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  1. Project Clover database Wed Oct 31 2018 15:13:58 GMT
  2. Package jalview.io

File CrossRef2xmlTests.java

 

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CrossRef2xmlTests 52 187 45 256
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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    import jalview.gui.JvOptionPane;
34    import jalview.util.DBRefUtils;
35   
36    import java.io.File;
37    import java.io.IOException;
38    import java.util.ArrayList;
39    import java.util.Arrays;
40    import java.util.HashMap;
41    import java.util.List;
42    import java.util.Map;
43   
44    import junit.extensions.PA;
45   
46    import org.testng.Assert;
47    import org.testng.annotations.BeforeClass;
48    import org.testng.annotations.DataProvider;
49    import org.testng.annotations.Test;
50   
51    @Test(singleThreaded = true)
 
52    public class CrossRef2xmlTests extends Jalview2xmlBase
53    {
54   
 
55  0 toggle @Override
56    @BeforeClass(alwaysRun = true)
57    public void setUpJvOptionPane()
58    {
59  0 JvOptionPane.setInteractiveMode(false);
60  0 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
61    }
62   
 
63  0 toggle @DataProvider(name = "initialAccessions")
64    static Object[][] getAccessions()
65    {
66  0 return new String[][] { { "UNIPROT", "P00338" },
67    { "UNIPROT", "Q8Z9G6" },
68    { "ENSEMBLGENOMES", "CAD01290" } };
69    }
70   
71    /**
72    * test store and recovery of all reachable cross refs from all reachable
73    * crossrefs for one or more fetched db refs. Currently, this test has a known
74    * failure case.
75    *
76    * @throws Exception
77    */
 
