def test_merging(self):
g = TypedDiGraph()
g.add_node(10, "agent", {"a": 0})
g.add_node(20, "agent", {"b": 0})
g.add_node(30, "action", {"c": 0})
g.add_edges_from([(10, 30), (20, 30)])
g.set_edge(10, 30, {"x": 0})
g.set_edge(20, 30, {"y": 0})
LHS = TypedDiGraph()
LHS.add_node(1, "agent")
LHS.add_node(2, "agent")
P = TypedDiGraph()
P.add_node("a", "agent")
P.add_node("b", "agent")
RHS = TypedDiGraph()
RHS.add_node("x", "agent")
h1 = Homomorphism(P, LHS, {"a": 1, "b": 2})
h2 = Homomorphism(P, RHS, {"a": "x", "b": "x"})
rw = Rewriter(g)
instances = rw.find_matching(LHS)
RHS_instance = rw.apply_rule(instances[0], h1, h2)
def test_undirected_dec_init(self):
__location__ = os.path.realpath(
os.path.join(os.getcwd(), os.path.dirname(__file__)))
g = TypedGraph()
g.add_node(1, "action")
g.add_node(2, "agent", {"u": {0, 1}})
g.add_node(3, "agent", {"u": {4}, "name": "Paul"})
g.add_node(4, "action")
g.add_node(5, "agent", {"u": {0}})
g.add_node(6, "agent", {"u": {7}})
g.add_node(7, "agent", {"u": {4}})
g.add_edges_from([(1, 2), (3, 2), (1, 5), (5, 4), (5, 6)])
g.set_edge(1, 2, {"a": {0}})
g.set_edge(2, 3, {"k": {1, 2, 3}})
rw = Rewriter(g)
LHS = TypedGraph()
LHS.add_nodes_from([(10, "action"), (20, "agent"), (30, "agent")])
LHS.node[20].attrs_ = {"u": {0}}
LHS.add_edges_from([(10, 20), (20, 30)])
LHS.set_edge(20, 30, {"k": {1, 2}})
P = TypedGraph()
P.add_node(100, "agent")
P.add_node(200, "agent", {"u": {0}})
P.add_node(300, "agent")
P.add_edges_from([(300, 100), (200, 300)])
P.set_edge(100, 300, {"k": {1, 2}})
P.set_edge(200, 300, {"k": set()})
RHS = TypedGraph()
RHS.add_node(1000, "region")
RHS.add_node(2000, "agent", {"u": {3}})
RHS.add_node(3000, "agent", {"u": {0, 2}})
RHS.add_edges_from([(1000, 3000), (2000, 3000), (3000, 3000)])
RHS.set_edge(3000, 3000, {"k": {5, 6}})
RHS.set_edge(2000, 3000, {"k": {1, 2, 10}})
RHS.set_edge(1000, 3000, {"a": {12}})
instances = rw.find_matching(LHS)
for i, instance in enumerate(instances):
plot_instance(
rw.graph_, LHS, instance,
os.path.join(__location__, "undir_dec_instance_%d.png" % i))
left_h = Homomorphism(P, LHS, {100: 20, 200: 20, 300: 30})
righ_h = Homomorphism(P, RHS, {100: 2000, 200: 3000, 300: 3000})
RHS_instance = rw.apply_rule(instances[0], left_h, righ_h)
plot_instance(rw.graph_,
RHS,
RHS_instance,
filename=os.path.join(__location__, "undir_dec_RHS.png"))
def __init__(self):
graph = TypedDiGraph()
graph.add_node(1, 'agent', {'name': 'EGFR', 'state': 'p'})
graph.add_node(2, 'action', attrs={'name': 'BND'})
graph.add_node(3, 'agent', {'name': 'Grb2', 'aa': 'S', 'loc': 90})
graph.add_node(4, 'region', attrs={'name': 'SH2'})
graph.add_node(5, 'agent', attrs={'name': 'EGFR'})
graph.add_node(6, 'action', attrs={'name': 'BND'})
graph.add_node(7, 'agent', attrs={'name': 'Grb2'})
graph.add_node(8, 'agent', attrs={'name': 'WAF1'})
graph.add_node(9, 'action', {'name': 'BND'})
graph.add_node(10, 'agent', {'name': 'G1-S/CDK', 'state': 'p'})
