Address some miscellaneous warnings

api/src/org/labkey/api/admin/AdminBean.java

@@ -80,9 +80,7 @@ public static class RecentUser
     public static final String servletContainer = ModuleLoader.getServletContext().getServerInfo();
     public static final String servletConfiguration = "Embedded";
     public static final String sessionTimeout = Formats.commaf0.format(ModuleLoader.getServletContext().getSessionTimeout());
-    @SuppressWarnings("unused") // Available substitution property, not used directly in code
     public static final String buildTime = ModuleLoader.getInstance().getCoreModule().getBuildTime();
-    @SuppressWarnings("unused") // Available substitution property, not used directly in code
     public static final String serverStartupTime = DateUtil.formatDateTime(ContainerManager.getRoot());
     public static final List<Module> modules;
 

api/src/org/labkey/api/exp/api/ExperimentService.java

@@ -79,6 +79,7 @@
 import org.labkey.api.reader.TabLoader;
 import org.labkey.api.security.User;
 import org.labkey.api.services.ServiceRegistry;
+import org.labkey.api.util.IntegerUtils;
 import org.labkey.api.util.Pair;
 import org.labkey.api.util.StringUtilsLabKey;
 import org.labkey.api.view.HttpView;
@@ -719,10 +720,8 @@ static void validateParentAlias(Map<String, String> aliasMap, Set<String> reserv
     ExpData getExpDataByURL(Path p, @Nullable Container c);
 
     /**
-     * Get all ExpData for the dataFileUrl.
-     *
-     * Having more than one ExpData for the same file path doesn't happen often but is allowed.
-     * Some examples:
+     * Get all ExpData for the dataFileUrl. Having more than one ExpData for the same file path doesn't happen often but
+     * is allowed. Some examples:
      * - The file or pipeline root may be shared by more than one container and an exp.data may be created in each container when importing assay data.
      * - In the MS2 analysis pipeline, there are tools that rewrite an input file to add more data. We model them as separate exp.data.
      */
@@ -1297,19 +1296,15 @@ public XarImportOptions setStrictValidateExistingSampleType(boolean strictValida
         }
     }
 
+    @Deprecated // Use IntegerUtils.asLong() instead
     static Long asLong(Object o)
     {
-        return null==o ? null : o.getClass() == Long.class ? (Long)o : ((Number)o).longValue();
+        return IntegerUtils.asLong(o);
     }
+
+    @Deprecated // Use IntegerUtils.asInteger() instead
     static Integer asInteger(Object o)
     {
-        if (null == o)
-            return null;
-        if (o.getClass() == Integer.class)
-            return (Integer)o;
-        long l = ((Number)o).longValue();
-        if (l < Integer.MIN_VALUE || l > Integer.MAX_VALUE)
-            throw new IllegalArgumentException("Invalid int value: " + l);
-        return (int)l;
+        return IntegerUtils.asInteger(o);
     }
 }

api/src/org/labkey/api/util/IntegerUtils.java

@@ -5,11 +5,11 @@
 
 /**
  * This Class to help with dealing with Object that may represent an integer number (char,short,int,long).  It
- * is meant to fill in the small gap between Java (e.g casts and instanceof) and ConvertUtils.  Hopefully, this
+ * is meant to fill in the small gap between Java (e.g. casts and instanceof) and ConvertUtils. Hopefully, this
  * class makes it just a little easier to deal with Integer valued Numbers.
  * <br>
- * Unfortunately, Number does not help with detecting integer/non-integer types, so this class only handles Object
- * instances that have corresponding to the primitive types.  {@code boolean}, {@code byte}, {@code char},
+ * Unfortunately, Number does not help with detecting integer/noninteger types, so this class only handles Object
+ * instances that have corresponding to the primitive types. {@code boolean}, {@code byte}, {@code char},
  * {@code short}, {@code int}, {@code long}, {@code float}, and {@code double})
  * <br>
  * Because "Integer" is kind of ambiguous, I will use "Integral" to mean any integer type.  For now, I am not including
@@ -27,15 +27,15 @@ public static boolean isIntegral(Object o)
         return c == Byte.class || c == Short.class || c==Integer.class || c==Long.class;
     }
 
-    /** returns Numeric object as a Long.  This method will throw if not Object is not Integral. */
+    /** returns Numeric object as a Long. This method will throw if Object is not Integral. */
     public static Long asLong(Object o)
     {
         if (!isIntegral(o))
             return (Long)o;  // throw ClassCastException
         return o.getClass() == Long.class ? (Long)o : Long.valueOf(((Number)o).longValue());
     }
 
-    /** returns Numeric object as an Integer.  This method will throw if not Object is not Integral or is out of range. */
+    /** returns Numeric object as an Integer. This method will throw if Object is not Integral or is out of range. */
     public static Integer asInteger(Object o) throws ClassCastException
     {
         if (null == o)

api/src/org/labkey/api/view/DataViewSnapshotSelectionForm.java

@@ -3,7 +3,6 @@
 import org.labkey.api.collections.LongHashSet;
 import org.labkey.api.data.DataRegionSelection;
 
-import java.util.HashSet;
 import java.util.Set;
 
 public class DataViewSnapshotSelectionForm extends DataViewSelectionForm

experiment/src/org/labkey/experiment/api/ExperimentServiceImpl.java

@@ -3610,6 +3610,7 @@ private void _verifyAllEdges(Container c, @Nullable Integer limit)
         }
     }
 