78  0 toggle @Test(
79    groups =
80    { "Operational" },
81    dataProvider = "initialAccessions",
82    enabled = true)
83    public void testRetrieveAndShowCrossref(String forSource,
84    String forAccession) throws Exception
85    {
86   
87  0 List<String> failedDBRetr = new ArrayList<>();
88  0 List<String> failedXrefMenuItems = new ArrayList<>();
89  0 List<String> failedProjectRecoveries = new ArrayList<>();
90    // only search for ensembl or Uniprot crossrefs
91  0 List<String> limit=Arrays.asList(new String[] {
92    DBRefUtils.getCanonicalName("ENSEMBL"),
93    DBRefUtils.getCanonicalName("Uniprot")});
94    // for every set of db queries
95    // retrieve db query
96    // verify presence of expected xrefs
97    // show xrefs - verify expected type of frame is shown for each xref
98    // show xrefs again
99    // - verify original -> xref -> xref(original) recovers frame containing at
100    // least the first retrieved sequence
101    // store
102    // 1. whole project
103    // 2. individual frames
104    // 3. load each one back and verify
105    // . aligned sequences (.toString() )
106    // . xrefs (.toString() )
107    // . codonframes
108    //
109    //
110  0 Map<String, String> dbtoviewBit = new HashMap<>();
111  0 List<String> keyseq = new ArrayList<>();
112  0 Map<String, File> savedProjects = new HashMap<>();
113   
114    // for (String[] did : new String[][] { { "UNIPROT", "P00338" } })
115    // {
116    // pass counters - 0 - first pass, 1 means retrieve project rather than
117    // perform action
118  0 int pass1 = 0, pass2 = 0, pass3 = 0;
119    // each do loop performs two iterations in the first outer loop pass, but
120    // only performs one iteration on the second outer loop
121    // ie. pass 1 = 0 {pass 2= 0 { pass 3 = 0,1 }, pass 2=1 { pass 3 = 0 }}, 1
122    // { pass 2 = 0 { pass 3 = 0 } }
123  0 do
124    {
125  0 String first = forSource + " " + forAccession;//did[0] + " " + did[1];
126  0 AlignFrame af = null;
127  0 boolean dna;
128  0 AlignmentI retral;
129  0 AlignmentI dataset;
130  0 SequenceI[] seqs;
131  0 List<String> ptypes = null;
132  0 if (pass1 == 0)
133    {
134    // retrieve dbref
135   
136  0 List<AlignFrame> afs = jalview.gui.SequenceFetcher.fetchAndShow(
137    forSource, forAccession);
138    // did[0], did[1]);
139  0 if (afs.size() == 0)
140    {
141  0 failedDBRetr.add("Didn't retrieve " + first);
142  0 break;
143    }
144  0 keyseq.add(first);
145  0 af = afs.get(0);
146   
147    // verify references for retrieved data
148  0 AlignmentTest.assertAlignmentDatasetRefs(af.getViewport()
149    .getAlignment(), "Pass (" + pass1 + "," + pass2 + ","
150    + pass3 + "): Fetch " + first + ":");
151  0 assertDatasetIsNormalisedKnownDefect(af.getViewport()
152    .getAlignment(), "Pass (" + pass1 + "," + pass2 + ","
153    + pass3 + "): Fetch " + first + ":");
154  0 dna = af.getViewport().getAlignment().isNucleotide();
155  0 retral = af.getViewport().getAlignment();
156  0 dataset = retral.getDataset();
157  0 seqs = retral.getSequencesArray();
158   
159    }
160    else
161    {
162  0 Desktop.instance.closeAll_actionPerformed(null);
163    // recover stored project
164  0 af = new FileLoader(false).LoadFileWaitTillLoaded(savedProjects
165    .get(first).toString(), DataSourceType.FILE);
166  0 System.out.println("Recovered view for '" + first + "' from '"
167    + savedProjects.get(first).toString() + "'");
168  0 dna = af.getViewport().getAlignment().isNucleotide();
169  0 retral = af.getViewport().getAlignment();
170  0 dataset = retral.getDataset();
171  0 seqs = retral.getSequencesArray();
172   
173    // verify references for recovered data
174  0 AlignmentTest.assertAlignmentDatasetRefs(af.getViewport()
175    .getAlignment(), "Pass (" + pass1 + "," + pass2 + ","
176    + pass3 + "): Recover " + first + ":");
177  0 assertDatasetIsNormalisedKnownDefect(af.getViewport()
178    .getAlignment(), "Pass (" + pass1 + "," + pass2 + ","
179    + pass3 + "): Recover " + first + ":");
180   
181    }
182   
183    // store project on first pass, compare next pass
184  0 stringify(dbtoviewBit, savedProjects, first, af.alignPanel);
185   
186  0 ptypes = (seqs == null || seqs.length == 0) ? null : new CrossRef(
187    seqs, dataset).findXrefSourcesForSequences(dna);
188  0 filterDbRefs(ptypes, limit);
189   
190    // start of pass2: retrieve each cross-ref for fetched or restored
191    // project.
192  0 do // first cross ref and recover crossref loop
193    {
194   
