test/jalview/gui/StructureChooserTest.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.gui;
  22
  23 import static org.testng.Assert.assertEquals;
  24 import static org.testng.AssertJUnit.assertNotNull;
  25 import static org.testng.AssertJUnit.assertTrue;
  26
  27
  28 import java.util.Collection;
  29 import java.util.Vector;
  30
  31 import org.junit.Assert;
  32 import org.testng.annotations.AfterMethod;
  33 import org.testng.annotations.BeforeClass;
  34 import org.testng.annotations.BeforeMethod;
  35 import org.testng.annotations.Test;
  36
  37 import jalview.datamodel.DBRefEntry;
  38 import jalview.datamodel.PDBEntry;
  39 import jalview.datamodel.Sequence;
  40 import jalview.datamodel.SequenceI;
  41 import jalview.fts.api.FTSData;
  42 import jalview.fts.core.FTSRestClient;
  43 import jalview.fts.service.pdb.PDBFTSRestClient;
  44 import jalview.fts.service.pdb.PDBFTSRestClientTest;
  45 import jalview.fts.service.threedbeacons.TDBeaconsFTSRestClient;
  46 import jalview.fts.threedbeacons.TDBeaconsFTSRestClientTest;
  47 import jalview.gui.structurechooser.PDBStructureChooserQuerySource;
  48 import jalview.jbgui.FilterOption;
  49 import junit.extensions.PA;
  50
  51 @Test(singleThreaded = true)
  52 public class StructureChooserTest
  53 {
  54
  55   @BeforeClass(alwaysRun = true)
  56   public void setUpJvOptionPane()
  57   {
  58     JvOptionPane.setInteractiveMode(false);
  59     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
  60   }
  61
  62   Sequence seq,upSeq,upSeq_nocanonical;
  63
  64   @BeforeMethod(alwaysRun = true)
  65   public void setUp() throws Exception
  66   {
  67     seq = new Sequence("PDB|4kqy|4KQY|A", "ABCDEFGHIJKLMNOPQRSTUVWXYZ", 1,
  68             26);
  69     seq.createDatasetSequence();
  70     for (int x = 1; x < 5; x++)
  71     {
  72       DBRefEntry dbRef = new DBRefEntry();
  73       dbRef.setAccessionId("XYZ_" + x);
  74       seq.addDBRef(dbRef);
  75     }
  76
  77     PDBEntry dbRef = new PDBEntry();
  78     dbRef.setId("1tim");
  79
  80     Vector<PDBEntry> pdbIds = new Vector<>();
  81     pdbIds.add(dbRef);
  82
  83     seq.setPDBId(pdbIds);
  84
  85     // Uniprot sequence for 3D-Beacons mocks
  86     upSeq = new Sequence("P38398",
  87             "MDLSALRVEEVQNVINAMQKILECPICLELIKEPVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRS\n"
  88             + "LQESTRFSQLVEELLKIICAFQLDTGLEYANSYNFAKKENNSPEHLKDEVSIIQSMGYRNRAKRLLQSEPEN\n"
  89             + "PSLQETSLSVQLSNLGTVRTLRTKQRIQPQKTSVYIELGSDSSEDTVNKATYCSVGDQELLQITPQGTRDEI\n"
  90             + "SLDSAKKAACEFSETDVTNTEHHQPSNNDLNTTEKRAAERHPEKYQGSSVSNLHVEPCGTNTHASSLQHENS\n"
  91             + "SLLLTKDRMNVEKAEFCNKSKQPGLARSQHNRWAGSKETCNDRRTPSTEKKVDLNADPLCERKEWNKQKLPC\n"
  92             + "SENPRDTEDVPWITLNSSIQKVNEWFSRSDELLGSDDSHDGESESNAKVADVLDVLNEVDEYSGSSEKIDLL\n"
  93             + "ASDPHEALICKSERVHSKSVESNIEDKIFGKTYRKKASLPNLSHVTENLIIGAFVTEPQIIQERPLTNKLKR\n"
  94             + "KRRPTSGLHPEDFIKKADLAVQKTPEMINQGTNQTEQNGQVMNITNSGHENKTKGDSIQNEKNPNPIESLEK\n"
  95             + "ESAFKTKAEPISSSISNMELELNIHNSKAPKKNRLRRKSSTRHIHALELVVSRNLSPPNCTELQIDSCSSSE\n"
  96             + "EIKKKKYNQMPVRHSRNLQLMEGKEPATGAKKSNKPNEQTSKRHDSDTFPELKLTNAPGSFTKCSNTSELKE\n"
  97             + "FVNPSLPREEKEEKLETVKVSNNAEDPKDLMLSGERVLQTERSVESSSISLVPGTDYGTQESISLLEVSTLG\n"
  98             + "KAKTEPNKCVSQCAAFENPKGLIHGCSKDNRNDTEGFKYPLGHEVNHSRETSIEMEESELDAQYLQNTFKVS\n"
