@gzoo/cortex 0.5.9

package/packages/graph/dist/sqlite-store.js

@@ -0,0 +1,632 @@
+import Database from 'better-sqlite3';
+import { randomUUID } from 'node:crypto';
+import { copyFileSync, statSync, mkdirSync, chmodSync } from 'node:fs';
+import { dirname } from 'node:path';
+import { homedir } from 'node:os';
+import { CortexError, GRAPH_DB_ERROR, GRAPH_ENTITY_NOT_FOUND, } from '@cortex/core';
+import { up as applyInitialMigration } from './migrations/001-initial.js';
+function resolveHomePath(p) {
+    return p.startsWith('~') ? p.replace('~', homedir()) : p;
+}
+function now() {
+    return new Date().toISOString();
+}
+function rowToContradiction(row) {
+    return {
+        id: row.id,
+        entityIds: [row.entity_id_a, row.entity_id_b],
+        description: row.description,
+        severity: row.severity,
+        suggestedResolution: row.suggested_resolution ?? undefined,
+        status: row.status,
+        resolvedAction: row.resolved_action ?? undefined,
+        resolvedAt: row.resolved_at ?? undefined,
+        detectedAt: row.detected_at,
+    };
+}
+function rowToEntity(row) {
+    return {
+        id: row.id,
+        type: row.type,
+        name: row.name,
+        content: row.content,
+        summary: row.summary ?? undefined,
+        properties: row.properties ? JSON.parse(row.properties) : {},
+        confidence: row.confidence,
+        sourceFile: row.source_file,
+        sourceRange: row.source_start_line != null && row.source_end_line != null
+            ? { startLine: row.source_start_line, endLine: row.source_end_line }
+            : undefined,
+        projectId: row.project_id,
+        extractedBy: JSON.parse(row.extracted_by),
+        tags: row.tags ? JSON.parse(row.tags) : [],
+        status: row.status,
+        createdAt: row.created_at,
+        updatedAt: row.updated_at,
+    };
+}
+function rowToRelationship(row) {
+    return {
+        id: row.id,
+        type: row.type,
+        sourceEntityId: row.source_entity_id,
+        targetEntityId: row.target_entity_id,
+        description: row.description ?? undefined,
+        confidence: row.confidence,
+        properties: row.properties ? JSON.parse(row.properties) : {},
+        extractedBy: JSON.parse(row.extracted_by),
+        createdAt: row.created_at,
+        updatedAt: row.updated_at,
+    };
+}
+function rowToFile(row) {
+    return {
+        id: row.id,
+        path: row.path,
+        relativePath: row.relative_path,
+        projectId: row.project_id,
+        contentHash: row.content_hash,
+        fileType: row.file_type,
+        sizeBytes: row.size_bytes,
+        lastModified: row.last_modified,
+        lastIngestedAt: row.last_ingested_at ?? undefined,
+        entityIds: row.entity_ids ? JSON.parse(row.entity_ids) : [],
+        status: row.status,
+        parseError: row.parse_error ?? undefined,
+    };
+}
+function rowToProject(row) {
+    return {
+        id: row.id,
+        name: row.name,
+        rootPath: row.root_path,
+        privacyLevel: row.privacy_level,
+        fileCount: row.file_count,
+        entityCount: row.entity_count,
+        lastIngestedAt: row.last_ingested_at ?? undefined,
+        createdAt: row.created_at,
+    };
+}
+export class SQLiteStore {
+    db;
+    dbPath;
+    constructor(options = {}) {
+        const { dbPath = '~/.cortex/cortex.db', walMode = true, backupOnStartup = true, } = options;
+        this.dbPath = resolveHomePath(dbPath);
+        mkdirSync(dirname(this.dbPath), { recursive: true });
+        if (backupOnStartup) {
+            this.backupSync();
+        }
+        this.db = new Database(this.dbPath);
+        if (walMode) {
+            this.db.pragma('journal_mode = WAL');
+        }
+        this.db.pragma('foreign_keys = ON');
+        this.db.pragma('busy_timeout = 5000');
+        this.migrate();
+    }
+    migrate() {
+        try {
+            applyInitialMigration(this.db);
+        }
+        catch (err) {
+            throw new CortexError(GRAPH_DB_ERROR, 'critical', 'graph', `Migration failed: ${err instanceof Error ? err.message : String(err)}`, undefined, 'Delete the database and restart.');
+        }
+    }
+    backupSync() {
+        try {
+            const stat = statSync(this.dbPath);
+            if (stat.isFile()) {
+                const backupPath = `${this.dbPath}.backup`;
+                copyFileSync(this.dbPath, backupPath);
+                try {
+                    chmodSync(backupPath, 0o600);
+                }
+                catch { /* Windows — ignore */ }
+            }
+        }
+        catch {
+            // DB doesn't exist yet — no backup needed
+        }
+    }
+    close() {
+        this.db.close();
+    }
+    // --- Entities ---
+    async createEntity(entity) {
+        const id = randomUUID();
+        const ts = now();
+        this.db.prepare(`
+      INSERT INTO entities (
+        id, type, name, content, summary, properties, confidence,
+        source_file, source_start_line, source_end_line,
+        project_id, extracted_by, tags, status, created_at, updated_at
+      ) VALUES (
+        ?, ?, ?, ?, ?, ?, ?,
+        ?, ?, ?,
+        ?, ?, ?, ?, ?, ?
+      )
+    `).run(id, entity.type, entity.name, entity.content, entity.summary ?? null, JSON.stringify(entity.properties), entity.confidence, entity.sourceFile, entity.sourceRange?.startLine ?? null, entity.sourceRange?.endLine ?? null, entity.projectId, JSON.stringify(entity.extractedBy), JSON.stringify(entity.tags), entity.status, ts, ts);
+        // Sync to FTS
+        this.db.prepare(`
+      INSERT INTO entities_fts (rowid, name, content, summary, tags)
+      VALUES (
+        (SELECT rowid FROM entities WHERE id = ?),
+        ?, ?, ?, ?
+      )
+    `).run(id, entity.name, entity.content, entity.summary ?? '', entity.tags.join(' '));
+        return { ...entity, id, createdAt: ts, updatedAt: ts };
+    }
+    async getEntity(id) {
+        const row = this.db.prepare('SELECT * FROM entities WHERE id = ? AND deleted_at IS NULL').get(id);
+        return row ? rowToEntity(row) : null;
+    }
+    async updateEntity(id, updates) {
+        const existing = await this.getEntity(id);
+        if (!existing) {
+            throw new CortexError(GRAPH_ENTITY_NOT_FOUND, 'low', 'graph', `Entity not found: ${id}`, { entityId: id });
+        }
+        const merged = { ...existing, ...updates, updatedAt: now() };
+        this.db.prepare(`
+      UPDATE entities SET
+        type = ?, name = ?, content = ?, summary = ?,
+        properties = ?, confidence = ?,
+        source_file = ?, source_start_line = ?, source_end_line = ?,
+        extracted_by = ?, tags = ?, status = ?, updated_at = ?
+      WHERE id = ?
+    `).run(merged.type, merged.name, merged.content, merged.summary ?? null, JSON.stringify(merged.properties), merged.confidence, merged.sourceFile, merged.sourceRange?.startLine ?? null, merged.sourceRange?.endLine ?? null, JSON.stringify(merged.extractedBy), JSON.stringify(merged.tags), merged.status, merged.updatedAt, id);
+        // Re-sync FTS
+        this.db.prepare(`
+      UPDATE entities_fts SET name = ?, content = ?, summary = ?, tags = ?
+      WHERE rowid = (SELECT rowid FROM entities WHERE id = ?)
