Mercurial > repos > shellac > sam_consensus_v3
diff env/lib/python3.9/site-packages/networkx/readwrite/tests/test_graphml.py @ 0:4f3585e2f14b draft default tip
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
| author | shellac |
|---|---|
| date | Mon, 22 Mar 2021 18:12:50 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/env/lib/python3.9/site-packages/networkx/readwrite/tests/test_graphml.py Mon Mar 22 18:12:50 2021 +0000 @@ -0,0 +1,1254 @@ +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")