Merge pull request #466 from ClearTK/refactoring/465-Remove-use-of-de…

…precated-OSS-Sonatype-parent-POM

Issue #465: Remove use of deprecated OSS Sonatype parent POM

.gitignore

@@ -7,3 +7,5 @@
 .factorypath
 .checkstyle
 target
+.apt_generated/
+.apt_generated_tests/

cleartk-clearnlp/src/main/java/org/cleartk/clearnlp/Tokenizer_ImplBase.java

@@ -60,7 +60,6 @@
  * <p>
  * 
  * @author Lee Becker
- * 
  */
 @Beta
 public abstract class Tokenizer_ImplBase<TOKEN_TYPE extends Annotation, SENTENCE_TYPE extends Annotation> extends

cleartk-corpus/src/main/java/org/cleartk/corpus/penntreebank/PennTreebankReader.java

@@ -32,17 +32,17 @@
 import org.apache.uima.UimaContext;
 import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
 import org.apache.uima.collection.CollectionException;
+import org.apache.uima.fit.component.JCasCollectionReader_ImplBase;
+import org.apache.uima.fit.component.ViewCreatorAnnotator;
+import org.apache.uima.fit.descriptor.ConfigurationParameter;
+import org.apache.uima.fit.descriptor.SofaCapability;
 import org.apache.uima.jcas.JCas;
 import org.apache.uima.resource.ResourceInitializationException;
 import org.apache.uima.util.FileUtils;
 import org.apache.uima.util.Level;
 import org.apache.uima.util.Progress;
 import org.apache.uima.util.ProgressImpl;
 import org.cleartk.util.ViewUriUtil;
-import org.apache.uima.fit.component.JCasCollectionReader_ImplBase;
-import org.apache.uima.fit.component.ViewCreatorAnnotator;
-import org.apache.uima.fit.descriptor.ConfigurationParameter;
-import org.apache.uima.fit.descriptor.SofaCapability;
 
 import com.google.common.annotations.Beta;
 
@@ -80,20 +80,18 @@ public class PennTreebankReader extends JCasCollectionReader_ImplBase {
   public static final String PARAM_CORPUS_DIRECTORY_NAME = "corpusDirectoryName";
 
   private static final String CORPUS_DIRECTORY_DESCRIPTION = "Specifies the location of WSJ/PennTreebank treebank files.  "
-      + "The directory should contain subdirectories corresponding to the sections (e.g. '00', '01', etc.) "
-      + "That is, if a local copy of PennTreebank sits at C:/Data/PTB/wsj/mrg, then the the subdirectory C:/Data/PTB/wsj/mrg/00 should exist. "
-      + "There are 24 sections in PTB corresponding to the directories 00, 01, 02, ... 24. ";
+          + "The directory should contain subdirectories corresponding to the sections (e.g. '00', '01', etc.) "
+          + "That is, if a local copy of PennTreebank sits at C:/Data/PTB/wsj/mrg, then the the subdirectory C:/Data/PTB/wsj/mrg/00 should exist. "
+          + "There are 24 sections in PTB corresponding to the directories 00, 01, 02, ... 24. ";
 
-  @ConfigurationParameter(
-      name = PARAM_CORPUS_DIRECTORY_NAME,
-      mandatory = true, description = CORPUS_DIRECTORY_DESCRIPTION)
+  @ConfigurationParameter(name = PARAM_CORPUS_DIRECTORY_NAME, mandatory = true, description = CORPUS_DIRECTORY_DESCRIPTION)
   private String corpusDirectoryName;
 
   public static final String PARAM_SECTIONS_SPECIFIER = "sectionsSpecifier";
 
   private static final String SECTIONS_DESCRIPTION = "specifies which sections of PTB to read in.  "
-      + "The required format for values of this parameter allows for comma-separated section numbers and section ranges, "
-      + "for example '02,07-12,16'.";
+          + "The required format for values of this parameter allows for comma-separated section numbers and section ranges, "
+          + "for example '02,07-12,16'.";
 
