Skip to content

Align version4 with RDF4J version used in version5 #1170

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
balhoff wants to merge 3 commits into
base: version4
Choose a base branch
from
+164 −178
Open

Align version4 with RDF4J version used in version5 #1170

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
2d47486
Issue #1145: Upgrade to RDF4J 5.x
reckart Jul 17, 2024
bf83722
GH-1145 update to RDF4J 5.0.2 and disable test case for handling of i…
hmottestad Aug 2, 2024
a2644c8
Fixes for RDF4J 5.
balhoff Jan 25, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
14 changes: 10 additions & 4 deletions contract/src/test/java/org/semanticweb/owlapi/api/test/baseclasses/TestBase.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -638,9 +638,13 @@ public OWLOntology roundTripOntology(OWLOntology ont, OWLDocumentFormat format)
format.setAddMissingTypes(addMissingTypes);
}
if (logger.isTraceEnabled()) {
logger.trace("TestBase.roundTripOntology() ontology originally");
ont.getAxioms().forEach(ax -> logger.trace(ax.toString()));
logger.trace("Original document (begin) ================");
StringDocumentTarget targetForDebug = new StringDocumentTarget();
m.saveOntology(ont, format, targetForDebug);
logger.trace(targetForDebug.toString());
logger.trace("Original document (end) ==================");
}
m.saveOntology(ont, format, target);
handleSaved(target, format);
Expand All @@ -650,10 +654,12 @@ public OWLOntology roundTripOntology(OWLOntology ont, OWLDocumentFormat format)
null), new OWLOntologyLoaderConfiguration().setReportStackTraces(true));
if (logger.isTraceEnabled()) {
logger.trace("TestBase.roundTripOntology() ontology parsed");
Set<OWLAxiom> axioms = ont2.getAxioms();
for (OWLAxiom ax : axioms) {
logger.trace(ax.toString());
}
ont2.getAxioms().forEach(ax -> logger.trace(ax.toString()));
logger.trace("Parsed document (begin) =================");
StringDocumentTarget targetForDebug = new StringDocumentTarget();
ont2.saveOntology(format, targetForDebug);
logger.trace(targetForDebug.toString());
logger.trace("Parsed document (end) ===================");
}
equal(ont, ont2);
return ont2;
Expand Down
3 changes: 3 additions & 0 deletions contract/src/test/java/org/semanticweb/owlapi/api/test/syntax/IRITestCase.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -3,6 +3,8 @@
import static org.junit.jupiter.api.Assertions.assertThrows;
import static org.junit.jupiter.api.Assertions.assertTrue;

import org.eclipse.rdf4j.rio.helpers.JSONLDSettings;
import org.junit.jupiter.api.Disabled;
import org.junit.jupiter.api.Test;
import org.semanticweb.owlapi.api.test.baseclasses.TestBase;
import org.semanticweb.owlapi.formats.FunctionalSyntaxDocumentFormat;
Expand Down Expand Up @@ -185,6 +187,7 @@ void shouldParseIRIAndSkipPrefixedSpaceRioTurtle() {
}

@Test
@Disabled("The correct behaviour for JSON-LD 1.1 is to skip invalid data, including IRIs that start with a space. A warning should be logged. To get an exception instead you can set JSONLDSettings.EXCEPTION_ON_WARNING.")
void shouldParseIRIAndSkipPrefixedSpaceJSONLD() {
roundTrip(new RDFJsonLDDocumentFormat(), BAD_JSON_LD);
}
Expand Down
6 changes: 3 additions & 3 deletions contract/src/test/java/org/semanticweb/owlapi/rio/RioRendererTestCase.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -15,7 +15,7 @@

import org.eclipse.rdf4j.model.Statement;
import org.eclipse.rdf4j.model.ValueFactory;
import org.eclipse.rdf4j.model.impl.ValueFactoryImpl;
import org.eclipse.rdf4j.model.impl.SimpleValueFactory;
import org.eclipse.rdf4j.model.vocabulary.OWL;
import org.eclipse.rdf4j.model.vocabulary.RDF;
import org.eclipse.rdf4j.rio.RDFFormat;
Expand Down Expand Up @@ -54,15 +54,15 @@ class RioRendererTestCase extends TestBase {

