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 import java.util.Collection;
  28 import java.util.Vector;
  29
  30 import org.junit.Assert;
  31 import org.testng.annotations.AfterMethod;
  32 import org.testng.annotations.BeforeClass;
  33 import org.testng.annotations.BeforeMethod;
  34 import org.testng.annotations.Test;
  35
  36 import jalview.datamodel.DBRefEntry;
  37 import jalview.datamodel.PDBEntry;
  38 import jalview.datamodel.Sequence;
  39 import jalview.datamodel.SequenceI;
  40 import jalview.fts.api.FTSData;
  41 import jalview.fts.core.FTSRestClient;
  42 import jalview.fts.service.pdb.PDBFTSRestClient;
  43 import jalview.fts.service.pdb.PDBFTSRestClientTest;
  44 import jalview.fts.service.threedbeacons.TDBeaconsFTSRestClient;
  45 import jalview.fts.threedbeacons.TDBeaconsFTSRestClientTest;
  46 import jalview.gui.structurechooser.PDBStructureChooserQuerySource;
  47 import jalview.jbgui.FilterOption;
  48 import junit.extensions.PA;
  49
  50 @Test(singleThreaded = true)
  51 public class StructureChooserTest
  52 {
  53
  54   @BeforeClass(alwaysRun = true)
  55   public void setUpJvOptionPane()
  56   {
  57     JvOptionPane.setInteractiveMode(false);
  58     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
  59   }
  60
  61   Sequence seq, upSeq, upSeq_nocanonical;
  62
  63   @BeforeMethod(alwaysRun = true)
  64   public void setUp() throws Exception
  65   {
  66     seq = new Sequence("PDB|4kqy|4KQY|A", "ABCDEFGHIJKLMNOPQRSTUVWXYZ", 1,
  67             26);
  68     seq.createDatasetSequence();
  69     for (int x = 1; x < 5; x++)
  70     {
  71       DBRefEntry dbRef = new DBRefEntry();
  72       dbRef.setAccessionId("XYZ_" + x);
  73       seq.addDBRef(dbRef);
  74     }
  75
  76     PDBEntry dbRef = new PDBEntry();
  77     dbRef.setId("1tim");
  78
  79     Vector<PDBEntry> pdbIds = new Vector<>();
  80     pdbIds.add(dbRef);
  81
  82     seq.setPDBId(pdbIds);
  83
  84     // Uniprot sequence for 3D-Beacons mocks
  85     upSeq = new Sequence("P38398",
  86             "MDLSALRVEEVQNVINAMQKILECPICLELIKEPVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRS\n"
  87                     + "LQESTRFSQLVEELLKIICAFQLDTGLEYANSYNFAKKENNSPEHLKDEVSIIQSMGYRNRAKRLLQSEPEN\n"
  88                     + "PSLQETSLSVQLSNLGTVRTLRTKQRIQPQKTSVYIELGSDSSEDTVNKATYCSVGDQELLQITPQGTRDEI\n"
  89                     + "SLDSAKKAACEFSETDVTNTEHHQPSNNDLNTTEKRAAERHPEKYQGSSVSNLHVEPCGTNTHASSLQHENS\n"
  90                     + "SLLLTKDRMNVEKAEFCNKSKQPGLARSQHNRWAGSKETCNDRRTPSTEKKVDLNADPLCERKEWNKQKLPC\n"
  91                     + "SENPRDTEDVPWITLNSSIQKVNEWFSRSDELLGSDDSHDGESESNAKVADVLDVLNEVDEYSGSSEKIDLL\n"
  92                     + "ASDPHEALICKSERVHSKSVESNIEDKIFGKTYRKKASLPNLSHVTENLIIGAFVTEPQIIQERPLTNKLKR\n"
  93                     + "KRRPTSGLHPEDFIKKADLAVQKTPEMINQGTNQTEQNGQVMNITNSGHENKTKGDSIQNEKNPNPIESLEK\n"
  94                     + "ESAFKTKAEPISSSISNMELELNIHNSKAPKKNRLRRKSSTRHIHALELVVSRNLSPPNCTELQIDSCSSSE\n"
  95                     + "EIKKKKYNQMPVRHSRNLQLMEGKEPATGAKKSNKPNEQTSKRHDSDTFPELKLTNAPGSFTKCSNTSELKE\n"
  96                     + "FVNPSLPREEKEEKLETVKVSNNAEDPKDLMLSGERVLQTERSVESSSISLVPGTDYGTQESISLLEVSTLG\n"
  97                     + "KAKTEPNKCVSQCAAFENPKGLIHGCSKDNRNDTEGFKYPLGHEVNHSRETSIEMEESELDAQYLQNTFKVS\n"
  98                     + "KRQSFAPFSNPGNAEEECATFSAHSGSLKKQSPKVTFECEQKEENQGKNESNIKPVQTVNITAGFPVVGQKD\n"
  99                     + "KPVDNAKCSIKGGSRFCLSSQFRGNETGLITPNKHGLLQNPYRIPPLFPIKSFVKTKCKKNLLEENFEEHSM\n"
