test/jalview/io/CrossRef2xmlTests.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.io;
  22
  23 import jalview.analysis.CrossRef;
  24 import jalview.api.AlignmentViewPanel;
  25 import jalview.datamodel.AlignedCodonFrame;
  26 import jalview.datamodel.AlignmentI;
  27 import jalview.datamodel.AlignmentTest;
  28 import jalview.datamodel.SequenceI;
  29 import jalview.gui.AlignFrame;
  30 import jalview.gui.CrossRefAction;
  31 import jalview.gui.Desktop;
  32 import jalview.gui.Jalview2XML;
  33
  34 import java.io.File;
  35 import java.io.IOException;
  36 import java.util.ArrayList;
  37 import java.util.HashMap;
  38 import java.util.List;
  39
  40 import org.testng.Assert;
  41 import org.testng.annotations.Test;
  42
  43 @Test(singleThreaded = true)
  44 public class CrossRef2xmlTests extends Jalview2xmlBase
  45 {
  46
  47   /**
  48    * test store and recovery of expanded views
  49    *
  50    * @throws Exception
  51    */
  52   @Test(groups = { "Operational" }, enabled = true)
  53   public void testRetrieveAndShowCrossref() throws Exception
  54   {
  55
  56     List<String> failedDBRetr = new ArrayList<String>();
  57     List<String> failedXrefMenuItems = new ArrayList<String>();
  58     List<String> failedProjectRecoveries = new ArrayList<String>();
  59
  60     // for every set of db queries
  61     // retrieve db query
  62     // verify presence of expected xrefs
  63     // show xrefs - verify expected type of frame is shown for each xref
  64     // show xrefs again
  65     // - verify original -> xref -> xref(original) recovers frame containing at
  66     // least the first retrieved sequence
  67     // store
  68     // 1. whole project
  69     // 2. individual frames
  70     // 3. load each one back and verify
  71     // . aligned sequences (.toString() )
  72     // . xrefs (.toString() )
  73     // . codonframes
  74     //
  75     //
  76     HashMap<String, String> dbtoviewBit = new HashMap<String, String>();
  77     List<String> keyseq = new ArrayList<String>();
  78     HashMap<String, File> savedProjects = new HashMap<String, File>();
  79
  80     for (String[] did : new String[][] { { "ENSEMBL", "ENSG00000157764" },
  81     { "UNIPROT", "P01731" } })
  82     {
  83       // pass counters - 0 - first pass, 1 means retrieve project rather than
  84       // perform action
  85       int pass1 = 0, pass2 = 0, pass3 = 0;
  86       // each do loop performs two iterations in the first outer loop pass, but
  87       // only performs one iteration on the second outer loop
  88       // ie. pass 1 = 0 {pass 2= 0 { pass 3 = 0,1 }, pass 2=1 { pass 3 = 0 }}, 1
  89       // { pass 2 = 0 { pass 3 = 0 } }
  90       do
  91       {
  92         String first = did[0] + " " + did[1];
  93         AlignFrame af = null;
  94         boolean dna;
  95         AlignmentI retral;
  96         AlignmentI dataset;
  97         SequenceI[] seqs;
  98         List<String> ptypes = null;
  99         if (pass1 == 0)
 100         {
 101           // retrieve dbref
 102
 103           List<AlignFrame> afs = jalview.gui.SequenceFetcher.fetchAndShow(
 104                   did[0], did[1]);
 105           if (afs.size() == 0)
 106           {
 107             failedDBRetr.add("Didn't retrieve " + first);
 108             break;
 109           }
 110           keyseq.add(first);
 111           af = afs.get(0);
 112
 113           // verify references for retrieved data
 114           AlignmentTest.assertAlignmentDatasetRefs(af.getViewport()
 115                   .getAlignment(), "Pass (" + pass1 + "," + pass2 + ","
 116                   + pass3 + "): Fetch " + first + ":");
 117           dna = af.getViewport().getAlignment().isNucleotide();
 118           retral = af.getViewport().getAlignment();
 119           dataset = retral.getDataset();
 120           seqs = retral.getSequencesArray();
 121
 122         }
 123         else
 124         {
 125           Desktop.instance.closeAll_actionPerformed(null);
 126           // recover stored project
 127           af = new FileLoader(false).LoadFileWaitTillLoaded(savedProjects
 128                   .get(first).toString(), FormatAdapter.FILE);
 129           System.out.println("Recovered view for '" + first + "' from '"
 130                   + savedProjects.get(first).toString() + "'");
 131           dna = af.getViewport().getAlignment().isNucleotide();
 132           retral = af.getViewport().getAlignment();
 133           dataset = retral.getDataset();
 134           seqs = retral.getSequencesArray();
 135
 136           // verify references for recovered data
 137           AlignmentTest.assertAlignmentDatasetRefs(af.getViewport()
 138                   .getAlignment(), "Pass (" + pass1 + "," + pass2 + ","
 139                   + pass3 + "): Recover " + first + ":");
 140
 141         }
 142
 143         // store project on first pass, compare next pass
 144         stringify(dbtoviewBit, savedProjects, first, af.alignPanel);
 145
 146         ptypes = (seqs == null || seqs.length == 0) ? null : new CrossRef(
 147                 seqs, dataset).findXrefSourcesForSequences(dna);
 148
 149         // start of pass2: retrieve each cross-ref for fetched or restored
 150         // project.
 151         do // first cross ref and recover crossref loop
 152         {
 153
 154           for (String db : ptypes)
 155           {
 156             // counter for splitframe views retrieved via crossref
 157             int firstcr_ap = 0;
 158             // build next key so we an retrieve all views
 159             String nextxref = first + " -> " + db + "{" + firstcr_ap + "}";
 160             // perform crossref action, or retrieve stored project
 161             List<AlignmentViewPanel> cra_views = new ArrayList<AlignmentViewPanel>();
 162             CrossRefAction cra = null;
 163
 164             if (pass2 == 0)
 165             { // retrieve and show cross-refs in this thread
 166               cra = new CrossRefAction(af, seqs, dna, db);
 167               cra.run();
 168               if (cra.getXrefViews().size() == 0)
 169               {
 170                 failedXrefMenuItems.add("No crossrefs retrieved for "
 171                         + first + " -> " + db);
 172                 continue;
 173               }
 174               cra_views = cra.getXrefViews();
 175               assertNucleotide(cra_views.get(0),
 176                       "Nucleotide panel included proteins for " + first
 177                               + " -> " + db);
 178               assertProtein(cra_views.get(1),
 179                       "Protein panel included nucleotides for " + first
 180                               + " -> " + db);
 181             }
 182             else
 183             {
 184               Desktop.instance.closeAll_actionPerformed(null);
 185               pass3 = 0;
 186               // recover stored project
 187               File storedProject = savedProjects.get(nextxref);
 188               if (storedProject == null)
 189               {
 190                 failedProjectRecoveries.add("Failed to store a view for '"
 191                         + nextxref + "'");
 192                 continue;
 193               }
 194
 195               // recover stored project
 196               AlignFrame af2 = new FileLoader(false)
 197                       .LoadFileWaitTillLoaded(savedProjects.get(nextxref)
 198                               .toString(), FormatAdapter.FILE);
 199               System.out.println("Recovered view for '" + nextxref
 200                       + "' from '" + savedProjects.get(nextxref).toString()
 201                       + "'");
 202               // gymnastics to recover the alignPanel/Complementary alignPanel
 203               if (af2.getViewport().isNucleotide())
 204               {
 205                 // top view, then bottom
 206                 cra_views.add(af2.getViewport().getAlignPanel());
 207                 cra_views.add(((jalview.gui.AlignViewport) af2
 208                         .getViewport().getCodingComplement())
 209                         .getAlignPanel());
 210
 211               }
 212               else
 213               {
 214                 // bottom view, then top
 215                 cra_views.add(((jalview.gui.AlignViewport) af2
 216                         .getViewport().getCodingComplement())
 217                         .getAlignPanel());
 218                 cra_views.add(af2.getViewport().getAlignPanel());
 219
 220               }
 221             }
 222             HashMap<String, List<String>> xrptypes = new HashMap<String, List<String>>();
 223             // first save/verify views.
