@omiron33/omi-neuron-web 0.1.0

package/dist/chunk-RQCGONPN.js.map

@@ -0,0 +1 @@
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type {\n  EventHandler,\n  EventSubscription,\n  EventSource,\n  NeuronEvent,\n  NeuronEventEmitter,\n  NeuronEventType,\n} from '../types/events';\n\nexport type EventMiddleware = (event: NeuronEvent, next: () => void | Promise<void>) =>\n  | void\n  | Promise<void>;\n\nexport class EventBus implements NeuronEventEmitter {\n  private subscribers = new Map<NeuronEventType, Set<EventHandler>>();\n  private globalSubscribers = new Set<EventHandler>();\n  private middleware: EventMiddleware[] = [];\n  private history: NeuronEvent[] = [];\n  private historyLimit = 200;\n\n  emit<T>(event: NeuronEvent<T>): void {\n    void this.emitAsync(event);\n  }\n\n  async emitAsync<T>(event: NeuronEvent<T>): Promise<void> {\n    await this.runMiddleware(event, async () => {\n      this.recordEvent(event);\n      const handlers = this.subscribers.get(event.type);\n      if (handlers) {\n        for (const handler of handlers) {\n          await handler(event);\n        }\n      }\n      for (const handler of this.globalSubscribers) {\n        await handler(event);\n      }\n    });\n  }\n\n  subscribe<T>(type: NeuronEventType, handler: EventHandler<T>): EventSubscription {\n    if (!this.subscribers.has(type)) {\n      this.subscribers.set(type, new Set());\n    }\n    this.subscribers.get(type)!.add(handler as EventHandler);\n    return {\n      unsubscribe: () => this.unsubscribe(type, handler as EventHandler),\n    };\n  }\n\n  subscribeMany(types: NeuronEventType[], handler: EventHandler): EventSubscription {\n    types.forEach((type) => this.subscribe(type, handler));\n    return {\n      unsubscribe: () => types.forEach((type) => this.unsubscribe(type, handler)),\n    };\n  }\n\n  subscribeAll(handler: EventHandler<unknown>): EventSubscription {\n    this.globalSubscribers.add(handler as EventHandler);\n    return {\n      unsubscribe: () => {\n        this.globalSubscribers.delete(handler as EventHandler);\n      },\n    };\n  }\n\n  unsubscribe(type: NeuronEventType, handler: EventHandler): void {\n    const handlers = this.subscribers.get(type);\n    if (!handlers) return;\n    handlers.delete(handler);\n    if (handlers.size === 0) {\n      this.subscribers.delete(type);\n    }\n  }\n\n  unsubscribeAll(): void {\n    this.subscribers.clear();\n    this.globalSubscribers.clear();\n  }\n\n  use(middleware: EventMiddleware): void {\n    this.middleware.push(middleware);\n  }\n\n  getSubscriberCount(type?: NeuronEventType): number {\n    if (!type) {\n      let count = this.globalSubscribers.size;\n      for (const handlers of this.subscribers.values()) {\n        count += handlers.size;\n      }\n      return count;\n    }\n    return this.subscribers.get(type)?.size ?? 0;\n  }\n\n  getEventHistory(limit?: number): NeuronEvent[] {\n    if (!limit) return [...this.history];\n    return this.history.slice(-limit);\n  }\n\n  clearHistory(): void {\n    this.history = [];\n  }\n\n  private recordEvent(event: NeuronEvent): void {\n    this.history.push(event);\n    if (this.history.length > this.historyLimit) {\n      this.history.shift();\n    }\n  }\n\n  private async runMiddleware(event: NeuronEvent, finalHandler: () => void | Promise<void>) {\n    const stack = [...this.middleware];\n    let index = -1;\n\n    const runner = async (): Promise<void> => {\n      index += 1;\n      if (index < stack.length) {\n        await stack[index](event, runner);\n      } else {\n        await finalHandler();\n      }\n    };\n\n    await runner();\n  }\n}\n\nexport const createEvent = <T>(\n  type: NeuronEventType,\n  payload: T,\n  source: EventSource = 'system'\n): NeuronEvent<T> => ({\n  type,\n  payload,\n  source,\n  timestamp: new Date(),\n});\n","import OpenAI from 'openai';\nimport type { Database } from '../../storage/database';\n\nexport interface EmbeddingsConfig {\n  openaiApiKey: string;\n  model: 'text-embedding-ada-002' | 'text-embedding-3-small' | 'text-embedding-3-large';\n  dimensions?: number;\n  batchSize: number;\n  rateLimit: number;\n  cacheTTL: number;\n  maxRetries: number;\n}\n\nexport interface EmbeddingResult {\n  nodeId: string;\n  embedding: number[];\n  model: string;\n  tokenCount: number;\n  cached: boolean;\n}\n\nexport class EmbeddingsService {\n  private client: OpenAI;\n\n  constructor(private config: EmbeddingsConfig, private db: Database) {\n    this.client = new OpenAI({ apiKey: config.openaiApiKey });\n  }\n\n  async generateEmbedding(text: string): Promise<number[]> {\n    const response = await this.client.embeddings.create({\n      model: this.config.model,\n      input: text,\n      dimensions: this.config.dimensions,\n    });\n    return response.data[0].embedding;\n  }\n\n  async generateBatchEmbeddings(texts: string[]): Promise<number[][]> {\n    const response = await this.client.embeddings.create({\n      model: this.config.model,\n      input: texts,\n      dimensions: this.config.dimensions,\n    });\n    return response.data.map((item) => item.embedding as