mindgraph-core 0.1.0

package/dist/storage/sqlite/sqlite-adapter.js

@@ -0,0 +1,497 @@
+import initSqlJs from 'sql.js';
+import { buildTraversalCTE } from './graph-traversal.js';
+function cosineSimilarity(a, b) {
+    let dot = 0, normA = 0, normB = 0;
+    for (let i = 0; i < a.length; i++) {
+        dot += a[i] * b[i];
+        normA += a[i] * a[i];
+        normB += b[i] * b[i];
+    }
+    const denom = Math.sqrt(normA) * Math.sqrt(normB);
+    return denom === 0 ? 0 : dot / denom;
+}
+/**
+ * Run a sql.js query and return results as an array of row objects.
+ */
+function queryAll(db, sql, params = []) {
+    const stmt = db.prepare(sql);
+    stmt.bind(params);
+    const rows = [];
+    while (stmt.step()) {
+        rows.push(stmt.getAsObject());
+    }
+    stmt.free();
+    return rows;
+}
+/**
+ * Run a sql.js query and return the first result row, or null.
+ */
+function queryOne(db, sql, params = []) {
+    const stmt = db.prepare(sql);
+    stmt.bind(params);
+    let row = null;
+    if (stmt.step()) {
+        row = stmt.getAsObject();
+    }
+    stmt.free();
+    return row;
+}
+// ─── Migrations (inline, no file reads) ────────────────────────────
+const MIGRATION_001 = `
+CREATE TABLE IF NOT EXISTS nodes (
+  id TEXT PRIMARY KEY,
+  node_type TEXT NOT NULL,
+  data TEXT NOT NULL DEFAULT '{}',
+  created_at TEXT NOT NULL,
+  updated_at TEXT NOT NULL
+);
+CREATE INDEX IF NOT EXISTS idx_nodes_type ON nodes(node_type);
+CREATE INDEX IF NOT EXISTS idx_nodes_updated ON nodes(updated_at);
+
+CREATE TABLE IF NOT EXISTS edges (
+  id TEXT PRIMARY KEY,
+  source_id TEXT NOT NULL,
+  target_id TEXT NOT NULL,
+  rel_type TEXT NOT NULL,
+  data TEXT NOT NULL DEFAULT '{}',
+  created_at TEXT NOT NULL,
+  FOREIGN KEY (source_id) REFERENCES nodes(id) ON DELETE CASCADE,
+  FOREIGN KEY (target_id) REFERENCES nodes(id) ON DELETE CASCADE
+);
+CREATE INDEX IF NOT EXISTS idx_edges_source ON edges(source_id);
+CREATE INDEX IF NOT EXISTS idx_edges_target ON edges(target_id);
+CREATE INDEX IF NOT EXISTS idx_edges_rel_type ON edges(rel_type);
+CREATE INDEX IF NOT EXISTS idx_edges_source_rel ON edges(source_id, rel_type);
+CREATE INDEX IF NOT EXISTS idx_edges_target_rel ON edges(target_id, rel_type);
+
+CREATE TABLE IF NOT EXISTS embeddings (
+  chunk_id TEXT PRIMARY KEY,
+  vector BLOB NOT NULL,
+  model_id TEXT NOT NULL,
+  dimensions INTEGER NOT NULL,
+  created_at TEXT NOT NULL,
+  FOREIGN KEY (chunk_id) REFERENCES nodes(id) ON DELETE CASCADE
+);
+
+CREATE VIRTUAL TABLE IF NOT EXISTS chunks_fts USING fts4(chunk_id, text, tokenize=porter);
+
+CREATE TABLE IF NOT EXISTS schema_migrations (
+  version INTEGER PRIMARY KEY,
+  applied_at TEXT NOT NULL
+);
+INSERT OR IGNORE INTO schema_migrations (version, applied_at) VALUES (1, datetime('now'));
+`;
+const MIGRATION_002 = `
+CREATE INDEX IF NOT EXISTS idx_edges_believes
+  ON edges(source_id, rel_type) WHERE rel_type = 'BELIEVES';
+CREATE INDEX IF NOT EXISTS idx_edges_contradicts
+  ON edges(source_id, rel_type) WHERE rel_type = 'CONTRADICTS';
+CREATE INDEX IF NOT EXISTS idx_edges_derived_from
+  ON edges(target_id, rel_type) WHERE rel_type = 'DERIVED_FROM';
+CREATE INDEX IF NOT EXISTS idx_edges_about
+  ON edges(source_id, rel_type) WHERE rel_type = 'ABOUT';
+INSERT OR IGNORE INTO schema_migrations (version, applied_at) VALUES (2, datetime('now'));
+`;
+const MIGRATION_003 = `
+CREATE TABLE IF NOT EXISTS meta (key TEXT PRIMARY KEY, value TEXT NOT NULL);
+INSERT OR REPLACE INTO meta (key, value) VALUES ('schemaVersion', '3');
+INSERT OR REPLACE INTO meta (key, value) VALUES ('createdAt', datetime('now'));
+INSERT OR REPLACE INTO meta (key, value) VALUES ('lastMigrationAt', datetime('now'));
+CREATE INDEX IF NOT EXISTS idx_edges_endorses
+  ON edges(source_id, rel_type) WHERE rel_type = 'ENDORSES';
