Upgrade Django from v3.2 to v4.2

django/applications/catmaid/control/authentication.py

@@ -26,7 +26,7 @@
 from django.core.exceptions import ObjectDoesNotExist
 from django.shortcuts import _get_queryset, render
 from django.template import Context, Template
-from django.utils.encoding import force_bytes, force_text
+from django.utils.encoding import force_bytes, force_str
 from django.utils.http import urlsafe_base64_encode, urlsafe_base64_decode
 from django.core.mail import EmailMessage
 
@@ -892,7 +892,7 @@ def register(request:HttpRequest) -> Union[HttpResponseRedirect, JsonResponse]:
 
 def activate(request:HttpRequest, uidb64, token):
     try:
-        uid = force_text(urlsafe_base64_decode(uidb64))
+        uid = force_str(urlsafe_base64_decode(uidb64))
         user = User.objects.get(pk=uid)
     except(TypeError, ValueError, OverflowError, User.DoesNotExist):
         user = None

django/applications/catmaid/control/client.py

@@ -32,7 +32,7 @@ class Meta:
 
 class ClientDatastoreList(APIView):
     @method_decorator(requires_user_role_for_any_project([UserRole.Browse, UserRole.Annotate]))
-    @never_cache
+    @method_decorator(never_cache)
     def get(self, request:Request, format=None) -> Response:
         """List key-value store datastores used by the client.
         ---
@@ -96,7 +96,7 @@ class Meta:
 
 class ClientDataList(APIView):
     @method_decorator(requires_user_role_for_any_project([UserRole.Browse, UserRole.Annotate]))
-    @never_cache
+    @method_decorator(never_cache)
     def get(self, request:Request, name=None, format=None) -> Response:
         """List key-value data in a datastore for the client.
 

django/applications/catmaid/control/deeplink.py

@@ -89,7 +89,7 @@ class Meta:
 class DeepLinkList(APIView):
 
     @method_decorator(requires_user_role([UserRole.Browse]))
-    @never_cache
+    @method_decorator(never_cache)
     def get(self, request:Request, project_id) -> Response:
         """List deep-links available to the client.
         ---
@@ -227,7 +227,7 @@ def post(self, request:Request, project_id) -> Response:
 
 class DeepLinkSelector(APIView):
 
-    @never_cache
+    @method_decorator(never_cache)
     def get(self, request:Request, project_id, alias) -> Response:
         """Get a deep-links available to the client.
 
@@ -242,7 +242,7 @@ def get(self, request:Request, project_id, alias) -> Response:
         return HttpResponseRedirect(url)
 
     @method_decorator(requires_user_role_for_any_project([UserRole.Browse]))
-    @never_cache
+    @method_decorator(never_cache)
     def head(self, request:Request, project_id, alias) -> Response:
         """Get a deep-links available to the client.
         ---
@@ -257,7 +257,7 @@ def head(self, request:Request, project_id, alias) -> Response:
             return Response('Link not found', status=status.HTTP_404_NOT_FOUND)
 
     @method_decorator(requires_user_role_for_any_project([UserRole.Annotate]))
-    @never_cache
+    @method_decorator(never_cache)
     def delete(self, request:Request, project_id, alias) -> Response:
         """Delete a deep-links available to the client.
         ---
@@ -278,7 +278,7 @@ def delete(self, request:Request, project_id, alias) -> Response:
 class DeepLinkDetails(APIView):
 
     @method_decorator(requires_user_role_for_any_project([UserRole.Browse]))
-    @never_cache
+    @method_decorator(never_cache)
     def get(self, request:Request, project_id, alias) -> Response:
         """Get details on a deep-link.
         ---
@@ -297,7 +297,7 @@ def get(self, request:Request, project_id, alias) -> Response:
 class DeepLinkByIdSelector(APIView):
 
     @method_decorator(requires_user_role_for_any_project([UserRole.Annotate]))
-    @never_cache
+    @method_decorator(never_cache)
     def delete(self, request:Request, project_id, link_id) -> Response:
         """Delete a deep-links available to the client.
         ---

django/applications/catmaid/control/project_token.py

@@ -84,7 +84,7 @@ class Meta:
 class ProjectTokenList(APIView):
 
     @method_decorator(requires_user_role([UserRole.Admin]))
-    @never_cache
+    @method_decorator(never_cache)
     def get(self, request:Request, project_id) -> Response:
         """List project tokens available for this project, if the user is an
         admin.
@@ -130,7 +130,7 @@ def post(self, request:Request, project_id) -> Response:
 
 class UserProjectTokenList(APIView):
 
-    @never_cache
+    @method_decorator(never_cache)
     def get(self, request:Request, project_id) -> JsonResponse:
         """List project tokens available for this project and user.
         ---

django/applications/catmaid/control/suppressed_virtual_treenode.py

@@ -24,7 +24,7 @@ class Meta:
 
 class SuppressedVirtualTreenodeList(APIView):
     @method_decorator(requires_user_role([UserRole.Browse, UserRole.Annotate]))
-    @never_cache
+    @method_decorator(never_cache)
     def get(self, request:Request, project_id=None, treenode_id=None, format=None) -> Response:
         """List suppressed virtual nodes along the edge to this node.
         ---

django/applications/catmaid/control/synapseclustering.py

@@ -104,8 +104,13 @@ def distanceMatrix(G, synNodes) -> Tuple[Any, Dict]:
     synNodes = set(synNodes)
     synIndices = tuple(i for i,node in enumerate(nodeList) if node in synNodes)
 
-    dmat = dijkstra(nx.to_scipy_sparse_matrix(G, nodeList),
-            directed=False, indices=synIndices)
+    # FIXME: The dtype paratmer and index overrides shouldn't be needed, but the
+    # Dijkstra implementation fails in SciPy >v1.10 and <v1.15. See PR #20913 in
+    # SciPy's GitHub repo.
+    mat = nx.to_scipy_sparse_matrix(G, nodeList, dtype=np.int32)
+    mat.indices = mat.indices.astype(np.int32)
+    mat.indptr = mat.indptr.astype(np.int32)
+    dmat = dijkstra(mat, directed=False, indices=synIndices)
 
     return dmat, {node: i for i,node in enumerate(nodeList)}
 

django/applications/catmaid/fields.py

@@ -80,7 +80,7 @@ def factory_class(self):
         return newclass
 
 
-composite_type_created = Signal(providing_args=['name'])
+composite_type_created = Signal()
 
 # Necessary when running in interactive contexts and from migrations.
 @receiver(composite_type_created)

django/applications/catmaid/management/commands/catmaid_update_project_configuration.py

@@ -15,7 +15,7 @@
 
 class Command(BaseCommand):
     help = 'Set up the required database entries for a project'
-    requires_system_checks = False
+    requires_system_checks = []
 
     def add_arguments(self, parser):
         parser.add_argument('--project_id', dest='project_id', required=False,

django/applications/catmaid/static/libs/cytoscapejs/cola.js

@@ -5052,7 +5052,6 @@ var cola;
         return LinkAccessor;
     })();
 })(cola || (cola = {}));
-//# sourceMappingURL=cola.js.map
 
 // patch in conditional cola commonjs support
 if( typeof module !== 'undefined' ){

django/applications/catmaid/tests/common.py

@@ -3,7 +3,7 @@
 from abc import ABC
 
 from django.db import connection
-from django.test import TestCase
+from django.test import TestCase, TransactionTestCase
 from django.test.client import Client
 from catmaid.apps import get_system_user
 from catmaid.models import Project
@@ -84,6 +84,32 @@ def fake_authentication(self):
         self.client.login(username='temporary', password='temporary')
 
 
+class CatmaidTransactionTestCase(TransactionTestCase, AssertStatusMixin):
+    fixtures = ['catmaid_testdata']
+
+    maxDiff = None
+
+    @classmethod
+    def setUpTestData(cls):
+        init_consistent_data()
+        # Set up data for the whole TestCase
+        cls.test_project_id = 3
+        cls.user = User.objects.create_user('temporary',
+                '[email protected]', 'temporary')
+
+        # Add admin user and test2 users to the test1 group
+        g = Group.objects.get(name='test1')
+        g.user_set.add(User.objects.get(username='admin'))
+        g.user_set.add(User.objects.get(username='test2'))
+        g.save()
+
+    def setUp(self):
+        self.client = Client()
+
+    def fake_authentication(self):
+        self.client.login(username='temporary', password='temporary')
+
+
 def round_list(l, digits=6):
     """Round floating point values in a list recursively to the specified number
     of digits.

django/applications/catmaid/tests/test_async.py

@@ -0,0 +1,56 @@
+import pytest
+from django.test import AsyncClient, TestCase, override_settings
+from channels.testing import WebsocketCommunicator
+from channels.auth import get_user, login, logout
+from channels.db import database_sync_to_async
+from catmaid.consumers import UpdateConsumer
+from catmaid.models import User
+from .common import CatmaidTestCase, CatmaidTransactionTestCase
+import functools
+from asgiref.sync import sync_to_async
+
+
+@database_sync_to_async
+def get_catmaid_user(username):
+    try:
+        return User.objects.get(username=username)
+    except User.DoesNotExist:
+        return User.objects.get(username='AnonymousUser')
+
+
+class AuthWebsocketCommunicator(WebsocketCommunicator):
+    def __init__(self, application, path, user, *args, **kwargs):
+        super().__init__(self._asgi_with_user(application, user), path,
+                         *args, **kwargs)
+
+    @classmethod
+    def _asgi_with_user(cls, asgi_app, user):
+        """
+        Update the scope of an ASGI app such that a particular user
+        is already assumed to have been authenticated.
+        """
+        async def app(scope, receive, send):
+            scope['user'] = user
+            return await asgi_app(scope, receive, send)
+        functools.update_wrapper(app, asgi_app)
+        return app
+
+
+@override_settings(CHANNEL_LAYERS={"default": {"BACKEND": "channels.layers.InMemoryChannelLayer"}})
+class TestWebsockets(CatmaidTransactionTestCase):
+
+    async def test_basic_connection(self):
+        client = AsyncClient()
+        user = await get_catmaid_user('temporary')
+
+        headers = [(b'origin', b'http://localhost:80')] # Bypass AllowedHostsOriginValidator
+        communicator = AuthWebsocketCommunicator(UpdateConsumer.as_asgi(),
+                                                 '/channels/updates', user,
+                                                 headers=headers)
+
+        #communicator = WebsocketCommunicator(UpdateConsumer.as_asgi(), "GET", "/channels/updates")
+        #communicator.instance.scope["user"] = await get_user(username='temporary')
+        connected, subprotocol = await communicator.connect()
+        assert connected
+
+        await communicator.disconnect()