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.AssertJUnit.assertEquals;
  24 import static org.testng.AssertJUnit.assertNotNull;
  25 import static org.testng.AssertJUnit.assertTrue;
  26
  27 import jalview.datamodel.DBRefEntry;
  28 import jalview.datamodel.DBRefSource;
  29 import jalview.datamodel.PDBEntry;
  30 import jalview.datamodel.Sequence;
  31 import jalview.datamodel.SequenceI;
  32 import jalview.fts.api.FTSData;
  33 import jalview.fts.api.FTSRestClientI;
  34 import jalview.fts.core.FTSRestClient;
  35 import jalview.fts.core.FTSRestRequest;
  36 import jalview.fts.service.pdb.PDBFTSRestClient;
  37 import jalview.fts.service.pdb.PDBFTSRestClientTest;
  38 import jalview.fts.service.threedbeacons.TDBeaconsFTSRestClient;
  39 import jalview.fts.threedbeacons.TDBeaconsFTSRestClientTest;
  40 import jalview.gui.structurechooser.PDBStructureChooserQuerySource;
  41 import jalview.gui.structurechooser.StructureChooserQuerySource;
  42 import jalview.gui.structurechooser.ThreeDBStructureChooserQuerySource;
  43 import jalview.jbgui.FilterOption;
  44 import jalview.ws.params.InvalidArgumentException;
  45
  46 import java.util.Collection;
  47 import java.util.Vector;
  48
  49 import org.junit.Assert;
  50 import org.testng.annotations.AfterMethod;
  51 import org.testng.annotations.BeforeClass;
  52 import org.testng.annotations.BeforeMethod;
  53 import org.testng.annotations.Test;
  54
  55 import junit.extensions.PA;
  56
  57 public class StructureChooserTest
  58 {
  59
  60   @BeforeClass(alwaysRun = true)
  61   public void setUpJvOptionPane()
  62   {
  63     JvOptionPane.setInteractiveMode(false);
  64     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
  65   }
  66
  67   Sequence seq,upSeq;
  68
  69   @BeforeMethod(alwaysRun = true)
  70   public void setUp() throws Exception
  71   {
  72     seq = new Sequence("PDB|4kqy|4KQY|A", "ABCDEFGHIJKLMNOPQRSTUVWXYZ", 1,
  73             26);
  74     seq.createDatasetSequence();
  75     for (int x = 1; x < 5; x++)
  76     {
  77       DBRefEntry dbRef = new DBRefEntry();
  78       dbRef.setAccessionId("XYZ_" + x);
  79       seq.addDBRef(dbRef);
  80     }
  81
  82     PDBEntry dbRef = new PDBEntry();
  83     dbRef.setId("1tim");
  84
  85     Vector<PDBEntry> pdbIds = new Vector<>();
  86     pdbIds.add(dbRef);
  87
  88     seq.setPDBId(pdbIds);
  89
  90     // Uniprot sequence for 3D-Beacons mocks
  91     upSeq = new Sequence("P38398",
  92             "MDLSALRVEEVQNVINAMQKILECPICLELIKEPVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRS\n"
  93             + "LQESTRFSQLVEELLKIICAFQLDTGLEYANSYNFAKKENNSPEHLKDEVSIIQSMGYRNRAKRLLQSEPEN\n"
  94             + "PSLQETSLSVQLSNLGTVRTLRTKQRIQPQKTSVYIELGSDSSEDTVNKATYCSVGDQELLQITPQGTRDEI\n"
  95             + "SLDSAKKAACEFSETDVTNTEHHQPSNNDLNTTEKRAAERHPEKYQGSSVSNLHVEPCGTNTHASSLQHENS\n"
