def test_build_edge_map_single_edge_of_each_type(self):
adjud = RedundantEdgeAdjudicator()
net = NiceCXNetwork()
# try empty network
neighbor, controls, other = adjud._build_edge_map(net)
self.assertEqual({}, neighbor)
self.assertEqual({}, controls)
self.assertEqual({}, other)
# try network with single neighbor, controls, and an another edge
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')
oid = net.create_edge(edge_source=0,
edge_target=1,
edge_interaction='somethingelse')
neighbor, controls, other = adjud._build_edge_map(net)
self.assertEqual(nid, neighbor[0][1])
self.assertEqual(nid, neighbor[1][0])
self.assertEqual({cid}, controls[0][1])
self.assertEqual({oid}, other[0][1])
def test_build_edge_map_multiple_edges_of_each_type(self):
# try network with multiple neighbor, controls, and an another edge
net = NiceCXNetwork()
adjud = RedundantEdgeAdjudicator()
nid = net.create_edge(edge_source=0,
edge_target=1,
edge_interaction='neighbor-of')
nidtwo = net.create_edge(edge_source=2,
edge_target=3,
edge_interaction='neighbor-of')
cid = net.create_edge(edge_source=0,
edge_target=1,
edge_interaction='controls-state-change-of')
cidtwo = net.create_edge(edge_source=3,
edge_target=4,
edge_interaction='controls-state-change-of')
oid = net.create_edge(edge_source=0,
edge_target=1,
edge_interaction='somethingelse')
oidtwo = net.create_edge(edge_source=5,
edge_target=6,
edge_interaction='anotherthingy')
neighbor, controls, other = adjud._build_edge_map(net)
self.assertEqual(nid, neighbor[0][1])
self.assertEqual(nid, neighbor[1][0])
self.assertEqual(nidtwo, neighbor[2][3])
self.assertEqual(nidtwo, neighbor[3][2])
self.assertEqual({cid}, controls[0][1])
self.assertEqual({cidtwo}, controls[3][4])
self.assertEqual({oid}, other[0][1])
self.assertEqual({oidtwo}, other[5][6])
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_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_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_edge_no_attributes(self):
adjud = RedundantEdgeAdjudicator()
net = NiceCXNetwork()
edgeid = net.create_edge(edge_source=0,
edge_target=1,
edge_interaction='foo')
self.assertEqual('foo', net.get_edge(edgeid)['i'])
adjud._remove_edge(net, edgeid)
self.assertEqual(None, net.get_edge(edgeid))
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_no_citation_on_edge(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')
self.assertEqual('neighbor-of', net.get_edge(nid)['i'])
adjud._remove_if_redundant(net, nid, [cid])
self.assertEqual(None, net.get_edge(nid))
def test_add_to_edge_map(self):
adjud = RedundantEdgeAdjudicator()
edgemap = {}
adjud._add_to_edge_map(edgemap, 0, 1, 2)
self.assertEqual({0}, edgemap[1][2])
self.assertEqual({0}, edgemap[2][1])
adjud._add_to_edge_map(edgemap, 0, 1, 2)
self.assertEqual({0}, edgemap[1][2])
self.assertEqual({0}, edgemap[2][1])
adjud._add_to_edge_map(edgemap, 1, 1, 2)
self.assertEqual({0, 1}, edgemap[1][2])
self.assertEqual({0, 1}, edgemap[2][1])
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_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_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_nonexistant_edge(self):
adjud = RedundantEdgeAdjudicator()
self.assertTrue('Removes' in adjud.get_description())
net = NiceCXNetwork()
adjud._remove_edge(net, 1)
def test_update_none_passed_in(self):
adjud = RedundantEdgeAdjudicator()
self.assertEqual(['Network passed in is None'], adjud.update(None))
def test_get_description(self):
adjud = RedundantEdgeAdjudicator()
self.assertTrue('Removes' in adjud.get_description())