work on NIHVIVO-205 ontology upgrade

webapp/config/web.xml

@@ -78,6 +78,12 @@
      <listener-class>edu.cornell.mannlib.vitro.webapp.servlet.setup.AttachSubmodels</listener-class>
   </listener>
 
+  <!-- Invokes process to perform updates to align with ontology changes if needed -->
+
+  <listener>
+     <listener-class>edu.cornell.mannlib.vitro.webapp.servlet.setup.UpdateKnowledgeBase</listener-class>
+  </listener>
+
   <!-- Pellet setup enables reasoning.  Inferences are cached in a separate DB graph. -->
   <!-- Changing the class name sets the kindss of inferences that are materialized. -->
   <!-- See documentation for details. -->

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

@@ -0,0 +1,72 @@
+package edu.cornell.mannlib.vitro.webapp.ontology.update;
+
+import edu.cornell.mannlib.vitro.webapp.dao.jena.OntModelSelector;
+
+public class OntologyUpdateSettings {
+
+	private String dataDir;
+	private String askQueryFile;
+	private String successAssertionsFile;
+	private String successRDFFormat = "N3";
+	private String diffFile;
+	private String logFile;
+	private String errorLogFile;
+	private String removedDataFile;
+	private OntModelSelector ontModelSelector;
+	
+	public String getDataDir() {
+		return dataDir;
+	}
+	public void setDataDir(String dataDir) {
+		this.dataDir = dataDir;
+	}
+	public String getAskQueryFile() {
+		return askQueryFile;
+	}
+	public void setAskQueryFile(String askQueryFile) {
+		this.askQueryFile = askQueryFile;
+	}
+	public String getSuccessAssertionsFile() {
+		return successAssertionsFile;
+	}
+	public void setSuccessAssertionsFile(String successAssertionsFile) {
+		this.successAssertionsFile = successAssertionsFile;
+	}
+	public String getSuccessRDFFormat() {
+		return successRDFFormat;
+	}
+	public void setSuccessRDFFormat(String successRDFFormat) {
+		this.successRDFFormat = successRDFFormat;
+	}
+	public String getDiffFile() {
+		return diffFile;
+	}
+	public void setDiffFile(String diffFile) {
+		this.diffFile = diffFile;
+	}
+	public OntModelSelector getOntModelSelector() {
+		return ontModelSelector;
+	}
+	public String getLogFile() {
+		return logFile;
+	}
+	public void setLogFile(String logFile) {
+		this.logFile = logFile;
+	}
+	public String getErrorLogFile() {
+		return errorLogFile;
+	}
+	public void setErrorLogFile(String errorLogFile) {
+		this.errorLogFile = errorLogFile;
+	}
+	public String getRemovedDataFile() {
+		return removedDataFile;
+	}
+	public void setRemovedDataFile(String removedDataFile) {
+		this.removedDataFile = removedDataFile;
+	}
+	public void setOntModelSelector(OntModelSelector ontModelSelector) {
+		this.ontModelSelector = ontModelSelector;
+	}
+	
+}

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

@@ -4,14 +4,13 @@ package edu.cornell.mannlib.vitro.webapp.ontology.update;
 
 import java.io.BufferedReader;
 import java.io.File;
+import java.io.FileInputStream;
 import java.io.FileNotFoundException;
 import java.io.FileReader;
 import java.io.IOException;
 import java.io.InputStream;
 import java.util.List;
 
-import javax.servlet.ServletContext;
-
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 
@@ -19,12 +18,9 @@ import com.hp.hpl.jena.query.Query;
 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.Syntax;
 import com.hp.hpl.jena.rdf.model.Model;
 import com.hp.hpl.jena.shared.Lock;
 
-import edu.cornell.mannlib.vitro.webapp.dao.jena.OntModelSelector;
-
 /**
  * Performs knowledge base updates if necessary to align with a
  * new ontology version.
@@ -37,21 +33,14 @@ import edu.cornell.mannlib.vitro.webapp.dao.jena.OntModelSelector;
  */
 public class OntologyUpdater {
 
