n  if (!cachedUnitTokens) {\n    cachedUnitTokens = new Set(\n      Object.keys(UNIT_TO_UCUM)\n        .map((unit) => normalize(unit).trim())\n        .filter(Boolean),\n    );\n  }\n  return cachedUnitTokens;\n}\n\ninterface PatternEntry {\n  ambiguous: boolean;\n  code: string;\n  loinc?: string;\n  original: string;\n}\n\ninterface NamePattern {\n  entries: PatternEntry[];\n  /** Built on first use — most names never match a given document. */\n  regex: RegExp | null;\n}\n\ninterface Candidate {\n  end: number;\n  entries: PatternEntry[];\n  start: number;\n}\n\nlet cachedPatterns: BiomarkerSearchPattern[] | null = null;\nlet cachedNamePatterns: Map<string, NamePattern> | null = null;\n\nfunction getPatterns(): BiomarkerSearchPattern[] {\n  if (!cachedPatterns) {\n    cachedPatterns = getAllSearchPatterns();\n  }\n  return cachedPatterns;\n}\n\nfunction escapeRegExp(text: string): string {\n  return text.replace(/[.*+?^${}()|[\\]\\\\]/g, '\\\\$&');\n}\n\n/**\n * Build a whole-token matcher for a normalized name.\n *\n * Lookarounds instead of `\\b` because names may start or end with a non-word\n * character (`Lp(a)`), where `\\b` asserts the wrong thing.\n *\n * A multi-word name must sit on a single line: in the column layouts labs\n * print, consecutive lines are separate biomarkers, and allowing a line break\n * inside a name turns \"Colesterol\\nHDL\" into the name \"Colesterol HDL\".\n * A wrapped name still anchors through its head token when that token is a\n * name of its own (\"Colesterol\\nTotal\" → `Cholesterol`).\n *\n * The trailing optional `s` keeps the plurals labs actually print\n * (\"Proteínas\", \"Cetonas\") anchored to the singular catalog name — without\n * letting `proteína` match inside `proteinúria`.\n */\nfunction buildNamePattern(normalizedName: string): RegExp {\n  const body = normalizedName.split(' ').map(escapeRegExp).join('[^\\\\S\\\\n]+');\n  const plural = /\\p{L}$/u.test(normalizedName) ? 's?' : '';\n  return new RegExp(`(?<![\\\\p{L}\\\\p{N}])${body}${plural}(?![\\\\p{L}\\\\p{N}])`, 'gu');\n}\n\nfunction isQualitativeUrine(pattern: BiomarkerSearchPattern): boolean {\n  const categories = Array.isArray(pattern.category) ? pattern.category : [pattern.category];\n  return categories.includes('urina') && !pattern.unit;\n}\n\n/**\n * A name is ambiguous when it is a single token that also reads as ordinary\n * text. Multi-word names (`Occult Blood`, `Urine Protein`) are specific enough\n * on their own.\n */\nfunction isAmbiguousName(normalizedName: string, pattern: BiomarkerSearchPattern): boolean {\n  if (normalizedName.includes(' ')) {\n    return false;\n  }\n  return CONTEXT_REQUIRED_NAMES.has(normalizedName) || isQualitativeUrine(pattern);\n}\n\nfunction getNamePatterns(): Map<string, NamePattern> {\n  if (!cachedNamePatterns) {\n    const map = new Map<string, NamePattern>();\n    for (const pattern of getPatterns()) {\n      for (const name of pattern.names) {\n        const normalized = normalize(name).trim();\n        if (!normalized) {\n          continue;\n        }\n        if (normalized.length < 3 && !UNAMBIGUOUS_SHORT_NAMES.has(normalized)) {\n          continue;\n        }\n        let slot = map.get(normalized);\n        if (!slot) {\n          slot = { entries: [], regex: null };\n          map.set(normalized, slot);\n        }\n        slot.entries.push({\n          ambiguous: isAmbiguousName(normalized, pattern),\n          code: pattern.code,\n          ...