def test_get_contigs(self):
self.csv_out.writerow(['ts', 'event', 'dur.sec', 'data.sec',
'op', 'sz.bytes', 'redis', 'cache', 'id'])
def print_stats(event, pevent):
#print('Completed: {}'.format(str(event)))
md = pevent.metadata # alias
row = [pevent.start, event, pevent.duration, md['get_data'],
md['op'], md['size'], md['redis'], md['cached'],
md['genome']]
self.csv_out.writerow(row)
perf = PerfCollector('get_contigs')
perf.add_observer('*', None, print_stats)
warmed_up = False
for redis_flag in (False, True, True):
set_redis(redis_flag) # both redis server and config. in cache
for genome, ref in self.genomes.items():
ga_obj = ga_api.GenomeAnnotationAPI(
shared.get_services(),
shared.token,
ref)
print("@@ REDIS={}".format(redis_flag))
asm_obj = ga_obj.get_assembly()
for type_, obj in (('assembly', asm_obj),):
for operation in ('SUBSET', 'ALL'):
event_key = '/'.join([genome, type_, operation])
perf.start_event('get_contigs', event_key)
if operation == 'ALL':
_log.debug('Get all contigs')
contigs = asm_obj.get_contigs()
nc = 0 # all
# timing of last get_data() call
get_data_sec = asm_obj.stats.get_event(
'ObjectAPI.get_data', limit=1)[0].duration
else:
contig_list = self.fetch_contigs[genome]
nc = len(contig_list)
_log.debug('Get {:d} contigs'.format(nc))
contigs = asm_obj.get_contigs(contig_list)
# timing of last get_data() call
get_data_sec = asm_obj.stats.get_event(
'ObjectAPI.get_data', limit=1)[0].duration
cached = 1 if (redis_flag and warmed_up) else 0
perf.set_metadata({'redis': redis_flag,
'cached': cached,
'op': operation,
'size': calc_size(contigs),
'genome': genome,
'num_contigs': nc,
'ref': ref,
'get_data': get_data_sec})
perf.end_event('get_contigs', event_key)
warmed_up = redis_flag
def test_get_contigs(self):
self.csv_out.writerow([
'ts', 'event', 'dur.sec', 'data.sec', 'op', 'sz.bytes', 'redis',
'cache', 'id'
])
def print_stats(event, pevent):
#print('Completed: {}'.format(str(event)))
md = pevent.metadata # alias
row = [
pevent.start, event, pevent.duration, md['get_data'], md['op'],
md['size'], md['redis'], md['cached'], md['genome']
]
self.csv_out.writerow(row)
perf = PerfCollector('get_contigs')
perf.add_observer('*', None, print_stats)
warmed_up = False
for redis_flag in (False, True, True):
set_redis(redis_flag) # both redis server and config. in cache
for genome, ref in self.genomes.items():
ga_obj = ga_api.GenomeAnnotationAPI(shared.get_services(),
shared.token, ref)
print("@@ REDIS={}".format(redis_flag))
asm_obj = ga_obj.get_assembly()
for type_, obj in (('assembly', asm_obj), ):
for operation in ('SUBSET', 'ALL'):
event_key = '/'.join([genome, type_, operation])
perf.start_event('get_contigs', event_key)
if operation == 'ALL':
_log.debug('Get all contigs')
contigs = asm_obj.get_contigs()
nc = 0 # all
# timing of last get_data() call
get_data_sec = asm_obj.stats.get_event(
'ObjectAPI.get_data', limit=1)[0].duration
else:
contig_list = self.fetch_contigs[genome]
nc = len(contig_list)
_log.debug('Get {:d} contigs'.format(nc))
contigs = asm_obj.get_contigs(contig_list)
# timing of last get_data() call
get_data_sec = asm_obj.stats.get_event(
'ObjectAPI.get_data', limit=1)[0].duration
cached = 1 if (redis_flag and warmed_up) else 0
perf.set_metadata({
'redis': redis_flag,
'cached': cached,
'op': operation,
'size': calc_size(contigs),
'genome': genome,
'num_contigs': nc,
'ref': ref,
'get_data': get_data_sec
})
perf.end_event('get_contigs', event_key)
warmed_up = redis_flag
class WriteNow(object):
"""Flush all writes to underlying stream immediately.
"""
def __init__(self, strm):
self._stream = strm
def write(self, *args, **kwargs):
r = self._stream.write(*args, **kwargs)
self._stream.flush()
return r
# ----------------------------------------------------
g_travis = shared.in_travis()
g_nocache = shared.get_services()["redis_host"] is None
@unittest.skipIf(g_travis, "Do not run in TravisCI")
@unittest.skipIf(g_nocache, "Do not run if caching is disabled")
class TestPerformance(unittest.TestCase):
def setUp(self):
self.public_workspace_name = "testOriginalGenome"
self.public_workspace_id = 641
self.genomes_order = ["kb|g.244916", "kb|g.0", "kb|g.3899",
"kb|g.140106"]
self.genomes = {'kb|g.166819': '1013/340/4'}
self.fetch_contigs = {'kb|g.166819': ['kb|g.166819.c.{:d}'.format(i)
for i in (2, 5)]}
opath = __name__ + '.csv'
opath = os.path.realpath(opath)
class WriteNow(object):
"""Flush all writes to underlying stream immediately.
"""
def __init__(self, strm):
self._stream = strm
def write(self, *args, **kwargs):
r = self._stream.write(*args, **kwargs)
self._stream.flush()
return r
# ----------------------------------------------------
g_travis = shared.in_travis()
g_nocache = shared.get_services()["redis_host"] is None
@unittest.skipIf(g_travis, "Do not run in TravisCI")
@unittest.skipIf(g_nocache, "Do not run if caching is disabled")
class TestPerformance(unittest.TestCase):
def setUp(self):
self.public_workspace_name = "testOriginalGenome"
self.public_workspace_id = 641
self.genomes_order = [
"kb|g.244916", "kb|g.0", "kb|g.3899", "kb|g.140106"
]
self.genomes = {'kb|g.166819': '1013/340/4'}
self.fetch_contigs = {
'kb|g.166819': ['kb|g.166819.c.{:d}'.format(i) for i in (2, 5)]
}
