Merge branch 'maint-rel-1.6' into develop
This commit is contained in:
j2blake
commit
0170b31b13
8 changed files with 320 additions and 41 deletions
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@ -11,12 +11,15 @@ CONSTRUCT {
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_:address v:region ?addressState .
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_:address v:postalCode ?addressPostalCode .
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_:address v:country ?addressCountry .
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_:address <http://purl.obolibrary.org/obo/RO_0001025> ?location .
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?location <http://purl.obolibrary.org/obo/RO_0001015> _:address .
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} WHERE {
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?s vivo:mailingAddress ?address .
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OPTIONAL { ?address vivo:addressCity ?addressCity }
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OPTIONAL { ?address vivo:addressState ?addressState }
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OPTIONAL { ?address vivo:addressPostalCode ?addressPostalCode }
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OPTIONAL { ?address vivo:addressCountry ?addressCountry }
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OPTIONAL { ?address vivo:hasGeographicLocation ?location }
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?s arg:ARG_2000028 ?vcard .
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OPTIONAL {
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?address vivo:address1 ?address1 .
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@ -17,6 +17,7 @@ CONSTRUCT {
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?s vivo:faxNumber ?faxNumber .
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?s vivo:mailingAddress ?address .
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?address ?addressP ?addressO .
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?addressS ?addressQ ?address .
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?s vivo:webpage ?webpage .
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?webpage ?webpageP ?webpageO .
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} WHERE {
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@ -58,6 +59,10 @@ CONSTRUCT {
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?s vivo:mailingAddress ?address .
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?address ?addressP ?addressO
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}
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UNION {
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?s vivo:mailingAddress ?address .
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?addressS ?addressQ ?address
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}
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UNION {
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?s vivo:webpage ?webpage
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}
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@ -296,36 +296,6 @@
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<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
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</owl:Class>
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<!-- http://purl.obolibrary.org/obo/ERO_0000715 -->
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<owl:Class rdf:about="http://purl.obolibrary.org/obo/ERO_0000715">
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<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/ERO_0000007"/>
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<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A technique used for identification, assessment, and prioritization of risks followed by coordinated and economical application of resources to minimize, monitor, and control the probability and/or impact of unfortunate events or to maximize the realization of opportunities.</obo:IAO_0000115>
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<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PERSON: Nicole Vasilevsky</obo:IAO_0000117>
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<obo:IAO_0000119 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://en.wikipedia.org/wiki/Risk_management</obo:IAO_0000119>
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<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000123"/>
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</owl:Class>
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<!-- http://purl.obolibrary.org/obo/ERO_0000742 -->
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<owl:Class rdf:about="http://purl.obolibrary.org/obo/ERO_0000742">
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<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/ERO_0000007"/>
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<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A technique designed for the collection of clinical data in electronic format for use mainly in human clinical trials.</obo:IAO_0000115>
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<obo:IAO_0000112 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Electronic health records.</obo:IAO_0000112>
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<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PERSON: Nicole Vasilevsky</obo:IAO_0000117>
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<obo:IAO_0000118 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">clinical database development</obo:IAO_0000118>
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<obo:IAO_0000119 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">http://en.wikipedia.org/wiki/Electronic_data_capture</obo:IAO_0000119>
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<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
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</owl:Class>
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<owl:Class rdf:about="http://purl.obolibrary.org/obo/ERO_0001245">
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@ -1774,9 +1774,6 @@ vivo:hasGoverningAuthority
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vitro:selectFromExistingAnnot
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"true"^^xsd:boolean .
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obo:ERO_0000715
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rdfs:label "Risk Management"@en-US .
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vcard:additionalName
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rdfs:label "additional name"@en-US .
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@ -2798,7 +2795,11 @@ vivo:GraduateAdvisingRelationship
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<http://vitro.mannlib.cornell.edu/ns/vitro/role#public> .
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obo:RO_0000052
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rdfs:label "inheres in"@en-US .
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rdfs:label "inheres in"@en-US ;
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vitro:hiddenFromDisplayBelowRoleLevelAnnot
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<http://vitro.mannlib.cornell.edu/ns/vitro/role#nobody> ;
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vitro:prohibitedFromUpdateBelowRoleLevelAnnot
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<http://vitro.mannlib.cornell.edu/ns/vitro/role#nobody> .