graph.add_node(11, 'agent')
graph.add_node(12, 'agent')
graph.add_node(13, 'agent')
edges = [(1, 2), (4, 2), (4, 3), (5, 6), (7, 6), (8, 9), (10, 9),
(11, 12), (12, 11), (12, 13), (13, 12), (11, 13), (13, 11),
(5, 2)]
graph.add_edges_from(edges)
graph.set_edge(1, 2, {'s': 'p'})
graph.set_edge(4, 2, {'s': 'u'})
graph.set_edge(5, 6, {'s': 'p'})
graph.set_edge(7, 6, {'s': 'u'})
graph.set_edge(5, 2, {'s': 'u'})
self.LHS_ = TypedDiGraph()
self.LHS_.add_node(1, 'agent', {'name': 'EGFR'})
self.LHS_.add_node(2, 'action', {'name': 'BND'})
self.LHS_.add_node(3, 'region')
self.LHS_.add_node(4, 'agent', {'name': 'Grb2'})
self.LHS_.add_node(5, 'agent', {'name': 'EGFR'})
self.LHS_.add_node(6, 'action', {'name': 'BND'})
self.LHS_.add_node(7, 'agent', {'name': 'Grb2'})
self.LHS_.add_edges_from([(1, 2), (3, 2), (3, 4), (5, 6), (7, 6)])
self.LHS_.set_edge(1, 2, {'s': 'p'})
self.LHS_.set_edge(5, 6, {'s': 'p'})
self.rw_ = Rewriter(graph)
self.instances_ = self.rw_.find_matching(self.LHS_)
def test_clonning_merging_sequence(self):
__location__ = os.path.realpath(
os.path.join(os.getcwd(), os.path.dirname(__file__)))
g = TypedDiGraph()
g.add_node(1, "agent", {"name": "John"})
g.add_node(2, "action", {})
g.add_edges_from([(1, 2), (2, 1)])
plot_graph(g, filename=os.path.join(__location__, "cms_test_init.png"))
LHS = TypedDiGraph()
LHS.add_node('entity', 'agent')
LHS.add_node('media', 'action')
LHS.add_edges_from([('entity', 'media'), ('media', 'entity')])
rewriter = Rewriter(g)
instances = rewriter.find_matching(LHS)
for i, instance in enumerate(instances):
plot_instance(
rewriter.graph_, LHS, instance,
os.path.join(__location__, "cms_instance_%d.png" % i))
for instance in instances:
new_name = rewriter.clone(instance, 'media')
rewriter.add_edge(instance, 'media', new_name)
# rewriter.merge(instance, ['media', new_name])
plot_graph(rewriter.graph_,
filename=os.path.join(__location__, "cms_test_clone1.png"))
def test_cloning_cases(self):
g = TypedDiGraph()
g.add_node(10, "agent", {"a": 0})
g.add_node(20, "agent", {"b": 0})
g.add_node(30, "action", {"c": 0})
g.add_edges_from([(10, 30), (20, 30)])
g.set_edge(10, 30, {"x": 0})
g.set_edge(20, 30, {"y": 0})
LHS = TypedDiGraph()
LHS.add_node(1, "agent")
rw = Rewriter(g)
instances = rw.find_matching(LHS)
# simple clone
P1 = TypedDiGraph()
P1.add_node("a", "agent")
P1.add_node("b", "agent")
RHS1 = TypedDiGraph()
RHS1.add_node("x", "agent")
RHS1.add_node("y", "agent")
h1 = Homomorphism(P1, LHS, {"a": 1, "b": 1})
h2 = Homomorphism(P1, RHS1, {"a": "x", "b": "y"})
RHS_instance = rw.apply_rule(instances[0], h1, h2)
# clone merge on the same nodes
RHS2 = TypedGraph()
RHS2.add_node("x", "agent")
h2 = Homomorphism(P1, RHS2, {"a": "x", "b": "x"})
RHS_instance = rw.apply_rule(instances[0], h1, h2)
# clone and merge one with other node
LHS.add_node(2, "agent")
# update matching
instances = rw.find_matching(LHS)
P3 = TypedDiGraph()
P3.add_node("a", "agent")
