From fb0359bd129a8f615f59817424bce2cc0d8fb71d Mon Sep 17 00:00:00 2001 From: gmungoc Date: Mon, 4 Feb 2019 12:18:29 +0000 Subject: [PATCH] JAL-3143 update unit test for ID -> id change --- test/jalview/analysis/AlignmentUtilsTests.java | 50 +++++++++++++----------- 1 file changed, 27 insertions(+), 23 deletions(-) diff --git a/test/jalview/analysis/AlignmentUtilsTests.java b/test/jalview/analysis/AlignmentUtilsTests.java index a7a7d34..70ae6a0 100644 --- a/test/jalview/analysis/AlignmentUtilsTests.java +++ b/test/jalview/analysis/AlignmentUtilsTests.java @@ -2040,44 +2040,48 @@ public class AlignmentUtilsTests String dbSnp = "dbSNP"; String cosmic = "COSMIC"; + /* + * NB setting "id" (as returned by Ensembl for features in JSON format); + * previously "ID" (as returned for GFF3 format) + */ SequenceFeature sf1 = new SequenceFeature("sequence_variant", "", 1, 1, 0f, ensembl); sf1.setValue("alleles", "A,G"); // AAA -> GAA -> K/E - sf1.setValue("ID", "var1.125A>G"); + sf1.setValue("id", "var1.125A>G"); SequenceFeature sf2 = new SequenceFeature("sequence_variant", "", 1, 1, 0f, dbSnp); sf2.setValue("alleles", "A,C"); // AAA -> CAA -> K/Q - sf2.setValue("ID", "var2"); + sf2.setValue("id", "var2"); sf2.setValue("clinical_significance", "Dodgy"); SequenceFeature sf3 = new SequenceFeature("sequence_variant", "", 1, 1, 0f, dbSnp); sf3.setValue("alleles", "A,T"); // AAA -> TAA -> stop codon - sf3.setValue("ID", "var3"); + sf3.setValue("id", "var3"); sf3.setValue("clinical_significance", "Bad"); SequenceFeature sf4 = new SequenceFeature("sequence_variant", "", 3, 3, 0f, cosmic); sf4.setValue("alleles", "A,G"); // AAA -> AAG synonymous - sf4.setValue("ID", "var4"); + sf4.setValue("id", "var4"); sf4.setValue("clinical_significance", "None"); SequenceFeature sf5 = new SequenceFeature("sequence_variant", "", 3, 3, 0f, ensembl); sf5.setValue("alleles", "A,T"); // AAA -> AAT -> K/N - sf5.setValue("ID", "sequence_variant:var5"); // prefix gets stripped off + sf5.setValue("id", "sequence_variant:var5"); // prefix gets stripped off sf5.setValue("clinical_significance", "Benign"); SequenceFeature sf6 = new SequenceFeature("sequence_variant", "", 6, 6, 0f, dbSnp); sf6.setValue("alleles", "T,C"); // TTT -> TTC synonymous - sf6.setValue("ID", "var6"); + sf6.setValue("id", "var6"); SequenceFeature sf7 = new SequenceFeature("sequence_variant", "", 8, 8, 0f, cosmic); sf7.setValue("alleles", "C,A,G"); // CCC -> CAC,CGC -> P/H/R - sf7.setValue("ID", "var7"); + sf7.setValue("id", "var7"); sf7.setValue("clinical_significance", "Good"); List codon1Variants = new ArrayList<>(); @@ -2149,9 +2153,9 @@ public class AlignmentUtilsTests assertEquals(1, sf.getEnd()); assertEquals("nonsynonymous_variant", sf.getType()); assertEquals("p.Lys1Asn", sf.getDescription()); - assertEquals("var5", sf.getValue("ID")); + assertEquals("var5", sf.getValue("id")); assertEquals("Benign", sf.getValue("clinical_significance")); - assertEquals("ID=var5;clinical_significance=Benign", + assertEquals("id=var5;clinical_significance=Benign", sf.getAttributes()); assertEquals(1, sf.links.size()); assertEquals( @@ -2165,9 +2169,9 @@ public class AlignmentUtilsTests assertEquals(1, sf.getEnd()); assertEquals("nonsynonymous_variant", sf.getType()); assertEquals("p.Lys1Gln", sf.getDescription()); - assertEquals("var2", sf.getValue("ID")); + assertEquals("var2", sf.getValue("id")); assertEquals("Dodgy", sf.getValue("clinical_significance")); - assertEquals("ID=var2;clinical_significance=Dodgy", sf.getAttributes()); + assertEquals("id=var2;clinical_significance=Dodgy", sf.getAttributes()); assertEquals(1, sf.links.size()); assertEquals( "p.Lys1Gln