updates for concept search and label management
This commit is contained in:
hudajkhan
parent
14ddc38177
commit
a9ebf8f94b
13 changed files with 171 additions and 76 deletions
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@ -1,47 +0,0 @@
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<rdf:RDF
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xmlns:vitro-public="http://vitro.mannlib.cornell.edu/ns/vitro/public#"
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xmlns:c4o="http://purl.org/spar/c4o/"
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xmlns:ero="http://purl.obolibrary.org/obo/"
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xmlns:pvs="http://vivoweb.org/ontology/provenance-support#"
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xmlns:owl2="http://www.w3.org/2006/12/owl2-xml#"
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xmlns:scirr="http://vivoweb.org/ontology/scientific-research-resource#"
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xmlns:vivo="http://vivoweb.org/ontology/core#"
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xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
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xmlns:bibo="http://purl.org/ontology/bibo/"
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xmlns:afn="http://jena.hpl.hp.com/ARQ/function#"
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xmlns:foaf="http://xmlns.com/foaf/0.1/"
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xmlns:scires="http://vivoweb.org/ontology/scientific-research#"
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xmlns:dcterms="http://purl.org/dc/terms/"
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xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
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xmlns:geo="http://aims.fao.org/aos/geopolitical.owl#"
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xmlns:skco="http://www.w3.org/2004/02/skos/core#"
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xmlns:event="http://purl.org/NET/c4dm/event.owl#"
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xmlns:dcelem="http://purl.org/dc/elements/1.1/"
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xmlns:vitro="http://vitro.mannlib.cornell.edu/ns/vitro/0.7#"
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xmlns:vann="http://purl.org/vocab/vann/"
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xmlns:skos="http://www.w3.org/2008/05/skos#"
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xmlns:swvs="http://www.w3.org/2003/06/sw-vocab-status/ns#"
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xmlns:owl="http://www.w3.org/2002/07/owl#"
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xmlns:fabio="http://purl.org/spar/fabio/"
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xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#">
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<owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#decimal"
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>0.7</owl:versionInfo>
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<owl:Class rdf:about="http://vivoweb.org/ontology/core#ConceptSemanticType">
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<vitro:exampleAnnot rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
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>Semantic Type for given concept, for example UMLS's type returned for concepts</vitro:exampleAnnot>
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<vitro:descriptionAnnot rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
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>Semantic Type for given concept, for example UMLS's type returned for concepts.</vitro:descriptionAnnot>
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<vitro:shortDef rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
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>Concept Semantic Type</vitro:shortDef>
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</owl:Class>
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<owl:ObjectProperty rdf:about="http://vivoweb.org/ontology/core#hasConceptSemanticType">
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<rdfs:range rdf:resource="http://vivoweb.org/ontology/core#ConceptSemanticType"/>
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<owl:inverseOf rdf:resource="http://vivoweb.org/ontology/core#isConceptSemanticTypeOf"/>
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</owl:ObjectProperty>
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</rdf:RDF>
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Before Width: | Height: | Size: 442 B |
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@ -10,6 +10,9 @@
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<#if !labelCount??>
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<#assign labelCount = 0 >
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</#if>
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<#if !localesCount??>
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<#assign localesCount = 1>
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</#if>
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<#assign qrCodeIcon = "qr-code-icon.png">
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<#assign visRequestingTemplate = "foaf-person-2column">
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<section id="individual-intro" class="vcard person" role="region">
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@ -40,7 +43,7 @@
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<#else>
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<h1 class="vcard foaf-person fn" <#if !editable>style="float:left;border-right:1px solid #A6B1B0;"</#if>>
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<#-- Label -->
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<@p.label individual editable labelCount/>
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<@p.label individual editable labelCount localesCount/>
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</h1>
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<#-- Display preferredTitle if it exists; otherwise mostSpecificTypes -->
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<#assign title = propertyGroups.pullProperty("${core}preferredTitle")!>
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@ -12,6 +12,9 @@
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<#if !labelCount??>
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<#assign labelCount = 0 >
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</#if>
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<#if !localesCount??>
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<#assign localesCount = 1>
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</#if>
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<#assign qrCodeIcon = "qr-code-icon.png">
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<#assign individualImage>
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<@p.image individual=individual
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@ -52,7 +55,7 @@
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<div id="photo-wrapper">${individualImage}</div>
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<h1 class="vcard foaf-person fn" <#if !editable>style="float:left;border-right:1px solid #A6B1B0;"</#if>>
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<#-- Label -->
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<@p.label individual editable labelCount/>
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<@p.label individual editable labelCount localesCount/>
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</h1>
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<#-- Display preferredTitle if it exists; otherwise mostSpecificTypes -->
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<#assign title = propertyGroups.pullProperty("${core}preferredTitle")!>
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@ -0,0 +1,4 @@
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<#-- $This file is distributed under the terms of the license in /doc/license.txt$ -->
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<#--Some values for labels etc. may be different between vitro and other systems -->
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<#assign returnText = "${i18n().return_to_profile}" />
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@ -51,6 +51,9 @@
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<#if existingConcept.vocabURI?has_content && existingConcept.vocabLabel?has_content>
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(${existingConcept.vocabLabel})
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</#if>
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<#if existingConcept.conceptSemanticTypeLabel?has_content>
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${existingConcept.conceptSemanticTypeLabel}
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</#if>
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</span>
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</span>
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<a href="${urls.base}/edit/primitiveRdfEdit" class="remove" title="${i18n().remove_capitalized}">${i18n().remove_capitalized}</a>
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@ -1,3 +1,6 @@
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<http://link.informatics.stonybrook.edu/umls> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2002/07/owl#Thing> .
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<http://aims.fao.org/aos/agrovoc/agrovocScheme> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2002/07/owl#Thing> .
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<http://www.eionet.europa.eu/gemet/gemetThesaurus> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2002/07/owl#Thing> .
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<http://www.eionet.europa.eu/gemet/gemetThesaurus> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/2002/07/owl#Thing> .
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<http://link.informatics.stonybrook.edu/umls> <http://www.w3.org/2000/01/rdf-schema#label> "UMLS"^^<http://www.w3.org/2001/XMLSchema#string> .
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<http://aims.fao.org/aos/agrovoc/agrovocScheme> <http://www.w3.org/2000/01/rdf-schema#label> "AGROVOC"^^<http://www.w3.org/2001/XMLSchema#string> .
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<http://www.eionet.europa.eu/gemet/gemetThesaurus> <http://www.w3.org/2000/01/rdf-schema#label> "GEMET"^^<http://www.w3.org/2001/XMLSchema#string> .
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@ -1,3 +0,0 @@
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<http://link.informatics.stonybrook.edu/umls> <http://www.w3.org/2000/01/rdf-schema#label> "UMLS"^^<http://www.w3.org/2001/XMLSchema#string> .
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<http://aims.fao.org/aos/agrovoc/agrovocScheme> <http://www.w3.org/2000/01/rdf-schema#label> "AGROVOC"^^<http://www.w3.org/2001/XMLSchema#string> .
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<http://www.eionet.europa.eu/gemet/gemetThesaurus> <http://www.w3.org/2000/01/rdf-schema#label> "GEMET"^^<http://www.w3.org/2001/XMLSchema#string> .
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@ -396,37 +396,38 @@ public class AddAssociatedConceptGenerator extends VivoBaseGenerator implements
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}
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//To determine whether or not a concept is a user generated or one from an external vocab source.
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//we cannot rely on whether or not it is a skos concept because incorporating UMLS semantic network classes as
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//SKOS concept subclasses means that even concepts from an external vocab source might be considered SKOS concepts
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//Instead, we will simply determine whether a concept is defined by an external vocabulary source and use that
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//as the primary indicator of whether a concept is from an external vocabulary source or a user generated concept
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private List<AssociatedConceptInfo> getAssociatedConceptInfo(
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List<Individual> concepts, VitroRequest vreq) {
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List<AssociatedConceptInfo> info = new ArrayList<AssociatedConceptInfo>();
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for ( Individual conceptIndividual : concepts ) {
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boolean isSKOSConcept = false;
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boolean userGenerated = true;
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//Note that this isn't technically
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String conceptUri = conceptIndividual.getURI();
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String conceptLabel = conceptIndividual.getName();
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//Check if SKOS Concept type
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List<ObjectPropertyStatement> osl = conceptIndividual.getObjectPropertyStatements(RDF.type.getURI());
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for(ObjectPropertyStatement os: osl) {
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if(os.getObjectURI().equals(SKOSConceptType)) {
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isSKOSConcept = true;
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break;
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}
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}
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//Check if defined by an external vocabulary source
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List<ObjectPropertyStatement> vocabList = conceptIndividual.getObjectPropertyStatements(RDFS.isDefinedBy.getURI());
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String vocabSource = null;
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String vocabLabel = null;
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if(vocabList != null && vocabList.size() > 0) {
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userGenerated = false;
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vocabSource = vocabList.get(0).getObjectURI();
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Individual sourceIndividual = EditConfigurationUtils.getIndividual(vreq, vocabSource);
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//Assuming name will get label
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vocabLabel = sourceIndividual.getName();
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}
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if(isSKOSConcept) {
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if(userGenerated) {
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//if the concept in question is skos - which would imply a user generated concept
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info.add(new AssociatedConceptInfo(conceptLabel, conceptUri, null, null, SKOSConceptType, null, null));
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} else {
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//Get the vocab source and vocab label
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List<ObjectPropertyStatement> vocabList = conceptIndividual.getObjectPropertyStatements(RDFS.isDefinedBy.getURI());
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String vocabSource = null;
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String vocabLabel = null;
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if(vocabList != null && vocabList.size() > 0) {
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vocabSource = vocabList.get(0).getObjectURI();
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Individual sourceIndividual = EditConfigurationUtils.getIndividual(vreq, vocabSource);
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//Assuming name will get label
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vocabLabel = sourceIndividual.getName();
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}
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String conceptSemanticTypeURI = null;
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String conceptSemanticTypeLabel = null;
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//Can a concept have multiple semantic types? Currently we are only returning the first one
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@ -438,7 +439,6 @@ public class AddAssociatedConceptGenerator extends VivoBaseGenerator implements
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if(typeAndLabel.containsKey("semanticTypeLabel")) {
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conceptSemanticTypeLabel = typeAndLabel.get("semanticTypeLabel");
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}
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//Assuming this is from an external vocabulary source
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info.add(new AssociatedConceptInfo(conceptLabel, conceptUri, vocabSource, vocabLabel, null, conceptSemanticTypeURI, conceptSemanticTypeLabel));
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@ -84,6 +84,8 @@ public class AddAssociatedConceptsPreprocessor extends
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//This will put the URI value in scope for the first semantic type label
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//and generate the rest if need be
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processConceptSemanticValues();
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//Also need to see if any broader or narrower uris for the concepts that already exist in the system
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//and set up the appropriate relationships between this concept and the broader/narrower uri
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if (numberConcepts > 1) {
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processConceptNodes(numberConcepts);
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}
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@ -0,0 +1,125 @@
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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.edit.n3editing.configuration.preprocessors;
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import javax.servlet.http.HttpServletRequest;
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import org.apache.commons.logging.Log;
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import org.apache.commons.logging.LogFactory;
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import com.hp.hpl.jena.ontology.OntModel;
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import com.hp.hpl.jena.query.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.QuerySolutionMap;
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import com.hp.hpl.jena.query.Syntax;
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import com.hp.hpl.jena.rdf.model.Literal;
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import com.hp.hpl.jena.rdf.model.Model;
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import com.hp.hpl.jena.rdf.model.ModelFactory;
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import com.hp.hpl.jena.rdf.model.Property;
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import com.hp.hpl.jena.rdf.model.ResIterator;
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import com.hp.hpl.jena.rdf.model.Resource;
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import com.hp.hpl.jena.rdf.model.ResourceFactory;
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import com.hp.hpl.jena.rdf.model.Statement;
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import com.hp.hpl.jena.shared.Lock;
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import com.hp.hpl.jena.vocabulary.RDF;
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import com.hp.hpl.jena.vocabulary.RDFS;
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import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;
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import edu.cornell.mannlib.vitro.webapp.dao.jena.DatasetWrapper;
