@the-cascade-protocol/cli 0.2.0

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

@@ -0,0 +1,242 @@
+/**
+ * FHIR -> Cascade converters for demographics and administrative types.
+ *
+ * Converts:
+ *   - Patient -> cascade:PatientProfile
+ *   - Immunization -> health:ImmunizationRecord
+ *   - Coverage -> coverage:InsurancePlan
+ */
+import { randomUUID } from 'node:crypto';
+import { NS, extractCodings, codeableConceptText, tripleStr, tripleInt, tripleType, tripleDateTime, tripleDate, commonTriples, quadsToJsonLd, } from './types.js';
+// ---------------------------------------------------------------------------
+// Patient converter
+// ---------------------------------------------------------------------------
+export function convertPatient(resource) {
+    const warnings = [];
+    const subjectUri = `urn:uuid:${randomUUID()}`;
+    const quads = [];
+    quads.push(tripleType(subjectUri, NS.cascade + 'PatientProfile'));
+    quads.push(...commonTriples(subjectUri));
+    if (resource.birthDate) {
+        quads.push(tripleDate(subjectUri, NS.cascade + 'dateOfBirth', resource.birthDate));
+        const dob = new Date(resource.birthDate);
+        const now = new Date();
+        let age = now.getFullYear() - dob.getFullYear();
+        const monthDiff = now.getMonth() - dob.getMonth();
+        if (monthDiff < 0 || (monthDiff === 0 && now.getDate() < dob.getDate())) {
+            age--;
+        }
+        quads.push(tripleInt(subjectUri, NS.cascade + 'computedAge', age));
+        let ageGroup;
+        if (age < 18)
+            ageGroup = 'pediatric';
+        else if (age < 40)
+            ageGroup = 'young_adult';
+        else if (age < 65)
+            ageGroup = 'adult';
+        else
+            ageGroup = 'senior';
+        quads.push(tripleStr(subjectUri, NS.cascade + 'ageGroup', ageGroup));
+    }
+    else {
+        warnings.push('No birthDate found in Patient resource');
+    }
+    if (resource.gender) {
+        const genderMap = {
+            male: 'male', female: 'female', other: 'intersex', unknown: 'intersex',
+        };
+        quads.push(tripleStr(subjectUri, NS.cascade + 'biologicalSex', genderMap[resource.gender] ?? resource.gender));
+    }
+    if (Array.isArray(resource.address) && resource.address.length > 0) {
+        const addr = resource.address[0];
+        if (addr.city)
+            quads.push(tripleStr(subjectUri, NS.cascade + 'addressCity', addr.city));
+        if (addr.state)
+            quads.push(tripleStr(subjectUri, NS.cascade + 'addressState', addr.state));
+        if (addr.postalCode)
+            quads.push(tripleStr(subjectUri, NS.cascade + 'addressPostalCode', addr.postalCode));
+        if (addr.country)
+            quads.push(tripleStr(subjectUri, NS.cascade + 'addressCountry', addr.country));
+        if (Array.isArray(addr.line)) {
+            for (const line of addr.line) {
+                quads.push(tripleStr(subjectUri, NS.cascade + 'addressLine', line));
+            }
+        }
+        warnings.push('Patient address flattened onto profile (blank node structure simplified)');
+    }
+    if (resource.maritalStatus) {
+        const maritalText = codeableConceptText(resource.maritalStatus);
+        if (maritalText) {
+            const maritalMap = {
+                S: 'single', M: 'married', D: 'divorced', W: 'widowed',
+                A: 'separated', T: 'domestic_partnership', UNK: 'prefer_not_to_say',
+                'Never Married': 'single', 'Married': 'married', 'Divorced': 'divorced',
+                'Widowed': 'widowed', 'Separated': 'separated',
+            };
+            const code = resource.maritalStatus.coding?.[0]?.code;
+            const mapped = maritalMap[code] ?? maritalMap[maritalText] ?? maritalText.toLowerCase();
