some kbm refactor and additional log messages
This commit is contained in:
stellamit
parent
d3ad1c1a5a
commit
0f9d1a79d1
2 changed files with 163 additions and 166 deletions
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@ -10,7 +10,6 @@ import java.io.FileNotFoundException;
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import java.io.FileReader;
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import java.io.IOException;
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import java.io.InputStream;
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import java.io.StringWriter;
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import java.util.ArrayList;
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import java.util.Iterator;
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import java.util.List;
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@ -30,16 +29,10 @@ import com.hp.hpl.jena.query.QueryFactory;
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import com.hp.hpl.jena.query.Syntax;
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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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import com.hp.hpl.jena.rdf.model.Resource;
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import com.hp.hpl.jena.rdf.model.ResourceFactory;
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import com.hp.hpl.jena.rdf.model.Statement;
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import com.hp.hpl.jena.rdf.model.StmtIterator;
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import com.hp.hpl.jena.shared.Lock;
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import com.hp.hpl.jena.vocabulary.RDF;
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import com.hp.hpl.jena.vocabulary.RDFS;
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import edu.cornell.mannlib.vitro.webapp.dao.DisplayVocabulary;
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import edu.cornell.mannlib.vitro.webapp.rdfservice.ChangeSet;
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import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFService;
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import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFServiceException;
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@ -371,144 +364,7 @@ public class KnowledgeBaseUpdater {
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}
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}
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//update migration model
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public void migrateDisplayModel() {
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OntModel displayModel = this.settings.getDisplayModel();
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Model addStatements = ModelFactory.createDefaultModel();
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Model removeStatements = ModelFactory.createDefaultModel();
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//remove old tbox and display metadata statements and add statements from new versions
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replaceTboxAndDisplayMetadata(displayModel, addStatements, removeStatements);
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//Update statements for data getter class types that have changed in 1.5
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updateDataGetterClassNames(displayModel, addStatements, removeStatements);
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//add cannot delete flags to pages that shouldn't allow deletion on page list
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addCannotDeleteFlagDisplayModel(displayModel, addStatements, removeStatements);
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//removes requiresTemplate statement for people page
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updatePeoplePageDisplayModel(displayModel, addStatements, removeStatements);
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//add page list
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addPageListDisplayModel(displayModel, addStatements, removeStatements);
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//update data getter labels
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updateDataGetterLabels(displayModel, addStatements, removeStatements);
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displayModel.enterCriticalSection(Lock.WRITE);
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try {
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if(log.isDebugEnabled()) {
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StringWriter sw = new StringWriter();
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addStatements.write(sw);
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log.debug("Statements to be added are: ");
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log.debug(sw.toString());
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sw.close();
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sw = new StringWriter();
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removeStatements.write(sw);
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log.debug("Statements to be removed are: ");
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log.debug(sw.toString());
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sw.close();
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}
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displayModel.remove(removeStatements);
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displayModel.add(addStatements);
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} catch(Exception ex) {
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log.error("An error occurred in migrating display model ", ex);
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} finally {
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displayModel.leaveCriticalSection();
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}
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}
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//replace
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private void replaceTboxAndDisplayMetadata(OntModel displayModel, Model addStatements, Model removeStatements) {
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OntModel oldDisplayModelTboxModel = this.settings.getOldDisplayModelTboxModel();
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OntModel oldDisplayModelDisplayMetadataModel = this.settings.getOldDisplayModelDisplayMetadataModel();
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OntModel newDisplayModelTboxModel = this.settings.getNewDisplayModelTboxModel();
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OntModel newDisplayModelDisplayMetadataModel = this.settings.getNewDisplayModelDisplayMetadataModel();
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OntModel loadedAtStartup = this.settings.getLoadedAtStartupDisplayModel();
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OntModel oldVivoListView = this.settings.getVivoListViewConfigDisplayModel();
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//Remove old display model tbox and display metadata statements from display model
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removeStatements.add(oldDisplayModelTboxModel);
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removeStatements.add(oldDisplayModelDisplayMetadataModel);
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//the old startup folder only contained by oldVivoListView
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removeStatements.add(oldVivoListView);
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//Add statements from new tbox and display metadata
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addStatements.add(newDisplayModelTboxModel);
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addStatements.add(newDisplayModelDisplayMetadataModel);
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//this should include the list view in addition to other files
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addStatements.add(loadedAtStartup);
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}
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//update statements for data getter classes
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private void updateDataGetterClassNames(OntModel displayModel, Model addStatements, Model removeStatements) {
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Resource classGroupOldType = ResourceFactory.createResource("java:edu.cornell.mannlib.vitro.webapp.utils.pageDataGetter.ClassGroupPageData");
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Resource browseOldType = ResourceFactory.createResource("java:edu.cornell.mannlib.vitro.webapp.utils.pageDataGetter.BrowseDataGetter");
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Resource individualsForClassesOldType = ResourceFactory.createResource("java:edu.cornell.mannlib.vitro.webapp.utils.pageDataGetter.IndividualsForClassesDataGetter");
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Resource internalClassesOldType = ResourceFactory.createResource("java:edu.cornell.mannlib.vitro.webapp.utils.pageDataGetter.InternalClassesDataGetter");
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Resource classGroupNewType = ResourceFactory.createResource("java:edu.cornell.mannlib.vitro.webapp.utils.dataGetter.ClassGroupPageData");
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Resource browseNewType = ResourceFactory.createResource("java:edu.cornell.mannlib.vitro.webapp.utils.dataGetter.BrowseDataGetter");
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Resource individualsForClassesNewType = ResourceFactory.createResource("java:edu.cornell.mannlib.vitro.webapp.utils.dataGetter.IndividualsForClassesDataGetter");
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Resource internalClassesNewType = ResourceFactory.createResource("java:edu.cornell.mannlib.vitro.webapp.utils.dataGetter.InternalClassesDataGetter");
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//Find statements where type is ClassGroupData
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updateAddRemoveDataGetterStatements(displayModel, removeStatements, addStatements, classGroupOldType, classGroupNewType);
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//Find statements where type is BrowseDataGetter
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updateAddRemoveDataGetterStatements(displayModel, removeStatements, addStatements, browseOldType, browseNewType);
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//Find statements where type is individuals for classes
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updateAddRemoveDataGetterStatements(displayModel, removeStatements, addStatements, individualsForClassesOldType, individualsForClassesNewType);
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//Find statements where type is internal class
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updateAddRemoveDataGetterStatements(displayModel, removeStatements, addStatements, internalClassesOldType, internalClassesNewType);
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}
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private void updateAddRemoveDataGetterStatements(OntModel displayModel,
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Model removeStatements, Model addStatements,
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Resource oldType, Resource newType) {
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removeStatements.add(displayModel.listStatements(null, RDF.type, oldType));
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StmtIterator oldStatements = displayModel.listStatements(null, RDF.type, oldType);
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while(oldStatements.hasNext()) {
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Statement stmt = oldStatements.nextStatement();
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addStatements.add(stmt.getSubject(), RDF.type, newType);
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}
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}
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//add cannotDeleteFlag to display model
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private void addCannotDeleteFlagDisplayModel(OntModel displayModel, Model addStatements, Model removeStatements) {
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Resource homePage = displayModel.getResource(DisplayVocabulary.HOME_PAGE_URI);
