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# -*- coding: utf-8 -*-
"""Tests for metadata transforations."""
import unittest
from pybel import BELGraph
from pybel.constants import (
ANNOTATIONS,
CITATION,
CITATION_AUTHORS,
CITATION_DATE,
CITATION_TYPE_PUBMED,
IDENTIFIER,
NAMESPACE,
)
from pybel.dsl import protein
from pybel.examples import sialic_acid_graph
from pybel.struct.mutation import (
add_annotation_value,
remove_annotation_value,
remove_extra_citation_metadata,
strip_annotations,
)
from pybel.testing.utils import n
class TestMetadata(unittest.TestCase):
"""Test metadata transformations."""
def test_strip_annotations(self):
"""Test the strip_annotation function."""
x = protein(namespace="HGNC", name="X")
y = protein(namespace="HGNC", name="X")
graph = BELGraph()
graph.annotation_list["A"] = set("ABC")
key = graph.add_increases(
x,
y,
citation="123456",
evidence="Fake",
annotations={"A": {"B": True}},
)
self.assertIn(ANNOTATIONS, graph[x][y][key])
strip_annotations(graph)
self.assertNotIn(ANNOTATIONS, graph[x][y][key])
def test_add_and_remove_annotation(self):
"""Test adding and removing annotations.
See: :func:`pybel.struct.mutation.add_annotation_value` and
:func:`pybel.struct.mutation.remove_annotation_value` functions.
"""
graph = sialic_acid_graph.copy()
annotation = "test-annotation"
value = "test-value"
url = n()
graph.annotation_url[annotation] = url
add_annotation_value(graph, annotation, value)
for u, v, d in graph.edges(data=True):
annotations = d.get(ANNOTATIONS)
if annotations is None:
continue
self.assertIn(annotation, annotations)
self.assertIn(value, annotations[annotation])
remove_annotation_value(graph, annotation, value)
for u, v, d in graph.edges(data=True):
annotations = d.get(ANNOTATIONS)
if annotations is None:
continue
annotation_values = annotations.get(annotation)
if annotation_values is None:
continue
self.assertNotIn(value, annotation_values)
def test_remove_citation_metadata(self):
"""Test removing citation metadata from a graph."""
x = protein(namespace="HGNC", name="X")
y = protein(namespace="HGNC", name="X")
graph = BELGraph()
graph.annotation_list["A"] = set("ABC")
k0 = graph.add_part_of(x, y)
k1 = graph.add_increases(
x,
y,
citation="123456",
evidence="Fake",
annotations={"A": {"B": True}},
)
k2 = graph.add_increases(
x,
y,
citation={
NAMESPACE: CITATION_TYPE_PUBMED,
IDENTIFIER: "12345678",
CITATION_DATE: "2018-12-10",
},
evidence="Fake",
annotations={"A": {"B": True}},
)
remove_extra_citation_metadata(graph)
self.assertNotIn(CITATION, graph[x][y][k0])
for k in k1, k2:
self.assertIn(CITATION, graph[x][y][k])
self.assertIn(NAMESPACE, graph[x][y][k][CITATION])
self.assertIn(IDENTIFIER, graph[x][y][k][CITATION])
self.assertNotIn(CITATION_DATE, graph[x][y][k][CITATION])
self.assertNotIn(CITATION_AUTHORS, graph[x][y][k][CITATION])
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