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updates to remove errant file and updates for adding concept

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This commit is contained in:
hudajkhan 2013-08-22 15:48:56 -04:00
parent 4b52ccd687
commit 0511404a47
5 changed files with 258 additions and 60 deletions
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1
.gitignore vendored
View file

@ -6,3 +6,4 @@
/deploy.properties
/build.properties
/runtime.properties
/ontology/public/catalog-v0001.xml

5
ontology/public/catalog-v001.xml
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@ -1,5 +0,0 @@
<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<catalog prefer="public" xmlns="urn:oasis:names:tc:entity:xmlns:xml:catalog">
<uri id="User Entered Import Resolution" name="http://vivoweb.org/ontology/core/vivo-c4o-public-1.5.owl" uri="vivo-core-public-1.5.owl"/>
<group id="Folder Repository, directory=, recursive=true, Auto-Update=true, version=2" prefer="public" xml:base=""/>
</catalog>

47
productMods/WEB-INF/filegraph/tbox/ConceptSemanticType.owl Normal file
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@ -0,0 +1,47 @@
<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>

36
src/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/generators/AddAssociatedConceptGenerator.java
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@ -16,6 +16,7 @@ import javax.servlet.http.HttpSession;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import com.hp.hpl.jena.ontology.OntModel;
import com.hp.hpl.jena.rdf.model.Literal;
import com.hp.hpl.jena.rdf.model.Model;
import com.hp.hpl.jena.vocabulary.RDF;
@ -27,6 +28,7 @@ import edu.cornell.mannlib.vitro.webapp.beans.ObjectProperty;
import edu.cornell.mannlib.vitro.webapp.beans.ObjectPropertyStatement;
import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
import edu.cornell.mannlib.vitro.webapp.controller.freemarker.UrlBuilder;
import edu.cornell.mannlib.vitro.webapp.dao.ModelAccess;
import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory;
import edu.cornell.mannlib.vitro.webapp.edit.n3editing.VTwo.EditConfigurationUtils;
import edu.cornell.mannlib.vitro.webapp.edit.n3editing.VTwo.EditConfigurationVTwo;
@ -85,7 +87,7 @@ public class AddAssociatedConceptGenerator extends VivoBaseGenerator implements
setTemplate(editConfiguration, vreq);
// No validators required here
// Add preprocessors
addPreprocessors(editConfiguration, vreq.getWebappDaoFactory());
addPreprocessors(editConfiguration, ModelAccess.on(vreq).getJenaOntModel());
// Adding additional data, specifically edit mode
addFormSpecificData(editConfiguration, vreq);
// One override for basic functionality, changing url pattern
@ -174,8 +176,10 @@ public class AddAssociatedConceptGenerator extends VivoBaseGenerator implements
private List<String> generateN3Optional() {
return list("?conceptNode <" + RDFS.label.getURI() + "> ?conceptLabel .\n" +
"?conceptNode <" + RDFS.isDefinedBy.getURI() + "> ?conceptSource .",
"?conceptNode <" + VIVOCore + "conceptSemanticType> ?conceptSemanticTypeURI ." +
"?conceptSemanticTypeURI <" + RDFS.label.getURI() + "> ?conceptSemanticTypeLabel ."
"?conceptNode <" + VIVOCore + "hasConceptSemanticType> ?conceptSemanticTypeURI ." +
"?conceptSemanticTypeURI <" + VIVOCore + "isConceptSemanticTypeOf> ?conceptNode ." +
"?conceptSemanticTypeURI <" + RDFS.label.getURI() + "> ?conceptSemanticTypeLabel ." +
"?conceptSemanticTypeURI <" + RDF.type.getURI() + "> <" + VIVOCore + "ConceptSemanticType> ."
