Merge pull request #106 from texttechnologylab/uima-3

Added latest Updates

src/main/java/org/texttechnologylab/DockerUnifiedUIMAInterface/DUUIDockerInterface.java

@@ -9,13 +9,17 @@
 import com.github.dockerjava.api.model.*;
 import com.github.dockerjava.core.DockerClientBuilder;
 import com.github.dockerjava.core.command.LogContainerResultCallback;
+import com.github.dockerjava.httpclient5.ApacheDockerHttpClient;
+import com.github.dockerjava.transport.DockerHttpClient;
 import com.google.common.collect.ImmutableList;
 
 import java.io.File;
 import java.io.IOException;
+import java.net.URI;
 import java.nio.file.Path;
 import java.nio.file.Paths;
 import java.security.InvalidParameterException;
+import java.time.Duration;
 import java.util.ArrayList;
 import java.util.LinkedList;
 import java.util.List;
@@ -162,22 +166,21 @@ public class DUUIDockerInterface {
      */
     public DUUIDockerInterface() throws IOException {
 
-        // GREAT TODO!!!
-        //URI dockerClientURI;
-        //if (System.getProperty("os.name").toLowerCase().contains("windows")) {
-        //    dockerClientURI = URI.create("npipe:////./pipe/docker_engine");
-        //} else {
-        //    dockerClientURI = URI.create("tcp://localhost:2375");
-        //}
-
-        //_docker = DockerClientBuilder.getInstance()
-//            .withDockerHttpClient(new ApacheDockerHttpClient.Builder()
-//                .dockerHost(dockerClientURI).build()).build();
-        _docker = DockerClientBuilder.getInstance().build();
-
+        if (!System.getProperty("os.name").contains("Windows")) {
+            _docker = DockerClientBuilder.getInstance().build();
+        } else {
+            // Windows
+            final DockerHttpClient http = new ApacheDockerHttpClient.Builder()
+                    .connectionTimeout(Duration.ofSeconds(5))
+                    .responseTimeout(Duration.ofMinutes(10))
+                    .dockerHost(URI.create("npipe:////./pipe/docker_engine"))
+                    // .dockerHost(URI.create("tcp://127.0.0.1:2375")) // if npipe doesn't work.
+                    .build();
+            _docker = DockerClientBuilder.getInstance()
+                    .withDockerHttpClient(http)
+                    .build();
 
-//        DockerClientConfig config = DefaultDockerClientConfig.createDefaultConfigBuilder().withDockerHost("tcp://localhost:2375").build();
-//        _docker = DockerClientBuilder.getInstance(config).build();
+        }
     }
 
     /**

src/main/java/org/texttechnologylab/DockerUnifiedUIMAInterface/IDUUICommunicationLayer.java

@@ -20,38 +20,43 @@ public interface IDUUICommunicationLayer {
 
   public void deserialize(JCas jc, ByteArrayInputStream input, String targetView) throws IOException, SAXException, CASException;
 
-    /**
-     * Serializes a JCas to a byte array output stream by using the LUA script provided by the component.
-     * @param jc Input JCas.
-     * @param out Output stream, i.e. the input to the component.
-     * @param parameters Parameters for use in the LUA script.
-     * @throws CompressorException
-     * @throws IOException
-     * @throws SAXException
-     */
-    public void serialize(JCas jc, ByteArrayOutputStream out, Map<String, String> parameters) throws CompressorException, IOException, SAXException, CASException;
-
-    /**
-     * Deserializes a byte array input stream to a JCas by using the LUA script provided by the component.
-     * @param jc Output JCas, note that the CAS is not reset before deserialization.
-     * @param input Input stream, i.e. the output of the component.
-     * @throws IOException
-     * @throws SAXException
-     */
-    public void deserialize(JCas jc, ByteArrayInputStream input) throws IOException, SAXException, CASException;
-
-    /**
-     *
-     * @return
-     */
-    public IDUUICommunicationLayer copy();
-
-    /**
-     *
-     * @param results
-     * @return
-     */
-    public ByteArrayInputStream merge(List<ByteArrayInputStream> results);
-
-    String myLuaTestMerging();
+  /**
+   * Serializes a JCas to a byte array output stream by using the LUA script provided by the component.
+   * @param jc Input JCas.
+   * @param out Output stream, i.e. the input to the component.
+   * @param parameters Parameters for use in the LUA script.
+   * @throws CompressorException
+   * @throws IOException
+   * @throws SAXException
+   */
+  default void serialize(JCas jc, ByteArrayOutputStream out, Map<String,String> parameters) throws CompressorException, IOException, SAXException, CASException {
+    serialize(jc, out, parameters, "_InitialView");
+  }
+
+  /**
+   * Deserializes a byte array input stream to a JCas by using the LUA script provided by the component.
+   * @param jc Output JCas, note that the CAS is not reset before deserialization.
+   * @param input Input stream, i.e. the output of the component.
+   * @throws IOException
+   * @throws SAXException
+   */
+  default void deserialize(JCas jc, ByteArrayInputStream input) throws IOException, SAXException, CASException {
+    deserialize(jc, input, "_InitialView");
+  }
+
+  /**
+   *
+   * @return
+   */
+  public IDUUICommunicationLayer copy();
+
+  /**
+   *
+   * @param results
+   * @return
+   */
+  public ByteArrayInputStream merge(List<ByteArrayInputStream> results);
+
+  String myLuaTestMerging();
+
 }

