def test_remove_edge(self):
collapser = RedundantEdgeCollapser()
net = NiceCXNetwork()
# test remove on non existant edge
collapser._remove_edge(net, 10)
# test removing edge with no attributes
eid = net.create_edge(edge_source=0,
edge_target=1,
edge_interaction='needs')
self.assertEqual('needs', net.get_edge(eid)['i'])
collapser._remove_edge(net, eid)
self.assertEqual(None, net.get_edge(eid))
# test removing edge with attributes
eid = net.create_edge(edge_source=0,
edge_target=1,
edge_interaction='needs')
net.set_edge_attribute(eid, 'foo', 'someval')
net.set_edge_attribute(eid, 'foo2', 'someval2')
self.assertEqual('needs', net.get_edge(eid)['i'])
self.assertEqual('someval', net.get_edge_attribute(eid, 'foo')['v'])
self.assertEqual('someval2', net.get_edge_attribute(eid, 'foo2')['v'])
collapser._remove_edge(net, eid)
self.assertEqual(None, net.get_edge(eid))
self.assertEqual((None, None), net.get_edge_attribute(eid, 'foo'))
self.assertEqual((None, None), net.get_edge_attribute(eid, 'foo2'))
def test_basic_network(self):
net = NiceCXNetwork()
adjud = RedundantEdgeAdjudicator()
nid = net.create_edge(edge_source=0,
edge_target=1,
edge_interaction='neighbor-of')
cid = net.create_edge(edge_source=0,
edge_target=1,
edge_interaction='controls-state-change-of')
net.set_edge_attribute(cid,
RedundantEdgeAdjudicator.CITATION,
['pubmed:123'],
type='list_of_string')
oid = net.create_edge(edge_source=0,
edge_target=1,
edge_interaction='someother')
net.set_edge_attribute(oid,
RedundantEdgeAdjudicator.CITATION,
['pubmed:123'],
type='list_of_string')
self.assertEqual('neighbor-of', net.get_edge(nid)['i'])
self.assertEqual('controls-state-change-of', net.get_edge(cid)['i'])
self.assertEqual('someother', net.get_edge(oid)['i'])
self.assertEqual([], adjud.update(net))
self.assertEqual(None, net.get_edge(nid))
self.assertEqual(None, net.get_edge(cid))
self.assertEqual('someother', net.get_edge(oid)['i'])
def test_update_edge_with_dict(self):
collapser = RedundantEdgeCollapser()
net = NiceCXNetwork()
eid = net.create_edge(edge_source=0,
edge_target=1,
edge_interaction='something')
net.set_edge_attribute(eid, 'sentence', 'hi', type='string')
edge_dict = {
'citation': (set(['pubmed:123']), 'list_of_string'),
'sentence': (set(['sentence1', 'sentence2']), 'string'),
'direct': (set([True, False]), 'boolean')
}
res = collapser._update_edge_with_dict(net, eid, edge_dict)
self.assertTrue('direct attribute has multiple values:' in res[0])
edata = net.get_edge_attribute(eid, 'citation')
self.assertEqual('list_of_string', edata['d'])
self.assertEqual(['pubmed:123'], edata['v'])
edata = net.get_edge_attribute(eid, 'sentence')
self.assertEqual('list_of_string', edata['d'])
self.assertTrue('sentence1' in edata['v'])
self.assertTrue('sentence2' in edata['v'])
self.assertEqual(2, len(edata['v']))
edata = net.get_edge_attribute(eid, 'direct')
self.assertEqual('boolean', edata['d'])
self.assertEqual(False, edata['v'])
def test_basic_network_where_neighbor_of_citations_merges_disabled(self):
net = NiceCXNetwork()
adjud = RedundantEdgeAdjudicator(disablcitededgemerge=True)
nid = net.create_edge(edge_source=0,
edge_target=1,
edge_interaction='neighbor-of')
net.set_edge_attribute(nid,
RedundantEdgeAdjudicator.CITATION, ['pubmed:5'],
type='list_of_string')
cid = net.create_edge(edge_source=0,
edge_target=1,
edge_interaction='controls-state-change-of')
oid = net.create_edge(edge_source=0,
edge_target=1,
edge_interaction='someother')
self.assertEqual('neighbor-of', net.get_edge(nid)['i'])
self.assertEqual('controls-state-change-of', net.get_edge(cid)['i'])
self.assertEqual('someother', net.get_edge(oid)['i'])
