1541 lines
66 KiB
Python
1541 lines
66 KiB
Python
import io
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import os
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import tempfile
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import pytest
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import networkx as nx
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from networkx.readwrite.graphml import GraphMLWriter
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from networkx.utils import edges_equal, nodes_equal
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class BaseGraphML:
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@classmethod
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def setup_class(cls):
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cls.simple_directed_data = """<?xml version="1.0" encoding="UTF-8"?>
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<!-- This file was written by the JAVA GraphML Library.-->
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<graphml xmlns="http://graphml.graphdrawing.org/xmlns"
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xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
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xsi:schemaLocation="http://graphml.graphdrawing.org/xmlns
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http://graphml.graphdrawing.org/xmlns/1.0/graphml.xsd">
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<graph id="G" edgedefault="directed">
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<node id="n0"/>
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<node id="n1"/>
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<node id="n2"/>
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<node id="n3"/>
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<node id="n4"/>
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<node id="n5"/>
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<node id="n6"/>
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<node id="n7"/>
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<node id="n8"/>
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<node id="n9"/>
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<node id="n10"/>
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<edge id="foo" source="n0" target="n2"/>
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<edge source="n1" target="n2"/>
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<edge source="n2" target="n3"/>
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<edge source="n3" target="n5"/>
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<edge source="n3" target="n4"/>
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<edge source="n4" target="n6"/>
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<edge source="n6" target="n5"/>
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<edge source="n5" target="n7"/>
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<edge source="n6" target="n8"/>
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<edge source="n8" target="n7"/>
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<edge source="n8" target="n9"/>
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</graph>
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</graphml>"""
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cls.simple_directed_graph = nx.DiGraph()
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cls.simple_directed_graph.add_node("n10")
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cls.simple_directed_graph.add_edge("n0", "n2", id="foo")
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cls.simple_directed_graph.add_edge("n0", "n2")
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cls.simple_directed_graph.add_edges_from(
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[
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("n1", "n2"),
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("n2", "n3"),
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("n3", "n5"),
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("n3", "n4"),
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("n4", "n6"),
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("n6", "n5"),
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("n5", "n7"),
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("n6", "n8"),
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("n8", "n7"),
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("n8", "n9"),
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]
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)
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cls.simple_directed_fh = io.BytesIO(cls.simple_directed_data.encode("UTF-8"))
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cls.attribute_data = """<?xml version="1.0" encoding="UTF-8"?>
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<graphml xmlns="http://graphml.graphdrawing.org/xmlns"
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xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
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xsi:schemaLocation="http://graphml.graphdrawing.org/xmlns
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http://graphml.graphdrawing.org/xmlns/1.0/graphml.xsd">
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<key id="d0" for="node" attr.name="color" attr.type="string">
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<default>yellow</default>
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</key>
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<key id="d1" for="edge" attr.name="weight" attr.type="double"/>
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<graph id="G" edgedefault="directed">
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<node id="n0">
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<data key="d0">green</data>
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</node>
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<node id="n1"/>
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<node id="n2">
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<data key="d0">blue</data>
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</node>
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<node id="n3">
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<data key="d0">red</data>
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</node>
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<node id="n4"/>
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<node id="n5">
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<data key="d0">turquoise</data>
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</node>
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<edge id="e0" source="n0" target="n2">
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<data key="d1">1.0</data>
