def test_dm_parser_limit(self):
dm = dotmotif.Motif(limit=3)
dm.from_motif(_DEMO_G_MIN)
self.assertTrue("LIMIT 3" in Neo4jExecutor.motif_to_cypher(dm).strip())
dm = dotmotif.Motif()
dm.from_motif(_DEMO_G_MIN)
self.assertFalse("LIMIT" in Neo4jExecutor.motif_to_cypher(dm).strip())
def test_alphanumeric_variables(self):
exp = """\
edge(A, B) {
A -> B
}
dualedge(A1, B) {
# Nested-inside comment!
edge(A1, B) # inline comment
B -> A1
}
dualedge(foo_1, bar_2) # inline comment
# standalone comment
foo_1 -> bar_2 # inline comment
"""
dm = dotmotif.Motif(exp)
edges = list(dm._g.edges(data=True))
self.assertEqual(len(edges), 2)
self.assertEqual(list(dm._g.nodes()), ["foo_1", "bar_2"])
self.assertEqual(type(list(dm._g.nodes())[0]), str)
new_exp = """
L1 -> Mi1
L1 -> Tm3
L3 -> Mi9
"""
dm = dotmotif.Motif(new_exp)
self.assertEqual(list(dm._g.nodes()),
["L1", "Mi1", "Tm3", "L3", "Mi9"])
def test_node_macro_attr(self):
exp = """\
macro(A) {
A.type = "excitatory"
A.size >= 4.0
}
Aaa -> Ba
macro(Aaa)
"""
dm = dotmotif.Motif(exp)
self.assertEqual(len(dm.list_node_constraints()), 1)
self.assertEqual(list(dm.list_node_constraints().keys()), ["Aaa"])
exp = """\
macro(A) {
A.type = "excitatory"
A.size >= 4.0
}
Aaa -> Ba
macro(Aaa)
macro(Ba)
"""
dm = dotmotif.Motif(exp)
self.assertEqual(len(dm.list_node_constraints()), 2)
self.assertEqual(list(dm.list_node_constraints().keys()),
["Aaa", "Ba"])
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 = GrandIsoExecutor(graph=G).find(motif)
self.assertEqual(len(res), 2)
motif = dotmotif.Motif(exclude_automorphisms=True).from_motif("""
A -> C
B -> C
A === B
""")
res = GrandIsoExecutor(graph=G).find(motif)
self.assertEqual(len(res), 1)
def test_dm_parser_actions(self):
dm = dotmotif.Motif(_THREE_CYCLE)
self.assertEqual([e[2]["action"] for e in dm._g.edges(data=True)],
["SYN"] * 3)
dm = dotmotif.Motif(_THREE_CYCLE_INH)
self.assertEqual([e[2]["action"] for e in dm._g.edges(data=True)],
["INH"] * 3)
def test_dm_parser_edge_exists(self):
dm = dotmotif.Motif(_THREE_CYCLE)
self.assertEqual([e[2]["exists"] for e in dm._g.edges(data=True)],
[True] * 3)
dm = dotmotif.Motif(_THREE_CYCLE_NEG)
self.assertEqual([e[2]["exists"] for e in dm._g.edges(data=True)],
[False] * 3)
dm = dotmotif.Motif(_THREE_CYCLE_NEG_INH)
self.assertEqual([e[2]["exists"] for e in dm._g.edges(data=True)],
[False] * 3)
def test_dm_parser_no_direction(self):
dm = dotmotif.Motif(ignore_direction=True)
dm.from_motif(_DEMO_G_MIN)
self.assertEqual(
Neo4jExecutor.motif_to_cypher(dm).strip(),
_DEMO_G_MIN_CYPHER.strip().replace("->", "-"),
)
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 = GrandIsoExecutor(graph=H).find(motif)
self.assertEqual(len(res), 3)
H.add_edge("Z", "C", weight=7)
res = GrandIsoExecutor(graph=H).find(motif)
self.assertEqual(len(res), 4)
H.add_edge("Z", "D", weight="no")
res = GrandIsoExecutor(graph=H).find(motif)
self.assertEqual(len(res), 4)
H.add_edge("y", "a")
self.assertEqual(len(GrandIsoExecutor(graph=H).find(motif)), 4)
H.add_edge("y", "a", other_weight=7, weight=8)
self.assertEqual(len(GrandIsoExecutor(graph=H).find(motif)), 5)
def test_dm_parser_no_pretty_print(self):
dm = dotmotif.Motif(pretty_print=False)
dm.from_motif(_DEMO_G_MIN)
self.assertEqual(
Neo4jExecutor.motif_to_cypher(dm).strip(),
_DEMO_G_MIN_CYPHER.strip().replace("\n", " "),
)
def test_edge_multi_attr(self):
exp = """\
Aa -> Ba [type != 1, type != 12]
"""
dm = dotmotif.Motif(exp)
self.assertEqual(len(dm._g.edges()), 1)
u, v, d = list(dm._g.edges(data=True))[0]
self.assertEqual(d["constraints"]["type"], {"!=": [1, 12]})
def test_macro_not_added(self):
exp = """\
edge(A, B) {
A -> B
}
"""
dm = dotmotif.Motif(exp)
self.assertEqual(len(dm._g.edges()), 0)
def test_automatic_autos(self):
exp = """\
A -> C
B -> C
"""
dm = dotmotif.Motif(exp, exclude_automorphisms=True)
cypher = Neo4jExecutor.motif_to_cypher(dm)
self.assertIn("id(A) < id(B)", cypher)
def test_simple_macro(self):
exp = """\
edge(A, B) {
A -> B
}
edge(C, D)
"""
dm = dotmotif.Motif(exp)
self.assertEqual(len(dm._g.edges()), 1)
def test_dm_parser_inequality(self):
dm = dotmotif.Motif(enforce_inequality=True)
dm.from_motif(_DEMO_G_MIN)
self.assertTrue("A<>B" in Neo4jExecutor.motif_to_cypher(dm).strip()
or "B<>A" in Neo4jExecutor.motif_to_cypher(dm).strip())
self.assertTrue("B<>C" in Neo4jExecutor.motif_to_cypher(dm).strip()
or "C<>B" in Neo4jExecutor.motif_to_cypher(dm).strip())
self.assertTrue("A<>C" in Neo4jExecutor.motif_to_cypher(dm).strip()
or "C<>A" in Neo4jExecutor.motif_to_cypher(dm).strip())
def test_basic_node_attr(self):
exp = """\
A -> C
B -> C
A === B
"""
dm = dotmotif.Motif(exp)
cypher = Neo4jExecutor.motif_to_cypher(dm)
self.assertIn("id(A) < id(B)", cypher)
def test_basic_node_attr(self):
exp = """\
Aa -> Ba
Aa.type = "excitatory"
"""
dm = dotmotif.Motif(exp)
self.assertEqual(len(dm.list_node_constraints()), 1)
self.assertEqual(list(dm.list_node_constraints().keys()), ["Aa"])
def test_multi_node_attr(self):
exp = """\
Aa -> Ba
Aa.type = "excitatory"
Ba.size=4.0
"""
dm = dotmotif.Motif(exp)
self.assertEqual(len(dm.list_node_constraints()), 2)
self.assertEqual(list(dm.list_node_constraints().keys()), ["Aa", "Ba"])
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(GrandIsoExecutor(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_cypher_edge_many_attributes(self):
dm = dotmotif.Motif()
dm.from_motif("""
A -> B [weight=4, area<=10, area<=20]
X -> Y [weight=2]
""")
self.assertEqual(
Neo4jExecutor.motif_to_cypher(dm).strip(),
_DEMO_EDGE_ATTR_CYPHER_2.strip())
def test_basic_edge_attr(self):
exp = """\
Aa -> Ba [type == 1]
"""
dm = dotmotif.Motif(exp)
self.assertEqual(len(dm._g.edges()), 1)
u, v, d = list(dm._g.edges(["Aa", "Bb"], data=True))[0]
self.assertEqual(type(list(dm._g.nodes())[0]), str)
self.assertEqual(type(list(dm._g.nodes())[1]), str)
self.assertEqual(d["constraints"]["type"], {"==": [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_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(GrandIsoExecutor(graph=H).find(motif)), 0)
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.Motif(ignore_direction=True).from_nx(g)
E = NetworkXExecutor(graph=G)
self.assertEqual(len(E.find(dm)), 4)
def test_wrong_args_macro(self):
exp = """\
edge(A, B) {
A -> B
B -> A
}
edge(C, D, E)
"""
# with self.assertRaises(ValueError):
with self.assertRaises(Exception):
dotmotif.Motif(exp)
def test_simple_macro_construction(self):
exp = """\
edge(A, B) {
A -> B
}
edge(C, D)
"""
dm = dotmotif.Motif(exp)
exp_edge = list(dm._g.edges(data=True))[0]
self.assertEqual(exp_edge[0], "C")
self.assertEqual(exp_edge[1], "D")
def test_dynamic_constraints_in_cypher(self):
dm = dotmotif.Motif(enforce_inequality=True)
dm.from_motif("""
A -> B
A.radius >= B.radius
A.zorf != B.zorf
""")
self.assertIn(
"WHERE A.radius >= B.radius AND A.zorf <> B.zorf",
Neo4jExecutor.motif_to_cypher(dm).strip(),
)
def test_undefined_macro(self):
exp = """\
dualedge(A, B) {
A -> B
B -> A
}
foo(C, D)
"""
# with self.assertRaises(ValueError):
with self.assertRaises(Exception):
dotmotif.Motif(exp)
def test_more_complex_macro(self):
exp = """\
tri(A, B, C) {
A -> B
B -> C
C -> A
}
tri(C, D, E)
"""
dm = dotmotif.Motif(exp)
edges = list(dm._g.edges(data=True))
self.assertEqual(len(edges), 3)
def test_cypher_node_attributes(self):
dm = dotmotif.Motif()
dm.from_motif("""
A -> B
A.size = "big"
""")
self.assertEqual(
Neo4jExecutor.motif_to_cypher(dm).strip(),
"""MATCH (A:Neuron)-[A_B:SYN]->(B:Neuron)\nWHERE A.size = "big"\nRETURN DISTINCT A,B"""
.strip(),
)