Merge pull request #65 from EBI-Metagenomics/develop

Develop

emgapi/filters.py

@@ -424,6 +424,7 @@ def filter_include(self, qs, name, value):
     class Meta:
         model = emg_models.Sample
         fields = (
+            'accession',
             'experiment_type',
             'biome_name',
             'lineage',
@@ -448,6 +449,21 @@ class Meta:
 
 class RunFilter(django_filters.FilterSet):
 
+    accession = filters.ModelMultipleChoiceFilter(
+        queryset=emg_models.Run.objects,
+        to_field_name='accession',
+        method='filter_accession',
+        distinct=True,
+        label='Run accession',
+        help_text='Run accession',
+        widget=QueryArrayWidget
+    )
+
+    def filter_accession(self, qs, name, values):
+        if values:
+            qs = qs.available(self.request).filter(accession__in=values)
+        return qs
+
     experiment_type = filters.ModelMultipleChoiceFilter(
         queryset=emg_models.ExperimentType.objects,
         to_field_name='experiment_type',
@@ -580,13 +596,19 @@ def filter_include(self, qs, name, value):
     class Meta:
         model = emg_models.Run
         fields = (
+            'accession',
+            'experiment_type',
             'biome_name',
             'lineage',
-            'experiment_type',
+            'species',
             'instrument_platform',
             'instrument_model',
-            'species',
+            'metadata_key',
+            'metadata_value_gte',
+            'metadata_value_lte',
+            'metadata_value',
             'sample_accession',
+            'study_accession',
             'include',
         )
 

emgapi/models.py

@@ -28,8 +28,8 @@
 from __future__ import unicode_literals
 
 from django.db import models
-from django.db.models import Sum, Count, Case, When
-from django.db.models import CharField, IntegerField, Value
+from django.db.models import Count
+from django.db.models import CharField, Value
 from django.db.models.functions import Concat, Cast
 from django.db.models import Q
 from django.db.models import Prefetch
@@ -106,7 +106,8 @@ def available(self, request=None):
             _instance = _query_filters[self.__class__.__name__]
             if isinstance(self, self.__class__):
                 if request is not None and request.user.is_authenticated():
-                    q.extend(_instance['authenticated'])
+                    if not request.user.is_superuser:
+                        q.extend(_instance['authenticated'])
                 else:
                     q.extend(_instance['all'])
             return self.distinct().filter(*q)
@@ -156,12 +157,20 @@ class PipelineManager(models.Manager):
 
     def get_queryset(self):
         return PipelineQuerySet(self.model, using=self._db) \
-            .annotate(analyses_count=Count('analyses', distinct=True)) \
-            .annotate(samples_count=Sum(Case(
-                When(analyses__sample__is_public=1, then=1),
-                default=0,
-                output_field=IntegerField()
-            )))
+            .annotate(
+                analyses_count=Count(
+                    'analyses', filter=(
+                        Q(analyses__analysis_status_id=3) |
+                        Q(analyses__analysis_status_id=6)
+                    ), distinct=True)
+            ) \
+            .annotate(
+                samples_count=Count(
+                    'analyses__sample', filter=(
+                        Q(analyses__analysis_status_id=3) |
+                        Q(analyses__analysis_status_id=6)
+                    ), distinct=True)
+            )
 
 
 class Pipeline(models.Model):
@@ -231,11 +240,7 @@ class BiomeManager(models.Manager):
 
     def get_queryset(self):
         return BiomeQuerySet(self.model, using=self._db) \
-            .annotate(samples_count=Sum(Case(
-                When(samples__is_public=1, then=1),
-                default=0,
-                output_field=IntegerField()
-            )))
+            .annotate(samples_count=Count('samples', distinct=True))
 
 
 class Biome(models.Model):
@@ -275,16 +280,8 @@ class PublicationManager(models.Manager):
 
     def get_queryset(self):
         return PublicationQuerySet(self.model, using=self._db) \
-            .annotate(studies_count=Sum(Case(
-                When(studies__is_public=1, then=1),
-                default=0,
-                output_field=IntegerField()
-            ))) \
-            .annotate(samples_count=Sum(Case(
-                When(studies__samples__is_public=1, then=1),
-                default=0,
-                output_field=IntegerField()
-            )))
+            .annotate(studies_count=Count('studies', distinct=True)) \
+            .annotate(samples_count=Count('studies__samples', distinct=True))
 
 
 class Publication(models.Model):
@@ -520,11 +517,7 @@ def get_queryset(self):
         # TODO: remove biome when schema updated
         return StudyQuerySet(self.model, using=self._db) \
             .defer('biome') \
-            .annotate(samples_count=Sum(Case(
-                When(samples__is_public=1, then=1),
-                default=0,
-                output_field=IntegerField()
-            )))
+            .annotate(samples_count=Count('samples'))
 
     def available(self, request):
         return self.get_queryset().available(request)
@@ -799,16 +792,14 @@ class ExperimentTypeManager(models.Manager):
 
     def get_queryset(self):
         return ExperimentTypeQuerySet(self.model, using=self._db) \
-            .annotate(runs_count=Sum(Case(
-                When(runs__status_id=4, then=1),
-                default=0,
-                output_field=IntegerField()
-            ))) \
-            .annotate(samples_count=Sum(Case(
-                When(runs__sample__is_public=1, then=1),
-                default=0,
-                output_field=IntegerField()
-            )))
+            .annotate(
+                samples_count=Count(
+                    'runs__sample', filter=Q(runs__status_id=4), distinct=True)
+            ) \
+            .annotate(
+                runs_count=Count(
+                    'runs', filter=Q(runs__status_id=4), distinct=True)
+            )
 
 
 class ExperimentType(models.Model):

emgapi/views_relations.py

@@ -419,7 +419,7 @@ def get_queryset(self):
             release_version=self.kwargs[self.lookup_field])
         queryset = emg_models.Sample.objects \
             .available(self.request, prefetch=True) \
-            .filter(analysis__pipeline=pipeline)
+            .filter(analyses__pipeline=pipeline)
         if 'runs' in self.request.GET.get('include', '').split(','):
             _qs = emg_models.Run.objects.available(self.request)
             queryset = queryset.prefetch_related(

requirements-test.txt

@@ -3,7 +3,7 @@
 # run pip install -r requirements-test
 
 pytest
-pytest-django
+pytest-django~=3.2.1
 
 model_mommy
 mock_services

setup.py

@@ -7,7 +7,7 @@
 _requirements = os.path.join(_base, 'requirements.txt')
 _requirements_test = os.path.join(_base, 'requirements-test.txt')
 
-version = "1.3.0"
+version = "1.3.1"
 
 install_requirements = []
 with open(_requirements) as f: