X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FCrossRef2xmlTests.java;h=53a0acb864ace38b2ef6d5c462cf9cc49ce076ff;hb=8669979d57e2019889afaefafe65b945ae7c172d;hp=154abc0065a49b9411ea989d9be9d3a63a6c5b89;hpb=57b6c602a430c5eaf7d413c0a9b6584eb066a8f4;p=jalview.git diff --git a/test/jalview/io/CrossRef2xmlTests.java b/test/jalview/io/CrossRef2xmlTests.java index 154abc0..53a0acb 100644 --- a/test/jalview/io/CrossRef2xmlTests.java +++ b/test/jalview/io/CrossRef2xmlTests.java @@ -20,8 +20,6 @@ */ package jalview.io; -import static org.testng.AssertJUnit.assertTrue; - import jalview.analysis.CrossRef; import jalview.api.AlignmentViewPanel; import jalview.datamodel.AlignedCodonFrame; @@ -31,30 +29,68 @@ import jalview.datamodel.SequenceI; import jalview.gui.AlignFrame; import jalview.gui.CrossRefAction; import jalview.gui.Desktop; -import jalview.gui.Jalview2XML; +import jalview.gui.JvOptionPane; +import jalview.project.Jalview2XML; +import jalview.util.DBRefUtils; import java.io.File; import java.io.IOException; import java.util.ArrayList; +import java.util.Arrays; import java.util.HashMap; -import java.util.IdentityHashMap; import java.util.List; +import java.util.Map; import org.testng.Assert; +import org.testng.annotations.BeforeClass; +import org.testng.annotations.DataProvider; import org.testng.annotations.Test; +import junit.extensions.PA; + @Test(singleThreaded = true) public class CrossRef2xmlTests extends Jalview2xmlBase { + @Override + @BeforeClass(alwaysRun = true) + public void setUpJvOptionPane() + { + JvOptionPane.setInteractiveMode(false); + JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION); + } + + @DataProvider(name = "initialAccessions") + static Object[][] getAccessions() + { + return new String[][] { { "UNIPROT", "P00338" }, + { "UNIPROT", "Q8Z9G6" }, + { "ENSEMBLGENOMES", "CAD01290" } }; + } + /** - * test store and recovery of expanded views + * test store and recovery of all reachable cross refs from all reachable + * crossrefs for one or more fetched db refs. Currently, this test has a known + * failure case. * * @throws Exception */ - @Test(groups = { "Operational" }, enabled = true) - public void testRetrieveAndShowCrossref() throws Exception + @Test( + groups = + { "Operational" }, + dataProvider = "initialAccessions", + enabled = true) + public void testRetrieveAndShowCrossref(String forSource, + String forAccession) throws Exception { + + List failedDBRetr = new ArrayList<>(); + List failedXrefMenuItems = new ArrayList<>(); + List failedProjectRecoveries = new ArrayList<>(); + // only search for ensembl or Uniprot crossrefs + List limit=Arrays.asList(new String[] { + DBRefUtils.getCanonicalName("ENSEMBL"), + DBRefUtils.getCanonicalName("Uniprot")}); // for every set of db queries // retrieve db query // verify presence of expected xrefs @@ -71,12 +107,12 @@ public class CrossRef2xmlTests extends Jalview2xmlBase // . codonframes // // - HashMap dbtoviewBit = new HashMap(); - List keyseq = new ArrayList(); - HashMap savedProjects = new HashMap(); + Map dbtoviewBit = new HashMap<>(); + List keyseq = new ArrayList<>(); + Map savedProjects = new HashMap<>(); - for (String[] did : new String[][] { { "UNIPROT", "P01731" } }) - { +// for (String[] did : new String[][] { { "UNIPROT", "P00338" } }) +// { // pass counters - 0 - first pass, 1 means retrieve project rather than // perform action int pass1 = 0, pass2 = 0, pass3 = 0; @@ -86,84 +122,125 @@ public class CrossRef2xmlTests extends Jalview2xmlBase // { pass 2 = 0 { pass 3 = 0 } } do { - String first = did[0] + " " + did[1]; + String first = forSource + " " + forAccession;//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( + forSource, forAccession); + // did[0], did[1]); + if (afs.size() == 0) + { + failedDBRetr.add("Didn't retrieve " + first); + break; + } keyseq.add(first); - - af = jalview.gui.SequenceFetcher.fetchAndShow(did[0], did[1]) - .get(0); - assertTrue("Didn't retrieve " + first, af != null); + af = afs.get(0); // verify references for retrieved