build(deps): bump butterfly from 1.0.4 to 1.1.1 (#3699)

* build(deps): bump butterfly from 1.0.4 to 1.1.0

Bumps [butterfly](https://github.com/OpenRefine/simile-butterfly) from 1.0.4 to 1.1.0.
- [Release notes](https://github.com/OpenRefine/simile-butterfly/releases)
- [Commits](https://github.com/OpenRefine/simile-butterfly/commits)

Signed-off-by: dependabot[bot] <support@github.com>

* Update Butterfly configuration after Jetty upgrade

* Fix main class name in web.xml

* Upgrade Butterfly to Jetty 9

* Temporary debugging output to understand why RefineServlet is not found

* Upgrade servlet-api

* Fix javax.servlet-api artifactId

* Reinstate debug logging temporarily

* Update butterfly to 1.1.1 to solve servlet-api version conflict

* Update javax.servlet-api in the rest of the code base

* Silence server logs in ./refine ui_test again

Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Antonin Delpeuch <antonin@delpeuch.eu>

benchmark/pom.xml

@@ -23,8 +23,8 @@
     </dependency>
     <dependency>
       <groupId>javax.servlet</groupId>
-      <artifactId>servlet-api</artifactId>
+      <artifactId>javax.servlet-api</artifactId>
-      <version>2.5</version>
+      <version>${servlet-api.version}</version>
       <scope>provided</scope>
     </dependency>
     <dependency>

main/pom.xml

@@ -171,14 +171,14 @@
   <dependencies>
     <dependency>
       <groupId>javax.servlet</groupId>
-      <artifactId>servlet-api</artifactId>
+      <artifactId>javax.servlet-api</artifactId>
-      <version>2.5</version>
+      <version>${servlet-api.version}</version>
       <scope>provided</scope>
     </dependency>
     <dependency>
       <groupId>org.openrefine.dependencies</groupId>
       <artifactId>butterfly</artifactId>
-      <version>1.0.4</version>
+      <version>${butterfly.version}</version>
     </dependency>
     <dependency>
       <groupId>org.mozilla</groupId>
@@ -367,6 +367,11 @@
       <artifactId>juniversalchardet</artifactId>
       <version>2.4.0</version>
     </dependency>
+    <dependency>
+      <groupId>org.eclipse.jetty</groupId>
+      <artifactId>jetty-servlets</artifactId>
+      <version>${jetty.version}</version>
+    </dependency>
 
     <!-- test dependencies -->
 

main/tests/server/src/com/google/refine/importing/ImportingUtilitiesTests.java

@@ -66,6 +66,7 @@ import com.google.refine.util.JSONUtilities;
 import com.google.refine.util.ParsingUtilities;
 import com.google.refine.util.TestUtils;
 
+import javax.servlet.ReadListener;
 import javax.servlet.ServletInputStream;
 import javax.servlet.http.HttpServletRequest;
 
@@ -167,6 +168,21 @@ public class ImportingUtilitiesTests extends ImporterTest {
             return delegate.read();
         }
 
+		@Override
+		public boolean isFinished() {
+			return false;
+		}
+
+		@Override
+		public boolean isReady() {
+			return true;
+		}
+
+		@Override
+		public void setReadListener(ReadListener readListener) {
+			
+		}
+
     }
 
     /**

main/webapp/WEB-INF/web.xml

@@ -1,10 +1,10 @@
-<?xml version="1.0"?>
+<?xml version="1.0" encoding="UTF-8"?>
-
+<web-app 
-<!DOCTYPE web-app
+   xmlns="http://xmlns.jcp.org/xml/ns/javaee" 
-    PUBLIC "-//Sun Microsystems, Inc.//DTD Web Application 2.3//EN"
+   xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
-    "http://java.sun.com/j2ee/dtds/web-app_2_3.dtd">
+   xsi:schemaLocation="http://xmlns.jcp.org/xml/ns/javaee http://xmlns.jcp.org/xml/ns/javaee/web-app_3_1.xsd"
-
+   metadata-complete="false"
-<web-app>
+   version="3.1">
     <display-name>OpenRefine</display-name>
     <description>OpenRefine Webapp</description>
 
@@ -22,7 +22,7 @@
 	
 	<filter>
       <filter-name>GzipFilter</filter-name>
-      <filter-class>org.mortbay.servlet.GzipFilter</filter-class>
+      <filter-class>org.eclipse.jetty.servlets.GzipFilter</filter-class>
       <init-param>
         <param-name>mimeTypes</param-name>
         <param-value>text/html,text/plain,text/xml,application/xhtml+xml,text/css,text/javascript,application/javascript,application/json,image/svg+xml</param-value>

pom.xml

@@ -61,7 +61,10 @@
     <surefireArgs/>
     <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
     <jackson.version>2.12.1</jackson.version>
+    <servlet-api.version>3.1.0</servlet-api.version>
+    <butterfly.version>1.1.1</butterfly.version>
     <slf4j.version>1.7.30</slf4j.version>
+    <jetty.version>9.4.26.v20200117</jetty.version>
   </properties>
 
