Merge branch 'releases/Release_2_10_2b1_Branch'

[jalview.git] / test / jalview / io / CrossRef2xmlTests.java

diff --git a/test/jalview/io/CrossRef2xmlTests.java b/test/jalview/io/CrossRef2xmlTests.java
index 070fa68..0715857 100644 (file)
--- a/test/jalview/io/CrossRef2xmlTests.java
+++ b/test/jalview/io/CrossRef2xmlTests.java
@@ -30,20 +30,32 @@ import jalview.gui.AlignFrame;
 import jalview.gui.CrossRefAction;
 import jalview.gui.Desktop;
 import jalview.gui.Jalview2XML;
+import jalview.gui.JvOptionPane;
+import jalview.util.DBRefUtils;
 
 import java.io.File;
 import java.io.IOException;
 import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.HashMap;
 import java.util.List;
 
 import org.testng.Assert;
+import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
 
 @Test(singleThreaded = true)
 public class CrossRef2xmlTests extends Jalview2xmlBase
 {
 
+  @Override
+  @BeforeClass(alwaysRun = true)
+  public void setUpJvOptionPane()
+  {
+    JvOptionPane.setInteractiveMode(false);
+    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+  }
+
   /**
    * 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
@@ -55,10 +67,13 @@ public class CrossRef2xmlTests extends Jalview2xmlBase
   public void testRetrieveAndShowCrossref() throws Exception
   {
 
-    List<String> failedDBRetr = new ArrayList<String>();
-    List<String> failedXrefMenuItems = new ArrayList<String>();
-    List<String> failedProjectRecoveries = new ArrayList<String>();
-
+    List<String> failedDBRetr = new ArrayList<>();
+    List<String> failedXrefMenuItems = new ArrayList<>();
+    List<String> failedProjectRecoveries = new ArrayList<>();
+    // only search for ensembl or Uniprot crossrefs
+    List<String> limit=Arrays.asList(new String[] {
+        DBRefUtils.getCanonicalName("ENSEMBL"), 
+        DBRefUtils.getCanonicalName("Uniprot")});
     // for every set of db queries
     // retrieve db query
     // verify presence of expected xrefs
@@ -75,12 +90,11 @@ public class CrossRef2xmlTests extends Jalview2xmlBase
     // . codonframes
     //
     //
-    HashMap<String, String> dbtoviewBit = new HashMap<String, String>();
-    List<String> keyseq = new ArrayList<String>();
-    HashMap<String, File> savedProjects = new HashMap<String, File>();
+    HashMap<String, String> dbtoviewBit = new HashMap<>();
+    List<String> keyseq = new ArrayList<>();
+    HashMap<String, File> savedProjects = new HashMap<>();
 
-    for (String[] did : new String[][] { { "ENSEMBL", "ENSG00000157764" },
-    { "UNIPROT", "P01731" } })
+    for (String[] did : new String[][] { { "UNIPROT", "P00338" } })
     {
       // pass counters - 0 - first pass, 1 means retrieve project rather than
       // perform action
@@ -153,7 +167,8 @@ public class CrossRef2xmlTests extends Jalview2xmlBase
 
         ptypes = (seqs == null || seqs.length == 0) ? null : new CrossRef(
                 seqs, dataset).findXrefSourcesForSequences(dna);
-
+        filterDbRefs(ptypes, limit);
+        
         // start of pass2: retrieve each cross-ref for fetched or restored
         // project.
         do // first cross ref and recover crossref loop
@@ -166,7 +181,7 @@ public class CrossRef2xmlTests extends Jalview2xmlBase
             // build next key so we an retrieve all views
             String nextxref = first + " -> " + db + "{" + firstcr_ap + "}";
             // perform crossref action, or retrieve stored project
-            List<AlignmentViewPanel> cra_views = new ArrayList<AlignmentViewPanel>();
+            List<AlignmentViewPanel> cra_views = new ArrayList<>();
             CrossRefAction cra = null;
 
             if (pass2 == 0)
@@ -227,7 +242,7 @@ public class CrossRef2xmlTests extends Jalview2xmlBase
 
               }
             }
-            HashMap<String, List<String>> xrptypes = new HashMap<String, List<String>>();
+            HashMap<String, List<String>> xrptypes = new HashMap<>();
             // first save/verify views.
             for (AlignmentViewPanel avp : cra_views)
             {
@@ -264,7 +279,7 @@ public class CrossRef2xmlTests extends Jalview2xmlBase
                 nextxref = first + " -> " + db + "{" + firstcr_ap++ + "}";
                 for (String xrefdb : xrptypes.get(nextxref))
                 {
-                  List<AlignmentViewPanel> cra_views2 = new ArrayList<AlignmentViewPanel>();
+                  List<AlignmentViewPanel> cra_views2 = new ArrayList<>();
                   int q = 0;
                   String nextnextxref = nextxref + " -> " + xrefdb + "{"
                           + q + "}";
@@ -427,6 +442,25 @@ public class CrossRef2xmlTests extends Jalview2xmlBase
     }
   }
 
+  private void filterDbRefs(List<String> ptypes, List<String> limit)
+  {
+    if (limit != null)
+    {
+      int p = 0;
+      while (ptypes.size() > p)
+      {
+        if (!limit.contains(ptypes.get(p)))
+        {
+          ptypes.remove(p);
+        }
+        else
+        {
+          p++;
+        }
+      }
+    }
+  }
+
   /**
    * wrapper to trap known defect for AH002001 testcase
    * 
@@ -470,7 +504,7 @@ public class CrossRef2xmlTests extends Jalview2xmlBase
   private void assertType(boolean expectProtein,
           AlignmentViewPanel alignmentViewPanel, String message)
   {
-    List<SequenceI> nonType = new ArrayList<SequenceI>();
+    List<SequenceI> nonType = new ArrayList<>();
     for (SequenceI sq : alignmentViewPanel.getAlignViewport()
             .getAlignment().getSequences())
     {