infrastructure for NIHVIVO-205 ontology upgrade

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

@@ -0,0 +1,31 @@
+package edu.cornell.mannlib.vitro.webapp.ontology.update;
+
+import java.util.List;
+
+import com.hp.hpl.jena.ontology.OntModel;
+
+public class ABoxUpdater {
+
+	private OntModel tboxModel;
+	private OntModel aboxModel;
+	private OntologyChangeLogger logger;  
+	private OntologyChangeRecord record;
+	
+	public ABoxUpdater(OntModel tboxModel, OntModel aboxModel,
+				OntologyChangeLogger logger, OntologyChangeRecord record) {
+		this.tboxModel = tboxModel;
+		this.aboxModel = aboxModel;
+		this.logger = logger;
+		this.record = record;
+	}
+	
+	public void processClassChanges(List<AtomicOntologyChange> changes) {
+		
+	}
+	
+	public void processPropertyChanges(List<AtomicOntologyChange> changes) {
+		
+	}
+	
+	
+}

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

@@ -0,0 +1,13 @@
+package edu.cornell.mannlib.vitro.webapp.ontology.update;
+
+import java.io.IOException;
+
+public interface OntologyChangeLogger {
+
+	public void log(String logMessage) throws IOException;
+	
+	public void logError(String errorMessage) throws IOException;
+	
+	public void closeLogs() throws IOException;
+	
+}

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

@@ -0,0 +1,11 @@
+package edu.cornell.mannlib.vitro.webapp.ontology.update;
+
+import com.hp.hpl.jena.rdf.model.Model;
+
+public interface OntologyChangeRecord {
+	
+	public void recordAdditions(Model incrementalAdditions);
+	
+	public void recordRetractions(Model incrementalRetractions);
+	
+}

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

@@ -14,6 +14,7 @@ import java.util.List;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 
+import com.hp.hpl.jena.ontology.OntModel;
 import com.hp.hpl.jena.query.Query;
 import com.hp.hpl.jena.query.QueryExecution;
 import com.hp.hpl.jena.query.QueryExecutionFactory;
@@ -54,7 +55,11 @@ public class OntologyUpdater {
 	}
 	
 	private void performUpdate() throws IOException {
-		List<AtomicOntologyChange> changes = getAtomicOntologyChanges();
+		List<AtomicOntologyChange> rawChanges = getAtomicOntologyChanges();
+		
+		AtomicOntologyChangeLists changes = 
+				new AtomicOntologyChangeLists(rawChanges, 
+						settings.getOntModelSelector().getTBoxModel());
 		
 		//updateTBox(changes);
 		//preprocessChanges(changes);
@@ -71,7 +76,9 @@ public class OntologyUpdater {
 		return (new OntologyChangeParser()).parseFile(settings.getDiffFile());
 	}
 	
-	private void updateABox(List<AtomicOntologyChange> changes) {
+
+	
+	private void updateABox(AtomicOntologyChangeLists changes) {
 		// perform operations based on change objects
 		// run additional SPARQL CONSTRUCTS 
 	}
@@ -140,6 +147,34 @@ public class OntologyUpdater {
 		
 	}
 	
+	/**
+	 * A class that allows to access two different ontology change lists,
+	 * one for class changes and the other for property changes.  The 
+	 * constructor will split a list containing both types of changes.
+	 * @author bjl23
+	 *
+	 */
+	private class AtomicOntologyChangeLists {
+		
+		private List<AtomicOntologyChange> atomicClassChanges;
+
+		private List<AtomicOntologyChange> atomicPropertyChanges;
+		
+		public AtomicOntologyChangeLists(
+				List<AtomicOntologyChange> changeList, OntModel tboxModel) {
+			// TODO: split the main list of change objects into two lists 
+			// depending on whether they refer to classes or properties
+		}
+		
+		public List<AtomicOntologyChange> getAtomicClassChanges() {
+			return atomicClassChanges;
+		}
+
+		public List<AtomicOntologyChange> getAtomicPropertyChanges() {
+			return atomicPropertyChanges;
+		}
+		
+	}
 	
 	
 }

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

@@ -0,0 +1,44 @@
+package edu.cornell.mannlib.vitro.webapp.ontology.update;
+
+import java.io.BufferedWriter;
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.io.Writer;
+
+public class SimpleOntologyChangeLogger implements OntologyChangeLogger {
+
+	private Writer logWriter;
+	private Writer errorWriter;
+	
+	public SimpleOntologyChangeLogger( String logPath, 
+									   String errorPath ) {
+		File logFile = new File(logPath);
+		File errorFile = new File(errorPath);
+		try {
+			logWriter = new BufferedWriter(new FileWriter(logFile));
+			errorWriter = new BufferedWriter(new FileWriter(errorFile));
+		} catch (IOException ioe) {
+			throw new RuntimeException ("Unable to open ontology change log " +
+										"files for writing", ioe);
+		}
+	}
+					
+	
+	public void log(String logMessage) throws IOException {
+		logWriter.write(logMessage + "\n");
+	}
+
+	public void logError(String errorMessage) throws IOException {
+		errorWriter.write(errorMessage + "\n");
+	}
+	
+	public void closeLogs() throws IOException {
+		logWriter.flush();
+		logWriter.close();
+		errorWriter.flush();
+		errorWriter.close();
+	}
+
+}

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

@@ -0,0 +1,61 @@
+package edu.cornell.mannlib.vitro.webapp.ontology.update;
+
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.FileOutputStream;
+
+import org.apache.commons.logging.Log;
+import org.apache.commons.logging.LogFactory;
+
+import com.hp.hpl.jena.rdf.model.Model;
+
+public class SimpleOntologyChangeRecord implements OntologyChangeRecord {
+
+	private final static Log log = 
+			LogFactory.getLog(SimpleOntologyChangeRecord.class);
+	
+	private final static String RDF_SYNTAX = "RDF/XML-ABBREV";
+	
+	private Model additionsModel;
+	private Model retractionsModel;
+	private File additionsFile;
+	private File retractionsFile;
+	
+	public SimpleOntologyChangeRecord(
+			Model additionsModel, Model retractionsModel,
+			String additionsFile, String retractionsFile) {
+		this.additionsModel = additionsModel;
+		this.retractionsModel = retractionsModel;
+		this.additionsFile = new File(additionsFile);
+		if (!this.additionsFile.exists()) {
+			throw new RuntimeException(this.getClass().getName() + 
+					" unable to create required file at " + additionsFile);
+		}
+		this.retractionsFile = new File(retractionsFile);
+		if (!this.retractionsFile.exists()) {
+			throw new RuntimeException(this.getClass().getName() + 
+					" unable to create required file at " + retractionsFile);			
+		}
+	}
+	
+	public void recordAdditions(Model incrementalAdditions) {
+		additionsModel.add(incrementalAdditions);
+		write(additionsModel, additionsFile);
+	}
+
+	public void recordRetractions(Model incrementalRetractions) {
+		retractionsModel.add(incrementalRetractions);
+		write(retractionsModel, retractionsFile);
+	}
+	
+	private void write(Model model, File file) {
+		try {
+			FileOutputStream fos = new FileOutputStream(file);
+			model.write(fos, RDF_SYNTAX);
+		} catch (FileNotFoundException fnfe) {
+			log.error(this.getClass().getName() + 
+					  " unable to write to RDF file", fnfe);
+		}
+	}
+
+}

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

@@ -0,0 +1,5 @@
+package edu.cornell.mannlib.vitro.webapp.ontology.update;
+
+public class TBoxUpdater {
+
+}