NIHVIVO-2416 Handle properties declared as both object and data properties in individual property display without throwing an error.

webapp/src/edu/cornell/mannlib/vitro/webapp/dao/ObjectPropertyStatementDao.java

@@ -31,7 +31,7 @@ public interface ObjectPropertyStatementDao {
 
     int insertNewObjectPropertyStatement(ObjectPropertyStatement objPropertyStmt );
     
-    public List<Map<String, String>> getObjectPropertyStatementsForIndividualByProperty(String subjectUri, String propertyUri, String query);
+    public List<Map<String, String>> getObjectPropertyStatementsForIndividualByProperty(String subjectUri, String propertyUri, String objectKey, String query);
     
-    public List<Map<String, String>> getObjectPropertyStatementsForIndividualByProperty(String subjectUri, String propertyUri, String query, Set<String> constructQueries);
+    public List<Map<String, String>> getObjectPropertyStatementsForIndividualByProperty(String subjectUri, String propertyUri, String objectKey, String query, Set<String> constructQueries);
 }

webapp/src/edu/cornell/mannlib/vitro/webapp/dao/filtering/ObjectPropertyStatementDaoFiltering.java

@@ -86,15 +86,15 @@ class ObjectPropertyStatementDaoFiltering extends BaseFiltering implements Objec
     @Override
     // RY What about filtering?
     public List<Map<String, String>> getObjectPropertyStatementsForIndividualByProperty(
-            String subjectUri, String propertyUri, String query) {
+            String subjectUri, String propertyUri, String objectKey, String query) {
-        return innerObjectPropertyStatementDao.getObjectPropertyStatementsForIndividualByProperty(subjectUri, propertyUri, query);
+        return innerObjectPropertyStatementDao.getObjectPropertyStatementsForIndividualByProperty(subjectUri, propertyUri, objectKey, query);
     }
     
     @Override
     // RY What about filtering?
     public List<Map<String, String>> getObjectPropertyStatementsForIndividualByProperty(
-            String subjectUri, String propertyUri, String query, Set<String> queryStrings) {
+            String subjectUri, String propertyUri, String objectKey, String query, Set<String> queryStrings) {
-        return innerObjectPropertyStatementDao.getObjectPropertyStatementsForIndividualByProperty(subjectUri, propertyUri, query, queryStrings);
+        return innerObjectPropertyStatementDao.getObjectPropertyStatementsForIndividualByProperty(subjectUri, propertyUri, objectKey, query, queryStrings);
     }
 
 

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

@@ -27,6 +27,7 @@ import com.hp.hpl.jena.query.Query;
 import com.hp.hpl.jena.query.QueryFactory;
 import com.hp.hpl.jena.query.QuerySolution;
 import com.hp.hpl.jena.query.ResultSet;
+import com.hp.hpl.jena.query.Syntax;
 import com.hp.hpl.jena.rdf.model.Property;
 import com.hp.hpl.jena.rdf.model.RDFNode;
 import com.hp.hpl.jena.rdf.model.Resource;
@@ -75,30 +76,13 @@ public class DataPropertyDaoJena extends PropertyDaoJena implements
      * This is a hack to throw out properties in the vitro, rdf, rdfs, and owl namespaces.
      * It will be implemented in a better way in v1.3 (Editing and Display Configuration).
      */
-    protected static String propertyFilters = null;
+    protected static final String PROPERTY_FILTERS;
     static {
         List<String> namespaceFilters = new ArrayList<String>();
-        for (String s : EXCLUDED_NAMESPACES) {
+        for (String namespace : EXCLUDED_NAMESPACES) {
-            namespaceFilters.add("(afn:namespace(?property) != \"" + s + "\")");
+            namespaceFilters.add("( afn:namespace(?property) != \"" + namespace + "\" )");
-        }
-        propertyFilters = "FILTER (" + StringUtils.join(namespaceFilters, " && ") + ")\n";
-    } 
-    protected static final String DATA_PROPERTY_QUERY_STRING = 
-        prefixes + "\n" +
-        "SELECT DISTINCT ?property WHERE { \n" +
-        "   ?subject ?property ?object . \n" + 
-        "   ?property rdf:type owl:DatatypeProperty . \n" +
-        propertyFilters +
-        "}";
-    
-    protected static Query dataPropertyQuery;
-    static {
-        try {
-            dataPropertyQuery = QueryFactory.create(DATA_PROPERTY_QUERY_STRING);
-        } catch(Throwable th){
-            log.error("could not create SPARQL query for DATA_PROPERTY_QUERY_STRING " + th.getMessage());
-            log.error(DATA_PROPERTY_QUERY_STRING);
         }
+        PROPERTY_FILTERS = StringUtils.join(namespaceFilters, " && ");
     } 
     
