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Merge branch 'maint-rel-1.6' of https://github.com/vivo-project/Vitro into maint-rel-1.6

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brianjlowe 2013-11-06 12:46:18 -05:00
commit 725b2e7a57
4 changed files with 13 additions and 304 deletions
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300
webapp/src/edu/cornell/mannlib/vitro/webapp/search/solr/documentBuilding/CalculateParameters.java
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@ -1,300 +0,0 @@
/* $This file is distributed under the terms of the license in /doc/license.txt$ */
package edu.cornell.mannlib.vitro.webapp.search.solr.documentBuilding;
import java.util.ArrayList;
import java.util.HashSet;
import java.util.Hashtable;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
import java.util.Set;
import java.util.StringTokenizer;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import org.apache.solr.common.SolrInputDocument;
import org.apache.solr.common.SolrInputField;
import com.hp.hpl.jena.query.Dataset;
import com.hp.hpl.jena.query.Query;
import com.hp.hpl.jena.query.QueryExecution;
import com.hp.hpl.jena.query.QueryExecutionFactory;
import com.hp.hpl.jena.query.QueryFactory;
import com.hp.hpl.jena.query.QuerySolution;
import com.hp.hpl.jena.query.QuerySolutionMap;
import com.hp.hpl.jena.query.ResultSet;
import com.hp.hpl.jena.query.Syntax;
import com.hp.hpl.jena.rdf.model.RDFNode;
import com.hp.hpl.jena.rdf.model.Resource;
import com.hp.hpl.jena.rdf.model.ResourceFactory;
import com.hp.hpl.jena.shared.Lock;
import edu.cornell.mannlib.vitro.webapp.beans.Individual;
import edu.cornell.mannlib.vitro.webapp.search.VitroSearchTermNames;
public class CalculateParameters implements DocumentModifier {
private boolean shutdown = false;
private Dataset dataset;
// public static int totalInd=1;
private static final String prefix = "prefix owl: <http://www.w3.org/2002/07/owl#> "
+ " prefix vitroDisplay: <http://vitro.mannlib.cornell.edu/ontologies/display/1.1#> "
+ " prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> "
+ " prefix core: <http://vivoweb.org/ontology/core#> "
+ " prefix foaf: <http://xmlns.com/foaf/0.1/> "
+ " prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> "
+ " prefix localNav: <http://vitro.mannlib.cornell.edu/ns/localnav#> "
+ " prefix bibo: <http://purl.org/ontology/bibo/> ";
private static final String betaQuery = prefix + " SELECT count(distinct ?inLinks) " +
" WHERE { " +
" ?uri rdf:type owl:Thing . " +
" ?inLinks ?prop ?uri . " +
" } ";
private static final String totalCountQuery = prefix + " SELECT count(distinct ?ind) " +
" WHERE { " +
" ?ind rdf:type owl:Thing . " +
" } ";
private static Log log = LogFactory.getLog(CalculateParameters.class);
public CalculateParameters(Dataset dataset){
this.dataset =dataset;
// new Thread(new TotalInd(this.dataset,totalCountQuery)).start();
}
public CalculateParameters(){
super();
}
public float calculateBeta(String uri){
float beta=0;
int Conn=0;
Query query;
QuerySolutionMap initialBinding = new QuerySolutionMap();
QuerySolution soln = null;
Resource uriResource = ResourceFactory.createResource(uri);
initialBinding.add("uri", uriResource);
dataset.getLock().enterCriticalSection(Lock.READ);
QueryExecution qexec=null;
try{
query = QueryFactory.create(betaQuery,Syntax.syntaxARQ);
qexec = QueryExecutionFactory.create(query,dataset,initialBinding);
ResultSet results = qexec.execSelect();
List<String> resultVars = results.getResultVars();
if(resultVars!=null && resultVars.size()!=0){
soln = results.next();
Conn = Integer.parseInt(soln.getLiteral(resultVars.get(0)).getLexicalForm());
}
}catch(Throwable t){
if( ! shutdown )
log.error(t,t);
}finally{
if( qexec != null )
qexec.close();
dataset.getLock().leaveCriticalSection();
}
beta = (float)Conn;
//beta *= 100;
