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

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

diff --git a/test/jalview/io/FileIOTester.java b/test/jalview/io/FileIOTester.java
index 700fd62..04d01b0 100644 (file)
--- a/test/jalview/io/FileIOTester.java
+++ b/test/jalview/io/FileIOTester.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -20,14 +20,23 @@
  */
 package jalview.io;
 
+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
  * 
@@ -35,12 +44,20 @@ 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
   {
+    Cache.initLogger();
   }
 
   /**
@@ -65,66 +82,90 @@ public class FileIOTester
   final static File STARS_FA_FILE2 = new File(
           "test/jalview/io/test_fasta_stars2.fa");
 
-  private void assertValidFormat(String fmt, String src, FileParse fp)
+  private void assertValidFormat(FileFormatI fmt, String src, FileParse fp)
+          throws FileFormatException
   {
     AssertJUnit.assertTrue("Couldn't resolve " + src + " as a valid file",
             fp.isValid());
-    String type = new IdentifyFile().identify(fp);
-    AssertJUnit.assertTrue("Data from '" + src + "' Expected to be '" + fmt
-            + "' identified as '" + type + "'", type.equalsIgnoreCase(fmt));
+    FileFormatI type = new IdentifyFile().identify(fp);
+    AssertJUnit.assertSame("Data from '" + src + "' Expected to be '" + fmt
+            + "' identified as '" + type + "'", type, fmt);
   }
 
   @Test(groups = { "Functional" })
   public void testStarsInFasta1() throws IOException
   {
     String uri;
-    FileParse fp = new FileParse(uri = STARS_FA_FILE1.getAbsoluteFile()
-            .toString(), AppletFormatAdapter.FILE);
-    assertValidFormat("FASTA", uri, fp);
+    FileParse fp = new FileParse(
+            uri = STARS_FA_FILE1.getAbsoluteFile().toString(),
+            DataSourceType.FILE);
+    assertValidFormat(FileFormat.Fasta, uri, fp);
   }
 
   @Test(groups = { "Functional" })
   public void testStarsInFasta2() throws IOException
   {
     String uri;
-    FileParse fp = new FileParse(uri = STARS_FA_FILE2.getAbsoluteFile()
-            .toString(), AppletFormatAdapter.FILE);
-    assertValidFormat("FASTA", uri, fp);
+    FileParse fp = new FileParse(
+            uri = STARS_FA_FILE2.getAbsoluteFile().toString(),
+            DataSourceType.FILE);
+    assertValidFormat(FileFormat.Fasta, uri, fp);
   }
 
   @Test(groups = { "Functional" })
   public void testGzipIo() throws IOException
   {
     String uri;
-    FileParse fp = new FileParse(uri = ALIGN_FILE.getAbsoluteFile().toURI()
-            .toString(), AppletFormatAdapter.URL);
-    assertValidFormat("FASTA", uri, fp);
+    FileParse fp = new FileParse(
+            uri = ALIGN_FILE.getAbsoluteFile().toURI().toString(),
+            DataSourceType.URL);
+    assertValidFormat(FileFormat.Fasta, uri, fp);
   }
 
   @Test(groups = { "Functional" })
   public void testGziplocalFileIO() throws IOException
   {
     String filepath;
-    FileParse fp = new FileParse(filepath = ALIGN_FILE.getAbsoluteFile()
-            .toString(), AppletFormatAdapter.FILE);
-    assertValidFormat("FASTA", filepath, fp);
+    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(), AppletFormatAdapter.URL);
-    assertValidFormat("FASTA", uri, fp);
+    FileParse fp = new FileParse(
+            uri = NOTGZALIGN_FILE.getAbsoluteFile().toURI().toString(),
+            DataSourceType.URL);
+    assertValidFormat(FileFormat.Fasta, uri, fp);
   }
 
   @Test(groups = { "Functional" })
   public void testNonGziplocalFileIO() throws IOException
   {
     String filepath;
-    FileParse fp = new FileParse(filepath = NOTGZALIGN_FILE
-            .getAbsoluteFile().toString(), AppletFormatAdapter.FILE);
-    assertValidFormat("FASTA", filepath, fp);
+    FileParse fp = new FileParse(
+            filepath = NOTGZALIGN_FILE.getAbsoluteFile().toString(),
+            DataSourceType.FILE);
+    assertValidFormat(FileFormat.Fasta, filepath, fp);
   }
 }