def test_node_and_edge_full_example(self):
H = nx.DiGraph()
H.add_edge("X", "Y", weight=10)
H.add_edge("Y", "Z", weight=9)
H.add_edge("Z", "X", weight=8)
motif = dotmotif.Motif("""
A -> B [weight>=7]
""".strip())
res = NetworkXExecutor(graph=H).find(motif)
self.assertEqual(len(res), 3)
H.add_edge("Z", "C", weight=7)
res = NetworkXExecutor(graph=H).find(motif)
self.assertEqual(len(res), 4)
H.add_edge("Z", "D", weight="no")
res = NetworkXExecutor(graph=H).find(motif)
self.assertEqual(len(res), 4)
H.add_edge("y", "a")
self.assertEqual(len(NetworkXExecutor(graph=H).find(motif)), 4)
H.add_edge("y", "a", other_weight=7, weight=8)
self.assertEqual(len(NetworkXExecutor(graph=H).find(motif)), 5)
def test_automorphism_reduction(self):
G = nx.DiGraph()
G.add_edge("X", "Z")
G.add_edge("Y", "Z")
motif = dotmotif.Motif("""
A -> C
B -> C
A === B
""")
res = NetworkXExecutor(graph=G).find(motif)
self.assertEqual(len(res), 2)
motif = dotmotif.Motif(exclude_automorphisms=True).from_motif("""
A -> C
B -> C
A === B
""")
res = NetworkXExecutor(graph=G).find(motif)
self.assertEqual(len(res), 1)
def test_edgecount_motif(self):
dm = dotmotif.Motif("""A->B""")
H = nx.DiGraph()
H.add_edge("x", "y")
self.assertEqual(len(NetworkXExecutor(graph=H).find(dm)), 1)
H.add_edge("x", "y")
self.assertEqual(len(NetworkXExecutor(graph=H).find(dm)), 1)
H.add_edge("x", "z")
self.assertEqual(len(NetworkXExecutor(graph=H).find(dm)), 2)
def test_from_nx_import(self):
G = nx.Graph()
G.add_edge("A", "B")
G.add_edge("B", "C")
g = nx.Graph()
g.add_edge("A", "B")
dm = dotmotif.dotmotif(ignore_direction=True).from_nx(g)
E = NetworkXExecutor(graph=G)
self.assertEqual(len(E.find(dm)), 4)
def test_fullyconnected_triangle_motif(self):
dm = dotmotif.Motif("""
A->B
B->C
C->A
""")
H = nx.DiGraph()
H.add_edge("x", "y")
self.assertEqual(len(NetworkXExecutor(graph=H).find(dm)), 0)
H.add_edge("y", "z")
self.assertEqual(len(NetworkXExecutor(graph=H).find(dm)), 0)
H.add_edge("z", "x")
self.assertEqual(len(NetworkXExecutor(graph=H).find(dm)), 3)
def test_mini_example(self):
H = nx.DiGraph()
H.add_edge("y", "x", ATTRIBUTE=7)
H.add_edge("y", "z", ATTRIBUTE=7)
motif = dotmotif.Motif("""
A -> B [ATTRIBUTE>=7]
""".strip())
self.assertEqual(len(NetworkXExecutor(graph=H).find(motif)), 2)
def test_edge_attribute_equality(self):
dm = dotmotif.Motif("""
A->B [weight==10, area==4]
""")
H = nx.DiGraph()
H.add_edge("z", "x", weight=10, area=4)
H.add_edge("x", "y")
H.add_edge("y", "z", weight=5)
self.assertEqual(len(NetworkXExecutor(graph=H).find(dm)), 1)
def test_one_instance(self):
H = nx.DiGraph()
H.add_edge("x", "y", weight=1)
H.add_edge("y", "z", weight=10)
H.add_edge("z", "x", weight=5)
motif = dotmotif.Motif("""
A -> B [weight>=11]
""".strip())
self.assertEqual(len(NetworkXExecutor(graph=H).find(motif)), 0)
def test_not_in(self):
m = dotmotif.Motif("""
A -> B
A.name !in "foo"
""")
host = nx.DiGraph()
host.add_edge("A", "B")
host.add_node("A", name="the foobar")
host.add_node("B", name="Barbaz")
res = NetworkXExecutor(graph=host).find(m)
self.assertEqual(len(res), 1)
def test_automorphism_flag_triangle(self):
G = nx.DiGraph()
G.add_edge("A", "B")
G.add_edge("B", "C")
G.add_edge("C", "A")
motif = dotmotif.Motif("""
A -> B
B -> C
C -> A
""")
res = NetworkXExecutor(graph=G).find(motif)
self.assertEqual(len(res), 3)
motif = dotmotif.Motif(exclude_automorphisms=True).from_motif("""
A -> B
B -> C
C -> A
""")
res = NetworkXExecutor(graph=G).find(motif)
self.assertEqual(len(res), 1)
def test_automorphism_notauto(self):
G = nx.DiGraph()
G.add_edge("X", "Z")
G.add_edge("Y", "Z")
motif = dotmotif.Motif("""
A -> C
B -> C
""")
res = NetworkXExecutor(graph=G).find(motif)
self.assertEqual(len(res), 2)
def test_two_instance(self):
H = nx.DiGraph()
H.add_edge("x", "y", weight=1)
H.add_edge("y", "z", weight=10)
H.add_edge("z", "x", weight=5)
H.add_edge("z", "a", weight=5)
H.add_edge("a", "b", weight=1)
H.add_edge("b", "c", weight=10)
H.add_edge("c", "a", weight=5)
motif = dotmotif.dotmotif().from_motif("""
A -> B [weight>=7]
""".strip())
self.assertEqual(len(NetworkXExecutor(graph=H).find(motif)), 2)
def find_motif(self):
# find motif and write out motif_df use dotmotif
'''
dotmotif need to cite
@article{matelsky_2020_dotmotif,
doi = {10.1101/2020.06.08.140533},
url = {https://www.biorxiv.org/content/10.1101/2020.06.08.140533v1},
year = 2020,
month = {june},
publisher = {BiorXiv},
author = {Matelsky, Jordan K. and Reilly, Elizabeth P. and Johnson,Erik C. and Wester, Brock A. and Gray-Roncal, William},
title = {{Connectome subgraph isomorphisms and graph queries with DotMotif}},
journal = {BiorXiv}
}
'''
if self.dataset == 'cn':
G = self.cn_G()
if self.dataset == 'mo':
G = self.mo_G()
if self.dataset == 'db':
G = self.db_G()
for root, _, files in os.walk('./data/' + self.dataset + '/motif'):
for file in files:
start = time.process_time()
motif_file_name = root + '/' + file
dm = dotmotif.dotmotif().from_motif(motif_file_name)
tmp_df = pd.DataFrame()
tmp_list = []
for i in NetworkXExecutor(graph=G).find(dm):
tmp_list.append(i)
if tmp_list:
tmp_df = tmp_df.append(tmp_list, ignore_index=True)
tmp_df = tmp_df.reindex(columns=['A', 'B', 'C'
]) # see floder '/motif'
tmp_df.to_csv('./data/' + self.dataset +
'/motif_unprocess/' + file,
sep='\t',
index=0,
header=0)
else:
print(file, ' not exsit')
elapsed = time.process_time() - start
print(file, 'motif created. time cost:', elapsed)
print(time.strftime('%y-%m-%d %I:%M:%S %p'))
def test_dynamic_constraints_one_result(self):
"""
Test that comparisons may be made between variables, e.g.:
A.type != B.type
"""
G = nx.DiGraph()
G.add_edge("A", "B")
G.add_edge("B", "C")
G.add_edge("C", "A")
G.add_node("A", radius=25)
G.add_node("B", radius=10)
exp = """\
A -> B
A.radius > B.radius
"""
dm = dotmotif.Motif(parser=ParserV2)
res = NetworkXExecutor(graph=G).find(dm.from_motif(exp))
self.assertEqual(len(res), 1)
