JAL-3829 pull out structure chooser query source tests to new class

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

diff --git a/test/jalview/gui/StructureChooserTest.java b/test/jalview/gui/StructureChooserTest.java
index 309b5ad..685e1bc 100644 (file)
--- a/test/jalview/gui/StructureChooserTest.java
+++ b/test/jalview/gui/StructureChooserTest.java
@@ -30,6 +30,8 @@ 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.service.pdb.PDBFTSRestClient;
 import jalview.fts.service.threedbeacons.TDBeaconsFTSRestClient;
 import jalview.fts.threedbeacons.TDBeaconsFTSRestClientTest;
 import jalview.gui.structurechooser.PDBStructureChooserQuerySource;
@@ -41,6 +43,7 @@ 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;
@@ -123,108 +126,6 @@ public class StructureChooserTest
     upSeq=null;
   }
 
-  @SuppressWarnings("deprecation")
-  @Test(groups = { "Functional" })
-  public void buildQueryTest()
-  {
-    System.out.println("seq >>>> " + seq);
-    
-    StructureChooserQuerySource scquery = StructureChooserQuerySource.getQuerySourceFor(new SequenceI[] { seq});
-    assertTrue(scquery instanceof PDBStructureChooserQuerySource);
-    String query = scquery.buildQuery(seq);
-    assertEquals("pdb_id:1tim", query);
-    seq.getAllPDBEntries().clear();
-    query = scquery.buildQuery(seq);
-    assertEquals(
-            "text:XYZ_1 OR text:XYZ_2 OR text:XYZ_3 OR text:XYZ_4 OR text:4kqy",
-            query);
-    seq.setDBRefs(null);
-    query = scquery.buildQuery(seq);
-    System.out.println(query);
-    assertEquals("text:4kqy", query);
-
-    DBRefEntry uniprotDBRef = new DBRefEntry();
-    uniprotDBRef.setAccessionId("P12345");
-    uniprotDBRef.setSource(DBRefSource.UNIPROT);
-    seq.addDBRef(uniprotDBRef);
-
-    DBRefEntry pdbDBRef = new DBRefEntry();
-    pdbDBRef.setAccessionId("1XYZ");
-    pdbDBRef.setSource(DBRefSource.PDB);
-    seq.addDBRef(pdbDBRef);
-
-    for (int x = 1; x < 5; x++)
-    {
-      DBRefEntry dbRef = new DBRefEntry();
-      dbRef.setAccessionId("XYZ_" + x);
-      seq.addDBRef(dbRef);
-    }
-    System.out.println("");
-    System.out.println(seq.getDBRefs());
-    System.out.println(query);
-    query = scquery.buildQuery(seq);
-    assertEquals(
-            "uniprot_accession:P12345 OR uniprot_id:P12345 OR pdb_id:1xyz",
-            query);
-  }
-
-  @SuppressWarnings("deprecation")
-  @Test(groups = { "Functional" })
-  public void buildThreeDBQueryTest()
-  {
-    System.out.println("seq >>>> " + upSeq);
-    TDBeaconsFTSRestClientTest.setMock();
-    StructureChooserQuerySource scquery = StructureChooserQuerySource.getQuerySourceFor(new SequenceI[] { upSeq});
-    assertTrue(scquery instanceof ThreeDBStructureChooserQuerySource);
-    String query = scquery.buildQuery(upSeq);
-    assertEquals("P38398", query);
-    
-    // query shouldn't change regardless of additional entries
-    // because 3DBeacons requires canonical entries.
-    upSeq.getAllPDBEntries().clear();
-    query = scquery.buildQuery(upSeq);
-    assertEquals("P38398", query);
-    upSeq.setDBRefs(null);
-    query = scquery.buildQuery(upSeq);
-    /*
-     * legacy projects/datasets will not have canonical flags set for uniprot dbrefs
-     * graceful behaviour would be to
-     *  - pick one ? not possible
-     *  - iterate through all until a 200 is obtained ?
-     *  ---> ideal but could be costly
-     *  ---> better to do a direct retrieval from uniprot to work out which is the canonical identifier..
-     *  ----> need a test to check that accessions can be promoted to canonical!
-     */
-    assertEquals(null, query);
-
-    // TODO: 
-//    
-//    DBRefEntry uniprotDBRef = new DBRefEntry();
-//    uniprotDBRef.setAccessionId("P12345");
-//    uniprotDBRef.setSource(DBRefSource.UNIPROT);
-//    upSeq.addDBRef(uniprotDBRef);
-//
-//    DBRefEntry pdbDBRef = new DBRefEntry();
-//    pdbDBRef.setAccessionId("1XYZ");
-//    pdbDBRef.setSource(DBRefSource.PDB);
-//    upSeq.addDBRef(pdbDBRef);
-//
-//    for (int x = 1; x < 5; x++)
-//    {
-//      DBRefEntry dbRef = new DBRefEntry();
-//      dbRef.setAccessionId("XYZ_" + x);
-//      seq.addDBRef(dbRef);
-//    }
-//    System.out.println("");
-//    System.out.println(seq.getDBRefs());
-//    System.out.println(query);
-//    query = scquery.buildQuery(seq);
-//    assertEquals(
-//            "uniprot_accession:P12345 OR uniprot_id:P12345 OR pdb_id:1xyz",
-//            query);
-  }
-  
-
   @Test(groups = { "Functional" })
   public void populateFilterComboBoxTest() throws InterruptedException
   {
@@ -257,7 +158,22 @@ public class StructureChooserTest
             "discoveredStructuresSet");
     assertNotNull(ss);
     assertTrue(ss.size() > 0);
+  }
 
+  @Test(groups = { "Functional" })
+  public void fetchStructuresInfoMockedTest()
+  {
+    Assert.fail("Not yet implemented");
+    TDBeaconsFTSRestClientTest.setMock();
+    
+    // PDBFTSRestClient.setMock();
+    SequenceI[] selectedSeqs = new SequenceI[] { upSeq };
+    StructureChooser sc = new StructureChooser(selectedSeqs, seq, null);
+    sc.fetchStructuresMetaData();
+    Collection<FTSData> ss = (Collection<FTSData>) PA.getValue(sc,
+            "discoveredStructuresSet");
+    assertNotNull(ss);
+    assertTrue(ss.size() > 0);
   }
 
   @Test(groups = { "Functional" })