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# -*- coding: utf-8 -*-
"""Tests for PyBEL induction functions."""
import string
import unittest
from pybel import BELGraph
from pybel.constants import (
CITATION_AUTHORS,
CITATION_TYPE_PUBMED,
IDENTIFIER,
NAMESPACE,
)
from pybel.dsl import BaseEntity, gene, protein, rna
from pybel.struct.mutation.expansion import expand_upstream_causal
from pybel.struct.mutation.induction import get_subgraph_by_annotation_value
from pybel.struct.mutation.induction.citation import (
get_subgraph_by_authors,
get_subgraph_by_pubmed,
)
from pybel.struct.mutation.induction.paths import (
get_nodes_in_all_shortest_paths,
get_subgraph_by_all_shortest_paths,
)
from pybel.struct.mutation.induction.upstream import get_upstream_causal_subgraph
from pybel.struct.mutation.induction.utils import get_subgraph_by_induction
from pybel.testing.utils import n
trem2_gene = gene(namespace="HGNC", name="TREM2")
trem2_rna = rna(namespace="HGNC", name="TREM2")
trem2_protein = protein(namespace="HGNC", name="TREM2")
class TestGraphMixin(unittest.TestCase):
"""A mixin to enable testing nodes and edge membership in the graph."""
def assert_in_edge(self, source, target, graph):
"""Assert the edge is in the graph.
:param source:
:param target:
:type graph: pybel.BELGraph
:rtype: bool
"""
self.assertIn(target, graph[source])
def assert_all_nodes_are_base_entities(self, graph):
"""Assert that all nodes are base entities."""
for node in graph:
self.assertIsInstance(node, BaseEntity)
class TestInduction(TestGraphMixin):
"""Test induction functions."""
def test_get_subgraph_by_induction(self):
"""Test get_subgraph_by_induction."""
graph = BELGraph()
keyword, url = n(), n()
graph.namespace_url[keyword] = url
a, b, c, d = [protein(namespace="test", name=str(i)) for i in range(4)]
graph.add_directly_increases(a, b, citation=n(), evidence=n())
graph.add_directly_increases(b, c, citation=n(), evidence=n())
graph.add_directly_increases(c, d, citation=n(), evidence=n())
graph.add_increases(a, d, citation=n(), evidence=n())
nodes = [b, c]
subgraph = get_subgraph_by_induction(graph, nodes)
self.assertIsInstance(subgraph, BELGraph)
self.assert_all_nodes_are_base_entities(subgraph)
self.assertNotEqual(
0,
len(subgraph.namespace_url),
msg="improperly found metadata: {}".format(subgraph.graph),
)
self.assertIn(keyword, subgraph.namespace_url)
self.assertEqual(url, subgraph.namespace_url[keyword])
self.assertNotIn(a, subgraph)
self.assertIn(b, subgraph)
self.assertIn(c, subgraph)
self.assertNotIn(d, subgraph)
def test_get_subgraph_by_all_shortest_paths(self):
"""Test get_subgraph_by_all_shortest_paths."""
graph = BELGraph()
keyword, url = n(), n()
graph.namespace_url[keyword] = url
a, b, c, d, e, f = [protein(namespace="test", name=n()) for _ in range(6)]
graph.add_increases(a, b, citation=n(), evidence=n())
graph.add_increases(a, c, citation=n(), evidence=n())
graph.add_increases(b, d, citation=n(), evidence=n())
graph.add_increases(c, d, citation=n(), evidence=n())
graph.add_increases(a, e, citation=n(), evidence=n())
graph.add_increases(e, f, citation=n(), evidence=n())
graph.add_increases(f, d, citation=n(), evidence=n())
query_nodes = [a, d]
shortest_paths_nodes = get_nodes_in_all_shortest_paths(graph, query_nodes)
self.assertIn(a, shortest_paths_nodes)
self.assertIn(b, shortest_paths_nodes)
self.assertIn(c, shortest_paths_nodes)
self.assertIn(d, shortest_paths_nodes)
subgraph = get_subgraph_by_all_shortest_paths(graph, query_nodes)
self.assert_all_nodes_are_base_entities(subgraph)
self.assertIsInstance(subgraph, BELGraph)
self.assertIn(keyword, subgraph.namespace_url)
self.assertEqual(url, subgraph.namespace_url[keyword])
self.assertIn(a, subgraph)
self.assertIn(b, subgraph)
self.assertIn(c, subgraph)
self.assertIn(d, subgraph)
self.assertNotIn(e, subgraph)
self.assertNotIn(f, subgraph)
def test_get_upstream_causal_subgraph(self):
"""Test get_upstream_causal_subgraph."""
