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