src/main/java/org/texttechnologylab/DockerUnifiedUIMAInterface/document_handler/DUUIDropboxDocumentHandler.java

@@ -12,7 +12,6 @@
 import java.util.ArrayList;
 import java.util.List;
 import java.util.Objects;
-import java.util.concurrent.ConcurrentLinkedQueue;
 import java.util.stream.Collectors;
 
 
@@ -281,47 +280,31 @@ public List<DUUIDocument> listDocuments(String path, String fileExtension, boole
 
     @Override
     public DUUIFolder getFolderStructure() {
+        return getFolderStructure("", "Files");
+    }
 
-        DUUIFolder root = new DUUIFolder("", "Files");
+    public DUUIFolder getFolderStructure(String path, String name) {
 
-        listFolderContents(root);
+        DUUIFolder root = new DUUIFolder(path, name);
 
-        return root;
-    }
+        ListFolderResult result = null;
 
-    /**
-     * Recursively traverses the dropbox directory and saves the directory
-     * tree in the root folder.
-     *
-     * @param root Root folder containing entire directory structure
-     */
-    private void listFolderContents(DUUIFolder root) {
         try {
-            ListFolderResult result = client.files().listFolderBuilder(root.id)
-                    .withRecursive(false)
-                    .withIncludeMediaInfo(false)
-                    .withIncludeDeleted(false)
-                    .withIncludeHasExplicitSharedMembers(false)
-                    .withIncludeMountedFolders(true)
-                    .withLimit(2000L)
+            result = client
+                    .files()
+                    .listFolderBuilder(path)
                     .start();
 
-            do {
-                result.getEntries().parallelStream()
-                        .filter(entry -> entry instanceof FolderMetadata)
-                        .map(entry -> (FolderMetadata) entry)
-                        .map(entry -> new DUUIFolder(entry.getPathDisplay(), entry.getName()))
-                        .peek(root::addChild)
-                        .forEach(this::listFolderContents);
-
-                if (result.getHasMore()) {
-                    result = client.files().listFolderContinue(result.getCursor());
-                } else break;
-
-            } while (true);
-        } catch (Exception e) {
-            new RuntimeException(e);
+        } catch (DbxException e) {
+            return null;
         }
 
+        result.getEntries().stream()
+            .filter(f -> f instanceof FolderMetadata)
+            .map(f -> getFolderStructure(((FolderMetadata) f).getId(), f.getName()))
+            .filter(Objects::nonNull)
+            .forEach(root::addChild);
+
+        return root;
     }
 }

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

@@ -665,6 +665,6 @@ public DUUISegmentationStrategy getSegmentationStrategy() {
     }
 
     public long getTimeout() {
-        return Long.valueOf(_options.getOrDefault(timeout, "60l"));
+        return Long.valueOf(_options.getOrDefault(timeout, "60"));
     }
 }

src/main/java/org/texttechnologylab/DockerUnifiedUIMAInterface/io/reader/DUUIYouTubeReader.java

@@ -461,8 +461,11 @@ private void setVideoMetadata(YouTubeVideo video, JCas jCas) throws IOException,
 
             FSList<Playlist> list = FSList.create(jCas, playlists);
             list.addToIndexes();
+
+            youTube.setPlaylist(list);
         }
 
+        youTube.setName(video._title);
         youTube.setUrl(video.getVideoUrl());
         youTube.setChannelName(video._channelName);
         youTube.setChannelURL(video._channelUrl);

src/main/java/org/texttechnologylab/DockerUnifiedUIMAInterface/tools/MultimodalUtil.java

@@ -445,16 +445,39 @@ private static void executeFFMpeg(String absoluteInputPath, List<String> command
         }
     }
 
+    /**
+     * Gets subimages as independent image files in .png
+     * @param jCas The JCas containing SubImage Annotations
+     * @return A List of files, each containing a SubImage. Files get deleted on exit
+     */
     public static List<File> getSubImages(JCas jCas){
-        return getSubImages(jCas, null);
+        return getSubImages(jCas, "png");
     }
 
-    public static List<File> getSubImages(JCas jCas, String overrideExtension) {
+    /**
+     * Gets subimages as independent image files
+     * @param jCas The JCas containing SubImage Annotations
+     * @param extension Changes the subimages images file extension
+     * @return A List of files, each containing a SubImage. Files get deleted on exit
+     */
+    public static List<File> getSubImages(JCas jCas, String extension) {
+
+        if(extension.startsWith("."))
+            extension = extension.substring(1);
+        String finalExtension = extension;
+
 
         List<File> subImages = new ArrayList<>();
 
         JCasUtil.select(jCas, SubImage.class).forEach(subImage -> {
-            byte[] base64Image = Base64.decodeBase64(subImage.getParent().getSrc());
+            String mainImageB64 = "";
+            if(subImage.getParent().getSrc() == null){
+                mainImageB64 = jCas.getSofaDataString();
+            }else{
+                mainImageB64 = subImage.getParent().getSrc();
+            }
+
+            byte[] base64Image = Base64.decodeBase64(mainImageB64);
             try {
                 BufferedImage bImage = ImageIO.read(new ByteArrayInputStream(base64Image));
 
@@ -468,45 +491,28 @@ public static List<File> getSubImages(JCas jCas, String overrideExtension) {
 
                 Rectangle bounds = polygon.getBounds();
 
-                BufferedImage bSubImage = new BufferedImage(bounds.width, bounds.height, BufferedImage.TYPE_INT_RGB);
-
-                Graphics2D graphics = bSubImage.createGraphics();
-
-                polygon.translate(-bounds.x, -bounds.y);
-
-                graphics.setClip(polygon);
-                graphics.drawImage(bImage, -bounds.x, -bounds.y, null);
-
-                // Create file
-
-                File tempInputFile = new File("tempInputImage");
-                tempInputFile.deleteOnExit();
-                try (OutputStream stream = new FileOutputStream(tempInputFile)) {
-                    stream.write(base64Image);
-                }
-
-                String mimeType = Files.probeContentType(tempInputFile.toPath());
-                String subType = "";
-
-                if(overrideExtension == null){
-                    if(mimeType != null && !mimeType.isEmpty()){
-                        subType = mimeType.split("/")[1];
-                    }else{
-                        subType = "jpg";
-                    }
-                }else{
-                    subType = overrideExtension;
-                    if(subType.startsWith(".")){
-                        if(subType.length() > 1)
-                            subType = subType.substring(1);
+                BufferedImage bSubImage;
+                if(finalExtension.equals("png") || finalExtension.equals("tiff") || finalExtension.equals("gif") || finalExtension.equals("apng"))
+                    bSubImage = new BufferedImage(bounds.width, bounds.height, BufferedImage.TYPE_INT_ARGB);  // Alpha channel support
+                else
+                    bSubImage = new BufferedImage(bounds.width, bounds.height, BufferedImage.TYPE_INT_RGB);  // No alpha
+
+                // Copy pixels form main image to new subimage
+                for (int x = bounds.x; x < bounds.x + bounds.width; x++) {
+                    for (int y = bounds.y; y < bounds.y + bounds.height; y++) {
+                        if(polygon.contains(x, y)){
+                            int iColor = bImage.getRGB(x, y);
+                            bSubImage.setRGB(x - bounds.x, y - bounds.y, iColor);
+                        }
                     }
                 }
 
-                File outputFile = new File(getOutputName(jCas, subImage, subType));
+                // Create output file
+                File outputFile = new File(getOutputName(jCas, subImage, finalExtension));
                 outputFile.deleteOnExit();
 
                 RenderedImage rendImage = bSubImage;
-                ImageIO.write(rendImage, subType, outputFile);
+                ImageIO.write(rendImage, finalExtension, outputFile);
 
                 subImages.add(outputFile);
             } catch (IOException e) {

src/test/java/TestDUUI.java

@@ -1171,7 +1171,6 @@ public void multimodalImageCutterTest() throws Exception{
 
         composer.add(new DUUIDockerDriver.Component("duui-yolo:latest")  // Image detection
                 .withScale(iWorkers)
-                .withRunningAfterDestroy(true)
                 .build());
 
         composer.add(new DUUIUIMADriver.Component(createEngineDescription(XmiWriter.class,