Add zip support (ported from SCIFIO)

src/main/java/org/scijava/io/handle/ZipHandle.java

@@ -0,0 +1,201 @@
+/*
+ * #%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.handle;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.zip.ZipEntry;
+import java.util.zip.ZipInputStream;
+
+import org.scijava.io.location.AbstractCompressedHandle;
+import org.scijava.io.location.Location;
+import org.scijava.io.location.ZipLocation;
+import org.scijava.plugin.Plugin;
+
+/**
+ * StreamHandle implementation for reading from Zip-compressed files or byte
+ * arrays. Instances of ZipHandle are read-only.
+ *
+ * @see StreamHandle
+ * @author Melissa Linkert
+ * @author Gabriel Einsdorf
+ */
+@Plugin(type = DataHandle.class)
+public class ZipHandle extends AbstractCompressedHandle<ZipLocation> {
+
+	// -- Fields --
+
+	private DataHandle<Location> in;
+
+	private String entryName;
+
+	private ZipEntry entry;
+
+	private long entryLength = -1l;
+
+	// -- ZipHandle API methods --
+
+	/** Get the name of the backing Zip entry. */
+	public String getEntryName() {
+		return entryName;
+	}
+
+	@Override
+	public void resetStream() throws IOException {
+
+		if (raw() instanceof ResettableStreamHandle<?>) {
+			((ResettableStreamHandle<?>) raw()).resetStream();
+		}
+		else {
+			raw().seek(0l);
+		}
+
+		inputStream = new ZipInputStream(new DataHandleInputStream<>(raw()));
+		// FIXME add Buffering
+
+		seekToEntry();
+
+	}
+
+	// -- IRandomAccess API methods --
+
+	@Override
+	public void close() throws IOException {
+		inputStream = null;
+		entryName = null;
+		entryLength = -1;
+		if (in != null) in.close();
+		in = null;
+	}
+
+	// -- Helper methods --
+
+	/**
+	 * Seeks to the relevant ZIP entry, populating the stream length accordingly.
+	 */
+	private void seekToEntry() throws IOException {
+
+		while (true) {
+			final ZipEntry e = ((ZipInputStream) inputStream).getNextEntry();
+			if (entryName == null) {
+				entry = e;
+				entryName = e.getName();
+			}
+			if (entryName.equals(e.getName())) {
+				// found the matching entry name (or first entry if the name is
+				// null)
+				if (entryLength < 0) {
+					final boolean resetNeeded = populateLength(e.getSize());
+					if (resetNeeded) {
+						// stream length was calculated by force, need to reset
+						resetStream();
+					}
+				}
+				break;
+			}
+		}
+	}
+
+	/**
+	 * Sets the stream length, computing it by force if necessary.
+	 *
+	 * @return if the Stream needs to be reset
+	 */
+	private boolean populateLength(final long size) throws IOException {
+		if (size >= 0) {
+			entryLength = size;
+			return false;
+		}
+		// size is unknown, so we must read the stream manually
+		long length = 0;
+		final DataHandle<Location> stream = raw();
+		while (true) {
+			final long skipped = stream.skip(Long.MAX_VALUE);
+			if (skipped == 0) {
+				// NB: End of stream, we hope. Technically there is no contract
+				// for when skip(long) returns 0, but in practice it seems to be
+				// when end of stream is reached.
+				break;
+			}
+			length += skipped;
+		}
+
+		entryLength = length;
+		return true;
+	}
+
+	@Override
+	public Class<ZipLocation> getType() {
+		return ZipLocation.class;
+	}
+
+	@Override
+	protected void initInputStream() throws IOException {
+		inputStream = new ZipInputStream(new DataHandleInputStream<>(raw()));
+
+		entry = get().getEntry();
+		if (entry == null) {
+			// strip off .zip extension and directory prefix
+			final String n = raw().get().getName();
+			String name = n.substring(0, n.length() - 4);
+
+			int slash = name.lastIndexOf(File.separator);
+			if (slash < 0) slash = name.lastIndexOf("/");
+			if (slash >= 0) name = name.substring(slash + 1);
+
+			// look for Zip entry with same prefix as the Zip file itself
+			boolean matchFound = false;
+			ZipEntry ze;
+			while ((ze = ((ZipInputStream) inputStream).getNextEntry()) != null) {
+				if (entryName == null) entryName = ze.getName();
+				if (!matchFound && ze.getName().startsWith(name)) {
+					// found entry with matching name
+					entryName = ze.getName();
+					entry = ze;
+					matchFound = true;
+				}
+			}
+			resetStream();
+		}
+	}
+
+	@Override
+	public long length() throws IOException {
+		if (entry == null) {
+			return -1;
+		}
+		return entry.getSize();
+	}
+
+	public long getEntryLength() {
+		return entryLength;
+	}
+}