);
}
@ -190,7 +194,7 @@ public class AddAssociatedConceptGenerator extends VivoBaseGenerator implements
//There are no new resources here, the concept node uri doesn't
//get created but already exists, and vocab uri should already exist as well
//Adding concept semantic type uri just to test - note this isn't really on the form at all
//newResources.put("conceptSemanticTypeURI", null);
newResources.put("conceptSemanticTypeURI", null);
return newResources;
}
@ -239,11 +243,11 @@ public class AddAssociatedConceptGenerator extends VivoBaseGenerator implements
//The URI of the node that defines the concept
urisOnForm.add("conceptNode");
urisOnForm.add("conceptSource");
// urisOnForm.add("conceptSemanticTypeURI");
urisOnForm.add("conceptSemanticTypeURI");
editConfiguration.setUrisOnform(urisOnForm);
//Also need to add the label of the concept
literalsOnForm.add("conceptLabel");
// literalsOnForm.add("conceptSemanticTypeLabel");
literalsOnForm.add("conceptSemanticTypeLabel");
editConfiguration.setLiteralsOnForm(literalsOnForm);
}
@ -272,8 +276,8 @@ public class AddAssociatedConceptGenerator extends VivoBaseGenerator implements
setConceptNodeField(editConfiguration, vreq);
setConceptLabelField(editConfiguration, vreq);
setVocabURIField(editConfiguration, vreq);
//setConceptSemanticTypeURIField(editConfiguration,vreq);
//setConceptSemanticTypeLabelField(editConfiguration,vreq);
setConceptSemanticTypeURIField(editConfiguration,vreq);
setConceptSemanticTypeLabelField(editConfiguration,vreq);
}
//this field will be hidden and include the concept node URI
@ -321,12 +325,14 @@ public class AddAssociatedConceptGenerator extends VivoBaseGenerator implements
//Add preprocessor
private void addPreprocessors(EditConfigurationVTwo editConfiguration, WebappDaoFactory wadf) {
private void addPreprocessors(EditConfigurationVTwo editConfiguration, OntModel ontModel) {
//An Edit submission preprocessor for enabling addition of multiple terms for a single search
//TODO: Check if this is the appropriate way of getting model
//Passing model to check for any URIs that are present
editConfiguration.addEditSubmissionPreprocessor(
new AddAssociatedConceptsPreprocessor(editConfiguration, wadf));
new AddAssociatedConceptsPreprocessor(editConfiguration, ontModel));
}
@ -412,13 +418,13 @@ public class AddAssociatedConceptGenerator extends VivoBaseGenerator implements
String conceptSemanticTypeURI = null;
String conceptSemanticTypeLabel = null;
//Can a concept have multiple semantic types? Currently we are only returning the first one
/*
List<ObjectPropertyStatement> semanticTypeStatements = conceptIndividual.getObjectPropertyStatements(VIVOCore + "conceptSemanticType");
List<ObjectPropertyStatement> semanticTypeStatements = conceptIndividual.getObjectPropertyStatements(VIVOCore + "hasConceptSemanticType");
if(semanticTypeStatements.size() > 0) {
conceptSemanticTypeURI = semanticTypeStatements.get(0).getObjectURI();
Individual conceptSemanticTypeIndividual = EditConfigurationUtils.getIndividual(vreq, conceptSemanticTypeURI);
conceptSemanticTypeLabel = conceptSemanticTypeIndividual.getName();
}*/
}
//get label
//Assuming this is from an external vocabulary source
@ -443,8 +449,8 @@ public class AddAssociatedConceptGenerator extends VivoBaseGenerator implements
this.vocabURI = inputVocabURI;
this.vocabLabel = inputVocabLabel;
this.type = inputType;
//this.conceptSemanticTypeURI = inputConceptSemanticTypeURI;
//this.conceptSemanticTypeLabel = inputConceptSemanticTypeLabel;
this.conceptSemanticTypeURI = inputConceptSemanticTypeURI;
this.conceptSemanticTypeLabel = inputConceptSemanticTypeLabel;
}
//Getters

227
src/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/preprocessors/AddAssociatedConceptsPreprocessor.java
View file

@ -4,18 +4,27 @@ package edu.cornell.mannlib.vitro.webapp.edit.n3editing.configuration.preprocess
import java.util.ArrayList;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
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.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.ResultSet;
import com.hp.hpl.jena.rdf.model.Literal;