+            quads.push(tripleStr(subjectUri, NS.cascade + 'maritalStatus', mapped));
+        }
+    }
+    if (resource.id) {
+        quads.push(tripleStr(subjectUri, NS.cascade + 'profileId', resource.id));
+    }
+    return {
+        turtle: '',
+        jsonld: quadsToJsonLd(quads, 'cascade:PatientProfile'),
+        warnings,
+        resourceType: 'Patient',
+        cascadeType: 'cascade:PatientProfile',
+        _quads: quads,
+    };
+}
+// ---------------------------------------------------------------------------
+// Immunization converter
+// ---------------------------------------------------------------------------
+export function convertImmunization(resource) {
+    const warnings = [];
+    const subjectUri = `urn:uuid:${randomUUID()}`;
+    const quads = [];
+    quads.push(tripleType(subjectUri, NS.health + 'ImmunizationRecord'));
+    quads.push(...commonTriples(subjectUri));
+    const vaccineName = codeableConceptText(resource.vaccineCode) ?? 'Unknown Vaccine';
+    quads.push(tripleStr(subjectUri, NS.health + 'vaccineName', vaccineName));
+    if (resource.occurrenceDateTime) {
+        quads.push(tripleDateTime(subjectUri, NS.health + 'administrationDate', resource.occurrenceDateTime));
+    }
+    else if (resource.occurrenceString) {
+        warnings.push(`Immunization date is a string: ${resource.occurrenceString}`);
+    }
+    quads.push(tripleStr(subjectUri, NS.health + 'status', resource.status ?? 'completed'));
+    const codings = extractCodings(resource.vaccineCode);
+    for (const c of codings) {
+        if (c.system === 'http://hl7.org/fhir/sid/cvx' || c.system === 'urn:oid:2.16.840.1.113883.12.292') {
+            quads.push(tripleStr(subjectUri, NS.health + 'vaccineCode', `CVX-${c.code}`));
+            break;
+        }
+    }
+    if (resource.manufacturer?.display) {
+        quads.push(tripleStr(subjectUri, NS.health + 'manufacturer', resource.manufacturer.display));
+    }
+    if (resource.lotNumber) {
+        quads.push(tripleStr(subjectUri, NS.health + 'lotNumber', resource.lotNumber));
+    }
+    if (resource.doseQuantity) {
+        const qty = `${resource.doseQuantity.value} ${resource.doseQuantity.unit ?? ''}`.trim();
+        quads.push(tripleStr(subjectUri, NS.health + 'doseQuantity', qty));
+    }
+    if (resource.route) {
+        const routeText = codeableConceptText(resource.route);
+        if (routeText)
+            quads.push(tripleStr(subjectUri, NS.health + 'route', routeText));
+    }
+    if (resource.site) {
+        const siteText = codeableConceptText(resource.site);
+        if (siteText)
+            quads.push(tripleStr(subjectUri, NS.health + 'site', siteText));
+    }
+    if (Array.isArray(resource.performer) && resource.performer.length > 0) {
+        const performer = resource.performer[0]?.actor?.display;
+        if (performer)
+            quads.push(tripleStr(subjectUri, NS.health + 'administeringProvider', performer));
+    }
+    if (resource.location?.display) {
+        quads.push(tripleStr(subjectUri, NS.health + 'administeringLocation', resource.location.display));
+    }
+    if (resource.note && Array.isArray(resource.note)) {
+        const noteText = resource.note.map((n) => n.text).filter(Boolean).join('; ');
+        if (noteText)
+            quads.push(tripleStr(subjectUri, NS.health + 'notes', noteText));
+    }
+    if (resource.id) {
+        quads.push(tripleStr(subjectUri, NS.health + 'sourceRecordId', resource.id));
+    }
+    return {
+        turtle: '',
+        jsonld: quadsToJsonLd(quads, 'health:ImmunizationRecord'),
+        warnings,
+        resourceType: 'Immunization',
+        cascadeType: 'health:ImmunizationRecord',
+        _quads: quads,
+    };
+}
+// ---------------------------------------------------------------------------
+// Coverage converter
+// ---------------------------------------------------------------------------
+export function convertCoverage(resource) {
+    const warnings = [];
+    const subjectUri = `urn:uuid:${randomUUID()}`;
+    const quads = [];
+    quads.push(tripleType(subjectUri, NS.coverage + 'InsurancePlan'));
+    quads.push(...commonTriples(subjectUri));
+    if (Array.isArray(resource.payor) && resource.payor.length > 0) {
+        const payorName = resource.payor[0]?.display ?? 'Unknown Insurance';
+        quads.push(tripleStr(subjectUri, NS.coverage + 'providerName', payorName));
+    }
+    else {
+        quads.push(tripleStr(subjectUri, NS.coverage + 'providerName', 'Unknown Insurance'));
+        warnings.push('No payor information found in Coverage resource');
+    }
+    if (resource.subscriberId) {
+        quads.push(tripleStr(subjectUri, NS.coverage + 'memberId', resource.subscriberId));
+        quads.push(tripleStr(subjectUri, NS.coverage + 'subscriberId', resource.subscriberId));
+    }
+    else if (resource.identifier && Array.isArray(resource.identifier) && resource.identifier.length > 0) {
+        const memberId = resource.identifier[0]?.value ?? '';
+        quads.push(tripleStr(subjectUri, NS.coverage + 'memberId', memberId));
+    }
+    else {
+        warnings.push('No member/subscriber ID found in Coverage resource');
+    }
+    if (resource.type) {
+        const typeText = resource.type.coding?.[0]?.code ?? codeableConceptText(resource.type) ?? 'primary';
+        quads.push(tripleStr(subjectUri, NS.coverage + 'coverageType', typeText));
+    }
+    else {
+        quads.push(tripleStr(subjectUri, NS.coverage + 'coverageType', 'primary'));
+    }
+    if (Array.isArray(resource.class)) {
+        for (const cls of resource.class) {
+            const clsType = cls.type?.coding?.[0]?.code ?? '';
+            if (clsType === 'group' && cls.value) {
+                quads.push(tripleStr(subjectUri, NS.coverage + 'groupNumber', cls.value));
+                if (cls.name)
+                    quads.push(tripleStr(subjectUri, NS.coverage + 'planName', cls.name));
+            }
+            else if (clsType === 'plan' && cls.value) {
+                quads.push(tripleStr(subjectUri, NS.coverage + 'planName', cls.name ?? cls.value));
+            }
+            else if (clsType === 'rxbin' && cls.value) {
+                quads.push(tripleStr(subjectUri, NS.coverage + 'rxBin', cls.value));
+            }
+            else if (clsType === 'rxpcn' && cls.value) {
+                quads.push(tripleStr(subjectUri, NS.coverage + 'rxPcn', cls.value));
+            }
+            else if (clsType === 'rxgroup' && cls.value) {
+                quads.push(tripleStr(subjectUri, NS.coverage + 'rxGroup', cls.value));
+            }
+        }
+    }
+    if (resource.relationship) {
+        const relCode = resource.relationship.coding?.[0]?.code ?? 'self';
+        quads.push(tripleStr(subjectUri, NS.coverage + 'subscriberRelationship', relCode));
+    }
+    if (resource.period?.start) {
+        quads.push(tripleDate(subjectUri, NS.coverage + 'effectiveStart', resource.period.start.substring(0, 10)));
+    }
+    if (resource.period?.end) {
+        quads.push(tripleDate(subjectUri, NS.coverage + 'effectiveEnd', resource.period.end.substring(0, 10)));
+    }
+    if (resource.id) {
+        quads.push(tripleStr(subjectUri, NS.health + 'sourceRecordId', resource.id));
+    }
+    return {
+        turtle: '',
+        jsonld: quadsToJsonLd(quads, 'coverage:InsurancePlan'),
+        warnings,
+        resourceType: 'Coverage',
+        cascadeType: 'coverage:InsurancePlan',
+        _quads: quads,
+    };
+}
+//# sourceMappingURL=converters-demographics.js.map

