Merged version1.2.5 into the master branch.

Author: MichaelRoeder

.gitignore

@@ -10,4 +10,6 @@ gerbil_data
 *.log
 google*.html
 export
-datadump.nt
+datadump.nt
+indexes
+dependency-reduced-pom.xml

.travis.yml

@@ -3,8 +3,9 @@ language: java
 before_install:
   - cp src/main/properties/log4j.properties src/test/resources/log4j.properties
   - mkdir -p "gerbil_data"
-  - curl --retry 4 -L -o "gerbil_data/gerbil_data.zip" "https://github.com/AKSW/gerbil/releases/download/v1.2.4/gerbil_data.zip"
+  - curl --retry 4 -L -o "gerbil_data/gerbil_data.zip" "https://github.com/AKSW/gerbil/releases/download/v1.2.5/gerbil_data.zip"
   - unzip "gerbil_data/gerbil_data.zip"
+  - touch src/main/properties/gerbil_keys.properties
 install:
   - mvn clean compile -DskipTests=true -Dmaven.javadoc.skip=true -B -V
 script:

index.sh

@@ -0,0 +1,29 @@
+mkdir dbpedia_dump
+cd dbpedia_dump
+
+wget -r --no-parent -R "*.txt, *.html, *.json" -A "*.nt, *.ttl, *.nt.bz2, *.ttl.bz2" http://downloads.dbpedia.org/2016-04/core-i18n/en/
+cd downloads.dbpedia.org/2016-04/core-i18n/en/
+
+wget http://www.l3s.de/~minack/rdf2rdf/downloads/rdf2rdf-1.0.1-2.3.1.jar
+
+
+rm *.json
+rm *.txt
+rm index.html
+
+for i in *.bz2; do
+	bzip2 -vd $i
+done
+
+for i in *.ttl; do
+	java -jar rdf2rdf-1.0.1-2.3.1.jar $i .nt
+done
+
+rm *.ttl
+rm rdf2rdf-1.0.1-2.3.1.jar
+
+cd ../../../../../../
+
+mvn exec:java -Dexec.mainClass="org.aksw.gerbil.tools.InitialIndexTool" -Dexec.args="dbpedia_dump/downloads.dbpedia.org/2016-04/core-i18n/en/"
+
+rm -rf dbpedia_dump/ 

pom.xml

@@ -12,8 +12,8 @@
 	xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
 	<modelVersion>4.0.0</modelVersion>
 	<groupId>org.aksw</groupId>
-	<artifactId>gerbil</artifactId>
-	<version>1.2.4</version>
+	<artifactId>gerbil</artifactId>
+	<version>1.2.5</version>
 	<name>General Entity Annotator Benchmark</name>
 	<description>This project is a benchmark for entity annotation and disambiguation tools.</description>
 	<inceptionYear>2014</inceptionYear>
@@ -55,8 +55,8 @@
 		<!-- NIF transfer lib -->
 		<dependency>
 			<groupId>org.aksw</groupId>
-			<artifactId>gerbil.nif.transfer</artifactId>
-			<version>1.2.2</version>
+			<artifactId>gerbil.nif.transfer</artifactId>
+			<version>1.2.3</version>
 		</dependency>
 		<!-- Jena for using JSON-LD -->
 		<dependency>
@@ -142,7 +142,7 @@
 		<dependency>
 			<groupId>org.apache.lucene</groupId>
 			<artifactId>lucene-core</artifactId>
-			<version>2.9.1</version>
+			<version>6.2.0</version>
 		</dependency>
 		<dependency>
 			<groupId>commons-configuration</groupId>
@@ -311,6 +311,11 @@
 			<artifactId>json</artifactId>
 			<version>20140107</version>
 		</dependency>
+		<dependency>
+			<groupId>org.apache.lucene</groupId>
+			<artifactId>lucene-analyzers-common</artifactId>
+			<version>6.2.0</version>
+		</dependency>
 	</dependencies>
 
