Add GZip support (adapted from SCIFIO)

Author: gab1one

src/main/java/org/scijava/io/location/gzip/GZipHandle.java

@@ -0,0 +1,69 @@
+/*
+ * #%L
+ * SCIFIO library for reading and converting scientific file formats.
+ * %%
+ * Copyright (C) 2011 - 2016 Board of Regents of the University of
+ * Wisconsin-Madison
+ * %%
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
+ *
+ * 1. Redistributions of source code must retain the above copyright notice,
+ *    this list of conditions and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above copyright notice,
+ *    this list of conditions and the following disclaimer in the documentation
+ *    and/or other materials provided with the distribution.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+ * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
+ * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+ * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+ * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+ * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+ * POSSIBILITY OF SUCH DAMAGE.
+ * #L%
+ */
+
+package org.scijava.io.location.gzip;
+
+import java.io.IOException;
+import java.util.zip.GZIPInputStream;
+
+import org.scijava.io.DataHandle;
+import org.scijava.io.DataHandleInputStream;
+import org.scijava.io.location.AbstractCompressedHandle;
+import org.scijava.plugin.Plugin;
+
+/**
+ * StreamHandle implementation for reading from gzip-compressed files or byte
+ * arrays. Instances of GZipHandle are read-only.
+ *
+ * @author Melissa Linkert
+ * @author Gabriel Einsdorf
+ */
+@Plugin(type = DataHandle.class)
+public class GZipHandle extends AbstractCompressedHandle<GZipLocation> {
+
+	@Override
+	public Class<GZipLocation> getType() {
+		return GZipLocation.class;
+	}
+
+	@Override
+	protected void initInputStream() throws IOException {
+		inputStream = new GZIPInputStream(new DataHandleInputStream<>(raw()));
+	}
+
+//	@Override
+//	public boolean isConstructable(final String file) throws IOException {
+//		final byte[] b = new byte[2];
+//		s.read(b);
+//		s.close();
+//		return Bytes.toInt(b, true) == GZIPInputStream.GZIP_MAGIC;
+//	}
+
+}

src/main/java/org/scijava/io/location/gzip/GZipLocation.java

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+
+package org.scijava.io.location.gzip;
+
+import org.scijava.io.DataHandle;
+import org.scijava.io.Location;
+import org.scijava.io.location.AbstractHigherOrderLocation;
+
+/**
+ * {@link Location} backed by a {@link DataHandle} that is <code>gzip</code>
+ * compressed.
+ * 
+ * @author Gabriel Einsdorf
+ * @see GZipHandle
+ */
+public class GZipLocation extends AbstractHigherOrderLocation {
+
+	public GZipLocation(Location location) {
+		super(location);
+	}
+
+}

src/test/java/org/scijava/io/GZipHandleTest.java

@@ -0,0 +1,81 @@
+/*
+ * #%L
+ * SciJava Common shared library for SciJava software.
+ * %%
+ * Copyright (C) 2009 - 2017 Board of Regents of the University of
+ * Wisconsin-Madison, Broad Institute of MIT and Harvard, and Max Planck
+ * Institute of Molecular Cell Biology and Genetics.
+ * %%
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
+ * 
+ * 1. Redistributions of source code must retain the above copyright notice,
+ *    this list of conditions and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above copyright notice,
+ *    this list of conditions and the following disclaimer in the documentation
+ *    and/or other materials provided with the distribution.
+ * 
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+ * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
+ * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+ * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+ * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+ * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+ * POSSIBILITY OF SUCH DAMAGE.
+ * #L%
+ */
+
+package org.scijava.io;
+
+import java.io.File;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.util.zip.GZIPOutputStream;
+
+import org.scijava.io.location.file.FileLocation;
+import org.scijava.io.location.gzip.GZipHandle;
+import org.scijava.io.location.gzip.GZipLocation;
+
+/**
+ * Tests {@link GZipHandle}.
+ *
+ * @author Gabriel Einsdorf
+ */
+public class GZipHandleTest extends DataHandleTest {
+
+	@Override
+	public Class<? extends DataHandle<?>> getExpectedHandleType() {
+		return GZipHandle.class;
+	}
+
+	@Override
+	public Location createLocation() throws IOException {
+		// create and populate a temp file
+		final File tmpFile = File.createTempFile("FileHandleTest",
+			"test-file.gzip");
+		tmpFile.deleteOnExit();
+
+		try (GZIPOutputStream out = new GZIPOutputStream(new FileOutputStream(
+			tmpFile)))
+		{
+			populateData(out);
+		}
+
+		return new GZipLocation(new FileLocation(tmpFile));
+	}
+
+	@Override
+	protected <L extends Location> void checkWrites(DataHandle<L> handle)
+		throws IOException
+	{
+		// NB Handle is read only
+	}
+	@Override
+	protected void setup() {
+		checkLength = false;
+	}
+}

src/test/java/org/scijava/io/GZipLocationTest.java

@@ -0,0 +1,63 @@
+/*
+ * #%L
+ * SciJava Common shared library for SciJava software.
+ * %%
+ * Copyright (C) 2009 - 2017 Board of Regents of the University of
+ * Wisconsin-Madison, Broad Institute of MIT and Harvard, and Max Planck
+ * Institute of Molecular Cell Biology and Genetics.
+ * %%
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
+ *
+ * 1. Redistributions of source code must retain the above copyright notice,
+ *    this list of conditions and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above copyright notice,
+ *    this list of conditions and the following disclaimer in the documentation
+ *    and/or other materials provided with the distribution.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+ * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
+ * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+ * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+ * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+ * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+ * POSSIBILITY OF SUCH DAMAGE.
+ * #L%
+ */
+
+package org.scijava.io;
+
+import static org.junit.Assert.assertEquals;
+
+import java.io.IOException;
+
+import org.junit.Test;
+import org.scijava.io.location.file.FileLocation;
+import org.scijava.io.location.gzip.GZipLocation;
+
+/**
+ * Tests {@link GZipLocation}.
+ *
+ * @author Gabriel Einsdorf
+ */
+public class GZipLocationTest {
+
+	/**
+	 * Tests {@link GZipLocation#GZipLocation(Location)}.
+	 *
+	 * @throws IOException
+	 */
+	@Test
+	public void testFile() throws IOException {
+		final String path = "/not/actually/a/real-file";
+		final FileLocation loc = new FileLocation(path);
+		GZipLocation zLoc = new GZipLocation(loc);
+
+		assertEquals(zLoc.getBaseLocation(), loc);
+	}
+
+}