number[]);\n  }\n\n  async embedNode(nodeId: string): Promise<EmbeddingResult> {\n    const node = await this.db.queryOne<{ id: string; content: string | null; embedding: number[] | null; embedding_generated_at: Date | null; }>(\n      'SELECT id, content, embedding, embedding_generated_at FROM nodes WHERE id = $1',\n      [nodeId]\n    );\n\n    if (!node) {\n      throw new Error(`Node not found: ${nodeId}`);\n    }\n\n    const cached = await this.getCachedEmbedding(nodeId);\n    if (cached) {\n      return {\n        nodeId,\n        embedding: cached,\n        model: this.config.model,\n        tokenCount: this.countTokens(node.content ?? ''),\n        cached: true,\n      };\n    }\n\n    const text = node.content ?? '';\n    const embedding = await this.withRetry(() => this.generateEmbedding(text));\n    await this.cacheEmbedding(nodeId, embedding, this.config.model);\n\n    return {\n      nodeId,\n      embedding,\n      model: this.config.model,\n      tokenCount: this.countTokens(text),\n      cached: false,\n    };\n  }\n\n  async embedNodes(nodeIds: string[]): Promise<{\n    results: EmbeddingResult[];\n    errors: Array<{ nodeId: string; error: string }>;\n  }> {\n    const results: EmbeddingResult[] = [];\n    const errors: Array<{ nodeId: string; error: string }> = [];\n\n    const batches = [];\n    for (let i = 0; i < nodeIds.length; i += this.config.batchSize) {\n      batches.push(nodeIds.slice(i, i + this.config.batchSize));\n    }\n\n    for (const batch of batches) {\n      try {\n        const nodes = await this.db.query<{ id: string; content: string | null }>(\n          'SELECT id, content FROM nodes WHERE id = ANY($1)',\n          [batch]\n        );\n\n        const texts = nodes.map((node) => node.content ?? '');\n        const embeddings = await this.withRetry(() => this.generateBatchEmbeddings(texts));\n\n        for (let idx = 0; idx < nodes.length; idx += 1) {\n          const node = nodes[idx];\n          const embedding = embeddings[idx];\n          await this.cacheEmbedding(node.id, embedding, this.config.model);\n          results.push({\n            nodeId: node.id,\n            embedding,\n            model: this.config.model,\n            tokenCount: this.countTokens(node.content ?? ''),\n            cached: false,\n          });\n        }\n\n        await this.applyRateLimit();\n      } catch (error) {\n        batch.forEach((nodeId) => {\n          errors.push({ nodeId, error: error instanceof Error ? error.message : String(error) });\n        });\n      }\n    }\n\n    return { results, errors };\n  }\n\n  async getCachedEmbedding(nodeId: string): Promise<number[] | null> {\n    const row = await this.db.queryOne<{ embedding: number[] | null; embedding_generated_at: Date | null; embedding_model: string | null }>(\n      'SELECT embedding, embedding_generated_at, embedding_model FROM nodes WHERE id = $1',\n      [nodeId]\n    );\n    if (!row?.embedding) return null;\n\n    if (row.embedding_model !== this.config.model) return null;\n    if (!row.embedding_generated_at) return row.embedding;\n\n    const ageSeconds = (Date.now() - row.embedding_generated_at.getTime()) / 1000;\n    if (ageSeconds > this.config.cacheTTL) return null;\n\n    return row.embedding;\n  }\n\n  async cacheEmbedding(nodeId: string, embedding: number[], model: string): Promise<void> {\n    await this.db.execute(\n      'UPDATE nodes SET embedding = $1, embedding_model = $2, embedding_generated_at = NOW() WHERE id = $3',\n      [embedding, model, nodeId]\n    );\n  }\n\n  async invalidateCache(nodeIds?: string[]): Promise<void> {\n    if (nodeIds?.length) {\n      await this.db.execute(\n        'UPDATE nodes SET embedding = NULL, embedding_model = NULL, embedding_generated_at = NULL WHERE id = ANY($1)',\n        [nodeIds]\n      );\n      return;\n    }\n    await this.db.execute(\n      'UPDATE nodes SET embedding = NULL, embedding_model = NULL, embedding_generated_at = NULL'\n    );\n  }\n\n  countTokens(text: string): number {\n    return Math.ceil(text.length / 4);\n  }\n\n  estimateCost(nodeCount: number): { tokens: number; cost: number } {\n    const tokens = nodeCount * 512;\n    const pricePerMillion = this.config.model === 'text-embedding-3-large'\n      ? 0.13\n      : this.config.model === 'text-embedding-3-small'\n      ? 0.02\n      : 0.1;\n    const cost = (tokens / 1_000_000) * pricePerMillion;\n    return { tokens, cost };\n  }\n\n  private async withRetry<T>(fn: () => Promise<T>): Promise<T> {\n    let attempt = 0;\n    while (attempt <= this.config.maxRetries) {\n      try {\n        return await fn();\n      } catch (error) {\n        attempt += 1;\n        if (attempt > this.config.maxRetries) {\n          throw error;\n        }\n        const delay = 500 * Math.pow(2, attempt);\n        await new Promise((resolve) => setTimeout(resolve, delay));\n      }\n    }\n    throw new Error('Exceeded retry attempts');\n  }\n\n  private async applyRateLimit(): Promise<void> {\n    const delayMs = Math.ceil(60_000 / this.config.rateLimit);\n    await new Promise((resolve) => setTimeout(resolve, delayMs));\n  }\n}\n","import crypto from 'node:crypto';\nimport type { Database } from '../../storage/database';\nimport type { ClusterMembership } from '../types/cluster';\nimport type { NeuronNode } from '../types/node';\nimport type { EmbeddingsService } from './embeddings-service';\n\nexport interface ClusteringConfig {\n  algorithm: 'kmeans' | 'dbscan' | 'hierarchical';\n  clusterCount?: number;\n  minClusterSize?: number;\n  similarityThreshold?: number;\n  epsilon?: number;\n  minSamples?: number;\n}\n\nexport interface ClusteringResult {\n  clusterId: string;\n  label: string;\n  nodeIds: string[];\n  centroid: number[];\n  avgSimilarity: number;\n  cohesion: number;\n}\n\nconst cosineSimilarity = (a: number[], b: number[]): number => {\n  let dot = 0;\n  let magA = 0;\n  let magB = 0;\n  for (let i = 0; i < a.length; i += 1) {\n    dot += a[i] * b[i];\n    magA += a[i] * a[i];\n    magB += b[i] * b[i];\n  }\n  if (magA === 0 || magB === 0) return 0;\n  return dot / (Math.sqrt(magA) * Math.sqrt(magB));\n};\n\nconst averageVector = (vectors: number[][]): number[] => {\n  const length = vectors[0]?.length ?? 0;\n  const sum = new Array(length).fill(0);\n  vectors.forEach((vector) => {\n    vector.forEach((value, idx) => {\n      sum[idx] += value;\n    });\n  });\n  return sum.map((value) => value / vectors.length);\n};\n\nexport class ClusteringEngine {\n  constructor(private db: Database, private embeddings: EmbeddingsService) {}\n\n  async clusterNodes(config: ClusteringConfig): Promise<{ clusters: ClusteringResult[]; unassigned: string[] }> {\n    const nodes = await this.fetchNodesWithEmbeddings();\n    if (nodes.length === 0) return { clusters: [], unassigned: [] };\n\n    let clusters: ClusteringResult[] = [];\n    if (config.algorithm === 'dbscan') {\n      clusters = this.runDbscan(nodes, config);\n    } else {\n      clusters = this.runKmeans(nodes, config);\n    }\n\n    await this.persistClusters(clusters);\n\n    const assigned = new Set(clusters.flatMap((cluster) => cluster.nodeIds));\n    const unassigned = nodes.map((node) => node.id).filter((id) => !assigned.has(id));\n\n    return { clusters, unassigned };\n  }\n\n  async recluster(config: ClusteringConfig): Promise<ClusteringResult[]> {\n    const { clusters } = await this.clusterNodes(config);\n    return clusters;\n  }\n\n  async assignToCluster(nodeId: string): Promise<ClusterMembership | null> {\n    const node = await this.db.queryOne<{ id: string; embedding: number[] | null }>(\n      'SELECT id, embedding FROM nodes WHERE id = $1',\n      [nodeId]\n    );\n    if (!node?.embedding) return null;\n\n    const best = await this.findBestCluster(node.embedding);\n    if (!best) return null;\n\n    await this.db.execute(\n      'INSERT INTO cluster_memberships (node_id, cluster_id, similarity_score, is_primary) VALUES ($1, $2, $3, true) ON CONFLICT (node_id, cluster_id) DO UPDATE SET similarity_score = $3, is_primary = true',\n      [nodeId, best.clusterId, best.similarity]\n    );\n    await this.db.execute('UPDATE nodes SET cluster_id = $1, cluster_similarity = $2 WHERE id = $3', [\n      best.clusterId,\n      best.similarity,\n      nodeId,\n    ]);\n\n    return {\n      nodeId,\n      clusterId: best.clusterId,\n      similarityScore: best.similarity,\n      isPrimary: true,\n      assignedAt: new Date(),\n    };\n  }\n\n  async findBestCluster(embedding: number[]): Promise<{ clusterId: string; similarity: number } | null> {\n    const clusters = await this.db.query<{ id: string; centroid: number[] | null }>(\n      'SELECT id, centroid FROM clusters WHERE centroid IS NOT NULL'\n    );\n    let best: { clusterId: string; similarity: number } | null = null;\n    clusters.forEach((cluster) => {\n      if (!cluster.centroid) return;\n      const similarity = cosineSimilarity(cluster.centroid, embedding);\n      if (!best || similarity > best.similarity) {\n        best = { clusterId: cluster.id, similarity };\n      }\n    });\n    return best;\n  }\n\n  async recomputeCentroid(clusterId: string): Promise<void> {\n    const rows = await this.db.query<{ embedding: number[] | null }>(\n      'SELECT n.embedding FROM nodes n JOIN cluster_memberships cm ON n.id = cm.node_id WHERE cm.cluster_id = $1',\n      [clusterId]\n    );\n    const vectors = rows.map((row) => row.embedding).filter(Boolean) as number[][];\n    if (vectors.length === 0) return;\n    const centroid = averageVector(vectors);\n    await this.db.execute('UPDATE clusters SET centroid = $1, last_recomputed_at = NOW() WHERE id = $2', [\n      centroid,\n      clusterId,\n    ]);\n  }\n\n  async recomputeAllCentroids(): Promise<void> {\n    const clusters = await this.db.query<{ id: string }>('SELECT id FROM clusters');\n    for (const cluster of clusters) {\n      await this.recomputeCentroid(cluster.id);\n    }\n  }\n\n  async generateClusterLabel(clusterId: string): Promise<string> {\n    const rows = await this.db.query<{ label: string }>(\n      'SELECT n.label FROM nodes n JOIN cluster_memberships cm ON n.id = cm.node_id WHERE cm.cluster_id = $1 LIMIT 5',\n      [clusterId]\n    );\n    const label = rows.map((row) => row.label).join(', ');\n    await this.db.execute('UPDATE clusters SET label = $1 WHERE id = $2', [label, clusterId]);\n    return label;\n  }\n\n  async generateAllLabels(): Promise<void> {\n    const clusters = await this.db.query<{ id: string }>('SELECT id FROM clusters');\n    for (const cluster of clusters) {\n      await this.generateClusterLabel(cluster.id);\n    }\n  }\n\n  calculateSilhouetteScore(clusters: ClusteringResult[]): number {\n    if (clusters.length === 0) return 0;\n    return clusters.reduce((acc, cluster) => acc + cluster.cohesion, 0) / clusters.length;\n  }\n\n  calculateCohesion(cluster: ClusteringResult): number {\n    return cluster.cohesion;\n  }\n\n  private async fetchNodesWithEmbeddings(): Promise<Array<NeuronNode & { embedding: number[] }>> {\n    const nodes = await this.db.query<NeuronNode & { embedding: number[] }>(\n      'SELECT * FROM nodes WHERE embedding IS NOT NULL'\n    );\n    return nodes as Array<NeuronNode & { embedding: number[] }>;\n  }\n\n  private runKmeans(nodes: Array<NeuronNode & { embedding: number[] }>, config: ClusteringConfig): ClusteringResult[] {\n    const k = Math.max(1, config.clusterCount ?? 3);\n    const centroids: number[][] = [];\n    const initialNodes = [...nodes].sort(() => Math.random() - 0.5).slice(0, k);\n    initialNodes.forEach((node) => centroids.push([...node.embedding]));\n\n    let assignments = new Map<string, number>();\n    for (let iteration = 0; iteration < 10; iteration += 1) {\n      assignments = new Map();\n      nodes.forEach((node) => {\n        let bestIndex = 0;\n        let bestScore = -Infinity;\n        centroids.forEach((centroid, idx) => {\n          const score = cosineSimilarity(node.embedding, centroid);\n          if (score > bestScore) {\n            bestScore = score;\n            bestIndex = idx;\n          }\n        });\n        assignments.set(node.id, bestIndex);\n      });\n\n      for (let i = 0; i < k; i += 1) {\n        const members = nodes.filter((node) => assignments.get(node.id) === i);\n        if (members.length === 0) continue;\n        centroids[i] = averageVector(members.map((node) => node.embedding));\n      }\n    }\n\n    const clusters: ClusteringResult[] = [];\n    for (let i = 0; i < k; i += 1) {\n      const members = nodes.filter((node) => assignments.get(node.id) === i);\n      if (members.length === 0) continue;\n      const centroid = centroids[i];\n      const similarities = members.map((node) => cosineSimilarity(node.embedding, centroid));\n      const avgSimilarity = similarities.reduce((acc, val) => acc + val, 0) / similarities.length;\n      clusters.push({\n        clusterId: crypto.randomUUID(),\n        label: members.map((node) => node.label).slice(0, 3).join(', '),\n        nodeIds: members.map((node) => node.id),\n        centroid,\n        avgSimilarity,\n        cohesion: avgSimilarity,\n      });\n    }\n\n    return clusters;\n  }\n\n  private runDbscan(nodes: Array<NeuronNode & { embedding: number[] }>, config: ClusteringConfig): ClusteringResult[] {\n    const epsilon = config.similarityThreshold ?? 0.75;\n    const minSamples = config.minSamples ?? 2;\n    const visited = new Set<string>();\n    const clusters: ClusteringResult[] = [];\n\n    for (const node of nodes) {\n      if (visited.has(node.id)) continue;\n      visited.add(node.id);\n      const neighbors = this.findNeighbors(nodes, node, epsilon);\n      if (neighbors.length < minSamples) {\n        continue;\n      }\n\n      const clusterMembers = new Set<string>([node.id, ...neighbors.map((n) => n.id)]);\n      let idx = 0;\n      const neighborList = [...neighbors];\n      while (idx < neighborList.length) {\n        const neighbor = neighborList[idx];\n        if (!visited.has(neighbor.id)) {\n          visited.add(neighbor.id);\n          const neighborNeighbors = this.findNeighbors(nodes, neighbor, epsilon);\n          if (neighborNeighbors.length >= minSamples) {\n            neighborNeighbors.forEach((n) => {\n              if (!clusterMembers.has(n.id)) {\n                clusterMembers.add(n.id);\n                neighborList.push(n);\n              }\n            });\n          }\n        }\n        idx += 1;\n      }\n\n      const members = nodes.filter((n) => clusterMembers.has(n.id));\n      const centroid = averageVector(members.map((member) => member.embedding));\n      const similarities = members.map((member) => cosineSimilarity(member.embedding, centroid));\n      const avgSimilarity = similarities.reduce((acc, val) => acc + val, 0) / similarities.length;\n      clusters.push({\n        clusterId: crypto.randomUUID(),\n        label: members.map((member) => member.label).slice(0, 3).join(', '),\n        nodeIds: members.map((member) => member.id),\n        centroid,\n        avgSimilarity,\n        cohesion: avgSimilarity,\n      });\n    }\n\n    return clusters;\n  }\n\n  private findNeighbors(\n    nodes: Array<NeuronNode & { embedding: number[] }>,\n    node: NeuronNode & { embedding: number[] },\n    threshold: number\n  ) {\n    return