test/jalview/gui/structurechooser/StructureChooserQuerySourceTest.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.structurechooser;
  22
  23
  24 import static org.testng.Assert.assertEquals;
  25 import static org.testng.Assert.assertTrue;
  26
  27 import java.util.Collection;
  28 import java.util.List;
  29 import java.util.Vector;
  30
  31 import org.junit.Assert;
  32 import org.testng.AssertJUnit;
  33 import org.testng.annotations.AfterMethod;
  34 import org.testng.annotations.BeforeClass;
  35 import org.testng.annotations.BeforeMethod;
  36 import org.testng.annotations.DataProvider;
  37 import org.testng.annotations.Test;
  38
  39 import jalview.datamodel.DBRefEntry;
  40 import jalview.datamodel.DBRefSource;
  41 import jalview.datamodel.PDBEntry;
  42 import jalview.datamodel.Sequence;
  43 import jalview.datamodel.SequenceI;
  44 import jalview.fts.api.FTSData;
  45 import jalview.fts.core.FTSRestRequest;
  46 import jalview.fts.core.FTSRestResponse;
  47 import jalview.fts.service.pdb.PDBFTSRestClient;
  48 import jalview.fts.service.pdb.PDBFTSRestClientTest;
  49 import jalview.fts.threedbeacons.TDBeaconsFTSRestClientTest;
  50 import jalview.gui.JvOptionPane;
  51 import jalview.gui.StructureChooser;
  52 import jalview.jbgui.FilterOption;
  53
  54 public class StructureChooserQuerySourceTest
  55 {
  56
  57   @BeforeClass(alwaysRun = true)
  58   public void setUpJvOptionPane()
  59   {
  60     JvOptionPane.setInteractiveMode(false);
  61     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
  62   }
  63
  64   Sequence seq,upSeq,upSeq_insulin;
  65
  66   // same set up as for structurechooser test
  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     upSeq_insulin=new Sequence("INS_HUMAN",
 124             "MALWMRLLPLLALLALWGPDPAAAFVNQHLCGSHLVEALYLVCGERGFFYTPKTRREAEDLQVGQVELGGGP"
 125             + "GAGSLQPLALEGSLQKRGIVEQCCTSICSLYQLENYCN");
 126     upSeq_insulin.createDatasetSequence();
 127     upSeq_insulin.setDescription("Insulin");
 128     upSeq_insulin.addDBRef(new DBRefEntry("UNIPROT","0","P01308",null,true));
 129   }
 130
 131 @AfterMethod(alwaysRun = true)
 132   public void tearDown() throws Exception
 133   {
 134     seq = null;
 135     upSeq=null;
 136   }
 137
 138   @SuppressWarnings("deprecation")
 139   @Test(groups = { "Functional" })
 140   public void buildPDBQueryTest()
 141   {
 142     System.out.println("seq >>>> " + seq);
 143
 144     StructureChooserQuerySource scquery = StructureChooserQuerySource.getQuerySourceFor(new SequenceI[] { seq});
 145     AssertJUnit.assertTrue(scquery instanceof PDBStructureChooserQuerySource);
 146     String query = scquery.buildQuery(seq);
 147     AssertJUnit.assertEquals("pdb_id:1tim", query);
 148     seq.getAllPDBEntries().clear();
 149     query = scquery.buildQuery(seq);
 150     AssertJUnit.assertEquals(
 151             "text:XYZ_1 OR text:XYZ_2 OR text:XYZ_3 OR text:XYZ_4 OR text:4kqy",
 152             query);
 153     seq.setDBRefs(null);
 154     query = scquery.buildQuery(seq);
 155     System.out.println(query);
 156     AssertJUnit.assertEquals("text:4kqy", query);
 157
 158     DBRefEntry uniprotDBRef = new DBRefEntry();
 159     uniprotDBRef.setAccessionId("P12345");
 160     uniprotDBRef.setSource(DBRefSource.UNIPROT);
 161     seq.addDBRef(uniprotDBRef);
 162
 163     DBRefEntry pdbDBRef = new DBRefEntry();
 164     pdbDBRef.setAccessionId("1XYZ");
 165     pdbDBRef.setSource(DBRefSource.PDB);
 166     seq.addDBRef(pdbDBRef);
 167
 168     for (int x = 1; x < 5; x++)
 169     {
 170       DBRefEntry dbRef = new DBRefEntry();
 171       dbRef.setAccessionId("XYZ_" + x);
 172       seq.addDBRef(dbRef);
 173     }
 174     System.out.println("");
 175     System.out.println(seq.getDBRefs());
 176     System.out.println(query);
 177     query = scquery.buildQuery(seq);
 178     AssertJUnit.assertEquals(
 179             "uniprot_accession:P12345 OR uniprot_id:P12345 OR pdb_id:1xyz",
 180             query);
 181   }
 182
 183   @SuppressWarnings("deprecation")
 184   @Test(groups = { "Functional" })
 185   public void buildThreeDBQueryTest()
 186   {
 187     System.out.println("seq >>>> " + upSeq);
 188     TDBeaconsFTSRestClientTest.setMock();
 189     PDBFTSRestClientTest.setMock();
 190     StructureChooserQuerySource scquery = StructureChooserQuerySource.getQuerySourceFor(new SequenceI[] { upSeq});
 191     // gets the lightweight proxy rather than the ThreeDBStructureChooserQuerySource
 192     AssertJUnit.assertTrue(scquery instanceof ThreeDBStructureChooserQuerySource);
 193     String query = scquery.buildQuery(upSeq);
 194     AssertJUnit.assertEquals("P38398", query);
 195
 196     // query shouldn't change regardless of additional entries
 197     // because 3DBeacons requires canonical entries.
