+
diff --git a/src/frontend/static/frontend/src/components/pipeline/experiment-result/gene-gem-details/survival-analysis/KaplanMeierUtils.tsx b/src/frontend/static/frontend/src/components/pipeline/experiment-result/gene-gem-details/survival-analysis/KaplanMeierUtils.tsx
index 12616511..d334f403 100644
--- a/src/frontend/static/frontend/src/components/pipeline/experiment-result/gene-gem-details/survival-analysis/KaplanMeierUtils.tsx
+++ b/src/frontend/static/frontend/src/components/pipeline/experiment-result/gene-gem-details/survival-analysis/KaplanMeierUtils.tsx
@@ -1,7 +1,7 @@
import React from 'react'
import * as d3 from 'd3'
import { Nullable } from '../../../../../utils/interfaces'
-
+import './kaplanMeier.css'
/** Needed structure for KaplanMeier chart */
type KaplanMeierSample = {
time: number,
@@ -174,7 +174,14 @@ const YAxis = (props: AxisProps) => {
className='axis axis-y'
transform={`translate(${props.left}, ${props.top})`}
>
-
+ {
+ /**
+ * g tag generate the dom structure of ...
+ * The idea es usign the first g wrapp the inside g tag and text to move it a few px to prevents being overwrite by Y axis.
+ * If the Dom change in the future, open the navigator inspect then verify the Dom and fix the new structure.
+ */
+ }
+
{
const colors = d3.scaleOrdinal(d3.schemeCategory10).range()
const yDomain = [1, 0]
- const seriesWidth = this.props.width - 64
+ const seriesWidth = this.props.width
const seriesHeight = this.props.height - 64
return (
diff --git a/src/frontend/static/frontend/src/components/pipeline/experiment-result/gene-gem-details/survival-analysis/kaplanMeier.css b/src/frontend/static/frontend/src/components/pipeline/experiment-result/gene-gem-details/survival-analysis/kaplanMeier.css
new file mode 100644
index 00000000..589bd9bc
--- /dev/null
+++ b/src/frontend/static/frontend/src/components/pipeline/experiment-result/gene-gem-details/survival-analysis/kaplanMeier.css
@@ -0,0 +1,3 @@
+.g-wrapper> g > text {
+ transform: translateX(-20px); /* Prevents Y axis overwrite text */
+}
\ No newline at end of file
diff --git a/src/frontend/static/frontend/src/utils/django_interfaces.ts b/src/frontend/static/frontend/src/utils/django_interfaces.ts
index e731cd33..c5751235 100644
--- a/src/frontend/static/frontend/src/utils/django_interfaces.ts
+++ b/src/frontend/static/frontend/src/utils/django_interfaces.ts
@@ -446,7 +446,19 @@ interface DjangoInstitution {
location: string,
email: string,
telephone_number: string,
- users: DjangoUser[]
+ users?: DjangoUser[]
+}
+
+/**
+ * Django Institution user
+ */
+interface DjangoInstitutionUser {
+ user: {
+ id: number,
+ username: string,
+ },
+ id: number,
+ is_institution_admin: boolean,
}
/**
@@ -530,7 +542,7 @@ interface DjangoNumberSamplesInCommonResult extends DjangoCommonResponse ({ ...command, functionToExecute: debounce(command.functionToExecute, 300) }))
+
+ this.websocket.onmessage = function (event) {
try {
const dataParsed: WebsocketMessage = JSON.parse(event.data)
const commandToAttend = config.commandsToAttend.find((commandToAttend) => commandToAttend.key === dataParsed.command)
// If matches with any function defined by the user, executes it
+
if (commandToAttend !== undefined) {
commandToAttend.functionToExecute()
}
@@ -38,7 +42,7 @@ class WebsocketClientCustom {
console.log('Data:', event.data)
console.log('Exception:', ex)
}
- }, 300)
+ }
this.websocket.onerror = function (event) {
console.log('Error establishing websocket connection', event)
diff --git a/src/frontend/templates/frontend/institutions.html b/src/frontend/templates/frontend/institutions.html
index bb76824b..f3139720 100644
--- a/src/frontend/templates/frontend/institutions.html
+++ b/src/frontend/templates/frontend/institutions.html
@@ -14,8 +14,13 @@
{% block js %}
{% render_bundle 'institutions' 'js' %}
diff --git a/src/frontend/urls.py b/src/frontend/urls.py
index 1aaa0b6e..256915fc 100644
--- a/src/frontend/urls.py
+++ b/src/frontend/urls.py
@@ -1,21 +1,12 @@
-from django.conf import settings
from django.urls import path
from . import views
urlpatterns = [
path('', views.index_action, name='index'),
path('gem', views.gem_action, name='gem'),
- path('login', views.login_action, name='login'),
path('my-datasets', views.datasets_action, name='datasets'),
path('survival', views.survival_action, name='survival'),
- path('authenticate', views.authenticate_action, name='authentication'),
- path('create-user', views.create_user_action, name='create_user'),
path('about-us', views.about_us_action, name='about_us'),
- path('site-policy', views.terms_and_privacy_policy_action, name='site_policy'),
- path('logout', views.logout_action, name='logout'),
- path('user', views.CurrentUserView.as_view(), name='current_user')
+ path('site-policy', views.terms_and_privacy_policy_action, name='site_policy')
]
-if settings.DEBUG:
- urlpatterns.append(path('new-user-email-test', views.test_new_user_email))
- urlpatterns.append(path('confirmation-email-test', views.test_confirmation_email))
diff --git a/src/frontend/views.py b/src/frontend/views.py
index f8fc9d65..68914f4c 100644
--- a/src/frontend/views.py
+++ b/src/frontend/views.py
@@ -1,17 +1,6 @@
-import logging
-from typing import Optional, Union
-from django.contrib.auth.base_user import AbstractBaseUser
-from django.shortcuts import render, redirect
-from django.contrib.auth import authenticate, logout, login
-from django.contrib.auth.models import User
+from django.shortcuts import render
from django.contrib.auth.decorators import login_required
-from django_email_verification import sendConfirm
-from rest_framework import permissions
-from rest_framework.response import Response
-from rest_framework.views import APIView
-from .serializers import UserSerializer
from django.conf import settings
-from django.db import transaction, InternalError
def index_action(request):
