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 import java.util.Collection;
  28 import java.util.Vector;
  29
  30 import org.junit.Assert;
  31 import org.testng.annotations.AfterMethod;
  32 import org.testng.annotations.BeforeClass;
  33 import org.testng.annotations.BeforeMethod;
  34 import org.testng.annotations.Test;
  35
  36 import jalview.datamodel.DBRefEntry;
  37 import jalview.datamodel.PDBEntry;
  38 import jalview.datamodel.Sequence;
  39 import jalview.datamodel.SequenceI;
  40 import jalview.fts.api.FTSData;
  41 import jalview.fts.core.FTSRestClient;
  42 import jalview.fts.service.pdb.PDBFTSRestClient;
  43 import jalview.fts.service.pdb.PDBFTSRestClientTest;
  44 import jalview.fts.service.threedbeacons.TDBeaconsFTSRestClient;
  45 import jalview.fts.threedbeacons.TDBeaconsFTSRestClientTest;
  46 import jalview.gui.structurechooser.PDBStructureChooserQuerySource;
  47 import jalview.jbgui.FilterOption;
  48 import junit.extensions.PA;
  49
  50 public class StructureChooserTest
  51 {
  52
  53   @BeforeClass(alwaysRun = true)
  54   public void setUpJvOptionPane()
  55   {
  56     JvOptionPane.setInteractiveMode(false);
  57     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
  58   }
  59
  60   Sequence seq,upSeq;
  61
  62   @BeforeMethod(alwaysRun = true)
  63   public void setUp() throws Exception
  64   {
  65     seq = new Sequence("PDB|4kqy|4KQY|A", "ABCDEFGHIJKLMNOPQRSTUVWXYZ", 1,
  66             26);
  67     seq.createDatasetSequence();
  68     for (int x = 1; x < 5; x++)
  69     {
  70       DBRefEntry dbRef = new DBRefEntry();
  71       dbRef.setAccessionId("XYZ_" + x);
  72       seq.addDBRef(dbRef);
  73     }
  74
  75     PDBEntry dbRef = new PDBEntry();
  76     dbRef.setId("1tim");
  77
  78     Vector<PDBEntry> pdbIds = new Vector<>();
  79     pdbIds.add(dbRef);
  80
  81     seq.setPDBId(pdbIds);
  82
  83     // Uniprot sequence for 3D-Beacons mocks
  84     upSeq = new Sequence("P38398",
  85             "MDLSALRVEEVQNVINAMQKILECPICLELIKEPVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRS\n"
  86             + "LQESTRFSQLVEELLKIICAFQLDTGLEYANSYNFAKKENNSPEHLKDEVSIIQSMGYRNRAKRLLQSEPEN\n"
  87             + "PSLQETSLSVQLSNLGTVRTLRTKQRIQPQKTSVYIELGSDSSEDTVNKATYCSVGDQELLQITPQGTRDEI\n"
  88             + "SLDSAKKAACEFSETDVTNTEHHQPSNNDLNTTEKRAAERHPEKYQGSSVSNLHVEPCGTNTHASSLQHENS\n"
  89             + "SLLLTKDRMNVEKAEFCNKSKQPGLARSQHNRWAGSKETCNDRRTPSTEKKVDLNADPLCERKEWNKQKLPC\n"
  90             + "SENPRDTEDVPWITLNSSIQKVNEWFSRSDELLGSDDSHDGESESNAKVADVLDVLNEVDEYSGSSEKIDLL\n"
  91             + "ASDPHEALICKSERVHSKSVESNIEDKIFGKTYRKKASLPNLSHVTENLIIGAFVTEPQIIQERPLTNKLKR\n"
  92             + "KRRPTSGLHPEDFIKKADLAVQKTPEMINQGTNQTEQNGQVMNITNSGHENKTKGDSIQNEKNPNPIESLEK\n"
  93             + "ESAFKTKAEPISSSISNMELELNIHNSKAPKKNRLRRKSSTRHIHALELVVSRNLSPPNCTELQIDSCSSSE\n"
