@the-cascade-protocol/cli 0.2.0

package/dist/lib/fhir-converter/cascade-to-fhir.d.ts

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+/**
+ * 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.
+ */
+/**
+ * Convert Cascade Turtle to FHIR R4 JSON.
+ */
+export declare function convertCascadeToFhir(turtle: string): Promise<{
+    resources: any[];
+    warnings: string[];
+}>;
+//# sourceMappingURL=cascade-to-fhir.d.ts.map

package/dist/lib/fhir-converter/cascade-to-fhir.d.ts.map

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+{"version":3,"file":"cascade-to-fhir.d.ts","sourceRoot":"","sources":["../../../src/lib/fhir-converter/cascade-to-fhir.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAKH;;GAEG;AACH,wBAAsB,oBAAoB,CAAC,MAAM,EAAE,MAAM,GAAG,OAAO,CAAC;IAClE,SAAS,EAAE,GAAG,EAAE,CAAC;IACjB,QAAQ,EAAE,MAAM,EAAE,CAAC;CACpB,CAAC,CA6VD"}

package/dist/lib/fhir-converter/cascade-to-fhir.js

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+/**
+ * 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 } from 'n3';
+import { NS } from './types.js';
+/**
+ * Convert Cascade Turtle to FHIR R4 JSON.
+ */
+export async function convertCascadeToFhir(turtle) {
+    const warnings = [];
+    const resources = [];
+    // Parse Turtle
+    const parser = new Parser();
+    const quads = [];
+    try {
+        const parsed = parser.parse(turtle);
+        quads.push(...parsed);
+    }
+    catch (err) {
+        return { resources: [], warnings: [`Turtle parse error: ${err.message}`] };
+    }
+    // Group quads by subject
+    const subjects = new Map();
+    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();
+        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) => pv.get(pred)?.[0];
+        if (rdfType === NS.health + 'MedicationRecord') {
+            const fhirResource = {
+                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 = [];
+            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 = {
+                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 = [];
+            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 = {
+                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 = {};
+                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 = {
+                resourceType: 'Observation',
+                code: { text: getFirst(NS.health + 'testName') ?? '' },
+                category: [{ coding: [{ code: 'laboratory' }] }],
+            };
+            // LOINC code
+            const testCode = pv.get(NS.health + 'testCode') ?? [];
+            const codingArr = [];
+            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 = {
+                    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 = {
+                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 = {
+                resourceType: 'Patient',
+            };
+            const dob = getFirst(NS.cascade + 'dateOfBirth');
+            if (dob)
+                fhirResource.birthDate = dob;
+            const sex = getFirst(NS.cascade + 'biologicalSex');
+            if (sex) {
+                const sexMap = { male: 'male', female: 'female', intersex: 'other' };
+                fhirResource.gender = sexMap[sex] ?? 'unknown';
+            }
+            const marital = getFirst(NS.cascade + 'maritalStatus');
+            if (marital) {
+                const maritalMap = {
+                    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 = {
+                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 = {
+                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 = [];
+            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 };
+}
+//# sourceMappingURL=cascade-to-fhir.js.map

package/dist/lib/fhir-converter/cascade-to-fhir.js.map

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package/dist/lib/fhir-converter/converters-clinical.d.ts

@@ -0,0 +1,29 @@
+/**
+ * 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 type { Quad } from 'n3';
+import { type ConversionResult } from './types.js';
+export declare function convertMedicationStatement(resource: any): ConversionResult & {
+    _quads: Quad[];
+};
+export declare function convertCondition(resource: any): ConversionResult & {
+    _quads: Quad[];
+};
+export declare function convertAllergyIntolerance(resource: any): ConversionResult & {
+    _quads: Quad[];
+};
+export declare function isVitalSignObservation(resource: any): boolean;
+export declare function convertObservationLab(resource: any): ConversionResult & {
+    _quads: Quad[];
+};
+export declare function convertObservationVital(resource: any): ConversionResult & {
+    _quads: Quad[];
+};
+//# sourceMappingURL=converters-clinical.d.ts.map

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

@@ -0,0 +1 @@
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