#!/usr/bin/env python
# -*- coding: utf-8 -*-
__author__ = 'Peter M. Landwehr <plandweh@cs.cmu.edu>'
import dynetmlparsingutils as dmlpu
from lxml import etree
from MetaNetwork import MetaNetwork
from networkx import nx
[docs]class MetaNetworkNX (MetaNetwork):
"""
A subclass of the MetaNetwork class that handles networks by storing them as instances of :class:`networkx.Graph` \
and :class:`networkx.DiGraph`.
"""
def _rename_network_nodes(self, nodeclass_name, nodeset_name, node_name, new_node_name):
new_mapping = {node_name: new_node_name}
for nk in self.networks:
if nk.graph['sourceType'] == nodeclass_name and nk.graph['source'] == nodeset_name or \
nk.graph['targetType'] == nodeclass_name and nk.graph['target'] == nodeset_name:
nx.relabel_nodes(nk, new_mapping)
def _parse_and_add_graph_tag(self, nk_tag):
if nk_tag.attrib['isDirected'] == 'true':
g = nx.DiGraph()
else:
g = nx.Graph()
g.graph['sourceType'] = nk_tag.attrib['sourceType']
g.graph['source'] = nk_tag.attrib['source']
g.graph['targetType'] = nk_tag.attrib['targetType']
g.graph['target'] = nk_tag.attrib['target']
g.graph['id'] = nk_tag.attrib['id']
g.graph['isDirected'] = nk_tag.attrib['isDirected'] == 'true'
g.graph['allowSelfLoops'] = nk_tag.attrib['allowSelfLoops'] == 'true'
g.graph['isBinary'] = nk_tag.attrib['isBinary'] == 'true'
#for attrib_key in nk_tag.attrib:
# g.graph[attrib_key] = format_prop(nk_tag.attrib[attrib_key])
link_list = list()
if g.graph['isBinary']:
for link in nk_tag.iterfind('link'):
link_list.append((link.attrib['source'], link.attrib['target']))
g.add_edges_from(link_list)
else:
for link in nk_tag.iterfind('link'):
weight = float(link.attrib['value']) if 'value' in link.attrib else 1.0
link_list.append((link.attrib['source'], link.attrib['target'], weight))
g.add_weighted_edges_from(link_list)
self.networks[nk_tag.attrib['id']] = g
def _get_networks_tag(self):
# bs = BeautifulSoup()
# networks_tag = bs.new_tag('networks')
# for key in self.networks:
# network_tag = bs.new_tag('network')
# network_tag['sourceType'] = self.networks[key].graph['sourceType']
# network_tag['source'] = self.networks[key].graph['source']
# network_tag['targetType'] = self.networks[key].graph['targetType']
# network_tag['target'] = self.networks[key].graph['target']
# network_tag['id'] = key
# network_tag['isDirected'] = dmlpu.unformat_prop(self.networks[key].graph['isDirected'])
# network_tag['allowSelfLoops'] = dmlpu.unformat_prop(self.networks[key].graph['allowSelfLoops'])
# network_tag['isBinary'] = dmlpu.unformat_prop(self.networks[key].graph['isBinary'])
#
# if self.networks[key].graph['isBinary']:
# for edge in self.networks[key].edges_iter(data=True):
# network_tag.append(bs.new_tag('link', source=edge[0], target=edge[1], value=edge[2]['weight']))
# else:
# for edge in self.networks[key].edges_iter():
# network_tag.append(bs.new_tag('link', source=edge[0], target=edge[1]))
#
# networks_tag.append(network_tag)
#
# return networks_tag
networks_tag = etree.Element('networks')
for key in self.networks:
network_tag = etree.SubElement(networks_tag, 'network', attrib={
'sourceType': self.networks[key].graph['sourceType'], 'source': self.networks[key].graph['source'],
'targetType': self.networks[key].graph['targetType'], 'target': self.networks[key].graph['target'],
'id': key, 'isDirected': dmlpu.unformat_prop(self.networks[key].graph['isDirected']),
'allowSelfLoops': dmlpu.unformat_prop(self.networks[key].graph['isBinary'])
})
if not self.networks[key].graph['isBinary']:
for edge in self.networks[key].edges_iter(data=True):
etree.SubElement(network_tag, 'link', attrib={'source': edge[0], 'target': edge[1],
'value': edge[2]['weight']})
else:
for edge in self.networks[key].edges_iter():
etree.SubElement(network_tag, 'link', attrib={'source': edge[0], 'target': edge[1]})
return networks_tag
def _pretty_print_networks(self):
print ' == Networks =='
network_count = 0
for nk_key in self.networks:
nk = self.networks[nk_key]
print u' Network {0}: {1}'.format(network_count, nk_key).encode('utf8')
for prop in nk.graph:
print u' {0}: {1}'.format(prop, nk.graph[prop]).encode('utf8')
print ' {0} nodes'.format(len(nk.nodes()))
print ' {0} edges'.format(len(nk.edges()))
network_count += 1
network_count += 1