Fixed wetlab API create-sample-data error. Included new API function lab-request-mapping.

CHANGELOG.md

@@ -21,6 +21,8 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 - Created graphics for the services that were re-analyzed [#290](https://github.com/BU-ISCIII/iskylims/pull/290)
 - Enhance both `install.sh` and `docker_install.sh`, fix data loading issues [#327](https://github.com/BU-ISCIII/iskylims/pull/327)
 - Included thorough description for wetlab API's update_lab() method [#361](https://github.com/BU-ISCIII/iskylims/pull/361)
+- Included new API function lab-request-mapping to get LabRequest fields ontology map [#377](https://github.com/BU-ISCIII/iskylims/pull/377)
+- Improved responses in API create-sample-data by adding ERROR messages and data [#377](https://github.com/BU-ISCIII/iskylims/pull/377)
 
 #### Fixes
 
@@ -56,8 +58,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 - Fixed wetlab API's labrequest.serializer update method to work properly [#361](https://github.com/BU-ISCIII/iskylims/pull/361)
 - Adapted update_lab serializer call to new serializer update method [#361](https://github.com/BU-ISCIII/iskylims/pull/361)
 - Leave missing submitting_fields as empty string instead of crashing in wetlab.api.create_sample_data [#363](https://github.com/BU-ISCIII/iskylims/pull/363)
-
-
+- Fixed wetlab API create-sample-data error when submitting_institution fields were not provided [#377](https://github.com/BU-ISCIII/iskylims/pull/377)
 
 #### Changed
 
@@ -69,6 +70,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 - Renamed method `get_delivery_date` to `get_delivered_date` for clarity.
 - Improved query performance and excluded rejected/archived services from ongoing list. (#299)
 - Updated sample metadata fields with standardized ontology mappings and schema alignment.[#358](https://github.com/BU-ISCIII/iskylims/pull/358)
+- API create-sample-data Lab data mapping moved to core_config.LAB_REQUEST_ONTOLOGY_MAP [#377](https://github.com/BU-ISCIII/iskylims/pull/377)
 
 #### Removed
 

core/core_config.py

@@ -334,3 +334,23 @@
 ]
 ERROR_PROJECT_FIELD_NOOPTION = ["Project field", "only has the following options:"]
 ERROR_PROJECT_FIELD_EMPTY = ["Project field", "is empty"]
+
+LAB_REQUEST_ONTOLOGY_MAP = {
+    "GENEPIO:0001153": ("lab_name", "collecting_institution"),
+    "SNOMED:423901009": ("lab_code_1", "collecting_institution_code_1"),
+    "NCIT:C101703": ("lab_code_2", "collecting_institution_code_2"),
+    "OBI:0001890": ("lab_email", "collecting_institution_email"),
+    "NCIT:C40978": ("lab_phone", "collecting_institution_phone"),
+    "GENEPIO:0001158": ("address", "collecting_institution_address"),
+    "GENEPIO:0001803": ("autonom_cod", "autonom_cod"),
+    "GENEPIO:0001185": ("geo_loc_state", "geo_loc_state"),
+    "GENEPIO:0001189": ("geo_loc_city", "geo_loc_city"),
+    "NCIT:C25621": ("post_code", "post_code"),
+    "mesh:D009935": ("dep_func", "dep_func"),
+    "NCIT:C93878": ("center_class_code", "center_class_code"),
+    "NCIT:C188820": ("lab_function", "collecting_institution_function"),
+    "EFO:0005020": ("lab_geo_loc_latitude", "lab_geo_loc_latitude"),
+    "EFO:0005021": ("lab_geo_loc_longitude", "lab_geo_loc_longitude"),
+    "OBI:0001620": ("geo_loc_latitude", "geo_loc_latitude"),
+    "OBI:0001621": ("geo_loc_longitude", "geo_loc_longitude"),
+}

wetlab/api/urls.py

@@ -29,4 +29,9 @@
         name="summarize_data_information",
     ),
     path("update-lab", views.update_lab, name="update_lab"),
+    path(
+        "lab-request-mapping",
+        views.get_lab_request_mapping,
+        name="get_lab_request_mapping",
+    ),
 ]

wetlab/api/utils/sample.py

@@ -2,6 +2,7 @@
 
 import core.models
 import core.utils.samples
+import core.core_config
 import wetlab.api.serializers
 import wetlab.config
 
@@ -353,31 +354,15 @@ def split_sample_data(data):
     lab_data["lab_unit"] = ""
     lab_data["lab_contact_name"] = ""
     lab_data["lab_phone"] = ""
-    lab_data_fields = [
-        ("lab_email", "collecting_institution_email"),
-        ("address", "collecting_institution_address"),
-        ("geo_loc_city", "geo_loc_city"),
-        ("geo_loc_state", "geo_loc_state"),
-        ("geo_loc_latitude", "geo_loc_latitude"),
-        ("geo_loc_longitude", "geo_loc_longitude"),
-    ]
+    lab_req_mapping = core.core_config.LAB_REQUEST_ONTOLOGY_MAP
+    lab_data_fields = lab_req_mapping.values()
     for l_data, i_data in lab_data_fields:
         try:
             lab_data[l_data] = data[i_data]
         except KeyError:
-            lab_data[l_data] = ""
-
-    """
-    lab_data["lab_email"] = data["collecting_institution_email"]
-    lab_data["address"] = data["collecting_institution_address"]
-    lab_data["geo_loc_city"] = data["geo_loc_city"]
-    lab_data["geo_loc_state"] = data["geo_loc_state"]
-    lab_data["geo_loc_latitude"] = data["geo_loc_latitude"]
-    lab_data["geo_loc_longitude"] = data["geo_loc_longitude"]
-    """
+            lab_data[l_data] = data.get(l_data, "")
 
