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# -*- coding: utf-8 -*-
"""Tests for the query builder."""
import logging
import unittest
from pybel import BELGraph
from pybel.dsl import Protein
from pybel.examples.egf_example import egf_graph
from pybel.struct.query import Seeding
from pybel.testing.generate import generate_random_graph
from pybel.testing.utils import n
log = logging.getLogger(__name__)
class TestSeedingConstructor(unittest.TestCase):
def test_none(self):
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)
def test_no_seeding(self):
graph = egf_graph.copy()
seeding = Seeding()
result = seeding.run(graph)
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())
seeding = Seeding()
seeding.append_neighbors(b)
result = seeding.run(graph)
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())
seeding = Seeding()
seeding.append_neighbors([b, c])
result = seeding.run(graph)
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):
graph = generate_random_graph(50, 1000)
seeding = Seeding()
seeding.append_sample(number_edges=10)
seeding.append_sample(number_edges=10)
result = seeding.run(graph)
# TODO this will fail randomly some times lol, so make allowed to be sort of wrong
self.assertIn(result.number_of_edges(), {18, 19, 20})
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