From: Jim Procter <jprocter@issues.jalview.org>
Date: Fri, 21 Aug 2020 10:45:26 +0000 (+0100)
Subject: JAL-3675 2.11.1.1 java 8 compatible patch for JAL-3615 from feature/JAL-3615gzipXfam
X-Git-Tag: Release_2_11_1_1~21^2~2
X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=2772202abb68d39691efc9064d927505d98f2aae

JAL-3675 2.11.1.1 java 8 compatible patch for JAL-3615 from feature/JAL-3615gzipXfam
---

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);
   }
 }