Merge branch 'master' into develop

Author: Peter J. Freeman

rest_VariantValidator/endpoints/lovd_endpoints.py

@@ -1,4 +1,6 @@
 # Import modules
+import json
+import ast
 from flask_restx import Namespace, Resource
 from . import request_parser
 from . import representations
@@ -9,6 +11,14 @@
 import VariantValidator
 vval = VariantValidator.Validator()
 
+
+def ordereddict_to_dict(value):
+    for k, v in value.items():
+        if isinstance(v, dict):
+            value[k] = ordereddict_to_dict(v)
+    return dict(value)
+
+
 """
 Create a parser object locally
 """
@@ -69,6 +79,11 @@ def get(self, genome_build, variant_description, transcript_model, select_transc
         content = VariantFormatter.simpleVariantFormatter.format(variant_description, genome_build, transcript_model,
                                                                  select_transcripts, checkonly, liftover)
 
+        to_dict = ordereddict_to_dict(content)
+        content = str(to_dict)
+        content = content.replace("'", '"')
+        content = ast.literal_eval(content)
+
         # Collect Arguments
         args = parser.parse_args()
 
@@ -78,7 +93,7 @@ def get(self, genome_build, variant_description, transcript_model, select_transc
             return representations.application_json(content, 200, None)
         # example: http://127.0.0.1:5000.....?content-type=application/xml
         elif args['content-type'] == 'application/xml':
-            return representations.xml(content, 200, None)
+            return representations.xml(str(content), 200, None)
         else:
             # Return the api default output
             return content

wsgi.py

@@ -1,4 +1,5 @@
-"""mod_wsgi gateway wsgi file
+"""
+mod_wsgi gateway wsgi file
 """
 
 from rest_VariantValidator.app import application as application
@@ -13,4 +14,4 @@
     else:
         application.debug = False
         application.config['PROPAGATE_EXCEPTIONS'] = False
-    application.run(host="127.0.0.1", port=5000)
+    application.run(host="127.0.0.1", port=8080)