konect.py 4.5 KB
Newer Older
Tiago Peixoto's avatar
Tiago Peixoto committed
1
2
3
4
5
 #! /usr/bin/env python
# -*- coding: utf-8 -*-
#
# graph_tool -- a general graph manipulation python module
#
Tiago Peixoto's avatar
Tiago Peixoto committed
6
# Copyright (C) 2006-2019 Tiago de Paula Peixoto <tiago@skewed.de>
Tiago Peixoto's avatar
Tiago Peixoto committed
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program.  If not, see <http://www.gnu.org/licenses/>.

from __future__ import division, absolute_import, print_function
import sys
if sys.version_info < (3,):
    range = xrange

import os.path
import tempfile
28
if sys.version_info < (3,):
29
    from urllib2 import urlopen, URLError
30
31
32
33
34
35
36
37
38
39
    import shutil
    class TemporaryDirectory(object):
        def __init__(self, suffix="", prefix="", dir=None):
            self.name = tempfile.mkdtemp(suffix, prefix, dir)

        def __enter__(self):
            return self.name

        def __exit__(self, exc, value, tb):
            shutil.rmtree(self.name)
40
else:
41
    from urllib.request import urlopen, URLError
42
    from tempfile import TemporaryDirectory
Tiago Peixoto's avatar
Tiago Peixoto committed
43
44
45
46
47
48
49
50
51
52
53
import tarfile
import warnings
import numpy

from .. import Graph

def load_koblenz_dir(dirname):
    g = Graph()
    g.gp.meta = g.new_graph_property("string")
    g.gp.readme = g.new_graph_property("string")
    for root, dirs, files in os.walk(dirname):
54
55
56
57
58
59
60
61
        for f in files:
            if f.startswith("README"):
                g.gp.readme = open(os.path.join(root, f)).read()
            if f.startswith("meta."):
                g.gp.meta = open(os.path.join(root, f)).read()
            if f.startswith("out."):
                edges = numpy.loadtxt(os.path.join(root, f), comments="%")
                line = next(open(os.path.join(root, f)))
Tiago Peixoto's avatar
Tiago Peixoto committed
62
63
64
                if "asym" not in line:
                    g.set_directed(False)
                edges[:,:2] -= 1  # we need zero-based indexing
65
66
                if "bip" in line: # bipartite graphs have non-unique indexing
                    edges[:,1] += edges[:,0].max() + 1
Tiago Peixoto's avatar
Tiago Peixoto committed
67
68
                g.add_edge_list(edges[:,:2])
                if edges.shape[1] > 2:
69
                    g.ep.weight = g.new_edge_property("double")
Tiago Peixoto's avatar
Tiago Peixoto committed
70
71
72
73
                    g.ep.weight.a = edges[:,2]
                if edges.shape[1] > 3:
                    g.ep.time = g.new_edge_property("int")
                    g.ep.time.a = edges[:,3]
74
75
        for f in files:
            if f.startswith("ent."):
Tiago Peixoto's avatar
Tiago Peixoto committed
76
77
78
79
                try:
                    g.vp.meta = g.new_vertex_property("string")
                    meta = g.vp.meta
                    count = 0
80
                    for line in open(os.path.join(root, f)):
Tiago Peixoto's avatar
Tiago Peixoto committed
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
                        vals = line.split()
                        if len(vals) == 1 and vals[0] == "%":
                            continue
                        if vals[0] == "%":
                            g.gp.meta_desc = g.new_graph_property("string", line)
                            continue
                        v = g.vertex(count)
                        meta[v] = line.strip()
                        count += 1
                except ValueError as e:
                    warnings.warn("error automatically reading node metadata from file '%s': %s" % (file, str(e)))
    return g

def get_koblenz_network_data(name):
    with tempfile.TemporaryFile(mode='w+b') as ftemp:
96
97
98
99
        try:
            response = urlopen('http://konect.cc/files/download.tsv.%s.tar.bz2' % name)
        except URLError:
            response = urlopen('http://konect.uni-koblenz.de/downloads/tsv/%s.tar.bz2' % name)
100
101
102
103
104
105
        buflen = 1 << 20
        while True:
            buf = response.read(buflen)
            ftemp.write(buf)
            if len(buf) < buflen:
                break
Tiago Peixoto's avatar
Tiago Peixoto committed
106
        ftemp.seek(0)
107
        with TemporaryDirectory(suffix=name) as tempdir:
Tiago Peixoto's avatar
Tiago Peixoto committed
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
            with tarfile.open(fileobj=ftemp, mode='r:bz2') as tar:
                tar.extractall(path=tempdir)
            g = load_koblenz_dir(tempdir)
            return g

class LazyKoblenzDataDict(dict):
    def __getitem__(self, k):
        if k not in self:
            g = get_koblenz_network_data(k)
            dict.__setitem__(self, k, g)
            return g
        return dict.__getitem__(self, k)


konect_data = LazyKoblenzDataDict()