@vinaes/succ 1.3.31 → 1.5.37

package/dist/lib/graph/graphology-bridge.js

@@ -0,0 +1,488 @@
+/**
+ * graphology integration for advanced graph algorithms.
+ *
+ * Provides: Personalized PageRank, Louvain communities, Dijkstra shortest path,
+ * articulation points, betweenness centrality, and PageRank.
+ *
+ * Loads memory links from StorageBackend into an in-memory graphology graph,
+ * runs algorithms, and returns results. Graph is cached and invalidated
+ * when links change.
+ */
+import { DirectedGraph } from 'graphology';
+import louvain from 'graphology-communities-louvain';
+import pagerank from 'graphology-metrics/centrality/pagerank.js';
+import betweennessCentrality from 'graphology-metrics/centrality/betweenness.js';
+import { bidirectional as dijkstraBidirectional } from 'graphology-shortest-path/dijkstra.js';
+import { getAllMemoryLinksForExport, getAllMemoriesForExport } from '../storage/index.js';
+import { getProjectRoot } from '../config.js';
+import { logInfo } from '../fault-logger.js';
+// Cache keyed by project root path so different projects never share a cached graph.
+const graphCache = new Map();
+const CACHE_TTL_MS = 5 * 60 * 1000; // 5 minutes
+/** Safe project key — falls back to '__default__' when no project is configured. */
+function safeProjectKey() {
+    try {
+        return getProjectRoot();
+    }
+    catch {
+        return '__default__';
+    }
+}
+/**
+ * Get or build the in-memory graphology graph from storage.
+ * Caches the graph per-project for CACHE_TTL_MS to avoid repeated DB reads.
+ */
+export async function getGraph(forceRefresh = false) {
+    const projectKey = safeProjectKey();
+    const now = Date.now();
+    const cached = graphCache.get(projectKey);
+    if (cached && !forceRefresh && now - cached.timestamp < CACHE_TTL_MS) {
+        return cached.graph;
+    }
+    // Use DirectedGraph so that directional relationships (A→B vs B→A) and
+    // multi-relational edges between the same pair of memories are preserved.
+    // All graph algorithms used here (PageRank, betweenness, Louvain, Dijkstra)
+    // support directed graphs.
+    const graph = new DirectedGraph();
+    // Load all links
+    const links = await getAllMemoryLinksForExport();
+    const memories = await getAllMemoriesForExport();
+    // Add all memory nodes (even isolated ones)
+    for (const mem of memories) {
+        if (!graph.hasNode(String(mem.id))) {
+            graph.addNode(String(mem.id), {
+                memoryId: mem.id,
+                content: mem.content?.slice(0, 200),
+                type: mem.type,
+            });
+        }
+    }
+    // Add edges
+    for (const link of links) {
+        const sourceKey = String(link.source_id);
+        const targetKey = String(link.target_id);
+        // Ensure nodes exist
+        if (!graph.hasNode(sourceKey)) {
+            graph.addNode(sourceKey, { memoryId: link.source_id });
+        }
+        if (!graph.hasNode(targetKey)) {
+            graph.addNode(targetKey, { memoryId: link.target_id });
+        }
+        // Add directed edge; skip if an edge with the same source, target, and relation
+        // already exists to avoid inflating weights. DirectedGraph only supports one edge
+        // per (source, target) pair, so multi-relational A→B edges (same pair, different
+        // relation) are deduplicated here — the first-encountered relation wins.
+        if (!graph.hasDirectedEdge(sourceKey, targetKey)) {
+            graph.addDirectedEdge(sourceKey, targetKey, {
+                weight: link.weight ?? 1.0,
+                relation: link.relation ?? 'related',
+            });
+        }
+    }
+    graphCache.set(projectKey, { graph, timestamp: now });
+    logInfo('graphology', `Graph loaded: ${graph.order} nodes, ${graph.size} edges`);
+    return graph;
+}
+/**
+ * Invalidate the graph cache for the current project (call after link mutations).
+ */
+export function invalidateGraphCache() {
+    const projectKey = safeProjectKey();
+    graphCache.delete(projectKey);
+}
+// ============================================================================
+// Personalized PageRank (PPR)
+// ============================================================================
+/**
+ * Run Personalized PageRank from seed nodes.
