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))