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