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Fix GH-6 migrate to rdf4j #7

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Fix GH-6 migrate to rdf4j #7

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f2eece0
protegeproject/rdf-library#6 pom dependencies migrated from sesame to…
abrokenjester Nov 17, 2018
9ed3cac
protegeproject/rdf-library#6 bumped owlapi to v5, got compilation err…
abrokenjester Nov 17, 2018
f4e47bb
protegeproject/rdf-library#6 replaced deprecated URI with IRI
abrokenjester Nov 17, 2018
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108 changes: 56 additions & 52 deletions pom.xml
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Original file line number Diff line number Diff line change
@@ -1,5 +1,7 @@
<?xml version="1.0" encoding="UTF-8"?>
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
<project xmlns="http://maven.apache.org/POM/4.0.0"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
<modelVersion>4.0.0</modelVersion>

<parent>
Expand Down Expand Up @@ -34,89 +36,91 @@
<email>tredmond@stanford.edu</email>
</developer>
</developers>

<scm>
<connection>scm:git:git@github.com:protegeproject/rdf-library.git</connection>
<developerConnection>scm:git:git@github.com:protegeproject/rdf-library.git</developerConnection>
<url>https://github.com/protegeproject/rdf-library</url>
</scm>

<properties>
<sesame.version>2.7.12</sesame.version>
<logback.version>1.1.3</logback.version>
<slf4j.version>1.7.12</slf4j.version>
<owlapi.version>4.2.8</owlapi.version>
<owlapi.version>5.1.7</owlapi.version>
<rdf4j.version>2.4.1</rdf4j.version>
</properties>

<dependencyManagement>
<dependencies>
<dependency>
<groupId>org.eclipse.rdf4j</groupId>
<artifactId>rdf4j-bom</artifactId>
<version>${rdf4j.version}</version>
<type>pom</type>
<scope>import</scope>
</dependency>
</dependencies>
</dependencyManagement>


<dependencies>
<dependency>
<groupId>org.openrdf.sesame</groupId>
<artifactId>sesame-repository-sail</artifactId>
<version>${sesame.version}</version>
<groupId>org.eclipse.rdf4j</groupId>
<artifactId>rdf4j-repository-sail</artifactId>
</dependency>

<dependency>
<groupId>org.openrdf.sesame</groupId>
<artifactId>sesame-sail-memory</artifactId>
<version>${sesame.version}</version>
<groupId>org.eclipse.rdf4j</groupId>
<artifactId>rdf4j-sail-memory</artifactId>
</dependency>

<dependency>
<groupId>org.openrdf.sesame</groupId>
<artifactId>sesame-rio-rdfxml</artifactId>
<version>${sesame.version}</version>
<groupId>org.eclipse.rdf4j</groupId>
<artifactId>rdf4j-rio-rdfxml</artifactId>
</dependency>

<dependency>
<groupId>org.openrdf.sesame</groupId>
<artifactId>sesame-model</artifactId>
<version>${sesame.version}</version>
<groupId>org.eclipse.rdf4j</groupId>
<artifactId>rdf4j-model</artifactId>
</dependency>

<dependency>
<groupId>org.openrdf.sesame</groupId>
<artifactId>sesame-queryparser-sparql</artifactId>
<version>${sesame.version}</version>
<groupId>org.eclipse.rdf4j</groupId>
<artifactId>rdf4j-queryparser-sparql</artifactId>
</dependency>

<dependency>
<groupId>org.openrdf.sesame</groupId>
<artifactId>sesame-queryparser-serql</artifactId>
<version>${sesame.version}</version>
<groupId>org.eclipse.rdf4j</groupId>
<artifactId>rdf4j-queryparser-serql</artifactId>
</dependency>

<dependency>
<groupId>ch.qos.logback</groupId>
<artifactId>logback-classic</artifactId>
<version>${logback.version}</version>
</dependency>

<dependency>
<groupId>ch.qos.logback</groupId>
<artifactId>logback-core</artifactId>
<version>${logback.version}</version>
</dependency>

<dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-api</artifactId>
<version>${slf4j.version}</version>
</dependency>

<dependency>
<groupId>net.sourceforge.owlapi</groupId>
<artifactId>owlapi-osgidistribution</artifactId>
<version>${owlapi.version}</version>
</dependency>

<dependency>
<groupId>org.testng</groupId>
<artifactId>testng</artifactId>
<version>6.8.21</version>
<scope>test</scope>
</dependency>
</dependencies>

<build>
<plugins>
<plugin>
Expand Down Expand Up @@ -157,7 +161,7 @@
</executions>
</plugin>

<plugin>
<plugin>
<groupId>org.apache.felix</groupId>
<artifactId>maven-bundle-plugin</artifactId>
<version>3.0.1</version>
Expand All @@ -166,24 +170,24 @@
<instructions>
<Bundle-SymbolicName>org.protege.owl.rdf;singleton:=true</Bundle-SymbolicName>
<Bundle-Vendor>The Protege Development Team</Bundle-Vendor>
<Embed-Dependency>sesame-queryparser-serql, sesame-queryparser-sparql</Embed-Dependency>
<Embed-Dependency>rdf4j-queryparser-serql,
rdf4j-queryparser-sparql</Embed-Dependency>
<Export-Package>
org.protege.owl.rdf*;version=${project.version},
info.aduna.*;version="2.7.0",
org.openrdf.*;version="2.7.0",
org.eclipse.rdf4j.*;version="2.4.1",
org.slf4j.*,
ch.qos.logback.*,
com.fasterxml.jackson.core.*;version="2.5.1"
</Export-Package>
<Export-Service>org.openrdf.query.parser.QueryParserFactory</Export-Service>
<Export-Service>org.eclipse.rdf4j.query.parser.QueryParserFactory</Export-Service>
<Import-Package>
!org.apache.commons.httpclient.*,
!groovy.lang,
!javax.jms,
!javax.mail.*,
!javax.servlet.*,
!org.codehaus.*,
!sun.reflect.*,
!org.apache.commons.httpclient.*,
!groovy.lang,
!javax.jms,
!javax.mail.*,
!javax.servlet.*,
!org.codehaus.*,
!sun.reflect.*,
*
</Import-Package>
</instructions>
Expand All @@ -197,7 +201,7 @@
</goals>
</execution>
</executions>
</plugin>
</plugin>

<plugin>
<groupId>org.apache.maven.plugins</groupId>
Expand All @@ -218,18 +222,18 @@
<suiteXmlFiles>
<suiteXmlFile>src/test/resources/unit-tests.xml</suiteXmlFile>
</suiteXmlFiles>
</configuration>
</configuration>
</execution>
</executions>
</plugin>

<plugin>
<artifactId>maven-eclipse-plugin</artifactId>
<version>2.9</version>
<configuration>
<pde>true</pde>
</configuration>
</plugin>
</plugin>
</plugins>
</build>
</project>
10 changes: 5 additions & 5 deletions src/main/java/org/protege/owl/rdf/Utilities.java
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@@ -1,10 +1,10 @@
package org.protege.owl.rdf;

import org.openrdf.repository.Repository;
import org.openrdf.repository.RepositoryException;
import org.openrdf.repository.sail.SailRepository;
import org.openrdf.sail.Sail;
import org.openrdf.sail.memory.MemoryStore;
import org.eclipse.rdf4j.repository.Repository;
import org.eclipse.rdf4j.repository.RepositoryException;
import org.eclipse.rdf4j.repository.sail.SailRepository;
import org.eclipse.rdf4j.sail.Sail;
import org.eclipse.rdf4j.sail.memory.MemoryStore;
import org.protege.owl.rdf.api.OwlTripleStore;
import org.protege.owl.rdf.impl.OwlTripleStoreImpl;
import org.protege.owl.rdf.impl.SynchronizeTripleStoreListener;
Expand Down
9 changes: 4 additions & 5 deletions src/main/java/org/protege/owl/rdf/api/OwlTripleStore.java
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Original file line number Diff line number Diff line change
@@ -1,10 +1,9 @@
package org.protege.owl.rdf.api;

import info.aduna.iteration.CloseableIteration;

import org.openrdf.model.BNode;
import org.openrdf.repository.Repository;
import org.openrdf.repository.RepositoryException;
import org.eclipse.rdf4j.common.iteration.CloseableIteration;
import org.eclipse.rdf4j.model.BNode;
import org.eclipse.rdf4j.repository.Repository;
import org.eclipse.rdf4j.repository.RepositoryException;
import org.semanticweb.owlapi.model.OWLAxiom;
import org.semanticweb.owlapi.model.OWLClassExpression;
import org.semanticweb.owlapi.model.OWLOntologyID;
Expand Down
33 changes: 18 additions & 15 deletions src/main/java/org/protege/owl/rdf/impl/AnonymousResourceHandler.java
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Original file line number Diff line number Diff line change
Expand Up @@ -17,6 +17,7 @@
import org.semanticweb.owlapi.model.OWLNamedIndividual;
import org.semanticweb.owlapi.model.OWLObject;
import org.semanticweb.owlapi.model.OWLOntologyID;
import org.semanticweb.owlapi.model.OWLOntologyManager;
import org.semanticweb.owlapi.util.OWLObjectDuplicator;

