Merge pull request #125 from EBI-Metagenomics/banner-message-api

Banner message api

emgapi/urls.py

@@ -12,6 +12,8 @@
 # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 # See the License for the specific language governing permissions and
 # limitations under the License.
+from django.conf.urls import url
+
 from rest_framework import routers
 
 from . import views
@@ -399,4 +401,10 @@
     r'antismash-geneclusters',
     views.AntiSmashGeneClustersViewSet,
     base_name='antismash-geneclusters'
-)
+)
+
+urlpatterns = [
+    url(r'^v1/banner-message',
+        views.BannerMessageView.as_view(),
+        name='banner-message'),
+]

emgapi/views.py

@@ -20,22 +20,18 @@
 
 from django.conf import settings
 from django.db.models import Prefetch, Count, Q
-from django.http import Http404
+from django.http import Http404, HttpResponse
 from django.middleware import csrf
-from django.http import HttpResponse
 from django.shortcuts import get_object_or_404
 from django.views.decorators.clickjacking import xframe_options_exempt
 
 from django_filters.rest_framework import DjangoFilterBackend
 
 from rest_framework.response import Response
 
-from rest_framework import filters
-from rest_framework import viewsets, mixins
+from rest_framework import filters, viewsets, mixins, permissions, renderers, status
 from rest_framework.decorators import detail_route, list_route
-from rest_framework import permissions
-from rest_framework import renderers
-from rest_framework import status
+from rest_framework.views import APIView
 
 from . import models as emg_models
 from . import serializers as emg_serializers
@@ -333,7 +329,7 @@ def list(self, request, *args, **kwargs):
         `/studies`
 
         `/studies?fields[studies]=accession,study_name,samples_count,biomes`
-        retrieve only selected fileds
+        retrieve only selected fields
 
         `/studies?include=biomes` with biomes
 
@@ -467,7 +463,7 @@ def list(self, request, *args, **kwargs):
         `/super-studies`
 
         `/super-studies?fields[super-studies]=super_study_id,title`
-        retrieve only selected fileds
+        retrieve only selected fields
 
         `/super-studies?include=biomes` with biomes
 
@@ -570,7 +566,7 @@ def list(self, request, *args, **kwargs):
         `/samples` retrieves list of samples
 
         `/samples?fields[samples]=accession,runs_count,biome`
-        retrieve only selected fileds
+        retrieve only selected fields
 
         `/samples?include=runs` with related runs
 
@@ -626,7 +622,7 @@ def list(self, request, *args, **kwargs):
         `/runs`
 
         `/runs?fields[runs]=accession,experiment_type` retrieve only
-        selected fileds
+        selected fields
 
         Filter by:
         ---
@@ -674,7 +670,7 @@ def list(self, request, *args, **kwargs):
         `/assembly`
 
         `/assembly?fields[assembly]=accession` retrieve only
-        selected fileds
+        selected fields
 
         Filter by:
         ---
@@ -1445,4 +1441,15 @@ class AntiSmashGeneClustersViewSet(mixins.RetrieveModelMixin,
     )
 
     ordering = ('-name',)
-
+
+
+class BannerMessageView(APIView):
+
+    def get(self, request):
+        """Get the content of the banner message if any
+        """
+        message = ""
+        if settings.BANNER_MESSAGE_FILE and os.path.isfile(settings.BANNER_MESSAGE_FILE):
+            with open(settings.BANNER_MESSAGE_FILE, 'r') as msg_file:
+                message = msg_file.read().strip()
+        return Response({"message": message})

emgapianns/views.py

@@ -35,8 +35,8 @@
 from rest_framework.views import APIView
 from rest_framework.response import Response
 from rest_framework.settings import api_settings
-from rest_framework import viewsets
-from rest_framework import status
+from rest_framework import viewsets, status
+from rest_framework.exceptions import NotFound
 
 from emgapi import serializers as emg_serializers
 from emgapi import models as emg_models
@@ -476,7 +476,7 @@ class AnalysisPfamRelationshipViewSet(  # NOQA
     m_mixins.AnalysisJobAnnotationMixin,
     m_viewsets.ListReadOnlyModelViewSet):
     """
-    Retrieves Pfram entries for the given accession
+    Retrieves Pfam entries for the given accession
     Example:
     ---
     `/analyses/MGYA00102827/pfam-entries`
@@ -872,14 +872,17 @@ def get_queryset(self):
             self.kwargs.get(self.lookup_field, None).strip())
         organism = m_models.Organism.objects.filter(lineage=lineage) \
             .only('id')
+
         if len(organism) == 0:
-            raise Http404(("Attribute error '%s'." % self.lookup_field))
+            raise NotFound("Lineage not found. Lineage: " + lineage)
+
         job_ids = m_models.AnalysisJobTaxonomy.objects \
             .filter(
                 M_Q(taxonomy__organism__in=organism) |
                 M_Q(taxonomy_lsu__organism__in=organism) |
                 M_Q(taxonomy_ssu__organism__in=organism)
             ).distinct('job_id')
+
         return emg_models.AnalysisJob.objects \
             .filter(job_id__in=job_ids) \
             .available(self.request)

emgcli/settings.py

@@ -573,3 +573,9 @@ def show_toolbar(request):
     RESULTS_DIR = EMG_CONF['emg']['results_dir']
 except KeyError:
     RESULTS_DIR = os.path.join(expanduser("~"), 'results')
+
+try:
+    # Banner message, the content of this file will be shown on the website.
+    BANNER_MESSAGE_FILE = EMG_CONF['emg']['banner_message_file']
+except KeyError:
+    BANNER_MESSAGE_FILE = None

emgcli/urls.py

@@ -30,9 +30,8 @@
 from rest_framework_jwt.views import verify_jwt_token
 
 from emgapi.urls import router as emg_router
-from emgapi.urls import mydata_router
-from emgapi.urls import utils_router
-from emgapianns.urls import mongo_router, urlpatterns as mongo_url_patterns
+from emgapi.urls import mydata_router, utils_router, urlpatterns as emgapi_urlpatterns 
+from emgapianns.urls import mongo_router, urlpatterns as mongo_urlpatterns
 from emgapianns.urls import router as emg_ext_router
 
 from openapi_codec import OpenAPICodec
@@ -109,10 +108,10 @@ def render(self, data, accepted_media_type=None, renderer_context=None):
         name='verify_jwt_token_v1'),
 ]
 
-# emgapianns custom endpoints
-urlpatterns += mongo_url_patterns
+urlpatterns += mongo_urlpatterns
+urlpatterns += emgapi_urlpatterns
 
-# Admin
+# admin
 urlpatterns += [
     url('admin/', admin.site.urls),
 ]