 224             for (AlignmentViewPanel avp : cra_views)
 225             {
 226               nextxref = first + " -> " + db + "{" + firstcr_ap++ + "}";
 227               // verify references for this panel
 228               AlignmentTest.assertAlignmentDatasetRefs(avp.getAlignment(),
 229                       "Pass (" + pass1 + "," + pass2 + "," + pass3
 230                               + "): before start of pass3: " + nextxref
 231                               + ":");
 232
 233               SequenceI[] xrseqs = avp.getAlignment().getSequencesArray();
 234
 235               List<String> _xrptypes = (seqs == null || seqs.length == 0) ? null
 236                       : new CrossRef(xrseqs, dataset)
 237                               .findXrefSourcesForSequences(avp
 238                                       .getAlignViewport().isNucleotide());
 239
 240               stringify(dbtoviewBit, savedProjects, nextxref, avp);
 241               xrptypes.put(nextxref, _xrptypes);
 242
 243             }
 244
 245             // now do the second xref pass starting from either saved or just
 246             // recovered split pane, in sequence
 247             do // retrieve second set of cross refs or recover and verify
 248             {
 249               firstcr_ap = 0;
 250               for (AlignmentViewPanel avp : cra_views)
 251               {
 252                 nextxref = first + " -> " + db + "{" + firstcr_ap++ + "}";
 253                 for (String xrefdb : xrptypes.get(nextxref))
 254                 {
 255                   List<AlignmentViewPanel> cra_views2 = new ArrayList<AlignmentViewPanel>();
 256                   int q = 0;
 257                   String nextnextxref = nextxref
 258                           + " -> " + xrefdb + "{" + q + "}";
 259
 260                   if (pass3 == 0)
 261                   {
 262
 263                     SequenceI[] xrseqs = avp.getAlignment()
 264                             .getSequencesArray();
 265                     AlignFrame nextaf = Desktop.getAlignFrameFor(avp
 266                             .getAlignViewport());
 267
 268                     cra = new CrossRefAction(nextaf, xrseqs, avp
 269                             .getAlignViewport().isNucleotide(), xrefdb);
 270                     cra.run();
 271                     if (cra.getXrefViews().size() == 0)
 272                     {
 273                       failedXrefMenuItems
 274                               .add("No crossrefs retrieved for '"
 275                               + nextxref + "' to " + xrefdb + " via '"
 276                               + nextaf.getTitle() + "'");
 277                       continue;
 278                     }
 279                     cra_views2 = cra.getXrefViews();
 280                     assertNucleotide(cra_views2.get(0),
 281                             "Nucleotide panel included proteins for '"
 282                                     + nextxref + "' to " + xrefdb
 283                                     + " via '" + nextaf.getTitle() + "'");
 284                     assertProtein(cra_views2.get(1),
 285                             "Protein panel included nucleotides for '"
 286                                     + nextxref + "' to " + xrefdb
 287                                     + " via '" + nextaf.getTitle() + "'");
 288
 289                   }
 290                   else
 291                   {
 292                     Desktop.instance.closeAll_actionPerformed(null);
 293                     // recover stored project
 294                     File storedProject = savedProjects.get(nextnextxref);
 295                     if (storedProject == null)
 296                     {
 297                       failedProjectRecoveries
 298                               .add("Failed to store a view for '"
 299                                       + nextnextxref + "'");
 300                       continue;
 301                     }
 302                     AlignFrame af2 = new FileLoader(false)
 303                             .LoadFileWaitTillLoaded(
 304                                     savedProjects.get(nextnextxref)
 305                                             .toString(), FormatAdapter.FILE);
 306                     System.out.println("Recovered view for '"
 307                             + nextnextxref + "' from '"
 308                             + savedProjects.get(nextnextxref).toString()
 309                             + "'");
 310                     // gymnastics to recover the alignPanel/Complementary
