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 all reachable cross refs from all reachable
  49    * crossrefs for one or more fetched db refs. Currently, this test has a known
  50    * failure case.
  51    *
  52    * @throws Exception
  53    */
  54   @Test(groups = { "Operational" }, enabled = true)
  55   public void testRetrieveAndShowCrossref() throws Exception
  56   {
  57
  58     List<String> failedDBRetr = new ArrayList<String>();
  59     List<String> failedXrefMenuItems = new ArrayList<String>();
  60     List<String> failedProjectRecoveries = new ArrayList<String>();
  61
  62     // for every set of db queries
  63     // retrieve db query
  64     // verify presence of expected xrefs
  65     // show xrefs - verify expected type of frame is shown for each xref
  66     // show xrefs again
  67     // - verify original -> xref -> xref(original) recovers frame containing at
  68     // least the first retrieved sequence
  69     // store
  70     // 1. whole project
  71     // 2. individual frames
  72     // 3. load each one back and verify
  73     // . aligned sequences (.toString() )
  74     // . xrefs (.toString() )
  75     // . codonframes
  76     //
  77     //
  78     HashMap<String, String> dbtoviewBit = new HashMap<String, String>();
  79     List<String> keyseq = new ArrayList<String>();
  80     HashMap<String, File> savedProjects = new HashMap<String, File>();
  81
  82     for (String[] did : new String[][] { { "ENSEMBL", "ENSG00000157764" },
  83     { "UNIPROT", "P01731" } })
  84     {
  85       // pass counters - 0 - first pass, 1 means retrieve project rather than
  86       // perform action
  87       int pass1 = 0, pass2 = 0, pass3 = 0;
  88       // each do loop performs two iterations in the first outer loop pass, but
  89       // only performs one iteration on the second outer loop
  90       // ie. pass 1 = 0 {pass 2= 0 { pass 3 = 0,1 }, pass 2=1 { pass 3 = 0 }}, 1
  91       // { pass 2 = 0 { pass 3 = 0 } }
  92       do
  93       {
  94         String first = did[0] + " " + did[1];
  95         AlignFrame af = null;
  96         boolean dna;
  97         AlignmentI retral;
  98         AlignmentI dataset;
  99         SequenceI[] seqs;
 100         List<String> ptypes = null;
 101         if (pass1 == 0)
 102         {
 103           // retrieve dbref
 104
 105           List<AlignFrame> afs = jalview.gui.SequenceFetcher.fetchAndShow(
 106                   did[0], did[1]);
 107           if (afs.size() == 0)
 108           {
 109             failedDBRetr.add("Didn't retrieve " + first);
 110             break;
 111           }
 112           keyseq.add(first);
 113           af = afs.get(0);
 114
 115           // verify references for retrieved data
 116           AlignmentTest.assertAlignmentDatasetRefs(af.getViewport()
 117                   .getAlignment(), "Pass (" + pass1 + "," + pass2 + ","
 118                   + pass3 + "): Fetch " + first + ":");
 119           assertDatasetIsNormalisedKnownDefect(af.getViewport()
 120                   .getAlignment(), "Pass (" + pass1 + "," + pass2 + ","
 121                   + pass3 + "): Fetch " + first + ":");
 122           dna = af.getViewport().getAlignment().isNucleotide();
 123           retral = af.getViewport().getAlignment();
 124           dataset = retral.getDataset();
 125           seqs = retral.getSequencesArray();
 126
 127         }
 128         else
 129         {
 130           Desktop.instance.closeAll_actionPerformed(null);
 131           // recover stored project
 132           af = new FileLoader(false).LoadFileWaitTillLoaded(savedProjects
 133                   .get(first).toString(), FormatAdapter.FILE);
 134           System.out.println("Recovered view for '" + first + "' from '"
 135                   + savedProjects.get(first).toString() + "'");
 136           dna = af.getViewport().getAlignment().isNucleotide();
 137           retral = af.getViewport().getAlignment();
 138           dataset = retral.getDataset();
 139           seqs = retral.getSequencesArray();
 140
 141           // verify references for recovered data
 142           AlignmentTest.assertAlignmentDatasetRefs(af.getViewport()
 143                   .getAlignment(), "Pass (" + pass1 + "," + pass2 + ","
 144                   + pass3 + "): Recover " + first + ":");
 145           assertDatasetIsNormalisedKnownDefect(af.getViewport()
 146                   .getAlignment(), "Pass (" + pass1 + "," + pass2 + ","
 147                   + pass3 + "): Recover " + first + ":");
 148
 149         }
 150
 151         // store project on first pass, compare next pass
 152         stringify(dbtoviewBit, savedProjects, first, af.alignPanel);
 153
 154         ptypes = (seqs == null || seqs.length == 0) ? null : new CrossRef(
 155                 seqs, dataset).findXrefSourcesForSequences(dna);
 156
 157         // start of pass2: retrieve each cross-ref for fetched or restored
 158         // project.
