def test_get_lat_longs(self):
exp = [
[74.0894932572, 65.3283470202],
[57.571893782, 32.5563076447],
[13.089194595, 92.5274472082],
[12.7065957714, 84.9722975792],
[44.9725384282, 66.1920014699],
[10.6655599093, 70.784770579],
[29.1499460692, 82.1270418227],
[35.2374368957, 68.5041623253],
[53.5050692395, 31.6056761814],
[60.1102854322, 74.7123248382],
[4.59216095574, 63.5115213108],
[68.0991287718, 34.8360987059],
[84.0030227585, 66.8954849864],
[3.21190859967, 26.8138925876],
[82.8302905615, 86.3615778099],
[12.6245524972, 96.0693176066],
[85.4121476399, 15.6526750776],
[23.1218032799, 42.838497795],
[43.9614715197, 82.8516734159],
[68.51099627, 2.35063674718],
[0.291867635913, 68.5945325743],
[40.8623799474, 6.66444220187],
[95.2060749748, 27.3592668624],
[78.3634273709, 74.423907894],
[38.2627021402, 3.48274264219]]
obs = get_lat_longs()
self.assertItemsEqual(obs, exp)
def _get_stats(self, callback):
# check if the key exists in redis
redis_lats_key = '%s:stats:sample_lats' % qiita_config.portal
redis_longs_key = '%s:stats:sample_longs' % qiita_config.portal
lats = r_client.lrange(redis_lats_key, 0, -1)
longs = r_client.lrange(redis_longs_key, 0, -1)
if not (lats and longs):
# if we don't have them, then fetch from disk and add to the
# redis server with a 24-hour expiration
lat_longs = get_lat_longs()
lats = [float(x[0]) for x in lat_longs]
longs = [float(x[1]) for x in lat_longs]
with r_client.pipeline() as pipe:
for latitude, longitude in lat_longs:
# storing as a simple data structure, hopefully this
# doesn't burn us later
pipe.rpush(redis_lats_key, latitude)
pipe.rpush(redis_longs_key, longitude)
# set the key to expire in 24 hours, so that we limit the
# number of times we have to go to the database to a reasonable
# amount
r_client.expire(redis_lats_key, 86400)
r_client.expire(redis_longs_key, 86400)
pipe.execute()
else:
# If we do have them, put the redis results into the same structure
# that would come back from the database
longs = [float(x) for x in longs]
lats = [float(x) for x in lats]
lat_longs = zip(lats, longs)
# Get the number of studies
num_studies = get_count('qiita.study')
# Get the number of samples
num_samples = len(lats)
# Get the number of users
num_users = get_count('qiita.qiita_user')
callback([num_studies, num_samples, num_users, lat_longs])
def _get_stats(self, callback):
# check if the key exists in redis
redis_lats_key = '%s:stats:sample_lats' % qiita_config.portal
redis_longs_key = '%s:stats:sample_longs' % qiita_config.portal
lats = r_client.lrange(redis_lats_key, 0, -1)
longs = r_client.lrange(redis_longs_key, 0, -1)
if not (lats and longs):
# if we don't have them, then fetch from disk and add to the
# redis server with a 24-hour expiration
lat_longs = get_lat_longs()
lats = [float(x[0]) for x in lat_longs]
longs = [float(x[1]) for x in lat_longs]
with r_client.pipeline() as pipe:
for latitude, longitude in lat_longs:
# storing as a simple data structure, hopefully this
# doesn't burn us later
pipe.rpush(redis_lats_key, latitude)
pipe.rpush(redis_longs_key, longitude)
# set the key to expire in 24 hours, so that we limit the
# number of times we have to go to the database to a reasonable
# amount
r_client.expire(redis_lats_key, 86400)
r_client.expire(redis_longs_key, 86400)
pipe.execute()
else:
# If we do have them, put the redis results into the same structure
# that would come back from the database
longs = [float(x) for x in longs]
lats = [float(x) for x in lats]
lat_longs = zip(lats, longs)
# Get the number of studies
num_studies = get_count('qiita.study')
# Get the number of samples
num_samples = len(lats)
# Get the number of users
num_users = get_count('qiita.qiita_user')
callback([num_studies, num_samples, num_users, lat_longs])
def test_get_lat_longs_EMP_portal(self):
info = {
'timeseries_type_id': 1,
'lab_person_id': None,
'principal_investigator_id': 3,
'metadata_complete': False,
'mixs_compliant': True,
'study_description': 'desc',
'study_alias': 'alias',
'study_abstract': 'abstract'}
study = Study.create(User('*****@*****.**'), 'test_study_1', efo=[1],
info=info)
Portal('EMP').add_studies([study.id])
md = {
'my.sample': {
'physical_specimen_location': 'location1',
'physical_specimen_remaining': True,
'dna_extracted': True,
'sample_type': 'type1',
'collection_timestamp': datetime(2014, 5, 29, 12, 24, 51),
'host_subject_id': 'NotIdentified',
'Description': 'Test Sample 4',
'str_column': 'Value for sample 4',
'int_column': 4,
'latitude': 42.42,
'longitude': 41.41,
'taxon_id': 9606,
'scientific_name': 'h**o sapiens'}
}
md_ext = pd.DataFrame.from_dict(md, orient='index')
SampleTemplate.create(md_ext, study)
qiita_config.portal = 'EMP'
obs = get_lat_longs()
exp = [[42.42, 41.41]]
self.assertItemsEqual(obs, exp)