self.assertEqual([], adjud.update(net))
self.assertEqual('neighbor-of', net.get_edge(nid)['i'])
self.assertEqual(None, net.get_edge(cid))
self.assertEqual('someother', net.get_edge(oid)['i'])
res = net.get_edge_attribute(nid, RedundantEdgeAdjudicator.CITATION)
res['v'].sort()
self.assertEqual(['pubmed:5'], res['v'])
res = net.get_edge_attribute(oid, RedundantEdgeAdjudicator.CITATION)
self.assertEqual((None, None), res)
def test_edge_with_emptystring(self):
updator = EmptyCitationAttributeRemover()
net = NiceCXNetwork()
edgeid = net.create_edge(edge_source=0, edge_target=1,
edge_interaction='foo')
net.set_edge_attribute(edgeid, 'citation', values=[''],
type='list_of_string')
self.assertEqual([], updator.update(net))
self.assertEqual((None, None), net.get_edge_attribute(edgeid,
'citation'))
def test_edge_with_emptyelementincitationlist(self):
updator = EmptyCitationAttributeRemover()
net = NiceCXNetwork()
edgeid = net.create_edge(edge_source=0, edge_target=1,
edge_interaction='foo')
net.set_edge_attribute(edgeid, 'citation',
values=['foo', 'pubmed:', 'hi'],
type='list_of_string')
self.assertEqual([], updator.update(net))
self.assertEqual(['foo', 'hi'],
net.get_edge_attribute(edgeid, 'citation')['v'])
def test_edge_with_emptylistcitation(self):
updator = EmptyCitationAttributeUpdator()
net = NiceCXNetwork()
edgeid = net.create_edge(edge_source=0,
edge_target=1,
edge_interaction='foo')
net.set_edge_attribute(edgeid,
'citation',
values=[],
type='list_of_string')
self.assertEqual([], updator.update(net))
edge = net.get_edge_attribute(edgeid, 'citation')
self.assertEqual([], edge['v'])
def test_remove_edge_with_attributes(self):
adjud = RedundantEdgeAdjudicator()
net = NiceCXNetwork()
edgeid = net.create_edge(edge_source=0,
edge_target=1,
edge_interaction='foo')
net.set_edge_attribute(edgeid, 'attr1', 'someval')
self.assertEqual('someval',
net.get_edge_attribute(edgeid, 'attr1')['v'])
self.assertEqual('foo', net.get_edge(edgeid)['i'])
adjud._remove_edge(net, edgeid)
self.assertEqual(None, net.get_edge(edgeid))
self.assertEqual((None, None), net.get_edge_attribute(edgeid, 'attr1'))
def test_remove_if_redundant_with_citation_and_other_lacks_citation(self):
net = NiceCXNetwork()
adjud = RedundantEdgeAdjudicator()
nid = net.create_edge(edge_source=0,
edge_target=1,
edge_interaction='neighbor-of')
net.set_edge_attribute(nid,
RedundantEdgeAdjudicator.CITATION,
['pubmed:123'],
type='list_of_string')
cid = net.create_edge(edge_source=0,
edge_target=1,
edge_interaction='controls-state-change-of')
self.assertEqual('neighbor-of', net.get_edge(nid)['i'])
adjud._remove_if_redundant(net, nid, [cid])
self.assertEqual('neighbor-of', net.get_edge(nid)['i'])
def test_basic_network_where_neighbor_of_citations_merges_enabled(self):
net = NiceCXNetwork()
adjud = RedundantEdgeAdjudicator()
edge_map = {}
nid = net.create_edge(edge_source=0,
edge_target=1,
edge_interaction='neighbor-of')
net.set_edge_attribute(nid,
RedundantEdgeAdjudicator.CITATION, ['pubmed:5'],
type='list_of_string')
cid = net.create_edge(edge_source=0,
edge_target=1,
edge_interaction='controls-state-change-of')
net.set_edge_attribute(cid,
RedundantEdgeAdjudicator.CITATION, ['pubmed:6'],
type='list_of_string')
neighbor_of_map = {}
controls_state_change_map = {}
other_edge_exists = {}
for k, v in net.get_edges():
s = v['s']
t = v['t']
i = v['i']
if i == 'neighbor-of':
if not s in neighbor_of_map:
neighbor_of_map[s] = {}
if not t in neighbor_of_map:
neighbor_of_map[t] = {}
neighbor_of_map[s][t] = k
neighbor_of_map[t][s] = k
elif i == 'controls-state-change-of':
adjud._add_to_edge_map(controls_state_change_map, k, s, t)
