allow retrieving fasta file from gene list

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

@@ -14,3 +14,4 @@ class GeneQueryParams(PaginatedQueryParams):
     tax_id = fields.Integer()
     function = fields.String()
     source = fields.String()
+    fasta = fields.Boolean()

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

+from io import StringIO
+
+from django.http import HttpResponse
 from drf_yasg.utils import swagger_auto_schema
+from marshmallow.exceptions import ValidationError
+from rest_framework.response import Response
+from rest_framework.status import HTTP_422_UNPROCESSABLE_ENTITY
 
 from metagenedb.apps.catalog.models import Gene
 from metagenedb.api.catalog.filters import GeneFilter
@@ -18,8 +24,26 @@ class GeneViewSet(BulkViewSet):
     @swagger_auto_schema(
         tags=['Genes'],
     )
-    def list(self, *args, **kwargs):
-        return super().list(*args, **kwargs)
+    def list(self, request, *args, **kwargs):
+        try:
+            query_params = self.query_params_parser().load(request.query_params)
+        except ValidationError as validation_error:
+            error_message = validation_error.normalized_messages()
+            error_message.update({
+                'allowed_query_params': ', '.join(self.query_params_parser().declared_fields.keys())
+            })
+            return Response(error_message, status=HTTP_422_UNPROCESSABLE_ENTITY)
+        if query_params.get('fasta', False) is True:
+            queryset = self.filter_queryset(self.get_queryset())
+            fasta_file = StringIO()
+            for gene in queryset.iterator():
+                fasta_file.write(gene.fasta)
+            # generate the file
+            response = HttpResponse(fasta_file.getvalue(), content_type='text/fasta')
+            filename = 'metagenedb_sequences.fasta'
+            response['Content-Disposition'] = 'attachment; filename=%s' % filename
+            return response
+        return super().list(request, *args, **kwargs)
 
     @swagger_auto_schema(
         tags=['Genes'],

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

@@ -28,6 +28,10 @@ class Gene(models.Model):
     def __str__(self):
         return self.gene_id
 
+    @property
+    def fasta(self):
+        return f">{self.gene_id}\n{self.sequence}\n"
+
     class Meta:
         ordering = ['-gene_id']
 

docker-compose.yaml

@@ -21,7 +21,7 @@ services:
   postgresql:
     container_name: postgresql
     image: postgres:11.4-alpine
-    shm_size: '2gb'
+    shm_size: '8gb'
     ports:
       - "5433:5432"
     volumes: