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

productMods/edit/forms/js/addConcept.js

@@ -206,7 +206,7 @@ var addConceptForm = {
     	var htmlAdd = "<li class='concepts'>" + 
     	"<div class='row'>" + 
     	"<span class='column conceptLabel'>" +
-    	addConceptForm.generateIndividualCUIInput(cuiURI, label, definition, type, definedBy) +  
+    	addConceptForm.generateIndividualCUIInput(cuiURI, label, type, definedBy) +  
     	label + addConceptForm.generateIndividualTypeDisplay(type) + "</span>" + 
     	addConceptForm.generateIndividualDefinitionDisplay(definition) + 
     	"</div>" +  

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

@@ -3,6 +3,7 @@
 
 <#assign existingConcepts = editConfiguration.pageData.existingConcepts/>
 <#assign userDefinedConceptUrl = editConfiguration.pageData.userDefinedConceptUrl/>
+<#assign sources = editConfiguration.pageData.searchServices/>
 
 <#--If edit submission exists, then retrieve validation errors if they exist-->
 <#if editSubmission?has_content && editSubmission.submissionExists = true && editSubmission.validationErrors?has_content>
@@ -10,10 +11,6 @@
 </#if>
 
 
-<#--This is set for testing purposes - will be retrieved dynamically from the generator later-->
-<#assign sources = [{"uri":"http://link.informatics.stonybrook.edu/umls/", "label":"UMLS"}, {"uri":"http://www.fao.org/webservices/Agrovoc", "label":"Agrovoc"}]/>
-<#assign selectedSource = "UMLS" />
-
 <h2>Manage Concepts</h2>
     
 
@@ -81,9 +78,9 @@
 </div> 
     <form id="addConceptForm" class="customForm" action="${submitUrl}">
 
-    <#list sources as source>
+    <#list sources?keys as sourceUri>
-        <input type="radio" id="source" name="source" value="${source.uri}" role="radio" <#if selectedSource = source.uri>checked</#if> />
+        <input type="radio" id="source" name="source" value="${sourceUri}" role="radio" />
-        <label class="inline" for="${source.label}"> ${source.label}</label>
+        <label class="inline" for="${sources[sourceUri]}"> ${sources[sourceUri]}</label>
         <br />
     </#list>
 

src/edu/cornell/mannlib/semservices/service/impl/AgrovocService.java

@@ -66,7 +66,7 @@ public class AgrovocService implements ExternalConceptService  {
             //XMLUtils.serializeNode(node); System.out.println();
 
             Concept concept = new Concept();
-            concept.setDefinedBy("Agrovoc");
+            concept.setDefinedBy("http://aims.fao.org/aos/agrovoc/agrovocScheme");
             concept.setConceptId(termcode);
 
             NamedNodeMap attrs = node.getAttributes();

src/edu/cornell/mannlib/semservices/service/impl/UMLSService.java

@@ -82,7 +82,7 @@ public class UMLSService implements ExternalConceptService {
                JSONObject o = bestMatchArray.getJSONObject(i);
                //System.out.println(o.toString());
                Concept concept = new Concept();
-               concept.setDefinedBy("UMLS");
+               concept.setDefinedBy("http://link.informatics.stonybrook.edu/umls");
                concept.setBestMatch("true");
                String cui = getJsonValue(o, "CUI");
                bestMatchIdList.add(cui);

