npm - @the-cascade-protocol/cli - Versions diffs - 0.2.3 → 0.2.5 - Mend

@the-cascade-protocol/cli 0.2.3 → 0.2.5

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (18) hide show

package/dist/commands/convert.d.ts.map +1 -1
package/dist/commands/convert.js +5 -1
package/dist/commands/convert.js.map +1 -1
package/dist/commands/reconcile.d.ts +32 -0
package/dist/commands/reconcile.d.ts.map +1 -0
package/dist/commands/reconcile.js +490 -0
package/dist/commands/reconcile.js.map +1 -0
package/dist/index.js +5 -3
package/dist/index.js.map +1 -1
package/dist/lib/fhir-converter/index.d.ts +1 -1
package/dist/lib/fhir-converter/index.d.ts.map +1 -1
package/dist/lib/fhir-converter/index.js +17 -2
package/dist/lib/fhir-converter/index.js.map +1 -1
package/dist/shapes/checkup.shapes.ttl +10 -0
package/package.json +1 -1
package/dist/commands/pod 2.js +0 -1017
package/dist/commands/pod.d.ts 2.map +0 -1
package/dist/commands/pod.js 2.map +0 -1

package/dist/commands/convert.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"convert.d.ts","sourceRoot":"","sources":["../../src/commands/convert.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;GAiBG;AAEH,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AAkBpC,wBAAgB,sBAAsB,CAAC,OAAO,EAAE,OAAO,GAAG,IAAI,~~CA8H7D~~"}
1	+ {"version":3,"file":"convert.d.ts","sourceRoot":"","sources":["../../src/commands/convert.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;GAiBG;AAEH,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AAkBpC,wBAAgB,sBAAsB,CAAC,OAAO,EAAE,OAAO,GAAG,IAAI,CAmI7D"}

package/dist/commands/convert.js CHANGED Viewed

@@ -39,6 +39,7 @@ export function registerConvertCommand(program) {
         .requiredOption('--from <format>', 'Source format (fhir|cascade|c-cda)')
         .requiredOption('--to <format>', 'Target format (turtle|jsonld|fhir|cascade)')
         .option('--format <output>', 'Output serialization format (turtle|jsonld)', 'turtle')
+        .option('--source-system <name>', 'Tag all records with a source system name (adds cascade:sourceSystem for reconciliation)')
         .action(async (file, options) => {
         const globalOpts = program.opts();
         printVerbose(`Converting from ${options.from} to ${options.to}`, globalOpts);
@@ -49,6 +50,9 @@ export function registerConvertCommand(program) {
             printVerbose('Reading from stdin', globalOpts);
         }
         printVerbose(`Output format: ${options.format}`, globalOpts);
+        if (options.sourceSystem) {
+            printVerbose(`Source system: ${options.sourceSystem}`, globalOpts);
+        }
         // 1. Read input
         let input;
         try {
@@ -84,7 +88,7 @@ export function registerConvertCommand(program) {
         }
         // 4. Run conversion
         const outputSerialization = (options.format === 'jsonld' ? 'jsonld' : 'turtle');
-        const result = await convert(input, options.from, options.to, outputSerialization);
+        const result = await convert(input, options.from, options.to, outputSerialization, options.sourceSystem);
         // 5. Output
         if (!result.success) {
             for (const err of result.errors) {

package/dist/commands/convert.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/commands/reconcile.d.ts ADDED Viewed

@@ -0,0 +1,32 @@
+/**
+ * cascade reconcile <file1> <file2> [file3...] [options]
+ *
+ * Reconcile Cascade Protocol Turtle files from multiple sources into a
+ * single normalized record set.
+ *
+ * Detects and resolves:
+ *   - Exact duplicates (same record from multiple systems)
+ *   - Near-duplicates (same record, minor value drift)
+ *   - Status conflicts (active vs resolved)
+ *   - Value conflicts (same test, different result)
+ *
+ * Adds reconciliation provenance to the merged output:
+ *   cascade:reconciliationStatus  "canonical" | "merged" | "conflict-resolved" | "unresolved-conflict"
+ *   cascade:mergedFrom            <source-uri1>, <source-uri2>, ...
+ *   cascade:mergedSources         "system-a, system-b"
+ *   cascade:conflictResolution    "trust_priority" | "merge_values"
+ *
+ * Options:
+ *   --output <file>                     Write merged Turtle to file (default: stdout)
+ *   --report <file>                     Write JSON transformation report to file
+ *   --trust <system=score,...>          Set trust scores (e.g. hospital=0.95,specialist=0.85)
+ *   --lab-tolerance <number>            Numeric tolerance for lab value matching (default: 0.05)
+ *   --json                              Output report as JSON to stdout
+ *
+ * Examples:
+ *   cascade reconcile primary-care.ttl specialist.ttl hospital.ttl --output merged.ttl --report report.json
+ *   cascade reconcile *.ttl --trust hospital=0.95
+ */
+import { Command } from 'commander';
+export declare function registerReconcileCommand(program: Command): void;
+//# sourceMappingURL=reconcile.d.ts.map

