JAL-3875 test case and patch to verify the query 3d beacons button is shown for prote...

[jalview.git] / test / jalview / gui / StructureChooserTest.java

diff --git a/test/jalview/gui/StructureChooserTest.java b/test/jalview/gui/StructureChooserTest.java
index 685e1bc..f183e5c 100644 (file)
--- a/test/jalview/gui/StructureChooserTest.java
+++ b/test/jalview/gui/StructureChooserTest.java
@@ -20,37 +20,34 @@
  */
 package jalview.gui;
 
-import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.Assert.assertEquals;
 import static org.testng.AssertJUnit.assertNotNull;
 import static org.testng.AssertJUnit.assertTrue;
 
+import java.util.Collection;
+import java.util.Vector;
+
+import org.junit.Assert;
+import org.testng.annotations.AfterMethod;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
 import jalview.datamodel.DBRefEntry;
-import jalview.datamodel.DBRefSource;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceI;
 import jalview.fts.api.FTSData;
-import jalview.fts.core.FTSRestRequest;
+import jalview.fts.core.FTSRestClient;
 import jalview.fts.service.pdb.PDBFTSRestClient;
+import jalview.fts.service.pdb.PDBFTSRestClientTest;
 import jalview.fts.service.threedbeacons.TDBeaconsFTSRestClient;
 import jalview.fts.threedbeacons.TDBeaconsFTSRestClientTest;
 import jalview.gui.structurechooser.PDBStructureChooserQuerySource;
-import jalview.gui.structurechooser.StructureChooserQuerySource;
-import jalview.gui.structurechooser.ThreeDBStructureChooserQuerySource;
 import jalview.jbgui.FilterOption;
-import jalview.ws.params.InvalidArgumentException;
-
-import java.util.Collection;
-import java.util.Vector;
-
-import org.junit.Assert;
-import org.testng.annotations.AfterMethod;
-import org.testng.annotations.BeforeClass;
-import org.testng.annotations.BeforeMethod;
-import org.testng.annotations.Test;
-
 import junit.extensions.PA;
 
+@Test(singleThreaded = true)
 public class StructureChooserTest
 {
 
@@ -61,7 +58,7 @@ public class StructureChooserTest
     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
   }
 
-  Sequence seq,upSeq;
+  Sequence seq,upSeq,upSeq_nocanonical;
 
   @BeforeMethod(alwaysRun = true)
   public void setUp() throws Exception
@@ -114,9 +111,15 @@ public class StructureChooserTest
             + "GTGVHPIVVVQPDAWTEDNGFHAIGQMCEAPVVTREWVLDSVALYQCQELDTYLIPQIPHSHY\n"
             + "", 1,
 1863);
-    upSeq.createDatasetSequence();
     upSeq.setDescription("Breast cancer type 1 susceptibility protein");
+    upSeq_nocanonical = new Sequence(upSeq);
+    upSeq.createDatasetSequence();
     upSeq.addDBRef(new DBRefEntry("UNIPROT","0","P38398",null,true));
+    
+    upSeq_nocanonical.createDatasetSequence();
+    // not a canonical reference
+    upSeq_nocanonical.addDBRef(new DBRefEntry("UNIPROT","0","P38398",null,false));
+
   }
 
   @AfterMethod(alwaysRun = true)
@@ -124,17 +127,33 @@ public class StructureChooserTest
   {
     seq = null;
     upSeq=null;
+    upSeq_nocanonical=null;
   }
 
   @Test(groups = { "Functional" })
   public void populateFilterComboBoxTest() throws InterruptedException
   {
+    TDBeaconsFTSRestClientTest.setMock();
+    PDBFTSRestClientTest.setMock();
+
     SequenceI[] selectedSeqs = new SequenceI[] { seq };
     StructureChooser sc = new StructureChooser(selectedSeqs, seq, null);
+    ThreadwaitFor(200, sc);
+    
+    // if structures are not discovered then don't
+    // populate filter options
     sc.populateFilterComboBox(false, false);
     int optionsSize = sc.getCmbFilterOption().getItemCount();
-    assertEquals(2, optionsSize); // if structures are not discovered then don't
-                                  // populate filter options
+    System.out.println("Items (no data, no cache): ");
+    StringBuilder items = new StringBuilder();
+    for (int p=0;p<optionsSize;p++)
+    {
+      items.append
+      ("- ").append(sc.getCmbFilterOption().getItemAt(p).getName()).append("\n");
+
+    }
+    // report items when this fails - seems to be a race condition
+    Assert.assertEquals(items.toString(),optionsSize,2); 
 
     sc.populateFilterComboBox(true, false);
     optionsSize = sc.getCmbFilterOption().getItemCount();
@@ -146,13 +165,35 @@ public class StructureChooserTest
     FilterOption filterOpt = (FilterOption) sc.getCmbFilterOption()
             .getSelectedItem();
     assertEquals("Cached Structures", filterOpt.getName());
+    FTSRestClient.unMock((FTSRestClient) TDBeaconsFTSRestClient.getInstance());
+    FTSRestClient.unMock((FTSRestClient) PDBFTSRestClient.getInstance());
+
+  }
+
+  @Test(groups = { "Functional" })
+  public void displayTDBQueryTest() throws InterruptedException
+  {
+    TDBeaconsFTSRestClientTest.setMock();
+    PDBFTSRestClientTest.setMock();
+
+    SequenceI[] selectedSeqs = new SequenceI[] { upSeq_nocanonical };
+    StructureChooser sc = new StructureChooser(selectedSeqs, upSeq_nocanonical, null);
+    // mock so should be quick. Exceptions from mocked PDBFTS are expected too
+    ThreadwaitFor(500, sc);
+    
+    assertTrue(sc.isCanQueryTDB() && sc.isNotQueriedTDBYet());
   }
 
   @Test(groups = { "Network" })
   public void fetchStructuresInfoTest()
   {
+    FTSRestClient.unMock((FTSRestClient) TDBeaconsFTSRestClient.getInstance());
+    PDBFTSRestClient.unMock((FTSRestClient) PDBFTSRestClient.getInstance());
     SequenceI[] selectedSeqs = new SequenceI[] { seq };
     StructureChooser sc = new StructureChooser(selectedSeqs, seq, null);
+    // not mocked, wait for 2s 
+    ThreadwaitFor(2000, sc);
+    
     sc.fetchStructuresMetaData();
     Collection<FTSData> ss = (Collection<FTSData>) PA.getValue(sc,
             "discoveredStructuresSet");
@@ -163,12 +204,12 @@ public class StructureChooserTest
   @Test(groups = { "Functional" })
   public void fetchStructuresInfoMockedTest()
   {
-    Assert.fail("Not yet implemented");
     TDBeaconsFTSRestClientTest.setMock();
-    
-    // PDBFTSRestClient.setMock();
+    PDBFTSRestClientTest.setMock();
     SequenceI[] selectedSeqs = new SequenceI[] { upSeq };
     StructureChooser sc = new StructureChooser(selectedSeqs, seq, null);
+    ThreadwaitFor(500, sc);
+    
     sc.fetchStructuresMetaData();
     Collection<FTSData> ss = (Collection<FTSData>) PA.getValue(sc,
             "discoveredStructuresSet");
@@ -176,6 +217,22 @@ public class StructureChooserTest
     assertTrue(ss.size() > 0);
   }
 
+  private void ThreadwaitFor(int i, StructureChooser sc)
+  {
+    long timeout = i+System.currentTimeMillis();
+    while (!sc.isDialogVisible() && timeout > System.currentTimeMillis())
+    {
+      try {
+        Thread.sleep(50);
+      } catch (InterruptedException x)
+      {
+        
+      }
+    }
+    
+  }
+
+
   @Test(groups = { "Functional" })
   public void sanitizeSeqNameTest()
   {