NIHVIVO-2660 Filter out data property statements that don't have a literal object. Some associated refactoring.

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

@@ -58,31 +58,6 @@ public class DataPropertyDaoJena extends PropertyDaoJena implements
     
     protected static final Log log = LogFactory.getLog(DataPropertyDaoJena.class.getName());
     
-    /* This may be the intent behind JenaBaseDao.NONUSER_NAMESPACES, but that
-     * value does not contain all of these namespaces.
-     */
-    protected static final List<String> EXCLUDED_NAMESPACES = Arrays.asList(
-            // Don't need to exclude these, because they are not owl:DatatypeProperty
-            //"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#",
-            "http://vitro.mannlib.cornell.edu/ns/vitro/0.7#",
-            "http://vitro.mannlib.cornell.edu/ns/vitro/public#"
-        ); 
-
-    /*
-     * 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 final String PROPERTY_FILTERS;
-    static {
-        List<String> namespaceFilters = new ArrayList<String>();
-        for (String namespace : EXCLUDED_NAMESPACES) {
-            namespaceFilters.add("( afn:namespace(?property) != \"" + namespace + "\" )");
-        }
-        PROPERTY_FILTERS = StringUtils.join(namespaceFilters, " && ");
-    } 
-    
     private class DataPropertyRanker implements Comparator {
         public int compare (Object o1, Object o2) {
             DataProperty dp1 = (DataProperty) o1;
@@ -735,28 +710,43 @@ public class DataPropertyDaoJena extends PropertyDaoJena implements
             return rootProperties;
     }
 
-    @Override
-    public List<DataProperty> getDataPropertyList(Individual subject) {
-        return getDataPropertyList(subject.getURI());
-    }
-    
-    @Override
     /*
-     * SPARQL-based method for getting the individual's data properties.
+     * SPARQL-based methods for getting the individual's data properties.
      * Ideally this implementation should replace the existing way of getting
      * the data property list, but the consequences of this may be far-reaching,
      * so we are implementing a new method now and will merge the old approach
      * into the new one in a future release.
      */
-    public List<DataProperty> getDataPropertyList(String subjectUri) {
     
-        // Due to a Jena bug, prebinding on ?subject combined with the isLiteral()
+    /* This may be the intent behind JenaBaseDao.NONUSER_NAMESPACES, but that
-        // filter causes the query to fail. Using string concatenation to insert the
+     * value does not contain all of these namespaces.
-        // subject uri instead.
+     */
-        String queryString = 
+    protected static final List<String> EXCLUDED_NAMESPACES = Arrays.asList(
-            prefixes + "\n" +
+            // Don't need to exclude these, because they are not owl:DatatypeProperty
+            //"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#",
+            "http://vitro.mannlib.cornell.edu/ns/vitro/0.7#",
+            "http://vitro.mannlib.cornell.edu/ns/vitro/public#"
+        ); 
+
+    /*
+     * 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 final String PROPERTY_FILTERS;
+    static {
+        List<String> namespaceFilters = new ArrayList<String>();
+        for (String namespace : EXCLUDED_NAMESPACES) {
+            namespaceFilters.add("( afn:namespace(?property) != \"" + namespace + "\" )");
+        }
+        PROPERTY_FILTERS = StringUtils.join(namespaceFilters, " && ");
+    } 
+    
+    protected static final String DATA_PROPERTY_QUERY_STRING = 
+        PREFIXES + "\n" +
         "SELECT DISTINCT ?property WHERE { \n" +
-            "   <" + subjectUri + "> ?property ?object . \n" + 
+        "   ?subject ?property ?object . \n" + 
         "   ?property a owl:DatatypeProperty . \n" +
         "   FILTER ( \n" +
         "       isLiteral(?object) && \n" +
@@ -764,6 +754,20 @@ public class DataPropertyDaoJena extends PropertyDaoJena implements
         "   ) \n" +
         "}";
     
+    @Override
+    public List<DataProperty> getDataPropertyList(Individual subject) {
+        return getDataPropertyList(subject.getURI());
+    }
+    
+    @Override
+    public List<DataProperty> getDataPropertyList(String subjectUri) {
+
+        // Due to a Jena bug, prebinding on ?subject combined with the isLiteral()
+        // filter causes the query to fail. Insert the subjectUri manually instead.
+        // QuerySolutionMap initialBindings = new QuerySolutionMap();
+        // initialBindings.add("subject", ResourceFactory.createResource(subjectUri));
+        String queryString = subUriForQueryVar(DATA_PROPERTY_QUERY_STRING, "subject", subjectUri);
+        
         Query query = null;
         try {
             query = QueryFactory.create(queryString);

