Minor auto-refactor code cleanup on a massive scale

announcements/src/org/labkey/announcements/AnnouncementUserListener.java

@@ -19,8 +19,6 @@
 import org.labkey.api.security.User;
 import org.labkey.api.security.UserManager.UserListener;
 
-import java.beans.PropertyChangeEvent;
-
 /**
  * User: adam
  * Date: Nov 5, 2008

announcements/src/org/labkey/announcements/NotificationSettingsImporterFactory.java

@@ -15,7 +15,6 @@
  */
 package org.labkey.announcements;
 
-import org.jetbrains.annotations.NotNull;
 import org.labkey.announcements.model.AnnouncementManager;
 import org.labkey.api.admin.AbstractFolderImportFactory;
 import org.labkey.api.admin.FolderArchiveDataTypes;
@@ -26,13 +25,9 @@
 import org.labkey.api.message.settings.MessageConfigService;
 import org.labkey.api.notification.EmailService;
 import org.labkey.api.pipeline.PipelineJob;
-import org.labkey.api.pipeline.PipelineJobWarning;
 import org.labkey.api.writer.VirtualFile;
 import org.labkey.folder.xml.NotificationsType;
 
-import java.util.Collection;
-import java.util.Collections;
-
 /**
  * User: cnathe
  * Date: 10/31/12

announcements/src/org/labkey/announcements/ToursController.java

@@ -53,7 +53,7 @@ public ToursController()
     // Anyone with read permission can attempt to view the list.  ToursTable will do further permission checking.
     @RequiresPermission(ReadPermission.class)
     @SuppressWarnings("UnusedDeclaration")
-    public class BeginAction extends SimpleViewAction<QueryForm>
+    public static class BeginAction extends SimpleViewAction<QueryForm>
     {
         @Override
         public ModelAndView getView(QueryForm queryForm, BindException errors)
@@ -86,7 +86,7 @@ public static ActionURL getEditTourURL(Container c)
 
     @ActionNames("edit, editTour")
     @RequiresPermission(ReadPermission.class) //will check below
-    public class EditTourAction extends SimpleViewAction<EditTourForm>
+    public static class EditTourAction extends SimpleViewAction<EditTourForm>
     {
         @Override
         public ModelAndView getView(EditTourForm editTourForm, BindException errors)
@@ -118,7 +118,7 @@ public void addNavTrail(NavTree root)
 
     @ActionNames("tours, saveTour")
     @RequiresPermission(ReadPermission.class) //will check below
-    public class SaveTourAction extends MutatingApiAction<SimpleApiJsonForm>
+    public static class SaveTourAction extends MutatingApiAction<SimpleApiJsonForm>
     {
         @Override
         public void validateForm(SimpleApiJsonForm form, Errors errors)
@@ -173,7 +173,7 @@ public Object execute(SimpleApiJsonForm form, BindException errors)
     }
 
     @RequiresPermission(ReadPermission.class)
-    public class GetTourAction extends MutatingApiAction<SimpleApiJsonForm>
+    public static class GetTourAction extends MutatingApiAction<SimpleApiJsonForm>
     {
 
         @Override

announcements/src/org/labkey/announcements/api/AnnouncementImpl.java

@@ -20,7 +20,6 @@
 import org.labkey.api.announcements.api.Announcement;
 import org.labkey.api.attachments.Attachment;
 import org.labkey.api.data.Container;
-import org.labkey.api.security.User;
 import org.labkey.api.wiki.WikiRendererType;
 
 import java.util.Collection;

announcements/src/org/labkey/announcements/api/AnnouncementServiceImpl.java

@@ -96,7 +96,7 @@ public Announcement insertAnnouncement(Container c, User u, String title, String
                 }
             }
 
-            if (validMemberListIds.size() > 0)
+            if (!validMemberListIds.isEmpty())
             {
                 // insert.setMemberListIds(validMemberListIds); // This gets set in AnnouncementManager.validateModelWithSideEffects by parsing the memberListInput
                 insert.setMemberListInput(StringUtils.join(validMemberListIds, "\n")); // Pretend this is coming as comma-separated input from a form

announcements/src/org/labkey/announcements/customizeAnnouncementWebPart.jsp

@@ -15,17 +15,17 @@
  * limitations under the License.
  */
 %>
-<%@ page import="org.apache.commons.lang3.StringUtils" %>
 <%@ page import="org.labkey.api.view.HttpView" %>
 <%@ page import="org.labkey.api.view.Portal" %>
 <%@ page import="org.labkey.api.view.ViewContext" %>
+<%@ page import="java.util.Objects" %>
 <%@ taglib prefix="labkey" uri="http://www.labkey.org/taglib" %>
 <%@ page extends="org.labkey.api.jsp.JspBase" %>
 
 <%
     Portal.WebPart webPart = (Portal.WebPart)HttpView.currentModel();
     ViewContext context = getViewContext();
-    String selected = StringUtils.defaultString(webPart.getPropertyMap().get("style"), "full");
+    String selected = Objects.toString(webPart.getPropertyMap().get("style"), "full");
 %>
 
 <labkey:form name="frmCustomize" method="post" action="<%=webPart.getCustomizePostURL(context)%>">

announcements/src/org/labkey/announcements/model/AnnouncementDigestProvider.java

@@ -174,7 +174,7 @@ private static String loadBody()
             }
             catch (IOException e)
             {
-                throw new UnexpectedException(e);
+                throw UnexpectedException.wrap(e);
             }
         }
 
@@ -194,20 +194,19 @@ protected void addCustomReplacements(Replacements replacements)
 
         private void initReason()
         {
-            StringBuilder sb = new StringBuilder();
-            sb.append("You have received this email because you are signed up for a daily digest of new posts to <a href=\"");
-            sb.append(PageFlowUtil.filter(dailyDigestBean.boardURL.getURIString()));
-            sb.append("\">");
-            sb.append(PageFlowUtil.filter(dailyDigestBean.boardPath));
-            sb.append("</a> at <a href=\"");
-            sb.append(PageFlowUtil.filter(dailyDigestBean.siteUrl));
-            sb.append("\">");
-            sb.append(PageFlowUtil.filter(dailyDigestBean.siteUrl));
-            sb.append("</a>. If you no longer wish to receive these notifications, please <a href=\"");
-            sb.append(PageFlowUtil.filter(dailyDigestBean.removeURL.getURIString()));
-            sb.append("\">change your email preferences</a>.");
-
-            reasonForEmail = sb.toString();
+            String sb = "You have received this email because you are signed up for a daily digest of new posts to <a href=\"" +
+                    PageFlowUtil.filter(dailyDigestBean.boardURL.getURIString()) +
+                    "\">" +
+                    PageFlowUtil.filter(dailyDigestBean.boardPath) +
+                    "</a> at <a href=\"" +
+                    PageFlowUtil.filter(dailyDigestBean.siteUrl) +
+                    "\">" +
+                    PageFlowUtil.filter(dailyDigestBean.siteUrl) +
+                    "</a>. If you no longer wish to receive these notifications, please <a href=\"" +
+                    PageFlowUtil.filter(dailyDigestBean.removeURL.getURIString()) +
+                    "\">change your email preferences</a>.";
+
+            reasonForEmail = sb;
         }
 
         private void initPosts()

announcements/src/org/labkey/announcements/model/AnnouncementManager.java

@@ -408,13 +408,12 @@ private static void notifyModerators(Container c, User user, AnnouncementModel a
                 msg.setFrom(LookAndFeelProperties.getInstance(c).getSystemEmailAddress());
                 msg.setSubject("New " + name.toLowerCase() + " in " + c.getPath() + " (" + c.getTitle() + ") requires moderator review");
 
-                StringBuilder content = new StringBuilder();
-                content.append("Please visit the Moderator Review page at ").append(new ActionURL(ModeratorReviewAction.class, c).getURIString());
-                content.append("\n\nSubject: ").append(ann.getTitle());
-                content.append("\nUser: ").append(user.getDisplayName(user)).append(" (").append(user.getEmail()).append(")");
-                content.append("\n").append(name).append(": ").append(AnnouncementsController.getThreadURL(c, ann.getEntityId(), ann.getRowId()).getURIString());
+                String content = "Please visit the Moderator Review page at " + new ActionURL(ModeratorReviewAction.class, c).getURIString() +
+                        "\n\nSubject: " + ann.getTitle() +
+                        "\nUser: " + user.getDisplayName(user) + " (" + user.getEmail() + ")" +
+                        "\n" + name + ": " + AnnouncementsController.getThreadURL(c, ann.getEntityId(), ann.getRowId()).getURIString();
 
-                msg.setTextContent(content.toString());
+                msg.setTextContent(content);
                 emailer.addMessage(toList, msg);
                 emailer.start();
             }
@@ -1248,7 +1247,7 @@ private static String loadBody()
             }
             catch (IOException e)
             {
-                throw new UnexpectedException(e);
+                throw UnexpectedException.wrap(e);
             }
         }
 

announcements/src/org/labkey/announcements/model/DiscussionServiceImpl.java

@@ -60,7 +60,7 @@
 public class DiscussionServiceImpl implements DiscussionService
 {
     @Override
-    public WebPartView startDiscussion(Container c, User user, String identifier, ActionURL pageURL, URLHelper cancelURL, String title, String summary, boolean allowMultipleDiscussions)
+    public WebPartView<?> startDiscussion(Container c, User user, String identifier, ActionURL pageURL, URLHelper cancelURL, String title, String summary, boolean allowMultipleDiscussions)
     {
         if (!allowMultipleDiscussions)
         {
@@ -110,7 +110,7 @@ public static ActionURL fromSaved(String saved)
     }
 
 
-    public WebPartView getDiscussion(Container c, URLHelper currentURL, AnnouncementModel ann, User user)
+    public WebPartView<?> getDiscussion(Container c, URLHelper currentURL, AnnouncementModel ann, User user)
     {
         // NOTE: don't pass in AnnouncementModel, it came from getBareAnnouncements()
         return new AnnouncementsController.ThreadView(c, currentURL, user, null, ann.getEntityId());
@@ -147,7 +147,7 @@ public DiscussionService.DiscussionView getDiscussionArea(Container c, User user
             {
                 discussionId = Integer.parseInt(id);
             }
-            else if (displayFirstDiscussionByDefault && params.isEmpty() && discussions.size() > 0)
+            else if (displayFirstDiscussionByDefault && params.isEmpty() && !discussions.isEmpty())
             {
                 discussionId = discussions.get(0).getRowId();
             }
@@ -168,7 +168,7 @@ else if (displayFirstDiscussionByDefault && params.isEmpty() && discussions.size
             // clean up discussion parameters (in case caller didn't)
             pageURL.deleteScopeParameters("discussion");
 
-            WebPartView start = startDiscussion(c, user, objectId, pageURL, adjustedCurrentURL, newDiscussionTitle, "", allowMultipleDiscussions);
+            WebPartView<?> start = startDiscussion(c, user, objectId, pageURL, adjustedCurrentURL, newDiscussionTitle, "", allowMultipleDiscussions);
             String title;
 
             if (start instanceof AnnouncementsController.ThreadView)
@@ -188,8 +188,8 @@ else if (displayFirstDiscussionByDefault && params.isEmpty() && discussions.size
         {
             AnnouncementModel selected = null;
 
-            WebPartView discussionView = null;
-            HttpView respondView = null;
+            WebPartView<?> discussionView = null;
+            HttpView<?> respondView = null;
 
             if (discussionId != 0)
             {
@@ -246,7 +246,7 @@ public void deleteDiscussions(Container c, User user, String... identifiers)
     @Override
     public void deleteDiscussions(Container container, User user, Collection<String> identifiers)
     {
-        Collection<AnnouncementModel> discussions = AnnouncementManager.getDiscussions(container, identifiers.toArray(new String[identifiers.size()]));
+        Collection<AnnouncementModel> discussions = AnnouncementManager.getDiscussions(container, identifiers.toArray(new String[0]));
         for (AnnouncementModel ann : discussions)
         {
             AnnouncementManager.deleteAnnouncement(container, ann.getRowId());
@@ -328,17 +328,17 @@ public static class AnchorView extends HtmlView
     }
 
 
-    public static class ThreadWrapper extends WebPartView
+    public static class ThreadWrapper extends WebPartView<Object>
     {
         String _id;
         String _class = "labkey-hidden";
         VBox _vbox;
 
-        ThreadWrapper(URLHelper currentURL, String caption, HttpView... views)
+        ThreadWrapper(URLHelper currentURL, String caption, HttpView<?>... views)
         {
             super(FrameType.NONE);
             _vbox = new VBox();
-            for (HttpView v : views)
+            for (HttpView<?> v : views)
             {
                 if (v != null)
                 {
@@ -354,7 +354,7 @@ public static class ThreadWrapper extends WebPartView
 
             _id = "discussionBox" + UniqueID.getRequestScopedUID(HttpView.currentRequest());
 
-            for (HttpView view : views)
+            for (HttpView<?> view : views)
             {
                 if (view != null)
                     addClientDependencies(view.getClientDependencies());
@@ -399,7 +399,7 @@ public void doEndTag(PrintWriter out)
     }
 
 
-    public static class PickerView extends JspView
+    public static class PickerView extends JspView<Object>
     {
         final public String discussionAreaId;
         final public URLHelper pageURL;

announcements/src/org/labkey/announcements/model/EmailPrefsSelector.java

@@ -105,7 +105,7 @@ public boolean shouldSend(@Nullable AnnouncementModel ann, User user)
         // log information to mothership (to help track this down) and return false (to avoid subsequent NPE).
         if (null == up)
         {
-            ExceptionUtil.logExceptionToMothership(HttpView.currentRequest(), new IllegalStateException("UserPreference is null for user: " + user.getEmail() + ", ann: " + (null != ann ? ann.getRowId() : null) + ", c: " + _c.toString() + "\n" + pp.toString()));
+            ExceptionUtil.logExceptionToMothership(HttpView.currentRequest(), new IllegalStateException("UserPreference is null for user: " + user.getEmail() + ", ann: " + (null != ann ? ann.getRowId() : null) + ", c: " + _c.toString() + "\n" + pp));
             return false;
         }
 