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

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

@@ -0,0 +1,17 @@
+/**
+ * FHIR -> Cascade dispatcher and public API.
+ *
+ * Routes FHIR resources to the appropriate per-type converter and
+ * provides the main public conversion functions.
+ *
+ * Individual converters are in:
+ *   - converters-clinical.ts     Medications, conditions, allergies, observations
+ *   - converters-demographics.ts Patient, immunization, coverage
+ */
+import type { Quad } from 'n3';
+import { type ConversionResult } from './types.js';
+export declare function convertFhirResourceToQuads(fhirResource: any): (ConversionResult & {
+    _quads: Quad[];
+}) | null;
+export declare function convertFhirToCascade(fhirResource: any): Promise<ConversionResult>;
+//# sourceMappingURL=fhir-to-cascade.d.ts.map

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

@@ -0,0 +1 @@
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package/dist/lib/fhir-converter/fhir-to-cascade.js

@@ -0,0 +1,63 @@
+/**
+ * FHIR -> Cascade dispatcher and public API.
+ *
+ * Routes FHIR resources to the appropriate per-type converter and
+ * provides the main public conversion functions.
+ *
+ * Individual converters are in:
+ *   - converters-clinical.ts     Medications, conditions, allergies, observations
+ *   - converters-demographics.ts Patient, immunization, coverage
+ */
+import { quadsToTurtle } from './types.js';
+import { convertMedicationStatement, convertCondition, convertAllergyIntolerance, isVitalSignObservation, convertObservationLab, convertObservationVital, } from './converters-clinical.js';
+import { convertPatient, convertImmunization, convertCoverage, } from './converters-demographics.js';
+// ---------------------------------------------------------------------------
+// Main dispatcher: single FHIR resource -> Cascade
+// ---------------------------------------------------------------------------
+export function convertFhirResourceToQuads(fhirResource) {
+    const resourceType = fhirResource?.resourceType;
+    if (!resourceType)
+        return null;
+    switch (resourceType) {
+        case 'MedicationStatement':
+        case 'MedicationRequest':
+            return convertMedicationStatement(fhirResource);
+        case 'Condition':
+            return convertCondition(fhirResource);
+        case 'AllergyIntolerance':
+            return convertAllergyIntolerance(fhirResource);
+        case 'Observation':
+            if (isVitalSignObservation(fhirResource)) {
+                return convertObservationVital(fhirResource);
+            }
+            return convertObservationLab(fhirResource);
+        case 'Patient':
+            return convertPatient(fhirResource);
+        case 'Immunization':
+            return convertImmunization(fhirResource);
+        case 'Coverage':
+            return convertCoverage(fhirResource);
+        default:
+            return null;
+    }
+}
+export async function convertFhirToCascade(fhirResource) {
+    const result = convertFhirResourceToQuads(fhirResource);
+    if (!result) {
+        return {
+            turtle: '',
+            warnings: [`Unsupported FHIR resource type: ${fhirResource?.resourceType ?? 'unknown'}`],
+            resourceType: fhirResource?.resourceType ?? 'unknown',
+            cascadeType: 'unknown',
+        };
+    }
+    const turtle = await quadsToTurtle(result._quads);
+    return {
+        turtle,
+        jsonld: result.jsonld,
+        warnings: result.warnings,
+        resourceType: result.resourceType,
+        cascadeType: result.cascadeType,
+    };
+}
+//# sourceMappingURL=fhir-to-cascade.js.map

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

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

@@ -0,0 +1,36 @@
+/**
+ * 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.
+ *
+ * This module re-exports all public API for backward compatibility.
+ * Internal implementation is split across:
+ *   - types.ts         Shared types, namespaces, and quad helpers
+ *   - fhir-to-cascade.ts  FHIR -> Cascade converters
+ *   - cascade-to-fhir.ts  Cascade -> FHIR converters
+ */
+import { type InputFormat, type OutputFormat, type ConversionResult, type BatchConversionResult } from './types.js';
+export type { InputFormat, OutputFormat, ConversionResult, BatchConversionResult };
+export { convertFhirResourceToQuads, convertFhirToCascade } from './fhir-to-cascade.js';
+export { convertCascadeToFhir } from './cascade-to-fhir.js';
+/**
+ * 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=index.d.ts.map

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

@@ -0,0 +1 @@
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package/dist/lib/fhir-converter/index.js