 159         do // first cross ref and recover crossref loop
 160         {
 161
 162           for (String db : ptypes)
 163           {
 164             // counter for splitframe views retrieved via crossref
 165             int firstcr_ap = 0;
 166             // build next key so we an retrieve all views
 167             String nextxref = first + " -> " + db + "{" + firstcr_ap + "}";
 168             // perform crossref action, or retrieve stored project
 169             List<AlignmentViewPanel> cra_views = new ArrayList<AlignmentViewPanel>();
 170             CrossRefAction cra = null;
 171
 172             if (pass2 == 0)
 173             { // retrieve and show cross-refs in this thread
 174               cra = new CrossRefAction(af, seqs, dna, db);
 175               cra.run();
 176               if (cra.getXrefViews().size() == 0)
 177               {
 178                 failedXrefMenuItems.add("No crossrefs retrieved for "
 179                         + first + " -> " + db);
 180                 continue;
 181               }
 182               cra_views = cra.getXrefViews();
 183               assertNucleotide(cra_views.get(0),
 184                       "Nucleotide panel included proteins for " + first
 185                               + " -> " + db);
 186               assertProtein(cra_views.get(1),
 187                       "Protein panel included nucleotides for " + first
 188                               + " -> " + db);
 189             }
 190             else
 191             {
 192               Desktop.instance.closeAll_actionPerformed(null);
 193               pass3 = 0;
 194               // recover stored project
 195               File storedProject = savedProjects.get(nextxref);
 196               if (storedProject == null)
 197               {
 198                 failedProjectRecoveries.add("Failed to store a view for '"
 199                         + nextxref + "'");
 200                 continue;
 201               }
 202
 203               // recover stored project
 204               AlignFrame af2 = new FileLoader(false)
 205                       .LoadFileWaitTillLoaded(savedProjects.get(nextxref)
 206                               .toString(), FormatAdapter.FILE);
 207               System.out.println("Recovered view for '" + nextxref
 208                       + "' from '" + savedProjects.get(nextxref).toString()
 209                       + "'");
 210               // gymnastics to recover the alignPanel/Complementary alignPanel
 211               if (af2.getViewport().isNucleotide())
 212               {
 213                 // top view, then bottom
 214                 cra_views.add(af2.getViewport().getAlignPanel());
 215                 cra_views.add(((jalview.gui.AlignViewport) af2
 216                         .getViewport().getCodingComplement())
 217                         .getAlignPanel());
 218
 219               }
 220               else
 221               {
 222                 // bottom view, then top
 223                 cra_views.add(((jalview.gui.AlignViewport) af2
 224                         .getViewport().getCodingComplement())
 225                         .getAlignPanel());
 226                 cra_views.add(af2.getViewport().getAlignPanel());
 227
 228               }
 229             }
 230             HashMap<String, List<String>> xrptypes = new HashMap<String, List<String>>();
 231             // first save/verify views.
