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# -*- coding: utf-8 -*-
"""Tests for the query builder."""
import logging
import unittest
from pybel import BELGraph, Pipeline
from pybel.dsl import Protein
from pybel.examples.egf_example import egf_graph, vcp
from pybel.examples.homology_example import (
homology_graph,
mouse_csf1_protein,
mouse_csf1_rna,
mouse_mapk1_protein,
mouse_mapk1_rna,
)
from pybel.examples.sialic_acid_example import (
cd33_phosphorylated,
dap12,
shp1,
shp2,
sialic_acid_graph,
syk,
trem2,
)
from pybel.struct import (
expand_node_neighborhood,
expand_nodes_neighborhoods,
get_subgraph_by_annotation_value,
)
from pybel.struct.mutation import collapse_to_genes, enrich_protein_and_rna_origins
from pybel.struct.query import Query, QueryMissingNetworksError, Seeding
from pybel.testing.generate import generate_random_graph
from pybel.testing.mock_manager import MockQueryManager
from pybel.testing.utils import n
log = logging.getLogger(__name__)
def add(query, manager, graph):
network = manager.insert_graph(graph)
query.append_network(network.id)
class TestSeedingConstructor(unittest.TestCase):
def test_none(self):
"""Test construction of a seeding container."""
seeding = Seeding()
self.assertEqual(0, len(seeding))
self.assertEqual("[]", seeding.dumps())
def test_append_sample(self):
seeding = Seeding()
seeding.append_sample()
self.assertEqual(1, len(seeding))
s = seeding.dumps()
self.assertIsInstance(s, str)
class TestQueryConstructor(unittest.TestCase):
"""Test the construction of a Query."""
def test_network_ids_none(self):
query = Query()
self.assertIsInstance(query.network_ids, list)
self.assertIsInstance(query.seeding, Seeding)
self.assertIsInstance(query.pipeline, Pipeline)
self.assertEqual(0, len(query.network_ids))
def test_network_ids_single(self):
query = Query(network_ids=1)
self.assertIsInstance(query.network_ids, list)
self.assertEqual(1, len(query.network_ids))
def test_network_ids_multiple(self):
query = Query(network_ids=[1, 2, 3])
self.assertIsInstance(query.network_ids, list)
self.assertEqual(3, len(query.network_ids))
def test_network_ids_type_error(self):
with self.assertRaises(TypeError):
Query(network_ids="a")
def test_seeding(self):
query = Query(seeding=Seeding())
self.assertEqual(0, len(query.seeding))
def test_pipeline(self):
query = Query(pipeline=Pipeline())
self.assertEqual(0, len(query.pipeline))
class QueryTestEgf(unittest.TestCase):
"""Test querying the EGF subgraph"""
def setUp(self):
"""Set up each test with a mock query manager."""
self.manager = MockQueryManager()
self.query = Query()
def add_query(self, graph):
add(self.query, self.manager, graph)
return self.query
def run_query(self):
return self.query.run(self.manager)
def test_fail_run_with_no_networks(self):
with self.assertRaises(QueryMissingNetworksError):
self.run_query()
def test_no_seeding_no_pipeline(self):
graph = egf_graph.copy()
self.add_query(graph)
result = self.run_query()
self.assertEqual(graph.number_of_nodes(), result.number_of_nodes())
self.assertEqual(graph.number_of_edges(), result.number_of_edges())
def test_seed_by_neighbor(self):
graph = BELGraph()
a, b, c, d = (Protein(namespace=n(), name=str(i)) for i in range(4))
graph.add_increases(a, b, citation=n(), evidence=n())
graph.add_increases(b, c, citation=n(), evidence=n())
graph.add_increases(c, d, citation=n(), evidence=n())
self.add_query(graph).append_seeding_neighbors(b)
result = self.run_query()
self.assertIsInstance(result, BELGraph)
# test nodes
self.assertIn(a, result)
self.assertIn(b, result)
self.assertIn(c, result)
self.assertNotIn(d, result)
# test edges
self.assertIn(b, result[a])
self.assertIn(c, result[b])
self.assertNotIn(d, result[c])
def test_seed_by_neighbors(self):
graph = BELGraph()
a, b, c, d, e = (Protein(namespace=n(), name=str(i)) for i in range(5))
graph.add_increases(a, b, citation=n(), evidence=n())
graph.add_increases(b, c, citation=n(), evidence=n())
graph.add_increases(c, d, citation=n(), evidence=n())
graph.add_increases(d, e, citation=n(), evidence=n())
self.add_query(graph).append_seeding_neighbors([b, c])
result = self.run_query()
self.assertIsInstance(result, BELGraph)
# test nodes
self.assertIn(a, result)
self.assertIn(b, result)
self.assertIn(c, result)
self.assertIn(d, result)
self.assertNotIn(e, result)
# test edges
self.assertIn(b, result[a])
self.assertIn(c, result[b])
self.assertIn(d, result[c])
self.assertNotIn(e, result[d])
def test_random_sample(self):
"""Test generating multiple random samples and combining them."""
