def from_family(family: Family, add_missing_members=True):
family_connections = FamilyConnections.from_family(
family, add_missing_members=add_missing_members
)
if not family_connections:
return [Layout._handle_broken_family_connections(family)]
if family_connections.is_connected():
logger.debug(
f"building layout for connected family: {family.family_id}")
return [Layout._build_family_layout(family, family_connections)]
layouts = []
for component in family_connections.connected_components():
members = [
m for m in family.full_members
if m.person_id in component
]
fam = Family.from_persons(members)
fc = FamilyConnections.from_family(fam)
# assert fc.is_connected(), fam.family_id
layouts.append(Layout._build_family_layout(fam, fc))
x_offset = 0.0
for layout in layouts:
layout.translate(x_offset, 0.0)
bbox = layout.get_bbox()
x_offset = bbox.max_x + IndividualWithCoordinates.SIZE + 4.0
return layouts
def test_family3_connections(family3):
assert len(family3.full_members) == 1
FamilyConnections.add_missing_members(family3)
assert len(family3.full_members) == 3
ids = [member.person_id for member in family3.full_members]
assert len(ids) == 3
assert sorted(ids) == sorted(["id3", "mom3", "mom3.father"])
def test_family2_connections(family2):
assert len(family2.full_members) == 3
FamilyConnections.add_missing_members(family2)
assert len(family2.full_members) == 3
ids = [member.person_id for member in family2.full_members]
assert len(ids) == 3
assert sorted(ids) == sorted(["id2", "mom2", "dad2"])
def test_family_connections_invalid(individual4, individual5, individual6):
id_to_mating_unit = [
{
"mom2,dad2":
MatingUnit(Individual(), individual6, SibshipUnit(individual4))
},
{
"mom2,dad2":
MatingUnit(individual5, Individual(), SibshipUnit(individual4))
},
{
"mom2,dad2":
MatingUnit(individual5, individual6, SibshipUnit([Individual()]))
},
]
assert FamilyConnections.is_valid_family(id_to_mating_unit[0]) is False
assert FamilyConnections.is_valid_family(id_to_mating_unit[1]) is False
assert FamilyConnections.is_valid_family(id_to_mating_unit[2]) is False
def from_family_layout(family):
if any([p.layout is None for p in family.full_members]):
print(
f"family {family.family_id} has member without layout",
file=sys.stderr,
)
return None
family_connections = FamilyConnections.from_family(
family, add_missing_members=False
)
if family_connections is None:
print(
f"can't build family connections for family "
f"{family.family_id}",
file=sys.stderr,
)
return None
layout_positions = defaultdict(list)
for person in family_connections.members:
position = layout_parser(person.layout)
if position is None:
print(
f"can't parse layout for person {person}: {person.layout}",
file=sys.stderr,
)
return None
individual = family_connections.get_individual(person.person_id)
assert isinstance(position["rank"], int), (
person,
person.layout,
position,
)
layout_positions[position["rank"]].append(
IndividualWithCoordinates(
individual, position["x"], position["y"]
)
)
individual_positions = [[]] * len(layout_positions)
for level, iwc in layout_positions.items():
individual_positions[level - 1] = iwc
individual_positions = [
sorted(level, key=lambda x: x.x) for level in individual_positions
]
layout = Layout()
layout.positions = individual_positions
layout._create_lines()
return layout
def _build_family_layout(
family: Family, family_connections: FamilyConnections):
if family_connections is None:
logger.warning(
f"missing family connections for family: {family.family_id}")
return Layout._handle_broken_family_connections(family)
assert family_connections.is_connected()
sandwich_instance = family_connections.create_sandwich_instance()
intervals = SandwichSolver.solve(sandwich_instance)
if intervals is None:
logger.warning(f"no intervals for family: {family.family_id}")
return Layout._handle_broken_family_connections(family)
individuals_intervals = [
interval
for interval in intervals
if interval.vertex.is_individual()
]
return Layout(individuals_intervals)
def test_family_connections_from_family_simple(family2):
family_connections = FamilyConnections.from_family(family2)
assert family_connections is not None
assert len(family_connections.members) == 3
sandwich_instance = family_connections.create_sandwich_instance()
assert len(sandwich_instance.vertices) == 5
assert len(sandwich_instance.required_graph) == 5
assert len(sandwich_instance.forbidden_graph) == 5
individuals_with_rank = family_connections.get_individuals_with_rank(1)
assert len(individuals_with_rank) == 1
assert "id2" in [el.member.person_id for el in individuals_with_rank]
def test_not_connected_aunts_roles(families_loader):
families = families_loader("test_not_connected_aunts.csv")
assert families is not None
fam = families["fam1"]
assert len(fam) == 7
assert len(fam.full_members) == 7
fc = FamilyConnections.from_family(fam)
fam1 = fc.family
assert len(fam) == 7
assert len(fam1.full_members) == 9
print(fam1.full_members)
aunt = fam1.get_member("aunt1")
assert aunt.role == Role.unknown
aunt_mating = fam.get_member("aunt1.father")
assert aunt_mating.role == Role.unknown
def test_not_connected_aunts(families_loader):
families = families_loader("test_not_connected_aunts.csv")
assert families is not None
fam = families["fam1"]
assert fam is not None
family_connections = FamilyConnections.from_family(fam)
assert family_connections is not None
print(family_connections.get_mating_units())
print(family_connections.get_sibship_units())
g = family_connections.get_graph()
print(g)
assert not family_connections.is_connected()
for comp in family_connections.connected_components():
print(comp, type(comp))
def test_family_connections_from_family_add_members(family2):
family2._members_in_order = list(
filter(lambda member: member.person_id != "mom2",
family2.members_in_order))
prb = list(
filter(lambda member: member.person_id == "id2",
family2.members_in_order))
assert len(prb) == 1
prb[0].mother = "0"
family_connections = FamilyConnections.from_family(
family2, add_missing_members=True)
assert family_connections is not None
assert len(family_connections.members) == 3
sandwich_instance = family_connections.create_sandwich_instance()
assert len(sandwich_instance.vertices) == 5
assert len(sandwich_instance.required_graph) == 5
assert len(sandwich_instance.forbidden_graph) == 5
individuals_with_rank = family_connections.get_individuals_with_rank(1)
assert len(individuals_with_rank) == 1
assert "id2" in [el.member.person_id for el in individuals_with_rank]
def fam1_family_connections(fam1):
return FamilyConnections.from_family(fam1)
def family_connections_from_family2(family2):
return FamilyConnections.from_family(family2)
def test_family_connections_valid(mating_unit2):
id_to_mating_unit = {"mom2,dad2": mating_unit2}
assert FamilyConnections.is_valid_family(id_to_mating_unit) is True
def test_family_connections_from_family_do_not_add_members(family3):
assert (FamilyConnections.from_family(family3, add_missing_members=False)
is None)
def test_family_connections_from_family1_simple(family1):
family_connections = FamilyConnections.from_family(family1)
assert family_connections is not None