Added patch script that will read in key files and a json object file…

… with patch objects. To identify the objects to patch use the @id key which can be UUID, accession or alias.

patch.py

@@ -0,0 +1,54 @@
+import os
+import sys
+import csv
+import json
+import requests
+import argparse
+
+def get_settings(key_file,server_name):
+    key_list = open(key_file)
+    keys = csv.DictReader(key_list,delimiter = '\t')
+    settings = {}
+    for key in keys:
+        if key.get('Server') == server_name:
+            settings['USER'] = key.get('User')
+            settings['SERVER'] = ('http://' + key.get('Server') + '.encodedcc.org')
+            settings['AUTHID'] = key.get('ID')
+            settings['AUTHPW'] = key.get('PW')
+    key_list.close()
+    return settings
+
+def read_objects(object_file):
+    json_file = open(object_file)
+    json_objects = json.load(json_file)
+    json_file.close()
+    return json_objects
+
+def filter_object(json_object,key):
+    json_duplicate = json_object
+    json_duplicate.pop(key)
+    return json.dumps(json_duplicate)
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser(description='Script to patch json objects with only fields you require.')
+    parser.add_argument('key_file', help='A tab delimited file that contains keys.')
+    parser.add_argument('server', help='The server you want to patch objects to.')
+    parser.add_argument('json_file', help='The JSON file that contains a list of objects you want to patch.')
+    args = parser.parse_args()
+
+    # set headers.  UNCLEAR IF THIS IS USED PROPERLY
+    HEADERS = {'content-type': 'application/json'}
+
+    settings = get_settings(args.key_file,str(args.server))
+
+    patch_objects = read_objects(args.json_file)
+
+    for i in range(0,len(patch_objects)-1):
+        object_id = patch_objects[i]['@id']
+        patch_object = filter_object(patch_objects[i], '@id')
+        url = (settings.get('SERVER') + '/' + str(object_id))
+        authid = settings.get('AUTHID')
+        authpw = settings.get('AUTHPW')
+        response = requests.patch(url, auth=(authid, authpw), headers=HEADERS, data=patch_object)
+        print response.text
+