[DS-2903] Fix potential Nullpointer exceptions indicated by FindBugs

dspace-api/src/main/java/org/dspace/app/itemimport/ItemImportServiceImpl.java

@@ -1840,6 +1840,7 @@ public class ItemImportServiceImpl implements ItemImportService, InitializingBea
 					
 					List<Collection> finalCollections = null;
 					if (theOwningCollection != null){
+                        finalCollections = new ArrayList<>();
 						finalCollections.add(theOwningCollection);
                         finalCollections.addAll(collectionList);
 					}

dspace-api/src/main/java/org/dspace/eperson/EPersonServiceImpl.java

@@ -99,7 +99,11 @@ public class EPersonServiceImpl extends DSpaceObjectServiceImpl<EPerson> impleme
 
     @Override
     public List<EPerson> search(Context context, String query) throws SQLException {
-        if(StringUtils.isBlank(query)) query = null;
+        if(StringUtils.isBlank(query))
+        {
+            //If we don't have a query, just return everything.
+            return findAll(context, EPerson.EMAIL);
+        }
         return search(context, query, -1, -1);
     }
 
@@ -116,7 +120,10 @@ public class EPersonServiceImpl extends DSpaceObjectServiceImpl<EPerson> impleme
         } catch(IllegalArgumentException e) {
             MetadataField firstNameField = metadataFieldService.findByElement(context, "eperson", "firstname", null);
             MetadataField lastNameField = metadataFieldService.findByElement(context, "eperson", "lastname", null);
-            if (StringUtils.isBlank(query)) query = null;
+            if (StringUtils.isBlank(query))
+            {
+                query = null;
+            }
             return ePersonDAO.search(context, query, Arrays.asList(firstNameField, lastNameField), Arrays.asList(firstNameField, lastNameField), offset, limit);
         }
     }

dspace-api/src/main/java/org/dspace/rdf/conversion/MetadataConverterPlugin.java

@@ -227,7 +227,11 @@ public class MetadataConverterPlugin implements ConverterPlugin
             }
             config.read(is, "file://" + mappingPath, FileUtils.guessLang(mappingPath));
             try {
-                is.close();
+                // Make sure that we have an input stream to avoid NullPointer
+                if(is != null)
+                {
+                    is.close();
+                }
             }
             catch (IOException ex)
             {

dspace-api/src/main/java/org/dspace/submit/lookup/NetworkSubmissionLookupDataLoader.java

@@ -14,10 +14,7 @@ import gr.ekt.bte.core.Value;
 import gr.ekt.bte.exceptions.MalformedSourceException;
 
 import java.io.IOException;
-import java.util.HashMap;
+import java.util.*;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
 
 import org.apache.commons.lang.StringUtils;
 import org.apache.http.HttpException;
@@ -78,7 +75,7 @@ public abstract class NetworkSubmissionLookupDataLoader implements
                         : null;
                 String year = getSearchTerms().get("year") != null ? getSearchTerms()
                         .get("year").iterator().next()
-                        : null;
+                        : String.valueOf(Calendar.getInstance().get(Calendar.YEAR));
                 int yearInt = Integer.parseInt(year);
                 results = search(null, title, authors, yearInt);
             }

dspace-api/src/main/java/org/dspace/xmlworkflow/XmlWorkflowServiceImpl.java

@@ -361,7 +361,7 @@ public class XmlWorkflowServiceImpl implements XmlWorkflowService {
                 e.printStackTrace();
             }
             finally {
-                if((nextStep != null && nextActionConfig != null) || wfi.getItem().isArchived()){
+                if((nextStep != null && currentStep != null && nextActionConfig != null) || (wfi.getItem().isArchived() && currentStep != null)){
                     logWorkflowEvent(c, currentStep.getWorkflow().getID(), currentStep.getId(), currentActionConfig.getId(), wfi, user, nextStep, nextActionConfig);
                 }
             }

dspace-api/src/main/java/org/dspace/xmlworkflow/state/actions/userassignment/AssignOriginalSubmitterAction.java

@@ -95,6 +95,12 @@ public class AssignOriginalSubmitterAction extends UserSelectionAction{
         while(nextAction != null && !nextAction.requiresUI()){
             nextAction = nextAction.getStep().getNextAction(nextAction);
         }
+        if(nextAction == null)
+        {
+            //Should never occur, but just in case
+            log.error("Could not find next action for step with id: " + step.getId() + " to assign a submitter to. Aborting the action.");
+            throw new IllegalStateException();
+        }
 
         createTaskForEPerson(c, wfi, step, nextAction, submitter);
 

dspace-jspui/src/main/java/org/dspace/app/webui/servlet/RequestItemServlet.java

@@ -311,14 +311,16 @@ public class RequestItemServlet extends DSpaceServlet
         {
 			Item item = requestItem.getItem();
 			String title = "";
+			String handle = "";
 			if (item != null) {
 				title = itemService.getMetadataFirstValue(item, "dc", "title", null, Item.ANY);
 				if (title == null) {
 					title = "";
 				}
+				handle = item.getHandle();
 			}
             request.setAttribute("request-name", requestItem.getReqName());
-            request.setAttribute("handle", item.getHandle());
+            request.setAttribute("handle", handle);
             request.setAttribute("title", title);
             
             JSPManager.showJSP(request, response,

dspace-jspui/src/main/java/org/dspace/app/webui/submit/step/JSPUploadStep.java

@@ -217,11 +217,11 @@ public class JSPUploadStep extends JSPStep
                 size = bitstream.getSize();
                 url = request.getContextPath() + "/retrieve/" + bitstreamID
                         + "/" + UIUtil.encodeBitstreamName(bitstreamName);
+                jsonResponse.addUploadFileStatus(bitstreamName, bitstreamID, size,
+                        url, status);
+                response.getWriter().print(gson.toJson(jsonResponse));
+                response.flushBuffer();
             }
-            jsonResponse.addUploadFileStatus(bitstreamName, bitstreamID, size,
-                    url, status);
-            response.getWriter().print(gson.toJson(jsonResponse));
-            response.flushBuffer();
             return;
         }
 

dspace-jspui/src/main/java/org/dspace/app/webui/submit/step/JSPUploadWithEmbargoStep.java

@@ -143,11 +143,11 @@ public class JSPUploadWithEmbargoStep extends JSPUploadStep
                 size = bitstream.getSize();
                 url = request.getContextPath() + "/retrieve/" + bitstreamID
                         + "/" + UIUtil.encodeBitstreamName(bitstreamName);
+                jsonResponse.addUploadFileStatus(bitstreamName, bitstreamID, size,
+                        url, status);
+                response.getWriter().print(gson.toJson(jsonResponse));
+                response.flushBuffer();
             }
-            jsonResponse.addUploadFileStatus(bitstreamName, bitstreamID, size,
-                    url, status);
-            response.getWriter().print(gson.toJson(jsonResponse));
-            response.flushBuffer();
             return;
         }
         

dspace-oai/src/main/java/org/dspace/xoai/services/api/CollectionsService.java

@@ -10,13 +10,14 @@ package org.dspace.xoai.services.api;
 import org.dspace.content.Collection;
 import org.dspace.content.Community;
 import org.dspace.content.Item;
+import org.dspace.xoai.services.api.context.ContextService;
 
 import java.sql.SQLException;
 import java.util.List;
 import java.util.UUID;
 
 public interface CollectionsService {
-    List<UUID> getAllSubCollections(UUID communityId) throws SQLException;
+    List<UUID> getAllSubCollections(ContextService contextService, UUID communityId) throws SQLException;
     List<Community> flatParentCommunities(Collection collection) throws SQLException;
     List<Community> flatParentCommunities(Community community) throws SQLException;
     List<Community> flatParentCommunities(Item item) throws SQLException;

dspace-oai/src/main/java/org/dspace/xoai/services/impl/DSpaceCollectionsService.java

@@ -25,12 +25,11 @@ import org.dspace.content.service.CommunityService;
 
 public class DSpaceCollectionsService implements CollectionsService {
 
-    private ContextService contextService;
     private static final CommunityService communityService
             = ContentServiceFactory.getInstance().getCommunityService();
 
     @Override
-    public List<UUID> getAllSubCollections(UUID communityId)
+    public List<UUID> getAllSubCollections(ContextService contextService, UUID communityId)
             throws SQLException
     {
         Queue<Community> comqueue = new LinkedList<>();

dspace-rest/src/main/java/org/dspace/rest/ItemsResource.java

@@ -919,7 +919,6 @@ public class ItemsResource extends Resource
         // Must used own style.
         if ((metadata.length < 2) || (metadata.length > 3))
         {
-            context.abort();
             log.error("Finding failed, bad metadata key.");
             throw new WebApplicationException(Response.Status.NOT_FOUND);
         }

dspace-xmlui/src/main/java/org/dspace/app/xmlui/aspect/administrative/FlowAuthorizationUtils.java

@@ -258,6 +258,9 @@ public class FlowAuthorizationUtils {
                         .authorizeManageItemPolicy(context, (Item) (bitstreamService.getParentObject(context, (Bitstream) policyParent)));
 			        break;
 				}
+			default:
+				//If we can't find a parent the policy will receive a NULL dspace object, this is not something we want.
+				throw new IllegalArgumentException("Invalid DSpaceObject type provided");
 			}
 			policy = resourcePolicyService.create(context);
 			policy.setdSpaceObject(policyParent);

dspace-xmlui/src/main/java/org/dspace/app/xmlui/aspect/administrative/item/EditItemMetadataForm.java

@@ -132,7 +132,7 @@ public class EditItemMetadataForm extends AbstractDSpaceTransformer {
         // Metadata editing is the only type of editing available for a template item.
         boolean editingTemplateItem = false;
         String templateCollectionID = parameters.getParameter("templateCollectionID", null);
-        Collection templateCollection = templateCollectionID != null ? null : collectionService.find(context, UUID.fromString(templateCollectionID));
+        Collection templateCollection = templateCollectionID == null ? null : collectionService.find(context, UUID.fromString(templateCollectionID));
         if (templateCollection != null)
         {
             Item templateItem = templateCollection.getTemplateItem();
@@ -144,7 +144,7 @@ public class EditItemMetadataForm extends AbstractDSpaceTransformer {
 
         // DIVISION: main
         Division main = body.addInteractiveDivision("edit-item-status", contextPath+"/admin/item", Division.METHOD_POST,"primary administrative item");
-        if (editingTemplateItem)
+        if (templateCollection != null && editingTemplateItem)
         {
             main.setHead(T_template_head.parameterize(templateCollection.getName()));
         }

dspace-xmlui/src/main/java/org/dspace/app/xmlui/aspect/artifactbrowser/ConfigurableBrowse.java

@@ -273,9 +273,16 @@ public class ConfigurableBrowse extends AbstractDSpaceTransformer implements
            HttpServletResponse response = (HttpServletResponse)objectModel
 		.get(HttpEnvironment.HTTP_RESPONSE_OBJECT);
 	    response.setStatus(HttpServletResponse.SC_NOT_FOUND);
+            return;
         }
 
         BrowseInfo info = getBrowseInfo();
+        if(info == null)
+        {
+            HttpServletResponse response = (HttpServletResponse)objectModel.get(HttpEnvironment.HTTP_RESPONSE_OBJECT);
+ 	        response.setStatus(HttpServletResponse.SC_NOT_FOUND);
+            return;
+        }
 
         String type = info.getBrowseIndex().getName();
 

dspace-xmlui/src/main/java/org/dspace/app/xmlui/aspect/artifactbrowser/ItemRequestResponseAction.java

@@ -81,7 +81,7 @@ public class ItemRequestResponseAction extends AbstractAction
         String title;
         Item item = requestItem.getItem();
         String titleDC = item.getName();
-        if (titleDC != null || titleDC.length() > 0)
+        if (titleDC != null && titleDC.length() > 0)
         	title=titleDC;
         else
         	title="untitled";

dspace-xmlui/src/main/java/org/dspace/app/xmlui/aspect/artifactbrowser/ItemRequestResponseTrueForm.java

@@ -124,7 +124,7 @@ public class ItemRequestResponseTrueForm extends AbstractDSpaceTransformer imple
 		String title;
 		Item item = requestItem.getItem();
 		String titleDC = item.getName();
-		if (titleDC != null || titleDC.length() > 0)
+		if (titleDC != null && titleDC.length() > 0)
 			title = titleDC;
 		else
 			title = "untitled";

dspace-xmlui/src/main/java/org/dspace/app/xmlui/aspect/handle/HandleResolverReader.java

@@ -142,6 +142,12 @@ public class HandleResolverReader extends AbstractReader implements Recyclable {
             log.error("SQLException: ", e);
             return;
         }
+        if(jsonString == null)
+        {
+            //No handle found bad request
+            resp.sendError(HttpServletResponse.SC_BAD_REQUEST);
+            return;
+        }
         
         try {
             ObjectModelHelper.getResponse(objectModel).setHeader("Content-Type", CONTENTTYPE);