X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FCrossRef2xmlTests.java;h=838aa7a09a12ff0e25f08063ab089758d55b4769;hb=ec58d7c6a3ceadb413a2e11247adef2eaee3382b;hp=dd6aac6ef8aba7ce2a0f62b77023afd7a4cb0031;hpb=c4baa6ec459f004be9c3b3d50cfbb29212b13312;p=jalview.git diff --git a/test/jalview/io/CrossRef2xmlTests.java b/test/jalview/io/CrossRef2xmlTests.java index dd6aac6..838aa7a 100644 --- a/test/jalview/io/CrossRef2xmlTests.java +++ b/test/jalview/io/CrossRef2xmlTests.java @@ -20,17 +20,21 @@ */ package jalview.io; -import static org.testng.AssertJUnit.assertTrue; - import jalview.analysis.CrossRef; import jalview.api.AlignmentViewPanel; +import jalview.datamodel.AlignedCodonFrame; import jalview.datamodel.AlignmentI; +import jalview.datamodel.AlignmentTest; import jalview.datamodel.SequenceI; import jalview.gui.AlignFrame; import jalview.gui.CrossRefAction; import jalview.gui.Desktop; +import jalview.gui.Jalview2XML; -import java.util.IdentityHashMap; +import java.io.File; +import java.io.IOException; +import java.util.ArrayList; +import java.util.HashMap; import java.util.List; import org.testng.Assert; @@ -48,6 +52,11 @@ public class CrossRef2xmlTests extends Jalview2xmlBase @Test(groups = { "Operational" }, enabled = true) public void testRetrieveAndShowCrossref() throws Exception { + + List failedDBRetr = new ArrayList(); + List failedXrefMenuItems = new ArrayList(); + List failedProjectRecoveries = new ArrayList(); + // for every set of db queries // retrieve db query // verify presence of expected xrefs @@ -64,70 +73,465 @@ public class CrossRef2xmlTests extends Jalview2xmlBase // . codonframes // // + HashMap dbtoviewBit = new HashMap(); + List keyseq = new ArrayList(); + HashMap savedProjects = new HashMap(); + for (String[] did : new String[][] { { "UNIPROT", "P01731" } }) { - AlignFrame af = jalview.gui.SequenceFetcher.fetchAndShow(did[0], - did[1]).get(0); - assertTrue("Didn't read in the example file correctly.", af != null); - boolean dna = af.getViewport().getAlignment().isNucleotide(); - AlignmentI retral = af.getViewport().getAlignment(); - AlignmentI dataset = retral.getDataset(); - SequenceI[] seqs = retral.getSequencesArray(); - List ptypes = (seqs == null || seqs.length == 0) ? null - : new CrossRef(seqs, dataset) - .findXrefSourcesForSequences(dna); - /* - * map between a view, and views generated after retrieving xrefs - */ - IdentityHashMap> viewxrefview = new IdentityHashMap>(); - /* - * map between a particular view and it's originating dbref path - */ - IdentityHashMap viewsourcedb = new IdentityHashMap(); - - String first = did[0] + " " + did[1]; - viewsourcedb.put(af.alignPanel, first); - for (String db : ptypes) + // pass counters - 0 - first pass, 1 means retrieve project rather than + // perform action + int pass1 = 0, pass2 = 0, pass3 = 0; + // each do loop performs two iterations in the first outer loop pass, but + // only performs one iteration on the second outer loop + // ie. pass 1 = 0 {pass 2= 0 { pass 3 = 0,1 }, pass 2=1 { pass 3 = 0 }}, 1 + // { pass 2 = 0 { pass 3 = 0 } } + do { - // retrieve and show cross-refs in this thread - CrossRefAction cra = new CrossRefAction(af, seqs, dna, db); - cra.run(); - Assert.assertTrue(cra.getXrefViews().size() > 0, - "No crossrefs retrieved for " + db); - viewxrefview.put(af.alignPanel, cra.getXrefViews()); - - for (AlignmentViewPanel avp : cra.getXrefViews()) + String first = did[0] + " " + did[1]; + AlignFrame af = null; + boolean dna; + AlignmentI retral; + AlignmentI dataset; + SequenceI[] seqs; + List ptypes = null; + if (pass1 == 0) + { + // retrieve dbref + + List afs = jalview.gui.SequenceFetcher.fetchAndShow( + did[0], did[1]); + if (afs.size() == 0) + { + failedDBRetr.add("Didn't retrieve " + first); + break; + } + keyseq.add(first); + af = afs.get(0); + + // verify references for retrieved data + AlignmentTest.assertAlignmentDatasetRefs(af.getViewport() + .getAlignment(), "Pass (" + pass1 + "," + pass2 + "," + + pass3 + "): Fetch " + first + ":"); + dna = af.getViewport().getAlignment().isNucleotide(); + retral = af.getViewport().getAlignment(); + dataset = retral.getDataset(); + seqs = retral.getSequencesArray(); + + } + else + { + Desktop.instance.closeAll_actionPerformed(null); + // recover stored project + af = new FileLoader(false).LoadFileWaitTillLoaded(savedProjects + .get(first).toString(), FormatAdapter.FILE); + System.out.println("Recovered view for '" + first + "' from '" + + savedProjects.get(first).toString() + "'"); + dna = af.getViewport().getAlignment().isNucleotide(); + retral = af.getViewport().getAlignment(); + dataset = retral.getDataset(); + seqs = retral.getSequencesArray(); + + // verify references for recovered data + AlignmentTest.assertAlignmentDatasetRefs(af.getViewport() + .getAlignment(), "Pass (" + pass1 + "," + pass2 + "," + + pass3 + "): Recover " + first + ":"); + + } + + // store project on first pass, compare next pass + stringify(dbtoviewBit, savedProjects, first, af.alignPanel); + + ptypes = (seqs == null || seqs.length == 0) ? null : new CrossRef( + seqs, dataset).findXrefSourcesForSequences(dna); + + // start of pass2: retrieve each cross-ref for fetched or restored + // project. + do // first cross ref and recover crossref loop { - SequenceI[] xrseqs = avp.getAlignment().getSequencesArray(); - String nextxref = first + " -> " + db; - viewsourcedb.put(avp, nextxref); - List xrptypes = (seqs == null || seqs.length == 0) ? null - : new CrossRef(xrseqs, dataset) - .findXrefSourcesForSequences(avp - .getAlignViewport().isNucleotide()); - for (String xrefdb : xrptypes) + for (String db : ptypes) { - AlignFrame nextaf = Desktop.getAlignFrameFor(avp - .getAlignViewport()); - cra = new CrossRefAction(nextaf, xrseqs, avp.getAlignViewport() - .isNucleotide(), xrefdb); - cra.run(); - Assert.assertTrue(cra.getXrefViews().size() > 0, - "No crossrefs found for '" + nextxref + "' to " - + xrefdb + " via '" + nextaf.getTitle() + "'"); - // save views for analysis - viewxrefview.put(avp, cra.getXrefViews()); - for (AlignmentViewPanel nextavp : cra.getXrefViews()) + // counter for splitframe views retrieved via crossref + int firstcr_ap = 0; + // build next key so we an retrieve all views + String nextxref = first + " -> " + db + "{" + firstcr_ap + "}"; + // perform crossref action, or retrieve stored project + List cra_views = new ArrayList(); + CrossRefAction cra = null; + + if (pass2 == 0) + { // retrieve and show cross-refs in this thread + cra = new CrossRefAction(af, seqs, dna, db); + cra.run(); + if (cra.getXrefViews().size() == 0) + { + failedXrefMenuItems.add("No crossrefs retrieved for " + + first + " -> " + db); + continue; + } + cra_views = cra.getXrefViews(); + assertNucleotide(cra_views.get(0), + "Nucleotide panel included proteins for " + first + + " -> " + db); + assertProtein(cra_views.get(1), + "Protein panel included nucleotides for " + first + + " -> " + db); + } + else + { + Desktop.instance.closeAll_actionPerformed(null); + pass3 = 0; + // recover stored project + File storedProject = savedProjects.get(nextxref); + if (storedProject == null) + { + failedProjectRecoveries.add("Failed to store a view for '" + + nextxref + "'"); + continue; + } + + // recover stored project + AlignFrame af2 = new FileLoader(false) + .LoadFileWaitTillLoaded(savedProjects.get(nextxref) + .toString(), FormatAdapter.FILE); + System.out.println("Recovered view for '" + nextxref + + "' from '" + savedProjects.get(nextxref).toString() + + "'"); + // gymnastics to recover the alignPanel/Complementary alignPanel + if (af2.getViewport().isNucleotide()) + { + // top view, then bottom + cra_views.add(af2.getViewport().getAlignPanel()); + cra_views.add(((jalview.gui.AlignViewport) af2 + .getViewport().getCodingComplement()) + .getAlignPanel()); + + } + else + { + // bottom view, then top + cra_views.add(((jalview.gui.AlignViewport) af2 + .getViewport().getCodingComplement()) + .getAlignPanel()); + cra_views.add(af2.getViewport().getAlignPanel()); + + } + } + HashMap> xrptypes = new HashMap>(); + // first save/verify views. + for (AlignmentViewPanel avp : cra_views) { + nextxref = first + " -> " + db + "{" + firstcr_ap++ + "}"; + // verify references for this panel + AlignmentTest.assertAlignmentDatasetRefs(avp.getAlignment(), + "Pass (" + pass1 + "," + pass2 + "," + pass3 + + "): before start of pass3: " + nextxref + + ":"); + + SequenceI[] xrseqs = avp.getAlignment().getSequencesArray(); + + List _xrptypes = (seqs == null || seqs.length == 0) ? null + : new CrossRef(xrseqs, dataset) + .findXrefSourcesForSequences(avp + .getAlignViewport().isNucleotide()); + + stringify(dbtoviewBit, savedProjects, nextxref, avp); + xrptypes.put(nextxref, _xrptypes); - viewsourcedb.put(nextavp, nextxref + " -> " + xrefdb); } + + // now do the second xref pass starting from either saved or just + // recovered split pane, in sequence + do // retrieve second set of cross refs or recover and verify + { + firstcr_ap = 0; + for (AlignmentViewPanel avp : cra_views) + { + nextxref = first + " -> " + db + "{" + firstcr_ap++ + "}"; + for (String xrefdb : xrptypes.get(nextxref)) + { + List cra_views2 = new ArrayList(); + int q = 0; + String nextnextxref = nextxref + + " -> " + xrefdb + "{" + q + "}"; + + if (pass3 == 0) + { + + SequenceI[] xrseqs = avp.getAlignment() + .getSequencesArray(); + AlignFrame nextaf = Desktop.getAlignFrameFor(avp + .getAlignViewport()); + + cra = new CrossRefAction(nextaf, xrseqs, avp + .getAlignViewport().isNucleotide(), xrefdb); + cra.run(); + if (cra.getXrefViews().size() == 0) + { + failedXrefMenuItems + .add("No crossrefs retrieved for '" + + nextxref + "' to " + xrefdb + " via '" + + nextaf.getTitle() + "'"); + continue; + } + cra_views2 = cra.getXrefViews(); + assertNucleotide(cra_views2.get(0), + "Nucleotide panel included proteins for '" + + nextxref + "' to " + xrefdb + + " via '" + nextaf.getTitle() + "'"); + assertProtein(cra_views2.get(1), + "Protein panel included nucleotides for '" + + nextxref + "' to " + xrefdb + + " via '" + nextaf.getTitle() + "'"); + + } + else + { + Desktop.instance.closeAll_actionPerformed(null); + // recover stored project + File storedProject = savedProjects.get(nextnextxref); + if (storedProject == null) + { + failedProjectRecoveries + .add("Failed to store a view for '" + + nextnextxref + "'"); + continue; + } + AlignFrame af2 = new FileLoader(false) + .LoadFileWaitTillLoaded( + savedProjects.get(nextnextxref) + .toString(), FormatAdapter.FILE); + System.out.println("Recovered view for '" + + nextnextxref + "' from '" + + savedProjects.get(nextnextxref).toString() + + "'"); + // gymnastics to recover the alignPanel/Complementary + // alignPanel + if (af2.getViewport().isNucleotide()) + { + // top view, then bottom + cra_views2.add(af2.getViewport().getAlignPanel()); + cra_views2.add(((jalview.gui.AlignViewport) af2 + .getViewport().getCodingComplement()) + .getAlignPanel()); + + } + else + { + // bottom view, then top + cra_views2.add(((jalview.gui.AlignViewport) af2 + .getViewport().getCodingComplement()) + .getAlignPanel()); + cra_views2.add(af2.getViewport().getAlignPanel()); + } + Assert.assertEquals(cra_views2.size(), 2); + Assert.assertNotNull(cra_views2.get(0)); + Assert.assertNotNull(cra_views2.get(1)); + } + + for (AlignmentViewPanel nextavp : cra_views2) + { + nextnextxref = nextxref + + " -> " + xrefdb + "{" + q++ + "}"; + + // verify references for this panel + AlignmentTest.assertAlignmentDatasetRefs( + nextavp.getAlignment(), "" + "Pass (" + pass1 + + "," + pass2 + "): For " + + nextnextxref + ":"); + + stringify(dbtoviewBit, savedProjects, nextnextxref, + nextavp); + keyseq.add(nextnextxref); + } + } // end of loop around showing all xrefdb for crossrf2 + + } // end of loop around all viewpanels from crossrf1 + } while (pass2 == 2 && pass3++ < 2); + // fetchdb->crossref1->crossref-2->verify for xrefs we + // either loop twice when pass2=0, or just once when pass2=1 + // (recovered project from previous crossref) + + } // end of loop over db-xrefs for crossref-2 + + // fetchdb-->crossref1 + // for each xref we try to retrieve xref, store and verify when + // pass1=0, or just retrieve and verify when pass1=1 + } while (pass1 == 1 && pass2++ < 2); + // fetchdb + // for each ref we + // loop twice: first, do the retrieve, second recover from saved project + + // increment pass counters, so we repeat traversal starting from the + // oldest saved project first. + if (pass1 == 0) + { + // verify stored projects for first set of cross references + pass1 = 1; + // and verify cross-references retrieved from stored projects + pass2 = 0; + pass3 = 0; + } + else + { + pass1++; + if (pass1 < 2) + { + // verify stored projects for second set of cross references + pass2 = 1; + // and verify cross-references retrievable from those stored projects. + pass3 = 0; } } + } while (pass3 < 2); + } + if (failedXrefMenuItems.size() > 0) + { + for (String s : failedXrefMenuItems) + { + System.err.println(s); } + Assert.fail("Faulty xref menu (" + failedXrefMenuItems.size() + + " counts)"); + } + if (failedProjectRecoveries.size() > 0) + { + + for (String s : failedProjectRecoveries) + { + System.err.println(s); + } + Assert.fail("Didn't recover projects for some retrievals (did they retrieve ?) (" + + failedProjectRecoveries.size() + " counts)"); + } + if (failedDBRetr.size() > 0) + { + for (String s : failedProjectRecoveries) + { + System.err.println(s); + } + Assert.fail("Didn't retrieve some db refs for checking cross-refs (" + + failedDBRetr.size() + " counts)"); + } + } + + private void assertProtein(AlignmentViewPanel alignmentViewPanel, + String message) + { + assertType(true, alignmentViewPanel, message); + } + + private void assertNucleotide(AlignmentViewPanel alignmentViewPanel, + String message) + { + assertType(false, alignmentViewPanel, message); + } + + private void assertType(boolean expectProtein, + AlignmentViewPanel alignmentViewPanel, String message) + { + List nonType = new ArrayList(); + for (SequenceI sq : alignmentViewPanel.getAlignViewport() + .getAlignment() + .getSequences()) + { + if (sq.isProtein() != expectProtein) + { + nonType.add(sq); + } + } + if (nonType.size() > 0) + { + Assert.fail(message + " [ " + + (expectProtein ? "nucleotides were " : "proteins were ") + + nonType.toString() + + " ]"); } - Thread.sleep(50000); } + /** + * first time called, record strings derived from alignment and + * alignedcodonframes, and save view to a project file. Second time called, + * compare strings to existing ones. org.testng.Assert.assertTrue on + * stringmatch + * + * @param dbtoviewBit + * map between xrefpath and view string + * @param savedProjects + * - map from xrefpath to saved project filename (createTempFile) + * @param xrefpath + * - xrefpath - unique ID for this context (composed of sequence of + * db-fetch/cross-ref actions preceeding state) + * @param avp + * - viewpanel to store (for viewpanels in splitframe, the same + * project should be written for both panels, only one needs + * recovering for comparison on the next stringify call, but each + * viewpanel needs to be called with a distinct xrefpath to ensure + * each one's strings are compared) + */ + private void stringify(HashMap dbtoviewBit, + HashMap savedProjects, String xrefpath, + AlignmentViewPanel avp) + { + if (savedProjects != null) + { + if (savedProjects.get(xrefpath) == null) + { + // write a project file for this view. On the second pass, this will be + // recovered and cross-references verified + try + { + File prfile = File.createTempFile("crossRefTest", ".jvp"); + AlignFrame af = Desktop.getAlignFrameFor(avp.getAlignViewport()); + new Jalview2XML(false).saveAlignment(af, prfile.toString(), + af.getTitle()); + System.out.println("Written view from '" + xrefpath + "' as '" + + prfile.getAbsolutePath() + "'"); + savedProjects.put(xrefpath, prfile); + } catch (IOException q) + { + Assert.fail("Unexpected IO Exception", q); + } + } + else + { + System.out.println("Stringify check on view from '" + xrefpath + + "' [ possibly retrieved from '" + + savedProjects.get(xrefpath).getAbsolutePath() + "' ]"); + + } + } + + StringBuilder sbr = new StringBuilder(); + sbr.append(avp.getAlignment().toString()); + sbr.append("\n"); + sbr.append(""); + sbr.append("\n"); + sbr.append(avp.getAlignment().getDataset()); + sbr.append("\n"); + sbr.append(""); + sbr.append("\n"); + int p = 0; + if (avp.getAlignment().getCodonFrames() != null) + { + for (AlignedCodonFrame ac : avp.getAlignment().getCodonFrames()) + { + sbr.append(""); + sbr.append("\n"); + sbr.append(ac.toString()); + sbr.append("\n"); + } + } + String dbt = dbtoviewBit.get(xrefpath); + if (dbt == null) + { + dbtoviewBit.put(xrefpath, sbr.toString()); + } + else + { + Assert.assertEquals(sbr.toString(), dbt, "stringify mismatch for " + + xrefpath); + } + } }