+INSERT OR IGNORE INTO schema_migrations (version, applied_at) VALUES (3, datetime('now'));
+`;
+class FilePersistence {
+    constructor(path) {
+        this.path = path;
+    }
+    async load() {
+        try {
+            // Dynamic import — only used in Node.js / Electron
+            const { readFileSync } = await import('fs');
+            const buf = readFileSync(this.path);
+            return new Uint8Array(buf.buffer, buf.byteOffset, buf.byteLength);
+        }
+        catch {
+            return null; // file doesn't exist yet
+        }
+    }
+    async save(data) {
+        const { writeFileSync, mkdirSync, renameSync, openSync, fsyncSync, closeSync } = await import('fs');
+        const { dirname } = await import('path');
+        try {
+            mkdirSync(dirname(this.path), { recursive: true });
+        }
+        catch {
+            // ignore
+        }
+        // Atomic write: write-to-tmp → fsync → rename
+        const tmpPath = this.path + '.tmp';
+        writeFileSync(tmpPath, data);
+        // fsync to ensure data is flushed to disk
+        const fd = openSync(tmpPath, 'r');
+        fsyncSync(fd);
+        closeSync(fd);
+        // Atomic rename
+        renameSync(tmpPath, this.path);
+    }
+}
+// ─── SqliteAdapter (sql.js) ────────────────────────────────────────
+export class SqliteAdapter {
+    constructor(dbPath) {
+        this.db = null;
+        this.saveTimer = null;
+        this.dirty = false;
+        this.saveDebounceMs = 1000;
+        this.persistence = new FilePersistence(dbPath);
+    }
+    async initialize() {
+        const SQL = await initSqlJs();
+        // Try to load existing database
+        const existing = await this.persistence.load();
+        this.db = existing ? new SQL.Database(existing) : new SQL.Database();
+        // Pragmas (no WAL — sql.js is in-memory)
+        this.db.run('PRAGMA foreign_keys = ON;');
+        await this.runMigrations();
+    }
+    async close() {
+        if (this.saveTimer) {
+            clearTimeout(this.saveTimer);
+            this.saveTimer = null;
+        }
+        await this.persist();
+        this.db?.close();
+        this.db = null;
+    }
+    getDb() {
+        if (!this.db)
+            throw new Error('Database not initialized. Call initialize() first.');
+        return this.db;
+    }
+    /** Write the in-memory database to disk. */
+    async persist() {
+        if (!this.dirty || !this.db)
+            return;
+        const data = this.db.export();
+        await this.persistence.save(data);
+        this.dirty = false;
+    }
+    /** Mark the database as changed and schedule a debounced save. */
+    markDirty() {
+        this.dirty = true;
+        if (this.saveTimer)
+            clearTimeout(this.saveTimer);
+        this.saveTimer = setTimeout(() => {
+            this.persist();
+        }, this.saveDebounceMs);
+    }
+    async runMigrations() {
+        const db = this.getDb();
+        const hasMigrationsTable = queryOne(db, "SELECT name FROM sqlite_master WHERE type='table' AND name='schema_migrations'");
+        let currentVersion = 0;
+        if (hasMigrationsTable) {
+            const row = queryOne(db, 'SELECT MAX(version) as version FROM schema_migrations');
+            currentVersion = row?.version ?? 0;
+        }
+        if (currentVersion < 1) {
+            db.exec(MIGRATION_001);
+        }
+        if (currentVersion < 2) {
+            db.exec(MIGRATION_002);
+        }
+        if (currentVersion < 3) {
+            db.exec(MIGRATION_003);
+        }
+        this.markDirty();
+    }
+    // ─── Node CRUD ───────────────────────────────────────────────────
+    async upsertNode(node) {
+        const db = this.getDb();
+        db.run(`INSERT INTO nodes (id, node_type, data, created_at, updated_at)