 232             for (AlignmentViewPanel avp : cra_views)
 233             {
 234               nextxref = first + " -> " + db + "{" + firstcr_ap++ + "}";
 235               // verify references for this panel
 236               AlignmentTest.assertAlignmentDatasetRefs(avp.getAlignment(),
 237                       "Pass (" + pass1 + "," + pass2 + "," + pass3
 238                               + "): before start of pass3: " + nextxref
 239                               + ":");
 240               assertDatasetIsNormalisedKnownDefect(avp.getAlignment(),
 241                       "Pass (" + pass1 + "," + pass2 + "," + pass3
 242                               + "): before start of pass3: " + nextxref
 243                               + ":");
 244
 245               SequenceI[] xrseqs = avp.getAlignment().getSequencesArray();
 246
 247               List<String> _xrptypes = (seqs == null || seqs.length == 0) ? null
 248                       : new CrossRef(xrseqs, dataset)
 249                               .findXrefSourcesForSequences(avp
 250                                       .getAlignViewport().isNucleotide());
 251
 252               stringify(dbtoviewBit, savedProjects, nextxref, avp);
 253               xrptypes.put(nextxref, _xrptypes);
 254
 255             }
 256
 257             // now do the second xref pass starting from either saved or just
 258             // recovered split pane, in sequence
 259             do // retrieve second set of cross refs or recover and verify
 260             {
 261               firstcr_ap = 0;
 262               for (AlignmentViewPanel avp : cra_views)
 263               {
 264                 nextxref = first + " -> " + db + "{" + firstcr_ap++ + "}";
 265                 for (String xrefdb : xrptypes.get(nextxref))
 266                 {
 267                   List<AlignmentViewPanel> cra_views2 = new ArrayList<AlignmentViewPanel>();
 268                   int q = 0;
 269                   String nextnextxref = nextxref + " -> " + xrefdb + "{"
 270                           + q + "}";
 271
 272                   if (pass3 == 0)
 273                   {
 274
 275                     SequenceI[] xrseqs = avp.getAlignment()
 276                             .getSequencesArray();
 277                     AlignFrame nextaf = Desktop.getAlignFrameFor(avp
 278                             .getAlignViewport());
 279
 280                     cra = new CrossRefAction(nextaf, xrseqs, avp
 281                             .getAlignViewport().isNucleotide(), xrefdb);
 282                     cra.run();
 283                     if (cra.getXrefViews().size() == 0)
 284                     {
 285                       failedXrefMenuItems
 286                               .add("No crossrefs retrieved for '"
 287                                       + nextxref + "' to " + xrefdb
 288                                       + " via '" + nextaf.getTitle() + "'");
 289                       continue;
 290                     }
 291                     cra_views2 = cra.getXrefViews();
 292                     assertNucleotide(cra_views2.get(0),
 293                             "Nucleotide panel included proteins for '"
 294                                     + nextxref + "' to " + xrefdb
 295                                     + " via '" + nextaf.getTitle() + "'");
 296                     assertProtein(cra_views2.get(1),
 297                             "Protein panel included nucleotides for '"
 298                                     + nextxref + "' to " + xrefdb
 299                                     + " via '" + nextaf.getTitle() + "'");
 300
 301                   }
 302                   else
 303                   {
 304                     Desktop.instance.closeAll_actionPerformed(null);
 305                     // recover stored project
 306                     File storedProject = savedProjects.get(nextnextxref);
 307                     if (storedProject == null)
 308                     {
 309                       failedProjectRecoveries
 310                               .add("Failed to store a view for '"
 311                                       + nextnextxref + "'");
 312                       continue;
 313                     }
 314                     AlignFrame af2 = new FileLoader(false)
 315                             .LoadFileWaitTillLoaded(
 316                                     savedProjects.get(nextnextxref)
 317                                             .toString(), FormatAdapter.FILE);
 318                     System.out.println("Recovered view for '"
 319                             + nextnextxref + "' from '"
 320                             + savedProjects.get(nextnextxref).toString()
 321                             + "'");
 322                     // gymnastics to recover the alignPanel/Complementary
