@semiont/graph 0.2.34-build.91 → 0.2.34-build.93

package/dist/index.js

@@ -145,6 +145,7 @@ var NeptuneGraphDatabase = class {
   neptuneEndpoint;
   neptunePort = 8182;
   region;
+  logger;
   g;
   // Gremlin graph traversal source
   connection;
@@ -164,6 +165,7 @@ var NeptuneGraphDatabase = class {
     if (config.endpoint) this.neptuneEndpoint = config.endpoint;
     this.neptunePort = config.port || 8182;
     if (config.region) this.region = config.region;
+    this.logger = config.logger;
   }
   async discoverNeptuneEndpoint() {
     if (this.neptuneEndpoint) {
@@ -199,9 +201,9 @@ var NeptuneGraphDatabase = class {
       }
       this.neptuneEndpoint = cluster.Endpoint;
       this.neptunePort = cluster.Port || 8182;
-      console.log(`Discovered Neptune endpoint: ${this.neptuneEndpoint}:${this.neptunePort}`);
+      this.logger?.info("Discovered Neptune endpoint", { endpoint: this.neptuneEndpoint, port: this.neptunePort });
     } catch (error) {
-      console.error("Failed to discover Neptune endpoint:", error);
+      this.logger?.error("Failed to discover Neptune endpoint", { error });
       throw error;
     }
   }
@@ -212,7 +214,7 @@ var NeptuneGraphDatabase = class {
       const traversal2 = gremlin.process.AnonymousTraversalSource.traversal;
       const DriverRemoteConnection2 = gremlin.driver.DriverRemoteConnection;
       const connectionUrl = `wss://${this.neptuneEndpoint}:${this.neptunePort}/gremlin`;
-      console.log(`Connecting to Neptune at ${connectionUrl}`);
+      this.logger?.info("Connecting to Neptune", { connectionUrl });
       this.connection = new DriverRemoteConnection2(connectionUrl, {
         authenticator: null,
         // Neptune uses IAM authentication via task role
@@ -221,10 +223,10 @@ var NeptuneGraphDatabase = class {
       });
       this.g = traversal2().withRemote(this.connection);
       const count = await this.g.V().limit(1).count().next();
-      console.log(`Connected to Neptune. Vertex count test: ${count.value}`);
+      this.logger?.info("Connected to Neptune", { vertexCountTest: count.value });
       this.connected = true;
     } catch (error) {
-      console.error("Failed to connect to Neptune:", error);
+      this.logger?.error("Failed to connect to Neptune", { error });
       throw error;
     }
   }
@@ -233,11 +235,11 @@ var NeptuneGraphDatabase = class {
       try {
         await this.connection.close();
       } catch (error) {
-        console.error("Error closing Neptune connection:", error);
+        this.logger?.error("Error closing Neptune connection", { error });
       }
     }
     this.connected = false;
-    console.log("Disconnected from Neptune");
+    this.logger?.info("Disconnected from Neptune");
   }
   isConnected() {
     return this.connected;
@@ -254,10 +256,10 @@ var NeptuneGraphDatabase = class {
         vertex.property("sourceResourceId", resource.sourceResourceId);
       }
       await vertex.next();
-      console.log(`Created resource vertex in Neptune: ${id}`);
+      this.logger?.info("Created resource vertex in Neptune", { id });
       return resource;
     } catch (error) {
-      console.error("Failed to create resource in Neptune:", error);
+      this.logger?.error("Failed to create resource in Neptune", { error });
       throw error;
     }
   }
@@ -269,7 +271,7 @@ var NeptuneGraphDatabase = class {
       }
       return vertexToResource(result.value);
     } catch (error) {
-      console.error("Failed to get resource from Neptune:", error);
+      this.logger?.error("Failed to get resource from Neptune", { error });
       throw error;
     }
   }
@@ -284,16 +286,16 @@ var NeptuneGraphDatabase = class {
       }
       return vertexToResource(result.value);
     } catch (error) {
-      console.error("Failed to update resource in Neptune:", error);
+      this.logger?.error("Failed to update resource in Neptune", { error });
       throw error;
     }
   }
   async deleteResource(id) {
     try {
       await this.g.V().hasLabel("Resource").has("id", id).drop().iterate();
-      console.log(`Deleted resource from Neptune: ${id}`);
