@the-cascade-protocol/cli 0.2.0 → 0.2.1

package/src/lib/fhir-converter/cascade-to-fhir.ts

@@ -1,369 +0,0 @@
-/**
- * Cascade -> FHIR (reverse conversion).
- *
- * Parses Cascade Protocol Turtle using n3, identifies the resource type from
- * rdf:type, and maps Cascade predicates back to FHIR R4 fields.
- *
- * Not all Cascade fields have FHIR equivalents -- lost fields are reported
- * as warnings.
- */
-
-import { Parser, type Quad } from 'n3';
-import { NS } from './types.js';
-
-/**
- * Convert Cascade Turtle to FHIR R4 JSON.
- */
-export async function convertCascadeToFhir(turtle: string): Promise<{
-  resources: any[];
-  warnings: string[];
-}> {
-  const warnings: string[] = [];
-  const resources: any[] = [];
-
-  // Parse Turtle
-  const parser = new Parser();
-  const quads: Quad[] = [];
-  try {
-    const parsed = parser.parse(turtle);
-    quads.push(...parsed);
-  } catch (err: any) {
-    return { resources: [], warnings: [`Turtle parse error: ${err.message}`] };
-  }
-
-  // Group quads by subject
-  const subjects = new Map<string, Quad[]>();
-  for (const q of quads) {
-    const subj = q.subject.value;
-    if (!subjects.has(subj)) subjects.set(subj, []);
-    subjects.get(subj)!.push(q);
-  }
-
-  for (const [_subjectUri, subjectQuads] of subjects) {
-    // Find rdf:type
-    const typeQuad = subjectQuads.find(q => q.predicate.value === NS.rdf + 'type');
-    if (!typeQuad) continue;
-
-    const rdfType = typeQuad.object.value;
-
-    // Build a predicate->value map for quick access
-    const pv = new Map<string, string[]>();
-    for (const q of subjectQuads) {
-      const pred = q.predicate.value;
-      if (!pv.has(pred)) pv.set(pred, []);
-      pv.get(pred)!.push(q.object.value);
-    }
-
-    const getFirst = (pred: string): string | undefined => pv.get(pred)?.[0];
-
-    if (rdfType === NS.health + 'MedicationRecord') {
-      const fhirResource: any = {
-        resourceType: 'MedicationStatement',
-        status: 'active',
-        medicationCodeableConcept: { text: getFirst(NS.health + 'medicationName') ?? '' },
-      };
-
-      // isActive -> status
-      const isActive = getFirst(NS.health + 'isActive');
-      if (isActive === 'false') fhirResource.status = 'stopped';
-
-      // Drug codes
-      const drugCodes = pv.get(NS.clinical + 'drugCode') ?? [];
-      const codingArr: any[] = [];
-      for (const uri of drugCodes) {
-        if (uri.startsWith(NS.rxnorm)) {
-          codingArr.push({ system: 'http://www.nlm.nih.gov/research/umls/rxnorm', code: uri.slice(NS.rxnorm.length) });
-        } else if (uri.startsWith(NS.sct)) {
-          codingArr.push({ system: 'http://snomed.info/sct', code: uri.slice(NS.sct.length) });
-        }
-      }
-      if (codingArr.length > 0) {
-        fhirResource.medicationCodeableConcept.coding = codingArr;
-      }
-
-      // Dosage
-      const doseText = getFirst(NS.health + 'dose');
-      if (doseText) {
-        fhirResource.dosage = [{ text: doseText }];
-      }
-
-      // Dates
-      const startDate = getFirst(NS.health + 'startDate');
-      const endDate = getFirst(NS.health + 'endDate');
-      if (startDate || endDate) {
-        fhirResource.effectivePeriod = {};
-        if (startDate) fhirResource.effectivePeriod.start = startDate;
-        if (endDate) fhirResource.effectivePeriod.end = endDate;
-      }
-
-      // Source record ID
-      const srcId = getFirst(NS.health + 'sourceRecordId');
-      if (srcId) fhirResource.id = srcId;
-
-      // Cascade-only fields that have no FHIR equivalent
-      const cascadeOnlyFields = [
-        NS.clinical + 'provenanceClass',
-        NS.clinical + 'clinicalIntent',
-        NS.cascade + 'schemaVersion',
-        NS.health + 'medicationClass',
-      ];
-      for (const field of cascadeOnlyFields) {
-        if (getFirst(field)) {
-          const shortName = field.split('#')[1] ?? field;
-          warnings.push(`Cascade field '${shortName}' has no FHIR equivalent and was not included in output`);
-        }
-      }
-
-      resources.push(fhirResource);
-    } else if (rdfType === NS.health + 'ConditionRecord') {
-      const fhirResource: any = {
-        resourceType: 'Condition',
-        code: {
-          text: getFirst(NS.health + 'conditionName') ?? '',
-        },
-      };
-
-      // Status
-      const status = getFirst(NS.health + 'status');
-      if (status) {
-        fhirResource.clinicalStatus = {
-          coding: [{ system: 'http://terminology.hl7.org/CodeSystem/condition-clinical', code: status }],
-        };
-      }
-
-      // Onset
