VIVO-483 Adjust indexing code for the ISF
This class should not have been in Vitro, since it uses VIVO URIs and is never referenced in Vitro. Also, it needed updating to match the ISF.
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j2blake
parent
171f47d392
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98f80dfd71
1 changed files with 0 additions and 300 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.solr.documentBuilding;
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import java.util.ArrayList;
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import java.util.HashSet;
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import java.util.Hashtable;
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import java.util.Iterator;
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import java.util.List;
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import java.util.Map;
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import java.util.Set;
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import java.util.StringTokenizer;
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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 org.apache.solr.common.SolrInputDocument;
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import org.apache.solr.common.SolrInputField;
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import com.hp.hpl.jena.query.Dataset;
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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.shared.Lock;
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import edu.cornell.mannlib.vitro.webapp.beans.Individual;
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import edu.cornell.mannlib.vitro.webapp.search.VitroSearchTermNames;
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public class CalculateParameters implements DocumentModifier {
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private boolean shutdown = false;
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private Dataset dataset;
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// public static int totalInd=1;
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private static final String prefix = "prefix owl: <http://www.w3.org/2002/07/owl#> "
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+ " prefix vitroDisplay: <http://vitro.mannlib.cornell.edu/ontologies/display/1.1#> "
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+ " prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> "
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+ " prefix core: <http://vivoweb.org/ontology/core#> "
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+ " prefix foaf: <http://xmlns.com/foaf/0.1/> "
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+ " prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> "
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+ " prefix localNav: <http://vitro.mannlib.cornell.edu/ns/localnav#> "
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+ " prefix bibo: <http://purl.org/ontology/bibo/> ";
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private static final String betaQuery = prefix + " SELECT count(distinct ?inLinks) " +
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" WHERE { " +
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" ?uri rdf:type owl:Thing . " +
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" ?inLinks ?prop ?uri . " +
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" } ";
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private static final String totalCountQuery = prefix + " SELECT count(distinct ?ind) " +
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" WHERE { " +
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" ?ind rdf:type owl:Thing . " +
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" } ";
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private static Log log = LogFactory.getLog(CalculateParameters.class);
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public CalculateParameters(Dataset dataset){
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this.dataset =dataset;
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// new Thread(new TotalInd(this.dataset,totalCountQuery)).start();
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}
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public CalculateParameters(){
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super();
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}
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public float calculateBeta(String uri){
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float beta=0;
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int Conn=0;
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Query query;
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QuerySolutionMap initialBinding = new QuerySolutionMap();
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QuerySolution soln = null;
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Resource uriResource = ResourceFactory.createResource(uri);
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initialBinding.add("uri", uriResource);
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dataset.getLock().enterCriticalSection(Lock.READ);
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QueryExecution qexec=null;
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try{
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query = QueryFactory.create(betaQuery,Syntax.syntaxARQ);
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qexec = QueryExecutionFactory.create(query,dataset,initialBinding);
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ResultSet results = qexec.execSelect();
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List<String> resultVars = results.getResultVars();
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if(resultVars!=null && resultVars.size()!=0){
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soln = results.next();
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Conn = Integer.parseInt(soln.getLiteral(resultVars.get(0)).getLexicalForm());
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}
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}catch(Throwable t){
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if( ! shutdown )
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log.error(t,t);
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}finally{
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if( qexec != null )
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qexec.close();
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dataset.getLock().leaveCriticalSection();
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}
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beta = (float)Conn;
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//beta *= 100;
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beta += 1;
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// sigmoid function to keep beta between 0 to 1;
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beta = (float) (1 / ( 1 + Math.pow(Math.E,(-beta))));
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if(beta > 1)
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log.info("Beta higher than 1 : " + beta);
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else if(beta <= 0)
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log.info("Beta lower < = 0 : " + beta);
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return beta;
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}
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public String[] getAdjacentNodes(String uri){
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List<String> queryList = new ArrayList<String>();
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Set<String> adjacentNodes = new HashSet<String>();
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Set<String> coauthorNames = new HashSet<String>();
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String[] info = new String[]{"",""};
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StringBuffer adjacentNodesConcat = new StringBuffer();
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StringBuffer coauthorBuff = new StringBuffer();
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adjacentNodesConcat.append("");
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coauthorBuff.append("");
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queryList.add(prefix +
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" SELECT ?adjobj (str(?adjobjLabel) as ?coauthor) " +
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" WHERE { " +
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" ?uri rdf:type <http://xmlns.com/foaf/0.1/Person> . " +
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" ?uri ?prop ?obj . " +
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" ?obj rdf:type <http://vivoweb.org/ontology/core#Relationship> . " +
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" ?obj ?prop2 ?obj2 . " +
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" ?obj2 rdf:type <http://vivoweb.org/ontology/core#InformationResource> . " +
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" ?obj2 ?prop3 ?obj3 . " +
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" ?obj3 rdf:type <http://vivoweb.org/ontology/core#Relationship> . " +
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" ?obj3 ?prop4 ?adjobj . " +
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" ?adjobj rdfs:label ?adjobjLabel . " +
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" ?adjobj rdf:type <http://xmlns.com/foaf/0.1/Person> . " +
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" FILTER (?prop !=rdf:type) . " +
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" FILTER (?prop2!=rdf:type) . " +
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" FILTER (?prop3!=rdf:type) . " +
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" FILTER (?prop4!=rdf:type) . " +
