Merge pull request #6 from gprodriguez/master

Merge

README.md

@@ -5,7 +5,12 @@
 ## Dummy Server in Java ##
 The code provided in this Github page is an Annotation Server prototype built in Java language. 
 
-The Dummy Server is designed to help researchers and developers to build a simply system in order to listen and respond BeCalm requests as quickly as possible, during the TIPS task in the BioCreative V.5 competition.
+The Dummy Server is designed to help researchers and developers to build a simply system in order to listen and respond 
+BeCalm requests as quickly as possible, during the TIPS task in the BioCreative V.5 competition. This example is done using only Java Sockets, so 
+it is recommended the implementation of a more complete and specific solution like 
+[HTTPServer](https://docs.oracle.com/javase/8/docs/jre/api/net/httpserver/spec/com/sun/net/httpserver/package-summary.html "HTTPServer"), 
+[NanoHTTPD](https://github.com/NanoHttpd/nanohttpd "NanoHTTPD") or 
+[Jetty](https://www.eclipse.org/jetty/ "Jetty").
 
 ### Glossary ###
 * [BioCreative V.5 competition](https://biocreative.bioinformatics.udel.edu/resources/publications/bcv5_proceedings "BioCreative V.5 competition")
@@ -17,8 +22,13 @@ Clone the repository and make a JAR (select the main class Server) or simply dow
 
 `java [-Xmx2G] [-Xms256M] -server -jar dummyserver.jar`
 
-Note that, the parameters between brackets are optional. However, it may be interesting to modify the maximum memory allocation and the initial memory allocation pool when starting the JVM (-Xmx and -Xms, respectively).
+Note that, the parameters between brackets are optional. However, it may be interesting to modify the maximum memory allocation and the initial memory allocation pool when starting the JVM (`-Xmx` and `-Xms`, respectively).
+
+Once the Annotation Server is running, it will be possible to make requests! At this point, you have two options to test the dummy server:
+
+1. If you clone the code and open it in a IDE, you will see a JUnit test to make this requests automatically. To do this, you must execute the Server class first. This JUnit test will send random requests to test the `getState` and `getAnnotations` methods.
+2. You can send POST requests to `127.0.0.1:8088` to test the `getState` method. The requests must be in JSON format and it is mandatory to use the correct `becalm_key`. See the following example:
+`curl -H "Content-Type: application/json" -X POST http://127.0.0.1:8088 -d "{\"name\": \"BeCalm\",\"method\": \"getState\",\"becalm_key\": \"b907e0df6bbc124844ae97dea98d3d0fc059c133\",\"custom_parameters\": {\"example\": true},\"parameters\": {}}"`
 
-Once the Annotation Server is running, it will be possible to make requests! If you clone the code and open it in a IDE, you will see a JUnit test to make this requests automatically. To do this, you must execute the Server class first.
 ### License ###
 Copyright © 2019, Aitor Blanco Míguez. Released under the Unlicense license.

src/main/java/es/uvigo/ei/sing/dummyserver/Functions.java

@@ -0,0 +1,39 @@
+package es.uvigo.ei.sing.dummyserver;
+
+import java.io.BufferedReader;
+import java.io.IOException;
+import java.io.PrintWriter;
+
+public class Functions {
+    public static String parseRequest(BufferedReader in) {
+        StringBuilder requestJson = new StringBuilder();
+
+        try {
+            // Read the headers
+            String headerLine;
+            while (!(headerLine = in.readLine()).isEmpty()) {
+                // TODO: Do something with the headers...
+            }
+
+            // Read the body (JSON)
+            while (in.ready()) {
+                // TODO: Do some content validations...
+                requestJson.append((char) in.read());
+            }
+        } catch (IOException e) {
+            e.printStackTrace();
+        }
+
+        return requestJson.toString();
+    }
+
+    public static void writeHeadersAndMessage(PrintWriter out, String message) {
+        // TODO: Add the desired headers...
+        out.println("POST  HTTP/1.1");
+        out.println("Content-Length:" + message.length());
+        out.println("Content-Type: application/json; charset=utf-8");
+        out.println("");
+        out.println(message);
+        out.flush();
+    }
+}

src/main/java/es/uvigo/ei/sing/dummyserver/Server.java

@@ -22,7 +22,7 @@ public static void main(String[] args) throws IOException {
         // Keep listening until a request is received
         while (listening)
             new ServerThread(serverSocket.accept()).start();
-        System.out.println("server> Server stoped");
+        System.out.println("server> Server stopped");
 
         serverSocket.close();
     }

src/main/java/es/uvigo/ei/sing/dummyserver/ServerThread.java

@@ -4,11 +4,10 @@
 import org.json.JSONException;
 import org.json.JSONObject;
 
-import java.io.IOException;
-import java.io.ObjectInputStream;
-import java.io.ObjectOutputStream;
+import java.io.*;
 import java.lang.management.ManagementFactory;
 import java.net.Socket;
+import java.nio.charset.StandardCharsets;
 import java.util.concurrent.CompletableFuture;
 
 import static es.uvigo.ei.sing.dummyserver.Constants.REQUEST_SECRET_KEY;
@@ -18,7 +17,6 @@
 @SuppressWarnings("restriction")
 public class ServerThread extends Thread {
     private Socket socket;
-    private Socket requestSocket;
 
     public ServerThread(Socket socket) {
         super("ServerThread");
@@ -30,11 +28,12 @@ public void run() {
             // Get the CPU state
             final OperatingSystemMXBean operatingSystemMXBean = (OperatingSystemMXBean) ManagementFactory.getOperatingSystemMXBean();
 
-            // Get the request
-            final ObjectOutputStream out = new ObjectOutputStream(socket.getOutputStream());
+            // Create the output stream to send the response
+            final PrintWriter out = new PrintWriter(new OutputStreamWriter(socket.getOutputStream(), StandardCharsets.UTF_8));
             out.flush();
-            final ObjectInputStream in = new ObjectInputStream(socket.getInputStream());
-            final String clientRequest = (String) in.readObject();
+            // Get the request (JSON format)
+            final BufferedReader in = new BufferedReader(new InputStreamReader(socket.getInputStream()));
+            final String clientRequest = Functions.parseRequest(in);
 
             // Transform the request to a JSON
             final JSONObject json = new JSONObject(clientRequest);
@@ -55,62 +54,63 @@ public void run() {
                         message = "{\"status\": 200, \"success\": true, \"becalm_key\":\"" + REST_API_KEY + "\", \"data\": {" +
                                 "\"state\":\"" + state + "\", \"version\":\"4.4.3\", \"version_changes\":\"Description of changes\", " +
                                 "\"max_analyzable_documents\":\"515\"} }";
-                        out.writeObject(message);
-                        out.flush();
+                        Functions.writeHeadersAndMessage(out, message);
                         break;
                     case "getAnnotations":
                         // TODO: getAnnotations method. Do something...
 
                         message = "{\"status\": 200, \"success\": true, \"becalm_key\":\"" + REST_API_KEY + "\", \"data\": {} }";
-                        out.writeObject(message);
-                        out.flush();
+                        Functions.writeHeadersAndMessage(out, message);
                         Thread.sleep(2000);
                         // Send an example annotation
-                        annottatePatents().exceptionally(err -> {
+                        annotatePatents().exceptionally(err -> {
                             System.out.println("Error while getting annotations: " + err);
                             return null;
                         });
                         break;
                     default:
                         // TODO: Invalid method. Do something...
                         message = "{\"status\": 500, \"success\": false, \"becalm_key\":\"" + REST_API_KEY + "\", \"data\": {} }";
-                        out.writeObject(message);
-                        out.flush();
+                        Functions.writeHeadersAndMessage(out, message);
                         break;
                 }
             } else {
                 // Bad key
                 message = "{\"status\": 401, \"success\": false, \"becalm_key\":\"" + REST_API_KEY + "\", \"data\": {} }";
-                out.writeObject(message);
-                out.flush();
+                Functions.writeHeadersAndMessage(out, message);
             }
             System.out.println("server> " + message);
+
+            // Close resources
+            in.close();
+            out.close();
+            socket.close();
         } catch (Exception e) {
             e.printStackTrace();
         }
     }
 
-    private CompletableFuture<Void> annottatePatents() {
+    private CompletableFuture<Void> annotatePatents() {
         // TODO: Method to make the annotations on the text... This only writes a dummy annotation
         return runAsync(() -> {
             final String annotations = "[ {\"document_id\": \"CA2073855C\", \"section\": \"T\", \"init\": 0, " +
                     "\"end\": 14, \"score\": 0.856016, \"annotated_text\": \"Glycoalkaloids\"," +
                     " \"type\": \"unknown\",  \"database_id\": \"ED5266\" } ]";
-            ObjectInputStream in = null;
-            ObjectOutputStream out = null;
+            BufferedReader in = null;
+            PrintWriter out = null;
+            Socket requestSocket = null;
 
             try {
                 requestSocket = new Socket("localhost", Constants.REQUESTERPORT);
                 System.out.println("server> Connected to localhost in port 8089");
-                out = new ObjectOutputStream(requestSocket.getOutputStream());
+                out = new PrintWriter(new OutputStreamWriter(requestSocket.getOutputStream(), StandardCharsets.UTF_8));
                 out.flush();
                 requestSocket.setSoTimeout(5000);
-                in = new ObjectInputStream(requestSocket.getInputStream());
+                in = new BufferedReader(new InputStreamReader(requestSocket.getInputStream()));
 
                 System.out.println("server> " + annotations);
 
-                out.writeObject(annotations);
-                out.flush();
+                Functions.writeHeadersAndMessage(out, annotations);
                 int tries = 0;
                 boolean exit = false;
                 do {
@@ -128,26 +128,27 @@ private CompletableFuture<Void> annottatePatents() {
                 try {
                     in.close();
                     out.close();
-                    requestSocket.close();
+                    if (requestSocket != null)
+                        requestSocket.close();
                 } catch (IOException ioException) {
                     ioException.printStackTrace();
                 }
             }
         });
     }
 
-    private boolean resendAnnotations(ObjectInputStream in, int tries) {
+    private boolean resendAnnotations(BufferedReader in, int tries) {
         try {
             System.out.println("server> Send annotations, try: " + tries);
-            String ok = (String) in.readObject();
+            String ok = in.readLine();
             final JSONObject json = new JSONObject(ok);
             if (json.getInt("status") == 200) {
                 System.out.println("client> " + ok);
                 return true;
             } else {
                 return false;
             }
-        } catch (ClassNotFoundException | IOException | JSONException e) {
+        } catch (IOException | JSONException e) {
             return false;
         }
     }

src/test/java/es/uvigo/ei/sing/dummyserver/Requester.java

@@ -2,12 +2,11 @@
 
 import junit.framework.TestCase;
 
-import java.io.IOException;
-import java.io.ObjectInputStream;
-import java.io.ObjectOutputStream;
+import java.io.*;
 import java.net.ServerSocket;
 import java.net.Socket;
 import java.net.UnknownHostException;
+import java.nio.charset.StandardCharsets;
 import java.util.Random;
 import java.util.concurrent.CompletableFuture;
 
@@ -17,8 +16,8 @@
 public class Requester extends TestCase {
     private ServerSocket serverSocket;
     private Socket requestSocket;
-    private ObjectOutputStream out;
-    private ObjectInputStream in;
+    private PrintWriter out;
+    private BufferedReader in;
 
     public void testRequest() {
         boolean listening = true;
@@ -34,7 +33,7 @@ public void testRequest() {
             while (listening)
                 new ClientThread(serverSocket.accept()).start();
 
-            System.out.println("server> Server stoped");
+            System.out.println("server> Server stopped");
 
             serverSocket.close();
         } catch (IOException e) {
@@ -44,15 +43,15 @@ public void testRequest() {
         assertTrue(true);
     }
 
-    private CompletableFuture<Void> request() throws IOException {
+    private CompletableFuture<Void> request() {
         return runAsync(() -> {
             try {
                 requestSocket = new Socket("localhost", SERVERPORT);
                 System.out.println("client> Connected to localhost in port " + SERVERPORT);
 
-                out = new ObjectOutputStream(requestSocket.getOutputStream());
+                out = new PrintWriter(new OutputStreamWriter(requestSocket.getOutputStream(), StandardCharsets.UTF_8));
                 out.flush();
-                in = new ObjectInputStream(requestSocket.getInputStream());
+                in = new BufferedReader(new InputStreamReader(requestSocket.getInputStream()));
 
                 // Use a random value to request one of the two methods
                 final Random random = new Random();
@@ -61,19 +60,15 @@ private CompletableFuture<Void> request() throws IOException {
                     method = "getAnnotations";
                 final String petition = "{\"name\":\"BeCalm\", \"method\":\"" + method + "\", \"becalm_key\":\"" + REQUEST_SECRET_KEY + "\"," +
                         "\"custom_parameters\" :{\"example\":true}, \"parameters\" : {} }";
-                out.writeObject(petition);
-                out.flush();
+                Functions.writeHeadersAndMessage(out, petition);
 
                 System.out.println("client> " + petition);
 
-                System.out.println("server> " + (String) in.readObject());
-
+                System.out.println("server> " + Functions.parseRequest(in));
             } catch (UnknownHostException unknownHost) {
                 System.err.println("client> You are trying to connect to an unknown host!");
             } catch (IOException ioException) {
                 ioException.printStackTrace();
-            } catch (ClassNotFoundException e) {
-                e.printStackTrace();
             } finally {
                 try {
                     in.close();
@@ -96,15 +91,13 @@ public ClientThread(Socket socket) {
 
         public void run() {
             try {
-                final ObjectOutputStream out = new ObjectOutputStream(this.socket.getOutputStream());
+                final PrintWriter out = new PrintWriter(new OutputStreamWriter(socket.getOutputStream(), StandardCharsets.UTF_8));
                 out.flush();
-                final ObjectInputStream in = new ObjectInputStream(this.socket.getInputStream());
-                System.out.println("server> " + (String) in.readObject());
+                final BufferedReader in = new BufferedReader(new InputStreamReader(socket.getInputStream()));
+                System.out.println("server> " + Functions.parseRequest(in));
                 final String ok = "{\"status\": 200, \"success\": true, \"becalm_key\":\"" + REQUEST_SECRET_KEY + "\", \"data\": {} }";
-                out.writeObject(ok);
-                out.flush();
+                Functions.writeHeadersAndMessage(out, ok);
                 System.out.println("client> " + ok);
-
             } catch (Exception e) {
                 e.printStackTrace();
             }