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# -*- coding: utf-8 -*-
"""Tests for functions for grouping BEL graphs into sub-graphs."""
import unittest
from pybel import BELGraph
from pybel.constants import CITATION_TYPE_PUBMED
from pybel.dsl import protein
from pybel.language import Entity
from pybel.struct.grouping import get_subgraphs_by_annotation, get_subgraphs_by_citation
from pybel.testing.utils import n
test_namespace_url = n()
test_annotation_url = n()
citation, evidence = n(), n()
a, b, c, d = [protein(namespace="test", name=str(i)) for i in range(4)]
class TestAnnotation(unittest.TestCase):
"""Tests for getting sub-graphs by annotation."""
def setUp(self):
"""Set up the test case with a pre-populated BEL graph."""
self.graph = BELGraph()
self.graph.namespace_url["test"] = test_namespace_url
self.graph.annotation_url["subgraph"] = test_annotation_url
self.graph.add_increases(
a,
b,
citation=citation,
evidence=evidence,
annotations={"subgraph": {"1", "2"}},
)
self.graph.add_increases(a, c, citation=citation, evidence=evidence, annotations={"subgraph": {"1"}})
self.graph.add_increases(
b,
d,
citation=citation,
evidence=evidence,
annotations={"subgraph": {"1", "2"}},
)
self.graph.add_increases(a, d, citation=citation, evidence=evidence, annotations={"subgraph": {"2"}})
self.graph.add_increases(c, d, citation=citation, evidence=evidence)
def test_get_subgraphs_by_annotation(self):
subgraphs = get_subgraphs_by_annotation(self.graph, annotation="subgraph")
self.assertEqual(2, len(subgraphs))
self.assertIn(Entity(namespace="subgraph", identifier="1"), subgraphs)
self.assertIn(Entity(namespace="subgraph", identifier="2"), subgraphs)
subgraph_1 = subgraphs[Entity(namespace="subgraph", identifier="1")]
self.assertIsInstance(subgraph_1, BELGraph)
self.assertIn("test", subgraph_1.namespace_url)
self.assertIn("subgraph", subgraph_1.annotation_url)
self.assertIn(a, subgraph_1)
self.assertIn(b, subgraph_1)
self.assertIn(c, subgraph_1)
self.assertIn(d, subgraph_1)
self.assertIn(b, subgraph_1[a])
self.assertIn(c, subgraph_1[a])
self.assertIn(d, subgraph_1[b])
self.assertNotIn(d, subgraph_1[a])
self.assertNotIn(d, subgraph_1[c])
subgraph_2 = subgraphs[Entity(namespace="subgraph", identifier="2")]
self.assertIsInstance(subgraph_2, BELGraph)
self.assertIn("test", subgraph_2.namespace_url)
self.assertIn("subgraph", subgraph_2.annotation_url)
self.assertIn(a, subgraph_2)
self.assertIn(b, subgraph_2)
self.assertNotIn(c, subgraph_2)
self.assertIn(d, subgraph_2)
self.assertIn(b, subgraph_2[a])
self.assertNotIn(c, subgraph_2[a])
self.assertIn(d, subgraph_2[b])
self.assertIn(d, subgraph_2[a])
def test_get_subgraphs_by_annotation_with_sentinel(self):
sentinel = n()
subgraphs = get_subgraphs_by_annotation(self.graph, annotation="subgraph", sentinel=sentinel)
self.assertEqual(3, len(subgraphs))
self.assertIn(Entity(namespace="subgraph", identifier="1"), subgraphs)
self.assertIn(Entity(namespace="subgraph", identifier="2"), subgraphs)
self.assertIn(sentinel, subgraphs)
class TestProvenance(unittest.TestCase):
"""Tests for getting sub-graphs by provenance information (citation, etc.)"""
def test_get_subgraphs_by_citation(self):
"""Test getting sub-graphs by citation."""
graph = BELGraph()
c1, c2, c3 = n(), n(), n()
graph.add_increases(a, b, citation=c1, evidence=n())
graph.add_increases(a, b, citation=c2, evidence=n())
graph.add_increases(b, c, citation=c1, evidence=n())
graph.add_increases(c, d, citation=c1, evidence=n())
graph.add_increases(a, d, citation=c3, evidence=n())
subgraphs = get_subgraphs_by_citation(graph)
# TODO tests for metadata
c1_pair = (CITATION_TYPE_PUBMED, c1)
self.assertIn(c1_pair, subgraphs)
c1_subgraph = subgraphs[c1_pair]
self.assertIn(a, c1_subgraph)
self.assertIn(b, c1_subgraph)
self.assertIn(c, c1_subgraph)
self.assertIn(d, c1_subgraph)
c2_pair = (CITATION_TYPE_PUBMED, c2)
self.assertIn(c2_pair, subgraphs)
c2_subgraph = subgraphs[c2_pair]
self.assertIn(a, c2_subgraph)
self.assertIn(b, c2_subgraph)
self.assertNotIn(c, c2_subgraph)
self.assertNotIn(d, c2_subgraph)
c3_pair = (CITATION_TYPE_PUBMED, c3)
self.assertIn(c3_pair, subgraphs)
c3_subgraph = subgraphs[c3_pair]
self.assertIn(a, c3_subgraph)
self.assertNotIn(b, c3_subgraph)
self.assertNotIn(c, c3_subgraph)
self.assertIn(d, c3_subgraph)
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