diff alveo_data_importer.py @ 14:a38315ecf593 draft

planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit b5b26e9118f2ad8af109d606746b39a5588f0511-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/alveo_data_importer.py	Wed Nov 01 01:18:15 2017 -0400
@@ -0,0 +1,37 @@
+from __future__ import print_function
+import argparse
+import pyalveo
+import sys
+from util import API_URL, write_key
+
+
+def parser():
+    p = argparse.ArgumentParser(description="Downloads documents in an Alveo Item List")
+    p.add_argument('--api_key', required=True, action="store", type=str, help="Alveo API key")
+    p.add_argument('--item_list_url', required=True, action="store", type=str, help="Item List to download")
+    p.add_argument('--output', required=True, action="store", type=str, help="output file name")
+    p.add_argument('--outputkey', required=True, action="store", type=str, help="output file name for API Key")
+    return p.parse_args()
+
+
+def main():
+    args = parser()
+    try:
+        write_key(args.api_key, args.outputkey)
+
+        client = pyalveo.Client(api_key=args.api_key, api_url=API_URL, use_cache=False)
+        item_list = client.get_item_list(args.item_list_url)
+
+        with open(args.output, 'w') as out:
+            out.write("ItemURL\n")
+            for item in item_list:
+                out.write(item + "\n")
+                print(item)
+
+    except pyalveo.APIError as e:
+        print("ERROR: " + str(e), file=sys.stderr)
+        sys.exit(1)
+
+
+if __name__ == '__main__':
+    main()