import pytest
import networkx as nx
from networkx.testing.utils import assert_edges_equal, assert_nodes_equal
import io
import tempfile
import os
from networkx.testing import almost_equal
class BaseGraphML:
@classmethod
def setup_class(cls):
cls.simple_directed_data = """<?xml version="1.0" encoding="UTF-8"?>
<!-- This file was written by the JAVA GraphML Library.-->
<graphml xmlns="http://graphml.graphdrawing.org/xmlns"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://graphml.graphdrawing.org/xmlns
http://graphml.graphdrawing.org/xmlns/1.0/graphml.xsd">
<graph id="G" edgedefault="directed">
<node id="n0"/>
<node id="n1"/>
<node id="n2"/>
<node id="n3"/>
<node id="n4"/>
<node id="n5"/>
<node id="n6"/>
<node id="n7"/>
<node id="n8"/>
<node id="n9"/>
<node id="n10"/>
<edge id="foo" source="n0" target="n2"/>
<edge source="n1" target="n2"/>
<edge source="n2" target="n3"/>
<edge source="n3" target="n5"/>
<edge source="n3" target="n4"/>
<edge source="n4" target="n6"/>
<edge source="n6" target="n5"/>
<edge source="n5" target="n7"/>
<edge source="n6" target="n8"/>
<edge source="n8" target="n7"/>
<edge source="n8" target="n9"/>
</graph>
</graphml>"""
cls.simple_directed_graph = nx.DiGraph()
cls.simple_directed_graph.add_node("n10")
cls.simple_directed_graph.add_edge("n0", "n2", id="foo")
cls.simple_directed_graph.add_edge("n0", "n2")
cls.simple_directed_graph.add_edges_from(
[
("n1", "n2"),
("n2", "n3"),
("n3", "n5"),
("n3", "n4"),
("n4", "n6"),
("n6", "n5"),
("n5", "n7"),
("n6", "n8"),
("n8", "n7"),
("n8", "n9"),
]
)
cls.simple_directed_fh = io.BytesIO(cls.simple_directed_data.encode("UTF-8"))
cls.attribute_data = """<?xml version="1.0" encoding="UTF-8"?>
<graphml xmlns="http://graphml.graphdrawing.org/xmlns"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://graphml.graphdrawing.org/xmlns
http://graphml.graphdrawing.org/xmlns/1.0/graphml.xsd">
<key id="d0" for="node" attr.name="color" attr.type="string">
<default>yellow</default>
</key>
<key id="d1" for="edge" attr.name="weight" attr.type="double"/>
<graph id="G" edgedefault="directed">
<node id="n0">
<data key="d0">green</data>
</node>
<node id="n1"/>
<node id="n2">
<data key="d0">blue</data>
</node>
<node id="n3">
<data key="d0">red</data>
</node>
<node id="n4"/>
<node id="n5">
<data key="d0">turquoise</data>
</node>
<edge id="e0" source="n0" target="n2">
<data key="d1">1.0</data>
</edge>
<edge id="e1" source="n0" target="n1">
<data key="d1">1.0</data>
</edge>
<edge id="e2" source="n1" target="n3">
<data key="d1">2.0</data>
</edge>
<edge id="e3" source="n3" target="n2"/>
<edge id="e4" source="n2" target="n4"/>
<edge id="e5" source="n3" target="n5"/>
<edge id="e6" source="n5" target="n4">
<data key="d1">1.1</data>
</edge>
</graph>
</graphml>
"""
cls.attribute_graph = nx.DiGraph(id="G")
cls.attribute_graph.graph["node_default"] = {"color": "yellow"}
cls.attribute_graph.add_node("n0", color="green")
cls.attribute_graph.add_node("n2", color="blue")
cls.attribute_graph.add_node("n3", color="red")
cls.attribute_graph.add_node("n4")
cls.attribute_graph.add_node("n5", color="turquoise")
cls.attribute_graph.add_edge("n0", "n2", id="e0", weight=1.0)
cls.attribute_graph.add_edge("n0", "n1", id="e1", weight=1.0)
cls.attribute_graph.add_edge("n1", "n3", id="e2", weight=2.0)
cls.attribute_graph.add_edge("n3", "n2", id="e3")
cls.attribute_graph.add_edge("n2", "n4", id="e4")
cls.attribute_graph.add_edge("n3", "n5", id="e5")
cls.attribute_graph.add_edge("n5", "n4", id="e6", weight=1.1)
cls.attribute_fh = io.BytesIO(cls.attribute_data.encode("UTF-8"))
cls.attribute_named_key_ids_data = """<?xml version='1.0' encoding='utf-8'?>
<graphml xmlns="http://graphml.graphdrawing.org/xmlns"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://graphml.graphdrawing.org/xmlns
http://graphml.graphdrawing.org/xmlns/1.0/graphml.xsd">
<key id="edge_prop" for="edge" attr.name="edge_prop" attr.type="string"/>
<key id="prop2" for="node" attr.name="prop2" attr.type="string"/>
<key id="prop1" for="node" attr.name="prop1" attr.type="string"/>
<graph edgedefault="directed">
<node id="0">
<data key="prop1">val1</data>
<data key="prop2">val2</data>
</node>
<node id="1">
<data key="prop1">val_one</data>
<data key="prop2">val2</data>
</node>
<edge source="0" target="1">
<data key="edge_prop">edge_value</data>
</edge>
</graph>
</graphml>
"""
cls.attribute_named_key_ids_graph = nx.DiGraph()
cls.attribute_named_key_ids_graph.add_node("0", prop1="val1", prop2="val2")
cls.attribute_named_key_ids_graph.add_node("1", prop1="val_one", prop2="val2")
cls.attribute_named_key_ids_graph.add_edge("0", "1", edge_prop="edge_value")
fh = io.BytesIO(cls.attribute_named_key_ids_data.encode("UTF-8"))
cls.attribute_named_key_ids_fh = fh
cls.attribute_numeric_type_data = """<?xml version='1.0' encoding='utf-8'?>
<graphml xmlns="http://graphml.graphdrawing.org/xmlns"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://graphml.graphdrawing.org/xmlns
http://graphml.graphdrawing.org/xmlns/1.0/graphml.xsd">
<key attr.name="weight" attr.type="double" for="node" id="d1" />
<key attr.name="weight" attr.type="double" for="edge" id="d0" />
<graph edgedefault="directed">
<node id="n0">
<data key="d1">1</data>
</node>
<node id="n1">
<data key="d1">2.0</data>
</node>
<edge source="n0" target="n1">
<data key="d0">1</data>
</edge>
<edge source="n1" target="n0">
<data key="d0">k</data>
</edge>
<edge source="n1" target="n1">
<data key="d0">1.0</data>
</edge>
</graph>
</graphml>
"""
cls.attribute_numeric_type_graph = nx.DiGraph()
cls.attribute_numeric_type_graph.add_node("n0", weight=1)
cls.attribute_numeric_type_graph.add_node("n1", weight=2.0)
cls.attribute_numeric_type_graph.add_edge("n0", "n1", weight=1)
