VIVO-469 run the URL Finders from an RDFService, not an OntModel

webapp/src/edu/cornell/mannlib/vitro/webapp/dao/jena/QueryUtils.java

@@ -6,6 +6,7 @@ import java.util.HashMap;
 import java.util.Iterator;
 import java.util.Map;
 
+import org.apache.commons.lang.StringUtils;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 
@@ -116,7 +117,11 @@ public class QueryUtils {
         return getQueryResults(queryStr, vreq.getRDFService());
     }
 
-    public static ResultSet getLanguageNeutralQueryResults(String queryStr, VitroRequest vreq) {
+    public static ResultSet getQueryResults(String queryStr, QuerySolution initialBindings, RDFService rdfService) {
+    	return getQueryResults(bindVariables(queryStr, initialBindings), rdfService);
+    }
+    
+	public static ResultSet getLanguageNeutralQueryResults(String queryStr, VitroRequest vreq) {
     	return getQueryResults(queryStr, vreq.getUnfilteredRDFService());
     }
 
@@ -130,4 +135,38 @@ public class QueryUtils {
 	    }
 	}
 
+	/**
+	 * The RDFService interface doesn't support initial bindings, so do text
+	 * substitutions instead.
+	 */
+	public static String bindVariables(String queryStr,
+			QuerySolution initialBindings) {
+		String bound = queryStr;
+		for (Iterator<String> it = initialBindings.varNames(); it.hasNext();) {
+			String name = it.next();
+			RDFNode node = initialBindings.get(name);
+			if (node.isLiteral()) {
+				bound = bound.replace('?' + name, literalToString(node.asLiteral()));
+			} else if (node.isURIResource()) {
+				bound = bound.replace('?' + name,  '<'+node.asResource().getURI()+ '>');
+			}else {
+				log.warn("Failed to bind anonymous resource variable '" + name
+						+ "' to query '" + bound + "'");
+			}
+		}
+		return bound;
+	}
+
+	private static String literalToString(Literal l) {
+		StringBuilder buffer = new StringBuilder();
+		buffer.append('"').append(l.getLexicalForm()).append('"');
+		if (l.getDatatypeURI() != null) {
+			buffer.append("^^<").append(l.getDatatypeURI()).append(">");
+		} else if (StringUtils.isNotEmpty(l.getLanguage())) {
+			buffer.append("@").append(l.getLanguage());
+		}
+		return buffer.toString();
+	}
+
+
 }

webapp/src/edu/cornell/mannlib/vitro/webapp/search/indexing/AdditionalURIsForObjectProperties.java

@@ -10,22 +10,17 @@ import java.util.List;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 
-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.QueryFactory;
 import com.hp.hpl.jena.query.QuerySolution;
 import com.hp.hpl.jena.query.QuerySolutionMap;
 import com.hp.hpl.jena.query.ResultSet;
-import com.hp.hpl.jena.query.Syntax;
-import com.hp.hpl.jena.rdf.model.Model;
 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.rdf.model.Statement;
-import com.hp.hpl.jena.shared.Lock;
 import com.hp.hpl.jena.vocabulary.RDFS;
 
+import edu.cornell.mannlib.vitro.webapp.dao.jena.QueryUtils;
+import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFService;
 import edu.cornell.mannlib.vitro.webapp.search.beans.StatementToURIsToUpdate;
 
 /**
@@ -38,13 +33,13 @@ import edu.cornell.mannlib.vitro.webapp.search.beans.StatementToURIsToUpdate;
 public class AdditionalURIsForObjectProperties implements StatementToURIsToUpdate {
     protected static final Log log = LogFactory.getLog(AdditionalURIsForObjectProperties.class);
     
-    protected Model model;              
+    protected final RDFService rdfService;
     
-    public AdditionalURIsForObjectProperties( Model model){
+    public AdditionalURIsForObjectProperties(RDFService rdfService) {
-        this.model = model;
+		this.rdfService = rdfService;
-    }
+	}
-    
+
-    @Override
+	@Override
     public List<String> findAdditionalURIsToIndex(Statement stmt) {
         if(  stmt == null )
             return Collections.emptyList();
@@ -102,37 +97,27 @@ public class AdditionalURIsForObjectProperties implements StatementToURIsToUpdat
         Resource uriResource = ResourceFactory.createResource(uri);        
         initialBinding.add("uri", uriResource);
         
