Merge branch 'maint-rel-1.6' into develop
This commit is contained in:
j2blake
commit
a2ab207ef9
5 changed files with 74 additions and 18 deletions
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@ -4,13 +4,13 @@
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DELETE FROM `orng_apps`;
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INSERT INTO `orng_apps` (`appid`, `name`, `url`, `PersonFilterID`, `enabled`, `channels`) VALUES
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(100, 'Google Search', 'http://dev-profiles.ucsf.edu/orng/GoogleSearch.xml', NULL, 1, NULL),
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(101, 'Featured Presentations', 'http://dev-profiles.ucsf.edu/orng/SlideShare.xml', NULL, 1, NULL),
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(102, 'Faculty Mentor', 'http://dev-profiles.ucsf.edu/orng/Mentor.xml', NULL, 0, NULL),
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(103, 'Websites', 'http://dev-profiles.ucsf.edu/orng/Links.xml', NULL, 1, NULL),
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(104, 'Profile List', 'http://dev-profiles.ucsf.edu/orng/ProfileListTool.xml', NULL, 1, 'JSONPersonIds'),
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(106, 'RDF Test Gadget', 'http://dev-profiles.ucsf.edu/orng/RDFTest.xml', NULL, 1, NULL),
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(112, 'Twitter', 'http://dev-profiles.ucsf.edu/ORNG/Twitter.xml', NULL, 1, NULL);
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(100, 'Google Search', 'http://stage-profiles.ucsf.edu/apps/ucsfsearch.xml', NULL, 1, NULL),
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(101, 'Featured Presentations', 'http://stage-profiles.ucsf.edu/apps/SlideShare.xml', NULL, 1, NULL),
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(102, 'Faculty Mentor', 'http://stage-profiles.ucsf.edu/apps/Mentor.xml', NULL, 0, NULL),
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(103, 'Websites', 'http://stage-profiles.ucsf.edu/apps/Links.xml', NULL, 1, NULL),
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(104, 'Profile List', 'http://stage-profiles.ucsf.edu/apps/ProfileListTool.xml', NULL, 1, 'JSONPersonIds'),
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(106, 'RDF Test Gadget', 'http://stage-profiles.ucsf.edu/apps/RDFTest.xml', NULL, 1, NULL),
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(112, 'Twitter', 'http://stage-profiles.ucsf.edu/apps/Twitter.xml', NULL, 1, NULL);
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DELETE FROM `orng_app_views`;
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@ -241,6 +241,9 @@ public class FormUtils {
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option.setValue(vclass.getURI());
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option.setBody(vclass.getPickListName());
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vclassOptionList.add(option);
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if(selectedVClassURI != null && selectedVClassURI.equals(vclass.getURI())) {
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option.setSelected(true);
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}
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}
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return vclassOptionList;
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}
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@ -2,6 +2,7 @@
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package edu.cornell.mannlib.vitro.webapp.controller.individual;
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import java.text.SimpleDateFormat;
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import java.util.Date;
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import java.util.HashSet;
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import java.util.Set;
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@ -343,7 +344,9 @@ public class IndividualRdfAssembler {
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}
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private Literal createDateLiteral(OntModel o) {
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return o.createTypedLiteral(new Date(), XSDDatatype.XSDdate);
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String date = new SimpleDateFormat("YYYY-MM-dd'T'HH:mm:ss")
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.format(new Date());
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return o.createTypedLiteral(date, XSDDatatype.XSDdateTime);
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}
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}
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@ -83,7 +83,7 @@ public class KnowledgeBaseUpdater {
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logger.closeLogs();
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long elapsedSecs = (System.currentTimeMillis() - startTime)/1000;
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log.info("Finished knowledge base migration in " + elapsedSecs + " second" + (elapsedSecs != 1 ? "s" : ""));
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log.info("Finished checking knowledge base in " + elapsedSecs + " second" + (elapsedSecs != 1 ? "s" : ""));
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return record.hasRecordedChanges();
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}
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@ -95,20 +95,20 @@ public class KnowledgeBaseUpdater {
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AtomicOntologyChangeLists changes = new AtomicOntologyChangeLists(rawChanges,settings.getNewTBoxModel(),settings.getOldTBoxModel());
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// update ABox data any time
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log.info("performing SPARQL CONSTRUCT additions");
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log.debug("performing SPARQL CONSTRUCT additions");
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performSparqlConstructs(settings.getSparqlConstructAdditionsDir(), settings.getRDFService(), ADD);
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log.info("performing SPARQL CONSTRUCT retractions");
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log.debug("performing SPARQL CONSTRUCT retractions");
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performSparqlConstructs(settings.getSparqlConstructDeletionsDir(), settings.getRDFService(), RETRACT);
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log.info("\tupdating the abox");
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log.info("\tchecking the abox");
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updateABox(changes);
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log.info("performing post-processing SPARQL CONSTRUCT additions");
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log.debug("performing post-processing SPARQL CONSTRUCT additions");
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performSparqlConstructs(settings.getSparqlConstructAdditionsDir() + "/post/",
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settings.getRDFService(), ADD);
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log.info("performing post-processing SPARQL CONSTRUCT retractions");
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log.debug("performing post-processing SPARQL CONSTRUCT retractions");
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performSparqlConstructs(settings.getSparqlConstructDeletionsDir() + "/post/",
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settings.getRDFService(), RETRACT);
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@ -145,7 +145,7 @@ public class KnowledgeBaseUpdater {
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boolean add) throws IOException {
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Dataset dataset = new RDFServiceDataset(rdfService);
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File sparqlConstructDirectory = new File(sparqlConstructDir);
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log.info("Using SPARQL CONSTRUCT directory " + sparqlConstructDirectory);
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log.debug("Using SPARQL CONSTRUCT directory " + sparqlConstructDirectory);
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if (!sparqlConstructDirectory.isDirectory()) {
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String logMsg = this.getClass().getName() +
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"performSparqlConstructs() expected to find a directory " +
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@ -178,7 +178,7 @@ public class KnowledgeBaseUpdater {
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}
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Model anonModel = ModelFactory.createDefaultModel();
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try {
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log.info("\t\tprocessing SPARQL construct query from file " + sparqlFile.getName());
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log.debug("\t\tprocessing SPARQL construct query from file " + sparqlFile.getName());
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anonModel = RDFServiceUtils.parseModel(
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rdfService.sparqlConstructQuery(fileContents.toString(),
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@ -12,6 +12,7 @@ import java.nio.file.Path;
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import java.nio.file.Paths;
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import java.text.SimpleDateFormat;
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import java.util.ArrayList;
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import java.util.Arrays;
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import java.util.Date;
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import java.util.List;
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@ -24,6 +25,10 @@ import org.apache.commons.logging.LogFactory;
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import com.hp.hpl.jena.ontology.OntModel;
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import com.hp.hpl.jena.ontology.OntModelSpec;
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import com.hp.hpl.jena.query.Query;
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import com.hp.hpl.jena.query.QueryExecution;
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import com.hp.hpl.jena.query.QueryExecutionFactory;
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import com.hp.hpl.jena.query.QueryFactory;
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import com.hp.hpl.jena.rdf.model.Model;
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import com.hp.hpl.jena.rdf.model.ModelFactory;
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import com.hp.hpl.jena.rdf.model.RDFNode;
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@ -42,8 +47,6 @@ import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory;
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import edu.cornell.mannlib.vitro.webapp.ontology.update.KnowledgeBaseUpdater;
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import edu.cornell.mannlib.vitro.webapp.ontology.update.UpdateSettings;
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import edu.cornell.mannlib.vitro.webapp.rdfservice.impl.RDFServiceUtils;
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import edu.cornell.mannlib.vitro.webapp.reasoner.ABoxRecomputer;
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import edu.cornell.mannlib.vitro.webapp.reasoner.SimpleReasoner;
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import edu.cornell.mannlib.vitro.webapp.startup.StartupStatus;
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/**
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@ -158,6 +161,8 @@ public class UpdateKnowledgeBase implements ServletContextListener {
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}
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}
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removeBadRestrictions(settings.getAssertionOntModelSelector().getTBoxModel());
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log.info("Simple reasoner connected for the ABox");
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if(JenaDataSourceSetupBase.isFirstStartup()
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|| (migrationChangesMade && requiredUpdate)) {
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@ -531,6 +536,51 @@ public class UpdateKnowledgeBase implements ServletContextListener {
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}
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}
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/**
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* Remove restrictions with missing owl:onProperty or obsolete core class
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* This should be worked into the main migration later.
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*/
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private void removeBadRestrictions(Model tboxModel) {
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List<String> queryStrs = Arrays.asList("PREFIX owl: <http://www.w3.org/2002/07/owl#> \n " +
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"CONSTRUCT { \n" +
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" ?rest ?p ?o . \n" +
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" ?oo ?pp ?rest \n" +
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"} WHERE { \n" +
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" ?rest a owl:Restriction . \n" +
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" FILTER NOT EXISTS { ?rest owl:onProperty ?x } \n" +
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" ?rest ?p ?o . \n" +
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" ?oo ?pp ?rest \n" +
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"} \n" ,
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"PREFIX owl: <http://www.w3.org/2002/07/owl#> \n " +
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"CONSTRUCT { \n" +
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" ?rest ?p ?o . \n" +
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" ?oo ?pp ?rest \n" +
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"} WHERE { \n" +
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" ?rest a owl:Restriction . \n" +
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" { ?rest owl:someValuesFrom ?c } UNION { ?rest owl:allValuesFrom ?c } \n" +
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" FILTER (regex(str(?c), \"vivoweb.org\")) \n" +
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" FILTER NOT EXISTS { ?c ?cp ?co } \n" +
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" ?rest ?p ?o . \n" +
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" ?oo ?pp ?rest \n" +
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"} \n" );
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for (String queryStr : queryStrs) {
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Query query = QueryFactory.create(queryStr);
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QueryExecution qe = QueryExecutionFactory.create(query, tboxModel);
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try {
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Model bad = qe.execConstruct();
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tboxModel.remove(bad);
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if (bad.size() > 0) {
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log.info("Deleted " + bad.size() +
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" triples of syntactically invalid restrictions");
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}
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} finally {
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if (qe != null) {
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qe.close();
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}
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}
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}
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}
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@Override
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public void contextDestroyed(ServletContextEvent arg0) {
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// nothing to do
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