X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fgui%2Fstructurechooser%2FStructureChooserQuerySourceTest.java;h=0254a776a553f67ceb7b3e4bf32034b8b208129a;hb=dfa42fba9774fe4659d234661c1e0d2c17980505;hp=f492ce6611cf2377c4bedfaaba6056b994667841;hpb=2e3c61cedbe9185548ecfecad806c9e4f67f43c2;p=jalview.git

diff --git a/test/jalview/gui/structurechooser/StructureChooserQuerySourceTest.java b/test/jalview/gui/structurechooser/StructureChooserQuerySourceTest.java
index f492ce6..0254a77 100644
--- a/test/jalview/gui/structurechooser/StructureChooserQuerySourceTest.java
+++ b/test/jalview/gui/structurechooser/StructureChooserQuerySourceTest.java
@@ -24,6 +24,8 @@ package jalview.gui.structurechooser;
 import static org.testng.Assert.assertEquals;
 import static org.testng.Assert.assertTrue;
 
+import java.util.Collection;
+import java.util.List;
 import java.util.Vector;
 
 import org.junit.Assert;
@@ -31,6 +33,7 @@ import org.testng.AssertJUnit;
 import org.testng.annotations.AfterMethod;
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
 
 import jalview.datamodel.DBRefEntry;
@@ -38,11 +41,13 @@ 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.FTSRestResponse;
 import jalview.fts.service.pdb.PDBFTSRestClient;
 import jalview.fts.threedbeacons.TDBeaconsFTSRestClientTest;
 import jalview.gui.JvOptionPane;
+import jalview.gui.StructureChooser;
 import jalview.jbgui.FilterOption;
 
 public class StructureChooserQuerySourceTest
@@ -55,7 +60,7 @@ public class StructureChooserQuerySourceTest
     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
   }
 
-  Sequence seq,upSeq;
+  Sequence seq,upSeq,upSeq_insulin;
 
   // same set up as for structurechooser test
   
@@ -113,6 +118,13 @@ public class StructureChooserQuerySourceTest
     upSeq.createDatasetSequence();
     upSeq.setDescription("Breast cancer type 1 susceptibility protein");
     upSeq.addDBRef(new DBRefEntry("UNIPROT","0","P38398",null,true));
+    
+    upSeq_insulin=new Sequence("INS_HUMAN",
+            "MALWMRLLPLLALLALWGPDPAAAFVNQHLCGSHLVEALYLVCGERGFFYTPKTRREAEDLQVGQVELGGGP"
+            + "GAGSLQPLALEGSLQKRGIVEQCCTSICSLYQLENYCN");
+    upSeq_insulin.createDatasetSequence();
+    upSeq_insulin.setDescription("Insulin");
+    upSeq_insulin.addDBRef(new DBRefEntry("UNIPROT","0","P01308",null,true));
   }
 
 @AfterMethod(alwaysRun = true)
@@ -173,7 +185,9 @@ public class StructureChooserQuerySourceTest
   {
     System.out.println("seq >>>> " + upSeq);
     TDBeaconsFTSRestClientTest.setMock();
+    PDBFTSRestClient.setMock();
     StructureChooserQuerySource scquery = StructureChooserQuerySource.getQuerySourceFor(new SequenceI[] { upSeq});
+    // gets the lightweight proxy rather than the ThreeDBStructureChooserQuerySource
     AssertJUnit.assertTrue(scquery instanceof ThreeDBStructureChooserQuerySource);
     String query = scquery.buildQuery(upSeq);
     AssertJUnit.assertEquals("P38398", query);
@@ -245,8 +259,8 @@ public class StructureChooserQuerySourceTest
 //            "uniprot_accession:P12345 OR uniprot_id:P12345 OR pdb_id:1xyz",
 //            query);
   }
-  @Test(groups= {"Functional"})
-  public void cascadingThreeDBandPDBQuerys()
+  @Test(groups= {"Functional"},dataProvider = "testUpSeqs")
+  public void cascadingThreeDBandPDBQuerys(SequenceI testUpSeq)
   {
     TDBeaconsFTSRestClientTest.setMock();
     PDBFTSRestClient.setMock();
@@ -257,9 +271,26 @@ public class StructureChooserQuerySourceTest
     
     FTSRestResponse upResponse = null;
     FTSRestResponse pdbResponse = null;
+    // TODO test available options
+    // Best coverage
+    // Best Alphafold Model
+    // Best model (by confidence score)
+    // Will also need to develop a more sophisticated filtering system
+    List<FilterOption> opts = tdbquery.getAvailableFilterOptions(StructureChooser.VIEWS_FILTER);
+    FilterOption opt_singlebest = opts.get(0);
+    FilterOption opt_manybest = opts.get(1);
+    assertEquals(opt_singlebest.getValue(), ThreeDBStructureChooserQuerySource.FILTER_FIRST_BEST_COVERAGE);
+    assertEquals(opt_manybest.getValue(), ThreeDBStructureChooserQuerySource.FILTER_TDBEACONS_COVERAGE);
     
     try {
-      upResponse = tdbquery.fetchStructuresMetaData(upSeq, tdbquery.getDocFieldPrefs().getStructureSummaryFields(),  null, false);
+      upResponse = tdbquery.fetchStructuresMetaData(testUpSeq, tdbquery.getDocFieldPrefs().getStructureSummaryFields(),  opt_singlebest, false);
+      tdbquery.updateAvailableFilterOptions(StructureChooser.VIEWS_FILTER,opts,upResponse.getSearchSummary());
+      // test ranking without additional PDBe data
+      FTSRestResponse firstRanked = tdbquery.selectFirstRankedQuery(testUpSeq, upResponse.getSearchSummary(), tdbquery.getDocFieldPrefs().getStructureSummaryFields(), opt_singlebest.getValue(), false);
+      assertEquals(firstRanked.getNumberOfItemsFound(),1);
+      // many best response
+      upResponse = tdbquery.fetchStructuresMetaData(testUpSeq, tdbquery.getDocFieldPrefs().getStructureSummaryFields(),  opt_manybest, false);
+      assertTrue(firstRanked.getSearchSummary().size()<upResponse.getSearchSummary().size());
       // NB Could have race condition here 
       String pdb_Query = tdbquery.buildPDBFTSQueryFor(upResponse);
       assertTrue(pdb_Query.trim().length()>0);
@@ -268,15 +299,23 @@ public class StructureChooserQuerySourceTest
       FTSRestResponse joinedResp = tdbquery.joinResponses(upResponse, pdbResponse);
       assertEquals(upResponse.getNumberOfItemsFound(),joinedResp.getNumberOfItemsFound());
       
+      
     } catch (Exception x)
     {
       x.printStackTrace();
       Assert.fail("Unexpected Exception");
     }
-    StructureChooserQuerySource scquery = StructureChooserQuerySource.getQuerySourceFor(new SequenceI[] { upSeq});
+    StructureChooserQuerySource scquery = StructureChooserQuerySource.getQuerySourceFor(new SequenceI[] { testUpSeq});
 
   }
   
+  @DataProvider(name = "testUpSeqs")
+  public Object[][] testUpSeqs() throws Exception
+  {
+    setUp();
+    return new Object[][] { {upSeq},{upSeq_insulin}};
+  }
+  
   @Test(groups = { "Functional" })
   public void sanitizeSeqNameTest()
   {