def test_inject_clone_node(self):
pattern = nx.DiGraph()
prim.add_nodes_from(pattern, [1, 2, 3])
prim.add_edges_from(pattern, [(1, 2), (3, 2)])
rule = Rule.from_transform(pattern)
new_p_node, new_rhs_node = rule.inject_clone_node(2)
check_homomorphism(rule.p, rule.lhs, rule.p_lhs)
check_homomorphism(rule.p, rule.rhs, rule.p_rhs)
assert (new_p_node in rule.p.nodes())
assert (new_rhs_node in rule.rhs.nodes())
assert (rule.p_rhs[new_p_node] == new_rhs_node)
assert ((1, new_p_node) in rule.p.edges())
assert ((3, new_p_node) in rule.p.edges())
assert ((1, new_rhs_node) in rule.rhs.edges())
assert ((3, new_rhs_node) in rule.rhs.edges())
new_p_node, new_rhs_node = rule.inject_clone_node(2)
assert (len(keys_by_value(rule.p_lhs, 2)) == 3)
check_homomorphism(rule.p, rule.lhs, rule.p_lhs)
check_homomorphism(rule.p, rule.rhs, rule.p_rhs)
rule.inject_remove_node(3)
try:
rule.inject_clone_node(3)
raise ValueError("Cloning of removed node was not caught")
except:
pass
def test_inject_clone_node(self):
pattern = nx.DiGraph()
prim.add_nodes_from(pattern, [1, 2, 3])
prim.add_edges_from(pattern, [(1, 2), (3, 2)])
rule = Rule.from_transform(pattern)
new_p_node, new_rhs_node = rule.inject_clone_node(2)
check_homomorphism(rule.p, rule.lhs, rule.p_lhs)
check_homomorphism(rule.p, rule.rhs, rule.p_rhs)
assert(new_p_node in rule.p.nodes())
assert(new_rhs_node in rule.rhs.nodes())
assert(rule.p_rhs[new_p_node] == new_rhs_node)
assert((1, new_p_node) in rule.p.edges())
assert((3, new_p_node) in rule.p.edges())
assert((1, new_rhs_node) in rule.rhs.edges())
assert((3, new_rhs_node) in rule.rhs.edges())
new_p_node, new_rhs_node = rule.inject_clone_node(2)
assert(len(keys_by_value(rule.p_lhs, 2)) == 3)
check_homomorphism(rule.p, rule.lhs, rule.p_lhs)
check_homomorphism(rule.p, rule.rhs, rule.p_rhs)
rule.inject_remove_node(3)
try:
rule.inject_clone_node(3)
raise ValueError("Cloning of removed node was not caught")
except:
pass
def test_rewrite(self):
pattern = nx.DiGraph()
prim.add_nodes_from(pattern, [1, (2, {"a": {1, 2}}), 3])
prim.add_edges_from(pattern, [(1, 2), (2, 3)])
lhs_typing = {
"g0": {
1: "circle",
2: "square",
3: "triangle"
},
"g00": {
1: "white",
2: "white",
3: "black"
}
}
p = nx.DiGraph()
p.add_nodes_from([1, 2, 3])
p.add_edges_from([(2, 3)])
rhs = nx.DiGraph()
prim.add_nodes_from(
rhs, [1, (2, {
"a": {3, 5}
}), (3, {
"new_attrs": {1}
}), 4])
prim.add_edges_from(rhs, [(2, 1, {
"new_attrs": {2}
}), (2, 4, {
"new_attrs": {3}
}), (2, 3, {
"new_attrs": {4}
})])
p_lhs = {1: 1, 2: 2, 3: 3}
p_rhs = {1: 1, 2: 2, 3: 3}
rule = Rule(p, pattern, rhs, p_lhs, p_rhs)
rhs_typing = {
"g0": {
1: "circle",
2: "square",
3: "triangle",
4: "triangle"
},
"g00": {
1: "white",
2: "white",
3: "black",
4: "black"
}
}
instances = self.hierarchy.find_matching("g1", pattern, lhs_typing)
# print(instances[0])
self.hierarchy.rewrite("g1", rule, instances[0], lhs_typing,
rhs_typing)
def test_inject_remove_node(self):
pattern = nx.DiGraph()
prim.add_nodes_from(pattern, [1, 2, 3])
prim.add_edges_from(pattern, [(1, 2), (3, 2)])
rule = Rule.from_transform(pattern)
rule.inject_remove_node(2)
check_homomorphism(rule.p, rule.lhs, rule.p_lhs)
check_homomorphism(rule.p, rule.rhs, rule.p_rhs)
assert (2 in rule.lhs.nodes())
assert (2 not in rule.p.nodes())
assert (2 not in rule.rhs.nodes())
def test_inject_remove_node(self):
pattern = nx.DiGraph()
prim.add_nodes_from(pattern, [1, 2, 3])
prim.add_edges_from(pattern, [(1, 2), (3, 2)])
rule = Rule.from_transform(pattern)
rule.inject_remove_node(2)
check_homomorphism(rule.p, rule.lhs, rule.p_lhs)
check_homomorphism(rule.p, rule.rhs, rule.p_rhs)
assert(2 in rule.lhs.nodes())
assert(2 not in rule.p.nodes())
assert(2 not in rule.rhs.nodes())
def test_find_matching(self):
pattern = nx.DiGraph()
prim.add_nodes_from(pattern, [(1, {
'state': 'p'
}), (2, {
'name': 'BND'
}), (3), (4)])
prim.add_edges_from(pattern, [(1, 2, {
's': 'p'
}), (3, 2, {
's': 'u'
}), (3, 4)])
find_matching(self.graph, pattern)
def test_find_matching(self):
pattern = nx.DiGraph()
prim.add_nodes_from(pattern,
[(1, {'state': 'p'}),
(2, {'name': 'BND'}),
(3),
(4)]
)
prim.add_edges_from(pattern,
[(1, 2, {'s': 'p'}),
(3, 2, {'s': 'u'}),
(3, 4)]
)
find_matching(self.graph, pattern)
def test_inject_add_node(self):
pattern = nx.DiGraph()
prim.add_nodes_from(pattern, [1, 2, 3])
prim.add_edges_from(pattern, [(1, 2), (3, 2)])
rule = Rule.from_transform(pattern)
try:
rule.inject_add_node(3)
raise ValueError("Node duplication was not caught")
except RuleError:
pass
rule.inject_add_node(4)
check_homomorphism(rule.p, rule.lhs, rule.p_lhs)
check_homomorphism(rule.p, rule.rhs, rule.p_rhs)
assert (4 in rule.rhs.nodes() and 4 not in rule.lhs.nodes()
and 4 not in rule.p.nodes())
def test_inject_add_node(self):
pattern = nx.DiGraph()
prim.add_nodes_from(pattern, [1, 2, 3])
prim.add_edges_from(pattern, [(1, 2), (3, 2)])
rule = Rule.from_transform(pattern)
try:
rule.inject_add_node(3)
raise ValueError("Node duplication was not caught")
except RuleError:
pass
rule.inject_add_node(4)
check_homomorphism(rule.p, rule.lhs, rule.p_lhs)
check_homomorphism(rule.p, rule.rhs, rule.p_rhs)
assert(4 in rule.rhs.nodes() and
4 not in rule.lhs.nodes() and
4 not in rule.p.nodes())
def test_inject_merge_nodes(self):
pattern = nx.DiGraph()
prim.add_nodes_from(pattern, [1, 2, 3])
prim.add_edges_from(pattern, [(1, 2), (3, 2)])
rule = Rule.from_transform(pattern)
new_name = rule.inject_merge_nodes([1, 2])
check_homomorphism(rule.p, rule.lhs, rule.p_lhs)
check_homomorphism(rule.p, rule.rhs, rule.p_rhs)
assert((new_name, new_name) in rule.rhs.edges())
assert((3, new_name) in rule.rhs.edges())
new_p_name, new_rhs_name = rule.inject_clone_node(2)
check_homomorphism(rule.p, rule.lhs, rule.p_lhs)
check_homomorphism(rule.p, rule.rhs, rule.p_rhs)
new_name = rule.inject_merge_nodes([2, 3])
check_homomorphism(rule.p, rule.lhs, rule.p_lhs)
check_homomorphism(rule.p, rule.rhs, rule.p_rhs)
assert(new_p_name in rule.rhs.nodes())
def test_find_matching(self):
pattern = nx.DiGraph()
prim.add_nodes_from(pattern, [1, (2, {"a": 1}), 3])
prim.add_edges_from(pattern, [(1, 2), (2, 3)])
pattern_typing = {1: "circle", 2: "square", 3: "triangle"}
instances = self.hierarchy.find_matching(graph_id="g1",
