X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FCrossRef2xmlTests.java;h=53a0acb864ace38b2ef6d5c462cf9cc49ce076ff;hb=8669979d57e2019889afaefafe65b945ae7c172d;hp=9e24262c89a38b53a5467e253b0ec4c85106913c;hpb=54dcb58375e9783c7bd4b793acd0b0aa485556ba;p=jalview.git diff --git a/test/jalview/io/CrossRef2xmlTests.java b/test/jalview/io/CrossRef2xmlTests.java index 9e24262..53a0acb 100644 --- a/test/jalview/io/CrossRef2xmlTests.java +++ b/test/jalview/io/CrossRef2xmlTests.java @@ -29,19 +29,25 @@ 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 { @@ -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 @@ -61,13 +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<>(); + // 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 @@ -84,13 +107,12 @@ 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[][] { { "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; @@ -100,7 +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; @@ -112,7 +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); @@ -162,7 +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 @@ -180,15 +204,16 @@ 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); @@ -280,16 +305,18 @@ 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 '" @@ -297,7 +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 @@ -405,7 +431,7 @@ public class CrossRef2xmlTests extends Jalview2xmlBase pass1++; } } while (pass1 < 3); - } + if (failedXrefMenuItems.size() > 0) { for (String s : failedXrefMenuItems) @@ -436,6 +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 * @@ -516,8 +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)