VIVO-1016 Avoid crashing on ABox.isEmpty()

1) Don't ask whether the ABox is empty, if you don't need to
2) If you must ask, ask the graph of the base model, to avoid SDB layers
3) change contains() to use SELECT instead of ASK, because SDB implements ASK very poorly.

webapp/config/log4j.properties

@@ -36,7 +36,7 @@ log4j.rootLogger=INFO, AllAppender
 # These classes are too chatty to display INFO messages.
 log4j.logger.edu.cornell.mannlib.vitro.webapp.startup.StartupStatus=WARN
 log4j.logger.edu.cornell.mannlib.vitro.webapp.servlet.setup.UpdateKnowledgeBase=WARN
-log4j.logger.org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer=WARN
+log4j.logger.org.semanticweb.owlapi.rdf.rdfxml.parser=WARN
 
 # Spring as a whole is too chatty to display INFO messages.
 log4j.logger.org.springframework=WARN

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

@@ -145,10 +145,12 @@ public class RDFServiceGraph implements GraphWithPerform {
 
     @Override
     public boolean contains(Node subject, Node predicate, Node object) {
-        if (subject.isBlank() || predicate.isBlank() || object.isBlank()) {
+		if ((subject != null && subject.isBlank())
+				|| (predicate != null && predicate.isBlank())
+				|| (object != null && object.isBlank())) {
             return false;
         }
-        StringBuffer containsQuery = new StringBuffer("ASK { \n");
+        StringBuffer containsQuery = new StringBuffer("SELECT * WHERE { \n");
         if (graphURI != null) {
             containsQuery.append("  GRAPH <" + graphURI + "> { ");
         }
@@ -160,9 +162,9 @@ public class RDFServiceGraph implements GraphWithPerform {
         if (graphURI != null) {
             containsQuery.append(" } \n");
         }
-        containsQuery.append("\n}");
+        containsQuery.append("} \nLIMIT 1 ");
-        boolean result = execAsk(containsQuery.toString());
+        ResultSet result = execSelect(containsQuery.toString());
-        return result;
+        return result.hasNext();
     }
 
     @Override
@@ -319,7 +321,7 @@ public class RDFServiceGraph implements GraphWithPerform {
 
     @Override
     public boolean isEmpty() {
-        return (size() == 0);
+        return !contains(null, null, null);
     }
 
     @Override

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

@@ -170,7 +170,9 @@ public class SparqlGraph implements GraphWithPerform {
 
     @Override
     public boolean contains(Node subject, Node predicate, Node object) {
-        if (subject.isBlank() || predicate.isBlank() || object.isBlank()) {
+		if ((subject != null && subject.isBlank())
+				|| (predicate != null && predicate.isBlank())
+				|| (object != null && object.isBlank())) {
             return false;
         }
         StringBuffer containsQuery = new StringBuffer("ASK { \n");
@@ -357,7 +359,7 @@ public class SparqlGraph implements GraphWithPerform {
 
     @Override
     public boolean isEmpty() {
-        return (size() == 0);
+        return !contains(null, null, null);
     }
 
     @Override

webapp/src/edu/cornell/mannlib/vitro/webapp/filestorage/serving/FileServingServlet.java

@@ -113,6 +113,8 @@ public class FileServingServlet extends VitroHttpServlet {
 			while (-1 != (howMany = in.read(buffer))) {
 				out.write(buffer, 0, howMany);
 			}
+		} catch (IOException e) {
+			log.warn("Failed to serve the file", e);
 		} finally {
 			try {
 				in.close();

webapp/src/edu/cornell/mannlib/vitro/webapp/rdfservice/impl/jena/ListeningGraph.java

@@ -163,7 +163,7 @@ public class ListeningGraph implements GraphWithPerform {
 
     @Override
     public boolean isEmpty() {
-        return (size() == 0);
+        return !contains(null, null, null);
     }
 
     @Override

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

@@ -32,6 +32,11 @@ import edu.cornell.mannlib.vitro.webapp.startup.StartupStatus;
 
 /**
  * Sets up the content models, OntModelSelectors and webapp DAO factories.
+ * 
+ * Why the firstTimeStartup flag? Because you can't ask a large SDB model
+ * whether it is empty. SDB translates  this into a call to size(), which
+ * in turn becomes find(null, null, null) and a count, and this gives an
+ * OutOfMemoryError because it tries to read the entire model into memory.
  */
 public class ContentModelSetup extends JenaDataSourceSetupBase 
         implements javax.servlet.ServletContextListener {
@@ -50,22 +55,24 @@ public class ContentModelSetup extends JenaDataSourceSetupBase
 
     private void setUpJenaDataSource(ServletContext ctx) {
         ContextModelAccess models = ModelAccess.on(ctx);
+        boolean firstTimeStartup = false;
     	
     	Model applicationMetadataModel = models.getOntModel(APPLICATION_METADATA);
-		if (applicationMetadataModel.size()== 0) {
+		if (applicationMetadataModel.isEmpty()) {
+			firstTimeStartup = true;
         	initializeApplicationMetadata(ctx, applicationMetadataModel);
 		} else {
         	checkForNamespaceMismatch( applicationMetadataModel, ctx );
 		}
 
         OntModel baseABoxModel = models.getOntModel(ABOX_ASSERTIONS);
-        if (baseABoxModel.size() == 0) {
+        if (firstTimeStartup) {
         	RDFFilesLoader.loadFirstTimeFiles("abox", baseABoxModel, true);
         }
         RDFFilesLoader.loadEveryTimeFiles("abox", baseABoxModel);
         
         OntModel baseTBoxModel = models.getOntModel(TBOX_ASSERTIONS);
-        if (baseTBoxModel.size() == 0) {
+        if (firstTimeStartup) {
         	RDFFilesLoader.loadFirstTimeFiles("tbox", baseTBoxModel, true);
         }
     	RDFFilesLoader.loadEveryTimeFiles("tbox", baseTBoxModel);

webapp/src/edu/cornell/mannlib/vitro/webapp/triplesource/impl/tdb/ContentTripleSourceTDB.java

@@ -106,7 +106,7 @@ public class ContentTripleSourceTDB extends ContentTripleSource {
 	}
 
 	private void checkForFirstTimeStartup() {
-		if (this.dataset.getNamedModel(ModelNames.TBOX_ASSERTIONS).size() == 0) {
+		if (this.dataset.getNamedModel(ModelNames.TBOX_ASSERTIONS).getGraph().isEmpty()) {
 			JenaDataSourceSetupBase.thisIsFirstStartup();
 		}
 	}