@dragonflymcp/plugin 1.0.0

package/dist/tools/knowledge/store.js

@@ -0,0 +1,562 @@
+/**
+ * Knowledge Graph Store
+ * SQLite-backed storage for entities and relations
+ */
+import { BaseStore } from "../../core/store.js";
+import { cosineSimilarity, numberArrayToBytes, bytesToNumberArray } from "../../utils/vectors.js";
+import { bfsTraverse } from "../../utils/graph.js";
+import { generateId } from "../../utils/ids.js";
+export class KnowledgeStore extends BaseStore {
+    constructor(dbPath) {
+        super(dbPath);
+        this.initTables();
+    }
+    initTables() {
+        this.db.exec(`
+      CREATE TABLE IF NOT EXISTS kg_entities (
+        id TEXT PRIMARY KEY,
+        name TEXT NOT NULL,
+        entity_type TEXT NOT NULL,
+        description TEXT,
+        properties TEXT,
+        source_memory_id TEXT,
+        created_at TEXT NOT NULL,
+        updated_at TEXT NOT NULL
+      );
+
+      CREATE INDEX IF NOT EXISTS idx_kg_entities_name ON kg_entities(name);
+      CREATE INDEX IF NOT EXISTS idx_kg_entities_type ON kg_entities(entity_type);
+
+      CREATE TABLE IF NOT EXISTS kg_entity_embeddings (
+        entity_id TEXT PRIMARY KEY,
+        embedding BLOB NOT NULL,
+        dimensions INTEGER NOT NULL,
+        FOREIGN KEY (entity_id) REFERENCES kg_entities(id) ON DELETE CASCADE
+      );
+
+      CREATE TABLE IF NOT EXISTS kg_relations (
+        id TEXT PRIMARY KEY,
+        source_id TEXT NOT NULL,
+        target_id TEXT NOT NULL,
+        relation_type TEXT NOT NULL,
+        weight REAL NOT NULL DEFAULT 1.0,
+        properties TEXT,
+        created_at TEXT NOT NULL,
+        FOREIGN KEY (source_id) REFERENCES kg_entities(id) ON DELETE CASCADE,
+        FOREIGN KEY (target_id) REFERENCES kg_entities(id) ON DELETE CASCADE,
+        UNIQUE(source_id, target_id, relation_type)
+      );
+
+      CREATE INDEX IF NOT EXISTS idx_kg_relations_source ON kg_relations(source_id);
+      CREATE INDEX IF NOT EXISTS idx_kg_relations_target ON kg_relations(target_id);
+      CREATE INDEX IF NOT EXISTS idx_kg_relations_type ON kg_relations(relation_type);
+
+      CREATE TABLE IF NOT EXISTS kg_communities (
+        id TEXT PRIMARY KEY,
+        name TEXT NOT NULL,
+        summary TEXT,
+        entity_ids TEXT NOT NULL,
+        level INTEGER NOT NULL DEFAULT 0,
+        created_at TEXT NOT NULL,
+        updated_at TEXT NOT NULL
+      );
+
+      CREATE TABLE IF NOT EXISTS kg_entity_memory_links (
+        entity_id TEXT NOT NULL,
+        memory_id TEXT NOT NULL,
+        relationship TEXT,
+        created_at TEXT NOT NULL,
+        PRIMARY KEY (entity_id, memory_id),
+        FOREIGN KEY (entity_id) REFERENCES kg_entities(id) ON DELETE CASCADE
+      );
+    `);
+        // Try to create FTS5 table with sync triggers (may fail on some SQLite builds)
+        try {
+            this.db.exec(`
+        CREATE VIRTUAL TABLE IF NOT EXISTS kg_entity_fts USING fts5(
+          name,
+          description,
+          content='kg_entities',
+          content_rowid='rowid'
+        );
+
+        -- Triggers to keep FTS5 in sync with kg_entities
+        CREATE TRIGGER IF NOT EXISTS kg_entity_fts_ai AFTER INSERT ON kg_entities BEGIN
+          INSERT INTO kg_entity_fts(rowid, name, description)
+            VALUES (new.rowid, new.name, new.description);
+        END;
+
+        CREATE TRIGGER IF NOT EXISTS kg_entity_fts_ad AFTER DELETE ON kg_entities BEGIN
+          INSERT INTO kg_entity_fts(kg_entity_fts, rowid, name, description)
+            VALUES ('delete', old.rowid, old.name, old.description);
+        END;
+
+        CREATE TRIGGER IF NOT EXISTS kg_entity_fts_au AFTER UPDATE ON kg_entities BEGIN
+          INSERT INTO kg_entity_fts(kg_entity_fts, rowid, name, description)
+            VALUES ('delete', old.rowid, old.name, old.description);
+          INSERT INTO kg_entity_fts(rowid, name, description)
+            VALUES (new.rowid, new.name, new.description);
+        END;
+      `);
+        }
+        catch {
+            // FTS5 not available, will use LIKE fallback
+        }
+    }
+    /**
+     * Rebuild FTS5 index from existing kg_entities data.
+     * Call after bulk-loading entities without triggers (e.g., migrating old data).
+     */
+    rebuildFts() {
+        try {
+            this.db.exec(`INSERT INTO kg_entity_fts(kg_entity_fts) VALUES ('rebuild')`);
+        }
+        catch {
+            // FTS5 not available
+        }
+    }
+    /**
+     * Clear all KG data (entities, relations, embeddings, communities)
+     */
+    clearAll() {
+        this.transaction(() => {
+            this.clearTable("kg_entity_memory_links");
+            this.clearTable("kg_relations");
+            this.clearTable("kg_entity_embeddings");
+            this.clearTable("kg_communities");
+            this.clearTable("kg_entities");
+        });
+    }
+    /**
+     * Insert or update an entity
+     */
+    upsertEntity(entity) {
+        // Check if entity with same name and type exists
+        const existing = this.queryOne(`SELECT id FROM kg_entities WHERE name = ? AND entity_type = ?`, [entity.name, entity.entityType]);
+        const now = new Date().toISOString();
+        if (existing) {
+            // Update
+            this.execute(`UPDATE kg_entities SET description = ?, properties = ?, updated_at = ? WHERE id = ?`, [
+                entity.description || null,
+                JSON.stringify(entity.properties || {}),
+                now,
+                existing.id,
+            ]);
+            return existing.id;
+        }
+        // Insert
+        const id = generateId("ent");
+        this.execute(`INSERT INTO kg_entities (id, name, entity_type, description, properties, source_memory_id, created_at, updated_at)
+       VALUES (?, ?, ?, ?, ?, ?, ?, ?)`, [
+            id,
+            entity.name,
+            entity.entityType,
+            entity.description || null,
+            JSON.stringify(entity.properties || {}),
+            entity.sourceMemoryId || null,
+            now,
+            now,
+        ]);
+        return id;
+    }
+    /**
+     * Get entity by ID
+     */
+    getEntity(id) {
+        const row = this.queryOne(`SELECT * FROM kg_entities WHERE id = ?`, [id]);
+        return row ? this.rowToEntity(row) : null;
+    }
+    /**
+     * Get entity by name
+     */
+    getEntityByName(name, entityType) {
+        let sql = `SELECT * FROM kg_entities WHERE name = ?`;
+        const params = [name];
+        if (entityType) {
+            sql += ` AND entity_type = ?`;
+            params.push(entityType);
+        }
+        const row = this.queryOne(sql, params);
+        return row ? this.rowToEntity(row) : null;
+    }
+    /**
+     * Insert embedding for entity
+     */
+    insertEmbedding(entityId, embedding) {
+        const buffer = numberArrayToBytes(embedding);
+        this.execute(`INSERT OR REPLACE INTO kg_entity_embeddings (entity_id, embedding, dimensions)
+       VALUES (?, ?, ?)`, [entityId, buffer, embedding.length]);
+    }
+    /**
+     * Insert a relation
+     */
+    insertRelation(relation) {
+        const id = generateId("rel");
+        try {
+            this.execute(`INSERT OR IGNORE INTO kg_relations (id, source_id, target_id, relation_type, weight, properties, created_at)
+         VALUES (?, ?, ?, ?, ?, ?, ?)`, [
+                id,
+                relation.sourceId,
+                relation.targetId,
+                relation.relationType,
+                relation.weight,
+                JSON.stringify(relation.properties || {}),
+                new Date().toISOString(),
+            ]);
+            return id;
+        }
+        catch {
+            return null;
+        }
+    }
+    /**
+     * Get relations for an entity
+     */
+    getRelations(entityId, relationTypes) {
+        let sql = `SELECT * FROM kg_relations WHERE source_id = ? OR target_id = ?`;
+        const params = [entityId, entityId];
+        if (relationTypes && relationTypes.length > 0) {
+            const placeholders = relationTypes.map(() => "?").join(", ");
+            sql += ` AND relation_type IN (${placeholders})`;
+            params.push(...relationTypes);
