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mightyscape-1.1-deprecated/extensions/networkx/readwrite/tests/test_gexf.py

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2020-07-30 01:16:18 +02:00
#!/usr/bin/env python
import io
import sys
import time
import pytest
import networkx as nx
class TestGEXF(object):
@classmethod
def setup_class(cls):
_ = pytest.importorskip("xml.etree.ElementTree")
cls.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>
"""
cls.simple_directed_graph = nx.DiGraph()
cls.simple_directed_graph.add_node('0', label='Hello')
cls.simple_directed_graph.add_node('1', label='World')
cls.simple_directed_graph.add_edge('0', '1', id='0')
cls.simple_directed_fh = \
io.BytesIO(cls.simple_directed_data.encode('UTF-8'))
cls.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>
"""
cls.attribute_graph = nx.DiGraph()
cls.attribute_graph.graph['node_default'] = {'frog': True}
cls.attribute_graph.add_node('0',
label='Gephi',
url='https://gephi.org',
indegree=1, frog=False)
cls.attribute_graph.add_node('1',
label='Webatlas',
url='http://webatlas.fr',
indegree=2, frog=False)
cls.attribute_graph.add_node('2',
label='RTGI',
url='http://rtgi.fr',
indegree=1, frog=True)
cls.attribute_graph.add_node('3',
label='BarabasiLab',
url='http://barabasilab.com',
indegree=1, frog=True)
cls.attribute_graph.add_edge('0', '1', id='0')
cls.attribute_graph.add_edge('0', '2', id='1')
cls.attribute_graph.add_edge('1', '0', id='2')
cls.attribute_graph.add_edge('2', '1', id='3')
cls.attribute_graph.add_edge('0', '3', id='4')
cls.attribute_fh = io.BytesIO(cls.attribute_data.encode('UTF-8'))
cls.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>
"""
cls.simple_undirected_graph = nx.Graph()
cls.simple_undirected_graph.add_node('0', label='Hello')
cls.simple_undirected_graph.add_node('1', label='World')
cls.simple_undirected_graph.add_edge('0', '1', id='0')
cls.simple_undirected_fh = io.BytesIO(cls.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 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_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 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_read_simple_undirected_graphml(self):
G = self.simple_undirected_graph
H = nx.read_gexf(self.simple_undirected_fh)
assert sorted(G.nodes()) == sorted(H.nodes())
assert (
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 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 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'))
pytest.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'))
pytest.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'))
pytest.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 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 sorted(G.nodes()) == sorted(H.nodes())
assert (
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 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 list(H) == [7]
assert H.nodes[7]['label'] == '77'
# FIXME: We should test xml without caring about their order This is causing a
# problem b/c of a change in Python 3.8
#
# "Prior to Python 3.8, the serialisation order of the XML attributes of
# elements was artificially made predictable by sorting the attributes by their
# name. Based on the now guaranteed ordering of dicts, this arbitrary
# reordering was removed in Python 3.8 to preserve the order in which
# attributes were originally parsed or created by user code."
#
# https://docs.python.org/3.8/library/xml.etree.elementtree.html
# https://bugs.python.org/issue34160
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
G.nodes[i]['start'] = i
G.nodes[i]['end'] = i + 1
if sys.version_info < (3, 8):
expected = """<gexf version="1.2" xmlns="http://www.gexf.net/1.2\
draft" 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="dynamic" name="" timeformat="long">
<nodes>
<node end="1" id="0" label="0" pid="0" start="0" />
<node end="2" id="1" label="1" pid="1" start="1" />
<node end="3" id="2" label="2" pid="2" start="2" />
<node end="4" id="3" label="3" pid="3" start="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(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="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'