@semiont/graph 0.2.28-build.40

package/dist/index.js.map

@@ -0,0 +1 @@
+{"version":3,"sources":["../src/implementations/neptune.ts","../src/implementations/neo4j.ts","../src/implementations/janusgraph.ts","../src/implementations/memorygraph.ts","../src/factory.ts"],"sourcesContent":["// AWS Neptune implementation of GraphDatabase interface\n// Uses Gremlin for graph traversal\n\nimport { GraphDatabase } from '../interface';\nimport { getBodySource } from '@semiont/api-client';\nimport { getEntityTypes } from '@semiont/ontology';\nimport type { components } from '@semiont/api-client';\nimport type {\n  AnnotationCategory,\n  GraphConnection,\n  GraphPath,\n  EntityTypeStats,\n  ResourceFilter,\n  UpdateResourceInput,\n  CreateAnnotationInternal,\n  ResourceId,\n  AnnotationId,\n} from '@semiont/core';\nimport type { ResourceUri, AnnotationUri } from '@semiont/api-client';\nimport { getExactText } from '@semiont/api-client';\nimport { v4 as uuidv4 } from 'uuid';\nimport { getTargetSource, getTargetSelector } from '@semiont/api-client';\nimport { getPrimaryRepresentation, getResourceId } from '@semiont/api-client';\n\ntype ResourceDescriptor = components['schemas']['ResourceDescriptor'];\ntype Annotation = components['schemas']['Annotation'];\n\n// Dynamic imports for AWS SDK and Gremlin\nlet NeptuneClient: any;\nlet DescribeDBClustersCommand: any;\nlet gremlin: any;\nlet process: any;\nlet TextP: any;\nlet order: any;\nlet cardinality: any;\nlet __: any;\n\nasync function loadDependencies() {\n  if (!NeptuneClient) {\n    const neptuneModule = await import('@aws-sdk/client-neptune');\n    NeptuneClient = neptuneModule.NeptuneClient;\n    DescribeDBClustersCommand = neptuneModule.DescribeDBClustersCommand;\n  }\n  if (!gremlin) {\n    // @ts-ignore - gremlin module has no types\n    gremlin = await import('gremlin');\n    process = gremlin.process;\n    TextP = process.TextP;\n    order = process.order;\n    cardinality = process.cardinality;\n    __ = process.statics;\n  }\n}\n\n// Helper function to convert Neptune vertex to ResourceDescriptor\nfunction vertexToResource(vertex: any): ResourceDescriptor {\n  const props = vertex.properties || vertex;\n\n  // Handle different property formats from Neptune\n  const getValue = (key: string, required: boolean = false) => {\n    const prop = props[key];\n    if (!prop) {\n      if (required) {\n        throw new Error(`Resource ${vertex.id || 'unknown'} missing required field: ${key}`);\n      }\n      return undefined;\n    }\n    if (Array.isArray(prop) && prop.length > 0) {\n      return prop[0].value !== undefined ? prop[0].value : prop[0];\n    }\n    return prop.value !== undefined ? prop.value : prop;\n  };\n\n  // Get all required fields and validate\n  const id = getValue('id', true);\n  const name = getValue('name', true);\n  const entityTypesRaw = getValue('entityTypes', true);\n  const mediaType = getValue('mediaType', true);\n  const archived = getValue('archived', true);\n  const dateCreated = getValue('dateCreated', true);\n  const checksum = getValue('checksum', true);\n  const creatorRaw = getValue('creator', true);\n\n  const resource: ResourceDescriptor = {\n    '@context': 'https://schema.org/',\n    '@id': id,\n    name,\n    entityTypes: JSON.parse(entityTypesRaw),\n    representations: [{\n      mediaType,\n      checksum,\n      rel: 'original',\n    }],\n    archived: archived === 'true' || archived === true,\n    dateCreated,\n    wasAttributedTo: typeof creatorRaw === 'string' ? JSON.parse(creatorRaw) : creatorRaw,\n    creationMethod: getValue('creationMethod', true),\n  };\n\n  const sourceResourceId = getValue('sourceResourceId');\n  if (sourceResourceId) resource.sourceResourceId = sourceResourceId;\n\n  return resource;\n}\n\n// Helper function to convert Neptune vertex to Annotation\nfunction vertexToAnnotation(vertex: any, entityTypes: string[] = []): Annotation {\n  const props = vertex.properties || vertex;\n\n  // Handle different property formats from Neptune\n  const getValue = (key: string, required: boolean = false) => {\n    const prop = props[key];\n    if (!prop) {\n      if (required) {\n        throw new Error(`Annotation ${vertex.id || 'unknown'} missing required field: ${key}`);\n      }\n      return undefined;\n    }\n    if (Array.isArray(prop) && prop.length > 0) {\n      return prop[0].value !== undefined ? prop[0].value : prop[0];\n    }\n    if (typeof prop === 'object' && 'value' in prop) return prop.value;\n    return prop;\n  };\n\n  // Get required fields\n  const id = getValue('id', true);\n  const resourceId = getValue('resourceId', true);\n  const selectorRaw = getValue('selector', true);\n  const creatorRaw = getValue('creator', true);\n  const createdRaw = getValue('created', true);\n\n  // Derive motivation from type if not present (backward compatibility)\n  const motivation = getValue('motivation') || 'linking';\n\n  // Parse creator - always stored as JSON string in DB\n  const creator = JSON.parse(creatorRaw);\n\n  // Reconstruct body array from entity tags and linking body\n  const bodyArray: Array<{type: 'TextualBody'; value: string; purpose: 'tagging'} | {type: 'SpecificResource'; source: string; purpose: 'linking'}> = [];\n\n  // Add entity tag bodies (TextualBody with purpose: \"tagging\")\n  for (const entityType of entityTypes) {\n    if (entityType) {\n      bodyArray.push({\n        type: 'TextualBody' as const,\n        value: entityType,\n        purpose: 'tagging' as const,\n      });\n    }\n  }\n\n  // Add linking body (SpecificResource) if annotation is resolved\n  const bodySource = getValue('source');\n  if (bodySource) {\n    bodyArray.push({\n      type: 'SpecificResource' as const,\n      source: bodySource,\n      purpose: 'linking' as const,\n    });\n  }\n\n  const annotation: Annotation = {\n    '@context': 'http://www.w3.org/ns/anno.jsonld' as const,\n    'type': 'Annotation' as const,\n    id,\n    motivation,\n    target: {\n      source: resourceId,\n      selector: JSON.parse(selectorRaw),\n    },\n    body: bodyArray,\n    creator,\n    created: createdRaw, // ISO string from DB\n  };\n\n  // W3C Web Annotation modification tracking\n  const modified = getValue('modified');\n  if (modified) annotation.modified = modified;\n\n  const generatorJson = getValue('generator');\n  if (generatorJson) {\n    try {\n      annotation.generator = JSON.parse(generatorJson);\n    } catch (e) {\n      // Ignore parse errors\n    }\n  }\n\n  return annotation;\n}\n\n\nexport class NeptuneGraphDatabase implements GraphDatabase {\n  private connected: boolean = false;\n  private neptuneEndpoint?: string;\n  private neptunePort: number = 8182;\n  private region?: string;\n  private g: any; // Gremlin graph traversal source\n  private connection: any; // Gremlin connection\n\n  // Helper method to fetch annotations with their entity types\n  private async fetchAnnotationsWithEntityTypes(annotationVertices: any[]): Promise<Annotation[]> {\n    const annotations: Annotation[] = [];\n\n    for (const vertex of annotationVertices) {\n      const id = vertex.properties?.id?.[0]?.value || vertex.id;\n\n      // Fetch entity types for this annotation\n      const entityTypesResult = await this.g.V()\n        .hasLabel('Annotation')\n        .has('id', id)\n        .out('TAGGED_AS')\n        .hasLabel('EntityType')\n        .values('name')\n        .toList();\n\n      const entityTypes = entityTypesResult || [];\n      annotations.push(vertexToAnnotation(vertex, entityTypes));\n    }\n\n    return annotations;\n  }\n  \n  constructor(config: {\n    endpoint?: string;\n    port?: number;\n    region?: string;\n  } = {}) {\n    if (config.endpoint) this.neptuneEndpoint = config.endpoint;\n    this.neptunePort = config.port || 8182;\n    if (config.region) this.region = config.region;\n  }\n  \n  private async discoverNeptuneEndpoint(): Promise<void> {\n    // If endpoint is already provided, use it\n    if (this.neptuneEndpoint) {\n      return;\n    }\n    \n    // In AWS environment, discover Neptune cluster endpoint\n    if (!this.region) {\n      throw new Error('AWS region must be configured in environment JSON file (aws.region) for Neptune endpoint discovery');\n    }\n\n    try {\n      // Load AWS SDK dynamically\n      await loadDependencies();\n      \n      // Create Neptune client\n      const client = new NeptuneClient({ region: this.region });\n      \n      // List all Neptune clusters\n      const command = new DescribeDBClustersCommand({});\n      const response = await client.send(command);\n      \n      if (!response.DBClusters || response.DBClusters.length === 0) {\n        throw new Error('No Neptune clusters found in region ' + this.region);\n      }\n      \n      // Find the Semiont cluster by tags\n      let cluster = null;\n      for (const dbCluster of response.DBClusters) {\n        // Check if this cluster has our application tag\n        const tagsCommand = new DescribeDBClustersCommand({\n          DBClusterIdentifier: dbCluster.DBClusterIdentifier\n        });\n        const clusterDetails = await client.send(tagsCommand);\n        \n        if (clusterDetails.DBClusters && clusterDetails.DBClusters[0]) {\n          const clusterInfo = clusterDetails.DBClusters[0];\n          // Check for Semiont tag or name pattern\n          if (clusterInfo.DBClusterIdentifier?.includes('Semiont') || \n              clusterInfo.DBClusterIdentifier?.includes('semiont')) {\n            cluster = clusterInfo;\n            break;\n          }\n        }\n      }\n      \n      if (!cluster) {\n        throw new Error('No Semiont Neptune cluster found in region ' + this.region);\n      }\n      \n      // Set the endpoint and port\n      this.neptuneEndpoint = cluster.Endpoint;\n      this.neptunePort = cluster.Port || 8182;\n      \n      console.log(`Discovered Neptune endpoint: ${this.neptuneEndpoint}:${this.neptunePort}`);\n    } catch (error: any) {\n      console.error('Failed to discover Neptune endpoint:', error);\n      throw error;\n    }\n  }\n  \n  async connect(): Promise<void> {\n    // Discover Neptune endpoint if needed\n    await this.discoverNeptuneEndpoint();\n    \n    try {\n      // Load Gremlin dynamically\n      await loadDependencies();\n      \n      // Create Gremlin connection\n      const traversal = gremlin.process.AnonymousTraversalSource.traversal;\n      const DriverRemoteConnection = gremlin.driver.DriverRemoteConnection;\n      \n      // Neptune requires WebSocket Secure (wss) protocol\n      const connectionUrl = `wss://${this.neptuneEndpoint}:${this.neptunePort}/gremlin`;\n      console.log(`Connecting to Neptune at ${connectionUrl}`);\n      \n      // Create the connection\n      this.connection = new DriverRemoteConnection(connectionUrl, {\n        authenticator: null, // Neptune uses IAM authentication via task role\n        rejectUnauthorized: true,\n        traversalSource: 'g'\n      });\n      \n      // Create the graph traversal source\n      this.g = traversal().withRemote(this.connection);\n      \n      // Test the connection\n      const count = await this.g.V().limit(1).count().next();\n      console.log(`Connected to Neptune. Vertex count test: ${count.value}`);\n      \n      this.connected = true;\n    } catch (error: any) {\n      console.error('Failed to connect to Neptune:', error);\n      throw error;\n    }\n  }\n  \n  async disconnect(): Promise<void> {\n    // Close Gremlin connection if it exists\n    if (this.connection) {\n      try {\n        await this.connection.close();\n      } catch (error) {\n        console.error('Error closing Neptune connection:', error);\n      }\n    }\n    \n    this.connected = false;\n    console.log('Disconnected from Neptune');\n  }\n  \n  isConnected(): boolean {\n    return this.connected;\n  }\n\n  async createResource(resource: ResourceDescriptor): Promise<ResourceDescriptor> {\n    const id = getResourceId(resource);\n    const primaryRep = getPrimaryRepresentation(resource);\n    if (!primaryRep) {\n      throw new Error('Resource must have at least one representation');\n    }\n\n    // Create vertex in Neptune\n    try {\n      const vertex = this.g.addV('Resource')\n        .property('id', id)\n        .property('name', resource.name)\n        .property('mediaType', primaryRep.mediaType)\n        .property('archived', resource.archived || false)\n        .property('dateCreated', resource.dateCreated)\n        .property('creator', JSON.stringify(resource.wasAttributedTo))\n        .property('creationMethod', resource.creationMethod)\n        .property('checksum', primaryRep.checksum)\n        .property('entityTypes', JSON.stringify(resource.entityTypes));\n\n      if (resource.sourceResourceId) {\n        vertex.property('sourceResourceId', resource.sourceResourceId);\n      }\n\n      await vertex.next();\n\n      console.log(`Created resource vertex in Neptune: ${id}`);\n      return resource;\n    } catch (error) {\n      console.error('Failed to create resource in Neptune:', error);\n      throw error;\n    }\n  }\n  \n  async getResource(id: ResourceUri): Promise<ResourceDescriptor | null> {\n    try {\n      const result = await this.g.V()\n        .hasLabel('Resource')\n        .has('id', id)\n        .elementMap()\n        .next();\n      \n      if (!result.value) {\n        return null;\n      }\n      \n      return vertexToResource(result.value);\n    } catch (error) {\n      console.error('Failed to get resource from Neptune:', error);\n      throw error;\n    }\n  }\n  \n  async updateResource(id: ResourceUri, input: UpdateResourceInput): Promise<ResourceDescriptor> {\n    // Resources are immutable - only archiving is allowed\n    if (Object.keys(input).length !== 1 || input.archived === undefined) {\n      throw new Error('Resources are immutable. Only archiving is allowed.');\n    }\n\n    try {\n      const result = await this.g.V()\n        .hasLabel('Resource')\n        .has('id', id)\n        .property('archived', input.archived)\n        .elementMap()\n        .next();\n\n      if (!result.value) {\n        throw new Error('Resource not found');\n      }\n\n      return vertexToResource(result.value);\n    } catch (error) {\n      console.error('Failed to update resource in Neptune:', error);\n      throw error;\n    }\n  }\n  \n  async deleteResource(id: ResourceUri): Promise<void> {\n    try {\n      // Delete the resource vertex and all connected edges\n      await this.g.V()\n        .hasLabel('Resource')\n        .has('id', id)\n        .drop()\n        .iterate();\n      \n      console.log(`Deleted resource from Neptune: ${id}`);\n    } catch (error) {\n      console.error('Failed to delete resource from Neptune:', error);\n      throw error;\n    }\n  }\n  \n  async listResources(filter: ResourceFilter): Promise<{ resources: ResourceDescriptor[]; total: number }> {\n    try {\n      let traversal = this.g.V().hasLabel('Resource');\n      \n      // Apply filters\n      if (filter.entityTypes && filter.entityTypes.length > 0) {\n        // Filter by entity types (stored as JSON string)\n        traversal = traversal.filter(\n          process.statics.or(\n            ...filter.entityTypes.map((type: string) =>\n              process.statics.has('entityTypes', TextP.containing(`\"${type}\"`))\n            )\n          )\n        );\n      }\n      \n      if (filter.search) {\n        // Case-insensitive search in resource name\n        traversal = traversal.has('name', TextP.containing(filter.search));\n      }\n      \n      // Count total before pagination\n      const totalResult = await traversal.clone().count().next();\n      const total = totalResult.value || 0;\n      \n      // Apply pagination\n      const offset = filter.offset || 0;\n      const limit = filter.limit || 20;\n      \n      const results = await traversal\n        .order().by('created', order.desc)\n        .range(offset, offset + limit)\n        .elementMap()\n        .toList();\n      \n      const resources = results.map(vertexToResource);\n      \n      return { resources, total };\n    } catch (error) {\n      console.error('Failed to list resources from Neptune:', error);\n      throw error;\n    }\n  }\n  \n  async searchResources(query: string, limit: number = 20): Promise<ResourceDescriptor[]> {\n    try {\n      // Use Neptune's text search capabilities\n      const results = await this.g.V()\n        .hasLabel('Resource')\n        .has('name', TextP.containing(query))\n        .order().by('created', order.desc)\n        .limit(limit)\n        .elementMap()\n        .toList();\n      \n      return results.map(vertexToResource);\n    } catch (error) {\n      console.error('Failed to search resources in Neptune:', error);\n      throw error;\n    }\n  }\n  \n  async createAnnotation(input: CreateAnnotationInternal): Promise<Annotation> {\n    const id = this.generateId();\n\n    // Only linking motivation with SpecificResource or empty array (stub)\n    const annotation: Annotation = {\n      '@context': 'http://www.w3.org/ns/anno.jsonld' as const,\n      'type': 'Annotation' as const,\n      id,\n      motivation: input.motivation,\n      target: input.target,\n      body: input.body,\n      creator: input.creator,\n      created: new Date().toISOString(),\n    };\n\n    // Extract values for Gremlin query\n    const targetSource = getTargetSource(input.target);\n    const targetSelector = getTargetSelector(input.target);\n    const bodySource = getBodySource(input.body);\n    const entityTypes = getEntityTypes(input);\n\n    try {\n      // Create Annotation vertex\n      const vertex = this.g.addV('Annotation')\n        .property('id', annotation.id)\n        .property('resourceId', targetSource) // Store full URI\n        .property('text', targetSelector ? getExactText(targetSelector) : '')\n        .property('selector', JSON.stringify(targetSelector || {}))\n        .property('type', 'SpecificResource')\n        .property('motivation', annotation.motivation)\n        .property('creator', JSON.stringify(annotation.creator))\n        .property('created', annotation.created);\n\n      // Add optional source property for resolved references\n      if (bodySource) {\n        vertex.property('source', bodySource);\n      }\n\n      const newVertex = await vertex.next();\n\n      // Create edge from Annotation to Resource (BELONGS_TO)\n      await this.g.V(newVertex.value)\n        .addE('BELONGS_TO')\n        .to(this.g.V().hasLabel('Resource').has('id', targetSource)) // Use full URI\n        .next();\n\n      // If it's a resolved reference, create edge to target resource (REFERENCES)\n      if (bodySource) {\n        await this.g.V(newVertex.value)\n          .addE('REFERENCES')\n          .to(this.g.V().hasLabel('Resource').has('id', bodySource)) // Use full URI\n          .next();\n      }\n\n      // Create TAGGED_AS relationships for entity types\n      for (const entityType of entityTypes) {\n        // Get or create EntityType vertex\n        const etVertex = await this.g.V()\n          .hasLabel('EntityType')\n          .has('name', entityType)\n          .fold()\n          .coalesce(\n            __.unfold(),\n            this.g.addV('EntityType').property('name', entityType)\n          )\n          .next();\n\n        // Create TAGGED_AS edge from Annotation to EntityType\n        await this.g.V(newVertex.value)\n          .addE('TAGGED_AS')\n          .to(this.g.V(etVertex.value))\n          .next();\n      }\n\n      console.log(`Created annotation vertex in Neptune: ${annotation.id}`);\n      return annotation;\n    } catch (error) {\n      console.error('Failed to create annotation in Neptune:', error);\n      throw error;\n    }\n  }\n  \n  async getAnnotation(id: AnnotationUri): Promise<Annotation | null> {\n    try {\n      const result = await this.g.V()\n        .hasLabel('Annotation')\n        .has('id', id)\n        .elementMap()\n        .next();\n\n      if (!result.value) {\n        return null;\n      }\n\n      // Fetch entity types from TAGGED_AS relationships\n      const entityTypesResult = await this.g.V()\n        .hasLabel('Annotation')\n        .has('id', id)\n        .out('TAGGED_AS')\n        .hasLabel('EntityType')\n        .values('name')\n        .toList();\n\n      const entityTypes = entityTypesResult || [];\n\n      return vertexToAnnotation(result.value, entityTypes);\n    } catch (error) {\n      console.error('Failed to get annotation from Neptune:', error);\n      throw error;\n    }\n  }\n  \n  async updateAnnotation(id: AnnotationUri, updates: Partial<Annotation>): Promise<Annotation> {\n    try {\n      let traversal = this.g.V()\n        .hasLabel('Annotation')\n        .has('id', id);\n\n      // Update target properties\n      if (updates.target !== undefined && typeof updates.target !== 'string') {\n        if (updates.target.selector !== undefined) {\n          traversal = traversal.property('text', getExactText(updates.target.selector));\n        }\n      }\n\n      // Update body properties and entity types\n      if (updates.body !== undefined) {\n        const bodySource = getBodySource(updates.body);\n        const entityTypes = getEntityTypes({ body: updates.body });\n\n        if (bodySource) {\n          traversal = traversal.property('source', bodySource);\n        }\n\n        // Update entity type relationships - remove old ones and create new ones\n        if (entityTypes.length >= 0) {\n          // Remove existing TAGGED_AS edges\n          await this.g.V()\n            .hasLabel('Annotation')\n            .has('id', id)\n            .outE('TAGGED_AS')\n            .drop()\n            .iterate();\n\n          // Create new TAGGED_AS edges\n          for (const entityType of entityTypes) {\n            const etVertex = await this.g.V()\n              .hasLabel('EntityType')\n              .has('name', entityType)\n              .fold()\n              .coalesce(\n                __.unfold(),\n                this.g.addV('EntityType').property('name', entityType)\n              )\n              .next();\n\n            await this.g.V()\n              .hasLabel('Annotation')\n              .has('id', id)\n              .addE('TAGGED_AS')\n              .to(this.g.V(etVertex.value))\n              .next();\n          }\n        }\n      }\n\n      if (updates.modified !== undefined) {\n        traversal = traversal.property('modified', updates.modified);\n      }\n      if (updates.generator !== undefined) {\n        traversal = traversal.property('generator', JSON.stringify(updates.generator));\n      }\n\n      const result = await traversal.elementMap().next();\n\n      if (!result.value) {\n        throw new Error('Annotation not found');\n      }\n\n      // Fetch entity types from TAGGED_AS relationships\n      const entityTypesResult = await this.g.V()\n        .hasLabel('Annotation')\n        .has('id', id)\n        .out('TAGGED_AS')\n        .hasLabel('EntityType')\n        .values('name')\n        .toList();\n\n      const entityTypes = entityTypesResult || [];\n\n      return vertexToAnnotation(result.value, entityTypes);\n    } catch (error) {\n      console.error('Failed to update annotation in Neptune:', error);\n      throw error;\n    }\n  }\n  \n  async deleteAnnotation(id: AnnotationUri): Promise<void> {\n    try {\n      await this.g.V()\n        .hasLabel('Annotation')\n        .has('id', id)\n        .drop()\n        .iterate();\n      \n      console.log(`Deleted annotation from Neptune: ${id}`);\n    } catch (error) {\n      console.error('Failed to delete annotation from Neptune:', error);\n      throw error;\n    }\n  }\n  \n  async listAnnotations(filter: { resourceId?: ResourceId; type?: AnnotationCategory }): Promise<{ annotations: Annotation[]; total: number }> {\n    try {\n      let traversal = this.g.V().hasLabel('Annotation');\n\n      // Apply filters\n      if (filter.resourceId) {\n        traversal = traversal.has('resourceId', filter.resourceId);\n      }\n\n      if (filter.type) {\n        const w3cType = filter.type === 'highlight' ? 'TextualBody' : 'SpecificResource';\n        traversal = traversal.has('type', w3cType);\n      }\n\n      const results = await traversal.elementMap().toList();\n      const annotations = await this.fetchAnnotationsWithEntityTypes(results);\n\n      return { annotations, total: annotations.length };\n    } catch (error) {\n      console.error('Failed to list annotations from Neptune:', error);\n      throw error;\n    }\n  }\n  \n  \n  async getHighlights(resourceId: ResourceId): Promise<Annotation[]> {\n    try {\n      const results = await this.g.V()\n        .hasLabel('Annotation')\n        .has('resourceId', resourceId)\n        .hasNot('resolvedResourceId')\n        .elementMap()\n        .toList();\n\n      return await this.fetchAnnotationsWithEntityTypes(results);\n    } catch (error) {\n      console.error('Failed to get highlights from Neptune:', error);\n      throw error;\n    }\n  }\n  \n  async resolveReference(annotationId: AnnotationId, source: ResourceId): Promise<Annotation> {\n    try {\n      // Get target resource name\n      const targetDocResult = await this.g.V()\n        .hasLabel('Resource')\n        .has('id', source)\n        .elementMap()\n        .next();\n      const targetDoc = targetDocResult.value ? vertexToResource(targetDocResult.value) : null;\n\n      // Update the existing Annotation vertex\n      const traversal = this.g.V()\n        .hasLabel('Annotation')\n        .has('id', annotationId)\n        .property('source', source)\n        .property('resolvedResourceName', targetDoc?.name)\n        .property('resolvedAt', new Date().toISOString());\n\n      const result = await traversal.elementMap().next();\n\n      if (!result.value) {\n        throw new Error('Annotation not found');\n      }\n\n      // Create REFERENCES edge to the resolved resource\n      const annVertex = await this.g.V()\n        .hasLabel('Annotation')\n        .has('id', annotationId)\n        .next();\n\n      await this.g.V(annVertex.value)\n        .addE('REFERENCES')\n        .to(this.g.V().hasLabel('Resource').has('id', source))\n        .next();\n\n      // Fetch entity types from TAGGED_AS relationships\n      const entityTypesResult = await this.g.V()\n        .hasLabel('Annotation')\n        .has('id', annotationId)\n        .out('TAGGED_AS')\n        .hasLabel('EntityType')\n        .values('name')\n        .toList();\n\n      const entityTypes = entityTypesResult || [];\n\n      return vertexToAnnotation(result.value, entityTypes);\n    } catch (error) {\n      console.error('Failed to resolve reference in Neptune:', error);\n      throw error;\n    }\n  }\n  \n  async getReferences(resourceId: ResourceId): Promise<Annotation[]> {\n    try {\n      const results = await this.g.V()\n        .hasLabel('Annotation')\n        .has('resourceId', resourceId)\n        .has('resolvedResourceId')\n        .elementMap()\n        .toList();\n\n      return await this.fetchAnnotationsWithEntityTypes(results);\n    } catch (error) {\n      console.error('Failed to get references from Neptune:', error);\n      throw error;\n    }\n  }\n  \n  async getEntityReferences(resourceId: ResourceId, entityTypes?: string[]): Promise<Annotation[]> {\n    try {\n      let traversal = this.g.V()\n        .hasLabel('Annotation')\n        .has('resourceId', resourceId)\n        .has('resolvedResourceId')\n        .has('entityTypes');\n      \n      if (entityTypes && entityTypes.length > 0) {\n        traversal = traversal.filter(\n          process.statics.or(\n            ...entityTypes.map((type: string) =>\n              process.statics.has('entityTypes', TextP.containing(`\"${type}\"`))\n            )\n          )\n        );\n      }\n      \n      const results = await traversal.elementMap().toList();\n\n      return await this.fetchAnnotationsWithEntityTypes(results);\n    } catch (error) {\n      console.error('Failed to get entity references from Neptune:', error);\n      throw error;\n    }\n  }\n  \n  async getResourceAnnotations(resourceId: ResourceId): Promise<Annotation[]> {\n    try {\n      const results = await this.g.V()\n        .hasLabel('Annotation')\n        .has('resourceId', resourceId)\n        .elementMap()\n        .toList();\n\n      return await this.fetchAnnotationsWithEntityTypes(results);\n    } catch (error) {\n      console.error('Failed to get resource annotations from Neptune:', error);\n      throw error;\n    }\n  }\n  \n  async getResourceReferencedBy(resourceUri: ResourceUri, _motivation?: string): Promise<Annotation[]> {\n    try {\n      const results = await this.g.V()\n        .hasLabel('Annotation')\n        .has('resolvedResourceId', resourceUri)\n        .elementMap()\n        .toList();\n\n      return await this.fetchAnnotationsWithEntityTypes(results);\n    } catch (error) {\n      console.error('Failed to get resource referenced by from Neptune:', error);\n      throw error;\n    }\n  }\n  \n  async getResourceConnections(resourceId: ResourceId): Promise<GraphConnection[]> {\n    try {\n      // Get all annotations from this resource that reference other resources\n      const outgoingAnnotations = await this.g.V()\n        .hasLabel('Annotation')\n        .has('resourceId', resourceId)\n        .has('source')\n        .elementMap()\n        .toList();\n\n      // Get all annotations that reference this resource\n      const incomingAnnotations = await this.g.V()\n        .hasLabel('Annotation')\n        .has('source', resourceId)\n        .elementMap()\n        .toList();\n\n      // Build connections map\n      const connectionsMap = new Map<string, GraphConnection>();\n\n      // Process outgoing references\n      for (const annVertex of outgoingAnnotations) {\n        const id = annVertex.properties?.id?.[0]?.value || annVertex.id;\n\n        // Fetch entity types for this annotation\n        const entityTypesResult = await this.g.V()\n          .hasLabel('Annotation')\n          .has('id', id)\n          .out('TAGGED_AS')\n          .hasLabel('EntityType')\n          .values('name')\n          .toList();\n\n        const entityTypes = entityTypesResult || [];\n        const annotation = vertexToAnnotation(annVertex, entityTypes);\n        const targetDocId = getBodySource(annotation.body);\n        if (!targetDocId) continue; // Skip stubs\n\n        // Get the target resource\n        const targetDocResult = await this.g.V()\n          .hasLabel('Resource')\n          .has('id', targetDocId)\n          .elementMap()\n          .next();\n\n        if (targetDocResult.value) {\n          const targetDoc = vertexToResource(targetDocResult.value);\n          const targetDocId = getResourceId(targetDoc);\n          if (!targetDocId) continue;\n          const existing = connectionsMap.get(targetDocId);\n          if (existing) {\n            existing.annotations.push(annotation);\n          } else {\n            connectionsMap.set(targetDocId, {\n              targetResource: targetDoc,\n              annotations: [annotation],\n              bidirectional: false,\n            });\n          }\n        }\n      }\n\n      // Check for bidirectional connections\n      for (const annVertex of incomingAnnotations) {\n        const id = annVertex.properties?.id?.