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add API tests for open, create and refactor tests structure
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‎src/test/java/dev/zarr/zarrjava/ZarrApiTest.java‎

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package dev.zarr.zarrjava;
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import dev.zarr.zarrjava.core.Node;
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import dev.zarr.zarrjava.store.FilesystemStore;
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import dev.zarr.zarrjava.store.StoreHandle;
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import dev.zarr.zarrjava.v2.ArrayMetadata;
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import dev.zarr.zarrjava.v3.Array;
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import dev.zarr.zarrjava.v3.Group;
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import org.junit.jupiter.api.Assertions;
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import org.junit.jupiter.api.Test;
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import java.io.IOException;
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import java.nio.file.Files;
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import java.nio.file.NoSuchFileException;
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import java.nio.file.Path;
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import java.nio.file.Paths;
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public class ZarrApiTest extends ZarrTest {
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@Test
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public void testGenericOpenV3() throws ZarrException, IOException {
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StoreHandle arrayHandle = new FilesystemStore(TESTDATA).resolve("l4_sample", "color", "1");
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StoreHandle groupHandle = new FilesystemStore(TESTDATA).resolve("l4_sample");
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StoreHandle v2Handle = new FilesystemStore(TESTDATA).resolve("v2_sample");
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Array array = (Array) Node.open(arrayHandle);
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Assertions.assertEquals(4, (array).metadata.shape.length);
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array = (Array) dev.zarr.zarrjava.core.Array.open(arrayHandle);
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Assertions.assertEquals(4, (array).metadata.shape.length);
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array = (Array) dev.zarr.zarrjava.v3.Node.open(arrayHandle);
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Assertions.assertEquals(4, (array).metadata.shape.length);
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Group group = (Group) Node.open(groupHandle);
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Assertions.assertInstanceOf(Group.class, group.get("color"));
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group = (Group) dev.zarr.zarrjava.core.Group.open(groupHandle);
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Assertions.assertInstanceOf(Group.class, group.get("color"));
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group = (Group) dev.zarr.zarrjava.v3.Node.open(groupHandle);
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Assertions.assertInstanceOf(Group.class, group.get("color"));
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Assertions.assertThrows(NoSuchFileException.class, () -> Node.open(new FilesystemStore(TESTDATA).resolve("non_existing")));
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Assertions.assertThrows(NoSuchFileException.class, () -> dev.zarr.zarrjava.v3.Node.open(v2Handle));
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Assertions.assertThrows(NoSuchFileException.class, () -> dev.zarr.zarrjava.v3.Group.open(v2Handle));
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Assertions.assertThrows(NoSuchFileException.class, () -> dev.zarr.zarrjava.v3.Array.open(v2Handle));
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}
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@Test
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public void testGenericOpenOverloadsV3() throws ZarrException, IOException {
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Path arrayPath = TESTDATA.resolve("l4_sample/color/1");
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Path groupPath = TESTDATA.resolve("l4_sample");
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Path v2GroupPath = TESTDATA.resolve("v2_sample");
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Array array = (Array) Node.open(arrayPath);
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Assertions.assertEquals(4, (array).metadata.shape.length);
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array = (Array) Node.open(arrayPath.toString());
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Assertions.assertEquals(4, (array).metadata.shape.length);
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array = (Array) dev.zarr.zarrjava.core.Array.open(arrayPath);
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Assertions.assertEquals(4, (array).metadata.shape.length);
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array = (Array) dev.zarr.zarrjava.core.Array.open(arrayPath.toString());
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Assertions.assertEquals(4, (array).metadata.shape.length);
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array = (Array) dev.zarr.zarrjava.v3.Node.open(arrayPath);
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Assertions.assertEquals(4, (array).metadata.shape.length);
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array = (Array) dev.zarr.zarrjava.v3.Node.open(arrayPath.toString());
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Assertions.assertEquals(4, (array).metadata.shape.length);
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Group group = (Group) Node.open(groupPath);
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Assertions.assertInstanceOf(Group.class, group.get("color"));
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group = (Group) Node.open(groupPath.toString());