beta += 1;
// sigmoid function to keep beta between 0 to 1;
beta = (float) (1 / ( 1 + Math.pow(Math.E,(-beta))));
if(beta > 1)
log.info("Beta higher than 1 : " + beta);
else if(beta <= 0)
log.info("Beta lower < = 0 : " + beta);
return beta;
}
public String[] getAdjacentNodes(String uri){
List<String> queryList = new ArrayList<String>();
Set<String> adjacentNodes = new HashSet<String>();
Set<String> coauthorNames = new HashSet<String>();
String[] info = new String[]{"",""};
StringBuffer adjacentNodesConcat = new StringBuffer();
StringBuffer coauthorBuff = new StringBuffer();
adjacentNodesConcat.append("");
coauthorBuff.append("");
queryList.add(prefix +
" SELECT ?adjobj (str(?adjobjLabel) as ?coauthor) " +
" WHERE { " +
" ?uri rdf:type <http://xmlns.com/foaf/0.1/Person> . " +
" ?uri ?prop ?obj . " +
" ?obj rdf:type <http://vivoweb.org/ontology/core#Relationship> . " +
" ?obj ?prop2 ?obj2 . " +
" ?obj2 rdf:type <http://vivoweb.org/ontology/core#InformationResource> . " +
" ?obj2 ?prop3 ?obj3 . " +
" ?obj3 rdf:type <http://vivoweb.org/ontology/core#Relationship> . " +
" ?obj3 ?prop4 ?adjobj . " +
" ?adjobj rdfs:label ?adjobjLabel . " +
" ?adjobj rdf:type <http://xmlns.com/foaf/0.1/Person> . " +
" FILTER (?prop !=rdf:type) . " +
" FILTER (?prop2!=rdf:type) . " +
" FILTER (?prop3!=rdf:type) . " +
" FILTER (?prop4!=rdf:type) . " +
" FILTER (?adjobj != ?uri) . " +
"}");
queryList.add(prefix +
" SELECT ?adjobj " +
" WHERE{ " +
" ?uri rdf:type foaf:Agent . " +
" ?uri ?prop ?obj . " +
" ?obj ?prop2 ?adjobj . " +
" FILTER (?prop !=rdf:type) . " +
" FILTER isURI(?obj) . " +
" FILTER (?prop2!=rdf:type) . " +
" FILTER (?adjobj != ?uri) . " +
" FILTER isURI(?adjobj) . " +
" { ?adjobj rdf:type <http://xmlns.com/foaf/0.1/Organization> . } " +
" UNION " +
" { ?adjobj rdf:type <http://xmlns.com/foaf/0.1/Person> . } " +
" UNION " +
" { ?adjobj rdf:type <http://vivoweb.org/ontology/core#InformationResource> . } " +
" UNION " +
" { ?adjobj rdf:type <http://vivoweb.org/ontology/core#Location> . } ." +
"}");
Query query;
QuerySolution soln;
QuerySolutionMap initialBinding = new QuerySolutionMap();
Resource uriResource = ResourceFactory.createResource(uri);
initialBinding.add("uri", uriResource);
Iterator<String> queryItr = queryList.iterator();
dataset.getLock().enterCriticalSection(Lock.READ);
Resource adjacentIndividual = null;
RDFNode coauthor = null;
try{
while(queryItr.hasNext()){
/*if(!isPerson){
queryItr.next(); // we don't want first query to execute if the ind is not a person.
}*/
query = QueryFactory.create(queryItr.next(),Syntax.syntaxARQ);
QueryExecution qexec = QueryExecutionFactory.create(query,dataset,initialBinding);
try{
ResultSet results = qexec.execSelect();
while(results.hasNext()){
soln = results.nextSolution();
adjacentIndividual = (Resource)soln.get("adjobj");
if(adjacentIndividual!=null){
adjacentNodes.add(adjacentIndividual.getURI());
}
coauthor = soln.get("coauthor");
if(coauthor!=null){
coauthorNames.add(" co-authors " + coauthor.toString() + " co-authors ");
}
}
}catch(Exception e){
if( ! shutdown )
log.error("Error found in getAdjacentNodes method of SearchQueryHandler");
}finally{
qexec.close();
}
}
queryList = null;
Iterator<String> itr = adjacentNodes.iterator();
while(itr.hasNext()){
adjacentNodesConcat.append(itr.next() + " ");
}
info[0] = adjacentNodesConcat.toString();
itr = coauthorNames.iterator();
while(itr.hasNext()){
coauthorBuff.append(itr.next());
}
info[1] = coauthorBuff.toString();
}
catch(Throwable t){
if( ! shutdown )
log.error(t,t);
}finally{
dataset.getLock().leaveCriticalSection();
adjacentNodes = null;
adjacentNodesConcat = null;
coauthorBuff = null;
}
return info;
}
@Override
public void modifyDocument(Individual individual, SolrInputDocument doc, StringBuffer addUri) {
// TODO Auto-generated method stub
// calculate beta value.
