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.assertEquals;
  25 import static org.testng.AssertJUnit.assertNotNull;
  26 import static org.testng.AssertJUnit.assertTrue;
  27
  28 import jalview.datamodel.DBRefEntry;
  29 import jalview.datamodel.DBRefSource;
  30 import jalview.datamodel.PDBEntry;
  31 import jalview.datamodel.Sequence;
  32 import jalview.datamodel.SequenceI;
  33 import jalview.fts.api.FTSData;
  34 import jalview.fts.api.FTSRestClientI;
  35 import jalview.fts.core.FTSRestClient;
  36 import jalview.fts.core.FTSRestRequest;
  37 import jalview.fts.service.pdb.PDBFTSRestClient;
  38 import jalview.fts.service.pdb.PDBFTSRestClientTest;
  39 import jalview.fts.service.threedbeacons.TDBeaconsFTSRestClient;
  40 import jalview.fts.threedbeacons.TDBeaconsFTSRestClientTest;
  41 import jalview.gui.structurechooser.PDBStructureChooserQuerySource;
  42 import jalview.gui.structurechooser.StructureChooserQuerySource;
  43 import jalview.gui.structurechooser.ThreeDBStructureChooserQuerySource;
  44 import jalview.jbgui.FilterOption;
  45 import jalview.ws.params.InvalidArgumentException;
  46
  47 import java.util.Collection;
  48 import java.util.Vector;
  49
  50 import javax.swing.JComboBox;
  51
  52 import org.junit.Assert;
  53 import org.testng.annotations.AfterMethod;
  54 import org.testng.annotations.BeforeClass;
  55 import org.testng.annotations.BeforeMethod;
  56 import org.testng.annotations.Test;
  57
  58 import junit.extensions.PA;
  59
  60 public class StructureChooserTest
  61 {
  62
  63   @BeforeClass(alwaysRun = true)
  64   public void setUpJvOptionPane()
  65   {
  66     JvOptionPane.setInteractiveMode(false);
  67     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
  68   }
  69
  70   Sequence seq,upSeq;
  71
  72   @BeforeMethod(alwaysRun = true)
  73   public void setUp() throws Exception
  74   {
  75     seq = new Sequence("PDB|4kqy|4KQY|A", "ABCDEFGHIJKLMNOPQRSTUVWXYZ", 1,
  76             26);
  77     seq.createDatasetSequence();
  78     for (int x = 1; x < 5; x++)
  79     {
  80       DBRefEntry dbRef = new DBRefEntry();
  81       dbRef.setAccessionId("XYZ_" + x);
  82       seq.addDBRef(dbRef);
  83     }
  84
  85     PDBEntry dbRef = new PDBEntry();
  86     dbRef.setId("1tim");
  87
  88     Vector<PDBEntry> pdbIds = new Vector<>();
  89     pdbIds.add(dbRef);
  90
  91     seq.setPDBId(pdbIds);
  92
  93     // Uniprot sequence for 3D-Beacons mocks
  94     upSeq = new Sequence("P38398",
  95             "MDLSALRVEEVQNVINAMQKILECPICLELIKEPVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRS\n"
  96             + "LQESTRFSQLVEELLKIICAFQLDTGLEYANSYNFAKKENNSPEHLKDEVSIIQSMGYRNRAKRLLQSEPEN\n"
  97             + "PSLQETSLSVQLSNLGTVRTLRTKQRIQPQKTSVYIELGSDSSEDTVNKATYCSVGDQELLQITPQGTRDEI\n"
  98             + "SLDSAKKAACEFSETDVTNTEHHQPSNNDLNTTEKRAAERHPEKYQGSSVSNLHVEPCGTNTHASSLQHENS\n"
