Work around some race conditions in MCP prototype

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

@@ -65,7 +65,9 @@
 import java.time.Duration;
 import java.util.ArrayList;
 import java.util.Arrays;
+import java.util.ConcurrentModificationException;
 import java.util.List;
+import java.util.NoSuchElementException;
 import java.util.Objects;
 import java.util.function.Supplier;
 
@@ -314,6 +316,7 @@ public ChatClient getChat(HttpSession session, String agentName, Supplier<String
                     .maxMessages(100)
                     .chatMemoryRepository(chatMemoryRepository)
                     .build();
+
             MessageChatMemoryAdvisor chatMemoryAdvisor = MessageChatMemoryAdvisor.builder(chatMemory)
                     .conversationId(conversationId)
                     .build();
@@ -335,46 +338,73 @@ public ChatClient getChat(HttpSession session, String agentName, Supplier<String
     @Override
     public MessageResponse sendMessage(ChatClient chatSession, String message)
     {
-        var callResponse = chatSession
-                .prompt(message)
-                .toolContext(McpContext.get().getToolContext().getContext())
-                .call();
-        StringBuilder sb = new StringBuilder();
-        for (Generation result : callResponse.chatResponse().getResults())
+        try
         {
-            var output = result.getOutput();
-            if (ASSISTANT == output.getMessageType())
+            var callResponse = chatSession
+                    .prompt(message)
+                    .toolContext(McpContext.get().getToolContext().getContext())
+                    .call();
+            StringBuilder sb = new StringBuilder();
+            for (Generation result : callResponse.chatResponse().getResults())
             {
-                sb.append(output.getText());
-                sb.append("\n\n");
+                var output = result.getOutput();
+                if (ASSISTANT == output.getMessageType())
+                {
+                    sb.append(output.getText());
+                    sb.append("\n\n");
+                }
             }
+            String md = sb.toString().strip();
+            HtmlString html = HtmlString.unsafe(MarkdownService.get().toHtml(md));
+            return new MessageResponse("text/markdown", md, html);
+        }
+        catch (java.util.NoSuchElementException x)
+        {
+            // Spring AI GoogleGenAiChatModel bug: empty candidates cause NoSuchElementException
+            // https://github.com/spring-projects/spring-ai/issues/4556
+            LOG.warn("Empty response from chat model (likely a filtered or empty candidate)", x);
+            return new MessageResponse("text/plain", "The model returned an empty response. Please try resubmitting and the problem continues, rephrase your question/prompt.", HtmlString.of("The model returned an empty response. Please try rephrasing your question."));
         }
-        String md = sb.toString().strip();
-        HtmlString html = HtmlString.unsafe(MarkdownService.get().toHtml(md));
-        return new MessageResponse("text/markdown", md, html);
     }
 
     @Override
     public List<MessageResponse> sendMessageEx(ChatClient chatSession, String message)
     {
         if (isBlank(message))
             return List.of();
-        var callResponse = chatSession
-                .prompt(message)
-                .toolContext(McpContext.get().getToolContext().getContext())
-                .call();
-        List<MessageResponse> ret = new ArrayList<>();
-        for (Generation result : callResponse.chatResponse().getResults())
+        try
         {
-            var output = result.getOutput();
-            if (ASSISTANT == output.getMessageType())
+            var callResponse = chatSession
+                    .prompt(message)
+                    .toolContext(McpContext.get().getToolContext().getContext())
+                    .call();
+            List<MessageResponse> ret = new ArrayList<>();
+            for (Generation result : callResponse.chatResponse().getResults())
             {
-                String md = output.getText();
-                HtmlString html = HtmlString.unsafe(MarkdownService.get().toHtml(md));
-                ret.add(new MessageResponse("text/markdown", md, html));
+                var output = result.getOutput();
+                if (ASSISTANT == output.getMessageType())
+                {
+                    String md = output.getText();
+                    HtmlString html = HtmlString.unsafe(MarkdownService.get().toHtml(md));
+                    ret.add(new MessageResponse("text/markdown", md, html));
+                }
             }
+            return ret;
+        }
+        catch (NoSuchElementException x)
+        {
+            // Spring AI GoogleGenAiChatModel bug: empty candidates cause NoSuchElementException
+            // https://github.com/spring-projects/spring-ai/issues/4556
+            LOG.warn("Empty response from chat model (likely a filtered or empty candidate)", x);
+            return List.of(new MessageResponse("text/plain", "The model returned an empty response. Please try rephrasing your question.", HtmlString.of("The model returned an empty response. Please try rephrasing your question.")));
+        }
+        catch (ConcurrentModificationException x)
+        {
+            // This can happen when the vector store is still loading, typically a problem shortly after startup
+            // Should do better synchronization or state checking
+            LOG.warn("Vector store not ready", x);
+            return List.of(new MessageResponse("text/plain", "Vector store likely not ready yet. Try again.", HtmlString.of("Vector store likely not ready yet. Try again.")));
         }
-        return ret;
     }
 
 
@@ -464,6 +494,7 @@ public String getModel()
             // gemini-2.5-flash
             // gemini-2.5-pro
             // gemini-3-flash-preview
+            // gemini-3-pro-preview
         }
 
         @Override

query/src/org/labkey/query/controllers/LabKeySql.md

@@ -57,16 +57,16 @@ A `PIVOT` query helps you summarize and re-visualize data by transforming rows i
   PIVOT new_column_name BY pivoting_column IN ('value1', 'value2')
   ```
   Note that pivot column names are case-sensitive. You may need to use `LOWER()` or `UPPER()` in your query to work around this issue.
-* **Pivoting by Two Columns:**
-  Two levels of `PIVOT` are not directly supported. However, you can achieve a similar result by concatenating the two values together and pivoting on that "calculated" column.
-  ```sql
-  SELECT
-    Run.SampleCondition || ' ' || PeakLabel AS ConditionPeak,
-    AVG(Data.PercTimeCorrArea) AS AvgPercTimeCorrArea
-  FROM Data
-  GROUP BY Run.SampleCondition || ' ' || PeakLabel
-  PIVOT AvgPercTimeCorrArea BY ConditionPeak
-  ```
+  * **Pivoting by Two Columns:**
+    Two levels of `PIVOT` are not directly supported. However, you can achieve a similar result by concatenating the two values together and pivoting on that "calculated" column.
+    ```sql
+    SELECT
+      Run.SampleCondition || ' ' || PeakLabel AS ConditionPeak,
+      AVG(Data.PercTimeCorrArea) AS AvgPercTimeCorrArea
+    FROM Data
+    GROUP BY Run.SampleCondition || ' ' || PeakLabel
+    PIVOT AvgPercTimeCorrArea BY ConditionPeak
+    ```
 
 -----
 
@@ -130,7 +130,26 @@ LabKey SQL allows you to directly annotate your SQL statements to override how c
 
 -----
 
-### **7. Available Methods**
+### **7. Container Filters**
+
+In addition to targeting a container by its path, LabKey SQL supports container filters to alter the scope
+of a query. Annotate tables in the FROM clause with an optional container filter. Syntax:
+
+SELECT * FROM Issues [ContainerFilter='CurrentAndSubfolders'] alias
+
+Possible values include:
+- AllFolders
+- AllInProject
+- AllInProjectPlusShared
+- Current
+- CurrentAndFirstChildren
+- CurrentAndParents
+- CurrentAndSubfolders
+- CurrentAndSubfoldersPlusShared
+- CurrentPlusProject
+- CurrentPlusProjectAndShared.
+
+### **8. Available Methods**
 
 Here is a summary of the available functions and methods in LabKey SQL.