     private class DataPropertyRanker implements Comparator {
@@ -767,9 +751,32 @@ public class DataPropertyDaoJena extends PropertyDaoJena implements
      * into the new one in a future release.
      */
     public List<DataProperty> getDataPropertyList(String subjectUri) {
-        log.debug("Data property query string:\n" + DATA_PROPERTY_QUERY_STRING);         
+
-        log.debug("Data property query:\n" + dataPropertyQuery);        
+        // Due to a Jena bug, prebinding on ?subject combined with the isLiteral()
-        Iterator<QuerySolution> results = getPropertyQueryResults(subjectUri, dataPropertyQuery);
+        // filter causes the query to fail. Using string concatenation to insert the
+        // subject uri instead.
+        String queryString = 
+            prefixes + "\n" +
+            "SELECT DISTINCT ?property WHERE { \n" +
+            "   <" + subjectUri + "> ?property ?object . \n" + 
+            "   ?property a owl:DatatypeProperty . \n" +
+            "   FILTER ( \n" +
+            "       isLiteral(?object) && \n" +
+                    PROPERTY_FILTERS + "\n" +
+            "   ) \n" +
+            "}";
+        
+        Query query = null;
+        try {
+            query = QueryFactory.create(queryString);
+        } catch(Throwable th){
+            log.error("could not create SPARQL query for query string " + th.getMessage());
+            log.error(queryString);
+            return null;
+        }                     
+        log.debug("Data property query string:\n" + query);         
+     
+        Iterator<QuerySolution> results = getPropertyQueryResults(subjectUri, query);
         List<DataProperty> properties = new ArrayList<DataProperty>();
         while (results.hasNext()) {
             QuerySolution sol = results.next();

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

@@ -26,6 +26,7 @@ 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.ResultSet;
+import com.hp.hpl.jena.query.Syntax;
 import com.hp.hpl.jena.rdf.model.Literal;
 import com.hp.hpl.jena.rdf.model.Property;
 import com.hp.hpl.jena.rdf.model.RDFNode;
@@ -55,44 +56,23 @@ public class ObjectPropertyDaoJena extends PropertyDaoJena implements ObjectProp
     private static final Log log = LogFactory.getLog(ObjectPropertyDaoJena.class.getName());
     
