X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FCrossRef2xmlTests.java;h=2b8a62f4d25de192b86f3906b14fa636f018d105;hb=3069ade337eb42af30baf34a69f0a7f4cefe3948;hp=ec5855f97e1b0d3e1e1c7877bdc6b7301c202bf3;hpb=483e7163b1fb8d4bcb9393014816c944befce328;p=jalview.git diff --git a/test/jalview/io/CrossRef2xmlTests.java b/test/jalview/io/CrossRef2xmlTests.java index ec5855f..2b8a62f 100644 --- a/test/jalview/io/CrossRef2xmlTests.java +++ b/test/jalview/io/CrossRef2xmlTests.java @@ -31,15 +31,21 @@ import jalview.gui.CrossRefAction; import jalview.gui.Desktop; import jalview.gui.Jalview2XML; import jalview.gui.JvOptionPane; +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 junit.extensions.PA; import org.testng.Assert; import org.testng.annotations.BeforeClass; +import org.testng.annotations.DataProvider; import org.testng.annotations.Test; @Test(singleThreaded = true) @@ -54,6 +60,14 @@ public class CrossRef2xmlTests extends Jalview2xmlBase 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 all reachable cross refs from all reachable * crossrefs for one or more fetched db refs. Currently, this test has a known @@ -61,14 +75,22 @@ 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(); - 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 @@ -85,13 +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[][] { { "ENSEMBL", "ENSG00000157764" }, - { "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; @@ -101,7 +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; @@ -113,7 +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); @@ -163,7 +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 @@ -176,20 +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); @@ -237,7 +261,7 @@ public class CrossRef2xmlTests extends Jalview2xmlBase } } - HashMap> xrptypes = new HashMap>(); + HashMap> xrptypes = new HashMap<>(); // first save/verify views. for (AlignmentViewPanel avp : cra_views) { @@ -274,23 +298,25 @@ 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 + "}"; 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 '" @@ -298,7 +324,6 @@ 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 @@ -406,7 +431,7 @@ public class CrossRef2xmlTests extends Jalview2xmlBase pass1++; } } while (pass1 < 3); - } + if (failedXrefMenuItems.size() > 0) { for (String s : failedXrefMenuItems) @@ -437,6 +462,25 @@ 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 * @@ -480,7 +524,7 @@ 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()) { @@ -517,8 +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)