@@ -52,169 +41,3 @@ def datasets_action(request):
def survival_action(request):
"""Survival Analysis view"""
return render(request, "frontend/survival.html")
-
-
-def login_action(request):
- """Login view"""
- if request.user.is_authenticated:
- return redirect('index')
-
- return render(request, "frontend/login.html")
-
-
-def view_bad_credentials(request):
- """Returns login template with bad credential error in Its context"""
- return render(request, "frontend/login.html", {'loginError': 'Your username or password is invalid'})
-
-
-def authenticate_action(request):
- """Authentication view"""
- username: Optional[str] = request.POST.get('username')
- password: Optional[str] = request.POST.get('password')
- if username is None or password is None:
- return view_bad_credentials(request)
-
- user: Union[AbstractBaseUser, AbstractBaseUser, None] = authenticate(username=username, password=password)
-
- if user is not None:
- login(request, user)
- # If 'next' param is specified, it redirects to that URL
- next_url = request.POST.get('next')
- return redirect(next_url if next_url is not None else 'index')
- else:
- # Checks if User is active
- try:
- user: User = User.objects.get(username=username)
- if user is not None and not user.is_active:
- return render(
- request,
- "frontend/login.html",
- {
- 'loginWarning': 'Your account has not been validated yet. Please, check your email account for '
- 'our verification email'
- }
- )
- return view_bad_credentials(request)
- except User.DoesNotExist:
- return view_bad_credentials(request)
-
-
-def is_sign_up_form_valid(username: str, email: str, password: str, password_repeated: str) -> bool:
- """
- Checks if Sign Up form is valid
- @param username: Username to check
- @param email: Email to check
- @param password: Password to check
- @param password_repeated: Repeated password to check
- @return: True if is all the field valid. False otherwise
- """
- password_striped = password.strip()
- password_repeated_striped = password_repeated.strip()
- return len(username.strip()) > 0 \
- and len(email.strip()) > 0 \
- and len(password_striped) > 0 \
- and len(password_repeated_striped) > 0 \
- and password_striped == password_repeated_striped
-
-
-def user_already_exists_username(username: str) -> bool:
- """
- Check if exists any user in the DB with the same username passed by parameter
- @param username: Username to check
- @return: True if exists the user. False otherwise
- """
- return User.objects.filter(username=username).exists()
-
-
-def user_already_exists_email(email: str) -> bool:
- """
- Check if exists any user in the DB with the same email passed by parameter
- @param email: Email to check
- @return: True if exists the user. False otherwise
- """
- return User.objects.filter(email=email).exists()
-
-
-@transaction.atomic
-def create_user_action(request):
- """User creation view"""
- username: str = request.POST.get('newUsername', '')
- email: str = request.POST.get('email', '')
- password: str = request.POST.get('newPassword', '')
- password_repeated: str = request.POST.get('newPasswordRepeated', '')
- if not is_sign_up_form_valid(username, email, password, password_repeated):
- return render(request, "frontend/login.html", {'loginError': 'Invalid fields'})
-
- if user_already_exists_username(username):
- return render(request, "frontend/login.html", {'loginError': 'There is already a user with that username'})
-
- if user_already_exists_email(email):
- return render(request, "frontend/login.html", {'loginError': 'There is already a user with that email'})
-
- # If it's set to not send an email asking for confirmation just creates the user and redirect to login
- if not settings.EMAIL_NEW_USER_CONFIRMATION_ENABLED:
- User.objects.create_user(username, email, password)
- return render(request, "frontend/login.html", {'loginSuccess': 'User created successfully'})
-
- # Creates the user and sends email
- # FIXME: library does not return exceptions thrown in sender thread. After a PR it should be tested
- error_sending_email = False
- try:
- with transaction.atomic():
- user = User.objects.create_user(username, email, password)
- try:
- sendConfirm(user)
- except Exception as ex:
- logging.warning(f'Error sending email -> {ex}')
- raise InternalError # Rollback
- except InternalError:
- error_sending_email = True
-
- if error_sending_email:
- return render(request, "frontend/login.html", {'loginError': 'An error have occurred. Please, try again. If the'
- ' problem persists contact us, please'})
-
- # Hides email
- idx_at = email.index('@')
- idx_to_replace = idx_at - 2
- hidden_email = '*' * idx_to_replace + email[idx_to_replace:]
-
- return render(
- request,
- "frontend/login.html",
- {'loginWarning': f'We have sent a confirmation email to {hidden_email}'}
- )
-
-
-def test_new_user_email(request):
- """
- To test new user email template in browser. Only accessible in DEBUG mode
- @param request: Request object
- @return: HTTP Response
- """
- return render(request, settings.EMAIL_MAIL_HTML, {'link': '#'})
-
-
-def test_confirmation_email(request):
- """
- To test confirmation email template in browser. Only accessible in DEBUG mode
- @param request: Request object
- @return: HTTP Response
- """
- return render(request, settings.EMAIL_PAGE_TEMPLATE, {'success': True})
-
-
-def logout_action(request):
- """Closes User session"""
- logout(request)
- return redirect('index')
-
-
-class CurrentUserView(APIView):
- """Gets current User info"""
- permission_classes = [permissions.IsAuthenticated]
-
- @staticmethod
- def get(request):
- serializer = UserSerializer(request.user)
- return Response(serializer.data)
diff --git a/src/genes/serializers.py b/src/genes/serializers.py
index c0dac294..b11a9b5a 100644
--- a/src/genes/serializers.py
+++ b/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()
+
diff --git a/src/institutions/__pycache__/models.cpython-312.pyc.2847318479840 b/src/institutions/__pycache__/models.cpython-312.pyc.2847318479840
new file mode 100644
index 00000000..2c0294ff
Binary files /dev/null and b/src/institutions/__pycache__/models.cpython-312.pyc.2847318479840 differ
diff --git a/src/institutions/models.py b/src/institutions/models.py
index 31171db3..93aff1da 100644
--- a/src/institutions/models.py
+++ b/src/institutions/models.py
@@ -1,5 +1,6 @@
from django.contrib.auth import get_user_model
from django.db import models
+from api_service.websocket_functions import send_update_institutions_command, send_update_user_for_institution_command
class Institution(models.Model):
@@ -10,6 +11,24 @@ class Institution(models.Model):
telephone_number = models.CharField(max_length=30, blank=True, null=True)
users = models.ManyToManyField(get_user_model(), through='InstitutionAdministration')
+ class Meta:
+ ordering = ['-id']
+
+ def delete(self, *args, **kwargs) -> None:
+ """Deletes the instance and sends a websockets message to update state in the frontend """
+ related_users = list(self.users.all())
+ super().delete(*args, **kwargs)
+ # Sends a websockets message to all users for update the institutions state in the frontend
+ for user in related_users:
+ send_update_institutions_command(user.id)
+
+ def save(self, *args, **kwargs) -> None:
+ """Everytime the institution status changes, uses websocket to update state in the frontend"""
+ super().save(*args, **kwargs)
+ # Sends a websockets message to all users for update the institutions state in the frontend
+ for user in self.users.all():
+ send_update_institutions_command(user.id)
+
def __str__(self):
return self.name
@@ -20,6 +39,27 @@ class InstitutionAdministration(models.Model):
institution = models.ForeignKey(Institution, on_delete=models.CASCADE)
is_institution_admin = models.BooleanField(default=False)
+ class Meta:
+ ordering = ['-id']
+
+ def delete(self, *args, **kwargs) -> None:
+ """Deletes the instance and sends a websockets message to update state in the frontend """
+ related_users = list(self.institution.users.all())
+ super().delete(*args, **kwargs)
+ # Sends a websockets message to all users for update the institutions state in the frontend
+ for user in related_users:
+ send_update_institutions_command(user.id)
+ send_update_user_for_institution_command(user.id)
+
+ def save(self, *args, **kwargs) -> None:
+ """Everytime the institution status changes, uses websocket to update state in the frontend"""
+ super().save(*args, **kwargs)
+ related_users = list(self.institution.users.all())
+ # Sends a websockets message to all users for update the institutions state in the frontend
+ for user in related_users:
+ send_update_institutions_command(user.id)
+ send_update_user_for_institution_command(user.id)
+
def __str__(self):
as_admin_label = '(as admin)' if self.is_institution_admin else ''
return f'{self.user} -> {self.institution} {as_admin_label}'
diff --git a/src/institutions/serializers.py b/src/institutions/serializers.py
index a2ce6426..bf1f1755 100644
--- a/src/institutions/serializers.py
+++ b/src/institutions/serializers.py
@@ -1,7 +1,7 @@
-from django.contrib.auth import get_user_model
from rest_framework import serializers
-from .models import Institution
-from frontend.serializers import UserSerializer
+from .models import Institution, InstitutionAdministration
+from users.serializers import UserSerializer
+from django.contrib.auth import get_user_model
class InstitutionSerializer(serializers.ModelSerializer):
@@ -19,9 +19,33 @@ class Meta:
model = Institution
fields = ['id', 'name']
+class InstitutionListSerializer(serializers.ModelSerializer):
+ """A simple serializer for get only the Institution fields"""
+ is_user_admin = serializers.SerializerMethodField(method_name='get_is_user_admin')
+ class Meta:
+ model = Institution
+ fields = ['id', 'name', 'location', 'email', 'telephone_number', 'is_user_admin']
+ def get_is_user_admin(self, obj: Institution) -> bool:
+ user = self.context['request'].user
+ return obj.institutionadministration_set.filter(user=user, is_institution_admin=True).exists()
+
+class LimitedUserSerializer(serializers.ModelSerializer):
+ """A lightweight serializer for User model"""
+ class Meta:
+ model = get_user_model()
+ fields = ['id', 'username']
class UserCandidateSerializer(serializers.ModelSerializer):
"""Serializer useful to add a User to an Institution"""
+ user = LimitedUserSerializer()
class Meta:
- model = get_user_model()
- fields = ['id', 'username', 'email']
+ model = InstitutionAdministration
+ fields = ['id', 'user', 'is_institution_admin']
+
+class InstitutionAdminUpdateSerializer(serializers.ModelSerializer):
+ """
+ Serializer for updating 'is_institution_admin' in InstitutionAdministration
+ """
+ class Meta:
+ model = InstitutionAdministration
+ fields = ['id', 'is_institution_admin']
diff --git a/src/institutions/urls.py b/src/institutions/urls.py
index 24fe9831..7bb42cac 100644
--- a/src/institutions/urls.py
+++ b/src/institutions/urls.py
@@ -4,9 +4,19 @@
urlpatterns = [
path('', views.institutions_action, name='institutions'),
- path('my-institutions-as-admin', views.InstitutionAsAdminList.as_view(), name='user_institutions_as_admin'),
- path('my-institutions', views.InstitutionList.as_view(), name='user_institutions'),
+ path('my-institutions', views.UserInstitution.as_view(), name='user_institutions'),
+ path('my-institutions-list', views.UserInstitutionList.as_view(), name='user_institutions_list'),
path('user-candidates', views.UserCandidatesList.as_view(), name='user_candidates'),
+ path('user-candidates//', views.UserCandidatesList.as_view()),
+ path('create', views.CreateInstitutionView.as_view(), name='create_institution'),
+ path('edit', views.UpdateInstitutionView.as_view(), name='edit_institution'),
