@the-cascade-protocol/cli 0.2.0

package/dist/lib/fhir-converter/types.d.ts

@@ -0,0 +1,77 @@
+/**
+ * Shared types and namespace constants for FHIR conversion.
+ *
+ * Used by both fhir-to-cascade and cascade-to-fhir converters.
+ */
+import { type Quad } from 'n3';
+export type InputFormat = 'fhir' | 'cascade' | 'c-cda';
+export type OutputFormat = 'turtle' | 'jsonld' | 'fhir' | 'cascade';
+export interface ConversionResult {
+    turtle: string;
+    jsonld?: object;
+    warnings: string[];
+    resourceType: string;
+    cascadeType: string;
+}
+export interface BatchConversionResult {
+    success: boolean;
+    output: string;
+    format: OutputFormat;
+    resourceCount: number;
+    warnings: string[];
+    errors: string[];
+    results: ConversionResult[];
+}
+export declare const NS: {
+    readonly cascade: "https://ns.cascadeprotocol.org/core/v1#";
+    readonly health: "https://ns.cascadeprotocol.org/health/v1#";
+    readonly clinical: "https://ns.cascadeprotocol.org/clinical/v1#";
+    readonly coverage: "https://ns.cascadeprotocol.org/coverage/v1#";
+    readonly fhir: "http://hl7.org/fhir/";
+    readonly sct: "http://snomed.info/sct/";
+    readonly loinc: "http://loinc.org/rdf#";
+    readonly rxnorm: "http://www.nlm.nih.gov/research/umls/rxnorm/";
+    readonly icd10: "http://hl7.org/fhir/sid/icd-10-cm/";
+    readonly xsd: "http://www.w3.org/2001/XMLSchema#";
+    readonly prov: "http://www.w3.org/ns/prov#";
+    readonly rdf: "http://www.w3.org/1999/02/22-rdf-syntax-ns#";
+};
+/** Standard Turtle prefix block for all generated output. */
+export declare const TURTLE_PREFIXES: Record<string, string>;
+export declare const CODING_SYSTEM_MAP: Record<string, string>;
+export declare const VITAL_LOINC_CODES: Record<string, {
+    type: string;
+    name: string;
+    unit: string;
+    snomedCode: string;
+}>;
+/** FHIR observation categories that indicate vital signs */
+export declare const VITAL_CATEGORIES: string[];
+/** Set of FHIR resource types supported for conversion */
+export declare const SUPPORTED_TYPES: Set<string>;
+/**
+ * Ensure an ISO 8601 dateTime string with timezone.
+ * Bare dates (YYYY-MM-DD) get T00:00:00Z appended.
+ */
+export declare function ensureDateTimeWithTz(dateStr: string): string;
+export interface CodingInfo {
+    system: string;
+    code: string;
+    display?: string;
+}
+export declare function extractCodings(codeableConcept: any): CodingInfo[];
+export declare function codeableConceptText(cc: any): string | undefined;
+export declare function tripleStr(subject: string, predicate: string, value: string): Quad;
+export declare function tripleTyped(subject: string, predicate: string, value: string, datatype: string): Quad;
+export declare function tripleBool(subject: string, predicate: string, value: boolean): Quad;
+export declare function tripleInt(subject: string, predicate: string, value: number): Quad;
+export declare function tripleDouble(subject: string, predicate: string, value: number): Quad;
+export declare function tripleRef(subject: string, predicate: string, object: string): Quad;
+export declare function tripleType(subject: string, rdfType: string): Quad;
+export declare function tripleDateTime(subject: string, predicate: string, dateStr: string): Quad;
+export declare function tripleDate(subject: string, predicate: string, dateStr: string): Quad;
+/** Common triples every Cascade resource gets */
+export declare function commonTriples(subject: string): Quad[];
+export declare function quadsToTurtle(quads: Quad[]): Promise<string>;
+export declare function quadsToJsonLd(quads: Quad[], _cascadeType: string): object;
+//# sourceMappingURL=types.d.ts.map

package/dist/lib/fhir-converter/types.d.ts.map

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package/dist/lib/fhir-converter/types.js

@@ -0,0 +1,236 @@
+/**
+ * Shared types and namespace constants for FHIR conversion.
+ *
+ * Used by both fhir-to-cascade and cascade-to-fhir converters.
+ */
+import { DataFactory, Writer } from 'n3';
+const { namedNode, literal, quad: makeQuad } = DataFactory;
+// ---------------------------------------------------------------------------
+// Namespace constants
+// ---------------------------------------------------------------------------
+export const NS = {
+    cascade: 'https://ns.cascadeprotocol.org/core/v1#',
+    health: 'https://ns.cascadeprotocol.org/health/v1#',
+    clinical: 'https://ns.cascadeprotocol.org/clinical/v1#',
+    coverage: 'https://ns.cascadeprotocol.org/coverage/v1#',
+    fhir: 'http://hl7.org/fhir/',
+    sct: 'http://snomed.info/sct/',
+    loinc: 'http://loinc.org/rdf#',
+    rxnorm: 'http://www.nlm.nih.gov/research/umls/rxnorm/',
+    icd10: 'http://hl7.org/fhir/sid/icd-10-cm/',
+    xsd: 'http://www.w3.org/2001/XMLSchema#',
+    prov: 'http://www.w3.org/ns/prov#',
+    rdf: 'http://www.w3.org/1999/02/22-rdf-syntax-ns#',
+};
+/** Standard Turtle prefix block for all generated output. */
+export const TURTLE_PREFIXES = {
+    cascade: NS.cascade,
+    health: NS.health,
+    clinical: NS.clinical,
+    coverage: NS.coverage,
+    fhir: NS.fhir,
+    sct: NS.sct,
+    loinc: NS.loinc,
+    rxnorm: NS.rxnorm,
+    xsd: NS.xsd,
+    prov: NS.prov,
+};
+// ---------------------------------------------------------------------------
+// FHIR coding-system to Cascade namespace mapping
+// ---------------------------------------------------------------------------
+export const CODING_SYSTEM_MAP = {
+    'http://www.nlm.nih.gov/research/umls/rxnorm': NS.rxnorm,
+    'urn:oid:2.16.840.1.113883.6.88': NS.rxnorm,
+    'http://snomed.info/sct': NS.sct,
+    'http://loinc.org': NS.loinc,
+    'http://hl7.org/fhir/sid/icd-10-cm': NS.icd10,
+    'http://hl7.org/fhir/sid/icd-10': NS.icd10,
+};
+// ---------------------------------------------------------------------------
+// FHIR vital-sign LOINC code mapping
+// ---------------------------------------------------------------------------
+export const VITAL_LOINC_CODES = {
+    '8480-6': { type: 'bloodPressureSystolic', name: 'Systolic Blood Pressure', unit: 'mmHg', snomedCode: '271649006' },
+    '8462-4': { type: 'bloodPressureDiastolic', name: 'Diastolic Blood Pressure', unit: 'mmHg', snomedCode: '271650006' },
+    '8867-4': { type: 'heartRate', name: 'Heart Rate', unit: 'bpm', snomedCode: '364075005' },
+    '9279-1': { type: 'respiratoryRate', name: 'Respiratory Rate', unit: 'breaths/min', snomedCode: '86290005' },
+    '8310-5': { type: 'bodyTemperature', name: 'Body Temperature', unit: 'degC', snomedCode: '386725007' },
+    '2708-6': { type: 'oxygenSaturation', name: 'Oxygen Saturation', unit: '%', snomedCode: '431314004' },
+    '29463-7': { type: 'bodyWeight', name: 'Body Weight', unit: 'kg', snomedCode: '27113001' },
+    '8302-2': { type: 'bodyHeight', name: 'Body Height', unit: 'cm', snomedCode: '50373000' },
+    '39156-5': { type: 'bmi', name: 'Body Mass Index', unit: 'kg/m2', snomedCode: '60621009' },
+};
+/** FHIR observation categories that indicate vital signs */
+export const VITAL_CATEGORIES = ['vital-signs', 'vital-sign'];
+/** Set of FHIR resource types supported for conversion */
+export const SUPPORTED_TYPES = new Set([
+    'MedicationStatement', 'MedicationRequest',
+    'Condition',
+    'AllergyIntolerance',
+    'Observation',
+    'Patient',
+    'Immunization',
+    'Coverage',
+]);
+// ---------------------------------------------------------------------------
+// Helper: date formatting
+// ---------------------------------------------------------------------------
+/**
+ * Ensure an ISO 8601 dateTime string with timezone.
+ * Bare dates (YYYY-MM-DD) get T00:00:00Z appended.
+ */
+export function ensureDateTimeWithTz(dateStr) {
+    if (!dateStr)
+        return '';
+    // Already has time component with timezone
+    if (/T.+Z$/.test(dateStr) || /T.+[+-]\d{2}:\d{2}$/.test(dateStr)) {
+        return dateStr;
+    }
+    // Has time component but no timezone -- append Z
+    if (/T/.test(dateStr)) {
+        return dateStr + 'Z';
+    }
+    // Date only -- append midnight UTC
+    return dateStr + 'T00:00:00Z';
+}
+export function extractCodings(codeableConcept) {
+    if (!codeableConcept)
+        return [];
+    const codings = [];
+    if (Array.isArray(codeableConcept.coding)) {
+        for (const c of codeableConcept.coding) {
+            if (c.system && c.code) {
+                codings.push({ system: c.system, code: c.code, display: c.display });
+            }
+        }
+    }
+    return codings;
+}
+export function codeableConceptText(cc) {
+    if (!cc)
+        return undefined;
+    if (cc.text)
+        return cc.text;
+    if (Array.isArray(cc.coding) && cc.coding.length > 0 && cc.coding[0].display) {
+        return cc.coding[0].display;
+    }
+    return undefined;
+}
