@the-cascade-protocol/cli 0.2.0

package/dist/lib/fhir-converter/converters-clinical.js

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+/**
+ * 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 { 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) {
+    const warnings = [];
+    const subjectUri = `urn:uuid:${randomUUID()}`;
+    const quads = [];
+    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;
+    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;
+    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) => 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,
+    };
+}
+// ---------------------------------------------------------------------------
+// Condition converter
+// ---------------------------------------------------------------------------
+export function convertCondition(resource) {
+    const warnings = [];
+    const subjectUri = `urn:uuid:${randomUUID()}`;
+    const quads = [];
+    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: ${coding.system}`);
+        }
+    }
+    if (resource.id) {
+        quads.push(tripleStr(subjectUri, NS.health + 'sourceRecordId', resource.id));
+    }
+    if (resource.note && Array.isArray(resource.note)) {
+        const noteText = resource.note.map((n) => n.text).filter(Boolean).join('; ');
+        if (noteText)
+            quads.push(tripleStr(subjectUri, NS.health + 'notes', noteText));
+    }
+    return {
+        turtle: '',
+        jsonld: quadsToJsonLd(quads, 'health:ConditionRecord'),
+        warnings,
+        resourceType: 'Condition',
+        cascadeType: 'health:ConditionRecord',
+        _quads: quads,
+    };
+}
+// ---------------------------------------------------------------------------
+// AllergyIntolerance converter
+// ---------------------------------------------------------------------------
+export function convertAllergyIntolerance(resource) {
+    const warnings = [];
+    const subjectUri = `urn:uuid:${randomUUID()}`;
+    const quads = [];
+    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) => r.manifestation ?? [])
+            .map((m) => 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 = { 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 = { 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) => 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) {
+    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) {
+    const warnings = [];
+    const subjectUri = `urn:uuid:${randomUUID()}`;
+    const quads = [];
+    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 = {
+            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 = [];
+        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]} ${unit}`.trim()));
+        }
+        else if (rr.text) {
+            quads.push(tripleStr(subjectUri, NS.health + 'referenceRange', rr.text));
+        }
+    }
+    if (resource.id) {
+        quads.push(tripleStr(subjectUri, NS.health + 'sourceRecordId', resource.id));
+    }
+    return {
+        turtle: '',
+        jsonld: quadsToJsonLd(quads, 'health:LabResultRecord'),
+        warnings,
+        resourceType: 'Observation',
+        cascadeType: 'health:LabResultRecord',
+        _quads: quads,
+    };
+}
+// ---------------------------------------------------------------------------
+// Observation (vital sign) converter
+// ---------------------------------------------------------------------------
+export function convertObservationVital(resource) {
+    const warnings = [];
+    const subjectUri = `urn:uuid:${randomUUID()}`;
+    const quads = [];
+    quads.push(tripleType(subjectUri, NS.clinical + 'VitalSign'));
+    quads.push(...commonTriples(subjectUri));
+    const codings = extractCodings(resource.code);
+    let vitalInfo;
+    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 = {
+            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,
+    };
+}
+//# sourceMappingURL=converters-clinical.js.map

package/dist/lib/fhir-converter/converters-clinical.js.map

@@ -0,0 +1 @@
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package/dist/lib/fhir-converter/converters-demographics.d.ts

@@ -0,0 +1,20 @@
+/**
+ * FHIR -> Cascade converters for demographics and administrative types.
+ *
+ * Converts:
+ *   - Patient -> cascade:PatientProfile
+ *   - Immunization -> health:ImmunizationRecord
+ *   - Coverage -> coverage:InsurancePlan
+ */
+import type { Quad } from 'n3';
+import { type ConversionResult } from './types.js';
+export declare function convertPatient(resource: any): ConversionResult & {
+    _quads: Quad[];
+};
+export declare function convertImmunization(resource: any): ConversionResult & {
+    _quads: Quad[];
+};
+export declare function convertCoverage(resource: any): ConversionResult & {
+    _quads: Quad[];
+};
+//# sourceMappingURL=converters-demographics.d.ts.map

package/dist/lib/fhir-converter/converters-demographics.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"converters-demographics.d.ts","sourceRoot":"","sources":["../../../src/lib/fhir-converter/converters-demographics.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAGH,OAAO,KAAK,EAAE,IAAI,EAAE,MAAM,IAAI,CAAC;AAE/B,OAAO,EACL,KAAK,gBAAgB,EAWtB,MAAM,YAAY,CAAC;AAMpB,wBAAgB,cAAc,CAAC,QAAQ,EAAE,GAAG,GAAG,gBAAgB,GAAG;IAAE,MAAM,EAAE,IAAI,EAAE,CAAA;CAAE,CA4EnF;AAMD,wBAAgB,mBAAmB,CAAC,QAAQ,EAAE,GAAG,GAAG,gBAAgB,GAAG;IAAE,MAAM,EAAE,IAAI,EAAE,CAAA;CAAE,CA4ExF;AAMD,wBAAgB,eAAe,CAAC,QAAQ,EAAE,GAAG,GAAG,gBAAgB,GAAG;IAAE,MAAM,EAAE,IAAI,EAAE,CAAA;CAAE,CA2EpF"}