public patient_result_collections AddResult(patient patient, result_files file, string name, string value, string externalId, string externalSource, DateTime resultedOn)
{
// First, identify the reference phenotype and if it exists
var phenotype = (from pheno in entities.phenotypes
where pheno.name == name && pheno.value == value
select pheno).FirstOrDefault();
if (phenotype == null)
{
phenotype = new phenotype()
{
name = name,
value = value,
external_source = externalSource,
external_id = externalId
};
entities.phenotypes.Add(phenotype);
entities.SaveChanges();
}
// Now add the patient phenotype
var patientPhenotype = new patient_phenotypes()
{
phenotype = phenotype,
resulted_on = resultedOn
};
entities.patient_phenotypes.Add(patientPhenotype);
entities.SaveChanges();
// Add the patient result collection for this entry
var collection = patientRepo.AddCollection(patient, file);
// Finally, link the collection to the phenotype
var member = new patient_result_members()
{
collection_id = collection.id,
member_id = patientPhenotype.id,
member_type = Enums.ResultMemberType.Phenotype,
};
entities.patient_result_members.Add(member);
entities.SaveChanges();
return collection;
}
public phenotype GetPhenotypeByExternalId(phenotype phenotype)
{
var existingPhenotype = (from pheno in entities.phenotypes
where pheno.external_id == phenotype.external_id && pheno.external_source == phenotype.external_source
select pheno).FirstOrDefault();
if (phenotype == null)
{
phenotype = new phenotype()
{
name = phenotype.name,
value = phenotype.value,
external_source = phenotype.external_source,
external_id = phenotype.external_id,
};
entities.phenotypes.Add(phenotype);
entities.SaveChanges();
}
return phenotype;
}
private phenotype CreatePhenotype(Pragma pragma)
{
phenotype phenotype = new phenotype();
var tag = pragma.Tags.FirstOrDefault(x => x.Name == "Ontology");
if (tag != null)
{
phenotype.external_source = tag.Value;
}
tag = pragma.Tags.FirstOrDefault(x => x.Name == "Term");
if (tag != null)
{
phenotype.external_id = tag.Value;
}
tag = pragma.Tags.FirstOrDefault(x => x.Name == "Comment");
if (tag != null)
{
phenotype.name = tag.Value;
}
return phenotype;
}