+    `).run(merged.name, merged.content, merged.summary ?? '', merged.tags.join(' '), id);
+        return merged;
+    }
+    async deleteEntity(id, soft = true) {
+        if (soft) {
+            this.db.prepare('UPDATE entities SET deleted_at = ?, status = ? WHERE id = ?').run(now(), 'deleted', id);
+        }
+        else {
+            // Remove FTS entry before deleting the entity
+            this.db.prepare('DELETE FROM entities_fts WHERE rowid = (SELECT rowid FROM entities WHERE id = ?)').run(id);
+            this.db.prepare('DELETE FROM entities WHERE id = ?').run(id);
+        }
+    }
+    async findEntities(query) {
+        const conditions = ['deleted_at IS NULL'];
+        const params = [];
+        if (query.type) {
+            conditions.push('type = ?');
+            params.push(query.type);
+        }
+        if (query.projectId) {
+            conditions.push('project_id = ?');
+            params.push(query.projectId);
+        }
+        if (query.status) {
+            conditions.push('status = ?');
+            params.push(query.status);
+        }
+        if (query.since) {
+            conditions.push('created_at >= ?');
+            params.push(query.since);
+        }
+        if (query.before) {
+            conditions.push('created_at < ?');
+            params.push(query.before);
+        }
+        let sql;
+        if (query.search) {
+            // Use FTS for text search
+            sql = `
+        SELECT e.* FROM entities e
+        JOIN entities_fts fts ON fts.rowid = e.rowid
+        WHERE fts.entities_fts MATCH ? AND ${conditions.join(' AND ')}
+        ORDER BY rank
+      `;
+            params.unshift(query.search);
+        }
+        else {
+            sql = `
+        SELECT * FROM entities
+        WHERE ${conditions.join(' AND ')}
+        ORDER BY created_at DESC
+      `;
+        }
+        if (query.limit) {
+            sql += ' LIMIT ?';
+            params.push(query.limit);
+        }
+        if (query.offset) {
+            sql += ' OFFSET ?';
+            params.push(query.offset);
+        }
+        const rows = this.db.prepare(sql).all(...params);
+        return rows.map(rowToEntity);
+    }
+    // --- Relationships ---
+    async createRelationship(rel) {
+        const id = randomUUID();
+        const ts = now();
+        this.db.prepare(`
+      INSERT INTO relationships (
+        id, type, source_entity_id, target_entity_id,
+        description, confidence, properties, extracted_by,
+        created_at, updated_at
+      ) VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?)
+    `).run(id, rel.type, rel.sourceEntityId, rel.targetEntityId, rel.description ?? null, rel.confidence, JSON.stringify(rel.properties), JSON.stringify(rel.extractedBy), ts, ts);
+        return { ...rel, id, createdAt: ts, updatedAt: ts };
+    }
+    async getRelationship(id) {
+        const row = this.db.prepare('SELECT * FROM relationships WHERE id = ?').get(id);
+        return row ? rowToRelationship(row) : null;
+    }
+    async getRelationshipsForEntity(entityId, direction = 'both') {
+        let sql;
+        let params;
+        if (direction === 'out') {
+            sql = 'SELECT * FROM relationships WHERE source_entity_id = ?';
+            params = [entityId];
+        }
+        else if (direction === 'in') {
+            sql = 'SELECT * FROM relationships WHERE target_entity_id = ?';
+            params = [entityId];
+        }
+        else {
+            sql = 'SELECT * FROM relationships WHERE source_entity_id = ? OR target_entity_id = ?';
+            params = [entityId, entityId];
+        }
+        const rows = this.db.prepare(sql).all(...params);
+        return rows.map(rowToRelationship);
+    }
+    async deleteRelationship(id) {
+        this.db.prepare('DELETE FROM relationships WHERE id = ?').run(id);
+    }
+    deleteBySourcePath(pathPrefix) {
+        // Normalize to backslashes (Windows DB storage), escape LIKE wildcards, then add wildcard
+        const normalized = pathPrefix.replace(/\//g, '\\');
+        const escaped = normalized.replace(/[%_\\]/g, '\\$&');
+        const pattern = escaped + '%';
+        return this.db.transaction(() => {
