incremental development for NIHVIVO-1286

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

@@ -634,17 +634,14 @@ public class ABoxUpdater {
 	}
 
 	public void logChange(Statement statement, boolean add) throws IOException {
-		logger.log( (add ? "Added " : "Removed") + "Statement: subject = " + statement.getSubject().getURI() +
+		logger.log( (add ? "Added" : "Removed") + stmtString(statement));
-				" property = " + statement.getPredicate().getURI() +
-                " object = " + (statement.getObject().isLiteral() ?  ((Literal)statement.getObject()).getLexicalForm()
-                		                                          : ((Resource)statement.getObject()).getURI()));	
 	}
 
     public static String stmtString(Statement statement) {
-    	return  " subject = " + statement.getSubject().getURI() +
+    	return  " [subject = " + statement.getSubject().getURI() +
-    			" property = " + statement.getPredicate().getURI() +
+    			"] [property = " + statement.getPredicate().getURI() +
-                " object = " + (statement.getObject().isLiteral() ? ((Literal)statement.getObject()).getLexicalForm() + " (Literal)"
+                "] [object = " + (statement.getObject().isLiteral() ? ((Literal)statement.getObject()).getLexicalForm() + " (Literal)"
-                		                                          : ((Resource)statement.getObject()).getURI() + " (Resource)");	
+                		                                          : ((Resource)statement.getObject()).getURI() + " (Resource)") + "]";	
     }    
 	
 }

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

@@ -175,7 +175,7 @@ public class DateTimeMigration {
 		               newStmt = ResourceFactory.createStatement(stmt.getSubject(), stmt.getPredicate(), getDateTimeLiteral(date) );
 		    	   } catch (ParseException pe) {
 		    		   logger.log("Parse Exception for year literal: " + stmt.getObject().asLiteral().getLexicalForm() + 
-		    				   ". The following statement has been removed from the knowledge base " + stmtString(stmt));
+		    				   ". The following statement has been removed from the knowledge base " + ABoxUpdater.stmtString(stmt));
 		    	   }		    	   		    	   
 		       } else  if (ymPrecisionURI.equals(precision)) {
 		    	   try {
@@ -183,7 +183,7 @@ public class DateTimeMigration {
 		               newStmt = ResourceFactory.createStatement(stmt.getSubject(), stmt.getPredicate(), getDateTimeLiteral(date) );
 		    	   } catch (ParseException pe) {
 		    		   logger.log("Parse Exception for yearMonth literal: " + stmt.getObject().asLiteral().getLexicalForm() + 
-		    				   ". The following statement has been removed from the knowledge base " + stmtString(stmt));
+		    				   ". The following statement has been removed from the knowledge base " + ABoxUpdater.stmtString(stmt));
 		    	   }
 		       } else  if (ymdPrecisionURI.equals(precision)) {
 		    	   try {
@@ -191,14 +191,14 @@ public class DateTimeMigration {
 		               newStmt = ResourceFactory.createStatement(stmt.getSubject(), stmt.getPredicate(), getDateTimeLiteral(date) );
 		    	   } catch (ParseException pe) {
 		    		   logger.log("Parse Exception for yearMonthDay literal: " + stmt.getObject().asLiteral().getLexicalForm() + 
-		    				   ". The following statement has been removed from the knowledge base " + stmtString(stmt));
+		    				   ". The following statement has been removed from the knowledge base " + ABoxUpdater.stmtString(stmt));
 		    	   }	   
 		       } else  if (ymdtPrecisionURI.equals(precision)) {
 		    	   logger.log("WARNING: unhandled precision found for individual " + stmt.getSubject().getURI() + ": " + precision +
-		    			      ". The following statement has been removed from the knowledge base " + stmtString(stmt));
+		    			      ". The following statement has been removed from the knowledge base " + ABoxUpdater.stmtString(stmt));
 		       } else {
 		    	   logger.log("WARNING: unrecognized precision found for individual " + stmt.getSubject().getURI() + ": " + precision +
-		    			      ". The following statement has been removed from the knowledge base " + stmtString(stmt));
+		    			      ". The following statement has been removed from the knowledge base " + ABoxUpdater.stmtString(stmt));
 		       }
 
 			   retractions.add(stmt);
@@ -256,11 +256,4 @@ public class DateTimeMigration {
 	    String dateString = dt.toString().substring(0, dt.toString().length()-1);
 	    return ResourceFactory.createTypedLiteral(dateString, XSDDatatype.XSDdateTime);
     }
-    
-    public static String stmtString(Statement statement) {
-        return  " subject = " + statement.getSubject().getURI() +
-        		" property = " + statement.getPredicate().getURI() +
-                " object = " + (statement.getObject().isLiteral() ? ((Literal)statement.getObject()).getLexicalForm() + " (Literal)"
-                    		                                      : ((Resource)statement.getObject()).getURI() + " (Resource)");	
-    }    
 }