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

@@ -54,6 +54,7 @@ import edu.cornell.mannlib.vitro.webapp.edit.n3editing.VTwo.FieldVTwo;
 import edu.cornell.mannlib.vitro.webapp.web.MiscWebUtils;
 import edu.cornell.mannlib.vitro.webapp.search.beans.ProhibitedFromSearch;
 import edu.cornell.mannlib.vitro.webapp.utils.FrontEndEditingUtils;
+import edu.cornell.mannlib.vitro.webapp.utils.ConceptSearchService.ConceptSearchServiceUtils;
 import edu.cornell.mannlib.vitro.webapp.utils.FrontEndEditingUtils.EditMode;
 import edu.cornell.mannlib.vitro.webapp.utils.generators.EditModeUtils;
 /**
@@ -306,19 +307,12 @@ public class AddAssociatedConceptGenerator  extends VivoBaseGenerator implements
 	//Form specific data
 	public void addFormSpecificData(EditConfigurationVTwo editConfiguration, VitroRequest vreq) {
 		HashMap<String, Object> formSpecificData = new HashMap<String, Object>();
-		//Existing concepts should probably be a hash map or a hash map of classes
+		//These are the concepts that already exist currently
-		//with URI of concept node to label and information about existing URI
+		formSpecificData.put("existingConcepts", getExistingConcepts(vreq));
-		//This would be a sparql query and would need to be run here?
-		//-------------------->For test purposes
-		List<AssociatedConceptInfo> testInfo = new ArrayList<AssociatedConceptInfo>();
-		testInfo.add(new AssociatedConceptInfo("testLabel", "testURI", "testVocabURI", "testVocabLabel", null));
-		testInfo.add(new AssociatedConceptInfo("user defined label", "testUserURI", null, null, "http://www.w3.org/2004/02/skos/core#Concept"));
-		
-		//Adding concepts
-		testInfo.addAll(getExistingConcepts(vreq));
-		formSpecificData.put("existingConcepts", testInfo);
 		//Return url for adding user defined concept
 		formSpecificData.put("userDefinedConceptUrl", getUserDefinedConceptUrl(vreq));
+		//Add URIs and labels for different services
+		formSpecificData.put("searchServices", ConceptSearchServiceUtils.getVocabSources());
 		editConfiguration.setFormSpecificData(formSpecificData);
 	}
 	
@@ -342,17 +336,17 @@ public class AddAssociatedConceptGenerator  extends VivoBaseGenerator implements
 	    //TODO: Check if sorted correctly
 	    sortConceptIndividuals(concepts);
 		
-		return getAssociatedConceptInfo(concepts);
+		return getAssociatedConceptInfo(concepts, vreq);
 	}
 	
 	
-	private void sortConceptIndividuals(List<Individual> authorships) {
+	private void sortConceptIndividuals(List<Individual> concepts) {
 		DataPropertyComparator comp = new DataPropertyComparator(RDFS.label.getURI());
-	    Collections.sort(authorships, comp);
+	    Collections.sort(concepts, comp);
 	}
 	
 	private List<AssociatedConceptInfo> getAssociatedConceptInfo(
-			List<Individual> concepts) {
+			List<Individual> concepts, VitroRequest vreq) {
 		List<AssociatedConceptInfo> info = new ArrayList<AssociatedConceptInfo>();
 		 for ( Individual conceptIndividual : concepts ) {
 			 	boolean isSKOSConcept = false;
@@ -376,8 +370,9 @@ public class AddAssociatedConceptGenerator  extends VivoBaseGenerator implements
 			 		String vocabLabel = null;
 			 		if(vocabList != null && vocabList.size() > 0) {
 			 			vocabSource = vocabList.get(0).getObjectURI();
-			 			//vocab label? Right now set as same to vocab source until we get the correct input
+			 			Individual sourceIndividual = EditConfigurationUtils.getIndividual(vreq, vocabSource);
-			 			vocabLabel = vocabSource;
+			 			//Assuming name will get label
+			 			vocabLabel = sourceIndividual.getName();
 			 		}
 			 		info.add(new AssociatedConceptInfo(conceptLabel, conceptUri, vocabSource, vocabLabel, null));
 

