Minor auto-refactor code cleanup on a massive scale

EHR_App/test/src/org/labkey/test/tests/EHRAppTestSetupHelper.java

@@ -13,7 +13,6 @@
 import java.io.File;
 import java.io.IOException;
 import java.util.Arrays;
-import java.util.Collections;
 import java.util.List;
 import java.util.Map;
 import java.util.Objects;

EHR_App/test/src/org/labkey/test/tests/EHR_AppTest.java

@@ -74,7 +74,7 @@ protected File getStudyPolicyXML()
     @BeforeClass
     public static void setupProject() throws Exception
     {
-        EHR_AppTest init = (EHR_AppTest) getCurrentTest();
+        EHR_AppTest init = getCurrentTest();
         init.doSetup();
     }
 

EHR_ComplianceDB/src/org/labkey/ehr_compliancedb/notification/EmployeeComplianceNotification.java

@@ -15,15 +15,10 @@
  */
 package org.labkey.ehr_compliancedb.notification;
 
-import org.jetbrains.annotations.Nullable;
 import org.labkey.api.data.Container;
 import org.apache.commons.lang3.time.DateUtils;
-import org.labkey.api.module.ModuleLoader;
-import org.labkey.api.module.Module;
 import org.labkey.api.data.CompareType;
-import org.labkey.api.data.Results;
 import org.labkey.api.data.ColumnInfo;
-import org.labkey.api.data.ResultsImpl;
 import org.labkey.api.data.Selector;
 import org.labkey.api.data.SimpleFilter;
 import org.labkey.api.data.Sort;
@@ -36,20 +31,15 @@
 import org.labkey.api.query.UserSchema;
 import org.labkey.api.ldk.notification.AbstractNotification;
 import org.labkey.api.util.DateUtil;
-import org.labkey.ehr_compliancedb.EHR_ComplianceDBModule;
-import org.labkey.ehr_compliancedb.EHR_ComplianceDBUserSchema;
 
 
-import java.util.Date;
 import java.sql.ResultSet;
 import java.sql.SQLException;
 import java.util.Calendar;
 import java.util.Date;
-import java.util.HashMap;
 import java.util.HashSet;
 import java.util.Map;
 import java.util.Set;
-import java.util.TreeMap;
 
 //Added 3-29-2016  Blasa
 
@@ -153,12 +143,12 @@ private void EmployeeComplianceNotification(Container c, User u, final StringBui
             msg.append("<tr style='font-weight: bold;'><td>Employee ID</td><td>First Name</td><td>Last Name</td><td>Category</td><td>Unit</td><td>Supervisor</td><td>Location</td></tr>\n");
 
 
-            ts.forEach(new Selector.ForEachBlock<ResultSet>()
+            ts.forEach(new Selector.ForEachBlock<>()
             {
                 @Override
                 public void exec(ResultSet rs) throws SQLException
                 {
-                    msg.append("<tr><td>" + (rs.getString("employeeid") == null ? "" : rs.getString("employeeid")) + "</td><td>" + rs.getString("firstName") + "</td><td>" + rs.getString("lastName")  + "</td><td>" + rs.getString("category")  + "</td><td>" + rs.getString("unit")  + "</td><td>" + rs.getString("supervisor") + "</td><td>" + rs.getString("location")+ "</td></tr>\n");
+                    msg.append("<tr><td>" + (rs.getString("employeeid") == null ? "" : rs.getString("employeeid")) + "</td><td>" + rs.getString("firstName") + "</td><td>" + rs.getString("lastName") + "</td><td>" + rs.getString("category") + "</td><td>" + rs.getString("unit") + "</td><td>" + rs.getString("supervisor") + "</td><td>" + rs.getString("location") + "</td></tr>\n");
 
                 }
             });

EHR_Purchasing/src/org/labkey/ehr_purchasing/EHR_PurchasingController.java

@@ -36,13 +36,15 @@ public EHR_PurchasingController()
     }
 
     @RequiresPermission(ReadPermission.class)
-    public class BeginAction extends SimpleViewAction
+    public static class BeginAction extends SimpleViewAction<Object>
     {
+        @Override
         public ModelAndView getView(Object o, BindException errors)
         {
-            return new JspView("/org/labkey/ehr_purchasing/view/hello.jsp");
+            return new JspView<>("/org/labkey/ehr_purchasing/view/hello.jsp");
         }
 
+        @Override
         public void addNavTrail(NavTree root) { }
     }
 }

EHR_SM/src/org/labkey/ehr_sm/EHR_SMController.java

@@ -48,15 +48,17 @@ public EHR_SMController()
     }
 
     @RequiresPermission(ReadPermission.class)
-    public class BeginAction extends SimpleViewAction
+    public static class BeginAction extends SimpleViewAction<Object>
     {
+        @Override
         public ModelAndView getView(Object o, BindException errors)
         {
             JspView<Void> view = new JspView<>("/org/labkey/ehr_sm/view/hello.jsp");
             view.setTitle("EHR Sample Manager");
             return view;
         }
 
+        @Override
         public void addNavTrail(NavTree root) { }
     }
 
@@ -100,6 +102,7 @@ public void setSelectedAnimalSampleTypes(String[] selectedAnimalSampleTypes)
     @RequiresPermission(AdminPermission.class)
     public class AdminAction extends FormViewAction<AdminForm>
     {
+        @Override
         public void addNavTrail(NavTree root) { }
 
         @Override

EHR_SM/test/src/org/labkey/test/tests/ehr_sm/EHR_SMTest.java

@@ -42,7 +42,7 @@ protected void doCleanup(boolean afterTest) throws TestTimeoutException
     @BeforeClass
     public static void setupProject()
     {
-        EHR_SMTest init = (EHR_SMTest)getCurrentTest();
+        EHR_SMTest init = getCurrentTest();
 
         init.doSetup();
     }

Viral_Load_Assay/src/org/labkey/viral_load_assay/assay/ABI7500ImportMethod.java

@@ -162,7 +162,7 @@ public JSONObject getMetadata(ViewContext ctx, ExpProtocol protocol)
         return meta;
     }
 
-    private class Parser extends DefaultAssayParser
+    private static class Parser extends DefaultAssayParser
     {
         private final Double CYCLE_LIMIT = 45.0;
         private static final String TASK_FIELD = "Task";
@@ -178,7 +178,7 @@ public Parser(AssayImportMethod method, Container c, User u, int assayId)
         @Override
         public Pair<ExpExperiment, ExpRun> saveBatch(JSONObject json, File file, String fileName, ViewContext ctx) throws BatchValidationException
         {
-            Integer templateId = json.getInt("TemplateId");
+            int templateId = json.getInt("TemplateId");
 
             Pair<ExpExperiment, ExpRun> result = super.saveBatch(json, file, fileName, ctx);
 
@@ -217,7 +217,7 @@ protected String readRawFile(ImportContext context) throws BatchValidationExcept
 
                     if (!inResults)
                     {
-                        if (row.size() == 0)
+                        if (row.isEmpty())
                             continue;
 
                         if (row.get(0).equals("Detector Name"))
@@ -229,7 +229,7 @@ protected String readRawFile(ImportContext context) throws BatchValidationExcept
                         if (inDetectors)
                         {
                             String detector = row.get(0);
-                            Map<String, Double> map = new HashMap<String, Double>();
+                            Map<String, Double> map = new HashMap<>();
                             map.put("slope", Double.parseDouble(row.get(1)));
                             map.put("intercept", Double.parseDouble(row.get(2)));
                             map.put("rSquared", Double.parseDouble(row.get(3)));
@@ -262,7 +262,7 @@ else if (row.get(0).startsWith("Document Name:"))
                     }
                     else
                     {
-                        out.writeNext(row.toArray(new String[row.size()]));
+                        out.writeNext(row.toArray(new String[0]));
                     }
                 }
 
@@ -284,7 +284,7 @@ else if (row.get(0).startsWith("Document Name:"))
         @Override
         protected List<Map<String, Object>> processRowsFromFile(List<Map<String, Object>> rows, ImportContext context) throws BatchValidationException
         {
-            List<Map<String, Object>> newRows = new ArrayList<Map<String, Object>>();
+            List<Map<String, Object>> newRows = new ArrayList<>();
             ParserErrors errors = context.getErrors();
 
             //add slope to run info
@@ -308,7 +308,7 @@ protected List<Map<String, Object>> processRowsFromFile(List<Map<String, Object>
                 {
                     rowIdx++;
                     Map<String, Object> row = rowsIter.next();
-                    Map<String, Object> map = new CaseInsensitiveHashMap<Object>(row);
+                    Map<String, Object> map = new CaseInsensitiveHashMap<>(row);
 
                     if (row.size() != 9)
                     {
@@ -444,7 +444,7 @@ private void calculateViralLoad(Map<String, Object> map, Double limitOfDetection
         {
             Map<String, Double> detectorInfo = _detectorMap.get(map.get(DETECTOR_FIELD));
             Double ct = map.get("cp") == null ? null : Double.parseDouble(map.get("cp").toString());
-            Double sampleVol = Double.parseDouble(String.valueOf(map.get("sampleVol")));
+            double sampleVol = Double.parseDouble(String.valueOf(map.get("sampleVol")));
             Double intercept = detectorInfo.get("intercept");
             Double slope = detectorInfo.get("slope");
             Double volPerRxn = Double.parseDouble(String.valueOf(map.get("volPerRxn")));
@@ -463,14 +463,14 @@ private void calculateViralLoad(Map<String, Object> map, Double limitOfDetection
 
         private void calculateViralLoads(List<Map<String, Object>> rows)
         {
-            Map<String, List<Map<String, Object>>> rowMap = new HashMap<String, List<Map<String, Object>>>();
+            Map<String, List<Map<String, Object>>> rowMap = new HashMap<>();
             Double lowestStd = 0.0;
             for (Map<String, Object> row : rows)
             {
                 String key = (String)row.get(NAME_FIELD);
                 List<Map<String, Object>> list = rowMap.get(key);
                 if (list == null)
-                    list = new ArrayList<Map<String, Object>>();
+                    list = new ArrayList<>();
 
                 if (TYPE.Standard.getTemplateText().equals(row.get(CATEGORY_FIELD)))
                 {
@@ -505,7 +505,7 @@ private void calculateViralLoads(List<Map<String, Object>> rows)
 
                 avgCopies = avgCopies / list.size();
                 Double stdDev = new StandardDeviation().evaluate(values);
-                Double cv = stdDev / avgCopies;
+                double cv = stdDev / avgCopies;
 
                 //NOTE: at some point I should make this configurable
                 //flag any record with %CV > 66, but only if at least 1 replicate has copies/rxn above limitOfDetection
@@ -573,14 +573,14 @@ public void doGenerateTemplate(JSONObject json, HttpServletRequest request, Http
             response.setHeader("Pragma", "private");
             response.setHeader("Cache-Control", "private");
 
-            Map<Integer, String[]> rowMap = new HashMap<Integer, String[]>();
+            Map<Integer, String[]> rowMap = new HashMap<>();
 
             int rowIdx = 0;
             for (JSONObject row : results)
             {
                 rowIdx++;
 
-                List<String> fields = new ArrayList<String>();
+                List<String> fields = new ArrayList<>();
 
                 //build the row
                 Integer wellNum = (Integer)wellMap.get(row.getString("well"));
@@ -594,13 +594,13 @@ public void doGenerateTemplate(JSONObject json, HttpServletRequest request, Http
                 fields.add(type.getTemplateText());
                 fields.add(TYPE.getQuantity(type, row.getString(SUBJECT_FIELD)));
 
-                rowMap.put(wellNum, fields.toArray(new String[fields.size()]));
+                rowMap.put(wellNum, fields.toArray(new String[0]));
             }
 
             if (errors.hasErrors())
                 throw errors;
 
-            List<String[]> rows = new ArrayList<String[]>();
+            List<String[]> rows = new ArrayList<>();
             rows.add(new String[]{"*** SDS Setup File Version", "3"});
             rows.add(new String[]{"*** Output Plate Size", "96"});
             rows.add(new String[]{"*** Output Plate ID", json.getString("templateName") + ".sds"});
@@ -642,21 +642,21 @@ public void doGenerateTemplate(JSONObject json, HttpServletRequest request, Http
 
     private Map<String, Map<String, String>> getDetectorsForResults(List<JSONObject> results)
     {
-        final Map<String, Map<String, String>> ret = new HashMap<String, Map<String, String>>();
-        Set<String> distinctAssays = new HashSet<String>();
+        final Map<String, Map<String, String>> ret = new HashMap<>();
+        Set<String> distinctAssays = new HashSet<>();
         for (JSONObject row : results)
         {
             distinctAssays.add(row.getString(ASSAYNAME_FIELD));
         }
 
         TableInfo table = Viral_Load_AssaySchema.getInstance().getSchema().getTable(Viral_Load_AssaySchema.TABLE_ABI7500_DETECTORS);
         TableSelector ts = new TableSelector(table, new SimpleFilter(FieldKey.fromString("assayName"), distinctAssays, CompareType.IN), null);
-        ts.forEach(new Selector.ForEachBlock<ResultSet>()
+        ts.forEach(new Selector.ForEachBlock<>()
         {
             @Override
             public void exec(ResultSet object) throws SQLException
             {
-                Map<String, String> row = new HashMap<String, String>();
+                Map<String, String> row = new HashMap<>();
                 row.put("detector", object.getString("detector"));
                 row.put("reporter", object.getString("reporter"));
                 row.put("quencher", object.getString("quencher"));
@@ -673,8 +673,8 @@ public void validateTemplate(User u, Container c, ExpProtocol protocol, @Nullabl
         //ensure each subject/date has at least 2 neg controls
         JSONObject resultDefaults = json.optJSONObject("Results");
         JSONArray rawResults = json.getJSONArray("ResultRows");
-        List<JSONObject> results = new ArrayList<JSONObject>();
-        Set<String> distinctWells = new HashSet<String>();
+        List<JSONObject> results = new ArrayList<>();
+        Set<String> distinctWells = new HashSet<>();
         Map<Object, Object> wellMap = getWellMap96("well_96", "addressbyrow_96");
 
         String[] requiredFields = new String[]{"well", SUBJECT_FIELD, CATEGORY_FIELD, ASSAYNAME_FIELD};
@@ -710,7 +710,7 @@ public void validateTemplate(User u, Container c, ExpProtocol protocol, @Nullabl
             if (missingRequired)
                 continue;
 
-            TYPE type = null;
+            TYPE type;
             try
             {
                 type = TYPE.getByDatabaseCategoryValue(row.getString(CATEGORY_FIELD));
@@ -782,7 +782,7 @@ public void validateTemplate(User u, Container c, ExpProtocol protocol, @Nullabl
         }
 
         Map<String, Map<String, String>> detectorRows = getDetectorsForResults(results);
-        if (detectorRows.size() == 0)
+        if (detectorRows.isEmpty())
         {
             errors.addRowError(new ValidationException("No detectors were found for these samples."));
             throw errors;

Viral_Load_Assay/src/org/labkey/viral_load_assay/assay/AbstractWNPRCImportMethod.java

@@ -401,10 +401,10 @@ protected void calculateViralLoadForRoche(Map<String, Object> map)
             map.put("sampleVol", 1.0);
 
         //This is the size (ml or mg) of the source material (plasma/serum/urine/etc.)
-        Double sampleVol = Double.parseDouble(map.get("sampleVol").toString());
+        double sampleVol = Double.parseDouble(map.get("sampleVol").toString());
 
-        Double viralLoad = 0.0;
-        Double dilutionFactor = 0.0;
+        double viralLoad = 0.0;
+        double dilutionFactor = 0.0;
         if (copiesPerRxn != null && sampleVol > 0)
         {
             dilutionFactor = (1.0 / sampleVol) * (eluateVol / volPerRxn);
@@ -417,8 +417,8 @@ protected void calculateViralLoadForRoche(Map<String, Object> map)
     }
 
     protected class Parser extends DefaultAssayParser {
-        private String HAS_RESULT = "__hasResult__";
-        private int _assayId;
+        private final String HAS_RESULT = "__hasResult__";
+        private final int _assayId;
         final String[] lookup = "0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ,.".split("");
         //The expected number of columns in the import data
         private int _expectedColumnCount = Integer.MAX_VALUE;
@@ -444,6 +444,7 @@ public Pair<ExpExperiment, ExpRun> saveBatch(JSONObject json, File file, String
         }
 
         //Needs to be overridden within the Parser class of each ImportMethod that extends AbstractWNPRCImportMethod
+        @Override
         protected TabLoader getTabLoader(String contents) throws IOException {
             return null;
         }
@@ -531,6 +532,7 @@ protected List<Map<String, Object>> processRowsFromFile(List<Map<String, Object>
             return newRows;
         }
 
+        @Override
         protected void ensureTemplateRowsHaveResults(Map<String, Map<String, Object>> templateRows, ImportContext context) throws BatchValidationException {
             for (String key : templateRows.keySet()) {
                 Map<String, Object> row = templateRows.get(key);
@@ -563,7 +565,7 @@ private String uncompressUUID(String compressObjectId) {
                 else if (hexString.length() == 2) {
                     hexString = "0" + hexString;
                 }
-                else if (hexString.length() == 0) {
+                else if (hexString.isEmpty()) {
                     hexString = "000" + hexString;
                 }
 
@@ -577,19 +579,17 @@ else if (hexString.length() == 0) {
             }
             char[] objectId = base16Duples.toString().toCharArray();
 
-            StringBuilder returnObjectId = new StringBuilder();
-
-            returnObjectId.append(objectId, 0, 8);
-            returnObjectId.append("-");
-            returnObjectId.append(objectId, 8, 4);
-            returnObjectId.append("-");
-            returnObjectId.append(objectId, 12, 4);
-            returnObjectId.append("-");
-            returnObjectId.append(objectId, 16, 4);
-            returnObjectId.append("-");
-            returnObjectId.append(objectId, 20, 12);
-
-            return returnObjectId.toString();
+            String returnObjectId = String.valueOf(objectId, 0, 8) +
+                    "-" +
+                    String.valueOf(objectId, 8, 4) +
+                    "-" +
+                    String.valueOf(objectId, 12, 4) +
+                    "-" +
+                    String.valueOf(objectId, 16, 4) +
+                    "-" +
+                    String.valueOf(objectId, 20, 12);
+
+            return returnObjectId;
         }
     }
 

Viral_Load_Assay/src/org/labkey/viral_load_assay/assay/DefaultVLImportMethod.java

@@ -157,7 +157,7 @@ protected void calculateViralLoadForRoche(Map<String, Object> map)
         if (!map.containsKey("sampleVol"))
             map.put("sampleVol", 1.0);
 
-        Double sampleVol = Double.parseDouble(map.get("sampleVol").toString());
+        double sampleVol = Double.parseDouble(map.get("sampleVol").toString());
 
         double viralLoad;
         if (copiesPerRxn != null)