VIVO-483 Obsolete VIVO URIs in Vitro search code.
Break out the mechanism for building a list of Additional URI Finder instances. Override that in VIVO. Move AdditionalURIsForContextNodes to VIVO. References to obsolete URIs are in comments.
This commit is contained in:
j2blake
parent
725b2e7a57
commit
bc0cf6be63
4 changed files with 32 additions and 1506 deletions
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/* $This file is distributed under the terms of the license in /doc/license.txt$ */
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package edu.cornell.mannlib.vitro.webapp.search.indexing;
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import java.util.ArrayList;
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import java.util.Collections;
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import java.util.HashSet;
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import java.util.Iterator;
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import java.util.List;
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import java.util.Set;
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import org.apache.commons.logging.Log;
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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.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.query.QuerySolution;
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import com.hp.hpl.jena.query.QuerySolutionMap;
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import com.hp.hpl.jena.query.ResultSet;
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import com.hp.hpl.jena.query.Syntax;
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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.shared.Lock;
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import edu.cornell.mannlib.vitro.webapp.search.beans.StatementToURIsToUpdate;
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public class AdditionalURIsForContextNodes implements StatementToURIsToUpdate {
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private OntModel model;
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private Set<String> alreadyChecked;
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private long accumulatedTime = 0;
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private static final List<String> multiValuedQueriesForAgent = new ArrayList<String>();
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private static final String multiValuedQueryForInformationResource;
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private static final List<String> multiValuedQueriesForRole = new ArrayList<String>();
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private static final List<String>queryList;
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private Log log = LogFactory.getLog(AdditionalURIsForContextNodes.class);
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public AdditionalURIsForContextNodes( OntModel jenaOntModel){
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this.model = jenaOntModel;
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}
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@Override
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public List<String> findAdditionalURIsToIndex(Statement stmt) {
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if( stmt != null ){
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long start = System.currentTimeMillis();
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List<String>urisToIndex = new ArrayList<String>();
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if(stmt.getSubject() != null && stmt.getSubject().isURIResource() ){
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String subjUri = stmt.getSubject().getURI();
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if( subjUri != null && ! alreadyChecked.contains( subjUri )){
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urisToIndex.addAll( findAdditionalURIsToIndex(subjUri));
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alreadyChecked.add(subjUri);
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}
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}
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if( stmt.getObject() != null && stmt.getObject().isURIResource() ){
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String objUri = stmt.getSubject().getURI();
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if( objUri != null && ! alreadyChecked.contains(objUri)){
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urisToIndex.addAll( findAdditionalURIsToIndex(objUri));
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alreadyChecked.add(objUri);
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}
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}
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accumulatedTime += (System.currentTimeMillis() - start ) ;
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return urisToIndex;
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}else{
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return Collections.emptyList();
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}
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}
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@Override
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public void startIndexing() {
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alreadyChecked = new HashSet<String>();
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accumulatedTime = 0L;
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}
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@Override
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public void endIndxing() {
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log.debug( "Accumulated time for this run of the index: " + accumulatedTime + " msec");
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alreadyChecked = null;
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}
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protected List<String> findAdditionalURIsToIndex(String uri) {
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List<String> uriList = new ArrayList<String>();
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for(String query : queryList){
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//log.info("Executing query: "+ query);
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QuerySolutionMap initialBinding = new QuerySolutionMap();
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Resource uriResource = ResourceFactory.createResource(uri);
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initialBinding.add("uri", uriResource);
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Query sparqlQuery = QueryFactory.create( query, Syntax.syntaxARQ);
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model.getLock().enterCriticalSection(Lock.READ);
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try{
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QueryExecution qExec = QueryExecutionFactory.create(sparqlQuery, model, initialBinding);
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try{
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ResultSet results = qExec.execSelect();
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while(results.hasNext()){
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QuerySolution soln = results.nextSolution();
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Iterator<String> iter = soln.varNames() ;
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while( iter.hasNext()){
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String name = iter.next();
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RDFNode node = soln.get( name );
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if( node != null ){
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uriList.add("" + node.toString());
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}else{
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log.debug(name + " is null");
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}
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}
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}
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}catch(Throwable t){
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log.error(t,t);
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} finally{
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qExec.close();
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}
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}finally{
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model.getLock().leaveCriticalSection();
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}
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}
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if( log.isDebugEnabled() )
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log.debug( "additional uris for " + uri + " are " + uriList);
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return uriList;
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}
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private static final String prefix = "prefix owl: <http://www.w3.org/2002/07/owl#> \n"
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+ " prefix vitroDisplay: <http://vitro.mannlib.cornell.edu/ontologies/display/1.1#> \n"
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+ " prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> \n"
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+ " prefix core: <http://vivoweb.org/ontology/core#> \n"
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+ " prefix foaf: <http://xmlns.com/foaf/0.1/> \n"
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+ " prefix obo: <http://purl.obolibrary.org/obo/> \n"
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+ " prefix vcard: <http://www.w3.org/2006/vcard/ns#> \n"
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+ " prefix event: <http://purl.org/NET/c4dm/event.owl#> \n"
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+ " prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> \n"
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+ " prefix localNav: <http://vitro.mannlib.cornell.edu/ns/localnav#> \n"
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+ " prefix bibo: <http://purl.org/ontology/bibo/> \n";
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static{
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// If a person changes then update
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// organizations for positions
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multiValuedQueriesForAgent.add(prefix +
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"SELECT DISTINCT \n" +
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" (str(?i) as ?positionInOrganization) \n" +
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" WHERE {\n"
