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.threedbeacons.TDBeaconsFTSRestClientTest;
  49 import jalview.gui.JvOptionPane;
  50 import jalview.gui.StructureChooser;
  51 import jalview.jbgui.FilterOption;
  52
  53 public class StructureChooserQuerySourceTest
  54 {
  55
  56   @BeforeClass(alwaysRun = true)
  57   public void setUpJvOptionPane()
  58   {
  59     JvOptionPane.setInteractiveMode(false);
  60     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
  61   }
  62
  63   Sequence seq,upSeq,upSeq_insulin;
  64
  65   // same set up as for structurechooser test
  66
  67 @BeforeMethod(alwaysRun = true)
  68   public void setUp() throws Exception
  69   {
  70     seq = new Sequence("PDB|4kqy|4KQY|A", "ABCDEFGHIJKLMNOPQRSTUVWXYZ", 1,
  71             26);
  72     seq.createDatasetSequence();
  73     for (int x = 1; x < 5; x++)
  74     {
  75       DBRefEntry dbRef = new DBRefEntry();
  76       dbRef.setAccessionId("XYZ_" + x);
  77       seq.addDBRef(dbRef);
  78     }
  79
  80     PDBEntry dbRef = new PDBEntry();
  81     dbRef.setId("1tim");
  82
  83     Vector<PDBEntry> pdbIds = new Vector<>();
  84     pdbIds.add(dbRef);
  85
  86     seq.setPDBId(pdbIds);
  87
  88     // Uniprot sequence for 3D-Beacons mocks
  89     upSeq = new Sequence("P38398",
  90             "MDLSALRVEEVQNVINAMQKILECPICLELIKEPVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRS\n"
  91             + "LQESTRFSQLVEELLKIICAFQLDTGLEYANSYNFAKKENNSPEHLKDEVSIIQSMGYRNRAKRLLQSEPEN\n"
  92             + "PSLQETSLSVQLSNLGTVRTLRTKQRIQPQKTSVYIELGSDSSEDTVNKATYCSVGDQELLQITPQGTRDEI\n"
  93             + "SLDSAKKAACEFSETDVTNTEHHQPSNNDLNTTEKRAAERHPEKYQGSSVSNLHVEPCGTNTHASSLQHENS\n"
  94             + "SLLLTKDRMNVEKAEFCNKSKQPGLARSQHNRWAGSKETCNDRRTPSTEKKVDLNADPLCERKEWNKQKLPC\n"
  95             + "SENPRDTEDVPWITLNSSIQKVNEWFSRSDELLGSDDSHDGESESNAKVADVLDVLNEVDEYSGSSEKIDLL\n"
  96             + "ASDPHEALICKSERVHSKSVESNIEDKIFGKTYRKKASLPNLSHVTENLIIGAFVTEPQIIQERPLTNKLKR\n"
  97             + "KRRPTSGLHPEDFIKKADLAVQKTPEMINQGTNQTEQNGQVMNITNSGHENKTKGDSIQNEKNPNPIESLEK\n"
  98             + "ESAFKTKAEPISSSISNMELELNIHNSKAPKKNRLRRKSSTRHIHALELVVSRNLSPPNCTELQIDSCSSSE\n"
  99             + "EIKKKKYNQMPVRHSRNLQLMEGKEPATGAKKSNKPNEQTSKRHDSDTFPELKLTNAPGSFTKCSNTSELKE\n"
 100             + "FVNPSLPREEKEEKLETVKVSNNAEDPKDLMLSGERVLQTERSVESSSISLVPGTDYGTQESISLLEVSTLG\n"
 101             + "KAKTEPNKCVSQCAAFENPKGLIHGCSKDNRNDTEGFKYPLGHEVNHSRETSIEMEESELDAQYLQNTFKVS\n"
 102             + "KRQSFAPFSNPGNAEEECATFSAHSGSLKKQSPKVTFECEQKEENQGKNESNIKPVQTVNITAGFPVVGQKD\n"
 103             + "KPVDNAKCSIKGGSRFCLSSQFRGNETGLITPNKHGLLQNPYRIPPLFPIKSFVKTKCKKNLLEENFEEHSM\n"
 104             + "SPEREMGNENIPSTVSTISRNNIRENVFKEASSSNINEVGSSTNEVGSSINEIGSSDENIQAELGRNRGPKL\n"
 105             + "NAMLRLGVLQPEVYKQSLPGSNCKHPEIKKQEYEEVVQTVNTDFSPYLISDNLEQPMGSSHASQVCSETPDD\n"
 106             + "LLDDGEIKEDTSFAENDIKESSAVFSKSVQKGELSRSPSPFTHTHLAQGYRRGAKKLESSEENLSSEDEELP\n"
 107             + "CFQHLLFGKVNNIPSQSTRHSTVATECLSKNTEENLLSLKNSLNDCSNQVILAKASQEHHLSEETKCSASLF\n"
 108             + "SSQCSELEDLTANTNTQDPFLIGSSKQMRHQSESQGVGLSDKELVSDDEERGTGLEENNQEEQSMDSNLGEA\n"
 109             + "ASGCESETSVSEDCSGLSSQSDILTTQQRDTMQHNLIKLQQEMAELEAVLEQHGSQPSNSYPSIISDSSALE\n"
 110             + "DLRNPEQSTSEKAVLTSQKSSEYPISQNPEGLSADKFEVSADSSTSKNKEPGVERSSPSKCPSLDDRWYMHS\n"
 111             + "CSGSLQNRNYPSQEELIKVVDVEEQQLEESGPHDLTETSYLPRQDLEGTPYLESGISLFSDDPESDPSEDRA\n"
