Merge commit 'alpha/update_2_12_for_2_11_2_series_merge^2' into HEAD

[jalview.git] / test / jalview / io / FileIOTester.java

diff --git a/test/jalview/io/FileIOTester.java b/test/jalview/io/FileIOTester.java
index f6480a6..e37ae3f 100644 (file)
--- a/test/jalview/io/FileIOTester.java
+++ b/test/jalview/io/FileIOTester.java
@@ -20,16 +20,25 @@
  */
 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.ByteArrayInputStream;
 import java.io.File;
+import java.io.FileInputStream;
 import java.io.IOException;
+import java.io.InputStream;
+import java.io.StringBufferInputStream;
 
 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 +59,7 @@ public class FileIOTester
   @BeforeClass(alwaysRun = true)
   public static void setUpBeforeClass() throws Exception
   {
+    Cache.initLogger();
   }
 
   /**
@@ -88,8 +98,9 @@ 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 +108,9 @@ 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 +118,9 @@ 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 +128,42 @@ 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));
+    
+    /*
+     * check recognition of non-gzipped input
+     */
+    assertFalse(FileParse.isGzipStream(new BufferedInputStream(
+            new ByteArrayInputStream("NOT A GZIP".getBytes()))));    
+  }
+
+  @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 +171,9 @@ 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);
   }
 }