Minor auto-refactor code cleanup on a massive scale

nirc_ehr/src/org/labkey/nirc_ehr/NIRCOrchardFileGenerator.java

@@ -1,14 +1,12 @@
 package org.labkey.nirc_ehr;
 
-import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
 import org.labkey.api.data.CompareType;
 import org.labkey.api.data.Container;
 import org.labkey.api.data.DbScope;
 import org.labkey.api.data.SimpleFilter;
 import org.labkey.api.data.TableInfo;
 import org.labkey.api.data.TableSelector;
-import org.labkey.api.exp.OntologyManager;
 import org.labkey.api.module.Module;
 import org.labkey.api.module.ModuleLoader;
 import org.labkey.api.module.ModuleProperty;

nirc_ehr/src/org/labkey/nirc_ehr/NIRC_EHRManager.java

@@ -12,7 +12,7 @@ public class NIRC_EHRManager
     public static final String SIB_OBS_TITLE = "SIB Observations";
     public static final List<String> SIB_OBS = List.of("Environmental Change", "Self Biting Observed", "Other Stereotopy", "New Injury Observed", "Special Enrichment", "Wound Status", "Wound Severity");
 
-    private static NIRCOrchardFileGenerator _orchardFileGenerator = new NIRCOrchardFileGenerator();
+    private static final NIRCOrchardFileGenerator _orchardFileGenerator = new NIRCOrchardFileGenerator();
     public static NIRCOrchardFileGenerator getOrchardFileGenerator()
     {
         return _orchardFileGenerator;

nirc_ehr/src/org/labkey/nirc_ehr/dataentry/form/NIRCArrivalFormType.java

@@ -8,8 +8,6 @@
 import org.labkey.nirc_ehr.dataentry.section.NIRCAnimalDetailsFormSection;
 import org.labkey.nirc_ehr.dataentry.section.NIRCArrivalFormSection;
 import org.labkey.nirc_ehr.dataentry.section.NIRCArrivalInstructionsFormSection;
-import org.labkey.nirc_ehr.dataentry.section.NIRCProjectAssignmentFormSection;
-import org.labkey.nirc_ehr.dataentry.section.NIRCProtocolAssignmentFormSection;
 import org.labkey.nirc_ehr.dataentry.section.NIRCTaskFormSection;
 import org.labkey.nirc_ehr.dataentry.section.NIRCWeightFormSection;
 

nirc_ehr/src/org/labkey/nirc_ehr/dataentry/form/NIRCBirthFormType.java

@@ -41,7 +41,7 @@ public NIRCBirthFormType (DataEntryFormContext ctx, Module owner)
     @Override
     protected List<String> getButtonConfigs()
     {
-        List<String> defaultButtons = new ArrayList<String>();
+        List<String> defaultButtons = new ArrayList<>();
         defaultButtons.add("SAVEDRAFT");
         defaultButtons.add("BIRTHARRIVALREVIEW");
         defaultButtons.add("BIRTHARRIVALFINAL");

nirc_ehr/src/org/labkey/nirc_ehr/dataentry/form/NIRCBulkBehaviorFormType.java

@@ -50,7 +50,7 @@ public NIRCBulkBehaviorFormType(DataEntryFormContext ctx, Module owner)
             s.addConfigSource("BehaviorDefaults");
             s.addConfigSource("TreatmentSchedule");
             s.addConfigSource("MedicationEndDate");
-        };
+        }
     }
 
     @Override

nirc_ehr/src/org/labkey/nirc_ehr/dataentry/form/NIRCBulkClinicalFormType.java

@@ -62,7 +62,7 @@ public NIRCBulkClinicalFormType(DataEntryFormContext ctx, Module owner)
             s.addConfigSource("BulkClinical");
             s.addConfigSource("TreatmentSchedule");
             s.addConfigSource("MedicationEndDate");
-        };
+        }
     }
 
