import argparse import time import arvados import arvados.collection import json import urllib.request import socket import getpass ARVADOS_API_HOST='lugli.arvadosapi.com' ARVADOS_API_TOKEN='2fbebpmbo3rw3x05ueu2i6nx70zhrsb1p22ycu3ry34m4x4462' UPLOAD_PROJECT='lugli-j7d0g-n5clictpuvwk8aa' def main(): parser = argparse.ArgumentParser(description='Upload SARS-CoV-19 sequences for analysis') parser.add_argument('sequence', type=argparse.FileType('r'), help='sequence FASTA') parser.add_argument('metadata', type=argparse.FileType('r'), help='sequence metadata json') args = parser.parse_args() api = arvados.api(host=ARVADOS_API_HOST, token=ARVADOS_API_TOKEN) col = arvados.collection.Collection(api_client=api) with col.open("sequence.fasta", "w") as f: r = args.sequence.read(65536) while r: f.write(r) r = args.sequence.read(65536) with col.open("metadata.jsonld", "w") as f: r = args.metadata.read(65536) while r: f.write(r) r = args.metadata.read(65536) external_ip = urllib.request.urlopen('https://ident.me').read().decode('utf8') properties = { "upload_app": "bh20-seq-uploader", "upload_ip": external_ip, "upload_user": "%s@%s" % (getpass.getuser(), socket.gethostname()) } col.save_new(owner_uuid=UPLOAD_PROJECT, name="Uploaded by %s from %s" % (properties['upload_user'], properties['upload_ip']), properties=properties, ensure_unique_name=True)