Merge pull request #788 from aaxelb/eng-2102--deps

[ENG-2102] upgrade all the dependencies

.github/workflows/run_tests.yml

@@ -69,7 +69,7 @@ jobs:
 
       - name: run tests
         run: |
-          coverage run -m pytest
+          coverage run -m pytest -x --create-db
           coverage run --append -m behave
         env:
           DATABASE_PASSWORD: postgres

api/authentication.py

@@ -1,5 +1,5 @@
 from rest_framework.authentication import SessionAuthentication
-from oauth2_provider.ext.rest_framework import OAuth2Authentication
+from oauth2_provider.contrib.rest_framework import OAuth2Authentication
 
 
 class NonCSRFSessionAuthentication(SessionAuthentication):

api/banners/urls.py

@@ -3,5 +3,5 @@
 
 
 router = SimpleRouter()
-router.register(r'^site_?banners', views.SiteBannerViewSet, base_name='site_banners')
+router.register(r'^site_?banners', views.SiteBannerViewSet, basename='site_banners')
 urlpatterns = router.urls

api/banners/views.py

@@ -2,12 +2,14 @@
 
 from api.banners.serializers import SiteBannerSerializer
 from api.base import ShareViewSet
+from api.pagination import CursorPagination
 
 from share.models import SiteBanner
 
 
 class SiteBannerViewSet(ShareViewSet, viewsets.ReadOnlyModelViewSet):
     """View showing all active site-wide announcements."""
+    pagination_class = CursorPagination
     serializer_class = SiteBannerSerializer
 
     ordering = ('id', )

api/formattedmetadatarecords/urls.py

@@ -3,5 +3,5 @@
 
 
 router = SimpleRouter()
-router.register(r'formattedmetadatarecords', views.FormattedMetadataRecordViewSet, base_name='formattedmetadatarecord')
+router.register(r'formattedmetadatarecords', views.FormattedMetadataRecordViewSet, basename='formattedmetadatarecord')
 urlpatterns = router.urls

api/ingestjobs/urls.py

@@ -3,5 +3,5 @@
 
 
 router = SimpleRouter()
-router.register(r'ingestjobs', views.IngestJobViewSet, base_name='ingestjob')
+router.register(r'ingestjobs', views.IngestJobViewSet, basename='ingestjob')
 urlpatterns = router.urls

api/migrations/0001_create_application.py

@@ -5,6 +5,7 @@
 from django.db import migrations
 from django.conf import settings
 
+
 def create_application(apps, schema_editor):
     from oauth2_provider.models import Application as ActualApplication
     Application = apps.get_model('oauth2_provider', 'Application')
@@ -16,7 +17,8 @@ def create_application(apps, schema_editor):
         name='Harvester API',
         user=share_user
     )
-    oauth_app = Application.objects.create(**fields)
+    Application.objects.create(**fields)
+
 
 class Migration(migrations.Migration):
 

api/migrations/0001_ensure_application.py

@@ -0,0 +1,33 @@
+# Generated by Django 3.2.5 on 2021-07-12 23:23
+
+from django.db import migrations
+from django.conf import settings
+
+
+def ensure_application(apps, schema_editor):
+    from oauth2_provider.models import Application as ActualApplication
+    Application = apps.get_model('oauth2_provider', 'Application')
+    ShareUser = apps.get_model('share', 'ShareUser')
+    share_user = ShareUser.objects.get(username=settings.APPLICATION_USERNAME)
+    Application.objects.get_or_create(
+        client_type=str(ActualApplication.CLIENT_TYPES[0][1]),
+        authorization_grant_type=str(ActualApplication.GRANT_TYPES[2][1]),
+        name='Harvester API',
+        user=share_user
+    )
+
+
+class Migration(migrations.Migration):
+
+    replaces = [
+        ('api', '0001_create_application'),
+    ]
+
+    dependencies = [
+        ('oauth2_provider', '0002_08_updates'),
+        ('share', '0061_ensure_auto_users'),
+    ]
+
+    operations = [
+        migrations.RunPython(ensure_application),
+    ]

api/normalizeddata/urls.py

@@ -3,5 +3,5 @@
 
 
 router = SimpleRouter()
-router.register(r'normalizeddata', views.NormalizedDataViewSet, base_name='normalizeddata')
+router.register(r'normalizeddata', views.NormalizedDataViewSet, basename='normalizeddata')
 urlpatterns = router.urls

api/normalizeddata/views.py

@@ -100,7 +100,6 @@ def _do_create(self, request, *args, **kwargs):
         with transaction.atomic():
             # Hack for back-compat: Ingest halfway synchronously, then apply changes asynchronously
             ingester = Ingester(data, suid).as_user(request.user).ingest(
-                apply_changes=False,
                 pls_format_metadata=False,
             )
             ingester.job.reschedule(claim=True)

api/pagination.py

@@ -6,7 +6,7 @@
 
 from rest_framework.views import Response
 from rest_framework_json_api.pagination import PageNumberPagination
-from rest_framework.pagination import CursorPagination
+from rest_framework.pagination import CursorPagination as DrfCursorPagination
 
 logger = logging.getLogger(__name__)
 
@@ -26,7 +26,7 @@ class FuzzyPageNumberPagination(PageNumberPagination):
     django_paginator_class = FuzzyPaginator
 
 
-class CursorPagination(CursorPagination):
+class CursorPagination(DrfCursorPagination):
     ordering = '-id'
     cursor_query_param = 'page[cursor]'
 

api/permissions.py

@@ -1,6 +1,6 @@
 import logging
 
-from oauth2_provider.ext.rest_framework import TokenHasScope
+from oauth2_provider.contrib.rest_framework import TokenHasScope
 from rest_framework.exceptions import PermissionDenied
 from rest_framework.permissions import BasePermission, IsAuthenticated, SAFE_METHODS
 

api/rawdata/urls.py

@@ -3,5 +3,5 @@
 
 
 router = SimpleRouter()
-router.register(r'rawdata', views.RawDataViewSet, base_name='rawdatum')
+router.register(r'rawdata', views.RawDataViewSet, basename='rawdatum')
 urlpatterns = router.urls

api/schemas/urls.py

@@ -1,4 +1,4 @@
-from django.conf.urls import url
+from django.urls import re_path as url
 
 from api.schemas import views
 

api/search/urls.py

@@ -1,4 +1,4 @@
-from django.conf.urls import url
+from django.urls import re_path as url
 from django.views.decorators.csrf import csrf_exempt
 
 from api.search import views

api/sourceconfigs/urls.py

@@ -3,5 +3,5 @@
 
 
 router = SimpleRouter()
-router.register(r'sourceconfigs', views.SourceConfigViewSet, base_name='sourceconfig')
+router.register(r'sourceconfigs', views.SourceConfigViewSet, basename='sourceconfig')
 urlpatterns = router.urls

api/sourceregistrations/urls.py

@@ -3,5 +3,5 @@
 
 
 router = SimpleRouter()
-router.register(r'sourceregistrations', views.ProviderRegistrationViewSet, base_name='sourceregistration')
+router.register(r'sourceregistrations', views.ProviderRegistrationViewSet, basename='sourceregistration')
 urlpatterns = router.urls

api/sourceregistrations/views.py

@@ -5,6 +5,7 @@
 
 from api.base.views import ShareViewSet
 from api.deprecation import deprecate
+from api.pagination import CursorPagination
 from api.sourceregistrations.serializers import ProviderRegistrationSerializer
 
 
@@ -40,6 +41,7 @@ class ProviderRegistrationViewSet(ShareViewSet, generics.ListCreateAPIView, gene
 
         Success:       201 CREATED
     """
+    pagination_class = CursorPagination
     permission_classes = (IsAuthenticated, )
     serializer_class = ProviderRegistrationSerializer
 

api/sources/urls.py

@@ -3,5 +3,5 @@
 
 
 router = SimpleRouter()
-router.register(r'sources', views.SourceViewSet, base_name='source')
+router.register(r'sources', views.SourceViewSet, basename='source')
 urlpatterns = router.urls