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+ "?uri rdf:type foaf:Agent ; core:relatedBy ?c . \n"
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+ " ?c rdf:type core:Position . \n"
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+ " OPTIONAL { ?c core:relates ?i . ?i rdf:type foaf:Organization } . \n"
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+ " }");
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// If a person changes then update
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// advisee, linkedAuthor and informationResource
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multiValuedQueriesForAgent.add(prefix +
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"SELECT (str(?d) as ?advisee) \n" +
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" (str(?f) as ?linkedAuthor) (str(?h) as ?linkedInformationResource) WHERE { {\n"
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+ "?uri rdf:type foaf:Agent . \n"
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+ "?uri core:relatedBy ?c . \n"
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+ "?c rdf:type core:AdvisingRelationship . \n"
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+ "?c core:relates ?d . \n"
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+ "?d rdf:type core:AdviseeRole . \n"
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+ "?d obo:RO_0000052 ?e . \n"
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+ "?e rdf:type foaf:Person . \n"
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+ "} \n"
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+ "UNION { \n"
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+ " ?uri rdf:type foaf:Agent . \n"
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+ " ?uri core:relatedBy ?c . \n"
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+ " ?c rdf:type core:Authorship . \n"
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+ " OPTIONAL {?c core:relates ?f . \n"
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+ " ?f rdf:type foaf:Person . } \n"
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+ " OPTIONAL { ?c core:relates ?h . \n"
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+ " ?h rdf:type obo:IAO_0000030 . } \n"
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+ " } } ");
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// If a person changes then update
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// award giver
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multiValuedQueriesForAgent.add(prefix +
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"SELECT (str(?d) as ?awardConferredBy) \n" +
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"WHERE {\n"
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+ "?uri rdf:type foaf:Agent ; ?b ?c . \n"
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+ " ?c rdf:type core:AwardReceipt . \n"
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+ " OPTIONAL { ?c core:assignedBy ?d . } . \n"
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+ " }");
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// If a person changes then update
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// organization for role
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multiValuedQueriesForAgent.add(prefix +
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"SELECT (str(?Organization) as ?organization) \n" +
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"WHERE {\n"
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+ "?uri rdf:type foaf:Agent ; ?b ?c . \n"
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+ " ?c rdf:type obo:BFO_0000023 ; obo:BFO_0000054 ?Organization .\n"
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+ " }");
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// If a person changes then update
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// organization in educational training
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multiValuedQueriesForAgent.add(prefix +
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"SELECT \n" +
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"(str(?e) as ?trainingAtOrganization) WHERE {\n"
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+ " ?uri rdf:type foaf:Agent ; ?b ?c . \n"
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+ " ?c rdf:type core:EducationalProcess . \n"
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+ " OPTIONAL { ?c obo:RO_0000057 ?e . \n"
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+ " ?e rdf:type foaf:Organization . } . "
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+"}");
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// If an organization changes then update
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// people in head of relations
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multiValuedQueriesForAgent.add(
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" # for organization, get leader \n" +
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prefix +
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"SELECT \n" +
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"(str(?e) as ?LeaderPerson ) WHERE {\n"
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+ " ?uri rdf:type foaf:Agent . \n"
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+ " ?uri core:contributingRole ?c . \n"
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+ " ?c rdf:type core:LeaderRole . \n"
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+ " OPTIONAL { ?c obo:RO_0000052 ?e . \n"
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+ " ?e rdf:type foaf:Person . } . "
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+"}");
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}
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//multivalued query for core:InformationResource
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static {
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multiValuedQueryForInformationResource = prefix +
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"SELECT (str(?b) as ?linkedAuthor) (str(?d) as ?linkedInformationResource) \n"
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+ "(str(?f) as ?editor) \n" +
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"(str(?i) as ?features) WHERE {\n"
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+ " ?uri rdf:type obo:IAO_0000030 . \n"
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+ " OPTIONAL { ?uri core:relatedBy ?a . \n"
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+ " ?a rdf:type core:Authorship . \n"
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+ " ?a core:relates ?b . ?b rdf:type foaf:Person .\n"
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+ " ?a core:relates ?d . ?d rdf:type obo:IAO_0000030 .\n"
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+ "} . "
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+ " OPTIONAL { ?uri core:relatedBy ?e . \n"
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+ " ?e rdf:type core:Editorship . \n"
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+ " ?e core:relates ?f . ?f rdf:type foaf:Person .\n"
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+ "} . "
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+ " OPTIONAL { ?uri core:features ?i . } . \n"
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+"}" ;
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}
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protected static List<String> queriesForAuthorship(){
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List<String> queries = new ArrayList<String>();
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//get additional URIs of information resources from author side
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queries.add(
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prefix
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+ "SELECT (str(?a) as ?infoResource) WHERE {\n"
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+ " ?uri rdf:type foaf:Person . \n"
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+ " ?uri core:relatedBy ?aship .\n"
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+ " ?aship rdf:type core:Authorship .\n"
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+ "OPTIONAL { ?aship core:relates ?a . ?a rdf:type obo:IAO_0000030 } .\n"
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+"}" );
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//get additional URIs of authors from information resource side
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queries.add(
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prefix
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+ "SELECT (str(?a) as ?author ) WHERE {\n"
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+ " ?uri rdf:type obo:IAO_0000030 . \n"
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+ " ?uri core:relatedBy ?aship . ?aship rdf:type core:Authorship . \n"
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+ "OPTIONAL { ?aship core:relates ?a . ?a rdf:type foaf:Person } .\n"
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+"}" );
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return queries;
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}
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protected static List<String> queriesForURLLink(){
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List<String> queries = new ArrayList<String>();
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//get additional URIs when URLLink is changed
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queries.add(
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prefix
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+ "SELECT (str(?x) as ?individual) WHERE {\n"
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+ " ?i rdf:type vcard:Individual . \n"
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+ " ?i vcard:hasURL ?uri . \n"
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+ " ?i obo:ARG_2000029 ?x . \n"
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+"}" );
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return queries;
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}
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protected static List<String> queriesForEducationalTraining(){
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List<String> queries = new ArrayList<String>();
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//if person changes, no additional URIs need to be
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//changed because the person is not displayed on the
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//degree individual or on the degree granting organization
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//if the degree changes, the person needs to be updated
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//since the degree name is shown on the person page.
