Merge pull request #229 from EBI-Metagenomics/feature/hybrid-and-long…

…-read-assemblies

Hybrid and LR assemblies - experyment tpe

emgapi/models.py

@@ -1023,7 +1023,7 @@ def get_queryset(self):
 
 class ExperimentType(models.Model):
     experiment_type_id = models.SmallIntegerField(
-        db_column='EXPERIMENT_TYPE_ID', primary_key=True, )
+        db_column='EXPERIMENT_TYPE_ID', primary_key=True)
     experiment_type = models.CharField(
         db_column='EXPERIMENT_TYPE', max_length=30,
         help_text="Experiment type, e.g. metagenomic")
@@ -1165,6 +1165,7 @@ class Assembly(models.Model):
         on_delete=models.SET_NULL, null=True, blank=True)
 
     coverage = models.IntegerField(db_column="COVERAGE", null=True, blank=True)
+
     min_gap_length = models.IntegerField(db_column="MIN_GAP_LENGTH", null=True, blank=True)
 
     objects = AssemblyManager()

emgapi/serializers.py

@@ -517,6 +517,9 @@ def get_experiment_type(self, obj):
         read_only=True,
         source='get_runs',
         model=emg_models.Run,
+        related_link_view_name='emgapi_v1:assemblies-runs-list',
+        related_link_url_kwarg='accession',
+        related_link_lookup_field='accession',
         related_link_self_view_name='emgapi_v1:runs-detail',
         related_link_self_lookup_field='accession'
     )
@@ -688,6 +691,7 @@ class BaseAnalysisSerializer(ExplicitFieldsModelSerializer,
         'sample': 'emgapi.serializers.SampleSerializer',
         'study': 'emgapi.serializers.StudySerializer',
         'downloads': 'emgapi.serializers.AnalysisJobDownloadSerializer',
+        'assembly': 'emgapi.serializers.AssemblySerializer',
     }
 
     url = serializers.HyperlinkedIdentityField(

emgapi/urls.py

@@ -164,6 +164,12 @@
     basename='assemblies-analyses'
 )
 
+router.register(
+    r'assemblies/(?P<accession>[^/]+)/runs',
+    views_relations.AssemblyRunsViewSet,
+    basename='assemblies-runs'
+)
+
 router.register(
     r'studies/(?P<accession>[^/]+)'
     r'/pipelines/(?P<release_version>[0-9\.]+)/file',

emgapi/views_relations.py

@@ -416,7 +416,6 @@ class RunAnalysisViewSet(emg_mixins.ListModelMixin,
 
     ordering_fields = (
         'pipeline',
-        # 'accession',
     )
 
     ordering = ('-pipeline',)
@@ -1004,7 +1003,6 @@ class AssemblyAnalysisViewSet(emg_mixins.ListModelMixin,
 
     ordering_fields = (
         'pipeline',
-        # 'accession',
     )
 
     ordering = ('-pipeline',)
@@ -1038,6 +1036,52 @@ def list(self, request, *args, **kwargs):
             .list(request, *args, **kwargs)
 
 
+class AssemblyRunsViewSet(emg_mixins.ListModelMixin,
+                          viewsets.GenericViewSet):
+
+    serializer_class = emg_serializers.RunSerializer
+
+    filter_class = emg_filters.RunFilter
+
+    filter_backends = (
+        DjangoFilterBackend,
+        filters.OrderingFilter,
+    )
+
+    ordering_fields = (
+        'accession',
+    )
+
+    ordering = ('-accession',)
+
+    lookup_field = 'accession'
+    lookup_value_regex = '[^/]+'
+
+    def get_serializer_class(self):
+        return super(AssemblyRunsViewSet, self).get_serializer_class()
+
+    def get_queryset(self):
+        assembly = get_object_or_404(
+            emg_models.Assembly,
+            Q(accession=self.kwargs['accession']) |
+            Q(wgs_accession=self.kwargs['accession']) |
+            Q(legacy_accession=self.kwargs['accession'])
+        )
+        queryset = emg_models.Run.objects \
+            .available(self.request) \
+            .filter(assemblies__in=[assembly])
+        return queryset
+
+    def list(self, request, *args, **kwargs):
+        """
+        Retrieves the runs for the given accession
+        Example:
+        ---
+        `/assemblies/ERZ1385375/runs`
+        """
+        return super(AssemblyRunsViewSet, self) \
+            .list(request, *args, **kwargs)
+
 class GenomeCogsRelationshipsViewSet(emg_mixins.ListModelMixin,
                                      viewsets.GenericViewSet):
     serializer_class = emg_serializers.CogCountSerializer