+            const relResult = this.db.prepare(`
+        DELETE FROM relationships
+        WHERE source_entity_id IN (SELECT id FROM entities WHERE source_file LIKE ? ESCAPE '\\')
+           OR target_entity_id IN (SELECT id FROM entities WHERE source_file LIKE ? ESCAPE '\\')
+      `).run(pattern, pattern);
+            this.db.prepare(`
+        DELETE FROM entities_fts
+        WHERE rowid IN (SELECT rowid FROM entities WHERE source_file LIKE ? ESCAPE '\\' AND deleted_at IS NULL)
+      `).run(pattern);
+            const entityResult = this.db.prepare("DELETE FROM entities WHERE source_file LIKE ? ESCAPE '\\'").run(pattern);
+            const fileResult = this.db.prepare("DELETE FROM files WHERE path LIKE ? ESCAPE '\\'").run(pattern);
+            return {
+                deletedEntities: entityResult.changes,
+                deletedRelationships: relResult.changes,
+                deletedFiles: fileResult.changes,
+            };
+        })();
+    }
+    resetDatabase() {
+        this.db.transaction(() => {
+            this.db.prepare('DELETE FROM contradictions').run();
+            this.db.prepare('DELETE FROM relationships').run();
+            this.db.prepare('DELETE FROM entities_fts').run();
+            this.db.prepare('DELETE FROM entities').run();
+            this.db.prepare('DELETE FROM files').run();
+        })();
+    }
+    pruneSoftDeleted() {
+        return this.db.transaction(() => {
+            const relResult = this.db.prepare(`
+        DELETE FROM relationships
+        WHERE source_entity_id IN (SELECT id FROM entities WHERE deleted_at IS NOT NULL)
+           OR target_entity_id IN (SELECT id FROM entities WHERE deleted_at IS NOT NULL)
+      `).run();
+            this.db.prepare(`
+        DELETE FROM entities_fts
+        WHERE rowid IN (SELECT rowid FROM entities WHERE deleted_at IS NOT NULL)
+      `).run();
+            const entityResult = this.db.prepare('DELETE FROM entities WHERE deleted_at IS NOT NULL').run();
+            return {
+                deletedEntities: entityResult.changes,
+                deletedRelationships: relResult.changes,
+            };
+        })();
+    }
+    // --- Files ---
+    async upsertFile(file) {
+        const existing = this.db.prepare('SELECT * FROM files WHERE path = ?').get(file.path);
+        if (existing) {
+            this.db.prepare(`
+        UPDATE files SET
+          relative_path = ?, project_id = ?, content_hash = ?,
+          file_type = ?, size_bytes = ?, last_modified = ?,
+          last_ingested_at = ?, entity_ids = ?, status = ?, parse_error = ?
+        WHERE path = ?
+      `).run(file.relativePath, file.projectId, file.contentHash, file.fileType, file.sizeBytes, file.lastModified, file.lastIngestedAt ?? null, JSON.stringify(file.entityIds), file.status, file.parseError ?? null, file.path);
+            return { ...file, id: existing.id };
+        }
+        const id = randomUUID();
+        this.db.prepare(`
+      INSERT INTO files (
+        id, path, relative_path, project_id, content_hash,
+        file_type, size_bytes, last_modified, last_ingested_at,
+        entity_ids, status, parse_error
+      ) VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)
+    `).run(id, file.path, file.relativePath, file.projectId, file.contentHash, file.fileType, file.sizeBytes, file.lastModified, file.lastIngestedAt ?? null, JSON.stringify(file.entityIds), file.status, file.parseError ?? null);
+        return { ...file, id };
+    }
+    async getFile(path) {
+        const row = this.db.prepare('SELECT * FROM files WHERE path = ?').get(path);
+        return row ? rowToFile(row) : null;
+    }
+    async getFilesByProject(projectId) {
+        const rows = this.db.prepare('SELECT * FROM files WHERE project_id = ?').all(projectId);
+        return rows.map(rowToFile);
+    }
+    // --- Projects ---
+    async createProject(project) {
+        const id = randomUUID();
+        const ts = now();
+        this.db.prepare(`
+      INSERT INTO projects (
+        id, name, root_path, privacy_level,
+        file_count, entity_count, last_ingested_at, created_at
+      ) VALUES (?, ?, ?, ?, ?, ?, ?, ?)
