Merge branch 'bug/JAL-2821' into develop

[jalview.git] / test / jalview / ws / dbsources / UniprotTest.java

diff --git a/test/jalview/ws/dbsources/UniprotTest.java b/test/jalview/ws/dbsources/UniprotTest.java
index 26fcaf0..f98ef85 100644 (file)
--- a/test/jalview/ws/dbsources/UniprotTest.java
+++ b/test/jalview/ws/dbsources/UniprotTest.java
@@ -22,20 +22,32 @@ package jalview.ws.dbsources;
 
 import static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertFalse;
+import static org.testng.AssertJUnit.assertNotNull;
 import static org.testng.AssertJUnit.assertNull;
 
 import jalview.datamodel.PDBEntry;
-import jalview.datamodel.SequenceFeature;
-import jalview.datamodel.UniprotEntry;
+import jalview.datamodel.SequenceI;
+import jalview.datamodel.xdb.uniprot.UniprotEntry;
+import jalview.datamodel.xdb.uniprot.UniprotFeature;
+import jalview.gui.JvOptionPane;
 
 import java.io.Reader;
 import java.io.StringReader;
 import java.util.Vector;
 
+import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
 
 public class UniprotTest
 {
+
+  @BeforeClass(alwaysRun = true)
+  public void setUpJvOptionPane()
+  {
+    JvOptionPane.setInteractiveMode(false);
+    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+  }
+
   // adapted from http://www.uniprot.org/uniprot/A9CKP4.xml
   private static final String UNIPROT_XML = "<?xml version='1.0' encoding='UTF-8'?>"
           + "<uniprot>"
@@ -47,6 +59,7 @@ public class UniprotTest
           + "<protein><recommendedName><fullName>Mitogen-activated protein kinase 13</fullName><fullName>Henry</fullName></recommendedName></protein>"
           + "<dbReference type=\"PDB\" id=\"2FSQ\"><property type=\"method\" value=\"X-ray\"/><property type=\"resolution\" value=\"1.40\"/></dbReference>"
           + "<dbReference type=\"PDBsum\" id=\"2FSR\"/>"
+          + "<dbReference type=\"EMBL\" id=\"AE007869\"><property type=\"protein sequence ID\" value=\"AAK85932.1\"/><property type=\"molecule type\" value=\"Genomic_DNA\"/></dbReference>"
           + "<feature type=\"signal peptide\" evidence=\"7\"><location><begin position=\"1\"/><end position=\"18\"/></location></feature>"
           + "<feature type=\"propeptide\" description=\"Activation peptide\" id=\"PRO_0000027399\" evidence=\"9 16 17 18\"><location><begin position=\"19\"/><end position=\"20\"/></location></feature>"
           + "<feature type=\"chain\" description=\"Granzyme B\" id=\"PRO_0000027400\"><location><begin position=\"21\"/><end position=\"247\"/></location></feature>"
@@ -84,13 +97,12 @@ public class UniprotTest
     /*
      * Check sequence features
      */
-    Vector<SequenceFeature> features = entry.getFeature();
+    Vector<UniprotFeature> features = entry.getFeature();
     assertEquals(3, features.size());
-    SequenceFeature sf = features.get(0);
+    UniprotFeature sf = features.get(0);
     assertEquals("signal peptide", sf.getType());
     assertNull(sf.getDescription());
     assertNull(sf.getStatus());
-    assertEquals(1, sf.getPosition());
     assertEquals(1, sf.getBegin());
     assertEquals(18, sf.getEnd());
     sf = features.get(1);
@@ -110,7 +122,7 @@ public class UniprotTest
      * Check cross-references
      */
     Vector<PDBEntry> xrefs = entry.getDbReference();
-    assertEquals(2, xrefs.size());
+    assertEquals(3, xrefs.size());
 
     PDBEntry xref = xrefs.get(0);
     assertEquals("2FSQ", xref.getId());
@@ -122,6 +134,23 @@ public class UniprotTest
     assertEquals("2FSR", xref.getId());
     assertEquals("PDBsum", xref.getType());
     assertFalse(xref.getProperties().hasMoreElements());
+
+    xref = xrefs.get(2);
+    assertEquals("AE007869", xref.getId());
+    assertEquals("EMBL", xref.getType());
+    assertEquals("AAK85932.1", xref.getProperty("protein sequence ID"));
+    assertEquals("Genomic_DNA", xref.getProperty("molecule type"));
+  }
+
+  @Test(groups = { "Functional" })
+  public void testGetUniprotSequence()
+  {
+    UniprotEntry entry = new Uniprot().getUniprotEntries(
+            new StringReader(UNIPROT_XML)).get(0);
+    SequenceI seq = new Uniprot().uniprotEntryToSequenceI(entry);
+    assertNotNull(seq);
+    assertEquals(6, seq.getDBRefs().length); // 2*Uniprot, PDB, PDBsum, 2*EMBL
+
   }
 
   /**
@@ -134,11 +163,11 @@ public class UniprotTest
             new StringReader(UNIPROT_XML)).get(0);
 
     /*
-     * name formatted as source | accession ids | names
-     * source database converted to Jalview canonical name
+     * name formatted with Uniprot Entry name
      */
-    String expectedName = "UNIPROT|A9CKP4|A9CKP5|A9CKP4_AGRT5|A9CKP4_AGRT6";
-    assertEquals(expectedName, Uniprot.getUniprotEntryId(entry));
+    String expectedName = "A9CKP4_AGRT5|A9CKP4_AGRT6";
+    assertEquals(expectedName,
+            Uniprot.getUniprotEntryId(entry));
   }
 
   /**
@@ -149,7 +178,7 @@ public class UniprotTest
   {
     UniprotEntry entry = new Uniprot().getUniprotEntries(
             new StringReader(UNIPROT_XML)).get(0);
-  
+
     /*
      * recommended names concatenated with space separator
      */