diff --git a/LDK/api-src/org/labkey/api/ldk/table/ContainerScopedTable.java b/LDK/api-src/org/labkey/api/ldk/table/ContainerScopedTable.java
index 975f117e..9a946cfe 100644
--- a/LDK/api-src/org/labkey/api/ldk/table/ContainerScopedTable.java
+++ b/LDK/api-src/org/labkey/api/ldk/table/ContainerScopedTable.java
@@ -122,7 +122,7 @@ public DataIteratorBuilder persistRows(DataIteratorBuilder data, DataIteratorCon
 
     protected class UpdateService extends SimpleQueryUpdateService
     {
-        private KeyManager _keyManager = new KeyManager();
+        private final KeyManager _keyManager = new KeyManager();
 
         public UpdateService(SimpleUserSchema.SimpleTable<?> ti)
         {
@@ -307,7 +307,7 @@ public Object call()
 
     private class KeyManager
     {
-        private Set<Object> _encounteredKeys = new HashSet<>();
+        private final Set<Object> _encounteredKeys = new HashSet<>();
 
         public KeyManager()
         {
@@ -337,7 +337,7 @@ public boolean rowExists(Container c, Object key)
 
             Container target = c.getContainerFor(ContainerType.DataType.sharedSchemaOwner);
             SimpleFilter filter = new SimpleFilter(FieldKey.fromString(_pseudoPk), key, CompareType.EQUAL);
-            filter.addClause(ContainerFilter.current(target).createFilterClause(_rootTable.getSchema(), getContainerFieldKey()));
+            filter.addClause(ContainerFilter.current(target, getUserSchema().getUser()).createFilterClause(_rootTable.getSchema(), getContainerFieldKey()));
             TableSelector ts = new TableSelector(_rootTable, Collections.singleton(_pseudoPk), filter, null);
 
             return ts.getRowCount() > 0;
diff --git a/LDK/src/org/labkey/ldk/notification/SiteSummaryNotification.java b/LDK/src/org/labkey/ldk/notification/SiteSummaryNotification.java
index 64bc49e5..3bddf0b4 100644
--- a/LDK/src/org/labkey/ldk/notification/SiteSummaryNotification.java
+++ b/LDK/src/org/labkey/ldk/notification/SiteSummaryNotification.java
@@ -677,11 +677,11 @@ private void getAssayRunSummary(Container c, User u, final StringBuilder msg, fi
             if (protocolMap == null)
                 protocolMap = new TreeMap<>();
 
-            ExpRunTable tiRun = AssayService.get().createRunTable(p, ap, u, p.getContainer(), ContainerFilter.EVERYTHING);
+            ExpRunTable tiRun = AssayService.get().createRunTable(p, ap, u, p.getContainer(), ContainerFilter.EVERYTHING_UNSAFE);
             TableSelector tsRun = new TableSelector(tiRun);
 
             AssayProtocolSchema schema = ap.createProtocolSchema(u, p.getContainer(), p, null);
-            TableInfo tiResult = schema.createDataTable(ContainerFilter.EVERYTHING);
+            TableInfo tiResult = schema.createDataTable(ContainerFilter.EVERYTHING_UNSAFE);
             TableSelector tsResult = new TableSelector(tiResult);
 
             protocolMap.put(p, new Long[]{tsRun.getRowCount(), tsResult.getRowCount()});
diff --git a/laboratory/api-src/org/labkey/api/laboratory/QueryCountNavItem.java b/laboratory/api-src/org/labkey/api/laboratory/QueryCountNavItem.java
index 1662c4a2..8c802af7 100644
--- a/laboratory/api-src/org/labkey/api/laboratory/QueryCountNavItem.java
+++ b/laboratory/api-src/org/labkey/api/laboratory/QueryCountNavItem.java
@@ -47,17 +47,17 @@ public Long getRowCount(Container c, User u)
         if (ti == null)
             return Long.valueOf(0);
 
