test/jalview/gui/StructureChooserTest.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;
  22
  23 import static org.testng.Assert.assertEquals;
  24 import static org.testng.AssertJUnit.assertNotNull;
  25 import static org.testng.AssertJUnit.assertTrue;
  26
  27 import java.io.File;
  28 import java.util.Collection;
  29 import java.util.List;
  30 import java.util.Vector;
  31
  32 import org.junit.Assert;
  33 import org.testng.annotations.AfterMethod;
  34 import org.testng.annotations.BeforeClass;
  35 import org.testng.annotations.BeforeMethod;
  36 import org.testng.annotations.DataProvider;
  37 import org.testng.annotations.Test;
  38
  39 import jalview.api.AlignViewportI;
  40 import jalview.bin.Cache;
  41 import jalview.bin.Jalview;
  42 import jalview.datamodel.AlignmentAnnotation;
  43 import jalview.datamodel.AlignmentI;
  44 import jalview.datamodel.DBRefEntry;
  45 import jalview.datamodel.PDBEntry;
  46 import jalview.datamodel.Sequence;
  47 import jalview.datamodel.SequenceI;
  48 import jalview.fts.api.FTSData;
  49 import jalview.fts.core.FTSRestClient;
  50 import jalview.fts.service.pdb.PDBFTSRestClient;
  51 import jalview.fts.service.pdb.PDBFTSRestClientTest;
  52 import jalview.fts.service.threedbeacons.TDBeaconsFTSRestClient;
  53 import jalview.fts.threedbeacons.TDBeaconsFTSRestClientTest;
  54 import jalview.gui.StructureViewer.ViewerType;
  55 import jalview.gui.structurechooser.PDBStructureChooserQuerySource;
  56 import jalview.io.DataSourceType;
  57 import jalview.io.FileFormatException;
  58 import jalview.io.FileFormatI;
  59 import jalview.io.FileLoader;
  60 import jalview.io.IdentifyFile;
  61 import jalview.jbgui.FilterOption;
  62 import jalview.structure.StructureImportSettings.TFType;
  63 import junit.extensions.PA;
  64
  65 @Test(singleThreaded = true)
  66 public class StructureChooserTest
  67 {
  68
  69   @BeforeClass(alwaysRun = true)
  70   public void setUpJvOptionPane()
  71   {
  72     JvOptionPane.setInteractiveMode(false);
  73     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
  74   }
  75
  76   Sequence seq, upSeq, upSeq_nocanonical;
  77
  78   @BeforeMethod(alwaysRun = true)
  79   public void setUp() throws Exception
  80   {
  81     seq = new Sequence("PDB|4kqy|4KQY|A", "ABCDEFGHIJKLMNOPQRSTUVWXYZ", 1,
  82             26);
  83     seq.createDatasetSequence();
  84     for (int x = 1; x < 5; x++)
  85     {
  86       DBRefEntry dbRef = new DBRefEntry();
  87       dbRef.setAccessionId("XYZ_" + x);
  88       seq.addDBRef(dbRef);
  89     }
  90
  91     PDBEntry dbRef = new PDBEntry();
  92     dbRef.setId("1tim");
  93
  94     Vector<PDBEntry> pdbIds = new Vector<>();
  95     pdbIds.add(dbRef);
  96
  97     seq.setPDBId(pdbIds);
  98
  99     // Uniprot sequence for 3D-Beacons mocks
 100     upSeq = new Sequence("P38398",
 101             "MDLSALRVEEVQNVINAMQKILECPICLELIKEPVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRS\n"
 102                     + "LQESTRFSQLVEELLKIICAFQLDTGLEYANSYNFAKKENNSPEHLKDEVSIIQSMGYRNRAKRLLQSEPEN\n"
 103                     + "PSLQETSLSVQLSNLGTVRTLRTKQRIQPQKTSVYIELGSDSSEDTVNKATYCSVGDQELLQITPQGTRDEI\n"
 104                     + "SLDSAKKAACEFSETDVTNTEHHQPSNNDLNTTEKRAAERHPEKYQGSSVSNLHVEPCGTNTHASSLQHENS\n"
 105                     + "SLLLTKDRMNVEKAEFCNKSKQPGLARSQHNRWAGSKETCNDRRTPSTEKKVDLNADPLCERKEWNKQKLPC\n"
