Merged with v1.2.6 and up to Jena3.1

pom.xml

@@ -24,7 +24,7 @@
 		<junit.version>4.11</junit.version>
 		<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
 		<spring.version>3.2.17.RELEASE</spring.version>
-		<jena.version>2.13.0</jena.version>
+		<jena.version>3.1.0</jena.version>
 		<jsonld-java-jena.version>0.4.1</jsonld-java-jena.version>
 	</properties>
 
@@ -53,11 +53,6 @@
 
 	<dependencies>
 		<!-- NIF transfer lib -->
-		<dependency>
-			<groupId>org.aksw</groupId>
-			<artifactId>gerbil.nif.transfer</artifactId>
-			<version>1.2.3</version>
-		</dependency>
 		<!-- Jena for using JSON-LD -->
 		<dependency>
 			<groupId>org.apache.jena</groupId>
@@ -316,6 +311,11 @@
 			<artifactId>lucene-analyzers-common</artifactId>
 			<version>6.2.0</version>
 		</dependency>
+		<dependency>
+			<groupId>org.aksw</groupId>
+			<artifactId>gerbil.nif.transfer</artifactId>
+			<version>1.2.5-jena3.1-SNAPSHOT</version>
+		</dependency>
 	</dependencies>
 
 	<build>

repository/org/apache/jena/jena-arq/2.12.1/jena-arq-2.12.1.pom

@@ -201,7 +201,7 @@
           <groups>
             <group>
               <title>SPARQL Query and Update</title>
-              <packages>com.hp.hpl.jena.query:com.hp.hpl.jena.update</packages>
+              <packages>org.apache.jena.query:org.apache.jena.update</packages>
             </group>
             <group>
               <title>RIOT</title>

repository/org/apache/jena/jena-core/2.12.1/jena-core-2.12.1.pom

@@ -145,23 +145,23 @@
           <windowtitle>Apache Jena</windowtitle>
           <doctitle>Apache Jena Core ${project.version}</doctitle>
           <bottom>Licenced under the Apache License, Version 2.0</bottom>
-          <excludePackageNames>com.hp.hpl.jena.shared.*:*.impl:com.hp.hpl.jena.assembler.assemblers:*.exceptions:*.regexptrees:com.hp.hpl.jena.mem:com.hp.hpl.jena.mem.*:com.hp.hpl.jena.n3:com.hp.hpl.jena.n3.*:com.hp.hpl.jena.rdf.arp.*:com.hp.hpl.jena.util.*:jena.cmdline:jena.util</excludePackageNames>
+          <excludePackageNames>org.apache.jena.shared.*:*.impl:org.apache.jena.assembler.assemblers:*.exceptions:*.regexptrees:org.apache.jena.mem:org.apache.jena.mem.*:org.apache.jena.n3:org.apache.jena.n3.*:org.apache.jena.rdf.arp.*:org.apache.jena.util.*:jena.cmdline:jena.util</excludePackageNames>
           <groups>
             <group>
               <title>API - Application Programming Interface</title>
-              <packages>com.hp.hpl.jena.db:com.hp.hpl.jena.rdf.model:com.hp.hpl.jena.rdf.listeners:com.hp.hpl.jena.rdf.arp:com.hp.hpl.jena.rdf.arp.lang:com.hp.hpl.jena.datatypes:com.hp.hpl.jena.datatypes.xsd:com.hp.hpl.jena.rdql:com.hp.hpl.jena.shared:com.hp.hpl.jena.vocabulary:com.hp.hpl.jena.xmloutput:com.hp.hpl.jena.ontology:com.hp.hpl.jena.ontology.daml:com.hp.hpl.jena.reasoner:com.hp.hpl.jena.reasoner.rulesys:com.hp.hpl.jena.reasoner.rulesys.builtins:com.hp.hpl.jena.reasoner.transitiveReasoner:com.hp.hpl.jena.reasoner.dig</packages>
+              <packages>org.apache.jena.db:org.apache.jena.rdf.model:org.apache.jena.rdf.listeners:org.apache.jena.rdf.arp:org.apache.jena.rdf.arp.lang:org.apache.jena.datatypes:org.apache.jena.datatypes.xsd:org.apache.jena.rdql:org.apache.jena.shared:org.apache.jena.vocabulary:org.apache.jena.xmloutput:org.apache.jena.ontology:org.apache.jena.ontology.daml:org.apache.jena.reasoner:org.apache.jena.reasoner.rulesys:org.apache.jena.reasoner.rulesys.builtins:org.apache.jena.reasoner.transitiveReasoner:org.apache.jena.reasoner.dig</packages>
             </group>
             <group>
               <title>SPI - System Programming Interface</title>
-              <packages>com.hp.hpl.jena.enhanced:com.hp.hpl.jena.graph:com.hp.hpl.jena.graph.compose:com.hp.hpl.jena.graph.query:com.hp.hpl.jena.util:com.hp.hpl.jena.util.iterator</packages>
+              <packages>org.apache.jena.enhanced:org.apache.jena.graph:org.apache.jena.graph.compose:org.apache.jena.graph.query:org.apache.jena.util:org.apache.jena.util.iterator</packages>
             </group>
             <group>
               <title>Command line tools</title>
               <packages>jena</packages>
             </group>
             <group>
               <title>Other Packages</title>
-              <packages>com.hp.hpl.jena.assembler</packages>
+              <packages>org.apache.jena.assembler</packages>
             </group>
           </groups>
         </configuration>

