715 lines
20 KiB
Python
715 lines
20 KiB
Python
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import codecs
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import io
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import math
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import os
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import tempfile
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from ast import literal_eval
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from contextlib import contextmanager
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from textwrap import dedent
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import pytest
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import networkx as nx
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from networkx.readwrite.gml import literal_destringizer, literal_stringizer
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class TestGraph:
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@classmethod
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def setup_class(cls):
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cls.simple_data = """Creator "me"
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Version "xx"
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graph [
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comment "This is a sample graph"
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directed 1
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IsPlanar 1
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pos [ x 0 y 1 ]
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node [
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id 1
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label "Node 1"
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pos [ x 1 y 1 ]
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]
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node [
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id 2
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pos [ x 1 y 2 ]
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label "Node 2"
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]
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node [
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id 3
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label "Node 3"
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pos [ x 1 y 3 ]
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]
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edge [
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source 1
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target 2
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label "Edge from node 1 to node 2"
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color [line "blue" thickness 3]
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]
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edge [
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source 2
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target 3
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label "Edge from node 2 to node 3"
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]
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edge [
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source 3
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target 1
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label "Edge from node 3 to node 1"
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]
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]
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"""
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def test_parse_gml_cytoscape_bug(self):
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# example from issue #321, originally #324 in trac
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cytoscape_example = """
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Creator "Cytoscape"
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Version 1.0
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graph [
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node [
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root_index -3
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id -3
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graphics [
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x -96.0
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y -67.0
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w 40.0
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h 40.0
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fill "#ff9999"
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type "ellipse"
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outline "#666666"
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outline_width 1.5
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]
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label "node2"
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]
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node [
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root_index -2
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id -2
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graphics [
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x 63.0
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y 37.0
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w 40.0
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h 40.0
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fill "#ff9999"
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type "ellipse"
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outline "#666666"
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outline_width 1.5
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]
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label "node1"
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]
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node [
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root_index -1
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id -1
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graphics [
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x -31.0
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y -17.0
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w 40.0
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h 40.0
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fill "#ff9999"
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type "ellipse"
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outline "#666666"
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outline_width 1.5
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]
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label "node0"
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]
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edge [
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root_index -2
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target -2
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source -1
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graphics [
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width 1.5
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fill "#0000ff"
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type "line"
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Line [
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]
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source_arrow 0
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target_arrow 3
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]
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label "DirectedEdge"
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]
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edge [
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root_index -1
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target -1
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source -3
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graphics [
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width 1.5
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fill "#0000ff"
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type "line"
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Line [
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]
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source_arrow 0
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target_arrow 3
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]
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label "DirectedEdge"
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]
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]
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"""
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nx.parse_gml(cytoscape_example)
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def test_parse_gml(self):
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G = nx.parse_gml(self.simple_data, label="label")
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assert sorted(G.nodes()) == ["Node 1", "Node 2", "Node 3"]
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assert [e for e in sorted(G.edges())] == [
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("Node 1", "Node 2"),
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("Node 2", "Node 3"),
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("Node 3", "Node 1"),
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]
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assert [e for e in sorted(G.edges(data=True))] == [
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(
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"Node 1",
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"Node 2",
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{
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"color": {"line": "blue", "thickness": 3},
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"label": "Edge from node 1 to node 2",
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},
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),
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("Node 2", "Node 3", {"label": "Edge from node 2 to node 3"}),
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("Node 3", "Node 1", {"label": "Edge from node 3 to node 1"}),
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]
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def test_read_gml(self):
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(fd, fname) = tempfile.mkstemp()
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fh = open(fname, "w")
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fh.write(self.simple_data)
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fh.close()
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Gin = nx.read_gml(fname, label="label")
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G = nx.parse_gml(self.simple_data, label="label")
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assert sorted(G.nodes(data=True)) == sorted(Gin.nodes(data=True))
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assert sorted(G.edges(data=True)) == sorted(Gin.edges(data=True))
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os.close(fd)
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os.unlink(fname)
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def test_labels_are_strings(self):
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# GML requires labels to be strings (i.e., in quotes)
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answer = """graph [
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node [
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id 0
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label "1203"
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]
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]"""
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G = nx.Graph()
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G.add_node(1203)
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data = "\n".join(nx.generate_gml(G, stringizer=literal_stringizer))
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assert data == answer
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def test_relabel_duplicate(self):
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data = """
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graph
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[
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label ""
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directed 1
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node
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[
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id 0
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label "same"
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]
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node
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[
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id 1
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label "same"
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]
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]
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"""
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fh = io.BytesIO(data.encode("UTF-8"))
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fh.seek(0)
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pytest.raises(nx.NetworkXError, nx.read_gml, fh, label="label")
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def test_tuplelabels(self):
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# https://github.com/networkx/networkx/pull/1048
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# Writing tuple labels to GML failed.