+        }
+        const rows = this.query(sql, params);
+        return rows.map(row => this.rowToRelation(row));
+    }
+    /**
+     * Semantic search for entities
+     */
+    searchSemantic(queryEmbedding, options = {}) {
+        const { limit = 20, entityType } = options;
+        let sql = `
+      SELECT e.*, emb.embedding
+      FROM kg_entities e
+      JOIN kg_entity_embeddings emb ON e.id = emb.entity_id
+    `;
+        const params = [];
+        if (entityType) {
+            sql += ` WHERE e.entity_type = ?`;
+            params.push(entityType);
+        }
+        const rows = this.query(sql, params);
+        const results = [];
+        for (const row of rows) {
+            const embedding = bytesToNumberArray(row.embedding);
+            const similarity = cosineSimilarity(queryEmbedding, embedding);
+            if (similarity > 0.3) {
+                results.push({
+                    entity: this.rowToEntity(row),
+                    finalScore: similarity,
+                    semanticScore: similarity,
+                    keywordScore: 0,
+                    graphScore: 0,
+                    communityScore: 0,
+                });
+            }
+        }
+        results.sort((a, b) => b.finalScore - a.finalScore);
+        return results.slice(0, limit);
+    }
+    /**
+     * Keyword search using FTS or LIKE fallback
+     */
+    searchKeyword(query, options = {}) {
+        const { limit = 20, entityType } = options;
+        const results = [];
+        // Try FTS5 first
+        try {
+            let sql = `
+        SELECT e.*, bm25(kg_entity_fts) as score
+        FROM kg_entity_fts fts
+        JOIN kg_entities e ON fts.rowid = e.rowid
+        WHERE kg_entity_fts MATCH ?
+      `;
+            const params = [query];
+            if (entityType) {
+                sql += ` AND e.entity_type = ?`;
+                params.push(entityType);
+            }
+            sql += ` ORDER BY score LIMIT ?`;
+            params.push(limit);
+            const rows = this.query(sql, params);
+            for (const row of rows) {
+                results.push({
+                    entity: this.rowToEntity(row),
+                    finalScore: Math.abs(row.score) / 10, // Normalize BM25
+                    semanticScore: 0,
+                    keywordScore: Math.abs(row.score) / 10,
+                    graphScore: 0,
+                    communityScore: 0,
+                });
+            }
+        }
+        catch {
+            // FTS5 failed, use LIKE fallback
+            const searchTerm = `%${query}%`;
+            let sql = `
+        SELECT * FROM kg_entities
+        WHERE (name LIKE ? OR description LIKE ?)
+      `;
+            const params = [searchTerm, searchTerm];
+            if (entityType) {
+                sql += ` AND entity_type = ?`;
+                params.push(entityType);
+            }
+            sql += ` LIMIT ?`;
+            params.push(limit);
+            const rows = this.query(sql, params);
+            for (const row of rows) {
+                results.push({
+                    entity: this.rowToEntity(row),
+                    finalScore: 0.5,
+                    semanticScore: 0,
+                    keywordScore: 0.5,
+                    graphScore: 0,
+                    communityScore: 0,
+                });
+            }
+        }
+        return results;
+    }
+    /**
+     * BFS traversal from entity
+     */
+    traverse(entityId, maxDepth, maxNodes, relationTypes) {
+        const results = bfsTraverse([entityId], {
+            getNode: (id) => this.getEntity(id),
+            getEdges: (id) => this.getRelations(id, relationTypes),
+            getNeighborId: (rel, currentId) => rel.sourceId === currentId ? rel.targetId : rel.sourceId,
+            maxDepth,
+            maxNodes,
+        });
+        return results.map(r => ({ entity: r.node, depth: r.depth, relations: r.edges }));
+    }
+    /**
+     * Detect communities using connected components.