api/sources/views.py

@@ -11,6 +11,7 @@
 
 from api.base import exceptions
 from api.base import ShareViewSet
+from api.pagination import CursorPagination
 from api.sources.serializers import (
     ReadonlySourceSerializer,
     CreateSourceSerializer,
@@ -25,6 +26,7 @@ class SourceViewSet(ShareViewSet, viewsets.ModelViewSet):
     filter_backends = (filters.OrderingFilter, )
     ordering = ('id', )
     ordering_fields = ('long_title', )
+    pagination_class = CursorPagination
     permission_classes = (DjangoModelPermissionsOrAnonReadOnly, )
 
     queryset = Source.objects.none()  # Required for DjangoModelPermissions

api/suids/urls.py

@@ -3,5 +3,5 @@
 
 
 router = SimpleRouter()
-router.register(r'suids', views.SuidViewSet, base_name='suid')
+router.register(r'suids', views.SuidViewSet, basename='suid')
 urlpatterns = router.urls

api/urls.py

@@ -1,5 +1,4 @@
-from django.conf.urls import include
-from django.conf.urls import url
+from django.urls import include, re_path as url
 
 from api import views
 from api.base.views import RootView

api/urls_v1.py

@@ -1,4 +1,4 @@
-from django.conf.urls import url
+from django.urls import re_path as url
 
 from api import views
 

api/users/serializers.py

@@ -36,7 +36,7 @@ class ShareUserWithTokenSerializer(ShareUserSerializer):
 
     def get_token(self, obj):
         try:
-            return obj.accesstoken_set.first().token
+            return obj.oauth2_provider_accesstoken.first().token
         except AttributeError:
             return None
 

api/users/urls.py

@@ -1,4 +1,4 @@
-from django.conf.urls import url
+from django.urls import re_path as url
 from django.views.decorators.csrf import ensure_csrf_cookie
 
 from rest_framework.routers import SimpleRouter
@@ -7,7 +7,7 @@
 
 
 router = SimpleRouter()
-router.register(r'users?', views.ShareUserViewSet, base_name='user')
+router.register(r'users?', views.ShareUserViewSet, basename='user')
 urlpatterns = router.urls + [
     url(r'userinfo/?', ensure_csrf_cookie(views.ShareUserView.as_view()), name='userinfo'),
 ]

dev-requirements.txt

@@ -1,15 +1,13 @@
 -r requirements.txt
 
-behave==1.2.5
-coveralls==2.1.2
-django-debug-toolbar==2.2
-factory-boy==2.8.1
-fake-factory==0.7.2
-faker==4.0.3
-flake8==3.8.4
-httpretty==0.8.14
-pytest-benchmark==3.0.0
-pytest-cov==2.5.1
-pytest==3.6.0
-pytest-django==3.2.1
-jedi==0.16.0
+behave==1.2.6
+coveralls==3.1.0
+django-debug-toolbar==3.2.1
+factory-boy==3.2.0
+faker==8.10.0
+flake8==3.9.2
+httpretty==1.1.3
+pytest-benchmark==3.4.1
+pytest==6.2.4
+pytest-django==4.4.0
+jedi==0.18.0

docker-compose.yml

@@ -73,9 +73,12 @@ services:
     command:
       - /bin/bash
       - -c
-      - pip install -r requirements.txt -r dev-requirements.txt &&
+      - apt-get update &&
+        apt-get install -y gcc &&
+        pip install -r requirements.txt -r dev-requirements.txt &&
         (python3 -m compileall /usr/local/lib/python3.6 || true) &&
         rm -Rf /python3.6/* &&
+        apt-get remove -y gcc &&
         cp -Rf -p /usr/local/lib/python3.6 / &&
         python3 setup.py develop
     restart: 'no'
@@ -94,7 +97,7 @@ services:
 
   worker:
     image: quay.io/centerforopenscience/share:develop
-    command: /usr/local/bin/celery worker -l INFO --app project --uid daemon
+    command: /usr/local/bin/celery --app project worker --uid daemon -l INFO
     depends_on:
       - postgres
       - rabbitmq
@@ -110,7 +113,7 @@ services:
 
   web:
     image: quay.io/centerforopenscience/share:develop
-    command: python manage.py runserver --noreload 0.0.0.0:8000
+    command: python manage.py runserver 0.0.0.0:8000
     ports:
       - 8003:8000
     depends_on: