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 java.util.Vector;
  25
  26 import org.testng.AssertJUnit;
  27 import org.testng.annotations.AfterMethod;
  28 import org.testng.annotations.BeforeClass;
  29 import org.testng.annotations.BeforeMethod;
  30 import org.testng.annotations.Test;
  31
  32 import jalview.datamodel.DBRefEntry;
  33 import jalview.datamodel.DBRefSource;
  34 import jalview.datamodel.PDBEntry;
  35 import jalview.datamodel.Sequence;
  36 import jalview.datamodel.SequenceI;
  37 import jalview.fts.core.FTSRestRequest;
  38 import jalview.fts.threedbeacons.TDBeaconsFTSRestClientTest;
  39 import jalview.gui.JvOptionPane;
  40
  41 public class StructureChooserQuerySourceTest
  42 {
  43
  44   @BeforeClass(alwaysRun = true)
  45   public void setUpJvOptionPane()
  46   {
  47     JvOptionPane.setInteractiveMode(false);
  48     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
  49   }
  50
  51   Sequence seq,upSeq;
  52
  53   // same set up as for structurechooser test
  54
  55 @BeforeMethod(alwaysRun = true)
  56   public void setUp() throws Exception
  57   {
  58     seq = new Sequence("PDB|4kqy|4KQY|A", "ABCDEFGHIJKLMNOPQRSTUVWXYZ", 1,
  59             26);
  60     seq.createDatasetSequence();
  61     for (int x = 1; x < 5; x++)
  62     {
  63       DBRefEntry dbRef = new DBRefEntry();
  64       dbRef.setAccessionId("XYZ_" + x);
  65       seq.addDBRef(dbRef);
  66     }
  67
  68     PDBEntry dbRef = new PDBEntry();
  69     dbRef.setId("1tim");
  70
  71     Vector<PDBEntry> pdbIds = new Vector<>();
  72     pdbIds.add(dbRef);
  73
  74     seq.setPDBId(pdbIds);
  75
  76     // Uniprot sequence for 3D-Beacons mocks
  77     upSeq = new Sequence("P38398",
  78             "MDLSALRVEEVQNVINAMQKILECPICLELIKEPVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRS\n"
  79             + "LQESTRFSQLVEELLKIICAFQLDTGLEYANSYNFAKKENNSPEHLKDEVSIIQSMGYRNRAKRLLQSEPEN\n"
  80             + "PSLQETSLSVQLSNLGTVRTLRTKQRIQPQKTSVYIELGSDSSEDTVNKATYCSVGDQELLQITPQGTRDEI\n"
  81             + "SLDSAKKAACEFSETDVTNTEHHQPSNNDLNTTEKRAAERHPEKYQGSSVSNLHVEPCGTNTHASSLQHENS\n"
  82             + "SLLLTKDRMNVEKAEFCNKSKQPGLARSQHNRWAGSKETCNDRRTPSTEKKVDLNADPLCERKEWNKQKLPC\n"
  83             + "SENPRDTEDVPWITLNSSIQKVNEWFSRSDELLGSDDSHDGESESNAKVADVLDVLNEVDEYSGSSEKIDLL\n"
  84             + "ASDPHEALICKSERVHSKSVESNIEDKIFGKTYRKKASLPNLSHVTENLIIGAFVTEPQIIQERPLTNKLKR\n"
  85             + "KRRPTSGLHPEDFIKKADLAVQKTPEMINQGTNQTEQNGQVMNITNSGHENKTKGDSIQNEKNPNPIESLEK\n"
  86             + "ESAFKTKAEPISSSISNMELELNIHNSKAPKKNRLRRKSSTRHIHALELVVSRNLSPPNCTELQIDSCSSSE\n"
  87             + "EIKKKKYNQMPVRHSRNLQLMEGKEPATGAKKSNKPNEQTSKRHDSDTFPELKLTNAPGSFTKCSNTSELKE\n"
  88             + "FVNPSLPREEKEEKLETVKVSNNAEDPKDLMLSGERVLQTERSVESSSISLVPGTDYGTQESISLLEVSTLG\n"
  89             + "KAKTEPNKCVSQCAAFENPKGLIHGCSKDNRNDTEGFKYPLGHEVNHSRETSIEMEESELDAQYLQNTFKVS\n"
  90             + "KRQSFAPFSNPGNAEEECATFSAHSGSLKKQSPKVTFECEQKEENQGKNESNIKPVQTVNITAGFPVVGQKD\n"
  91             + "KPVDNAKCSIKGGSRFCLSSQFRGNETGLITPNKHGLLQNPYRIPPLFPIKSFVKTKCKKNLLEENFEEHSM\n"
  92             + "SPEREMGNENIPSTVSTISRNNIRENVFKEASSSNINEVGSSTNEVGSSINEIGSSDENIQAELGRNRGPKL\n"
  93             + "NAMLRLGVLQPEVYKQSLPGSNCKHPEIKKQEYEEVVQTVNTDFSPYLISDNLEQPMGSSHASQVCSETPDD\n"
  94             + "LLDDGEIKEDTSFAENDIKESSAVFSKSVQKGELSRSPSPFTHTHLAQGYRRGAKKLESSEENLSSEDEELP\n"
  95             + "CFQHLLFGKVNNIPSQSTRHSTVATECLSKNTEENLLSLKNSLNDCSNQVILAKASQEHHLSEETKCSASLF\n"
  96             + "SSQCSELEDLTANTNTQDPFLIGSSKQMRHQSESQGVGLSDKELVSDDEERGTGLEENNQEEQSMDSNLGEA\n"
  97             + "ASGCESETSVSEDCSGLSSQSDILTTQQRDTMQHNLIKLQQEMAELEAVLEQHGSQPSNSYPSIISDSSALE\n"
  98             + "DLRNPEQSTSEKAVLTSQKSSEYPISQNPEGLSADKFEVSADSSTSKNKEPGVERSSPSKCPSLDDRWYMHS\n"
  99             + "CSGSLQNRNYPSQEELIKVVDVEEQQLEESGPHDLTETSYLPRQDLEGTPYLESGISLFSDDPESDPSEDRA\n"
 100             + "PESARVGNIPSSTSALKVPQLKVAESAQSPAAAHTTDTAGYNAMEESVSREKPELTASTERVNKRMSMVVSG\n"
 101             + "LTPEEFMLVYKFARKHHITLTNLITEETTHVVMKTDAEFVCERTLKYFLGIAGGKWVVSYFWVTQSIKERKM\n"
 102             + "LNEHDFEVRGDVVNGRNHQGPKRARESQDRKIFRGLEICCYGPFTNMPTDQLEWMVQLCGASVVKELSSFTL\n"
 103             + "GTGVHPIVVVQPDAWTEDNGFHAIGQMCEAPVVTREWVLDSVALYQCQELDTYLIPQIPHSHY\n"
 104             + "", 1,
 105 1863);
 106     upSeq.createDatasetSequence();
 107     upSeq.setDescription("Breast cancer type 1 susceptibility protein");
 108     upSeq.addDBRef(new DBRefEntry("UNIPROT","0","P38398",null,true));
 109   }
 110
 111 @AfterMethod(alwaysRun = true)
 112   public void tearDown() throws Exception
 113   {
 114     seq = null;
 115     upSeq=null;
 116   }
 117
 118   @SuppressWarnings("deprecation")
 119   @Test(groups = { "Functional" })
 120   public void buildPDBQueryTest()
 121   {
 122     System.out.println("seq >>>> " + seq);
 123
 124     StructureChooserQuerySource scquery = StructureChooserQuerySource.getQuerySourceFor(new SequenceI[] { seq});
 125     AssertJUnit.assertTrue(scquery instanceof PDBStructureChooserQuerySource);
 126     String query = scquery.buildQuery(seq);
 127     AssertJUnit.assertEquals("pdb_id:1tim", query);
 128     seq.getAllPDBEntries().clear();
 129     query = scquery.buildQuery(seq);
 130     AssertJUnit.assertEquals(
 131             "text:XYZ_1 OR text:XYZ_2 OR text:XYZ_3 OR text:XYZ_4 OR text:4kqy",
 132             query);
 133     seq.setDBRefs(null);
 134     query = scquery.buildQuery(seq);
 135     System.out.println(query);
 136     AssertJUnit.assertEquals("text:4kqy", query);
 137
 138     DBRefEntry uniprotDBRef = new DBRefEntry();
 139     uniprotDBRef.setAccessionId("P12345");
 140     uniprotDBRef.setSource(DBRefSource.UNIPROT);
 141     seq.addDBRef(uniprotDBRef);
 142
 143     DBRefEntry pdbDBRef = new DBRefEntry();
 144     pdbDBRef.setAccessionId("1XYZ");
 145     pdbDBRef.setSource(DBRefSource.PDB);
 146     seq.addDBRef(pdbDBRef);
 147
 148     for (int x = 1; x < 5; x++)
 149     {
 150       DBRefEntry dbRef = new DBRefEntry();
 151       dbRef.setAccessionId("XYZ_" + x);
 152       seq.addDBRef(dbRef);
 153     }
 154     System.out.println("");
 155     System.out.println(seq.getDBRefs());
 156     System.out.println(query);
 157     query = scquery.buildQuery(seq);
 158     AssertJUnit.assertEquals(
 159             "uniprot_accession:P12345 OR uniprot_id:P12345 OR pdb_id:1xyz",
 160             query);
 161   }
 162
 163   @SuppressWarnings("deprecation")
 164   @Test(groups = { "Functional" })
 165   public void buildThreeDBQueryTest()
 166   {
 167     System.out.println("seq >>>> " + upSeq);
 168     TDBeaconsFTSRestClientTest.setMock();
 169     StructureChooserQuerySource scquery = StructureChooserQuerySource.getQuerySourceFor(new SequenceI[] { upSeq});
 170     AssertJUnit.assertTrue(scquery instanceof ThreeDBStructureChooserQuerySource);
 171     String query = scquery.buildQuery(upSeq);
 172     AssertJUnit.assertEquals("P38398", query);
 173
 174     // query shouldn't change regardless of additional entries
 175     // because 3DBeacons requires canonical entries.