195  0 for (String db : ptypes)
196    {
197    // counter for splitframe views retrieved via crossref
198  0 int firstcr_ap = 0;
199    // build next key so we an retrieve all views
200  0 String nextxref = first + " -> " + db + "{" + firstcr_ap + "}";
201    // perform crossref action, or retrieve stored project
202  0 List<AlignmentViewPanel> cra_views = new ArrayList<>();
203  0 CrossRefAction cra = null;
204   
205  0 if (pass2 == 0)
206    { // retrieve and show cross-refs in this thread
207  0 cra = CrossRefAction.getHandlerFor(seqs, dna, db, af);
208  0 cra.run();
209  0 cra_views = (List<AlignmentViewPanel>) PA.getValue(cra,
210    "xrefViews");
211  0 if (cra_views.size() == 0)
212    {
213  0 failedXrefMenuItems.add("No crossrefs retrieved for "
214    + first + " -> " + db);
215  0 continue;
216    }
217  0 assertNucleotide(cra_views.get(0),
218    "Nucleotide panel included proteins for " + first
219    + " -> " + db);
220  0 assertProtein(cra_views.get(1),
221    "Protein panel included nucleotides for " + first
222    + " -> " + db);
223    }
224    else
225    {
226  0 Desktop.instance.closeAll_actionPerformed(null);
227  0 pass3 = 0;
228    // recover stored project
229  0 File storedProject = savedProjects.get(nextxref);
230  0 if (storedProject == null)
231    {
232  0 failedProjectRecoveries.add("Failed to store a view for '"
233    + nextxref + "'");
234  0 continue;
235    }
236   
237    // recover stored project
238  0 AlignFrame af2 = new FileLoader(false)
239    .LoadFileWaitTillLoaded(savedProjects.get(nextxref)
240    .toString(), DataSourceType.FILE);
241  0 System.out.println("Recovered view for '" + nextxref
242    + "' from '" + savedProjects.get(nextxref).toString()
243    + "'");
244    // gymnastics to recover the alignPanel/Complementary alignPanel
245  0 if (af2.getViewport().isNucleotide())
246    {
247    // top view, then bottom
248  0 cra_views.add(af2.getViewport().getAlignPanel());
249  0 cra_views.add(((jalview.gui.AlignViewport) af2
250    .getViewport().getCodingComplement())
251    .getAlignPanel());
252   
253    }
254    else
255    {
256    // bottom view, then top
257  0 cra_views.add(((jalview.gui.AlignViewport) af2
258    .getViewport().getCodingComplement())
259    .getAlignPanel());
260  0 cra_views.add(af2.getViewport().getAlignPanel());
261   
262    }
263    }
264  0 HashMap<String, List<String>> xrptypes = new HashMap<>();
265    // first save/verify views.
266  0 for (AlignmentViewPanel avp : cra_views)
267    {
268  0 nextxref = first + " -> " + db + "{" + firstcr_ap++ + "}";
269    // verify references for this panel
270  0 AlignmentTest.assertAlignmentDatasetRefs(avp.getAlignment(),
271    "Pass (" + pass1 + "," + pass2 + "," + pass3
272    + "): before start of pass3: " + nextxref
273    + ":");
274  0 assertDatasetIsNormalisedKnownDefect(avp.getAlignment(),
275    "Pass (" + pass1 + "," + pass2 + "," + pass3
276    + "): before start of pass3: " + nextxref
277    + ":");
278   
279  0 SequenceI[] xrseqs = avp.getAlignment().getSequencesArray();
280   
281  0 List<String> _xrptypes = (seqs == null || seqs.length == 0) ? null
282    : new CrossRef(xrseqs, dataset)
283    .findXrefSourcesForSequences(avp
284    .getAlignViewport().isNucleotide());
285   
286  0 stringify(dbtoviewBit, savedProjects, nextxref, avp);
287  0 xrptypes.put(nextxref, _xrptypes);
288   
289    }
290   
291    // now do the second xref pass starting from either saved or just
292    // recovered split pane, in sequence
293  0 do // retrieve second set of cross refs or recover and verify
294    {
295  0 firstcr_ap = 0;
296  0 for (AlignmentViewPanel avp : cra_views)
297    {
298  0 nextxref = first + " -> " + db + "{" + firstcr_ap++ + "}";
299  0 for (String xrefdb : xrptypes.get(nextxref))
300    {
301  0 List<AlignmentViewPanel> cra_views2 = new ArrayList<>();
302  0 int q = 0;
303  0 String nextnextxref = nextxref + " -> " + xrefdb + "{"
304    + q + "}";
305   
306  0 if (pass3 == 0)
307    {
308  0 SequenceI[] xrseqs = avp.getAlignment()
309    .getSequencesArray();
310  0 AlignFrame nextaf = Desktop.getAlignFrameFor(avp
311    .getAlignViewport());
312   
313  0 cra = CrossRefAction.getHandlerFor(xrseqs, avp
314    .getAlignViewport().isNucleotide(), xrefdb,
315    nextaf);
316  0 cra.run();
317  0 cra_views2 = (List<AlignmentViewPanel>) PA.getValue(
318    cra, "xrefViews");
319  0 if (cra_views2.size() == 0)
320    {
321  0 failedXrefMenuItems
322    .add("No crossrefs retrieved for '"
323    + nextxref + "' to " + xrefdb