graph = generate_random_graph(50, 1000)
query = self.add_query(graph)
query.append_seeding_sample(number_edges=10)
query.append_seeding_sample(number_edges=10)
result = self.run_query()
self.assertIn(
result.number_of_edges(),
{16, 17, 18, 19, 20},
msg="This will rail randomly sometimes, lol",
)
class QueryTest(unittest.TestCase):
"""Test the query"""
def setUp(self):
"""Setup each test with an empty mock query manager."""
self.manager = MockQueryManager()
def test_pipeline(self):
graph = egf_graph.copy()
enrich_protein_and_rna_origins(graph)
self.assertEqual(
32, # 10 protein nodes already there + complex + bp + 2*10 (genes and rnas)
graph.number_of_nodes(),
)
# 6 already there + 5 complex hasComponent edges + new 2*10 edges
self.assertEqual(31, graph.number_of_edges())
network = self.manager.insert_graph(graph)
pipeline = Pipeline()
pipeline.append(collapse_to_genes)
query = Query(network_ids=[network.id], pipeline=pipeline)
result_graph = query.run(self.manager)
self.assertEqual(12, result_graph.number_of_nodes()) # same number of nodes than there were
self.assertEqual(11, result_graph.number_of_edges()) # same number of edges than there were
def test_pipeline_2(self):
graph = egf_graph.copy()
network = self.manager.insert_graph(graph)
network_id = network.id
query = Query(network_ids=[network_id])
query.append_seeding_neighbors(vcp)
query.append_pipeline(get_subgraph_by_annotation_value, "Species", "9606")
result = query.run(self.manager)
self.assertIsNotNone(result, msg="Query returned none")
self.assertEqual(3, result.number_of_nodes())
def test_query_multiple_networks(self):
sialic_acid_graph_id = self.manager.insert_graph(sialic_acid_graph.copy()).id
egf_graph_id = self.manager.insert_graph(egf_graph.copy()).id
query = Query()
query.append_network(sialic_acid_graph_id)
query.append_network(egf_graph_id)
query.append_seeding_neighbors([syk])
query.append_pipeline(enrich_protein_and_rna_origins)
result = query.run(self.manager)
self.assertIsNotNone(result, msg="Query returned none")
self.assertIn(shp1, result)
self.assertIn(shp2, result)
self.assertIn(trem2, result)
self.assertIn(dap12, result)
self.assertEqual(15, result.number_of_nodes())
self.assertEqual(14, result.number_of_edges())
def test_get_subgraph_by_annotation_value(self):
graph = homology_graph.copy()
result = get_subgraph_by_annotation_value(graph, "Species", "10090")
self.assertIsNotNone(result, msg="Query returned none")
self.assertIsInstance(result, BELGraph)
self.assertLess(0, result.number_of_nodes())
self.assertIn(mouse_mapk1_protein, result, msg="nodes:\n{}".format(list(map(repr, graph))))
self.assertIn(mouse_csf1_protein, result)
self.assertEqual(2, result.number_of_nodes())
self.assertEqual(1, result.number_of_edges())
def test_seeding_1(self):
test_network_1 = self.manager.insert_graph(homology_graph.copy())
query = Query(network_ids=[test_network_1.id])
query.append_seeding_neighbors([mouse_csf1_rna, mouse_mapk1_rna])
result = query.run(self.manager)
self.assertIsNotNone(result, msg="Query returned none")
self.assertIsInstance(result, BELGraph)
self.assertIn(mouse_mapk1_rna, result)
self.assertIn(mouse_csf1_rna, result)
self.assertIn(mouse_mapk1_protein, result)
self.assertIn(mouse_csf1_protein, result)
self.assertEqual(6, result.number_of_nodes())
self.assertEqual(4, result.number_of_edges())
def test_seeding_with_pipeline(self):
test_network_1 = self.manager.insert_graph(sialic_acid_graph.copy())
query = Query(network_ids=[test_network_1.id])
query.append_seeding_neighbors([trem2, dap12, shp2])
query.append_pipeline(expand_nodes_neighborhoods, [trem2, dap12, shp2])
result = query.run(self.manager)
self.assertIsNotNone(result, msg="Query returned none")
self.assertIsInstance(result, BELGraph)
self.assertIn(trem2, result)
self.assertIn(dap12, result)
self.assertIn(shp2, result)
self.assertIn(syk, result)
self.assertIn(cd33_phosphorylated, result)
self.assertEqual(5, result.number_of_nodes())
self.assertEqual(4, result.number_of_edges())
def test_query_multiple_networks_with_api(self):
test_network_1 = self.manager.insert_graph(homology_graph.copy())
pipeline = Pipeline()
pipeline.append(expand_node_neighborhood, mouse_mapk1_protein)
query = Query(network_ids=[test_network_1.id], pipeline=pipeline)
query.append_seeding_annotation("Species", {"10090"})
result = query.run(self.manager)
self.assertIsNotNone(result, msg="Query returned none")
self.assertEqual(3, result.number_of_nodes())
self.assertIn(mouse_mapk1_protein, result)
self.assertIn(mouse_csf1_protein, result)
self.assertEqual(2, result.number_of_edges())
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