def test_composite(self, mock):
interleukin_23_complex = NamedComplexAbundance(
'GO', 'interleukin-23 complex')
il6 = hgnc(name='IL6')
interleukin_23_and_il6 = CompositeAbundance(
[interleukin_23_complex, il6])
self._help_reconstitute(interleukin_23_and_il6, 3, 2)
def test_component_list(self):
s = 'complex(SCOMP:"C1 Complex") hasComponents list(p(HGNC:C1QB), p(HGNC:C1S))'
result = self.parser.relation.parseString(s)
expected_result_list = [[COMPLEX, 'SCOMP', 'C1 Complex'],
'hasComponents',
[[PROTEIN, 'HGNC', 'C1QB'],
[PROTEIN, 'HGNC', 'C1S']]]
self.assertEqual(expected_result_list, result.asList())
sub = named_complex_abundance('SCOMP', 'C1 Complex')
self.assert_has_node(sub)
child_1 = hgnc('C1QB')
self.assert_has_node(child_1)
self.assert_has_edge(sub, child_1, **{RELATION: HAS_COMPONENT})
child_2 = hgnc('C1S')
self.assert_has_node(child_2)
self.assert_has_edge(sub, child_2, **{RELATION: HAS_COMPONENT})
def test_component_list(self):
s = 'complex(FPLX:C1) hasComponents list(p(HGNC:C1QB), p(HGNC:C1S))'
result = self.parser.relation.parseString(s)
expected_result_list = [[COMPLEX, ['FPLX', 'C1']], 'hasComponents',
[
[PROTEIN, ['HGNC', 'C1QB']],
[PROTEIN, ['HGNC', 'C1S']],
]]
self.assertEqual(expected_result_list, result.asList())
sub = named_complex_abundance('FPLX', 'C1')
self.assert_has_node(sub)
child_1 = hgnc(name='C1QB')
self.assert_has_node(child_1)
self.assert_has_edge(child_1, sub, **{RELATION: PART_OF})
child_2 = hgnc(name='C1S')
self.assert_has_node(child_2)
self.assert_has_edge(child_2, sub, **{RELATION: PART_OF})
test_citation_dict = {
CITATION_TYPE: 'PubMed',
CITATION_NAME: 'TestName',
CITATION_REFERENCE: '1235813'
}
SET_CITATION_TEST = 'SET Citation = {{"{type}","{name}","{reference}"}}'.format(
**test_citation_dict)
test_evidence_text = 'I read it on Twitter'
test_set_evidence = 'SET Evidence = "{}"'.format(test_evidence_text)
HGNC_KEYWORD = 'HGNC'
HGNC_URL = hbp_namespace('hgnc')
MESH_DISEASES_KEYWORD = 'MeSHDisease'
MESH_DISEASES_URL = OPENBEL_ANNOTATION_RESOURCES + "mesh-diseases.belanno"
akt1 = hgnc(name='AKT1')
egfr = hgnc(name='EGFR')
fadd = hgnc(name='FADD')
casp8 = hgnc(name='CASP8')
def update_provenance(control_parser: ControlParser) -> None:
"""Put a default evidence and citation in a BEL parser."""
control_parser.citation.update(test_citation_dict)
control_parser.evidence = test_evidence_text
def assert_has_node(self: unittest.TestCase, node: BaseEntity, graph: BELGraph,
**kwargs):
"""Check if a node with the given properties is contained within a graph."""
