Merge branch '27-backend-cleaning' into 'master'

Resolve "Reorganize backend architecture"

Closes #27 and #33

See merge request !7

backend/metagenedb/apps/accounts/tests.py → backend/metagenedb/api/accounts/tests.py

@@ -12,7 +12,7 @@ class TestAccounts(APITestCase):
     def test_obtain_jwt(self):
 
         # create an inactive user
-        url = reverse('api-jwt-auth')
+        url = reverse('api:auth:api-jwt-auth')
         u = User.objects.create_user(username='user', email='user@foo.com', password='pass')
         u.is_active = False
         u.save()
@@ -39,7 +39,7 @@ class TestAccounts(APITestCase):
         payload = jwt_payload_handler(user)
         token = jwt_encode_handler(payload)
 
-        verify_url = reverse('api-jwt-verify')
+        verify_url = reverse('api:auth:api-jwt-verify')
         credentials = {
             'token': token
         }

backend/metagenedb/apps/accounts/urls.py → backend/metagenedb/api/accounts/urls.py

@@ -8,17 +8,17 @@ from rest_framework_jwt.views import (
 
 urlpatterns = [
     re_path(
-        r'^auth/obtain_token/',
+        r'^obtain_token/',
         obtain_jwt_token,
         name='api-jwt-auth'
     ),
     re_path(
-        r'^auth/refresh_token/',
+        r'^refresh_token/',
         refresh_jwt_token,
         name='api-jwt-refresh'
     ),
     re_path(
-        r'^auth/verify_token/',
+        r'^verify_token/',
         verify_jwt_token,
         name='api-jwt-verify'
     ),

backend/metagenedb/api/catalog/urls.py

+from django.conf.urls import url, include
+from rest_framework.routers import DefaultRouter
+
+from metagenedb.api.catalog.views import GeneViewSet
+
+
+api_router = DefaultRouter()
+api_router.register(r'genes', GeneViewSet, base_name='genes')
+
+
+urlpatterns = [
+    url(r'v1/', include((api_router.urls, 'v1')))
+]

backend/metagenedb/api/catalog/views/__init__.py

+from .gene import GeneViewSet  # noqa
+
+__all__ = ['GeneViewSet']

backend/metagenedb/api/catalog/views/gene.py

+import pandas as pd
+from rest_framework.viewsets import GenericViewSet
+from rest_framework import mixins
+from rest_framework.decorators import action
+from rest_framework.response import Response
+
+from metagenedb.common.utils.df_operations import get_mask
+from metagenedb.apps.catalog.models import Gene
+from metagenedb.apps.catalog.serializers import GeneSerializer
+
+
+class GeneViewSet(mixins.ListModelMixin,
+                  mixins.RetrieveModelMixin,
+                  GenericViewSet):
+    queryset = Gene.objects.all()
+    serializer_class = GeneSerializer
+    GENE_LENGTH_COL = 'gene_length'
+
+    def _count_windows(self, df, window_size=10000, window_col=GENE_LENGTH_COL):
+        """
+        Count how many line of the df belong to each windows defined by the window_size for the window_col
+        :param df:
+        :param window_col: column concerned by the window
+        :param window_size: size of the window
+        :return: {'data': COUNTS_BY_WINDOW, 'labels': START-END}
+        """
+        all_ranges = [(i, i + window_size) for i in range(0, df[window_col].max(), window_size)]
+        data = []
+        labels = []
+        for rg in all_ranges:
+            labels.append(f"{rg[0]}-{rg[1]-1}")
+            data.append(df[get_mask(df, rg, window_col)].count()['gene_length'])
+        return {
+            'counts': data,
+            'labels': labels
+        }
+
+    @action(methods=['get'], detail=False)
+    def gene_length(self, request, window_size=10000):
+        if 'window_size' in request.query_params:
+            window_size = int(request.query_params.get('window_size'))
+        df = pd.DataFrame(list(self.queryset.values(self.GENE_LENGTH_COL)))
+        return Response(
+            {'results': self._count_windows(df, window_size)}
+        )

backend/metagenedb/apps/catalog/views/test_gene.py → backend/metagenedb/api/catalog/views/test_gene.py