-        Query sparqlQuery = QueryFactory.create( QUERY_FOR_RELATED );
+		ResultSet results = QueryUtils.getQueryResults(QUERY_FOR_RELATED,
-        model.getLock().enterCriticalSection(Lock.READ);
+				initialBinding, rdfService);
-        try{
+
-            QueryExecution qExec = QueryExecutionFactory.create(sparqlQuery, model, initialBinding);
+        while(results.hasNext()){                    
-            try{                
+            QuerySolution soln = results.nextSolution();                                   
-                ResultSet results = qExec.execSelect();                
+            Iterator<String> iter =  soln.varNames() ;
-                while(results.hasNext()){                    
+            while( iter.hasNext()){
-                    QuerySolution soln = results.nextSolution();                                   
+                String name = iter.next();
-                    Iterator<String> iter =  soln.varNames() ;
+                RDFNode node = soln.get( name );
-                    while( iter.hasNext()){
+                if( node != null ){
-                        String name = iter.next();
+                    if( node.isURIResource() ){
-                        RDFNode node = soln.get( name );
+                        additionalUris.add( node.as( Resource.class ).getURI()  );
-                        if( node != null ){
+                    }else{
-                            if( node.isURIResource() ){
+                        log.warn( "value from query for var " + name + "  was not a URIResource, it was " + node);    
-                                additionalUris.add( node.as( Resource.class ).getURI()  );
-                            }else{
-                                log.warn( "value from query for var " + name + "  was not a URIResource, it was " + node);    
-                            }
-                        }else{
-                            log.warn("value for query for var " + name + " was null");
-                        }                        
                     }
-                }
+                }else{
-            }catch(Throwable t){
+                    log.warn("value for query for var " + name + " was null");
-                    log.error(t,t);
+                }                        
-            } finally{
+            }
-                qExec.close();
-            } 
-        }finally{
-            model.getLock().leaveCriticalSection();
         }
+
         return additionalUris;
     }
 

webapp/src/edu/cornell/mannlib/vitro/webapp/search/indexing/AdditionalUriFinders.java

@@ -5,9 +5,8 @@ package edu.cornell.mannlib.vitro.webapp.search.indexing;
 import java.util.ArrayList;
 import java.util.List;
 
-import com.hp.hpl.jena.ontology.OntModel;
-
 import edu.cornell.mannlib.vitro.webapp.dao.IndividualDao;
+import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFService;
 import edu.cornell.mannlib.vitro.webapp.search.beans.StatementToURIsToUpdate;
 
 /**
@@ -16,12 +15,12 @@ import edu.cornell.mannlib.vitro.webapp.search.beans.StatementToURIsToUpdate;
  */
 public class AdditionalUriFinders {
 
-	public static List<StatementToURIsToUpdate> getList(OntModel jenaOntModel,
+	public static List<StatementToURIsToUpdate> getList(RDFService rdfService,
 			IndividualDao indDao) {
 		// TODO How many of these are only relevant to VIVO?
 		List<StatementToURIsToUpdate> uriFinders = new ArrayList<>();
 		uriFinders.add(new AdditionalURIsForDataProperties());
-		uriFinders.add(new AdditionalURIsForObjectProperties(jenaOntModel));
+		uriFinders.add(new AdditionalURIsForObjectProperties(rdfService));
 		uriFinders.add(new AdditionalURIsForTypeStatements());
 		uriFinders.add(new URIsForClassGroupChange(indDao));
 		return uriFinders;

webapp/src/edu/cornell/mannlib/vitro/webapp/search/solr/SolrSetup.java

@@ -23,6 +23,7 @@ import edu.cornell.mannlib.vitro.webapp.dao.filtering.WebappDaoFactoryFiltering;
 import edu.cornell.mannlib.vitro.webapp.dao.filtering.filters.VitroFilterUtils;
 import edu.cornell.mannlib.vitro.webapp.dao.filtering.filters.VitroFilters;
 import edu.cornell.mannlib.vitro.webapp.dao.jena.ModelContext;
+import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFService;
 import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFServiceFactory;
 import edu.cornell.mannlib.vitro.webapp.rdfservice.impl.RDFServiceUtils;
 import edu.cornell.mannlib.vitro.webapp.search.beans.StatementToURIsToUpdate;
@@ -133,7 +134,8 @@ public class SolrSetup implements javax.servlet.ServletContextListener{
             wadf = new WebappDaoFactoryFiltering(wadf, vf);            
             
             // make objects that will find additional URIs for context nodes etc
-            List<StatementToURIsToUpdate> uriFinders = AdditionalUriFinders.getList(jenaOntModel,wadf.getIndividualDao());
+            RDFService rdfService = RDFServiceUtils.getRDFServiceFactory(context).getRDFService();
+			List<StatementToURIsToUpdate> uriFinders = AdditionalUriFinders.getList(rdfService,wadf.getIndividualDao());
             
             // Make the IndexBuilder
             IndexBuilder builder = new IndexBuilder( solrIndexer, wadf, uriFinders );