 	<build>

src/main/java/org/aksw/gerbil/annotator/OKETask1Annotator.java

@@ -22,7 +22,7 @@
 import org.aksw.gerbil.transfer.nif.Document;
 import org.aksw.gerbil.transfer.nif.data.TypedNamedEntity;
 
-public interface OKETask1Annotator extends A2KBAnnotator, EntityTyper {
+public interface OKETask1Annotator extends A2KBAnnotator, RT2KBAnnotator {
 
     public List<TypedNamedEntity> performTask1(Document document) throws GerbilException;
 }

src/main/java/org/aksw/gerbil/annotator/RT2KBAnnotator.java

@@ -0,0 +1,28 @@
+/**
+ * This file is part of General Entity Annotator Benchmark.
+ *
+ * General Entity Annotator Benchmark is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * General Entity Annotator Benchmark is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with General Entity Annotator Benchmark.  If not, see <http://www.gnu.org/licenses/>.
+ */
+package org.aksw.gerbil.annotator;
+
+import java.util.List;
+
+import org.aksw.gerbil.exceptions.GerbilException;
+import org.aksw.gerbil.transfer.nif.Document;
+import org.aksw.gerbil.transfer.nif.TypedSpan;
+
+public interface RT2KBAnnotator extends EntityRecognizer, EntityTyper {
+
+    public List<TypedSpan> performRT2KBTask(Document document) throws GerbilException;
+}

src/main/java/org/aksw/gerbil/annotator/decorator/ErrorCountingAnnotatorDecorator.java

@@ -27,6 +27,7 @@
 import org.aksw.gerbil.annotator.EntityTyper;
 import org.aksw.gerbil.annotator.OKETask1Annotator;
 import org.aksw.gerbil.annotator.OKETask2Annotator;
+import org.aksw.gerbil.annotator.RT2KBAnnotator;
 import org.aksw.gerbil.datatypes.ErrorTypes;
 import org.aksw.gerbil.datatypes.ExperimentType;
 import org.aksw.gerbil.evaluate.EvaluationResultContainer;
@@ -52,8 +53,8 @@
  * @author Michael Röder ([email protected])
  * 
  */
-public abstract class ErrorCountingAnnotatorDecorator extends AbstractAnnotatorDecorator
-        implements Evaluator<Marking>, ErrorCounter {
+public abstract class ErrorCountingAnnotatorDecorator extends AbstractAnnotatorDecorator implements Evaluator<Marking>,
+        ErrorCounter {
 
     private static final Logger LOGGER = LoggerFactory.getLogger(ErrorCountingAnnotatorDecorator.class);
 
@@ -82,6 +83,8 @@ public static ErrorCountingAnnotatorDecorator createDecorator(ExperimentType typ
             return new ErrorCountingOKETask1Annotator((OKETask1Annotator) annotator, maxErrors);
         case OKE_Task2:
             return new ErrorCountingOKETask2Annotator((OKETask2Annotator) annotator, maxErrors);
+        case RT2KB:
+            return new ErrorCountingRT2KBAnnotator((RT2KBAnnotator) annotator, maxErrors);
         case Rc2KB:
             break;
         case Sa2KB:
@@ -125,8 +128,8 @@ public List<MeaningSpan> performD2KBTask(Document document) throws GerbilExcepti
         }
     }
 
-    private static class ErrorCountingEntityRecognizer extends ErrorCountingAnnotatorDecorator
-            implements EntityRecognizer {
+    private static class ErrorCountingEntityRecognizer extends ErrorCountingAnnotatorDecorator implements
+            EntityRecognizer {
 
         public ErrorCountingEntityRecognizer(EntityRecognizer decoratedAnnotator, int maxErrors) {
             super(decoratedAnnotator, maxErrors);
@@ -173,8 +176,24 @@ public List<TypedSpan> performTyping(Document document) throws GerbilException {
         }
     }
 
-    private static class ErrorCountingOKETask1Annotator extends ErrorCountingA2KBAnnotator
-            implements OKETask1Annotator {
+    private static class ErrorCountingRT2KBAnnotator extends ErrorCountingEntityRecognizer implements RT2KBAnnotator {
+
+        protected ErrorCountingRT2KBAnnotator(RT2KBAnnotator decoratedAnnotator, int maxErrors) {
+            super(decoratedAnnotator, maxErrors);
+        }
+
+        @Override
+        public List<TypedSpan> performTyping(Document document) throws GerbilException {
+            return ErrorCountingAnnotatorDecorator.performTyping(this, document);
+        }
+
+        @Override
+        public List<TypedSpan> performRT2KBTask(Document document) throws GerbilException {
+            return ErrorCountingAnnotatorDecorator.performRT2KBTask(this, document);
+        }
+    }
+
+    private static class ErrorCountingOKETask1Annotator extends ErrorCountingA2KBAnnotator implements OKETask1Annotator {
 
         protected ErrorCountingOKETask1Annotator(OKETask1Annotator decoratedAnnotator, int maxErrors) {
             super(decoratedAnnotator, maxErrors);
@@ -185,14 +204,19 @@ public List<TypedSpan> performTyping(Document document) throws GerbilException {
             return ErrorCountingAnnotatorDecorator.performTyping(this, document);
         }
 
+        @Override
+        public List<TypedSpan> performRT2KBTask(Document document) throws GerbilException {
+            return ErrorCountingAnnotatorDecorator.performRT2KBTask(this, document);
+        }
+
         @Override
         public List<TypedNamedEntity> performTask1(Document document) throws GerbilException {
             return ErrorCountingAnnotatorDecorator.performOKETask1(this, document);
         }
     }
 
-    private static class ErrorCountingOKETask2Annotator extends ErrorCountingAnnotatorDecorator
-            implements OKETask2Annotator {
+    private static class ErrorCountingOKETask2Annotator extends ErrorCountingAnnotatorDecorator implements
+            OKETask2Annotator {
 
         protected ErrorCountingOKETask2Annotator(OKETask2Annotator decoratedAnnotator, int maxErrors) {
             super(decoratedAnnotator, maxErrors);
@@ -269,8 +293,8 @@ protected static List<MeaningSpan> performD2KBTask(ErrorCountingAnnotatorDecorat
         return result;
     }
 
-    protected static List<MeaningSpan> performExtraction(ErrorCountingAnnotatorDecorator errorCounter,
-            Document document) throws GerbilException {
+    protected static List<MeaningSpan> performExtraction(ErrorCountingAnnotatorDecorator errorCounter, Document document)
+            throws GerbilException {
         List<MeaningSpan> result = null;
         try {
             result = ((A2KBAnnotator) errorCounter.getDecoratedAnnotator()).performA2KBTask(document);
@@ -384,6 +408,29 @@ protected static List<TypedNamedEntity> performOKETask2(ErrorCountingAnnotatorDe
         return result;
     }
 
+    public static List<TypedSpan> performRT2KBTask(ErrorCountingAnnotatorDecorator errorCounter, Document document)
+            throws GerbilException {
+        List<TypedSpan> result = null;
+        try {
+            result = ((RT2KBAnnotator) errorCounter.getDecoratedAnnotator()).performRT2KBTask(document);
+        } catch (Exception e) {
+            if (errorCounter.getErrorCount() == 0) {
+                // Log only the first exception completely
+                LOGGER.error("Got an Exception from the annotator (" + errorCounter.getName() + ")", e);
+            } else {
+                // Log only the Exception message without the stack trace
+                LOGGER.error("Got an Exception from the annotator (" + errorCounter.getName() + "): "
+                        + e.getLocalizedMessage());
+            }
+            errorCounter.increaseErrorCount();
+            return new ArrayList<TypedSpan>(0);
+        }
+        if (printDebugMsg && LOGGER.isDebugEnabled()) {
+            logResult(result, errorCounter.getName(), "TypedNamedEntity");
+        }
+        return result;
+    }
+
     protected int errorCount = 0;
     protected int maxErrors;