2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
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.
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.
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.
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;
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;
43 import org.testng.Assert;
44 import org.testng.annotations.BeforeClass;
45 import org.testng.annotations.DataProvider;
46 import org.testng.annotations.Test;
48 @Test(singleThreaded = true)
49 public class CrossRef2xmlTests extends Jalview2xmlBase
53 @BeforeClass(alwaysRun = true)
54 public void setUpJvOptionPane()
56 JvOptionPane.setInteractiveMode(false);
57 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
60 @DataProvider(name = "initialAccessions")
61 static Object[][] getAccessions()
63 return new String[][] { { "UNIPROT", "P00338" },
64 { "UNIPROT", "Q8Z9G6" },
65 { "ENSEMBLGENOMES", "CAD01290" } };
69 * test store and recovery of all reachable cross refs from all reachable
70 * crossrefs for one or more fetched db refs. Currently, this test has a known
78 dataProvider = "initialAccessions",
80 public void testRetrieveAndShowCrossref(String forSource,
81 String forAccession) throws Exception
84 List<String> failedDBRetr = new ArrayList<>();
85 List<String> failedXrefMenuItems = new ArrayList<>();
86 List<String> failedProjectRecoveries = new ArrayList<>();
87 // only search for ensembl or Uniprot crossrefs
88 List<String> limit=Arrays.asList(new String[] {
89 DBRefUtils.getCanonicalName("ENSEMBL"),
90 DBRefUtils.getCanonicalName("Uniprot")});
91 // for every set of db queries
93 // verify presence of expected xrefs
94 // show xrefs - verify expected type of frame is shown for each xref
96 // - verify original -> xref -> xref(original) recovers frame containing at
97 // least the first retrieved sequence
100 // 2. individual frames
101 // 3. load each one back and verify
102 // . aligned sequences (.toString() )
103 // . xrefs (.toString() )
107 HashMap<String, String> dbtoviewBit = new HashMap<>();
108 List<String> keyseq = new ArrayList<>();
109 HashMap<String, File> savedProjects = new HashMap<>();
111 // for (String[] did : new String[][] { { "UNIPROT", "P00338" } })
113 // pass counters - 0 - first pass, 1 means retrieve project rather than
115 int pass1 = 0, pass2 = 0, pass3 = 0;
116 // each do loop performs two iterations in the first outer loop pass, but
117 // only performs one iteration on the second outer loop
118 // ie. pass 1 = 0 {pass 2= 0 { pass 3 = 0,1 }, pass 2=1 { pass 3 = 0 }}, 1
119 // { pass 2 = 0 { pass 3 = 0 } }
122 String first = forSource + " " + forAccession;//did[0] + " " + did[1];
123 AlignFrame af = null;
128 List<String> ptypes = null;
133 List<AlignFrame> afs = jalview.gui.SequenceFetcher.fetchAndShow(
134 forSource, forAccession);
138 failedDBRetr.add("Didn't retrieve " + first);
144 // verify references for retrieved data
145 AlignmentTest.assertAlignmentDatasetRefs(af.getViewport()
146 .getAlignment(), "Pass (" + pass1 + "," + pass2 + ","
147 + pass3 + "): Fetch " + first + ":");
148 assertDatasetIsNormalisedKnownDefect(af.getViewport()
149 .getAlignment(), "Pass (" + pass1 + "," + pass2 + ","
150 + pass3 + "): Fetch " + first + ":");
151 dna = af.getViewport().getAlignment().isNucleotide();
152 retral = af.getViewport().getAlignment();
153 dataset = retral.getDataset();
154 seqs = retral.getSequencesArray();
159 Desktop.instance.closeAll_actionPerformed(null);
160 // recover stored project
161 af = new FileLoader(false).LoadFileWaitTillLoaded(savedProjects
162 .get(first).toString(), DataSourceType.FILE);
