3 files changed, 113 insertions, 0 deletions
diff --git a/bh20sequploader/bh20seq-schema.yml b/bh20sequploader/bh20seq-schema.yml
new file mode 100644
index 0000000..6e0973a
--- /dev/null
+++ b/bh20sequploader/bh20seq-schema.yml
@@ -0,0 +1,36 @@
+$graph:
+
+- name: sampleInformationSchema
+  type: record
+  fields:
+    location: string
+    host: string
+    sequenceTechnology: string
+    assemblyMethod: string
+
+- name: InstituteInformationSchema
+  type: record
+  fields:
+    OriginatingLab: string
+    SubmittingLab: string
+
+- name: SubmitterInformationSchema
+  type: record
+  fields:
+    Submitter: string
+    submissionDate: string
+
+- name: VirusDetailSchema
+  type: record
+  fields:
+    VirusName: string
+    AccessionId: string
+
+- name: MainSchema
+  type: record
+  documentRoot: true
+  fields:
+    sampleInformation: sampleInformationSchema
+    InstituteInformation: InstituteInformationSchema
+    SubmitterInformation: SubmitterInformationSchema
+    VirusDetail: VirusDetailSchema
diff --git a/bh20sequploader/main.py b/bh20sequploader/main.py
new file mode 100644
index 0000000..8b8fefe
--- /dev/null
+++ b/bh20sequploader/main.py
@@ -0,0 +1,56 @@
+import argparse
+import time
+import arvados
+import arvados.collection
+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'
+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('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)
+
+    qc_metadata(args.metadata.name)
+
+    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 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)
+
+    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)
+
+if __name__ == "__main__":
+    main()
diff --git a/bh20sequploader/qc_metadata.py b/bh20sequploader/qc_metadata.py
new file mode 100644
index 0000000..78b31b2
--- /dev/null
+++ b/bh20sequploader/qc_metadata.py
@@ -0,0 +1,21 @@
+import schema_salad.schema
+import logging
+import pkg_resources
+
+def qc_metadata(metadatafile):
+    schema_resource = pkg_resources.resource_stream(__name__, "bh20seq-schema.yml")
+    cache = {"https://raw.githubusercontent.com/arvados/bh20-seq-resource/master/bh20sequploader/bh20seq-schema.yml": schema_resource.read().decode("utf-8")}
+    (document_loader,
+     avsc_names,
+     schema_metadata,
+     metaschema_loader) = schema_salad.schema.load_schema("https://raw.githubusercontent.com/arvados/bh20-seq-resource/master/bh20sequploader/bh20seq-schema.yml", cache=cache)
+
+    if not isinstance(avsc_names, schema_salad.avro.schema.Names):
+        print(avsc_names)
+        return False
+
+    try:
+        doc, metadata = schema_salad.schema.load_and_validate(document_loader, avsc_names, metadatafile, True)
+        return True
+    except:
+        return False