Java tutorial
/* * Copyright (c) 2012 The Broad Institute * * Permission is hereby granted, free of charge, to any person * obtaining a copy of this software and associated documentation * files (the "Software"), to deal in the Software without * restriction, including without limitation the rights to use, * copy, modify, merge, publish, distribute, sublicense, and/or sell * copies of the Software, and to permit persons to whom the * Software is furnished to do so, subject to the following * conditions: * * The above copyright notice and this permission notice shall be * included in all copies or substantial portions of the Software. * * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR * THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ package org.broadinstitute.sting.utils.io; import org.apache.commons.io.FileUtils; import org.broadinstitute.sting.BaseTest; import java.io.File; import java.io.FileInputStream; import java.io.FileOutputStream; import java.io.IOException; import java.util.Arrays; import java.util.List; import java.util.Random; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.UserException; import org.testng.Assert; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; public class IOUtilsUnitTest extends BaseTest { @Test public void testGoodTempDir() { IOUtils.checkTempDir(new File("/tmp/queue")); } @Test(expectedExceptions = UserException.BadTmpDir.class) public void testBadTempDir() { IOUtils.checkTempDir(new File("/tmp")); } @Test public void testAbsoluteSubDir() { File subDir = IOUtils.absolute(new File("."), new File("/path/to/file")); Assert.assertEquals(subDir, new File("/path/to/file")); subDir = IOUtils.absolute(new File("/different/path"), new File("/path/to/file")); Assert.assertEquals(subDir, new File("/path/to/file")); subDir = IOUtils.absolute(new File("/different/path"), new File(".")); Assert.assertEquals(subDir, new File("/different/path")); } @Test public void testRelativeSubDir() throws IOException { File subDir = IOUtils.absolute(new File("."), new File("path/to/file")); Assert.assertEquals(subDir.getCanonicalFile(), new File("path/to/file").getCanonicalFile()); subDir = IOUtils.absolute(new File("/different/path"), new File("path/to/file")); Assert.assertEquals(subDir, new File("/different/path/path/to/file")); } @Test public void testDottedSubDir() throws IOException { File subDir = IOUtils.absolute(new File("."), new File("path/../to/file")); Assert.assertEquals(subDir.getCanonicalFile(), new File("path/../to/./file").getCanonicalFile()); subDir = IOUtils.absolute(new File("."), new File("/path/../to/file")); Assert.assertEquals(subDir, new File("/path/../to/file")); subDir = IOUtils.absolute(new File("/different/../path"), new File("path/to/file")); Assert.assertEquals(subDir, new File("/different/../path/path/to/file")); subDir = IOUtils.absolute(new File("/different/./path"), new File("/path/../to/file")); Assert.assertEquals(subDir, new File("/path/../to/file")); } @Test public void testTempDir() { File tempDir = IOUtils.tempDir("Q-Unit-Test", "", new File("queueTempDirToDelete")); Assert.assertTrue(tempDir.exists()); Assert.assertFalse(tempDir.isFile()); Assert.assertTrue(tempDir.isDirectory()); boolean deleted = IOUtils.tryDelete(tempDir); Assert.assertTrue(deleted); Assert.assertFalse(tempDir.exists()); } @Test public void testDirLevel() { File dir = IOUtils.dirLevel(new File("/path/to/directory"), 1); Assert.assertEquals(dir, new File("/path")); dir = IOUtils.dirLevel(new File("/path/to/directory"), 2); Assert.assertEquals(dir, new File("/path/to")); dir = IOUtils.dirLevel(new File("/path/to/directory"), 