causantic 0.2.0

package/dist/storage/vector-store.js

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+/**
+ * In-memory vector store with SQLite persistence.
+ *
+ * Provides vector similarity search for chunk embeddings using angular distance.
+ * Embeddings are stored as Float32Array blobs in SQLite and loaded into memory
+ * on first access for fast brute-force search.
+ *
+ * ## Architecture
+ *
+ * ```
+ * ┌─────────────────────────────────────────────────────────────┐
+ * │                     VectorStore                             │
+ * │  ┌─────────────────────┐    ┌─────────────────────────────┐ │
+ * │  │  In-Memory Index    │    │    SQLite Persistence       │ │
+ * │  │  Map<id, number[]>  │ ◄──┤  vectors (id, embedding,    │ │
+ * │  └─────────────────────┘    │           last_accessed)    │ │
+ * │                             └─────────────────────────────┘ │
+ * └─────────────────────────────────────────────────────────────┘
+ * ```
+ *
+ * ## TTL (Time To Live)
+ *
+ * Vectors have a `last_accessed` timestamp that is updated when they are
+ * returned from search. Vectors that haven't been accessed within the TTL
+ * period can be cleaned up by the maintenance task.
+ *
+ * This allows vectors to persist for semantic search even after their
+ * associated chunks are pruned from the causal graph, while still eventually
+ * cleaning up truly stale vectors.
+ *
+ * ## Usage
+ *
+ * ```typescript
+ * import { vectorStore } from './vector-store.js';
+ *
+ * // Insert an embedding
+ * await vectorStore.insert('chunk-123', embedding);
+ *
+ * // Search for similar vectors
+ * const results = await vectorStore.search(queryEmbedding, 10);
+ * // Returns: [{ id: 'chunk-456', distance: 0.15 }, ...]
+ * // (also updates last_accessed for returned vectors)
+ * ```
+ *
+ * ## Distance Metric
+ *
+ * Uses angular distance (0 = identical, 2 = opposite):
+ * - `0.0`: Identical vectors
+ * - `0.5`: ~60° angle
+ * - `1.0`: Orthogonal (90°)
+ * - `2.0`: Opposite vectors
+ *
+ * ## Performance Notes
+ *
+ * - Initial load: O(n) to deserialize all vectors from SQLite
+ * - Insert: O(1) amortized (memory + single row insert)
+ * - Search: O(n) brute-force (sufficient for <100k vectors)
+ * - Memory: ~4KB per vector (1024 dimensions × 4 bytes)
+ *
+ * For larger scale, consider upgrading to LanceDB or FAISS.
+ *
+ * @module storage/vector-store
+ */
+import { getDb } from './db.js';
+import { angularDistance } from '../utils/angular-distance.js';
+import { createLogger } from '../utils/logger.js';
+import { serializeEmbedding, deserializeEmbedding } from '../utils/embedding-utils.js';
+const log = createLogger('vector-store');
+/**
+ * In-memory vector index backed by SQLite for persistence.
+ *
+ * Uses lazy loading — vectors are loaded from SQLite on first operation.
+ * All operations are async to support future migration to async storage backends.
+ *
+ * Thread safety: Single-threaded (Node.js). For concurrent access, use
+ * the singleton `vectorStore` export which ensures consistent state.
+ */
+// Export class for testing (allows creating fresh instances)
+export class VectorStore {
+    vectors = new Map();
+    loaded = false;
+    /** chunkId → projectSlug index for project-filtered search */
+    chunkProjectIndex = new Map();
+    /**
+     * Load vectors from database into memory.