-	private final String DATA_DIR = "/WEB-INF/ontologies/update/";
+	
-	private final String ASK_QUERY_FILE = DATA_DIR + "ask.sparql";
-	private final String SUCCESS_ASSERTIONS_FILE = DATA_DIR + "success.n3";
-	private final String SUCCESS_RDF_FORMAT = "N3";
-	private final String DIFF_FILE = DATA_DIR + "diff.tab.txt";
 	
 	private final Log log = LogFactory.getLog(OntologyUpdater.class);
 	
-	private ServletContext context;
+	private OntologyUpdateSettings settings;
-	private OntModelSelector ontModelSelector;
 	
-	public OntologyUpdater(ServletContext context, 
+	public OntologyUpdater(OntologyUpdateSettings settings) {
-			OntModelSelector ontModelSelector) {
+		this.settings = settings;
-		this.context = context;
-		this.ontModelSelector = ontModelSelector;
 	}
 	
 	public void update() throws IOException {	
@@ -67,12 +56,12 @@ public class OntologyUpdater {
 	private void performUpdate() {
 		List<AtomicOntologyChange> changes = getAtomicOntologyChanges();
 		
-		//preprocessChanges(changes);
 		//updateTBox(changes);
+		//preprocessChanges(changes);
 		
 		updateABox(changes);
 		
-		updateAnnotations();
+		updateTBoxAnnotations();
 		
 		// perform additional additions and retractions
 	}
@@ -84,10 +73,9 @@ public class OntologyUpdater {
 	private void updateABox(List<AtomicOntologyChange> changes) {
 		// perform operations based on change objects
 		// run additional SPARQL CONSTRUCTS 
-
 	}
 	
-	private void updateAnnotations() {
+	private void updateTBoxAnnotations() {
 		// Stella's code is called here
 	}
 	
@@ -96,11 +84,11 @@ public class OntologyUpdater {
 	 * needs to be updated to conform to a new ontology version
 	 */
 	private boolean updateRequired() throws IOException {
-		String sparqlQueryStr = loadSparqlQuery(ASK_QUERY_FILE);
+		String sparqlQueryStr = loadSparqlQuery(settings.getAskQueryFile());
 		if (sparqlQueryStr == null) {
 			return false;
 		}
-		Model m = ontModelSelector.getApplicationMetadataModel();
+		Model m = settings.getOntModelSelector().getApplicationMetadataModel();
 		Query query = QueryFactory.create(sparqlQueryStr);
 		QueryExecution qexec = QueryExecutionFactory.create(query, m);
 		
@@ -117,7 +105,7 @@ public class OntologyUpdater {
 	 * @return the query string or null if file not found
 	 */
 	private String loadSparqlQuery(String filePath) throws IOException {
-		File file = new File(context.getRealPath(filePath));	
+		File file = new File(settings.getAskQueryFile());	
 		if (!file.exists()) {
 			return null;
 		}
@@ -130,15 +118,21 @@ public class OntologyUpdater {
 		return fileContents.toString();				
 	}
 	
-	private void assertSuccess() {
+	private void assertSuccess() throws FileNotFoundException {
-	    Model m = ontModelSelector.getApplicationMetadataModel();
+		try {
-	    InputStream inStream = context.getResourceAsStream(SUCCESS_ASSERTIONS_FILE);
+		    Model m = settings.getOntModelSelector().getApplicationMetadataModel();
-	    m.enterCriticalSection(Lock.WRITE);
+		    File successAssertionsFile = 
-	    try {
+		    	new File(settings.getSuccessAssertionsFile()); 
-	    	m.read(inStream, SUCCESS_RDF_FORMAT);
+		    InputStream inStream = new FileInputStream(successAssertionsFile);
-	    } finally {
+		    m.enterCriticalSection(Lock.WRITE);
-	    	m.leaveCriticalSection();
+		    try {
-	    }
+		    	m.read(inStream, settings.getSuccessRDFFormat());
+		    } finally {
+		    	m.leaveCriticalSection();
+		    }
+		} catch (Exception e) {
+			// TODO: log something to the error log
+		}
 	}
 	