  94             + "EIKKKKYNQMPVRHSRNLQLMEGKEPATGAKKSNKPNEQTSKRHDSDTFPELKLTNAPGSFTKCSNTSELKE\n"
  95             + "FVNPSLPREEKEEKLETVKVSNNAEDPKDLMLSGERVLQTERSVESSSISLVPGTDYGTQESISLLEVSTLG\n"
  96             + "KAKTEPNKCVSQCAAFENPKGLIHGCSKDNRNDTEGFKYPLGHEVNHSRETSIEMEESELDAQYLQNTFKVS\n"
  97             + "KRQSFAPFSNPGNAEEECATFSAHSGSLKKQSPKVTFECEQKEENQGKNESNIKPVQTVNITAGFPVVGQKD\n"
  98             + "KPVDNAKCSIKGGSRFCLSSQFRGNETGLITPNKHGLLQNPYRIPPLFPIKSFVKTKCKKNLLEENFEEHSM\n"
  99             + "SPEREMGNENIPSTVSTISRNNIRENVFKEASSSNINEVGSSTNEVGSSINEIGSSDENIQAELGRNRGPKL\n"
 100             + "NAMLRLGVLQPEVYKQSLPGSNCKHPEIKKQEYEEVVQTVNTDFSPYLISDNLEQPMGSSHASQVCSETPDD\n"
 101             + "LLDDGEIKEDTSFAENDIKESSAVFSKSVQKGELSRSPSPFTHTHLAQGYRRGAKKLESSEENLSSEDEELP\n"
 102             + "CFQHLLFGKVNNIPSQSTRHSTVATECLSKNTEENLLSLKNSLNDCSNQVILAKASQEHHLSEETKCSASLF\n"
 103             + "SSQCSELEDLTANTNTQDPFLIGSSKQMRHQSESQGVGLSDKELVSDDEERGTGLEENNQEEQSMDSNLGEA\n"
 104             + "ASGCESETSVSEDCSGLSSQSDILTTQQRDTMQHNLIKLQQEMAELEAVLEQHGSQPSNSYPSIISDSSALE\n"
 105             + "DLRNPEQSTSEKAVLTSQKSSEYPISQNPEGLSADKFEVSADSSTSKNKEPGVERSSPSKCPSLDDRWYMHS\n"
 106             + "CSGSLQNRNYPSQEELIKVVDVEEQQLEESGPHDLTETSYLPRQDLEGTPYLESGISLFSDDPESDPSEDRA\n"
 107             + "PESARVGNIPSSTSALKVPQLKVAESAQSPAAAHTTDTAGYNAMEESVSREKPELTASTERVNKRMSMVVSG\n"
 108             + "LTPEEFMLVYKFARKHHITLTNLITEETTHVVMKTDAEFVCERTLKYFLGIAGGKWVVSYFWVTQSIKERKM\n"
 109             + "LNEHDFEVRGDVVNGRNHQGPKRARESQDRKIFRGLEICCYGPFTNMPTDQLEWMVQLCGASVVKELSSFTL\n"
 110             + "GTGVHPIVVVQPDAWTEDNGFHAIGQMCEAPVVTREWVLDSVALYQCQELDTYLIPQIPHSHY\n"
 111             + "", 1,
 112 1863);
 113     upSeq.createDatasetSequence();
 114     upSeq.setDescription("Breast cancer type 1 susceptibility protein");
 115     upSeq.addDBRef(new DBRefEntry("UNIPROT","0","P38398",null,true));
 116   }
 117
 118   @AfterMethod(alwaysRun = true)
 119   public void tearDown() throws Exception
 120   {
 121     seq = null;
 122     upSeq=null;
 123   }
 124
 125   @Test(groups = { "Functional" })
 126   public void populateFilterComboBoxTest() throws InterruptedException
 127   {
 128     TDBeaconsFTSRestClientTest.setMock();
 129     PDBFTSRestClientTest.setMock();
 130
 131     SequenceI[] selectedSeqs = new SequenceI[] { seq };
 132     StructureChooser sc = new StructureChooser(selectedSeqs, seq, null);
 133
 134     // if structures are not discovered then don't
 135     // populate filter options
 136     sc.populateFilterComboBox(false, false);
 137     int optionsSize = sc.getCmbFilterOption().getItemCount();
 138     System.out.println("Items (no data, no cache): ");
 139     StringBuilder items = new StringBuilder();
 140     for (int p=0;p<optionsSize;p++)
 141     {
 142       items.append
 143       ("- ").append(sc.getCmbFilterOption().getItemAt(p).getName()).append("\n");
