private static List <string> GetSignificances(XElement interpretations)
{
if (interpretations == null || interpretations.IsEmpty)
{
return(null);
}
var significanceList = new List <string>();
foreach (var interpretation in interpretations.Elements(InterpretationTag))
{
var type = interpretation.Attribute(TypeTag)?.Value;
if (type == null || type != "Clinical significance")
{
continue;
}
var significanceString = interpretation.Element(DescriptionTag)?.Value.ToLower();
if (significanceString == null)
{
continue;
}
var significances = ClinVarCommon.GetSignificances(significanceString, null);
foreach (var significance in significances)
{
if (!ClinVarCommon.ValidPathogenicity.Contains(significance))
{
throw new InvalidDataException($"Invalid clinical significance found. Observed: {significance}");
}
significanceList.Add(significance);
}
}
return(significanceList);
}
public string GetJsonString()
{
var sb = StringBuilderCache.Acquire();
var jsonObject = new JsonObject(sb);
jsonObject.AddStringValue("id", $"{_accession}.{_version}");
jsonObject.AddStringValue("reviewStatus", ClinVarCommon.ReviewStatusStrings[_reviewStatus]);
jsonObject.AddStringValues("significance", _significances);
jsonObject.AddStringValue("refAllele", ClinVarCommon.NormalizeAllele(RefAllele));
jsonObject.AddStringValue("altAllele", ClinVarCommon.NormalizeAllele(AltAllele));
jsonObject.AddStringValue("lastUpdatedDate", _lastUpdatedDate.ToString("yyyy-MM-dd"));
return(StringBuilderCache.GetStringAndRelease(sb));
}
private void GetClinicalSignificance(XElement xElement)
{
if (xElement == null || xElement.IsEmpty)
{
return;
}
_reviewStatus = xElement.Element(ReviewStatusTag)?.Value;
var description = xElement.Element(DescriptionTag)?.Value;
var explanation = xElement.Element(ExplanationTag)?.Value;
_significances = ClinVarCommon.GetSignificances(description, explanation);
ValidateSignificance(_significances);
}
