webapp/src/edu/cornell/mannlib/vitro/webapp/ontology/update/ABoxUpdater.java

@@ -39,9 +39,7 @@ public class ABoxUpdater {
 	private OntModel newTBoxAnnotationsModel;
 	private OntologyChangeLogger logger;  
 	private OntologyChangeRecord record;
-	private OntClass OWL_THING = (ModelFactory
+	private OntClass OWL_THING = (ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM)).createClass(OWL.Thing.getURI());
-			.createOntologyModel(OntModelSpec.OWL_MEM))
-			.createClass(OWL.Thing.getURI());
 
 	/**
 	 * 
@@ -311,7 +309,7 @@ public class ABoxUpdater {
 				namedClassList.add(ontClass);
 			}
 		}
-		OntClass parent = (namedClassList.isEmpty()) 
+		OntClass parent = (!namedClassList.isEmpty()) 
 								? namedClassList.get(0) 
 								: OWL_THING;
 		
@@ -323,10 +321,9 @@ public class ABoxUpdater {
 		} 
 
 	   //log summary of changes
-	   //logger.log("Class " + deletedClass.getURI() + " has been deleted. Any references to it in the knowledge base will be changed to " + 
+	   logger.log("Class " + deletedClass.getURI() + " has been deleted. Any references to it in the knowledge base will be changed to " +   replacementClass.getURI());
-	   //		        replacementClass.getURI());
 
-		AtomicOntologyChange chg = new AtomicOntologyChange(deletedClass.getURI(), replacementClass.getURI(), AtomicChangeType.RENAME);
+		AtomicOntologyChange chg = new AtomicOntologyChange(deletedClass.getURI(), replacementClass.getURI(), AtomicChangeType.RENAME, change.getNotes());
 		renameClass(chg);		
 	}
 	
@@ -349,18 +346,59 @@ public class ABoxUpdater {
 	}
 	
 	private void addProperty(AtomicOntologyChange propObj) throws IOException{
-		OntProperty tempProperty = newTboxModel.getOntProperty
+		OntProperty addedProperty = newTboxModel.getOntProperty 	(propObj.getDestinationURI());
-			(propObj.getDestinationURI());
+		
-		if (tempProperty == null) {
+		if (addedProperty == null) {
-			logger.logError("Unable to find property " + 
+			logger.logError("Unable to find property " + propObj.getDestinationURI() + 	" in new TBox");
-					propObj.getDestinationURI() +
-					" in newTBoxModel");
 			return;
 		}
-		OntProperty superProperty = tempProperty.getSuperProperty();
+		
+		//  if the newly added property has an inverse in the new TBox, then for all  existing
+		//  ABox statements involving that inverse (if the inverse is new also there won't be
+		//  any) add the corresponding statement with the new property.
+		//  
+		//  Shouldn't a reasoner be doing this?
+		
+		
+		OntProperty inverseOfAddedProperty = addedProperty.getInverseOf();
+		
+		if (inverseOfAddedProperty != null) {
+			Model additions = ModelFactory.createDefaultModel();
+			aboxModel.enterCriticalSection(Lock.WRITE);
+			
+			try {
+				StmtIterator iter = aboxModel.listStatements((Resource) null, inverseOfAddedProperty, (RDFNode) null);
+		
+				while (iter.hasNext()) {
+					
+					Statement stmt = iter.next();
+					Statement newStmt = ResourceFactory.createStatement(stmt.getObject().asResource(), addedProperty, stmt.getSubject());
+					additions.add(newStmt);
+				}
+				
+				aboxModel.add(additions);
+				record.recordAdditions(additions);
+				
+				if (additions.size() > 0) {
+					logger.log(additions.size() + " statement" + 
+							((additions.size() > 1) ? "s" : "") +
+							" with predicate " + addedProperty.getURI() + " " + 
+							((additions.size() > 1) ? "were" : "was") 
+							+ " added (as an inverse to existing  " + inverseOfAddedProperty.getURI() + 
+							" assertions");
+				}
+				
+			} finally {
+				aboxModel.leaveCriticalSection();
+			}
+			
+		}
+		
+/*		OntProperty superProperty = addedProperty.getSuperProperty();
 		if (superProperty == null) {
 			return;
 		}
+		
 		int count = aboxModel.listStatements(
 				(Resource) null, superProperty, (RDFNode) null).toSet().size();
 		if (count > 0) {
@@ -369,7 +407,7 @@ public class ABoxUpdater {
 							"a new subproperty " + propObj.getDestinationURI() +
 					" in the new ontology version. ");
 			logger.log("Please review uses of this property to see if " + propObj.getDestinationURI() + " is a more appropriate choice.");
-		}
+		}*/
 	}
 	
