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Merge branch 'develop' of https://github.com/vivo-project/VIVO into develop

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This commit is contained in:
Holly Mistlebauer 2013-11-12 11:49:10 -05:00
commit 328d023b43
9 changed files with 14449 additions and 14498 deletions
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2
languages/example/rdf/display/everytime/PropertyConfig_es.n3
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@ -42,3 +42,5 @@
<http://vitro.mannlib.cornell.edu/ns/vitro/siteConfig/hasLeaderRoleConfig> <http://vitro.mannlib.cornell.edu/ns/vitro/ApplicationConfiguration#displayName> "jefe de"@es . <http://vitro.mannlib.cornell.edu/ns/vitro/siteConfig/hasLeaderRoleConfig> <http://vitro.mannlib.cornell.edu/ns/vitro/ApplicationConfiguration#displayName> "jefe de"@es .
<http://vitro.mannlib.cornell.edu/ns/vitro/siteConfig/hasMemberRoleConfig> <http://vitro.mannlib.cornell.edu/ns/vitro/ApplicationConfiguration#displayName> "miembro de"@es . <http://vitro.mannlib.cornell.edu/ns/vitro/siteConfig/hasMemberRoleConfig> <http://vitro.mannlib.cornell.edu/ns/vitro/ApplicationConfiguration#displayName> "miembro de"@es .
<http://vitro.mannlib.cornell.edu/ns/vitro/siteConfig/personTelephoneConfig> <http://vitro.mannlib.cornell.edu/ns/vitro/ApplicationConfiguration#displayName> "tel\u00E9fono"@es . <http://vitro.mannlib.cornell.edu/ns/vitro/siteConfig/personTelephoneConfig> <http://vitro.mannlib.cornell.edu/ns/vitro/ApplicationConfiguration#displayName> "tel\u00E9fono"@es .
<http://vitro.mannlib.cornell.edu/ns/vitro/siteConfig/hasSubOrganizationConfig> <http://vitro.mannlib.cornell.edu/ns/vitro/ApplicationConfiguration#displayName> "tiene sub-organización"@es .
<http://vitro.mannlib.cornell.edu/ns/vitro/siteConfig/subOrganizationWithinConfig> <http://vitro.mannlib.cornell.edu/ns/vitro/ApplicationConfiguration#displayName> "organización dentro de"@es .

2
productMods/templates/freemarker/lib/lib-vivo-properties.ftl
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@ -25,7 +25,7 @@
<#if webpage?has_content> <#-- true when the property is in the list, even if not populated (when editing) --> <#if webpage?has_content> <#-- true when the property is in the list, even if not populated (when editing) -->
<nav role="navigation"> <nav role="navigation">
<#local label = "Websites"> <#local label = "${i18n().websites}">
<@p.addLinkWithLabel webpage editable label /> <@p.addLinkWithLabel webpage editable label />
<#if webpage.statements?has_content> <#-- if there are any statements --> <#if webpage.statements?has_content> <#-- if there are any statements -->
<#include "individual-webpage.ftl" > <#include "individual-webpage.ftl" >

4
rdf/tbox/firsttime/initialTBoxAnnotations.n3
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@ -3684,6 +3684,8 @@ vivo:hasPredecessorOrganization
<http://vivoweb.org/ontology#vitroPropertyGroupoverview> ; <http://vivoweb.org/ontology#vitroPropertyGroupoverview> ;
vitro:prohibitedFromUpdateBelowRoleLevelAnnot vitro:prohibitedFromUpdateBelowRoleLevelAnnot
<http://vitro.mannlib.cornell.edu/ns/vitro/role#public> ; <http://vitro.mannlib.cornell.edu/ns/vitro/role#public> ;
vitro:offerCreateNewOptionAnnot
"true"^^xsd:boolean ;
vitro:selectFromExistingAnnot vitro:selectFromExistingAnnot
"true"^^xsd:boolean . "true"^^xsd:boolean .