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addStatements.add(homePage,
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ResourceFactory.createProperty(DisplayVocabulary.DISPLAY_NS + "cannotDeletePage"),
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ResourceFactory.createPlainLiteral("true"));
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}
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//remove requires template
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private void updatePeoplePageDisplayModel(OntModel displayModel, Model addStatements, Model removeStatements) {
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Resource peoplePage = displayModel.getResource(DisplayVocabulary.DISPLAY_NS + "People");
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if(peoplePage != null) {
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removeStatements.add(peoplePage, DisplayVocabulary.REQUIRES_BODY_TEMPLATE,
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ResourceFactory.createPlainLiteral("menupage--classgroup-people.ftl"));
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}
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}
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//add page list sparql query
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private void addPageListDisplayModel(OntModel displayModel, Model addStatements, Model removeStatements) {
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OntModel newDisplayModel = this.settings.getNewDisplayModelFromFile();
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//Get all statements about pageList and pageListData
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Resource pageList = newDisplayModel.getResource(DisplayVocabulary.DISPLAY_NS + "pageList");
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Resource pageListData = newDisplayModel.getResource(DisplayVocabulary.DISPLAY_NS + "pageListData");
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addStatements.add(newDisplayModel.listStatements(pageList, null, (RDFNode) null));
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addStatements.add(newDisplayModel.listStatements(pageListData, null, (RDFNode) null));
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}
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//update any new labels
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private void updateDataGetterLabels(OntModel displayModel, Model addStatements, Model removeStatements) {
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OntModel newDisplayModel = this.settings.getNewDisplayModelFromFile();
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List<Resource> resourcesForLabels = new ArrayList<Resource>();
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resourcesForLabels.add(ResourceFactory.createResource("java:edu.cornell.mannlib.vitro.webapp.utils.dataGetter.ClassGroupPageData"));
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resourcesForLabels.add(ResourceFactory.createResource("java:edu.cornell.mannlib.vitro.webapp.utils.dataGetter.BrowseDataGetter"));
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resourcesForLabels.add(ResourceFactory.createResource("java:edu.cornell.mannlib.vitro.webapp.utils.dataGetter.IndividualsForClassesDataGetter"));
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resourcesForLabels.add(ResourceFactory.createResource("java:edu.cornell.mannlib.vitro.webapp.utils.dataGetter.InternalClassesDataGetter"));
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resourcesForLabels.add(ResourceFactory.createResource("java:edu.cornell.mannlib.vitro.webapp.utils.dataGetter.SparqlQueryDataGetter"));
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for(Resource r: resourcesForLabels) {
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addStatements.add(newDisplayModel.listStatements(r, RDFS.label, (RDFNode)null));
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}
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}
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/**
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* A class that allows to access two different ontology change lists,
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@ -572,8 +428,6 @@ public class KnowledgeBaseUpdater {
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public List<AtomicOntologyChange> getAtomicPropertyChanges() {
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return atomicPropertyChanges;
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}
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}
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}
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}
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@ -5,10 +5,11 @@ package edu.cornell.mannlib.vitro.webapp.servlet.setup;
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import java.io.File;
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import java.io.FileInputStream;
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import java.io.FileNotFoundException;
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import java.io.IOException;
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import java.io.InputStream;
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import java.io.StringWriter;
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import java.text.SimpleDateFormat;
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import java.util.ArrayList;
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import java.util.Date;
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import java.util.List;
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import javax.servlet.ServletContext;
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import javax.servlet.ServletContextEvent;
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@ -21,18 +22,20 @@ 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.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.Property;
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import com.hp.hpl.jena.rdf.model.RDFNode;
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import com.hp.hpl.jena.rdf.model.Resource;
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import com.hp.hpl.jena.rdf.model.ResourceFactory;
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import com.hp.hpl.jena.rdf.model.Statement;
