@mcp-graph-workflow/mcp-graph 5.8.0 → 5.9.1

package/dist/core/rag/entity-store.d.ts

@@ -0,0 +1,91 @@
+/**
+ * Entity Store — SQLite CRUD and graph traversal for the Knowledge Graph.
+ *
+ * Stores entities, relations between entities, and mentions linking
+ * entities to knowledge documents. Provides FTS5 search and BFS
+ * traversal for subgraph extraction.
+ */
+import type Database from "better-sqlite3";
+import type { Entity, EntityType, EntityRelationType, EntityRelation, EntityMention } from "../../schemas/entity.schema.js";
+export interface EntitySubgraph {
+    entities: Entity[];
+    relations: EntityRelation[];
+    docIds: string[];
+}
+export declare class EntityStore {
+    private readonly db;
+    constructor(db: Database.Database);
+    /**
+     * Check if the kg_entities table exists (graceful degradation).
+     */
+    hasKgTables(): boolean;
+    /**
+     * Upsert entity — insert if new, increment mention_count if existing.
+     * Deduplication key: normalized_name + type.
+     */
+    upsertEntity(name: string, type: EntityType, docId?: string): Entity;
+    /**
+     * Add a relation between two entities.
+     */
+    addRelation(fromEntityId: string, toEntityId: string, relationType: EntityRelationType, weight?: number, sourceDocId?: string | null): EntityRelation | null;
+    /**
+     * Add a mention linking an entity to a knowledge document.
+     */
+    addMention(entityId: string, docId: string, context: string | null, position: number): EntityMention;
+    /**
+     * Get entity by ID.
+     */
+    getById(id: string): Entity | undefined;
+    /**
+     * Find entities by FTS5 search on name, aliases, description.
+     */
+    findByName(query: string, limit?: number): Entity[];
+    /**
+     * Get all relations from/to an entity.
+     */
+    getRelations(entityId: string): EntityRelation[];
+    /**
+     * Get relations originating from an entity.
+     */
+    getRelationsFrom(entityId: string): EntityRelation[];
+    /**
+     * Get relations pointing to an entity.
+     */
+    getRelationsTo(entityId: string): EntityRelation[];
+    /**
+     * Get all entities mentioned in a specific document.
+     */
+    getEntitiesForDoc(docId: string): Entity[];
+    /**
+     * Get all document IDs that mention an entity.
+     */
+    getDocIdsForEntity(entityId: string): string[];
+    /**
+     * Get mentions for an entity.
+     */
+    getMentions(entityId: string): EntityMention[];
+    /**
+     * BFS traversal from seed entities — extract subgraph up to maxDepth hops.
+     * Returns entities, relations, and associated document IDs.
+     * Caps at maxEntities to prevent unbounded growth.
+     */
+    extractSubgraph(seedEntityIds: string[], maxDepth?: number, maxEntities?: number): EntitySubgraph;
+    /**
+     * Merge two entities — move all mentions and relations from mergeId to keepId,
+     * then delete the merged entity.
+     */
+    mergeEntities(keepId: string, mergeId: string): void;
+    /**
+     * Get stats for the knowledge graph.
+     */
+    stats(): {
+        entities: number;
+        relations: number;
+        mentions: number;
+    };
+    /**
+     * Clear all KG data (for reindexing).
+     */
+    clear(): void;
+}
+//# sourceMappingURL=entity-store.d.ts.map

package/dist/core/rag/entity-store.d.ts.map

@@ -0,0 +1 @@
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package/dist/core/rag/entity-store.js

@@ -0,0 +1,395 @@
+/**
+ * Entity Store — SQLite CRUD and graph traversal for the Knowledge Graph.
+ *
+ * Stores entities, relations between entities, and mentions linking
+ * entities to knowledge documents. Provides FTS5 search and BFS
+ * traversal for subgraph extraction.
+ */
+import { generateId } from "../utils/id.js";
+import { now } from "../utils/time.js";
+import { logger } from "../utils/logger.js";
+// ── Mappers ──────────────────────────────────────────────
+function rowToEntity(row) {
+    return {
+        id: row.id,
+        name: row.name,
+        type: row.type,
+        normalizedName: row.normalized_name,
+        aliases: JSON.parse(row.aliases),
+        description: row.description,
+        metadata: JSON.parse(row.metadata),
+        mentionCount: row.mention_count,
+        createdAt: row.created_at,
+        updatedAt: row.updated_at,
+    };
+}
+function rowToRelation(row) {
+    return {
+        id: row.id,
+        fromEntityId: row.from_entity_id,
+        toEntityId: row.to_entity_id,
+        relationType: row.relation_type,
+        weight: row.weight,
+        sourceDocId: row.source_doc_id,
+        createdAt: row.created_at,
+    };
+}
+function rowToMention(row) {
+    return {
+        id: row.id,
+        entityId: row.entity_id,
+        docId: row.doc_id,
+        context: row.context,
+        position: row.position,
+        createdAt: row.created_at,
+    };
+}
+// ── Normalize ────────────────────────────────────────────
+function normalizeName(name) {
+    return name.toLowerCase().trim();
+}
+// ── Entity Store ─────────────────────────────────────────
+export class EntityStore {
+    db;
+    constructor(db) {
+        this.db = db;
+    }
+    /**
+     * Check if the kg_entities table exists (graceful degradation).
+     */
+    hasKgTables() {
+        const row = this.db
+            .prepare("SELECT name FROM sqlite_master WHERE type='table' AND name='kg_entities'")
+            .get();
+        return row !== undefined;
+    }
+    /**
+     * Upsert entity — insert if new, increment mention_count if existing.
+     * Deduplication key: normalized_name + type.
+     */
+    upsertEntity(name, type, docId) {
+        const normalized = normalizeName(name);
+        const timestamp = now();
+        const existing = this.db
+            .prepare("SELECT * FROM kg_entities WHERE normalized_name = ? AND type = ?")
+            .get(normalized, type);
+        if (existing) {
+            this.db
+                .prepare("UPDATE kg_entities SET mention_count = mention_count + 1, updated_at = ? WHERE id = ?")
+                .run(timestamp, existing.id);
+            if (docId) {
+                this.addMention(existing.id, docId, null, 0);
+            }
+            return rowToEntity({
+                ...existing,
+                mention_count: existing.mention_count + 1,
+                updated_at: timestamp,
+            });
+        }
+        const id = generateId("ent");
+        this.db
+            .prepare(`INSERT INTO kg_entities (id, name, type, normalized_name, aliases, description, metadata, mention_count, created_at, updated_at)
+         VALUES (?, ?, ?, ?, '[]', NULL, '{}', 1, ?, ?)`)
+            .run(id, name, type, normalized, timestamp, timestamp);
+        // Sync FTS — standalone FTS table, use auto-generated rowid
+        const entityRowid = this.db
+            .prepare("SELECT rowid FROM kg_entities WHERE id = ?")
+            .get(id);
+        if (entityRowid) {
+            this.db
+                .prepare("INSERT INTO kg_entities_fts (rowid, name, aliases, description) VALUES (?, ?, '[]', '')")
+                .run(entityRowid.rowid, name);
+        }
+        if (docId) {
+            this.addMention(id, docId, null, 0);
+        }
+        logger.debug("entity-store:upsert", { id, name, type });
+        return {
+            id,
+            name,
+            type,
+            normalizedName: normalized,
+            aliases: [],
+            description: null,
+            metadata: {},
+            mentionCount: 1,
+            createdAt: timestamp,
+            updatedAt: timestamp,
+        };
+    }
+    /**
+     * Add a relation between two entities.
+     */
+    addRelation(fromEntityId, toEntityId, relationType, weight = 1.0, sourceDocId = null) {
+        const id = generateId("kgrel");
+        const timestamp = now();
+        try {
+            this.db
+                .prepare(`INSERT OR IGNORE INTO kg_relations (id, from_entity_id, to_entity_id, relation_type, weight, source_doc_id, created_at)
+           VALUES (?, ?, ?, ?, ?, ?, ?)`)
+                .run(id, fromEntityId, toEntityId, relationType, weight, sourceDocId, timestamp);
+            return {
+                id,
+                fromEntityId,
+                toEntityId,
