From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Thu, 15 Mar 2018 16:24:06 +0000 (+0000)
Subject: JAL-2893 enabling Get Crossreferences to ENSEMBLGENOMES
X-Git-Tag: Release_2_10_4~42
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=5af80dd011bdfeab879472802bf2a9646e538f68;p=jalview.git

JAL-2893 enabling Get Crossreferences to ENSEMBLGENOMES
---

diff --git a/src/jalview/ext/ensembl/EnsemblGenomes.java b/src/jalview/ext/ensembl/EnsemblGenomes.java
index 6dd69a8..9fc6a53 100644
--- a/src/jalview/ext/ensembl/EnsemblGenomes.java
+++ b/src/jalview/ext/ensembl/EnsemblGenomes.java
@@ -21,6 +21,7 @@
 package jalview.ext.ensembl;
 
 import jalview.bin.Cache;
+import jalview.datamodel.DBRefSource;
 
 /**
  * A class to behave much like EnsemblGene but referencing the ensemblgenomes
@@ -45,7 +46,7 @@ public class EnsemblGenomes extends EnsemblGene
   @Override
   public String getDbName()
   {
-    return "EnsemblGenomes";
+    return DBRefSource.ENSEMBLGENOMES;
   }
 
   @Override
@@ -60,7 +61,7 @@ public class EnsemblGenomes extends EnsemblGene
   @Override
   public String getDbSource()
   {
-    return "EnsemblGenomes";
+    return DBRefSource.ENSEMBLGENOMES;
   }
 
 }
diff --git a/test/jalview/analysis/CrossRefTest.java b/test/jalview/analysis/CrossRefTest.java
index 95be1ff..0265af3 100644
--- a/test/jalview/analysis/CrossRefTest.java
+++ b/test/jalview/analysis/CrossRefTest.java
@@ -106,7 +106,7 @@ public class CrossRefTest
   public void testFindXrefSourcesForSequence_proteinToDna()
   {
     SequenceI seq = new Sequence("Seq1", "MGKYQARLSS");
-    List<String> sources = new ArrayList<String>();
+    List<String> sources = new ArrayList<>();
     AlignmentI al = new Alignment(new SequenceI[] {});
 
     /*
@@ -132,8 +132,9 @@ public class CrossRefTest
     sources = new CrossRef(new SequenceI[] { seq }, al)
             .findXrefSourcesForSequences(false);
     // method is patched to remove EMBL from the sources to match
-    assertEquals(3, sources.size());
-    assertEquals("[EMBLCDS, GENEDB, ENSEMBL]", sources.toString());
+    assertEquals(4, sources.size());
+    assertEquals("[EMBLCDS, GENEDB, ENSEMBL, ENSEMBLGENOMES]",
+            sources.toString());
 
     /*
      * add a sequence to the alignment which has a dbref to UNIPROT|A1234
@@ -270,7 +271,7 @@ public class CrossRefTest
     pep1.addDBRef(new DBRefEntry("UNIPROT", "0", "Q9ZTS2"));
     AlignmentI al = new Alignment(new SequenceI[] { dna1, pep1 });
 
-    List<SequenceI> result = new ArrayList<SequenceI>();
+    List<SequenceI> result = new ArrayList<>();
 
     /*
      * first search for a dbref nowhere on the alignment:
diff --git a/test/jalview/datamodel/AlignmentTest.java b/test/jalview/datamodel/AlignmentTest.java
index 266b90a..1d1ebd6 100644
--- a/test/jalview/datamodel/AlignmentTest.java
+++ b/test/jalview/datamodel/AlignmentTest.java
@@ -248,7 +248,9 @@ public class AlignmentTest
                   if (raiseAssert)
                   {
                     Assert.fail(message
-                            + " DBRefEntry for sequence in alignment had map to sequence not in dataset");
+                            + " DBRefEntry " + dbr + " for sequence "
+                            + seqds
+                            + " in alignment has map to sequence not in dataset");
                   }
                   return false;
                 }
diff --git a/test/jalview/io/CrossRef2xmlTests.java b/test/jalview/io/CrossRef2xmlTests.java
index 0715857..ef7615b 100644
--- a/test/jalview/io/CrossRef2xmlTests.java
+++ b/test/jalview/io/CrossRef2xmlTests.java
@@ -42,6 +42,7 @@ import java.util.List;
 
 import org.testng.Assert;
 import org.testng.annotations.BeforeClass;
+import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
 
 @Test(singleThreaded = true)
@@ -56,6 +57,14 @@ public class CrossRef2xmlTests extends Jalview2xmlBase
     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
   }
 
+  @DataProvider(name = "initialAccessions")
+  static Object[][] getAccessions()
+  {
+    return new String[][] { { "UNIPROT", "P00338" },
+        { "UNIPROT", "Q8Z9G6" },
+        { "ENSEMBLGENOMES", "CAD01290" } };
+  }
+
   /**
    * test store and recovery of all reachable cross refs from all reachable
    * crossrefs for one or more fetched db refs. Currently, this test has a known
@@ -63,8 +72,13 @@ public class CrossRef2xmlTests extends Jalview2xmlBase
    * 
    * @throws Exception
    */
-  @Test(groups = { "Operational" }, enabled = true)
-  public void testRetrieveAndShowCrossref() throws Exception
+  @Test(
+    groups =
+    { "Operational" },
+    dataProvider = "initialAccessions",
+    enabled = true)
+  public void testRetrieveAndShowCrossref(String forSource,
+          String forAccession) throws Exception
   {
 
     List<String> failedDBRetr = new ArrayList<>();
@@ -94,8 +108,8 @@ public class CrossRef2xmlTests extends Jalview2xmlBase
     List<String> keyseq = new ArrayList<>();
     HashMap<String, File> savedProjects = new HashMap<>();
 
-    for (String[] did : new String[][] { { "UNIPROT", "P00338" } })
-    {
+//    for (String[] did : new String[][] { { "UNIPROT", "P00338" } })
+//    {
       // pass counters - 0 - first pass, 1 means retrieve project rather than
       // perform action
       int pass1 = 0, pass2 = 0, pass3 = 0;
@@ -105,7 +119,7 @@ public class CrossRef2xmlTests extends Jalview2xmlBase
       // { pass 2 = 0 { pass 3 = 0 } }
       do
       {
-        String first = did[0] + " " + did[1];
+        String first = forSource + " " + forAccession;//did[0] + " " + did[1];
         AlignFrame af = null;
         boolean dna;
         AlignmentI retral;
@@ -117,7 +131,8 @@ public class CrossRef2xmlTests extends Jalview2xmlBase
           // retrieve dbref
 
           List<AlignFrame> afs = jalview.gui.SequenceFetcher.fetchAndShow(
-                  did[0], did[1]);
+                forSource, forAccession);
+        // did[0], did[1]);
           if (afs.size() == 0)
           {
             failedDBRetr.add("Didn't retrieve " + first);
@@ -411,7 +426,7 @@ public class CrossRef2xmlTests extends Jalview2xmlBase
           pass1++;
         }
       } while (pass1 < 3);
-    }
+
     if (failedXrefMenuItems.size() > 0)
     {
       for (String s : failedXrefMenuItems)