#442 - Upgrade to UIMAv3

cleartk-corpus/src/main/java/org/cleartk/corpus/conll2005/Conll2005GoldAnnotator.java

@@ -35,6 +35,10 @@
 import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
 import org.apache.uima.cas.CAS;
 import org.apache.uima.cas.CASException;
+import org.apache.uima.fit.component.JCasAnnotator_ImplBase;
+import org.apache.uima.fit.descriptor.ConfigurationParameter;
+import org.apache.uima.fit.descriptor.SofaCapability;
+import org.apache.uima.fit.util.FSCollectionFactory;
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.jcas.cas.FSArray;
 import org.apache.uima.jcas.tcas.Annotation;
@@ -43,16 +47,13 @@
 import org.cleartk.srl.type.Chunk;
 import org.cleartk.srl.type.Predicate;
 import org.cleartk.srl.type.SemanticArgument;
+import org.cleartk.syntax.constituent.type.TerminalTreebankNode;
 import org.cleartk.syntax.constituent.type.TopTreebankNode;
 import org.cleartk.syntax.constituent.type.TreebankNode;
 import org.cleartk.syntax.constituent.type.TreebankNodeUtil;
 import org.cleartk.token.type.Sentence;
 import org.cleartk.token.type.Token;
 import org.cleartk.util.AnnotationUtil;
-import org.apache.uima.fit.component.JCasAnnotator_ImplBase;
-import org.apache.uima.fit.descriptor.ConfigurationParameter;
-import org.apache.uima.fit.descriptor.SofaCapability;
-import org.apache.uima.fit.util.FSCollectionFactory;
 
 /**
  * <br>
@@ -98,14 +99,17 @@ public void process(JCas jCas) throws AnalysisEngineProcessException {
       CharniakParseParser parser = new CharniakParseParser(initView);
 
       int numberOfPredicates = 0;
-      for (Conll2005Line line : conll2005Lines)
-        if (!line.targetVerb.equals("-"))
+      for (Conll2005Line line : conll2005Lines) {
+        if (!line.targetVerb.equals("-")) {
           numberOfPredicates += 1;
+        }
+      }
 
       int currentPredicate = 0;
       PredicateParser predicateParsers[] = new PredicateParser[numberOfPredicates];
-      for (int i = 0; i < numberOfPredicates; i++)
+      for (int i = 0; i < numberOfPredicates; i++) {
         predicateParsers[i] = new PredicateParser(initView);
+      }
 
       NamedEntityParser namedEntityParser = new NamedEntityParser(initView);
 
@@ -128,7 +132,7 @@ public void process(JCas jCas) throws AnalysisEngineProcessException {
         token.setPos(line.pos);
         token.addToIndexes();
 
-        TreebankNode terminal = new TreebankNode(initView, startIndex, endIndex);
+        TerminalTreebankNode terminal = new TerminalTreebankNode(initView, startIndex, endIndex);
         terminal.setNodeType(line.pos);
         terminal.setNodeValue(line.word);
         terminal.setChildren(new FSArray(jCas, 0));
@@ -162,8 +166,9 @@ public void process(JCas jCas) throws AnalysisEngineProcessException {
 
       parser.makeParse();
 
-      for (PredicateParser predicateParser : predicateParsers)
+      for (PredicateParser predicateParser : predicateParsers) {
         predicateParser.makePredicate();
+      }
 
     } catch (CASException e) {
       throw new AnalysisEngineProcessException(e);
@@ -237,8 +242,9 @@ public TreebankNode makeTreebankNode(JCas jCas) {
         node.setNodeType(this.type);
         node.setChildren(new FSArray(jCas, this.children.size()));
         FSCollectionFactory.fillArrayFS(node.getChildren(), this.children);
-        for (TreebankNode child : this.children)
+        for (TreebankNode child : this.children) {
           child.setParent(node);
+        }
         node.addToIndexes();
         return node;
       }
@@ -248,18 +254,18 @@ public TreebankNode makeTreebankNode(JCas jCas) {
   private static class CharniakParseParser {
     Stack<Constituent> parseStack;
 
-    List<TreebankNode> terminals;
+    List<TerminalTreebankNode> terminals;
 
     JCas jCas;
 
     CharniakParseParser(JCas jCas) {
       parseStack = new Stack<Constituent>();
       parseStack.push(new Constituent("TOP"));
-      terminals = new ArrayList<TreebankNode>();
+      terminals = new ArrayList<>();
       this.jCas = jCas;
     }
 
