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.Vector;
  28
  29 import org.junit.Assert;
  30 import org.testng.AssertJUnit;
  31 import org.testng.annotations.AfterMethod;
  32 import org.testng.annotations.BeforeClass;
  33 import org.testng.annotations.BeforeMethod;
  34 import org.testng.annotations.Test;
  35
  36 import jalview.datamodel.DBRefEntry;
  37 import jalview.datamodel.DBRefSource;
  38 import jalview.datamodel.PDBEntry;
  39 import jalview.datamodel.Sequence;
  40 import jalview.datamodel.SequenceI;
  41 import jalview.fts.core.FTSRestRequest;
  42 import jalview.fts.core.FTSRestResponse;
  43 import jalview.fts.service.pdb.PDBFTSRestClient;
  44 import jalview.fts.threedbeacons.TDBeaconsFTSRestClientTest;
  45 import jalview.gui.JvOptionPane;
  46 import jalview.jbgui.FilterOption;
  47
  48 public class StructureChooserQuerySourceTest
  49 {
  50
  51   @BeforeClass(alwaysRun = true)
  52   public void setUpJvOptionPane()
  53   {
  54     JvOptionPane.setInteractiveMode(false);
  55     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
  56   }
  57
  58   Sequence seq,upSeq;
  59
  60   // same set up as for structurechooser test
  61
  62 @BeforeMethod(alwaysRun = true)
  63   public void setUp() throws Exception
  64   {
  65     seq = new Sequence("PDB|4kqy|4KQY|A", "ABCDEFGHIJKLMNOPQRSTUVWXYZ", 1,
  66             26);
  67     seq.createDatasetSequence();
  68     for (int x = 1; x < 5; x++)
  69     {
  70       DBRefEntry dbRef = new DBRefEntry();
  71       dbRef.setAccessionId("XYZ_" + x);
  72       seq.addDBRef(dbRef);
  73     }
  74
  75     PDBEntry dbRef = new PDBEntry();
  76     dbRef.setId("1tim");
  77
  78     Vector<PDBEntry> pdbIds = new Vector<>();
  79     pdbIds.add(dbRef);
  80
  81     seq.setPDBId(pdbIds);
  82
  83     // Uniprot sequence for 3D-Beacons mocks
  84     upSeq = new Sequence("P38398",
  85             "MDLSALRVEEVQNVINAMQKILECPICLELIKEPVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRS\n"
  86             + "LQESTRFSQLVEELLKIICAFQLDTGLEYANSYNFAKKENNSPEHLKDEVSIIQSMGYRNRAKRLLQSEPEN\n"
  87             + "PSLQETSLSVQLSNLGTVRTLRTKQRIQPQKTSVYIELGSDSSEDTVNKATYCSVGDQELLQITPQGTRDEI\n"
  88             + "SLDSAKKAACEFSETDVTNTEHHQPSNNDLNTTEKRAAERHPEKYQGSSVSNLHVEPCGTNTHASSLQHENS\n"
  89             + "SLLLTKDRMNVEKAEFCNKSKQPGLARSQHNRWAGSKETCNDRRTPSTEKKVDLNADPLCERKEWNKQKLPC\n"
  90             + "SENPRDTEDVPWITLNSSIQKVNEWFSRSDELLGSDDSHDGESESNAKVADVLDVLNEVDEYSGSSEKIDLL\n"
  91             + "ASDPHEALICKSERVHSKSVESNIEDKIFGKTYRKKASLPNLSHVTENLIIGAFVTEPQIIQERPLTNKLKR\n"
  92             + "KRRPTSGLHPEDFIKKADLAVQKTPEMINQGTNQTEQNGQVMNITNSGHENKTKGDSIQNEKNPNPIESLEK\n"
  93             + "ESAFKTKAEPISSSISNMELELNIHNSKAPKKNRLRRKSSTRHIHALELVVSRNLSPPNCTELQIDSCSSSE\n"