@@ -0,0 +1,187 @@
+/**
+ * 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.
+ *
+ * This module re-exports all public API for backward compatibility.
+ * Internal implementation is split across:
+ *   - types.ts         Shared types, namespaces, and quad helpers
+ *   - fhir-to-cascade.ts  FHIR -> Cascade converters
+ *   - cascade-to-fhir.ts  Cascade -> FHIR converters
+ */
+import { SUPPORTED_TYPES, quadsToTurtle, quadsToJsonLd, } from './types.js';
+import { convertFhirResourceToQuads } from './fhir-to-cascade.js';
+import { convertCascadeToFhir } from './cascade-to-fhir.js';
+// Re-export public functions from sub-modules
+export { convertFhirResourceToQuads, convertFhirToCascade } from './fhir-to-cascade.js';
+export { convertCascadeToFhir } from './cascade-to-fhir.js';
+// ---------------------------------------------------------------------------
+// Batch conversion (FHIR Bundle support)
+// ---------------------------------------------------------------------------
+/**
+ * Convert an entire FHIR input (single resource or Bundle) to Cascade format.
+ */
+export async function convert(input, from, to, outputSerialization = 'turtle') {
+    const warnings = [];
+    const errors = [];
+    const results = [];
+    if (from === 'fhir' && (to === 'cascade' || to === 'turtle' || to === 'jsonld')) {
+        // FHIR -> Cascade
+        let parsed;
+        try {
+            parsed = JSON.parse(input);
+        }
+        catch {
+            return {
+                success: false, output: '', format: to, resourceCount: 0,
+                warnings: [], errors: ['Invalid JSON input'], results: [],
+            };
+        }
+        // Collect resources from Bundle or single resource
+        const fhirResources = [];
+        if (parsed.resourceType === 'Bundle' && Array.isArray(parsed.entry)) {
+            for (const entry of parsed.entry) {
+                if (entry.resource)
+                    fhirResources.push(entry.resource);
+            }
+        }
+        else if (parsed.resourceType) {
+            fhirResources.push(parsed);
+        }
+        else {
+            return {
+                success: false, output: '', format: to, resourceCount: 0,
+                warnings: [], errors: ['Input does not appear to be a FHIR resource or Bundle'], results: [],
+            };
+        }
+        const allQuads = [];
+        for (const res of fhirResources) {
+            if (!SUPPORTED_TYPES.has(res.resourceType)) {
+                warnings.push(`Skipping unsupported FHIR resource type: ${res.resourceType}`);
+                continue;
+            }
+            const result = convertFhirResourceToQuads(res);
+            if (result) {
+                allQuads.push(...result._quads);
+                results.push({
+                    turtle: '', // will be filled with combined output
+                    jsonld: result.jsonld,
+                    warnings: result.warnings,
+                    resourceType: result.resourceType,
+                    cascadeType: result.cascadeType,
+                });
+                warnings.push(...result.warnings);
+            }
+        }
+        if (allQuads.length === 0) {
+            return {
+                success: false, output: '', format: to, resourceCount: 0,
+                warnings, errors: ['No convertible FHIR resources found'], results: [],
+            };
+        }
+        // Determine output format
+        let output;
+        if (outputSerialization === 'jsonld' || to === 'jsonld') {
+            const jsonLd = quadsToJsonLd(allQuads, results[0]?.cascadeType ?? '');
+            output = JSON.stringify(jsonLd, null, 2);
+        }
+        else {
+            output = await quadsToTurtle(allQuads);
+        }
+        return {
+            success: true,
+            output,
+            format: to === 'cascade' ? (outputSerialization === 'jsonld' ? 'jsonld' : 'turtle') : to,
+            resourceCount: results.length,
+            warnings,
+            errors,
+            results,
+        };
+    }
+    else if (from === 'cascade' && to === 'fhir') {
+        // Cascade -> FHIR
+        const { resources, warnings: convWarnings } = await convertCascadeToFhir(input);
+        warnings.push(...convWarnings);
+        if (resources.length === 0) {
+            return {
+                success: false, output: '', format: 'fhir', resourceCount: 0,
+                warnings, errors: ['No resources converted from Cascade Turtle'], results: [],
+            };
+        }
+        const output = resources.length === 1
+            ? JSON.stringify(resources[0], null, 2)
+            : JSON.stringify({ resourceType: 'Bundle', type: 'collection', entry: resources.map(r => ({ resource: r })) }, null, 2);
+        return {
+            success: true,
+            output,
+            format: 'fhir',
+            resourceCount: resources.length,
+            warnings,
+            errors,
+            results: resources.map(r => ({
+                turtle: '',
+                warnings: [],
+                resourceType: r.resourceType,
+                cascadeType: 'fhir',
+            })),
+        };
+    }
+    else if (from === 'c-cda') {
+        return {
+            success: false, output: '', format: to, resourceCount: 0,
+            warnings: [], errors: ['C-CDA conversion is not yet supported'], results: [],
+        };
+    }
+    else {
+        return {
+            success: false, output: '', format: to, resourceCount: 0,
+            warnings: [], errors: [`Unsupported conversion: ${from} -> ${to}`], results: [],
+        };
+    }
+}
+// ---------------------------------------------------------------------------
+// Format detection
+// ---------------------------------------------------------------------------
+/**
+ * Detect the format of input data by inspecting its content.
+ */
+export function detectFormat(input) {
+    const trimmed = input.trim();
+    // Check for FHIR JSON (has "resourceType")
+    if (trimmed.startsWith('{') || trimmed.startsWith('[')) {
+        try {
+            const parsed = JSON.parse(trimmed);
+            if (parsed.resourceType)
+                return 'fhir';
+            if (parsed['@context'] || parsed['@type'])
+                return 'cascade'; // JSON-LD
+        }
+        catch {
+            // Not valid JSON
+        }
+    }
+    // Check for Turtle (has @prefix declarations or common Cascade namespace URIs)
+    if (trimmed.includes('@prefix') ||
+        trimmed.includes('ns.cascadeprotocol.org') ||
+        /^<[^>]+>\s+a\s+/.test(trimmed)) {
+        return 'cascade';
+    }
+    // Check for C-CDA (XML with ClinicalDocument root)
+    if (trimmed.startsWith('<?xml') || trimmed.includes('<ClinicalDocument')) {
+        return 'c-cda';
+    }
+    return null;
+}
+//# sourceMappingURL=index.js.map

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

@@ -0,0 +1 @@
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