pattern=pattern,
pattern_typing={
"g0": pattern_typing,
"g00": {
1: "white",
2: "white",
3: "black"
}
})
assert (len(instances) == 1)
def test_inject_merge_nodes(self):
pattern = NXGraph()
prim.add_nodes_from(pattern, [1, 2, 3])
prim.add_edges_from(pattern, [(1, 2), (3, 2)])
rule = Rule.from_transform(pattern)
new_name = rule.inject_merge_nodes([1, 2])
check_homomorphism(rule.p, rule.lhs, rule.p_lhs)
check_homomorphism(rule.p, rule.rhs, rule.p_rhs)
assert ((new_name, new_name) in rule.rhs.edges())
assert ((3, new_name) in rule.rhs.edges())
new_p_name, new_rhs_name = rule.inject_clone_node(2)
check_homomorphism(rule.p, rule.lhs, rule.p_lhs)
check_homomorphism(rule.p, rule.rhs, rule.p_rhs)
new_name = rule.inject_merge_nodes([2, 3])
check_homomorphism(rule.p, rule.lhs, rule.p_lhs)
check_homomorphism(rule.p, rule.rhs, rule.p_rhs)
assert (new_rhs_name in rule.rhs.nodes())
def test_controlled_up_propagation(self):
pattern = nx.DiGraph()
pattern.add_nodes_from(["A"])
rule = Rule.from_transform(pattern)
p_clone, _ = rule.inject_clone_node("A")
rule.inject_add_node("D")
p_typing = {
"nn1": {
"A_bye": {},
"A_hello": {p_clone}
},
"n1": {
"A": p_clone
}
}
instance = {"A": "A"}
nugget_1 = nx.DiGraph()
primitives.add_nodes_from(
nugget_1, ["A_bye", "A_hello", "A_res_1", "p", "B", "mod"])
primitives.add_edges_from(nugget_1, [("A_res_1", "A_hello"),
("A_res_1", "A_bye"),
("p", "A_res_1"), ("mod", "p"),
("B", "mod")])
self.hierarchy.add_graph("nn1", nugget_1)
self.hierarchy.add_typing(
"nn1", "n1", {
"A_bye": "A",
"A_hello": "A",
"A_res_1": "A_res_1",
"p": "p",
"B": "B",
"mod": "mod"
})
new_hierarchy, _ = self.hierarchy.rewrite("ag",
rule,
instance,
p_typing=p_typing,
inplace=False)
primitives.print_graph(new_hierarchy.get_graph("nn1"))
print(new_hierarchy.typing["nn1"]["n1"])
def test_inject_remove_edge_attrs(self):
pattern = nx.DiGraph()
prim.add_nodes_from(pattern, [1, 2, 3])
prim.add_edges_from(pattern, [(1, 2, {
"a12": {True}
}), (3, 2, {
"a32": {True}
})])
rule = Rule.from_transform(pattern)
rule.inject_remove_edge_attrs(1, 2, {"a12": {True}})
assert ("a12" not in rule.p.edge[1][2])
new_p_node, new_rhs_node = rule.inject_clone_node(2)
assert ("a12" not in rule.p.edge[1][new_p_node])
rule.inject_remove_edge_attrs(3, new_p_node, {"a32": {True}})
assert ("a32" in rule.p.edge[3][2])
assert ("a32" not in rule.p.edge[3][new_p_node])
assert ("a32" in rule.rhs.edge[3][rule.p_rhs[2]])
assert ("a32" not in rule.rhs.edge[3][new_rhs_node])
def test_inject_remove_edge_attrs(self):
pattern = nx.DiGraph()
prim.add_nodes_from(
pattern,
[1, 2, 3])
prim.add_edges_from(
pattern,
[(1, 2, {"a12": {True}}), (3, 2, {"a32": {True}})])
rule = Rule.from_transform(pattern)
rule.inject_remove_edge_attrs(1, 2, {"a12": {True}})
assert("a12" not in rule.p.adj[1][2])
new_p_node, new_rhs_node = rule.inject_clone_node(2)
assert("a12" not in rule.p.adj[1][new_p_node])
rule.inject_remove_edge_attrs(3, new_p_node, {"a32": {True}})
assert("a32" in rule.p.adj[3][2])
assert("a32" not in rule.p.adj[3][new_p_node])
assert("a32" in rule.rhs.adj[3][rule.p_rhs[2]])
assert("a32" not in rule.rhs.adj[3][new_rhs_node])
def test_component_getters(self):
pattern = nx.DiGraph()
prim.add_nodes_from(
pattern,
[(1, {"a1": {1}}), (2, {"a2": {2}}), (3, {"a3": {3}})]
)
prim.add_edges_from(
pattern,
[
(1, 2, {"a12": {12}}),
(2, 3),
(3, 2, {"a32": {32}})
]
)
rule = Rule.from_transform(pattern)
rule.remove_node(1)
rule.remove_edge(2, 3)
new_name, _ = rule.clone_node(2)
print(new_name)
rule.remove_node_attrs(3, {"a3": {3}})
rule.remove_edge_attrs(3, 2, {"a32": {32}})
rule.add_node_attrs(3, {"a3": {100}})
rule.add_node(4)
rule.add_edge_rhs(4, "21")
assert(rule.removed_nodes() == {1})
print(rule.removed_edges())
assert(rule.removed_edges() == {(2, 3), (new_name[0], 3)})
assert(len(rule.cloned_nodes()) == 1 and
2 in rule.cloned_nodes().keys())
assert(len(rule.removed_node_attrs()) == 1 and
3 in rule.removed_node_attrs()[3]["a3"])
assert(len(rule.removed_edge_attrs()) == 1 and
32 in rule.removed_edge_attrs()[(3, 2)]["a32"])
assert(rule.added_nodes() == {4})
assert(rule.added_edges() == {(4, "21")})
# rule.merged_nodes()
# rule.added_edge_attrs()
assert(len(rule.added_node_attrs()) == 1 and
100 in rule.added_node_attrs()[3]["a3"])
assert(rule.is_restrictive() and rule.is_relaxing())
def test_inject_add_node_attrs(self):
pattern = NXGraph()
prim.add_nodes_from(pattern, [1, 2, 3])
prim.add_edges_from(pattern, [(1, 2), (3, 2)])
rule = Rule.from_transform(pattern)
clone_name_p, clone_name_rhs = rule.inject_clone_node(2)
rule.inject_add_node(4)
merge = rule.inject_merge_nodes([1, 3])
rule.inject_add_node_attrs(2, {"a": {True}})
assert ("a" in rule.rhs.get_node(2))
rule.inject_add_node_attrs(clone_name_p, {"b": {True}})
assert ("b" in rule.rhs.get_node(clone_name_rhs))
assert ("b" not in rule.rhs.get_node(2))
rule.inject_add_node_attrs(4, {"c": {True}})
assert ("c" in rule.rhs.get_node(4))
rule.inject_add_node_attrs(merge, {"d": {True}})
assert ("d" in rule.rhs.get_node(merge))
check_homomorphism(rule.p, rule.lhs, rule.p_lhs)
check_homomorphism(rule.p, rule.rhs, rule.p_rhs)
def test_inject_add_edge(self):
pattern = nx.DiGraph()
prim.add_nodes_from(pattern, [1, 2, 3])
prim.add_edges_from(pattern, [(1, 2), (3, 2)])
rule = Rule.from_transform(pattern)
rule.inject_add_node(4)
rule.inject_add_edge(1, 4)
check_homomorphism(rule.p, rule.lhs, rule.p_lhs)
check_homomorphism(rule.p, rule.rhs, rule.p_rhs)
assert ((1, 4) in rule.rhs.edges())
merge_node = rule.inject_merge_nodes([1, 2])
rule.inject_add_edge(merge_node, 3)
check_homomorphism(rule.p, rule.lhs, rule.p_lhs)
check_homomorphism(rule.p, rule.rhs, rule.p_rhs)
assert ((merge_node, 3) in rule.rhs.edges())
new_p_node, new_rhs_node = rule.inject_clone_node(2)
rule.inject_add_edge(new_p_node, merge_node)
check_homomorphism(rule.p, rule.lhs, rule.p_lhs)
check_homomorphism(rule.p, rule.rhs, rule.p_rhs)
assert ((new_rhs_node, merge_node) in rule.rhs.edges())
def test_inject_add_edge(self):
pattern = nx.DiGraph()
prim.add_nodes_from(pattern, [1, 2, 3])
prim.add_edges_from(pattern, [(1, 2), (3, 2)])
rule = Rule.from_transform(pattern)
rule.inject_add_node(4)
rule.inject_add_edge(1, 4)
check_homomorphism(rule.p, rule.lhs, rule.p_lhs)
