def test_merge_copies_property_chain_axioms():
nucleus_ontology = ontol_factory.OntologyFactory().create(
"tests/resources/nucleus.json")
assert len(nucleus_ontology.all_property_chain_axioms) == 0
goslim_ontology = ontol_factory.OntologyFactory().create(
"tests/resources/goslim_generic.json")
assert len(goslim_ontology.all_property_chain_axioms) == 2
# Test property chain axiom copy in merge
nucleus_ontology.merge([goslim_ontology])
assert len(nucleus_ontology.all_property_chain_axioms) == 2
def test_merge_copies_logical_definitions():
pombe_ontology = ontol_factory.OntologyFactory().create(
"tests/resources/goslim_pombe.json")
assert len(pombe_ontology.all_logical_definitions) == 0
nucleus_ontology = ontol_factory.OntologyFactory().create(
"tests/resources/nucleus.json")
assert len(nucleus_ontology.all_logical_definitions) == 2
# Test logical definition copy in merge
pombe_ontology.merge([nucleus_ontology])
assert len(pombe_ontology.all_property_chain_axioms) == 2
def test_go_rules_15():
assoc = make_annotation(goid="GO:0044419",
taxon="taxon:123|taxon:456").associations[0]
ontology = ontol_factory.OntologyFactory().create(
"tests/resources/go-interspecies-20210520.json")
test_result = qc.GoRule15().test(assoc,
all_rules_config(ontology=ontology))
assert test_result.result_type == qc.ResultType.PASS
assoc.object.id = Curie.from_str("GO:1234567")
test_result = qc.GoRule15().test(assoc,
all_rules_config(ontology=ontology))
assert test_result.result_type == qc.ResultType.WARNING
assoc.object.id = Curie.from_str("GO:0002812")
test_result = qc.GoRule15().test(assoc,
all_rules_config(ontology=ontology))
assert test_result.result_type == qc.ResultType.PASS
assoc.object.id = Curie.from_str("GO:0044215")
assoc.object.id = Curie.from_str("NCBITaxon:123")
assoc.interacting_taxon = None # This is the important part, no interacting taxon
test_result = qc.GoRule15().test(assoc,
all_rules_config(ontology=ontology))
assert test_result.result_type == qc.ResultType.PASS
def test_ontology_synonyms():
ontology = ontol_factory.OntologyFactory().create(
"tests/resources/nucleus_new.json")
syn = ontology.synonyms("GO:0005634")
assert syn[0].__dict__ == ontol.Synonym(
"GO:0005634",
val="cell nucleus",
pred="hasExactSynonym",
lextype=None,
xrefs=[],
ontology=None,
confidence=1.0,
synonymType="http://purl.obolibrary.org/obo/go-test#systematic_synonym"
).__dict__
def make_ontology(input_ontology):
click.echo("Loading ontology...")
ontology_factory = ontol_factory.OntologyFactory()
return ontology_factory.create(input_ontology)
def make_ontology(input_ontology):
ontology_factory = ontol_factory.OntologyFactory()
return ontology_factory.create(input_ontology)
import datetime
import yaml
import json
from ontobio.model import association
from ontobio.model.association import Curie
from ontobio.io import qc
from ontobio.io import gaference
from ontobio.io import assocparser
from ontobio.io import gafparser
from ontobio.io import gpadparser
from ontobio import ontol, ontol_factory
import copy
ontology = ontol_factory.OntologyFactory().create(
"tests/resources/goslim_generic.json")
def make_annotation(db="blah",
db_id="blah12345",
db_obj_symb="blah",
qualifier="",
negated=False,
goid="GO:1234567",
references="BLAH:54321",
evidence="IDA",
withfrom="BLAH:12345",
aspect="C",
db_obj_name="",
db_obj_syn="",
db_obj_type="blah",
def test_missing_node_is_none():
ontology = ontol_factory.OntologyFactory().create(
"tests/resources/goslim_generic.json")
assert ontology.node("GO:0") == None