+ *
+ * PPR biases the random walk to restart at seed nodes, making it
+ * discover nodes that are structurally relevant to the seeds.
+ * This is SOTA for graph-enhanced retrieval (HippoRAG2: 95% accuracy).
+ *
+ * @param seedNodeIds - Memory IDs to seed from (e.g., top-k search results)
+ * @param topK - Number of top PPR-scored nodes to return
+ * @param alpha - Restart probability (default: 0.85 — standard PageRank value)
+ * @returns Sorted array of { memoryId, score } pairs
+ */
+export async function personalizedPageRank(seedNodeIds, topK = 20, alpha = 0.85) {
+    const graph = await getGraph();
+    if (graph.order === 0)
+        return [];
+    // Build personalization vector: uniform over seed nodes
+    const validSeeds = seedNodeIds.filter((id) => graph.hasNode(String(id)));
+    if (validSeeds.length === 0)
+        return [];
+    // graphology's pagerank doesn't natively support personalization vector,
+    // so we implement PPR using power iteration manually
+    const pprScores = computePPR(graph, validSeeds.map(String), alpha, 50);
+    // Convert to sorted array
+    const results = [];
+    for (const [nodeKey, score] of pprScores.entries()) {
+        const memId = parseInt(nodeKey, 10);
+        if (!isNaN(memId)) {
+            results.push({ memoryId: memId, score });
+        }
+    }
+    results.sort((a, b) => b.score - a.score);
+    return results.slice(0, topK);
+}
+/**
+ * Power iteration for Personalized PageRank.
+ *
+ * PPR(v) = (1-alpha) * personalization(v) + alpha * sum(PPR(u) * w(u,v) / deg(u))
+ */
+function computePPR(graph, seedNodes, alpha, maxIterations) {
+    const n = graph.order;
+    if (n === 0)
+        return new Map();
+    // Initialize personalization vector
+    const personalization = new Map();
+    const seedWeight = 1.0 / seedNodes.length;
+    for (const seed of seedNodes) {
+        if (graph.hasNode(seed)) {
+            personalization.set(seed, seedWeight);
+        }
+    }
+    // Initialize scores uniformly
+    let scores = new Map();
+    const initScore = 1.0 / n;
+    graph.forEachNode((node) => {
+        scores.set(node, initScore);
+    });
+    // Precompute weighted out-degrees for all nodes (O(E) total, done once).
+    // In a directed graph, a node distributes its score along its OUT-edges,
+    // so we sum weights over outgoing edges only.
+    const weightedDegrees = new Map();
+    graph.forEachNode((node) => {
+        let wDeg = 0;
+        graph.forEachOutEdge(node, (_edge, attr) => {
+            wDeg += attr.weight ?? 1.0;
+        });
+        weightedDegrees.set(node, wDeg);
+    });
+    // Identify dangling nodes (zero weighted degree) — their mass must be redistributed
+    // to prevent score mass from collapsing each iteration.
+    const danglingNodes = [];
+    graph.forEachNode((node) => {
+        if ((weightedDegrees.get(node) ?? 0) === 0) {
+            danglingNodes.push(node);
+        }
+    });
+    // Power iteration
+    for (let iter = 0; iter < maxIterations; iter++) {
+        const newScores = new Map();
+        let diff = 0;
+        // Collect dangling mass — redistribute uniformly across all nodes
+        let danglingMass = 0;
+        for (const d of danglingNodes) {
+            danglingMass += scores.get(d) ?? 0;
+        }
+        const danglingShare = (alpha * danglingMass) / n;
+        graph.forEachNode((node) => {
+            // Contribution from in-neighbors (nodes that have an out-edge pointing TO this node).
