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.service.threedbeacons.TDBeaconsFTSRestClient;
  34 import jalview.fts.threedbeacons.TDBeaconsFTSRestClientTest;
  35 import jalview.gui.structurechooser.PDBStructureChooserQuerySource;
  36 import jalview.gui.structurechooser.StructureChooserQuerySource;
  37 import jalview.gui.structurechooser.ThreeDBStructureChooserQuerySource;
  38 import jalview.jbgui.FilterOption;
  39 import jalview.ws.params.InvalidArgumentException;
  40
  41 import java.util.Collection;
  42 import java.util.Vector;
  43
  44 import org.testng.annotations.AfterMethod;
  45 import org.testng.annotations.BeforeClass;
  46 import org.testng.annotations.BeforeMethod;
  47 import org.testng.annotations.Test;
  48
  49 import junit.extensions.PA;
  50
  51 public class StructureChooserTest
  52 {
  53
  54   @BeforeClass(alwaysRun = true)
  55   public void setUpJvOptionPane()
  56   {
  57     JvOptionPane.setInteractiveMode(false);
  58     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
  59   }
  60
  61   Sequence seq,upSeq;
  62
  63   @BeforeMethod(alwaysRun = true)
  64   public void setUp() throws Exception
  65   {
  66     seq = new Sequence("PDB|4kqy|4KQY|A", "ABCDEFGHIJKLMNOPQRSTUVWXYZ", 1,
  67             26);
  68     seq.createDatasetSequence();
  69     for (int x = 1; x < 5; x++)
  70     {
  71       DBRefEntry dbRef = new DBRefEntry();
  72       dbRef.setAccessionId("XYZ_" + x);
  73       seq.addDBRef(dbRef);
  74     }
  75
  76     PDBEntry dbRef = new PDBEntry();
  77     dbRef.setId("1tim");
  78
  79     Vector<PDBEntry> pdbIds = new Vector<>();
  80     pdbIds.add(dbRef);
  81
  82     seq.setPDBId(pdbIds);
  83
  84     // Uniprot sequence for 3D-Beacons mocks
  85     upSeq = new Sequence("P38398",
  86             "MDLSALRVEEVQNVINAMQKILECPICLELIKEPVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRS\n"
  87             + "LQESTRFSQLVEELLKIICAFQLDTGLEYANSYNFAKKENNSPEHLKDEVSIIQSMGYRNRAKRLLQSEPEN\n"
  88             + "PSLQETSLSVQLSNLGTVRTLRTKQRIQPQKTSVYIELGSDSSEDTVNKATYCSVGDQELLQITPQGTRDEI\n"
  89             + "SLDSAKKAACEFSETDVTNTEHHQPSNNDLNTTEKRAAERHPEKYQGSSVSNLHVEPCGTNTHASSLQHENS\n"
  90             + "SLLLTKDRMNVEKAEFCNKSKQPGLARSQHNRWAGSKETCNDRRTPSTEKKVDLNADPLCERKEWNKQKLPC\n"
  91             + "SENPRDTEDVPWITLNSSIQKVNEWFSRSDELLGSDDSHDGESESNAKVADVLDVLNEVDEYSGSSEKIDLL\n"
  92             + "ASDPHEALICKSERVHSKSVESNIEDKIFGKTYRKKASLPNLSHVTENLIIGAFVTEPQIIQERPLTNKLKR\n"
  93             + "KRRPTSGLHPEDFIKKADLAVQKTPEMINQGTNQTEQNGQVMNITNSGHENKTKGDSIQNEKNPNPIESLEK\n"
  94             + "ESAFKTKAEPISSSISNMELELNIHNSKAPKKNRLRRKSSTRHIHALELVVSRNLSPPNCTELQIDSCSSSE\n"
  95             + "EIKKKKYNQMPVRHSRNLQLMEGKEPATGAKKSNKPNEQTSKRHDSDTFPELKLTNAPGSFTKCSNTSELKE\n"
  96             + "FVNPSLPREEKEEKLETVKVSNNAEDPKDLMLSGERVLQTERSVESSSISLVPGTDYGTQESISLLEVSTLG\n"
  97             + "KAKTEPNKCVSQCAAFENPKGLIHGCSKDNRNDTEGFKYPLGHEVNHSRETSIEMEESELDAQYLQNTFKVS\n"
  98             + "KRQSFAPFSNPGNAEEECATFSAHSGSLKKQSPKVTFECEQKEENQGKNESNIKPVQTVNITAGFPVVGQKD\n"
  99             + "KPVDNAKCSIKGGSRFCLSSQFRGNETGLITPNKHGLLQNPYRIPPLFPIKSFVKTKCKKNLLEENFEEHSM\n"
 100             + "SPEREMGNENIPSTVSTISRNNIRENVFKEASSSNINEVGSSTNEVGSSINEIGSSDENIQAELGRNRGPKL\n"
 101             + "NAMLRLGVLQPEVYKQSLPGSNCKHPEIKKQEYEEVVQTVNTDFSPYLISDNLEQPMGSSHASQVCSETPDD\n"
 102             + "LLDDGEIKEDTSFAENDIKESSAVFSKSVQKGELSRSPSPFTHTHLAQGYRRGAKKLESSEENLSSEDEELP\n"
 103             + "CFQHLLFGKVNNIPSQSTRHSTVATECLSKNTEENLLSLKNSLNDCSNQVILAKASQEHHLSEETKCSASLF\n"