+    `).run(id, project.name, project.rootPath, project.privacyLevel, project.fileCount, project.entityCount, project.lastIngestedAt ?? null, ts);
+        return { ...project, id, createdAt: ts };
+    }
+    async getProject(id) {
+        const row = this.db.prepare('SELECT * FROM projects WHERE id = ?').get(id);
+        return row ? rowToProject(row) : null;
+    }
+    async listProjects() {
+        const rows = this.db.prepare('SELECT * FROM projects ORDER BY created_at DESC').all();
+        return rows.map(rowToProject);
+    }
+    // --- Contradictions ---
+    async createContradiction(contradiction) {
+        const id = randomUUID();
+        this.db.prepare(`
+      INSERT INTO contradictions (
+        id, entity_id_a, entity_id_b, description, severity,
+        suggested_resolution, status, resolved_action, resolved_at, detected_at
+      ) VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?)
+    `).run(id, contradiction.entityIds[0], contradiction.entityIds[1], contradiction.description, contradiction.severity, contradiction.suggestedResolution ?? null, contradiction.status, contradiction.resolvedAction ?? null, contradiction.resolvedAt ?? null, contradiction.detectedAt);
+        return { ...contradiction, id };
+    }
+    async findContradictions(query = {}) {
+        const conditions = [];
+        const params = [];
+        if (query.status) {
+            conditions.push('status = ?');
+            params.push(query.status);
+        }
+        if (query.entityId) {
+            conditions.push('(entity_id_a = ? OR entity_id_b = ?)');
+            params.push(query.entityId, query.entityId);
+        }
+        const where = conditions.length > 0 ? `WHERE ${conditions.join(' AND ')}` : '';
+        let sql = `SELECT * FROM contradictions ${where} ORDER BY detected_at DESC`;
+        if (query.limit) {
+            sql += ' LIMIT ?';
+            params.push(query.limit);
+        }
+        const rows = this.db.prepare(sql).all(...params);
+        return rows.map(rowToContradiction);
+    }
+    async updateContradiction(id, update) {
+        this.db.prepare(`
+      UPDATE contradictions SET status = ?, resolved_action = ?, resolved_at = ? WHERE id = ?
+    `).run(update.status, update.resolvedAction ?? null, update.resolvedAt ?? null, id);
+    }
+    // --- Search ---
+    async searchEntities(text, limit = 20) {
+        // Sanitize input: strip FTS5 operators to prevent injection via MATCH syntax
+        const sanitized = text.replace(/[^a-zA-Z0-9\s]/g, ' ').trim();
+        if (!sanitized)
+            return [];
+        const rows = this.db.prepare(`
+      SELECT e.* FROM entities e
+      JOIN entities_fts fts ON fts.rowid = e.rowid
+      WHERE fts.entities_fts MATCH ? AND e.deleted_at IS NULL
+      ORDER BY rank
+      LIMIT ?
+    `).all(sanitized, limit);
+        return rows.map(rowToEntity);
+    }
+    async semanticSearch(_embedding, _limit = 20) {
+        // Vector search is delegated to VectorStore.
+        // This method exists to satisfy the GraphStore interface.
+        // The QueryEngine will combine results from both stores.
