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_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_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_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_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_edge_with_no_edgecitation(self):
updator = EmptyCitationAttributeRemover()
net = NiceCXNetwork()
edgeid = net.create_edge(edge_source=0, edge_target=1,
edge_interaction='foo')
self.assertEqual([], updator.update(net))
self.assertEqual((None, None), net.get_edge_attribute(edgeid,
'citation'))
def test_with_network_with_edge_not_supposed_to_be_directed(self):
setter = DirectedEdgeSetter()
net = NiceCXNetwork()
edgeid = net.create_edge(edge_source=0,
edge_target=1,
edge_interaction='foo')
self.assertEqual([], setter.update(net))
directed = DirectedEdgeSetter.DIRECTED_ATTRIB
self.assertEqual(False, net.get_edge_attribute(edgeid, directed)['v'])
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_no_edgecitation(self):
updator = EmptyCitationAttributeUpdator()
net = NiceCXNetwork()
edgeid = net.create_edge(edge_source=0,
edge_target=1,
edge_interaction='foo')
self.assertEqual([], updator.update(net))
edge = net.get_edge_attribute(edgeid, 'citation')
self.assertEqual([], edge['v'])
self.assertEqual('list_of_string', edge['d'])
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_emptypubmedcitation(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=['pubmed:'],
type='list_of_string')
self.assertEqual([], updator.update(net))
edge = net.get_edge_attribute(edgeid, 'citation')
self.assertEqual([], edge['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)
def test_with_network_with_edges_that_are_directed(self):
setter = DirectedEdgeSetter()
net = NiceCXNetwork()
directed = DirectedEdgeSetter.DIRECTED_ATTRIB
cntr = 1
for entry in loadndexncipidloader.DIRECTED_INTERACTIONS:
edgeid = net.create_edge(edge_source=0,
edge_target=cntr,
edge_interaction=entry)
self.assertEqual([], setter.update(net))
self.assertEqual(True,
net.get_edge_attribute(edgeid, directed)['v'])
cntr = cntr + 1
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'])
# 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[ ]:
#This method has been deprecated. Please use get_edge_attributes()
# #### get_edge_attributes(edge)
# In[ ]:
NiceCX_creatures = NiceCXNetwork()
edge_id = NiceCX_creatures.create_edge("A", "B")
# add 5 attributes to the edge
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'])