P3.add_node("b", "agent")
P3.add_node("c", "agent")
RHS3 = TypedDiGraph()
RHS3.add_node("x", "agent")
RHS3.add_node("y", "agent")
h1 = Homomorphism(P3, LHS, {"a": 1, "b": 1, "c": 2})
h2 = Homomorphism(P3, RHS3, {"a": "x", "b": "y", "c": "y"})
RHS_instance = rw.apply_rule(instances[0], h1, h2)
def test_rule_to_homomorphism(self):
__location__ = os.path.realpath(
os.path.join(os.getcwd(), os.path.dirname(__file__)))
g = TypedGraph()
g.add_node(1, "action")
g.add_node(2, "agent", {"u": {0, 1}})
g.add_node(3, "agent", {"u": {4}, "name": "Paul"})
g.add_node(4, "action")
g.add_node(5, "agent", {"u": {0}})
g.add_node(6, "agent", {"u": {7}})
g.add_node(7, "agent", {"u": {4}})
g.add_edges_from([(1, 2), (3, 2), (1, 5), (5, 4), (5, 6)])
g.set_edge(1, 2, {"a": {0}})
g.set_edge(2, 3, {"k": {1, 2, 3}})
rw = Rewriter(g)
LHS = TypedGraph()
LHS.add_nodes_from([(1, "action"), (2, "agent"), (3, "agent")])
LHS.node[2].set_attrs({"u": 0})
LHS.add_edges_from([(1, 2), (2, 3)])
LHS.set_edge(2, 3, {"k": {1, 2}})
instances = rw.find_matching(LHS)
rw.add_node_attrs(instances[0], 1, {"u": 55, "x": 0})
h1, h2 = rw.generate_rule(
LHS, """delete_node 1.
clone 2 as 'clone'.
delete_node_attrs 'clone' {'u': 0}.
delete_edge 2 3.
delete_edge_attrs 'clone' 3 {'k': {1}}.
update_edge_attrs 'clone' 3 {'t': 333}.
update_node_attrs 2 {'u': {12, 13}}.
merge ['clone', 3] as 'merged'.
add_node_attrs 'merged' {'m': 1}.
add_node 'new_node' type 'region'.
add_node_attrs 'new_node' {'x': 1}.
add_edge 'new_node' 'merged'.
add_edge_attrs 'merged' 'new_node' {'j': 33}.""")
RHS_instance = rw.apply_rule(instances[0], h1, h2)
plot_instance(rw.graph_,
h2.target_,
RHS_instance,
filename=os.path.join(__location__,
"undir_rule_to_hom_RHS.png"))
def test_rewriting_with_metamodel(self):
meta_meta = TypedDiGraph()
meta_meta.add_node("agent", "node")
meta_meta.add_node("action", "node")
meta_meta.add_edges_from([("agent", "agent"), ("action", "action"),
("action", "agent"), ("agent", "action")])
meta = TypedDiGraph(meta_meta)
meta.add_node("protein", "agent")
meta.add_node("region", "agent")
meta.add_node("action", "agent")
meta.add_edges_from([
("protein", "protein"),
("region", "region"),
("action", "action"),
("region", "protein"),
("region", "action"),
("action", "region"),
])
graph = TypedDiGraph(meta)
graph.add_nodes_from([(1, "protein"), (2, "region"), (3, "action"),
(4, "region"), (5, "protein"), (6, "region"),
(7, "protein")])
graph.add_edge(2, 1)
graph.add_edge(2, 3)
graph.add_edge(4, 3)
graph.add_edge(4, 5)
graph.add_edge(6, 3)
graph.add_edge(6, 7)
rw = Rewriter(graph)
LHS = TypedDiGraph()
LHS.add_node("a", "protein")
LHS.add_node("b", "region")
LHS.add_node(33, "action")
LHS.add_edges_from([("b", "a"), ("b", 33)])
instances = rw.find_matching(LHS)
try:
rw.add_node(instances[0], "new_type", 2)
assert False
except:
assert True
try:
rw.add_edge(instances[0], "a", 33)
assert False
except:
assert True
class TestRewrites(object):
"""."""
