Merge pull request #42 from ola-t/swagger-3

Upgrade to Swagger 3

emgapi/models.py

@@ -298,7 +298,7 @@ def mydata(self, request):
             _username = request.user.username
             return self.distinct() \
                 .filter(Q(submission_account_id=_username))
-        return self.available(request)
+        return ()
 
     def recent(self):
         return self.order_by('-last_update')

emgapi/urls.py

@@ -179,13 +179,13 @@
     base_name='samples-studies'
 )
 
-router.register(
-    (r'studies/(?P<accession>[a-zA-Z0-9\-\_]+)/'
-     r'pipelines/(?P<release_version>[0-9\.]+)/'
-     r'summary'),
-    views_relations.StudySummaryViewSet,
-    base_name='studies-pipelines-summary'
-)
+# router.register(
+#     (r'studies/(?P<accession>[a-zA-Z0-9\-\_]+)/'
+#      r'pipelines/(?P<release_version>[0-9\.]+)/'
+#      r'summary'),
+#     views_relations.StudySummaryViewSet,
+#     base_name='studies-pipelines-summary'
+# )
 
 
 mydata_router = routers.DefaultRouter(trailing_slash=False)

emgapi/views.py

@@ -55,8 +55,7 @@ class MyDataViewSet(mixins.ListModelMixin,
 
     def get_queryset(self):
         queryset = emg_models.Study.objects \
-            .mydata(self.request) \
-            .select_related('biome')
+            .mydata(self.request)
         return queryset
 
     def get_serializer_class(self):

emgcli/settings.py

@@ -32,6 +32,7 @@
 import warnings
 import logging
 import binascii
+import datetime
 
 from os.path import expanduser
 
@@ -165,11 +166,10 @@ def create_secret_key(var_dir):
     'corsheaders',
     # rest framework
     'rest_framework',
-    'rest_framework.authtoken',
-    'rest_framework_swagger',
+    # 'rest_framework.authtoken',
     'rest_framework_mongoengine',
+    'rest_framework_jwt',
     'django_filters',
-    'rest_auth',
     # apps
     'emgapi',
     'emgapianns',
@@ -276,7 +276,7 @@ def create_secret_key(var_dir):
 
 REST_FRAMEWORK = {
 
-    'DEFAULT_VERSION': '0.3',
+    'DEFAULT_VERSION': '0.4',
 
     'PAGE_SIZE': 20,
 
@@ -316,9 +316,9 @@ def create_secret_key(var_dir):
         'rest_framework_json_api.metadata.JSONAPIMetadata',
 
     'DEFAULT_AUTHENTICATION_CLASSES': (
-        # 'rest_framework.authentication.BasicAuthentication',
+        'rest_framework_jwt.authentication.JSONWebTokenAuthentication',
         'rest_framework.authentication.SessionAuthentication',
-        'rest_framework.authentication.TokenAuthentication',
+        # 'rest_framework.authentication.BasicAuthentication',
     ),
     'DEFAULT_PERMISSION_CLASSES': [
         'rest_framework.permissions.IsAuthenticatedOrReadOnly',
@@ -340,20 +340,6 @@ def create_secret_key(var_dir):
 LOGIN_URL = 'rest_framework:login'
 LOGOUT_URL = 'rest_framework:logout'
 
-SWAGGER_SETTINGS = {
-    'ENABLED_METHODS': [
-        'get',
-        'post',
-    ],
-    'SECURITY_DEFINITIONS': {
-        # 'basic': {
-        #     'type': 'basic'
-        # }
-    },
-    'USE_SESSION_AUTH': True,
-    'VALIDATOR_URL': None
-}
-
 # Custom settings
 try:
     EMG_DEFAULT_LIMIT = REST_FRAMEWORK['PAGE_SIZE']
@@ -414,6 +400,11 @@ def create_secret_key(var_dir):
     'OPTIONS'
 )
 
+JWT_AUTH = {
+    'JWT_EXPIRATION_DELTA': datetime.timedelta(seconds=108000),
+    'JWT_AUTH_HEADER_PREFIX': 'Bearer',
+}
+
 try:
     ADMINS = EMG_CONF['emg']['admins']
     MANAGERS = ADMINS

emgcli/urls.py

@@ -20,20 +20,26 @@
 from django.views.generic import RedirectView
 from django.views.generic import TemplateView
 
+from rest_framework import status
 from rest_framework.schemas import get_schema_view
-from rest_framework_swagger.views import get_swagger_view
+from rest_framework.renderers import BaseRenderer, JSONRenderer
 