@ -5088,6 +5090,8 @@ vivo:termLabel
skos:related skos:related
rdfs:label "related"@en-US ; rdfs:label "related"@en-US ;
vitro:customEntryFormAnnot
"edu.cornell.mannlib.vitro.webapp.edit.n3editing.configuration.generators.AddConceptThroughObjectPropertyGenerator"^^xsd:string ;
vitro:displayLimitAnnot vitro:displayLimitAnnot
"5"^^xsd:int ; "5"^^xsd:int ;
vitro:displayRankAnnot vitro:displayRankAnnot

13
src/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/generators/AddEditWebpageFormGenerator.java
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@ -240,11 +240,22 @@ public class AddEditWebpageFormGenerator extends BaseEditConfigurationGenerator
private String getUrlPatternToReturnTo(VitroRequest vreq) { private String getUrlPatternToReturnTo(VitroRequest vreq) {
String subjectUri = EditConfigurationUtils.getSubjectUri(vreq); String subjectUri = EditConfigurationUtils.getSubjectUri(vreq);
String predicateUri = EditConfigurationUtils.getPredicateUri(vreq); String predicateUri = EditConfigurationUtils.getPredicateUri(vreq);
//Also add domain and range uris if they exist to enable cancel to work properly
String domainUri = (String) vreq.getParameter("domainUri");
String rangeUri = (String) vreq.getParameter("rangeUri");
String generatorName = "edu.cornell.mannlib.vitro.webapp.edit.n3editing.configuration.generators.ManageWebpagesForIndividualGenerator"; String generatorName = "edu.cornell.mannlib.vitro.webapp.edit.n3editing.configuration.generators.ManageWebpagesForIndividualGenerator";
String editUrl = EditConfigurationUtils.getEditUrlWithoutContext(vreq); String editUrl = EditConfigurationUtils.getEditUrlWithoutContext(vreq);
return editUrl + "?subjectUri=" + UrlBuilder.urlEncode(subjectUri) + String returnPath = editUrl + "?subjectUri=" + UrlBuilder.urlEncode(subjectUri) +
"&predicateUri=" + UrlBuilder.urlEncode(predicateUri) + "&predicateUri=" + UrlBuilder.urlEncode(predicateUri) +
"&editForm=" + UrlBuilder.urlEncode(generatorName); "&editForm=" + UrlBuilder.urlEncode(generatorName);
if(domainUri != null && !domainUri.isEmpty()) {
returnPath += "&domainUri=" + UrlBuilder.urlEncode(domainUri);
}
if(rangeUri != null && !rangeUri.isEmpty()) {
returnPath += "&rangeUri=" + UrlBuilder.urlEncode(rangeUri);
}
return returnPath;
} }
private String getLinkUri(VitroRequest vreq) { private String getLinkUri(VitroRequest vreq) {

72
src/edu/cornell/mannlib/vitro/webapp/search/indexing/AdditionalURIsForContextNodes.java
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@ -12,26 +12,21 @@ import java.util.Set;
import org.apache.commons.logging.Log; import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory; import org.apache.commons.logging.LogFactory;
import com.hp.hpl.jena.ontology.OntModel;
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.QuerySolution;
import com.hp.hpl.jena.query.QuerySolutionMap; import com.hp.hpl.jena.query.QuerySolutionMap;
import com.hp.hpl.jena.query.ResultSet; 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.RDFNode;
import com.hp.hpl.jena.rdf.model.Resource; import com.hp.hpl.jena.rdf.model.Resource;
import com.hp.hpl.jena.rdf.model.ResourceFactory; import com.hp.hpl.jena.rdf.model.ResourceFactory;
import com.hp.hpl.jena.rdf.model.Statement; import com.hp.hpl.jena.rdf.model.Statement;
import com.hp.hpl.jena.shared.Lock;
import edu.cornell.mannlib.vitro.webapp.dao.jena.QueryUtils;
import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFService;
import edu.cornell.mannlib.vitro.webapp.search.beans.StatementToURIsToUpdate; import edu.cornell.mannlib.vitro.webapp.search.beans.StatementToURIsToUpdate;
public class AdditionalURIsForContextNodes implements StatementToURIsToUpdate { public class AdditionalURIsForContextNodes implements StatementToURIsToUpdate {
private OntModel model; private final RDFService rdfService;
private Set<String> alreadyChecked; private Set<String> alreadyChecked;
private long accumulatedTime = 0; private long accumulatedTime = 0;
@ -43,8 +38,8 @@ public class AdditionalURIsForContextNodes implements StatementToURIsToUpdate {
private Log log = LogFactory.getLog(AdditionalURIsForContextNodes.class); private Log log = LogFactory.getLog(AdditionalURIsForContextNodes.class);
public AdditionalURIsForContextNodes( OntModel jenaOntModel){ public AdditionalURIsForContextNodes( RDFService rdfService){
this.model = jenaOntModel; this.rdfService = rdfService;
} }
@Override @Override
@ -93,42 +88,27 @@ public class AdditionalURIsForContextNodes implements StatementToURIsToUpdate {
List<String> uriList = new ArrayList<String>(); List<String> uriList = new ArrayList<String>();
for(String query : queryList){ for (String query : queryList) {
QuerySolutionMap initialBinding = new QuerySolutionMap();