src/main/java/org/scijava/io/location/ZipLocation.java

@@ -0,0 +1,86 @@
+/*
+ * #%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.location;
+
+import java.util.zip.ZipEntry;
+
+import org.scijava.io.handle.DataHandle;
+import org.scijava.io.handle.ZipHandle;
+import org.scijava.plugin.Plugin;
+
+/**
+ * {@link Location} backed by a {@link DataHandle} that is <code>zip</code>
+ * compressed.
+ * 
+ * @author Gabriel Einsdorf
+ * @see ZipHandle
+ */
+@Plugin(type = DataHandle.class)
+public class ZipLocation extends AbstractHigherOrderLocation {
+
+	private ZipEntry entry;
+
+	public ZipLocation(Location location) {
+		super(location);
+	}
+
+	public ZipLocation(Location location, ZipEntry entry) {
+		super(location);
+		this.entry = entry;
+	}
+
+	public ZipEntry getEntry() {
+		return entry;
+	}
+
+	@Override
+	public int hashCode() {
+		final int prime = 31;
+		int result = super.hashCode();
+		result = prime * result + ((entry == null) ? 0 : entry.hashCode());
+		return result;
+	}
+
+	@Override
+	public boolean equals(Object obj) {
+		if (this == obj) return true;
+		if (!super.equals(obj)) return false;
+		if (getClass() != obj.getClass()) return false;
+		ZipLocation other = (ZipLocation) obj;
+		if (entry == null) {
+			if (other.entry != null) return false;
+		}
+		else if (!entry.equals(other.entry)) return false;
+		return true;
+	}
+
+}

src/test/java/org/scijava/io/handle/ZipHandleTest.java

@@ -0,0 +1,89 @@
+/*
+ * #%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.handle;
+
+import java.io.File;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.util.zip.ZipEntry;
+import java.util.zip.ZipOutputStream;
+
+import org.junit.Ignore;
+import org.junit.Test;
+import org.scijava.io.handle.DataHandle;
+import org.scijava.io.location.FileLocation;
+import org.scijava.io.location.Location;
+import org.scijava.io.location.ZipLocation;
+
+/**
+ * Tests {@link ZipHandle}.
+ *
+ * @author Gabriel Einsdorf
+ */
+public class ZipHandleTest extends DataHandleTest {
+
+	@Override
+	public Class<? extends DataHandle<?>> getExpectedHandleType() {
+		return ZipHandle.class;
+	}
+
+	@Override
+	public Location createLocation() throws IOException {
+		// create and populate a temp file
+		final File tmpFile = File.createTempFile("FileHandleTest", "test-file.zip");
+		tmpFile.deleteOnExit();
+
+		try (ZipOutputStream out = new ZipOutputStream(new FileOutputStream(
+			tmpFile)))
+		{
+			out.putNextEntry(new ZipEntry(tmpFile.getName()));
+			populateData(out);
+		}
+
+		return new ZipLocation(new FileLocation(tmpFile));
+	}
+
+	@Test
+	@Override
+	public void testWriting() throws IOException {
+		// no Op
+	}
+
+	@Override
+	@Test
+	public void testReading() throws IOException {
+		try (final DataHandle<? extends Location> handle = createHandle()) {
+			checkBasicReadMethods(handle, false);
+			checkEndiannessReading(handle);
+		}
+	}
+}