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authorAdam Novak2020-04-09 15:52:23 -0700
committerAdam Novak2020-04-09 15:52:23 -0700
commit2cd6623aa0ddfe4e42b2d434e0523773bb3536ef (patch)
tree6c8a99afdf03837dba83e9d956f60316c09391d3 /bh20sequploader/main.py
parentec6f3ad6268f576c1302101c7f0761fbf1d3dc55 (diff)
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Copy over/combine top-level project components
Diffstat (limited to 'bh20sequploader/main.py')
-rw-r--r--bh20sequploader/main.py7
1 files changed, 2 insertions, 5 deletions
diff --git a/bh20sequploader/main.py b/bh20sequploader/main.py
index 8b8fefe..d3ebc0c 100644
--- a/bh20sequploader/main.py
+++ b/bh20sequploader/main.py
@@ -6,7 +6,6 @@ import json
import urllib.request
import socket
import getpass
-from .qc_metadata import qc_metadata
ARVADOS_API_HOST='lugli.arvadosapi.com'
ARVADOS_API_TOKEN='2fbebpmbo3rw3x05ueu2i6nx70zhrsb1p22ycu3ry34m4x4462'
@@ -20,8 +19,6 @@ def main():
api = arvados.api(host=ARVADOS_API_HOST, token=ARVADOS_API_TOKEN, insecure=True)
- qc_metadata(args.metadata.name)
-
col = arvados.collection.Collection(api_client=api)
print("Reading FASTA")
@@ -32,8 +29,8 @@ def main():
f.write(r)
r = args.sequence.read(65536)
- print("Reading metadata")
- with col.open("metadata.yaml", "w") as f:
+ print("Reading JSONLD")
+ with col.open("metadata.jsonld", "w") as f:
r = args.metadata.read(65536)
print(r[0:20])
while r: