X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fws%2Fseqfetcher%2FDbRefFetcherTest.java;h=8b223d1efb5432486347e79299cc3a663bd78189;hb=57738a1f3c19b1c3a00bd3ac5108f8cd0af32f99;hp=5265a72d14e557a2033dec7b59abb63d8d3f3a51;hpb=c7e8d3a34d2bac0206a942b393e9b6d4d52c55a2;p=jalview.git

diff --git a/test/jalview/ws/seqfetcher/DbRefFetcherTest.java b/test/jalview/ws/seqfetcher/DbRefFetcherTest.java
index 5265a72..8b223d1 100644
--- 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;
 
@@ -29,14 +30,18 @@ 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;
 
 import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.List;
 
 import org.testng.annotations.AfterClass;
@@ -50,23 +55,52 @@ import org.testng.annotations.Test;
 public class DbRefFetcherTest
 {
 
+  @BeforeClass(alwaysRun = true)
+  public void setUpJvOptionPane()
+  {
+    JvOptionPane.setInteractiveMode(false);
+    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+  }
+
   /**
    * @throws java.lang.Exception
    */
   @BeforeClass(alwaysRun = true)
   public static void setUpBeforeClass() throws Exception
   {
-    jalview.bin.Cache.initLogger();
+    jalview.bin.Console.initLogger();
   }
 
   /**
    * @throws java.lang.Exception
    */
-  @AfterClass
+  @AfterClass(alwaysRun = true)
   public static void tearDownAfterClass() throws Exception
   {
   }
 
+  @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
@@ -75,7 +109,9 @@ public class DbRefFetcherTest
   @Test(groups = { "Functional" })
   public void testStandardProtDbs()
   {
-    String[] defdb = DBRefSource.PROTEINDBS;
+    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;
@@ -123,8 +159,8 @@ 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);
   }
@@ -139,8 +175,8 @@ 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);
   }
@@ -160,35 +196,33 @@ 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());
-    SequenceFeature[] sfs = seq.getSequenceFeatures();
-    assertNotNull("Sequence features missing", sfs);
-    assertTrue(
-            "Feature not CDS",
-            FeatureProperties.isCodingFeature(embl.getDbSource(),
-                    sfs[0].getType()));
-    assertEquals(embl.getDbSource(), sfs[0].getFeatureGroup());
-    DBRefEntry[] dr = DBRefUtils.selectRefs(seq.getDBRef(),
-            DBRefSource.PROTEINSEQ);
+    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.length);
-    assertEquals("Expected cross reference map to be one amino acid", dr[0]
-            .getMap().getMappedWidth(), 1);
-    assertEquals("Expected local reference map to be 3 nucleotides", dr[0]
-            .getMap().getWidth(), 3);
-    AlignmentI sprods = CrossRef.findXrefSequences(
-            alsq.getSequencesArray(), true, dr[0].getSource(),
-            alsq.getDataset());
+    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[0].getMap().getTo()
-            .getSequenceAsString());
-    assertEquals(dr[0].getSource() + "|" + dr[0].getAccessionId(),
+    assertEquals(proteinSeq.getSequenceAsString(),
+            dr.get(0).getMap().getTo().getSequenceAsString());
+    assertEquals(dr.get(0).getSource() + "|" + dr.get(0).getAccessionId(),
             proteinSeq.getName());
   }
 }