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import com.hp.hpl.jena.rdf.model.StmtIterator;
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import com.hp.hpl.jena.shared.Lock;
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import com.hp.hpl.jena.vocabulary.RDF;
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import com.hp.hpl.jena.vocabulary.RDFS;
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import edu.cornell.mannlib.vitro.webapp.dao.DisplayVocabulary;
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import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory;
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import edu.cornell.mannlib.vitro.webapp.dao.jena.ModelContext;
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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.ChangeSet;
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import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFService;
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import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFService.ModelSerializationFormat;
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import edu.cornell.mannlib.vitro.webapp.rdfservice.impl.RDFServiceUtils;
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/**
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* Invokes process to test whether the knowledge base needs any updating
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@ -93,8 +96,9 @@ public class UpdateKnowledgeBase implements ServletContextListener {
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settings.setAssertionOntModelSelector(ModelContext.getBaseOntModelSelector(ctx));
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settings.setInferenceOntModelSelector(ModelContext.getInferenceOntModelSelector(ctx));
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settings.setUnionOntModelSelector(ModelContext.getUnionOntModelSelector(ctx));
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settings.setDisplayModel(ModelContext.getDisplayModel(ctx));
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boolean tryMigrateDisplay = true;
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try {
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settings.setDisplayModel(ModelContext.getDisplayModel(ctx));
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OntModel oldTBoxModel = loadModelFromDirectory(ctx.getRealPath(OLD_TBOX_MODEL_DIR));
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settings.setOldTBoxModel(oldTBoxModel);
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OntModel newTBoxModel = loadModelFromDirectory(ctx.getRealPath(NEW_TBOX_MODEL_DIR));
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@ -123,11 +127,9 @@ public class UpdateKnowledgeBase implements ServletContextListener {
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settings.setLoadedAtStartupDisplayModel(loadedAtStartupFiles);
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OntModel oldDisplayModelVivoListView = loadModelFromFile(ctx.getRealPath(OLD_DISPLAYMODEL_VIVOLISTVIEW_PATH));
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settings.setVivoListViewConfigDisplayModel(oldDisplayModelVivoListView);
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} catch (ModelDirectoryNotFoundException e) {
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log.info("Knowledge base update directories not found. " +
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"No update will be performed.");
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return;
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} catch (Exception e) {
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log.info("unable to read display model migration files, display model not migrated. " + e.getMessage());
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tryMigrateDisplay = false;
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}
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try {
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@ -137,10 +139,17 @@ public class UpdateKnowledgeBase implements ServletContextListener {
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if (ontologyUpdater.updateRequired(ctx)) {
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ctx.setAttribute(KBM_REQURIED_AT_STARTUP, Boolean.TRUE);
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ontologyUpdater.update(ctx);
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migrateDisplayModel(ontologyUpdater);
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if (tryMigrateDisplay) {
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try {
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migrateDisplayModel(settings);
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log.info("Migrated display model");
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} catch (Exception e) {
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log.info("unable to update display model: " + e.getMessage());
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}
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}
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}
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} catch (IOException ioe) {
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String errMsg = "IOException updating knowledge base " +
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} catch (Exception ioe) {
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String errMsg = "Exception updating knowledge base " +
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"for ontology changes: ";
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// Tomcat doesn't always seem to print exceptions thrown from
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// context listeners
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@ -157,10 +166,143 @@ public class UpdateKnowledgeBase implements ServletContextListener {
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}
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//Multiple changes from 1.4 to 1.5 will occur
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//update migration model
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public void migrateDisplayModel(UpdateSettings settings) {
