Clear Thought 1.5

/** * PDR Knowledge Graph Implementation * In-memory graph with hierarchical + network structure */ export class PDRKnowledgeGraph { constructor(sessionId, mode = "standard") { this.sessionId = sessionId; this.mode = mode; this.nodes = new Map(); this.edges = new Map(); this.edgesBySource = new Map(); this.hierarchy = { root: "", levels: new Map(), parentChild: new Map(), }; this.clusters = new Map(); this.metrics = { nodeCount: 0, edgeCount: 0, avgDegree: 0, maxDepth: 0, clusterCount: 0, gaps: [], }; } get limits() { return PDRKnowledgeGraph.LIMITS[this.mode]; } createNode(data) { // Enforce resource limits if (this.nodes.size >= this.limits.nodes) { throw new Error(`Maximum node limit (${this.limits.nodes}) reached for mode ${this.mode}`); } if (data.depth && data.depth > this.limits.depth) { throw new Error(`Maximum depth (${this.limits.depth}) exceeded`); } // Generate ID const id = `node-${Date.now()}-${Math.random().toString(36).substr(2, 9)}`; const node = { id, content: data.content || "", type: data.type || "subject", depth: data.depth || 0, parentId: data.parentId, childrenIds: new Set(data.childrenIds || []), incomingEdges: new Set(), outgoingEdges: new Set(), scores: { confidence: data.scores?.confidence || 0.5, centrality: 0, passScores: new Map(), }, metadata: { createdInPass: data.metadata?.createdInPass || "initial", lastModified: new Date().toISOString(), tags: new Set(data.metadata?.tags || []), patternUsed: data.metadata?.patternUsed, selected: false, }, artifacts: data.artifacts, }; this.nodes.set(id, node); // Update hierarchy if (node.parentId && this.nodes.has(node.parentId)) { const parent = this.nodes.get(node.parentId); parent.childrenIds.add(id); if (!this.hierarchy.parentChild.has(node.parentId)) { this.hierarchy.parentChild.set(node.parentId, []); } this.hierarchy.parentChild.get(node.parentId)?.push(id); } // Update depth levels if (!this.hierarchy.levels.has(node.depth)) { this.hierarchy.levels.set(node.depth, new Set()); } this.hierarchy.levels.get(node.depth)?.add(id); // Set root if first node if (this.nodes.size === 1) { this.hierarchy.root = id; } // Update metrics this.metrics.nodeCount = this.nodes.size; this.metrics.maxDepth = Math.max(this.metrics.maxDepth, node.depth); return id; } addEdge(data) { // Enforce resource limits if (this.edges.size >= this.limits.edges) { throw new Error(`Maximum edge limit (${this.limits.edges}) reached for mode ${this.mode}`); } // Validate nodes exist if (!data.sourceId || !data.targetId) { throw new Error("Source and target IDs are required"); } if (!this.nodes.has(data.sourceId) || !this.nodes.has(data.targetId)) { throw new Error("Source or target node does not exist"); } // Validate weight if (data.weight !== undefined && (data.weight < 0 || data.weight > 1)) { throw new Error("Edge weight must be between 0 and 1"); } const id = `edge-${Date.now()}-${Math.random().toString(36).substr(2, 9)}`; const edge = { id, sourceId: data.sourceId, targetId: data.targetId, type: data.type || "relates-to", weight: data.weight || 0.5, metadata: { createdInPass: data.metadata?.createdInPass || "initial", confidence: data.metadata?.confidence || 0.5, justification: data.metadata?.justification, bidirectional: data.metadata?.bidirectional || false, }, }; // Store edge this.edges.set(id, edge); // Update source index if (!this.edgesBySource.has(edge.sourceId)) { this.edgesBySource.set(edge.sourceId, new Set()); } this.edgesBySource.get(edge.sourceId)?.add(id); // Update node references this.nodes.get(edge.sourceId)?.outgoingEdges.add(id); this.nodes.get(edge.targetId)?.incomingEdges.add(id); // Handle bidirectional edges if (edge.metadata.bidirectional) { this.nodes.get(edge.targetId)?.outgoingEdges.add(id); this.nodes.get(edge.sourceId)?.incomingEdges.add(id); } // Update metrics this.metrics.edgeCount = this.edges.size; this.updateAverageDegree(); return id; } updateAverageDegree() { if (this.nodes.size === 0) { this.metrics.avgDegree = 0; return; } let totalDegree = 0; this.nodes.forEach((node) => { totalDegree += node.incomingEdges.size + node.outgoingEdges.size; }); this.metrics.avgDegree = totalDegree / this.nodes.size; } // Query methods getNode(nodeId) { return this.nodes.get(nodeId); } getEdge(edgeId) { return this.edges.get(edgeId); } getAllNodes() { return Array.from(this.nodes.values()); } getAllEdges() { return Array.from(this.edges.values()); } getOutgoingEdges(nodeId) { const node = this.nodes.get(nodeId); if (!node) return []; return Array.from(node.outgoingEdges) .map((edgeId) => this.edges.get(edgeId)) .filter((edge) => edge !== undefined); } getIncomingEdges(nodeId) { const node = this.nodes.get(nodeId); if (!node) return []; return Array.from(node.incomingEdges) .map((edgeId) => this.edges.get(edgeId)) .filter((edge) => edge !