+            // PPR formula: score(v) ← sum over u where u→v exists of: score(u) * w(u,v) / outDeg(u)
+            let neighborContrib = 0;
+            graph.forEachInNeighbor(node, (neighbor) => {
+                const wDeg = weightedDegrees.get(neighbor) ?? 0;
+                if (wDeg > 0) {
+                    // Edge runs neighbor → node (confirmed by forEachInNeighbor)
+                    const edgeWeight = graph.hasDirectedEdge(neighbor, node)
+                        ? (graph.getEdgeAttribute(graph.directedEdge(neighbor, node), 'weight') ?? 1.0)
+                        : 1.0;
+                    neighborContrib += ((scores.get(neighbor) ?? 0) * edgeWeight) / wDeg;
+                }
+            });
+            // PPR formula: (1-alpha) * personalization + alpha * neighbor_contrib + dangling_share
+            const p = personalization.get(node) ?? 0;
+            const newScore = (1 - alpha) * p + alpha * neighborContrib + danglingShare;
+            newScores.set(node, newScore);
+            diff += Math.abs(newScore - (scores.get(node) ?? 0));
+        });
+        scores = newScores;
+        // Early convergence
+        if (diff < 1e-8)
+            break;
+    }
+    return scores;
+}
+/**
+ * Detect communities using Louvain modularity optimization.
+ * Superior to Label Propagation — produces higher-quality communities.
+ *
+ * @returns Communities sorted by size (largest first)
+ */
+export async function detectLouvainCommunities(minSize = 2) {
+    const graph = await getGraph();
+    if (graph.order === 0) {
+        return { communities: [], modularity: 0, isolated: 0 };
+    }
+    // Run Louvain with detailed output (includes modularity)
+    const detailed = louvain.detailed(graph, {
+        getEdgeWeight: 'weight',
+        resolution: 1.0,
+    });
+    const communities = detailed.communities;
+    const modularity = detailed.modularity;
+    // Group by community
+    const communityMap = new Map();
+    for (const [nodeKey, communityId] of Object.entries(communities)) {
+        const memId = parseInt(nodeKey, 10);
+        if (isNaN(memId))
+            continue;
+        const members = communityMap.get(communityId) ?? [];
+        members.push(memId);
+        communityMap.set(communityId, members);
+    }
+    // Build result
+    const result = [];
+    let isolated = 0;
+    let nextId = 0;
+    for (const [, members] of communityMap) {
+        if (members.length < minSize) {
+            isolated += members.length;
+        }
+        else {
+            result.push({
+                id: nextId++,
+                size: members.length,
+                members: members.sort((a, b) => a - b),
+            });
+        }
+    }
+    result.sort((a, b) => b.size - a.size);
+    return { communities: result, modularity, isolated };
+}
+// ============================================================================
+// Shortest Path (Dijkstra)
+// ============================================================================
+/**
+ * Convert edge similarity weight (higher = stronger relation) to distance
+ * cost (lower = closer) for Dijkstra. Avoids zero/negative/non-finite costs.
+ *
+ * Only guards the lower bound and non-finite values — weights above 1.0 are
+ * intentionally preserved so that Dijkstra and betweenness centrality can
+ * distinguish between links of different strengths. Clamping to 1.0 would
+ * collapse all high-weight edges to an identical cost of 1.0 and lose ordering.
+ */
+function similarityToDistance(_edge, attr) {
+    const raw = typeof attr.weight === 'number' ? attr.weight : 1.0;
+    const safe = Number.isFinite(raw) && raw > 0 ? raw : 0.01;
+    return 1.0 / safe;
+}
+/**
+ * Find shortest path between two memories using Dijkstra.
+ * Edge weights in the graph represent similarity/strength (higher = stronger).
+ * Dijkstra needs cost/distance (lower = closer), so weights are inverted
+ * via 1/weight before path-finding.
+ *
+ * @returns Path as array of memory IDs, or null if no path exists
+ */
+export async function shortestPath(fromId, toId) {
+    const graph = await getGraph();
+    const fromKey = String(fromId);
+    const toKey = String(toId);
+    if (!graph.hasNode(fromKey) || !graph.hasNode(toKey)) {
+        return null;
+    }
+    const pathNodes = dijkstraBidirectional(graph, fromKey, toKey, similarityToDistance);
+    if (!pathNodes || pathNodes.length === 0)
+        return null;
+    // Calculate total original weight (similarity, not distance)
+    let totalWeight = 0;
+    for (let i = 0; i < pathNodes.length - 1; i++) {
+        const edge = graph.edge(pathNodes[i], pathNodes[i + 1]);
+        if (edge) {
+            totalWeight += graph.getEdgeAttribute(edge, 'weight') ?? 1.0;
+        }
+    }
+    return {
+        path: pathNodes.map((n) => parseInt(n, 10)),
+        weight: totalWeight,
+    };
+}
+// ============================================================================
+// Articulation Points (Critical Nodes)
+// ============================================================================
+/**
+ * Find articulation points — nodes whose removal disconnects the graph.