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Assertions.assertInstanceOf(Group.class, group.get("color"));
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group = (Group) dev.zarr.zarrjava.core.Group.open(groupPath);
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Assertions.assertInstanceOf(Group.class, group.get("color"));
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group = (Group) dev.zarr.zarrjava.core.Group.open(groupPath.toString());
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Assertions.assertInstanceOf(Group.class, group.get("color"));
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group = (Group) dev.zarr.zarrjava.v3.Node.open(groupPath);
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Assertions.assertInstanceOf(Group.class, group.get("color"));
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group = (Group) dev.zarr.zarrjava.v3.Node.open(groupPath.toString());
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Assertions.assertInstanceOf(Group.class, group.get("color"));
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Assertions.assertThrows(NoSuchFileException.class, () -> Node.open(new FilesystemStore(TESTDATA).resolve("non_existing")));
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Assertions.assertThrows(NoSuchFileException.class, () -> Node.open(new FilesystemStore(TESTDATA).resolve("non_existing").toString()));
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Assertions.assertThrows(NoSuchFileException.class, () -> dev.zarr.zarrjava.v3.Node.open(v2GroupPath));
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Assertions.assertThrows(NoSuchFileException.class, () -> dev.zarr.zarrjava.v3.Node.open(v2GroupPath.toString()));
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Assertions.assertThrows(NoSuchFileException.class, () -> dev.zarr.zarrjava.v3.Group.open(v2GroupPath));
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Assertions.assertThrows(NoSuchFileException.class, () -> dev.zarr.zarrjava.v3.Group.open(v2GroupPath.toString()));
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Assertions.assertThrows(NoSuchFileException.class, () -> dev.zarr.zarrjava.v3.Array.open(v2GroupPath));
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Assertions.assertThrows(NoSuchFileException.class, () -> dev.zarr.zarrjava.v3.Array.open(v2GroupPath.toString()));
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}
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@Test
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public void testGenericOpenV2() throws ZarrException, IOException {
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StoreHandle arrayHandle = new FilesystemStore(TESTDATA).resolve("v2_sample", "subgroup", "array");
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StoreHandle groupHandle = new FilesystemStore(TESTDATA).resolve("v2_sample");
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StoreHandle v3Handle = new FilesystemStore(TESTDATA).resolve("l4_sample");
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dev.zarr.zarrjava.v2.Array array = (dev.zarr.zarrjava.v2.Array) Node.open(arrayHandle);
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Assertions.assertEquals(3, (array).metadata.shape.length);
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array = (dev.zarr.zarrjava.v2.Array) dev.zarr.zarrjava.core.Array.open(arrayHandle);
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Assertions.assertEquals(3, (array).metadata.shape.length);
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array = (dev.zarr.zarrjava.v2.Array) dev.zarr.zarrjava.v2.Node.open(arrayHandle);
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Assertions.assertEquals(3, (array).metadata.shape.length);
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dev.zarr.zarrjava.v2.Group group = (dev.zarr.zarrjava.v2.Group) Node.open(groupHandle);
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Assertions.assertInstanceOf(dev.zarr.zarrjava.v2.Group.class, group.get("subgroup"));
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group = (dev.zarr.zarrjava.v2.Group) dev.zarr.zarrjava.core.Group.open(groupHandle);
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Assertions.assertInstanceOf(dev.zarr.zarrjava.v2.Group.class, group.get("subgroup"));
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group = (dev.zarr.zarrjava.v2.Group) dev.zarr.zarrjava.v2.Node.open(groupHandle);
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Assertions.assertInstanceOf(dev.zarr.zarrjava.v2.Group.class, group.get("subgroup"));
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Assertions.assertThrows(NoSuchFileException.class, () -> Node.open(new FilesystemStore(TESTDATA).resolve("non_existing")));
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Assertions.assertThrows(NoSuchFileException.class, () -> dev.zarr.zarrjava.v2.Node.open(v3Handle));
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Assertions.assertThrows(NoSuchFileException.class, () -> dev.zarr.zarrjava.v2.Group.open(v3Handle));
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Assertions.assertThrows(NoSuchFileException.class, () -> dev.zarr.zarrjava.v2.Array.open(v3Handle));
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}
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@Test
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public void testGenericOpenOverloadsV2() throws ZarrException, IOException {
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Path arrayPath = TESTDATA.resolve("v2_sample/subgroup/array");
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Path groupPath = TESTDATA.resolve("v2_sample");
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Path v3GroupPath = TESTDATA.resolve("l4_sample");
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dev.zarr.zarrjava.v2.Array array = (dev.zarr.zarrjava.v2.Array) Node.open(arrayPath);
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Assertions.assertEquals(3, (array).metadata.shape.length);
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array = (dev.zarr.zarrjava.v2.Array) Node.open(arrayPath.toString());
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Assertions.assertEquals(3, (array).metadata.shape.length);
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array = (dev.zarr.zarrjava.v2.Array) dev.zarr.zarrjava.core.Array.open(arrayPath);