+    @Override
     public void clearAncestors(ExpRunItem runItem)
     {
         boolean isSample = runItem instanceof ExpMaterial;
@@ -3619,16 +3620,19 @@ public void clearAncestors(ExpRunItem runItem)
             clearDataAncestors(List.of(runItem.getRowId()));
     }
 
+    @Override
     public void repopulateAncestors()
     {
         ClosureQueryHelper.truncateAndRecreate();
     }
 
+    @Override
     public void clearDataAncestors(Collection<Long> dataRowIds)
     {
         ClosureQueryHelper.clearAncestorsForDataObjects(dataRowIds);
     }
 
+    @Override
     public void clearMaterialAncestors(Collection<Long> materialRowIds)
     {
         ClosureQueryHelper.clearAncestorsForMaterials(materialRowIds);

query/src/org/labkey/query/QueryServiceImpl.java

@@ -385,18 +385,16 @@ private static SQLFragment getColumnInSql(@NotNull FieldKey fieldKey, Object val
 
         SQLFragment fromSql = t.getFromSQL("_");
 
-        SQLFragment sqlFragment = new SQLFragment()
-                .append("(").appendIdentifier(col.getAlias())
-                .append(")")
-                .append(negate ? " NOT" : "")
-                .append(" IN (")
-                .append(" SELECT ")
-                .append(t.getColumns().get(0).getValueSql("_"))
-                .append(" FROM ")
-                .append(fromSql)
-                .append(")");
-
-        return sqlFragment;
+        return new SQLFragment()
+            .append("(").appendIdentifier(col.getAlias())
+            .append(")")
+            .append(negate ? " NOT" : "")
+            .append(" IN (")
+            .append(" SELECT ")
+            .append(t.getColumns().get(0).getValueSql("_"))
+            .append(" FROM ")
+            .append(fromSql)
+            .append(")");
     }
 
     /**

query/src/org/labkey/query/reports/AttachmentReport.java

@@ -80,7 +80,7 @@ public String getType()
     @Override
     public boolean canEdit(User user, Container container, List<ValidationError> errors)
     {
-        // disallow a non site admin user from editing a server AttachmentReport
+        // disallow a non-site-admin user from editing a server AttachmentReport
         if (StringUtils.isNotEmpty(getFilePath()) && !container.hasPermission(user, AdminOperationsPermission.class))
         {
             errors.add(new SimpleValidationError("You must be an administrator in order to edit this report."));

search/src/org/labkey/search/view/SearchWebPartFactory.java

@@ -18,20 +18,13 @@
 import org.jetbrains.annotations.NotNull;
 import org.labkey.api.data.BooleanFormat;
 import org.labkey.api.view.AlwaysAvailableWebPartFactory;
-import org.labkey.api.view.HttpView;
 import org.labkey.api.view.JspView;
-import org.labkey.api.view.Portal;
+import org.labkey.api.view.Portal.WebPart;
 import org.labkey.api.view.ViewContext;
 import org.labkey.api.view.WebPartFactory;
-import org.labkey.api.view.WebPartView;
 
 import java.text.ParseException;
 
-/**
- * User: adam
- * Date: Jan 19, 2010
- * Time: 2:03:13 PM
- */
 public class SearchWebPartFactory extends AlwaysAvailableWebPartFactory
 {
     public SearchWebPartFactory()
@@ -41,7 +34,7 @@ public SearchWebPartFactory()
     }
 
     @Override
-    public WebPartView<?> getWebPartView(@NotNull ViewContext portalCtx, @NotNull Portal.WebPart webPart)
+    public SearchWebPart getWebPartView(@NotNull ViewContext portalCtx, @NotNull WebPart webPart)
     {
         boolean includeSubfolders = includeSubfolders(webPart);
 
@@ -57,13 +50,13 @@ public WebPartView<?> getWebPartView(@NotNull ViewContext portalCtx, @NotNull Po
 
 
     @Override
-    public HttpView<?> getEditView(Portal.WebPart webPart, ViewContext context)
+    public JspView<WebPart> getEditView(WebPart webPart, ViewContext context)
     {
         return new JspView<>("/org/labkey/search/view/customizeSearchWebPart.jsp", webPart);
     }
 
 
-    public static boolean includeSubfolders(Portal.WebPart part)
+    public static boolean includeSubfolders(WebPart part)
     {
         String value = part.getPropertyMap().get("includeSubfolders");
 
@@ -77,5 +70,3 @@ public static boolean includeSubfolders(Portal.WebPart part)
         }
     }
 }
-
-

study/src/org/labkey/study/query/DatasetQueryView.java

@@ -594,13 +594,11 @@ private MenuButton createQCStateButton()
         }
 
         boolean addSeparator = false;
+
         if (getContainer().hasPermission(getUser(), QCAnalystPermission.class))
         {
-            if (!addSeparator)
-            {
-                addSeparator = true;
-                button.addSeparator();
-            }
+            addSeparator = true;
+            button.addSeparator();
             ActionURL updateAction = new ActionURL(StudyController.UpdateQCStateAction.class, getContainer());
             updateAction.addReturnUrl(getViewContext().getActionURL());
             button.addMenuItem("Update state of selected rows", "if (verifySelected(" + DataRegion.getJavaScriptObjectReference(getDataRegionName()) + ".form, \"" +