@@ -2,18 +2,21 @@ from django.contrib.auth.models import User
 from django.test import TestCase
 from django.urls import reverse
 
+import pandas as pd
 from rest_framework import status
 from rest_framework_jwt.settings import api_settings
 
+from metagenedb.api.catalog.views.gene import GeneViewSet
+
 
 class TestGenes(TestCase):
-    """Post Tests"""
 
     def test_get_genes_no_auth(self):
         """
         Unauthenticated users should be able to access genes
+        @TODO make unaccessible
         """
-        url = reverse('genes')
+        url = reverse('api:catalog:v1:genes-list')
         resp = self.client.get(url)
         self.assertEqual(resp.status_code, status.HTTP_200_OK)
 
@@ -31,6 +34,25 @@ class TestGenes(TestCase):
         payload = jwt_payload_handler(user)
         token = jwt_encode_handler(payload)
 
-        url = reverse('genes')
+        url = reverse('api:catalog:v1:genes-list')
         resp = self.client.get(url, format='json', HTTP_AUTHORIZATION=f"JWT {token}")
         self.assertEqual(resp.status_code, status.HTTP_200_OK)
+
+
+class TestCountWindows(TestCase):
+
+    def setUp(self):
+        self.window_col = "gene_length"
+        self.df = pd.DataFrame(
+            [22, 29, 35],
+            columns=[self.window_col]
+        )
+
+    def test_simple_count_window10(self):
+        expected_dict = {
+            'labels': ['0-9', '10-19', '20-29', '30-39'],
+            'counts': [0, 0, 2, 1]
+        }
+        geneviewset = GeneViewSet()
+        test_dict = geneviewset._count_windows(self.df, 10, window_col=self.window_col)
+        self.assertDictEqual(test_dict, expected_dict)

backend/metagenedb/api/urls.py

+from django.urls import include, path
+
+
+urlpatterns = [
+    path('auth/', include(('metagenedb.api.accounts.urls', 'auth'))),
+    path('catalog/', include(('metagenedb.api.catalog.urls', 'catalog')))
+]

backend/metagenedb/apps/accounts/apps.py

-from django.apps import AppConfig
-
-
-class AccountsConfig(AppConfig):
-    name = 'accounts'

backend/metagenedb/apps/catalog/serializers.py

-from rest_framework import serializers
-from .models import Gene, Function
-
-
-class FunctionSerializer(serializers.ModelSerializer):
-    class Meta:
-        model = Function
-        fields = ('function_id', 'source', 'name')
-
-
-class GeneSerializer(serializers.ModelSerializer):
-    functions = FunctionSerializer(many=True, read_only=True)
-
-    class Meta:
-        model = Gene
-        fields = ('gene_id', 'gene_length', 'functions')

backend/metagenedb/apps/catalog/urls.py

-from django.urls import re_path
-
-from . import views
-
-
-urlpatterns = [
-    re_path(r'^api/genes/$', views.gene_list, name='genes'),
-    re_path(r'^api/genes/(?P<gene_id>.*)$', views.gene_detail),
-    re_path(r'^api/gene_length$', views.gene_length, name='gene_length'),
-]

backend/metagenedb/apps/catalog/views/__init__.py

-from .gene import gene_detail, gene_list  # noqa
-from .statistics import gene_length  # noqa
\ No newline at end of file

