def test_create_network_symmetric_wrong_input():
"""Test if function is used with non-symmetric scores object"""
scores = create_dummy_scores()
msnet = SimilarityNetwork()
with pytest.raises(AssertionError) as msg:
msnet.create_network(scores)
expected_msg = "Expected symmetric scores object with queries==references"
assert expected_msg in str(msg), "Expected different exception"
def test_create_network_symmetric_modified_cosine():
"""Test creating a graph from a symmetric Scores object using ModifiedCosine"""
cutoff = 0.7
scores = create_dummy_scores_symmetric_modified_cosine()
msnet = SimilarityNetwork(score_cutoff=cutoff)
msnet.create_network(scores)
edges_list = list(msnet.graph.edges())
edges_list.sort()
assert len(edges_list) == 28, "Expected different number of edges"
def test_create_network_symmetric_higher_cutoff():
cutoff = 0.9
scores = create_dummy_scores_symmetric()
msnet = SimilarityNetwork(score_cutoff=cutoff)
msnet.create_network(scores)
edges_list = list(msnet.graph.edges())
edges_list.sort()
assert len(edges_list) == 1, "Expected only one link"
assert edges_list[0][0] in ['query_spec_0', 'ref_spec_4'], \
"Expected different node to have a link"
assert edges_list[0][1] in ['query_spec_0', 'ref_spec_4'], \
"Expected different node to have a link"
def test_create_network_symmetric():
"""Test creating a graph from a symmetric Scores object"""
cutoff = 0.7
scores = create_dummy_scores_symmetric()
msnet = SimilarityNetwork(score_cutoff=cutoff)
msnet.create_network(scores)
nodes_list = list(msnet.graph.nodes())
edges_list = list(msnet.graph.edges())
edges_list.sort()
nodes_without_edges = ['ref_spec_0', 'ref_spec_1', 'ref_spec_2']
assert len(nodes_list) == 8, "Expected different number of nodes"
assert len(edges_list) == 5, "Expected different number of edges"
assert np.all([(x[0] not in nodes_without_edges) for x in edges_list]), \
"Expected this node to have no edges"
assert np.all([(x[1] not in nodes_without_edges) for x in edges_list]), \
"Expected this node to have no edges"
def test_create_network_symmetric_remove_unconnected_nodes():
"""Test if unconnected nodes are removed"""
cutoff = 0.7
scores = create_dummy_scores_symmetric()
msnet = SimilarityNetwork(score_cutoff=cutoff,
keep_unconnected_nodes=False)
msnet.create_network(scores)
nodes_list = list(msnet.graph.nodes())
edges_list = list(msnet.graph.edges())
edges_list.sort()
nodes_with_edges = [
'query_spec_0', 'ref_spec_4', 'query_spec_2', 'ref_spec_3',
'query_spec_1'
]
assert len(nodes_list) == 5, "Expected different number of nodes"
assert np.all([(x in nodes_with_edges) for x in nodes_list]), \
"Expected this node to have edges"
def test_create_network_export_to_graphml(filename):
"""Test creating a graph from a symmetric Scores object using ModifiedCosine"""
cutoff = 0.7
scores = create_dummy_scores_symmetric_modified_cosine()
msnet = SimilarityNetwork(score_cutoff=cutoff)
msnet.create_network(scores)
msnet.export_to_graphml(filename)
assert os.path.isfile(filename), "graphml file not found"
def test_create_network_symmetric_mutual_method():
"""Test creating a graph from a Scores object"""
cutoff = 0.7
scores = create_dummy_scores_symmetric()
# change some scores
scores.scores[7, 6] = scores.scores[6, 7] = 0.85
scores.scores[7, 5] = scores.scores[5, 7] = 0.75
scores.scores[7, 3] = scores.scores[3, 7] = 0.7
msnet = SimilarityNetwork(score_cutoff=cutoff,
top_n=3,
max_links=3,
link_method="mutual")
msnet.create_network(scores)
nodes_with_edges = [
'query_spec_0', 'query_spec_1', 'query_spec_2', 'ref_spec_4'
]
edges_list = list(msnet.graph.edges())
edges_list.sort()
assert len(edges_list) == 4, "Expected four links"
assert np.all([(x[0] in nodes_with_edges)
for x in edges_list]), "Expected different edges in graph"
assert np.all([(x[1] in nodes_with_edges)
for x in edges_list]), "Expected different edges in graph"