+                relationType,
+                weight,
+                sourceDocId,
+                createdAt: timestamp,
+            };
+        }
+        catch {
+            logger.debug("entity-store:relation-exists", { fromEntityId, toEntityId, relationType });
+            return null;
+        }
+    }
+    /**
+     * Add a mention linking an entity to a knowledge document.
+     */
+    addMention(entityId, docId, context, position) {
+        const id = generateId("kgm");
+        const timestamp = now();
+        this.db
+            .prepare(`INSERT INTO kg_mentions (id, entity_id, doc_id, context, position, created_at)
+         VALUES (?, ?, ?, ?, ?, ?)`)
+            .run(id, entityId, docId, context, position, timestamp);
+        return {
+            id,
+            entityId,
+            docId,
+            context,
+            position,
+            createdAt: timestamp,
+        };
+    }
+    /**
+     * Get entity by ID.
+     */
+    getById(id) {
+        const row = this.db
+            .prepare("SELECT * FROM kg_entities WHERE id = ?")
+            .get(id);
+        return row ? rowToEntity(row) : undefined;
+    }
+    /**
+     * Find entities by FTS5 search on name, aliases, description.
+     */
+    findByName(query, limit = 10) {
+        if (!query.trim())
+            return [];
+        try {
+            // Try FTS5 prefix match first (append *)
+            const ftsQuery = query.trim().replace(/[^a-zA-Z0-9\s]/g, "") + "*";
+            const ftsRows = this.db
+                .prepare(`SELECT e.* FROM kg_entities e
+           JOIN kg_entities_fts fts ON e.rowid = fts.rowid
+           WHERE kg_entities_fts MATCH ?
+           LIMIT ?`)
+                .all(ftsQuery, limit);
+            if (ftsRows.length > 0) {
+                return ftsRows.map(rowToEntity);
+            }
+        }
+        catch {
+            // FTS query syntax error — fall through to LIKE
+        }
+        // Fallback to LIKE for substring matching
+        const likeRows = this.db
+            .prepare("SELECT * FROM kg_entities WHERE normalized_name LIKE ? OR name LIKE ? LIMIT ?")
+            .all(`%${normalizeName(query)}%`, `%${query}%`, limit);
+        return likeRows.map(rowToEntity);
+    }
+    /**
+     * Get all relations from/to an entity.
+     */
+    getRelations(entityId) {
+        const rows = this.db
+            .prepare("SELECT * FROM kg_relations WHERE from_entity_id = ? OR to_entity_id = ?")
+            .all(entityId, entityId);
+        return rows.map(rowToRelation);
+    }
+    /**
+     * Get relations originating from an entity.
+     */
+    getRelationsFrom(entityId) {
+        const rows = this.db
+            .prepare("SELECT * FROM kg_relations WHERE from_entity_id = ?")
+            .all(entityId);
+        return rows.map(rowToRelation);
+    }
+    /**
+     * Get relations pointing to an entity.
+     */
+    getRelationsTo(entityId) {
+        const rows = this.db
+            .prepare("SELECT * FROM kg_relations WHERE to_entity_id = ?")
+            .all(entityId);
+        return rows.map(rowToRelation);
+    }
+    /**
+     * Get all entities mentioned in a specific document.
+     */
+    getEntitiesForDoc(docId) {
+        const rows = this.db
+            .prepare(`SELECT DISTINCT e.* FROM kg_entities e
+         JOIN kg_mentions m ON e.id = m.entity_id
+         WHERE m.doc_id = ?`)
+            .all(docId);
+        return rows.map(rowToEntity);
+    }
+    /**
+     * Get all document IDs that mention an entity.
+     */
+    getDocIdsForEntity(entityId) {
+        const rows = this.db
+            .prepare("SELECT DISTINCT doc_id FROM kg_mentions WHERE entity_id = ?")
+            .all(entityId);
+        return rows.map((r) => r.doc_id);
+    }
+    /**
+     * Get mentions for an entity.
+     */
+    getMentions(entityId) {
+        const rows = this.db
+            .prepare("SELECT * FROM kg_mentions WHERE entity_id = ?")
+            .all(entityId);
+        return rows.map(rowToMention);
+    }
+    /**
+     * BFS traversal from seed entities — extract subgraph up to maxDepth hops.
+     * Returns entities, relations, and associated document IDs.
+     * Caps at maxEntities to prevent unbounded growth.
+     */
+    extractSubgraph(seedEntityIds, maxDepth = 2, maxEntities = 50) {
+        const visited = new Set();
+        const collectedRelations = new Map();
+        const docIdSet = new Set();
+        let frontier = seedEntityIds.filter((id) => {
+            if (visited.has(id))
+                return false;
+            visited.add(id);
+            return true;
+        });
+        // Collect doc IDs for seeds
+        for (const id of frontier) {
+            for (const docId of this.getDocIdsForEntity(id)) {
+                docIdSet.add(docId);
+            }
+        }
