Minor auto-refactor code cleanup on a massive scale

OConnorExperiments/src/org/labkey/oconnorexperiments/OConnorExperimentsController.java

@@ -17,7 +17,6 @@
 package org.labkey.oconnorexperiments;
 
 import org.apache.commons.io.FileUtils;
-import org.apache.logging.log4j.Logger;
 import org.apache.logging.log4j.LogManager;
 import org.labkey.api.action.ApiResponse;
 import org.labkey.api.action.ApiSimpleResponse;
@@ -93,7 +92,7 @@ public OConnorExperimentsController()
     }
 
     @RequiresPermission(ReadPermission.class)
-    public class BeginAction extends SimpleViewAction
+    public static class BeginAction extends SimpleViewAction<Object>
     {
         @Override
         public ModelAndView getView(Object o, BindException errors)
@@ -108,7 +107,7 @@ public void addNavTrail(NavTree root)
     }
 
     @RequiresPermission(AdminPermission.class)
-    public class MigrateDataAction extends FormViewAction<UserForm>
+    public static class MigrateDataAction extends FormViewAction<UserForm>
     {
         @Override
         public void validateCommand(UserForm target, Errors errors)
@@ -234,7 +233,7 @@ public boolean handlePost(UserForm form, BindException errors) throws Exception
                     // Move files
                     File sourceFile = new File(fileContentService.getFileRoot(sourceContainer).getPath() + File.separator + "@files", databaseMap.get("expnumber").toString());
                     File targetDir = new File(fileContentService.getFileRoot(targetContainer).getPath() + File.separator + databaseMap.get("expnumber").toString() + File.separator + "@files");
-                    LogManager.getLogger(OConnorExperimentsController.class).info("Copy from file '" + sourceFile.toString() + "' to directory '" + targetDir.toString() +"'" );
+                    LogManager.getLogger(OConnorExperimentsController.class).info("Copy from file '" + sourceFile + "' to directory '" + targetDir +"'" );
                     if (sourceFile.exists())
                     {
                         FileUtils.copyDirectory(sourceFile, targetDir);
@@ -258,7 +257,7 @@ public boolean handlePost(UserForm form, BindException errors) throws Exception
                     Map<String, Object> map = new CaseInsensitiveHashMap<>();
                     map.put("container", databaseMap.get("ContainerStr"));
 
-                    String[] parents = new String[0];
+                    String[] parents;
                     ArrayList<String> parentsEntityId = new ArrayList<>();
                     if (databaseMap.get("expParent") != null)
                     {
@@ -280,9 +279,9 @@ public boolean handlePost(UserForm form, BindException errors) throws Exception
                                 }
                             }
                         }
-                        if (parentsEntityId.size() > 0)
+                        if (!parentsEntityId.isEmpty())
                         {
-                            map.put("ParentExperiments", parentsEntityId.toArray(new String[parentsEntityId.size()]));
+                            map.put("ParentExperiments", parentsEntityId.toArray(new String[0]));
 
                             // workaround, pass user, container - databaseMap.get("Container"), singleton list
                             LogManager.getLogger(OConnorExperimentsController.class).info("Update rows on experiment " + databaseMap.get("expnumber"));
@@ -423,7 +422,7 @@ public void setFinalMigration(boolean finalMigration)
      */
     @RequiresLogin
     @RequiresPermission(InsertPermission.class)
-    public class InsertExperimentAction extends FormHandlerAction
+    public static class InsertExperimentAction extends FormHandlerAction<Object>
     {
         private Container newExperiment;
 
@@ -465,7 +464,7 @@ public boolean handlePost(Object o, BindException errors) throws Exception
 
     @RequiresLogin
     @RequiresPermission(ReadPermission.class)
-    public class GetExperimentAction extends ReadOnlyApiAction
+    public static class GetExperimentAction extends ReadOnlyApiAction<Object>
     {
         @Override
         public ApiResponse execute(Object o, BindException errors) throws Exception
@@ -474,7 +473,7 @@ public ApiResponse execute(Object o, BindException errors) throws Exception
             TableInfo table = schema.getTable(OConnorExperimentsUserSchema.Table.Experiments.name());
             QueryUpdateService qus = table.getUpdateService();
 