data - AlignmentTest.verifyAlignmentDatasetRefs(af.getViewport() - .getAlignment(), true); + AlignmentTest.assertAlignmentDatasetRefs(af.getViewport() + .getAlignment(), "Pass (" + pass1 + "," + pass2 + "," + + pass3 + "): Fetch " + first + ":"); + assertDatasetIsNormalisedKnownDefect(af.getViewport() + .getAlignment(), "Pass (" + pass1 + "," + pass2 + "," + + pass3 + "): Fetch " + first + ":"); + dna = af.getViewport().getAlignment().isNucleotide(); + retral = af.getViewport().getAlignment(); + dataset = retral.getDataset(); + seqs = retral.getSequencesArray(); - // store project to recover on next pass - stringify(dbtoviewBit, savedProjects, first, af.alignPanel); } else { Desktop.instance.closeAll_actionPerformed(null); // recover stored project af = new FileLoader(false).LoadFileWaitTillLoaded(savedProjects - .get(first).toString(), FormatAdapter.FILE); + .get(first).toString(), DataSourceType.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.verifyAlignmentDatasetRefs(af.getViewport() - .getAlignment(), true); + AlignmentTest.assertAlignmentDatasetRefs(af.getViewport() + .getAlignment(), "Pass (" + pass1 + "," + pass2 + "," + + pass3 + "): Recover " + first + ":"); + assertDatasetIsNormalisedKnownDefect(af.getViewport() + .getAlignment(), "Pass (" + pass1 + "," + pass2 + "," + + pass3 + "): Recover " + first + ":"); } - 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(); - - viewsourcedb.put(af.alignPanel, first); - for (String db : ptypes) + // 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); + filterDbRefs(ptypes, limit); + + // start of pass2: retrieve each cross-ref for fetched or restored + // project. + do // first cross ref and recover crossref loop { - pass2 = 0; - do // second cross ref and recover crossref loop + + for (String db : ptypes) { // counter for splitframe views retrieved via crossref - int p = 0; + int firstcr_ap = 0; // build next key so we an retrieve all views - String nextxref = first + " -> " + db + "{" + p + "}"; + String nextxref = first + " -> " + db + "{" + firstcr_ap + "}"; // perform crossref action, or retrieve stored project - List cra_views = new ArrayList(); + 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 = CrossRefAction.getHandlerFor(seqs, dna, db, af); cra.run(); - Assert.assertTrue(cra.getXrefViews().size() > 0, - "No crossrefs retrieved for " + db); - cra_views = cra.getXrefViews(); - viewxrefview.put(af.alignPanel, cra.getXrefViews()); + cra_views = (List) PA.getValue(cra, + "xrefViews"); + if (cra_views.size() == 0) + { + failedXrefMenuItems.add("No crossrefs retrieved for " + + first + " -> " + db); + continue; + } + 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); + .toString(), DataSourceType.FILE); + System.out.println("Recovered view for '" + nextxref + + "' from '" + savedProjects.get(nextxref).toString() + + "'"); // gymnastics to recover the alignPanel/Complementary alignPanel if (af2.getViewport().isNucleotide()) { @@ -184,55 +261,100 @@ public class CrossRef2xmlTests extends Jalview2xmlBase } } + HashMap> xrptypes = new HashMap<>(); + // first save/verify views. for (AlignmentViewPanel avp : cra_views) { + nextxref = first + " -> " + db + "{" + firstcr_ap++ + "}"; // verify references for this panel - AlignmentTest.verifyAlignmentDatasetRefs(avp.getAlignment(), - true); + AlignmentTest.assertAlignmentDatasetRefs(avp.getAlignment(), + "Pass (" + pass1 + "," + pass2 + "," + pass3 + + "): before start of pass3: " + nextxref + + ":"); + assertDatasetIsNormalisedKnownDefect(avp.getAlignment(), + "Pass (" + pass1 + "," + pass2 + "," + pass3 + + "): before start of pass3: " + nextxref + + ":"); SequenceI[] xrseqs = avp.getAlignment().getSequencesArray(); - nextxref = first + " -> " + db + "{" + p++ + "}"; - - viewsourcedb.put(avp, nextxref); - stringify(dbtoviewBit, savedProjects, nextxref, avp); - keyseq.add(nextxref); - List xrptypes = (seqs == null || seqs.length == 0) ? null + List _xrptypes = (seqs == null || seqs.length == 0) ? null : new