Upgrade back-end code from Django 4.2 to 5.2 LTS

requirements-testing.txt

@@ -1,8 +1,12 @@
-django-stubs==1.12.0
-mypy==1.5.1
+# django-stubs==1.12.0
+django-stubs==5.2.9
+mypy==1.13.0
 hypothesis>=6.131.9,<7
 hypothesis-jsonschema==0.19.0
 types-requests==2.28.5
 lxml
-coverage
-pytest-django
+debugpy==1.6.5
+pytest==7.2.1
+pytest-django==4.12.0
+django-extensions==4.1
+coverage==7.15.2

requirements.txt

@@ -5,14 +5,14 @@ wheel
 kombu==5.5.2
 redis==6.4.0
 celery==5.5.1
-Django==4.2.30
+Django==5.2.13
 mysqlclient==2.1.1
 SQLAlchemy==1.4.54
 sqlalchemy2-stubs
 requests==2.32.4
 pycryptodome==3.21.0
-PyJWT==2.12.1
-django-auth-ldap==1.2.17
+PyJWT==2.13.0
+django-auth-ldap==5.3.0
 jsonschema==4.0.1
 typing-extensions==4.12.2
 stream-zip==0.0.83

specifyweb/backend/accounts/views.py

@@ -193,7 +193,7 @@ def oic_callback(request: http.HttpRequest) -> http.HttpResponse:
     spuserexternalid.save()
 
     login(request,
-          cast(AbstractBaseUser, spuserexternalid.specifyuser),
+          cast(Specifyuser, spuserexternalid.specifyuser),
           backend='django.contrib.auth.backends.ModelBackend')
     return http.HttpResponseRedirect('/accounts/choose_collection')
 

specifyweb/backend/batch_identify/urls.py

@@ -1,9 +1,9 @@
-from django.urls import re_path
+from django.urls import path
 
 from . import views
 
 urlpatterns = [
-    re_path(r'^batch_identify/resolve/$', views.batch_identify_resolve),
-    re_path(r'^batch_identify/validate_record_set/$', views.batch_identify_validate_record_set),
-    re_path(r'^batch_identify/$', views.batch_identify),
+    path('batch_identify/resolve/', views.batch_identify_resolve),
+    path('batch_identify/validate_record_set/', views.batch_identify_validate_record_set),
+    path('batch_identify/', views.batch_identify),
 ]

specifyweb/backend/context/testurls.py

@@ -2,15 +2,15 @@
 Provides urls to access the mocked views
 """
 
-from django.urls import path, re_path
+from django.urls import path
 
 from . import testsviews as views
 
 urlpatterns = [
     path('collection/', views.collection),
-    re_path(r'^domain.json$', views.domain),
-    re_path(r'^viewsets/(?P<level>\d+).xml$', views.viewsets),
-    re_path(r'^schema_localization.json$', views.schema_localization),
-    re_path(r'^app.resource$', views.app_resource),
-    re_path(r'^available_related_searches.json$', views.available_related_searches),
+    path('domain.json', views.domain),
+    path('viewsets/<str:level>.xml', views.viewsets),
+    path('schema_localization.json', views.schema_localization),
+    path('app.resource', views.app_resource),
+    path('available_related_searches.json', views.available_related_searches),
 ]

specifyweb/backend/context/urls.py

@@ -2,7 +2,7 @@
 Defines the urls for the app context subsystem
 """
 
-from django.urls import path, re_path
+from django.urls import path
 from django.urls import path
 
 from . import views, user_resources, collection_resources
@@ -16,26 +16,26 @@
     path('language/', views.languages),
     path('schema/language/', views.schema_language),
 
-    re_path(r'^api_endpoints.json$', views.api_endpoints),
-    re_path(r'^api_endpoints_all.json$', views.api_endpoints_all),
-    re_path(r'^user.json$', views.user),
-    re_path(r'^stats_counts.json$', views.stats_counts),
-    re_path(r'^system_info.json$', views.system_info),
-    re_path(r'^all_system_data.json$', views.all_system_data),
-    re_path(r'^all_system_config_data.json$', views.all_system_config_data),
-    re_path(r'^server_time.json$', views.get_server_time),
-    re_path(r'^domain.json$', views.domain),
-    re_path(r'^view.json$', views.view),
-    re_path(r'^views.json$', views.views),
-    re_path(r'^viewsets.json$', views.viewsets),
-    re_path(r'^datamodel.json$', views.datamodel),
-    re_path(r'^schema_localization.json$', views.schema_localization),
-    re_path(r'^app.resource$', views.app_resource),
-    re_path(r'^available_related_searches.json$', views.available_related_searches),
-    re_path(r'^remoteprefs.properties$', views.remote_prefs),
-
-    re_path(r'^attachment_settings.json$', attachment_settings),
-    re_path(r'^report_runner_status.json$', report_runner_status),
+    path('api_endpoints.json', views.api_endpoints),
+    path('api_endpoints_all.json', views.api_endpoints_all),
+    path('user.json', views.user),
+    path('stats_counts.json', views.stats_counts),
+    path('system_info.json', views.system_info),
+    path('all_system_data.json', views.all_system_data),
+    path('all_system_config_data.json', views.all_system_config_data),
+    path('server_time.json', views.get_server_time),
+    path('domain.json', views.domain),
+    path('view.json', views.view),
+    path('views.json', views.views),
+    path('viewsets.json', views.viewsets),
+    path('datamodel.json', views.datamodel),
+    path('schema_localization.json', views.schema_localization),
+    path('app.resource', views.app_resource),
+    path('available_related_searches.json', views.available_related_searches),
+    path('remoteprefs.properties', views.remote_prefs),
+
+    path('attachment_settings.json', attachment_settings),
+    path('report_runner_status.json', report_runner_status),
 
