Generate biomarker from the result of a momix pipeline

src/biomarkers/serializers.py

@@ -1,4 +1,5 @@
 from rest_framework import serializers
+from genes.serializers import GeneGEMWithType
 from user_files.models_choices import MoleculeType
 from .models import Biomarker, MRNAIdentifier, MethylationIdentifier, CNAIdentifier, MiRNAIdentifier, MoleculeIdentifier
 from tags.serializers import TagSerializer
@@ -164,5 +165,14 @@ def get_was_already_used(ins: Biomarker) -> bool:
         This avoids the user to edit a Biomarker that was already used and generate inconsistencies.
         """
         return ins.was_already_used
+
+
+class BiomarkerFromCorrelationAnalysisSerializer(serializers.Serializer):
+    """
+    Serializer for BiomarkerFromCorrelationAnalysis, including correlation analysis ID, gene GEM list, and correlation threshold.
+    """
+    correlation_analysis_id = serializers.IntegerField()
+    gene_gem_list = GeneGEMWithType(many=True, required=False)
+    correlation_threshold = serializers.IntegerField(required=False)
 
 

src/biomarkers/urls.py

@@ -18,4 +18,5 @@
     path('methylation-sites', views.MethylationSites.as_view(), name='methylation_sites'),
     path('methylation-sites-finder', views.MethylationSites.as_view(), name='methylation_sites_finder'),
     path('biomarker-molecules', views.BiomarkerMolecules.as_view(), name='biomarker_molecules'),
+    path('biomarker-correlation-api', views.BiomarkerCorrelationAPIView.as_view(), name='biomarker_correlation_api'),
 ]

src/biomarkers/views.py

@@ -10,15 +10,17 @@
 from rest_framework.request import Request
 from rest_framework.response import Response
 from rest_framework.views import APIView
+from api_service.models import Experiment
 from api_service.mrna_service import global_mrna_service
 from biomarkers.models import Biomarker, BiomarkerState, BiomarkerOrigin, MoleculeIdentifier
-from biomarkers.serializers import BiomarkerSerializer, MoleculeIdentifierSerializer, \
+from biomarkers.serializers import BiomarkerFromCorrelationAnalysisSerializer, BiomarkerSerializer, MoleculeIdentifierSerializer, \
     BiomarkerSimpleSerializer, BiomarkerSimpleUpdateSerializer
 from common.pagination import StandardResultsSetPagination
 from common.response import generate_json_response_or_404
 from django.db.models import QuerySet, Q
 
 
+
 class BiomarkerList(generics.ListAPIView):
     """REST endpoint: list for Biomarker model"""
 
@@ -276,3 +278,22 @@ def get_queryset(self):
     filter_backends = [filters.OrderingFilter, filters.SearchFilter, DjangoFilterBackend]
     search_fields = ['identifier']
     ordering_fields = ['identifier']
+
+
+class BiomarkerCorrelationAPIView(APIView):
+    """Validates the request data and retrieves the corresponding experiment."""
+
+    def post(self, request, *args, **kwargs):
+        # Instantiate the serializer with the received data
+        serializer = BiomarkerFromCorrelationAnalysisSerializer(data=request.data)
+
+        # Validate the data (returns a 400 error if the structure is incorrect)
+        serializer.is_valid(raise_exception=True)
+        validated_data = serializer.validated_data
+
+        # Here the Biomarker is created validating which parameters were sent from the frontend
+        cor_analysis = get_object_or_404(Experiment, pk=validated_data['correlation_analysis_id'])
+
+        return Response({
+            "ok": True,
+        })

src/genes/serializers.py

@@ -7,3 +7,9 @@ class GeneForResultTableSerializer(serializers.ModelSerializer):
     class Meta:
         model = Gene
         fields = ['type', 'chromosome', 'start', 'end', 'description']
+
+class GeneGEMWithType(serializers.Serializer):
+    """Serializer for GeneGEMWithType"""
+    id = serializers.IntegerField()
+    molecule_type = serializers.IntegerField()
+