Merge branch 'maint-rel-1.6' into develop

opensocial/shindig_example_gadgets.sql

@@ -4,13 +4,13 @@
 DELETE FROM `orng_apps`;
 
 INSERT INTO `orng_apps` (`appid`, `name`, `url`, `PersonFilterID`, `enabled`, `channels`) VALUES
-(100, 'Google Search', 'http://dev-profiles.ucsf.edu/orng/GoogleSearch.xml', NULL, 1, NULL),
+(100, 'Google Search', 'http://stage-profiles.ucsf.edu/apps/ucsfsearch.xml', NULL, 1, NULL),
-(101, 'Featured Presentations', 'http://dev-profiles.ucsf.edu/orng/SlideShare.xml', NULL, 1, NULL),
+(101, 'Featured Presentations', 'http://stage-profiles.ucsf.edu/apps/SlideShare.xml', NULL, 1, NULL),
-(102, 'Faculty Mentor', 'http://dev-profiles.ucsf.edu/orng/Mentor.xml', NULL, 0, NULL),
+(102, 'Faculty Mentor', 'http://stage-profiles.ucsf.edu/apps/Mentor.xml', NULL, 0, NULL),
-(103, 'Websites', 'http://dev-profiles.ucsf.edu/orng/Links.xml', NULL, 1, NULL),
+(103, 'Websites', 'http://stage-profiles.ucsf.edu/apps/Links.xml', NULL, 1, NULL),
-(104, 'Profile List', 'http://dev-profiles.ucsf.edu/orng/ProfileListTool.xml', NULL, 1, 'JSONPersonIds'),
+(104, 'Profile List', 'http://stage-profiles.ucsf.edu/apps/ProfileListTool.xml', NULL, 1, 'JSONPersonIds'),
-(106, 'RDF Test Gadget', 'http://dev-profiles.ucsf.edu/orng/RDFTest.xml', NULL, 1, NULL),
+(106, 'RDF Test Gadget', 'http://stage-profiles.ucsf.edu/apps/RDFTest.xml', NULL, 1, NULL),
-(112, 'Twitter', 'http://dev-profiles.ucsf.edu/ORNG/Twitter.xml', NULL, 1, NULL);
+(112, 'Twitter', 'http://stage-profiles.ucsf.edu/apps/Twitter.xml', NULL, 1, NULL);
 
 DELETE FROM `orng_app_views`;
 

webapp/src/edu/cornell/mannlib/vedit/util/FormUtils.java

@@ -241,6 +241,9 @@ public class FormUtils {
         	option.setValue(vclass.getURI());
         	option.setBody(vclass.getPickListName());
         	vclassOptionList.add(option);
+        	if(selectedVClassURI != null && selectedVClassURI.equals(vclass.getURI())) {
+        	    option.setSelected(true);
+        	}
         }
         return vclassOptionList;
     }

webapp/src/edu/cornell/mannlib/vitro/webapp/controller/individual/IndividualRdfAssembler.java

@@ -2,6 +2,7 @@
 
 package edu.cornell.mannlib.vitro.webapp.controller.individual;
 
+import java.text.SimpleDateFormat;
 import java.util.Date;
 import java.util.HashSet;
 import java.util.Set;
@@ -343,7 +344,9 @@ public class IndividualRdfAssembler {
 	}
 
 	private Literal createDateLiteral(OntModel o) {
-		return o.createTypedLiteral(new Date(), XSDDatatype.XSDdate);
+		String date = new SimpleDateFormat("YYYY-MM-dd'T'HH:mm:ss")
+				.format(new Date());
+		return o.createTypedLiteral(date, XSDDatatype.XSDdateTime);
 	}
 
 }

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

@@ -83,7 +83,7 @@ public class KnowledgeBaseUpdater {
 		logger.closeLogs();
 
 		long elapsedSecs = (System.currentTimeMillis() - startTime)/1000;		
-		log.info("Finished knowledge base migration in " + elapsedSecs + " second" + (elapsedSecs != 1 ? "s" : ""));
+		log.info("Finished checking knowledge base in " + elapsedSecs + " second" + (elapsedSecs != 1 ? "s" : ""));
 		
 		return record.hasRecordedChanges();
 	}
@@ -95,20 +95,20 @@ public class KnowledgeBaseUpdater {
 		AtomicOntologyChangeLists changes = new AtomicOntologyChangeLists(rawChanges,settings.getNewTBoxModel(),settings.getOldTBoxModel());
 	        	
 		// update ABox data any time
-    	log.info("performing SPARQL CONSTRUCT additions");
+    	log.debug("performing SPARQL CONSTRUCT additions");
     	performSparqlConstructs(settings.getSparqlConstructAdditionsDir(), settings.getRDFService(), ADD);
     	
-        log.info("performing SPARQL CONSTRUCT retractions");
+        log.debug("performing SPARQL CONSTRUCT retractions");
         performSparqlConstructs(settings.getSparqlConstructDeletionsDir(), settings.getRDFService(), RETRACT);
         
-        log.info("\tupdating the abox");
+        log.info("\tchecking the abox");
         updateABox(changes);
         
-        log.info("performing post-processing SPARQL CONSTRUCT additions");
+        log.debug("performing post-processing SPARQL CONSTRUCT additions");
         performSparqlConstructs(settings.getSparqlConstructAdditionsDir() + "/post/", 
                 settings.getRDFService(), ADD);
         
-        log.info("performing post-processing SPARQL CONSTRUCT retractions");
+        log.debug("performing post-processing SPARQL CONSTRUCT retractions");
         performSparqlConstructs(settings.getSparqlConstructDeletionsDir() + "/post/", 
                 settings.getRDFService(), RETRACT);
         
@@ -145,7 +145,7 @@ public class KnowledgeBaseUpdater {
             boolean add)   throws IOException {
         Dataset dataset = new RDFServiceDataset(rdfService);
         File sparqlConstructDirectory = new File(sparqlConstructDir);
-        log.info("Using SPARQL CONSTRUCT directory " + sparqlConstructDirectory);
+        log.debug("Using SPARQL CONSTRUCT directory " + sparqlConstructDirectory);
         if (!sparqlConstructDirectory.isDirectory()) {
             String logMsg = this.getClass().getName() + 
                     "performSparqlConstructs() expected to find a directory " +
@@ -178,7 +178,7 @@ public class KnowledgeBaseUpdater {
             }   
             Model anonModel = ModelFactory.createDefaultModel();
             try {
-                log.info("\t\tprocessing SPARQL construct query from file " + sparqlFile.getName());
+                log.debug("\t\tprocessing SPARQL construct query from file " + sparqlFile.getName());
                 
                 anonModel = RDFServiceUtils.parseModel(
                         rdfService.sparqlConstructQuery(fileContents.toString(), 

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

@@ -12,6 +12,7 @@ import java.nio.file.Path;
 import java.nio.file.Paths;
 import java.text.SimpleDateFormat;
 import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.Date;
 import java.util.List;
 
@@ -24,6 +25,10 @@ import org.apache.commons.logging.LogFactory;
 
 import com.hp.hpl.jena.ontology.OntModel;
 import com.hp.hpl.jena.ontology.OntModelSpec;
+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.rdf.model.Model;
 import com.hp.hpl.jena.rdf.model.ModelFactory;
 import com.hp.hpl.jena.rdf.model.RDFNode;
@@ -42,8 +47,6 @@ import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory;
 import edu.cornell.mannlib.vitro.webapp.ontology.update.KnowledgeBaseUpdater;
 import edu.cornell.mannlib.vitro.webapp.ontology.update.UpdateSettings;
 import edu.cornell.mannlib.vitro.webapp.rdfservice.impl.RDFServiceUtils;
-import edu.cornell.mannlib.vitro.webapp.reasoner.ABoxRecomputer;
-import edu.cornell.mannlib.vitro.webapp.reasoner.SimpleReasoner;
 import edu.cornell.mannlib.vitro.webapp.startup.StartupStatus;
 
 /**
@@ -158,6 +161,8 @@ public class UpdateKnowledgeBase implements ServletContextListener {
     			}	
 			}
 			
+			removeBadRestrictions(settings.getAssertionOntModelSelector().getTBoxModel());
+			
             log.info("Simple reasoner connected for the ABox");
             if(JenaDataSourceSetupBase.isFirstStartup() 
                     || (migrationChangesMade && requiredUpdate)) {
@@ -531,6 +536,51 @@ public class UpdateKnowledgeBase implements ServletContextListener {
 		}	
 	}
 	
+	/**
+	 *  Remove restrictions with missing owl:onProperty or obsolete core class
+	 *  This should be worked into the main migration later.
+	 */
+	private void removeBadRestrictions(Model tboxModel) {
+	    List<String> queryStrs = Arrays.asList("PREFIX owl:   <http://www.w3.org/2002/07/owl#> \n " +
+	            "CONSTRUCT { \n" +
+	            "    ?rest ?p ?o . \n" +
+	            "    ?oo ?pp ?rest \n" +
+	            "} WHERE { \n" +
+	            "    ?rest a owl:Restriction . \n" + 
+	            "    FILTER NOT EXISTS { ?rest owl:onProperty ?x } \n" +
+	            "    ?rest ?p ?o . \n" +
+	            "    ?oo ?pp ?rest \n" +
+	            "} \n" ,
+	            "PREFIX owl:   <http://www.w3.org/2002/07/owl#> \n " +
+                "CONSTRUCT { \n" +
+                "    ?rest ?p ?o . \n" +
+                "    ?oo ?pp ?rest \n" +
+                "} WHERE { \n" +
+                "    ?rest a owl:Restriction . \n" +
+                "    { ?rest owl:someValuesFrom ?c } UNION { ?rest owl:allValuesFrom ?c } \n" +
+                "    FILTER (regex(str(?c), \"vivoweb.org\")) \n" +
+                "    FILTER NOT EXISTS { ?c ?cp ?co } \n" +
+                "    ?rest ?p ?o . \n" +
+                "    ?oo ?pp ?rest \n" +
+                "} \n" );
+	    for (String queryStr : queryStrs) {
+            Query query = QueryFactory.create(queryStr);
+            QueryExecution qe = QueryExecutionFactory.create(query, tboxModel);
+            try {
+                Model bad = qe.execConstruct();
+                tboxModel.remove(bad);
+                if (bad.size() > 0) {
+                    log.info("Deleted " + bad.size() + 
+                            " triples of syntactically invalid restrictions");
+                }
+            } finally {
+                if (qe != null) {
+                    qe.close();
+                }
+            }
+	    }
+	}
+	
 	@Override
 	public void contextDestroyed(ServletContextEvent arg0) {
 		// nothing to do