     @Override

nirc_ehr/src/org/labkey/nirc_ehr/dataentry/form/NIRCDeathNecropsyFormType.java

@@ -45,7 +45,7 @@ public NIRCDeathNecropsyFormType(DataEntryFormContext ctx, Module owner)
     @Override
     protected List<String> getButtonConfigs()
     {
-        List<String> defaultButtons = new ArrayList<String>();
+        List<String> defaultButtons = new ArrayList<>();
         boolean isVetTech = getCtx().getContainer().hasPermission(getCtx().getUser(), NIRCEHRVetTechPermission.class);
         boolean isVet = getCtx().getContainer().hasPermission(getCtx().getUser(), EHRVeterinarianPermission.class);
 

nirc_ehr/src/org/labkey/nirc_ehr/dataentry/form/NIRCDepartureFormType.java

@@ -1,9 +1,7 @@
 package org.labkey.nirc_ehr.dataentry.form;
 
 import org.labkey.api.ehr.dataentry.DataEntryFormContext;
-import org.labkey.api.ehr.dataentry.TaskForm;
 import org.labkey.api.module.Module;
-import org.labkey.api.view.template.ClientDependency;
 import org.labkey.nirc_ehr.dataentry.section.NIRCAnimalDetailsFormSection;
 import org.labkey.nirc_ehr.dataentry.section.NIRCDepartureFormSection;
 import org.labkey.nirc_ehr.dataentry.section.NIRCTaskFormSection;

nirc_ehr/src/org/labkey/nirc_ehr/dataentry/form/NIRCHousingFormType.java

@@ -3,7 +3,6 @@
 import org.labkey.api.ehr.dataentry.DataEntryFormContext;
 import org.labkey.api.ehr.security.EHRHousingTransferPermission;
 import org.labkey.api.module.Module;
-import org.labkey.api.view.template.ClientDependency;
 import org.labkey.nirc_ehr.dataentry.section.NIRCAnimalDetailsFormSection;
 import org.labkey.nirc_ehr.dataentry.section.NIRCHousingFormSection;
 import org.labkey.nirc_ehr.dataentry.section.NIRCTaskFormSection;

nirc_ehr/src/org/labkey/nirc_ehr/dataentry/form/NIRCWeightFormType.java

@@ -2,7 +2,6 @@
 
 import org.labkey.api.ehr.dataentry.DataEntryFormContext;
 import org.labkey.api.module.Module;
-import org.labkey.api.view.template.ClientDependency;
 import org.labkey.nirc_ehr.dataentry.section.NIRCAnimalDetailsFormSection;
 import org.labkey.nirc_ehr.dataentry.section.NIRCTaskFormSection;
 import org.labkey.nirc_ehr.dataentry.section.NIRCWeightFormSection;

nirc_ehr/src/org/labkey/nirc_ehr/dataentry/section/NIRCArrivalFormSection.java

@@ -3,7 +3,6 @@
 import org.json.JSONObject;
 import org.labkey.api.data.TableInfo;
 import org.labkey.api.ehr.dataentry.DataEntryFormContext;
-import org.labkey.api.ehr.dataentry.forms.NewAnimalFormSection;
 import org.labkey.api.query.FieldKey;
 
 import java.util.List;

nirc_ehr/src/org/labkey/nirc_ehr/dataentry/section/NIRCBloodDrawFormSection.java

@@ -10,9 +10,9 @@
 
 public class NIRCBloodDrawFormSection extends BloodDrawFormSection
 {
-    private boolean _collapsible = false;
-    private boolean _initCollapsed = false;
-    private boolean _addCopyFromSection = false;
+    private boolean _collapsible;
+    private boolean _initCollapsed;
+    private boolean _addCopyFromSection;
 
     public NIRCBloodDrawFormSection(boolean collapsible, boolean initCollapsed, boolean addCopyFromSection)
     {
@@ -41,6 +41,7 @@ public NIRCBloodDrawFormSection(boolean isChild, String parentQueryName)
         }
     }
 
+    @Override
     public List<String> getTbarButtons()
     {
         List<String> defaultButtons = super.getTbarButtons();

nirc_ehr/src/org/labkey/nirc_ehr/dataentry/section/NIRCCasesFormPanelSection.java