//log.info("Executing query: "+ query); Resource uriResource = ResourceFactory.createResource(uri);
initialBinding.add("uri", uriResource);
QuerySolutionMap initialBinding = new QuerySolutionMap();
Resource uriResource = ResourceFactory.createResource(uri); ResultSet results = QueryUtils.getQueryResults(query,
initialBinding.add("uri", uriResource); initialBinding, rdfService);
while (results.hasNext()) {
Query sparqlQuery = QueryFactory.create( query, Syntax.syntaxARQ); QuerySolution soln = results.nextSolution();
model.getLock().enterCriticalSection(Lock.READ); Iterator<String> iter = soln.varNames();
try{ while (iter.hasNext()) {
QueryExecution qExec = QueryExecutionFactory.create(sparqlQuery, model, initialBinding); String name = iter.next();
try{ RDFNode node = soln.get(name);
ResultSet results = qExec.execSelect(); if (node != null) {
while(results.hasNext()){ uriList.add("" + node.toString());
QuerySolution soln = results.nextSolution(); } else {
Iterator<String> iter = soln.varNames() ; log.debug(name + " is null");
while( iter.hasNext()){ }
String name = iter.next(); }
RDFNode node = soln.get( name ); }
if( node != null ){ }
uriList.add("" + node.toString());
}else{
log.debug(name + " is null");
}
}
}
}catch(Throwable t){
log.error(t,t);
} finally{
qExec.close();
}
}finally{
model.getLock().leaveCriticalSection();
}
}
if( log.isDebugEnabled() ) if( log.isDebugEnabled() )
log.debug( "additional uris for " + uri + " are " + uriList); log.debug( "additional uris for " + uri + " are " + uriList);

9
src/edu/cornell/mannlib/vitro/webapp/search/indexing/AdditionalUriFinders.java
View file

@ -5,9 +5,8 @@ package edu.cornell.mannlib.vitro.webapp.search.indexing;
import java.util.ArrayList; import java.util.ArrayList;
import java.util.List; 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.dao.IndividualDao;
import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFService;
import edu.cornell.mannlib.vitro.webapp.search.beans.StatementToURIsToUpdate; import edu.cornell.mannlib.vitro.webapp.search.beans.StatementToURIsToUpdate;
/** /**
@ -16,12 +15,12 @@ import edu.cornell.mannlib.vitro.webapp.search.beans.StatementToURIsToUpdate;
*/ */
public class AdditionalUriFinders { public class AdditionalUriFinders {
public static List<StatementToURIsToUpdate> getList(OntModel jenaOntModel, public static List<StatementToURIsToUpdate> getList(RDFService rdfService,
IndividualDao indDao) { IndividualDao indDao) {
List<StatementToURIsToUpdate> uriFinders = new ArrayList<>(); List<StatementToURIsToUpdate> uriFinders = new ArrayList<>();
uriFinders.add(new AdditionalURIsForDataProperties()); uriFinders.add(new AdditionalURIsForDataProperties());
uriFinders.add(new AdditionalURIsForObjectProperties(jenaOntModel)); uriFinders.add(new AdditionalURIsForObjectProperties(rdfService));
uriFinders.add(new AdditionalURIsForContextNodes(jenaOntModel)); uriFinders.add(new AdditionalURIsForContextNodes(rdfService));
uriFinders.add(new AdditionalURIsForTypeStatements()); uriFinders.add(new AdditionalURIsForTypeStatements());
uriFinders.add(new URIsForClassGroupChange(indDao)); uriFinders.add(new URIsForClassGroupChange(indDao));
return uriFinders; return uriFinders;

136
test/edu/cornell/mannlib/vitro/webapp/search/indexing/AdditionalURIsForContextNodesTest.java
View file

@ -12,11 +12,13 @@ import org.junit.Test;
import com.hp.hpl.jena.ontology.OntModel; import com.hp.hpl.jena.ontology.OntModel;
import com.hp.hpl.jena.rdf.model.ModelFactory; import com.hp.hpl.jena.rdf.model.ModelFactory;
import edu.cornell.mannlib.vitro.webapp.search.indexing.AdditionalURIsForContextNodes; import edu.cornell.mannlib.vitro.webapp.rdfservice.impl.jena.model.RDFServiceModel;
public class AdditionalURIsForContextNodesTest { public class AdditionalURIsForContextNodesTest {
private AdditionalURIsForContextNodes uriFinder;
@Test @Test
public void testPositionChanges(){ public void testPositionChanges(){
String n3 = String n3 =
@ -59,12 +61,7 @@ public class AdditionalURIsForContextNodesTest {
"<http://vivoweb.org/ontology/core#DateTimeInterval> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2002/07/owl#Class> . \n" + "<http://vivoweb.org/ontology/core#DateTimeInterval> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2002/07/owl#Class> . \n" +
"<http://vivoweb.org/ontology/core#Department> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2002/07/owl#Class> . \n" ; "<http://vivoweb.org/ontology/core#Department> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2002/07/owl#Class> . \n" ;
//make a test model with an person, an authorship context node and a book populateModelAndCreateUriFinder(n3);
OntModel model = ModelFactory.createOntologyModel();
