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# -*- coding: utf-8 -*-
import os
from pathlib import Path
from pybel import BELGraph, Manager
from pybel.constants import ANNOTATIONS
from pybel.resources import HGNC_URL
from pybel.testing.cases import TemporaryCacheClsMixin
from pybel.testing.constants import belns_dir_path
from pybel.testing.mocks import mock_bel_resources
from tests.constants import OPENBEL_ANNOTATION_RESOURCES
ns1 = Path(os.path.join(belns_dir_path, "disease-ontology.belns")).as_uri()
ns1_url = "http://resources.openbel.org/belframework/20150611/namespace/disease-ontology-ids.belns"
ns2 = Path(os.path.join(belns_dir_path, "mesh-diseases.belns")).as_uri()
ns2_url = "http://resources.openbel.org/belframework/20150611/namespace/mesh-diseases.belns"
CELL_LINE_URL = OPENBEL_ANNOTATION_RESOURCES + "cell-line.belanno"
CELL_LINE_KEYWORD = "CellLine"
class TestDefinitionManagers(TemporaryCacheClsMixin):
def _help_check_hgnc(self, manager: Manager) -> None:
"""Help check the HGNC namespace was loaded properly."""
entry = manager.get_namespace_entry(HGNC_URL, "MHS2")
self.assertIsNotNone(entry)
self.assertEqual("MHS2", entry.name)
self.assertIn("G", entry.encoding)
entry = manager.get_namespace_entry(HGNC_URL, "MIATNB")
self.assertIsNotNone(entry)
self.assertEqual("MIATNB", entry.name)
self.assertIn("G", entry.encoding)
self.assertIn("R", entry.encoding)
entry = manager.get_namespace_entry(HGNC_URL, "MIA")
self.assertIsNotNone(entry)
self.assertEqual("MIA", entry.name)
self.assertIn("G", entry.encoding)
self.assertIn("P", entry.encoding)
self.assertIn("R", entry.encoding)
@mock_bel_resources
def test_insert_namespace_persistent(self, mock_get):
self.assertEqual(0, self.manager.count_namespaces())
self.assertEqual(0, self.manager.count_namespace_entries())
self.manager.get_or_create_namespace(HGNC_URL)
self._help_check_hgnc(self.manager)
self.manager.get_or_create_namespace(HGNC_URL)
self._help_check_hgnc(self.manager)
self.manager.drop_namespace_by_url(HGNC_URL)
self.assertEqual(0, self.manager.count_namespaces())
self.assertEqual(0, self.manager.count_namespace_entries())
@mock_bel_resources
def test_insert_annotation(self, mock_get):
self.assertEqual(0, self.manager.count_annotations())
self.assertEqual(0, self.manager.count_annotation_entries())
annotation = self.manager.get_or_create_annotation(CELL_LINE_URL)
self.assertIsNotNone(annotation)
self.assertEqual(CELL_LINE_URL, annotation.url)
entry = self.manager.get_namespace_entry(CELL_LINE_URL, "1321N1 cell")
self.assertEqual("1321N1 cell", entry.name)
self.assertEqual("CLO_0001072", entry.identifier)
entries = self.manager.get_annotation_entries_by_names(CELL_LINE_URL, ["1321N1 cell"])
self.assertIsNotNone(entries)
self.assertEqual(1, len(entries))
entry = entries[0]
self.assertEqual("1321N1 cell", entry.name)
self.assertEqual("CLO_0001072", entry.identifier)
graph = BELGraph()
graph.annotation_url[CELL_LINE_KEYWORD] = CELL_LINE_URL
data = {
ANNOTATIONS: {
CELL_LINE_KEYWORD: {
"1321N1 cell": True,
},
},
}
annotations_iter = dict(self.manager._iter_from_annotations_dict(graph, annotations_dict=data[ANNOTATIONS]))
self.assertIn(CELL_LINE_URL, annotations_iter)
self.assertIn("1321N1 cell", annotations_iter[CELL_LINE_URL])
entries = self.manager._get_annotation_entries_from_data(graph, data)
self.assertIsNotNone(entries)
self.assertEqual(1, len(entries))
entry = entries[0]
self.assertEqual("1321N1 cell", entry.name)
self.assertEqual("CLO_0001072", entry.identifier)
self.manager.drop_namespace_by_url(CELL_LINE_URL)
self.assertEqual(0, self.manager.count_annotations())
self.assertEqual(0, self.manager.count_annotation_entries())
def test_get_annotation_entries_no_data(self):
"""Test that if there's no ANNOTATIONS entry in the data, it just returns none."""
graph = BELGraph()
data = {}
entries = self.manager._get_annotation_entries_from_data(graph, data)
self.assertIsNone(entries)
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