-from rest_auth import views as rest_auth_views
+from rest_framework_jwt.views import obtain_jwt_token
+from rest_framework_jwt.views import verify_jwt_token
 
 from emgapi.urls import router as emg_router
 from emgapi.urls import mydata_router
 from emgapianns.urls import mongo_router
 from emgapianns.urls import router as emg_ext_router
 
+from openapi_codec import OpenAPICodec
+
 from . import routers
 
+
 api_version = settings.REST_FRAMEWORK['DEFAULT_VERSION']
 
+
 # merge all routers
 router = routers.DefaultRouter(trailing_slash=False)
 router.extend(emg_router)
@@ -42,50 +48,57 @@
 router.extend(mydata_router)
 
 
-# Wire up our API using automatic URL routing.
-# Additionally, we include login URLs for the browsable API.
+# API URL routing.
 urlpatterns = [
 
     # url(r'^admin/', admin.site.urls),
 
     url(r'^$', RedirectView.as_view(
         pattern_name='emgapi:api-root', permanent=False)),
 
-    url(r'^500$', TemplateView.as_view(template_name='500.html')),
+    url(r'^v%s/' % api_version, include(router.urls,
+                                        namespace='emgapi')),
+
+]
+
+# API authentication routing.
+urlpatterns += [
 
     url(r'^http-auth/', include('rest_framework.urls',
                                 namespace='rest_framework')),
 
-    url(
-        r'^v%s/auth/login' % api_version,
-        rest_auth_views.LoginView.as_view(),
-        name='rest_auth_login'
-    ),
+    url(r'^v%s/utils/token/obtain' % api_version, obtain_jwt_token,
+        name='obtain_jwt_token'),
+    url(r'^v%s/utils/token/verify' % api_version, verify_jwt_token,
+        name='verify_jwt_token'),
 
-    url(
-        r'^v%s/auth/logout' % api_version,
-        rest_auth_views.LogoutView.as_view(),
-        name='rest_auth_logout'
-    ),
-
-    url(r'^v%s/' % api_version, include(router.urls,
-                                        namespace='emgapi')),
+    # url(r'^500$', TemplateView.as_view(template_name='500.html')),
 
 ]
 
-# schema_prefix
+
+class OpenAPIRenderer(BaseRenderer):
+    media_type = 'application/openapi+json'
+    charset = None
+    format = 'openapi'
+
+    def render(self, data, accepted_media_type=None, renderer_context=None):
+        if renderer_context['response'].status_code != status.HTTP_200_OK:
+            return JSONRenderer().render(data)
+        return OpenAPICodec().encode(data)
+
+
 schema_view = get_schema_view(
     title=settings.EMG_TITLE, url=settings.EMG_URL,
-    description=settings.EMG_DESC)
-
-docs_schema_view = get_swagger_view(
-    title=settings.EMG_TITLE, url=settings.EMG_URL)
+    description=settings.EMG_DESC, renderer_classes=[OpenAPIRenderer]
+)
 
 
 urlpatterns += [
 
-    url(r'^schema/', schema_view),
+    url(r'^schema/$', schema_view, name="schema_view"),
 
-    url(r'^docs/', docs_schema_view),
+    url(r'^docs/',
+        TemplateView.as_view(template_name='swagger-ui/index.html')),
 
 ]

emgui/templates/rest_framework/base.html

@@ -147,7 +147,7 @@
 
           <!-- local-title -->
           <div class="columns medium-12" id="local-title">
-            {% include "rest_framework_swagger/include/header.html" %}
+            {% include "swagger-ui/include/header.html" %}
           </div>
           <!-- /local-title -->
 

emgui/templates/swagger-ui/include/swagger_css.html

@@ -0,0 +1,22 @@
+{% load staticfiles %}
+
+  <link rel="stylesheet" type="text/css" href='{% static "swagger-ui-3.4.3/swagger-ui.css" %}' >
+  <style>
+    html
+    {
+      box-sizing: border-box;
+      overflow: -moz-scrollbars-vertical;
+      overflow-y: scroll;
+    }
+    *,
+    *:before,
+    *:after
+    {
+      box-sizing: inherit;
+    }
+
+    body {
+      margin:0;
+      background: #fafafa;
+    }
+  </style>

