Minor auto-refactor code cleanup on a massive scale

elisa/src/org/labkey/elisa/ElisaAssayProvider.java

@@ -71,6 +71,7 @@
 import org.labkey.elisa.plate.BioTekPlateReader;
 import org.springframework.web.servlet.ModelAndView;
 
+import java.lang.reflect.InvocationTargetException;
 import java.util.Arrays;
 import java.util.Collection;
 import java.util.Collections;
@@ -141,10 +142,10 @@ enum PlateReaderType
     {
         BIOTEK(BioTekPlateReader.LABEL, BioTekPlateReader.class);
 
-        private String _label;
-        private Class _class;
+        private final String _label;
+        private final Class<? extends PlateReader> _class;
 
-        private PlateReaderType(String label, Class cls)
+        PlateReaderType(String label, Class<? extends PlateReader> cls)
         {
             _label = label;
             _class = cls;
@@ -159,9 +160,9 @@ public PlateReader getInstance()
         {
             try
             {
-                return (PlateReader)_class.newInstance();
+                return _class.getDeclaredConstructor().newInstance();
             }
-            catch (InstantiationException | IllegalAccessException x)
+            catch (InstantiationException | IllegalAccessException | InvocationTargetException | NoSuchMethodException x)
             {
                 throw new RuntimeException(x);
             }
@@ -295,11 +296,11 @@ private DomainProperty addPropertyWithFormat(Domain domain, String name, String
     }
 
     @Override
-    public HttpView getDataDescriptionView(AssayRunUploadForm form)
+    public HttpView<?> getDataDescriptionView(AssayRunUploadForm form)
     {
-        if (form instanceof ElisaRunUploadForm)
+        if (form instanceof ElisaRunUploadForm eForm)
         {
-            if (((ElisaRunUploadForm)form).getSampleMetadataInputFormat() == SampleMetadataInputFormat.COMBINED)
+            if (eForm.getSampleMetadataInputFormat() == SampleMetadataInputFormat.COMBINED)
                 return new JspView<>("/org/labkey/assay/view/tsvDataDescription.jsp", form);
         }
         return new HtmlView(HtmlString.of("The ELISA data files must be in the BioTek Microplate Reader Excel file format (.xls or .xlsx extension)."));
@@ -438,7 +439,7 @@ protected void moveAssayResults(List<ExpRun> runs, ExpProtocol protocol, Contain
         // move specimen
         String tableName = AssayProtocolSchema.DATA_TABLE_NAME;
         AssaySchema schema = createProtocolSchema(user, targetContainer, protocol, null);
-        FilteredTable assayResultTable = (FilteredTable) schema.getTable(tableName);
+        FilteredTable<?> assayResultTable = (FilteredTable<?>) schema.getTable(tableName);
         if (assayResultTable != null)
         {
             TableInfo expMaterialTable = ExperimentService.get().getTinfoMaterial();

elisa/src/org/labkey/elisa/ElisaController.java

@@ -102,7 +102,7 @@ public void setProtocolId(int protocolId)
     }
 
     @RequiresPermission(ReadPermission.class)
-    public class GetCurveFitXYPairs extends ReadOnlyApiAction<GetCurveFitXYPairsForm>
+    public static class GetCurveFitXYPairs extends ReadOnlyApiAction<GetCurveFitXYPairsForm>
     {
         ExpRun _run;
 

elisa/src/org/labkey/elisa/ElisaImportHelper.java

@@ -14,7 +14,7 @@
 
 public interface ElisaImportHelper
 {
-    public static String PLACEHOLDER_PLATE_NAME = "PLACEHOLDER_PLATE";
+    String PLACEHOLDER_PLATE_NAME = "PLACEHOLDER_PLATE";
 
     /**
      * Gets the set of plate names in this import

elisa/src/org/labkey/elisa/ElisaProtocolSchema.java

@@ -23,7 +23,6 @@
 import org.labkey.api.data.DbSchema;
 import org.labkey.api.data.TableInfo;
 import org.labkey.api.exp.api.ExpProtocol;
-import org.labkey.api.query.FilteredTable;
 import org.labkey.api.security.User;
 import org.labkey.elisa.query.CurveFitTable;
 import org.labkey.elisa.query.ElisaResultsTable;
@@ -67,7 +66,7 @@ protected TableInfo createProviderTable(String name, ContainerFilter cf)
     }
 