log.debug("Parameter calculation starts..");
float beta = calculateBeta(individual.getURI());
doc.addField(VitroSearchTermNames.BETA, beta);
doc.setDocumentBoost(beta + doc.getDocumentBoost() );
log.debug("Parameter calculation is done");
}
public void shutdown(){
shutdown=true;
}
}
class TotalInd implements Runnable{
private Dataset dataset;
private String totalCountQuery;
private static Log log = LogFactory.getLog(TotalInd.class);
public TotalInd(Dataset dataset,String totalCountQuery){
this.dataset = dataset;
this.totalCountQuery = totalCountQuery;
}
public void run(){
int totalInd=0;
Query query;
QuerySolution soln = null;
dataset.getLock().enterCriticalSection(Lock.READ);
QueryExecution qexec = null;
try{
query = QueryFactory.create(totalCountQuery,Syntax.syntaxARQ);
qexec = QueryExecutionFactory.create(query,dataset);
ResultSet results = qexec.execSelect();
List<String> resultVars = results.getResultVars();
if(resultVars!=null && resultVars.size()!=0){
soln = results.next();
totalInd = Integer.parseInt(soln.getLiteral(resultVars.get(0)).getLexicalForm());
}
//CalculateParameters.totalInd = totalInd;
//log.info("Total number of individuals in the system are : " + CalculateParameters.totalInd);
}catch(Throwable t){
log.error(t,t);
}finally{
if( qexec != null )
qexec.close();
dataset.getLock().leaveCriticalSection();
}
}
}

2
webapp/src/edu/cornell/mannlib/vitro/webapp/services/shortview/FakeApplicationOntologyService.java
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@ -442,7 +442,7 @@ public class FakeApplicationOntologyService {
private static String QUERY_STRING = ""
+ "PREFIX obo: <http://purl.obolibrary.org/obo/> \n"
+ "PREFIX vcard: <http://www.w3.org/2006/vcard/ns#> \n"
+ "SELECT ?uri ?pt \n" + "WHERE { \n"
+ "SELECT ?pt \n" + "WHERE { \n"
+ " ?uri obo:ARG_2000028 ?vIndividual . \n"
+ " ?vIndividual vcard:hasTitle ?vTitle . \n"
+ " ?vTitle vcard:title ?pt . \n" + "} LIMIT 1";

3
webapp/src/edu/cornell/mannlib/vitro/webapp/servlet/setup/SimpleReasonerSetup.java
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@ -33,6 +33,7 @@ import edu.cornell.mannlib.vitro.webapp.reasoner.ReasonerPlugin;
import edu.cornell.mannlib.vitro.webapp.reasoner.SimpleReasoner;
import edu.cornell.mannlib.vitro.webapp.reasoner.SimpleReasonerTBoxListener;
import edu.cornell.mannlib.vitro.webapp.startup.StartupStatus;
import edu.cornell.mannlib.vitro.webapp.utils.threads.VitroBackgroundThread;
public class SimpleReasonerSetup implements ServletContextListener {
@ -121,7 +122,7 @@ public class SimpleReasonerSetup implements ServletContextListener {
simpleReasoner.recompute();
} else if (RecomputeMode.BACKGROUND.equals(mode)) {
log.info("starting ABox inference recompute in a separate thread.");
new Thread(
new VitroBackgroundThread(
new ABoxRecomputer(
simpleReasoner),"ABoxRecomputer").start();
}

12
webapp/src/edu/cornell/mannlib/vitro/webapp/utils/dataGetter/SparqlQueryDataGetter.java
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@ -148,6 +148,10 @@ public class SparqlQueryDataGetter extends DataGetterBase implements DataGetter{
for (String key: pageData.keySet()) {
merged.put(key, String.valueOf(pageData.get(key)));
}
if (log.isDebugEnabled()) {
log.debug("Merging request parameters " + parameterMap
+ " with page data " + pageData + " results in " + merged);
}
return merged;
}
@ -161,9 +165,13 @@ public class SparqlQueryDataGetter extends DataGetterBase implements DataGetter{
private String bindParameters(String text, Map<String, String> merged) {
String bound = text;
for (String key : merged.keySet()) {
bound.replace('?' + key, '<' + merged.get(key) + '>');
bound = bound.replace('?' + key, '<' + merged.get(key) + '>');
}
if (log.isDebugEnabled()) {
log.debug("parameters: " + merged);
log.debug("query before binding parameters:" + text);
log.debug("query after binding parameters: " + bound);
}
log.debug("query after binding parameters: " + bound);
return bound;
}