+      this.logger?.info("Deleted resource from Neptune", { id });
     } catch (error) {
-      console.error("Failed to delete resource from Neptune:", error);
+      this.logger?.error("Failed to delete resource from Neptune", { error });
       throw error;
     }
   }
@@ -320,7 +322,7 @@ var NeptuneGraphDatabase = class {
       const resources = results.map(vertexToResource);
       return { resources, total };
     } catch (error) {
-      console.error("Failed to list resources from Neptune:", error);
+      this.logger?.error("Failed to list resources from Neptune", { error });
       throw error;
     }
   }
@@ -329,7 +331,7 @@ var NeptuneGraphDatabase = class {
       const results = await this.g.V().hasLabel("Resource").has("name", TextP.containing(query)).order().by("created", order.desc).limit(limit).elementMap().toList();
       return results.map(vertexToResource);
     } catch (error) {
-      console.error("Failed to search resources in Neptune:", error);
+      this.logger?.error("Failed to search resources in Neptune", { error });
       throw error;
     }
   }
@@ -366,10 +368,10 @@ var NeptuneGraphDatabase = class {
         ).next();
         await this.g.V(newVertex.value).addE("TAGGED_AS").to(this.g.V(etVertex.value)).next();
       }
-      console.log(`Created annotation vertex in Neptune: ${annotation.id}`);
+      this.logger?.info("Created annotation vertex in Neptune", { id: annotation.id });
       return annotation;
     } catch (error) {
-      console.error("Failed to create annotation in Neptune:", error);
+      this.logger?.error("Failed to create annotation in Neptune", { error });
       throw error;
     }
   }
@@ -383,7 +385,7 @@ var NeptuneGraphDatabase = class {
       const entityTypes = entityTypesResult || [];
       return vertexToAnnotation(result.value, entityTypes);
     } catch (error) {
-      console.error("Failed to get annotation from Neptune:", error);
+      this.logger?.error("Failed to get annotation from Neptune", { error });
       throw error;
     }
   }
@@ -426,16 +428,16 @@ var NeptuneGraphDatabase = class {
       const entityTypes = entityTypesResult || [];
       return vertexToAnnotation(result.value, entityTypes);
     } catch (error) {
-      console.error("Failed to update annotation in Neptune:", error);
+      this.logger?.error("Failed to update annotation in Neptune", { error });
       throw error;
     }
   }
   async deleteAnnotation(id) {
     try {
       await this.g.V().hasLabel("Annotation").has("id", id).drop().iterate();
-      console.log(`Deleted annotation from Neptune: ${id}`);
+      this.logger?.info("Deleted annotation from Neptune", { id });
     } catch (error) {
-      console.error("Failed to delete annotation from Neptune:", error);
+      this.logger?.error("Failed to delete annotation from Neptune", { error });
       throw error;
     }
   }
@@ -453,7 +455,7 @@ var NeptuneGraphDatabase = class {
       const annotations = await this.fetchAnnotationsWithEntityTypes(results);
       return { annotations, total: annotations.length };
     } catch (error) {
-      console.error("Failed to list annotations from Neptune:", error);
+      this.logger?.error("Failed to list annotations from Neptune", { error });
       throw error;
     }
   }
@@ -462,7 +464,7 @@ var NeptuneGraphDatabase = class {
       const results = await this.g.V().hasLabel("Annotation").has("resourceId", resourceId).hasNot("resolvedResourceId").elementMap().toList();
       return await this.fetchAnnotationsWithEntityTypes(results);
     } catch (error) {
-      console.error("Failed to get highlights from Neptune:", error);
+      this.logger?.error("Failed to get highlights from Neptune", { error });
       throw error;
     }
   }
@@ -481,7 +483,7 @@ var NeptuneGraphDatabase = class {
       const entityTypes = entityTypesResult || [];
       return vertexToAnnotation(result.value, entityTypes);
     } catch (error) {
-      console.error("Failed to resolve reference in Neptune:", error);
+      this.logger?.error("Failed to resolve reference in Neptune", { error });