 

server/pom.xml

@@ -154,18 +154,23 @@
     </dependency>
     <dependency>
       <groupId>javax.servlet</groupId>
-      <artifactId>servlet-api</artifactId>
+      <artifactId>javax.servlet-api</artifactId>
-      <version>2.5</version>
+      <version>${servlet-api.version}</version>
     </dependency>
     <dependency>
-      <groupId>org.mortbay.jetty</groupId>
+      <groupId>org.eclipse.jetty</groupId>
-      <artifactId>jetty</artifactId>
+      <artifactId>jetty-server</artifactId>
-      <version>6.1.26</version>
+      <version>${jetty.version}</version>
     </dependency>
     <dependency>
-      <groupId>org.mortbay.jetty</groupId>
+      <groupId>org.eclipse.jetty</groupId>
-      <artifactId>jetty-util</artifactId>
+      <artifactId>jetty-servlet</artifactId>
-      <version>6.1.26</version>
+      <version>${jetty.version}</version>
+    </dependency>
+    <dependency>
+      <groupId>org.eclipse.jetty</groupId>
+      <artifactId>jetty-webapp</artifactId>
+      <version>${jetty.version}</version>
     </dependency>
     <dependency>
       <groupId>org.openrefine.dependencies</groupId>
@@ -175,7 +180,7 @@
     <dependency>
       <groupId>org.openrefine.dependencies</groupId>
       <artifactId>butterfly</artifactId>
-      <version>1.0.4</version>
+      <version>${butterfly.version}</version>
     </dependency>
     <dependency>
       <groupId>org.mozilla</groupId>

server/src/com/google/refine/Refine.java

@@ -51,18 +51,23 @@ import java.util.concurrent.TimeUnit;
 import javax.swing.JFrame;
 
 import org.apache.log4j.Level;
-import org.mortbay.jetty.Connector;
+import org.eclipse.jetty.server.HttpConfiguration;
-import org.mortbay.jetty.Server;
+import org.eclipse.jetty.server.HttpConnectionFactory;
-import org.mortbay.jetty.bio.SocketConnector;
+import org.eclipse.jetty.server.Server;
-import org.mortbay.jetty.servlet.ServletHolder;
+import org.eclipse.jetty.server.ServerConnector;
-import org.mortbay.jetty.webapp.WebAppContext;
+import org.eclipse.jetty.server.handler.StatisticsHandler;
-import org.mortbay.util.Scanner;
+import org.eclipse.jetty.servlet.ServletHolder;
+import org.eclipse.jetty.webapp.WebAppContext;
+import org.eclipse.jetty.util.Scanner;
+import org.eclipse.jetty.util.thread.ThreadPool;
+import com.google.util.threads.ThreadPoolExecutorAdapter;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
 import com.codeberry.jdatapath.DataPath;
 import com.codeberry.jdatapath.JDataPathSystem;
-import com.google.util.threads.ThreadPoolExecutorAdapter;
+
+import com.google.refine.Configurations;
 
 /**
  * Main class for Refine server application.  Starts an instance of the
@@ -82,7 +87,7 @@ public class Refine {
         
         // tell jetty to use SLF4J for logging instead of its own stuff
         System.setProperty("VERBOSE","false");
-        System.setProperty("org.mortbay.log.class","org.mortbay.log.Slf4jLog");
+        System.setProperty("org.eclipse.jetty.log.class","org.eclipse.jetty.util.log.Slf4jLog");
         
         // tell macosx to keep the menu associated with the screen and what the app title is
         System.setProperty("apple.laf.useScreenMenuBar", "true");  
@@ -136,6 +141,18 @@ class RefineServer extends Server {
     
     final static Logger logger = LoggerFactory.getLogger("refine_server");
     
+    public RefineServer() {
+        super(createThreadPool());
+    }
+    
+    private static ThreadPool createThreadPool() {
+        int maxThreads = Configurations.getInteger("refine.queue.size", 30);
+        int maxQueue = Configurations.getInteger("refine.queue.max_size", 300);
+        long keepAliveTime = Configurations.getInteger("refine.queue.idle_time", 60);
+        LinkedBlockingQueue<Runnable> queue = new LinkedBlockingQueue<Runnable>(maxQueue);
+        return new ThreadPoolExecutorAdapter(new ThreadPoolExecutor(maxThreads, maxQueue, keepAliveTime, TimeUnit.SECONDS, queue));
+    }
+        
     private ThreadPoolExecutor threadPool;
     
     public void init(String host, int port) throws Exception {
@@ -146,21 +163,13 @@ class RefineServer extends Server {
             logger.info("refine.memory size: " + memory + " JVM Max heap: " + Runtime.getRuntime().maxMemory());
         }
         
