@the-cascade-protocol/cli 0.3.1 → 0.3.3

package/dist/commands/capabilities.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"capabilities.d.ts","sourceRoot":"","sources":["../../src/commands/capabilities.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AAiNpC,wBAAgB,2BAA2B,CAAC,OAAO,EAAE,OAAO,GAAG,IAAI,CAkBlE"}
+{"version":3,"file":"capabilities.d.ts","sourceRoot":"","sources":["../../src/commands/capabilities.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AA2QpC,wBAAgB,2BAA2B,CAAC,OAAO,EAAE,OAAO,GAAG,IAAI,CAkBlE"}

package/dist/commands/capabilities.js

@@ -53,6 +53,28 @@ function getCapabilities(version) {
                 examples: ['cascade pod init ./my-pod'],
                 status: 'implemented',
             },
+            {
+                name: 'pod import',
+                description: 'Import FHIR R4 JSON or Cascade Turtle files into a Pod, converting and reconciling records into the Pod directory structure',
+                usage: 'cascade pod import <pod-dir> <files...> [options]',
+                parameters: [
+                    { name: 'pod-dir', type: 'string', required: true, description: 'Path to the target Cascade Pod' },
+                    { name: 'files', type: 'string[]', required: true, description: 'One or more FHIR R4 JSON or Cascade Turtle files to import' },
+                    { name: '--source-system', type: 'string', required: false, description: 'Label for the source health system (e.g., "Virginia Mason")' },
+                    { name: '--no-reconcile', type: 'boolean', required: false, description: 'Skip reconciliation; append records without merging duplicates' },
+                    { name: '--trust', type: 'string', required: false, description: 'Comma-separated trust scores per source (0.0–1.0), in file order' },
+                    { name: '--report', type: 'string', required: false, description: 'Write a JSON import report to this file path' },
+                    { name: '--dry-run', type: 'boolean', required: false, description: 'Parse and convert without writing to the Pod' },
+                    { name: '--passthrough', type: 'string', required: false, description: 'Passthrough mode for unconverted records', choices: ['full', 'minimal'] },
+                    { name: '--json', type: 'boolean', required: false, description: 'Output results as JSON' },
+                ],
+                examples: [
+                    'cascade pod import ./my-pod patient.json --source-system "Virginia Mason"',
+                    'cascade pod import ./my-pod vm.json swedish.json --source-system "primary,specialist" --report report.json',
+                    'cascade pod import ./my-pod records.ttl --no-reconcile',
+                ],
+                status: 'implemented',
+            },
             {
                 name: 'pod query',
                 description: 'Query data within a Cascade Pod by type',
@@ -63,10 +85,19 @@ function getCapabilities(version) {
                     { name: '--conditions', type: 'boolean', required: false, description: 'Query conditions' },
                     { name: '--allergies', type: 'boolean', required: false, description: 'Query allergies' },
                     { name: '--lab-results', type: 'boolean', required: false, description: 'Query lab results' },
-                    { name: '--all', type: 'boolean', required: false, description: 'Query all data' },
-                    { name: '--json', type: 'boolean', required: false, description: 'Output as JSON' },
+                    { name: '--immunizations', type: 'boolean', required: false, description: 'Query immunizations' },
+                    { name: '--vital-signs', type: 'boolean', required: false, description: 'Query vital signs' },
+                    { name: '--supplements', type: 'boolean', required: false, description: 'Query supplements' },
+                    { name: '--procedures', type: 'boolean', required: false, description: 'Query procedures' },
+                    { name: '--encounters', type: 'boolean', required: false, description: 'Query clinical encounters' },
+                    { name: '--all', type: 'boolean', required: false, description: 'Query all data types' },