 	private void deleteProperty(AtomicOntologyChange propObj) throws IOException{
@@ -413,7 +451,7 @@ public class ABoxUpdater {
 						propObj.getSourceURI() + " " + (plural ? "were" : "was") + " removed. ");
 			}
 		} else {
-			AtomicOntologyChange chg = new AtomicOntologyChange(deletedProperty.getURI(), replacementProperty.getURI(), AtomicChangeType.RENAME);
+			AtomicOntologyChange chg = new AtomicOntologyChange(deletedProperty.getURI(), replacementProperty.getURI(), AtomicChangeType.RENAME, propObj.getNotes());
 			renameProperty(chg);
 		}		
 		
@@ -435,8 +473,7 @@ public class ABoxUpdater {
 		}
 		
 		Model renamePropAddModel = ModelFactory.createDefaultModel();
-		Model renamePropRetractModel = 
+		Model renamePropRetractModel = 	ModelFactory.createDefaultModel();
-			ModelFactory.createDefaultModel();
 		
 		aboxModel.enterCriticalSection(Lock.WRITE);
 		try {

webapp/src/edu/cornell/mannlib/vitro/webapp/ontology/update/AtomicOntologyChange.java

@@ -13,6 +13,7 @@ public class AtomicOntologyChange {
 	private String sourceURI;	
 	private String destinationURI;
 	private AtomicChangeType atomicChangeType;
+	private String notes;
 
 	public AtomicOntologyChange() {
 
@@ -20,11 +21,13 @@ public class AtomicOntologyChange {
 
 	public AtomicOntologyChange(String sourceURI,
 	                            String destinationURI,
-	                            AtomicChangeType atomicChangeType) {
+	                            AtomicChangeType atomicChangeType,
+	                            String notes) {
 		
 		this.sourceURI = sourceURI;
 		this.destinationURI = destinationURI;
 		this.atomicChangeType = atomicChangeType;
+		this.notes = notes;
     }
 
 	
@@ -63,9 +66,17 @@ public class AtomicOntologyChange {
 	public void setAtomicChangeType(AtomicChangeType atomicChangeType) {
 		this.atomicChangeType = atomicChangeType;
 	}
-	
+
+	public String getNotes() {
+		return notes;
+	}
+
+	public void setNotes(String notes) {
+		this.notes = notes;
+	}
+
 	public enum AtomicChangeType {
 		ADD, DELETE, RENAME
 	}
-	
+
 }

webapp/src/edu/cornell/mannlib/vitro/webapp/ontology/update/DateTimeMigration.java

@@ -2,9 +2,26 @@
 
 package edu.cornell.mannlib.vitro.webapp.ontology.update;
 
+import java.io.IOException;
+import java.text.DateFormat;
+import java.text.ParseException;
+import java.text.SimpleDateFormat;
+import java.util.Calendar;
+import java.util.Date;
+
+import com.hp.hpl.jena.datatypes.xsd.XSDDateTime;
+import com.hp.hpl.jena.ontology.DatatypeProperty;
+import com.hp.hpl.jena.ontology.ObjectProperty;
 import com.hp.hpl.jena.ontology.OntModel;
+import com.hp.hpl.jena.ontology.OntModelSpec;
+import com.hp.hpl.jena.rdf.model.Literal;
 import com.hp.hpl.jena.rdf.model.Model;
 import com.hp.hpl.jena.rdf.model.ModelFactory;
+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.rdf.model.StmtIterator;
 import com.hp.hpl.jena.shared.Lock;
 