       throw error;
     }
   }
@@ -490,7 +492,7 @@ var NeptuneGraphDatabase = class {
       const results = await this.g.V().hasLabel("Annotation").has("resourceId", resourceId).has("resolvedResourceId").elementMap().toList();
       return await this.fetchAnnotationsWithEntityTypes(results);
     } catch (error) {
-      console.error("Failed to get references from Neptune:", error);
+      this.logger?.error("Failed to get references from Neptune", { error });
       throw error;
     }
   }
@@ -509,7 +511,7 @@ var NeptuneGraphDatabase = class {
       const results = await traversal2.elementMap().toList();
       return await this.fetchAnnotationsWithEntityTypes(results);
     } catch (error) {
-      console.error("Failed to get entity references from Neptune:", error);
+      this.logger?.error("Failed to get entity references from Neptune", { error });
       throw error;
     }
   }
@@ -518,7 +520,7 @@ var NeptuneGraphDatabase = class {
       const results = await this.g.V().hasLabel("Annotation").has("resourceId", resourceId).elementMap().toList();
       return await this.fetchAnnotationsWithEntityTypes(results);
     } catch (error) {
-      console.error("Failed to get resource annotations from Neptune:", error);
+      this.logger?.error("Failed to get resource annotations from Neptune", { error });
       throw error;
     }
   }
@@ -527,7 +529,7 @@ var NeptuneGraphDatabase = class {
       const results = await this.g.V().hasLabel("Annotation").has("resolvedResourceId", resourceUri3).elementMap().toList();
       return await this.fetchAnnotationsWithEntityTypes(results);
     } catch (error) {
-      console.error("Failed to get resource referenced by from Neptune:", error);
+      this.logger?.error("Failed to get resource referenced by from Neptune", { error });
       throw error;
     }
   }
@@ -573,7 +575,7 @@ var NeptuneGraphDatabase = class {
       }
       return Array.from(connectionsMap.values());
     } catch (error) {
-      console.error("Failed to get resource connections from Neptune:", error);
+      this.logger?.error("Failed to get resource connections from Neptune", { error });
       throw error;
     }
   }
@@ -596,7 +598,7 @@ var NeptuneGraphDatabase = class {
       }
       return paths;
     } catch (error) {
-      console.error("Failed to find paths in Neptune:", error);
+      this.logger?.error("Failed to find paths in Neptune", { error });
       throw error;
     }
   }
@@ -617,7 +619,7 @@ var NeptuneGraphDatabase = class {
       }
       return stats;
     } catch (error) {
-      console.error("Failed to get entity type stats from Neptune:", error);
+      this.logger?.error("Failed to get entity type stats from Neptune", { error });
       throw error;
     }
   }
@@ -650,7 +652,7 @@ var NeptuneGraphDatabase = class {
         contentTypes
       };
     } catch (error) {
-      console.error("Failed to get stats from Neptune:", error);
+      this.logger?.error("Failed to get stats from Neptune", { error });
       throw error;
     }
   }
@@ -663,7 +665,7 @@ var NeptuneGraphDatabase = class {
       }
       return results;
     } catch (error) {
-      console.error("Failed to create annotations in Neptune:", error);
+      this.logger?.error("Failed to create annotations in Neptune", { error });
       throw error;
     }
   }
@@ -676,7 +678,7 @@ var NeptuneGraphDatabase = class {
       }
       return results;
     } catch (error) {
-      console.error("Failed to resolve references in Neptune:", error);
+      this.logger?.error("Failed to resolve references in Neptune", { error });
       throw error;
     }
   }
@@ -702,7 +704,7 @@ var NeptuneGraphDatabase = class {
         __.addV("TagCollection").property("type", "entity-types")
       ).property(cardinality.set, "tags", tag).iterate();
     } catch (error) {
-      console.error("Failed to add entity type:", error);
+      this.logger?.error("Failed to add entity type", { error });
     }
   }
   async addEntityTypes(tags) {
@@ -719,7 +721,7 @@ var NeptuneGraphDatabase = class {
