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