cls.attribute_numeric_type_graph.add_edge("n1", "n1", weight=1.0)
fh = io.BytesIO(cls.attribute_numeric_type_data.encode("UTF-8"))
cls.attribute_numeric_type_fh = fh
cls.simple_undirected_data = """<?xml version="1.0" encoding="UTF-8"?>
<graphml xmlns="http://graphml.graphdrawing.org/xmlns"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://graphml.graphdrawing.org/xmlns
http://graphml.graphdrawing.org/xmlns/1.0/graphml.xsd">
<graph id="G">
<node id="n0"/>
<node id="n1"/>
<node id="n2"/>
<node id="n10"/>
<edge id="foo" source="n0" target="n2"/>
<edge source="n1" target="n2"/>
<edge source="n2" target="n3"/>
</graph>
</graphml>"""
# <edge source="n8" target="n10" directed="false"/>
cls.simple_undirected_graph = nx.Graph()
cls.simple_undirected_graph.add_node("n10")
cls.simple_undirected_graph.add_edge("n0", "n2", id="foo")
cls.simple_undirected_graph.add_edges_from([("n1", "n2"), ("n2", "n3")])
fh = io.BytesIO(cls.simple_undirected_data.encode("UTF-8"))
cls.simple_undirected_fh = fh
cls.undirected_multigraph_data = """<?xml version="1.0" encoding="UTF-8"?>
<graphml xmlns="http://graphml.graphdrawing.org/xmlns"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://graphml.graphdrawing.org/xmlns
http://graphml.graphdrawing.org/xmlns/1.0/graphml.xsd">
<graph id="G">
<node id="n0"/>
<node id="n1"/>
<node id="n2"/>
<node id="n10"/>
<edge id="e0" source="n0" target="n2"/>
<edge id="e1" source="n1" target="n2"/>
<edge id="e2" source="n2" target="n1"/>
</graph>
</graphml>"""
cls.undirected_multigraph = nx.MultiGraph()
cls.undirected_multigraph.add_node("n10")
cls.undirected_multigraph.add_edge("n0", "n2", id="e0")
cls.undirected_multigraph.add_edge("n1", "n2", id="e1")
cls.undirected_multigraph.add_edge("n2", "n1", id="e2")
fh = io.BytesIO(cls.undirected_multigraph_data.encode("UTF-8"))
cls.undirected_multigraph_fh = fh
cls.undirected_multigraph_no_multiedge_data = """<?xml version="1.0" encoding="UTF-8"?>
<graphml xmlns="http://graphml.graphdrawing.org/xmlns"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://graphml.graphdrawing.org/xmlns
http://graphml.graphdrawing.org/xmlns/1.0/graphml.xsd">
<graph id="G">
<node id="n0"/>
<node id="n1"/>
<node id="n2"/>
<node id="n10"/>
<edge id="e0" source="n0" target="n2"/>
<edge id="e1" source="n1" target="n2"/>
<edge id="e2" source="n2" target="n3"/>
</graph>
</graphml>"""
cls.undirected_multigraph_no_multiedge = nx.MultiGraph()
cls.undirected_multigraph_no_multiedge.add_node("n10")
cls.undirected_multigraph_no_multiedge.add_edge("n0", "n2", id="e0")
cls.undirected_multigraph_no_multiedge.add_edge("n1", "n2", id="e1")
cls.undirected_multigraph_no_multiedge.add_edge("n2", "n3", id="e2")
fh = io.BytesIO(cls.undirected_multigraph_no_multiedge_data.encode("UTF-8"))
cls.undirected_multigraph_no_multiedge_fh = fh
cls.multigraph_only_ids_for_multiedges_data = """<?xml version="1.0" encoding="UTF-8"?>
<graphml xmlns="http://graphml.graphdrawing.org/xmlns"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://graphml.graphdrawing.org/xmlns
http://graphml.graphdrawing.org/xmlns/1.0/graphml.xsd">
<graph id="G">
<node id="n0"/>
<node id="n1"/>
<node id="n2"/>
<node id="n10"/>
<edge source="n0" target="n2"/>
<edge id="e1" source="n1" target="n2"/>
<edge id="e2" source="n2" target="n1"/>
</graph>
</graphml>"""
cls.multigraph_only_ids_for_multiedges = nx.MultiGraph()
cls.multigraph_only_ids_for_multiedges.add_node("n10")
cls.multigraph_only_ids_for_multiedges.add_edge("n0", "n2")
cls.multigraph_only_ids_for_multiedges.add_edge("n1", "n2", id="e1")
cls.multigraph_only_ids_for_multiedges.add_edge("n2", "n1", id="e2")
fh = io.BytesIO(cls.multigraph_only_ids_for_multiedges_data.encode("UTF-8"))
cls.multigraph_only_ids_for_multiedges_fh = fh
class TestReadGraphML(BaseGraphML):
def test_read_simple_directed_graphml(self):
G = self.simple_directed_graph
H = nx.read_graphml(self.simple_directed_fh)
assert sorted(G.nodes()) == sorted(H.nodes())
assert sorted(G.edges()) == sorted(H.edges())
assert sorted(G.edges(data=True)) == sorted(H.edges(data=True))
self.simple_directed_fh.seek(0)
PG = nx.parse_graphml(self.simple_directed_data)
assert sorted(G.nodes()) == sorted(PG.nodes())
assert sorted(G.edges()) == sorted(PG.edges())
assert sorted(G.edges(data=True)) == sorted(PG.edges(data=True))
def test_read_simple_undirected_graphml(self):
G = self.simple_undirected_graph
H = nx.read_graphml(self.simple_undirected_fh)
assert_nodes_equal(G.nodes(), H.nodes())
assert_edges_equal(G.edges(), H.edges())
self.simple_undirected_fh.seek(0)
PG = nx.parse_graphml(self.simple_undirected_data)
assert_nodes_equal(G.nodes(), PG.nodes())
assert_edges_equal(G.edges(), PG.edges())
def test_read_undirected_multigraph_graphml(self):
G = self.undirected_multigraph
H = nx.read_graphml(self.undirected_multigraph_fh)
assert_nodes_equal(G.nodes(), H.nodes())
assert_edges_equal(G.edges(), H.edges())
self.undirected_multigraph_fh.seek(0)
PG = nx.parse_graphml(self.undirected_multigraph_data)
assert_nodes_equal(G.nodes(), PG.nodes())
assert_edges_equal(G.edges(), PG.edges())
def test_read_undirected_multigraph_no_multiedge_graphml(self):
G = self.undirected_multigraph_no_multiedge
H = nx.read_graphml(self.undirected_multigraph_no_multiedge_fh)
assert_nodes_equal(G.nodes(), H.nodes())
assert_edges_equal(G.edges(), H.edges())
self.undirected_multigraph_no_multiedge_fh.seek(0)
PG = nx.parse_graphml(self.undirected_multigraph_no_multiedge_data)
assert_nodes_equal(G.nodes(), PG.nodes())
assert_edges_equal(G.edges(), PG.edges())
def test_read_undirected_multigraph_only_ids_for_multiedges_graphml(self):
G = self.multigraph_only_ids_for_multiedges
H = nx.read_graphml(self.multigraph_only_ids_for_multiedges_fh)
assert_nodes_equal(G.nodes(), H.nodes())
