JAL-3174 Merging in some test filename-case fixes

[jalview.git] / test / jalview / ext / htsjdk / TestHtsContigDb.java

diff --git a/test/jalview/ext/htsjdk/TestHtsContigDb.java b/test/jalview/ext/htsjdk/TestHtsContigDb.java
index 9fc5fb9..ad9bf03 100644 (file)
--- a/test/jalview/ext/htsjdk/TestHtsContigDb.java
+++ b/test/jalview/ext/htsjdk/TestHtsContigDb.java
@@ -1,14 +1,39 @@
-/**
+/*
+ * 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.ext.htsjdk;
 
+import static org.testng.Assert.assertEquals;
+import static org.testng.Assert.assertFalse;
+import static org.testng.Assert.assertNotNull;
+import static org.testng.Assert.assertTrue;
+import static org.testng.Assert.fail;
+
 import jalview.datamodel.SequenceI;
 
 import java.io.File;
+import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.StandardCopyOption;
 
-import org.junit.Assert;
-import org.junit.Test;
+import org.testng.annotations.Test;
 
 /**
  * @author jprocter
@@ -16,17 +41,112 @@ import org.junit.Test;
  */
 public class TestHtsContigDb
 {
-  @Test
-  public final void testHTSReferenceSequence() throws Exception
+  @Test(groups = "Functional")
+  public final void testGetSequenceProxy() throws Exception
   {
-    HtsContigDb remmadb = new HtsContigDb("REEMADB", new File(
-            "D:\\Jims\\Jalview\\Reema\\pgmb.fasta"));
+    String pathname = "test/jalview/ext/htsjdk/pgmB.fasta";
+    HtsContigDb db = new HtsContigDb("ADB", new File(pathname));
+
+    assertTrue(db.isValid());
+    assertTrue(db.isIndexed()); // htsjdk opens the .fai file
 
-    Assert.assertTrue(remmadb.isValid());
+    SequenceI sq = db.getSequenceProxy("Deminut");
+    assertNotNull(sq);
+    assertEquals(sq.getLength(), 606);
 
-    SequenceI sq = remmadb.getSequenceProxy("Deminut");
-    Assert.assertNotNull(sq);
-    Assert.assertNotEquals(0, sq.getLength());
+    /*
+     * read a sequence earlier in the file
+     */
+    sq = db.getSequenceProxy("PPL_06716");
+    assertNotNull(sq);
+    assertEquals(sq.getLength(), 602);
+
+    // dict = db.getDictionary(f, truncate))
   }
 
+  /**
+   * Trying to open a .fai file directly results in IllegalArgumentException -
+   * have to provide the unindexed file name instead
+   */
+  @Test(
+    groups = "Functional",
+    expectedExceptions = java.lang.IllegalArgumentException.class)
+  public final void testGetSequenceProxy_indexed()
+  {
+    String pathname = "test/jalview/ext/htsjdk/pgmB.fasta.fai";
+    new HtsContigDb("ADB", new File(pathname));
+    fail("Expected exception opening .fai file");
+  }
+
+  /**
+   * Tests that exercise
+   * <ul>
+   * <li>opening an unindexed fasta file</li>
+   * <li>creating a .fai index</li>
+   * <li>opening the fasta file, now using the index</li>
+   * <li>error on creating index if overwrite not allowed</li>
+   * </ul>
+   * 
+   * @throws IOException
+   */
+  @Test(groups = "Functional")
+  public void testCreateFastaSequenceIndex() throws IOException
+  {
+    File fasta = new File("test/jalview/ext/htsjdk/pgmB.fasta");
+
+    /*
+     * create .fai with no overwrite fails if it exists
+     */
+    try
+    {
+      HtsContigDb.createFastaSequenceIndex(fasta.toPath(), false);
+      fail("Expected exception");
+    } catch (IOException e)
+    {
+      System.out.println(
+              "Caught IOException in testCreateFastaSequenceIndex");
+      e.printStackTrace();
+      // expected
+    }
+
+    /*
+     * create a copy of the .fasta (as a temp file)
+     */
+    File copyFasta = File.createTempFile("copyFasta", ".fasta");
+    copyFasta.deleteOnExit();
+    assertTrue(copyFasta.exists());
+    Files.copy(fasta.toPath(), copyFasta.toPath(),
+            StandardCopyOption.REPLACE_EXISTING);
+
+    /*
+     * open the Fasta file - not indexed, as no .fai file yet exists
+     */
+    HtsContigDb db = new HtsContigDb("ADB", copyFasta);
+    assertTrue(db.isValid());
+    assertFalse(db.isIndexed());
+    db.close();
+
+    /*
+     * create the .fai index, re-open the .fasta file - now indexed
+     */
+    HtsContigDb.createFastaSequenceIndex(copyFasta.toPath(), true);
+    db = new HtsContigDb("ADB", copyFasta);
+    assertTrue(db.isValid());
+    assertTrue(db.isIndexed());
+    db.close();
+  }
+
+  /**
+   * A convenience 'test' that may be run to create a .fai file for any given
+   * fasta file
+   * 
+   * @throws IOException
+   */
+  @Test(enabled = false)
+  public void testCreateIndex() throws IOException
+  {
+
+    File fasta = new File("test/jalview/io/vcf/contigs.fasta");
+    HtsContigDb.createFastaSequenceIndex(fasta.toPath(), true);
+  }
 }