test: fix STDIO integration test and quiet expected error logs

Run MCP client verification synchronously, launch the STDIO subprocess with the correct config, and avoid starting STDIO in-process during config tests. Suppress intentional ERROR logs in test logback configuration.

Co-authored-by: Cursor <cursoragent@cursor.com>

Author: codeboyzhou

src/test/java/com/github/thought2code/mcp/annotated/integration/McpApplicationIntegrationTest.java

@@ -26,7 +26,6 @@
 import io.modelcontextprotocol.json.McpJsonDefaults;
 import java.time.Duration;
 import java.util.Random;
-import java.util.concurrent.Executors;
 import org.junit.jupiter.api.BeforeAll;
 import org.junit.jupiter.api.Tag;
 import org.junit.jupiter.api.Test;
@@ -59,14 +58,8 @@ private void startServer(McpServerConfiguration configuration) {
     mcpServer.start();
   }
 
-  private void startServer(String configFileName) {
-    startServer(new McpConfigurationLoader(configFileName).loadConfig());
-  }
-
   @Test
   void stdioTransport_shouldServeAllFixtureComponents() {
-    TestMcpStdioServer.main(new String[] {});
-
     String classpath = System.getProperty("java.class.path");
     ServerParameters serverParameters =
         ServerParameters.builder("java")
@@ -76,8 +69,7 @@ void stdioTransport_shouldServeAllFixtureComponents() {
         new StdioClientTransport(serverParameters, McpJsonDefaults.getMapper());
 
     try (McpSyncClient client = McpClient.sync(transport).requestTimeout(requestTimeout).build()) {
-      Executors.newSingleThreadExecutor()
-          .execute(() -> McpClientVerificationSupport.verifyAll(client));
+      McpClientVerificationSupport.verifyAll(client);
     }
   }
 
@@ -126,11 +118,14 @@ void disabledConfiguration_shouldNotStartServer() {
     assertFalse(configuration.enabled());
   }
 
+  /**
+   * STDIO mode binds to System.in/out, starting it in-process would block or break subprocess
+   * tests.
+   */
   @Test
-  void stdioModeConfig_shouldLoadAndStartWithoutError() {
+  void stdioModeConfig_shouldLoadWithoutStartingInProcessServer() {
     McpServerConfiguration configuration =
         new McpConfigurationLoader("test-mcp-server-enable-stdio-mode.yml").loadConfig();
-    assertDoesNotThrow(() -> startServer(configuration));
     assertEquals(ServerMode.STDIO, configuration.mode());
   }
 
@@ -154,6 +149,9 @@ void streamableModeConfig_shouldLoadAndStartWithoutError() {
   void unknownModeConfig_shouldFailDuringLoad() {
     assertThrows(
         McpServerConfigurationException.class,
-        () -> startServer("test-mcp-server-enable-unknown-mode.yml"));
+        () ->
+            startServer(
+                new McpConfigurationLoader("test-mcp-server-enable-unknown-mode.yml")
+                    .loadConfig()));
   }
 }

src/test/java/com/github/thought2code/mcp/annotated/test/TestMcpStdioServer.java

@@ -4,7 +4,9 @@
 
 public class TestMcpStdioServer {
 
+  private static final String STDIO_CONFIG = "test-mcp-server-enable-stdio-mode.yml";
+
   public static void main(String[] args) {
-    McpApplication.run(TestMcpStdioServer.class, args);
+    McpApplication.run(TestMcpStdioServer.class, args, STDIO_CONFIG);
   }
 }

src/test/resources/logback.xml

@@ -12,8 +12,15 @@
     </appender>
 
     <logger name="org.eclipse.jetty" level="WARN"/>
+    <logger name="io.modelcontextprotocol" level="WARN"/>
 
-    <root level="DEBUG">
+    <!-- Expected failure paths in unit/integration tests intentionally emit ERROR logs. -->
+    <logger name="com.github.thought2code.mcp.annotated.util.JacksonHelper" level="OFF"/>
+    <logger name="com.github.thought2code.mcp.annotated.reflect.MethodInvoker" level="OFF"/>
+    <logger name="com.github.thought2code.mcp.annotated.reflect.ComponentInvocationSupport" level="OFF"/>
+    <logger name="com.github.thought2code.mcp.annotated.server.JettyHttpServer" level="OFF"/>
+
+    <root level="WARN">
         <appender-ref ref="CONSOLE"/>
     </root>
 

src/test/resources/test-mcp-server-enable-stdio-mode.yml

@@ -3,7 +3,7 @@ mode: STDIO
 name: mcp-server
 version: 1.0.0
 type: SYNC
-instructions: You are a helpful AI assistant
+instructions: test
 request-timeout: 60000
 capabilities:
   resource: true