 /**  
@@ -17,7 +34,19 @@ public class DateTimeMigration {
 	private OntModel aboxModel;
 	private OntologyChangeLogger logger;  
 	private OntologyChangeRecord record;
+	
+	private static final String dateTimeURI = "http://vivoweb.org/ontology/core#dateTime";
+	private static final String dateTimePrecisionURI = "http://vivoweb.org/ontology/core#dateTimePrecision";
 
+	private static final String yPrecisionURI = "http://vivoweb.org/ontology/core#yearPrecision";
+	private static final String ymPrecisionURI = "http://vivoweb.org/ontology/core#yearMonthPrecision";
+	private static final String ymdPrecisionURI = "http://vivoweb.org/ontology/core#yearMonthDayPrecision";
+	private static final String ymdtPrecisionURI = "http://vivoweb.org/ontology/core#yearMonthDayTimePrecision";
+	
+	private DatatypeProperty dateTimeProp = (ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM)).createDatatypeProperty(dateTimeURI);
+	private ObjectProperty dateTimePrecisionProp = (ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM)).createObjectProperty(dateTimePrecisionURI);
+	
+	
 	/**
 	 * Constructor 
 	 *  
@@ -40,24 +69,110 @@ public class DateTimeMigration {
 	 * and property definitions in the transition from version 1.1 to 1.2.
 	 *  
 	 */
-	public void updateABox() {
+	public void updateABox() throws IOException {
-				
+
+		// note: not handling timezones - they are not expected to be in the 1.1.1 data
+		DateFormat yearFormat = new SimpleDateFormat("yyyy");
+		DateFormat yearMonthFormat = new SimpleDateFormat("yyyy-mm");
+		DateFormat yearMonthDayFormat = new SimpleDateFormat("yyyy-mm-dd");
+	 	
+		aboxModel.enterCriticalSection(Lock.WRITE);
+		
+		try {			
+	        Model additions = ModelFactory.createDefaultModel();
+	        Model retractions = ModelFactory.createDefaultModel();
+
+		    StmtIterator iter = aboxModel.listStatements((Resource) null, dateTimeProp, (RDFNode) null);
+	       
+		    while (iter.hasNext()) {
+		       Statement newStmt = null;
+		       Date date = null;
+			   Statement stmt = iter.next();
+			   String precision = getPrecision(stmt);
+
+		       if (precision == null) {
+		    	   logger.log("WARNING: no precision found for individual " + stmt.getSubject().getURI() );
+		       } else  if (yPrecisionURI.equals(precision)) {
+		    	   try {
+		               date = yearFormat.parse(stmt.getObject().asLiteral().getLexicalForm());
+		    	   } catch (ParseException pe) {
+		    		   logger.log("Parse Exception for year literal: " + stmt.getObject().asLiteral().getLexicalForm() + ". skipping statement.");
+		    	   }
+		    	   
+		    	   newStmt = ResourceFactory.createStatement(stmt.getSubject(), stmt.getPredicate(), getDateTimeLiteral(date) );
+		    	   
+		       } else  if (ymPrecisionURI.equals(precision)) {
+		    	   try {
+		               date = yearMonthFormat.parse(stmt.getObject().asLiteral().getLexicalForm());
+		    	   } catch (ParseException pe) {
+		    		   logger.log("Parse Exception for year literal: " + stmt.getObject().asLiteral().getLexicalForm() + ". skipping statement.");
+		    	   }
+		    	   
+		    	   newStmt = ResourceFactory.createStatement(stmt.getSubject(), stmt.getPredicate(), getDateTimeLiteral(date) );
+		       } else  if (ymdPrecisionURI.equals(precision)) {
+		    	   try {
+		               date = yearMonthDayFormat.parse(stmt.getObject().asLiteral().getLexicalForm());
+		    	   } catch (ParseException pe) {
+		    		   logger.log("Parse Exception for year literal: " + stmt.getObject().asLiteral().getLexicalForm() + ". skipping statement.");
+		    	   }
+		    	   
+		    	   newStmt = ResourceFactory.createStatement(stmt.getSubject(), stmt.getPredicate(), getDateTimeLiteral(date) );
+	   
+		       } else  if (ymdtPrecisionURI.equals(precision)) {
+		    	   logger.log("WARNING: unhandled precision found for individual " + stmt.getSubject().getURI() + ": " + precision );
+		       } else {
+		    	   logger.log("WARNING: unrecognized precision found for individual " + stmt.getSubject().getURI() + ": " + precision );
+		       }
+			   
+		       if (newStmt != null ) {
+			     additions.add(newStmt);
+			     retractions.add(stmt);
+		       }		   
+		    }
+		   
+		    aboxModel.remove(retractions);
+		    record.recordRetractions(retractions);
+		    aboxModel.add(additions);
+		    record.recordAdditions(additions);
+		   
+		} finally {
+			aboxModel.leaveCriticalSection();
+		}	
+	}
+	
+	public String getPrecision(Statement stmt) {
+		
+		String precision = null;
+		
 		aboxModel.enterCriticalSection(Lock.WRITE);
 		