 144
 145     }
 146     // report items when this fails - seems to be a race condition
 147     Assert.assertEquals(items.toString(),optionsSize,2);
 148
 149     sc.populateFilterComboBox(true, false);
 150     optionsSize = sc.getCmbFilterOption().getItemCount();
 151     assertTrue(optionsSize > 3); // if structures are found, filter options
 152                                  // should be populated
 153
 154     sc.populateFilterComboBox(true, true);
 155     assertTrue(sc.getCmbFilterOption().getSelectedItem() != null);
 156     FilterOption filterOpt = (FilterOption) sc.getCmbFilterOption()
 157             .getSelectedItem();
 158     assertEquals("Cached Structures", filterOpt.getName());
 159     FTSRestClient.unMock((FTSRestClient) TDBeaconsFTSRestClient.getInstance());
 160     FTSRestClient.unMock((FTSRestClient) PDBFTSRestClient.getInstance());
 161
 162   }
 163
 164   @Test(groups = { "Network" })
 165   public void fetchStructuresInfoTest()
 166   {
 167     FTSRestClient.unMock((FTSRestClient) TDBeaconsFTSRestClient.getInstance());
 168     PDBFTSRestClient.unMock((FTSRestClient) PDBFTSRestClient.getInstance());
 169     SequenceI[] selectedSeqs = new SequenceI[] { seq };
 170     StructureChooser sc = new StructureChooser(selectedSeqs, seq, null);
 171     sc.fetchStructuresMetaData();
 172     Collection<FTSData> ss = (Collection<FTSData>) PA.getValue(sc,
 173             "discoveredStructuresSet");
 174     assertNotNull(ss);
 175     assertTrue(ss.size() > 0);
 176   }
 177
 178   @Test(groups = { "Functional" })
 179   public void fetchStructuresInfoMockedTest()
 180   {
 181     TDBeaconsFTSRestClientTest.setMock();
 182     PDBFTSRestClientTest.setMock();
 183     SequenceI[] selectedSeqs = new SequenceI[] { upSeq };
 184     StructureChooser sc = new StructureChooser(selectedSeqs, seq, null);
 185     sc.fetchStructuresMetaData();
 186     Collection<FTSData> ss = (Collection<FTSData>) PA.getValue(sc,
 187             "discoveredStructuresSet");
 188     assertNotNull(ss);
 189     assertTrue(ss.size() > 0);
 190   }
 191
 192   @Test(groups = { "Functional" })
 193   public void sanitizeSeqNameTest()
 194   {
 195     String name = "ab_cdEF|fwxyz012349";
 196     assertEquals(name, PDBStructureChooserQuerySource.sanitizeSeqName(name));
 197
 198     // remove a [nn] substring
 199     name = "abcde12[345]fg";
 200     assertEquals("abcde12fg", PDBStructureChooserQuerySource.sanitizeSeqName(name));
 201
 202     // remove characters other than a-zA-Z0-9 | or _
 203     name = "ab[cd],.\t£$*!- \\\"@:e";
 204     assertEquals("abcde", PDBStructureChooserQuerySource.sanitizeSeqName(name));
 205
 206     name = "abcde12[345a]fg";
 207     assertEquals("abcde12345afg", PDBStructureChooserQuerySource.sanitizeSeqName(name));
 208   }
 209 }