(pattern.loinc && { loinc: pattern.loinc }),\n          original: name,\n        });\n      }\n    }\n    cachedNamePatterns = map;\n  }\n  return cachedNamePatterns;\n}\n\nfunction getLineBounds(text: string, position: number): { end: number; start: number } {\n  const start = text.lastIndexOf('\\n', position) + 1;\n  const nextBreak = text.indexOf('\\n', position);\n  return { end: nextBreak === -1 ? text.length : nextBreak, start };\n}\n\nfunction hasGeneticContext(line: string): boolean {\n  return GENETIC_CONTEXT_PATTERNS.some((pattern) => pattern.test(line));\n}\n\n/**\n * Does this line carry something that looks like a measured result?\n * A digit, a known unit, or an expected qualitative term.\n */\nfunction hasValueEvidence(line: string): boolean {\n  if (DIGIT_PATTERN.test(line)) {\n    return true;\n  }\n  const unitTokens = getUnitTokens();\n  for (const token of line.split(/[^\\p{L}\\p{N}%/]+/u)) {\n    if (token && (unitTokens.has(token) || QUALITATIVE_VALUE_TERMS.has(token))) {\n      return true;\n    }\n  }\n  return false;\n}\n\n/**\n * Cheap pre-filter before the (much costlier) boundary regex.\n *\n * Sound because `normalize` collapses horizontal whitespace to a single space\n * and a name never spans a line break: whenever the pattern can match, the\n * literal name is a substring of the text.\n */\nfunction collectCandidates(normalizedText: string): Candidate[] {\n  const candidates: Candidate[] = [];\n  for (const [name, slot] of getNamePatterns()) {\n    if (!normalizedText.includes(name)) {\n      continue;\n    }\n    const { entries } = slot;\n    const regex = (slot.regex ??= buildNamePattern(name));\n    regex.lastIndex = 0;\n    let occurrences = 0;\n    let match = regex.exec(normalizedText);\n    while (match !== null && occurrences < MAX_OCCURRENCES_PER_NAME) {\n      candidates.push({ end: match.index + match[0].length, entries, start: match.index });\n      occurrences += 1;\n      match = regex.exec(normalizedText);\n    }\n  }\n  return candidates;\n}\n\n/**\n * Longest match wins: drop a match fully contained in a longer one, so\n * `Cholesterol` doesn't anchor inside `HDL Cholesterol` and `Blood` doesn't\n * anchor inside `Blood Glucose`.\n *\n * Strictly longer, not longer-or-equal: containment plus equal length means an\n * identical span, which only happens when two distinct catalog names match the\n * same text (a singular and its plural form, say). Dropping one of those by\n * catalog order would silently lose a code, and losing an anchor is worse than\n * keeping both — `findBiomarkersInText` dedups per code anyway.\n */\nfunction resolveOverlaps(candidates: Candidate[]): Candidate[] {\n  const sorted = [...candidates].sort(\n    (a, b) => b.end - b.start - (a.end - a.start) || a.start - b.start,\n  );\n  const accepted: Candidate[] = [];\n  for (const candidate of sorted) {\n    const length = candidate.end - candidate.start;\n    const swallowed = accepted.some(\n      (other) =>\n        other.start <= candidate.start &&\n        candidate.end <= other.end &&\n        other.end - other.start > length,\n    );\n    if (!swallowed) {\n      accepted.push(candidate);\n    }\n  }\n  return accepted;\n}\n\n/**\n * Find all biomarker names present in OCR text.\n *\n * Matching is whole-token, longest-match-wins, and context-aware: matches\n * inside genetic report lines are discarded, and generic names only anchor\n * when a value sits on the same line. Returns one match per biomarker code —\n * the highest-confidence occurrence.