public void SerializeJson(StringBuilder sb)
{
var jsonObject = new JsonObject(sb);
//converting empty alleles to '-'
var refAllele = string.IsNullOrEmpty(ReferenceAllele)? "-":ReferenceAllele;
var altAllele = string.IsNullOrEmpty(AltAllele) ? "-" : AltAllele;
sb.Append(JsonObject.OpenBrace);
jsonObject.AddStringValue("id", ID);
jsonObject.AddStringValue("reviewStatus", ReviewStatusStrings[ReviewStatus]);
jsonObject.AddStringValue("isAlleleSpecific", IsAlleleSpecific, false);
jsonObject.AddStringValues("alleleOrigins", _alleleOrigins);
jsonObject.AddStringValue("refAllele", "N" == refAllele ? null : refAllele);
jsonObject.AddStringValue("altAllele", "N" == altAllele ? null : altAllele);
jsonObject.AddStringValues("phenotypes", Phenotypes);
jsonObject.AddStringValues("medGenIDs", _medgenIds);
jsonObject.AddStringValues("omimIDs", OmimIDs);
jsonObject.AddStringValues("orphanetIDs", OrphanetIDs);
jsonObject.AddStringValue("significance", Significance);
if (LastUpdatedDate != long.MinValue)
{
jsonObject.AddStringValue("lastUpdatedDate", Date.GetDate(LastUpdatedDate));
}
jsonObject.AddStringValues("pubMedIds", PubmedIds?.Select(id => id.ToString()));
sb.Append(JsonObject.CloseBrace);
}
public string GetJsonString()
{
var sb = StringBuilderCache.Acquire();
var jsonObject = new JsonObject(sb);
//converting empty alleles to '-'
var refAllele = string.IsNullOrEmpty(ReferenceAllele) ? "-" : ReferenceAllele;
var altAllele = string.IsNullOrEmpty(AlternateAllele) ? "-" : AlternateAllele;
//the reduced alt allele should never be output
altAllele = SupplementaryAnnotationUtilities.ReverseSaReducedAllele(altAllele);
jsonObject.AddStringValue("id", Id);
jsonObject.AddStringValue("reviewStatus", ReviewStatusStrings[ReviewStatus]);
jsonObject.AddStringValue("isAlleleSpecific", IsAlleleSpecific, false);
jsonObject.AddStringValues("alleleOrigins", AlleleOrigins);
jsonObject.AddStringValue("refAllele", "N" == refAllele ? null : refAllele);
jsonObject.AddStringValue("altAllele", "N" == altAllele ? null : altAllele);
jsonObject.AddStringValues("phenotypes", Phenotypes);
jsonObject.AddStringValues("medGenIds", MedGenIDs);
jsonObject.AddStringValues("omimIds", OmimIDs);
jsonObject.AddStringValues("orphanetIds", OrphanetIDs);
jsonObject.AddStringValue("significance", Significance);
if (LastUpdatedDate != long.MinValue)
{
jsonObject.AddStringValue("lastUpdatedDate", new DateTime(LastUpdatedDate).ToString("yyyy-MM-dd"));
}
jsonObject.AddStringValues("pubMedIds", PubmedIds?.Select(id => id.ToString()));
return(StringBuilderCache.GetStringAndRelease(sb));
}
private List <string[]> GetValues()
{
var values = new List <string[]>
{
//the exact order of adding values has to be preserved. the order is dictated by the json schema
new[] { Id },
new[] { VariationId },
new[] { ClinVarCommon.ReviewStatusStrings[ReviewStatus] },
AlleleOrigins?.ToArray(),
new[] { ClinVarCommon.NormalizeAllele(RefAllele) },
new[] { ClinVarCommon.NormalizeAllele(AltAllele) },
Phenotypes?.ToArray(),
MedGenIds?.ToArray(),
OmimIds?.ToArray(),
OrphanetIds?.ToArray(),
Significances,
new[] { new DateTime(LastUpdatedDate).ToString("yyyy-MM-dd") },
PubmedIds?.OrderBy(x => x).Select(x => x.ToString()).ToArray()
};
return(values);
}