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</edge>
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<edge id="e1" source="n0" target="n1">
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<data key="d1">1.0</data>
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</edge>
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<edge id="e2" source="n1" target="n3">
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<data key="d1">2.0</data>
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</edge>
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<edge id="e3" source="n3" target="n2"/>
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<edge id="e4" source="n2" target="n4"/>
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<edge id="e5" source="n3" target="n5"/>
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<edge id="e6" source="n5" target="n4">
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<data key="d1">1.1</data>
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</edge>
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</graph>
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</graphml>
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"""
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cls.attribute_graph = nx.DiGraph(id="G")
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cls.attribute_graph.graph["node_default"] = {"color": "yellow"}
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cls.attribute_graph.add_node("n0", color="green")
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cls.attribute_graph.add_node("n2", color="blue")
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cls.attribute_graph.add_node("n3", color="red")
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cls.attribute_graph.add_node("n4")
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cls.attribute_graph.add_node("n5", color="turquoise")
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cls.attribute_graph.add_edge("n0", "n2", id="e0", weight=1.0)
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cls.attribute_graph.add_edge("n0", "n1", id="e1", weight=1.0)
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cls.attribute_graph.add_edge("n1", "n3", id="e2", weight=2.0)
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cls.attribute_graph.add_edge("n3", "n2", id="e3")
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cls.attribute_graph.add_edge("n2", "n4", id="e4")
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cls.attribute_graph.add_edge("n3", "n5", id="e5")
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cls.attribute_graph.add_edge("n5", "n4", id="e6", weight=1.1)
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cls.attribute_fh = io.BytesIO(cls.attribute_data.encode("UTF-8"))
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cls.node_attribute_default_data = """<?xml version="1.0" encoding="UTF-8"?>
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<graphml xmlns="http://graphml.graphdrawing.org/xmlns"
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xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
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xsi:schemaLocation="http://graphml.graphdrawing.org/xmlns
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http://graphml.graphdrawing.org/xmlns/1.0/graphml.xsd">
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<key id="d0" for="node" attr.name="boolean_attribute" attr.type="boolean"><default>false</default></key>
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<key id="d1" for="node" attr.name="int_attribute" attr.type="int"><default>0</default></key>
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<key id="d2" for="node" attr.name="long_attribute" attr.type="long"><default>0</default></key>
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<key id="d3" for="node" attr.name="float_attribute" attr.type="float"><default>0.0</default></key>
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<key id="d4" for="node" attr.name="double_attribute" attr.type="double"><default>0.0</default></key>
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<key id="d5" for="node" attr.name="string_attribute" attr.type="string"><default>Foo</default></key>
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<graph id="G" edgedefault="directed">
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<node id="n0"/>
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<node id="n1"/>
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<edge id="e0" source="n0" target="n1"/>
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</graph>
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</graphml>
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"""
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cls.node_attribute_default_graph = nx.DiGraph(id="G")
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cls.node_attribute_default_graph.graph["node_default"] = {
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"boolean_attribute": False,
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"int_attribute": 0,
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"long_attribute": 0,
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"float_attribute": 0.0,
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"double_attribute": 0.0,
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"string_attribute": "Foo",
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}
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cls.node_attribute_default_graph.add_node("n0")
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cls.node_attribute_default_graph.add_node("n1")
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cls.node_attribute_default_graph.add_edge("n0", "n1", id="e0")
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cls.node_attribute_default_fh = io.BytesIO(
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cls.node_attribute_default_data.encode("UTF-8")
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)
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cls.attribute_named_key_ids_data = """<?xml version='1.0' encoding='utf-8'?>
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<graphml xmlns="http://graphml.graphdrawing.org/xmlns"
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xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
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xsi:schemaLocation="http://graphml.graphdrawing.org/xmlns
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http://graphml.graphdrawing.org/xmlns/1.0/graphml.xsd">
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<key id="edge_prop" for="edge" attr.name="edge_prop" attr.type="string"/>
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<key id="prop2" for="node" attr.name="prop2" attr.type="string"/>
