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Added option to download a limited number of directories for testing #2

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3 changes: 2 additions & 1 deletion bin/update_microbedb.py
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Original file line number Diff line number Diff line change
Expand Up @@ -39,7 +39,7 @@ def main():

fetcher = ncbi_fetcher()

fetcher.sync_version()
fetcher.sync_version(opts.test)

# We're done so set the current microbedb version to the new current one
Version.set_current(version)
Expand All @@ -49,6 +49,7 @@ def argParser():
parser = argparse.ArgumentParser(description='Update MicrobeDB from NCBI\'s ftp site')
parser.add_argument('-c','--config', dest='config', help='Config file', required=True)
parser.add_argument('-n','--noversion', action='store_true', default=False, dest='noversion', help='Don\'t create a new version, use the latest', required=False)
parser.add_argument('-t','--test', type=int, default=0, help='To test MicrobeDBv2, number of directories to try downloading from NCBI bacterial genome ftp (typically 5-10)')

return parser

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6 changes: 5 additions & 1 deletion lib/microbedb/ncbi.py
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Expand Up @@ -70,11 +70,15 @@ def check_and_reconnect(self):
genomes, for each send it for processing all the
isolates within.
'''
def sync_version(self):
def sync_version(self, test):

# First we fetch all the files
files = self.ftp.nlst()

if test!=0:
self.logger.info("We are testing MicrobeDBv2, only considering the first %s directories" % test)
files = files[:test]

for file in files:
self.logger.info("Processing remote directory: {}".format(file))

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