def download(self, subtype, output=True, count=True, **kwargs):
'''
download documents from table
'''
import time
start_time = time.time()
self.connect_rethink(**kwargs)
self.vdb_download = vdb_download(database=self.database,
virus=self.virus)
select, present, interval, = self.vdb_download.parse_subset_arguments(
**kwargs)
select.append(('subtype', [subtype]))
sequence_count = r.table(self.virus).count().run()
print(sequence_count, "measurements in table:", self.virus)
print("Downloading titer measurements from the table: " + self.virus)
measurements = self.rethinkdb_download(self.virus,
presents=present,
selections=select,
intervals=interval,
**kwargs)
print("Downloaded " + str(len(measurements)) + " measurements")
if output:
self.output(measurements, **kwargs)
if count:
self.write_count(measurements, **kwargs)
print("--- %s minutes to download ---" %
((time.time() - start_time) / 60))
def download(self, subtype=None, **kwargs):
'''
download documents from table
'''
start_time = time.time()
self.connect_rethink(**kwargs)
self.vdb_download = vdb_download(database=self.database,
virus=self.virus)
select, present, interval, = self.vdb_download.parse_subset_arguments(
**kwargs)
if subtype is not None:
select.append(('subtype', [subtype]))
measurement_count = r.table(self.virus).count().run()
print(measurement_count, "measurements in table:", self.virus)
print("Downloading titer measurements from the table: " + self.virus)
measurements = self.rethinkdb_download(self.virus,
presents=present,
selections=select,
intervals=interval,
**kwargs)
self.rename_strains_with_passage(measurements)
print("Downloaded " + str(len(measurements)) + " measurements")
print("--- %s minutes to download ---" %
((time.time() - start_time) / 60))
return measurements
def download(self, subtype, output=True, count=True, **kwargs):
'''
download documents from table
'''
import time
start_time = time.time()
self.connect_rethink(**kwargs)
self.vdb_download = vdb_download(database=self.database, virus=self.virus)
select, present, interval, = self.vdb_download.parse_subset_arguments(**kwargs)
select.append(('subtype', [subtype]))
sequence_count = r.table(self.virus).count().run()
print(sequence_count, "measurements in table:", self.virus)
print("Downloading titer measurements from the table: " + self.virus)
measurements = self.rethinkdb_download(self.virus, presents=present, selections=select, intervals=interval, **kwargs)
print("Downloaded " + str(len(measurements)) + " measurements")
if output:
self.output(measurements, subtype=subtype, **kwargs)
if count:
self.write_count(measurements, subtype=subtype, **kwargs)
print("--- %s minutes to download ---" % ((time.time() - start_time)/60))