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OntModel displayModel = settings.getDisplayModel();
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Model addStatements = ModelFactory.createDefaultModel();
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Model removeStatements = ModelFactory.createDefaultModel();
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//remove old tbox and display metadata statements and add statements from new versions
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replaceTboxAndDisplayMetadata(displayModel, addStatements, removeStatements,settings);
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//Update statements for data getter class types that have changed in 1.5
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updateDataGetterClassNames(displayModel, addStatements, removeStatements);
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//add cannot delete flags to pages that shouldn't allow deletion on page list
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addCannotDeleteFlagDisplayModel(displayModel, addStatements, removeStatements);
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//removes requiresTemplate statement for people page
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updatePeoplePageDisplayModel(displayModel, addStatements, removeStatements);
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//add page list
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addPageListDisplayModel(displayModel, addStatements, removeStatements,settings);
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//update data getter labels
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updateDataGetterLabels(displayModel, addStatements, removeStatements,settings);
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displayModel.enterCriticalSection(Lock.WRITE);
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try {
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if(log.isDebugEnabled()) {
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StringWriter sw = new StringWriter();
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addStatements.write(sw);
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log.debug("Statements to be added are: ");
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log.debug(sw.toString());
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sw.close();
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sw = new StringWriter();
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removeStatements.write(sw);
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log.debug("Statements to be removed are: ");
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log.debug(sw.toString());
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sw.close();
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}
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displayModel.remove(removeStatements);
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displayModel.add(addStatements);
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} catch(Exception ex) {
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log.error("An error occurred in migrating display model ", ex);
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} finally {
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displayModel.leaveCriticalSection();
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}
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}
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//replace
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private void replaceTboxAndDisplayMetadata(OntModel displayModel, Model addStatements, Model removeStatements, UpdateSettings settings) {
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OntModel oldDisplayModelTboxModel = settings.getOldDisplayModelTboxModel();
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OntModel oldDisplayModelDisplayMetadataModel = settings.getOldDisplayModelDisplayMetadataModel();
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OntModel newDisplayModelTboxModel = settings.getNewDisplayModelTboxModel();
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OntModel newDisplayModelDisplayMetadataModel = settings.getNewDisplayModelDisplayMetadataModel();
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OntModel loadedAtStartup = settings.getLoadedAtStartupDisplayModel();
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OntModel oldVivoListView = settings.getVivoListViewConfigDisplayModel();
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//Remove old display model tbox and display metadata statements from display model
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removeStatements.add(oldDisplayModelTboxModel);
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removeStatements.add(oldDisplayModelDisplayMetadataModel);
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//the old startup folder only contained by oldVivoListView
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removeStatements.add(oldVivoListView);
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//Add statements from new tbox and display metadata
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addStatements.add(newDisplayModelTboxModel);
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addStatements.add(newDisplayModelDisplayMetadataModel);
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//this should include the list view in addition to other files
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addStatements.add(loadedAtStartup);
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}
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//update statements for data getter classes
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private void updateDataGetterClassNames(OntModel displayModel, Model addStatements, Model removeStatements) {
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Resource classGroupOldType = ResourceFactory.createResource("java:edu.cornell.mannlib.vitro.webapp.utils.pageDataGetter.ClassGroupPageData");
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Resource browseOldType = ResourceFactory.createResource("java:edu.cornell.mannlib.vitro.webapp.utils.pageDataGetter.BrowseDataGetter");
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Resource individualsForClassesOldType = ResourceFactory.createResource("java:edu.cornell.mannlib.vitro.webapp.utils.pageDataGetter.IndividualsForClassesDataGetter");