public class AnonymousResourceHandler {
Expand Down Expand Up @@ -108,15 +109,16 @@ private Set<OWLAnnotation> duplicateAxiomAnnotations(OWLAxiom axiom, OWLObjectDu

private class SurrogateInserter extends OWLObjectDuplicator {
public SurrogateInserter(OWLDataFactory factory) {
super(factory);
// FIXME this cast is _very_ likely not correct.
super((OWLOntologyManager)factory);
}

public void visit(OWLAnonymousIndividual i) {
public OWLAnonymousIndividual visit(OWLAnonymousIndividual i) {
IRI iri = getSurrogateId(i);
setLastObject(factory.getOWLNamedIndividual(iri));
return (OWLAnonymousIndividual)t(factory.getOWLNamedIndividual(iri));
}

public void visit(OWLAnnotationAssertionAxiom axiom) {
public OWLAnnotationAssertionAxiom visit(OWLAnnotationAssertionAxiom axiom) {
OWLObject rawSubject = duplicateObject(axiom.getSubject());
OWLAnnotationSubject subject;
if (rawSubject instanceof OWLNamedIndividual) {
Expand All @@ -134,10 +136,10 @@ public void visit(OWLAnnotationAssertionAxiom axiom) {
else {
value = (OWLAnnotationValue) rawValue;
}
setLastObject(factory.getOWLAnnotationAssertionAxiom(prop, subject, value, duplicateAxiomAnnotations(axiom, this)));
return t(factory.getOWLAnnotationAssertionAxiom(prop, subject, value, duplicateAxiomAnnotations(axiom, this)));
}

public void visit(OWLAnnotation node) {
public OWLAnnotation visit(OWLAnnotation node) {
OWLAnnotationProperty prop = duplicateObject(node.getProperty());
OWLObject rawValue = duplicateObject(node.getValue());
OWLAnnotationValue val;
Expand All @@ -147,27 +149,28 @@ public void visit(OWLAnnotation node) {
else {
val = (OWLAnnotationValue) rawValue;
}
setLastObject(factory.getOWLAnnotation(prop, val));
return t(factory.getOWLAnnotation(prop, val));
}

}

private class SurrogateRemover extends OWLObjectDuplicator {

public SurrogateRemover(OWLDataFactory factory) {
super(factory);
// FIXME this cast is _very_ likely not correct.
super((OWLOntologyManager)factory);
}

public void visit(OWLNamedIndividual i) {
public OWLNamedIndividual visit(OWLNamedIndividual i) {
if (isSurrogate(i.getIRI())) {
setLastObject(getAnonymousIndividual(i.getIRI()));
return (OWLNamedIndividual)t(getAnonymousIndividual(i.getIRI()));
}
else {
setLastObject(i);
return t(i);
}
}

public void visit(OWLAnnotationAssertionAxiom axiom) {
public OWLAnnotationAssertionAxiom visit(OWLAnnotationAssertionAxiom axiom) {
OWLAnnotationSubject subject = duplicateObject(axiom.getSubject());
if (subject instanceof IRI && isSurrogate((IRI) subject)) {
subject = getAnonymousIndividual((IRI) subject);
Expand All @@ -177,17 +180,17 @@ public void visit(OWLAnnotationAssertionAxiom axiom) {
if (value instanceof IRI && isSurrogate((IRI) value)) {
value = getAnonymousIndividual((IRI) value);
}
setLastObject(factory.getOWLAnnotationAssertionAxiom(prop, subject, value, duplicateAxiomAnnotations(axiom, this)));
return t(factory.getOWLAnnotationAssertionAxiom(prop, subject, value, duplicateAxiomAnnotations(axiom, this)));
}

public void visit(OWLAnnotation node) {
public OWLAnnotation visit(OWLAnnotation node) {
node.getProperty().accept(this);
OWLAnnotationProperty prop = (OWLAnnotationProperty) duplicateObject(node.getProperty());
OWLAnnotationValue val = (OWLAnnotationValue) duplicateObject(node.getValue());
if (val instanceof IRI && isSurrogate((IRI) val)) {
val = getAnonymousIndividual((IRI) val);
}
setLastObject(factory.getOWLAnnotation(prop, val));
return t(factory.getOWLAnnotation(prop, val));
}
}
}