-    void feed(String segment, TreebankNode terminal) throws IOException {
+    void feed(String segment, TerminalTreebankNode terminal) throws IOException {
       BufferedReader r = new BufferedReader(new StringReader(segment));
 
       terminals.add(terminal);
@@ -291,8 +297,9 @@ public TopTreebankNode makeParse() {
       List<TreebankNode> children = parseStack.peek().children;
       node.setChildren(new FSArray(jCas, children.size()));
       FSCollectionFactory.fillArrayFS(node.getChildren(), children);
-      for (TreebankNode child : parseStack.peek().children)
+      for (TreebankNode child : parseStack.peek().children) {
         child.setParent(node);
+      }
       node.setTerminals(new FSArray(jCas, this.terminals.size()));
       FSCollectionFactory.fillArrayFS(node.getTerminals(), this.terminals);
       node.addToIndexes();
@@ -376,8 +383,9 @@ void feed(String segment, Token token) throws IOException {
             this.argumentTokens = null;
             break;
           case '*':
-            if (this.argumentTokens != null)
+            if (this.argumentTokens != null) {
               this.argumentTokens.add(token);
+            }
             break;
           default:
             throw new IOException("unexpected character in string: " + String.valueOf(c) + " ("
@@ -409,8 +417,9 @@ private static String readArgumentType(BufferedReader r) throws IOException {
       while (true) {
         r.mark(1);
         int i = r.read();
-        if (i == -1)
+        if (i == -1) {
           break;
+        }
 
         char c = (char) i;
         if (c == '(' || c == ')' || c == '*') {
@@ -476,8 +485,9 @@ private static String readName(BufferedReader r) throws IOException {
       while (true) {
         r.mark(1);
         int i = r.read();
-        if (i == -1)
+        if (i == -1) {
           break;
+        }
 
         char c = (char) i;
         if (c == '*') {

cleartk-corpus/src/main/java/org/cleartk/corpus/timeml/TempEval2013Writer.java

@@ -30,6 +30,7 @@
 import java.util.Collections;
 import java.util.List;
 import java.util.TreeMap;
+import java.util.function.IntPredicate;
 
 import org.apache.uima.analysis_engine.AnalysisEngineDescription;
 import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
@@ -490,5 +491,35 @@ public int getEnd() {
     public String getCoveredText() {
       throw new UnsupportedOperationException();
     }
+
+    @Override
+    public int _id() {
+      throw new UnsupportedOperationException();
+    }
+
+    @Override
+    public int _getTypeCode() {
+      throw new UnsupportedOperationException();
+    }
+
+    @Override
+    public int getAddress() {
+      throw new UnsupportedOperationException();
+    }
+
+    @Override
+    public void setBegin(int aBegin) {
+      throw new UnsupportedOperationException();
+    }
+
+    @Override
+    public void setEnd(int aEnd) {
+      throw new UnsupportedOperationException();
+    }
+
+    @Override
+    public void trim(IntPredicate aPredicate) {
+      throw new UnsupportedOperationException();
+    }
   }
 }

cleartk-ml-crfsuite/pom.xml

@@ -42,9 +42,23 @@
 			<artifactId>cleartk-ml</artifactId>
 		</dependency>
 		<dependency>
-			<groupId>de.tudarmstadt.ukp.dkpro.core</groupId>
-			<artifactId>de.tudarmstadt.ukp.dkpro.core.api.resources-asl</artifactId>
-			<version>1.6.0</version>
+			<groupId>org.dkpro.core</groupId>
+			<artifactId>dkpro-core-api-resources-asl</artifactId>
+			<version>2.2.0</version>
+			<exclusions>
+				<exclusion>
+					<groupId>org.springframework</groupId>
+					<artifactId>spring-core</artifactId>
+				</exclusion>
+				<exclusion>
+					<groupId>org.springframework</groupId>
+					<artifactId>spring-context</artifactId>
+				</exclusion>
+				<exclusion>
+					<groupId>org.springframework</groupId>
+					<artifactId> spring-beans</artifactId>
+				</exclusion>
+			</exclusions>
 		</dependency>
 		<dependency>
 			<groupId>org.cleartk</groupId>

cleartk-ml-crfsuite/src/main/java/org/cleartk/ml/crfsuite/CrfSuiteWrapper.java

@@ -58,7 +58,7 @@
 import org.cleartk.util.InputStreamHandler;
 import org.cleartk.util.PlatformDetection;
 
