Merge branch 'master' of gitlab.iric.ca:bioinfo_iric/iric-data

iric_data/settings.py

@@ -51,6 +51,7 @@ INSTALLED_APPS = [
     'chartjs',
     'private_storage',
     'loginas',
+    'graphene_django',
     'portal'
 ]
 
@@ -238,6 +239,7 @@ USE_I18N = True
 USE_L10N = True
 USE_TZ = True
 
+
 ENV_PATH = os.path.abspath(os.path.dirname(__file__))
 MEDIA_ROOT = os.path.join(ENV_PATH, 'media/')
 MEDIA_URL = "/media/"

iric_data/urls.py

@@ -13,12 +13,14 @@ Including another URLconf
     1. Import the include() function: from django.urls import include, path
     2. Add a URL to urlpatterns:  path('blog/', include('blog.urls'))
 """
+import private_storage.urls
 from django.conf import settings
 from django.conf.urls.static import static
 from django.contrib import admin
 from django.urls import include, path
-
-import private_storage.urls
+from django.views.decorators.csrf import csrf_exempt
+from portal.graphql_schema import schema
+from portal.graphql_schema import PrivateGraphQLView
 
 urlpatterns = [
     path('', include('portal.urls')),
@@ -27,4 +29,5 @@ urlpatterns = [
     path('private-media/', include(private_storage.urls)),
     path("admin/", include('loginas.urls')),
     path('oauth/', include('social_django.urls', namespace='social')),
+    path("graphql/", csrf_exempt(PrivateGraphQLView.as_view(graphiql=True, schema=schema))),
 ] + static(settings.MEDIA_URL, document_root=settings.MEDIA_ROOT)

portal/graphql_schema.py

+import graphene
+from django.contrib.auth import get_user_model
+from graphene_django.types import DjangoObjectType
+from graphene_django.views import GraphQLView
+
+from portal.models import DataFile, DataSet, Profile
+from portal.views import TokenLoginMixin
+
+
+# Protect graphql API page
+class PrivateGraphQLView(TokenLoginMixin, GraphQLView):
+    pass
+
+
+# Create a GraphQL type for the various models
+class DataFileType(DjangoObjectType):
+    class Meta:
+        model = DataFile
+        fields = "__all__"
+
+
+class DataSetType(DjangoObjectType):
+    class Meta:
+        model = DataSet
+        fields = "__all__"
+
+
+class ProfileSetType(DjangoObjectType):
+    class Meta:
+        model = Profile
+
+
+class UserType(DjangoObjectType):
+    class Meta:
+        model = get_user_model()
+
+
+# Create a Query type
+class Query(graphene.ObjectType):
+    datafile = graphene.Field(DataFileType, id=graphene.String(), dbid=graphene.Int())
+    dataset = graphene.Field(DataSetType, id=graphene.String())
+    datafiles = graphene.List(DataFileType, key=graphene.String(), value=graphene.String(), dataset=graphene.String())
+    datasets = graphene.List(DataSetType)
+
+    def resolve_datafile(self, info, **kwargs):
+        id = kwargs.get('id')
+        dbid = kwargs.get('dbid')
+
+        if id is not None:
+            return DataFile.objects.get(iric_data_id=id)
+        elif dbid is not None:
+            return DataFile.objects.get(pk=dbid)
+
+    def resolve_dataset(self, info, **kwargs):
+        id = kwargs.get('id')
+
+        if id is not None:
+            return DataSet.objects.get(iric_data_id=id)
+
+        return None
+
+    def resolve_datafiles(self, info, **kwargs):
+        # qs = DataFile.objects.accessible_to_profile(self.request.user.profile)
+        qs = DataFile.objects
+        key = kwargs.get('key', None)
+        value = kwargs.get('value', None)
+        dataset = kwargs.get('dataset', None)
+
+        if key and value:
+            qs = qs.filter(annotations__contains={key: value})
+        elif key:
+            qs = qs.filter(annotations__has_key=key)
+        elif value:
+            qs = qs.filter(annotations__values__icontains=value)
+
+        if dataset:
+            qs = qs.filter(datasets__iric_data_id=dataset)
+
+        return qs.distinct()
+
+    def resolve_datasets(self, info, **kwargs):
+        return DataSet.objects.all()
+
+
+class Mutation(graphene.ObjectType):
+    pass
+
+
+schema = graphene.Schema(query=Query, auto_camelcase=False)

portal/models.py

@@ -3,7 +3,7 @@ import binascii
 import hashlib
 
 from django.conf import settings
-from django.contrib.auth.models import User
+from django.contrib.auth import get_user_model
 from django.contrib.postgres.fields import HStoreField
 from django.db import models
 from django.db.models import Q
@@ -14,11 +14,11 @@ from private_storage.fields import PrivateFileField
 from portal.storage import HashStorage
 
 
-
 class ProfileManager(models.Manager):
     def exclude_profile(self, profile):
         return super().get_queryset().exclude(id=profile.id)
 
+
 class Profile(models.Model):
     """example Documentation:
     https://simpleisbetterthancomplex.com/tutorial/2016/07/22/how-to-extend-django-user-model.html#onetoone
@@ -31,7 +31,7 @@ class Profile(models.Model):
     accountname = models.CharField(max_length=150, null=True, blank=True)
     unix_username = models.CharField(max_length=150, null=True, blank=True, verbose_name=_("Unix username"))
 