assert_edges_equal(G.edges(), H.edges())
self.multigraph_only_ids_for_multiedges_fh.seek(0)
PG = nx.parse_graphml(self.multigraph_only_ids_for_multiedges_data)
assert_nodes_equal(G.nodes(), PG.nodes())
assert_edges_equal(G.edges(), PG.edges())
def test_read_attribute_graphml(self):
G = self.attribute_graph
H = nx.read_graphml(self.attribute_fh)
assert_nodes_equal(G.nodes(True), sorted(H.nodes(data=True)))
ge = sorted(G.edges(data=True))
he = sorted(H.edges(data=True))
for a, b in zip(ge, he):
assert a == b
self.attribute_fh.seek(0)
PG = nx.parse_graphml(self.attribute_data)
assert sorted(G.nodes(True)) == sorted(PG.nodes(data=True))
ge = sorted(G.edges(data=True))
he = sorted(PG.edges(data=True))
for a, b in zip(ge, he):
assert a == b
def test_directed_edge_in_undirected(self):
s = """<?xml version="1.0" encoding="UTF-8"?>
<graphml xmlns="http://graphml.graphdrawing.org/xmlns"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://graphml.graphdrawing.org/xmlns
http://graphml.graphdrawing.org/xmlns/1.0/graphml.xsd">
<graph id="G">
<node id="n0"/>
<node id="n1"/>
<node id="n2"/>
<edge source="n0" target="n1"/>
<edge source="n1" target="n2" directed='true'/>
</graph>
</graphml>"""
fh = io.BytesIO(s.encode("UTF-8"))
pytest.raises(nx.NetworkXError, nx.read_graphml, fh)
pytest.raises(nx.NetworkXError, nx.parse_graphml, s)
def test_undirected_edge_in_directed(self):
s = """<?xml version="1.0" encoding="UTF-8"?>
<graphml xmlns="http://graphml.graphdrawing.org/xmlns"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://graphml.graphdrawing.org/xmlns
http://graphml.graphdrawing.org/xmlns/1.0/graphml.xsd">
<graph id="G" edgedefault='directed'>
<node id="n0"/>
<node id="n1"/>
<node id="n2"/>
<edge source="n0" target="n1"/>
<edge source="n1" target="n2" directed='false'/>
</graph>
</graphml>"""
fh = io.BytesIO(s.encode("UTF-8"))
pytest.raises(nx.NetworkXError, nx.read_graphml, fh)
pytest.raises(nx.NetworkXError, nx.parse_graphml, s)
def test_key_raise(self):
s = """<?xml version="1.0" encoding="UTF-8"?>
<graphml xmlns="http://graphml.graphdrawing.org/xmlns"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://graphml.graphdrawing.org/xmlns
http://graphml.graphdrawing.org/xmlns/1.0/graphml.xsd">
<key id="d0" for="node" attr.name="color" attr.type="string">
<default>yellow</default>
</key>
<key id="d1" for="edge" attr.name="weight" attr.type="double"/>
<graph id="G" edgedefault="directed">
<node id="n0">
<data key="d0">green</data>
</node>
<node id="n1"/>
<node id="n2">
<data key="d0">blue</data>
</node>
<edge id="e0" source="n0" target="n2">
<data key="d2">1.0</data>
</edge>
</graph>
</graphml>
"""
fh = io.BytesIO(s.encode("UTF-8"))
pytest.raises(nx.NetworkXError, nx.read_graphml, fh)
pytest.raises(nx.NetworkXError, nx.parse_graphml, s)
def test_hyperedge_raise(self):
s = """<?xml version="1.0" encoding="UTF-8"?>
<graphml xmlns="http://graphml.graphdrawing.org/xmlns"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://graphml.graphdrawing.org/xmlns
http://graphml.graphdrawing.org/xmlns/1.0/graphml.xsd">
<key id="d0" for="node" attr.name="color" attr.type="string">
<default>yellow</default>
</key>
<key id="d1" for="edge" attr.name="weight" attr.type="double"/>
<graph id="G" edgedefault="directed">
<node id="n0">
<data key="d0">green</data>
</node>
<node id="n1"/>
<node id="n2">
<data key="d0">blue</data>
</node>
<hyperedge id="e0" source="n0" target="n2">
<endpoint node="n0"/>
<endpoint node="n1"/>
<endpoint node="n2"/>
</hyperedge>
</graph>
</graphml>
"""
fh = io.BytesIO(s.encode("UTF-8"))
pytest.raises(nx.NetworkXError, nx.read_graphml, fh)
pytest.raises(nx.NetworkXError, nx.parse_graphml, s)
def test_multigraph_keys(self):
# Test that reading multigraphs uses edge id attributes as keys
s = """<?xml version="1.0" encoding="UTF-8"?>
<graphml xmlns="http://graphml.graphdrawing.org/xmlns"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://graphml.graphdrawing.org/xmlns
http://graphml.graphdrawing.org/xmlns/1.0/graphml.xsd">
<graph id="G" edgedefault="directed">
<node id="n0"/>
<node id="n1"/>
<edge id="e0" source="n0" target="n1"/>
<edge id="e1" source="n0" target="n1"/>
</graph>
</graphml>
"""
fh = io.BytesIO(s.encode("UTF-8"))
G = nx.read_graphml(fh)
expected = [("n0", "n1", "e0"), ("n0", "n1", "e1")]
assert sorted(G.edges(keys=True)) == expected
fh.seek(0)
H = nx.parse_graphml(s)
assert sorted(H.edges(keys=True)) == expected
def test_preserve_multi_edge_data(self):
"""
Test that data and keys of edges are preserved on consequent
write and reads
"""
G = nx.MultiGraph()
G.add_node(1)
G.add_node(2)
G.add_edges_from(
[
# edges with no data, no keys:
(1, 2),
# edges with only data:
(1, 2, dict(key="data_key1")),
(1, 2, dict(id="data_id2")),
(1, 2, dict(key="data_key3", id="data_id3")),
# edges with both data and keys:
(1, 2, 103, dict(key="data_key4")),
(1, 2, 104, dict(id="data_id5")),
(1, 2, 105, dict(key="data_key6", id="data_id7")),
]
)
fh = io.BytesIO()
nx.write_graphml(G, fh)
fh.seek(0)
H = nx.read_graphml(fh, node_type=int)
assert_edges_equal(G.edges(data=True, keys=True), H.edges(data=True, keys=True))
assert G._adj == H._adj
Gadj = {
str(node): {
str(nbr): {str(ekey): dd for ekey, dd in key_dict.items()}
for nbr, key_dict in nbr_dict.items()
}
for node, nbr_dict in G._adj.items()
}
fh.seek(0)
HH = nx.read_graphml(fh, node_type=str, edge_key_type=str)
assert Gadj == HH._adj
fh.seek(0)
string_fh = fh.read()
HH = nx.parse_graphml(string_fh, node_type=str, edge_key_type=str)
assert Gadj == HH._adj
def test_yfiles_extension(self):
data = """<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<graphml xmlns="http://graphml.graphdrawing.org/xmlns"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xmlns:y="http://www.yworks.com/xml/graphml"
xmlns:yed="http://www.yworks.com/xml/yed/3"
xsi:schemaLocation="http://graphml.graphdrawing.org/xmlns
http://graphml.graphdrawing.org/xmlns/1.0/graphml.xsd">
<!--Created by yFiles for Java 2.7-->
<key for="graphml" id="d0" yfiles.type="resources"/>
<key attr.name="url" attr.type="string" for="node" id="d1"/>
<key attr.name="description" attr.type="string" for="node" id="d2"/>
<key for="node" id="d3" yfiles.type="nodegraphics"/>
<key attr.name="Description" attr.type="string" for="graph" id="d4">
<default/>
</key>
<key attr.name="url" attr.type="string" for="edge" id="d5"/>
<key attr.name="description" attr.type="string" for="edge" id="d6"/>
<key for="edge" id="d7" yfiles.type="edgegraphics"/>
<graph edgedefault="directed" id="G">
<node id="n0">
<data key="d3">
<y:ShapeNode>
<y:Geometry height="30.0" width="30.0" x="125.0" y="100.0"/>
<y:Fill color="#FFCC00" transparent="false"/>
<y:BorderStyle color="#000000" type="line" width="1.0"/>
<y:NodeLabel alignment="center" autoSizePolicy="content"
borderDistance="0.0" fontFamily="Dialog" fontSize="13"
fontStyle="plain" hasBackgroundColor="false" hasLineColor="false"
height="19.1328125" modelName="internal" modelPosition="c"
textColor="#000000" visible="true" width="12.27099609375"
x="8.864501953125" y="5.43359375">1</y:NodeLabel>
<y:Shape type="rectangle"/>
</y:ShapeNode>
</data>
</node>
<node id="n1">
<data key="d3">
<y:ShapeNode>
<y:Geometry height="30.0" width="30.0" x="183.0" y="205.0"/>
<y:Fill color="#FFCC00" transparent="false"/>
<y:BorderStyle color="#000000" type="line" width="1.0"/>
<y:NodeLabel alignment="center" autoSizePolicy="content"
borderDistance="0.0" fontFamily="Dialog" fontSize="13"
fontStyle="plain" hasBackgroundColor="false" hasLineColor="false"
height="19.1328125" modelName="internal" modelPosition="c"
textColor="#000000" visible="true" width="12.27099609375"
x="8.864501953125" y="5.43359375">2</y:NodeLabel>
<y:Shape type="rectangle"/>
</y:ShapeNode>
</data>
</node>
<edge id="e0" source="n0" target="n1">
<data key="d7">
<y:PolyLineEdge>
<y:Path sx="0.0" sy="0.0" tx="0.0" ty="0.0"/>
<y:LineStyle color="#000000" type="line" width="1.0"/>
<y:Arrows source="none" target="standard"/>
<y:BendStyle smoothed="false"/>
</y:PolyLineEdge>
</data>
</edge>
</graph>
<data key="d0">
<y:Resources/>
</data>
</graphml>
"""
fh = io.BytesIO(data.encode("UTF-8"))
G = nx.read_graphml(fh, force_multigraph=True)
assert list(G.edges()) == [("n0", "n1")]
assert G.has_edge("n0", "n1", key="e0")
assert G.nodes["n0"]["label"] == "1"
assert G.nodes["n1"]["label"] == "2"
fh.seek(0)
G = nx.read_graphml(fh)
assert list(G.edges()) == [("n0", "n1")]
assert G["n0"]["n1"]["id"] == "e0"
assert G.nodes["n0"]["label"] == "1"
assert G.nodes["n1"]["label"] == "2"
H = nx.parse_graphml(data, force_multigraph=True)
assert list(H.edges()) == [("n0", "n1")]
assert H.has_edge("n0", "n1", key="e0")
assert H.nodes["n0"]["label"] == "1"
assert H.nodes["n1"]["label"] == "2"
H = nx.parse_graphml(data)
assert list(H.edges()) == [("n0", "n1")]
assert H["n0"]["n1"]["id"] == "e0"
assert H.nodes["n0"]["label"] == "1"
assert H.nodes["n1"]["label"] == "2"
def test_bool(self):
s = """<?xml version="1.0" encoding="UTF-8"?>
<graphml xmlns="http://graphml.graphdrawing.org/xmlns"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://graphml.graphdrawing.org/xmlns
http://graphml.graphdrawing.org/xmlns/1.0/graphml.xsd">
<key id="d0" for="node" attr.name="test" attr.type="boolean">
<default>false</default>
</key>
<graph id="G" edgedefault="directed">
<node id="n0">
<data key="d0">true</data>
</node>
<node id="n1"/>
<node id="n2">
<data key="d0">false</data>
</node>
<node id="n3">
<data key="d0">FaLsE</data>
</node>
<node id="n4">
<data key="d0">True</data>
</node>
<node id="n5">
<data key="d0">0</data>
</node>
<node id="n6">
<data key="d0">1</data>
</node>
</graph>
</graphml>
"""
fh = io.BytesIO(s.encode("UTF-8"))
G = nx.read_graphml(fh)
H = nx.parse_graphml(s)
for graph in [G, H]:
assert graph.nodes["n0"]["test"]
assert not graph.nodes["n2"]["test"]
assert not graph.nodes["n3"]["test"]
assert graph.nodes["n4"]["test"]
assert not graph.nodes["n5"]["test"]
assert graph.nodes["n6"]["test"]
def test_graphml_header_line(self):
good = """<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<graphml xmlns="http://graphml.graphdrawing.org/xmlns"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://graphml.graphdrawing.org/xmlns
http://graphml.graphdrawing.org/xmlns/1.0/graphml.xsd">
<key id="d0" for="node" attr.name="test" attr.type="boolean">
<default>false</default>
</key>
<graph id="G">
<node id="n0">
<data key="d0">true</data>
</node>
</graph>
</graphml>
"""
bad = """<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<graphml>
<key id="d0" for="node" attr.name="test" attr.type="boolean">
<default>false</default>
</key>
<graph id="G">
<node id="n0">
<data key="d0">true</data>
</node>
</graph>
</graphml>
"""
ugly = """<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<graphml xmlns="https://ghghgh">
<key id="d0" for="node" attr.name="test" attr.type="boolean">
<default>false</default>
</key>
<graph id="G">
<node id="n0">
<data key="d0">true</data>
</node>
</graph>
</graphml>
"""
for s in (good, bad):
fh = io.BytesIO(s.encode("UTF-8"))
G = nx.read_graphml(fh)
H = nx.parse_graphml(s)
for graph in [G, H]:
assert graph.nodes["n0"]["test"]
fh = io.BytesIO(ugly.encode("UTF-8"))
pytest.raises(nx.NetworkXError, nx.read_graphml, fh)
pytest.raises(nx.NetworkXError, nx.parse_graphml, ugly)
def test_read_attributes_with_groups(self):
data = """\
