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test na to ze se bude removovat positive match #1209

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test na to ze se bude removovat positive match #1209

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5e75dab
tests: show that set size changes during iteration
kristinagalik May 15, 2023
5807276
tests: fix donor and recipient id retrieval
kristinagalik May 15, 2023
fe19759
tests: fix set manipulation for positive matches so tests pass
kristinagalik May 15, 2023
e1baaf6
Merge branch 'master' into set_manipulation_tests
kristinagalik May 20, 2023
04a08bd
tests: fix test assert for positive crossmatch
kristinagalik May 20, 2023
c84e036
Merge branch 'master' into set_manipulation_tests
kristinagalik May 22, 2023
e0ade93
Merge branch 'master' into set_manipulation_tests
kristinagalik May 25, 2023
34ea9a9
tests: rewirte tests for positive matches
kristinagalik May 25, 2023
f2b1223
tests: prove that the fixed code works
kristinagalik May 25, 2023
ed3c0a4
tests: add comment to tests
kristinagalik May 26, 2023
048681c
Reformat code.
abragtim May 27, 2023
6470937
Merge branch 'master' into set_manipulation_tests
kristinagalik Jun 3, 2023
d466264
Merge branch 'master' into set_manipulation_tests
kubantjan Nov 26, 2024
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46 changes: 41 additions & 5 deletions tests/utils/hla_system/test_crossmatch.py
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Original file line number Diff line number Diff line change
Expand Up @@ -4,19 +4,18 @@
from typing import Callable, List

from local_testing_utilities.generate_patients import LARGE_DATA_FOLDER
from txmatching.utils.hla_system.hla_preparation_utils import create_hla_typing, create_hla_type, \
create_antibodies, create_antibody, create_antibody_parsed
from tests.utils.hla_system.type_a_example_recipient import TYPE_A_EXAMPLE_REC
from txmatching.patients.hla_code import HLACode
from txmatching.patients.hla_model import HLAAntibodyRaw
from txmatching.patients.hla_model import HLAAntibody, HLAAntibodyRaw
from txmatching.utils.constants import \
SUFFICIENT_NUMBER_OF_ANTIBODIES_IN_HIGH_RES
from txmatching.utils.enums import (AntibodyMatchTypes, HLAAntibodyType,
HLACrossmatchLevel)
from txmatching.utils.hla_system.hla_crossmatch import (
AntibodyMatch, do_crossmatch_in_type_a, do_crossmatch_in_type_b,
AntibodyMatch, add_theoretical_crossmatch_type, do_crossmatch_in_type_a, do_crossmatch_in_type_b,
is_positive_hla_crossmatch, is_recipient_type_a)

from txmatching.utils.hla_system.hla_preparation_utils import create_hla_typing, create_hla_type, \
create_antibodies, create_antibody, create_antibody_parsed
logger = logging.getLogger(__name__)


Expand Down Expand Up @@ -595,3 +594,40 @@ def test_crossmatch_for_antibodies_with_two_codes(self):
)

self.assertEqual(crossmatch_result[4].antibody_matches[0].match_type, AntibodyMatchTypes.HIGH_RES_WITH_SPLIT)

def test_positive_crossmatch_theoretical_antibody(self):
# add_theoretical_crossmatch_type changes match_type of theoretical antibodies
# to theoretical, thus these two antibodies will be equal
positive_matches = {AntibodyMatch(
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Jako tohle by se ale nikdy nemelo stat, ze budou protilatky, co maji stejny hla kod ale ruzny typ preci ne?

Obecne chceme mit v testech realna data a ne nejaky situace, ktery v realite nesmi nastat

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@kristinagalik kristinagalik May 29, 2023 •
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toto je priklad co sa stal, tak je asi problem niekde inde... :/ @kubantjan

mam zalozit novu issue ci to riesit vramci tejto

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Aha! tak to urcite zkusme vyresit v ramci teto, ale priorita je nizsi nez ty jine veci :)

hla_antibody=HLAAntibody(raw_code='DQA1*02:03',
code=HLACode('DQA1*02:03', 'DQA2', 'DQA2'),
mfi=2100,
cutoff=2000,
second_raw_code=None,
second_code=None,
type=HLAAntibodyType.THEORETICAL),
match_type=AntibodyMatchTypes.HIGH_RES),
AntibodyMatch(
hla_antibody=HLAAntibody(raw_code='DQA1*02:03',
code=HLACode('DQA1*02:03', 'DQA2', 'DQA2'),
mfi=2100,
cutoff=2000,
second_raw_code=None,
second_code=None,
type=HLAAntibodyType.THEORETICAL),
match_type=AntibodyMatchTypes.HIGH_RES_WITH_SPLIT)
}

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expected_positive_matches = {AntibodyMatch(
hla_antibody=HLAAntibody(raw_code='DQA1*02:03',
code=HLACode('DQA1*02:03', 'DQA2', 'DQA2'),
mfi=2100,
cutoff=2000,
second_raw_code=None,
second_code=None,
type=HLAAntibodyType.THEORETICAL),
match_type=AntibodyMatchTypes.THEORETICAL)
}

add_theoretical_crossmatch_type(positive_matches)
self.assertEqual(positive_matches, expected_positive_matches)
6 changes: 3 additions & 3 deletions txmatching/utils/hla_system/hla_crossmatch.py
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Original file line number Diff line number Diff line change
Expand Up @@ -303,7 +303,7 @@ def do_crossmatch_in_type_a(donor_hla_typing: HLATyping,
_do_crossmatch_for_hlas_recipient_was_not_tested_for(
hla_per_group, [antibody], antibodies, positive_matches, use_high_resolution)

_add_theoretical_crossmatch_type(positive_matches)
add_theoretical_crossmatch_type(positive_matches)
_add_none_crossmatch_type(_get_antibodies_over_cutoff(antibodies), positive_matches)
antibody_matches_for_groups.append(AntibodyMatchForHLAGroup(hla_per_group.hla_group, list(positive_matches)))
return antibody_matches_for_groups
Expand Down Expand Up @@ -388,7 +388,7 @@ def do_crossmatch_in_type_b(donor_hla_typing: HLATyping,
if _add_broad_crossmatch_type(hla_type, tested_antibodies_that_match, positive_matches):
continue

_add_theoretical_crossmatch_type(positive_matches)
add_theoretical_crossmatch_type(positive_matches)
_add_none_crossmatch_type(antibodies, positive_matches)

antibody_matches_for_groups.append(AntibodyMatchForHLAGroup(hla_per_group.hla_group, list(positive_matches)))
Expand Down Expand Up @@ -497,7 +497,7 @@ def _add_undecidable_crossmatch_type(antibodies: List[HLAAntibody],
positive_matches.add(AntibodyMatch(antibody, AntibodyMatchTypes.UNDECIDABLE))


def _add_theoretical_crossmatch_type(positive_matches: Set[AntibodyMatch]):
def add_theoretical_crossmatch_type(positive_matches: Set[AntibodyMatch]):
matches_to_remove = set()
for match in positive_matches:
if match.hla_antibody.type == HLAAntibodyType.THEORETICAL and match.match_type != AntibodyMatchTypes.UNDECIDABLE:
Expand Down