324    + " via '" + nextaf.getTitle() + "'");
325  0 continue;
326    }
327  0 assertNucleotide(cra_views2.get(0),
328    "Nucleotide panel included proteins for '"
329    + nextxref + "' to " + xrefdb
330    + " via '" + nextaf.getTitle() + "'");
331  0 assertProtein(cra_views2.get(1),
332    "Protein panel included nucleotides for '"
333    + nextxref + "' to " + xrefdb
334    + " via '" + nextaf.getTitle() + "'");
335   
336    }
337    else
338    {
339  0 Desktop.instance.closeAll_actionPerformed(null);
340    // recover stored project
341  0 File storedProject = savedProjects.get(nextnextxref);
342  0 if (storedProject == null)
343    {
344  0 failedProjectRecoveries
345    .add("Failed to store a view for '"
346    + nextnextxref + "'");
347  0 continue;
348    }
349  0 AlignFrame af2 = new FileLoader(false)
350    .LoadFileWaitTillLoaded(
351    savedProjects.get(nextnextxref)
352    .toString(),
353    DataSourceType.FILE);
354  0 System.out.println("Recovered view for '"
355    + nextnextxref + "' from '"
356    + savedProjects.get(nextnextxref).toString()
357    + "'");
358    // gymnastics to recover the alignPanel/Complementary
359    // alignPanel
360  0 if (af2.getViewport().isNucleotide())
361    {
362    // top view, then bottom
363  0 cra_views2.add(af2.getViewport().getAlignPanel());
364  0 cra_views2.add(((jalview.gui.AlignViewport) af2
365    .getViewport().getCodingComplement())
366    .getAlignPanel());
367   
368    }
369    else
370    {
371    // bottom view, then top
372  0 cra_views2.add(((jalview.gui.AlignViewport) af2
373    .getViewport().getCodingComplement())
374    .getAlignPanel());
375  0 cra_views2.add(af2.getViewport().getAlignPanel());
376    }
377  0 Assert.assertEquals(cra_views2.size(), 2);
378  0 Assert.assertNotNull(cra_views2.get(0));
379  0 Assert.assertNotNull(cra_views2.get(1));
380    }
381   
382  0 for (AlignmentViewPanel nextavp : cra_views2)
383    {
384  0 nextnextxref = nextxref + " -> " + xrefdb + "{" + q++
385    + "}";
386   
387    // verify references for this panel
388  0 AlignmentTest.assertAlignmentDatasetRefs(
389    nextavp.getAlignment(), "" + "Pass (" + pass1
390    + "," + pass2 + "): For "
391    + nextnextxref + ":");
392  0 assertDatasetIsNormalisedKnownDefect(
393    nextavp.getAlignment(), "" + "Pass (" + pass1
394    + "," + pass2 + "): For "
395    + nextnextxref + ":");
396   
397  0 stringify(dbtoviewBit, savedProjects, nextnextxref,
398    nextavp);
399  0 keyseq.add(nextnextxref);
400    }
401    } // end of loop around showing all xrefdb for crossrf2
402   
403    } // end of loop around all viewpanels from crossrf1
404  0 } while (pass2 == 2 && pass3++ < 2);
405    // fetchdb->crossref1->crossref-2->verify for xrefs we
406    // either loop twice when pass2=0, or just once when pass2=1
407    // (recovered project from previous crossref)
408   
409    } // end of loop over db-xrefs for crossref-2
410   
411    // fetchdb-->crossref1
412    // for each xref we try to retrieve xref, store and verify when
413    // pass1=0, or just retrieve and verify when pass1=1
414  0 } while (pass1 == 1 && pass2++ < 2);
415    // fetchdb
416    // for each ref we
417    // loop twice: first, do the retrieve, second recover from saved project
418   
419    // increment pass counters, so we repeat traversal starting from the
420    // oldest saved project first.
421  0 if (pass1 == 0)
422    {
423    // verify stored projects for first set of cross references
424  0 pass1 = 1;
425    // and verify cross-references retrieved from stored projects
426  0 pass2 = 0;
427  0 pass3 = 0;
428    }
429    else
430    {
431  0 pass1++;
432    }
433  0 } while (pass1 < 3);
434   
435  0 if (failedXrefMenuItems.size() > 0)
436    {
437  0 for (String s : failedXrefMenuItems)
438    {
439  0 System.err.println(s);
440    }
441  0 Assert.fail("Faulty xref menu (" + failedXrefMenuItems.size()
442    + " counts)");
443    }
444  0 if (failedProjectRecoveries.size() > 0)
445    {
446   
447  0 for (String s : failedProjectRecoveries)
448    {
449  0 System.err.println(s);
450    }
451  0 Assert.fail("Didn't recover projects for some retrievals (did they retrieve ?) ("
452    + failedProjectRecoveries.size() + " counts)");
453    }
454  0 if (failedDBRetr.size() > 0)
455    {
456  0 for (String s : failedProjectRecoveries)
457    {
458  0 System.err.println(s);
459    }
460  0 Assert.fail("Didn't retrieve some db refs for checking cross-refs ("
461    + failedDBRetr.size() + " counts)");
462    }
463    }
464   
 