     @Override
-    public FilteredTable createDataTable(ContainerFilter cf, boolean includeLinkedToStudyColumns)
+    public ElisaResultsTable createDataTable(ContainerFilter cf, boolean includeLinkedToStudyColumns)
     {
         return new ElisaResultsTable(this, cf, includeLinkedToStudyColumns);
     }

elisa/src/org/labkey/elisa/HighThroughputImportHelper.java

@@ -33,7 +33,7 @@ public class HighThroughputImportHelper extends AbstractElisaImportHelper
 {
     private static final Logger LOG = LogManager.getLogger(HighThroughputImportHelper.class);
 
-    private Map<String, AnalytePlate> _plateMap = new HashMap<>();
+    private final Map<String, AnalytePlate> _plateMap = new HashMap<>();
     private Plate _plateTemplate;
 
     public HighThroughputImportHelper(AssayUploadXarContext context, PlateBasedAssayProvider provider, ExpProtocol protocol, File dataFile) throws ExperimentException
@@ -77,7 +77,7 @@ private void ensureData() throws ExperimentException
                     }
                 }
                 else
-                    LOG.warn("No well location and plate name for row : " + row.toString());
+                    LOG.warn("No well location and plate name for row : " + row);
             }
         }
         catch (IOException e)
@@ -171,12 +171,12 @@ public Map<String, Object> getExtraProperties(String plateName, Position positio
 
     private static class AnalytePlate
     {
-        private Map<Integer, Map<String, Double>> _stdConcentrations = new HashMap<>();
-        private Map<Integer, double[][]> _dataMap = new HashMap<>();
-        private String _plateName;
-        private Plate _plateTemplate;
+        private final Map<Integer, Map<String, Double>> _stdConcentrations = new HashMap<>();
+        private final Map<Integer, double[][]> _dataMap = new HashMap<>();
+        private final String _plateName;
+        private final Plate _plateTemplate;
         // contains the mapping of (well/analyte) to extra row data to merge during data import
-        private Map<String, Map<String, Object>> _extraWellData = new HashMap<>();
+        private final Map<String, Map<String, Object>> _extraWellData = new HashMap<>();
         public static final String CONTROL_ID_COLUMN = "Sample";
 
         public AnalytePlate(String plateName, Plate plateTemplate)

elisa/src/org/labkey/elisa/actions/ElisaUploadWizardAction.java

@@ -29,7 +29,6 @@
 import org.labkey.api.data.DataRegion;
 import org.labkey.api.exp.ExperimentException;
 import org.labkey.api.exp.api.ExpProtocol;
-import org.labkey.api.exp.api.ExpRun;
 import org.labkey.api.exp.api.ExperimentService;
 import org.labkey.api.exp.property.DomainProperty;
 import org.labkey.api.query.PropertyValidationError;
@@ -117,7 +116,7 @@ public boolean executeStep(ElisaRunUploadForm form, BindException errors) throws
             }
 
             @Override
-            public ModelAndView getNextStep(ElisaRunUploadForm form, BindException errors) throws ServletException, SQLException, ExperimentException
+            public ModelAndView getNextStep(ElisaRunUploadForm form, BindException errors) throws ExperimentException
             {
                 if (form.isResetDefaultValues() || errors.hasErrors())
                     return getRunPropertiesView(form, !form.isResetDefaultValues(), false, errors);
@@ -230,15 +229,14 @@ public void validateStep(ElisaRunUploadForm form, Errors errors)
         @Override
         public boolean executeStep(ElisaRunUploadForm form, BindException errors) throws ServletException, SQLException, ExperimentException
         {
-            ExpRun run;
             try
             {
                 PlateConcentrationPropertyHelper helper = createConcentrationPropertyHelper(form.getContainer(), form.getProtocol(), form.getProvider());
 
                 Map<String, Map<DomainProperty, String>> postedProps = helper.getPostedPropertyValues(form.getRequest());
                 form.setConcentrationProperties(postedProps);
 
-                run = saveExperimentRun(form);
+                saveExperimentRun(form);
 
                 for (Map.Entry<String, Map<DomainProperty, String>> entry : postedProps.entrySet())
                     form.saveDefaultValues(entry.getValue(), entry.getKey());
@@ -263,7 +261,7 @@ public boolean executeStep(ElisaRunUploadForm form, BindException errors) throws
         }
 
         @Override
-        public ModelAndView getNextStep(ElisaRunUploadForm form, BindException errors) throws ServletException, SQLException, ExperimentException
+        public ModelAndView getNextStep(ElisaRunUploadForm form, BindException errors) throws ExperimentException
         {
             if (form.isResetDefaultValues() || errors.hasErrors())
                 return getConcentrationsView(form, !form.isResetDefaultValues(), errors);

elisa/src/org/labkey/elisa/actions/PlateConcentrationPropertyHelper.java

@@ -96,7 +96,7 @@ protected boolean isCopyable(DomainProperty pd)
     @Override
     public List<String> getSampleNames()
     {
-        return Arrays.asList(_controlNames.toArray(new String[_controlNames.size()]));
+        return Arrays.asList(_controlNames.toArray(new String[0]));
     }
 
     @Override

elisa/src/org/labkey/elisa/query/CurveFitTable.java

@@ -5,10 +5,8 @@
 import org.labkey.api.assay.AssayProtocolSchema;
 import org.labkey.api.data.ColumnInfo;
 import org.labkey.api.data.ContainerFilter;
-import org.labkey.api.data.ContainerForeignKey;
 import org.labkey.api.exp.api.ExpProtocol;
 import org.labkey.api.query.FilteredTable;
-import org.labkey.api.query.UserIdForeignKey;
 import org.labkey.elisa.ElisaProtocolSchema;
 
 public class CurveFitTable extends FilteredTable<AssayProtocolSchema>

elisa/src/org/labkey/elisa/query/ElisaResultsTable.java

@@ -27,7 +27,6 @@
 import org.labkey.api.exp.api.SampleTypeService;
 import org.labkey.api.exp.property.DomainProperty;
 import org.labkey.api.exp.query.ExpMaterialTable;
-import org.labkey.api.exp.query.ExpSchema;
 import org.labkey.api.query.FieldKey;
 import org.labkey.api.query.LookupForeignKey;
 import org.labkey.api.query.PropertyForeignKey;

elispotassay/src/org/labkey/elispot/ElispotAssayProvider.java

@@ -58,6 +58,7 @@
 import org.labkey.elispot.plate.AIDPlateReader;
 import org.labkey.elispot.query.ElispotAntigenDomainKind;
 
+import java.lang.reflect.InvocationTargetException;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collection;
@@ -102,10 +103,10 @@ enum PlateReaderType
         AID("AID", AIDPlateReader.class),
         ZEISS("Zeiss", TextPlateReader.class);
 
-        private String _label;
-        private Class _class;
+        private final String _label;
+        private final Class<? extends PlateReader> _class;
 
-        PlateReaderType(String label, Class cls)
+        PlateReaderType(String label, Class<? extends PlateReader> cls)
         {
             _label = label;
             _class = cls;
@@ -120,9 +121,9 @@ public PlateReader getInstance()
         {
             try
             {
-                return (PlateReader)_class.newInstance();
+                return _class.getDeclaredConstructor().newInstance();
             }
-            catch (InstantiationException | IllegalAccessException x)
+            catch (InstantiationException | IllegalAccessException | InvocationTargetException | NoSuchMethodException x)
             {
                 throw new RuntimeException(x);
             }
@@ -238,7 +239,7 @@ public List<Pair<Domain, Map<DomainProperty, Object>>> createDefaultDomains(Cont
     }
 
     @Override
-    public HttpView getDataDescriptionView(AssayRunUploadForm form)
+    public HttpView<?> getDataDescriptionView(AssayRunUploadForm form)
     {
         return HtmlView.of("The data file is the output file from the plate reader that has been selected.");
     }

elispotassay/src/org/labkey/elispot/ElispotController.java

@@ -89,7 +89,7 @@ public ElispotController()
     }
 
     @RequiresPermission(ReadPermission.class)
-    public class BeginAction extends SimpleViewAction
+    public static class BeginAction extends SimpleViewAction<Object>
     {
         @Override
         public ModelAndView getView(Object o, BindException errors)
@@ -255,7 +255,7 @@ private void addRunFilter(ExpProtocol protocol, ActionURL url, int rowId)
         url.addFilter(ElispotProtocolSchema.ANTIGEN_STATS_TABLE_NAME, provider.getTableMetadata(protocol).getRunRowIdFieldKeyFromResults(), CompareType.EQUAL, rowId);
     }
 
-    private class ElispotDetailsHeaderView extends AssayHeaderView
+    private static class ElispotDetailsHeaderView extends AssayHeaderView
     {
         List<NavTree> _links = new ArrayList<>();
 
@@ -341,7 +341,7 @@ public ApiResponse execute(DetailsForm form, BindException errors)
                     }
                 }
                 response.put("summary", rows);
-                if (analyteMap.size() > 0)
+                if (!analyteMap.isEmpty())
                 {
                     response.put("analytes", analyteMap.keySet());
                     response.put("analyteMap", analyteMap);
@@ -374,9 +374,9 @@ public static class WellInfo
         private String _spotSize = "";
         private String _activity = "";
         private String _intensity = "";
-        private Map<String, ObjectProperty> _wellProperties = new LinkedHashMap<>();
+        private final Map<String, ObjectProperty> _wellProperties = new LinkedHashMap<>();
         private final RunDataRow _runDataRow;
-        private Position _position;
+        private final Position _position;
 
         public WellInfo(@Nullable RunDataRow runDataRow, Position position)
         {
@@ -530,7 +530,7 @@ public void setFluorospot(boolean fluorospot)
     }
 
     @RequiresPermission(InsertPermission.class)
-    public class BackgroundSubtractionAction extends FormHandlerAction<Object>
+    public static class BackgroundSubtractionAction extends FormHandlerAction<Object>
     {
         @Override
         public void validateCommand(Object target, Errors errors)

elispotassay/src/org/labkey/elispot/ElispotDataExchangeHandler.java

@@ -32,7 +32,6 @@
 import org.labkey.api.view.ViewContext;
 import org.labkey.vfs.FileLike;
 
-import java.io.File;
 import java.util.List;
 import java.util.Map;
 import java.util.Set;
@@ -79,9 +78,8 @@ public void createSampleData(
     ) throws Exception
     {
         AssayProvider provider = AssayService.get().getProvider(protocol);
-        if (provider instanceof ElispotAssayProvider)
+        if (provider instanceof ElispotAssayProvider plateProvider)
         {
-            ElispotAssayProvider plateProvider = (ElispotAssayProvider)provider;
             Plate template = plateProvider.getPlate(viewContext.getContainer(), protocol);
             if (template != null)
             {

elispotassay/src/org/labkey/elispot/ElispotManager.java

@@ -160,7 +160,7 @@ public Map<String, Set<Integer>> getAntigenHeadings(Container container, TableIn
                 if (null != antigenHeading)
                 {
                     if (!antigenHeadingMap.containsKey(antigenHeading))
-                        antigenHeadingMap.put(antigenHeading, new HashSet<Integer>());
+                        antigenHeadingMap.put(antigenHeading, new HashSet<>());
                     antigenHeadingMap.get(antigenHeading).add((Integer)object.get("RunId"));
                 }
             });

elispotassay/src/org/labkey/elispot/ElispotProviderSchema.java

@@ -58,7 +58,7 @@ public TableInfo createTable(String name, ContainerFilter cf)
     {
         if (name.equalsIgnoreCase(ELISPOT_PLATE_READER_TABLE))
         {
-            EnumTableInfo<ElispotAssayProvider.PlateReaderType> result = new EnumTableInfo<>(ElispotAssayProvider.PlateReaderType.class, this, new EnumTableInfo.EnumValueGetter<ElispotAssayProvider.PlateReaderType>()
+            EnumTableInfo<ElispotAssayProvider.PlateReaderType> result = new EnumTableInfo<>(ElispotAssayProvider.PlateReaderType.class, this, new EnumTableInfo.EnumValueGetter<>()
             {
                 @Override
                 public String getValue(ElispotAssayProvider.PlateReaderType e)

elispotassay/src/org/labkey/elispot/plate/FluorescentPlateInfo.java

@@ -27,8 +27,8 @@
  */
 public class FluorescentPlateInfo implements PlateInfo
 {
-    private String _measurement;
-    private String _analyte;
+    private final String _measurement;
+    private final String _analyte;
 
     private FluorescentPlateInfo(String measurement, String analyte)
     {
@@ -52,7 +52,6 @@ public String getAnalyte()
 
     /**
      * Factory to parse annotations and create PlateInfo instances
-     * @return
      */
     @Nullable
     public static FluorescentPlateInfo create(List<String> annotations)

elispotassay/src/org/labkey/elispot/plate/PlateInfo.java

@@ -1,18 +1,18 @@
-/*
- * Copyright (c) 2015 LabKey Corporation
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- *     http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
+/*
+ * Copyright (c) 2015 LabKey Corporation
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
 package org.labkey.elispot.plate;
 
 import org.jetbrains.annotations.NotNull;
@@ -27,13 +27,11 @@ public interface PlateInfo
      * Returns the type of measurement the corresponding plate contains
      * @return the measurement name
      */
-    @NotNull
-    public String getMeasurement();
+    @NotNull String getMeasurement();
 
     /**
      * Returns the name of the analyte used for a corresponding plate data
      * @return the name of the analyte
      */
-    @Nullable
-    public String getAnalyte();
+    @Nullable String getAnalyte();
 }