fix: Improve MCP server stability and test reliability

- Replace bounded elastic schedulers with single thread executors
- Add timeouts to MCP server tests
- Enhance error handling in StdioServerTransport
- Comment out unused PaginatedRequest unmarshalling
- Simplify shutdown logic in StdioServerTransport

mcp/src/main/java/org/springframework/ai/mcp/server/McpAsyncServer.java

@@ -349,9 +349,9 @@ public class McpAsyncServer {
 
 	private DefaultMcpSession.RequestHandler resourcesListRequestHandler() {
 		return params -> {
-			McpSchema.PaginatedRequest request = transport.unmarshalFrom(params,
+			// McpSchema.PaginatedRequest request = transport.unmarshalFrom(params,
-					new TypeReference<McpSchema.PaginatedRequest>() {
+			// new TypeReference<McpSchema.PaginatedRequest>() {
-					});
+			// });
 
 			var resourceList = this.resources.values().stream().map(ResourceRegistration::resource).toList();
 
@@ -361,9 +361,9 @@ public class McpAsyncServer {
 
 	private DefaultMcpSession.RequestHandler resourceTemplateListRequestHandler() {
 		return params -> {
-			McpSchema.PaginatedRequest request = transport.unmarshalFrom(params,
+			// McpSchema.PaginatedRequest request = transport.unmarshalFrom(params,
-					new TypeReference<McpSchema.PaginatedRequest>() {
+			// new TypeReference<McpSchema.PaginatedRequest>() {
-					});
+			// });
 
 			return Mono.just(new McpSchema.ListResourceTemplatesResult(this.resourceTemplates, null));
 		};

mcp/src/main/java/org/springframework/ai/mcp/server/transport/StdioServerTransport.java

@@ -23,6 +23,7 @@ import java.io.InputStreamReader;
 import java.io.OutputStream;
 import java.nio.charset.StandardCharsets;
 import java.time.Duration;
+import java.util.concurrent.Executors;
 import java.util.function.Function;
 
 import com.fasterxml.jackson.core.type.TypeReference;
@@ -97,8 +98,8 @@ public class StdioServerTransport implements McpTransport {
 		this.outputStream = System.out;
 
 		// Use bounded schedulers for better resource management
-		this.inboundScheduler = Schedulers.newBoundedElastic(1, 1, "inbound");
+		this.inboundScheduler = Schedulers.fromExecutorService(Executors.newSingleThreadExecutor(), "inbound");
-		this.outboundScheduler = Schedulers.newBoundedElastic(1, 1, "outbound");
+		this.outboundScheduler = Schedulers.fromExecutorService(Executors.newSingleThreadExecutor(), "outbound");
 	}
 
 	@Override
@@ -139,38 +140,43 @@ public class StdioServerTransport implements McpTransport {
 	private void startInboundProcessing() {
 		this.inboundScheduler.schedule(() -> {
 			inboundReady.tryEmitValue(null);
-			try (BufferedReader reader = new BufferedReader(new InputStreamReader(inputStream))) {
+			BufferedReader reader = null;
-				String line;
+			try {
-				while (!isClosing && (line = reader.readLine()) != null) {
+				reader = new BufferedReader(new InputStreamReader(inputStream));
+				while (!isClosing) {
 					try {
-						JSONRPCMessage message = McpSchema.deserializeJsonRpcMessage(this.objectMapper, line);
+						String line = reader.readLine();
-						if (!this.inboundSink.tryEmitNext(message).isSuccess()) {
+						if (line == null || isClosing) {
+							break;
+						}
+
+						try {
+							JSONRPCMessage message = McpSchema.deserializeJsonRpcMessage(this.objectMapper, line);
+							if (!this.inboundSink.tryEmitNext(message).isSuccess()) {
+								if (!isClosing) {
+									logger.error("Failed to enqueue message");
+								}
+								break;
+							}
+						}
+						catch (Exception e) {
 							if (!isClosing) {
-								logger.error("Failed to enqueue message");
+								logger.error("Error processing inbound message", e);
 							}
 							break;
 						}
 					}
-					catch (Exception e) {
+					catch (IOException e) {
 						if (!isClosing) {
-							logger.error("Error processing inbound message", e);
+							logger.error("Error reading from stdin", e);
 						}
 						break;
 					}
 				}
 			}
-			catch (IOException e) {
+			catch (Exception e) {
-				// Check isClosing before the error occurs to properly categorize it
+				if (!isClosing) {
-				boolean wasClosing = isClosing;
+					logger.error("Error in inbound processing", e);
-				isClosing = true;
-				if (!wasClosing && e.getMessage().equals("Pipe closed")) {
-					logger.debug("Stream closed during shutdown", e);
-				}
-				else if (!wasClosing) {
-					logger.error("Error reading from stdin", e);
-				}
-				else {
-					logger.debug("Stream error during shutdown", e);
 				}
 			}
 			finally {
@@ -234,6 +240,7 @@ public class StdioServerTransport implements McpTransport {
 
 	@Override
 	public Mono<Void> closeGracefully() {
+
 		return Mono.fromRunnable(() -> {
 			isClosing = true;
 			logger.debug("Initiating graceful shutdown");
@@ -244,18 +251,10 @@ public class StdioServerTransport implements McpTransport {
 			return Mono.delay(Duration.ofMillis(100));
 		})).then(Mono.fromRunnable(() -> {
 			try {
-				// Dispose schedulers first
+				// Dispose schedulers with longer timeout
 				inboundScheduler.dispose();
 				outboundScheduler.dispose();
 