@@ -14,10 +14,10 @@
 
 public class NIRCCasesFormPanelSection extends ParentFormPanelSection
 {
-    private boolean isVetTech;
-    private boolean isVet;
-    private boolean isFolderAdmin;
-    private boolean isBehavior;
+    private final boolean isVetTech;
+    private final boolean isVet;
+    private final boolean isFolderAdmin;
+    private final boolean isBehavior;
 
     public NIRCCasesFormPanelSection(String label, DataEntryFormContext ctx, boolean isBehavior)
     {

nirc_ehr/src/org/labkey/nirc_ehr/dataentry/section/NIRCClinicalObservationsFormSection.java

@@ -7,7 +7,7 @@
 public class NIRCClinicalObservationsFormSection extends BaseFormSection
 {
     public static final String LABEL = "Observations";
-    private boolean _autoPopulateDailyObs = true;
+    private boolean _autoPopulateDailyObs;
 
     public NIRCClinicalObservationsFormSection(boolean autoPopulateDailyObs, boolean initCollapsed)
     {

nirc_ehr/src/org/labkey/nirc_ehr/dataentry/section/NIRCClinicalRemarksFormSection.java

@@ -8,9 +8,9 @@
 public class NIRCClinicalRemarksFormSection extends BaseFormSection
 {
     public static final String LABEL = "Clinical Remarks";
-    private boolean isVetTech;
-    private boolean isVet;
-    private boolean isFolderAdmin;
+    private final boolean isVetTech;
+    private final boolean isVet;
+    private final boolean isFolderAdmin;
 
     public NIRCClinicalRemarksFormSection(boolean isVetTech, boolean isVet, boolean isFolderAdmin)
     {

nirc_ehr/src/org/labkey/nirc_ehr/dataentry/section/NIRCDeathFormSection.java

@@ -12,6 +12,7 @@ public NIRCDeathFormSection()
         setSupportFormSort(false);
     }
 
+    @Override
     public JSONObject toJSON(DataEntryFormContext ctx, boolean includeFormElements)
     {
         JSONObject json = super.toJSON(ctx, includeFormElements);

nirc_ehr/src/org/labkey/nirc_ehr/dataentry/section/NIRCExemptionsFormSection.java

@@ -1,7 +1,5 @@
 package org.labkey.nirc_ehr.dataentry.section;
 
-import org.labkey.api.ehr.EHRService;
-
 public class NIRCExemptionsFormSection extends BaseFormSection
 {
     public NIRCExemptionsFormSection(String label)

nirc_ehr/src/org/labkey/nirc_ehr/dataentry/section/NIRCFlagsFormSection.java

@@ -1,7 +1,5 @@
 package org.labkey.nirc_ehr.dataentry.section;
 
-import org.labkey.api.ehr.EHRService;
-
 public class NIRCFlagsFormSection extends BaseFormSection
 {
     public NIRCFlagsFormSection(String label)

nirc_ehr/src/org/labkey/nirc_ehr/dataentry/section/NIRCGrossPathologyFormSection.java

@@ -1,7 +1,5 @@
 package org.labkey.nirc_ehr.dataentry.section;
 
-import org.json.JSONObject;
-import org.labkey.api.ehr.dataentry.DataEntryFormContext;
 import org.labkey.api.view.template.ClientDependency;
 
 import java.util.List;

nirc_ehr/src/org/labkey/nirc_ehr/dataentry/section/NIRCNecropsyFormSection.java

@@ -1,14 +1,10 @@
 package org.labkey.nirc_ehr.dataentry.section;
 
 import org.json.JSONObject;
-import org.labkey.api.data.TableInfo;
 import org.labkey.api.ehr.dataentry.DataEntryFormContext;
 import org.labkey.api.ehr.dataentry.SimpleFormPanelSection;
-import org.labkey.api.query.FieldKey;
 import org.labkey.api.view.template.ClientDependency;
 
-import java.util.List;
-
 public class NIRCNecropsyFormSection extends SimpleFormPanelSection
 {
 

nirc_ehr/src/org/labkey/nirc_ehr/dataentry/section/NIRCObservationOrdersFormSection.java