CrossRef(xrseqs, dataset) .findXrefSourcesForSequences(avp .getAlignViewport().isNucleotide()); - for (String xrefdb : xrptypes) + + stringify(dbtoviewBit, savedProjects, nextxref, avp); + xrptypes.put(nextxref, _xrptypes); + + } + + // 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) { - pass3 = 0; - do // 3rd cross ref and recover crossref loop + nextxref = first + " -> " + db + "{" + firstcr_ap++ + "}"; + for (String xrefdb : xrptypes.get(nextxref)) { - List cra_views2 = new ArrayList(); + List cra_views2 = new ArrayList<>(); int q = 0; - String nextnextxref = "{" + p + "}" + nextxref + " -> " - + xrefdb + "{" + q + "}"; + String nextnextxref = nextxref + " -> " + xrefdb + "{" + + q + "}"; - AlignFrame nextaf = Desktop.getAlignFrameFor(avp - .getAlignViewport()); if (pass3 == 0) { + SequenceI[] xrseqs = avp.getAlignment() + .getSequencesArray(); + AlignFrame nextaf = Desktop.getAlignFrameFor(avp + .getAlignViewport()); - cra = new CrossRefAction(nextaf, xrseqs, avp - .getAlignViewport().isNucleotide(), xrefdb); + cra = CrossRefAction.getHandlerFor(xrseqs, avp + .getAlignViewport().isNucleotide(), xrefdb, + nextaf); cra.run(); - Assert.assertTrue(cra.getXrefViews().size() > 0, - "No crossrefs found for '" + nextxref + "' to " - + xrefdb + " via '" + nextaf.getTitle() - + "'"); - cra_views2 = cra.getXrefViews(); + cra_views2 = (List) PA.getValue( + cra, "xrefViews"); + if (cra_views2.size() == 0) + { + failedXrefMenuItems + .add("No crossrefs retrieved for '" + + nextxref + "' to " + xrefdb + + " via '" + nextaf.getTitle() + "'"); + continue; + } + 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); + .toString(), + DataSourceType.FILE); + System.out.println("Recovered view for '" + + nextnextxref + "' from '" + + savedProjects.get(nextnextxref).toString() + + "'"); // gymnastics to recover the alignPanel/Complementary // alignPanel if (af2.getViewport().isNucleotide()) @@ -259,24 +381,163 @@ public class CrossRef2xmlTests extends Jalview2xmlBase for (AlignmentViewPanel nextavp : cra_views2) { - nextnextxref = "{" + p + "}" + nextxref + " -> " - + xrefdb + "{" + q++ + "}"; + nextnextxref = nextxref + " -> " + xrefdb + "{" + q++ + + "}"; // verify references for this panel - AlignmentTest.verifyAlignmentDatasetRefs( - nextavp.getAlignment(), true); + AlignmentTest.assertAlignmentDatasetRefs( + nextavp.getAlignment(), "" + "Pass (" + pass1 + + "," + pass2 + "): For " + + nextnextxref + ":"); + assertDatasetIsNormalisedKnownDefect( + nextavp.getAlignment(), "" + "Pass (" + pass1 + + "," + pass2 + "): For " + + nextnextxref + ":"); - viewsourcedb.put(nextavp, nextnextxref); stringify(dbtoviewBit, savedProjects, nextnextxref, nextavp); keyseq.add(nextnextxref); } - } while (pass3++ < 2 && pass2 < 1); - } - } - } while (pass2++ < 2 && pass1 < 1); + } // 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++; + } + } while (pass1 < 3); + + 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 filterDbRefs(List ptypes, List limit) + { + if (limit != null) + { + int p = 0; + while (ptypes.size() > p) + { + if (!limit.contains(ptypes.get(p))) + { + ptypes.remove(p); } - } while (++pass1 < 2); + else + { + p++; + } + } + } + } + + /** + * wrapper to trap known defect for AH002001 testcase + * + * @param alignment + * @param string + */ + private void assertDatasetIsNormalisedKnownDefect(AlignmentI al, + String message) + { + try + { + AlignmentTest.assertDatasetIsNormalised(al, message); + } catch (AssertionError ae) + { + if (!ae.getMessage().endsWith("EMBL|AH002001")) + { + throw ae; + } + else + { + System.out + .println("Ignored exception for known defect: JAL-2179 : " + + message); + } + + } + } + + 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() + " ]"); } } @@ -300,29 +561,29 @@ public class CrossRef2xmlTests extends Jalview2xmlBase * 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, + private void stringify(Map dbtoviewBit, + Map 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); - } + // 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 {