   @ConfigurationParameter(name = PARAM_SECTIONS_SPECIFIER, defaultValue = "00-24", description = SECTIONS_DESCRIPTION)
   private String sectionsSpecifier;
@@ -119,7 +117,7 @@ public void initialize(UimaContext context) throws ResourceInitializationExcepti
   }
 
   /**
-   * This will add all the <tt>.mrg</tt> files in the given WSJ sections to <em>treebankFiles</em>.
+   * This will add all the {@code .mrg} files in the given WSJ sections to <em>treebankFiles</em>.
    * 
    * @param wsjDirectory
    *          The top level of the WSJ part of Treebank. Underneath here are the section
@@ -130,22 +128,23 @@ public void initialize(UimaContext context) throws ResourceInitializationExcepti
    *          The set of sections to include.
    */
   @Beta
-  public static void collectSections(
-      File wsjDirectory,
-      List<File> treebankFiles,
-      ListSpecification wsjSections) {
-    if (!wsjDirectory.isDirectory())
+  public static void collectSections(File wsjDirectory, List<File> treebankFiles,
+          ListSpecification wsjSections) {
+    if (!wsjDirectory.isDirectory()) {
       return;
+    }
 
     for (File subFile : wsjDirectory.listFiles()) {
-      if (!subFile.isDirectory())
+      if (!subFile.isDirectory()) {
         continue;
+      }
 
       try {
         int section = Integer.valueOf(subFile.getName());
 
-        if (!wsjSections.contains(section))
+        if (!wsjSections.contains(section)) {
           continue;
+        }
       } catch (NumberFormatException e) {
         continue;
       }
@@ -167,37 +166,37 @@ static void collectFiles(File file, List<File> treebankFiles) {
   /**
    * Reads the next file and stores its text in <b>cas</b> as the "TreebankView" SOFA.
    */
+  @Override
   public void getNext(JCas jCas) throws IOException, CollectionException {
     File treebankFile = files.removeFirst();
-    getUimaContext().getLogger().log(
-        Level.FINEST,
-        "reading treebank file: " + treebankFile.getPath());
+    getUimaContext().getLogger().log(Level.FINEST,
+            "reading treebank file: " + treebankFile.getPath());
     ViewUriUtil.setURI(jCas, treebankFile.toURI());
     try {
-      JCas treebankView = ViewCreatorAnnotator.createViewSafely(
-          jCas,
-          TREEBANK_VIEW);
+      JCas treebankView = ViewCreatorAnnotator.createViewSafely(jCas, TREEBANK_VIEW);
       treebankView.setSofaDataString(FileUtils.file2String(treebankFile), "text/plain");
     } catch (AnalysisEngineProcessException aepe) {
       throw new CollectionException(aepe);
     }
   }
 
+  @Override
   public void close() throws IOException {
   }
 
+  @Override
   public Progress[] getProgress() {
-    return new Progress[] { new ProgressImpl(
-        numberOfFiles - files.size(),
-        numberOfFiles,
-        Progress.ENTITIES) };
+    return new Progress[] {
+        new ProgressImpl(numberOfFiles - files.size(), numberOfFiles, Progress.ENTITIES) };
   }
 
+  @Override
   public boolean hasNext() throws IOException, CollectionException {
-    if (files.size() > 0)
+    if (files.size() > 0) {
       return true;
-    else
+    } else {
       return false;
+    }
   }
 
   @Beta

cleartk-corpus/src/main/java/org/cleartk/corpus/propbank/PropbankGoldReader.java

@@ -55,7 +55,7 @@
  * 
  * 
  * <p>
- * PropbankCollectionReader reads all <tt>.mrg</tt> files of the WSJ part of Treebank in lexical
+ * PropbankCollectionReader reads all {@code .mrg} files of the WSJ part of Treebank in lexical
  * order, then reads the corresponding Propbank entries, and populates the "TreebankView" and
  * "PropbankView" SOFAs.
  * </p>