@@ -213,7 +213,7 @@ UserPreference getApplicablePreference(@Nullable AnnouncementModel ann)
         @Override
         public String toString()
         {
-            return "PreferencePicker: " + _c.getId() + " " + _preferenceMap.toString();
+            return "PreferencePicker: " + _c.getId() + " " + _preferenceMap;
         }
     }
 }

announcements/src/org/labkey/announcements/model/TourModel.java

@@ -111,7 +111,7 @@ public JSONObject abbrevDef()
     public JSONObject toJSON()
     {
         JSONObject out = new JSONObject();
-        if (!getJson().equals(""))
+        if (!getJson().isEmpty())
         {
               out = new JSONObject(getJson());
         }

announcements/src/org/labkey/announcements/query/ForumSubscriptionTable.java

@@ -116,9 +116,9 @@ public QueryUpdateService getUpdateService()
 
     private static class SubscriptionTarget
     {
-        @NotNull private User _user;
-        @NotNull private Container _container;
-        @NotNull private String _srcIdentifier;
+        @NotNull private final User _user;
+        @NotNull private final Container _container;
+        @NotNull private final String _srcIdentifier;
 
         private SubscriptionTarget(@NotNull User user, @NotNull Container container, @NotNull String srcIdentifier)
         {
@@ -203,7 +203,7 @@ private SubscriptionTarget getTargets(Map<String, Object> row, User user, Contai
                 targetContainer = ContainerManager.getForId(folderId.toString());
                 if (targetContainer == null)
                 {
-                    throw new InvalidKeyException("No such Folder: " + folderId.toString());
+                    throw new InvalidKeyException("No such Folder: " + folderId);
                 }
             }
 

announcements/src/org/labkey/announcements/update.jsp

@@ -144,8 +144,8 @@ if (settings.hasExpires())
                     for (Attachment att : ann.getAttachments())
                 {
                     x++;
-                    id = makeId("remove_");
-                    %><tr id="attach-<%=x%>">
+                    makeId("remove_");
+                %><tr id="attach-<%=x%>">
                         <td><img src="<%=getWebappURL(att.getFileIcon())%>" alt="logo"/>&nbsp;<%= h(att.getName()) %></td>
                         <td><%= link("remove").onClick("LABKEY.discuss.removeAttachment(" + q(ann.getEntityId()) + "," + q(att.getName()) + "," +  q("attach-"+x) + ");") %></td>
                     </tr><%

api/gwtsrc/org/labkey/api/gwt/client/AuditBehaviorType.java

@@ -25,7 +25,7 @@ public enum AuditBehaviorType
     DETAILED("Detailed"),
     SUMMARY("Summary");
 
-    private String _label;
+    private final String _label;
 
     AuditBehaviorType(String label)
     {

api/gwtsrc/org/labkey/api/gwt/client/DefaultScaleType.java

@@ -24,7 +24,7 @@ public enum DefaultScaleType
     LINEAR("Linear"),
     LOG("Log");
 
-    private String _label;
+    private final String _label;
 
     DefaultScaleType(String label)
     {

api/gwtsrc/org/labkey/api/gwt/client/assay/model/GWTProtocol.java

@@ -46,16 +46,16 @@ public class GWTProtocol implements IsSerializable
     private List<GWTDomain<GWTPropertyDescriptor>> _domains;
 
     private List<String> _availablePlateTemplates;
-    private Map<String, String> _availableMetadataInputFormats = new HashMap<String, String>();
+    private Map<String, String> _availableMetadataInputFormats = new HashMap<>();
     private String _metadataInputFormatHelp;
 
     private String _selectedPlateTemplate;
     private String _selectedMetadataInputFormat;
 
     /** Scripts defined in the module itself, associated with the assay provider */
-    private List<String> _moduleTransformScripts = new ArrayList<String>();
+    private List<String> _moduleTransformScripts = new ArrayList<>();
     /** Scripts defined in the assay definition */
-    private List<Map<String, Object>> _protocolTransformScripts = new ArrayList<>();
+    private final List<Map<String, Object>> _protocolTransformScripts = new ArrayList<>();
 
     private List<String> _availableDetectionMethods;
     private String _selectedDetectionMethod;