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obo:OBI_0000299
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rdfs:label "has specified output"@en-US .
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@ -5568,9 +5569,6 @@ geo:countryAreaUnit
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vitro:prohibitedFromUpdateBelowRoleLevelAnnot
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<http://vitro.mannlib.cornell.edu/ns/vitro/role#public> .
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obo:ERO_0000742
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rdfs:label "Research Electronic Datacapture"@en-US .
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vcard:geo
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rdfs:label "geo"@en-US .
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@ -6053,7 +6051,11 @@ obo:RO_0001018
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rdfs:label "contained in"@en-US .
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obo:ERO_0000033
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rdfs:label "has expertise"@en-US .
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rdfs:label "has expertise in technique"@en-US ;
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vitro:selectFromExistingAnnot
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"true"^^xsd:boolean ;
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vitro:offerCreateNewOptionAnnot
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"true"^^xsd:boolean .
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bibo:peerReviewed
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rdfs:label "peer reviewed"@en-US .
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@ -0,0 +1,298 @@
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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;
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import java.util.ArrayList;
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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 org.apache.solr.common.SolrInputDocument;
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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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import edu.cornell.mannlib.vitro.webapp.search.solr.documentBuilding.DocumentModifier;
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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 obo: <http://purl.obolibrary.org/obo/> "
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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 obo:IAO_0000030 . " +
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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 obo:IAO_0000030 . } " +
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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");
|
||||
}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;
|
||||
}
|
||||
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||||
@Override
|
||||
public void modifyDocument(Individual individual, SolrInputDocument doc, StringBuffer addUri) {
|
||||
// TODO Auto-generated method stub
|
||||
// calculate beta value.
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||||
log.debug("Parameter calculation starts..");
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||||
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){
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||||
this.dataset = dataset;
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||||
this.totalCountQuery = totalCountQuery;
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||||
|
||||
}
|
||||
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);
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||||
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();
|
||||
}
|
||||
|
||||
}
|
||||
}
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||||
|
|
@ -13,7 +13,6 @@ import com.hp.hpl.jena.query.DatasetFactory;
|
|||
import edu.cornell.mannlib.vitro.webapp.dao.ModelAccess;
|
||||
import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFServiceFactory;
|
||||
import edu.cornell.mannlib.vitro.webapp.rdfservice.impl.RDFServiceUtils;
|
||||
import edu.cornell.mannlib.vitro.webapp.search.solr.documentBuilding.CalculateParameters;
|
||||
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.SearchIndexExcluder;
|
||||
|
|
|
|||
|
|
@ -48,7 +48,7 @@ public class VivoInformationResourceContextNodeFields extends ContextNodeFields{
|
|||
+ "?uri core:relatedBy ?a . "
|
||||
+ "?a rdf:type core:Authorship ."
|
||||
+ "?a core:relates ?b ."
|
||||
+ "?b rdf:type foaf:Person ."
|
||||
+ "?b rdf:type foaf:Agent ."
|
||||
+ "?b rdfs:label ?ContextNodeProperty .}");
|
||||
|
||||
/* features */
|
||||
|
|
@ -69,7 +69,7 @@ public class VivoInformationResourceContextNodeFields extends ContextNodeFields{
|
|||
+ "?uri core:relatedBy ?e . "
|
||||
+ "?e rdf:type core:Editorship ."
|
||||
+ "?e core:relates ?i ."
|
||||
+ "?i rdf:type foaf:Person ."
|
||||
+ "?i rdf:type foaf:Agent ."
|
||||
+ "?i rdfs:label ?ContextNodeProperty ."
|
||||
+ "}");
|
||||
|
||||
|
|
|
|||
2
utilities/languageSupport/i18nChecker/check
Executable file
2
utilities/languageSupport/i18nChecker/check
Executable file
|
|
@ -0,0 +1,2 @@
|
|||
ruby i18nChecker.rb '/Library/Tomcat/webapps/vivo/i18n/*.properties' complete
|
||||
ruby i18nChecker.rb '/Library/Tomcat/webapps/vivo/themes/wilma/i18n/*.properties' complete
|
||||
Loading…
Add table
Reference in a new issue