@semiont/graph 0.5.30 → 0.5.32

package/dist/index.js.map

@@ -1 +1 @@
-{"version":3,"sources":["../src/interface.ts","../src/resource-query.ts","../src/implementations/neptune.ts","../src/annotation-codec.ts","../src/implementations/neo4j.ts","../src/implementations/janusgraph.ts","../src/implementations/memorygraph.ts","../src/factory.ts"],"sourcesContent":["// Graph database interface - all implementations must follow this contract\n\nimport type {\n  Annotation,\n  AnnotationCategory,\n  AnnotationId,\n  CreateAnnotationInternal,\n  EntityTypeStats,\n  GraphConnection,\n  GraphPath,\n  ResourceDescriptor,\n  ResourceFilter,\n  ResourceId,\n  UpdateResourceInput,\n} from '@semiont/core';\n\nconst MUTABLE_RESOURCE_FACETS = new Set<string>(['archived', 'entityTypes']);\n\n/**\n * Resources are immutable apart from two facets: archival state, and entity\n * tags (mutable since the controlled-vocabulary decision — the Weaver folds\n * `mark:archived`/`mark:unarchived` and `mark:entity-tag-added`/`-removed`\n * through `updateResource`). Every implementation validates its input with\n * this one guard so the mutability contract cannot drift per gateway.\n */\nexport function assertMutableResourceUpdate(input: UpdateResourceInput): void {\n  const keys = Object.keys(input);\n  if (keys.length === 0 || keys.some((k) => !MUTABLE_RESOURCE_FACETS.has(k))) {\n    throw new Error('Resources are immutable apart from archival state and entity tags.');\n  }\n}\n\n/**\n * Newest first, ties broken by id — the ordering every `listResources` result\n * must carry.\n *\n * The tiebreak is not cosmetic: browse pages these results with offset/limit,\n * and a partial order lets two pages repeat or drop rows. Ids compare by code\n * point rather than locale so the JS gateways agree with the engines, whose\n * `ORDER BY` is codepoint-ordered.\n */\nexport function compareByRecencyThenId(a: ResourceDescriptor, b: ResourceDescriptor): number {\n  const aTime = a.dateCreated ? Date.parse(a.dateCreated) : 0;\n  const bTime = b.dateCreated ? Date.parse(b.dateCreated) : 0;\n  if (aTime !== bTime) return bTime - aTime;\n  const aId = String(a['@id']);\n  const bId = String(b['@id']);\n  return aId < bId ? -1 : aId > bId ? 1 : 0;\n}\n\nexport interface GraphDatabase {\n  // Connection management\n  connect(): Promise<void>;\n  disconnect(): Promise<void>;\n  isConnected(): boolean;\n\n  // Resource operations\n  // Accepts W3C ResourceDescriptor directly - GraphDB stores W3C compliant resources\n  createResource(resource: ResourceDescriptor): Promise<ResourceDescriptor>;\n  getResource(id: ResourceId): Promise<ResourceDescriptor | null>;\n  updateResource(id: ResourceId, input: UpdateResourceInput): Promise<ResourceDescriptor>;\n  deleteResource(id: ResourceId): Promise<void>;\n  listResources(filter: ResourceFilter): Promise<{ resources: ResourceDescriptor[]; total: number }>;\n\n  // Annotation operations\n  createAnnotation(input: CreateAnnotationInternal): Promise<Annotation>;\n  getAnnotation(id: AnnotationId): Promise<Annotation | null>;\n  updateAnnotation(id: AnnotationId, updates: Partial<Annotation>): Promise<Annotation>;\n  deleteAnnotation(id: AnnotationId): Promise<void>;\n  listAnnotations(filter: { resourceId?: ResourceId; type?: AnnotationCategory }): Promise<{ annotations: Annotation[]; total: number }>;\n\n  // Highlight operations\n  getHighlights(resourceId: ResourceId): Promise<Annotation[]>;\n\n  // Reference operations\n  resolveReference(annotationId: AnnotationId, source: ResourceId): Promise<Annotation>;\n  getReferences(resourceId: ResourceId): Promise<Annotation[]>;\n  getEntityReferences(resourceId: ResourceId, entityTypes?: string[]): Promise<Annotation[]>;\n\n  // Relationship queries\n  getResourceAnnotations(resourceId: ResourceId): Promise<Annotation[]>;\n  getResourceReferencedBy(resourceId: ResourceId, motivation?: string): Promise<Annotation[]>;\n\n  // Graph traversal\n  getResourceConnections(resourceId: ResourceId): Promise<GraphConnection[]>;\n  findPath(fromResourceId: ResourceId, toResourceId: ResourceId, maxDepth?: number): Promise<GraphPath[]>;\n  \n  // Analytics\n  getEntityTypeStats(): Promise<EntityTypeStats[]>;\n  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  \n  // Bulk operations\n  batchCreateResources(resources: ResourceDescriptor[]): Promise<ResourceDescriptor[]>;\n  createAnnotations(inputs: CreateAnnotationInternal[]): Promise<Annotation[]>;\n  resolveReferences(inputs: { annotationId: AnnotationId; source: ResourceId }[]): Promise<Annotation[]>;\n\n  // Auto-detection\n  detectAnnotations(resourceId: ResourceId): Promise<Annotation[]>;\n  \n  // Tag Collections\n  getEntityTypes(): Promise<string[]>;\n  addEntityType(tag: string): Promise<void>;\n  addEntityTypes(tags: string[]): Promise<void>;\n  \n  // Utility\n  generateId(): string;\n  clearDatabase(): Promise<void>; // For testing\n}","/**\n * The resource query — filtering, ranking and pagination — expressed in JS.\n *\n * Shared by every gateway whose engine does not express it directly (memory,\n * JanusGraph, Neptune) so those three cannot drift apart. Neo4j expresses the\n * same semantics in Cypher, and the interface contract tests pin both shapes to\n * one behaviour.\n */\n\nimport { getResourceEntityTypes, getStorageUri } from '@semiont/core';\nimport type { ResourceDescriptor, ResourceFilter } from '@semiont/core';\nimport { compareByRecencyThenId } from './interface';\n\n/**\n * Split a query into the terms every match must satisfy. Blank input yields no\n * terms, which callers read as \"no query\" — a bare substring match on `\" \"`\n * would otherwise match every name containing a space.\n */\nexport function searchTerms(query: string): string[] {\n  return query.toLowerCase().split(/\\s+/).filter(Boolean);\n}\n\n/**\n * How directly a resource answers the query: 0 exact name, 1 name prefix,\n * 2 every term present in the name, 3 something other than the name — the path\n * or an entity type — had to supply a term.\n *\n * Those assisted hits rank last deliberately. Someone searching \"Marathon\"\n * wants the document *called* Marathon before every file that merely lives\n * under a folder of that name or is tagged with it.\n */\nexport function searchRank(resource: ResourceDescriptor, query: string): number {\n  const whole = query.trim().toLowerCase();\n  const name = (resource.name ?? '').toLowerCase();\n  if (name === whole) return 0;\n  if (name.startsWith(whole)) return 1;\n  if (searchTerms(query).every((term) => name.includes(term))) return 2;\n  return 3;\n}\n\n/**\n * Every term must appear, though each may come from the name, the path or an\n * entity type — so \"Aeschylus Marathon\" finds a resource named for one and\n * filed under the other, and \"Historian\" finds what is tagged as one.\n */\nfunction matchesSearch(resource: ResourceDescriptor, terms: string[]): boolean {\n  const name = (resource.name ?? '').toLowerCase();\n  const uri = getStorageUri(resource)?.toLowerCase() ?? '';\n  const types = getResourceEntityTypes(resource).map((t) => t.toLowerCase());\n  return terms.every((term) =>\n    name.includes(term) || uri.includes(term) || types.some((t) => t.includes(term)));\n}\n\n/**\n * Filter, order and page a resource set. Filters always run before pagination,\n * so `total` describes the match set rather than the page.\n */\nexport function queryResources(\n  all: ResourceDescriptor[],\n  filter: ResourceFilter,\n): { resources: ResourceDescriptor[]; total: number } {\n  let matches = all;\n\n  if (filter.entityTypes && filter.entityTypes.length > 0) {\n    matches = matches.filter((doc) =>\n      filter.entityTypes!.some((type) => getResourceEntityTypes(doc).includes(type)));\n  }\n\n  // A query of only whitespace has no terms, and so filters nothing.\n  const terms = filter.search ? searchTerms(filter.search) : [];\n  if (terms.length > 0) {\n    matches = matches.filter((doc) => matchesSearch(doc, terms));\n  }\n\n  if (filter.archived !== undefined) {\n    matches = matches.filter((doc) => (doc.archived ?? false) === filter.archived);\n  }\n\n  const search = terms.length > 0 ? filter.search! : undefined;\n  const ordered = [...matches].sort(\n    search\n      ? (a, b) => (searchRank(a, search) - searchRank(b, search)) || compareByRecencyThenId(a, b)\n      : compareByRecencyThenId,\n  );\n\n  const offset = filter.offset ?? 0;\n  const limit = filter.limit ?? 20;\n  return { resources: ordered.slice(offset, offset + limit), total: ordered.length };\n}\n","// AWS Neptune implementation of GraphDatabase interface\n// Uses Gremlin for graph traversal\n\nimport { GraphDatabase } from '../interface';\nimport { assertMutableResourceUpdate } from '../interface';\nimport { queryResources } from '../resource-query';\nimport { getEntityTypes } from '@semiont/ontology';\nimport type { Logger } from '@semiont/core';\nimport {\n  buildAnnotation,\n  decodeAnnotation,\n  encodeAnnotation,\n  encodeSelector,\n  motivationForCategory,\n  storedAnnotationType,\n  type AnnotationProperties,\n} from '../annotation-codec';\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 { v4 as uuidv4 } from 'uuid';\nimport { getBodySource, getTargetSource, getPrimaryRepresentation, getResourceId, getStorageUri } from '@semiont/core';\nimport type { ResourceDescriptor } from '@semiont/core';\nimport type { Annotation } from '@semiont/core';\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 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    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      storageUri: getValue('storageUri') || undefined,\n    }],\n    archived: archived === 'true' || archived === true,\n    dateCreated,\n    wasAttributedTo: typeof creatorRaw === 'string' ? JSON.parse(creatorRaw) : creatorRaw,\n  };\n\n  const sourceResourceId = getValue('sourceResourceId');\n  if (sourceResourceId) resource.sourceResourceId = sourceResourceId;\n\n  return resource;\n}\n\n/**\n * Convert a Neptune vertex to an Annotation.\n *\n * Exported so the cross-store conformance suite can run this store's decode\n * path with no live Neptune: everything past the flattening below is the\n * shared codec's.\n */\nexport function vertexToAnnotation(vertex: any, entityTypes: string[] = []): Annotation {\n  return decodeAnnotation(normalizeProperties(vertex.properties || vertex), entityTypes);\n}\n\n/** Neptune returns each property in one of several shapes depending on the traversal. */\nfunction normalizeProperties(props: any): AnnotationProperties {\n  const normalized: AnnotationProperties = {};\n  for (const [key, raw] of Object.entries(props ?? {})) {\n    const value = unwrap(raw);\n    if (value === undefined || value === null) continue;\n    normalized[key] = typeof value === 'string' ? value : String(value);\n  }\n  return normalized;\n}\n\nfunction unwrap(prop: any): any {\n  if (prop === undefined || prop === null) return undefined;\n  if (Array.isArray(prop)) return prop.length > 0 ? unwrap(prop[0]) : undefined;\n  if (typeof prop === 'object' && 'value' in prop) return prop.value;\n  return prop;\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 logger?: Logger;\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    logger?: Logger;\n  } = {}) {\n    if (config.endpoint) this.neptuneEndpoint = config.endpoint;\n    this.neptunePort = config.port || 8182;\n    if (config.region) this.region = config.region;\n    this.logger = config.logger;\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      this.logger?.info('Discovered Neptune endpoint', { endpoint: this.neptuneEndpoint, port: this.neptunePort });\n    } catch (error: any) {\n      this.logger?.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      this.logger?.info('Connecting to Neptune', { 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      this.logger?.info('Connected to Neptune', { vertexCountTest: count.value });\n\n      this.connected = true;\n    } catch (error: any) {\n      this.logger?.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        this.logger?.error('Error closing Neptune connection', { error });\n      }\n    }\n\n    this.connected = false;\n    this.logger?.info('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('checksum', primaryRep.checksum)\n        .property('entityTypes', JSON.stringify(resource.entityTypes));\n\n      if (resource.sourceResourceId) {\n        vertex.property('sourceResourceId', resource.sourceResourceId);\n      }\n      const storageUri = getStorageUri(resource);\n      if (storageUri) {\n        vertex.property('storageUri', storageUri);\n      }\n\n      await vertex.next();\n\n      this.logger?.info('Created resource vertex in Neptune', { id });\n      return resource;\n    } catch (error) {\n      this.logger?.error('Failed to create resource in Neptune', { error });\n      throw error;\n    }\n  }\n  \n  async getResource(id: ResourceId): 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      this.logger?.error('Failed to get resource from Neptune', { error });\n      throw error;\n    }\n  }\n  \n  async updateResource(id: ResourceId, input: UpdateResourceInput): Promise<ResourceDescriptor> {\n    assertMutableResourceUpdate(input);\n\n    try {\n      let traversal = this.g.V()\n        .hasLabel('Resource')\n        .has('id', id);\n      if (input.archived !== undefined) {\n        traversal = traversal.property('archived', input.archived);\n      }\n      if (input.entityTypes !== undefined) {\n        // Mirrors createResource's storage idiom: entityTypes ride as JSON.\n        traversal = traversal.property('entityTypes', JSON.stringify(input.entityTypes));\n      }\n      const result = await traversal\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      this.logger?.error('Failed to update resource in Neptune', { error });\n      throw error;\n    }\n  }\n  \n  async deleteResource(id: ResourceId): 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      this.logger?.info('Deleted resource from Neptune', { id });\n    } catch (error) {\n      this.logger?.error('Failed to delete resource from Neptune', { error });\n      throw error;\n    }\n  }\n  \n  /**\n   * Filtering, ranking and pagination happen in JS rather than in Gremlin.\n   *\n   * The ranking ladder (exact name over prefix over substring over path- or\n   * tag-assisted) has no natural Gremlin expression, and a rank applied after\n   * `range()` would order one page instead of the match set. JanusGraph\n   * post-filters for the same reason. Both share `queryResources` with the\n   * memory backend so search cannot mean three different things across three\n   * gateways.\n   *\n   * The cost is explicit and accepted: this materializes every `Resource`\n   * vertex per call, so it is O(N) in the size of the KB rather than in the\n   * size of the result. Neo4j is the production path and pushes the whole\n   * query — filter, rank, page — into Cypher; Neptune and JanusGraph are not\n   * deployment targets today. If either becomes one at scale, the fix is a\n   * Gremlin rank expression (`choose` over `toLower`, engine-version\n   * permitting), not a return to per-gateway search semantics.