-            List<Map<String, Object>> pks = Collections.singletonList(Collections.singletonMap("Container", (Object)getContainer().getId()));
+            List<Map<String, Object>> pks = Collections.singletonList(Collections.singletonMap("Container", getContainer().getId()));
             List<Map<String, Object>> result = qus.getRows(getUser(), getContainer(), pks);
 
             ApiSimpleResponse resp = new ApiSimpleResponse();
@@ -495,14 +494,14 @@ public ApiResponse execute(Object o, BindException errors) throws Exception
     }
 
     @RequiresPermission(UpdatePermission.class)
-    public class HistoryAction extends SimpleViewAction
+    public static class HistoryAction extends SimpleViewAction<Object>
     {
         @Override
         public ModelAndView getView(Object o, BindException errors)
         {
             getPageConfig().setNoIndex();
             getPageConfig().setNoFollow();
-            return new JspView("/org/labkey/oconnorexperiments/view/history.jsp", null, errors);
+            return new JspView<>("/org/labkey/oconnorexperiments/view/history.jsp", null, errors);
         }
 
         @Override
@@ -528,7 +527,7 @@ public void setId(String id)
     }
 
     @RequiresPermission(ReadPermission.class)
-    public class LookupWorkbookAction extends SimpleViewAction<LookupWorkbookForm>
+    public static class LookupWorkbookAction extends SimpleViewAction<LookupWorkbookForm>
     {
         @Override
         public ModelAndView getView(LookupWorkbookForm form, BindException errors)

OConnorExperiments/src/org/labkey/oconnorexperiments/OConnorExperimentsModule.java

@@ -128,7 +128,7 @@ public Set<String> getSchemaNames()
     }
 
     // Listener that just updates the experiment changed date when a wiki is modified.
-    private class OConnorWikiChangeListener implements WikiChangeListener
+    private static class OConnorWikiChangeListener implements WikiChangeListener
     {
         @Override
         public void wikiCreated(User user, Container c, String name)
@@ -150,7 +150,7 @@ public void wikiDeleted(User user, Container c, String name)
     }
 
     // Listener that just updates the experiment changed date when a file is uploaded/renamed.
-    private class OConnorFileChangeListener implements FileListener
+    private static class OConnorFileChangeListener implements FileListener
     {
         @Override
         public void fileCreated(@NotNull File created, @Nullable User user, @Nullable Container container)

OConnorExperiments/src/org/labkey/oconnorexperiments/query/ExperimentsTable.java

@@ -505,7 +505,7 @@ public boolean next() throws BatchValidationException
             }
 
             Collection<String> parentExperiments = (Collection<String>)o;
-            if (parentExperiments.size() == 0)
+            if (parentExperiments.isEmpty())
                 return true;
 
             // Validate each ParentExperiment is a workbook and create list of maps for insertion

OConnorExperiments/test/src/org/labkey/test/tests/OConnorExperimentTest.java

@@ -64,7 +64,7 @@ public class OConnorExperimentTest extends BaseWebDriverTest implements Postgres
     private static final String TABLE_NAME = "Experiments";
     private static final String EXPERIMENT_TYPE_TABLE_NAME = "ExperimentType";
     private static final String EXPERIMENT_SAVE_SIGNAL = "experimentDataSave"; // See experimentField.html
-    private ArrayList<String> pkeys = new ArrayList<>();
+    private final ArrayList<String> pkeys = new ArrayList<>();
 
     @Nullable
     @Override
@@ -327,7 +327,7 @@ protected void deleteViaJavaApi()
             DeleteRowsCommand cmd = new DeleteRowsCommand(SCHEMA_NAME, TABLE_NAME);
             Connection cn = WebTestHelper.getRemoteApiConnection();
             for (String pk : pkeys)
-                cmd.addRow(Collections.singletonMap("container", (Object) pk));
+                cmd.addRow(Collections.singletonMap("container", pk));
 
             SaveRowsResponse resp = cmd.execute(cn, getProjectName());
             assertEquals("Expected to delete " + pkeys.size() + " rows", pkeys.size(), resp.getRowsAffected().intValue());

OConnorExperiments/test/src/org/labkey/test/tests/OConnorListTest.java

@@ -70,7 +70,7 @@ public List<String> getAssociatedModules()
     @LogMethod
     public static void setup()
     {
-        OConnorListTest initTest = (OConnorListTest)getCurrentTest();
+        OConnorListTest initTest = getCurrentTest();
         initTest.setupOConnorProject();
     }
 

genotyping/src/org/labkey/genotyping/GenotypingController.java

@@ -154,7 +154,7 @@ public GenotypingController()
     }
 
     @RequiresPermission(ReadPermission.class)
-    public class BeginAction extends SimpleRedirectAction
+    public static class BeginAction extends SimpleRedirectAction<Object>
     {
         @Override
         public ActionURL getRedirectURL(Object o)
@@ -222,7 +222,7 @@ public void setError(String error)
 
 
     @RequiresPermission(ReadPermission.class)
-    public class AnalysisAction extends QueryViewAction<AnalysisForm, QueryView>
+    public static class AnalysisAction extends QueryViewAction<AnalysisForm, QueryView>
     {
         private GenotypingAnalysis _analysis = null;
 
@@ -316,7 +316,7 @@ private ActionURL getDeleteMatchesURL(int analysisId)
 
     // TODO: Delete this action? No longer used?
     @RequiresPermission(DeletePermission.class)
-    public class DeleteMatchesAction extends FormHandlerAction<MatchesForm>
+    public static class DeleteMatchesAction extends FormHandlerAction<MatchesForm>
     {
         private int _count = 0;
         private String _error = null;
@@ -363,7 +363,7 @@ public boolean handlePost(MatchesForm form, BindException errors)
 
 
     @RequiresPermission(AdminPermission.class)
-    public class LoadSequencesAction extends FormHandlerAction<ReturnUrlForm>
+    public static class LoadSequencesAction extends FormHandlerAction<ReturnUrlForm>
     {
         @Override
         public void validateCommand(ReturnUrlForm target, Errors errors)
@@ -581,7 +581,7 @@ public void addNavTrail(NavTree root)
 
     @RequiresPermission(ReadPermission.class)
     @IgnoresTermsOfUse
-    public class MergeFastqFilesAction extends ExportAction<MergeFastqFilesForm>
+    public static class MergeFastqFilesAction extends ExportAction<MergeFastqFilesForm>
     {
         @Override
         public void export(MergeFastqFilesForm form, HttpServletResponse response, BindException errors) throws Exception
@@ -698,7 +698,7 @@ public static ActionURL getMySettingsURL(Container c, ActionURL returnUrl)
 
 
     @RequiresPermission(ReadPermission.class)
-    public class MySettingsAction extends FormViewAction<MySettingsForm>
+    public static class MySettingsAction extends FormViewAction<MySettingsForm>
     {
         @Override
         public void validateCommand(MySettingsForm form, Errors errors)
@@ -890,10 +890,10 @@ public void setPrefix(String prefix)
 
     public static class ImportReadsBean
     {
-        private List<Integer> _runs;
-        private SEQUENCE_PLATFORMS _platform;
-        private String _readsPath;
-        private String _path;
+        private final List<Integer> _runs;
+        private final SEQUENCE_PLATFORMS _platform;
+        private final String _readsPath;
+        private final String _path;
         private String _prefix;
 
         private ImportReadsBean(List<Integer> runs, String readsPath, String path, @Nullable String platform, @Nullable String prefix)
@@ -1124,7 +1124,7 @@ private ActionURL getAnalyzeURL(int runId, ActionURL cancelURL)
 
 
     @RequiresPermission(InsertPermission.class)
-    public class AnalyzeAction extends FormViewAction<AnalyzeForm>
+    public static class AnalyzeAction extends FormViewAction<AnalyzeForm>
     {
         @Override
         public void validateCommand(AnalyzeForm target, Errors errors)
@@ -1501,7 +1501,7 @@ public static ActionURL getSequencesURL(Container c, @Nullable Integer dictionar
 
 
     @RequiresPermission(ReadPermission.class)
-    public class SequencesAction extends QueryViewAction<SequencesForm, QueryView>
+    public static class SequencesAction extends QueryViewAction<SequencesForm, QueryView>
     {
         public SequencesAction()
         {
@@ -1563,7 +1563,7 @@ public void setAnalysis(Integer analysis)
 
