Minor auto-refactor code cleanup on a massive scale

hdrl/src/org/labkey/hdrl/HDRLContainerListener.java

@@ -28,7 +28,6 @@
 import org.labkey.api.security.User;
 import org.labkey.api.util.ContainerUtil;
 import org.labkey.hdrl.query.LabWareQuerySchema;
-import org.labkey.remoteapi.assay.Data;
 
 import java.util.Collections;
 import java.util.Collection;

hdrl/src/org/labkey/hdrl/HDRLController.java

@@ -132,7 +132,7 @@ public void addNavTrail(NavTree root)
 
 
     @RequiresPermission(ReadPermission.class)
-    public class RequestDetailsAction extends SimpleViewAction
+    public static class RequestDetailsAction extends SimpleViewAction<Object>
     {
         @Override
         public ModelAndView getView(Object o, BindException errors)
@@ -141,7 +141,7 @@ public ModelAndView getView(Object o, BindException errors)
             if (requestId != null)
             {
                 InboundRequestBean bean = HDRLManager.get().getInboundRequest(getUser(), getContainer(), Integer.parseInt(requestId));
-                JspView jsp = new JspView("/org/labkey/hdrl/view/requestDetails.jsp", bean);
+                JspView jsp = new JspView<>("/org/labkey/hdrl/view/requestDetails.jsp", bean);
                 jsp.setTitle("Test Request");
 
                 UserSchema schema = QueryService.get().getUserSchema(getUser(), getContainer(), HDRLQuerySchema.NAME);
@@ -166,7 +166,7 @@ public void addNavTrail(NavTree root)
     }
 
     @RequiresPermission(InsertPermission.class)
-    public class EditRequestAction extends SimpleViewAction<RequestForm>
+    public static class EditRequestAction extends SimpleViewAction<RequestForm>
     {
         private String _navLabel = "Create a new Test Request";
 
@@ -259,7 +259,7 @@ public void setTestTypeId(Integer testTypeId)
     }
 
     @RequiresPermission(ReadPermission.class)
-    public class VerifySpecimenAction extends ReadOnlyApiAction<VerifyForm>
+    public static class VerifySpecimenAction extends ReadOnlyApiAction<VerifyForm>
     {
         @Override
         public Object execute(VerifyForm form, BindException errors)
@@ -310,7 +310,7 @@ public static class VerifyForm extends SimpleApiJsonForm
 
 
     @RequiresPermission(ReadPermission.class)
-    public class DownloadClinicalReportAction extends ExportAction<SpecimenForm>
+    public static class DownloadClinicalReportAction extends ExportAction<SpecimenForm>
     {
         @Override
         public void export(SpecimenForm form, HttpServletResponse response, BindException errors) throws Exception
@@ -361,7 +361,7 @@ public void setSpecimenId(Integer specimenId)
     }
 
     @RequiresPermission(ReadPermission.class)
-    public class DownloadSpecimenTemplateAction extends ExportAction
+    public static class DownloadSpecimenTemplateAction extends ExportAction<Object>
     {
         @Override
         public void export(Object o, HttpServletResponse response, BindException errors)
@@ -385,7 +385,7 @@ public void export(Object o, HttpServletResponse response, BindException errors)
     }
 
     @RequiresPermission(ReadPermission.class)
-    public class PrintPackingListAction extends SimpleViewAction<PackingListBean>
+    public static class PrintPackingListAction extends SimpleViewAction<PackingListBean>
     {
         @Override
         public ModelAndView getView(PackingListBean packingListBean, BindException errors)
@@ -483,7 +483,7 @@ public void setShippingNumber(String shippingNumber)
 
     @AdminConsoleAction
     @RequiresPermission(AdminPermission.class)
-    public class HDRLSensitiveDataAdminAction extends FormViewAction<SensitiveDataForm>
+    public static class HDRLSensitiveDataAdminAction extends FormViewAction<SensitiveDataForm>
     {
         @Override
         public void validateCommand(SensitiveDataForm target, Errors errors)
@@ -537,7 +537,7 @@ public void setTimeWindowInDays(int timeWindowInDays)
 