+        for (let depth = 0; depth < maxDepth && frontier.length > 0; depth++) {
+            if (visited.size >= maxEntities)
+                break;
+            const nextFrontier = [];
+            for (const entityId of frontier) {
+                const relations = this.getRelations(entityId);
+                for (const rel of relations) {
+                    collectedRelations.set(rel.id, rel);
+                    const neighborId = rel.fromEntityId === entityId
+                        ? rel.toEntityId
+                        : rel.fromEntityId;
+                    if (!visited.has(neighborId) && visited.size < maxEntities) {
+                        visited.add(neighborId);
+                        nextFrontier.push(neighborId);
+                        for (const docId of this.getDocIdsForEntity(neighborId)) {
+                            docIdSet.add(docId);
+                        }
+                    }
+                }
+            }
+            frontier = nextFrontier;
+        }
+        // Fetch full entity objects
+        const entities = [];
+        for (const id of visited) {
+            const entity = this.getById(id);
+            if (entity)
+                entities.push(entity);
+        }
+        logger.debug("entity-store:subgraph", {
+            seeds: seedEntityIds.length,
+            entities: entities.length,
+            relations: collectedRelations.size,
+            docs: docIdSet.size,
+        });
+        return {
+            entities,
+            relations: Array.from(collectedRelations.values()),
+            docIds: Array.from(docIdSet),
+        };
+    }
+    /**
+     * Merge two entities — move all mentions and relations from mergeId to keepId,
+     * then delete the merged entity.
+     */
+    mergeEntities(keepId, mergeId) {
+        this.db.transaction(() => {
+            // Move mentions
+            this.db
+                .prepare("UPDATE kg_mentions SET entity_id = ? WHERE entity_id = ?")
+                .run(keepId, mergeId);
+            // Move outgoing relations (ignore duplicates)
+            this.db
+                .prepare(`UPDATE OR IGNORE kg_relations SET from_entity_id = ? WHERE from_entity_id = ?`)
+                .run(keepId, mergeId);
+            // Move incoming relations (ignore duplicates)
+            this.db
+                .prepare(`UPDATE OR IGNORE kg_relations SET to_entity_id = ? WHERE to_entity_id = ?`)
+                .run(keepId, mergeId);
+            // Delete orphaned relations that couldn't be moved (duplicates)
+            this.db
+                .prepare("DELETE FROM kg_relations WHERE from_entity_id = ? OR to_entity_id = ?")
+                .run(mergeId, mergeId);
+            // Update mention count on keeper
+            const mentionCount = this.db
+                .prepare("SELECT COUNT(*) as cnt FROM kg_mentions WHERE entity_id = ?")
+                .get(keepId).cnt;
+            this.db
+                .prepare("UPDATE kg_entities SET mention_count = ?, updated_at = ? WHERE id = ?")
+                .run(mentionCount, now(), keepId);
+            // Delete FTS entry for merged entity
+            const mergedRowid = this.db
+                .prepare("SELECT rowid FROM kg_entities WHERE id = ?")
+                .get(mergeId);
+            if (mergedRowid) {
+                const merged = this.db
+                    .prepare("SELECT * FROM kg_entities WHERE id = ?")
+                    .get(mergeId);
+                if (merged) {
+                    this.db
+                        .prepare("DELETE FROM kg_entities_fts WHERE rowid = ?")
+                        .run(mergedRowid.rowid);
+                }
+            }
+            // Delete merged entity
+            this.db.prepare("DELETE FROM kg_entities WHERE id = ?").run(mergeId);
+            logger.debug("entity-store:merge", { keepId, mergeId, mentionCount });
+        })();
+    }
+    /**
+     * Get stats for the knowledge graph.
+     */
+    stats() {
+        const entities = this.db
+            .prepare("SELECT COUNT(*) as cnt FROM kg_entities")
+            .get().cnt;
+        const relations = this.db
+            .prepare("SELECT COUNT(*) as cnt FROM kg_relations")
+            .get().cnt;
+        const mentions = this.db
+            .prepare("SELECT COUNT(*) as cnt FROM kg_mentions")
+            .get().cnt;
+        return { entities, relations, mentions };
+    }
+    /**
+     * Clear all KG data (for reindexing).
+     */
+    clear() {
+        this.db.transaction(() => {
+            this.db.exec("DELETE FROM kg_mentions");
+            this.db.exec("DELETE FROM kg_relations");
+            this.db.exec("DELETE FROM kg_entities_fts");
+            this.db.exec("DELETE FROM kg_entities");
+        })();
+    }
+}
+//# sourceMappingURL=entity-store.js.map