 311                     // alignPanel
 312                     if (af2.getViewport().isNucleotide())
 313                     {
 314                       // top view, then bottom
 315                       cra_views2.add(af2.getViewport().getAlignPanel());
 316                       cra_views2.add(((jalview.gui.AlignViewport) af2
 317                               .getViewport().getCodingComplement())
 318                               .getAlignPanel());
 319
 320                     }
 321                     else
 322                     {
 323                       // bottom view, then top
 324                       cra_views2.add(((jalview.gui.AlignViewport) af2
 325                               .getViewport().getCodingComplement())
 326                               .getAlignPanel());
 327                       cra_views2.add(af2.getViewport().getAlignPanel());
 328                     }
 329                     Assert.assertEquals(cra_views2.size(), 2);
 330                     Assert.assertNotNull(cra_views2.get(0));
 331                     Assert.assertNotNull(cra_views2.get(1));
 332                   }
 333
 334                   for (AlignmentViewPanel nextavp : cra_views2)
 335                   {
 336                     nextnextxref = nextxref
 337                             + " -> " + xrefdb + "{" + q++ + "}";
 338
 339                     // verify references for this panel
 340                     AlignmentTest.assertAlignmentDatasetRefs(
 341                             nextavp.getAlignment(), "" + "Pass (" + pass1
 342                                     + "," + pass2 + "): For "
 343                                     + nextnextxref + ":");
 344
 345                     stringify(dbtoviewBit, savedProjects, nextnextxref,
 346                             nextavp);
 347                     keyseq.add(nextnextxref);
 348                   }
 349                 } // end of loop around showing all xrefdb for crossrf2
 350
 351               } // end of loop around all viewpanels from crossrf1
 352             } while (pass2 == 2 && pass3++ < 2);
 353             // fetchdb->crossref1->crossref-2->verify for xrefs we
 354             // either loop twice when pass2=0, or just once when pass2=1
 355             // (recovered project from previous crossref)
 356
 357           } // end of loop over db-xrefs for crossref-2
 358
 359           // fetchdb-->crossref1
 360           // for each xref we try to retrieve xref, store and verify when
 361           // pass1=0, or just retrieve and verify when pass1=1
 362         } while (pass1 == 1 && pass2++ < 2);
 363         // fetchdb
 364         // for each ref we
 365         // loop twice: first, do the retrieve, second recover from saved project
 366
 367         // increment pass counters, so we repeat traversal starting from the
 368         // oldest saved project first.
 369         if (pass1 == 0)
 370         {
 371           // verify stored projects for first set of cross references
 372           pass1 = 1;
 373           // and verify cross-references retrieved from stored projects
 374           pass2 = 0;
 375           pass3 = 0;
 376         }
 377         else
 378         {
 379           pass1++;
 380           if (pass1 < 2)
 381           {
 382             // verify stored projects for second set of cross references
 383             pass2 = 1;
 384           // and verify cross-references retrievable from those stored projects.
 385             pass3 = 0;
 386           }
 387         }
 388       } while (pass3 < 2);
 389     }
 390     if (failedXrefMenuItems.size() > 0)
 391     {
 392       for (String s : failedXrefMenuItems)
 393       {
 394         System.err.println(s);
 395       }
 396       Assert.fail("Faulty xref menu (" + failedXrefMenuItems.size()
 397               + " counts)");
 398     }
 399     if (failedProjectRecoveries.size() > 0)
 400     {
 401
 402       for (String s : failedProjectRecoveries)
 403       {
 404         System.err.println(s);
 405       }
 406       Assert.fail("Didn't recover projects for some retrievals (did they retrieve ?) ("
 407               + failedProjectRecoveries.size() + " counts)");
 408     }
 409     if (failedDBRetr.size() > 0)
 410     {
 411       for (String s : failedProjectRecoveries)
 412       {
 413         System.err.println(s);
 414       }
 415       Assert.fail("Didn't retrieve some db refs for checking cross-refs ("
 416               + failedDBRetr.size() + " counts)");
