Merge pull request #51 from ola-t/master

minor fixes
EBI-Metagenomics · Jan 18, 2018 · 669c2dd · 669c2dd
2 parents b8aa942 + 4a9e488
commit 669c2dd
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Showing 2 changed files with 9 additions and 7 deletions.
diff --git a/emgapi/models.py b/emgapi/models.py
@@ -28,7 +28,7 @@
 from __future__ import unicode_literals
 
 from django.db import models
-from django.db.models import Count, Case, When, IntegerField
+from django.db.models import Sum, Count, Case, When, IntegerField
 from django.db.models import Q
 from django.db.models import Prefetch
 
@@ -140,7 +140,7 @@ class PipelineManager(models.Manager):
     def get_queryset(self):
         return PipelineQuerySet(self.model, using=self._db) \
             .annotate(analysis_count=Count('analysis', distinct=True)) \
-            .annotate(samples_count=Count(Case(
+            .annotate(samples_count=Sum(Case(
                 When(analysis__sample__is_public=1, then=1),
                 default=0,
                 output_field=IntegerField()
@@ -214,7 +214,7 @@ class BiomeManager(models.Manager):
 
     def get_queryset(self):
         return BiomeQuerySet(self.model, using=self._db) \
-            .annotate(samples_count=Count(Case(
+            .annotate(samples_count=Sum(Case(
                 When(samples__is_public=1, then=1),
                 default=0,
                 output_field=IntegerField()
@@ -258,12 +258,12 @@ class PublicationManager(models.Manager):
 
     def get_queryset(self):
         return PublicationQuerySet(self.model, using=self._db) \
-            .annotate(studies_count=Count(Case(
+            .annotate(studies_count=Sum(Case(
                 When(studies__is_public=1, then=1),
                 default=0,
                 output_field=IntegerField()
             ))) \
-            .annotate(samples_count=Count(Case(
+            .annotate(samples_count=Sum(Case(
                 When(studies__samples__is_public=1, then=1),
                 default=0,
                 output_field=IntegerField()
@@ -345,7 +345,7 @@ def get_queryset(self):
         # TODO: remove biome when schema updated
         return StudyQuerySet(self.model, using=self._db) \
             .defer('biome') \
-            .annotate(samples_count=Count(Case(
+            .annotate(samples_count=Sum(Case(
                 When(samples__is_public=1, then=1),
                 default=0,
                 output_field=IntegerField()
@@ -582,7 +582,7 @@ class ExperimentTypeManager(models.Manager):
     def get_queryset(self):
         return ExperimentTypeQuerySet(self.model, using=self._db) \
             .annotate(runs_count=Count('runs', distinct=True)) \
-            .annotate(samples_count=Count(Case(
+            .annotate(samples_count=Sum(Case(
                 When(runs__sample__is_public=1, then=1),
                 default=0,
                 output_field=IntegerField()

diff --git a/emgapianns/management/commands/import_taxonomy.py b/emgapianns/management/commands/import_taxonomy.py
@@ -22,6 +22,8 @@
             'species'],
     '4.0': ['super kingdom', 'kingdom', 'phylum', 'class', 'order', 'family',
             'genus', 'species'],
+    '4.1': ['super kingdom', 'kingdom', 'phylum', 'class', 'order', 'family',
+            'genus', 'species'],
 }