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G = nx.OrderedGraph()
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G.add_edge((0, 1), (1, 0))
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data = "\n".join(nx.generate_gml(G, stringizer=literal_stringizer))
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answer = """graph [
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node [
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id 0
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label "(0,1)"
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]
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node [
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id 1
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label "(1,0)"
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]
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edge [
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source 0
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target 1
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]
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]"""
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assert data == answer
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def test_quotes(self):
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# https://github.com/networkx/networkx/issues/1061
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# Encoding quotes as HTML entities.
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G = nx.path_graph(1)
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G.name = "path_graph(1)"
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attr = 'This is "quoted" and this is a copyright: ' + chr(169)
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G.nodes[0]["demo"] = attr
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fobj = tempfile.NamedTemporaryFile()
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nx.write_gml(G, fobj)
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fobj.seek(0)
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# Should be bytes in 2.x and 3.x
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data = fobj.read().strip().decode("ascii")
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answer = """graph [
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name "path_graph(1)"
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node [
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id 0
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label "0"
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demo "This is "quoted" and this is a copyright: ©"
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]
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]"""
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assert data == answer
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def test_unicode_node(self):
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node = "node" + chr(169)
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G = nx.Graph()
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G.add_node(node)
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fobj = tempfile.NamedTemporaryFile()
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nx.write_gml(G, fobj)
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fobj.seek(0)
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# Should be bytes in 2.x and 3.x
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data = fobj.read().strip().decode("ascii")
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answer = """graph [
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node [
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id 0
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label "node©"
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]
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]"""
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assert data == answer
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def test_float_label(self):
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node = 1.0
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G = nx.Graph()
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G.add_node(node)
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fobj = tempfile.NamedTemporaryFile()
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nx.write_gml(G, fobj)
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fobj.seek(0)
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# Should be bytes in 2.x and 3.x
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data = fobj.read().strip().decode("ascii")
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answer = """graph [
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node [
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id 0
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label "1.0"
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]
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]"""
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assert data == answer