 417     }
 418   }
 419
 420   private void assertProtein(AlignmentViewPanel alignmentViewPanel,
 421           String message)
 422   {
 423     assertType(true, alignmentViewPanel, message);
 424   }
 425
 426   private void assertNucleotide(AlignmentViewPanel alignmentViewPanel,
 427           String message)
 428   {
 429     assertType(false, alignmentViewPanel, message);
 430   }
 431
 432   private void assertType(boolean expectProtein,
 433           AlignmentViewPanel alignmentViewPanel, String message)
 434   {
 435     List<SequenceI> nonType = new ArrayList<SequenceI>();
 436     for (SequenceI sq : alignmentViewPanel.getAlignViewport()
 437             .getAlignment()
 438             .getSequences())
 439     {
 440       if (sq.isProtein() != expectProtein)
 441       {
 442         nonType.add(sq);
 443       }
 444     }
 445     if (nonType.size() > 0)
 446     {
 447       Assert.fail(message + " [ "
 448               + (expectProtein ? "nucleotides were " : "proteins were ")
 449               + nonType.toString()
 450               + " ]");
 451     }
 452   }
 453
 454   /**
 455    * first time called, record strings derived from alignment and
 456    * alignedcodonframes, and save view to a project file. Second time called,
 457    * compare strings to existing ones. org.testng.Assert.assertTrue on
 458    * stringmatch
 459    *
 460    * @param dbtoviewBit
 461    *          map between xrefpath and view string
 462    * @param savedProjects
 463    *          - map from xrefpath to saved project filename (createTempFile)
 464    * @param xrefpath
 465    *          - xrefpath - unique ID for this context (composed of sequence of
 466    *          db-fetch/cross-ref actions preceeding state)
 467    * @param avp
 468    *          - viewpanel to store (for viewpanels in splitframe, the same
 469    *          project should be written for both panels, only one needs
 470    *          recovering for comparison on the next stringify call, but each
 471    *          viewpanel needs to be called with a distinct xrefpath to ensure
 472    *          each one's strings are compared)
 473    */
 474   private void stringify(HashMap<String, String> dbtoviewBit,
 475           HashMap<String, File> savedProjects, String xrefpath,
 476           AlignmentViewPanel avp)
 477   {
 478     if (savedProjects != null)
 479     {
 480       if (savedProjects.get(xrefpath) == null)
 481       {
 482         // write a project file for this view. On the second pass, this will be
 483         // recovered and cross-references verified
 484         try
 485         {
 486           File prfile = File.createTempFile("crossRefTest", ".jvp");
 487           AlignFrame af = Desktop.getAlignFrameFor(avp.getAlignViewport());
 488           new Jalview2XML(false).saveAlignment(af, prfile.toString(),
 489                   af.getTitle());
 490           System.out.println("Written view from '" + xrefpath + "' as '"
 491                   + prfile.getAbsolutePath() + "'");
 492           savedProjects.put(xrefpath, prfile);
 493         } catch (IOException q)
 494         {
 495           Assert.fail("Unexpected IO Exception", q);
 496         }
 497       }
 498       else
 499       {
 500         System.out.println("Stringify check on view from '" + xrefpath
 501                 + "' [ possibly retrieved from '"
 502                 + savedProjects.get(xrefpath).getAbsolutePath() + "' ]");
 503
 504       }
 505     }
 506
 507     StringBuilder sbr = new StringBuilder();
 508     sbr.append(avp.getAlignment().toString());
 509     sbr.append("\n");
 510     sbr.append("<End of alignment>");
 511     sbr.append("\n");
 512     sbr.append(avp.getAlignment().getDataset());
 513     sbr.append("\n");
 514     sbr.append("<End of dataset>");
 515     sbr.append("\n");
 516     int p = 0;
 517     if (avp.getAlignment().getCodonFrames() != null)
 518     {
 519       for (AlignedCodonFrame ac : avp.getAlignment().getCodonFrames())
 520       {
 521         sbr.append("<AlignedCodonFrame " + p++ + ">");
 522         sbr.append("\n");
 523         sbr.append(ac.toString());
 524         sbr.append("\n");
 525       }
 526     }
 527     String dbt = dbtoviewBit.get(xrefpath);
 528     if (dbt == null)
 529     {
 530       dbtoviewBit.put(xrefpath, sbr.toString());
 531     }
 532     else
 533     {
 534       Assert.assertEquals(sbr.toString(), dbt, "stringify mismatch for "
 535               + xrefpath);
 536     }
 537   }
 538 }