 104             + "SSQCSELEDLTANTNTQDPFLIGSSKQMRHQSESQGVGLSDKELVSDDEERGTGLEENNQEEQSMDSNLGEA\n"
 105             + "ASGCESETSVSEDCSGLSSQSDILTTQQRDTMQHNLIKLQQEMAELEAVLEQHGSQPSNSYPSIISDSSALE\n"
 106             + "DLRNPEQSTSEKAVLTSQKSSEYPISQNPEGLSADKFEVSADSSTSKNKEPGVERSSPSKCPSLDDRWYMHS\n"
 107             + "CSGSLQNRNYPSQEELIKVVDVEEQQLEESGPHDLTETSYLPRQDLEGTPYLESGISLFSDDPESDPSEDRA\n"
 108             + "PESARVGNIPSSTSALKVPQLKVAESAQSPAAAHTTDTAGYNAMEESVSREKPELTASTERVNKRMSMVVSG\n"
 109             + "LTPEEFMLVYKFARKHHITLTNLITEETTHVVMKTDAEFVCERTLKYFLGIAGGKWVVSYFWVTQSIKERKM\n"
 110             + "LNEHDFEVRGDVVNGRNHQGPKRARESQDRKIFRGLEICCYGPFTNMPTDQLEWMVQLCGASVVKELSSFTL\n"
 111             + "GTGVHPIVVVQPDAWTEDNGFHAIGQMCEAPVVTREWVLDSVALYQCQELDTYLIPQIPHSHY\n"
 112             + "", 1,
 113 1863);
 114     upSeq.createDatasetSequence();
 115     upSeq.setDescription("Breast cancer type 1 susceptibility protein");
 116     upSeq.addDBRef(new DBRefEntry("UNIPROT","0","P38398",null,true));
 117   }
 118
 119   @AfterMethod(alwaysRun = true)
 120   public void tearDown() throws Exception
 121   {
 122     seq = null;
 123     upSeq=null;
 124   }
 125
 126   @SuppressWarnings("deprecation")
 127   @Test(groups = { "Functional" })
 128   public void buildQueryTest()
 129   {
 130     System.out.println("seq >>>> " + seq);
 131
 132     StructureChooserQuerySource scquery = StructureChooserQuerySource.getQuerySourceFor(new SequenceI[] { seq});
 133     assertTrue(scquery instanceof PDBStructureChooserQuerySource);
 134     String query = scquery.buildQuery(seq);
 135     assertEquals("pdb_id:1tim", query);
 136     seq.getAllPDBEntries().clear();
 137     query = scquery.buildQuery(seq);
 138     assertEquals(
 139             "text:XYZ_1 OR text:XYZ_2 OR text:XYZ_3 OR text:XYZ_4 OR text:4kqy",
 140             query);
 141     seq.setDBRefs(null);
 142     query = scquery.buildQuery(seq);
 143     System.out.println(query);
 144     assertEquals("text:4kqy", query);
 145
 146     DBRefEntry uniprotDBRef = new DBRefEntry();
 147     uniprotDBRef.setAccessionId("P12345");
 148     uniprotDBRef.setSource(DBRefSource.UNIPROT);
 149     seq.addDBRef(uniprotDBRef);
 150
 151     DBRefEntry pdbDBRef = new DBRefEntry();
 152     pdbDBRef.setAccessionId("1XYZ");
 153     pdbDBRef.setSource(DBRefSource.PDB);
 154     seq.addDBRef(pdbDBRef);
 155
 156     for (int x = 1; x < 5; x++)
 157     {
 158       DBRefEntry dbRef = new DBRefEntry();
 159       dbRef.setAccessionId("XYZ_" + x);
 160       seq.addDBRef(dbRef);
 161     }
 162     System.out.println("");
 163     System.out.println(seq.getDBRefs());
 164     System.out.println(query);
 165     query = scquery.buildQuery(seq);
 166     assertEquals(
 167             "uniprot_accession:P12345 OR uniprot_id:P12345 OR pdb_id:1xyz",
 168             query);
 169   }
 170
 171   @SuppressWarnings("deprecation")
 172   @Test(groups = { "Functional" })
 173   public void buildThreeDBQueryTest()
 174   {
 175     System.out.println("seq >>>> " + upSeq);
 176     TDBeaconsFTSRestClientTest.setMock();
 177     StructureChooserQuerySource scquery = StructureChooserQuerySource.getQuerySourceFor(new SequenceI[] { upSeq});
 178     assertTrue(scquery instanceof ThreeDBStructureChooserQuerySource);
 179     String query = scquery.buildQuery(upSeq);
 180     assertEquals("P38398", query);
 181
 182     // query shouldn't change regardless of additional entries
 183     // because 3DBeacons requires canonical entries.
