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brokkoli71brokkoli71
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reformat src/test
1 parent 9d571f9 commit 467b478

12 files changed

Lines changed: 399 additions & 404 deletions

‎src/test/java/dev/zarr/zarrjava/TestUtils.java‎

Lines changed: 2 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -8,11 +8,10 @@
88

99
import static dev.zarr.zarrjava.utils.Utils.inversePermutation;
1010
import static dev.zarr.zarrjava.utils.Utils.isPermutation;
11-
import static org.junit.Assert.assertFalse;
1211

1312
public class TestUtils {
1413
@Test
15-
public void testIsPermutation(){
14+
public void testIsPermutation() {
1615
assert isPermutation(new int[]{2, 1, 0});
1716
assert isPermutation(new int[]{4, 2, 1, 3, 0});
1817
assert !isPermutation(new int[]{0, 1, 2, 0});
@@ -21,7 +20,7 @@ public void testIsPermutation(){
2120
}
2221

2322
@Test
24-
public void testInversePermutation(){
23+
public void testInversePermutation() {
2524
Assertions.assertArrayEquals(new int[]{1, 0, 2}, inversePermutation(new int[]{1, 0, 2}));
2625
Assertions.assertArrayEquals(new int[]{2, 0, 1}, inversePermutation(new int[]{1, 2, 0}));
2726
Assertions.assertArrayEquals(new int[]{0, 3, 2, 4, 1}, inversePermutation(new int[]{0, 4, 2, 1, 3}));

‎src/test/java/dev/zarr/zarrjava/ZarrPythonTests.java‎

Lines changed: 88 additions & 89 deletions
Original file line numberDiff line numberDiff line change
@@ -17,13 +17,14 @@
1717
import org.junit.jupiter.params.provider.CsvSource;
1818
import org.junit.jupiter.params.provider.MethodSource;
1919

20-
import java.io.*;
20+
import java.io.BufferedReader;
21+
import java.io.FileOutputStream;
22+
import java.io.IOException;
23+
import java.io.InputStreamReader;
2124
import java.nio.ByteBuffer;
2225
import java.nio.file.Path;
2326
import java.nio.file.Paths;
2427
import java.util.Arrays;
25-
import java.util.HashMap;
26-
import java.util.Map;
2728
import java.util.stream.Stream;
2829

2930

@@ -66,19 +67,13 @@ public static void setupUV() {
6667
}
6768
}
6869

69-
public void run_python_script(String scriptName, String... args) throws IOException, InterruptedException {
70-
int exitCode = runCommand(Stream.concat(Stream.of("uv", "run", PYTHON_TEST_PATH.resolve(scriptName)
71-
.toString()), Arrays.stream(args)).toArray(String[]::new));
72-
assert exitCode == 0;
73-
}
74-
75-
static ucar.ma2.Array testdata(dev.zarr.zarrjava.core.DataType dt){
70+
static ucar.ma2.Array testdata(dev.zarr.zarrjava.core.DataType dt) {
7671
ucar.ma2.DataType ma2Type = dt.getMA2DataType();
77-
ucar.ma2.Array array = ucar.ma2.Array.factory(ma2Type, new int[]{16, 16, 16});
72+
ucar.ma2.Array array = ucar.ma2.Array.factory(ma2Type, new int[]{16, 16, 16});
7873
for (int i = 0; i < array.getSize(); i++) {
7974
switch (ma2Type) {
8075
case BOOLEAN:
81-
array.setBoolean(i, i%2 == 0);
76+
array.setBoolean(i, i % 2 == 0);
8277
break;
8378
case BYTE:
8479
case UBYTE:
@@ -151,45 +146,79 @@ static void assertIsTestdata(ucar.ma2.Array result, dev.zarr.zarrjava.core.DataT
151146