+ path('edit//', views.UpdateInstitutionView.as_view()),
+ path('delete', views.DeleteInstitutionView.as_view(), name='delete-institution'),
+ path('delete//', views.DeleteInstitutionView.as_view()),
+ path('admin-update', views.UpdateInstitutionAdminView.as_view(), name='update-institution-admin'),
+ path('admin-update//', views.UpdateInstitutionAdminView.as_view()),
+ path('non-users', views.InstitutionNonUsersListView.as_view(), name='institution-non-users-list'),
+ path('non-users//', views.InstitutionNonUsersListView.as_view()),
path(
'add-remove-user-to-institution',
views.add_remove_user_to_institution_action,
diff --git a/src/institutions/views.py b/src/institutions/views.py
index 70789e0c..bfbc7ecd 100644
--- a/src/institutions/views.py
+++ b/src/institutions/views.py
@@ -1,56 +1,62 @@
from django.contrib.auth.decorators import login_required
from django.shortcuts import render
-from rest_framework import generics, permissions
+from rest_framework import generics, permissions, filters
import json
from common.enums import ResponseCode
from common.functions import encode_json_response_status
from common.response import ResponseStatus
from .enums import AddRemoveUserToInstitutionStatusErrorCode
-from .models import Institution
-from .serializers import InstitutionSerializer, UserCandidateSerializer
+from .models import Institution, InstitutionAdministration
+from .serializers import InstitutionSerializer, UserCandidateSerializer, InstitutionListSerializer, InstitutionAdminUpdateSerializer, LimitedUserSerializer
from django.contrib.auth.models import User
+from common.pagination import StandardResultsSetPagination
+from django_filters.rest_framework import DjangoFilterBackend
+from rest_framework.response import Response
+from rest_framework.views import APIView
+from django.shortcuts import get_object_or_404
+from rest_framework.exceptions import ValidationError
+from django.contrib.auth import get_user_model
+from api_service.websocket_functions import send_update_institutions_command, send_update_user_for_institution_command
-class InstitutionAsAdminList(generics.ListAPIView):
- """REST endpoint: list for Institution model of which the current user is admin"""
+
+class UserInstitutionList(generics.ListAPIView):
+ """REST endpoint: list for Institution model of which the current user is part"""
def get_queryset(self):
return Institution.objects.filter(
- institutionadministration__user=self.request.user,
- institutionadministration__is_institution_admin=True
- )
+ institutionadministration__user=self.request.user
+ ).distinct()
- serializer_class = InstitutionSerializer
+ serializer_class = InstitutionListSerializer
permission_classes = [permissions.IsAuthenticated]
-
-
-class InstitutionList(generics.ListAPIView):
+ pagination_class = StandardResultsSetPagination
+ filter_backends = [filters.OrderingFilter, filters.SearchFilter]
+ search_fields = ['name', 'location']
+ ordering_fields = ['name', 'location', 'email', 'telephone_number']
+class UserInstitution(generics.ListAPIView):
"""REST endpoint: list for Institution model of which the current user is part"""
def get_queryset(self):
return Institution.objects.filter(institutionadministration__user=self.request.user)
-
serializer_class = InstitutionSerializer
permission_classes = [permissions.IsAuthenticated]
-
class UserCandidatesList(generics.ListAPIView):
"""REST endpoint: list for User model. Used to add to an Institution"""
def get_queryset(self):
- # Parses the request search param
- query_search = self.request.GET.get('querySearch', '')
- query_search = query_search.strip()
-
- if not query_search:
- return User.objects.none()
-
- # Returns only 3 results
- return User.objects.filter(username__icontains=query_search)[:3]
-
+ institution_id = self.kwargs.get('institution_id')
+ return InstitutionAdministration.objects.filter(
+ institution_id=institution_id
+ )
serializer_class = UserCandidateSerializer
permission_classes = [permissions.IsAuthenticated]
-
+
+ pagination_class = StandardResultsSetPagination
+ filter_backends = [filters.OrderingFilter, filters.SearchFilter]
+ search_fields = ['user__username']
+ ordering_fields = ['user__username']
@login_required
def add_remove_user_to_institution_action(request):
@@ -81,13 +87,17 @@ def add_remove_user_to_institution_action(request):
institutionadministration__is_institution_admin=True
)
+
# Adds/Remove user
if is_adding:
institution.users.add(user)
else:
institution.users.remove(user)
- institution.save()
+ for user in institution.users.all():
+ send_update_institutions_command(user.id)
+ send_update_user_for_institution_command(user.id)
+
response = {
'status': ResponseStatus(ResponseCode.SUCCESS)
@@ -119,6 +129,147 @@ def add_remove_user_to_institution_action(request):
return encode_json_response_status(response)
+class CreateInstitutionView(generics.CreateAPIView):
+ """
+ REST endpoint: Create an Institution and assign the creator as admin
+ """
+ serializer_class = InstitutionSerializer
+ permission_classes = [permissions.IsAuthenticated]
+
+ def perform_create(self, serializer):
+ """
+ Overrides the create method to add the creator as admin
+ """
+ # Save the institution instance
+ institution = serializer.save()
+ # Create a relationship between the creator and the institution as admin
+ InstitutionAdministration.objects.create(
+ user=self.request.user,
+ institution=institution,
+ is_institution_admin=True
+ )
+
+ def create(self, request, *args, **kwargs):
+ """
+ Handles the POST request to create an institution
+ """
+ serializer = self.get_serializer(data=request.data)
+ serializer.is_valid(raise_exception=True)
+ self.perform_create(serializer)
+ return Response(
+ serializer.data
+ )
+
+class UpdateInstitutionView(generics.UpdateAPIView):
+ """
+ REST endpoint: Update an Institution
+ Allows editing 'name', 'location', 'email', and 'telephone_number'.