-import de.tudarmstadt.ukp.dkpro.core.api.resources.ResourceUtils;
+import org.dkpro.core.api.resources.ResourceUtils;
 
 /**
  * <br>

cleartk-ml-liblinear/src/test/java/org/cleartk/ml/liblinear/LibLinearTest.java

@@ -30,18 +30,12 @@
 import java.util.List;
 import java.util.Map;
 
-import org.apache.commons.lang.SerializationUtils;
+import org.apache.commons.lang3.SerializationUtils;
 import org.cleartk.ml.Feature;
 import org.cleartk.ml.Instance;
 import org.cleartk.ml.jar.DefaultDataWriterFactory;
 import org.cleartk.ml.jar.DirectoryDataWriterFactory;
 import org.cleartk.ml.jar.Train;
-import org.cleartk.ml.liblinear.LibLinearBooleanOutcomeClassifier;
-import org.cleartk.ml.liblinear.LibLinearBooleanOutcomeClassifierBuilder;
-import org.cleartk.ml.liblinear.LibLinearBooleanOutcomeDataWriter;
-import org.cleartk.ml.liblinear.LibLinearStringOutcomeClassifier;
-import org.cleartk.ml.liblinear.LibLinearStringOutcomeClassifierBuilder;
-import org.cleartk.ml.liblinear.LibLinearStringOutcomeDataWriter;
 import org.cleartk.ml.liblinear.ExampleInstanceFactory.BooleanAnnotator;
 import org.cleartk.ml.liblinear.ExampleInstanceFactory.StringAnnotator;
 import org.cleartk.ml.liblinear.encoder.FeatureNodeArrayEncoder;

cleartk-ml-tksvmlight/src/main/java/org/cleartk/ml/tksvmlight/kernel/TreeKernel_ImplBase.java

@@ -26,7 +26,7 @@
 import java.util.ArrayList;
 import java.util.List;
 
-import org.apache.commons.lang.NotImplementedException;
+import org.apache.commons.lang3.NotImplementedException;
 import org.cleartk.ml.tksvmlight.TreeFeature;
 import org.cleartk.ml.tksvmlight.TreeFeatureVector;
 /**
@@ -46,6 +46,7 @@ public abstract class TreeKernel_ImplBase implements ComposableTreeKernel {
 
   protected ForestSumMethod sumMethod = ForestSumMethod.SEQUENTIAL;
 
+  @Override
   public double evaluate(TreeFeatureVector fv1, TreeFeatureVector fv2) {
     double sim = 0.0;
     if (sumMethod == ForestSumMethod.SEQUENTIAL) {
@@ -62,6 +63,7 @@ public double evaluate(TreeFeatureVector fv1, TreeFeatureVector fv2) {
     return sim;
   }
 
+  @Override
   public abstract double evaluate(TreeFeature tf1, TreeFeature tf2);
 
 }

cleartk-ml-weka/src/main/java/org/cleartk/ml/weka/WekaStringOutcomeClassifier.java

@@ -21,7 +21,7 @@
 import java.util.List;
 import java.util.Map;
 
-import org.apache.commons.lang.NotImplementedException;
+import org.apache.commons.lang3.NotImplementedException;
 import org.cleartk.ml.CleartkProcessingException;
 import org.cleartk.ml.Feature;
 import org.cleartk.ml.encoder.features.FeaturesEncoder;

cleartk-ml/pom.xml

@@ -17,7 +17,8 @@
       <groupId>org.cleartk</groupId>
       <artifactId>cleartk-util</artifactId>
     </dependency>
-    <!-- test only -->
+
+		<!-- test only -->
     <dependency>
       <groupId>junit</groupId>
       <artifactId>junit</artifactId>
@@ -38,5 +39,10 @@
       <artifactId>uimaj-document-annotation</artifactId>
       <scope>test</scope>
     </dependency>
+    <dependency>
+      <groupId>org.assertj</groupId>
+      <artifactId>assertj-core</artifactId>
+      <scope>test</scope>
+    </dependency>
   </dependencies>
 </project>

cleartk-ml/src/test/java/org/cleartk/ml/jar/JarDataWriterTest.java

@@ -23,14 +23,15 @@
  */
 package org.cleartk.ml.jar;
 
