def test_shortest_simple_paths_mod_signed():
seg, sng, all_ns = _setup_signed_graph()
# Add a very long path
sng.add_edge(('B3', INT_PLUS), ('Z1', INT_PLUS),
belief=0.6,
weight=-np.log(0.6))
source = ('B2', INT_PLUS)
target = ('D1', INT_PLUS) # D1 upregulated
# Check that beliafs and weights have been set
assert sng.edges[(source, ('C1', INT_PLUS))].get('weight', False)
assert sng.edges[(source, ('C1', INT_PLUS))].get('belief', False)
# Unweighted search
expected_paths = {(source, ('C1', INT_PLUS), target),
(source, ('C1', INT_MINUS), target)}
paths = [tuple(p) for p in shortest_simple_paths(sng, source, target)]
assert len(paths) == 2
assert set(paths) == expected_paths, 'sets of paths not equal'
# Weighted search
source = ('B3', INT_PLUS)
expected_paths = {
(source, ('C1', 1), target),
(source, ('Z1', 0), ('A1', 0), ('B1', 0), ('C1', 0), target),
(source, ('Z1', 0), ('A1', 1), ('B1', 1), ('C1', 1), target)
}
paths = tuple([
tuple(p)
for p in shortest_simple_paths(sng, source, target, weight='weight')
])
assert len(paths) == 3
assert set(paths) == expected_paths, 'sets of paths not equal'
def test_shortest_simple_paths_mod_unsigned():
dg, all_ns = _setup_unsigned_graph()
dg.add_edge('B1', 'A3', belief=0.7, weight=-np.log(0.7)) # Add long path
# between
# B1 and C1
source, target = 'B1', 'D1'
# Unweighted searches
paths = [p for p in shortest_simple_paths(dg, source, target)]
assert len(paths) == 2
assert tuple(paths[0]) == ('B1', 'C1', 'D1')
assert tuple(paths[1]) == ('B1', 'A3', 'B2', 'C1', 'D1')
assert len([
p
for p in shortest_simple_paths(dg, source, target, ignore_nodes={'A3'})
]) == 1
# Test nx.NoPathFound
try:
len([
p for p in shortest_simple_paths(
dg, source, target, ignore_nodes={'C1'})
]) == 0
except Exception as exc:
assert isinstance(exc, nx.NetworkXNoPath)
# Weighted searches
paths = [
p for p in shortest_simple_paths(dg, source, target, weight='weight')
]
assert tuple(paths[0]) == ('B1', 'C1', 'D1')
assert tuple(paths[1]) == ('B1', 'A3', 'B2', 'C1', 'D1')
def find_paths(hashes):
def ref_counts_function(G, u, v):
edge_hashes = G.graph['hashes']
edge_hashes[('A3', 'B1')] = [14]
try:
return \
len(set(hashes).intersection(set(edge_hashes[(u, v)]))),\
sum(hashes)
except KeyError:
return 0, sum(hashes)
return list(
shortest_simple_paths(G,
source,
target,
hashes=hashes,
ref_counts_function=ref_counts_function))
def count_paths(source, target, hashes):
def ref_counts_function(G, u, v):
edge_hashes = G.graph['hashes']
edge_hashes[('A2', 'B3')] = [14]
edge_hashes[('B3', 'B1')] = [15]
try:
return len(set(hashes).intersection(set(
edge_hashes[(u, v)]))), None
except KeyError:
return 0, None
try:
paths = list(
shortest_simple_paths(G,
source,
target,
hashes=hashes,
weight='weight',
strict_mesh_id_filtering=True,
ref_counts_function=ref_counts_function))
return len(paths)
except nx.NetworkXNoPath:
return 0