\n */\nexport function findBiomarkersInText(ocrText: string): AnchorResult {\n  const startTime = Date.now();\n  const normalizedText = normalize(ocrText);\n  const bestByCode = new Map<string, AnchorMatch>();\n  const geneticLines = new Map<number, boolean>();\n  const valueLines = new Map<number, boolean>();\n  const girthLines = new Map<number, boolean>();\n\n  for (const candidate of resolveOverlaps(collectCandidates(normalizedText))) {\n    const { end: lineEnd, start: lineStart } = getLineBounds(normalizedText, candidate.start);\n\n    let genetic = geneticLines.get(lineStart);\n    if (genetic === undefined) {\n      genetic = hasGeneticContext(normalizedText.slice(lineStart, lineEnd));\n      geneticLines.set(lineStart, genetic);\n    }\n    if (genetic) {\n      continue;\n    }\n\n    let hasValue = valueLines.get(lineStart);\n    if (hasValue === undefined) {\n      hasValue = hasValueEvidence(normalizedText.slice(lineStart, lineEnd));\n      valueLines.set(lineStart, hasValue);\n    }\n\n    let girth = girthLines.get(lineStart);\n    if (girth === undefined) {\n      girth = hasGirthContext(normalizedText.slice(lineStart, lineEnd));\n      girthLines.set(lineStart, girth);\n    }\n\n    for (const entry of candidate.entries) {\n      if (entry.ambiguous && !hasValue) {\n        continue;\n      }\n\n      if (girth && SKINFOLD_SITE_CODES.has(entry.code)) {\n        continue;\n      }\n\n      let confidence = CONFIDENCE_NAME_ONLY;\n      if (entry.ambiguous) {\n        confidence = CONFIDENCE_AMBIGUOUS;\n      } else if (hasValue) {\n        confidence = CONFIDENCE_VALUE_ADJACENT;\n      }\n\n      const existing = bestByCode.get(entry.code);\n      const better =\n        !existing ||\n        confidence > existing.confidence ||\n        (confidence === existing.confidence && candidate.start < existing.position);\n      if (better) {\n        bestByCode.set(entry.code, {\n          code: entry.code,\n          confidence,\n          loinc: entry.loinc,\n          matchedName: entry.original,\n          position: candidate.start,\n        });\n      }\n    }\n  }\n\n  const matches = Array.from(bestByCode.values()).sort((a, b) => a.position - b.position);\n  const scanTimeMs = Date.now() - startTime;\n\n  return {\n    filteredReference: generateFilteredLLMReference(matches.map((m) => m.code)),\n    matches,\n    stats: {\n      matchedCount: matches.length,\n      scanTimeMs,\n      totalPatterns: getPatterns().length,\n    },\n  };\n}\n\n/**\n * Get the list of matched biomarker codes from an anchor result.\n */\nexport function getMatchedCodes(result: AnchorResult): string[] {\n  return result.matches.map((m) => m.code);\n}\n"]}

package/dist/index.js

@@ -138,6 +138,28 @@ var GENETIC_CONTEXT_PATTERNS = [
   /\bhomozigot/,
   /\bsequence change\b/
 ];
+var SKINFOLD_SITE_CODES = /* @__PURE__ */ new Set([
+  "SkinfoldAbdominal",
+  "SkinfoldChest",
+  "SkinfoldMidaxillary",
+  "SkinfoldSubscapular",
+  "SkinfoldSuprailiac",
+  "SkinfoldThigh",
+  "SkinfoldTriceps"
+]);
+var GIRTH_CONTEXT_PATTERNS = [
+  /\bcircumference\b/,
+  /\bcircunferencias?\b/,
+  /\bperimetros?\b/,
+  /\bgirth\b/
+];
+var SKINFOLD_CONTEXT_PATTERNS = [/\bdobras?\b/, /\bskin ?folds?\b/, /\bpregas?\b/];
+function hasGirthContext(line) {
+  if (SKINFOLD_CONTEXT_PATTERNS.some((re) => re.test(line))) {
+    return false;
+  }
+  return GIRTH_CONTEXT_PATTERNS.some((re) => re.test(line));
+}
 var DIGIT_PATTERN = /\d/;