+ * These are "load-bearing" memories, architectural bottlenecks.
+ *
+ * Uses Tarjan's algorithm (O(V+E)).
+ *
+ * @returns Array of memory IDs that are articulation points
+ */
+export async function getArticulationPoints() {
+    const graph = await getGraph();
+    if (graph.order < 3)
+        return [];
+    return findArticulationPointsTarjan(graph)
+        .map((n) => parseInt(n, 10))
+        .filter((id) => !isNaN(id));
+}
+/**
+ * Tarjan's algorithm for finding articulation points in an undirected graph.
+ * A node is an articulation point if:
+ * 1. It is the root of the DFS tree and has 2+ children, OR
+ * 2. It is not root and has a child with no back-edge above it (low[child] >= disc[node])
+ */
+function findArticulationPointsTarjan(graph) {
+    const disc = new Map();
+    const low = new Map();
+    const parent = new Map();
+    const childCount = new Map();
+    const ap = new Set();
+    let time = 0;
+    // Iterative DFS to avoid stack overflow on large graphs
+    function dfsIterative(root) {
+        const stack = [];
+        disc.set(root, time);
+        low.set(root, time);
+        time++;
+        childCount.set(root, 0);
+        const rootNeighbors = graph.neighbors(root);
+        stack.push({ node: root, idx: 0, neighbors: rootNeighbors });
+        while (stack.length > 0) {
+            const frame = stack[stack.length - 1];
+            const u = frame.node;
+            if (frame.idx < frame.neighbors.length) {
+                const v = frame.neighbors[frame.idx];
+                frame.idx++;
+                if (!disc.has(v)) {
+                    // Tree edge
+                    parent.set(v, u);
+                    childCount.set(u, (childCount.get(u) ?? 0) + 1);
+                    disc.set(v, time);
+                    low.set(v, time);
+                    time++;
+                    childCount.set(v, 0);
+                    const vNeighbors = graph.neighbors(v);
+                    stack.push({ node: v, idx: 0, neighbors: vNeighbors });
+                }
+                else if (v !== parent.get(u)) {
+                    // Back edge
+                    low.set(u, Math.min(low.get(u), disc.get(v)));
+                }
+            }
+            else {
+                // All neighbors processed — pop and update parent
+                stack.pop();
+                if (stack.length > 0) {
+                    const parentFrame = stack[stack.length - 1];
+                    const pu = parentFrame.node;
+                    low.set(pu, Math.min(low.get(pu), low.get(u)));
+                    // Root with 2+ children
+                    if (parent.get(pu) === null && (childCount.get(pu) ?? 0) > 1) {
+                        ap.add(pu);
+                    }
+                    // Non-root with child that can't reach above
+                    if (parent.get(pu) !== null && low.get(u) >= disc.get(pu)) {
+                        ap.add(pu);
+                    }
+                }
+            }
+        }
+    }
+    graph.forEachNode((node) => {
+        if (!disc.has(node)) {
+            parent.set(node, null);
+            dfsIterative(node);
+        }
+    });
+    return [...ap];
+}
+// ============================================================================
+// PageRank (Global Importance)
+// ============================================================================
+/**
+ * Compute global PageRank for all nodes.
+ * Higher-ranked memories are more "important" (more connections, central position).
+ *
+ * @returns Map of memoryId → PageRank score (0-1)
+ */
+export async function computePageRank() {
+    const graph = await getGraph();
+    if (graph.order === 0)
+        return new Map();
+    const scores = pagerank(graph, {
+        alpha: 0.85,
+        maxIterations: 100,
+        tolerance: 1e-6,
+        getEdgeWeight: 'weight',
+    });
+    const result = new Map();
+    graph.forEachNode((node) => {
+        const memId = parseInt(node, 10);
+        if (!isNaN(memId)) {
+            result.set(memId, scores[node] ?? 0);
+        }
+    });
+    return result;
+}
+// ============================================================================
+// Betweenness Centrality
+// ============================================================================
+/**
+ * Compute betweenness centrality for all nodes.
