import io
import sys
import time
import pytest
import networkx as nx
class TestGEXF:
@classmethod
def setup_class(cls):
_ = pytest.importorskip("xml.etree.ElementTree")
cls.simple_directed_data = """
"""
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 = """\
Gephi.org
A Web network
true
"""
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", label="foo")
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 = """
"""
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 = """
"""
fh = io.BytesIO(s.encode("UTF-8"))
pytest.raises(nx.NetworkXError, nx.read_gexf, fh)
def test_undirected_edge_in_directed(self):
s = """
"""
fh = io.BytesIO(s.encode("UTF-8"))
pytest.raises(nx.NetworkXError, nx.read_gexf, fh)
def test_key_raises(self):
s = """
"""
fh = io.BytesIO(s.encode("UTF-8"))
pytest.raises(nx.NetworkXError, nx.read_gexf, fh)
def test_relabel(self):
s = """
"""
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 = f"""
NetworkX {nx.__version__}
"""
else:
expected = f"""
NetworkX {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 = f"""
NetworkX {nx.__version__}
"""
else:
expected = f"""
NetworkX {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)
if sys.version_info < (3, 8):
expected = f"""
NetworkX {nx.__version__}
"""
else:
expected = f"""
NetworkX {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"]
# 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"
def test_simple_list(self):
G = nx.Graph()
list_value = [(1, 2, 3), (9, 1, 2)]
G.add_node(1, key=list_value)
fh = io.BytesIO()
nx.write_gexf(G, fh)
fh.seek(0)
H = nx.read_gexf(fh, node_type=int)
assert H.nodes[1]["networkx_key"] == list_value
def test_dynamic_mode(self):
G = nx.Graph()
G.add_node(1, label="1", color="green")
G.graph["mode"] = "dynamic"
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()
)
def test_multigraph_with_missing_attributes(self):
G = nx.MultiGraph()
G.add_node(0, label="1", color="green")
G.add_node(1, label="2", color="green")
G.add_edge(0, 1, id="0", wight=3, type="undirected", start=0, end=1)
G.add_edge(0, 1, id="1", label="foo", start=0, end=1)
G.add_edge(0, 1)
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()
)
def test_missing_viz_attributes(self):
G = nx.Graph()
G.add_node(0, label="1", color="green")
G.nodes[0]["viz"] = {"size": 54}
G.nodes[0]["viz"]["position"] = {"x": 0, "y": 1, "z": 0}
G.nodes[0]["viz"]["color"] = {"r": 0, "g": 0, "b": 256}
G.nodes[0]["viz"]["shape"] = "http://random.url"
G.nodes[0]["viz"]["thickness"] = 2
fh = io.BytesIO()
nx.write_gexf(G, fh, version="1.1draft")
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()
)
# Second graph for the other branch
G = nx.Graph()
G.add_node(0, label="1", color="green")
G.nodes[0]["viz"] = {"size": 54}
G.nodes[0]["viz"]["position"] = {"x": 0, "y": 1, "z": 0}
G.nodes[0]["viz"]["color"] = {"r": 0, "g": 0, "b": 256, "a": 0.5}
G.nodes[0]["viz"]["shape"] = "ftp://random.url"
G.nodes[0]["viz"]["thickness"] = 2
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()
)
def test_slice_and_spell(self):
# Test spell first, so version = 1.2
G = nx.Graph()
G.add_node(0, label="1", color="green")
G.nodes[0]["spells"] = [(1, 2)]
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()
)
G = nx.Graph()
G.add_node(0, label="1", color="green")
G.nodes[0]["slices"] = [(1, 2)]
fh = io.BytesIO()
nx.write_gexf(G, fh, version="1.1draft")
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()
)
def test_add_parent(self):
G = nx.Graph()
G.add_node(0, label="1", color="green", parents=[1, 2])
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()
)