docs

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

@@ -4,24 +4,36 @@
 import org.apache.commons.compress.compressors.CompressorInputStream;
 import org.apache.commons.compress.compressors.CompressorOutputStream;
 import org.apache.commons.compress.compressors.CompressorStreamFactory;
-import org.apache.uima.util.TypeSystemUtil;
 
 import java.io.ByteArrayInputStream;
 import java.io.ByteArrayOutputStream;
 import java.io.IOException;
-import java.io.StringWriter;
 import java.nio.charset.StandardCharsets;
 import java.util.Base64;
 
+/**
+ * Helper class for compression and decompression of strings.
+ */
 public class DUUICompressionHelper {
     CompressorStreamFactory _factory;
     String _method;
 
+    /**
+     * Constructor using a {@link CompressorStreamFactory} and a compression method.
+     * @param method
+     */
     public DUUICompressionHelper(String method) {
         _factory = new CompressorStreamFactory();
         _method = method;
     }
 
+    /**
+     * Compresses a string.
+     * @param input The string to compress.
+     * @return The compressed string as a base64 encoded string.
+     * @throws IOException
+     * @throws CompressorException
+     */
     public String compress(String input) throws IOException, CompressorException {
         ByteArrayOutputStream out = new ByteArrayOutputStream();
         CompressorOutputStream output = _factory.createCompressorOutputStream(_method,out);
@@ -30,6 +42,13 @@ public String compress(String input) throws IOException, CompressorException {
         return new String(Base64.getEncoder().encode(out.toByteArray()), StandardCharsets.UTF_8);
     }
 
+    /**
+     * Decompresses a string.
+     * @param input The compressed string as a base64 encoded string.
+     * @return The decompressed string.
+     * @throws IOException
+     * @throws CompressorException
+     */
     public String decompress(String input) throws IOException, CompressorException {
         ByteArrayInputStream inputstream = new ByteArrayInputStream(Base64.getDecoder().decode(input.getBytes(StandardCharsets.UTF_8)));
         CompressorInputStream inpst = _factory.createCompressorInputStream(_method, inputstream);

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

@@ -10,13 +10,24 @@
 import java.net.URISyntaxException;
 import java.util.Vector;
 
+/**
+ * Description of a pipeline for the DUUI composer that holds all components.
+ */
 public class DUUIPipelineDescription {
     private Vector<DUUIPipelineAnnotationComponent> _components;
 
+    /**
+     * Constructor
+     * @param components List of components of the pipeline.
+     */
     public DUUIPipelineDescription(Vector<DUUIPipelineAnnotationComponent> components) {
         _components = components;
     }
 
+    /**
+     * Get the components of the pipeline.
+     * @return List of components.
+     */
     public Vector<DUUIPipelineAnnotationComponent> getComponents() {
         return _components;
     }

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

@@ -8,10 +8,41 @@
 import java.util.List;
 import java.util.Map;
 
+/**
+ * Interface for communication between the DUUI composer {@link DUUIComposer} and the components {@link org.texttechnologylab.DockerUnifiedUIMAInterface.driver.IDUUIDriverInterface}.
+ */
 public interface IDUUICommunicationLayer {
+    /**
+     * 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;
+
+    /**
+     * 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;
+
+    /**
+     *
+     * @return
+     */
     public IDUUICommunicationLayer copy();
+
+    /**
+     *
+     * @param results
+     * @return
+     */
     public ByteArrayInputStream merge(List<ByteArrayInputStream> results);
 
     String myLuaTestMerging();

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

@@ -5,6 +5,9 @@
 import java.util.List;
 import java.util.concurrent.Future;
 
+/**
+ * Interface for execution plans of the DUUI composer pipleine.
+ */
 public interface IDUUIExecutionPlan {
     public List<IDUUIExecutionPlan> getNextExecutionPlans();
 

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

@@ -2,6 +2,14 @@
 
 import org.apache.uima.jcas.JCas;
 
+/**
+ * Interface for generating execution plans {@link IDUUIExecutionPlan}.
+ */
 public interface IDUUIExecutionPlanGenerator {
+    /**
+     * Generates an execution plan for a given JCas.
+     * @param jc The JCas to generate the execution plan for.
+     * @return The generated execution plan.
+     */
     public IDUUIExecutionPlan generate(JCas jc);
 }