  94             + "EIKKKKYNQMPVRHSRNLQLMEGKEPATGAKKSNKPNEQTSKRHDSDTFPELKLTNAPGSFTKCSNTSELKE\n"
  95             + "FVNPSLPREEKEEKLETVKVSNNAEDPKDLMLSGERVLQTERSVESSSISLVPGTDYGTQESISLLEVSTLG\n"
  96             + "KAKTEPNKCVSQCAAFENPKGLIHGCSKDNRNDTEGFKYPLGHEVNHSRETSIEMEESELDAQYLQNTFKVS\n"
  97             + "KRQSFAPFSNPGNAEEECATFSAHSGSLKKQSPKVTFECEQKEENQGKNESNIKPVQTVNITAGFPVVGQKD\n"
  98             + "KPVDNAKCSIKGGSRFCLSSQFRGNETGLITPNKHGLLQNPYRIPPLFPIKSFVKTKCKKNLLEENFEEHSM\n"
  99             + "SPEREMGNENIPSTVSTISRNNIRENVFKEASSSNINEVGSSTNEVGSSINEIGSSDENIQAELGRNRGPKL\n"
 100             + "NAMLRLGVLQPEVYKQSLPGSNCKHPEIKKQEYEEVVQTVNTDFSPYLISDNLEQPMGSSHASQVCSETPDD\n"
 101             + "LLDDGEIKEDTSFAENDIKESSAVFSKSVQKGELSRSPSPFTHTHLAQGYRRGAKKLESSEENLSSEDEELP\n"
 102             + "CFQHLLFGKVNNIPSQSTRHSTVATECLSKNTEENLLSLKNSLNDCSNQVILAKASQEHHLSEETKCSASLF\n"
 103             + "SSQCSELEDLTANTNTQDPFLIGSSKQMRHQSESQGVGLSDKELVSDDEERGTGLEENNQEEQSMDSNLGEA\n"
 104             + "ASGCESETSVSEDCSGLSSQSDILTTQQRDTMQHNLIKLQQEMAELEAVLEQHGSQPSNSYPSIISDSSALE\n"
 105             + "DLRNPEQSTSEKAVLTSQKSSEYPISQNPEGLSADKFEVSADSSTSKNKEPGVERSSPSKCPSLDDRWYMHS\n"
 106             + "CSGSLQNRNYPSQEELIKVVDVEEQQLEESGPHDLTETSYLPRQDLEGTPYLESGISLFSDDPESDPSEDRA\n"
 107             + "PESARVGNIPSSTSALKVPQLKVAESAQSPAAAHTTDTAGYNAMEESVSREKPELTASTERVNKRMSMVVSG\n"
 108             + "LTPEEFMLVYKFARKHHITLTNLITEETTHVVMKTDAEFVCERTLKYFLGIAGGKWVVSYFWVTQSIKERKM\n"
 109             + "LNEHDFEVRGDVVNGRNHQGPKRARESQDRKIFRGLEICCYGPFTNMPTDQLEWMVQLCGASVVKELSSFTL\n"
 110             + "GTGVHPIVVVQPDAWTEDNGFHAIGQMCEAPVVTREWVLDSVALYQCQELDTYLIPQIPHSHY\n"
 111             + "", 1,
 112 1863);
 113     upSeq.createDatasetSequence();
 114     upSeq.setDescription("Breast cancer type 1 susceptibility protein");
 115     upSeq.addDBRef(new DBRefEntry("UNIPROT","0","P38398",null,true));
 116   }
 117
 118 @AfterMethod(alwaysRun = true)
 119   public void tearDown() throws Exception
 120   {
 121     seq = null;
 122     upSeq=null;
 123   }
 124
 125   @SuppressWarnings("deprecation")
 126   @Test(groups = { "Functional" })
 127   public void buildPDBQueryTest()
 128   {
 129     System.out.println("seq >>>> " + seq);
 130
 131     StructureChooserQuerySource scquery = StructureChooserQuerySource.getQuerySourceFor(new SequenceI[] { seq});
 132     AssertJUnit.assertTrue(scquery instanceof PDBStructureChooserQuerySource);
 133     String query = scquery.buildQuery(seq);
 134     AssertJUnit.assertEquals("pdb_id:1tim", query);
 135     seq.getAllPDBEntries().clear();
 136     query = scquery.buildQuery(seq);
 137     AssertJUnit.assertEquals(
 138             "text:XYZ_1 OR text:XYZ_2 OR text:XYZ_3 OR text:XYZ_4 OR text:4kqy",