else:
adjud._add_to_edge_map(other_edge_exists, k, s, t)
adjud.remove_and_merge_neighbor_of(net, neighbor_of_map, edge_map)
net.print_summary()
def test_remove_node_from_network_with_edges_and_attrs(self):
net = NiceCXNetwork()
node_id = net.create_node('node1', node_represents='ha')
other_node_id = net.create_node('node2', node_represents='ha')
edge_id = net.create_edge(edge_source=node_id,
edge_target=other_node_id,
edge_interaction='activates')
net.set_node_attribute(node_id, 'nodeattr', values='foo')
net.set_node_attribute(node_id, 'nodeattr2', values='foo2')
net.set_edge_attribute(edge_id, 'edgeattr', values='hello')
net.set_edge_attribute(edge_id, 'edgeattr2', values='hello2')
nef = NetworkNodeFactory()
nn = nef.get_network_node_from_network(net_cx=net, node_id=node_id)
nn.remove_node_from_network(net_cx=net)
self.assertEqual(1, len(net.get_nodes()))
self.assertEqual(0, len(net.get_edges()))
def test_remove_if_redundant_with_multiple_edges_same_citations(self):
net = NiceCXNetwork()
adjud = RedundantEdgeAdjudicator()
nid = net.create_edge(edge_source=0,
edge_target=1,
edge_interaction='neighbor-of')
net.set_edge_attribute(nid,
RedundantEdgeAdjudicator.CITATION,
['pubmed:4', 'pubmed:123'],
type='list_of_string')
cid = net.create_edge(edge_source=0,
edge_target=1,
edge_interaction='controls-state-change-of')
net.set_edge_attribute(cid,
RedundantEdgeAdjudicator.CITATION,
['pubmed:555', 'pubmed:4'],
type='list_of_string')
cidtwo = net.create_edge(edge_source=0,
edge_target=1,
edge_interaction='controls-state-change-of')
net.set_edge_attribute(cidtwo,
RedundantEdgeAdjudicator.CITATION,
['pubmed:4', 'pubmed:123'],
type='list_of_string')
self.assertEqual('neighbor-of', net.get_edge(nid)['i'])
adjud._remove_if_redundant(net, nid, [cid, cidtwo])
self.assertEqual(None, net.get_edge(nid))
def test_remove_if_redundant_mergecitations_true(self):
net = NiceCXNetwork()
adjud = RedundantEdgeAdjudicator()
nid = net.create_edge(edge_source=0,
edge_target=1,
edge_interaction='neighbor-of')
net.set_edge_attribute(nid,
RedundantEdgeAdjudicator.CITATION,
['pubmed:4', 'pubmed:123'],
type='list_of_string')
cid = net.create_edge(edge_source=0,
edge_target=1,
edge_interaction='controls-state-change-of')
self.assertEqual('neighbor-of', net.get_edge(nid)['i'])
adjud._remove_if_redundant(net, nid, [cid], mergecitations=True)
self.assertEqual(None, net.get_edge(nid))
res = net.get_edge_attribute(cid, RedundantEdgeAdjudicator.CITATION)
res['v'].sort()
self.assertEqual(['pubmed:123', 'pubmed:4'], res['v'])
def test_update_network_with_pmc_citation(self):
updator = InvalidEdgeCitationRemover()
net = NiceCXNetwork()
noattredge = net.create_edge(edge_source=0,
edge_target=1,
edge_interaction='foo')
t_edge = net.create_edge(edge_source=2,
edge_target=3,
edge_interaction='blah')
net.set_edge_attribute(t_edge,
InvalidEdgeCitationRemover.CITATION_ATTRIB,
['pubmed:PMC3619734'],
type='list_of_string')
issues = updator.update(net)
self.assertEqual(1, len(issues))
self.assertTrue('Replacing' in issues[0])
res = net.get_edge_attribute(
t_edge, InvalidEdgeCitationRemover.CITATION_ATTRIB)
self.assertEqual(['pubmed:15109499'], res['v'])
def test_update_network_containing_all_types(self):
updator = DirectEdgeAttributeUpdator()
net = NiceCXNetwork()
noattredge = net.create_edge(edge_source=0, edge_target=1,
edge_interaction='foo')
t_edge = net.create_edge(edge_source=2, edge_target=3,
edge_interaction='blah')
net.set_edge_attribute(t_edge,
DirectEdgeAttributeUpdator.DIRECTED_ATTRIB,
't', type='string')
f_edge = net.create_edge(edge_source=3, edge_target=4,
edge_interaction='blah')
