NIHVIVO-2039 improvement to population of applicable object properties

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

@@ -14,17 +14,22 @@ import java.util.List;
 import java.util.Map;
 import java.util.Set;
 
+import com.hp.hpl.jena.ontology.AllValuesFromRestriction;
 import com.hp.hpl.jena.ontology.ObjectProperty;
 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.ontology.Restriction;
+import com.hp.hpl.jena.ontology.SomeValuesFromRestriction;
 import com.hp.hpl.jena.rdf.model.Property;
+import com.hp.hpl.jena.rdf.model.ResIterator;
 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.rdf.model.StmtIterator;
 import com.hp.hpl.jena.shared.Lock;
 import com.hp.hpl.jena.vocabulary.OWL;
+import com.hp.hpl.jena.vocabulary.RDFS;
 
 import edu.cornell.mannlib.vitro.webapp.beans.Individual;
 import edu.cornell.mannlib.vitro.webapp.beans.ObjectPropertyStatement;
@@ -95,23 +100,40 @@ public class PropertyInstanceDaoJena extends JenaBaseDao implements
 
     public Collection<PropertyInstance> getAllPossiblePropInstForIndividual(String individualURI) {
     	Individual ind = getWebappDaoFactory().getIndividualDao().getIndividualByURI(individualURI);
-    	Map<String, PropertyInstance> propURI2propInst = new HashMap<String, PropertyInstance>();
+    	VClassDao vcDao = getWebappDaoFactory().getVClassDao();
+    	
     	List<VClass> allTypes = ind.getVClasses(false); // include indirect types
-    	Collections.sort(allTypes, new VClassHierarchyRanker(this.getWebappDaoFactory().getVClassDao()));
+        
-    	for (VClass currClass : allTypes) {
+        Set<String> allSuperclassURIs = new HashSet<String>();
-			Collection<PropertyInstance> propInstsForClass = getAllPropInstByVClass(currClass.getURI());
+       
-			for (PropertyInstance propInst : propInstsForClass) {
+        for (VClass type : allTypes) {
-				if (propURI2propInst.get(propInst.getPropertyURI()) == null) {
+            String classURI = type.getURI();
-					propURI2propInst.put(propInst.getPropertyURI(), propInst);
+            if (classURI != null) {
-				}
+                allSuperclassURIs.add(type.getURI());
-			}
+            }
+            for (String equivURI : vcDao.getEquivalentClassURIs(classURI)) {
+                allSuperclassURIs.add(equivURI);
+                allSuperclassURIs.addAll(vcDao.getAllSuperClassURIs(equivURI));
+            }
+            allSuperclassURIs.addAll(vcDao.getAllSuperClassURIs(classURI));
+        }
+        
+        List<VClass> vclasses = new ArrayList<VClass>();
+        for(String vclassURI : allSuperclassURIs) {
+            VClass vclass = vcDao.getVClassByURI(vclassURI);
+            if (vclass != null) {
+                vclasses.add(vclass);
+            }
+        }
+    	
+    	Collection<PropertyInstance> piList = getAllPropInstByVClasses(vclasses);
+    	
+    	for (PropertyInstance pi : piList) {
+    		pi.setDomainClassURI(ind.getVClassURI());
+    		// TODO: improve.  This is so the DWR property editing passes the 
+    		// individual's VClass to get the right restrictions
     	}
-    	for (PropertyInstance pi : propURI2propInst.values()) {
+
-    		pi.setDomainClassURI(ind.getVClassURI()); // TODO: improve.  This is so the DWR property editing passes the individual's VClass to get the right restrictions
-    	}
-    	List<PropertyInstance> piList = new ArrayList<PropertyInstance>();
-    	piList.addAll(propURI2propInst.values());
-		Collections.sort(piList, new PropInstSorter());
 		return piList;
     }
     
@@ -126,15 +148,19 @@ public class PropertyInstanceDaoJena extends JenaBaseDao implements
     	public int compare(VClass vc1, VClass vc2) {
     		if (vcDao.isSubClassOf(vc1, vc2)) {
     			return -1;
-    		} else return 0;
+    		} else if (vcDao.isSubClassOf(vc2, vc1)) {
+    		    return 1;
+    		} else {
+    		    return 0;
+    		}
     	}
     }
     