@BeforeEach
void setUp() {
vf = new ValueFactoryImpl();
vf = SimpleValueFactory.getInstance();
m.getOntologyStorers().set(new RioNTriplesStorerFactory(), new RioRDFXMLStorerFactory(),
new RioTurtleStorerFactory());
testOntologyEmpty = create(testOntologyUri1);
testOntologyKoala = loadOntologyFrom(getClass().getResourceAsStream("/koala.owl"));
assertEquals(70, testOntologyKoala.getAxiomCount());
testHandlerStatementCollector = new StatementCollector();
testOntologyEmptyStatement =
vf.createStatement(vf.createURI("urn:test:ontology:uri:1"), RDF.TYPE, OWL.ONTOLOGY);
vf.createStatement(vf.createIRI("urn:test:ontology:uri:1"), RDF.TYPE, OWL.ONTOLOGY);
testRdfXmlStringWriter = new StringWriter();
testRdfXmlRioWriter = Rio.createWriter(RDFFormat.RDFXML, testRdfXmlStringWriter);
testTurtleStringWriter = new StringWriter();
Expand Down
14 changes: 7 additions & 7 deletions contract/src/test/java/org/semanticweb/owlapi/rio/RioUtilsTestCase.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -8,9 +8,9 @@
import org.eclipse.rdf4j.model.BNode;
import org.eclipse.rdf4j.model.Literal;
import org.eclipse.rdf4j.model.Statement;
import org.eclipse.rdf4j.model.URI;
import org.eclipse.rdf4j.model.IRI;
import org.eclipse.rdf4j.model.ValueFactory;
import org.eclipse.rdf4j.model.impl.ValueFactoryImpl;
import org.eclipse.rdf4j.model.impl.SimpleValueFactory;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.BeforeEach;
import org.semanticweb.owlapi.api.test.baseclasses.TestBase;
Expand All @@ -26,7 +26,7 @@
class RioUtilsTestCase extends TestBase {

