Minor auto-refactor code cleanup on a massive scale

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.

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

@@ -35,7 +35,6 @@ public interface AlignmentStep extends PipelineStep
 {
     /**
      * Creates any indexes needed by this aligner if not already present.
-     * @throws PipelineJobException
      */
     IndexOutput createIndex(ReferenceGenome referenceGenome, File outputDir) throws PipelineJobException;
 
@@ -49,7 +48,6 @@ default String getIndexCachedDirName(PipelineJob job)
      * @param inputFastqs1 The forward FASTQ file(s). In most cases this is a single FASTQ. The aligner must return true for canAlignMultiplePairsAtOnce() otherwise.
      * @param inputFastqs2 The second FASTQ(s), if using paired end data
      * @param basename The basename to use as the output
-     * @throws PipelineJobException
      */
     AlignmentOutput performAlignment(Readset rs, List<File> inputFastqs1, @Nullable List<File> inputFastqs2, File outputDirectory, ReferenceGenome referenceGenome, String basename, String readGroupId, @Nullable String platformUnit) throws PipelineJobException;
 
@@ -102,7 +100,6 @@ interface AlignmentOutput extends PipelineStepOutput
     /**
      * Optional.  Allows this analysis to gather any information from the server required to execute the alignment.  This information needs to be serialized
      * to run remotely, which could be as simple as writing to a text file.
-     * @throws PipelineJobException
      */
     default void init(SequenceAnalysisJobSupport support) throws PipelineJobException
     {

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

@@ -31,7 +31,6 @@ public interface AnalysisStep extends PipelineStep
     /**
      * Optional.  Allows this analysis to gather any information from the server required to execute the analysis.  This information needs to be serialized
      * to run remotely, which could be as simple as writing to a text file.
-     * @throws PipelineJobException
      */
     default void init(SequenceAnalysisJobSupport support) throws PipelineJobException
     {

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

@@ -3,7 +3,6 @@
 import org.jetbrains.annotations.Nullable;
 import org.labkey.api.pipeline.PipelineJobException;
 import org.labkey.api.sequenceanalysis.model.Readset;
-import org.labkey.api.util.Pair;
 
 import java.io.File;
 

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

@@ -29,7 +29,7 @@
 public class CommandLineParam
 {
     private final String _argName;
-    protected boolean _isSwitch = false;
+    protected boolean _isSwitch;
 
     private CommandLineParam(String argName, boolean isSwitch)
     {

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

@@ -9,21 +9,13 @@ public interface PipelineOutputTracker
 {
     /**
      * Add an intermediate file.  If the user selected 'delete intermediates', this will be deleted on job success.
-     * @param file
      */
     void addIntermediateFile(File file);
 
     void addIntermediateFiles(Collection<File> files);
 
     /**
      * Add a SequenceOutputFile for this job.  These files are tracked and displayed through the browser UI.
-     * @param file
-     * @param label
-     * @param category
-     * @param readsetId
-     * @param analysisId
-     * @param genomeId
-     * @param description
      */
     void addSequenceOutput(File file, String label, String category, @Nullable Integer readsetId, @Nullable Integer analysisId, @Nullable Integer genomeId, @Nullable String description);
 

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

@@ -16,7 +16,6 @@
 package org.labkey.api.sequenceanalysis.pipeline;
 
 import org.jetbrains.annotations.Nullable;
-import org.labkey.api.sequenceanalysis.model.Readset;
 import org.labkey.api.util.Pair;
 
 import java.io.File;
@@ -34,15 +33,11 @@ public interface PipelineStepOutput extends PipelineOutputTracker
 {
     /**
      * Add an experiment input to this pipeline step
-     * @param input
-     * @param role
      */
     void addInput(File input, String role);
 
     /**
      * Add an experiment output to this pipeline step
-     * @param output
-     * @param role
      */
     void addOutput(File output, String role);
 
@@ -65,8 +60,6 @@ public interface PipelineStepOutput extends PipelineOutputTracker
     /**
      * Add an intermediate file.  If the user selected 'delete intermediates', this will be deleted on job success.
      * This will also be recorded as a step output with this role.
-     * @param file
-     * @param role
      */
     void addIntermediateFile(File file, String role);
 

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

@@ -3,7 +3,6 @@
 import org.apache.commons.io.IOUtils;
 import org.apache.logging.log4j.Level;
 import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
 import org.labkey.api.util.StringUtilsLabKey;
 
 import java.io.BufferedInputStream;

