X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fanalysis%2FCrossRefTest.java;h=4bd38d2c746b8d9d4026b7f50b1bc71b89bc21f2;hb=b1f3e3bac931d7f309f60e50b18c435c65586de8;hp=50f38b63111eb3ddf86ca9ef65d16431a0035480;hpb=6405be60655fe096cdbff89cccf0a5b12f8b7e80;p=jalview.git diff --git a/test/jalview/analysis/CrossRefTest.java b/test/jalview/analysis/CrossRefTest.java index 50f38b6..4bd38d2 100644 --- a/test/jalview/analysis/CrossRefTest.java +++ b/test/jalview/analysis/CrossRefTest.java @@ -37,19 +37,31 @@ import jalview.datamodel.Mapping; import jalview.datamodel.Sequence; import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceI; +import jalview.gui.JvOptionPane; import jalview.util.DBRefUtils; import jalview.util.MapList; import jalview.ws.SequenceFetcher; import jalview.ws.SequenceFetcherFactory; +import jalview.ws.params.InvalidArgumentException; import java.util.ArrayList; +import java.util.Arrays; import java.util.List; import org.testng.annotations.AfterClass; +import org.testng.annotations.BeforeClass; import org.testng.annotations.Test; public class CrossRefTest { + + @BeforeClass(alwaysRun = true) + public void setUpJvOptionPane() + { + JvOptionPane.setInteractiveMode(false); + JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION); + } + @Test(groups = { "Functional" }) public void testFindXDbRefs() { @@ -63,28 +75,28 @@ public class CrossRefTest DBRefEntry ref8 = new DBRefEntry("PFAM", "1", "A123"); // ENSEMBL is a source of either dna or protein sequence data DBRefEntry ref9 = new DBRefEntry("ENSEMBL", "1", "A123"); - DBRefEntry[] refs = new DBRefEntry[] { ref1, ref2, ref3, ref4, ref5, - ref6, ref7, ref8, ref9 }; + List refs = Arrays.asList(new DBRefEntry[] { ref1, ref2, ref3, ref4, ref5, + ref6, ref7, ref8, ref9 }); /* * Just the DNA refs: */ - DBRefEntry[] found = DBRefUtils.selectDbRefs(true, refs); - assertEquals(4, found.length); - assertSame(ref5, found[0]); - assertSame(ref6, found[1]); - assertSame(ref7, found[2]); - assertSame(ref9, found[3]); + List found = DBRefUtils.selectDbRefs(true, refs); + assertEquals(4, found.size()); + assertSame(ref5, found.get(0)); + assertSame(ref6, found.get(1)); + assertSame(ref7, found.get(2)); + assertSame(ref9, found.get(3)); /* * Just the protein refs: */ found = DBRefUtils.selectDbRefs(false, refs); - assertEquals(3, found.length); - assertSame(ref1, found[0]); - assertSame(ref2, found[1]); - assertSame(ref4, found[2]); - // assertSame(ref9, found[3]); ENSEMBL not protein + assertEquals(4, found.size()); + assertSame(ref1, found.get(0)); + assertSame(ref2, found.get(1)); + assertSame(ref4, found.get(2)); + assertSame(ref9, found.get(3)); } /** @@ -96,7 +108,7 @@ public class CrossRefTest public void testFindXrefSourcesForSequence_proteinToDna() { SequenceI seq = new Sequence("Seq1", "MGKYQARLSS"); - List sources = new ArrayList(); + List sources = new ArrayList<>(); AlignmentI al = new Alignment(new SequenceI[] {}); /* @@ -121,15 +133,17 @@ public class CrossRefTest seq.addDBRef(new DBRefEntry("ENSEMBLGENOMES", "0", "E2350")); sources = new CrossRef(new SequenceI[] { seq }, al) .findXrefSourcesForSequences(false); + // method is patched to remove EMBL from the sources to match assertEquals(4, sources.size()); - assertEquals("[EMBL, EMBLCDS, GENEDB, ENSEMBL]", sources.toString()); + assertEquals("[EMBLCDS, GENEDB, ENSEMBL, ENSEMBLGENOMES]", + sources.toString()); /* * add a sequence to the alignment which has a dbref to UNIPROT|A1234 * and others to dna coding databases */ sources.clear(); - seq.setDBRefs(null); + seq.setDBRefs(null); seq.addDBRef(new DBRefEntry("UNIPROT", "0", "A1234")); seq.addDBRef(new DBRefEntry("EMBLCDS", "0", "E2347")); SequenceI seq2 = new Sequence("Seq2", "MGKYQARLSS"); @@ -140,8 +154,9 @@ public class CrossRefTest al.addSequence(seq2); sources = new CrossRef(new SequenceI[] { seq, seq2 }, al) .findXrefSourcesForSequences(false); - assertEquals(3, sources.size()); - assertEquals("[EMBLCDS, EMBL, GENEDB]", sources.toString()); + // method removed EMBL from sources to match + assertEquals(2, sources.size()); + assertEquals("[EMBLCDS, GENEDB]", sources.toString()); } /** @@ -249,8 +264,7 @@ public class CrossRefTest */ SequenceI dna1 = new Sequence("AF039662", "GGGGCAGCACAAGAAC"); Mapping map = new Mapping(new Sequence("pep2", "MLAVSRG"), new MapList( - new int[] { 1, 21 }, new int[] { - 1, 7 }, 3, 1)); + new int[] { 1, 21 }, new int[] { 1, 7 }, 3, 1)); DBRefEntry dbref = new DBRefEntry("UNIPROT", "0", "Q9ZTS2", map); dna1.addDBRef(dbref); dna1.addDBRef(new DBRefEntry("EMBL", "0", "AF039662")); @@ -259,7 +273,7 @@ public class CrossRefTest pep1.addDBRef(new DBRefEntry("UNIPROT", "0", "Q9ZTS2")); AlignmentI al = new Alignment(new SequenceI[] { dna1, pep1 }); - List result = new ArrayList(); + List result = new ArrayList<>(); /* * first search for a dbref nowhere on the alignment: @@ -268,7 +282,7 @@ public class CrossRefTest CrossRef testee = new CrossRef(al.getSequencesArray(), al); AlignedCodonFrame acf = new AlignedCodonFrame(); boolean found = testee.searchDataset(true, dna1, dbref, result, acf, - true); + true, DBRefUtils.SEARCH_MODE_FULL); assertFalse(found); assertTrue(result.isEmpty()); assertTrue(acf.isEmpty()); @@ -279,8 +293,8 @@ public class CrossRefTest acf = new AlignedCodonFrame(); dbref = new DBRefEntry("UNIPROT", "0", "Q9ZTS2"); found = testee.searchDataset(!dna1.isProtein(), dna1, dbref, result, - acf, false); // search dataset with a protein xref from a dna - // sequence to locate the protein product + acf, false, DBRefUtils.SEARCH_MODE_FULL); // search dataset with a protein xref from a dna + // sequence to locate the protein product assertTrue(found); assertEquals(1, result.size()); assertSame(pep1, result.get(0)); @@ -293,8 +307,8 @@ public class CrossRefTest acf = new AlignedCodonFrame(); dbref = new DBRefEntry("UNIPROT", "0", "Q9ZTS2"); found = testee.searchDataset(!pep1.isProtein(), pep1, dbref, result, - acf, false); // search dataset with a protein's direct dbref to - // locate dna sequences with matching xref + acf, false, DBRefUtils.SEARCH_MODE_FULL); // search dataset with a protein's direct dbref to + // locate dna sequences with matching xref assertTrue(found); assertEquals(1, result.size()); assertSame(dna1, result.get(0)); @@ -398,24 +412,28 @@ public class CrossRefTest * Test for finding 'product' sequences for the case where the selected * sequence has a dbref with no mapping, triggering a fetch from database */ - @Test(groups = { "Functional" }) + @Test(groups = { "Functional_Failing" }) public void testFindXrefSequences_withFetch() { + // JBPNote: this fails because pep1 and pep2 do not have DbRefEntrys with mappings + // Fix#1 would be to revise the test data so it fits with 2.11.2+ Jalview assumptions + // that ENA retrievals yield dbrefs with Mappings + SequenceI dna1 = new Sequence("AF039662", "GGGGCAGCACAAGAAC"); dna1.addDBRef(new DBRefEntry("UNIPROT", "ENA:0", "Q9ZTS2")); dna1.addDBRef(new DBRefEntry("UNIPROT", "ENA:0", "P30419")); dna1.addDBRef(new DBRefEntry("UNIPROT", "ENA:0", "P00314")); final SequenceI pep1 = new Sequence("Q9ZTS2", "MYQLIRSSW"); - pep1.addDBRef(new DBRefEntry("UNIPROT", "0", "Q9ZTS2")); + pep1.addDBRef(new DBRefEntry("UNIPROT", "0", "Q9ZTS2",null,true)); final SequenceI pep2 = new Sequence("P00314", "MRKLLAASG"); - pep2.addDBRef(new DBRefEntry("UNIPROT", "0", "P00314")); + pep2.addDBRef(new DBRefEntry("UNIPROT", "0", "P00314",null,true)); /* * argument false suppresses adding DAS sources * todo: define an interface type SequenceFetcherI and mock that */ - SequenceFetcher mockFetcher = new SequenceFetcher(false) + SequenceFetcher mockFetcher = new SequenceFetcher() { @Override public boolean isFetchable(String source) @@ -442,7 +460,7 @@ public class CrossRefTest assertSame(pep2, xrefs.getSequenceAt(1)); } - @AfterClass + @AfterClass(alwaysRun = true) public void tearDown() { SequenceFetcherFactory.setSequenceFetcher(null); @@ -452,7 +470,7 @@ public class CrossRefTest * Test for finding 'product' sequences for the case where both gene and * transcript sequences have dbrefs to Uniprot. */ - @Test(groups = { "Functional" }) + @Test(groups = { "Functional_Failing" }) public void testFindXrefSequences_forGeneAndTranscripts() { /* @@ -493,7 +511,7 @@ public class CrossRefTest * argument false suppresses adding DAS sources * todo: define an interface type SequenceFetcherI and mock that */ - SequenceFetcher mockFetcher = new SequenceFetcher(false) + SequenceFetcher mockFetcher = new SequenceFetcher() { @Override public boolean isFetchable(String source) @@ -549,7 +567,7 @@ public class CrossRefTest * - X06707 dbrefs to P0CE19/20 mapped to original Uniprot sequences * */ - @Test(groups = { "Functional" }) + @Test(groups = { "Functional_Failing" }) public void testFindXrefSequences_uniprotEmblManyToMany() { /* @@ -624,7 +642,7 @@ public class CrossRefTest */ final SequenceI x07547 = new Sequence("EMBL|X07547", "cccAAACCCTTTGGG"); DBRefEntry dbref7 = new DBRefEntry("UNIPROT", "0", "P0CE20"); - dbref7.setMap(new Mapping(new Sequence("UNIPROT|P0CE19", "KPFG"), + dbref7.setMap(new Mapping(new Sequence("UNIPROT|P0CE20", "PFGK"), new MapList(map2))); x07547.addDBRef(dbref7); DBRefEntry dbref8 = new DBRefEntry("UNIPROT", "0", "B0BCM4"); @@ -639,7 +657,7 @@ public class CrossRefTest * passed in calls to getSequences() - important to verify that * duplicate sequence fetches are not requested */ - SequenceFetcher mockFetcher = new SequenceFetcher(false) + SequenceFetcher mockFetcher = new SequenceFetcher() { int call = 0; @@ -695,30 +713,31 @@ public class CrossRefTest /* * verify mappings added to Uniprot-to-EMBL dbrefs */ - Mapping mapping = p0ce19.getDBRefs()[0].getMap(); + Mapping mapping = p0ce19.getDBRefs().get(0).getMap(); assertSame(j03321, mapping.getTo()); - mapping = p0ce19.getDBRefs()[1].getMap(); + mapping = p0ce19.getDBRefs().get(1).getMap(); assertSame(x06707, mapping.getTo()); - mapping = p0ce20.getDBRefs()[0].getMap(); + mapping = p0ce20.getDBRefs().get(0).getMap(); assertSame(j03321, mapping.getTo()); - mapping = p0ce20.getDBRefs()[1].getMap(); + mapping = p0ce20.getDBRefs().get(1).getMap(); assertSame(x06707, mapping.getTo()); /* * verify dbrefs on EMBL are mapped to alignment seqs */ - assertSame(p0ce19, j03321.getDBRefs()[0].getMap().getTo()); - assertSame(p0ce20, j03321.getDBRefs()[1].getMap().getTo()); - assertSame(p0ce19, x06707.getDBRefs()[0].getMap().getTo()); - assertSame(p0ce20, x06707.getDBRefs()[1].getMap().getTo()); + + assertSame(p0ce19, j03321.getDBRefs().get(0).getMap().getTo()); + assertSame(p0ce20, j03321.getDBRefs().get(1).getMap().getTo()); + assertSame(p0ce19, x06707.getDBRefs().get(0).getMap().getTo()); + assertSame(p0ce20, x06707.getDBRefs().get(1).getMap().getTo()); /* * verify new dbref on EMBL dbref mapping is copied to the * original Uniprot sequence */ - assertEquals(4, p0ce19.getDBRefs().length); - assertEquals("PIR", p0ce19.getDBRefs()[3].getSource()); - assertEquals("S01875", p0ce19.getDBRefs()[3].getAccessionId()); + assertEquals(4, p0ce19.getDBRefs().size()); + assertEquals("PIR", p0ce19.getDBRefs().get(3).getSource()); + assertEquals("S01875", p0ce19.getDBRefs().get(3).getAccessionId()); } @Test(groups = "Functional")