+                    { name: '--json', type: 'boolean', required: false, description: 'Output results as JSON (machine-readable)' },
+                ],
+                examples: [
+                    'cascade pod query ./my-pod --medications --json',
+                    'cascade pod query ./my-pod --encounters --conditions --json',
+                    'cascade pod query ./my-pod --all --json',
                 ],
-                examples: ['cascade pod query ./my-pod --medications --json', 'cascade pod query ./my-pod --all --json'],
                 status: 'implemented',
             },
             {
@@ -88,6 +119,23 @@ function getCapabilities(version) {
                 examples: ['cascade pod export ./my-pod', 'cascade pod export ./my-pod --format directory'],
                 status: 'implemented',
             },
+            {
+                name: 'reconcile',
+                description: 'Reconcile Cascade RDF records from multiple sources into a normalized record set, resolving conflicts using trust-weighted scoring',
+                usage: 'cascade reconcile <files...> [options]',
+                parameters: [
+                    { name: 'files', type: 'string[]', required: true, description: 'Two or more Cascade Turtle files to reconcile' },
+                    { name: '--output', type: 'string', required: false, description: 'Write merged output to this file (defaults to stdout)' },
+                    { name: '--report', type: 'string', required: false, description: 'Write a JSON reconciliation report to this file path' },
+                    { name: '--trust', type: 'string', required: false, description: 'Comma-separated trust scores per source (0.0–1.0), in file order' },
+                    { name: '--json', type: 'boolean', required: false, description: 'Output results as JSON' },
+                ],
+                examples: [
+                    'cascade reconcile system-a.ttl system-b.ttl --output merged.ttl --report report.json',
+                    'cascade reconcile vm.ttl swedish.ttl --trust 0.9,0.7 --output merged.ttl',
+                ],
+                status: 'implemented',
+            },
             {
                 name: 'conformance run',
                 description: 'Run conformance test suite (53 fixtures)',
@@ -128,12 +176,22 @@ function getCapabilities(version) {
                 description: 'Read a Cascade Pod and return a JSON summary of all contents',
                 parameters: { path: { type: 'string', description: 'Pod directory path (optional, uses CASCADE_POD_PATH)', required: false } },
             },
+            {
+                name: 'cascade_pod_import',
+                description: 'Import FHIR R4 JSON or Cascade Turtle files into a Pod, converting and reconciling records',
+                parameters: {
+                    podPath: { type: 'string', description: 'Pod directory path', required: true },
+                    files: { type: 'array', description: 'File paths to import (FHIR JSON or Cascade Turtle)', required: true },
+                    sourceSystem: { type: 'string', description: 'Label for the source health system', required: false },
+                    noReconcile: { type: 'boolean', description: 'Skip reconciliation', required: false },
+                },
+            },
             {
                 name: 'cascade_pod_query',
                 description: 'Query records from a Pod by data type',
                 parameters: {
                     path: { type: 'string', description: 'Pod directory path (optional)', required: false },
-                    dataType: { type: 'string', description: 'Data type to query', required: true, enum: ['medications', 'conditions', 'allergies', 'lab-results', 'immunizations', 'vital-signs', 'supplements', 'insurance', 'patient-profile', 'heart-rate', 'blood-pressure', 'activity', 'sleep', 'all'] },
+                    dataType: { type: 'string', description: 'Data type to query', required: true, enum: ['medications', 'conditions', 'allergies', 'lab-results', 'immunizations', 'vital-signs', 'supplements', 'procedures', 'encounters', 'insurance', 'patient-profile', 'heart-rate', 'blood-pressure', 'activity', 'sleep', 'all'] },
                 },
             },
             {

package/dist/commands/capabilities.js.map

@@ -1 +1 @@
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package/dist/lib/fhir-converter/converters-clinical.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"converters-clinical.d.ts","sourceRoot":"","sources":["../../../src/lib/fhir-converter/converters-clinical.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;GAgBG;AAEH,OAAO,KAAK,EAAE,IAAI,EAAE,MAAM,IAAI,CAAC;AAE/B,OAAO,EACL,KAAK,gBAAgB,EAkBtB,MAAM,YAAY,CAAC;AAMpB,wBAAgB,0BAA0B,CAAC,QAAQ,EAAE,GAAG,GAAG,gBAAgB,GAAG;IAAE,MAAM,EAAE,IAAI,EAAE,CAAA;CAAE,CA2F/F;AAMD,wBAAgB,gBAAgB,CAAC,QAAQ,EAAE,GAAG,GAAG,gBAAgB,GAAG;IAAE,MAAM,EAAE,IAAI,EAAE,CAAA;CAAE,CAqDrF;AAMD,wBAAgB,yBAAyB,CAAC,QAAQ,EAAE,GAAG,GAAG,gBAAgB,GAAG;IAAE,MAAM,EAAE,IAAI,EAAE,CAAA;CAAE,CAwD9F;AAMD,wBAAgB,sBAAsB,CAAC,QAAQ,EAAE,GAAG,GAAG,OAAO,CAoB7D;AAMD,wBAAgB,qBAAqB,CAAC,QAAQ,EAAE,GAAG,GAAG,gBAAgB,GAAG;IAAE,MAAM,EAAE,IAAI,EAAE,CAAA;CAAE,CAiH1F;AAMD,wBAAgB,uBAAuB,CAAC,QAAQ,EAAE,GAAG,GAAG,gBAAgB,GAAG;IAAE,MAAM,EAAE,IAAI,EAAE,CAAA;CAAE,CAiG5F;AAMD,wBAAgB,gBAAgB,CAAC,QAAQ,EAAE,GAAG,GAAG,gBAAgB,GAAG;IAAE,MAAM,EAAE,IAAI,EAAE,CAAA;CAAE,CAgDrF;AAMD,wBAAgB,uBAAuB,CAAC,QAAQ,EAAE,GAAG,GAAG,gBAAgB,GAAG;IAAE,MAAM,EAAE,IAAI,EAAE,CAAA;CAAE,CAgD5F;AAMD,wBAAgB,gBAAgB,CAAC,QAAQ,EAAE,GAAG,GAAG,gBAAgB,GAAG;IAAE,MAAM,EAAE,IAAI,EAAE,CAAA;CAAE,CAsErF;AAMD,wBAAgB,uBAAuB,CAAC,QAAQ,EAAE,GAAG,GAAG,gBAAgB,GAAG;IAAE,MAAM,EAAE,IAAI,EAAE,CAAA;CAAE,CAkF5F;AAMD,wBAAgB,+BAA+B,CAAC,QAAQ,EAAE,GAAG,GAAG,gBAAgB,GAAG;IAAE,MAAM,EAAE,IAAI,EAAE,CAAA;CAAE,CAmDpG;AAMD,wBAAgB,aAAa,CAAC,QAAQ,EAAE,GAAG,GAAG,gBAAgB,GAAG;IAAE,MAAM,EAAE,IAAI,EAAE,CAAA;CAAE,CA+ClF;AAMD,wBAAgB,mBAAmB,CAAC,QAAQ,EAAE,GAAG,GAAG,gBAAgB,GAAG;IAAE,MAAM,EAAE,IAAI,EAAE,CAAA;CAAE,CAuDxF"}

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

@@ -631,11 +631,16 @@ export function convertLaboratoryReport(resource) {
             quads.push(tripleStr(subjectUri, NS.clinical + 'reportCategory', catCode));
         }
     }
-    // Effective date
+    // Effective date (when procedure/analysis was performed)
     const effectiveDate = resource.effectiveDateTime ?? resource.effectivePeriod?.start;
     if (effectiveDate) {
         quads.push(tripleDateTime(subjectUri, NS.clinical + 'performedDate', effectiveDate));
     }
+    // documentDate (when results were finalized/issued) — required by LaboratoryReportShape
+    const issuedDate = resource.issued ?? resource.effectiveDateTime ?? resource.effectivePeriod?.start;
+    if (issuedDate) {
+        quads.push(tripleDateTime(subjectUri, NS.clinical + 'documentDate', issuedDate));
+    }
     // Provider from first performer
     if (Array.isArray(resource.performer) && resource.performer.length > 0) {
         const provName = resource.performer[0]?.display;
@@ -661,7 +666,9 @@ export function convertLaboratoryReport(resource) {
     }
     if (resource.id) {
         quads.push(tripleStr(subjectUri, NS.clinical + 'sourceRecordId', resource.id));
+        quads.push(tripleStr(subjectUri, NS.clinical + 'fhirResourceId', resource.id));
     }
+    quads.push(tripleStr(subjectUri, NS.clinical + 'fhirResourceType', 'DiagnosticReport'));
     quads.push(tripleRef(subjectUri, NS.cascade + 'layerPromotionStatus', NS.cascade + 'FullyMapped'));
     return {
         turtle: '',

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

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

@@ -1 +1 @@
-{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../src/lib/fhir-converter/index.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GAsCG;AAMH,OAAO,EACL,KAAK,WAAW,EAChB,KAAK,YAAY,EACjB,KAAK,gBAAgB,EACrB,KAAK,qBAAqB,EAI3B,MAAM,YAAY,CAAC;AASpB,YAAY,EAAE,WAAW,EAAE,YAAY,EAAE,gBAAgB,EAAE,qBAAqB,EAAE,CAAC;AAGnF,OAAO,EAAE,0BAA0B,EAAE,oBAAoB,EAAE,MAAM,sBAAsB,CAAC;AACxF,OAAO,EAAE,oBAAoB,EAAE,MAAM,sBAAsB,CAAC;AAM5D;;;;;;GAMG;AACH,wBAAsB,OAAO,CAC3B,KAAK,EAAE,MAAM,EACb,IAAI,EAAE,WAAW,EACjB,EAAE,EAAE,YAAY,EAChB,mBAAmB,GAAE,QAAQ,GAAG,QAAmB,EACnD,YAAY,CAAC,EAAE,MAAM,EACrB,kBAAkB,UAAQ,GACzB,OAAO,CAAC,qBAAqB,CAAC,CA0IhC;AAMD;;GAEG;AACH,wBAAgB,YAAY,CAAC,KAAK,EAAE,MAAM,GAAG,WAAW,GAAG,IAAI,CA6B9D"}
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../src/lib/fhir-converter/index.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GAsCG;AAMH,OAAO,EACL,KAAK,WAAW,EAChB,KAAK,YAAY,EACjB,KAAK,gBAAgB,EACrB,KAAK,qBAAqB,EAI3B,MAAM,YAAY,CAAC;AASpB,YAAY,EAAE,WAAW,EAAE,YAAY,EAAE,gBAAgB,EAAE,qBAAqB,EAAE,CAAC;AAGnF,OAAO,EAAE,0BAA0B,EAAE,oBAAoB,EAAE,MAAM,sBAAsB,CAAC;AACxF,OAAO,EAAE,oBAAoB,EAAE,MAAM,sBAAsB,CAAC;AAM5D;;;;;;GAMG;AACH,wBAAsB,OAAO,CAC3B,KAAK,EAAE,MAAM,EACb,IAAI,EAAE,WAAW,EACjB,EAAE,EAAE,YAAY,EAChB,mBAAmB,GAAE,QAAQ,GAAG,QAAmB,EACnD,YAAY,CAAC,EAAE,MAAM,EACrB,kBAAkB,UAAQ,GACzB,OAAO,CAAC,qBAAqB,CAAC,CAiKhC;AAMD;;GAEG;AACH,wBAAgB,YAAY,CAAC,KAAK,EAAE,MAAM,GAAG,WAAW,GAAG,IAAI,CA6B9D"}

