Merge pull request #433 from bento-platform/feat/individual-phenopackets

feat(patients): add individual phenopackets endpoint w/ attachment option

chord_metadata_service/patients/api_views.py

@@ -1,9 +1,12 @@
+import re
+
 from datetime import datetime
 
 from rest_framework import viewsets, filters, mixins, serializers
+from rest_framework.decorators import action
 from rest_framework.response import Response
-from rest_framework.views import APIView
 from rest_framework.settings import api_settings
+from rest_framework.views import APIView
 from django.conf import settings
 from django.utils.decorators import method_decorator
 from django.views.decorators.cache import cache_page
@@ -22,6 +25,7 @@
 from chord_metadata_service.logger import logger
 from chord_metadata_service.phenopackets.api_views import BIOSAMPLE_PREFETCH, PHENOPACKET_PREFETCH
 from chord_metadata_service.phenopackets.models import Phenopacket
+from chord_metadata_service.phenopackets.serializers import PhenopacketSerializer
 from chord_metadata_service.restapi.api_renderers import (
     FHIRRenderer,
     PhenopacketsRenderer,
@@ -97,6 +101,27 @@ def list(self, request, *args, **kwargs):
 
         return super(IndividualViewSet, self).list(request, *args, **kwargs)
 
+    @action(detail=True, methods=["GET", "POST"])
+    def phenopackets(self, request, *_args, **_kwargs):
+        as_attachment = request.query_params.get("attachment", "") in ("1", "true", "yes")
+        individual = self.get_object()
+
+        phenopackets = (
+            Phenopacket.objects
+            .filter(subject=individual)
+            .prefetch_related(*PHENOPACKET_PREFETCH)
+            .order_by("id")
+        )
+
+        filename_safe_id = re.sub(r"[\\/:*?\"<>|]", "_", individual.id)
+        return Response(
+            PhenopacketSerializer(phenopackets, many=True).data,
+            headers=(
+                {"Content-Disposition": f"attachment; filename=\"{filename_safe_id}_phenopackets.json\""}
+                if as_attachment else {}
+            ),
+        )
+
 
 class BatchViewSet(mixins.ListModelMixin, viewsets.GenericViewSet):
     """

chord_metadata_service/patients/tests/test_api.py

@@ -154,7 +154,7 @@ def test_csv_export(self):
             self.assertIn(column, [column_name.lower() for column_name in headers])
 
 
-class IndividualFullTextSearchTest(APITestCase):
+class IndividualWithPhenopacketSearchTest(APITestCase):
     """ Test for api/individuals?search= """
 
     def setUp(self):
@@ -165,7 +165,7 @@ def setUp(self):
             **ph_c.valid_phenopacket(subject=self.individual_one, meta_data=self.metadata_1)
         )
 
-    def test_search(self):
+    def test_search(self):  # test full-text search
         get_resp_1 = self.client.get('/api/individuals?search=P49Y')
         self.assertEqual(get_resp_1.status_code, status.HTTP_200_OK)
         response_obj_1 = get_resp_1.json()
@@ -176,13 +176,25 @@ def test_search(self):
         response_obj_2 = get_resp_2.json()
         self.assertEqual(len(response_obj_2['results']), 2)
 
-    def test_search_bento_search_format(self):
+    def test_search_bento_search_format(self):  # test full-text search - bento search result format
         get_resp_1 = self.client.get('/api/individuals?search=P49Y&format=bento_search_result')
         self.assertEqual(get_resp_1.status_code, status.HTTP_200_OK)
         response_obj_1 = get_resp_1.json()
         self.assertEqual(len(response_obj_1['results']), 1)
         self.assertEqual(len(response_obj_1['results'][0]), 4)  # 4 fields in the bento search response
 
+    def test_individual_phenopackets(self):
+        get_resp = self.client.get(f"/api/individuals/{self.individual_one.id}/phenopackets")
+        self.assertEqual(get_resp.status_code, status.HTTP_200_OK)
+        response_obj_1 = get_resp.json()
+        self.assertEqual(len(response_obj_1), 1)  # 1 phenopacket for individual
+
+        post_resp = self.client.post(f"/api/individuals/{self.individual_one.id}/phenopackets?attachment=1")
+        self.assertEqual(post_resp.status_code, status.HTTP_200_OK)
+        self.assertIn("attachment; filename=", post_resp.headers.get("Content-Disposition", ""))
+        response_obj_2 = post_resp.json()
+        self.assertEqual(len(response_obj_2), 1)  # 1 phenopacket for individual, still
+
 
 # Note: the next five tests use the same setUp method. Initially they were
 # all combined in the same class. But this caused bugs with regard to unavailable