JAL-2656 Java 8 compatible test for gzipped, refactored for unit test

diff --git a/src/jalview/io/FileParse.java b/src/jalview/io/FileParse.java
index 39d8ad4..3726c6b 100755 (executable)
--- 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 (file)
--- 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);
   }
 }