X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FFileIOTester.java;h=b693d516c674c4fe3ba3e2d8f833db5f0e7adffb;hb=cb8e52fbbc5f725e3f7f48c672cdddb0690bd978;hp=4fb2ee630179c384c1cb4a472c7b7906938a5d45;hpb=ee198b3ca3687f18a2ee186f4e7c7330f4ea30f0;p=jalview.git

diff --git a/test/jalview/io/FileIOTester.java b/test/jalview/io/FileIOTester.java
index 4fb2ee6..b693d51 100644
--- a/test/jalview/io/FileIOTester.java
+++ b/test/jalview/io/FileIOTester.java
@@ -20,14 +20,25 @@
  */
 package jalview.io;
 
+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.Console;
+import jalview.gui.JvOptionPane;
+
 /**
  * @author jimp
  * 
@@ -35,12 +46,20 @@ import org.testng.annotations.Test;
 public class FileIOTester
 {
 
+  @BeforeClass(alwaysRun = true)
+  public void setUpJvOptionPane()
+  {
+    JvOptionPane.setInteractiveMode(false);
+    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+  }
+
   /**
    * @throws java.lang.Exception
    */
   @BeforeClass(alwaysRun = true)
   public static void setUpBeforeClass() throws Exception
   {
+    Console.initLogger();
   }
 
   /**
@@ -79,8 +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);
   }
 
@@ -88,8 +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);
   }
 
@@ -97,8 +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);
   }
 
@@ -106,17 +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);
   }
 
@@ -124,8 +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);
   }
 }