 100                     + "SPEREMGNENIPSTVSTISRNNIRENVFKEASSSNINEVGSSTNEVGSSINEIGSSDENIQAELGRNRGPKL\n"
 101                     + "NAMLRLGVLQPEVYKQSLPGSNCKHPEIKKQEYEEVVQTVNTDFSPYLISDNLEQPMGSSHASQVCSETPDD\n"
 102                     + "LLDDGEIKEDTSFAENDIKESSAVFSKSVQKGELSRSPSPFTHTHLAQGYRRGAKKLESSEENLSSEDEELP\n"
 103                     + "CFQHLLFGKVNNIPSQSTRHSTVATECLSKNTEENLLSLKNSLNDCSNQVILAKASQEHHLSEETKCSASLF\n"
 104                     + "SSQCSELEDLTANTNTQDPFLIGSSKQMRHQSESQGVGLSDKELVSDDEERGTGLEENNQEEQSMDSNLGEA\n"
 105                     + "ASGCESETSVSEDCSGLSSQSDILTTQQRDTMQHNLIKLQQEMAELEAVLEQHGSQPSNSYPSIISDSSALE\n"
 106                     + "DLRNPEQSTSEKAVLTSQKSSEYPISQNPEGLSADKFEVSADSSTSKNKEPGVERSSPSKCPSLDDRWYMHS\n"
 107                     + "CSGSLQNRNYPSQEELIKVVDVEEQQLEESGPHDLTETSYLPRQDLEGTPYLESGISLFSDDPESDPSEDRA\n"
 108                     + "PESARVGNIPSSTSALKVPQLKVAESAQSPAAAHTTDTAGYNAMEESVSREKPELTASTERVNKRMSMVVSG\n"
 109                     + "LTPEEFMLVYKFARKHHITLTNLITEETTHVVMKTDAEFVCERTLKYFLGIAGGKWVVSYFWVTQSIKERKM\n"
 110                     + "LNEHDFEVRGDVVNGRNHQGPKRARESQDRKIFRGLEICCYGPFTNMPTDQLEWMVQLCGASVVKELSSFTL\n"
 111                     + "GTGVHPIVVVQPDAWTEDNGFHAIGQMCEAPVVTREWVLDSVALYQCQELDTYLIPQIPHSHY\n"
 112                     + "",
 113             1, 1863);
 114     upSeq.setDescription("Breast cancer type 1 susceptibility protein");
 115     upSeq_nocanonical = new Sequence(upSeq);
 116     upSeq.createDatasetSequence();
 117     upSeq.addDBRef(new DBRefEntry("UNIPROT", "0", "P38398", null, true));
 118
 119     upSeq_nocanonical.createDatasetSequence();
 120     // not a canonical reference
 121     upSeq_nocanonical.addDBRef(
 122             new DBRefEntry("UNIPROT", "0", "P38398", null, false));
 123
 124   }
 125
 126   @AfterMethod(alwaysRun = true)
 127   public void tearDown() throws Exception
 128   {
 129     seq = null;
 130     upSeq = null;
 131     upSeq_nocanonical = null;
 132   }
 133
 134   @Test(groups = { "Functional" })
 135   public void populateFilterComboBoxTest() throws InterruptedException
 136   {
 137     TDBeaconsFTSRestClientTest.setMock();
 138     PDBFTSRestClientTest.setMock();
 139
 140     SequenceI[] selectedSeqs = new SequenceI[] { seq };
 141     StructureChooser sc = new StructureChooser(selectedSeqs, seq, null);
 142     ThreadwaitFor(200, sc);
 143
 144     // if structures are not discovered then don't
 145     // populate filter options
 146     sc.populateFilterComboBox(false, false);
 147     int optionsSize = sc.getCmbFilterOption().getItemCount();
 148     System.out.println("Items (no data, no cache): ");
 149     StringBuilder items = new StringBuilder();
 150     for (int p = 0; p < optionsSize; p++)
 151     {
 152       items.append("- ")
 153               .append(sc.getCmbFilterOption().getItemAt(p).getName())
 154               .append("\n");
 155
 156     }
 157     // report items when this fails - seems to be a race condition
 158     Assert.assertEquals(items.toString(), optionsSize, 2);
 159
 160     sc.populateFilterComboBox(true, false);
 161     optionsSize = sc.getCmbFilterOption().getItemCount();
 162     assertTrue(optionsSize > 3); // if structures are found, filter options
 163                                  // should be populated
 164
 165     sc.populateFilterComboBox(true, true);
 166     assertTrue(sc.getCmbFilterOption().getSelectedItem() != null);
 167     FilterOption filterOpt = (FilterOption) sc.getCmbFilterOption()
 168             .getSelectedItem();
 169     assertEquals("Cached Structures", filterOpt.getName());
 170     FTSRestClient
 171             .unMock((FTSRestClient) TDBeaconsFTSRestClient.getInstance());
 172     FTSRestClient.unMock((FTSRestClient) PDBFTSRestClient.getInstance());
 173
 174   }
 175
 176   @Test(groups = { "Functional" })
 177   public void displayTDBQueryTest() throws InterruptedException
 178   {
 179     TDBeaconsFTSRestClientTest.setMock();
 180     PDBFTSRestClientTest.setMock();
 181
 182     SequenceI[] selectedSeqs = new SequenceI[] { upSeq_nocanonical };
 183     StructureChooser sc = new StructureChooser(selectedSeqs,
 184             upSeq_nocanonical, null);
 185     // mock so should be quick. Exceptions from mocked PDBFTS are expected too
 186     ThreadwaitFor(500, sc);
 187
 188     assertTrue(sc.isCanQueryTDB() && sc.isNotQueriedTDBYet());
 189   }
 190
 191   @Test(groups = { "Network" })
 192   public void fetchStructuresInfoTest()
 193   {
 194     FTSRestClient
 195             .unMock((FTSRestClient) TDBeaconsFTSRestClient.getInstance());
 196     PDBFTSRestClient.unMock((FTSRestClient) PDBFTSRestClient.getInstance());
 197     SequenceI[] selectedSeqs = new SequenceI[] { seq };
 198     StructureChooser sc = new StructureChooser(selectedSeqs, seq, null);
 199     // not mocked, wait for 2s
 200     ThreadwaitFor(2000, sc);
 201
 202     sc.fetchStructuresMetaData();
 203     Collection<FTSData> ss = (Collection<FTSData>) PA.getValue(sc,
 204             "discoveredStructuresSet");
 205     assertNotNull(ss);
 206     assertTrue(ss.size() > 0);
 207   }
 208
 209   @Test(groups = { "Functional" })
 210   public void fetchStructuresInfoMockedTest()
 211   {
 212     TDBeaconsFTSRestClientTest.setMock();
 213     PDBFTSRestClientTest.setMock();
 214     SequenceI[] selectedSeqs = new SequenceI[] { upSeq };
 215     StructureChooser sc = new StructureChooser(selectedSeqs, seq, null);
 216     ThreadwaitFor(500, sc);
 217
 218     sc.fetchStructuresMetaData();
 219     Collection<FTSData> ss = (Collection<FTSData>) PA.getValue(sc,
 220             "discoveredStructuresSet");
 221     assertNotNull(ss);
 222     assertTrue(ss.size() > 0);
 223   }
 224
 225   private void ThreadwaitFor(int i, StructureChooser sc)
 226   {
 227     long timeout = i + System.currentTimeMillis();
 228     while (!sc.isDialogVisible() && timeout > System.currentTimeMillis())
 229     {
 230       try
 231       {
 232         Thread.sleep(50);
 233       } catch (InterruptedException x)
 234       {
 235
 236       }
 237     }
 238
 239   }
 240
 241   @Test(groups = { "Functional" })
 242   public void sanitizeSeqNameTest()
 243   {
 244     String name = "ab_cdEF|fwxyz012349";
 245     assertEquals(name,
 246             PDBStructureChooserQuerySource.sanitizeSeqName(name));
 247
 248     // remove a [nn] substring
 249     name = "abcde12[345]fg";
 250     assertEquals("abcde12fg",
 251             PDBStructureChooserQuerySource.sanitizeSeqName(name));
 252
 253     // remove characters other than a-zA-Z0-9 | or _
 254     name = "ab[cd],.\t£$*!- \\\"@:e";
 255     assertEquals("abcde",
 256             PDBStructureChooserQuerySource.sanitizeSeqName(name));
 257
 258     name = "abcde12[345a]fg";
 259     assertEquals("abcde12345afg",
 260             PDBStructureChooserQuerySource.sanitizeSeqName(name));
 261   }
 262 }