 106                     + "SENPRDTEDVPWITLNSSIQKVNEWFSRSDELLGSDDSHDGESESNAKVADVLDVLNEVDEYSGSSEKIDLL\n"
 107                     + "ASDPHEALICKSERVHSKSVESNIEDKIFGKTYRKKASLPNLSHVTENLIIGAFVTEPQIIQERPLTNKLKR\n"
 108                     + "KRRPTSGLHPEDFIKKADLAVQKTPEMINQGTNQTEQNGQVMNITNSGHENKTKGDSIQNEKNPNPIESLEK\n"
 109                     + "ESAFKTKAEPISSSISNMELELNIHNSKAPKKNRLRRKSSTRHIHALELVVSRNLSPPNCTELQIDSCSSSE\n"
 110                     + "EIKKKKYNQMPVRHSRNLQLMEGKEPATGAKKSNKPNEQTSKRHDSDTFPELKLTNAPGSFTKCSNTSELKE\n"
 111                     + "FVNPSLPREEKEEKLETVKVSNNAEDPKDLMLSGERVLQTERSVESSSISLVPGTDYGTQESISLLEVSTLG\n"
 112                     + "KAKTEPNKCVSQCAAFENPKGLIHGCSKDNRNDTEGFKYPLGHEVNHSRETSIEMEESELDAQYLQNTFKVS\n"
 113                     + "KRQSFAPFSNPGNAEEECATFSAHSGSLKKQSPKVTFECEQKEENQGKNESNIKPVQTVNITAGFPVVGQKD\n"
 114                     + "KPVDNAKCSIKGGSRFCLSSQFRGNETGLITPNKHGLLQNPYRIPPLFPIKSFVKTKCKKNLLEENFEEHSM\n"
 115                     + "SPEREMGNENIPSTVSTISRNNIRENVFKEASSSNINEVGSSTNEVGSSINEIGSSDENIQAELGRNRGPKL\n"
 116                     + "NAMLRLGVLQPEVYKQSLPGSNCKHPEIKKQEYEEVVQTVNTDFSPYLISDNLEQPMGSSHASQVCSETPDD\n"
 117                     + "LLDDGEIKEDTSFAENDIKESSAVFSKSVQKGELSRSPSPFTHTHLAQGYRRGAKKLESSEENLSSEDEELP\n"
 118                     + "CFQHLLFGKVNNIPSQSTRHSTVATECLSKNTEENLLSLKNSLNDCSNQVILAKASQEHHLSEETKCSASLF\n"
 119                     + "SSQCSELEDLTANTNTQDPFLIGSSKQMRHQSESQGVGLSDKELVSDDEERGTGLEENNQEEQSMDSNLGEA\n"
 120                     + "ASGCESETSVSEDCSGLSSQSDILTTQQRDTMQHNLIKLQQEMAELEAVLEQHGSQPSNSYPSIISDSSALE\n"
 121                     + "DLRNPEQSTSEKAVLTSQKSSEYPISQNPEGLSADKFEVSADSSTSKNKEPGVERSSPSKCPSLDDRWYMHS\n"
 122                     + "CSGSLQNRNYPSQEELIKVVDVEEQQLEESGPHDLTETSYLPRQDLEGTPYLESGISLFSDDPESDPSEDRA\n"
 123                     + "PESARVGNIPSSTSALKVPQLKVAESAQSPAAAHTTDTAGYNAMEESVSREKPELTASTERVNKRMSMVVSG\n"
 124                     + "LTPEEFMLVYKFARKHHITLTNLITEETTHVVMKTDAEFVCERTLKYFLGIAGGKWVVSYFWVTQSIKERKM\n"
 125                     + "LNEHDFEVRGDVVNGRNHQGPKRARESQDRKIFRGLEICCYGPFTNMPTDQLEWMVQLCGASVVKELSSFTL\n"
 126                     + "GTGVHPIVVVQPDAWTEDNGFHAIGQMCEAPVVTREWVLDSVALYQCQELDTYLIPQIPHSHY\n"
 127                     + "",
 128             1, 1863);
 129     upSeq.setDescription("Breast cancer type 1 susceptibility protein");
 130     upSeq_nocanonical = new Sequence(upSeq);
 131     upSeq.createDatasetSequence();
 132     upSeq.addDBRef(new DBRefEntry("UNIPROT", "0", "P38398", null, true));
 133
 134     upSeq_nocanonical.createDatasetSequence();
 135     // not a canonical reference
 136     upSeq_nocanonical.addDBRef(
 137             new DBRefEntry("UNIPROT", "0", "P38398", null, false));
 138
 139   }
 140
 141   @AfterMethod(alwaysRun = true)
 142   public void tearDown() throws Exception
 143   {
 144     seq = null;
 145     upSeq = null;
 146     upSeq_nocanonical = null;
 147   }
 148
 149   @Test(groups = { "Functional" })
 150   public void populateFilterComboBoxTest() throws InterruptedException
 151   {
 152     TDBeaconsFTSRestClientTest.setMock();
 153     PDBFTSRestClientTest.setMock();
 154
 155     SequenceI[] selectedSeqs = new SequenceI[] { seq };
 156     StructureChooser sc = new StructureChooser(selectedSeqs, seq, null);
 157     ThreadwaitFor(200, sc);
 158
