From 2772202abb68d39691efc9064d927505d98f2aae Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Fri, 21 Aug 2020 11:45:26 +0100 Subject: [PATCH] JAL-3675 2.11.1.1 java 8 compatible patch for JAL-3615 from feature/JAL-3615gzipXfam --- src/jalview/io/FileParse.java | 49 +++++++++++++++++++++---------- test/jalview/io/FileIOTester.java | 57 ++++++++++++++++++++++++++++--------- 2 files changed, 78 insertions(+), 28 deletions(-) diff --git a/src/jalview/io/FileParse.java b/src/jalview/io/FileParse.java index f1d79fe..3013c0b 100755 --- a/src/jalview/io/FileParse.java +++ b/src/jalview/io/FileParse.java @@ -24,6 +24,7 @@ import jalview.api.AlignExportSettingI; import jalview.api.AlignViewportI; import jalview.api.AlignmentViewPanel; import jalview.api.FeatureSettingsModelI; +import jalview.bin.Cache; import jalview.util.MessageManager; import java.io.BufferedInputStream; @@ -201,18 +202,41 @@ public class FileParse } return error; } - + /** - * Recognise the 2-byte magic header for gzip streams + * Recognise the 2-byte magic header indicating a gzipped stream * + * see * https://recalll.co/ask/v/topic/java-How-to-check-if-InputStream-is-Gzipped/555aadd62bd27354438b90f6 * - * @param bytes - at least two bytes - * @return + * @param input + * - input stream that supports mark and contains at least two bytes + * + * @return false if mark not supported or no magic header found + * + * @throws IOException */ - private static boolean isGzipStream(byte[] bytes) { - int head = ((int) bytes[0] & 0xff) | ((bytes[1] << 8) & 0xff00); - return (GZIPInputStream.GZIP_MAGIC == head); + public static boolean isGzipStream(InputStream input) throws IOException + { + if (!input.markSupported()) + { + Cache.log.error( + "FileParse.izGzipStream: input stream must support mark/reset"); + return false; + } + input.mark(4); + + // get first 2 bytes or return false + byte[] bytes = new byte[2]; + int read = input.read(bytes); + input.reset(); + if (read != bytes.length) + { + return false; + } + + int header = (bytes[0] & 0xff) | ((bytes[1] << 8) & 0xff00); + return (GZIPInputStream.GZIP_MAGIC == header); } /** @@ -226,16 +250,11 @@ public class FileParse // NB: stackoverflow https://stackoverflow.com/questions/4818468/how-to-check-if-inputstream-is-gzipped // could use a PushBackInputStream rather than a BufferedInputStream - - BufferedInputStream bufinput; + if (!input.markSupported()) { - bufinput= new BufferedInputStream(input,16); - input = bufinput; + input = new BufferedInputStream(input,16); } - input.mark(4); - byte[] bytes=input.readNBytes(2); - input.reset(); - if (bytes.length==2 && isGzipStream(bytes)) { + if (isGzipStream(input)) { return getGzipReader(input); } // return a buffered reader for the stream. diff --git a/test/jalview/io/FileIOTester.java b/test/jalview/io/FileIOTester.java index f6480a6..04d01b0 100644 --- a/test/jalview/io/FileIOTester.java +++ b/test/jalview/io/FileIOTester.java @@ -20,16 +20,23 @@ */ package jalview.io; -import jalview.gui.JvOptionPane; +import static org.testng.Assert.assertFalse; +import static org.testng.Assert.assertTrue; +import java.io.BufferedInputStream; import java.io.File; +import java.io.FileInputStream; import java.io.IOException; +import java.io.InputStream; import org.testng.AssertJUnit; import org.testng.annotations.AfterClass; import org.testng.annotations.BeforeClass; import org.testng.annotations.Test; +import jalview.bin.Cache; +import jalview.gui.JvOptionPane; + /** * @author jimp * @@ -50,6 +57,7 @@ public class FileIOTester @BeforeClass(alwaysRun = true) public static void setUpBeforeClass() throws Exception { + Cache.initLogger(); } /** @@ -88,8 +96,9 @@ public class FileIOTester public void testStarsInFasta1() throws IOException { String uri; - FileParse fp = new FileParse(uri = STARS_FA_FILE1.getAbsoluteFile() - .toString(), DataSourceType.FILE); + FileParse fp = new FileParse( + uri = STARS_FA_FILE1.getAbsoluteFile().toString(), + DataSourceType.FILE); assertValidFormat(FileFormat.Fasta, uri, fp); } @@ -97,8 +106,9 @@ public class FileIOTester public void testStarsInFasta2() throws IOException { String uri; - FileParse fp = new FileParse(uri = STARS_FA_FILE2.getAbsoluteFile() - .toString(), DataSourceType.FILE); + FileParse fp = new FileParse( + uri = STARS_FA_FILE2.getAbsoluteFile().toString(), + DataSourceType.FILE); assertValidFormat(FileFormat.Fasta, uri, fp); } @@ -106,8 +116,9 @@ public class FileIOTester public void testGzipIo() throws IOException { String uri; - FileParse fp = new FileParse(uri = ALIGN_FILE.getAbsoluteFile().toURI() - .toString(), DataSourceType.URL); + FileParse fp = new FileParse( + uri = ALIGN_FILE.getAbsoluteFile().toURI().toString(), + DataSourceType.URL); assertValidFormat(FileFormat.Fasta, uri, fp); } @@ -115,17 +126,36 @@ public class FileIOTester public void testGziplocalFileIO() throws IOException { String filepath; - FileParse fp = new FileParse(filepath = ALIGN_FILE.getAbsoluteFile() - .toString(), DataSourceType.FILE); + FileParse fp = new FileParse( + filepath = ALIGN_FILE.getAbsoluteFile().toString(), + DataSourceType.FILE); assertValidFormat(FileFormat.Fasta, filepath, fp); } @Test(groups = { "Functional" }) + public void testIsGzipInputStream() throws IOException + { + InputStream is = new FileInputStream(ALIGN_FILE); + + /* + * first try fails - FileInputStream does not support mark/reset + */ + assertFalse(FileParse.isGzipStream(is)); + + /* + * wrap in a BufferedInputStream and try again + */ + is = new BufferedInputStream(is, 16); + assertTrue(FileParse.isGzipStream(is)); + } + + @Test(groups = { "Functional" }) public void testNonGzipURLIO() throws IOException { String uri; - FileParse fp = new FileParse(uri = NOTGZALIGN_FILE.getAbsoluteFile() - .toURI().toString(), DataSourceType.URL); + FileParse fp = new FileParse( + uri = NOTGZALIGN_FILE.getAbsoluteFile().toURI().toString(), + DataSourceType.URL); assertValidFormat(FileFormat.Fasta, uri, fp); } @@ -133,8 +163,9 @@ public class FileIOTester public void testNonGziplocalFileIO() throws IOException { String filepath; - FileParse fp = new FileParse(filepath = NOTGZALIGN_FILE - .getAbsoluteFile().toString(), DataSourceType.FILE); + FileParse fp = new FileParse( + filepath = NOTGZALIGN_FILE.getAbsoluteFile().toString(), + DataSourceType.FILE); assertValidFormat(FileFormat.Fasta, filepath, fp); } } -- 1.7.10.2