  99             + "SLLLTKDRMNVEKAEFCNKSKQPGLARSQHNRWAGSKETCNDRRTPSTEKKVDLNADPLCERKEWNKQKLPC\n"
 100             + "SENPRDTEDVPWITLNSSIQKVNEWFSRSDELLGSDDSHDGESESNAKVADVLDVLNEVDEYSGSSEKIDLL\n"
 101             + "ASDPHEALICKSERVHSKSVESNIEDKIFGKTYRKKASLPNLSHVTENLIIGAFVTEPQIIQERPLTNKLKR\n"
 102             + "KRRPTSGLHPEDFIKKADLAVQKTPEMINQGTNQTEQNGQVMNITNSGHENKTKGDSIQNEKNPNPIESLEK\n"
 103             + "ESAFKTKAEPISSSISNMELELNIHNSKAPKKNRLRRKSSTRHIHALELVVSRNLSPPNCTELQIDSCSSSE\n"
 104             + "EIKKKKYNQMPVRHSRNLQLMEGKEPATGAKKSNKPNEQTSKRHDSDTFPELKLTNAPGSFTKCSNTSELKE\n"
 105             + "FVNPSLPREEKEEKLETVKVSNNAEDPKDLMLSGERVLQTERSVESSSISLVPGTDYGTQESISLLEVSTLG\n"
 106             + "KAKTEPNKCVSQCAAFENPKGLIHGCSKDNRNDTEGFKYPLGHEVNHSRETSIEMEESELDAQYLQNTFKVS\n"
 107             + "KRQSFAPFSNPGNAEEECATFSAHSGSLKKQSPKVTFECEQKEENQGKNESNIKPVQTVNITAGFPVVGQKD\n"
 108             + "KPVDNAKCSIKGGSRFCLSSQFRGNETGLITPNKHGLLQNPYRIPPLFPIKSFVKTKCKKNLLEENFEEHSM\n"
 109             + "SPEREMGNENIPSTVSTISRNNIRENVFKEASSSNINEVGSSTNEVGSSINEIGSSDENIQAELGRNRGPKL\n"
 110             + "NAMLRLGVLQPEVYKQSLPGSNCKHPEIKKQEYEEVVQTVNTDFSPYLISDNLEQPMGSSHASQVCSETPDD\n"
 111             + "LLDDGEIKEDTSFAENDIKESSAVFSKSVQKGELSRSPSPFTHTHLAQGYRRGAKKLESSEENLSSEDEELP\n"
 112             + "CFQHLLFGKVNNIPSQSTRHSTVATECLSKNTEENLLSLKNSLNDCSNQVILAKASQEHHLSEETKCSASLF\n"
 113             + "SSQCSELEDLTANTNTQDPFLIGSSKQMRHQSESQGVGLSDKELVSDDEERGTGLEENNQEEQSMDSNLGEA\n"
 114             + "ASGCESETSVSEDCSGLSSQSDILTTQQRDTMQHNLIKLQQEMAELEAVLEQHGSQPSNSYPSIISDSSALE\n"
 115             + "DLRNPEQSTSEKAVLTSQKSSEYPISQNPEGLSADKFEVSADSSTSKNKEPGVERSSPSKCPSLDDRWYMHS\n"
 116             + "CSGSLQNRNYPSQEELIKVVDVEEQQLEESGPHDLTETSYLPRQDLEGTPYLESGISLFSDDPESDPSEDRA\n"
 117             + "PESARVGNIPSSTSALKVPQLKVAESAQSPAAAHTTDTAGYNAMEESVSREKPELTASTERVNKRMSMVVSG\n"
 118             + "LTPEEFMLVYKFARKHHITLTNLITEETTHVVMKTDAEFVCERTLKYFLGIAGGKWVVSYFWVTQSIKERKM\n"
 119             + "LNEHDFEVRGDVVNGRNHQGPKRARESQDRKIFRGLEICCYGPFTNMPTDQLEWMVQLCGASVVKELSSFTL\n"
 120             + "GTGVHPIVVVQPDAWTEDNGFHAIGQMCEAPVVTREWVLDSVALYQCQELDTYLIPQIPHSHY\n"
 121             + "", 1,
 122 1863);
 123     upSeq.createDatasetSequence();
 124     upSeq.setDescription("Breast cancer type 1 susceptibility protein");
 125     upSeq.addDBRef(new DBRefEntry("UNIPROT","0","P38398",null,true));
 126   }
 127
 128   @AfterMethod(alwaysRun = true)
 129   public void tearDown() throws Exception
 130   {
 131     seq = null;
 132     upSeq=null;
 133   }
 134
 135   @Test(groups = { "Functional" })
 136   public void populateFilterComboBoxTest() throws InterruptedException
 137   {
 138     TDBeaconsFTSRestClientTest.setMock();
 139     PDBFTSRestClientTest.setMock();
 140
 141     SequenceI[] selectedSeqs = new SequenceI[] { seq };
 142     StructureChooser sc = new StructureChooser(selectedSeqs, seq, null);
 143
 144     // if structures are not discovered then don't
 145     // populate filter options
 146     sc.populateFilterComboBox(false, false);
 147     int optionsSize = sc.getCmbFilterOption().getItemCount();
 148     System.out.println("Items (no data, no cache): ");
 149     StringBuilder items = new StringBuilder();
 150     for (int p=0;p<optionsSize;p++)
 151     {
 152       items.append
 153       ("- ").append(sc.getCmbFilterOption().getItemAt(p).getName()).append("\n");
 154
 155     }
 156     // report items when this fails - seems to be a race condition
 157     assertEquals(optionsSize,2,items.toString());
 158
 159     sc.populateFilterComboBox(true, false);
 160     optionsSize = sc.getCmbFilterOption().getItemCount();
 161     assertTrue(optionsSize > 3); // if structures are found, filter options
 162                                  // should be populated
 163
 164     sc.populateFilterComboBox(true, true);
 165     assertTrue(sc.getCmbFilterOption().getSelectedItem() != null);
 166     FilterOption filterOpt = (FilterOption) sc.getCmbFilterOption()
 167             .getSelectedItem();
 168     assertEquals("Cached Structures", filterOpt.getName());
 169     FTSRestClient.unMock((FTSRestClient) TDBeaconsFTSRestClient.getInstance());
 170     FTSRestClient.unMock((FTSRestClient) PDBFTSRestClient.getInstance());
 171
 172   }
 173
 174   @Test(groups = { "Network" })
 175   public void fetchStructuresInfoTest()
 176   {
 177     FTSRestClient.unMock((FTSRestClient) TDBeaconsFTSRestClient.getInstance());
 178     PDBFTSRestClient.unMock((FTSRestClient) PDBFTSRestClient.getInstance());
 179     SequenceI[] selectedSeqs = new SequenceI[] { seq };
 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 fetchStructuresInfoMockedTest()
 190   {
 191     TDBeaconsFTSRestClientTest.setMock();
 192     PDBFTSRestClientTest.setMock();
 193     SequenceI[] selectedSeqs = new SequenceI[] { upSeq };
 194     StructureChooser sc = new StructureChooser(selectedSeqs, seq, null);
 195     sc.fetchStructuresMetaData();
 196     Collection<FTSData> ss = (Collection<FTSData>) PA.getValue(sc,
 197             "discoveredStructuresSet");
 198     assertNotNull(ss);
 199     assertTrue(ss.size() > 0);
 200   }
 201
 202   @Test(groups = { "Functional" })
 203   public void sanitizeSeqNameTest()
 204   {
 205     String name = "ab_cdEF|fwxyz012349";
 206     assertEquals(name, PDBStructureChooserQuerySource.sanitizeSeqName(name));
 207
 208     // remove a [nn] substring
 209     name = "abcde12[345]fg";
 210     assertEquals("abcde12fg", PDBStructureChooserQuerySource.sanitizeSeqName(name));
 211
 212     // remove characters other than a-zA-Z0-9 | or _
 213     name = "ab[cd],.\t£$*!- \\\"@:e";
 214     assertEquals("abcde", PDBStructureChooserQuerySource.sanitizeSeqName(name));
 215
 216     name = "abcde12[345a]fg";
 217     assertEquals("abcde12345afg", PDBStructureChooserQuerySource.sanitizeSeqName(name));
 218   }
 219 }