+       VALUES (?, ?, ?, ?, ?)
+       ON CONFLICT(id) DO UPDATE SET
+         node_type = excluded.node_type,
+         data = excluded.data,
+         updated_at = excluded.updated_at`, [node.id, node.nodeType, JSON.stringify(node.data), node.createdAt, node.updatedAt]);
+        this.markDirty();
+    }
+    async getNode(id) {
+        const row = queryOne(this.getDb(), 'SELECT * FROM nodes WHERE id = ?', [id]);
+        return row ? this.rowToNode(row) : null;
+    }
+    async queryNodes(query) {
+        const db = this.getDb();
+        // Build query (simplified — no json_extract, filter in TS)
+        let sql = 'SELECT * FROM nodes';
+        const params = [];
+        const conditions = [];
+        if (query.nodeType) {
+            conditions.push('node_type = ?');
+            params.push(query.nodeType);
+        }
+        if (conditions.length > 0) {
+            sql += ' WHERE ' + conditions.join(' AND ');
+        }
+        sql += ' ORDER BY updated_at DESC';
+        if (query.limit) {
+            sql += ' LIMIT ?';
+            params.push(query.limit);
+        }
+        if (query.offset) {
+            sql += ' OFFSET ?';
+            params.push(query.offset);
+        }
+        let rows = queryAll(db, sql, params).map((r) => this.rowToNode(r));
+        // Apply JSON field filters in TypeScript
+        if (query.where) {
+            rows = rows.filter((node) => {
+                for (const [key, value] of Object.entries(query.where)) {
+                    if (node.data[key] !== value)
+                        return false;
+                }
+                return true;
+            });
+        }
+        return rows;
+    }
+    async deleteNode(id) {
+        this.getDb().run('DELETE FROM nodes WHERE id = ?', [id]);
+        this.markDirty();
+    }
+    async deleteNodesByData(nodeType, field, value) {
+        // Fetch, filter in TS, delete by ID
+        const candidates = queryAll(this.getDb(), 'SELECT id, data FROM nodes WHERE node_type = ?', [nodeType]);
+        let count = 0;
+        for (const row of candidates) {
+            const data = JSON.parse(row.data);
+            if (data[field] === value) {
+                this.getDb().run('DELETE FROM nodes WHERE id = ?', [row.id]);
+                count++;
+            }
+        }
+        if (count > 0)
+            this.markDirty();
+        return count;
+    }
+    // ─── Edge CRUD ───────────────────────────────────────────────────
+    async upsertEdge(edge) {
+        this.getDb().run(`INSERT INTO edges (id, source_id, target_id, rel_type, data, created_at)
+       VALUES (?, ?, ?, ?, ?, ?)
+       ON CONFLICT(id) DO UPDATE SET
+         source_id = excluded.source_id,
+         target_id = excluded.target_id,
+         rel_type = excluded.rel_type,
+         data = excluded.data`, [edge.id, edge.sourceId, edge.targetId, edge.relType, JSON.stringify(edge.data), edge.createdAt]);
+        this.markDirty();
+    }
+    async getEdge(id) {
+        const row = queryOne(this.getDb(), 'SELECT * FROM edges WHERE id = ?', [id]);
+        return row ? this.rowToEdge(row) : null;
+    }
+    async queryEdges(query) {
+        const conditions = [];
+        const params = [];
+        if (query.sourceId) {
+            conditions.push('source_id = ?');
+            params.push(query.sourceId);
+        }
+        if (query.targetId) {
+            conditions.push('target_id = ?');
+            params.push(query.targetId);
+        }
+        if (query.relType) {
+            conditions.push('rel_type = ?');
+            params.push(query.relType);
+        }
+        let sql = 'SELECT * FROM edges';
+        if (conditions.length > 0)
+            sql += ' WHERE ' + conditions.join(' AND ');
+        sql += ' ORDER BY created_at DESC';
+        if (query.limit) {
+            sql += ' LIMIT ?';
+            params.push(query.limit);
+        }
+        return queryAll(this.getDb(), sql, params).map((r) => this.rowToEdge(r));
+    }
+    async deleteEdge(id) {
+        this.getDb().run('DELETE FROM edges WHERE id = ?', [id]);
+        this.markDirty();
+    }
+    async deleteEdgesByNode(nodeId) {
+        const db = this.getDb();
+        const before = queryOne(db, 'SELECT COUNT(*) as c FROM edges WHERE source_id = ? OR target_id = ?', [nodeId, nodeId]);
+        db.run('DELETE FROM edges WHERE source_id = ? OR target_id = ?', [nodeId, nodeId]);
+        const count = before?.c ?? 0;
+        if (count > 0)
+            this.markDirty();
+        return count;
+    }
+    // ─── Graph traversal ────────────────────────────────────────────
+    async traverse(options) {
+        const { sql, params } = buildTraversalCTE(options);
+        return queryAll(this.getDb(), sql, params).map((r) => this.rowToNode(r));
+    }
+    // ─── Embeddings ──────────────────────────────────────────────────
+    async upsertEmbedding(record) {
+        const vectorBytes = new Uint8Array(record.vector.buffer, record.vector.byteOffset, record.vector.byteLength);
+        this.getDb().run(`INSERT INTO embeddings (chunk_id, vector, model_id, dimensions, created_at)
+       VALUES (?, ?, ?, ?, ?)
+       ON CONFLICT(chunk_id) DO UPDATE SET
+         vector = excluded.vector,
+         model_id = excluded.model_id,
+         dimensions = excluded.dimensions`, [record.chunkId, vectorBytes, record.modelId, record.dimensions, record.createdAt]);
+        this.markDirty();
+    }
+    async getEmbedding(chunkId) {
+        const row = queryOne(this.getDb(), 'SELECT * FROM embeddings WHERE chunk_id = ?', [chunkId]);
+        if (!row)
+            return null;
+        const bytes = new Uint8Array(row.vector);
+        const dims = row.dimensions;
+        const vector = new Float32Array(bytes.buffer, bytes.byteOffset, dims);
+        return {
+            chunkId: row.chunk_id,
+            vector,
+            modelId: row.model_id,
+            dimensions: dims,
+            createdAt: row.created_at,
+        };
+    }
+    async similaritySearch(query) {
+        let sql = 'SELECT * FROM embeddings';
+        const params = [];
+        if (query.modelId) {
+            sql += ' WHERE model_id = ?';
+            params.push(query.modelId);
+        }
+        const rows = queryAll(this.getDb(), sql, params);
+        const scored = [];
+        for (const row of rows) {
+            const bytes = new Uint8Array(row.vector);
+            const dims = row.dimensions;
+            const vec = new Float32Array(bytes.buffer, bytes.byteOffset, dims);
+            const score = cosineSimilarity(query.vector, vec);
+            if (!query.threshold || score >= query.threshold) {
+                scored.push({ chunkId: row.chunk_id, score });
+            }
+        }
+        scored.sort((a, b) => b.score - a.score);
+        const topK = scored.slice(0, query.topK);
+        const results = [];
+        for (const item of topK) {
+            const node = await this.getNode(item.chunkId);
+            if (node) {
+                results.push({
+                    chunkId: item.chunkId,
+                    nodeId: item.chunkId,
+                    score: item.score,
+                    text: node.data.text ?? '',
+                    notePath: node.data.notePath ?? '',
+                });
+            }
+        }
+        return results;
+    }
+    async deleteEmbedding(chunkId) {
+        this.getDb().run('DELETE FROM embeddings WHERE chunk_id = ?', [chunkId]);
+        this.markDirty();
+    }
+    // ─── Full-text search (FTS4) ─────────────────────────────────────
+    async fullTextSearch(query) {
+        const limit = query.limit ?? 20;
+        const rows = queryAll(this.getDb(), `SELECT chunk_id, text FROM chunks_fts WHERE chunks_fts MATCH ? LIMIT ?`, [query.query, limit]);
+        const results = [];
+        for (const row of rows) {
+            const node = await this.getNode(row.chunk_id);
+            results.push({
+                chunkId: row.chunk_id,
+                nodeId: row.chunk_id,
+                score: 1.0,
+                text: row.text,
+                notePath: node ? node.data.notePath ?? '' : '',
+            });
+        }
+        return results;
+    }
+    async upsertFTSEntry(chunkId, text) {
+        const db = this.getDb();
+        db.run('DELETE FROM chunks_fts WHERE chunk_id = ?', [chunkId]);
+        db.run('INSERT INTO chunks_fts (chunk_id, text) VALUES (?, ?)', [chunkId, text]);
+        this.markDirty();
+    }
+    async deleteFTSEntry(chunkId) {
+        this.getDb().run('DELETE FROM chunks_fts WHERE chunk_id = ?', [chunkId]);
+        this.markDirty();
+    }
+    // ─── Bulk operations ─────────────────────────────────────────────
+    async transaction(fn) {
+        const db = this.getDb();
+        db.run('BEGIN TRANSACTION');
+        try {
+            const result = await fn();
+            db.run('COMMIT');
+            this.markDirty();
+            return result;
+        }
+        catch (err) {
+            db.run('ROLLBACK');
+            throw err;
+        }
+    }
+    // ─── Schema version ────────────────────────────────────────────
+    getSchemaVersion() {
+        const db = this.getDb();
+        const row = queryOne(db, "SELECT value FROM meta WHERE key = 'schemaVersion'");
+        return row ? Number(row.value) : 0;
+    }
+    getMetaValue(key) {
+        const db = this.getDb();
+        const row = queryOne(db, 'SELECT value FROM meta WHERE key = ?', [key]);
+        return row ? String(row.value) : null;
+    }
+    setMetaValue(key, value) {
+        this.getDb().run('INSERT OR REPLACE INTO meta (key, value) VALUES (?, ?)', [key, value]);
+        this.markDirty();
+    }
+    // ─── Integrity ─────────────────────────────────────────────────
+    async checkIntegrity() {
+        const db = this.getDb();
+        const row = queryOne(db, 'PRAGMA integrity_check');
+        const result = row ? String(Object.values(row)[0]) : 'unknown';
+        return { ok: result === 'ok', details: result };
+    }
+    // ─── Stats ───────────────────────────────────────────────────────
+    async getStats() {
+        const db = this.getDb();
+        const nodeCount = queryOne(db, 'SELECT COUNT(*) as c FROM nodes')?.c ?? 0;
+        const edgeCount = queryOne(db, 'SELECT COUNT(*) as c FROM edges')?.c ?? 0;
+        const embeddingCount = queryOne(db, 'SELECT COUNT(*) as c FROM embeddings')?.c ?? 0;
+        const typeRows = queryAll(db, 'SELECT node_type, COUNT(*) as c FROM nodes GROUP BY node_type');
+        const nodeCountByType = {};
+        for (const row of typeRows) {
+            nodeCountByType[row.node_type] = row.c;
+        }
+        return { nodeCount, edgeCount, embeddingCount, nodeCountByType };
+    }
+    // ─── Row mapping ─────────────────────────────────────────────────
+    rowToNode(row) {
+        return {
+            id: row.id,
+            nodeType: row.node_type,
+            data: JSON.parse(row.data),
+            createdAt: row.created_at,
+            updatedAt: row.updated_at ?? row.created_at,
+        };
+    }
+    rowToEdge(row) {
+        return {
+            id: row.id,
+            sourceId: row.source_id,
+            targetId: row.target_id,
+            relType: row.rel_type,
+            data: JSON.parse(row.data),
+            createdAt: row.created_at,
+        };
+    }
+}
+//# sourceMappingURL=sqlite-adapter.js.map

package/dist/storage/sqlite/sqlite-adapter.js.map

@@ -0,0 +1 @@
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package/dist/storage/storage-interface.d.ts

@@ -0,0 +1,64 @@
+import type { GraphNode, GraphEdge, EmbeddingRecord, SearchResult, NodeType, RelType } from '../schema/types.js';
+export interface NodeQuery {
+    nodeType?: NodeType;
+    where?: Record<string, unknown>;
+    limit?: number;
+    offset?: number;
+}
+export interface EdgeQuery {
+    sourceId?: string;
+    targetId?: string;
+    relType?: RelType;
+    limit?: number;
+}
+export interface TraversalOptions {
+    startNodeId: string;
+    relTypes?: RelType[];
+    direction?: 'outbound' | 'inbound' | 'both';
+    maxDepth?: number;
+    nodeTypeFilter?: NodeType[];
+}
+export interface SimilarityQuery {
+    vector: Float32Array;
+    topK: number;
+    threshold?: number;
+    modelId?: string;
+}
+export interface FullTextQuery {
+    query: string;
+    limit?: number;
+}
+export interface StorageAdapter {
+    initialize(): Promise<void>;
+    close(): Promise<void>;
+    upsertNode(node: GraphNode): Promise<void>;
+    getNode(id: string): Promise<GraphNode | null>;
+    queryNodes(query: NodeQuery): Promise<GraphNode[]>;
+    deleteNode(id: string): Promise<void>;
+    deleteNodesByData(nodeType: NodeType, field: string, value: unknown): Promise<number>;
+    upsertEdge(edge: GraphEdge): Promise<void>;
+    getEdge(id: string): Promise<GraphEdge | null>;
+    queryEdges(query: EdgeQuery): Promise<GraphEdge[]>;
+    deleteEdge(id: string): Promise<void>;
+    deleteEdgesByNode(nodeId: string): Promise<number>;
+    traverse(options: TraversalOptions): Promise<GraphNode[]>;
+    upsertEmbedding(record: EmbeddingRecord): Promise<void>;
+    getEmbedding(chunkId: string): Promise<EmbeddingRecord | null>;
+    similaritySearch(query: SimilarityQuery): Promise<SearchResult[]>;
+    deleteEmbedding(chunkId: string): Promise<void>;
+    fullTextSearch(query: FullTextQuery): Promise<SearchResult[]>;
+    upsertFTSEntry(chunkId: string, text: string): Promise<void>;
+    deleteFTSEntry(chunkId: string): Promise<void>;
+    transaction<T>(fn: () => Promise<T>): Promise<T>;
+    checkIntegrity?(): Promise<{
+        ok: boolean;
+        details: string;
+    }>;
+    getStats(): Promise<{
+        nodeCount: number;
+        edgeCount: number;
+        embeddingCount: number;
+        nodeCountByType: Record<string, number>;
+    }>;
+}
+//# sourceMappingURL=storage-interface.d.ts.map

package/dist/storage/storage-interface.d.ts.map

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package/dist/storage/storage-interface.js

@@ -0,0 +1,2 @@
+export {};
+//# sourceMappingURL=storage-interface.js.map

package/dist/storage/storage-interface.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"storage-interface.js","sourceRoot":"","sources":["../../src/storage/storage-interface.ts"],"names":[],"mappings":""}

package/dist/utils/retry-fetch.d.ts

@@ -0,0 +1,20 @@
+export interface RetryFetchOptions {
+    maxRetries?: number;
+    baseDelayMs?: number;
+    timeoutMs?: number;
+}
+/**
+ * Structured error for non-retryable HTTP responses (4xx except 429).
+ * Exposes status and response body for programmatic handling.
+ */
+export declare class FetchError extends Error {
+    readonly status: number;
+    readonly body: string;
+    constructor(status: number, body: string);
+}
+/**
+ * Wraps fetch() with exponential backoff retry for 429/5xx and network errors.
+ * 4xx errors (except 429) fail immediately.
+ */
+export declare function retryFetch(url: string, init: RequestInit, options?: RetryFetchOptions): Promise<Response>;
+//# sourceMappingURL=retry-fetch.d.ts.map

package/dist/utils/retry-fetch.d.ts.map

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