updates for semantic services, temporarily commenting out concept semantic type which is still in progress

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

@@ -95,9 +95,9 @@
     </p><span id="createOwnOne"> ${i18n().or} &nbsp;<a href="${userDefinedConceptUrl}" title="${i18n().create_own_concept}">${i18n().create_own_concept}&nbsp;</a></span>
     <input type="hidden" id="conceptNode" name="conceptNode" value=""/> <!-- Field value populated by JavaScript -->
     <input type="hidden" id="conceptLabel" name="conceptLabel" value="" />  <!-- Field value populated by JavaScript -->
-		<input type="hidden" id="conceptSource" name="conceptSource" value="" /> <!-- Field value populated by JavaScript -->
+	<input type="hidden" id="conceptSource" name="conceptSource" value="" /> <!-- Field value populated by JavaScript -->
-    		<input type="hidden" id="conceptSemanticTypeURI" name="conceptSemanticTypeURI" value="" /> <!-- Field value populated by JavaScript -->
+    <input type="hidden" id="conceptSemanticTypeURI" name="conceptSemanticTypeURI" value="" /> <!-- Field value populated by JavaScript -->
-        		<input type="hidden" id="conceptSemanticTypeLabel" name="conceptSemanticTypeLabel" value="" /> <!-- Field value populated by JavaScript -->
+    <input type="hidden" id="conceptSemanticTypeLabel" name="conceptSemanticTypeLabel" value="" /> <!-- Field value populated by JavaScript -->
     
     <div id="selectedConcept" name="selectedConcept" class="acSelection">
         <p class="inline">

src/edu/cornell/mannlib/semservices/bo/Concept.java

@@ -17,7 +17,8 @@ public class Concept {
    private List<String> narrowerURIList;
    private List<String> exactMatchURIList;
    private List<String> closeMatchURIList;
-
+   private List<String> altLabelList;
+   
    /**
     * default constructor
     */
@@ -149,4 +150,12 @@ public void setCloseMatchURIList(List<String> closeMatchURIList) {
 	this.closeMatchURIList = closeMatchURIList;
 }
 
+public List<String> getAltLabelList() {
+	return altLabelList;
+}
+
+public void setAltLabelList(List<String> altLabelList) {
+	this.altLabelList = altLabelList;
+}
+
 }

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

@@ -65,7 +65,6 @@ public class AgrovocService implements ExternalConceptService  {
    private final String codeName = "hasCodeAgrovoc";
    private final String searchMode = "Exact Match";
    protected final String dbpedia_endpoint = " http://dbpedia.org/sparql";
-
   
    
 	@Override
@@ -94,16 +93,16 @@ public class AgrovocService implements ExternalConceptService  {
 			return conceptList;
 		}
 		
-		System.out.println("uri: "+uri); 
+		//System.out.println("uri: "+uri); 
         SKOSDataset dataset = manager.loadDataset(uri);
         
         for (SKOSConcept skosConcept : dataset.getSKOSConcepts()) {
         	Concept concept = new Concept();
-            System.out.println("Concept: " + skosConcept.getURI());
+            //System.out.println("Concept: " + skosConcept.getURI());
             concept.setUri(skosConcept.getURI().toString());
             concept.setConceptId(stripConceptId(skosConcept.getURI().toString()));
             concept.setBestMatch("true");
-            concept.setDefinedBy(this.schemeUri);
+            concept.setDefinedBy(schemeUri);
             concept.setSchemeURI(this.schemeUri);
             concept.setType("");
             String lang = "";
@@ -126,6 +125,32 @@ public class AgrovocService implements ExternalConceptService  {
               }
             }
             