-        SimpleFilter filter = getFilter(c, ti);
+        SimpleFilter filter = getFilter(c, u, ti);
         TableSelector ts = new TableSelector(ti, ti.getPkColumns(), filter, null);
         return ts.getRowCount();
     }
 
-    protected SimpleFilter getFilter(Container c, TableInfo ti)
+    protected SimpleFilter getFilter(Container c, User u, TableInfo ti)
     {
         SimpleFilter filter = new SimpleFilter();
 
-        if (ti.getColumn("container") != null && !(ti.supportsContainerFilter() && ContainerFilter.current(c).equals(ti.getContainerFilter())))
-            filter.addClause(ContainerFilter.current(c).createFilterClause(ti.getSchema(), FieldKey.fromString("container")));
+        if (ti.getColumn("container") != null && !(ti.supportsContainerFilter() && ContainerFilter.current(c, u).equals(ti.getContainerFilter())))
+            filter.addClause(ContainerFilter.current(c, u).createFilterClause(ti.getSchema(), FieldKey.fromString("container")));
 
         if (_filter != null)
         {
diff --git a/laboratory/src/org/labkey/laboratory/SamplesCountNavItem.java b/laboratory/src/org/labkey/laboratory/SamplesCountNavItem.java
index c22e4c08..88953025 100644
--- a/laboratory/src/org/labkey/laboratory/SamplesCountNavItem.java
+++ b/laboratory/src/org/labkey/laboratory/SamplesCountNavItem.java
@@ -8,6 +8,7 @@
 import org.labkey.api.laboratory.LaboratoryService;
 import org.labkey.api.laboratory.QueryCountNavItem;
 import org.labkey.api.query.FieldKey;
+import org.labkey.api.security.User;
 
 /**
  * User: bimber
@@ -22,9 +23,9 @@ public SamplesCountNavItem(DataProvider provider, String schema, String query, L
     }
 
     @Override
-    protected SimpleFilter getFilter(Container c, TableInfo ti)
+    protected SimpleFilter getFilter(Container c, User u, TableInfo ti)
     {
-        SimpleFilter filter = super.getFilter(c, ti);
+        SimpleFilter filter = super.getFilter(c, u, ti);
         filter.addCondition(FieldKey.fromString("dateremoved"), null, CompareType.ISBLANK);
         return filter;
     }
diff --git a/laboratory/src/org/labkey/laboratory/query/LaboratoryTableCustomizer.java b/laboratory/src/org/labkey/laboratory/query/LaboratoryTableCustomizer.java
index af8a869d..d37f31e2 100644
--- a/laboratory/src/org/labkey/laboratory/query/LaboratoryTableCustomizer.java
+++ b/laboratory/src/org/labkey/laboratory/query/LaboratoryTableCustomizer.java
@@ -982,7 +982,7 @@ public void customizeButtonBar(AbstractTableInfo ti)
                 newIncludes.addAll(Arrays.asList(includes));
             }
 
-            ti.getButtonBarConfig().setScriptIncludes(newIncludes.toArray(new String[newIncludes.size()]));
+            ti.getButtonBarConfig().setScriptIncludes(newIncludes.toArray(new String[0]));
         }
     }
 
@@ -993,7 +993,7 @@ private void customzieSamplesTable(AbstractTableInfo ti)
         {
             Container c = ti.getUserSchema().getContainer();
             c = c.isWorkbook() ? c.getParent() : c;
-            SQLFragment containerSql = ContainerFilter.current(c).getSQLFragment(LaboratorySchema.getInstance().getSchema(), new SQLFragment(ti.getContainerFieldKey().toString()));
+            SQLFragment containerSql = ContainerFilter.current(c, ti.getUserSchema().getUser()).getSQLFragment(LaboratorySchema.getInstance().getSchema(), new SQLFragment(ti.getContainerFieldKey().toString()));
 
             SQLFragment sql = new SQLFragment("(SELECT count(*) as _expr FROM laboratory.samples s WHERE " +
                     " (s.").append(containerSql).append(")" + " AND ").