 		try {
 			
-	       Model additions = ModelFactory.createDefaultModel();
-	       Model retractions = ModelFactory.createDefaultModel();
 	       
-
+		   StmtIterator iter = aboxModel.listStatements(stmt.getSubject(), dateTimePrecisionProp, (RDFNode) null);
-	    
+	       
-		   aboxModel.remove(retractions);
+		   while (iter.hasNext()) {
-		   record.recordRetractions(retractions);
+			   Statement statement = iter.next();
-		   aboxModel.add(additions);
+			   precision = ((Resource)statement.getObject()).getURI();
-		   record.recordAdditions(additions);
+		   }
+		   
+		   return precision;
 		   
 		} finally {
 			aboxModel.leaveCriticalSection();
 		}	
 	}	
+
+     
+    public static Literal getDateTimeLiteral(Date date) {
+
+      // Note this loses time zone info, don't know how get parser to extract that
+      //Calendar cal  = Calendar.getInstance( TimeZone.getTimeZone("GMT") );
+    	
+      Calendar cal = Calendar.getInstance();
+      cal.setTime(date);
+      XSDDateTime dt = new XSDDateTime(cal);
+      return ResourceFactory.createTypedLiteral(dt);
+        
+    }
 }

webapp/src/edu/cornell/mannlib/vitro/webapp/ontology/update/OntologyChangeParser.java

@@ -2,18 +2,17 @@
 
 package edu.cornell.mannlib.vitro.webapp.ontology.update;
 
-import edu.cornell.mannlib.vitro.webapp.ontology.update.AtomicOntologyChange;
+import java.io.File;
-import edu.cornell.mannlib.vitro.webapp.ontology.update.AtomicOntologyChange.AtomicChangeType;
+import java.io.FileInputStream;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.StringTokenizer;
 
 import org.skife.csv.CSVReader;
 import org.skife.csv.SimpleReader;
 
-import java.io.FileInputStream;
+import edu.cornell.mannlib.vitro.webapp.ontology.update.AtomicOntologyChange.AtomicChangeType;
-import java.io.File;
-import java.io.IOException;
-import java.util.List;
-import java.util.StringTokenizer;
-import java.util.ArrayList;
 
 /**
  * Performs parsing on Prompt output and provides change object list.
@@ -61,12 +60,19 @@ public class OntologyChangeParser {
 			} else {
 		
 				changeObj = new AtomicOntologyChange();
+				
 				if (cols[0] != null && cols[0].length() > 0) {
 					changeObj.setSourceURI(cols[0]);
 				}
+				
 				if (cols[1] != null && cols[1].length() > 0) {
 					changeObj.setDestinationURI(cols[1]);
 				}
+
+				if (cols[4] != null && cols[4].length() > 0) {
+                  changeObj.setNotes(cols[4]);
+                }
+
 				if ("Yes".equals(cols[2])) {
 					changeObj.setAtomicChangeType(AtomicChangeType.RENAME);
 				} else if ("Delete".equals(cols[3])) {
@@ -77,6 +83,8 @@ public class OntologyChangeParser {
 					logger.logError("Invalid rename or change type data: '" +
 							cols[2] + " " + cols[3] + "'");
 				}
+				
+				
 				changeObjects.add(changeObj);
 					
 			}

webapp/src/edu/cornell/mannlib/vitro/webapp/ontology/update/OntologyUpdater.java

@@ -65,7 +65,6 @@ public class OntologyUpdater {
 			if (!logger.errorsWritten()) {
 				// add assertions to the knowledge base showing that the 
 				// update was successful, so we don't need to run it again.
-				// TODO improve error handling in future version.
 				assertSuccess();
 			}
 			
