From: Jim Procter <jprocter@dundee.ac.uk>
Date: Sun, 14 Dec 2014 21:36:17 +0000 (+0000)
Subject: JAL-1617 test to verify Uniprot cross-references are available for EMBL records with... 
X-Git-Tag: Release_2_8_2b1^2~1
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=6797d65989b01c8fa5bdeaf6a66e35279b66a7f7;p=jalview.git

JAL-1617 test to verify Uniprot cross-references are available for EMBL records with Uniprot cross references, and that Jalview recovers the protein sequences
---

diff --git a/test/jalview/ws/seqfetcher/DbRefFetcherTest.java b/test/jalview/ws/seqfetcher/DbRefFetcherTest.java
index 07167bd..785ca42 100644
--- a/test/jalview/ws/seqfetcher/DbRefFetcherTest.java
+++ b/test/jalview/ws/seqfetcher/DbRefFetcherTest.java
@@ -20,16 +20,19 @@
  */
 package jalview.ws.seqfetcher;
 
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertTrue;
+import jalview.analysis.CrossRef;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.DBRefSource;
+import jalview.util.DBRefUtils;
+import jalview.ws.SequenceFetcher;
 
 import java.util.ArrayList;
 import java.util.List;
 
-import jalview.datamodel.DBRefSource;
-import jalview.ws.DBRefFetcher;
-import jalview.ws.SequenceFetcher;
-import jalview.ws.dbsources.das.api.jalviewSourceI;
-
 import org.junit.AfterClass;
 import org.junit.BeforeClass;
 import org.junit.Test;
@@ -94,4 +97,23 @@ public class DbRefFetcherTest
             uniprot != null && i < 2);
   }
 
+  @Test
+  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);
+    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);
+    assertNotNull(dr);
+    assertEquals("Expected a single Uniprot cross reference", 1, dr.length);
+    AlignmentI sprods = CrossRef.findXrefSequences(alsq.getSequencesArray(), true, dr[0].getSource(), alsq.getDataset());
+    assertNotNull(
+            "Couldn't recover cross reference sequence from dataset. Was it ever added ?",
+            sprods);
+    
+    
+  }
 }