JAL-2037 set DBRefEntry.version to "0" not "" in EMBL xrefs

[jalview.git] / test / jalview / datamodel / xdb / embl / EmblFileTest.java

diff --git a/test/jalview/datamodel/xdb/embl/EmblFileTest.java b/test/jalview/datamodel/xdb/embl/EmblFileTest.java
index 81aae0b..c6a94d7 100644 (file)
--- a/test/jalview/datamodel/xdb/embl/EmblFileTest.java
+++ b/test/jalview/datamodel/xdb/embl/EmblFileTest.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.datamodel.xdb.embl;
 
 import static org.testng.AssertJUnit.assertEquals;
@@ -15,23 +35,23 @@ import org.testng.annotations.Test;
 public class EmblFileTest
 {
   // adapted from http://www.ebi.ac.uk/Tools/dbfetch/dbfetch/embl/x53828/emblxml
-  private static final String TESTDATA = 
-          "<?xml version=\"1.0\" encoding=\"UTF-8\" ?>"
+  private static final String TESTDATA = "<?xml version=\"1.0\" encoding=\"UTF-8\" ?>"
           + "<EMBL_Services>"
           + "<entry accession=\"X53828\" version=\"3\" lastUpdated=\"2005-04-18\" releaseCreated=\"25\" releaseLastUpdated=\"83\">"
           + "<description>Chicken LDH-A mRNA for lactate dehydrogenase A chain (EC 1.1.1.27)</description>"
           + "<keyword>L-lactate dehydrogenase</keyword><keyword>chutney</keyword>"
           + "<dbreference db=\"EuropePMC\" primary=\"PMC1460223\" secondary=\"9649548\" />"
+          + "<dbreference db=\"MD5\" primary=\"d3b68\" />"
           + "<feature name=\"CDS\"><dbreference db=\"GOA\" primary=\"P00340\" secondary=\"2.1\" /><dbreference db=\"InterPro\" primary=\"IPR001236\" />"
           + "<qualifier name=\"note\"><value>L-lactate dehydrogenase A-chain</value><value>pickle</value></qualifier>"
           + "<qualifier name=\"translation\"><value>MSLKDHLIHN</value><evidence>Keith</evidence></qualifier>"
           + "<location type=\"single\" complement=\"true\">"
-              + "<locationElement type=\"range\" accession=\"X53828\" version=\"1\" complement=\"false\">"
+          + "<locationElement type=\"range\" accession=\"X53828\" version=\"1\" complement=\"false\">"
           + "<basePosition type=\"simple\">60</basePosition><basePosition type=\"join\">1058</basePosition>"
-              + "</locationElement></location></feature>"
+          + "</locationElement></location></feature>"
           + "<sequence type=\"mRNA\" version=\"2\">GTGACG</sequence></entry></EMBL_Services>";
 
-  @Test(groups ={ "Functional" })
+  @Test(groups = { "Functional" })
   public void testGetEmblFile()
   {
     Vector<EmblEntry> entries = EmblFile.getEmblFile(
@@ -60,11 +80,16 @@ public class EmblFileTest
     /*
      * dbrefs
      */
-    assertEquals(1, entry.getDbRefs().size());
+    assertEquals(2, entry.getDbRefs().size());
     DBRefEntry dbref = entry.getDbRefs().get(0);
     assertEquals("EuropePMC", dbref.getSource());
     assertEquals("PMC1460223", dbref.getAccessionId());
     assertEquals("9649548", dbref.getVersion());
+    dbref = entry.getDbRefs().get(1);
+    assertEquals("MD5", dbref.getSource());
+    assertEquals("d3b68", dbref.getAccessionId());
+    // blank version has been converted to "0"
+    assertEquals("0", dbref.getVersion());
 
     /*
      * sequence features
@@ -80,7 +105,8 @@ public class EmblFileTest
     dbref = ef.getDbRefs().get(1);
     assertEquals("InterPro", dbref.getSource());
     assertEquals("IPR001236", dbref.getAccessionId());
-    assertEquals("", dbref.getVersion());
+    // blank version converted to "0":
+    assertEquals("0", dbref.getVersion());
     assertEquals(2, ef.getQualifiers().size());
 
     // feature qualifiers
@@ -123,5 +149,12 @@ public class EmblFileTest
     assertEquals("mRNA", seq.getType());
     assertEquals("2", seq.getVersion());
     assertEquals("GTGACG", seq.getSequence());
+
+    /*
+     * getSequence() converts empty DBRefEntry.version to "0"
+     */
+    assertEquals("0", entry.getDbRefs().get(1).getVersion());
+    assertEquals("0", entry.getFeatures().get(0).getDbRefs().get(1)
+            .getVersion());
   }
 }