@@ -80,19 +79,19 @@ public class OntologyUpdater {
 	
 	private void performUpdate() throws IOException {
 		
-		DateTimeMigration dtMigration = new DateTimeMigration(settings.getOntModelSelector().getABoxModel(), logger, record);
-        dtMigration.updateABox();
-		
 		performSparqlConstructAdditions(settings.getSparqlConstructAdditionsDir(), settings.getOntModelSelector().getABoxModel());
 		performSparqlConstructRetractions(settings.getSparqlConstructDeletionsDir(), settings.getOntModelSelector().getABoxModel());
-		
+
+		DateTimeMigration dtMigration = new DateTimeMigration(settings.getOntModelSelector().getABoxModel(), logger, record);
+        dtMigration.updateABox();
+        
 		List<AtomicOntologyChange> rawChanges = getAtomicOntologyChanges();
 		
 		AtomicOntologyChangeLists changes = new AtomicOntologyChangeLists(rawChanges, 
 						                                                  settings.getNewTBoxModel(), 
 						                                                  settings.getOldTBoxModel());
 		   //process the TBox before the ABox
-	       updateTBoxAnnotations();
+	       //TODO: uncomment updateTBoxAnnotations();
 
     	   updateABox(changes);
 		
@@ -226,8 +225,7 @@ public class OntologyUpdater {
 	
 	private List<AtomicOntologyChange> getAtomicOntologyChanges() 
 			throws IOException {
-		return (new OntologyChangeParser(logger))
+		return (new OntologyChangeParser(logger)).parseFile(settings.getDiffFile());
-				.parseFile(settings.getDiffFile());
 	}
 	
 
@@ -339,18 +337,19 @@ public class OntologyUpdater {
 				if (changeObj.getSourceURI() != null){
 			
 					if (oldTboxModel.getOntProperty(changeObj.getSourceURI()) != null){
-						atomicPropertyChanges.add(changeObj);
+						 atomicPropertyChanges.add(changeObj);
-					}
+					} else if (oldTboxModel.getOntClass(changeObj.getSourceURI()) != null) {
-					else if (oldTboxModel.getOntClass(changeObj.getSourceURI()) != null) {
+						 atomicClassChanges.add(changeObj);
-						atomicClassChanges.add(changeObj);
+					} else if ("Prop".equals(changeObj.getNotes())) {
-					}
+						 atomicPropertyChanges.add(changeObj);
-					else{
+					} else if ("Class".equals(changeObj.getNotes())) {
-						logger.logError("Source URI is neither a Property" +
+						 atomicClassChanges.add(changeObj);
-								" nor a Class. " + "Change Object skipped for sourceURI: " + changeObj.getSourceURI());
+					} else{
+						 logger.log("WARNING: Source URI is neither a Property" +
+						    		" nor a Class. " + "Change Object skipped for sourceURI: " + changeObj.getSourceURI());
 					}
 					
-				}
+				} else if(changeObj.getDestinationURI() != null){
-				else if(changeObj.getDestinationURI() != null){
 					
 					if (newTboxModel.getOntProperty(changeObj.getDestinationURI()) != null) {
 						atomicPropertyChanges.add(changeObj);
@@ -358,16 +357,14 @@ public class OntologyUpdater {
 						getDestinationURI()) != null) {
 						atomicClassChanges.add(changeObj);
 					} else{
-						logger.logError("Destination URI is neither a Property" +
+						logger.log("WARNING: Destination URI is neither a Property" +
 								" nor a Class. " + "Change Object skipped for destinationURI: " + changeObj.getDestinationURI());
 					}
-				}
+				} else{
-				else{
+					logger.log("WARNING: Source and Destination URI can't be null. " + "Change Object skipped" );
-					logger.logError("Source and Destination URI can't be null. " 
-							+ "Change Object skipped" );
 				}
 			}
-			//logger.log("Property and Class change Object lists separated");
+			//logger.log("Property and Class change Object lists have been created");
 		}
 		
 		public List<AtomicOntologyChange> getAtomicClassChanges() {