 159     // if structures are not discovered then don't
 160     // populate filter options
 161     sc.populateFilterComboBox(false, false);
 162     int optionsSize = sc.getCmbFilterOption().getItemCount();
 163     System.out.println("Items (no data, no cache): ");
 164     StringBuilder items = new StringBuilder();
 165     for (int p = 0; p < optionsSize; p++)
 166     {
 167       items.append("- ")
 168               .append(sc.getCmbFilterOption().getItemAt(p).getName())
 169               .append("\n");
 170
 171     }
 172     // report items when this fails - seems to be a race condition
 173     Assert.assertEquals(items.toString(), optionsSize, 2);
 174
 175     sc.populateFilterComboBox(true, false);
 176     optionsSize = sc.getCmbFilterOption().getItemCount();
 177     assertTrue(optionsSize > 3); // if structures are found, filter options
 178                                  // should be populated
 179
 180     sc.populateFilterComboBox(true, true);
 181     assertTrue(sc.getCmbFilterOption().getSelectedItem() != null);
 182     FilterOption filterOpt = (FilterOption) sc.getCmbFilterOption()
 183             .getSelectedItem();
 184     assertEquals("Cached Structures", filterOpt.getName());
 185     FTSRestClient
 186             .unMock((FTSRestClient) TDBeaconsFTSRestClient.getInstance());
 187     FTSRestClient.unMock((FTSRestClient) PDBFTSRestClient.getInstance());
 188
 189   }
 190
 191   @Test(groups = { "Functional" })
 192   public void displayTDBQueryTest() throws InterruptedException
 193   {
 194     TDBeaconsFTSRestClientTest.setMock();
 195     PDBFTSRestClientTest.setMock();
 196
 197     SequenceI[] selectedSeqs = new SequenceI[] { upSeq_nocanonical };
 198     StructureChooser sc = new StructureChooser(selectedSeqs,
 199             upSeq_nocanonical, null);
 200     // mock so should be quick. Exceptions from mocked PDBFTS are expected too
 201     ThreadwaitFor(500, sc);
 202
 203     assertTrue(sc.isCanQueryTDB() && sc.isNotQueriedTDBYet());
 204   }
 205
 206   @Test(groups = { "Network" })
 207   public void fetchStructuresInfoTest()
 208   {
 209     FTSRestClient
 210             .unMock((FTSRestClient) TDBeaconsFTSRestClient.getInstance());
 211     PDBFTSRestClient.unMock((FTSRestClient) PDBFTSRestClient.getInstance());
 212     SequenceI[] selectedSeqs = new SequenceI[] { seq };
 213     StructureChooser sc = new StructureChooser(selectedSeqs, seq, null);
 214     // not mocked, wait for 2s
 215     ThreadwaitFor(2000, sc);
 216
 217     sc.fetchStructuresMetaData();
 218     Collection<FTSData> ss = (Collection<FTSData>) PA.getValue(sc,
 219             "discoveredStructuresSet");
 220     assertNotNull(ss);
 221     assertTrue(ss.size() > 0);
 222   }
 223
 224   @Test(groups = { "Functional" })
 225   public void fetchStructuresInfoMockedTest()
 226   {
 227     TDBeaconsFTSRestClientTest.setMock();
 228     PDBFTSRestClientTest.setMock();
 229     SequenceI[] selectedSeqs = new SequenceI[] { upSeq };
 230     StructureChooser sc = new StructureChooser(selectedSeqs, seq, null);
 231     ThreadwaitFor(500, sc);
 232
 233     sc.fetchStructuresMetaData();
 234     Collection<FTSData> ss = (Collection<FTSData>) PA.getValue(sc,
 235             "discoveredStructuresSet");
 236     assertNotNull(ss);
 237     assertTrue(ss.size() > 0);
 238   }
 239