+     */
+    async load() {
+        if (this.loaded)
+            return;
+        const db = getDb();
+        // Ensure vectors table exists with TTL columns
+        db.exec(`
+      CREATE TABLE IF NOT EXISTS vectors (
+        id TEXT PRIMARY KEY,
+        embedding BLOB NOT NULL,
+        orphaned_at TEXT DEFAULT NULL,
+        last_accessed TEXT DEFAULT CURRENT_TIMESTAMP
+      )
+    `);
+        // Migrate existing tables
+        const columns = db.prepare("PRAGMA table_info(vectors)").all();
+        const hasOrphanedAt = columns.some((c) => c.name === 'orphaned_at');
+        const hasLastAccessed = columns.some((c) => c.name === 'last_accessed');
+        if (!hasOrphanedAt) {
+            db.exec("ALTER TABLE vectors ADD COLUMN orphaned_at TEXT DEFAULT NULL");
+        }
+        if (!hasLastAccessed) {
+            db.exec("ALTER TABLE vectors ADD COLUMN last_accessed TEXT DEFAULT CURRENT_TIMESTAMP");
+            db.exec("UPDATE vectors SET last_accessed = CURRENT_TIMESTAMP WHERE last_accessed IS NULL");
+        }
+        const rows = db.prepare('SELECT id, embedding FROM vectors').all();
+        for (const row of rows) {
+            const embedding = deserializeEmbedding(row.embedding);
+            this.vectors.set(row.id, embedding);
+        }
+        // Populate chunk→project index from chunks table
+        try {
+            const chunkRows = db.prepare("SELECT id, session_slug FROM chunks WHERE session_slug != ''").all();
+            for (const row of chunkRows) {
+                this.chunkProjectIndex.set(row.id, row.session_slug);
+            }
+        }
+        catch {
+            // chunks table may not exist yet (e.g., during migrations)
+        }
+        this.loaded = true;
+    }
+    /**
+     * Insert a vector.
+     */
+    async insert(id, embedding) {
+        await this.load();
+        const db = getDb();
+        const blob = serializeEmbedding(embedding);
+        db.prepare('INSERT OR REPLACE INTO vectors (id, embedding, orphaned_at, last_accessed) VALUES (?, ?, NULL, CURRENT_TIMESTAMP)').run(id, blob);
+        this.vectors.set(id, embedding);
+        // Update project index
+        try {
+            const row = db.prepare('SELECT session_slug FROM chunks WHERE id = ?').get(id);
+            if (row?.session_slug) {
+                this.chunkProjectIndex.set(id, row.session_slug);
+            }
+        }
+        catch {
+            // chunks table may not exist
+        }
+    }
+    /**
+     * Insert multiple vectors in a transaction.
+     */
+    async insertBatch(items) {
+        await this.load();
+        const db = getDb();
+        const stmt = db.prepare('INSERT OR REPLACE INTO vectors (id, embedding, orphaned_at, last_accessed) VALUES (?, ?, NULL, CURRENT_TIMESTAMP)');
+        const insertMany = db.transaction((items) => {
+            for (const item of items) {
+                const blob = serializeEmbedding(item.embedding);
+                stmt.run(item.id, blob);
+                this.vectors.set(item.id, item.embedding);
+            }
+        });
+        insertMany(items);
+        // Update project index for batch
+        try {
+            const ids = items.map(i => i.id);
+            if (ids.length > 0) {
+                const placeholders = ids.map(() => '?').join(',');
+                const rows = db.prepare(`SELECT id, session_slug FROM chunks WHERE id IN (${placeholders}) AND session_slug != ''`).all(...ids);
+                for (const row of rows) {
+                    this.chunkProjectIndex.set(row.id, row.session_slug);
+                }
+            }
+        }
+        catch {
+            // chunks table may not exist
+        }
+    }
+    /**
+     * Get a vector by ID.
+     */
+    async get(id) {
+        await this.load();
+        return this.vectors.get(id) ?? null;
+    }
+    /**
+     * Search for similar vectors using angular distance.
+     *
+     * Uses brute-force search over all vectors in memory. For small to medium
+     * datasets (<100k vectors), this is fast enough. For larger datasets,
+     * consider approximate nearest neighbor (ANN) algorithms.
+     *
+     * Also updates `last_accessed` timestamp for returned vectors, keeping
+     * them alive for TTL purposes.
+     *
+     * @param query - Query embedding vector (must match stored dimensionality)
+     * @param limit - Maximum number of results to return
+     * @returns Results sorted by distance ascending (closest first)
+     *
+     * @example
+     * ```typescript
+     * const results = await vectorStore.search(queryEmbedding, 10);
+     * for (const { id, distance } of results) {
+     *   console.log(`${id}: distance=${distance.toFixed(3)}`);
+     * }
+     * ```
+     */
+    async search(query, limit) {
+        await this.load();
+        const results = [];
+        for (const [id, embedding] of this.vectors) {
+            const distance = angularDistance(query, embedding);
+            results.push({ id, distance });
+        }
+        // Sort by distance and take top k
+        results.sort((a, b) => a.distance - b.distance);
+        const topResults = results.slice(0, limit);
+        // Touch last_accessed for returned vectors (async, non-blocking)
+        if (topResults.length > 0) {
+            this.touchLastAccessed(topResults.map((r) => r.id));
+        }
+        return topResults;
+    }
+    /**
+     * Search within a subset of IDs.
+     * Also updates last_accessed for returned vectors.
+     */
+    async searchWithinIds(query, candidateIds, limit) {
+        await this.load();
+        const results = [];
+        const idSet = new Set(candidateIds);
+        for (const [id, embedding] of this.vectors) {
+            if (!idSet.has(id))
+                continue;
+            const distance = angularDistance(query, embedding);
+            results.push({ id, distance });
+        }
+        results.sort((a, b) => a.distance - b.distance);
+        const topResults = results.slice(0, limit);
+        // Touch last_accessed for returned vectors
+        if (topResults.length > 0) {
+            this.touchLastAccessed(topResults.map((r) => r.id));
+        }
+        return topResults;
+    }
+    /**
+     * Search for similar vectors filtered to specific project(s).
+     *
+     * Skips vectors not belonging to the specified project(s) during
+     * distance computation (more efficient than post-filtering).
+     *
+     * @param query - Query embedding vector
+     * @param projects - Single project slug or array of project slugs
+     * @param limit - Maximum results
+     * @returns Results sorted by distance ascending
+     */
+    async searchByProject(query, projects, limit) {
+        await this.load();
+        const projectSet = new Set(Array.isArray(projects) ? projects : [projects]);
+        const results = [];
+        for (const [id, embedding] of this.vectors) {
+            const project = this.chunkProjectIndex.get(id);
+            if (!project || !projectSet.has(project))
+                continue;
+            const distance = angularDistance(query, embedding);
+            results.push({ id, distance });
+        }
+        results.sort((a, b) => a.distance - b.distance);
+        const topResults = results.slice(0, limit);
+        if (topResults.length > 0) {
+            this.touchLastAccessed(topResults.map((r) => r.id));
+        }
+        return topResults;
+    }
+    /**
+     * Get the project slug for a chunk ID.
+     */
+    getChunkProject(id) {
+        return this.chunkProjectIndex.get(id);
+    }
+    /**
+     * Delete a vector.
+     */
+    async delete(id) {
+        await this.load();
+        const db = getDb();
+        const result = db.prepare('DELETE FROM vectors WHERE id = ?').run(id);
+        this.vectors.delete(id);
+        return result.changes > 0;
+    }
+    /**
+     * Delete multiple vectors.
+     */
+    async deleteBatch(ids) {
+        if (ids.length === 0)
+            return 0;
+        await this.load();
+        const db = getDb();
+        const placeholders = ids.map(() => '?').join(',');
+        const result = db.prepare(`DELETE FROM vectors WHERE id IN (${placeholders})`).run(...ids);
+        for (const id of ids) {
+            this.vectors.delete(id);
+        }
+        return result.changes;
+    }
+    /**
+     * Get vector count.
+     */
+    async count() {
+        await this.load();
+        return this.vectors.size;
+    }
+    /**
+     * Check if a vector exists.
+     */
+    async has(id) {
+        await this.load();
+        return this.vectors.has(id);
+    }
+    /**
+     * Clear all vectors (for testing).
+     */
+    async clear() {
+        const db = getDb();
+        db.exec('DELETE FROM vectors');
+        this.vectors.clear();
+    }
+    /**
+     * Get all vector IDs.
+     */
+    async getAllIds() {
+        await this.load();
+        return Array.from(this.vectors.keys());
+    }
+    /**
+     * Get all vectors as an array (for clustering).
+     */
+    async getAllVectors() {
+        await this.load();
+        return Array.from(this.vectors.entries()).map(([id, embedding]) => ({
+            id,
+            embedding,
+        }));
+    }
+    /**
+     * Reset loaded state (for testing).
+     */
+    reset() {
+        this.vectors.clear();
+        this.chunkProjectIndex.clear();
+        this.loaded = false;
+    }
+    // ─── TTL Management ─────────────────────────────────────────────────────────
+    /**
+     * Update last_accessed timestamp for vectors.
+     * Called when vectors are returned from search to keep them alive.
+     */
+    touchLastAccessed(ids) {
+        if (ids.length === 0)
+            return;
+        const db = getDb();
+        const placeholders = ids.map(() => '?').join(',');
+        db.prepare(`UPDATE vectors SET last_accessed = CURRENT_TIMESTAMP WHERE id IN (${placeholders})`).run(...ids);
+    }
+    /**
+     * Mark a vector as orphaned (its associated chunk was deleted).
+     * The vector will be subject to TTL cleanup after this.
+     * Called by pruner when deleting orphaned chunks.
+     */
+    async markOrphaned(id) {
+        await this.load();
+        const db = getDb();
+        db.prepare('UPDATE vectors SET orphaned_at = CURRENT_TIMESTAMP, last_accessed = CURRENT_TIMESTAMP WHERE id = ?').run(id);
+    }
+    /**
+     * Mark multiple vectors as orphaned.
+     */
+    async markOrphanedBatch(ids) {
+        if (ids.length === 0)
+            return;
+        await this.load();
+        const db = getDb();
+        const placeholders = ids.map(() => '?').join(',');
+        db.prepare(`UPDATE vectors SET orphaned_at = CURRENT_TIMESTAMP, last_accessed = CURRENT_TIMESTAMP WHERE id IN (${placeholders})`).run(...ids);
+    }
+    /**
+     * Clean up expired orphaned vectors and their corresponding chunks.
+     * Removes vectors that are orphaned AND haven't been accessed within the TTL period.
+     * Also deletes the corresponding chunks (FK cascades handle cluster assignments and edges).
+     *
+     * @param ttlDays - Number of days after which orphaned vectors expire
+     * @returns Number of vectors deleted
+     */
+    async cleanupExpired(ttlDays) {
+        await this.load();
+        const db = getDb();
+        // Find expired orphaned vectors
+        const expiredRows = db.prepare(`
+      SELECT id FROM vectors
+      WHERE orphaned_at IS NOT NULL
+        AND last_accessed < datetime('now', '-' || ? || ' days')
+    `).all(ttlDays);
+        if (expiredRows.length === 0) {
+            return 0;
+        }
+        const expiredIds = expiredRows.map((r) => r.id);
+        const placeholders = expiredIds.map(() => '?').join(',');
+        // Delete chunks first (FK cascades handle chunk_clusters and edges)
+        db.prepare(`DELETE FROM chunks WHERE id IN (${placeholders})`).run(...expiredIds);
+        // Delete vectors
+        const result = db.prepare(`DELETE FROM vectors WHERE id IN (${placeholders})`).run(...expiredIds);
+        // Remove empty clusters (no remaining members after chunk deletion)
+        db.prepare(`
+      DELETE FROM clusters WHERE id NOT IN (
+        SELECT DISTINCT cluster_id FROM chunk_clusters
+      )
+    `).run();
+        // Remove from memory
+        for (const id of expiredIds) {
+            this.vectors.delete(id);
+        }
+        return result.changes;
+    }
+    /**
+     * Get count of orphaned vectors.
+     */
+    async getOrphanedCount() {
+        await this.load();
+        const db = getDb();
+        const row = db.prepare('SELECT COUNT(*) as count FROM vectors WHERE orphaned_at IS NOT NULL').get();
+        return row.count;
+    }
+}
+/**
+ * Singleton vector store instance.
+ *
+ * Use this for all vector operations to ensure consistent state.
+ * The instance lazy-loads vectors from SQLite on first operation.
+ */
+export const vectorStore = new VectorStore();
+//# sourceMappingURL=vector-store.js.map

package/dist/storage/vector-store.js.map

@@ -0,0 +1 @@
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package/dist/temporal/clock-compactor.d.ts

@@ -0,0 +1,65 @@
+/**
+ * Clock compaction for reference clocks.
