Feature/286 (#330)

* #294 fix: Update experiment update conditions

* fix: Fix registration of fiducial experiments

* feat: Move populations to error state if cordmap doesn't produce cell files

* fix: Rollback custom cordmap changes

* #294 fix: Improve update experiment logic

* #286 feat: Change csv headers at download time

* fix: Update population cells file location

applications/portal/backend/api/helpers/download_populations.py

@@ -0,0 +1,48 @@
+import csv
+import io
+import os
+import tempfile
+import zipfile
+
+from django.db.models import Q
+from django.http import HttpResponse
+
+from api.models import Population
+
+
+def get_populations_zip(active_populations, experiment):
+    filename_prefix = f'{experiment.name}' if experiment else 'population'
+    filename_suffix = 's' if len(active_populations) > 1 else ''
+
+    temp_file = tempfile.TemporaryFile()
+    with zipfile.ZipFile(temp_file, 'w') as zip_file:
+        for population in Population.objects.filter(Q(experiment=experiment) | Q(experiment=None), id__in=active_populations):
+            if population.cells:
+                modified_csv_content = modify_csv_headers(population.cells.path)
+                zip_file.writestr(os.path.basename(population.cells.path), modified_csv_content)
+                filename_prefix += f"_{population.name}"
+
+    temp_file.seek(0)  # Reset file pointer
+    return temp_file, f"{filename_prefix}_population{filename_suffix}.zip"
+
+
+
+def modify_csv_headers(csv_file_path):
+    with open(csv_file_path, 'r') as csvfile:
+        reader = csv.reader(csvfile)
+        modified_data = io.StringIO()
+        writer = csv.writer(modified_data)
+
+        # Swap 'x' and 'y' in headers
+        headers = next(reader)
+        x_index = headers.index('x')
+        y_index = headers.index('y')
+        headers[x_index], headers[y_index] = headers[y_index], headers[x_index]
+        writer.writerow(headers)
+
+        # Write the rest of the rows as they are
+        for row in reader:
+            writer.writerow(row)
+
+        modified_data.seek(0)
+        return modified_data.getvalue()

applications/portal/backend/api/helpers/population_cells.py

@@ -15,7 +15,7 @@ def associate_population_cells_file(population, storage_path, csv_suffix):
         new_file_name = f"{csv_suffix}_{str(uuid.uuid4())[:8]}.csv"
         new_file_path = move_file(
             original_file_path,
-            os.path.join(population.storage_path, str(population.id)),
+            population.storage_path,
             new_file_name
         )
         with open(new_file_path, 'rb') as file:

applications/portal/backend/api/views/rest/experiment.py

@@ -1,19 +1,16 @@
 import logging
-import os
-import tempfile
-import zipfile
 
-from django.db.models import Q
 from django.http import HttpResponse
+from django.shortcuts import get_object_or_404
 from dry_rest_permissions.generics import DRYPermissions
 from rest_framework import status, viewsets
 from rest_framework.decorators import action
 from rest_framework.parsers import MultiPartParser
 from rest_framework.response import Response
-from django.shortcuts import get_object_or_404
 
+from api.helpers.download_populations import get_populations_zip
 from api.helpers.exceptions import InvalidPopulationFile, DuplicatedPopulationError, InvalidInputError
-from api.models import Experiment, Population
+from api.models import Experiment
 from api.serializers import (
     ExperimentPairFileUploadSerializer,
     ExperimentSerializer,
@@ -68,7 +65,7 @@ def destroy(self, request, *args, **kwargs):
         pk = kwargs.get("pk")
         queryset = self.get_queryset()
         instance = get_object_or_404(queryset, pk=pk)
-        if request.user==instance.owner:
+        if request.user == instance.owner:
             self.perform_destroy(instance)
             return Response(status=status.HTTP_204_NO_CONTENT)
         return Response(status=status.HTTP_403_FORBIDDEN)
@@ -190,22 +187,11 @@ def download_populations(self, request, pk=None, active_populations=None):
         if not active_populations or len(active_populations) == 0:
             return Response(status=status.HTTP_204_NO_CONTENT)
 
-        filename_prefix = f'{experiment.name}' if experiment else 'population'
-        filename_suffix = 's' if len(active_populations) > 1 else ''
-        with tempfile.TemporaryFile() as temp_file:
-            with zipfile.ZipFile(temp_file, 'w') as zip_file:
-                for population in Population.objects.filter(Q(experiment=experiment) | Q(experiment=None),
-                                                            id__in=active_populations):
-                    if population.cells:
-                        zip_file.write(population.cells.path, arcname=os.path.basename(population.cells.path))
-                        filename_prefix += f"_{population.name}"
-
-            temp_file.seek(0)  # move the file pointer to the beginning of the file
-
-            response = HttpResponse(temp_file.read(), content_type='application/octet-stream')
-            response[
-                'Content-Disposition'] = f'attachment; filename="{filename_prefix}_population{filename_suffix}.zip"'
-            return response
+        zip_file, filename = get_populations_zip(active_populations, experiment)
+        response = HttpResponse(zip_file.read(), content_type='application/octet-stream')
+        response['Content-Disposition'] = f'attachment; filename="{filename}"'
+        zip_file.close()
+        return response
 
     def perform_create(self, serializer):
         experiment = serializer.save(owner=self.request.user)