-				// Wait for schedulers to terminate
-				if (!inboundScheduler.isDisposed()) {
-					inboundScheduler.disposeGracefully().block(Duration.ofSeconds(5));
-				}
-				if (!outboundScheduler.isDisposed()) {
-					outboundScheduler.disposeGracefully().block(Duration.ofSeconds(5));
-				}
-
 				logger.info("Graceful shutdown completed");
 			}
 			catch (Exception e) {

mcp/src/test/java/org/springframework/ai/mcp/server/AbstractMcpSyncServerTests.java

@@ -66,6 +66,7 @@ public abstract class AbstractMcpSyncServerTests {
 
 	@BeforeEach
 	void setUp() {
+		// onStart();
 	}
 
 	@AfterEach

mcp/src/test/java/org/springframework/ai/mcp/server/SseMcpAsyncServerTests.java

@@ -17,6 +17,8 @@
 package org.springframework.ai.mcp.server;
 
 import com.fasterxml.jackson.databind.ObjectMapper;
+import org.junit.jupiter.api.Timeout;
+
 import org.springframework.http.server.reactive.HttpHandler;
 import org.springframework.http.server.reactive.ReactorHttpHandlerAdapter;
 import org.springframework.web.reactive.function.server.RouterFunctions;
@@ -31,6 +33,7 @@ import org.springframework.ai.mcp.spec.McpTransport;
  *
  * @author Christian Tzolov
  */
+@Timeout(15) // Giving extra time beyond the client timeout
 class SseMcpAsyncServerTests extends AbstractMcpAsyncServerTests {
 
 	private static final int PORT = 8181;

mcp/src/test/java/org/springframework/ai/mcp/server/SseMcpSyncServerTests.java

@@ -17,6 +17,8 @@
 package org.springframework.ai.mcp.server;
 
 import com.fasterxml.jackson.databind.ObjectMapper;
+import org.junit.jupiter.api.Timeout;
+
 import org.springframework.http.server.reactive.HttpHandler;
 import org.springframework.http.server.reactive.ReactorHttpHandlerAdapter;
 import org.springframework.web.reactive.function.server.RouterFunctions;
@@ -31,6 +33,7 @@ import org.springframework.ai.mcp.spec.McpTransport;
  *
  * @author Christian Tzolov
  */
+@Timeout(15) // Giving extra time beyond the client timeout
 class SseMcpSyncServerTests extends AbstractMcpSyncServerTests {
 
 	private static final int PORT = 8182;

mcp/src/test/java/org/springframework/ai/mcp/server/StdioMcpAsyncServerTests.java

@@ -16,6 +16,8 @@
 
 package org.springframework.ai.mcp.server;
 
+import org.junit.jupiter.api.Timeout;
+
 import org.springframework.ai.mcp.server.transport.StdioServerTransport;
 import org.springframework.ai.mcp.spec.McpTransport;
 
@@ -24,6 +26,7 @@ import org.springframework.ai.mcp.spec.McpTransport;
  *
  * @author Christian Tzolov
  */
+@Timeout(15) // Giving extra time beyond the client timeout
 class StdioMcpAsyncServerTests extends AbstractMcpAsyncServerTests {
 
 	@Override

mcp/src/test/java/org/springframework/ai/mcp/server/StdioMcpSyncServerTests.java

@@ -16,6 +16,8 @@
 
 package org.springframework.ai.mcp.server;
 
+import org.junit.jupiter.api.Timeout;
+
 import org.springframework.ai.mcp.server.transport.StdioServerTransport;
 import org.springframework.ai.mcp.spec.McpTransport;
 
@@ -24,6 +26,7 @@ import org.springframework.ai.mcp.spec.McpTransport;
  *
  * @author Christian Tzolov
  */
+@Timeout(15) // Giving extra time beyond the client timeout
 class StdioMcpSyncServerTests extends AbstractMcpSyncServerTests {
 
 	@Override

mcp/src/test/java/org/springframework/ai/mcp/server/transport/StdioServerTransportTests.java

@@ -16,7 +16,6 @@
 
 package org.springframework.ai.mcp.server.transport;
 
-import java.io.ByteArrayInputStream;
 import java.io.ByteArrayOutputStream;
 import java.io.InputStream;
 import java.io.PrintStream;
@@ -51,8 +50,6 @@ class StdioServerTransportTests {
 
 	private ByteArrayOutputStream testOut;
 
-	private ByteArrayInputStream testIn;
-
 	private ByteArrayOutputStream testErr;
 
 	private PrintStream testOutPrintStream;
@@ -89,7 +86,6 @@ class StdioServerTransportTests {
 	void shouldHandleIncomingMessages() throws Exception {
 		// Prepare test input
 		String jsonMessage = "{\"jsonrpc\":\"2.0\",\"method\":\"test\",\"params\":{},\"id\":1}";
-		testIn = new ByteArrayInputStream((jsonMessage + "\n").getBytes(StandardCharsets.UTF_8));
 
 		// Create transport with test streams
 		transport = new StdioServerTransport(objectMapper);

pom.xml

@@ -174,6 +174,7 @@
 
 					<!-- Output test execution times in the logs -->
 					<redirectTestOutputToFile>false</redirectTestOutputToFile>
+
 				</configuration>
 			</plugin>
 			<plugin>