  99             + "KRQSFAPFSNPGNAEEECATFSAHSGSLKKQSPKVTFECEQKEENQGKNESNIKPVQTVNITAGFPVVGQKD\n"
 100             + "KPVDNAKCSIKGGSRFCLSSQFRGNETGLITPNKHGLLQNPYRIPPLFPIKSFVKTKCKKNLLEENFEEHSM\n"
 101             + "SPEREMGNENIPSTVSTISRNNIRENVFKEASSSNINEVGSSTNEVGSSINEIGSSDENIQAELGRNRGPKL\n"
 102             + "NAMLRLGVLQPEVYKQSLPGSNCKHPEIKKQEYEEVVQTVNTDFSPYLISDNLEQPMGSSHASQVCSETPDD\n"
 103             + "LLDDGEIKEDTSFAENDIKESSAVFSKSVQKGELSRSPSPFTHTHLAQGYRRGAKKLESSEENLSSEDEELP\n"
 104             + "CFQHLLFGKVNNIPSQSTRHSTVATECLSKNTEENLLSLKNSLNDCSNQVILAKASQEHHLSEETKCSASLF\n"
 105             + "SSQCSELEDLTANTNTQDPFLIGSSKQMRHQSESQGVGLSDKELVSDDEERGTGLEENNQEEQSMDSNLGEA\n"
 106             + "ASGCESETSVSEDCSGLSSQSDILTTQQRDTMQHNLIKLQQEMAELEAVLEQHGSQPSNSYPSIISDSSALE\n"
 107             + "DLRNPEQSTSEKAVLTSQKSSEYPISQNPEGLSADKFEVSADSSTSKNKEPGVERSSPSKCPSLDDRWYMHS\n"
 108             + "CSGSLQNRNYPSQEELIKVVDVEEQQLEESGPHDLTETSYLPRQDLEGTPYLESGISLFSDDPESDPSEDRA\n"
 109             + "PESARVGNIPSSTSALKVPQLKVAESAQSPAAAHTTDTAGYNAMEESVSREKPELTASTERVNKRMSMVVSG\n"
 110             + "LTPEEFMLVYKFARKHHITLTNLITEETTHVVMKTDAEFVCERTLKYFLGIAGGKWVVSYFWVTQSIKERKM\n"
 111             + "LNEHDFEVRGDVVNGRNHQGPKRARESQDRKIFRGLEICCYGPFTNMPTDQLEWMVQLCGASVVKELSSFTL\n"
 112             + "GTGVHPIVVVQPDAWTEDNGFHAIGQMCEAPVVTREWVLDSVALYQCQELDTYLIPQIPHSHY\n"
 113             + "", 1,
 114 1863);
 115     upSeq.setDescription("Breast cancer type 1 susceptibility protein");
 116     upSeq_nocanonical = new Sequence(upSeq);
 117     upSeq.createDatasetSequence();
 118     upSeq.addDBRef(new DBRefEntry("UNIPROT","0","P38398",null,true));
 119
 120     upSeq_nocanonical.createDatasetSequence();
 121     // not a canonical reference
 122     upSeq_nocanonical.addDBRef(new DBRefEntry("UNIPROT","0","P38398",null,false));
 123   }
 124
 125   @AfterMethod(alwaysRun = true)
 126   public void tearDown() throws Exception
 127   {
 128     seq = null;
 129     upSeq=null;
 130     upSeq_nocanonical=null;
 131   }
 132
 133   @Test(groups = { "Functional" })
 134   public void populateFilterComboBoxTest() throws InterruptedException
 135   {
 136     TDBeaconsFTSRestClientTest.setMock();
 137     PDBFTSRestClientTest.setMock();
 138
 139     SequenceI[] selectedSeqs = new SequenceI[] { seq };
 140     StructureChooser sc = new StructureChooser(selectedSeqs, seq, null);
 141     ThreadwaitFor(200, sc);
 142
 143     // if structures are not discovered then don't
 144     // populate filter options
 145     sc.populateFilterComboBox(false, false);
 146     int optionsSize = sc.getCmbFilterOption().getItemCount();
 147     System.out.println("Items (no data, no cache): ");
 148     StringBuilder items = new StringBuilder();
 149     for (int p=0;p<optionsSize;p++)
 150     {
 151       items.append
 152       ("- ").append(sc.getCmbFilterOption().getItemAt(p).getName()).append("\n");
 153
 154     }
 155     // report items when this fails - seems to be a race condition
 156     Assert.assertEquals(items.toString(),optionsSize,2);
 157
 158     sc.populateFilterComboBox(true, false);
 159     optionsSize = sc.getCmbFilterOption().getItemCount();
 160     assertTrue(optionsSize > 3); // if structures are found, filter options
 161                                  // should be populated
 162
 163     sc.populateFilterComboBox(true, true);
