G2P-418 and G2P-432

gene2phenotype_project/gene2phenotype_app/models.py

@@ -574,7 +574,7 @@ class Meta:
 class Panel(models.Model):
     id = models.AutoField(primary_key=True)
     name = models.CharField(max_length=100, unique=True, null=False)
-    description = models.CharField(max_length=255, null=True)
+    description = models.CharField(max_length=255, null=False, default="before_G2P_2025")
     is_visible = models.SmallIntegerField(null=False)
 
     def __str__(self):

gene2phenotype_project/gene2phenotype_app/serializers/__init__.py

@@ -2,7 +2,7 @@
 
 from .user import UserSerializer, LoginSerializer, CreateUserSerializer, AddUserToPanelSerializer, LogoutSerializer, ChangePasswordSerializer, VerifyEmailSerializer, PasswordResetSerializer
 
-from .panel import PanelDetailSerializer, LGDPanelSerializer
+from .panel import PanelCreateSerializer, PanelDetailSerializer, LGDPanelSerializer
 
 from .publication import PublicationSerializer, LGDPublicationSerializer, LGDPublicationListSerializer
 

gene2phenotype_project/gene2phenotype_app/serializers/panel.py

@@ -1,10 +1,100 @@
 from rest_framework import serializers
 from django.db.models import Q
+from django.core.exceptions import ObjectDoesNotExist
 
 from ..models import Panel, User, UserPanel, LGDPanel, Attrib
 
 from ..utils import get_date_now
 
+
+class PanelCreateSerializer(serializers.ModelSerializer):
+    """
+        Panel Creation Serializer
+
+        Args:
+            name: short name of the panel (mandatory)
+            description: complete name of the panel (mandatory)
+            is_visible: panel visible to authenticated or non authenticated users
+
+
+        Raises:
+            serializers.ValidationError: Raises a validation error when the panel exists
+
+        Returns:
+            _type_: A created panel
+    """    
+    name = serializers.CharField(required=True)
+    description = serializers.CharField(required=True)
+    is_visible = serializers.BooleanField(required=True)
+
+    def validate(self, attrs):
+        """
+            Validate the request data 
+
+            Args:
+                attrs (_type_): A dictionary like object containing the request data
+
+            Raises:
+                serializers.ValidationError: Raises a validation error when the panel exists
+
+            Returns:
+                _type_: A validated request object
+        """        
+        name = attrs.get('name')
+        if Panel.objects.filter(name=name, is_visible=1).exists():
+            raise serializers.ValidationError({'message': 'Can not create an existing panel'})
+
+        return attrs
+
+    def create(self, validated_data):
+        """
+            Creation of the panel if panel does not exist
+            Updating the panel if is_visible = 0
+
+            Args:
+                validated_data (_type_): validated request object
+
+            Returns:
+                _type_: Created panel
+        """        
+        name = validated_data.get('name')
+        description = validated_data.get('description')
+        is_visible = validated_data.get('is_visible')
+
+        if Panel.objects.filter(name=name, is_visible=0).exists() and is_visible is True:
+            self.update(name, is_visible, description)
+
+        if Panel.objects.filter(name=name, is_visible=0).exists() and is_visible is False:
+            raise serializers.ValidationError({"message" : f"{name} exist. It is only visible to authenticated users"})
+
+        panel = Panel.objects.create(name=name, description=description, is_visible=is_visible)
+
+        return panel
+
+    def update(self, name, is_visible, description):
+        """
+            Updating the panel if the panel is_visible = 0 
+
+            Args:
+                name (_type_): name of the panel 
+
+            Returns:
+                _type_: Updated panel
+        """   
+        try:     
+            panel = Panel.objects.get(name=name, is_visible=0)
+            panel.is_visible = is_visible
+            panel.description = description
+            panel.save()
+        except ObjectDoesNotExist:
+            raise serializers.ValidationError({"message": f"{panel} does not exist"})
+
+        return panel
+
+    class Meta:
+        model = Panel
+        fields = ['name', 'description', 'is_visible']
+
 class PanelDetailSerializer(serializers.ModelSerializer):
     """
         Serializer for the Panel model.

gene2phenotype_project/gene2phenotype_app/serializers/user.py

@@ -8,6 +8,8 @@
 from rest_framework_simplejwt.tokens import RefreshToken, TokenError
 from rest_framework.validators import UniqueValidator
 from django.contrib.auth.models import update_last_login
+from django.core.exceptions import ObjectDoesNotExist
+
 
 from ..utils import CustomMail
 from ..models import User, UserPanel, Panel
@@ -230,10 +232,40 @@ class Meta:
                         }
 
 class AddUserToPanelSerializer(serializers.ModelSerializer):
+    """
+        Adds User to a Panel serializer 
+        Args:
+            serializers (_type_): 
+                user : Serializers CharField
+                panel : Serializers ListField that only accepts CharField and can not be empty
+
+        Raises:
+            serializers.ValidationError: If UserEmail is not sent in the request
+            serializers.ValidationError: If User does not exists
+            serializers.ValidationError: If Panel does not exists
+            serializers.ValidationError: If UserPanel already exists
+
+        Returns:
+            _type_: Created UserPanel or Updated UserPanel
+    """    
     user = serializers.CharField(write_only=True)
     panel = serializers.ListField(child=serializers.CharField(), allow_empty=False, write_only=True)
 
     def validate(self, attrs):
+        """
+            Validation step for the AddUserPanelSerializer
+
+            Args:
+                attrs (_type_): The request data that will be validated
+
+            Raises:
+                serializers.ValidationError: If UserEmail is not sent in the request
+                serializers.ValidationError: If User does not exists
+                serializers.ValidationError: If Panel does not exists
+
+            Returns:
+                _type_: Validated data
+        """        
         user = attrs.get('user', '')
         if user is None:
             raise serializers.ValidationError({'message': 'user email is required to add user to panel'})
@@ -251,24 +283,64 @@ def validate(self, attrs):
 
 
     def create(self, validated_data):
+        """
+            Creates the User panel, taking the User and a list of panels from validated data 
+            Also calls the update function if UserPanel already exists
+
+            Args:
+                validated_data (_type_): A dictionary object containing a list of panels and user_email
+
+            Raises:
+                serializers.ValidationError: If UserPanel already exists and it is not deleted 
+
+            Returns:
+                _type_: Created UserPanel
+        """        
         user_email = validated_data.get('user')
         panels = validated_data.get('panel')
-
         user_obj = User.objects.get(email=user_email)
         for panel in panels:
             panel_obj = Panel.objects.get(name=panel)
 
             if UserPanel.objects.filter(user=user_obj, panel=panel_obj, is_deleted=1).exists():
-                raise serializers.ValidationError({'message': f"User {user_email} used to exists in this {panel}, Update instead"})
-
+                self.update(user_obj, panel_obj)
+                continue
+
             if not UserPanel.objects.filter(user=user_obj, panel=panel_obj, is_deleted=0).exists():
                 user_panel = UserPanel.objects.create(user=user_obj, panel=panel_obj, is_deleted=0)
             else:
                 raise serializers.ValidationError({'message': f"User {user_email} already exists in this {panel}"})
-
+        
         return user_panel
 
+    def update(self, user, panel):
+        """
+            Updates the UserPanel, if UserPanel exists
+            Changes from is_deleted = 1 to is_deleted = 0
+
+            Args:
+                user (_type_): user object 
+                panel (_type_): Panel object
+
+        Returns:
+            _type_: The updated user panel
+        """       
+        try: 
+            user_panel = UserPanel.objects.get(user=user, panel=panel, is_deleted=1)
+            user_panel.is_deleted = 0
+            user_panel.save()
+
+
+            user_info =  {
+                "message" : f"{user} has been updated in this {panel}"
+                }
+
+        except ObjectDoesNotExist:
+            return {
+                "message": f"{user} does not exist in this panel "
+            }
 
+        return user_info
     class Meta:
         model = UserPanel
         fields = ['user', 'panel']

gene2phenotype_project/gene2phenotype_app/urls.py

@@ -71,8 +71,8 @@ def perform_create(self, serializer):
     path('curation/publish/<str:stable_id>/', views.PublishRecord.as_view(), name="publish_record"),
 
     #user management
-    path("create/user/", views.CreateUserView.as_view(), name="create"),
-    path('add_user/panel/', views.AddUserToPanelView.as_view(), name="add_user"),
+    path("create/user/", views.CreateUserView.as_view(), name="create_user"),
+    path('add_user/panel/', views.AddUserToPanelView.as_view(), name="add_user_panel"),
     path('profile/', views.ManageUserView.as_view(), name='profile'),
     path('change_password/', views.ChangePasswordView.as_view(), name='change_password'),
     path('reset_password/<uid>/<token>/', views.ResetPasswordView.as_view(), name='reset_password'),
@@ -81,5 +81,8 @@ def perform_create(self, serializer):
     path('logout/', views.LogOutView.as_view(), name='logout'),
     path('token/refresh/', views.CustomTokenRefreshView.as_view(), name='token_refresh'),
 
+    #panels management 
+    path("create/panel/", views.PanelCreateView.as_view(), name="panel_create")
+
 ]
 urlpatterns = format_suffix_patterns(urlpatterns)

gene2phenotype_project/gene2phenotype_app/views/__init__.py

@@ -1,6 +1,6 @@
 from .base import BaseView, BaseAdd, BaseUpdate, ListEndpoints
 
-from .panel import (PanelList, PanelDetail, PanelRecordsSummary, 
+from .panel import (PanelCreateView, PanelList, PanelDetail, PanelRecordsSummary, 
                     PanelDownload, LGDEditPanel)
 
 from .locus import LocusGene, LocusGeneSummary, GeneFunction

gene2phenotype_project/gene2phenotype_app/views/panel.py

@@ -15,10 +15,16 @@
                                        LGDPublication, LGDCrossCuttingModifier,
                                        LGDPanel, LGDComment)
 
-from gene2phenotype_app.serializers import PanelDetailSerializer, LGDPanelSerializer, UserSerializer
+from gene2phenotype_app.serializers import PanelCreateSerializer, PanelDetailSerializer, LGDPanelSerializer, UserSerializer
 
 from .base import BaseView, IsSuperUser, CustomPermissionAPIView
 
+class PanelCreateView(generics.CreateAPIView):
+    """ 
+        Panel Creation View 
+    """    
+    serializer_class = PanelCreateSerializer
+    permission_classes = [permissions.IsAdminUser]
 
 class PanelList(generics.ListAPIView):
     """
@@ -143,7 +149,7 @@ class LGDEditPanel(CustomPermissionAPIView):
     # Define specific permissions
     method_permissions = {
         "post": [permissions.IsAuthenticated],
-        "update": [permissions.IsAuthenticated, IsSuperUser],
+        "update": [IsSuperUser],
     }
 
     @transaction.atomic

gene2phenotype_project/gene2phenotype_app/views/user.py

@@ -104,6 +104,12 @@ class CreateUserView(generics.CreateAPIView):
     permission_classes = [permissions.IsAdminUser]
 
 class AddUserToPanelView(generics.CreateAPIView):
+    """
+        Add User to Panel view
+
+        Args:
+            generics (_type_): Adds User to panel, permissions is AdminUser, so views only available to AdminUser
+    """    
     serializer_class = AddUserToPanelSerializer
     permission_classes = [permissions.IsAdminUser]