def test_none_passed_into_get_graph(self):
fac = LegacyNetworkXVersionTwoPlusFactory()
try:
fac.get_graph(None)
self.fail('Expected NDExError')
except NDExError as ne:
self.assertEqual('Input network is None', str(ne))
def test_empty_network_passed_in_with_various_legacy_modes(self):
net = NiceCXNetwork()
fac = LegacyNetworkXVersionTwoPlusFactory()
g = fac.get_graph(net)
self.assertTrue(isinstance(g, networkx.Graph))
self.assertEqual(0, len(g))
self.assertEqual(0, g.number_of_edges())
def test_empty_network_passed_in_with_various_legacy_modes(self):
net = NiceCXNetwork()
fac = LegacyNetworkXVersionTwoPlusFactory()
g = fac.get_graph(net)
self.assertTrue(isinstance(g, networkx.Graph))
self.assertEqual(0, len(g))
self.assertEqual(0, g.number_of_edges())
def test_none_passed_into_get_graph(self):
fac = LegacyNetworkXVersionTwoPlusFactory()
try:
fac.get_graph(None)
self.fail('Expected NDExError')
except NDExError as ne:
self.assertEqual('Input network is None', str(ne))
def test_one_node_no_edge_network(self):
net = NiceCXNetwork()
net.create_node('first')
net.set_name('bob')
fac = LegacyNetworkXVersionTwoPlusFactory()
g = fac.get_graph(net)
self.assertEqual('bob', g.graph['name'])
self.assertEqual(1, len(g))
self.assertEqual(0, g.number_of_edges())
self.assertTrue('first' in g)
nodelist = g.nodes(data=True)
self.assertEqual('first', nodelist['first']['represents'])
def test_darktheme_network(self):
net = ndex2\
.create_nice_cx_from_file(TestLegacyNetworkXVersionTwoPlusFactory
.DARKTHEME_FILE)
fac = LegacyNetworkXVersionTwoPlusFactory()
g = fac.get_graph(net)
self.assertEqual('Dark theme final version', g.graph['name'])
self.assertTrue('Perfetto L.,' in g.graph['reference'])
self.assertEqual('Theodora Pavlidou', g.graph['author'])
self.assertEqual('SIGNOR-EGF', g.graph['labels'])
self.assertEqual('18-Jan-2019', g.graph['version'])
self.assertEqual('Human, 9606, H**o sapiens', g.graph['organism'])
self.assertEqual('SIGNOR-EGF', g.graph['labels'])
self.assertTrue('epidermal growth factor' in g.graph['description'])
self.assertEqual(34, len(g))
self.assertEqual(50, g.number_of_edges())
self.assertTrue('STAT3' in g)
self.assertTrue('MAX' in g)
nodelist = list(g.nodes(data=True))
edgelist = list(g.edges(data=True))
statthree = -1
for i in range(0, len(nodelist)):
if nodelist[i][0] == 'STAT3':
statthree = i
break
self.assertEqual('STAT3', nodelist[statthree][0])
self.assertEqual('protein', nodelist[statthree][1]['type'])
self.assertEqual('uniprot:P40763',
nodelist[statthree][1]['represents'])
stat_edge = -2
for i in range(0, len(edgelist)):
if edgelist[i][0] == 'STAT3' and edgelist[i][1] == 'JAK1/' \
'STAT1/STAT3':
stat_edge = i
break
if edgelist[i][0] == 'JAK1/STAT1/' \
'STAT3' and edgelist[i][1] == 'STAT3':
stat_edge = i
break
self.assertTrue(stat_edge >= 0)
self.assertEqual('form complex', edgelist[stat_edge][2]['interaction'])
self.assertEqual('true', edgelist[stat_edge][2]['directed'])
self.assertEqual('"pubmed:15284024"',
edgelist[stat_edge][2]['citation'])
# check coordinates
self.assertTrue((g.pos[1655][0] + 90.96) < 1.0)
self.assertTrue((g.pos[1655][1] - 145.72) < 1.0)
def test_one_node_no_edge_network(self):
net = NiceCXNetwork()
net.create_node('first')
net.set_name('bob')
fac = LegacyNetworkXVersionTwoPlusFactory()
g = fac.get_graph(net)
self.assertEqual('bob', g.graph['name'])
self.assertEqual(1, len(g))
self.assertEqual(0, g.number_of_edges())
self.assertTrue('first' in g)
nodelist = g.nodes(data=True)
self.assertEqual('first', nodelist['first']['represents'])
def test_darktheme_network(self):
net = ndex2.create_nice_cx_from_file(TestLegacyNetworkXVersionTwoPlusFactory.DARKTHEME_FILE)
fac = LegacyNetworkXVersionTwoPlusFactory()
g = fac.get_graph(net)
self.assertEqual('Dark theme final version', g.graph['name'])