package/dist/commands/reconcile.d.ts.map ADDED Viewed

	@@ -0,0 +1 @@
1	+ {"version":3,"file":"reconcile.d.ts","sourceRoot":"","sources":["../../src/commands/reconcile.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;;;;;;;;;GA4BG;AAEH,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAC;AAoWpC,wBAAgB,wBAAwB,CAAC,OAAO,EAAE,OAAO,GAAG,IAAI,CAsL/D"}

package/dist/commands/reconcile.js ADDED Viewed

@@ -0,0 +1,490 @@
+/**
+ * cascade reconcile <file1> <file2> [file3...] [options]
+ *
+ * Reconcile Cascade Protocol Turtle files from multiple sources into a
+ * single normalized record set.
+ *
+ * Detects and resolves:
+ *   - Exact duplicates (same record from multiple systems)
+ *   - Near-duplicates (same record, minor value drift)
+ *   - Status conflicts (active vs resolved)
+ *   - Value conflicts (same test, different result)
+ *
+ * Adds reconciliation provenance to the merged output:
+ *   cascade:reconciliationStatus  "canonical" | "merged" | "conflict-resolved" | "unresolved-conflict"
+ *   cascade:mergedFrom            <source-uri1>, <source-uri2>, ...
+ *   cascade:mergedSources         "system-a, system-b"
+ *   cascade:conflictResolution    "trust_priority" | "merge_values"
+ *
+ * Options:
+ *   --output <file>                     Write merged Turtle to file (default: stdout)
+ *   --report <file>                     Write JSON transformation report to file
+ *   --trust <system=score,...>          Set trust scores (e.g. hospital=0.95,specialist=0.85)
+ *   --lab-tolerance <number>            Numeric tolerance for lab value matching (default: 0.05)
+ *   --json                              Output report as JSON to stdout
+ *
+ * Examples:
+ *   cascade reconcile primary-care.ttl specialist.ttl hospital.ttl --output merged.ttl --report report.json
+ *   cascade reconcile *.ttl --trust hospital=0.95
+ */
+import { readFileSync, writeFileSync } from 'node:fs';
+import { basename } from 'node:path';
+import { Parser, Writer, DataFactory } from 'n3';
+import { printResult, printError, printVerbose } from '../lib/output.js';
+import { NS, TURTLE_PREFIXES } from '../lib/fhir-converter/types.js';
+const { namedNode, literal, quad: makeQuad } = DataFactory;
+const KNOWN_TYPES = {
+    [NS.health + 'MedicationRecord']: 'health:MedicationRecord',
+    [NS.health + 'ConditionRecord']: 'health:ConditionRecord',
+    [NS.health + 'AllergyRecord']: 'health:AllergyRecord',
+    [NS.health + 'LabResultRecord']: 'health:LabResultRecord',
+    [NS.health + 'ImmunizationRecord']: 'health:ImmunizationRecord',
+    [NS.clinical + 'VitalSign']: 'clinical:VitalSign',
+    [NS.cascade + 'PatientProfile']: 'cascade:PatientProfile',
+    [NS.coverage + 'InsurancePlan']: 'coverage:InsurancePlan',
+};
+async function parseTurtle(turtle, defaultSystem) {
+    return new Promise((resolve, reject) => {
+        const parser = new Parser({ format: 'Turtle' });
+        const bySubject = new Map();
+        parser.parse(turtle, (error, quad) => {
+            if (error) {
+                reject(error);
+                return;
+            }
+            if (!quad) {
+                const records = [];
+                for (const [uri, triples] of bySubject) {
+                    const typeTriple = triples.find(t => t.pred === NS.rdf + 'type');
+                    if (!typeTriple || !KNOWN_TYPES[typeTriple.obj])
+                        continue;
+                    const properties = new Map();
+                    for (const t of triples) {
+                        const existing = properties.get(t.pred);
+                        if (existing)
+                            existing.push(t.obj);
+                        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 });
+                }
+                resolve(records);
+                return;
+            }
+            const subj = quad.subject.value;
+            if (!bySubject.has(subj))
+                bySubject.set(subj, []);
+            bySubject.get(subj).push({ pred: quad.predicate.value, obj: quad.object.value });