a, b, c, d, e, f = [protein(namespace="test", name=n()) for _ in range(6)]
universe = BELGraph()
universe.namespace_pattern["test"] = "test-url"
universe.add_increases(a, b, citation=n(), evidence=n())
universe.add_increases(b, c, citation=n(), evidence=n())
universe.add_association(d, a, citation=n(), evidence=n())
universe.add_increases(e, a, citation=n(), evidence=n())
universe.add_decreases(f, b, citation=n(), evidence=n())
subgraph = get_upstream_causal_subgraph(universe, [a, b])
self.assertIsInstance(subgraph, BELGraph)
self.assert_all_nodes_are_base_entities(subgraph)
self.assertIn("test", subgraph.namespace_pattern)
self.assertEqual("test-url", subgraph.namespace_pattern["test"])
self.assertIn(a, subgraph)
self.assertIn(b, subgraph)
self.assertNotIn(c, subgraph)
self.assertNotIn(d, subgraph)
self.assertIn(e, subgraph)
self.assertIn(f, subgraph)
self.assertEqual(4, subgraph.number_of_nodes())
self.assert_in_edge(e, a, subgraph)
self.assert_in_edge(a, b, subgraph)
self.assert_in_edge(f, b, subgraph)
self.assertEqual(3, subgraph.number_of_edges())
def test_expand_upstream_causal_subgraph(self):
"""Test expanding on the upstream causal subgraph."""
a, b, c, d, e, f = [protein(namespace="test", name=i) for i in string.ascii_lowercase[:6]]
universe = BELGraph()
universe.add_increases(a, b, citation=n(), evidence=n())
universe.add_increases(b, c, citation=n(), evidence=n())
universe.add_association(d, a, citation=n(), evidence=n())
universe.add_increases(e, a, citation=n(), evidence=n())
universe.add_decreases(f, b, citation=n(), evidence=n())
subgraph = BELGraph()
subgraph.add_increases(a, b, citation=n(), evidence=n())
expand_upstream_causal(universe, subgraph)
self.assertIsInstance(subgraph, BELGraph)
self.assert_all_nodes_are_base_entities(subgraph)
self.assertIn(a, subgraph)
self.assertIn(b, subgraph)
self.assertNotIn(c, subgraph)
self.assertNotIn(d, subgraph)
self.assertIn(e, subgraph)
self.assertIn(f, subgraph)
self.assertEqual(4, subgraph.number_of_nodes())
self.assert_in_edge(e, a, subgraph)
self.assert_in_edge(a, b, subgraph)
self.assert_in_edge(f, b, subgraph)
self.assertEqual(2, len(subgraph[a][b]))
self.assertEqual(4, subgraph.number_of_edges(), msg="\n".join(map(str, subgraph.edges())))
class TestEdgePredicateBuilders(TestGraphMixin):
"""Tests for edge predicate builders."""
def test_build_pmid_inclusion_filter(self):
"""Test getting a sub-graph by a single PubMed identifier."""
a, b, c, d = [protein(namespace="test", name=n()) for _ in range(4)]
p1, p2, p3, p4 = n(), n(), n(), n()
graph = BELGraph()
keyword, url = n(), n()
graph.namespace_url[keyword] = url
graph.add_increases(a, b, evidence=n(), citation=p1)
graph.add_increases(a, b, evidence=n(), citation=p2)
graph.add_increases(b, c, evidence=n(), citation=p1)
graph.add_increases(b, c, evidence=n(), citation=p3)
graph.add_increases(c, d, evidence=n(), citation=p3)
subgraph = get_subgraph_by_pubmed(graph, p1)
self.assertIsInstance(subgraph, BELGraph)
self.assert_all_nodes_are_base_entities(subgraph)
self.assertIn(keyword, subgraph.namespace_url)
self.assertEqual(url, subgraph.namespace_url[keyword])
self.assertIn(a, subgraph)
self.assertIn(b, subgraph)
self.assertIn(c, subgraph)
self.assertNotIn(d, subgraph)
empty_subgraph = get_subgraph_by_pubmed(graph, p4)
self.assertIn(keyword, subgraph.namespace_url)
self.assertEqual(url, subgraph.namespace_url[keyword])
self.assertEqual(0, empty_subgraph.number_of_nodes())
def test_build_pmid_set_inclusion_filter(self):
"""Test getting a sub-graph by a set of PubMed identifiers."""
a, b, c, d, e, f = [protein(namespace="test", name=n()) for _ in range(6)]
p1, p2, p3, p4, p5, p6 = n(), n(), n(), n(), n(), n()
graph = BELGraph()
keyword, url = n(), n()
graph.namespace_url[keyword] = url
graph.add_increases(a, b, evidence=n(), citation=p1)
graph.add_increases(a, b, evidence=n(), citation=p2)
graph.add_increases(b, c, evidence=n(), citation=p1)
graph.add_increases(b, c, evidence=n(), citation=p3)
graph.add_increases(c, d, evidence=n(), citation=p3)
graph.add_increases(e, f, evidence=n(), citation=p4)
subgraph = get_subgraph_by_pubmed(graph, [p1, p4])
self.assertIsInstance(subgraph, BELGraph)
self.assert_all_nodes_are_base_entities(subgraph)
self.assertIn(keyword, subgraph.namespace_url)
self.assertEqual(url, subgraph.namespace_url[keyword])
self.assertIn(a, subgraph)
self.assertIn(b, subgraph)
self.assertIn(c, subgraph)
self.assertNotIn(d, subgraph)
self.assertIn(e, subgraph)
self.assertIn(f, subgraph)
empty_subgraph = get_subgraph_by_pubmed(graph, [p5, p6])
self.assertIn(keyword, subgraph.namespace_url)
self.assertEqual(url, subgraph.namespace_url[keyword])
self.assertEqual(0, empty_subgraph.number_of_nodes())
def test_build_author_inclusion_filter(self):
"""Test getting a sub-graph by a single author."""
a, b, c, d = [protein(namespace="test", name=n()) for _ in range(4)]
a1, a2, a3, a4, a5 = n(), n(), n(), n(), n()
c1 = {
NAMESPACE: CITATION_TYPE_PUBMED,
IDENTIFIER: n(),
CITATION_AUTHORS: [a1, a2, a3],
}
c2 = {
NAMESPACE: CITATION_TYPE_PUBMED,
IDENTIFIER: n(),
CITATION_AUTHORS: [a1, a4],
}
graph = BELGraph()
keyword, url = n(), n()
graph.namespace_url[keyword] = url
graph.add_increases(a, b, evidence=n(), citation=c1)
graph.add_increases(a, b, evidence=n(), citation=c2)
graph.add_increases(b, c, evidence=n(), citation=c1)
graph.add_increases(c, d, evidence=n(), citation=c2)
subgraph1 = get_subgraph_by_authors(graph, a1)
self.assertIsInstance(subgraph1, BELGraph)
self.assert_all_nodes_are_base_entities(subgraph1)
self.assertIn(keyword, subgraph1.namespace_url)
self.assertEqual(url, subgraph1.namespace_url[keyword])
self.assertIn(a, subgraph1)
self.assertIn(b, subgraph1)
self.assertIn(c, subgraph1)
self.assertIn(d, subgraph1)
subgraph2 = get_subgraph_by_authors(graph, a2)
self.assertIsInstance(subgraph2, BELGraph)
self.assert_all_nodes_are_base_entities(subgraph2)
self.assertIn(keyword, subgraph2.namespace_url)
self.assertEqual(url, subgraph2.namespace_url[keyword])
self.assertIn(a, subgraph2)
self.assertIn(b, subgraph2)
self.assertIn(c, subgraph2)
self.assertNotIn(d, subgraph2)
subgraph3 = get_subgraph_by_authors(graph, a5)
self.assertIsInstance(subgraph3, BELGraph)
self.assert_all_nodes_are_base_entities(subgraph3)
self.assertIn(keyword, subgraph3.namespace_url)
self.assertEqual(url, subgraph3.namespace_url[keyword])
self.assertEqual(0, subgraph3.number_of_nodes())
def test_build_author_set_inclusion_filter(self):
"""Test getting a sub-graph by a set of authors."""
