From 5d692fe353d79edf544e9100716c22eef07e010e Mon Sep 17 00:00:00 2001
From: Jan Weber <st157366@stud.uni-stuttgart.de>
Date: Tue, 23 Jul 2024 16:09:40 +0200
Subject: [PATCH 01/14] Update dependencies

---
 .../api/v1_api/ontology_type_validation.py    |    4 +-
 muse_for_anything/db/cli.py                   |   10 -
 muse_for_anything/db/models/model_helpers.py  |   25 +-
 .../db/models/object_relation_tables.py       |   75 +-
 .../db/models/ontology_objects.py             |   99 +-
 muse_for_anything/db/models/taxonomies.py     |   70 +-
 muse_for_anything/db/models/users.py          |   35 +-
 muse_for_anything/oso_helpers.py              |  130 +-
 poetry.lock                                   | 1191 +++++++++--------
 pyproject.toml                                |   54 +-
 10 files changed, 925 insertions(+), 768 deletions(-)

diff --git a/muse_for_anything/api/v1_api/ontology_type_validation.py b/muse_for_anything/api/v1_api/ontology_type_validation.py
index 5e2a8eb..0c6afd0 100644
--- a/muse_for_anything/api/v1_api/ontology_type_validation.py
+++ b/muse_for_anything/api/v1_api/ontology_type_validation.py
@@ -2,7 +2,7 @@
 
 from dataclasses import dataclass
 from muse_for_anything.db.models.taxonomies import Taxonomy
-from flask.globals import _request_ctx_stack
+from flask.globals import request_ctx
 from werkzeug.urls import url_parse
 from werkzeug.routing import MapAdapter
 
@@ -152,7 +152,7 @@ def visit(self, data, walker: SchemaWalker) -> None:
         else:
             url = url_parse(data["$ref"])
 
-            ctx = _request_ctx_stack.top
+            ctx = request_ctx
             if ctx is None:
                 raise DataVisitorException(
                     "No request context to check schema url against!"
diff --git a/muse_for_anything/db/cli.py b/muse_for_anything/db/cli.py
index 757ff26..c26ec41 100644
--- a/muse_for_anything/db/cli.py
+++ b/muse_for_anything/db/cli.py
@@ -4,7 +4,6 @@
 
 import click
 from flask import Blueprint, Flask, current_app
-from flask.cli import with_appcontext
 
 from ..util.logging import get_logger
 
@@ -22,7 +21,6 @@
 
 
 @DB_CLI.command("create-db")
-@with_appcontext
 def create_db():
     """Create all db tables."""
     create_db_function(current_app)
@@ -36,7 +34,6 @@ def create_db_function(app: Flask):
 
 @DB_CLI.command("create-admin-user")
 @click.option("-f", "--force", is_flag=True, default=False)
-@with_appcontext
 def create_admin_user_cli(force: bool = False):
     """Create an admin user with username and password 'admin'."""
     result = create_admin_user(current_app, force)
@@ -70,7 +67,6 @@ def create_admin_user(app: Flask, force: bool = False):
 @click.password_option("--password")
 @click.option("-r", "--role", default=None)
 @click.option("-f", "--force", is_flag=True, default=False)
-@with_appcontext
 def create_user_cli(
     username: str, password: str, role: Optional[str] = None, force: bool = False
 ):
@@ -120,7 +116,6 @@ def create_user(
 
 @DB_CLI.command("delete-user")
 @click.option("-u", "--username")
-@with_appcontext
 def delete_user_cli(username: str):
     """Delete the user with the given username."""
     click.confirm(
@@ -151,7 +146,6 @@ def delete_user(app: Flask, username: str):
 
 @DB_CLI.command("list-roles")
 @click.option("-u", "--username", default=None)
-@with_appcontext
 def list_roles_cli(username: Optional[str]):
     """List all user roles.
 
@@ -171,7 +165,6 @@ def list_roles_cli(username: Optional[str]):
 @DB_CLI.command("add-role")
 @click.option("-u", "--username")
 @click.option("-r", "--role")
-@with_appcontext
 def add_user_role_cli(username: str, role: str):
     """Add a role to an existing user."""
     user: Optional[User] = User.query.filter(User.username == username).first()
@@ -187,7 +180,6 @@ def add_user_role_cli(username: str, role: str):
 @DB_CLI.command("remove-role")
 @click.option("-u", "--username")
 @click.option("-r", "--role")
-@with_appcontext
 def remove_user_role_cli(username: str, role: str):
     """Remove a role from an existing user."""
     user: Optional[User] = User.query.filter(User.username == username).first()
@@ -202,7 +194,6 @@ def remove_user_role_cli(username: str, role: str):
 
 
 @DB_CLI.command("drop-db")
-@with_appcontext
 def drop_db():
     """Drop all db tables."""
     drop_db_function(current_app)
@@ -222,7 +213,6 @@ def register_cli_blueprint(app: Flask):
 
 @DB_CLI.command("export-namespace")
 @click.option("-n", "--namespace")
-@with_appcontext
 def map_namespace_to_owl_cli(namespace: int):
     """
     Export the specified namespace to an OWL file.
diff --git a/muse_for_anything/db/models/model_helpers.py b/muse_for_anything/db/models/model_helpers.py
index 7c2df31..b8c8cfb 100644
--- a/muse_for_anything/db/models/model_helpers.py
+++ b/muse_for_anything/db/models/model_helpers.py
@@ -1,7 +1,10 @@
 from datetime import datetime
 from typing import Any, Sequence
+from sqlalchemy import DateTime
 from sqlalchemy.sql.elements import literal
 from sqlalchemy.sql.schema import Column
+from sqlalchemy.types import Unicode, UnicodeText
+from sqlalchemy.orm import Mapped, mapped_column
 
 from ...util.import_helpers import get_all_classes_of_module
 
@@ -24,32 +27,28 @@ def exists(cls, query_filter: Sequence[Any] = tuple()):
 class IdMixin:
     """Add an 'id' column that is the primary key for this table."""
 
-    id: Column = DB.Column(DB.Integer, primary_key=True)
+    id: Mapped[int] = mapped_column(primary_key=True)
 
 
 class NameDescriptionMixin:
     """Add a 'name' and 'description' column to the table."""
 
-    name: Column = DB.Column(
-        DB.Unicode, nullable=False, index=True, info={"collate": "NOCASE"}
-    )
-    description: Column = DB.Column(DB.UnicodeText, nullable=True, index=True)
+    name: Mapped[str] = mapped_column(DB.Unicode, nullable=False, index=True, info={"collate": "NOCASE"})
+    description: Mapped[str] = mapped_column(DB.UnicodeText, nullable=True, index=True)
 
 
 class UniqueNameDescriptionMixin:
     """Add a 'name' (with a unique constraint) and 'description' column to the table."""
 
-    name: Column = DB.Column(
-        DB.Unicode, nullable=False, unique=True, index=True, info={"collate": "NOCASE"}
-    )
-    description: Column = DB.Column(DB.UnicodeText, nullable=True, index=True)
+    name: Mapped[str] = mapped_column(DB.Unicode, nullable=False, unique=True, index=True, info={"collate": "NOCASE"})
+    description: Mapped[str] = mapped_column(DB.UnicodeText, nullable=True, index=True)
 
 
 class CreateDeleteMixin:
     """Add the columns 'created_on' and 'deleted_on' to track creation and deletion of immutable database entries."""
 
-    created_on: Column = DB.Column(DB.DateTime, default=datetime.utcnow, nullable=False)
-    deleted_on: Column = DB.Column(DB.DateTime, nullable=True)
+    created_on: Mapped[datetime] = mapped_column(DateTime(timezone=True), default=datetime.utcnow, nullable=False)
+    deleted_on: Mapped[datetime] = mapped_column(DateTime(timezone=True), nullable=True)
 
     @property
     def is_deleted(self) -> bool:
@@ -59,9 +58,7 @@ def is_deleted(self) -> bool:
 class ChangesMixin(CreateDeleteMixin):
     """Add the columns 'created_on', 'updated_on' and 'deleted_on' to track changes to the database entries."""
 
-    updated_on: Column = DB.Column(
-        DB.DateTime, default=datetime.utcnow, onupdate=datetime.utcnow, nullable=False
-    )
+    updated_on: Mapped[datetime] = mapped_column(DateTime(timezone=True), default=datetime.utcnow, onupdate=datetime.utcnow, nullable=False)
 
 
 __all__ = list(get_all_classes_of_module(__name__))
diff --git a/muse_for_anything/db/models/object_relation_tables.py b/muse_for_anything/db/models/object_relation_tables.py
index 2d3423e..7431259 100644
--- a/muse_for_anything/db/models/object_relation_tables.py
+++ b/muse_for_anything/db/models/object_relation_tables.py
@@ -1,8 +1,8 @@
 """Module containing relation tables."""
 
 from typing import Any, Dict, Optional, cast
-from sqlalchemy.sql.schema import ForeignKey, Column, Index
-from sqlalchemy.orm import relationship
+from sqlalchemy.sql.schema import ForeignKey, Index
+from sqlalchemy.orm import Mapped, mapped_column, relationship
 from sqlalchemy.ext.declarative import declared_attr
 
 from ..db import DB, MODEL
@@ -30,24 +30,19 @@ class OntologyTypeVersionToTypeVersion(MODEL, IdMixin):
     __tablename__ = "TypeVersionToTypeVersion"
 
     # the type version importing
-    type_version_source_id: Column = DB.Column(
-        DB.Integer, ForeignKey(OntologyObjectTypeVersion.id), nullable=False
-    )
+    type_version_source_id: Mapped[int] = mapped_column(ForeignKey("OntologyObjectTypeVersion.id"), nullable=False)
+    
     # the imported type version
-    type_version_target_id: Column = DB.Column(
-        DB.Integer, ForeignKey(OntologyObjectTypeVersion.id), nullable=False
-    )
+    type_version_target_id: Mapped[int] = mapped_column(ForeignKey("OntologyObjectTypeVersion.id"), nullable=False)
 
     # relationships
-    type_version_source: OntologyObjectTypeVersion = relationship(
-        OntologyObjectTypeVersion,
+    type_version_source: Mapped[OntologyObjectTypeVersion] = relationship(
         lazy="select",  # is nearly always in cache anyway
         back_populates="imported_types",
         primaryjoin=OntologyObjectTypeVersion.id == type_version_source_id,
     )
 
-    type_version_target: OntologyObjectTypeVersion = relationship(
-        OntologyObjectTypeVersion,
+    type_version_target: Mapped[OntologyObjectTypeVersion] = relationship(
         lazy="select",  # is nearly always in cache anyway
         back_populates="imported_by_types",
         primaryjoin=OntologyObjectTypeVersion.id == type_version_target_id,
@@ -67,23 +62,17 @@ class OntologyTypeVersionToType(MODEL, IdMixin):
 
     __tablename__ = "TypeVersionToType"
 
-    type_version_source_id: Column = DB.Column(
-        DB.Integer, ForeignKey(OntologyObjectTypeVersion.id), nullable=False
-    )
-    type_target_id: Column = DB.Column(
-        DB.Integer, ForeignKey(OntologyObjectType.id), nullable=False
-    )
+    type_version_source_id: Mapped[int] = mapped_column(ForeignKey("OntologyObjectTypeVersion.id"), nullable=False)
+    type_target_id: Mapped[int] = mapped_column(ForeignKey("OntologyObjectType.id"), nullable=False)
 
     # relationships
-    type_version_source: OntologyObjectTypeVersion = relationship(
-        OntologyObjectTypeVersion,
+    type_version_source: Mapped[OntologyObjectTypeVersion] = relationship(
         lazy="select",  # is nearly always in cache anyway
         back_populates="referenced_types",
         primaryjoin=OntologyObjectTypeVersion.id == type_version_source_id,
     )
 
-    type_target: OntologyObjectType = relationship(
-        OntologyObjectType,
+    type_target: Mapped[OntologyObjectType] = relationship(
         lazy="select",  # is nearly always in cache anyway
         back_populates="referenced_by_types",
         primaryjoin=OntologyObjectType.id == type_target_id,
@@ -103,23 +92,17 @@ class OntologyTypeVersionToTaxonomy(MODEL, IdMixin):
 
     __tablename__ = "TypeVersionToTaxonomy"
 
-    type_version_source_id: Column = DB.Column(
-        DB.Integer, ForeignKey(OntologyObjectTypeVersion.id), nullable=False
-    )
-    taxonomy_target_id: Column = DB.Column(
-        DB.Integer, ForeignKey(Taxonomy.id), nullable=False
-    )
+    type_version_source_id: Mapped[int] = mapped_column(ForeignKey("OntologyObjectTypeVersion.id"), nullable=False)
+    taxonomy_target_id: Mapped[int] = mapped_column(ForeignKey("Taxonomy.id"), nullable=False)
 
     # relationships
-    type_version_source: OntologyObjectTypeVersion = relationship(
-        OntologyObjectTypeVersion,
+    type_version_source: Mapped[OntologyObjectTypeVersion] = relationship(
         lazy="select",  # is nearly always in cache anyway
         back_populates="referenced_taxonomies",
         primaryjoin=OntologyObjectTypeVersion.id == type_version_source_id,
     )
 
-    taxonomy_target: Taxonomy = relationship(
-        Taxonomy,
+    taxonomy_target: Mapped[Taxonomy] = relationship(
         lazy="select",  # is nearly always in cache anyway
         back_populates="referenced_by_types",
         primaryjoin=Taxonomy.id == taxonomy_target_id,
@@ -139,23 +122,17 @@ class OntologyObjectVersionToObject(MODEL, IdMixin):
 
     __tablename__ = "ObjectVersionToObject"
 
-    object_version_source_id: Column = DB.Column(
-        DB.Integer, ForeignKey(OntologyObjectVersion.id), nullable=False
-    )
-    object_target_id: Column = DB.Column(
-        DB.Integer, ForeignKey(OntologyObject.id), nullable=False
-    )
+    object_version_source_id: Mapped[int] = mapped_column(ForeignKey("OntologyObjectTypeVersion.id"), nullable=False)
+    object_target_id: Mapped[int] = mapped_column(ForeignKey("OntologyObject.id"), nullable=False)
 
     # relationships
-    object_version_source: OntologyObjectVersion = relationship(
-        OntologyObjectVersion,
+    object_version_source: Mapped[OntologyObjectVersion] = relationship(
         lazy="select",  # is nearly always in cache anyway
         back_populates="referenced_objects",
         primaryjoin=OntologyObjectVersion.id == object_version_source_id,
     )
 
-    object_target: OntologyObject = relationship(
-        OntologyObject,
+    object_target: Mapped[OntologyObject] = relationship(
         lazy="select",  # is nearly always in cache anyway
         back_populates="referenced_by_objects",
         primaryjoin=OntologyObject.id == object_target_id,
@@ -175,23 +152,17 @@ class OntologyObjectVersionToTaxonomyItem(MODEL, IdMixin):
 
     __tablename__ = "ObjectVersionToTaxonomyItem"
 
-    object_version_source_id: Column = DB.Column(
-        DB.Integer, ForeignKey(OntologyObjectVersion.id), nullable=False
-    )
-    taxonomy_item_target_id: Column = DB.Column(
-        DB.Integer, ForeignKey(TaxonomyItem.id), nullable=False
-    )
+    object_version_source_id: Mapped[int] = mapped_column(ForeignKey("OntologyObjectVersion.id"), nullable=False)
+    taxonomy_item_target_id: Mapped[int] = mapped_column(ForeignKey("TaxonomyItem.id"), nullable=False)
 
     # relationships
-    object_version_source: OntologyObjectVersion = relationship(
-        OntologyObjectVersion,
+    object_version_source: Mapped[OntologyObjectVersion] = relationship(
         lazy="select",  # is nearly always in cache anyway
         back_populates="referenced_taxonomy_items",
         primaryjoin=OntologyObjectVersion.id == object_version_source_id,
     )
 
-    taxonomy_item_target: TaxonomyItem = relationship(
-        TaxonomyItem,
+    taxonomy_item_target: Mapped[TaxonomyItem] = relationship(
         lazy="select",  # is nearly always in cache anyway
         back_populates="referenced_by_objects",
         primaryjoin=TaxonomyItem.id == taxonomy_item_target_id,
diff --git a/muse_for_anything/db/models/ontology_objects.py b/muse_for_anything/db/models/ontology_objects.py
index 7aee99e..b10b751 100644
--- a/muse_for_anything/db/models/ontology_objects.py
+++ b/muse_for_anything/db/models/ontology_objects.py
@@ -1,9 +1,10 @@
 """Module containing ontology object table definitions."""
 
 from typing import Any, Dict, List, Optional, cast
-from sqlalchemy.sql.schema import ForeignKey, Column, Index
-from sqlalchemy.orm import relationship
+from sqlalchemy.sql.schema import ForeignKey, Index
+from sqlalchemy.orm import Mapped, mapped_column, relationship
 from sqlalchemy.ext.declarative import declared_attr
+from sqlalchemy.types import Text
 
 from ..db import DB, MODEL
 from .model_helpers import (
@@ -22,16 +23,13 @@ class OntologyObjectType(MODEL, IdMixin, NameDescriptionMixin, ChangesMixin):
 
     __tablename__ = "Type"
 
-    namespace_id: Column = DB.Column(DB.Integer, ForeignKey(Namespace.id), nullable=False)
-    current_version_id: Column = DB.Column(
-        DB.Integer, ForeignKey("TypeVersion.id"), nullable=True
-    )
-    is_toplevel_type: Column = DB.Column(DB.Boolean, nullable=False)
-
+    namespace_id: Mapped[int] = mapped_column(ForeignKey("Namespace.id"), nullable=False)
+    current_version_id: Mapped[int] = mapped_column(ForeignKey("TypeVesion.id"), nullable=True)
+    is_toplevel_type: Mapped[int] = mapped_column(nullable=False)
+    
     # relationships
-    namespace: Namespace = relationship(Namespace, innerjoin=True, lazy="selectin")
-    current_version: "OntologyObjectTypeVersion" = relationship(
-        "OntologyObjectTypeVersion",
+    namespace: Mapped[Namespace] = relationship(innerjoin=True, lazy="selectin")
+    current_version: Mapped["OntologyObjectTypeVersion"] = relationship(
         post_update=True,
         innerjoin=True,
         lazy="joined",
@@ -44,14 +42,12 @@ class OntologyObjectType(MODEL, IdMixin, NameDescriptionMixin, ChangesMixin):
         back_populates="ontology_type",
         primaryjoin="OntologyObjectType.id == OntologyObjectTypeVersion.object_type_id",
     )
-    ontology_objects: "OntologyObject" = relationship(
-        "OntologyObject",
+    ontology_objects: Mapped["OntologyObject"] = relationship(
         lazy="select",
         back_populates="ontology_type",
     )
 
-    referenced_by_types: List["rel.OntologyTypeVersionToType"] = relationship(
-        "OntologyTypeVersionToType",
+    referenced_by_types: Mapped[List["rel.OntologyTypeVersionToType"]] = relationship(
         lazy="select",
         order_by="OntologyTypeVersionToType.id",
         back_populates="type_target",
@@ -114,12 +110,10 @@ class OntologyObjectTypeVersion(MODEL, IdMixin, CreateDeleteMixin):
 
     __tablename__ = "TypeVersion"
 
-    id: Column = DB.Column(DB.Integer, primary_key=True)
-    object_type_id: Column = DB.Column(
-        DB.Integer, ForeignKey(OntologyObjectType.id), nullable=False
-    )
-    version: Column = DB.Column(DB.Integer, nullable=False)
-    data: Column = DB.Column(DB.JSON, nullable=False)
+    id: Mapped[int] = mapped_column(primary_key=True)
+    object_type_id: Mapped[int] = mapped_column(ForeignKey("OntologyObjectType.id"), nullable=False)
+    version: Mapped[int] = mapped_column(nullable=False)
+    data: Mapped[Text] = mapped_column(DB.JSON, nullable=False)
 
     @declared_attr
     def __table_args__(cls):
@@ -133,43 +127,37 @@ def __table_args__(cls):
         )
 
     # relationships
-    ontology_type: OntologyObjectType = relationship(
-        OntologyObjectType,
+    ontology_type: Mapped[OntologyObjectType] = relationship(
         lazy="select",  # should already be in chache in most cases
         back_populates="versions",
         primaryjoin=OntologyObjectType.id == object_type_id,
     )
-    ontology_object_versions: "OntologyObjectVersion" = relationship(
-        "OntologyObjectVersion",
+    ontology_object_versions: Mapped["OntologyObjectVersion"] = relationship(
         lazy="select",
         back_populates="ontology_type_version",
     )
 
-    imported_types: List["rel.OntologyTypeVersionToTypeVersion"] = relationship(
-        "OntologyTypeVersionToTypeVersion",
+    imported_types: Mapped[List["rel.OntologyTypeVersionToTypeVersion"]] = relationship(
         lazy="select",
         order_by="OntologyTypeVersionToTypeVersion.id",
         back_populates="type_version_source",
         primaryjoin="OntologyObjectTypeVersion.id == OntologyTypeVersionToTypeVersion.type_version_source_id",
     )
-    imported_by_types: List["rel.OntologyTypeVersionToTypeVersion"] = relationship(
-        "OntologyTypeVersionToTypeVersion",
+    imported_by_types: Mapped[List["rel.OntologyTypeVersionToTypeVersion"]] = relationship(
         lazy="select",
         order_by="OntologyTypeVersionToTypeVersion.id",
         back_populates="type_version_target",
         primaryjoin="OntologyObjectTypeVersion.id == OntologyTypeVersionToTypeVersion.type_version_target_id",
     )
 
-    referenced_types: List["rel.OntologyTypeVersionToType"] = relationship(
-        "OntologyTypeVersionToType",
+    referenced_types: Mapped[List["rel.OntologyTypeVersionToType"]] = relationship(
         lazy="select",
         order_by="OntologyTypeVersionToType.id",
         back_populates="type_version_source",
         primaryjoin="OntologyObjectTypeVersion.id == OntologyTypeVersionToType.type_version_source_id",
     )
 
-    referenced_taxonomies: List["rel.OntologyTypeVersionToTaxonomy"] = relationship(
-        "OntologyTypeVersionToTaxonomy",
+    referenced_taxonomies: Mapped[List["rel.OntologyTypeVersionToTaxonomy"]] = relationship(
         lazy="select",
         order_by="OntologyTypeVersionToTaxonomy.id",
         back_populates="type_version_source",
@@ -218,24 +206,18 @@ class OntologyObject(MODEL, IdMixin, NameDescriptionMixin, ChangesMixin):
 
     __tablename__ = "Object"
 
-    namespace_id: Column = DB.Column(DB.Integer, ForeignKey(Namespace.id), nullable=False)
-    object_type_id: Column = DB.Column(
-        DB.Integer, ForeignKey(OntologyObjectType.id), nullable=False
-    )
-    current_version_id: Column = DB.Column(
-        DB.Integer, ForeignKey("ObjectVersion.id"), nullable=True
-    )
+    namespace_id: Mapped[int] = mapped_column(ForeignKey("Namespace.id"), nullable=False)
+    object_type_id: Mapped[int] = mapped_column(ForeignKey("OnotologyObjectType.id"), nullable=False)
+    current_version_id: Mapped[int] = mapped_column(ForeignKey("ObjectVersion.id"), nullable=True)
 
     # relationships
-    namespace: Namespace = relationship(Namespace, innerjoin=True, lazy="selectin")
-    ontology_type: OntologyObjectType = relationship(
-        OntologyObjectType,
+    namespace: Mapped[Namespace] = relationship(innerjoin=True, lazy="selectin")
+    ontology_type: Mapped[OntologyObjectType] = relationship(
         innerjoin=True,
         lazy="selectin",  # load the type in a seperate query (and maybe benefit from session chache)
         back_populates="ontology_objects",
     )
-    current_version: "OntologyObjectVersion" = relationship(
-        "OntologyObjectVersion",
+    current_version: Mapped["OntologyObjectVersion"] = relationship(
         post_update=True,
         innerjoin=True,
         lazy="joined",
@@ -249,8 +231,7 @@ class OntologyObject(MODEL, IdMixin, NameDescriptionMixin, ChangesMixin):
         primaryjoin="OntologyObject.id == OntologyObjectVersion.object_id",
     )
 
-    referenced_by_objects: List["rel.OntologyObjectVersionToObject"] = relationship(
-        "OntologyObjectVersionToObject",
+    referenced_by_objects: Mapped[List["rel.OntologyObjectVersionToObject"]] = relationship(
         lazy="select",
         order_by="OntologyObjectVersionToObject.id",
         back_populates="object_target",
@@ -304,14 +285,10 @@ class OntologyObjectVersion(MODEL, IdMixin, NameDescriptionMixin, CreateDeleteMi
 
     __tablename__ = "ObjectVersion"
 
-    object_id: Column = DB.Column(
-        DB.Integer, ForeignKey(OntologyObject.id), nullable=False
-    )
-    version: Column = DB.Column(DB.Integer, nullable=False)
-    object_type_version_id: Column = DB.Column(
-        DB.Integer, ForeignKey(OntologyObjectTypeVersion.id), nullable=False
-    )
-    data: Column = DB.Column(DB.JSON, nullable=False)
+    object_id: Mapped[int] = mapped_column(ForeignKey("OntologyObject.id"), nullable=False)
+    version: Mapped[int] = mapped_column(nullable=False)
+    object_type_version_id: Mapped[int] = mapped_column(ForeignKey("OntologyObjectTypeVersion.id"), nullable=False)
+    data: Mapped[Text] = mapped_column(DB.JSON, nullable=False)
 
     @declared_attr
     def __table_args__(cls):
@@ -322,30 +299,26 @@ def __table_args__(cls):
         )
 
     # relationships
-    ontology_object: OntologyObject = relationship(
-        OntologyObject,
+    ontology_object: Mapped[OntologyObject] = relationship(
         innerjoin=True,
         lazy="select",  # should already be in session cache
         back_populates="versions",
         primaryjoin=OntologyObject.id == object_id,
     )
-    ontology_type_version: OntologyObjectTypeVersion = relationship(
-        OntologyObjectTypeVersion,
+    ontology_type_version: Mapped[OntologyObjectTypeVersion] = relationship(
         innerjoin=True,
         lazy="selectin",  # selectin uses a second (or more) queries and is more memory efficient compared to direct join
         back_populates="ontology_object_versions",
     )
 
-    referenced_objects: List["rel.OntologyObjectVersionToObject"] = relationship(
-        "OntologyObjectVersionToObject",
+    referenced_objects: Mapped[List["rel.OntologyObjectVersionToObject"]] = relationship(
         lazy="select",
         order_by="OntologyObjectVersionToObject.id",
         back_populates="object_version_source",
         primaryjoin="OntologyObjectVersion.id == OntologyObjectVersionToObject.object_version_source_id",
     )
 
-    referenced_taxonomy_items: List["rel.OntologyObjectVersionToTaxonomyItem"] = relationship(
-        "OntologyObjectVersionToTaxonomyItem",
+    referenced_taxonomy_items: Mapped[List["rel.OntologyObjectVersionToTaxonomyItem"]] = relationship(
         lazy="select",
         order_by="OntologyObjectVersionToTaxonomyItem.id",
         back_populates="object_version_source",
diff --git a/muse_for_anything/db/models/taxonomies.py b/muse_for_anything/db/models/taxonomies.py
index c51120a..4f136d1 100644
--- a/muse_for_anything/db/models/taxonomies.py
+++ b/muse_for_anything/db/models/taxonomies.py
@@ -3,7 +3,7 @@
 from typing import Any, Dict, List, Optional, cast
 from sqlalchemy.orm.query import Query
 from sqlalchemy.sql.schema import ForeignKey, Column, Index
-from sqlalchemy.orm import relationship, selectinload
+from sqlalchemy.orm import Mapped, mapped_column, relationship, selectinload
 from sqlalchemy.ext.declarative import declared_attr
 
 from ..db import DB, MODEL
@@ -23,20 +23,18 @@ class Taxonomy(MODEL, IdMixin, NameDescriptionMixin, ChangesMixin):
 
     __tablename__ = "Taxonomy"
 
-    namespace_id: Column = DB.Column(DB.Integer, ForeignKey(Namespace.id), nullable=False)
+    namespace_id: Mapped[int] = mapped_column(ForeignKey("Namespace.id"), nullable=False)
 
     # relationships
     namespace = relationship(Namespace, innerjoin=True, lazy="selectin")
 
-    items: List["TaxonomyItem"] = relationship(
-        "TaxonomyItem",
+    items: Mapped[List["TaxonomyItem"]] = relationship(
         lazy="select",  # do not always load this
         order_by="TaxonomyItem.id",
         back_populates="taxonomy",
         primaryjoin="Taxonomy.id == TaxonomyItem.taxonomy_id",
     )
-    current_items: List["TaxonomyItem"] = relationship(
-        "TaxonomyItem",
+    current_items: Mapped[List["TaxonomyItem"]] = relationship(
         viewonly=True,
         # lazy="select",  # do not always load this
         order_by="TaxonomyItem.id",
@@ -44,8 +42,7 @@ class Taxonomy(MODEL, IdMixin, NameDescriptionMixin, ChangesMixin):
         primaryjoin="and_(Taxonomy.id == TaxonomyItem.taxonomy_id, TaxonomyItem.deleted_on == None)",
     )
 
-    referenced_by_types: List["rel.OntologyTypeVersionToTaxonomy"] = relationship(
-        "OntologyTypeVersionToTaxonomy",
+    referenced_by_types: Mapped[List["rel.OntologyTypeVersionToTaxonomy"]] = relationship(
         lazy="select",
         order_by="OntologyTypeVersionToTaxonomy.id",
         back_populates="taxonomy_target",
@@ -83,64 +80,54 @@ class TaxonomyItem(MODEL, IdMixin, ChangesMixin):
 
     __tablename__ = "TaxonomyItem"
 
-    taxonomy_id: Column = DB.Column(DB.Integer, ForeignKey(Taxonomy.id), nullable=False)
-    current_version_id: Column = DB.Column(
-        DB.Integer, ForeignKey("TaxonomyItemVersion.id"), nullable=True
-    )
+    taxonomy_id: Mapped[int] = mapped_column(ForeignKey("Taxonomy.id"), nullable=False)
+    current_version_id: Mapped[int] = mapped_column(ForeignKey("TaxonomyItemVersion.id"), nullable=True)
 
     # relationships
-    taxonomy: Taxonomy = relationship(
-        Taxonomy,
+    taxonomy: Mapped[Taxonomy] = relationship(
         innerjoin=True,
         lazy="selectin",
         back_populates="items",
         sync_backref=False,
     )
-    current_version: "TaxonomyItemVersion" = relationship(
-        "TaxonomyItemVersion",
+    current_version: Mapped["TaxonomyItemVersion"] = relationship(
         post_update=True,
         innerjoin=True,
         lazy="joined",
         primaryjoin="TaxonomyItem.current_version_id == TaxonomyItemVersion.id",
     )
-    versions: List["TaxonomyItemVersion"] = relationship(
-        "TaxonomyItemVersion",
+    versions: Mapped[List["TaxonomyItemVersion"]] = relationship(
         lazy="select",
         order_by="TaxonomyItemVersion.version",
         back_populates="taxonomy_item",
         primaryjoin="TaxonomyItem.id == TaxonomyItemVersion.taxonomy_item_id",
     )
-    related: List["TaxonomyItemRelation"] = relationship(
-        "TaxonomyItemRelation",
+    related: Mapped[List["TaxonomyItemRelation"]] = relationship(
         lazy="select",
         order_by="TaxonomyItemRelation.id",
         back_populates="taxonomy_item_source",
         primaryjoin="TaxonomyItem.id == TaxonomyItemRelation.taxonomy_item_source_id",
     )
-    ancestors: List["TaxonomyItemRelation"] = relationship(
-        "TaxonomyItemRelation",
+    ancestors: Mapped[List["TaxonomyItemRelation"]] = relationship(
         lazy="select",
         order_by="TaxonomyItemRelation.id",
         back_populates="taxonomy_item_target",
         primaryjoin="TaxonomyItem.id == TaxonomyItemRelation.taxonomy_item_target_id",
     )
-    current_related: List["TaxonomyItemRelation"] = relationship(
-        "TaxonomyItemRelation",
+    current_related: Mapped[List["TaxonomyItemRelation"]] = relationship(
         viewonly=True,
         lazy="selectin",  # deals better with multiple levels of hierarchy
         order_by="TaxonomyItemRelation.id",
         primaryjoin="and_(TaxonomyItem.id == TaxonomyItemRelation.taxonomy_item_source_id, TaxonomyItemRelation.deleted_on == None)",
     )
-    current_ancestors: List["TaxonomyItemRelation"] = relationship(
-        "TaxonomyItemRelation",
+    current_ancestors: Mapped[List["TaxonomyItemRelation"]] = relationship(
         viewonly=True,
         lazy="selectin",  # deals better with multiple levels of hierarchy
         order_by="TaxonomyItemRelation.id",
         primaryjoin="and_(TaxonomyItem.id == TaxonomyItemRelation.taxonomy_item_target_id, TaxonomyItemRelation.deleted_on == None)",
     )
 
-    referenced_by_objects: List["rel.OntologyObjectVersionToTaxonomyItem"] = relationship(
-        "OntologyObjectVersionToTaxonomyItem",
+    referenced_by_objects: Mapped[List["rel.OntologyObjectVersionToTaxonomyItem"]] = relationship(
         lazy="select",
         order_by="OntologyObjectVersionToTaxonomyItem.id",
         back_populates="taxonomy_item_target",
@@ -187,12 +174,10 @@ class TaxonomyItemVersion(MODEL, IdMixin, NameDescriptionMixin, CreateDeleteMixi
 
     __tablename__ = "TaxonomyItemVersion"
 
-    taxonomy_item_id: Column = DB.Column(
-        DB.Integer, ForeignKey(TaxonomyItem.id), nullable=False
-    )
-    version: Column = DB.Column(DB.Integer, nullable=False)
-    sort_key: Column = DB.Column(DB.Float, nullable=True)
-
+    taxonomy_item_id: Mapped[int] = mapped_column(ForeignKey("TaxonomyItem.id"), nullable=False)
+    version: Mapped[int] = mapped_column(nullable=False)
+    sort_key: Mapped[float] = mapped_column(nullable=True)
+    
     @declared_attr
     def __table_args__(cls):
         return (
@@ -211,8 +196,7 @@ def __table_args__(cls):
         )
 
     # relationships
-    taxonomy_item: TaxonomyItem = relationship(
-        TaxonomyItem,
+    taxonomy_item: Mapped[TaxonomyItem] = relationship(
         innerjoin=True,
         lazy="select",  # normally loaded from the taxonmy item -> less queries needed
         back_populates="versions",
@@ -240,24 +224,18 @@ class TaxonomyItemRelation(MODEL, IdMixin, CreateDeleteMixin):
 
     __tablename__ = "TaxonomyItemRelation"
 
-    taxonomy_item_source_id: Column = DB.Column(
-        DB.Integer, ForeignKey(TaxonomyItem.id), nullable=False
-    )
+    taxonomy_item_source_id: Mapped[int] = mapped_column(ForeignKey("TaxonomyItem.id"), nullable=False)
 
-    taxonomy_item_target_id: Column = DB.Column(
-        DB.Integer, ForeignKey(TaxonomyItem.id), nullable=False
-    )
+    taxonomy_item_target_id: Mapped[int] = mapped_column(ForeignKey("TaxonomyItem.id"), nullable=False)
 
     # relationships
-    taxonomy_item_source: TaxonomyItem = relationship(
-        TaxonomyItem,
+    taxonomy_item_source: Mapped[TaxonomyItem] = relationship(
         lazy="select",  # is nearly always in cache anyway
         back_populates="related",
         primaryjoin=TaxonomyItem.id == taxonomy_item_source_id,
     )
 
-    taxonomy_item_target: TaxonomyItem = relationship(
-        TaxonomyItem,
+    taxonomy_item_target: Mapped[TaxonomyItem] = relationship(
         lazy="select",  # is nearly always in cache anyway
         back_populates="ancestors",
         primaryjoin=TaxonomyItem.id == taxonomy_item_target_id,
diff --git a/muse_for_anything/db/models/users.py b/muse_for_anything/db/models/users.py
index c3ec22b..cd6297a 100644
--- a/muse_for_anything/db/models/users.py
+++ b/muse_for_anything/db/models/users.py
@@ -3,9 +3,10 @@
 from typing import List, Optional, Set, Union
 
 from flask_babel import gettext
-from sqlalchemy.orm import relationship
+from sqlalchemy.orm import Mapped, mapped_column, relationship
 from sqlalchemy.sql.elements import literal
-from sqlalchemy.sql.schema import Column, ForeignKey
+from sqlalchemy.sql.schema import ForeignKey
+from sqlalchemy.types import Text
 
 from .model_helpers import CreateDeleteMixin, ExistsMixin, IdMixin
 from .namespace import Namespace
@@ -55,19 +56,17 @@ class User(MODEL, IdMixin, CreateDeleteMixin, ExistsMixin):
 
