501 lines
17 KiB
Python
501 lines
17 KiB
Python
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#!/usr/bin/env python
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import io
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import sys
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import time
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import pytest
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import networkx as nx
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class TestGEXF(object):
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@classmethod
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def setup_class(cls):
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_ = pytest.importorskip("xml.etree.ElementTree")
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cls.simple_directed_data = """<?xml version="1.0" encoding="UTF-8"?>
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<gexf xmlns="http://www.gexf.net/1.2draft" version="1.2">
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<graph mode="static" defaultedgetype="directed">
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<nodes>
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<node id="0" label="Hello" />
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<node id="1" label="Word" />
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</nodes>
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<edges>
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<edge id="0" source="0" target="1" />
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</edges>
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</graph>
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</gexf>
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"""
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cls.simple_directed_graph = nx.DiGraph()
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cls.simple_directed_graph.add_node('0', label='Hello')
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cls.simple_directed_graph.add_node('1', label='World')
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cls.simple_directed_graph.add_edge('0', '1', id='0')
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cls.simple_directed_fh = \
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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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<gexf xmlns="http://www.gexf.net/1.2draft" xmlns:xsi="http://www.w3.\
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org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.gexf.net/\
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1.2draft http://www.gexf.net/1.2draft/gexf.xsd" version="1.2">
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<meta lastmodifieddate="2009-03-20">
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<creator>Gephi.org</creator>
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<description>A Web network</description>
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</meta>
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<graph defaultedgetype="directed">
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<attributes class="node">
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<attribute id="0" title="url" type="string"/>
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<attribute id="1" title="indegree" type="integer"/>
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<attribute id="2" title="frog" type="boolean">
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<default>true</default>
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</attribute>
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</attributes>
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<nodes>
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<node id="0" label="Gephi">
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<attvalues>
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<attvalue for="0" value="https://gephi.org"/>
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<attvalue for="1" value="1"/>
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<attvalue for="2" value="false"/>
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</attvalues>
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</node>
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<node id="1" label="Webatlas">
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<attvalues>
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<attvalue for="0" value="http://webatlas.fr"/>
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<attvalue for="1" value="2"/>
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<attvalue for="2" value="false"/>
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</attvalues>
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</node>
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<node id="2" label="RTGI">
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<attvalues>
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<attvalue for="0" value="http://rtgi.fr"/>
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<attvalue for="1" value="1"/>
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<attvalue for="2" value="true"/>
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</attvalues>
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</node>
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<node id="3" label="BarabasiLab">
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<attvalues>
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<attvalue for="0" value="http://barabasilab.com"/>
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<attvalue for="1" value="1"/>
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<attvalue for="2" value="true"/>
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</attvalues>
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</node>
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</nodes>
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<edges>
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<edge id="0" source="0" target="1"/>
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<edge id="1" source="0" target="2"/>
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<edge id="2" source="1" target="0"/>
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<edge id="3" source="2" target="1"/>
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<edge id="4" source="0" target="3"/>
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</edges>
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</graph>
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</gexf>
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"""
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cls.attribute_graph = nx.DiGraph()
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cls.attribute_graph.graph['node_default'] = {'frog': True}
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cls.attribute_graph.add_node('0',
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label='Gephi',
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url='https://gephi.org',
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indegree=1, frog=False)
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cls.attribute_graph.add_node('1',
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label='Webatlas',
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url='http://webatlas.fr',
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indegree=2, frog=False)
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cls.attribute_graph.add_node('2',
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label='RTGI',
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url='http://rtgi.fr',
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indegree=1, frog=True)
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cls.attribute_graph.add_node('3',
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label='BarabasiLab',
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url='http://barabasilab.com',
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indegree=1, frog=True)
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cls.attribute_graph.add_edge('0', '1', id='0')
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cls.attribute_graph.add_edge('0', '2', id='1')
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cls.attribute_graph.add_edge('1', '0', id='2')
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cls.attribute_graph.add_edge('2', '1', id='3')
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cls.attribute_graph.add_edge('0', '3', id='4')
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cls.attribute_fh = io.BytesIO(cls.attribute_data.encode('UTF-8'))
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cls.simple_undirected_data = """<?xml version="1.0" encoding="UTF-8"?>
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<gexf xmlns="http://www.gexf.net/1.2draft" version="1.2">
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<graph mode="static" defaultedgetype="undirected">
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<nodes>
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<node id="0" label="Hello" />
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<node id="1" label="Word" />
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</nodes>
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<edges>
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<edge id="0" source="0" target="1" />
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</edges>