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<key id="prop1" for="node" attr.name="prop1" attr.type="string"/>
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<graph edgedefault="directed">
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<node id="0">
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<data key="prop1">val1</data>
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<data key="prop2">val2</data>
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</node>
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<node id="1">
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<data key="prop1">val_one</data>
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<data key="prop2">val2</data>
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</node>
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<edge source="0" target="1">
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<data key="edge_prop">edge_value</data>
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</edge>
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</graph>
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</graphml>
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"""
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cls.attribute_named_key_ids_graph = nx.DiGraph()
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cls.attribute_named_key_ids_graph.add_node("0", prop1="val1", prop2="val2")
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cls.attribute_named_key_ids_graph.add_node("1", prop1="val_one", prop2="val2")
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cls.attribute_named_key_ids_graph.add_edge("0", "1", edge_prop="edge_value")
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fh = io.BytesIO(cls.attribute_named_key_ids_data.encode("UTF-8"))
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cls.attribute_named_key_ids_fh = fh
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cls.attribute_numeric_type_data = """<?xml version='1.0' encoding='utf-8'?>
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<graphml xmlns="http://graphml.graphdrawing.org/xmlns"
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xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
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xsi:schemaLocation="http://graphml.graphdrawing.org/xmlns
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http://graphml.graphdrawing.org/xmlns/1.0/graphml.xsd">
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<key attr.name="weight" attr.type="double" for="node" id="d1" />
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<key attr.name="weight" attr.type="double" for="edge" id="d0" />
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<graph edgedefault="directed">
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<node id="n0">
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<data key="d1">1</data>
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</node>
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<node id="n1">
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<data key="d1">2.0</data>
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</node>
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<edge source="n0" target="n1">
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<data key="d0">1</data>
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</edge>
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<edge source="n1" target="n0">
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<data key="d0">k</data>
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</edge>
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<edge source="n1" target="n1">
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<data key="d0">1.0</data>
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</edge>
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</graph>
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</graphml>
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"""
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cls.attribute_numeric_type_graph = nx.DiGraph()
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cls.attribute_numeric_type_graph.add_node("n0", weight=1)
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cls.attribute_numeric_type_graph.add_node("n1", weight=2.0)
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cls.attribute_numeric_type_graph.add_edge("n0", "n1", weight=1)
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cls.attribute_numeric_type_graph.add_edge("n1", "n1", weight=1.0)
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fh = io.BytesIO(cls.attribute_numeric_type_data.encode("UTF-8"))
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cls.attribute_numeric_type_fh = fh
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cls.simple_undirected_data = """<?xml version="1.0" encoding="UTF-8"?>
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<graphml xmlns="http://graphml.graphdrawing.org/xmlns"
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xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
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xsi:schemaLocation="http://graphml.graphdrawing.org/xmlns
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http://graphml.graphdrawing.org/xmlns/1.0/graphml.xsd">
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<graph id="G">
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<node id="n0"/>
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<node id="n1"/>
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<node id="n2"/>
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<node id="n10"/>
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<edge id="foo" source="n0" target="n2"/>
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<edge source="n1" target="n2"/>
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<edge source="n2" target="n3"/>
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</graph>
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</graphml>"""
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# <edge source="n8" target="n10" directed="false"/>
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cls.simple_undirected_graph = nx.Graph()
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cls.simple_undirected_graph.add_node("n10")
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cls.simple_undirected_graph.add_edge("n0", "n2", id="foo")
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cls.simple_undirected_graph.add_edges_from([("n1", "n2"), ("n2", "n3")])
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fh = io.BytesIO(cls.simple_undirected_data.encode("UTF-8"))
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cls.simple_undirected_fh = fh
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cls.undirected_multigraph_data = """<?xml version="1.0" encoding="UTF-8"?>
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<graphml xmlns="http://graphml.graphdrawing.org/xmlns"
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xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
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xsi:schemaLocation="http://graphml.graphdrawing.org/xmlns
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http://graphml.graphdrawing.org/xmlns/1.0/graphml.xsd">
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<graph id="G">
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<node id="n0"/>
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<node id="n1"/>
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<node id="n2"/>
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<node id="n10"/>
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<edge id="e0" source="n0" target="n2"/>
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<edge id="e1" source="n1" target="n2"/>
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<edge id="e2" source="n2" target="n1"/>
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</graph>
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</graphml>"""
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cls.undirected_multigraph = nx.MultiGraph()
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cls.undirected_multigraph.add_node("n10")
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cls.undirected_multigraph.add_edge("n0", "n2", id="e0")
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cls.undirected_multigraph.add_edge("n1", "n2", id="e1")
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cls.undirected_multigraph.add_edge("n2", "n1", id="e2")
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fh = io.BytesIO(cls.undirected_multigraph_data.encode("UTF-8"))
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cls.undirected_multigraph_fh = fh
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cls.undirected_multigraph_no_multiedge_data = """<?xml version="1.0" encoding="UTF-8"?>
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<graphml xmlns="http://graphml.graphdrawing.org/xmlns"
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xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
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xsi:schemaLocation="http://graphml.graphdrawing.org/xmlns
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http://graphml.graphdrawing.org/xmlns/1.0/graphml.xsd">
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<graph id="G">
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<node id="n0"/>
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<node id="n1"/>
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<node id="n2"/>
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<node id="n10"/>
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<edge id="e0" source="n0" target="n2"/>
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<edge id="e1" source="n1" target="n2"/>
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<edge id="e2" source="n2" target="n3"/>
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</graph>
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</graphml>"""
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cls.undirected_multigraph_no_multiedge = nx.MultiGraph()
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cls.undirected_multigraph_no_multiedge.add_node("n10")
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cls.undirected_multigraph_no_multiedge.add_edge("n0", "n2", id="e0")
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cls.undirected_multigraph_no_multiedge.add_edge("n1", "n2", id="e1")
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cls.undirected_multigraph_no_multiedge.add_edge("n2", "n3", id="e2")
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fh = io.BytesIO(cls.undirected_multigraph_no_multiedge_data.encode("UTF-8"))
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cls.undirected_multigraph_no_multiedge_fh = fh
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cls.multigraph_only_ids_for_multiedges_data = """<?xml version="1.0" encoding="UTF-8"?>
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<graphml xmlns="http://graphml.graphdrawing.org/xmlns"
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xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
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xsi:schemaLocation="http://graphml.graphdrawing.org/xmlns
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http://graphml.graphdrawing.org/xmlns/1.0/graphml.xsd">
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<graph id="G">
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<node id="n0"/>
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<node id="n1"/>
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<node id="n2"/>
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<node id="n10"/>
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<edge source="n0" target="n2"/>
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<edge id="e1" source="n1" target="n2"/>
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<edge id="e2" source="n2" target="n1"/>
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</graph>
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</graphml>"""
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cls.multigraph_only_ids_for_multiedges = nx.MultiGraph()
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cls.multigraph_only_ids_for_multiedges.add_node("n10")
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cls.multigraph_only_ids_for_multiedges.add_edge("n0", "n2")
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cls.multigraph_only_ids_for_multiedges.add_edge("n1", "n2", id="e1")
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cls.multigraph_only_ids_for_multiedges.add_edge("n2", "n1", id="e2")
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fh = io.BytesIO(cls.multigraph_only_ids_for_multiedges_data.encode("UTF-8"))
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cls.multigraph_only_ids_for_multiedges_fh = fh
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class TestReadGraphML(BaseGraphML):
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def test_read_simple_directed_graphml(self):
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G = self.simple_directed_graph
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H = nx.read_graphml(self.simple_directed_fh)
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assert sorted(G.nodes()) == sorted(H.nodes())
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assert sorted(G.edges()) == sorted(H.edges())
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assert sorted(G.edges(data=True)) == sorted(H.edges(data=True))
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self.simple_directed_fh.seek(0)