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

@@ -1,7 +1,6 @@
 package org.labkey.api.sequenceanalysis.pipeline;
 
 import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
 import org.labkey.api.pipeline.PipelineJobException;
 
 import java.io.File;

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

@@ -1,7 +1,6 @@
 package org.labkey.api.sequenceanalysis.pipeline;
 
 import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
 import org.jetbrains.annotations.Nullable;
 import org.labkey.api.sequenceanalysis.run.AbstractCommandWrapper;
 

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

@@ -136,7 +136,6 @@ default boolean isVisible()
 
     /**
      * Provides the opportunity for the handler to validate parameters prior to running
-     * @param params
      * @return List of error messages.  Null or empty list indicates no errors.
      */
     default List<String> validateParameters(List<SequenceOutputFile> outputFiles, JSONObject params)
@@ -174,8 +173,6 @@ interface SequenceOutputProcessor extends SequenceProcessor
          * Allows handlers to perform setup on the webserver prior to remote running.  This will be run in the background as a pipeline job.
          * @param ctx Provides context about the active pipeline job
          * @param inputFiles      The list of input files to process
-         * @param actions
-         * @param outputsToCreate
          */
         default void init(JobContext ctx, List<SequenceOutputFile> inputFiles, List<RecordedAction> actions, List<SequenceOutputFile> outputsToCreate) throws UnsupportedOperationException, PipelineJobException
         {
@@ -189,10 +186,6 @@ default void init(JobContext ctx, List<SequenceOutputFile> inputFiles, List<Reco
          *
          * @param support Provides context about the active pipeline job
          * @param inputFiles The list of input files to process
-         * @param params
-         * @param outputDir
-         * @param actions
-         * @param outputsToCreate
          */
         void processFilesOnWebserver(PipelineJob job, SequenceAnalysisJobSupport support, List<SequenceOutputFile> inputFiles, JSONObject params, File outputDir, List<RecordedAction> actions, List<SequenceOutputFile> outputsToCreate) throws UnsupportedOperationException, PipelineJobException;
 
@@ -211,21 +204,13 @@ interface SequenceReadsetProcessor extends SequenceProcessor
          * @param job             The pipeline job running this task
          * @param support Provides context about the active pipeline job
          * @param readsets      The list of readsets to process
-         * @param params
-         * @param outputDir
-         * @param actions
-         * @param outputsToCreate
          */
         void init(PipelineJob job, SequenceAnalysisJobSupport support, List<Readset> readsets, JSONObject params, File outputDir, List<RecordedAction> actions, List<SequenceOutputFile> outputsToCreate) throws UnsupportedOperationException, PipelineJobException;
 
         /**
          *
          * @param support Provides context about the active pipeline job
          * @param readsets The list of readsets to process
-         * @param params
-         * @param outputDir
-         * @param actions
-         * @param outputsToCreate
          */
         void processFilesOnWebserver(PipelineJob job, SequenceAnalysisJobSupport support, List<Readset> readsets, JSONObject params, File outputDir, List<RecordedAction> actions, List<SequenceOutputFile> outputsToCreate) throws UnsupportedOperationException, PipelineJobException;
 

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

@@ -129,11 +129,6 @@ static public void setInstance(SequencePipelineService instance)
 
     /**
      *
-     * @param input
-     * @param log
-     * @param startColumnIdx The 1-based column on which to sort.  BED files are 2 and GTF/GFF are 4
-     * @throws IOException
-     * @throws PipelineJobException
      */
     abstract public void sortROD(File input, Logger log, Integer startColumnIdx) throws IOException, PipelineJobException;
 

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

@@ -4,7 +4,6 @@
 import org.apache.commons.io.FileUtils;
 import org.apache.commons.lang3.time.DurationFormatUtils;
 import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
 import org.jetbrains.annotations.Nullable;
 import org.labkey.api.pipeline.PipelineJobException;
 import org.labkey.api.sequenceanalysis.run.PicardWrapper;

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

@@ -56,7 +56,7 @@ public interface TaskFileManager extends PipelineOutputTracker
 
     boolean isDeleteIntermediateFiles();
 
-    public boolean performCleanupAfterEachStep();
+    boolean performCleanupAfterEachStep();
 
     boolean isCopyInputsLocally();
 

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

@@ -27,7 +27,6 @@
 
 import java.util.ArrayList;
 import java.util.List;
-import java.util.Map;
 
 /**
  * User: bimber