updates for concept search and label management

productMods/WEB-INF/filegraph/tbox/ConceptSemanticType.owl

@@ -1,47 +0,0 @@
-<rdf:RDF
-    xmlns:vitro-public="http://vitro.mannlib.cornell.edu/ns/vitro/public#"
-    xmlns:c4o="http://purl.org/spar/c4o/"
-    xmlns:ero="http://purl.obolibrary.org/obo/"
-    xmlns:pvs="http://vivoweb.org/ontology/provenance-support#"
-    xmlns:owl2="http://www.w3.org/2006/12/owl2-xml#"
-    xmlns:scirr="http://vivoweb.org/ontology/scientific-research-resource#"
-    xmlns:vivo="http://vivoweb.org/ontology/core#"
-    xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
-    xmlns:bibo="http://purl.org/ontology/bibo/"
-    xmlns:afn="http://jena.hpl.hp.com/ARQ/function#"
-    xmlns:foaf="http://xmlns.com/foaf/0.1/"
-    xmlns:scires="http://vivoweb.org/ontology/scientific-research#"
-    xmlns:dcterms="http://purl.org/dc/terms/"
-    xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
-    xmlns:geo="http://aims.fao.org/aos/geopolitical.owl#"
-    xmlns:skco="http://www.w3.org/2004/02/skos/core#"
-    xmlns:event="http://purl.org/NET/c4dm/event.owl#"
-    xmlns:dcelem="http://purl.org/dc/elements/1.1/"
-    xmlns:vitro="http://vitro.mannlib.cornell.edu/ns/vitro/0.7#"
-    xmlns:vann="http://purl.org/vocab/vann/"
-    xmlns:skos="http://www.w3.org/2008/05/skos#"
-    xmlns:swvs="http://www.w3.org/2003/06/sw-vocab-status/ns#"
-    xmlns:owl="http://www.w3.org/2002/07/owl#"
-    xmlns:fabio="http://purl.org/spar/fabio/"
-    xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#">
-  
-    <owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#decimal"
-    >0.7</owl:versionInfo>
-
- 
-  <owl:Class rdf:about="http://vivoweb.org/ontology/core#ConceptSemanticType">
-    <vitro:exampleAnnot rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
-    >Semantic Type for given concept, for example UMLS's type returned for concepts</vitro:exampleAnnot>
-    <vitro:descriptionAnnot rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
-    >Semantic Type for given concept, for example UMLS's type returned for concepts.</vitro:descriptionAnnot>
-    
-    <vitro:shortDef rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
-    >Concept Semantic Type</vitro:shortDef>
-  </owl:Class>
-  
-   <owl:ObjectProperty rdf:about="http://vivoweb.org/ontology/core#hasConceptSemanticType">
-    <rdfs:range rdf:resource="http://vivoweb.org/ontology/core#ConceptSemanticType"/>
-    <owl:inverseOf rdf:resource="http://vivoweb.org/ontology/core#isConceptSemanticTypeOf"/>
-  </owl:ObjectProperty>
- 
-</rdf:RDF>

productMods/templates/freemarker/body/individual/individual--foaf-person-2column.ftl

@@ -10,6 +10,9 @@
 <#if !labelCount??>
     <#assign labelCount = 0 >
 </#if>
+<#if !localesCount??>
+	<#assign localesCount = 1>
+</#if>
 <#assign qrCodeIcon = "qr-code-icon.png">
 <#assign visRequestingTemplate = "foaf-person-2column">
 <section id="individual-intro" class="vcard person" role="region">
@@ -40,7 +43,7 @@
             <#else>  
                 <h1 class="vcard foaf-person fn" <#if !editable>style="float:left;border-right:1px solid #A6B1B0;"</#if>> 
                     <#-- Label -->
-                    <@p.label individual editable labelCount/>
+                    <@p.label individual editable labelCount localesCount/>
                 </h1>
                 <#--  Display preferredTitle if it exists; otherwise mostSpecificTypes -->
                 <#assign title = propertyGroups.pullProperty("${core}preferredTitle")!>

productMods/templates/freemarker/body/individual/individual--foaf-person-quickview.ftl

@@ -12,6 +12,9 @@
 <#if !labelCount??>
     <#assign labelCount = 0 >
 </#if>
+<#if !localesCount??>
+	<#assign localesCount = 1>
+</#if>
 <#assign qrCodeIcon = "qr-code-icon.png">
 <#assign individualImage>
     <@p.image individual=individual 
@@ -52,7 +55,7 @@
                 <div id="photo-wrapper">${individualImage}</div>
                 <h1 class="vcard foaf-person fn" <#if !editable>style="float:left;border-right:1px solid #A6B1B0;"</#if>> 
                     <#-- Label -->
-                    <@p.label individual editable labelCount/>
+                    <@p.label individual editable labelCount localesCount/>
                 </h1>
                 <#--  Display preferredTitle if it exists; otherwise mostSpecificTypes -->
                 <#assign title = propertyGroups.pullProperty("${core}preferredTitle")!>

productMods/templates/freemarker/body/individual/manageLabelsForIndividualTerms.ftl