net.set_edge_attribute(f_edge,
DirectEdgeAttributeUpdator.DIRECTED_ATTRIB,
'f', type='string')
o_edge = net.create_edge(edge_source=3, edge_target=4,
edge_interaction='blah')
net.set_edge_attribute(o_edge,
DirectEdgeAttributeUpdator.DIRECTED_ATTRIB,
'blah', type='string')
self.assertEqual([],
updator.update(net))
d_attrib = DirectEdgeAttributeUpdator.DIRECTED_ATTRIB
res = net.get_edge_attribute(noattredge, d_attrib)
self.assertEqual((None, None), res)
res = net.get_edge_attribute(t_edge, d_attrib)
self.assertEqual(res['v'], True)
res = net.get_edge_attribute(f_edge, d_attrib)
self.assertEqual(res['v'], False)
res = net.get_edge_attribute(o_edge, d_attrib)
self.assertEqual(res['v'], False)
class NiceCxAssembler(object):
"""Assembles a Nice CX network from a set of INDRA Statements.
Parameters
----------
stmts : Optional[list[indra.statements.Statement]]
A list of INDRA Statements to be assembled.
network_name : Optional[str]
The name of the network to be assembled. Default: indra_assembled
Attributes
----------
network : ndex2.nice_cx_network.NiceCXNetwork
A Nice CX network object that is assembled from Statements.
"""
def __init__(self, stmts=None, network_name=None):
self.statements = stmts if stmts else []
self.network = NiceCXNetwork()
self.network.set_network_attribute(
'name', (network_name if network_name else 'indra_assembled'))
self.node_keys = {}
self.context_prefixes = {
'pubmed': 'https://identifiers.org/pubmed:',
'hgnc.symbol': 'https://identifiers.org/hgnc.symbol:'
}
def make_model(self, self_loops=False, network_attributes=None):
"""Return a Nice CX network object after running assembly.
Parameters
----------
self_loops : Optional[bool]
If False, self-loops are excluded from the network. Default: False
network_attributes : Optional[dict]
A dictionary containing attributes to be added to the
assembled network.
Returns
-------
ndex2.nice_cx_network.NiceCXNetwork
The assembled Nice CX network.
"""
for stmt in self.statements:
agents = stmt.agent_list()
not_none_agents = [a for a in agents if a is not None]
if len(not_none_agents) < 2:
continue
for a1, a2 in itertools.combinations(not_none_agents, 2):
a1_id = self.add_node(a1)
a2_id = self.add_node(a2)
if not self_loops and a1_id == a2_id:
continue
edge_id = self.add_edge(a1_id, a2_id, stmt)
self.network.set_network_attribute('@context',
json.dumps(self.context_prefixes))
if network_attributes:
for k, v in network_attributes.items():
self.network.set_network_attribute(k, v, 'string')
return self.network
def add_node(self, agent):
"""Add an Agent to the network as a node."""
agent_key = self.get_agent_key(agent)
# If the node already exists
if agent_key in self.node_keys:
return self.node_keys[agent_key]
# If the node doesn't exist yet
db_ns, db_id = agent.get_grounding()
# TODO: handle more represents name spaces
if db_ns == 'HGNC':
represents = 'hgnc.symbol:%s' % agent.name
else:
represents = None
node_id = self.network.create_node(agent.name,
node_represents=represents)
self.node_keys[agent_key] = node_id
# Add db_refs as aliases
db_refs_list = [
'%s:%s' % (db_name, db_id)
for db_name, db_id in agent.db_refs.items()
if db_name in url_prefixes
]
if db_refs_list:
self.network.add_node_attribute(property_of=node_id,
name='aliases',
values=db_refs_list,
type='list_of_string')
# Add the type of the node, inferred from grounding
if db_ns:
mapped_type = db_ns_type_mappings.get(db_ns)
if mapped_type:
self.network.add_node_attribute(property_of=node_id,
name='type',
values=mapped_type,
type='string')
return node_id
def add_edge(self, a1_id, a2_id, stmt):
"""Add a Statement to the network as an edge."""