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def test_special_float_label(self):
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special_floats = [float("nan"), float("+inf"), float("-inf")]
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try:
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import numpy as np
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special_floats += [np.nan, np.inf, np.inf * -1]
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except ImportError:
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special_floats += special_floats
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G = nx.cycle_graph(len(special_floats))
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attrs = dict(enumerate(special_floats))
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nx.set_node_attributes(G, attrs, "nodefloat")
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edges = list(G.edges)
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attrs = {edges[i]: value for i, value in enumerate(special_floats)}
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nx.set_edge_attributes(G, attrs, "edgefloat")
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fobj = tempfile.NamedTemporaryFile()
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nx.write_gml(G, fobj)
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fobj.seek(0)
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# Should be bytes in 2.x and 3.x
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data = fobj.read().strip().decode("ascii")
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answer = """graph [
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node [
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id 0
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label "0"
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nodefloat NAN
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]
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node [
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id 1
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label "1"
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nodefloat +INF
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]
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node [
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id 2
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label "2"
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nodefloat -INF
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]
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node [
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id 3
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label "3"
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nodefloat NAN
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]
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node [
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id 4
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label "4"
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nodefloat +INF
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]
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node [
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id 5
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label "5"
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nodefloat -INF
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]
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edge [
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source 0
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target 1
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edgefloat NAN
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]
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edge [
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source 0
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target 5
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edgefloat +INF
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]
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edge [
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source 1
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target 2
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edgefloat -INF
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]
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edge [
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source 2
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target 3
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edgefloat NAN
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]
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edge [
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source 3
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target 4
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edgefloat +INF
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]
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edge [
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source 4