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

@@ -115,18 +115,36 @@ export async function convert(input, from, to, outputSerialization = 'turtle', s
             };
         }
         // Inject cascade:sourceSystem into every record if --source-system was given.
-        // We add one triple per unique subject that has an rdf:type (i.e. a real record).
-        if (sourceSystem) {
-            const recordSubjects = new Set();
-            for (const q of allQuads) {
-                if (q.predicate.value === NS.rdf + 'type') {
-                    recordSubjects.add(q.subject.value);
+        // Also inject clinical:importedAt and clinical:sourceEHR for ClinicalDocument subtypes
+        // (LaboratoryReport, ImagingReport, etc.) which require these fields per the SHACL shapes.
+        const clinicalDocTypes = new Set([
+            NS.clinical + 'LaboratoryReport',
+            NS.clinical + 'ImagingReport',
+            NS.clinical + 'ClinicalDocument',
+            NS.clinical + 'VisitSummary',
+        ]);
+        const conversionTimestamp = new Date().toISOString();
+        const clinicalDocSubjects = new Set();
+        const recordSubjects = new Set();
+        for (const q of allQuads) {
+            if (q.predicate.value === NS.rdf + 'type') {
+                recordSubjects.add(q.subject.value);
+                if (clinicalDocTypes.has(q.object.value)) {
+                    clinicalDocSubjects.add(q.subject.value);
                 }
             }
+        }
+        if (sourceSystem) {
             for (const subjectUri of recordSubjects) {
                 allQuads.push(makeQuad(namedNode(subjectUri), namedNode(NS.cascade + 'sourceSystem'), literal(sourceSystem)));
             }
         }
+        for (const subjectUri of clinicalDocSubjects) {
+            allQuads.push(makeQuad(namedNode(subjectUri), namedNode(NS.clinical + 'importedAt'), literal(conversionTimestamp, namedNode(NS.xsd + 'dateTime'))));
+            if (sourceSystem) {
+                allQuads.push(makeQuad(namedNode(subjectUri), namedNode(NS.clinical + 'sourceEHR'), literal(sourceSystem)));
+            }
+        }
         // Determine output format
         let output;
         if (outputSerialization === 'jsonld' || to === 'jsonld') {

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

@@ -1 +1 @@
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package/dist/lib/reconciler.d.ts

@@ -32,11 +32,16 @@ export interface ReconcilerResult {
     };
 }
 type CascadeRecordType = 'health:MedicationRecord' | 'health:ConditionRecord' | 'health:AllergyRecord' | 'health:LabResultRecord' | 'health:ImmunizationRecord' | 'clinical:VitalSign' | 'cascade:PatientProfile' | 'coverage:InsurancePlan';
+interface RdfValue {
+    value: string;
+    /** xsd:* datatype URI for typed literals; undefined for URIs and plain strings */
+    datatype?: string;
+}
 interface ParsedRecord {
     uri: string;
     type: CascadeRecordType;
     sourceSystem: string;
-    properties: Map<string, string[]>;
+    properties: Map<string, RdfValue[]>;
 }
 export declare function parseTurtle(turtle: string, defaultSystem: string): Promise<ParsedRecord[]>;
 export declare function normalizeMedName(name: string): string;

