public patient_result_collections AddCollection(patient patient, result_files file)
{
// Add the patient result collection for this entry
var collection = new patient_result_collections()
{
patient_id = patient.id,
received_on = DateTime.Now,
result_file_id = file.id
};
entities.patient_result_collections.Add(collection);
entities.SaveChanges();
return collection;
}
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 AddPatient(string mrn, string mrnSource, string firstName, string lastName, DateTime? dateOfBirth)
{
var result = (from existingPatient in entities.patients
where existingPatient.external_source == mrnSource && existingPatient.external_id == mrn
select existingPatient).FirstOrDefault();
if (result == null)
{
patient newPatient = new patient()
{
external_source = mrnSource,
external_id = mrn,
date_of_birth = dateOfBirth,
first_name = firstName,
last_name = lastName
};
entities.patients.Add(newPatient);
entities.SaveChanges();
result = newPatient;
}
return result;
}
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;
}
public override void LoadData(string filePath)
{
var vcfParser = new VCFParser(filePath);
var header = vcfParser.Header;
var collectionInformationList = new List<patient_variant_information>();
var patient = new patient();
// We pull out all of the metadata from the header (all lines) and write them as information
// lines associated with this result.
foreach (var headerItem in header.MetaDataInInputOrder)
{
if (headerItem.Key == "individual-id")
{
var individualParts = headerItem.Value.Replace("<", "").Replace(">", "").Split(new char[] { ',' });
var individualData = individualParts.Select(x => x.Split(new char[] { '=' })).ToArray();
var mrnParts = individualData.FirstOrDefault(x => x[0] == "Dbxref")[1].Split(':');
patient = patientRepo.AddPatient(mrnParts[1], mrnParts[0],
individualData.FirstOrDefault(x => x[0] == "First_name")[1],
individualData.FirstOrDefault(x => x[0] == "Last_name")[1],
DateTime.Parse(individualData.FirstOrDefault(x => x[0] == "DOB")[1]));
}
else if (headerItem.GetType() == typeof(VCFInfoHeaderLine))
{
var info = headerItem as VCFInfoHeaderLine;
collectionInformationList.Add(AddHeaderInformation(string.Format("VCF:{0}", headerItem.Key), CleanHeaderValue("INFO", info.ToString())));
}
else if (headerItem.GetType() == typeof(VCFFilterHeaderLine))
{
var filter = headerItem as VCFFilterHeaderLine;
collectionInformationList.Add(AddHeaderInformation(string.Format("VCF:{0}", headerItem.Key), CleanHeaderValue("FILTER", filter.ToString())));
}
else if (headerItem.GetType() == typeof(VCFFormatHeaderLine))
{
var format = headerItem as VCFFormatHeaderLine;
collectionInformationList.Add(AddHeaderInformation(string.Format("VCF:{0}", headerItem.Key), CleanHeaderValue("FORMAT", format.ToString())));
}
else
{
collectionInformationList.Add(AddHeaderInformation(string.Format("VCF:{0}", headerItem.Key), headerItem.Value));
}
}
var reference = header.MetaDataInInputOrder.First(x => x.Key == "reference").Value;
DateTime? resultDate = DateTime.ParseExact(header.MetaDataInInputOrder.First(x => x.Key == "fileDate").Value,
"yyyyMMdd", CultureInfo.InvariantCulture, DateTimeStyles.None);
var patientVariants = new List<patient_variants>();
var featureInformationList = new Dictionary<patient_variants, List<patient_variant_information>>();
while (vcfParser.MoveNext())
{
var current = vcfParser.Current;
var variant = variantRepo.AddVariant(null, current.ID, "dbSNP",
current.Chr, current.Start, current.End,
reference, current.Reference.BaseString);
var patientVariant = new patient_variants()
{
patient_id = patient.id,
reference_id = variant.id,
resulted_on = resultDate,
variant_type = Enums.PatientVariantType.SNP
};
SetVariantValues(patientVariant, current);
patientVariants.Add(patientVariant);
var attributeList = new List<patient_variant_information>();
foreach (var attribute in current.Attributes)
{
attributeList.Add(AddVariantInformation(string.Format("VCF:{0}", attribute.Key), attribute.Value.ToString()));
}
if (current.FiltersMaybeNull != null)
{
foreach (var filter in current.FiltersMaybeNull)
{
attributeList.Add(AddVariantInformation("VCF:Filter", filter));
}
}
foreach (var genotype in current.Genotypes)
{
attributeList.Add(AddVariantInformation("VCF:Genotype", genotype.ToMHGRString()));
}
attributeList.Add(AddVariantInformation("VCF:Quality", current.PhredScaledQual.ToString()));
attributeList.Add(AddVariantInformation("VCF:Filter", string.Join(",", current.Filters.ToArray())));
featureInformationList.Add(patientVariant, attributeList);
}
// Save the collection to get its ID
var source = sourceRepo.AddSource("VCF", "VCF file");
var file = AddResultFile(filePath, source);
var collection = patientRepo.AddCollection(patient, file);
// Save the collection-level header data
collectionInformationList.ForEach(x => x.item_id = collection.id);
variantRepo.AddPatientVariantInformationList(collectionInformationList);
variantRepo.AddPatientVariants(patientVariants);
// Save the individual attributes associated with each feature.
// Must be done after the patient variants are written to DB (above), since we
// rely on the ID being set.
foreach (var pair in featureInformationList)
{
foreach (var attribute in pair.Value)
{
attribute.item_id = pair.Key.id;
}
variantRepo.AddPatientVariantInformationList(pair.Value);
}
variantRepo.AddPatientVariantsToCollection(collection, patientVariants);
featureInformationList.Clear();
collectionInformationList.Clear();
patientVariants.Clear();
}
