X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FCrossRef2xmlTests.java;h=9e24262c89a38b53a5467e253b0ec4c85106913c;hb=54dcb58375e9783c7bd4b793acd0b0aa485556ba;hp=64c800b7452572c7dd7dcd1d9070b7a1ccc7fa80;hpb=d8965731a376fef5d414c64ec9865f643665119e;p=jalview.git diff --git a/test/jalview/io/CrossRef2xmlTests.java b/test/jalview/io/CrossRef2xmlTests.java index 64c800b..9e24262 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; @@ -32,6 +30,7 @@ import jalview.gui.AlignFrame; import jalview.gui.CrossRefAction; import jalview.gui.Desktop; import jalview.gui.Jalview2XML; +import jalview.gui.JvOptionPane; import java.io.File; import java.io.IOException; @@ -40,20 +39,35 @@ import java.util.HashMap; import java.util.List; import org.testng.Assert; +import org.testng.annotations.BeforeClass; import org.testng.annotations.Test; @Test(singleThreaded = true) public class CrossRef2xmlTests extends Jalview2xmlBase { + @Override + @BeforeClass(alwaysRun = true) + public void setUpJvOptionPane() + { + JvOptionPane.setInteractiveMode(false); + JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION); + } + /** - * 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 { + + 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 @@ -70,11 +84,12 @@ public class CrossRef2xmlTests extends Jalview2xmlBase // . codonframes // // - HashMap dbtoviewBit = new HashMap(); - List keyseq = new ArrayList(); - HashMap savedProjects = new HashMap(); + HashMap dbtoviewBit = new HashMap<>(); + List keyseq = new ArrayList<>(); + HashMap savedProjects = new HashMap<>(); - for (String[] did : new String[][] { { "UNIPROT", "P01731" } }) + for (String[] did : new String[][] { { "ENSEMBL", "ENSG00000157764" }, + { "UNIPROT", "P01731" } }) { // pass counters - 0 - first pass, 1 means retrieve project rather than // perform action @@ -96,16 +111,23 @@ public class CrossRef2xmlTests extends Jalview2xmlBase { // 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 = 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.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(); @@ -117,7 +139,7 @@ public class CrossRef2xmlTests extends Jalview2xmlBase 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(); @@ -129,6 +151,9 @@ public class CrossRef2xmlTests extends Jalview2xmlBase AlignmentTest.assertAlignmentDatasetRefs(af.getViewport() .getAlignment(), "Pass (" + pass1 + "," + pass2 + "," + pass3 + "): Recover " + first + ":"); + assertDatasetIsNormalisedKnownDefect(af.getViewport() + .getAlignment(), "Pass (" + pass1 + "," + pass2 + "," + + pass3 + "): Recover " + first + ":"); } @@ -140,8 +165,7 @@ public class CrossRef2xmlTests extends Jalview2xmlBase // start of pass2: retrieve each cross-ref for fetched or restored // project. - pass2 = 0; - do // second cross ref and recover crossref loop + do // first cross ref and recover crossref loop { for (String db : ptypes) @@ -151,23 +175,44 @@ public class CrossRef2xmlTests extends Jalview2xmlBase // 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(); + 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(); - Assert.assertTrue(cra.getXrefViews().size() > 0, - "No crossrefs retrieved for " + db); + 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); + .toString(), DataSourceType.FILE); System.out.println("Recovered view for '" + nextxref + "' from '" + savedProjects.get(nextxref).toString() + "'"); @@ -191,7 +236,7 @@ public class CrossRef2xmlTests extends Jalview2xmlBase } } - HashMap> xrptypes = new HashMap>(); + HashMap> xrptypes = new HashMap<>(); // first save/verify views. for (AlignmentViewPanel avp : cra_views) { @@ -201,6 +246,10 @@ public class CrossRef2xmlTests extends Jalview2xmlBase "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(); @@ -208,16 +257,15 @@ public class CrossRef2xmlTests extends Jalview2xmlBase : new CrossRef(xrseqs, dataset) .findXrefSourcesForSequences(avp .getAlignViewport().isNucleotide()); - + stringify(dbtoviewBit, savedProjects, nextxref, avp); xrptypes.put(nextxref, _xrptypes); } - // now do the next xref pass starting from either saved or just + + // now do the second xref pass starting from either saved or just // recovered split pane, in sequence - pass3 = 0; - do // 3rd cross ref and recover crossref loop, for each view from - // second xref view set or recover viewset + do // retrieve second set of cross refs or recover and verify { firstcr_ap = 0; for (AlignmentViewPanel avp : cra_views) @@ -225,10 +273,10 @@ public class CrossRef2xmlTests extends Jalview2xmlBase 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 = nextxref - + " -> " + xrefdb + "{" + q + "}"; + String nextnextxref = nextxref + " -> " + xrefdb + "{" + + q + "}"; if (pass3 == 0) { @@ -241,21 +289,42 @@ public class CrossRef2xmlTests extends Jalview2xmlBase cra = new CrossRefAction(nextaf, xrseqs, avp .getAlignViewport().isNucleotide(), xrefdb); cra.run(); - Assert.assertTrue( - cra.getXrefViews().size() > 0, - "No crossrefs found for '" + nextnextxref - + "' to " + xrefdb + " via '" - + nextaf.getTitle() + "'"); + 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); + .toString(), + DataSourceType.FILE); System.out.println("Recovered view for '" + nextnextxref + "' from '" + savedProjects.get(nextnextxref).toString() @@ -286,14 +355,18 @@ public class CrossRef2xmlTests extends Jalview2xmlBase for (AlignmentViewPanel nextavp : cra_views2) { - nextnextxref = nextxref - + " -> " + xrefdb + "{" + q++ + "}"; + nextnextxref = nextxref + " -> " + xrefdb + "{" + q++ + + "}"; // verify references for this panel AlignmentTest.assertAlignmentDatasetRefs( nextavp.getAlignment(), "" + "Pass (" + pass1 + "," + pass2 + "): For " + nextnextxref + ":"); + assertDatasetIsNormalisedKnownDefect( + nextavp.getAlignment(), "" + "Pass (" + pass1 + + "," + pass2 + "): For " + + nextnextxref + ":"); stringify(dbtoviewBit, savedProjects, nextnextxref, nextavp); @@ -302,20 +375,124 @@ public class CrossRef2xmlTests extends Jalview2xmlBase } // end of loop around showing all xrefdb for crossrf2 } // end of loop around all viewpanels from crossrf1 - } while (pass3++ < 2 && pass2 < 1); + } 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 (pass2++ < 2 && pass1 < 1); + } while (pass1 == 1 && pass2++ < 2); // fetchdb // for each ref we // loop twice: first, do the retrieve, second recover from saved project - } while (pass1++ < 2); + + // 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)"); + } + } + + /** + * 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() + " ]"); } }