#288 feat: WIP - Update PDF upload and render logic

applications/portal/api/openapi.yaml

@@ -1216,31 +1216,6 @@ paths:
           description: ''
       tags:
       - api
-  /api/population/{id}/upload-pdf-files/:
-    post:
-      operationId: uploadPdfFilePopulation
-      description: This viewset automatically provides `list` actions.
-      parameters:
-      - name: id
-        in: path
-        required: true
-        description: A unique integer value identifying this population.
-        schema:
-          type: string
-      requestBody:
-        content:
-          multipart/form-data:
-            schema:
-              $ref: '#/components/schemas/PopulationPDFUpload'
-      responses:
-        '201':
-          content:
-            application/json:
-              schema:
-                $ref: '#/components/schemas/PopulationPDFUpload'
-          description: ''
-      tags:
-      - api
   /api/teams/{id}/add_members/:
     post:
       operationId: addMembersGroup
@@ -1579,7 +1554,7 @@ components:
           readOnly: true
         name:
           type: string
-          maxLength: 40
+          maxLength: 100
         category:
           enum:
           - ELECTROPHYSIOLOGY
@@ -1591,15 +1566,21 @@ components:
           format: date-time
           readOnly: true
         created_by:
-          type: integer
+          type: string
+          readOnly: true
         file:
           type: string
           format: binary
           nullable: true
+        experiment:
+          type: string
+          readOnly: true
+        population:
+          type: string
+          readOnly: true
       required:
       - name
       - category
-      - created_by
     Tag:
       type: object
       properties:
@@ -1729,21 +1710,6 @@ components:
           format: binary
       required:
       - file
-    PopulationPDFUpload:
-      type: object
-      properties:
-        pdf_file:
-          type: string
-          format: binary
-        category:
-          enum:
-          - ELECTROPHYSIOLOGY
-          - BEHAVIOUR
-          - IO_MAPPING
-          type: string
-      required:
-      - pdf_file
-      - category
     Member:
       type: object
       properties:

applications/portal/backend/api/admin.py

@@ -1,6 +1,6 @@
 from django.contrib import admin
 
-from api.models import Collaborator, Experiment, Population, Tag, UserDetail
+from api.models import Collaborator, Experiment, Population, Tag, UserDetail, Pdf
 
 
 class PopulationInline(admin.TabularInline):
@@ -39,7 +39,12 @@ class TagAdmin(admin.ModelAdmin):
     pass
 
 
+class PDFAdmin(admin.ModelAdmin):
+    pass
+
+
 admin.site.register(UserDetail, UserDetailAdmin)
 admin.site.register(Experiment, ExperimentAdmin)
 admin.site.register(Collaborator, CollaboratorAdmin)
 admin.site.register(Tag, TagAdmin)
+admin.site.register(Pdf, PDFAdmin)

applications/portal/backend/api/migrations/0004_pdf.py

@@ -1,4 +1,4 @@
-# Generated by Django 4.2 on 2023-11-28 14:41
+# Generated by Django 4.2 on 2023-11-29 02:51
 
 from django.conf import settings
 from django.db import migrations, models
@@ -51,6 +51,14 @@ class Migration(migrations.Migration):
                         to=settings.AUTH_USER_MODEL,
                     ),
                 ),
+                (
+                    "experiment",
+                    models.ForeignKey(
+                        on_delete=django.db.models.deletion.CASCADE,
+                        related_name="experiment_pdfs",
+                        to="api.experiment",
+                    ),
+                ),
                 (
                     "population",
                     models.ForeignKey(

applications/portal/backend/api/models/pdf.py

@@ -1,50 +1,56 @@
-
 from django.db import models
 from django.contrib.auth.models import User
+
+from . import Experiment
 from .population import Population
 