\n   */\n  async listResources(filter: ResourceFilter): Promise<{ resources: ResourceDescriptor[]; total: number }> {\n    try {\n      const results = await this.g.V().hasLabel('Resource').elementMap().toList();\n      return queryResources(results.map(vertexToResource), filter);\n    } catch (error) {\n      this.logger?.error('Failed to list resources from Neptune', { error });\n      throw error;\n    }\n  }\n\n  \n  async createAnnotation(input: CreateAnnotationInternal): Promise<Annotation> {\n    // The caller's id is the system of record's — never mint a fresh one\n    // (the event-log id is what deletes and lookups arrive under).\n    const annotation = buildAnnotation(input, new Date().toISOString());\n    const props = encodeAnnotation(annotation);\n    const targetSource = props.resourceId!;\n    const bodySource = props.source;\n    const entityTypes = getEntityTypes(input);\n\n    try {\n      // Create Annotation vertex — every property comes from the codec, so\n      // a source-only target contributes no `selector` property at all.\n      let vertex = this.g.addV('Annotation');\n      for (const [key, value] of Object.entries(props)) {\n        vertex = vertex.property(key, value);\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      this.logger?.info('Created annotation vertex in Neptune', { id: annotation.id });\n      return annotation;\n    } catch (error) {\n      this.logger?.error('Failed to create annotation in Neptune', { error });\n      throw error;\n    }\n  }\n  \n  async getAnnotation(id: AnnotationId): 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      this.logger?.error('Failed to get annotation from Neptune', { error });\n      throw error;\n    }\n  }\n  \n  async updateAnnotation(id: AnnotationId, 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          for (const [key, value] of Object.entries(encodeSelector(updates.target.selector))) {\n            traversal = traversal.property(key, value);\n          }\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      this.logger?.error('Failed to update annotation in Neptune', { error });\n      throw error;\n    }\n  }\n  \n  async deleteAnnotation(id: AnnotationId): Promise<void> {\n    try {\n      await this.g.V()\n        .hasLabel('Annotation')\n        .has('id', id)\n        .drop()\n        .iterate();\n\n      this.logger?.info('Deleted annotation from Neptune', { id });\n    } catch (error) {\n      this.logger?.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        traversal = traversal.has('type', storedAnnotationType(motivationForCategory(filter.type)));\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      this.logger?.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      this.logger?.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      this.logger?.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      this.logger?.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      this.logger?.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      this.logger?.error('Failed to get resource annotations from Neptune', { error });\n      throw error;\n    }\n  }\n  \n  async getResourceReferencedBy(resourceId: ResourceId, _motivation?: string): Promise<Annotation[]> {\n    try {\n      const results = await this.g.V()\n        .hasLabel('Annotation')\n        .has('resolvedResourceId', resourceId)\n        .elementMap()\n        .toList();\n\n      return await this.fetchAnnotationsWithEntityTypes(results);\n    } catch (error) {\n      this.logger?.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      this.logger?.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      this.logger?.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      this.logger?.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      this.logger?.error('Failed to get stats from Neptune', { error });\n      throw error;\n    }\n  }\n  \n  async batchCreateResources(resources: ResourceDescriptor[]): Promise<ResourceDescriptor[]> {\n    const results: ResourceDescriptor[] = [];\n    for (const resource of resources) {\n      results.push(await this.createResource(resource));\n    }\n    return results;\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      this.logger?.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      this.logger?.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      this.logger?.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      this.logger?.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      this.logger?.debug('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        this.logger?.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      this.logger?.info('Cleared all data from Neptune');\n      // Reset tag collections\n      this.entityTypesCollection = null;\n    } catch (error) {\n      this.logger?.error('Failed to clear Neptune database', { error });\n      throw error;\n    }\n  }\n}","/**\n * The annotation codec — the one module that decides how a W3C annotation\n * becomes stored properties and back.\n *\n * Every store keeps its own dialect (Cypher parameters, Gremlin\n * `.property()` chains, a Map) and its own way of flattening what the driver\n * hands back into a property bag. What none of them owns any more is the\n * SHAPE: the W3C envelope, which fields are required, how a selector is\n * serialized, how the body array is reconstructed from entity tags and a\n * linking source. Those lived in three near-verbatim copies that disagreed\n * in four places, and each disagreement was a bug — a resource-level\n * annotation came back carrying `selector: {}`, which is not a legal\n * selector, and a motivation-less row was silently relabelled `'linking'`.\n *\n * The codec manufactures nothing. Absence is stored as absence and read back\n * as absence, in both directions.\n */\n\nimport { annotationId as makeAnnotationId } from '@semiont/core';\nimport { getBodySource, getExactText, getTargetSelector, getTargetSource } from '@semiont/core';\nimport type { Annotation, AnnotationCategory, CreateAnnotationInternal } from '@semiont/core';\n\n/**\n * A store's property bag, flattened. Producing this is the store's job (D3):\n * neo4j unwraps `node.properties` and its native temporals, the Gremlin\n * stores unwrap `[{value}]` lists. What the values MEAN is the codec's.\n */\nexport type AnnotationProperties = Record<string, string | undefined>;\n\ntype AnnotationTarget = Exclude<Annotation['target'], string>;\ntype AnnotationSelector = NonNullable<AnnotationTarget['selector']>;\ntype AnnotationBody = NonNullable<Annotation['body']>;\n\n/**\n * The stored `type` property, which the category filters match on. It\n * restates the motivation, so it is derived from it here and nowhere else —\n * the three filters that used to hand-write the same mapping had drifted\n * into asking for a value no store ever wrote.\n */\nexport function storedAnnotationType(motivation: Annotation['motivation']): string {\n  return motivation === 'highlighting' ? 'TextualBody' : 'SpecificResource';\n}\n\n/** The category a caller filters by, in the vocabulary the annotation stores. */\nexport function motivationForCategory(category: AnnotationCategory): Annotation['motivation'] {\n  return category === 'highlight' ? 'highlighting' : 'linking';\n}\n\n/**\n * Mint the annotation a create request describes.\n *\n * `created` is a parameter rather than a `new Date()` here so the codec stays\n * pure — and so it is visible at each call site that the graph stamps its own\n * write time. `CreateAnnotationInternal` carries no timestamp, so the event's\n * own time does not reach this projection at all.\n */\nexport function buildAnnotation(input: CreateAnnotationInternal, created: string): Annotation {\n  const annotation: Annotation = {\n    '@context': 'http://www.w3.org/ns/anno.jsonld',\n    type: 'Annotation',\n    id: makeAnnotationId(input.id),\n    motivation: input.motivation,\n    target: input.target,\n    creator: input.creator,\n    created,\n  };\n  if (input.body && (!Array.isArray(input.body) || input.body.length > 0)) {\n    annotation.body = input.body;\n  }\n  return annotation;\n}\n\n/**\n * The annotation's stored properties. Entity tags are not among them — those\n * are edges, and the store writes them from `getEntityTypes(annotation)`.\n */\nexport function encodeAnnotation(annotation: Annotation): Record<string, string> {\n  const selector = getTargetSelector(annotation.target);\n  const bodySource = getBodySource(annotation.body);\n\n  // `created` is optional on the wire but not in the store: a row without it\n  // cannot be read back, so refuse to write one rather than mint a timestamp.\n  const resourceId = getTargetSource(annotation.target);\n  if (!resourceId) throw new Error(`Annotation ${annotation.id} has no target source`);\n  if (!annotation.created) throw new Error(`Annotation ${annotation.id} has no created timestamp`);\n\n  const props: Record<string, string> = {\n    id: annotation.id,\n    resourceId,\n    type: storedAnnotationType(annotation.motivation),\n    motivation: annotation.motivation,\n    creator: JSON.stringify(annotation.creator),\n    created: annotation.created,\n  };\n\n  if (selector) Object.assign(props, encodeSelector(selector));\n  if (bodySource) props.source = bodySource;\n  if (annotation.modified) props.modified = annotation.modified;\n  if (annotation.generator) props.generator = JSON.stringify(annotation.generator);\n\n  return props;\n}\n\n/**\n * The properties a selector contributes: its serialization, plus the quoted\n * text pulled out beside it. Targeted selector updates go through here too,\n * so no store decides on its own what a selector is called on disk.\n */\nexport function encodeSelector(selector: AnnotationSelector): Record<string, string> {\n  const props: Record<string, string> = { selector: JSON.stringify(selector) };\n  const exact = getExactText(selector);\n  if (exact) props.exact = exact;\n  return props;\n}\n\n/**\n * Rebuild the annotation from stored properties and the entity-tag edges the\n * store resolved separately.\n *\n * A field the properties do not carry is omitted, never invented: a\n * source-only target (legal since RESOURCE-LEVEL-ANCHOR) comes back with no\n * `selector`, and a row missing a required field fails loudly by name rather\n * than acquiring a default.\n */\nexport function decodeAnnotation(props: AnnotationProperties, entityTypes: string[] = []): Annotation {\n  const id = props.id;\n  if (!id) throw new Error('Annotation missing required field: id');\n\n  const required = (key: string): string => {\n    const value = props[key];\n    if (!value) throw new Error(`Annotation ${id} missing required field: ${key}`);\n    return value;\n  };\n\n  const resourceId = required('resourceId');\n  const creator = JSON.parse(required('creator'));\n  // The stored value is one of the wire vocabulary's, which the event that\n  // produced it was validated against; the projection does not re-police it.\n  const motivation = required('motivation') as Annotation['motivation'];\n  const created = required('created');\n\n  const body: AnnotationBody = [];\n  for (const entityType of entityTypes) {\n    if (entityType) body.push({ type: 'TextualBody', value: entityType, purpose: 'tagging' });\n  }\n  if (props.source) {\n    body.push({ type: 'SpecificResource', source: props.source, purpose: 'linking' });\n  }\n\n  const selector = decodeSelector(props.selector);\n  const target: AnnotationTarget = selector ? { source: resourceId, selector } : { source: resourceId };\n\n  const annotation: Annotation = {\n    '@context': 'http://www.w3.org/ns/anno.jsonld',\n    type: 'Annotation',\n    id: makeAnnotationId(id),\n    motivation,\n    target,\n    creator,\n    created,\n  };\n\n  if (body.length > 0) annotation.body = body;\n  if (props.modified) annotation.modified = props.modified;\n  if (props.generator) {\n    try {\n      annotation.generator = JSON.parse(props.generator);\n    } catch {\n      // A corrupt generator is not worth failing the whole read over — the\n      // annotation itself is intact, and provenance is advisory.\n    }\n  }\n\n  return annotation;\n}\n\n/**\n * Rows written before RESOURCE-LEVEL-ANCHOR reached the stores hold `'{}'`\n * where a resource-level annotation has no selector at all. `{}` satisfies no\n * branch of the selector union, so it fails validation on the first round\n * trip through a validated channel — reading it back as absent is what makes\n * those rows harmless without a migration.\n */\nfunction decodeSelector(raw: string | undefined): AnnotationSelector | undefined {\n  if (!raw) return undefined;\n  const parsed = JSON.parse(raw);\n  if (!parsed || Object.keys(parsed).length === 0) return undefined;\n  return parsed;\n}\n","// Neo4j implementation of GraphDatabase interface\n// Uses Cypher query language\n\nimport type { Driver, Session } from 'neo4j-driver';\nimport { GraphDatabase } from '../interface';\nimport { assertMutableResourceUpdate } from '../interface';\nimport { searchTerms } from '../resource-query';\nimport type { Logger } from '@semiont/core';\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 { v4 as uuidv4 } from 'uuid';\nimport { getPrimaryRepresentation, getStorageUri } from '@semiont/core';\nimport { getEntityTypes } from '@semiont/ontology';\nimport {\n  buildAnnotation,\n  decodeAnnotation,\n  encodeAnnotation,\n  motivationForCategory,\n  storedAnnotationType,\n  type AnnotationProperties,\n} from '../annotation-codec';\n\nimport type { ResourceDescriptor } from '@semiont/core';\nimport type { Annotation } from '@semiont/core';\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 neo4j!: typeof import('neo4j-driver');\n  private connected: boolean = false;\n  private logger?: Logger;\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    logger?: Logger;\n  } = {}) {\n    this.config = config;\n    this.logger = config.logger;\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      this.logger?.info('Connecting to Neo4j', { uri });\n\n      this.neo4j = await import('neo4j-driver');\n      this.driver = this.neo4j.driver(\n        uri,\n        this.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      this.logger?.info('Successfully connected to Neo4j');\n      this.connected = true;\n    } catch (error) {\n      this.logger?.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            this.logger?.warn('Schema creation warning', { message: 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            this.logger?.warn('Index creation warning', { message: 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      // Use MERGE instead of CREATE for idempotence and to enrich stub nodes\n      // Stub nodes may be created by REFERENCES edge creation before resource.created event\n      const result = await session.run(\n        `MERGE (d:Resource {id: $id})\n         SET d.name = $name,\n             d.entityTypes = $entityTypes,\n             d.format = $format,\n             d.archived = $archived,\n             d.created = datetime($created),\n             d.creator = $creator,\n             d.contentChecksum = $contentChecksum,\n             d.sourceAnnotationId = $sourceAnnotationId,\n             d.sourceResourceId = $sourceResourceId,\n             d.storageUri = $storageUri,\n             d.stub = false\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          contentChecksum: primaryRep.checksum,\n          sourceAnnotationId: resource.sourceAnnotationId ?? null,\n          sourceResourceId: resource.sourceResourceId ?? null,\n          storageUri: getStorageUri(resource) ?? null,\n        }\n      );\n\n      this.logger?.info('Resource created/enriched', { id });\n      return this.parseResourceNode(result.records[0]!.get('d'));\n    } finally {\n      await session.close();\n    }\n  }\n\n  async getResource(id: ResourceId): 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: ResourceId, input: UpdateResourceInput): Promise<ResourceDescriptor> {\n    assertMutableResourceUpdate(input);\n\n    const sets: string[] = [];\n    const params: Record<string, unknown> = { id };\n    if (input.archived !