cleartk-corpus/src/main/java/org/cleartk/corpus/propbank/util/Propbank.java

@@ -46,7 +46,7 @@
  * 
  * <p>
  * A <em>Propbank object</em> represents one entry in Propbank. It closely reflects the structure of
- * one line in <tt>prop.txt</tt>.
+ * one line in {@code prop.txt}.
  * </p>
  * 
  * @author Philipp Wetzler, Philip Ogren, Steven Bethard
@@ -57,7 +57,7 @@ public class Propbank {
    * Parses one Propbank entry and returns its representation as a <em>Propbank</em> object.
    * 
    * @param propTxt
-   *          one line from <tt>prop.txt</tt>
+   *          one line from {@code prop.txt}
    * 
    * @return a <em>Propbank</em> object representing <b>propTxt</b>
    */
@@ -104,10 +104,10 @@ public static Propbank fromString(String propTxt) {
 
   /**
    * A convenience funtion to quickly read only the filename portion of a line from
-   * <tt>prop.txt</tt>.
+   * {@code prop.txt}.
    * 
    * @param propTxt
-   *          one line from <tt>prop.txt</tt>
+   *          one line from {@code prop.txt}
    * 
    * @return the filename part of <b>propTxt</b>
    */

cleartk-corpus/src/main/java/org/cleartk/corpus/propbank/util/PropbankRelation.java

@@ -50,7 +50,7 @@ public abstract class PropbankRelation {
    * <em>PropbankRelation</em> object.
    * 
    * @param s
-   *          the textual representation of a relation taken from <tt>prop.txt</tt>
+   *          the textual representation of a relation taken from {@code prop.txt}
    * 
    * @return a <em>PropbankRelation</em> object representing <b>s</b>
    */

cleartk-corpus/src/main/java/org/cleartk/corpus/propbank/util/Proplabel.java

@@ -29,13 +29,13 @@
 import java.util.List;
 import java.util.Set;
 
+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;
 import org.cleartk.srl.type.SemanticArgument;
 import org.cleartk.syntax.constituent.type.TopTreebankNode;
 import org.cleartk.util.AnnotationUtil;
-import org.apache.uima.fit.util.FSCollectionFactory;
 
 import com.google.common.annotations.Beta;
 
@@ -58,7 +58,7 @@ public class Proplabel {
    * <em>Proplabel</em> object.
    * 
    * @param lblTxt
-   *          one label part of one line from <tt>prop.txt</tt>
+   *          one label part of one line from {@code prop.txt}
    * 
    * @return a <em>Proplabel</em> object representing <b>lblTxt</b>
    */
@@ -103,16 +103,13 @@ static Proplabel fromString(String lblTxt) {
 
     // throw some exceptions for bad input
     if (columns.length != expectedLength) {
-      throw new PropbankFormatException(String.format(
-          "Expected %d items, found %d",
-          expectedLength,
-          columns.length));
+      throw new PropbankFormatException(
+              String.format("Expected %d items, found %d", expectedLength, columns.length));
     }
     if (Proplabel.labelsRequiringFeatures.contains(columns[1])) {
       if (proplabel.getFeature() == null) {
-        throw new PropbankFormatException(String.format(
-            "Label %s requires a feature",
-            proplabel.getLabel()));
+        throw new PropbankFormatException(
+                String.format("Label %s requires a feature", proplabel.getLabel()));
       }
     }
     return proplabel;
@@ -247,26 +244,29 @@ public String toString() {
 
     buffer.append(getRelation().toString());
     buffer.append("-" + getLabel());
-    if (getFeature() != null)
+    if (getFeature() != null) {
       buffer.append("-" + getFeature());
-    if (getHyphenTag() != null)
+    }
+    if (getHyphenTag() != null) {
       buffer.append("-" + getHyphenTag());
-    if (getPreposition() != null)
+    }
+    if (getPreposition() != null) {
       buffer.append("-" + getPreposition());
+    }
 
     return buffer.toString();
   }
 
   private static final Set<String> labels = new HashSet<String>(
-      Arrays.asList("rel|Support|ARG0|ARG1|ARG2|ARG3|ARG4|ARG5|ARGA|ARGM".split("\\|")));
+          Arrays.asList("rel|Support|ARG0|ARG1|ARG2|ARG3|ARG4|ARG5|ARGA|ARGM".split("\\|")));
 
