X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fws%2Fseqfetcher%2FDbRefFetcherTest.java;h=0a565bda2ef3c92c62d67b0587ddd6bf9a88c5cd;hb=37de9310bec3501cbc6381e0c3dcb282fcaad812;hp=8a18494c9ea0a2db6e6a16f335dd3a5d8b6c7de1;hpb=ab43013b7e357b84b4abade0dba949668dfb2a0e;p=jalview.git

diff --git a/test/jalview/ws/seqfetcher/DbRefFetcherTest.java b/test/jalview/ws/seqfetcher/DbRefFetcherTest.java
index 8a18494..0a565bd 100644
--- a/test/jalview/ws/seqfetcher/DbRefFetcherTest.java
+++ b/test/jalview/ws/seqfetcher/DbRefFetcherTest.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
- * Copyright (C) 2014 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.
  * 
@@ -20,22 +20,29 @@
  */
 package jalview.ws.seqfetcher;
 
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertTrue;
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertNotNull;
+import static org.testng.AssertJUnit.assertTrue;
+
 import jalview.analysis.CrossRef;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.DBRefSource;
+import jalview.datamodel.FeatureProperties;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
 import jalview.util.DBRefUtils;
 import jalview.ws.SequenceFetcher;
+import jalview.ws.dbsources.Pdb;
+import jalview.ws.dbsources.Uniprot;
 
 import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.List;
 
-import org.junit.AfterClass;
-import org.junit.BeforeClass;
-import org.junit.Test;
+import org.testng.annotations.AfterClass;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
 
 /**
  * @author jimp
@@ -47,73 +54,143 @@ public class DbRefFetcherTest
   /**
    * @throws java.lang.Exception
    */
-  @BeforeClass
+  @BeforeClass(alwaysRun = true)
   public static void setUpBeforeClass() throws Exception
   {
+    jalview.bin.Cache.initLogger();
   }
 
   /**
    * @throws java.lang.Exception
    */
-  @AfterClass
+  @AfterClass(alwaysRun = true)
   public static void tearDownAfterClass() throws Exception
   {
   }
 
-  @Test
+  /**
+   * Tests that standard protein database sources include Uniprot (as the first)
+   * and also PDB. (Additional sources are dependent on availability of DAS
+   * services.)
+   */
+  @Test(groups = { "Functional" })
   public void testStandardProtDbs()
   {
-    String[] defdb = DBRefSource.PROTEINDBS;
+    List<String> defdb = new ArrayList<String>();
+    defdb.addAll(Arrays.asList(DBRefSource.PROTEINDBS));
+    defdb.add(DBRefSource.PDB);
     List<DbSourceProxy> srces = new ArrayList<DbSourceProxy>();
+    SequenceFetcher sfetcher = new SequenceFetcher();
+    boolean pdbFound = false;
+
     for (String ddb : defdb)
     {
-      SequenceFetcher sfetcher = new SequenceFetcher();
       List<DbSourceProxy> srcesfordb = sfetcher.getSourceProxy(ddb);
 
       if (srcesfordb != null)
       {
+        // TODO is this right? get duplicate entries
         srces.addAll(srcesfordb);
       }
     }
-    DbSourceProxy uniprot = null;
+
     int i = 0;
-    // append the selected sequence sources to the default dbs
+    int uniprotPos = -1;
     for (DbSourceProxy s : srces)
     {
-      if (s.getDbSource().equalsIgnoreCase(DBRefSource.UNIPROT))
+      if (s instanceof Uniprot && uniprotPos == -1)
       {
-        i++;
+        uniprotPos = i;
       }
-
-      if (s instanceof jalview.ws.dbsources.Uniprot)
+      if (s instanceof Pdb)
       {
-        uniprot = s;
-        break;
+        pdbFound = true;
       }
+      i++;
     }
 
     assertTrue("Failed to find Uniprot source as first source amongst "
-            + srces.size() + " sources (source was at position " + i + ")",
-            uniprot != null && i < 2);
+            + srces.size() + " sources (source was at position "
+            + uniprotPos + ")", uniprotPos == 0);
+    assertTrue("Failed to find PDB source amongst " + srces.size()
+            + " sources", pdbFound);
   }
 
