JAL-3863 passing test to verify a uniprot accession with canonical flag set is transf...

[jalview.git] / test / jalview / ws / seqfetcher / DbRefFetcherTest.java

diff --git a/test/jalview/ws/seqfetcher/DbRefFetcherTest.java b/test/jalview/ws/seqfetcher/DbRefFetcherTest.java
index e35f83e..914520f 100644 (file)
--- a/test/jalview/ws/seqfetcher/DbRefFetcherTest.java
+++ b/test/jalview/ws/seqfetcher/DbRefFetcherTest.java
@@ -21,6 +21,7 @@
 package jalview.ws.seqfetcher;
 
 import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertFalse;
 import static org.testng.AssertJUnit.assertNotNull;
 import static org.testng.AssertJUnit.assertTrue;
 
@@ -29,10 +30,12 @@ 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.Pdb;
 import jalview.ws.dbsources.Uniprot;
@@ -76,6 +79,26 @@ public class DbRefFetcherTest
   {
   }
 
+  @Test(groups= {"Network"})
+  public void checkUniprotCanonicalFlagSet()
+  {
+    // 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);
+  }
   /**
    * Tests that standard protein database sources include Uniprot (as the first)
    * and also PDB. (Additional sources are dependent on availability of DAS
@@ -173,32 +196,32 @@ public class DbRefFetcherTest
     SequenceI seq = alsq.getSequenceAt(0);
     assertEquals("Wrong sequence name", embl.getDbSource() + "|"
             + retrievalId, seq.getName());
-    SequenceFeature[] sfs = seq.getSequenceFeatures();
-    assertNotNull("Sequence features missing", sfs);
+    List<SequenceFeature> sfs = seq.getSequenceFeatures();
+    assertFalse("Sequence features missing", sfs.isEmpty());
     assertTrue(
             "Feature not CDS",
             FeatureProperties.isCodingFeature(embl.getDbSource(),
-                    sfs[0].getType()));
-    assertEquals(embl.getDbSource(), sfs[0].getFeatureGroup());
-    DBRefEntry[] dr = DBRefUtils.selectRefs(seq.getDBRefs(),
+ 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.length);
-    assertEquals("Expected cross reference map to be one amino acid", dr[0]
+    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[0]
+    assertEquals("Expected local reference map to be 3 nucleotides", dr.get(0)
             .getMap().getWidth(), 3);
     AlignmentI sprods = new CrossRef(alsq.getSequencesArray(), alsq)
-            .findXrefSequences(dr[0].getSource(), true);
+            .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[0].getMap().getTo()
+    assertEquals(proteinSeq.getSequenceAsString(), dr.get(0).getMap().getTo()
             .getSequenceAsString());
-    assertEquals(dr[0].getSource() + "|" + dr[0].getAccessionId(),
+    assertEquals(dr.get(0).getSource() + "|" + dr.get(0).getAccessionId(),
             proteinSeq.getName());
   }
 }