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queries.add(
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prefix
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+ " SELECT (str(?person) as ?personUri) WHERE {\n"
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+ " ?uri rdf:type core:AcademicDegree . \n"
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+ " ?uri core:relatedBy ?awardedDegree .\n"
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+ " ?awardedDegree rdf:type core:AwardedDegree .\n"
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+ " ?awardedDegree core:relates ?person .\n"
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+ " ?person rdf:type foaf:Person .\n"
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+"}" );
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//if the organization changes the person needs to be updated
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//since the organization name is shown on the person page.
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queries.add(
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prefix
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+ " SELECT (str(?person) as ?personUri) WHERE {\n"
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+ " ?uri rdf:type foaf:Organization . \n"
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+ " ?uri obo:RO_0000056 ?edTrainingNode .\n"
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+ " ?edTrainingNode rdf:type core:EducationalProcess . \n"
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+ " ?edTrainingNode obo:RO_0000057 ?person . \n"
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+ " ?person rdf:type foaf:Person ."
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+"}" );
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return queries;
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}
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protected static List<String> queriesForPosition(){
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List<String> queries = new ArrayList<String>();
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//If an organization changes, update people
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queries.add(
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prefix
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+ " SELECT (str(?person) as ?personUri) WHERE {\n"
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+ " ?uri rdf:type foaf:Organization . \n"
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+ " ?uri core:relatedBy ?positionNode .\n"
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+ " ?positionNode rdf:type core:Position .\n"
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+ " ?positionNode core:relates ?person . \n"
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+ " ?person rdf:type foaf:Person .\n"
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+"}" );
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//if people change, update organizations
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queries.add(
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prefix
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+ " SELECT (str(?org) as ?orgUri) WHERE {\n"
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+ " ?uri rdf:type foaf:Person . \n"
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+ " ?uri core:relatedBy ?positionNode .\n"
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+ " ?positionNode rdf:type core:Position .\n"
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+ " ?positionNode core:relates ?org . \n"
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+ " ?org rdf:type foaf:Organization .\n"
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+"}" );
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return queries;
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}
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static{
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// core:AttendeeRole
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// If the person changes, update the attendee role in organization
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// core:AttendeeRole applies to events, not organizations; updating accordingly - tlw72
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multiValuedQueriesForRole.add(prefix +
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"SELECT (str(?d) as ?event) \n " +
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"WHERE {\n"
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+ "?uri rdf:type foaf:Person . \n"