 112             + "PESARVGNIPSSTSALKVPQLKVAESAQSPAAAHTTDTAGYNAMEESVSREKPELTASTERVNKRMSMVVSG\n"
 113             + "LTPEEFMLVYKFARKHHITLTNLITEETTHVVMKTDAEFVCERTLKYFLGIAGGKWVVSYFWVTQSIKERKM\n"
 114             + "LNEHDFEVRGDVVNGRNHQGPKRARESQDRKIFRGLEICCYGPFTNMPTDQLEWMVQLCGASVVKELSSFTL\n"
 115             + "GTGVHPIVVVQPDAWTEDNGFHAIGQMCEAPVVTREWVLDSVALYQCQELDTYLIPQIPHSHY\n"
 116             + "", 1,
 117 1863);
 118     upSeq.createDatasetSequence();
 119     upSeq.setDescription("Breast cancer type 1 susceptibility protein");
 120     upSeq.addDBRef(new DBRefEntry("UNIPROT","0","P38398",null,true));
 121
 122     upSeq_insulin=new Sequence("INS_HUMAN",
 123             "MALWMRLLPLLALLALWGPDPAAAFVNQHLCGSHLVEALYLVCGERGFFYTPKTRREAEDLQVGQVELGGGP"
 124             + "GAGSLQPLALEGSLQKRGIVEQCCTSICSLYQLENYCN");
 125     upSeq_insulin.createDatasetSequence();
 126     upSeq_insulin.setDescription("Insulin");
 127     upSeq_insulin.addDBRef(new DBRefEntry("UNIPROT","0","P01308",null,true));
 128   }
 129
 130 @AfterMethod(alwaysRun = true)
 131   public void tearDown() throws Exception
 132   {
 133     seq = null;
 134     upSeq=null;
 135   }
 136
 137   @SuppressWarnings("deprecation")
 138   @Test(groups = { "Functional" })
 139   public void buildPDBQueryTest()
 140   {
 141     System.out.println("seq >>>> " + seq);
 142
 143     StructureChooserQuerySource scquery = StructureChooserQuerySource.getQuerySourceFor(new SequenceI[] { seq});
 144     AssertJUnit.assertTrue(scquery instanceof PDBStructureChooserQuerySource);
 145     String query = scquery.buildQuery(seq);
 146     AssertJUnit.assertEquals("pdb_id:1tim", query);
 147     seq.getAllPDBEntries().clear();
 148     query = scquery.buildQuery(seq);
 149     AssertJUnit.assertEquals(
 150             "text:XYZ_1 OR text:XYZ_2 OR text:XYZ_3 OR text:XYZ_4 OR text:4kqy",
 151             query);
 152     seq.setDBRefs(null);
 153     query = scquery.buildQuery(seq);
 154     System.out.println(query);
 155     AssertJUnit.assertEquals("text:4kqy", query);
 156
 157     DBRefEntry uniprotDBRef = new DBRefEntry();
 158     uniprotDBRef.setAccessionId("P12345");
 159     uniprotDBRef.setSource(DBRefSource.UNIPROT);
 160     seq.addDBRef(uniprotDBRef);
 161
 162     DBRefEntry pdbDBRef = new DBRefEntry();
 163     pdbDBRef.setAccessionId("1XYZ");
 164     pdbDBRef.setSource(DBRefSource.PDB);
 165     seq.addDBRef(pdbDBRef);
 166
 167     for (int x = 1; x < 5; x++)
 168     {
 169       DBRefEntry dbRef = new DBRefEntry();
 170       dbRef.setAccessionId("XYZ_" + x);
 171       seq.addDBRef(dbRef);
 172     }
 173     System.out.println("");
 174     System.out.println(seq.getDBRefs());
 175     System.out.println(query);
 176     query = scquery.buildQuery(seq);
 177     AssertJUnit.assertEquals(
 178             "uniprot_accession:P12345 OR uniprot_id:P12345 OR pdb_id:1xyz",
 179             query);
 180   }
 181
 182   @SuppressWarnings("deprecation")
 183   @Test(groups = { "Functional" })
 184   public void buildThreeDBQueryTest()
 185   {
 186     System.out.println("seq >>>> " + upSeq);
 187     TDBeaconsFTSRestClientTest.setMock();
 188     PDBFTSRestClient.setMock();
 189     StructureChooserQuerySource scquery = StructureChooserQuerySource.getQuerySourceFor(new SequenceI[] { upSeq});
 190     // gets the lightweight proxy rather than the ThreeDBStructureChooserQuerySource
 191     AssertJUnit.assertTrue(scquery instanceof ThreeDBStructureChooserQuerySource);