self.assertIsInstance(node, BaseEntity)
METADATA_NAME: "PyBEL Test Thorough",
METADATA_DESCRIPTION: "Statements made up to contain many conceivable variants of nodes from BEL",
METADATA_VERSION: "1.0.0",
METADATA_COPYRIGHT: "Copyright (c) Charles Tapley Hoyt. All Rights Reserved.",
METADATA_AUTHORS: "Charles Tapley Hoyt",
METADATA_LICENSES: "WTF License",
METADATA_CONTACT: "*****@*****.**",
}
citation_1 = citation_dict(db=CITATION_TYPE_PUBMED, db_id='123455')
citation_2 = citation_dict(db=CITATION_TYPE_PUBMED, db_id='123456')
evidence_1 = "Evidence 1"
dummy_evidence = 'These are mostly made up'
akt1 = hgnc(name='AKT1')
egfr = hgnc(name='EGFR')
fadd = hgnc(name='FADD')
casp8 = hgnc(name='CASP8')
mia = hgnc(name='MIA')
il6 = Protein('HGNC', 'IL6')
adgrb1 = Protein(namespace='HGNC', name='ADGRB1')
adgrb2 = Protein(namespace='HGNC', name='ADGRB2')
adgrb_complex = ComplexAbundance([adgrb1, adgrb2])
achlorhydria = Pathology(namespace='MESHD', name='Achlorhydria')
akt1_rna = akt1.get_rna()
akt1_gene = akt1_rna.get_gene()
akt_methylated = akt1_gene.with_variants(GeneModification('Me'))
from pybel.testing.cases import FleetingTemporaryCacheMixin, TemporaryCacheClsMixin, TemporaryCacheMixin
from pybel.testing.constants import test_bel_simple
from pybel.testing.mocks import mock_bel_resources
from pybel.testing.utils import make_dummy_annotations, make_dummy_namespaces, n
from tests.constants import (
BelReconstitutionMixin,
akt1,
casp8,
egfr,
expected_test_simple_metadata,
fadd,
test_citation_dict,
test_evidence_text,
)
fos = hgnc(name='FOS')
jun = hgnc(name='JUN')
mirna_1 = mirbase(name=n())
mirna_2 = mirbase(name=n())
pathology_1 = Pathology('DO', n())
ap1_complex = ComplexAbundance([fos, jun])
egfr_dimer = ComplexAbundance([egfr, egfr])
yfg_data = hgnc(name='YFG')
e2f4_data = hgnc(name='E2F4')
bound_ap1_e2f4 = ComplexAbundance([ap1_complex, e2f4_data])
superoxide = chebi(name='superoxide')
hydrogen_peroxide = chebi(name='hydrogen peroxide')
oxygen = chebi(name='oxygen')
from pybel.testing.cases import FleetingTemporaryCacheMixin, TemporaryCacheClsMixin, TemporaryCacheMixin
from pybel.testing.constants import test_bel_simple
from pybel.testing.mocks import mock_bel_resources
from pybel.testing.utils import make_dummy_annotations, make_dummy_namespaces, n
from tests.constants import (
BelReconstitutionMixin,
akt1,
casp8,
egfr,
expected_test_simple_metadata,
fadd,
test_citation_dict,
test_evidence_text,
)
fos = hgnc('FOS')
jun = hgnc('JUN')
mirna_1 = mirbase(n())
mirna_2 = mirbase(n())
pathology_1 = Pathology('DO', n())
ap1_complex = ComplexAbundance([fos, jun])
egfr_dimer = ComplexAbundance([egfr, egfr])
yfg_data = hgnc('YFG')
e2f4_data = hgnc('E2F4')
bound_ap1_e2f4 = ComplexAbundance([ap1_complex, e2f4_data])
superoxide = chebi('superoxide')
hydrogen_peroxide = chebi('hydrogen peroxide')
oxygen = chebi('oxygen')
# -*- coding: utf-8 -*-
import unittest
from pybel import BELGraph
from pybel.dsl import ComplexAbundance, Fragment, Protein
from pybel.dsl.namespaces import hgnc
from pybel_tools.selection.group_nodes import get_mapped_nodes
ccl2 = hgnc(name='CCL2')
ccr2 = hgnc(name='CCR2')
ccl2_mgi = Protein('MGI', 'Ccl2')
ccl2_ccr2_complex = ComplexAbundance([ccl2, ccr2])
chemokine_family = Protein('FPLX', 'chemokine protein family')
HGNC = 'hgnc'
class TestMapping(unittest.TestCase):
def test_variants_mapping(self):
graph = BELGraph()
app = Protein(HGNC, 'APP')
app_fragment = app.with_variants(Fragment('1_49'))
graph.add_node_from_data(app_fragment)
mapped_nodes = get_mapped_nodes(graph, HGNC, {'APP'})
self.assertEqual(1, len(mapped_nodes))
self.assertIn(app, mapped_nodes)
self.assertEqual({app_fragment}, mapped_nodes[app])