+        });
+    });
+}
+// ---------------------------------------------------------------------------
+// Matching helpers
+// ---------------------------------------------------------------------------
+function normalizeMedName(name) {
+    return name.toLowerCase()
+        .replace(/\d+(\.\d+)?\s*(mg|mcg|g|ml|%|iu|units?|meq)\b/gi, '')
+        .replace(/\b(oral|tablet|capsule|solution|injection|extended|release|er|xr|cr|sr|hr)\b/gi, '')
+        .replace(/\s+/g, ' ').trim();
+}
+function normalizeConditionName(name) {
+    return name.toLowerCase().replace(/\([^)]*\)/g, '').replace(/\s+/g, ' ').trim();
+}
+function getProp(r, pred) {
+    return r.properties.get(pred)?.[0];
+}
+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 shared = rxA.find(c => c && rxB.includes(c));
+    if (shared)
+        return { match: true, confidence: 1.0, matchedOn: `rxnorm:${shared}` };
+    const nA = normalizeMedName(getProp(a, NS.health + 'medicationName') ?? '');
+    const nB = normalizeMedName(getProp(b, NS.health + 'medicationName') ?? '');
+    if (nA && nB && nA === nB)
+        return { match: true, confidence: 0.85, matchedOn: `name:"${nA}"` };
+    if (nA && nB && (nA.includes(nB) || nB.includes(nA)))
+        return { match: true, confidence: 0.70, matchedOn: `partial-name` };
+    return { match: false, confidence: 0, matchedOn: '' };
+}
+function matchConditions(a, b) {
+    const sA = getProp(a, NS.health + 'snomedCode');
+    const sB = getProp(b, NS.health + 'snomedCode');
+    if (sA && sB && codeFromUri(sA) === codeFromUri(sB))
+        return { match: true, confidence: 1.0, matchedOn: `snomed:${codeFromUri(sA)}` };
+    const iA = getProp(a, NS.health + 'icd10Code');
+    const iB = getProp(b, NS.health + 'icd10Code');
+    if (iA && iB && codeFromUri(iA) === codeFromUri(iB))
+        return { match: true, confidence: 0.95, matchedOn: `icd10:${codeFromUri(iA)}` };
+    const nA = normalizeConditionName(getProp(a, NS.health + 'conditionName') ?? '');
+    const nB = normalizeConditionName(getProp(b, NS.health + 'conditionName') ?? '');
+    if (nA && nB && nA === nB)
+        return { match: true, confidence: 0.80, matchedOn: `name:"${nA}"` };
+    return { match: false, confidence: 0, matchedOn: '' };
+}
+function matchAllergies(a, b) {
+    const nA = (getProp(a, NS.health + 'allergen') ?? '').toLowerCase().trim();
+    const nB = (getProp(b, NS.health + 'allergen') ?? '').toLowerCase().trim();
+    if (nA && nB && nA === nB)
+        return { match: true, confidence: 0.90, matchedOn: `allergen:"${nA}"` };
+    return { match: false, confidence: 0, matchedOn: '' };
+}
+function matchLabs(a, b, tol) {
+    const lA = getProp(a, NS.health + 'testCode');
+    const lB = getProp(b, NS.health + 'testCode');
+    const dA = dateOnly(getProp(a, NS.health + 'performedDate') ?? '');
+    const dB = dateOnly(getProp(b, NS.health + 'performedDate') ?? '');
+    const vA = parseFloat(getProp(a, NS.health + 'resultValue') ?? 'NaN');
+    const vB = parseFloat(getProp(b, NS.health + 'resultValue') ?? 'NaN');
+    const sameDay = dA && dB && dA === dB;
+    const sameLoinc = lA && lB && codeFromUri(lA) === codeFromUri(lB);
+    if (sameLoinc && sameDay) {
+        if (!isNaN(vA) && !isNaN(vB)) {
+            const diff = Math.abs(vA - vB) / Math.max(Math.abs(vA), 0.001);
+            const conf = diff <= tol ? (diff === 0 ? 1.0 : 0.90) : 0.85;
+            return { match: true, confidence: conf, matchedOn: `loinc:${codeFromUri(lA)}+${dA}` };
+        }
+        return { match: true, confidence: 0.90, matchedOn: `loinc:${codeFromUri(lA)}+${dA}` };
+    }
+    const nA = (getProp(a, NS.health + 'testName') ?? '').toLowerCase().trim();
+    const nB = (getProp(b, NS.health + 'testName') ?? '').toLowerCase().trim();
+    if (nA && nB && nA === nB && sameDay)
+        return { match: true, confidence: 0.75, matchedOn: `name:"${nA}"+${dA}` };
+    return { match: false, confidence: 0, matchedOn: '' };
+}
