def testSingleTerm(self):
self.loader.options['process_relations'] = True
self.loader.options['process_parents'] = True
with dal.session_scope() as session:
m_ontology = self.loader.load_ontology('fypo', session)
session.add(m_ontology)
term = helpers.Term(
ontology_name='fypo',
iri='http://purl.obolibrary.org/obo/FYPO_0000257')
o_term = self.client.detail(term)
m_term = self.loader.load_term(o_term, m_ontology, session)
session.commit()
self.assertGreaterEqual(len(m_term.parent_terms), 1)
self.loader.options['process_relations'] = False
self.loader.options['process_parents'] = False
o_ontology = self.client.ontology('GO')
term = helpers.Term(
ontology_name='GO',
iri='http://purl.obolibrary.org/obo/GO_0000002')
o_term = self.client.detail(term)
m_term = self.loader.load_term(o_term, o_ontology, session)
self.assertEqual(m_term.ontology.name, 'GO')
with self.assertRaises(RuntimeError):
self.loader.load_term(o_term, 33, session)
def test_dynamic_links(self):
term = helpers.Term(ontology_name='aero',
iri='http://purl.obolibrary.org/obo/IAO_0000630')
for relation in term.relations_types:
related = term.load_relation(relation)
if related:
self._checkTerms(related)
self.assertIn('has_part', term.relations_types)
term = helpers.Term(ontology_name='aero',
iri='http://purl.obolibrary.org/obo/IAO_0000314')
self.assertIn('part_of', term.relations_types)
def test_namespace(self):
# retrieved from namespace annotation
h_term = helpers.Term(ontology_name='aero',
iri='http://purl.obolibrary.org/obo/IAO_0000314')
self.client.detail(h_term)
self.assertEqual(h_term.namespace, 'aero')
# retrieved from obo_name_space annotation
h_term = helpers.Term(ontology_name='duo',
iri='http://purl.obolibrary.org/obo/DUO_0000017')
self.client.detail(h_term)
self.assertEqual(h_term.namespace, 'duo')
def testRelationsShips(self):
with dal.session_scope() as session:
m_ontology = self.loader.load_ontology('bto', session)
session.add(m_ontology)
term = helpers.Term(
ontology_name='bto',
iri='http://purl.obolibrary.org/obo/BTO_0000005')
o_term = self.client.detail(term)
m_term = self.loader.load_term(o_term, m_ontology, session)
session.add(m_term)
self.assertGreaterEqual(len(m_term.parent_terms), 0)
def test_terms(self):
"""
Test direct calls to terms entry point.
Should warn that test may be long according to the nnumber of terms involved
:return:
"""
term_1 = helpers.Term(ontology_name='duo',
iri='http://purl.obolibrary.org/obo/DUO_0000026')
ancestors = term_1.load_relation('ancestors')
for ancestor in ancestors:
self._checkTerm(ancestor)
self._checkTerm(term_1)
def testRelationOtherOntology(self):
self.loader.options['process_relations'] = True
self.loader.options['process_parents'] = True
with dal.session_scope() as session:
m_ontology = self.loader.load_ontology('efo', session)
session.add(m_ontology)
term = helpers.Term(ontology_name='efo',
iri='http://www.ebi.ac.uk/efo/EFO_0002215')
o_term = self.client.detail(term)
m_term = self.loader.load_term(o_term, m_ontology, session)
session.add(m_term)
self.assertGreaterEqual(session.query(Ontology).count(), 2)
term = session.query(Term).filter_by(accession='BTO:0000164')
self.assertEqual(1, term.count())
def elem_class_instance(self, **kwargs):
"""
Search OLS api returns mixed types elements, get current element class to return accordingly
:param kwargs: type items
:return: mixed
"""
import ebi.ols.api.helpers as helpers
type_item = kwargs.pop('type', None)
if type_item == 'property':
return helpers.Property(**kwargs)
elif type_item == 'individual':
return helpers.Individual(**kwargs)
elif type_item == 'ontology':
return helpers.Ontology(**kwargs)
else:
return helpers.Term(**kwargs)
def test_exception_retry(self):
# unknown URI
with self.assertRaises(ebi.ols.api.exceptions.NotFoundException):
h_term = helpers.Term(
ontology_name='so',
iri='http://purl.obolibrary.org/obo/SO_99999999')
self.client.detail(h_term)
with self.assertRaises(ebi.ols.api.exceptions.NotFoundException):
self.client.ontology('unexisting_ontology')
with self.assertRaises(ebi.ols.api.exceptions.BadFilters):
filters = {'accession': 'EFO:0000405'}
self.client.terms(filters=filters)
with self.assertRaises(ebi.ols.api.exceptions.ObjectNotRetrievedError):
prop = helpers.Property(
iri=
'http://purl.obolibrary.org/obo/uberon/insect-anatomy#efo_slim',
ontology_name='efo')
self.client.detail(prop)
def testSubsets(self):
self.loader.options['process_relations'] = False
self.loader.options['process_parents'] = False
with dal.session_scope() as session:
term = helpers.Term(
ontology_name='go',
iri='http://purl.obolibrary.org/obo/GO_0099565')
o_term = self.client.detail(term)
m_term = self.loader.load_term(o_term, 'go', session)
session.add(m_term)
subsets = session.query(Subset).all()
for subset in subsets:
self.assertIsNotNone(subset.definition)
subset = helpers.Property(
ontology_name='go',
iri=
'http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym')
details = self.client.detail(subset)
self.assertNotEqual(details.definition, '')