JAL-3423 test coverage

[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 44cefe2..f752235 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;
 
@@ -31,12 +32,14 @@ import jalview.datamodel.DBRefSource;
 import jalview.datamodel.FeatureProperties;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
+import jalview.gui.JvOptionPane;
 import jalview.util.DBRefUtils;
 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;
@@ -50,6 +53,13 @@ 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
    */
@@ -62,7 +72,7 @@ public class DbRefFetcherTest
   /**
    * @throws java.lang.Exception
    */
-  @AfterClass
+  @AfterClass(alwaysRun = true)
   public static void tearDownAfterClass() throws Exception
   {
   }
@@ -75,9 +85,11 @@ public class DbRefFetcherTest
   @Test(groups = { "Functional" })
   public void testStandardProtDbs()
   {
-    String[] defdb = DBRefSource.PROTEINDBS;
-    List<DbSourceProxy> srces = new ArrayList<DbSourceProxy>();
-    SequenceFetcher sfetcher = new SequenceFetcher();
+    List<String> defdb = new ArrayList<>();
+    defdb.addAll(Arrays.asList(DBRefSource.PROTEINDBS));
+    defdb.add(DBRefSource.PDB);
+    List<DbSourceProxy> srces = new ArrayList<>();
+    SequenceFetcher sfetcher = SequenceFetcher.getInstance();
     boolean pdbFound = false;
 
     for (String ddb : defdb)
@@ -123,7 +135,7 @@ public class DbRefFetcherTest
   public void testEmblUniprotProductRecovery() throws Exception
   {
     String retrievalId = "V00488";
-    DbSourceProxy embl = new SequenceFetcher().getSourceProxy(
+    DbSourceProxy embl = SequenceFetcher.getInstance().getSourceProxy(
             DBRefSource.EMBL).get(0);
     assertNotNull("Couldn't find the EMBL retrieval client", embl);
     verifyProteinNucleotideXref(retrievalId, embl);
@@ -139,7 +151,8 @@ public class DbRefFetcherTest
   public void testEmblCDSUniprotProductRecovery() throws Exception
   {
     String retrievalId = "AAH29712";
-    DbSourceProxy embl = new SequenceFetcher().getSourceProxy(
+    DbSourceProxy embl = SequenceFetcher.getInstance()
+            .getSourceProxy(
             DBRefSource.EMBLCDS).get(0);
     assertNotNull("Couldn't find the EMBL retrieval client", embl);
     verifyProteinNucleotideXref(retrievalId, embl);
@@ -162,33 +175,32 @@ 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(),
-            new String[] { DBRefSource.UNIPROT, DBRefSource.UNIPROTKB,
-                DBRefSource.EMBLCDSProduct, DBRefSource.ENSEMBL });
+ 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());
+            .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());
   }
 }