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</graph>
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</gexf>
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"""
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cls.simple_undirected_graph = nx.Graph()
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cls.simple_undirected_graph.add_node('0', label='Hello')
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cls.simple_undirected_graph.add_node('1', label='World')
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cls.simple_undirected_graph.add_edge('0', '1', id='0')
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cls.simple_undirected_fh = io.BytesIO(cls.simple_undirected_data
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.encode('UTF-8'))
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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_gexf(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)) ==
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sorted(H.edges(data=True)))
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self.simple_directed_fh.seek(0)
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def test_write_read_simple_directed_graphml(self):
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G = self.simple_directed_graph
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fh = io.BytesIO()
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nx.write_gexf(G, fh)
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fh.seek(0)
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H = nx.read_gexf(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)) ==
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sorted(H.edges(data=True)))
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self.simple_directed_fh.seek(0)
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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_gexf(self.simple_undirected_fh)
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assert sorted(G.nodes()) == sorted(H.nodes())
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assert (
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sorted(sorted(e) for e in G.edges()) ==
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sorted(sorted(e) for e in H.edges()))
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self.simple_undirected_fh.seek(0)
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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_gexf(self.attribute_fh)
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assert sorted(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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def test_directed_edge_in_undirected(self):
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s = """<?xml version="1.0" encoding="UTF-8"?>
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<gexf xmlns="http://www.gexf.net/1.2draft" version='1.2'>
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<graph mode="static" defaultedgetype="undirected" name="">
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<nodes>
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<node id="0" label="Hello" />
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<node id="1" label="Word" />
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</nodes>
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<edges>
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<edge id="0" source="0" target="1" type="directed"/>
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</edges>
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</graph>
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</gexf>
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"""
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fh = io.BytesIO(s.encode('UTF-8'))
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pytest.raises(nx.NetworkXError, nx.read_gexf, fh)
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def test_undirected_edge_in_directed(self):
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s = """<?xml version="1.0" encoding="UTF-8"?>
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<gexf xmlns="http://www.gexf.net/1.2draft" version='1.2'>
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<graph mode="static" defaultedgetype="directed" name="">
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<nodes>
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<node id="0" label="Hello" />
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<node id="1" label="Word" />
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</nodes>
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<edges>
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<edge id="0" source="0" target="1" type="undirected"/>
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</edges>
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</graph>
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</gexf>
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"""
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fh = io.BytesIO(s.encode('UTF-8'))
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pytest.raises(nx.NetworkXError, nx.read_gexf, fh)
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def test_key_raises(self):
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s = """<?xml version="1.0" encoding="UTF-8"?>
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<gexf xmlns="http://www.gexf.net/1.2draft" version='1.2'>
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<graph mode="static" defaultedgetype="directed" name="">
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<nodes>
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<node id="0" label="Hello">
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<attvalues>
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<attvalue for='0' value='1'/>
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</attvalues>
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</node>
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<node id="1" label="Word" />
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</nodes>
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<edges>
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<edge id="0" source="0" target="1" type="undirected"/>
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</edges>
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</graph>
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</gexf>
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"""
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fh = io.BytesIO(s.encode('UTF-8'))
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pytest.raises(nx.NetworkXError, nx.read_gexf, fh)
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def test_relabel(self):
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s = """<?xml version="1.0" encoding="UTF-8"?>
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<gexf xmlns="http://www.gexf.net/1.2draft" version='1.2'>
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<graph mode="static" defaultedgetype="directed" name="">
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<nodes>
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<node id="0" label="Hello" />
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<node id="1" label="Word" />
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</nodes>
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<edges>
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<edge id="0" source="0" target="1"/>
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</edges>
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</graph>
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</gexf>
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"""
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fh = io.BytesIO(s.encode('UTF-8'))
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G = nx.read_gexf(fh, relabel=True)
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assert sorted(G.nodes()) == ["Hello", "Word"]
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def test_default_attribute(self):
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G = nx.Graph()
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G.add_node(1, label='1', color='green')
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nx.add_path(G, [0, 1, 2, 3])
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G.add_edge(1, 2, foo=3)
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G.graph['node_default'] = {'color': 'yellow'}
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G.graph['edge_default'] = {'foo': 7}
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fh = io.BytesIO()
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nx.write_gexf(G, fh)
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fh.seek(0)
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H = nx.read_gexf(fh, node_type=int)
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assert sorted(G.nodes()) == sorted(H.nodes())
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assert (
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sorted(sorted(e) for e in G.edges()) ==
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sorted(sorted(e) for e in H.edges()))
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# Reading a gexf graph always sets mode attribute to either
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# 'static' or 'dynamic'. Remove the mode attribute from the
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# read graph for the sake of comparing remaining attributes.
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del H.graph['mode']
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assert G.graph == H.graph
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def test_serialize_ints_to_strings(self):
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G = nx.Graph()
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G.add_node(1, id=7, label=77)
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fh = io.BytesIO()
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nx.write_gexf(G, fh)
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fh.seek(0)
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H = nx.read_gexf(fh, node_type=int)
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assert list(H) == [7]
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assert H.nodes[7]['label'] == '77'
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# FIXME: We should test xml without caring about their order This is causing a
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# problem b/c of a change in Python 3.8
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#
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# "Prior to Python 3.8, the serialisation order of the XML attributes of
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# elements was artificially made predictable by sorting the attributes by their
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# name. Based on the now guaranteed ordering of dicts, this arbitrary
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# reordering was removed in Python 3.8 to preserve the order in which
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# attributes were originally parsed or created by user code."
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#
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# https://docs.python.org/3.8/library/xml.etree.elementtree.html
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# https://bugs.python.org/issue34160
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def test_write_with_node_attributes(self):
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# Addresses #673.
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G = nx.OrderedGraph()
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G.add_edges_from([(0, 1), (1, 2), (2, 3)])
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for i in range(4):
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G.nodes[i]['id'] = i
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G.nodes[i]['label'] = i
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G.nodes[i]['pid'] = i
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G.nodes[i]['start'] = i
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G.nodes[i]['end'] = i + 1
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if sys.version_info < (3, 8):
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expected = """<gexf version="1.2" xmlns="http://www.gexf.net/1.2\
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draft" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:\
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schemaLocation="http://www.gexf.net/1.2draft http://www.gexf.net/1.2draft/\
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gexf.xsd">
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<meta lastmodifieddate="{}">
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<creator>NetworkX {}</creator>
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</meta>
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<graph defaultedgetype="undirected" mode="dynamic" name="" timeformat="long">
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<nodes>
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<node end="1" id="0" label="0" pid="0" start="0" />
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<node end="2" id="1" label="1" pid="1" start="1" />
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<node end="3" id="2" label="2" pid="2" start="2" />
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<node end="4" id="3" label="3" pid="3" start="3" />
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</nodes>
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<edges>
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<edge id="0" source="0" target="1" />
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<edge id="1" source="1" target="2" />
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<edge id="2" source="2" target="3" />
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</edges>
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</graph>
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</gexf>""".format(time.strftime('%Y-%m-%d'), nx.__version__)
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else:
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expected = """<gexf xmlns="http://www.gexf.net/1.2draft" xmlns:xsi\
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="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation=\
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"http://www.gexf.net/1.2draft http://www.gexf.net/1.2draft/\
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gexf.xsd" version="1.2">
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<meta lastmodifieddate="{}">
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<creator>NetworkX {}</creator>
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</meta>
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<graph defaultedgetype="undirected" mode="dynamic" name="" timeformat="long">
|
||
|
|
<nodes>
|
||
|
|
<node id="0" label="0" pid="0" start="0" end="1" />
|
||
|
|
<node id="1" label="1" pid="1" start="1" end="2" />
|
||
|
|
<node id="2" label="2" pid="2" start="2" end="3" />
|
||
|
|
<node id="3" label="3" pid="3" start="3" end="4" />
|
||
|
|
</nodes>
|
||
|
|
<edges>
|
||
|
|
<edge source="0" target="1" id="0" />
|
||
|
|
<edge source="1" target="2" id="1" />
|
||
|
|
<edge source="2" target="3" id="2" />
|
||
|
|
</edges>
|
||
|
|
</graph>
|
||
|
|
</gexf>""".format(time.strftime('%Y-%m-%d'), nx.__version__)
|
||
|
|
obtained = '\n'.join(nx.generate_gexf(G))
|
||
|
|
assert expected == obtained
|
||
|
|
|
||
|
|
def test_edge_id_construct(self):
|
||
|
|
G = nx.Graph()
|
||
|
|
G.add_edges_from([(0, 1, {'id': 0}), (1, 2, {'id': 2}), (2, 3)])
|
||
|
|
|
||
|
|
if sys.version_info < (3, 8):
|
||
|
|
expected = """<gexf version="1.2" xmlns="http://www.gexf.net/\
|
||
|
|
1.2draft" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:\
|
||
|
|
schemaLocation="http://www.gexf.net/1.2draft http://www.gexf.net/1.2draft/\
|
||
|
|
gexf.xsd">
|
||
|
|
<meta lastmodifieddate="{}">
|
||
|
|
<creator>NetworkX {}</creator>
|
||
|
|
</meta>
|
||
|
|
<graph defaultedgetype="undirected" mode="static" name="">
|
||
|
|
<nodes>
|
||
|
|
<node id="0" label="0" />
|
||
|
|
<node id="1" label="1" />
|
||
|
|
<node id="2" label="2" />
|
||
|
|
<node id="3" label="3" />
|
||
|
|
</nodes>
|
||
|
|
<edges>
|
||
|
|
<edge id="0" source="0" target="1" />
|
||
|
|
<edge id="2" source="1" target="2" />
|
||
|
|
<edge id="1" source="2" target="3" />
|
||
|
|
</edges>
|
||
|
|
</graph>
|
||
|
|
</gexf>""".format(time.strftime('%Y-%m-%d'), nx.__version__)
|
||
|
|
else:
|
||
|
|
expected = """<gexf xmlns="http://www.gexf.net/1.2draft" xmlns:xsi\
|
||
|
|
="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.\
|
||
|
|
gexf.net/1.2draft http://www.gexf.net/1.2draft/gexf.xsd" version="1.2">
|
||
|
|
<meta lastmodifieddate="{}">
|
||
|
|
<creator>NetworkX {}</creator>
|
||
|
|
</meta>
|
||
|
|
<graph defaultedgetype="undirected" mode="static" name="">
|
||
|
|
<nodes>
|
||
|