+
 class PDFCategory(models.TextChoices):
-	ELECTROPHYSIOLOGY = 'ELECTROPHYSIOLOGY'
-	BEHAVIOUR = 'BEHAVIOUR'
-	IO_MAPPING = 'IO_MAPPING'
+    ELECTROPHYSIOLOGY = 'ELECTROPHYSIOLOGY'
+    BEHAVIOUR = 'BEHAVIOUR'
+    IO_MAPPING = 'IO_MAPPING'
 
 
 '''
 	PopulationPDF associate to each population. 
 	Population can have multiple PDFs of any of following categories:
 		- ELECTROPHYSIOLOGY, BEHAVIOUR, IO_MAPPING
 '''
+
+
 class Pdf(models.Model):
     name = models.CharField(max_length=100)
     category = models.CharField(max_length=40, choices=PDFCategory.choices)
     created_at = models.DateTimeField(auto_now_add=True)
     created_by = models.ForeignKey(
-		User,
-		related_name="pdf_created_by",
-		on_delete=models.CASCADE,
-	)
+        User,
+        related_name="pdf_created_by",
+        on_delete=models.CASCADE,
+    )
     file = models.FileField(null=True, blank=True, max_length=255)
     population = models.ForeignKey(
-		Population,
-		related_name="population_pdf",
-		on_delete=models.CASCADE,
-	)
-
+        Population,
+        related_name="population_pdf",
+        on_delete=models.CASCADE,
+    )
+    experiment = models.ForeignKey(
+        Experiment,
+        on_delete=models.CASCADE,
+        related_name="experiment_pdfs"
+    )
 
     @staticmethod
     def has_read_permission(request):
         return True
 
     @staticmethod
-    def has_list_permission(request):
-        return True
-
-    @staticmethod
-    def has_destroy_permission(request):
-        return True
-
-    def has_object_write_permission(self, request):
-        # return self.population.experiment and self.population.experiment.has_object_write_permission(request)
+    def has_write_permission(request):
         return True
 
+    def has_object_read_permission(self, request):
+        if request.user == self.created_by:
+            return True
+        return not self.experiment.is_private
 
+    def has_object_destroy_permission(self, request):
+        return request.user == self.created_by

applications/portal/backend/api/models/population.py

@@ -148,8 +148,7 @@ def has_object_read_permission(self, request):
         return self.experiment is None or self.experiment.has_object_read_permission(request)
 
     def has_object_write_permission(self, request):
-        # return self.experiment and self.experiment.has_object_write_permission(request)
-        return True
+        return self.experiment and self.experiment.has_object_write_permission(request)
 
     def update_color(self):
         if not is_valid_hex_str(self.color):

applications/portal/backend/api/serializers/pdf.py

@@ -1,20 +1,25 @@
 from rest_framework import serializers
-from api.models import Pdf, PDFCategory
-import os
+
+from api.models import Pdf
 
 
 class PdfSerializer(serializers.ModelSerializer):
-	created_by = serializers.SerializerMethodField()
-	class Meta:
-		model = Pdf
-		fields = (
-			"id",
-			"name",
-			"category",
-			"created_at",
-			"created_by",
-			"file"
-		)
+    created_by = serializers.SerializerMethodField()
+    experiment = serializers.PrimaryKeyRelatedField(read_only=True)
+    population = serializers.PrimaryKeyRelatedField(read_only=True)
+
+    class Meta:
+        model = Pdf
+        fields = (
+            "id",
+            "name",
+            "category",
+            "created_at",
+            "created_by",
+            "file",
+            "experiment",
+            "population",
+        )
 
-	def get_created_by(self, obj):
-		return obj.created_by.first_name + " " + obj.created_by.last_name
+    def get_created_by(self, obj):
+        return obj.created_by.first_name + " " + obj.created_by.last_name

applications/portal/backend/api/serializers/population.py

@@ -1,6 +1,6 @@
 from rest_framework import serializers
 
-from api.models import AtlasesChoice, Population, PDFCategory
+from api.models import AtlasesChoice, Population, Pdf
 from api.serializers.pdf import PdfSerializer
 