<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<graphml xmlns="http://graphml.graphdrawing.org/xmlns" xmlns:java="http://www.yworks.com/xml/yfiles-common/1.0/java" xmlns:sys="http://www.yworks.com/xml/yfiles-common/markup/primitives/2.0" xmlns:x="http://www.yworks.com/xml/yfiles-common/markup/2.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:y="http://www.yworks.com/xml/graphml" xmlns:yed="http://www.yworks.com/xml/yed/3" xsi:schemaLocation="http://graphml.graphdrawing.org/xmlns http://www.yworks.com/xml/schema/graphml/1.1/ygraphml.xsd">
<!--Created by yEd 3.17-->
<key attr.name="Description" attr.type="string" for="graph" id="d0"/>
<key for="port" id="d1" yfiles.type="portgraphics"/>
<key for="port" id="d2" yfiles.type="portgeometry"/>
<key for="port" id="d3" yfiles.type="portuserdata"/>
<key attr.name="CustomProperty" attr.type="string" for="node" id="d4">
<default/>
</key>
<key attr.name="url" attr.type="string" for="node" id="d5"/>
<key attr.name="description" attr.type="string" for="node" id="d6"/>
<key for="node" id="d7" yfiles.type="nodegraphics"/>
<key for="graphml" id="d8" yfiles.type="resources"/>
<key attr.name="url" attr.type="string" for="edge" id="d9"/>
<key attr.name="description" attr.type="string" for="edge" id="d10"/>
<key for="edge" id="d11" yfiles.type="edgegraphics"/>
<graph edgedefault="directed" id="G">
<data key="d0"/>
<node id="n0">
<data key="d4"><![CDATA[CustomPropertyValue]]></data>
<data key="d6"/>
<data key="d7">
<y:ShapeNode>
<y:Geometry height="30.0" width="30.0" x="125.0" y="-255.4611111111111"/>
<y:Fill color="#FFCC00" transparent="false"/>
<y:BorderStyle color="#000000" raised="false" type="line" width="1.0"/>
<y:NodeLabel alignment="center" autoSizePolicy="content" fontFamily="Dialog" fontSize="12" fontStyle="plain" hasBackgroundColor="false" hasLineColor="false" height="17.96875" horizontalTextPosition="center" iconTextGap="4" modelName="custom" textColor="#000000" verticalTextPosition="bottom" visible="true" width="11.634765625" x="9.1826171875" y="6.015625">2<y:LabelModel>
<y:SmartNodeLabelModel distance="4.0"/>
</y:LabelModel>
<y:ModelParameter>
<y:SmartNodeLabelModelParameter labelRatioX="0.0" labelRatioY="0.0" nodeRatioX="0.0" nodeRatioY="0.0" offsetX="0.0" offsetY="0.0" upX="0.0" upY="-1.0"/>
</y:ModelParameter>
</y:NodeLabel>
<y:Shape type="rectangle"/>
</y:ShapeNode>
</data>
</node>
<node id="n1" yfiles.foldertype="group">
<data key="d4"><![CDATA[CustomPropertyValue]]></data>
<data key="d5"/>
<data key="d6"/>
<data key="d7">
<y:ProxyAutoBoundsNode>
<y:Realizers active="0">
<y:GroupNode>
<y:Geometry height="250.38333333333333" width="140.0" x="-30.0" y="-330.3833333333333"/>
<y:Fill color="#F5F5F5" transparent="false"/>
<y:BorderStyle color="#000000" type="dashed" width="1.0"/>
<y:NodeLabel alignment="right" autoSizePolicy="node_width" backgroundColor="#EBEBEB" borderDistance="0.0" fontFamily="Dialog" fontSize="15" fontStyle="plain" hasLineColor="false" height="21.4609375" horizontalTextPosition="center" iconTextGap="4" modelName="internal" modelPosition="t" textColor="#000000" verticalTextPosition="bottom" visible="true" width="140.0" x="0.0" y="0.0">Group 3</y:NodeLabel>
<y:Shape type="roundrectangle"/>
<y:State closed="false" closedHeight="50.0" closedWidth="50.0" innerGraphDisplayEnabled="false"/>
<y:Insets bottom="15" bottomF="15.0" left="15" leftF="15.0" right="15" rightF="15.0" top="15" topF="15.0"/>
<y:BorderInsets bottom="1" bottomF="1.0" left="0" leftF="0.0" right="0" rightF="0.0" top="1" topF="1.0001736111111086"/>
</y:GroupNode>
<y:GroupNode>
<y:Geometry height="50.0" width="50.0" x="0.0" y="60.0"/>
<y:Fill color="#F5F5F5" transparent="false"/>
<y:BorderStyle color="#000000" type="dashed" width="1.0"/>
<y:NodeLabel alignment="right" autoSizePolicy="node_width" backgroundColor="#EBEBEB" borderDistance="0.0" fontFamily="Dialog" fontSize="15" fontStyle="plain" hasLineColor="false" height="21.4609375" horizontalTextPosition="center" iconTextGap="4" modelName="internal" modelPosition="t" textColor="#000000" verticalTextPosition="bottom" visible="true" width="65.201171875" x="-7.6005859375" y="0.0">Folder 3</y:NodeLabel>
<y:Shape type="roundrectangle"/>
<y:State closed="true" closedHeight="50.0" closedWidth="50.0" innerGraphDisplayEnabled="false"/>
<y:Insets bottom="5" bottomF="5.0" left="5" leftF="5.0" right="5" rightF="5.0" top="5" topF="5.0"/>
<y:BorderInsets bottom="0" bottomF="0.0" left="0" leftF="0.0" right="0" rightF="0.0" top="0" topF="0.0"/>
</y:GroupNode>
</y:Realizers>
</y:ProxyAutoBoundsNode>
</data>
<graph edgedefault="directed" id="n1:">
<node id="n1::n0" yfiles.foldertype="group">
<data key="d4"><![CDATA[CustomPropertyValue]]></data>
<data key="d5"/>
<data key="d6"/>
<data key="d7">
<y:ProxyAutoBoundsNode>
<y:Realizers active="0">
<y:GroupNode>
<y:Geometry height="83.46111111111111" width="110.0" x="-15.0" y="-292.9222222222222"/>
<y:Fill color="#F5F5F5" transparent="false"/>
<y:BorderStyle color="#000000" type="dashed" width="1.0"/>
<y:NodeLabel alignment="right" autoSizePolicy="node_width" backgroundColor="#EBEBEB" borderDistance="0.0" fontFamily="Dialog" fontSize="15" fontStyle="plain" hasLineColor="false" height="21.4609375" horizontalTextPosition="center" iconTextGap="4" modelName="internal" modelPosition="t" textColor="#000000" verticalTextPosition="bottom" visible="true" width="110.0" x="0.0" y="0.0">Group 1</y:NodeLabel>
<y:Shape type="roundrectangle"/>
<y:State closed="false" closedHeight="50.0" closedWidth="50.0" innerGraphDisplayEnabled="false"/>
<y:Insets bottom="15" bottomF="15.0" left="15" leftF="15.0" right="15" rightF="15.0" top="15" topF="15.0"/>
<y:BorderInsets bottom="1" bottomF="1.0" left="0" leftF="0.0" right="0" rightF="0.0" top="1" topF="1.0001736111111086"/>
</y:GroupNode>
<y:GroupNode>
<y:Geometry height="50.0" width="50.0" x="0.0" y="60.0"/>
