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VIVO-389 pellet exception

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brianjlowe 2013-11-05 12:39:45 -05:00
parent 93d941412f
commit 447c677c39
1 changed files with 53 additions and 2 deletions
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55
webapp/src/edu/cornell/mannlib/vitro/webapp/servlet/setup/UpdateKnowledgeBase.java
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@ -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 +536,52 @@ 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");
bad.write(System.out);
}
} finally {
if (qe != null) {
qe.close();
}
}
}
}
@Override
public void contextDestroyed(ServletContextEvent arg0) {
// nothing to do