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.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.Test;
  36
  37 import jalview.datamodel.DBRefEntry;
  38 import jalview.datamodel.DBRefSource;
  39 import jalview.datamodel.PDBEntry;
  40 import jalview.datamodel.Sequence;
  41 import jalview.datamodel.SequenceI;
  42 import jalview.fts.api.FTSData;
  43 import jalview.fts.core.FTSRestRequest;
  44 import jalview.fts.core.FTSRestResponse;
  45 import jalview.fts.service.pdb.PDBFTSRestClient;
  46 import jalview.fts.threedbeacons.TDBeaconsFTSRestClientTest;
  47 import jalview.gui.JvOptionPane;
  48 import jalview.gui.StructureChooser;
  49 import jalview.jbgui.FilterOption;
  50
  51 public class StructureChooserQuerySourceTest
  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   // same set up as for structurechooser test
  64
  65 @BeforeMethod(alwaysRun = true)
  66   public void setUp() throws Exception
  67   {
  68     seq = new Sequence("PDB|4kqy|4KQY|A", "ABCDEFGHIJKLMNOPQRSTUVWXYZ", 1,
  69             26);
  70     seq.createDatasetSequence();
  71     for (int x = 1; x < 5; x++)
  72     {
  73       DBRefEntry dbRef = new DBRefEntry();
  74       dbRef.setAccessionId("XYZ_" + x);
  75       seq.addDBRef(dbRef);
  76     }
  77
  78     PDBEntry dbRef = new PDBEntry();
  79     dbRef.setId("1tim");
  80
  81     Vector<PDBEntry> pdbIds = new Vector<>();
  82     pdbIds.add(dbRef);
  83
  84     seq.setPDBId(pdbIds);
  85
  86     // Uniprot sequence for 3D-Beacons mocks
  87     upSeq = new Sequence("P38398",
  88             "MDLSALRVEEVQNVINAMQKILECPICLELIKEPVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRS\n"
  89             + "LQESTRFSQLVEELLKIICAFQLDTGLEYANSYNFAKKENNSPEHLKDEVSIIQSMGYRNRAKRLLQSEPEN\n"
  90             + "PSLQETSLSVQLSNLGTVRTLRTKQRIQPQKTSVYIELGSDSSEDTVNKATYCSVGDQELLQITPQGTRDEI\n"
  91             + "SLDSAKKAACEFSETDVTNTEHHQPSNNDLNTTEKRAAERHPEKYQGSSVSNLHVEPCGTNTHASSLQHENS\n"
  92             + "SLLLTKDRMNVEKAEFCNKSKQPGLARSQHNRWAGSKETCNDRRTPSTEKKVDLNADPLCERKEWNKQKLPC\n"
  93             + "SENPRDTEDVPWITLNSSIQKVNEWFSRSDELLGSDDSHDGESESNAKVADVLDVLNEVDEYSGSSEKIDLL\n"
  94             + "ASDPHEALICKSERVHSKSVESNIEDKIFGKTYRKKASLPNLSHVTENLIIGAFVTEPQIIQERPLTNKLKR\n"
  95             + "KRRPTSGLHPEDFIKKADLAVQKTPEMINQGTNQTEQNGQVMNITNSGHENKTKGDSIQNEKNPNPIESLEK\n"
  96             + "ESAFKTKAEPISSSISNMELELNIHNSKAPKKNRLRRKSSTRHIHALELVVSRNLSPPNCTELQIDSCSSSE\n"
  97             + "EIKKKKYNQMPVRHSRNLQLMEGKEPATGAKKSNKPNEQTSKRHDSDTFPELKLTNAPGSFTKCSNTSELKE\n"
  98             + "FVNPSLPREEKEEKLETVKVSNNAEDPKDLMLSGERVLQTERSVESSSISLVPGTDYGTQESISLLEVSTLG\n"
