X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FCrossRef2xmlTests.java;h=ae5ed2598f64008929f5240f273ee7ea2da0fc8f;hb=582096635d0502a9bc8415c8f1ef3bcc9c545a44;hp=071585785605cd2e3a6d68b2afe41d4c62340512;hpb=f4766a7bbcfae845fc95923b01fa14ff83d589ff;p=jalview.git diff --git a/test/jalview/io/CrossRef2xmlTests.java b/test/jalview/io/CrossRef2xmlTests.java index 0715857..ae5ed25 100644 --- a/test/jalview/io/CrossRef2xmlTests.java +++ b/test/jalview/io/CrossRef2xmlTests.java @@ -20,6 +20,10 @@ */ package jalview.io; +import static org.testng.Assert.assertEquals; +import static org.testng.Assert.assertNotNull; +import static org.testng.Assert.assertTrue; + import jalview.analysis.CrossRef; import jalview.api.AlignmentViewPanel; import jalview.datamodel.AlignedCodonFrame; @@ -29,8 +33,8 @@ 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; @@ -39,11 +43,15 @@ import java.util.ArrayList; import java.util.Arrays; import java.util.HashMap; 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 { @@ -56,6 +64,59 @@ public class CrossRef2xmlTests extends Jalview2xmlBase JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION); } + @Test(groups = { "Functional" }, enabled = true) + public void openCrossrefsForEnsemblTwice() + { + AlignFrame af = new FileLoader(false).LoadFileWaitTillLoaded( + "examples/testdata/CantShowEnsemblCrossrefsTwice.jvp", + DataSourceType.FILE); + assertNotNull(af, "Couldn't load test's project."); + AlignmentI origAlig = af.getViewport().getAlignment(); + List source = new CrossRef(origAlig.getSequencesArray(), + origAlig.getDataset()).findXrefSourcesForSequences(true); + assertEquals(source.size(), 1, "Expected just one crossref to show."); + List views; + { + // try to show once - in a code block so handler is forgotten about + CrossRefAction xref1 = CrossRefAction.getHandlerFor( + origAlig.getSequencesArray(), true, source.get(0), af); + try + { + xref1.run(); + views = (List) PA.getValue(xref1, "xrefViews"); + assertTrue(views.size() > 0, + "Couldn't get cross ref on first attempt (SERIOUS FAIL)."); + } catch (Exception ex) + { + Assert.fail("Unexpected Exception for first xref action", ex); + } + } + + views = null; + // now just try it again + CrossRefAction xref2 = CrossRefAction.getHandlerFor( + origAlig.getSequencesArray(), true, source.get(0), af); + try + { + xref2.run(); + views = (List) PA.getValue(xref2, "xrefViews"); + assertTrue(views.size() > 0, + "Couldn't get cross ref on second attempt (SERIOUS FAIL)."); + } catch (Exception ex) + { + Assert.fail("Unexpected Exception for second xref action", ex); + } + // TODO : check that both views contain the same data + } + + @DataProvider(name = "initialAccessions") + static Object[][] getAccessions() + { + return new String[][] { { "UNIPROT", "P00338" }, + { "UNIPROT", "Q8Z9G6" }, + { "ENSEMBLGENOMES", "CAD01290" } }; + } + /** * 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 @@ -63,8 +124,13 @@ public class CrossRef2xmlTests extends Jalview2xmlBase * * @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<>(); @@ -90,12 +156,12 @@ public class CrossRef2xmlTests extends Jalview2xmlBase // . codonframes // // - HashMap dbtoviewBit = new HashMap<>(); + Map dbtoviewBit = new HashMap<>(); List keyseq = new ArrayList<>(); - HashMap savedProjects = new HashMap<>(); + Map savedProjects = new HashMap<>(); - for (String[] did : new String[][] { { "UNIPROT", "P00338" } }) - { +// 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; @@ -105,7 +171,7 @@ 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; @@ -117,7 +183,8 @@ public class CrossRef2xmlTests extends Jalview2xmlBase // retrieve dbref List afs = jalview.gui.SequenceFetcher.fetchAndShow( - did[0], did[1]); + forSource, forAccession); + // did[0], did[1]); if (afs.size() == 0) { failedDBRetr.add("Didn't retrieve " + first); @@ -186,15 +253,16 @@ public class CrossRef2xmlTests extends Jalview2xmlBase 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(); - if (cra.getXrefViews().size() == 0) + cra_views = (List) PA.getValue(cra, + "xrefViews"); + if (cra_views.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); @@ -286,16 +354,18 @@ public class CrossRef2xmlTests extends Jalview2xmlBase 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(); - if (cra.getXrefViews().size() == 0) + cra_views2 = (List) PA.getValue( + cra, "xrefViews"); + if (cra_views2.size() == 0) { failedXrefMenuItems .add("No crossrefs retrieved for '" @@ -303,7 +373,6 @@ public class CrossRef2xmlTests extends Jalview2xmlBase + " via '" + nextaf.getTitle() + "'"); continue; } - cra_views2 = cra.getXrefViews(); assertNucleotide(cra_views2.get(0), "Nucleotide panel included proteins for '" + nextxref + "' to " + xrefdb @@ -411,7 +480,7 @@ public class CrossRef2xmlTests extends Jalview2xmlBase pass1++; } } while (pass1 < 3); - } + if (failedXrefMenuItems.size() > 0) { for (String s : failedXrefMenuItems) @@ -541,8 +610,8 @@ 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)