+            // get altLabels
+            List<String> altLabelList = new ArrayList<String>();
+			for (SKOSLiteral literal : skosConcept
+					.getSKOSRelatedConstantByProperty(dataset, manager
+							.getSKOSDataFactory().getSKOSAltLabelProperty())) {
+
+				if (!literal.isTyped()) {
+					// if it has language
+					SKOSUntypedLiteral untypedLiteral = literal
+							.getAsSKOSUntypedLiteral();
+					if (untypedLiteral.hasLang()) {
+						lang = untypedLiteral.getLang();
+					} else {
+						lang = "";
+					}
+				}
+				//System.out.println("literal: "+ literal.getLiteral());
+				if (lang.equals("en")) {
+					//System.out.println("altLabel: " + literal.getLiteral());
+					altLabelList.add(literal.getLiteral());
+				}
+			}
+            concept.setAltLabelList(altLabelList);
+            
+            
+            
             // get the broader property URI
             List<String> broaderURIList = new ArrayList<String>();
             for (SKOSAnnotation annotation: skosConcept.getSKOSAnnotationsByURI(dataset, manager.getSKOSDataFactory().getSKOSBroaderProperty().getURI())) {
@@ -347,9 +372,9 @@ public class AgrovocService implements ExternalConceptService  {
 
 
    public List<Concept> getConceptsByURIWithSparql(String uri) throws Exception {
-	 //John Ferreira's original code has implementation
+	  // deprecating this method...just return an empty list
-	      List<Concept> newConceptList = new ArrayList<Concept>();
+      List<Concept> conceptList = new ArrayList<Concept>();      
-	      return newConceptList;
+      return conceptList;
    }
    
    protected String getAgrovocTermCode(String rdf) throws Exception {

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

@@ -34,8 +34,7 @@ public class GemetService implements ExternalConceptService  {
    private final String endpoint = "http://cr.eionet.europa.eu/sparql";
    private final String schemeURI = "http://www.eionet.europa.eu/gemet/gemetThesaurus";
 
-
+   
-  
 	@Override
 	public List<Concept> getConcepts(String term) throws Exception {
 		List<Concept> conceptList = new ArrayList<Concept>();
@@ -65,11 +64,12 @@ public class GemetService implements ExternalConceptService  {
 
    }
 
-   public List<Concept> getConceptsByURIWithSparql(String uri) throws Exception {
+	public List<Concept> getConceptsByURIWithSparql(String uri)
-     //John Ferreira's original code has implementation
+			throws Exception {
-      List<Concept> newConceptList = new ArrayList<Concept>();
+		// deprecating this method...just return an empty list
-      return newConceptList;
+		List<Concept> conceptList = new ArrayList<Concept>();
-   }
+		return conceptList;
+	}
 
    /**
     * @param results
@@ -87,7 +87,7 @@ public class GemetService implements ExternalConceptService  {
 
          for (int i = 0; i < jsonArray.size(); i++) {
             Concept concept = new Concept();
-            concept.setDefinedBy(this.schemeURI);
+            concept.setDefinedBy(schemeURI);
             concept.setBestMatch("true");
             JSONObject json = jsonArray.getJSONObject(i);
             String uri = getJsonValue(json, "uri");
@@ -124,7 +124,7 @@ public class GemetService implements ExternalConceptService  {
             for (String s: relatedURIList) {
             	System.out.println("related uri: "+s);
             }*/
-            
+            //String altLabels = getAllTranslationsForConcept(uri, "nonPreferredLabels");
             
             conceptList.add(concept);
 
@@ -218,9 +218,10 @@ public class GemetService implements ExternalConceptService  {
       "?concept_uri=" + concept_uri +
       "&property_uri=" + property_uri +
       "&language=en";
-
       try {
          result = getGemetResults(serviceUrl);
+         List<String> props = getPropertyFromJson(result);
+          
       } catch (Exception e) {
          e.printStackTrace();
          throw e;
@@ -310,6 +311,7 @@ public class GemetService implements ExternalConceptService  {
       return results;
    }
    
+    
    protected List<String> getRelatedUris(String json) {
 	   List<String> uriList = new ArrayList<String>();
 	   String uri = new String();
@@ -327,6 +329,19 @@ public class GemetService implements ExternalConceptService  {
 	   
    }
    
+	protected List<String> getPropertyFromJson(String json) {
+		List<String> props = new ArrayList<String>();
+		JSONArray jsonArray = (JSONArray) JSONSerializer.toJSON(json);
+		if (jsonArray.size() == 0) {
+			return new ArrayList<String>();
+		}
+		for (int i = 0; i < jsonArray.size(); i++) {
+			JSONObject jsonObj = jsonArray.getJSONObject(i);
+			System.out.println(jsonObj.toString());
+		}
+		return props;
+	}
+
    protected String stripConceptId(String uri) {
 	     String conceptId = new String();
 	     int lastslash = uri.lastIndexOf('/');

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

@@ -29,14 +29,14 @@ public class UMLSService implements ExternalConceptService {
    private static final String baseUri = "http://link.informatics.stonybrook.edu/umls/CUI/";
    private static final String endpoint = "http://link.informatics.stonybrook.edu/sparql/";
    private static final String schemeURI = "http://link.informatics.stonybrook.edu/umls";
-
+   
+   
    
 	@Override
 	public List<Concept> getConcepts(String term) throws Exception {
 		List<Concept> conceptList = new ArrayList<Concept>();
 
 		String results = null;
-		//Format in rdf/xml is possible but would require separate processing method
 		String dataUrl = submissionUrl + "textToProcess="
 				+ URLEncoder.encode(term, "UTF-8") 
 				+ "&format=json";
@@ -98,11 +98,12 @@ public class UMLSService implements ExternalConceptService {
     * @param uri
     * @return
     */
-   public List<Concept> getConceptsByURIWithSparql(String uri) throws Exception {
+	public List<Concept> getConceptsByURIWithSparql(String uri)
-	 //John Ferreira's original code has implementation
+			throws Exception {
-	      List<Concept> newConceptList = new ArrayList<Concept>();
+		// deprecating this method...just return an empty list
-	      return newConceptList;
+		List<Concept> conceptList = new ArrayList<Concept>();
-   }
+		return conceptList;
+	}
 
    /**
     * @param results

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

@@ -190,7 +190,7 @@ 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 +239,11 @@ 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 +272,8 @@ public class AddAssociatedConceptGenerator  extends VivoBaseGenerator implements
     	setConceptNodeField(editConfiguration, vreq);
     	setConceptLabelField(editConfiguration, vreq);
     	setVocabURIField(editConfiguration, vreq);
-    	setConceptSemanticTypeURIField(editConfiguration,vreq);
+    	//setConceptSemanticTypeURIField(editConfiguration,vreq);
-    	setConceptSemanticTypeLabelField(editConfiguration,vreq);
+    	//setConceptSemanticTypeLabelField(editConfiguration,vreq);
     }
     
 	//this field will be hidden and include the concept node URI
@@ -325,7 +325,7 @@ public class AddAssociatedConceptGenerator  extends VivoBaseGenerator implements
 	  //An Edit submission preprocessor for enabling addition of multiple terms for a single search
 	  
 	   editConfiguration.addEditSubmissionPreprocessor(
-			   new AddAssociatedConceptsPreprocessor(editConfiguration));
+			   new AddAssociatedConceptsPreprocessor(editConfiguration, wadf));
 	  
 	}
      
@@ -411,12 +411,13 @@ 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");
 				 	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
@@ -441,8 +442,8 @@ public class AddAssociatedConceptGenerator  extends VivoBaseGenerator implements
 			this.vocabURI = inputVocabURI;
 			this.vocabLabel = inputVocabLabel;
 			this.type = inputType;
-			this.conceptSemanticTypeURI = inputConceptSemanticTypeURI;
+			//this.conceptSemanticTypeURI = inputConceptSemanticTypeURI;
-			this.conceptSemanticTypeLabel = inputConceptSemanticTypeLabel;
+			//this.conceptSemanticTypeLabel = inputConceptSemanticTypeLabel;
 		}
 		
 		//Getters

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

@@ -13,6 +13,9 @@ import org.apache.commons.logging.LogFactory;
 import com.hp.hpl.jena.rdf.model.Literal;
 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;
@@ -24,6 +27,7 @@ public class AddAssociatedConceptsPreprocessor extends
 
 	protected static final Log log = LogFactory
 			.getLog(AddAssociatedConceptsPreprocessor.class.getName());
+    protected WebappDaoFactory wadf = null;
 
