diff --git a/api/src/org/labkey/api/exp/api/ExperimentService.java b/api/src/org/labkey/api/exp/api/ExperimentService.java
index d317517c57b..2ce76f42943 100644
--- a/api/src/org/labkey/api/exp/api/ExperimentService.java
+++ b/api/src/org/labkey/api/exp/api/ExperimentService.java
@@ -82,7 +82,6 @@
 import org.labkey.api.util.Pair;
 import org.labkey.api.util.StringUtilsLabKey;
 import org.labkey.api.view.HttpView;
-import org.labkey.api.view.NotFoundException;
 import org.labkey.api.view.ViewBackgroundInfo;
 import org.labkey.api.view.ViewContext;
 import org.labkey.vfs.FileLike;
@@ -1183,6 +1182,11 @@ List<? extends ExpProtocol> getExpProtocolsWithParameterValue(
 
     Map<String, Map<String, Object>> getDomainMetrics();
 
+    void clearAncestors(ExpRunItem runItem);
+    void clearDataAncestors(Collection<Long> dataRowIds);
+    void clearMaterialAncestors(Collection<Long> materialRowIds);
+    void repopulateAncestors();
+
     class XarExportOptions
     {
         String _lsidRelativizer = LSID_OPTION_FOLDER_RELATIVE;
diff --git a/experiment/src/org/labkey/experiment/api/ClosureQueryHelper.java b/experiment/src/org/labkey/experiment/api/ClosureQueryHelper.java
index f2daaf48d46..909ff74ed46 100644
--- a/experiment/src/org/labkey/experiment/api/ClosureQueryHelper.java
+++ b/experiment/src/org/labkey/experiment/api/ClosureQueryHelper.java
@@ -17,6 +17,7 @@
 import org.labkey.api.data.MutableColumnInfo;
 import org.labkey.api.data.SQLFragment;
 import org.labkey.api.data.SqlExecutor;
+import org.labkey.api.data.Table;
 import org.labkey.api.data.TableInfo;
 import org.labkey.api.data.TempTableTracker;
 import org.labkey.api.data.VirtualTable;
@@ -349,26 +350,26 @@ private static void incrementalRecomputeFromTempTable(SQLFragment familyTempTabl
         }
     }
 
-    public static void clearAncestorsForMaterial(long rowId)
+    public static void clearAncestorsForMaterials(Collection<Long> materialRowIds)
     {
         var tx = getScope().getCurrentTransaction();
         if (null != tx)
         {
-            tx.addCommitTask(() -> clearAncestorsForMaterial(rowId), DbScope.CommitTaskOption.POSTCOMMIT);
+            tx.addCommitTask(() -> clearAncestorsForMaterials(materialRowIds), DbScope.CommitTaskOption.POSTCOMMIT);
             return;
         }
-        recomputeMaterialAncestors(rowId);
+        recomputeMaterialAncestors(materialRowIds);
     }
 
-    public static void clearAncestorsForDataObject(long rowId)
+    public static void clearAncestorsForDataObjects(Collection<Long> dataRowIds)
     {
         var tx = getScope().getCurrentTransaction();
         if (null != tx)
         {
-            tx.addCommitTask(() -> clearAncestorsForDataObject(rowId), DbScope.CommitTaskOption.POSTCOMMIT);
+            tx.addCommitTask(() -> clearAncestorsForDataObjects(dataRowIds), DbScope.CommitTaskOption.POSTCOMMIT);
             return;
         }
-        recomputeDataObjectAncestors(rowId);
+        recomputeDataObjectAncestors(dataRowIds);
     }
 
     public static void populateMaterialAncestors(Logger logger)
@@ -425,14 +426,12 @@ public static void truncateAndRecreate()
 
     public static void truncateAndRecreate(Logger logger)
     {
-        try (DbScope.Transaction transaction = ExperimentService.get().getSchema().getScope().ensureTransaction())
+        try (DbScope.Transaction transaction = ExperimentService.get().ensureTransaction())
         {
-            TableInfo tInfo = ExperimentServiceImpl.get().getTinfoMaterialAncestors();
-            new SqlExecutor(tInfo.getSchema()).execute("TRUNCATE TABLE " + tInfo);
+            Table.truncate(ExperimentServiceImpl.get().getTinfoMaterialAncestors());
             ClosureQueryHelper.populateMaterialAncestors(logger);
 
-            tInfo = ExperimentServiceImpl.get().getTinfoDataAncestors();
-            new SqlExecutor(tInfo.getSchema()).execute("TRUNCATE TABLE " + tInfo);
+            Table.truncate(ExperimentServiceImpl.get().getTinfoDataAncestors());
             ClosureQueryHelper.populateDataAncestors(logger);
 
             transaction.commit();
@@ -485,11 +484,11 @@ public static void recomputeFromSeeds(SQLFragment selectSeedsSql, boolean isSamp
         }
     }
 
-    private static void recomputeMaterialAncestors(long rowId)
+    private static void recomputeMaterialAncestors(Collection<Long> rowIds)
     {
         SQLFragment selectSeedsSql = new SQLFragment()
                 .append("SELECT m.RowId, m.ObjectId, 'm' AS ObjectType FROM exp.material m\n")
-                .append("WHERE m.RowId = ").appendValue(rowId);
+                .append("WHERE m.RowId ").appendInClause(rowIds, getScope().getSqlDialect());
         recomputeFromSeeds(selectSeedsSql, true);
     }
 
@@ -525,18 +524,16 @@ private static void recomputeMaterialAncestorsForRuns(Collection<Long> runIds)
                 .append("SELECT m.RowId, m.ObjectId, 'm' AS ObjectType FROM exp.material m\n")
                 .append("INNER JOIN exp.MaterialInput mi ON m.rowId = mi.materialId\n")
                 .append("INNER JOIN exp.ProtocolApplication pa ON mi.TargetApplicationId = pa.RowId\n")
-                .append("WHERE pa.RunId ");
-        getScope().getSqlDialect().appendInClauseSql(selectSeedsSql, runIds);
-        selectSeedsSql
+                .append("WHERE pa.RunId ").appendInClause(runIds, getScope().getSqlDialect())
                 .append(" AND pa.CpasType = ").appendValue(ExperimentRunOutput);
         recomputeFromSeeds(selectSeedsSql, true);
     }
 
-    private static void recomputeDataObjectAncestors(long rowId)
+    private static void recomputeDataObjectAncestors(Collection<Long> rowIds)
     {
         SQLFragment selectSeedsSql = new SQLFragment()
                 .append("SELECT d.RowId, d.ObjectId, 'd' AS ObjectType FROM exp.data d\n")
-                .append("WHERE d.RowId = ").appendValue(rowId);
+                .append("WHERE d.RowId ").appendInClause(rowIds, getScope().getSqlDialect());
         recomputeFromSeeds(selectSeedsSql, false);
     }
 
@@ -572,9 +569,7 @@ private static void recomputeDataAncestorsForRuns(Collection<Long> runIds)
                 .append("SELECT d.RowId, d.ObjectId, 'd' AS ObjectType FROM exp.data d\n")
                 .append("INNER JOIN exp.DataInput di ON d.rowId = di.dataId\n")
                 .append("INNER JOIN exp.ProtocolApplication pa ON di.TargetApplicationId = pa.RowId\n")
-                .append("WHERE pa.RunId ");
-        getScope().getSqlDialect().appendInClauseSql(selectSeedsSql, runIds);
-        selectSeedsSql
+                .append("WHERE pa.RunId ").appendInClause(runIds, getScope().getSqlDialect())
                 .append(" AND pa.CpasType = ").appendValue(ExperimentRunOutput);
         recomputeFromSeeds(selectSeedsSql, false);
     }
diff --git a/experiment/src/org/labkey/experiment/api/ExperimentServiceImpl.java b/experiment/src/org/labkey/experiment/api/ExperimentServiceImpl.java
index e3bc1bbb24b..b9b8859e1e4 100644
--- a/experiment/src/org/labkey/experiment/api/ExperimentServiceImpl.java
+++ b/experiment/src/org/labkey/experiment/api/ExperimentServiceImpl.java
@@ -236,7 +236,6 @@
 import org.labkey.api.view.HttpView;
 import org.labkey.api.view.JspTemplate;
 import org.labkey.api.view.JspView;
-import org.labkey.api.view.NotFoundException;
 import org.labkey.api.view.UnauthorizedException;
 import org.labkey.api.view.ViewBackgroundInfo;
 import org.labkey.api.view.ViewContext;
@@ -244,7 +243,6 @@
 import org.labkey.experiment.FileLinkFileListener;
 import org.labkey.experiment.MissingFilesCheckInfo;
 import org.labkey.experiment.XarExportType;
-import org.labkey.experiment.XarExporter;
 import org.labkey.experiment.XarReader;
 import org.labkey.experiment.api.property.DomainPropertyManager;
 import org.labkey.experiment.controllers.exp.ExperimentController;
@@ -253,13 +251,11 @@
 import org.labkey.experiment.pipeline.ExperimentPipelineJob;
 import org.labkey.experiment.pipeline.MoveRunsPipelineJob;
 import org.labkey.experiment.xar.AutoFileLSIDReplacer;
-import org.labkey.experiment.xar.XarExportSelection;
 import org.labkey.vfs.FileLike;
 import org.springframework.dao.DataIntegrityViolationException;
 import org.springframework.dao.PessimisticLockingFailureException;
 
 import java.io.File;
-import java.io.FileOutputStream;
 import java.io.IOException;
 import java.io.UncheckedIOException;
 import java.net.MalformedURLException;
@@ -3615,9 +3611,24 @@ public void clearAncestors(ExpRunItem runItem)
     {
         boolean isSample = runItem instanceof ExpMaterial;
         if (isSample)
-            ClosureQueryHelper.clearAncestorsForMaterial(runItem.getRowId());
+            clearMaterialAncestors(List.of(runItem.getRowId()));
         else
-            ClosureQueryHelper.clearAncestorsForDataObject(runItem.getRowId());
+            clearDataAncestors(List.of(runItem.getRowId()));
+    }
+
+    public void repopulateAncestors()
+    {
+        ClosureQueryHelper.truncateAndRecreate();
+    }
+
+    public void clearDataAncestors(Collection<Long> dataRowIds)
+    {
+        ClosureQueryHelper.clearAncestorsForDataObjects(dataRowIds);
+    }
+
+    public void clearMaterialAncestors(Collection<Long> materialRowIds)
+    {
+        ClosureQueryHelper.clearAncestorsForMaterials(materialRowIds);
     }
 
     public List<ProtocolApplication> getProtocolApplicationsForRun(long runId)