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Fix validation issues 1/n #105

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Merged
merged 1 commit into from
Aug 26, 2021
Merged

Fix validation issues 1/n #105

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27 changes: 18 additions & 9 deletions pyard/pyard.py
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Original file line number Diff line number Diff line change
Expand Up @@ -271,8 +271,8 @@ def is_serology(allele: str) -> bool:
@staticmethod
def is_mac(gl: str) -> bool:
"""
MAC has there are non-digit characters after the : character,
then it's a MAC.
MAC has non-digit characters after the : character.

:param gl: glstring to test if it has a MAC code
:return: True if MAC
"""
Expand All @@ -283,11 +283,14 @@ def is_v2(allele: str) -> bool:
"""
Version 2 of the nomenclature is a single field.
It does not have any ':' field separator.
Eg: A*0104
Eg: A*0104
Exceptions:
DRB3*NNNN is not v2 allele
:param allele: Possible allele
:return: Is the allele in V2 nomenclature
"""
return '*' in allele and ':' not in allele
return '*' in allele and ':' not in allele \
and not allele.endswith('*NNNN')

def _is_who_allele(self, allele):
"""
Expand Down Expand Up @@ -395,20 +398,26 @@ def isvalid(self, allele: str) -> bool:
:return: allele or empty
:rtype: bool
"""
if allele == '':
if allele == '' or allele.endswith('*'):
return False

# validate allele without the 'HLA-' prefix
if HLA_regex.search(allele):
# remove 'HLA-' prefix
allele = allele[4:]
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@mmaiers-nmdp mmaiers-nmdp Aug 26, 2021

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nice


if '*' in allele:
alphanum_allele = allele.replace('*', '').replace(':', '')
if not alphanum_allele.isalnum():
return False

if not self.is_mac(allele) and \
not self.is_serology(allele) and \
not self.is_v2(allele):
# Alleles ending with P or G are valid_alleles
if allele.endswith(('P', 'G')):
# remove the last character
allele = allele[:-1]
# validate allele without the 'HLA-' prefix
if HLA_regex.search(allele):
# remove 'HLA-' prefix
allele = allele[4:]
return self._is_valid_allele(allele)
return True

Expand Down