Upgrade SPIN API dependency to 2.0.0 (and Jena to 3.0.1)

pom.xml

@@ -71,6 +71,12 @@
             <artifactId>saxon</artifactId>
             <version>9.1.0.8</version>
         </dependency>
+        <dependency>
+            <groupId>javax.servlet</groupId>
+            <artifactId>servlet-api</artifactId>
+            <version>2.5</version>
+            <scope>provided</scope>
+        </dependency>
         <dependency>
             <groupId>${project.groupId}</groupId>
             <artifactId>core</artifactId>
@@ -79,7 +85,7 @@
         <dependency>
             <groupId>org.topbraid</groupId>
             <artifactId>spin</artifactId>
-            <version>1.4.0</version>
+            <version>2.0.0</version>
         </dependency>        
     </dependencies>
 

src/main/java/org/graphity/client/Application.java

@@ -16,9 +16,9 @@
  */
 package org.graphity.client;
 
-import com.hp.hpl.jena.ontology.OntDocumentManager;
-import com.hp.hpl.jena.util.FileManager;
-import com.hp.hpl.jena.util.LocationMapper;
+import org.apache.jena.ontology.OntDocumentManager;
+import org.apache.jena.util.FileManager;
+import org.apache.jena.util.LocationMapper;
 import java.io.IOException;
 import java.net.URISyntaxException;
 import java.util.HashSet;
@@ -29,7 +29,6 @@
 import javax.ws.rs.core.UriInfo;
 import javax.xml.transform.Source;
 import javax.xml.transform.TransformerConfigurationException;
-import org.apache.jena.riot.IO_Jena;
 import org.apache.jena.riot.RDFFormat;
 import org.apache.jena.riot.RDFWriterRegistry;
 import org.graphity.client.locator.PrefixMapper;
@@ -41,7 +40,6 @@
 import org.graphity.client.provider.DataManagerProvider;
 import org.graphity.client.provider.MediaTypesProvider;
 import org.graphity.client.provider.TemplatesProvider;
-import org.graphity.client.riot.lang.JSONLDWriterAdapter;
 import org.graphity.client.riot.lang.JSONLDWriterFactory;
 import org.graphity.client.writer.ModelXSLTWriter;
 import org.graphity.core.provider.QueryParamProvider;
@@ -147,7 +145,7 @@ public void init()
             RDFFormat jsonLdFormat = new RDFFormat(RDFLanguages.JSONLD);
             RDFWriterRegistry.register(RDFLanguages.JSONLD, jsonLdFormat);
             RDFWriterRegistry.register(jsonLdFormat, new JSONLDWriterFactory(jsonLdTemplates));
-            IO_Jena.registerForModelWrite(RDFLanguages.strLangJSONLD, JSONLDWriterAdapter.class);
+            //IO_Jena.registerForModelWrite(RDFLanguages.strLangJSONLD, JSONLDWriterAdapter.class);
 	}
 	catch (TransformerConfigurationException ex)
 	{

src/main/java/org/graphity/client/filter/response/ConstructorBase.java

@@ -16,25 +16,25 @@
 
 package org.graphity.client.filter.response;
 
-import com.hp.hpl.jena.ontology.AllValuesFromRestriction;
-import com.hp.hpl.jena.ontology.OntClass;
-import com.hp.hpl.jena.ontology.OntModel;
-import com.hp.hpl.jena.ontology.OntProperty;
-import com.hp.hpl.jena.query.ParameterizedSparqlString;
-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.QuerySolutionMap;
-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 com.hp.hpl.jena.util.iterator.ExtendedIterator;
-import com.hp.hpl.jena.vocabulary.RDF;
-import com.hp.hpl.jena.vocabulary.RDFS;
+import org.apache.jena.ontology.AllValuesFromRestriction;
+import org.apache.jena.ontology.OntClass;
+import org.apache.jena.ontology.OntModel;
+import org.apache.jena.ontology.OntProperty;
+import org.apache.jena.query.ParameterizedSparqlString;
+import org.apache.jena.query.Query;
+import org.apache.jena.query.QueryExecution;
+import org.apache.jena.query.QueryExecutionFactory;
+import org.apache.jena.query.QuerySolutionMap;
+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 org.apache.jena.util.iterator.ExtendedIterator;
+import org.apache.jena.vocabulary.RDF;
+import org.apache.jena.vocabulary.RDFS;
 import java.util.ArrayList;
 import java.util.HashSet;
 import java.util.List;
@@ -82,7 +82,7 @@ public OntModel fixOntModel(OntModel ontModel)
             while (it.hasNext())
             {
                 Statement stmt = it.next();
-                com.hp.hpl.jena.rdf.model.Resource queryOrTemplateCall = stmt.getSubject();
+                Resource queryOrTemplateCall = stmt.getSubject();
                 StmtIterator propIt = queryOrTemplateCall.listProperties();
                 try
                 {
@@ -123,10 +123,10 @@ public void addInstance(OntClass forClass, Property property, Resource instance,
             throw new SitemapException("Constructor is invoked but '" + property.getURI() + "' not defined for class '" + forClass.getURI() +"'");
         }
 
