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update.py
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update.py
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import argparse
import datetime
from trialstreamer import pubmed
from trialstreamer.dbutil import db, log_update
if __name__ == "__main__":
parser = argparse.ArgumentParser(description='Trialstreamer daily update script')
parser.add_argument('--source', type=str, help='pubmed|medrxiv')
args = parser.parse_args()
print("""
Welcome to the TrialStreamer daily update script
NB Please this will only work if RobotReviewer is running locally using the API mode
""")
# FIRST DO UPDATES
# NB! RobotReviewer MUST be running locally in API mode (ideally on a GPU)
if not args.source:
print("Missing --source argument")
parser.print_help()
elif args.source == 'pubmed':
print("Downloading any updates from PubMed")
pubmed.download_ftp_updates()
print("Annotating using RobotReviewer")
pubmed.annotate_rcts()
print("Updating counts")
pubmed.update_counts()
print("Updating logs")
log_update(update_type="fullcheck", download_date=datetime.datetime.utcnow())
print("Done! :)")
elif args.source == 'medrxiv':
print("Updating MedRxiv COVID-19 articles")
from trialstreamer import medrxiv_cov
medrxiv_cov.update()
print("Updating logs")
log_update(update_type="medrxiv", download_date=datetime.datetime.utcnow())
else:
print("Invalid --source argument, must be one of the following: (pubmed|medrxiv)")
parser.print_help()