 240   private void ThreadwaitFor(int i, StructureChooser sc)
 241   {
 242     long timeout = i + System.currentTimeMillis();
 243     while (!sc.isDialogVisible() && timeout > System.currentTimeMillis())
 244     {
 245       try
 246       {
 247         Thread.sleep(50);
 248       } catch (InterruptedException x)
 249       {
 250
 251       }
 252     }
 253
 254   }
 255
 256   @Test(groups = { "Functional" })
 257   public void sanitizeSeqNameTest()
 258   {
 259     String name = "ab_cdEF|fwxyz012349";
 260     assertEquals(name,
 261             PDBStructureChooserQuerySource.sanitizeSeqName(name));
 262
 263     // remove a [nn] substring
 264     name = "abcde12[345]fg";
 265     assertEquals("abcde12fg",
 266             PDBStructureChooserQuerySource.sanitizeSeqName(name));
 267
 268     // remove characters other than a-zA-Z0-9 | or _
 269     name = "ab[cd],.\t£$*!- \\\"@:e";
 270     assertEquals("abcde",
 271             PDBStructureChooserQuerySource.sanitizeSeqName(name));
 272
 273     name = "abcde12[345a]fg";
 274     assertEquals("abcde12345afg",
 275             PDBStructureChooserQuerySource.sanitizeSeqName(name));
 276   }
 277
 278   @Test(groups = { "Functional" }, dataProvider = "openStructureFileParams")
 279   public void openStructureFileForSequenceTest(String alfile, String seqid,
 280           String sFilename, TFType tft, String paeFilename,
 281           boolean showRefAnnotations, boolean doXferSettings,
 282           ViewerType viewerType, int seqNum, int annNum, int viewerNum,
 283           String propsFile)
 284   {
 285     Cache.loadProperties(
 286             propsFile == null ? "test/jalview/io/testProps.jvprops"
 287                     : propsFile);
 288
 289     Jalview.main(
 290             propsFile == null ? null : new String[]
 291             { "--props", propsFile });
 292     if (Desktop.instance != null)
 293       Desktop.instance.closeAll_actionPerformed(null);
 294     JvOptionPane.setInteractiveMode(false);
 295     JvOptionPane.setMockResponse(JvOptionPane.OK_OPTION);
 296
 297     FileLoader fileLoader = new FileLoader(true);
 298     FileFormatI format = null;
 299     File alFile = new File(alfile);
 300     try
 301     {
 302       format = new IdentifyFile().identify(alFile, DataSourceType.FILE);
 303     } catch (FileFormatException e1)
 304     {
 305       Assert.fail(
 306               "Unknown file format for '" + alFile.getAbsolutePath() + "'");
 307     }
 308
 309     AlignFrame af = fileLoader.LoadFileWaitTillLoaded(alFile,
 310             DataSourceType.FILE, format);
 311     AlignmentPanel ap = af.alignPanel;
 312     Assert.assertNotNull("No alignPanel", ap);
 313
 314     AlignmentI al = ap.getAlignment();
 315     Assert.assertNotNull(al);
 316
 317     SequenceI seq = al.findName(seqid);
 318     Assert.assertNotNull("Sequence '" + seqid + "' not found in alignment",
 319             seq);
 320
 321     StructureChooser.openStructureFileForSequence(null, null, ap, seq,
 322             false, sFilename, tft, paeFilename, false, showRefAnnotations,
 323             doXferSettings, viewerType);
 324
 325     List<SequenceI> seqs = al.getSequences();
 326     Assert.assertNotNull(seqs);
 327
 328     Assert.assertEquals("Wrong number of sequences", seqNum, seqs.size());
 329