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+ "?uri obo:RO_0000053 ?c . \n"
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+ "?c rdf:type core:AttendeeRole . \n"
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+ "?c obo:BFO_0000054 ?d . \n"
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+ "?d rdf:type event:Event .\n"
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+ " }");
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// If the organization changes, update the attendee role of person
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// core:AttendeeRole applies to events, not organizations; updating accordingly - tlw72
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multiValuedQueriesForRole.add(prefix +
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"SELECT (str(?d) as ?person) \n" +
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"WHERE {\n"
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+ "?uri rdf:type event:Event . \n"
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+ "?uri obo:BFO_0000055 ?c . \n"
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+ "?c rdf:type core:AttendeeRole . \n"
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+ "?c obo:RO_0000052 ?d . \n"
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+ "?d rdf:type foaf:Person .\n"
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+ " }");
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// core:ClinicalRole -- core:clinicalRoleOf
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// If the person changes, update the clinical role in project
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multiValuedQueriesForRole.add(prefix +
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"SELECT (str(?d) as ?project) \n" +
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"WHERE {\n"
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+ "?uri rdf:type foaf:Person . \n"
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+ "?uri obo:RO_0000053 ?c . \n"
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+ "?c rdf:type core:ClinicalRole . \n"
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+ "?c obo:BFO_0000054 ?d .\n"
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+ "?d rdf:type core:Project .\n"
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+ " }");
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// If the person changes, update the clinical role in service
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multiValuedQueriesForRole.add(prefix +
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"SELECT (str(?d) as ?service) \n" +
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"WHERE {\n"
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+ "?uri rdf:type foaf:Person . \n"
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+ "?uri obo:RO_0000053 ?c . \n"
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+ "?c rdf:type core:ClinicalRole . \n"
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+ "?c core:roleContributesTo ?d .\n"
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+ "?d rdf:type obo:ERO_0000005 .\n"
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+ " }");
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// If the project changes, update the clinical role of person
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multiValuedQueriesForRole.add(prefix +
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"SELECT (str(?d) as ?person) \n" +
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"WHERE {\n"
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+ "?uri rdf:type core:Project . \n"
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+ "?uri obo:BFO_0000055 ?c . \n"
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+ "?c rdf:type core:ClinicalRole . \n"
|
||||
+ "?c obo:RO_0000052 ?d .\n "
|
||||
+ "?d rdf:type foaf:Person .\n "
|
||||
+ " }");
|
||||
|
||||
// If the service changes, update the clinical role of person
|
||||
multiValuedQueriesForRole.add(prefix +
|
||||
"SELECT (str(?d) as ?person) \n" +
|
||||
"WHERE {\n"
|
||||
+ "?uri rdf:type obo:ERO_0000005 . \n"
|
||||
+ "?uri core:contributingRole ?c . \n"
|
||||
+ "?c rdf:type core:ClinicalRole . \n"
|
||||
+ "?c obo:RO_0000052 ?d .\n "
|
||||
+ "?d rdf:type foaf:Person .\n "
|
||||
+ " }");
|
||||
|
||||
// If the person changes, update the leader role in organization
|
||||
multiValuedQueriesForRole.add(prefix +
|
||||
"SELECT (str(?d) as ?organization) \n" +
|
||||
"WHERE {\n"
|
||||
+ "?uri rdf:type foaf:Person . \n"
|
||||
+ "?uri obo:RO_0000053 ?c . \n"
|
||||
+ "?c rdf:type core:LeaderRole . \n"
|
||||
+ "?c core:roleContributesTo ?d .\n"
|
||||
+ "?d rdf:type foaf:Organization .\n "
|
||||
+ " }");
|
||||
|
||||
// If the organization changes, update the leader role of person
|
||||
multiValuedQueriesForRole.add(prefix +
|
||||
"SELECT (str(?d) as ?person) \n" +
|
||||
"WHERE {\n"
|
||||
+ "?uri rdf:type foaf:Organization . \n"
|
||||
+ "?uri core:contributingRole ?c . \n"
|
||||
+ "?c rdf:type core:LeaderRole . \n"
|
||||
+ "?c obo:RO_0000052 ?d .\n "
|
||||
+ "?d rdf:type foaf:Person .\n "
|
||||
+ " }");
|
||||
|
||||
// core:MemberRole -- core:memberRoleOf
|
||||
|
||||
// If the person changes, update the member role in organization
|
||||
multiValuedQueriesForRole.add(prefix +
|
||||
"SELECT (str(?d) as ?organization) \n" +
|
||||
"WHERE \n{"
|
||||
+ "?uri rdf:type foaf:Person . \n"
|
||||
+ "?uri obo:RO_0000053 ?c . \n"
|
||||
+ "?c rdf:type core:MemberRole . \n"
|
||||
+ "?c core:roleContributesTo ?d .\n"
|
||||
+ "?d rdf:type foaf:Organization .\n "
|
||||
+ " }");
|
||||
|
||||
// If the organization changes, update the member role of person
|
||||
multiValuedQueriesForRole.add(prefix +
|
||||
"SELECT (str(?d) as ?person) \n" +
|
||||
"WHERE {"
|
||||
+ "?uri rdf:type foaf:Organization . \n"
|
||||
+ "?uri core:contributingRole ?c . \n"
|
||||
+ "?c rdf:type core:MemberRole . \n"
|
||||
+ "?c obo:RO_0000052 ?d .\n "
|
||||
+ "?d rdf:type foaf:Person .\n "
|
||||
+ " }");
|
||||
|
||||
// core:OrganizerRole -- core:organizerRoleOf
|
||||
|
||||
// If the person changes, update the organizer role in organization
|
||||
// organizerRole appplies to events not organizations; updating accordingly - tlw72
|
||||
multiValuedQueriesForRole.add(prefix +
|
||||
"SELECT (str(?d) as ?event) \n" +
|
||||
"WHERE {"
|
||||
+ "?uri rdf:type foaf:Person . \n"
|
||||
+ "?uri obo:RO_0000053 ?c . \n"
|
||||
+ "?c rdf:type core:OrganizerRole .\n"
|
||||
+ "?c obo:BFO_0000054 ?d .\n"
|
||||
+ "?d rdf:type event:Event .\n "
|
||||
+ " }");
|
||||
|
||||
// If the organization changes, update the organizer role of person
|
||||
// organizerRole appplies to events not organizations; updating accordingly - tlw72
|
||||
multiValuedQueriesForRole.add(prefix +
|
||||
"SELECT (str(?d) as ?person) \n" +
|
||||
"WHERE {\n"
|
||||
+ "?uri rdf:type event:Event . \n"
|
||||
+ "?uri obo:BFO_0000055 ?c . \n"
|
||||
+ "?c rdf:type core:OrganizerRole . \n"
|
||||
+ "?c obo:RO_0000052 ?d .\n "
|
||||
+ "?d rdf:type foaf:Person .\n "
|
||||
+ " }");
|
||||
|
||||
// core:OutreachProviderRole -- core:outreachProviderRoleOf
|
||||
|
||||
// If the person changes, update the outreach provider role in organization
|
||||
multiValuedQueriesForRole.add(prefix +
|
||||
"SELECT (str(?d) as ?organization) \n" +
|
||||
"WHERE {\n"
|
||||
+ "?uri rdf:type foaf:Person . \n"
|
||||
+ "?uri obo:RO_0000053 ?c . \n"
|
||||
+ "?c rdf:type core:OutreachProviderRole .\n"
|
||||
+ "?c core:roleContributesTo ?d .\n"
|
||||
+ "?d rdf:type foaf:Organization .\n "
|
||||
+ " }");
|
||||
|
||||
// If the organization changes, update the outreach provider role of person
|
||||
multiValuedQueriesForRole.add(prefix +
|
||||
"SELECT (str(?d) as ?person) \n" +
|
||||
"WHERE {\n"
|
||||
+ "?uri rdf:type foaf:Organization . \n"
|
||||
+ "?uri core:contributingRole ?c . \n"
|
||||
+ "?c rdf:type core:OutreachProviderRole . \n"
|
||||
+ "?c obo:RO_0000052 ?d .\n "
|
||||
+ "?d rdf:type foaf:Person .\n "
|
||||
+ " }");
|
||||
|
||||
// core:PresenterRole -- core:presenterRoleOf
|
||||
|
||||
// If the person changes, update the presentation
|
||||
multiValuedQueriesForRole.add(prefix +
|
||||
"SELECT (str(?d) as ?presentation) \n" +
|
||||
"WHERE {\n"
|
||||
+ "?uri rdf:type foaf:Person . \n"
|
||||
+ "?uri obo:RO_0000053 ?c . \n"
|
||||
+ " ?c rdf:type core:PresenterRole . \n"
|
||||
+ " ?c obo:BFO_0000054 ?d .\n"
|
||||
+ " ?d rdf:type core:Presentation . \n"
|
||||
+ " }");
|
||||
|
||||
// If the presentation changes, update the person
|
||||
multiValuedQueriesForRole.add(prefix +
|
||||
"SELECT (str(?d) as ?person) \n" +
|
||||
"WHERE {\n"
|
||||
+ "?uri rdf:type core:Presentation . \n"
|
||||
+ "?uri obo:BFO_0000055 ?c . \n"
|
||||
+ " ?c rdf:type core:PresenterRole . \n "
|
||||
+ "?c obo:RO_0000052 ?d .\n "
|
||||
+ "?d rdf:type foaf:Person .\n "
|
||||
+ " }");
|
||||
|
||||
// core:ResearcherRole -- core:researcherRoleOf
|
||||
|
||||
// If the person changes, update the grant
|
||||
multiValuedQueriesForRole.add(prefix +
|
||||
"SELECT (str(?d) as ?grant) \n" +
|
||||
"WHERE {\n"
|
||||
+ "?uri rdf:type foaf:Person . \n"
|
||||
+ "?uri obo:RO_0000053 ?c . \n"
|
||||
+ " ?c rdf:type core:ResearcherRole . \n "
|
||||
+ " ?c core:relatedBy ?d .\n"
|
||||
+ " ?d rdf:type core:Grant . \n"
|
||||
+ " }");
|
||||
|
||||
