def post(self):
"""
returns leader match status of single HLA-B-mismatched transplants sorted via a three-letter nomenclature: (1) non-shared patient's mismatch, (2) non-shared donor's mismatch, (3) shared allotype.
"""
try:
patient = request.json['hla-b_genotype_patient']
donors = request.json['hla-b_genotype_donors']
match = HlaBGenotypeMatch(HlaBGenotype(patient['genotype'], id=patient['id']),
[HlaBGenotype(donor['genotype'], id=donor['id']) for donor in donors])
results = LeaderMapper().get_match_status_info(match)
return jsonify(results)
except Exception as e:
return e.__dict__, 500
def __init__(self, genotype_patient: HlaBGenotype, genotypes_donors: list) -> None:
"""
Represents the match status between two HLA-B genotypes as a
two-element list of HlaBAllotypeMatches. Also, aligns the genotypes
with the match grades. The first genotype represents the patient/recipient while
the second genotype represents the potential donor.
:param genotype_patient: HlaBGenotype object
:param genotypes_donors: List of HlaBGenotype objects
"""
if not isinstance(genotypes_donors, list):
genotypes_donors = [genotypes_donors]
if not (isinstance(genotype_patient, HlaBGenotype) and
False not in [isinstance(geno_donor, HlaBGenotype) for geno_donor in genotypes_donors]):
genotype_patient = HlaBGenotype(str(genotype_patient))
genotypes_donors = [HlaBGenotype(str(geno_donor)) for geno_donor in genotypes_donors]
self.matches = self._get_matches(genotype_patient, genotypes_donors)
def get_leader_genotype_info(self, inp_genotype: HlaBGenotype):
"""
Returns leader genotype information from a HLA-B genotype
:param: HLA-B genotype
:type: HlaBGenotype or str
"""
if not isinstance(inp_genotype, HlaBGenotype):
inp_genotype = HlaBGenotype(inp_genotype)
allotype_one = self.get_leader_allotype_info(inp_genotype.first())
allotype_two = self.get_leader_allotype_info(inp_genotype.second())
return {
"leader_genotype":
str(allotype_one["common_leader"]) +
str(allotype_two["common_leader"]),
"hla-b_genotype":
dict(inp_genotype),
"hla-b_allotype_one":
allotype_one,
"hla-b_allotype_two":
allotype_two,
}
def step_impl(context):
context.genotype_one = HlaBGenotype(context.genotype_name_one)
context.genotype_two = HlaBGenotype(context.genotype_name_two)
context.sort_one = context.genotype_one.flip_sorted and "sorted" or "unsorted"
context.sort_two = context.genotype_two.flip_sorted and "sorted" or "unsorted"
def step_impl(context, sorted_genotype):
context.sorted_genotype = HlaBGenotype(sorted_genotype)
def step_impl(context, genotype):
try:
context.genotype = HlaBGenotype(genotype)
except InvalidHlaBGenotypeError:
context.genotype = "invalid"
def step_impl(context, genotype_name):
context.genotype = HlaBGenotype(genotype_name)
def step_impl(context):
donors = []
for row in context.table:
donors.append(HlaBGenotype(row["HLA-B Genotype"]))
context.genotypes_donors = donors
def step_impl(context, genotype_patient):
context.genotype_patient = HlaBGenotype(genotype_patient)
def step_impl(context):
context.genotype_one = HlaBGenotype(context.genotype_name_one)
context.genotype_two = HlaBGenotype(context.genotype_name_two)
context.sort_one = context.genotype_one.flip_sorted and 'sorted' or 'unsorted'
context.sort_two = context.genotype_two.flip_sorted and 'sorted' or 'unsorted'