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;
}
protected result_files AddResultFile(string filePath, result_sources source)
{
string hash = GetFileHash(filePath);
var file = new result_files()
{
md5 = hash,
name = filePath,
received_on = DateTime.Now,
result_source_id = source.id
};
return fileRepo.AddResultFile(file);
}
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;
}
public result_files AddResultFile(result_files file)
{
entities.result_files.Add(file);
entities.SaveChanges();
return file;
}
private List<string> GetPhenotypeDetails(result_files file, string phenotype)
{
List<string> details = new List<string>();
var geneIds = GetGeneFilterForPhenotype(phenotype);
if (geneIds == null)
{
return details;
}
foreach (var collection in file.patient_result_collections)
{
foreach (var member in collection.patient_result_members)
{
switch (member.member_type)
{
case Enums.ResultMemberType.Phenotype:
var patientPhenotype = entities.patient_phenotypes.Where(x => x.id == member.member_id).FirstOrDefault();
details.Add(string.Format("<div>The phenotype {0} {1} was resulted on {2} <small>{3} {4}</small></div>",
patientPhenotype.phenotype.name, patientPhenotype.phenotype.value, patientPhenotype.resulted_on.Value.ToShortDateString(), patientPhenotype.phenotype.external_source, patientPhenotype.phenotype.external_id));
break;
case Enums.ResultMemberType.Variant:
StringBuilder builder = new StringBuilder();
var patientVariant = entities.patient_variants.Where(x => x.id == member.member_id).FirstOrDefault();
variant variant = null;
switch (patientVariant.variant_type)
{
case Enums.PatientVariantType.SNP:
variant = entities.variants.Where(x =>
x.id == patientVariant.reference_id && x.gene_id.HasValue && geneIds.Contains(x.gene_id.Value)).FirstOrDefault();
if (variant != null)
{
builder.AppendFormat("<div class='variant'>{0}: ", variant.external_id);
builder.AppendFormat("<span class='{0}'>{1}</span>",
variant.reference_bases == patientVariant.value1 ? "normal" : "alternate",
patientVariant.value1);
builder.AppendFormat("<span class='{0}'>{1}</span>",
variant.reference_bases == patientVariant.value2 ? "normal" : "alternate",
patientVariant.value2);
builder.AppendFormat("<small>On chr{0}, Reference is {1} from {2}</small></div>", variant.chromosome, variant.reference_bases, variant.reference_genome);
}
break;
case Enums.PatientVariantType.StarVariant:
variant = entities.variants.Where(x =>
x.id == patientVariant.reference_id && x.gene_id.HasValue && geneIds.Contains(x.gene_id.Value)).FirstOrDefault();
if (variant != null)
{
builder.AppendFormat("<div class='variant'>{0}: ", variant.gene.name);
builder.AppendFormat("<span class='{0}'>*{1}</span>/",
"1" == patientVariant.value1 ? "normal" : "alternate",
patientVariant.value1);
builder.AppendFormat("<span class='{0}'>{1}</span>",
"1" == patientVariant.value2 ? "normal" : "alternate",
patientVariant.value2);
}
break;
case Enums.PatientVariantType.Collection:
break;
default:
details.Add(string.Format("The variant type {0} for variant {1} could not be displayed", patientVariant.variant_type, patientVariant.reference_id));
break;
}
details.Add(builder.ToString());
//details.Add(string.Format("<div>{0} = {1}{2} ({3})</div>", formattedVariant, patientVariant.value1, patientVariant.value2, patientVariant.resulted_on.Value.ToShortDateString()));
break;
}
}
}
return details;
}