// If the grant changes, update the researcher
|
||||
multiValuedQueriesForRole.add(prefix +
|
||||
"SELECT (str(?d) as ?person) \n" +
|
||||
"WHERE {\n"
|
||||
+ "?uri rdf:type core:Grant . \n"
|
||||
+ "?uri core:relates ?c . \n"
|
||||
+ " ?c rdf:type core:ResearcherRole . \n "
|
||||
+ " ?c obo:RO_0000052 ?d .\n"
|
||||
+ "?d rdf:type foaf:Person .\n "
|
||||
+ " }");
|
||||
|
||||
// If the grant changes, update the principal investigator
|
||||
multiValuedQueriesForRole.add(prefix +
|
||||
"SELECT (str(?d) as ?person) \n" +
|
||||
"WHERE {\n"
|
||||
+ "?uri rdf:type core:Grant . \n"
|
||||
+ " ?uri core:relates ?c . \n"
|
||||
+ " ?c rdf:type core:PrincipalInvestigatorRole . \n "
|
||||
+ " ?c obo:RO_0000052 ?d .\n"
|
||||
+ "?d rdf:type foaf:Person .\n "
|
||||
+ " }");
|
||||
|
||||
// If the grant changes, update the co-principal investigator
|
||||
multiValuedQueriesForRole.add(prefix +
|
||||
"SELECT (str(?d) as ?person) \n" +
|
||||
"WHERE {\n"
|
||||
+ "?uri rdf:type core:Grant . \n"
|
||||
+ " ?uri core:relates ?c . \n"
|
||||
+ " ?c rdf:type core:CoPrincipalInvestigatorRole . \n "
|
||||
+ " ?c obo:RO_0000052 ?d .\n"
|
||||
+ "?d rdf:type foaf:Person .\n "
|
||||
+ " }");
|
||||
|
||||
|
||||
// If the grant changes, update the investigator
|
||||
multiValuedQueriesForRole.add(prefix +
|
||||
"SELECT (str(?d) as ?person) \n" +
|
||||
"WHERE {\n"
|
||||
+ "?uri rdf:type core:Grant . \n"
|
||||
+ " ?uri core:relates ?c . \n"
|
||||
+ " ?c rdf:type core:InvestigatorRole . \n "
|
||||
+ " ?c obo:RO_0000052 ?d .\n"
|
||||
+ "?d rdf:type foaf:Person .\n "
|
||||
+ " }");
|
||||
|
||||
// If the person changes, update the project
|
||||
multiValuedQueriesForRole.add(prefix +
|
||||
"SELECT (str(?d) as ?project) \n" +
|
||||
"WHERE {\n"
|
||||
+ "?uri rdf:type foaf:Person . \n"
|
||||
+ "?uri obo:RO_0000053 ?c . \n"
|
||||
+ " ?c rdf:type core:ResearcherRole . \n "
|
||||
+ " ?c obo:BFO_0000054 ?d .\n"
|
||||
+ " ?d rdf:type core:Project . \n"
|
||||
+ " }");
|
||||
|
||||
// If the project changes, update the researcher
|
||||
multiValuedQueriesForRole.add(prefix +
|
||||
"SELECT (str(?d) as ?person) \n" +
|
||||
"WHERE {\n"
|
||||
+ "?uri rdf:type core:Project . \n"
|
||||
+ " ?uri obo:BFO_0000055 ?c .\n"
|
||||
+ " ?c rdf:type core:ResearcherRole . \n "
|
||||
+ " ?c obo:RO_0000052 ?d .\n"
|
||||
+ "?d rdf:type foaf:Person .\n "
|
||||
+ " }");
|
||||
|
||||
// core:EditorRole -- core:editorRoleOf, core:forInformationResource (person, informationresource)
|
||||
|
||||
// If the person changes, update the editor role of the info resource
|
||||
// changing foaf:Organization to info content entity. Org no longer applies here - tlw72
|
||||
multiValuedQueriesForRole.add(prefix +
|
||||
"SELECT (str(?d) as ?informationResource) \n" +
|
||||
"WHERE {\n"
|
||||
+ "?uri rdf:type foaf:Person . \n"
|
||||
+ "?uri obo:RO_0000053 ?c . \n"
|
||||
+ " ?c rdf:type core:EditorRole . \n "
|
||||
+ " ?c core:roleContributesTo ?d .\n"
|
||||
+ "?d rdf:type obo:IAO_0000030 .\n "
|
||||
+ " }");
|
||||
|
||||
|
||||
// If the info respource changes, update the editor role of person
|
||||
// changing foaf:Organization to info content entity. Org no longer applies here - tlw72
|
||||
multiValuedQueriesForRole.add(prefix +
|
||||
"SELECT (str(?d) as ?person) \n" +
|
||||
"WHERE {\n"
|
||||
+ "?uri rdf:type obo:IAO_0000030 . \n"
|
||||
+ "?uri core:contributingRole ?c . \n"
|
||||
+ " ?c rdf:type core:EditorRole . \n "
|
||||
+ " ?c obo:RO_0000052 ?d .\n"
|
||||
+ "?d rdf:type foaf:Person .\n "
|
||||
+ " }");
|
||||
|
||||
// Next two queries are covered by the previous two. Commenting them out - tlw72
|
||||
// If the person changes, update the information resource associated with editor role
|
||||
/* multiValuedQueriesForRole.add(prefix +
|
||||
"SELECT (str(?d) as ?informationResource) \n" +
|
||||
"WHERE {\n"
|
||||
|
||||
+ "?uri rdf:type foaf:Person ; ?b ?c . \n"
|
||||
+ " ?c rdf:type core:EditorRole ; core:forInformationResource ?d .\n"
|
||||
+ " }");
|
||||
|
||||
// If the organization changes, update the information resource associated with editor role
|
||||
multiValuedQueriesForRole.add(prefix +
|
||||
"SELECT (str(?d) as ?informationResource) \n" +
|
||||
"WHERE {\n"
|
||||
|
||||
+ "?uri rdf:type foaf:Organization ; ?b ?c . \n"
|
||||
+ " ?c rdf:type core:EditorRole ; core:forInformationResource ?d .\n"
|
||||
+ " }");
|
||||
*/
|
||||
// core:ServiceProviderRole -- core:serviceProviderRoleOf
|
||||
|
||||
// If the person changes, update the service provider role in organization
|
||||
multiValuedQueriesForRole.add(prefix +
|
||||
"SELECT (str(?d) as ?organization) \n" +
|
||||
"WHERE {\n"
|
||||
+ "?uri rdf:type foaf:Person . \n"
|
||||