[0]?.value || annVertex.id;\n\n        // Fetch entity types for this annotation\n        const entityTypesResult = await this.g.V()\n          .hasLabel('Annotation')\n          .has('id', id)\n          .out('TAGGED_AS')\n          .hasLabel('EntityType')\n          .values('name')\n          .toList();\n\n        const entityTypes = entityTypesResult || [];\n        const annotation = vertexToAnnotation(annVertex, entityTypes);\n        const sourceDocId = getTargetSource(annotation.target);\n        const existing = connectionsMap.get(sourceDocId);\n        if (existing) {\n          existing.bidirectional = true;\n        }\n      }\n\n      return Array.from(connectionsMap.values());\n    } catch (error) {\n      console.error('Failed to get resource connections from Neptune:', error);\n      throw error;\n    }\n  }\n  \n  async findPath(fromResourceId: string, toResourceId: string, maxDepth: number = 5): Promise<GraphPath[]> {\n    try {\n      // Use Neptune's optimized path queries\n      const results = await this.g.V()\n        .hasLabel('Resource')\n        .has('id', fromResourceId)\n        .repeat(\n          process.statics.both('REFERENCES')\n            .simplePath()\n        )\n        .times(maxDepth)\n        .emit()\n        .has('id', toResourceId)\n        .path()\n        .by(process.statics.elementMap())\n        .limit(10)\n        .toList();\n      \n      const paths: GraphPath[] = [];\n      \n      for (const pathResult of results) {\n        const resources: ResourceDescriptor[] = [];\n\n        // Process path elements (alternating vertices and edges)\n        for (let i = 0; i < pathResult.objects.length; i++) {\n          const element = pathResult.objects[i];\n\n          if (i % 2 === 0) {\n            // Vertex (Resource)\n            resources.push(vertexToResource(element));\n          } else {\n            // Edge - skip for now as we're using vertex-based annotations\n            // We'd need to query for annotations between resources\n          }\n        }\n\n        paths.push({ resources, annotations: [] });\n      }\n      \n      return paths;\n    } catch (error) {\n      console.error('Failed to find paths in Neptune:', error);\n      throw error;\n    }\n  }\n  \n  async getEntityTypeStats(): Promise<EntityTypeStats[]> {\n    try {\n      // Use Neptune's analytics capabilities\n      const results = await this.g.V()\n        .hasLabel('Resource')\n        .values('entityTypes')\n        .map((entityTypesJson: string) => {\n          const types = JSON.parse(entityTypesJson);\n          return types;\n        })\n        .unfold()\n        .groupCount()\n        .next();\n      \n      const stats: EntityTypeStats[] = [];\n      \n      if (results.value) {\n        for (const [type, count] of Object.entries(results.value)) {\n          stats.push({\n            type,\n            count: count as number,\n          });\n        }\n      }\n      \n      return stats;\n    } catch (error) {\n      console.error('Failed to get entity type stats from Neptune:', error);\n      throw error;\n    }\n  }\n  \n  async getStats(): Promise<{\n    resourceCount: number;\n    annotationCount: number;\n    highlightCount: number;\n    referenceCount: number;\n    entityReferenceCount: number;\n    entityTypes: Record<string, number>;\n    contentTypes: Record<string, number>;\n  }> {\n    try {\n      // Get resource count\n      const docCountResult = await this.g.V()\n        .hasLabel('Resource')\n        .count()\n        .next();\n      const resourceCount = docCountResult.value || 0;\n      \n      // Get annotation count\n      const selCountResult = await this.g.V()\n        .hasLabel('Annotation')\n        .count()\n        .next();\n      const annotationCount = selCountResult.value || 0;\n\n      // Get highlight count (annotations without resolved resource)\n      const highlightCountResult = await this.g.V()\n        .hasLabel('Annotation')\n        .hasNot('resolvedResourceId')\n        .count()\n        .next();\n      const highlightCount = highlightCountResult.value || 0;\n\n      // Get reference count (annotations with resolved resource)\n      const referenceCountResult = await this.g.V()\n        .hasLabel('Annotation')\n        .has('resolvedResourceId')\n        .count()\n        .next();\n      const referenceCount = referenceCountResult.value || 0;\n\n      // Get entity reference count\n      const entityRefCountResult = await this.g.V()\n        .hasLabel('Annotation')\n        .has('resolvedResourceId')\n        .has('entityTypes')\n        .count()\n        .next();\n      const entityReferenceCount = entityRefCountResult.value || 0;\n      \n      // Get entity type stats\n      const entityTypeStats = await this.getEntityTypeStats();\n      const entityTypes: Record<string, number> = {};\n      for (const stat of entityTypeStats) {\n        entityTypes[stat.type] = stat.count;\n      }\n      \n      // Get content type stats\n      const contentTypeResult = await this.g.V()\n        .hasLabel('Resource')\n        .groupCount()\n        .by('contentType')\n        .next();\n      const contentTypes = contentTypeResult.value || {};\n      \n      return {\n        resourceCount,\n        annotationCount,\n        highlightCount,\n        referenceCount,\n        entityReferenceCount,\n        entityTypes,\n        contentTypes,\n      };\n    } catch (error) {\n      console.error('Failed to get stats from Neptune:', error);\n      throw error;\n    }\n  }\n  \n  async createAnnotations(inputs: CreateAnnotationInternal[]): Promise<Annotation[]> {\n    const results: Annotation[] = [];\n\n    try {\n      for (const input of inputs) {\n        const annotation = await this.createAnnotation(input);\n        results.push(annotation);\n      }\n\n      return results;\n    } catch (error) {\n      console.error('Failed to create annotations in Neptune:', error);\n      throw error;\n    }\n  }\n\n\n  async resolveReferences(inputs: { annotationId: AnnotationId; source: ResourceId }[]): Promise<Annotation[]> {\n    const results: Annotation[] = [];\n\n    try {\n      for (const input of inputs) {\n        const annotation = await this.resolveReference(input.annotationId, input.source);\n        results.push(annotation);\n      }\n\n      return results;\n    } catch (error) {\n      console.error('Failed to resolve references in Neptune:', error);\n      throw error;\n    }\n  }\n  \n  async detectAnnotations(_resourceId: ResourceId): Promise<Annotation[]> {\n    // This would use AI/ML to detect annotations in a resource\n    // For now, return empty array as a placeholder\n    return [];\n  }\n  \n  // Tag Collections - stored as special vertices in the graph\n  private entityTypesCollection: Set<string> | null = null;\n  \n  async getEntityTypes(): Promise<string[]> {\n    // Initialize if not already loaded\n    if (this.entityTypesCollection === null) {\n      await this.initializeTagCollections();\n    }\n    return Array.from(this.entityTypesCollection!).sort();\n  }\n  \n  async addEntityType(tag: string): Promise<void> {\n    if (this.entityTypesCollection === null) {\n      await this.initializeTagCollections();\n    }\n    this.entityTypesCollection!.add(tag);\n    // Persist to Neptune\n    try {\n      await this.g.V()\n        .has('tagCollection', 'type', 'entity-types')\n        .fold()\n        .coalesce(\n          __.unfold(),\n          __.addV('TagCollection').property('type', 'entity-types')\n        )\n        .property(cardinality.set, 'tags', tag)\n        .iterate();\n    } catch (error) {\n      console.error('Failed to add entity type:', error);\n    }\n  }\n  \n  async addEntityTypes(tags: string[]): Promise<void> {\n    if (this.entityTypesCollection === null) {\n      await this.initializeTagCollections();\n    }\n    tags.forEach(tag => this.entityTypesCollection!.add(tag));\n    // Persist to Neptune\n    try {\n      const vertex = await this.g.V()\n        .has('tagCollection', 'type', 'entity-types')\n        .fold()\n        .coalesce(\n          __.unfold(),\n          __.addV('TagCollection').property('type', 'entity-types')\n        );\n      \n      for (const tag of tags) {\n        await vertex.property(cardinality.set, 'tags', tag).iterate();\n      }\n    } catch (error) {\n      console.error('Failed to add entity types:', error);\n    }\n  }\n  \n  private async initializeTagCollections(): Promise<void> {\n    try {\n      // Check Neptune for existing collections\n      const collections = await this.g.V()\n        .hasLabel('TagCollection')\n        .project('type', 'tags')\n        .by('type')\n        .by(__.values('tags').fold())\n        .toList();\n\n      // Process existing collections\n      for (const col of collections) {\n        if (col.type === 'entity-types') {\n          this.entityTypesCollection = new Set(col.tags as string[]);\n        }\n      }\n    } catch (error) {\n      console.log('No existing tag collections found, will initialize with defaults');\n    }\n\n    // Initialize with defaults if not present\n    if (this.entityTypesCollection === null) {\n      const { DEFAULT_ENTITY_TYPES } = await import('@semiont/ontology');\n      this.entityTypesCollection = new Set(DEFAULT_ENTITY_TYPES);\n      // Persist defaults to Neptune\n      try {\n        const vertex = await this.g.addV('TagCollection')\n          .property('type', 'entity-types')\n          .next();\n        for (const tag of DEFAULT_ENTITY_TYPES) {\n          await this.g.V(vertex.value.id)\n            .property(cardinality.set, 'tags', tag)\n            .iterate();\n        }\n      } catch (error) {\n        console.error('Failed to initialize entity types:', error);\n      }\n    }\n  }\n  \n  generateId(): string {\n    return uuidv4().replace(/-/g, '').substring(0, 12);\n  }\n  \n  async clearDatabase(): Promise<void> {\n    try {\n      // CAREFUL! This clears the entire graph\n      await this.g.V().drop().iterate();\n      console.log('Cleared all data from Neptune');\n      // Reset tag collections\n      this.entityTypesCollection = null;\n    } catch (error) {\n      console.error('Failed to clear Neptune database:', error);\n      throw error;\n    }\n  }\n}","// Neo4j implementation of GraphDatabase interface\n// Uses Cypher query language\n\nimport neo4j, { Driver, Session } from 'neo4j-driver';\nimport { GraphDatabase } from '../interface';\nimport type { components } from '@semiont/api-client';\nimport type {\n  AnnotationCategory,\n  GraphConnection,\n  GraphPath,\n  EntityTypeStats,\n  ResourceFilter,\n  UpdateResourceInput,\n  CreateAnnotationInternal,\n  ResourceId,\n  AnnotationId,\n} from '@semiont/core';\nimport type { ResourceUri, AnnotationUri } from '@semiont/api-client';\nimport { getExactText } from '@semiont/api-client';\nimport { v4 as uuidv4 } from 'uuid';\nimport { getBodySource, getTargetSource, getTargetSelector } from '@semiont/api-client';\nimport { getEntityTypes } from '@semiont/ontology';\nimport { getPrimaryRepresentation } from '@semiont/api-client';\n\ntype ResourceDescriptor = components['schemas']['ResourceDescriptor'];\ntype Annotation = components['schemas']['Annotation'];\n\n/**\n * Convert motivation to a valid Neo4j label name\n *\n * Annotations get both a property (`motivation: \"linking\"`) and a label (`:Linking`)\n * for the same motivation value. This enables:\n * - Fast filtering: `MATCH (a:Annotation:Linking)` vs `MATCH (a:Annotation) WHERE a.motivation = 'linking'`\n * - Automatic indexing: Neo4j indexes labels by default\n * - Visual exploration: Graph visualization tools prominently display labels\n *\n * Example: \"linking\" -> \"Linking\", \"commenting\" -> \"Commenting\"\n *\n * W3C Motivation values:\n * assessing, bookmarking, classifying, commenting, describing, editing,\n * highlighting, identifying, linking, moderating, questioning, replying, tagging\n */\nfunction motivationToLabel(motivation: string): string {\n  return motivation.charAt(0).toUpperCase() + motivation.slice(1);\n}\n\nexport class Neo4jGraphDatabase implements GraphDatabase {\n  private driver: Driver | null = null;\n  private connected: boolean = false;\n  private config: {\n    uri?: string;\n    username?: string;\n    password?: string;\n    database?: string;\n  };\n\n  // Tag Collections - cached in memory for performance\n  private entityTypesCollection: Set<string> | null = null;\n\n  constructor(config: {\n    uri?: string;\n    username?: string;\n    password?: string;\n    database?: string;\n  } = {}) {\n    this.config = config;\n  }\n\n  async connect(): Promise<void> {\n    try {\n      const uri = this.config.uri;\n      const username = this.config.username;\n      const password = this.config.password;\n      const database = this.config.database;\n\n      if (!uri) {\n        throw new Error('Neo4j URI not configured! Pass uri in config.');\n      }\n      if (!username) {\n        throw new Error('Neo4j username not configured! Pass username in config.');\n      }\n      if (!password) {\n        throw new Error('Neo4j password not configured! Pass password in config.');\n      }\n      if (!database) {\n        throw new Error('Neo4j database not configured! Pass database in config.');\n      }\n\n      console.log(`Connecting to Neo4j at ${uri}...`);\n\n      this.driver = neo4j.driver(\n        uri,\n        neo4j.auth.basic(username, password),\n        {\n          maxConnectionPoolSize: 50,\n          connectionAcquisitionTimeout: 60000,\n        }\n      );\n\n      // Test connection\n      const session = this.driver.session({ database });\n\n      await session.run('RETURN 1 as test');\n      await session.close();\n\n      // Create constraints and indexes if they don't exist\n      await this.ensureSchemaExists();\n\n      console.log('Successfully connected to Neo4j');\n      this.connected = true;\n    } catch (error) {\n      console.error('Failed to connect to Neo4j:', error);\n      throw new Error(`Neo4j connection failed: ${error}`);\n    }\n  }\n\n  async disconnect(): Promise<void> {\n    if (this.driver) {\n      await this.driver.close();\n      this.driver = null;\n    }\n    this.connected = false;\n  }\n\n  isConnected(): boolean {\n    return this.connected;\n  }\n\n  private getSession(): Session {\n    if (!this.driver) {\n      throw new Error('Neo4j driver not initialized');\n    }\n    if (!this.config.database) {\n      throw new Error('Neo4j database not configured! Pass database in config.');\n    }\n    return this.driver.session({\n      database: this.config.database\n    });\n  }\n\n  private async ensureSchemaExists(): Promise<void> {\n    const session = this.getSession();\n    try {\n      // Create constraints for unique IDs\n      const constraints = [\n        'CREATE CONSTRAINT doc_id IF NOT EXISTS FOR (d:Resource) REQUIRE d.id IS UNIQUE',\n        'CREATE CONSTRAINT sel_id IF NOT EXISTS FOR (s:Annotation) REQUIRE s.id IS UNIQUE',\n        'CREATE CONSTRAINT tag_id IF NOT EXISTS FOR (t:TagCollection) REQUIRE t.type IS UNIQUE'\n      ];\n\n      for (const constraint of constraints) {\n        try {\n          await session.run(constraint);\n        } catch (error: any) {\n          // Ignore if constraint already exists\n          if (!error.message?.includes('already exists')) {\n            console.warn(`Schema creation warning: ${error.message}`);\n          }\n        }\n      }\n\n      // Create indexes for common queries\n      const indexes = [\n        'CREATE INDEX doc_name IF NOT EXISTS FOR (d:Resource) ON (d.name)',\n        'CREATE INDEX doc_entity_types IF NOT EXISTS FOR (d:Resource) ON (d.entityTypes)',\n        'CREATE INDEX sel_doc_id IF NOT EXISTS FOR (s:Annotation) ON (s.resourceId)',\n        'CREATE INDEX sel_resolved_id IF NOT EXISTS FOR (s:Annotation) ON (s.resolvedResourceId)'\n      ];\n\n      for (const index of indexes) {\n        try {\n          await session.run(index);\n        } catch (error: any) {\n          // Ignore if index already exists\n          if (!error.message?.includes('already exists')) {\n            console.warn(`Index creation warning: ${error.message}`);\n          }\n        }\n      }\n    } finally {\n      await session.close();\n    }\n  }\n\n  async createResource(resource: ResourceDescriptor): Promise<ResourceDescriptor> {\n    const session = this.getSession();\n    try {\n      const id = resource['@id']; // Use full URI for consistency\n      const primaryRep = getPrimaryRepresentation(resource);\n      if (!primaryRep) {\n        throw new Error('Resource must have at least one representation');\n      }\n\n      const result = await session.run(\n        `CREATE (d:Resource {\n          id: $id,\n          name: $name,\n          entityTypes: $entityTypes,\n          format: $format,\n          archived: $archived,\n          created: datetime($created),\n          creator: $creator,\n          creationMethod: $creationMethod,\n          contentChecksum: $contentChecksum,\n          sourceAnnotationId: $sourceAnnotationId,\n          sourceResourceId: $sourceResourceId\n        }) RETURN d`,\n        {\n          id,\n          name: resource.name,\n          entityTypes: resource.entityTypes,\n          format: primaryRep.mediaType,\n          archived: resource.archived || false,\n          created: resource.dateCreated,\n          creator: JSON.stringify(resource.wasAttributedTo),\n          creationMethod: resource.creationMethod,\n          contentChecksum: primaryRep.checksum,\n          sourceAnnotationId: resource.sourceAnnotationId ?? null,\n          sourceResourceId: resource.sourceResourceId ?? null,\n        }\n      );\n\n      return this.parseResourceNode(result.records[0]!.get('d'));\n    } finally {\n      await session.close();\n    }\n  }\n\n  async getResource(id: ResourceUri): Promise<ResourceDescriptor | null> {\n    const session = this.getSession();\n    try {\n      const result = await session.run(\n        'MATCH (d:Resource {id: $id}) RETURN d',\n        { id }\n      );\n\n      if (result.records.length === 0) return null;\n      return this.parseResourceNode(result.records[0]!.get('d'));\n    } finally {\n      await session.close();\n    }\n  }\n\n  async updateResource(id: ResourceUri, input: UpdateResourceInput): Promise<ResourceDescriptor> {\n    // Resources are immutable - only archiving is allowed\n    if (Object.keys(input).length !== 1 || input.archived === undefined) {\n      throw new Error('Resources are immutable. Only archiving is allowed.');\n    }\n\n    const session = this.getSession();\n    try {\n      const result = await session.run(\n        `MATCH (d:Resource {id: $id})\n         SET d.archived = $archived\n         RETURN d`,\n        { id, archived: input.archived }\n      );\n\n      if (result.records.length === 0) {\n        throw new Error('Resource not found');\n      }\n\n      return this.parseResourceNode(result.records[0]!.get('d'));\n    } finally {\n      await session.close();\n    }\n  }\n\n  async deleteResource(id: ResourceUri): Promise<void> {\n    const session = this.getSession();\n    try {\n      // Delete resource and all its annotations\n      await session.run(\n        `MATCH (d:Resource {id: $id})\n         OPTIONAL MATCH (a:Annotation)-[:BELONGS_TO|:REFERENCES]->(d)\n         DETACH DELETE d, a`,\n        { id }\n      );\n    } finally {\n      await session.close();\n    }\n  }\n\n  async listResources(filter: ResourceFilter): Promise<{ resources: ResourceDescriptor[]; total: number }> {\n    const session = this.getSession();\n    try {\n      let whereClause = '';\n      const params: any = {};\n      const conditions: string[] = [];\n\n      if (filter.entityTypes && filter.entityTypes.length > 0) {\n        conditions.push('ANY(type IN $entityTypes WHERE type IN d.entityTypes)');\n        params.entityTypes = filter.entityTypes;\n      }\n\n      if (filter.search) {\n        conditions.push('toLower(d.name) CONTAINS toLower($search)');\n        params.search = filter.search;\n      }\n\n      if (conditions.length > 0) {\n        whereClause = 'WHERE ' + conditions.join(' AND ');\n      }\n\n      // Get total count\n      const countResult = await session.run(\n        `MATCH (d:Resource) ${whereClause} RETURN count(d) as total`,\n        params\n      );\n      const total = countResult.records[0]!.get('total').toNumber();\n\n      // Get paginated results - ensure integers for Neo4j\n      params.skip = neo4j.int(filter.offset || 0);\n      params.limit = neo4j.int(filter.limit || 20);\n\n      const result = await session.run(\n        `MATCH (d:Resource) ${whereClause}\n         RETURN d\n         ORDER BY d.updatedAt DESC\n         SKIP $skip LIMIT $limit`,\n        params\n      );\n\n      const resources = result.records.map(record => this.parseResourceNode(record.get('d')));\n\n      return { resources, total };\n    } finally {\n      await session.close();\n    }\n  }\n\n  async searchResources(query: string, limit: number = 20): Promise<ResourceDescriptor[]> {\n    const session = this.getSession();\n    try {\n      const result = await session.run(\n        `MATCH (d:Resource)\n         WHERE toLower(d.name) CONTAINS toLower($query)\n         RETURN d\n         ORDER BY d.updatedAt DESC\n         LIMIT $limit`,\n        { query, limit: neo4j.int(limit) }\n      );\n\n      return result.records.map(record => this.parseResourceNode(record.get('d')));\n    } finally {\n      await session.close();\n    }\n  }\n\n  async createAnnotation(input: CreateAnnotationInternal): Promise<Annotation> {\n    const session = this.getSession();\n    try {\n      const id = input.id;\n\n      const annotation: Annotation = {\n        '@context': 'http://www.w3.org/ns/anno.jsonld' as const,\n        'type': 'Annotation' as const,\n        id,\n        motivation: input.motivation,\n        target: input.target,\n        body: input.body,\n        creator: input.creator,\n        created: new Date().toISOString(),\n      };\n\n      // Extract values for Cypher query\n      const targetSource = getTargetSource(input.target);\n      const targetSelector = getTargetSelector(input.target);\n      const bodySource = getBodySource(input.body);\n\n      // Extract entity types from TextualBody bodies with purpose: \"tagging\"\n      const entityTypes = getEntityTypes(input);\n\n      // Convert motivation to label (e.g., \"linking\" -> \"Linking\")\n      const motivationLabel = motivationToLabel(annotation.motivation);\n\n      // Create the annotation node and relationships\n      let cypher: string;\n      if (bodySource) {\n        // Resolved reference with target resource\n        // Add motivation as both a property and a label for efficient querying\n        cypher = `MATCH (from:Resource {id: $fromId})\n           MATCH (to:Resource {id: $toId})\n           CREATE (a:Annotation:${motivationLabel} {\n             id: $id,\n             resourceId: $resourceId,\n             exact: $exact,\n             selector: $selector,\n             type: $type,\n             motivation: $motivation,\n             creator: $creator,\n             created: datetime($created),\n             source: $source\n           })\n           CREATE (a)-[:BELONGS_TO]->(from)\n           CREATE (a)-[:REFERENCES]->(to)\n           FOREACH (entityType IN $entityTypes |\n             MERGE (et:EntityType {name: entityType})\n             CREATE (a)-[:TAGGED_AS]->(et)\n           )\n           RETURN a`;\n      } else {\n        // Stub reference (unresolved)\n        // Add motivation as both a property and a label for efficient querying\n        cypher = `MATCH (d:Resource {id: $resourceId})\n           CREATE (a:Annotation:${motivationLabel} {\n             id: $id,\n             resourceId: $resourceId,\n             exact: $exact,\n             selector: $selector,\n             type: $type,\n             motivation: $motivation,\n             creator: $creator,\n             created: datetime($created)\n           })\n           CREATE (a)-[:BELONGS_TO]->(d)\n           FOREACH (entityType IN $entityTypes |\n             MERGE (et:EntityType {name: entityType})\n             CREATE (a)-[:TAGGED_AS]->(et)\n           )\n           RETURN a`;\n      }\n\n      const params: any = {\n        id,\n        resourceId: targetSource, // Store full URI\n        fromId: targetSource, // Store full URI\n        toId: bodySource || null, // Store full URI\n        exact: targetSelector ? getExactText(targetSelector) : '',\n        selector: JSON.stringify(targetSelector || {}),\n        type: 'SpecificResource',\n        motivation: annotation.motivation,\n        creator: JSON.stringify(annotation.creator),\n        created: annotation.created,\n        entityTypes,\n        source: bodySource || null,\n      };\n\n      const result = await session.run(cypher, params);\n\n      if (result.records.length === 0) {\n        throw new Error(`Failed to create annotation: Resource ${targetSource} not found in graph database`);\n      }\n\n      return this.parseAnnotationNode(result.records[0]!.get('a'), entityTypes);\n    } finally {\n      await session.close();\n    }\n  }\n\n  async getAnnotation(id: AnnotationUri): Promise<Annotation | null> {\n    console.log(`[Neo4j] getAnnotation called for: ${id}`);\n    const session = this.getSession();\n    try {\n      const result = await session.run(\n        `MATCH (a:Annotation {id: $id})\n         OPTIONAL MATCH (a)-[:TAGGED_AS]->(et:EntityType)\n         RETURN a, collect(et.name) as entityTypes`,\n        { id }\n      );\n\n      if (result.records.length === 0) {\n        console.log(`[Neo4j] getAnnotation: Annotation ${id} NOT FOUND`);\n        return null;\n      }\n      console.log(`[Neo4j] getAnnotation: Annotation ${id} FOUND`);\n      return this.parseAnnotationNode(\n        result.records[0]!.get('a'),\n        result.records[0]!.get('entityTypes')\n      );\n    } finally {\n      await session.close();\n    }\n  }\n\n  async updateAnnotation(id: AnnotationUri, updates: Partial<Annotation>): Promise<Annotation> {\n    const session = this.getSession();\n    try {\n      const setClauses: string[] = ['a.updatedAt = datetime()'];\n      const params: any = { id };\n\n      // Build SET clauses dynamically\n      Object.entries(updates).forEach(([key, value]) => {\n        if (key !== 'id' && key !== 'updatedAt') {\n          setClauses.push(`a.${key} = $${key}`);\n          if (key === 'selector' || key === 'metadata' || key === 'body') {\n            params[key] = JSON.stringify(value);\n          } else if (key === 'created' || key === 'resolvedAt') {\n            params[key] = value ? new Date(value as any).toISOString() : null;\n          } else {\n            params[key] = value;\n          }\n        }\n      });\n\n      // Update annotation properties\n      const result = await session.run(\n        `MATCH (a:Annotation {id: $id})\n         SET ${setClauses.join(', ')}\n         WITH a\n         OPTIONAL MATCH (a)-[:TAGGED_AS]->(et:EntityType)\n         RETURN a, collect(et.name) as entityTypes`,\n        params\n      );\n\n      if (result.records.length === 0) {\n        throw new Error('Annotation not found');\n      }\n\n      // If motivation was updated, update the label\n      if (updates.motivation) {\n        const newLabel = motivationToLabel(updates.motivation);\n        console.log(`[Neo4j] Updating motivation label to: ${newLabel}`);\n\n        // Remove all possible motivation labels and add the new one\n        const allMotivations = ['Assessing', 'Bookmarking', 'Classifying', 'Commenting',\n                                'Describing', 'Editing', 'Highlighting', 'Identifying',\n                                'Linking', 'Moderating', 'Questioning', 'Replying', 'Tagging'];\n        const removeLabels = allMotivations.filter(m => m !== newLabel).map(m => `a:${m}`).join(', ');\n\n        await session.run(\n          `MATCH (a:Annotation {id: $id})\n           REMOVE ${removeLabels}\n           SET a:${newLabel}`,\n          { id }\n        );\n        console.log(`[Neo4j] ✅ Motivation label updated to: ${newLabel}`);\n      }\n\n      // If body was updated and contains a SpecificResource, create REFERENCES relationship\n      if (updates.body) {\n        console.log(`[Neo4j] ====== BODY UPDATE for Annotation ${id} ======`);\n        console.log(`[Neo4j] updates.body:`, JSON.stringify(updates.body));\n        const bodyArray = Array.isArray(updates.body) ? updates.body : [updates.body];\n        console.log(`[Neo4j] bodyArray length: ${bodyArray.length}`);\n\n        bodyArray.forEach((item, idx) => {\n          console.log(`[Neo4j]   Body item ${idx}:`, JSON.stringify(item));\n        });\n\n        const specificResource = bodyArray.find((item: any) => item.type === 'SpecificResource' && item.purpose === 'linking');\n        console.log(`[Neo4j] Found SpecificResource:`, specificResource ? JSON.stringify(specificResource) : 'null');\n\n        if (specificResource && 'source' in specificResource && specificResource.source) {\n          console.log(`[Neo4j] ✅ Creating REFERENCES edge: ${id} -> ${specificResource.source}`);\n          // Create REFERENCES relationship to the target resource\n          const refResult = await session.run(\n            `MATCH (a:Annotation {id: $annotationId})\n             MATCH (target:Resource {id: $targetResourceId})\n             MERGE (a)-[:REFERENCES]->(target)\n             RETURN a, target`,\n            {\n              annotationId: id,\n              targetResourceId: specificResource.source\n            }\n          );\n          console.log(`[Neo4j] ✅ REFERENCES edge created! Matched ${refResult.records.length} nodes`);\n          if (refResult.records.length > 0) {\n            console.log(`[Neo4j]   Annotation: ${refResult.records[0]!.get('a').properties.id}`);\n            console.log(`[Neo4j]   Target Resource: ${refResult.records[0]!.get('target').properties.id}`);\n          }\n        } else {\n          console.log(`[Neo4j] No SpecificResource in body - this is a stub reference (not yet resolved)`);\n        }\n      } else {\n        console.log(`[Neo4j] No body update for annotation ${id}`);\n      }\n\n      return this.parseAnnotationNode(\n        result.records[0]!.get('a'),\n        result.records[0]!.get('entityTypes')\n      );\n    } finally {\n      await session.close();\n    }\n  }\n\n  async deleteAnnotation(id: AnnotationUri): Promise<void> {\n    const session = this.getSession();\n    try {\n      await session.run(\n        'MATCH (a:Annotation {id: $id}) DETACH DELETE a',\n        { id }\n      );\n    } finally {\n      await session.close();\n    }\n  }\n\n  async listAnnotations(filter: { resourceId?: ResourceId; type?: AnnotationCategory }): Promise<{ annotations: Annotation[]; total: number }> {\n    const session = this.getSession();\n    try {\n      const conditions: string[] = [];\n      const params: any = {};\n\n      if (filter.resourceId) {\n        conditions.push('a.resourceId = $resourceId');\n        params.resourceId = filter.resourceId;\n      }\n\n      if (filter.type) {\n        const w3cType = filter.type === 'highlight' ? 'TextualBody' : 'SpecificResource';\n        conditions.push('a.type = $type');\n        params.type = w3cType;\n      }\n\n      const whereClause = conditions.length > 0 ? 'WHERE ' + conditions.join(' AND ') : '';\n\n      // Get all results (no pagination in new simplified interface)\n      const result = await session.run(\n        `MATCH (a:Annotation) ${whereClause}\n         OPTIONAL MATCH (a)-[:TAGGED_AS]->(et:EntityType)\n         RETURN a, collect(et.name) as entityTypes`,\n        params\n      );\n\n      const annotations = result.records.map(record =>\n        this.parseAnnotationNode(record.get('a'), record.get('entityTypes'))\n      );\n\n      return { annotations, total: annotations.length };\n    } finally {\n      await session.close();\n    }\n  }\n\n  async getHighlights(resourceId: ResourceId): Promise<Annotation[]> {\n    const session = this.getSession();\n    try {\n      const result = await session.run(\n        `MATCH (a:Annotation {resourceId: $resourceId})\n         WHERE a.annotationCategory = 'highlight'\n         OPTIONAL MATCH (a)-[:TAGGED_AS]->(et:EntityType)\n         RETURN a, collect(et.name) as entityTypes\n         ORDER BY a.created DESC`,\n        { resourceId }\n      );\n\n      return result.records.map(record =>\n        this.parseAnnotationNode(record.get('a'), record.get('entityTypes'))\n      );\n    } finally {\n      await session.close();\n    }\n  }\n\n  async resolveReference(annotationId: AnnotationId, source: ResourceId): Promise<Annotation> {\n    const session = this.getSession();\n    try {\n      // Get the target resource's name\n      const docResult = await session.run(\n        'MATCH (d:Resource {id: $id}) RETURN d.name as name',\n        { id: source }\n      );\n      const resourceName = docResult.records[0]?.get('name');\n\n      // Update annotation and create REFERENCES relationship\n      const result = await session.run(\n        `MATCH (a:Annotation {id: $annotationId})\n         MATCH (to:Resource {id: $source})\n         SET a.source = $source,\n             a.resolvedResourceName = $resourceName,\n             a.resolvedAt = datetime()\n         MERGE (a)-[:REFERENCES]->(to)\n         OPTIONAL MATCH (a)-[:TAGGED_AS]->(et:EntityType)\n         RETURN a, collect(et.name) as entityTypes`,\n        { annotationId, source, resourceName }\n      );\n\n      if (result.records.length === 0) {\n        throw new Error('Annotation not found');\n      }\n\n      return this.parseAnnotationNode(\n        result.records[0]!.get('a'),\n        result.records[0]!.get('entityTypes')\n      );\n    } finally {\n      await session.close();\n    }\n  }\n\n  async getReferences(resourceId: ResourceId): Promise<Annotation[]> {\n    const session = this.getSession();\n    try {\n      const result = await session.run(\n        `MATCH (a:Annotation {resourceId: $resourceId})\n         WHERE a.annotationCategory IN ['stub_reference', 'resolved_reference']\n         OPTIONAL MATCH (a)-[:TAGGED_AS]->(et:EntityType)\n         RETURN a, collect(et.name) as entityTypes\n         ORDER BY a.created DESC`,\n        { resourceId }\n      );\n\n      return result.records.map(record =>\n        this.parseAnnotationNode(record.get('a'), record.get('entityTypes'))\n      );\n    } finally {\n      await session.close();\n    }\n  }\n\n  async getEntityReferences(resourceId: ResourceId, entityTypes?: string[]): Promise<Annotation[]> {\n    const session = this.getSession();\n    try {\n      let cypher = `MATCH (a:Annotation {resourceId: $resourceId})\n                    WHERE a.source IS NOT NULL`;\n\n      const params: any = { resourceId };\n\n      if (entityTypes && entityTypes.length > 0) {\n        cypher += `\n          MATCH (a)-[:TAGGED_AS]->(et:EntityType)\n          WHERE et.name IN $entityTypes`;\n        params.entityTypes = entityTypes;\n      }\n\n      cypher += `\n        OPTIONAL MATCH (a)-[:TAGGED_AS]->(et2:EntityType)\n        RETURN a, collect(et2.name) as entityTypes\n        ORDER BY a.created DESC`;\n\n      const result = await session.run(cypher, params);\n\n      return result.records.map(record =>\n        this.parseAnnotationNode(record.get('a'), record.get('entityTypes'))\n      );\n    } finally {\n      await session.close();\n    }\n  }\n\n  async getResourceAnnotations(resourceId: ResourceId): Promise<Annotation[]> {\n    const session = this.getSession();\n    try {\n      const result = await session.run(\n        `MATCH (a:Annotation {resourceId: $resourceId})\n         OPTIONAL MATCH (a)-[:TAGGED_AS]->(et:EntityType)\n         RETURN a, collect(et.name) as entityTypes\n         ORDER BY a.created DESC`,\n        { resourceId }\n      );\n\n      return result.records.map(record =>\n        this.parseAnnotationNode(record.get('a'), record.get('entityTypes'))\n      );\n    } finally {\n      await session.close();\n    }\n  }\n\n  async getResourceReferencedBy(resourceUri: ResourceUri, motivation?: string): Promise<Annotation[]> {\n    const session = this.getSession();\n    try {\n      const filterDesc = motivation ? ` with motivation=${motivation}` : '';\n      console.log(`[Neo4j] getResourceReferencedBy: Searching for annotations${filterDesc} referencing ${resourceUri}`);\n\n      // Build query with optional motivation label filter\n      // If motivation is specified, use the label for efficient filtering\n      const motivationLabel = motivation ? `:${motivationToLabel(motivation)}` : '';\n      const cypher = `MATCH (a:Annotation${motivationLabel})-[:REFERENCES]->(d:Resource {id: $resourceUri})\n         OPTIONAL MATCH (a)-[:TAGGED_AS]->(et:EntityType)\n         RETURN a, collect(et.name) as entityTypes\n         ORDER BY a.created DESC`;\n\n      const result = await session.run(cypher, { resourceUri });\n\n      console.log(`[Neo4j] getResourceReferencedBy: Found ${result.records.length} annotations`);\n\n      return result.records.map(record =>\n        this.parseAnnotationNode(record.get('a'), record.get('entityTypes'))\n      );\n    } finally {\n      await session.close();\n    }\n  }\n\n  async getResourceConnections(resourceId: ResourceId): Promise<GraphConnection[]> {\n    const session = this.getSession();\n    try {\n      const result = await session.run(\n        `MATCH (d:Resource {id: $resourceId})\n         OPTIONAL MATCH (d)<-[:BELONGS_TO]-(a1:Annotation)-[:REFERENCES]->(other:Resource)\n         OPTIONAL MATCH (other)<-[:BELONGS_TO]-(a2:Annotation)-[:REFERENCES]->(d)\n         WITH other, COLLECT(DISTINCT a1) as outgoing, COLLECT(DISTINCT a2) as incoming\n         WHERE other IS NOT NULL\n         RETURN other, outgoing, incoming`,\n        { resourceId }\n      );\n\n      const connections: GraphConnection[] = [];\n\n      for (const record of result.records) {\n        const targetResource = this.parseResourceNode(record.get('other'));\n\n        // Fetch entity types for outgoing annotations\n        const outgoingNodes = record.get('outgoing');\n        const outgoing: Annotation[] = [];\n        for (const annNode of outgoingNodes) {\n          const annId = annNode.properties.id;\n          const annResult = await session.run(\n            `MATCH (a:Annotation {id: $id})\n             OPTIONAL MATCH (a)-[:TAGGED_AS]->(et:EntityType)\n             RETURN a, collect(et.name) as entityTypes`,\n            { id: annId }\n          );\n          if (annResult.records.length > 0) {\n            outgoing.push(this.parseAnnotationNode(\n              annResult.records[0]!.get('a'),\n              annResult.records[0]!.get('entityTypes')\n            ));\n          }\n        }\n\n        // Fetch entity types for incoming annotations\n        const incomingNodes = record.get('incoming');\n        const incoming: Annotation[] = [];\n        for (const annNode of incomingNodes) {\n          const annId = annNode.properties.id;\n          const annResult = await session.run(\n            `MATCH (a:Annotation {id: $id})\n             OPTIONAL MATCH (a)-[:TAGGED_AS]->(et:EntityType)\n             RETURN a, collect(et.name) as entityTypes`,\n            { id: annId }\n          );\n          if (annResult.records.length > 0) {\n            incoming.push(this.parseAnnotationNode(\n              annResult.records[0]!.get('a'),\n              annResult.records[0]!.get('entityTypes')\n            ));\n          }\n        }\n\n        connections.push({\n          targetResource,\n          annotations: outgoing,\n          bidirectional: incoming.length > 0\n        });\n      }\n\n      return connections;\n    } finally {\n      await session.close();\n    }\n  }\n\n  async findPath(fromResourceId: string, toResourceId: string, maxDepth: number = 5): Promise<GraphPath[]> {\n    const session = this.getSession();\n    try {\n      const result = await session.run(\n        `MATCH path = shortestPath((from:Resource {id: $fromId})-[:REFERENCES*..${maxDepth}]-(to:Resource {id: $toId}))\n         WITH path, nodes(path) as docs, relationships(path) as rels\n         RETURN docs, rels\n         LIMIT 10`,\n        { fromId: fromResourceId, toId: toResourceId }\n      );\n\n      const paths: GraphPath[] = [];\n\n      for (const record of result.records) {\n        const docs = record.get('docs').map((node: any) => this.parseResourceNode(node));\n        const rels = record.get('rels');\n\n        // Get annotation details for the relationships\n        const annotationIds = rels.map((rel: any) => rel.properties.id).filter((id: any) => id);\n        const annotations: Annotation[] = [];\n\n        if (annotationIds.length > 0) {\n          const selResult = await session.run(\n            `MATCH (a:Annotation) WHERE a.id IN $ids\n             OPTIONAL MATCH (a)-[:TAGGED_AS]->(et:EntityType)\n             RETURN a, collect(et.name) as entityTypes`,\n            { ids: annotationIds }\n          );\n          selResult.records.forEach(rec => {\n            annotations.push(this.parseAnnotationNode(\n              rec.get('a'),\n              rec.get('entityTypes')\n            ));\n          });\n        }\n\n        paths.push({\n          resources: docs,\n          annotations: annotations\n        });\n      }\n\n      return paths;\n    } finally {\n      await session.close();\n    }\n  }\n\n  async getEntityTypeStats(): Promise<EntityTypeStats[]> {\n    const session = this.getSession();\n    try {\n      const result = await session.run(\n        `MATCH (d:Resource)\n         UNWIND d.entityTypes AS type\n         RETURN type, count(*) AS count\n         ORDER BY count DESC`\n      );\n\n      return result.records.map(record => ({\n        type: record.get('type'),\n        count: record.get('count').toNumber()\n      }));\n    } finally {\n      await session.close();\n    }\n  }\n\n  async getStats(): Promise<{\n    resourceCount: number;\n    annotationCount: number;\n    highlightCount: number;\n    referenceCount: number;\n    entityReferenceCount: number;\n    entityTypes: Record<string, number>;\n    contentTypes: Record<string, number>;\n  }> {\n    const session = this.getSession();\n    try {\n      // Get resource count\n      const docCountResult = await session.run('MATCH (d:Resource) RETURN count(d) as count');\n      const resourceCount = docCountResult.records[0]!.get('count').toNumber();\n\n      // Get annotation counts\n      const selCountResult = await session.run('MATCH (a:Annotation) RETURN count(a) as count');\n      const annotationCount = selCountResult.records[0]!.get('count').toNumber();\n\n      const highlightCountResult = await session.run(\n        'MATCH (a:Annotation) WHERE a.resolvedResourceId IS NULL RETURN count(a) as count'\n      );\n      const highlightCount = highlightCountResult.records[0]!.get('count').toNumber();\n\n      const referenceCountResult = await session.run(\n        'MATCH (a:Annotation) WHERE a.resolvedResourceId IS NOT NULL RETURN count(a) as count'\n      );\n      const referenceCount = referenceCountResult.records[0]!.get('count').toNumber();\n\n      const entityRefCountResult = await session.run(\n        'MATCH (a:Annotation) WHERE a.resolvedResourceId IS NOT NULL AND size(a.entityTypes) > 0 RETURN count(a) as count'\n      );\n      const entityReferenceCount = entityRefCountResult.records[0]!.get('count').toNumber();\n\n      // Get entity type stats\n      const entityTypeResult = await session.run(\n        `MATCH (d:Resource)\n         UNWIND d.entityTypes AS type\n         RETURN type, count(*) AS count`\n      );\n\n      const entityTypes: Record<string, number> = {};\n      entityTypeResult.records.forEach(record => {\n        entityTypes[record.get('type')] = record.get('count').toNumber();\n      });\n\n      // Get content type stats\n      const contentTypeResult = await session.run(\n        `MATCH (d:Resource)\n         RETURN d.format as type, count(*) AS count`\n      );\n\n      const contentTypes: Record<string, number> = {};\n      contentTypeResult.records.forEach(record => {\n        contentTypes[record.get('type')] = record.get('count').toNumber();\n      });\n\n      return {\n        resourceCount,\n        annotationCount,\n        highlightCount,\n        referenceCount,\n        entityReferenceCount,\n        entityTypes,\n        contentTypes\n      };\n    } finally {\n      await session.close();\n    }\n  }\n\n  async createAnnotations(inputs: CreateAnnotationInternal[]): Promise<Annotation[]> {\n    const results: Annotation[] = [];\n    for (const input of inputs) {\n      results.push(await this.createAnnotation(input));\n    }\n    return results;\n  }\n\n  async resolveReferences(inputs: { annotationId: AnnotationId; source: ResourceId }[]): Promise<Annotation[]> {\n    const results: Annotation[] = [];\n    for (const input of inputs) {\n      results.push(await this.resolveReference(input.annotationId, input.source));\n    }\n    return results;\n  }\n\n  async detectAnnotations(_resourceId: ResourceId): Promise<Annotation[]> {\n    // This would use AI/ML to detect annotations in a resource\n    // For now, return empty array as a placeholder\n    return [];\n  }\n\n  // Tag Collections\n  async getEntityTypes(): Promise<string[]> {\n    if (this.entityTypesCollection === null) {\n      await this.initializeTagCollections();\n    }\n    return Array.from(this.entityTypesCollection!).sort();\n  }\n\n  async addEntityType(tag: string): Promise<void> {\n    if (this.entityTypesCollection === null) {\n      await this.initializeTagCollections();\n    }\n    this.entityTypesCollection!.add(tag);\n    await this.persistTagCollection('entity-types', this.entityTypesCollection!);\n  }\n\n  async addEntityTypes(tags: string[]): Promise<void> {\n    if (this.entityTypesCollection === null) {\n      await this.initializeTagCollections();\n    }\n    tags.forEach(tag => this.entityTypesCollection!.add(tag));\n    await this.persistTagCollection('entity-types', this.entityTypesCollection!);\n  }\n\n  private async initializeTagCollections(): Promise<void> {\n    const session = this.getSession();\n    try {\n      // Load existing collections from Neo4j\n      const result = await session.run(\n        'MATCH (t:TagCollection {type: \"entity-types\"}) RETURN t.tags as tags'\n      );\n\n      let entityTypesFromDb: string[] = [];\n\n      if (result.records.length > 0) {\n        const record = result.records[0];\n        if (record) {\n          const tags = record.get('tags');\n          entityTypesFromDb = tags || [];\n        }\n      }\n\n      // Load defaults\n      const { DEFAULT_ENTITY_TYPES } = await import('@semiont/ontology');\n\n      // Merge with defaults\n      this.entityTypesCollection = new Set([...DEFAULT_ENTITY_TYPES, ...entityTypesFromDb]);\n\n      // Persist merged collection back to Neo4j\n      await this.persistTagCollection('entity-types', this.entityTypesCollection);\n    } finally {\n      await session.close();\n    }\n  }\n\n  private async persistTagCollection(type: string, collection: Set<string>): Promise<void> {\n    const session = this.getSession();\n    try {\n      await session.run(\n        'MERGE (t:TagCollection {type: $type}) SET t.tags = $tags',\n        { type, tags: Array.from(collection) }\n      );\n    } finally {\n      await session.close();\n    }\n  }\n\n  generateId(): string {\n    return uuidv4().replace(/-/g, '').substring(0, 12);\n  }\n\n  async clearDatabase(): Promise<void> {\n    const session = this.getSession();\n    try {\n      // CAREFUL! This clears the entire database\n      await session.run('MATCH (n) DETACH DELETE n');\n      this.entityTypesCollection = null;\n    } finally {\n      await session.close();\n    }\n  }\n\n  // Helper methods to parse Neo4j nodes\n  private parseResourceNode(node: any): ResourceDescriptor {\n    const props = node.properties;\n\n    // Validate all required fields\n    if (!props.id) throw new Error('Resource missing required field: id');\n    if (!props.name) throw new Error(`Resource ${props.id} missing required field: name`);\n    if (!props.entityTypes) throw new Error(`Resource ${props.id} missing required field: entityTypes`);\n    if (!props.format) throw new Error(`Resource ${props.id} missing required field: contentType`);\n    if (props.archived === undefined || props.archived === null) throw new Error(`Resource ${props.id} missing required field: archived`);\n    if (!props.created) throw new Error(`Resource ${props.id} missing required field: created`);\n    if (!props.creator) throw new Error(`Resource ${props.id} missing required field: creator`);\n    if (!props.creationMethod) throw new Error(`Resource ${props.id} missing required field: creationMethod`);\n    if (!props.contentChecksum) throw new Error(`Resource ${props.id} missing required field: contentChecksum`);\n\n    const resource: ResourceDescriptor = {\n      '@context': 'https://schema.org/',\n      '@id': props.id,\n      name: props.name,\n      entityTypes: props.entityTypes,\n      representations: [{\n        mediaType: props.format,\n        checksum: props.contentChecksum,\n        rel: 'original',\n      }],\n      archived: props.archived,\n      dateCreated: props.created.toString(),\n      wasAttributedTo: typeof props.creator === 'string' ? JSON.parse(props.creator) : props.creator,\n      creationMethod: props.creationMethod,\n    };\n\n    if (props.sourceResourceId) resource.sourceResourceId = props.sourceResourceId;\n\n    return resource;\n  }\n\n  private parseAnnotationNode(node: any, entityTypes: string[] = []): Annotation {\n    const props = node.properties;\n\n    // Validate required fields\n    if (!props.id) throw new Error('Annotation missing required field: id');\n    if (!props.resourceId) throw new Error(`Annotation ${props.id} missing required field: resourceId`);\n    // props.exact is optional - not all annotation types have selected text (e.g., image annotations)\n    if (!props.type) throw new Error(`Annotation ${props.id} missing required field: type`);\n    if (!props.selector) throw new Error(`Annotation ${props.id} missing required field: selector`);\n    if (!props.creator) throw new Error(`Annotation ${props.id} missing required field: creator`);\n\n    if (!props.motivation) throw new Error(`Annotation ${props.id} missing required field: motivation`);\n\n    // Parse creator - always stored as JSON string in DB\n    const creator = JSON.parse(props.creator);\n\n    // Reconstruct body array from entity tags and linking body\n    const bodyArray: Array<{type: 'TextualBody'; value: string; purpose: 'tagging'} | {type: 'SpecificResource'; source: string; purpose: 'linking'}> = [];\n\n    // Add entity tag bodies (TextualBody with purpose: \"tagging\")\n    for (const entityType of entityTypes) {\n      if (entityType) {  // Filter out nulls\n        bodyArray.push({\n          type: 'TextualBody' as const,\n          value: entityType,\n          purpose: 'tagging' as const,\n        });\n      }\n    }\n\n    // Add linking body (SpecificResource) if annotation is resolved\n    if (props.source) {\n      bodyArray.push({\n        type: 'SpecificResource' as const,\n        source: props.source,\n        purpose: 'linking' as const,\n      });\n    }\n\n    const annotation: Annotation = {\n      '@context': 'http://www.w3.org/ns/anno.jsonld' as const,\n      'type': 'Annotation' as const,\n      id: props.id,\n      motivation: props.motivation,\n      target: {\n        source: props.resourceId,\n        selector: JSON.parse(props.selector),\n      },\n      body: bodyArray as Annotation['body'],\n      creator,\n      created: props.created, // ISO string from DB\n    };\n\n    // W3C Web Annotation modification tracking\n    if (props.modified) annotation.modified = props.modified.toString();\n    if (props.generator) {\n      try {\n        annotation.generator = JSON.parse(props.generator);\n      } catch (e) {\n        // Ignore parse errors\n      }\n    }\n\n    return annotation;\n  }\n}","// JanusGraph implementation with real Gremlin connection\n// This replaces the mock in-memory implementation\n\nimport gremlin from 'gremlin';\nimport { GraphDatabase } from '../interface';\nimport {\n  getBodySource,\n  getPrimaryRepresentation,\n  getResourceId,\n  getExactText,\n  type components,\n  type ResourceUri,\n  type AnnotationUri,\n  resourceUri,\n} from '@semiont/api-client';\nimport { getEntityTypes } from '@semiont/ontology';\nimport { annotationIdToURI } from '@semiont/core';\nimport type {\n  AnnotationCategory,\n  GraphConnection,\n  GraphPath,\n  EntityTypeStats,\n  ResourceFilter,\n  UpdateResourceInput,\n  CreateAnnotationInternal,\n  ResourceId,\n  AnnotationId,\n  EnvironmentConfig,\n} from '@semiont/core';\nimport { v4 as uuidv4 } from 'uuid';\n\ntype ResourceDescriptor = components['schemas']['ResourceDescriptor'];\ntype Annotation = components['schemas']['Annotation'];\n\nconst traversal = gremlin.process.AnonymousTraversalSource.traversal;\nconst DriverRemoteConnection = gremlin.driver.DriverRemoteConnection;\n\nexport class JanusGraphDatabase implements GraphDatabase {\n  private connected: boolean = false;\n  private connection: gremlin.driver.DriverRemoteConnection | null = null;\n  private g: gremlin.process.GraphTraversalSource | null = null;\n\n  // Tag Collections - cached in memory for performance\n  private entityTypesCollection: Set<string> | null = null;\n\n\n  constructor(\n    private graphConfig: {\n      host?: string;\n      port?: number;\n      storageBackend?: 'cassandra' | 'hbase' | 'berkeleydb';\n      indexBackend?: 'elasticsearch' | 'solr' | 'lucene';\n    },\n    private envConfig: EnvironmentConfig\n  ) {}\n  \n  async connect(): Promise<void> {\n    // Configuration must be provided via constructor\n    const host = this.graphConfig.host;\n    if (!host) {\n      throw new Error('JanusGraph host is required: provide in config');\n    }\n\n    const port = this.graphConfig.port;\n    if (!port) {\n      throw new Error('JanusGraph port is required: provide in config');\n    }\n\n    console.log(`Attempting to connect to JanusGraph at ws://${host}:${port}/gremlin`);\n\n    this.connection = new DriverRemoteConnection(\n      `ws://${host}:${port}/gremlin`,\n      {}\n    );\n\n    this.g = traversal().withRemote(this.connection);\n\n    // Test the connection with a simple query\n    await this.g.V().limit(1).toList();\n\n    this.connected = true;\n    console.log('Successfully connected to JanusGraph');\n\n    // Initialize schema if needed\n    await this.initializeSchema();\n  }\n  \n  async disconnect(): Promise<void> {\n    if (this.connection) {\n      await this.connection.close();\n    }\n    this.connected = false;\n  }\n  \n  isConnected(): boolean {\n    return this.connected;\n  }\n  \n  private async initializeSchema(): Promise<void> {\n    // Note: Schema management in JanusGraph typically requires direct access\n    // to the management API, which isn't available through Gremlin.\n    // In production, you'd run schema initialization scripts separately.\n    console.log('Schema initialization would happen here in production');\n  }\n  \n  // Helper function to convert vertex to Resource\n  private vertexToResource(vertex: any): ResourceDescriptor {\n    const props = vertex.properties || {};\n    const id = this.getPropertyValue(props, 'id');\n\n    // Validate required fields\n    const creatorRaw = this.getPropertyValue(props, 'creator');\n    const creationMethod = this.getPropertyValue(props, 'creationMethod');\n    const contentChecksum = this.getPropertyValue(props, 'contentChecksum');\n    const mediaType = this.getPropertyValue(props, 'contentType');\n\n    if (!creatorRaw) throw new Error(`Resource ${id} missing required field: creator`);\n    if (!creationMethod) throw new Error(`Resource ${id} missing required field: creationMethod`);\n    if (!contentChecksum) throw new Error(`Resource ${id} missing required field: contentChecksum`);\n    if (!mediaType) throw new Error(`Resource ${id} missing required field: contentType`);\n\n    const creator = typeof creatorRaw === 'string' ? JSON.parse(creatorRaw) : creatorRaw;\n\n    const resource: ResourceDescriptor = {\n      '@context': 'https://schema.org/',\n      '@id': id,\n      name: this.getPropertyValue(props, 'name'),\n      entityTypes: JSON.parse(this.getPropertyValue(props, 'entityTypes') || '[]'),\n      representations: [{\n        mediaType,\n        checksum: contentChecksum,\n        rel: 'original',\n      }],\n      archived: this.getPropertyValue(props, 'archived') === 'true',\n      dateCreated: this.getPropertyValue(props, 'created'),\n      wasAttributedTo: creator,\n      creationMethod,\n    };\n\n    const sourceAnnotationId = this.getPropertyValue(props, 'sourceAnnotationId');\n    const sourceResourceId = this.getPropertyValue(props, 'sourceResourceId');\n\n    if (sourceAnnotationId) resource.sourceAnnotationId = sourceAnnotationId;\n    if (sourceResourceId) resource.sourceResourceId = sourceResourceId;\n\n    return resource;\n  }\n  \n  // Helper to get property value from Gremlin vertex properties\n  private getPropertyValue(props: any, key: string): any {\n    if (!props[key]) return undefined;\n    const prop = Array.isArray(props[key]) ? props[key][0] : props[key];\n    return prop?.value || prop;\n  }\n\n  // Helper method to fetch annotations with their entity types\n  private async fetchAnnotationsWithEntityTypes(annotationVertices: any[]): Promise<Annotation[]> {\n    const annotations: Annotation[] = [];\n\n    for (const vertex of annotationVertices) {\n      const id = this.getPropertyValue(vertex.properties || {}, 'id');\n\n      // Fetch entity types for this annotation\n      const entityTypeVertices = await this.g!\n        .V()\n        .has('Annotation', 'id', id)\n        .out('TAGGED_AS')\n        .has('EntityType')\n        .toList();\n\n      const entityTypes = entityTypeVertices.map((v: any) =>\n        this.getPropertyValue(v.properties || {}, 'name')\n      ).filter(Boolean);\n\n      annotations.push(this.vertexToAnnotation(vertex, entityTypes));\n    }\n\n    return annotations;\n  }\n\n  // Helper function to convert vertex to Annotation\n  private vertexToAnnotation(vertex: any, entityTypes: string[] = []): Annotation {\n    const props = vertex.properties || {};\n\n    // Derive motivation from type if not present (backward compatibility)\n    const motivation = this.getPropertyValue(props, 'motivation') || 'linking';\n\n    // Parse creator - always stored as JSON string in DB\n    const creatorJson = this.getPropertyValue(props, 'creator');\n    const creator = JSON.parse(creatorJson);\n\n    // Reconstruct body array from entity tags and linking body\n    const bodyArray: Array<{type: 'TextualBody'; value: string; purpose: 'tagging'} | {type: 'SpecificResource'; source: string; purpose: 'linking'}> = [];\n\n    // Add entity tag bodies (TextualBody with purpose: \"tagging\")\n    for (const entityType of entityTypes) {\n      if (entityType) {\n        bodyArray.push({\n          type: 'TextualBody' as const,\n          value: entityType,\n          purpose: 'tagging' as const,\n        });\n      }\n    }\n\n    // Add linking body (SpecificResource) if annotation is resolved\n    const bodySource = this.getPropertyValue(props, 'source');\n    if (bodySource) {\n      bodyArray.push({\n        type: 'SpecificResource' as const,\n        source: bodySource,\n        purpose: 'linking' as const,\n      });\n    }\n\n    const annotation: Annotation = {\n      '@context': 'http://www.w3.org/ns/anno.jsonld' as const,\n      'type': 'Annotation' as const,\n      id: this.getPropertyValue(props, 'id'),\n      motivation,\n      target: {\n        source: this.getPropertyValue(props, 'resourceId'),\n        selector: JSON.parse(this.getPropertyValue(props, 'selector') || '{}'),\n      },\n      body: bodyArray,\n      creator,\n      created: this.getPropertyValue(props, 'created'), // ISO string from DB\n    };\n\n    // W3C Web Annotation modification tracking\n    const modified = this.getPropertyValue(props, 'modified');\n    if (modified) {\n      annotation.modified = modified;\n    }\n\n    const generatorJson = this.getPropertyValue(props, 'generator');\n    if (generatorJson) {\n      try {\n        annotation.generator = JSON.parse(generatorJson);\n      } catch (e) {\n        // Ignore parse errors\n      }\n    }\n\n    return annotation;\n  }\n\n  async createResource(resource: ResourceDescriptor): Promise<ResourceDescriptor> {\n    const id = getResourceId(resource);\n    const primaryRep = getPrimaryRepresentation(resource);\n    if (!primaryRep) {\n      throw new Error('Resource must have at least one representation');\n    }\n\n    // Create vertex in JanusGraph using fields from ResourceDescriptor\n    const vertex = this.g!\n      .addV('Resource')\n      .property('id', id)\n      .property('name', resource.name)\n      .property('entityTypes', JSON.stringify(resource.entityTypes))\n      .property('contentType', primaryRep.mediaType)\n      .property('archived', resource.archived || false)\n      .property('created', resource.dateCreated)\n      .property('creator', JSON.stringify(resource.wasAttributedTo))\n      .property('creationMethod', resource.creationMethod)\n      .property('contentChecksum', primaryRep.checksum);\n\n    if (resource.sourceAnnotationId) {\n      vertex.property('sourceAnnotationId', resource.sourceAnnotationId);\n    }\n    if (resource.sourceResourceId) {\n      vertex.property('sourceResourceId', resource.sourceResourceId);\n    }\n\n    await vertex.next();\n\n    console.log('Created resource vertex in JanusGraph:', id);\n    return resource;\n  }\n  \n  async getResource(id: ResourceUri): Promise<ResourceDescriptor | null> {\n    const vertices = await this.g!\n      .V()\n      .has('Resource', 'id', id)\n      .toList();\n\n    if (vertices.length === 0) {\n      return null;\n    }\n\n    return this.vertexToResource(vertices[0] as any);\n  }\n  \n  async updateResource(id: ResourceUri, input: UpdateResourceInput): Promise<ResourceDescriptor> {\n    // Resources are immutable - only archiving is allowed\n    if (Object.keys(input).length !== 1 || input.archived === undefined) {\n      throw new Error('Resources are immutable. Only archiving is allowed.');\n    }\n\n    await this.g!\n      .V()\n      .has('Resource', 'id', id)\n      .property('archived', input.archived)\n      .next();\n\n    const updatedResource = await this.getResource(id);\n    if (!updatedResource) {\n      throw new Error('Resource not found');\n    }\n\n    return updatedResource;\n  }\n  \n  async deleteResource(id: ResourceUri): Promise<void> {\n    // Delete the vertex and all its edges\n    await this.g!\n      .V()\n      .has('Resource', 'id', id)\n      .drop()\n      .next();\n\n    console.log('Deleted resource from JanusGraph:', id);\n  }\n  \n  async listResources(filter: ResourceFilter): Promise<{ resources: ResourceDescriptor[]; total: number }> {\n    let traversalQuery = this.g!.V().hasLabel('Resource');\n\n    // Apply filters\n    if (filter.search) {\n      // Note: This is a simple text search. In production, you'd use\n      // JanusGraph's full-text search capabilities with Elasticsearch\n      traversalQuery = traversalQuery.has('name', gremlin.process.TextP.containing(filter.search));\n    }\n\n    const docs = await traversalQuery.toList();\n    let resources = docs.map((v: any) => this.vertexToResource(v));\n\n    // Apply entity type filtering after retrieval since JanusGraph stores as JSON\n    if (filter.entityTypes && filter.entityTypes.length > 0) {\n      resources = resources.filter(doc =>\n        filter.entityTypes!.some((type: string) => doc.entityTypes?.includes(type))\n      );\n    }\n\n    const total = resources.length;\n    const offset = filter.offset || 0;\n    const limit = filter.limit || 50;\n\n    return {\n      resources: resources.slice(offset, offset + limit),\n      total\n    };\n  }\n  \n  async searchResources(query: string, limit?: number): Promise<ResourceDescriptor[]> {\n    const result = await this.listResources({ search: query, limit: limit || 10 });\n    return result.resources;\n  }\n  \n  async createAnnotation(input: CreateAnnotationInternal): Promise<Annotation> {\n    const id = this.generateId();\n\n    // Only linking motivation with SpecificResource or empty array (stub)\n    const motivation = input.motivation;\n\n    const annotation: Annotation = {\n      '@context': 'http://www.w3.org/ns/anno.jsonld' as const,\n      'type': 'Annotation' as const,\n      id,\n      motivation,\n      target: input.target,\n      body: input.body,\n      creator: input.creator,\n      created: new Date().toISOString(),\n    };\n\n    // Extract source from body using helper\n    const bodySource = getBodySource(input.body);\n    const entityTypes = getEntityTypes(input);\n    const bodyType = Array.isArray(input.body) ? 'SpecificResource' : input.body.type;\n\n    // Extract target source and selector\n    const targetSource = typeof input.target === 'string' ? input.target : input.target.source;\n    const targetSelector = typeof input.target === 'string' ? undefined : input.target.selector;\n\n    // Create annotation vertex\n    const vertex = this.g!\n      .addV('Annotation')\n      .property('id', id)\n      .property('resourceId', targetSource) // Store full URI\n      .property('text', targetSelector ? getExactText(targetSelector) : '')\n      .property('selector', JSON.stringify(targetSelector || {}))\n      .property('type', bodyType)\n      .property('motivation', motivation)\n      .property('creator', JSON.stringify(input.creator))\n      .property('created', annotation.created);\n\n    if (bodySource) {\n      vertex.property('source', bodySource);\n    }\n\n    const annVertex = await vertex.next();\n\n    // Create edge from annotation to resource (BELONGS_TO)\n    await this.g!\n      .V(annVertex.value)\n      .addE('BELONGS_TO')\n      .to(this.g!.V().has('Resource', 'id', targetSource))\n      .next();\n\n    // If it's a resolved reference, create edge to target resource\n    if (bodySource) {\n      await this.g!\n        .V(annVertex.value)\n        .addE('REFERENCES')\n        .to(this.g!.V().has('Resource', 'id', bodySource))\n        .next();\n    }\n\n    // Create TAGGED_AS relationships for entity types\n    for (const entityType of entityTypes) {\n      // Get or create EntityType vertex\n      const etResults = await this.g!\n        .V()\n        .has('EntityType', 'name', entityType)\n        .toList();\n\n      let etVertex;\n      if (etResults.length === 0) {\n        // Create new EntityType vertex\n        etVertex = await this.g!\n          .addV('EntityType')\n          .property('name', entityType)\n          .next();\n      } else {\n        etVertex = { value: etResults[0] };\n      }\n\n      // Create TAGGED_AS edge from Annotation to EntityType\n      await this.g!\n        .V(annVertex.value)\n        .addE('TAGGED_AS')\n        .to(this.g!.V(etVertex.value))\n        .next();\n    }\n\n    console.log('Created annotation in JanusGraph:', id);\n    return annotation;\n  }\n  \n  async getAnnotation(id: AnnotationUri): Promise<Annotation | null> {\n    const vertices = await this.g!\n      .V()\n      .has('Annotation', 'id', id)\n      .toList();\n\n    if (vertices.length === 0) {\n      return null;\n    }\n\n    // Fetch entity types from TAGGED_AS relationships\n    const entityTypeVertices = await this.g!\n      .V()\n      .has('Annotation', 'id', id)\n      .out('TAGGED_AS')\n      .has('EntityType')\n      .toList();\n\n    const entityTypes = entityTypeVertices.map((v: any) =>\n      this.getPropertyValue(v.properties || {}, 'name')\n    ).filter(Boolean);\n\n    return this.vertexToAnnotation(vertices[0] as any, entityTypes);\n  }\n  \n  async updateAnnotation(id: AnnotationUri, updates: Partial<Annotation>): Promise<Annotation> {\n    const traversalQuery = this.g!\n      .V()\n      .has('Annotation', 'id', id);\n\n    // Update target properties\n    if (updates.target !== undefined && typeof updates.target !== 'string') {\n      if (updates.target.selector !== undefined) {\n        await traversalQuery.property('text', getExactText(updates.target.selector)).next();\n        await traversalQuery.property('selector', JSON.stringify(updates.target.selector)).next();\n      }\n    }\n\n    // Update body properties and entity types\n    if (updates.body !== undefined) {\n      const bodySource = getBodySource(updates.body);\n      const entityTypes = getEntityTypes({ body: updates.body });\n\n      if (bodySource) {\n        await traversalQuery.property('source', bodySource).next();\n      }\n\n      // Update entity type relationships - remove old ones and create new ones\n      if (entityTypes.length >= 0) {\n        // Remove existing TAGGED_AS edges\n        await this.g!