@@ -8,7 +8,7 @@ public class NIRCObservationOrdersFormSection extends BaseFormSection
 {
 
     public static final String LABEL = "Observation Orders";
-    private String _dailyObsOption;
+    private final String _dailyObsOption;
 
     public NIRCObservationOrdersFormSection(String dailyObsOption, boolean initCollapsed)
     {

nirc_ehr/src/org/labkey/nirc_ehr/dataentry/section/NIRCWeightFormSection.java

@@ -1,6 +1,5 @@
 package org.labkey.nirc_ehr.dataentry.section;
 
-import org.labkey.api.ehr.EHRService;
 import org.labkey.api.view.template.ClientDependency;
 
 public class NIRCWeightFormSection extends BaseFormSection

nirc_ehr/src/org/labkey/nirc_ehr/demographics/ActiveAssignmentsDemographicsProvider.java

@@ -35,7 +35,7 @@ public ActiveAssignmentsDemographicsProvider(Module owner)
     @Override
     protected Set<FieldKey> getFieldKeys()
     {
-        Set<FieldKey> keys = new HashSet<FieldKey>();
+        Set<FieldKey> keys = new HashSet<>();
         keys.add(FieldKey.fromString("lsid"));
         keys.add(FieldKey.fromString("Id"));
         keys.add(FieldKey.fromString("project"));

nirc_ehr/src/org/labkey/nirc_ehr/demographics/ActiveCasesDemographicsProvider.java

@@ -21,7 +21,7 @@ public ActiveCasesDemographicsProvider(Module module)
     @Override
     protected Set<FieldKey> getFieldKeys()
     {
-        Set<FieldKey> keys = new HashSet<FieldKey>();
+        Set<FieldKey> keys = new HashSet<>();
         keys.add(FieldKey.fromString("lsid"));
         keys.add(FieldKey.fromString("objectid"));
         keys.add(FieldKey.fromString("Id"));

nirc_ehr/src/org/labkey/nirc_ehr/demographics/ActiveFlagsDemographicsProvider.java

@@ -39,7 +39,7 @@ public ActiveFlagsDemographicsProvider(Module module)
     @Override
     protected Set<FieldKey> getFieldKeys()
     {
-        Set<FieldKey> keys = new HashSet<FieldKey>();
+        Set<FieldKey> keys = new HashSet<>();
         keys.add(FieldKey.fromString("lsid"));
         keys.add(FieldKey.fromString("Id"));
         keys.add(FieldKey.fromString("date"));

nirc_ehr/src/org/labkey/nirc_ehr/demographics/ActiveTreatmentsDemographicsProvider.java

@@ -20,7 +20,7 @@ public ActiveTreatmentsDemographicsProvider(Module owner)
     @Override
     protected Set<FieldKey> getFieldKeys()
     {
-        Set<FieldKey> keys = new HashSet<FieldKey>();
+        Set<FieldKey> keys = new HashSet<>();
         keys.add(FieldKey.fromString("lsid"));
         keys.add(FieldKey.fromString("Id"));
         keys.add(FieldKey.fromString("code"));
@@ -60,6 +60,7 @@ public Collection<String> getKeysToTest()
         return keys;
     }
 
+    @Override
     protected SimpleFilter getFilter(Collection<String> ids)
     {
         SimpleFilter filter = super.getFilter(ids);

nirc_ehr/src/org/labkey/nirc_ehr/demographics/NecropsyStatusDemographicsProvider.java

@@ -31,13 +31,14 @@ public boolean requiresRecalc(String schema, String query)
     @Override
     protected Collection<FieldKey> getFieldKeys()
     {
-        Set<FieldKey> keys = new HashSet<FieldKey>();
+        Set<FieldKey> keys = new HashSet<>();
         keys.add(FieldKey.fromString("Id"));
         keys.add(FieldKey.fromString("necropsy_status"));
 
         return keys;
     }
 
+    @Override
     protected SimpleFilter getFilter(Collection<String> ids)
     {
         List<String> qcStates = new ArrayList<>();

nirc_ehr/src/org/labkey/nirc_ehr/demographics/ProtocolAssignmentDemographicsProvider.java