163 System.out.println("Recovered view for '" + first + "' from '"
164 + savedProjects.get(first).toString() + "'");
165 dna = af.getViewport().getAlignment().isNucleotide();
166 retral = af.getViewport().getAlignment();
167 dataset = retral.getDataset();
168 seqs = retral.getSequencesArray();
170 // verify references for recovered data
171 AlignmentTest.assertAlignmentDatasetRefs(af.getViewport()
172 .getAlignment(), "Pass (" + pass1 + "," + pass2 + ","
173 + pass3 + "): Recover " + first + ":");
174 assertDatasetIsNormalisedKnownDefect(af.getViewport()
175 .getAlignment(), "Pass (" + pass1 + "," + pass2 + ","
176 + pass3 + "): Recover " + first + ":");
180 // store project on first pass, compare next pass
181 stringify(dbtoviewBit, savedProjects, first, af.alignPanel);
183 ptypes = (seqs == null || seqs.length == 0) ? null : new CrossRef(
184 seqs, dataset).findXrefSourcesForSequences(dna);
185 filterDbRefs(ptypes, limit);
187 // start of pass2: retrieve each cross-ref for fetched or restored
189 do // first cross ref and recover crossref loop
192 for (String db : ptypes)
194 // counter for splitframe views retrieved via crossref
196 // build next key so we an retrieve all views
197 String nextxref = first + " -> " + db + "{" + firstcr_ap + "}";
198 // perform crossref action, or retrieve stored project
199 List<AlignmentViewPanel> cra_views = new ArrayList<>();
200 CrossRefAction cra = null;
203 { // retrieve and show cross-refs in this thread
204 cra = new CrossRefAction(af, seqs, dna, db);
206 if (cra.getXrefViews().size() == 0)
208 failedXrefMenuItems.add("No crossrefs retrieved for "
209 + first + " -> " + db);
212 cra_views = cra.getXrefViews();
213 assertNucleotide(cra_views.get(0),
214 "Nucleotide panel included proteins for " + first
216 assertProtein(cra_views.get(1),
217 "Protein panel included nucleotides for " + first
222 Desktop.instance.closeAll_actionPerformed(null);
224 // recover stored project
225 File storedProject = savedProjects.get(nextxref);
226 if (storedProject == null)
228 failedProjectRecoveries.add("Failed to store a view for '"
233 // recover stored project
234 AlignFrame af2 = new FileLoader(false)
235 .LoadFileWaitTillLoaded(savedProjects.get(nextxref)
236 .toString(), DataSourceType.FILE);
237 System.out.println("Recovered view for '" + nextxref
238 + "' from '" + savedProjects.get(nextxref).toString()
240 // gymnastics to recover the alignPanel/Complementary alignPanel
241 if (af2.getViewport().isNucleotide())
243 // top view, then bottom
244 cra_views.add(af2.getViewport().getAlignPanel());
245 cra_views.add(((jalview.gui.AlignViewport) af2
246 .getViewport().getCodingComplement())
252 // bottom view, then top
253 cra_views.add(((jalview.gui.AlignViewport) af2
254 .getViewport().getCodingComplement())
256 cra_views.add(af2.getViewport().getAlignPanel());
260 HashMap<String, List<String>> xrptypes = new HashMap<>();
261 // first save/verify views.
262 for (AlignmentViewPanel avp : cra_views)
264 nextxref = first + " -> " + db + "{" + firstcr_ap++ + "}";
265 // verify references for this panel
266 AlignmentTest.assertAlignmentDatasetRefs(avp.getAlignment(),
267 "Pass (" + pass1 + "," + pass2 + "," + pass3
268 + "): before start of pass3: " + nextxref
270 assertDatasetIsNormalisedKnownDefect(avp.getAlignment(),
271 "Pass (" + pass1 + "," + pass2 + "," + pass3
272 + "): before start of pass3: " + nextxref
275 SequenceI[] xrseqs = avp.getAlignment().getSequencesArray();
277 List<String> _xrptypes = (seqs == null || seqs.length == 0) ? null
278 : new CrossRef(xrseqs, dataset)
279 .findXrefSourcesForSequences(avp
280 .getAlignViewport().isNucleotide());
282 stringify(dbtoviewBit, savedProjects, nextxref, avp);
