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 import static org.testng.Assert.assertEquals;
  24 import static org.testng.Assert.assertTrue;
  25
  26 import java.util.Collection;
  27 import java.util.List;
  28 import java.util.Vector;
  29
  30 import org.junit.Assert;
  31 import org.testng.AssertJUnit;
  32 import org.testng.annotations.AfterMethod;
  33 import org.testng.annotations.BeforeClass;
  34 import org.testng.annotations.BeforeMethod;
  35 import org.testng.annotations.DataProvider;
  36 import org.testng.annotations.Test;
  37
  38 import jalview.datamodel.DBRefEntry;
  39 import jalview.datamodel.DBRefSource;
  40 import jalview.datamodel.PDBEntry;
  41 import jalview.datamodel.Sequence;
  42 import jalview.datamodel.SequenceI;
  43 import jalview.fts.api.FTSData;
  44 import jalview.fts.core.FTSRestRequest;
  45 import jalview.fts.core.FTSRestResponse;
  46 import jalview.fts.service.pdb.PDBFTSRestClient;
  47 import jalview.fts.service.pdb.PDBFTSRestClientTest;
  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                     + "",
 117             1, 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
 128             .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
 145             .getQuerySourceFor(new SequenceI[]
 146             { seq });
 147     AssertJUnit
 148             .assertTrue(scquery instanceof PDBStructureChooserQuerySource);
 149     String query = scquery.buildQuery(seq);
 150     AssertJUnit.assertEquals("pdb_id:1tim", query);
 151     seq.getAllPDBEntries().clear();
 152     query = scquery.buildQuery(seq);
 153     AssertJUnit.assertEquals(
 154             "text:XYZ_1 OR text:XYZ_2 OR text:XYZ_3 OR text:XYZ_4 OR text:4kqy",
 155             query);
 156     seq.setDBRefs(null);
 157     query = scquery.buildQuery(seq);
 158     System.out.println(query);
 159     AssertJUnit.assertEquals("text:4kqy", query);
 160
 161     DBRefEntry uniprotDBRef = new DBRefEntry();
 162     uniprotDBRef.setAccessionId("P12345");
 163     uniprotDBRef.setSource(DBRefSource.UNIPROT);
 164     seq.addDBRef(uniprotDBRef);
 165
 166     DBRefEntry pdbDBRef = new DBRefEntry();
 167     pdbDBRef.setAccessionId("1XYZ");
 168     pdbDBRef.setSource(DBRefSource.PDB);
 169     seq.addDBRef(pdbDBRef);
 170
 171     for (int x = 1; x < 5; x++)
 172     {
 173       DBRefEntry dbRef = new DBRefEntry();
 174       dbRef.setAccessionId("XYZ_" + x);
 175       seq.addDBRef(dbRef);
 176     }
 177     System.out.println("");
 178     System.out.println(seq.getDBRefs());
 179     System.out.println(query);
 180     query = scquery.buildQuery(seq);
 181     AssertJUnit.assertEquals(
 182             "uniprot_accession:P12345 OR uniprot_id:P12345 OR pdb_id:1xyz",
 183             query);
 184   }
 185
 186   @SuppressWarnings("deprecation")
 187   @Test(groups = { "Functional" })
 188   public void buildThreeDBQueryTest()
 189   {
 190     System.out.println("seq >>>> " + upSeq);
 191     TDBeaconsFTSRestClientTest.setMock();
 192     PDBFTSRestClientTest.setMock();
 193     StructureChooserQuerySource scquery = StructureChooserQuerySource
 194             .getQuerySourceFor(new SequenceI[]
 195             { upSeq });
 196     // gets the lightweight proxy rather than the
 197     // ThreeDBStructureChooserQuerySource
 198     AssertJUnit.assertTrue(
 199             scquery instanceof ThreeDBStructureChooserQuerySource);
 200     String query = scquery.buildQuery(upSeq);
 201     AssertJUnit.assertEquals("P38398", query);
 202
 203     // query shouldn't change regardless of additional entries
 204     // because 3DBeacons requires canonical entries.
