@the-cascade-protocol/cli 0.2.4 → 0.3.0

package/dist/lib/reconciler.js

@@ -0,0 +1,397 @@
+/**
+ * Core reconciliation logic extracted from the reconcile command.
+ *
+ * Exported so that other commands (e.g., pod import) can reuse reconciliation
+ * without going through the CLI layer.
+ */
+import { Parser, Writer, DataFactory } from 'n3';
+import { NS, TURTLE_PREFIXES } from './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',
+};
+export 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
+// ---------------------------------------------------------------------------
+export 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));
+    });
+}
+// ---------------------------------------------------------------------------
+// Main exported function
+// ---------------------------------------------------------------------------
+export async function runReconciliation(inputs, options) {
+    const trustScores = {
+        'primary-care': 0.90,
+        'specialist': 0.85,
+        'hospital': 0.95,
+        ...(options?.trustScores ?? {}),
+    };
+    const defaultTrust = 0.80;
+    const labTol = options?.labTolerance ?? 0.05;
+    // Parse all inputs
+    const allRecords = [];
+    const sourceInfo = [];
+    for (const input of inputs) {
+        const records = await parseTurtle(input.content, input.systemName);
+        allRecords.push(...records);
+        sourceInfo.push({ system: input.systemName, count: records.length });
+    }
+    // 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 turtle = await serializeGroups(groups, resolutions);
+    // Build report
+    let exactDups = 0, nearDups = 0, resolved = 0, unresolved = 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;
+        }
+        if (g.matchType !== 'pass_through')
+            transformations.push(t);
+        if (!res.resolved)
+            unresolvedList.push(t);
+    }
+    return {
+        turtle,
+        report: {
+            sources: sourceInfo,
+            summary: {
+                totalInputRecords: allRecords.length,
+                exactDuplicatesRemoved: exactDups,
+                nearDuplicatesMerged: nearDups,
+                conflictsResolved: resolved,
+                conflictsUnresolved: unresolved,
+                finalRecordCount: groups.length,
+            },
+            transformations,
+            unresolvedConflicts: unresolvedList,
+        },
+    };
+}
+//# sourceMappingURL=reconciler.js.map

package/dist/lib/reconciler.js.map

@@ -0,0 +1 @@
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package/dist/shapes/checkup.shapes.ttl

@@ -476,6 +476,16 @@ checkup:MedicationSummaryShape a sh:NodeShape ;
         sh:severity sh:Info ;
         sh:name "Concerns For Doctor" ;
         sh:message "Concerns patient wants to discuss with provider"
+    ] ;
+
+    # v3.2: Computed supply end date (startDate + supplyDurationDays)
+    sh:property [
+        sh:path checkup:supplyEndDate ;
+        sh:datatype xsd:date ;
+        sh:maxCount 1 ;
+        sh:severity sh:Info ;
+        sh:name "Supply End Date" ;
+        sh:message "Computed date when medication supply is expected to be exhausted; used to infer currency when adherenceStatus is absent"
     ] .
 
 # ============================================================================

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@the-cascade-protocol/cli",
-  "version": "0.2.4",
+  "version": "0.3.0",
   "description": "Cascade Protocol CLI - Validate, convert, and manage health data",
   "bin": {
     "cascade": "dist/index.js"