Merge pull request #11 from tpietzsch/readdata

ReadData and DataBlockCodec

Author: bogovicj

.github/workflows/build-pr.yml

@@ -6,6 +6,9 @@ on:
       - master
     tags:
       - "*-[0-9]+.*"
+  pull_request:
+    branches:
+      - master
 
 jobs:
   build:
@@ -14,7 +17,7 @@ jobs:
     steps:
       - uses: actions/checkout@v2
       - name: Set up Java
-        uses: actions/setup-java@v2
+        uses: actions/setup-java@v3
         with:
           java-version: '8'
           distribution: 'zulu'
@@ -28,5 +31,6 @@ jobs:
           GPG_PASSPHRASE: ${{ secrets.GPG_PASSPHRASE }}
           MAVEN_USER: ${{ secrets.MAVEN_USER }}
           MAVEN_PASS: ${{ secrets.MAVEN_PASS }}
+          OSSRH_USER: ${{ secrets.OSSRH_USER }}
           OSSRH_PASS: ${{ secrets.OSSRH_PASS }}
           SIGNING_ASC: ${{ secrets.SIGNING_ASC }}

.github/workflows/build-main.yml .github/workflows/build.yml.github/workflows/build-main.yml renamed to .github/workflows/build.yml

@@ -1,3 +1,5 @@
+[![Build Status](https://github.com/saalfeldlab/n5-blosc/actions/workflows/build.yml/badge.svg)](https://github.com/saalfeldlab/n5-blosc/actions/workflows/build.yml)
+
 [![Build Status](https://github.com/saalfeldlab/n5-blosc/actions/workflows/build-main.yml/badge.svg)](https://github.com/saalfeldlab/n5-blosc/actions/workflows/build-main.yml)
 
 # n5-blosc

README.md

@@ -5,7 +5,7 @@
 	<parent>
 		<groupId>org.scijava</groupId>
 		<artifactId>pom-scijava</artifactId>
-		<version>37.0.0</version>
+		<version>40.0.0</version>
 		<relativePath />
 	</parent>
 
@@ -83,19 +83,10 @@
 		<license.organizationName>Saalfeld Lab</license.organizationName>
 		<license.copyrightOwners>Stephan Saalfeld</license.copyrightOwners>
 
-		<scijava.jvm.build.version>[1.8.0-101,11]</scijava.jvm.build.version>
-
 		<!-- NB: Deploy releases to the SciJava Maven repository. -->
 		<releaseProfiles>sign,deploy-to-scijava</releaseProfiles>
 
-		<!-- TODO remove when pom-scijava-base is updated -->
-		<scijava.jvm.version>8</scijava.jvm.version>
-		<scijava.jvm.build.version>[1.8.0-101,)</scijava.jvm.build.version>
-
-		<maven-enforcer-plugin.version>3.0.0-M3</maven-enforcer-plugin.version>
-		<jacoco-maven-plugin.version>0.8.6</jacoco-maven-plugin.version>
-
-		<n5.version>3.1.2</n5.version>
+		<n5.version>4.0.0-alpha-1</n5.version>
 	</properties>
 
 	<dependencies>

pom.xml

@@ -26,26 +26,20 @@
 package org.janelia.saalfeldlab.n5.blosc;
 
 import java.io.IOException;
-import java.io.InputStream;
-import java.io.OutputStream;
 import java.nio.ByteBuffer;
-
-import org.apache.commons.compress.utils.IOUtils;
 import org.blosc.BufferSizes;
 import org.blosc.JBlosc;
 import org.janelia.saalfeldlab.n5.Compression;
 import org.janelia.saalfeldlab.n5.Compression.CompressionType;
-import org.janelia.saalfeldlab.n5.DataBlock;
-import org.janelia.saalfeldlab.n5.DefaultBlockReader;
-import org.janelia.saalfeldlab.n5.DefaultBlockWriter;
+import org.janelia.saalfeldlab.n5.readdata.ReadData;
 
 /**
  * Compression using JBlosc (https://github.com/Blosc/JBlosc) compressors.
  *
  * @author Stephan Saalfeld <saalfelds@janelia.hhmi.org>
  */
 @CompressionType("blosc")
-public class BloscCompression implements DefaultBlockReader, DefaultBlockWriter, Compression  {
+public class BloscCompression implements Compression  {
 
 	public static final int NOSHUFFLE = 0;
 	public static final int SHUFFLE = 1;
@@ -138,68 +132,33 @@ public BloscCompression(final BloscCompression template) {
 		this.nthreads = template.nthreads;
 	}
 
-	@Override
-	public <T, B extends DataBlock<T>> void read(
-			final B dataBlock,
-			final InputStream in) throws IOException {
-
-		final ByteBuffer src = ByteBuffer.wrap(IOUtils.toByteArray(in));
-		final boolean isByte = dataBlock.getData() instanceof byte[];
+	private byte[] decode(final byte[] data, final byte[] dstBuffer) {
+		final ByteBuffer src = ByteBuffer.wrap(data);
 		final ByteBuffer dst;
-		if (isByte)
-			dst = dataBlock.toByteBuffer();
-		else {
+		if (dstBuffer != null) {
+			dst = ByteBuffer.wrap(dstBuffer);
+		} else {
 			final BufferSizes sizes = blosc.cbufferSizes(src);
 			final int dstSize = (int)sizes.getNbytes();
-			dst = ByteBuffer.allocateDirect(dstSize);
+			dst = ByteBuffer.allocate(dstSize);
 		}
 		JBlosc.decompressCtx(src, dst, dst.capacity(), nthreads);
-		dataBlock.readData(dst);
+		return dst.array();
 	}
 
 	@Override
-	public <T> void write(
-			final DataBlock<T> dataBlock,
-			final OutputStream out) throws IOException {
+	public ReadData decode(final ReadData readData) throws IOException {
+		return ReadData.from(decode(readData.allBytes(), null));
+	}
 
-		final ByteBuffer src = dataBlock.toByteBuffer();
-		final ByteBuffer dst = ByteBuffer.allocate(src.limit() + JBlosc.OVERHEAD);
+	@Override
+	public ReadData encode(final ReadData readData) throws IOException {
+		final byte[] serialized = readData.allBytes();
+		final ByteBuffer src = ByteBuffer.wrap(serialized);
+		final ByteBuffer dst = ByteBuffer.allocate(serialized.length + JBlosc.OVERHEAD);
 		JBlosc.compressCtx(clevel, shuffle, 1, src, src.limit(), dst, dst.limit(), cname, blocksize, nthreads);
 		final BufferSizes sizes = blosc.cbufferSizes(dst);
 		final int dstSize = (int)sizes.getCbytes();
-		out.write(dst.array(), 0, dstSize);
-		out.flush();
-	}
-
-	@Override
-	public BloscCompression getReader() {
-
-		return this;
-	}
-
-	@Override
-	public BloscCompression getWriter() {
-
-		return this;
-	}
-
-	/**
-	 * Not used in this implementation of {@link DefaultBlockWriter} as
-	 * {@link JBlosc} decompresses from and into {@link ByteBuffer}.
-	 */
-	@Override
-	public OutputStream getOutputStream(final OutputStream out) throws IOException {
-
-		return null;
-	}
-
-	/**
-	 * Not used in this implementation of {@link DefaultBlockReader} as
-	 * {@link JBlosc} compresses from and into {@link ByteBuffer}.
-	 */
-	@Override
-	public InputStream getInputStream(final InputStream in) throws IOException {
-
-		return null;
+		return ReadData.from(dst.array(), 0, dstSize);
 	}
 }