 323                     // alignPanel
 324                     if (af2.getViewport().isNucleotide())
 325                     {
 326                       // top view, then bottom
 327                       cra_views2.add(af2.getViewport().getAlignPanel());
 328                       cra_views2.add(((jalview.gui.AlignViewport) af2
 329                               .getViewport().getCodingComplement())
 330                               .getAlignPanel());
 331
 332                     }
 333                     else
 334                     {
 335                       // bottom view, then top
 336                       cra_views2.add(((jalview.gui.AlignViewport) af2
 337                               .getViewport().getCodingComplement())
 338                               .getAlignPanel());
 339                       cra_views2.add(af2.getViewport().getAlignPanel());
 340                     }
 341                     Assert.assertEquals(cra_views2.size(), 2);
 342                     Assert.assertNotNull(cra_views2.get(0));
 343                     Assert.assertNotNull(cra_views2.get(1));
 344                   }
 345
 346                   for (AlignmentViewPanel nextavp : cra_views2)
 347                   {
 348                     nextnextxref = nextxref + " -> " + xrefdb + "{" + q++
 349                             + "}";
 350
 351                     // verify references for this panel
 352                     AlignmentTest.assertAlignmentDatasetRefs(
 353                             nextavp.getAlignment(), "" + "Pass (" + pass1
 354                                     + "," + pass2 + "): For "
 355                                     + nextnextxref + ":");
 356                     assertDatasetIsNormalisedKnownDefect(
 357                             nextavp.getAlignment(), "" + "Pass (" + pass1
 358                                     + "," + pass2 + "): For "
 359                                     + nextnextxref + ":");
 360
 361                     stringify(dbtoviewBit, savedProjects, nextnextxref,
 362                             nextavp);
 363                     keyseq.add(nextnextxref);
 364                   }
 365                 } // end of loop around showing all xrefdb for crossrf2
 366
 367               } // end of loop around all viewpanels from crossrf1
 368             } while (pass2 == 2 && pass3++ < 2);
 369             // fetchdb->crossref1->crossref-2->verify for xrefs we
 370             // either loop twice when pass2=0, or just once when pass2=1
 371             // (recovered project from previous crossref)
 372
 373           } // end of loop over db-xrefs for crossref-2
 374
 375           // fetchdb-->crossref1
 376           // for each xref we try to retrieve xref, store and verify when
 377           // pass1=0, or just retrieve and verify when pass1=1
 378         } while (pass1 == 1 && pass2++ < 2);
 379         // fetchdb
 380         // for each ref we
 381         // loop twice: first, do the retrieve, second recover from saved project
 382
 383         // increment pass counters, so we repeat traversal starting from the
 384         // oldest saved project first.
 385         if (pass1 == 0)
 386         {
 387           // verify stored projects for first set of cross references
 388           pass1 = 1;
 389           // and verify cross-references retrieved from stored projects
 390           pass2 = 0;
 391           pass3 = 0;
 392         }
 393         else
 394         {
 395           pass1++;
 396         }
 397       } while (pass1 < 3);
 398     }
 399     if (failedXrefMenuItems.size() > 0)
 400     {
 401       for (String s : failedXrefMenuItems)
 402       {
 403         System.err.println(s);
 404       }
 405       Assert.fail("Faulty xref menu (" + failedXrefMenuItems.size()
 406               + " counts)");
 407     }
 408     if (failedProjectRecoveries.size() > 0)
 409     {
 410
 411       for (String s : failedProjectRecoveries)
 412       {
 413         System.err.println(s);
 414       }
 415       Assert.fail("Didn't recover projects for some retrievals (did they retrieve ?) ("
 416               + failedProjectRecoveries.size() + " counts)");
 417     }
 418     if (failedDBRetr.size() > 0)
 419     {
 420       for (String s : failedProjectRecoveries)
 421       {
 422         System.err.println(s);
 423       }
 424       Assert.fail("Didn't retrieve some db refs for checking cross-refs ("
 425               + failedDBRetr.size() + " counts)");
 426     }
 427   }
 428
 429   /**
 430    * wrapper to trap known defect for AH002001 testcase
 431    *
 432    * @param alignment
 433    * @param string
 434    */
 435   private void assertDatasetIsNormalisedKnownDefect(AlignmentI al,
 436           String message)
 437   {
 438     try
 439     {
 440       AlignmentTest.assertDatasetIsNormalised(al, message);
