public virtual NeisseriaPubMlstIsolate GetIsolateById(int id)
{
try
{
var isolateJson = JObject.Parse(callGetUrl($"{BaseUrl}/{id}"));
var allelesJson = JObject.Parse(callGetUrl($"{BaseUrl}/{id}/allele_ids?return_all=1"));
var alleles = ConvertToDictionary(allelesJson.GetValue("allele_ids"));
var isolate = new NeisseriaPubMlstIsolate
{
PubMlstId = id,
PorAVr1 = alleles.Get(PorAVr1, ""),
PorAVr2 = alleles.Get(PorAVr2, ""),
FetAVr = alleles.Get(FetAVr, ""),
PorB = alleles.Get(PorB, ""),
Fhbp = alleles.Get(Fhbp, ""),
Nhba = alleles.Get(NhbaPeptide, ""),
NadA = alleles.Get(NadaPeptide, ""),
PenA = alleles.Get(PenA, ""),
GyrA = alleles.Get(GyrA, ""),
ParC = alleles.Get(Neis1525, ""),
ParE = alleles.Get(Neis1600, ""),
RpoB = alleles.Get(RpoB, ""),
RplF = alleles.Get(RplF, ""),
};
var fields = isolateJson.GetValue("schemes")?.First["fields"];
if (fields != null)
{
isolate.SequenceType = fields[SequenceType]?.Value <string>();
isolate.ClonalComplex = fields[ClonalComplex]?.Value <string>();
}
var phenotypic = isolateJson["phenotypic"];
if (phenotypic != null)
{
isolate.BexseroReactivity = phenotypic.Value <string>(BexseroReactivity);
isolate.TrumenbaReactivity = phenotypic.Value <string>(TrumenbaReactivity);
}
return(isolate);
}
catch (WebException e)
{
Log.Error(e, "$Failed to call PubMLST REST API.");
return(null);
}
}
private NeisseriaPubMlstIsolate CreateOrUpdatePubMlstIsolate(MeningoIsolate isolate, NeisseriaPubMlstIsolate pubMlstIsolate)
{
//TODO fix this duplication from MeningoIsolateController and try to find a
//mapping framework which does not mess with EntityFramework context as automapper
var pubMlstIsolateFromDatabase =
_db.NeisseriaPubMlstIsolates.SingleOrDefault(n =>
n.PubMlstId == pubMlstIsolate.PubMlstId);
if (pubMlstIsolateFromDatabase == null)
{
pubMlstIsolateFromDatabase = pubMlstIsolate;
_db.NeisseriaPubMlstIsolates.Add(pubMlstIsolateFromDatabase);
}
else
{
pubMlstIsolateFromDatabase.PorAVr1 = pubMlstIsolate.PorAVr1;
pubMlstIsolateFromDatabase.PorAVr2 = pubMlstIsolate.PorAVr2;
pubMlstIsolateFromDatabase.FetAVr = pubMlstIsolate.FetAVr;
pubMlstIsolateFromDatabase.PorB = pubMlstIsolate.PorB;
pubMlstIsolateFromDatabase.Fhbp = pubMlstIsolate.Fhbp;
pubMlstIsolateFromDatabase.Nhba = pubMlstIsolate.Nhba;
pubMlstIsolateFromDatabase.NadA = pubMlstIsolate.NadA;
pubMlstIsolateFromDatabase.PenA = pubMlstIsolate.PenA;
pubMlstIsolateFromDatabase.GyrA = pubMlstIsolate.GyrA;
pubMlstIsolateFromDatabase.ParC = pubMlstIsolate.ParC;
pubMlstIsolateFromDatabase.ParE = pubMlstIsolate.ParE;
pubMlstIsolateFromDatabase.RpoB = pubMlstIsolate.RpoB;
pubMlstIsolateFromDatabase.RplF = pubMlstIsolate.RplF;
pubMlstIsolateFromDatabase.SequenceType = pubMlstIsolate.SequenceType;
pubMlstIsolateFromDatabase.ClonalComplex = pubMlstIsolate.ClonalComplex;
pubMlstIsolateFromDatabase.BexseroReactivity = pubMlstIsolate.BexseroReactivity;
pubMlstIsolateFromDatabase.TrumenbaReactivity = pubMlstIsolate.TrumenbaReactivity;
}
isolate.NeisseriaPubMlstIsolate = pubMlstIsolateFromDatabase;
return(pubMlstIsolateFromDatabase);
}
public MeningoIsolateViewModel()
{
EpsilometerTestViewModels = new List <EpsilometerTestViewModel>();
NeisseriaPubMlstIsolate = new NeisseriaPubMlstIsolate();
Report = new string[0];
}