     split_data["lab_data"] = lab_data
-
     return split_data
 
 

wetlab/api/views.py

@@ -13,6 +13,7 @@
 from rest_framework.response import Response
 
 import core.models
+import core.core_config
 import wetlab.api.serializers
 import wetlab.api.utils.lab
 import wetlab.api.utils.sample
@@ -182,7 +183,13 @@ def create_sample_data(request):
         if isinstance(data, QueryDict):
             data = data.dict()
         if "sample_name" not in data or "sample_project" not in data:
-            return Response(status=status.HTTP_400_BAD_REQUEST)
+            return Response(
+                {
+                    "ERROR": "Missing fields `sample_name` or `sample_project` in data",
+                    "data": data,
+                },
+                status=status.HTTP_400_BAD_REQUEST,
+            )
         not_allowed_sample_names = []
         allowed_sample_repeat = (
             False
@@ -228,26 +235,19 @@ def create_sample_data(request):
                 return Response(error, status=status.HTTP_400_BAD_REQUEST)
         split_data = wetlab.api.utils.sample.split_sample_data(data)
         if not isinstance(split_data, dict):
-            return Response(split_data, status=status.HTTP_400_BAD_REQUEST)
+            return Response(
+                {"ERROR": "Error splitting data", "data": split_data},
+                status=status.HTTP_400_BAD_REQUEST,
+            )
         apps_name = __package__.split(".")[0]
         inst_req_sample = wetlab.api.utils.sample.include_instances_in_sample(
             split_data["s_data"], split_data["lab_data"], apps_name
         )
-        required_submit_inst_fieldmap = {
-            "submitting_institution": "lab_name",
-            "submitting_institution_email": "lab_email",
-            "submitting_institution_address": "address",
-        }
-        if all(k in data for k in required_submit_inst_fieldmap.keys()):
-            submit_inst_data = split_data["lab_data"].copy()
-            for field, keymap in required_submit_inst_fieldmap.items():
-                submit_inst_data[keymap] = data.get(field, "")
-            submit_inst_data["lab_name_coding"] = "".join(
-                [x[0] for x in data["lab_name"].strip().split(" ")]
-            )
-            wetlab.api.utils.sample.create_new_laboratory(submit_inst_data)
         if not isinstance(inst_req_sample, dict):
-            return Response(inst_req_sample, status=status.HTTP_400_BAD_REQUEST)
+            return Response(
+                {"ERROR": "Error including data", "data": inst_req_sample},
+                status=status.HTTP_400_BAD_REQUEST,
+            )
         split_data["s_data"] = inst_req_sample
         split_data["s_data"]["sample_user"] = request.user.pk
         # Adding coding for sample
@@ -261,7 +261,11 @@ def create_sample_data(request):
         )
         if not sample_serializer.is_valid():
             return Response(
-                sample_serializer.errors, status=status.HTTP_400_BAD_REQUEST
+                {
+                    "ERROR": f"Error serializing sample {data['sample_name']}",
+                    "data": sample_serializer.errors,
+                },
+                status=status.HTTP_400_BAD_REQUEST,
             )
         new_sample_id = sample_serializer.save().get_sample_id()
         for d_field in split_data["p_data"]:
@@ -271,12 +275,23 @@ def create_sample_data(request):
             )
             if not s_project_serializer.is_valid():
                 return Response(
-                    s_project_serializer.errors, status=status.HTTP_400_BAD_REQUEST
+                    {
+                        "ERROR": "Error serializing project",
+                        "data": s_project_serializer.errors,
+                    },
+                    status=status.HTTP_400_BAD_REQUEST,
                 )
             s_project_serializer.save()
 
-        return Response("Successful upload information", status=status.HTTP_201_CREATED)
-    return Response(status=status.HTTP_400_BAD_REQUEST)
+        return Response(
+            {"message": "Successful upload information", "data": split_data["s_data"]},
+            status=status.HTTP_201_CREATED,
+        )
+    else:
+        return Response(
+            {"ERROR": f"Request method must be POST, received {request.method}"},
+            status=status.HTTP_400_BAD_REQUEST,
+        )
 
 
 @swagger_auto_schema(
@@ -419,6 +434,18 @@ def sample_project_fields(request):
     return Response(status=status.HTTP_400_BAD_REQUEST)
 
 
+@swagger_auto_schema(
+    method="get",
+    operation_description="Use this request to get the fields used to fill lab_request model",
+    manual_parameters=[laboratory],
+)
+@api_view(["GET"])
+def get_lab_request_mapping(request):
+    return Response(
+        {"data": core.core_config.LAB_REQUEST_ONTOLOGY_MAP}, status=status.HTTP_200_OK
+    )
+
+
 @swagger_auto_schema(method="get", manual_parameters=[laboratory])
 @api_view(["GET"])
 def get_lab_information_contact(request):