 441     } catch (AssertionError ae)
 442     {
 443       if (!ae.getMessage().endsWith("EMBL|AH002001"))
 444       {
 445         throw ae;
 446       }
 447       else
 448       {
 449         System.out
 450                 .println("Ignored exception for known defect: JAL-2179 : "
 451                         + message);
 452       }
 453
 454     }
 455   }
 456
 457   private void assertProtein(AlignmentViewPanel alignmentViewPanel,
 458           String message)
 459   {
 460     assertType(true, alignmentViewPanel, message);
 461   }
 462
 463   private void assertNucleotide(AlignmentViewPanel alignmentViewPanel,
 464           String message)
 465   {
 466     assertType(false, alignmentViewPanel, message);
 467   }
 468
 469   private void assertType(boolean expectProtein,
 470           AlignmentViewPanel alignmentViewPanel, String message)
 471   {
 472     List<SequenceI> nonType = new ArrayList<SequenceI>();
 473     for (SequenceI sq : alignmentViewPanel.getAlignViewport()
 474             .getAlignment().getSequences())
 475     {
 476       if (sq.isProtein() != expectProtein)
 477       {
 478         nonType.add(sq);
 479       }
 480     }
 481     if (nonType.size() > 0)
 482     {
 483       Assert.fail(message + " [ "
 484               + (expectProtein ? "nucleotides were " : "proteins were ")
 485               + nonType.toString() + " ]");
 486     }
 487   }
 488
 489   /**
 490    * first time called, record strings derived from alignment and
 491    * alignedcodonframes, and save view to a project file. Second time called,
 492    * compare strings to existing ones. org.testng.Assert.assertTrue on
 493    * stringmatch
 494    *
 495    * @param dbtoviewBit
 496    *          map between xrefpath and view string
 497    * @param savedProjects
 498    *          - map from xrefpath to saved project filename (createTempFile)
 499    * @param xrefpath
 500    *          - xrefpath - unique ID for this context (composed of sequence of
 501    *          db-fetch/cross-ref actions preceeding state)
 502    * @param avp
 503    *          - viewpanel to store (for viewpanels in splitframe, the same
 504    *          project should be written for both panels, only one needs
 505    *          recovering for comparison on the next stringify call, but each
 506    *          viewpanel needs to be called with a distinct xrefpath to ensure
 507    *          each one's strings are compared)
 508    */
 509   private void stringify(HashMap<String, String> dbtoviewBit,
 510           HashMap<String, File> savedProjects, String xrefpath,
 511           AlignmentViewPanel avp)
 512   {
 513     if (savedProjects != null)
 514     {
 515       if (savedProjects.get(xrefpath) == null)
 516       {
 517         // write a project file for this view. On the second pass, this will be
 518         // recovered and cross-references verified
 519         try
 520         {
 521           File prfile = File.createTempFile("crossRefTest", ".jvp");
 522           AlignFrame af = Desktop.getAlignFrameFor(avp.getAlignViewport());
 523           new Jalview2XML(false).saveAlignment(af, prfile.toString(),
 524                   af.getTitle());
 525           System.out.println("Written view from '" + xrefpath + "' as '"
 526                   + prfile.getAbsolutePath() + "'");
 527           savedProjects.put(xrefpath, prfile);
 528         } catch (IOException q)
 529         {
 530           Assert.fail("Unexpected IO Exception", q);
 531         }
 532       }
 533       else
 534       {
 535         System.out.println("Stringify check on view from '" + xrefpath
 536                 + "' [ possibly retrieved from '"
 537                 + savedProjects.get(xrefpath).getAbsolutePath() + "' ]");
 538
 539       }
 540     }
 541
 542     StringBuilder sbr = new StringBuilder();
 543     sbr.append(avp.getAlignment().toString());
 544     sbr.append("\n");
 545     sbr.append("<End of alignment>");
 546     sbr.append("\n");
 547     sbr.append(avp.getAlignment().getDataset());
 548     sbr.append("\n");
 549     sbr.append("<End of dataset>");
 550     sbr.append("\n");
 551     int p = 0;
 552     if (avp.getAlignment().getCodonFrames() != null)
 553     {
 554       for (AlignedCodonFrame ac : avp.getAlignment().getCodonFrames())
 555       {
 556         sbr.append("<AlignedCodonFrame " + p++ + ">");
 557         sbr.append("\n");
 558         sbr.append(ac.toString());
 559         sbr.append("\n");
 560       }
 561     }
 562     String dbt = dbtoviewBit.get(xrefpath);
 563     if (dbt == null)
 564     {
 565       dbtoviewBit.put(xrefpath, sbr.toString());
 566     }
 567     else
 568     {
 569       Assert.assertEquals(sbr.toString(), dbt, "stringify mismatch for "
 570               + xrefpath);
 571     }
 572   }
 573 }