package/dist/lib/reconciler.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"reconciler.d.ts","sourceRoot":"","sources":["../../src/lib/reconciler.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAWH,MAAM,WAAW,iBAAiB;IAChC,WAAW,CAAC,EAAE,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;IACrC,YAAY,CAAC,EAAE,MAAM,CAAC;CACvB;AAED,MAAM,WAAW,eAAe;IAC9B,OAAO,EAAE,MAAM,CAAC;IAChB,UAAU,EAAE,MAAM,CAAC;CACpB;AAED,MAAM,WAAW,gBAAgB;IAC/B,MAAM,EAAE,MAAM,CAAC;IACf,MAAM,EAAE;QACN,OAAO,EAAE,KAAK,CAAC;YAAE,MAAM,EAAE,MAAM,CAAC;YAAC,KAAK,EAAE,MAAM,CAAA;SAAE,CAAC,CAAC;QAClD,OAAO,EAAE;YACP,iBAAiB,EAAE,MAAM,CAAC;YAC1B,sBAAsB,EAAE,MAAM,CAAC;YAC/B,oBAAoB,EAAE,MAAM,CAAC;YAC7B,iBAAiB,EAAE,MAAM,CAAC;YAC1B,mBAAmB,EAAE,MAAM,CAAC;YAC5B,gBAAgB,EAAE,MAAM,CAAC;SAC1B,CAAC;QACF,eAAe,EAAE,MAAM,EAAE,CAAC;QAC1B,mBAAmB,EAAE,MAAM,EAAE,CAAC;KAC/B,CAAC;CACH;AAMD,KAAK,iBAAiB,GAClB,yBAAyB,GACzB,wBAAwB,GACxB,sBAAsB,GACtB,wBAAwB,GACxB,2BAA2B,GAC3B,oBAAoB,GACpB,wBAAwB,GACxB,wBAAwB,CAAC;AAiB7B,UAAU,YAAY;IACpB,GAAG,EAAE,MAAM,CAAC;IACZ,IAAI,EAAE,iBAAiB,CAAC;IACxB,YAAY,EAAE,MAAM,CAAC;IACrB,UAAU,EAAE,GAAG,CAAC,MAAM,EAAE,MAAM,EAAE,CAAC,CAAC;CACnC;AAED,wBAAsB,WAAW,CAAC,MAAM,EAAE,MAAM,EAAE,aAAa,EAAE,MAAM,GAAG,OAAO,CAAC,YAAY,EAAE,CAAC,CA+BhG;AAMD,wBAAgB,gBAAgB,CAAC,IAAI,EAAE,MAAM,GAAG,MAAM,CAKrD;AA6QD,wBAAsB,iBAAiB,CACrC,MAAM,EAAE,eAAe,EAAE,EACzB,OAAO,CAAC,EAAE,iBAAiB,GAC1B,OAAO,CAAC,gBAAgB,CAAC,CA8G3B"}
+{"version":3,"file":"reconciler.d.ts","sourceRoot":"","sources":["../../src/lib/reconciler.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAWH,MAAM,WAAW,iBAAiB;IAChC,WAAW,CAAC,EAAE,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;IACrC,YAAY,CAAC,EAAE,MAAM,CAAC;CACvB;AAED,MAAM,WAAW,eAAe;IAC9B,OAAO,EAAE,MAAM,CAAC;IAChB,UAAU,EAAE,MAAM,CAAC;CACpB;AAED,MAAM,WAAW,gBAAgB;IAC/B,MAAM,EAAE,MAAM,CAAC;IACf,MAAM,EAAE;QACN,OAAO,EAAE,KAAK,CAAC;YAAE,MAAM,EAAE,MAAM,CAAC;YAAC,KAAK,EAAE,MAAM,CAAA;SAAE,CAAC,CAAC;QAClD,OAAO,EAAE;YACP,iBAAiB,EAAE,MAAM,CAAC;YAC1B,sBAAsB,EAAE,MAAM,CAAC;YAC/B,oBAAoB,EAAE,MAAM,CAAC;YAC7B,iBAAiB,EAAE,MAAM,CAAC;YAC1B,mBAAmB,EAAE,MAAM,CAAC;YAC5B,gBAAgB,EAAE,MAAM,CAAC;SAC1B,CAAC;QACF,eAAe,EAAE,MAAM,EAAE,CAAC;QAC1B,mBAAmB,EAAE,MAAM,EAAE,CAAC;KAC/B,CAAC;CACH;AAMD,KAAK,iBAAiB,GAClB,yBAAyB,GACzB,wBAAwB,GACxB,sBAAsB,GACtB,wBAAwB,GACxB,2BAA2B,GAC3B,oBAAoB,GACpB,wBAAwB,GACxB,wBAAwB,CAAC;AAiB7B,UAAU,QAAQ;IAChB,KAAK,EAAE,MAAM,CAAC;IACd,kFAAkF;IAClF,QAAQ,CAAC,EAAE,MAAM,CAAC;CACnB;AAED,UAAU,YAAY;IACpB,GAAG,EAAE,MAAM,CAAC;IACZ,IAAI,EAAE,iBAAiB,CAAC;IACxB,YAAY,EAAE,MAAM,CAAC;IACrB,UAAU,EAAE,GAAG,CAAC,MAAM,EAAE,QAAQ,EAAE,CAAC,CAAC;CACrC;AAED,wBAAsB,WAAW,CAAC,MAAM,EAAE,MAAM,EAAE,aAAa,EAAE,MAAM,GAAG,OAAO,CAAC,YAAY,EAAE,CAAC,CAmChG;AAMD,wBAAgB,gBAAgB,CAAC,IAAI,EAAE,MAAM,GAAG,MAAM,CAKrD;AAiRD,wBAAsB,iBAAiB,CACrC,MAAM,EAAE,eAAe,EAAE,EACzB,OAAO,CAAC,EAAE,iBAAiB,GAC1B,OAAO,CAAC,gBAAgB,CAAC,CA8G3B"}