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Assertions.assertEquals(3, (array).metadata.shape.length);
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array = (dev.zarr.zarrjava.v2.Array) dev.zarr.zarrjava.core.Array.open(arrayPath.toString());
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Assertions.assertEquals(3, (array).metadata.shape.length);
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array = (dev.zarr.zarrjava.v2.Array) dev.zarr.zarrjava.v2.Node.open(arrayPath);
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Assertions.assertEquals(3, (array).metadata.shape.length);
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array = (dev.zarr.zarrjava.v2.Array) dev.zarr.zarrjava.v2.Node.open(arrayPath.toString());
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Assertions.assertEquals(3, (array).metadata.shape.length);
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dev.zarr.zarrjava.v2.Group group = (dev.zarr.zarrjava.v2.Group) Node.open(groupPath);
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Assertions.assertInstanceOf(dev.zarr.zarrjava.v2.Group.class, group.get("subgroup"));
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group = (dev.zarr.zarrjava.v2.Group) Node.open(groupPath.toString());
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Assertions.assertInstanceOf(dev.zarr.zarrjava.v2.Group.class, group.get("subgroup"));
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group = (dev.zarr.zarrjava.v2.Group) dev.zarr.zarrjava.core.Group.open(groupPath);
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Assertions.assertInstanceOf(dev.zarr.zarrjava.v2.Group.class, group.get("subgroup"));
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group = (dev.zarr.zarrjava.v2.Group) dev.zarr.zarrjava.core.Group.open(groupPath.toString());
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Assertions.assertInstanceOf(dev.zarr.zarrjava.v2.Group.class, group.get("subgroup"));
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group = (dev.zarr.zarrjava.v2.Group) dev.zarr.zarrjava.v2.Node.open(groupPath);
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Assertions.assertInstanceOf(dev.zarr.zarrjava.v2.Group.class, group.get("subgroup"));
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group = (dev.zarr.zarrjava.v2.Group) dev.zarr.zarrjava.v2.Node.open(groupPath.toString());
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Assertions.assertInstanceOf(dev.zarr.zarrjava.v2.Group.class, group.get("subgroup"));
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Assertions.assertThrows(NoSuchFileException.class, () -> Node.open(new FilesystemStore(TESTDATA).resolve("non_existing")));
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Assertions.assertThrows(NoSuchFileException.class, () -> Node.open(new FilesystemStore(TESTDATA).resolve("non_existing").toString()));
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Assertions.assertThrows(NoSuchFileException.class, () -> dev.zarr.zarrjava.v2.Node.open(v3GroupPath));
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Assertions.assertThrows(NoSuchFileException.class, () -> dev.zarr.zarrjava.v2.Node.open(v3GroupPath.toString()));
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Assertions.assertThrows(NoSuchFileException.class, () -> dev.zarr.zarrjava.v2.Group.open(v3GroupPath));
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Assertions.assertThrows(NoSuchFileException.class, () -> dev.zarr.zarrjava.v2.Group.open(v3GroupPath.toString()));
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Assertions.assertThrows(NoSuchFileException.class, () -> dev.zarr.zarrjava.v2.Array.open(v3GroupPath));
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Assertions.assertThrows(NoSuchFileException.class, () -> dev.zarr.zarrjava.v2.Array.open(v3GroupPath.toString()));
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}
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@Test
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public void testCreateArrayV2() throws ZarrException, IOException {
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StoreHandle storeHandle = new FilesystemStore(TESTOUTPUT).resolve("testCreateArrayV2");
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Path storeHandlePath = TESTOUTPUT.resolve("testCreateArrayV2Path");
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String storeHandleString = String.valueOf(TESTOUTPUT.resolve("testCreateArrayV2String"));
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ArrayMetadata arrayMetadata = dev.zarr.zarrjava.v2.Array.metadataBuilder()
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.withShape(10, 10)
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.withDataType(dev.zarr.zarrjava.v2.DataType.UINT8)
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.withChunks(5, 5)
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.build();
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dev.zarr.zarrjava.v2.Array.create(storeHandle, arrayMetadata);
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Assertions.assertTrue(storeHandle.resolve(".zarray").exists());
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dev.zarr.zarrjava.v2.Array.create(storeHandlePath, arrayMetadata);
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Assertions.assertTrue(Files.exists(storeHandlePath.resolve(".zarray")));
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dev.zarr.zarrjava.v2.Array.create(storeHandleString, arrayMetadata);
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Assertions.assertTrue(Files.exists(Paths.get(storeHandleString).resolve(".zarray")));
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}
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@Test
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public void testCreateGroupV2() throws ZarrException, IOException {
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StoreHandle storeHandle = new FilesystemStore(TESTOUTPUT).resolve("testCreateGroupV2");
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Path storeHandlePath = TESTOUTPUT.resolve("testCreateGroupV2Path");
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String storeHandleString = String.valueOf(TESTOUTPUT.resolve("testCreateGroupV2String"));
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dev.zarr.zarrjava.v2.Group.create(storeHandle);
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Assertions.assertTrue(storeHandle.resolve(".zgroup").exists());
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dev.zarr.zarrjava.v2.Group.create(storeHandlePath);
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Assertions.assertTrue(Files.exists(storeHandlePath.resolve(".zgroup")));
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dev.zarr.zarrjava.v2.Group.create(storeHandleString);
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Assertions.assertTrue(Files.exists(Paths.get(storeHandleString).resolve(".zgroup")));
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}
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@Test
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public void testCreateArrayV3() throws ZarrException, IOException {
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StoreHandle storeHandle = new FilesystemStore(TESTOUTPUT).resolve("testCreateArrayV3");
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Path storeHandlePath = TESTOUTPUT.resolve("testCreateArrayV3Path");
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String storeHandleString = String.valueOf(TESTOUTPUT.resolve("testCreateArrayV3String"));
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dev.zarr.zarrjava.v3.ArrayMetadata arrayMetadata = dev.zarr.zarrjava.v3.Array.metadataBuilder()
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.withShape(10, 10)
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.withDataType(dev.zarr.zarrjava.v3.DataType.UINT8)
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.withChunkShape(5, 5)
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.build();
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dev.zarr.zarrjava.v3.Array.create(storeHandle, arrayMetadata);
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Assertions.assertTrue(storeHandle.resolve("zarr.json").exists());
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dev.zarr.zarrjava.v3.Array.create(storeHandlePath, arrayMetadata);
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Assertions.assertTrue(Files.exists(storeHandlePath.resolve("zarr.json")));
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dev.zarr.zarrjava.v3.Array.create(storeHandleString, arrayMetadata);
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Assertions.assertTrue(Files.exists(Paths.get(storeHandleString).resolve("zarr.json")));
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}
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@Test
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public void testCreateGroupV3() throws ZarrException, IOException {
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StoreHandle storeHandle = new FilesystemStore(TESTOUTPUT).resolve("testCreateGroupV3");
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Path storeHandlePath = TESTOUTPUT.resolve("testCreateGroupV3Path");
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String storeHandleString = String.valueOf(TESTOUTPUT.resolve("testCreateGroupV3String"));
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dev.zarr.zarrjava.v3.Group.create(storeHandle);
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Assertions.assertTrue(storeHandle.resolve("zarr.json").exists());
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dev.zarr.zarrjava.v3.Group.create(storeHandlePath);
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Assertions.assertTrue(Files.exists(storeHandlePath.resolve("zarr.json")));
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dev.zarr.zarrjava.v3.Group.create(storeHandleString);
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Assertions.assertTrue(Files.exists(Paths.get(storeHandleString).resolve("zarr.json")));
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}
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}

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

Lines changed: 1 addition & 13 deletions
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import java.io.*;
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import java.nio.ByteBuffer;
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import java.nio.file.Files;
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import java.nio.file.Path;
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import java.nio.file.Paths;
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import java.util.Arrays;
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import java.util.Comparator;
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import java.util.HashMap;
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import java.util.Map;
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import java.util.stream.Stream;
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public class ZarrPythonTests {
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public class ZarrPythonTests extends ZarrTest {
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final static Path TESTOUTPUT = Paths.get("testoutput");
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final static Path PYTHON_TEST_PATH = Paths.get("src/test/python-scripts/");
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@BeforeAll
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public static void clearTestoutputFolder() throws IOException {
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if (Files.exists(TESTOUTPUT)) {
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try (Stream<Path> walk = Files.walk(TESTOUTPUT)) {
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walk.sorted(Comparator.reverseOrder()).map(Path::toFile).forEach(File::delete);
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}
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}
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Files.createDirectory(TESTOUTPUT);
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}
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public static int runCommand(String... command) throws IOException, InterruptedException {
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ProcessBuilder pb = new ProcessBuilder();

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