== undefined) {\n      sets.push('d.archived = $archived');\n      params.archived = input.archived;\n    }\n    if (input.entityTypes !== undefined) {\n      sets.push('d.entityTypes = $entityTypes');\n      params.entityTypes = input.entityTypes;\n    }\n\n    const session = this.getSession();\n    try {\n      const result = await session.run(\n        `MATCH (d:Resource {id: $id})\n         SET ${sets.join(', ')}\n         RETURN d`,\n        params\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: ResourceId): 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      // Stub nodes are id-only placeholders that `MERGE` creates when a\n      // REFERENCES edge points at a resource whose `resource.created` event\n      // hasn't landed yet. They carry no name, so they are not listable — and\n      // `parseResourceNode` throws on the missing field rather than inventing one.\n      const conditions: string[] = ['coalesce(d.stub, false) = false'];\n\n      if (filter.archived !== undefined) {\n        conditions.push('d.archived = $archived');\n        params.archived = filter.archived;\n      }\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      // Every term must appear, each satisfiable by the name or the path. A\n      // whitespace-only query yields no terms and so is not a search at all.\n      const terms = filter.search ? searchTerms(filter.search) : [];\n      if (terms.length > 0) {\n        conditions.push(\n          `ALL(t IN $terms WHERE toLower(d.name) CONTAINS t\n                             OR toLower(coalesce(d.storageUri, \"\")) CONTAINS t\n                             OR ANY(e IN coalesce(d.entityTypes, []) WHERE toLower(e) CONTAINS t))`\n        );\n        params.terms = terms;\n        params.search = filter.search!.trim().toLowerCase();\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 = this.neo4j.int(filter.offset || 0);\n      params.limit = this.neo4j.int(filter.limit || 20);\n\n      // Rank only means something against a query; an unsearched listing orders\n      // on recency alone. Ranking must happen here rather than over the returned\n      // page, or it would sort one page instead of the match set.\n      const rankClause = terms.length > 0\n        ? `WITH d, CASE\n             WHEN toLower(d.name) = $search THEN 0\n             WHEN toLower(d.name) STARTS WITH $search THEN 1\n             WHEN ALL(t IN $terms WHERE toLower(d.name) CONTAINS t) THEN 2\n             ELSE 3\n           END AS rank\n         `\n        : '';\n      const orderClause = terms.length > 0\n        ? 'ORDER BY rank, d.created DESC, d.id'\n        : 'ORDER BY d.created DESC, d.id';\n\n      const result = await session.run(\n        `MATCH (d:Resource) ${whereClause}\n         ${rankClause}RETURN d\n         ${orderClause}\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\n  async createAnnotation(input: CreateAnnotationInternal): Promise<Annotation> {\n    const session = this.getSession();\n    try {\n      const annotation = buildAnnotation(input, new Date().toISOString());\n      const props = encodeAnnotation(annotation);\n      const targetSource = props.resourceId!;\n      const bodySource = props.source;\n\n      // Entity tags are edges, not properties, so they travel beside the bag.\n      const entityTypes = getEntityTypes(input);\n\n      // Convert motivation to label (e.g., \"linking\" -> \"Linking\")\n      const motivationLabel = motivationToLabel(annotation.motivation);\n\n      // The codec's property bag is applied verbatim; `created` is then\n      // re-set as a native temporal, which is the one property this store\n      // stores in a type of its own.\n      const cypher = bodySource\n        ? `MATCH (from:Resource {id: $targetSource})\n           MATCH (to:Resource {id: $bodySource})\n           CREATE (a:Annotation:${motivationLabel})\n           SET a = $props, a.created = datetime($created)\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        : `MATCH (d:Resource {id: $targetSource})\n           CREATE (a:Annotation:${motivationLabel})\n           SET a = $props, a.created = datetime($created)\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      const result = await session.run(cypher, {\n        props,\n        created: annotation.created,\n        targetSource,\n        bodySource: bodySource ?? null,\n        entityTypes,\n      });\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 parseAnnotationNode(result.records[0]!.get('a'), entityTypes);\n    } finally {\n      await session.close();\n    }\n  }\n\n  async getAnnotation(id: AnnotationId): Promise<Annotation | null> {\n    this.logger?.debug('Getting annotation', { id });\n    const session = this.getSession();\n    try {\n      const result = await session.run(\n        `MATCH (a:Annotation {id: $id})\n         OPTIONAL MATCH (a)-[:TAGGED_AS]->(et:EntityType)\n         RETURN a, collect(et.name) as entityTypes`,\n        { id }\n      );\n\n      if (result.records.length === 0) {\n        this.logger?.debug('Annotation not found', { id });\n        return null;\n      }\n      this.logger?.debug('Annotation found', { id });\n      return parseAnnotationNode(\n        result.records[0]!.get('a'),\n        result.records[0]!.get('entityTypes')\n      );\n    } finally {\n      await session.close();\n    }\n  }\n\n  async updateAnnotation(id: AnnotationId, updates: Partial<Annotation>): Promise<Annotation> {\n    const session = this.getSession();\n    try {\n      const setClauses: string[] = ['a.updatedAt = datetime()'];\n      const params: any = { id };\n\n      // Build SET clauses dynamically\n      Object.entries(updates).forEach(([key, value]) => {\n        if (key !== 'id' && key !== 'updatedAt') {\n          setClauses.push(`a.${key} = $${key}`);\n          if (key === 'body') {\n            params[key] = JSON.stringify(value);\n          } else if (key === 'created') {\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        this.logger?.debug('Updating motivation label', { 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        this.logger?.debug('Motivation label updated', { newLabel });\n      }\n\n      // If body was updated and contains a SpecificResource, create REFERENCES relationship\n      if (updates.body) {\n        this.logger?.debug('Body update for annotation', { id, body: updates.body });\n        const bodyArray = Array.isArray(updates.body) ? updates.body : [updates.body];\n\n        const specificResource = bodyArray.find((item: any) => item.type === 'SpecificResource' && item.purpose === 'linking');\n\n        if (specificResource && 'source' in specificResource && specificResource.source) {\n          this.logger?.debug('Creating REFERENCES edge', { annotationId: id, targetResourceId: specificResource.source });\n          // Create REFERENCES relationship to the target resource\n          // Use MERGE for target to create stub node if it doesn't exist yet (eventual consistency)\n          // Stub will be enriched when resource.created event arrives\n          const refResult = await session.run(\n            `MATCH (a:Annotation {id: $annotationId})\n             MERGE (target:Resource {id: $targetResourceId})\n             ON CREATE SET target.stub = true\n             MERGE (a)-[:REFERENCES]->(target)\n             RETURN a, target, target.stub AS wasStub`,\n            {\n              annotationId: id,\n              targetResourceId: specificResource.source\n            }\n          );\n\n          if (refResult.records.length > 0) {\n            const wasStub = refResult.records[0]!.get('wasStub');\n            if (wasStub) {\n              this.logger?.debug('REFERENCES edge created with stub node', { targetResourceId: specificResource.source });\n            } else {\n              this.logger?.debug('REFERENCES edge created to existing resource', { targetResourceId: specificResource.source });\n            }\n          } else {\n            this.logger?.warn('REFERENCES edge creation returned no records');\n          }\n        } else {\n          this.logger?.debug('No SpecificResource in body - stub reference not yet resolved');\n        }\n      } else {\n        this.logger?.debug('No body update for annotation', { id });\n      }\n\n      return 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: AnnotationId): 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        conditions.push('a.type = $type');\n        params.type = storedAnnotationType(motivationForCategory(filter.type));\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        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        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 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        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        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        parseAnnotationNode(record.get('a'), record.get('entityTypes'))\n      );\n    } finally {\n      await session.close();\n    }\n  }\n\n  async getResourceReferencedBy(resourceId: ResourceId, motivation?: string): Promise<Annotation[]> {\n    const session = this.getSession();\n    try {\n      this.logger?.debug('Searching for annotations referencing resource', { resourceId, motivation });\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: $resourceId})\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, { resourceId });\n\n      this.logger?.debug('Found annotations', { count: result.records.length });\n\n      return result.records.map(record =>\n        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(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(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(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 batchCreateResources(resources: ResourceDescriptor[]): Promise<ResourceDescriptor[]> {\n    if (resources.length === 0) return [];\n    const session = this.getSession();\n    try {\n      const params = resources.map(resource => {\n        const primaryRep = getPrimaryRepresentation(resource);\n        if (!primaryRep) throw new Error('Resource must have at least one representation');\n        return {\n          id: resource['@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          contentChecksum: primaryRep.checksum,\n          sourceAnnotationId: resource.sourceAnnotationId ?? null,\n          sourceResourceId: resource.sourceResourceId ?? null,\n          storageUri: getStorageUri(resource) ?? null,\n        };\n      });\n\n      const result = await session.run(\n        `UNWIND $resources AS r\n         MERGE (d:Resource {id: r.id})\n         SET d.name = r.name,\n             d.entityTypes = r.entityTypes,\n             d.format = r.format,\n             d.archived = r.archived,\n             d.created = datetime(r.created),\n             d.creator = r.creator,\n             d.contentChecksum = r.contentChecksum,\n             d.sourceAnnotationId = r.sourceAnnotationId,\n             d.sourceResourceId = r.sourceResourceId,\n             d.storageUri = r.storageUri,\n             d.stub = false\n         RETURN d`,\n        { resources: params }\n      );\n\n      this.logger?.info('Batch created/enriched resources', { count: resources.length });\n      return result.records.map(record => this.parseResourceNode(record.get('d')));\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.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        storageUri: props.storageUri ?? undefined,\n      }],\n      archived: props.archived,\n      dateCreated: props.created.toString(),\n      wasAttributedTo: typeof props.creator === 'string' ? JSON.parse(props.creator) : props.creator,\n    };\n\n    if (props.sourceResourceId) resource.sourceResourceId = props.sourceResourceId;\n\n    return resource;\n  }\n\n}\n\n/**\n * Project a neo4j annotation node to the wire `Annotation`.\n *\n * Module-level (not a method) so the projection is unit-testable without a\n * driver: `node` is untyped at this seam, which is exactly how a native\n * neo4j DateTime once reached the wire as `created` unseen by tsc.\n */\nexport function parseAnnotationNode(node: any, entityTypes: string[] = []): Annotation {\n  return decodeAnnotation(normalizeProperties(node.properties), entityTypes);\n}\n\n/**\n * Flatten a node's properties to the strings the codec reads.\n *\n * `created` is stored as `datetime($created)`, so the driver hands back a\n * native temporal object whose `toString()` is the ISO form — the coercion\n * that has to happen before the codec sees a value it is entitled to treat\n * as a string. This seam is untyped, so only a test can see it slip.\n */\nfunction normalizeProperties(props: any): AnnotationProperties {\n  const normalized: AnnotationProperties = {};\n  for (const [key, value] of Object.entries(props ?? {})) {\n    if (value === null || value === undefined) continue;\n    normalized[key] = typeof value === 'string' ? value : String(value);\n  }\n  return normalized;\n}\n","// JanusGraph implementation with real Gremlin connection\n// This replaces the mock in-memory implementation\n\nimport { GraphDatabase } from '../interface';\nimport { assertMutableResourceUpdate } from '../interface';\nimport { queryResources } from '../resource-query';\nimport type { Logger } from '@semiont/core';\nimport { resourceId as makeResourceId } from '@semiont/core';\nimport { getBodySource, getPrimaryRepresentation, getResourceId, getStorageUri } from '@semiont/core';\nimport { getEntityTypes } from '@semiont/ontology';\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 { v4 as uuidv4 } from 'uuid';\nimport {\n  buildAnnotation,\n  decodeAnnotation,\n  encodeAnnotation,\n  encodeSelector,\n  motivationForCategory,\n  storedAnnotationType,\n  type AnnotationProperties,\n} from '../annotation-codec';\n\nimport type { ResourceDescriptor } from '@semiont/core';\nimport type { Annotation } from '@semiont/core';\n\n/** Helper to get property value from Gremlin vertex properties */\nfunction 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/**\n * Convert a JanusGraph vertex to an Annotation.\n *\n * Module-level so the cross-store conformance suite can run this store's\n * decode path with no live JanusGraph: everything past the flattening is the\n * shared codec's. This is where a missing selector used to become `'{}'` and\n * a missing motivation used to become `'linking'`.