def __init__(self):
graph = TypedDiGraph()
graph.add_node(1, 'agent', {'name': 'EGFR', 'state': 'p'})
graph.add_node(2, 'action', attrs={'name': 'BND'})
graph.add_node(3, 'agent', {'name': 'Grb2', 'aa': 'S', 'loc': 90})
graph.add_node(4, 'region', attrs={'name': 'SH2'})
graph.add_node(5, 'agent', attrs={'name': 'EGFR'})
graph.add_node(6, 'action', attrs={'name': 'BND'})
graph.add_node(7, 'agent', attrs={'name': 'Grb2'})
graph.add_node(8, 'agent', attrs={'name': 'WAF1'})
graph.add_node(9, 'action', {'name': 'BND'})
graph.add_node(10, 'agent', {'name': 'G1-S/CDK', 'state': 'p'})
graph.add_node(11, 'agent')
graph.add_node(12, 'agent')
graph.add_node(13, 'agent')
edges = [(1, 2), (4, 2), (4, 3), (5, 6), (7, 6), (8, 9), (10, 9),
(11, 12), (12, 11), (12, 13), (13, 12), (11, 13), (13, 11),
(5, 2)]
graph.add_edges_from(edges)
graph.set_edge(1, 2, {'s': 'p'})
graph.set_edge(4, 2, {'s': 'u'})
graph.set_edge(5, 6, {'s': 'p'})
graph.set_edge(7, 6, {'s': 'u'})
graph.set_edge(5, 2, {'s': 'u'})
self.LHS_ = TypedDiGraph()
self.LHS_.add_node(1, 'agent', {'name': 'EGFR'})
self.LHS_.add_node(2, 'action', {'name': 'BND'})
self.LHS_.add_node(3, 'region')
self.LHS_.add_node(4, 'agent', {'name': 'Grb2'})
self.LHS_.add_node(5, 'agent', {'name': 'EGFR'})
self.LHS_.add_node(6, 'action', {'name': 'BND'})
self.LHS_.add_node(7, 'agent', {'name': 'Grb2'})
self.LHS_.add_edges_from([(1, 2), (3, 2), (3, 4), (5, 6), (7, 6)])
self.LHS_.set_edge(1, 2, {'s': 'p'})
self.LHS_.set_edge(5, 6, {'s': 'p'})
self.rw_ = Rewriter(graph)
self.instances_ = self.rw_.find_matching(self.LHS_)
def test_find_matching(self):
assert_equals(self.instances_, [{
1: 1,
2: 2,
3: 4,
4: 3,
5: 5,
6: 6,
7: 7
}])
new_pattern = TypedDiGraph()
new_pattern.add_node("a", "agent")
new_pattern.add_node("b", "agent")
new_pattern.add_node("c", "agent")
new_pattern.add_edges_from([("a", "b"), ("a", "c")])
instances = self.rw_.find_matching(new_pattern)
assert_equals(6, len(instances))
def test_transform_instance(self):
self.rw_.transform_instance(
self.instances_[0], """delete_node 6.\n"""
"""merge [1, 5] method union as 'merge_1'.\n"""
"""merge [4, 7] as 'merge_2'.\n"""
"""add_edge 'merge_1' 'merge_2'.\n"""
"""clone 'merge_1' as 'clone_1'.\n"""
"""clone 3 as 'clone_2'.""")
