Minor code improvements

api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/harvester/FileHarvestController.java

@@ -456,8 +456,8 @@ public class FileHarvestController extends FreemarkerHttpServlet {
                 }
 
                 StringBuilder progressSinceLastCheck = new StringBuilder();
-                for(int i = 0; i < unsentLogLines.length; i++) {
+                for (String unsentLogLine : unsentLogLines) {
-                    progressSinceLastCheck.append(unsentLogLines[i]).append(newline);
+                    progressSinceLastCheck.append(unsentLogLine).append(newline);
                 }
 
                 boolean finished = sessionInfo.isFinished();

api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/harvester/Harvester.java

@@ -173,12 +173,12 @@ class Harvester {
      */
     public static String[] stringsToArray(Object ... args) {
         ArrayList<String> allData = new ArrayList<String>();
-        for(int i = 0; i < args.length; i++) {
+        for (Object arg : args) {
-            if(args[i] instanceof String[]) {
+            if (arg instanceof String[]) {
-                String[] array = (String[])(args[i]);
+                String[] array = (String[]) (arg);
                 Collections.addAll(allData, array);
             } else {
-                allData.add(args[i].toString());
+                allData.add(arg.toString());
             }
         }
         return allData.toArray(new String[allData.size()]);

api/src/main/java/edu/cornell/mannlib/vitro/webapp/visualization/temporalgraph/OrganizationUtilityFunctions.java

@@ -27,40 +27,14 @@ import edu.cornell.mannlib.vitro.webapp.visualization.visutils.QueryRunner;
 
 public class OrganizationUtilityFunctions {
 
-	public static String getHighestLevelOrganizationURI(ResultSet resultSet,
+	public static String getHighestLevelOrganizationURI(ResultSet resultSet, Map<String, String> fieldLabelToOutputFieldLabel) {
-			Map<String, String> fieldLabelToOutputFieldLabel) {
-
-		GenericQueryMap queryResult = new GenericQueryMap();
-
 		while (resultSet.hasNext()) {
 			QuerySolution solution = resultSet.nextSolution();
 
-			RDFNode organizationNode = solution
+			RDFNode organizationNode = solution.get(fieldLabelToOutputFieldLabel.get("organization"));
-					.get(fieldLabelToOutputFieldLabel.get("organization"));
 
 			if (organizationNode != null) {
-				queryResult.addEntry(
-						fieldLabelToOutputFieldLabel.get("organization"),
-						organizationNode.toString());
-
 				return organizationNode.toString();
-
-			}
-
-			RDFNode organizationLabelNode = solution
-					.get(fieldLabelToOutputFieldLabel.get("organizationLabel"));
-
-			if (organizationLabelNode != null) {
-				queryResult.addEntry(
-						fieldLabelToOutputFieldLabel.get("organizationLabel"),
-						organizationLabelNode.toString());
-			}
-
-			RDFNode numberOfChildrenNode = solution.getLiteral("numOfChildren");
-
-			if (numberOfChildrenNode != null) {
-				queryResult.addEntry("numOfChildren", String
-						.valueOf(numberOfChildrenNode.asLiteral().getInt()));
 			}
 		}
 

api/src/main/java/edu/cornell/mannlib/vitro/webapp/visualization/utilities/UtilitiesRequestHandler.java

@@ -350,7 +350,6 @@ public class UtilitiesRequestHandler implements VisualizationRequestHandler {
 		private VitroRequest vitroRequest;
 		private Map<String, String> fieldLabelToOutputFieldLabel;
 		private String topLevelURL = null;
-		private GenericQueryMap queryResult = new GenericQueryMap();
 
 		HighetTopLevelOrgTemporalGraphURLConsumer(VitroRequest vitroRequest, Map<String, String> fieldLabelToOutputFieldLabel) {
 			this.vitroRequest = vitroRequest;
@@ -366,8 +365,6 @@ public class UtilitiesRequestHandler implements VisualizationRequestHandler {
 			RDFNode organizationNode = qs.get(fieldLabelToOutputFieldLabel.get("organization"));
 
 			if (organizationNode != null) {
-				queryResult.addEntry(fieldLabelToOutputFieldLabel.get("organization"), organizationNode.toString());
-
 				String individualLocalName = UtilityFunctions.getIndividualLocalName(organizationNode.toString(), vitroRequest);
 
 				if (StringUtils.isNotBlank(individualLocalName)) {
@@ -388,19 +385,6 @@ public class UtilitiesRequestHandler implements VisualizationRequestHandler {
 							highestLevelOrganizationTemporalGraphVisURLParams);
 
 				}
-			} else {
-				RDFNode organizationLabelNode = qs.get(fieldLabelToOutputFieldLabel.get("organizationLabel"));
-
-				if (organizationLabelNode != null) {
-					queryResult.addEntry(fieldLabelToOutputFieldLabel.get("organizationLabel"), organizationLabelNode.toString());
-				}
-
-				RDFNode numberOfChildrenNode = qs.getLiteral("numOfChildren");
-
-				if (numberOfChildrenNode != null) {
-					queryResult.addEntry("numOfChildren",
-							String.valueOf(numberOfChildrenNode.asLiteral().getInt()));
-				}
 			}
 		}
 

api/src/main/java/edu/cornell/mannlib/vitro/webapp/visualization/visutils/CollaborationDataViewHelper.java

@@ -102,12 +102,6 @@ public class CollaborationDataViewHelper {
         // Now add the person that is the focus to the start of the list
         collaborators.add(0, data.getEgoCollaborator());
 
-        // Generate a list of collaborator IDs for use in filling the matrix
-        List<Integer> collabIDs = new ArrayList<Integer>(collaborators.size());
-        for (Collaborator collaborator : collaborators) {
-            collabIDs.add(collaborator.getCollaboratorID());
-        }
-
         // If we only want to visualize collaborations between the main focus and others, set this to false
         boolean fullMatrix = true;
 

api/src/test/resources/log4j.properties

@@ -4,7 +4,7 @@
 # It's not very important, because the tests themselves will override this 
 # configuration in AbstractTestClass.initializeLogging().
 #
-log4j.rootLogger=WARN, AllAppender 
+log4j.rootLogger=WARN, AllAppender
-log4j.appender.AllAppender=org.apache.log4j.ConsoleAppender 
+log4j.appender.AllAppender=org.apache.log4j.ConsoleAppender
-log4j.appender.AllAppender.layout=org.apache.log4j.PatternLayout 
+log4j.appender.AllAppender.layout=org.apache.log4j.PatternLayout
-log4j.appender.AllAppender.layout.ConversionPattern=%p %t %c - %m%n 
+log4j.appender.AllAppender.layout.ConversionPattern=%p %t %c - %m%n

home/src/main/resources/config/example.runtime.properties

@@ -334,7 +334,7 @@ http.createCacheHeaders = true
   # VIVO 1.3 release mitigates this problem by the way of a caching mechanism & 
   # hence we can safely set this to be enabled by default.
   #
-visualization.temporal = enabled 
+visualization.temporal = enabled
 
   #
   # Types of individual for which we can create proxy editors.
@@ -354,4 +354,4 @@ Vitro.reconcile.defaultTypeList = http://vivoweb.org/ontology/core#Role, core:Ro
     http://vivoweb.org/ontology/core#Location, core:Location; \
     http://xmlns.com/foaf/0.1/Organization, foaf:Organization; \
     http://xmlns.com/foaf/0.1/Person, foaf:Person; \
-    http://purl.obolibrary.org/obo/IAO_0000030, obo:IAO_0000030 
+    http://purl.obolibrary.org/obo/IAO_0000030, obo:IAO_0000030

legacy/config/licenser/licenser.properties

@@ -10,7 +10,7 @@ source_dir = ../../
 # (if relative, then relative to this file)
 target_dir = 
 
-# A list of filename globs that match the files we want to license, 
+# A list of filename globs that match the files we want to license,
 # delimited by commas with optional white-space.
 file_matchers = *.java, *.jsp, *.tld, *.xsl, *.xslt, *.css, *.js, *.ftl, *.xml