\n */\nexport function vertexToAnnotation(vertex: any, entityTypes: string[] = []): Annotation {\n  const props = vertex.properties || {};\n  const normalized: AnnotationProperties = {};\n  for (const key of Object.keys(props)) {\n    const value = getPropertyValue(props, key);\n    if (value === undefined || value === null) continue;\n    normalized[key] = typeof value === 'string' ? value : String(value);\n  }\n  return decodeAnnotation(normalized, entityTypes);\n}\n\nexport class JanusGraphDatabase implements GraphDatabase {\n  private connected: boolean = false;\n  private connection: any | null = null;\n  private g: any | null = null;\n  private logger?: Logger;\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      logger?: Logger;\n    },\n  ) {\n    this.logger = graphConfig.logger;\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    this.logger?.info('Connecting to JanusGraph', { host, port });\n\n    const gremlin = await import('gremlin');\n    const DriverRemoteConnection = gremlin.driver.DriverRemoteConnection;\n    const traversal = gremlin.process.AnonymousTraversalSource.traversal;\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    this.logger?.info('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    this.logger?.debug('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 = getPropertyValue(props, 'id');\n\n    // Validate required fields\n    const creatorRaw = getPropertyValue(props, 'creator');\n    const contentChecksum = getPropertyValue(props, 'contentChecksum');\n    const mediaType = getPropertyValue(props, 'contentType');\n\n    if (!creatorRaw) throw new Error(`Resource ${id} missing required field: creator`);\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: getPropertyValue(props, 'name'),\n      entityTypes: JSON.parse(getPropertyValue(props, 'entityTypes') || '[]'),\n      representations: [{\n        mediaType,\n        checksum: contentChecksum,\n        rel: 'original',\n        storageUri: getPropertyValue(props, 'storageUri') || undefined,\n      }],\n      archived: getPropertyValue(props, 'archived') === 'true',\n      dateCreated: getPropertyValue(props, 'created'),\n      wasAttributedTo: creator,\n    };\n\n    const sourceAnnotationId = getPropertyValue(props, 'sourceAnnotationId');\n    const sourceResourceId = getPropertyValue(props, 'sourceResourceId');\n\n    if (sourceAnnotationId) resource.sourceAnnotationId = sourceAnnotationId;\n    if (sourceResourceId) resource.sourceResourceId = sourceResourceId;\n\n    return resource;\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 = 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        getPropertyValue(v.properties || {}, 'name')\n      ).filter(Boolean);\n\n      annotations.push(vertexToAnnotation(vertex, entityTypes));\n    }\n\n    return annotations;\n  }\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('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    const storageUri = getStorageUri(resource);\n    if (storageUri) {\n      vertex.property('storageUri', storageUri);\n    }\n\n    await vertex.next();\n\n    this.logger?.info('Created resource vertex in JanusGraph', { id });\n    return resource;\n  }\n  \n  async getResource(id: ResourceId): 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: ResourceId, input: UpdateResourceInput): Promise<ResourceDescriptor> {\n    assertMutableResourceUpdate(input);\n\n    let traversal = this.g!\n      .V()\n      .has('Resource', 'id', id);\n    if (input.archived !== undefined) {\n      traversal = traversal.property('archived', input.archived);\n    }\n    if (input.entityTypes !== undefined) {\n      // Mirrors createResource's storage idiom: entityTypes ride as JSON.\n      traversal = traversal.property('entityTypes', JSON.stringify(input.entityTypes));\n    }\n    await traversal.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: ResourceId): 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    this.logger?.info('Deleted resource from JanusGraph', { id });\n  }\n  \n  async listResources(filter: ResourceFilter): Promise<{ resources: ResourceDescriptor[]; total: number }> {\n    // Note: filtering is done client-side after retrieval. In production,\n    // JanusGraph supports server-side text predicates via Elasticsearch,\n    // but composing OR across multiple text properties requires the\n    // anonymous-traversal API; for a gateway that's not the production\n    // target today, JS post-filtering is simpler and adequate at our scale.\n    const docs = await this.g!.V().hasLabel('Resource').toList();\n    return queryResources(docs.map((v: any) => this.vertexToResource(v)), filter);\n  }\n\n  \n  async createAnnotation(input: CreateAnnotationInternal): Promise<Annotation> {\n    // The caller's id is the system of record's — never mint a fresh one\n    // (the event-log id is what deletes and lookups arrive under).\n    const annotation = buildAnnotation(input, new Date().toISOString());\n    const props = encodeAnnotation(annotation);\n    const targetSource = props.resourceId!;\n    const bodySource = props.source;\n    const entityTypes = getEntityTypes(input);\n\n    // Create annotation vertex — every property comes from the codec, so a\n    // source-only target contributes no `selector` property at all.\n    let vertex = this.g!.addV('Annotation');\n    for (const [key, value] of Object.entries(props)) {\n      vertex = vertex.property(key, value);\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    this.logger?.info('Created annotation in JanusGraph', { id: annotation.id });\n    return annotation;\n  }\n  \n  async getAnnotation(id: AnnotationId): 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      getPropertyValue(v.properties || {}, 'name')\n    ).filter(Boolean);\n\n    return vertexToAnnotation(vertices[0] as any, entityTypes);\n  }\n  \n  async updateAnnotation(id: AnnotationId, 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        for (const [key, value] of Object.entries(encodeSelector(updates.target.selector))) {\n          await traversalQuery.property(key, value).next();\n        }\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: AnnotationId): Promise<void> {\n    await this.g!\n      .V()\n      .has('Annotation', 'id', id)\n      .drop()\n      .next();\n\n    this.logger?.info('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      traversalQuery = traversalQuery.has('type', storedAnnotationType(motivationForCategory(filter.type)));\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 annotation = await this.getAnnotation(annotationId);\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(annotationId, {\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(annotationId);\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(resourceId: ResourceId, _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', resourceId)\n      .toList();\n\n    return 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    this.logger?.debug('Found paths', { count: 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(makeResourceId(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 batchCreateResources(resources: ResourceDescriptor[]): Promise<ResourceDescriptor[]> {\n    const results: ResourceDescriptor[] = [];\n    for (const resource of resources) {\n      results.push(await this.createResource(resource));\n    }\n    return results;\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      this.logger?.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      this.logger?.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 = getPropertyValue(props, 'type');\n      const tagsJson = 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    this.logger?.info('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 { assertMutableResourceUpdate } from '../interface';\nimport { queryResources } from '../resource-query';\nimport type { Logger } from '@semiont/core';\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 { v4 as uuidv4 } from 'uuid';\nimport { getBodySource, getTargetSource, getResourceId, getPrimaryRepresentation, getResourceEntityTypes } from '@semiont/core';\nimport { getEntityTypes } from '@semiont/ontology';\nimport { buildAnnotation, decodeAnnotation, encodeAnnotation } from '../annotation-codec';\nimport type { ResourceDescriptor } from '@semiont/core';\nimport type { Annotation } from '@semiont/core';\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  private logger?: Logger;\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: { logger?: Logger } = {}) {\n    this.logger = config.logger;\n  }\n  \n  async connect(): Promise<void> {\n    // No actual connection needed for in-memory storage\n    this.logger?.info('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: ResourceId): Promise<ResourceDescriptor | null> {\n    return this.resources.get(String(id)) || null;\n  }\n\n  async updateResource(id: ResourceId, input: UpdateResourceInput): Promise<ResourceDescriptor> {\n    assertMutableResourceUpdate(input);\n\n    const doc = this.resources.get(String(id));\n    if (!doc) throw new Error('Resource not found');\n\n    if (input.archived !== undefined) doc.archived = input.archived;\n    if (input.entityTypes !== undefined) doc.entityTypes = input.entityTypes;\n    return doc;\n  }\n\n  async deleteResource(id: ResourceId): Promise<void> {\n    this.resources.delete(String(id));\n\n    // Delete annotations targeting or referencing this resource\n    const idStr = String(id);\n    for (const [selId, sel] of this.annotations) {\n      if (getTargetSource(sel.target) === idStr || getBodySource(sel.body) === idStr) {\n        this.annotations.delete(selId);\n      }\n    }\n  }\n  \n  async listResources(filter: ResourceFilter): Promise<{ resources: ResourceDescriptor[]; total: number }> {\n    return queryResources(Array.from(this.resources.values()), filter);\n  }\n\n  \n  async createAnnotation(input: CreateAnnotationInternal): Promise<Annotation> {\n    // The caller's id is the system of record's — never mint a fresh one\n    // (the event-log id is what deletes and lookups arrive under).\n    const id = input.id;\n\n    // Nothing here needs serializing — but this store is the reference the\n    // interface-contract suite runs against, and a reference that cannot\n    // exhibit what the real stores exhibit is why four codec divergences\n    // survived. So the annotation round-trips through the codec: what a Map\n    // hands back is exactly what Cypher and Gremlin hand back.\n    const annotation = decodeAnnotation(\n      encodeAnnotation(buildAnnotation(input, new Date().toISOString())),\n      getEntityTypes(input)\n    );\n\n    this.annotations.set(id, annotation);\n    this.logger?.debug('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: AnnotationId): Promise<Annotation | null> {\n    return this.annotations.get(id) || null;\n  }\n  \n  async updateAnnotation(id: AnnotationId, 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: AnnotationId): 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 => getTargetSource(a.target) === resourceIdStr);\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  async getHighlights(resourceId: ResourceId): Promise<Annotation[]> {\n    const resourceIdStr = String(resourceId);\n    const highlights = Array.from(this.annotations.values())\n      .filter(sel => getTargetSource(sel.target) === resourceIdStr && sel.motivation === 'highlighting');\n    this.logger?.debug('Got highlights for resource', { resourceId, count: highlights.length });\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: String(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 => getTargetSource(sel.target) === resourceIdStr && sel.motivation === 'linking');\n    this.logger?.debug('Got references for resource', { resourceId, count: references.length });\n    return references;\n  }\n\n  async getEntityReferences(resourceId: ResourceId, entityTypes?: string[]): Promise<Annotation[]> {\n    const resourceIdStr = String(resourceId);\n    let refs = Array.from(this.annotations.values())\n      .filter(sel => getTargetSource(sel.target) === resourceIdStr && getEntityTypes(sel).length > 0);\n\n    if (entityTypes && entityTypes.length > 0) {\n      refs = refs.filter(sel => getEntityTypes(sel).some(type => entityTypes.includes(type)));\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 => getTargetSource(sel.target) === resourceIdStr);\n  }\n\n  async getResourceReferencedBy(resourceId: ResourceId, _motivation?: string): Promise<Annotation[]> {\n    return Array.from(this.annotations.values())\n      .filter(sel => getBodySource(sel.body) === String(resourceId));\n  }\n\n  async getResourceConnections(resourceId: ResourceId): Promise<GraphConnection[]> {\n    const connections: GraphConnection[] = [];\n    const refs = await this.getReferences(resourceId);\n    const resourceIdStr = String(resourceId);\n\n    for (const ref of refs) {\n      const bodySource = getBodySource(ref.body);\n      if (bodySource) {\n        const targetDoc = await this.getResource(makeResourceId(bodySource));\n        if (targetDoc) {\n          const reverseRefs = await this.getReferences(makeResourceId(bodySource));\n          const bidirectional = reverseRefs.some(r => getBodySource(r.body) === resourceIdStr);\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    const visited = new Set<string>();\n    const queue: { docId: string; path: ResourceDescriptor[]; sels: Annotation[] }[] = [];\n    const fromDoc = await this.getResource(makeResourceId(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    // Extract entity types from annotation body\n    const entityReferenceCount = annotations.filter(\n      a => a.motivation === 'linking' && getEntityTypes(a).length > 0\n    ).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 batchCreateResources(resources: ResourceDescriptor[]): Promise<ResourceDescriptor[]> {\n    const results: ResourceDescriptor[] = [];\n    for (const resource of resources) {\n      results.push(await this.createResource(resource));\n    }\n    return results;\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  \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! This would clear the entire graph\n    // await this.client.submit(`g.V().drop()`);\n    this.resources.clear();\n    this.annotations.clear();\n    this.entityTypesCollection = null;\n  }\n}","// Factory for creating graph database instances based on configuration\n\nimport { GraphDatabase } from './interface';\nimport { NeptuneGraphDatabase } from './implementations/neptune';\nimport { Neo4jGraphDatabase } from './implementations/neo4j';\nimport { JanusGraphDatabase } from './implementations/janusgraph';\nimport { MemoryGraphDatabase } from './implementations/memorygraph';\nimport type { GraphServiceConfig } from '@semiont/core';\n\nexport type GraphDatabaseType = 'neptune' | 'neo4j' | 'janusgraph' | 'memory';\n\nexport interface GraphDatabaseConfig {\n  type: GraphDatabaseType;\n\n  // Neptune config\n  neptuneEndpoint?: string;\n  neptunePort?: number;\n  neptuneRegion?: string;\n\n  // Neo4j config\n  neo4jUri?: string;\n  neo4jUsername?: string;\n  neo4jPassword?: string;\n  neo4jDatabase?: string;\n\n  // JanusGraph config\n  janusHost?: string;\n  janusPort?: number;\n  janusStorageBackend?: 'cassandra' | 'hbase' | 'berkeleydb';\n  janusIndexBackend?: 'elasticsearch' | 'solr' | 'lucene';\n}\n\n// Singleton instance\nlet graphDatabaseInstance: GraphDatabase | null = null;\n\nexport function createGraphDatabase(config: GraphDatabaseConfig): GraphDatabase {\n  switch (config.type) {\n    case 'neptune': {\n      const neptuneConfig: any = {};\n      if (config.neptuneEndpoint !== undefined) neptuneConfig.endpoint = config.neptuneEndpoint;\n      if (config.neptunePort !