  99             + "KAKTEPNKCVSQCAAFENPKGLIHGCSKDNRNDTEGFKYPLGHEVNHSRETSIEMEESELDAQYLQNTFKVS\n"
 100             + "KRQSFAPFSNPGNAEEECATFSAHSGSLKKQSPKVTFECEQKEENQGKNESNIKPVQTVNITAGFPVVGQKD\n"
 101             + "KPVDNAKCSIKGGSRFCLSSQFRGNETGLITPNKHGLLQNPYRIPPLFPIKSFVKTKCKKNLLEENFEEHSM\n"
 102             + "SPEREMGNENIPSTVSTISRNNIRENVFKEASSSNINEVGSSTNEVGSSINEIGSSDENIQAELGRNRGPKL\n"
 103             + "NAMLRLGVLQPEVYKQSLPGSNCKHPEIKKQEYEEVVQTVNTDFSPYLISDNLEQPMGSSHASQVCSETPDD\n"
 104             + "LLDDGEIKEDTSFAENDIKESSAVFSKSVQKGELSRSPSPFTHTHLAQGYRRGAKKLESSEENLSSEDEELP\n"
 105             + "CFQHLLFGKVNNIPSQSTRHSTVATECLSKNTEENLLSLKNSLNDCSNQVILAKASQEHHLSEETKCSASLF\n"
 106             + "SSQCSELEDLTANTNTQDPFLIGSSKQMRHQSESQGVGLSDKELVSDDEERGTGLEENNQEEQSMDSNLGEA\n"
 107             + "ASGCESETSVSEDCSGLSSQSDILTTQQRDTMQHNLIKLQQEMAELEAVLEQHGSQPSNSYPSIISDSSALE\n"
 108             + "DLRNPEQSTSEKAVLTSQKSSEYPISQNPEGLSADKFEVSADSSTSKNKEPGVERSSPSKCPSLDDRWYMHS\n"
 109             + "CSGSLQNRNYPSQEELIKVVDVEEQQLEESGPHDLTETSYLPRQDLEGTPYLESGISLFSDDPESDPSEDRA\n"
 110             + "PESARVGNIPSSTSALKVPQLKVAESAQSPAAAHTTDTAGYNAMEESVSREKPELTASTERVNKRMSMVVSG\n"
 111             + "LTPEEFMLVYKFARKHHITLTNLITEETTHVVMKTDAEFVCERTLKYFLGIAGGKWVVSYFWVTQSIKERKM\n"
 112             + "LNEHDFEVRGDVVNGRNHQGPKRARESQDRKIFRGLEICCYGPFTNMPTDQLEWMVQLCGASVVKELSSFTL\n"
 113             + "GTGVHPIVVVQPDAWTEDNGFHAIGQMCEAPVVTREWVLDSVALYQCQELDTYLIPQIPHSHY\n"
 114             + "", 1,
 115 1863);
 116     upSeq.createDatasetSequence();
 117     upSeq.setDescription("Breast cancer type 1 susceptibility protein");
 118     upSeq.addDBRef(new DBRefEntry("UNIPROT","0","P38398",null,true));
 119   }
 120
 121 @AfterMethod(alwaysRun = true)
 122   public void tearDown() throws Exception
 123   {
 124     seq = null;
 125     upSeq=null;
 126   }
 127
 128   @SuppressWarnings("deprecation")
 129   @Test(groups = { "Functional" })
 130   public void buildPDBQueryTest()
 131   {
 132     System.out.println("seq >>>> " + seq);
 133
 134     StructureChooserQuerySource scquery = StructureChooserQuerySource.getQuerySourceFor(new SequenceI[] { seq});
 135     AssertJUnit.assertTrue(scquery instanceof PDBStructureChooserQuerySource);
 136     String query = scquery.buildQuery(seq);
 137     AssertJUnit.assertEquals("pdb_id:1tim", query);
 138     seq.getAllPDBEntries().clear();
 139     query = scquery.buildQuery(seq);
 140     AssertJUnit.assertEquals(
 141             "text:XYZ_1 OR text:XYZ_2 OR text:XYZ_3 OR text:XYZ_4 OR text:4kqy",
 142             query);
 143     seq.setDBRefs(null);
 144     query = scquery.buildQuery(seq);
 145     System.out.println(query);
 146     AssertJUnit.assertEquals("text:4kqy", query);
 147
 148     DBRefEntry uniprotDBRef = new DBRefEntry();
 149     uniprotDBRef.setAccessionId("P12345");
 150     uniprotDBRef.setSource(DBRefSource.UNIPROT);
 151     seq.addDBRef(uniprotDBRef);
 152
 153     DBRefEntry pdbDBRef = new DBRefEntry();
 154     pdbDBRef.setAccessionId("1XYZ");
 155     pdbDBRef.setSource(DBRefSource.PDB);
 156     seq.addDBRef(pdbDBRef);
 157
 158     for (int x = 1; x < 5; x++)
 159     {
 160       DBRefEntry dbRef = new DBRefEntry();
 161       dbRef.setAccessionId("XYZ_" + x);
 162       seq.addDBRef(dbRef);
 163     }
 164     System.out.println("");
 165     System.out.println(seq.getDBRefs());
 166     System.out.println(query);
 167     query = scquery.buildQuery(seq);
 168     AssertJUnit.assertEquals(
 169             "uniprot_accession:P12345 OR uniprot_id:P12345 OR pdb_id:1xyz",
 170             query);
 171   }
 172
 173   @SuppressWarnings("deprecation")
 174   @Test(groups = { "Functional" })
 175   public void buildThreeDBQueryTest()
 176   {
 177     System.out.println("seq >>>> " + upSeq);
 178     TDBeaconsFTSRestClientTest.setMock();
 179     PDBFTSRestClient.setMock();
 180     StructureChooserQuerySource scquery = StructureChooserQuerySource.getQuerySourceFor(new SequenceI[] { upSeq});
 181     // gets the lightweight proxy rather than the ThreeDBStructureChooserQuerySource
 182     AssertJUnit.assertTrue(scquery instanceof ThreeDBStructureChooserQuerySource);
 183     String query = scquery.buildQuery(upSeq);
 184     AssertJUnit.assertEquals("P38398", query);
 185
 186     // query shouldn't change regardless of additional entries
 187     // because 3DBeacons requires canonical entries.
 188     upSeq.getAllPDBEntries().clear();
 189     query = scquery.buildQuery(upSeq);
 190     AssertJUnit.assertEquals("P38398", query);
 191     upSeq.setDBRefs(null);
 192     query = scquery.buildQuery(upSeq);
 193     /*
 194      * legacy projects/datasets will not have canonical flags set for uniprot dbrefs
 195      * graceful behaviour would be to
 196      *  - pick one ? not possible
 197      *  - iterate through all until a 200 is obtained ?
 198      *  ---> ideal but could be costly
 199      *  ---> better to do a direct retrieval from uniprot to work out which is the canonical identifier..
 200      *  ----> need a test to check that accessions can be promoted to canonical!
 201      */
 202     //FIXME - need to be able to use ID to query here ?
 203     AssertJUnit.assertEquals(null, query);
 204
 205
 206
 207     // TODO:
 208     /**
 209      * set of sequences:
 210      * - no protein -> TDB not applicable, query PDBe only (consider RNA or DNA - specific query adapter ?)
 211      * - protein but no uniprot -> first consider trying to get uniprot refs (need a mark to say none are available)
 212      * - protein and uniprot - no canonicals -> resolve to uniprot automatically to get canonicals
 213      * - query uniprot against 3DBeacons
 214      * --> decorate experimental structures with additional data from PDBe
 215      * - query remaining against PDBe
 216      * Ranking
 217      * - 3D Beacons
 218      *  --> in memory ranking - no need to query twice
 219      *  Rank by
 220      *  - experimental > AlphaFold -> Model
 221      *  - start > end
 222      *  -> filters for
 223      *  -> experimental only
 224      *  -> experimental plus best models for other regions
 225      *  -> "best cover"
 226      *  -> need to be able to select correct reference (the longest one that covers all) for superposition
 227      */
 228 //
 229 //    DBRefEntry uniprotDBRef = new DBRefEntry();
 230 //    uniprotDBRef.setAccessionId("P12345");
 231 //    uniprotDBRef.setSource(DBRefSource.UNIPROT);
 232 //    upSeq.addDBRef(uniprotDBRef);
 233 //
 234 //    DBRefEntry pdbDBRef = new DBRefEntry();
 235 //    pdbDBRef.setAccessionId("1XYZ");
 236 //    pdbDBRef.setSource(DBRefSource.PDB);
 237 //    upSeq.addDBRef(pdbDBRef);
 238 //
 239 //    for (int x = 1; x < 5; x++)
 240 //    {
 241 //      DBRefEntry dbRef = new DBRefEntry();
 242 //      dbRef.setAccessionId("XYZ_" + x);
 243 //      seq.addDBRef(dbRef);
 244 //    }
 245 //    System.out.println("");
 246 //    System.out.println(seq.getDBRefs());
 247 //    System.out.println(query);
 248 //    query = scquery.buildQuery(seq);
 249 //    assertEquals(
 250 //            "uniprot_accession:P12345 OR uniprot_id:P12345 OR pdb_id:1xyz",
 251 //            query);
 252   }
 253   @Test(groups= {"Functional"})
 254   public void cascadingThreeDBandPDBQuerys()
 255   {
 256     TDBeaconsFTSRestClientTest.setMock();
 257     PDBFTSRestClient.setMock();
 258     ThreeDBStructureChooserQuerySource tdbquery = new ThreeDBStructureChooserQuerySource();
 259     PDBStructureChooserQuerySource pdbquery  = new PDBStructureChooserQuerySource();
 260
 261
 262
 263     FTSRestResponse upResponse = null;
 264     FTSRestResponse pdbResponse = null;
 265     // TODO test available options
 266     // Best coverage
 267     // Best Alphafold Model
 268     // Best model (by confidence score)
 269     // Will also need to develop a more sophisticated filtering system
 270     FilterOption opt = tdbquery.getAvailableFilterOptions(StructureChooser.VIEWS_FILTER).get(0);
 271     try {
 272       upResponse = tdbquery.fetchStructuresMetaData(upSeq, tdbquery.getDocFieldPrefs().getStructureSummaryFields(),  opt, false);
 273       // test ranking without additional PDBe data
 274       FTSRestResponse firstRanked = tdbquery.selectFirstRankedQuery(upSeq, upResponse.getSearchSummary(), tdbquery.getDocFieldPrefs().getStructureSummaryFields(), opt.getValue(), false);
 275       assertTrue(firstRanked.getNumberOfItemsFound()<upResponse.getNumberOfItemsFound());
 276       // NB Could have race condition here
 277       String pdb_Query = tdbquery.buildPDBFTSQueryFor(upResponse);
 278       assertTrue(pdb_Query.trim().length()>0);
 279       pdbResponse = tdbquery.fetchStructuresMetaDataFor(pdbquery, upResponse);
 280       assertTrue(pdbResponse.getNumberOfItemsFound()>0);
 281       FTSRestResponse joinedResp = tdbquery.joinResponses(upResponse, pdbResponse);
 282       assertEquals(upResponse.getNumberOfItemsFound(),joinedResp.getNumberOfItemsFound());
 283
 284
 285     } catch (Exception x)
 286     {
 287       x.printStackTrace();
 288       Assert.fail("Unexpected Exception");
 289     }
 290     StructureChooserQuerySource scquery = StructureChooserQuerySource.getQuerySourceFor(new SequenceI[] { upSeq});
 291
 292   }
 293
 294   @Test(groups = { "Functional" })
 295   public void sanitizeSeqNameTest()
 296   {
 297     String name = "ab_cdEF|fwxyz012349";
 298     AssertJUnit.assertEquals(name, PDBStructureChooserQuerySource.sanitizeSeqName(name));
 299
 300     // remove a [nn] substring
 301     name = "abcde12[345]fg";
 302     AssertJUnit.assertEquals("abcde12fg", PDBStructureChooserQuerySource.sanitizeSeqName(name));
 303
 304     // remove characters other than a-zA-Z0-9 | or _
 305     name = "ab[cd],.\t£$*!- \\\"@:e";
 306     AssertJUnit.assertEquals("abcde", PDBStructureChooserQuerySource.sanitizeSeqName(name));
 307
 308     name = "abcde12[345a]fg";
 309     AssertJUnit.assertEquals("abcde12345afg", PDBStructureChooserQuerySource.sanitizeSeqName(name));
 310   }
 311 }