+function matchImmunizations(a, b) {
+    const cA = getProp(a, NS.health + 'cvxCode');
+    const cB = getProp(b, NS.health + 'cvxCode');
+    const dA = dateOnly(getProp(a, NS.health + 'administrationDate') ?? getProp(a, NS.health + 'startDate') ?? '');
+    const dB = dateOnly(getProp(b, NS.health + 'administrationDate') ?? getProp(b, NS.health + 'startDate') ?? '');
+    if (cA && cB && codeFromUri(cA) === codeFromUri(cB) && dA && dA === dB)
+        return { match: true, confidence: 1.0, matchedOn: `cvx:${codeFromUri(cA)}+${dA}` };
+    return { match: false, confidence: 0, matchedOn: '' };
+}
+function doRecordsMatch(a, b, tol) {
+    if (a.type !== b.type)
+        return { match: false, confidence: 0, matchedOn: '' };
+    switch (a.type) {
+        case 'health:MedicationRecord': return matchMedications(a, b);
+        case 'health:ConditionRecord': return matchConditions(a, b);
+        case 'health:AllergyRecord': return matchAllergies(a, b);
+        case 'health:LabResultRecord': return matchLabs(a, b, tol);
+        case 'health:ImmunizationRecord': return matchImmunizations(a, b);
+        default: return { match: false, confidence: 0, matchedOn: '' };
+    }
+}
+function classifyGroup(records, tol) {
+    if (records.length < 2)
+        return { matchType: 'pass_through' };
+    const [a, b] = records;
+    if (a.type === 'health:ConditionRecord') {
+        const sA = getProp(a, NS.health + 'status');
+        const sB = getProp(b, NS.health + 'status');
+        if (sA && sB && sA !== sB)
+            return { matchType: 'status_conflict', conflictField: 'health:status', conflictValues: { [a.sourceSystem]: sA, [b.sourceSystem]: sB } };
+    }
+    if (a.type === 'health:AllergyRecord') {
+        const sA = getProp(a, NS.health + 'allergySeverity');
+        const sB = getProp(b, NS.health + 'allergySeverity');
+        if (sA && sB && sA !== sB)
+            return { matchType: 'value_conflict', conflictField: 'health:allergySeverity', conflictValues: { [a.sourceSystem]: sA, [b.sourceSystem]: sB } };
+    }
+    if (a.type === 'health:LabResultRecord') {
+        const vA = parseFloat(getProp(a, NS.health + 'resultValue') ?? 'NaN');
+        const vB = parseFloat(getProp(b, NS.health + 'resultValue') ?? 'NaN');
+        if (!isNaN(vA) && !isNaN(vB)) {
+            const diff = Math.abs(vA - vB) / Math.max(Math.abs(vA), 0.001);
+            if (diff > tol)
+                return { matchType: 'value_conflict', conflictField: 'health:resultValue', conflictValues: { [a.sourceSystem]: String(vA), [b.sourceSystem]: String(vB) } };
+            if (diff > 0)
+                return { matchType: 'near_duplicate' };
+        }
+    }
+    if (a.type === 'health:MedicationRecord') {
+        const nA = normalizeMedName(getProp(a, NS.health + 'medicationName') ?? '');
+        const nB = normalizeMedName(getProp(b, NS.health + 'medicationName') ?? '');
+        if (nA !== nB)
+            return { matchType: 'near_duplicate' };
+    }
+    return { matchType: 'exact_duplicate' };
+}
+function completeness(r) {
+    const skip = new Set([NS.rdf + 'type', NS.cascade + 'dataProvenance', NS.cascade + 'schemaVersion', NS.cascade + 'sourceSystem']);
+    let n = 0;
+    for (const [p] of r.properties)
+        if (!skip.has(p))
+            n++;
+    return n;
+}
+function resolveGroup(g, trustScores, defaultTrust) {
+    const trust = (sys) => trustScores[sys] ?? defaultTrust;
+    if (g.records.length === 1) {
+        return { canonical: g.records[0], mergedUris: [g.records[0].uri], mergedSystems: [g.records[0].sourceSystem], strategy: 'pass_through', resolved: true };
+    }
+    const ranked = [...g.records].sort((a, b) => {
+        const td = trust(b.sourceSystem) - trust(a.sourceSystem);
+        return td !== 0 ? td : completeness(b) - completeness(a);
+    });
+    const winner = ranked[0];
+    const losers = ranked.slice(1);
+    let strategy = 'trust_priority';
+    let resolved = true;
+    if (g.matchType === 'near_duplicate') {
