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                     + "",
 114             1, 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())
 153               .append("\n");
 154
 155     }
 156     // report items when this fails - seems to be a race condition
 157     Assert.assertEquals(items.toString(), optionsSize, 2);
 158
 159     sc.populateFilterComboBox(true, false);
 160     optionsSize = sc.getCmbFilterOption().getItemCount();
 161     assertTrue(optionsSize > 3); // if structures are found, filter options
 162                                  // should be populated
 163
 164     sc.populateFilterComboBox(true, true);
 165     assertTrue(sc.getCmbFilterOption().getSelectedItem() != null);
 166     FilterOption filterOpt = (FilterOption) sc.getCmbFilterOption()
 167             .getSelectedItem();
 168     assertEquals("Cached Structures", filterOpt.getName());
 169     FTSRestClient
 170             .unMock((FTSRestClient) TDBeaconsFTSRestClient.getInstance());
 171     FTSRestClient.unMock((FTSRestClient) PDBFTSRestClient.getInstance());
 172
 173   }
 174
 175   @Test(groups = { "Functional" })
 176   public void displayTDBQueryTest() throws InterruptedException
 177   {
 178     TDBeaconsFTSRestClientTest.setMock();
 179     PDBFTSRestClientTest.setMock();
 180
 181     SequenceI[] selectedSeqs = new SequenceI[] { upSeq_nocanonical };
 182     StructureChooser sc = new StructureChooser(selectedSeqs,
 183             upSeq_nocanonical, null);
 184     // mock so should be quick. Exceptions from mocked PDBFTS are expected too
 185     ThreadwaitFor(500, sc);
 186
 187     assertTrue(sc.isCanQueryTDB() && sc.isNotQueriedTDBYet());
 188   }
 189
 190   @Test(groups = { "Network" })
 191   public void fetchStructuresInfoTest()
 192   {
 193     FTSRestClient
 194             .unMock((FTSRestClient) TDBeaconsFTSRestClient.getInstance());
 195     PDBFTSRestClient.unMock((FTSRestClient) PDBFTSRestClient.getInstance());
 196     SequenceI[] selectedSeqs = new SequenceI[] { seq };
 197     StructureChooser sc = new StructureChooser(selectedSeqs, seq, null);
 198     // not mocked, wait for 2s
 199     ThreadwaitFor(2000, sc);
 200
 201     sc.fetchStructuresMetaData();
 202     Collection<FTSData> ss = (Collection<FTSData>) PA.getValue(sc,
 203             "discoveredStructuresSet");
 204     assertNotNull(ss);
 205     assertTrue(ss.size() > 0);
 206   }
 207
 208   @Test(groups = { "Functional" })
 209   public void fetchStructuresInfoMockedTest()
 210   {
 211     TDBeaconsFTSRestClientTest.setMock();
 212     PDBFTSRestClientTest.setMock();
 213     SequenceI[] selectedSeqs = new SequenceI[] { upSeq };
 214     StructureChooser sc = new StructureChooser(selectedSeqs, seq, null);
 215     ThreadwaitFor(500, sc);
 216
 217     sc.fetchStructuresMetaData();
 218     Collection<FTSData> ss = (Collection<FTSData>) PA.getValue(sc,
 219             "discoveredStructuresSet");
 220     assertNotNull(ss);
 221     assertTrue(ss.size() > 0);
 222   }
 223
 224   private void ThreadwaitFor(int i, StructureChooser sc)
 225   {
 226     long timeout = i + System.currentTimeMillis();
 227     while (!sc.isDialogVisible() && timeout > System.currentTimeMillis())
 228     {
 229       try
 230       {
 231         Thread.sleep(50);
 232       } catch (InterruptedException x)
 233       {
 234
 235       }
 236     }
 237   }
 238   @Test(groups = { "Functional" })
 239   public void sanitizeSeqNameTest()
 240   {
 241     String name = "ab_cdEF|fwxyz012349";
 242     assertEquals(name,
 243             PDBStructureChooserQuerySource.sanitizeSeqName(name));
 244
 245     // remove a [nn] substring
 246     name = "abcde12[345]fg";
 247     assertEquals("abcde12fg",
 248             PDBStructureChooserQuerySource.sanitizeSeqName(name));
 249
 250     // remove characters other than a-zA-Z0-9 | or _
 251     name = "ab[cd],.\t£$*!- \\\"@:e";
 252     assertEquals("abcde",
 253             PDBStructureChooserQuerySource.sanitizeSeqName(name));
 254
 255     name = "abcde12[345a]fg";
 256     assertEquals("abcde12345afg",
 257             PDBStructureChooserQuerySource.sanitizeSeqName(name));
 258   }
 259 }