+        return [];
+    }
+    // --- Stats ---
+    async getStats() {
+        const entityCount = this.db.prepare("SELECT COUNT(*) as count FROM entities WHERE deleted_at IS NULL AND status != 'deleted'").get().count;
+        const relationshipCount = this.db.prepare('SELECT COUNT(*) as count FROM relationships').get().count;
+        const fileCount = this.db.prepare('SELECT COUNT(*) as count FROM files').get().count;
+        const projectCount = this.db.prepare('SELECT COUNT(*) as count FROM projects').get().count;
+        const contradictionCount = this.db.prepare("SELECT COUNT(*) as count FROM contradictions WHERE status = 'active'").get().count;
+        let dbSizeBytes = 0;
+        try {
+            dbSizeBytes = statSync(this.dbPath).size;
+        }
+        catch {
+            // DB file may not exist yet
+        }
+        return {
+            entityCount,
+            relationshipCount,
+            fileCount,
+            projectCount,
+            contradictionCount,
+            dbSizeBytes,
+            vectorDbSizeBytes: 0, // Managed by VectorStore
+        };
+    }
+    // --- Report ---
+    getReportData() {
+        // File status breakdown
+        const fileRows = this.db.prepare('SELECT status, COUNT(*) as count FROM files GROUP BY status').all();
+        const fileStatus = { ingested: 0, failed: 0, skipped: 0, pending: 0 };
+        for (const row of fileRows) {
+            if (row.status in fileStatus) {
+                fileStatus[row.status] = row.count;
+            }
+        }
+        // Failed files with error messages
+        const failedFiles = this.db.prepare(`SELECT path, relative_path, parse_error FROM files
+       WHERE status = 'failed' AND parse_error IS NOT NULL
+       ORDER BY path LIMIT 50`).all()
+            .map((r) => ({ path: r.path, relativePath: r.relative_path, parseError: r.parse_error }));
+        // Entity breakdown by type (active only)
+        const entityRows = this.db.prepare(`SELECT type, COUNT(*) as count, AVG(confidence) as avg_confidence
+       FROM entities WHERE deleted_at IS NULL AND status = 'active'
+       GROUP BY type ORDER BY count DESC`).all();
+        const entityBreakdown = entityRows.map((r) => ({
+            type: r.type, count: r.count, avgConfidence: r.avg_confidence,
+        }));
+        // Superseded entity count (proxy for merges)
+        const supersededCount = this.db.prepare("SELECT COUNT(*) as count FROM entities WHERE status = 'superseded'").get().count;
+        // Relationship breakdown by type
+        const relRows = this.db.prepare('SELECT type, COUNT(*) as count FROM relationships GROUP BY type ORDER BY count DESC').all();
+        const relationshipBreakdown = relRows.map((r) => ({ type: r.type, count: r.count }));
+        // Contradictions breakdown by status and severity
+        const contrRows = this.db.prepare('SELECT status, severity, COUNT(*) as count FROM contradictions GROUP BY status, severity').all();
+        const contradictions = {
+            active: 0, resolved: 0, dismissed: 0,
+            highSeverity: 0, mediumSeverity: 0, lowSeverity: 0,
+        };
+        for (const r of contrRows) {
+            if (r.status === 'active')
+                contradictions.active += r.count;
+            if (r.status === 'resolved')
+                contradictions.resolved += r.count;
+            if (r.status === 'dismissed')
+                contradictions.dismissed += r.count;
+            if (r.severity === 'high' || r.severity === 'critical')
+                contradictions.highSeverity += r.count;
+            if (r.severity === 'medium')
+                contradictions.mediumSeverity += r.count;
+            if (r.severity === 'low')
+                contradictions.lowSeverity += r.count;
+        }
+        // Top active contradictions (high first, then medium, limit 10)
+        const topContrRows = this.db.prepare(`SELECT c.id, c.severity, c.description, ea.name as entity_a, eb.name as entity_b
+       FROM contradictions c
+       LEFT JOIN entities ea ON c.entity_id_a = ea.id
+       LEFT JOIN entities eb ON c.entity_id_b = eb.id
+       WHERE c.status = 'active'
+       ORDER BY CASE c.severity
+         WHEN 'critical' THEN 0 WHEN 'high' THEN 1 WHEN 'medium' THEN 2 ELSE 3
+       END, c.detected_at DESC
+       LIMIT 10`).all();
+        const topContradictions = topContrRows.map((r) => ({
