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Migrate to Jena 4.10 #389

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Migrate to Jena 4.10 #389

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44e06ef
build: switch to Jena SNAPSHOT
berezovskyi Aug 14, 2023
7a196df
finish Jena 5 move
berezovskyi Aug 14, 2023
cb21e4e
feat: initial support for ReifierStd
berezovskyi Aug 21, 2023
176a8b9
chore: cleanup
berezovskyi Aug 21, 2023
1b3ff4a
chore: typo
berezovskyi Aug 21, 2023
fef35e4
Target Jena 4.11 SNAPSHOT
berezovskyi Nov 6, 2023
cedf991
build: convergence
berezovskyi Nov 6, 2023
aa86ea7
build: typo
berezovskyi Nov 6, 2023
61282a6
feat: target Jena 5
berezovskyi Nov 6, 2023
c2e9400
try dropping down to 4.10.0
berezovskyi Oct 9, 2024
b7d396b
Merge branch 'master' into b-jena-next
berezovskyi Oct 9, 2024
571db3c
fix: Guava import
berezovskyi Oct 9, 2024
0d72ba8
Merge branch 'master' into b-jena-next
berezovskyi Oct 9, 2024
1128498
Merge branch 'master' into b-jena-next
berezovskyi Oct 21, 2024
b5dd083
Merge branch 'master' into b-jena-next
berezovskyi Nov 6, 2024
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4 changes: 4 additions & 0 deletions core/lyo-core-settings/pom.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -82,6 +82,10 @@
<artifactId>jersey-common</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>com.google.guava</groupId>
<artifactId>guava</artifactId>
</dependency>
</dependencies>

<build>
Expand Down
2 changes: 1 addition & 1 deletion core/lyo-core-settings/src/main/java/org/eclipse/lyo/oslc4j/core/OSLC4JUtils.java
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Original file line number Diff line number Diff line change
Expand Up @@ -36,13 +36,13 @@
import javax.xml.parsers.DocumentBuilderFactory;
import javax.xml.parsers.ParserConfigurationException;

import com.google.common.base.Strings;
import org.apache.jena.datatypes.DatatypeFormatException;
import org.apache.jena.datatypes.RDFDatatype;
import org.apache.jena.datatypes.TypeMapper;
import org.apache.jena.datatypes.xsd.XSDDatatype;
import org.apache.jena.datatypes.xsd.XSDDateTime;
import org.apache.jena.datatypes.xsd.impl.XMLLiteralType;
import org.apache.jena.ext.com.google.common.base.Strings;
import org.apache.jena.rdf.model.Property;
import org.eclipse.lyo.oslc4j.core.model.ResourceShape;
import org.eclipse.lyo.oslc4j.core.model.XMLLiteral;
Expand Down
10 changes: 10 additions & 0 deletions core/oslc4j-core/pom.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -113,6 +113,16 @@
<artifactId>jersey-common</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.junit.jupiter</groupId>
<artifactId>junit-jupiter-api</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.junit.jupiter</groupId>
<artifactId>junit-jupiter-engine</artifactId>
<scope>test</scope>
</dependency>
</dependencies>
<build>
<plugins>
Expand Down
165 changes: 120 additions & 45 deletions core/oslc4j-core/src/main/java/org/eclipse/lyo/oslc4j/provider/jena/JenaModelHelper.java
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
/*
* Copyright (c) 2020 Contributors to the Eclipse Foundation
* Copyright (c) 2023 Contributors to the Eclipse Foundation
*
* See the NOTICE file(s) distributed with this work for additional
* information regarding copyright ownership.
Expand All @@ -13,40 +13,71 @@
*/
package org.eclipse.lyo.oslc4j.provider.jena;

import org.apache.jena.rdf.model.Container;
import org.apache.jena.rdf.model.NodeIterator;
import org.apache.jena.rdf.model.Literal;
import org.apache.jena.rdf.model.Model;
import org.apache.jena.rdf.model.Property;
import org.apache.jena.datatypes.DatatypeFormatException;
import org.apache.jena.datatypes.RDFDatatype;
import org.apache.jena.rdf.model.ReifiedStatement;
import org.apache.jena.rdf.model.Resource;
import org.apache.jena.rdf.model.Statement;