== undefined); } getEdgesByType(type) { return Array.from(this.edges.values()).filter((edge) => edge.type === type); } hasNode(nodeId) { return this.nodes.has(nodeId); } hasEdgeBetween(nodeId1, nodeId2) { const edges1 = this.getOutgoingEdges(nodeId1); return edges1.some((edge) => edge.targetId === nodeId2); } // Modification methods updateNode(nodeId, updates) { const node = this.nodes.get(nodeId); if (!node) throw new Error(`Node ${nodeId} not found`); // Update allowed fields if (updates.content !== undefined) node.content = updates.content; if (updates.type !== undefined) node.type = updates.type; if (updates.scores) { Object.assign(node.scores, updates.scores); } if (updates.metadata) { Object.assign(node.metadata, updates.metadata); node.metadata.lastModified = new Date().toISOString(); } if (updates.artifacts) { node.artifacts = { ...node.artifacts, ...updates.artifacts }; } } markSelected(nodeId, selected) { const node = this.nodes.get(nodeId); if (node) { node.metadata.selected = selected; } } getSelectedNodes() { return Array.from(this.nodes.values()).filter((node) => node.metadata.selected); } // Cluster management setClusters(clusters) { this.clusters = clusters; this.metrics.clusterCount = clusters.size; } getClusters() { return this.clusters; } getCluster(clusterId) { return this.clusters.get(clusterId); } // Centrality update updateCentrality(centrality) { centrality.forEach((score, nodeId) => { const node = this.nodes.get(nodeId); if (node) { node.scores.centrality = score; } }); } // Gap tracking setGaps(gaps) { this.metrics.gaps = gaps; } getGaps() { return this.metrics.gaps; } // Metrics getMetrics() { return { ...this.metrics }; } getNodeCount() { return this.nodes.size; } getEdgeCount() { return this.edges.size; } // Serialization serialize() { return JSON.stringify({ sessionId: this.sessionId, mode: this.mode, nodes: Array.from(this.nodes.entries()).map(([id, node]) => [ id, { ...node, childrenIds: Array.from(node.childrenIds), incomingEdges: Array.from(node.incomingEdges), outgoingEdges: Array.from(node.outgoingEdges), metadata: { ...node.metadata, tags: Array.from(node.metadata.tags), }, scores: { ...node.scores, passScores: Array.from(node.scores.passScores.entries()), }, }, ]), edges: Array.from(this.edges.entries()), edgesBySource: Array.from(this.edgesBySource.entries()).map(([k, v]) => [ k, Array.from(v), ]), hierarchy: { ...this.hierarchy, levels: Array.from(this.hierarchy.levels.entries()).map(([k, v]) => [ k, Array.from(v), ]), }, clusters: Array.from(this.clusters.entries()).map(([id, cluster]) => [ id, { ...cluster, nodeIds: Array.from(cluster.nodeIds), }, ]), metrics: this.metrics, }); } static deserialize(data) { const parsed = JSON.parse(data); const graph = new PDRKnowledgeGraph(parsed.sessionId, parsed.mode); // Restore nodes parsed.nodes.forEach(([id, nodeData]) => { const node = { ...nodeData, childrenIds: new Set(nodeData.childrenIds), incomingEdges: new Set(nodeData.incomingEdges), outgoingEdges: new Set(nodeData.outgoingEdges), metadata: { ...nodeData.metadata, tags: new Set(nodeData.metadata.tags), }, scores: { ...nodeData.scores, passScores: new Map(nodeData.scores.passScores), }, }; graph.nodes.set(id, node); }); // Restore edges parsed.edges.forEach(([id, edge]) => { graph.edges.set(id, edge); }); // Restore indices parsed.edgesBySource.forEach(([k, v]) => { graph.edgesBySource.set(k, new Set(v)); }); // Restore hierarchy graph.hierarchy = { ...parsed.hierarchy, levels: new Map(parsed.hierarchy.levels.map(([k, v]) => [ k, new Set(v), ])), }; // Restore clusters parsed.clusters.forEach(([id, clusterData]) => { graph.clusters.set(id, { ...clusterData, nodeIds: new Set(clusterData.nodeIds), }); }); graph.metrics = parsed.metrics; return graph; } getMode() { return this.mode; } getSessionId() { return this.sessionId; } getResourceLimits() { return PDRKnowledgeGraph.LIMITS[this.mode]; } removeNode(nodeId) { const node = this.nodes.get(nodeId); if (!node) return false; // Remove all edges connected to this node const edgesToRemove = [ ...this.getIncomingEdges(nodeId), ...this.getOutgoingEdges(nodeId), ]; edgesToRemove.forEach((edge) => this.removeEdge(edge.id)); // Remove from parent's children if (node.parentId) { const parent = this.nodes.get(node.parentId); if (parent) { parent.childrenIds.delete(nodeId); } } // Remove node this.nodes.delete(nodeId); return true; } removeEdge(edgeId) { return this.edges.delete(edgeId); } } // Resource limits based on Node.js/V8 constraints PDRKnowledgeGraph.LIMITS = { development: { nodes: 500, edges: 2500, depth: 8, targetMemoryMB: 10, }, standard: { nodes: 5000, edges: 25000, depth: 10, targetMemoryMB: 50, }, extended: { nodes: 20000, edges: 100000, depth: 12, targetMemoryMB: 200, }, cloud: { nodes: 50000, edges: 250000, depth: 15, targetMemoryMB: 500, requiresFlag: "--max-old-space-size=2048", }, };