webapp/test/edu/cornell/mannlib/vitro/webapp/dao/jena/QueryUtilsTest.java

@@ -0,0 +1,65 @@
+/* $This file is distributed under the terms of the license in /doc/license.txt$ */
+
+package edu.cornell.mannlib.vitro.webapp.dao.jena;
+
+import static org.junit.Assert.*;
+
+import org.junit.Ignore;
+import org.junit.Test;
+
+import com.hp.hpl.jena.query.QuerySolutionMap;
+import com.hp.hpl.jena.rdf.model.Literal;
+import com.hp.hpl.jena.rdf.model.ModelFactory;
+import com.hp.hpl.jena.rdf.model.ResourceFactory;
+
+import edu.cornell.mannlib.vitro.testing.AbstractTestClass;
+
+/**
+ * TODO
+ */
+public class QueryUtilsTest extends AbstractTestClass {
+	private QuerySolutionMap bindings = new QuerySolutionMap();
+
+	@Test
+	public void bindResource() {
+		bindings.add("uri", ResourceFactory.createResource("http://my.uri"));
+		assertBoundQueryEquals("a resource ?uri", "a resource <http://my.uri>");
+	}
+
+	@Test
+	public void bindPlainLiteral() {
+		bindings.add("plain", ResourceFactory.createPlainLiteral("too easy"));
+		assertBoundQueryEquals("This is ?plain ?plain",
+				"This is \"too easy\" \"too easy\"");
+	}
+
+	@Test
+	public void bindTypedLiteral() {
+		bindings.add("typed", ResourceFactory.createTypedLiteral(100L));
+		assertBoundQueryEquals("take this ?typed number",
+				"take this \"100\"^^<http://www.w3.org/2001/XMLSchema#long> number");
+	}
+
+	@Test
+	public void bindLanguageLiteral() {
+		Literal l = ModelFactory.createDefaultModel().createLiteral("Spanish",
+				"es-ES");
+		bindings.add("lang", l);
+		assertBoundQueryEquals("speak my ?lang?", "speak my \"Spanish\"@es-ES?");
+	}
+
+	@Ignore
+	@Test
+	public void bindAnon() {
+		fail("bindAnon not implemented");
+	}
+
+	// ----------------------------------------------------------------------
+	// Helper methods
+	// ----------------------------------------------------------------------
+
+	private void assertBoundQueryEquals(String template, String expected) {
+		String actual = QueryUtils.bindVariables(template, bindings);
+		assertEquals("bounding results", expected, actual);
+	}
+}

webapp/test/edu/cornell/mannlib/vitro/webapp/search/indexing/AdditionalURIsForObjectPropertiesTest.java

@@ -15,9 +15,13 @@ import com.hp.hpl.jena.rdf.model.ResourceFactory;
 import com.hp.hpl.jena.vocabulary.OWL;
 import com.hp.hpl.jena.vocabulary.RDFS;
 
+import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFService;
+import edu.cornell.mannlib.vitro.webapp.rdfservice.impl.jena.model.RDFServiceModel;
+
 public class AdditionalURIsForObjectPropertiesTest {
 
     Model model;
+    RDFService rdfService;
     
     String testNS = "http://example.com/test#";
     String n3 = "" +
@@ -39,11 +43,12 @@ public class AdditionalURIsForObjectPropertiesTest {
     public void setUp() throws Exception {
         model = ModelFactory.createDefaultModel();
         model.read(new StringReader(n3 ), null , "N3");
+        rdfService = new RDFServiceModel(model);
     }
 
     @Test
     public void testChangeOfRdfsLabel() {
-        AdditionalURIsForObjectProperties aufop = new AdditionalURIsForObjectProperties(model);
+        AdditionalURIsForObjectProperties aufop = new AdditionalURIsForObjectProperties(rdfService);
         List<String> uris = aufop.findAdditionalURIsToIndex( 
                 ResourceFactory.createStatement(
                         ResourceFactory.createResource(testNS + "bob"),
@@ -66,7 +71,7 @@ public class AdditionalURIsForObjectPropertiesTest {
     @Test
     public void testChangeOfObjPropStmt() {
         
-        AdditionalURIsForObjectProperties aufop = new AdditionalURIsForObjectProperties(model);
+        AdditionalURIsForObjectProperties aufop = new AdditionalURIsForObjectProperties(rdfService);
         List<String> uris = aufop.findAdditionalURIsToIndex( 
                 ResourceFactory.createStatement(
                         ResourceFactory.createResource(testNS + "bob"),
@@ -88,7 +93,7 @@ public class AdditionalURIsForObjectPropertiesTest {
     
     @Test
     public void testOfDataPropChange() {
-        AdditionalURIsForObjectProperties aufop = new AdditionalURIsForObjectProperties(model);
+        AdditionalURIsForObjectProperties aufop = new AdditionalURIsForObjectProperties(rdfService);
         List<String> uris = aufop.findAdditionalURIsToIndex( 
                 ResourceFactory.createStatement(
                         ResourceFactory.createResource(testNS + "bob"),
@@ -107,8 +112,9 @@ public class AdditionalURIsForObjectPropertiesTest {
         
         Model model = ModelFactory.createDefaultModel();
         model.read(new StringReader( n3ForNIHVIVO_2902 ), null , "N3");
-        
+        RDFService rdfService = new RDFServiceModel(model);
-        AdditionalURIsForObjectProperties aufop = new AdditionalURIsForObjectProperties(model);
+
+        AdditionalURIsForObjectProperties aufop = new AdditionalURIsForObjectProperties(rdfService);
         List<String> uris = aufop.findAdditionalURIsToIndex( 
                 ResourceFactory.createStatement(
                         ResourceFactory.createResource("http://caruso-laptop.mannlib.cornell.edu:8090/vivo/individual/n2241"),