a, b, c, d = [protein(namespace="test", name=n()) for _ in range(4)]
a1, a2, a3, a4 = n(), n(), n(), n()
c1 = {
NAMESPACE: CITATION_TYPE_PUBMED,
IDENTIFIER: n(),
CITATION_AUTHORS: [a1, a2, a3],
}
c2 = {
NAMESPACE: CITATION_TYPE_PUBMED,
IDENTIFIER: n(),
CITATION_AUTHORS: [a1, a4],
}
graph = BELGraph()
keyword, url = n(), n()
graph.namespace_url[keyword] = url
graph.add_increases(a, b, evidence=n(), citation=c1)
graph.add_increases(a, b, evidence=n(), citation=c2)
graph.add_increases(b, c, evidence=n(), citation=c1)
graph.add_increases(c, d, evidence=n(), citation=c2)
subgraph1 = get_subgraph_by_authors(graph, [a1, a2])
self.assertIsInstance(subgraph1, BELGraph)
self.assert_all_nodes_are_base_entities(subgraph1)
self.assertIn(keyword, subgraph1.namespace_url)
self.assertEqual(url, subgraph1.namespace_url[keyword])
self.assertIn(a, subgraph1)
self.assertIn(b, subgraph1)
self.assertIn(c, subgraph1)
self.assertIn(d, subgraph1)
class TestEdgeInduction(unittest.TestCase):
"""Test induction over edges."""
def test_get_subgraph_by_annotation_value(self):
"""Test getting a subgraph by a single annotation value."""
graph = BELGraph()
graph.annotation_url["Subgraph"] = n()
a, b, c, d = [protein(namespace="test", name=n()) for _ in range(4)]
k1 = graph.add_increases(a, b, citation=n(), evidence=n(), annotations={"Subgraph": {"A"}})
k2 = graph.add_increases(a, b, citation=n(), evidence=n(), annotations={"Subgraph": {"B"}})
k3 = graph.add_increases(a, b, citation=n(), evidence=n(), annotations={"Subgraph": {"A", "C", "D"}})
subgraph = get_subgraph_by_annotation_value(graph, "Subgraph", "A")
self.assertIsInstance(subgraph, BELGraph)
self.assertIn(a, subgraph)
self.assertIn(b, subgraph)
self.assertIn(b, subgraph[a])
self.assertIn(k1, subgraph[a][b])
self.assertNotIn(k2, subgraph[a][b])
self.assertIn(k3, subgraph[a][b])
def test_get_subgraph_by_annotation_values(self):
"""Test getting a subgraph by multiple annotation value."""
graph = BELGraph()
graph.annotation_list["Subgraph"] = set("ABCDE")
a, b, c, d = [protein(namespace="test", name=n()) for _ in range(4)]
k1 = graph.add_increases(a, b, citation=n(), evidence=n(), annotations={"Subgraph": {"A"}})
k2 = graph.add_increases(a, b, citation=n(), evidence=n(), annotations={"Subgraph": {"B"}})
k3 = graph.add_increases(a, b, citation=n(), evidence=n(), annotations={"Subgraph": {"A", "C", "D"}})
k4 = graph.add_increases(a, b, citation=n(), evidence=n(), annotations={"Subgraph": {"C", "D"}})
subgraph = get_subgraph_by_annotation_value(graph, "Subgraph", {"A", "C"})
self.assertIsInstance(subgraph, BELGraph)
self.assertIn(a, subgraph)
self.assertIn(b, subgraph)
self.assertIn(b, subgraph[a])
self.assertIn(k1, subgraph[a][b])
self.assertNotIn(k2, subgraph[a][b])
self.assertIn(k3, subgraph[a][b])
self.assertIn(k4, subgraph[a][b])
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