1. Addition of new scimaps vis related jar file.

2. COmpleted the task of providing subdiscipline activity for an entity & other metadata to the front-end in the json format.
3/ Minor refactor of utility functions.

src/edu/cornell/mannlib/vitro/webapp/controller/visualization/VisualizationFrameworkConstants.java

@@ -52,6 +52,7 @@ public class VisualizationFrameworkConstants {
 	public static final String INDIVIDUAL_URI_KEY = "uri";
 	public static final String VIS_MODE_KEY = "vis_mode";
 	public static final String RENDER_MODE_KEY = "render_mode";
+	public static final String OUTPUT_FORMAT_KEY = "output";
 
 	/*
 	 * These values represent possible render modes.
@@ -121,7 +122,9 @@ public class VisualizationFrameworkConstants {
 	
 	
 	/*
-	 * These values represent possible vis-modes for temporal graph vis 
+	 * These values represent possible data serialization formats corresponding to 
+	 * output format key. 
 	 * */
-	public static final String TEMPORAL_GRAPH_JSON_DATA_VIS_MODE = "json";
+	public static final String JSON_OUTPUT_FORMAT = "json";
+	public static final String CSV_OUTPUT_FORMAT = "csv";
 }

src/edu/cornell/mannlib/vitro/webapp/visualization/entitycomparison/EntityPublicationCountRequestHandler.java

@@ -138,7 +138,7 @@ public class EntityPublicationCountRequestHandler implements
 		/*
 		 * This will provide the data in json format mainly used for standalone tmeporal vis. 
 		 * */
-		if (VisualizationFrameworkConstants.TEMPORAL_GRAPH_JSON_DATA_VIS_MODE
+		if (VisualizationFrameworkConstants.JSON_OUTPUT_FORMAT
 					.equalsIgnoreCase(vitroRequest.getParameter(
 							VisualizationFrameworkConstants.VIS_MODE_KEY))) {
 			
@@ -306,7 +306,7 @@ public class EntityPublicationCountRequestHandler implements
 			
 			entityJson.setEntityURI(subentity.getIndividualURI());
 			
-			boolean isPerson = UtilityFunctions.isEntityAPerson(vreq, subentity);
+			boolean isPerson = UtilityFunctions.isEntityAPerson(vreq, subentity.getIndividualURI());
 			
 			if (isPerson) {
 				entityJson.setVisMode("PERSON");

src/edu/cornell/mannlib/vitro/webapp/visualization/entitycomparison/cached/TemporalGrantVisualizationRequestHandler.java

@@ -95,7 +95,7 @@ public class TemporalGrantVisualizationRequestHandler implements
 		/*
 		 * This will provide the data in json format mainly used for standalone temporal vis. 
 		 * */
-		if (VisualizationFrameworkConstants.TEMPORAL_GRAPH_JSON_DATA_VIS_MODE
+		if (VisualizationFrameworkConstants.JSON_OUTPUT_FORMAT
 					.equalsIgnoreCase(vitroRequest
 							.getParameter(VisualizationFrameworkConstants.VIS_MODE_KEY))) {
 			

src/edu/cornell/mannlib/vitro/webapp/visualization/entitycomparison/cached/TemporalPublicationVisualizationRequestHandler.java

@@ -207,7 +207,7 @@ public class TemporalPublicationVisualizationRequestHandler implements
 		/*
 		 * This will provide the data in json format mainly used for standalone tmeporal vis. 
 		 * */
-		if (VisualizationFrameworkConstants.TEMPORAL_GRAPH_JSON_DATA_VIS_MODE
+		if (VisualizationFrameworkConstants.JSON_OUTPUT_FORMAT
 					.equalsIgnoreCase(vitroRequest.getParameter(
 							VisualizationFrameworkConstants.VIS_MODE_KEY))) {
 			

src/edu/cornell/mannlib/vitro/webapp/visualization/entitygrantcount/EntityGrantCountRequestHandler.java

@@ -85,7 +85,7 @@ public class EntityGrantCountRequestHandler implements
 		/*
 		 * This will provide the data in json format mainly used for standalone temporal vis. 
 		 * */
-		if (VisualizationFrameworkConstants.TEMPORAL_GRAPH_JSON_DATA_VIS_MODE
+		if (VisualizationFrameworkConstants.JSON_OUTPUT_FORMAT
 					.equalsIgnoreCase(vitroRequest
 							.getParameter(VisualizationFrameworkConstants.VIS_MODE_KEY))) {
 			
@@ -304,7 +304,7 @@ public class EntityGrantCountRequestHandler implements
 
 			entityJson.setEntityURI(subentity.getIndividualURI());
 			
-			if (UtilityFunctions.isEntityAPerson(vreq, subentity)) {
+			if (UtilityFunctions.isEntityAPerson(vreq, subentity.getIndividualURI())) {
 				entityJson.setVisMode("PERSON");
 			} else {
 				entityJson.setVisMode("ORGANIZATION");

src/edu/cornell/mannlib/vitro/webapp/visualization/mapofscience/MapOfScienceVisualizationRequestHandler.java

@@ -2,11 +2,15 @@
 
 package edu.cornell.mannlib.vitro.webapp.visualization.mapofscience;
 
+import java.io.IOException;
 import java.util.HashMap;
 import java.util.HashSet;
 import java.util.Map;
 import java.util.Set;
 
+import mapping.ScienceMapping;
+import mapping.ScienceMappingResult;
+
 import org.apache.commons.lang.StringEscapeUtils;
 import org.apache.commons.lang.StringUtils;
 import org.apache.commons.logging.Log;
@@ -130,7 +134,7 @@ public class MapOfScienceVisualizationRequestHandler implements
 			if (VisConstants.DataVisMode.JSON.equals(visMode)) {
 				return prepareStandaloneDataResponse(vitroRequest, organizationEntity);
 			} else {
-				return prepareDataResponse(organizationEntity);
+				return prepareDataResponse(vitroRequest, organizationEntity);
 			}
 		}
 	}
@@ -138,12 +142,13 @@ public class MapOfScienceVisualizationRequestHandler implements
 	/**
 	 * Provides response when json file containing the publication count over the
 	 * years is requested.
+	 * @param vitroRequest 
 	 * 
 	 * @param entity
 	 * @param subentities
 	 * @param subOrganizationTypesResult
 	 */
-	private Map<String, String> prepareDataResponse(Entity entity) {
+	private Map<String, String> prepareDataResponse(VitroRequest vitroRequest, Entity entity) {
 
 		String entityLabel = entity.getEntityLabel();
 
@@ -190,7 +195,7 @@ public class MapOfScienceVisualizationRequestHandler implements
 		fileData.put(DataVisualizationController.FILE_CONTENT_TYPE_KEY, 
 					 "application/octet-stream");
 		fileData.put(DataVisualizationController.FILE_CONTENT_KEY, 
-					 "{\"error\" : \"No Publications for this Organization found in VIVO.\"}");
+					 "{\"error\" : \"No Publications for this Entity found in VIVO.\"}");
 		return fileData;
 	}
 
@@ -202,48 +207,29 @@ public class MapOfScienceVisualizationRequestHandler implements
 		String entityURI = vitroRequest
 				.getParameter(VisualizationFrameworkConstants.INDIVIDUAL_URI_KEY);
 		
-		/*
+		if (StringUtils.isBlank(entityURI)) {
-		 * This will provide the data in json format mainly used for standalone tmeporal vis. 
+			entityURI = OrganizationUtilityFunctions
-		 * */
-		if (VisualizationFrameworkConstants.TEMPORAL_GRAPH_JSON_DATA_VIS_MODE
-					.equalsIgnoreCase(vitroRequest.getParameter(
-							VisualizationFrameworkConstants.VIS_MODE_KEY))) {
-			
-			if (StringUtils.isNotBlank(entityURI)) {
-				
-				return getSubjectEntityAndGenerateDataResponse(
-								vitroRequest, 
-								log,
-								dataset, 
-								entityURI,
-								VisConstants.DataVisMode.JSON);
-			} else {
-				
-				return getSubjectEntityAndGenerateDataResponse(
-								vitroRequest, 
-								log,
-								dataset,
-								OrganizationUtilityFunctions
 							.getStaffProvidedOrComputedHighestLevelOrganization(
 									log,
 									dataset,
-												vitroRequest),
+									vitroRequest);
-								VisConstants.DataVisMode.JSON);
+		}
+		
+		VisConstants.DataVisMode currentDataVisMode = VisConstants.DataVisMode.CSV;
+		
+		if (VisualizationFrameworkConstants.JSON_OUTPUT_FORMAT
+				.equalsIgnoreCase(vitroRequest.getParameter(
+						VisualizationFrameworkConstants.OUTPUT_FORMAT_KEY))) {
+			currentDataVisMode = VisConstants.DataVisMode.JSON;
 		}
 		
-		} else {
-			/*
-			 * This provides csv download files for the content in the tables.
-			 * */
 
 		return getSubjectEntityAndGenerateDataResponse(
 				vitroRequest, 
 				log,
 				dataset,
 				entityURI,
-						VisConstants.DataVisMode.CSV);
+				currentDataVisMode);
-			
-		}
 		
 	}
 	
@@ -251,7 +237,7 @@ public class MapOfScienceVisualizationRequestHandler implements
 	@Override
 	public Object generateAjaxVisualization(VitroRequest vitroRequest, Log log,
 			Dataset dataset) throws MalformedQueryParametersException {
-		throw new UnsupportedOperationException("Entity Pub Count does not provide Ajax Response.");
+		throw new UnsupportedOperationException("Map of Science Vis does not provide Ajax Response.");
 	}
 
 	private Map<String, String> prepareStandaloneDataResponse(
@@ -299,27 +285,60 @@ public class MapOfScienceVisualizationRequestHandler implements
 		Gson json = new Gson();
 		Set jsonContent = new HashSet();
 
-		for (SubEntity subentity : subjectEntity.getSubEntities()) {
+		MapOfScience entityJson = new MapOfScience(subjectEntity.getIndividualURI());
+		entityJson.setLabel(subjectEntity.getIndividualLabel());
 		
-			MapOfScience entityJson = new MapOfScience(subentity.getIndividualURI());
+		if (UtilityFunctions.isEntityAPerson(vreq, subjectEntity.getEntityURI())) {
-			
-			entityJson.setLabel(subentity.getIndividualLabel());
-			
-			entityJson.setLastCachedAtDateTime(subentity.getLastCachedAtDateTime());
-			
-			if (subentity.getEntityClass().equals(VOConstants.EntityClassType.PERSON)) {
 			entityJson.setType("PERSON");
-			} else if (subentity.getEntityClass().equals(VOConstants.EntityClassType.ORGANIZATION)) {
+		} else {
 			entityJson.setType("ORGANIZATION");
 		}
 		
+		Set<Activity> publicationsForEntity = new HashSet<Activity>();
+		
+		for (SubEntity subentity : subjectEntity.getSubEntities()) {
+			
+			Set<Activity> subEntityActivities = subentity.getActivities();
+			publicationsForEntity.addAll(subEntityActivities);
+			
+			
+			String subEntityType = "ORGANIZATION";
+			
+			if (subentity.getEntityClass().equals(VOConstants.EntityClassType.PERSON)) {
+				subEntityType = "PERSON";
+			} 
+			
+			entityJson.addSubEntity(subentity.getIndividualURI(), 
+									subentity.getIndividualLabel(), 
+									subEntityType, 
+									subEntityActivities.size());
+			
+		}
+		
+		PublicationJournalStats publicationStats = getPublicationJournalStats(publicationsForEntity);
+		
+		entityJson.setPubsWithNoJournals(publicationStats.noJournalCount);
+		
+		/*
+		 * This method side-effects entityJson by updating its counts for mapped publications, 
+		 * publications with no journal names & publications with invalid journal names & 
+		 * map of subdiscipline to activity.
+		 * */
+		updateEntityMapOfScienceInformation(entityJson,
+											publicationStats.journalToPublicationCount);
+		
+		jsonContent.add(entityJson);
+		
+		return json.toJson(jsonContent);
+	}
+
+	private PublicationJournalStats getPublicationJournalStats(
+			Set<Activity> subEntityActivities) {
 		
 		Map<String, Integer> journalToPublicationCount = new HashMap<String, Integer>();
+		int publicationsWithNoJournalCount = 0;
 		
-			int mappedPublicationCount = 0;
+		for (Activity activity : subEntityActivities) {
-			int unMappedPublicationCount = 0;
-			
-			for (Activity activity : subentity.getActivities()) {
 			
 			if (StringUtils.isNotBlank(((MapOfScienceActivity) activity).getPublishedInJournal())) {
 				
@@ -333,23 +352,50 @@ public class MapOfScienceVisualizationRequestHandler implements
 					journalToPublicationCount.put(journalName, 1);
 				}
 				
-					mappedPublicationCount++;
-					
 			} else {
 				
-					unMappedPublicationCount++;
+				publicationsWithNoJournalCount++;
 			}
 			
 		} 
 		
+		return new PublicationJournalStats(publicationsWithNoJournalCount, journalToPublicationCount);
+	}
+
+	private void updateEntityMapOfScienceInformation(MapOfScience entityJson,
+			Map<String, Integer> journalToPublicationCount) {
+//		System.out.println("journalToPublicationCount " + journalToPublicationCount);
+		
+		int mappedPublicationCount = 0;
+		int publicationsWithInvalidJournalCount = 0;
+		
+		ScienceMappingResult result = null;
+		Map<Integer, Float> subdisciplineToActivity = new HashMap<Integer, Float>();
+		
+		try {
+			result = (new ScienceMapping()).generateScienceMappingResult(journalToPublicationCount);
+		} catch (NumberFormatException e) {
+			System.err.println("NumberFormatException coming from Map Of Science Vis");
+			e.printStackTrace();
+		} catch (IOException e) {
+			System.err.println("IOException coming from Map Of Science Vis");
+			e.printStackTrace();
+		} finally {
+			
+			if (result != null) {
+				subdisciplineToActivity = result.getMappedResult();
+				publicationsWithInvalidJournalCount = Math.round(result.getUnMappedPublications());
+				mappedPublicationCount = Math.round(result.getMappedPublications());
+			}
+			
+		}
+		
+//		System.out.println("subdisciplineToActivity " + subdisciplineToActivity);
+		
 		entityJson.setPubsMapped(mappedPublicationCount);
-			entityJson.setPubsUnmapped(unMappedPublicationCount);
+		entityJson.setPubsWithInvalidJournals(publicationsWithInvalidJournalCount);
-			entityJson.setSubdisciplineActivity(journalToPublicationCount);
 		
-			jsonContent.add(entityJson);
+		entityJson.setSubdisciplineActivity(subdisciplineToActivity);
-		}
-		
-		return json.toJson(jsonContent);
 	}
 
 	private String getEntityPublicationsPerYearCSVContent(Entity entity) {
@@ -373,4 +419,18 @@ public class MapOfScienceVisualizationRequestHandler implements
 		return csvFileContent.toString();
 	}
 	
+	private class PublicationJournalStats {
+		
+		int noJournalCount;
+		Map<String, Integer> journalToPublicationCount;
+		
+		public PublicationJournalStats(int noJournalCount,
+								Map<String, Integer> journalToPublicationCount) {
+
+			this.noJournalCount = noJournalCount;
+			this.journalToPublicationCount = journalToPublicationCount;
+		}
+		
+	} 
+
 }	

src/edu/cornell/mannlib/vitro/webapp/visualization/valueobjects/json/MapOfScience.java

@@ -2,7 +2,9 @@
 package edu.cornell.mannlib.vitro.webapp.visualization.valueobjects.json;
 
 import java.util.HashMap;
+import java.util.HashSet;
 import java.util.Map;
+import java.util.Set;
 
 public class MapOfScience {
 	
@@ -10,9 +12,11 @@ public class MapOfScience {
 	private String label;
 	private String type;
 	private int pubsMapped;
-	private int pubsUnmapped;
+	private int pubsWithNoJournals;
+	private int pubsWithInvalidJournals;
 	private String lastCachedAtDateTime;
-	private Map<String, Integer> subdisciplineActivity = new HashMap<String, Integer>();
+	private Map<Integer, Float> subdisciplineActivity = new HashMap<Integer, Float>();
+	private Set<SubEntityInfo> subEntities = new HashSet<SubEntityInfo>();
 
 	public MapOfScience(String uri) {
 		this.uri = uri;
@@ -43,16 +47,24 @@ public class MapOfScience {
 	public int getPubsMapped() {
 		return pubsMapped;
 	}
-	public void setPubsUnmapped(int pubsUnmapped) {
+	public void setPubsWithNoJournals(int pubsUnmapped) {
-		this.pubsUnmapped = pubsUnmapped;
+		this.pubsWithNoJournals = pubsUnmapped;
 	}
-	public int getPubsUnmapped() {
+	public int getPubsWithNoJournals() {
-		return pubsUnmapped;
+		return pubsWithNoJournals;
 	}
-	public void setSubdisciplineActivity(Map<String, Integer> subdisciplineActivity) {
+	public void setPubsWithInvalidJournals(int pubsWithInvalidJournals) {
+		this.pubsWithInvalidJournals = pubsWithInvalidJournals;
+	}
+
+	public int getPubsWithInvalidJournals() {
+		return pubsWithInvalidJournals;
+	}
+
+	public void setSubdisciplineActivity(Map<Integer, Float> subdisciplineActivity) {
 		this.subdisciplineActivity = subdisciplineActivity;
 	}
-	public Map<String, Integer> getSubdisciplineActivity() {
+	public Map<Integer, Float> getSubdisciplineActivity() {
 		return subdisciplineActivity;
 	}
 
@@ -64,4 +76,60 @@ public class MapOfScience {
 		return lastCachedAtDateTime;
 	}
 
+	public void addSubEntity(String uri, String label, String type, int pubs) {
+		this.subEntities.add(new SubEntityInfo(uri, label, type, pubs));
+	}
+
+	public Set<SubEntityInfo> getSubEntities() {
+		return subEntities;
+	}
+
+	private class SubEntityInfo {
+		
+		private String uri;
+		private String label;
+		private String type;
+		private int pubs;
+		
+		public SubEntityInfo(String uri, String label, String type, int pubs) {
+			this.uri = uri;
+			this.label = label;
+			this.type = type;
+			this.pubs = pubs;
+		}
+
+		public String getUri() {
+			return uri;
+		}
+
+		public void setUri(String uri) {
+			this.uri = uri;
+		}
+
+		public String getLabel() {
+			return label;
+		}
+
+		public void setLabel(String label) {
+			this.label = label;
+		}
+
+		public String getType() {
+			return type;
+		}
+
+		public void setType(String type) {
+			this.type = type;
+		}
+
+		public int getPubs() {
+			return pubs;
+		}
+
+		public void setPubs(int pubs) {
+			this.pubs = pubs;
+		}
+		
+		
+	}
 }

src/edu/cornell/mannlib/vitro/webapp/visualization/visutils/UtilityFunctions.java

@@ -251,10 +251,10 @@ public class UtilityFunctions {
 		return collaboratorshipNetworkURL != null ? collaboratorshipNetworkURL : "" ;
 	}
 	
-	public static boolean isEntityAPerson(VitroRequest vreq, SubEntity subentity) {
+	public static boolean isEntityAPerson(VitroRequest vreq, String individualURI) {
 		return vreq.getWebappDaoFactory()
 					.getIndividualDao()
-					.getIndividualByURI(subentity.getIndividualURI())
+					.getIndividualByURI(individualURI)
 					.isVClass("http://xmlns.com/foaf/0.1/Person");
 	}