Upgrade to Spring AI 2, add logging, use Gemini 3 by default

api/build.gradle

@@ -466,6 +466,7 @@ dependencies {
         )
     )
 
+    // Jackson 2
     BuildUtils.addExternalDependency(
         project,
         new ExternalDependency(

core/src/org/labkey/core/mpc/McpServiceImpl.java

@@ -60,9 +60,15 @@
 import org.springframework.ai.google.genai.text.GoogleGenAiTextEmbeddingModel;
 import org.springframework.ai.google.genai.text.GoogleGenAiTextEmbeddingOptions;
 import org.springframework.ai.mcp.McpToolUtils;
+import org.springframework.ai.chat.model.ToolContext;
 import org.springframework.ai.tool.ToolCallback;
+import org.springframework.ai.tool.definition.ToolDefinition;
+import org.springframework.ai.tool.metadata.ToolMetadata;
+import org.springframework.ai.document.Document;
+import org.springframework.ai.vectorstore.SearchRequest;
 import org.springframework.ai.vectorstore.SimpleVectorStore;
 import org.springframework.ai.vectorstore.VectorStore;
+import org.springframework.ai.vectorstore.filter.Filter;
 import org.springframework.mock.web.MockHttpServletRequest;
 import org.springframework.mock.web.MockHttpServletResponse;
 import reactor.core.publisher.Mono;
@@ -171,7 +177,7 @@ public boolean isReady()
     @Override
     public void registerTools(@NotNull List<ToolCallback> tools)
     {
-        tools.forEach(tool -> toolMap.put(tool.getToolDefinition().name(), tool));
+        tools.forEach(tool -> toolMap.put(tool.getToolDefinition().name(), new _LoggingToolCallback(tool)));
     }
 
     @Override
@@ -316,6 +322,65 @@ public void shutdownStarted()
         }
     }
 
+
+    /** Delegating wrapper that logs vector store similarity searches */
+    private static class _LoggingVectorStore implements VectorStore
+    {
+        private final VectorStore delegate;
+
+        _LoggingVectorStore(VectorStore delegate)
+        {
+            this.delegate = delegate;
+        }
+
+        @Override
+        public void add(List<Document> documents)
+        {
+            delegate.add(documents);
+        }
+
+        @Override
+        public void delete(Filter.Expression filterExpression)
+        {
+            delegate.delete(filterExpression);
+        }
+
+        @Override
+        public void delete(List<String> idList)
+        {
+            delegate.delete(idList);
+        }
+
+        @Override
+        public List<Document> similaritySearch(SearchRequest request)
+        {
+            LOG.info("Vector store search: query=\"{}\"", request.getQuery());
+            List<Document> results = delegate.similaritySearch(request);
+            if (results.isEmpty())
+            {
+                LOG.info("Vector store search returned no results");
+            }
+            else
+            {
+                LOG.info("Vector store search returned {} result(s):", results.size());
+                for (Document doc : results)
+                {
+                    String content = doc.getText();
+                    String snippet = content.length() > 200 ? content.substring(0, 200) + "..." : content;
+                    LOG.info("  - [{}] {}", doc.getMetadata(), snippet);
+                }
+            }
+            return results;
+        }
+
+        @Override
+        public String getName()
+        {
+            return delegate.getName();
+        }
+    }
+
+
     @Override
     public ChatClient getChat(HttpSession session, String agentName, Supplier<String> systemPromptSupplier, boolean createIfNotExists)
     {
@@ -352,7 +417,7 @@ private ChatClient createSpringChat(HttpSession session, String agentName, Suppl
 
         VectorStore vs = getVectorStore();
         if (null != vs)
-            advisors.add(QuestionAnswerAdvisor.builder(vs).build());
+            advisors.add(QuestionAnswerAdvisor.builder(new _LoggingVectorStore(vs)).build());
 
         return ChatClient.builder(modelProvider.getChatModel())
                 .defaultOptions(modelProvider.getChatOptions())
@@ -558,11 +623,11 @@ class _GeminiProvider implements _ModelProvider
         @Override
         public String getModel()
         {
-            return "gemini-2.5-flash";
+//            return "gemini-2.5-flash";
             // gemini-2.5-flash
             // gemini-2.5-pro
             // gemini-3-flash-preview
-            // gemini-3-pro-preview
+            return "gemini-3-pro-preview";
         }
 
         @Override
@@ -630,6 +695,43 @@ public EmbeddingModel createEmbeddingModel()
     }
 
 
+    private static class _LoggingToolCallback implements ToolCallback
+    {
+        private final ToolCallback delegate;
+
+        _LoggingToolCallback(ToolCallback delegate)
+        {
+            this.delegate = delegate;
+        }
+
+        @Override
+        public ToolDefinition getToolDefinition()
+        {
+            return delegate.getToolDefinition();
+        }
+
+        @Override
+        public ToolMetadata getToolMetadata()
+        {
+            return delegate.getToolMetadata();
+        }
+
+        @Override
+        public String call(String toolInput)
+        {
+            LOG.info("MCP tool invoked: {}", delegate.getToolDefinition().name());
+            return delegate.call(toolInput);
+        }
+
+        @Override
+        public String call(String toolInput, ToolContext toolContext)
+        {
+            LOG.info("MCP tool invoked: {}", delegate.getToolDefinition().name());
+            return delegate.call(toolInput, toolContext);
+        }
+    }
+
+
     class _ClaudeProvider implements _ModelProvider
     {
         @Override