Merge pull request #59 from abrami/paper

Paper

src/main/java/org/texttechnologylab/DockerUnifiedUIMAInterface/connection/DUUIWebsocketAlt.java

@@ -5,8 +5,6 @@
 import java.io.ByteArrayInputStream;
 import java.io.IOException;
 import java.net.URI;
-import java.nio.ByteBuffer;
-import java.nio.charset.StandardCharsets;
 import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.List;
@@ -18,6 +16,7 @@
  *
  * Interface between DUUIComposer and WebsocketClient.
  */
+@Deprecated
 public class DUUIWebsocketAlt implements IDUUIConnectionHandler{
 
     private static List<DUUIWebsocketAlt> clients = new ArrayList<>();

src/main/java/org/texttechnologylab/DockerUnifiedUIMAInterface/connection/IDUUIConnectionHandler.java

@@ -3,6 +3,12 @@
 import java.io.ByteArrayInputStream;
 import java.util.List;
 
+/**
+ * Interface for socket connections
+ *
+ * @author Dawit Terefe, Givara Ebo
+ */
+@Deprecated
 public interface IDUUIConnectionHandler {
 
     List<ByteArrayInputStream> send(byte[] jc);

src/main/java/org/texttechnologylab/DockerUnifiedUIMAInterface/connection/WebsocketClient.java

@@ -1,6 +1,7 @@
 package org.texttechnologylab.DockerUnifiedUIMAInterface.connection;
 
 import com.fasterxml.jackson.core.JsonProcessingException;
+import com.fasterxml.jackson.databind.ObjectMapper;
 import org.java_websocket.client.WebSocketClient;
 import org.java_websocket.handshake.ServerHandshake;
 
@@ -15,8 +16,11 @@
 import java.util.stream.Collectors;
 import java.util.stream.Stream;
 
-import com.fasterxml.jackson.databind.ObjectMapper;
-
+/**
+ * Interface for WebSocket connections
+ *
+ * @author David Terefe
+ */
 public class WebsocketClient extends WebSocketClient{
 
     List<byte []> messageStack = new ArrayList<>();
@@ -117,21 +121,21 @@ public void onMessage(ByteBuffer b) {
     public void onMessage(String s) {
 //        System.out.println("[WebsocketClient]: Message Received: " + s);
         System.out.println("[WebsocketClient]: Message Received: ");
-
     }
+
     @Override
     public void onOpen(ServerHandshake serverHandshake) {
         System.out.println("[WebsocketClient]: Opened websocket connection...");
-
     }
 
     @Override
     public void onClose(int i, String s, boolean b) {
         System.out.println("[WebsocketClient]: CLOSED: i="+i+", s="+s+", b="+b );
-
     }
 
     @Override
     public void onError(Exception e) {
+        System.err.println("[WebsocketClient]: ERROR:" + e.getMessage());
+        e.getStackTrace();
     }
 }

src/main/java/org/texttechnologylab/DockerUnifiedUIMAInterface/connection/mongodb/MongoDBConnectionHandler.java

@@ -262,14 +262,5 @@ public Set<String> listCollections() {
         return rSet;
     }
 
-
-    public String createIndex(String sCollection, String sField) {
-
-        BasicDBObject query = new BasicDBObject();
-        query.put(sField, "text");
-        String rString = this.getCollection(sCollection).createIndex(query);
-
-        return rString;
-    }
 }
 

src/main/java/org/texttechnologylab/DockerUnifiedUIMAInterface/driver/DUUIDockerDriver.java

@@ -46,10 +46,19 @@
 
 import static java.lang.String.format;
 
+/**
+ * Interface for all drivers
+ *
+ * @author Alexander Leonhardt
+ */
 interface ResponsiveMessageCallback {
     public void operation(String message);
 }
 
+/**
+ * Driver for the use of Docker
+ * @author Alexander Leonhardt
+ */
 public class DUUIDockerDriver implements IDUUIDriverInterface {
     private DUUIDockerInterface _interface;
     private HttpClient _client;
@@ -78,6 +87,13 @@ public DUUIDockerDriver() throws IOException, UIMAException, SAXException {
         _luaContext = null;
     }
 
+    /**
+     * Constructor with built-in timeout
+     * @param timeout
+     * @throws IOException
+     * @throws UIMAException
+     * @throws SAXException
+     */
     public DUUIDockerDriver(int timeout) throws IOException, UIMAException, SAXException {
         _interface = new DUUIDockerInterface();
         _client = HttpClient.newBuilder().connectTimeout(Duration.ofSeconds(timeout)).build();
@@ -87,16 +103,18 @@ public DUUIDockerDriver(int timeout) throws IOException, UIMAException, SAXExcep
         _active_components = new HashMap<String, InstantiatedComponent>();
     }
 
-    public void setLuaContext(DUUILuaContext luaContext) {
-        _luaContext = luaContext;
-    }
-
-    public DUUIDockerDriver withTimeout(int container_timeout_ms) {
-        _container_timeout = container_timeout_ms;
-        return this;
-    }
-
-    // TODO: Fragen, ob ich eine analoge Funktion auch für den KubernetesDriver schreiben sollte.
+    /**
+     * Creation of the communication layer based on the Driver
+     * @param url
+     * @param jc
+     * @param timeout_ms
+     * @param client
+     * @param printfunc
+     * @param context
+     * @param skipVerification
+     * @return
+     * @throws Exception
+     */
     public static IDUUICommunicationLayer responsiveAfterTime(String url, JCas jc, int timeout_ms, HttpClient client, ResponsiveMessageCallback printfunc, DUUILuaContext context, boolean skipVerification) throws Exception {
         long start = System.currentTimeMillis();
         IDUUICommunicationLayer layer = new DUUIFallbackCommunicationLayer();  // Hier wird layer zum ersten mal erstellt.
@@ -139,8 +157,6 @@ else if(e instanceof CompletionException){
                     String body2 = new String(resp.body(), Charset.defaultCharset());
                     try {
                         printfunc.operation("Component lua communication layer, loading...");
-
-//                        System.out.printf("Got script %s\n", body2);
                         IDUUICommunicationLayer lua_com = new DUUILuaCommunicationLayer(body2,"requester",context);
                         layer = lua_com;
                         printfunc.operation("Component lua communication layer, loaded.");
@@ -211,10 +227,41 @@ else if(e instanceof CompletionException){
                 }
     }
 
+    /**
+     * Set Lua-Context
+     * @param luaContext
+     */
+    public void setLuaContext(DUUILuaContext luaContext) {
+        _luaContext = luaContext;
+    }
+
+    /**
+     * Set Timeout
+     * @param container_timeout_ms
+     * @return
+     */
+    public DUUIDockerDriver withTimeout(int container_timeout_ms) {
+        _container_timeout = container_timeout_ms;
+        return this;
+    }
+
+    /**
+     * Check whether the image is available.
+     * @param comp
+     * @return
+     */
     public boolean canAccept(DUUIPipelineComponent comp) {
         return comp.getDockerImageName()!=null;
     }
 
+    /**
+     * Instantiate the component
+     * @param component
+     * @param jc
+     * @param skipVerification
+     * @return
+     * @throws Exception
+     */
     public String instantiate(DUUIPipelineComponent component, JCas jc, boolean skipVerification) throws Exception {
         String uuid = UUID.randomUUID().toString();
         while (_active_components.containsKey(uuid.toString())) {
@@ -293,6 +340,10 @@ public String instantiate(DUUIPipelineComponent component, JCas jc, boolean skip
         return uuid;
     }
 
+    /**
+     * Show the maximum parallelism
+     * @param uuid
+     */
     public void printConcurrencyGraph(String uuid) {
         InstantiatedComponent component = _active_components.get(uuid);
         if (component == null) {
@@ -301,6 +352,16 @@ public void printConcurrencyGraph(String uuid) {
         System.out.printf("[DockerLocalDriver][%s]: Maximum concurrency %d\n",uuid,component.getInstances().size());
     }
 
+    /**
+     * Return the TypeSystem used by the given Component
+     * @param uuid
+     * @return
+     * @throws InterruptedException
+     * @throws IOException
+     * @throws SAXException
+     * @throws CompressorException
+     * @throws ResourceInitializationException
+     */
     public TypeSystemDescription get_typesystem(String uuid) throws InterruptedException, IOException, SAXException, CompressorException, ResourceInitializationException {
         InstantiatedComponent comp = _active_components.get(uuid);
         if (comp == null) {
@@ -309,6 +370,17 @@ public TypeSystemDescription get_typesystem(String uuid) throws InterruptedExcep
         return IDUUIInstantiatedPipelineComponent.getTypesystem(uuid,comp);
     }
 
+    /**
+     * Execute a component in the driver
+     * @param uuid
+     * @param aCas
+     * @param perf
+     * @throws InterruptedException
+     * @throws IOException
+     * @throws SAXException
+     * @throws CompressorException
+     * @throws CASException
+     */
     public void run(String uuid, JCas aCas, DUUIPipelineDocumentPerformance perf) throws InterruptedException, IOException, SAXException, CompressorException, CASException {
         long mutexStart = System.nanoTime();
         InstantiatedComponent comp = _active_components.get(uuid);
@@ -323,10 +395,18 @@ public void run(String uuid, JCas aCas, DUUIPipelineDocumentPerformance perf) th
         }
     }
 
+    /**
+     * Shutdown of the Docker-Driver
+     * @hidden
+     */
     public void shutdown() {
 
     }
 
+    /**
+     * Terminate a component
+     * @param uuid
+     */
     public void destroy(String uuid) {
         InstantiatedComponent comp = _active_components.remove(uuid);
         if (comp == null) {

src/main/java/org/texttechnologylab/DockerUnifiedUIMAInterface/driver/DUUIKubernetesDriver.java

@@ -37,6 +37,11 @@
 import static io.fabric8.kubernetes.client.impl.KubernetesClientImpl.logger;
 import static java.lang.String.format;
 
+/**
+ * Driver for the running of components in Kubernetes
+ *
+ * @author Markos Genios, Filip Fitzermann
+ */
 public class DUUIKubernetesDriver implements IDUUIDriverInterface {
 
     private final KubernetesClient _kube_client;

src/main/java/org/texttechnologylab/DockerUnifiedUIMAInterface/driver/IDUUIDriverInterface.java

@@ -13,6 +13,11 @@
 
 import java.io.IOException;
 
+/**
+ * Interface for all drivers
+ *
+ * @author Alexander Leonhardt
+ */
 public interface IDUUIDriverInterface {
     public void setLuaContext(DUUILuaContext luaContext);
     public boolean canAccept(DUUIPipelineComponent component) throws InvalidXMLException, IOException, SAXException;

src/main/java/org/texttechnologylab/DockerUnifiedUIMAInterface/io/DUUIAsynchronousProcessor.java

@@ -9,8 +9,7 @@
 import java.util.stream.LongStream;
 
 /**
- * Class for asynchronous processing of DUUI processes
- *
+ * Class for asynchronous processing of DUUI readers
  * @author Giuseppe Abrami
  */
 public class DUUIAsynchronousProcessor {

src/main/java/org/texttechnologylab/DockerUnifiedUIMAInterface/io/DUUICollectionReader.java

@@ -5,19 +5,39 @@
 
 /**
  * Interface for a CollectionReader
- *
  * @author Giuseppe Abrami
  */
 public interface DUUICollectionReader {
 
+    /**
+     * Get the Progress
+     *
+     * @return
+     */
     ProgressMeter getProgress();
 
+    /**
+     * Fill and get the next JCas
+     * @param pCas
+     */
     public void getNextCas(JCas pCas);
 
+    /**
+     * Are there still cas to be processed?
+     * @return
+     */
     public boolean hasNext();
 
+    /**
+     * Get size of Collection
+     * @return
+     */
     long getSize();
 
+    /**
+     * How many JCas have already been processed?
+     * @return
+     */
     long getDone();
 
 }

src/main/java/org/texttechnologylab/DockerUnifiedUIMAInterface/io/SerializeJSON.java

@@ -1,7 +1,16 @@
 package org.texttechnologylab.DockerUnifiedUIMAInterface.io;
 
+/**
+ * Serialization interface
+ *
+ * @param <T>
+ */
 public interface SerializeJSON<T> {
 
+    /**
+     * Serialize
+     * @return
+     */
     String serialize();
 
 }