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

@@ -4,10 +4,11 @@ package edu.cornell.mannlib.vitro.webapp.dao.jena;
 
 import java.util.ArrayList;
 import java.util.Collection;
+import java.util.HashMap;
 import java.util.List;
+import java.util.Map;
 
 import com.hp.hpl.jena.datatypes.TypeMapper;
-import com.hp.hpl.jena.ontology.DatatypeProperty;
 import com.hp.hpl.jena.ontology.OntModel;
 import com.hp.hpl.jena.ontology.OntResource;
 import com.hp.hpl.jena.query.Dataset;
@@ -16,7 +17,6 @@ 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.rdf.model.AnonId;
 import com.hp.hpl.jena.rdf.model.Literal;
@@ -42,21 +42,6 @@ public class DataPropertyStatementDaoJena extends JenaBaseDao implements DataPro
 
     private DatasetWrapperFactory dwf;
     
-    protected static final String DATA_PROPERTY_VALUE_QUERY_STRING = 
-        "SELECT ?value WHERE { \n" +
-        "    ?subject ?property ?value . \n" +        
-        "}";
-    
-    static protected Query dataPropertyValueQuery;
-    static {
-        try {
-            dataPropertyValueQuery = QueryFactory.create(DATA_PROPERTY_VALUE_QUERY_STRING);
-        } catch(Throwable th){
-            log.error("could not create SPARQL query for DATA_PROPERTY_VALUE_QUERY_STRING " + th.getMessage());
-            log.error(DATA_PROPERTY_VALUE_QUERY_STRING);
-        }             
-    }
-    
     public DataPropertyStatementDaoJena(DatasetWrapperFactory dwf, 
                                         WebappDaoFactoryJena wadf) {
         super(wadf);
@@ -311,6 +296,23 @@ public class DataPropertyStatementDaoJena extends JenaBaseDao implements DataPro
      * SPARQL-based methods for getting the individual's values for a single data property.
      */
     
+    protected static final String DATA_PROPERTY_VALUE_QUERY_STRING = 
+        "SELECT ?value WHERE { \n" +
+        "    ?subject ?property ?value . \n" +
+        // ignore statements with uri values
+        " FILTER ( isLiteral(?value) ) " +
+        "} ";
+    
+    protected static Query dataPropertyValueQuery;
+    static {
+        try {
+            dataPropertyValueQuery = QueryFactory.create(DATA_PROPERTY_VALUE_QUERY_STRING);
+        } catch(Throwable th) {
+            log.error("could not create SPARQL query for DATA_PROPERTY_VALUE_QUERY_STRING " + th.getMessage());
+            log.error(DATA_PROPERTY_VALUE_QUERY_STRING);
+        }             
+    }
+    
     @Override
     public List<Literal> getDataPropertyValuesForIndividualByProperty(Individual subject, DataProperty property) {
         return getDataPropertyValuesForIndividualByProperty(subject.getURI(), property.getURI());
@@ -321,9 +323,15 @@ public class DataPropertyStatementDaoJena extends JenaBaseDao implements DataPro
         log.debug("Data property value query string:\n" + DATA_PROPERTY_VALUE_QUERY_STRING);         
         log.debug("Data property value:\n" + dataPropertyValueQuery); 
 
-        QuerySolutionMap initialBindings = new QuerySolutionMap();
+        // Due to a Jena bug, prebinding on ?subject combined with the isLiteral()
-        initialBindings.add("subject", ResourceFactory.createResource(subjectUri));
+        // filter causes the query to fail. Insert the subjectUri manually instead.
-        initialBindings.add("property", ResourceFactory.createResource(propertyUri));
+        // QuerySolutionMap initialBindings = new QuerySolutionMap();
+        // initialBindings.add("subject", ResourceFactory.createResource(subjectUri));
+        // initialBindings.add("property", ResourceFactory.createResource(propertyUri));
+        Map<String, String> bindings = new HashMap<String, String>();
+        bindings.put("subject", subjectUri);
+        bindings.put("property", propertyUri);
+        String queryString = subUrisForQueryVars(DATA_PROPERTY_VALUE_QUERY_STRING, bindings);
 
         // Run the SPARQL query to get the properties
         List<Literal> values = new ArrayList<Literal>();                
@@ -332,7 +340,7 @@ public class DataPropertyStatementDaoJena extends JenaBaseDao implements DataPro
         dataset.getLock().enterCriticalSection(Lock.READ);
         try {
             QueryExecution qexec = QueryExecutionFactory.create(
-                    dataPropertyValueQuery, dataset, initialBindings);
+                    queryString, dataset);
             ResultSet results = qexec.execSelect(); 
     
             while (results.hasNext()) {

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

@@ -1071,5 +1071,21 @@ public class JenaBaseDao extends JenaBaseDaoCon {
 		return temp;
     }
 
