ENH: Expose species (#32)

ccdb/api/urls.py

@@ -7,6 +7,7 @@ from ..utils import viewsets as utils_viewsets
 from ..collections_ccdb import viewsets as collections_viewsets
 from ..projects import viewsets as projects_viewsets
 from ..locations import viewsets as locations_viewsets
+from ..species import viewsets as species_viewsets
 
 
 router = routers.DefaultRouter(trailing_slash=False)
@@ -28,6 +29,10 @@ router.register(r'projects', projects_viewsets.ProjectViewSet)
 router.register(r'regions', locations_viewsets.RegionViewSet)
 router.register(r'sites', locations_viewsets.SiteViewSet)
 router.register(r'study-locations', locations_viewsets.StudyLocationViewSet)
+# Species
+router.register(r'species', species_viewsets.SpeciesViewSet)
+router.register(r'collection-species',
+                species_viewsets.CollectionSpeciesViewSet)
 
 urlpatterns = [
     url(r'^auth/login/', api_v.Login.as_view()),

ccdb/collections_ccdb/filters.py

@@ -4,6 +4,7 @@ from django_filters import rest_framework as filters
 from .models import Collection, CollectionMethod, ADFGPermit
 from ccdb.projects.models import Project
 from ccdb.locations.models import Region, Site, StudyLocation
+from ccdb.species.models import Species
 
 
 class CollectionFilter(filters.FilterSet):
@@ -43,9 +44,15 @@ class CollectionFilter(filters.FilterSet):
         queryset=ADFGPermit.objects.all(),
     )
 
+    species = ModelMultipleChoiceFilter(
+        name='collection_species__species__id',
+        to_field_name='id',
+        queryset=Species.objects.all(),
+    )
+
     class Meta:
         model = Collection
         fields = ['project', 'region', 'site', 'study_location',
                   'collection_method', 'number_of_traps',
                   'collection_start_date', 'collection_end_date',
-                  'adfg_permit']
+                  'adfg_permit', 'species']

ccdb/collections_ccdb/serializers.py

@@ -16,6 +16,8 @@ class CollectionSerializer(serializers.ModelSerializer):
         'collection_type':
             'ccdb.collections_ccdb.serializers.CollectionTypeSerializer',
         'flaw': 'ccdb.collections_ccdb.serializers.FlawSerializer',
+        'collection_species':
+            'ccdb.species.serializers.CollectionSpeciesSerializer',
     }
 
     class Meta:
@@ -25,7 +27,8 @@ class CollectionSerializer(serializers.ModelSerializer):
                   'collection_start_date', 'collection_start_time',
                   'collection_end_date', 'collection_end_time',
                   'storage_location', 'specimen_state', 'process_type',
-                  'reagent', 'adfg_permit', 'flaw', 'display_name')
+                  'reagent', 'adfg_permit', 'flaw', 'display_name',
+                  'collection_species')
 
 
 class ADFGPermitSerializer(serializers.ModelSerializer):

ccdb/species/serializers.py

@@ -0,0 +1,21 @@
+from rest_framework_json_api import serializers
+
+from .models import Species, CollectionSpecies
+
+
+class SpeciesSerializer(serializers.ModelSerializer):
+    class Meta:
+        model = Species
+        fields = ('common_name', 'genus', 'species', 'parasite', 'sort_order')
+
+
+class CollectionSpeciesSerializer(serializers.ModelSerializer):
+    included_serializers = {
+        'collection': 'ccdb.collections_ccdb.serializers.CollectionSerializer',
+        'species': 'ccdb.species.serializers.SpeciesSerializer',
+    }
+
+    class Meta:
+        model = CollectionSpecies
+        fields = ('id', 'sex', 'count', 'count_estimated', 'collection',
+                  'species')

ccdb/species/viewsets.py

@@ -0,0 +1,14 @@
+from rest_framework import viewsets
+
+from .models import Species, CollectionSpecies
+from .serializers import SpeciesSerializer, CollectionSpeciesSerializer
+
+
+class SpeciesViewSet(viewsets.ModelViewSet):
+    queryset = Species.objects.all()
+    serializer_class = SpeciesSerializer
+
+
+class CollectionSpeciesViewSet(viewsets.ModelViewSet):
+    queryset = CollectionSpecies.objects.all()
+    serializer_class = CollectionSpeciesSerializer