From fd137721188b0044b9259b3a9aed14c155477888 Mon Sep 17 00:00:00 2001
From: Peter Amstutz
Date: Mon, 6 Apr 2020 12:46:38 -0400
Subject: Now uploads data

---
 bh20sequploader/main.py | 47 ++++++++++++++++++++++++++++++++++++++++++++++-
 setup.py                |  4 ++--
 2 files changed, 48 insertions(+), 3 deletions(-)

diff --git a/bh20sequploader/main.py b/bh20sequploader/main.py
index e3095b2..049a21c 100644
--- a/bh20sequploader/main.py
+++ b/bh20sequploader/main.py
@@ -1,2 +1,47 @@
+import argparse
+import time
+import arvados
+import arvados.collection
+import json
+import urllib.request
+import socket
+import getpass
+
+ARVADOS_API_HOST='lugli.arvadosapi.com'
+ARVADOS_API_TOKEN='2fbebpmbo3rw3x05ueu2i6nx70zhrsb1p22ycu3ry34m4x4462'
+UPLOAD_PROJECT='lugli-j7d0g-n5clictpuvwk8aa'
+WORKFLOW=''
+
 def main():
-    print("hello world")
+    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)
+
+    col = arvados.collection.Collection(api_client=api)
+
+    with col.open("sequence.fasta", "w") as f:
+        r = args.sequence.read(65536)
+        while r:
+            f.write(r)
+            r = args.sequence.read(65536)
+
+    with col.open("metadata.jsonld", "w") as f:
+        r = args.metadata.read(65536)
+        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)
diff --git a/setup.py b/setup.py
index acff69b..d5c71b2 100644
--- a/setup.py
+++ b/setup.py
@@ -15,7 +15,7 @@ try:
 except ImportError:
     tagger = egg_info_cmd.egg_info
 
-install_requires = []
+install_requires = ["arvados-python-client"]
 
 needs_pytest = {"pytest", "test", "ptr"}.intersection(sys.argv)
 pytest_runner = ["pytest < 6", "pytest-runner < 5"] if needs_pytest else []
@@ -35,7 +35,7 @@ setup(
     tests_require=["pytest<5"],
     entry_points={
         "console_scripts": [
-            "bh20sequploader=bh20sequploader.main:main"
+            "bh20-seq-uploader=bh20sequploader.main:main"
         ]
     },
     zip_safe=True,
-- 
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