X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fgui%2FStructureChooserTest.java;h=918b85789db55a5dcdc0797e89c5103d004fcb8e;hb=60b467249ff016c9376474933fc46598ddb027bf;hp=073bde83e22375ecfe5f99a4604377b1f534f4ec;hpb=253eb09c3a7682a9183c7ee647ce17e7fcc6ecb8;p=jalview.git

diff --git a/test/jalview/gui/StructureChooserTest.java b/test/jalview/gui/StructureChooserTest.java
index 073bde8..918b857 100644
--- a/test/jalview/gui/StructureChooserTest.java
+++ b/test/jalview/gui/StructureChooserTest.java
@@ -20,27 +20,31 @@
  */
 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 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.jbgui.GStructureChooser.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 jalview.datamodel.DBRefEntry;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+import jalview.fts.api.FTSData;
+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.jbgui.FilterOption;
 import junit.extensions.PA;
 
 public class StructureChooserTest
@@ -53,7 +57,7 @@ public class StructureChooserTest
     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
   }
 
-  Sequence seq;
+  Sequence seq,upSeq;
 
   @BeforeMethod(alwaysRun = true)
   public void setUp() throws Exception
@@ -75,60 +79,72 @@ public class StructureChooserTest
     pdbIds.add(dbRef);
 
     seq.setPDBId(pdbIds);
+    
+    // Uniprot sequence for 3D-Beacons mocks
+    upSeq = new Sequence("P38398", 
+            "MDLSALRVEEVQNVINAMQKILECPICLELIKEPVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRS\n"
+            + "LQESTRFSQLVEELLKIICAFQLDTGLEYANSYNFAKKENNSPEHLKDEVSIIQSMGYRNRAKRLLQSEPEN\n"
+            + "PSLQETSLSVQLSNLGTVRTLRTKQRIQPQKTSVYIELGSDSSEDTVNKATYCSVGDQELLQITPQGTRDEI\n"
+            + "SLDSAKKAACEFSETDVTNTEHHQPSNNDLNTTEKRAAERHPEKYQGSSVSNLHVEPCGTNTHASSLQHENS\n"
+            + "SLLLTKDRMNVEKAEFCNKSKQPGLARSQHNRWAGSKETCNDRRTPSTEKKVDLNADPLCERKEWNKQKLPC\n"
+            + "SENPRDTEDVPWITLNSSIQKVNEWFSRSDELLGSDDSHDGESESNAKVADVLDVLNEVDEYSGSSEKIDLL\n"
+            + "ASDPHEALICKSERVHSKSVESNIEDKIFGKTYRKKASLPNLSHVTENLIIGAFVTEPQIIQERPLTNKLKR\n"
+            + "KRRPTSGLHPEDFIKKADLAVQKTPEMINQGTNQTEQNGQVMNITNSGHENKTKGDSIQNEKNPNPIESLEK\n"
+            + "ESAFKTKAEPISSSISNMELELNIHNSKAPKKNRLRRKSSTRHIHALELVVSRNLSPPNCTELQIDSCSSSE\n"
+            + "EIKKKKYNQMPVRHSRNLQLMEGKEPATGAKKSNKPNEQTSKRHDSDTFPELKLTNAPGSFTKCSNTSELKE\n"
+            + "FVNPSLPREEKEEKLETVKVSNNAEDPKDLMLSGERVLQTERSVESSSISLVPGTDYGTQESISLLEVSTLG\n"
+            + "KAKTEPNKCVSQCAAFENPKGLIHGCSKDNRNDTEGFKYPLGHEVNHSRETSIEMEESELDAQYLQNTFKVS\n"
+            + "KRQSFAPFSNPGNAEEECATFSAHSGSLKKQSPKVTFECEQKEENQGKNESNIKPVQTVNITAGFPVVGQKD\n"
+            + "KPVDNAKCSIKGGSRFCLSSQFRGNETGLITPNKHGLLQNPYRIPPLFPIKSFVKTKCKKNLLEENFEEHSM\n"
+            + "SPEREMGNENIPSTVSTISRNNIRENVFKEASSSNINEVGSSTNEVGSSINEIGSSDENIQAELGRNRGPKL\n"
+            + "NAMLRLGVLQPEVYKQSLPGSNCKHPEIKKQEYEEVVQTVNTDFSPYLISDNLEQPMGSSHASQVCSETPDD\n"
+            + "LLDDGEIKEDTSFAENDIKESSAVFSKSVQKGELSRSPSPFTHTHLAQGYRRGAKKLESSEENLSSEDEELP\n"
+            + "CFQHLLFGKVNNIPSQSTRHSTVATECLSKNTEENLLSLKNSLNDCSNQVILAKASQEHHLSEETKCSASLF\n"
+            + "SSQCSELEDLTANTNTQDPFLIGSSKQMRHQSESQGVGLSDKELVSDDEERGTGLEENNQEEQSMDSNLGEA\n"
+            + "ASGCESETSVSEDCSGLSSQSDILTTQQRDTMQHNLIKLQQEMAELEAVLEQHGSQPSNSYPSIISDSSALE\n"
+            + "DLRNPEQSTSEKAVLTSQKSSEYPISQNPEGLSADKFEVSADSSTSKNKEPGVERSSPSKCPSLDDRWYMHS\n"
+            + "CSGSLQNRNYPSQEELIKVVDVEEQQLEESGPHDLTETSYLPRQDLEGTPYLESGISLFSDDPESDPSEDRA\n"
+            + "PESARVGNIPSSTSALKVPQLKVAESAQSPAAAHTTDTAGYNAMEESVSREKPELTASTERVNKRMSMVVSG\n"
+            + "LTPEEFMLVYKFARKHHITLTNLITEETTHVVMKTDAEFVCERTLKYFLGIAGGKWVVSYFWVTQSIKERKM\n"
+            + "LNEHDFEVRGDVVNGRNHQGPKRARESQDRKIFRGLEICCYGPFTNMPTDQLEWMVQLCGASVVKELSSFTL\n"
+            + "GTGVHPIVVVQPDAWTEDNGFHAIGQMCEAPVVTREWVLDSVALYQCQELDTYLIPQIPHSHY\n"
+            + "", 1,
+1863);
+    upSeq.createDatasetSequence();
+    upSeq.setDescription("Breast cancer type 1 susceptibility protein");
+    upSeq.addDBRef(new DBRefEntry("UNIPROT","0","P38398",null,true));
   }
 
