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Merged
merged 4 commits into from
Dec 17, 2018
Merged

Bugfix/travis mysql #21

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8880de5
Changed line ending to LF
marcoooo Dec 13, 2018
b4f8dcd
Updated requirements.txt to ols-client:1.0.7
marcoooo Dec 14, 2018
354c2f0
Moved travis-test onto mysql
marcoooo Dec 14, 2018
33c95d4
Revert MySQL testing - back to in memory SQLite for now
marcoooo Dec 17, 2018
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12 changes: 10 additions & 2 deletions bio/ensembl/ontology/loader/db.py
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Original file line number Diff line number Diff line change
Expand Up @@ -38,18 +38,26 @@ class DataAccessLayer:
session = None

def db_init(self, conn_string, **options):
extra_params = {}
if 'mysql' in conn_string:
extra_params = dict(
pool_recycle = options.get('pool_recycle', 280),
pool_size = options.get('pool_size', 100)
)

self.engine = sqlalchemy.create_engine(conn_string,
pool_recycle=options.get('pool_recycle', 280),
pool_size=options.get('pool_size', 100),
echo=options.get('echo', False),
encoding='utf8',
**extra_params,
convert_unicode=True)
self.options = options or {}
self.metadata.create_all(self.engine)
self.connection = self.engine.connect()

def wipe_schema(self, conn_string):
engine = sqlalchemy.create_engine(conn_string, echo=False)
if not engine:
raise RuntimeError("Can't wipe schema prior to init db")
Base.metadata.drop_all(engine)

def get_session(self):
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5 changes: 3 additions & 2 deletions requirements.txt
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@@ -1,6 +1,7 @@
requests==2.20.0
SQLAlchemy==1.2.11
ebi-ols-client==1.0.6
ebi-ols-client==1.0.7
mysqlclient==1.3.13
dateutils==0.6.6
coreapi==2.3.3
coreapi==2.3.3
PyMySQL==0.9.2
2 changes: 1 addition & 1 deletion scripts/loader.py
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Expand Up @@ -36,7 +36,7 @@
logger.debug('Script arguments %s', arguments)
args = vars(parser.parse_args())
db_name = 'ensembl_ontology_{}'.format(arguments.release)
options = {'drop': not arguments.keep, 'echo': arguments.verbose}
options = {'drop': not arguments.keep, 'echo': arguments.verbose, 'db_version': arguments.release}
if arguments.host_url is None:
db_url = 'sqlite:///' + expanduser("~") + '/' + db_name + '.sqlite'
options.update({'pool_size':None})
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97 changes: 44 additions & 53 deletions tests/test_basic.py
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Expand Up @@ -79,11 +79,6 @@ def testLoadOntology(self):
self.assertEqual(5, session.query(Term).count())
ontologies = session.query(Ontology).filter_by(name=ontology_name)
self.assertEqual(ontologies.count(), 2)
if self.db_url.startswith('mysql'):
session = dal.get_session()
self.loader.wipe_ontology(ontology_name=ontology_name)
ontologies = session.query(Ontology).filter_by(name=ontology_name).count()
self.assertEqual(ontologies, 0)

def testLoadOntologyTerms(self):
session = dal.get_session()
Expand Down Expand Up @@ -117,55 +112,51 @@ def testLoadTimeMeta(self):
self.fail('Wrong date format')

def testCascadeDelete(self):
self.skipTest('mysql' in self.db_url)
with dal.session_scope() as session:
m_ontology = Ontology(name='GO', _namespace='namespace', version='1', title='Ontology test')
m_ontology_2 = Ontology(name='GO', _namespace='namespace 2', version='1', title='Ontology test 2')
m_ontology_3 = Ontology(name='FPO', _namespace='namespace 3', version='1', title='Ontology test 2')
session.add(m_ontology)
session.add(m_ontology_2)
session.add(m_ontology_3)
rel_type, created = get_one_or_create(RelationType,
session,
name='is_a')
for i in range(0, 5):
m_term = Term(accession='GO:0000%s' % i, name='Term %s' % i, ontology=m_ontology)
m_term_2 = Term(accession='GO:1000%s' % i, name='Term %s' % i, ontology=m_ontology_2)
m_term_3 = Term(accession='T3:0000%s' % i, name='Term %s' % i, ontology=m_ontology_3)
syn_1 = Synonym(name='TS:000%s' % i, type=SynonymTypeEnum.EXACT, db_xref='REF:000%s' % i)
m_term.synonyms.append(syn_1)
syn_2 = Synonym(name='TS2:000%s' % i, type=SynonymTypeEnum.EXACT, db_xref='REF:000%s' % i)
m_term_2.synonyms.append(syn_2)
session.add_all([syn_1, syn_2])
alt_id = AltId(accession='ATL:000%s' % i)
m_term.alt_ids.append(alt_id)
session.add(alt_id)
m_term.add_child_relation(session=session, rel_type=rel_type, child_term=m_term_3)
m_term.add_parent_relation(session=session, rel_type=rel_type, parent_term=m_term_2)
closure_1 = Closure(child_term=m_term, parent_term=m_term_2, distance=1, ontology=m_ontology)
closure_2 = Closure(parent_term=m_term, child_term=m_term_3, distance=3, ontology=m_ontology_2)
closure_3 = Closure(parent_term=m_term_2, child_term=m_term_3, subparent_term=m_term, distance=2,
ontology=m_ontology_3)
session.add_all([closure_1, closure_2, closure_3])

self.assertEqual(session.query(Synonym).count(), 10)
self.assertEqual(session.query(AltId).count(), 5)
self.assertEqual(session.query(Relation).count(), 10)
self.assertEqual(session.query(Closure).count(), 12)

if self.db_url.startswith('mysql'):

with dal.session_scope() as session:
m_ontology = Ontology(name='GO', _namespace='namespace', version='1', title='Ontology test')
m_ontology_2 = Ontology(name='GO', _namespace='namespace 2', version='1', title='Ontology test 2')
m_ontology_3 = Ontology(name='FPO', _namespace='namespace 3', version='1', title='Ontology test 2')
session.add(m_ontology)
session.add(m_ontology_2)
session.add(m_ontology_3)
rel_type, created = get_one_or_create(RelationType,
session,
name='is_a')
for i in range(0, 5):
m_term = Term(accession='GO:0000%s' % i, name='Term %s' % i, ontology=m_ontology)
m_term_2 = Term(accession='GO:1000%s' % i, name='Term %s' % i, ontology=m_ontology_2)
m_term_3 = Term(accession='T3:0000%s' % i, name='Term %s' % i, ontology=m_ontology_3)
syn_1 = Synonym(name='TS:000%s' % i, type=SynonymTypeEnum.EXACT, db_xref='REF:000%s' % i)
m_term.synonyms.append(syn_1)
syn_2 = Synonym(name='TS2:000%s' % i, type=SynonymTypeEnum.EXACT, db_xref='REF:000%s' % i)
m_term_2.synonyms.append(syn_2)
session.add_all([syn_1, syn_2])
alt_id = AltId(accession='ATL:000%s' % i)
m_term.alt_ids.append(alt_id)
session.add(alt_id)
m_term.add_child_relation(session=session, rel_type=rel_type, child_term=m_term_3)
m_term.add_parent_relation(session=session, rel_type=rel_type, parent_term=m_term_2)
closure_1 = Closure(child_term=m_term, parent_term=m_term_2, distance=1, ontology=m_ontology)
closure_2 = Closure(parent_term=m_term, child_term=m_term_3, distance=3, ontology=m_ontology_2)
closure_3 = Closure(parent_term=m_term_2, child_term=m_term_3, subparent_term=m_term, distance=2,
ontology=m_ontology_3)
session.add_all([closure_1, closure_2, closure_3])

self.assertEqual(session.query(Synonym).count(), 10)
self.assertEqual(session.query(AltId).count(), 5)
self.assertEqual(session.query(Relation).count(), 10)
self.assertEqual(session.query(Closure).count(), 12)

with dal.session_scope() as session:
self.loader.wipe_ontology('GO')
[self.assertTrue(term.accession.startswith('T3')) for term in session.query(Term).all()]
self.assertEqual(0, session.query(Term).filter(Term.ontology_id == 1).count())
self.assertEqual(session.query(Term).count(), 5)
self.assertEqual(session.query(Synonym).count(), 0)
self.assertEqual(session.query(AltId).count(), 0)
self.assertEqual(session.query(Relation).count(), 0)
self.assertEqual(session.query(Closure).count(), 0)
else:
self.skipTest('No suitable engine for testing')
with dal.session_scope() as session:
self.loader.wipe_ontology('GO')
[self.assertTrue(term.accession.startswith('T3')) for term in session.query(Term).all()]
self.assertEqual(0, session.query(Term).filter(Term.ontology_id == 1).count())
self.assertEqual(session.query(Term).count(), 5)
self.assertEqual(session.query(Synonym).count(), 0)
self.assertEqual(session.query(AltId).count(), 0)
self.assertEqual(session.query(Relation).count(), 0)
self.assertEqual(session.query(Closure).count(), 0)

def testMeta(self):
session = dal.get_session()
Expand Down