+import static java.nio.charset.StandardCharsets.UTF_8;
 import static org.assertj.core.api.Assertions.assertThat;
+import static org.assertj.core.api.Assertions.contentOf;
 import static org.junit.Assert.assertTrue;
 
 import java.io.File;
 
 import org.apache.uima.UimaContext;
 import org.apache.uima.fit.factory.UimaContextFactory;
-import org.apache.uima.util.FileUtils;
 import org.cleartk.ml.DataWriter;
 import org.cleartk.ml.encoder.features.FeaturesEncoder_ImplBase;
 import org.cleartk.ml.encoder.features.NameNumberFeaturesEncoder;
@@ -59,10 +60,9 @@ public void testManifest() throws Throwable {
     dataWriter.setFeaturesEncoder(new NameNumberFeaturesEncoder(false, false));
     dataWriter.setOutcomeEncoder(new StringToStringOutcomeEncoder());
     dataWriter.finish();
-    File manifestFile = new File(outputDirectory, "MANIFEST.MF");
-    String actualManifest = FileUtils.file2String(manifestFile);
-
-    assertThat(actualManifest).isEqualToIgnoringWhitespace(expectedManifest);
+
+    assertThat(contentOf(new File(outputDirectory, "MANIFEST.MF"), UTF_8)) //
+        .isEqualToIgnoringWhitespace(expectedManifest);
   }
 
   @Test

cleartk-ml/src/test/java/org/cleartk/ml/viterbi/ViterbiDataWriterTest.java

@@ -118,15 +118,13 @@ public void testConsumeAll() throws Exception {
     String expectedManifest = "Manifest-Version: 1.0\n"
         + "classifierBuilderClass: org.cleartk.ml.viterbi.ViterbiClassifierBuilde\n" + " r";
 
-    File manifestFile = new File(outputDirectoryName, "MANIFEST.MF");
-    String actualManifest = contentOf(manifestFile, UTF_8);
-    assertThat(actualManifest).isEqualToIgnoringWhitespace(expectedManifest);
+    assertThat(contentOf(new File(outputDirectoryName, "MANIFEST.MF"), UTF_8)) //
+        .isEqualToIgnoringWhitespace(expectedManifest);
 
     ViterbiClassifierBuilder<String> builder = new ViterbiClassifierBuilder<String>();
     File delegatedOutputDirectory = builder.getDelegatedModelDirectory(outputDirectory);
-    String[] trainingData = FileUtil.loadListOfStrings(new File(
-        delegatedOutputDirectory,
-        "training-data.test"));
+    String[] trainingData = FileUtil.loadListOfStrings(
+        new File(delegatedOutputDirectory, "training-data.test"));
     testFeatures(trainingData[1], "PreviousOutcome_L1_D");
     testFeatures(
         trainingData[2],

cleartk-opennlp-tools/src/main/java/org/cleartk/opennlp/tools/PosTagger.java

@@ -51,9 +51,9 @@ public static AnalysisEngineDescription getDescription(String languageCode)
     return AnalysisEngineFactory.createEngineDescription(
         opennlp.uima.postag.POSTagger.class,
         opennlp.uima.util.UimaUtil.MODEL_PARAMETER,
-        ExternalResourceFactory.createExternalResourceDescription(
-            POSModelResourceImpl.class,
-            PosTagger.class.getResource(modelPath).toString()),
+        ExternalResourceFactory.createSharedResourceDescription(
+            PosTagger.class.getResource(modelPath).toString(),
+            POSModelResourceImpl.class),
         opennlp.uima.util.UimaUtil.SENTENCE_TYPE_PARAMETER,
         Sentence.class.getName(),
         opennlp.uima.util.UimaUtil.TOKEN_TYPE_PARAMETER,

cleartk-opennlp-tools/src/main/java/org/cleartk/opennlp/tools/Tokenizer.java

@@ -51,9 +51,9 @@ public static AnalysisEngineDescription getDescription(String languageCode)
     return AnalysisEngineFactory.createEngineDescription(
         opennlp.uima.tokenize.Tokenizer.class,
         opennlp.uima.util.UimaUtil.MODEL_PARAMETER,
-        ExternalResourceFactory.createExternalResourceDescription(
-            TokenizerModelResourceImpl.class,
-            Tokenizer.class.getResource(modelPath).toString()),
+        ExternalResourceFactory.createSharedResourceDescription(
+            Tokenizer.class.getResource(modelPath).toString(),
+            TokenizerModelResourceImpl.class),
         opennlp.uima.util.UimaUtil.SENTENCE_TYPE_PARAMETER,
         Sentence.class.getName(),
         opennlp.uima.util.UimaUtil.TOKEN_TYPE_PARAMETER,