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Address FileChannel.lock runtime exception, address aliquot rollup deadlock #6721

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Address FileChannel.lock runtime exception, address aliquot rollup deadlock #6721

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14 changes: 13 additions & 1 deletion api/src/org/labkey/api/util/FileUtil.java
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Original file line number Diff line number Diff line change
Expand Up @@ -61,6 +61,7 @@
import java.nio.CharBuffer;
import java.nio.channels.FileChannel;
import java.nio.channels.FileLock;
import java.nio.channels.OverlappingFileLockException;
import java.nio.channels.ReadableByteChannel;
import java.nio.file.FileSystems;
import java.nio.file.FileVisitResult;
Expand Down Expand Up @@ -1078,6 +1079,17 @@ public static void copyFile(File src, File dst) throws IOException
}
}

private static FileLock acquireLock(FileChannel out) throws IOException
{
try
{
return out.lock();
}
catch (OverlappingFileLockException e)
{
throw new IOException(e);
}
}

// FileUtil.copyFile() does not use transferTo() or sync()
public static void copyFile(ReadableByteChannel in, long expected, File dst) throws IOException
Expand All @@ -1092,7 +1104,7 @@ public static void copyFile(ReadableByteChannel in, long expected, File dst) thr

try (FileOutputStream os = new FileOutputStream(dst);
FileChannel out = os.getChannel();
FileLock lockOut = out.lock())
FileLock lockOut = acquireLock(out))
{
do
{
Expand Down
5 changes: 3 additions & 2 deletions experiment/src/org/labkey/experiment/api/SampleTypeServiceImpl.java
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Original file line number Diff line number Diff line change
Expand Up @@ -118,6 +118,7 @@
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;
Expand Down Expand Up @@ -1700,7 +1701,7 @@ 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())
Expand Down Expand Up @@ -1761,7 +1762,7 @@ 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())
Expand Down