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PG = nx.parse_graphml(self.simple_directed_data)
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assert sorted(G.nodes()) == sorted(PG.nodes())
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assert sorted(G.edges()) == sorted(PG.edges())
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assert sorted(G.edges(data=True)) == sorted(PG.edges(data=True))
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def test_read_simple_undirected_graphml(self):
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G = self.simple_undirected_graph
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H = nx.read_graphml(self.simple_undirected_fh)
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assert nodes_equal(G.nodes(), H.nodes())
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assert edges_equal(G.edges(), H.edges())
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self.simple_undirected_fh.seek(0)
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PG = nx.parse_graphml(self.simple_undirected_data)
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assert nodes_equal(G.nodes(), PG.nodes())
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assert edges_equal(G.edges(), PG.edges())
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def test_read_undirected_multigraph_graphml(self):
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G = self.undirected_multigraph
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H = nx.read_graphml(self.undirected_multigraph_fh)
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assert nodes_equal(G.nodes(), H.nodes())
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assert edges_equal(G.edges(), H.edges())
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self.undirected_multigraph_fh.seek(0)
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PG = nx.parse_graphml(self.undirected_multigraph_data)
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assert nodes_equal(G.nodes(), PG.nodes())
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assert edges_equal(G.edges(), PG.edges())
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def test_read_undirected_multigraph_no_multiedge_graphml(self):
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G = self.undirected_multigraph_no_multiedge
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H = nx.read_graphml(self.undirected_multigraph_no_multiedge_fh)
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assert nodes_equal(G.nodes(), H.nodes())
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assert edges_equal(G.edges(), H.edges())
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self.undirected_multigraph_no_multiedge_fh.seek(0)
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PG = nx.parse_graphml(self.undirected_multigraph_no_multiedge_data)
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assert nodes_equal(G.nodes(), PG.nodes())
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assert edges_equal(G.edges(), PG.edges())
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def test_read_undirected_multigraph_only_ids_for_multiedges_graphml(self):
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G = self.multigraph_only_ids_for_multiedges
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H = nx.read_graphml(self.multigraph_only_ids_for_multiedges_fh)
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assert nodes_equal(G.nodes(), H.nodes())
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assert edges_equal(G.edges(), H.edges())
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self.multigraph_only_ids_for_multiedges_fh.seek(0)
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PG = nx.parse_graphml(self.multigraph_only_ids_for_multiedges_data)
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assert nodes_equal(G.nodes(), PG.nodes())
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assert edges_equal(G.edges(), PG.edges())
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def test_read_attribute_graphml(self):
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G = self.attribute_graph
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H = nx.read_graphml(self.attribute_fh)
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assert nodes_equal(G.nodes(True), sorted(H.nodes(data=True)))
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ge = sorted(G.edges(data=True))
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he = sorted(H.edges(data=True))
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for a, b in zip(ge, he):
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assert a == b
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self.attribute_fh.seek(0)
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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_node_default_attribute_graphml(self):
|
|
G = self.node_attribute_default_graph
|
|
H = nx.read_graphml(self.node_attribute_default_fh)
|
|
assert G.graph["node_default"] == H.graph["node_default"]
|
|
|
|
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>
|
|
<node id="n2">
|
|
<data key="d6" xml:space="preserve"><![CDATA[description
|
|
line1
|
|
line2]]></data>
|
|
<data key="d3">
|
|
<y:GenericNode configuration="com.yworks.flowchart.terminator">
|
|
<y:Geometry height="40.0" width="80.0" x="950.0" y="286.0"/>
|
|
<y:Fill color="#E8EEF7" color2="#B7C9E3" transparent="false"/>
|
|
<y:BorderStyle color="#000000" 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="67.984375" x="6.0078125" xml:space="preserve"
|
|
y="11.015625">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:GenericNode>
|
|
</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"
|
|
assert G.nodes["n2"]["label"] == "3"
|
|
assert G.nodes["n0"]["shape_type"] == "rectangle"
|
|
assert G.nodes["n1"]["shape_type"] == "rectangle"
|
|
assert G.nodes["n2"]["shape_type"] == "com.yworks.flowchart.terminator"
|
|
assert G.nodes["n2"]["description"] == "description\nline1\nline2"
|
|
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"
|
|
assert G.nodes["n2"]["label"] == "3"
|
|
assert G.nodes["n0"]["shape_type"] == "rectangle"
|
|
assert G.nodes["n1"]["shape_type"] == "rectangle"
|
|
assert G.nodes["n2"]["shape_type"] == "com.yworks.flowchart.terminator"
|
|
assert G.nodes["n2"]["description"] == "description\nline1\nline2"
|
|
|
|
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"
|
|
assert H.nodes["n2"]["label"] == "3"
|
|
|
|
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"
|
|
assert H.nodes["n2"]["label"] == "3"
|
|
|
|
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"/>
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<key for="port" id="d1" yfiles.type="portgraphics"/>
|
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<key for="port" id="d2" yfiles.type="portgeometry"/>
|
|
<key for="port" id="d3" yfiles.type="portuserdata"/>
