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networkx / readwrite / tests / test_gexf.py
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#!/usr/bin/env python
import io
import time
from nose import SkipTest
from nose.tools import *

import networkx as nx


class TestGEXF(object):
    @classmethod
    def setupClass(cls):
        try:
            import xml.etree.ElementTree
        except ImportError:
            raise SkipTest('xml.etree.ElementTree not available.')

    def setUp(self):
        self.simple_directed_data = """<?xml version="1.0" encoding="UTF-8"?>
<gexf xmlns="http://www.gexf.net/1.2draft" version="1.2">
    <graph mode="static" defaultedgetype="directed">
        <nodes>
            <node id="0" label="Hello" />
            <node id="1" label="Word" />
        </nodes>
        <edges>
            <edge id="0" source="0" target="1" />
        </edges>
    </graph>
</gexf>
"""
        self.simple_directed_graph = nx.DiGraph()
        self.simple_directed_graph.add_node('0', label='Hello')
        self.simple_directed_graph.add_node('1', label='World')
        self.simple_directed_graph.add_edge('0', '1', id='0')

        self.simple_directed_fh = \
            io.BytesIO(self.simple_directed_data.encode('UTF-8'))

        self.attribute_data = """<?xml version="1.0" encoding="UTF-8"?>
<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="2009-03-20">
    <creator>Gephi.org</creator>
    <description>A Web network</description>
  </meta>
  <graph defaultedgetype="directed">
    <attributes class="node">
      <attribute id="0" title="url" type="string"/>
      <attribute id="1" title="indegree" type="integer"/>
      <attribute id="2" title="frog" type="boolean">
        <default>true</default>
      </attribute>
    </attributes>
    <nodes>
      <node id="0" label="Gephi">
        <attvalues>
          <attvalue for="0" value="https://gephi.org"/>
          <attvalue for="1" value="1"/>
          <attvalue for="2" value="false"/>
        </attvalues>
      </node>
      <node id="1" label="Webatlas">
        <attvalues>
          <attvalue for="0" value="http://webatlas.fr"/>
          <attvalue for="1" value="2"/>
          <attvalue for="2" value="false"/>
        </attvalues>
      </node>
      <node id="2" label="RTGI">
        <attvalues>
          <attvalue for="0" value="http://rtgi.fr"/>
          <attvalue for="1" value="1"/>
          <attvalue for="2" value="true"/>
        </attvalues>
      </node>
      <node id="3" label="BarabasiLab">
        <attvalues>
          <attvalue for="0" value="http://barabasilab.com"/>
          <attvalue for="1" value="1"/>
          <attvalue for="2" value="true"/>
        </attvalues>
      </node>
    </nodes>
    <edges>
      <edge id="0" source="0" target="1"/>
      <edge id="1" source="0" target="2"/>
      <edge id="2" source="1" target="0"/>
      <edge id="3" source="2" target="1"/>
      <edge id="4" source="0" target="3"/>
    </edges>
  </graph>
</gexf>
"""
        self.attribute_graph = nx.DiGraph()
        self.attribute_graph.graph['node_default'] = {'frog': True}
        self.attribute_graph.add_node('0',
                                      label='Gephi',
                                      url='https://gephi.org',
                                      indegree=1, frog=False)
        self.attribute_graph.add_node('1',
                                      label='Webatlas',
                                      url='http://webatlas.fr',
                                      indegree=2, frog=False)
        self.attribute_graph.add_node('2',
                                      label='RTGI',
                                      url='http://rtgi.fr',
                                      indegree=1, frog=True)
        self.attribute_graph.add_node('3',
                                      label='BarabasiLab',
                                      url='http://barabasilab.com',
                                      indegree=1, frog=True)
        self.attribute_graph.add_edge('0', '1', id='0')
        self.attribute_graph.add_edge('0', '2', id='1')
        self.attribute_graph.add_edge('1', '0', id='2')
        self.attribute_graph.add_edge('2', '1', id='3')
        self.attribute_graph.add_edge('0', '3', id='4')
        self.attribute_fh = io.BytesIO(self.attribute_data.encode('UTF-8'))

        self.simple_undirected_data = """<?xml version="1.0" encoding="UTF-8"?>
<gexf xmlns="http://www.gexf.net/1.2draft" version="1.2">
    <graph mode="static" defaultedgetype="undirected">
        <nodes>
            <node id="0" label="Hello" />
            <node id="1" label="Word" />
        </nodes>
        <edges>
            <edge id="0" source="0" target="1" />
        </edges>
    </graph>
</gexf>
"""
        self.simple_undirected_graph = nx.Graph()
        self.simple_undirected_graph.add_node('0', label='Hello')
        self.simple_undirected_graph.add_node('1', label='World')
        self.simple_undirected_graph.add_edge('0', '1', id='0')

        self.simple_undirected_fh = io.BytesIO(self.simple_undirected_data.encode('UTF-8'))

    def test_read_simple_directed_graphml(self):
        G = self.simple_directed_graph
        H = nx.read_gexf(self.simple_directed_fh)
        assert_equal(sorted(G.nodes()), sorted(H.nodes()))
        assert_equal(sorted(G.edges()), sorted(H.edges()))
        assert_equal(sorted(G.edges(data=True)),
                     sorted(H.edges(data=True)))
        self.simple_directed_fh.seek(0)

    def test_write_read_simple_directed_graphml(self):
        G = self.simple_directed_graph
        fh = io.BytesIO()
        nx.write_gexf(G, fh)
        fh.seek(0)
        H = nx.read_gexf(fh)
        assert_equal(sorted(G.nodes()), sorted(H.nodes()))
        assert_equal(sorted(G.edges()), sorted(H.edges()))
        assert_equal(sorted(G.edges(data=True)),
                     sorted(H.edges(data=True)))
        self.simple_directed_fh.seek(0)

    def test_read_simple_undirected_graphml(self):
        G = self.simple_undirected_graph
        H = nx.read_gexf(self.simple_undirected_fh)
        assert_equal(sorted(G.nodes()), sorted(H.nodes()))
        assert_equal(
            sorted(sorted(e) for e in G.edges()),
            sorted(sorted(e) for e in H.edges()))
        self.simple_undirected_fh.seek(0)

    def test_read_attribute_graphml(self):
        G = self.attribute_graph
        H = nx.read_gexf(self.attribute_fh)
        assert_equal(sorted(G.nodes(True)), sorted(H.nodes(data=True)))
        ge = sorted(G.edges(data=True))
        he = sorted(H.edges(data=True))
        for a, b in zip(ge, he):
            assert_equal(a, b)
        self.attribute_fh.seek(0)

    def test_directed_edge_in_undirected(self):
        s = """<?xml version="1.0" encoding="UTF-8"?>
<gexf xmlns="http://www.gexf.net/1.2draft" version='1.2'>
    <graph mode="static" defaultedgetype="undirected" name="">
        <nodes>
            <node id="0" label="Hello" />
            <node id="1" label="Word" />
        </nodes>
        <edges>
            <edge id="0" source="0" target="1" type="directed"/>
        </edges>
    </graph>
</gexf>
"""
        fh = io.BytesIO(s.encode('UTF-8'))
        assert_raises(nx.NetworkXError, nx.read_gexf, fh)

    def test_undirected_edge_in_directed(self):
        s = """<?xml version="1.0" encoding="UTF-8"?>
<gexf xmlns="http://www.gexf.net/1.2draft" version='1.2'>
    <graph mode="static" defaultedgetype="directed" name="">
        <nodes>
            <node id="0" label="Hello" />
            <node id="1" label="Word" />
        </nodes>
        <edges>
            <edge id="0" source="0" target="1" type="undirected"/>
        </edges>
    </graph>
</gexf>
"""
        fh = io.BytesIO(s.encode('UTF-8'))
        assert_raises(nx.NetworkXError, nx.read_gexf, fh)