     protected static final List<String> EXCLUDED_NAMESPACES = Arrays.asList(
-            // Don't need to exclude these, because they are not owl:ObjectProperty
-            //"http://www.w3.org/1999/02/22-rdf-syntax-ns#",
-            //"http://www.w3.org/2000/01/rdf-schema#",
             "http://www.w3.org/2002/07/owl#"            
         ); 
     /*
      * This is a hack to throw out properties in the vitro, rdf, rdfs, and owl namespaces.
      * It will be implemented in a better way in v1.3 (Editing and Display Configuration).
      */
-    protected static String propertyFilters = "";
+    protected static final String PROPERTY_FILTERS;
     static {
         List<String> namespaceFilters = new ArrayList<String>();
-        for (String s : EXCLUDED_NAMESPACES) {
+        for (String namespace : EXCLUDED_NAMESPACES) {
-            namespaceFilters.add("(afn:namespace(?property) != \"" + s + "\")");
+            namespaceFilters.add("( afn:namespace(?property) != \"" + namespace + "\" )");
         }
         // A hack to include the vitro:primaryLink and vitro:additionalLink properties in the list
         namespaceFilters.add("( ?property = vitro:primaryLink ||" +
                                "?property = vitro:additionalLink ||" +
                                "afn:namespace(?property) != \"http://vitro.mannlib.cornell.edu/ns/vitro/0.7#\" )");
-        propertyFilters = "FILTER (" + StringUtils.join(namespaceFilters, " && ") + ")\n";
+        PROPERTY_FILTERS = StringUtils.join(namespaceFilters, " && ");
-    }
-    
-    protected static final String OBJECT_PROPERTY_QUERY_STRING = 
-        prefixes + "\n" +
-        "SELECT DISTINCT ?property WHERE { \n" +
-        "   ?subject ?property ?object . \n" + 
-        "   ?property rdf:type owl:ObjectProperty . \n" +
-        propertyFilters +
-        "}";
-
-    protected static Query objectPropertyQuery;
-    static {
-        try {
-            objectPropertyQuery = QueryFactory.create(OBJECT_PROPERTY_QUERY_STRING);
-        } catch(Throwable th){
-            log.error("could not create SPARQL query for OBJECT_PROPERTY_QUERY_STRING " + th.getMessage());
-            log.error(OBJECT_PROPERTY_QUERY_STRING);
-        }           
     }
     
     protected static final String LIST_VIEW_CONFIG_FILE_QUERY_STRING =
@@ -101,7 +81,7 @@ public class ObjectPropertyDaoJena extends PropertyDaoJena implements ObjectProp
         "    ?property display:listViewConfigFile ?filename . \n" +
         "}";
     
-    protected static Query listViewConfigFileQuery;
+    protected static Query listViewConfigFileQuery = null;
     static {
         try {
             listViewConfigFileQuery = QueryFactory.create(LIST_VIEW_CONFIG_FILE_QUERY_STRING);
@@ -884,9 +864,32 @@ public class ObjectPropertyDaoJena extends PropertyDaoJena implements ObjectProp
      * into the new one in a future release.
      */
     public List<ObjectProperty> getObjectPropertyList(String subjectUri) {
-        log.debug("Object property query string:\n" + OBJECT_PROPERTY_QUERY_STRING);
+
-        log.debug("Object property query:\n" + objectPropertyQuery);
+        // Due to a Jena bug, prebinding on ?subject combined with the isURI()
-        Iterator<QuerySolution> results = getPropertyQueryResults(subjectUri, objectPropertyQuery);
+        // filter causes the query to fail. Using string concatenation to insert the
+        // subject uri instead.
+        String queryString =  
+            prefixes + "\n" +
+            "SELECT DISTINCT ?property WHERE { \n" +
+            "   <" + subjectUri + "> ?property ?object . \n" + 
+            "   ?property a owl:ObjectProperty . \n" +
+            "   FILTER ( \n" +
+            "       isURI(?object) && \n" +
+                    PROPERTY_FILTERS + "\n" +
+            "   ) \n" +
+            "}";
+
+        Query query = null;
+        try {
+            query = QueryFactory.create(queryString);
+        } catch(Throwable th){
+            log.error("could not create SPARQL query for query string " + th.getMessage());
+            log.error(queryString);
+            return null;
+        } 
+        log.debug("Object property query:\n" + query);
+        
+        Iterator<QuerySolution> results = getPropertyQueryResults(subjectUri, query);
         List<ObjectProperty> properties = new ArrayList<ObjectProperty>();
         while (results.hasNext()) {
             QuerySolution soln = results.next();

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

@@ -25,6 +25,7 @@ import com.hp.hpl.jena.query.Syntax;
 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.ResourceFactory;
 import com.hp.hpl.jena.rdf.model.Statement;
@@ -254,10 +255,10 @@ public class ObjectPropertyStatementDaoJena extends JenaBaseDao implements Objec
     public List<Map<String, String>> getObjectPropertyStatementsForIndividualByProperty(
             String subjectUri, 
             String propertyUri, 
-            String queryString) {
+            String objectKey, String queryString) {
         
         return getObjectPropertyStatementsForIndividualByProperty(
-                subjectUri, propertyUri, null);
+                subjectUri, propertyUri, objectKey, objectKey, null);
         
     }
     
@@ -272,8 +273,8 @@ public class ObjectPropertyStatementDaoJena extends JenaBaseDao implements Objec
     public List<Map<String, String>> getObjectPropertyStatementsForIndividualByProperty(
             String subjectUri, 
             String propertyUri, 
-            String queryString, 
+            String objectKey, 
-            Set<String> constructQueryStrings ) {  
+            String queryString, Set<String> constructQueryStrings ) {  
         
         Model constructedModel = constructModelForSelectQueries(
                 subjectUri, propertyUri, constructQueryStrings);
@@ -313,8 +314,11 @@ public class ObjectPropertyStatementDaoJena extends JenaBaseDao implements Objec
 
             while (results.hasNext()) {
                 QuerySolution soln = results.nextSolution();
+                RDFNode node = soln.get(objectKey);
+                if (node.isResource()) {
                     list.add(QueryUtils.querySolutionToStringValueMap(soln));
                 }
+            }
             
         } finally {
             dataset.getLock().leaveCriticalSection();

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

@@ -404,10 +404,12 @@ public class PropertyDaoJena extends JenaBaseDao implements PropertyDao {
      
     protected Iterator<QuerySolution> getPropertyQueryResults(String subjectUri, Query query) {        
         log.debug("SPARQL query:\n" + query.toString());
-        // Bind the subject's uri to the ?subject query term
+        
-        QuerySolutionMap subjectBinding = new QuerySolutionMap();
+        // RY Removing prebinding due to Jena bug: when isLiteral(?object) or 
-        subjectBinding.add("subject", 
+        // isURI(?object) is added to the query as a filter, the query fails with prebinding
-                ResourceFactory.createResource(subjectUri));
+        // but succeeds when the subject uri is concatenated into the query string.
+        //QuerySolutionMap subjectBinding = new QuerySolutionMap();
+        //subjectBinding.add("subject", ResourceFactory.createResource(subjectUri));
                 
         // Run the SPARQL query to get the properties
         DatasetWrapper w = dwf.getDatasetWrapper();
@@ -415,7 +417,7 @@ public class PropertyDaoJena extends JenaBaseDao implements PropertyDao {
         dataset.getLock().enterCriticalSection(Lock.READ);
         try {
             QueryExecution qexec = QueryExecutionFactory.create(
-                    query, dataset, subjectBinding);
+                    query, dataset); //, subjectBinding);
             try {
                 ResultSet rs = qexec.execSelect();
                 // consume iterator before wrapper w is closed in finally block

webapp/src/edu/cornell/mannlib/vitro/webapp/web/templatemodels/individual/CollatedObjectPropertyTemplateModel.java

@@ -61,7 +61,7 @@ public class CollatedObjectPropertyTemplateModel extends ObjectPropertyTemplateM
             String subjectUri = subject.getURI();
             String propertyUri = op.getURI();
             List<Map<String, String>> statementData = 
-                opDao.getObjectPropertyStatementsForIndividualByProperty(subjectUri, propertyUri, getSelectQuery(), getConstructQueries());
+                opDao.getObjectPropertyStatementsForIndividualByProperty(subjectUri, propertyUri, getObjectKey(), getSelectQuery(), getConstructQueries());
     
             /* Apply post-processing */
             postprocess(statementData, wdf);

webapp/src/edu/cornell/mannlib/vitro/webapp/web/templatemodels/individual/UncollatedObjectPropertyTemplateModel.java

@@ -37,7 +37,7 @@ public class UncollatedObjectPropertyTemplateModel extends ObjectPropertyTemplat
             String subjectUri = subject.getURI();
             String propertyUri = op.getURI();
             List<Map<String, String>> statementData = 
-                opDao.getObjectPropertyStatementsForIndividualByProperty(subjectUri, propertyUri, getSelectQuery(), getConstructQueries());
+                opDao.getObjectPropertyStatementsForIndividualByProperty(subjectUri, propertyUri, getObjectKey(), getSelectQuery(), getConstructQueries());
             
             /* Apply postprocessing */
             postprocess(statementData, wdf);