== undefined) neptuneConfig.port = config.neptunePort;\n      if (config.neptuneRegion !== undefined) neptuneConfig.region = config.neptuneRegion;\n      return new NeptuneGraphDatabase(neptuneConfig);\n    }\n\n    case 'neo4j': {\n      const neo4jConfig: any = {};\n      if (config.neo4jUri !== undefined) neo4jConfig.uri = config.neo4jUri;\n      if (config.neo4jUsername !== undefined) neo4jConfig.username = config.neo4jUsername;\n      if (config.neo4jPassword !== undefined) neo4jConfig.password = config.neo4jPassword;\n      if (config.neo4jDatabase !== undefined) neo4jConfig.database = config.neo4jDatabase;\n      return new Neo4jGraphDatabase(neo4jConfig);\n    }\n\n    case 'janusgraph': {\n      const janusConfig: any = {};\n      if (config.janusHost !== undefined) janusConfig.host = config.janusHost;\n      if (config.janusPort !== undefined) janusConfig.port = config.janusPort;\n      if (config.janusStorageBackend !== undefined) janusConfig.storageBackend = config.janusStorageBackend;\n      if (config.janusIndexBackend !== undefined) janusConfig.indexBackend = config.janusIndexBackend;\n      return new JanusGraphDatabase(janusConfig);\n    }\n\n    case 'memory':\n      // Hermetic TEST sink only (WEAVER-ISOLATION D4 refinement): a heap-\n      // local graph cannot be shared with a standalone Weaver, so no\n      // deployment configures it — and none does. weaver-main refuses it.\n      return new MemoryGraphDatabase({});\n\n    default:\n      throw new Error(`Unsupported graph database type: ${config.type}`);\n  }\n}\n\n// Helper function to evaluate environment variable placeholders\nfunction evaluateEnvVar(value: string | undefined): string | undefined {\n  if (!value) return undefined;\n\n  // Replace ${VAR_NAME} with actual environment variable value\n  return value.replace(/\\$\\{([^}]+)\\}/g, (match, varName) => {\n    const envValue = process.env[varName];\n    if (!envValue) {\n      throw new Error(`Environment variable ${varName} is not set. Referenced in configuration as ${match}`);\n    }\n    return envValue;\n  });\n}\n\nexport async function getGraphDatabase(graphConfig: GraphServiceConfig): Promise<GraphDatabase> {\n  if (!graphDatabaseInstance) {\n    const config: GraphDatabaseConfig = {\n      type: graphConfig.type,\n    };\n\n    // Apply configuration based on type\n    if (graphConfig.type === 'janusgraph') {\n      if (graphConfig.host) {\n        config.janusHost = graphConfig.host;\n      }\n      if (graphConfig.port) {\n        config.janusPort = graphConfig.port;\n      }\n      if (graphConfig.storage) {\n        config.janusStorageBackend = graphConfig.storage as any;\n      }\n      if (graphConfig.index && graphConfig.index !== 'none') {\n        config.janusIndexBackend = graphConfig.index as any;\n      }\n    } else if (graphConfig.type === 'neptune') {\n      if (graphConfig.endpoint) {\n        config.neptuneEndpoint = graphConfig.endpoint;\n      }\n      if (graphConfig.port) {\n        config.neptunePort = graphConfig.port;\n      }\n      if (graphConfig.region) {\n        config.neptuneRegion = graphConfig.region;\n      }\n    } else if (graphConfig.type === 'neo4j') {\n      if (graphConfig.uri) {\n        config.neo4jUri = evaluateEnvVar(graphConfig.uri);\n      }\n      if (graphConfig.username) {\n        config.neo4jUsername = evaluateEnvVar(graphConfig.username);\n      }\n      if (graphConfig.password) {\n        config.neo4jPassword = evaluateEnvVar(graphConfig.password);\n      }\n      if (graphConfig.database) {\n        config.neo4jDatabase = evaluateEnvVar(graphConfig.database);\n      }\n    }\n\n    graphDatabaseInstance = createGraphDatabase(config);\n    await graphDatabaseInstance.connect();\n  }\n\n  if (!graphDatabaseInstance.isConnected()) {\n    await graphDatabaseInstance.connect();\n  }\n\n  return graphDatabaseInstance;\n}\n\nexport async function closeGraphDatabase(): Promise<void> {\n  if (graphDatabaseInstance) {\n    await graphDatabaseInstance.disconnect();\n    graphDatabaseInstance = null;\n  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Every implementation validates its input with\n * this one guard so the mutability contract cannot drift per gateway.\n */\nexport function assertMutableResourceUpdate(input: UpdateResourceInput): void {\n  const keys = Object.keys(input);\n  if (keys.length === 0 || keys.some((k) => !MUTABLE_RESOURCE_FACETS.has(k))) {\n    throw new Error('Resources are immutable apart from archival state and entity tags.');\n  }\n}\n\n/**\n * Newest first, ties broken by id — the ordering every `listResources` result\n * must carry.\n *\n * The tiebreak is not cosmetic: browse pages these results with offset/limit,\n * and a partial order lets two pages repeat or drop rows. Ids compare by code\n * point rather than locale so the JS gateways agree with the engines, whose\n * `ORDER BY` is codepoint-ordered.\n */\nexport function compareByRecencyThenId(a: ResourceDescriptor, b: ResourceDescriptor): number {\n  const aTime = a.dateCreated ? 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Neo4j expresses the\n * same semantics in Cypher, and the interface contract tests pin both shapes to\n * one behaviour.\n */\n\nimport { getResourceEntityTypes, getStorageUri } from '@semiont/core';\nimport type { ResourceDescriptor, ResourceFilter } from '@semiont/core';\nimport { compareByRecencyThenId } from './interface';\n\n/**\n * Split a query into the terms every match must satisfy. Blank input yields no\n * terms, which callers read as \"no query\" — a bare substring match on `\" \"`\n * would otherwise match every name containing a space.\n */\nexport function searchTerms(query: string): string[] {\n  return query.toLowerCase().split(/\\s+/).filter(Boolean);\n}\n\n/**\n * How directly a resource answers the query: 0 exact name, 1 name prefix,\n * 2 every term present in the name, 3 something other than the name — the path\n * or an entity type — had to supply a term.\n *\n * Those assisted hits rank last deliberately. Someone searching \"Marathon\"\n * wants the document *called* Marathon before every file that merely lives\n * under a folder of that name or is tagged with it.\n */\nexport function searchRank(resource: ResourceDescriptor, query: string): number {\n  const whole = query.trim().toLowerCase();\n  const name = (resource.name ?? '').toLowerCase();\n  if (name === whole) return 0;\n  if (name.startsWith(whole)) return 1;\n  if (searchTerms(query).every((term) => name.includes(term))) return 2;\n  return 3;\n}\n\n/**\n * Every term must appear, though each may come from the name, the path or an\n * entity type — so \"Aeschylus Marathon\" finds a resource named for one and\n * filed under the other, and \"Historian\" finds what is tagged as one.\n */\nfunction matchesSearch(resource: ResourceDescriptor, terms: string[]): boolean {\n  const name = (resource.name ?? '').toLowerCase();\n  const uri = getStorageUri(resource)?.toLowerCase() ?? '';\n  const types = getResourceEntityTypes(resource).map((t) => t.toLowerCase());\n  return terms.every((term) =>\n    name.includes(term) || uri.includes(term) || types.some((t) => t.includes(term)));\n}\n\n/**\n * Filter, order and page a resource set. Filters always run before pagination,\n * so `total` describes the match set rather than the page.\n */\nexport function queryResources(\n  all: ResourceDescriptor[],\n  filter: ResourceFilter,\n): { resources: ResourceDescriptor[]; total: number } {\n  let matches = all;\n\n  if (filter.entityTypes && filter.entityTypes.length > 0) {\n    matches = matches.filter((doc) =>\n      filter.entityTypes!.some((type) => getResourceEntityTypes(doc).includes(type)));\n  }\n\n  // A query of only whitespace has no terms, and so filters nothing.\n  const terms = filter.search ? searchTerms(filter.search) : [];\n  if (terms.length > 0) {\n    matches = matches.filter((doc) => matchesSearch(doc, terms));\n  }\n\n  if (filter.archived !== undefined) {\n    matches = matches.filter((doc) => (doc.archived ?? false) === filter.archived);\n  }\n\n  const search = terms.length > 0 ? filter.search! : undefined;\n  const ordered = [...matches].sort(\n    search\n      ? (a, b) => (searchRank(a, search) - searchRank(b, search)) || compareByRecencyThenId(a, b)\n      : compareByRecencyThenId,\n  );\n\n  const offset = filter.offset ?? 0;\n  const limit = filter.limit ?? 20;\n  return { resources: ordered.slice(offset, offset + limit), total: ordered.length };\n}\n","// AWS Neptune implementation of GraphDatabase interface\n// Uses Gremlin for graph traversal\n\nimport { GraphDatabase } from '../interface';\nimport { assertMutableResourceUpdate } from '../interface';\nimport { queryResources } from '../resource-query';\nimport { getEntityTypes } from '@semiont/ontology';\nimport type { Logger } from '@semiont/core';\nimport {\n  buildAnnotation,\n  decodeAnnotation,\n  encodeAnnotation,\n  encodeSelector,\n  motivationForCategory,\n  storedAnnotationType,\n  type AnnotationProperties,\n} from '../annotation-codec';\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 { v4 as uuidv4 } from 'uuid';\nimport { getBodySource, getTargetSource, getPrimaryRepresentation, getResourceId, getStorageUri } from '@semiont/core';\nimport type { ResourceDescriptor } from '@semiont/core';\nimport type { Annotation } from '@semiont/core';\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 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    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      storageUri: getValue('storageUri') || undefined,\n    }],\n    archived: archived === 'true' || archived === true,\n    dateCreated,\n    wasAttributedTo: typeof creatorRaw === 'string' ? JSON.parse(creatorRaw) : creatorRaw,\n  };\n\n  const sourceResourceId = getValue('sourceResourceId');\n  if (sourceResourceId) resource.sourceResourceId = sourceResourceId;\n\n  return resource;\n}\n\n/**\n * Convert a Neptune vertex to an Annotation.\n *\n * Exported so the cross-store conformance suite can run this store's decode\n * path with no live Neptune: everything past the flattening below is the\n * shared codec's.\n */\nexport function vertexToAnnotation(vertex: any, entityTypes: string[] = []): Annotation {\n  return decodeAnnotation(normalizeProperties(vertex.properties || vertex), entityTypes);\n}\n\n/** Neptune returns each property in one of several shapes depending on the traversal. */\nfunction normalizeProperties(props: any): AnnotationProperties {\n  const normalized: AnnotationProperties = {};\n  for (const [key, raw] of Object.entries(props ?? {})) {\n    const value = unwrap(raw);\n    if (value === undefined || value === null) continue;\n    normalized[key] = typeof value === 'string' ? value : String(value);\n  }\n  return normalized;\n}\n\nfunction unwrap(prop: any): any {\n  if (prop === undefined || prop === null) return undefined;\n  if (Array.isArray(prop)) return prop.length > 0 ? unwrap(prop[0]) : undefined;\n  if (typeof prop === 'object' && 'value' in prop) return prop.value;\n  return prop;\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 logger?: Logger;\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    logger?: Logger;\n  } = {}) {\n    if (config.endpoint) this.neptuneEndpoint = config.endpoint;\n    this.neptunePort = config.port || 8182;\n    if (config.region) this.region = config.region;\n    this.logger = config.logger;\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      this.logger?.info('Discovered Neptune endpoint', { endpoint: this.neptuneEndpoint, port: this.neptunePort });\n    } catch (error: any) {\n      this.logger?.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      this.logger?.info('Connecting to Neptune', { 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      this.logger?.info('Connected to Neptune', { vertexCountTest: count.value });\n\n      this.connected = true;\n    } catch (error: any) {\n      this.logger?.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        this.logger?.error('Error closing Neptune connection', { error });\n      }\n    }\n\n    this.connected = false;\n    this.logger?.info('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('checksum', primaryRep.checksum)\n        .property('entityTypes', JSON.stringify(resource.entityTypes));\n\n      if (resource.sourceResourceId) {\n        vertex.property('sourceResourceId', resource.sourceResourceId);\n      }\n      const storageUri = getStorageUri(resource);\n      if (storageUri) {\n        vertex.property('storageUri', storageUri);\n      }\n\n      await vertex.next();\n\n      this.logger?.info('Created resource vertex in Neptune', { id });\n      return resource;\n    } catch (error) {\n      this.logger?.error('Failed to create resource in Neptune', { error });\n      throw error;\n    }\n  }\n  \n  async getResource(id: ResourceId): 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      this.logger?.error('Failed to get resource from Neptune', { error });\n      throw error;\n    }\n  }\n  \n  async updateResource(id: ResourceId, input: UpdateResourceInput): Promise<ResourceDescriptor> {\n    assertMutableResourceUpdate(input);\n\n    try {\n      let traversal = this.g.V()\n        .hasLabel('Resource')\n        .has('id', id);\n      if (input.archived !== undefined) {\n        traversal = traversal.property('archived', input.archived);\n      }\n      if (input.entityTypes !== undefined) {\n        // Mirrors createResource's storage idiom: entityTypes ride as JSON.\n        traversal = traversal.property('entityTypes', JSON.stringify(input.entityTypes));\n      }\n      const result = await traversal\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      this.logger?.error('Failed to update resource in Neptune', { error });\n      throw error;\n    }\n  }\n  \n  async deleteResource(id: ResourceId): 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      this.logger?.info('Deleted resource from Neptune', { id });\n    } catch (error) {\n      this.logger?.error('Failed to delete resource from Neptune', { error });\n      throw error;\n    }\n  }\n  \n  /**\n   * Filtering, ranking and pagination happen in JS rather than in Gremlin.\n   *\n   * The ranking ladder (exact name over prefix over substring over path- or\n   * tag-assisted) has no natural Gremlin expression, and a rank applied after\n   * `range()` would order one page instead of the match set. JanusGraph\n   * post-filters for the same reason. Both share `queryResources` with the\n   * memory backend so search cannot mean three different things across three\n   * gateways.\n   *\n   * The cost is explicit and accepted: this materializes every `Resource`\n   * vertex per call, so it is O(N) in the size of the KB rather than in the\n   * size of the result. Neo4j is the production path and pushes the whole\n   * query — filter, rank, page — into Cypher; Neptune and JanusGraph are not\n   * deployment targets today. If either becomes one at scale, the fix is a\n   * Gremlin rank expression (`choose` over `toLower`, engine-version\n   * permitting), not a return to per-gateway search semantics.