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" FILTER (?adjobj != ?uri) . " +
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"}");
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queryList.add(prefix +
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" SELECT ?adjobj " +
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" WHERE{ " +
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" ?uri rdf:type foaf:Agent . " +
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" ?uri ?prop ?obj . " +
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" ?obj ?prop2 ?adjobj . " +
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" FILTER (?prop !=rdf:type) . " +
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" FILTER isURI(?obj) . " +
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" FILTER (?prop2!=rdf:type) . " +
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" FILTER (?adjobj != ?uri) . " +
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" FILTER isURI(?adjobj) . " +
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" { ?adjobj rdf:type <http://xmlns.com/foaf/0.1/Organization> . } " +
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" UNION " +
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" { ?adjobj rdf:type <http://xmlns.com/foaf/0.1/Person> . } " +
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" UNION " +
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" { ?adjobj rdf:type <http://vivoweb.org/ontology/core#InformationResource> . } " +
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" UNION " +
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" { ?adjobj rdf:type <http://vivoweb.org/ontology/core#Location> . } ." +
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"}");
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Query query;
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QuerySolution soln;
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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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Iterator<String> queryItr = queryList.iterator();
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dataset.getLock().enterCriticalSection(Lock.READ);
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Resource adjacentIndividual = null;
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RDFNode coauthor = null;
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try{
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while(queryItr.hasNext()){
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/*if(!isPerson){
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queryItr.next(); // we don't want first query to execute if the ind is not a person.
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}*/
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query = QueryFactory.create(queryItr.next(),Syntax.syntaxARQ);
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QueryExecution qexec = QueryExecutionFactory.create(query,dataset,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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soln = results.nextSolution();
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adjacentIndividual = (Resource)soln.get("adjobj");
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if(adjacentIndividual!=null){
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adjacentNodes.add(adjacentIndividual.getURI());
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}
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coauthor = soln.get("coauthor");
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if(coauthor!=null){
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coauthorNames.add(" co-authors " + coauthor.toString() + " co-authors ");
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}
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}
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}catch(Exception e){
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if( ! shutdown )
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log.error("Error found in getAdjacentNodes method of SearchQueryHandler");
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}finally{
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qexec.close();
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}
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}
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queryList = null;
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Iterator<String> itr = adjacentNodes.iterator();
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while(itr.hasNext()){
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adjacentNodesConcat.append(itr.next() + " ");
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}
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info[0] = adjacentNodesConcat.toString();
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itr = coauthorNames.iterator();
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while(itr.hasNext()){
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coauthorBuff.append(itr.next());
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}
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info[1] = coauthorBuff.toString();
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}
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catch(Throwable t){
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if( ! shutdown )
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log.error(t,t);
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}finally{
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dataset.getLock().leaveCriticalSection();
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adjacentNodes = null;
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adjacentNodesConcat = null;
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coauthorBuff = null;
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}
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return info;
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}
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@Override
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public void modifyDocument(Individual individual, SolrInputDocument doc, StringBuffer addUri) {
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// TODO Auto-generated method stub
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// calculate beta value.
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log.debug("Parameter calculation starts..");
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float beta = calculateBeta(individual.getURI());
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doc.addField(VitroSearchTermNames.BETA, beta);
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doc.setDocumentBoost(beta + doc.getDocumentBoost() );
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log.debug("Parameter calculation is done");
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}
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public void shutdown(){
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shutdown=true;
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}
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}
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class TotalInd implements Runnable{
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private Dataset dataset;
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private String totalCountQuery;
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private static Log log = LogFactory.getLog(TotalInd.class);
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public TotalInd(Dataset dataset,String totalCountQuery){
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this.dataset = dataset;
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this.totalCountQuery = totalCountQuery;
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}
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public void run(){
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int totalInd=0;
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Query query;
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QuerySolution soln = null;
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dataset.getLock().enterCriticalSection(Lock.READ);
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QueryExecution qexec = null;
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try{
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query = QueryFactory.create(totalCountQuery,Syntax.syntaxARQ);
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qexec = QueryExecutionFactory.create(query,dataset);
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ResultSet results = qexec.execSelect();
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List<String> resultVars = results.getResultVars();
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if(resultVars!=null && resultVars.size()!=0){
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soln = results.next();
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totalInd = Integer.parseInt(soln.getLiteral(resultVars.get(0)).getLexicalForm());
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}
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//CalculateParameters.totalInd = totalInd;
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//log.info("Total number of individuals in the system are : " + CalculateParameters.totalInd);
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}catch(Throwable t){
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log.error(t,t);
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}finally{
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if( qexec != null )
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qexec.close();
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dataset.getLock().leaveCriticalSection();
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}
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}
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}
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