         await vertex.property(cardinality.set, "tags", tag).iterate();
       }
     } catch (error) {
-      console.error("Failed to add entity types:", error);
+      this.logger?.error("Failed to add entity types", { error });
     }
   }
   async initializeTagCollections() {
@@ -731,7 +733,7 @@ var NeptuneGraphDatabase = class {
         }
       }
     } catch (error) {
-      console.log("No existing tag collections found, will initialize with defaults");
+      this.logger?.debug("No existing tag collections found, will initialize with defaults");
     }
     if (this.entityTypesCollection === null) {
       const { DEFAULT_ENTITY_TYPES } = await import("@semiont/ontology");
@@ -742,7 +744,7 @@ var NeptuneGraphDatabase = class {
           await this.g.V(vertex.value.id).property(cardinality.set, "tags", tag).iterate();
         }
       } catch (error) {
-        console.error("Failed to initialize entity types:", error);
+        this.logger?.error("Failed to initialize entity types", { error });
       }
     }
   }
@@ -752,10 +754,10 @@ var NeptuneGraphDatabase = class {
   async clearDatabase() {
     try {
       await this.g.V().drop().iterate();
-      console.log("Cleared all data from Neptune");
+      this.logger?.info("Cleared all data from Neptune");
       this.entityTypesCollection = null;
     } catch (error) {
-      console.error("Failed to clear Neptune database:", error);
+      this.logger?.error("Failed to clear Neptune database", { error });
       throw error;
     }
   }
@@ -778,11 +780,13 @@ function motivationToLabel(motivation) {
 var Neo4jGraphDatabase = class {
   driver = null;
   connected = false;
+  logger;
   config;
   // Tag Collections - cached in memory for performance
   entityTypesCollection = null;
   constructor(config = {}) {
     this.config = config;
+    this.logger = config.logger;
   }
   async connect() {
     try {
@@ -802,7 +806,7 @@ var Neo4jGraphDatabase = class {
       if (!database) {
         throw new Error("Neo4j database not configured! Pass database in config.");
       }
-      console.log(`Connecting to Neo4j at ${uri}...`);
+      this.logger?.info("Connecting to Neo4j", { uri });
       this.driver = neo4j.driver(
         uri,
         neo4j.auth.basic(username, password),
@@ -815,10 +819,10 @@ var Neo4jGraphDatabase = class {
       await session.run("RETURN 1 as test");
       await session.close();
       await this.ensureSchemaExists();
-      console.log("Successfully connected to Neo4j");
+      this.logger?.info("Successfully connected to Neo4j");
       this.connected = true;
     } catch (error) {
-      console.error("Failed to connect to Neo4j:", error);
+      this.logger?.error("Failed to connect to Neo4j", { error });
       throw new Error(`Neo4j connection failed: ${error}`);
     }
   }
@@ -856,7 +860,7 @@ var Neo4jGraphDatabase = class {
           await session.run(constraint);
         } catch (error) {
           if (!error.message?.includes("already exists")) {
-            console.warn(`Schema creation warning: ${error.message}`);
+            this.logger?.warn("Schema creation warning", { message: error.message });
           }
         }
       }
@@ -871,7 +875,7 @@ var Neo4jGraphDatabase = class {
           await session.run(index);
         } catch (error) {
           if (!error.message?.includes("already exists")) {
-            console.warn(`Index creation warning: ${error.message}`);
+            this.logger?.warn("Index creation warning", { message: error.message });
           }
         }
       }
@@ -915,7 +919,7 @@ var Neo4jGraphDatabase = class {
           sourceResourceId: resource.sourceResourceId ?? null
         }
       );
-      console.log(`[Neo4j] Resource created/enriched: ${id}`);
+      this.logger?.info("Resource created/enriched", { id });
       return this.parseResourceNode(result.records[0].get("d"));
     } finally {
       await session.close();
@@ -1107,7 +1111,7 @@ var Neo4jGraphDatabase = class {
     }
   }
   async getAnnotation(id) {
-    console.log(`[Neo4j] getAnnotation called for: ${id}`);