src/main/java/org/aksw/gerbil/annotator/OKE2018Task4Annotator.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.Marking;
+
+public interface OKE2018Task4Annotator extends REAnnotator, A2KBAnnotator  {
+
+    public List<Marking> performOKE2018Task4(Document document) throws GerbilException;
+}

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

@@ -0,0 +1,29 @@
+/**
+ * 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.Relation;
+import org.aksw.gerbil.transfer.nif.Span;
+
+public interface REAnnotator extends Annotator {
+
+    public List<Relation> performRETask(Document document) throws GerbilException;
+}

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

@@ -25,8 +25,10 @@
 import org.aksw.gerbil.annotator.D2KBAnnotator;
 import org.aksw.gerbil.annotator.EntityRecognizer;
 import org.aksw.gerbil.annotator.EntityTyper;
+import org.aksw.gerbil.annotator.OKE2018Task4Annotator;
 import org.aksw.gerbil.annotator.OKETask1Annotator;
 import org.aksw.gerbil.annotator.OKETask2Annotator;
+import org.aksw.gerbil.annotator.REAnnotator;
 import org.aksw.gerbil.annotator.RT2KBAnnotator;
 import org.aksw.gerbil.datatypes.ErrorTypes;
 import org.aksw.gerbil.datatypes.ExperimentType;
@@ -38,6 +40,7 @@
 import org.aksw.gerbil.transfer.nif.Marking;
 import org.aksw.gerbil.transfer.nif.Meaning;
 import org.aksw.gerbil.transfer.nif.MeaningSpan;
+import org.aksw.gerbil.transfer.nif.Relation;
 import org.aksw.gerbil.transfer.nif.Span;
 import org.aksw.gerbil.transfer.nif.TypedSpan;
 import org.aksw.gerbil.transfer.nif.data.TypedNamedEntity;
@@ -85,6 +88,10 @@ public static ErrorCountingAnnotatorDecorator createDecorator(ExperimentType typ
             return new ErrorCountingOKETask2Annotator((OKETask2Annotator) annotator, maxErrors);
         case RT2KB:
             return new ErrorCountingRT2KBAnnotator((RT2KBAnnotator) annotator, maxErrors);
+        case RE:
+        	return new ErrorCountingREAnnotator((REAnnotator) annotator, maxErrors);
+        case OKE2018Task4:
+        	return new ErrorCountingOKE2018Task4Annotator((OKE2018Task4Annotator) annotator, maxErrors);
         case Rc2KB:
             break;
         case Sa2KB:
@@ -141,6 +148,59 @@ public List<Span> performRecognition(Document document) throws GerbilException {
         }
     }
 
+    private static class ErrorCountingOKE2018Task4Annotator extends ErrorCountingAnnotatorDecorator implements OKE2018Task4Annotator {
+
+		protected ErrorCountingOKE2018Task4Annotator(Annotator decoratedAnnotator, int maxErrors) {
+			super(decoratedAnnotator, maxErrors);
+		}
+
+		@Override
+		public List<Relation> performRETask(Document document) throws GerbilException {
+			return ErrorCountingAnnotatorDecorator.performRE(this, document);
+		}
+
+		@Override
+		public List<Span> performRecognition(Document document) throws GerbilException {
+			return ErrorCountingAnnotatorDecorator.performRecognition(this, document);
+
+		}
+
+		@Override
+		public List<Marking> performOKE2018Task4(Document document) throws GerbilException {
+			return ErrorCountingAnnotatorDecorator.performOKE2018Task4(this, document);
+
+		}
+
+		@Override
+		public List<MeaningSpan> performA2KBTask(Document document) throws GerbilException {
+			return ErrorCountingAnnotatorDecorator.performExtraction(this, document);
+		}
+
+		@Override
+		public List<MeaningSpan> performD2KBTask(Document document) throws GerbilException {
+			return ErrorCountingAnnotatorDecorator.performD2KBTask(this, document);
+		}
+
+		@Override
+		public List<Meaning> performC2KB(Document document) throws GerbilException {
+			return ErrorCountingAnnotatorDecorator.performC2KB(this, document);
+		}
+
+    }
+
+    private static class ErrorCountingREAnnotator extends ErrorCountingAnnotatorDecorator implements REAnnotator {
+
+		protected ErrorCountingREAnnotator(Annotator decoratedAnnotator, int maxErrors) {
+			super(decoratedAnnotator, maxErrors);
+		}
+
+		@Override
+		public List<Relation> performRETask(Document document) throws GerbilException {
+			return ErrorCountingAnnotatorDecorator.performRE(this, document);
+		}
+
+    }
+
     private static class ErrorCountingA2KBAnnotator extends ErrorCountingD2KBAnnotator implements A2KBAnnotator {
 
         public ErrorCountingA2KBAnnotator(A2KBAnnotator decoratedAnnotator, int maxErrors) {
@@ -247,7 +307,53 @@ protected static void logResult(List<? extends Marking> result, String annotator
         LOGGER.debug(builder.toString());
     }
 
-    protected static List<Meaning> performC2KB(ErrorCountingAnnotatorDecorator errorCounter, Document document)
+    public static List<Relation> performRE(ErrorCountingAnnotatorDecorator errorCounter,
+			Document document) throws GerbilException {
+    	List<Relation> result = null;
+        try {
+            result = ((REAnnotator) errorCounter.getDecoratedAnnotator()).performRETask(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<Relation>(0);
+        }
+        if (printDebugMsg && LOGGER.isDebugEnabled()) {
+            logResult(result, errorCounter.getName(), "Relation");
+        }
+        return result;
+	}
+
+    public static List<Marking> performOKE2018Task4(ErrorCountingAnnotatorDecorator errorCounter,
+			Document document) throws GerbilException {
+    	List<Marking> result = null;
+        try {
+            result = ((OKE2018Task4Annotator) errorCounter.getDecoratedAnnotator()).performOKE2018Task4(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<Marking>(0);
+        }
+        if (printDebugMsg && LOGGER.isDebugEnabled()) {
+            logResult(result, errorCounter.getName(), "Meaning");
+        }
+        return result;
+	}
+
+	protected static List<Meaning> performC2KB(ErrorCountingAnnotatorDecorator errorCounter, Document document)
             throws GerbilException {
         List<Meaning> result = null;
         try {