     __tablename__ = "User"
 
-    username: Column = DB.Column(DB.String(120), unique=True, index=True)
-    e_mail: Column = DB.Column(DB.Text, unique=True, index=True, nullable=True)
-    password: Column = DB.Column(DB.String(120))
+    username: Mapped[str] = mapped_column(DB.String(120), unique=True, index=True)
+    e_mail: Mapped[Text] = mapped_column(DB.Text, unique=True, index=True, nullable=True)
+    password: Mapped[str] = mapped_column(DB.String(120))
 
     # references
-    roles: List["UserRole"] = relationship(
-        "UserRole",
+    roles: Mapped[List["UserRole"]] = relationship(
         lazy="joined",
         back_populates="user",
     )
 
-    grants: List["UserGrant"] = relationship(
-        "UserGrant",
+    grants: Mapped[List["UserGrant"]] = relationship(
         lazy="select",
         back_populates="user",
     )
@@ -159,12 +158,11 @@ class UserRole(MODEL, IdMixin):
 
     __tablename__ = "UserRole"
 
-    user_id: Column = DB.Column(DB.Integer, ForeignKey(User.id), nullable=False)
-    role: Column = DB.Column(DB.String(64))
+    user_id: Mapped[int] = mapped_column(ForeignKey("User.id"), nullable=False)
+    role: Mapped[str] = mapped_column(DB.String(64))
 
     # references
-    user: User = relationship(
-        User,
+    user: Mapped[User] = relationship(
         innerjoin=True,
         lazy="selectin",
         back_populates="roles",
@@ -249,13 +247,12 @@ class UserGrant(MODEL, IdMixin):
 
     __tablename__ = "UserGrant"
 
-    user_id: Column = DB.Column(DB.Integer, ForeignKey(User.id), nullable=True)
-    role: Column = DB.Column(DB.String(64), index=True)
-    resource_type: Column = DB.Column(DB.String(64), index=True)
-    resource_id: Column = DB.Column(DB.Integer(), index=True)
+    user_id: Mapped[int] = mapped_column(ForeignKey("User.id"), nullable=True)
+    role: Mapped[str] = mapped_column(DB.String(64), index=True)
+    resource_type: Mapped[str] = mapped_column(DB.String(64), index=True)
+    resource_id: Mapped[int] = mapped_column(index=True)
 
-    user: User = relationship(
-        User,
+    user: Mapped[User] = relationship(
         innerjoin=True,
         lazy="selectin",
         back_populates="grants",
diff --git a/muse_for_anything/oso_helpers.py b/muse_for_anything/oso_helpers.py
index 342b5e7..2cd11fb 100644
--- a/muse_for_anything/oso_helpers.py
+++ b/muse_for_anything/oso_helpers.py
@@ -1,14 +1,15 @@
 """Module for setting up oso support for flask app."""
 
 from dataclasses import dataclass
-from typing import Any, Dict, Optional, Sequence, Type
+from typing import Any, Callable, Dict, NoReturn, Optional, Sequence, Type
 
-from flask import Flask
-from flask.globals import g, request
-from flask_oso import FlaskOso
+from flask import Flask, current_app, g, request
+from flask.globals import request_ctx, g, request
+from flask.wrappers import Request, Response
 from oso import Oso
 from polar.exceptions import OsoError
 from sqlalchemy.exc import ArgumentError
+from werkzeug.exceptions import Forbidden
 
 from muse_for_anything.db.models.namespace import Namespace
 from muse_for_anything.db.models.ontology_objects import (
@@ -56,25 +57,81 @@ class OsoResource:
     arguments: Optional[Dict[str, Any]] = None
 
 
-class CustomFlaskOso(FlaskOso):
+class CustomFlaskOso():
 
     _oso: Oso
     _app: Flask
     _allowed_methods: Optional[Sequence[str]]
 
-    def __init__(self, *, oso: Optional[Oso] = None, app: Optional[Flask] = None):
-        super().__init__(oso=oso, app=app)
+    def __init__(self, oso: Optional[Oso] = None, app: Optional[Flask] = None) -> None:
+        self._app = app
+        self._oso = None
+        
+        def unauthorized() -> NoReturn:
+            raise Forbidden("Unauthorized")
+        
+        self._unauthorized_action = unauthorized
+        
+        self._get_actor = lambda: g.current_user
+        
+        if self._app is not None:
+            self.init_app(self._app)
+        if oso is not None:
+            self.set_oso(oso)
+        
         self._allowed_methods = None
 
+    def set_oso(self, oso: Oso) -> None:
+        if oso == self._oso:
+            return
+        self._oso = oso
+        self._oso.register_class(Request)
+
     def init_app(self, app: Flask):
-        super().init_app(app)
+        app.teardown_appcontext(self.teardown)
+        app.before_request(self._provide_oso)
         app.before_request(self._clear_old_cache)
 
+    def teardown(self, exception):
+        pass
+    
+    def _provide_oso(self) -> None:
+        top = _app_context()
+        if not hasattr(top, "oso_flask_oso"):
+            top.oso_flask_oso = self
+
     def _clear_old_cache(
         self,
     ):
         self._allowed_methods = None
 
+    def set_get_actor(self, func:Callable[[], Any]) -> None:
+        self._get_actor = func
+        
+    def set_unauthorize_action(self, func:Callable[[], Any]) -> None:
+        self._unauthorized_action = func
+        
+    def require_authorization(self, app:Optional[Flask] = None) -> None:
+        if app is None:
+            app = self._app
+        if app is None:
+            raise OsoError(
+                "Cannot require authorization without Flask app object"
+            )
+        app.after_request(self._require_authorization)
+        
+    def perform_route_authorization(self, app: Optional[Flask] = None) -> None:
+        if app is None:
+            app = self._app
+        if app is None:
+            raise OsoError(
+                "Cannot perform route authorization without Flask app object"
+            )
+        app.before_request(self.perform_route_authorization)
+        
+    def skip_authorization(self, reason: Optional[str] = None) -> None:
+        _authorize_called()
+
     def _get_resource(self):
         if g.current_resource:
             return g.current_resource
@@ -111,7 +168,51 @@ def authorize(
     ):
         if resource is None:
             resource = self._get_resource()
-        super().authorize(resource, actor=actor, action=action)
+        if actor is None:
+            try:
+                actor = self.current_actor
+            except AttributeError as e:
+                raise OsoError(
+                    "Getting the current actor failed. "
+                    "You may need to override the current actor function with "
+                    "FlaskOso#set_get_actor"
+                ) from e
+        if action is None:
+            action = request.method
+        if resource is request:
+            resource = request._get_currect_object()
+        if self.oso is None:
+            raise OsoError("Cannot perform authorization without oso instance")
+        
+        allowed = self.oso.is_allowed(actor, action, resource)
+        _authorize_called()
+        
+        if not allowed:
+            self._unauthorized_action()
+        
+    @property
+    def app(self) -> Flask:
+        return self._app or current_app
+    
+    @property
+    def oso(self) -> Optional[Oso]:
+        return self._oso
+    
+    @property
+    def current_actor(self) -> Any:
+        return self._get_actor()
+
+    def _perform_route_authorization(self) -> None:
+        if not request.url_rule:
+            return
+        self.authorize(resource=request)
+        
+    def _require_authorization(self, response: Response) -> Response:
+        if not request.url_rule:
+            return Response
+        if not getattr(_app_context(), "oso_flask_authorize_called", False):
+            raise OsoError("Authorize not called.")
+        return response
 
     def is_admin(
         self,
@@ -172,6 +273,17 @@ def get_allowed_actions(
 
 FLASK_OSO = CustomFlaskOso(oso=OSO)
 
+def _authorize_called() -> None:
+    _app_context().oso_flask_authorize_called = True
+
+def _app_context():
+    top = request_ctx
+    if top is None:
+        raise OsoError(
+            "Application context doesn't exist. Did you use oso outside the context of a request? "
+            "See https://flask.palletsprojects.com/en/1.1.x/appcontext/#manually-push-a-context"
+        )
+    return top
 
 def register_oso(app: Flask):
     """Register oso to enable access management for this app."""
diff --git a/poetry.lock b/poetry.lock
index 12dd35b..82568d4 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,4 +1,4 @@
-# This file is automatically @generated by Poetry 1.8.2 and should not be changed by hand.
+# This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand.
 
 [[package]]
 name = "alabaster"
@@ -13,13 +13,13 @@ files = [
 
 [[package]]
 name = "alembic"
-version = "1.13.1"
+version = "1.13.2"
 description = "A database migration tool for SQLAlchemy."
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "alembic-1.13.1-py3-none-any.whl", hash = "sha256:2edcc97bed0bd3272611ce3a98d98279e9c209e7186e43e75bbb1b2bdfdbcc43"},
-    {file = "alembic-1.13.1.tar.gz", hash = "sha256:4932c8558bf68f2ee92b9bbcb8218671c627064d5b08939437af6d77dc05e595"},
+    {file = "alembic-1.13.2-py3-none-any.whl", hash = "sha256:6b8733129a6224a9a711e17c99b08462dbf7cc9670ba8f2e2ae9af860ceb1953"},
+    {file = "alembic-1.13.2.tar.gz", hash = "sha256:1ff0ae32975f4fd96028c39ed9bb3c867fe3af956bd7bb37343b54c9fe7445ef"},
 ]
 
 [package.dependencies]
@@ -32,37 +32,26 @@ tz = ["backports.zoneinfo"]
 
 [[package]]
 name = "apispec"
-version = "5.2.2"
+version = "6.6.1"
 description = "A pluggable API specification generator. Currently supports the OpenAPI Specification (f.k.a. the Swagger specification)."
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "apispec-5.2.2-py3-none-any.whl", hash = "sha256:f5f0d6b452c3e4a0e0922dce8815fac89dc4dbc758acef21fb9e01584d6602a5"},
-    {file = "apispec-5.2.2.tar.gz", hash = "sha256:6ea6542e1ebffe9fd95ba01ef3f51351eac6c200a974562c7473059b9cd20aa7"},
+    {file = "apispec-6.6.1-py3-none-any.whl", hash = "sha256:6460315cb38ac6a2ff42d9e2b8dc0435c37d4428d3abeda96ff97b5dc8eb6b94"},
+    {file = "apispec-6.6.1.tar.gz", hash = "sha256:f5caa47cee75fe03b9c50b5594048b4c052eeca2c212e0dac12dbb6175d9a659"},
 ]
 
 [package.dependencies]
-marshmallow = {version = ">=3.13.0", optional = true, markers = "extra == \"marshmallow\""}
+marshmallow = {version = ">=3.18.0", optional = true, markers = "extra == \"marshmallow\""}
+packaging = ">=21.3"
 
 [package.extras]
-dev = ["PyYAML (>=3.10)", "flake8 (==4.0.1)", "flake8-bugbear (==22.4.25)", "marshmallow (>=3.13.0)", "mock", "mypy (==0.950)", "prance[osv] (>=0.11)", "pre-commit (>=2.4,<3.0)", "pytest", "tox", "types-PyYAML"]
-docs = ["marshmallow (>=3.13.0)", "pyyaml (==6.0)", "sphinx (==4.5.0)", "sphinx-issues (==3.0.1)", "sphinx-rtd-theme (==1.0.0)"]
-lint = ["flake8 (==4.0.1)", "flake8-bugbear (==22.4.25)", "mypy (==0.950)", "pre-commit (>=2.4,<3.0)", "types-PyYAML"]
-marshmallow = ["marshmallow (>=3.13.0)"]
-tests = ["PyYAML (>=3.10)", "marshmallow (>=3.13.0)", "mock", "prance[osv] (>=0.11)", "pytest"]
-validation = ["prance[osv] (>=0.11)"]
+dev = ["apispec[tests]", "pre-commit (>=3.5,<4.0)", "tox"]
+docs = ["apispec[marshmallow]", "pyyaml (==6.0.1)", "sphinx (==7.3.7)", "sphinx-issues (==4.1.0)", "sphinx-rtd-theme (==2.0.0)"]
+marshmallow = ["marshmallow (>=3.18.0)"]
+tests = ["apispec[marshmallow,yaml]", "openapi-spec-validator (==0.7.1)", "pytest"]
 yaml = ["PyYAML (>=3.10)"]
 
-[[package]]
-name = "atomicwrites"
-version = "1.4.1"
-description = "Atomic file writes."
-optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
-files = [
-    {file = "atomicwrites-1.4.1.tar.gz", hash = "sha256:81b2c9071a49367a7f770170e5eec8cb66567cfbbc8c73d20ce5ca4a8d71cf11"},
-]
-
 [[package]]
 name = "attrs"
 version = "23.2.0"
@@ -84,13 +73,13 @@ tests-no-zope = ["attrs[tests-mypy]", "cloudpickle", "hypothesis", "pympler", "p
 