private static final String TEST_LITERAL = "Test literal";
private static final ValueFactory VF = ValueFactoryImpl.getInstance();
private static final ValueFactory VF = SimpleValueFactory.getInstance();
private RDFTriple testOwlApiTripleAllIRI;
private RDFTriple testOwlApiTriplePlainLiteral;
private RDFTriple testOwlApiTripleLangLiteral;
Expand Down Expand Up @@ -71,13 +71,13 @@ void setUp() {
new RDFTriple(testOwlApiSubjectUri1, testOwlApiPredicateUri1, testOwlApiObjectBNode1);
testOwlApiTripleSubjectObjectBNode =
new RDFTriple(testOwlApiSubjectBNode1, testOwlApiPredicateUri1, testOwlApiObjectBNode1);
URI testSesameSubjectUri1 = VF.createURI("urn:test:subject:uri:1");
URI testSesamePredicateUri1 = VF.createURI("urn:test:predicate:uri:1");
URI testSesameObjectUri1 = VF.createURI("urn:test:object:uri:1");
IRI testSesameSubjectUri1 = VF.createIRI("urn:test:subject:uri:1");
IRI testSesamePredicateUri1 = VF.createIRI("urn:test:predicate:uri:1");
IRI testSesameObjectUri1 = VF.createIRI("urn:test:object:uri:1");
Literal testSesameObjectPlainLiteral1 = VF.createLiteral(TEST_LITERAL);
Literal testSesameObjectLangLiteral1 = VF.createLiteral(TEST_LITERAL, "en");
Literal testSesameObjectTypedLiteral1 =
VF.createLiteral(TEST_LITERAL, VF.createURI("urn:test:datatype:1"));
VF.createLiteral(TEST_LITERAL, VF.createIRI("urn:test:datatype:1"));
BNode testSesameSubjectBNode1 = VF.createBNode("subjectBnode1");
BNode testSesameObjectBNode1 = VF.createBNode("objectBnode1");
testSesameTripleAllIRI = VF.createStatement(testSesameSubjectUri1, testSesamePredicateUri1,
Expand Down
2 changes: 1 addition & 1 deletion distribution/pom.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -47,7 +47,7 @@
<dependency><groupId>org.eclipse.rdf4j</groupId><artifactId>rdf4j-rio-trix</artifactId><version>${inherited.rdf4j.version}</version></dependency>
<dependency><groupId>org.eclipse.rdf4j</groupId><artifactId>rdf4j-rio-turtle</artifactId><version>${inherited.rdf4j.version}</version></dependency>
<dependency><groupId>org.eclipse.rdf4j</groupId><artifactId>rdf4j-rio-trig</artifactId><version>${inherited.rdf4j.version}</version></dependency>
<dependency><groupId>org.eclipse.rdf4j</groupId><artifactId>rdf4j-util</artifactId><version>${inherited.rdf4j.version}</version></dependency>
<dependency><groupId>org.eclipse.rdf4j</groupId><artifactId>rdf4j-rio-hdt</artifactId><version>${inherited.rdf4j.version}</version></dependency>
<dependency><groupId>com.github.jsonld-java</groupId><artifactId>jsonld-java</artifactId><version>0.13.6</version></dependency>
</dependencies>

