Minor auto-refactor code cleanup on a massive scale (#354)

* Minor auto-refactor code cleanup on a massive scale

* Remove unnecessary cast

Author: labkey-jeckels

OpenLdapSync/src/org/labkey/openldapsync/OpenLdapSyncController.java

@@ -57,7 +57,7 @@ public OpenLdapSyncController()
     }
 
     @RequiresPermission(AdminOperationsPermission.class)
-    public class InitiateLdapSyncAction extends MutatingApiAction<InitiateLdapSyncForm>
+    public static class InitiateLdapSyncAction extends MutatingApiAction<InitiateLdapSyncForm>
     {
         @Override
         public ApiResponse execute(InitiateLdapSyncForm form, BindException errors) throws Exception
@@ -100,7 +100,7 @@ public void setForPreview(boolean forPreview)
     }
 
     @RequiresPermission(AdminPermission.class)
-    public class ListLdapGroupsAction extends ReadOnlyApiAction<LdapForm>
+    public static class ListLdapGroupsAction extends ReadOnlyApiAction<LdapForm>
     {
         @Override
         public ApiResponse execute(LdapForm form, BindException errors) throws Exception
@@ -495,7 +495,7 @@ public void setMemberSyncMode(String memberSyncMode)
     }
 
     @RequiresPermission(AdminOperationsPermission.class)
-    public class TestLdapConnectionAction extends MutatingApiAction<Object>
+    public static class TestLdapConnectionAction extends MutatingApiAction<Object>
     {
         @Override
         public ApiResponse execute(Object form, BindException errors) throws Exception
@@ -545,7 +545,7 @@ public ApiResponse execute(Object form, BindException errors) throws Exception
     }
 
     @RequiresPermission(AdminOperationsPermission.class)
-    public class GetLdapSettingsAction extends ReadOnlyApiAction<Object>
+    public static class GetLdapSettingsAction extends ReadOnlyApiAction<Object>
     {
         @Override
         public ApiResponse execute(Object form, BindException errors)
@@ -569,7 +569,7 @@ public ApiResponse execute(Object form, BindException errors)
 
     @Marshal(Marshaller.Jackson)
     @RequiresPermission(AdminOperationsPermission.class)
-    public class SetLdapSettingsAction extends MutatingApiAction<LdapForm>
+    public static class SetLdapSettingsAction extends MutatingApiAction<LdapForm>
     {
         @Override
         public ApiResponse execute(LdapForm form, BindException errors)
@@ -668,7 +668,7 @@ public ApiResponse execute(LdapForm form, BindException errors)
             if (form.getSyncMode() != null)
                 props.put(LdapSettings.SYNC_MODE_PROP, form.getSyncMode());
 
-            if (form.getAllowedDn() != null && form.getAllowedDn().length() > 0)
+            if (form.getAllowedDn() != null && !form.getAllowedDn().isEmpty())
             {
                 String allowed = StringUtils.join(form.getAllowedDn().toList(), LdapSettings.DELIM);
                 props.put(LdapSettings.ALLOWED_DN_PROP, allowed);

OpenLdapSync/src/org/labkey/openldapsync/ldap/LdapEntry.java

@@ -75,8 +75,8 @@ public boolean isEnabled()
 
         try
         {
-            Integer value = Integer.parseInt(a);
-            return (value.intValue() & 2) == 0;
+            int value = Integer.parseInt(a);
+            return (value & 2) == 0;
         }
         catch (NumberFormatException e)
         {

OpenLdapSync/src/org/labkey/openldapsync/ldap/LdapSettings.java

@@ -466,7 +466,6 @@ public Integer getFrequency()
 
     /**
      * Provides a brief sanity check of the settings, designed to identify problems if a sync will run.
-     * @throws LdapException
      */
     public void validateSettings() throws LdapException
     {
@@ -495,7 +494,7 @@ public void validateSettings() throws LdapException
 
         if (LdapSyncMode.groupWhitelist.equals(mode))
         {
-            if (getGroupWhiteList().size() == 0)
+            if (getGroupWhiteList().isEmpty())
             {
                 throw new LdapException("Cannot choose to sync based on specific groups unless you provide a list of groups to sync");
             }

OpenLdapSync/src/org/labkey/openldapsync/ldap/LdapSyncRunner.java

@@ -14,7 +14,6 @@
 import org.labkey.api.data.Container;
 import org.labkey.api.data.ContainerManager;
 import org.labkey.api.data.RuntimeSQLException;
-import org.labkey.api.data.Selector;
 import org.labkey.api.data.SimpleFilter;
 import org.labkey.api.data.Table;
 import org.labkey.api.data.TableInfo;
@@ -1058,7 +1057,7 @@ public void testIndividualOperations() throws Exception
         }
 
         // This can be used to return LdapEntry objects to support some degree of automated testing without needing a functional LDAP Server
-        public class DummyConnectionWrapper extends LdapConnectionWrapper
+        public static class DummyConnectionWrapper extends LdapConnectionWrapper
         {
             private final List<LdapEntry> _users = new ArrayList<>();
             private final Map<String, MockLdapEntry> _groupMap = new HashMap<>();

QueryExtensions/src/org/labkey/queryextensions/QueryExtensionsController.java

@@ -16,14 +16,7 @@
 
 package org.labkey.queryextensions;
 
-import org.labkey.api.action.SimpleViewAction;
 import org.labkey.api.action.SpringActionController;
-import org.labkey.api.security.RequiresPermission;
-import org.labkey.api.security.permissions.ReadPermission;
-import org.labkey.api.view.JspView;
-import org.labkey.api.view.NavTree;
-import org.springframework.validation.BindException;
-import org.springframework.web.servlet.ModelAndView;
 
 public class QueryExtensionsController extends SpringActionController
 {

QueryExtensions/test/src/org/labkey/test/tests/queryextensions/QueryExtensionsTest.java

@@ -39,7 +39,7 @@ protected void doCleanup(boolean afterTest) throws TestTimeoutException
     @BeforeClass
     public static void setupProject()
     {
-        QueryExtensionsTest init = (QueryExtensionsTest)getCurrentTest();
+        QueryExtensionsTest init = getCurrentTest();
 
         init.doSetup();
     }

SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/GenomeTrigger.java

@@ -16,7 +16,6 @@
 package org.labkey.api.sequenceanalysis;
 
 import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
 import org.labkey.api.data.Container;
 import org.labkey.api.security.User;
 

SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/SequenceAnalysisService.java

@@ -113,10 +113,10 @@ static public void setInstance(SequenceAnalysisService instance)
 
     abstract public void registerReadsetListener(ReadsetListener listener);
 
-    public static interface ReadsetListener
+    public interface ReadsetListener
     {
-        public void onReadsetCreate(User u, Readset rs, @Nullable Readset replacedReadset, @Nullable PipelineJob job);
+        void onReadsetCreate(User u, Readset rs, @Nullable Readset replacedReadset, @Nullable PipelineJob job);
 
-        public boolean isAvailable(Container c, User u);
+        boolean isAvailable(Container c, User u);
     }
 }

SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/AbstractPipelineStepProvider.java

@@ -20,7 +20,6 @@
 import org.json.JSONObject;
 import org.labkey.api.view.template.ClientDependency;
 
-import java.lang.reflect.ParameterizedType;
 import java.util.Collection;
 import java.util.Collections;
 import java.util.LinkedHashSet;
@@ -39,7 +38,7 @@ abstract public class AbstractPipelineStepProvider<StepType extends PipelineStep
     private final String _websiteURL;
     private final String _description;
     private final LinkedHashSet<String> _clientDependencyPaths;
-    private List<ToolParameterDescriptor> _parameters;
+    private final List<ToolParameterDescriptor> _parameters;
 
     public AbstractPipelineStepProvider(String name, String label, @Nullable String toolName, String description, @Nullable List<ToolParameterDescriptor> parameters, @Nullable Collection<String> clientDependencyPaths, @Nullable String websiteURL)
     {

SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/AlignerIndexUtil.java

@@ -1,17 +1,13 @@
 package org.labkey.api.sequenceanalysis.pipeline;
 
 import org.apache.commons.io.FileUtils;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
 import org.jetbrains.annotations.Nullable;
 import org.labkey.api.data.ConvertHelper;
 import org.labkey.api.pipeline.PipelineJobException;
 import org.labkey.api.pipeline.WorkDirectory;
-import org.labkey.api.sequenceanalysis.run.SimpleScriptWrapper;
 
 import java.io.File;
 import java.io.IOException;
-import java.util.Arrays;
 
 /**
  * Created by bimber on 9/6/2014.