add route to get gene length repartition

backend/metagenedb/apps/catalog/admin/admin.py

-from django.contrib import admin
-
-from metagenedb.apps.catalog.models import Gene, Function, KeggOrthology
-
-
-@admin.register(Gene)
-class GeneAdmin(admin.ModelAdmin):
-
-    list_display = ('gene_id', 'gene_length', 'get_functions')
-    search_fields = ('gene_id',)
-
-    def get_functions(self, obj):
-        return ",".join([str(f) for f in obj.functions.all()])
-    get_functions.short_description = 'Functions'
-
-
-@admin.register(KeggOrthology)
-class KeggOrthologyAdmin(admin.ModelAdmin):
-
-    list_display = ('function_id', 'name', 'long_name', 'ec_number', 'source')
-    search_fields = ('function_id',)
-
-
-@admin.register(Function)
-class FunctionAdmin(admin.ModelAdmin):
-
-    list_display = ('function_id', 'name', 'source')
-    search_fields = ('function_id',)

backend/metagenedb/apps/catalog/urls.py

@@ -5,4 +5,5 @@ 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 .genes import gene_detail, gene_list  # noqa
\ No newline at end of file
+from .genes import gene_detail, gene_list  # noqa
+from .statistics import gene_length  # noqa
\ No newline at end of file

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

@@ -30,9 +30,11 @@ def gene_list(request):
     if data.has_previous():
         previousPage = data.previous_page_number()
 
-    return Response({'data': serializer.data, 'count': paginator.count, 'numpages': paginator.num_pages,
-                     'nextlink': '/api/genes/?page=' + str(nextPage),
-                     'prevlink': '/api/genes/?page=' + str(previousPage)})
+    return Response(
+        {'data': serializer.data, 'count': paginator.count, 'numpages': paginator.num_pages,
+         'nextlink': '/api/genes/?page=' + str(nextPage),
+         'prevlink': '/api/genes/?page=' + str(previousPage)}
+    )
 
 
 @api_view(['GET'])

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 {
+        'data': data,
+        'labels': labels
+    }
+
+@api_view(['GET'])
+def gene_length(request):
+    df = pd.DataFrame(list(Gene.objects.all().values(GENE_LENGTH_COL)))
+    return Response({
+        'data': _count_windows(df, GENE_LENGTH_COL)
+    })

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'],
+            'data': [0, 0, 2, 1]
+        }
+        test_dict = _count_windows(self.df, self.window_col, 10)
+        self.assertDictEqual(test_dict, expected_dict)