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

@@ -243,9 +243,13 @@ public class OntologyUpdater {
 	}
 	
 	private void updateTBoxAnnotations() throws IOException {
-		(new TBoxUpdater(settings.getOldTBoxAnnotationsModel(),
+		
+		TBoxUpdater tboxUpdater = new TBoxUpdater(settings.getOldTBoxAnnotationsModel(),
 		                                          settings.getNewTBoxAnnotationsModel(),
-		                 settings.getOntModelSelector().getABoxModel(), logger, record)).updateVitroPropertyDefaultValues();
+                                                  settings.getOntModelSelector().getABoxModel(), logger, record);
+                                                  
+        tboxUpdater.updateVitroPropertyDefaultValues();
+        tboxUpdater.updateVitroAnnotationsModel();
 	}
 	
 	/**

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

@@ -5,7 +5,9 @@ package edu.cornell.mannlib.vitro.webapp.ontology.update;
 import java.io.IOException;
 import java.util.List;
 
+import com.hp.hpl.jena.ontology.DatatypeProperty;
 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;
@@ -16,6 +18,7 @@ import com.hp.hpl.jena.rdf.model.Resource;
 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.RDF;
 import com.hp.hpl.jena.vocabulary.RDFS;
 
 import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;
@@ -33,6 +36,11 @@ public class TBoxUpdater {
 	private OntologyChangeRecord record;
 	private boolean detailLogs = false;
 	
+    private static final String classGroupURI = "http://vitro.mannlib.cornell.edu/ns/vitro/0.7#ClassGroup";
+	private Resource classGroupClass = (ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM)).createResource(classGroupURI);
+    private static final String inClassGroupURI = "http://vitro.mannlib.cornell.edu/ns/vitro/0.7#inClassGroup";
+	private Property inClassGroupProp = (ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM)).createProperty(inClassGroupURI);
+
 	/**
 	 * 
 	 * Constructor 
@@ -297,4 +305,75 @@ public class TBoxUpdater {
 		siteModel.leaveCriticalSection();
 	}
 }
+	
+/**
+ * 
+ * Update a knowledge base to align with changes to the vitro annotation model  
+ * in a new version of the ontology. The two versions of the ontology and the
+ * knowledge base to be updated are provided in the class constructor and are
+ * referenced via class level variables. 
+ *                    
+ * Currently, this method only handles deletions of a ClassGroup
+ *                    
+ *  Writes to the change log file, the error log file, and the incremental change
+ *  knowledge base.                  
+ *  
+ */	
+public void updateVitroAnnotationsModel() throws IOException {
+		
+	   // for each ClassGroup in the old vitro annotations model: if it is not in 
+	   // the new vitro annotations model and the site has no classes asserted to 
+	   // be in that class group then delete it.
+	   // TODO: the site will have classes asserted to be in it if we have switched
+	   // the default assignment in the new version but haven't migration yet. How
+	   // to handle this?
+	   
+	   siteModel.enterCriticalSection(Lock.WRITE);
+	   
+	   try {	
+		    Model retractions = ModelFactory.createDefaultModel();
+		    
+			StmtIterator iter = oldTboxAnnotationsModel.listStatements((Resource) null, RDF.type, classGroupClass);
+	  	
+			int count = 0;
+			while (iter.hasNext()) {  
+			  Statement stmt = iter.next();
+			  
+			  if (!newTboxAnnotationsModel.contains(stmt) && !usesGroup(siteModel, stmt.getSubject())) {
+				  count++;
+				  retractions.add(siteModel.listStatements(stmt.getSubject(),(Property) null,(RDFNode)null));
+			  }
+			}
+	    	
+			if (retractions.size() > 0) {
+			   siteModel.remove(retractions);
+			   record.recordRetractions(retractions);
+			
+			   // log summary of changes
+			   if (retractions.size() > 0) {
+		          logger.log("Removed " + count + " Class Group" + (count > 1 ? "s" : "") + " from the annotations model."); 		   
+			   }
+			}  
+		} finally {
+			siteModel.leaveCriticalSection();
+		}
+
+	   // If we were going to handle add, this is the logic:
+	   // for each ClassGroup in new old vitro annotations model: if it is not in 
+	   // the old vitro annotations and it is not in the site model, then 
+	   // add it.
+	   
+}
+
+public boolean usesGroup(Model model, Resource theClassGroup) throws IOException {
+	
+   model.enterCriticalSection(Lock.READ);
+     
+   try {
+	    return (model.contains((Resource) null, inClassGroupProp, theClassGroup) ? true : false);
+   } finally {
+	    model.leaveCriticalSection();
+   }
+}
+
 }