public void AddPatientVariantsToCollection(patient_result_collections collection, List<patient_variants> patientVariants)
{
foreach (var variant in patientVariants)
{
var member = new patient_result_members()
{
collection_id = collection.id,
member_id = variant.id,
member_type = Enums.ResultMemberType.Variant,
};
entities.patient_result_members.Add(member);
}
entities.SaveChanges();
}
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 patient_result_collections AddSnps(patient patient, result_files file, DateTime resultedOn, List<SnpResult> snps)
{
// Create a collection
var collection = patientRepo.AddCollection(patient, file);
// Create patient variant entries
List<patient_variants> variants = new List<patient_variants>();
foreach (var snp in snps)
{
var variant = GetVariant(snp.RSID, "dbSNP", snp.Position, snp.Position);
var patientVariant = new patient_variants()
{
patient_id = patient.id,
variant_type = Enums.PatientVariantType.SNP,
reference_id = variant.id,
resulted_on = resultedOn,
value1 = snp.Genotype[0].ToString(),
value2 = snp.Genotype[1].ToString()
};
variants.Add(patientVariant);
}
entities.patient_variants.AddRange(variants);
entities.SaveChanges();
// Finally, link the collection to the SNPs
foreach (var variant in variants)
{
var member = new patient_result_members()
{
collection_id = collection.id,
member_id = variant.id,
member_type = Enums.ResultMemberType.Variant,
};
entities.patient_result_members.Add(member);
}
entities.SaveChanges();
return collection;
}
public patient_result_collections AddStarVariants(patient patient, result_files file, DateTime resultedOn, List<StarVariantResult> stars)
{
// Create a collection
var collection = patientRepo.AddCollection(patient, file);
// Create patient variant entries
List<patient_variants> variants = new List<patient_variants>();
foreach (var star in stars)
{
var gene = AddGene(star.Gene, star.Gene, null, null, null);
var variant = AddVariant(star.Gene, star.Result, "Star Variant", null, null, null, null, null);
string[] splitStars = star.Result.Split(new string[]{"*"}, StringSplitOptions.RemoveEmptyEntries);
var patientVariant = new patient_variants()
{
patient_id = patient.id,
variant_type = Enums.PatientVariantType.StarVariant,
reference_id = variant.id,
resulted_on = resultedOn,
value1 = splitStars[0],
value2 = splitStars[1]
};
variants.Add(patientVariant);
}
entities.patient_variants.AddRange(variants);
entities.SaveChanges();
// Finally, link the collection to the stars
foreach (var variant in variants)
{
var member = new patient_result_members()
{
collection_id = collection.id,
member_id = variant.id,
member_type = Enums.ResultMemberType.Variant,
};
entities.patient_result_members.Add(member);
}
entities.SaveChanges();
return collection;
}