--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/data_manager.py	Fri Jul 08 11:17:50 2016 -0400
@@ -0,0 +1,73 @@
+import os
+import sys
+import uuid
+import json
+import argparse
+import requests
+from requests.exceptions import ContentDecodingError
+
+
+def url_download(url):
+    """Attempt to download gene annotation file from a given url
+    :param url: full url to gene annotation file
+    :type url: str.
+    :returns: name of downloaded gene annotation file
+    :raises: ContentDecodingError, IOError
+    """
+    response = requests.get(url=url, stream=True)
+
+    # Generate file_name
+    file_name = response.url.split("/")[-1]
+
+    block_size = 10 * 1024 * 1024  # 10MB chunked download
+    with open(file_name, 'w+') as f:
+        try:
+            # Good to note here that requests' iter_content() will
+            # automatically handle decoding "gzip" and "deflate" encoding
+            # formats
+            for buf in response.iter_content(block_size):
+                f.write(buf)
+        except (ContentDecodingError, IOError) as e:
+            sys.stderr.write("Error occured downloading reference file: %s"
+                             % e)
+            os.remove(file_name)
+
+    return file_name
+
+
+def main():
+
+    # Generate and parse command line args
+    parser = argparse.ArgumentParser(description='Create data manager JSON.')
+    parser.add_argument('--out', dest='output', action='store',
+                        help='JSON filename')
+    parser.add_argument('--name', dest='name', action='store',
+                        default=uuid.uuid4(), help='Data table entry unique ID'
+                        )
+    parser.add_argument('--url', dest='url', action='store',
+                        help='Url to download gtf file from')
+
+    args = parser.parse_args()
+
+    work_dir = os.getcwd()
+
+    # Attempt to download gene annotation file from given url
+    gene_annotation_file_name = url_download(args.url)
+
+    # Update Data Manager JSON and write to file
+    data_manager_entry = {
+        'data_tables': {
+            'gene_annotation': {
+                'value': str(args.name),
+                'dbkey': str(args.name),
+                'name': gene_annotation_file_name,
+                'path': os.path.join(work_dir, gene_annotation_file_name)
+            }
+        }
+    }
+
+    with open(os.path.join(args.output), "w+") as f:
+        f.write(json.dumps(data_manager_entry))
+
+if __name__ == '__main__':
+    main()