152147
static Stream<Object[]> compressorAndDataTypeProviderV3() {
153148
Stream<Object[]> datatypeTests = Stream.of(
154-
DataType.BOOL,
155-
DataType.INT8,
156-
DataType.UINT8,
157-
DataType.INT16,
158-
DataType.UINT16,
159-
DataType.INT32,
160-
DataType.UINT32,
161-
DataType.INT64,
162-
DataType.UINT64,
163-
DataType.FLOAT32,
164-
DataType.FLOAT64
149+
DataType.BOOL,
150+
DataType.INT8,
151+
DataType.UINT8,
152+
DataType.INT16,
153+
DataType.UINT16,
154+
DataType.INT32,
155+
DataType.UINT32,
156+
DataType.INT64,
157+
DataType.UINT64,
158+
DataType.FLOAT32,
159+
DataType.FLOAT64
165160
).flatMap(dt -> Stream.of(
166-
new Object[]{"sharding", "end", dt},
167-
new Object[]{"blosc", "blosclz_shuffle_3", dt}
161+
new Object[]{"sharding", "end", dt},
162+
new Object[]{"blosc", "blosclz_shuffle_3", dt}
168163
));
169164

170165
Stream<Object[]> codecsTests = Stream.of(
171-
new Object[]{"blosc", "blosclz_noshuffle_0", DataType.INT32},
172-
new Object[]{"blosc", "lz4_shuffle_6", DataType.INT32},
173-
new Object[]{"blosc", "lz4hc_bitshuffle_3", DataType.INT32},
174-
new Object[]{"blosc", "zlib_shuffle_5", DataType.INT32},
175-
new Object[]{"blosc", "zstd_bitshuffle_9", DataType.INT32},
176-
new Object[]{"gzip", "0", DataType.INT32},
177-
new Object[]{"gzip", "5", DataType.INT32},
178-
new Object[]{"zstd", "0_true", DataType.INT32},
179-
new Object[]{"zstd", "5_true", DataType.INT32},
180-
new Object[]{"zstd", "0_false", DataType.INT32},
181-
new Object[]{"zstd", "5_false", DataType.INT32},
182-
new Object[]{"bytes", "BIG", DataType.INT32},
183-
new Object[]{"bytes", "LITTLE", DataType.INT32},
184-
new Object[]{"transpose", "_", DataType.INT32},
185-
new Object[]{"sharding", "start", DataType.INT32},
186-
new Object[]{"sharding_nested", "_", DataType.INT32},
187-
new Object[]{"crc32c", "_", DataType.INT32}
166+
new Object[]{"blosc", "blosclz_noshuffle_0", DataType.INT32},
167+
new Object[]{"blosc", "lz4_shuffle_6", DataType.INT32},
168+
new Object[]{"blosc", "lz4hc_bitshuffle_3", DataType.INT32},
169+
new Object[]{"blosc", "zlib_shuffle_5", DataType.INT32},
170+
new Object[]{"blosc", "zstd_bitshuffle_9", DataType.INT32},
171+
new Object[]{"gzip", "0", DataType.INT32},
172+
new Object[]{"gzip", "5", DataType.INT32},
173+
new Object[]{"zstd", "0_true", DataType.INT32},
174+
new Object[]{"zstd", "5_true", DataType.INT32},
175+
new Object[]{"zstd", "0_false", DataType.INT32},
176+
new Object[]{"zstd", "5_false", DataType.INT32},
177+
new Object[]{"bytes", "BIG", DataType.INT32},
178+
new Object[]{"bytes", "LITTLE", DataType.INT32},
179+
new Object[]{"transpose", "_", DataType.INT32},
180+
new Object[]{"sharding", "start", DataType.INT32},
181+
new Object[]{"sharding_nested", "_", DataType.INT32},
182+
new Object[]{"crc32c", "_", DataType.INT32}
188183
);
189184

190185
return Stream.concat(datatypeTests, codecsTests);
191186
}
192187

188+
static Stream<Object[]> compressorAndDataTypeProviderV2() {
189+
Stream<Object[]> datatypeTests = Stream.of(
190+
dev.zarr.zarrjava.v2.DataType.BOOL,
191+
dev.zarr.zarrjava.v2.DataType.INT8,
192+
dev.zarr.zarrjava.v2.DataType.UINT8,
193+
dev.zarr.zarrjava.v2.DataType.INT16,
194+
dev.zarr.zarrjava.v2.DataType.UINT16,
195+
dev.zarr.zarrjava.v2.DataType.INT32,
196+
dev.zarr.zarrjava.v2.DataType.UINT32,
197+
dev.zarr.zarrjava.v2.DataType.INT64,
198+
dev.zarr.zarrjava.v2.DataType.UINT64,
199+
dev.zarr.zarrjava.v2.DataType.FLOAT32,
200+
dev.zarr.zarrjava.v2.DataType.FLOAT64
201+
).flatMap(dt -> Stream.of(
202+
new Object[]{"zlib", "0", dt},
203+
new Object[]{"blosc", "blosclz_shuffle_3", dt}
204+
));
205+
206+
Stream<Object[]> bloscTests = Stream.of(
207+
new Object[]{"blosc", "blosclz_noshuffle_0", dev.zarr.zarrjava.v2.DataType.INT32},
208+
new Object[]{"blosc", "lz4_shuffle_6", dev.zarr.zarrjava.v2.DataType.INT32},
209+
new Object[]{"blosc", "lz4hc_bitshuffle_3", dev.zarr.zarrjava.v2.DataType.INT32},
210+
new Object[]{"blosc", "zlib_shuffle_5", dev.zarr.zarrjava.v2.DataType.INT32},
211+
new Object[]{"blosc", "zstd_bitshuffle_9", dev.zarr.zarrjava.v2.DataType.INT32}
212+
);
213+
214+
return Stream.concat(datatypeTests, bloscTests);
215+
}
216+
217+
public void run_python_script(String scriptName, String... args) throws IOException, InterruptedException {
218+
int exitCode = runCommand(Stream.concat(Stream.of("uv", "run", PYTHON_TEST_PATH.resolve(scriptName)
219+
.toString()), Arrays.stream(args)).toArray(String[]::new));
220+
assert exitCode == 0;
221+
}
193222

194223
@ParameterizedTest
195224
@MethodSource("compressorAndDataTypeProviderV3")
@@ -215,11 +244,11 @@ public void testWriteV3(String codec, String codecParam, DataType dataType) thro
215244
StoreHandle storeHandle = new FilesystemStore(TESTOUTPUT).resolve("testWriteV3", codec, codecParam, dataType.name());
216245

217246
ArrayMetadataBuilder builder = Array.metadataBuilder()
218-
.withShape(16, 16, 16)
219-
.withDataType(dataType)
220-
.withChunkShape(2, 4, 8)
221-
.withFillValue(0)
222-
.withAttributes(attributes);
247+
.withShape(16, 16, 16)
248+
.withDataType(dataType)
249+
.withChunkShape(2, 4, 8)
250+
.withFillValue(0)
251+
.withAttributes(attributes);
223252

224253
switch (codec) {
225254
case "blosc":
@@ -273,36 +302,6 @@ public void testWriteV3(String codec, String codecParam, DataType dataType) thro
273302
run_python_script("zarr_python_read.py", codec, codecParam, dataType.name().toLowerCase(), storeHandle.toPath().toString());
274303
}
275304