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import edu.cornell.mannlib.vitro.webapp.dao.jena.DatasetWrapperFactory;
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//We are representing semantic types from the UMLS Semantic Network as OWL Classes
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//and this preprocessor will add the appropriate class information to the TBox
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public class ConceptSemanticTypesPreprocessor implements ModelChangePreprocessor {
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private static String VIVOCore = "http://vivoweb.org/ontology/core#";
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private static String SKOSConceptType = "http://www.w3.org/2004/02/skos/core#Concept";
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private Log log = LogFactory.getLog(ConceptSemanticTypesPreprocessor.class);
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private OntModel toUpdateModel = null;
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//Custom constructor
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public ConceptSemanticTypesPreprocessor(OntModel updateModel) {
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this.toUpdateModel = updateModel;
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}
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@Override
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public void preprocess(Model retractionsModel, Model additionsModel,
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HttpServletRequest request) {
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//Run a construct query against the additions model
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String prefixes = "PREFIX rdfs:<" + RDFS.getURI() + "> " +
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"PREFIX owl:<http://www.w3.org/2002/07/owl#> " +
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"PREFIX rdf:<" + RDF.getURI() + ">" +
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"PREFIX skos:<http://www.w3.org/2004/02/skos/core#>";
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String constructQuery = prefixes + " CONSTRUCT { " +
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"?semanticType rdf:type owl:Class. " +
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"?semanticType rdfs:subClassOf skos:Concept . " +
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"?semanticType rdfs:label ?label. " +
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"} WHERE { " +
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"?concept rdf:type ?semanticType. " +
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"?semanticType rdfs:label ?label . " +
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"?semanticType rdfs:subClassOf skos:Concept . " +
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"}";
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//Execute construct query
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Model constructedModel = ModelFactory.createDefaultModel();
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log.debug("CONSTRUCT query string " + constructQuery);
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Query query = null;
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try {
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query = QueryFactory.create(constructQuery, Syntax.syntaxARQ);
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} catch(Throwable th){
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log.error("Could not create CONSTRUCT SPARQL query for query " +
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"string. " + th.getMessage());
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log.error(constructQuery);
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return;
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}
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additionsModel.getLock().enterCriticalSection(Lock.READ);
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QueryExecution qe = null;
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try {
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qe = QueryExecutionFactory.create(
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query, additionsModel);
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qe.execConstruct(constructedModel);
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} catch (Exception e) {
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log.error("Error getting constructed model for query string " + constructQuery);
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} finally {
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if (qe != null) {
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qe.close();
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}
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additionsModel.getLock().leaveCriticalSection();
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}
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//Add constructed model to the designated update model
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toUpdateModel.enterCriticalSection(Lock.WRITE);
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try {
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toUpdateModel.add(constructedModel);
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} catch (Exception e) {
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log.error("Error adding statements to update model for " + constructQuery);
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} finally {
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toUpdateModel.leaveCriticalSection();
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}
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//Take this constructed model and remove from the additions model
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additionsModel.enterCriticalSection(Lock.WRITE);
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try {
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additionsModel.remove(constructedModel.listStatements().toList());
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} catch (Exception e) {
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log.error("Error removing statements from additions model for " + constructQuery);
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} finally {
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additionsModel.leaveCriticalSection();
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}
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}
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}
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# custom form templates ( /templates/freemarker/edit/forms )
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#
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manage_concepts = Manage Concepts
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remove_capitalized = Remove
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no_concepts_specified = There are currently no concepts specified.
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return_to_profile = Return to Profile Page
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external_vocabulary_services = External Vocabulary Services
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<#if !labelCount??>
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<#assign labelCount = 0 >
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</#if>
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<#if !localesCount??>
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<#assign localesCount = 1>
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</#if>
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<#assign visRequestingTemplate = "foaf-person-wilma">
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<section id="individual-intro" class="vcard person" role="region">
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<#else>
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<h1 class="vcard foaf-person">
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<#-- Label -->
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<span class="fn"><@p.label individual editable labelCount/></span>
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<span class="fn"><@p.label individual editable labelCount localesCount/></span>
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<#-- Display preferredTitle if it exists; otherwise mostSpecificTypes -->
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<#assign title = propertyGroups.pullProperty("${core}preferredTitle")!>
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