 205     upSeq.getAllPDBEntries().clear();
 206     query = scquery.buildQuery(upSeq);
 207     AssertJUnit.assertEquals("P38398", query);
 208     upSeq.setDBRefs(null);
 209     query = scquery.buildQuery(upSeq);
 210     /*
 211      * legacy projects/datasets will not have canonical flags set for uniprot dbrefs
 212      * graceful behaviour would be to
 213      *  - pick one ? not possible
 214      *  - iterate through all until a 200 is obtained ?
 215      *  ---> ideal but could be costly
 216      *  ---> better to do a direct retrieval from uniprot to work out which is the canonical identifier..
 217      *  ----> need a test to check that accessions can be promoted to canonical!
 218      */
 219     // FIXME - need to be able to use ID to query here ?
 220     AssertJUnit.assertEquals(null, query);
 221
 222     // TODO:
 223     /**
 224      * set of sequences: - no protein -> TDB not applicable, query PDBe only
 225      * (consider RNA or DNA - specific query adapter ?) - protein but no uniprot
 226      * -> first consider trying to get uniprot refs (need a mark to say none are
 227      * available) - protein and uniprot - no canonicals -> resolve to uniprot
 228      * automatically to get canonicals - query uniprot against 3DBeacons -->
 229      * decorate experimental structures with additional data from PDBe - query
 230      * remaining against PDBe Ranking - 3D Beacons --> in memory ranking - no
 231      * need to query twice Rank by - experimental > AlphaFold -> Model - start >
 232      * end -> filters for -> experimental only -> experimental plus best models
 233      * for other regions -> "best cover" -> need to be able to select correct
 234      * reference (the longest one that covers all) for superposition
 235      */
 236     //
 237     // DBRefEntry uniprotDBRef = new DBRefEntry();
 238     // uniprotDBRef.setAccessionId("P12345");
 239     // uniprotDBRef.setSource(DBRefSource.UNIPROT);
 240     // upSeq.addDBRef(uniprotDBRef);
 241     //
 242     // DBRefEntry pdbDBRef = new DBRefEntry();
 243     // pdbDBRef.setAccessionId("1XYZ");
 244     // pdbDBRef.setSource(DBRefSource.PDB);
 245     // upSeq.addDBRef(pdbDBRef);
 246     //
 247     // for (int x = 1; x < 5; x++)
 248     // {
 249     // DBRefEntry dbRef = new DBRefEntry();
 250     // dbRef.setAccessionId("XYZ_" + x);
 251     // seq.addDBRef(dbRef);
 252     // }
 253     // System.out.println("");
 254     // System.out.println(seq.getDBRefs());
 255     // System.out.println(query);
 256     // query = scquery.buildQuery(seq);
 257     // assertEquals(
 258     // "uniprot_accession:P12345 OR uniprot_id:P12345 OR pdb_id:1xyz",
 259     // query);
 260   }
 261
 262   @Test(groups = { "Functional" }, dataProvider = "testUpSeqs")
 263   public void cascadingThreeDBandPDBQuerys(SequenceI testUpSeq)
 264   {
 265     TDBeaconsFTSRestClientTest.setMock();
 266     PDBFTSRestClientTest.setMock();
 267     ThreeDBStructureChooserQuerySource tdbquery = new ThreeDBStructureChooserQuerySource();
 268     PDBStructureChooserQuerySource pdbquery = new PDBStructureChooserQuerySource();
 269
 270     FTSRestResponse upResponse = null;
 271     FTSRestResponse pdbResponse = null;
 272     // TODO test available options
 273     // Best coverage
 274     // Best Alphafold Model
 275     // Best model (by confidence score)
 276     // Will also need to develop a more sophisticated filtering system