-  @Test
+  /**
+   * Tests retrieval of one entry from EMBL. Test is dependent on availability
+   * of network and the EMBL service.
+   * 
+   * @throws Exception
+   */
+  @Test(groups = { "External" })
   public void testEmblUniprotProductRecovery() throws Exception
   {
-    String retrievalId = "CAA23748"; // "V00488";
-    DbSourceProxy embl = new SequenceFetcher().getSourceProxy(DBRefSource.EMBL).get(0);
-    assertNotNull("Couldn't find the EMBL retrieval client",embl);
+    String retrievalId = "V00488";
+    DbSourceProxy embl = new SequenceFetcher().getSourceProxy(
+            DBRefSource.EMBL).get(0);
+    assertNotNull("Couldn't find the EMBL retrieval client", embl);
+    verifyProteinNucleotideXref(retrievalId, embl);
+  }
+
+  /**
+   * Tests retrieval of one entry from EMBLCDS. Test is dependent on
+   * availability of network and the EMBLCDS service.
+   * 
+   * @throws Exception
+   */
+  @Test(groups = { "External" })
+  public void testEmblCDSUniprotProductRecovery() throws Exception
+  {
+    String retrievalId = "AAH29712";
+    DbSourceProxy embl = new SequenceFetcher().getSourceProxy(
+            DBRefSource.EMBLCDS).get(0);
+    assertNotNull("Couldn't find the EMBL retrieval client", embl);
+    verifyProteinNucleotideXref(retrievalId, embl);
+  }
+
+  /**
+   * Helper method to perform database retrieval and verification of results.
+   * 
+   * @param retrievalId
+   * @param embl
+   * @throws Exception
+   */
+  private void verifyProteinNucleotideXref(String retrievalId,
+          DbSourceProxy embl) throws Exception
+  {
     AlignmentI alsq = embl.getSequenceRecords(retrievalId);
     assertNotNull("Couldn't find the EMBL record " + retrievalId, alsq);
-    assertEquals("Didn't retrieve right number of records", 1, alsq.getHeight());
-    DBRefEntry[] dr = DBRefUtils.selectRefs(alsq.getSequenceAt(0).getDBRef(), DBRefSource.PROTEINSEQ);
+    assertEquals("Didn't retrieve right number of records", 1,
+            alsq.getHeight());
+    SequenceI seq = alsq.getSequenceAt(0);
+    assertEquals("Wrong sequence name", embl.getDbSource() + "|"
+            + retrievalId, seq.getName());
+    SequenceFeature[] sfs = seq.getSequenceFeatures();
+    assertNotNull("Sequence features missing", sfs);
+    assertTrue(
+            "Feature not CDS",
+            FeatureProperties.isCodingFeature(embl.getDbSource(),
+                    sfs[0].getType()));
+    assertEquals(embl.getDbSource(), sfs[0].getFeatureGroup());
+    DBRefEntry[] dr = DBRefUtils.selectRefs(seq.getDBRefs(),
+            new String[] { DBRefSource.UNIPROT });
     assertNotNull(dr);
     assertEquals("Expected a single Uniprot cross reference", 1, dr.length);
-    AlignmentI sprods = CrossRef.findXrefSequences(alsq.getSequencesArray(), true, dr[0].getSource(), alsq.getDataset());
+    assertEquals("Expected cross reference map to be one amino acid", dr[0]
+            .getMap().getMappedWidth(), 1);
+    assertEquals("Expected local reference map to be 3 nucleotides", dr[0]
+            .getMap().getWidth(), 3);
+    AlignmentI sprods = new CrossRef(alsq.getSequencesArray(), alsq)
+            .findXrefSequences(dr[0].getSource(), true);
     assertNotNull(
             "Couldn't recover cross reference sequence from dataset. Was it ever added ?",
             sprods);
-    
-    
+    assertEquals("Didn't xref right number of records", 1,
+            sprods.getHeight());
+    SequenceI proteinSeq = sprods.getSequenceAt(0);
+    assertEquals(proteinSeq.getSequenceAsString(), dr[0].getMap().getTo()
+            .getSequenceAsString());
+    assertEquals(dr[0].getSource() + "|" + dr[0].getAccessionId(),
+            proteinSeq.getName());
   }
 }