 }

webapp/src/edu/cornell/mannlib/vitro/webapp/servlet/setup/UpdateKnowledgeBase.java

@@ -4,6 +4,7 @@ package edu.cornell.mannlib.vitro.webapp.servlet.setup;
 
 import java.io.IOException;
 
+import javax.servlet.ServletContext;
 import javax.servlet.ServletContextEvent;
 import javax.servlet.ServletContextListener;
 
@@ -12,6 +13,7 @@ import com.hp.hpl.jena.ontology.OntModel;
 import edu.cornell.mannlib.vitro.webapp.dao.jena.JenaBaseDao;
 import edu.cornell.mannlib.vitro.webapp.dao.jena.OntModelSelector;
 import edu.cornell.mannlib.vitro.webapp.dao.jena.SimpleOntModelSelector;
+import edu.cornell.mannlib.vitro.webapp.ontology.update.OntologyUpdateSettings;
 import edu.cornell.mannlib.vitro.webapp.ontology.update.OntologyUpdater;
 
 /**
@@ -22,14 +24,41 @@ import edu.cornell.mannlib.vitro.webapp.ontology.update.OntologyUpdater;
  */
 public class UpdateKnowledgeBase implements ServletContextListener {
 
+	private final String DATA_DIR = "/WEB-INF/ontologies/update/";
+	private final String LOG_DIR = "logs/";
+	private final String REMOVED_DATA_DIR = "removedData/";
+	private final String ASK_QUERY_FILE = DATA_DIR + "ask.sparql";
+	private final String SUCCESS_ASSERTIONS_FILE = DATA_DIR + "success.n3";
+	private final String SUCCESS_RDF_FORMAT = "N3";
+	private final String DIFF_FILE = DATA_DIR + "diff.tab.txt";
+	private final String LOG_FILE = DATA_DIR + LOG_DIR + 
+									"knowledgeBaseUpdate.log";
+	private final String ERROR_LOG_FILE = DATA_DIR + LOG_DIR +
+									"knowledgeBaseUpdate.error.log";
+	private final String REMOVED_DATA_FILE = DATA_DIR + REMOVED_DATA_DIR +
+									"removedData.rdf";
+	
 	public void contextInitialized(ServletContextEvent sce) {
 		
+		ServletContext ctx = sce.getServletContext();
+		
 		OntModelSelector oms = new SimpleOntModelSelector(
 				(OntModel) sce.getServletContext().getAttribute(
 						JenaBaseDao.ASSERTIONS_ONT_MODEL_ATTRIBUTE_NAME));
 		
+		OntologyUpdateSettings settings = new OntologyUpdateSettings();
+		settings.setAskQueryFile(ctx.getRealPath(ASK_QUERY_FILE));
+		settings.setDataDir(ctx.getRealPath(DATA_DIR));
+		settings.setDiffFile(ctx.getRealPath(DIFF_FILE));
+		settings.setSuccessAssertionsFile(
+				ctx.getRealPath(SUCCESS_ASSERTIONS_FILE));
+		settings.setSuccessRDFFormat(ctx.getRealPath(SUCCESS_RDF_FORMAT));
+		settings.setLogFile(ctx.getRealPath(LOG_FILE));
+		settings.setErrorLogFile(ctx.getRealPath(ERROR_LOG_FILE));
+		settings.setRemovedDataFile(ctx.getRealPath(REMOVED_DATA_FILE));
+		
 		try {
-			(new OntologyUpdater(sce.getServletContext(), oms)).update(); 
+			(new OntologyUpdater(settings)).update(); 
 		} catch (IOException ioe) {
 			throw new RuntimeException("IOException updating knowledge base " +
 					"for ontology changes", ioe);