package/dist/lib/reconciler.js

@@ -30,7 +30,7 @@ export async function parseTurtle(turtle, defaultSystem) {
                 const records = [];
                 for (const [uri, triples] of bySubject) {
                     const typeTriple = triples.find(t => t.pred === NS.rdf + 'type');
-                    if (!typeTriple || !KNOWN_TYPES[typeTriple.obj])
+                    if (!typeTriple || !KNOWN_TYPES[typeTriple.obj.value])
                         continue;
                     const properties = new Map();
                     for (const t of triples) {
@@ -40,8 +40,8 @@ export async function parseTurtle(turtle, defaultSystem) {
                         else
                             properties.set(t.pred, [t.obj]);
                     }
-                    const sourceSystem = properties.get(NS.cascade + 'sourceSystem')?.[0] ?? defaultSystem;
-                    records.push({ uri, type: KNOWN_TYPES[typeTriple.obj], sourceSystem, properties });
+                    const sourceSystem = properties.get(NS.cascade + 'sourceSystem')?.[0]?.value ?? defaultSystem;
+                    records.push({ uri, type: KNOWN_TYPES[typeTriple.obj.value], sourceSystem, properties });
                 }
                 resolve(records);
                 return;
@@ -49,7 +49,11 @@ export async function parseTurtle(turtle, defaultSystem) {
             const subj = quad.subject.value;
             if (!bySubject.has(subj))
                 bySubject.set(subj, []);
-            bySubject.get(subj).push({ pred: quad.predicate.value, obj: quad.object.value });
+            const obj = quad.object;
+            const rdfVal = obj.termType === 'Literal' && obj.datatype?.value && obj.datatype.value !== NS.xsd + 'string'
+                ? { value: obj.value, datatype: obj.datatype.value }
+                : { value: obj.value };
+            bySubject.get(subj).push({ pred: quad.predicate.value, obj: rdfVal });
         });
     });
 }
@@ -66,15 +70,15 @@ function normalizeConditionName(name) {
     return name.toLowerCase().replace(/\([^)]*\)/g, '').replace(/\s+/g, ' ').trim();
 }
 function getProp(r, pred) {
-    return r.properties.get(pred)?.[0];
+    return r.properties.get(pred)?.[0]?.value;
 }
 function codeFromUri(uri) {
     return uri.split('/').pop() ?? uri.split('#').pop() ?? uri;
 }
 function dateOnly(dt) { return dt.split('T')[0] ?? dt; }
 function matchMedications(a, b) {
-    const rxA = (a.properties.get(NS.health + 'rxNormCode') ?? []).map(codeFromUri);
-    const rxB = (b.properties.get(NS.health + 'rxNormCode') ?? []).map(codeFromUri);
+    const rxA = (a.properties.get(NS.health + 'rxNormCode') ?? []).map(v => codeFromUri(v.value));
+    const rxB = (b.properties.get(NS.health + 'rxNormCode') ?? []).map(v => codeFromUri(v.value));
     const shared = rxA.find(c => c && rxB.includes(c));
     if (shared)
         return { match: true, confidence: 1.0, matchedOn: `rxnorm:${shared}` };
@@ -251,7 +255,11 @@ async function serializeGroups(groups, resolutions) {
             const subj = namedNode(res.canonical.uri);
             for (const [pred, vals] of res.canonical.properties) {
                 for (const val of vals) {
-                    const obj = val.startsWith('http') || val.startsWith('urn:') ? namedNode(val) : literal(val);
+                    const obj = val.value.startsWith('http') || val.value.startsWith('urn:')
+                        ? namedNode(val.value)
+                        : val.datatype
+                            ? literal(val.value, namedNode(val.datatype))
+                            : literal(val.value);
                     writer.addQuad(makeQuad(subj, namedNode(pred), obj));
                 }
             }