 277     List<FilterOption> opts = tdbquery
 278             .getAvailableFilterOptions(StructureChooser.VIEWS_FILTER);
 279     FilterOption opt_singlebest = opts.get(0);
 280     FilterOption opt_manybest = opts.get(1);
 281     assertEquals(opt_singlebest.getValue(),
 282             ThreeDBStructureChooserQuerySource.FILTER_FIRST_BEST_COVERAGE);
 283     assertEquals(opt_manybest.getValue(),
 284             ThreeDBStructureChooserQuerySource.FILTER_TDBEACONS_COVERAGE);
 285
 286     try
 287     {
 288       upResponse = tdbquery.fetchStructuresMetaData(testUpSeq,
 289               tdbquery.getDocFieldPrefs().getStructureSummaryFields(),
 290               opt_singlebest, false);
 291       tdbquery.updateAvailableFilterOptions(StructureChooser.VIEWS_FILTER,
 292               opts, upResponse.getSearchSummary());
 293       // test ranking without additional PDBe data
 294       FTSRestResponse firstRanked = tdbquery.selectFirstRankedQuery(
 295               testUpSeq, upResponse.getSearchSummary(),
 296               tdbquery.getDocFieldPrefs().getStructureSummaryFields(),
 297               opt_singlebest.getValue(), false);
 298       assertEquals(firstRanked.getNumberOfItemsFound(), 1);
 299       // many best response
 300       upResponse = tdbquery.fetchStructuresMetaData(testUpSeq,
 301               tdbquery.getDocFieldPrefs().getStructureSummaryFields(),
 302               opt_manybest, false);
 303       assertTrue(firstRanked.getSearchSummary().size() < upResponse
 304               .getSearchSummary().size());
 305       // NB Could have race condition here
 306       String pdb_Query = tdbquery.buildPDBFTSQueryFor(upResponse);
 307       assertTrue(pdb_Query.trim().length() > 0);
 308       pdbResponse = tdbquery.fetchStructuresMetaDataFor(pdbquery,
 309               upResponse);
 310       assertTrue(pdbResponse.getNumberOfItemsFound() > 0);
 311       FTSRestResponse joinedResp = tdbquery.joinResponses(upResponse,
 312               pdbResponse);
 313       assertEquals(upResponse.getNumberOfItemsFound(),
 314               joinedResp.getNumberOfItemsFound());
 315
 316     } catch (Exception x)
 317     {
 318       x.printStackTrace();
 319       Assert.fail("Unexpected Exception");
 320     }
 321     StructureChooserQuerySource scquery = StructureChooserQuerySource
 322             .getQuerySourceFor(new SequenceI[]
 323             { testUpSeq });
 324
 325   }
 326
 327   @DataProvider(name = "testUpSeqs")
 328   public Object[][] testUpSeqs() throws Exception
 329   {
 330     setUp();
 331     return new Object[][] { { upSeq }, { upSeq_insulin } };
 332   }
 333
 334   @Test(groups = { "Functional" })
 335   public void sanitizeSeqNameTest()
 336   {
 337     String name = "ab_cdEF|fwxyz012349";
 338     AssertJUnit.assertEquals(name,
 339             PDBStructureChooserQuerySource.sanitizeSeqName(name));
 340
 341     // remove a [nn] substring
 342     name = "abcde12[345]fg";
 343     AssertJUnit.assertEquals("abcde12fg",
 344             PDBStructureChooserQuerySource.sanitizeSeqName(name));
 345
 346     // remove characters other than a-zA-Z0-9 | or _
 347     name = "ab[cd],.\t£$*!- \\\"@:e";
 348     AssertJUnit.assertEquals("abcde",
 349             PDBStructureChooserQuerySource.sanitizeSeqName(name));
 350
 351     name = "abcde12[345a]fg";
 352     AssertJUnit.assertEquals("abcde12345afg",
 353             PDBStructureChooserQuerySource.sanitizeSeqName(name));
 354   }
 355 }