def setUp(self):
services = shared.get_services()
if services["redis_host"] is not None:
cache.ObjectCache.cache_class = cache.RedisCache
cache.ObjectCache.cache_params = {'redis_host': 'localhost'}
else:
_log.warn("KB_REDIS_HOST not defined, using 'null' cache")
cache.ObjectCache.cache_class = cache.NullCache
cache.ObjectCache.cache_params = {}
_log.debug('Fetching old object')
self.old_object = ObjectAPI(services=services, ref=self.genome_old)
_log.debug('Fetching new object')
self.new_object = ObjectAPI(services=services, ref=self.genome_new)
def setUp(self):
services = shared.get_services()
if services["redis_host"] is not None:
cache.ObjectCache.cache_class = cache.RedisCache
cache.ObjectCache.cache_params = {'redis_host': 'localhost'}
else:
_log.warn("KB_REDIS_HOST not defined, using 'null' cache")
cache.ObjectCache.cache_class = cache.NullCache
cache.ObjectCache.cache_params = {}
_log.debug('Fetching old object')
self.old_object = ObjectAPI(services=services,
ref=self.genome_old)
_log.debug('Fetching new object')
self.new_object = ObjectAPI(services=services,
ref=self.genome_new)
def test_perf_stats(self):
g = ObjectAPI(services=shared.get_services(), ref=self.genome_old)
for method in ('get_schema', 'get_history', 'get_data',
'get_referrers', 'copy', 'get_provenance'):
getattr(self.old_object, method)()
assert method in g.stats.get_last().event
_log.info('Old genome {:20s} {:.3f} seconds'.format(
method,
g.stats.get_last().duration))
getattr(self.new_object, method)()
assert method in g.stats.get_last().event
_log.info('New genome {:20s} {:.3f} seconds'.format(
method,
g.stats.get_last().duration))
def can_connect(ref=genome):
"""See if we can get a connection to the workspace and access the
given reference.
Args:
ref (str): Workspace object reference
Returns:
(bool) if it can be accessed
"""
try:
_ = ObjectAPI(services=get_services(), ref=ref)
except Exception as err:
_log.exception(err)
_log.warn('Connect and fetch object failed: {}'.format(err))
return False
return True
class TestCachedObjectAPI(unittest.TestCase):
genome_new = "ReferenceGenomeAnnotations/kb|g.166819"
genome_old = "OriginalReferenceGenomes/kb|g.166819"
def setUp(self):
services = shared.get_services()
if services["redis_host"] is not None:
cache.ObjectCache.cache_class = cache.RedisCache
cache.ObjectCache.cache_params = {'redis_host': 'localhost'}
else:
_log.warn("KB_REDIS_HOST not defined, using 'null' cache")
cache.ObjectCache.cache_class = cache.NullCache
cache.ObjectCache.cache_params = {}
_log.debug('Fetching old object')
self.old_object = ObjectAPI(services=services, ref=self.genome_old)
_log.debug('Fetching new object')
self.new_object = ObjectAPI(services=services, ref=self.genome_new)
# def test_extract_paths(self):
# data = {'a1': {'b1': {'c1': 1, 'c2': 2}, 'b2': {'d1': 3}}}
# paths = ['a1/b1', 'a1/b1/c2', 'a1/b2/d1', 'a1/b1/N', 'N', 'a1/N']
# r = cache.ObjectCache.extract_paths(data, paths)
# assert len(r) == 3, 'Wrong number of results, got {:d} expected {:d}'.\
# format(len(r), 3)
# msg = 'Invalid result "{r}" for path "{p}"'
# assert r['a1/b1'] == {'a1': {'b1': {'c1': 1, 'c2': 2}}}, \
# msg.format(r=r[0], p=paths[0])
# assert r['a1/b1/c2'] == {'a1': {'b1': {'c2': 2}}}, msg.format(r=r[1],
# p=paths[1])
# assert r['a1/b2/d1'] == {'a1': {'b2':{'d1': 3}}}, msg.format(r=r[2],
# p=paths[2])
def test_get_new_data(self):
self.new_object.get_data()
event = self.new_object.cache_stats.get_last()
_log.info('Get new genome #1: {:.3f}'.format(event.duration))
self.new_object.get_data()
event = self.new_object.cache_stats.get_last()
_log.info('Get new genome #2: {:.3f}'.format(event.duration))
def test_get_old_data(self):
self.old_object.get_data()
event = self.old_object.cache_stats.get_last()
_log.info('Get old genome #1: {:.3f}'.format(event.duration))
self.old_object.get_data()
event = self.old_object.cache_stats.get_last()
_log.info('Get old genome #2: {:.3f}'.format(event.duration))
def test_perf_stats(self):
g = ObjectAPI(services=shared.get_services(), ref=self.genome_old)
for method in ('get_schema', 'get_history', 'get_data',
'get_referrers', 'copy', 'get_provenance'):
getattr(self.old_object, method)()
assert method in g.stats.get_last().event
_log.info('Old genome {:20s} {:.3f} seconds'.format(
method,
g.stats.get_last().duration))
getattr(self.new_object, method)()
assert method in g.stats.get_last().event
_log.info('New genome {:20s} {:.3f} seconds'.format(
method,
g.stats.get_last().duration))
def setup():
shared.setup()
global t
t = ObjectAPI(shared.services, shared.token, t_ref)
class TestCachedObjectAPI(unittest.TestCase):
genome_new = "ReferenceGenomeAnnotations/kb|g.166819"
genome_old = "OriginalReferenceGenomes/kb|g.166819"
def setUp(self):
services = shared.get_services()
if services["redis_host"] is not None:
cache.ObjectCache.cache_class = cache.RedisCache
cache.ObjectCache.cache_params = {'redis_host': 'localhost'}
else:
_log.warn("KB_REDIS_HOST not defined, using 'null' cache")
cache.ObjectCache.cache_class = cache.NullCache
cache.ObjectCache.cache_params = {}
_log.debug('Fetching old object')
self.old_object = ObjectAPI(services=services,
ref=self.genome_old)
_log.debug('Fetching new object')
self.new_object = ObjectAPI(services=services,
ref=self.genome_new)
# def test_extract_paths(self):
# data = {'a1': {'b1': {'c1': 1, 'c2': 2}, 'b2': {'d1': 3}}}
# paths = ['a1/b1', 'a1/b1/c2', 'a1/b2/d1', 'a1/b1/N', 'N', 'a1/N']
# r = cache.ObjectCache.extract_paths(data, paths)
# assert len(r) == 3, 'Wrong number of results, got {:d} expected {:d}'.\
# format(len(r), 3)
# msg = 'Invalid result "{r}" for path "{p}"'
# assert r['a1/b1'] == {'a1': {'b1': {'c1': 1, 'c2': 2}}}, \
# msg.format(r=r[0], p=paths[0])
# assert r['a1/b1/c2'] == {'a1': {'b1': {'c2': 2}}}, msg.format(r=r[1],
# p=paths[1])
# assert r['a1/b2/d1'] == {'a1': {'b2':{'d1': 3}}}, msg.format(r=r[2],
# p=paths[2])
def test_get_new_data(self):
self.new_object.get_data()
event = self.new_object.cache_stats.get_last()
_log.info('Get new genome #1: {:.3f}'.format(event.duration))
self.new_object.get_data()
event = self.new_object.cache_stats.get_last()
_log.info('Get new genome #2: {:.3f}'.format(event.duration))
def test_get_old_data(self):
self.old_object.get_data()
event = self.old_object.cache_stats.get_last()
_log.info('Get old genome #1: {:.3f}'.format(event.duration))
self.old_object.get_data()
event = self.old_object.cache_stats.get_last()
_log.info('Get old genome #2: {:.3f}'.format(event.duration))
def test_perf_stats(self):
g = ObjectAPI(services=shared.get_services(), ref=self.genome_old)
for method in ('get_schema', 'get_history', 'get_data', 'get_referrers',
'copy', 'get_provenance'):
getattr(self.old_object, method)()
assert method in g.stats.get_last().event
_log.info('Old genome {:20s} {:.3f} seconds'.format(
method, g.stats.get_last().duration))
getattr(self.new_object, method)()
assert method in g.stats.get_last().event
_log.info('New genome {:20s} {:.3f} seconds'.format(
method, g.stats.get_last().duration))