self.assertTrue('Perfetto L.,' in g.graph['reference'])
self.assertEqual('Theodora Pavlidou', g.graph['author'])
self.assertEqual('SIGNOR-EGF', g.graph['labels'])
self.assertEqual('18-Jan-2019', g.graph['version'])
self.assertEqual('Human, 9606, H**o sapiens', g.graph['organism'])
self.assertEqual('SIGNOR-EGF', g.graph['labels'])
self.assertTrue('epidermal growth factor' in g.graph['description'])
self.assertEqual(34, len(g))
self.assertEqual(50, g.number_of_edges())
self.assertTrue('STAT3' in g)
self.assertTrue('MAX' in g)
nodelist = list(g.nodes(data=True))
edgelist = list(g.edges(data=True))
statthree = -1
for i in range(0, len(nodelist)):
if nodelist[i][0] == 'STAT3':
statthree = i
break
self.assertEqual('STAT3', nodelist[statthree][0])
self.assertEqual('protein', nodelist[statthree][1]['type'])
self.assertEqual('uniprot:P40763', nodelist[statthree][1]['represents'])
stat_edge = -2
for i in range(0, len(edgelist)):
if edgelist[i][0] == 'STAT3' and edgelist[i][1] == 'JAK1/STAT1/STAT3':
stat_edge = i
break
if edgelist[i][0] == 'JAK1/STAT1/STAT3' and edgelist[i][1] == 'STAT3':
stat_edge = i
break
self.assertTrue(stat_edge >= 0)
self.assertEqual('form complex', edgelist[stat_edge][2]['interaction'])
self.assertEqual('true', edgelist[stat_edge][2]['directed'])
self.assertEqual('"pubmed:15284024"', edgelist[stat_edge][2]['citation'])
# check coordinates
self.assertTrue((g.pos[1655][0] + 90.96) < 1.0)
self.assertTrue((g.pos[1655][1] - 145.72) < 1.0)
def test_two_node_one_edge_network(self):
net = NiceCXNetwork()
net.create_node('first')
net.create_node('second')
net.create_edge(edge_source=0, edge_target=1)
net.set_name('bob')
fac = LegacyNetworkXVersionTwoPlusFactory()
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('first' in g)
self.assertTrue('second' in g)
edgelist = list(g.edges(data=True))
self.assertTrue(('first' == edgelist[0][0] and 'second' == edgelist[0][1]) or
('second' == edgelist[0][0] and 'first' == edgelist[0][1]))
self.assertEqual(None, edgelist[0][2]['interaction'])
def test_two_node_one_edge_network(self):
net = NiceCXNetwork()
net.create_node('first')
net.create_node('second')
net.create_edge(edge_source=0, edge_target=1)
net.set_name('bob')
fac = LegacyNetworkXVersionTwoPlusFactory()
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('first' in g)
self.assertTrue('second' in g)
edgelist = list(g.edges(data=True))
self.assertTrue(
('first' == edgelist[0][0] and 'second' == edgelist[0][1])
or ('second' == edgelist[0][0] and 'first' == edgelist[0][1]))
self.assertEqual(None, edgelist[0][2]['interaction'])
def test_glypican_network_legacyfalse(self):
net = ndex2\
.create_nice_cx_from_file(TestLegacyNetworkXVersionTwoPlusFactory
.GLYPICAN_FILE)
fac = LegacyNetworkXVersionTwoPlusFactory()
g = fac.get_graph(net)
self.assertEqual('Glypican 2 network', g.graph['name'])
self.assertEqual('', g.graph['reference'])
self.assertEqual('Mirko von Elstermann', g.graph['author'])
self.assertEqual('Jorge Filmus', g.graph['reviewers'])
self.assertEqual('glypican_2pathway', g.graph['labels'])
self.assertEqual('APR-2018', g.graph['version'])
self.assertEqual('human', g.graph['organism'])
self.assertEqual('<i>Glypican 2 network</i> was derived from '
'the latest BioPAX3 version of the Pathway '
'Interaction Database (PID) curated by NCI/Nature. '
'The BioPAX was first converted to Extended Binary '
'SIF (EBS) by the PAXTools v5 utility. It was then '
'processed to remove redundant edges, to add a '
'\'directed flow\' layout, and to add a graphic '
'style using Cytoscape Visual Properties. This '
'network can be found in searches using its original '
'PID accession id, present in the \'labels\' '
'property.', g.graph['description'])
self.assertEqual(2, len(g))
