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 result_entities AddPhenotype(result_files resultFile, patient patient, attribute attribute, DateTime? resultedOn)
{
result_entities rootEntity = new result_entities()
{
patient_id = patient.id,
result_file_id = resultFile.id,
attribute_id = attribute.id,
};
result_entities resultedOnEntity = new result_entities()
{
patient_id = patient.id,
result_file_id = resultFile.id,
attribute_id = GetAttribute(null, null, "Resulted on", null).id,
parent = rootEntity,
value_date_time = resultedOn
};
entities.result_entities.AddRange(new[] { rootEntity, resultedOnEntity });
entities.SaveChanges();
return rootEntity;
}
public result_files AddResultFile(result_files file)
{
entities.result_files.Add(file);
entities.SaveChanges();
return file;
}
public result_entities[] AddSnps(result_files resultFile, patient patient, DateTime? resultedOn, List<SnpResult> snps)
{
var results = new List<result_entities>();
var snpAlleleAttributeId = GetAttribute(null, null, "SNP allele", null).id;
var referenceBaseAttributeId = GetAttribute(null, null, "Reference base", null).id;
var resultedOnAttributeId = GetAttribute(null, null, "Resulted on", null).id;
foreach (var snp in snps)
{
var entityParts = new List<result_entities>();
result_entities rootEntity = new result_entities()
{
patient_id = patient.id,
result_file_id = resultFile.id,
attribute_id = GetAttribute(snp.RSID, "dbSNP", snp.RSID, snp.RSID).id,
};
result_entities resultedOnEntity = new result_entities()
{
patient_id = patient.id,
result_file_id = resultFile.id,
attribute_id = resultedOnAttributeId,
parent = rootEntity,
value_date_time = resultedOn
};
result_entities referenceBaseEntity = new result_entities()
{
patient_id = patient.id,
result_file_id = resultFile.id,
attribute_id = referenceBaseAttributeId,
parent = rootEntity,
value_short_text = snp.ReferenceBase
};
result_entities allele1Entity = new result_entities()
{
patient_id = patient.id,
result_file_id = resultFile.id,
attribute_id = snpAlleleAttributeId,
parent = rootEntity,
value_short_text = snp.Genotype[0].ToString()
};
result_entities allele2Entity = new result_entities()
{
patient_id = patient.id,
result_file_id = resultFile.id,
attribute_id = snpAlleleAttributeId,
parent = rootEntity,
value_short_text = snp.Genotype[1].ToString()
};
entities.result_entities.AddRange(new[] { rootEntity, resultedOnEntity, referenceBaseEntity, allele1Entity, allele2Entity });
results.Add(rootEntity);
}
entities.SaveChanges();
return results.ToArray();
}
public result_entities[] AddStarVariants(patient patient, result_files resultFile, DateTime resultedOn, List<StarVariantResult> stars)
{
var results = new List<result_entities>();
foreach (var star in stars)
{
var entityParts = new List<result_entities>();
result_entities rootEntity = new result_entities()
{
patient_id = patient.id,
result_file_id = resultFile.id,
attribute_id = GetAttribute(star.Gene, "HGNC", star.Gene, star.Gene).id
};
entityParts.Add(rootEntity);
result_entities resultedOnEntity = new result_entities()
{
patient_id = patient.id,
result_file_id = resultFile.id,
attribute_id = GetAttribute(null, null, "Resulted on", null).id,
parent = rootEntity,
value_date_time = resultedOn
};
entityParts.Add(resultedOnEntity);
string[] splitStars = star.Result.Split(new string[] { "*" }, StringSplitOptions.RemoveEmptyEntries);
foreach (var value in splitStars)
{
result_entities alleleEntity = new result_entities()
{
patient_id = patient.id,
result_file_id = resultFile.id,
attribute_id = GetAttribute(null, null, "Star allele", null).id,
parent = rootEntity,
value_short_text = value
};
entityParts.Add(alleleEntity);
}
entities.result_entities.AddRange(entityParts);
results.Add(rootEntity);
}
entities.SaveChanges();
return results.ToArray();
}
private List<string> GetPhenotypeDetailsForStar(result_files file, string phenotype)
{
List<string> details = new List<string>();
var geneIds = GetGeneFilterForPhenotype(phenotype);
if (geneIds == null)
{
return details;
}
var results = (from re in entities.result_entities
join parentEnt in entities.result_entities on re.parent_id equals parentEnt.id
join attr in entities.attributes on parentEnt.attribute_id equals attr.id
where geneIds.Contains(attr.id)
&& re.result_file_id == file.id && re.attribute_id == 129
select new DetailResult() { AttributeName = attr.name, Result = re }).ToArray();
string currentGene = "";
foreach (var result in results)
{
if (string.IsNullOrEmpty(currentGene))
{
details.Add(string.Format("<div>{0}: *{1}", result.AttributeName, FormatResultEntityValue(result.Result)));
}
else if (currentGene != result.AttributeName)
{
details.Add(string.Format("</div><div>{0}: {1}", result.AttributeName, FormatResultEntityValue(result.Result)));
}
else
{
details.Add(string.Format("/*{0}", FormatResultEntityValue(result.Result)));
}
currentGene = result.AttributeName;
}
details.Add("</div>");
return details;
}
private List<string> GetPhenotypeDetailsForSNP(result_files file, string phenotype)
{
List<string> details = new List<string>();
var geneIds = GetGeneFilterForPhenotype(phenotype);
if (geneIds == null)
{
return details;
}
var results = (from valRes in entities.result_entities
join varRes in entities.result_entities on valRes.parent_id equals varRes.id
join attr in entities.attributes on varRes.attribute_id equals attr.id
join rel in entities.attribute_relationships on attr.id equals rel.attribute1_id
where rel.relationship_id == 5 && geneIds.Contains(rel.attribute2_id) && varRes.result_file_id == file.id
&& (valRes.attribute_id == 128 || valRes.attribute_id == 129)
orderby attr.name
select new DetailResult() { AttributeName = attr.name, Result = valRes }).ToArray();
string currentVariant = "";
foreach (var result in results)
{
if (string.IsNullOrEmpty(currentVariant))
{
details.Add(string.Format("<div>{0}: {1}", result.AttributeName, FormatResultEntityValue(result.Result)));
}
else if (currentVariant != result.AttributeName)
{
details.Add(string.Format("</div><div>{0}: {1}", result.AttributeName, FormatResultEntityValue(result.Result)));
}
else
{
details.Add(FormatResultEntityValue(result.Result));
}
currentVariant = result.AttributeName;
}
details.Add("</div>");
return details;
}
private List<string> GetPhenotypeDetails(result_files file, string phenotype)
{
List<string> details = new List<string>();
var geneIds = GetGeneFilterForPhenotype(phenotype);
if (geneIds == null)
{
return details;
}
var results = (from re in entities.result_entities
join attr in entities.attributes on re.attribute_id equals attr.id
join phenRel in entities.attribute_relationships on attr.id equals phenRel.attribute1_id
join phenAttr in entities.attributes on phenRel.attribute2_id equals phenAttr.id
join geneRel in entities.attribute_relationships on phenRel.attribute2_id equals geneRel.attribute1_id
where phenRel.relationship_id == 2 && geneIds.Contains(geneRel.attribute2_id) && geneRel.relationship_id == 3
&& re.result_file_id == file.id
select new List<string>() { phenAttr.name, attr.name }).ToArray();
List<string> uniqueValues = new List<string>();
foreach (var result in results)
{
string value = string.Format("<div>{0}: {1}</div>", result[0], result[1]);
if (!uniqueValues.Contains(value))
{
details.Add(value);
uniqueValues.Add(value);
}
}
return details;
}