 var cachedUnitTokens = null;
 function getUnitTokens() {
@@ -264,6 +286,7 @@ function findBiomarkersInText(ocrText) {
   const bestByCode = /* @__PURE__ */ new Map();
   const geneticLines = /* @__PURE__ */ new Map();
   const valueLines = /* @__PURE__ */ new Map();
+  const girthLines = /* @__PURE__ */ new Map();
   for (const candidate of resolveOverlaps(collectCandidates(normalizedText))) {
     const { end: lineEnd, start: lineStart } = getLineBounds(normalizedText, candidate.start);
     let genetic = geneticLines.get(lineStart);
@@ -279,10 +302,18 @@ function findBiomarkersInText(ocrText) {
       hasValue = hasValueEvidence(normalizedText.slice(lineStart, lineEnd));
       valueLines.set(lineStart, hasValue);
     }
+    let girth = girthLines.get(lineStart);
+    if (girth === void 0) {
+      girth = hasGirthContext(normalizedText.slice(lineStart, lineEnd));
+      girthLines.set(lineStart, girth);
+    }
     for (const entry of candidate.entries) {
       if (entry.ambiguous && !hasValue) {
         continue;
       }
+      if (girth && SKINFOLD_SITE_CODES.has(entry.code)) {
+        continue;
+      }
       let confidence = CONFIDENCE_NAME_ONLY;
       if (entry.ambiguous) {
         confidence = CONFIDENCE_AMBIGUOUS;

package/dist/index.js.map

@@ -1 +1 @@
-{"version":3,"sources":["../src/anchor.ts"],"sourcesContent":["/**\n * OCR Anchor — Biomarker text anchoring\n *\n * Scans OCR text for biomarker names BEFORE sending to LLM.\n * This prevents hallucination by constraining what biomarkers\n * the LLM is allowed to extract.\n *\n * Matching is deliberately conservative: a name only anchors when it appears\n * as a whole token, is not swallowed by a longer biomarker name, is not inside\n * a genetic report line, and — for generic single-word names — sits on a line\n * that actually carries a value.\n */\n\nimport {\n  type BiomarkerSearchPattern,\n  generateFilteredLLMReference,\n  getAllSearchPatterns,\n  UNIT_TO_UCUM,\n} from '@precisa-saude/fhir';\n\nexport interface AnchorMatch {\n  code: string;\n  confidence: number;\n  loinc?: string;\n  matchedName: string;\n  position: number;\n}\n\nexport interface AnchorResult {\n  filteredReference: string;\n  matches: AnchorMatch[];\n  stats: {\n    totalPatterns: number;\n    matchedCount: number;\n    scanTimeMs: number;\n  };\n}\n\n/**\n * Confidence assigned to a specific biomarker name found on a line that also\n * carries a value (a number, a unit, or an expected qualitative term).\n */\nexport const CONFIDENCE_VALUE_ADJACENT = 1.0;\n\n/**\n * Confidence assigned to a specific biomarker name with no value evidence\n * nearby — a section heading, or a mention in prose.\n */\nexport const CONFIDENCE_NAME_ONLY = 0.7;\n\n/**\n * Confidence assigned to a generic/ambiguous name (`Color`, `Protein`,\n * `Blood`, …) that only anchored because a value was found next to it.\n */\nexport const CONFIDENCE_AMBIGUOUS = 0.4;\n\n/** Cap on how many occurrences of the same name are inspected per document. */\nconst MAX_OCCURRENCES_PER_NAME = 5;\n\n/**\n * Normalize text for comparison:\n * - Removes diacritics (ã→a, ç→c, é→e)\n * - Converts to lowercase\n * - Collapses horizontal whitespace, but KEEPS line breaks — the line is the\n *   context window used to decide whether a match is a real biomarker mention\n */\nfunction normalize(text: string): string {\n  return text\n    .normalize('NFD')\n    .replace(/[\\u0300-\\u036f]/g, '')\n    .toLowerCase()\n    .replace(/[^\\S\\n]+/g, ' ');\n}\n\nconst UNAMBIGUOUS_SHORT_NAMES = new Set([\n  'hdl',\n  'ldl',\n  'lh',\n  'tsh',\n  'crp',\n  'pcr',\n  'ggt',\n  'alt',\n  'ast',\n  'bun',\n  'wbc',\n  'rbc',\n  'mcv',\n  'mch',\n  'rdw',\n  'mpv',\n  'psa',\n  'fsh',\n  'hba1c',\n  'egfr',\n  'acr',\n  'esr',\n  'vhs',\n  'bmc',\n  'bmd',\n  'vat',\n  'dxa',\n  'dmo',\n  'cmo',\n  'ffm',\n  'lbm',\n  'mlg',\n  'tav',\n]);\n\n/**\n * Single-word catalog names that are ordinary words in EN/PT, so seeing them\n * proves nothing on its own. They only anchor when the line also carries a\n * value. Qualitative urine markers (`Color`, `Protein`, `Blood`, …) are\n * detected automatically — see `isQualitativeUrine` — and don't belong here.\n */\nconst CONTEXT_REQUIRED_NAMES = new Set([\n  'bacteria', // Bacteria_Urine — tem unidade, escapa da regra automática\n  'bacterias', // Bacteria_Urine\n  'lead', // Lead — verbo/substantivo comuníssimo em inglês\n  'peso', // TotalMass\n  'saturation', // TransferrinSaturation — \"oxygen saturation\", \"saturation index\"\n  'tap', // ProthrombinTime — \"tap\" em inglês\n  'volume', // VATVolume\n  'weight', // TotalMass\n]);\n\n/**\n * Qualitative results expected next to a non-numeric biomarker\n * (urine dipstick, sediment, appearance). Normalized, single tokens —\n * \"não reagente\" is covered by `reagente`, \"não detectado\" by `detectado`.\n */\nconst QUALITATIVE_VALUE_TERMS = new Set([\n  'absent',\n  'alguns',\n  'amarela',\n  'amarelo',\n  'anormal',\n  'ausencia',\n  'ausente',\n  'ausentes',\n  'citrino',\n  'claro',\n  'clear',\n  'cloudy',\n  'colorless',\n  'detectado',\n  'detected',\n  'escuro',\n  'incolor',\n  'indetectavel',\n  'limpido',\n  'moderada',\n  'moderado',\n  'negativa',\n  'negative',\n  'negativo',\n  'normais',\n  'normal',\n  'numerosos',\n  'ocasional',\n  'positiva',\n  'positive',\n  'positivo',\n  'present',\n  'presente',\n  'presentes',\n  'raras',\n  'raro',\n  'raros',\n  'reagente',\n  'trace',\n  'traces',\n  'tracos',\n  'turvo',\n  'undetectable',\n  'yellow',\n]);\n\n/**\n * Signals that a line comes from a genetic/molecular report rather than from a\n * panel of measured values. Gene symbols collide with biomarker names (`APOB`\n * the gene vs. `ApoB` the lipoprotein), so the context — not a static HGNC\n * blocklist — is what tells them apart. 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Dropping one of those by\n * catalog order would silently lose a code, and losing an anchor is worse than\n * keeping both — `findBiomarkersInText` dedups per code anyway.\n */\nfunction resolveOverlaps(candidates: Candidate[]): Candidate[] {\n  const sorted = [...candidates].sort(\n    (a, b) => b.end - b.start - (a.end - a.start) || a.start - b.start,\n  );\n  const accepted: Candidate[] = [];\n  for (const candidate of sorted) {\n    const length = candidate.end - candidate.start;\n    const swallowed = accepted.some(\n      (other) =>\n        other.start <= candidate.start &&\n        candidate.end <= other.end &&\n        other.end - other.start > length,\n    );\n    if (!swallowed) {\n      accepted.push(candidate);\n    }\n  }\n  return accepted;\n}\n\n/**\n * Find all biomarker names present in OCR text.\n *\n * Matching is whole-token, longest-match-wins, and context-aware: matches\n * inside genetic report lines are discarded, and generic names only anchor\n * when a value sits on the same line. 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valueLines.set(lineStart, hasValue);\n    }\n\n    for (const entry of candidate.entries) {\n      if (entry.ambiguous && !hasValue) {\n        continue;\n      }\n\n      let confidence = CONFIDENCE_NAME_ONLY;\n      if (entry.ambiguous) {\n        confidence = CONFIDENCE_AMBIGUOUS;\n      } else if (hasValue) {\n        confidence = CONFIDENCE_VALUE_ADJACENT;\n      }\n\n      const existing = bestByCode.get(entry.code);\n      const better =\n        !existing ||\n        confidence > existing.confidence ||\n        (confidence === existing.confidence && candidate.start < existing.position);\n      if (better) {\n        bestByCode.set(entry.code, {\n          code: entry.code,\n          confidence,\n          loinc: entry.loinc,\n          matchedName: entry.original,\n          position: candidate.start,\n        });\n      }\n    }\n  }\n\n  const matches = Array.from(bestByCode.values()).sort((a, b) => a.position - b.position);\n  const scanTimeMs = Date.now() - startTime;\n\n  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+{"version":3,"sources":["../src/anchor.ts"],"sourcesContent":["/**\n * OCR Anchor — Biomarker text anchoring\n *\n * Scans OCR text for biomarker names BEFORE sending to LLM.\n * This prevents hallucination by constraining what biomarkers\n * the LLM is allowed to extract.\n *\n * Matching is deliberately conservative: a name only anchors when it appears\n * as a whole token, is not swallowed by a longer biomarker name, is not inside\n * a genetic report line, and — for generic single-word names — sits on a line\n * that actually carries a value.\n */\n\nimport {\n  type BiomarkerSearchPattern,\n  generateFilteredLLMReference,\n  getAllSearchPatterns,\n  UNIT_TO_UCUM,\n} from '@precisa-saude/fhir';\n\nexport interface AnchorMatch {\n  code: string;\n  confidence: number;\n  loinc?: string;\n  matchedName: string;\n  position: number;\n}\n\nexport interface AnchorResult {\n  filteredReference: string;\n  matches: AnchorMatch[];\n  stats: {\n    totalPatterns: number;\n    matchedCount: number;\n    scanTimeMs: number;\n  };\n}\n\n/**\n * Confidence assigned to a specific biomarker name found on a line that also\n * carries a value (a number, a unit, or an expected qualitative term).\n */\nexport const CONFIDENCE_VALUE_ADJACENT = 1.0;\n\n/**\n * Confidence assigned to a specific biomarker name with no value evidence\n * nearby — a section heading, or a mention in prose.\n */\nexport const CONFIDENCE_NAME_ONLY = 0.7;\n\n/**\n * Confidence assigned to a generic/ambiguous name (`Color`, `Protein`,\n * `Blood`, …) that only anchored because a value was found next to it.\n */\nexport const CONFIDENCE_AMBIGUOUS = 0.4;\n\n/** Cap on how many occurrences of the same name are inspected per document. */\nconst MAX_OCCURRENCES_PER_NAME = 5;\n\n/**\n * Normalize text for comparison:\n * - Removes diacritics (ã→a, ç→c, é→e)\n * - Converts to lowercase\n * - Collapses horizontal whitespace, but KEEPS line breaks — the line is the\n *   context window used to decide whether a match is a real biomarker mention\n */\nfunction normalize(text: string): string {\n  return text\n    .normalize('NFD')\n    .replace(/[\\u0300-\\u036f]/g, '')\n    .toLowerCase()\n    .replace(/[^\\S\\n]+/g, ' ');\n}\n\nconst UNAMBIGUOUS_SHORT_NAMES = new Set([\n  'hdl',\n  'ldl',\n  'lh',\n  'tsh',\n  'crp',\n  'pcr',\n  'ggt',\n  'alt',\n  'ast',\n  'bun',\n  'wbc',\n  'rbc',\n  'mcv',\n  'mch',\n  'rdw',\n  'mpv',\n  'psa',\n  'fsh',\n  'hba1c',\n  'egfr',\n  'acr',\n  'esr',\n  'vhs',\n  'bmc',\n  'bmd',\n  'vat',\n  'dxa',\n  'dmo',\n  'cmo',\n  'ffm',\n  'lbm',\n  'mlg',\n  'tav',\n]);\n\n/**\n * Single-word catalog names that are ordinary words in EN/PT, so seeing them\n * proves nothing on its own. They only anchor when the line also carries a\n * value. Qualitative urine markers (`Color`, `Protein`, `Blood`, …) are\n * detected automatically — see `isQualitativeUrine` — and don't belong here.