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# This script is the CLI uploader for http://covid19.genenetwork.org/
#
# To upload a sequence with its metadata:
#
# python3 bh20sequploader/main.py example/sequence.fasta example/maximum_metadata_example.yaml
#
# Usage: described in http://covid19.genenetwork.org/blog?id=using-covid-19-pubseq-part3
import argparse
import time
import arvados
import arvados.collection
import json
import logging
import magic
from pathlib import Path
import urllib.request
import socket
import getpass
import sys
sys.path.insert(0,'.')
from bh20sequploader.qc_metadata import qc_metadata
from bh20sequploader.qc_fasta import qc_fasta
logging.basicConfig(level=logging.DEBUG)
log = logging.getLogger(__name__ )
log.debug("Entering sequence uploader")
# ---- Tokens for uploading data to Arvados
ARVADOS_API_HOST='lugli.arvadosapi.com'
UPLOADER_API_TOKEN='2fbebpmbo3rw3x05ueu2i6nx70zhrsb1p22ycu3ry34m4x4462'
ANONYMOUS_API_TOKEN='5o42qdxpxp5cj15jqjf7vnxx5xduhm4ret703suuoa3ivfglfh'
UPLOAD_PROJECT='lugli-j7d0g-n5clictpuvwk8aa'
VALIDATED_PROJECT='lugli-j7d0g-5ct8p1i1wrgyjvp'
def qc_stuff(metadata, sequence_p1, sequence_p2, do_qc=True):
"""Quality control. Essentially it checks the RDF schema and the FASTA
sequence for enough overlap with the reference genome
"""
failed = False
sample_id = ''
try:
log.debug("Checking metadata" if do_qc else "Skipping metadata check")
if do_qc:
sample_id = qc_metadata(metadata.name)
if not sample_id:
log.warning("Failed metadata QC")
failed = True
except Exception as e:
log.exception("Failed metadata QC")
failed = True # continue with the FASTA checker
target = []
if sequence_p1:
try:
log.debug("FASTA/FASTQ QC" if do_qc else "Limited FASTA/FASTQ QC")
target.append(qc_fasta(sequence_p1, check_with_mimimap2=do_qc))
if sequence_p2:
if target[0][2] == 'text/fasta':
raise ValueError("It is possible to upload just one FASTA file at a time")
target.append(qc_fasta(sequence_p2))
target[0] = ("reads_1."+target[0][0][6:], target[0][1], target[0][2])
target[1] = ("reads_2."+target[1][0][6:], target[1][1], target[1][2])
if do_qc and target[0][2] == 'text/fasta' and sample_id != target[0][1]:
raise ValueError(f"The sample_id field in the metadata ({sample_id}) must be the same as the FASTA header ({target[0][1]})")
except Exception as e:
log.exception("Failed sequence QC")
failed = True
if failed:
log.debug("Bailing out!")
exit(1)
return target
def upload_sequence(col, target, sequence):
with col.open(target[0], "wb") as f:
r = sequence.read(65536)
while r:
f.write(r)
r = sequence.read(65536)
def main():
parser = argparse.ArgumentParser(description='Upload SARS-CoV-19 sequences for analysis')
parser.add_argument('metadata', type=argparse.FileType('r'), help='sequence metadata json')
parser.add_argument('sequence_p1', type=argparse.FileType('rb'), default=None, nargs='?', help='sequence FASTA/FASTQ')
parser.add_argument('sequence_p2', type=argparse.FileType('rb'), default=None, nargs='?', help='sequence FASTQ pair')
parser.add_argument("--validate", action="store_true", help="Dry run, validate only")
parser.add_argument("--skip-qc", action="store_true", help="Skip local qc check")
parser.add_argument("--trusted", action="store_true", help="Trust local validation and add directly to validated project")
args = parser.parse_args()
if args.trusted:
# Use credentials from environment
api = arvados.api()
else:
api = arvados.api(host=ARVADOS_API_HOST, token=UPLOADER_API_TOKEN, insecure=True)
# ---- First the QC
target = qc_stuff(args.metadata, args.sequence_p1, args.sequence_p2, not args.skip_qc)
if target:
seqlabel = target[0][1]
else:
seqlabel = ""
if args.validate:
log.info("Valid")
exit(0)
col = arvados.collection.Collection(api_client=api)
# ---- Upload the sequence to Arvados
if args.sequence_p1:
upload_sequence(col, target[0], args.sequence_p1)
if args.sequence_p2:
upload_sequence(col, target[1], args.sequence_p2)
# ---- Make sure the metadata YAML is valid
log.info("Reading metadata")
with col.open("metadata.yaml", "w") as f:
r = args.metadata.read(65536)
log.info(r[0:20])
while r:
f.write(r)
r = args.metadata.read(65536)
# ---- Get the uploader IP address (gateway) and local user info
external_ip = urllib.request.urlopen('https://ident.me').read().decode('utf8')
try:
username = getpass.getuser()
except KeyError:
username = "unknown"
properties = {
"sequence_label": seqlabel,
"upload_app": "bh20-seq-uploader",
"upload_ip": external_ip,
"upload_user": "%s@%s" % (username, socket.gethostname())
}
# ---- Get ready for actual uploading
api2 = arvados.api(host=ARVADOS_API_HOST, token=ANONYMOUS_API_TOKEN, insecure=True)
dup = api2.collections().list(filters=[["owner_uuid", "in", [VALIDATED_PROJECT, UPLOAD_PROJECT]],
["portable_data_hash", "=", col.portable_data_hash()]]).execute()
if dup["items"]:
# This exact collection has been uploaded before.
log.error("Duplicate of %s" % ([d["uuid"] for d in dup["items"]]))
exit(1)
if args.trusted:
properties["status"] = "validated"
owner_uuid = VALIDATED_PROJECT
else:
owner_uuid = UPLOAD_PROJECT
# ---- and stream the 'collection' up
col.save_new(owner_uuid=owner_uuid, name="%s uploaded by %s from %s" %
(seqlabel, properties['upload_user'], properties['upload_ip']),
properties=properties, ensure_unique_name=True)
log.info("Saved to %s" % col.manifest_locator())
log.info("Done")
exit(0)
if __name__ == "__main__":
main()
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