    def test_key_raises(self):
        s = """<?xml version="1.0" encoding="UTF-8"?>
<gexf xmlns="http://www.gexf.net/1.2draft" version='1.2'>
    <graph mode="static" defaultedgetype="directed" name="">
        <nodes>
            <node id="0" label="Hello">
              <attvalues>
                <attvalue for='0' value='1'/>
              </attvalues>
            </node>
            <node id="1" label="Word" />
        </nodes>
        <edges>
            <edge id="0" source="0" target="1" type="undirected"/>
        </edges>
    </graph>
</gexf>
"""
        fh = io.BytesIO(s.encode('UTF-8'))
        assert_raises(nx.NetworkXError, nx.read_gexf, fh)

    def test_relabel(self):
        s = """<?xml version="1.0" encoding="UTF-8"?>
<gexf xmlns="http://www.gexf.net/1.2draft" version='1.2'>
    <graph mode="static" defaultedgetype="directed" name="">
        <nodes>
            <node id="0" label="Hello" />
            <node id="1" label="Word" />
        </nodes>
        <edges>
            <edge id="0" source="0" target="1"/>
        </edges>
    </graph>
</gexf>
"""
        fh = io.BytesIO(s.encode('UTF-8'))
        G = nx.read_gexf(fh, relabel=True)
        assert_equal(sorted(G.nodes()), ["Hello", "Word"])

    def test_default_attribute(self):
        G = nx.Graph()
        G.add_node(1, label='1', color='green')
        nx.add_path(G, [0, 1, 2, 3])
        G.add_edge(1, 2, foo=3)
        G.graph['node_default'] = {'color': 'yellow'}
        G.graph['edge_default'] = {'foo': 7}
        fh = io.BytesIO()
        nx.write_gexf(G, fh)
        fh.seek(0)
        H = nx.read_gexf(fh, node_type=int)
        assert_equal(sorted(G.nodes()), sorted(H.nodes()))
        assert_equal(
            sorted(sorted(e) for e in G.edges()),
            sorted(sorted(e) for e in H.edges()))
        # Reading a gexf graph always sets mode attribute to either
        # 'static' or 'dynamic'. Remove the mode attribute from the
        # read graph for the sake of comparing remaining attributes.
        del H.graph['mode']
        assert_equal(G.graph, H.graph)

    def test_serialize_ints_to_strings(self):
        G = nx.Graph()
        G.add_node(1, id=7, label=77)
        fh = io.BytesIO()
        nx.write_gexf(G, fh)
        fh.seek(0)
        H = nx.read_gexf(fh, node_type=int)
        assert_equal(list(H), [7])
        assert_equal(H.nodes[7]['label'], '77')

    def test_write_with_node_attributes(self):
        # Addresses #673.
        G = nx.OrderedGraph()
        G.add_edges_from([(0, 1), (1, 2), (2, 3)])
        for i in range(4):
            G.nodes[i]['id'] = i
            G.nodes[i]['label'] = i
            G.nodes[i]['pid'] = i

        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.w3.org/2001/XMLSchema-instance">
  <graph defaultedgetype="undirected" mode="static" name="">
    <meta>
      <creator>NetworkX {}</creator>
      <lastmodified>{}</lastmodified>
    </meta>
    <nodes>
      <node id="0" label="0" pid="0" />
      <node id="1" label="1" pid="1" />
      <node id="2" label="2" pid="2" />
      <node id="3" label="3" pid="3" />
    </nodes>
    <edges>
      <edge id="0" source="0" target="1" />
      <edge id="1" source="1" target="2" />
      <edge id="2" source="2" target="3" />
    </edges>
  </graph>
</gexf>""".format(nx.__version__, time.strftime('%d/%m/%Y'))
        obtained = '\n'.join(nx.generate_gexf(G))
        assert_equal(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_equal(H.nodes[1]['testattr'], True)