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| author | Peter Amstutz | 2020-04-07 15:28:42 -0400 |
|---|---|---|
| committer | Peter Amstutz | 2020-04-07 15:28:42 -0400 |
| commit | 07bc4c65535437b8e9e0744f08da8cea541d0116 (patch) | |
| tree | 201cd544a87aebf0ba6978c42d61df1e90d7d836 /bh20sequploader/main.py | |
| parent | 4215a82af730ff05b8fe98e226b759413cdf95f7 (diff) | |
| download | bh20-seq-resource-07bc4c65535437b8e9e0744f08da8cea541d0116.tar.gz bh20-seq-resource-07bc4c65535437b8e9e0744f08da8cea541d0116.tar.lz bh20-seq-resource-07bc4c65535437b8e9e0744f08da8cea541d0116.zip | |
Add metadata validation with schema-salad
Diffstat (limited to 'bh20sequploader/main.py')
| -rw-r--r-- | bh20sequploader/main.py | 7 |
1 files changed, 5 insertions, 2 deletions
diff --git a/bh20sequploader/main.py b/bh20sequploader/main.py index d3ebc0c..8b8fefe 100644 --- a/bh20sequploader/main.py +++ b/bh20sequploader/main.py @@ -6,6 +6,7 @@ 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' @@ -19,6 +20,8 @@ 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") @@ -29,8 +32,8 @@ def main(): f.write(r) r = args.sequence.read(65536) - print("Reading JSONLD") - with col.open("metadata.jsonld", "w") as f: + print("Reading metadata") + with col.open("metadata.yaml", "w") as f: r = args.metadata.read(65536) print(r[0:20]) while r: |