\n   */\n  async listResources(filter: ResourceFilter): Promise<{ resources: ResourceDescriptor[]; total: number }> {\n    try {\n      const results = await this.g.V().hasLabel('Resource').elementMap().toList();\n      return queryResources(results.map(vertexToResource), filter);\n    } catch (error) {\n      this.logger?.error('Failed to list resources from Neptune', { error });\n      throw error;\n    }\n  }\n\n  \n  async createAnnotation(input: CreateAnnotationInternal): Promise<Annotation> {\n    // The caller's id is the system of record's — never mint a fresh one\n    // (the event-log id is what deletes and lookups arrive under).\n    const annotation = buildAnnotation(input);\n    const props = encodeAnnotation(annotation);\n    const targetSource = props.resourceId!;\n    const bodySource = props.source;\n    const entityTypes = getEntityTypes(input);\n\n    try {\n      // Create Annotation vertex — every property comes from the codec, so\n      // a source-only target contributes no `selector` property at all.\n      let vertex = this.g.addV('Annotation');\n      for (const [key, value] of Object.entries(props)) {\n        vertex = vertex.property(key, value);\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      this.logger?.info('Created annotation vertex in Neptune', { id: annotation.id });\n      return annotation;\n    } catch (error) {\n      this.logger?.error('Failed to create annotation in Neptune', { error });\n      throw error;\n    }\n  }\n  \n  async getAnnotation(id: AnnotationId): 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      this.logger?.error('Failed to get annotation from Neptune', { error });\n      throw error;\n    }\n  }\n  \n  async updateAnnotation(id: AnnotationId, 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          for (const [key, value] of Object.entries(encodeSelector(updates.target.selector))) {\n            traversal = traversal.property(key, value);\n          }\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      this.logger?.error('Failed to update annotation in Neptune', { error });\n      throw error;\n    }\n  }\n  \n  async deleteAnnotation(id: AnnotationId): Promise<void> {\n    try {\n      await this.g.V()\n        .hasLabel('Annotation')\n        .has('id', id)\n        .drop()\n        .iterate();\n\n      this.logger?.info('Deleted annotation from Neptune', { id });\n    } catch (error) {\n      this.logger?.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        traversal = traversal.has('type', storedAnnotationType(motivationForCategory(filter.type)));\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      this.logger?.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      this.logger?.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      this.logger?.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      this.logger?.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      this.logger?.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      this.logger?.error('Failed to get resource annotations from Neptune', { error });\n      throw error;\n    }\n  }\n  \n  async getResourceReferencedBy(resourceId: ResourceId, _motivation?: string): Promise<Annotation[]> {\n    try {\n      const results = await this.g.V()\n        .hasLabel('Annotation')\n        .has('resolvedResourceId', resourceId)\n        .elementMap()\n        .toList();\n\n      return await this.fetchAnnotationsWithEntityTypes(results);\n    } catch (error) {\n      this.logger?.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      this.logger?.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      this.logger?.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      this.logger?.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      this.logger?.error('Failed to get stats from Neptune', { error });\n      throw error;\n    }\n  }\n  \n  async batchCreateResources(resources: ResourceDescriptor[]): Promise<ResourceDescriptor[]> {\n    const results: ResourceDescriptor[] = [];\n    for (const resource of resources) {\n      results.push(await this.createResource(resource));\n    }\n    return results;\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      this.logger?.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      this.logger?.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      this.logger?.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      this.logger?.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      this.logger?.debug('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        this.logger?.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      this.logger?.info('Cleared all data from Neptune');\n      // Reset tag collections\n      this.entityTypesCollection = null;\n    } catch (error) {\n      this.logger?.error('Failed to clear Neptune database', { error });\n      throw error;\n    }\n  }\n}","/**\n * The annotation codec — the one module that decides how a W3C annotation\n * becomes stored properties and back.\n *\n * Every store keeps its own dialect (Cypher parameters, Gremlin\n * `.property()` chains, a Map) and its own way of flattening what the driver\n * hands back into a property bag. What none of them owns any more is the\n * SHAPE: the W3C envelope, which fields are required, how a selector is\n * serialized, how the body array is reconstructed from entity tags and a\n * linking source. Those lived in three near-verbatim copies that disagreed\n * in four places, and each disagreement was a bug — a resource-level\n * annotation came back carrying `selector: {}`, which is not a legal\n * selector, and a motivation-less row was silently relabelled `'linking'`.\n *\n * The codec manufactures nothing. Absence is stored as absence and read back\n * as absence, in both directions.\n */\n\nimport { annotationId as makeAnnotationId } from '@semiont/core';\nimport { getBodySource, getExactText, getTargetSelector, getTargetSource } from '@semiont/core';\nimport { getEntityTypes } from '@semiont/ontology';\nimport type { Annotation, AnnotationCategory, CreateAnnotationInternal } from '@semiont/core';\n\n/**\n * A store's property bag, flattened. Producing this is the store's job (D3):\n * neo4j unwraps `node.properties` and its native temporals, the Gremlin\n * stores unwrap `[{value}]` lists. What the values MEAN is the codec's.\n */\nexport type AnnotationProperties = Record<string, string | undefined>;\n\ntype AnnotationTarget = Exclude<Annotation['target'], string>;\ntype AnnotationSelector = NonNullable<AnnotationTarget['selector']>;\ntype AnnotationBody = NonNullable<Annotation['body']>;\n\n/**\n * The stored `type` property, which the category filters match on. It\n * restates the motivation, so it is derived from it here and nowhere else —\n * the three filters that used to hand-write the same mapping had drifted\n * into asking for a value no store ever wrote.\n */\nexport function storedAnnotationType(motivation: Annotation['motivation']): string {\n  return motivation === 'highlighting' ? 'TextualBody' : 'SpecificResource';\n}\n\n/** The category a caller filters by, in the vocabulary the annotation stores. */\nexport function motivationForCategory(category: AnnotationCategory): Annotation['motivation'] {\n  return category === 'highlight' ? 'highlighting' : 'linking';\n}\n\n/**\n * Mint the annotation a create request describes.\n *\n * `created` comes from the input, which carries the AUTHORED moment from the\n * event. It used to be a second parameter, and every store passed\n * `new Date().toISOString()` into it — so the graph stamped its own write time\n * and a rebuild collapsed every annotation to the rebuild moment.\n */\nexport function buildAnnotation(input: CreateAnnotationInternal): Annotation {\n  const annotation: Annotation = {\n    '@context': 'http://www.w3.org/ns/anno.jsonld',\n    type: 'Annotation',\n    id: makeAnnotationId(input.id),\n    motivation: input.motivation,\n    target: input.target,\n    creator: input.creator,\n    created: input.created,\n  };\n  if (input.body && (!Array.isArray(input.body) || input.body.length > 0)) {\n    annotation.body = input.body;\n  }\n  return annotation;\n}\n\n/**\n * The annotation's stored properties. Entity tags are not among them — those\n * are edges, and the store writes them from `getEntityTypes(annotation)`.\n */\nexport function encodeAnnotation(annotation: Annotation): Record<string, string> {\n  const selector = getTargetSelector(annotation.target);\n  const bodySource = getBodySource(annotation.body);\n\n  const resourceId = getTargetSource(annotation.target);\n  if (!resourceId) throw new Error(`Annotation ${annotation.id} has no target source`);\n\n  const props: Record<string, string> = {\n    id: annotation.id,\n    resourceId,\n    type: storedAnnotationType(annotation.motivation),\n    motivation: annotation.motivation,\n    creator: JSON.stringify(annotation.creator),\n    created: annotation.created,\n  };\n\n  if (selector) Object.assign(props, encodeSelector(selector));\n  if (bodySource) props.source = bodySource;\n  if (annotation.modified) props.modified = annotation.modified;\n  if (annotation.generator) props.generator = JSON.stringify(annotation.generator);\n\n  return props;\n}\n\n/**\n * The properties a selector contributes: its serialization, plus the quoted\n * text pulled out beside it. Targeted selector updates go through here too,\n * so no store decides on its own what a selector is called on disk.\n */\nexport function encodeSelector(selector: AnnotationSelector): Record<string, string> {\n  const props: Record<string, string> = { selector: JSON.stringify(selector) };\n  const exact = getExactText(selector);\n  if (exact) props.exact = exact;\n  return props;\n}\n\n/**\n * Rebuild the annotation from stored properties and the entity-tag edges the\n * store resolved separately.\n *\n * A field the properties do not carry is omitted, never invented: a\n * source-only target (legal since RESOURCE-LEVEL-ANCHOR) comes back with no\n * `selector`, and a row missing a required field fails loudly by name rather\n * than acquiring a default.\n */\nexport function decodeAnnotation(props: AnnotationProperties, entityTypes: string[] = []): Annotation {\n  const id = props.id;\n  if (!id) throw new Error('Annotation missing required field: id');\n\n  const required = (key: string): string => {\n    const value = props[key];\n    if (!value) throw new Error(`Annotation ${id} missing required field: ${key}`);\n    return value;\n  };\n\n  const resourceId = required('resourceId');\n  const creator = JSON.parse(required('creator'));\n  // The stored value is one of the wire vocabulary's, which the event that\n  // produced it was validated against; the projection does not re-police it.\n  const motivation = required('motivation') as Annotation['motivation'];\n  const created = required('created');\n\n  const body: AnnotationBody = [];\n  for (const entityType of entityTypes) {\n    if (entityType) body.push({ type: 'TextualBody', value: entityType, purpose: 'tagging' });\n  }\n  if (props.source) {\n    body.push({ type: 'SpecificResource', source: props.source, purpose: 'linking' });\n  }\n\n  const selector = decodeSelector(props.selector);\n  const target: AnnotationTarget = selector ? { source: resourceId, selector } : { source: resourceId };\n\n  const annotation: Annotation = {\n    '@context': 'http://www.w3.org/ns/anno.jsonld',\n    type: 'Annotation',\n    id: makeAnnotationId(id),\n    motivation,\n    target,\n    creator,\n    created,\n  };\n\n  if (body.length > 0) annotation.body = body;\n  if (props.modified) annotation.modified = props.modified;\n  if (props.generator) {\n    try {\n      annotation.generator = JSON.parse(props.generator);\n    } catch {\n      // A corrupt generator is not worth failing the whole read over — the\n      // annotation itself is intact, and provenance is advisory.\n    }\n  }\n\n  return annotation;\n}\n\n/**\n * Rows written before RESOURCE-LEVEL-ANCHOR reached the stores hold `'{}'`\n * where a resource-level annotation has no selector at all. `{}` satisfies no\n * branch of the selector union, so it fails validation on the first round\n * trip through a validated channel — reading it back as absent is what makes\n * those rows harmless without a migration.\n */\nfunction decodeSelector(raw: string | undefined): AnnotationSelector | undefined {\n  if (!raw) return undefined;\n  const parsed = JSON.parse(raw);\n  if (!parsed || Object.keys(parsed).length === 0) return undefined;\n  return parsed;\n}\n\n/**\n * What the graph is SUPPOSED to hold for this annotation — the codec's own\n * statement of it, obtained by round-tripping through both halves.\n *\n * The graph is a purpose-built projection, not a copy of the views: it stores\n * what graph queries need and nothing else. `wasAttributedTo`, for instance,\n * rides on almost every annotation in the log and the encoder deliberately\n * writes none of it. So \"is the graph correct?\" cannot be answered by comparing\n * it to a view — only by comparing it to what this module says it should be.\n *\n * Callers get a value scoped to exactly the fields the encoder writes, in the\n * decoded shape, free of any store's physical dialect. Widen or narrow the\n * encoder and this follows automatically; there is no second list to maintain.\n */\nexport function intendedGraphAnnotation(annotation: Annotation): Annotation {\n  return decodeAnnotation(encodeAnnotation(annotation), getEntityTypes(annotation));\n}\n","// Neo4j implementation of GraphDatabase interface\n// Uses Cypher query language\n\nimport type { Driver, Session } from 'neo4j-driver';\nimport { GraphDatabase } from '../interface';\nimport { assertMutableResourceUpdate } from '../interface';\nimport { searchTerms } from '../resource-query';\nimport type { Logger } from '@semiont/core';\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 { v4 as uuidv4 } from 'uuid';\nimport { getPrimaryRepresentation, getStorageUri } from '@semiont/core';\nimport { getEntityTypes } from '@semiont/ontology';\nimport {\n  buildAnnotation,\n  decodeAnnotation,\n  encodeAnnotation,\n  motivationForCategory,\n  storedAnnotationType,\n  type AnnotationProperties,\n} from '../annotation-codec';\n\nimport type { ResourceDescriptor } from '@semiont/core';\nimport type { Annotation } from '@semiont/core';\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 neo4j!: typeof import('neo4j-driver');\n  private connected: boolean = false;\n  private logger?: Logger;\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    logger?: Logger;\n  } = {}) {\n    this.config = config;\n    this.logger = config.logger;\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      this.logger?.info('Connecting to Neo4j', { uri });\n\n      this.neo4j = await import('neo4j-driver');\n      this.driver = this.neo4j.driver(\n        uri,\n        this.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      this.logger?.info('Successfully connected to Neo4j');\n      this.connected = true;\n    } catch (error) {\n      this.logger?.