+    /** Manually replace query variables with uris when prebinding causes the query to fail, probably
+     * due to a Jena bug.
+     */
+    protected static String subUrisForQueryVars(String queryString, Map<String, String> varsToUris) {
         
+        for (String var : varsToUris.keySet()) {
+           queryString = subUriForQueryVar(queryString, var, varsToUris.get(var));
+        }
+        return queryString;
+    }
+
+    /** Manually replace a query variable with a uri when prebinding causes the query to fail, probably
+     * due to a Jena bug.
+     */
+    protected static String subUriForQueryVar(String queryString, String varName, String uri) {
+        return queryString.replaceAll("\\?" + varName + "\\b", "<" + uri + ">");
+    }
 }

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

@@ -52,44 +52,6 @@ import edu.cornell.mannlib.vitro.webapp.dao.jena.event.EditEvent;
 public class ObjectPropertyDaoJena extends PropertyDaoJena implements ObjectPropertyDao {
     private static final Log log = LogFactory.getLog(ObjectPropertyDaoJena.class.getName());
     
-    protected static final List<String> EXCLUDED_NAMESPACES = Arrays.asList(
-            "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 final String PROPERTY_FILTERS;
-    static {
-        List<String> namespaceFilters = new ArrayList<String>();
-        for (String namespace : EXCLUDED_NAMESPACES) {
-            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#\" )");
-        PROPERTY_FILTERS = StringUtils.join(namespaceFilters, " && ");
-    }
-    
-    protected static final String LIST_VIEW_CONFIG_FILE_QUERY_STRING =
-        "PREFIX display: <http://vitro.mannlib.cornell.edu/ontologies/display/1.1#>" +
-        "SELECT ?property ?filename WHERE { \n" +
-        "    ?property display:listViewConfigFile ?filename . \n" +
-        "}";
-    
-    protected static Query listViewConfigFileQuery = null;
-    static {
-        try {
-            listViewConfigFileQuery = QueryFactory.create(LIST_VIEW_CONFIG_FILE_QUERY_STRING);
-        } catch(Throwable th){
-            log.error("could not create SPARQL query for LIST_VIEW_CONFIG_FILE_QUERY_STRING " + th.getMessage());
-            log.error(LIST_VIEW_CONFIG_FILE_QUERY_STRING);
-        }           
-    }
-    
-    Map<ObjectProperty, String> customListViewConfigFileMap = null;
-    
     public ObjectPropertyDaoJena(DatasetWrapperFactory dwf, 
                                  WebappDaoFactoryJena wadf) {
         super(dwf, wadf);
@@ -847,28 +809,38 @@ public class ObjectPropertyDaoJena extends PropertyDaoJena implements ObjectProp
     	return false;
     }
 
-    @Override
-    public List<ObjectProperty> getObjectPropertyList(Individual subject) {
-        return getObjectPropertyList(subject.getURI());
-    }
-    
-    @Override
     /*
-     * SPARQL-based method for getting the individual's object properties.
+     * SPARQL-based methods for getting the individual's object properties.
      * Ideally this implementation should replace the existing way of getting
      * the object property list, but the consequences of this may be far-reaching,
      * so we are implementing a new method now and will merge the old approach
      * into the new one in a future release.
      */
-    public List<ObjectProperty> getObjectPropertyList(String subjectUri) {
     
-        // Due to a Jena bug, prebinding on ?subject combined with the isURI()
+    protected static final List<String> EXCLUDED_NAMESPACES = Arrays.asList(
-        // filter causes the query to fail. Using string concatenation to insert the
+            "http://www.w3.org/2002/07/owl#"            
-        // subject uri instead.
+        ); 
-        String queryString =  
+    /*
-            prefixes + "\n" +
+     * 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 final String PROPERTY_FILTERS;
+    static {
+        List<String> namespaceFilters = new ArrayList<String>();
+        for (String namespace : EXCLUDED_NAMESPACES) {
+            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#\" )");
+        PROPERTY_FILTERS = StringUtils.join(namespaceFilters, " && ");
+    }
+    
+    protected static final String OBJECT_PROPERTY_QUERY_STRING = 
+        PREFIXES + "\n" +
         "SELECT DISTINCT ?property WHERE { \n" +
-            "   <" + subjectUri + "> ?property ?object . \n" + 
+        "   ?subject ?property ?object . \n" + 
         "   ?property a owl:ObjectProperty . \n" +
         "   FILTER ( \n" +
         "       isURI(?object) && \n" +
@@ -876,6 +848,19 @@ public class ObjectPropertyDaoJena extends PropertyDaoJena implements ObjectProp
         "   ) \n" +
         "}";    
     
