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gab1onectrueden
gab1one
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ctrueden
committedNov 12, 2021
Add BZip2 support (Ported from SCIFIO)
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Diff for: ‎src/main/java/org/scijava/io/handle/BZip2Handle.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.handle;
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import java.io.IOException;
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import org.scijava.io.handle.bzip2.CBZip2InputStream;
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import org.scijava.io.location.AbstractCompressedHandle;
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import org.scijava.io.location.BZip2Location;
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import org.scijava.plugin.Plugin;
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/**
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* {@link DataHandle} for a {@link BZip2Location}.
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*
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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 BZip2Handle extends AbstractCompressedHandle<BZip2Location> {
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@Override
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protected void initInputStream() throws IOException {
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int skipped = 0;
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// ensure 2 bytes are skipped
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while (skipped < 2) {
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skipped += raw().skip(2l - skipped);
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}
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inputStream = new CBZip2InputStream(raw(), log());
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}
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@Override
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public Class<BZip2Location> getType() {
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return BZip2Location.class;
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}
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}

Diff for: ‎src/main/java/org/scijava/io/handle/bzip2/CBZip2InputStream.java

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Diff for: ‎src/main/java/org/scijava/io/handle/bzip2/CRC.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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/*
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* Copyright 2001-2002,2004 The Apache Software Foundation
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*
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* Licensed under the Apache License, Version 2.0 (the "License");
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* you may not use this file except in compliance with the License.
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* You may obtain a copy of the License at
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*
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* http://www.apache.org/licenses/LICENSE-2.0
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*
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* Unless required by applicable law or agreed to in writing, software
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* distributed under the License is distributed on an "AS IS" BASIS,
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* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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* See the License for the specific language governing permissions and
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* limitations under the License.
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*/
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/*
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* This package is based on the work done by Keiron Liddle, Aftex Software
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* <keiron@aftexsw.com> to whom the Ant project is very grateful for his
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* great code.
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*/
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package org.scijava.io.handle.bzip2;
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/** Holds and calculates a CRC for verifying data integrity. */
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public class CRC {
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// -- Constants --
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public static final int[] CRC_32_TABLE = { 0x00000000, 0x04c11db7, 0x09823b6e,
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0x0d4326d9, 0x130476dc, 0x17c56b6b, 0x1a864db2, 0x1e475005, 0x2608edb8,
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0x22c9f00f, 0x2f8ad6d6, 0x2b4bcb61, 0x350c9b64, 0x31cd86d3, 0x3c8ea00a,
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0x384fbdbd, 0x4c11db70, 0x48d0c6c7, 0x4593e01e, 0x4152fda9, 0x5f15adac,
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0x5bd4b01b, 0x569796c2, 0x52568b75, 0x6a1936c8, 0x6ed82b7f, 0x639b0da6,
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0x675a1011, 0x791d4014, 0x7ddc5da3, 0x709f7b7a, 0x745e66cd, 0x9823b6e0,
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0x9ce2ab57, 0x91a18d8e, 0x95609039, 0x8b27c03c, 0x8fe6dd8b, 0x82a5fb52,
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0x8664e6e5, 0xbe2b5b58, 0xbaea46ef, 0xb7a96036, 0xb3687d81, 0xad2f2d84,
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0xa9ee3033, 0xa4ad16ea, 0xa06c0b5d, 0xd4326d90, 0xd0f37027, 0xddb056fe,
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0xd9714b49, 0xc7361b4c, 0xc3f706fb, 0xceb42022, 0xca753d95, 0xf23a8028,
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0xf6fb9d9f, 0xfbb8bb46, 0xff79a6f1, 0xe13ef6f4, 0xe5ffeb43, 0xe8bccd9a,
