Merge branch 'dev'

GeoKnow · Mar 17, 2017 · 1de8dea · 1de8dea
2 parents 6215a72 + 4bf19be
commit 1de8dea
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Showing 48 changed files with 23,776 additions and 4,827 deletions.
diff --git a/pom.xml b/pom.xml
diff --git a/src/main/java/org/aksw/deer/helper/datastructure/FMeasure.java b/src/main/java/org/aksw/deer/helper/datastructure/FMeasure.java
@@ -3,7 +3,7 @@
  */
 package org.aksw.deer.helper.datastructure;
 
-import com.hp.hpl.jena.rdf.model.Model;
+import org.apache.jena.rdf.model.Model;
 
 /**
  * @author sherif

diff --git a/src/main/java/org/aksw/deer/helper/kb/KBSampler.java b/src/main/java/org/aksw/deer/helper/kb/KBSampler.java
@@ -6,11 +6,11 @@
 import org.aksw.deer.workflow.specslearner.SimplePipeLineLearner;
 import org.apache.log4j.Logger;
 
-import com.hp.hpl.jena.query.QueryExecution;
-import com.hp.hpl.jena.query.QueryExecutionFactory;
-import com.hp.hpl.jena.query.QueryFactory;
-import com.hp.hpl.jena.rdf.model.Model;
-import com.hp.hpl.jena.rdf.model.Resource;
+import org.apache.jena.query.QueryExecution;
+import org.apache.jena.query.QueryExecutionFactory;
+import org.apache.jena.query.QueryFactory;
+import org.apache.jena.rdf.model.Model;
+import org.apache.jena.rdf.model.Resource;
 
 /**
  * @author sherif

diff --git a/src/main/java/org/aksw/deer/helper/vacabularies/DBpedia.java b/src/main/java/org/aksw/deer/helper/vacabularies/DBpedia.java
@@ -3,8 +3,8 @@
  */
 package org.aksw.deer.helper.vacabularies;
 
-import com.hp.hpl.jena.rdf.model.Property;
-import com.hp.hpl.jena.rdf.model.ResourceFactory;
+import org.apache.jena.rdf.model.Property;
+import org.apache.jena.rdf.model.ResourceFactory;
 
 public class DBpedia{
 	public static final String endPoint 		= "http://dbpedia.org/sparql";

diff --git a/src/main/java/org/aksw/deer/helper/vacabularies/SCMSANN.java b/src/main/java/org/aksw/deer/helper/vacabularies/SCMSANN.java
@@ -3,8 +3,8 @@
  */
 package org.aksw.deer.helper.vacabularies;
 
-import com.hp.hpl.jena.rdf.model.Property;
-import com.hp.hpl.jena.rdf.model.ResourceFactory;
+import org.apache.jena.rdf.model.Property;
+import org.apache.jena.rdf.model.ResourceFactory;
 
 public class SCMSANN{
 	public static final String scmsAnnotation	= "http://ns.aksw.org/scms/annotations/";

diff --git a/src/main/java/org/aksw/deer/helper/vacabularies/SPECS.java b/src/main/java/org/aksw/deer/helper/vacabularies/SPECS.java
@@ -3,9 +3,9 @@
  */
 package org.aksw.deer.helper.vacabularies;
 
-import com.hp.hpl.jena.rdf.model.Property;
-import com.hp.hpl.jena.rdf.model.Resource;
-import com.hp.hpl.jena.rdf.model.ResourceFactory;
+import org.apache.jena.rdf.model.Property;
+import org.apache.jena.rdf.model.Resource;
+import org.apache.jena.rdf.model.ResourceFactory;
 
 /**
  * @author sherif

diff --git a/src/main/java/org/aksw/deer/io/Reader.java b/src/main/java/org/aksw/deer/io/Reader.java
@@ -5,9 +5,9 @@
 
 import org.apache.log4j.Logger;
 