 139             query);
 140     seq.setDBRefs(null);
 141     query = scquery.buildQuery(seq);
 142     System.out.println(query);
 143     AssertJUnit.assertEquals("text:4kqy", query);
 144
 145     DBRefEntry uniprotDBRef = new DBRefEntry();
 146     uniprotDBRef.setAccessionId("P12345");
 147     uniprotDBRef.setSource(DBRefSource.UNIPROT);
 148     seq.addDBRef(uniprotDBRef);
 149
 150     DBRefEntry pdbDBRef = new DBRefEntry();
 151     pdbDBRef.setAccessionId("1XYZ");
 152     pdbDBRef.setSource(DBRefSource.PDB);
 153     seq.addDBRef(pdbDBRef);
 154
 155     for (int x = 1; x < 5; x++)
 156     {
 157       DBRefEntry dbRef = new DBRefEntry();
 158       dbRef.setAccessionId("XYZ_" + x);
 159       seq.addDBRef(dbRef);
 160     }
 161     System.out.println("");
 162     System.out.println(seq.getDBRefs());
 163     System.out.println(query);
 164     query = scquery.buildQuery(seq);
 165     AssertJUnit.assertEquals(
 166             "uniprot_accession:P12345 OR uniprot_id:P12345 OR pdb_id:1xyz",
 167             query);
 168   }
 169
 170   @SuppressWarnings("deprecation")
 171   @Test(groups = { "Functional" })
 172   public void buildThreeDBQueryTest()
 173   {
 174     System.out.println("seq >>>> " + upSeq);
 175     TDBeaconsFTSRestClientTest.setMock();
 176     StructureChooserQuerySource scquery = StructureChooserQuerySource.getQuerySourceFor(new SequenceI[] { upSeq});
 177     AssertJUnit.assertTrue(scquery instanceof ThreeDBStructureChooserQuerySource);
 178     String query = scquery.buildQuery(upSeq);
 179     AssertJUnit.assertEquals("P38398", query);
 180
 181     // query shouldn't change regardless of additional entries
 182     // because 3DBeacons requires canonical entries.
 183     upSeq.getAllPDBEntries().clear();
 184     query = scquery.buildQuery(upSeq);
 185     AssertJUnit.assertEquals("P38398", query);
 186     upSeq.setDBRefs(null);
 187     query = scquery.buildQuery(upSeq);
 188     /*
 189      * legacy projects/datasets will not have canonical flags set for uniprot dbrefs
 190      * graceful behaviour would be to
 191      *  - pick one ? not possible
 192      *  - iterate through all until a 200 is obtained ?
 193      *  ---> ideal but could be costly
 194      *  ---> better to do a direct retrieval from uniprot to work out which is the canonical identifier..
 195      *  ----> need a test to check that accessions can be promoted to canonical!
 196      */
 197     //FIXME - need to be able to use ID to query here ?
 198     AssertJUnit.assertEquals(null, query);
 199
 200
 201
 202     // TODO:
 203     /**
 204      * set of sequences:
 205      * - no protein -> TDB not applicable, query PDBe only (consider RNA or DNA - specific query adapter ?)