stmt_type = stmt.__class__.__name__
edge_id = self.network.create_edge(a1_id, a2_id, stmt_type)
evs = []
for ev in stmt.evidence:
# We skip evidences with no PMID
if not ev.pmid:
continue
# We take a maximum 200 character snippet of the evidence text
if not ev.text:
ev_txt = 'Evidence text not available.'
elif len(ev.text) > 200:
ev_txt = ev.text[:200] + '...'
else:
ev_txt = ev.text
# Construct a clickable PMID link with the source and evidence text
ev_str = ('<a target="_blank" '
'href="https://identifiers.org/pubmed:%s">'
'pubmed:%s</a> (%s) %s') % (ev.pmid, ev.pmid,
ev.source_api, ev_txt)
evs.append((ev_str, 0 if ev.text is None else 1))
# Reorder to have ones with text first
evs = sorted(evs, key=lambda x: x[1], reverse=True)
# Cap at 10 pieces of evidence
evs = [e[0] for e in evs[:10]]
self.network.set_edge_attribute(edge_id,
'citation',
evs,
type='list_of_string')
return edge_id
def print_model(self):
"""Return the CX string of the assembled model."""
return self.network.to_cx()
@staticmethod
def get_agent_key(agent):
return agent.name
def test_update(self):
collapser = RedundantEdgeCollapser()
net = NiceCXNetwork()
ctext = {'pubmed': 'http://p/'}
net.set_network_attribute('@context', values=json.dumps(ctext))
collapser._set_pubmedurl_from_network(net)
eid = net.create_edge(edge_source=0,
edge_target=1,
edge_interaction='something')
net.set_edge_attribute(eid, 'sentence', 'sent1', type='string')
net.set_edge_attribute(eid, 'direct', True, type='boolean')
net.set_edge_attribute(eid, 'citation', 'pubmed:123', type='string')
eidtwo = net.create_edge(edge_source=0,
edge_target=1,
edge_interaction='something')
net.set_edge_attribute(eidtwo, 'sentence', 'sent2', type='string')
net.set_edge_attribute(eidtwo, 'direct', True, type='boolean')
net.set_edge_attribute(eidtwo, 'citation', 'pubmed:456', type='string')
res = collapser.update(net)
self.assertEqual([], res)
edata = net.get_edge_attribute(eid, 'sentence')
self.assertEqual(2, len(edata['v']))
self.assertTrue('<a target="_blank" href="http://p/456">'
'pubmed:456</a> sent2' in edata['v'])
self.assertTrue('<a target="_blank" href="http://p/123">'
'pubmed:123</a> sent1' in edata['v'])
def test_update_network_containing_several_citations(self):
updator = InvalidEdgeCitationRemover()
net = NiceCXNetwork()
noattredge = net.create_edge(edge_source=0,
edge_target=1,
edge_interaction='foo')
t_edge = net.create_edge(edge_source=2,
edge_target=3,
edge_interaction='blah')
net.set_edge_attribute(t_edge,
InvalidEdgeCitationRemover.CITATION_ATTRIB, [],
type='list_of_string')
v_edge = net.create_edge(edge_source=3,
edge_target=4,
edge_interaction='blah')
net.set_edge_attribute(v_edge,
InvalidEdgeCitationRemover.CITATION_ATTRIB,
['pubmed:1234'],
type='list_of_string')
o_edge = net.create_edge(edge_source=3,
edge_target=4,
edge_interaction='blah')
net.set_edge_attribute(o_edge,
InvalidEdgeCitationRemover.CITATION_ATTRIB,
['pubmed:Other'],
type='list_of_string')
neg_edge = net.create_edge(edge_source=5,
edge_target=6,
edge_interaction='blah')
net.set_edge_attribute(neg_edge,
InvalidEdgeCitationRemover.CITATION_ATTRIB,
['pubmed:-100', 'pubmed:5'],
type='list_of_string')
issues = updator.update(net)
self.assertEqual(2, len(issues))
self.assertTrue('Removing invalid citation id: '
'pubmed:Other on edge id: ' + str(o_edge) in issues)
self.assertTrue('Removing invalid citation id: '
'pubmed:-100 on edge id: ' + str(neg_edge) in issues)
d_attrib = InvalidEdgeCitationRemover.CITATION_ATTRIB