+        strategy = 'merge_values';
+    }
+    else if (g.matchType === 'status_conflict') {
+        const diff = Math.abs(trust(ranked[0].sourceSystem) - trust(ranked[1].sourceSystem));
+        if (diff < 0.05) {
+            strategy = 'flag_unresolved';
+            resolved = false;
+        }
+    }
+    // Merge missing fields from lower-trust sources
+    let canonical = winner;
+    if (strategy === 'merge_values') {
+        const mergedProps = new Map(winner.properties);
+        const metaPreds = new Set([NS.rdf + 'type', NS.cascade + 'dataProvenance', NS.cascade + 'schemaVersion', NS.cascade + 'sourceSystem']);
+        for (const src of losers) {
+            for (const [pred, vals] of src.properties) {
+                if (!metaPreds.has(pred) && !mergedProps.has(pred))
+                    mergedProps.set(pred, vals);
+            }
+        }
+        canonical = { ...winner, properties: mergedProps };
+    }
+    return {
+        canonical,
+        mergedUris: g.records.map(r => r.uri),
+        mergedSystems: g.records.map(r => r.sourceSystem),
+        strategy,
+        resolved,
+    };
+}
+// ---------------------------------------------------------------------------
+// Serializer: resolved groups → Turtle
+// ---------------------------------------------------------------------------
+async function serializeGroups(groups, resolutions) {
+    return new Promise((resolve, reject) => {
+        const writer = new Writer({ prefixes: TURTLE_PREFIXES });
+        for (let i = 0; i < groups.length; i++) {
+            const g = groups[i];
+            const res = resolutions[i];
+            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);
+                    writer.addQuad(makeQuad(subj, namedNode(pred), obj));
+                }
+            }
+            // Reconciliation status
+            const status = !res.resolved ? 'unresolved-conflict'
+                : g.matchType === 'pass_through' ? 'canonical'
+                    : (g.matchType === 'status_conflict' || g.matchType === 'value_conflict') ? 'conflict-resolved'
+                        : 'merged';
+            writer.addQuad(makeQuad(subj, namedNode(NS.cascade + 'reconciliationStatus'), literal(status)));
+            writer.addQuad(makeQuad(subj, namedNode(NS.cascade + 'sourceSystem'), literal(res.canonical.sourceSystem)));
+            if (g.matchType !== 'pass_through' && res.mergedUris.length > 1) {
+                for (const srcUri of res.mergedUris) {
+                    writer.addQuad(makeQuad(subj, namedNode(NS.cascade + 'mergedFrom'), namedNode(srcUri)));
+                    writer.addQuad(makeQuad(subj, namedNode(NS.prov + 'wasDerivedFrom'), namedNode(srcUri)));
+                }
+                writer.addQuad(makeQuad(subj, namedNode(NS.cascade + 'mergedSources'), literal(res.mergedSystems.join(', '))));
+                writer.addQuad(makeQuad(subj, namedNode(NS.cascade + 'conflictResolution'), literal(res.strategy)));
+                if (g.conflictField)
+                    writer.addQuad(makeQuad(subj, namedNode(NS.cascade + 'conflictField'), literal(g.conflictField)));
+                if (g.conflictValues) {
+                    const valDesc = Object.entries(g.conflictValues).map(([s, v]) => `${s}: "${v}"`).join(' vs ');
+                    writer.addQuad(makeQuad(subj, namedNode(NS.cascade + 'conflictValues'), literal(valDesc)));
+                }
+            }
+        }
+        writer.end((err, result) => err ? reject(err) : resolve(result));
+    });
+}
+// ---------------------------------------------------------------------------
+// Command registration
+// ---------------------------------------------------------------------------
+export function registerReconcileCommand(program) {
+    program
+        .command('reconcile')
+        .description('Reconcile Cascade RDF from multiple sources into a normalized record set')
+        .argument('<files...>', 'Cascade Turtle files to reconcile (2 or more)')
