@the-cascade-protocol/cli 0.2.0 → 0.2.1

package/src/lib/fhir-converter/converters-clinical.ts

@@ -1,446 +0,0 @@
-/**
- * FHIR -> Cascade converters for clinical record types.
- *
- * Converts:
- *   - MedicationStatement / MedicationRequest -> health:MedicationRecord
- *   - Condition -> health:ConditionRecord
- *   - AllergyIntolerance -> health:AllergyRecord
- *   - Observation (lab) -> health:LabResultRecord
- *   - Observation (vital) -> clinical:VitalSign
- */
-
-import { randomUUID } from 'node:crypto';
-import type { Quad } from 'n3';
-
-import {
-  type ConversionResult,
-  NS,
-  CODING_SYSTEM_MAP,
-  VITAL_LOINC_CODES,
-  VITAL_CATEGORIES,
-  extractCodings,
-  codeableConceptText,
-  tripleStr,
-  tripleBool,
-  tripleDouble,
-  tripleRef,
-  tripleType,
-  tripleDateTime,
-  commonTriples,
-  quadsToJsonLd,
-} from './types.js';
-
-// ---------------------------------------------------------------------------
-// Medication converter
-// ---------------------------------------------------------------------------
-
-export function convertMedicationStatement(resource: any): ConversionResult & { _quads: Quad[] } {
-  const warnings: string[] = [];
-  const subjectUri = `urn:uuid:${randomUUID()}`;
-  const quads: Quad[] = [];
-
-  quads.push(tripleType(subjectUri, NS.health + 'MedicationRecord'));
-  quads.push(...commonTriples(subjectUri));
-
-  // Medication name
-  const medName = codeableConceptText(resource.medicationCodeableConcept)
-    ?? resource.medicationReference?.display
-    ?? 'Unknown Medication';
-  quads.push(tripleStr(subjectUri, NS.health + 'medicationName', medName));
-
-  // isActive from FHIR status
-  const status = resource.status as string | undefined;
-  const isActive = status === 'active' || status === 'intended' || status === 'on-hold';
-  quads.push(tripleBool(subjectUri, NS.health + 'isActive', isActive));
-
-  // Drug codes
-  const codings = extractCodings(resource.medicationCodeableConcept);
-  for (const coding of codings) {
-    const nsUri = CODING_SYSTEM_MAP[coding.system];
-    if (nsUri) {
-      quads.push(tripleRef(subjectUri, NS.clinical + 'drugCode', nsUri + coding.code));
-      if (nsUri === NS.rxnorm) {
-        quads.push(tripleRef(subjectUri, NS.health + 'rxNormCode', nsUri + coding.code));
-      }
-    } else {
-      warnings.push(`Unknown coding system: ${coding.system} (code ${coding.code})`);
-    }
-  }
-
-  // Dosage
-  const dosage = Array.isArray(resource.dosage) ? resource.dosage[0] : undefined;
-  if (dosage) {
-    if (dosage.text) {
-      quads.push(tripleStr(subjectUri, NS.health + 'dose', dosage.text));
-    }
-    if (dosage.route?.text) {
-      quads.push(tripleStr(subjectUri, NS.health + 'route', dosage.route.text));
-    } else if (dosage.route?.coding?.[0]?.display) {
-      quads.push(tripleStr(subjectUri, NS.health + 'route', dosage.route.coding[0].display));
-    }
-    if (dosage.timing?.repeat?.frequency) {
-      const freq = dosage.timing.repeat.frequency;
-      const periodUnit = dosage.timing.repeat.periodUnit ?? 'd';
-      const unitLabel = periodUnit === 'd' ? 'daily' : periodUnit === 'wk' ? 'weekly' : periodUnit;
-      const freqText = freq === 1 ? `once ${unitLabel}` : `${freq} times ${unitLabel}`;
-      quads.push(tripleStr(subjectUri, NS.health + 'frequency', freqText));
-    }
-  }
-
-  // Effective period
-  if (resource.effectivePeriod?.start) {
-    quads.push(tripleDateTime(subjectUri, NS.health + 'startDate', resource.effectivePeriod.start));
-  } else if (resource.effectiveDateTime) {
-    quads.push(tripleDateTime(subjectUri, NS.health + 'startDate', resource.effectiveDateTime));
