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| author | Peter Amstutz | 2020-04-06 17:54:37 -0400 |
|---|---|---|
| committer | GitHub | 2020-04-06 17:54:37 -0400 |
| commit | 9b1c125f91469074c7586a1278d89b85919e3eae (patch) | |
| tree | 6d6a69ef2ebf4a9481a2c350914373ad25f63d00 /bh20sequploader | |
| parent | 2c69ca48ce1a9ab431afcc891bdad8c495c9768e (diff) | |
| parent | 762b770eda79fd4006b767e2dd768746232995ba (diff) | |
| download | bh20-seq-resource-9b1c125f91469074c7586a1278d89b85919e3eae.tar.gz bh20-seq-resource-9b1c125f91469074c7586a1278d89b85919e3eae.tar.lz bh20-seq-resource-9b1c125f91469074c7586a1278d89b85919e3eae.zip | |
Merge pull request #1 from pjotrp/master
Installation notes
Diffstat (limited to 'bh20sequploader')
| -rw-r--r-- | bh20sequploader/main.py | 8 | ||||
| -rw-r--r-- | bh20sequploader/main.py~ | 2 |
2 files changed, 7 insertions, 3 deletions
diff --git a/bh20sequploader/main.py b/bh20sequploader/main.py index 9de51f4..17ad492 100644 --- a/bh20sequploader/main.py +++ b/bh20sequploader/main.py @@ -17,18 +17,22 @@ def main(): 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) + api = arvados.api(host=ARVADOS_API_HOST, token=ARVADOS_API_TOKEN, insecure=True) col = arvados.collection.Collection(api_client=api) + print("Reading FASTA") with col.open("sequence.fasta", "w") as f: r = args.sequence.read(65536) + print(r[0:20]) while r: f.write(r) r = args.sequence.read(65536) + print("Reading JSONLD") with col.open("metadata.jsonld", "w") as f: r = args.metadata.read(65536) + print(r[0:20]) while r: f.write(r) r = args.metadata.read(65536) @@ -44,3 +48,5 @@ def main(): 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) + +main() diff --git a/bh20sequploader/main.py~ b/bh20sequploader/main.py~ deleted file mode 100644 index 336e825..0000000 --- a/bh20sequploader/main.py~ +++ /dev/null @@ -1,2 +0,0 @@ -def main(): - pass |