 	// Field names/variables names for n3 - these will have numbers added as
 	// suffix if more than one term
@@ -34,14 +38,17 @@ public class AddAssociatedConceptsPreprocessor extends
 	private static String conceptNodeValues = null;
 	private static String conceptLabelValues = null;
 	private static String conceptSourceValues = null;
+	private static String conceptSemanticTypeLabelValues = null;
+	private static String conceptSemanticTypeURIValues = null;
 	private static MultiValueEditSubmission submission = null;
 
 	// String datatype
 
 	// Will be editing the edit configuration as well as edit submission here
 
-	public AddAssociatedConceptsPreprocessor(EditConfigurationVTwo editConfig) {
+	public AddAssociatedConceptsPreprocessor(EditConfigurationVTwo editConfig, WebappDaoFactory wadf) {
 		super(editConfig);
+		this.wadf = wadf;
 	}
 
 	public void preprocess(MultiValueEditSubmission inputSubmission) {
@@ -50,7 +57,9 @@ 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;
@@ -71,8 +80,26 @@ public class AddAssociatedConceptsPreprocessor extends
 		conceptLabelValues = getConceptLabelValues();
 		conceptNodeValues = getConceptNodeValues();
 		conceptSourceValues = getConceptSourceValues();
+
+	}
+	
+	//
+	private void processConceptSemanticValues() {
+		conceptSemanticTypeLabelValues = getConceptSemanticTypeLabelValues();
+		conceptSemanticTypeURIValues = getConceptSemanticTypeURIValues();
+		
+		//We are first going to handle the single value case and then handle additional values
+		//where the rest of the additional values are handled
+		
 	}
 
+
+	
+	
+	
+	
+
+	//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
 		// Add N3Required
@@ -98,6 +125,9 @@ public class AddAssociatedConceptsPreprocessor extends
 		addConceptNodeInputs(numberConcepts);
 		addConceptSourceInputs(numberConcepts);
 		addConceptLabelInputs(numberConcepts);
+		//for concept semantic type  labels and uris where they exist
+		//addConceptSemanticTypeLabelInputs(numberConcepts);
+		//addConceptSemanticTypeURIInputs(numberConcepts);
 		
 	}
 
@@ -167,8 +197,17 @@ public class AddAssociatedConceptsPreprocessor extends
 			log.error("Concept labels returned were null");
 		}
 	}
+	
+	private void addConceptSemanticTypeLabelInputs(int numberConcepts) {
+		
+	}
+	
+	private void addConceptSemanticTypeURIInputs(int numberConcepts) {
+		
+	}
 
-
+	//Fields
+	
 	private void addFields(int numberConcepts) {
 		//Clear out all fields in edit configuration first
 		editConfiguration.setFields(new HashMap<String, FieldVTwo>());
@@ -290,6 +329,7 @@ public class AddAssociatedConceptsPreprocessor extends
 	}
 	
 	
+	//Get values from submission 
 	private String getConceptNodeValues() {
 		Map<String, List<String>> urisFromForm = submission.getUrisFromForm();
 		List<String> conceptNodes =  urisFromForm.get("conceptNode");
@@ -308,6 +348,40 @@ public class AddAssociatedConceptsPreprocessor extends
 
 	}
 	
+	private String getConceptSemanticTypeLabelValues() {
+		Map<String, List<Literal>> literalsFromForm = submission.getLiteralsFromForm();
+		Map<String, List<String>> transformed = EditConfigurationUtils.transformLiteralMap(literalsFromForm);
+		return (String) getFirstElement(transformed.get("conceptSemanticTypeLabel"));
+	}
+	
+	//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);
+			int numberLabels = conceptSemanticTypeLabels.length;
+			
+			for(int i = 0; i < numberLabels; i++) {
+				String label = conceptSemanticTypeLabels[i];
+				//Make or retrieve URI for this label
+				String  uri = getURIForSemanticTypeLabel(label);
+				conceptSemanticTypeURIs.add(uri);
+			}
+			
+			//Set uris as string
+			//Essentially this will allow the URI to be put in scope 
+			return conceptSemanticTypeURIs.toString();
+		}
+		
+	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 concepts
+		return null;
+		
+	}
+	
 	private Object getFirstElement(List inputList) {
 		if(inputList == null || inputList.size() == 0)
 			return null;