diff options
| -rw-r--r-- | bh20sequploader/main.py | 47 | ||||
| -rw-r--r-- | setup.py | 4 |
2 files changed, 48 insertions, 3 deletions
diff --git a/bh20sequploader/main.py b/bh20sequploader/main.py index e3095b2..049a21c 100644 --- a/bh20sequploader/main.py +++ b/bh20sequploader/main.py @@ -1,2 +1,47 @@ +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' +WORKFLOW='' + def main(): - print("hello world") + 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) @@ -15,7 +15,7 @@ try: except ImportError: tagger = egg_info_cmd.egg_info -install_requires = [] +install_requires = ["arvados-python-client"] needs_pytest = {"pytest", "test", "ptr"}.intersection(sys.argv) pytest_runner = ["pytest < 6", "pytest-runner < 5"] if needs_pytest else [] @@ -35,7 +35,7 @@ setup( tests_require=["pytest<5"], entry_points={ "console_scripts": [ - "bh20sequploader=bh20sequploader.main:main" + "bh20-seq-uploader=bh20sequploader.main:main" ] }, zip_safe=True, |