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 62ce958..04d01b0 100644 (file)
--- a/test/jalview/io/FileIOTester.java
+++ b/test/jalview/io/FileIOTester.java
@@ -1,49 +1,171 @@
-/**
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
  * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.io;
 
-import static org.junit.Assert.*;
+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.junit.AfterClass;
-import org.junit.BeforeClass;
-import org.junit.Test;
+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
- *
+ * 
  */
 public class FileIOTester
 {
 
+  @BeforeClass(alwaysRun = true)
+  public void setUpJvOptionPane()
+  {
+    JvOptionPane.setInteractiveMode(false);
+    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+  }
+
   /**
    * @throws java.lang.Exception
    */
-  @BeforeClass
+  @BeforeClass(alwaysRun = true)
   public static void setUpBeforeClass() throws Exception
   {
+    Cache.initLogger();
   }
 
   /**
    * @throws java.lang.Exception
    */
-  @AfterClass
+  @AfterClass(alwaysRun = true)
   public static void tearDownAfterClass() throws Exception
   {
   }
-final static File ALIGN_FILE = new File("test/jalview/io/test_gz_fasta.gz");
 
-  @Test
+  // TODO: make a better/more comprehensive test harness for identify/io
+
+  final static File ALIGN_FILE = new File(
+          "test/jalview/io/test_gz_fasta.gz");
+
+  final static File NOTGZALIGN_FILE = new File(
+          "test/jalview/io/test_gz_fasta_notgz.gz");
+
+  final static File STARS_FA_FILE1 = new File(
+          "test/jalview/io/test_fasta_stars.fa");
+
+  final static File STARS_FA_FILE2 = new File(
+          "test/jalview/io/test_fasta_stars2.fa");
+
+  private void assertValidFormat(FileFormatI fmt, String src, FileParse fp)
+          throws FileFormatException
+  {
+    AssertJUnit.assertTrue("Couldn't resolve " + src + " as a valid file",
+            fp.isValid());
+    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(),
+            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(),
+            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(),
+            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(),
+            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=ALIGN_FILE.getAbsoluteFile().toURI().toString(),AppletFormatAdapter.URL);
-    assertTrue("Couldn't resolve "+uri+" as a valid file",fp.isValid());
-    String type = new IdentifyFile().Identify(fp);
-    assertTrue("Gzipped data from '"+uri+"' identified as '"+type+"'",type.equalsIgnoreCase("FASTA"));
+    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(),
+            DataSourceType.FILE);
+    assertValidFormat(FileFormat.Fasta, filepath, fp);
+  }
 }