Expand Down
23 changes: 18 additions & 5 deletions osgidistribution/pom.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -34,10 +34,14 @@
<dependency><groupId>org.tukaani</groupId><artifactId>xz</artifactId><version>1.9</version></dependency>
<dependency><groupId>org.slf4j</groupId><artifactId>slf4j-api</artifactId><version>2.0.11</version></dependency>
<dependency><groupId>org.slf4j</groupId><artifactId>jcl-over-slf4j</artifactId><version>2.0.11</version></dependency>
<dependency><groupId>org.eclipse.rdf4j</groupId><artifactId>rdf4j-model</artifactId><version>${inherited.rdf4j.version}</version></dependency>
<dependency><groupId>org.eclipse.rdf4j</groupId><artifactId>rdf4j-model-api</artifactId><version>${inherited.rdf4j.version}</version></dependency>
<dependency><groupId>org.eclipse.rdf4j</groupId><artifactId>rdf4j-model-vocabulary</artifactId><version>${inherited.rdf4j.version}</version></dependency>
<dependency><groupId>org.eclipse.rdf4j</groupId><artifactId>rdf4j-rio-api</artifactId><version>${inherited.rdf4j.version}</version></dependency>
<dependency><groupId>org.slf4j</groupId><artifactId>slf4j-api</artifactId><version>1.7.30</version></dependency>
<dependency><groupId>org.slf4j</groupId><artifactId>jcl-over-slf4j</artifactId><version>1.7.30</version></dependency>
<dependency><groupId>org.eclipse.rdf4j</groupId><artifactId>rdf4j-rio-api</artifactId><version>${inherited.rdf4j.version}</version>
<exclusions>
<exclusion><groupId>javax.xml.bind</groupId><artifactId>jaxb-api</artifactId></exclusion>
<exclusion><groupId>jakarta.xml.bind</groupId><artifactId>jakarta.xml.bind-api</artifactId></exclusion>
</exclusions>
</dependency>
<dependency><groupId>org.eclipse.rdf4j</groupId><artifactId>rdf4j-rio-languages</artifactId><version>${inherited.rdf4j.version}</version></dependency>
<dependency><groupId>org.eclipse.rdf4j</groupId><artifactId>rdf4j-rio-datatypes</artifactId><version>${inherited.rdf4j.version}</version></dependency>
<dependency><groupId>org.eclipse.rdf4j</groupId><artifactId>rdf4j-rio-binary</artifactId><version>${inherited.rdf4j.version}</version></dependency>
Expand All @@ -50,7 +54,16 @@
<dependency><groupId>org.eclipse.rdf4j</groupId><artifactId>rdf4j-rio-trix</artifactId><version>${inherited.rdf4j.version}</version></dependency>
<dependency><groupId>org.eclipse.rdf4j</groupId><artifactId>rdf4j-rio-turtle</artifactId><version>${inherited.rdf4j.version}</version></dependency>
<dependency><groupId>org.eclipse.rdf4j</groupId><artifactId>rdf4j-rio-trig</artifactId><version>${inherited.rdf4j.version}</version></dependency>
<dependency><groupId>org.eclipse.rdf4j</groupId><artifactId>rdf4j-util</artifactId><version>${inherited.rdf4j.version}</version></dependency>
<dependency><groupId>org.eclipse.rdf4j</groupId><artifactId>rdf4j-rio-hdt</artifactId><version>${inherited.rdf4j.version}</version></dependency>
<dependency><groupId>org.eclipse.rdf4j</groupId><artifactId>rdf4j-common-annotation</artifactId><version>${inherited.rdf4j.version}</version></dependency>
<dependency><groupId>org.eclipse.rdf4j</groupId><artifactId>rdf4j-common-exception</artifactId><version>${inherited.rdf4j.version}</version></dependency>
<dependency><groupId>org.eclipse.rdf4j</groupId><artifactId>rdf4j-model-vocabulary</artifactId><version>${inherited.rdf4j.version}</version></dependency>
<dependency><groupId>org.eclipse.rdf4j</groupId><artifactId>rdf4j-model-api</artifactId><version>${inherited.rdf4j.version}</version></dependency>
<dependency><groupId>org.eclipse.rdf4j</groupId><artifactId>rdf4j-common-text</artifactId><version>${inherited.rdf4j.version}</version></dependency>
<dependency><groupId>org.eclipse.rdf4j</groupId><artifactId>rdf4j-common-io</artifactId><version>${inherited.rdf4j.version}</version></dependency>
<dependency><groupId>org.eclipse.rdf4j</groupId><artifactId>rdf4j-common-iterator</artifactId><version>${inherited.rdf4j.version}</version></dependency>
<dependency><groupId>org.eclipse.rdf4j</groupId><artifactId>rdf4j-model</artifactId><version>${inherited.rdf4j.version}</version></dependency>
<dependency><groupId>org.eclipse.rdf4j</groupId><artifactId>rdf4j-common-xml</artifactId><version>${inherited.rdf4j.version}</version></dependency>
<dependency><groupId>com.github.jsonld-java</groupId><artifactId>jsonld-java</artifactId><version>0.13.6</version></dependency>
<dependency><groupId>org.apache.httpcomponents</groupId><artifactId>httpclient</artifactId><version>4.5.14</version></dependency>
<dependency><groupId>org.apache.httpcomponents</groupId><artifactId>httpclient-cache</artifactId><version>4.5.14</version></dependency>
Expand Down
5 changes: 3 additions & 2 deletions pom.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -24,8 +24,9 @@
<properties>
<!-- Specify the encoding of the source files. -->
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<rdf4j.version>3.7.7</rdf4j.version>
<!-- remove this line for releases, if the release process fails because of missing javadoc jars -->
<rdf4j.version>5.0.2</rdf4j.version>
<!-- remove this line for releases, if the release process fails because
of missing javadoc jars -->
<no-javadoc>false</no-javadoc>
<!-- 4.0.0 is the earliest release on Maven Central for this series -->
<last.japicmp.compare.version>4.0.0</last.japicmp.compare.version>
Expand Down
20 changes: 10 additions & 10 deletions rio/src/main/java/org/semanticweb/owlapi/rio/OWLAPIRioTrixParser.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -42,11 +42,11 @@
import org.eclipse.rdf4j.model.Statement;
import org.eclipse.rdf4j.model.Value;
import org.eclipse.rdf4j.model.ValueFactory;
import org.eclipse.rdf4j.model.impl.ValueFactoryImpl;
import org.eclipse.rdf4j.model.impl.SimpleValueFactory;
import org.eclipse.rdf4j.rio.RDFFormat;
import org.eclipse.rdf4j.rio.RDFHandlerException;
import org.eclipse.rdf4j.rio.RDFParseException;
import org.eclipse.rdf4j.rio.helpers.RDFParserBase;
import org.eclipse.rdf4j.rio.helpers.AbstractRDFParser;
import org.eclipse.rdf4j.rio.helpers.TriXParserSettings;
import org.semanticweb.owlapi.rio.utils.OWLAPISimpleSAXParser;
import org.xml.sax.SAXException;
Expand All @@ -59,14 +59,14 @@
* @author Arjohn Kampman Modified to install error handler by Simon Spero, because error handler.
*/