backend/metagenedb/apps/catalog/views/gene.py

-import logging
-
-from rest_framework import status
-from rest_framework.decorators import (
-    api_view,
-    authentication_classes,
-    permission_classes
-)
-from rest_framework.response import Response
-from django.core.paginator import Paginator, EmptyPage, PageNotAnInteger
-
-from metagenedb.apps.catalog.models import Gene
-from metagenedb.apps.catalog.serializers import GeneSerializer
-
-logging.basicConfig(level=logging.INFO)
-_LOGGER = logging.getLogger(__name__)
-
-
-@api_view(['GET'])
-@authentication_classes(())
-@permission_classes(())
-def gene_list(request):
-    """
-    List genes
-    """
-    next_page = 1
-    previous_page = 1
-    genes = Gene.objects.all()
-    page = request.GET.get('page', 1)
-    paginator = Paginator(genes, 10)
-    try:
-        data = paginator.page(page)
-    except PageNotAnInteger:
-        data = paginator.page(1)
-    except EmptyPage:
-        data = paginator.page(paginator.num_pages)
-
-    serializer = GeneSerializer(data, context={'request': request}, many=True)
-    if data.has_next():
-        next_page = data.next_page_number()
-    if data.has_previous():
-        previous_page = data.previous_page_number()
-
-    return Response(
-        {'data': serializer.data, 'count': paginator.count, 'numpages': paginator.num_pages,
-         'nextlink': '/api/genes/?page=' + str(next_page),
-         'prevlink': '/api/genes/?page=' + str(previous_page)}
-    )
-
-
-@api_view(['GET'])
-def gene_detail(request, gene_id):
-    """
-    Retrieve, update or delete a gene instance.
-    """
-    try:
-        gene = Gene.objects.get(gene_id=gene_id)
-    except Gene.DoesNotExist:
-        return Response(status=status.HTTP_404_NOT_FOUND)
-
-    serializer = GeneSerializer(gene, context={'request': request})
-    return Response(serializer.data)

backend/metagenedb/apps/catalog/views/statistics.py

-import pandas as pd
-from rest_framework.decorators import api_view
-from rest_framework.response import Response
-
-from metagenedb.apps.catalog.models import Gene
-
-
-GENE_LENGTH_COL = 'gene_length'
-
-
-def _get_mask(df, rg, col_name):
-    """
-    rg is a range, e.g. (10-20)
-    """
-    return (df[col_name] >= rg[0]) & (df[col_name] < rg[1])
-
-
-def _count_windows(df, window_col, window_size=10000):
-    """
-    Count how many line of the df belong to each windows defined by the window_size for the window_col
-    :param df:
-    :param window_col: column concerned by the window
-    :param window_size: size of the window
-    :return: {'data': COUNTS_BY_WINDOW, 'labels': START-END}
-    """
-    all_ranges = [(i, i + window_size) for i in range(0, df[window_col].max(), window_size)]
-    data = []
-    labels = []
-    for rg in all_ranges:
-        labels.append(f"{rg[0]}-{rg[1]-1}")
-        data.append(df[_get_mask(df, rg, window_col)].count()['gene_length'])
-    return {
-        'counts': data,
-        'labels': labels
-    }
-
-
-@api_view(['GET'])
-def gene_length(request, window_size=10000):
-    if 'window_size' in request.query_params:
-        window_size = int(request.query_params.get('window_size'))
-    df = pd.DataFrame(list(Gene.objects.all().values(GENE_LENGTH_COL)))
-    return Response({
-        'data': _count_windows(df, GENE_LENGTH_COL, window_size)
-    })

backend/metagenedb/apps/catalog/views/test_statistics.py

-import pandas as pd
-from unittest import TestCase
-
-from .statistics import _count_windows
-
-
-class TestCountWindows(TestCase):
-
-    def setUp(self):
-        self.window_col = "gene_length"
-        self.df = pd.DataFrame(
-            [22, 29, 35],
-            columns=[self.window_col]
-        )
-
-    def test_simple_count_window10(self):
-        expected_dict = {
-            'labels': ['0-9', '10-19', '20-29', '30-39'],
-            'counts': [0, 0, 2, 1]
-        }
-        test_dict = _count_windows(self.df, self.window_col, 10)
-        self.assertDictEqual(test_dict, expected_dict)

backend/metagenedb/common/utils/df_operations.py

+def get_mask(df, range, col_name):
+    """
+    Get mask for a dataframe for a given range on a column defined by col_name
+    Lower is included but not upper:
+      e.g (4,8): 4, 5, 6 and 7 are selected
+    """
+    return (df[col_name] >= range[0]) & (df[col_name] < range[1])