|
<node id="0" label="0" />
|
||
|
|
<node id="1" label="1" />
|
||
|
|
<node id="2" label="2" />
|
||
|
|
<node id="3" label="3" />
|
||
|
|
</nodes>
|
||
|
|
<edges>
|
||
|
|
<edge source="0" target="1" id="0" />
|
||
|
|
<edge source="1" target="2" id="2" />
|
||
|
|
<edge source="2" target="3" id="1" />
|
||
|
|
</edges>
|
||
|
|
</graph>
|
||
|
|
</gexf>""".format(time.strftime('%Y-%m-%d'), nx.__version__)
|
||
|
|
|
||
|
|
obtained = '\n'.join(nx.generate_gexf(G))
|
||
|
|
assert expected == obtained
|
||
|
|
|
||
|
|
def test_numpy_type(self):
|
||
|
|
G = nx.path_graph(4)
|
||
|
|
try:
|
||
|
|
import numpy
|
||
|
|
except ImportError:
|
||
|
|
return
|
||
|
|
nx.set_node_attributes(G, {n: n for n in numpy.arange(4)}, 'number')
|
||
|
|
G[0][1]['edge-number'] = numpy.float64(1.1)
|
||
|
|
|
||
|
|
expected = """<gexf version="1.2" xmlns="http://www.gexf.net/1.2draft"\
|
||
|
|
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation\
|
||
|
|
="http://www.gexf.net/1.2draft http://www.gexf.net/1.2draft/gexf.xsd">
|
||
|
|
<meta lastmodifieddate="{}">
|
||
|
|
<creator>NetworkX {}</creator>
|
||
|
|
</meta>
|
||
|
|
<graph defaultedgetype="undirected" mode="static" name="">
|
||
|
|
<attributes class="edge" mode="static">
|
||
|
|
<attribute id="1" title="edge-number" type="float" />
|
||
|
|
</attributes>
|
||
|
|
<attributes class="node" mode="static">
|
||
|
|
<attribute id="0" title="number" type="int" />
|
||
|
|
</attributes>
|
||
|
|
<nodes>
|
||
|
|
<node id="0" label="0">
|
||
|
|
<attvalues>
|
||
|
|
<attvalue for="0" value="0" />
|
||
|
|
</attvalues>
|
||
|
|
</node>
|
||
|
|
<node id="1" label="1">
|
||
|
|
<attvalues>
|
||
|
|
<attvalue for="0" value="1" />
|
||
|
|
</attvalues>
|
||
|
|
</node>
|
||
|
|
<node id="2" label="2">
|
||
|
|
<attvalues>
|
||
|
|
<attvalue for="0" value="2" />
|
||
|
|
</attvalues>
|
||
|
|
</node>
|
||
|
|
<node id="3" label="3">
|
||
|
|
<attvalues>
|
||
|
|
<attvalue for="0" value="3" />
|
||
|
|
</attvalues>
|
||
|
|
</node>
|
||
|
|
</nodes>
|
||
|
|
<edges>
|
||
|
|
<edge id="0" source="0" target="1">
|
||
|
|
<attvalues>
|
||
|
|
<attvalue for="1" value="1.1" />
|
||
|
|
</attvalues>
|
||
|
|
</edge>
|
||
|
|
<edge id="1" source="1" target="2" />
|
||
|
|
<edge id="2" source="2" target="3" />
|
||
|
|
</edges>
|
||
|
|
</graph>
|
||
|
|
</gexf>""".format(time.strftime('%Y-%m-%d'), nx.__version__)
|
||
|
|
obtained = '\n'.join(nx.generate_gexf(G))
|
||
|
|
assert expected == obtained
|
||
|
|
|
||
|
|
def test_bool(self):
|
||
|
|
G = nx.Graph()
|
||
|
|
G.add_node(1, testattr=True)
|
||
|
|
fh = io.BytesIO()
|
||
|
|
nx.write_gexf(G, fh)
|
||
|
|
fh.seek(0)
|
||
|
|
H = nx.read_gexf(fh, node_type=int)
|
||
|
|
assert H.nodes[1]['testattr'] == True
|
||
|
|
|
||
|
|
# Test for NaN, INF and -INF
|
||
|
|
def test_specials(self):
|
||
|
|
from math import isnan
|
||
|
|
inf, nan = float('inf'), float('nan')
|
||
|
|
G = nx.Graph()
|
||
|
|
G.add_node(1, testattr=inf, strdata='inf', key='a')
|
||
|
|
G.add_node(2, testattr=nan, strdata='nan', key='b')
|
||
|
|
G.add_node(3, testattr=-inf, strdata='-inf', key='c')
|
||
|
|
|
||
|
|
fh = io.BytesIO()
|
||
|
|
nx.write_gexf(G, fh)
|
||
|
|
fh.seek(0)
|
||
|
|
filetext = fh.read()
|
||
|
|
fh.seek(0)
|
||
|
|
H = nx.read_gexf(fh, node_type=int)
|
||
|
|
|
||
|
|
assert b'INF' in filetext
|
||
|
|
assert b'NaN' in filetext
|
||
|
|
assert b'-INF' in filetext
|
||
|
|
|
||
|
|
assert H.nodes[1]['testattr'] == inf
|
||
|
|
assert isnan(H.nodes[2]['testattr'])
|
||
|
|
assert H.nodes[3]['testattr'] == -inf
|
||
|
|
|
||
|
|
assert H.nodes[1]['strdata'] == 'inf'
|
||
|
|
assert H.nodes[2]['strdata'] == 'nan'
|
||
|
|
assert H.nodes[3]['strdata'] == '-inf'
|
||
|
|
|
||
|
|
assert H.nodes[1]['networkx_key'] == 'a'
|
||
|
|
assert H.nodes[2]['networkx_key'] == 'b'
|
||
|
|
assert H.nodes[3]['networkx_key'] == 'c'
|