 176     upSeq.getAllPDBEntries().clear();
 177     query = scquery.buildQuery(upSeq);
 178     AssertJUnit.assertEquals("P38398", query);
 179     upSeq.setDBRefs(null);
 180     query = scquery.buildQuery(upSeq);
 181     /*
 182      * legacy projects/datasets will not have canonical flags set for uniprot dbrefs
 183      * graceful behaviour would be to
 184      *  - pick one ? not possible
 185      *  - iterate through all until a 200 is obtained ?
 186      *  ---> ideal but could be costly
 187      *  ---> better to do a direct retrieval from uniprot to work out which is the canonical identifier..
 188      *  ----> need a test to check that accessions can be promoted to canonical!
 189      */
 190     //FIXME - need to be able to use ID to query here ?
 191     AssertJUnit.assertEquals(null, query);
 192
 193
 194
 195     // TODO:
 196     /**
 197      * set of sequences:
 198      * - no protein -> TDB not applicable, query PDBe only (consider RNA or DNA - specific query adapter ?)
 199      * - protein but no uniprot -> first consider trying to get uniprot refs (need a mark to say none are available)
 200      * - protein and uniprot - no canonicals -> resolve to uniprot automatically to get canonicals
 201      * - query uniprot against 3DBeacons
 202      * --> decorate experimental structures with additional data from PDBe
 203      * - query remaining against PDBe
 204      * Ranking
 205      * - 3D Beacons
 206      *  --> in memory ranking - no need to query twice
 207      *  Rank by
 208      *  - experimental > AlphaFold -> Model
 209      *  - start > end
 210      *  -> filters for
 211      *  -> experimental only
 212      *  -> experimental plus best models for other regions
 213      *  -> "best cover"
 214      *  -> need to be able to select correct reference (the longest one that covers all) for superposition
 215      */
 216 //
 217 //    DBRefEntry uniprotDBRef = new DBRefEntry();
 218 //    uniprotDBRef.setAccessionId("P12345");
 219 //    uniprotDBRef.setSource(DBRefSource.UNIPROT);
 220 //    upSeq.addDBRef(uniprotDBRef);
 221 //
 222 //    DBRefEntry pdbDBRef = new DBRefEntry();
 223 //    pdbDBRef.setAccessionId("1XYZ");
 224 //    pdbDBRef.setSource(DBRefSource.PDB);
 225 //    upSeq.addDBRef(pdbDBRef);
 226 //
 227 //    for (int x = 1; x < 5; x++)
 228 //    {
 229 //      DBRefEntry dbRef = new DBRefEntry();
 230 //      dbRef.setAccessionId("XYZ_" + x);
 231 //      seq.addDBRef(dbRef);
 232 //    }
 233 //    System.out.println("");
 234 //    System.out.println(seq.getDBRefs());
 235 //    System.out.println(query);
 236 //    query = scquery.buildQuery(seq);
 237 //    assertEquals(
 238 //            "uniprot_accession:P12345 OR uniprot_id:P12345 OR pdb_id:1xyz",
 239 //            query);
 240   }
 241   @Test(groups= {"Functional"})
 242   public void cascadingThreeDBandPDBQuerys()
 243   {
 244     TDBeaconsFTSRestClientTest.setMock();
 245
 246     StructureChooserQuerySource scquery = StructureChooserQuerySource.getQuerySourceFor(new SequenceI[] { upSeq});
 247
 248     // query TDB for doc
 249     // query PDBe for PDB entry metadata
 250     // Combine
 251
 252     FTSRestRequest tdbQuery = new FTSRestRequest();
 253     tdbQuery.setResponseSize(100);
 254     tdbQuery.setFieldToSearchBy("");
 255     tdbQuery.setSearchTerm(scquery.buildQuery(upSeq));
 256     tdbQuery.setWantedFields(scquery.getDocFieldPrefs().getStructureSummaryFields());
 257     //scquery.fetchStructuresMetaData(upSeq, null, null, false);
 258     String secondaryPdbQuery;
 259     //secondaryPdbQuery = ((ThreeDBStructureChooserQuerySource)scquery).buildPDBFTSquery();
 260
 261   }
 262
 263   @Test(groups = { "Functional" })
 264   public void sanitizeSeqNameTest()
 265   {
 266     String name = "ab_cdEF|fwxyz012349";
 267     AssertJUnit.assertEquals(name, PDBStructureChooserQuerySource.sanitizeSeqName(name));
 268
 269     // remove a [nn] substring
 270     name = "abcde12[345]fg";
 271     AssertJUnit.assertEquals("abcde12fg", PDBStructureChooserQuerySource.sanitizeSeqName(name));
 272
 273     // remove characters other than a-zA-Z0-9 | or _
 274     name = "ab[cd],.\t£$*!- \\\"@:e";
 275     AssertJUnit.assertEquals("abcde", PDBStructureChooserQuerySource.sanitizeSeqName(name));
 276
 277     name = "abcde12[345a]fg";
 278     AssertJUnit.assertEquals("abcde12345afg", PDBStructureChooserQuerySource.sanitizeSeqName(name));
 279   }
 280 }