+        .option('--output <file>', 'Write merged Turtle output to file (default: stdout)')
+        .option('--report <file>', 'Write JSON transformation report to file')
+        .option('--trust <scores>', 'Source trust scores: system1=0.9,system2=0.85')
+        .option('--lab-tolerance <number>', 'Lab value match tolerance as fraction (default: 0.05)', '0.05')
+        .action(async (files, options) => {
+        const globalOpts = program.opts();
+        if (files.length < 2) {
+            printError('reconcile requires at least 2 input files', globalOpts);
+            process.exitCode = 1;
+            return;
+        }
+        const trustScores = { 'primary-care': 0.90, 'specialist': 0.85, 'hospital': 0.95 };
+        if (options.trust) {
+            for (const pair of options.trust.split(',')) {
+                const [sys, score] = pair.split('=');
+                if (sys && score)
+                    trustScores[sys] = parseFloat(score);
+            }
+        }
+        const defaultTrust = 0.80;
+        const labTol = parseFloat(options.labTolerance);
+        printVerbose(`Reconciling ${files.length} files`, globalOpts);
+        printVerbose(`Trust scores: ${JSON.stringify(trustScores)}`, globalOpts);
+        // Parse all files
+        const allRecords = [];
+        const sourceInfo = [];
+        for (const filePath of files) {
+            let turtle;
+            try {
+                turtle = readFileSync(filePath, 'utf-8');
+            }
+            catch (err) {
+                printError(`Cannot read file: ${filePath}`, globalOpts);
+                process.exitCode = 1;
+                return;
+            }
+            const systemName = basename(filePath, '.ttl').replace(/_/g, '-');
+            const records = await parseTurtle(turtle, systemName);
+            // Use the cascade:sourceSystem from the file if present, otherwise derive from filename
+            const systemNames = [...new Set(records.map(r => r.sourceSystem).filter(s => s !== systemName))];
+            const effectiveSystem = systemNames[0] ?? systemName;
+            // Re-tag with effective system if all records share one
+            for (const r of records) {
+                if (r.sourceSystem === systemName && systemNames.length > 0)
+                    r.sourceSystem = effectiveSystem;
+            }
+            allRecords.push(...records);
+            sourceInfo.push({ system: effectiveSystem, file: filePath, count: records.length });
+            printVerbose(`  ${filePath}: ${records.length} records (system: ${effectiveSystem})`, globalOpts);
+        }
+        // Match and group
+        const groups = [];
+        const assigned = new Set();
+        for (let i = 0; i < allRecords.length; i++) {
+            const a = allRecords[i];
+            if (assigned.has(a.uri))
+                continue;
+            if (a.type === 'cascade:PatientProfile' || a.type === 'coverage:InsurancePlan') {
+                groups.push({ matchType: 'pass_through', confidence: 1.0, records: [a], matchedOn: 'profile' });
+                assigned.add(a.uri);
+                continue;
+            }
+            const matched = [a];
+            let matchedOn = '';
+            let bestConf = 1.0;
+            for (let j = i + 1; j < allRecords.length; j++) {
+                const b = allRecords[j];
+                if (assigned.has(b.uri) || a.sourceSystem === b.sourceSystem)
+                    continue;
+                const { match, confidence, matchedOn: mo } = doRecordsMatch(a, b, labTol);
+                if (match && confidence >= 0.65) {
+                    matched.push(b);
+                    assigned.add(b.uri);
+                    if (!matchedOn) {
+                        matchedOn = mo;
+                        bestConf = confidence;
+                    }
+                }
+            }
+            assigned.add(a.uri);
+            if (matched.length === 1) {
+                groups.push({ matchType: 'pass_through', confidence: 1.0, records: matched, matchedOn: '' });