model.read( new StringReader(n3), null, "N3");
//make an AdditionalURIsForContextNodesTest object with that model
AdditionalURIsForContextNodes uriFinder = new AdditionalURIsForContextNodes( model );
//if the person changes then the org needs to be updated //if the person changes then the org needs to be updated
List<String> uris = uriFinder.findAdditionalURIsToIndex( "http://caruso-laptop.mannlib.cornell.edu:8090/vivo/individual/n932"); List<String> uris = uriFinder.findAdditionalURIsToIndex( "http://caruso-laptop.mannlib.cornell.edu:8090/vivo/individual/n932");
@ -107,21 +104,15 @@ public class AdditionalURIsForContextNodesTest {
" core:contributingRole <http://caruso-laptop.mannlib.cornell.edu:8090/vivo/individual/n2577> . \n" + " core:contributingRole <http://caruso-laptop.mannlib.cornell.edu:8090/vivo/individual/n2577> . \n" +
" <http://vivo.scripps.edu/individual/n14979> a <http://xmlns.com/foaf/0.1/Person> , owl:Thing , <http://xmlns.com/foaf/0.1/Agent> . \n"; " <http://vivo.scripps.edu/individual/n14979> a <http://xmlns.com/foaf/0.1/Person> , owl:Thing , <http://xmlns.com/foaf/0.1/Agent> . \n";
//make a test model with an person, an authorship context node and a book //make a test model with an person, an authorship context node and a book
OntModel model = ModelFactory.createOntologyModel(); populateModelAndCreateUriFinder(n3);
model.read( new StringReader(n3), null, "N3");
//make an AdditionalURIsForContextNodesTest object with that model
AdditionalURIsForContextNodes uriFinder = new AdditionalURIsForContextNodes( model );
//get additional uris for org //get additional uris for org
List<String> uris = uriFinder.findAdditionalURIsToIndex( "http://caruso-laptop.mannlib.cornell.edu:8090/vivo/individual/n2592"); List<String> uris = uriFinder.findAdditionalURIsToIndex( "http://caruso-laptop.mannlib.cornell.edu:8090/vivo/individual/n2592");
assertTrue("did not find person for context node", uris.contains("http://vivo.scripps.edu/individual/n14979" )); assertTrue("did not find person for context node", uris.contains("http://vivo.scripps.edu/individual/n14979" ));
} }
@Test @Test
public void testLeaderRoleChanges(){ public void testLeaderRoleChanges(){
@ -153,13 +144,7 @@ public class AdditionalURIsForContextNodesTest {
"<http://vivo.scripps.edu/individual/n7080> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2002/07/owl#Thing> . \n " + "<http://vivo.scripps.edu/individual/n7080> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2002/07/owl#Thing> . \n " +
"<http://vivo.scripps.edu/individual/n7080> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://xmlns.com/foaf/0.1/Organization> . \n " ; "<http://vivo.scripps.edu/individual/n7080> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://xmlns.com/foaf/0.1/Organization> . \n " ;
populateModelAndCreateUriFinder(n3);
//make a test model with an person, a leader role node and a university
OntModel model = ModelFactory.createOntologyModel();
model.read( new StringReader(n3), null, "N3");
//make an AdditionalURIsForContextNodesTest object with that model
AdditionalURIsForContextNodes uriFinder = new AdditionalURIsForContextNodes( model );
//if the person changes then the university needs to be updated //if the person changes then the university needs to be updated
List<String> uris = uriFinder.findAdditionalURIsToIndex( "http://vivo.scripps.edu/individual/n2027"); List<String> uris = uriFinder.findAdditionalURIsToIndex( "http://vivo.scripps.edu/individual/n2027");
@ -168,8 +153,6 @@ public class AdditionalURIsForContextNodesTest {
//if the university changes then the person needs to be updated //if the university changes then the person needs to be updated
uris = uriFinder.findAdditionalURIsToIndex( "http://vivo.scripps.edu/individual/n7080"); uris = uriFinder.findAdditionalURIsToIndex( "http://vivo.scripps.edu/individual/n7080");
assertTrue("did not find person for context node", uris.contains("http://vivo.scripps.edu/individual/n2027" )); assertTrue("did not find person for context node", uris.contains("http://vivo.scripps.edu/individual/n2027" ));
} }
@ -204,14 +187,7 @@ public class AdditionalURIsForContextNodesTest {
"<http://vivo.scripps.edu/individual/n6004> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2002/07/owl#Thing> . \n " + "<http://vivo.scripps.edu/individual/n6004> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2002/07/owl#Thing> . \n " +
"<http://vivo.scripps.edu/individual/n6004> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://xmlns.com/foaf/0.1/Organization> . \n " ; "<http://vivo.scripps.edu/individual/n6004> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://xmlns.com/foaf/0.1/Organization> . \n " ;
populateModelAndCreateUriFinder(n3);
//make a test model with an person, a member role node and a university
OntModel model = ModelFactory.createOntologyModel();
model.read( new StringReader(n3), null, "N3");
//make an AdditionalURIsForContextNodesTest object with that model
AdditionalURIsForContextNodes uriFinder = new AdditionalURIsForContextNodes( model );
//if the person changes then the university needs to be updated //if the person changes then the university needs to be updated
List<String> uris = uriFinder.findAdditionalURIsToIndex( "http://vivo.scripps.edu/individual/n4519"); List<String> uris = uriFinder.findAdditionalURIsToIndex( "http://vivo.scripps.edu/individual/n4519");
@ -254,15 +230,8 @@ public class AdditionalURIsForContextNodesTest {
"<http://vivo.scripps.edu/individual/n5177> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://vivoweb.org/ontology/core#Project> . \n" + "<http://vivo.scripps.edu/individual/n5177> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://vivoweb.org/ontology/core#Project> . \n" +
"<http://vivo.scripps.edu/individual/n5177> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2002/07/owl#Thing> . \n" + "<http://vivo.scripps.edu/individual/n5177> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2002/07/owl#Thing> . \n" +
"<http://vivo.scripps.edu/individual/n5177> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://vivoweb.org/ontology/core#Process> . \n" ; "<http://vivo.scripps.edu/individual/n5177> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://vivoweb.org/ontology/core#Process> . \n" ;
//make a test model with an person, a clinical role node and a project populateModelAndCreateUriFinder(n3);
OntModel model = ModelFactory.createOntologyModel();
model.read( new StringReader(n3), null, "N3");
//make an AdditionalURIsForContextNodesTest object with that model
AdditionalURIsForContextNodes uriFinder = new AdditionalURIsForContextNodes( model );
//if the person changes then the project needs to be updated //if the person changes then the project needs to be updated
List<String> uris = uriFinder.findAdditionalURIsToIndex( "http://vivo.scripps.edu/individual/n4858"); List<String> uris = uriFinder.findAdditionalURIsToIndex( "http://vivo.scripps.edu/individual/n4858");
@ -303,12 +272,7 @@ public class AdditionalURIsForContextNodesTest {
"<http://vivo.scripps.edu/individual/n4442> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2002/07/owl#Thing> . \n" + "<http://vivo.scripps.edu/individual/n4442> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2002/07/owl#Thing> . \n" +
"<http://vivo.scripps.edu/individual/n4442> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://purl.obolibrary.org/obo/ERO_0000005> . \n" ; "<http://vivo.scripps.edu/individual/n4442> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://purl.obolibrary.org/obo/ERO_0000005> . \n" ;
//make a test model with an person, a clinical role node and a service populateModelAndCreateUriFinder(n3);
OntModel model = ModelFactory.createOntologyModel();
model.read( new StringReader(n3), null, "N3");
//make an AdditionalURIsForContextNodesTest object with that model
AdditionalURIsForContextNodes uriFinder = new AdditionalURIsForContextNodes( model );
//if the person changes then the service needs to be updated //if the person changes then the service needs to be updated
List<String> uris = uriFinder.findAdditionalURIsToIndex( "http://vivo.scripps.edu/individual/n5651"); List<String> uris = uriFinder.findAdditionalURIsToIndex( "http://vivo.scripps.edu/individual/n5651");
@ -350,13 +314,7 @@ public class AdditionalURIsForContextNodesTest {
"<http://vivo.scripps.edu/individual/n1305> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://purl.org/NET/c4dm/event.owl#Event> . \n" + "<http://vivo.scripps.edu/individual/n1305> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://purl.org/NET/c4dm/event.owl#Event> . \n" +
"<http://vivo.scripps.edu/individual/n1305> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2002/07/owl#Thing> . \n" ; "<http://vivo.scripps.edu/individual/n1305> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2002/07/owl#Thing> . \n" ;
populateModelAndCreateUriFinder(n3);
//make a test model with an person, a presenter role node and a presentation
OntModel model = ModelFactory.createOntologyModel();
model.read( new StringReader(n3), null, "N3");
//make an AdditionalURIsForContextNodesTest object with that model
AdditionalURIsForContextNodes uriFinder = new AdditionalURIsForContextNodes( model );
//if the person changes then the presentation needs to be updated //if the person changes then the presentation needs to be updated
