work in progress on data migration and related changes to support ISF

webapp/src/edu/cornell/mannlib/vitro/webapp/controller/jena/RDFUploadController.java

@@ -77,11 +77,16 @@ public class RDFUploadController extends JenaIngestController {
         VitroRequest request = new VitroRequest(req);        
         LoginStatusBean loginBean = LoginStatusBean.getBean(request);
         
+        try {
             String modelName = req.getParameter("modelName");
             if(modelName!=null){
                 loadRDF(req,request,response);
                 return;
             }    
+        } catch (Exception e) {
+            log.error(e,e);
+            throw new RuntimeException(e);
+        }
                        
         boolean remove = "remove".equals(request.getParameter("mode"));
         String verb = remove?"Removed":"Added";

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

@@ -905,8 +905,8 @@ public class ObjectPropertyDaoJena extends PropertyDaoJena implements ObjectProp
         "SELECT ?property ?range ?filename WHERE { \n" +
         "    { ?property display:listViewConfigFile ?filename \n" +
         "    } UNION { \n" +
-        "        ?lv config:listViewConfigFile ?filename . \n " +
+        "        ?configuration config:listViewConfigFile ?filename . \n " +
-        "        ?configuration config:hasListView ?lv . " +
+//        "        ?configuration config:hasListView ?lv . " +
         "        ?context config:hasConfiguration ?configuration . \n" +
         "        ?context config:configContextFor ?property . \n" +
         "        ?context config:qualifiedBy ?range . \n" +
@@ -955,6 +955,7 @@ public class ObjectPropertyDaoJena extends PropertyDaoJena implements ObjectProp
                 	}
                 } else {
                     String filename = soln.getLiteral("filename").getLexicalForm();
+                    log.info("putting " + prop.getURI() + " " + rangeUri + " " + filename + " into list view map");
                     customListViewConfigFileMap.put(new Pair<ObjectProperty, String>(prop, rangeUri), filename);     
                 }
             }       
@@ -963,6 +964,7 @@ public class ObjectPropertyDaoJena extends PropertyDaoJena implements ObjectProp
         
         String customListViewConfigFileName = customListViewConfigFileMap.get(new Pair<ObjectProperty, String>(op, op.getRangeVClassURI()));
         if (customListViewConfigFileName == null) {
+            log.info("no list view found for " + op.getURI() + " qualified by " + op.getRangeVClassURI());
             customListViewConfigFileName = customListViewConfigFileMap.get(new Pair<ObjectProperty, String>(op, OWL.Thing.getURI()));
         }
         

webapp/src/edu/cornell/mannlib/vitro/webapp/filestorage/uploadrequest/MultipartHttpServletRequest.java

@@ -57,6 +57,7 @@ public class MultipartHttpServletRequest extends FileUploadServletRequest {
         throws IOException{
         super(request);
         storeFilesToTempDir = false;
+        setup(request);
         
     }
             
@@ -73,6 +74,7 @@ public class MultipartHttpServletRequest extends FileUploadServletRequest {
         storeFilesToTempDir = true;
         this.maxFileSize = maxFileSize;
         this.tempDir = figureTemporaryDirectory(request);
+        setup(request);
 	}
 
     private void setup(HttpServletRequest request){

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

@@ -4,10 +4,12 @@ package edu.cornell.mannlib.vitro.webapp.ontology.update;
 
 import java.io.IOException;
 import java.util.ArrayList;
-import java.util.HashSet;
 import java.util.Iterator;
 import java.util.List;
 
+import org.apache.commons.logging.Log;
+import org.apache.commons.logging.LogFactory;
+
 import com.hp.hpl.jena.ontology.OntClass;
 import com.hp.hpl.jena.ontology.OntModel;
 import com.hp.hpl.jena.ontology.OntModelSpec;
@@ -24,7 +26,6 @@ import com.hp.hpl.jena.rdf.model.StmtIterator;
 import com.hp.hpl.jena.shared.Lock;
 import com.hp.hpl.jena.vocabulary.OWL;
 import com.hp.hpl.jena.vocabulary.RDF;
-import com.hp.hpl.jena.vocabulary.RDFS;
 
 import edu.cornell.mannlib.vitro.webapp.ontology.update.AtomicOntologyChange.AtomicChangeType;
 
@@ -34,6 +35,7 @@ import edu.cornell.mannlib.vitro.webapp.ontology.update.AtomicOntologyChange.Ato
 */ 
 public class ABoxUpdater {
 
