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 a7e5806..914520f 100644 (file)
--- a/test/jalview/ws/seqfetcher/DbRefFetcherTest.java
+++ b/test/jalview/ws/seqfetcher/DbRefFetcherTest.java
@@ -30,10 +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;
@@ -77,6 +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