private void SetupXlMod() { var parser = new XlmodOboParser(); XlmodTerm[] modifications = parser.Parse(XlmodOboParserTest.GetFilePath()).ToArray(); _xlmodLookup = XlModModificationLookup.CreateFromModifications(modifications, _elementProvider); }
public void BasicTest() { var parser = new XlmodOboParser(); var result = new List <XlmodTerm>(parser.Parse(GetFilePath())); Assert.IsNotNull(result); Assert.AreEqual(1102, result.Count); Assert.AreEqual("XLMOD:00004", result[4].Id); Assert.AreEqual("cross-linking entity", result[1].Name); Assert.AreEqual("Dead-end modification resulting from a cross-linker reagent reacting only with one peptide.", result[2].Definition); Assert.IsNull(result[0].IsA); Assert.IsNull(result[0].PropertyValues); Assert.IsNull(result[0].Relationships); Assert.IsNull(result[0].Synonyms); // External References Assert.IsNotNull(result[166].ExternalReferences); Assert.AreEqual(1, result[166].ExternalReferences.Count); Assert.AreEqual("21557289", result[166].ExternalReferences.Single(x => x.Name == "PMID").Id); var term7091 = result.Single(x => x.Id == "XLMOD:07091"); Assert.IsNotNull(term7091.ExternalReferences); Assert.AreEqual(4, term7091.ExternalReferences.Count); Assert.AreEqual("18704-37-5", term7091.ExternalReferences.Single(x => x.Name == "CAS").Id); Assert.AreEqual("29220", term7091.ExternalReferences.Single(x => x.Name == "PubChem_Compound").Id); Assert.AreEqual("27177", term7091.ExternalReferences.Single(x => x.Name == "ChemSpiderID").Id); Assert.AreEqual("CB8329163", term7091.ExternalReferences.Single(x => x.Name == "ChemicalBookNo").Id); // Is A Assert.IsNotNull(result[4].IsA); Assert.AreEqual(1, result[4].IsA.Count); // Property values Assert.IsNotNull(result[101].PropertyValues); Assert.AreEqual(2, result[101].PropertyValues.Count); Assert.AreEqual("(K,Protein N-term)", result[101].PropertyValues.Single(x => x.Name == "specificities").Value); Assert.AreEqual("xsd:string", result[101].PropertyValues.Single(x => x.Name == "secondarySpecificities").DataType); // Relationships Assert.IsNotNull(result[103].Relationships); Assert.AreEqual(2, result[103].Relationships.Count); Assert.AreEqual("XLMOD:00149", result[103].Relationships.Single(x => x.Type == "is_activatable").Id); Assert.AreEqual("XLMOD:00037", result[103].Relationships.Single(x => x.Type == "is_reactive_with").Id); // Synonyms Assert.IsNotNull(result[102].Synonyms); Assert.AreEqual(1, result[102].Synonyms.Count); Assert.AreEqual("N-hydroxysulfosuccinimide ester", result[102].Synonyms.Single().Text); Assert.AreEqual("EXACT", result[102].Synonyms.Single().Type); var term2001 = result.Single(x => x.Id == "XLMOD:02001"); Assert.AreEqual("EXACT", term2001.Synonyms.Single(x => x.Text == "1,1'-[(1,8-Dioxooctane-1,8-diyl)bis(oxy)]dipyrrolidine-2,5-dione").Type); }