Merge pull request #86 from openvar/develop

Develop

Author: Peter J. Freeman

REQUIREMENTS.txt

@@ -8,20 +8,14 @@ httplib2>=0.9.0
 configparser>=3.5.0
 pyliftover>=0.3
 biotools>=0.3.0
-mysql-connector-python
 requests
 dicttoxml
-notebook
-jupyter_contrib_nbextensions
-jupyter_nbextensions_configurator
 pytest>=3.6
 pytest-cov
 codecov
-
-# flask restplus is out of date, requiring these
-flask-restplus
-flask==1.1.1
-Werkzeug==0.16.1
-itsdangerous==2.0.1
-jinja2<3.1.0
-
+flask-restx
+flask-socketio
+flask == 1.1.4
+jinja2==2.11.3
+Werkzeug==1.0.1
+markupsafe==2.0.1

rest_VariantValidator/endpoints/__init__.py

@@ -1,7 +1,7 @@
 import rest_VariantValidator
 import VariantValidator
 import VariantFormatter
-from flask_restplus import Api
+from flask_restx import Api
 from flask import url_for
 from .variantvalidator_endpoints import api as ns_vv
 from .variantformatter_endpoints import api as ns_vf

rest_VariantValidator/endpoints/hello.py

@@ -1,4 +1,4 @@
-from flask_restplus import Namespace, Resource
+from flask_restx import Namespace, Resource
 from . import request_parser
 from . import representations
 

rest_VariantValidator/endpoints/lovd_endpoints.py

@@ -1,7 +1,7 @@
 # Import modules
 import json
 import ast
-from flask_restplus import Namespace, Resource
+from flask_restx import Namespace, Resource
 from . import request_parser
 from . import representations
 

rest_VariantValidator/endpoints/request_parser.py

@@ -1,4 +1,4 @@
-from flask_restplus import reqparse
+from flask_restx import reqparse
 
 
 # Create a RequestParser object to identify specific content-type requests in HTTP URLs

rest_VariantValidator/endpoints/variantformatter_endpoints.py

@@ -1,5 +1,5 @@
 # Import modules
-from flask_restplus import Namespace, Resource
+from flask_restx import Namespace, Resource
 from . import request_parser
 from . import representations
 

rest_VariantValidator/endpoints/variantvalidator_endpoints.py

@@ -1,5 +1,5 @@
 # Import modules
-from flask_restplus import Namespace, Resource
+from flask_restx import Namespace, Resource
 from . import request_parser
 from . import representations
 from . import exceptions

rest_VariantValidator/endpoints/vijs_endpoints.py

@@ -1,5 +1,5 @@
 # Import modules
-from flask_restplus import Namespace, Resource
+from flask_restx import Namespace, Resource
 from . import request_parser
 from . import representations