def test_has_nodetypes_actuallyhas(self, mock_keggapi_link):
mock_keggapi_link.return_value = [hsa_nodes, enzyme_nodes]
graph = kgu.kegg_link_graph("hsa", "enzyme")
self.assertTrue(kgu.has_nodetypes(graph))
def test_get_nodes_by_nodetype_missingnodetype(self, mock_keggapi_link):
mock_keggapi_link.return_value = [hsa_nodes, enzyme_nodes]
graph = kgu.kegg_link_graph("hsa", "enzyme")
with self.assertRaises(errors.MissingNodetypeError):
kgu.get_nodes_by_nodetype(graph, "map")
def test_get_nodes_by_nodetype_invalidgraph(self, mock_keggapi_link):
mock_keggapi_link.return_value = [hsa_nodes, enzyme_nodes]
graph = nx.Graph()
with self.assertRaises(errors.NotAKeggGraphError):
kgu.get_nodes_by_nodetype(graph, "hsa")
def test_get_nodes_by_nodetype(self, mock_keggapi_link):
mock_keggapi_link.return_value = [hsa_nodes, enzyme_nodes]
graph = kgu.kegg_link_graph("hsa", "enzyme")
self.assertEqual(
kgu.get_nodes_by_nodetype(graph, "hsa", return_dict=True),
dict.fromkeys(hsa_nodes, "hsa"))
def test_neighbor_graph_edges(self):
self.assertEqual(
set(
list(
kgu.neighbor_graph(testgraph, {
hsa_nodes[0]: 'hsa'
}).edges)[0]), set([hsa_nodes[0], enzyme_nodes[0]]))
def test_kegg_link_graph_returns_bipartite_graphs(self, mocker):
mocker.return_value = [hsa_nodes, enzyme_nodes]
graph = kgu.kegg_link_graph("hsa", "enzyme")
self.assertTrue(nx.is_bipartite(graph), "Graph is not bipartite")
def test_kegg_link_graph_adds_nodes(self, mock_keggapi_link):
mock_keggapi_link.return_value = [hsa_nodes, enzyme_nodes]
graph = kgu.kegg_link_graph("hsa", "enzyme")
self.assertTrue(
set(graph.nodes) == set(hsa_nodes + enzyme_nodes),
"Different number of nodes")
def test_kegg_link_graph_all_nodes_are_correctly_copied(self, mocker):
mocker.return_value = [hsa_nodes, enzyme_nodes]
graph = kgu.kegg_link_graph("hsa", "enzyme")
self.assertEqual(
len(hsa_nodes) + len(enzyme_nodes), len(graph.nodes),
"Not all nodes are being copied")
def test_has_nodetype_doesnthave(self):
graph = nx.Graph()
self.assertFalse(kgu.has_nodetypes(graph))
def test_neighbor_graph_nodes(self):
self.assertEqual(
set(kgu.neighbor_graph(testgraph, {
hsa_nodes[0]: "hsa"
}).nodes), set([hsa_nodes[0], enzyme_nodes[0]]))
def test_linked_nodes(self):
self.assertEqual(
kgu.linked_nodes(testgraph, hsa_nodes[0], return_dict=True),
{enzyme_nodes[0]: "enzyme"})
def test_unique_nodetypes(self):
self.assertEqual(kgu.get_unique_nodetypes(testgraph),
['enzyme', 'hsa'])
def test_get_nodes_by_nodetype_correct_nodetype_dict(self):
hsa_nodetypes = dict.fromkeys(hsa_nodes, "hsa")
self.assertEqual(
kgu.get_nodes_by_nodetype(testgraph, "hsa", return_dict=True),
hsa_nodetypes)