Zip Store #37
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Zip Store #37
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# Conflicts: # src/test/java/dev/zarr/zarrjava/ZarrV2Test.java
…ault to a new MemoryStore
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I wonder how writing would be implemented on the ZipStore? Maybe it could have an internal Reading could use a different implementation that works on the zip file directly. Maybe it even makes sense to have 2 separate ZipStore implementations. In any case, it would be cool if the ZipStore(s) could wrap around any other store so that zip files can be written to disk, s3 etc. |
diff --git c/src/main/java/dev/zarr/zarrjava/store/ZipStore.java i/src/main/java/dev/zarr/zarrjava/store/ZipStore.java new file mode 100644 index 0000000..054917f --- /dev/null +++ i/src/main/java/dev/zarr/zarrjava/store/ZipStore.java @@ -0,0 +1,72 @@ +package dev.zarr.zarrjava.store; + +import javax.annotation.Nonnull; +import javax.annotation.Nullable; +import java.nio.ByteBuffer; +import java.nio.file.Path; +import java.nio.file.Paths; +import java.util.stream.Stream; + +public class ZipStore implements Store, Store.ListableStore { + @nonnull + private final Path path; + + public ZipStore(@nonnull Path path) { + this.path = path; + } + + public ZipStore(@nonnull String path) { + this.path = Paths.get(path); + } + + + @OverRide + public Stream<String> list(String[] keys) { + return Stream.empty(); + } + + @OverRide + public boolean exists(String[] keys) { + return false; + } + + @nullable + @OverRide + public ByteBuffer get(String[] keys) { + return null; + } + + @nullable + @OverRide + public ByteBuffer get(String[] keys, long start) { + return null; + } + + @nullable + @OverRide + public ByteBuffer get(String[] keys, long start, long end) { + return null; + } + + @OverRide + public void set(String[] keys, ByteBuffer bytes) { + + } + + @OverRide + public void delete(String[] keys) { + + } + + @nonnull + @OverRide + public StoreHandle resolve(String... keys) { + return new StoreHandle(this, keys); + } + + @OverRide + public String toString() { + return this.path.toUri().toString().replaceAll("\\/$", ""); + } + +} diff --git c/src/test/java/dev/zarr/zarrjava/Utils.java i/src/test/java/dev/zarr/zarrjava/Utils.java new file mode 100644 index 0000000..0026200 --- /dev/null +++ i/src/test/java/dev/zarr/zarrjava/Utils.java @@ -0,0 +1,40 @@ +package dev.zarr.zarrjava; + +import java.io.File; +import java.io.FileInputStream; +import java.io.IOException; +import java.util.zip.ZipEntry; +import java.util.zip.ZipOutputStream; + +public class Utils { + + static void zipFile(File fileToZip, String fileName, ZipOutputStream zipOut) throws IOException { + if (fileToZip.isHidden()) { + return; + } + if (fileToZip.isDirectory()) { + if (fileName.endsWith("/")) { + zipOut.putNextEntry(new ZipEntry(fileName)); + zipOut.closeEntry(); + } else { + zipOut.putNextEntry(new ZipEntry(fileName + "/")); + zipOut.closeEntry(); + } + File[] children = fileToZip.listFiles(); + for (File childFile : children) { + zipFile(childFile, fileName + "/" + childFile.getName(), zipOut); + } + return; + } + FileInputStream fis = new FileInputStream(fileToZip); + ZipEntry zipEntry = new ZipEntry(fileName); + zipOut.putNextEntry(zipEntry); + byte[] bytes = new byte[1024]; + int length; + while ((length = fis.read(bytes)) >= 0) { + zipOut.write(bytes, 0, length); + } + fis.close(); + } + +} diff --git c/src/test/java/dev/zarr/zarrjava/ZarrStoreTest.java i/src/test/java/dev/zarr/zarrjava/ZarrStoreTest.java index 4a369c9..c7d2ab4 100644 --- c/src/test/java/dev/zarr/zarrjava/ZarrStoreTest.java +++ i/src/test/java/dev/zarr/zarrjava/ZarrStoreTest.java @@ -7,16 +7,22 @@ import dev.zarr.zarrjava.v3.