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0xec7dd02d, 0x34867077, 0x30476dc0, 0x3d044b19, 0x39c556ae, 0x278206ab,
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0x23431b1c, 0x2e003dc5, 0x2ac12072, 0x128e9dcf, 0x164f8078, 0x1b0ca6a1,
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0x1fcdbb16, 0x018aeb13, 0x054bf6a4, 0x0808d07d, 0x0cc9cdca, 0x7897ab07,
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0x7c56b6b0, 0x71159069, 0x75d48dde, 0x6b93dddb, 0x6f52c06c, 0x6211e6b5,
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0x66d0fb02, 0x5e9f46bf, 0x5a5e5b08, 0x571d7dd1, 0x53dc6066, 0x4d9b3063,
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0x495a2dd4, 0x44190b0d, 0x40d816ba, 0xaca5c697, 0xa864db20, 0xa527fdf9,
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0xa1e6e04e, 0xbfa1b04b, 0xbb60adfc, 0xb6238b25, 0xb2e29692, 0x8aad2b2f,
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0x8e6c3698, 0x832f1041, 0x87ee0df6, 0x99a95df3, 0x9d684044, 0x902b669d,
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0x94ea7b2a, 0xe0b41de7, 0xe4750050, 0xe9362689, 0xedf73b3e, 0xf3b06b3b,
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0xf771768c, 0xfa325055, 0xfef34de2, 0xc6bcf05f, 0xc27dede8, 0xcf3ecb31,
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0xcbffd686, 0xd5b88683, 0xd1799b34, 0xdc3abded, 0xd8fba05a, 0x690ce0ee,
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0x6dcdfd59, 0x608edb80, 0x644fc637, 0x7a089632, 0x7ec98b85, 0x738aad5c,
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0x774bb0eb, 0x4f040d56, 0x4bc510e1, 0x46863638, 0x42472b8f, 0x5c007b8a,
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0x58c1663d, 0x558240e4, 0x51435d53, 0x251d3b9e, 0x21dc2629, 0x2c9f00f0,
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0x285e1d47, 0x36194d42, 0x32d850f5, 0x3f9b762c, 0x3b5a6b9b, 0x0315d626,
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0x07d4cb91, 0x0a97ed48, 0x0e56f0ff, 0x1011a0fa, 0x14d0bd4d, 0x19939b94,
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0x1d528623, 0xf12f560e, 0xf5ee4bb9, 0xf8ad6d60, 0xfc6c70d7, 0xe22b20d2,
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0xe6ea3d65, 0xeba91bbc, 0xef68060b, 0xd727bbb6, 0xd3e6a601, 0xdea580d8,
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0xda649d6f, 0xc423cd6a, 0xc0e2d0dd, 0xcda1f604, 0xc960ebb3, 0xbd3e8d7e,
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0xb9ff90c9, 0xb4bcb610, 0xb07daba7, 0xae3afba2, 0xaafbe615, 0xa7b8c0cc,
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0xa379dd7b, 0x9b3660c6, 0x9ff77d71, 0x92b45ba8, 0x9675461f, 0x8832161a,
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0x8cf30bad, 0x81b02d74, 0x857130c3, 0x5d8a9099, 0x594b8d2e, 0x5408abf7,
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0x50c9b640, 0x4e8ee645, 0x4a4ffbf2, 0x470cdd2b, 0x43cdc09c, 0x7b827d21,
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0x7f436096, 0x7200464f, 0x76c15bf8, 0x68860bfd, 0x6c47164a, 0x61043093,
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0x65c52d24, 0x119b4be9, 0x155a565e, 0x18197087, 0x1cd86d30, 0x029f3d35,
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0x065e2082, 0x0b1d065b, 0x0fdc1bec, 0x3793a651, 0x3352bbe6, 0x3e119d3f,
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0x3ad08088, 0x2497d08d, 0x2056cd3a, 0x2d15ebe3, 0x29d4f654, 0xc5a92679,
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0xc1683bce, 0xcc2b1d17, 0xc8ea00a0, 0xd6ad50a5, 0xd26c4d12, 0xdf2f6bcb,
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0xdbee767c, 0xe3a1cbc1, 0xe760d676, 0xea23f0af, 0xeee2ed18, 0xf0a5bd1d,
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0xf464a0aa, 0xf9278673, 0xfde69bc4, 0x89b8fd09, 0x8d79e0be, 0x803ac667,
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0x84fbdbd0, 0x9abc8bd5, 0x9e7d9662, 0x933eb0bb, 0x97ffad0c, 0xafb010b1,
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0xab710d06, 0xa6322bdf, 0xa2f33668, 0xbcb4666d, 0xb8757bda, 0xb5365d03,
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0xb1f740b4 };
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// -- Fields --
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private int globalCrc;
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// -- Constructor --
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public CRC() {
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initialiseCRC();
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}
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// -- CRC API methods --
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public void initialiseCRC() {
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globalCrc = 0xffffffff;
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}
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public int getFinalCRC() {
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return ~globalCrc;
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}
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public int getGlobalCRC() {
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return globalCrc;
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}
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public void setGlobalCRC(final int newCrc) {
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globalCrc = newCrc;
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}
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public void updateCRC(final int inCh) {
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int temp = (globalCrc >> 24) ^ inCh;
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if (temp < 0) {
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temp = 256 + temp;
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}
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globalCrc = (globalCrc << 8) ^ CRC.CRC_32_TABLE[temp];
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}
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}