+    this.logger?.debug("Getting annotation", { id });
     const session = this.getSession();
     try {
       const result = await session.run(
@@ -1117,10 +1121,10 @@ var Neo4jGraphDatabase = class {
         { id }
       );
       if (result.records.length === 0) {
-        console.log(`[Neo4j] getAnnotation: Annotation ${id} NOT FOUND`);
+        this.logger?.debug("Annotation not found", { id });
         return null;
       }
-      console.log(`[Neo4j] getAnnotation: Annotation ${id} FOUND`);
+      this.logger?.debug("Annotation found", { id });
       return this.parseAnnotationNode(
         result.records[0].get("a"),
         result.records[0].get("entityTypes")
@@ -1159,7 +1163,7 @@ var Neo4jGraphDatabase = class {
       }
       if (updates.motivation) {
         const newLabel = motivationToLabel(updates.motivation);
-        console.log(`[Neo4j] Updating motivation label to: ${newLabel}`);
+        this.logger?.debug("Updating motivation label", { newLabel });
         const allMotivations = [
           "Assessing",
           "Bookmarking",
@@ -1182,20 +1186,14 @@ var Neo4jGraphDatabase = class {
            SET a:${newLabel}`,
           { id }
         );
-        console.log(`[Neo4j] \u2705 Motivation label updated to: ${newLabel}`);
+        this.logger?.debug("Motivation label updated", { newLabel });
       }
       if (updates.body) {
-        console.log(`[Neo4j] ====== BODY UPDATE for Annotation ${id} ======`);
-        console.log(`[Neo4j] updates.body:`, JSON.stringify(updates.body));
+        this.logger?.debug("Body update for annotation", { id, body: updates.body });
         const bodyArray = Array.isArray(updates.body) ? updates.body : [updates.body];
-        console.log(`[Neo4j] bodyArray length: ${bodyArray.length}`);
-        bodyArray.forEach((item, idx) => {
-          console.log(`[Neo4j]   Body item ${idx}:`, JSON.stringify(item));
-        });
         const specificResource = bodyArray.find((item) => item.type === "SpecificResource" && item.purpose === "linking");
-        console.log(`[Neo4j] Found SpecificResource:`, specificResource ? JSON.stringify(specificResource) : "null");
         if (specificResource && "source" in specificResource && specificResource.source) {
-          console.log(`[Neo4j] \u2705 Creating REFERENCES edge: ${id} -> ${specificResource.source}`);
+          this.logger?.debug("Creating REFERENCES edge", { annotationId: id, targetResourceId: specificResource.source });
           const refResult = await session.run(
             `MATCH (a:Annotation {id: $annotationId})
              MERGE (target:Resource {id: $targetResourceId})
@@ -1210,18 +1208,18 @@ var Neo4jGraphDatabase = class {
           if (refResult.records.length > 0) {
             const wasStub = refResult.records[0].get("wasStub");
             if (wasStub) {
-              console.log(`[Neo4j] \u2705 REFERENCES edge created with stub node for ${specificResource.source} (will be enriched by resource.created event)`);
+              this.logger?.debug("REFERENCES edge created with stub node", { targetResourceId: specificResource.source });
             } else {
-              console.log(`[Neo4j] \u2705 REFERENCES edge created to existing resource ${specificResource.source}`);
+              this.logger?.debug("REFERENCES edge created to existing resource", { targetResourceId: specificResource.source });
             }
           } else {
-            console.log(`[Neo4j] \u26A0\uFE0F  REFERENCES edge creation returned no records`);
+            this.logger?.warn("REFERENCES edge creation returned no records");
           }
         } else {
-          console.log(`[Neo4j] No SpecificResource in body - this is a stub reference (not yet resolved)`);
+          this.logger?.debug("No SpecificResource in body - stub reference not yet resolved");
         }
       } else {
-        console.log(`[Neo4j] No body update for annotation ${id}`);
+        this.logger?.debug("No body update for annotation", { id });
       }
       return this.parseAnnotationNode(
         result.records[0].get("a"),
