MCP Server MVP

api/src/org/labkey/api/mcp/McpException.java

@@ -0,0 +1,11 @@
+package org.labkey.api.mcp;
+
+// A special exception that MCP endpoints can throw when they want to provide guidance to the client without making
+// it a big red error. The message will be extracted and sent as text to the client.
+public class McpException extends RuntimeException
+{
+    public McpException(String message)
+    {
+        super(message);
+    }
+}

api/src/org/labkey/api/mcp/McpService.java

@@ -5,11 +5,15 @@
 import jakarta.servlet.http.HttpSession;
 import org.jetbrains.annotations.NotNull;
 import org.jspecify.annotations.NonNull;
+import org.labkey.api.data.Container;
 import org.labkey.api.module.McpProvider;
+import org.labkey.api.security.User;
 import org.labkey.api.services.ServiceRegistry;
 import org.labkey.api.util.HtmlString;
-import org.springaicommunity.mcp.provider.resource.SyncMcpResourceProvider;
+import org.labkey.api.writer.ContainerUser;
 import org.springframework.ai.chat.client.ChatClient;
+import org.springframework.ai.chat.model.ToolContext;
+import org.springframework.ai.mcp.annotation.provider.resource.SyncMcpResourceProvider;
 import org.springframework.ai.support.ToolCallbacks;
 import org.springframework.ai.tool.ToolCallback;
 import org.springframework.ai.tool.ToolCallbackProvider;
@@ -31,7 +35,28 @@
 public interface McpService extends ToolCallbackProvider
 {
     // marker interface for classes that we will "ingest" using Spring annotations
-    interface McpImpl {}
+    interface McpImpl
+    {
+        default ContainerUser getContext(ToolContext toolContext)
+        {
+            User user = (User)toolContext.getContext().get("user");
+            Container container = (Container)toolContext.getContext().get("container");
+            if (container == null)
+                throw new McpException("No container path is set. Ask the user which container/folder they want to use (you can call listContainers to show available options), then call setContainer before retrying.");
+            return ContainerUser.create(container, user);
+        }
+
+        default User getUser(ToolContext toolContext)
+        {
+            return (User)toolContext.getContext().get("user");
+        }
+
+        // Every MCP resource should call this on every invocation
+        default void incrementResourceReadCount(String resource)
+        {
+            get().incrementResourceCount(resource);
+        }
+    }
 
     static @NotNull McpService get()
     {
@@ -79,6 +104,10 @@ default ChatClient getChat(HttpSession session, String agentName, Supplier<Strin
         return getChat(session, agentName, systemPromptSupplier, true);
     }
 
+    void saveSessionContainer(ToolContext context, Container container);
+
+    void incrementResourceCount(String resource);
+
     ChatClient getChat(HttpSession session, String agentName, Supplier<String> systemPromptSupplier, boolean createIfNotExists);
 
     void close(HttpSession session, ChatClient chat);

core/src/org/labkey/core/CoreMcp.java

@@ -1,16 +1,20 @@
 package org.labkey.core;
 
 import org.json.JSONObject;
+import org.labkey.api.collections.LabKeyCollectors;
 import org.labkey.api.data.Container;
-import org.labkey.api.mcp.McpContext;
+import org.labkey.api.data.ContainerManager;
 import org.labkey.api.mcp.McpService;
 import org.labkey.api.security.User;
+import org.labkey.api.security.permissions.ReadPermission;
 import org.labkey.api.settings.AppProps;
 import org.labkey.api.settings.LookAndFeelProperties;
 import org.labkey.api.study.Study;
 import org.labkey.api.study.StudyService;
 import org.labkey.api.util.HtmlString;
+import org.springframework.ai.chat.model.ToolContext;
 import org.springframework.ai.tool.annotation.Tool;
+import org.springframework.ai.tool.annotation.ToolParam;
 