     path('user_resource/', user_resources.user_resources),
     path('user_resource/<int:resourceid>/', user_resources.user_resource),

specifyweb/backend/inheritance/urls.py

@@ -1,12 +1,12 @@
 
-from django.urls import include, path, re_path
+from django.urls import path
 
 from specifyweb.backend.inheritance import views
 
 urlpatterns = [
     # cat num for siblings
-    re_path(r'^catalog_number_for_sibling/$', views.catalog_number_for_sibling),
+    path('catalog_number_for_sibling/', views.catalog_number_for_sibling),
 
     # cat num for parent
-    re_path(r'^catalog_number_from_parent/$', views.catalog_number_from_parent), 
-]
+    path('catalog_number_from_parent/', views.catalog_number_from_parent), 
+]

specifyweb/backend/setup_tool/urls.py

@@ -1,17 +1,16 @@
 
-from django.urls import re_path
+from django.urls import path
 
 from . import views
 
 urlpatterns = [
     # check if the db is new at login
-    re_path(r'^setup_progress/$', views.get_setup_progress),
-    re_path(r'^config_progress/$', views.get_setup_progress),
+    path('setup_progress/', views.get_setup_progress),
+    path('config_progress/', views.get_setup_progress),
+    path('setup_database/create/', views.setup_database_view),
 
-    re_path(r'^setup_database/create/$', views.setup_database_view),
-
-    re_path(r'^discipline_and_trees/create/$', views.create_discipline_and_trees),
-    re_path(r'^running_worker_tasks/$', views.get_running_worker_tasks),
+    path('discipline_and_trees/create/', views.create_discipline_and_trees),
+    path('running_worker_tasks/', views.get_running_worker_tasks),
 
     # These urls are functional but unused by the setup process. The API can be used instead.
     # re_path(r'^institution/create/$', views.create_institution_view),
@@ -22,4 +21,4 @@
     # re_path(f'^taxontreedef/create/$', views.create_taxon_tree_view),
     # re_path(f'^collection/create/$', views.create_collection_view),
     # re_path(f'^specifyuser/create/$', views.create_specifyuser_view),
-]
+]

specifyweb/backend/trees/urls.py

@@ -23,8 +23,8 @@
 
     # Create new trees
     path('create_default_tree/', views.create_default_tree_view),
-    re_path(r'^create_default_tree/status/(?P<task_id>[^/]+)/$', views.default_tree_upload_status),
-    re_path(r'^create_default_tree/abort/(?P<task_id>[^/]+)/$', views.abort_default_tree_creation),
+    path('create_default_tree/status/<str:task_id>/', views.default_tree_upload_status),
+    path('create_default_tree/abort/<str:task_id>/', views.abort_default_tree_creation),
     path('default_tree_mapping/', views.default_tree_mapping),
     path('db_encoding/', views.get_db_encoding),
 ]

specifyweb/backend/workbench/models.py

@@ -172,7 +172,7 @@ def get_dataset_as_dict(self):
         return ds_dict
 
     def was_uploaded(self) -> bool:
-        return self.uploadresult and self.uploadresult["success"]
+        return bool(self.uploadresult and self.uploadresult["success"])
 
 class Spdatasetattachment(models.Model):
     specify_model = datamodel.get_table_strict('spdatasetattachment')
@@ -202,4 +202,4 @@ class Meta:
         ]
 
 
-    # save = partialmethod(custom_save)
+    # save = partialmethod(custom_save)

specifyweb/backend/workbench/tests.py

@@ -174,8 +174,11 @@ def test_create_record_set(self) -> None:
             no_commit=False,
             allow_partial=False,
         )
-
-        self.assertTrue(dataset.uploadresult["success"])
+
+        # ignoring this mympy type error becuase mypy deduces that the type of `uploadresult` is 
+        # Any | None. we know it is a JSONField, but since that is a field of the parent of Spdataset, mypy can't find it.
+        # TODO (mypy): figure out how to tell mypy that uploadresult is iterable
+        self.assertTrue(dataset.uploadresult["success"]) #type: ignore
 
         response = c.post(
             f"/api/workbench/create_recordset/{datasetid}/",
@@ -337,4 +340,4 @@ def test_transfer_dataset_rejects_invalid_user(self) -> None:
         self.assertEqual(response.status_code, 400)
         self.dataset.refresh_from_db()
         self.assertEqual(self.dataset.specifyuser, self.specifyuser)
-        self.assertFalse(Message.objects.exists())
+        self.assertFalse(Message.objects.exists())

specifyweb/backend/workbench/upload/predicates.py

@@ -283,7 +283,7 @@ def canonicalize_remove_node(node: ToRemoveNode) -> Q:
 
 
 def _map_matchee(matchee: list[ToRemoveMatchee], model_name: str) -> Exists:
-    model: Model = get_model(model_name)
+    model = get_model(model_name)
     qs = [Q(**match["filter_on"]) for match in matchee]
     qs_or = Func.make_ors(qs)
     query = model.objects.filter(qs_or)
@@ -309,7 +309,7 @@ class ContetRef(Exception):
 ]
 
 
-def safe_fetch(model: Model, filters, version):
+def safe_fetch(model, filters, version):
     if filters is None:
         return None
     try:
@@ -354,4 +354,4 @@ def resolve_reference_attributes(
 
     clone_attrs = {field: getattr(reference_record, field) for field in all_fields}
 
-    return clone_attrs
+    return clone_attrs

specifyweb/frontend/js_src/lib/components/ChooseCollection/index.tsx

@@ -172,9 +172,9 @@ function Wrapped({
             <Button.BorderedGray
               onClick={(): void =>
                 loading(
-                  ping('/accounts/logout/').then(() =>
+                  ping('/accounts/logout/', {method: 'POST'}).then(() =>
                     globalThis.location.assign(
-                      formatUrl('/accounts/logout/', { next: nextUrl })
+                      formatUrl('/specify/command/logout/', { next: nextUrl })
                     )
                   )
                 )

specifyweb/frontend/js_src/lib/components/Core/Main.tsx

@@ -102,7 +102,7 @@ function MissingAgent(): JSX.Element {
       }}
       forceToTop
       header={userText.noAgent()}
-      onClose={(): void => globalThis.location.assign('/accounts/logout/')}
+      onClose={(): void => globalThis.location.assign('/specify/command/logout/')}
     >
       {userText.noAgentDescription()}
     </Dialog>

specifyweb/frontend/js_src/lib/components/Header/userToolDefinitions.ts

@@ -27,7 +27,7 @@ const rawUserTools = ensure<IR<IR<Omit<MenuItem, 'name'>>>>()({
   [userText.userAccount()]: {
     logOut: {
       title: userText.logOut(),
-      url: '/accounts/logout/',
+      url: '/specify/command/logout/',
       icon: icons.logout,
       enabled: () => userInformation.isauthenticated,
       onClick: async () =>

specifyweb/frontend/js_src/lib/components/Logout/index.tsx

@@ -0,0 +1,28 @@
+import React from 'react';
+import { useSearchParameter } from '../../hooks/navigation';
+import { ajax } from '../../utils/ajax';
+import { LoadingScreen } from '../Molecules/Dialog';
+import { formatUrl } from '../Router/queryString';
+import { LoadingContext } from '../Core/Contexts';
+import { softError } from '../Errors/assert';
+
+export function Logout(): JSX.Element {
+  const loading = React.useContext(LoadingContext);
+  const [nextUrl = '/specify/'] = useSearchParameter('nextUrl');
+
+  console.log('next => ' + nextUrl);
+
+  React.useEffect(() => {
+    loading(
+      ajax<string>('/accounts/logout/', { method: 'POST', headers: {} })
+        .catch((error) => softError(error))
+        .finally(() =>
+          globalThis.location.assign(
+            formatUrl('/accounts/login/', { next: nextUrl })
+          )
+        )
+    );
+  }, [loading]);
+
+  return <LoadingScreen />;
+}

specifyweb/frontend/js_src/lib/components/Router/Routes.tsx

@@ -466,6 +466,14 @@ export const routes: RA<EnhancedRoute> = [
             ({ CacheBuster }) => CacheBuster
           ),
       },
+	  {
+		path: 'logout',
+		title: userText.logOut(),
+		element: () => 
+		  import('../Logout').then(
+			({ Logout }) => Logout
+		  )
+	  },
     ],
   },
   {

specifyweb/settings/__init__.py

@@ -143,14 +143,12 @@ def get_sa_db_url(db_name):
 
 SITE_ID = 1
 
+USE_TZ=False
+
 # If you set this to False, Django will make some optimizations so as not
 # to load the internationalization machinery.
 USE_I18N = True
 
-# If you set this to False, Django will not format dates, numbers and
-# calendars according to the current locale
-USE_L10N = True
-
 LANGUAGE_COOKIE_NAME='language'
 
 # Absolute filesystem path to the directory that will hold user-uploaded files.

specifyweb/specify/migrations/0045_add_indexes.py

@@ -5,7 +5,7 @@
 class Migration(migrations.Migration):
 
     dependencies = [
-        ('specify', '0044_alter_deletion_cascade'),
+        ('specify', '0044_alter_deletion_cascade')
     ]
 
     operations = [