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AML Project ported to OWLApi v4.x #3

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f1085c4
Create README.md
teymourlouie Dec 9, 2015
9d0cdd4
AML ported to OWL Api v4.x
teymourlouie Dec 10, 2015
c6c3ec0
change uri getting code wrt. Optional<> class used in getting OntologyID
teymourlouie Dec 10, 2015
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5 changes: 3 additions & 2 deletions AgreementMakerLight/.classpath
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Original file line number Diff line number Diff line change
Expand Up @@ -6,8 +6,9 @@
<classpathentry kind="lib" path="src/lib/jaws.jar"/>
<classpathentry kind="lib" path="src/lib/simmetrics.jar"/>
<classpathentry kind="lib" path="src/lib/gephi-toolkit.jar"/>
<classpathentry kind="lib" path="src/lib/elk.jar"/>
<classpathentry kind="lib" path="src/lib/owlapi.jar"/>
<classpathentry kind="lib" path="src/lib/net.sourceforge.owlapi/pellet-core-ignazio1977/2.4.0-ignazio1977/pellet-core-ignazio1977-2.4.0-ignazio1977.jar"/>
<classpathentry kind="lib" path="src/lib/net.sourceforge.owlapi/pellet-core-ignazio1977/2.4.0-ignazio1977/pellet-owlapi-ignazio1977-2.4.0-ignazio1977.jar"/>
<classpathentry kind="lib" path="src/lib/owlapi-distribution-4.1.3.jar"/>
<classpathentry kind="lib" path="src/lib/log4j.jar"/>
<classpathentry kind="lib" path="src/lib/microsoft-translator.jar"/>
<classpathentry kind="lib" path="src/lib/commons-lang-2.6.jar"/>
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61 changes: 53 additions & 8 deletions AgreementMakerLight/pom.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@
<groupId>aml</groupId>
<artifactId>aml</artifactId>
<packaging>jar</packaging>
<version>2.1-SNAPSHOT</version>
<version>2.1-owlapi4</version>

<name>AgreementMakerLight</name>
<url>http://somer.fc.ul.pt/aml.php</url>
Expand All @@ -30,6 +30,11 @@
<checksumPolicy>fail</checksumPolicy>
</releases>
</repository>
<repository>
<id>in-project</id>
<name>In Project Repo</name>
<url>file://${project.basedir}/src/lib</url>
</repository>
</repositories>

<build>
Expand Down Expand Up @@ -68,6 +73,15 @@
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.3</version>
<configuration>
<source>1.8</source>
<target>1.8</target>
</configuration>
</plugin>
</plugins>
</build>

Expand All @@ -82,16 +96,17 @@
<artifactId>dom4j</artifactId>
<version>1.6.1</version>
</dependency>
<dependency>
<groupId>org.semanticweb.elk</groupId>
<artifactId>elk-owlapi-standalone</artifactId>
<version>0.4.1</version>
<classifier>bin</classifier>
</dependency>
<dependency>
<groupId>org.gephi</groupId>
<artifactId>gephi-toolkit</artifactId>
<version>0.8.2</version>
<exclusions>
<exclusion>
<!-- whatever the correct values are -->
<artifactId>google-collections</artifactId>
<groupId>com.google.collections</groupId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>edu.smu.tspell.wordnet</groupId>
Expand All @@ -112,7 +127,7 @@
<dependency>
<groupId>net.sourceforge.owlapi</groupId>
<artifactId>owlapi-distribution</artifactId>
<version>3.4.10</version>
<version>4.1.3</version>
</dependency>
<dependency>
<groupId>uk.ac.shef.wit</groupId>
Expand All @@ -124,5 +139,35 @@
<artifactId>swingx-all</artifactId>
<version>1.6.4</version>
</dependency>

<!--Pellet Reasoner-->
<dependency>
<groupId>net.sourceforge.owlapi</groupId>
<artifactId>pellet-core-ignazio1977</artifactId>
<version>2.4.0-ignazio1977</version>
</dependency>

<dependency>
<groupId>net.sourceforge.owlapi</groupId>
<artifactId>pellet-owlapi-ignazio1977</artifactId>
<version>2.4.0-ignazio1977</version>
</dependency>

<dependency>
<groupId>com.github.ansell.aterms</groupId>
<artifactId>aterm-java</artifactId>
<version>1.8.2-p1</version>
<scope>runtime</scope>
</dependency>

<dependency>
<groupId>org.jgrapht</groupId>
<artifactId>jgrapht-core</artifactId>
<version>0.9.1</version>
<scope>runtime</scope>
</dependency>


<!-- end Pellet Reasoner-->
</dependencies>
</project>
189 changes: 92 additions & 97 deletions AgreementMakerLight/src/aml/ontology/BKOntology.java
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Original file line number Diff line number Diff line change
@@ -1,49 +1,44 @@
/******************************************************************************
* Copyright 2013-2015 LASIGE *
* *
* Licensed under the Apache License, Version 2.0 (the "License"); you may *
* not use this file except in compliance with the License. You may obtain a *
* copy of the License at http://www.apache.org/licenses/LICENSE-2.0 *
* *
* Unless required by applicable law or agreed to in writing, software *
* distributed under the License is distributed on an "AS IS" BASIS, *
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. *
* See the License for the specific language governing permissions and *
* limitations under the License. *
* *
*******************************************************************************
* An Ontology object, loaded using the OWL API. *
* *
* @author Daniel Faria *
* @date 13-08-2015 *
******************************************************************************/
* Copyright 2013-2015 LASIGE *
* *
* Licensed under the Apache License, Version 2.0 (the "License"); you may *
* not use this file except in compliance with the License. You may obtain a *
* copy of the License at http://www.apache.org/licenses/LICENSE-2.0 *
* *
* Unless required by applicable law or agreed to in writing, software *
* distributed under the License is distributed on an "AS IS" BASIS, *
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. *
* See the License for the specific language governing permissions and *
* limitations under the License. *
* *
*******************************************************************************
* An Ontology object, loaded using the OWL API. *
* *
* @author Daniel Faria *
* @date 13-08-2015 *
******************************************************************************/
package aml.ontology;

import java.io.File;
import java.util.Set;

import org.semanticweb.owlapi.model.IRI;
import org.semanticweb.owlapi.model.OWLAnnotation;
import org.semanticweb.owlapi.model.OWLAnnotationProperty;
import org.semanticweb.owlapi.model.OWLClass;
import org.semanticweb.owlapi.model.OWLLiteral;
import org.semanticweb.owlapi.model.OWLNamedIndividual;
import org.semanticweb.owlapi.model.OWLOntology;
import org.semanticweb.owlapi.model.OWLOntologyCreationException;
import org.semanticweb.owlapi.vocab.OWLRDFVocabulary;

import aml.settings.LexicalType;
import aml.util.StringParser;
import org.semanticweb.owlapi.model.*;
import org.semanticweb.owlapi.model.parameters.Imports;
import org.semanticweb.owlapi.search.EntitySearcher;
import org.semanticweb.owlapi.vocab.OWLRDFVocabulary;

import java.io.File;
import java.util.HashSet;
import java.util.Set;

public class BKOntology extends Ontology
{

//Attributes

//Its map of cross-references
protected ReferenceMap refs;


//Constructors

/**
Expand All @@ -54,26 +49,26 @@ public BKOntology()
super();
refs = new ReferenceMap();
}

/**
* Constructs an Ontology from file
* Constructs an Ontology from file
* @param path: the path to the input Ontology file
* @throws OWLOntologyCreationException
* @throws OWLOntologyCreationException
*/
public BKOntology(String path) throws OWLOntologyCreationException
{
this();
//Load the local ontology
File f = new File(path);
OWLOntology o;
//Load the local ontology
File f = new File(path);
OWLOntology o;
o = manager.loadOntologyFromOntologyDocument(f);
uri = f.getAbsolutePath();
init(o);
//Close the OntModel
manager.removeOntology(o);
//Reset the entity expansion limit
System.clearProperty(LIMIT);
//Check if a xrefs file with the same name as the ontology exists
manager.removeOntology(o);
//Reset the entity expansion limit
System.clearProperty(LIMIT);
//Check if a xrefs file with the same name as the ontology exists
String refName = path.substring(0,path.lastIndexOf(".")) + ".xrefs";
f = new File(refName);
if(f.exists())
Expand All @@ -89,35 +84,35 @@ public void close()
super.close();
refs = null;
}

/**
* @return the ReferenceMap of the Ontology
*/
public ReferenceMap getReferenceMap()
{
return refs;
}
//Private Methods