+ * Nodes with high betweenness sit on many shortest paths — they're "bridges"
+ * between different parts of the knowledge graph.
+ *
+ * @returns Map of memoryId → betweenness score (0-1 normalized)
+ */
+export async function computeBetweennessCentrality() {
+    const graph = await getGraph();
+    if (graph.order === 0)
+        return new Map();
+    const scores = betweennessCentrality(graph, {
+        getEdgeWeight: similarityToDistance,
+        normalized: true,
+    });
+    const result = new Map();
+    graph.forEachNode((node) => {
+        const memId = parseInt(node, 10);
+        if (!isNaN(memId)) {
+            result.set(memId, scores[node] ?? 0);
+        }
+    });
+    return result;
+}
+// ============================================================================
+// Why Related (Explain Path)
+// ============================================================================
+/**
+ * Explain why two memories are related by finding the shortest path
+ * and returning the relationship chain with edge types.
+ */
+export async function whyRelated(fromId, toId) {
+    const graph = await getGraph();
+    const fromKey = String(fromId);
+    const toKey = String(toId);
+    if (!graph.hasNode(fromKey) || !graph.hasNode(toKey)) {
+        return null;
+    }
+    const pathNodes = dijkstraBidirectional(graph, fromKey, toKey, similarityToDistance);
+    if (!pathNodes || pathNodes.length === 0) {
+        return { connected: false, path: [], distance: Number.MAX_SAFE_INTEGER };
+    }
+    const path = [];
+    let totalWeight = 0;
+    for (let i = 0; i < pathNodes.length; i++) {
+        const memId = parseInt(pathNodes[i], 10);
+        let relation;
+        if (i < pathNodes.length - 1) {
+            const edge = graph.edge(pathNodes[i], pathNodes[i + 1]);
+            if (edge) {
+                relation = graph.getEdgeAttribute(edge, 'relation');
+                const w = graph.getEdgeAttribute(edge, 'weight');
+                totalWeight += Number.isFinite(w) ? w : 1.0;
+            }
+        }
+        path.push({ memoryId: memId, relation });
+    }
+    return {
+        connected: true,
+        path,
+        distance: totalWeight, // Cumulative edge similarity (higher = stronger connection)
+    };
+}
+//# sourceMappingURL=graphology-bridge.js.map

package/dist/lib/graph/graphology-bridge.js.map

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package/dist/lib/graph/llm-relations.d.ts.map

@@ -1 +1 @@
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package/dist/lib/graph/llm-relations.js

@@ -10,45 +10,9 @@
 import { callLLM } from '../llm.js';
 import { LINK_RELATIONS } from '../storage/types.js';
 import { getAllMemoryLinksForExport, getMemoryById, updateMemoryLink, getMemoryLinks, } from '../storage/index.js';
-// ============================================================================
-// Relation Classification
-// ============================================================================
-const CLASSIFY_PROMPT_SINGLE = `Given two memories from a knowledge base, determine their relationship.
-
-Memory A (type: {typeA}): {contentA}
-
-Memory B (type: {typeB}): {contentB}
-
-Choose ONE relation from: caused_by, leads_to, contradicts, implements, supersedes, references, related, similar_to
-
-Rules:
-- caused_by: A was caused by or resulted from B
-- leads_to: A leads to or enables B
-- contradicts: A and B conflict or disagree
-- implements: A is an implementation/action based on B (a decision)
-- supersedes: A replaces or updates B
-- references: A mentions or cites B
-- related: connected but none of the above fit
-- similar_to: nearly identical content (keep only if truly duplicate-like)
-
-Reply with ONLY valid JSON: {"relation": "...", "confidence": 0.0-1.0}`;
-const CLASSIFY_PROMPT_BATCH = `Given pairs of memories from a knowledge base, determine the relationship for each pair.
