Merge branch 'develop' into features/phenov2-1394

chord_metadata_service/chord/api_views.py

@@ -12,6 +12,7 @@
 from django_filters.rest_framework import DjangoFilterBackend
 from chord_metadata_service.cleanup.run_all import run_all_cleanup
 
+from chord_metadata_service.resources.serializers import ResourceSerializer
 from chord_metadata_service.restapi.api_renderers import PhenopacketsRenderer, JSONLDDatasetRenderer, RDFDatasetRenderer
 from chord_metadata_service.restapi.pagination import LargeResultsSetPagination
 
@@ -85,6 +86,15 @@ def dats(self, _request, *_args, **_kwargs):
         dataset = self.get_object()
         return Response(json.loads(dataset.dats_file))
 
+    @action(detail=True, methods=["get"])
+    def resources(self, _request, *_args, **_kwargs):
+        """
+        Retrieve all resources (phenopackets/additional_resources) for a dataset and return a JSON response serialized
+        using ResourceSerializer
+        """
+        dataset = self.get_object()
+        return Response(ResourceSerializer(dataset.resources.all(), many=True).data)
+
     @async_to_sync
     async def destroy(self, request, *args, **kwargs):
         get_obj_async = sync_to_async(self.get_object)

chord_metadata_service/chord/tests/test_api.py

@@ -111,6 +111,35 @@ def test_dats(self):
         self.assertEqual(response.status_code, status.HTTP_200_OK)
         self.assertDictEqual(response.data, json.loads(payload['dats_file']))
 
+    def test_resources(self):
+        resource = {
+            "id": "NCBITaxon:2023-09-14",
+            "name": "NCBI Taxonomy OBO Edition",
+            "version": "2023-09-14",
+            "namespace_prefix": "NCBITaxon",
+            "url": "http://purl.obolibrary.org/obo/ncbitaxon/2023-09-14/ncbitaxon.owl",
+            "iri_prefix": "http://purl.obolibrary.org/obo/NCBITaxon_",
+        }
+
+        r = self.client.post("/api/resources", data=json.dumps(resource), content_type="application/json")
+        self.assertEqual(r.status_code, status.HTTP_201_CREATED)
+
+        r = self.client.post(
+            "/api/datasets",
+            data=json.dumps({
+                **valid_dataset_1(self.project["identifier"]),
+                "additional_resources": [resource["id"]],
+            }),
+            content_type="application/json")
+        self.assertEqual(r.status_code, status.HTTP_201_CREATED)
+
+        dataset_id = Dataset.objects.first().identifier
+        r = self.client.get(f"/api/datasets/{dataset_id}/resources")
+        self.assertEqual(r.status_code, status.HTTP_200_OK)
+        self.assertEqual(len(r.data), 1)
+        self.assertEqual(r.data[0]["id"], resource["id"])
+
+
 # TODO: Update Dataset
 # TODO: Delete Dataset
 

chord_metadata_service/experiments/schemas.py

@@ -96,7 +96,7 @@
             "enum": ["DNA Methylation", "mRNA-Seq", "smRNA-Seq", "RNA-Seq", "WES",
                      "WGS", "Genotyping", "Proteomic profiling",
                      "Neutralizing antibody titers", "Metabolite profiling",
-                     "Antibody measurement", "Other"]
+                     "Antibody measurement", "Viral WGS", "Other"]
         },
         "experiment_ontology": ONTOLOGY_CLASS_LIST,
         "molecule": {
@@ -107,7 +107,7 @@
         "molecule_ontology": ONTOLOGY_CLASS_LIST,
         "library_strategy": {
             "type": "string",
-            "enum": ["Bisulfite-Seq", "RNA-Seq", "ChIP-Seq", "WES", "Other"]
+            "enum": ["Bisulfite-Seq", "RNA-Seq", "ChIP-Seq", "WES", "WGS", "RAD-Seq", "AMPLICON", "Other"]
         },
         "library_source": {
             "type": "string",

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

chord_metadata_service/phenopackets/autocomplete_views.py

@@ -7,10 +7,10 @@ class DiseaseTermAutocomplete(autocomplete.Select2QuerySetView):
 
     # get_result_value return result.pk
 
-    def get_result_label(self, item):
-        return item.term["label"]
+    def get_result_value(self, item):
+        return item.term["id"]
 
-    def get_selected_result_label(self, item):
+    def get_result_label(self, item):
         return item.term["label"]
 
     def get_queryset(self):

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "poetry.core.masonry.api"
 
 [tool.poetry]
 name = "chord_metadata_service"  # can be renamed to katsu if inner module directory is renamed too
-version = "4.0.0"
+version = "4.4.0"
 description = "An implementation of a clin/pheno metadata store for the Bento platform."
 authors = [
     "Ksenia Zaytseva",