 198     upSeq.getAllPDBEntries().clear();
 199     query = scquery.buildQuery(upSeq);
 200     AssertJUnit.assertEquals("P38398", query);
 201     upSeq.setDBRefs(null);
 202     query = scquery.buildQuery(upSeq);
 203     /*
 204      * legacy projects/datasets will not have canonical flags set for uniprot dbrefs
 205      * graceful behaviour would be to
 206      *  - pick one ? not possible
 207      *  - iterate through all until a 200 is obtained ?
 208      *  ---> ideal but could be costly
 209      *  ---> better to do a direct retrieval from uniprot to work out which is the canonical identifier..
 210      *  ----> need a test to check that accessions can be promoted to canonical!
 211      */
 212     //FIXME - need to be able to use ID to query here ?
 213     AssertJUnit.assertEquals(null, query);
 214
 215
 216
 217     // TODO:
 218     /**
 219      * set of sequences:
 220      * - no protein -> TDB not applicable, query PDBe only (consider RNA or DNA - specific query adapter ?)
 221      * - protein but no uniprot -> first consider trying to get uniprot refs (need a mark to say none are available)
 222      * - protein and uniprot - no canonicals -> resolve to uniprot automatically to get canonicals
 223      * - query uniprot against 3DBeacons
 224      * --> decorate experimental structures with additional data from PDBe
 225      * - query remaining against PDBe
 226      * Ranking
 227      * - 3D Beacons
 228      *  --> in memory ranking - no need to query twice
 229      *  Rank by
 230      *  - experimental > AlphaFold -> Model
 231      *  - start > end
 232      *  -> filters for
 233      *  -> experimental only
 234      *  -> experimental plus best models for other regions
 235      *  -> "best cover"
 236      *  -> need to be able to select correct reference (the longest one that covers all) for superposition
 237      */
 238 //
 239 //    DBRefEntry uniprotDBRef = new DBRefEntry();
 240 //    uniprotDBRef.setAccessionId("P12345");
 241 //    uniprotDBRef.setSource(DBRefSource.UNIPROT);
 242 //    upSeq.addDBRef(uniprotDBRef);
 243 //
 244 //    DBRefEntry pdbDBRef = new DBRefEntry();
 245 //    pdbDBRef.setAccessionId("1XYZ");
 246 //    pdbDBRef.setSource(DBRefSource.PDB);
 247 //    upSeq.addDBRef(pdbDBRef);
 248 //
 249 //    for (int x = 1; x < 5; x++)
 250 //    {
 251 //      DBRefEntry dbRef = new DBRefEntry();
 252 //      dbRef.setAccessionId("XYZ_" + x);
 253 //      seq.addDBRef(dbRef);
 254 //    }
 255 //    System.out.println("");
 256 //    System.out.println(seq.getDBRefs());
 257 //    System.out.println(query);
 258 //    query = scquery.buildQuery(seq);
 259 //    assertEquals(
 260 //            "uniprot_accession:P12345 OR uniprot_id:P12345 OR pdb_id:1xyz",
 261 //            query);
 262   }
 263   @Test(groups= {"Functional"},dataProvider = "testUpSeqs")
 264   public void cascadingThreeDBandPDBQuerys(SequenceI testUpSeq)
 265   {
 266     TDBeaconsFTSRestClientTest.setMock();
 267     PDBFTSRestClientTest.setMock();
 268     ThreeDBStructureChooserQuerySource tdbquery = new ThreeDBStructureChooserQuerySource();
 269     PDBStructureChooserQuerySource pdbquery  = new PDBStructureChooserQuerySource();
 270
 271
 272
 273     FTSRestResponse upResponse = null;
 274     FTSRestResponse pdbResponse = null;