     @RequiresPermission(AdminPermission.class)
     @Marshal(Marshaller.Jackson)
-    public class AddLabWareOutboundRequestAction extends MutatingApiAction<LabWareOutboundRequestForm>
+    public static class AddLabWareOutboundRequestAction extends MutatingApiAction<LabWareOutboundRequestForm>
     {
         @Override
         public Object execute(LabWareOutboundRequestForm form, BindException errors)
@@ -633,7 +633,7 @@ public void setDateModified(Date dateModified)
 
     @RequiresPermission(AdminPermission.class)
     @Marshal(Marshaller.Jackson)
-    public class AddLabWareOutboundSpecimenAction extends MutatingApiAction<LabWareOutboundSpecimenForm>
+    public static class AddLabWareOutboundSpecimenAction extends MutatingApiAction<LabWareOutboundSpecimenForm>
     {
         @Override
         public Object execute(LabWareOutboundSpecimenForm form, BindException errors) throws Exception

hdrl/src/org/labkey/hdrl/HDRLFolderType.java

@@ -15,7 +15,6 @@
  */
 package org.labkey.hdrl;
 
-import org.labkey.api.module.Module;
 import org.labkey.api.module.MultiPortalFolderType;
 import org.labkey.api.view.Portal;
 

hdrl/src/org/labkey/hdrl/HDRLMaintenanceTask.java

@@ -16,7 +16,6 @@
 package org.labkey.hdrl;
 
 import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
 import org.labkey.api.data.DbSchema;
 import org.labkey.api.data.DbScope;
 import org.labkey.api.data.SQLFragment;

hdrl/src/org/labkey/hdrl/query/HDRLQuerySchema.java

@@ -79,7 +79,7 @@ public class HDRLQuerySchema extends SimpleUserSchema
     public static final String TABLE_LABWARE_OUTBOUND_RESULTS = "LabwareOutboundRequests";
     public static final String TABLE_LABWARE_OUTBOUND_SPECIMENS = "LabwareOutboundSpecimens";
 
-    public static final String COL_REQUEST_STATUS_ID = "RequestStatusId";;
+    public static final String COL_REQUEST_STATUS_ID = "RequestStatusId";
     public static final String COL_INBOUND_REQUEST_ID = "InboundRequestId";
     public static final String COL_ARCHIVED_REQUEST_COUNT = "ArchivedRequestCount";
 

hdrl/src/org/labkey/hdrl/query/InboundRequestTable.java

@@ -17,7 +17,6 @@
 
 import org.jetbrains.annotations.NotNull;
 import org.jetbrains.annotations.Nullable;
-import org.labkey.api.data.ColumnInfo;
 import org.labkey.api.data.ContainerFilter;
 import org.labkey.api.data.ContainerForeignKey;
 import org.labkey.api.data.DatabaseTableType;

hdrl/src/org/labkey/hdrl/query/InboundRequestUpdateService.java

@@ -107,33 +107,33 @@ public static void validateUniqueness(Integer requestId) throws QueryUpdateServi
         // check that there are no duplicate barcodes
         List<String> duplicates = findDuplicates(requestId, "CustomerBarcode");
         StringBuilder message = new StringBuilder();
-        if (duplicates.size() > 0)
+        if (!duplicates.isEmpty())
         {
             message.append("Request has specimens with duplicate fields: Customer Barcode - ").append(StringUtils.join(duplicates, ", "));
         }
 
         // check that all existing DODId in the specimens in this request are unique
         duplicates = findDuplicates(requestId, "DoDId");
-        if (duplicates.size() > 0)
+        if (!duplicates.isEmpty())
         {
-            if (message.length() == 0)
+            if (message.isEmpty())
                 message.append("Request has specimens with duplicate fields: ");
             else
                 message.append("; ");
             message.append("DoDID - ").append(StringUtils.join(duplicates, ", "));
         }
         // check that all the existing SSN + FMP pairs in this request are unique
         duplicates = findDuplicates(requestId, "SSN, FMPId");
-        if (duplicates.size() > 0)
+        if (!duplicates.isEmpty())
         {
-            if (message.length() == 0)
+            if (message.isEmpty())
                 message.append("Request has specimens with duplicate fields: ");
             else
                 message.append("; ");
             message.append("SSN + FMP - ").append(StringUtils.join(duplicates, ", "));
         }
 