   @AfterMethod(alwaysRun = true)
   public void tearDown() throws Exception
   {
     seq = null;
-  }
-
-  @Test(groups = { "Functional" })
-  public void buildQueryTest()
-  {
-    String query = StructureChooser.buildQuery(seq);
-    assertEquals("pdb_id:1tim", query);
-    System.out.println("seq >>>> " + seq);
-    seq.getAllPDBEntries().clear();
-    query = StructureChooser.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 = StructureChooser.buildQuery(seq);
-    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);
-    }
-    query = StructureChooser.buildQuery(seq);
-    assertEquals(
-            "uniprot_accession:P12345 OR uniprot_id:P12345 OR pdb_id:1xyz",
-            query);
+    upSeq=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);
+    
+    // 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();
@@ -140,11 +156,16 @@ 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 = { "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);
     sc.fetchStructuresMetaData();
@@ -152,24 +173,37 @@ public class StructureChooserTest
             "discoveredStructuresSet");
     assertNotNull(ss);
     assertTrue(ss.size() > 0);
+  }
 
+  @Test(groups = { "Functional" })
+  public void fetchStructuresInfoMockedTest()
+  {
+    TDBeaconsFTSRestClientTest.setMock();
+    PDBFTSRestClientTest.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" })
   public void sanitizeSeqNameTest()
   {
     String name = "ab_cdEF|fwxyz012349";
-    assertEquals(name, StructureChooser.sanitizeSeqName(name));
+    assertEquals(name, PDBStructureChooserQuerySource.sanitizeSeqName(name));
 
     // remove a [nn] substring
     name = "abcde12[345]fg";
-    assertEquals("abcde12fg", StructureChooser.sanitizeSeqName(name));
+    assertEquals("abcde12fg", PDBStructureChooserQuerySource.sanitizeSeqName(name));
 
     // remove characters other than a-zA-Z0-9 | or _
     name = "ab[cd],.\t£$*!- \\\"@:e";
-    assertEquals("abcde", StructureChooser.sanitizeSeqName(name));
+    assertEquals("abcde", PDBStructureChooserQuerySource.sanitizeSeqName(name));
 
     name = "abcde12[345a]fg";
-    assertEquals("abcde12345afg", StructureChooser.sanitizeSeqName(name));
+    assertEquals("abcde12345afg", PDBStructureChooserQuerySource.sanitizeSeqName(name));
   }
 }