  96             + "SLLLTKDRMNVEKAEFCNKSKQPGLARSQHNRWAGSKETCNDRRTPSTEKKVDLNADPLCERKEWNKQKLPC\n"
  97             + "SENPRDTEDVPWITLNSSIQKVNEWFSRSDELLGSDDSHDGESESNAKVADVLDVLNEVDEYSGSSEKIDLL\n"
  98             + "ASDPHEALICKSERVHSKSVESNIEDKIFGKTYRKKASLPNLSHVTENLIIGAFVTEPQIIQERPLTNKLKR\n"
  99             + "KRRPTSGLHPEDFIKKADLAVQKTPEMINQGTNQTEQNGQVMNITNSGHENKTKGDSIQNEKNPNPIESLEK\n"
 100             + "ESAFKTKAEPISSSISNMELELNIHNSKAPKKNRLRRKSSTRHIHALELVVSRNLSPPNCTELQIDSCSSSE\n"
 101             + "EIKKKKYNQMPVRHSRNLQLMEGKEPATGAKKSNKPNEQTSKRHDSDTFPELKLTNAPGSFTKCSNTSELKE\n"
 102             + "FVNPSLPREEKEEKLETVKVSNNAEDPKDLMLSGERVLQTERSVESSSISLVPGTDYGTQESISLLEVSTLG\n"
 103             + "KAKTEPNKCVSQCAAFENPKGLIHGCSKDNRNDTEGFKYPLGHEVNHSRETSIEMEESELDAQYLQNTFKVS\n"
 104             + "KRQSFAPFSNPGNAEEECATFSAHSGSLKKQSPKVTFECEQKEENQGKNESNIKPVQTVNITAGFPVVGQKD\n"
 105             + "KPVDNAKCSIKGGSRFCLSSQFRGNETGLITPNKHGLLQNPYRIPPLFPIKSFVKTKCKKNLLEENFEEHSM\n"
 106             + "SPEREMGNENIPSTVSTISRNNIRENVFKEASSSNINEVGSSTNEVGSSINEIGSSDENIQAELGRNRGPKL\n"
 107             + "NAMLRLGVLQPEVYKQSLPGSNCKHPEIKKQEYEEVVQTVNTDFSPYLISDNLEQPMGSSHASQVCSETPDD\n"
 108             + "LLDDGEIKEDTSFAENDIKESSAVFSKSVQKGELSRSPSPFTHTHLAQGYRRGAKKLESSEENLSSEDEELP\n"
 109             + "CFQHLLFGKVNNIPSQSTRHSTVATECLSKNTEENLLSLKNSLNDCSNQVILAKASQEHHLSEETKCSASLF\n"
 110             + "SSQCSELEDLTANTNTQDPFLIGSSKQMRHQSESQGVGLSDKELVSDDEERGTGLEENNQEEQSMDSNLGEA\n"
 111             + "ASGCESETSVSEDCSGLSSQSDILTTQQRDTMQHNLIKLQQEMAELEAVLEQHGSQPSNSYPSIISDSSALE\n"
 112             + "DLRNPEQSTSEKAVLTSQKSSEYPISQNPEGLSADKFEVSADSSTSKNKEPGVERSSPSKCPSLDDRWYMHS\n"
 113             + "CSGSLQNRNYPSQEELIKVVDVEEQQLEESGPHDLTETSYLPRQDLEGTPYLESGISLFSDDPESDPSEDRA\n"
 114             + "PESARVGNIPSSTSALKVPQLKVAESAQSPAAAHTTDTAGYNAMEESVSREKPELTASTERVNKRMSMVVSG\n"
 115             + "LTPEEFMLVYKFARKHHITLTNLITEETTHVVMKTDAEFVCERTLKYFLGIAGGKWVVSYFWVTQSIKERKM\n"
 116             + "LNEHDFEVRGDVVNGRNHQGPKRARESQDRKIFRGLEICCYGPFTNMPTDQLEWMVQLCGASVVKELSSFTL\n"
 117             + "GTGVHPIVVVQPDAWTEDNGFHAIGQMCEAPVVTREWVLDSVALYQCQELDTYLIPQIPHSHY\n"
 118             + "", 1,
 119 1863);
 120     upSeq.createDatasetSequence();
 121     upSeq.setDescription("Breast cancer type 1 susceptibility protein");
 122     upSeq.addDBRef(new DBRefEntry("UNIPROT","0","P38398",null,true));
 123   }
 124
 125   @AfterMethod(alwaysRun = true)
 126   public void tearDown() throws Exception
 127   {
 128     seq = null;
 129     upSeq=null;
 130   }
 131
 132   @Test(groups = { "Functional" })
 133   public void populateFilterComboBoxTest() throws InterruptedException
 134   {
 135     TDBeaconsFTSRestClientTest.setMock();
 136     PDBFTSRestClientTest.setMock();
 137
 138     SequenceI[] selectedSeqs = new SequenceI[] { seq };
 139     StructureChooser sc = new StructureChooser(selectedSeqs, seq, null);
 140     sc.populateFilterComboBox(false, false);
 141     int optionsSize = sc.getCmbFilterOption().getItemCount();
 142     assertEquals(2, optionsSize); // if structures are not discovered then don't
 143                                   // populate filter options
 144
 145     sc.populateFilterComboBox(true, false);
 146     optionsSize = sc.getCmbFilterOption().getItemCount();
 147     assertTrue(optionsSize > 3); // if structures are found, filter options
 148                                  // should be populated
 149
 150     sc.populateFilterComboBox(true, true);
 151     assertTrue(sc.getCmbFilterOption().getSelectedItem() != null);
 152     FilterOption filterOpt = (FilterOption) sc.getCmbFilterOption()
 153             .getSelectedItem();
 154     assertEquals("Cached Structures", filterOpt.getName());
 155     FTSRestClient.unMock((FTSRestClient) TDBeaconsFTSRestClient.getInstance());
 156     FTSRestClient.unMock((FTSRestClient) PDBFTSRestClient.getInstance());
 157
 158   }
 159
 160   @Test(groups = { "Network" })
 161   public void fetchStructuresInfoTest()
 162   {
 163     FTSRestClient.unMock((FTSRestClient) TDBeaconsFTSRestClient.getInstance());
 164     PDBFTSRestClient.unMock((FTSRestClient) PDBFTSRestClient.getInstance());
 165     SequenceI[] selectedSeqs = new SequenceI[] { seq };
 166     StructureChooser sc = new StructureChooser(selectedSeqs, seq, null);
 167     sc.fetchStructuresMetaData();
 168     Collection<FTSData> ss = (Collection<FTSData>) PA.getValue(sc,
 169             "discoveredStructuresSet");
 170     assertNotNull(ss);
 171     assertTrue(ss.size() > 0);
 172   }
 173
 174   @Test(groups = { "Functional" })
 175   public void fetchStructuresInfoMockedTest()
 176   {
 177     TDBeaconsFTSRestClientTest.setMock();
 178     PDBFTSRestClientTest.setMock();
 179     SequenceI[] selectedSeqs = new SequenceI[] { upSeq };
 180     StructureChooser sc = new StructureChooser(selectedSeqs, seq, null);
 181     sc.fetchStructuresMetaData();
 182     Collection<FTSData> ss = (Collection<FTSData>) PA.getValue(sc,
 183             "discoveredStructuresSet");
 184     assertNotNull(ss);
 185     assertTrue(ss.size() > 0);
 186   }
 187
 188   @Test(groups = { "Functional" })
 189   public void sanitizeSeqNameTest()
 190   {
 191     String name = "ab_cdEF|fwxyz012349";
 192     assertEquals(name, PDBStructureChooserQuerySource.sanitizeSeqName(name));
 193
 194     // remove a [nn] substring
 195     name = "abcde12[345]fg";
 196     assertEquals("abcde12fg", PDBStructureChooserQuerySource.sanitizeSeqName(name));
 197
 198     // remove characters other than a-zA-Z0-9 | or _
 199     name = "ab[cd],.\t£$*!- \\\"@:e";
 200     assertEquals("abcde", PDBStructureChooserQuerySource.sanitizeSeqName(name));
 201
 202     name = "abcde12[345a]fg";
 203     assertEquals("abcde12345afg", PDBStructureChooserQuerySource.sanitizeSeqName(name));
 204   }
 205 }