+    private final Log log = LogFactory.getLog(ABoxUpdater.class);
 	private OntModel oldTboxModel;
 	private OntModel newTboxModel;
 	private OntModel aboxModel;
@@ -388,20 +390,33 @@ public class ABoxUpdater {
 		Iterator<AtomicOntologyChange> propItr = changes.iterator();
 		while(propItr.hasNext()){
 			AtomicOntologyChange propChangeObj = propItr.next();
+			log.info("processing " + propChangeObj);
+			try {
+			    if (propChangeObj.getAtomicChangeType() == null) {
+			        log.error("Missing change type; skipping " + propChangeObj);
+			        continue;
+			    }
     			switch (propChangeObj.getAtomicChangeType()){
     			  case ADD: 
+    			   log.info("add");
     			   addProperty(propChangeObj);
     			   break;
     			case DELETE: 
+    			   log.info("delete");
     			   deleteProperty(propChangeObj);
     			   break;
     			case RENAME: 
+    			   log.info("rename");
     			   renameProperty(propChangeObj);
     			   break;
     			default: 
+    			   log.info("unknown");
     			   logger.logError("unexpected change type indicator: " + propChangeObj.getAtomicChangeType());
     			   break;
     		    }	
+			} catch (Exception e) {
+			    log.error(e,e);
+			}
 		}
 	}
 	
@@ -518,7 +533,7 @@ public class ABoxUpdater {
 	
 	private void renameProperty(AtomicOntologyChange propObj) throws IOException {
 		
-		//logger.log("Processing a property rename from: " + propObj.getSourceURI() + " to " + propObj.getDestinationURI());
+		logger.log("Processing a property rename from: " + propObj.getSourceURI() + " to " + propObj.getDestinationURI());
 		
 		OntProperty oldProperty = oldTboxModel.getOntProperty(propObj.getSourceURI());
 		OntProperty newProperty = newTboxModel.getOntProperty(propObj.getDestinationURI());

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

@@ -30,6 +30,11 @@ public class AtomicOntologyChange {
 		this.notes = notes;
     }
 
+	@Override
+	public String toString() {
+	    return "Source: " + sourceURI + "; Destination: " + destinationURI +
+	            "; Type: " + atomicChangeType + "; Notes:" + notes;
+	}
 	
 	/**
 	 * Contains the URI of a class or property in the previous version of

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

@@ -98,14 +98,18 @@ public class KnowledgeBaseUpdater {
 		AtomicOntologyChangeLists changes = new AtomicOntologyChangeLists(rawChanges,settings.getNewTBoxModel(),settings.getOldTBoxModel());
 		
         //process the TBox before the ABox
+		try {
 		    log.info("\tupdating tbox annotations");
 	        updateTBoxAnnotations();
+		} catch (Exception e) {
+		    log.error(e,e);
+		}
 	    
 	    try {
     	    migrateMigrationMetadata(servletContext);
 		    logger.log("Migrated migration metadata");
 	    } catch (Exception e) {
-	    	log.debug("unable to migrate migration metadata " + e.getMessage());
+	    	log.error("unable to migrate migration metadata " + e.getMessage());
 	    }
 	    
 		log.info("\tupdating the abox");
@@ -390,11 +394,13 @@ public class KnowledgeBaseUpdater {
 			while(listItr.hasNext()) {
 				AtomicOntologyChange changeObj = listItr.next();
 				if (changeObj.getSourceURI() != null){
-			
+			        log.info("triaging " + changeObj);
 					if (oldTboxModel.getOntProperty(changeObj.getSourceURI()) != null){
 						 atomicPropertyChanges.add(changeObj);
+						 log.info("added to property changes");
 					} else if (oldTboxModel.getOntClass(changeObj.getSourceURI()) != null) {
 						 atomicClassChanges.add(changeObj);
+						 log.info("added to class changes");
 					} else if ("Prop".equals(changeObj.getNotes())) {
 						 atomicPropertyChanges.add(changeObj);
 					} else if ("Class".equals(changeObj.getNotes())) {

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

@@ -9,6 +9,8 @@ import java.util.ArrayList;
 import java.util.List;
 import java.util.StringTokenizer;
 
+import org.apache.commons.logging.Log;
+import org.apache.commons.logging.LogFactory;
 import org.skife.csv.CSVReader;
 import org.skife.csv.SimpleReader;
 
@@ -23,6 +25,8 @@ import edu.cornell.mannlib.vitro.webapp.ontology.update.AtomicOntologyChange.Ato
 
 public class OntologyChangeParser {
 
+    private final Log log = LogFactory.getLog(OntologyChangeParser.class);
+    
 	private ChangeLogger logger;
 	
 	public OntologyChangeParser(ChangeLogger logger) {
@@ -85,6 +89,8 @@ public class OntologyChangeParser {
 				}
 				
 				
+				log.info(changeObj);
+				
 				changeObjects.add(changeObj);
 					
 			}

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

@@ -104,6 +104,11 @@ public class TBoxUpdater {
          //  if the default has changed in the new version of the ontology AND if 
          //  the site hasn't overidden the previous default in their knowledge base.
     		    
+	      if(oldTboxAnnotationsModel == null) {
+	          logger.log("oldTboxAnnotationModel is null; aborting update of annotation values");
+	          return;
+	      }
+	       
 		  StmtIterator iter = oldTboxAnnotationsModel.listStatements();
 		  		  		  
 		  while (iter.hasNext()) {