class OWLAPIRioTrixParser extends RDFParserBase {
class OWLAPIRioTrixParser extends AbstractRDFParser {

/*--------------*
* Constructors *
*--------------*/

/**
* Creates a new TriXParser that will use a {@link ValueFactoryImpl} to create objects for
* Creates a new TriXParser that will use a {@link SimpleValueFactory} to create objects for
* resources, bNodes, literals and statements.
*/
public OWLAPIRioTrixParser() {
Expand Down Expand Up @@ -180,7 +180,7 @@ public void startTag(String tagName, Map<String, String> atts, String text)

if (datatype == null) {
reportError(DATATYPE_ATT + " attribute missing for typed literal",
TriXParserSettings.FAIL_ON_TRIX_MISSING_DATATYPE);
TriXParserSettings.FAIL_ON_MISSING_DATATYPE);
valueList.add(createLiteral(text, null, null));
} else {
IRI dtURI = createURI(datatype);
Expand All @@ -193,11 +193,11 @@ public void startTag(String tagName, Map<String, String> atts, String text)
// context information
if (valueList.size() > 1) {
reportError("At most 1 resource can be specified for the context",
TriXParserSettings.FAIL_ON_TRIX_INVALID_STATEMENT);
TriXParserSettings.FAIL_ON_INVALID_STATEMENT);
} else if (valueList.size() == 1) {
if (!(valueList.get(0) instanceof Resource)) {
reportError("Context identifier should be a URI or blank node",
TriXParserSettings.FAIL_ON_TRIX_INVALID_STATEMENT);
TriXParserSettings.FAIL_ON_INVALID_STATEMENT);
} else {
currentContext = (Resource) valueList.get(0);
}
Expand Down Expand Up @@ -234,17 +234,17 @@ private void reportStatement() throws RDFParseException, RDFHandlerException {
try {
if (valueList.size() != 3) {
reportError("exactly 3 values are required for a triple",
TriXParserSettings.FAIL_ON_TRIX_INVALID_STATEMENT);
TriXParserSettings.FAIL_ON_INVALID_STATEMENT);
return;
}
if (!(valueList.get(0) instanceof Resource)) {
reportError("First value for a triple should be a URI or blank node",
TriXParserSettings.FAIL_ON_TRIX_INVALID_STATEMENT);
TriXParserSettings.FAIL_ON_INVALID_STATEMENT);
return;
}
if (!(valueList.get(1) instanceof IRI)) {
reportError("Second value for a triple should be a URI",
TriXParserSettings.FAIL_ON_TRIX_INVALID_STATEMENT);
TriXParserSettings.FAIL_ON_INVALID_STATEMENT);
return;
}

Expand Down
Loading