+            id: r.id.slice(0, 8),
+            severity: r.severity,
+            description: r.description,
+            entityA: r.entity_a ?? 'unknown',
+            entityB: r.entity_b ?? 'unknown',
+        }));
+        // Token estimate from entity extracted_by JSON
+        const tokenRow = this.db.prepare(`SELECT
+        SUM(CAST(JSON_EXTRACT(extracted_by, '$.tokensUsed.input') AS INTEGER)) as total_input,
+        SUM(CAST(JSON_EXTRACT(extracted_by, '$.tokensUsed.output') AS INTEGER)) as total_output
+       FROM entities WHERE deleted_at IS NULL`).get();
+        return {
+            generatedAt: new Date().toISOString(),
+            fileStatus,
+            failedFiles,
+            entityBreakdown,
+            supersededCount,
+            relationshipBreakdown,
+            contradictions,
+            topContradictions,
+            tokenEstimate: {
+                totalInput: tokenRow.total_input ?? 0,
+                totalOutput: tokenRow.total_output ?? 0,
+            },
+        };
+    }
+    // --- Maintenance ---
+    async backup() {
+        const backupPath = `${this.dbPath}.backup-${Date.now()}`;
+        await this.db.backup(backupPath);
+        try {
+            chmodSync(backupPath, 0o600);
+        }
+        catch { /* Windows — ignore */ }
+        return backupPath;
+    }
+    async integrityCheck() {
+        const details = [];
+        // Check for orphaned relationships
+        const orphanedRels = this.db.prepare(`
+      SELECT COUNT(*) as count FROM relationships r
+      WHERE NOT EXISTS (SELECT 1 FROM entities WHERE id = r.source_entity_id)
+         OR NOT EXISTS (SELECT 1 FROM entities WHERE id = r.target_entity_id)
+    `).get().count;
+        if (orphanedRels > 0) {
+            details.push(`Found ${orphanedRels} orphaned relationships`);
+        }
+        // Check for files referencing missing projects
+        const missingProjects = this.db.prepare(`
+      SELECT COUNT(*) as count FROM files f
+      WHERE NOT EXISTS (SELECT 1 FROM projects WHERE id = f.project_id)
+    `).get().count;
+        if (missingProjects > 0) {
+            details.push(`Found ${missingProjects} files referencing missing projects`);
+        }
+        // SQLite integrity check
+        const integrityResult = this.db.pragma('integrity_check');
+        const sqliteOk = integrityResult.length === 1 && integrityResult[0].integrity_check === 'ok';
+        if (!sqliteOk) {
+            details.push('SQLite integrity check failed');
+        }
+        return {
+            ok: orphanedRels === 0 && missingProjects === 0 && sqliteOk,
+            orphanedRelationships: orphanedRels,
+            missingFiles: missingProjects,
+            details,
+        };
+    }
+    // --- Graph visualization data ---
+    getGraphData(options = {}) {
+        const limit = options.limit ?? 2000;
+        let entitySql = `SELECT id, name, type, confidence, source_file FROM entities WHERE status = 'active'`;
+        const params = [];
+        if (options.projectId) {
+            entitySql += ` AND project_id = ?`;
+            params.push(options.projectId);
+        }
+        entitySql += ` ORDER BY confidence DESC LIMIT ?`;
+        params.push(limit);
+        const entityRows = this.db.prepare(entitySql).all(...params);
+        const entityIds = new Set(entityRows.map(e => e.id));
+        const relRows = this.db.prepare(`SELECT id, type, source_entity_id, target_entity_id, confidence
+       FROM relationships
+       LIMIT ?`).all(limit * 2);
+        // Only include edges where both endpoints are in our node set
+        const edges = relRows
+            .filter(r => entityIds.has(r.source_entity_id) && entityIds.has(r.target_entity_id))
+            .map(r => ({
+            id: r.id,
+            source: r.source_entity_id,
+            target: r.target_entity_id,
+            type: r.type,
+            confidence: r.confidence,
+        }));
+        return {
+            nodes: entityRows.map(e => ({
+                id: e.id,
+                name: e.name,
+                type: e.type,
+                confidence: e.confidence,
+                sourceFile: e.source_file,
+            })),
+            edges,
+        };
+    }
+}
+//# sourceMappingURL=sqlite-store.js.map

package/packages/graph/dist/sqlite-store.js.map

@@ -0,0 +1 @@
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