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<key attr.name="CustomProperty" attr.type="string" for="node" id="d4">
|
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<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">
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<data key="d0"/>
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<node id="n0">
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<data key="d4"><![CDATA[CustomPropertyValue]]></data>
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<data key="d6"/>
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<data key="d7">
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<y:ShapeNode>
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<y:Geometry height="30.0" width="30.0" x="125.0" y="-255.4611111111111"/>
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<y:Fill color="#FFCC00" transparent="false"/>
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<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>
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|
<y:SmartNodeLabelModel distance="4.0"/>
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|
</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"/>
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|
</y:ModelParameter>
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|
</y:NodeLabel>
|
|
<y:Shape type="rectangle"/>
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|
</y:ShapeNode>
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|
</data>
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|
</node>
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|
<node id="n1" yfiles.foldertype="group">
|
|
<data key="d4"><![CDATA[CustomPropertyValue]]></data>
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|
<data key="d5"/>
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|
<data key="d6"/>
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|
<data key="d7">
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<y:ProxyAutoBoundsNode>
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|
<y:Realizers active="0">
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<y:GroupNode>
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<y:Geometry height="250.38333333333333" width="140.0" x="-30.0" y="-330.3833333333333"/>
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<y:Fill color="#F5F5F5" transparent="false"/>
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<y:BorderStyle color="#000000" type="dashed" width="1.0"/>
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<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"/>
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<y:State closed="false" closedHeight="50.0" closedWidth="50.0" innerGraphDisplayEnabled="false"/>
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<y:Insets bottom="15" bottomF="15.0" left="15" leftF="15.0" right="15" rightF="15.0" top="15" topF="15.0"/>
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|
<y:BorderInsets bottom="1" bottomF="1.0" left="0" leftF="0.0" right="0" rightF="0.0" top="1" topF="1.0001736111111086"/>
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</y:GroupNode>
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<y:GroupNode>
|
|
<y:Geometry height="50.0" width="50.0" x="0.0" y="60.0"/>
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<y:Fill color="#F5F5F5" transparent="false"/>
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<y:BorderStyle color="#000000" type="dashed" width="1.0"/>
|
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<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>
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<y:Shape type="roundrectangle"/>
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<y:State closed="true" closedHeight="50.0" closedWidth="50.0" innerGraphDisplayEnabled="false"/>
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<y:Insets bottom="5" bottomF="5.0" left="5" leftF="5.0" right="5" rightF="5.0" top="5" topF="5.0"/>
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<y:BorderInsets bottom="0" bottomF="0.0" left="0" leftF="0.0" right="0" rightF="0.0" top="0" topF="0.0"/>
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</y:GroupNode>
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</y:Realizers>
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</y:ProxyAutoBoundsNode>
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</data>
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<graph edgedefault="directed" id="n1:">
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<node id="n1::n0" yfiles.foldertype="group">
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<data key="d4"><![CDATA[CustomPropertyValue]]></data>
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|
<data key="d5"/>
|
|
<data key="d6"/>
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|
<data key="d7">
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<y:ProxyAutoBoundsNode>
|
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<y:Realizers active="0">
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<y:GroupNode>
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<y:Geometry height="83.46111111111111" width="110.0" x="-15.0" y="-292.9222222222222"/>
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<y:Fill color="#F5F5F5" transparent="false"/>
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<y:BorderStyle color="#000000" type="dashed" width="1.0"/>
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<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>
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<y:Shape type="roundrectangle"/>
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<y:State closed="false" closedHeight="50.0" closedWidth="50.0" innerGraphDisplayEnabled="false"/>
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<y:Insets bottom="15" bottomF="15.0" left="15" leftF="15.0" right="15" rightF="15.0" top="15" topF="15.0"/>
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<y:BorderInsets bottom="1" bottomF="1.0" left="0" leftF="0.0" right="0" rightF="0.0" top="1" topF="1.0001736111111086"/>
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</y:GroupNode>
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<y:GroupNode>
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<y:Geometry height="50.0" width="50.0" x="0.0" y="60.0"/>
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<y:Fill color="#F5F5F5" transparent="false"/>
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<y:BorderStyle color="#000000" type="dashed" width="1.0"/>
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|
<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>
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<y:Shape type="roundrectangle"/>
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<y:State closed="true" closedHeight="50.0" closedWidth="50.0" innerGraphDisplayEnabled="false"/>