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target 5
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edgefloat -INF
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]
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]"""
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assert data == answer
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fobj.seek(0)
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graph = nx.read_gml(fobj)
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for indx, value in enumerate(special_floats):
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node_value = graph.nodes[str(indx)]["nodefloat"]
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if math.isnan(value):
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assert math.isnan(node_value)
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else:
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assert node_value == value
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edge = edges[indx]
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string_edge = (str(edge[0]), str(edge[1]))
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edge_value = graph.edges[string_edge]["edgefloat"]
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if math.isnan(value):
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assert math.isnan(edge_value)
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else:
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assert edge_value == value
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def test_name(self):
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G = nx.parse_gml('graph [ name "x" node [ id 0 label "x" ] ]')
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assert "x" == G.graph["name"]
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G = nx.parse_gml('graph [ node [ id 0 label "x" ] ]')
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assert "" == G.name
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assert "name" not in G.graph
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def test_graph_types(self):
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for directed in [None, False, True]:
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for multigraph in [None, False, True]:
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gml = "graph ["
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if directed is not None:
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gml += " directed " + str(int(directed))
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if multigraph is not None:
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gml += " multigraph " + str(int(multigraph))
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gml += ' node [ id 0 label "0" ]'
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gml += " edge [ source 0 target 0 ]"
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gml += " ]"
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G = nx.parse_gml(gml)
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assert bool(directed) == G.is_directed()
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assert bool(multigraph) == G.is_multigraph()
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gml = "graph [\n"
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if directed is True:
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|
|
gml += " directed 1\n"
|
||
|
|
if multigraph is True:
|
||
|
|
gml += " multigraph 1\n"
|
||
|
|
gml += """ node [
|
||
|
|
id 0
|
||
|
|
label "0"
|
||
|
|
]
|
||
|
|
edge [
|
||
|
|
source 0
|
||
|
|
target 0
|
||
|
|
"""
|
||
|
|
if multigraph:
|
||
|
|
gml += " key 0\n"
|
||
|
|
gml += " ]\n]"
|
||
|
|
assert gml == "\n".join(nx.generate_gml(G))
|
||
|
|
|
||
|
|
def test_data_types(self):
|
||
|
|
data = [
|
||
|
|
True,
|
||
|
|
False,
|
||
|
|
10**20,
|
||
|
|
-2e33,
|
||
|
|
"'",
|
||
|
|
'"&&&""',
|
||
|
|
[{(b"\xfd",): "\x7f", chr(0x4444): (1, 2)}, (2, "3")],
|
||
|
|
]
|
||
|
|
data.append(chr(0x14444))
|
||
|
|
data.append(literal_eval("{2.3j, 1 - 2.3j, ()}"))
|
||
|
|
G = nx.Graph()
|
||
|
|
G.name = data
|
||
|
|
G.graph["data"] = data
|
||
|
|
G.add_node(0, int=-1, data=dict(data=data))
|
||
|
|
G.add_edge(0, 0, float=-2.5, data=data)
|
||
|
|
gml = "\n".join(nx.generate_gml(G, stringizer=literal_stringizer))
|
||
|
|
G = nx.parse_gml(gml, destringizer=literal_destringizer)
|
||
|
|
assert data == G.name
|
||
|
|
assert {"name": data, "data": data} == G.graph
|
||
|
|
assert list(G.nodes(data=True)) == [(0, dict(int=-1, data=dict(data=data)))]
|
||
|
|
assert list(G.edges(data=True)) == [(0, 0, dict(float=-2.5, data=data))]
|
||
|
|
G = nx.Graph()
|
||
|
|
G.graph["data"] = "frozenset([1, 2, 3])"
|
||
|
|
G = nx.parse_gml(nx.generate_gml(G), destringizer=literal_eval)
|
||
|
|
assert G.graph["data"] == "frozenset([1, 2, 3])"
|
||
|
|
|
||
|
|
def test_escape_unescape(self):
|
||
|
|
gml = """graph [
|
||
|
|
name "&"䑄��&unknown;"
|
||
|
|
]"""
|
||
|
|
G = nx.parse_gml(gml)
|
||
|
|
assert (
|
||
|
|