\n */\nconst CONTEXT_REQUIRED_NAMES = new Set([\n  'bacteria', // Bacteria_Urine — tem unidade, escapa da regra automática\n  'bacterias', // Bacteria_Urine\n  'lead', // Lead — verbo/substantivo comuníssimo em inglês\n  'peso', // TotalMass\n  'saturation', // TransferrinSaturation — \"oxygen saturation\", \"saturation index\"\n  'tap', // ProthrombinTime — \"tap\" em inglês\n  'volume', // VATVolume\n  'weight', // TotalMass\n]);\n\n/**\n * Qualitative results expected next to a non-numeric biomarker\n * (urine dipstick, sediment, appearance). Normalized, single tokens —\n * \"não reagente\" is covered by `reagente`, \"não detectado\" by `detectado`.\n */\nconst QUALITATIVE_VALUE_TERMS = new Set([\n  'absent',\n  'alguns',\n  'amarela',\n  'amarelo',\n  'anormal',\n  'ausencia',\n  'ausente',\n  'ausentes',\n  'citrino',\n  'claro',\n  'clear',\n  'cloudy',\n  'colorless',\n  'detectado',\n  'detected',\n  'escuro',\n  'incolor',\n  'indetectavel',\n  'limpido',\n  'moderada',\n  'moderado',\n  'negativa',\n  'negative',\n  'negativo',\n  'normais',\n  'normal',\n  'numerosos',\n  'ocasional',\n  'positiva',\n  'positive',\n  'positivo',\n  'present',\n  'presente',\n  'presentes',\n  'raras',\n  'raro',\n  'raros',\n  'reagente',\n  'trace',\n  'traces',\n  'tracos',\n  'turvo',\n  'undetectable',\n  'yellow',\n]);\n\n/**\n * Signals that a line comes from a genetic/molecular report rather than from a\n * panel of measured values. Gene symbols collide with biomarker names (`APOB`\n * the gene vs. `ApoB` the lipoprotein), so the context — not a static HGNC\n * blocklist — is what tells them apart. Blocking the token itself would break\n * real lipid panels.\n */\nconst GENETIC_CONTEXT_PATTERNS: RegExp[] = [\n  /\\b[nx][mrpc]_\\d{6,}/, // RefSeq: NM_000384.2, NP_, NR_, XM_\n  /\\bens[gtp]\\d{6,}/, // Ensembl: ENSG00000084674\n  /\\bp\\.[a-z]{3}\\d/, // HGVS proteína: p.Trp448*\n  /\\bc\\.\\d+[acgt]?[>_+-]/, // HGVS codificante: c.1234A>G, c.76_78del\n  /\\brs\\d{4,}\\b/, // dbSNP\n  /\\bgenes?\\b/,\n  /\\bvariante?s?\\b/,\n  /\\bexons?\\b/,\n  /\\bzygosity\\b/,\n  /\\bzigosidade\\b/,\n  /\\balleles?\\b/,\n  /\\balelos?\\b/,\n  /\\bmutations?\\b/,\n  /\\bmutac(ao|oes)\\b/,\n  /\\bpathogenic/,\n  /\\bpatogenic/,\n  /\\bheterozyg/,\n  /\\bhomozyg/,\n  /\\bheterozigot/,\n  /\\bhomozigot/,\n  /\\bsequence change\\b/,\n];\n\n/**\n * Sítios de dobra cutânea cujo nome nu também nomeia uma circunferência:\n * \"Coxa\" aparece tanto em \"Dobra Cutânea Coxa\" quanto em \"Circunferência da\n * Coxa\". 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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@precisa-saude/fhir-ocr-utils",
-  "version": "0.20.2",
+  "version": "0.20.3",
   "description": "Utilitários de ancoragem OCR para extração de biomarcadores de PDFs de resultados laboratoriais",
   "keywords": [
     "fhir",
@@ -41,7 +41,7 @@
     "dist"
   ],
   "dependencies": {
-    "@precisa-saude/fhir": "^0.20.2"
+    "@precisa-saude/fhir": "^0.20.3"
   },
   "devDependencies": {
     "tsup": "^8.3.5",