1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
|
# -*- coding: utf-8 -*-
from pybel.examples import sialic_acid_graph
from pybel.examples.sialic_acid_example import (
cd33,
cd33_phosphorylated,
shp2,
syk,
trem2,
)
from pybel.manager.models import Edge, Namespace, Network
from pybel.manager.query_manager import graph_from_edges
from pybel.resources import CHEBI_URL, GO_URL, HGNC_URL
from pybel.testing.cases import TemporaryCacheClsMixin
from pybel.testing.mocks import mock_bel_resources
class TestSeeding(TemporaryCacheClsMixin):
"""This module tests the seeding functions in the query manager."""
@classmethod
def setUpClass(cls):
"""Add the Sialic Acid subgraph for all query tests."""
super().setUpClass()
with mock_bel_resources:
cls.manager.insert_graph(sialic_acid_graph)
def test_namespace_existence(self):
"""Check the sialic acid graph has the right namespaces, and they're uploaded properly."""
ns = self.manager.session.query(Namespace).filter(Namespace.url == HGNC_URL).one()
self.assertIsNotNone(ns)
ns = self.manager.session.query(Namespace).filter(Namespace.url == CHEBI_URL).one()
self.assertIsNotNone(ns)
ns = self.manager.session.query(Namespace).filter(Namespace.url == GO_URL).one()
self.assertIsNotNone(ns)
def test_sialic_acid_in_node_store(self):
r = "sialic acid"
n = self.manager.get_namespace_entry(CHEBI_URL, r)
self.assertIsNotNone(n)
self.assertEqual(r, n.name)
def test_network_existence(self):
networks = self.manager.session.query(Network).all()
self.assertEqual(1, len(networks))
def test_edge_existence(self):
edges = self.manager.session.query(Edge).all()
self.assertEqual(11, len(edges))
def test_seed_by_pmid(self):
pmids = ["26438529"]
edges = self.manager.query_edges_by_pubmed_identifiers(pmids)
self.assertLessEqual(1, len(edges))
def test_seed_by_pmid_no_result(self):
missing_pmids = ["11111"]
edges = self.manager.query_edges_by_pubmed_identifiers(missing_pmids)
self.assertEqual(0, len(edges))
def test_seed_by_induction_raise(self):
"""Test that seeding by induction fails when an empty list is given."""
with self.assertRaises(ValueError):
self.manager.query_induction([])
def test_seed_by_induction_raise_length_one(self):
"""Test that seeding by induction fails when a list of length one is given."""
shp2_model = self.manager.get_node_by_dsl(shp2)
with self.assertRaises(ValueError):
self.manager.query_induction([shp2_model])
def test_seed_by_induction(self):
"""Test seeding by inducing over a list of nodes."""
shp2_model = self.manager.get_node_by_dsl(shp2)
self.assertIsNotNone(shp2_model)
syk_model = self.manager.get_node_by_dsl(syk)
self.assertIsNotNone(syk_model)
trem2_model = self.manager.get_node_by_dsl(trem2)
self.assertIsNotNone(trem2_model)
edges = self.manager.query_induction([shp2_model, syk_model, trem2_model])
self.assertEqual(2, len(edges))
graph = graph_from_edges(edges)
self.assertEqual(3, graph.number_of_nodes())
self.assertIn(trem2, graph)
self.assertIn(syk, graph)
self.assertIn(shp2, graph)
self.assertEqual(3, graph.number_of_nodes())
self.assertEqual(2, graph.number_of_edges())
def test_seed_by_neighbors(self):
"""Test seeding a graph by neighbors of a list of nodes."""
shp2_model = self.manager.get_node_by_dsl(shp2)
self.assertIsNotNone(shp2_model)
edges = self.manager.query_neighbors([shp2_model])
self.assertEqual(2, len(edges))
graph = graph_from_edges(edges)
self.assertEqual(3, graph.number_of_edges())
self.assertEqual(4, graph.number_of_nodes())
self.assertIn(cd33_phosphorylated, graph)
self.assertIn(cd33, graph)
self.assertIn(syk, graph)
self.assertIn(shp2, graph)
self.assertEqual(3, graph.number_of_edges())
|