-        List<com.hp.hpl.jena.rdf.model.Resource> newResources = new ArrayList<>();
-        Set<com.hp.hpl.jena.rdf.model.Resource> reachedTypes = new HashSet<>();
+        List<Resource> newResources = new ArrayList<>();
+        Set<Resource> reachedTypes = new HashSet<>();
         OntModel fixedModel = fixOntModel(forClass.getOntModel());
-        Map<com.hp.hpl.jena.rdf.model.Resource, List<CommandWrapper>> class2Constructor = SPINQueryFinder.getClass2QueryMap(fixedModel, fixedModel, property, false, false);
+        Map<Resource, List<CommandWrapper>> class2Constructor = SPINQueryFinder.getClass2QueryMap(fixedModel, fixedModel, property, false, false);
         SPINConstructors.constructInstance(fixedModel, instance, forClass, targetModel, newResources, reachedTypes, class2Constructor, null, null, null);
         instance.addProperty(RDF.type, forClass);
 
@@ -145,7 +145,7 @@ public void addInstance(OntClass forClass, Property property, Resource instance,
                         OntClass valueClass = avfr.getAllValuesFrom().as(OntClass.class);
                         if (!valueClass.equals(forClass)) // avoid circular restrictions
                         {
-                            com.hp.hpl.jena.rdf.model.Resource value = targetModel.createResource().
+                            Resource value = targetModel.createResource().
                                 addProperty(RDF.type, valueClass);
                             instance.addProperty(avfr.getOnProperty(), value);
 

src/main/java/org/graphity/client/filter/response/HypermediaFilter.java

@@ -16,20 +16,20 @@
 
 package org.graphity.client.filter.response;
 
-import com.hp.hpl.jena.ontology.AnnotationProperty;
-import com.hp.hpl.jena.ontology.OntClass;
-import com.hp.hpl.jena.ontology.OntDocumentManager;
-import com.hp.hpl.jena.ontology.OntModel;
-import com.hp.hpl.jena.ontology.OntModelSpec;
-import com.hp.hpl.jena.rdf.model.Model;
-import com.hp.hpl.jena.rdf.model.NodeIterator;
-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.reasoner.Reasoner;
-import com.hp.hpl.jena.reasoner.rulesys.GenericRuleReasoner;
-import com.hp.hpl.jena.reasoner.rulesys.Rule;
-import com.hp.hpl.jena.vocabulary.RDF;
+import org.apache.jena.ontology.AnnotationProperty;
+import org.apache.jena.ontology.OntClass;
+import org.apache.jena.ontology.OntDocumentManager;
+import org.apache.jena.ontology.OntModel;
+import org.apache.jena.ontology.OntModelSpec;
+import org.apache.jena.rdf.model.Model;
+import org.apache.jena.rdf.model.NodeIterator;
+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.reasoner.Reasoner;
+import org.apache.jena.reasoner.rulesys.GenericRuleReasoner;
+import org.apache.jena.reasoner.rulesys.Rule;
+import org.apache.jena.vocabulary.RDF;
 import com.sun.jersey.spi.container.ContainerRequest;
 import com.sun.jersey.spi.container.ContainerResponse;
 import com.sun.jersey.spi.container.ContainerResponseFilter;

src/main/java/org/graphity/client/filter/response/SubjectRewriteFilter.java

@@ -16,12 +16,12 @@
 
 package org.graphity.client.filter.response;
 
-import com.hp.hpl.jena.rdf.model.Model;
-import com.hp.hpl.jena.rdf.model.NodeIterator;
-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.util.ResourceUtils;
+import org.apache.jena.rdf.model.Model;
+import org.apache.jena.rdf.model.NodeIterator;
+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.util.ResourceUtils;
 import com.sun.jersey.api.uri.UriComponent;
 import com.sun.jersey.spi.container.ContainerRequest;
 import com.sun.jersey.spi.container.ContainerResponse;

src/main/java/org/graphity/client/locator/LocatorGRDDL.java

@@ -17,7 +17,7 @@
 package org.graphity.client.locator;
 
 import org.graphity.core.locator.LocatorLinkedData;
-import com.hp.hpl.jena.util.TypedStream;
+import org.apache.jena.util.TypedStream;
 import com.sun.jersey.api.uri.UriTemplate;
 import java.io.BufferedInputStream;
 import java.io.ByteArrayInputStream;

src/main/java/org/graphity/client/locator/PrefixMapper.java

@@ -16,12 +16,12 @@
  */
 package org.graphity.client.locator;
 