-  }
-  if (resource.effectivePeriod?.end) {
-    quads.push(tripleDateTime(subjectUri, NS.health + 'endDate', resource.effectivePeriod.end));
-  }
-
-  // Provenance class -- based on resource type
-  const fhirResourceType = resource.resourceType as string;
-  if (fhirResourceType === 'MedicationStatement') {
-    quads.push(tripleStr(subjectUri, NS.clinical + 'sourceFhirResourceType', 'MedicationStatement'));
-    quads.push(tripleStr(subjectUri, NS.clinical + 'clinicalIntent', 'reportedUse'));
-  } else if (fhirResourceType === 'MedicationRequest') {
-    quads.push(tripleStr(subjectUri, NS.clinical + 'sourceFhirResourceType', 'MedicationRequest'));
-    quads.push(tripleStr(subjectUri, NS.clinical + 'clinicalIntent', 'prescribed'));
-  }
-  quads.push(tripleStr(subjectUri, NS.clinical + 'provenanceClass', 'imported'));
-
-  if (resource.id) {
-    quads.push(tripleStr(subjectUri, NS.health + 'sourceRecordId', resource.id));
-  }
-
-  if (resource.note && Array.isArray(resource.note)) {
-    const noteText = resource.note.map((n: any) => n.text).filter(Boolean).join('; ');
-    if (noteText) quads.push(tripleStr(subjectUri, NS.health + 'notes', noteText));
-  }
-
-  return {
-    turtle: '',
-    warnings,
-    resourceType: fhirResourceType,
-    cascadeType: 'health:MedicationRecord',
-    jsonld: quadsToJsonLd(quads, 'health:MedicationRecord'),
-    _quads: quads,
-  } as ConversionResult & { _quads: Quad[] };
-}
-
-// ---------------------------------------------------------------------------
-// Condition converter
-// ---------------------------------------------------------------------------
-
-export function convertCondition(resource: any): ConversionResult & { _quads: Quad[] } {
-  const warnings: string[] = [];
-  const subjectUri = `urn:uuid:${randomUUID()}`;
-  const quads: Quad[] = [];
-
-  quads.push(tripleType(subjectUri, NS.health + 'ConditionRecord'));
-  quads.push(...commonTriples(subjectUri));
-
-  const condName = codeableConceptText(resource.code) ?? 'Unknown Condition';
-  quads.push(tripleStr(subjectUri, NS.health + 'conditionName', condName));
-
-  const clinicalStatus = resource.clinicalStatus?.coding?.[0]?.code ?? 'active';
-  quads.push(tripleStr(subjectUri, NS.health + 'status', clinicalStatus));
-
-  if (resource.onsetDateTime) {
-    quads.push(tripleDateTime(subjectUri, NS.health + 'onsetDate', resource.onsetDateTime));
-  } else if (resource.onsetPeriod?.start) {
-    quads.push(tripleDateTime(subjectUri, NS.health + 'onsetDate', resource.onsetPeriod.start));
-  }
-
-  if (resource.abatementDateTime) {
-    quads.push(tripleDateTime(subjectUri, NS.health + 'abatementDate', resource.abatementDateTime));
-  }
-
-  const codings = extractCodings(resource.code);
-  for (const coding of codings) {
-    const nsUri = CODING_SYSTEM_MAP[coding.system];
-    if (nsUri === NS.icd10) {
-      quads.push(tripleRef(subjectUri, NS.health + 'icd10Code', nsUri + coding.code));
-    } else if (nsUri === NS.sct) {
-      quads.push(tripleRef(subjectUri, NS.health + 'snomedCode', nsUri + coding.code));
-    } else if (nsUri) {
-      warnings.push(`Condition code from non-standard system: ${coding.system}`);
-    }
-  }
-
-  if (resource.id) {
-    quads.push(tripleStr(subjectUri, NS.health + 'sourceRecordId', resource.id));
-  }
-
-  if (resource.note && Array.isArray(resource.note)) {
-    const noteText = resource.note.map((n: any) => n.text).filter(Boolean).join('; ');
-    if (noteText) quads.push(tripleStr(subjectUri, NS.health + 'notes', noteText));
-  }
-
-  return {
-    turtle: '',
-    jsonld: quadsToJsonLd(quads, 'health:ConditionRecord'),
-    warnings,
-    resourceType: 'Condition',
-    cascadeType: 'health:ConditionRecord',
-    _quads: quads,
-  };
-}
-
-// ---------------------------------------------------------------------------
-// AllergyIntolerance converter
-// ---------------------------------------------------------------------------
-
-export function convertAllergyIntolerance(resource: any): ConversionResult & { _quads: Quad[] } {
-  const warnings: string[] = [];
-  const subjectUri = `urn:uuid:${randomUUID()}`;
-  const quads: Quad[] = [];
-
-  quads.push(tripleType(subjectUri, NS.health + 'AllergyRecord'));
-  quads.push(...commonTriples(subjectUri));
-
-  const allergen = codeableConceptText(resource.code) ?? 'Unknown Allergen';
-  quads.push(tripleStr(subjectUri, NS.health + 'allergen', allergen));
-
-  if (Array.isArray(resource.category) && resource.category.length > 0) {
-    quads.push(tripleStr(subjectUri, NS.health + 'allergyCategory', resource.category[0]));
-  }
-
-  if (Array.isArray(resource.reaction) && resource.reaction.length > 0) {
-    const manifestations = resource.reaction
-      .flatMap((r: any) => r.manifestation ?? [])
-      .map((m: any) => codeableConceptText(m))
-      .filter(Boolean);
-    if (manifestations.length > 0) {
-      quads.push(tripleStr(subjectUri, NS.health + 'reaction', manifestations.join(', ')));
-    }
-    const severity = resource.reaction[0]?.severity;
-    if (severity) {
-      const severityMap: Record<string, string> = { mild: 'mild', moderate: 'moderate', severe: 'severe' };
-      quads.push(tripleStr(subjectUri, NS.health + 'allergySeverity', severityMap[severity] ?? severity));
-    }
-  }
-
-  if (resource.criticality && !(Array.isArray(resource.reaction) && resource.reaction[0]?.severity)) {
-    const critMap: Record<string, string> = { low: 'mild', high: 'severe', 'unable-to-assess': 'moderate' };
-    quads.push(tripleStr(subjectUri, NS.health + 'allergySeverity', critMap[resource.criticality] ?? resource.criticality));
-  }
-
-  if (resource.onsetDateTime) {
-    quads.push(tripleDateTime(subjectUri, NS.health + 'onsetDate', resource.onsetDateTime));
-  }
-
-  if (resource.id) {
-    quads.push(tripleStr(subjectUri, NS.health + 'sourceRecordId', resource.id));
-  }
-
-  if (resource.note && Array.isArray(resource.note)) {
-    const noteText = resource.note.map((n: any) => n.text).filter(Boolean).join('; ');
-    if (noteText) quads.push(tripleStr(subjectUri, NS.health + 'notes', noteText));
-  }
-
-  return {
-    turtle: '',
-    jsonld: quadsToJsonLd(quads, 'health:AllergyRecord'),
-    warnings,
-    resourceType: 'AllergyIntolerance',
-    cascadeType: 'health:AllergyRecord',
-    _quads: quads,
-  };
-}
-
-// ---------------------------------------------------------------------------
-// Observation: vital sign detection
-// ---------------------------------------------------------------------------
-
-export function isVitalSignObservation(resource: any): boolean {
-  if (Array.isArray(resource.category)) {
-    for (const cat of resource.category) {
-      if (Array.isArray(cat.coding)) {
-        for (const c of cat.coding) {
-          if (VITAL_CATEGORIES.includes(c.code)) return true;
-        }
-      }
-    }
-  }
-  const codings = extractCodings(resource.code);
-  for (const c of codings) {
-    if (c.system === 'http://loinc.org' && VITAL_LOINC_CODES[c.code]) return true;
-  }
-  return false;
-}
-
-// ---------------------------------------------------------------------------
-// Observation (lab) converter
-// ---------------------------------------------------------------------------
-
-export function convertObservationLab(resource: any): ConversionResult & { _quads: Quad[] } {
-  const warnings: string[] = [];
-  const subjectUri = `urn:uuid:${randomUUID()}`;
-  const quads: Quad[] = [];
-
-  quads.push(tripleType(subjectUri, NS.health + 'LabResultRecord'));
-  quads.push(...commonTriples(subjectUri));
-
-  const testName = codeableConceptText(resource.code) ?? 'Unknown Lab Test';
-  quads.push(tripleStr(subjectUri, NS.health + 'testName', testName));
-
-  if (resource.valueQuantity) {
-    quads.push(tripleStr(subjectUri, NS.health + 'resultValue', String(resource.valueQuantity.value)));
-    if (resource.valueQuantity.unit) {
-      quads.push(tripleStr(subjectUri, NS.health + 'resultUnit', resource.valueQuantity.unit));
-    }
-  } else if (resource.valueString) {
-    quads.push(tripleStr(subjectUri, NS.health + 'resultValue', resource.valueString));
-  } else if (resource.valueCodeableConcept) {
-    const valText = codeableConceptText(resource.valueCodeableConcept) ?? '';
-    quads.push(tripleStr(subjectUri, NS.health + 'resultValue', valText));
-  } else {
-    quads.push(tripleStr(subjectUri, NS.health + 'resultValue', ''));
-    warnings.push('No result value found in Observation resource');
-  }
-
-  if (resource.interpretation && Array.isArray(resource.interpretation) && resource.interpretation.length > 0) {
-    const interpCode = resource.interpretation[0]?.coding?.[0]?.code ?? 'unknown';
-    const interpMap: Record<string, string> = {
-      N: 'normal', H: 'abnormal', L: 'abnormal', A: 'abnormal',
-      HH: 'critical', LL: 'critical', AA: 'critical',
-      HU: 'critical', LU: 'critical',
-    };
-    quads.push(tripleStr(subjectUri, NS.health + 'interpretation', interpMap[interpCode] ?? 'unknown'));
-  } else {
-    quads.push(tripleStr(subjectUri, NS.health + 'interpretation', 'unknown'));
-  }
-
-  const effectiveDate = resource.effectiveDateTime ?? resource.effectivePeriod?.start ?? resource.issued;
-  if (effectiveDate) {
-    quads.push(tripleDateTime(subjectUri, NS.health + 'performedDate', effectiveDate));
-  } else {
-    warnings.push('No effective date found in Observation resource');
-  }
-
-  const codings = extractCodings(resource.code);
-  for (const c of codings) {
-    if (c.system === 'http://loinc.org') {
-      quads.push(tripleRef(subjectUri, NS.health + 'testCode', NS.loinc + c.code));
-    }
-  }
-
-  if (Array.isArray(resource.category)) {
-    for (const cat of resource.category) {
-      if (Array.isArray(cat.coding)) {
-        for (const c of cat.coding) {
-          if (c.code && c.code !== 'laboratory') {
-            quads.push(tripleStr(subjectUri, NS.health + 'labCategory', c.code));
-          }
-        }
-      }
-      if (cat.text) {
-        quads.push(tripleStr(subjectUri, NS.health + 'labCategory', cat.text));
-      }
-    }
-  }
-
-  if (Array.isArray(resource.referenceRange) && resource.referenceRange.length > 0) {
-    const rr = resource.referenceRange[0];
-    const parts: string[] = [];
-    if (rr.low?.value !== undefined) parts.push(String(rr.low.value));
-    if (rr.high?.value !== undefined) parts.push(String(rr.high.value));
-    const unit = rr.low?.unit ?? rr.high?.unit ?? '';
-    if (parts.length === 2) {
-      quads.push(tripleStr(subjectUri, NS.health + 'referenceRange', `${parts[0]}-${parts[1]} ${unit}`.trim()));
-    } else if (rr.text) {
-      quads.push(tripleStr(subjectUri, NS.health + 'referenceRange', rr.text));
-    }
-  }
-
-  if (resource.id) {
