def test_namespace_url(self):
uploaded = datetime.datetime.now()
model = Namespace(
keyword='TEST',
url='http://test.com',
name='Test Namespace',
domain=NAMESPACE_DOMAIN_OTHER,
species='9606',
version='1.0.0',
author='Charles Tapley Hoyt',
contact='*****@*****.**',
uploaded=uploaded,
)
expected = dict(
keyword='TEST',
url='http://test.com',
name='Test Namespace',
version='1.0.0',
)
self.assertEqual(model.to_json(), expected)
expected['id'] = model.id = 1
self.assertEqual(model.to_json(include_id=True), expected)
def test_drop_namespace(self):
keyword, url = n(), n()
namespace = Namespace(keyword=keyword, url=url)
self.manager.session.add(namespace)
n_entries = 5
for _ in range(n_entries):
entry = NamespaceEntry(name=n(), namespace=namespace)
self.manager.session.add(entry)
self.manager.session.commit()
self.assertEqual(1,
self.manager.count_namespaces(),
msg='Should have one namespace')
self.assertEqual(n_entries,
self.manager.count_namespace_entries(),
msg='Should have {} entries'.format(n_entries))
self.manager.drop_namespace_by_url(url)
self.assertEqual(0,
self.manager.count_namespaces(),
msg='Should have no namespaces')
self.assertEqual(0,
self.manager.count_namespace_entries(),
msg='Entries should have been dropped')
def test_namespace_pattern(self):
uploaded = datetime.datetime.now()
model = Namespace(keyword='TEST',
pattern='\w+',
name='Test Namespace',
domain=NAMESPACE_DOMAIN_OTHER,
species='9606',
version='1.0.0',
author='Charles Tapley Hoyt',
contact='*****@*****.**',
uploaded=uploaded)
expected = dict(
keyword='TEST',
pattern='\w+',
name='Test Namespace',
version='1.0.0',
)
self.assertEqual(model.to_json(), expected)
def test_namespace_entry(self):
model = NamespaceEntry(name='entry',
namespace=Namespace(keyword='test'))
expected = {NAMESPACE: 'test', NAME: 'entry'}
self.assertEqual(model.to_json(), expected)
expected['id'] = model.id = 1
self.assertEqual(model.to_json(include_id=True), expected)
expected[IDENTIFIER] = model.identifier = 'test:00001'
self.assertEqual(model.to_json(include_id=True), expected)
def _make_namespace(self) -> Namespace:
"""Make a namespace."""
namespace = Namespace(
name=self._get_namespace_name(),
keyword=self._get_namespace_keyword(),
url=self._get_namespace_url(),
version=str(time.asctime()),
)
self.session.add(namespace)
entries = self._get_namespace_entries(namespace)
self.session.add_all(entries)
t = time.time()
logger.info('committing models')
self.session.commit()
logger.info('committed models in %.2f seconds', time.time() - t)
return namespace
def make_dummy_namespaces(manager, graph, namespaces):
"""
:param pybel.manager.Manager manager:
:param pybel.BELGraph graph:
:param dict[str,iter[str]] namespaces:
"""
for keyword, names in namespaces.items():
url = n()
graph.namespace_url[keyword] = url
namespace = Namespace(keyword=keyword, url=url)
manager.session.add(namespace)
manager.namespace_model[url] = namespace
for name in names:
entry = manager.namespace_object_cache[url][
entry.name] = NamespaceEntry(name=name, namespace=namespace)
manager.session.add(entry)
manager.session.commit()