276-
277-
static Stream<Object[]> compressorAndDataTypeProviderV2() {
278-
Stream<Object[]> datatypeTests = Stream.of(
279-
dev.zarr.zarrjava.v2.DataType.BOOL,
280-
dev.zarr.zarrjava.v2.DataType.INT8,
281-
dev.zarr.zarrjava.v2.DataType.UINT8,
282-
dev.zarr.zarrjava.v2.DataType.INT16,
283-
dev.zarr.zarrjava.v2.DataType.UINT16,
284-
dev.zarr.zarrjava.v2.DataType.INT32,
285-
dev.zarr.zarrjava.v2.DataType.UINT32,
286-
dev.zarr.zarrjava.v2.DataType.INT64,
287-
dev.zarr.zarrjava.v2.DataType.UINT64,
288-
dev.zarr.zarrjava.v2.DataType.FLOAT32,
289-
dev.zarr.zarrjava.v2.DataType.FLOAT64
290-
).flatMap(dt -> Stream.of(
291-
new Object[]{"zlib", "0", dt},
292-
new Object[]{"blosc", "blosclz_shuffle_3", dt}
293-
));
294-
295-
Stream <Object[]> bloscTests = Stream.of(
296-
new Object[]{"blosc", "blosclz_noshuffle_0", dev.zarr.zarrjava.v2.DataType.INT32},
297-
new Object[]{"blosc", "lz4_shuffle_6", dev.zarr.zarrjava.v2.DataType.INT32},
298-
new Object[]{"blosc", "lz4hc_bitshuffle_3", dev.zarr.zarrjava.v2.DataType.INT32},
299-
new Object[]{"blosc", "zlib_shuffle_5", dev.zarr.zarrjava.v2.DataType.INT32},
300-
new Object[]{"blosc", "zstd_bitshuffle_9", dev.zarr.zarrjava.v2.DataType.INT32}
301-
);
302-
303-
return Stream.concat(datatypeTests, bloscTests);
304-
}
305-
306305
@ParameterizedTest
307306
@MethodSource("compressorAndDataTypeProviderV2")
308307
public void testReadV2(String compressor, String compressorParam, dev.zarr.zarrjava.v2.DataType dt) throws IOException, ZarrException, InterruptedException {
@@ -329,11 +328,11 @@ public void testWriteV2(String compressor, String compressorParam, dev.zarr.zarr
329328
StoreHandle storeHandle = new FilesystemStore(TESTOUTPUT).resolve("testCodecsWriteV2", compressor, compressorParam, dt.name());
330329

331330
dev.zarr.zarrjava.v2.ArrayMetadataBuilder builder = dev.zarr.zarrjava.v2.Array.metadataBuilder()
332-
.withShape(16, 16, 16)
333-
.withDataType(dt)
334-
.withChunks(2, 4, 8)
335-
.withAttributes(attributes)
336-
.withFillValue(0);
331+
.withShape(16, 16, 16)
332+
.withDataType(dt)
333+
.withChunks(2, 4, 8)
334+
.withAttributes(attributes)
335+
.withFillValue(0);
337336

338337
switch (compressor) {
339338
case "blosc":
@@ -391,11 +390,11 @@ public void testZstdLibrary(int clevel, boolean checksumFlag) throws IOException
391390

392391
//decompress in python
393392
int exitCode = ZarrPythonTests.runCommand(
394-
"uv",
395-
"run",
396-
PYTHON_TEST_PATH.resolve("zstd_decompress.py").toString(),
397-
compressedDataPath,
398-
Integer.toString(number)
393+
"uv",
394+
"run",
395+
PYTHON_TEST_PATH.resolve("zstd_decompress.py").toString(),
396+
compressedDataPath,
397+
Integer.toString(number)
399398
);
400399
assert exitCode == 0;
401400
}
@@ -410,7 +409,7 @@ public void testGroupReadWriteV2() throws Exception {
410409
.withShape(16, 16, 16)
411410
.withDataType(dataType)
412411
.withChunks(2, 4, 8)
413-
);
412+
);
414413

415414
array.write(testdata(dataType));
416415

@@ -437,7 +436,7 @@ public void testGroupReadWriteV3() throws Exception {
437436
.withShape(16, 16, 16)
438437
.withDataType(dataType)
439438
.withChunkShape(2, 4, 8)
440-
);
439+
);
441440

442441
array.write(testdata(dataType));
443442

‎src/test/java/dev/zarr/zarrjava/ZarrStoreTest.java‎

Lines changed: 20 additions & 17 deletions
Original file line numberDiff line numberDiff line change
@@ -2,9 +2,11 @@
22

33
import com.fasterxml.jackson.databind.ObjectMapper;
44
import dev.zarr.zarrjava.core.Attributes;
5-
import dev.zarr.zarrjava.store.*;
5+
import dev.zarr.zarrjava.store.FilesystemStore;
6+
import dev.zarr.zarrjava.store.HttpStore;
7+
import dev.zarr.zarrjava.store.MemoryStore;
8+
import dev.zarr.zarrjava.store.S3Store;
69
import dev.zarr.zarrjava.v3.*;
7-
import java.net.URI;
810
import org.junit.jupiter.api.Assertions;
911
import org.junit.jupiter.api.Test;
1012
import org.junit.jupiter.params.ParameterizedTest;
@@ -15,6 +17,7 @@
1517
import software.amazon.awssdk.services.s3.S3Configuration;
1618

