updates for adding concepts, including urls for agrovoc and umls services and updating person has educational training to add the inverse property from organization to educational training
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hjkhjk54
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c240321458
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49ff104d3a
7 changed files with 39 additions and 33 deletions
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@ -206,7 +206,7 @@ var addConceptForm = {
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var htmlAdd = "<li class='concepts'>" +
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"<div class='row'>" +
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"<span class='column conceptLabel'>" +
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addConceptForm.generateIndividualCUIInput(cuiURI, label, definition, type, definedBy) +
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addConceptForm.generateIndividualCUIInput(cuiURI, label, type, definedBy) +
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label + addConceptForm.generateIndividualTypeDisplay(type) + "</span>" +
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addConceptForm.generateIndividualDefinitionDisplay(definition) +
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"</div>" +
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@ -3,6 +3,7 @@
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<#assign existingConcepts = editConfiguration.pageData.existingConcepts/>
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<#assign userDefinedConceptUrl = editConfiguration.pageData.userDefinedConceptUrl/>
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<#assign sources = editConfiguration.pageData.searchServices/>
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<#--If edit submission exists, then retrieve validation errors if they exist-->
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<#if editSubmission?has_content && editSubmission.submissionExists = true && editSubmission.validationErrors?has_content>
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@ -10,10 +11,6 @@
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</#if>
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<#--This is set for testing purposes - will be retrieved dynamically from the generator later-->
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<#assign sources = [{"uri":"http://link.informatics.stonybrook.edu/umls/", "label":"UMLS"}, {"uri":"http://www.fao.org/webservices/Agrovoc", "label":"Agrovoc"}]/>
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<#assign selectedSource = "UMLS" />
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<h2>Manage Concepts</h2>
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@ -81,9 +78,9 @@
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</div>
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<form id="addConceptForm" class="customForm" action="${submitUrl}">
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<#list sources as source>
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<input type="radio" id="source" name="source" value="${source.uri}" role="radio" <#if selectedSource = source.uri>checked</#if> />
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<label class="inline" for="${source.label}"> ${source.label}</label>
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<#list sources?keys as sourceUri>
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<input type="radio" id="source" name="source" value="${sourceUri}" role="radio" />
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<label class="inline" for="${sources[sourceUri]}"> ${sources[sourceUri]}</label>
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<br />
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</#list>
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@ -66,7 +66,7 @@ public class AgrovocService implements ExternalConceptService {
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//XMLUtils.serializeNode(node); System.out.println();
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Concept concept = new Concept();
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concept.setDefinedBy("Agrovoc");
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concept.setDefinedBy("http://aims.fao.org/aos/agrovoc/agrovocScheme");
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concept.setConceptId(termcode);
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NamedNodeMap attrs = node.getAttributes();
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@ -82,7 +82,7 @@ public class UMLSService implements ExternalConceptService {
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JSONObject o = bestMatchArray.getJSONObject(i);
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//System.out.println(o.toString());
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Concept concept = new Concept();
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concept.setDefinedBy("UMLS");
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concept.setDefinedBy("http://link.informatics.stonybrook.edu/umls");
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concept.setBestMatch("true");
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String cui = getJsonValue(o, "CUI");
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bestMatchIdList.add(cui);
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@ -54,6 +54,7 @@ import edu.cornell.mannlib.vitro.webapp.edit.n3editing.VTwo.FieldVTwo;
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import edu.cornell.mannlib.vitro.webapp.web.MiscWebUtils;
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import edu.cornell.mannlib.vitro.webapp.search.beans.ProhibitedFromSearch;
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import edu.cornell.mannlib.vitro.webapp.utils.FrontEndEditingUtils;
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import edu.cornell.mannlib.vitro.webapp.utils.ConceptSearchService.ConceptSearchServiceUtils;
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import edu.cornell.mannlib.vitro.webapp.utils.FrontEndEditingUtils.EditMode;
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import edu.cornell.mannlib.vitro.webapp.utils.generators.EditModeUtils;
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/**
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@ -306,19 +307,12 @@ public class AddAssociatedConceptGenerator extends VivoBaseGenerator implements
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//Form specific data
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public void addFormSpecificData(EditConfigurationVTwo editConfiguration, VitroRequest vreq) {
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HashMap<String, Object> formSpecificData = new HashMap<String, Object>();
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//Existing concepts should probably be a hash map or a hash map of classes
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//with URI of concept node to label and information about existing URI
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//This would be a sparql query and would need to be run here?
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//-------------------->For test purposes
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List<AssociatedConceptInfo> testInfo = new ArrayList<AssociatedConceptInfo>();
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testInfo.add(new AssociatedConceptInfo("testLabel", "testURI", "testVocabURI", "testVocabLabel", null));
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testInfo.add(new AssociatedConceptInfo("user defined label", "testUserURI", null, null, "http://www.w3.org/2004/02/skos/core#Concept"));
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//Adding concepts
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testInfo.addAll(getExistingConcepts(vreq));
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formSpecificData.put("existingConcepts", testInfo);
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//These are the concepts that already exist currently
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formSpecificData.put("existingConcepts", getExistingConcepts(vreq));
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//Return url for adding user defined concept
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formSpecificData.put("userDefinedConceptUrl", getUserDefinedConceptUrl(vreq));
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//Add URIs and labels for different services
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formSpecificData.put("searchServices", ConceptSearchServiceUtils.getVocabSources());
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editConfiguration.setFormSpecificData(formSpecificData);
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}
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@ -342,17 +336,17 @@ public class AddAssociatedConceptGenerator extends VivoBaseGenerator implements
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//TODO: Check if sorted correctly
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sortConceptIndividuals(concepts);
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return getAssociatedConceptInfo(concepts);
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return getAssociatedConceptInfo(concepts, vreq);
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}
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private void sortConceptIndividuals(List<Individual> authorships) {
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private void sortConceptIndividuals(List<Individual> concepts) {
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DataPropertyComparator comp = new DataPropertyComparator(RDFS.label.getURI());
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Collections.sort(authorships, comp);
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Collections.sort(concepts, comp);
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}
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private List<AssociatedConceptInfo> getAssociatedConceptInfo(
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List<Individual> concepts) {
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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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@ -376,8 +370,9 @@ public class AddAssociatedConceptGenerator extends VivoBaseGenerator implements
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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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//vocab label? Right now set as same to vocab source until we get the correct input
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vocabLabel = vocabSource;
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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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info.add(new AssociatedConceptInfo(conceptLabel, conceptUri, vocabSource, vocabLabel, null));
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@ -89,7 +89,7 @@ public class PersonHasEducationalTraining extends VivoBaseGenerator implements
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conf.setN3Optional(Arrays.asList(
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n3ForEdTrainingToOrg, majorFieldAssertion, degreeAssertion,
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deptAssertion, infoAssertion,
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n3ForStart, n3ForEnd ));
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n3ForStart, n3ForEnd, n3ForOrgToEdTraining ));
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conf.addNewResource("edTraining", DEFAULT_NS_FOR_NEW_RESOURCE);
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conf.addNewResource("org",DEFAULT_NS_FOR_NEW_RESOURCE);
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@ -119,6 +119,8 @@ public class PersonHasEducationalTraining extends VivoBaseGenerator implements
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conf.addSparqlForExistingUris("endNode", existingEndNodeQuery);
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conf.addSparqlForExistingUris("startField-precision", existingStartPrecisionQuery);
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conf.addSparqlForExistingUris("endField-precision", existingEndPrecisionQuery);
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//Add sparql to include inverse property as well
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conf.addSparqlForAdditionalUrisInScope("inverseTrainingAtOrg", inverseTrainingAtOrgQuery);
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conf.addField( new FieldVTwo().
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setName("degree").
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@ -228,7 +230,9 @@ public class PersonHasEducationalTraining extends VivoBaseGenerator implements
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final static String n3ForEdTrainingToOrg =
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"?edTraining <"+ trainingAtOrg +"> ?org .";
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//The inverse of the above
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final static String n3ForOrgToEdTraining =
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"?org ?inverseTrainingAtOrg ?edTraining .";
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/* Queries for editing an existing educational training entry */
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final static String orgQuery =
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@ -318,6 +322,13 @@ public class PersonHasEducationalTraining extends VivoBaseGenerator implements
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"?endNode <"+ type +"> <"+ dateTimeValueType +"> .\n"+
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"?endNode <"+ dateTimePrecision +"> ?existingEndPrecision . }";
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//Query for inverse property
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final static String inverseTrainingAtOrgQuery =
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"PREFIX owl: <http://www.w3.org/2002/07/owl#>"
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+ " SELECT ?inverseTrainingAtOrg "
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+ " WHERE { ?inverseTrainingAtOrg owl:inverseOf <"+ trainingAtOrg +"> . } ";
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//Adding form specific data such as edit mode
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public void addFormSpecificData(EditConfigurationVTwo editConfiguration, VitroRequest vreq) {
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HashMap<String, Object> formSpecificData = new HashMap<String, Object>();
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@ -331,4 +342,6 @@ public class PersonHasEducationalTraining extends VivoBaseGenerator implements
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return EditModeUtils.getEditMode(vreq, predicates);
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}
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}
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@ -19,8 +19,9 @@ import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
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public class ConceptSearchServiceUtils {
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private static final Log log = LogFactory.getLog(ConceptSearchServiceUtils.class);
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//Get the appropriate search service class
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private static final String UMLSVocabSource = "http://link.informatics.stonybrook.edu/umls/";
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private static final String AgrovocVocabSource = "http://www.fao.org/webservices/Agrovoc";
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//TODO: Change this so retrieved from the system instead using a query
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private static final String UMLSVocabSource = "http://link.informatics.stonybrook.edu/umls";
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private static final String AgrovocVocabSource = "http://aims.fao.org/aos/agrovoc/agrovocScheme";
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//Get the class that corresponds to the appropriate search
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public static String getConceptSearchServiceClassName(String searchServiceName) {
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HashMap<String, String> map = getMapping();
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@ -44,8 +45,8 @@ public class ConceptSearchServiceUtils {
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//Get the hashmap mapping service name to Service class
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private static HashMap<String, String> getMapping() {
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HashMap<String, String> map = new HashMap<String, String>();
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map.put("http://link.informatics.stonybrook.edu/umls/", "edu.cornell.mannlib.semservices.service.impl.UMLSService");
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map.put("http://www.fao.org/webservices/Agrovoc", "edu.cornell.mannlib.semservices.service.impl.AgrovocService");
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map.put(UMLSVocabSource, "edu.cornell.mannlib.semservices.service.impl.UMLSService");
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map.put(AgrovocVocabSource, "edu.cornell.mannlib.semservices.service.impl.AgrovocService");
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return map;
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}
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