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fix: handle case where constraint.relations=None #33

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Merged
jsstevenson merged 4 commits into from
Feb 12, 2026
Merged

fix: handle case where constraint.relations=None #33

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6a4a31e
fix: handle case where constraint.relations=None
jsstevenson Feb 12, 2026
09d709b
add test
jsstevenson Feb 12, 2026
3b4493a
does this work?
jsstevenson Feb 12, 2026
ba21ff8
Merge branch 'main' into fix-nonetype-relations-error
jsstevenson Feb 12, 2026
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3 changes: 2 additions & 1 deletion src/ga4gh/cat_vrs/recipes.py
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Original file line number Diff line number Diff line change
Expand Up @@ -180,7 +180,8 @@ def validate_constraints(cls, v: list[Constraint]) -> list[Constraint]:
):
def_loc_constr_found = True

for r in constraint.relations:
relations = constraint.relations or []
for r in relations:
if r.primaryCoding and (
r.primaryCoding.code.root == Relation.LIFTOVER_TO.value
and r.primaryCoding.system
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20 changes: 19 additions & 1 deletion tests/validation/test_cat_vrs_models.py
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Original file line number Diff line number Diff line change
Expand Up @@ -366,7 +366,11 @@ def test_canonical_allele(defining_loc_constr, members_and_name):
recipes.CanonicalAllele(**valid_params)


def test_categorical_cnv(members_and_name, defining_loc_constr, copy_change_constr):
def test_categorical_cnv(
members_and_name: dict,
defining_loc_constr: models.DefiningLocationConstraint,
copy_change_constr: models.CopyChangeConstraint,
):
"""Test the CategoricalCnv validator"""
# Valid CategoricalCnv with CopyChangeConstraint
valid_params = deepcopy(members_and_name)
Expand All @@ -384,6 +388,20 @@ def test_categorical_cnv(members_and_name, defining_loc_constr, copy_change_cons
]
assert recipes.CategoricalCnv(**valid_params)

# Invalid CategoricalCnv: relations unset on DLC
invalid_params = deepcopy(members_and_name)
invalid_dlc = deepcopy(defining_loc_constr)
invalid_dlc.relations = None
invalid_params["constraints"] = [
models.Constraint(root=invalid_dlc),
models.Constraint(root=models.CopyCountConstraint(copies=[1, 2])),
]
with pytest.raises(
ValueError,
match="`DefiningLocationConstraint` found, but must contain at least one relation where `primaryCoding.code` is 'liftover_to' and `primaryCoding.system` is 'ga4gh-gks-term:allele-relation'.",
):
recipes.CategoricalCnv(**invalid_params)

# Invalid CategoricalCnv: No DefiningLocationConstraint
invalid_params = deepcopy(members_and_name)
invalid_params["constraints"] = [
Expand Down