+ *
+ * Reference clocks accumulate agent entries over time. This module provides
+ * compaction to prune entries only when ALL edges referencing that agent
+ * have fully decayed.
+ *
+ * Why not prune by tick recency:
+ * An agent may not tick for a long time, but edges referencing it could still
+ * be queried. Pruning based on tick recency would break hop count calculation
+ * for those edges.
+ */
+import { type VectorClock } from './vector-clock.js';
+import { type VectorDecayConfig } from '../storage/decay.js';
+/**
+ * Result of clock compaction.
+ */
+export interface CompactionResult {
+    /** Agent IDs that were pruned */
+    prunedAgents: string[];
+    /** Number of agent entries remaining */
+    remainingAgents: number;
+    /** Duration of compaction in milliseconds */
+    durationMs: number;
+}
+/**
+ * Compact the reference clock for a project by removing agent entries
+ * that no longer have any live edges referencing them.
+ *
+ * @param projectSlug - Project identifier
+ * @param vectorConfig - Vector decay configuration (optional)
+ * @returns Compaction result
+ */
+export declare function compactReferenceClock(projectSlug: string, vectorConfig?: VectorDecayConfig): Promise<CompactionResult>;
+/**
+ * Get statistics about clock entries for a project.
+ *
+ * @param projectSlug - Project identifier
+ * @returns Clock statistics
+ */
+export declare function getClockStats(projectSlug: string): {
+    agentCount: number;
+    totalTicks: number;
+    agents: Array<{
+        agentId: string;
+        ticks: number;
+    }>;
+};
+/**
+ * Estimate the "age" of edges in hop count terms.
+ * Returns distribution of edges by hop count.
+ *
+ * @param projectSlug - Project identifier
+ * @returns Histogram of hop counts
+ */
+export declare function getHopCountDistribution(projectSlug: string): Promise<Map<number, number>>;
+/**
+ * Force refresh the reference clock by merging all agent clocks.
+ * Useful after data recovery or manual edits.
+ *
+ * @param projectSlug - Project identifier
+ * @returns The refreshed reference clock
+ */
+export declare function refreshReferenceClock(projectSlug: string): VectorClock;
+//# sourceMappingURL=clock-compactor.d.ts.map

package/dist/temporal/clock-compactor.d.ts.map

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package/dist/temporal/clock-compactor.js

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+/**
+ * Clock compaction for reference clocks.
+ *
+ * Reference clocks accumulate agent entries over time. This module provides
+ * compaction to prune entries only when ALL edges referencing that agent
+ * have fully decayed.
+ *
+ * Why not prune by tick recency:
+ * An agent may not tick for a long time, but edges referencing it could still
+ * be queried. Pruning based on tick recency would break hop count calculation
+ * for those edges.
+ */
+import { getDb } from '../storage/db.js';
+import { getReferenceClock, setReferenceClock, getAllAgentClocks, } from '../storage/clock-store.js';
+import { hopCount, deserialize, } from './vector-clock.js';
+import { DEFAULT_VECTOR_DECAY } from '../storage/decay.js';
+import { getConfig } from '../config/memory-config.js';
+/**
+ * Compact the reference clock for a project by removing agent entries
+ * that no longer have any live edges referencing them.
+ *
+ * @param projectSlug - Project identifier
+ * @param vectorConfig - Vector decay configuration (optional)
+ * @returns Compaction result
+ */
+export async function compactReferenceClock(projectSlug, vectorConfig) {
+    const startTime = Date.now();
+    const config = vectorConfig ?? getConfig().vectorDecay ?? DEFAULT_VECTOR_DECAY;
+    const refClock = getReferenceClock(projectSlug);
+    const agentIds = Object.keys(refClock);
+    if (agentIds.length === 0) {
+        return {
+            prunedAgents: [],
+            remainingAgents: 0,
+            durationMs: Date.now() - startTime,
+        };
+    }
+    const prunedAgents = [];
+    for (const agentId of agentIds) {
+        const hasLiveEdges = await hasEdgesReferencingAgent(projectSlug, agentId, refClock, config);
+        if (!hasLiveEdges) {
+            prunedAgents.push(agentId);
+        }
+    }
+    if (prunedAgents.length > 0) {
+        // Remove pruned agents from reference clock
+        const newClock = {};
+        for (const [id, ticks] of Object.entries(refClock)) {
+            if (!prunedAgents.includes(id)) {
+                newClock[id] = ticks;
+            }
+        }
+        setReferenceClock(projectSlug, newClock);
+    }
+    return {
+        prunedAgents,
+        remainingAgents: agentIds.length - prunedAgents.length,
+        durationMs: Date.now() - startTime,
+    };
+}
+/**
+ * Check if any live edges reference a specific agent in their vector clock.