+ """
+ queryset = Institution.objects.all()
+ serializer_class = InstitutionListSerializer
+ permission_classes = [permissions.IsAuthenticated]
+ lookup_field = 'id'
+
+ def get_queryset(self):
+ """
+ Allow only admins of the institution to edit
+ """
+ return Institution.objects.filter(
+ institutionadministration__user=self.request.user,
+ institutionadministration__is_institution_admin=True
+ )
+
+ def update(self, request, *args, **kwargs):
+ """
+ Handle partial updates
+ """
+ partial = kwargs.pop('partial', True) # Permite actualizaciones parciales
+ instance = self.get_object()
+ serializer = self.get_serializer(instance, data=request.data, partial=partial)
+ serializer.is_valid(raise_exception=True)
+ self.perform_update(serializer)
+
+ return Response(serializer.data)
+
+class DeleteInstitutionView(generics.DestroyAPIView):
+ """
+ REST endpoint: Delete an Institution
+ Allows deletion only if the user is an admin of the institution.
+ """
+ queryset = Institution.objects.all()
+ permission_classes = [permissions.IsAuthenticated]
+ lookup_field = 'id'
+
+ def get_queryset(self):
+ """
+ Allow only admins of the institution to delete it.
+ """
+ return Institution.objects.filter(
+ institutionadministration__user=self.request.user,
+ institutionadministration__is_institution_admin=True
+ )
+
+ def delete(self, request, *args, **kwargs):
+ """
+ Handle the delete operation with additional checks.
+ """
+ try:
+ instance = self.get_object()
+ self.perform_destroy(instance)
+ response = {
+ 'status': ResponseStatus(
+ ResponseCode.ERROR,
+ message="Institution deleted successfully."
+ )
+ }
+ return encode_json_response_status(response)
+
+ except Institution.DoesNotExist:
+ response = {
+ 'status': ResponseStatus(
+ ResponseCode.ERROR,
+ message="Institution not found or you do not have permission to delete it."
+ )
+ }
+ return encode_json_response_status(response)
+
+
+class UpdateInstitutionAdminView(APIView):
+ """
+ REST endpoint: Update the 'is_institution_admin' field in InstitutionAdministration
+ """
+ queryset = InstitutionAdministration.objects.all()
+ serializer_class = InstitutionAdminUpdateSerializer
+ permission_classes = [permissions.IsAuthenticated]
+ def patch(self, request, id):
+ """
+ Ensure that only an institution admin can update this relationship.
+ """
+ relation = get_object_or_404(InstitutionAdministration, institution__institutionadministration__user=self.request.user, id=id)
+ if relation.user.id == self.request.user.id:
+ raise ValidationError('Can not change admin for current user.')
+ relation.is_institution_admin = not relation.is_institution_admin
+ relation.save(update_fields=['is_institution_admin'])
+ return Response({'ok': True})
+
+class InstitutionNonUsersListView(generics.ListAPIView):
+ """
+ REST endpoint: Get all users NOT associated with a specific institution.
+ """
+ serializer_class = LimitedUserSerializer
+ permission_classes = [permissions.IsAuthenticated]
+
+ def get_queryset(self):
+ """
+ Return all users not associated with a specific institution.