@@ -1381,15 +1379,14 @@ var Neo4jGraphDatabase = class {
   async getResourceReferencedBy(resourceUri3, motivation) {
     const session = this.getSession();
     try {
-      const filterDesc = motivation ? ` with motivation=${motivation}` : "";
-      console.log(`[Neo4j] getResourceReferencedBy: Searching for annotations${filterDesc} referencing ${resourceUri3}`);
+      this.logger?.debug("Searching for annotations referencing resource", { resourceUri: resourceUri3, motivation });
       const motivationLabel = motivation ? `:${motivationToLabel(motivation)}` : "";
       const cypher = `MATCH (a:Annotation${motivationLabel})-[:REFERENCES]->(d:Resource {id: $resourceUri})
          OPTIONAL MATCH (a)-[:TAGGED_AS]->(et:EntityType)
          RETURN a, collect(et.name) as entityTypes
          ORDER BY a.created DESC`;
       const result = await session.run(cypher, { resourceUri: resourceUri3 });
-      console.log(`[Neo4j] getResourceReferencedBy: Found ${result.records.length} annotations`);
+      this.logger?.debug("Found annotations", { count: result.records.length });
       return result.records.map(
         (record) => this.parseAnnotationNode(record.get("a"), record.get("entityTypes"))
       );
@@ -1743,10 +1740,12 @@ var JanusGraphDatabase = class {
   constructor(graphConfig, envConfig) {
     this.graphConfig = graphConfig;
     this.envConfig = envConfig;
+    this.logger = graphConfig.logger;
   }
   connected = false;
   connection = null;
   g = null;
+  logger;
   // Tag Collections - cached in memory for performance
   entityTypesCollection = null;
   async connect() {
@@ -1758,7 +1757,7 @@ var JanusGraphDatabase = class {
     if (!port) {
       throw new Error("JanusGraph port is required: provide in config");
     }
-    console.log(`Attempting to connect to JanusGraph at ws://${host}:${port}/gremlin`);
+    this.logger?.info("Connecting to JanusGraph", { host, port });
     this.connection = new DriverRemoteConnection(
       `ws://${host}:${port}/gremlin`,
       {}
@@ -1766,7 +1765,7 @@ var JanusGraphDatabase = class {
     this.g = traversal().withRemote(this.connection);
     await this.g.V().limit(1).toList();
     this.connected = true;
-    console.log("Successfully connected to JanusGraph");
+    this.logger?.info("Successfully connected to JanusGraph");
     await this.initializeSchema();
   }
   async disconnect() {
@@ -1779,7 +1778,7 @@ var JanusGraphDatabase = class {
     return this.connected;
   }
   async initializeSchema() {
-    console.log("Schema initialization would happen here in production");
+    this.logger?.debug("Schema initialization would happen here in production");
   }
   // Helper function to convert vertex to Resource
   vertexToResource(vertex) {
@@ -1899,7 +1898,7 @@ var JanusGraphDatabase = class {
       vertex.property("sourceResourceId", resource.sourceResourceId);
     }
     await vertex.next();
-    console.log("Created resource vertex in JanusGraph:", id);
+    this.logger?.info("Created resource vertex in JanusGraph", { id });
     return resource;
   }
   async getResource(id) {
@@ -1922,7 +1921,7 @@ var JanusGraphDatabase = class {
   }
   async deleteResource(id) {
     await this.g.V().has("Resource", "id", id).drop().next();
-    console.log("Deleted resource from JanusGraph:", id);
+    this.logger?.info("Deleted resource from JanusGraph", { id });
   }
   async listResources(filter) {
     let traversalQuery = this.g.V().hasLabel("Resource");
@@ -1985,7 +1984,7 @@ var JanusGraphDatabase = class {
       }
       await this.g.V(annVertex.value).addE("TAGGED_AS").to(this.g.V(etVertex.value)).next();
     }
-    console.log("Created annotation in JanusGraph:", id);
+    this.logger?.info("Created annotation in JanusGraph", { id });
     return annotation;
   }
   async getAnnotation(id) {
@@ -2044,7 +2043,7 @@ var JanusGraphDatabase = class {
   }
   async deleteAnnotation(id) {
     await this.g.V().has("Annotation", "id", id).drop().next();
-    console.log("Deleted annotation from JanusGraph:", id);
+    this.logger?.info("Deleted annotation from JanusGraph", { id });
