Merge branch 'master' into patch-1

1 files changed, 20 insertions, 6 deletions

diff --git a/bh20sequploader/main.py b/bh20sequploader/main.py
index 17ad492..4a225f6 100644
--- a/bh20sequploader/main.py
+++ b/bh20sequploader/main.py
@@ -3,9 +3,13 @@ import time
 import arvados
 import arvados.collection
 import json
+import magic
+from pathlib import Path
 import urllib.request
 import socket
 import getpass
+from .qc_metadata import qc_metadata
+from .qc_fasta import qc_fasta
 
 ARVADOS_API_HOST='lugli.arvadosapi.com'
 ARVADOS_API_TOKEN='2fbebpmbo3rw3x05ueu2i6nx70zhrsb1p22ycu3ry34m4x4462'
@@ -13,29 +17,36 @@ UPLOAD_PROJECT='lugli-j7d0g-n5clictpuvwk8aa'
 
 def main():
     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('sequence', type=argparse.FileType('r'), help='sequence FASTA/FASTQ')
     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, insecure=True)
 
+    target = qc_fasta(args.sequence)
+
+    if not qc_metadata(args.metadata.name):
+        print("Failed metadata qc")
+        exit(1)
+
     col = arvados.collection.Collection(api_client=api)
 
-    print("Reading FASTA")
-    with col.open("sequence.fasta", "w") as f:
+    with col.open(target, "w") as f:
         r = args.sequence.read(65536)
         print(r[0:20])
         while r:
             f.write(r)
             r = args.sequence.read(65536)
+    args.sequence.close()
 
-    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:
             f.write(r)
             r = args.metadata.read(65536)
+    args.metadata.close()
 
     external_ip = urllib.request.urlopen('https://ident.me').read().decode('utf8')
 
@@ -49,4 +60,7 @@ def main():
                  (properties['upload_user'], properties['upload_ip']),
                  properties=properties, ensure_unique_name=True)
 
-main()
+    print("Done")
+
+if __name__ == "__main__":
+    main()