+ """
+ institution_id = self.kwargs.get('institution_id')
+
+ associated_user_ids = InstitutionAdministration.objects.filter(
+ institution_id=institution_id
+ ).values_list('user_id', flat=True)
+
+ return get_user_model().objects.exclude(id__in=associated_user_ids)
@login_required
def institutions_action(request):
diff --git a/src/multiomics_intermediate/settings.py b/src/multiomics_intermediate/settings.py
index beaf5106..182a0c45 100644
--- a/src/multiomics_intermediate/settings.py
+++ b/src/multiomics_intermediate/settings.py
@@ -62,6 +62,7 @@
'inferences',
'molecules_details',
'chunked_upload',
+ 'users',
]
MIDDLEWARE = [
@@ -151,6 +152,8 @@
},
]
+MIN_PASSWORD_LEN: int = int(os.getenv('MIN_PASSWORD_LEN', 8))
+
# Internationalization
# https://docs.djangoproject.com/en/3.0/topics/i18n/
@@ -296,17 +299,18 @@
EMAIL_PAGE_TEMPLATE = 'confirm_template.html'
EMAIL_PAGE_DOMAIN = 'https://multiomix.org'
-
# Modulector settings
MODULECTOR_SETTINGS = {
- 'host': os.getenv('MODULECTOR_HOST', '127.0.0.1'),
- 'port': os.getenv('MODULECTOR_PORT', '8001')
+ 'host': os.getenv('MODULECTOR_HOST', 'modulector.multiomix.org'),
+ 'port': os.getenv('MODULECTOR_PORT', 443),
+ 'protocol': os.getenv('BIOAPI_PROTOCOL', 'https')
}
# BioAPI settings
BIOAPI_SETTINGS = {
- 'host': os.getenv('BIOAPI_HOST', '127.0.0.1'),
- 'port': os.getenv('BIOAPI_PORT', '8002')
+ 'host': os.getenv('BIOAPI_HOST', 'bioapi.multiomix.org'),
+ 'port': os.getenv('BIOAPI_PORT', 443),
+ 'protocol': os.getenv('BIOAPI_PROTOCOL', 'https')
}
# Multiomix-aws-emr
diff --git a/src/multiomics_intermediate/urls.py b/src/multiomics_intermediate/urls.py
index f277e55f..e5029a6b 100644
--- a/src/multiomics_intermediate/urls.py
+++ b/src/multiomics_intermediate/urls.py
@@ -36,4 +36,5 @@
path('molecules/', include('molecules_details.urls')),
path('admin/', admin.site.urls),
path('email/', include(mail_urls)),
+ path('users/', include('users.urls')),
] + static(settings.MEDIA_URL, document_root=settings.MEDIA_ROOT)
diff --git a/src/statistical_properties/stats_service.py b/src/statistical_properties/stats_service.py
index d27bc9d1..c82d8f71 100644
--- a/src/statistical_properties/stats_service.py
+++ b/src/statistical_properties/stats_service.py
@@ -3,8 +3,9 @@
import numpy as np
import pandas as pd
from lifelines import CoxPHFitter
-from sklearn.metrics import mean_squared_error, r2_score
+from sklearn.metrics import mean_squared_error, r2_score, silhouette_score
from sklearn.model_selection import GridSearchCV, StratifiedKFold
+from sklearn.cluster import AgglomerativeClustering
from sksurv.metrics import concordance_index_censored
from common.datasets_utils import get_common_samples, generate_molecules_file, format_data, \
generate_clinical_file, generate_molecules_dataframe, check_sample_classes, \
@@ -113,13 +114,19 @@ def __compute_stat_validation(stat_validation: StatisticalValidation, molecules_
# Makes predictions
if is_regression:
check_if_stopped(is_aborted, ExperimentStopped)
- predictions = classifier.predict(molecules_df)
+ if isinstance(classifier, AgglomerativeClustering):
+ predictions = classifier.fit_predict(molecules_df)
+ else:
+ predictions = classifier.predict(molecules_df)
# Gets all the metrics for the SVM or RF
check_if_stopped(is_aborted, ExperimentStopped)
y_true = clinical_data['time']
stat_validation.mean_squared_error = mean_squared_error(y_true, predictions)
- stat_validation.c_index = classifier.score(molecules_df, clinical_data)
+ if isinstance(classifier, AgglomerativeClustering):
+ stat_validation.c_index = silhouette_score(molecules_df, predictions)
+ else:
+ stat_validation.c_index = classifier.score(molecules_df, clinical_data)
stat_validation.r2_score = r2_score(y_true, predictions)
# TODO: add here all the metrics for every Source type
diff --git a/src/statistical_properties/survival_functions.py b/src/statistical_properties/survival_functions.py
index bde6f60d..66e37760 100644
--- a/src/statistical_properties/survival_functions.py
+++ b/src/statistical_properties/survival_functions.py
@@ -5,6 +5,7 @@
from lifelines.statistics import logrank_test
from common.utils import get_subset_of_features
from feature_selection.fs_models import ClusteringModels
+from sklearn.cluster import AgglomerativeClustering
KaplanMeierSample = Tuple[
int,
@@ -138,7 +139,10 @@ def generate_survival_groups_by_clustering(
molecules_df = get_subset_of_features(molecules_df, molecules_df.index)
# Gets the groups
- clustering_result = classifier.predict(molecules_df.values)
+ if isinstance(classifier, AgglomerativeClustering):
+ clustering_result = classifier.fit_predict(molecules_df.values)
+ else:
+ clustering_result = classifier.predict(molecules_df.values)
# Retrieves the data for every group and stores the survival function
data: List[Dict[str, LabelOrKaplanMeierResult]] = []
diff --git a/src/statistical_properties/views.py b/src/statistical_properties/views.py
index ed9a7940..39c732f7 100644
--- a/src/statistical_properties/views.py
+++ b/src/statistical_properties/views.py
@@ -163,6 +163,8 @@ def get_queryset(self):
ordering_fields = ['name', 'description', 'state', 'created']
+
+# Todo: Verificar
class StatisticalValidationDestroy(generics.DestroyAPIView):
"""REST endpoint: delete for StatisticalValidation model."""