-import com.hp.hpl.jena.rdf.model.*;
-import com.hp.hpl.jena.shared.JenaException;
-import com.hp.hpl.jena.util.FileManager;
-import com.hp.hpl.jena.util.FileUtils;
-import com.hp.hpl.jena.util.LocationMapper;
-import com.hp.hpl.jena.vocabulary.LocationMappingVocab;
+import org.apache.jena.rdf.model.*;
+import org.apache.jena.shared.JenaException;
+import org.apache.jena.util.FileManager;
+import org.apache.jena.util.FileUtils;
+import org.apache.jena.util.LocationMapper;
+import org.apache.jena.vocabulary.LocationMappingVocab;
 import java.io.InputStream;
 import java.util.HashMap;
 import java.util.Iterator;

src/main/java/org/graphity/client/mapper/ExceptionMapperBase.java

@@ -16,11 +16,11 @@
 
 package org.graphity.client.mapper;
 
-import com.hp.hpl.jena.rdf.model.Model;
-import com.hp.hpl.jena.rdf.model.ModelFactory;
-import com.hp.hpl.jena.rdf.model.Resource;
-import com.hp.hpl.jena.vocabulary.DCTerms;
-import com.hp.hpl.jena.vocabulary.RDF;
+import org.apache.jena.rdf.model.Model;
+import org.apache.jena.rdf.model.ModelFactory;
+import org.apache.jena.rdf.model.Resource;
+import org.apache.jena.vocabulary.DCTerms;
+import org.apache.jena.vocabulary.RDF;
 import java.util.ArrayList;
 import java.util.List;
 import java.util.Locale;

src/main/java/org/graphity/client/mapper/NotFoundExceptionMapper.java

@@ -16,7 +16,7 @@
  */
 package org.graphity.client.mapper;
 
-import com.hp.hpl.jena.rdf.model.ResourceFactory;
+import org.apache.jena.rdf.model.ResourceFactory;
 import javax.ws.rs.core.Response;
 import javax.ws.rs.ext.ExceptionMapper;
 import javax.ws.rs.ext.Provider;

src/main/java/org/graphity/client/model/impl/ProxyResourceBase.java

@@ -16,7 +16,7 @@
  */
 package org.graphity.client.model.impl;
 
-import com.hp.hpl.jena.rdf.model.Model;
+import org.apache.jena.rdf.model.Model;
 import com.sun.jersey.api.client.Client;
 import com.sun.jersey.api.client.ClientResponse;
 import com.sun.jersey.api.client.WebResource;

src/main/java/org/graphity/client/provider/DataManagerProvider.java

@@ -16,10 +16,10 @@
  */
 package org.graphity.client.provider;
 
-import com.hp.hpl.jena.query.ARQ;
-import com.hp.hpl.jena.rdf.model.Property;
-import com.hp.hpl.jena.util.FileManager;
-import com.hp.hpl.jena.util.LocationMapper;
+import org.apache.jena.query.ARQ;
+import org.apache.jena.rdf.model.Property;
+import org.apache.jena.util.FileManager;
+import org.apache.jena.util.LocationMapper;
 import com.sun.jersey.core.spi.component.ComponentContext;
 import com.sun.jersey.spi.inject.Injectable;
 import com.sun.jersey.spi.inject.PerRequestTypeInjectableProvider;
@@ -91,11 +91,11 @@ public boolean getBooleanParam(ServletConfig servletConfig, Property property)
 
         boolean value = false;
         if (servletConfig.getInitParameter(property.getURI()) != null)
-            value = Boolean.parseBoolean(servletConfig.getInitParameter(property.getURI()).toString());
+            value = Boolean.parseBoolean(servletConfig.getInitParameter(property.getURI()));
         return value;
     }
 
-    public DataManager getDataManager(LocationMapper mapper, com.hp.hpl.jena.sparql.util.Context context, 
+    public DataManager getDataManager(LocationMapper mapper, org.apache.jena.sparql.util.Context context, 
             boolean cacheModelLoads, boolean preemptiveAuth, boolean resolvingUncached)
     {
         return (DataManager)FileManager.get();

src/main/java/org/graphity/client/provider/MediaTypesProvider.java

@@ -16,8 +16,8 @@
 
 package org.graphity.client.provider;
 
-import com.hp.hpl.jena.query.ResultSet;
-import com.hp.hpl.jena.rdf.model.Model;
+import org.apache.jena.query.ResultSet;
+import org.apache.jena.rdf.model.Model;
 import java.util.ArrayList;
 import java.util.Collections;
 import java.util.HashMap;

src/main/java/org/graphity/client/provider/TemplatesProvider.java

@@ -16,7 +16,7 @@
  */
 package org.graphity.client.provider;
 
-import com.hp.hpl.jena.rdf.model.Property;
+import org.apache.jena.rdf.model.Property;
 import com.sun.jersey.core.spi.component.ComponentContext;
 import com.sun.jersey.spi.inject.Injectable;
 import com.sun.jersey.spi.inject.PerRequestTypeInjectableProvider;

src/main/java/org/graphity/client/provider/URIRewritingModelProvider.java

@@ -16,10 +16,10 @@
 
 package org.graphity.client.provider;
 
-import com.hp.hpl.jena.rdf.model.Model;
-import com.hp.hpl.jena.rdf.model.ResIterator;
-import com.hp.hpl.jena.rdf.model.Resource;
-import com.hp.hpl.jena.util.ResourceUtils;
+import org.apache.jena.rdf.model.Model;
+import org.apache.jena.rdf.model.ResIterator;
+import org.apache.jena.rdf.model.Resource;
+import org.apache.jena.util.ResourceUtils;
 import java.io.IOException;
 import java.io.InputStream;
 import java.lang.annotation.Annotation;

src/main/java/org/graphity/client/reader/ModelXSLTReader.java

@@ -16,18 +16,18 @@
  */
 package org.graphity.client.reader;
 
-import com.hp.hpl.jena.rdf.model.Model;
-import com.hp.hpl.jena.rdf.model.ModelFactory;
-import com.hp.hpl.jena.rdf.model.RDFErrorHandler;
-import com.hp.hpl.jena.rdf.model.RDFReader;
-import com.hp.hpl.jena.shared.JenaException;
-import com.hp.hpl.jena.util.FileUtils;
+import org.apache.jena.rdf.model.Model;
+import org.apache.jena.rdf.model.ModelFactory;
+import org.apache.jena.rdf.model.RDFErrorHandler;
+import org.apache.jena.rdf.model.RDFReader;
+import org.apache.jena.shared.JenaException;
 import java.io.*;
 import java.lang.annotation.Annotation;
 import java.lang.reflect.Type;
 import java.net.URI;
 import java.net.URL;
 import java.net.URLConnection;
+import java.nio.charset.StandardCharsets;
 import javax.ws.rs.Consumes;
 import javax.ws.rs.WebApplicationException;
 import javax.ws.rs.core.*;
@@ -120,7 +120,7 @@ public void read(Model model, String url)
             // Inc .gz streams.
 
             if ( encoding == null )
-                read(model, new InputStreamReader(conn.getInputStream(), FileUtils.encodingUTF8), url);
+                read(model, new InputStreamReader(conn.getInputStream(), StandardCharsets.UTF_8), url);
             else
             {
                 if ( ! encoding.equalsIgnoreCase("UTF-8") )

src/main/java/org/graphity/client/riot/JSONLDWriter.java

@@ -16,9 +16,9 @@
  */
 package org.graphity.client.riot;
 
-import com.hp.hpl.jena.graph.Graph;
-import com.hp.hpl.jena.rdf.model.ModelFactory;
-import com.hp.hpl.jena.sparql.util.Context;
+import org.apache.jena.graph.Graph;
+import org.apache.jena.rdf.model.ModelFactory;
+import org.apache.jena.sparql.util.Context;
 import java.io.ByteArrayInputStream;
 import java.io.ByteArrayOutputStream;
 import java.io.OutputStream;

src/main/java/org/graphity/client/util/DataManager.java

@@ -16,10 +16,10 @@
  */
 package org.graphity.client.util;
 
-import com.hp.hpl.jena.query.*;
-import com.hp.hpl.jena.rdf.model.Model;
-import com.hp.hpl.jena.rdf.model.ModelFactory;
-import com.hp.hpl.jena.util.LocationMapper;
+import org.apache.jena.query.*;
+import org.apache.jena.rdf.model.Model;
+import org.apache.jena.rdf.model.ModelFactory;
+import org.apache.jena.util.LocationMapper;
 import com.sun.jersey.api.client.ClientResponse;
 import java.io.ByteArrayInputStream;
 import java.io.ByteArrayOutputStream;
@@ -57,8 +57,8 @@ public DataManager(LocationMapper mapper, MediaTypes mediaTypes,
         this.resolvingUncached = resolvingUncached;
 
         List<javax.ws.rs.core.MediaType> acceptedTypeList = new ArrayList();
-        acceptedTypeList.addAll(getMediaTypes().getReadable(Model.class));
-        acceptedTypeList.addAll(getMediaTypes().getReadable(ResultSet.class));
+        acceptedTypeList.addAll(mediaTypes.getReadable(Model.class));
+        acceptedTypeList.addAll(mediaTypes.getReadable(ResultSet.class));
         acceptedTypes = acceptedTypeList.toArray(new javax.ws.rs.core.MediaType[acceptedTypeList.size()]);        
     }