+     *
+     * By default, excludes "universal connector" relation types (configures, depends_on, guards)
+     * that link cross-cutting patterns to every module, collapsing the graph into one component.
+     * Override with includeRelationTypes to use only specific types, or excludeRelationTypes
+     * to exclude specific types.
+     */
+    detectCommunities(options = {}) {
+        // Default: exclude universal connectors and hierarchical relations that collapse communities.
+        // configures/depends_on/guards = cross-cutting patterns connecting all modules
+        // contains/defined_in = structural hierarchy (module→file→symbol) forming one tree
+        const defaultExclude = ["configures", "depends_on", "guards", "contains", "defined_in"];
+        let sql = `SELECT source_id, target_id FROM kg_relations`;
+        const params = [];
+        if (options.includeRelationTypes && options.includeRelationTypes.length > 0) {
+            // Whitelist: only use these relation types
+            const placeholders = options.includeRelationTypes.map(() => "?").join(", ");
+            sql += ` WHERE relation_type IN (${placeholders})`;
+            params.push(...options.includeRelationTypes);
+        }
+        else {
+            // Blacklist: exclude universal connectors
+            const exclude = options.excludeRelationTypes ?? defaultExclude;
+            if (exclude.length > 0) {
+                const placeholders = exclude.map(() => "?").join(", ");
+                sql += ` WHERE relation_type NOT IN (${placeholders})`;
+                params.push(...exclude);
+            }
+        }
+        // Build adjacency list (read-only, outside transaction)
+        const relations = this.query(sql, params);
+        const adj = new Map();
+        for (const rel of relations) {
+            if (!adj.has(rel.source_id))
+                adj.set(rel.source_id, new Set());
+            if (!adj.has(rel.target_id))
+                adj.set(rel.target_id, new Set());
+            adj.get(rel.source_id).add(rel.target_id);
+            adj.get(rel.target_id).add(rel.source_id);
+        }
+        // Find connected components via BFS (in-memory)
+        const visited = new Set();
+        const components = [];
+        for (const [startId] of adj) {
+            if (visited.has(startId))
+                continue;
+            const component = [];
+            const queue = [startId];
+            while (queue.length > 0) {
+                const id = queue.shift();
+                if (visited.has(id))
+                    continue;
+                visited.add(id);
+                component.push(id);
+                const neighbors = adj.get(id) || new Set();
+                for (const neighbor of neighbors) {
+                    if (!visited.has(neighbor)) {
+                        queue.push(neighbor);
+                    }
+                }
+            }
+            // Skip singletons
+            if (component.length < 2)
+                continue;
+            // Name by highest-degree entity
+            let maxDegree = 0;
+            let centerName = "";
+            for (const id of component) {
+                const degree = adj.get(id)?.size || 0;
+                if (degree > maxDegree) {
+                    maxDegree = degree;
+                    const entity = this.getEntity(id);
+                    if (entity)
+                        centerName = entity.name;
+                }
+            }
+            components.push({ entityIds: component, centerName: centerName || "Unnamed" });
+        }
+        // Atomic clear + insert in a single transaction to prevent duplicates
+        // from concurrent processes or interleaved calls
+        return this.transaction(() => {
+            this.clearTable("kg_communities");
+            const communities = [];
+            const now = new Date().toISOString();
+            for (const comp of components) {
+                const community = {
+                    id: generateId("com"),
+                    name: comp.centerName,
+                    summary: `${comp.entityIds.length} entities`,
+                    entityIds: comp.entityIds,
+                    level: 0,
+                    createdAt: now,
+                    updatedAt: now,
+                };
+                this.execute(`INSERT INTO kg_communities (id, name, summary, entity_ids, level, created_at, updated_at)
+           VALUES (?, ?, ?, ?, ?, ?, ?)`, [community.id, community.name, community.summary, JSON.stringify(community.entityIds), community.level, community.createdAt, community.updatedAt]);