 330     AlignViewportI av = ap.getAlignViewport();
 331     Assert.assertNotNull(av);
 332
 333     AlignmentAnnotation[] aas = al.getAlignmentAnnotation();
 334     int visibleAnn = 0;
 335     for (AlignmentAnnotation aa : aas)
 336     {
 337       if (aa.visible)
 338         visibleAnn++;
 339     }
 340     Assert.assertEquals("Wrong number of viewed annotations", annNum,
 341             visibleAnn);
 342
 343     if (viewerNum > -1)
 344     {
 345       try
 346       {
 347         Thread.sleep(100);
 348       } catch (InterruptedException e)
 349       {
 350         // TODO Auto-generated catch block
 351         e.printStackTrace();
 352       }
 353       List<StructureViewerBase> openViewers = Desktop.instance
 354               .getStructureViewers(ap, null);
 355       Assert.assertNotNull(openViewers);
 356       Assert.assertEquals("Wrong number of structure viewers opened",
 357               viewerNum, openViewers.size());
 358     }
 359
 360     if (af != null)
 361     {
 362       af.setVisible(false);
 363       af.dispose();
 364     }
 365   }
 366
 367   @DataProvider(name = "openStructureFileParams")
 368   public Object[][] openStructureFileParams()
 369   {
 370     /*
 371         String alFile,
 372         String seqid,
 373         String structureFilename,
 374         TFType tft,
 375         String paeFilename,
 376         boolean showRefAnnotations,
 377         boolean doXferSettings, // false for Commands
 378         ViewerType viewerType,
 379         int seqNum,
 380         int annNum,
 381         int viewerNum,
 382         String propsFile
 383      */
 384     return new Object[][] {
 385         /*
 386         */
 387         { "examples/uniref50.fa", "FER1_SPIOL",
 388             "examples/AlphaFold/AF-P00221-F1-model_v4.cif", TFType.DEFAULT,
 389             "examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json",
 390             true, false, null, 15, 7, 0, null },
 391         { "examples/uniref50.fa", "FER1_SPIOL",
 392             "examples/AlphaFold/AF-P00221-F1-model_v4.cif", TFType.PLDDT,
 393             "examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json",
 394             true, false, null, 15, 7, 0, null },
 395         { "examples/uniref50.fa", "FER1_SPIOL",
 396             "examples/AlphaFold/AF-P00221-F1-model_v4.cif", TFType.PLDDT,
 397             "examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json",
 398             false, false, null, 15, 4, 0, null },
 399         { "examples/uniref50.fa", "FER1_SPIOL",
 400             "examples/AlphaFold/AF-P00221-F1-model_v4.cif", TFType.DEFAULT,
 401             "examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json",
 402             true, false, ViewerType.JMOL, 15, 7, 1, null },
 403         { "examples/uniref50.fa", "FER1_SPIOL",
 404             "examples/AlphaFold/AF-P00221-F1-model_v4.cif", TFType.PLDDT,
 405             "examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json",
 406             true, false, ViewerType.JMOL, 15, 7, 1, null },
 407         { "examples/uniref50.fa", "FER1_SPIOL",
 408             "examples/AlphaFold/AF-P00221-F1-model_v4.cif", TFType.PLDDT,
 409             "examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json",
 410             false, false, ViewerType.JMOL, 15, 4, 1, null }, };
 411   }
 412
 413 }