+ *
+ * @param projectSlug - Project identifier
+ * @param agentId - Agent ID to check
+ * @param refClock - Current reference clock
+ * @param config - Vector decay configuration
+ * @returns true if at least one live edge references this agent
+ */
+async function hasEdgesReferencingAgent(projectSlug, agentId, refClock, config) {
+    const db = getDb();
+    // Find edges in this project whose vector_clock contains this agentId
+    // We use LIKE to find JSON containing the agent ID
+    const rows = db.prepare(`
+    SELECT e.vector_clock FROM edges e
+    JOIN chunks c ON e.source_chunk_id = c.id
+    WHERE c.session_slug = ?
+      AND e.vector_clock LIKE ?
+  `).all(projectSlug, `%"${agentId}":%`);
+    for (const row of rows) {
+        if (!row.vector_clock)
+            continue;
+        const edgeClock = deserialize(row.vector_clock);
+        if (!(agentId in edgeClock))
+            continue;
+        // Calculate if edge is still alive
+        const hops = hopCount(edgeClock, refClock);
+        const weight = Math.pow(config.weightPerHop, hops);
+        if (weight >= config.minWeight) {
+            return true; // At least one live edge references this agent
+        }
+    }
+    return false; // No live edges reference this agent
+}
+/**
+ * Get statistics about clock entries for a project.
+ *
+ * @param projectSlug - Project identifier
+ * @returns Clock statistics
+ */
+export function getClockStats(projectSlug) {
+    const refClock = getReferenceClock(projectSlug);
+    const agents = Object.entries(refClock).map(([agentId, ticks]) => ({
+        agentId,
+        ticks,
+    }));
+    return {
+        agentCount: agents.length,
+        totalTicks: agents.reduce((sum, a) => sum + a.ticks, 0),
+        agents: agents.sort((a, b) => b.ticks - a.ticks),
+    };
+}
+/**
+ * Estimate the "age" of edges in hop count terms.
+ * Returns distribution of edges by hop count.
+ *
+ * @param projectSlug - Project identifier
+ * @returns Histogram of hop counts
+ */
+export async function getHopCountDistribution(projectSlug) {
+    const db = getDb();
+    const refClock = getReferenceClock(projectSlug);
+    const distribution = new Map();
+    const rows = db.prepare(`
+    SELECT e.vector_clock FROM edges e
+    JOIN chunks c ON e.source_chunk_id = c.id
+    WHERE c.session_slug = ?
+      AND e.vector_clock IS NOT NULL
+  `).all(projectSlug);
+    for (const row of rows) {
+        if (!row.vector_clock)
+            continue;
+        const edgeClock = deserialize(row.vector_clock);
+        const hops = hopCount(edgeClock, refClock);
+        distribution.set(hops, (distribution.get(hops) ?? 0) + 1);
+    }
+    return distribution;
+}
+/**
+ * Force refresh the reference clock by merging all agent clocks.
+ * Useful after data recovery or manual edits.
+ *
+ * @param projectSlug - Project identifier
+ * @returns The refreshed reference clock
+ */
+export function refreshReferenceClock(projectSlug) {
+    const agentClocks = getAllAgentClocks(projectSlug);
+    const refClock = {};
+    for (const [, clock] of agentClocks) {
+        for (const [agentId, ticks] of Object.entries(clock)) {
+            refClock[agentId] = Math.max(refClock[agentId] ?? 0, ticks);
+        }
+    }
+    setReferenceClock(projectSlug, refClock);
+    return refClock;
+}
+//# sourceMappingURL=clock-compactor.js.map