283 xrptypes.put(nextxref, _xrptypes);
287 // now do the second xref pass starting from either saved or just
288 // recovered split pane, in sequence
289 do // retrieve second set of cross refs or recover and verify
292 for (AlignmentViewPanel avp : cra_views)
294 nextxref = first + " -> " + db + "{" + firstcr_ap++ + "}";
295 for (String xrefdb : xrptypes.get(nextxref))
297 List<AlignmentViewPanel> cra_views2 = new ArrayList<>();
299 String nextnextxref = nextxref + " -> " + xrefdb + "{"
305 SequenceI[] xrseqs = avp.getAlignment()
306 .getSequencesArray();
307 AlignFrame nextaf = Desktop.getAlignFrameFor(avp
308 .getAlignViewport());
310 cra = new CrossRefAction(nextaf, xrseqs, avp
311 .getAlignViewport().isNucleotide(), xrefdb);
313 if (cra.getXrefViews().size() == 0)
316 .add("No crossrefs retrieved for '"
317 + nextxref + "' to " + xrefdb
318 + " via '" + nextaf.getTitle() + "'");
321 cra_views2 = cra.getXrefViews();
322 assertNucleotide(cra_views2.get(0),
323 "Nucleotide panel included proteins for '"
324 + nextxref + "' to " + xrefdb
325 + " via '" + nextaf.getTitle() + "'");
326 assertProtein(cra_views2.get(1),
327 "Protein panel included nucleotides for '"
328 + nextxref + "' to " + xrefdb
329 + " via '" + nextaf.getTitle() + "'");
334 Desktop.instance.closeAll_actionPerformed(null);
335 // recover stored project
336 File storedProject = savedProjects.get(nextnextxref);
337 if (storedProject == null)
339 failedProjectRecoveries
340 .add("Failed to store a view for '"
341 + nextnextxref + "'");
344 AlignFrame af2 = new FileLoader(false)
345 .LoadFileWaitTillLoaded(
346 savedProjects.get(nextnextxref)
348 DataSourceType.FILE);
349 System.out.println("Recovered view for '"
350 + nextnextxref + "' from '"
351 + savedProjects.get(nextnextxref).toString()
353 // gymnastics to recover the alignPanel/Complementary
355 if (af2.getViewport().isNucleotide())
357 // top view, then bottom
358 cra_views2.add(af2.getViewport().getAlignPanel());
359 cra_views2.add(((jalview.gui.AlignViewport) af2
360 .getViewport().getCodingComplement())
366 // bottom view, then top
367 cra_views2.add(((jalview.gui.AlignViewport) af2
368 .getViewport().getCodingComplement())
370 cra_views2.add(af2.getViewport().getAlignPanel());
372 Assert.assertEquals(cra_views2.size(), 2);
373 Assert.assertNotNull(cra_views2.get(0));
374 Assert.assertNotNull(cra_views2.get(1));
377 for (AlignmentViewPanel nextavp : cra_views2)
379 nextnextxref = nextxref + " -> " + xrefdb + "{" + q++
382 // verify references for this panel
383 AlignmentTest.assertAlignmentDatasetRefs(
384 nextavp.getAlignment(), "" + "Pass (" + pass1
385 + "," + pass2 + "): For "
386 + nextnextxref + ":");
387 assertDatasetIsNormalisedKnownDefect(
388 nextavp.getAlignment(), "" + "Pass (" + pass1
389 + "," + pass2 + "): For "
390 + nextnextxref + ":");
392 stringify(dbtoviewBit, savedProjects, nextnextxref,
394 keyseq.add(nextnextxref);
396 } // end of loop around showing all xrefdb for crossrf2
398 } // end of loop around all viewpanels from crossrf1
399 } while (pass2 == 2 && pass3++ < 2);
400 // fetchdb->crossref1->crossref-2->verify for xrefs we
401 // either loop twice when pass2=0, or just once when pass2=1
402 // (recovered project from previous crossref)
404 } // end of loop over db-xrefs for crossref-2
406 // fetchdb-->crossref1
407 // for each xref we try to retrieve xref, store and verify when
408 // pass1=0, or just retrieve and verify when pass1=1
409 } while (pass1 == 1 && pass2++ < 2);
412 // loop twice: first, do the retrieve, second recover from saved project
414 // increment pass counters, so we repeat traversal starting from the
415 // oldest saved project first.