 import java.util.Map;
 import java.util.Objects;
@@ -19,13 +23,13 @@
 
 public class CoreMcp implements McpService.McpImpl
 {
-    // TODO ChatSessions are currently per session.  The McpService should detect change of folder.
-    @Tool(description = "Call this tool before answering any prompts!  This tool provides useful context information about the current user (name, userid), webserver (name, url, description), and current folder (name, path, url, description).")
-    String whereAmIWhoAmITalkingTo()
+    @Tool(description = "This tool provides useful context information about the current user (name, userid), webserver " +
+        "(name, url, description), and current folder (name, path, url, description) once the container is set via setContainer.")
+    String whereAmIWhoAmITalkingTo(ToolContext context)
     {
-        McpContext context = McpContext.get();
-        User user = context.getUser();
-        Container folder = context.getContainer();
+        var cu = getContext(context);
+        User user = cu.getUser();
+        Container folder = cu.getContainer();
         AppProps appProps = AppProps.getInstance();
         Study study = null != StudyService.get() ? Objects.requireNonNull(StudyService.get()).getStudy(folder) : null;
         LookAndFeelProperties laf = LookAndFeelProperties.getInstance(folder);
@@ -63,4 +67,41 @@ String whereAmIWhoAmITalkingTo()
             "site", siteObj
         )).toString();
     }
+
+    @Tool(description = "List the hierarchical path for every container in the server where the user has read permissions.")
+    String listContainers(ToolContext toolContext)
+    {
+        return ContainerManager.getAllChildren(ContainerManager.getRoot(), getUser(toolContext), ReadPermission.class)
+            .stream()
+            .map(Container::getPath)
+            .collect(LabKeyCollectors.toJSONArray())
+            .toString();
+    }
+
+    @Tool(description = "Every tool in this MCP requires a container path, e.g. /MyProject/MyFolder. A container is also called a folder or project. Please prompt the user for a container path and use this tool to save the path for this session.")
+    String setContainer(ToolContext context, @ToolParam(description = "Container path, e.g. /MyProject/MyFolder", required = true) String containerPath)
+    {
+        final String message;
+
+        if (containerPath == null)
+        {
+            message = "Container path was null. Please enter a valid container path. Try using listContainers to see them.";
+        }
+        else
+        {
+            Container container = ContainerManager.getForPath(containerPath);
+
+            if (container == null)
+            {
+                message = "That's not a valid container path. Try using listContainers to see them.";
+            }
+            else
+            {
+                McpService.get().saveSessionContainer(context, container);
+                message = "Container has been set";
+            }
+        }
+
+        return message;
+    }
 }

core/src/org/labkey/core/CoreModule.java

@@ -255,7 +255,6 @@
 import org.labkey.core.login.DbLoginAuthenticationProvider;
 import org.labkey.core.login.DbLoginManager;
 import org.labkey.core.login.LoginController;
-import org.labkey.core.mcp.McpServiceImpl;
 import org.labkey.core.metrics.SimpleMetricsServiceImpl;
 import org.labkey.core.metrics.WebSocketConnectionManager;
 import org.labkey.core.notification.EmailPreferenceConfigServiceImpl;
@@ -1288,8 +1287,6 @@ public void moduleStartupComplete(ServletContext servletContext)
         UserManager.addUserListener(new EmailPreferenceUserListener());
 
         Encryption.checkMigration();
-
-        McpServiceImpl.get().startMpcServer();
     }
 
     // Issue 7527: Auto-detect missing SQL views and attempt to recreate
@@ -1324,9 +1321,6 @@ public void registerServlets(ServletContext servletCtx)
         _webdavServletDynamic = servletCtx.addServlet("static", new WebdavServlet(true));
         _webdavServletDynamic.setMultipartConfig(SpringActionController.getMultiPartConfigElement());
         _webdavServletDynamic.addMapping("/_webdav/*");
-
-        McpService.setInstance(new McpServiceImpl());
-        McpServiceImpl.get().registerServlets(servletCtx);
     }
 
     @Override