Skip to content

Test of detection of invalid codec order and invalid TransposeCodec #7

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
merged 1 commit into from
Aug 15, 2024
Merged
Changes from all commits
Commits
File filter

Filter by extension

Filter by extension

Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
81 changes: 60 additions & 21 deletions src/test/java/dev/zarr/zarrjava/ZarrTest.java
Original file line number Diff line number Diff line change
Expand Up @@ -13,6 +13,7 @@
import dev.zarr.zarrjava.utils.MultiArrayUtils;
import dev.zarr.zarrjava.v3.*;
import dev.zarr.zarrjava.v3.codec.CodecBuilder;
import dev.zarr.zarrjava.v3.codec.core.BytesCodec;
import dev.zarr.zarrjava.v3.codec.core.TransposeCodec;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.BeforeAll;
Expand All @@ -32,6 +33,7 @@
import java.util.Comparator;
import java.util.HashMap;
import java.util.Map;
import java.util.function.Function;
import java.util.stream.Stream;

import static org.junit.Assert.assertThrows;
Expand Down Expand Up @@ -231,17 +233,39 @@ public void testWriteReadWithZarrita(String codec, String codecParam) throws Exc
assert exitCode == 0;
}

static Stream<int[]> invalidchunkSizes() {
static Stream<Function<CodecBuilder, CodecBuilder>> invalidCodecBuilder(){
return Stream.of(
new int[] {1} ,
new int[] {1, 1, 1},
c -> c.withBytes(BytesCodec.Endian.LITTLE).withBytes(BytesCodec.Endian.LITTLE),
c -> c.withBlosc().withBytes(BytesCodec.Endian.LITTLE),
c -> c.withBytes(BytesCodec.Endian.LITTLE).withTranspose(new int[]{1,0}),
c -> c.withTranspose(new int[]{1,0}).withBytes(BytesCodec.Endian.LITTLE).withTranspose(new int[]{1,0})
);
}

@ParameterizedTest
@MethodSource("invalidCodecBuilder")
public void testCheckInvalidCodecConfiguration(Function<CodecBuilder, CodecBuilder> codecBuilder) throws Exception {
StoreHandle storeHandle = new FilesystemStore(TESTOUTPUT).resolve("invalid_codec_config", String.valueOf(codecBuilder.hashCode()));
ArrayMetadataBuilder builder = Array.metadataBuilder()
.withShape(new long[] {4, 4})
.withDataType(DataType.UINT32)
.withChunkShape(new int[]{2,2})
.withCodecs(codecBuilder);

assertThrows(ZarrException.class, () -> Array.create(storeHandle, builder.build()));
}

static Stream<int[]> invalidChunkSizes() {
return Stream.of(
new int[]{1},
new int[]{1, 1, 1},
new int[] {5, 1},
new int[] {1, 5}
);
}

@ParameterizedTest
@MethodSource("invalidchunkSizes")
@MethodSource("invalidChunkSizes")
public void testCheckInvalidChunkBounds(int[] chunkSize) throws Exception {
long[] shape = new long[] {4, 4};

Expand Down Expand Up @@ -310,31 +334,46 @@ public void testZstdCodecReadWrite(int clevel, boolean checksum) throws ZarrExce
@Test
public void testTransposeCodec() throws ZarrException {
ucar.ma2.Array testData = ucar.ma2.Array.factory(ucar.ma2.DataType.UINT, new int[]{2, 3, 3}, new int[]{
0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17});
0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17});
ucar.ma2.Array testDataTransposed120 = ucar.ma2.Array.factory(ucar.ma2.DataType.UINT, new int[]{3, 3, 2}, new int[]{
0, 9, 1, 10, 2, 11, 3, 12, 4, 13, 5, 14, 6, 15, 7, 16, 8, 17});
0, 9, 1, 10, 2, 11, 3, 12, 4, 13, 5, 14, 6, 15, 7, 16, 8, 17});

ArrayMetadata.CoreArrayMetadata metadata = new ArrayMetadata.CoreArrayMetadata(
new long[]{2, 3, 3},
new int[]{2, 3, 3},
DataType.UINT32,
null);
TransposeCodec transposeCodec = new TransposeCodec(new TransposeCodec.Configuration(new int[]{1, 2, 0}));
TransposeCodec transposeCodecWrongOrder1 = new TransposeCodec(new TransposeCodec.Configuration(new int[]{1, 2, 2}));
TransposeCodec transposeCodecWrongOrder2 = new TransposeCodec(new TransposeCodec.Configuration(new int[]{1, 2, 3}));
TransposeCodec transposeCodecWrongOrder3 = new TransposeCodec(new TransposeCodec.Configuration(new int[]{1, 2, 3, 0}));
transposeCodec.setCoreArrayMetadata(metadata);
transposeCodecWrongOrder1.setCoreArrayMetadata(metadata);
transposeCodecWrongOrder2.setCoreArrayMetadata(metadata);
transposeCodecWrongOrder3.setCoreArrayMetadata(metadata);
transposeCodec.setCoreArrayMetadata(new ArrayMetadata.CoreArrayMetadata(
new long[]{2, 3, 3},
new int[]{2, 3, 3},
DataType.UINT32,
null));

assert MAMath.equals(testDataTransposed120, transposeCodec.encode(testData));
assert MAMath.equals(testData, transposeCodec.decode(testDataTransposed120));
assertThrows(ZarrException.class, () -> transposeCodecWrongOrder1.encode(testData));
assertThrows(ZarrException.class, () -> transposeCodecWrongOrder2.encode(testData));
assertThrows(ZarrException.class, () -> transposeCodecWrongOrder3.encode(testData));
}

static Stream<int[]> invalidTransposeOrder() {
return Stream.of(
new int[]{1, 0, 0},
new int[]{1, 2, 3},
new int[]{1,2,3,0},
new int[]{1,2}
);
}

@ParameterizedTest
@MethodSource("invalidChunkSizes")
public void testCheckInvalidTransposeOrder(int[] transposeOrder) throws Exception {
int[] shapeInt = new int[]{2, 3, 3};
long[] shapeLong = new long[]{2, 3, 3};

TransposeCodec transposeCodec = new TransposeCodec(new TransposeCodec.Configuration(transposeOrder));
transposeCodec.setCoreArrayMetadata(new ArrayMetadata.CoreArrayMetadata(
shapeLong,
shapeInt,
DataType.UINT32,
null));

ucar.ma2.Array testData = ucar.ma2.Array.factory(ucar.ma2.DataType.UINT, shapeInt);
assertThrows(ZarrException.class, () -> transposeCodec.encode(testData));
}
@Test
public void testFileSystemStores() throws IOException, ZarrException {
FilesystemStore fsStore = new FilesystemStore(TESTDATA);
Expand Down
Loading