Diff for: ‎src/main/java/org/scijava/io/location/BZip2Location.java

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package org.scijava.io.location;
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import org.scijava.io.handle.BZip2Handle;
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import org.scijava.io.handle.DataHandle;
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/**
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* {@link Location} backed by a {@link DataHandle} that is BZip2 compressed.
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*
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* @author Gabriel Einsdorf
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* @see BZip2Handle
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*/
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public class BZip2Location extends AbstractHigherOrderLocation {
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/**
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* Creates a {@link BZip2Location} wrapping the given location
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*
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* @param location the location to operate on
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*/
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public BZip2Location(final Location location) {
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super(location);
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}
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}

Diff for: ‎src/test/java/org/scijava/io/handle/BZip2HandleTest.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
10+
* 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.
14+
* 2. Redistributions in binary form must reproduce the above copyright notice,
15+
* this list of conditions and the following disclaimer in the documentation
16+
* 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"
19+
* AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
20+
* IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
21+
* 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
23+
* CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
24+
* SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
25+
* INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
26+
* CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
27+
* ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
28+
* POSSIBILITY OF SUCH DAMAGE.
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* #L%
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*/
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package org.scijava.io.handle;
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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 org.junit.Ignore;
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import org.junit.Test;
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import org.scijava.io.handle.DataHandle;
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import org.scijava.io.location.BZip2Location;
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import org.scijava.io.location.FileLocation;
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import org.scijava.io.location.Location;
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/**
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* Tests {@link BZip2Handle}.
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*
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* @author Gabriel Einsdorf
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*/
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public class BZip2HandleTest extends DataHandleTest {
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@Override
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public Class<? extends DataHandle<?>> getExpectedHandleType() {
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return BZip2Handle.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");
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tmpFile.deleteOnExit();
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try (FileOutputStream out = new FileOutputStream(tmpFile)) {
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populateData(out);
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}
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final Runtime rt = Runtime.getRuntime();
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final Process p = rt.exec(new String[] { "bzip2", tmpFile
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.getAbsolutePath() });
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try {
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p.waitFor();
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}
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catch (final InterruptedException e) {
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throw new RuntimeException(e);
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}
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final File bzip2File = new File(tmpFile.getAbsolutePath() + ".bz2");
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bzip2File.deleteOnExit();
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return new BZip2Location(new FileLocation(bzip2File));
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}
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@Test
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@Override
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public void testWriting() throws IOException {
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// no Op
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}
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@Override
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@Test
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public void testReading() throws IOException {
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try (final DataHandle<? extends Location> handle = createHandle()) {
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checkBasicReadMethods(handle, false);
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checkEndiannessReading(handle);
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}
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}
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}

Diff for: ‎src/test/java/org/scijava/io/location/BZip2LocationTest.java

+63
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/*
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* #%L
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* SciJava Common shared library for SciJava software.
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* %%
5+
* Copyright (C) 2009 - 2017 Board of Regents of the University of
6+
* Wisconsin-Madison, Broad Institute of MIT and Harvard, and Max Planck
7+
* Institute of Molecular Cell Biology and Genetics.
8+
* %%
9+
* Redistribution and use in source and binary forms, with or without
10+
* modification, are permitted provided that the following conditions are met:
11+
*
12+
* 1. Redistributions of source code must retain the above copyright notice,
13+
* this list of conditions and the following disclaimer.
14+
* 2. Redistributions in binary form must reproduce the above copyright notice,
15+
* this list of conditions and the following disclaimer in the documentation
16+
* and/or other materials provided with the distribution.
17+
*
18+
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
19+
* AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
20+
* IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
21+
* ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
22+
* LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
23+
* CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
24+
* SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
25+
* INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
26+
* CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
27+
* ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
28+
* POSSIBILITY OF SUCH DAMAGE.
29+
* #L%
30+
*/
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package org.scijava.io.location;
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import static org.junit.Assert.assertEquals;
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import java.io.IOException;
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import org.junit.Test;
39+
import org.scijava.io.location.FileLocation;
40+
import org.scijava.io.location.Location;
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/**
43+
* Tests {@link BZip2Location}.
44+
*
45+
* @author Gabriel Einsdorf
46+
*/
47+
public class BZip2LocationTest {
48+
49+
/**
50+
* Tests {@link BZip2Location#BZip2Location(Location)}.
51+
*
52+
* @throws IOException
53+
*/
54+
@Test
55+
public void testFile() throws IOException {
56+
final String path = "/not/actually/a/real-file";
57+
final FileLocation loc = new FileLocation(path);
58+
BZip2Location zLoc = new BZip2Location(loc);
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assertEquals(zLoc.getBaseLocation(), loc);
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}
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}

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