-      const onset = getFirst(NS.health + 'onsetDate');
-      if (onset) fhirResource.onsetDateTime = onset;
-
-      // Codes
-      const codingArr: any[] = [];
-      const icd10 = pv.get(NS.health + 'icd10Code') ?? [];
-      for (const uri of icd10) {
-        codingArr.push({ system: 'http://hl7.org/fhir/sid/icd-10-cm', code: uri.startsWith(NS.icd10) ? uri.slice(NS.icd10.length) : uri });
-      }
-      const snomed = pv.get(NS.health + 'snomedCode') ?? [];
-      for (const uri of snomed) {
-        codingArr.push({ system: 'http://snomed.info/sct', code: uri.startsWith(NS.sct) ? uri.slice(NS.sct.length) : uri });
-      }
-      if (codingArr.length > 0) fhirResource.code.coding = codingArr;
-
-      const srcId = getFirst(NS.health + 'sourceRecordId');
-      if (srcId) fhirResource.id = srcId;
-
-      resources.push(fhirResource);
-    } else if (rdfType === NS.health + 'AllergyRecord') {
-      const fhirResource: any = {
-        resourceType: 'AllergyIntolerance',
-        code: { text: getFirst(NS.health + 'allergen') ?? '' },
-      };
-
-      const cat = getFirst(NS.health + 'allergyCategory');
-      if (cat) fhirResource.category = [cat];
-
-      const severity = getFirst(NS.health + 'allergySeverity');
-      const reaction = getFirst(NS.health + 'reaction');
-      if (reaction || severity) {
-        const rxn: any = {};
-        if (reaction) rxn.manifestation = [{ text: reaction }];
-        if (severity) rxn.severity = severity;
-        fhirResource.reaction = [rxn];
-      }
-
-      const onset = getFirst(NS.health + 'onsetDate');
-      if (onset) fhirResource.onsetDateTime = onset;
-
-      const srcId = getFirst(NS.health + 'sourceRecordId');
-      if (srcId) fhirResource.id = srcId;
-
-      resources.push(fhirResource);
-    } else if (rdfType === NS.health + 'LabResultRecord') {
-      const fhirResource: any = {
-        resourceType: 'Observation',
-        code: { text: getFirst(NS.health + 'testName') ?? '' },
-        category: [{ coding: [{ code: 'laboratory' }] }],
-      };
-
-      // LOINC code
-      const testCode = pv.get(NS.health + 'testCode') ?? [];
-      const codingArr: any[] = [];
-      for (const uri of testCode) {
-        const code = uri.startsWith(NS.loinc) ? uri.slice(NS.loinc.length) : uri;
-        codingArr.push({ system: 'http://loinc.org', code });
-      }
-      if (codingArr.length > 0) fhirResource.code.coding = codingArr;
-
-      // Value
-      const resultVal = getFirst(NS.health + 'resultValue');
-      const resultUnit = getFirst(NS.health + 'resultUnit');
-      if (resultVal) {
-        const numVal = parseFloat(resultVal);
-        if (!isNaN(numVal)) {
-          fhirResource.valueQuantity = { value: numVal };
-          if (resultUnit) fhirResource.valueQuantity.unit = resultUnit;
-        } else {
-          fhirResource.valueString = resultVal;
-        }
-      }
-
-      // Date
-      const perfDate = getFirst(NS.health + 'performedDate');
-      if (perfDate) fhirResource.effectiveDateTime = perfDate;
-
-      // Interpretation
-      const interp = getFirst(NS.health + 'interpretation');
-      if (interp) {
-        const revInterpMap: Record<string, string> = {
-          normal: 'N', abnormal: 'A', critical: 'HH', unknown: 'UNK',
-        };
-        fhirResource.interpretation = [{
-          coding: [{ code: revInterpMap[interp] ?? interp }],
-        }];
-      }
-
-      const srcId = getFirst(NS.health + 'sourceRecordId');
-      if (srcId) fhirResource.id = srcId;
-
-      resources.push(fhirResource);
-    } else if (rdfType === NS.clinical + 'VitalSign') {
-      const fhirResource: any = {
-        resourceType: 'Observation',
-        code: {},
-        category: [{ coding: [{ system: 'http://terminology.hl7.org/CodeSystem/observation-category', code: 'vital-signs' }] }],
-      };
-
-      // LOINC code
-      const loincUri = getFirst(NS.clinical + 'loincCode');
-      if (loincUri) {
-        const code = loincUri.startsWith(NS.loinc) ? loincUri.slice(NS.loinc.length) : loincUri;
-        fhirResource.code.coding = [{ system: 'http://loinc.org', code }];
-      }
-      const vitalName = getFirst(NS.clinical + 'vitalTypeName');
-      if (vitalName) fhirResource.code.text = vitalName;
-
-      // Value
-      const value = getFirst(NS.clinical + 'value');
-      const unit = getFirst(NS.clinical + 'unit');
-      if (value) {
-        fhirResource.valueQuantity = { value: parseFloat(value) };
-        if (unit) fhirResource.valueQuantity.unit = unit;
-      }
-
-      // Date
-      const effDate = getFirst(NS.clinical + 'effectiveDate');