nodes.filter((candidate) => {\n      if (candidate.id === node.id) return false;\n      return cosineSimilarity(candidate.embedding, node.embedding) >= threshold;\n    });\n  }\n\n  private async persistClusters(clusters: ClusteringResult[]): Promise<void> {\n    await this.db.transaction(async (client) => {\n      await client.query('DELETE FROM cluster_memberships');\n      await client.query('DELETE FROM clusters');\n\n      for (const cluster of clusters) {\n        await client.query(\n          'INSERT INTO clusters (id, label, centroid, member_count, avg_similarity, cohesion, created_at, updated_at) VALUES ($1, $2, $3, $4, $5, $6, NOW(), NOW())',\n          [\n            cluster.clusterId,\n            cluster.label,\n            cluster.centroid,\n            cluster.nodeIds.length,\n            cluster.avgSimilarity,\n            cluster.cohesion,\n          ]\n        );\n\n        for (const nodeId of cluster.nodeIds) {\n          await client.query(\n            'INSERT INTO cluster_memberships (node_id, cluster_id, similarity_score, is_primary) VALUES ($1, $2, $3, true)',\n            [nodeId, cluster.clusterId, cluster.avgSimilarity]\n          );\n          await client.query('UPDATE nodes SET cluster_id = $1, cluster_similarity = $2 WHERE id = $3', [\n            cluster.clusterId,\n            cluster.avgSimilarity,\n            nodeId,\n          ]);\n        }\n      }\n    });\n  }\n}\n","import OpenAI from 'openai';\nimport type { Database } from '../../storage/database';\nimport type { EdgeEvidence, NeuronEdge, RelationshipType } from '../types/edge';\n\nexport interface InferenceConfig {\n  model: string;\n  minConfidence: number;\n  maxPerNode: number;\n  similarityThreshold: number;\n  includeExisting: boolean;\n  batchSize: number;\n  rateLimit: number;\n}\n\nexport interface InferredRelationship {\n  fromNodeId: string;\n  toNodeId: string;\n  relationshipType: RelationshipType;\n  confidence: number;\n  reasoning: string;\n  evidence: EdgeEvidence[];\n}\n\nconst INFERENCE_PROMPT = `You are analyzing potential relationships between concepts in a knowledge graph.\n\nNode A:\n- Label: {nodeA.label}\n- Summary: {nodeA.summary}\n- Content: {nodeA.content}\n\nNode B:\n- Label: {nodeB.label}\n- Summary: {nodeB.summary}\n- Content: {nodeB.content}\n\nDetermine if there is a meaningful relationship between these nodes.\n\nRespond in JSON:\n{\n  \"hasRelationship\": boolean,\n  \"relationshipType\": \"related_to\" | \"derives_from\" | \"contradicts\" | \"supports\" | \"references\" | \"part_of\" | \"leads_to\" | \"similar_to\",\n  \"confidence\": 0.0-1.0,\n  \"reasoning\": \"Brief explanation\",\n  \"evidence\": [\"Specific quote or fact supporting this\"]\n}\n`;\n\nexport class RelationshipEngine {\n  private client: OpenAI;\n\n  constructor(private db: Database, private config: InferenceConfig) {\n    this.client = new OpenAI({ apiKey: process.env.OPENAI_API_KEY ?? '' });\n  }\n\n  async inferForNode(nodeId: string): Promise<InferredRelationship[]> {\n    const candidates = await this.findCandidates(nodeId);\n    const inferred: InferredRelationship[] = [];\n\n    for (const candidate of candidates.slice(0, this.config.maxPerNode)) {\n      const inference = await this.inferPair(nodeId, candidate.nodeId);\n      if (inference && inference.confidence >= this.config.minConfidence) {\n        inferred.push(inference);\n      }\n      await this.applyRateLimit();\n    }\n\n    return inferred;\n  }\n\n  async inferForNodes(nodeIds: string[]): Promise<{\n    inferred: InferredRelationship[];\n    errors: Array<{ nodeId: string; error: string }>;\n  }> {\n    const inferred: InferredRelationship[] = [];\n    const errors: Array<{ nodeId: string; error: string }> = [];\n\n    for (const nodeId of nodeIds) {\n      try {\n        const results = await this.inferForNode(nodeId);\n        inferred.push(...results);\n      } catch (error) {\n        errors.push({ nodeId, error: error instanceof Error ? error.message : String(error) });\n      }\n    }\n\n    return { inferred, errors };\n  }\n\n  async inferAll(): Promise<InferredRelationship[]> {\n    const nodes = await this.db.query<{ id: string }>('SELECT id FROM nodes');\n    const result = await this.inferForNodes(nodes.map((node) => node.id));\n    return result.inferred;\n  }\n\n  async findCandidates(nodeId: string): Promise<Array<{ nodeId: string; similarity: number }>> {\n    const rows = await this.db.query<{ id: string; similarity: number }>(\n      `SELECT id, 1 - (embedding <=> (SELECT embedding FROM nodes WHERE id = $1)) as similarity\n       FROM nodes\n       WHERE embedding IS NOT NULL AND id != $1\n       ORDER BY embedding <=> (SELECT embedding FROM nodes WHERE id = $1)\n       LIMIT $2`,\n      [nodeId, this.config.maxPerNode * 3]\n    );\n\n    return rows\n      .filter((row) => row.similarity >= this.config.similarityThreshold)\n      .map((row) => ({ nodeId: row.id, similarity: row.similarity }));\n  }\n\n  async validateRelationship(rel: InferredRelationship): Promise<boolean> {\n    return rel.confidence >= this.config.minConfidence;\n  }\n\n  async createEdgesFromInferences(\n    inferences: InferredRelationship[],\n    autoApprove = true\n  ): Promise<NeuronEdge[]> {\n    const created: NeuronEdge[] = [];\n    if (!autoApprove) return created;\n\n    for (const inference of inferences) {\n      const rows = await this.db.query<NeuronEdge>(\n        `INSERT INTO edges (from_node_id, to_node_id, relationship_type, strength, confidence, evidence, source, source_model)\n         VALUES ($1, $2, $3, $4, $5, $6, 'ai_inferred', $7)\n         ON CONFLICT (from_node_id, to_node_id, relationship_type) DO NOTHING\n         RETURNING *`,\n        [\n          inference.fromNodeId,\n          inference.toNodeId,\n          inference.relationshipType,\n          inference.confidence,\n          inference.confidence,\n          JSON.stringify(inference.evidence),\n          this.config.model,\n        ]\n      );\n      if (rows[0]) {\n        created.push(rows[0]);\n      }\n    }\n\n    return created;\n  }\n\n  private async inferPair(\n    fromNodeId: string,\n    toNodeId: string\n  ): Promise<InferredRelationship | null> {\n    const [nodeA, nodeB] = await Promise.all([\n      this.db.queryOne<{ id: string; label: string; summary: string | null; content: string | null }>(\n        'SELECT id, label, summary, content FROM nodes WHERE id = $1',\n        [fromNodeId]\n      ),\n      this.db.queryOne<{ id: string; label: string; summary: string | null; content: string | null }>(\n        'SELECT id, label, summary, content FROM nodes WHERE id = $1',\n        [toNodeId]\n      ),\n    ]);\n\n    if (!nodeA || !nodeB) return null;\n\n    const prompt = INFERENCE_PROMPT.replace('{nodeA.label}', nodeA.label)\n      .replace('{nodeA.summary}', nodeA.summary ?? '')\n      .replace('{nodeA.content}', nodeA.content ?? '')\n      .replace('{nodeB.label}', nodeB.label)\n      .replace('{nodeB.summary}', nodeB.summary ?? '')\n      .replace('{nodeB.content}', nodeB.content ?? '');\n\n    const response = await this.client.chat.completions.create({\n      model: this.config.model,\n      messages: [{ role: 'user', content: prompt }],\n      response_format: { type: 'json_object' },\n    });\n\n    const content = response.choices[0]?.message?.content;\n    if (!content) return null;\n\n    const parsed = JSON.parse(content) as {\n      hasRelationship: boolean;\n      relationshipType: RelationshipType;\n      confidence: number;\n      reasoning: string;\n      evidence: string[];\n    };\n\n    if (!parsed.hasRelationship) return null;\n\n    return {\n      fromNodeId,\n      toNodeId,\n      relationshipType: parsed.relationshipType ?? 'related_to',\n      confidence: parsed.confidence ?? 0,\n      reasoning: parsed.reasoning ?? '',\n      evidence: (parsed.evidence ?? []).map((text) => ({ type: 'text', content: text })),\n    };\n  }\n\n  private async applyRateLimit(): Promise<void> {\n    const delayMs = Math.ceil(60_000 / this.config.rateLimit);\n    await new Promise((resolve) => setTimeout(resolve, delayMs));\n  }\n}\n","import type { Database } from '../../storage/database';\nimport type { AnalysisRun, AnalysisRunType } from '../types/analysis';\nimport type { ClusteringAlgorithm } from '../types/cluster';\nimport type { EventBus } from '../events/event-bus';\nimport type { EmbeddingsService } from './embeddings-service';\nimport type { ClusteringEngine } from './clustering-engine';\nimport type { RelationshipEngine } from './relationship-engine';\n\nexport interface PipelineOptions {\n  nodeIds?: string[];\n  forceRecompute?: boolean;\n  skipEmbeddings?: boolean;\n  embeddingModel?: string;\n  skipClustering?: boolean;\n  clusterCount?: number;\n  clusteringAlgorithm?: ClusteringAlgorithm;\n  skipRelationships?: boolean;\n  relationshipThreshold?: number;\n  maxRelationshipsPerNode?: number;\n  onProgress?: (progress: PipelineProgress) => void;\n  webhookUrl?: string;\n}\n\nexport interface PipelineProgress {\n  stage: 'embeddings' | 'clustering' | 'relationships' | 'complete';\n  progress: number;\n  currentItem: string;\n  itemsProcessed: number;\n  totalItems: number;\n  estimatedTimeRemaining?: number;\n}\n\nexport class AnalysisPipeline {\n  private activeJobs = new Map<string, AbortController>();\n\n  constructor(\n    private db: Database,\n    private embeddings: EmbeddingsService,\n    private clustering: ClusteringEngine,\n    private relationships: RelationshipEngine,\n    private events: EventBus\n  ) {}\n\n  async runFull(options: PipelineOptions = {}): Promise<AnalysisRun> {\n    const job = await this.createJob('full_analysis', options);\n    try {\n      if (!options.skipEmbeddings) {\n        await this.runEmbeddingsStage(job, options);\n      }\n      if (!options.skipClustering) {\n        await this.runClusteringStage(job, options);\n      }\n      if (!options.skipRelationships) {\n        await this.runRelationshipsStage(job, options);\n      }\n      return await this.completeJob(job.id);\n    } catch (error) {\n      return await this.failJob(job.id, error);\n    }\n  }\n\n  async runEmbeddings(options: PipelineOptions = {}): Promise<AnalysisRun> {\n    const job = await this.createJob('embedding', options);\n    try {\n      await this.runEmbeddingsStage(job, options);\n      return await this.completeJob(job.id);\n    } catch (error) {\n      return await this.failJob(job.id, error);\n    }\n  }\n\n  async runClustering(options: PipelineOptions = {}): Promise<AnalysisRun> {\n    const job = await this.createJob('clustering', options);\n    try {\n      await this.runClusteringStage(job, options);\n      return await this.completeJob(job.id);\n    } catch (error) {\n      return await this.failJob(job.id, error);\n    }\n  }\n\n  async runRelationships(options: PipelineOptions = {}): Promise<AnalysisRun> {\n    const job = await this.createJob('relationship_inference', options);\n    try {\n      await this.runRelationshipsStage(job, options);\n      return await this.completeJob(job.id);\n    } catch (error) {\n      return await this.failJob(job.id, error);\n    }\n  }\n\n  async getJob(jobId: string): Promise<AnalysisRun | null> {\n    const row = await this.db.queryOne<AnalysisRun>('SELECT * FROM analysis_runs WHERE id = $1', [jobId]);\n    return row ?? null;\n  }\n\n  async listJobs(options?: { status?: string; limit?: number }): Promise<AnalysisRun[]> {\n    const where = options?.status ? 'WHERE status = $1' : '';\n    const limit = options?.limit ? `LIMIT ${options.limit}` : '';\n    const rows = await this.db.query<AnalysisRun>(\n      `SELECT * FROM analysis_runs ${where} ORDER BY created_at DESC ${limit}`,\n      options?.status ? [options.status] : []\n    );\n    return rows;\n  }\n\n  async cancelJob(jobId: string): Promise<boolean> {\n    const controller = this.activeJobs.get(jobId);\n    if (!controller) return false;\n    controller.abort();\n    await this.db.execute('UPDATE analysis_runs SET status = $1 WHERE id = $2', [\n      'cancelled',\n      jobId,\n    ]);\n    return true;\n  }\n\n  getActiveJobs(): AnalysisRun[] {\n    return [];\n  }\n\n  isRunning(): boolean {\n    return this.activeJobs.size > 0;\n  }\n\n  private async runEmbeddingsStage(job: AnalysisRun, options: PipelineOptions): Promise<void> {\n    const nodeIds = await this.resolveNodeIds(options.nodeIds, options.forceRecompute);\n    const { results, errors } = await this.embeddings.embedNodes(nodeIds);\n    await this.updateJobResults(job.id, {\n      embeddingsGenerated: results.length,\n      errors,\n    });\n    options.onProgress?.({\n      stage: 'embeddings',\n      progress: 100,\n      currentItem: 'complete',\n      itemsProcessed: results.length,\n      totalItems: nodeIds.length,\n    });\n  }\n\n  private async runClusteringStage(job: AnalysisRun, options: PipelineOptions): Promise<void> {\n    const clusterCount = options.clusterCount;\n    const algorithm = options.clusteringAlgorithm ?? 'kmeans';\n    const result = await this.clustering.clusterNodes({\n      algorithm,\n      clusterCount,\n      similarityThreshold: options.relationshipThreshold,\n    });\n    await this.updateJobResults(job.id, {\n      clustersCreated: result.clusters.length,\n    });\n    options.onProgress?.({\n      stage: 'clustering',\n      progress: 100,\n      currentItem: 'complete',\n      itemsProcessed: result.clusters.length,\n      totalItems: result.clusters.length,\n    });\n  }\n\n  private async runRelationshipsStage(job: AnalysisRun, options: PipelineOptions): Promise<void> {\n    const nodeIds = options.nodeIds ?? (await this.resolveNodeIds());\n    const { inferred, errors } = await this.relationships.inferForNodes(nodeIds);\n    await this.relationships.createEdgesFromInferences(inferred, true);\n    await this.updateJobResults(job.id, {\n      relationshipsInferred: inferred.length,\n      errors,\n    });\n    options.onProgress?.({\n      stage: 'relationships',\n      progress: 100,\n      currentItem: 'complete',\n      itemsProcessed: inferred.length,\n      totalItems: inferred.length,\n    });\n  }\n\n  private async createJob(runType: AnalysisRunType, options: PipelineOptions): Promise<AnalysisRun> {\n    const controller = new AbortController();\n    const row = await this.db.queryOne<AnalysisRun>(\n      `INSERT INTO analysis_runs (run_type, input_params, status, progress, started_at)\n       VALUES ($1, $2, 'running', 0, NOW())\n       RETURNING *`,\n      [runType, options]\n    );\n    if (!row) throw new Error('Failed to create analysis job');\n    this.activeJobs.set(row.id, controller);\n    return row;\n  }\n\n  private async completeJob(jobId: string): Promise<AnalysisRun> {\n    const row = await this.db.queryOne<AnalysisRun>(\n      `UPDATE analysis_runs\n       SET status = 'completed', progress = 100, completed_at = NOW(), duration_ms = EXTRACT(EPOCH FROM (NOW() - started_at)) * 1000\n       WHERE id = $1\n       RETURNING *`,\n      [jobId]\n    );\n    this.activeJobs.delete(jobId);\n    return row as AnalysisRun;\n  }\n\n  private async failJob(jobId: string, error: unknown): Promise<AnalysisRun> {\n    const message = error instanceof Error ? error.message : String(error);\n    const stack = error instanceof Error ? error.stack : undefined;\n    const row = await this.db.queryOne<AnalysisRun>(\n      `UPDATE analysis_runs\n       SET status = 'failed', error_message = $2, error_stack = $3, completed_at = NOW(), duration_ms = EXTRACT(EPOCH FROM (NOW() - started_at)) * 1000\n       WHERE id = $1\n       RETURNING *`,\n      [jobId, message, stack]\n    );\n    this.activeJobs.delete(jobId);\n    return row as AnalysisRun;\n  }\n\n  private async updateJobResults(jobId: string, updates: Partial<AnalysisRun['results']>) {\n    const row = await this.db.queryOne<{ results: AnalysisRun['results'] }>(\n      'SELECT results FROM analysis_runs WHERE id = $1',\n      [jobId]\n    );\n    const current = row?.results ?? {\n      nodesProcessed: 0,\n      embeddingsGenerated: 0,\n      clustersCreated: 0,\n      relationshipsInferred: 0,\n      errors: [],\n    };\n    const next = { ...current, ...updates };\n    await this.db.execute('UPDATE analysis_runs SET results = $1 WHERE id = $2', [next, jobId]);\n  }\n\n  private async resolveNodeIds(nodeIds?: string[], forceRecompute = false): Promise<string[]> {\n    if (nodeIds?.length) return nodeIds;\n    if (forceRecompute) {\n      const rows = await this.db.query<{ id: string }>('SELECT id FROM nodes');\n      return rows.map((row) => row.id);\n    }\n    const rows = await this.db.query<{ id: string }>('SELECT id FROM nodes WHERE embedding IS NULL');\n    return rows.map((row) => row.id);\n  }\n}\n","import { Pool, type PoolClient, type PoolConfig } from 'pg';\n\nexport interface DatabaseConfig {\n  connectionString?: string;\n  host?: string;\n  port?: number;\n  user?: string;\n  password?: string;\n  database?: string;\n  pool?: {\n    min: number;\n    max: number;\n    idleTimeoutMs: number;\n    connectionTimeoutMs: number;\n  };\n  ssl?: boolean | object;\n  slowQueryThresholdMs?: number;\n}\n\nexport interface PoolStats {\n  totalCount: number;\n  idleCount: number;\n  waitingCount: number;\n}\n\nexport class Database {\n  private pool: Pool;\n  private slowQueryThresholdMs?: number;\n\n  constructor(config: DatabaseConfig) {\n    const poolConfig: PoolConfig = {\n      connectionString: config.connectionString ?? this.buildConnectionString(config),\n      ssl: config.ssl,\n      min: config.pool?.min,\n      max: config.pool?.max,\n      idleTimeoutMillis: config.pool?.idleTimeoutMs,\n      connectionTimeoutMillis: config.pool?.connectionTimeoutMs,\n    };\n\n    this.pool = new Pool(poolConfig);\n    this.slowQueryThresholdMs = config.slowQueryThresholdMs;\n  }\n\n  async connect(): Promise<void> {\n    const client = await this.pool.connect();\n    client.release();\n  }\n\n  async disconnect(): Promise<void> {\n    await this.pool.end();\n  }\n\n  async isConnected(): Promise<boolean> {\n    try {\n      await this.query('SELECT 1');\n      return true;\n    } catch {\n      return false;\n    }\n  }\n\n  async query<T>(sql: string, params: unknown[] = []): Promise<T[]> {\n    const start = Date.now();\n    const result = await this.pool.query(sql, params);\n    this.logSlowQuery(sql, Date.now() - start);\n    return result.rows as T[];\n  }\n\n  async queryOne<T>(sql: string, params: unknown[] = []): Promise<T | null> {\n    const rows = await this.query<T>(sql, params);\n    return rows[0] ?? null;\n  }\n\n  async execute(sql: string, params: unknown[] = []): Promise<number> {\n    const start = Date.now();\n    const result = await this.pool.query(sql, params);\n    this.logSlowQuery(sql, Date.now() - start);\n    return result.rowCount ?? 0;\n  }\n\n  async transaction<T>(fn: (client: PoolClient) => Promise<T>): Promise<T> {\n    const client = await this.pool.connect();\n    try {\n      await client.query('BEGIN');\n      const result = await fn(client);\n      await client.query('COMMIT');\n      return result;\n    } catch (error) {\n      await client.query('ROLLBACK');\n      throw error;\n    } finally {\n      client.release();\n    }\n  }\n\n  async tableExists(tableName: string): Promise<boolean> {\n    const result = await this.queryOne<{ exists: boolean }>(\n      'SELECT EXISTS (SELECT 1 FROM information_schema.tables WHERE table_name = $1) as exists',\n      [tableName]\n    );\n    return result?.exists ?? false;\n  }\n\n  async getPoolStats(): Promise<PoolStats> {\n    return {\n      totalCount: this.pool.totalCount,\n      idleCount: this.pool.idleCount,\n      waitingCount: this.pool.waitingCount,\n    };\n  }\n\n  private buildConnectionString(config: DatabaseConfig): string | undefined {\n    if (config.host && config.port && config.user && config.database) {\n      const password = config.password ? `:${config.password}` : '';\n      return `postgresql://${config.user}${password}@${config.host}:${config.port}/${config.database}`;\n    }\n\n    return undefined;\n  }\n\n  private logSlowQuery(sql: string, durationMs: number): void {\n    if (!this.slowQueryThresholdMs || durationMs < this.slowQueryThresholdMs) {\n      return;\n    }\n\n    // eslint-disable-next-line no-console\n    console.warn(`[omi-neuron] Slow query (${durationMs}ms): ${sql}`);\n  }\n}\n"]}