check_homomorphism(rule.p, rule.rhs, rule.p_rhs)
assert((1, 4) in rule.rhs.edges())
merge_node = rule.inject_merge_nodes([1, 2])
rule.inject_add_edge(merge_node, 3)
check_homomorphism(rule.p, rule.lhs, rule.p_lhs)
check_homomorphism(rule.p, rule.rhs, rule.p_rhs)
assert((merge_node, 3) in rule.rhs.edges())
new_p_node, new_rhs_node = rule.inject_clone_node(2)
rule.inject_add_edge(new_p_node, merge_node)
check_homomorphism(rule.p, rule.lhs, rule.p_lhs)
check_homomorphism(rule.p, rule.rhs, rule.p_rhs)
assert((new_rhs_node, merge_node) in rule.rhs.edges())
def test_inject_remove_node_attrs(self):
pattern = nx.DiGraph()
prim.add_nodes_from(
pattern,
[1, (2, {"a2": {True}}), (3, {"a3": {False}})])
prim.add_edges_from(pattern, [(1, 2), (3, 2)])
rule = Rule.from_transform(pattern)
rule.inject_remove_node_attrs(3, {"a3": {False}})
check_homomorphism(rule.p, rule.lhs, rule.p_lhs)
check_homomorphism(rule.p, rule.rhs, rule.p_rhs)
assert("a3" not in rule.p.node[3])
assert("a3" in rule.lhs.node[3])
new_p_node, new_rhs_node = rule.inject_clone_node(2)
rule.inject_remove_node_attrs(new_p_node, {"a2": {True}})
check_homomorphism(rule.p, rule.lhs, rule.p_lhs)
check_homomorphism(rule.p, rule.rhs, rule.p_rhs)
assert("a2" not in rule.p.node[new_p_node])
assert("a2" in rule.p.node[2])
assert("a2" not in rule.rhs.node[new_rhs_node])
assert("a2" in rule.rhs.node[2])
def test_inject_add_node_attrs(self):
pattern = nx.DiGraph()
prim.add_nodes_from(pattern, [1, 2, 3])
prim.add_edges_from(pattern, [(1, 2), (3, 2)])
rule = Rule.from_transform(pattern)
clone_name_p, clone_name_rhs = rule.inject_clone_node(2)
rule.inject_add_node(4)
merge = rule.inject_merge_nodes([1, 3])
rule.inject_add_node_attrs(2, {"a": {True}})
assert("a" in rule.rhs.node[2])
assert("a" in rule.rhs.node[clone_name_rhs])
rule.inject_add_node_attrs(clone_name_p, {"b": {True}})
assert("b" in rule.rhs.node[clone_name_rhs])
assert("b" not in rule.rhs.node[2])
rule.inject_add_node_attrs(4, {"c": {True}})
assert("c" in rule.rhs.node[4])
rule.inject_add_node_attrs(merge, {"d": {True}})
assert("d" in rule.rhs.node[merge])
check_homomorphism(rule.p, rule.lhs, rule.p_lhs)
check_homomorphism(rule.p, rule.rhs, rule.p_rhs)
def test_inject_remove_node_attrs(self):
pattern = nx.DiGraph()
prim.add_nodes_from(
pattern,
[1, (2, {"a2": {True}}), (3, {"a3": {False}})])
prim.add_edges_from(pattern, [(1, 2), (3, 2)])
rule = Rule.from_transform(pattern)
rule.inject_remove_node_attrs(3, {"a3": {False}})
check_homomorphism(rule.p, rule.lhs, rule.p_lhs)
check_homomorphism(rule.p, rule.rhs, rule.p_rhs)
assert("a3" not in rule.p.node[3])
assert("a3" in rule.lhs.node[3])
new_p_node, new_rhs_node = rule.inject_clone_node(2)
rule.inject_remove_node_attrs(new_p_node, {"a2": {True}})
check_homomorphism(rule.p, rule.lhs, rule.p_lhs)
check_homomorphism(rule.p, rule.rhs, rule.p_rhs)
assert("a2" not in rule.p.node[new_p_node])
assert("a2" in rule.p.node[2])
assert("a2" not in rule.rhs.node[new_rhs_node])
assert("a2" in rule.rhs.node[2])
def test_inject_add_edge_attrs(self):
pattern = nx.DiGraph()
prim.add_nodes_from(pattern, [0, 1, 2, 3])
prim.add_edges_from(pattern, [(0, 1), (0, 2), (1, 2), (3, 2)])
rule = Rule.from_transform(pattern)
clone_name_p, clone_name_rhs = rule.inject_clone_node(2)
rule.inject_add_node(4)
rule.inject_add_edge(4, 3)
merge = rule.inject_merge_nodes([1, 3])
rule.inject_add_edge_attrs(0, 1, {"a": {True}})
assert ("a" in rule.rhs.edge[0][merge])
rule.inject_add_edge_attrs(0, clone_name_p, {"b": {True}})
assert ("b" in rule.rhs.edge[0][clone_name_rhs])
rule.inject_add_edge_attrs(merge, clone_name_p, {"c": {True}})
assert ("c" in rule.rhs.edge[merge][clone_name_rhs])
assert ("c" not in rule.rhs.edge[merge][2])
rule.inject_add_edge_attrs(4, merge, {"d": {True}})
assert ("d" in rule.rhs.edge[4][merge])
check_homomorphism(rule.p, rule.lhs, rule.p_lhs)
check_homomorphism(rule.p, rule.rhs, rule.p_rhs)
def test_find_matching(self):
pattern = nx.DiGraph()
prim.add_nodes_from(pattern, [
1,
(2, {"a": 1}),
3
])
prim.add_edges_from(pattern, [
(1, 2),
(2, 3)
])
pattern_typing = {1: "circle", 2: "square", 3: "triangle"}
instances = self.hierarchy.find_matching(
graph_id="g1",
pattern=pattern,
pattern_typing={
"g0": pattern_typing,
"g00": {1: "white", 2: "white", 3: "black"}
}
)
assert(len(instances) == 1)
def test_from_commands(self):
pattern = nx.DiGraph()
prim.add_nodes_from(pattern, [(1, {
'state': 'p'
}), (2, {
'name': 'BND'
}), 3, 4])
prim.add_edges_from(pattern, [(1, 2, {
's': 'p'
}), (3, 2, {
's': 'u'
}), (3, 4)])
p = nx.DiGraph()
prim.add_nodes_from(p, [(1, {
'state': 'p'
}), ("1_clone", {
'state': 'p'
}), (2, {
'name': 'BND'
}), 3, 4])
prim.add_edges_from(p, [(1, 2), ('1_clone', 2), (3, 4)])
rhs = nx.DiGraph()
prim.add_nodes_from(rhs, [(1, {
'state': 'p'
}), ("1_clone", {
'state': 'p'
}), (2, {
'name': 'BND'
}), 3, 4, 5])
prim.add_edges_from(rhs, [(1, 2, {
's': 'u'
}), ('1_clone', 2), (2, 4), (3, 4), (5, 3)])
p_lhs = {1: 1, '1_clone': 1, 2: 2, 3: 3, 4: 4}
p_rhs = {1: 1, '1_clone': '1_clone', 2: 2, 3: 3, 4: 4}
rule1 = Rule(p, pattern, rhs, p_lhs, p_rhs)
commands = "clone 1.\n" +\
"delete_edge 3 2.\n" +\
"add_node 5.\n" +\
"add_edge 2 4.\n" +\
"add_edge 5 3."
rule2 = Rule.from_transform(pattern, commands)
assert ((5, 3) in rule2.rhs.edges())
assert (5 in rule2.rhs.nodes() and 5 not in rule2.p.nodes())
assert ((2, 4) in rule2.rhs.edges())
def test_from_commands(self):
pattern = nx.DiGraph()
prim.add_nodes_from(
pattern,
[(1, {'state': 'p'}),
(2, {'name': 'BND'}),
3,
4]
)
prim.add_edges_from(
pattern,
[(1, 2, {'s': 'p'}),
(3, 2, {'s': 'u'}),
(3, 4)]
)
p = nx.DiGraph()
prim.add_nodes_from(
p,
[(1, {'state': 'p'}), ("1_clone", {'state': 'p'}), (2, {'name': 'BND'}), 3, 4])
prim.add_edges_from(
p, [(1, 2), ('1_clone', 2), (3, 4)])
rhs = nx.DiGraph()
prim.add_nodes_from(
rhs,
[(1, {'state': 'p'}), ("1_clone", {'state': 'p'}), (2, {'name': 'BND'}), 3, 4, 5])
prim.add_edges_from(
rhs, [(1, 2, {'s': 'u'}), ('1_clone', 2), (2, 4), (3, 4), (5, 3)])
p_lhs = {1: 1, '1_clone': 1, 2: 2, 3: 3, 4: 4}
p_rhs = {1: 1, '1_clone': '1_clone', 2: 2, 3: 3, 4: 4}
rule1 = Rule(p, pattern, rhs, p_lhs, p_rhs)
commands = "clone 1.\n" +\
"delete_edge 3 2.\n" +\
"add_node 5.\n" +\
"add_edge 2 4.\n" +\
"add_edge 5 3."
