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Add Zip support (adapted from SCIFIO)
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‎src/main/java/org/scijava/io/location/zip/ZipHandle.java

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/*
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* #%L
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* SCIFIO library for reading and converting scientific file formats.
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* %%
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* Copyright (C) 2011 - 2016 Board of Regents of the University of
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* Wisconsin-Madison
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* %%
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* Redistribution and use in source and binary forms, with or without
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* modification, are permitted provided that the following conditions are met:
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*
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* 1. Redistributions of source code must retain the above copyright notice,
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* this list of conditions and the following disclaimer.
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* 2. Redistributions in binary form must reproduce the above copyright notice,
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* this list of conditions and the following disclaimer in the documentation
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* and/or other materials provided with the distribution.
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*
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* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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* AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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* IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
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* ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
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* LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
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* CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
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* SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
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* INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
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* CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
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* ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
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* POSSIBILITY OF SUCH DAMAGE.
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* #L%
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*/
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package org.scijava.io.location.zip;
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import java.io.File;
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import java.io.IOException;
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import java.util.zip.ZipEntry;
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import java.util.zip.ZipInputStream;
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import org.scijava.io.DataHandle;
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import org.scijava.io.DataHandleInputStream;
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import org.scijava.io.Location;
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import org.scijava.io.location.AbstractCompressedHandle;
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import org.scijava.io.location.ResettableStreamHandle;
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import org.scijava.io.location.StreamHandle;
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import org.scijava.plugin.Plugin;
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/**
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* StreamHandle implementation for reading from Zip-compressed files or byte
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* arrays. Instances of ZipHandle are read-only.
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*
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* @see StreamHandle
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* @author Melissa Linkert
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* @author Gabriel Einsdorf
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*/
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@Plugin(type = DataHandle.class)
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public class ZipHandle extends AbstractCompressedHandle<ZipLocation> {
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// -- Fields --
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private DataHandle<Location> in;
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private String entryName;
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private ZipEntry entry;
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private long entryLength = -1l;
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// -- Constructor --
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// @Override
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// public boolean isConstructable(final String file) throws IOException {
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//
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// final byte[] b = new byte[2];
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// if (handle.length() >= 2) {
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// handle.read(b);
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// }
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// handle.close();
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// return new String(b, Constants.ENCODING).equals("PK");
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// }
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// -- ZipHandle API methods --
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/** Get the name of the backing Zip entry. */
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public String getEntryName() {
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return entryName;
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}
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@Override
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public void resetStream() throws IOException {
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if (raw() instanceof ResettableStreamHandle<?>) {
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((ResettableStreamHandle<?>) raw()).resetStream();
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}
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else {
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raw().seek(0l);
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}
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inputStream = new ZipInputStream(new DataHandleInputStream<>(raw()));
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// FIXME add Buffering
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seekToEntry();
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}
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// -- IRandomAccess API methods --
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@Override
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public void close() throws IOException {
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inputStream = null;
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entryName = null;
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entryLength = -1;
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if (in != null) in.close();
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in = null;
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}
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// -- Helper methods --
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/**
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* Seeks to the relevant ZIP entry, populating the stream length accordingly.
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*/
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private void seekToEntry() throws IOException {
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while (true) {
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final ZipEntry e = ((ZipInputStream) inputStream).getNextEntry();
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if (entryName == null) {
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entry = e;
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entryName = e.getName();
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}
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if (entryName.equals(e.getName())) {
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// found the matching entry name (or first entry if the name is
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// null)
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if (entryLength < 0) {
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final boolean resetNeeded = populateLength(e.getSize());
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if (resetNeeded) {
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// stream length was calculated by force, need to reset
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resetStream();
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}
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}
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break;
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}
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}
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}
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/**
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* Sets the stream length, computing it by force if necessary.
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*
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* @return if the Stream needs to be reset
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*/
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private boolean populateLength(final long size) throws IOException {
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if (size >= 0) {
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entryLength = size;
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return false;
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}
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// size is unknown, so we must read the stream manually
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long length = 0;
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final DataHandle<Location> stream = raw();
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while (true) {
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final long skipped = stream.skip(Long.MAX_VALUE);
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if (skipped == 0) {
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// NB: End of stream, we hope. Technically there is no contract
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// for when skip(long) returns 0, but in practice it seems to be
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// when end of stream is reached.
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break;
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}
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length += skipped;
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}
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entryLength = length;
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return true;
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}
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@Override
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public Class<ZipLocation> getType() {
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return ZipLocation.class;
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}
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@Override
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protected void initInputStream() throws IOException {
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inputStream = new ZipInputStream(new DataHandleInputStream<>(raw()));
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entry = get().getEntry();
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if (entry == null) {
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// strip off .zip extension and directory prefix
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final String n = raw().get().getName();
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String name = n.substring(0, n.length() - 4);
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int slash = name.lastIndexOf(File.separator);
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if (slash < 0) slash = name.lastIndexOf("/");
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if (slash >= 0) name = name.substring(slash + 1);
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// look for Zip entry with same prefix as the Zip file itself
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boolean matchFound = false;
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ZipEntry ze;
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while ((ze = ((ZipInputStream) inputStream).getNextEntry()) != null) {
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if (entryName == null) entryName = ze.getName();
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if (!matchFound && ze.getName().startsWith(name)) {
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// found entry with matching name
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entryName = ze.getName();
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entry = ze;
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matchFound = true;
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}
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}
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resetStream();
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}
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}
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}