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            this.logger?.warn('Schema creation warning', { message: 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            this.logger?.warn('Index creation warning', { message: 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      // Use MERGE instead of CREATE for idempotence and to enrich stub nodes\n      // Stub nodes may be created by REFERENCES edge creation before resource.created event\n      const result = await session.run(\n        `MERGE (d:Resource {id: $id})\n         SET d.name = $name,\n             d.entityTypes = $entityTypes,\n             d.format = $format,\n             d.archived = $archived,\n             d.created = $created,\n             d.creator = $creator,\n             d.contentChecksum = $contentChecksum,\n             d.sourceAnnotationId = $sourceAnnotationId,\n             d.sourceResourceId = $sourceResourceId,\n             d.storageUri = $storageUri,\n             d.stub = false\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          contentChecksum: primaryRep.checksum,\n          sourceAnnotationId: resource.sourceAnnotationId ?? null,\n          sourceResourceId: resource.sourceResourceId ?? null,\n          storageUri: getStorageUri(resource) ?? null,\n        }\n      );\n\n      this.logger?.info('Resource created/enriched', { id });\n      return this.parseResourceNode(result.records[0]!.get('d'));\n    } finally {\n      await session.close();\n    }\n  }\n\n  async getResource(id: ResourceId): 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: ResourceId, input: UpdateResourceInput): Promise<ResourceDescriptor> {\n    assertMutableResourceUpdate(input);\n\n    const sets: string[] = [];\n    const params: Record<string, unknown> = { id };\n    if (input.archived !== undefined) {\n      sets.push('d.archived = $archived');\n      params.archived = input.archived;\n    }\n    if (input.entityTypes !== undefined) {\n      sets.push('d.entityTypes = $entityTypes');\n      params.entityTypes = input.entityTypes;\n    }\n\n    const session = this.getSession();\n    try {\n      const result = await session.run(\n        `MATCH (d:Resource {id: $id})\n         SET ${sets.join(', ')}\n         RETURN d`,\n        params\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: ResourceId): 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      // Stub nodes are id-only placeholders that `MERGE` creates when a\n      // REFERENCES edge points at a resource whose `resource.created` event\n      // hasn't landed yet. They carry no name, so they are not listable — and\n      // `parseResourceNode` throws on the missing field rather than inventing one.\n      const conditions: string[] = ['coalesce(d.stub, false) = false'];\n\n      if (filter.archived !== undefined) {\n        conditions.push('d.archived = $archived');\n        params.archived = filter.archived;\n      }\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      // Every term must appear, each satisfiable by the name or the path. A\n      // whitespace-only query yields no terms and so is not a search at all.\n      const terms = filter.search ? searchTerms(filter.search) : [];\n      if (terms.length > 0) {\n        conditions.push(\n          `ALL(t IN $terms WHERE toLower(d.name) CONTAINS t\n                             OR toLower(coalesce(d.storageUri, \"\")) CONTAINS t\n                             OR ANY(e IN coalesce(d.entityTypes, []) WHERE toLower(e) CONTAINS t))`\n        );\n        params.terms = terms;\n        params.search = filter.search!.trim().toLowerCase();\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 = this.neo4j.int(filter.offset || 0);\n      params.limit = this.neo4j.int(filter.limit || 20);\n\n      // Rank only means something against a query; an unsearched listing orders\n      // on recency alone. Ranking must happen here rather than over the returned\n      // page, or it would sort one page instead of the match set.\n      const rankClause = terms.length > 0\n        ? `WITH d, CASE\n             WHEN toLower(d.name) = $search THEN 0\n             WHEN toLower(d.name) STARTS WITH $search THEN 1\n             WHEN ALL(t IN $terms WHERE toLower(d.name) CONTAINS t) THEN 2\n             ELSE 3\n           END AS rank\n         `\n        : '';\n      const orderClause = terms.length > 0\n        ? 'ORDER BY rank, d.created DESC, d.id'\n        : 'ORDER BY d.created DESC, d.id';\n\n      const result = await session.run(\n        `MATCH (d:Resource) ${whereClause}\n         ${rankClause}RETURN d\n         ${orderClause}\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\n  async createAnnotation(input: CreateAnnotationInternal): Promise<Annotation> {\n    const session = this.getSession();\n    try {\n      const annotation = buildAnnotation(input);\n      const props = encodeAnnotation(annotation);\n      const targetSource = props.resourceId!;\n      const bodySource = props.source;\n\n      // Entity tags are edges, not properties, so they travel beside the bag.\n      const entityTypes = getEntityTypes(input);\n\n      // Convert motivation to label (e.g., \"linking\" -> \"Linking\")\n      const motivationLabel = motivationToLabel(annotation.motivation);\n\n      // The codec's property bag is applied verbatim; `created` is then\n      // re-set as a native temporal, which is the one property this store\n      // stores in a type of its own.\n      const cypher = bodySource\n        ? `MATCH (from:Resource {id: $targetSource})\n           MATCH (to:Resource {id: $bodySource})\n           CREATE (a:Annotation:${motivationLabel})\n           SET a = $props\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        : `MATCH (d:Resource {id: $targetSource})\n           CREATE (a:Annotation:${motivationLabel})\n           SET a = $props\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      const result = await session.run(cypher, {\n        props,\n        targetSource,\n        bodySource: bodySource ?? null,\n        entityTypes,\n      });\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 parseAnnotationNode(result.records[0]!.get('a'), entityTypes);\n    } finally {\n      await session.close();\n    }\n  }\n\n  async getAnnotation(id: AnnotationId): Promise<Annotation | null> {\n    this.logger?.debug('Getting annotation', { 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        this.logger?.debug('Annotation not found', { id });\n        return null;\n      }\n      this.logger?.debug('Annotation found', { id });\n      return 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: AnnotationId, 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 === 'body') {\n            params[key] = JSON.stringify(value);\n          } else if (key === 'created') {\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 ${setClauses.join(', ')}\n         WITH a\n         OPTIONAL MATCH (a)-[:TAGGED_AS]->(et:EntityType)\n         RETURN a, collect(et.name) as entityTypes`,\n        params\n      );\n\n      if (result.records.length === 0) {\n        throw new Error('Annotation not found');\n      }\n\n      // If motivation was updated, update the label\n      if (updates.motivation) {\n        const newLabel = motivationToLabel(updates.motivation);\n        this.logger?.debug('Updating motivation label', { newLabel });\n\n        // Remove all possible motivation labels and add the new one\n        const allMotivations = ['Assessing', 'Bookmarking', 'Classifying', 'Commenting',\n                                'Describing', 'Editing', 'Highlighting', 'Identifying',\n                                'Linking', 'Moderating', 'Questioning', 'Replying', 'Tagging'];\n        const removeLabels = allMotivations.filter(m => m !== newLabel).map(m => `a:${m}`).join(', ');\n\n        await session.run(\n          `MATCH (a:Annotation {id: $id})\n           REMOVE ${removeLabels}\n           SET a:${newLabel}`,\n          { id }\n        );\n        this.logger?.debug('Motivation label updated', { newLabel });\n      }\n\n      // If body was updated and contains a SpecificResource, create REFERENCES relationship\n      if (updates.body) {\n        this.logger?.debug('Body update for annotation', { id, body: updates.body });\n        const bodyArray = Array.isArray(updates.body) ? updates.body : [updates.body];\n\n        const specificResource = bodyArray.find((item: any) => item.type === 'SpecificResource' && item.purpose === 'linking');\n\n        if (specificResource && 'source' in specificResource && specificResource.source) {\n          this.logger?.debug('Creating REFERENCES edge', { annotationId: id, targetResourceId: specificResource.source });\n          // Create REFERENCES relationship to the target resource\n          // Use MERGE for target to create stub node if it doesn't exist yet (eventual consistency)\n          // Stub will be enriched when resource.created event arrives\n          const refResult = await session.run(\n            `MATCH (a:Annotation {id: $annotationId})\n             MERGE (target:Resource {id: $targetResourceId})\n             ON CREATE SET target.stub = true\n             MERGE (a)-[:REFERENCES]->(target)\n             RETURN a, target, target.stub AS wasStub`,\n            {\n              annotationId: id,\n              targetResourceId: specificResource.source\n            }\n          );\n\n          if (refResult.records.length > 0) {\n            const wasStub = refResult.records[0]!.get('wasStub');\n            if (wasStub) {\n              this.logger?.debug('REFERENCES edge created with stub node', { targetResourceId: specificResource.source });\n            } else {\n              this.logger?.debug('REFERENCES edge created to existing resource', { targetResourceId: specificResource.source });\n            }\n          } else {\n            this.logger?.warn('REFERENCES edge creation returned no records');\n          }\n        } else {\n          this.logger?.debug('No SpecificResource in body - stub reference not yet resolved');\n        }\n      } else {\n        this.logger?.debug('No body update for annotation', { id });\n      }\n\n      return 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: AnnotationId): 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        conditions.push('a.type = $type');\n        params.type = storedAnnotationType(motivationForCategory(filter.type));\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        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        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 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        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        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: $resourceId})\n         OPTIONAL MATCH (a)-[:TAGGED_AS]->(et:EntityType)\n         RETURN a, collect(et.name) as entityTypes\n         ORDER BY a.created DESC`,\n        { resourceId }\n      );\n\n      return result.records.map(record =>\n        parseAnnotationNode(record.get('a'), record.get('entityTypes'))\n      );\n    } finally {\n      await session.close();\n    }\n  }\n\n  async getResourceReferencedBy(resourceId: ResourceId, motivation?: string): Promise<Annotation[]> {\n    const session = this.getSession();\n    try {\n      this.logger?.debug('Searching for annotations referencing resource', { resourceId, motivation });\n\n      // Build query with optional motivation label filter\n      // If motivation is specified, use the label for efficient filtering\n      const motivationLabel = motivation ? `:${motivationToLabel(motivation)}` : '';\n      const cypher = `MATCH (a:Annotation${motivationLabel})-[:REFERENCES]->(d:Resource {id: $resourceId})\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, { resourceId });\n\n      this.logger?.debug('Found annotations', { count: result.records.length });\n\n      return result.records.map(record =>\n        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(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(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(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 batchCreateResources(resources: ResourceDescriptor[]): Promise<ResourceDescriptor[]> {\n    if (resources.length === 0) return [];\n    const session = this.getSession();\n    try {\n      const params = resources.map(resource => {\n        const primaryRep = getPrimaryRepresentation(resource);\n        if (!primaryRep) throw new Error('Resource must have at least one representation');\n        return {\n          id: resource['@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          contentChecksum: primaryRep.checksum,\n          sourceAnnotationId: resource.sourceAnnotationId ?? null,\n          sourceResourceId: resource.sourceResourceId ?? null,\n          storageUri: getStorageUri(resource) ?? null,\n        };\n      });\n\n      const result = await session.run(\n        `UNWIND $resources AS r\n         MERGE (d:Resource {id: r.id})\n         SET d.name = r.name,\n             d.entityTypes = r.entityTypes,\n             d.format = r.format,\n             d.archived = r.archived,\n             d.created = r.created,\n             d.creator = r.creator,\n             d.contentChecksum = r.contentChecksum,\n             d.sourceAnnotationId = r.sourceAnnotationId,\n             d.sourceResourceId = r.sourceResourceId,\n             d.storageUri = r.storageUri,\n             d.stub = false\n         RETURN d`,\n        { resources: params }\n      );\n\n      this.logger?.info('Batch created/enriched resources', { count: resources.length });\n      return result.records.map(record => this.parseResourceNode(record.get('d')));\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.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        storageUri: props.storageUri ?? undefined,\n      }],\n      archived: props.archived,\n      dateCreated: props.created.toString(),\n      wasAttributedTo: typeof props.creator === 'string' ? JSON.parse(props.creator) : props.creator,\n    };\n\n    if (props.sourceResourceId) resource.sourceResourceId = props.sourceResourceId;\n\n    return resource;\n  }\n\n}\n\n/**\n * Project a neo4j annotation node to the wire `Annotation`.\n *\n * Module-level (not a method) so the projection is unit-testable without a\n * driver: `node` is untyped at this seam, which is exactly how a native\n * neo4j DateTime once reached the wire as `created` unseen by tsc.\n */\nexport function parseAnnotationNode(node: any, entityTypes: string[] = []): Annotation {\n  return decodeAnnotation(normalizeProperties(node.properties), entityTypes);\n}\n\n/**\n * Flatten a node's properties to the strings the codec reads.\n *\n * `created` is stored as the codec's own string, so it round-trips verbatim.\n * Rows written before that change hold a native temporal instead, and the\n * driver hands those back as an object whose `toString()` REFORMATS the value\n * (a zero fraction elided, any other padded to nanoseconds) — so a legacy row\n * reads back with a different string than the log carried, until a rebuild\n * replaces it. The coercion\n * that has to happen before the codec sees a value it is entitled to treat\n * as a string. This seam is untyped, so only a test can see it slip.\n */\nfunction normalizeProperties(props: any): AnnotationProperties {\n  const normalized: AnnotationProperties = {};\n  for (const [key, value] of Object.entries(props ?? {})) {\n    if (value === null || value === undefined) continue;\n    normalized[key] = typeof value === 'string' ? value : String(value);\n  }\n  return normalized;\n}\n","// JanusGraph implementation with real Gremlin connection\n// This replaces the mock in-memory implementation\n\nimport { GraphDatabase } from '../interface';\nimport { assertMutableResourceUpdate } from '../interface';\nimport { queryResources } from '../resource-query';\nimport type { Logger } from '@semiont/core';\nimport { resourceId as makeResourceId } from '@semiont/core';\nimport { getBodySource, getPrimaryRepresentation, getResourceId, getStorageUri } from '@semiont/core';\nimport { getEntityTypes } from '@semiont/ontology';\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 { v4 as uuidv4 } from 'uuid';\nimport {\n  buildAnnotation,\n  decodeAnnotation,\n  encodeAnnotation,\n  encodeSelector,\n  motivationForCategory,\n  storedAnnotationType,\n  type AnnotationProperties,\n} from '../annotation-codec';\n\nimport type { ResourceDescriptor } from '@semiont/core';\nimport type { Annotation } from '@semiont/core';\n\n/** Helper to get property value from Gremlin vertex properties */\nfunction 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/**\n * Convert a JanusGraph vertex to an Annotation.\n *\n * Module-level so the cross-store conformance suite can run this store's\n * decode path with no live JanusGraph: everything past the flattening is the\n * shared codec's. This is where a missing selector used to become `'{}'` and\n * a missing motivation used to become `'linking'`.\n */\nexport function vertexToAnnotation(vertex: any, entityTypes: string[] = []): Annotation {\n  const props = vertex.properties || {};\n  const normalized: AnnotationProperties = {};\n  for (const key of Object.keys(props)) {\n    const value = getPropertyValue(props, key);\n    if (value === undefined || value === null) continue;\n    normalized[key] = typeof value === 'string' ? value : String(value);\n  }\n  return decodeAnnotation(normalized, entityTypes);\n}\n\nexport class JanusGraphDatabase implements GraphDatabase {\n  private connected: boolean = false;\n  private connection: any | null = null;\n  private g: any | null = null;\n  private logger?: Logger;\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      logger?: Logger;\n    },\n  ) {\n    this.logger = graphConfig.logger;\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    this.logger?.info('Connecting to JanusGraph', { host, port });\n\n    const gremlin = await import('gremlin');\n    const DriverRemoteConnection = gremlin.driver.DriverRemoteConnection;\n    const traversal = gremlin.process.AnonymousTraversalSource.traversal;\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    this.logger?.info('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    this.logger?.debug('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 = getPropertyValue(props, 'id');\n\n    // Validate required fields\n    const creatorRaw = getPropertyValue(props, 'creator');\n    const contentChecksum = getPropertyValue(props, 'contentChecksum');\n    const mediaType = getPropertyValue(props, 'contentType');\n\n    if (!creatorRaw) throw new Error(`Resource ${id} missing required field: creator`);\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: getPropertyValue(props, 'name'),\n      entityTypes: JSON.parse(getPropertyValue(props, 'entityTypes') || '[]'),\n      representations: [{\n        mediaType,\n        checksum: contentChecksum,\n        rel: 'original',\n        storageUri: getPropertyValue(props, 'storageUri') || undefined,\n      }],\n      archived: getPropertyValue(props, 'archived') === 'true',\n      dateCreated: getPropertyValue(props, 'created'),\n      wasAttributedTo: creator,\n    };\n\n    const sourceAnnotationId = getPropertyValue(props, 'sourceAnnotationId');\n    const sourceResourceId = getPropertyValue(props, 'sourceResourceId');\n\n    if (sourceAnnotationId) resource.sourceAnnotationId = sourceAnnotationId;\n    if (sourceResourceId) resource.sourceResourceId = sourceResourceId;\n\n    return resource;\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 = 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        getPropertyValue(v.properties || {}, 'name')\n      ).filter(Boolean);\n\n      annotations.push(vertexToAnnotation(vertex, entityTypes));\n    }\n\n    return annotations;\n  }\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('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    const storageUri = getStorageUri(resource);\n    if (storageUri) {\n      vertex.property('storageUri', storageUri);\n    }\n\n    await vertex.next();\n\n    this.logger?.info('Created resource vertex in JanusGraph', { id });\n    return resource;\n  }\n  \n  async getResource(id: ResourceId): 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: ResourceId, input: UpdateResourceInput): Promise<ResourceDescriptor> {\n    assertMutableResourceUpdate(input);\n\n    let traversal = this.g!\n      .V()\n      .has('Resource', 'id', id);\n    if (input.archived !== undefined) {\n      traversal = traversal.property('archived', input.archived);\n    }\n    if (input.entityTypes !== undefined) {\n      // Mirrors createResource's storage idiom: entityTypes ride as JSON.\n      traversal = traversal.property('entityTypes', JSON.stringify(input.entityTypes));\n    }\n    await traversal.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: ResourceId): 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    this.logger?.info('Deleted resource from JanusGraph', { id });\n  }\n  \n  async listResources(filter: ResourceFilter): Promise<{ resources: ResourceDescriptor[]; total: number }> {\n    // Note: filtering is done client-side after retrieval. In production,\n    // JanusGraph supports server-side text predicates via Elasticsearch,\n    // but composing OR across multiple text properties requires the\n    // anonymous-traversal API; for a gateway that's not the production\n    // target today, JS post-filtering is simpler and adequate at our scale.\n    const docs = await this.g!.V().hasLabel('Resource').toList();\n    return queryResources(docs.map((v: any) => this.vertexToResource(v)), filter);\n  }\n\n  \n  async createAnnotation(input: CreateAnnotationInternal): Promise<Annotation> {\n    // The caller's id is the system of record's — never mint a fresh one\n    // (the event-log id is what deletes and lookups arrive under).\n    const annotation = buildAnnotation(input);\n    const props = encodeAnnotation(annotation);\n    const targetSource = props.resourceId!;\n    const bodySource = props.source;\n    const entityTypes = getEntityTypes(input);\n\n    // Create annotation vertex — every property comes from the codec, so a\n    // source-only target contributes no `selector` property at all.\n    let vertex = this.g!.addV('Annotation');\n    for (const [key, value] of Object.entries(props)) {\n      vertex = vertex.property(key, value);\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    this.logger?.info('Created annotation in JanusGraph', { id: annotation.id });\n    return annotation;\n  }\n  \n  async getAnnotation(id: AnnotationId): 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      getPropertyValue(v.properties || {}, 'name')\n    ).filter(Boolean);\n\n    return vertexToAnnotation(vertices[0] as any, entityTypes);\n  }\n  \n  async updateAnnotation(id: AnnotationId, 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        for (const [key, value] of Object.entries(encodeSelector(updates.target.selector))) {\n          await traversalQuery.property(key, value).next();\n        }\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: AnnotationId): Promise<void> {\n    await this.g!\n      .V()\n      .has('Annotation', 'id', id)\n      .drop()\n      .next();\n\n    this.logger?.info('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      traversalQuery = traversalQuery.has('type', storedAnnotationType(motivationForCategory(filter.type)));\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 annotation = await this.getAnnotation(annotationId);\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(annotationId, {\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(annotationId);\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(resourceId: ResourceId, _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', resourceId)\n      .toList();\n\n    return 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    this.logger?.debug('Found paths', { count: 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(makeResourceId(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 batchCreateResources(resources: ResourceDescriptor[]): Promise<ResourceDescriptor[]> {\n    const results: ResourceDescriptor[] = [];\n    for (const resource of resources) {\n      results.push(await this.createResource(resource));\n    }\n    return results;\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      this.logger?.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      this.logger?.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 = getPropertyValue(props, 'type');\n      const tagsJson = 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    this.logger?.info('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 { assertMutableResourceUpdate } from '../interface';\nimport { queryResources } from '../resource-query';\nimport type { Logger } from '@semiont/core';\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 { v4 as uuidv4 } from 'uuid';\nimport { getBodySource, getTargetSource, getResourceId, getPrimaryRepresentation, getResourceEntityTypes } from '@semiont/core';\nimport { getEntityTypes } from '@semiont/ontology';\nimport { buildAnnotation, decodeAnnotation, encodeAnnotation } from '../annotation-codec';\nimport type { ResourceDescriptor } from '@semiont/core';\nimport type { Annotation } from '@semiont/core';\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  private logger?: Logger;\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: { logger?: Logger } = {}) {\n    this.logger = config.logger;\n  }\n  \n  async connect(): Promise<void> {\n    // No actual connection needed for in-memory storage\n    this.logger?.info('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: ResourceId): Promise<ResourceDescriptor | null> {\n    return this.resources.get(String(id)) || null;\n  }\n\n  async updateResource(id: ResourceId, input: UpdateResourceInput): Promise<ResourceDescriptor> {\n    assertMutableResourceUpdate(input);\n\n    const doc = this.resources.get(String(id));\n    if (!doc) throw new Error('Resource not found');\n\n    if (input.archived !== undefined) doc.archived = input.archived;\n    if (input.entityTypes !== undefined) doc.entityTypes = input.entityTypes;\n    return doc;\n  }\n\n  async deleteResource(id: ResourceId): Promise<void> {\n    this.resources.delete(String(id));\n\n    // Delete annotations targeting or referencing this resource\n    const idStr = String(id);\n    for (const [selId, sel] of this.annotations) {\n      if (getTargetSource(sel.target) === idStr || getBodySource(sel.body) === idStr) {\n        this.annotations.delete(selId);\n      }\n    }\n  }\n  \n  async listResources(filter: ResourceFilter): Promise<{ resources: ResourceDescriptor[]; total: number }> {\n    return queryResources(Array.from(this.resources.values()), filter);\n  }\n\n  \n  async createAnnotation(input: CreateAnnotationInternal): Promise<Annotation> {\n    // The caller's id is the system of record's — never mint a fresh one\n    // (the event-log id is what deletes and lookups arrive under).\n    const id = input.id;\n\n    // Nothing here needs serializing — but this store is the reference the\n    // interface-contract suite runs against, and a reference that cannot\n    // exhibit what the real stores exhibit is why four codec divergences\n    // survived. So the annotation round-trips through the codec: what a Map\n    // hands back is exactly what Cypher and Gremlin hand back.\n    const annotation = decodeAnnotation(\n      encodeAnnotation(buildAnnotation(input)),\n      getEntityTypes(input)\n    );\n\n    this.annotations.set(id, annotation);\n    this.logger?.debug('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: AnnotationId): Promise<Annotation | null> {\n    return this.annotations.get(id) || null;\n  }\n  \n  async updateAnnotation(id: AnnotationId, 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: AnnotationId): 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 => getTargetSource(a.target) === resourceIdStr);\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  async getHighlights(resourceId: ResourceId): Promise<Annotation[]> {\n    const resourceIdStr = String(resourceId);\n    const highlights = Array.from(this.annotations.values())\n      .filter(sel => getTargetSource(sel.target) === resourceIdStr && sel.motivation === 'highlighting');\n    this.logger?.debug('Got highlights for resource', { resourceId, count: highlights.length });\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: String(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 => getTargetSource(sel.target) === resourceIdStr && sel.motivation === 'linking');\n    this.logger?.debug('Got references for resource', { resourceId, count: references.length });\n    return references;\n  }\n\n  async getEntityReferences(resourceId: ResourceId, entityTypes?: string[]): Promise<Annotation[]> {\n    const resourceIdStr = String(resourceId);\n    let refs = Array.from(this.annotations.values())\n      .filter(sel => getTargetSource(sel.target) === resourceIdStr && getEntityTypes(sel).length > 0);\n\n    if (entityTypes && entityTypes.length > 0) {\n      refs = refs.filter(sel => getEntityTypes(sel).some(type => entityTypes.includes(type)));\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 => getTargetSource(sel.target) === resourceIdStr);\n  }\n\n  async getResourceReferencedBy(resourceId: ResourceId, _motivation?: string): Promise<Annotation[]> {\n    return Array.from(this.annotations.values())\n      .filter(sel => getBodySource(sel.body) === String(resourceId));\n  }\n\n  async getResourceConnections(resourceId: ResourceId): Promise<GraphConnection[]> {\n    const connections: GraphConnection[] = [];\n    const refs = await this.getReferences(resourceId);\n    const resourceIdStr = String(resourceId);\n\n    for (const ref of refs) {\n      const bodySource = getBodySource(ref.body);\n      if (bodySource) {\n        const targetDoc = await this.getResource(makeResourceId(bodySource));\n        if (targetDoc) {\n          const reverseRefs = await this.getReferences(makeResourceId(bodySource));\n          const bidirectional = reverseRefs.some(r => getBodySource(r.body) === resourceIdStr);\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    const visited = new Set<string>();\n    const queue: { docId: string; path: ResourceDescriptor[]; sels: Annotation[] }[] = [];\n    const fromDoc = await this.getResource(makeResourceId(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    // Extract entity types from annotation body\n    const entityReferenceCount = annotations.filter(\n      a => a.motivation === 'linking' && getEntityTypes(a).length > 0\n    ).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 batchCreateResources(resources: ResourceDescriptor[]): Promise<ResourceDescriptor[]> {\n    const results: ResourceDescriptor[] = [];\n    for (const resource of resources) {\n      results.push(await this.createResource(resource));\n    }\n    return results;\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  \n  async resolveReferences(inputs: { annotationId: AnnotationId; 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