 192     String query = scquery.buildQuery(upSeq);
 193     AssertJUnit.assertEquals("P38398", query);
 194
 195     // query shouldn't change regardless of additional entries
 196     // because 3DBeacons requires canonical entries.
 197     upSeq.getAllPDBEntries().clear();
 198     query = scquery.buildQuery(upSeq);
 199     AssertJUnit.assertEquals("P38398", query);
 200     upSeq.setDBRefs(null);
 201     query = scquery.buildQuery(upSeq);
 202     /*
 203      * legacy projects/datasets will not have canonical flags set for uniprot dbrefs
 204      * graceful behaviour would be to
 205      *  - pick one ? not possible
 206      *  - iterate through all until a 200 is obtained ?
 207      *  ---> ideal but could be costly
 208      *  ---> better to do a direct retrieval from uniprot to work out which is the canonical identifier..
 209      *  ----> need a test to check that accessions can be promoted to canonical!
 210      */
 211     //FIXME - need to be able to use ID to query here ?
 212     AssertJUnit.assertEquals(null, query);
 213
 214
 215
 216     // TODO:
 217     /**
 218      * set of sequences:
 219      * - no protein -> TDB not applicable, query PDBe only (consider RNA or DNA - specific query adapter ?)
 220      * - protein but no uniprot -> first consider trying to get uniprot refs (need a mark to say none are available)
 221      * - protein and uniprot - no canonicals -> resolve to uniprot automatically to get canonicals
 222      * - query uniprot against 3DBeacons
 223      * --> decorate experimental structures with additional data from PDBe
 224      * - query remaining against PDBe
 225      * Ranking
 226      * - 3D Beacons
 227      *  --> in memory ranking - no need to query twice
 228      *  Rank by
 229      *  - experimental > AlphaFold -> Model
 230      *  - start > end
 231      *  -> filters for
 232      *  -> experimental only
 233      *  -> experimental plus best models for other regions
 234      *  -> "best cover"
 235      *  -> need to be able to select correct reference (the longest one that covers all) for superposition
 236      */
 237 //
 238 //    DBRefEntry uniprotDBRef = new DBRefEntry();
 239 //    uniprotDBRef.setAccessionId("P12345");
 240 //    uniprotDBRef.setSource(DBRefSource.UNIPROT);
 241 //    upSeq.addDBRef(uniprotDBRef);
 242 //
 243 //    DBRefEntry pdbDBRef = new DBRefEntry();
 244 //    pdbDBRef.setAccessionId("1XYZ");
 245 //    pdbDBRef.setSource(DBRefSource.PDB);
 246 //    upSeq.addDBRef(pdbDBRef);
 247 //
 248 //    for (int x = 1; x < 5; x++)
 249 //    {
 250 //      DBRefEntry dbRef = new DBRefEntry();
 251 //      dbRef.setAccessionId("XYZ_" + x);
 252 //      seq.addDBRef(dbRef);
 253 //    }
 254 //    System.out.println("");
 255 //    System.out.println(seq.getDBRefs());
 256 //    System.out.println(query);
 257 //    query = scquery.buildQuery(seq);
 258 //    assertEquals(
 259 //            "uniprot_accession:P12345 OR uniprot_id:P12345 OR pdb_id:1xyz",
 260 //            query);
 261   }
 262   @Test(groups= {"Functional"},dataProvider = "testUpSeqs")
 263   public void cascadingThreeDBandPDBQuerys(SequenceI testUpSeq)
 264   {
 265     TDBeaconsFTSRestClientTest.setMock();
 266     PDBFTSRestClient.setMock();
 267     ThreeDBStructureChooserQuerySource tdbquery = new ThreeDBStructureChooserQuerySource();
 268     PDBStructureChooserQuerySource pdbquery  = new PDBStructureChooserQuerySource();