 275     // TODO test available options
 276     // Best coverage
 277     // Best Alphafold Model
 278     // Best model (by confidence score)
 279     // Will also need to develop a more sophisticated filtering system
 280     List<FilterOption> opts = tdbquery.getAvailableFilterOptions(StructureChooser.VIEWS_FILTER);
 281     FilterOption opt_singlebest = opts.get(0);
 282     FilterOption opt_manybest = opts.get(1);
 283     assertEquals(opt_singlebest.getValue(), ThreeDBStructureChooserQuerySource.FILTER_FIRST_BEST_COVERAGE);
 284     assertEquals(opt_manybest.getValue(), ThreeDBStructureChooserQuerySource.FILTER_TDBEACONS_COVERAGE);
 285
 286     try {
 287       upResponse = tdbquery.fetchStructuresMetaData(testUpSeq, tdbquery.getDocFieldPrefs().getStructureSummaryFields(),  opt_singlebest, false);
 288       tdbquery.updateAvailableFilterOptions(StructureChooser.VIEWS_FILTER,opts,upResponse.getSearchSummary());
 289       // test ranking without additional PDBe data
 290       FTSRestResponse firstRanked = tdbquery.selectFirstRankedQuery(testUpSeq, upResponse.getSearchSummary(), tdbquery.getDocFieldPrefs().getStructureSummaryFields(), opt_singlebest.getValue(), false);
 291       assertEquals(firstRanked.getNumberOfItemsFound(),1);
 292       // many best response
 293       upResponse = tdbquery.fetchStructuresMetaData(testUpSeq, tdbquery.getDocFieldPrefs().getStructureSummaryFields(),  opt_manybest, false);
 294       assertTrue(firstRanked.getSearchSummary().size()<upResponse.getSearchSummary().size());
 295       // NB Could have race condition here
 296       String pdb_Query = tdbquery.buildPDBFTSQueryFor(upResponse);
 297       assertTrue(pdb_Query.trim().length()>0);
 298       pdbResponse = tdbquery.fetchStructuresMetaDataFor(pdbquery, upResponse);
 299       assertTrue(pdbResponse.getNumberOfItemsFound()>0);
 300       FTSRestResponse joinedResp = tdbquery.joinResponses(upResponse, pdbResponse);
 301       assertEquals(upResponse.getNumberOfItemsFound(),joinedResp.getNumberOfItemsFound());
 302
 303
 304     } catch (Exception x)
 305     {
 306       x.printStackTrace();
 307       Assert.fail("Unexpected Exception");
 308     }
 309     StructureChooserQuerySource scquery = StructureChooserQuerySource.getQuerySourceFor(new SequenceI[] { testUpSeq});
 310
 311   }
 312
 313   @DataProvider(name = "testUpSeqs")
 314   public Object[][] testUpSeqs() throws Exception
 315   {
 316     setUp();
 317     return new Object[][] { {upSeq},{upSeq_insulin}};
 318   }
 319
 320   @Test(groups = { "Functional" })
 321   public void sanitizeSeqNameTest()
 322   {
 323     String name = "ab_cdEF|fwxyz012349";
 324     AssertJUnit.assertEquals(name, PDBStructureChooserQuerySource.sanitizeSeqName(name));
 325
 326     // remove a [nn] substring
 327     name = "abcde12[345]fg";
 328     AssertJUnit.assertEquals("abcde12fg", PDBStructureChooserQuerySource.sanitizeSeqName(name));
 329
 330     // remove characters other than a-zA-Z0-9 | or _
 331     name = "ab[cd],.\t£$*!- \\\"@:e";
 332     AssertJUnit.assertEquals("abcde", PDBStructureChooserQuerySource.sanitizeSeqName(name));
 333
 334     name = "abcde12[345a]fg";
 335     AssertJUnit.assertEquals("abcde12345afg", PDBStructureChooserQuerySource.sanitizeSeqName(name));
 336   }
 337 }