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<y:Insets bottom="5" bottomF="5.0" left="5" leftF="5.0" right="5" rightF="5.0" top="5" topF="5.0"/>
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<y:BorderInsets bottom="0" bottomF="0.0" left="0" leftF="0.0" right="0" rightF="0.0" top="0" topF="0.0"/>
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|
</y:GroupNode>
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|
</y:Realizers>
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</y:ProxyAutoBoundsNode>
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|
</data>
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|
<graph edgedefault="directed" id="n1::n0:">
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|
<node id="n1::n0::n0">
|
|
<data key="d4"><![CDATA[CustomPropertyValue]]></data>
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|
<data key="d6"/>
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<data key="d7">
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<y:ShapeNode>
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|
<y:Geometry height="30.0" width="30.0" x="50.0" y="-255.4611111111111"/>
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|
<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>
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|
<y:SmartNodeLabelModel distance="4.0"/>
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|
</y:LabelModel>
|
|
<y:ModelParameter>
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|
<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"/>
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|
</y:ShapeNode>
|
|
</data>
|
|
</node>
|
|
<node id="n1::n0::n1">
|
|
<data key="d4"><![CDATA[CustomPropertyValue]]></data>
|
|
<data key="d6"/>
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|
<data key="d7">
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<y:ShapeNode>
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|
<y:Geometry height="30.0" width="30.0" x="0.0" y="-255.4611111111111"/>
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|
<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"/>
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|
</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>
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|
</data>
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|
</node>
|
|
</graph>
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|
</node>
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|
<node id="n1::n1" yfiles.foldertype="group">
|
|
<data key="d4"><![CDATA[CustomPropertyValue]]></data>
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|
<data key="d5"/>
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|
<data key="d6"/>
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|
<data key="d7">
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|
<y:ProxyAutoBoundsNode>
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<y:Realizers active="0">
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<y:GroupNode>
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|
<y:Geometry height="83.46111111111111" width="110.0" x="-15.0" y="-179.4611111111111"/>
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|
<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>
|
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<y:Shape type="roundrectangle"/>
|
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<y:State closed="false" closedHeight="50.0" closedWidth="50.0" innerGraphDisplayEnabled="false"/>
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<y:Insets bottom="15" bottomF="15.0" left="15" leftF="15.0" right="15" rightF="15.0" top="15" topF="15.0"/>
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|
<y:BorderInsets bottom="1" bottomF="1.0" left="0" leftF="0.0" right="0" rightF="0.0" top="1" topF="1.0001736111111086"/>
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|
</y:GroupNode>
|
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<y:GroupNode>
|
|
<y:Geometry height="50.0" width="50.0" x="0.0" y="60.0"/>
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<y:Fill color="#F5F5F5" transparent="false"/>
|
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<y:BorderStyle color="#000000" type="dashed" width="1.0"/>
|
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<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"/>
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|
<y:Insets bottom="5" bottomF="5.0" left="5" leftF="5.0" right="5" rightF="5.0" top="5" topF="5.0"/>
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|
<y:BorderInsets bottom="0" bottomF="0.0" left="0" leftF="0.0" right="0" rightF="0.0" top="0" topF="0.0"/>
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|
</y:GroupNode>
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|
</y:Realizers>
|
|
</y:ProxyAutoBoundsNode>
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|
</data>
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<graph edgedefault="directed" id="n1::n1:">
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|
<node id="n1::n1::n0">
|
|
<data key="d4"><![CDATA[CustomPropertyValue]]></data>
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|
<data key="d6"/>
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<data key="d7">
|
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<y:ShapeNode>
|
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<y:Geometry height="30.0" width="30.0" x="0.0" y="-142.0"/>
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<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"] != ""
|
|
|
|
def test_long_attribute_type(self):
|
|
# test that graphs with attr.type="long" (as produced by botch and
|
|
# dose3) can be parsed
|
|
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 attr.name="cudfversion" attr.type="long" for="node" id="d6" />
|
|
<graph edgedefault="directed">
|
|
<node id="n1">
|
|
<data key="d6">4284</data>
|
|
</node>
|
|
</graph>
|
|
</graphml>"""
|
|
fh = io.BytesIO(s.encode("UTF-8"))
|
|
G = nx.read_graphml(fh)
|
|
expected = [("n1", {"cudfversion": 4284})]
|
|
assert sorted(G.nodes(data=True)) == expected
|
|
fh.seek(0)
|
|
H = nx.parse_graphml(s)
|
|
assert sorted(H.nodes(data=True)) == expected
|
|
|
|
|
|
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_GraphMLWriter_add_graphs(self):
|
|
gmlw = GraphMLWriter()
|
|
G = self.simple_directed_graph
|
|
H = G.copy()
|
|
gmlw.add_graphs([G, H])
|
|
|
|
def test_write_read_simple_no_prettyprint(self):
|
|
G = self.simple_directed_graph
|
|
G.graph["hi"] = "there"
|
|
G.graph["id"] = "1"
|
|
fh = io.BytesIO()
|
|
self.writer(G, fh, prettyprint=False)
|
|
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_str_number_mixed_type_attributes(self):
|
|
G = nx.MultiGraph()
|
|
G.add_node("n0", special="hello")
|
|
G.add_node("n1", special=0)
|
|
G.add_edge("n0", "n1", special="hello")
|
|
G.add_edge("n0", "n1", special=0)