diff --git a/src/user_files/serializers.py b/src/user_files/serializers.py
index f6b78b5d..b957cbe0 100644
--- a/src/user_files/serializers.py
+++ b/src/user_files/serializers.py
@@ -5,12 +5,12 @@
from rest_framework import serializers
from common.functions import get_enum_from_value, create_survival_columns_from_json
from datasets_synchronization.models import SurvivalColumnsTupleUserFile
-from .models_choices import FileType
-from .utils import has_uploaded_file_valid_format, get_invalid_format_response
-from frontend.serializers import UserSimpleSerializer
+from user_files.models_choices import FileType
+from user_files.utils import has_uploaded_file_valid_format, get_invalid_format_response
+from users.serializers import UserSimpleSerializer
from institutions.serializers import InstitutionSimpleSerializer
from tags.serializers import TagSerializer
-from .models import UserFile
+from user_files.models import UserFile
class SurvivalColumnsTupleUserFileSimpleSerializer(serializers.ModelSerializer):
diff --git a/src/user_files/views.py b/src/user_files/views.py
index 7aeff2ef..e3b9cd19 100644
--- a/src/user_files/views.py
+++ b/src/user_files/views.py
@@ -11,7 +11,7 @@
from rest_framework.exceptions import ValidationError
from rest_framework.views import APIView
from common.pagination import StandardResultsSetPagination
-from .serializers import UserFileSerializer, UserFileWithoutFileObjSerializer
+from user_files.serializers import UserFileSerializer, UserFileWithoutFileObjSerializer
from .models import UserFile
from rest_framework.response import Response
diff --git a/src/users/admin.py b/src/users/admin.py
new file mode 100644
index 00000000..e69de29b
diff --git a/src/users/apps.py b/src/users/apps.py
new file mode 100644
index 00000000..72b14010
--- /dev/null
+++ b/src/users/apps.py
@@ -0,0 +1,6 @@
+from django.apps import AppConfig
+
+
+class UsersConfig(AppConfig):
+ default_auto_field = 'django.db.models.BigAutoField'
+ name = 'users'
diff --git a/src/users/migrations/__init__.py b/src/users/migrations/__init__.py
new file mode 100644
index 00000000..e69de29b
diff --git a/src/users/models.py b/src/users/models.py
new file mode 100644
index 00000000..8b137891
--- /dev/null
+++ b/src/users/models.py
@@ -0,0 +1 @@
+
diff --git a/src/users/serializers.py b/src/users/serializers.py
new file mode 100644
index 00000000..d3ea7a20
--- /dev/null
+++ b/src/users/serializers.py
@@ -0,0 +1,67 @@
+from django.forms import ValidationError
+from rest_framework import serializers
+from django.contrib.auth import get_user_model
+from institutions.models import Institution
+from django.db import transaction
+from django.contrib.auth.hashers import make_password
+
+from multiomics_intermediate import settings
+
+
+
+class UserSerializer(serializers.ModelSerializer):
+ class Meta:
+ model = get_user_model()
+ fields = ['id', 'username', 'is_superuser', 'first_name', 'last_name']
+
+ def to_representation(self, instance):
+ # Adds custom fields
+ data = super(UserSerializer, self).to_representation(instance)
+
+ # Check if current user has any institutions where he's admin
+ data['is_institution_admin'] = Institution.objects.filter(
+ institutionadministration__user=instance,
+ institutionadministration__is_institution_admin=True
+ ).exists()
+
+ # User at this point is not anonymous
+ data['is_anonymous'] = False
+
+ return data
+
+
+class UserSimpleSerializer(serializers.ModelSerializer):
+ """User serializer with fewer data"""
+ class Meta:
+ model = get_user_model()
+ fields = ['id', 'username']
+
+class UserUpdateSerializer(serializers.ModelSerializer):
+ """"fields that are received to update the user"""
+ first_name = serializers.CharField()
+ last_name = serializers.CharField()
+ password = serializers.CharField(write_only=True, required=False, min_length=8)
+
+ class Meta:
+ model = get_user_model()
+ fields = ['first_name', 'last_name', 'password']
+
+ def update(self, instance, validated_data):
+ """Updates the users first_name, last_name, and password fields."""
+ with transaction.atomic():
+ instance.first_name = validated_data.get('first_name', instance.first_name)
+ instance.last_name = validated_data.get('last_name', instance.last_name)
+
+ password = validated_data.pop('password', '')
+ password_length = len(password)
+
+ if password_length != 0:
+ minimum_password_len = settings.MIN_PASSWORD_LEN
+ if password_length < minimum_password_len:
+ raise ValidationError(f'Password must be at least {minimum_password_len} chars long')
+ else:
+ instance.set_password(password)
+
+ instance.save()
+ return instance
+
\ No newline at end of file
diff --git a/src/users/urls.py b/src/users/urls.py
new file mode 100644
index 00000000..ae789c04
--- /dev/null
+++ b/src/users/urls.py
@@ -0,0 +1,16 @@
+from django.conf import settings
+from django.urls import path
+from users import views
+
+urlpatterns = [
+ path('login', views.login_action, name='login'),
+ path('authenticate', views.authenticate_action, name='authentication'),
+ path('create-user', views.create_user_action, name='create_user'),
+ path('logout', views.logout_action, name='logout'),
+ path('user', views.CurrentUserView.as_view(), name='current_user'),
+ path('edit-profile', views.UserRetrieveUpdateView.as_view(), name='update_user')
+]
+
+if settings.DEBUG:
+ urlpatterns.append(path('new-user-email-test', views.test_new_user_email))
+ urlpatterns.append(path('confirmation-email-test', views.test_confirmation_email))
\ No newline at end of file
diff --git a/src/users/views.py b/src/users/views.py
new file mode 100644
index 00000000..fdfbea18
--- /dev/null
+++ b/src/users/views.py
@@ -0,0 +1,188 @@
+import logging
+from typing import Optional, Union
+from django.contrib.auth.base_user import AbstractBaseUser
+from django.shortcuts import render, redirect
+from django.contrib.auth import authenticate, logout, login
+from django.contrib.auth.models import User
+from django_email_verification import sendConfirm
+from rest_framework import permissions, generics