     @SuppressWarnings({"UnusedDeclaration"})  // URL defined on sequences.rowId column in genotyping.xml
     @RequiresPermission(ReadPermission.class)
-    public class SequenceAction extends SimpleViewAction<SequenceForm>
+    public static class SequenceAction extends SimpleViewAction<SequenceForm>
     {
         @Override
         public ModelAndView getView(SequenceForm form, BindException errors)
@@ -1607,7 +1607,7 @@ public static ActionURL getRunsURL(Container c)
 
 
     @RequiresPermission(ReadPermission.class)
-    public class RunsAction extends QueryViewAction<QueryExportForm, QueryView>
+    public static class RunsAction extends QueryViewAction<QueryExportForm, QueryView>
     {
         public RunsAction()
         {
@@ -1636,7 +1636,7 @@ public static ActionURL getAnalysesURL(Container c)
 
 
     @RequiresPermission(ReadPermission.class)
-    public class AnalysesAction extends QueryViewAction<QueryExportForm, QueryView>
+    public static class AnalysesAction extends QueryViewAction<QueryExportForm, QueryView>
     {
         public AnalysesAction()
         {
@@ -1727,7 +1727,7 @@ public static ActionURL getRunURL(Container c, GenotypingRun run)
     public static final String FASTQ_FILE_FORMAT = "FASTQ_FILE";
     public static final String FASTQ_FORMAT = "FASTQ";
 
-    private abstract class ReadsAction<FORM extends RunForm> extends QueryViewAction<FORM, QueryView>
+    private abstract static class ReadsAction<FORM extends RunForm> extends QueryViewAction<FORM, QueryView>
     {
         private static final String DATA_REGION_NAME = "Reads";
 
@@ -1905,7 +1905,7 @@ protected void handleSettings(QuerySettings settings)
 
 
     @RequiresPermission(AdminPermission.class)
-    public class DeleteRunsAction extends FormHandlerAction
+    public static class DeleteRunsAction extends FormHandlerAction<Object>
     {
         @Override
         public void validateCommand(Object target, Errors errors)
@@ -1936,7 +1936,7 @@ public ActionURL getSuccessURL(Object o)
 
 
     @RequiresPermission(DeletePermission.class)
-    public class DeleteAnalysesAction extends FormHandlerAction
+    public static class DeleteAnalysesAction extends FormHandlerAction<Object>
     {
         @Override
         public void validateCommand(Object target, Errors errors)
@@ -2036,7 +2036,7 @@ protected void handleSettings(QuerySettings settings)
         }
     }
 
-    public class AssignmentReportBean
+    public static class AssignmentReportBean
     {
         private final Collection<Integer> _ids;
         private final String _assayName;
@@ -2101,7 +2101,7 @@ public void addNavTrail(NavTree root)
     }
 
     @RequiresPermission(ReadPermission.class)
-    public class DuplicateAssignmentReportAction extends BaseAssayAction<ProtocolIdForm>
+    public static class DuplicateAssignmentReportAction extends BaseAssayAction<ProtocolIdForm>
     {
         private ExpProtocol _protocol;
 
@@ -2128,7 +2128,7 @@ public void addNavTrail(NavTree root)
     }
 
     @RequiresPermission(ReadPermission.class)
-    public class STRDiscrepanciesAssignmentReportAction extends SimpleViewAction<STRDiscrepancies>
+    public static class STRDiscrepanciesAssignmentReportAction extends SimpleViewAction<STRDiscrepancies>
     {
         private ExpProtocol _protocol;
         private static final String DELIM = "[;,/]";
@@ -2355,7 +2355,7 @@ public void addNavTrail(NavTree root)
     }
 
     @RequiresPermission(UpdatePermission.class)
-    public class EditHaplotypeAssignmentAction extends SimpleViewAction<AssignmentForm>
+    public static class EditHaplotypeAssignmentAction extends SimpleViewAction<AssignmentForm>
     {
         @Override
         public ModelAndView getView(AssignmentForm form, BindException errors)

genotyping/src/org/labkey/genotyping/GenotypingManager.java

@@ -443,7 +443,7 @@ public int deleteMatches(Container c, User user, int analysisId, List<Integer> m
         GenotypingAnalysis analysis = GenotypingManager.get().getAnalysis(c, analysisId);
 
         // Verify that matches were posted
-        if (matchIds.size() < 1)
+        if (matchIds.isEmpty())
             throw new IllegalStateException("No matches were selected");
 
         // Count the corresponding matches in the database, making sure they belong to this analysis