package/dist/core/rag/entity-store.js.map

@@ -0,0 +1 @@
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package/dist/core/rag/multi-strategy-retrieval.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"multi-strategy-retrieval.d.ts","sourceRoot":"","sources":["../../../src/core/rag/multi-strategy-retrieval.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;GAWG;AAEH,OAAO,KAAK,QAAQ,MAAM,gBAAgB,CAAC;AAO3C,MAAM,WAAW,YAAY;IAC3B,EAAE,EAAE,MAAM,CAAC;IACX,UAAU,EAAE,MAAM,CAAC;IACnB,QAAQ,EAAE,MAAM,CAAC;IACjB,KAAK,EAAE,MAAM,CAAC;IACd,OAAO,EAAE,MAAM,CAAC;IAChB,KAAK,EAAE,MAAM,CAAC;IACd,YAAY,EAAE,MAAM,CAAC;IACrB,UAAU,EAAE,MAAM,EAAE,CAAC;CACtB;AAED,UAAU,aAAa;IACrB,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,UAAU,CAAC,EAAE,MAAM,CAAC;IACpB,KAAK,CAAC,EAAE,MAAM,CAAC;CAChB;AAID;;;GAGG;AACH,wBAAgB,oBAAoB,CAClC,WAAW,EAAE,KAAK,CAAC,KAAK,CAAC;IAAE,EAAE,EAAE,MAAM,CAAC;IAAC,KAAK,EAAE,MAAM,CAAA;CAAE,CAAC,CAAC,GACvD,KAAK,CAAC;IAAE,EAAE,EAAE,MAAM,CAAC;IAAC,QAAQ,EAAE,MAAM,CAAA;CAAE,CAAC,CAczC;AAED;;;GAGG;AACH,wBAAgB,mBAAmB,CACjC,EAAE,EAAE,QAAQ,CAAC,QAAQ,EACrB,KAAK,EAAE,MAAM,EACb,OAAO,CAAC,EAAE,aAAa,GACtB,YAAY,EAAE,CAoKhB"}

package/dist/core/rag/multi-strategy-retrieval.js

@@ -12,6 +12,8 @@
  */
 import { KnowledgeStore } from "../store/knowledge-store.js";
 import { findCrossSourceContext } from "./knowledge-linker.js";
+import { EntityStore } from "./entity-store.js";
+import { decomposeQuery } from "./query-understanding.js";
 import { logger } from "../utils/logger.js";
 const RRF_K = 60;
 /**
@@ -77,11 +79,49 @@ export function multiStrategySearch(db, query, options) {
             return { id, score: recencyScore };
         });
     }
-    if (ftsResults.length === 0 && graphResults.length === 0) {
+    // Strategy 4: Entity Graph Traversal — find docs via KG entities
+    const entityGraphResults = [];
+    try {
+        const entityStore = new EntityStore(db);
+        if (entityStore.hasKgTables() && entityStore.stats().entities > 0) {
+            const decomposed = decomposeQuery(query, db);
+            if (decomposed.entityMatches.length > 0) {
+                // Extract subgraph around matched entities (2 hops)
+                const seedIds = decomposed.entityMatches.slice(0, 5).map((m) => m.entityId);
+                const subgraph = entityStore.extractSubgraph(seedIds, 2, 50);
+                // Convert doc IDs to scored results
+                const docScoreMap = new Map();
+                for (const docId of subgraph.docIds) {
+                    docScoreMap.set(docId, 0.5);
+                }
+                // Boost docs that contain directly matched entities
+                for (const match of decomposed.entityMatches) {
+                    const docIds = entityStore.getDocIdsForEntity(match.entityId);
+                    for (const docId of docIds) {
+                        const current = docScoreMap.get(docId) ?? 0;
+                        docScoreMap.set(docId, Math.min(current + match.score * 0.3, 1.0));
+                    }
+                }
+                for (const [id, score] of docScoreMap) {
+                    entityGraphResults.push({ id, score });
+                }
+                // Sort by score descending for RRF
+                entityGraphResults.sort((a, b) => b.score - a.score);
+            }
+        }
+    }
+    catch {
+        logger.debug("Entity graph strategy skipped — KG not available");
+    }
+    if (ftsResults.length === 0 && graphResults.length === 0 && entityGraphResults.length === 0) {
         return [];
     }
-    // Merge via RRF
-    const merged = reciprocalRankFusion([ftsResults, graphResults, recencyResults]);
+    // Merge via RRF — add entity graph results as 4th list
+    const rankedLists = [ftsResults, graphResults, recencyResults];
+    if (entityGraphResults.length > 0) {
+        rankedLists.push(entityGraphResults);
+    }
+    const merged = reciprocalRankFusion(rankedLists);
     // Fetch full docs and apply quality multiplier
     const results = [];
     const strategyMap = new Map();
@@ -95,6 +135,11 @@ export function multiStrategySearch(db, query, options) {
         strategies.push("graph");
         strategyMap.set(gr.id, strategies);
     }
+    for (const eg of entityGraphResults) {
+        const strategies = strategyMap.get(eg.id) ?? [];
+        strategies.push("entity_graph");
+        strategyMap.set(eg.id, strategies);
+    }
     for (const item of merged.slice(0, limit)) {
         const doc = knowledgeStore.getById(item.id);
         if (!doc)
@@ -133,6 +178,7 @@ export function multiStrategySearch(db, query, options) {
         query,
         ftsCount: ftsResults.length,
         graphCount: graphResults.length,
+        entityGraphCount: entityGraphResults.length,
         resultCount: results.length,
     });
     return results;

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package/dist/core/rag/node-indexer.d.ts

@@ -0,0 +1,26 @@
+/**
+ * Node Indexer — indexes graph nodes into the Knowledge Store
+ * so they become discoverable via RAG search.
+ *
+ * Converts node content (title, description, AC, tags) into
+ * knowledge documents with sourceType "graph_node".
+ */
+import type Database from "better-sqlite3";
+import type { GraphNode } from "../graph/graph-types.js";
+/**
+ * Index a single graph node as a knowledge document.
+ * If a doc already exists for this node (same sourceId), it is replaced.
+ */
+export declare function indexNodeAsKnowledge(db: Database.Database, node: GraphNode): void;
+/**
+ * Remove a node's knowledge document.
+ */
+export declare function removeNodeFromKnowledge(db: Database.Database, nodeId: string): void;
+/**
+ * Index all existing graph nodes into the Knowledge Store.
+ * Used by reindex_knowledge with source "graph".
+ */
+export declare function indexAllNodes(db: Database.Database, projectId?: string): {
+    indexed: number;
+};
+//# sourceMappingURL=node-indexer.d.ts.map

package/dist/core/rag/node-indexer.d.ts.map

@@ -0,0 +1 @@
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