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