+// ---------------------------------------------------------------------------
+// Quad-building helpers
+// ---------------------------------------------------------------------------
+export function tripleStr(subject, predicate, value) {
+    return makeQuad(namedNode(subject), namedNode(predicate), literal(value));
+}
+export function tripleTyped(subject, predicate, value, datatype) {
+    return makeQuad(namedNode(subject), namedNode(predicate), literal(value, namedNode(datatype)));
+}
+export function tripleBool(subject, predicate, value) {
+    return makeQuad(namedNode(subject), namedNode(predicate), literal(String(value), namedNode(NS.xsd + 'boolean')));
+}
+export function tripleInt(subject, predicate, value) {
+    return makeQuad(namedNode(subject), namedNode(predicate), literal(String(value), namedNode(NS.xsd + 'integer')));
+}
+export function tripleDouble(subject, predicate, value) {
+    return makeQuad(namedNode(subject), namedNode(predicate), literal(String(value), namedNode(NS.xsd + 'double')));
+}
+export function tripleRef(subject, predicate, object) {
+    return makeQuad(namedNode(subject), namedNode(predicate), namedNode(object));
+}
+export function tripleType(subject, rdfType) {
+    return tripleRef(subject, NS.rdf + 'type', rdfType);
+}
+export function tripleDateTime(subject, predicate, dateStr) {
+    return tripleTyped(subject, predicate, ensureDateTimeWithTz(dateStr), NS.xsd + 'dateTime');
+}
+export function tripleDate(subject, predicate, dateStr) {
+    return tripleTyped(subject, predicate, dateStr, NS.xsd + 'date');
+}
+/** Common triples every Cascade resource gets */
+export function commonTriples(subject) {
+    return [
+        tripleRef(subject, NS.cascade + 'dataProvenance', NS.cascade + 'ClinicalGenerated'),
+        tripleStr(subject, NS.cascade + 'schemaVersion', '1.3'),
+    ];
+}
+// ---------------------------------------------------------------------------
+// Quads -> Turtle serialization
+// ---------------------------------------------------------------------------
+export function quadsToTurtle(quads) {
+    return new Promise((resolve, reject) => {
+        const writer = new Writer({ prefixes: TURTLE_PREFIXES });
+        for (const q of quads) {
+            writer.addQuad(q);
+        }
+        writer.end((error, result) => {
+            if (error)
+                reject(error);
+            else
+                resolve(result);
+        });
+    });
+}
+// ---------------------------------------------------------------------------
+// Quads -> JSON-LD object (lightweight, no @context resolution)
+// ---------------------------------------------------------------------------
+export function quadsToJsonLd(quads, _cascadeType) {
+    // Build a simple JSON-LD representation grouped by subject
+    const subjects = new Map();
+    for (const q of quads) {
+        const subj = q.subject.value;
+        if (!subjects.has(subj)) {
+            subjects.set(subj, {
+                '@context': 'https://ns.cascadeprotocol.org/context/v1/cascade.jsonld',
+                '@id': subj,
+            });
+        }
+        const obj = subjects.get(subj);
+        const pred = q.predicate.value;
+        if (pred === NS.rdf + 'type') {
+            obj['@type'] = q.object.value;
+            continue;
+        }
+        // Compact the predicate using known prefixes
+        let key = pred;
+        for (const [prefix, uri] of Object.entries(TURTLE_PREFIXES)) {
+            if (pred.startsWith(uri)) {
+                key = `${prefix}:${pred.slice(uri.length)}`;
+                break;
+            }
+        }
+        // Handle object vs literal
+        if (q.object.termType === 'NamedNode') {
+            // Check if this is a provenance reference
+            let idVal = q.object.value;
+            for (const [prefix, uri] of Object.entries(TURTLE_PREFIXES)) {
+                if (idVal.startsWith(uri)) {
+                    idVal = `${prefix}:${idVal.slice(uri.length)}`;
+                    break;
+                }
+            }
+            obj[key] = { '@id': idVal };
+        }
+        else {
+            // Literal
+            const dt = q.object.datatype?.value;
+            if (dt === NS.xsd + 'dateTime' || dt === NS.xsd + 'date') {
+                obj[key] = { '@value': q.object.value, '@type': dt === NS.xsd + 'dateTime' ? 'xsd:dateTime' : 'xsd:date' };
+            }
+            else if (dt === NS.xsd + 'boolean') {
+                obj[key] = q.object.value === 'true';
+            }
+            else if (dt === NS.xsd + 'integer') {
+                obj[key] = parseInt(q.object.value, 10);
+            }
+            else if (dt === NS.xsd + 'double' || dt === NS.xsd + 'decimal') {
+                obj[key] = parseFloat(q.object.value);
+            }
+            else {
+                obj[key] = q.object.value;
+            }
+        }
+    }
+    const entries = Array.from(subjects.values());
+    return entries.length === 1 ? entries[0] : entries;
+}
+//# sourceMappingURL=types.js.map

