wehub-resource-sync
448 lines
15 KiB
Python
448 lines
15 KiB
Python
import io
|
|
import sys
|
|
import time
|
|
|
|
import easygraph as eg
|
|
import pytest
|
|
|
|
|
|
class TestGEXF:
|
|
@classmethod
|
|
def setup_class(cls):
|
|
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 = eg.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" label="foo"/>
|
|
<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 = eg.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 = """<?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 = eg.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 = eg.read_gexf(self.simple_directed_fh)
|
|
assert sorted(G.nodes) == sorted(H.nodes)
|
|
assert sorted(G.edges) == sorted(H.edges)
|
|
self.simple_directed_fh.seek(0)
|
|
|
|
def test_write_read_simple_directed_graphml(self):
|
|
G = self.simple_directed_graph
|
|
fh = io.BytesIO()
|
|
eg.write_gexf(G, fh)
|
|
fh.seek(0)
|
|
H = eg.read_gexf(fh)
|
|
assert sorted(G.nodes) == sorted(H.nodes)
|
|
assert sorted(G.edges) == sorted(H.edges)
|
|
self.simple_directed_fh.seek(0)
|
|
|
|
def test_read_simple_undirected_graphml(self):
|
|
G = self.simple_undirected_graph
|
|
H = eg.read_gexf(self.simple_undirected_fh)
|
|
assert sorted(G.nodes) == sorted(H.nodes)
|
|
assert sorted(G.edges) == sorted(H.edges)
|
|
self.simple_undirected_fh.seek(0)
|
|
|
|
def test_read_attribute_graphml(self):
|
|
G = self.attribute_graph
|
|
H = eg.read_gexf(self.attribute_fh)
|
|
assert sorted(G.nodes) == sorted(H.nodes)
|
|
ge = sorted(G.edges)
|
|
he = sorted(H.edges)
|
|
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(eg.EasyGraphError, eg.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(eg.EasyGraphError, eg.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(eg.EasyGraphError, eg.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 = eg.read_gexf(fh, relabel=True)
|
|
assert sorted(G.nodes) == ["Hello", "Word"]
|
|
|
|
def test_default_attribute(self):
|
|
G = eg.Graph()
|
|
G.add_node(1, label="1", color="green")
|
|
eg.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()
|
|
eg.write_gexf(G, fh)
|
|
fh.seek(0)
|
|
H = eg.read_gexf(fh, node_type=int)
|
|
assert sorted(G.nodes) == sorted(H.nodes)
|
|
# 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 = eg.Graph()
|
|
G.add_node(1, id=7, label=77)
|
|
fh = io.BytesIO()
|
|
eg.write_gexf(G, fh)
|
|
fh.seek(0)
|
|
H = eg.read_gexf(fh, node_type=int)
|
|
assert list(H) == [7]
|
|
assert H.nodes[7]["label"] == "77"
|
|
|
|
@pytest.mark.skipif(sys.version_info < (3, 8), reason="requires >= python3.8")
|
|
def test_edge_id_construct(self):
|
|
G = eg.Graph()
|
|
G.add_edges_from([(0, 1, {"id": 0}), (1, 2, {"id": 2}), (2, 3)])
|
|
|
|
expected = f"""<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="{time.strftime('%Y-%m-%d')}">
|
|
<creator>EasyGraph</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>"""
|
|
|
|
obtained = "\n".join(eg.generate_gexf(G))
|
|
assert expected == obtained
|
|
|
|
@pytest.mark.skipif(sys.version_info < (3, 8), reason="requires >= python3.8")
|
|
def test_numpy_type(self):
|
|
np = pytest.importorskip("numpy")
|
|
G = eg.path_graph(4)
|
|
eg.set_node_attributes(G, {n: n for n in np.arange(4)}, "number")
|
|
G[0][1]["edge-number"] = np.float64(1.1)
|
|
expected = f"""<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="{time.strftime('%Y-%m-%d')}">
|
|
<creator>EasyGraph</creator>
|
|
</meta>
|
|
<graph defaultedgetype="undirected" mode="static" name="">
|
|
<attributes mode="static" class="edge">
|
|
<attribute id="1" title="edge-number" type="float" />
|
|
</attributes>
|
|
<attributes mode="static" class="node">
|
|
<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 source="0" target="1" id="0">
|
|
<attvalues>
|
|
<attvalue for="1" value="1.1" />
|
|
</attvalues>
|
|
</edge>
|
|
<edge source="1" target="2" id="1" />
|
|
<edge source="2" target="3" id="2" />
|
|
</edges>
|
|
</graph>
|
|
</gexf>"""
|
|
obtained = "\n".join(eg.generate_gexf(G))
|
|
assert expected == obtained
|
|
|
|
def test_bool(self):
|
|
G = eg.Graph()
|
|
G.add_node(1, testattr=True)
|
|
fh = io.BytesIO()
|
|
eg.write_gexf(G, fh)
|
|
fh.seek(0)
|
|
H = eg.read_gexf(fh, node_type=int)
|
|
assert H.nodes[1]["testattr"]
|
|
|
|
def test_specials(self):
|
|
from math import isnan
|
|
|
|
inf, nan = float("inf"), float("nan")
|
|
G = eg.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()
|
|
eg.write_gexf(G, fh)
|
|
fh.seek(0)
|
|
filetext = fh.read()
|
|
fh.seek(0)
|
|
H = eg.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]["easygraph_key"] == "a"
|
|
assert H.nodes[2]["easygraph_key"] == "b"
|
|
assert H.nodes[3]["easygraph_key"] == "c"
|
|
|
|
def test_simple_list(self):
|
|
G = eg.Graph()
|
|
list_value = [(1, 2, 3), (9, 1, 2)]
|
|
G.add_node(1, key=list_value)
|
|
fh = io.BytesIO()
|
|
eg.write_gexf(G, fh)
|
|
fh.seek(0)
|
|
H = eg.read_gexf(fh, node_type=int)
|
|
assert H.nodes[1]["easygraph_key"] == list_value
|
|
|
|
def test_dynamic_mode(self):
|
|
G = eg.Graph()
|
|
G.add_node(1, label="1", color="green")
|
|
G.graph["mode"] = "dynamic"
|
|
fh = io.BytesIO()
|
|
eg.write_gexf(G, fh)
|
|
fh.seek(0)
|
|
H = eg.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 = eg.Graph()
|
|
G.add_node(0, label="1", color="green")
|
|
G.nodes[0]["spells"] = [(1, 2)]
|
|
fh = io.BytesIO()
|
|
eg.write_gexf(G, fh)
|
|
fh.seek(0)
|
|
H = eg.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 = eg.Graph()
|
|
G.add_node(0, label="1", color="green")
|
|
G.nodes[0]["slices"] = [(1, 2)]
|
|
fh = io.BytesIO()
|
|
eg.write_gexf(G, fh, version="1.1draft")
|
|
fh.seek(0)
|
|
H = eg.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 = eg.Graph()
|
|
G.add_node(0, label="1", color="green", parents=[1, 2])
|
|
fh = io.BytesIO()
|
|
eg.write_gexf(G, fh)
|
|
fh.seek(0)
|
|
H = eg.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)
|