-import com.hp.hpl.jena.rdf.model.Model;
-import com.hp.hpl.jena.rdf.model.ModelFactory;
-import com.hp.hpl.jena.util.FileManager;
+import org.apache.jena.rdf.model.Model;
+import org.apache.jena.rdf.model.ModelFactory;
+import org.apache.jena.util.FileManager;
 
 /**
  * @author sherif

diff --git a/src/main/java/org/aksw/deer/io/Writer.java b/src/main/java/org/aksw/deer/io/Writer.java
@@ -8,7 +8,7 @@
 
 import org.apache.log4j.Logger;
 
-import com.hp.hpl.jena.rdf.model.Model;
+import org.apache.jena.rdf.model.Model;
 
 /**
  * @author sherif
@@ -25,4 +25,4 @@ public static void writeModel(Model model, String format, String outputFile) thr
 		model.write(fileWriter, format);
 		logger.info("Saving file done in " + (System.currentTimeMillis() - starTime) +"ms.");
 	}
-}
+}
diff --git a/src/main/java/org/aksw/deer/modules/DeerModule.java b/src/main/java/org/aksw/deer/modules/DeerModule.java
@@ -8,8 +8,8 @@
 
 import org.aksw.deer.json.ParameterType;
 
-import com.hp.hpl.jena.rdf.model.Model;
-import com.hp.hpl.jena.rdf.model.Resource;
+import org.apache.jena.rdf.model.Model;
+import org.apache.jena.rdf.model.Resource;
 
 /**
  * @author sherif

diff --git a/src/main/java/org/aksw/deer/modules/Dereferencing/DereferencingModule.java b/src/main/java/org/aksw/deer/modules/Dereferencing/DereferencingModule.java
@@ -21,20 +21,20 @@
 import org.apache.log4j.Logger;
 
 import com.google.common.collect.Sets;
-import com.hp.hpl.jena.query.Query;
-import com.hp.hpl.jena.query.QueryExecution;
-import com.hp.hpl.jena.query.QueryExecutionFactory;
-import com.hp.hpl.jena.query.QueryFactory;
-import com.hp.hpl.jena.query.QuerySolution;
-import com.hp.hpl.jena.query.ResultSet;
-import com.hp.hpl.jena.rdf.model.Model;
-import com.hp.hpl.jena.rdf.model.ModelFactory;
-import com.hp.hpl.jena.rdf.model.Property;
-import com.hp.hpl.jena.rdf.model.RDFNode;
-import com.hp.hpl.jena.rdf.model.Resource;
-import com.hp.hpl.jena.rdf.model.ResourceFactory;
-import com.hp.hpl.jena.rdf.model.Statement;
-import com.hp.hpl.jena.rdf.model.StmtIterator;
+import org.apache.jena.query.Query;
+import org.apache.jena.query.QueryExecution;
+import org.apache.jena.query.QueryExecutionFactory;
+import org.apache.jena.query.QueryFactory;
+import org.apache.jena.query.QuerySolution;
+import org.apache.jena.query.ResultSet;
+import org.apache.jena.rdf.model.Model;
+import org.apache.jena.rdf.model.ModelFactory;
+import org.apache.jena.rdf.model.Property;
+import org.apache.jena.rdf.model.RDFNode;
+import org.apache.jena.rdf.model.Resource;
+import org.apache.jena.rdf.model.ResourceFactory;
+import org.apache.jena.rdf.model.Statement;
+import org.apache.jena.rdf.model.StmtIterator;
 /**
  * @author mofeed
  * This class includes methods in order to load dataset in Model from file.

diff --git a/src/main/java/org/aksw/deer/modules/authorityconformation/AuthorityConformationModule.java b/src/main/java/org/aksw/deer/modules/authorityconformation/AuthorityConformationModule.java
@@ -15,15 +15,15 @@
 
 import com.google.common.collect.HashMultiset;
 import com.google.common.collect.Multiset;
-import com.hp.hpl.jena.rdf.model.Model;
-import com.hp.hpl.jena.rdf.model.ModelFactory;
-import com.hp.hpl.jena.rdf.model.Property;
-import com.hp.hpl.jena.rdf.model.RDFNode;
-import com.hp.hpl.jena.rdf.model.ResIterator;
-import com.hp.hpl.jena.rdf.model.Resource;
-import com.hp.hpl.jena.rdf.model.ResourceFactory;
-import com.hp.hpl.jena.rdf.model.Statement;
-import com.hp.hpl.jena.rdf.model.StmtIterator;
+import org.apache.jena.rdf.model.Model;
+import org.apache.jena.rdf.model.ModelFactory;
+import org.apache.jena.rdf.model.Property;
+import org.apache.jena.rdf.model.RDFNode;
+import org.apache.jena.rdf.model.ResIterator;
+import org.apache.jena.rdf.model.Resource;
+import org.apache.jena.rdf.model.ResourceFactory;
+import org.apache.jena.rdf.model.Statement;
+import org.apache.jena.rdf.model.StmtIterator;
 
 /**
  * @author sherif
@@ -122,7 +122,7 @@ public static void main(String[] args) {
 	}
 
 	/* (non-Javadoc)
-	 * @see org.aksw.geolift.modules.GeoLiftModule#process(com.hp.hpl.jena.rdf.model.Model, java.util.Map)
+	 * @see org.aksw.geolift.modules.GeoLiftModule#process(org.apache.jena.rdf.model.Model, java.util.Map)
 	 */
 	@Override
 	public Model process(Model inputModel, Map<String, String> parameters) {

diff --git a/src/main/java/org/aksw/deer/modules/filter/FilterModule.java b/src/main/java/org/aksw/deer/modules/filter/FilterModule.java
@@ -13,13 +13,13 @@
 import org.aksw.deer.modules.DeerModule;
 import org.apache.log4j.Logger;
 
-import com.hp.hpl.jena.rdf.model.Model;
-import com.hp.hpl.jena.rdf.model.ModelFactory;
-import com.hp.hpl.jena.rdf.model.Property;
-import com.hp.hpl.jena.rdf.model.Resource;
-import com.hp.hpl.jena.rdf.model.ResourceFactory;
-import com.hp.hpl.jena.rdf.model.Statement;
-import com.hp.hpl.jena.rdf.model.StmtIterator;
+import org.apache.jena.rdf.model.Model;
+import org.apache.jena.rdf.model.ModelFactory;
+import org.apache.jena.rdf.model.Property;
+import org.apache.jena.rdf.model.Resource;
+import org.apache.jena.rdf.model.ResourceFactory;
+import org.apache.jena.rdf.model.Statement;
+import org.apache.jena.rdf.model.StmtIterator;
 
 /**
  * @author sherif
@@ -71,7 +71,7 @@ public static void main(String[] args) {
 	}
 
 	/* (non-Javadoc)
-	 * @see org.aksw.geolift.modules.GeoLiftModule#process(com.hp.hpl.jena.rdf.model.Model, java.util.Map)
+	 * @see org.aksw.geolift.modules.GeoLiftModule#process(org.apache.jena.rdf.model.Model, java.util.Map)
 	 */
 	@Override
 	public Model process(Model model, Map<String, String> parameters) {
@@ -115,7 +115,7 @@ public Model filterModel(){
 		//				Resource o = ResourceFactory.createResource(str.split(">")[2].replaceAll("<", "").replaceAll(">", "").trim());
 		//				accepted.add(s, p, o);
 		//			}else if(str.split(">")[2].trim().startsWith("\"")){
-		//				com.hp.hpl.jena.rdf.model.Literal o = ResourceFactory.createPlainLiteral(str.split(">")[2]);
+		//				org.apache.jena.rdf.model.Literal o = ResourceFactory.createPlainLiteral(str.split(">")[2]);
 		//				accepted.add(s, p, o);
 		//			}
 		//		}
@@ -166,7 +166,7 @@ public List<String> getNecessaryParameters() {
 	}
 
 	/* (non-Javadoc)
-	 * @see org.aksw.geolift.modules.GeoLiftModule#selfConfig(com.hp.hpl.jena.rdf.model.Model, com.hp.hpl.jena.rdf.model.Model)
+	 * @see org.aksw.geolift.modules.GeoLiftModule#selfConfig(org.apache.jena.rdf.model.Model, org.apache.jena.rdf.model.Model)
 	 */
 	@Override
 	public Map<String, String> selfConfig(Model source, Model target) {

diff --git a/src/main/java/org/aksw/deer/modules/linking/LinkingModule.java b/src/main/java/org/aksw/deer/modules/linking/LinkingModule.java
@@ -9,51 +9,52 @@
 import org.aksw.deer.helper.vacabularies.SPECS;
 import org.aksw.deer.json.ParameterType;
 import org.aksw.deer.modules.DeerModule;
+import org.aksw.limes.core.io.config.reader.xml.XMLConfigurationReader;
 import org.apache.log4j.Logger;
 
-import com.hp.hpl.jena.rdf.model.Model;
-import com.hp.hpl.jena.rdf.model.ModelFactory;
-import com.hp.hpl.jena.rdf.model.Property;
-import com.hp.hpl.jena.rdf.model.RDFNode;
-import com.hp.hpl.jena.rdf.model.Resource;
-import com.hp.hpl.jena.rdf.model.Statement;
-import com.hp.hpl.jena.rdf.model.StmtIterator;
+import org.apache.jena.rdf.model.Model;
+import org.apache.jena.rdf.model.ModelFactory;
+import org.apache.jena.rdf.model.Property;
+import org.apache.jena.rdf.model.RDFNode;
+import org.apache.jena.rdf.model.Resource;
+import org.apache.jena.rdf.model.Statement;
+import org.apache.jena.rdf.model.StmtIterator;
 
-import de.uni_leipzig.simba.controller.PPJoinController;
+import org.aksw.limes.core.controller.Controller;
 
 /**
  * @author mofeed
  *
  */
 public class LinkingModule implements DeerModule{
 	private static final Logger logger = Logger.getLogger(LinkingModule.class.getName());
-	
+
 	private static final String LINKS_PART = "linkspart";
 	private static final String LINKS_FILE = "linksfile";
 	private static final String SPEC_FILE = "specfile";
-	
+
 	private static final String LINKS_PART_DESC = "Represents the position of the URI to be enriched in the links file";
 	private static final String LINKS_FILE_DESC = "file to save links resulted from the linking process";
 	private static final String SPEC_FILE_DESC = "The specification file used for linking process";
 
-	
+
 	private String specFilePath;
 	private String linksFilePath;
 	private String linksPart;
-	
+
 	/**
 	 * @param model: the model of the dataset to be enriched
 	 * @param parameters: list of parameters needed for the processing include:
 	 * datasetFilePath,specFilePath,linksFilePath,linksPart
 	 * @return model enriched with links generated from a linking tool
 	 */
 
-	public Model process(Model model, Map<String, String> parameters) 
+	public Model process(Model model, Map<String, String> parameters)
 	{
 		logger.info("--------------- Linking Module ---------------");
 		//Copy parameters from Map into List
-//		String datasetSource = parameters.get("datasetSource"); 
-		
+//		String datasetSource = parameters.get("datasetSource");
+
 		for(String key : parameters.keySet()){
 			if(key.equalsIgnoreCase(SPEC_FILE)){
 				specFilePath = parameters.get(SPEC_FILE);
@@ -67,14 +68,14 @@ public Model process(Model model, Map<String, String> parameters)
 				System.exit(1);
 			}
 		}
-	
+
 		model = setPrefixes(model);
 		linkingProcess(specFilePath);
 		model= addLinksToModel(model, linksFilePath,linksPart);
 		return model;
 	}
 
-	public List<String> getParameters() 
+	public List<String> getParameters()
 	{
 		List<String> parameters = new ArrayList<String>();
 //		parameters.add("datasetSource");
@@ -83,7 +84,7 @@ public List<String> getParameters()
 		parameters.add(LINKS_PART);
 		return parameters;
 	}
-	
+
 	/* (non-Javadoc)
 	 * @see org.aksw.geolift.modules.GeoLiftModule#getNecessaryParameters()
 	 */
@@ -99,7 +100,7 @@ public List<String> getNecessaryParameters() {
 	 */
 	private void linkingProcess(String specFilePath)
 	{
-		PPJoinController.run(specFilePath); 
+	    Controller.getMapping(new XMLConfigurationReader(specFilePath).read());
 	}
 	/**
 	 * @param model: the model of the dataset to be enriched
@@ -115,7 +116,7 @@ private Model addLinksToModel(Model model,String linksFilePath, String linksPart
 		StmtIterator iter = linksModel.listStatements();
 
 		// print out the predicate, subject and object of each statement
-		while (iter.hasNext()) 
+		while (iter.hasNext())
 		{
 			Statement stmt      = iter.nextStatement();  // get next statement
 			Resource  subject   = stmt.getSubject();     // get the subject
@@ -133,8 +134,8 @@ private Model addLinksToModel(Model model,String linksFilePath, String linksPart
 				resource = model.getResource(object.toString());
 				resource.addProperty(predicate, subject);
 			}
-		} 
-		return model; 
+		}
+		return model;
 	}
 
 	/**
@@ -143,7 +144,7 @@ private Model addLinksToModel(Model model,String linksFilePath, String linksPart
 	 * This function reads the links generated by a linking tool into a model
 	 */
 	private Model getLinks(String linksFilePath)
-	{ 	
+	{
 		Model model= ModelFactory.createDefaultModel();
 		model=org.aksw.deer.io.Reader.readModel(linksFilePath);
 		return model;
@@ -234,7 +235,7 @@ public static void main(String[] args) {
 	}
 
 	/* (non-Javadoc)
-	 * @see org.aksw.geolift.modules.GeoLiftModule#selfConfig(com.hp.hpl.jena.rdf.model.Model, com.hp.hpl.jena.rdf.model.Model)
+	 * @see org.aksw.geolift.modules.GeoLiftModule#selfConfig(org.apache.jena.rdf.model.Model, org.apache.jena.rdf.model.Model)
 	 */
 	@Override
 	public Map<String, String> selfConfig(Model source, Model target) {

diff --git a/src/main/java/org/aksw/deer/modules/nlp/LiteralPropertyRanker.java b/src/main/java/org/aksw/deer/modules/nlp/LiteralPropertyRanker.java
@@ -11,18 +11,18 @@
 
 import org.apache.log4j.Logger;
 
-import com.hp.hpl.jena.query.QueryExecution;
-import com.hp.hpl.jena.query.QueryExecutionFactory;
-import com.hp.hpl.jena.query.QueryFactory;
-import com.hp.hpl.jena.query.QuerySolution;
-import com.hp.hpl.jena.query.ResultSet;
-import com.hp.hpl.jena.rdf.model.Model;
-import com.hp.hpl.jena.rdf.model.ModelFactory;
-import com.hp.hpl.jena.rdf.model.NodeIterator;
-import com.hp.hpl.jena.rdf.model.Property;
-import com.hp.hpl.jena.rdf.model.RDFNode;
-import com.hp.hpl.jena.rdf.model.ResourceFactory;
-import com.hp.hpl.jena.util.FileManager;
+import org.apache.jena.query.QueryExecution;
+import org.apache.jena.query.QueryExecutionFactory;
+import org.apache.jena.query.QueryFactory;
+import org.apache.jena.query.QuerySolution;
+import org.apache.jena.query.ResultSet;
+import org.apache.jena.rdf.model.Model;
+import org.apache.jena.rdf.model.ModelFactory;
+import org.apache.jena.rdf.model.NodeIterator;
+import org.apache.jena.rdf.model.Property;
+import org.apache.jena.rdf.model.RDFNode;
+import org.apache.jena.rdf.model.ResourceFactory;
+import org.apache.jena.util.FileManager;
 
 
 /**