<y:Fill color="#F5F5F5" transparent="false"/>
<y:BorderStyle color="#000000" type="dashed" width="1.0"/>
<y:NodeLabel alignment="right" autoSizePolicy="node_width" backgroundColor="#EBEBEB" borderDistance="0.0" fontFamily="Dialog" fontSize="15" fontStyle="plain" hasLineColor="false" height="21.4609375" horizontalTextPosition="center" iconTextGap="4" modelName="internal" modelPosition="t" textColor="#000000" verticalTextPosition="bottom" visible="true" width="65.201171875" x="-7.6005859375" y="0.0">Folder 1</y:NodeLabel>
<y:Shape type="roundrectangle"/>
<y:State closed="true" closedHeight="50.0" closedWidth="50.0" innerGraphDisplayEnabled="false"/>
<y:Insets bottom="5" bottomF="5.0" left="5" leftF="5.0" right="5" rightF="5.0" top="5" topF="5.0"/>
<y:BorderInsets bottom="0" bottomF="0.0" left="0" leftF="0.0" right="0" rightF="0.0" top="0" topF="0.0"/>
</y:GroupNode>
</y:Realizers>
</y:ProxyAutoBoundsNode>
</data>
<graph edgedefault="directed" id="n1::n0:">
<node id="n1::n0::n0">
<data key="d4"><![CDATA[CustomPropertyValue]]></data>
<data key="d6"/>
<data key="d7">
<y:ShapeNode>
<y:Geometry height="30.0" width="30.0" x="50.0" y="-255.4611111111111"/>
<y:Fill color="#FFCC00" transparent="false"/>
<y:BorderStyle color="#000000" raised="false" type="line" width="1.0"/>
<y:NodeLabel alignment="center" autoSizePolicy="content" fontFamily="Dialog" fontSize="12" fontStyle="plain" hasBackgroundColor="false" hasLineColor="false" height="17.96875" horizontalTextPosition="center" iconTextGap="4" modelName="custom" textColor="#000000" verticalTextPosition="bottom" visible="true" width="11.634765625" x="9.1826171875" y="6.015625">1<y:LabelModel>
<y:SmartNodeLabelModel distance="4.0"/>
</y:LabelModel>
<y:ModelParameter>
<y:SmartNodeLabelModelParameter labelRatioX="0.0" labelRatioY="0.0" nodeRatioX="0.0" nodeRatioY="0.0" offsetX="0.0" offsetY="0.0" upX="0.0" upY="-1.0"/>
</y:ModelParameter>
</y:NodeLabel>
<y:Shape type="rectangle"/>
</y:ShapeNode>
</data>
</node>
<node id="n1::n0::n1">
<data key="d4"><![CDATA[CustomPropertyValue]]></data>
<data key="d6"/>
<data key="d7">
<y:ShapeNode>
<y:Geometry height="30.0" width="30.0" x="0.0" y="-255.4611111111111"/>
<y:Fill color="#FFCC00" transparent="false"/>
<y:BorderStyle color="#000000" raised="false" type="line" width="1.0"/>
<y:NodeLabel alignment="center" autoSizePolicy="content" fontFamily="Dialog" fontSize="12" fontStyle="plain" hasBackgroundColor="false" hasLineColor="false" height="17.96875" horizontalTextPosition="center" iconTextGap="4" modelName="custom" textColor="#000000" verticalTextPosition="bottom" visible="true" width="11.634765625" x="9.1826171875" y="6.015625">3<y:LabelModel>
<y:SmartNodeLabelModel distance="4.0"/>
</y:LabelModel>
<y:ModelParameter>
<y:SmartNodeLabelModelParameter labelRatioX="0.0" labelRatioY="0.0" nodeRatioX="0.0" nodeRatioY="0.0" offsetX="0.0" offsetY="0.0" upX="0.0" upY="-1.0"/>
</y:ModelParameter>
</y:NodeLabel>
<y:Shape type="rectangle"/>
</y:ShapeNode>
</data>
</node>
</graph>
</node>
<node id="n1::n1" yfiles.foldertype="group">
<data key="d4"><![CDATA[CustomPropertyValue]]></data>
<data key="d5"/>
<data key="d6"/>
<data key="d7">
<y:ProxyAutoBoundsNode>
<y:Realizers active="0">
<y:GroupNode>
<y:Geometry height="83.46111111111111" width="110.0" x="-15.0" y="-179.4611111111111"/>
<y:Fill color="#F5F5F5" transparent="false"/>
<y:BorderStyle color="#000000" type="dashed" width="1.0"/>
<y:NodeLabel alignment="right" autoSizePolicy="node_width" backgroundColor="#EBEBEB" borderDistance="0.0" fontFamily="Dialog" fontSize="15" fontStyle="plain" hasLineColor="false" height="21.4609375" horizontalTextPosition="center" iconTextGap="4" modelName="internal" modelPosition="t" textColor="#000000" verticalTextPosition="bottom" visible="true" width="110.0" x="0.0" y="0.0">Group 2</y:NodeLabel>
<y:Shape type="roundrectangle"/>
<y:State closed="false" closedHeight="50.0" closedWidth="50.0" innerGraphDisplayEnabled="false"/>
<y:Insets bottom="15" bottomF="15.0" left="15" leftF="15.0" right="15" rightF="15.0" top="15" topF="15.0"/>
<y:BorderInsets bottom="1" bottomF="1.0" left="0" leftF="0.0" right="0" rightF="0.0" top="1" topF="1.0001736111111086"/>
</y:GroupNode>
<y:GroupNode>
<y:Geometry height="50.0" width="50.0" x="0.0" y="60.0"/>
<y:Fill color="#F5F5F5" transparent="false"/>
<y:BorderStyle color="#000000" type="dashed" width="1.0"/>
<y:NodeLabel alignment="right" autoSizePolicy="node_width" backgroundColor="#EBEBEB" borderDistance="0.0" fontFamily="Dialog" fontSize="15" fontStyle="plain" hasLineColor="false" height="21.4609375" horizontalTextPosition="center" iconTextGap="4" modelName="internal" modelPosition="t" textColor="#000000" verticalTextPosition="bottom" visible="true" width="65.201171875" x="-7.6005859375" y="0.0">Folder 2</y:NodeLabel>
<y:Shape type="roundrectangle"/>
<y:State closed="true" closedHeight="50.0" closedWidth="50.0" innerGraphDisplayEnabled="false"/>
<y:Insets bottom="5" bottomF="5.0" left="5" leftF="5.0" right="5" rightF="5.0" top="5" topF="5.0"/>
<y:BorderInsets bottom="0" bottomF="0.0" left="0" leftF="0.0" right="0" rightF="0.0" top="0" topF="0.0"/>
</y:GroupNode>
</y:Realizers>
</y:ProxyAutoBoundsNode>
</data>
<graph edgedefault="directed" id="n1::n1:">
<node id="n1::n1::n0">
<data key="d4"><![CDATA[CustomPropertyValue]]></data>
<data key="d6"/>
<data key="d7">
<y:ShapeNode>
<y:Geometry height="30.0" width="30.0" x="0.0" y="-142.0"/>
<y:Fill color="#FFCC00" transparent="false"/>
<y:BorderStyle color="#000000" raised="false" type="line" width="1.0"/>
<y:NodeLabel alignment="center" autoSizePolicy="content" fontFamily="Dialog" fontSize="12" fontStyle="plain" hasBackgroundColor="false" hasLineColor="false" height="17.96875" horizontalTextPosition="center" iconTextGap="4" modelName="custom" textColor="#000000" verticalTextPosition="bottom" visible="true" width="11.634765625" x="9.1826171875" y="6.015625">5<y:LabelModel>
<y:SmartNodeLabelModel distance="4.0"/>
</y:LabelModel>
<y:ModelParameter>
<y:SmartNodeLabelModelParameter labelRatioX="0.0" labelRatioY="0.0" nodeRatioX="0.0" nodeRatioY="0.0" offsetX="0.0" offsetY="0.0" upX="0.0" upY="-1.0"/>
</y:ModelParameter>
</y:NodeLabel>
<y:Shape type="rectangle"/>
</y:ShapeNode>
</data>
</node>
<node id="n1::n1::n1">
<data key="d4"><![CDATA[CustomPropertyValue]]></data>
<data key="d6"/>
<data key="d7">
<y:ShapeNode>
<y:Geometry height="30.0" width="30.0" x="50.0" y="-142.0"/>
<y:Fill color="#FFCC00" transparent="false"/>
<y:BorderStyle color="#000000" raised="false" type="line" width="1.0"/>
<y:NodeLabel alignment="center" autoSizePolicy="content" fontFamily="Dialog" fontSize="12" fontStyle="plain" hasBackgroundColor="false" hasLineColor="false" height="17.96875" horizontalTextPosition="center" iconTextGap="4" modelName="custom" textColor="#000000" verticalTextPosition="bottom" visible="true" width="11.634765625" x="9.1826171875" y="6.015625">6<y:LabelModel>
<y:SmartNodeLabelModel distance="4.0"/>
</y:LabelModel>
<y:ModelParameter>
<y:SmartNodeLabelModelParameter labelRatioX="0.0" labelRatioY="0.0" nodeRatioX="0.0" nodeRatioY="0.0" offsetX="0.0" offsetY="0.0" upX="0.0" upY="-1.0"/>
</y:ModelParameter>
</y:NodeLabel>
<y:Shape type="rectangle"/>
</y:ShapeNode>
</data>
</node>
</graph>
</node>
</graph>
</node>
<node id="n2">
<data key="d4"><![CDATA[CustomPropertyValue]]></data>
<data key="d6"/>
<data key="d7">
<y:ShapeNode>
<y:Geometry height="30.0" width="30.0" x="125.0" y="-142.0"/>
<y:Fill color="#FFCC00" transparent="false"/>
<y:BorderStyle color="#000000" raised="false" type="line" width="1.0"/>
<y:NodeLabel alignment="center" autoSizePolicy="content" fontFamily="Dialog" fontSize="12" fontStyle="plain" hasBackgroundColor="false" hasLineColor="false" height="17.96875" horizontalTextPosition="center" iconTextGap="4" modelName="custom" textColor="#000000" verticalTextPosition="bottom" visible="true" width="11.634765625" x="9.1826171875" y="6.015625">9<y:LabelModel>
<y:SmartNodeLabelModel distance="4.0"/>
</y:LabelModel>
<y:ModelParameter>
<y:SmartNodeLabelModelParameter labelRatioX="0.0" labelRatioY="0.0" nodeRatioX="0.0" nodeRatioY="0.0" offsetX="0.0" offsetY="0.0" upX="0.0" upY="-1.0"/>
</y:ModelParameter>
</y:NodeLabel>
<y:Shape type="rectangle"/>
</y:ShapeNode>
</data>
</node>
<edge id="n1::n1::e0" source="n1::n1::n0" target="n1::n1::n1">
<data key="d10"/>
<data key="d11">
<y:PolyLineEdge>
<y:Path sx="15.0" sy="-0.0" tx="-15.0" ty="-0.0"/>
<y:LineStyle color="#000000" type="line" width="1.0"/>
<y:Arrows source="none" target="standard"/>
<y:BendStyle smoothed="false"/>
</y:PolyLineEdge>
</data>
</edge>
<edge id="n1::n0::e0" source="n1::n0::n1" target="n1::n0::n0">
<data key="d10"/>
<data key="d11">
<y:PolyLineEdge>
<y:Path sx="15.0" sy="-0.0" tx="-15.0" ty="-0.0"/>
<y:LineStyle color="#000000" type="line" width="1.0"/>
<y:Arrows source="none" target="standard"/>
<y:BendStyle smoothed="false"/>
</y:PolyLineEdge>
</data>
</edge>
<edge id="e0" source="n1::n0::n0" target="n0">
<data key="d10"/>
<data key="d11">
<y:PolyLineEdge>
<y:Path sx="15.0" sy="-0.0" tx="-15.0" ty="-0.0"/>
<y:LineStyle color="#000000" type="line" width="1.0"/>
<y:Arrows source="none" target="standard"/>
<y:BendStyle smoothed="false"/>
</y:PolyLineEdge>
</data>
</edge>
<edge id="e1" source="n1::n1::n1" target="n2">
<data key="d10"/>
<data key="d11">
<y:PolyLineEdge>
<y:Path sx="15.0" sy="-0.0" tx="-15.0" ty="-0.0"/>
<y:LineStyle color="#000000" type="line" width="1.0"/>
<y:Arrows source="none" target="standard"/>
<y:BendStyle smoothed="false"/>
</y:PolyLineEdge>
</data>
</edge>
</graph>
<data key="d8">
<y:Resources/>
</data>
</graphml>
"""
# verify that nodes / attributes are correctly read when part of a group
fh = io.BytesIO(data.encode("UTF-8"))
G = nx.read_graphml(fh)
data = [x for _, x in G.nodes(data=True)]
assert len(data) == 9
for node_data in data:
assert node_data["CustomProperty"] != ""
class TestWriteGraphML(BaseGraphML):
writer = staticmethod(nx.write_graphml_lxml)
@classmethod
def setup_class(cls):
BaseGraphML.setup_class()
_ = pytest.importorskip("lxml.etree")
def test_write_interface(self):
try:
import lxml.etree
assert nx.write_graphml == nx.write_graphml_lxml
except ImportError:
assert nx.write_graphml == nx.write_graphml_xml
def test_write_read_simple_directed_graphml(self):
G = self.simple_directed_graph
G.graph["hi"] = "there"
fh = io.BytesIO()
self.writer(G, fh)
fh.seek(0)
H = nx.read_graphml(fh)
assert sorted(G.nodes()) == sorted(H.nodes())
assert sorted(G.edges()) == sorted(H.edges())
assert sorted(G.edges(data=True)) == sorted(H.edges(data=True))
self.simple_directed_fh.seek(0)
def test_write_read_attribute_named_key_ids_graphml(self):
from xml.etree.ElementTree import parse
G = self.attribute_named_key_ids_graph
fh = io.BytesIO()
self.writer(G, fh, named_key_ids=True)
fh.seek(0)
H = nx.read_graphml(fh)
fh.seek(0)
assert_nodes_equal(G.nodes(), H.nodes())
assert_edges_equal(G.edges(), H.edges())
assert_edges_equal(G.edges(data=True), H.edges(data=True))
self.attribute_named_key_ids_fh.seek(0)
xml = parse(fh)
# Children are the key elements, and the graph element
children = list(xml.getroot())
assert len(children) == 4
keys = [child.items() for child in children[:3]]
assert len(keys) == 3
assert ("id", "edge_prop") in keys[0]
assert ("attr.name", "edge_prop") in keys[0]
assert ("id", "prop2") in keys[1]
assert ("attr.name", "prop2") in keys[1]
assert ("id", "prop1") in keys[2]
assert ("attr.name", "prop1") in keys[2]