3); Assert.assertEquals(dir, new File("/path/to/directory")); dir = IOUtils.dirLevel(new File("/path/to/directory"), 4); Assert.assertEquals(dir, new File("/path/to/directory")); } @Test public void testAbsolute() { File dir = IOUtils.absolute(new File("/path/./to/./directory/.")); Assert.assertEquals(dir, new File("/path/to/directory")); dir = IOUtils.absolute(new File("/")); Assert.assertEquals(dir, new File("/")); dir = IOUtils.absolute(new File("/.")); Assert.assertEquals(dir, new File("/")); dir = IOUtils.absolute(new File("/././.")); Assert.assertEquals(dir, new File("/")); dir = IOUtils.absolute(new File("/./directory/.")); Assert.assertEquals(dir, new File("/directory")); dir = IOUtils.absolute(new File("/./directory/./")); Assert.assertEquals(dir, new File("/directory")); dir = IOUtils.absolute(new File("/./directory./")); Assert.assertEquals(dir, new File("/directory.")); dir = IOUtils.absolute(new File("/./.directory/")); Assert.assertEquals(dir, new File("/.directory")); } @Test public void testTail() throws IOException { List<String> lines = Arrays.asList("chr18_random 4262 3154410390 50 51", "chr19_random 301858 3154414752 50 51", "chr21_random 1679693 3154722662 50 51", "chr22_random 257318 3156435963 50 51", "chrX_random 1719168 3156698441 50 51"); List<String> tail = IOUtils.tail(new File(BaseTest.hg18Reference + ".fai"), 5); Assert.assertEquals(tail.size(), 5); for (int i = 0; i < 5; i++) Assert.assertEquals(tail.get(i), lines.get(i)); } @Test public void testWriteSystemFile() throws IOException { File temp = createTempFile("temp.", ".properties"); try { IOUtils.writeResource(new Resource("StingText.properties", null), temp); } finally { FileUtils.deleteQuietly(temp); } } @Test public void testWriteSystemTempFile() throws IOException { File temp = IOUtils.writeTempResource(new Resource("StingText.properties", null)); try { Assert.assertTrue(temp.getName().startsWith("StingText"), "File does not start with 'StingText.': " + temp); Assert.assertTrue(temp.getName().endsWith(".properties"), "File does not end with '.properties': " + temp); } finally { FileUtils.deleteQuietly(temp); } } @Test(expectedExceptions = IllegalArgumentException.class) public void testMissingSystemFile() throws IOException { File temp = createTempFile("temp.", ".properties"); try { IOUtils.writeResource(new Resource("MissingStingText.properties", null), temp); } finally { FileUtils.deleteQuietly(temp); } } @Test public void testWriteRelativeFile() throws IOException { File temp = createTempFile("temp.", ".properties"); try { IOUtils.writeResource(new Resource("/StingText.properties", IOUtils.class), temp); } finally { FileUtils.deleteQuietly(temp); } } @Test public void testWriteRelativeTempFile() throws IOException { File temp = IOUtils.writeTempResource(new Resource("/StingText.properties", IOUtils.class)); try { Assert.assertTrue(temp.getName().startsWith("StingText"), "File does not start with 'StingText.': " + temp); Assert.assertTrue(temp.getName().endsWith(".properties"), "File does not end with '.properties': " + temp); } finally { FileUtils.deleteQuietly(temp); } } @Test(expectedExceptions = IllegalArgumentException.class) public void testMissingRelativeFile() throws IOException { File temp = createTempFile("temp.", ".properties"); try { // Looking for /org/broadinstitute/sting/utils/file/StingText.properties IOUtils.writeResource(new Resource("StingText.properties", IOUtils.class), temp); } finally { FileUtils.deleteQuietly(temp); } } @Test public void testResourceProperties() { Resource resource = new