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

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/*
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* #%L
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* SciJava Common shared library for SciJava software.
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* %%
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* Copyright (C) 2009 - 2017 Board of Regents of the University of
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* Wisconsin-Madison, Broad Institute of MIT and Harvard, and Max Planck
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* Institute of Molecular Cell Biology and Genetics.
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* %%
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* Redistribution and use in source and binary forms, with or without
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* modification, are permitted provided that the following conditions are met:
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*
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* 1. Redistributions of source code must retain the above copyright notice,
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* this list of conditions and the following disclaimer.
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* 2. Redistributions in binary form must reproduce the above copyright notice,
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* this list of conditions and the following disclaimer in the documentation
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* and/or other materials provided with the distribution.
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*
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* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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* AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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* IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
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* ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
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* LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
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* CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
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* SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
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* INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
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* CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
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* ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
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* POSSIBILITY OF SUCH DAMAGE.
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* #L%
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*/
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package org.scijava.io.location.zip;
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import java.util.zip.ZipEntry;
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import org.scijava.io.DataHandle;
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import org.scijava.io.Location;
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import org.scijava.io.location.AbstractHigherOrderLocation;
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import org.scijava.plugin.Plugin;
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/**
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* {@link Location} backed by a {@link DataHandle} that is <code>zip</code>
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* compressed.
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*
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* @author Gabriel Einsdorf
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* @see ZipHandle
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*/
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@Plugin(type = DataHandle.class)
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public class ZipLocation extends AbstractHigherOrderLocation {
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private ZipEntry entry;
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public ZipLocation(Location location) {
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super(location);
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}
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public ZipLocation(Location location, ZipEntry entry) {
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super(location);
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this.entry = entry;
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}
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public ZipEntry getEntry() {
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return entry;
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}
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@Override
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public int hashCode() {
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final int prime = 31;
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int result = super.hashCode();
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result = prime * result + ((entry == null) ? 0 : entry.hashCode());
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return result;
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}
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@Override
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public boolean equals(Object obj) {
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if (this == obj) return true;
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if (!super.equals(obj)) return false;
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if (getClass() != obj.getClass()) return false;
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ZipLocation other = (ZipLocation) obj;
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if (entry == null) {
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if (other.entry != null) return false;
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}
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else if (!entry.equals(other.entry)) return false;
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return true;
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}
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}

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

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

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