+from rest_framework.response import Response
+from rest_framework.permissions import IsAuthenticated
+from rest_framework.views import APIView
+from users.serializers import UserSerializer, UserUpdateSerializer
+from django.conf import settings
+from django.db import transaction, InternalError
+
+
+def login_action(request):
+ """Login view"""
+ if request.user.is_authenticated:
+ return redirect('index')
+
+ return render(request, "frontend/login.html")
+
+
+def view_bad_credentials(request):
+ """Returns login template with bad credential error in Its context"""
+ return render(request, "frontend/login.html", {'loginError': 'Your username or password is invalid'})
+
+
+def authenticate_action(request):
+ """Authentication view"""
+ username: Optional[str] = request.POST.get('username')
+ password: Optional[str] = request.POST.get('password')
+ if username is None or password is None:
+ return view_bad_credentials(request)
+
+ user: Union[AbstractBaseUser, AbstractBaseUser, None] = authenticate(username=username, password=password)
+
+ if user is not None:
+ login(request, user)
+ # If 'next' param is specified, it redirects to that URL
+ next_url = request.POST.get('next')
+ return redirect(next_url if next_url is not None else 'index')
+ else:
+ # Checks if User is active
+ try:
+ user: User = User.objects.get(username=username)
+ if user is not None and not user.is_active:
+ return render(
+ request,
+ "frontend/login.html",
+ {
+ 'loginWarning': 'Your account has not been validated yet. Please, check your email account for '
+ 'our verification email'
+ }
+ )
+ return view_bad_credentials(request)
+ except User.DoesNotExist:
+ return view_bad_credentials(request)
+
+
+def is_sign_up_form_valid(username: str, email: str, password: str, password_repeated: str) -> bool:
+ """
+ Checks if Sign Up form is valid
+ @param username: Username to check
+ @param email: Email to check
+ @param password: Password to check
+ @param password_repeated: Repeated password to check
+ @return: True if is all the field valid. False otherwise
+ """
+ password_striped = password.strip()
+ password_repeated_striped = password_repeated.strip()
+ return len(username.strip()) > 0 \
+ and len(email.strip()) > 0 \
+ and len(password_striped) > 0 \
+ and len(password_repeated_striped) > 0 \
+ and password_striped == password_repeated_striped
+
+
+def user_already_exists_username(username: str) -> bool:
+ """
+ Check if exists any user in the DB with the same username passed by parameter
+ @param username: Username to check
+ @return: True if exists the user. False otherwise
+ """
+ return User.objects.filter(username=username).exists()
+
+
+def user_already_exists_email(email: str) -> bool:
+ """
+ Check if exists any user in the DB with the same email passed by parameter
+ @param email: Email to check
+ @return: True if exists the user. False otherwise
+ """
+ return User.objects.filter(email=email).exists()
+
+
+@transaction.atomic
+def create_user_action(request):
+ """User creation view"""
+ username: str = request.POST.get('newUsername', '')
+ email: str = request.POST.get('email', '')
+ password: str = request.POST.get('newPassword', '')
+ password_repeated: str = request.POST.get('newPasswordRepeated', '')
+ if not is_sign_up_form_valid(username, email, password, password_repeated):
+ return render(request, "frontend/login.html", {'loginError': 'Invalid fields'})
+
+ if user_already_exists_username(username):
+ return render(request, "frontend/login.html", {'loginError': 'There is already a user with that username'})
+
+ if user_already_exists_email(email):
+ return render(request, "frontend/login.html", {'loginError': 'There is already a user with that email'})
+
+ # If it's set to not send an email asking for confirmation just creates the user and redirect to login
+ if not settings.EMAIL_NEW_USER_CONFIRMATION_ENABLED:
+ User.objects.create_user(username, email, password)
+ return render(request, "frontend/login.html", {'loginSuccess': 'User created successfully'})
+
+ # Creates the user and sends email
+ # FIXME: library does not return exceptions thrown in sender thread. After a PR it should be tested
+ error_sending_email = False
+ try:
+ with transaction.atomic():
+ user = User.objects.create_user(username, email, password)
+ try:
+ sendConfirm(user)
+ except Exception as ex:
+ logging.warning(f'Error sending email -> {ex}')
+ raise InternalError # Rollback
+ except InternalError:
+ error_sending_email = True
+
+ if error_sending_email:
+ return render(request, "frontend/login.html", {'loginError': 'An error have occurred. Please, try again. If the'
+ ' problem persists contact us, please'})
+
+ # Hides email
+ idx_at = email.index('@')
+ idx_to_replace = idx_at - 2
+ hidden_email = '*' * idx_to_replace + email[idx_to_replace:]
+
+ return render(
+ request,
+ "frontend/login.html",
+ {'loginWarning': f'We have sent a confirmation email to {hidden_email}'}
+ )
+
+
+def test_new_user_email(request):
+ """
+ To test new user email template in browser. Only accessible in DEBUG mode
+ @param request: Request object
+ @return: HTTP Response
+ """
+ return render(request, settings.EMAIL_MAIL_HTML, {'link': '#'})
+
+
+def test_confirmation_email(request):
+ """
+ To test confirmation email template in browser. Only accessible in DEBUG mode
+ @param request: Request object
+ @return: HTTP Response
+ """
+ return render(request, settings.EMAIL_PAGE_TEMPLATE, {'success': True})
+
+
+def logout_action(request):
+ """Closes User session"""
+ logout(request)
+ return redirect('index')
+
+
+class CurrentUserView(APIView):
+ """Gets current User info"""
+ permission_classes = [permissions.IsAuthenticated]
+
+ @staticmethod
+ def get(request):
+ serializer = UserSerializer(request.user)
+ return Response(serializer.data)
+
+
+class UserRetrieveUpdateView(generics.RetrieveUpdateAPIView):
+ serializer_class = UserUpdateSerializer
+ permission_classes = [IsAuthenticated]
+
+ def get_object(self):
+ return self.request.user