-        if (message.length() > 0)
+        if (!message.isEmpty())
             throw new QueryUpdateServiceException(message.toString());
 
     }

hdrl/src/org/labkey/hdrl/query/InboundSpecimenUpdateService.java

@@ -125,8 +125,8 @@ public static void validate(Map<String, Object> row) throws ValidationException
         calendar.set(Calendar.SECOND, 0);
         calendar.set(Calendar.MILLISECOND, 0);
         Date today = calendar.getTime();
-        List<String> errors = new ArrayList<String>();
-        List<String> missingFields = new ArrayList<String>();
+        List<String> errors = new ArrayList<>();
+        List<String> missingFields = new ArrayList<>();
         if (row.get("FMPId") == null)
             missingFields.add("FMP");
         if (row.get("DrawDate") == null)
@@ -151,30 +151,34 @@ public static void validate(Map<String, Object> row) throws ValidationException
                 }
             }
         }
-        if (row.get("BirthDate") != null)
+        Object birthDateObj = row.get("BirthDate");
+        if (birthDateObj != null)
         {
             Date birthDate = null;
-            if (row.get("BirthDate") instanceof Date)
-                birthDate = (Date) row.get("BirthDate");
+            if (birthDateObj instanceof Date d)
+                birthDate = d;
             else
             {
                 try
                 {
                     birthDate = dateFormat.parse((String) row.get("BirthDate"));
-                    if (birthDate.after(today))
-                    {
-                        errors.add("Birth date cannot be in the future");
-                    }
-                    else if ((drawDate != null) && (drawDate.before(birthDate)))
-                    {
-                        errors.add("Draw date cannot be before birth date");
-                    }
                 }
                 catch (ParseException e)
                 {
                     errors.add("Invalid birth date format");
                 }
             }
+            if (birthDate != null)
+            {
+                if (birthDate.after(today))
+                {
+                    errors.add("Birth date cannot be in the future");
+                }
+                else if ((drawDate != null) && (drawDate.before(birthDate)))
+                {
+                    errors.add("Draw date cannot be before birth date");
+                }
+            }
         }
         if (row.get("SSN") == null || StringUtils.isEmpty(String.valueOf(row.get("SSN"))))
             missingFields.add("SSN");

hdrl/src/org/labkey/hdrl/query/ResultTable.java

@@ -30,7 +30,6 @@
 import org.labkey.api.security.UserPrincipal;
 import org.labkey.api.security.permissions.Permission;
 
-import java.sql.SQLException;
 import java.util.Map;
 
 /**

hdrl/test/src/org/labkey/test/tests/HDRLTest.java

@@ -66,8 +66,8 @@ public class HDRLTest extends BaseWebDriverTest implements PostgresOnlyTest
     public static final Locator.XPathLocator enabledSave = Locator.xpath("//a[not(contains(normalize-space(@class), 'x4-btn-disable'))]//span[text()='" + SAVE_BUTTON_TEXT + "']");
     public static final Locator.XPathLocator enabledPrintPackingList = Locator.xpath("//a[not(contains(normalize-space(@class), 'x4-btn-disable'))]//span[text()='" + PRINT_PACKING_LIST_TEXT + "']");
 
-    private static int CARRIER_COLUMN_INDEX = 2;
-    private static int STATUS_COLUMN_INDEX = 13;
+    private static final int CARRIER_COLUMN_INDEX = 2;
+    private static final int STATUS_COLUMN_INDEX = 13;
 
     @Override
     protected String getProjectName()
@@ -78,7 +78,7 @@ protected String getProjectName()
     @BeforeClass
     public static void initProject()
     {
-        HDRLTest init = (HDRLTest)getCurrentTest();
+        HDRLTest init = getCurrentTest();
         init.setupFolder();
     }
 