'&"\x0f' + chr(0x4444) + "��&unknown;"
|
||
|
|
== G.name
|
||
|
|
)
|
||
|
|
gml = "\n".join(nx.generate_gml(G))
|
||
|
|
alnu = "#1234567890;&#x1234567890abcdef"
|
||
|
|
answer = (
|
||
|
|
"""graph [
|
||
|
|
name "&"䑄&"""
|
||
|
|
+ alnu
|
||
|
|
+ """;&unknown;"
|
||
|
|
]"""
|
||
|
|
)
|
||
|
|
assert answer == gml
|
||
|
|
|
||
|
|
def test_exceptions(self):
|
||
|
|
pytest.raises(ValueError, literal_destringizer, "(")
|
||
|
|
pytest.raises(ValueError, literal_destringizer, "frozenset([1, 2, 3])")
|
||
|
|
pytest.raises(ValueError, literal_destringizer, literal_destringizer)
|
||
|
|
pytest.raises(ValueError, literal_stringizer, frozenset([1, 2, 3]))
|
||
|
|
pytest.raises(ValueError, literal_stringizer, literal_stringizer)
|
||
|
|
with tempfile.TemporaryFile() as f:
|
||
|
|
f.write(codecs.BOM_UTF8 + b"graph[]")
|
||
|
|
f.seek(0)
|
||
|
|
pytest.raises(nx.NetworkXError, nx.read_gml, f)
|
||
|
|
|
||
|
|
def assert_parse_error(gml):
|
||
|
|
pytest.raises(nx.NetworkXError, nx.parse_gml, gml)
|
||
|
|
|
||
|
|
assert_parse_error(["graph [\n\n", "]"])
|
||
|
|
assert_parse_error("")
|
||
|
|
assert_parse_error('Creator ""')
|
||
|
|
assert_parse_error("0")
|
||
|
|
assert_parse_error("graph ]")
|
||
|
|
assert_parse_error("graph [ 1 ]")
|
||
|
|
assert_parse_error("graph [ 1.E+2 ]")
|
||
|
|
assert_parse_error('graph [ "A" ]')
|
||
|
|
assert_parse_error("graph [ ] graph ]")
|
||
|
|
assert_parse_error("graph [ ] graph [ ]")
|
||
|
|
assert_parse_error("graph [ data [1, 2, 3] ]")
|
||
|
|
assert_parse_error("graph [ node [ ] ]")
|
||
|
|
assert_parse_error("graph [ node [ id 0 ] ]")
|
||
|
|
nx.parse_gml('graph [ node [ id "a" ] ]', label="id")
|
||
|
|
assert_parse_error("graph [ node [ id 0 label 0 ] node [ id 0 label 1 ] ]")
|
||
|
|
assert_parse_error("graph [ node [ id 0 label 0 ] node [ id 1 label 0 ] ]")
|
||
|
|
assert_parse_error("graph [ node [ id 0 label 0 ] edge [ ] ]")
|
||
|
|
assert_parse_error("graph [ node [ id 0 label 0 ] edge [ source 0 ] ]")
|
||
|
|
nx.parse_gml("graph [edge [ source 0 target 0 ] node [ id 0 label 0 ] ]")
|
||
|
|
assert_parse_error("graph [ node [ id 0 label 0 ] edge [ source 1 target 0 ] ]")
|
||
|
|
assert_parse_error("graph [ node [ id 0 label 0 ] edge [ source 0 target 1 ] ]")
|
||
|
|
assert_parse_error(
|
||
|
|
"graph [ node [ id 0 label 0 ] node [ id 1 label 1 ] "
|
||
|
|
"edge [ source 0 target 1 ] edge [ source 1 target 0 ] ]"
|
||
|
|
)
|
||
|
|
nx.parse_gml(
|
||
|
|
"graph [ node [ id 0 label 0 ] node [ id 1 label 1 ] "
|
||
|
|
"edge [ source 0 target 1 ] edge [ source 1 target 0 ] "
|
||
|
|
"directed 1 ]"
|
||
|
|
)
|
||
|
|
nx.parse_gml(
|
||
|
|
"graph [ node [ id 0 label 0 ] node [ id 1 label 1 ] "
|
||
|
|
"edge [ source 0 target 1 ] edge [ source 0 target 1 ]"
|
||
|
|
"multigraph 1 ]"
|
||
|
|
)
|
||
|
|
nx.parse_gml(
|
||
|
|
"graph [ node [ id 0 label 0 ] node [ id 1 label 1 ] "
|
||
|
|
"edge [ source 0 target 1 key 0 ] edge [ source 0 target 1 ]"
|
||
|
|
"multigraph 1 ]"
|
||
|
|
)
|
||
|
|
assert_parse_error(
|
||
|
|
"graph [ node [ id 0 label 0 ] node [ id 1 label 1 ] "
|
||
|
|
"edge [ source 0 target 1 key 0 ] edge [ source 0 target 1 key 0 ]"
|
||
|
|
"multigraph 1 ]"
|
||
|
|
)
|
||
|
|
nx.parse_gml(
|
||
|
|
"graph [ node [ id 0 label 0 ] node [ id 1 label 1 ] "
|
||
|
|
"edge [ source 0 target 1 key 0 ] edge [ source 1 target 0 key 0 ]"
|
||
|
|
"directed 1 multigraph 1 ]"
|
||
|
|
)
|
||
|
|
|
||
|
|
# Tests for string convertable alphanumeric id and label values
|
||
|
|
nx.parse_gml("graph [edge [ source a target a ] node [ id a label b ] ]")
|
||
|
|
nx.parse_gml(
|
||
|
|
"graph [ node [ id n42 label 0 ] node [ id x43 label 1 ]"
|
||
|
|
"edge [ source n42 target x43 key 0 ]"
|
||
|
|
"edge [ source x43 target n42 key 0 ]"
|
||
|
|
"directed 1 multigraph 1 ]"
|
||
|
|
)
|
||
|
|
assert_parse_error(
|
||
|
|
"graph [edge [ source u'u\4200' target u'u\4200' ] "
|
||
|
|
+ "node [ id u'u\4200' label b ] ]"
|
||
|
|
)
|
||
|
|
|
||
|
|
def assert_generate_error(*args, **kwargs):
|
||
|
|
pytest.raises(
|
||
|
|
nx.NetworkXError, lambda: list(nx.generate_gml(*args, **kwargs))
|
||
|
|
)
|
||
|
|
|
||
|
|
G = nx.Graph()
|
||
|
|
G.graph[3] = 3
|
||
|
|
assert_generate_error(G)
|
||
|
|
G = nx.Graph()
|
||
|
|
G.graph["3"] = 3
|
||
|
|
assert_generate_error(G)
|
||
|
|
G = nx.Graph()
|
||
|
|
G.graph["data"] = frozenset([1, 2, 3])
|
||
|
|
assert_generate_error(G, stringizer=literal_stringizer)
|
||
|
|
G = nx.Graph()
|
||
|
|
G.graph["data"] = []
|
||
|
|
assert_generate_error(G)
|
||
|
|
assert_generate_error(G, stringizer=len)
|
||
|
|
|
||
|
|
def test_label_kwarg(self):
|
||
|
|
G = nx.parse_gml(self.simple_data, label="id")
|
||
|
|
assert sorted(G.nodes) == [1, 2, 3]
|
||
|
|
labels = [G.nodes[n]["label"] for n in sorted(G.nodes)]
|
||
|
|
assert labels == ["Node 1", "Node 2", "Node 3"]
|
||
|
|
|
||
|
|
G = nx.parse_gml(self.simple_data, label=None)
|
||
|
|
assert sorted(G.nodes) == [1, 2, 3]
|
||
|
|
labels = [G.nodes[n]["label"] for n in sorted(G.nodes)]
|
||
|
|
assert labels == ["Node 1", "Node 2", "Node 3"]
|
||
|
|
|
||
|
|
def test_outofrange_integers(self):
