Upgrade back-end code from Django 4.2 to 5.2 LTS

pytest.ini

@@ -0,0 +1,2 @@
+[pytest]
+DJANGO_SETTINGS_MODULE = specifyweb.settings

requirements-testing.txt

@@ -1,6 +1,12 @@
-django-stubs==1.12.0
+# django-stubs==1.12.0
+django-stubs==5.2.9
 mypy==1.5.1
 hypothesis>=6.131.9,<7
 hypothesis-jsonschema==0.19.0
 types-requests==2.28.5
-lxml
+lxml
+debugpy==1.6.5
+pytest==7.2.1
+pytest-django==4.12.0
+django-extensions==4.1
+# django-debug-toolbar==4.4.6

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
+django-auth-ldap==5.3.0
 jsonschema==4.0.1
 typing-extensions==4.12.2
 stream-zip==0.0.83

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/<int: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 include, 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 +1,17 @@
 
-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_config_progress),
+    path('setup_progress/', views.get_setup_progress),
+    path('config_progress/', views.get_config_progress),
 
-    re_path(r'^setup_database/create/$', views.setup_database_view),
+    path('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),

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/frontend/js_src/lib/components/Atoms/Icons.tsx

@@ -151,11 +151,7 @@ export const dialogIcons: RR<
 > = {
   none: undefined,
   error: <span className="text-red-500">{icons.exclamationCircle}</span>,
-  warning: (
-    <span className="text-red-500">
-      {icons.exclamation}
-    </span>
-  ),
+  warning: <span className="text-red-500">{icons.exclamation}</span>,
   success: <span className="text-green-500">{icons.checkCircle}</span>,
   info: icons.informationCircle,
   question: icons.questionCircle,

specifyweb/settings/__init__.py

@@ -150,10 +150,6 @@ def get_sa_db_url(db_name):
 # 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/settings/specify_settings.py

@@ -45,31 +45,31 @@
 # want to access which must be a Specify database already
 # be initialized from a backup or by using the Specify Wizard
 # from a Specify 6 installation.
-DATABASE_NAME = 'SpecifyDB'
+DATABASE_NAME = os.environ.get("DATABASE_NAME", "")
 
 # Database hostname or IP. Will use localhost:3306 by default.
-DATABASE_HOST = ''
-DATABASE_PORT = ''
+DATABASE_HOST = os.environ.get("DATABASE_HOST", "")
+DATABASE_PORT = os.environ.get("DATABASE_PORT", "")
 
 # Any extra options for the database connection
 # https://docs.djangoproject.com/en/4.2/ref/settings/#std-setting-OPTIONS
 DATABASE_OPTIONS = {}
 
 # The master user login. This is the MySQL user used to connect to the
 # database. This can be the same as the Specify 6 master user.
-MASTER_NAME = 'MasterUser'
-MASTER_PASSWORD = 'MasterPassword'
-MIGRATOR_NAME = 'MasterUser'
-MIGRATOR_PASSWORD = 'MasterPassword'
-APP_USER_NAME = 'MasterUser'
-APP_USER_PASSWORD = 'MasterPassword'
-
-# MASTER_NAME = os.environ.get('MASTER_NAME', 'root')
-# MASTER_PASSWORD = os.environ.get('MASTER_NAME', 'password')
-# MIGRATOR_NAME = os.environ.get('MIGRATOR_NAME', MASTER_NAME)
-# MIGRATOR_PASSWORD = os.environ.get('MIGRATOR_PASSWORD', MASTER_PASSWORD)
-# APP_USER_NAME = os.environ.get('APP_USER_NAME', MIGRATOR_NAME)
-# APP_USER_PASSWORD = os.environ.get('APP_USER_PASSWORD', MIGRATOR_PASSWORD)
+MASTER_NAME = os.environ.get("MASTER_NAME", "")
+MASTER_PASSWORD = os.environ.get("MASTER_PASSWORD", "")
+MIGRATOR_NAME = os.environ.get("MIGRATOR_NAME", "")
+MIGRATOR_PASSWORD = os.environ.get("MIGRATOR_PASSWORD", "")
+APP_USER_NAME = os.environ.get("APP_USER_NAME", "")
+APP_USER_PASSWORD = os.environ.get("APP_USER_PASSWORD", "")
+
+# MASTER_NAME = os.environ.get("MASTER_NAME", "")
+# MASTER_PASSWORD = os.environ.get("MASTER_PASSWORD", "")
+# MIGRATOR_NAME = os.environ.get("MIGRATOR_NAME", "")
+# MIGRATOR_PASSWORD = os.environ.get("MIGRATOR_PASSWORD", "")
+# APP_USER_NAME = os.environ.get("APP_USER_NAME", "")
+# APP_USER_PASSWORD = os.environ.get("APP_USER_PASSWORD", "")
 
 # The Specify web attachment server URL.
 WEB_ATTACHMENT_URL = None

specifyweb/specify/migrations/0045_alter_many_to_many_through_fields.py

@@ -0,0 +1,46 @@
+# Generated by Django 5.2.13 on 2026-04-30
+
+from django.db import migrations, models
+
+class Migration(migrations.Migration):
+    dependencies = [
+        ('specify', '0044_alter_deletion_cascade'),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name='autonumberingscheme',
+            name='collections',
+            field=models.ManyToManyField(related_name='numberingschemes', through='specify.Autonumschcoll', through_fields=('autonumberingscheme', 'collection'), to='specify.collection'),
+        ),
+        migrations.AlterField(
+            model_name='autonumberingscheme',
+            name='disciplines',
+            field=models.ManyToManyField(related_name='numberingschemes', through='specify.Autonumschdsp', through_fields=('autonumberingscheme', 'discipline'), to='specify.discipline'),
+        ),
+        migrations.AlterField(
+            model_name='autonumberingscheme',
+            name='divisions',
+            field=models.ManyToManyField(related_name='numberingschemes', through='specify.Autonumschdiv', through_fields=('autonumberingscheme', 'division'), to='specify.division'),
+        ),
+        migrations.AlterField(
+            model_name='project',
+            name='collectionobjects',
+            field=models.ManyToManyField(related_name='projects', through='specify.Project_colobj', through_fields=('project', 'collectionobject'), to='specify.collectionobject'),
+        ),
+        migrations.AlterField(
+            model_name='specifyuser',
+            name='spprincipals',
+            field=models.ManyToManyField(related_name='specifyusers', through='specify.Specifyuser_spprincipal', through_fields=('specifyuser', 'spprincipal'), to='specify.spprincipal'),
+        ),
+        migrations.AlterField(
+            model_name='spexportschema',
+            name='mappings',
+            field=models.ManyToManyField(related_name='spexportschemas', through='specify.Spexportschema_exportmapping', through_fields=('spexportschema', 'spexportschemamapping'), to='specify.spexportschemamapping'),
+        ),
+        migrations.AlterField(
+            model_name='spprincipal',
+            name='sppermissions',
+            field=models.ManyToManyField(related_name='spprincipals', through='specify.Spprincipal_sppermission', through_fields=('spprincipal', 'sppermission'), to='specify.sppermission'),
+        ),
+    ]

specifyweb/specify/urls.py

@@ -1,15 +1,16 @@
 # Entrypoint for the routing of the app
 
+from django.urls import path
 from django.urls import include, re_path
 
 from specifyweb.specify import views
 from specifyweb.specify.models_utils import schema
 
 urlpatterns = [
     # the main business data API
-    re_path(r'^specify_schema/openapi.json$', schema.openapi),
+    path('specify_schema/openapi.json', schema.openapi),
     re_path(r'^specify_schema/(?P<model>\w+)/$', schema.view),
-    re_path(r'^specify/', include('specifyweb.backend.batch_identify.urls')), # batch identify
+    path('specify/', include('specifyweb.backend.batch_identify.urls')), # batch identify
     re_path(r'^specify/(?P<model>\w+)/(?P<id>\d+)/$', views.resource), # permissions added
     re_path(r'^specify/(?P<model>\w+)/$', views.collection), # permissions added
 
@@ -19,29 +20,29 @@
     # === Backwards compatibility ===
 
     # Merge endpoints
-    re_path(r'^specify/merge/', include('specifyweb.backend.merge.urls')),
+    path('specify/merge/', include('specifyweb.backend.merge.urls')),
 
     # Inheritance (catalog number endpoints)
-    re_path(r'^specify/', include('specifyweb.backend.inheritance.urls')),
+    path('specify/', include('specifyweb.backend.inheritance.urls')),
 
     # Series endpoints
-    re_path(r'^specify', include('specifyweb.backend.series.urls')),
+    path('specify', include('specifyweb.backend.series.urls')),
 
     # Table rows
-    re_path(r'^', include('specifyweb.backend.table_rows.urls')),
+    path('', include('specifyweb.backend.table_rows.urls')),
 
     # Delete blockers
-    re_path(r'^', include('specifyweb.backend.delete_blockers.urls')),
+    path('', include('specifyweb.backend.delete_blockers.urls')),
 
     ## Bulk copy
-    re_path(r'^specify', include('specifyweb.backend.bulk_copy.urls')),
+    path('specify', include('specifyweb.backend.bulk_copy.urls')),
 
     # Trees
-    re_path(r'^', include('specifyweb.backend.trees.urls')),
+    path('', include('specifyweb.backend.trees.urls')),
 
     # Locality update tool
-    re_path(r'^', include('specifyweb.backend.locality_update_tool.urls')),
+    path('', include('specifyweb.backend.locality_update_tool.urls')),
 
     # Master key + User management
-    re_path(r'^', include('specifyweb.backend.accounts.urls')),
+    path('', include('specifyweb.backend.accounts.urls')),
 ]

specifyweb/specify/utils/case_insensitive_bool.py

@@ -9,7 +9,12 @@ def to_python(self, value):
             return False
         return super().to_python(value)
 
-class NullBooleanField(models.NullBooleanField):
+class NullBooleanField(BooleanField):
+    def __init__(self, *args, **kwargs):
+        kwargs.setdefault('null', True)
+        kwargs.setdefault('blank', True)
+        super().__init__(*args, **kwargs)
+
     def to_python(self, value):
         if value == 'true':
             return True

specifyweb/urls.py

@@ -41,7 +41,7 @@
     # just redirect root url to the main specify view
     path('', skip_collection_access_check(RedirectView.as_view(url='/specify/'))),
 
-    re_path(r'^opensearch.xml$', search_view),
+    path('opensearch.xml', search_view),
 
     # This is the main specify view.
     # Every URL beginning with '/specify/' is handled
@@ -53,7 +53,7 @@
     path('api/', include(api_urls)),
     path('api/backup/', include(backup_urls)),
     path('images/<path:path>', images),
-    re_path(r'^properties/(?P<name>.+).properties$', properties), # Note fully supported since remmoving dependence on specify.jar
+    path('properties/<path:name>.properties', properties), # Note fully supported since remmoving dependence on specify.jar
 
     path('documentation/', include(doc_urls)),