+ "?uri obo:RO_0000053 ?c . \n"
|
||||
+ " ?c rdf:type obo:ERO_0000012 . \n"
|
||||
+ " ?c core:roleContributesTo ?d .\n"
|
||||
+ " ?d rdf:type foaf:Organization .\n "
|
||||
+ " }");
|
||||
|
||||
// If the organization changes, update the service provider role of person
|
||||
multiValuedQueriesForRole.add(prefix +
|
||||
"SELECT (str(?d) as ?person) \n" +
|
||||
"WHERE {\n"
|
||||
+ "?uri rdf:type foaf:Organization . \n"
|
||||
+ "?uri core:contributingRole ?c . \n"
|
||||
+ " ?c rdf:type obo:ERO_0000012 . \n "
|
||||
+ " ?c obo:RO_0000052 ?d .\n"
|
||||
+ "?d rdf:type foaf:Person .\n "
|
||||
+ " }");
|
||||
|
||||
|
||||
// core:TeacherRole -- core:teacherRoleOf
|
||||
|
||||
// If the person changes, update the teacher role in organization
|
||||
// updated to make this an Event (e.g., a course) not an organization - tlw72
|
||||
multiValuedQueriesForRole.add(prefix +
|
||||
"SELECT (str(?d) as ?event) \n" +
|
||||
"WHERE {\n"
|
||||
+ "?uri rdf:type foaf:Person . \n"
|
||||
+ "?uri obo:RO_0000053 ?c . \n"
|
||||
+ " ?c rdf:type core:TeacherRole . \n"
|
||||
+ " ?c obo:BFO_0000054 ?d .\n"
|
||||
+ " ?d rdf:type event:Event .\n "
|
||||
+ " }");
|
||||
|
||||
// If the organization changes, update the teacher role of person
|
||||
// updated to make this an Event (e.g., a course) not an organization - tlw72
|
||||
multiValuedQueriesForRole.add(prefix +
|
||||
"SELECT (str(?d) as ?person) \n" +
|
||||
"WHERE {\n"
|
||||
+ "?uri rdf:type event:Event . \n"
|
||||
+ "?uri obo:BFO_0000055 ?c . \n"
|
||||
+ " ?c rdf:type core:TeacherRole . \n "
|
||||
+ " ?c obo:RO_0000052 ?d .\n"
|
||||
+ "?d rdf:type foaf:Person .\n "
|
||||
+ " }");
|
||||
|
||||
|
||||
// core:ReviewerRole -- core:forInformationResource, core:reviewerRoleOf
|
||||
// core:PeerReviewerRole -- core:forInformationResource, core:reviewerRoleOf
|
||||
|
||||
// If the person changes, update the reviewer role in organization
|
||||
// There is no relationship between a reviewerRole and an organization; commenting
|
||||
// the next two queries out - tlw72
|
||||
/* multiValuedQueriesForRole.add(prefix +
|
||||
"SELECT (str(?d) as ?organization) \n" +
|
||||
"WHERE {\n"
|
||||
|
||||
+ "?uri rdf:type foaf:Person ; ?b ?c . \n"
|
||||
+ " ?c rdf:type core:ReviewerRole ; core:roleIn ?d .\n"
|
||||
+ " }");
|
||||
|
||||
|
||||
// If the organization changes, update the reviewer role of person
|
||||
|
||||
multiValuedQueriesForRole.add(prefix +
|
||||
"SELECT (str(?d) as ?person) \n" +
|
||||
"WHERE {\n"
|
||||
|
||||
+ "?uri rdf:type foaf:Organization ; ?b ?c . \n"
|
||||
+ " ?c rdf:type core:ReviewerRole ; core:reviewerRoleOf ?d .\n"
|
||||
+ " }");
|
||||
*/
|
||||
// If the person changes, update the information resource associated with reviewer role
|
||||
multiValuedQueriesForRole.add(prefix +
|
||||
"SELECT (str(?d) as ?informationResource) \n " +
|
||||
"WHERE {\n"
|
||||
+ "?uri rdf:type foaf:Person . \n"
|
||||
+ "?uri obo:RO_0000053 ?c . \n"
|
||||
+ " ?c rdf:type core:ReviewerRole . \n"
|
||||
+ " ?c core:roleContributesTo ?d .\n"
|
||||
+ " ?d rdf:type obo:IAO_0000030 .\n "
|
||||
+ " }");
|
||||
|
||||
// If the organization changes, update the information resource associated with reviewer role
|
||||
multiValuedQueriesForRole.add(prefix +
|
||||
"SELECT (str(?d) as ?informationResource) \n" +
|
||||
"WHERE {\n"
|
||||
+ "?uri rdf:type obo:IAO_0000030 . \n"
|
||||
+ "?uri core:contributingRole ?c . \n"
|
||||
+ " ?c rdf:type core:ReviewerRole. \n "
|
||||
+ " ?c obo:RO_0000052 ?d .\n"
|
||||
+ "?d rdf:type foaf:Person .\n "
|
||||
+ " }");
|
||||
|
||||
}
|
||||
|
||||
static{
|
||||
List<String> tmpList = new ArrayList<String>();
|
||||
tmpList.add(multiValuedQueryForInformationResource);
|
||||
tmpList.addAll(multiValuedQueriesForAgent);
|
||||
tmpList.addAll(multiValuedQueriesForRole);
|
||||
tmpList.addAll( queriesForAuthorship());
|
||||
tmpList.addAll(queriesForURLLink());
|
||||
tmpList.addAll(queriesForEducationalTraining());
|
||||
tmpList.addAll(queriesForPosition());
|
||||
|
||||
queryList = Collections.unmodifiableList(tmpList);
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -0,0 +1,30 @@
|
|||
/* $This file is distributed under the terms of the license in /doc/license.txt$ */
|
||||
|
||||
package edu.cornell.mannlib.vitro.webapp.search.indexing;
|
||||
|
||||
import java.util.ArrayList;
|
||||
import java.util.List;
|
||||
|
||||
import com.hp.hpl.jena.ontology.OntModel;
|
||||
|
||||
import edu.cornell.mannlib.vitro.webapp.dao.IndividualDao;
|
||||
import edu.cornell.mannlib.vitro.webapp.search.beans.StatementToURIsToUpdate;
|
||||
|
||||
/**
|
||||
* Make a list of StatementToURIsToUpdate objects for use by the
|
||||
* IndexBuidler.
