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_basic_network_where_neighbor_of_citations_merges(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: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(None, net.get_edge(nid))
self.assertEqual(None, net.get_edge(cid))
self.assertEqual('someother', net.get_edge(oid)['i'])
res = net.get_edge_attribute(oid, RedundantEdgeAdjudicator.CITATION)
res['v'].sort()
self.assertEqual(['pubmed:5'], res['v'])
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_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_create_edge_with_int_for_edge_ids(self):
net = NiceCXNetwork()
net.create_edge(edge_source=0, edge_target=1)
res = net.get_edge(0)
self.assertEqual(0, res[constants.EDGE_ID])
self.assertEqual(0, res[constants.EDGE_SOURCE])
self.assertEqual(1, res[constants.EDGE_TARGET])
def test_create_edge_with_interaction(self):
net = NiceCXNetwork()
edge_id = net.create_edge(edge_source=10, edge_target=20, edge_interaction='blah')
res = net.get_edge(edge_id)
self.assertEqual(edge_id, res[constants.EDGE_ID])
self.assertEqual(10, res[constants.EDGE_SOURCE])
self.assertEqual(20, res[constants.EDGE_TARGET])
self.assertEqual('blah', res[constants.EDGE_INTERACTION])
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_create_edge_with_node_dict_passed_in_for_edge_ids(self):
net = NiceCXNetwork()
nodeone = net.get_node(net.create_node('node1'))
nodetwo = net.get_node(net.create_node('node2'))
edge_id = net.create_edge(edge_source=nodeone,
edge_target=nodetwo)
res = net.get_edge(edge_id)
self.assertEqual(edge_id, res[constants.EDGE_ID])
self.assertEqual(0, res[constants.EDGE_SOURCE])
self.assertEqual(1, res[constants.EDGE_TARGET])
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'])