-        int maxThreads = Configurations.getInteger("refine.queue.size", 30);
+        HttpConfiguration httpConfig = new HttpConfiguration();
-        int maxQueue = Configurations.getInteger("refine.queue.max_size", 300);
+        httpConfig.setSendServerVersion(false);
-        long keepAliveTime = Configurations.getInteger("refine.queue.idle_time", 60);
+        HttpConnectionFactory httpFactory = new HttpConnectionFactory(httpConfig);
-
+        ServerConnector connector = new ServerConnector(this, httpFactory);
-        LinkedBlockingQueue<Runnable> queue = new LinkedBlockingQueue<Runnable>(maxQueue);
-        
-        threadPool = new ThreadPoolExecutor(maxThreads, maxQueue, keepAliveTime, TimeUnit.SECONDS, queue);
-
-        this.setThreadPool(new ThreadPoolExecutorAdapter(threadPool));
-        
-        Connector connector = new SocketConnector();
         connector.setPort(port);
         connector.setHost(host);
-        connector.setMaxIdleTime(Configurations.getInteger("refine.connection.max_idle_time",60000));
+        connector.setIdleTimeout(Configurations.getInteger("server.connection.max_idle_time",60000));
-        connector.setStatsOn(false);
         this.addConnector(connector);
 
         File webapp = new File(Configurations.get("refine.webapp","main/webapp"));
@@ -185,7 +194,17 @@ class RefineServer extends Server {
 
         this.setHandler(context);
         this.setStopAtShutdown(true);
-        this.setSendServerVersion(true);
+        StatisticsHandler handler = new StatisticsHandler();
+        handler.setServer(this);
+        handler.setHandler(this.getHandler());
+        this.addBean(handler);
+        // Tell the server we want to try and shutdown gracefully
+        // this means that the server will stop accepting new connections
+        // right away but it will continue to process the ones that
+        // are in execution for the given timeout before attempting to stop
+        // NOTE: this is *not* a blocking method, it just sets a parameter
+        //       that _server.stop() will rely on
+        this.setStopTimeout(30000);
 
         // Enable context autoreloading
         if (Configurations.getBoolean("refine.autoreload",false)) {
@@ -210,7 +229,7 @@ class RefineServer extends Server {
             if (threadPool != null) {
                 threadPool.shutdown();
             }
-            
+            Thread.sleep(3000);
             // then let the parent stop
             super.doStop();
         } catch (InterruptedException e) {
@@ -260,7 +279,11 @@ class RefineServer extends Server {
             }
         });
 
-        scanner.start();
+        try {
+            scanner.start();
+        } catch (Exception e) {
+            e.printStackTrace();
+        }
     }
     
     static private void findFiles(final String extension, File baseDir, final Collection<File> found) {
@@ -502,14 +525,6 @@ class ShutdownSignalHandler implements Runnable {
     @Override
     public void run() {
 
-        // Tell the server we want to try and shutdown gracefully
-        // this means that the server will stop accepting new connections
-        // right away but it will continue to process the ones that
-        // are in execution for the given timeout before attempting to stop
-        // NOTE: this is *not* a blocking method, it just sets a parameter
-        //       that _server.stop() will rely on
-        _server.setGracefulShutdown(3000);
-
         try {
             _server.stop();
         } catch (Exception e) {

server/src/com/google/util/threads/ThreadPoolExecutorAdapter.java

@@ -19,9 +19,9 @@ import java.util.concurrent.RejectedExecutionException;
 import java.util.concurrent.ThreadPoolExecutor;
 import java.util.concurrent.TimeUnit;
 
-import org.mortbay.component.LifeCycle;
+import org.eclipse.jetty.util.component.LifeCycle;
-import org.mortbay.log.Log;
+import org.eclipse.jetty.util.log.Log;
-import org.mortbay.thread.ThreadPool;
+import org.eclipse.jetty.util.thread.ThreadPool;
 
 /**
  * Jetty {@link ThreadPool} that bridges requests to a
@@ -36,13 +36,11 @@ public class ThreadPoolExecutorAdapter implements ThreadPool, LifeCycle {
     }
 
     @Override
-    public boolean dispatch(Runnable job) {
+    public void execute(Runnable job) {
         try {
             executor.execute(job);
-            return true;
         } catch (RejectedExecutionException e) {
-            Log.warn(e);
+            Log.getLog().warn(e);
-            return false;
         }
     }