515 lines
16 KiB
Python
515 lines
16 KiB
Python
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#!/usr/bin/env python
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# encoding: utf-8
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from ast import literal_eval
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import codecs
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import io
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import pytest
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import networkx as nx
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from networkx.readwrite.gml import literal_stringizer, literal_destringizer
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import os
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import tempfile
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try:
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unicode
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except NameError:
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unicode = str
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try:
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unichr
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except NameError:
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unichr = chr
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class TestGraph(object):
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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()) ==
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['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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assert ([e for e in sorted(G.edges(data=True))] ==
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[('Node 1', 'Node 2',
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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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('Node 2', 'Node 3',
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{'label': 'Edge from node 2 to node 3'}),
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('Node 3', 'Node 1',
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{'label': 'Edge from node 3 to node 1'})])
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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(
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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: ' + unichr(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' + unichr(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_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'
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if multigraph is True:
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gml += ' multigraph 1\n'
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gml += """ node [
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id 0
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label "0"
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]
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edge [
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source 0
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target 0
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"""
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if multigraph:
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gml += ' key 0\n'
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gml += ' ]\n]'
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assert gml == '\n'.join(nx.generate_gml(G))
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def test_data_types(self):
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data = [True, False, 10 ** 20, -2e33, "'", '"&&&""',
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[{(b'\xfd',): '\x7f', unichr(0x4444): (1, 2)}, (2, "3")]]
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try: # fails under IronPython
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data.append(unichr(0x14444))
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except ValueError:
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data.append(unichr(0x1444))
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try: # fails under Python 2.7
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data.append(literal_eval('{2.3j, 1 - 2.3j, ()}'))
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except ValueError:
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data.append([2.3j, 1 - 2.3j, ()])
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G = nx.Graph()
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G.name = data
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G.graph['data'] = data
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G.add_node(0, int=-1, data=dict(data=data))
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G.add_edge(0, 0, float=-2.5, data=data)
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gml = '\n'.join(nx.generate_gml(G, stringizer=literal_stringizer))
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G = nx.parse_gml(gml, destringizer=literal_destringizer)
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assert data == G.name
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assert {'name': data, unicode('data'): data} == G.graph
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assert (list(G.nodes(data=True)) ==
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[(0, dict(int=-1, data=dict(data=data)))])
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assert (list(G.edges(data=True)) ==
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[(0, 0, dict(float=-2.5, data=data))])
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G = nx.Graph()
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G.graph['data'] = 'frozenset([1, 2, 3])'
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G = nx.parse_gml(nx.generate_gml(G), destringizer=literal_eval)
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assert G.graph['data'] == 'frozenset([1, 2, 3])'
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def test_escape_unescape(self):
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gml = """graph [
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name "&"䑄��&unknown;"
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]"""
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G = nx.parse_gml(gml)
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assert (
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'&"\x0f' + unichr(0x4444) +
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'��&unknown;' ==
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G.name)
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gml = '\n'.join(nx.generate_gml(G))
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alnu = "#1234567890;&#x1234567890abcdef"
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answer = """graph [
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name "&"䑄&""" + alnu + """;&unknown;"
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]"""
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assert answer == gml
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def test_exceptions(self):
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pytest.raises(ValueError, literal_destringizer, '(')
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pytest.raises(ValueError, literal_destringizer, 'frozenset([1, 2, 3])')
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pytest.raises(ValueError, literal_destringizer, literal_destringizer)
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pytest.raises(ValueError, literal_stringizer, frozenset([1, 2, 3]))
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pytest.raises(ValueError, literal_stringizer, literal_stringizer)
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with tempfile.TemporaryFile() as f:
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f.write(codecs.BOM_UTF8 + 'graph[]'.encode('ascii'))
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f.seek(0)
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pytest.raises(nx.NetworkXError, nx.read_gml, f)
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def assert_parse_error(gml):
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|
|
pytest.raises(nx.NetworkXError, nx.parse_gml, gml)
|
||
|
|
|
||
|
|
assert_parse_error(['graph [\n\n', unicode(']')])
|
||
|
|
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)
|