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# -*- coding: utf-8 -*-
"""Test summary functions for edges."""
import unittest
from collections import Counter
from pybel import BELGraph
from pybel.dsl import protein
from pybel.examples import sialic_acid_graph
from pybel.language import Entity
from pybel.struct.summary.edge_summary import (
count_annotations,
get_annotation_values,
get_annotation_values_by_annotation,
get_annotations,
get_unused_annotations,
get_unused_list_annotation_values,
iter_annotation_value_pairs,
iter_annotation_values,
)
from pybel.testing.utils import n
class TestEdgeSummary(unittest.TestCase):
"""Test summary functions for edges."""
def test_1(self):
"""Test iterating over annotation/value pairs."""
graph = BELGraph()
graph.annotation_list.update(
{
"A": set("1234"),
"B": set("XYZ"),
"C": set("abcde"),
}
)
u = protein("HGNC", name="U")
v = protein("HGNC", name="V")
w = protein("HGNC", name="W")
graph.add_increases(u, v, evidence=n(), citation=n(), annotations={"A": {"1", "2"}, "B": {"X"}})
graph.add_increases(
u,
w,
evidence=n(),
citation=n(),
annotations={
"A": {"1", "3"},
"C": {"a"},
},
)
graph.add_increases(
w,
v,
evidence=n(),
citation=n(),
)
x = dict(Counter((key, entity.identifier) for key, entity in iter_annotation_value_pairs(graph)))
self.assertEqual(
{
("A", "1"): 2,
("A", "2"): 1,
("A", "3"): 1,
("B", "X"): 1,
("C", "a"): 1,
},
x,
)
y = Counter(iter_annotation_values(graph, "A"))
self.assertEqual(x["A", "1"] + x["A", "2"] + x["A", "3"], sum(y.values()))
y = Counter(iter_annotation_values(graph, "B"))
self.assertEqual(x["B", "X"], sum(y.values()))
y = Counter(iter_annotation_values(graph, "C"))
self.assertEqual(x["C", "a"], sum(y.values()))
def test_get_annotation_values(self):
"""Test getting annotation values."""
expected = {
"Confidence": {
Entity(namespace="Confidence", identifier="High"),
Entity(namespace="Confidence", identifier="Low"),
},
"Species": {
Entity(namespace="Species", identifier="9606"),
},
}
self.assertEqual({"Confidence", "Species"}, get_annotations(sialic_acid_graph))
self.assertEqual({"Confidence": 8, "Species": 8}, dict(count_annotations(sialic_acid_graph)))
annotation_values_by_annotation = get_annotation_values_by_annotation(sialic_acid_graph)
self.assertEqual(expected, annotation_values_by_annotation)
annotation_values = get_annotation_values(sialic_acid_graph, "Confidence")
self.assertEqual(expected["Confidence"], annotation_values)
def test_get_unused_annotation_url(self):
graph = BELGraph()
name = n()
graph.annotation_url[name] = n()
self.assertEqual({name}, get_unused_annotations(graph))
def test_get_unused_annotation_pattern(self):
graph = BELGraph()
name = n()
graph.annotation_pattern[name] = n()
self.assertEqual({name}, get_unused_annotations(graph))
def test_get_unused_annotation_list(self):
graph = BELGraph()
name = n()
graph.annotation_pattern[name] = {n(), n(), n()}
self.assertEqual({name}, get_unused_annotations(graph))
def test_get_unused_annotation_list_values(self):
"""Test getting unused annotation list values."""
graph = BELGraph()
annotation_key = "test"
graph.annotation_list[annotation_key] = set("abc")
graph.add_increases(
protein(n(), n()),
protein(n(), n()),
citation=n(),
evidence=n(),
annotations={annotation_key: {"a"}},
)
rv = get_unused_list_annotation_values(graph)
self.assertIsInstance(rv, dict)
self.assertEqual({annotation_key: set("bc")}, rv)
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