emgui/templates/swagger-ui/include/swagger_doc.html

@@ -0,0 +1,35 @@
+<svg xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" style="position:absolute;width:0;height:0">
+  <defs>
+    <symbol viewBox="0 0 20 20" id="unlocked">
+          <path d="M15.8 8H14V5.6C14 2.703 12.665 1 10 1 7.334 1 6 2.703 6 5.6V6h2v-.801C8 3.754 8.797 3 10 3c1.203 0 2 .754 2 2.199V8H4c-.553 0-1 .646-1 1.199V17c0 .549.428 1.139.951 1.307l1.197.387C5.672 18.861 6.55 19 7.1 19h5.8c.549 0 1.428-.139 1.951-.307l1.196-.387c.524-.167.953-.757.953-1.306V9.199C17 8.646 16.352 8 15.8 8z"></path>
+    </symbol>
+
+    <symbol viewBox="0 0 20 20" id="locked">
+      <path d="M15.8 8H14V5.6C14 2.703 12.665 1 10 1 7.334 1 6 2.703 6 5.6V8H4c-.553 0-1 .646-1 1.199V17c0 .549.428 1.139.951 1.307l1.197.387C5.672 18.861 6.55 19 7.1 19h5.8c.549 0 1.428-.139 1.951-.307l1.196-.387c.524-.167.953-.757.953-1.306V9.199C17 8.646 16.352 8 15.8 8zM12 8H8V5.199C8 3.754 8.797 3 10 3c1.203 0 2 .754 2 2.199V8z"/>
+    </symbol>
+
+    <symbol viewBox="0 0 20 20" id="close">
+      <path d="M14.348 14.849c-.469.469-1.229.469-1.697 0L10 11.819l-2.651 3.029c-.469.469-1.229.469-1.697 0-.469-.469-.469-1.229 0-1.697l2.758-3.15-2.759-3.152c-.469-.469-.469-1.228 0-1.697.469-.469 1.228-.469 1.697 0L10 8.183l2.651-3.031c.469-.469 1.228-.469 1.697 0 .469.469.469 1.229 0 1.697l-2.758 3.152 2.758 3.15c.469.469.469 1.229 0 1.698z"/>
+    </symbol>
+
+    <symbol viewBox="0 0 20 20" id="large-arrow">
+      <path d="M13.25 10L6.109 2.58c-.268-.27-.268-.707 0-.979.268-.27.701-.27.969 0l7.83 7.908c.268.271.268.709 0 .979l-7.83 7.908c-.268.271-.701.27-.969 0-.268-.269-.268-.707 0-.979L13.25 10z"/>
+    </symbol>
+
+    <symbol viewBox="0 0 20 20" id="large-arrow-down">
+      <path d="M17.418 6.109c.272-.268.709-.268.979 0s.271.701 0 .969l-7.908 7.83c-.27.268-.707.268-.979 0l-7.908-7.83c-.27-.268-.27-.701 0-.969.271-.268.709-.268.979 0L10 13.25l7.418-7.141z"/>
+    </symbol>
+
+
+    <symbol viewBox="0 0 24 24" id="jump-to">
+      <path d="M19 7v4H5.83l3.58-3.59L8 6l-6 6 6 6 1.41-1.41L5.83 13H21V7z"/>
+    </symbol>
+
+    <symbol viewBox="0 0 24 24" id="expand">
+      <path d="M10 18h4v-2h-4v2zM3 6v2h18V6H3zm3 7h12v-2H6v2z"/>
+    </symbol>
+
+  </defs>
+</svg>
+
+<div id="swagger-ui"></div>

emgui/templates/swagger-ui/include/swagger_js.html

@@ -0,0 +1,33 @@
+{% load staticfiles %}
+
+<script src='{% static "swagger-ui-3.4.3/swagger-ui-bundle.js" %}'> </script>
+<script src='{% static "swagger-ui-3.4.3/swagger-ui-standalone-preset.js" %}'> </script>
+<script>
+
+var baseUrl = window.location.protocol + "//" + window.location.host 
+
+window.onload = function() {
+
+  // Build a system
+  const ui = SwaggerUIBundle({
+    url: baseUrl + "{% url 'schema_view' %}?format=openapi",
+    dom_id: '#swagger-ui',
+    deepLinking: true,
+    docExpansion: null,
+    validatorUrl: null,
+    supportHeaderParams: false,
+    jsonEditor: true,
+    supportedSubmitMethods: ["get", "post"],
+    presets: [
+      SwaggerUIBundle.presets.apis,
+      // SwaggerUIStandalonePreset
+    ],
+    plugins: [
+      SwaggerUIBundle.plugins.DownloadUrl
+    ],
+    // layout: "StandaloneLayout"
+  })
+
+  window.ui = ui
+}
+</script>