Minor auto-refactor code cleanup on a massive scale

SkylineToolsStore/src/org/labkey/skylinetoolsstore/RatingManager.java

@@ -87,7 +87,7 @@ public Rating[] getRatingsByToolAllVersions(String toolLsid)
             for (SkylineTool tool : tools)
                 ratings.addAll(Arrays.asList(getRatingsByToolId(tool.getRowId())));
         }
-        return ratings.toArray(new Rating[ratings.size()]);
+        return ratings.toArray(new Rating[0]);
     }
 
     public boolean userLeftRating(String toolLsid, User user)

SkylineToolsStore/src/org/labkey/skylinetoolsstore/SkylineToolsStoreController.java

@@ -129,7 +129,7 @@ public SkylineToolsStoreController()
     }
 
     @RequiresPermission(ReadPermission.class)
-    public class BeginAction extends SimpleViewAction
+    public static class BeginAction extends SimpleViewAction<Object>
     {
         @Override
         public ModelAndView getView(Object o, BindException errors) throws Exception
@@ -460,7 +460,7 @@ public ModelAndView handleRequestInternal(HttpServletRequest httpServletRequest,
                 ArrayList<User> toolOwnersUsers = parsedOwners.first;
                 ArrayList<String> toolOwnersInvalid = parsedOwners.second;
 
-                if (toolOwnersInvalid.size() > 0)
+                if (!toolOwnersInvalid.isEmpty())
                 {
                     getViewContext().getRequest().setAttribute(BindingResult.MODEL_KEY_PREFIX + "form",
                         UNKNOWN_USERS + StringUtils.join(toolOwnersInvalid, ", "));
@@ -607,7 +607,7 @@ else if (!getContainer().hasPermission(getUser(), InsertPermission.class))
             getViewContext().getRequest().setAttribute(BindingResult.MODEL_KEY_PREFIX + "sender", sender);
             getViewContext().getRequest().setAttribute(BindingResult.MODEL_KEY_PREFIX + "updatetarget", updateTargetString);
             getViewContext().getRequest().setAttribute(BindingResult.MODEL_KEY_PREFIX + "toolowners", toolOwners);
-            return new JspView("/org/labkey/skylinetoolsstore/view/SkylineToolsStoreUpload.jsp", null);
+            return new JspView<>("/org/labkey/skylinetoolsstore/view/SkylineToolsStoreUpload.jsp", null);
         }
 
         @Override
@@ -667,9 +667,9 @@ protected ModelAndView handleRequestInternal(HttpServletRequest httpServletReque
             final String ratingIdString = httpServletRequest.getParameter("ratingId");
             int ratingId;
             try {
-                ratingId = (ratingIdString != null && !ratingIdString.isEmpty()) ? Integer.parseInt(ratingIdString) : -1;;
+                ratingId = (ratingIdString != null && !ratingIdString.isEmpty()) ? Integer.parseInt(ratingIdString) : -1;
             } catch(Exception e) {
-                return new JspView("/org/labkey/skylinetoolsstore/view/SkylineRating.jsp", null);
+                return new JspView<>("/org/labkey/skylinetoolsstore/view/SkylineRating.jsp", null);
             }
             Rating rating = (ratingId < 0) ? null : RatingManager.get().getRatingById(ratingId);
             final SkylineTool tool = SkylineToolsStoreManager.get().getTool((toolId >= 0) ? toolId : rating.getToolId());
@@ -679,7 +679,7 @@ protected ModelAndView handleRequestInternal(HttpServletRequest httpServletReque
             try {
                 ratingValue = Integer.parseInt(ratingValueString);
             } catch(Exception e) {
-                return new JspView("/org/labkey/skylinetoolsstore/view/SkylineRating.jsp", null);
+                return new JspView<>("/org/labkey/skylinetoolsstore/view/SkylineRating.jsp", null);
             }
             final String ratingTitle = httpServletRequest.getParameter("title");
             final String review = httpServletRequest.getParameter("review");
@@ -701,7 +701,7 @@ else if (ratingValue < 1 || ratingValue > 5)
                 getViewContext().getRequest().setAttribute(BindingResult.MODEL_KEY_PREFIX + "form",
                     NO_RATING);
             }
-            else if (review == null || review.length() == 0)
+            else if (review == null || review.isEmpty())
             {
                 getViewContext().getRequest().setAttribute(BindingResult.MODEL_KEY_PREFIX + "form",
                     NO_REVIEW);
@@ -748,7 +748,7 @@ else if (tool == null || (ratingId >= 0 && rating == null))
             if (review != null)
                 getViewContext().getRequest().setAttribute(BindingResult.MODEL_KEY_PREFIX + "formReview", review);
 
-            return new JspView("/org/labkey/skylinetoolsstore/view/SkylineRating.jsp", null);
+            return new JspView<>("/org/labkey/skylinetoolsstore/view/SkylineRating.jsp", null);
         }
 
         @Override
@@ -813,7 +813,7 @@ public ModelAndView handleRequestInternal(HttpServletRequest httpServletRequest,
             {
                 httpServletRequest.setAttribute(BindingResult.MODEL_KEY_PREFIX + "form", INVALID_TOOL_ID + " " + suppTargetString);
                 httpServletRequest.setAttribute(BindingResult.MODEL_KEY_PREFIX + "supptarget", suppTargetString);
-                return new JspView("/org/labkey/skylinetoolsstore/view/SkylineToolSupplementUpload.jsp", null);
+                return new JspView<>("/org/labkey/skylinetoolsstore/view/SkylineToolSupplementUpload.jsp", null);
             }
 
             SkylineTool tool = SkylineToolsStoreManager.get().getTool(suppTarget);
@@ -846,7 +846,7 @@ public ModelAndView handleRequestInternal(HttpServletRequest httpServletRequest,
             }
 
             getViewContext().getRequest().setAttribute(BindingResult.MODEL_KEY_PREFIX + "supptarget", suppTargetString);
-            return new JspView("/org/labkey/skylinetoolsstore/view/SkylineToolSupplementUpload.jsp", null);
+            return new JspView<>("/org/labkey/skylinetoolsstore/view/SkylineToolSupplementUpload.jsp", null);
         }
 
         @Override
@@ -902,7 +902,7 @@ public void checkPermissions() throws UnauthorizedException
     }
 
     @RequiresLogin
-    public class DeleteAction extends FormHandlerAction<IdForm>
+    public static class DeleteAction extends FormHandlerAction<IdForm>
     {
         @Override
         public URLHelper getSuccessURL(IdForm idForm)
@@ -1002,7 +1002,7 @@ public class DeleteLatestAction extends AbstractController implements Permission
         @Override
         public ModelAndView handleRequestInternal(HttpServletRequest httpServletRequest, HttpServletResponse httpServletResponse) throws Exception
         {
-            Integer id;
+            int id;
             try {
                 id = Integer.parseInt(httpServletRequest.getParameter("id"));
             }
@@ -1156,7 +1156,7 @@ public void checkPermissions() throws UnauthorizedException
 
     @RequiresNoPermission
     @ActionNames("downloadFile")
-    public class DownloadToolFileAction extends SimpleViewAction<DownloadFileForm> implements PermissionCheckable
+    public static class DownloadToolFileAction extends SimpleViewAction<DownloadFileForm> implements PermissionCheckable
     {
         @Override
         public ModelAndView getView(DownloadFileForm form, BindException errors) throws Exception
@@ -1243,8 +1243,7 @@ public ModelAndView getView(ViewToolDetailsForm form, BindException errors) thro
                 _tool = SkylineToolsStoreManager.get().getTool(toolId);
                 if (_tool == null)
                 {
-                    StringBuilder msg = new StringBuilder("Could not find tool ").append(" by Id ").append(toolId);
-                    errors.reject(SpringActionController.ERROR_MSG,  msg.toString());
+                    errors.reject(SpringActionController.ERROR_MSG, "Could not find tool " + " by Id " + toolId);
                     return new SimpleErrorView(errors);
                 }
             }
@@ -1396,7 +1395,7 @@ public ModelAndView handleRequestInternal(HttpServletRequest httpServletRequest,
             getViewContext().getRequest().setAttribute(BindingResult.MODEL_KEY_PREFIX + "toolowners", toolOwners);
             getViewContext().getRequest().setAttribute(BindingResult.MODEL_KEY_PREFIX + "sender", sender);
             getViewContext().getRequest().setAttribute(BindingResult.MODEL_KEY_PREFIX + "updatetarget", updateTargetString);
-            return new JspView("/org/labkey/skylinetoolsstore/view/SkylineToolManageOwners.jsp", null);
+            return new JspView<>("/org/labkey/skylinetoolsstore/view/SkylineToolManageOwners.jsp", null);
         }
 
         @Override
@@ -1414,7 +1413,7 @@ public class UpdatePropertyAction extends AbstractController implements Permissi
         @Override
         public ModelAndView handleRequestInternal(HttpServletRequest httpServletRequest, HttpServletResponse httpServletResponse) throws Exception
         {
-            final Integer id = Integer.parseInt(httpServletRequest.getParameter("id"));
+            final int id = Integer.parseInt(httpServletRequest.getParameter("id"));
 
             final SkylineTool tool = SkylineToolsStoreManager.get().getTool(id);
             if(tool == null)

SkylineToolsStore/src/org/labkey/skylinetoolsstore/SkylineToolsStoreModule.java

@@ -32,7 +32,6 @@
 import org.labkey.skylinetoolsstore.model.SkylineTool;
 import org.labkey.skylinetoolsstore.view.SkylineToolsStoreWebPart;
 
-import java.lang.reflect.InvocationTargetException;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collection;
@@ -66,19 +65,21 @@ public boolean hasScripts()
     @NotNull
     protected Collection<WebPartFactory> createWebPartFactories()
     {
-        return new ArrayList<WebPartFactory>(
-            Arrays.asList(
-                    new BaseWebPartFactory("Skyline Tool Store") {
+        return new ArrayList<>(
+                Arrays.asList(
+                        new BaseWebPartFactory("Skyline Tool Store")
                         {
-                            addLegacyNames("Skyline Tools Store");
-                        }
-                        @Override
-                        public WebPartView getWebPartView(@NotNull ViewContext portalCtx, Portal.@NotNull WebPart webPart) throws WebPartConfigurationException
-                        {
-                            return new SkylineToolsStoreWebPart();
+                            {
+                                addLegacyNames("Skyline Tools Store");
+                            }
+
+                            @Override
+                            public WebPartView getWebPartView(@NotNull ViewContext portalCtx, Portal.@NotNull WebPart webPart) throws WebPartConfigurationException
+                            {
+                                return new SkylineToolsStoreWebPart();
+                            }
                         }
-                    }
-            ));
+                ));
     }
 
     @Override

SkylineToolsStore/src/org/labkey/skylinetoolsstore/SkylineToolsStoreSchema.java

@@ -20,8 +20,6 @@
 import org.labkey.api.data.dialect.SqlDialect;
 import org.labkey.api.data.TableInfo;
 
-import java.lang.String;
-
 public class SkylineToolsStoreSchema
 {
     private static final SkylineToolsStoreSchema _instance = new SkylineToolsStoreSchema();

SkylineToolsStore/src/org/labkey/skylinetoolsstore/model/Rating.java

@@ -76,9 +76,8 @@ public void setRowId(Integer rowId)
 
     public boolean equals(Object obj)
     {
-        if (!(obj instanceof Rating))
+        if (!(obj instanceof Rating p))
             return false;
-        Rating p = (Rating)obj;
 
         return Objects.equals(_rating, p.getRating()) &&
                Objects.equals(_toolId, p.getToolId()) &&

SkylineToolsStore/src/org/labkey/skylinetoolsstore/model/SkylineTool.java

@@ -177,9 +177,8 @@ public void setRowId(Integer rowId)
 
     public boolean equals(Object obj)
     {
-        if (!(obj instanceof SkylineTool))
+        if (!(obj instanceof SkylineTool p))
             return false;
-        SkylineTool p = (SkylineTool)obj;
 
         return Objects.equals(_name, p.getName()) &&
                Objects.equals(_authors, p.getAuthors()) &&

lincs/src/org/labkey/lincs/DocImportListener.java

@@ -29,7 +29,7 @@
 
 public class DocImportListener implements ExperimentListener, SkylineDocumentImportListener
 {
-    private static Logger _log = LogManager.getLogger(DocImportListener.class);
+    private static final Logger _log = LogManager.getLogger(DocImportListener.class);
 
     @Override
     public void beforeRunDelete(ExpProtocol protocol, ExpRun run, User user)

lincs/src/org/labkey/lincs/Gct.java

@@ -32,11 +32,11 @@
  */
 public class Gct
 {
-    private List<GctEntity> _probes;
-    private Map<String, Integer> _probeIndexMap;
-    private List<GctEntity> _replicates;
-    private Map<String, Integer> _replicateIndexMap;
-    private GctTable<ProbeReplicate> _areaRatios;
+    private final List<GctEntity> _probes;
+    private final Map<String, Integer> _probeIndexMap;
+    private final List<GctEntity> _replicates;
+    private final Map<String, Integer> _replicateIndexMap;
+    private final GctTable<ProbeReplicate> _areaRatios;
 
     private List<String> _probeAnnotationNames;
     private List<String> _replicateAnnotationNames;
@@ -164,7 +164,7 @@ public List<GctEntity> getSortedReplicates()
         // Sort replicates by the value of the det_plate annotation, and then
         // by replicate name. For custom GCT, the replicate name is:
         // <exp_type>_<plate_number>_<original_replicate_name>
-        List<GctEntity> sortedReplicates = new ArrayList<GctEntity>(_replicates.size());
+        List<GctEntity> sortedReplicates = new ArrayList<>(_replicates.size());
         sortedReplicates.addAll(_replicates);
         sortedReplicates.sort((rep1, rep2) ->
         {
@@ -262,7 +262,7 @@ public void setIgnoredProbeAnnotations(Set<String> ignored)
     public static class GctEntity
     {
         private final String _name;
-        private Map<String, String> _annotations;
+        private final Map<String, String> _annotations;
 
         public GctEntity(String name)
         {
@@ -418,7 +418,7 @@ public String toString()
 
     public interface GctKeyBuilder <T extends GctKey>
     {
-        public T build(String key1, String key2);
+        T build(String key1, String key2);
     }
 
     public static class ProbePlateKeyBuilder implements GctKeyBuilder<ProbeExpTypePlate>
@@ -446,7 +446,7 @@ public GctFileException(String message, Throwable cause)
 
     public static class GctTable <T extends GctKey>
     {
-        private Map<T, String> _map;
+        private final Map<T, String> _map;
         private List<String> _sortedKey2;
 
         public GctTable()