+    
     public Collection<PropertyInstance> getAllPropInstByVClass(String classURI) {
         if (classURI==null || classURI.length()<1) {
             return null;
         }
-        List<PropertyInstance> propInsts = new ArrayList();
         
         VClassDao vcDao = getWebappDaoFactory().getVClassDao();
         
@@ -142,56 +168,135 @@ public class PropertyInstanceDaoJena extends JenaBaseDao implements
        
         allSuperclassURIs.add(classURI);
         for (String equivURI : vcDao.getEquivalentClassURIs(classURI)) {
-        	allSuperclassURIs.add(equivURI);
+            allSuperclassURIs.add(equivURI);
-        	allSuperclassURIs.addAll(vcDao.getAllSuperClassURIs(equivURI));
+            allSuperclassURIs.addAll(vcDao.getAllSuperClassURIs(equivURI));
         }
         allSuperclassURIs.addAll(vcDao.getAllSuperClassURIs(classURI));
         
+        List<VClass> vclasses = new ArrayList<VClass>();
+        for(String vclassURI : allSuperclassURIs) {
+            VClass vclass = vcDao.getVClassByURI(vclassURI);
+            if (vclass != null) {
+                vclasses.add(vclass);
+            }
+        }
+        return getAllPropInstByVClasses(vclasses);
+    }
+    
+    private void updatePropertyRangeMap(Map<String, Resource[]> map, 
+                                        String propURI, 
+                                        Resource[] ranges) {
+        Resource[] existingRanges = map.get(propURI);
+        if (existingRanges == null) {
+            map.put(propURI, ranges);
+        } else if (existingRanges[0] == null && existingRanges[1] != null) {
+            existingRanges[0] = ranges[0];
+            map.put(propURI, existingRanges);
+        } else if (existingRanges[0] != null && existingRanges[1] == null) {
+            existingRanges[1] = ranges[1];
+            map.put(propURI, existingRanges);            
+        }
+    }
+    
+    public Collection<PropertyInstance> getAllPropInstByVClasses(List<VClass> vclasses) {
+        
+        List<PropertyInstance> propInsts = new ArrayList<PropertyInstance>();
+        
+        if(vclasses == null || vclasses.isEmpty()) {
+            return propInsts;
+        }
+        
+        Collections.sort(vclasses, new VClassHierarchyRanker(this.getWebappDaoFactory().getVClassDao()));
+        
         OntModel ontModel = getOntModelSelector().getTBoxModel();
         
         try {
         
         	ontModel.enterCriticalSection(Lock.READ);
         	
-        	Set<ObjectProperty> applicableProperties = new HashSet<ObjectProperty>();
+        	// map object property URI to an array of two resources:
+        	// the first is the "allValuesFrom" resource and the second is
+        	// "someValuesFrom"
+        	Map<String, Resource[]> applicableProperties = 
+        	        new HashMap<String, Resource[]>();
         	
         	try {
-		        for (String VClassURI : allSuperclassURIs) {
+		        for (VClass vclass : vclasses) {
+		            if (vclass.isAnonymous()) {
+		                continue; 
+		            }
+		            String VClassURI = vclass.getURI();
+		            
 		        	OntClass ontClass = getOntClass(ontModel,VClassURI);
 		        	if (ontClass != null) {
-		        		if (ontClass.isRestriction()) {
+		        	    List<OntClass> relatedClasses = new ArrayList<OntClass>();
-		        			// TODO: check if restriction is something like
+		        	    relatedClasses.addAll(ontClass.listEquivalentClasses().toList());
-		        			// maxCardinality 0 or allValuesFrom owl:Nothing,
+		        	    relatedClasses.addAll(ontClass.listSuperClasses().toList());
-		        			// in which case the property is NOT applicable!
+		        	    for (OntClass relatedClass : relatedClasses) {
-		        			Restriction rest = (Restriction) ontClass.as(Restriction.class);
+    		        	    // find properties in restrictions
-		        			OntProperty onProperty = rest.getOnProperty();
+    		        		if (relatedClass.isRestriction()) {
-		        			if (onProperty != null && onProperty.canAs(ObjectProperty.class)) {
+    		        			// TODO: check if restriction is something like
-		        				applicableProperties.add((ObjectProperty)onProperty.as(ObjectProperty.class));
+    		        			// maxCardinality 0 or allValuesFrom owl:Nothing,
-		        			}
+    		        			// in which case the property is NOT applicable!
+    		        			Restriction rest = (Restriction) relatedClass.as(Restriction.class);
+    		        			OntProperty onProperty = rest.getOnProperty();
+    		        			if (onProperty != null && onProperty.canAs(ObjectProperty.class)) {
+    		        			    Resource[] ranges = new Resource[2];
+    		        			    if (rest.isAllValuesFromRestriction()) {
+    		        			        ranges[0] = (rest.asAllValuesFromRestriction()).getAllValuesFrom();
+    		        			    } else if (rest.isSomeValuesFromRestriction()) {
+                                        ranges[1] = (rest.asSomeValuesFromRestriction()).getSomeValuesFrom();
+                                    }
+    		        				updatePropertyRangeMap(applicableProperties, onProperty.getURI(), ranges);
+    		        			}
+    		        		}
+		        	    }
+		        		
+		        		// find properties with class in domain
+		        		ResIterator pit = ontModel.listSubjectsWithProperty(
+		        		        RDFS.domain, ontClass);
+		        		while (pit.hasNext()) {
+		        		    Resource prop = pit.nextResource();
+		        		    if (prop.getNameSpace() != null 
+		        		            && !NONUSER_NAMESPACES.contains(
+		        		                    prop.getNameSpace()) ) {
+		        		        StmtIterator rangeSit = prop.listProperties(
+		        		                RDFS.range);
+		        		        Resource rangeRes = null;
+		        		        while (rangeSit.hasNext()) {    
+		        		            Statement s = rangeSit.nextStatement();
+		        		            if (s.getObject().isURIResource()) {
+		        		                rangeRes = (Resource) s.getObject();
+		        		            }
+		        		        }
+		        		        Resource[] ranges = new Resource[2];
+		        		        ranges[0] = rangeRes;
+		        		        updatePropertyRangeMap(
+		        		                applicableProperties, prop.getURI(), ranges);
+		        		        
+		        		    }
 		        		}
 		        		
 		        	}
 		        }       
         	} catch (Exception e) {
-        		log.error("Unable to get applicable properties for " + classURI
+        		log.error("Unable to get applicable properties " +
-        				+ " by examining property restrictions", e);
+        		          "by examining property restrictions and domains", e);
         	}
         	
-	        HashSet allSuperclassURIset = new HashSet(allSuperclassURIs);
+        	// make the PropertyInstance objects
-	        Iterator ops = ontModel.listObjectProperties();
+	        for (String propertyURI : applicableProperties.keySet()) {
-	        while (ops.hasNext()) {
+	        	ObjectProperty op = ontModel.getObjectProperty(propertyURI);
-	            ObjectProperty op = (ObjectProperty) ops.next();
+	        	if (op == null) {
-	            if (op.getNameSpace() != null && !NONUSER_NAMESPACES.contains(op.getNameSpace()) ) {
+	        	    continue;
-	                Resource domainRes = op.getDomain();         
+	        	}
-	                if (domainRes != null && allSuperclassURIset.contains(getURIStr(domainRes))) {
-	                	applicableProperties.add(op);
-	                }	                
-	            }
-	        }
-	        for (Iterator<ObjectProperty> appPropIt = applicableProperties.iterator(); appPropIt.hasNext();) {
-	        	ObjectProperty op = appPropIt.next();
 	        	String domainURIStr = getURIStr(op.getDomain());
-	        	Resource rangeRes = op.getRange();
+	        	Resource[] foundRanges = applicableProperties.get(propertyURI);
+	        	Resource rangeRes = (foundRanges[0] != null) 
+	        	        ? foundRanges[0]
+	        	        : (op.getRange() == null && foundRanges[1] != null)
+	        	                ? foundRanges[1]
+	        	                : op.getRange();
                 PropertyInstance pi = new PropertyInstance();
                 if (rangeRes != null) {
                 	String rangeClassURI;
@@ -220,7 +325,6 @@ public class PropertyInstanceDaoJena extends JenaBaseDao implements
                 pi.setDomainPublic(getLabelOrId(op));
                 propInsts.add(pi);
 	        }      
-        
         } finally {
         	ontModel.leaveCriticalSection();
         }