 269
 270
 271
 272     FTSRestResponse upResponse = null;
 273     FTSRestResponse pdbResponse = null;
 274     // TODO test available options
 275     // Best coverage
 276     // Best Alphafold Model
 277     // Best model (by confidence score)
 278     // Will also need to develop a more sophisticated filtering system
 279     List<FilterOption> opts = tdbquery.getAvailableFilterOptions(StructureChooser.VIEWS_FILTER);
 280     FilterOption opt_singlebest = opts.get(0);
 281     FilterOption opt_manybest = opts.get(1);
 282     assertEquals(opt_singlebest.getValue(), ThreeDBStructureChooserQuerySource.FILTER_FIRST_BEST_COVERAGE);
 283     assertEquals(opt_manybest.getValue(), ThreeDBStructureChooserQuerySource.FILTER_TDBEACONS_COVERAGE);
 284
 285     try {
 286       upResponse = tdbquery.fetchStructuresMetaData(testUpSeq, tdbquery.getDocFieldPrefs().getStructureSummaryFields(),  opt_singlebest, false);
 287       tdbquery.updateAvailableFilterOptions(StructureChooser.VIEWS_FILTER,opts,upResponse.getSearchSummary());
 288       // test ranking without additional PDBe data
 289       FTSRestResponse firstRanked = tdbquery.selectFirstRankedQuery(testUpSeq, upResponse.getSearchSummary(), tdbquery.getDocFieldPrefs().getStructureSummaryFields(), opt_singlebest.getValue(), false);
 290       assertEquals(firstRanked.getNumberOfItemsFound(),1);
 291       // many best response
 292       upResponse = tdbquery.fetchStructuresMetaData(testUpSeq, tdbquery.getDocFieldPrefs().getStructureSummaryFields(),  opt_manybest, false);
 293       assertTrue(firstRanked.getSearchSummary().size()<upResponse.getSearchSummary().size());
 294       // NB Could have race condition here
 295       String pdb_Query = tdbquery.buildPDBFTSQueryFor(upResponse);
 296       assertTrue(pdb_Query.trim().length()>0);
 297       pdbResponse = tdbquery.fetchStructuresMetaDataFor(pdbquery, upResponse);
 298       assertTrue(pdbResponse.getNumberOfItemsFound()>0);
 299       FTSRestResponse joinedResp = tdbquery.joinResponses(upResponse, pdbResponse);
 300       assertEquals(upResponse.getNumberOfItemsFound(),joinedResp.getNumberOfItemsFound());
 301
 302
 303     } catch (Exception x)
 304     {
 305       x.printStackTrace();
 306       Assert.fail("Unexpected Exception");
 307     }
 308     StructureChooserQuerySource scquery = StructureChooserQuerySource.getQuerySourceFor(new SequenceI[] { testUpSeq});
 309
 310   }
 311
 312   @DataProvider(name = "testUpSeqs")
 313   public Object[][] testUpSeqs() throws Exception
 314   {
 315     setUp();
 316     return new Object[][] { {upSeq},{upSeq_insulin}};
 317   }
 318
 319   @Test(groups = { "Functional" })
 320   public void sanitizeSeqNameTest()
 321   {
 322     String name = "ab_cdEF|fwxyz012349";
 323     AssertJUnit.assertEquals(name, PDBStructureChooserQuerySource.sanitizeSeqName(name));
 324
 325     // remove a [nn] substring
 326     name = "abcde12[345]fg";
 327     AssertJUnit.assertEquals("abcde12fg", PDBStructureChooserQuerySource.sanitizeSeqName(name));
 328
 329     // remove characters other than a-zA-Z0-9 | or _
 330     name = "ab[cd],.\t£$*!- \\\"@:e";
 331     AssertJUnit.assertEquals("abcde", PDBStructureChooserQuerySource.sanitizeSeqName(name));
 332
 333     name = "abcde12[345a]fg";
 334     AssertJUnit.assertEquals("abcde12345afg", PDBStructureChooserQuerySource.sanitizeSeqName(name));
 335   }
 336 }