var2|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var2", @@ -2180,9 +2184,9 @@ public class AlignmentUtilsTests assertEquals(1, sf.getEnd()); assertEquals("nonsynonymous_variant", sf.getType()); assertEquals("p.Lys1Glu", sf.getDescription()); - assertEquals("var1.125A>G", sf.getValue("ID")); + assertEquals("var1.125A>G", sf.getValue("id")); assertNull(sf.getValue("clinical_significance")); - assertEquals("ID=var1.125A>G", sf.getAttributes()); + assertEquals("id=var1.125A>G", sf.getAttributes()); assertEquals(1, sf.links.size()); // link to variation is urlencoded assertEquals( @@ -2196,9 +2200,9 @@ public class AlignmentUtilsTests assertEquals(1, sf.getEnd()); assertEquals("stop_gained", sf.getType()); assertEquals("Aaa/Taa", sf.getDescription()); - assertEquals("var3", sf.getValue("ID")); + assertEquals("var3", sf.getValue("id")); assertEquals("Bad", sf.getValue("clinical_significance")); - assertEquals("ID=var3;clinical_significance=Bad", sf.getAttributes()); + assertEquals("id=var3;clinical_significance=Bad", sf.getAttributes()); assertEquals(1, sf.links.size()); assertEquals( "Aaa/Taa var3|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var3", @@ -2211,9 +2215,9 @@ public class AlignmentUtilsTests assertEquals(1, sf.getEnd()); assertEquals("synonymous_variant", sf.getType()); assertEquals("aaA/aaG", sf.getDescription()); - assertEquals("var4", sf.getValue("ID")); + assertEquals("var4", sf.getValue("id")); assertEquals("None", sf.getValue("clinical_significance")); - assertEquals("ID=var4;clinical_significance=None", sf.getAttributes()); + assertEquals("id=var4;clinical_significance=None", sf.getAttributes()); assertEquals(1, sf.links.size()); assertEquals( "aaA/aaG var4|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var4", @@ -2226,9 +2230,9 @@ public class AlignmentUtilsTests assertEquals(2, sf.getEnd()); assertEquals("synonymous_variant", sf.getType()); assertEquals("ttT/ttC", sf.getDescription()); - assertEquals("var6", sf.getValue("ID")); + assertEquals("var6", sf.getValue("id")); assertNull(sf.getValue("clinical_significance")); - assertEquals("ID=var6", sf.getAttributes()); + assertEquals("id=var6", sf.getAttributes()); assertEquals(1, sf.links.size()); assertEquals( "ttT/ttC var6|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var6", @@ -2242,9 +2246,9 @@ public class AlignmentUtilsTests assertEquals(3, sf.getEnd()); assertEquals("nonsynonymous_variant", sf.getType()); assertEquals("p.Pro3Arg", sf.getDescription()); - assertEquals("var7", sf.getValue("ID")); + assertEquals("var7", sf.getValue("id")); assertEquals("Good", sf.getValue("clinical_significance")); - assertEquals("ID=var7;clinical_significance=Good", sf.getAttributes()); + assertEquals("id=var7;clinical_significance=Good", sf.getAttributes()); assertEquals(1, sf.links.size()); assertEquals( "p.Pro3Arg var7|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var7", @@ -2257,9 +2261,9 @@ public class AlignmentUtilsTests assertEquals(3, sf.getEnd()); assertEquals("nonsynonymous_variant", sf.getType()); assertEquals("p.Pro3His", sf.getDescription()); - assertEquals("var7", sf.getValue("ID")); + assertEquals("var7", sf.getValue("id")); assertEquals("Good", sf.getValue("clinical_significance")); - assertEquals("ID=var7;clinical_significance=Good", sf.getAttributes()); + assertEquals("id=var7;clinical_significance=Good", sf.getAttributes()); assertEquals(1, sf.links.size()); assertEquals( "p.Pro3His var7|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var7", -- 1.7.10.2