Resource("foo", Resource.class); Assert.assertEquals(resource.getPath(), "foo"); Assert.assertEquals(resource.getRelativeClass(), Resource.class); } @Test public void testIsSpecialFile() { Assert.assertTrue(IOUtils.isSpecialFile(new File("/dev"))); Assert.assertTrue(IOUtils.isSpecialFile(new File("/dev/null"))); Assert.assertTrue(IOUtils.isSpecialFile(new File("/dev/full"))); Assert.assertTrue(IOUtils.isSpecialFile(new File("/dev/stdout"))); Assert.assertTrue(IOUtils.isSpecialFile(new File("/dev/stderr"))); Assert.assertFalse(IOUtils.isSpecialFile(null)); Assert.assertFalse(IOUtils.isSpecialFile(new File("/home/user/my.file"))); Assert.assertFalse(IOUtils.isSpecialFile(new File("/devfake/null"))); } @DataProvider(name = "ByteArrayIOTestData") public Object[][] byteArrayIOTestDataProvider() { return new Object[][] { // file size, read buffer size { 0, 4096 }, { 1, 4096 }, { 2000, 4096 }, { 4095, 4096 }, { 4096, 4096 }, { 4097, 4096 }, { 6000, 4096 }, { 8191, 4096 }, { 8192, 4096 }, { 8193, 4096 }, { 10000, 4096 } }; } @Test(dataProvider = "ByteArrayIOTestData") public void testWriteThenReadFileIntoByteArray(int fileSize, int readBufferSize) throws Exception { File tempFile = createTempFile( String.format("testWriteThenReadFileIntoByteArray_%d_%d", fileSize, readBufferSize), "tmp"); byte[] dataWritten = getDeterministicRandomData(fileSize); IOUtils.writeByteArrayToFile(dataWritten, tempFile); byte[] dataRead = IOUtils.readFileIntoByteArray(tempFile, readBufferSize); Assert.assertEquals(dataRead.length, dataWritten.length); Assert.assertTrue(Arrays.equals(dataRead, dataWritten)); } @Test(dataProvider = "ByteArrayIOTestData") public void testWriteThenReadStreamIntoByteArray(int fileSize, int readBufferSize) throws Exception { File tempFile = createTempFile( String.format("testWriteThenReadStreamIntoByteArray_%d_%d", fileSize, readBufferSize), "tmp"); byte[] dataWritten = getDeterministicRandomData(fileSize); IOUtils.writeByteArrayToStream(dataWritten, new FileOutputStream(tempFile)); byte[] dataRead = IOUtils.readStreamIntoByteArray(new FileInputStream(tempFile), readBufferSize); Assert.assertEquals(dataRead.length, dataWritten.length); Assert.assertTrue(Arrays.equals(dataRead, dataWritten)); } @Test(expectedExceptions = UserException.CouldNotReadInputFile.class) public void testReadNonExistentFileIntoByteArray() { File nonExistentFile = new File("djfhsdkjghdfk"); Assert.assertFalse(nonExistentFile.exists()); IOUtils.readFileIntoByteArray(nonExistentFile); } @Test(expectedExceptions = ReviewedStingException.class) public void testReadNullStreamIntoByteArray() { IOUtils.readStreamIntoByteArray(null); } @Test(expectedExceptions = ReviewedStingException.class) public void testReadStreamIntoByteArrayInvalidBufferSize() throws Exception { IOUtils.readStreamIntoByteArray( new FileInputStream(createTempFile("testReadStreamIntoByteArrayInvalidBufferSize", "tmp")), -1); } @Test(expectedExceptions = UserException.CouldNotCreateOutputFile.class) public void testWriteByteArrayToUncreatableFile() { IOUtils.writeByteArrayToFile(new byte[] { 0 }, new File("/dev/foo/bar")); } @Test(expectedExceptions = ReviewedStingException.class) public void testWriteNullByteArrayToFile() { IOUtils.writeByteArrayToFile(null, createTempFile("testWriteNullByteArrayToFile", "tmp")); } @Test(expectedExceptions = ReviewedStingException.class) public void testWriteByteArrayToNullStream() { IOUtils.writeByteArrayToStream(new byte[] { 0 }, null); } private byte[] getDeterministicRandomData(int size) { GenomeAnalysisEngine.resetRandomGenerator(); Random rand = GenomeAnalysisEngine.getRandomGenerator(); byte[] randomData = new byte[size]; rand.nextBytes(randomData); return randomData; } }