res = net.get_edge_attribute(noattredge, d_attrib)
self.assertEqual((None, None), res)
res = net.get_edge_attribute(t_edge, d_attrib)
self.assertEqual([], res['v'])
res = net.get_edge_attribute(v_edge, d_attrib)
self.assertEqual(['pubmed:1234'], res['v'])
res = net.get_edge_attribute(o_edge, d_attrib)
self.assertEqual([], res['v'])
res = net.get_edge_attribute(neg_edge, d_attrib)
self.assertEqual(['pubmed:5'], res['v'])
print(NiceCX_creatures.create_edge("C", "D"))
print(NiceCX_creatures.create_edge("B", "C"))
# #### add_edge(edge)
# In[ ]:
#This method has been deprecated. Please use create_edge()
# #### set_edge_attribute(edge, attribute_name, values, type=None, subnetwork=None)
# In[ ]:
NiceCX_creatures = NiceCXNetwork()
edge_id = NiceCX_creatures.create_edge("A", "B")
NiceCX_creatures.set_edge_attribute(edge_id, "new edge attribute",
"edge attribute value is nnnnn")
# #### get_edge_attribute(edge, attribute_name, subnetwork=None)
# In[ ]:
NiceCX_creatures = NiceCXNetwork()
edge_id = NiceCX_creatures.create_edge("A", "B")
NiceCX_creatures.set_edge_attribute(edge_id, "new edge attribute",
"new edge attribute value is nnnnn")
NiceCX_creatures.get_edge_attribute(edge_id, "new edge attribute")
# #### get_edge_attribute_objects(edge, attribute_name)
# In[ ]:
def test_two_node_one_edge_network(self):
net = NiceCXNetwork()
net.create_node('first')
net.create_node('second')
edge_one = net.create_edge(edge_source=0, edge_target=1)
net.set_name('bob')
net.set_edge_attribute(edge_one,
'booleanattrib',
'false',
type='boolean')
net.set_edge_attribute(edge_one, 'integerattrib', '1', type='integer')
net.set_edge_attribute(edge_one, 'doubleattrib', '2.0', type='double')
net.set_edge_attribute(edge_one, 'longattrib', '3', type='long')
net.set_edge_attribute(edge_one,
'stringattrib',
'false',
type='string')
net.set_edge_attribute(edge_one,
'list_of_booleanattrib', ['True'],
type='list_of_boolean')
net.set_edge_attribute(edge_one,
'list_of_doubleattrib', ['4.0'],
type='list_of_double')
net.set_edge_attribute(edge_one,
'list_of_integerattrib', ['5'],
type='list_of_integer')
net.set_edge_attribute(edge_one,
'list_of_longattrib', ['6'],
type='list_of_long')
net.set_edge_attribute(edge_one,
'list_of_stringattrib', ['false'],
type='list_of_string')
fac = DefaultNetworkXFactory()
g = fac.get_graph(net)
self.assertEqual('bob', g.graph['name'])
self.assertEqual(2, len(g))
self.assertEqual(1, g.number_of_edges())
self.assertTrue(0 in g)
if NETWORKX_MAJOR_VERSION >= 2:
nodelist = list(g.nodes(data=True))
edgelist = list(g.edges(data=True))
else:
nodelist = g.nodes(data=True)
edgelist = g.edges(data=True)
self.assertEqual('first', nodelist[0][1]['name'])
self.assertEqual('second', nodelist[1][1]['name'])
self.assertEqual(0, edgelist[0][0])
self.assertEqual(1, edgelist[0][1])
self.assertEqual(None, edgelist[0][2]['interaction'])
self.assertEqual('false', edgelist[0][2]['booleanattrib'])
self.assertEqual('1', edgelist[0][2]['integerattrib'])
self.assertEqual('2.0', edgelist[0][2]['doubleattrib'])
self.assertEqual('3', edgelist[0][2]['longattrib'])
self.assertEqual('false', edgelist[0][2]['stringattrib'])
self.assertEqual(['True'], edgelist[0][2]['list_of_booleanattrib'])
self.assertEqual(['4.0'], edgelist[0][2]['list_of_doubleattrib'])
self.assertEqual(['5'], edgelist[0][2]['list_of_integerattrib'])
self.assertEqual(['6'], edgelist[0][2]['list_of_longattrib'])
self.assertEqual(['false'], edgelist[0][2]['list_of_stringattrib'])
