Merge branch 'features/r2_11_2_alphafold/JAL-2349_JAL-3855' into develop

[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 bf34ea5..6769d39 100644 (file)
--- a/test/jalview/ws/seqfetcher/DbRefFetcherTest.java
+++ b/test/jalview/ws/seqfetcher/DbRefFetcherTest.java
@@ -32,10 +32,12 @@ 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.EBIAlfaFold;
 import jalview.ws.dbsources.Pdb;
@@ -70,7 +72,7 @@ public class DbRefFetcherTest
   @BeforeClass(alwaysRun = true)
   public static void setUpBeforeClass() throws Exception
   {
-    jalview.bin.Cache.initLogger();
+    jalview.bin.Console.initLogger();
   }
 
   /**
@@ -81,6 +83,28 @@ 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
@@ -139,8 +163,8 @@ public class DbRefFetcherTest
   public void testEmblUniprotProductRecovery() throws Exception
   {
     String retrievalId = "V00488";
-    DbSourceProxy embl = new SequenceFetcher().getSourceProxy(
-            DBRefSource.EMBL).get(0);
+    DbSourceProxy embl = new SequenceFetcher()
+            .getSourceProxy(DBRefSource.EMBL).get(0);
     assertNotNull("Couldn't find the EMBL retrieval client", embl);
     verifyProteinNucleotideXref(retrievalId, embl);
   }
@@ -155,8 +179,8 @@ public class DbRefFetcherTest
   public void testEmblCDSUniprotProductRecovery() throws Exception
   {
     String retrievalId = "AAH29712";
-    DbSourceProxy embl = new SequenceFetcher().getSourceProxy(
-            DBRefSource.EMBLCDS).get(0);
+    DbSourceProxy embl = new SequenceFetcher()
+            .getSourceProxy(DBRefSource.EMBLCDS).get(0);
     assertNotNull("Couldn't find the EMBL retrieval client", embl);
     verifyProteinNucleotideXref(retrievalId, embl);
   }
@@ -176,23 +200,22 @@ public class DbRefFetcherTest
     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());
+    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()));
+    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 });
+            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);
+    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(
@@ -201,8 +224,8 @@ public class DbRefFetcherTest
     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(proteinSeq.getSequenceAsString(),
+            dr.get(0).getMap().getTo().getSequenceAsString());
     assertEquals(dr.get(0).getSource() + "|" + dr.get(0).getAccessionId(),
             proteinSeq.getName());
   }