@@ -150,7 +150,7 @@ public void testRetrievalOfResultsAndArchiving() throws Exception
         clickButton(SUBMIT_BUTTON_TEXT);
         DataRegionTable drt = new DataRegionTable("query", this);
         int idx = drt.getRowIndex("ShippingNumber", "testRetrievalOfResults");
-        assertNotEquals(idx, -1);
+        assertNotEquals(-1, idx);
         String requestId = drt.getDataAsText(idx, "RequestId");
 
         Map<String, Object> result = new HashMap<>();
@@ -236,7 +236,7 @@ public void testRetrievalOfResultsAndArchiving() throws Exception
         click(Locator.linkContainingText("View test requests"));
         drt = new DataRegionTable("query", this);
         idx = drt.getRowIndex("RequestId", requestId);
-        assertNotEquals(idx, -1);
+        assertNotEquals(-1, idx);
         log("view test results");
         assertEquals("VIEW", drt.getDataAsText(idx, 0));
         clickAndWait(drt.link(idx, 0));
@@ -395,7 +395,7 @@ public void testFileUploadAndSubmit()
 
         DataRegionTable drt = new DataRegionTable("query", this);
         int idx = drt.getRowIndex("ShippingCarrier", "FedEx");
-        assertNotEquals(idx, -1);
+        assertNotEquals(-1, idx);
         clickAndWait(drt.link(idx, 0));
         log("submitting an existing request");
         waitForElement(Locator.tagContainingText("div", "222-33-4444"));
@@ -404,7 +404,7 @@ public void testFileUploadAndSubmit()
 
         drt = new DataRegionTable("query", this);
         idx = drt.getRowIndex("ShippingCarrier", "FedEx");
-        assertNotEquals(idx, -1);
+        assertNotEquals(-1, idx);
         Assert.assertFalse(drt.getDataAsText(idx, "Submitted By").trim().isEmpty()); // "submitted by" field should be filled in
         Assert.assertFalse(drt.getDataAsText(idx, "Submitted").trim().isEmpty()); // submitted date should be filled in
 
@@ -423,7 +423,7 @@ public void testFileUploadAndSubmit()
         clickAndWait(Locator.linkContainingText("View test requests"));
         drt = new DataRegionTable("query", this);
         idx = drt.getRowIndex("ShippingCarrier", "FedEx");
-        assertNotEquals(idx, -1);
+        assertNotEquals(-1, idx);
         log("ensure submitted requests are still editable by admins");
         assertEquals("VIEW", drt.getDataAsText(idx, 0));
         clickAndWait(drt.link(idx, 0));
@@ -454,7 +454,7 @@ public void testEditSubmittedRequest()
         log("Edit the submitted request as admin");
         DataRegionTable drt = new DataRegionTable("query", this);
         int idx = drt.getRowIndex("ShippingNumber", "testEditSubmittedRequest");
-        assertNotEquals(idx, -1);
+        assertNotEquals(-1, idx);
         assertEquals("Submitted", drt.getDataAsText(idx, STATUS_COLUMN_INDEX));
         String submittedDate = drt.getDataAsText(idx, 6).trim();
 
@@ -476,7 +476,7 @@ public void testEditSubmittedRequest()
         log("Test that not saving request does not change anything");
         clickButton("Cancel", 0); // takes you back to the view test requests page
         idx = drt.getRowIndex("ShippingNumber", "testEditSubmittedRequest");
-        assertNotEquals(idx, -1);
+        assertNotEquals(-1, idx);
         assertEquals("Submitted", drt.getDataAsText(idx, STATUS_COLUMN_INDEX));
         assertNotEquals("DHL", drt.getDataAsText(idx, CARRIER_COLUMN_INDEX));
         assertEquals("EDIT", drt.getDataAsText(idx, 0));
@@ -491,7 +491,7 @@ public void testEditSubmittedRequest()
 
         log("Test that saving request does not change the request status");
         idx = drt.getRowIndex("ShippingNumber", "testEditSubmittedRequest");
-        assertNotEquals(idx, -1);
+        assertNotEquals(-1, idx);
         assertEquals("Submitted", drt.getDataAsText(idx, STATUS_COLUMN_INDEX));
         assertEquals("DHL", drt.getDataAsText(idx, CARRIER_COLUMN_INDEX));
         // submitted date should still be the same
@@ -528,7 +528,7 @@ public void testDataDeletion()
         click(Locator.linkWithText("View test requests"));
         DataRegionTable drt = new DataRegionTable("query", this);
         int idx = drt.getRowIndex("ShippingNumber", "testRetrievalOfResults");
-        assertNotEquals(idx, -1);
+        assertNotEquals(-1, idx);
         String requestId = drt.getDataAsText(idx, "RequestId");
         Assert.assertEquals("Archived", drt.getDataAsText(idx, "Status"));
         List<String> specimenIds = getSpecimenIds(requestId, "hdrl", "InboundSpecimen", "RowId");
@@ -600,7 +600,7 @@ private void verifyDataRegionRows(String tableName, List<Map<String, String>> ex
         for (Map<String, String> expectedRow : expectedRows)
         {
             int idx = drt.getRowIndex(key, expectedRow.get(key));
-            assertNotEquals(String.format("Didn't find row with %s = %s", key, expectedRow.get(key)), idx, -1);
+            assertNotEquals(String.format("Didn't find row with %s = %s", key, expectedRow.get(key)), -1, idx);
 
             Map<String, String> actualRow = new HashMap<>();
             for (Map.Entry<String, String> field : expectedRow.entrySet())

ms2extensions/src/org/labkey/ms2extensions/MS2ExtensionsController.java

@@ -96,7 +96,7 @@ private static String getPreference(ViewContext viewContext, String preferenceNa
     }
 
     @RequiresPermission(AdminOperationsPermission.class)
-    public class UpdatePeptideCountsAction extends SimpleViewAction<Object>
+    public static class UpdatePeptideCountsAction extends SimpleViewAction<Object>
     {
         @Override
         public ModelAndView getView(Object o, BindException errors)
@@ -105,7 +105,7 @@ public ModelAndView getView(Object o, BindException errors)
             {
                 List<DOM.Renderable> warnings = new ArrayList<>();
                 updatePeptideCounts(warnings, getContainer());
-                if (warnings.size() == 0)
+                if (warnings.isEmpty())
                 {
                     return new HtmlView(DOM.DIV("Success!"));
                 }
@@ -139,7 +139,7 @@ public void addNavTrail(NavTree root)
     }
 
     @RequiresPermission(ReadPermission.class)
-    public class SetPreferencesAction extends MutatingApiAction<SimpleApiJsonForm>
+    public static class SetPreferencesAction extends MutatingApiAction<SimpleApiJsonForm>
     {
         @Override
         public ApiResponse execute(SimpleApiJsonForm simpleApiJsonForm, BindException errors)

ms2extensions/src/org/labkey/ms2extensions/PeptideCountPepXmlDataHandler.java

@@ -16,7 +16,6 @@
 package org.labkey.ms2extensions;
 
 import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
 import org.jetbrains.annotations.Nullable;
 import org.labkey.api.data.Container;
 import org.labkey.api.exp.ExperimentDataHandler;

pepdb/src/org/scharp/atlas/pepdb/PepDBBaseController.java

@@ -215,7 +215,7 @@ && validateInteger(getAAStart().trim()) > validateInteger(getAAEnd().trim()))
             {
                 if (StringUtils.trimToNull(qValue) == null)
                     errors.reject(null, "The Peptide Id range must be entered.");
-                if (qValue != null && qValue.length() > 0)
+                if (qValue != null && !qValue.isEmpty())
                 {
                     if (!(qValue.matches("\\d+-\\d+")))
                     {
@@ -423,7 +423,7 @@ public boolean validate(Errors errors, AttachmentFile file) throws Exception
                     errors.reject(null, "File name must end with in .txt.\nFile should be tab delimited text file and the number of field vary depending on file type.");
                 }
             }
-            if (getActionType() == null || getActionType().length() == 0)
+            if (getActionType() == null || getActionType().isEmpty())
                 errors.reject(null, "File Type is required");
             if(errors.getErrorCount() > 0)
                 return false;