fix merge and put back index fix

Author: XingY

experiment/src/client/test/integration/DataClassCrud.ispec.ts

@@ -233,7 +233,7 @@ describe('Import with update / merge', () => {
    it ("Issue 52922: Blank sample id in the file are getting ignored in update from file", async () => {
        const BLANK_KEY_UPDATE_ERROR_NO_EXPRESSION = 'Missing value for required property: Name';
        const BLANK_KEY_UPDATE_ERROR_WITH_EXPRESSION = 'Name value not provided on row ';
-       const BOGUS_KEY_UPDATE_ERROR = 'Data not found: ';
+       const BOGUS_KEY_UPDATE_ERROR = 'Data not found for ';
        const DUPLICATE_KEY_ERROR = 'duplicate key value';
 
        const dataType = "NoExpressionNameRequired52922";

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

@@ -136,6 +136,7 @@
 import java.util.Optional;
 import java.util.Set;
 import java.util.SortedSet;
+import java.util.TreeMap;
 import java.util.TreeSet;
 import java.util.function.Function;
 import java.util.function.Predicate;
@@ -1718,7 +1719,7 @@ private Map<Integer, Pair<Integer, String>> getSampleAliquotCounts(Collection<In
                 .append(")-1 AS CreatedAliquotCount FROM exp.material AS m WHERE m.rowid\s");
         dialect.appendInClauseSql(sql, sampleIds);
 
-        Map<Integer, Pair<Integer, String>> sampleAliquotCounts = new HashMap<>();
+        Map<Integer, Pair<Integer, String>> sampleAliquotCounts = new TreeMap<>(); // Order sample by rowId to reduce probability of deadlock with search indexer
         try (ResultSet rs = new SqlSelector(dbSchema, sql).getResultSet())
         {
             while (rs.next())
@@ -1779,7 +1780,7 @@ SELECT RootMaterialRowId as rootRowId, COUNT(*) as aliquotCount
         }
         dialect.appendInClauseSql(sql, sampleIds);
 
-        Map<Integer, Pair<Integer, String>> sampleAliquotCounts = new HashMap<>();
+        Map<Integer, Pair<Integer, String>> sampleAliquotCounts = new TreeMap<>(); // Order by rowId to reduce deadlock with search indexer
         try (ResultSet rs = new SqlSelector(dbSchema, sql).getResultSet())
         {
             while (rs.next())