418 // verify stored projects for first set of cross references
420 // and verify cross-references retrieved from stored projects
430 if (failedXrefMenuItems.size() > 0)
432 for (String s : failedXrefMenuItems)
434 System.err.println(s);
436 Assert.fail("Faulty xref menu (" + failedXrefMenuItems.size()
439 if (failedProjectRecoveries.size() > 0)
442 for (String s : failedProjectRecoveries)
444 System.err.println(s);
446 Assert.fail("Didn't recover projects for some retrievals (did they retrieve ?) ("
447 + failedProjectRecoveries.size() + " counts)");
449 if (failedDBRetr.size() > 0)
451 for (String s : failedProjectRecoveries)
453 System.err.println(s);
455 Assert.fail("Didn't retrieve some db refs for checking cross-refs ("
456 + failedDBRetr.size() + " counts)");
460 private void filterDbRefs(List<String> ptypes, List<String> limit)
465 while (ptypes.size() > p)
467 if (!limit.contains(ptypes.get(p)))
480 * wrapper to trap known defect for AH002001 testcase
485 private void assertDatasetIsNormalisedKnownDefect(AlignmentI al,
490 AlignmentTest.assertDatasetIsNormalised(al, message);
491 } catch (AssertionError ae)
493 if (!ae.getMessage().endsWith("EMBL|AH002001"))
500 .println("Ignored exception for known defect: JAL-2179 : "
507 private void assertProtein(AlignmentViewPanel alignmentViewPanel,
510 assertType(true, alignmentViewPanel, message);
513 private void assertNucleotide(AlignmentViewPanel alignmentViewPanel,
516 assertType(false, alignmentViewPanel, message);
519 private void assertType(boolean expectProtein,
520 AlignmentViewPanel alignmentViewPanel, String message)
522 List<SequenceI> nonType = new ArrayList<>();
523 for (SequenceI sq : alignmentViewPanel.getAlignViewport()
524 .getAlignment().getSequences())
526 if (sq.isProtein() != expectProtein)
531 if (nonType.size() > 0)
533 Assert.fail(message + " [ "
534 + (expectProtein ? "nucleotides were " : "proteins were ")
535 + nonType.toString() + " ]");
540 * first time called, record strings derived from alignment and
541 * alignedcodonframes, and save view to a project file. Second time called,
542 * compare strings to existing ones. org.testng.Assert.assertTrue on
546 * map between xrefpath and view string
547 * @param savedProjects
548 * - map from xrefpath to saved project filename (createTempFile)
550 * - xrefpath - unique ID for this context (composed of sequence of
551 * db-fetch/cross-ref actions preceeding state)
553 * - viewpanel to store (for viewpanels in splitframe, the same
554 * project should be written for both panels, only one needs
555 * recovering for comparison on the next stringify call, but each
556 * viewpanel needs to be called with a distinct xrefpath to ensure
557 * each one's strings are compared)
559 private void stringify(HashMap<String, String> dbtoviewBit,
560 HashMap<String, File> savedProjects, String xrefpath,
561 AlignmentViewPanel avp)
563 if (savedProjects != null)
565 if (savedProjects.get(xrefpath) == null)
567 // write a project file for this view. On the second pass, this will be
568 // recovered and cross-references verified
571 File prfile = File.createTempFile("crossRefTest", ".jvp");
572 AlignFrame af = Desktop.getAlignFrameFor(avp.getAlignViewport());
573 new Jalview2XML(false).saveAlignment(af, prfile.toString(),
575 System.out.println("Written view from '" + xrefpath + "' as '"
576 + prfile.getAbsolutePath() + "'");
577 savedProjects.put(xrefpath, prfile);
578 } catch (IOException q)
580 Assert.fail("Unexpected IO Exception", q);
585 System.out.println("Stringify check on view from '" + xrefpath
586 + "' [ possibly retrieved from '"
587 + savedProjects.get(xrefpath).getAbsolutePath() + "' ]");
592 StringBuilder sbr = new StringBuilder();
593 sbr.append(avp.getAlignment().toString());
595 sbr.append("<End of alignment>");
597 sbr.append(avp.getAlignment().getDataset());
599 sbr.append("<End of dataset>");
602 if (avp.getAlignment().getCodonFrames() != null)
604 for (AlignedCodonFrame ac : avp.getAlignment().getCodonFrames())
606 sbr.append("<AlignedCodonFrame " + p++ + ">");
608 sbr.append(ac.toString());
612 String dbt = dbtoviewBit.get(xrefpath);
615 dbtoviewBit.put(xrefpath, sbr.toString());
619 Assert.assertEquals(sbr.toString(), dbt, "stringify mismatch for "