//Private Methods

//Builds the ontology data structures
private void init(OWLOntology o)
{
//Update the URI of the ontology (if it lists one)
if(o.getOntologyID().getOntologyIRI() != null)
uri = o.getOntologyID().getOntologyIRI().toString();
if(o.getOntologyID().getOntologyIRI().isPresent())
uri = o.getOntologyID().getOntologyIRI().get().toString();

//Get the classes and their lexical and cross-reference information
//The internal index of the class
int id = 0;
//The Lexical type and weight
LexicalType type;
double weight;

//The label property
OWLAnnotationProperty label = factory.getOWLAnnotationProperty(OWLRDFVocabulary.RDFS_LABEL.getIRI());
//Get an iterator over the ontology classes
Set<OWLClass> owlClasses = o.getClassesInSignature(true);
Set<OWLClass> owlClasses = o.getClassesInSignature(Imports.INCLUDED);
//Then get the URI for each class
for(OWLClass c : owlClasses)
{
Expand All @@ -128,7 +123,7 @@ private void init(OWLOntology o)
classes.add(++id);
//Get the local name from the URI
String name = getLocalName(classUri);

//If the local name is not an alphanumeric code, add it to the lexicon
if(!StringParser.isNumericId(name))
{
Expand All @@ -138,56 +133,56 @@ private void init(OWLOntology o)
}

//Now get the class's annotations (including imports)
Set<OWLAnnotation> annots = c.getAnnotations(o);
Set<OWLAnnotation> annots = new HashSet<>(EntitySearcher.getAnnotations(c, o));
for(OWLOntology ont : o.getImports())
annots.addAll(c.getAnnotations(ont));
for(OWLAnnotation annotation : annots)
{
//Labels and synonyms go to the Lexicon
String propUri = annotation.getProperty().getIRI().toString();
type = LexicalType.getLexicalType(propUri);
if(type != null)
{
weight = type.getDefaultWeight();
if(annotation.getValue() instanceof OWLLiteral)
{
OWLLiteral val = (OWLLiteral) annotation.getValue();
name = val.getLiteral();
String lang = val.getLang();
if(lang.equals(""))
lang = "en";
lex.addClass(id, name, lang, type, "", weight);
}
else if(annotation.getValue() instanceof IRI)
{
OWLNamedIndividual ni = factory.getOWLNamedIndividual((IRI) annotation.getValue());
for(OWLAnnotation a : ni.getAnnotations(o,label))
{
if(a.getValue() instanceof OWLLiteral)
{
OWLLiteral val = (OWLLiteral) a.getValue();
name = val.getLiteral();
String lang = val.getLang();
if(lang.equals(""))
lang = "en";
lex.addClass(id, name, lang, type, "", weight);
}
}
}
}
//xRefs go to the ReferenceMap
else if(propUri.endsWith("hasDbXref") &&
annotation.getValue() instanceof OWLLiteral)
{
OWLLiteral val = (OWLLiteral) annotation.getValue();
annots.addAll(EntitySearcher.getAnnotations(c, ont));
for(OWLAnnotation annotation : annots)
{
//Labels and synonyms go to the Lexicon
String propUri = annotation.getProperty().getIRI().toString();
type = LexicalType.getLexicalType(propUri);
if(type != null)
{
weight = type.getDefaultWeight();
if(annotation.getValue() instanceof OWLLiteral)
{
OWLLiteral val = (OWLLiteral) annotation.getValue();
name = val.getLiteral();
String lang = val.getLang();
if(lang.equals(""))
lang = "en";
lex.addClass(id, name, lang, type, "", weight);
}
else if(annotation.getValue() instanceof IRI)
{
OWLNamedIndividual ni = factory.getOWLNamedIndividual((IRI) annotation.getValue());
for(OWLAnnotation a : EntitySearcher.getAnnotations(ni, o, label))
{
if(a.getValue() instanceof OWLLiteral)
{
OWLLiteral val = (OWLLiteral) a.getValue();
name = val.getLiteral();
String lang = val.getLang();
if(lang.equals(""))
lang = "en";
lex.addClass(id, name, lang, type, "", weight);
}
}
}
}
//xRefs go to the ReferenceMap
else if(propUri.endsWith("hasDbXref") &&
annotation.getValue() instanceof OWLLiteral)
{
OWLLiteral val = (OWLLiteral) annotation.getValue();
String xRef = val.getLiteral();
if(!xRef.startsWith("http"))
refs.add(id,xRef.replace(':','_'));
}
}
}
}
}
}

//Get the local name of an entity from its URI
private String getLocalName(String uri)
{
Expand Down
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