rule2 = Rule.from_transform(pattern, commands)
assert((5, 3) in rule2.rhs.edges())
assert(5 in rule2.rhs.nodes() and 5 not in rule2.p.nodes())
assert((2, 4) in rule2.rhs.edges())
def test_add_rule_multiple_typing(self):
lhs = nx.DiGraph()
prim.add_nodes_from(lhs, [1, 2, 3, 4])
prim.add_edges_from(lhs, [(1, 3), (2, 3), (4, 3)])
p = nx.DiGraph()
prim.add_nodes_from(p, [1, 3, 31, 4])
prim.add_edges_from(p, [(1, 3), (1, 31), (4, 3), (4, 31)])
rhs = copy.deepcopy(p)
p_lhs = {1: 1, 3: 3, 31: 3, 4: 4}
p_rhs = {1: 1, 3: 3, 31: 31, 4: 4}
lhs_typing_g2 = {1: 1, 2: 1, 3: 2, 4: 4}
rhs_typing_g2 = {1: 1, 3: 2, 31: 2, 4: 4}
lhs_typing_g3 = {1: 1, 2: 1, 3: 1, 4: 2}
rhs_typing_g3 = {1: 1, 3: 1, 31: 1, 4: 2}
rule = Rule(p, lhs, rhs, p_lhs, p_rhs)
self.hierarchy.add_rule("r2", rule,
{"name": "Second rule: with multiple typing"})
self.hierarchy.add_rule_typing("r2", "g2", lhs_typing_g2,
rhs_typing_g2)
self.hierarchy.add_rule_typing("r2", "g3", lhs_typing_g3,
rhs_typing_g3)
pattern = nx.DiGraph()
prim.add_nodes_from(pattern, [1, 2])
prim.add_edges_from(pattern, [(2, 1)])
lhs_typing = {
"g0": {
1: "circle",
2: "circle"
},
"g00": {
1: "black",
2: "white"
}
}
p = nx.DiGraph()
prim.add_nodes_from(p, [1, 2, 21])
prim.add_edges_from(p, [(21, 1)])
rhs = copy.deepcopy(p)
p_lhs = {1: 1, 2: 2, 21: 2}
p_rhs = {1: 1, 2: 2, 21: 21}
rule = Rule(p, pattern, rhs, p_lhs, p_rhs)
rhs_typing = {
"g0": ({
1: "circle",
2: "circle",
21: "circle",
}),
"g00": ({
1: "black",
2: "white",
21: "white"
})
}
instances = self.hierarchy.find_matching("g1", pattern, lhs_typing)
self.hierarchy.rewrite("g1", rule, instances[0], lhs_typing,
rhs_typing)
def __init__(self):
self.hierarchy = NetworkXHierarchy()
a = nx.DiGraph()
primitives.add_nodes_from(a, [
("red", {"sex": {"male", "female"}}),
("blue", {"location": {"far", "close"}})
])
primitives.add_edges_from(a, [
("red", "red", {"type": {"friend", "supervisor"}}),
("red", "blue", {"type": "works"}),
("blue", "blue")
])
self.hierarchy.add_graph("a", a)
b = nx.DiGraph()
primitives.add_nodes_from(b, [
("prof", {"sex": {"male", "female"}}),
("student", {"sex": {"male", "female"}}),
("school", {"location": {"far", "close"}}),
("institute", {"location": {"far", "close"}})
])
primitives.add_edges_from(
b,
[
("prof", "prof", {"type": "friend"}),
("student", "student", {"type": "friend"}),
("prof", "student", {"type": {"friend", "supervisor"}}),
("student", "prof", {"type": "friend"}),
("prof", "school"),
("prof", "institute"),
("student", "school"),
("institute", "school")
])
self.hierarchy.add_graph("b", b)
b_a = {
"prof": "red",
"student": "red",
"school": "blue",
"institute": "blue"
}
self.hierarchy.add_graph("bb", b)
self.hierarchy.add_typing("b", "bb",
{n: n for n in b.nodes()})
self.hierarchy.add_typing("b", "a", b_a)
self.hierarchy.add_typing("bb", "a", b_a)
c = nx.DiGraph()
primitives.add_nodes_from(c, [
("Alice", {"sex": "female"}),
("Bob", {"sex": "male"}),
("John", {"sex": "male"}),
("Nancy", {"sex": "female"}),
("ENS", {"location": "close"}),
("INRIA")
])
primitives.add_edges_from(c, [
("Alice", "Bob", {"type": "friend"}),
("Alice", "ENS"),
("John", "Alice", {"type": "supervisor"}),
("John", "ENS"),
("Nancy", "John", {"type": "friend"}),
("Nancy", "INRIA")
])
c_b = {
"Alice": "student",
"Bob": "student",
"John": "prof",
"Nancy": "prof",
"ENS": "school",
"INRIA": "institute"
}
self.hierarchy.add_graph("c", c)
self.hierarchy.add_typing("c", "b", c_b)
def __init__(self):
self.hierarchy = Hierarchy(directed=True)
g0 = nx.DiGraph()
prim.add_node(g0, "circle", {"a": {1, 2, 3}})
prim.add_node(g0, "square", {"a": {1, 2, 3, 5}})
prim.add_node(g0, "triangle", {"new_attrs": {1}})
prim.add_edges_from(
g0,
[
("circle", "circle"), # , {"b": {1, 2, 3, 4}}),
("circle", "square"),
("square", "circle", {
"new_attrs": {2}
}),
("square", "triangle", {
"new_attrs": {3, 4}
})
])
self.hierarchy.add_graph("g0", g0, {"name": "Shapes"})
g00 = nx.DiGraph()
prim.add_node(g00, 'black', {"a": {1, 2, 3}, "new_attrs": {1}})
prim.add_node(g00, 'white', {"a": {1, 2, 3, 5}})
prim.add_edges_from(g00, [('white', 'white', {
"new_attrs": 2
}), ('white', 'black', {
"new_attrs": {4, 3}
}), ('black', 'black'), ('black', 'white')])
self.hierarchy.add_graph("g00", g00, {"name": "Colors"})
g1 = nx.DiGraph()
prim.add_nodes_from(g1, [("black_circle", {
"a": {1, 2, 3}
}), "white_circle", "black_square", ("white_square", {
"a": {1, 2}
}), "black_triangle", "white_triangle"])
prim.add_edges_from(
g1,
[
("black_circle", "black_circle"), # {"b": {1, 2, 3, 4}}),
("black_circle", "white_circle"),
("black_circle", "black_square"),
("white_circle", "black_circle"),
("white_circle", "white_square"),
("black_square", "black_circle"),
("black_square", "black_triangle"),
("black_square", "white_triangle"),
("white_square", "white_circle"),
("white_square", "black_triangle"),
("white_square", "white_triangle")
])
self.hierarchy.add_graph("g1", g1)
self.hierarchy.add_typing(
"g1", "g0", {
"black_circle": "circle",
"white_circle": "circle",
"black_square": "square",
"white_square": "square",
"black_triangle": "triangle",
"white_triangle": "triangle"
})
self.hierarchy.add_typing(
"g1", "g00", {
"black_square": "black",
"black_circle": "black",
"black_triangle": "black",
"white_square": "white",
"white_circle": "white",
"white_triangle": "white"
})
g2 = nx.DiGraph()
prim.add_nodes_from(g2, [
(1, {
"a": {1, 2}
}),
2,
3,
4,
(5, {
"a": {1}
}),
6,
7,
])
prim.add_edges_from(
g2,
[
(1, 2), # {"b": {1, 2, 3}}),
(2, 3),
(3, 6),
(3, 7),
(4, 2),
(4, 5),
(5, 7)
])
self.hierarchy.add_graph("g2", g2)
self.hierarchy.add_typing(
"g2", "g1", {
1: "black_circle",
2: "black_circle",
3: "black_square",
4: "white_circle",
5: "white_square",
6: "white_triangle",
7: "black_triangle"
})
g3 = nx.DiGraph()
prim.add_nodes_from(
g3,
[
(1), # {"a": {1, 2}}),
2,
3,
5,
(4), # {"a": {1}}),
6,
7,
])
prim.add_edges_from(
g3,
[
(1, 1), # , {"b": {1, 2, 3}}),
(1, 2),
(1, 3),
(1, 5),
(2, 1),
(3, 4),
(4, 7),
(4, 6),
(5, 6),
(5, 7)
])
self.hierarchy.add_graph("g3", g3)
self.hierarchy.add_typing(
"g3", "g1", {
1: "black_circle",
2: "white_circle",
3: "white_circle",
5: "black_square",
4: "white_square",
6: "white_triangle",
7: "black_triangle"
})
g4 = nx.DiGraph()
prim.add_nodes_from(g4, [1, 2, 3])
prim.add_edges_from(g4, [(1, 2), (2, 3)])
self.hierarchy.add_graph("g4", g4)
self.hierarchy.add_typing("g4", "g2", {1: 2, 2: 3, 3: 6})
self.hierarchy.add_typing("g4", "g3", {1: 1, 2: 5, 3: 6})
g5 = nx.DiGraph()
prim.add_nodes_from(
g5,
[
("black_circle"), # {"a": {255}}),
("black_square"), # {"a": {256}}),
("white_triangle"), # {"a": {257}}),
("star") # , {"a": {258}})
])
prim.add_edges_from(
g5,
[
("black_circle", "black_square"),
("black_square", "white_triangle"), # , {"b": {11}}),
("star", "black_square"),
("star", "white_triangle")
])
self.hierarchy.add_graph("g5", g5)
def __init__(self):
hierarchy = NetworkXHierarchy()
base = nx.DiGraph()
prim.add_nodes_from(base, [
("circle", {"a": {1, 2, 3}}),
("square", {"b": {1, 2, 3}})
])
prim.add_edges_from(base, [
("circle", "circle"),
("square", "square"),
("circle", "square", {"c": {5, 6, 7}}),
("square", "circle")
])
hierarchy.add_graph("base", base)
a1 = nx.DiGraph()
prim.add_nodes_from(a1, [
("black_circle", {"a": {1}}),
("white_circle", {"a": {2}}),
("black_square", {"b": {1}}),
("white_square", {"b": {1}})
])
prim.add_edges_from(a1, [
("white_circle", "white_circle"),
("white_circle", "white_square", {"c": {5}}),
("black_circle", "black_square"),
("black_square", "white_square"),
("black_circle", "white_square", {"c": {6}})
])
hierarchy.add_graph("a1", a1)
hierarchy.add_typing(
"a1", "base",
{
"black_circle": "circle",
"white_circle": "circle",
"white_square": "square",
"black_square": "square"
}
)
a2 = nx.DiGraph()
prim.add_nodes_from(a2, [
("right_circle", {"a": {1, 2}}),
("middle_square", {"b": {1}}),
("left_circle", {"a": 1})
])
prim.add_edges_from(a2, [
("right_circle", "middle_square", {"c": {5, 6, 7}}),
("left_circle", "middle_square", {"c": {6, 7}})
])
hierarchy.add_graph("a2", a2)
hierarchy.add_typing(
"a2", "base",
{
"right_circle": "circle",
"middle_square": "square",
"left_circle": "circle"
}
)
self.hierarchy = hierarchy
def get_rule_projections(tx, hierarchy, graph_id, rule, instance, rhs_typing=None):
"""Execute the query finding rule liftings."""