-    user = models.OneToOneField(User, on_delete=models.CASCADE, related_name='profile')
+    user = models.OneToOneField(get_user_model(), on_delete=models.CASCADE, related_name='profile')
     labs = models.ManyToManyField('Lab', related_name='members')
 
     api_token = models.CharField(max_length=64, null=True, unique=True, blank=False, default=None)

portal/storage.py

@@ -34,4 +34,3 @@ class HashStorage(PrivateStorage):
         if not os.listdir(hashdir):
             # clean up
             os.rmdir(hashdir)
-

portal/templates/portal/secure/user/api.html

@@ -16,8 +16,12 @@
         </div>
         <p>
         {% trans 'Use this token to authenticate your API calls by inserting it in the request header under "Iric-Auth-Token".' %}
-        Ex.
         </p>
+        <p>
+        {% trans 'Two APIs exists to query IRIC Data :' %}
+        </p>
+
+        <h3> {% trans 'IRIC Data API v1 (python requests example)' %} </h3>
         <div class="col-10 alert alert-secondary">
             <pre class='mb-0'><code>import requests
 url = '{{ request.scheme }}://{{ request.get_host }}/api/v1/my-datasets/list/json/'
@@ -25,6 +29,24 @@ headers = {'Iric-Auth-Token': '{{user.profile.api_token}}'}
 r = requests.get(url, headers=headers)
 r.json()</code></pre>
         </div>
+        <h3> {% trans 'GraphQL API (python requests example)' %} </h3>
+        <p>
+        <i>{% trans 'NOTE: A GraphQL sandbox is also available online' %} :  <a href="{{ request.scheme }}://{{ request.get_host }}/graphql/">{{ request.scheme }}://{{ request.get_host }}/graphql/<a></i>
+        </p>
+        <div class="col-10 alert alert-secondary">
+            <pre class='mb-0'><code>import requests
+url = '{{ request.scheme }}://{{ request.get_host }}/graphql/'
+headers = {'Iric-Auth-Token': '{{user.profile.api_token}}'}
+query = """{
+  datafiles {
+    filename
+  }
+}
+"""
+r = requests.post(url, headers=headers, json={'query': query})
+r.json()</code></pre>
+        </div>
+
     </div>
 </div>
 

portal/urls.py

@@ -8,19 +8,18 @@ from .views.public import IndexView
 from .views.secure.alert import (AlertCreateView, AlertDeleteView,
                                  AlertJSONListView, AlertListView,
                                  AlertUpdateView)
-from .views.secure.api import (APIView,
-                               AdminDataSetJSONListView,
+from .views.secure.api import (AdminDataSetJSONListView, APIView,
                                DataFileAnnotationJSONView,
+                               DataFileDeleteJSONView,
                                DataFileLookupJSONListView,
                                DataFileMetadataJSONView,
-                               UserDataSetJSONListView,
-                               DataFileDeleteJSONView)
+                               UserDataSetJSONListView)
 from .views.secure.dashboard import AdminDashboardView, DashboardView
 from .views.secure.datafile import (DataFileAnnotateView,
                                     DataFileAnnotationDownloadView,
                                     DataFileBatchAddAnnotation,
+                                    DataFileBatchDelete,
                                     DataFileBatchRemoveAnnotation,
-                                    DataFileBatchDelete,  ########### xj
                                     DataFileDeleteView, DataFileDetailsView,
                                     DataFileDownloadView,
                                     DataFilesJSONListView, DataFilesView,

portal/views/secure/api.py

@@ -2,18 +2,16 @@ import logging
 
 from django.contrib.auth.mixins import LoginRequiredMixin
 from django.db.models import Q
-from django.shortcuts import get_object_or_404
-from django.views.generic import TemplateView
 from django.http import JsonResponse
-from django.views.generic.detail import BaseDetailView
+from django.shortcuts import get_object_or_404
+from django.utils.decorators import method_decorator
 from django.utils.translation import ugettext_lazy as _
-from portal.views import TokenLoginMixin, SlugMixin
 from django.views.decorators.csrf import csrf_exempt
-from django.utils.decorators import method_decorator
-
-from ...models import DataFile, DataSet, Profile
-from ...views import JSONListView, JSONView, StaffViewMixin, ActivePageViewMixin
-
+from django.views.generic import TemplateView
+from django.views.generic.detail import BaseDetailView
+from portal.models import DataFile, DataSet, Profile
+from portal.views import (ActivePageViewMixin, JSONListView, JSONView,
+                          SlugMixin, TokenLoginMixin)
 
 logger = logging.getLogger('debug')
 
@@ -105,7 +103,7 @@ class DataFileDeleteJSONView(TokenLoginMixin, SlugMixin, BaseDetailView):
     def delete(self, request, *args, **kwargs):
         try:
             o = self.get_object()
-        except Exception as e:
+        except Exception:
             return JsonResponse({'error': _('File cannot be found')}, status=403)
 
         if o in DataFile.objects.editable_by_profile(self.request.user.profile).all():

requirements.txt

+aniso8601==7.0.0
 autopep8==1.4.3
 certifi==2018.11.29
 cffi==1.14.3
@@ -12,6 +13,10 @@ django-loginas==0.3.8
 django-model-utils==3.1.2
 django-private-storage==2.2
 flake8==3.6.0
+graphene==2.1.8
+graphene-django==2.15.0
+graphql-core==2.3.2
+graphql-relay==2.0.1
 idna==2.8
 mccabe==0.6.1
 oauthlib==3.1.0
@@ -30,6 +35,8 @@ python3-openid==3.2.0
 pytz==2018.7
 requests==2.21.0
 requests-oauthlib==1.3.0
+Rx==1.6.1
+singledispatch==3.4.0.3
 six==1.12.0
 social-auth-app-django==3.1.0
 social-auth-core==3.3.3