+    @Override
+    public List<ObjectProperty> getObjectPropertyList(Individual subject) {
+        return getObjectPropertyList(subject.getURI());
+    }
+    
+    @Override
+    public List<ObjectProperty> getObjectPropertyList(String subjectUri) {
+
+        // Due to a Jena bug, prebinding on ?subject combined with the isURI()
+        // filter causes the query to fail. Using string concatenation to insert the
+        // subject uri instead.
+        String queryString = subUriForQueryVar(OBJECT_PROPERTY_QUERY_STRING, "subject", subjectUri); 
+
         Query query = null;
         try {
             query = QueryFactory.create(queryString);
@@ -901,6 +886,24 @@ public class ObjectPropertyDaoJena extends PropertyDaoJena implements ObjectProp
         return properties; 
     }
 
+    protected static final String LIST_VIEW_CONFIG_FILE_QUERY_STRING =
+        "PREFIX display: <http://vitro.mannlib.cornell.edu/ontologies/display/1.1#>" +
+        "SELECT ?property ?filename WHERE { \n" +
+        "    ?property display:listViewConfigFile ?filename . \n" +
+        "}";
+    
+    protected static Query listViewConfigFileQuery = null;
+    static {
+        try {
+            listViewConfigFileQuery = QueryFactory.create(LIST_VIEW_CONFIG_FILE_QUERY_STRING);
+        } catch(Throwable th){
+            log.error("could not create SPARQL query for LIST_VIEW_CONFIG_FILE_QUERY_STRING " + th.getMessage());
+            log.error(LIST_VIEW_CONFIG_FILE_QUERY_STRING);
+        }           
+    }
+    
+    Map<ObjectProperty, String> customListViewConfigFileMap = null;
+    
     @Override
     public String getCustomListViewConfigFileName(ObjectProperty op) {
         if (customListViewConfigFileMap == null) {

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

@@ -251,6 +251,14 @@ public class ObjectPropertyStatementDaoJena extends JenaBaseDao implements Objec
         return 0;
     }
 
+    /*
+     * SPARQL-based method for getting values related to a single object property.
+     * We cannot return a List<ObjectPropertyStatement> here, the way the corresponding method of
+     * DataPropertyStatementDaoJena returns a List<DataPropertyStatement>. We need to accomodate
+     * custom queries that could request any data in addition to just the object of the statement.
+     * However, we do need to get the object of the statement so that we have it to create editing links.
+     */
+    
     @Override 
     public List<Map<String, String>> getObjectPropertyStatementsForIndividualByProperty(
             String subjectUri, 
@@ -263,13 +271,6 @@ public class ObjectPropertyStatementDaoJena extends JenaBaseDao implements Objec
     }
     
     @Override
-    /*
-     * SPARQL-based method for getting values related to a single object property.
-     * We cannot return a List<ObjectPropertyStatement> here, the way the corresponding method of
-     * DataPropertyStatementDaoJena returns a List<DataPropertyStatement>. We need to accomodate
-     * custom queries that could request any data in addition to just the object of the statement.
-     * However, we do need to get the object of the statement so that we have it to create editing links.
-     */
     public List<Map<String, String>> getObjectPropertyStatementsForIndividualByProperty(
             String subjectUri, 
             String propertyUri, 
@@ -315,7 +316,7 @@ public class ObjectPropertyStatementDaoJena extends JenaBaseDao implements Objec
             while (results.hasNext()) {
                 QuerySolution soln = results.nextSolution();
                 RDFNode node = soln.get(objectKey);
-                if (node.isResource()) {
+                if (node.isURIResource()) {
                     list.add(QueryUtils.querySolutionToStringValueMap(soln));
                 }
             }

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

@@ -53,12 +53,14 @@ public class PropertyDaoJena extends JenaBaseDao implements PropertyDao {
         put("vitroPublic", VitroVocabulary.VITRO_PUBLIC);
     }};
     
-    protected static String prefixes = "";
+    protected static final String PREFIXES;
     static {
+        String prefixes = "";
         for (String key : NAMESPACES.keySet()) {
             prefixes += "PREFIX " + key + ": <" + NAMESPACES.get(key) + ">\n";
         }
-        log.debug("Query prefixes: " + prefixes);
+        PREFIXES = prefixes;
+        log.debug("Query prefixes: " + PREFIXES);
     }
     
     protected DatasetWrapperFactory dwf;

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

@@ -109,7 +109,7 @@ public class GroupedPropertyList extends BaseTemplateModel {
     
     }
     
-    // It's possible that a collated object property retrieved in the call to getPopulatedObjectPropertyList()
+    // It's possible that an object property retrieved in the call to getPopulatedObjectPropertyList()
     // is now empty of statements, because if not editing, some statements without a linked individual
     // are not retrieved by the query. (See <linked-individual-required> elements in queries.)
     // Remove these properties, and also remove any groups with no remaining properties.