-      if (effDate) fhirResource.effectiveDateTime = effDate;
-
-      const srcId = getFirst(NS.health + 'sourceRecordId');
-      if (srcId) fhirResource.id = srcId;
-
-      // Warn about Cascade-specific fields
-      if (getFirst(NS.clinical + 'snomedCode')) {
-        warnings.push("Cascade field 'snomedCode' has no standard FHIR Observation field and was not included");
-      }
-
-      resources.push(fhirResource);
-    } else if (rdfType === NS.cascade + 'PatientProfile') {
-      const fhirResource: any = {
-        resourceType: 'Patient',
-      };
-
-      const dob = getFirst(NS.cascade + 'dateOfBirth');
-      if (dob) fhirResource.birthDate = dob;
-
-      const sex = getFirst(NS.cascade + 'biologicalSex');
-      if (sex) {
-        const sexMap: Record<string, string> = { male: 'male', female: 'female', intersex: 'other' };
-        fhirResource.gender = sexMap[sex] ?? 'unknown';
-      }
-
-      const marital = getFirst(NS.cascade + 'maritalStatus');
-      if (marital) {
-        const maritalMap: Record<string, string> = {
-          single: 'S', married: 'M', divorced: 'D', widowed: 'W',
-          separated: 'A', domestic_partnership: 'T',
-        };
-        fhirResource.maritalStatus = {
-          coding: [{ code: maritalMap[marital] ?? 'UNK' }],
-          text: marital,
-        };
-      }
-
-      const profileId = getFirst(NS.cascade + 'profileId');
-      if (profileId) fhirResource.id = profileId;
-
-      // Warn about Cascade-only fields
-      const cascadeOnly = ['computedAge', 'ageGroup', 'genderIdentity'];
-      for (const field of cascadeOnly) {
-        if (getFirst(NS.cascade + field)) {
-          warnings.push(`Cascade field '${field}' has no FHIR Patient equivalent and was not included`);
-        }
-      }
-
-      resources.push(fhirResource);
-    } else if (rdfType === NS.health + 'ImmunizationRecord') {
-      const fhirResource: any = {
-        resourceType: 'Immunization',
-        status: getFirst(NS.health + 'status') ?? 'completed',
-        vaccineCode: { text: getFirst(NS.health + 'vaccineName') ?? '' },
-      };
-
-      const adminDate = getFirst(NS.health + 'administrationDate');
-      if (adminDate) fhirResource.occurrenceDateTime = adminDate;
-
-      const vaccineCode = getFirst(NS.health + 'vaccineCode');
-      if (vaccineCode) {
-        // Strip "CVX-" prefix
-        const code = vaccineCode.startsWith('CVX-') ? vaccineCode.slice(4) : vaccineCode;
-        fhirResource.vaccineCode.coding = [{ system: 'http://hl7.org/fhir/sid/cvx', code }];
-      }
-
-      const manufacturer = getFirst(NS.health + 'manufacturer');
-      if (manufacturer) fhirResource.manufacturer = { display: manufacturer };
-
-      const lotNumber = getFirst(NS.health + 'lotNumber');
-      if (lotNumber) fhirResource.lotNumber = lotNumber;
-
-      const srcId = getFirst(NS.health + 'sourceRecordId');
-      if (srcId) fhirResource.id = srcId;
-
-      resources.push(fhirResource);
-    } else if (rdfType === NS.coverage + 'InsurancePlan') {
-      const fhirResource: any = {
-        resourceType: 'Coverage',
-        status: 'active',
-      };
-
-      const providerName = getFirst(NS.coverage + 'providerName');
-      if (providerName) fhirResource.payor = [{ display: providerName }];
-
-      const memberId = getFirst(NS.coverage + 'memberId');
-      if (memberId) fhirResource.subscriberId = memberId;
-
-      const groupNum = getFirst(NS.coverage + 'groupNumber');
-      const planName = getFirst(NS.coverage + 'planName');
-      const classArr: any[] = [];
-      if (groupNum) classArr.push({ type: { coding: [{ code: 'group' }] }, value: groupNum, name: planName });
-      else if (planName) classArr.push({ type: { coding: [{ code: 'plan' }] }, value: planName });
-      if (classArr.length > 0) fhirResource.class = classArr;
-
-      const start = getFirst(NS.coverage + 'effectiveStart');
-      const end = getFirst(NS.coverage + 'effectiveEnd');
-      if (start || end) {
-        fhirResource.period = {};
-        if (start) fhirResource.period.start = start;
-        if (end) fhirResource.period.end = end;
-      }
-
-      const rel = getFirst(NS.coverage + 'subscriberRelationship');
-      if (rel) fhirResource.relationship = { coding: [{ code: rel }] };
-
-      const srcId = getFirst(NS.health + 'sourceRecordId');
-      if (srcId) fhirResource.id = srcId;
-
-      resources.push(fhirResource);
-    } else {
-      warnings.push(`Unknown Cascade RDF type: ${rdfType}`);
-    }
-  }
-
-  return { resources, warnings };
-}