def test_clonning_merging_sequence(self):
__location__ = os.path.realpath(
os.path.join(os.getcwd(), os.path.dirname(__file__)))
g = TypedDiGraph()
g.add_node(1, "agent", {"name": "John"})
g.add_node(2, "action", {})
g.add_edges_from([(1, 2), (2, 1)])
plot_graph(g, filename=os.path.join(__location__, "cms_test_init.png"))
LHS = TypedDiGraph()
LHS.add_node('entity', 'agent')
LHS.add_node('media', 'action')
LHS.add_edges_from([('entity', 'media'), ('media', 'entity')])
rewriter = Rewriter(g)
instances = rewriter.find_matching(LHS)
for i, instance in enumerate(instances):
plot_instance(
rewriter.graph_, LHS, instance,
os.path.join(__location__, "cms_instance_%d.png" % i))
for instance in instances:
new_name = rewriter.clone(instance, 'media')
rewriter.add_edge(instance, 'media', new_name)
# rewriter.merge(instance, ['media', new_name])
plot_graph(rewriter.graph_,
filename=os.path.join(__location__, "cms_test_clone1.png"))
def test_undirected_imp_init(self):
__location__ = os.path.realpath(
os.path.join(os.getcwd(), os.path.dirname(__file__)))
g = TypedGraph()
g.add_node(1, "agent", {"name": "John"})
g.add_node(2, "action")
g.add_node(3, "agent", {"name": "Paul"})
g.add_edges_from([(1, 2), (3, 2)])
g.set_edge(1, 2, {"a": 0})
rw = Rewriter(g)
LHS = TypedGraph()
LHS.add_nodes_from([(1, "agent"), (2, "action")])
LHS.add_edges_from([(1, 2)])
instances = rw.find_matching(LHS)
for i, instance in enumerate(instances):
plot_instance(
rw.graph_, LHS, instance,
os.path.join(__location__, "undir_instance_%d.png" % i))
rw.add_node(instances[0], 'region', 'Europe', {"a": 44})
rw.delete_node(instances[0], 1)
rw.delete_edge(instances[0], 2, 3)
rw.clone(instances[0], 2)
cast_node(rw.graph_, "Europe", "action")
rw.merge(instances[0], ["Europe", 2])
plot_graph(rw.graph_,
filename=os.path.join(__location__, "undir_cloned.png"))
def test_undirected_dec_init(self):
__location__ = os.path.realpath(
os.path.join(os.getcwd(), os.path.dirname(__file__)))
g = TypedGraph()
g.add_node(1, "action")
g.add_node(2, "agent", {"u": {0, 1}})
g.add_node(3, "agent", {"u": {4}, "name": "Paul"})
g.add_node(4, "action")
g.add_node(5, "agent", {"u": {0}})
g.add_node(6, "agent", {"u": {7}})
g.add_node(7, "agent", {"u": {4}})
g.add_edges_from([(1, 2), (3, 2), (1, 5), (5, 4), (5, 6)])
g.set_edge(1, 2, {"a": {0}})
g.set_edge(2, 3, {"k": {1, 2, 3}})
rw = Rewriter(g)
LHS = TypedGraph()
LHS.add_nodes_from([(10, "action"), (20, "agent"), (30, "agent")])
LHS.node[20].attrs_ = {"u": {0}}
LHS.add_edges_from([(10, 20), (20, 30)])
LHS.set_edge(20, 30, {"k": {1, 2}})
P = TypedGraph()
P.add_node(100, "agent")
P.add_node(200, "agent", {"u": {0}})
P.add_node(300, "agent")
P.add_edges_from([(300, 100), (200, 300)])
P.set_edge(100, 300, {"k": {1, 2}})
P.set_edge(200, 300, {"k": set()})
RHS = TypedGraph()
RHS.add_node(1000, "region")
RHS.add_node(2000, "agent", {"u": {3}})
RHS.add_node(3000, "agent", {"u": {0, 2}})
RHS.add_edges_from([(1000, 3000), (2000, 3000), (3000, 3000)])
RHS.set_edge(3000, 3000, {"k": {5, 6}})
