JAL-1766 additional tests for stub htsjdk wrapper

diff --git a/src/jalview/ext/htsjdk/HtsContigDb.java b/src/jalview/ext/htsjdk/HtsContigDb.java
index 37ce625..729f658 100644 (file)
--- a/src/jalview/ext/htsjdk/HtsContigDb.java
+++ b/src/jalview/ext/htsjdk/HtsContigDb.java
@@ -20,17 +20,13 @@
  */
 package jalview.ext.htsjdk;
 
-import htsjdk.samtools.SAMSequenceDictionary;
-import htsjdk.samtools.SAMSequenceRecord;
-import htsjdk.samtools.reference.ReferenceSequence;
-import htsjdk.samtools.reference.ReferenceSequenceFile;
-import htsjdk.samtools.reference.ReferenceSequenceFileFactory;
-import htsjdk.samtools.util.StringUtil;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceI;
 
 import java.io.File;
+import java.io.IOException;
 import java.math.BigInteger;
+import java.nio.file.Path;
 import java.security.MessageDigest;
 import java.security.NoSuchAlgorithmException;
 import java.util.ArrayList;
@@ -38,6 +34,15 @@ import java.util.HashSet;
 import java.util.List;
 import java.util.Set;
 
+import htsjdk.samtools.SAMException;
+import htsjdk.samtools.SAMSequenceDictionary;
+import htsjdk.samtools.SAMSequenceRecord;
+import htsjdk.samtools.reference.FastaSequenceIndexCreator;
+import htsjdk.samtools.reference.ReferenceSequence;
+import htsjdk.samtools.reference.ReferenceSequenceFile;
+import htsjdk.samtools.reference.ReferenceSequenceFileFactory;
+import htsjdk.samtools.util.StringUtil;
+
 /**
  * a source of sequence data accessed via the HTSJDK
  * 
@@ -46,14 +51,25 @@ import java.util.Set;
  */
 public class HtsContigDb
 {
-
   private String name;
 
   private File dbLocation;
 
   private htsjdk.samtools.reference.ReferenceSequenceFile refFile = null;
 
-  public HtsContigDb(String name, File descriptor) throws Exception
+  public static void createFastaSequenceIndex(Path path, boolean overwrite)
+          throws IOException
+  {
+    try
+    {
+      FastaSequenceIndexCreator.create(path, overwrite);
+    } catch (SAMException e)
+    {
+      throw new IOException(e.getMessage());
+    }
+  }
+
+  public HtsContigDb(String name, File descriptor)
   {
     if (descriptor.isFile())
     {
@@ -63,7 +79,21 @@ public class HtsContigDb
     initSource();
   }
 
-  private void initSource() throws Exception
+  public void close()
+  {
+    if (refFile != null)
+    {
+      try
+      {
+        refFile.close();
+      } catch (IOException e)
+      {
+        // ignore
+      }
+    }
+  }
+
+  private void initSource()
   {
     if (refFile != null)
     {
@@ -142,8 +172,8 @@ public class HtsContigDb
     final ReferenceSequenceFile refSeqFile = ReferenceSequenceFileFactory
             .getReferenceSequenceFile(f, truncate);
     ReferenceSequence refSeq;
-    List<SAMSequenceRecord> ret = new ArrayList<SAMSequenceRecord>();
-    Set<String> sequenceNames = new HashSet<String>();
+    List<SAMSequenceRecord> ret = new ArrayList<>();
+    Set<String> sequenceNames = new HashSet<>();
     for (int numSequences = 0; (refSeq = refSeqFile
             .nextSequence()) != null; ++numSequences)
     {
@@ -220,7 +250,7 @@ public class HtsContigDb
 
   // ///// end of hts bits.
 
-  SequenceI getSequenceProxy(String id)
+  public SequenceI getSequenceProxy(String id)
   {
     if (!isValid())
     {
@@ -230,4 +260,10 @@ public class HtsContigDb
     ReferenceSequence sseq = refFile.getSequence(id);
     return new Sequence(sseq.getName(), new String(sseq.getBases()));
   }
+
+  public boolean isIndexed()
+  {
+    return refFile != null && refFile.isIndexed();
+  }
+
 }

diff --git a/test/jalview/ext/htsjdk/TestHtsContigDb.java b/test/jalview/ext/htsjdk/TestHtsContigDb.java
index 350b599..29303d0 100644 (file)
--- a/test/jalview/ext/htsjdk/TestHtsContigDb.java
+++ b/test/jalview/ext/htsjdk/TestHtsContigDb.java
@@ -20,13 +20,19 @@
  */
 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 jalview.gui.JvOptionPane;
 
 import java.io.File;
+import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.StandardCopyOption;
 
-import org.testng.Assert;
-import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
 
 /**
@@ -35,25 +41,83 @@ import org.testng.annotations.Test;
  */
 public class TestHtsContigDb
 {
+  @Test(groups = "Functional")
+  public final void testGetSequenceProxy() throws Exception
+  {
+    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
+    
+    SequenceI sq = db.getSequenceProxy("Deminut");
+    assertNotNull(sq);
+    assertEquals(sq.getLength(), 606);
 
-  @BeforeClass(alwaysRun = true)
-  public void setUpJvOptionPane()
+    /*
+     * 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()
   {
-    JvOptionPane.setInteractiveMode(false);
-    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+    String pathname = "test/jalview/ext/htsjdk/pgmb.fasta.fai";
+    new HtsContigDb("ADB", new File(pathname));
+    fail("Expected exception opening .fai file");
   }
 
   @Test(groups = "Functional")
-  public final void testHTSReferenceSequence() throws Exception
+  public void testCreateFastaSequenceIndex() throws IOException
   {
-    HtsContigDb remmadb = new HtsContigDb("REEMADB", new File(
-            "test/jalview/ext/htsjdk/pgmb.fasta"));
+    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)
+    {
+      // expected
+    }
 
-    Assert.assertTrue(remmadb.isValid());
+    /*
+     * 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);
 
-    SequenceI sq = remmadb.getSequenceProxy("Deminut");
-    Assert.assertNotNull(sq);
-    Assert.assertNotEquals(0, sq.getLength());
-  }
+    /*
+     * 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();
+  }
 }