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Resource internalClassesOldType = ResourceFactory.createResource("java:edu.cornell.mannlib.vitro.webapp.utils.pageDataGetter.InternalClassesDataGetter");
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Resource classGroupNewType = ResourceFactory.createResource("java:edu.cornell.mannlib.vitro.webapp.utils.dataGetter.ClassGroupPageData");
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Resource browseNewType = ResourceFactory.createResource("java:edu.cornell.mannlib.vitro.webapp.utils.dataGetter.BrowseDataGetter");
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Resource individualsForClassesNewType = ResourceFactory.createResource("java:edu.cornell.mannlib.vitro.webapp.utils.dataGetter.IndividualsForClassesDataGetter");
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Resource internalClassesNewType = ResourceFactory.createResource("java:edu.cornell.mannlib.vitro.webapp.utils.dataGetter.InternalClassesDataGetter");
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//Find statements where type is ClassGroupData
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updateAddRemoveDataGetterStatements(displayModel, removeStatements, addStatements, classGroupOldType, classGroupNewType);
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//Find statements where type is BrowseDataGetter
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updateAddRemoveDataGetterStatements(displayModel, removeStatements, addStatements, browseOldType, browseNewType);
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//Find statements where type is individuals for classes
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updateAddRemoveDataGetterStatements(displayModel, removeStatements, addStatements, individualsForClassesOldType, individualsForClassesNewType);
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//Find statements where type is internal class
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updateAddRemoveDataGetterStatements(displayModel, removeStatements, addStatements, internalClassesOldType, internalClassesNewType);
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}
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private void updateAddRemoveDataGetterStatements(OntModel displayModel,
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Model removeStatements, Model addStatements,
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Resource oldType, Resource newType) {
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removeStatements.add(displayModel.listStatements(null, RDF.type, oldType));
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StmtIterator oldStatements = displayModel.listStatements(null, RDF.type, oldType);
|
||||
while(oldStatements.hasNext()) {
|
||||
Statement stmt = oldStatements.nextStatement();
|
||||
addStatements.add(stmt.getSubject(), RDF.type, newType);
|
||||
}
|
||||
}
|
||||
|
||||
//add cannotDeleteFlag to display model
|
||||
private void addCannotDeleteFlagDisplayModel(OntModel displayModel, Model addStatements, Model removeStatements) {
|
||||
Resource homePage = displayModel.getResource(DisplayVocabulary.HOME_PAGE_URI);
|
||||
addStatements.add(homePage,
|
||||
ResourceFactory.createProperty(DisplayVocabulary.DISPLAY_NS + "cannotDeletePage"),
|
||||
ResourceFactory.createPlainLiteral("true"));
|
||||
}
|
||||
|
||||
//remove requires template
|
||||
private void updatePeoplePageDisplayModel(OntModel displayModel, Model addStatements, Model removeStatements) {
|
||||
Resource peoplePage = displayModel.getResource(DisplayVocabulary.DISPLAY_NS + "People");
|
||||
if(peoplePage != null) {
|
||||
removeStatements.add(peoplePage, DisplayVocabulary.REQUIRES_BODY_TEMPLATE,
|
||||
ResourceFactory.createPlainLiteral("menupage--classgroup-people.ftl"));
|
||||
}
|
||||
}
|
||||
|
||||
//add page list sparql query
|
||||
private void addPageListDisplayModel(OntModel displayModel, Model addStatements, Model removeStatements, UpdateSettings settings) {
|
||||
OntModel newDisplayModel = settings.getNewDisplayModelFromFile();
|
||||
//Get all statements about pageList and pageListData
|
||||
Resource pageList = newDisplayModel.getResource(DisplayVocabulary.DISPLAY_NS + "pageList");
|
||||
Resource pageListData = newDisplayModel.getResource(DisplayVocabulary.DISPLAY_NS + "pageListData");
|
||||
|
||||
addStatements.add(newDisplayModel.listStatements(pageList, null, (RDFNode) null));
|
||||
addStatements.add(newDisplayModel.listStatements(pageListData, null, (RDFNode) null));
|
||||
}
|
||||
|
||||
//update any new labels
|
||||
private void updateDataGetterLabels(OntModel displayModel, Model addStatements, Model removeStatements, UpdateSettings settings) {
|
||||
OntModel newDisplayModel = settings.getNewDisplayModelFromFile();
|
||||
List<Resource> resourcesForLabels = new ArrayList<Resource>();
|
||||
resourcesForLabels.add(ResourceFactory.createResource("java:edu.cornell.mannlib.vitro.webapp.utils.dataGetter.ClassGroupPageData"));
|
||||
resourcesForLabels.add(ResourceFactory.createResource("java:edu.cornell.mannlib.vitro.webapp.utils.dataGetter.BrowseDataGetter"));
|
||||
resourcesForLabels.add(ResourceFactory.createResource("java:edu.cornell.mannlib.vitro.webapp.utils.dataGetter.IndividualsForClassesDataGetter"));
|
||||
resourcesForLabels.add(ResourceFactory.createResource("java:edu.cornell.mannlib.vitro.webapp.utils.dataGetter.InternalClassesDataGetter"));
|
||||
resourcesForLabels.add(ResourceFactory.createResource("java:edu.cornell.mannlib.vitro.webapp.utils.dataGetter.SparqlQueryDataGetter"));
|
||||
for(Resource r: resourcesForLabels) {
|
||||
addStatements.add(newDisplayModel.listStatements(r, RDFS.label, (RDFNode)null));
|
||||
}
|
||||
}
|
||||
|
||||
private void migrateDisplayModel(KnowledgeBaseUpdater ontologyUpdater) {
|
||||
ontologyUpdater.migrateDisplayModel();
|
||||
}
|
||||
|
||||
private OntModel loadModelFromDirectory(String directoryPath) {
|
||||
|
||||
|
|
@ -190,6 +332,7 @@ public class UpdateKnowledgeBase implements ServletContextListener {
|
|||
return om;
|
||||
}
|
||||
|
||||
|
||||
private void readFile(File f, OntModel om, String path) {
|
||||
try {
|
||||
FileInputStream fis = new FileInputStream(f);
|
||||
|
|
|
|||
Loading…
Add table
Reference in a new issue