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

@@ -3,14 +3,20 @@
 package edu.cornell.mannlib.vitro.webapp.dao.jena;
 
 import java.io.StringReader;
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
 
 import junit.framework.Assert;
 
 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.ModelFactory;
 import com.hp.hpl.jena.vocabulary.XSD;
 
+import edu.cornell.mannlib.vitro.webapp.beans.PropertyInstance;
 import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;
 import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory;
 
@@ -135,4 +141,66 @@ public class PropertyInstanceDaoJenaTest {
     void wipeOutModTime(Model model){
 		model.removeAll(null, model.createProperty(VitroVocabulary.MODTIME), null);
 	}
+    
+    @org.junit.Test
+    public void testGetAllPossiblePropInstForIndividual() {
+        String n3 = prefixesN3 +
+            "ex:hasMold a owl:ObjectProperty . \n" +
+            "ex:hasSpore a owl:ObjectProperty . \n" +
+            "ex:hasFungus a owl:ObjectProperty . \n" +
+            "ex:redHerring a owl:ObjectProperty . \n" +
+            "ex:Person a owl:Class . \n" +
+            "ex:Agent a owl:Class . \n" +
+            "ex:Mold a owl:Class . \n" +
+            "ex:Spore a owl:Class . \n" +
+            "ex:Fungus a owl:Class . \n" +
+            "ex:Organism a owl:Class . \n" +
+            "ex:Mold rdfs:subClassOf ex:Organism . \n" +
+            "ex:Spore rdfs:subClassOf ex:Organism . \n" +
+            "ex:Fungus rdfs:subClassOf ex:Organism . \n" +
+            "ex:Person rdfs:subClassOf ex:Agent . \n" +
+            "ex:hasFungus rdfs:range ex:Fungus . \n" +
+            "ex:hasFungus rdfs:domain ex:Agent . \n" +
+            "ex:Agent rdfs:subClassOf [ a owl:Restriction ; \n" +
+                                       "owl:onProperty ex:hasMold ; \n" +
+                                       "owl:allValuesFrom ex:Organism ] . \n" +
+            "ex:Person rdfs:subClassOf [ a owl:Restriction ; \n" +
+                                       "owl:onProperty ex:hasMold ; \n" +
+                                       "owl:allValuesFrom ex:Mold ] . \n" +
+            "ex:Agent rdfs:subClassOf [ a owl:Restriction ; \n" +
+                                       "owl:onProperty ex:hasSpore ; \n" +
+                                       "owl:allValuesFrom ex:Organism ] . \n" +
+            "ex:Person rdfs:subClassOf [ a owl:Restriction ; \n" +
+                                       "owl:onProperty ex:hasSpore ; \n" +
+                                       "owl:someValuesFrom ex:Spore ] . \n" +            
+            "ex:bob a ex:Person ; a ex:Agent . \n";
+        
+        // The applicable properties for bob should be:
+        // 1. hasMold (values from Mold)
+        // 2. hasSpore (values from Organism)
+        // 3. hasFungus (values from Fungus)
+        
+        OntModel ontModel = (ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM));
+        ontModel.read(new StringReader(n3), null, "N3");
+        
+        WebappDaoFactory wadf = new WebappDaoFactoryJena(ontModel);
+        Assert.assertEquals(4, wadf.getObjectPropertyDao().getAllObjectProperties().size());
+        Assert.assertEquals(6, wadf.getVClassDao().getAllVclasses().size());
+        Assert.assertNotNull(wadf.getIndividualDao().getIndividualByURI("http://example.com/bob"));
+        
+        Collection<PropertyInstance> pinsts = wadf.getPropertyInstanceDao()
+                .getAllPossiblePropInstForIndividual("http://example.com/bob");
+        
+        Assert.assertEquals(3, pinsts.size());
+        
+        Map<String, String> propToRange = new HashMap<String,String>();
+        for (PropertyInstance pi : pinsts) {
+            propToRange.put(pi.getPropertyURI(), pi.getRangeClassURI());
+        }
+        
+        Assert.assertEquals("http://example.com/Mold", propToRange.get("http://example.com/hasMold"));
+        Assert.assertEquals("http://example.com/Organism", propToRange.get("http://example.com/hasSpore"));
+        Assert.assertEquals("http://example.com/Fungus", propToRange.get("http://example.com/hasFungus"));    
+            
+    }
 }