X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fws%2Fseqfetcher%2FDbRefFetcherTest.java;h=914520f8a87634ebb0cde4dd7c42fc06836f87e7;hb=41b0e9331ac71787c1280aa1d809f54c575fbf97;hp=a269eccc823bd7503e70b4a0661f23b9f35c279e;hpb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;p=jalview.git

diff --git a/test/jalview/ws/seqfetcher/DbRefFetcherTest.java b/test/jalview/ws/seqfetcher/DbRefFetcherTest.java
index a269ecc..914520f 100644
--- a/test/jalview/ws/seqfetcher/DbRefFetcherTest.java
+++ b/test/jalview/ws/seqfetcher/DbRefFetcherTest.java
@@ -1,93 +1,227 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * 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.
  * 
  * 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.
+ * 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/>.
+ * 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.ws.seqfetcher;
 
-import static org.junit.Assert.*;
-
-import java.util.ArrayList;
-import java.util.List;
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertFalse;
+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.Sequence;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.gui.JvOptionPane;
+import jalview.util.DBRefUtils;
 import jalview.ws.DBRefFetcher;
 import jalview.ws.SequenceFetcher;
-import jalview.ws.dbsources.das.api.jalviewSourceI;
+import jalview.ws.dbsources.Pdb;
+import jalview.ws.dbsources.Uniprot;
 
-import org.junit.AfterClass;
-import org.junit.BeforeClass;
-import org.junit.Test;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+
+import org.testng.annotations.AfterClass;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
 
 /**
  * @author jimp
- *
+ * 
  */
 public class DbRefFetcherTest
 {
 
+  @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
   {
+    jalview.bin.Cache.initLogger();
   }
 
   /**
    * @throws java.lang.Exception
    */
-  @AfterClass
+  @AfterClass(alwaysRun = true)
   public static void tearDownAfterClass() throws Exception
   {
   }
 
-  @Test
-  public void testStandardProtDbs()
-  {
-    String[] defdb = DBRefSource.PROTEINDBS;
-  List<DbSourceProxy> srces = new ArrayList<DbSourceProxy>();
-  for (String ddb : defdb)
+  @Test(groups= {"Network"})
+  public void checkUniprotCanonicalFlagSet()
   {
-    SequenceFetcher sfetcher= new SequenceFetcher();
-    List<DbSourceProxy> srcesfordb = sfetcher.getSourceProxy(ddb);
-    
-    if (srcesfordb != null)
-    {
-      srces.addAll(srcesfordb);
+    // TODO - mock this  - for moment it is a live request.
+    SequenceI uniprotSeq = new Sequence("FER1_SPIOL",
+            "MAATTTTMMGMATTFVPKPQAPPMMAALPSNTGRSLFGLKTGSRGGRMTMAAYKVTLVTPTGNVEFQCPDDV"
+            + "YILDAAEEEGIDLPYSCRAGSCSSCAGKLKTGSLNQDDQSFLDDDQIDEGWVLTCAAYPVSDVTIETHKEEE"
+            + "LTA");
+    DBRefFetcher dbr = new DBRefFetcher(new SequenceI[] { uniprotSeq });
+    dbr.fetchDBRefs(true);
+    List<DBRefEntry> primRefs = uniprotSeq.getPrimaryDBRefs();
+    assertNotNull(primRefs);
+    assertTrue(primRefs.size()>0);
+    boolean canonicalUp=false;
+    for (DBRefEntry ref:primRefs) {
+      assertEquals(DBRefSource.UNIPROT, ref.getCanonicalSourceName());
+      canonicalUp |= ref.isCanonical();
     }
+    assertTrue("No Canonical Uniprot reference detected", canonicalUp);
   }
-  DbSourceProxy uniprot=null;
-  int i=0;
-  // append the selected sequence sources to the default dbs
-  for (DbSourceProxy s:srces)
+  /**
+   * 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()
   {
-    if (s.getDbSource().equalsIgnoreCase(DBRefSource.UNIPROT))
+    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)
     {
-      i++;
+      List<DbSourceProxy> srcesfordb = sfetcher.getSourceProxy(ddb);
+
+      if (srcesfordb != null)
+      {
+        // TODO is this right? get duplicate entries
+        srces.addAll(srcesfordb);
+      }
     }
-    
-    if (s instanceof jalview.ws.dbsources.Uniprot)
+
+    int i = 0;
+    int uniprotPos = -1;
+    for (DbSourceProxy s : srces)
     {
-      uniprot = s;
-      break;
+      if (s instanceof Uniprot && uniprotPos == -1)
+      {
+        uniprotPos = i;
+      }
+      if (s instanceof Pdb)
+      {
+        pdbFound = true;
+      }
+      i++;
     }
+
+    assertTrue("Failed to find Uniprot source as first source amongst "
+            + srces.size() + " sources (source was at position "
+            + uniprotPos + ")", uniprotPos == 0);
+    assertTrue("Failed to find PDB source amongst " + srces.size()
+            + " sources", pdbFound);
   }
-          
-  assertTrue("Failed to find Uniprot source as first source amongst "+srces.size()+" sources (source was at position "+i+")", uniprot!=null && i<2);
+
+  /**
+   * 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 = "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());
+    SequenceI seq = alsq.getSequenceAt(0);
+    assertEquals("Wrong sequence name", embl.getDbSource() + "|"
+            + retrievalId, seq.getName());
+    List<SequenceFeature> sfs = seq.getSequenceFeatures();
+    assertFalse("Sequence features missing", sfs.isEmpty());
+    assertTrue(
+            "Feature not CDS",
+            FeatureProperties.isCodingFeature(embl.getDbSource(),
+ sfs.get(0).getType()));
+    assertEquals(embl.getDbSource(), sfs.get(0).getFeatureGroup());
+    List<DBRefEntry> dr = DBRefUtils.selectRefs(seq.getDBRefs(),
+            new String[] { DBRefSource.UNIPROT });
+    assertNotNull(dr);
+    assertEquals("Expected a single Uniprot cross reference", 1, dr.size());
+    assertEquals("Expected cross reference map to be one amino acid", dr.get(0)
+            .getMap().getMappedWidth(), 1);
+    assertEquals("Expected local reference map to be 3 nucleotides", dr.get(0)
+            .getMap().getWidth(), 3);
+    AlignmentI sprods = new CrossRef(alsq.getSequencesArray(), alsq)
+            .findXrefSequences(dr.get(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.get(0).getMap().getTo()
+            .getSequenceAsString());
+    assertEquals(dr.get(0).getSource() + "|" + dr.get(0).getAccessionId(),
+            proteinSeq.getName());
+  }
 }