465  0 toggle private void filterDbRefs(List<String> ptypes, List<String> limit)
466    {
467  0 if (limit != null)
468    {
469  0 int p = 0;
470  0 while (ptypes.size() > p)
471    {
472  0 if (!limit.contains(ptypes.get(p)))
473    {
474  0 ptypes.remove(p);
475    }
476    else
477    {
478  0 p++;
479    }
480    }
481    }
482    }
483   
484    /**
485    * wrapper to trap known defect for AH002001 testcase
486    *
487    * @param alignment
488    * @param string
489    */
 
490  0 toggle private void assertDatasetIsNormalisedKnownDefect(AlignmentI al,
491    String message)
492    {
493  0 try
494    {
495  0 AlignmentTest.assertDatasetIsNormalised(al, message);
496    } catch (AssertionError ae)
497    {
498  0 if (!ae.getMessage().endsWith("EMBL|AH002001"))
499    {
500  0 throw ae;
501    }
502    else
503    {
504  0 System.out
505    .println("Ignored exception for known defect: JAL-2179 : "
506    + message);
507    }
508   
509    }
510    }
511   
 
512  0 toggle private void assertProtein(AlignmentViewPanel alignmentViewPanel,
513    String message)
514    {
515  0 assertType(true, alignmentViewPanel, message);
516    }
517   
 
518  0 toggle private void assertNucleotide(AlignmentViewPanel alignmentViewPanel,
519    String message)
520    {
521  0 assertType(false, alignmentViewPanel, message);
522    }
523   
 
524  0 toggle private void assertType(boolean expectProtein,
525    AlignmentViewPanel alignmentViewPanel, String message)
526    {
527  0 List<SequenceI> nonType = new ArrayList<>();
528  0 for (SequenceI sq : alignmentViewPanel.getAlignViewport()
529    .getAlignment().getSequences())
530    {
531  0 if (sq.isProtein() != expectProtein)
532    {
533  0 nonType.add(sq);
534    }
535    }
536  0 if (nonType.size() > 0)
537    {
538  0 Assert.fail(message + " [ "
539  0 + (expectProtein ? "nucleotides were " : "proteins were ")
540    + nonType.toString() + " ]");
541    }
542    }
543   
544    /**
545    * first time called, record strings derived from alignment and
546    * alignedcodonframes, and save view to a project file. Second time called,
547    * compare strings to existing ones. org.testng.Assert.assertTrue on
548    * stringmatch
549    *
550    * @param dbtoviewBit
551    * map between xrefpath and view string
552    * @param savedProjects
553    * - map from xrefpath to saved project filename (createTempFile)
554    * @param xrefpath
555    * - xrefpath - unique ID for this context (composed of sequence of
556    * db-fetch/cross-ref actions preceeding state)
557    * @param avp
558    * - viewpanel to store (for viewpanels in splitframe, the same
559    * project should be written for both panels, only one needs
560    * recovering for comparison on the next stringify call, but each
561    * viewpanel needs to be called with a distinct xrefpath to ensure
562    * each one's strings are compared)
563    */
 
564  0 toggle private void stringify(Map<String, String> dbtoviewBit,
565    Map<String, File> savedProjects, String xrefpath,
566    AlignmentViewPanel avp)
567    {
568  0 if (savedProjects != null)
569    {
570  0 if (savedProjects.get(xrefpath) == null)
571    {
572    // write a project file for this view. On the second pass, this will be
573    // recovered and cross-references verified
574  0 try
575    {
576  0 File prfile = File.createTempFile("crossRefTest", ".jvp");
577  0 AlignFrame af = Desktop.getAlignFrameFor(avp.getAlignViewport());
578  0 new Jalview2XML(false).saveAlignment(af, prfile.toString(),
579    af.getTitle());
580  0 System.out.println("Written view from '" + xrefpath + "' as '"
581    + prfile.getAbsolutePath() + "'");
582  0 savedProjects.put(xrefpath, prfile);
583    } catch (IOException q)
584    {
585  0 Assert.fail("Unexpected IO Exception", q);
586    }
587    }
588    else
589    {
590  0 System.out.println("Stringify check on view from '" + xrefpath
591    + "' [ possibly retrieved from '"
592    + savedProjects.get(xrefpath).getAbsolutePath() + "' ]");
593   
594    }
595    }
596   
597  0 StringBuilder sbr = new StringBuilder();
598  0 sbr.append(avp.getAlignment().toString());
599  0 sbr.append("\n");
600  0 sbr.append("<End of alignment>");
601  0 sbr.append("\n");
602  0 sbr.append(avp.getAlignment().getDataset());
603  0 sbr.append("\n");
604  0 sbr.append("<End of dataset>");
605  0 sbr.append("\n");
606  0 int p = 0;
607  0 if (avp.getAlignment().getCodonFrames() != null)
608    {
609  0 for (AlignedCodonFrame ac : avp.getAlignment().getCodonFrames())
610    {
611  0 sbr.append("<AlignedCodonFrame " + p++ + ">");
612  0 sbr.append("\n");
613  0 sbr.append(ac.toString());
614  0 sbr.append("\n");
615    }
616    }
617  0 String dbt = dbtoviewBit.get(xrefpath);
618  0 if (dbt == null)
619    {
620  0 dbtoviewBit.put(xrefpath, sbr.toString());
621    }
622    else
623    {
624  0 Assert.assertEquals(sbr.toString(), dbt, "stringify mismatch for "
625    + xrefpath);
626    }
627    }
628    }
  • Report generated by OpenClover v 4.2.1 on Wed Oct 31 2018 15:15:54 GMT using coverage data from Wed Oct 31 2018 15:15:47 GMT.
  • Clover free edition.