+                communities.push(community);
+            }
+            return communities;
+        });
+    }
+    /**
+     * Get all communities
+     */
+    getCommunities() {
+        const rows = this.query(`SELECT * FROM kg_communities`);
+        return rows.map(row => this.rowToCommunity(row));
+    }
+    /**
+     * Get community by ID
+     */
+    getCommunity(id) {
+        const row = this.queryOne(`SELECT * FROM kg_communities WHERE id = ?`, [id]);
+        if (!row)
+            return null;
+        return this.rowToCommunity(row);
+    }
+    /**
+     * Find community for entity
+     */
+    findCommunityForEntity(entityId) {
+        const rows = this.query(`SELECT * FROM kg_communities`);
+        for (const row of rows) {
+            const community = this.rowToCommunity(row);
+            if (community.entityIds.includes(entityId)) {
+                return community;
+            }
+        }
+        return null;
+    }
+    /**
+     * Convert database row to Community object
+     */
+    rowToCommunity(row) {
+        return {
+            id: row.id,
+            name: row.name,
+            summary: row.summary,
+            entityIds: JSON.parse(row.entity_ids),
+            level: row.level,
+            createdAt: row.created_at,
+            updatedAt: row.updated_at,
+        };
+    }
+    /**
+     * Get knowledge graph statistics
+     */
+    getKGStats() {
+        const totalEntities = this.queryOne(`SELECT COUNT(*) as count FROM kg_entities`)?.count ?? 0;
+        const totalRelations = this.queryOne(`SELECT COUNT(*) as count FROM kg_relations`)?.count ?? 0;
+        const totalCommunities = this.queryOne(`SELECT COUNT(*) as count FROM kg_communities`)?.count ?? 0;
+        const byEntityType = {
+            function: 0,
+            type: 0,
+            package: 0,
+            file: 0,
+            concept: 0,
+            pattern: 0,
+            tool: 0,
+            module: 0,
+            store: 0,
+            table: 0,
+            config: 0,
+            method: 0,
+            variable: 0,
+            interface: 0,
+        };
+        const typeRows = this.query(`SELECT entity_type, COUNT(*) as count FROM kg_entities GROUP BY entity_type`);
+        for (const row of typeRows) {
+            byEntityType[row.entity_type] = row.count;
+        }
+        const byRelationType = {
+            calls: 0,
+            imports: 0,
+            implements: 0,
+            contains: 0,
+            depends_on: 0,
+            related_to: 0,
+            defined_in: 0,
+            tested_by: 0,
+            guards: 0,
+            stores_in: 0,
+            configures: 0,
+        };
+        const relRows = this.query(`SELECT relation_type, COUNT(*) as count FROM kg_relations GROUP BY relation_type`);
+        for (const row of relRows) {
+            byRelationType[row.relation_type] = row.count;
+        }
+        return {
+            totalEntities,
+            totalRelations,
+            totalCommunities,
+            byEntityType,
+            byRelationType,
+            avgRelationsPerEntity: totalEntities > 0 ? totalRelations / totalEntities : 0,
+        };
+    }
+    /**
+     * Convert row to Entity
+     */
+    rowToEntity(row) {
+        return {
+            id: row.id,
+            name: row.name,
+            entityType: row.entity_type,
+            description: row.description,
+            properties: JSON.parse(row.properties || "{}"),
+            sourceMemoryId: row.source_memory_id,
+            createdAt: row.created_at,
+            updatedAt: row.updated_at,
+        };
+    }
+    /**
+     * Convert row to Relation
+     */
+    rowToRelation(row) {
+        return {
+            id: row.id,
+            sourceId: row.source_id,
+            targetId: row.target_id,
+            relationType: row.relation_type,
+            weight: row.weight,
+            properties: JSON.parse(row.properties || "{}"),
+            createdAt: row.created_at,
+        };
+    }
+}
+//# sourceMappingURL=store.js.map

package/dist/tools/knowledge/store.js.map

@@ -0,0 +1 @@
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package/dist/tools/knowledge/store.test.d.ts

@@ -0,0 +1,6 @@
+/**
+ * Knowledge Graph Store Tests
+ * Comprehensive tests for KG storage, retrieval, and community detection
+ */
+export {};
+//# sourceMappingURL=store.test.d.ts.map

package/dist/tools/knowledge/store.test.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"store.test.d.ts","sourceRoot":"","sources":["../../../src/tools/knowledge/store.test.ts"],"names":[],"mappings":"AAAA;;;GAGG"}