if rhs_typing is None:
rhs_typing = {}
projections = {}
if rule.is_relaxing():
if len(rule.lhs.nodes()) > 0:
lhs_instance = {
n: instance[n] for n in rule.lhs.nodes()
}
lhs_vars = {
n: n for n in rule.lhs.nodes()}
match_instance_vars = {
v: lhs_instance[k] for k, v in lhs_vars.items()
}
# Match nodes
query = "// Match nodes the instance of the rewritten graph \n"
query += "MATCH {}".format(
", ".join([
"({}:{} {{id: '{}'}})".format(k, graph_id, v)
for k, v in match_instance_vars.items()
])
)
query += "\n\n"
carry_vars = list(lhs_vars.values())
for k, v in lhs_vars.items():
query += (
"OPTIONAL MATCH (n)<-[:typing*1..]-({})\n".format(v) +
"WITH {} \n".format(
", ".join(
carry_vars +
["collect(DISTINCT {{type:'node', origin: {}.id, id: n.id, graph:labels(n)[0], attrs: properties(n)}}) as {}_dict\n".format(
v, v)])
)
)
carry_vars.append("{}_dict".format(v))
# Match edges
for (u, v) in rule.p.edges():
edge_var = "{}_{}".format(lhs_vars[u], lhs_vars[v])
query += "OPTIONAL MATCH ({}_instance)-[{}:edge]->({}_instance)\n".format(
lhs_vars[u],
edge_var,
lhs_vars[v])
query += "WHERE ({})<-[:typing*1..]-({}) AND ({})<-[:typing*1..]-({})\n".format(
"{}_instance".format(lhs_vars[u]), lhs_vars[u],
"{}_instance".format(lhs_vars[v]), lhs_vars[v])
query += (
"WITH {} \n".format(
", ".join(carry_vars + [
"collect({{type: 'edge', source: {}.id, target: {}.id, graph:labels({})[0], attrs: properties({})}}) as {}\n".format(
"{}_instance".format(lhs_vars[u]),
"{}_instance".format(lhs_vars[v]),
"{}_instance".format(lhs_vars[u]),
edge_var,
edge_var)
])
)
)
carry_vars.append(edge_var)
query += "RETURN {}".format(
", ".join(
["{}_dict as {}".format(v, v) for v in lhs_vars.values()] +
["{}_{}".format(lhs_vars[u], lhs_vars[v]) for u, v in rule.p.edges()]))
result = tx.run(query)
record = result.single()
l_l_ts = {}
l_nodes = {}
l_edges = {}
for k, v in record.items():
if len(v) > 0:
if v[0]["type"] == "node":
for el in v:
l_node = keys_by_value(instance, el["origin"])[0]
if el["graph"] not in l_nodes:
l_nodes[el["graph"]] = {}
l_l_ts[el["graph"]] = {}
if el["id"] not in l_nodes[el["graph"]]:
l_nodes[el["graph"]][el["id"]] = {}
l_nodes[el["graph"]][el["id"]] = attrs_union(
l_nodes[el["graph"]][el["id"]],
attrs_intersection(
generic.convert_props_to_attrs(el["attrs"]),
get_node(rule.lhs, l_node)))
l_l_ts[el["graph"]][l_node] = el["id"]
else:
for el in v:
l_sources = keys_by_value(l_l_ts[el["graph"]], el["source"])
l_targets = keys_by_value(l_l_ts[el["graph"]], el["target"])
for l_source in l_sources:
for l_target in l_targets:
if exists_edge(rule.l, l_source, l_target):
if el["graph"] not in l_edges:
l_edges[el["graph"]] = {}
if (el["source"], el["target"]) not in l_edges[el["graph"]]:
l_edges[el["graph"]][(el["source"], el["target"])] = {}
l_edges[el["graph"]][(el["source"], el["target"])] =\
attrs_union(
l_edges[el["graph"]][(el["source"], el["target"])],
attrs_intersection(
generic.convert_props_to_attrs(el["attrs"]),
get_edge(rule.lhs, l_source, l_target)))
for graph, typing in hierarchy.get_descendants(graph_id).items():
if graph in l_nodes:
nodes = l_nodes[graph]
else:
nodes = {}
if graph in l_edges:
edges = l_edges[graph]
else:
edges = {}
l = nx.DiGraph()
add_nodes_from(l, [(k, v) for k, v in nodes.items()])
if graph in l_edges:
add_edges_from(
l,
[(s, t, v) for (s, t), v in edges.items()])
rhs, p_rhs, r_r_t = pushout(
rule.p, l, rule.rhs, compose(rule.p_lhs, l_l_ts[graph]), rule.p_rhs)
l_t_t = {n: n for n in nodes}
# Modify P_T and R_T according to the controlling
# relation rhs_typing
if graph in rhs_typing.keys():
r_t_factorization = {
r_r_t[k]: v
for k, v in rhs_typing[graph].items()
}
added_t_nodes = set()
for n in rhs.nodes():
if n in r_t_factorization.keys():
# If corresponding R_T node is specified in
# the controlling relation add nodes of T
# that type it to P
t_nodes = r_t_factorization[n]
for t_node in t_nodes:
if t_node not in l_t_t.values() and\
t_node not in added_t_nodes:
new_p_node = generate_new_id(
l.nodes(), t_node)
l.add_node(new_p_node)
added_t_nodes.add(t_node)
p_rhs[new_p_node] = n
l_t_t[new_p_node] = t_node
else:
p_rhs[keys_by_value(l_t_t, t_node)[0]] = n
projections[graph] = {
"rule": Rule(p=l, rhs=rhs, p_rhs=p_rhs),
"instance": l_t_t,
"l_l_t": l_l_ts[graph],
"p_p_t": {k: l_l_ts[graph][v] for k, v in rule.p_lhs.items()},
"r_r_t": r_r_t
}
return projections
"""ReGraph hierarchy tutorial ex 1."""
import networkx as nx
from regraph import Hierarchy, plot_graph, primitives
# create an empty hierarchy
hierarchy = Hierarchy()
# initialize graphs `t` & `g`
t = nx.DiGraph()
primitives.add_nodes_from(t, ["agent", "action", "state"])
primitives.add_edges_from(t, [("agent", "agent"), ("state", "agent"),
("agent", "action"), ("action", "state")])
g = nx.DiGraph()
primitives.add_nodes_from(g, ["protein", "region", "activity", "mod"])
primitives.add_edges_from(g, [("region", "protein"), ("activity", "protein"),
("activity", "region"), ("protein", "mod"),
("region", "mod"), ("mod", "activity")])
# add graphs to the hierarchy
hierarchy.add_graph("T", t)
hierarchy.add_graph("G", g)
# add typing of `g` by `t`
mapping = {
"protein": "agent",
"region": "agent",
"activity": "state",
"mod": "action"
}
def test_neo4j_hierarchy_versioning(self):
"""Test hierarchy versioning functionality."""
try:
hierarchy = Neo4jHierarchy(uri="bolt://localhost:7687",
user="******",
password="******")
hierarchy._clear()
hierarchy.add_graph("shapes",
node_list=[("c", {
"a": 1
}), ("s", {
"b": 2
})])
hierarchy.add_graph("colors",
node_list=[("w", {
"a": 1,
"b": 2
}), ("b", {
"a": 1,
"b": 2
})])
hierarchy.add_graph("ag",
node_list=[("wc", {
"a": 1
}), "bc", "ws", ("bs", {
"b": 2
})])
hierarchy.add_graph("nugget",
node_list=[("wc1", {
"a": 1
}), "wc2", "bc1", "ws1", ("bs2", {
"b": 2
})])
hierarchy.add_typing("ag", "shapes", {
"wc": "c",
"bc": "c",
"ws": "s",
"bs": "s"
})
hierarchy.add_typing("ag", "colors", {
"wc": "w",
"bc": "b",
"ws": "w",
"bs": "b"
})
hierarchy.add_typing("nugget", "ag", {
"wc1": "wc",
"wc2": "wc",
"bc1": "bc",
"ws1": "ws",
"bs2": "bs"
})
hierarchy.add_typing("nugget", "colors", {
"wc1": "w",
"wc2": "w",
"bc1": "b",
"ws1": "w",
"bs2": "b"
})
hierarchy.add_graph("base", node_list=[("node", {"a": 1, "b": 2})])
hierarchy.add_typing("colors", "base", {"w": "node", "b": "node"})
pattern = nx.DiGraph()
pattern.add_nodes_from(["s", "c"])
rule = Rule.from_transform(pattern)
rule.inject_add_edge("s", "c", {"c": 3})
hierarchy.rewrite("nugget", rule, {"s": "bs2", "c": "wc1"})
h = VersionedHierarchy(hierarchy)
rollback_commit = h._heads["master"]
pattern = nx.DiGraph()
primitives.add_nodes_from(pattern, [("s", {
"b": 2
}), ("c", {
"a": 1
})])
primitives.add_edges_from(pattern, [("s", "c", {"c": 3})])
rule2 = Rule.from_transform(pattern)
clone, _ = rule2.inject_clone_node("s")
rule2.inject_add_node("new_node")
rule2.inject_add_edge("new_node", "s", {"d": 4})
merged_rule_node = rule2.inject_merge_nodes([clone, "c"])
rule2.inject_remove_edge("s", "c")
rhs_instances, first_commit = h.rewrite(
"ag",
rule2, {
"s": "bs",
"c": "wc"
},
message="Rewriting neo4j graph")
merged_ag_node = rhs_instances["ag"][merged_rule_node]
h.branch('test')
pattern = nx.DiGraph()
pattern.add_nodes_from(["ws"])
rule3 = Rule.from_transform(pattern)
rule3.inject_remove_node("ws")
h.rewrite("ag", rule3, {"ws": "ws"}, message="Removed ws from ag")
h.switch_branch("master")
pattern = nx.DiGraph()
pattern.add_nodes_from([merged_ag_node])
rule4 = Rule.from_transform(pattern)
rule4.inject_clone_node(merged_ag_node)
h.rewrite("ag",
rule4, {merged_ag_node: merged_ag_node},
message="Cloned merged from ag")
h.merge_with("test")
data = h.to_json()
h1 = VersionedHierarchy.from_json(hierarchy, data)
h1.print_history()
h1.rollback(rollback_commit)
# except ServiceUnavailable as e:
# print(e)
except:
print()
def get_rule_liftings(tx, graph_id, rule, instance, p_typing=None):
"""Execute the query finding rule liftings."""