List<String> uris = uriFinder.findAdditionalURIsToIndex( "http://vivo.scripps.edu/individual/n5596"); List<String> uris = uriFinder.findAdditionalURIsToIndex( "http://vivo.scripps.edu/individual/n5596");
@ -398,13 +356,8 @@ public class AdditionalURIsForContextNodesTest {
"<http://vivo.scripps.edu/individual/n4107> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://purl.org/NET/c4dm/event.owl#Event> . \n " + "<http://vivo.scripps.edu/individual/n4107> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://purl.org/NET/c4dm/event.owl#Event> . \n " +
"<http://vivo.scripps.edu/individual/n4107> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2002/07/owl#Thing> . \n " + "<http://vivo.scripps.edu/individual/n4107> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2002/07/owl#Thing> . \n " +
"<http://vivo.scripps.edu/individual/n4107> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://vivoweb.org/ontology/core#InvitedTalk> . \n " ; "<http://vivo.scripps.edu/individual/n4107> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://vivoweb.org/ontology/core#InvitedTalk> . \n " ;
//make a test model with an person, a presenter role node and an invited talk populateModelAndCreateUriFinder(n3);
OntModel model = ModelFactory.createOntologyModel();
model.read( new StringReader(n3), null, "N3");
//make an AdditionalURIsForContextNodesTest object with that model
AdditionalURIsForContextNodes uriFinder = new AdditionalURIsForContextNodes( model );
//if the person changes then the invited talk needs to be updated //if the person changes then the invited talk needs to be updated
List<String> uris = uriFinder.findAdditionalURIsToIndex( "http://vivo.scripps.edu/individual/n4112"); List<String> uris = uriFinder.findAdditionalURIsToIndex( "http://vivo.scripps.edu/individual/n4112");
@ -447,13 +400,7 @@ public class AdditionalURIsForContextNodesTest {
"<http://vivo.scripps.edu/individual/n4252> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2002/07/owl#Thing> . \n" + "<http://vivo.scripps.edu/individual/n4252> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2002/07/owl#Thing> . \n" +
"<http://vivo.scripps.edu/individual/n4252> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://vivoweb.org/ontology/core#Grant> . \n" ; "<http://vivo.scripps.edu/individual/n4252> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://vivoweb.org/ontology/core#Grant> . \n" ;
populateModelAndCreateUriFinder(n3);
//make a test model with an person, a researcher role node and a grant
OntModel model = ModelFactory.createOntologyModel();
model.read( new StringReader(n3), null, "N3");
//make an AdditionalURIsForContextNodesTest object with that model
AdditionalURIsForContextNodes uriFinder = new AdditionalURIsForContextNodes( model );
//if the person changes then the grant needs to be updated //if the person changes then the grant needs to be updated
List<String> uris = uriFinder.findAdditionalURIsToIndex( "http://vivo.scripps.edu/individual/n4957"); List<String> uris = uriFinder.findAdditionalURIsToIndex( "http://vivo.scripps.edu/individual/n4957");
@ -497,14 +444,7 @@ public class AdditionalURIsForContextNodesTest {
"<http://vivo.scripps.edu/individual/n564> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2002/07/owl#Thing> . \n " + "<http://vivo.scripps.edu/individual/n564> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2002/07/owl#Thing> . \n " +
"<http://vivo.scripps.edu/individual/n564> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://vivoweb.org/ontology/core#Process> . \n " ; "<http://vivo.scripps.edu/individual/n564> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://vivoweb.org/ontology/core#Process> . \n " ;
populateModelAndCreateUriFinder(n3);
//make a test model with an person, a researcher role node and a project
OntModel model = ModelFactory.createOntologyModel();
model.read( new StringReader(n3), null, "N3");
//make an AdditionalURIsForContextNodesTest object with that model
AdditionalURIsForContextNodes uriFinder = new AdditionalURIsForContextNodes( model );
//if the person changes then the project needs to be updated //if the person changes then the project needs to be updated
List<String> uris = uriFinder.findAdditionalURIsToIndex( "http://vivo.scripps.edu/individual/n2029"); List<String> uris = uriFinder.findAdditionalURIsToIndex( "http://vivo.scripps.edu/individual/n2029");
@ -548,13 +488,7 @@ public class AdditionalURIsForContextNodesTest {
"<http://vivo.scripps.edu/individual/n1742> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2002/07/owl#Thing> . \n" + "<http://vivo.scripps.edu/individual/n1742> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2002/07/owl#Thing> . \n" +