@@ -8,7 +8,6 @@
 
 import java.util.Collection;
 import java.util.HashSet;
-import java.util.List;
 import java.util.Set;
 
 public class ProtocolAssignmentDemographicsProvider extends AbstractListDemographicsProvider

nirc_ehr/src/org/labkey/nirc_ehr/history/BloodDrawDataSource.java

@@ -41,12 +41,11 @@ protected Set<String> getColumnNames()
     @Override
     protected String getHtml(Container c, Results rs, boolean redacted) throws SQLException
     {
-        StringBuilder sb = new StringBuilder();
 
-        sb.append(safeAppend(rs, "Total Quantity", "quantity", " mL"));
-        sb.append(safeAppend(rs, "Sample Type", "type"));
-        sb.append(safeAppend(rs, "Remark", "remark"));
+        String sb = safeAppend(rs, "Total Quantity", "quantity", " mL") +
+                safeAppend(rs, "Sample Type", "type") +
+                safeAppend(rs, "Remark", "remark");
 
-        return sb.toString();
+        return sb;
     }
 }

nirc_ehr/src/org/labkey/nirc_ehr/history/BreederDataSource.java

@@ -32,12 +32,11 @@ public BreederDataSource(Module module)
     @Override
     protected String getHtml(Container c, Results rs, boolean redacted) throws SQLException
     {
-        StringBuilder sb = new StringBuilder();
 
-        sb.append(safeAppend(rs, "Type", "type"));
-        sb.append(safeAppend(rs, "Result", "result"));
-        sb.append(safeAppend(rs, "Remark", "remark"));
+        String sb = safeAppend(rs, "Type", "type") +
+                safeAppend(rs, "Result", "result") +
+                safeAppend(rs, "Remark", "remark");
 
-        return sb.toString();
+        return sb;
     }
 }

nirc_ehr/src/org/labkey/nirc_ehr/history/FosteringDataSource.java

@@ -40,11 +40,10 @@ protected Set<String> getColumnNames()
     @Override
     protected String getHtml(Container c, Results rs, boolean redacted) throws SQLException
     {
-        StringBuilder sb = new StringBuilder();
 
-        sb.append(safeAppend(rs, "Type", "type"));
-        sb.append(safeAppend(rs, "Remark", "remark"));
+        String sb = safeAppend(rs, "Type", "type") +
+                safeAppend(rs, "Remark", "remark");
 
-        return sb.toString();
+        return sb;
     }
 }

nirc_ehr/src/org/labkey/nirc_ehr/history/HistopathologyDataSource.java

@@ -40,11 +40,10 @@ protected Set<String> getColumnNames()
     @Override
     protected String getHtml(Container c, Results rs, boolean redacted) throws SQLException
     {
-        StringBuilder sb = new StringBuilder();
 
-        sb.append(safeAppend(rs, "Diagnosis", "diagnosis"));
-        sb.append(safeAppend(rs, "Remark", "remark"));
+        String sb = safeAppend(rs, "Diagnosis", "diagnosis") +
+                safeAppend(rs, "Remark", "remark");
 
-        return sb.toString();
+        return sb;
     }
 }

nirc_ehr/src/org/labkey/nirc_ehr/history/NIRCCaseCloseDataSource.java

@@ -1,6 +1,5 @@
 package org.labkey.nirc_ehr.history;
 
-import org.apache.commons.lang3.time.DateUtils;
 import org.jetbrains.annotations.NotNull;
 import org.labkey.api.data.CompareType;
 import org.labkey.api.data.Container;
@@ -31,14 +30,12 @@ protected String getHtml(Container c, Results rs, boolean redacted) throws SQLEx
     {
         Date start = rs.getDate(FieldKey.fromString("date"));
 
-        StringBuilder sb = new StringBuilder();
+        String sb = "Opened Date: " + DateUtil.formatDate(c, start) +
+                "\n" +
+                safeAppend(rs, "Problem Area", "problemCategory") +
+                safeAppend(rs, "Close Remark", "closeRemark");
 
-        sb.append("Opened Date: ").append(DateUtil.formatDate(c, start));
-        sb.append("\n");
-        sb.append(safeAppend(rs, "Problem Area", "problemCategory"));
-        sb.append(safeAppend(rs, "Close Remark", "closeRemark"));
-
-        return sb.toString();
+        return sb;
     }
 
     @Override