+            }
+            else {
+                const { matchType, conflictField, conflictValues } = classifyGroup(matched, labTol);
+                groups.push({ matchType, confidence: bestConf, records: matched, matchedOn, conflictField, conflictValues });
+            }
+        }
+        // Resolve
+        const resolutions = groups.map(g => resolveGroup(g, trustScores, defaultTrust));
+        // Serialize
+        const mergedTurtle = await serializeGroups(groups, resolutions);
+        // Build report
+        let exactDups = 0, nearDups = 0, resolved = 0, unresolved = 0, passThrough = 0;
+        const transformations = [];
+        const unresolvedList = [];
+        for (let i = 0; i < groups.length; i++) {
+            const g = groups[i];
+            const res = resolutions[i];
+            const t = {
+                type: g.matchType,
+                recordType: g.records[0].type,
+                canonicalUri: res.canonical.uri,
+                sources: g.records.map(r => r.sourceSystem),
+                matchedOn: g.matchedOn,
+                strategy: res.strategy,
+                conflictField: g.conflictField,
+                conflictValues: g.conflictValues,
+                resolved: res.resolved,
+            };
+            switch (g.matchType) {
+                case 'exact_duplicate':
+                    exactDups++;
+                    break;
+                case 'near_duplicate':
+                    nearDups++;
+                    break;
+                case 'status_conflict':
+                case 'value_conflict':
+                    res.resolved ? resolved++ : unresolved++;
+                    break;
+                case 'pass_through':
+                    passThrough++;
+                    break;
+            }
+            if (g.matchType !== 'pass_through')
+                transformations.push(t);
+            if (!res.resolved)
+                unresolvedList.push(t);
+        }
+        const report = {
+            generatedAt: new Date().toISOString(),
+            sources: sourceInfo.map(s => ({ ...s, trustScore: trustScores[s.system] ?? defaultTrust })),
+            summary: {
+                totalInputRecords: allRecords.length,
+                exactDuplicatesRemoved: exactDups,
+                nearDuplicatesMerged: nearDups,
+                conflictsResolved: resolved,
+                conflictsUnresolved: unresolved,
+                passThrough,
+                finalRecordCount: groups.length,
+            },
+            transformations,
+            unresolvedConflicts: unresolvedList,
+        };
+        // Output
+        if (options.output) {
+            writeFileSync(options.output, mergedTurtle);
+            console.error(`Merged Turtle written to: ${options.output}`);
+        }
+        else {
+            console.log(mergedTurtle);
+        }
+        if (options.report) {
+            writeFileSync(options.report, JSON.stringify(report, null, 2));
+            console.error(`Report written to: ${options.report}`);
+        }
+        // Summary to stderr
+        const { summary } = report;
+        console.error(`\nReconciliation summary:`);
+        console.error(`  Input records:       ${summary.totalInputRecords}`);
+        console.error(`  Exact duplicates:    -${summary.exactDuplicatesRemoved}`);
+        console.error(`  Near-duplicates:     ~${summary.nearDuplicatesMerged} merged`);
+        console.error(`  Conflicts resolved:  ${summary.conflictsResolved}`);
+        if (summary.conflictsUnresolved > 0) {
+            console.error(`  ⚠️  Unresolved:       ${summary.conflictsUnresolved}`);
+        }
+        console.error(`  Final records:       ${summary.finalRecordCount}`);
+        if (globalOpts.json) {
+            printResult(report, globalOpts);
+        }
+    });
+}
+//# sourceMappingURL=reconcile.js.map

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+ 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