|
|
fh = io.BytesIO()
|
|
self.writer(G, fh)
|
|
fh.seek(0)
|
|
H = nx.read_graphml(fh)
|
|
assert H.nodes["n0"]["special"] == "hello"
|
|
assert H.nodes["n1"]["special"] == 0
|
|
assert H.edges["n0", "n1", 0]["special"] == "hello"
|
|
assert H.edges["n0", "n1", 1]["special"] == 0
|
|
|
|
def test_mixed_int_type_number_attributes(self):
|
|
np = pytest.importorskip("numpy")
|
|
G = nx.MultiGraph()
|
|
G.add_node("n0", special=np.int64(0))
|
|
G.add_node("n1", special=1)
|
|
G.add_edge("n0", "n1", special=np.int64(2))
|
|
G.add_edge("n0", "n1", special=3)
|
|
fh = io.BytesIO()
|
|
self.writer(G, fh)
|
|
fh.seek(0)
|
|
H = nx.read_graphml(fh)
|
|
assert H.nodes["n0"]["special"] == 0
|
|
assert H.nodes["n1"]["special"] == 1
|
|
assert H.edges["n0", "n1", 0]["special"] == 2
|
|
assert H.edges["n0", "n1", 1]["special"] == 3
|
|
|
|
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_write_generate_edge_id_from_attribute(self):
|
|
from xml.etree.ElementTree import parse
|
|
|
|
G = nx.Graph()
|
|
G.add_edges_from([("a", "b"), ("b", "c"), ("a", "c")])
|
|
edge_attributes = {e: str(e) for e in G.edges}
|
|
nx.set_edge_attributes(G, edge_attributes, "eid")
|
|
fd, fname = tempfile.mkstemp()
|
|
# set edge_id_from_attribute e.g. "eid" for write_graphml()
|
|
self.writer(G, fname, edge_id_from_attribute="eid")
|
|
# set edge_id_from_attribute e.g. "eid" for generate_graphml()
|
|
generator = nx.generate_graphml(G, edge_id_from_attribute="eid")
|
|
|
|
H = nx.read_graphml(fname)
|
|
assert nodes_equal(G.nodes(), H.nodes())
|
|
assert edges_equal(G.edges(), H.edges())
|
|
# NetworkX adds explicit edge "id" from file as attribute
|
|
nx.set_edge_attributes(G, edge_attributes, "id")
|
|
assert edges_equal(G.edges(data=True), H.edges(data=True))
|
|
|
|
tree = parse(fname)
|
|
children = list(tree.getroot())
|
|
assert len(children) == 2
|
|
edge_ids = [
|
|
edge.attrib["id"]
|
|
for edge in tree.getroot().findall(
|
|
".//{http://graphml.graphdrawing.org/xmlns}edge"
|
|
)
|
|
]
|
|
# verify edge id value is equal to sepcified attribute value
|
|
assert sorted(edge_ids) == sorted(edge_attributes.values())
|
|
|
|
# check graphml generated from generate_graphml()
|
|
data = "".join(generator)
|
|
J = nx.parse_graphml(data)
|
|
assert sorted(G.nodes()) == sorted(J.nodes())
|
|
assert sorted(G.edges()) == sorted(J.edges())
|
|
# NetworkX adds explicit edge "id" from file as attribute
|
|
nx.set_edge_attributes(G, edge_attributes, "id")
|
|
assert edges_equal(G.edges(data=True), J.edges(data=True))
|
|
|
|
os.close(fd)
|
|
os.unlink(fname)
|
|
|
|
def test_multigraph_write_generate_edge_id_from_attribute(self):
|
|
from xml.etree.ElementTree import parse
|
|
|
|
G = nx.MultiGraph()
|
|
G.add_edges_from([("a", "b"), ("b", "c"), ("a", "c"), ("a", "b")])
|
|
edge_attributes = {e: str(e) for e in G.edges}
|
|
nx.set_edge_attributes(G, edge_attributes, "eid")
|
|
fd, fname = tempfile.mkstemp()
|
|
# set edge_id_from_attribute e.g. "eid" for write_graphml()
|
|
self.writer(G, fname, edge_id_from_attribute="eid")
|
|
# set edge_id_from_attribute e.g. "eid" for generate_graphml()
|
|
generator = nx.generate_graphml(G, edge_id_from_attribute="eid")
|
|
|
|
H = nx.read_graphml(fname)
|
|
assert H.is_multigraph()
|
|
H = nx.read_graphml(fname, force_multigraph=True)
|
|
assert H.is_multigraph()
|
|
|
|
assert nodes_equal(G.nodes(), H.nodes())
|
|
assert edges_equal(G.edges(), H.edges())
|
|
assert sorted(data.get("eid") for u, v, data in H.edges(data=True)) == sorted(
|
|
edge_attributes.values()
|
|
)
|
|
# NetworkX uses edge_ids as keys in multigraphs if no key
|
|
assert sorted(key for u, v, key in H.edges(keys=True)) == sorted(
|
|
edge_attributes.values()
|
|
)
|
|
|
|
tree = parse(fname)
|
|
children = list(tree.getroot())
|
|
assert len(children) == 2
|
|
edge_ids = [
|
|
edge.attrib["id"]
|
|
for edge in tree.getroot().findall(
|
|
".//{http://graphml.graphdrawing.org/xmlns}edge"
|
|
)
|
|
]
|
|
# verify edge id value is equal to sepcified attribute value
|
|
assert sorted(edge_ids) == sorted(edge_attributes.values())
|
|
|
|
# check graphml generated from generate_graphml()
|
|
graphml_data = "".join(generator)
|
|
J = nx.parse_graphml(graphml_data)
|
|
assert J.is_multigraph()
|
|
|
|
assert nodes_equal(G.nodes(), J.nodes())
|
|
assert edges_equal(G.edges(), J.edges())
|
|
assert sorted(data.get("eid") for u, v, data in J.edges(data=True)) == sorted(
|
|
edge_attributes.values()
|
|
)
|
|
# NetworkX uses edge_ids as keys in multigraphs if no key
|
|
assert sorted(key for u, v, key in J.edges(keys=True)) == sorted(
|
|
edge_attributes.values()
|
|
)
|
|
|
|
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 wtG == pytest.approx(wtH, abs=1e-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 wtG == pytest.approx(wtH, abs=1e-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()
|
|
|
|
|
|
def test_exception_for_unsupported_datatype_node_attr():
|
|
"""Test that a detailed exception is raised when an attribute is of a type
|
|
not supported by GraphML, e.g. a list"""
|
|
pytest.importorskip("lxml.etree")
|
|
# node attribute
|
|
G = nx.Graph()
|
|
G.add_node(0, my_list_attribute=[0, 1, 2])
|
|
fh = io.BytesIO()
|
|
with pytest.raises(TypeError, match="GraphML does not support"):
|
|
nx.write_graphml(G, fh)
|
|
|
|
|
|
def test_exception_for_unsupported_datatype_edge_attr():
|
|
"""Test that a detailed exception is raised when an attribute is of a type
|
|
not supported by GraphML, e.g. a list"""
|
|
pytest.importorskip("lxml.etree")
|
|
# edge attribute
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G = nx.Graph()
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G.add_edge(0, 1, my_list_attribute=[0, 1, 2])
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fh = io.BytesIO()
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with pytest.raises(TypeError, match="GraphML does not support"):
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nx.write_graphml(G, fh)
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|
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def test_exception_for_unsupported_datatype_graph_attr():
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"""Test that a detailed exception is raised when an attribute is of a type
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not supported by GraphML, e.g. a list"""
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pytest.importorskip("lxml.etree")
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# graph attribute
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G = nx.Graph()
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G.graph["my_list_attribute"] = [0, 1, 2]
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|
fh = io.BytesIO()
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with pytest.raises(TypeError, match="GraphML does not support"):
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|
nx.write_graphml(G, fh)
|