package/dist/lib/fhir-converter/types.js.map

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

@@ -0,0 +1,62 @@
+/**
+ * FHIR conversion utilities.
+ *
+ * Converts between FHIR R4 JSON and Cascade Protocol RDF (Turtle/JSON-LD).
+ *
+ * Supported FHIR R4 resource types:
+ *   - MedicationStatement / MedicationRequest -> health:MedicationRecord
+ *   - Condition -> health:ConditionRecord
+ *   - AllergyIntolerance -> health:AllergyRecord
+ *   - Observation (lab) -> health:LabResultRecord
+ *   - Observation (vital) -> clinical:VitalSign
+ *   - Patient -> cascade:PatientProfile
+ *   - Immunization -> health:ImmunizationRecord
+ *   - Coverage -> coverage:InsurancePlan
+ *
+ * Zero network calls. All conversion is local.
+ */
+import { type Quad } from 'n3';
+export type InputFormat = 'fhir' | 'cascade' | 'c-cda';
+export type OutputFormat = 'turtle' | 'jsonld' | 'fhir' | 'cascade';
+export interface ConversionResult {
+    turtle: string;
+    jsonld?: object;
+    warnings: string[];
+    resourceType: string;
+    cascadeType: string;
+}
+export interface BatchConversionResult {
+    success: boolean;
+    output: string;
+    format: OutputFormat;
+    resourceCount: number;
+    warnings: string[];
+    errors: string[];
+    results: ConversionResult[];
+}
+export declare function convertFhirResourceToQuads(fhirResource: any): (ConversionResult & {
+    _quads: Quad[];
+}) | null;
+export declare function convertFhirToCascade(fhirResource: any): Promise<ConversionResult>;
+/**
+ * Convert Cascade Turtle to FHIR R4 JSON.
+ *
+ * Parses the Turtle using n3, identifies the resource type from rdf:type,
+ * and maps Cascade predicates back to FHIR fields.
+ *
+ * Not all Cascade fields have FHIR equivalents -- lost fields are reported
+ * as warnings.
+ */
+export declare function convertCascadeToFhir(turtle: string): Promise<{
+    resources: any[];
+    warnings: string[];
+}>;
+/**
+ * Convert an entire FHIR input (single resource or Bundle) to Cascade format.
+ */
+export declare function convert(input: string, from: InputFormat, to: OutputFormat, outputSerialization?: 'turtle' | 'jsonld'): Promise<BatchConversionResult>;
+/**
+ * Detect the format of input data by inspecting its content.
+ */
+export declare function detectFormat(input: string): InputFormat | null;
+//# sourceMappingURL=fhir-converter.d.ts.map

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

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