 164     assertTrue(sc.getCmbFilterOption().getSelectedItem() != null);
 165     FilterOption filterOpt = (FilterOption) sc.getCmbFilterOption()
 166             .getSelectedItem();
 167     assertEquals("Cached Structures", filterOpt.getName());
 168     FTSRestClient.unMock((FTSRestClient) TDBeaconsFTSRestClient.getInstance());
 169     FTSRestClient.unMock((FTSRestClient) PDBFTSRestClient.getInstance());
 170
 171   }
 172
 173   @Test(groups = { "Functional" })
 174   public void displayTDBQueryTest() throws InterruptedException
 175   {
 176     TDBeaconsFTSRestClientTest.setMock();
 177     PDBFTSRestClientTest.setMock();
 178
 179     SequenceI[] selectedSeqs = new SequenceI[] { upSeq_nocanonical };
 180     StructureChooser sc = new StructureChooser(selectedSeqs, upSeq_nocanonical, null);
 181     // mock so should be quick. Exceptions from mocked PDBFTS are expected too
 182     ThreadwaitFor(500, sc);
 183
 184     assertTrue(sc.isCanQueryTDB() && sc.isNotQueriedTDBYet());
 185   }
 186
 187   @Test(groups = { "Network" })
 188   public void fetchStructuresInfoTest()
 189   {
 190     FTSRestClient.unMock((FTSRestClient) TDBeaconsFTSRestClient.getInstance());
 191     PDBFTSRestClient.unMock((FTSRestClient) PDBFTSRestClient.getInstance());
 192     SequenceI[] selectedSeqs = new SequenceI[] { seq };
 193     StructureChooser sc = new StructureChooser(selectedSeqs, seq, null);
 194     // not mocked, wait for 2s
 195     ThreadwaitFor(2000, sc);
 196
 197     sc.fetchStructuresMetaData();
 198     Collection<FTSData> ss = (Collection<FTSData>) PA.getValue(sc,
 199             "discoveredStructuresSet");
 200     assertNotNull(ss);
 201     assertTrue(ss.size() > 0);
 202   }
 203
 204   @Test(groups = { "Functional" })
 205   public void fetchStructuresInfoMockedTest()
 206   {
 207     TDBeaconsFTSRestClientTest.setMock();
 208     PDBFTSRestClientTest.setMock();
 209     SequenceI[] selectedSeqs = new SequenceI[] { upSeq };
 210     StructureChooser sc = new StructureChooser(selectedSeqs, seq, null);
 211     ThreadwaitFor(500, sc);
 212
 213     sc.fetchStructuresMetaData();
 214     Collection<FTSData> ss = (Collection<FTSData>) PA.getValue(sc,
 215             "discoveredStructuresSet");
 216     assertNotNull(ss);
 217     assertTrue(ss.size() > 0);
 218   }
 219
 220   private void ThreadwaitFor(int i, StructureChooser sc)
 221   {
 222     long timeout = i+System.currentTimeMillis();
 223     while (!sc.isDialogVisible() && timeout > System.currentTimeMillis())
 224     {
 225       try {
 226         Thread.sleep(50);
 227       } catch (InterruptedException x)
 228       {
 229
 230       }
 231     }
 232
 233   }
 234   @Test(groups = { "Functional" })
 235   public void sanitizeSeqNameTest()
 236   {
 237     String name = "ab_cdEF|fwxyz012349";
 238     assertEquals(name, PDBStructureChooserQuerySource.sanitizeSeqName(name));
 239
 240     // remove a [nn] substring
 241     name = "abcde12[345]fg";
 242     assertEquals("abcde12fg", PDBStructureChooserQuerySource.sanitizeSeqName(name));
 243
 244     // remove characters other than a-zA-Z0-9 | or _
 245     name = "ab[cd],.\t£$*!- \\\"@:e";
 246     assertEquals("abcde", PDBStructureChooserQuerySource.sanitizeSeqName(name));
 247
 248     name = "abcde12[345a]fg";
 249     assertEquals("abcde12345afg", PDBStructureChooserQuerySource.sanitizeSeqName(name));
 250   }
 251 }