\n          .V()\n          .has('Annotation', 'id', id)\n          .outE('TAGGED_AS')\n          .drop()\n          .iterate();\n\n        // Create new TAGGED_AS edges\n        for (const entityType of entityTypes) {\n          // Get or create EntityType vertex\n          const etResults = await this.g!\n            .V()\n            .has('EntityType', 'name', entityType)\n            .toList();\n\n          let etVertex;\n          if (etResults.length === 0) {\n            // Create new EntityType vertex\n            etVertex = await this.g!\n              .addV('EntityType')\n              .property('name', entityType)\n              .next();\n          } else {\n            etVertex = { value: etResults[0] };\n          }\n\n          // Create TAGGED_AS edge from Annotation to EntityType\n          const annVertices = await this.g!\n            .V()\n            .has('Annotation', 'id', id)\n            .toList();\n\n          if (annVertices.length > 0) {\n            await this.g!\n              .V(annVertices[0])\n              .addE('TAGGED_AS')\n              .to(this.g!.V(etVertex.value))\n              .next();\n          }\n        }\n      }\n    }\n\n    if (updates.modified !== undefined) {\n      await traversalQuery.property('modified', updates.modified).next();\n    }\n    if (updates.generator !== undefined) {\n      await traversalQuery.property('generator', JSON.stringify(updates.generator)).next();\n    }\n\n    const updatedAnnotation = await this.getAnnotation(id);\n    if (!updatedAnnotation) {\n      throw new Error('Annotation not found');\n    }\n\n    return updatedAnnotation;\n  }\n  \n  async deleteAnnotation(id: AnnotationUri): Promise<void> {\n    await this.g!\n      .V()\n      .has('Annotation', 'id', id)\n      .drop()\n      .next();\n\n    console.log('Deleted annotation from JanusGraph:', id);\n  }\n  \n  async listAnnotations(filter: { resourceId?: ResourceId; type?: AnnotationCategory }): Promise<{ annotations: Annotation[]; total: number }> {\n    let traversalQuery = this.g!.V().hasLabel('Annotation');\n\n    // Apply filters\n    if (filter.resourceId) {\n      traversalQuery = traversalQuery.has('resourceId', filter.resourceId);\n    }\n\n    if (filter.type) {\n      const w3cType = filter.type === 'highlight' ? 'TextualBody' : 'SpecificResource';\n      traversalQuery = traversalQuery.has('type', w3cType);\n    }\n\n    const vertices = await traversalQuery.toList();\n    const annotations = await this.fetchAnnotationsWithEntityTypes(vertices);\n\n    return {\n      annotations,\n      total: annotations.length\n    };\n  }\n\n  async getHighlights(resourceId: ResourceId): Promise<Annotation[]> {\n    const { annotations } = await this.listAnnotations({\n      resourceId,\n      type: 'highlight'\n    });\n    return annotations;\n  }\n\n  async resolveReference(annotationId: AnnotationId, source: ResourceId): Promise<Annotation> {\n    const publicURL = this.envConfig.services.backend!.publicURL;\n    const annotation = await this.getAnnotation(annotationIdToURI(annotationId, publicURL));\n    if (!annotation) throw new Error('Annotation not found');\n\n    // TODO Preserve existing TextualBody entities, add SpecificResource\n    // For now, just update with SpecificResource (losing entity tags)\n    await this.updateAnnotation(annotationIdToURI(annotationId, publicURL), {\n      body: [\n        {\n          type: 'SpecificResource',\n          source,\n          purpose: 'linking' as const,\n        },\n      ],\n    });\n\n    // Create edge from annotation to target resource\n    await this.g!\n      .V()\n      .has('Annotation', 'id', annotationId)\n      .addE('REFERENCES')\n      .to(this.g!.V().has('Resource', 'id', source))\n      .next();\n\n    const updatedAnnotation = await this.getAnnotation(annotationIdToURI(annotationId, publicURL));\n    if (!updatedAnnotation) {\n      throw new Error('Annotation not found after update');\n    }\n\n    return updatedAnnotation;\n  }\n\n  async getReferences(resourceId: ResourceId): Promise<Annotation[]> {\n    const { annotations } = await this.listAnnotations({\n      resourceId,\n      type: 'reference'\n    });\n    return annotations;\n  }\n\n  async getEntityReferences(resourceId: ResourceId, entityTypes?: string[]): Promise<Annotation[]> {\n    const { annotations } = await this.listAnnotations({\n      resourceId,\n      type: 'reference'\n    });\n\n    // TODO Extract entity types from body using helper\n    if (entityTypes && entityTypes.length > 0) {\n      return annotations.filter(ann => {\n        const annEntityTypes = getEntityTypes(ann);\n        return annEntityTypes.some((type: string) => entityTypes.includes(type));\n      });\n    }\n\n    return annotations.filter(ann => getEntityTypes(ann).length > 0);\n  }\n\n  async getResourceAnnotations(resourceId: ResourceId): Promise<Annotation[]> {\n    const { annotations } = await this.listAnnotations({ resourceId });\n    return annotations;\n  }\n\n  async getResourceReferencedBy(resourceUri: ResourceUri, _motivation?: string): Promise<Annotation[]> {\n    // Find annotations that reference this resource\n    const vertices = await this.g!\n      .V()\n      .hasLabel('Annotation')\n      .has('source', resourceUri)\n      .toList();\n\n    return await this.fetchAnnotationsWithEntityTypes(vertices);\n  }\n  \n  async getResourceConnections(resourceId: ResourceId): Promise<GraphConnection[]> {\n    // Use Gremlin to find connected resources\n    const paths = await this.g!\n      .V()\n      .has('Resource', 'id', resourceId)\n      .inE('BELONGS_TO')\n      .outV()\n      .outE('REFERENCES')\n      .inV()\n      .path()\n      .toList();\n\n    // Convert paths to connections\n    // This is simplified - real implementation would process paths properly\n    console.log('Found paths:', paths.length);\n\n    // For now, also build connections from references\n    const connections: GraphConnection[] = [];\n    const refs = await this.getReferences(resourceId);\n\n    for (const ref of refs) {\n      // Extract source from body using helper\n      const bodySource = getBodySource(ref.body);\n      if (bodySource) {\n        const targetDoc = await this.getResource(resourceUri(bodySource));\n        if (targetDoc) {\n          const existing = connections.find(c => c.targetResource.id === targetDoc.id);\n          if (existing) {\n            existing.annotations.push(ref);\n          } else {\n            connections.push({\n              targetResource: targetDoc,\n              annotations: [ref],\n              relationshipType: undefined,\n              bidirectional: false,\n            });\n          }\n        }\n      }\n    }\n\n    return connections;\n  }\n  \n  async findPath(_fromResourceId: string, _toResourceId: string, _maxDepth?: number): Promise<GraphPath[]> {\n    // TODO: Implement real graph traversal with JanusGraph\n    // For now, return empty array\n    return [];\n  }\n  \n  async getEntityTypeStats(): Promise<EntityTypeStats[]> {\n    const docs = await this.g!.V().hasLabel('Resource').toList();\n    const resources = docs.map((v: any) => this.vertexToResource(v));\n\n    const stats = new Map<string, number>();\n\n    for (const doc of resources) {\n      for (const type of doc.entityTypes || []) {\n        stats.set(type, (stats.get(type) || 0) + 1);\n      }\n    }\n\n    return Array.from(stats.entries()).map(([type, count]) => ({ type, count }));\n  }\n  \n  async getStats(): Promise<any> {\n    const entityTypes: Record<string, number> = {};\n    const contentTypes: Record<string, number> = {};\n\n    // Get all resources\n    const docs = await this.g!.V().hasLabel('Resource').toList();\n    const resources = docs.map((v: any) => this.vertexToResource(v));\n\n    for (const doc of resources) {\n      for (const type of doc.entityTypes || []) {\n        entityTypes[type] = (entityTypes[type] || 0) + 1;\n      }\n      const primaryRep = getPrimaryRepresentation(doc);\n      if (primaryRep?.mediaType) {\n        contentTypes[primaryRep.mediaType] = (contentTypes[primaryRep.mediaType] || 0) + 1;\n      }\n    }\n\n    // Get all annotations\n    const anns = await this.g!.V().hasLabel('Annotation').toList();\n    const annotations = await this.fetchAnnotationsWithEntityTypes(anns);\n\n    const highlights = annotations.filter(a => a.motivation === 'highlighting');\n    const references = annotations.filter(a => a.motivation === 'linking');\n    const entityReferences = references.filter(a => getEntityTypes(a).length > 0);\n\n    return {\n      resourceCount: resources.length,\n      annotationCount: annotations.length,\n      highlightCount: highlights.length,\n      referenceCount: references.length,\n      entityReferenceCount: entityReferences.length,\n      entityTypes,\n      contentTypes,\n    };\n  }\n\n  async createAnnotations(inputs: CreateAnnotationInternal[]): Promise<Annotation[]> {\n    const results = [];\n    for (const input of inputs) {\n      results.push(await this.createAnnotation(input));\n    }\n    return results;\n  }\n\n  async resolveReferences(inputs: Array<{ annotationId: AnnotationId; source: ResourceId }>): Promise<Annotation[]> {\n    const results = [];\n    for (const input of inputs) {\n      results.push(await this.resolveReference(input.annotationId, input.source));\n    }\n    return results;\n  }\n\n  async detectAnnotations(_resourceId: ResourceId): Promise<Annotation[]> {\n    // Auto-detection would analyze resource content\n    return [];\n  }\n  \n  async getEntityTypes(): Promise<string[]> {\n    if (this.entityTypesCollection === null) {\n      await this.initializeTagCollections();\n    }\n    return Array.from(this.entityTypesCollection!).sort();\n  }\n  \n  async addEntityType(tag: string): Promise<void> {\n    if (this.entityTypesCollection === null) {\n      await this.initializeTagCollections();\n    }\n    this.entityTypesCollection!.add(tag);\n\n    // Persist to JanusGraph\n    try {\n      // Find or create the TagCollection vertex\n      const existing = await this.g!.V()\n        .hasLabel('TagCollection')\n        .has('type', 'entity-types')\n        .toList();\n\n      if (existing.length > 0) {\n        // Update existing collection\n        await this.g!.V(existing[0])\n          .property('tags', JSON.stringify(Array.from(this.entityTypesCollection!)))\n          .next();\n      } else {\n        // Create new collection\n        await this.g!.addV('TagCollection')\n          .property('type', 'entity-types')\n          .property('tags', JSON.stringify(Array.from(this.entityTypesCollection!)))\n          .next();\n      }\n    } catch (error) {\n      console.error('Failed to add entity type:', error);\n    }\n  }\n\n  async addEntityTypes(tags: string[]): Promise<void> {\n    if (this.entityTypesCollection === null) {\n      await this.initializeTagCollections();\n    }\n    tags.forEach(tag => this.entityTypesCollection!.add(tag));\n\n    // Persist all at once\n    try {\n      const existing = await this.g!.V()\n        .hasLabel('TagCollection')\n        .has('type', 'entity-types')\n        .toList();\n\n      if (existing.length > 0) {\n        await this.g!.V(existing[0])\n          .property('tags', JSON.stringify(Array.from(this.entityTypesCollection!)))\n          .next();\n      } else {\n        await this.g!.addV('TagCollection')\n          .property('type', 'entity-types')\n          .property('tags', JSON.stringify(Array.from(this.entityTypesCollection!)))\n          .next();\n      }\n    } catch (error) {\n      console.error('Failed to add entity types:', error);\n    }\n  }\n\n  private async initializeTagCollections(): Promise<void> {\n    // Load existing collections from JanusGraph\n    const collections = await this.g!.V()\n      .hasLabel('TagCollection')\n      .toList();\n\n    let entityTypesFromDb: string[] = [];\n\n    for (const vertex of collections) {\n      const props = (vertex as any).properties || {};\n      const type = this.getPropertyValue(props, 'type');\n      const tagsJson = this.getPropertyValue(props, 'tags');\n      const tags = tagsJson ? JSON.parse(tagsJson) : [];\n\n      if (type === 'entity-types') {\n        entityTypesFromDb = tags;\n      }\n    }\n\n    // Load defaults\n    const { DEFAULT_ENTITY_TYPES } = await import('@semiont/ontology');\n\n    // Merge with defaults\n    this.entityTypesCollection = new Set([...DEFAULT_ENTITY_TYPES, ...entityTypesFromDb]);\n\n    // Persist merged collection back to JanusGraph if it doesn't exist\n    if (entityTypesFromDb.length === 0) {\n      await this.addEntityTypes([]);\n    }\n  }\n\n  generateId(): string {\n    return uuidv4().replace(/-/g, '').substring(0, 12);\n  }\n  \n  async clearDatabase(): Promise<void> {\n    // Drop all vertices in JanusGraph\n    await this.g!.V().drop().next();\n    // Reset cached collections\n    this.entityTypesCollection = null;\n    console.log('Cleared JanusGraph database');\n  }\n}","// In-memory implementation of GraphDatabase interface\n// Used for development and testing without requiring a real graph database\n\nimport { GraphDatabase } from '../interface';\nimport { getResourceEntityTypes } from '@semiont/api-client';\nimport { getEntityTypes } from '@semiont/ontology';\nimport type { components } from '@semiont/api-client';\nimport type {\n  AnnotationCategory,\n  GraphConnection,\n  GraphPath,\n  EntityTypeStats,\n  ResourceFilter,\n  UpdateResourceInput,\n  CreateAnnotationInternal,\n  ResourceId,\n  AnnotationId,\n} from '@semiont/core';\nimport { resourceId as makeResourceId } from '@semiont/core';\nimport type { ResourceUri, AnnotationUri } from '@semiont/api-client';\nimport { resourceUri } from '@semiont/api-client';\nimport { v4 as uuidv4 } from 'uuid';\nimport { getBodySource, getTargetSource } from '@semiont/api-client';\nimport { getResourceId, getPrimaryRepresentation } from '@semiont/api-client';\n\ntype ResourceDescriptor = components['schemas']['ResourceDescriptor'];\ntype Annotation = components['schemas']['Annotation'];\n\n// Simple in-memory storage using Maps\n// Useful for development and testing\n\nexport class MemoryGraphDatabase implements GraphDatabase {\n  private connected: boolean = false;\n  \n  // In-memory storage using Maps\n  private resources: Map<string, ResourceDescriptor> = new Map();\n  private annotations: Map<string, Annotation> = new Map();\n  \n  constructor(config: any = {}) {\n    // Config is ignored for in-memory implementation\n    void config;\n  }\n  \n  async connect(): Promise<void> {\n    // No actual connection needed for in-memory storage\n    console.log('Using in-memory graph database...');\n    this.connected = true;\n  }\n  \n  async disconnect(): Promise<void> {\n    // Nothing to close for in-memory storage\n    this.connected = false;\n  }\n  \n  isConnected(): boolean {\n    return this.connected;\n  }\n\n  async createResource(resource: ResourceDescriptor): Promise<ResourceDescriptor> {\n    const id = getResourceId(resource);\n    if (!id) {\n      throw new Error('Resource must have an id');\n    }\n\n    // Simply add to in-memory map\n    // await this.client.submit(`\n    //   graph.tx().rollback()\n    //   g.addV('Resource')\n    //     .property('id', id)\n    //     .property('name', name)\n    //     .property('entityTypes', entityTypes)\n    //     .property('contentType', contentType)\n    //     .property('created', created)\n    //     .property('updatedAt', updatedAt)\n    //   graph.tx().commit()\n    // `, { id, name, entityTypes, ... });\n\n    this.resources.set(id, resource);\n    return resource;\n  }\n  \n  async getResource(id: ResourceUri): Promise<ResourceDescriptor | null> {\n    // Simply retrieve from map\n    // const result = await this.client.submit(`\n    //   g.V().hasLabel('Resource').has('id', id).valueMap(true)\n    // `, { id });\n\n    return this.resources.get(id) || null;\n  }\n\n  async updateResource(id: ResourceUri, input: UpdateResourceInput): Promise<ResourceDescriptor> {\n    // Resources are immutable - only archiving is allowed\n    if (Object.keys(input).length !== 1 || input.archived === undefined) {\n      throw new Error('Resources are immutable. Only archiving is allowed.');\n    }\n\n    const doc = this.resources.get(id);\n    if (!doc) throw new Error('Resource not found');\n\n    doc.archived = input.archived;\n    return doc;\n  }\n  \n  async deleteResource(id: ResourceUri): Promise<void> {\n    // Simply delete from map\n    // await this.client.submit(`\n    //   graph.tx().rollback()\n    //   g.V().has('id', id).drop()\n    //   graph.tx().commit()\n    // `, { id });\n    \n    this.resources.delete(id);\n    \n    // Delete annotations\n    for (const [selId, sel] of this.annotations) {\n      if (getTargetSource(sel.target) === id || getBodySource(sel.body) === id) {\n        this.annotations.delete(selId);\n      }\n    }\n  }\n  \n  async listResources(filter: ResourceFilter): Promise<{ resources: ResourceDescriptor[]; total: number }> {\n    let docs = Array.from(this.resources.values());\n\n    if (filter.entityTypes && filter.entityTypes.length > 0) {\n      docs = docs.filter(doc =>\n        doc.entityTypes && doc.entityTypes.some((type: string) => filter.entityTypes!.includes(type))\n      );\n    }\n\n    if (filter.search) {\n      const searchLower = filter.search.toLowerCase();\n      docs = docs.filter(doc =>\n        doc.name.toLowerCase().includes(searchLower)\n      );\n    }\n\n    const total = docs.length;\n    const offset = filter.offset || 0;\n    const limit = filter.limit || 20;\n    docs = docs.slice(offset, offset + limit);\n\n    return { resources: docs, total };\n  }\n\n  async searchResources(query: string, limit: number = 20): Promise<ResourceDescriptor[]> {\n    // Simple text search in memory\n    // const results = await this.client.submit(`\n    //   g.V().has('Resource', 'name', textContains(query)).limit(limit).valueMap(true)\n    // `, { query, limit });\n\n    const searchLower = query.toLowerCase();\n    const results = Array.from(this.resources.values())\n      .filter(doc => doc.name.toLowerCase().includes(searchLower))\n      .slice(0, limit);\n    \n    return results;\n  }\n  \n  async createAnnotation(input: CreateAnnotationInternal): Promise<Annotation> {\n    const id = this.generateId();\n\n    // Only linking motivation with SpecificResource or empty array (stub)\n    const annotation: Annotation = {\n      '@context': 'http://www.w3.org/ns/anno.jsonld' as const,\n      'type': 'Annotation' as const,\n      id,\n      motivation: input.motivation,\n      target: input.target,\n      body: input.body,\n      creator: input.creator,\n      created: new Date().toISOString(),\n    };\n\n    this.annotations.set(id, annotation);\n    console.log('Memory: Created annotation:', {\n      id,\n      motivation: annotation.motivation,\n      hasSource: !!getBodySource(annotation.body),\n      targetSource: getTargetSource(annotation.target)\n    });\n    return annotation;\n  }\n  \n  async getAnnotation(id: AnnotationUri): Promise<Annotation | null> {\n    return this.annotations.get(id) || null;\n  }\n  \n  async updateAnnotation(id: AnnotationUri, updates: Partial<Annotation>): Promise<Annotation> {\n    const annotation = this.annotations.get(id);\n    if (!annotation) throw new Error('Annotation not found');\n\n    const updated: Annotation = {\n      ...annotation,\n      ...updates,\n    };\n\n    // Motivation should come from updates if provided\n    // No need to derive from body type\n\n    this.annotations.set(id, updated);\n    return updated;\n  }\n  \n  async deleteAnnotation(id: AnnotationUri): Promise<void> {\n    this.annotations.delete(id);\n  }\n  \n  async listAnnotations(filter: { resourceId?: ResourceId; type?: AnnotationCategory }): Promise<{ annotations: Annotation[]; total: number }> {\n    let results = Array.from(this.annotations.values());\n\n    if (filter.resourceId) {\n      const resourceIdStr = String(filter.resourceId);\n      results = results.filter(a => {\n        const targetSource = getTargetSource(a.target);\n        return targetSource === resourceIdStr || targetSource === resourceUri(resourceIdStr);\n      });\n    }\n\n    // Only SpecificResource supported, use motivation to distinguish\n    if (filter.type) {\n      const motivation = filter.type === 'highlight' ? 'highlighting' : 'linking';\n      results = results.filter(a => a.motivation === motivation);\n    }\n\n    return { annotations: results, total: results.length };\n  }\n  \n  \n  async getHighlights(resourceId: ResourceId): Promise<Annotation[]> {\n    const resourceIdStr = String(resourceId);\n    const highlights = Array.from(this.annotations.values())\n      .filter(sel => {\n        const targetSource = getTargetSource(sel.target);\n        return (targetSource === resourceIdStr || targetSource === resourceUri(resourceIdStr)) && sel.motivation === 'highlighting';\n      });\n    console.log(`Memory: getHighlights for ${resourceId} found ${highlights.length} highlights`);\n    return highlights;\n  }\n\n  async resolveReference(annotationId: AnnotationId, source: ResourceId): Promise<Annotation> {\n    const annotation = this.annotations.get(annotationId);\n    if (!annotation) throw new Error('Annotation not found');\n\n    // Convert stub (empty array) to resolved SpecificResource\n    const updated: Annotation = {\n      ...annotation,\n      body: {\n        type: 'SpecificResource',\n        source,\n        purpose: 'linking',\n      },\n    };\n\n    this.annotations.set(annotationId, updated);\n    return updated;\n  }\n\n  async getReferences(resourceId: ResourceId): Promise<Annotation[]> {\n    const resourceIdStr = String(resourceId);\n    const references = Array.from(this.annotations.values())\n      .filter(sel => {\n        const targetSource = getTargetSource(sel.target);\n        return (targetSource === resourceIdStr || targetSource === resourceUri(resourceIdStr)) && sel.motivation === 'linking';\n      });\n    console.log(`Memory: getReferences for ${resourceId} found ${references.length} references`);\n    references.forEach(ref => {\n      console.log('  Reference:', {\n        id: ref.id,\n        source: getBodySource(ref.body),\n        entityTypes: getEntityTypes(ref) // from body\n      });\n    });\n    return references;\n  }\n\n  async getEntityReferences(resourceId: ResourceId, entityTypes?: string[]): Promise<Annotation[]> {\n    // TODO Extract entity types from body\n    const resourceIdStr = String(resourceId);\n    let refs = Array.from(this.annotations.values())\n      .filter(sel => {\n        const selEntityTypes = getEntityTypes(sel);\n        const targetSource = getTargetSource(sel.target);\n        return (targetSource === resourceIdStr || targetSource === resourceUri(resourceIdStr)) && selEntityTypes.length > 0;\n      });\n\n    if (entityTypes && entityTypes.length > 0) {\n      refs = refs.filter(sel => {\n        const selEntityTypes = getEntityTypes(sel);\n        return selEntityTypes.some((type: string) => entityTypes.includes(type));\n      });\n    }\n\n    return refs;\n  }\n\n  async getResourceAnnotations(resourceId: ResourceId): Promise<Annotation[]> {\n    const resourceIdStr = String(resourceId);\n    return Array.from(this.annotations.values())\n      .filter(sel => {\n        const targetSource = getTargetSource(sel.target);\n        return targetSource === resourceIdStr || targetSource === resourceUri(resourceIdStr);\n      });\n  }\n\n  async getResourceReferencedBy(resourceUri: ResourceUri, _motivation?: string): Promise<Annotation[]> {\n    return Array.from(this.annotations.values())\n      .filter(sel => getBodySource(sel.body) === resourceUri);\n  }\n  \n  async getResourceConnections(resourceId: ResourceId): Promise<GraphConnection[]> {\n    // Simple in-memory traversal\n    // const results = await this.client.submit(`\n    //   g.V().has('id', resourceId)\n    //     .bothE('REFERENCES').as('e')\n    //     .otherV().as('v')\n    //     .select('e', 'v')\n    // `, { resourceId });\n    \n    const connections: GraphConnection[] = [];\n    const refs = await this.getReferences(resourceId);\n    \n    for (const ref of refs) {\n      const bodySource = getBodySource(ref.body);\n      if (bodySource) {\n        const targetDoc = await this.getResource(resourceUri(bodySource));\n        if (targetDoc) {\n          const reverseRefs = await this.getReferences(makeResourceId(bodySource));\n          const resourceIdStr = String(resourceId);\n          const bidirectional = reverseRefs.some(r => {\n            const reverseBodySource = getBodySource(r.body);\n            return reverseBodySource === resourceIdStr || reverseBodySource === resourceUri(resourceIdStr);\n          });\n\n          connections.push({\n            targetResource: targetDoc,\n            annotations: [ref],\n            bidirectional,\n          });\n        }\n      }\n    }\n    \n    return connections;\n  }\n  \n  async findPath(fromResourceId: string, toResourceId: string, maxDepth: number = 5): Promise<GraphPath[]> {\n    // Path finding not implemented in memory version\n    // const results = await this.client.submit(`\n    //   g.V().has('id', fromResourceId)\n    //     .repeat(both().simplePath()).times(maxDepth).emit()\n    //     .has('id', toResourceId)\n    //     .path()\n    //     .by(valueMap(true))\n    //     .limit(10)\n    // `, { fromResourceId, toResourceId, maxDepth });\n\n    // Using BFS implementation for stub\n    const visited = new Set<string>();\n    const queue: { docId: string; path: ResourceDescriptor[]; sels: Annotation[] }[] = [];\n    const fromDoc = await this.getResource(resourceUri(fromResourceId));\n\n    if (!fromDoc) return [];\n\n    queue.push({ docId: fromResourceId, path: [fromDoc], sels: [] });\n    visited.add(fromResourceId);\n\n    const paths: GraphPath[] = [];\n\n    while (queue.length > 0 && paths.length < 10) {\n      const { docId, path, sels } = queue.shift()!;\n\n      if (path.length > maxDepth) continue;\n\n      if (docId === toResourceId) {\n        paths.push({ resources: path, annotations: sels });\n        continue;\n      }\n\n      const connections = await this.getResourceConnections(makeResourceId(docId));\n\n      for (const conn of connections) {\n        const targetId = getResourceId(conn.targetResource);\n        if (targetId && !visited.has(targetId)) {\n          visited.add(targetId);\n          queue.push({\n            docId: targetId,\n            path: [...path, conn.targetResource],\n            sels: [...sels, ...conn.annotations],\n          });\n        }\n      }\n    }\n\n    return paths;\n  }\n  \n  async getEntityTypeStats(): Promise<EntityTypeStats[]> {\n    // Simple in-memory statistics\n    // const results = await this.client.submit(`\n    //   g.V().hasLabel('Resource')\n    //     .values('entityTypes').unfold()\n    //     .groupCount()\n    // `);\n\n    const typeCounts = new Map<string, number>();\n\n    for (const doc of this.resources.values()) {\n      const types = getResourceEntityTypes(doc);\n      for (const type of types) {\n        typeCounts.set(type, (typeCounts.get(type) || 0) + 1);\n      }\n    }\n    \n    return Array.from(typeCounts.entries()).map(([type, count]) => ({\n      type,\n      count,\n    }));\n  }\n  \n  async getStats(): Promise<{\n    resourceCount: number;\n    annotationCount: number;\n    highlightCount: number;\n    referenceCount: number;\n    entityReferenceCount: number;\n    entityTypes: Record<string, number>;\n    contentTypes: Record<string, number>;\n  }> {\n    const entityTypes: Record<string, number> = {};\n    const contentTypes: Record<string, number> = {};\n\n    for (const doc of this.resources.values()) {\n      for (const type of doc.entityTypes || []) {\n        entityTypes[type] = (entityTypes[type] || 0) + 1;\n      }\n      const primaryRep = getPrimaryRepresentation(doc);\n      if (primaryRep?.mediaType) {\n        contentTypes[primaryRep.mediaType] = (contentTypes[primaryRep.mediaType] || 0) + 1;\n      }\n    }\n    \n    const annotations = Array.from(this.annotations.values());\n    // Use motivation to distinguish types\n    const highlightCount = annotations.filter(a => a.motivation === 'highlighting').length;\n    const referenceCount = annotations.filter(a => a.motivation === 'linking').length;\n    // TODO Extract entity types from body\n    const entityReferenceCount = annotations.filter(a => a.motivation === 'linking' && getEntityTypes(a).length > 0).length;\n    \n    return {\n      resourceCount: this.resources.size,\n      annotationCount: this.annotations.size,\n      highlightCount,\n      referenceCount,\n      entityReferenceCount,\n      entityTypes,\n      contentTypes,\n    };\n  }\n  \n  async createAnnotations(inputs: CreateAnnotationInternal[]): Promise<Annotation[]> {\n    // In production: Use batch operations for better performance\n    // const tx = graph.tx()\n    // tx.rollback()\n    // ... batch operations ...\n    // tx.commit()\n    \n    const results: Annotation[] = [];\n    for (const input of inputs) {\n      results.push(await this.createAnnotation(input));\n    }\n    return results;\n  }\n  \n  \n  async resolveReferences(inputs: { annotationId: AnnotationId; source: ResourceId }[]): Promise<Annotation[]> {\n    const results: Annotation[] = [];\n    for (const input of inputs) {\n      results.push(await this.resolveReference(input.annotationId, input.source));\n    }\n    return results;\n  }\n  \n  async detectAnnotations(_resourceId: ResourceId): Promise<Annotation[]> {\n    // This would use AI/ML to detect annotations in a resource\n    // For now, return empty array as a placeholder\n    return [];\n  }\n  \n  // Tag Collections - stored as special vertices in the graph\n  private entityTypesCollection: Set<string> | null = null;\n  \n  async getEntityTypes(): Promise<string[]> {\n    // Initialize if not already loaded\n    if (this.entityTypesCollection === null) {\n      await this.initializeTagCollections();\n    }\n    return Array.from(this.entityTypesCollection!).sort();\n  }\n\n  async addEntityType(tag: string): Promise<void> {\n    if (this.entityTypesCollection === null) {\n      await this.initializeTagCollections();\n    }\n    this.entityTypesCollection!.add(tag);\n    // Simply add to set\n    // await this.client.submit(`g.V().has('tagCollection', 'type', 'entity-types')\n    //   .property(set, 'tags', '${tag}')`, {});\n  }\n\n  async addEntityTypes(tags: string[]): Promise<void> {\n    if (this.entityTypesCollection === null) {\n      await this.initializeTagCollections();\n    }\n    tags.forEach(tag => this.entityTypesCollection!.add(tag));\n    // Simply add to set\n  }\n  \n  private async initializeTagCollections(): Promise<void> {\n    // Initialize in-memory collections\n    // const result = await this.client.submit(\n    //   `g.V().has('tagCollection', 'type', 'entity-types')\n    //    .project('type', 'tags').by('type').by('tags')`, {}\n    // );\n\n    // For now, initialize with defaults if not present\n    if (this.entityTypesCollection === null) {\n      const { DEFAULT_ENTITY_TYPES } = await import('@semiont/ontology');\n      this.entityTypesCollection = new Set(DEFAULT_ENTITY_TYPES);\n    }\n  }\n  \n  generateId(): string {\n    return uuidv4().replace(/-/g, '').substring(0, 12);\n  }\n  \n  async clearDatabase(): Promise<void> {\n    // In production: CAREFUL! 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package/package.json

@@ -0,0 +1,72 @@
+{
+  "name": "@semiont/graph",
+  "version": "0.2.28-build.40",
+  "type": "module",
+  "description": "Graph database abstraction with Neo4j, Neptune, JanusGraph, and in-memory implementations",
+  "main": "./dist/index.js",
+  "types": "./dist/index.d.ts",
+  "exports": {
+    ".": {
+      "types": "./dist/index.d.ts",
+      "import": "./dist/index.js"
+    }
+  },
+  "files": [
+    "dist",
+    "README.md"
+  ],
+  "scripts": {
+    "build": "npm run typecheck && tsup",
+    "typecheck": "tsc --noEmit",
+    "clean": "rm -rf dist",
+    "test": "vitest run",
+    "test:watch": "vitest"
+  },
+  "dependencies": {
+    "@semiont/api-client": "*",
+    "@semiont/core": "*",
+    "@semiont/ontology": "*",
+    "uuid": "^9.0.1"
+  },
+  "peerDependencies": {
+    "@aws-sdk/client-neptune": "^3.600.0",
+    "gremlin": "^3.7.4",
+    "neo4j-driver": "^5.28.2"
+  },
+  "peerDependenciesMeta": {
+    "neo4j-driver": {
+      "optional": true
+    },
+    "gremlin": {
+      "optional": true
+    },
+    "@aws-sdk/client-neptune": {
+      "optional": true
+    }
+  },
+  "devDependencies": {
+    "@types/uuid": "^9.0.8",
+    "tsup": "^8.0.1",
+    "typescript": "^5.6.3",
+    "vitest": "^3.2.4"
+  },
+  "publishConfig": {
+    "access": "public"
+  },
+  "keywords": [
+    "graph-database",
+    "neo4j",
+    "neptune",
+    "janusgraph",
+    "gremlin",
+    "knowledge-graph",
+    "semantic-web"
+  ],
+  "author": "The AI Alliance",
+  "license": "Apache-2.0",
+  "repository": {
+    "type": "git",
+    "url": "https://github.com/The-AI-Alliance/semiont.git",
+    "directory": "packages/graph"
+  }
+}