-
-{pairs}
-
-For each pair, choose ONE relation from: caused_by, leads_to, contradicts, implements, supersedes, references, related, similar_to
-
-Rules:
-- caused_by: A was caused by or resulted from B
-- leads_to: A leads to or enables B
-- contradicts: A and B conflict or disagree
-- implements: A is an implementation/action based on B (a decision)
-- supersedes: A replaces or updates B
-- references: A mentions or cites B
-- related: connected but none of the above fit
-- similar_to: nearly identical content (keep only if truly duplicate-like)
-
-Reply with ONLY a valid JSON array: [{"pair": 1, "relation": "...", "confidence": 0.0-1.0}, ...]`;
+import { logWarn } from '../fault-logger.js';
+import { invalidateGraphCache } from './graphology-bridge.js';
+import { CLASSIFY_SYSTEM, CLASSIFY_PROMPT_SINGLE, CLASSIFY_PROMPT_BATCH, } from '../../prompts/index.js';
 /**
  * Classify the relation between two memories using LLM.
  */
@@ -58,10 +22,17 @@ export async function classifyRelation(memoryA, memoryB) {
         .replace('{typeB}', memoryB.type)
         .replace('{contentB}', memoryB.content.substring(0, 500));
     try {
-        const response = await callLLM(prompt, { maxTokens: 100, temperature: 0.1 });
+        const response = await callLLM(prompt, {
+            maxTokens: 100,
+            temperature: 0.1,
+            systemPrompt: CLASSIFY_SYSTEM,
+        });
         return parseClassifyResponse(response);
     }
-    catch {
+    catch (error) {
+        logWarn('llm-relations', 'LLM call failed for single relation classification', {
+            error: error instanceof Error ? error.message : String(error),
+        });
         return { relation: 'similar_to', confidence: 0 };
     }
 }
@@ -84,10 +55,14 @@ export async function classifyRelationsBatch(pairs) {
         const response = await callLLM(prompt, {
             maxTokens: 50 * pairs.length,
             temperature: 0.1,
+            systemPrompt: CLASSIFY_SYSTEM,
         });
         return parseBatchResponse(response, pairs);
     }
-    catch {
+    catch (error) {
+        logWarn('llm-relations', 'LLM call failed for batch relation classification', {
+            error: error instanceof Error ? error.message : String(error),
+        });
         // Fallback: keep all as similar_to
         return pairs.map((p) => ({
             linkId: p.linkId,
@@ -134,7 +109,10 @@ export async function enrichExistingLinks(options = {}) {
                         try {
                             return JSON.parse(mem.tags);
                         }
-                        catch {
+                        catch (error) {
+                            logWarn('llm-relations', 'Failed to parse memory tags JSON string for relation enrichment', {
+                                error: error instanceof Error ? error.message : String(error),
+                            });
                             return [];
                         }
                     })()
@@ -190,6 +168,11 @@ export async function enrichExistingLinks(options = {}) {
             }
         }
     }
+    // Invalidate the graph cache once after all link mutations so that subsequent
+    // graph algorithm calls (PPR, betweenness, etc.) see the updated relations.
+    if (enriched > 0 || failed > 0) {
+        invalidateGraphCache();
+    }
     return { enriched, failed, skipped };
 }
 /**
@@ -220,7 +203,10 @@ function parseClassifyResponse(response) {
         const confidence = typeof parsed.confidence === 'number' ? Math.max(0, Math.min(1, parsed.confidence)) : 0.5;
         return { relation, confidence };
     }
-    catch {
+    catch (error) {
+        logWarn('llm-relations', 'Failed to parse classify JSON response', {
+            error: error instanceof Error ? error.message : String(error),
+        });
         return { relation: 'similar_to', confidence: 0 };
     }
 }
@@ -247,7 +233,10 @@ function parseBatchResponse(response, pairs) {
             };
         });
     }
-    catch {
+    catch (error) {
+        logWarn('llm-relations', 'Failed to parse batch classify JSON response', {
+            error: error instanceof Error ? error.message : String(error),
+        });
         return pairs.map((p) => ({
             linkId: p.linkId,
             relation: 'similar_to',