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Fix BloscCompression class poisoning when Blosc is unavailable #6

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Merged
ksugar merged 1 commit into from
Jun 23, 2026
Merged

Fix BloscCompression class poisoning when Blosc is unavailable #6

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29 changes: 21 additions & 8 deletions src/main/java/org/mastodon/geff/GeffUtils.java
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Original file line number Diff line number Diff line change
Expand Up @@ -35,7 +35,20 @@ public class GeffUtils
{
private static final Logger LOG = LoggerFactory.getLogger( GeffUtils.class );

private static final Compression DEFAULT_COMPRESSION = createDefaultCompression();
// Lazy-initialization holder: BloscCompression is only instantiated the first
// time a write method is called, NOT when GeffUtils class is loaded (e.g. by
// computeFirstDimChunk). This avoids permanently poisoning the BloscCompression
// class before N5ZarrWriter has had a chance to handle the UnsatisfiedLinkError
// itself, which would cause N5ZarrWriter to crash with NoClassDefFoundError.
private static final class DefaultCompressionHolder
{
static final Compression INSTANCE = createDefaultCompression();
}

private static Compression defaultCompression()
{
return DefaultCompressionHolder.INSTANCE;
}

private static Compression createDefaultCompression()
{
Expand Down Expand Up @@ -157,7 +170,7 @@ public static < T > void writeIntArray(
new long[] { size },
new int[] { chunkSize },
DataType.INT32,
DEFAULT_COMPRESSION );
defaultCompression() );
writer.createDataset( dataset, attributes );
write( data, writer, dataset, attributes );
}
Expand Down Expand Up @@ -199,7 +212,7 @@ public static void writeIntMatrix(
new long[] { numColumns, numRows },
new int[] { numColumns, chunkSize },
DataType.INT32,
DEFAULT_COMPRESSION );
defaultCompression() );
writer.createDataset( dataset, attributes );
write( data, writer, dataset, attributes );
}
Expand All @@ -218,7 +231,7 @@ public static < T > void writeDoubleArray(
new long[] { size },
new int[] { chunkSize },
DataType.FLOAT64,
DEFAULT_COMPRESSION );
defaultCompression() );
writer.createDataset( dataset, attributes );
write( data, writer, dataset, attributes );
}
Expand All @@ -244,7 +257,7 @@ public static < T > void writeDoubleMatrix(
new long[] { numColumns, size },
new int[] { numColumns, chunkSize },
DataType.FLOAT64,
DEFAULT_COMPRESSION );
defaultCompression() );
writer.createDataset( dataset, attributes );
write( data, writer, dataset, attributes );
}
Expand Down Expand Up @@ -1013,7 +1026,7 @@ private static void writeDataArray(
new long[] { numElements },
new int[] { Math.min( chunkSize, ( int ) numElements ) },
dataType,
DEFAULT_COMPRESSION );
defaultCompression() );
writer.createDataset( dataset, attributes );
write( data, writer, dataset, attributes );
}
Expand Down Expand Up @@ -1044,7 +1057,7 @@ private static void writeOffsetsArray(
new long[] { numColumns, numNodes },
new int[] { numColumns, Math.min( chunkSize, numNodes ) },
DataType.UINT64,
DEFAULT_COMPRESSION );
defaultCompression() );
writer.createDataset( dataset, attributes );
write( flatOffsets, writer, dataset, attributes );
}
Expand All @@ -1064,7 +1077,7 @@ private static void writeMissingArray(
new long[] { missing.length },
new int[] { Math.min( chunkSize, missing.length ) },
DataType.UINT8,
DEFAULT_COMPRESSION );
defaultCompression() );
writer.createDataset( dataset, attributes );

final byte[] boolAsBytes = new byte[ missing.length ];
Expand Down
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