RHS.set_edge(2000, 3000, {"k": {1, 2, 10}})
RHS.set_edge(1000, 3000, {"a": {12}})
instances = rw.find_matching(LHS)
for i, instance in enumerate(instances):
plot_instance(
rw.graph_, LHS, instance,
os.path.join(__location__, "undir_dec_instance_%d.png" % i))
left_h = Homomorphism(P, LHS, {100: 20, 200: 20, 300: 30})
righ_h = Homomorphism(P, RHS, {100: 2000, 200: 3000, 300: 3000})
RHS_instance = rw.apply_rule(instances[0], left_h, righ_h)
plot_instance(rw.graph_,
RHS,
RHS_instance,
filename=os.path.join(__location__, "undir_dec_RHS.png"))
def test_rule_to_homomorphism(self):
__location__ = os.path.realpath(
os.path.join(os.getcwd(), os.path.dirname(__file__)))
g = TypedGraph()
g.add_node(1, "action")
g.add_node(2, "agent", {"u": {0, 1}})
g.add_node(3, "agent", {"u": {4}, "name": "Paul"})
g.add_node(4, "action")
g.add_node(5, "agent", {"u": {0}})
g.add_node(6, "agent", {"u": {7}})
g.add_node(7, "agent", {"u": {4}})
g.add_edges_from([(1, 2), (3, 2), (1, 5), (5, 4), (5, 6)])
g.set_edge(1, 2, {"a": {0}})
g.set_edge(2, 3, {"k": {1, 2, 3}})
rw = Rewriter(g)
LHS = TypedGraph()
LHS.add_nodes_from([(1, "action"), (2, "agent"), (3, "agent")])
LHS.node[2].set_attrs({"u": 0})
LHS.add_edges_from([(1, 2), (2, 3)])
LHS.set_edge(2, 3, {"k": {1, 2}})
instances = rw.find_matching(LHS)
rw.add_node_attrs(instances[0], 1, {"u": 55, "x": 0})
h1, h2 = rw.generate_rule(
LHS, """delete_node 1.
clone 2 as 'clone'.
delete_node_attrs 'clone' {'u': 0}.
delete_edge 2 3.
delete_edge_attrs 'clone' 3 {'k': {1}}.
update_edge_attrs 'clone' 3 {'t': 333}.
update_node_attrs 2 {'u': {12, 13}}.
merge ['clone', 3] as 'merged'.
add_node_attrs 'merged' {'m': 1}.
add_node 'new_node' type 'region'.
add_node_attrs 'new_node' {'x': 1}.
add_edge 'new_node' 'merged'.
add_edge_attrs 'merged' 'new_node' {'j': 33}.""")
RHS_instance = rw.apply_rule(instances[0], h1, h2)
plot_instance(rw.graph_,
h2.target_,
RHS_instance,
filename=os.path.join(__location__,
"undir_rule_to_hom_RHS.png"))
def test_cloning_cases(self):
g = TypedDiGraph()
g.add_node(10, "agent", {"a": 0})
g.add_node(20, "agent", {"b": 0})
g.add_node(30, "action", {"c": 0})
g.add_edges_from([(10, 30), (20, 30)])
g.set_edge(10, 30, {"x": 0})
g.set_edge(20, 30, {"y": 0})
LHS = TypedDiGraph()
LHS.add_node(1, "agent")
rw = Rewriter(g)
instances = rw.find_matching(LHS)
# simple clone
P1 = TypedDiGraph()
P1.add_node("a", "agent")
P1.add_node("b", "agent")
RHS1 = TypedDiGraph()
RHS1.add_node("x", "agent")
RHS1.add_node("y", "agent")
h1 = Homomorphism(P1, LHS, {"a": 1, "b": 1})
h2 = Homomorphism(P1, RHS1, {"a": "x", "b": "y"})
RHS_instance = rw.apply_rule(instances[0], h1, h2)
# clone merge on the same nodes
RHS2 = TypedGraph()
RHS2.add_node("x", "agent")
h2 = Homomorphism(P1, RHS2, {"a": "x", "b": "x"})
RHS_instance = rw.apply_rule(instances[0], h1, h2)
# clone and merge one with other node
LHS.add_node(2, "agent")
# update matching
instances = rw.find_matching(LHS)
P3 = TypedDiGraph()
P3.add_node("a", "agent")