if p_typing is None:
p_typing = {}
liftings = {}
if len(rule.lhs.nodes()) > 0:
lhs_vars = {
n: n for n in rule.lhs.nodes()}
match_instance_vars = {lhs_vars[k]: v for k, v in instance.items()}
# Match nodes
query = "// Match nodes the instance of the rewritten graph \n"
query += "MATCH {}".format(
", ".join([
"({}:{} {{id: '{}'}})".format(k, graph_id, v)
for k, v in match_instance_vars.items()
])
)
query += "\n\n"
carry_vars = list(lhs_vars.values())
for k, v in lhs_vars.items():
query += (
"OPTIONAL MATCH (n)-[:typing*1..]->({})\n".format(v) +
"WITH {} \n".format(
", ".join(carry_vars + [
"collect({{type:'node', origin: {}.id, id: n.id, graph:labels(n)[0], attrs: properties(n)}}) as {}_dict\n".format(
v, v)])
)
)
carry_vars.append("{}_dict".format(v))
# Match edges
for (u, v) in rule.lhs.edges():
edge_var = "{}_{}".format(lhs_vars[u], lhs_vars[v])
query += "OPTIONAL MATCH ({}_instance)-[{}:edge]->({}_instance)\n".format(
lhs_vars[u],
edge_var,
lhs_vars[v])
query += "WHERE ({})-[:typing*1..]->({}) AND ({})-[:typing*1..]->({})\n".format(
"{}_instance".format(lhs_vars[u]), lhs_vars[u],
"{}_instance".format(lhs_vars[v]), lhs_vars[v])
query += (
"WITH {} \n".format(
", ".join(carry_vars + [
"collect({{type: 'edge', source: {}.id, target: {}.id, attrs: properties({}), graph:labels({})[0]}}) as {}\n".format(
"{}_instance".format(lhs_vars[u]),
"{}_instance".format(lhs_vars[v]),
edge_var,
"{}_instance".format(lhs_vars[u]),
edge_var)
])
)
)
carry_vars.append(edge_var)
query += "RETURN {}".format(
", ".join(
["{}_dict as {}".format(v, v) for v in lhs_vars.values()] +
["{}_{}".format(lhs_vars[u], lhs_vars[v]) for u, v in rule.lhs.edges()]))
result = tx.run(query)
record = result.single()
l_g_ls = {}
lhs_nodes = {}
lhs_edges = {}
for k, v in record.items():
if len(v) > 0:
if v[0]["type"] == "node":
for el in v:
if el["graph"] not in lhs_nodes:
lhs_nodes[el["graph"]] = []
l_g_ls[el["graph"]] = {}
l_g_ls[el["graph"]][el["id"]] = keys_by_value(
instance, el["origin"])[0]
# compute attr intersection
attrs = attrs_intersection(
generic.convert_props_to_attrs(el["attrs"]),
get_node(rule.lhs, l_g_ls[el["graph"]][el["id"]]))
lhs_nodes[el["graph"]].append((el["id"], attrs))
else:
for el in v:
if el["graph"] not in lhs_edges:
lhs_edges[el["graph"]] = []
# compute attr intersection
attrs = attrs_intersection(
generic.convert_props_to_attrs(el["attrs"]),
get_edge(
rule.lhs,
l_g_ls[el["graph"]][el["source"]],
l_g_ls[el["graph"]][el["target"]]))
lhs_edges[el["graph"]].append(
(el["source"], el["target"], attrs)
)
for graph, nodes in lhs_nodes.items():
lhs = nx.DiGraph()
add_nodes_from(lhs, nodes)
if graph in lhs_edges:
add_edges_from(
lhs, lhs_edges[graph])
p, p_lhs, p_g_p = pullback(
lhs, rule.p, rule.lhs, l_g_ls[graph], rule.p_lhs)
l_g_g = {n[0]: n[0] for n in nodes}
# Remove controlled things from P_G
if graph in p_typing.keys():
l_g_factorization = {
keys_by_value(l_g_g, k)[0]: v
for k, v in p_typing[graph].items()
}
p_g_nodes_to_remove = set()
for n in p.nodes():
l_g_node = p_lhs[n]
# If corresponding L_G node is specified in
# the controlling relation, remove all
# the instances of P nodes not mentioned
# in this relations
if l_g_node in l_g_factorization.keys():
p_nodes = l_g_factorization[l_g_node]
if p_g_p[n] not in p_nodes:
del p_g_p[n]
del p_lhs[n]
p_g_nodes_to_remove.add(n)
for n in p_g_nodes_to_remove:
p.remove_node(n)
liftings[graph] = {
"rule": Rule(p=p, lhs=lhs, p_lhs=p_lhs),
"instance": l_g_g,
"l_g_l": l_g_ls[graph],
"p_g_p": p_g_p
}
else:
query = generic.ancestors_query(graph_id, "graph", "homomorphism")
result = tx.run(query)
ancestors = [record["ancestor"] for record in result]
for a in ancestors:
liftings[a] = {
"rule": Rule.identity_rule(),
"instance": {},
"l_g_l": {},
"p_g_p": {}
}
return liftings
def test_rewrite(self):
pattern = nx.DiGraph()
prim.add_nodes_from(pattern, [
1,
(2, {"a": {1, 2}}),
3
])
prim.add_edges_from(pattern, [
(1, 2),
(2, 3)
])
lhs_typing = {
"g0": {1: "circle", 2: "square", 3: "triangle"},
"g00": {1: "white", 2: "white", 3: "black"}
}
p = nx.DiGraph()
p.add_nodes_from([
1,
2,
3
])
p.add_edges_from([
(2, 3)
])
rhs = nx.DiGraph()
prim.add_nodes_from(rhs, [
1,
(2, {"a": {3, 5}}),
(3, {"new_attrs": {1}}),
4
])
prim.add_edges_from(rhs, [
(2, 1, {"new_attrs": {2}}),
(2, 4, {"new_attrs": {3}}),
(2, 3, {"new_attrs": {4}})
])
p_lhs = {1: 1, 2: 2, 3: 3}
p_rhs = {1: 1, 2: 2, 3: 3}
rule = Rule(p, pattern, rhs, p_lhs, p_rhs)
rhs_typing = {
"g0": {
1: "circle",
2: "square",
3: "triangle",
4: "triangle"
},
"g00": {
1: "white",
2: "white",
3: "black",
4: "black"
}
}
instances = self.hierarchy.find_matching(
"g1",
pattern,
lhs_typing
)
# print(instances[0])
self.hierarchy.rewrite(
"g1",
rule,
instances[0],
lhs_typing,
rhs_typing
)
def __init__(self):
hierarchy = Hierarchy()
hierarchy = Hierarchy()
colors = nx.DiGraph()
primitives.add_nodes_from(
colors,
[("red", {"r": 255, "g": 0, "b": 0}),
("blue", {"r": 0, "g": 0, "b": 255})]
)
primitives.add_edges_from(
colors,
[("red", "red"), ("blue", "red"), ("red", "blue")]
)
hierarchy.add_graph("colors", colors)
mmm = nx.DiGraph()
primitives.add_nodes_from(
mmm,
["component", "state", "action"]
)
primitives.add_edges_from(
mmm,
[("component", "action"),
("component", "component"),
("state", "component"),
("action", "state")]
)
hierarchy.add_graph("mmm", mmm)
mm = nx.DiGraph()
primitives.add_nodes_from(
mm,
["gene", "residue", "state", "mod"]
)
primitives.add_edges_from(
mm,
[("residue", "gene"),
("state", "gene"),
("state", "residue"),
("mod", "state"),
("gene", "mod")]
)
hierarchy.add_graph("mm", mm)
action_graph = nx.DiGraph()
primitives.add_nodes_from(
action_graph,
["A", "A_res_1", "p_a", "B", "mod1",
"mod2", "C", "p_c", "activity"]
)
primitives.add_edges_from(
action_graph,
[("A_res_1", "A"),
("p_a", "A_res_1"),
("mod1", "p_a"),
("B", "mod1"),
("p_c", "C"),
("B", "mod2"),
("activity", "B"),
("mod2", "p_c")]
)
hierarchy.add_graph("ag", action_graph)
nugget_1 = nx.DiGraph()
primitives.add_nodes_from(
nugget_1,
["A", "A_res_1", "p", "B", "mod"]
)
primitives.add_edges_from(
nugget_1,
[("A_res_1", "A"),
("p", "A_res_1"),
("mod", "p"),
("B", "mod")]
)
hierarchy.add_graph("n1", nugget_1)
nugget_2 = nx.DiGraph()
primitives.add_nodes_from(
nugget_2,
["B", "activity", "mod", "p", "C"])
primitives.add_edges_from(nugget_2, [
("activity", "B"),
("B", "mod"),
("mod", "p"),
("p", "C")])
hierarchy.add_graph("n2", nugget_2)