*; import org.junit.jupiter.api.Assertions; import org.junit.jupiter.api.Test; import org.junit.jupiter.params.ParameterizedTest; +import org.junit.jupiter.params.provider.MethodSource; import org.junit.jupiter.params.provider.CsvSource; import software.amazon.awssdk.auth.credentials.AnonymousCredentialsProvider; import software.amazon.awssdk.regions.Region; import software.amazon.awssdk.services.s3.S3Client; +import java.io.File; +import java.io.FileOutputStream; import java.io.IOException; import java.nio.file.Files; import java.util.Arrays; import java.util.stream.Stream; +import java.nio.file.Path; +import java.util.zip.ZipOutputStream; +import static dev.zarr.zarrjava.Utils.zipFile; import static dev.zarr.zarrjava.v3.Node.makeObjectMapper; public class ZarrStoreTest extends ZarrTest { @@ -132,4 +138,72 @@ public class ZarrStoreTest extends ZarrTest { Assertions.assertEquals("test group", attrs.getString("description")); } + + @test + public void testZipStore() throws ZarrException, IOException { + Path sourceDir = TESTOUTPUT.resolve("testZipStore"); + Path targetDir = TESTOUTPUT.resolve("testZipStore.zip"); + FilesystemStore fsStore = new FilesystemStore(sourceDir); + writeTestGroupV3(fsStore, true); + + FileOutputStream fos = new FileOutputStream(targetDir.toFile()); + ZipOutputStream zipOut = new ZipOutputStream(fos); + + File fileToZip = new File(sourceDir.toUri()); + zipFile(fileToZip, fileToZip.getName(), zipOut); + zipOut.close(); + fos.close(); + + ZipStore zipStore = new ZipStore(targetDir); + assertIsTestGroupV3(Group.open(zipStore.resolve()), true); + } + + static Stream<Store> localStores() { + return Stream.of( +// new ConcurrentMemoryStore(), + new FilesystemStore(TESTOUTPUT.resolve("testLocalStoresFS")), + new ZipStore(TESTOUTPUT.resolve("testLocalStoresZIP.zip")) + ); + } + + @ParameterizedTest + @MethodSource("localStores") + public void testLocalStores(Store store) throws IOException, ZarrException { + boolean useParallel = true; + Group group = writeTestGroupV3(store, useParallel); + assertIsTestGroupV3(group, useParallel); + } + + int[] testData(){ + int[] testData = new int[1024 * 1024]; + Arrays.setAll(testData, p -> p); + return testData; + } + + Group writeTestGroupV3(Store store, boolean useParallel) throws ZarrException, IOException { + StoreHandle storeHandle = store.resolve(); + + Group group = Group.create(storeHandle); + Array array = group.createArray("array", b -> b + .withShape(1024, 1024) + .withDataType(DataType.UINT32) + .withChunkShape(5, 5) + ); + array.write(ucar.ma2.Array.factory(ucar.ma2.DataType.UINT, new int[]{1024, 1024}, testData()), useParallel); + group.createGroup("subgroup"); + group.setAttributes(new Attributes(b -> b.set("some", "value"))); + return group; + } + + void assertIsTestGroupV3(Group group, boolean useParallel) throws ZarrException { + Stream<dev.zarr.zarrjava.core.Node> nodes = group.list(); + Assertions.assertEquals(2, nodes.count()); + Array array = (Array) group.get("array"); + Assertions.assertNotNull(array); + ucar.ma2.Array result = array.read(useParallel); + Assertions.assertArrayEquals(testData(), (int[]) result.get1DJavaArray(ucar.ma2.DataType.UINT)); + Attributes attrs = group.metadata().attributes; + Assertions.assertNotNull(attrs); + Assertions.assertEquals("value", attrs.getString("some")); + } }
# Conflicts: # src/test/java/dev/zarr/zarrjava/ZarrStoreTest.java
There are apparently cases where release: [created] leads to the deploy not being triggered. Attempting an expansion to [created, published].
Removed setup steps for zarr-python from the workflow.
Use new sonatype plugin for upload
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TODO:
Requirements derived from https://ngff.openmicroscopy.org/rfc/9/index.html
EDIT:
enforcing zip64 on smaller files resulted in header errors when writing with
org.apache.commons.compress. For now zip64 will only be used when needed