 206      * - protein but no uniprot -> first consider trying to get uniprot refs (need a mark to say none are available)
 207      * - protein and uniprot - no canonicals -> resolve to uniprot automatically to get canonicals
 208      * - query uniprot against 3DBeacons
 209      * --> decorate experimental structures with additional data from PDBe
 210      * - query remaining against PDBe
 211      * Ranking
 212      * - 3D Beacons
 213      *  --> in memory ranking - no need to query twice
 214      *  Rank by
 215      *  - experimental > AlphaFold -> Model
 216      *  - start > end
 217      *  -> filters for
 218      *  -> experimental only
 219      *  -> experimental plus best models for other regions
 220      *  -> "best cover"
 221      *  -> need to be able to select correct reference (the longest one that covers all) for superposition
 222      */
 223 //
 224 //    DBRefEntry uniprotDBRef = new DBRefEntry();
 225 //    uniprotDBRef.setAccessionId("P12345");
 226 //    uniprotDBRef.setSource(DBRefSource.UNIPROT);
 227 //    upSeq.addDBRef(uniprotDBRef);
 228 //
 229 //    DBRefEntry pdbDBRef = new DBRefEntry();
 230 //    pdbDBRef.setAccessionId("1XYZ");
 231 //    pdbDBRef.setSource(DBRefSource.PDB);
 232 //    upSeq.addDBRef(pdbDBRef);
 233 //
 234 //    for (int x = 1; x < 5; x++)
 235 //    {
 236 //      DBRefEntry dbRef = new DBRefEntry();
 237 //      dbRef.setAccessionId("XYZ_" + x);
 238 //      seq.addDBRef(dbRef);
 239 //    }
 240 //    System.out.println("");
 241 //    System.out.println(seq.getDBRefs());
 242 //    System.out.println(query);
 243 //    query = scquery.buildQuery(seq);
 244 //    assertEquals(
 245 //            "uniprot_accession:P12345 OR uniprot_id:P12345 OR pdb_id:1xyz",
 246 //            query);
 247   }
 248   @Test(groups= {"Functional"})
 249   public void cascadingThreeDBandPDBQuerys()
 250   {
 251     TDBeaconsFTSRestClientTest.setMock();
 252     PDBFTSRestClient.setMock();
 253     ThreeDBStructureChooserQuerySource tdbquery = new ThreeDBStructureChooserQuerySource();
 254     PDBStructureChooserQuerySource pdbquery  = new PDBStructureChooserQuerySource();
 255
 256
 257
 258     FTSRestResponse upResponse = null;
 259     FTSRestResponse pdbResponse = null;
 260
 261     try {
 262       upResponse = tdbquery.fetchStructuresMetaData(upSeq, tdbquery.getDocFieldPrefs().getStructureSummaryFields(),  null, false);
 263       // NB Could have race condition here
 264       String pdb_Query = tdbquery.buildPDBFTSQueryFor(upResponse);
 265       assertTrue(pdb_Query.trim().length()>0);
 266       pdbResponse = tdbquery.fetchStructuresMetaDataFor(pdbquery, upResponse);
 267       assertTrue(pdbResponse.getNumberOfItemsFound()>0);
 268       FTSRestResponse joinedResp = tdbquery.joinResponses(upResponse, pdbResponse);
 269       assertEquals(upResponse.getNumberOfItemsFound(),joinedResp.getNumberOfItemsFound());
 270
 271     } catch (Exception x)
 272     {
 273       x.printStackTrace();
 274       Assert.fail("Unexpected Exception");
 275     }
 276     StructureChooserQuerySource scquery = StructureChooserQuerySource.getQuerySourceFor(new SequenceI[] { upSeq});
 277
 278   }
 279
 280   @Test(groups = { "Functional" })
 281   public void sanitizeSeqNameTest()
 282   {
 283     String name = "ab_cdEF|fwxyz012349";
 284     AssertJUnit.assertEquals(name, PDBStructureChooserQuerySource.sanitizeSeqName(name));
 285
 286     // remove a [nn] substring
 287     name = "abcde12[345]fg";
 288     AssertJUnit.assertEquals("abcde12fg", PDBStructureChooserQuerySource.sanitizeSeqName(name));
 289
 290     // remove characters other than a-zA-Z0-9 | or _
 291     name = "ab[cd],.\t£$*!- \\\"@:e";
 292     AssertJUnit.assertEquals("abcde", PDBStructureChooserQuerySource.sanitizeSeqName(name));
 293
 294     name = "abcde12[345a]fg";
 295     AssertJUnit.assertEquals("abcde12345afg", PDBStructureChooserQuerySource.sanitizeSeqName(name));
 296   }
 297 }