-    quads.push(tripleStr(subjectUri, NS.health + 'sourceRecordId', resource.id));
-  }
-
-  return {
-    turtle: '',
-    jsonld: quadsToJsonLd(quads, 'health:LabResultRecord'),
-    warnings,
-    resourceType: 'Observation',
-    cascadeType: 'health:LabResultRecord',
-    _quads: quads,
-  };
-}
-
-// ---------------------------------------------------------------------------
-// Observation (vital sign) converter
-// ---------------------------------------------------------------------------
-
-export function convertObservationVital(resource: any): ConversionResult & { _quads: Quad[] } {
-  const warnings: string[] = [];
-  const subjectUri = `urn:uuid:${randomUUID()}`;
-  const quads: Quad[] = [];
-
-  quads.push(tripleType(subjectUri, NS.clinical + 'VitalSign'));
-  quads.push(...commonTriples(subjectUri));
-
-  const codings = extractCodings(resource.code);
-  let vitalInfo: { type: string; name: string; unit: string; snomedCode: string } | undefined;
-  for (const c of codings) {
-    if (c.system === 'http://loinc.org' && VITAL_LOINC_CODES[c.code]) {
-      vitalInfo = VITAL_LOINC_CODES[c.code];
-      quads.push(tripleRef(subjectUri, NS.clinical + 'loincCode', NS.loinc + c.code));
-      break;
-    }
-  }
-
-  if (vitalInfo) {
-    quads.push(tripleStr(subjectUri, NS.clinical + 'vitalType', vitalInfo.type));
-    quads.push(tripleStr(subjectUri, NS.clinical + 'vitalTypeName', vitalInfo.name));
-    quads.push(tripleRef(subjectUri, NS.clinical + 'snomedCode', NS.sct + vitalInfo.snomedCode));
-  } else {
-    const name = codeableConceptText(resource.code) ?? 'Unknown Vital';
-    quads.push(tripleStr(subjectUri, NS.clinical + 'vitalType', name.toLowerCase().replace(/\s+/g, '_')));
-    quads.push(tripleStr(subjectUri, NS.clinical + 'vitalTypeName', name));
-    warnings.push(`Unknown vital sign LOINC code -- using display name: ${name}`);
-  }
-
-  if (resource.valueQuantity) {
-    quads.push(tripleDouble(subjectUri, NS.clinical + 'value', resource.valueQuantity.value));
-    quads.push(tripleStr(subjectUri, NS.clinical + 'unit', resource.valueQuantity.unit ?? vitalInfo?.unit ?? ''));
-  } else {
-    warnings.push('No valueQuantity found in vital sign Observation');
-  }
-
-  const effectiveDate = resource.effectiveDateTime ?? resource.effectivePeriod?.start;
-  if (effectiveDate) {
-    quads.push(tripleDateTime(subjectUri, NS.clinical + 'effectiveDate', effectiveDate));
-  }
-
-  if (Array.isArray(resource.referenceRange) && resource.referenceRange.length > 0) {
-    const rr = resource.referenceRange[0];
-    if (rr.low?.value !== undefined) {
-      quads.push(tripleDouble(subjectUri, NS.clinical + 'referenceRangeLow', rr.low.value));
-    }
-    if (rr.high?.value !== undefined) {
-      quads.push(tripleDouble(subjectUri, NS.clinical + 'referenceRangeHigh', rr.high.value));
-    }
-  }
-
-  if (resource.interpretation && Array.isArray(resource.interpretation) && resource.interpretation.length > 0) {
-    const interpCode = resource.interpretation[0]?.coding?.[0]?.code ?? 'unknown';
-    const interpMap: Record<string, string> = {
-      N: 'normal', H: 'high', L: 'low', A: 'abnormal',
-      HH: 'critical', LL: 'critical',
-    };
-    quads.push(tripleStr(subjectUri, NS.clinical + 'interpretation', interpMap[interpCode] ?? interpCode));
-  }
-
-  if (resource.id) {
-    quads.push(tripleStr(subjectUri, NS.health + 'sourceRecordId', resource.id));
-  }
-
-  return {
-    turtle: '',
-    jsonld: quadsToJsonLd(quads, 'clinical:VitalSign'),
-    warnings,
-    resourceType: 'Observation',
-    cascadeType: 'clinical:VitalSign',
-    _quads: quads,
-  };
-}