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