   }
   async listAnnotations(filter) {
     let traversalQuery = this.g.V().hasLabel("Annotation");
@@ -2119,7 +2118,7 @@ var JanusGraphDatabase = class {
   }
   async getResourceConnections(resourceId) {
     const paths = await this.g.V().has("Resource", "id", resourceId).inE("BELONGS_TO").outV().outE("REFERENCES").inV().path().toList();
-    console.log("Found paths:", paths.length);
+    this.logger?.debug("Found paths", { count: paths.length });
     const connections = [];
     const refs = await this.getReferences(resourceId);
     for (const ref of refs) {
@@ -2222,7 +2221,7 @@ var JanusGraphDatabase = class {
         await this.g.addV("TagCollection").property("type", "entity-types").property("tags", JSON.stringify(Array.from(this.entityTypesCollection))).next();
       }
     } catch (error) {
-      console.error("Failed to add entity type:", error);
+      this.logger?.error("Failed to add entity type", { error });
     }
   }
   async addEntityTypes(tags) {
@@ -2238,7 +2237,7 @@ var JanusGraphDatabase = class {
         await this.g.addV("TagCollection").property("type", "entity-types").property("tags", JSON.stringify(Array.from(this.entityTypesCollection))).next();
       }
     } catch (error) {
-      console.error("Failed to add entity types:", error);
+      this.logger?.error("Failed to add entity types", { error });
     }
   }
   async initializeTagCollections() {
@@ -2265,12 +2264,11 @@ var JanusGraphDatabase = class {
   async clearDatabase() {
     await this.g.V().drop().next();
     this.entityTypesCollection = null;
-    console.log("Cleared JanusGraph database");
+    this.logger?.info("Cleared JanusGraph database");
   }
 };
 
 // src/implementations/memorygraph.ts
-import { getEntityTypes as getEntityTypes4 } from "@semiont/ontology";
 import { resourceId as makeResourceId, uriToResourceId, resourceUri as resourceUri2 } from "@semiont/core";
 import { v4 as uuidv44 } from "uuid";
 import {
@@ -2282,14 +2280,15 @@ import {
 } from "@semiont/api-client";
 var MemoryGraphDatabase = class {
   connected = false;
+  logger;
   // In-memory storage using Maps
   resources = /* @__PURE__ */ new Map();
   annotations = /* @__PURE__ */ new Map();
   constructor(config = {}) {
-    void config;
+    this.logger = config.logger;
   }
   async connect() {
-    console.log("Using in-memory graph database...");
+    this.logger?.info("Using in-memory graph database");
     this.connected = true;
   }
   async disconnect() {
@@ -2372,7 +2371,7 @@ var MemoryGraphDatabase = class {
       created: (/* @__PURE__ */ new Date()).toISOString()
     };
     this.annotations.set(id, annotation);
-    console.log("Memory: Created annotation:", {
+    this.logger?.debug("Created annotation", {
       id,
       motivation: annotation.motivation,
       hasSource: !!getBodySource4(annotation.body),
@@ -2419,7 +2418,7 @@ var MemoryGraphDatabase = class {
       const targetResourceId = targetSource ? uriToResourceId(targetSource) : null;
       return targetResourceId === resourceIdStr && sel.motivation === "highlighting";
     });
-    console.log(`Memory: getHighlights for ${resourceId} found ${highlights.length} highlights`);
+    this.logger?.debug("Got highlights for resource", { resourceId, count: highlights.length });
     return highlights;
   }
   async resolveReference(annotationId, source) {
@@ -2445,15 +2444,7 @@ var MemoryGraphDatabase = class {
       const targetResourceId = targetSource ? uriToResourceId(targetSource) : null;
       return targetResourceId === resourceIdStr && sel.motivation === "linking";
     });
-    console.log(`Memory: getReferences for ${resourceId} found ${references.length} references`);
-    references.forEach((ref) => {
-      console.log("  Reference:", {
-        id: ref.id,
-        source: getBodySource4(ref.body),
-        entityTypes: getEntityTypes4(ref)
-        // from body
-      });
-    });
+    this.logger?.debug("Got references for resource", { resourceId, count: references.length });
     return references;
   }
   async getEntityReferences(resourceId, entityTypes) {