|
||||
*/
|
||||
public class AdditionalUriFinders {
|
||||
|
||||
public static List<StatementToURIsToUpdate> getList(OntModel jenaOntModel,
|
||||
IndividualDao indDao) {
|
||||
// TODO How many of these are only relevant to VIVO?
|
||||
List<StatementToURIsToUpdate> uriFinders = new ArrayList<>();
|
||||
uriFinders.add(new AdditionalURIsForDataProperties());
|
||||
uriFinders.add(new AdditionalURIsForObjectProperties(jenaOntModel));
|
||||
uriFinders.add(new AdditionalURIsForTypeStatements());
|
||||
uriFinders.add(new URIsForClassGroupChange(indDao));
|
||||
return uriFinders;
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -2,8 +2,6 @@
|
|||
|
||||
package edu.cornell.mannlib.vitro.webapp.search.solr;
|
||||
|
||||
import java.net.MalformedURLException;
|
||||
import java.net.URL;
|
||||
import java.util.ArrayList;
|
||||
import java.util.List;
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@ -18,7 +16,6 @@ import com.hp.hpl.jena.rdf.model.Model;
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import com.hp.hpl.jena.vocabulary.OWL;
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import edu.cornell.mannlib.vitro.webapp.config.ConfigurationProperties;
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import edu.cornell.mannlib.vitro.webapp.dao.IndividualDao;
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import edu.cornell.mannlib.vitro.webapp.dao.ModelAccess;
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import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;
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import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory;
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@ -29,13 +26,9 @@ import edu.cornell.mannlib.vitro.webapp.dao.jena.ModelContext;
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import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFServiceFactory;
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import edu.cornell.mannlib.vitro.webapp.rdfservice.impl.RDFServiceUtils;
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import edu.cornell.mannlib.vitro.webapp.search.beans.StatementToURIsToUpdate;
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||||
import edu.cornell.mannlib.vitro.webapp.search.indexing.AdditionalURIsForContextNodes;
|
||||
import edu.cornell.mannlib.vitro.webapp.search.indexing.AdditionalURIsForDataProperties;
|
||||
import edu.cornell.mannlib.vitro.webapp.search.indexing.AdditionalURIsForObjectProperties;
|
||||
import edu.cornell.mannlib.vitro.webapp.search.indexing.AdditionalURIsForTypeStatements;
|
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import edu.cornell.mannlib.vitro.webapp.search.indexing.AdditionalUriFinders;
|
||||
import edu.cornell.mannlib.vitro.webapp.search.indexing.IndexBuilder;
|
||||
import edu.cornell.mannlib.vitro.webapp.search.indexing.SearchReindexingListener;
|
||||
import edu.cornell.mannlib.vitro.webapp.search.indexing.URIsForClassGroupChange;
|
||||
import edu.cornell.mannlib.vitro.webapp.search.solr.documentBuilding.DocumentModifier;
|
||||
import edu.cornell.mannlib.vitro.webapp.search.solr.documentBuilding.ExcludeBasedOnNamespace;
|
||||
import edu.cornell.mannlib.vitro.webapp.search.solr.documentBuilding.ExcludeBasedOnType;
|
||||
|
|
@ -140,7 +133,7 @@ public class SolrSetup implements javax.servlet.ServletContextListener{
|
|||
wadf = new WebappDaoFactoryFiltering(wadf, vf);
|
||||
|
||||
// make objects that will find additional URIs for context nodes etc
|
||||
List<StatementToURIsToUpdate> uriFinders = makeURIFinders(jenaOntModel,wadf.getIndividualDao());
|
||||
List<StatementToURIsToUpdate> uriFinders = AdditionalUriFinders.getList(jenaOntModel,wadf.getIndividualDao());
|
||||
|
||||
// Make the IndexBuilder
|
||||
IndexBuilder builder = new IndexBuilder( solrIndexer, wadf, uriFinders );
|
||||
|
|
@ -159,22 +152,6 @@ public class SolrSetup implements javax.servlet.ServletContextListener{
|
|||
|
||||
}
|
||||
|
||||
/**
|
||||
* Make a list of StatementToURIsToUpdate objects for use by the
|
||||
* IndexBuidler.
|
||||
* @param indDao
|
||||
*/
|
||||
public List<StatementToURIsToUpdate> makeURIFinders( OntModel jenaOntModel, IndividualDao indDao ){
|
||||
List<StatementToURIsToUpdate> uriFinders = new ArrayList<StatementToURIsToUpdate>();
|
||||
uriFinders.add( new AdditionalURIsForDataProperties() );
|
||||
uriFinders.add( new AdditionalURIsForObjectProperties(jenaOntModel) );
|
||||
uriFinders.add( new AdditionalURIsForContextNodes(jenaOntModel) );
|
||||
uriFinders.add( new AdditionalURIsForTypeStatements() );
|
||||
uriFinders.add( new URIsForClassGroupChange( indDao ));
|
||||
return uriFinders;
|
||||
}
|
||||
|
||||
|
||||
@Override
|
||||
public void contextDestroyed(ServletContextEvent sce) {
|
||||
IndexBuilder builder = (IndexBuilder)sce.getServletContext().getAttribute(IndexBuilder.class.getName());
|
||||
|
|
|
|||
Loading…
Add table
Add a link
Reference in a new issue