# Confirm the read graph nodes/edge are identical when compared to
# default writing behavior.
default_behavior_fh = io.BytesIO()
nx.write_graphml(G, default_behavior_fh)
default_behavior_fh.seek(0)
H = nx.read_graphml(default_behavior_fh)
named_key_ids_behavior_fh = io.BytesIO()
nx.write_graphml(G, named_key_ids_behavior_fh, named_key_ids=True)
named_key_ids_behavior_fh.seek(0)
J = nx.read_graphml(named_key_ids_behavior_fh)
assert all(n1 == n2 for (n1, n2) in zip(H.nodes, J.nodes))
assert all(e1 == e2 for (e1, e2) in zip(H.edges, J.edges))
def test_write_read_attribute_numeric_type_graphml(self):
from xml.etree.ElementTree import parse
G = self.attribute_numeric_type_graph
fh = io.BytesIO()
self.writer(G, fh, infer_numeric_types=True)
fh.seek(0)
H = nx.read_graphml(fh)
fh.seek(0)
assert_nodes_equal(G.nodes(), H.nodes())
assert_edges_equal(G.edges(), H.edges())
assert_edges_equal(G.edges(data=True), H.edges(data=True))
self.attribute_numeric_type_fh.seek(0)
xml = parse(fh)
# Children are the key elements, and the graph element
children = list(xml.getroot())
assert len(children) == 3
keys = [child.items() for child in children[:2]]
assert len(keys) == 2
assert ("attr.type", "double") in keys[0]
assert ("attr.type", "double") in keys[1]
def test_more_multigraph_keys(self):
"""Writing keys as edge id attributes means keys become strings.
The original keys are stored as data, so read them back in
if `str(key) == edge_id`
This allows the adjacency to remain the same.
"""
G = nx.MultiGraph()
G.add_edges_from([("a", "b", 2), ("a", "b", 3)])
fd, fname = tempfile.mkstemp()
self.writer(G, fname)
H = nx.read_graphml(fname)
assert H.is_multigraph()
assert_edges_equal(G.edges(keys=True), H.edges(keys=True))
assert G._adj == H._adj
os.close(fd)
os.unlink(fname)
def test_default_attribute(self):
G = nx.Graph(name="Fred")
G.add_node(1, label=1, color="green")
nx.add_path(G, [0, 1, 2, 3])
G.add_edge(1, 2, weight=3)
G.graph["node_default"] = {"color": "yellow"}
G.graph["edge_default"] = {"weight": 7}
fh = io.BytesIO()
self.writer(G, fh)
fh.seek(0)
H = nx.read_graphml(fh, node_type=int)
assert_nodes_equal(G.nodes(), H.nodes())
assert_edges_equal(G.edges(), H.edges())
assert G.graph == H.graph
def test_mixed_type_attributes(self):
G = nx.MultiGraph()
G.add_node("n0", special=False)
G.add_node("n1", special=0)
G.add_edge("n0", "n1", special=False)
G.add_edge("n0", "n1", special=0)
fh = io.BytesIO()
self.writer(G, fh)
fh.seek(0)
H = nx.read_graphml(fh)
assert not H.nodes["n0"]["special"]
assert H.nodes["n1"]["special"] == 0
assert not H.edges["n0", "n1", 0]["special"]
assert H.edges["n0", "n1", 1]["special"] == 0
def test_numpy_float(self):
np = pytest.importorskip("numpy")
wt = np.float(3.4)
G = nx.Graph([(1, 2, {"weight": wt})])
fd, fname = tempfile.mkstemp()
self.writer(G, fname)
H = nx.read_graphml(fname, node_type=int)
assert G._adj == H._adj
os.close(fd)
os.unlink(fname)
def test_multigraph_to_graph(self):
# test converting multigraph to graph if no parallel edges found
G = nx.MultiGraph()
G.add_edges_from([("a", "b", 2), ("b", "c", 3)]) # no multiedges
fd, fname = tempfile.mkstemp()
self.writer(G, fname)
H = nx.read_graphml(fname)
assert not H.is_multigraph()
H = nx.read_graphml(fname, force_multigraph=True)
assert H.is_multigraph()
os.close(fd)
os.unlink(fname)
# add a multiedge
G.add_edge("a", "b", "e-id")
fd, fname = tempfile.mkstemp()
self.writer(G, fname)
H = nx.read_graphml(fname)
assert H.is_multigraph()
H = nx.read_graphml(fname, force_multigraph=True)
assert H.is_multigraph()
os.close(fd)
os.unlink(fname)
def test_numpy_float64(self):
np = pytest.importorskip("numpy")
wt = np.float64(3.4)
G = nx.Graph([(1, 2, {"weight": wt})])
fd, fname = tempfile.mkstemp()
self.writer(G, fname)
H = nx.read_graphml(fname, node_type=int)
assert G.edges == H.edges
wtG = G[1][2]["weight"]
wtH = H[1][2]["weight"]
assert almost_equal(wtG, wtH, places=6)
assert type(wtG) == np.float64
assert type(wtH) == float
os.close(fd)
os.unlink(fname)
def test_numpy_float32(self):
np = pytest.importorskip("numpy")
wt = np.float32(3.4)
G = nx.Graph([(1, 2, {"weight": wt})])
fd, fname = tempfile.mkstemp()
self.writer(G, fname)
H = nx.read_graphml(fname, node_type=int)
assert G.edges == H.edges
wtG = G[1][2]["weight"]
wtH = H[1][2]["weight"]
assert almost_equal(wtG, wtH, places=6)
assert type(wtG) == np.float32
assert type(wtH) == float
os.close(fd)
os.unlink(fname)
def test_numpy_float64_inference(self):
np = pytest.importorskip("numpy")
G = self.attribute_numeric_type_graph
G.edges[("n1", "n1")]["weight"] = np.float64(1.1)
fd, fname = tempfile.mkstemp()
self.writer(G, fname, infer_numeric_types=True)
H = nx.read_graphml(fname)
assert G._adj == H._adj
os.close(fd)
os.unlink(fname)
def test_unicode_attributes(self):
G = nx.Graph()
name1 = chr(2344) + chr(123) + chr(6543)
name2 = chr(5543) + chr(1543) + chr(324)
node_type = str
G.add_edge(name1, "Radiohead", foo=name2)
fd, fname = tempfile.mkstemp()
self.writer(G, fname)
H = nx.read_graphml(fname, node_type=node_type)
assert G._adj == H._adj
os.close(fd)
os.unlink(fname)
def test_unicode_escape(self):
# test for handling json escaped stings in python 2 Issue #1880
import json
a = dict(a='{"a": "123"}') # an object with many chars to escape
sa = json.dumps(a)
G = nx.Graph()
G.graph["test"] = sa
fh = io.BytesIO()
self.writer(G, fh)
fh.seek(0)
H = nx.read_graphml(fh)
assert G.graph["test"] == H.graph["test"]
class TestXMLGraphML(TestWriteGraphML):
writer = staticmethod(nx.write_graphml_xml)
@classmethod
def setup_class(cls):
TestWriteGraphML.setup_class()
pytest.importorskip("xml.etree.ElementTree")