# add typings
hierarchy.add_typing(
"mm", "mmm",
{
"gene": "component",
"residue": "component",
"state": "state",
"mod": "action"
}, total=True
)
hierarchy.add_typing(
"mm", "colors",
{
"gene": "red",
"residue": "red",
"state": "red",
"mod": "blue"
}
)
hierarchy.add_typing(
"ag", "mm",
{
"A": "gene",
"B": "gene",
"A_res_1": "residue",
"mod1": "mod",
"p_a": "state",
"C": "gene",
"activity": "state",
"p_c": "state",
"mod2": "mod"
}, total=True
)
hierarchy.add_typing(
"n1", "ag",
{
"A": "A",
"B": "B",
"A_res_1": "A_res_1",
"mod": "mod1",
"p": "p_a",
}, total=True
)
hierarchy.add_typing(
"n2", "ag",
{
"B": "B",
"C": "C",
"p": "p_c",
"activity": "activity",
"mod": "mod2",
}, total=True
)
self.hierarchy = hierarchy
def test_add_rule(self):
lhs = nx.DiGraph()
prim.add_nodes_from(lhs, [1, 2, 3])
prim.add_edges_from(lhs, [(1, 2), (2, 1), (2, 3)])
p = nx.DiGraph()
prim.add_nodes_from(p, [1, 2, 3, 31])
prim.add_edges_from(p, [(1, 2), (2, 3), (2, 31)])
rhs = nx.DiGraph()
prim.add_nodes_from(rhs, [1, 2, 3, 31, 4])
prim.add_edges_from(rhs, [(1, 2), (4, 2), (2, 3), (2, 31)])
p_lhs = {1: 1, 2: 2, 3: 3, 31: 3}
p_rhs = {1: 1, 2: 2, 3: 3, 31: 3}
rule = Rule(p, lhs, rhs, p_lhs, p_rhs)
lhs_typing = {1: "black_circle", 2: "white_circle", 3: "white_square"}
rhs_typing = {
1: "black_circle",
2: "white_circle",
3: "white_square",
31: "white_square",
4: "black_circle"
}
self.hierarchy.add_rule("r1", rule, {"name": "First rule"})
self.hierarchy.add_rule_typing("r1", "g1", lhs_typing, rhs_typing)
pattern = nx.DiGraph()
prim.add_nodes_from(pattern, [1, (2, {"a": {1, 2}}), 3])
prim.add_edges_from(pattern, [(1, 2), (2, 3)])
lhs_typing = {
"g0": {
1: "circle",
2: "square",
3: "triangle"
},
"g00": {
1: 'white',
2: 'white',
3: 'black'
}
}
p = nx.DiGraph()
prim.add_nodes_from(p, [1, 11, 2, 3])
prim.add_edges_from(p, [(2, 3)])
rhs = nx.DiGraph()
prim.add_nodes_from(rhs, [
1,
11,
(2, {
"a": {3, 5}
}),
(3, {
"new_attrs": {1}
}),
])
prim.add_edges_from(rhs, [(2, 3, {"new_attrs": {4}})])
p_lhs = {1: 1, 11: 1, 2: 2, 3: 3}
p_rhs = {1: 1, 11: 11, 2: 2, 3: 3}
rule = Rule(p, pattern, rhs, p_lhs, p_rhs)
rhs_typing = {
"g0": {
1: "circle",
11: "circle",
2: "square",
3: "triangle"
},
"g00": {
1: "white",
11: "white",
2: "white",
3: "black"
}
}
instances = self.hierarchy.find_matching("g1", pattern, lhs_typing)
self.hierarchy.rewrite("g1", rule, instances[0], lhs_typing,
rhs_typing)
def test_add_rule_multiple_typing(self):
lhs = nx.DiGraph()
prim.add_nodes_from(lhs, [1, 2, 3, 4])
prim.add_edges_from(lhs, [
(1, 3),
(2, 3),
(4, 3)
])
p = nx.DiGraph()
prim.add_nodes_from(p, [1, 3, 31, 4])
prim.add_edges_from(p, [
(1, 3),
(1, 31),
(4, 3),
(4, 31)
])
rhs = copy.deepcopy(p)
p_lhs = {1: 1, 3: 3, 31: 3, 4: 4}
p_rhs = {1: 1, 3: 3, 31: 31, 4: 4}
lhs_typing_g2 = {
1: 1,
2: 1,
3: 2,
4: 4
}
rhs_typing_g2 = {
1: 1,
3: 2,
31: 2,
4: 4
}
lhs_typing_g3 = {
1: 1,
2: 1,
3: 1,
4: 2
}
rhs_typing_g3 = {
1: 1,
3: 1,
31: 1,
4: 2
}
rule = Rule(p, lhs, rhs, p_lhs, p_rhs)
self.hierarchy.add_rule(
"r2", rule, {"name": "Second rule: with multiple typing"})
self.hierarchy.add_rule_typing(
"r2", "g2", lhs_typing_g2, rhs_typing_g2)
self.hierarchy.add_rule_typing(
"r2", "g3", lhs_typing_g3, rhs_typing_g3)
pattern = nx.DiGraph()
prim.add_nodes_from(pattern, [
1,
2
])
prim.add_edges_from(pattern, [
(2, 1)
])
lhs_typing = {
"g0": {1: "circle", 2: "circle"},
"g00": {1: "black", 2: "white"}
}
p = nx.DiGraph()
prim.add_nodes_from(p, [
1,
2,
21
])
prim.add_edges_from(p, [
(21, 1)
])
rhs = copy.deepcopy(p)
p_lhs = {1: 1, 2: 2, 21: 2}
p_rhs = {1: 1, 2: 2, 21: 21}
rule = Rule(p, pattern, rhs, p_lhs, p_rhs)
rhs_typing = {
"g0": ({
1: "circle",
2: "circle",
21: "circle",
}),
"g00": ({
1: "black",
2: "white",
21: "white"
})
}
instances = self.hierarchy.find_matching(
"g1",
pattern,
lhs_typing
)
self.hierarchy.rewrite(
"g1",
rule,
instances[0],
lhs_typing,
rhs_typing
)
def __init__(self):
hierarchy = NetworkXHierarchy()
base = nx.DiGraph()
prim.add_nodes_from(base, [("circle", {
"a": {1, 2, 3}
}), ("square", {
"b": {1, 2, 3}
})])
prim.add_edges_from(base, [("circle", "circle"), ("square", "square"),
("circle", "square", {
"c": {5, 6, 7}
}), ("square", "circle")])
hierarchy.add_graph("base", base)
a1 = nx.DiGraph()
prim.add_nodes_from(a1, [("black_circle", {
"a": {1}
}), ("white_circle", {
"a": {2}
}), ("black_square", {
"b": {1}
}), ("white_square", {
"b": {1}
})])
prim.add_edges_from(a1, [("white_circle", "white_circle"),
("white_circle", "white_square", {
"c": {5}
}), ("black_circle", "black_square"),
("black_square", "white_square"),
("black_circle", "white_square", {
"c": {6}
})])
hierarchy.add_graph("a1", a1)
hierarchy.add_typing(
"a1", "base", {
"black_circle": "circle",
"white_circle": "circle",
"white_square": "square",
"black_square": "square"
})
a2 = nx.DiGraph()
prim.add_nodes_from(a2, [("right_circle", {
"a": {1, 2}
}), ("middle_square", {
"b": {1}
}), ("left_circle", {
"a": 1
})])
prim.add_edges_from(a2, [("right_circle", "middle_square", {
"c": {5, 6, 7}
}), ("left_circle", "middle_square", {
"c": {6, 7}
})])
hierarchy.add_graph("a2", a2)
hierarchy.add_typing(
"a2", "base", {
"right_circle": "circle",
"middle_square": "square",
"left_circle": "circle"
})
self.hierarchy = hierarchy
def test_add_rule(self):
lhs = nx.DiGraph()
prim.add_nodes_from(lhs, [
1, 2, 3
])
prim.add_edges_from(lhs, [
(1, 2),
(2, 1),
(2, 3)
])
p = nx.DiGraph()
prim.add_nodes_from(p, [
1, 2, 3, 31
])
prim.add_edges_from(p, [
(1, 2),
(2, 3),
(2, 31)
])
rhs = nx.DiGraph()
prim.add_nodes_from(rhs, [
1, 2, 3, 31, 4
])
prim.add_edges_from(rhs, [
(1, 2),
(4, 2),
(2, 3),
(2, 31)
])
p_lhs = {1: 1, 2: 2, 3: 3, 31: 3}
p_rhs = {1: 1, 2: 2, 3: 3, 31: 3}
rule = Rule(p, lhs, rhs, p_lhs, p_rhs)
lhs_typing = {
1: "black_circle",
2: "white_circle",
3: "white_square"
}
rhs_typing = {
1: "black_circle",
2: "white_circle",
3: "white_square",
31: "white_square",
4: "black_circle"
}
self.hierarchy.add_rule("r1", rule, {"name": "First rule"})
self.hierarchy.add_rule_typing("r1", "g1", lhs_typing, rhs_typing)
pattern = nx.DiGraph()
prim.add_nodes_from(pattern, [
1,
(2, {"a": {1, 2}}),
3
])
prim.add_edges_from(pattern, [
(1, 2),
(2, 3)
])
lhs_typing = {
"g0": {1: "circle", 2: "square", 3: "triangle"},
"g00": {1: 'white', 2: 'white', 3: 'black'}
}
p = nx.DiGraph()
prim.add_nodes_from(p, [
1,
11,
2,
3
])
prim.add_edges_from(p, [
(2, 3)
])
rhs = nx.DiGraph()
prim.add_nodes_from(rhs, [
1,
11,
(2, {"a": {3, 5}}),