@@ -0,0 +1,4 @@
+<#-- $This file is distributed under the terms of the license in /doc/license.txt$ -->
+
+<#--Some values for labels etc. may be different between vitro and other systems -->
+<#assign returnText = "${i18n().return_to_profile}" />

productMods/templates/freemarker/edit/forms/addAssociatedConcept.ftl

@@ -51,6 +51,9 @@
                    	<#if existingConcept.vocabURI?has_content && existingConcept.vocabLabel?has_content>
                    		(${existingConcept.vocabLabel})
                    	</#if>
+                   	<#if existingConcept.conceptSemanticTypeLabel?has_content>
+                   	 ${existingConcept.conceptSemanticTypeLabel}
+                   	</#if>
                    </span> 
                 </span>
                 &nbsp;<a href="${urls.base}/edit/primitiveRdfEdit" class="remove" title="${i18n().remove_capitalized}">${i18n().remove_capitalized}</a>

rdf/abox/filegraph/vocabularySource.n3

@@ -1,3 +1,6 @@
 <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> .
 <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> .
 <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> .
+<http://link.informatics.stonybrook.edu/umls> <http://www.w3.org/2000/01/rdf-schema#label> "UMLS"^^<http://www.w3.org/2001/XMLSchema#string>  .
+<http://aims.fao.org/aos/agrovoc/agrovocScheme> <http://www.w3.org/2000/01/rdf-schema#label> "AGROVOC"^^<http://www.w3.org/2001/XMLSchema#string>  .
+<http://www.eionet.europa.eu/gemet/gemetThesaurus> <http://www.w3.org/2000/01/rdf-schema#label> "GEMET"^^<http://www.w3.org/2001/XMLSchema#string>  . 

rdf/abox/firsttime/vocabularySource-labels.n3

@@ -1,3 +0,0 @@
-<http://link.informatics.stonybrook.edu/umls> <http://www.w3.org/2000/01/rdf-schema#label> "UMLS"^^<http://www.w3.org/2001/XMLSchema#string>  .
-<http://aims.fao.org/aos/agrovoc/agrovocScheme> <http://www.w3.org/2000/01/rdf-schema#label> "AGROVOC"^^<http://www.w3.org/2001/XMLSchema#string>  .
-<http://www.eionet.europa.eu/gemet/gemetThesaurus> <http://www.w3.org/2000/01/rdf-schema#label> "GEMET"^^<http://www.w3.org/2001/XMLSchema#string>  . 

src/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/generators/AddAssociatedConceptGenerator.java

@@ -396,37 +396,38 @@ public class AddAssociatedConceptGenerator  extends VivoBaseGenerator implements
 	}
 	
     
+	//To determine whether or not a concept is a user generated or one from an external vocab source.
+	//we cannot rely on whether or not it is a skos concept because incorporating UMLS semantic network classes as
+	//SKOS concept subclasses means that even concepts from an external vocab source might be considered SKOS concepts
+	//Instead, we will simply determine whether a concept is defined by an external vocabulary source and use that
+	//as the primary indicator of whether a concept is from an external vocabulary source or a user generated concept
 	private List<AssociatedConceptInfo> getAssociatedConceptInfo(
 			List<Individual> concepts, VitroRequest vreq) {
 		List<AssociatedConceptInfo> info = new ArrayList<AssociatedConceptInfo>();
 		 for ( Individual conceptIndividual : concepts ) {
-			 	boolean isSKOSConcept = false;
+			 	boolean userGenerated = true;
+			 	//Note that this isn't technically 
 			 	String conceptUri =  conceptIndividual.getURI();
 			 	String conceptLabel = conceptIndividual.getName();
 
-			 	//Check if SKOS Concept type
+			 	//Check if defined by an external vocabulary source
-			 	List<ObjectPropertyStatement> osl = conceptIndividual.getObjectPropertyStatements(RDF.type.getURI());
+		 		List<ObjectPropertyStatement> vocabList = conceptIndividual.getObjectPropertyStatements(RDFS.isDefinedBy.getURI());
-			 	for(ObjectPropertyStatement os: osl) {
+		 		String vocabSource = null;
-			 		if(os.getObjectURI().equals(SKOSConceptType)) {
+		 		String vocabLabel = null;
-			 			isSKOSConcept = true;
+		 		if(vocabList != null && vocabList.size() > 0) {
-			 			break;
+		 			userGenerated = false;
-			 		}
+		 			vocabSource = vocabList.get(0).getObjectURI();
-			 	}
+		 			Individual sourceIndividual = EditConfigurationUtils.getIndividual(vreq, vocabSource);
+		 			//Assuming name will get label
+		 			vocabLabel = sourceIndividual.getName();
+		 		}
 		 		
-			 	if(isSKOSConcept) {
+			 	
+			 	
+			 	if(userGenerated) {
 			 		//if the concept in question is skos - which would imply a user generated concept
 			 		info.add(new AssociatedConceptInfo(conceptLabel, conceptUri, null, null, SKOSConceptType, null, null));
 			 	} else {
-			 		//Get the vocab source and vocab label
-			 		List<ObjectPropertyStatement> vocabList = conceptIndividual.getObjectPropertyStatements(RDFS.isDefinedBy.getURI());
-			 		String vocabSource = null;
-			 		String vocabLabel = null;
-			 		if(vocabList != null && vocabList.size() > 0) {
-			 			vocabSource = vocabList.get(0).getObjectURI();
-			 			Individual sourceIndividual = EditConfigurationUtils.getIndividual(vreq, vocabSource);
-			 			//Assuming name will get label
-			 			vocabLabel = sourceIndividual.getName();
-			 		}
 			 		String conceptSemanticTypeURI = null;
 			 		String conceptSemanticTypeLabel = null;
 			 		//Can a concept have multiple semantic types?  Currently we are only returning the first one
@@ -439,7 +440,6 @@ public class AddAssociatedConceptGenerator  extends VivoBaseGenerator implements
 			 			conceptSemanticTypeLabel = typeAndLabel.get("semanticTypeLabel");
 			 		}
 
-
 			 		//Assuming this is from an external vocabulary source
 			 		info.add(new AssociatedConceptInfo(conceptLabel, conceptUri, vocabSource, vocabLabel, null, conceptSemanticTypeURI, conceptSemanticTypeLabel));
 

src/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/preprocessors/AddAssociatedConceptsPreprocessor.java

@@ -84,6 +84,8 @@ public class AddAssociatedConceptsPreprocessor extends
 			//This will put the URI value in scope for the first semantic type label
 			//and generate the rest if need be
 			processConceptSemanticValues();
+			//Also need to see if any broader or narrower uris for the concepts that already exist in the system
+			//and set up the appropriate relationships between this concept and the broader/narrower uri
 			if (numberConcepts > 1) {
 				processConceptNodes(numberConcepts);
 			}

src/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/preprocessors/ConceptSemanticTypesPreprocessor.java

@@ -0,0 +1,125 @@
+/* $This file is distributed under the terms of the license in /doc/license.txt$ */
+
+package edu.cornell.mannlib.vitro.webapp.edit.n3editing.configuration.preprocessors;
+
+import javax.servlet.http.HttpServletRequest;
+
+import org.apache.commons.logging.Log;
+import org.apache.commons.logging.LogFactory;
+
+import com.hp.hpl.jena.ontology.OntModel;
+import com.hp.hpl.jena.query.Dataset;
+import com.hp.hpl.jena.query.Query;
+import com.hp.hpl.jena.query.QueryExecution;
+import com.hp.hpl.jena.query.QueryExecutionFactory;
+import com.hp.hpl.jena.query.QueryFactory;
+import com.hp.hpl.jena.query.QuerySolutionMap;
+import com.hp.hpl.jena.query.Syntax;
+import com.hp.hpl.jena.rdf.model.Literal;
+import com.hp.hpl.jena.rdf.model.Model;
+import com.hp.hpl.jena.rdf.model.ModelFactory;
+import com.hp.hpl.jena.rdf.model.Property;
+import com.hp.hpl.jena.rdf.model.ResIterator;
+import com.hp.hpl.jena.rdf.model.Resource;
+import com.hp.hpl.jena.rdf.model.ResourceFactory;
+import com.hp.hpl.jena.rdf.model.Statement;
+import com.hp.hpl.jena.shared.Lock;
+import com.hp.hpl.jena.vocabulary.RDF;
+import com.hp.hpl.jena.vocabulary.RDFS;
+
+import edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary;
+import edu.cornell.mannlib.vitro.webapp.dao.jena.DatasetWrapper;
+import edu.cornell.mannlib.vitro.webapp.dao.jena.DatasetWrapperFactory;
+
+//We are representing semantic types from the UMLS Semantic Network as OWL Classes
+//and this preprocessor will add the appropriate class information to the TBox
+
+public class ConceptSemanticTypesPreprocessor implements ModelChangePreprocessor {
+
+	private static String VIVOCore = "http://vivoweb.org/ontology/core#";
+	private static String SKOSConceptType = "http://www.w3.org/2004/02/skos/core#Concept";	
+	private Log log = LogFactory.getLog(ConceptSemanticTypesPreprocessor.class);
+
+	private OntModel toUpdateModel = null;
+	
+	//Custom constructor
+	public ConceptSemanticTypesPreprocessor(OntModel updateModel) {
+		this.toUpdateModel = updateModel;
+	}
+	
+	@Override
+	public void preprocess(Model retractionsModel, Model additionsModel,
+			HttpServletRequest request) {
+		//Run a construct query against the additions model
+		String prefixes = "PREFIX rdfs:<" + RDFS.getURI() + "> " + 
+		"PREFIX owl:<http://www.w3.org/2002/07/owl#> " + 
+		"PREFIX rdf:<" + RDF.getURI() + ">" + 
+		"PREFIX skos:<http://www.w3.org/2004/02/skos/core#>";		
+		String constructQuery = prefixes + " CONSTRUCT { " + 
+				"?semanticType rdf:type owl:Class.  " + 
+				"?semanticType rdfs:subClassOf skos:Concept .  " + 
+				"?semanticType rdfs:label ?label.  " + 
+			"} WHERE { " + 
+				"?concept rdf:type ?semanticType.  " + 
+				"?semanticType rdfs:label ?label . " + 
+				"?semanticType rdfs:subClassOf skos:Concept . " + 
+			"}";
+		
+		//Execute construct query 
+		 Model constructedModel = ModelFactory.createDefaultModel();
+	        
+	       
+        log.debug("CONSTRUCT query string " + constructQuery);
+        
+        Query query = null;
+        try {
+            query = QueryFactory.create(constructQuery, Syntax.syntaxARQ);
+        } catch(Throwable th){
+            log.error("Could not create CONSTRUCT SPARQL query for query " +
+                      "string. " + th.getMessage());
+            log.error(constructQuery);
+            return;
+        } 
+	        
+	           
+	        
+        additionsModel.getLock().enterCriticalSection(Lock.READ);
+        QueryExecution qe = null;
+        try {                           
+            qe = QueryExecutionFactory.create(
+                    query, additionsModel);
+            qe.execConstruct(constructedModel);
+        } catch (Exception e) {
+            log.error("Error getting constructed model for query string " + constructQuery);
+        } finally {
+            if (qe != null) {
+                qe.close();
+            }
+            additionsModel.getLock().leaveCriticalSection();
+        }
+        
+        //Add constructed model to the designated update model
+        toUpdateModel.enterCriticalSection(Lock.WRITE);
+        try {
+        	toUpdateModel.add(constructedModel);
+        } catch (Exception e) {
+            log.error("Error adding statements to update model for " + constructQuery);
+        } finally {
+        	toUpdateModel.leaveCriticalSection();
+        }
+        
+        //Take this constructed model and remove from the additions model
+        additionsModel.enterCriticalSection(Lock.WRITE);
+        try {
+        	additionsModel.remove(constructedModel.listStatements().toList());
+        } catch (Exception e) {
+            log.error("Error removing statements from additions model for " + constructQuery);
+        } finally {
+            additionsModel.leaveCriticalSection();
+        }
+        
+    }
+		
+
+
+}

themes/wilma/i18n/all.properties

@@ -280,7 +280,6 @@ change_selection = change selection
 # custom form templates ( /templates/freemarker/edit/forms ) 
 #
 manage_concepts = Manage Concepts
-remove_capitalized = Remove
 no_concepts_specified = There are currently no concepts specified.
 return_to_profile = Return to Profile Page
 external_vocabulary_services = External Vocabulary Services

themes/wilma/templates/individual--foaf-person.ftl

@@ -11,6 +11,9 @@
 <#if !labelCount??>
     <#assign labelCount = 0 >
 </#if>
+<#if !localesCount??>
+	<#assign localesCount = 1>
+</#if>
 <#assign visRequestingTemplate = "foaf-person-wilma">
 <section id="individual-intro" class="vcard person" role="region">
 
@@ -55,7 +58,7 @@
             <#else>                
                 <h1 class="vcard foaf-person">
                     <#-- Label -->
-                    <span class="fn"><@p.label individual editable labelCount/></span>
+                    <span class="fn"><@p.label individual editable labelCount localesCount/></span>
 
                     <#--  Display preferredTitle if it exists; otherwise mostSpecificTypes -->
                     <#assign title = propertyGroups.pullProperty("${core}preferredTitle")!>