|
||
|
|
# GML restricts integers to 32 signed bits.
|
||
|
|
# Check that we honor this restriction on export
|
||
|
|
G = nx.Graph()
|
||
|
|
# Test export for numbers that barely fit or don't fit into 32 bits,
|
||
|
|
# and 3 numbers in the middle
|
||
|
|
numbers = {
|
||
|
|
"toosmall": (-(2**31)) - 1,
|
||
|
|
"small": -(2**31),
|
||
|
|
"med1": -4,
|
||
|
|
"med2": 0,
|
||
|
|
"med3": 17,
|
||
|
|
"big": (2**31) - 1,
|
||
|
|
"toobig": 2**31,
|
||
|
|
}
|
||
|
|
G.add_node("Node", **numbers)
|
||
|
|
|
||
|
|
fd, fname = tempfile.mkstemp()
|
||
|
|
try:
|
||
|
|
nx.write_gml(G, fname)
|
||
|
|
# Check that the export wrote the nonfitting numbers as strings
|
||
|
|
G2 = nx.read_gml(fname)
|
||
|
|
for attr, value in G2.nodes["Node"].items():
|
||
|
|
if attr == "toosmall" or attr == "toobig":
|
||
|
|
assert type(value) == str
|
||
|
|
else:
|
||
|
|
assert type(value) == int
|
||
|
|
finally:
|
||
|
|
os.close(fd)
|
||
|
|
os.unlink(fname)
|
||
|
|
|
||
|
|
|
||
|
|
@contextmanager
|
||
|
|
def byte_file():
|
||
|
|
_file_handle = io.BytesIO()
|
||
|
|
yield _file_handle
|
||
|
|
_file_handle.seek(0)
|
||
|
|
|
||
|
|
|
||
|
|
class TestPropertyLists:
|
||
|
|
def test_writing_graph_with_multi_element_property_list(self):
|
||
|
|
g = nx.Graph()
|
||
|
|
g.add_node("n1", properties=["element", 0, 1, 2.5, True, False])
|
||
|
|
with byte_file() as f:
|
||
|
|
nx.write_gml(g, f)
|
||
|
|
result = f.read().decode()
|
||
|
|
|
||
|
|
assert result == dedent(
|
||
|
|
"""\
|
||
|
|
graph [
|
||
|
|
node [
|
||
|
|
id 0
|
||
|
|
label "n1"
|
||
|
|
properties "element"
|
||
|
|
properties 0
|
||
|
|
properties 1
|
||
|
|
properties 2.5
|
||
|
|
properties 1
|
||
|
|
properties 0
|
||
|
|
]
|
||
|
|
]
|
||
|
|
"""
|
||
|
|
)
|
||
|
|
|
||
|
|
def test_writing_graph_with_one_element_property_list(self):
|
||
|
|
g = nx.Graph()
|
||
|
|
g.add_node("n1", properties=["element"])
|
||
|
|
with byte_file() as f:
|
||
|
|
nx.write_gml(g, f)
|
||
|
|
result = f.read().decode()
|
||
|
|
|
||
|
|
assert result == dedent(
|
||
|
|
"""\
|
||
|
|
graph [
|
||
|
|
node [
|
||
|
|
id 0
|
||
|
|
label "n1"
|
||
|
|
properties "_networkx_list_start"
|
||
|
|
properties "element"
|
||
|
|
]
|
||
|
|
]
|
||
|
|
"""
|
||
|
|
)
|
||
|
|
|
||
|
|
def test_reading_graph_with_list_property(self):
|
||
|
|
with byte_file() as f:
|
||
|
|
f.write(
|
||
|
|
dedent(
|
||
|
|
"""
|
||
|
|
graph [
|
||
|
|
node [
|
||
|
|
id 0
|
||
|
|
label "n1"
|
||
|
|
properties "element"
|
||
|
|
properties 0
|
||
|
|
properties 1
|
||
|
|
properties 2.5
|
||
|
|
]
|
||
|
|
]
|
||
|
|
"""
|
||
|
|
).encode("ascii")
|
||
|
|
)
|
||
|
|
f.seek(0)
|
||
|
|
graph = nx.read_gml(f)
|
||
|
|
assert graph.nodes(data=True)["n1"] == {"properties": ["element", 0, 1, 2.5]}
|
||
|
|
|
||
|
|
def test_reading_graph_with_single_element_list_property(self):
|
||
|
|
with byte_file() as f:
|
||
|
|
f.write(
|
||
|
|
dedent(
|
||
|
|
"""
|
||
|
|
graph [
|
||
|
|
node [
|
||
|
|
id 0
|
||
|
|
label "n1"
|
||
|
|
properties "_networkx_list_start"
|
||
|
|
properties "element"
|
||
|
|
]
|
||
|
|
]
|
||
|
|
"""
|
||
|
|
).encode("ascii")
|
||
|
|
)
|
||
|
|
f.seek(0)
|
||
|
|
graph = nx.read_gml(f)
|
||
|
|
assert graph.nodes(data=True)["n1"] == {"properties": ["element"]}
|