Minor auto-refactor code cleanup on a massive scale

Original PR: LabKey/platform#6742

* Minor auto-refactor code cleanup on a massive scale

* Fix DomainDesignerTest, reduce usage of deprecated methods

* Fix merge

Author: labkey-jeckels

studydesign/src/org/labkey/studydesign/StudyDesignController.java

@@ -120,7 +120,7 @@ private Study getStudy(Container container)
 
     @ActionNames("manageAssaySchedule, manageAssaySpecimen")
     @RequiresPermission(UpdatePermission.class)
-    public class ManageAssayScheduleAction extends SimpleViewAction<AssayScheduleForm>
+    public static class ManageAssayScheduleAction extends SimpleViewAction<AssayScheduleForm>
     {
         @Override
         public ModelAndView getView(AssayScheduleForm form, BindException errors)
@@ -154,7 +154,7 @@ public void setUseAlternateLookupFields(boolean useAlternateLookupFields)
     }
 
     @RequiresPermission(UpdatePermission.class)
-    public class ManageStudyProductsAction extends SimpleViewAction<ReturnUrlForm>
+    public static class ManageStudyProductsAction extends SimpleViewAction<ReturnUrlForm>
     {
         @Override
         public ModelAndView getView(ReturnUrlForm form, BindException errors)
@@ -188,7 +188,7 @@ public void setSingleTable(boolean singleTable)
     }
 
     @RequiresPermission(UpdatePermission.class)
-    public class ManageTreatmentsAction extends SimpleViewAction<ManageTreatmentsBean>
+    public static class ManageTreatmentsAction extends SimpleViewAction<ManageTreatmentsBean>
     {
         @Override
         public ModelAndView getView(ManageTreatmentsBean form, BindException errors)
@@ -633,10 +633,10 @@ private List<Integer> updateTreatments(List<TreatmentImpl> treatments) throws Ex
     @RequiresPermission(UpdatePermission.class)
     public class UpdateTreatmentScheduleAction extends MutatingApiAction<StudyTreatmentSchedule>
     {
-        private Map<String, Integer> _tempTreatmentIdMap = new HashMap<>();
-        private Set<Integer> usedTreatmentIds = new HashSet<>(); // treatmentIds referenced in single table Treatment Schedule UI
-        private List<Integer> treatmentRowIds = new ArrayList<>(); // treatmentIds defined in 2 table UI's Treatment section
-        private List<Integer> cohortRowIds = new ArrayList<>();
+        private final Map<String, Integer> _tempTreatmentIdMap = new HashMap<>();
+        private final Set<Integer> usedTreatmentIds = new HashSet<>(); // treatmentIds referenced in single table Treatment Schedule UI
+        private final List<Integer> treatmentRowIds = new ArrayList<>(); // treatmentIds defined in 2 table UI's Treatment section
+        private final List<Integer> cohortRowIds = new ArrayList<>();
 
         @Override
         public void validateForm(StudyTreatmentSchedule form, Errors errors)

studydesign/src/org/labkey/studydesign/model/TreatmentManager.java

@@ -805,11 +805,11 @@ private void populateTreatmentSchedule() throws ValidationException
         {
             _cohorts.add(CohortService.get().createCohort(_junitStudy, _user, "Cohort1", true, 10, null));
             _cohorts.add(CohortService.get().createCohort(_junitStudy, _user, "Cohort2", true, 20, null));
-            assertEquals(_cohorts.size(), 2);
+            assertEquals(2, _cohorts.size());
 
             _visits.add(VisitService.get().createVisit(_junitStudy, _user, BigDecimal.valueOf(1.0), "Visit 1", Visit.Type.BASELINE));
             _visits.add(VisitService.get().createVisit(_junitStudy, _user, BigDecimal.valueOf(2.0), "Visit 2", Visit.Type.SCHEDULED_FOLLOWUP));
-            assertEquals(_visits.size(), 2);
+            assertEquals(2, _visits.size());
 
             for (Cohort cohort : _cohorts)
             {
@@ -843,7 +843,7 @@ private void populateTreatments()
                 _treatments.add(treatment2);
             }
 
-            assertEquals(_treatments.size(), 2);
+            assertEquals(2, _treatments.size());
         }
 
         private void addProductsForTreatment(int treatmentId)
@@ -887,7 +887,7 @@ private void populateStudyProducts()
                 _products.add(Table.insert(_user, ti, product4));
             }
 
-            assertEquals(_products.size(), 4);
+            assertEquals(4, _products.size());
 
             for (ProductImpl product : _products)
                 addAntigenToProduct(product.getRowId());
@@ -942,7 +942,7 @@ private void populateLookupTables()
             assertNull("Unexpected study design lookup label", _manager.getStudyDesignRouteLabelByName(_container, "UNK"));
             _lookups.put("Route", name);
 
-            assertEquals(_lookups.keySet().size(), 4);
+            assertEquals(4, _lookups.keySet().size());
         }
 
         private void verifyTreatmentVisitMapRecords(int expectedCount)
@@ -1079,7 +1079,7 @@ private void populateAssaySchedule()
         {
             _visits.add(VisitService.get().createVisit(_junitStudy, _user, BigDecimal.valueOf(1.0), "Visit 1", Visit.Type.BASELINE));
             _visits.add(VisitService.get().createVisit(_junitStudy, _user, BigDecimal.valueOf(2.0), "Visit 2", Visit.Type.SCHEDULED_FOLLOWUP));
-            assertEquals(_visits.size(), 2);
+            assertEquals(2, _visits.size());
 
             for (AssaySpecimenConfigImpl assay : _assays)
             {
@@ -1123,7 +1123,7 @@ private void populateLookupTables()
             _lookups.put("Lab", name);
 
             data.put("Name", name = "Test Sample Type");
-            data.put("Label", label = "Test Sample Type Label");
+            data.put("Label", "Test Sample Type Label");
             data.put("PrimaryType", "Test Primary Type");
             data.put("ShortSampleCode", "TP");
             Table.insert(_user, StudyDesignSchema.getInstance().getTableInfoStudyDesignSampleTypes(), data);

studydesign/src/org/labkey/studydesign/view/immunizationScheduleWebpart.jsp

@@ -103,7 +103,7 @@
 %>
                 </tr>
 <%
-                if (cohorts.size() == 0)
+                if (cohorts.isEmpty())
                 {
                     %><tr><td class="cell-display empty" colspan="2">No data to show.</td></tr><%
                 }