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);
}