"<http://vivo.scripps.edu/individual/n1742> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://vivoweb.org/ontology/core#Grant> . \n" ; "<http://vivo.scripps.edu/individual/n1742> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://vivoweb.org/ontology/core#Grant> . \n" ;
populateModelAndCreateUriFinder(n3);
//make a test model with an person, a principal investigator role node and a grant
OntModel model = ModelFactory.createOntologyModel();
model.read( new StringReader(n3), null, "N3");
//make an AdditionalURIsForContextNodesTest object with that model
AdditionalURIsForContextNodes uriFinder = new AdditionalURIsForContextNodes( model );
//if the person changes then the grant needs to be updated //if the person changes then the grant needs to be updated
List<String> uris = uriFinder.findAdditionalURIsToIndex( "http://vivo.scripps.edu/individual/n2368"); List<String> uris = uriFinder.findAdditionalURIsToIndex( "http://vivo.scripps.edu/individual/n2368");
@ -598,13 +532,8 @@ public class AdditionalURIsForContextNodesTest {
"<http://vivo.scripps.edu/individual/n4931> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2002/07/owl#Thing> . \n" + "<http://vivo.scripps.edu/individual/n4931> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2002/07/owl#Thing> . \n" +
"<http://vivo.scripps.edu/individual/n4931> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://vivoweb.org/ontology/core#Grant> . \n" ; "<http://vivo.scripps.edu/individual/n4931> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://vivoweb.org/ontology/core#Grant> . \n" ;
//make a test model with an person, a co-principal investigator role node and a grant populateModelAndCreateUriFinder(n3);
OntModel model = ModelFactory.createOntologyModel();
model.read( new StringReader(n3), null, "N3");
//make an AdditionalURIsForContextNodesTest object with that model
AdditionalURIsForContextNodes uriFinder = new AdditionalURIsForContextNodes( model );
//if the copi changes then the grant needs to be updated //if the copi changes then the grant needs to be updated
List<String> uris = uriFinder.findAdditionalURIsToIndex( "http://vivo.scripps.edu/individual/n1373"); List<String> uris = uriFinder.findAdditionalURIsToIndex( "http://vivo.scripps.edu/individual/n1373");
assertTrue("did not find grant for co-pi", uris.contains("http://vivo.scripps.edu/individual/n4931" )); assertTrue("did not find grant for co-pi", uris.contains("http://vivo.scripps.edu/individual/n4931" ));
@ -646,14 +575,8 @@ public class AdditionalURIsForContextNodesTest {
"<http://vivo.scripps.edu/individual/n160> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2002/07/owl#Thing> . \n" + "<http://vivo.scripps.edu/individual/n160> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2002/07/owl#Thing> . \n" +
"<http://vivo.scripps.edu/individual/n160> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://vivoweb.org/ontology/core#Grant> . \n" ; "<http://vivo.scripps.edu/individual/n160> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://vivoweb.org/ontology/core#Grant> . \n" ;
populateModelAndCreateUriFinder(n3);
//make a test model with an person, a investigator role node and a grant
OntModel model = ModelFactory.createOntologyModel();
model.read( new StringReader(n3), null, "N3");
//make an AdditionalURIsForContextNodesTest object with that model
AdditionalURIsForContextNodes uriFinder = new AdditionalURIsForContextNodes( model );
//if the investigator changes then the grant needs to be updated //if the investigator changes then the grant needs to be updated
List<String> uris = uriFinder.findAdditionalURIsToIndex( "http://vivo.scripps.edu/individual/n5282"); List<String> uris = uriFinder.findAdditionalURIsToIndex( "http://vivo.scripps.edu/individual/n5282");
assertTrue("did not find grant for investigator", uris.contains("http://vivo.scripps.edu/individual/n160" )); assertTrue("did not find grant for investigator", uris.contains("http://vivo.scripps.edu/individual/n160" ));
@ -661,10 +584,21 @@ public class AdditionalURIsForContextNodesTest {
//if the grant changes then the investigator needs to be updated //if the grant changes then the investigator needs to be updated
uris = uriFinder.findAdditionalURIsToIndex( "http://vivo.scripps.edu/individual/n160"); uris = uriFinder.findAdditionalURIsToIndex( "http://vivo.scripps.edu/individual/n160");
assertTrue("did not find investigator for grant", uris.contains("http://vivo.scripps.edu/individual/n5282" )); assertTrue("did not find investigator for grant", uris.contains("http://vivo.scripps.edu/individual/n5282" ));
} }
// ----------------------------------------------------------------------
// Helper methods
// ----------------------------------------------------------------------
/**
* Build a Model from this N3 string, and create a URI Finder based on that
* Model.
