X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fgui%2FStructureChooserTest.java;h=918b85789db55a5dcdc0797e89c5103d004fcb8e;hb=60b467249ff016c9376474933fc46598ddb027bf;hp=1e73d3e95a915ef4ac92383af3133e87b279d7df;hpb=43a44d10c88ef1ebb6e149b0a48f890c0f803247;p=jalview.git

diff --git a/test/jalview/gui/StructureChooserTest.java b/test/jalview/gui/StructureChooserTest.java
index 1e73d3e..918b857 100644
--- a/test/jalview/gui/StructureChooserTest.java
+++ b/test/jalview/gui/StructureChooserTest.java
@@ -1,28 +1,70 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.gui;
 
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertTrue;
+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.PDBEntry;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceI;
-
-import java.util.Vector;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
+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
 {
-  Sequence seq;
 
-  @Before
+  @BeforeClass(alwaysRun = true)
+  public void setUpJvOptionPane()
+  {
+    JvOptionPane.setInteractiveMode(false);
+    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+  }
+
+  Sequence seq,upSeq;
+
+  @BeforeMethod(alwaysRun = true)
   public void setUp() throws Exception
   {
     seq = new Sequence("PDB|4kqy|4KQY|A", "ABCDEFGHIJKLMNOPQRSTUVWXYZ", 1,
             26);
-    seq.setDatasetSequence(seq);
+    seq.createDatasetSequence();
     for (int x = 1; x < 5; x++)
     {
       DBRefEntry dbRef = new DBRefEntry();
@@ -33,58 +75,135 @@ public class StructureChooserTest
     PDBEntry dbRef = new PDBEntry();
     dbRef.setId("1tim");
 
-    Vector<PDBEntry> pdbIds = new Vector<PDBEntry>();
+    Vector<PDBEntry> pdbIds = new Vector<>();
     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));
   }
 
-  @After
+  @AfterMethod(alwaysRun = true)
   public void tearDown() throws Exception
   {
     seq = null;
+    upSeq=null;
   }
 
-
-
-  @Test
-  public void buildQueryTest()
+  @Test(groups = { "Functional" })
+  public void populateFilterComboBoxTest() throws InterruptedException
   {
-    String query = StructureChooser.buildQuery(seq);
-    System.out.println(">>>>>>>>>> query : " + query);
-    assertEquals(
-            "4kqy OR text:1tim OR text:XYZ_1 OR text:XYZ_2 OR text:XYZ_3 OR text:XYZ_4",
-            query);
-  }
+    TDBeaconsFTSRestClientTest.setMock();
+    PDBFTSRestClientTest.setMock();
 
-  @Test
-  public void populateFilterComboBoxTest()
-  {
-    SequenceI[] selectedSeqs = new SequenceI[]
-    { seq };
-    StructureChooser sc = new StructureChooser(selectedSeqs, seq,
-            null);
-    sc.populateFilterComboBox();
+    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(3, 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.setStructuresDiscovered(true);
-    sc.populateFilterComboBox();
+    sc.populateFilterComboBox(true, false);
     optionsSize = sc.getCmbFilterOption().getItemCount();
     assertTrue(optionsSize > 3); // if structures are found, filter options
                                  // should be populated
+
+    sc.populateFilterComboBox(true, true);
+    assertTrue(sc.getCmbFilterOption().getSelectedItem() != null);
+    FilterOption filterOpt = (FilterOption) sc.getCmbFilterOption()
+            .getSelectedItem();
+    assertEquals("Cached Structures", filterOpt.getName());
+    FTSRestClient.unMock((FTSRestClient) TDBeaconsFTSRestClient.getInstance());
+    FTSRestClient.unMock((FTSRestClient) PDBFTSRestClient.getInstance());
+
   }
 
-  @Test
+  @Test(groups = { "Network" })
   public void fetchStructuresInfoTest()
   {
-    SequenceI[] selectedSeqs = new SequenceI[]
-    { seq };
+    FTSRestClient.unMock((FTSRestClient) TDBeaconsFTSRestClient.getInstance());
+    PDBFTSRestClient.unMock((FTSRestClient) PDBFTSRestClient.getInstance());
+    SequenceI[] selectedSeqs = new SequenceI[] { seq };
     StructureChooser sc = new StructureChooser(selectedSeqs, seq, null);
     sc.fetchStructuresMetaData();
-    assertTrue(sc.getDiscoveredStructuresSet() != null);
-    assertTrue(sc.getDiscoveredStructuresSet().size() > 0);
+    Collection<FTSData> ss = (Collection<FTSData>) PA.getValue(sc,
+            "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, PDBStructureChooserQuerySource.sanitizeSeqName(name));
+
+    // remove a [nn] substring
+    name = "abcde12[345]fg";
+    assertEquals("abcde12fg", PDBStructureChooserQuerySource.sanitizeSeqName(name));
+
+    // remove characters other than a-zA-Z0-9 | or _
+    name = "ab[cd],.\t£$*!- \\\"@:e";
+    assertEquals("abcde", PDBStructureChooserQuerySource.sanitizeSeqName(name));
 
+    name = "abcde12[345a]fg";
+    assertEquals("abcde12345afg", PDBStructureChooserQuerySource.sanitizeSeqName(name));
   }
 }