 184     upSeq.getAllPDBEntries().clear();
 185     query = scquery.buildQuery(upSeq);
 186     assertEquals("P38398", query);
 187     upSeq.setDBRefs(null);
 188     query = scquery.buildQuery(upSeq);
 189     /*
 190      * legacy projects/datasets will not have canonical flags set for uniprot dbrefs
 191      * graceful behaviour would be to
 192      *  - pick one ? not possible
 193      *  - iterate through all until a 200 is obtained ?
 194      *  ---> ideal but could be costly
 195      *  ---> better to do a direct retrieval from uniprot to work out which is the canonical identifier..
 196      *  ----> need a test to check that accessions can be promoted to canonical!
 197      */
 198     assertEquals(null, query);
 199
 200     // TODO:
 201 //
 202 //    DBRefEntry uniprotDBRef = new DBRefEntry();
 203 //    uniprotDBRef.setAccessionId("P12345");
 204 //    uniprotDBRef.setSource(DBRefSource.UNIPROT);
 205 //    upSeq.addDBRef(uniprotDBRef);
 206 //
 207 //    DBRefEntry pdbDBRef = new DBRefEntry();
 208 //    pdbDBRef.setAccessionId("1XYZ");
 209 //    pdbDBRef.setSource(DBRefSource.PDB);
 210 //    upSeq.addDBRef(pdbDBRef);
 211 //
 212 //    for (int x = 1; x < 5; x++)
 213 //    {
 214 //      DBRefEntry dbRef = new DBRefEntry();
 215 //      dbRef.setAccessionId("XYZ_" + x);
 216 //      seq.addDBRef(dbRef);
 217 //    }
 218 //    System.out.println("");
 219 //    System.out.println(seq.getDBRefs());
 220 //    System.out.println(query);
 221 //    query = scquery.buildQuery(seq);
 222 //    assertEquals(
 223 //            "uniprot_accession:P12345 OR uniprot_id:P12345 OR pdb_id:1xyz",
 224 //            query);
 225   }
 226
 227
 228   @Test(groups = { "Functional" })
 229   public void populateFilterComboBoxTest() throws InterruptedException
 230   {
 231     SequenceI[] selectedSeqs = new SequenceI[] { seq };
 232     StructureChooser sc = new StructureChooser(selectedSeqs, seq, null);
 233     sc.populateFilterComboBox(false, false);
 234     int optionsSize = sc.getCmbFilterOption().getItemCount();
 235     assertEquals(2, optionsSize); // if structures are not discovered then don't
 236                                   // populate filter options
 237
 238     sc.populateFilterComboBox(true, false);
 239     optionsSize = sc.getCmbFilterOption().getItemCount();
 240     assertTrue(optionsSize > 3); // if structures are found, filter options
 241                                  // should be populated
 242
 243     sc.populateFilterComboBox(true, true);
 244     assertTrue(sc.getCmbFilterOption().getSelectedItem() != null);
 245     FilterOption filterOpt = (FilterOption) sc.getCmbFilterOption()
 246             .getSelectedItem();
 247     assertEquals("Cached Structures", filterOpt.getName());
 248   }
 249
 250   @Test(groups = { "Network" })
 251   public void fetchStructuresInfoTest()
 252   {
 253     SequenceI[] selectedSeqs = new SequenceI[] { seq };
 254     StructureChooser sc = new StructureChooser(selectedSeqs, seq, null);
 255     sc.fetchStructuresMetaData();
 256     Collection<FTSData> ss = (Collection<FTSData>) PA.getValue(sc,
 257             "discoveredStructuresSet");
 258     assertNotNull(ss);
 259     assertTrue(ss.size() > 0);
 260
 261   }
 262
 263   @Test(groups = { "Functional" })
 264   public void sanitizeSeqNameTest()
 265   {
 266     String name = "ab_cdEF|fwxyz012349";
 267     assertEquals(name, PDBStructureChooserQuerySource.sanitizeSeqName(name));
 268
 269     // remove a [nn] substring
 270     name = "abcde12[345]fg";
 271     assertEquals("abcde12fg", PDBStructureChooserQuerySource.sanitizeSeqName(name));
 272
 273     // remove characters other than a-zA-Z0-9 | or _
 274     name = "ab[cd],.\t£$*!- \\\"@:e";
 275     assertEquals("abcde", PDBStructureChooserQuerySource.sanitizeSeqName(name));
 276
 277     name = "abcde12[345a]fg";
 278     assertEquals("abcde12345afg", PDBStructureChooserQuerySource.sanitizeSeqName(name));
 279   }
 280 }