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

@@ -89,7 +89,7 @@ public class PersonHasEducationalTraining  extends VivoBaseGenerator implements
         conf.setN3Optional(Arrays.asList( 
                 n3ForEdTrainingToOrg, majorFieldAssertion, degreeAssertion, 
                 deptAssertion, infoAssertion, 
-                n3ForStart, n3ForEnd  ));
+                n3ForStart, n3ForEnd, n3ForOrgToEdTraining  ));
         
         conf.addNewResource("edTraining", DEFAULT_NS_FOR_NEW_RESOURCE);
         conf.addNewResource("org",DEFAULT_NS_FOR_NEW_RESOURCE);
@@ -119,6 +119,8 @@ public class PersonHasEducationalTraining  extends VivoBaseGenerator implements
         conf.addSparqlForExistingUris("endNode", existingEndNodeQuery);
         conf.addSparqlForExistingUris("startField-precision", existingStartPrecisionQuery);
         conf.addSparqlForExistingUris("endField-precision", existingEndPrecisionQuery);
+        //Add sparql to include inverse property as well
+        conf.addSparqlForAdditionalUrisInScope("inverseTrainingAtOrg", inverseTrainingAtOrgQuery);
                         
         conf.addField( new FieldVTwo().                        
                 setName("degree").
@@ -228,7 +230,9 @@ public class PersonHasEducationalTraining  extends VivoBaseGenerator implements
     final static String n3ForEdTrainingToOrg  =      
         "?edTraining <"+ trainingAtOrg +"> ?org .";
     
-    
+    //The inverse of the above
+    final static String n3ForOrgToEdTraining  =      
+        "?org ?inverseTrainingAtOrg ?edTraining .";
     /* Queries for editing an existing educational training entry */
 
     final static String orgQuery  =      
@@ -318,6 +322,13 @@ public class PersonHasEducationalTraining  extends VivoBaseGenerator implements
         "?endNode <"+ type +"> <"+ dateTimeValueType +"> .\n"+
         "?endNode <"+ dateTimePrecision +"> ?existingEndPrecision . }";
     
+    //Query for inverse property
+    final static String inverseTrainingAtOrgQuery  =
+    	  "PREFIX owl:  <http://www.w3.org/2002/07/owl#>"
+			+ " SELECT ?inverseTrainingAtOrg "
+			+ "    WHERE { ?inverseTrainingAtOrg owl:inverseOf <"+ trainingAtOrg +"> . } ";
+    
+    
   //Adding form specific data such as edit mode
 	public void addFormSpecificData(EditConfigurationVTwo editConfiguration, VitroRequest vreq) {
 		HashMap<String, Object> formSpecificData = new HashMap<String, Object>();
@@ -331,4 +342,6 @@ public class PersonHasEducationalTraining  extends VivoBaseGenerator implements
 		return EditModeUtils.getEditMode(vreq, predicates);
 	}
 
+	
+	
 }

src/edu/cornell/mannlib/vitro/webapp/utils/ConceptSearchService/ConceptSearchServiceUtils.java

@@ -19,8 +19,9 @@ import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
 public class ConceptSearchServiceUtils {
     private static final Log log = LogFactory.getLog(ConceptSearchServiceUtils.class);
     //Get the appropriate search service class
-    private static final String UMLSVocabSource = "http://link.informatics.stonybrook.edu/umls/";
+    //TODO: Change this so retrieved from the system instead using a query
-    private static final String AgrovocVocabSource = "http://www.fao.org/webservices/Agrovoc";
+    private static final String UMLSVocabSource = "http://link.informatics.stonybrook.edu/umls";
+    private static final String AgrovocVocabSource = "http://aims.fao.org/aos/agrovoc/agrovocScheme";
     //Get the class that corresponds to the appropriate search
 	public static String getConceptSearchServiceClassName(String searchServiceName) {
 		HashMap<String, String> map = getMapping();
@@ -44,8 +45,8 @@ public class ConceptSearchServiceUtils {
     //Get the hashmap mapping service name to Service class
     private static HashMap<String, String> getMapping() {
     	HashMap<String, String> map = new HashMap<String, String>();
-    	map.put("http://link.informatics.stonybrook.edu/umls/", "edu.cornell.mannlib.semservices.service.impl.UMLSService");
+    	map.put(UMLSVocabSource, "edu.cornell.mannlib.semservices.service.impl.UMLSService");
-    	map.put("http://www.fao.org/webservices/Agrovoc", "edu.cornell.mannlib.semservices.service.impl.AgrovocService");
+    	map.put(AgrovocVocabSource, "edu.cornell.mannlib.semservices.service.impl.AgrovocService");
 
     	return map;
     }