X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FCrossRef2xmlTests.java;h=53a0acb864ace38b2ef6d5c462cf9cc49ce076ff;hb=8669979d57e2019889afaefafe65b945ae7c172d;hp=838aa7a09a12ff0e25f08063ab089758d55b4769;hpb=ec58d7c6a3ceadb413a2e11247adef2eaee3382b;p=jalview.git diff --git a/test/jalview/io/CrossRef2xmlTests.java b/test/jalview/io/CrossRef2xmlTests.java index 838aa7a..53a0acb 100644 --- a/test/jalview/io/CrossRef2xmlTests.java +++ b/test/jalview/io/CrossRef2xmlTests.java @@ -29,34 +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.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(); - + 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 @@ -73,12 +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; @@ -88,7 +122,7 @@ 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; @@ -100,7 +134,8 @@ 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); @@ -113,6 +148,9 @@ public class CrossRef2xmlTests extends Jalview2xmlBase 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(); @@ -124,7 +162,7 @@ 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(); @@ -136,6 +174,9 @@ 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 + ":"); } @@ -144,7 +185,8 @@ public class CrossRef2xmlTests extends Jalview2xmlBase 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 @@ -157,20 +199,21 @@ 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 = 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); @@ -194,7 +237,7 @@ public class CrossRef2xmlTests extends Jalview2xmlBase // 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() + "'"); @@ -218,7 +261,7 @@ public class CrossRef2xmlTests extends Jalview2xmlBase } } - HashMap> xrptypes = new HashMap>(); + HashMap> xrptypes = new HashMap<>(); // first save/verify views. for (AlignmentViewPanel avp : cra_views) { @@ -228,6 +271,10 @@ 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(); @@ -235,7 +282,7 @@ public class CrossRef2xmlTests extends Jalview2xmlBase : new CrossRef(xrseqs, dataset) .findXrefSourcesForSequences(avp .getAlignViewport().isNucleotide()); - + stringify(dbtoviewBit, savedProjects, nextxref, avp); xrptypes.put(nextxref, _xrptypes); @@ -251,31 +298,32 @@ 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) { - 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 '" - + nextxref + "' to " + xrefdb + " via '" - + nextaf.getTitle() + "'"); + + nextxref + "' to " + xrefdb + + " via '" + nextaf.getTitle() + "'"); continue; } - cra_views2 = cra.getXrefViews(); assertNucleotide(cra_views2.get(0), "Nucleotide panel included proteins for '" + nextxref + "' to " + xrefdb @@ -301,7 +349,8 @@ public class CrossRef2xmlTests extends Jalview2xmlBase 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() @@ -332,14 +381,18 @@ 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); @@ -376,16 +429,9 @@ public class CrossRef2xmlTests extends Jalview2xmlBase 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); - } + } while (pass1 < 3); + if (failedXrefMenuItems.size() > 0) { for (String s : failedXrefMenuItems) @@ -416,6 +462,53 @@ public class CrossRef2xmlTests extends Jalview2xmlBase } } + 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); + } + 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) { @@ -431,10 +524,9 @@ public class CrossRef2xmlTests extends Jalview2xmlBase private void assertType(boolean expectProtein, AlignmentViewPanel alignmentViewPanel, String message) { - List nonType = new ArrayList(); + List nonType = new ArrayList<>(); for (SequenceI sq : alignmentViewPanel.getAlignViewport() - .getAlignment() - .getSequences()) + .getAlignment().getSequences()) { if (sq.isProtein() != expectProtein) { @@ -445,8 +537,7 @@ public class CrossRef2xmlTests extends Jalview2xmlBase { Assert.fail(message + " [ " + (expectProtein ? "nucleotides were " : "proteins were ") - + nonType.toString() - + " ]"); + + nonType.toString() + " ]"); } } @@ -470,8 +561,8 @@ 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)