(3, {"new_attrs": {1}}),
])
prim.add_edges_from(rhs, [
(2, 3, {"new_attrs": {4}})
])
p_lhs = {1: 1, 11: 1, 2: 2, 3: 3}
p_rhs = {1: 1, 11: 11, 2: 2, 3: 3}
rule = Rule(p, pattern, rhs, p_lhs, p_rhs)
rhs_typing = {
"g0": {
1: "circle",
11: "circle",
2: "square",
3: "triangle"
},
"g00": {
1: "white",
11: "white",
2: "white",
3: "black"
}
}
instances = self.hierarchy.find_matching(
"g1", pattern, lhs_typing)
self.hierarchy.rewrite(
"g1", rule, instances[0], lhs_typing, rhs_typing)
def test_refinement(self):
graph = NXGraph()
prim.add_nodes_from(graph, [
("a", {
"name": "Bob"
}),
("b", {
"name": "Jane"
}),
("c", {
"name": "Alice"
}),
("d", {
"name": "Joe"
}),
])
prim.add_edges_from(graph, [("a", "a", {
"type": "friends"
}), ("a", "b", {
"type": "enemies"
}), ("c", "a", {
"type": "colleages"
}), ("d", "a", {
"type": "siblings"
})])
pattern = NXGraph()
pattern.add_nodes_from(["x", "y"])
pattern.add_edges_from([("y", "x")])
instance = {"x": "a", "y": "d"}
# Remove node side-effects
rule = Rule.from_transform(NXGraph.copy(pattern))
rule.inject_remove_node("x")
new_instance = rule.refine(graph, instance)
assert (new_instance == {"x": "a", "y": "d", "b": "b", "c": "c"})
assert (prim.get_node(rule.lhs, "x") == prim.get_node(graph, "a"))
assert (prim.get_edge(rule.lhs, "x",
"b") == prim.get_edge(graph, "a", "b"))
assert (prim.get_edge(rule.lhs, "c",
"x") == prim.get_edge(graph, "c", "a"))
# Remove edge side-effects
rule = Rule.from_transform(NXGraph.copy(pattern))
rule.inject_remove_edge("y", "x")
new_instance = rule.refine(graph, instance)
assert (prim.get_edge(rule.lhs, "y",
"x") == prim.get_edge(graph, "d", "a"))
# Merge side-effects
rule = Rule.from_transform(NXGraph.copy(pattern))
rule.inject_merge_nodes(["x", "y"])
new_instance = rule.refine(graph, instance)
assert (new_instance == {"x": "a", "y": "d", "b": "b", "c": "c"})
assert (rule.lhs.get_node("x") == graph.get_node("a"))
assert (rule.lhs.get_node("y") == graph.get_node("d"))
assert (rule.lhs.get_edge("y", "x") == graph.get_edge("d", "a"))
# Combined side-effects
# Ex1: Remove cloned edge + merge with some node
graph.remove_edge("a", "a")
pattern.add_node("z")
pattern.add_edge("x", "z")
instance["z"] = "b"
rule = Rule.from_transform(NXGraph.copy(pattern))
p_node, _ = rule.inject_clone_node("x")
rule.inject_remove_node("z")
rule.inject_remove_edge("y", p_node)
rule.inject_merge_nodes([p_node, "y"])
new_instance = rule.refine(graph, instance)
assert (new_instance == {"x": "a", "y": "d", "z": "b", "c": "c"})
assert (prim.get_node(rule.lhs, "x") == prim.get_node(graph, "a"))
assert (prim.get_node(rule.lhs, "y") == prim.get_node(graph, "d"))
assert (prim.get_edge(rule.lhs, "y",
"x") == prim.get_edge(graph, "d", "a"))
# test with rule inversion
backup = NXGraph.copy(graph)
rhs_g = graph.rewrite(rule, new_instance)
inverted = rule.get_inverted_rule()
rhs_gg = graph.rewrite(inverted, rhs_g)
# print(rhs_gg)
old_node_labels = {v: new_instance[k] for k, v in rhs_gg.items()}
graph.relabel_nodes(old_node_labels)
assert (backup == graph)
def __init__(self):
self.hierarchy = NetworkXHierarchy(directed=True)
g0 = nx.DiGraph()
prim.add_node(g0, "circle", {"a": {1, 2, 3}})
prim.add_node(g0, "square", {"a": {1, 2, 3, 5}})
prim.add_node(g0, "triangle", {"new_attrs": {1}})
prim.add_edges_from(g0, [
("circle", "circle"), # , {"b": {1, 2, 3, 4}}),
("circle", "square"),
("square", "circle", {"new_attrs": {2}}),
("square", "triangle", {"new_attrs": {3, 4}})
])
self.hierarchy.add_graph("g0", g0, {"name": "Shapes"})
g00 = nx.DiGraph()
prim.add_node(g00, 'black', {"a": {1, 2, 3}, "new_attrs": {1}})
prim.add_node(g00, 'white', {"a": {1, 2, 3, 5}})
prim.add_edges_from(g00, [
('white', 'white', {"new_attrs": 2}),
('white', 'black', {"new_attrs": {4, 3}}),
('black', 'black'),
('black', 'white')
])
self.hierarchy.add_graph("g00", g00, {"name": "Colors"})
g1 = nx.DiGraph()
prim.add_nodes_from(g1, [
("black_circle", {"a": {1, 2, 3}}),
"white_circle",
"black_square",
("white_square", {"a": {1, 2}}),
"black_triangle",
"white_triangle"
])
prim.add_edges_from(g1, [
("black_circle", "black_circle"), # {"b": {1, 2, 3, 4}}),
("black_circle", "white_circle"),
("black_circle", "black_square"),
("white_circle", "black_circle"),
("white_circle", "white_square"),
("black_square", "black_circle"),
("black_square", "black_triangle"),
("black_square", "white_triangle"),
("white_square", "white_circle"),
("white_square", "black_triangle"),
("white_square", "white_triangle")
])
self.hierarchy.add_graph("g1", g1)
self.hierarchy.add_typing(
"g1", "g0",
{"black_circle": "circle",
"white_circle": "circle",
"black_square": "square",
"white_square": "square",
"black_triangle": "triangle",
"white_triangle": "triangle"}
)
self.hierarchy.add_typing(
"g1", "g00",
{
"black_square": "black",
"black_circle": "black",
"black_triangle": "black",
"white_square": "white",
"white_circle": "white",
"white_triangle": "white"
}
)
g2 = nx.DiGraph()
prim.add_nodes_from(g2, [
(1, {"a": {1, 2}}),
2,
3,
4,
(5, {"a": {1}}),
6,
7,
])
prim.add_edges_from(g2, [
(1, 2), # {"b": {1, 2, 3}}),
(2, 3),
(3, 6),
(3, 7),
(4, 2),
(4, 5),
(5, 7)
])
self.hierarchy.add_graph("g2", g2)
self.hierarchy.add_typing(
"g2", "g1",
{1: "black_circle",
2: "black_circle",
3: "black_square",
4: "white_circle",
5: "white_square",
6: "white_triangle",
7: "black_triangle"}
)
g3 = nx.DiGraph()
prim.add_nodes_from(g3, [
(1), # {"a": {1, 2}}),
2,
3,
5,
(4), # {"a": {1}}),
6,
7,
])
prim.add_edges_from(g3, [
(1, 1), # , {"b": {1, 2, 3}}),
(1, 2),
(1, 3),
(1, 5),
(2, 1),
(3, 4),
(4, 7),
(4, 6),
(5, 6),
(5, 7)
])
self.hierarchy.add_graph("g3", g3)
self.hierarchy.add_typing(
"g3", "g1",
{1: "black_circle",
2: "white_circle",
3: "white_circle",
5: "black_square",
4: "white_square",
6: "white_triangle",
7: "black_triangle"}
)
g4 = nx.DiGraph()
prim.add_nodes_from(g4, [1, 2, 3])
prim.add_edges_from(g4, [
(1, 2),
(2, 3)
])
self.hierarchy.add_graph("g4", g4)
self.hierarchy.add_typing("g4", "g2", {1: 2, 2: 3, 3: 6})
self.hierarchy.add_typing("g4", "g3", {1: 1, 2: 5, 3: 6})
g5 = nx.DiGraph()
prim.add_nodes_from(g5, [
("black_circle"), # {"a": {255}}),
("black_square"), # {"a": {256}}),
("white_triangle"), # {"a": {257}}),
("star") # , {"a": {258}})
])
prim.add_edges_from(g5, [
("black_circle", "black_square"),
("black_square", "white_triangle"), # , {"b": {11}}),
("star", "black_square"),
("star", "white_triangle")
])
self.hierarchy.add_graph("g5", g5)