From f60987555392a60449a37fe08a0f53003c26937b Mon Sep 17 00:00:00 2001 From: gmungoc Date: Tue, 18 Aug 2020 17:07:21 +0100 Subject: [PATCH] JAL-2656 Java 8 compatible test for gzipped, refactored for unit test --- src/jalview/io/FileParse.java | 83 +++++++++++++++++++++++-------------- test/jalview/io/FileIOTester.java | 57 +++++++++++++++++++------ 2 files changed, 95 insertions(+), 45 deletions(-) diff --git a/src/jalview/io/FileParse.java b/src/jalview/io/FileParse.java index 39d8ad4..3726c6b 100755 --- a/src/jalview/io/FileParse.java +++ b/src/jalview/io/FileParse.java @@ -20,12 +20,6 @@ */ package jalview.io; -import jalview.api.AlignExportSettingsI; -import jalview.api.AlignViewportI; -import jalview.api.AlignmentViewPanel; -import jalview.api.FeatureSettingsModelI; -import jalview.util.MessageManager; - import java.io.BufferedInputStream; import java.io.BufferedReader; import java.io.ByteArrayInputStream; @@ -43,6 +37,12 @@ import java.net.URL; import java.net.URLConnection; import java.util.zip.GZIPInputStream; +import jalview.api.AlignExportSettingsI; +import jalview.api.AlignViewportI; +import jalview.api.AlignmentViewPanel; +import jalview.api.FeatureSettingsModelI; +import jalview.bin.Cache; +import jalview.util.MessageManager; import jalview.util.Platform; /** @@ -210,18 +210,33 @@ public class FileParse } return error; } - + /** * Recognise the 2-byte magic header for gzip streams * * https://recalll.co/ask/v/topic/java-How-to-check-if-InputStream-is-Gzipped/555aadd62bd27354438b90f6 * - * @param bytes - at least two bytes - * @return + * @param bytes + * - at least two bytes + * @return + * @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); + byte[] bytes = { (byte) input.read(), (byte) input.read() }; // input.readNBytes(2); + input.reset(); + if (bytes.length == 2) + { + int header = (bytes[0] & 0xff) | ((bytes[1] << 8) & 0xff00); + return (GZIPInputStream.GZIP_MAGIC == header); + } + return false; } /** @@ -231,27 +246,26 @@ public class FileParse * @param input * @return */ - private BufferedReader checkForGzipStream(InputStream input) throws Exception { - - // NB: stackoverflow https://stackoverflow.com/questions/4818468/how-to-check-if-inputstream-is-gzipped + private BufferedReader checkForGzipStream(InputStream input) + throws Exception + { + // 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; + if (!input.markSupported()) + { + 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. - InputStreamReader isReader= new InputStreamReader(input); - BufferedReader toReadFrom=new BufferedReader(isReader); + InputStreamReader isReader = new InputStreamReader(input); + BufferedReader toReadFrom = new BufferedReader(isReader); return toReadFrom; } + /** * Returns a {@code BufferedReader} which wraps the input stream with a * GZIPInputStream. Throws a {@code ZipException} if a GZIP format error @@ -304,16 +318,21 @@ public class FileParse throw new IOException( "Response status from " + urlStr + " was " + rc); } - } else { - try { - dataIn = checkForGzipStream(_conn.getInputStream()); - dataName=urlStr; + } + else + { + try + { + dataIn = checkForGzipStream(_conn.getInputStream()); + dataName = urlStr; } catch (IOException ex) { - throw new IOException("Failed to handle non-HTTP URI stream",ex); + throw new IOException("Failed to handle non-HTTP URI stream", ex); } catch (Exception ex) { - throw new IOException("Failed to determine type of input stream for given URI",ex); + throw new IOException( + "Failed to determine type of input stream for given URI", + ex); } return; } 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