   private static final Set<String> labelsRequiringFeatures = new HashSet<String>(
-      Arrays.asList(new String[] { "ARGM" }));
+          Arrays.asList(new String[] { "ARGM" }));
 
   private static final Set<String> features = new HashSet<String>(
-      Arrays.asList("ADV|CAU|DIR|DIS|EXT|LOC|MNR|MOD|NEG|PNC|PRD|REC|TMP".split("\\|")));
+          Arrays.asList("ADV|CAU|DIR|DIS|EXT|LOC|MNR|MOD|NEG|PNC|PRD|REC|TMP".split("\\|")));
 
   private static final Set<String> hyphenTags = new HashSet<String>(
-      Arrays.asList("H0|H1|H2|H3|H4|H5|H6|H7|H8|H9|XX".split("\\|")));
+          Arrays.asList("H0|H1|H2|H3|H4|H5|H6|H7|H8|H9|XX".split("\\|")));
 
 }

cleartk-eval/src/main/java/org/cleartk/eval/Evaluation_ImplBase.java

@@ -70,7 +70,7 @@ public Evaluation_ImplBase(File baseDirectory) {
    * @return The statistics that result from testing the model.
    */
   public STATS_TYPE trainAndTest(List<ITEM_TYPE> trainItems, List<ITEM_TYPE> testItems)
-      throws Exception {
+          throws Exception {
     File subDirectory = new File(this.baseDirectory, "train_and_test");
     subDirectory.mkdirs();
     this.train(this.getCollectionReader(trainItems), subDirectory);
@@ -120,7 +120,8 @@ public List<STATS_TYPE> crossValidation(List<ITEM_TYPE> items, int nFolds) throw
    * @param nFolds
    *          The total number of folds in this cross validation.
    * @param fold
-   *          The index of the fold (0 <= fold < nFolds) whose training items are to be selected.
+   *          The index of the fold (0 &lt;= fold &lt; nFolds) whose training items are to be
+   *          selected.
    * @return The items that should be used for training.
    */
   protected List<ITEM_TYPE> selectFoldTrainItems(List<ITEM_TYPE> items, int nFolds, int fold) {
@@ -144,7 +145,7 @@ protected List<ITEM_TYPE> selectFoldTrainItems(List<ITEM_TYPE> items, int nFolds
    * @param nFolds
    *          The total number of folds in this cross validation.
    * @param fold
-   *          The index of the fold (0 <= fold < nFolds) whose test items are to be selected.
+   *          The index of the fold (0 &lt;= fold &lt; nFolds) whose test items are to be selected.
    * @return The items that should be used for testing.
    */
   protected List<ITEM_TYPE> selectFoldTestItems(List<ITEM_TYPE> items, int nFolds, int fold) {
@@ -192,6 +193,6 @@ protected List<ITEM_TYPE> selectFoldTestItems(List<ITEM_TYPE> items, int nFolds,
    * @return The statistics that result from testing the model
    */
   protected abstract STATS_TYPE test(CollectionReader collectionReader, File directory)
-      throws Exception;
+          throws Exception;
 
 }

cleartk-feature/src/main/java/org/cleartk/feature/syntax/SyntacticPathExtractor.java

@@ -60,9 +60,9 @@ public class SyntacticPathExtractor implements FeatureExtractor2<TreebankNode, T
    * @param pathMemberExtractor
    *          this extractor will be used to get a feature for every node on the path, which will
    *          then be combined to form a single string. The extractor should preferably generate
-   *          exactly one <tt>StringFeature</tt>, but must generate at least one
-   *          <tt>StringFeature</tt>, <tt>LongFeature</tt>, <tt>DoubleFeature</tt>, or
-   *          <tt>BooleanFeature</tt>. Only the first feature will then be used and naively
+   *          exactly one {@code StringFeature}, but must generate at least one
+   *          {@code StringFeature}, {@code LongFeature}, {@code DoubleFeature}, or
+   *          {@code BooleanFeature}. Only the first feature will then be used and naively
    *          converted to a string.
    * @param partial
    *          if true, generate a partial path only, i.e. from the first node up to the lowest