P3.add_node("b", "agent")
P3.add_node("c", "agent")
RHS3 = TypedDiGraph()
RHS3.add_node("x", "agent")
RHS3.add_node("y", "agent")
h1 = Homomorphism(P3, LHS, {"a": 1, "b": 1, "c": 2})
h2 = Homomorphism(P3, RHS3, {"a": "x", "b": "y", "c": "y"})
RHS_instance = rw.apply_rule(instances[0], h1, h2)
def test_merging(self):
g = TypedDiGraph()
g.add_node(10, "agent", {"a": 0})
g.add_node(20, "agent", {"b": 0})
g.add_node(30, "action", {"c": 0})
g.add_edges_from([(10, 30), (20, 30)])
g.set_edge(10, 30, {"x": 0})
g.set_edge(20, 30, {"y": 0})
LHS = TypedDiGraph()
LHS.add_node(1, "agent")
LHS.add_node(2, "agent")
P = TypedDiGraph()
P.add_node("a", "agent")
P.add_node("b", "agent")
RHS = TypedDiGraph()
RHS.add_node("x", "agent")
h1 = Homomorphism(P, LHS, {"a": 1, "b": 2})
h2 = Homomorphism(P, RHS, {"a": "x", "b": "x"})
rw = Rewriter(g)
instances = rw.find_matching(LHS)
RHS_instance = rw.apply_rule(instances[0], h1, h2)
def test_rewriting_with_metamodel(self):
meta_meta = TypedDiGraph()
meta_meta.add_node("agent", "node")
meta_meta.add_node("action", "node")
meta_meta.add_edges_from([("agent", "agent"), ("action", "action"),
("action", "agent"), ("agent", "action")])
meta = TypedDiGraph(meta_meta)
meta.add_node("protein", "agent")
meta.add_node("region", "agent")
meta.add_node("action", "agent")
meta.add_edges_from([
("protein", "protein"),
("region", "region"),
("action", "action"),
("region", "protein"),
("region", "action"),
("action", "region"),
])
graph = TypedDiGraph(meta)
graph.add_nodes_from([(1, "protein"), (2, "region"), (3, "action"),
(4, "region"), (5, "protein"), (6, "region"),
(7, "protein")])
graph.add_edge(2, 1)
graph.add_edge(2, 3)
graph.add_edge(4, 3)
graph.add_edge(4, 5)
graph.add_edge(6, 3)
graph.add_edge(6, 7)
rw = Rewriter(graph)
LHS = TypedDiGraph()
LHS.add_node("a", "protein")
LHS.add_node("b", "region")
LHS.add_node(33, "action")
LHS.add_edges_from([("b", "a"), ("b", 33)])
instances = rw.find_matching(LHS)
try:
rw.add_node(instances[0], "new_type", 2)
assert False
except:
assert True
try:
rw.add_edge(instances[0], "a", 33)
assert False
except:
assert True
def test_undirected_imp_init(self):
__location__ = os.path.realpath(
os.path.join(os.getcwd(), os.path.dirname(__file__)))
g = TypedGraph()
g.add_node(1, "agent", {"name": "John"})
g.add_node(2, "action")
g.add_node(3, "agent", {"name": "Paul"})
g.add_edges_from([(1, 2), (3, 2)])
g.set_edge(1, 2, {"a": 0})
rw = Rewriter(g)
LHS = TypedGraph()
LHS.add_nodes_from([(1, "agent"), (2, "action")])
LHS.add_edges_from([(1, 2)])
instances = rw.find_matching(LHS)
for i, instance in enumerate(instances):
plot_instance(
rw.graph_, LHS, instance,
os.path.join(__location__, "undir_instance_%d.png" % i))
rw.add_node(instances[0], 'region', 'Europe', {"a": 44})
rw.delete_node(instances[0], 1)
rw.delete_edge(instances[0], 2, 3)
rw.clone(instances[0], 2)
cast_node(rw.graph_, "Europe", "action")
rw.merge(instances[0], ["Europe", 2])
plot_graph(rw.graph_,
filename=os.path.join(__location__, "undir_cloned.png"))