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