import org.apache.jena.datatypes.xsd.XSDDatatype;
import org.apache.jena.datatypes.xsd.XSDDateTime;
import org.apache.jena.datatypes.xsd.impl.XMLLiteralType;
import org.apache.jena.datatypes.xsd.impl.XSDDateType;
import org.apache.jena.graph.BlankNodeId;
import org.apache.jena.graph.Graph;
import org.apache.jena.graph.Node;
import org.apache.jena.rdf.model.Alt;
import org.apache.jena.rdf.model.AnonId;
import org.apache.jena.rdf.model.Bag;
import org.apache.jena.rdf.model.Container;
import org.apache.jena.rdf.model.Literal;
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.RDFList;
import org.apache.jena.rdf.model.RDFNode;
import org.apache.jena.rdf.model.RSIterator;
import org.apache.jena.rdf.model.ReifiedStatement;
import org.apache.jena.rdf.model.ResIterator;
import org.apache.jena.rdf.model.Resource;
import org.apache.jena.rdf.model.Seq;
import org.apache.jena.rdf.model.SimpleSelector;
import org.apache.jena.rdf.model.Statement;
import org.apache.jena.rdf.model.StmtIterator;
import org.apache.jena.graph.BlankNodeId;
import org.apache.jena.datatypes.DatatypeFormatException;
import org.apache.jena.datatypes.xsd.XSDDatatype;
import org.apache.jena.datatypes.xsd.XSDDateTime;
import org.apache.jena.datatypes.xsd.impl.XMLLiteralType;
import org.apache.jena.datatypes.xsd.impl.XSDDateType;
import org.apache.jena.rdf.model.impl.ReifierStd;
import org.apache.jena.util.ResourceUtils;
import org.apache.jena.util.iterator.ExtendedIterator;
import org.apache.jena.vocabulary.RDF;
import org.apache.jena.vocabulary.RDFS;
import org.apache.jena.util.ResourceUtils;

import org.eclipse.lyo.oslc4j.core.*;
import org.eclipse.lyo.oslc4j.core.annotation.*;
import org.eclipse.lyo.oslc4j.core.exception.*;
import org.eclipse.lyo.oslc4j.core.model.*;
import org.eclipse.lyo.oslc4j.core.NestedWildcardProperties;
import org.eclipse.lyo.oslc4j.core.OSLC4JConstants;
import org.eclipse.lyo.oslc4j.core.OSLC4JUtils;
import org.eclipse.lyo.oslc4j.core.OslcGlobalNamespaceProvider;
import org.eclipse.lyo.oslc4j.core.SingletonWildcardProperties;
import org.eclipse.lyo.oslc4j.core.UnparseableLiteral;
import org.eclipse.lyo.oslc4j.core.annotation.OslcName;
import org.eclipse.lyo.oslc4j.core.annotation.OslcNamespaceDefinition;
import org.eclipse.lyo.oslc4j.core.annotation.OslcPropertyDefinition;
import org.eclipse.lyo.oslc4j.core.annotation.OslcRdfCollectionType;
import org.eclipse.lyo.oslc4j.core.annotation.OslcResourceShape;
import org.eclipse.lyo.oslc4j.core.annotation.OslcSchema;
import org.eclipse.lyo.oslc4j.core.annotation.OslcValueType;
import org.eclipse.lyo.oslc4j.core.exception.LyoModelException;
import org.eclipse.lyo.oslc4j.core.exception.OslcCoreApplicationException;
import org.eclipse.lyo.oslc4j.core.exception.OslcCoreInvalidPropertyDefinitionException;
import org.eclipse.lyo.oslc4j.core.exception.OslcCoreMissingSetMethodException;
import org.eclipse.lyo.oslc4j.core.exception.OslcCoreMisusedOccursException;
import org.eclipse.lyo.oslc4j.core.exception.OslcCoreRelativeURIException;
import org.eclipse.lyo.oslc4j.core.model.AbstractResource;
import org.eclipse.lyo.oslc4j.core.model.AnyResource;
import org.eclipse.lyo.oslc4j.core.model.FilteredResource;
import org.eclipse.lyo.oslc4j.core.model.IExtendedResource;
import org.eclipse.lyo.oslc4j.core.model.IOslcCustomNamespaceProvider;
import org.eclipse.lyo.oslc4j.core.model.IReifiedResource;
import org.eclipse.lyo.oslc4j.core.model.IResource;
import org.eclipse.lyo.oslc4j.core.model.InheritedMethodAnnotationHelper;
import org.eclipse.lyo.oslc4j.core.model.Link;
import org.eclipse.lyo.oslc4j.core.model.OslcConstants;
import org.eclipse.lyo.oslc4j.core.model.ResponseInfo;
import org.eclipse.lyo.oslc4j.core.model.TypeFactory;
import org.eclipse.lyo.oslc4j.core.model.ValueType;
import org.eclipse.lyo.oslc4j.core.model.XMLLiteral;
import org.eclipse.lyo.oslc4j.provider.jena.ordfm.ResourcePackages;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
Expand All @@ -63,14 +94,40 @@
import javax.xml.transform.dom.DOMSource;
import javax.xml.transform.stream.StreamResult;
import java.io.StringWriter;
import java.lang.reflect.*;
import java.lang.reflect.Array;
import java.lang.reflect.InvocationTargetException;
import java.lang.reflect.Method;
import java.lang.reflect.ParameterizedType;
import java.lang.reflect.Type;
import java.math.BigDecimal;
import java.math.BigInteger;
import java.net.URI;
import java.net.URISyntaxException;
import java.time.Duration;
import java.time.Instant;
import java.util.*;
import java.util.AbstractCollection;
import java.util.AbstractList;
import java.util.AbstractSequentialList;
import java.util.AbstractSet;
import java.util.ArrayList;
import java.util.Calendar;
import java.util.Collection;
import java.util.Collections;
import java.util.Date;
import java.util.Deque;
import java.util.GregorianCalendar;
import java.util.HashMap;
import java.util.HashSet;
import java.util.LinkedList;
import java.util.List;
import java.util.Locale;
import java.util.Map;
import java.util.NavigableSet;
import java.util.Optional;
import java.util.Queue;
import java.util.Set;
import java.util.SortedSet;
import java.util.TreeSet;
import java.util.function.Function;

@SuppressWarnings({"unused", "WeakerAccess"})
Expand Down Expand Up @@ -363,7 +420,7 @@ public static Object fromJenaResource(final Resource resource, Class<?> beanClas
if (mostConcreteResourceClass.isPresent()) {
beanClass = mostConcreteResourceClass.get();
}
final Object newInstance = beanClass.newInstance();
final Object newInstance = beanClass.getDeclaredConstructor().newInstance();
final Map<Class<?>, Map<String, Method>> classPropertyDefinitionsToSetMethods = new HashMap<>();
final Map<String,Object> visitedResources = new HashMap<>();
final HashSet<String> rdfTypes = new HashSet<>();
Expand Down Expand Up @@ -553,7 +610,7 @@ private static List<Object> createObjectResultList(Class<?> beanClass,
continue;
}
}
final Object newInstance = beanClass.newInstance();
final Object newInstance = beanClass.getDeclaredConstructor().newInstance();
final Map<String,Object> visitedResources = new HashMap<>();
final HashSet<String> rdfTypes = new HashSet<>();

Expand Down Expand Up @@ -912,7 +969,7 @@ else if (o.isResource())
Class<?> resourceClass = optionalResourceClass.isPresent()
? optionalResourceClass.get()
: setMethodComponentParameterClass;
final Object nestedBean = resourceClass.newInstance();
final Object nestedBean = resourceClass.getDeclaredConstructor().newInstance();
fromResource(classPropertyDefinitionsToSetMethods,
nestedBean.getClass(),
nestedBean,
Expand All @@ -930,7 +987,7 @@ else if (o.isResource())
{
// This property supports reified statements. Create the
// new resource to hold the value and any metadata.
final Object reifiedResource = reifiedClass.newInstance();
final Object reifiedResource = reifiedClass.getDeclaredConstructor().newInstance();

// Find a setter for the actual value.
for (Method method : reifiedClass.getMethods())
Expand All @@ -949,10 +1006,12 @@ else if (o.isResource())
}

// Fill in any reified statements.
RSIterator rsIter = statement.listReifiedStatements();
while (rsIter.hasNext())
Graph stmtGraph = statement.getModel().getGraph();
ExtendedIterator<Node> reifiedTriplesIter = ReifierStd.allNodes(stmtGraph, statement.asTriple());
while (reifiedTriplesIter.hasNext())
{
ReifiedStatement reifiedStatement = rsIter.next();
Node reifiedNode = reifiedTriplesIter.next();
Resource reifiedStatement = getResource(statement.getModel(), reifiedNode);
fromResource(classPropertyDefinitionsToSetMethods,
reifiedClass,
reifiedResource,
Expand Down Expand Up @@ -1051,7 +1110,7 @@ else if ((SortedSet.class == parameterClass) ||
// Not handled above. Let's try newInstance with possible failure.
else
{
collection = ((Collection<Object>) parameterClass.newInstance());
collection = ((Collection<Object>) parameterClass.getDeclaredConstructor().newInstance());
}

collection.addAll(values);
Expand All @@ -1062,6 +1121,23 @@ else if ((SortedSet.class == parameterClass) ||
}
}

/*
Adapted from https://github.com/spdx/tools/blob/bc35e25dacb728bf8332b82b509bb3efacd6c64e/src/org/spdx/rdfparser/SPDXDocument.java#L1225
Copyright (c) 2010, 2011 Source Auditor Inc.
SPDX-License-Identifier: Apache-2.0
*/
private static Resource getResource(Model model, Node node) {
Resource s;
if (node.isURI()) {
s = model.createResource(node.getURI());
} else if (node.isBlank()) {
s = model.createResource(new AnonId(node.getBlankNodeId()));
} else {
throw(new IllegalArgumentException("Only returning nodes for URI or bnode subjects"));
}
return s;
}

/**
* Returns a hash set of rdf:types for a given resource object. If the set
* was populated before, returns the given list. This list will only be
Expand Down Expand Up @@ -1463,9 +1539,8 @@ else if (properties instanceof NestedWildcardProperties)
final Property property = model.createProperty(propertyName);
final Object value = extendedProperty.getValue();

if (value instanceof Collection)
if (value instanceof Collection<?> collection)
{
final Collection<?> collection = (Collection<?>) value;
for (Object next : collection)
{
handleExtendedValue(resourceClass,
Expand Down Expand Up @@ -1509,14 +1584,13 @@ private static void handleExtendedValue(final Class<?> objectClass,
InvocationTargetException,
OslcCoreApplicationException
{
if (value instanceof UnparseableLiteral)
if (value instanceof UnparseableLiteral unparseable)
{
if (onlyNested)
{
return;
}

final UnparseableLiteral unparseable = (UnparseableLiteral) value;
resource.addProperty(property, model.createLiteral(unparseable.getRawValue()));
}
else if (value instanceof AnyResource)
Expand Down Expand Up @@ -2169,7 +2243,7 @@ private static void recursivelyCollectNamespaceMappings(final Map<String, String
{
try {
IOslcCustomNamespaceProvider customNamespaceProviderImpl
= customNamespaceProvider.newInstance();
= customNamespaceProvider.getDeclaredConstructor().newInstance();
Map<String, String> customNamespacePrefixes = customNamespaceProviderImpl
.getCustomNamespacePrefixes();
if(null != customNamespacePrefixes)
Expand All @@ -2183,6 +2257,12 @@ private static void recursivelyCollectNamespaceMappings(final Map<String, String
} catch (InstantiationException e) {
throw new RuntimeException("The custom namespace provider must not be a abstract," +
" nor interface class and must have a public no args constructor", e);
} catch (InvocationTargetException e) {
throw new RuntimeException(
"Class '%s' does not have a no-args constructor required for Lyo Beans"
.formatted(customNamespaceProvider.getSimpleName()), e);
} catch (NoSuchMethodException e) {
throw new RuntimeException(e);
}
}
}
Expand All @@ -2197,13 +2277,8 @@ private static void recursivelyCollectNamespaceMappings(final Map<String, String

final Class<?>[] interfaces = resourceClass.getInterfaces();

if (interfaces != null)
{
for (final Class<?> interfac : interfaces)
{
recursivelyCollectNamespaceMappings(namespaceMappings,
interfac);
}
for (final Class<?> iface : interfaces) {
recursivelyCollectNamespaceMappings(namespaceMappings, iface);
}
}

Expand Down
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