*/
private void populateModelAndCreateUriFinder(String n3String) {
OntModel model = ModelFactory.createOntologyModel();
model.read(new StringReader(n3String), null, "N3");
uriFinder = new AdditionalURIsForContextNodes(
new RDFServiceModel(model));
}
} }

28623
test/edu/cornell/mannlib/vitro/webapp/search/solr/NIHVIVO3853_DataSet1.rdf
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File diff suppressed because it is too large Load diff

86
test/edu/cornell/mannlib/vitro/webapp/search/solr/VivoAgentContextNodeFieldsTest.java
View file

@ -1,13 +1,12 @@
/* $This file is distributed under the terms of the license in /doc/license.txt$ */ /* $This file is distributed under the terms of the license in /doc/license.txt$ */
package edu.cornell.mannlib.vitro.webapp.search.solr; package edu.cornell.mannlib.vitro.webapp.search.solr;
import static org.junit.Assert.assertNotNull; import static org.junit.Assert.*;
import static org.junit.Assert.assertTrue;
import java.io.InputStream; import java.io.InputStream;
import org.apache.solr.common.SolrInputDocument;
import org.junit.BeforeClass; import org.junit.BeforeClass;
import org.junit.Ignore;
import org.junit.Test; import org.junit.Test;
import com.hp.hpl.jena.rdf.model.Model; import com.hp.hpl.jena.rdf.model.Model;
@ -25,33 +24,33 @@ import edu.cornell.mannlib.vitro.webapp.rdfservice.impl.RDFServiceFactorySingle;
import edu.cornell.mannlib.vitro.webapp.rdfservice.impl.jena.model.RDFServiceModel; import edu.cornell.mannlib.vitro.webapp.rdfservice.impl.jena.model.RDFServiceModel;
public class VivoAgentContextNodeFieldsTest extends AbstractTestClass{ public class VivoAgentContextNodeFieldsTest extends AbstractTestClass{
static String SPCA = "http://vivo.mydomain.edu/individual/n8087"; static String SPCA = "http://vivo.mydomain.edu/individual/n8087";
static RDFServiceFactory rdfServiceFactory; static RDFServiceFactory rdfServiceFactory;
@BeforeClass @BeforeClass
public static void setup(){ public static void setup(){
Model m = ModelFactory.createDefaultModel(); Model m = ModelFactory.createDefaultModel();
InputStream stream = VivoAgentContextNodeFieldsTest InputStream stream = VivoAgentContextNodeFieldsTest
.class.getResourceAsStream("./NIHVIVO3853_DataSet1.rdf"); .class.getResourceAsStream("./NIHVIVO3853_DataSet1.rdf");
long preloadSize = m.size(); long preloadSize = m.size();
m.read(stream, null); m.read(stream, null);
assertTrue("expected to load statements from file", m.size() > preloadSize ); assertTrue("expected to load statements from file", m.size() > preloadSize );
assertTrue("expect statements about SPCA", assertTrue("expect statements about SPCA",
m.contains(ResourceFactory.createResource(SPCA),(Property) null,(RDFNode) null)); m.contains(ResourceFactory.createResource(SPCA),(Property) null,(RDFNode) null));
RDFService rdfService = new RDFServiceModel(m); RDFService rdfService = new RDFServiceModel(m);
rdfServiceFactory = new RDFServiceFactorySingle(rdfService); rdfServiceFactory = new RDFServiceFactorySingle(rdfService);
} }
@Test @Test
public void testJane(){ public void testJane(){
Individual ind = new IndividualImpl(); Individual ind = new IndividualImpl();
ind.setURI(SPCA); ind.setURI(SPCA);
VivoAgentContextNodeFields vacnf = new VivoAgentContextNodeFields(rdfServiceFactory); VivoAgentContextNodeFields vacnf = new VivoAgentContextNodeFields(rdfServiceFactory);
@ -61,13 +60,12 @@ public class VivoAgentContextNodeFieldsTest extends AbstractTestClass{
String values = sb.toString(); String values = sb.toString();
boolean hasJane = values.toLowerCase().indexOf("jane") > 0; boolean hasJane = values.toLowerCase().indexOf("jane") > 0;
assertTrue("expected to have jane because SPCA advises jane", hasJane); assertTrue("expected to have jane because SPCA advises jane", hasJane);
} }
@Ignore @Test
@Test public void testWonder(){
public void testWonder(){ Individual ind = new IndividualImpl();
Individual ind = new IndividualImpl();
ind.setURI(SPCA); ind.setURI(SPCA);
VivoAgentContextNodeFields vacnf = new VivoAgentContextNodeFields(rdfServiceFactory); VivoAgentContextNodeFields vacnf = new VivoAgentContextNodeFields(rdfServiceFactory);
@ -77,12 +75,12 @@ public class VivoAgentContextNodeFieldsTest extends AbstractTestClass{
String values = sb.toString(); String values = sb.toString();
boolean hasWonder = values.toLowerCase().indexOf("wonders") > 0; boolean hasWonder = values.toLowerCase().indexOf("wonders") > 0;
assertTrue("expected to have jane because SPCA won wonders award", hasWonder); assertTrue("expected to have jane because SPCA won wonders award", hasWonder);
} }
@Test @Test
public void testChimp(){ public void testChimp(){
Individual ind = new IndividualImpl(); Individual ind = new IndividualImpl();
ind.setURI(SPCA); ind.setURI(SPCA);
VivoAgentContextNodeFields vacnf = new VivoAgentContextNodeFields(rdfServiceFactory); VivoAgentContextNodeFields vacnf = new VivoAgentContextNodeFields(rdfServiceFactory);
@ -92,6 +90,6 @@ public class VivoAgentContextNodeFieldsTest extends AbstractTestClass{
String values = sb.toString(); String values = sb.toString();
boolean hasNotChimp = ! (values.toLowerCase().indexOf("chimp") > 0); boolean hasNotChimp = ! (values.toLowerCase().indexOf("chimp") > 0);
assertTrue("expected to not have chimp because jane won chimp award, not SPCA", hasNotChimp); assertTrue("expected to not have chimp because jane won chimp award, not SPCA", hasNotChimp);
} }
} }