self.assertEqual(1, g.number_of_edges())
self.assertTrue('MDK' in g)
self.assertTrue('GPC2' in g)
nodelist = list(g.nodes(data=True))
edgelist = list(g.edges(data=True))
mdk = -1
for i in range(0, len(nodelist)):
if nodelist[i][0] == 'MDK':
mdk = i
break
self.assertEqual('MDK', nodelist[mdk][0])
self.assertEqual('Protein', nodelist[mdk][1]['type'])
aliaslist = nodelist[mdk][1]['alias']
self.assertEqual(2, len(aliaslist))
self.assertTrue('uniprot knowledgebase:Q2LEK4' in aliaslist)
self.assertTrue('uniprot knowledgebase:Q9UCC7' in aliaslist)
gp = -1
for i in range(0, len(nodelist)):
if nodelist[i][0] == 'GPC2':
gp = i
break
self.assertEqual('GPC2', nodelist[gp][0])
self.assertEqual('Protein', nodelist[gp][1]['type'])
aliaslist = nodelist[gp][1]['alias']
self.assertEqual(1, len(aliaslist))
self.assertTrue('uniprot knowledgebase:Q8N158' in aliaslist)
self.assertTrue(('MDK' == edgelist[0][0] and 'GPC2',
edgelist[0][1]) or
('GPC2' == edgelist[0][0] and 'MDK',
edgelist[0][1]))
self.assertEqual('in-complex-with', edgelist[0][2]['interaction'])
self.assertEqual('false', edgelist[0][2]['directed'])
# check coordinates
self.assertTrue((g.pos[0][0] + 398.3) < 1.0)
self.assertTrue((g.pos[0][1] - 70.71) < 1.0)
self.assertTrue((g.pos[1][0] + 353.49) < 1.0)
self.assertTrue((g.pos[1][1] - 70.71) < 1.0)
def test_glypican_network_legacyfalse(self):
net = ndex2.create_nice_cx_from_file(TestLegacyNetworkXVersionTwoPlusFactory.GLYPICAN_FILE)
fac = LegacyNetworkXVersionTwoPlusFactory()
g = fac.get_graph(net)
self.assertEqual('Glypican 2 network', g.graph['name'])
self.assertEqual('', g.graph['reference'])
self.assertEqual('Mirko von Elstermann', g.graph['author'])
self.assertEqual('Jorge Filmus', g.graph['reviewers'])
self.assertEqual('glypican_2pathway', g.graph['labels'])
self.assertEqual('APR-2018', g.graph['version'])
self.assertEqual('human', g.graph['organism'])
self.assertEqual('<i>Glypican 2 network</i> was derived from '
'the latest BioPAX3 version of the Pathway '
'Interaction Database (PID) curated by NCI/Nature. '
'The BioPAX was first converted to Extended Binary '
'SIF (EBS) by the PAXTools v5 utility. It was then '
'processed to remove redundant edges, to add a '
'\'directed flow\' layout, and to add a graphic '
'style using Cytoscape Visual Properties. This '
'network can be found in searches using its original '
'PID accession id, present in the \'labels\' '
'property.', g.graph['description'])
self.assertEqual(2, len(g))
self.assertEqual(1, g.number_of_edges())
self.assertTrue('MDK' in g)
self.assertTrue('GPC2' in g)
nodelist = list(g.nodes(data=True))
edgelist = list(g.edges(data=True))
mdk = -1
for i in range(0, len(nodelist)):
if nodelist[i][0] == 'MDK':
mdk = i
break
self.assertEqual('MDK', nodelist[mdk][0])
self.assertEqual('Protein', nodelist[mdk][1]['type'])
aliaslist = nodelist[mdk][1]['alias']
self.assertEqual(2, len(aliaslist))
self.assertTrue('uniprot knowledgebase:Q2LEK4' in aliaslist)
self.assertTrue('uniprot knowledgebase:Q9UCC7' in aliaslist)
gp = -1
for i in range(0, len(nodelist)):
if nodelist[i][0] == 'GPC2':
gp = i
break
self.assertEqual('GPC2', nodelist[gp][0])
self.assertEqual('Protein', nodelist[gp][1]['type'])
aliaslist = nodelist[gp][1]['alias']
self.assertEqual(1, len(aliaslist))
self.assertTrue('uniprot knowledgebase:Q8N158' in aliaslist)
self.assertTrue(('MDK' == edgelist[0][0] and 'GPC2', edgelist[0][1]) or
('GPC2' == edgelist[0][0] and 'MDK', edgelist[0][1]))
self.assertEqual('in-complex-with', edgelist[0][2]['interaction'])
self.assertEqual('false', edgelist[0][2]['directed'])
# check coordinates
self.assertTrue((g.pos[0][0] + 398.3) < 1.0)
self.assertTrue((g.pos[0][1] - 70.71) < 1.0)
self.assertTrue((g.pos[1][0] + 353.49) < 1.0)
self.assertTrue((g.pos[1][1] - 70.71) < 1.0)