import com.hp.hpl.jena.rdf.model.Resource;
import com.hp.hpl.jena.vocabulary.RDF;
import com.hp.hpl.jena.vocabulary.RDFS;
import com.hp.hpl.jena.vocabulary.XSD;
import edu.cornell.mannlib.vitro.webapp.beans.Individual;
import edu.cornell.mannlib.vitro.webapp.dao.WebappDaoFactory;
import edu.cornell.mannlib.vitro.webapp.edit.n3editing.VTwo.BaseEditSubmissionPreprocessorVTwo;
import edu.cornell.mannlib.vitro.webapp.edit.n3editing.VTwo.EditConfigurationUtils;
import edu.cornell.mannlib.vitro.webapp.edit.n3editing.VTwo.EditConfigurationVTwo;
@ -27,13 +36,18 @@ public class AddAssociatedConceptsPreprocessor extends
protected static final Log log = LogFactory
.getLog(AddAssociatedConceptsPreprocessor.class.getName());
protected WebappDaoFactory wadf = null;
//TODO: Check if better way to do this?
protected OntModel ontModel = null;
// Field names/variables names for n3 - these will have numbers added as
// suffix if more than one term
private static String conceptNodeBase = "conceptNode";
private static String sourceBase = "conceptSource";
private static String labelBase = "conceptLabel";
private static String conceptSemanticTypeLabelBase = "conceptSemanticTypeLabel";
private static String conceptSemanticTypeURIBase = "conceptSemanticTypeURI";
//keyed off label variable, specifies which uri variable should be used, useful if same label repeated twice
private HashMap<String, String> labelVarToUriVarHash = null;
//Also storing submission values
private static String conceptNodeValues = null;
private static String conceptLabelValues = null;
@ -46,9 +60,10 @@ public class AddAssociatedConceptsPreprocessor extends
// Will be editing the edit configuration as well as edit submission here
public AddAssociatedConceptsPreprocessor(EditConfigurationVTwo editConfig, WebappDaoFactory wadf) {
public AddAssociatedConceptsPreprocessor(EditConfigurationVTwo editConfig, OntModel ontModel) {
super(editConfig);
this.wadf = wadf;
this.ontModel = ontModel;
this.labelVarToUriVarHash = new HashMap<String, String>();
}
public void preprocess(MultiValueEditSubmission inputSubmission) {
@ -57,12 +72,14 @@ public class AddAssociatedConceptsPreprocessor extends
// as vocab uri (which is based on thge
// For query parameters, check whether CUI
copySubmissionValues();
//This will put the URI value in scope for the first semantic type label
//and generate the rest if need be
//processConceptSemanticValues();
if (conceptNodeValues != null) {
String[] conceptNodes = convertDelimitedStringToArray(conceptNodeValues);
int numberConcepts = conceptNodes.length;
//This will put the URI value in scope for the first semantic type label
//and generate the rest if need be
processConceptSemanticValues();
if (numberConcepts > 1) {
processConceptNodes(numberConcepts);
}
@ -80,6 +97,7 @@ public class AddAssociatedConceptsPreprocessor extends
conceptLabelValues = getConceptLabelValues();
conceptNodeValues = getConceptNodeValues();
conceptSourceValues = getConceptSourceValues();
log.debug("concept label values are " + conceptLabelValues);
}
@ -94,14 +112,11 @@ public class AddAssociatedConceptsPreprocessor extends
}
//This is for additional concept nodes (i.e. if user selects more than one concept)
private void processConceptNodes(int numberConcepts) {
//There are no "new" resources b/c the concept nodes are URIs from external vocabularies
//New resources for concept semantic type uris
addNewResources(numberConcepts);
// Add N3Required
addN3Required(numberConcepts);
//Add N3 Optional as well
@ -115,6 +130,31 @@ public class AddAssociatedConceptsPreprocessor extends
}
//This is specifically for concept semantic type URIs which may need to be generated
private void addNewResources(int numberConcepts) {
// TODO Auto-generated method stub
addConceptSemanticTypeURIResources(numberConcepts);
}
private void addConceptSemanticTypeURIResources(int numberConcepts) {
String[] conceptSemanticTypeURIs= convertDelimitedStringToArray(conceptSemanticTypeURIValues);
//the number of existing values may not match up, or at least existing populated ones
if(conceptSemanticTypeURIs != null && conceptSemanticTypeURIs.length == numberConcepts) {
int i;
for(i = 0; i < numberConcepts; i++) {
int suffix = i + 1;
String newResourceName = conceptSemanticTypeURIBase + suffix;
editConfiguration.addNewResource(newResourceName, null);
}
} else if(conceptSemanticTypeURIs != null && conceptSemanticTypeURIs.length != numberConcepts){
log.error("Number of concept semantic type uris does not match the number of concepts");
} else{
log.error("Concept semantic type uris returned as null");
}
}
//This is where the actual values will be submitted as if they were separate input fields
//Each field name will correspond to the names of the fileds/uris on form/literals on form
//generated here
@ -126,8 +166,8 @@ public class AddAssociatedConceptsPreprocessor extends
addConceptSourceInputs(numberConcepts);
addConceptLabelInputs(numberConcepts);
//for concept semantic type labels and uris where they exist
//addConceptSemanticTypeLabelInputs(numberConcepts);
//addConceptSemanticTypeURIInputs(numberConcepts);
addConceptSemanticTypeLabelInputs(numberConcepts);
addConceptSemanticTypeURIInputs(numberConcepts);
}
@ -199,11 +239,51 @@ public class AddAssociatedConceptsPreprocessor extends
}
private void addConceptSemanticTypeLabelInputs(int numberConcepts) {
String[] labels = convertDelimitedStringToArray(conceptSemanticTypeLabelValues);
if(labels != null && labels.length == numberConcepts) {
int i;
for(i = 0; i < numberConcepts; i++) {
int suffix = i + 1;
String labelInputName = conceptSemanticTypeLabelBase + suffix;
String[] labelValues = new String[1];
labelValues[0] = labels[i];
//TODO: Check if there are no funky typed information also stored
//At this point the field should already have been added to edit configuration
FieldVTwo labelField = editConfiguration.getField(labelInputName);
//TODO: Also check to see whether the label is actually populate or will n3 editing take care of that?
if(labelField != null) {
submission.addLiteralToForm(editConfiguration, labelField, labelInputName, labelValues);
} else {
log.error("Corresponding field for " + labelInputName + " was not added to edit configuration");
}
}
} else if(labels != null && labels.length != numberConcepts){
log.error("Number of concept semantic type labels did not match the number of concepts to be added");
} else{
log.error("Concept labels returned were null");
}
}
private void addConceptSemanticTypeURIInputs(int numberConcepts) {
String[] conceptSemanticTypeURIs= convertDelimitedStringToArray(conceptSemanticTypeURIValues);
//the number of existing values may not match up, or at least existing populated ones
if(conceptSemanticTypeURIs != null && conceptSemanticTypeURIs.length == numberConcepts) {
int i;
for(i = 0; i < numberConcepts; i++) {
int suffix = i + 1;
String conceptInputName = conceptSemanticTypeURIBase + suffix;
String[] uriValues = new String[1];
uriValues[0] = conceptSemanticTypeURIs[i];
//Add value for uri to form
//TODO: Check if value is empty in which case don't add to submission
submission.addUriToForm(editConfiguration, conceptInputName, uriValues);
}
} else if(conceptSemanticTypeURIs != null && conceptSemanticTypeURIs.length != numberConcepts){
log.error("Number of concept nodes did not match the number of concepts to be added");
} else{
log.error("Concept nodes returned were null");
}
}
//Fields
@ -218,10 +298,16 @@ public class AddAssociatedConceptsPreprocessor extends
String conceptNode = conceptNodeBase + suffix;
String label = labelBase + suffix;
String source = sourceBase + suffix;
String conceptSemanticTypeLabel = conceptSemanticTypeLabelBase + suffix;
String conceptSemanticTypeURI = conceptSemanticTypeURIBase + suffix;
addConceptNodeField(conceptNode);
addLabelField(label);
addSourceField(source);
//Also add fields for concept semantic type label
addConceptSemanticTypeLabelField(conceptSemanticTypeLabel);
//and concept semantic type URI
addConceptSemanticTypeURIField(conceptSemanticTypeURI);
}
}
@ -247,6 +333,21 @@ public class AddAssociatedConceptsPreprocessor extends
}
//Will need to check whether or not semantic type label even exists though?
private void addConceptSemanticTypeLabelField(String label) {
editConfiguration.addField(new FieldVTwo().
setName(label).
setRangeDatatypeUri(XSD.xstring.toString())
);
}
private void addConceptSemanticTypeURIField(String conceptSemanticTypeURI) {
editConfiguration.addField(new FieldVTwo().
setName(conceptSemanticTypeURI));
}
//original literals on form: label, uris on form: conceptNode and conceptSource
//This will overwrite the original values in the edit configuration
private void addLiteralsAndUrisOnForm(int numberTerms) {
@ -261,9 +362,13 @@ public class AddAssociatedConceptsPreprocessor extends
String conceptNode = conceptNodeBase + suffix;
String label = labelBase + suffix;
String source = sourceBase + suffix;
String conceptSemanticTypeLabel = conceptSemanticTypeLabelBase + suffix;
String conceptSemanticTypeURI = conceptSemanticTypeURIBase + suffix;
urisOnForm.add(conceptNode);
urisOnForm.add(source);
urisOnForm.add(conceptSemanticTypeURI);
literalsOnForm.add(label);
literalsOnForm.add(conceptSemanticTypeLabel);
}
editConfiguration.setUrisOnform(urisOnForm);
editConfiguration.setLiteralsOnForm(literalsOnForm);
@ -279,8 +384,7 @@ public class AddAssociatedConceptsPreprocessor extends
List<String> n3Required = new ArrayList<String>();
int index;
String nodeBase = "?" + conceptNodeBase;
String labelVar = "?" + labelBase;
String sourceVar = "?" + sourceBase;
String prefixStr = "@prefix core: <http://vivoweb.org/ontology/core#> .";
// First one already included so add new ones here
for (index = 1; index <= numberConcepts; index++) {
@ -293,23 +397,30 @@ public class AddAssociatedConceptsPreprocessor extends
editConfiguration.setN3Required(n3Required);
}
//Add n3 optional
//TODO: Rewrite optional N3
private void addN3Optional(int numberConcepts) {
List<String> n3Optional = new ArrayList<String>();
int index;
String nodeBase = "?" + conceptNodeBase;
String labelVar = "?" + labelBase;
String sourceVar = "?" + sourceBase;
String conceptSemanticTypeLabelVar = "?" + conceptSemanticTypeLabelBase;
String conceptSemanticTypeURIVar = "?" + conceptSemanticTypeURIBase;
String prefixStr = "@prefix core: <http://vivoweb.org/ontology/core#> .";
// First one already included so add new ones here
for (index = 1; index <= numberConcepts; index++) {
int suffix = index;
String node = nodeBase + suffix;
String label = labelVar + suffix;
String source = sourceVar + suffix;
String conceptSemanticTypeLabel = conceptSemanticTypeLabelVar + suffix;
String conceptSemanticTypeURI = conceptSemanticTypeURIVar + suffix;
String n3String = prefixStr;
n3String += node + " <" + RDFS.label.getURI() + "> " + label + " .\n" +
node + " <" + RDFS.isDefinedBy.getURI() + "> " + source + " .";
n3String += node + " core:hasConceptSemanticType " + conceptSemanticTypeURI + " ." +
conceptSemanticTypeURI + " core:isConceptSemanticTypeOf " + node + ". " +
conceptSemanticTypeURI + " <" + RDFS.label.getURI() + "> " + conceptSemanticTypeLabel + " .\n" +
conceptSemanticTypeURI + " <" + RDF.type.getURI() + "> core:ConceptSemanticType .\n" ;
n3Optional.add(n3String);
}
//Already have n3 required so need to add to that
@ -357,33 +468,71 @@ public class AddAssociatedConceptsPreprocessor extends
//This will either generate or retrieve URIs for the concept semantic type labels if they exist
//We will then update the submission to include this
private String getConceptSemanticTypeURIValues() {
List<String> conceptSemanticTypeURIs = new ArrayList<String>();
String[] conceptSemanticTypeLabels = convertDelimitedStringToArray(conceptSemanticTypeLabelValues);
//keep track of unique labels
HashSet<String> allSemanticTypeLabels = new HashSet<String>();
int numberLabels = conceptSemanticTypeLabels.length;
String pseudoInputString = "";
for(int i = 0; i < numberLabels; i++) {
String label = conceptSemanticTypeLabels[i];
//if label not already in the hash, then create key
if(!allSemanticTypeLabels.contains(label)) {
}
//Make or retrieve URI for this label
String uri = getURIForSemanticTypeLabel(label);
conceptSemanticTypeURIs.add(uri);
if(i != 0) {
pseudoInputString += ",";
}
pseudoInputString += uri;
}
//Set uris as string
//Essentially this will allow the URI to be put in scope
return conceptSemanticTypeURIs.toString();
String[] urisToAdd = new String[1];
urisToAdd[0] = pseudoInputString;
log.debug("uris to add" + pseudoInputString);
submission.addUriToForm(this.editConfiguration, "conceptSemanticTypeURI", urisToAdd);
return pseudoInputString;
}
private String getURIForSemanticTypeLabel(String label) {
//Check if system has an individual with this URI
//
List<Individual> individualsWithLabel = this.wadf.getIndividualDao().getIndividualsByDataProperty(RDFS.label.getURI(), label);
//We are only interested in semantic type objects and this may return multiple elements (perhaps too many?
//getting the model requires servlet and context and we don't want to pass that here do we//Return all semantic type objects with this label
//this.modelSelector.
return null;
String existingURI = this.getExistingSemanticTypeURI(label);
if(existingURI != null) {
return existingURI;
}
//if we leave this as null, we should be able to generate a new resource
//empty string because there may be more than one value returned for labels
else return "";
}
private String getExistingSemanticTypeURI(String label) {
String queryStr = "SELECT ?semanticType WHERE { ?semanticType <" + RDF.type.getURI() + "> <http://vivoweb.org/ontology/core#ConceptSemanticType> . " +
"?semanticType <" + RDFS.label.getURI() + "> \"" + label + "\"^^<http://www.w3.org/2001/XMLSchema#string> . }";
QueryExecution qe = null;
try{
Query query = QueryFactory.create(queryStr);
qe = QueryExecutionFactory.create(query, this.ontModel);
ResultSet results = null;
results = qe.execSelect();
while( results.hasNext()){
QuerySolution qs = results.nextSolution();
if(qs.get("semanticType") != null) {
Resource semanticTypeURI = qs.getResource("semanticType");
log.debug("Semantic Type URI returned " + semanticTypeURI.getURI());
return semanticTypeURI.getURI();
}
}
}catch(Exception ex){
throw new Error("Error in executing query string: \n" + queryStr + '\n' + ex.getMessage());
}finally{
if( qe != null)
qe.close();
}
return null;
}
private Object getFirstElement(List inputList) {
if(inputList == null || inputList.size() == 0)
return null;