 
@@ -27,19 +27,19 @@ class Meta:
         )
 
     def get_pdfs(self, obj):
-        pdfs = obj.population_pdf.filter(
-            created_by=self.context["request"].user
-        ).order_by("-created_at")
-        return PdfSerializer(pdfs, many=True).data
+        request = self.context.get("request")
 
+        # Check if there's an experiment ID in the request
+        experiment_id = request.query_params.get("experiment") if request else None
+
+        if experiment_id:
+            pdfs = obj.population_pdf.filter(
+                experiment_id=experiment_id,
+            ).order_by("-created_at")
+        else:
+            pdfs = Pdf.objects.none()
+
+        return PdfSerializer(pdfs, many=True).data
 
 
-class PopulationPDFUploadSerializer(serializers.Serializer):
-    pdf_file = serializers.FileField(required=True)
-    category = serializers.ChoiceField(
-        choices=PDFCategory.choices, required=True
-    )
 
-    class Meta:
-        model = Population
-        fields = ()

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

@@ -2,12 +2,15 @@
 
 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 api.models import Pdf
+from api.helpers.exceptions import InvalidPDFFile
+from api.models import Pdf, Population, Experiment
 from api.serializers import PdfSerializer
 from api.services.user_service import is_user_owner
-from api.services.pdf_service import get_pdf_save_dir
+from api.services.pdf_service import get_pdf_save_dir, save_pdf_and_get_path
 import os
 
 log = logging.getLogger("__name__")
@@ -22,17 +25,60 @@ class PDFViewSet(viewsets.ModelViewSet):
     serializer_class = PdfSerializer
     queryset = Pdf.objects.all()
 
+    def partial_update(self, request, *args, **kwargs):
+        # Disable PATCH
+        return Response(status=status.HTTP_405_METHOD_NOT_ALLOWED)
+
+    def update(self, request, *args, **kwargs):
+        # Disable PUT
+        return Response(status=status.HTTP_405_METHOD_NOT_ALLOWED)
+
     def destroy(self, request, *args, **kwargs):
         instance = self.get_object()
         population_obj = instance.population
 
         if population_obj.experiment and (not is_user_owner(request, population_obj)):
             return Response(status=status.HTTP_403_FORBIDDEN)
-        
+
         pdf_storage_path = get_pdf_save_dir(
             population_obj.storage_path, instance)
         if os.path.exists(pdf_storage_path):
             os.remove(pdf_storage_path)
-        
+
         instance.delete()
         return Response(status=status.HTTP_204_NO_CONTENT)
+
+    def create(self, request, **kwargs):
+        pdf_file = request.FILES.get("pdf_file")
+        category = request.data.get("category")
+        population_id = request.data.get("population_id")
+        experiment_id = request.data.get("experiment_id")
+
+        # Retrieve the Population and Experiment instances
+        try:
+            population = Population.objects.get(id=population_id)
+            experiment = Experiment.objects.get(id=experiment_id)
+        except (Population.DoesNotExist, Experiment.DoesNotExist):
+            return Response(status=status.HTTP_404_NOT_FOUND)
+
+        if experiment and (not is_user_owner(request, experiment)):
+            return Response(status=status.HTTP_403_FORBIDDEN)
+
+        try:
+            pdf_obj = Pdf.objects.create(
+                population=population, experiment=experiment,
+                created_by=request.user, category=category, name=pdf_file.name
+            )
+            pdf_path = save_pdf_and_get_path(
+                pdf_obj=pdf_obj,
+                population_storage_path=population.storage_path, pdf_file=pdf_file
+            )
+            pdf_obj.file = pdf_path
+            pdf_obj.save()
+
+            pdf_serializer = PdfSerializer(pdf_obj)
+            return Response(pdf_serializer.data, status=status.HTTP_201_CREATED)
+        except InvalidPDFFile as e:
+            return Response(data={'detail': str(e)}, status=status.HTTP_422_UNPROCESSABLE_ENTITY)
+        except Exception as e:
+            return Response(data={'detail': str(e)}, status=status.HTTP_400_BAD_REQUEST)