X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FCrossRef2xmlTests.java;h=ef7615bc5a64f843b346901a24b42492f808ff20;hb=483abbfd34bb2e47698f4cb04e21531c2b11924a;hp=c55ddd95d63266f0e8379adbd33ba6637c09c635;hpb=528c0f1815bc67b54618ad5b16c2162946974caf;p=jalview.git

diff --git a/test/jalview/io/CrossRef2xmlTests.java b/test/jalview/io/CrossRef2xmlTests.java
index c55ddd9..ef7615b 100644
--- a/test/jalview/io/CrossRef2xmlTests.java
+++ b/test/jalview/io/CrossRef2xmlTests.java
@@ -30,20 +30,41 @@ 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.DataProvider;
 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);
+  }
+
+  @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
@@ -51,14 +72,22 @@ 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<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
@@ -75,13 +104,12 @@ 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
       int pass1 = 0, pass2 = 0, pass3 = 0;
@@ -91,7 +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;
@@ -103,7 +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);
@@ -130,7 +159,7 @@ public class CrossRef2xmlTests extends Jalview2xmlBase
           Desktop.instance.closeAll_actionPerformed(null);
           // recover stored project
           af = new FileLoader(false).LoadFileWaitTillLoaded(savedProjects
-                  .get(first).toString(), FormatAdapter.FILE);
+                  .get(first).toString(), DataSourceType.FILE);
           System.out.println("Recovered view for '" + first + "' from '"
                   + savedProjects.get(first).toString() + "'");
           dna = af.getViewport().getAlignment().isNucleotide();
@@ -153,7 +182,8 @@ 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 +196,7 @@ 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)
@@ -203,7 +233,7 @@ public class CrossRef2xmlTests extends Jalview2xmlBase
               // recover stored project
               AlignFrame af2 = new FileLoader(false)
                       .LoadFileWaitTillLoaded(savedProjects.get(nextxref)
-                              .toString(), FormatAdapter.FILE);
+                              .toString(), DataSourceType.FILE);
               System.out.println("Recovered view for '" + nextxref
                       + "' from '" + savedProjects.get(nextxref).toString()
                       + "'");
@@ -227,7 +257,7 @@ 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 +294,7 @@ 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 + "}";
@@ -314,7 +344,8 @@ public class CrossRef2xmlTests extends Jalview2xmlBase
                     AlignFrame af2 = new FileLoader(false)
                             .LoadFileWaitTillLoaded(
                                     savedProjects.get(nextnextxref)
-                                            .toString(), FormatAdapter.FILE);
+                                            .toString(),
+                                    DataSourceType.FILE);
                     System.out.println("Recovered view for '"
                             + nextnextxref + "' from '"
                             + savedProjects.get(nextnextxref).toString()
@@ -395,7 +426,7 @@ public class CrossRef2xmlTests extends Jalview2xmlBase
           pass1++;
         }
       } while (pass1 < 3);
-    }
+
     if (failedXrefMenuItems.size() > 0)
     {
       for (String s : failedXrefMenuItems)
@@ -426,6 +457,25 @@ 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
    * 
@@ -469,7 +519,7 @@ 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())
     {