1719
import java.io.IOException;
20+
import java.net.URI;
1821
import java.nio.file.Files;
1922
import java.util.Arrays;
2023
import java.util.stream.Stream;
@@ -28,17 +31,17 @@ public void testFileSystemStores() throws IOException, ZarrException {
2831
ObjectMapper objectMapper = makeObjectMapper();
2932

3033
GroupMetadata groupMetadata = objectMapper.readValue(
31-
Files.readAllBytes(TESTDATA.resolve("l4_sample").resolve("zarr.json")),
32-
GroupMetadata.class
34+
Files.readAllBytes(TESTDATA.resolve("l4_sample").resolve("zarr.json")),
35+
GroupMetadata.class
3336
);
3437

3538
String groupMetadataString = objectMapper.writeValueAsString(groupMetadata);
3639
Assertions.assertTrue(groupMetadataString.contains("\"zarr_format\":3"));
3740
Assertions.assertTrue(groupMetadataString.contains("\"node_type\":\"group\""));
3841

3942
ArrayMetadata arrayMetadata = objectMapper.readValue(Files.readAllBytes(TESTDATA.resolve(
40-
"l4_sample").resolve("color").resolve("1").resolve("zarr.json")),
41-
ArrayMetadata.class);
43+
"l4_sample").resolve("color").resolve("1").resolve("zarr.json")),
44+
ArrayMetadata.class);
4245

4346
String arrayMetadataString = objectMapper.writeValueAsString(arrayMetadata);
4447
Assertions.assertTrue(arrayMetadataString.contains("\"zarr_format\":3"));
@@ -63,23 +66,23 @@ public void testFileSystemStores() throws IOException, ZarrException {
6366
@Test
6467
public void testS3Store() throws IOException, ZarrException {
6568
S3Store s3Store = new S3Store(S3Client.builder()
66-
.endpointOverride(URI.create("https://uk1s3.embassy.ebi.ac.uk"))
67-
.region(Region.US_EAST_1) // required, but ignored
68-
.serviceConfiguration(
69-
S3Configuration.builder()
70-
.pathStyleAccessEnabled(true) // required
71-
.build()
72-
)
73-
.credentialsProvider(AnonymousCredentialsProvider.create())
74-
.build(), "idr", "zarr/v0.5/idr0033A");
69+
.endpointOverride(URI.create("https://uk1s3.embassy.ebi.ac.uk"))
70+
.region(Region.US_EAST_1) // required, but ignored
71+
.serviceConfiguration(
72+
S3Configuration.builder()
73+
.pathStyleAccessEnabled(true) // required
74+
.build()
75+
)
76+
.credentialsProvider(AnonymousCredentialsProvider.create())
77+
.build(), "idr", "zarr/v0.5/idr0033A");
7578

7679
Array arrayV3 = Array.open(s3Store.resolve("BR00109990_C2.zarr", "0", "0"));
7780
Assertions.assertArrayEquals(new long[]{5, 1552, 2080}, arrayV3.metadata().shape);
78-
Assertions.assertEquals(574, arrayV3.read(new long[]{0,0,0}, new int[]{1,1,1}).getInt(0));
81+
Assertions.assertEquals(574, arrayV3.read(new long[]{0, 0, 0}, new int[]{1, 1, 1}).getInt(0));
7982

8083
dev.zarr.zarrjava.core.Array arrayCore = dev.zarr.zarrjava.core.Array.open(s3Store.resolve("BR00109990_C2.zarr", "0", "0"));
8184
Assertions.assertArrayEquals(new long[]{5, 1552, 2080}, arrayCore.metadata().shape);
82-
Assertions.assertEquals(574, arrayCore.read(new long[]{0,0,0}, new int[]{1,1,1}).getInt(0));
85+
Assertions.assertEquals(574, arrayCore.read(new long[]{0, 0, 0}, new int[]{1, 1, 1}).getInt(0));
8386
}
8487

8588
@Test

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