Merge branch 'develop' into features/last-data-ingestion-for-public

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

@@ -104,7 +104,7 @@
         "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/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):