 [[package]]
 name = "babel"
-version = "2.14.0"
+version = "2.15.0"
 description = "Internationalization utilities"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "Babel-2.14.0-py3-none-any.whl", hash = "sha256:efb1a25b7118e67ce3a259bed20545c29cb68be8ad2c784c83689981b7a57287"},
-    {file = "Babel-2.14.0.tar.gz", hash = "sha256:6919867db036398ba21eb5c7a0f6b28ab8cbc3ae7a73a44ebe34ae74a4e7d363"},
+    {file = "Babel-2.15.0-py3-none-any.whl", hash = "sha256:08706bdad8d0a3413266ab61bd6c34d0c28d6e1e7badf40a2cebe67644e2e1fb"},
+    {file = "babel-2.15.0.tar.gz", hash = "sha256:8daf0e265d05768bc6c7a314cf1321e9a123afc328cc635c18622a2f30a04413"},
 ]
 
 [package.extras]
@@ -98,60 +87,73 @@ dev = ["freezegun (>=1.0,<2.0)", "pytest (>=6.0)", "pytest-cov"]
 
 [[package]]
 name = "bcrypt"
-version = "3.2.2"
+version = "4.2.0"
 description = "Modern password hashing for your software and your servers"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
 files = [
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 ]
 
-[package.dependencies]
-cffi = ">=1.1"
-
 [package.extras]
 tests = ["pytest (>=3.2.1,!=3.3.0)"]
 typecheck = ["mypy"]
 
 [[package]]
 name = "black"
-version = "23.12.1"
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 description = "The uncompromising code formatter."
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
@@ -171,24 +173,24 @@ uvloop = ["uvloop (>=0.15.2)"]
 
 [[package]]
 name = "blinker"
-version = "1.7.0"
+version = "1.8.2"
 description = "Fast, simple object-to-object and broadcast signaling"
 optional = false
 python-versions = ">=3.8"
 files = [
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+    {file = "blinker-1.8.2.tar.gz", hash = "sha256:8f77b09d3bf7c795e969e9486f39c2c5e9c39d4ee07424be2bc594ece9642d83"},
 ]
 
 [[package]]
 name = "certifi"
-version = "2023.11.17"
+version = "2024.7.4"
 description = "Python package for providing Mozilla's CA Bundle."
 optional = false
 python-versions = ">=3.6"
 files = [
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 ]
 
 [[package]]
@@ -381,48 +383,62 @@ files = [
 
 [[package]]
 name = "docutils"
-version = "0.18.1"
+version = "0.20.1"
 description = "Docutils -- Python Documentation Utilities"
 optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
+python-versions = ">=3.7"
 files = [
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+    {file = "docutils-0.20.1-py3-none-any.whl", hash = "sha256:96f387a2c5562db4476f09f13bbab2192e764cac08ebbf3a34a95d9b1e4a59d6"},
+    {file = "docutils-0.20.1.tar.gz", hash = "sha256:f08a4e276c3a1583a86dce3e34aba3fe04d02bba2dd51ed16106244e8a923e3b"},
 ]
 
+[[package]]
+name = "exceptiongroup"
+version = "1.2.2"
+description = "Backport of PEP 654 (exception groups)"
+optional = false
+python-versions = ">=3.7"
+files = [
+    {file = "exceptiongroup-1.2.2-py3-none-any.whl", hash = "sha256:3111b9d131c238bec2f8f516e123e14ba243563fb135d3fe885990585aa7795b"},
+    {file = "exceptiongroup-1.2.2.tar.gz", hash = "sha256:47c2edf7c6738fafb49fd34290706d1a1a2f4d1c6df275526b62cbb4aa5393cc"},
+]
+
+[package.extras]
+test = ["pytest (>=6)"]
+
 [[package]]
 name = "flake8"
-version = "3.9.2"
+version = "7.1.0"
 description = "the modular source code checker: pep8 pyflakes and co"
 optional = false
-python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,>=2.7"
+python-versions = ">=3.8.1"
 files = [
-    {file = "flake8-3.9.2-py2.py3-none-any.whl", hash = "sha256:bf8fd333346d844f616e8d47905ef3a3384edae6b4e9beb0c5101e25e3110907"},
-    {file = "flake8-3.9.2.tar.gz", hash = "sha256:07528381786f2a6237b061f6e96610a4167b226cb926e2aa2b6b1d78057c576b"},
+    {file = "flake8-7.1.0-py2.py3-none-any.whl", hash = "sha256:2e416edcc62471a64cea09353f4e7bdba32aeb079b6e360554c659a122b1bc6a"},
+    {file = "flake8-7.1.0.tar.gz", hash = "sha256:48a07b626b55236e0fb4784ee69a465fbf59d79eec1f5b4785c3d3bc57d17aa5"},
 ]
 
 [package.dependencies]
-mccabe = ">=0.6.0,<0.7.0"
-pycodestyle = ">=2.7.0,<2.8.0"
-pyflakes = ">=2.3.0,<2.4.0"
+mccabe = ">=0.7.0,<0.8.0"
+pycodestyle = ">=2.12.0,<2.13.0"
+pyflakes = ">=3.2.0,<3.3.0"
 
 [[package]]
 name = "flake8-bugbear"
-version = "21.11.29"
+version = "24.4.26"
 description = "A plugin for flake8 finding likely bugs and design problems in your program. Contains warnings that don't belong in pyflakes and pycodestyle."
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.8.1"
 files = [
-    {file = "flake8-bugbear-21.11.29.tar.gz", hash = "sha256:8b04cb2fafc6a78e1a9d873bd3988e4282f7959bb6b0d7c1ae648ec09b937a7b"},
-    {file = "flake8_bugbear-21.11.29-py36.py37.py38-none-any.whl", hash = "sha256:179e41ddae5de5e3c20d1f61736feeb234e70958fbb56ab3c28a67739c8e9a82"},
+    {file = "flake8_bugbear-24.4.26-py3-none-any.whl", hash = "sha256:cb430dd86bc821d79ccc0b030789a9c87a47a369667f12ba06e80f11305e8258"},
+    {file = "flake8_bugbear-24.4.26.tar.gz", hash = "sha256:ff8d4ba5719019ebf98e754624c30c05cef0dadcf18a65d91c7567300e52a130"},
 ]
 
 [package.dependencies]
 attrs = ">=19.2.0"
-flake8 = ">=3.0.0"
+flake8 = ">=6.0.0"
 
 [package.extras]
-dev = ["coverage", "hypothesis", "hypothesmith (>=0.2)", "pre-commit"]
+dev = ["coverage", "hypothesis", "hypothesmith (>=0.2)", "pre-commit", "pytest", "tox"]
 
 [[package]]
 name = "flake8-docstrings"
@@ -441,13 +457,13 @@ pydocstyle = ">=2.1"
 
 [[package]]
 name = "flask"
-version = "2.3.3"
+version = "3.0.3"
 description = "A simple framework for building complex web applications."
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "flask-2.3.3-py3-none-any.whl", hash = "sha256:f69fcd559dc907ed196ab9df0e48471709175e696d6e698dd4dbe940f96ce66b"},
-    {file = "flask-2.3.3.tar.gz", hash = "sha256:09c347a92aa7ff4a8e7f3206795f30d826654baf38b873d0744cd571ca609efc"},
+    {file = "flask-3.0.3-py3-none-any.whl", hash = "sha256:34e815dfaa43340d1d15a5c3a02b8476004037eb4840b34910c6e21679d288f3"},
+    {file = "flask-3.0.3.tar.gz", hash = "sha256:ceb27b0af3823ea2737928a4d99d125a06175b8512c445cbd9a9ce200ef76842"},
 ]
 
 [package.dependencies]
@@ -456,7 +472,7 @@ click = ">=8.1.3"
 itsdangerous = ">=2.1.2"
 Jinja2 = ">=3.1.2"
 python-dotenv = {version = "*", optional = true, markers = "extra == \"dotenv\""}
-Werkzeug = ">=2.3.7"
+Werkzeug = ">=3.0.0"
 
 [package.extras]
 async = ["asgiref (>=3.2)"]
@@ -464,38 +480,34 @@ dotenv = ["python-dotenv"]
 
 [[package]]
 name = "flask-babel"
-version = "2.0.0"
-description = "Adds i18n/l10n support to Flask applications"
+version = "4.0.0"
+description = "Adds i18n/l10n support for Flask applications."
 optional = false
-python-versions = "*"
+python-versions = ">=3.8,<4.0"
 files = [
-    {file = "Flask-Babel-2.0.0.tar.gz", hash = "sha256:f9faf45cdb2e1a32ea2ec14403587d4295108f35017a7821a2b1acb8cfd9257d"},
-    {file = "Flask_Babel-2.0.0-py3-none-any.whl", hash = "sha256:e6820a052a8d344e178cdd36dd4bb8aea09b4bda3d5f9fa9f008df2c7f2f5468"},
+    {file = "flask_babel-4.0.0-py3-none-any.whl", hash = "sha256:638194cf91f8b301380f36d70e2034c77ee25b98cb5d80a1626820df9a6d4625"},
+    {file = "flask_babel-4.0.0.tar.gz", hash = "sha256:dbeab4027a3f4a87678a11686496e98e1492eb793cbdd77ab50f4e9a2602a593"},
 ]
 
 [package.dependencies]
-Babel = ">=2.3"
-Flask = "*"
-Jinja2 = ">=2.5"
-pytz = "*"
-
-[package.extras]
-dev = ["Pallets-Sphinx-Themes", "bumpversion", "ghp-import", "pytest", "pytest-mock", "sphinx"]
+Babel = ">=2.12"
+Flask = ">=2.0"
+Jinja2 = ">=3.1"
+pytz = ">=2022.7"
 
 [[package]]
 name = "flask-cors"
-version = "3.0.10"
+version = "4.0.1"
 description = "A Flask extension adding a decorator for CORS support"
 optional = false
 python-versions = "*"
 files = [
-    {file = "Flask-Cors-3.0.10.tar.gz", hash = "sha256:b60839393f3b84a0f3746f6cdca56c1ad7426aa738b70d6c61375857823181de"},
-    {file = "Flask_Cors-3.0.10-py2.py3-none-any.whl", hash = "sha256:74efc975af1194fc7891ff5cd85b0f7478be4f7f59fe158102e91abb72bb4438"},
+    {file = "Flask_Cors-4.0.1-py2.py3-none-any.whl", hash = "sha256:f2a704e4458665580c074b714c4627dd5a306b333deb9074d0b1794dfa2fb677"},
+    {file = "flask_cors-4.0.1.tar.gz", hash = "sha256:eeb69b342142fdbf4766ad99357a7f3876a2ceb77689dc10ff912aac06c389e4"},
 ]
 
 [package.dependencies]
 Flask = ">=0.9"
-Six = "*"
 
 [[package]]
 name = "flask-jwt-extended"
@@ -517,86 +529,91 @@ Werkzeug = ">=0.14"
 asymmetric-crypto = ["cryptography (>=3.3.1)"]
 
 [[package]]
-name = "flask-migrate"
-version = "3.1.0"
-description = "SQLAlchemy database migrations for Flask applications using Alembic."
+name = "flask-login"
+version = "0.6.3"
+description = "User authentication and session management for Flask."
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
 files = [
-    {file = "Flask-Migrate-3.1.0.tar.gz", hash = "sha256:57d6060839e3a7f150eaab6fe4e726d9e3e7cffe2150fb223d73f92421c6d1d9"},
-    {file = "Flask_Migrate-3.1.0-py3-none-any.whl", hash = "sha256:a6498706241aba6be7a251078de9cf166d74307bca41a4ca3e403c9d39e2f897"},
+    {file = "Flask-Login-0.6.3.tar.gz", hash = "sha256:5e23d14a607ef12806c699590b89d0f0e0d67baeec599d75947bf9c147330333"},
+    {file = "Flask_Login-0.6.3-py3-none-any.whl", hash = "sha256:849b25b82a436bf830a054e74214074af59097171562ab10bfa999e6b78aae5d"},
 ]
 
 [package.dependencies]
-alembic = ">=0.7"
-Flask = ">=0.9"
-Flask-SQLAlchemy = ">=1.0"
+Flask = ">=1.0.4"
+Werkzeug = ">=1.0.1"
 
 [[package]]
-name = "flask-oso"
-version = "0.26.0"
-description = "oso flask integration"
+name = "flask-migrate"
+version = "4.0.7"
+description = "SQLAlchemy database migrations for Flask applications using Alembic."
 optional = false
 python-versions = ">=3.6"
 files = [
-    {file = "flask_oso-0.26.0-py3-none-any.whl", hash = "sha256:86694a0d4643f05c8342c2d616048c1a44c2cf762d8327c6fbd84a0fa8f7a7ba"},
+    {file = "Flask-Migrate-4.0.7.tar.gz", hash = "sha256:dff7dd25113c210b069af280ea713b883f3840c1e3455274745d7355778c8622"},
+    {file = "Flask_Migrate-4.0.7-py3-none-any.whl", hash = "sha256:5c532be17e7b43a223b7500d620edae33795df27c75811ddf32560f7d48ec617"},
 ]
 
 [package.dependencies]
-flask = ">=0.12.0"
-oso = ">=0.26.0,<0.27.0"
+alembic = ">=1.9.0"
+Flask = ">=0.9"
+Flask-SQLAlchemy = ">=1.0"
 
 [[package]]
 name = "flask-smorest"
-version = "0.39.0"
+version = "0.44.0"
 description = "Flask/Marshmallow-based REST API framework"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "flask-smorest-0.39.0.tar.gz", hash = "sha256:b72b068283176c8dc7bb0e3cfbc2721fc5c9efdcf719eac76604d78223adb99c"},
-    {file = "flask_smorest-0.39.0-py3-none-any.whl", hash = "sha256:0b31c01f5fd3f7c2bc7f9e700e387e326939529edeabbe45963d352caca99f12"},
+    {file = "flask-smorest-0.44.0.tar.gz", hash = "sha256:13f6e39d807c8847a56dc40656c2bbc0a2b2a430d8a4bb4a21836046757f7cef"},
+    {file = "flask_smorest-0.44.0-py3-none-any.whl", hash = "sha256:a35d088d0f62e9ff7e94ed996601e04fcc17cbacfb43b52543b596b933db4f72"},
 ]
 
 [package.dependencies]
-apispec = {version = ">=5.1.0,<6", extras = ["marshmallow"]}
-flask = ">=2.0,<3"
-marshmallow = ">=3.13.0,<4"
+apispec = {version = ">=6.0.0,<7", extras = ["marshmallow"]}
+flask = ">=3.0.2,<4"
+marshmallow = ">=3.18.0,<4"
 webargs = ">=8.0.0,<9"
-werkzeug = ">=2.0,<3"
+werkzeug = ">=3.0.1,<4"
 
 [package.extras]
-dev = ["PyYAML (==6.0)", "apispec (==5.2.2)", "coverage (==6.4.3)", "flake8 (==5.0.4)", "flake8-bugbear (==22.7.1)", "flask (==2.2.2)", "marshmallow (==3.17.0)", "pre-commit (==2.20.0)", "pytest (==7.1.2)", "pytest-cov (==3.0.0)", "webargs (==8.2.0)", "werkzeug (==2.2.2)"]
-lint = ["flake8 (==5.0.4)", "flake8-bugbear (==22.7.1)", "pre-commit (==2.20.0)"]
-tests = ["PyYAML (==6.0)", "apispec (==5.2.2)", "coverage (==6.4.3)", "flask (==2.2.2)", "marshmallow (==3.17.0)", "pytest (==7.1.2)", "pytest-cov (==3.0.0)", "webargs (==8.2.0)", "werkzeug (==2.2.2)"]
+dev = ["PyYAML (==6.0.1)", "apispec (==6.4.0)", "coverage (==7.4.3)", "flask (==3.0.2)", "marshmallow (==3.20.2)", "pre-commit (==3.6.2)", "pytest (==8.0.2)", "pytest-cov (==4.1.0)", "webargs (==8.4.0)", "werkzeug (==3.0.1)"]
+lint = ["pre-commit (==3.6.2)"]
+tests = ["PyYAML (==6.0.1)", "apispec (==6.4.0)", "coverage (==7.4.3)", "flask (==3.0.2)", "marshmallow (==3.20.2)", "pytest (==8.0.2)", "pytest-cov (==4.1.0)", "webargs (==8.4.0)", "werkzeug (==3.0.1)"]
 
 [[package]]
 name = "flask-sqlalchemy"
-version = "2.5.1"
-description = "Adds SQLAlchemy support to your Flask application."
+version = "3.1.1"
+description = "Add SQLAlchemy support to your Flask application."
 optional = false
-python-versions = ">= 2.7, != 3.0.*, != 3.1.*, != 3.2.*, != 3.3.*"
+python-versions = ">=3.8"
 files = [
-    {file = "Flask-SQLAlchemy-2.5.1.tar.gz", hash = "sha256:2bda44b43e7cacb15d4e05ff3cc1f8bc97936cc464623424102bfc2c35e95912"},
-    {file = "Flask_SQLAlchemy-2.5.1-py2.py3-none-any.whl", hash = "sha256:f12c3d4cc5cc7fdcc148b9527ea05671718c3ea45d50c7e732cceb33f574b390"},
+    {file = "flask_sqlalchemy-3.1.1-py3-none-any.whl", hash = "sha256:4ba4be7f419dc72f4efd8802d69974803c37259dd42f3913b0dcf75c9447e0a0"},
+    {file = "flask_sqlalchemy-3.1.1.tar.gz", hash = "sha256:e4b68bb881802dda1a7d878b2fc84c06d1ee57fb40b874d3dc97dabfa36b8312"},
 ]
 
 [package.dependencies]
-Flask = ">=0.10"
-SQLAlchemy = ">=0.8.0"
+flask = ">=2.2.5"
+sqlalchemy = ">=2.0.16"
 
 [[package]]
 name = "flask-static-digest"
-version = "0.2.1"
-description = "Flask extension for md5 tagging and gzipping static files."
+version = "0.4.1"
+description = "Flask extension for md5 tagging and compressing (gzip / brotli) static files."
 optional = false
 python-versions = ">=3.6"
 files = [
-    {file = "Flask-Static-Digest-0.2.1.tar.gz", hash = "sha256:7528b08a2c12dc3a828096b66ee2612f323d50be36d01f2817b767fbb1ceca6e"},
+    {file = "Flask_Static_Digest-0.4.1-py3-none-any.whl", hash = "sha256:72bed5f614bcb57a81d2ebf6aa9ee3158a6057114b441ee791340b2c0df962b1"},
+    {file = "flask_static_digest-0.4.1.tar.gz", hash = "sha256:a6b38e953a4cfaac092e0ae40feea82a4f098bfac50969cefc48d4a9e7492e14"},
 ]
 
 [package.dependencies]
 Flask = ">=1.0"
 
+[package.extras]
+brotli = ["Brotli (>=1.0.9)"]
+
 [[package]]
 name = "greenlet"
 version = "3.0.3"
@@ -670,13 +687,13 @@ test = ["objgraph", "psutil"]
 
 [[package]]
 name = "idna"
-version = "3.6"
+version = "3.7"
 description = "Internationalized Domain Names in Applications (IDNA)"
 optional = false
 python-versions = ">=3.5"
 files = [
-    {file = "idna-3.6-py3-none-any.whl", hash = "sha256:c05567e9c24a6b9faaa835c4821bad0590fbb9d5779e7caa6e1cc4978e7eb24f"},
-    {file = "idna-3.6.tar.gz", hash = "sha256:9ecdbbd083b06798ae1e86adcbfe8ab1479cf864e4ee30fe4e46a003d12491ca"},
+    {file = "idna-3.7-py3-none-any.whl", hash = "sha256:82fee1fc78add43492d3a1898bfa6d8a904cc97d8427f683ed8e798d07761aa0"},
+    {file = "idna-3.7.tar.gz", hash = "sha256:028ff3aadf0609c1fd278d8ea3089299412a7a8b9bd005dd08b9f8285bcb5cfc"},
 ]
 
 [[package]]
@@ -714,24 +731,24 @@ files = [
 
 [[package]]
 name = "itsdangerous"
-version = "2.1.2"
+version = "2.2.0"
 description = "Safely pass data to untrusted environments and back."
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "itsdangerous-2.1.2-py3-none-any.whl", hash = "sha256:2c2349112351b88699d8d4b6b075022c0808887cb7ad10069318a8b0bc88db44"},
-    {file = "itsdangerous-2.1.2.tar.gz", hash = "sha256:5dbbc68b317e5e42f327f9021763545dc3fc3bfe22e6deb96aaf1fc38874156a"},
+    {file = "itsdangerous-2.2.0-py3-none-any.whl", hash = "sha256:c6242fc49e35958c8b15141343aa660db5fc54d4f13a1db01a3f5891b98700ef"},
+    {file = "itsdangerous-2.2.0.tar.gz", hash = "sha256:e0050c0b7da1eea53ffaf149c0cfbb5c6e2e2b69c4bef22c81fa6eb73e5f6173"},
 ]
 
 [[package]]
 name = "jinja2"
-version = "3.1.2"
+version = "3.1.4"
 description = "A very fast and expressive template engine."
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "Jinja2-3.1.2-py3-none-any.whl", hash = "sha256:6088930bfe239f0e6710546ab9c19c9ef35e29792895fed6e6e31a023a182a61"},
-    {file = "Jinja2-3.1.2.tar.gz", hash = "sha256:31351a702a408a9e7595a8fc6150fc3f43bb6bf7e319770cbc0db9df9437e852"},
+    {file = "jinja2-3.1.4-py3-none-any.whl", hash = "sha256:bc5dd2abb727a5319567b7a813e6a2e7318c39f4f487cfe6c89c6f9c7d25197d"},
+    {file = "jinja2-3.1.4.tar.gz", hash = "sha256:4a3aee7acbbe7303aede8e9648d13b8bf88a429282aa6122a993f0ac800cb369"},
 ]
 
 [package.dependencies]
@@ -742,34 +759,48 @@ i18n = ["Babel (>=2.7)"]
 
 [[package]]
 name = "jsonschema"
-version = "3.2.0"
+version = "4.23.0"
 description = "An implementation of JSON Schema validation for Python"
 optional = false
-python-versions = "*"
+python-versions = ">=3.8"
 files = [
-    {file = "jsonschema-3.2.0-py2.py3-none-any.whl", hash = "sha256:4e5b3cf8216f577bee9ce139cbe72eca3ea4f292ec60928ff24758ce626cd163"},
-    {file = "jsonschema-3.2.0.tar.gz", hash = "sha256:c8a85b28d377cc7737e46e2d9f2b4f44ee3c0e1deac6bf46ddefc7187d30797a"},
+    {file = "jsonschema-4.23.0-py3-none-any.whl", hash = "sha256:fbadb6f8b144a8f8cf9f0b89ba94501d143e50411a1278633f56a7acf7fd5566"},
+    {file = "jsonschema-4.23.0.tar.gz", hash = "sha256:d71497fef26351a33265337fa77ffeb82423f3ea21283cd9467bb03999266bc4"},
 ]
 
 [package.dependencies]
-attrs = ">=17.4.0"
-pyrsistent = ">=0.14.0"
-setuptools = "*"
-six = ">=1.11.0"
+attrs = ">=22.2.0"
+jsonschema-specifications = ">=2023.03.6"
+referencing = ">=0.28.4"
+rpds-py = ">=0.7.1"
 
 [package.extras]
-format = ["idna", "jsonpointer (>1.13)", "rfc3987", "strict-rfc3339", "webcolors"]
-format-nongpl = ["idna", "jsonpointer (>1.13)", "rfc3339-validator", "rfc3986-validator (>0.1.0)", "webcolors"]
+format = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339-validator", "rfc3987", "uri-template", "webcolors (>=1.11)"]
+format-nongpl = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339-validator", "rfc3986-validator (>0.1.0)", "uri-template", "webcolors (>=24.6.0)"]
+
+[[package]]
+name = "jsonschema-specifications"
+version = "2023.12.1"
+description = "The JSON Schema meta-schemas and vocabularies, exposed as a Registry"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "jsonschema_specifications-2023.12.1-py3-none-any.whl", hash = "sha256:87e4fdf3a94858b8a2ba2778d9ba57d8a9cafca7c7489c46ba0d30a8bc6a9c3c"},
+    {file = "jsonschema_specifications-2023.12.1.tar.gz", hash = "sha256:48a76787b3e70f5ed53f1160d2b81f586e4ca6d1548c5de7085d1682674764cc"},
+]
+
+[package.dependencies]
+referencing = ">=0.31.0"
 
 [[package]]
 name = "mako"
-version = "1.3.0"
+version = "1.3.5"
 description = "A super-fast templating language that borrows the best ideas from the existing templating languages."
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
@@ -806,81 +837,90 @@ testing = ["coverage", "pytest", "pytest-cov", "pytest-regressions"]
 
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 description = "A lightweight library for converting complex datatypes to and from native Python datatypes."
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 python-versions = ">=3.8"
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-lint = ["pre-commit (>=2.4,<4.0)"]
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 tests = ["pytest", "pytz", "simplejson"]
 
 [[package]]
@@ -903,24 +943,24 @@ union = ["marshmallow-union"]
 
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 [package.dependencies]
@@ -955,17 +995,17 @@ files = [
 
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 markdown-it-py = ">=3.0,<4.0"
 mdit-py-plugins = ">=0.4,<1.0"
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 ]
 
 [package.dependencies]
@@ -1034,13 +1078,13 @@ jwt = ["authlib"]
 
 [[package]]
 name = "packaging"
-version = "23.2"
+version = "24.1"
 description = "Core utilities for Python packages"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
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+    {file = "packaging-24.1-py3-none-any.whl", hash = "sha256:5b8f2217dbdbd2f7f384c41c628544e6d52f2d0f53c6d0c3ea61aa5d1d7ff124"},
+    {file = "packaging-24.1.tar.gz", hash = "sha256:026ed72c8ed3fcce5bf8950572258698927fd1dbda10a5e981cdf0ac37f4f002"},
 ]
 
 [[package]]
@@ -1056,51 +1100,70 @@ files = [
 
 [[package]]
 name = "pip-licenses"
-version = "3.5.5"
+version = "4.5.1"
 description = "Dump the software license list of Python packages installed with pip."
 optional = false
-python-versions = "~=3.7"
+python-versions = "~=3.8"
 files = [
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 ]
 
 [package.dependencies]
-PTable = "*"
+prettytable = ">=2.3.0"
+tomli = ">=2"
 
 [package.extras]
-test = ["docutils", "pytest-cov", "pytest-pycodestyle", "pytest-runner"]
+test = ["docutils", "mypy", "pytest-cov", "pytest-pycodestyle", "pytest-runner", "tomli-w"]
 
 [[package]]
 name = "platformdirs"
-version = "4.1.0"
-description = "A small Python package for determining appropriate platform-specific dirs, e.g. a \"user data dir\"."
+version = "4.2.2"
+description = "A small Python package for determining appropriate platform-specific dirs, e.g. a `user data dir`."
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "platformdirs-4.1.0-py3-none-any.whl", hash = "sha256:11c8f37bcca40db96d8144522d925583bdb7a31f7b0e37e3ed4318400a8e2380"},
-    {file = "platformdirs-4.1.0.tar.gz", hash = "sha256:906d548203468492d432bcb294d4bc2fff751bf84971fbb2c10918cc206ee420"},
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 ]
 
 [package.extras]
-docs = ["furo (>=2023.7.26)", "proselint (>=0.13)", "sphinx (>=7.1.1)", "sphinx-autodoc-typehints (>=1.24)"]
-test = ["appdirs (==1.4.4)", "covdefaults (>=2.3)", "pytest (>=7.4)", "pytest-cov (>=4.1)", "pytest-mock (>=3.11.1)"]
+docs = ["furo (>=2023.9.10)", "proselint (>=0.13)", "sphinx (>=7.2.6)", "sphinx-autodoc-typehints (>=1.25.2)"]
+test = ["appdirs (==1.4.4)", "covdefaults (>=2.3)", "pytest (>=7.4.3)", "pytest-cov (>=4.1)", "pytest-mock (>=3.12)"]
+type = ["mypy (>=1.8)"]
 
 [[package]]
 name = "pluggy"
-version = "1.3.0"
+version = "1.5.0"
 description = "plugin and hook calling mechanisms for python"
 optional = false
 python-versions = ">=3.8"
 files = [
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+    {file = "pluggy-1.5.0-py3-none-any.whl", hash = "sha256:44e1ad92c8ca002de6377e165f3e0f1be63266ab4d554740532335b9d75ea669"},
+    {file = "pluggy-1.5.0.tar.gz", hash = "sha256:2cffa88e94fdc978c4c574f15f9e59b7f4201d439195c3715ca9e2486f1d0cf1"},
 ]
 
 [package.extras]
 dev = ["pre-commit", "tox"]
 testing = ["pytest", "pytest-benchmark"]
 
+[[package]]
+name = "prettytable"
+version = "3.10.2"
+description = "A simple Python library for easily displaying tabular data in a visually appealing ASCII table format"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "prettytable-3.10.2-py3-none-any.whl", hash = "sha256:1cbfdeb4bcc73976a778a0fb33cb6d752e75396f16574dcb3e2d6332fd93c76a"},
+    {file = "prettytable-3.10.2.tar.gz", hash = "sha256:29ec6c34260191d42cd4928c28d56adec360ac2b1208a26c7e4f14b90cc8bc84"},
+]
+
+[package.dependencies]
+wcwidth = "*"
+
+[package.extras]
+tests = ["pytest", "pytest-cov", "pytest-lazy-fixtures"]
+
 [[package]]
 name = "psycopg2"
 version = "2.9.9"
@@ -1123,47 +1186,26 @@ files = [
     {file = "psycopg2-2.9.9.tar.gz", hash = "sha256:d1454bde93fb1e224166811694d600e746430c006fbb031ea06ecc2ea41bf156"},
 ]
 
-[[package]]
-name = "ptable"
-version = "0.9.2"
-description = "A simple Python library for easily displaying tabular data in a visually appealing ASCII table format"
-optional = false
-python-versions = "*"
-files = [
-    {file = "PTable-0.9.2.tar.gz", hash = "sha256:aa7fc151cb40f2dabcd2275ba6f7fd0ff8577a86be3365cd3fb297cbe09cc292"},
-]
-
-[[package]]
-name = "py"
-version = "1.11.0"
-description = "library with cross-python path, ini-parsing, io, code, log facilities"
-optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
-files = [
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-]
-
 [[package]]
 name = "pycodestyle"
-version = "2.7.0"
+version = "2.12.0"
 description = "Python style guide checker"
 optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
+python-versions = ">=3.8"
 files = [
-    {file = "pycodestyle-2.7.0-py2.py3-none-any.whl", hash = "sha256:514f76d918fcc0b55c6680472f0a37970994e07bbb80725808c17089be302068"},
-    {file = "pycodestyle-2.7.0.tar.gz", hash = "sha256:c389c1d06bf7904078ca03399a4816f974a1d590090fecea0c63ec26ebaf1cef"},
+    {file = "pycodestyle-2.12.0-py2.py3-none-any.whl", hash = "sha256:949a39f6b86c3e1515ba1787c2022131d165a8ad271b11370a8819aa070269e4"},
+    {file = "pycodestyle-2.12.0.tar.gz", hash = "sha256:442f950141b4f43df752dd303511ffded3a04c2b6fb7f65980574f0c31e6e79c"},
 ]
 
 [[package]]
 name = "pycparser"
-version = "2.21"
+version = "2.22"
 description = "C parser in Python"
 optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
+python-versions = ">=3.8"
 files = [
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-    {file = "pycparser-2.21.tar.gz", hash = "sha256:e644fdec12f7872f86c58ff790da456218b10f863970249516d60a5eaca77206"},
+    {file = "pycparser-2.22-py3-none-any.whl", hash = "sha256:c3702b6d3dd8c7abc1afa565d7e63d53a1d0bd86cdc24edd75470f4de499cfcc"},
+    {file = "pycparser-2.22.tar.gz", hash = "sha256:491c8be9c040f5390f5bf44a5b07752bd07f56edf992381b05c701439eec10f6"},
 ]
 
 [[package]]
@@ -1185,28 +1227,27 @@ toml = ["tomli (>=1.2.3)"]
 
 [[package]]
 name = "pyflakes"
-version = "2.3.1"
+version = "3.2.0"
 description = "passive checker of Python programs"
 optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
+python-versions = ">=3.8"
 files = [
-    {file = "pyflakes-2.3.1-py2.py3-none-any.whl", hash = "sha256:7893783d01b8a89811dd72d7dfd4d84ff098e5eed95cfa8905b22bbffe52efc3"},
-    {file = "pyflakes-2.3.1.tar.gz", hash = "sha256:f5bc8ecabc05bb9d291eb5203d6810b49040f6ff446a756326104746cc00c1db"},
+    {file = "pyflakes-3.2.0-py2.py3-none-any.whl", hash = "sha256:84b5be138a2dfbb40689ca07e2152deb896a65c3a3e24c251c5c62489568074a"},
+    {file = "pyflakes-3.2.0.tar.gz", hash = "sha256:1c61603ff154621fb2a9172037d84dca3500def8c8b630657d1701f026f8af3f"},
 ]
 
 [[package]]
 name = "pygments"
-version = "2.17.2"
+version = "2.18.0"
 description = "Pygments is a syntax highlighting package written in Python."
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "pygments-2.17.2-py3-none-any.whl", hash = "sha256:b27c2826c47d0f3219f29554824c30c5e8945175d888647acd804ddd04af846c"},
-    {file = "pygments-2.17.2.tar.gz", hash = "sha256:da46cec9fd2de5be3a8a784f434e4c4ab670b4ff54d605c4c2717e9d49c4c367"},
+    {file = "pygments-2.18.0-py3-none-any.whl", hash = "sha256:b8e6aca0523f3ab76fee51799c488e38782ac06eafcf95e7ba832985c8e7b13a"},
+    {file = "pygments-2.18.0.tar.gz", hash = "sha256:786ff802f32e91311bff3889f6e9a86e81505fe99f2735bb6d60ae0c5004f199"},
 ]
 
 [package.extras]
-plugins = ["importlib-metadata"]
 windows-terminal = ["colorama (>=0.4.6)"]
 
 [[package]]
@@ -1228,93 +1269,50 @@ tests = ["coverage[toml] (==5.0.4)", "pytest (>=6.0.0,<7.0.0)"]
 
 [[package]]
 name = "pymysql"
-version = "1.1.0"
+version = "1.1.1"
 description = "Pure Python MySQL Driver"
 optional = true
 python-versions = ">=3.7"
 files = [
-    {file = "PyMySQL-1.1.0-py3-none-any.whl", hash = "sha256:8969ec6d763c856f7073c4c64662882675702efcb114b4bcbb955aea3a069fa7"},
-    {file = "PyMySQL-1.1.0.tar.gz", hash = "sha256:4f13a7df8bf36a51e81dd9f3605fede45a4878fe02f9236349fd82a3f0612f96"},
+    {file = "PyMySQL-1.1.1-py3-none-any.whl", hash = "sha256:4de15da4c61dc132f4fb9ab763063e693d521a80fd0e87943b9a453dd4c19d6c"},
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 [package.extras]
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 [package.extras]
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 ]
 
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 description = "Python HTTP for Humans."
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 ]
 
 [package.dependencies]
@@ -1402,21 +1426,113 @@ socks = ["PySocks (>=1.5.6,!=1.5.7)"]
 use-chardet-on-py3 = ["chardet (>=3.0.2,<6)"]
 
 [[package]]
-name = "setuptools"
-version = "69.0.3"
-description = "Easily download, build, install, upgrade, and uninstall Python packages"
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+version = "0.19.0"
+description = "Python bindings to Rust's persistent data structures (rpds)"
 optional = false
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-[package.extras]
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-
 [[package]]
 name = "six"
 version = "1.16.0"
@@ -1441,68 +1557,69 @@ files = [
 
 [[package]]
 name = "sphinx"
-version = "6.2.1"
+version = "7.4.7"
 description = "Python documentation generator"
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.9"
 files = [
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 [package.dependencies]
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-docutils = ">=0.18.1,<0.20"
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+docutils = ">=0.20,<0.22"
 imagesize = ">=1.3"
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-packaging = ">=21.0"
-Pygments = ">=2.13"
-requests = ">=2.25.0"
-snowballstemmer = ">=2.0"
+Jinja2 = ">=3.1"
+packaging = ">=23.0"
+Pygments = ">=2.17"
+requests = ">=2.30.0"
+snowballstemmer = ">=2.2"
 sphinxcontrib-applehelp = "*"
 sphinxcontrib-devhelp = "*"
 sphinxcontrib-htmlhelp = ">=2.0.0"
 sphinxcontrib-jsmath = "*"
 sphinxcontrib-qthelp = "*"
-sphinxcontrib-serializinghtml = ">=1.1.5"
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 [package.extras]
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-test = ["cython", "filelock", "html5lib", "pytest (>=4.6)"]
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+test = ["cython (>=3.0)", "defusedxml (>=0.7.1)", "pytest (>=8.0)", "setuptools (>=70.0)", "typing_extensions (>=4.9)"]
 
 [[package]]
 name = "sphinx-click"
-version = "4.4.0"
+version = "6.0.0"
 description = "Sphinx extension that automatically documents click applications"
 optional = false
-python-versions = ">=3.7"
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 files = [
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 [package.dependencies]
-click = ">=7.0"
+click = ">=8.0"
 docutils = "*"
-sphinx = ">=2.0"
+sphinx = ">=4.0"
 
 [[package]]
 name = "sphinx-rtd-theme"
-version = "1.3.0"
+version = "2.0.0"
 description = "Read the Docs theme for Sphinx"
 optional = false
-python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,>=2.7"
+python-versions = ">=3.6"
 files = [
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 [package.dependencies]
-docutils = "<0.19"
-sphinx = ">=1.6,<8"
+docutils = "<0.21"
+sphinx = ">=5,<8"
 sphinxcontrib-jquery = ">=4,<5"
 
 [package.extras]
@@ -1510,56 +1627,50 @@ dev = ["bump2version", "sphinxcontrib-httpdomain", "transifex-client", "wheel"]
 
 [[package]]
 name = "sphinxcontrib-applehelp"
-version = "1.0.7"
+version = "1.0.8"
 description = "sphinxcontrib-applehelp is a Sphinx extension which outputs Apple help books"
 optional = false
 python-versions = ">=3.9"
 files = [
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-[package.dependencies]
-Sphinx = ">=5"
-
 [package.extras]
 lint = ["docutils-stubs", "flake8", "mypy"]
+standalone = ["Sphinx (>=5)"]
 test = ["pytest"]
 
 [[package]]
 name = "sphinxcontrib-devhelp"
-version = "1.0.5"
+version = "1.0.6"
 description = "sphinxcontrib-devhelp is a sphinx extension which outputs Devhelp documents"
 optional = false
 python-versions = ">=3.9"
 files = [
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 ]
 
-[package.dependencies]
-Sphinx = ">=5"
-
 [package.extras]
 lint = ["docutils-stubs", "flake8", "mypy"]
+standalone = ["Sphinx (>=5)"]
 test = ["pytest"]
 
 [[package]]
 name = "sphinxcontrib-htmlhelp"
-version = "2.0.4"
+version = "2.0.6"
 description = "sphinxcontrib-htmlhelp is a sphinx extension which renders HTML help files"
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 python-versions = ">=3.9"
 files = [
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-[package.dependencies]
-Sphinx = ">=5"
-
 [package.extras]
 lint = ["docutils-stubs", "flake8", "mypy"]
+standalone = ["Sphinx (>=5)"]
 test = ["html5lib", "pytest"]
 
 [[package]]
@@ -1592,21 +1703,19 @@ test = ["flake8", "mypy", "pytest"]
 
 [[package]]
 name = "sphinxcontrib-qthelp"
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+version = "1.0.8"
 description = "sphinxcontrib-qthelp is a sphinx extension which outputs QtHelp documents"
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 python-versions = ">=3.9"
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-[package.dependencies]
-Sphinx = ">=5"
-
 [package.extras]
 lint = ["docutils-stubs", "flake8", "mypy"]
-test = ["pytest"]
+standalone = ["Sphinx (>=5)"]
+test = ["defusedxml (>=0.7.1)", "pytest"]
 
 [[package]]
 name = "sphinxcontrib-redoc"
@@ -1627,91 +1736,107 @@ sphinx = ">=1.5"
 
 [[package]]
 name = "sphinxcontrib-serializinghtml"
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 description = "sphinxcontrib-serializinghtml is a sphinx extension which outputs \"serialized\" HTML files (json and pickle)"
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 python-versions = ">=3.9"
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-[package.dependencies]
-Sphinx = ">=5"
-
 [package.extras]
 lint = ["docutils-stubs", "flake8", "mypy"]
+standalone = ["Sphinx (>=5)"]
 test = ["pytest"]
 
 [[package]]
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 description = "Database Abstraction Library"
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+typing-extensions = ">=4.6.0"
 
 [package.extras]
 aiomysql = ["aiomysql (>=0.2.0)", "greenlet (!=0.4.17)"]
+aioodbc = ["aioodbc", "greenlet (!=0.4.17)"]
 aiosqlite = ["aiosqlite", "greenlet (!=0.4.17)", "typing_extensions (!=3.10.0.1)"]
 asyncio = ["greenlet (!=0.4.17)"]
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-mariadb-connector = ["mariadb (>=1.0.1,!=1.1.2)"]
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+mariadb-connector = ["mariadb (>=1.0.1,!=1.1.2,!=1.1.5)"]
 mssql = ["pyodbc"]
 mssql-pymssql = ["pymssql"]
 mssql-pyodbc = ["pyodbc"]
-mypy = ["mypy (>=0.910)", "sqlalchemy2-stubs"]
-mysql = ["mysqlclient (>=1.4.0)", "mysqlclient (>=1.4.0,<2)"]
+mypy = ["mypy (>=0.910)"]
+mysql = ["mysqlclient (>=1.4.0)"]
 mysql-connector = ["mysql-connector-python"]
-oracle = ["cx_oracle (>=7)", "cx_oracle (>=7,<8)"]
+oracle = ["cx_oracle (>=8)"]
+oracle-oracledb = ["oracledb (>=1.0.1)"]
 postgresql = ["psycopg2 (>=2.7)"]
 postgresql-asyncpg = ["asyncpg", "greenlet (!=0.4.17)"]
-postgresql-pg8000 = ["pg8000 (>=1.16.6,!=1.29.0)"]
+postgresql-pg8000 = ["pg8000 (>=1.29.1)"]
+postgresql-psycopg = ["psycopg (>=3.0.7)"]
 postgresql-psycopg2binary = ["psycopg2-binary"]
 postgresql-psycopg2cffi = ["psycopg2cffi"]
-pymysql = ["pymysql", "pymysql (<1)"]
+postgresql-psycopgbinary = ["psycopg[binary] (>=3.0.7)"]
+pymysql = ["pymysql"]
 sqlcipher = ["sqlcipher3_binary"]
 
-[[package]]
-name = "toml"
-version = "0.10.2"
-description = "Python Library for Tom's Obvious, Minimal Language"
-optional = false
-python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*"
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-
 [[package]]
 name = "tomli"
 version = "2.0.1"
@@ -1725,31 +1850,43 @@ files = [
 
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+version = "4.12.2"
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 ]
 
 [[package]]
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-version = "2.1.0"
+version = "2.2.2"
 description = "HTTP library with thread-safe connection pooling, file post, and more."
 optional = false
 python-versions = ">=3.8"
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 ]
 
 [package.extras]
 brotli = ["brotli (>=1.0.9)", "brotlicffi (>=0.8.0)"]
+h2 = ["h2 (>=4,<5)"]
 socks = ["pysocks (>=1.5.6,!=1.5.7,<2.0)"]
 zstd = ["zstandard (>=0.18.0)"]
 
+[[package]]
+name = "wcwidth"
+version = "0.2.13"
+description = "Measures the displayed width of unicode strings in a terminal"
+optional = false
+python-versions = "*"
+files = [
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+]
+
 [[package]]
 name = "webargs"
 version = "8.4.0"
@@ -1774,13 +1911,13 @@ tests = ["Django (>=2.2.0)", "Flask (>=0.12.5)", "aiohttp (>=3.0.8)", "bottle (>
 
 [[package]]
 name = "werkzeug"
-version = "2.3.8"
+version = "3.0.1"
 description = "The comprehensive WSGI web application library."
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "werkzeug-2.3.8-py3-none-any.whl", hash = "sha256:bba1f19f8ec89d4d607a3bd62f1904bd2e609472d93cd85e9d4e178f472c3748"},
-    {file = "werkzeug-2.3.8.tar.gz", hash = "sha256:554b257c74bbeb7a0d254160a4f8ffe185243f52a52035060b761ca62d977f03"},
+    {file = "werkzeug-3.0.1-py3-none-any.whl", hash = "sha256:90a285dc0e42ad56b34e696398b8122ee4c681833fb35b8334a095d82c56da10"},
+    {file = "werkzeug-3.0.1.tar.gz", hash = "sha256:507e811ecea72b18a404947aded4b3390e1db8f826b494d76550ef45bb3b1dcc"},
 ]
 
 [package.dependencies]
@@ -1796,4 +1933,4 @@ pymysql = ["PyMySQL"]
 [metadata]
 lock-version = "2.0"
 python-versions = "^3.10"
-content-hash = "6baf20773f3c4dbe2c313217230660174184a9b5c374197e8934425cfd91deef"
+content-hash = "08e5fe91bda8f623c9270a733539d03a582de54b09c2b99ce8401e125c813d85"
diff --git a/pyproject.toml b/pyproject.toml
index cdd7d31..4feddeb 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -8,36 +8,38 @@ readme = "README.md"
 
 [tool.poetry.dependencies]
 python = "^3.10"
-flask = { extras = ["dotenv"], version = "^2.0.0" }
-invoke = "^2.0.0"
-Flask-JWT-Extended = "^4.0.0"
-Flask-Cors = "^3.0.10"
-Flask-SQLAlchemy = "^2.5.1"
-SQLAlchemy = "^1.4.40"
-Flask-Migrate = "^3.0.0"
-flask-babel = "^2.0.0"
-flask-smorest = "^0.39.0"
-Flask-Static-Digest = "^0.2.1"
-flask-oso = "^0.26.0"
+flask = { extras = ["dotenv"], version = "^3.0.0" }
+invoke = "^2.2.0"
+Flask-JWT-Extended = "^4.6.0"
+Flask-Cors = "^4.0.0"
+Flask-SQLAlchemy = "^3.1.1"
+SQLAlchemy = "^2.0.23"
+Flask-Login = "^0.6.3"
+Flask-Migrate = "^4.0.5"
+flask-babel = "^4.0.0"
+flask-smorest = "^0.44.0"
+Flask-Static-Digest = "^0.4.1"
+oso = "^0.27.3"
 tomli = "^2.0.0"
 marshmallow-jsonschema = "^0.13.0"
-jsonschema = "3.2.0"
-bcrypt = "^3.2.0"
-psycopg2 = { version = "^2.9.3", optional = true }
-PyMySQL = { version = "^1.0.2", optional = true }
+jsonschema = "4.23.0"
+bcrypt = "^4.0.0"
+werkzeug = "3.0.1"
+psycopg2 = { version = "^2.9.9", optional = true }
+PyMySQL = { version = "^1.1.1", optional = true }
 
-[tool.poetry.dev-dependencies]
-black = "^23.1.0"
-flake8 = "^3.9.2"
-pytest = "^6.2.4"
-flake8-docstrings = "^1.6.0"
-flake8-bugbear = "^21.4.3"
-Sphinx = "^6.0.0"
+[tool.poetry.group.dev.dependencies]
+black = "^24.4.2"
+flake8 = "^7.1.0"
+pytest = "^8.3.1"
+flake8-docstrings = "^1.7.0"
+flake8-bugbear = "^24.4.26"
+Sphinx = "^7.4.7"
 sphinxcontrib-redoc = "^1.6.0"
-sphinx-click = "^4.4.0"
-myst-parser = "^2.0.0"
-sphinx-rtd-theme = "^1.2.2"
-pip-licenses = "^3.5.3"
+sphinx-click = "^6.0.0"
+myst-parser = "^3.0.1"
+sphinx-rtd-theme = "^2.0.0"
+pip-licenses = "^4.5.1"
 
 [tool.poetry.extras]
 psycopg2 = ["psycopg2"]

From ae9a5359790e57a72127000d293582b158145e85 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Fabian=20B=C3=BChler?=
 <fabian.buehler@iaas.uni-stuttgart.de>
Date: Tue, 23 Jul 2024 16:38:57 +0200
Subject: [PATCH 02/14] Fix using of non timezone aware datetime object for
 timezone aware db columns

The DB column change may require a migration!
---
 muse_for_anything/api/v1_api/namespace.py     |  4 ++--
 .../api/v1_api/ontology_objects.py            |  4 ++--
 .../api/v1_api/ontology_types.py              |  4 ++--
 muse_for_anything/api/v1_api/taxonomy.py      |  4 ++--
 .../api/v1_api/taxonomy_items.py              |  6 ++---
 muse_for_anything/db/models/model_helpers.py  | 23 +++++++++++++++----
 6 files changed, 29 insertions(+), 16 deletions(-)

diff --git a/muse_for_anything/api/v1_api/namespace.py b/muse_for_anything/api/v1_api/namespace.py
index f5821de..2a69840 100644
--- a/muse_for_anything/api/v1_api/namespace.py
+++ b/muse_for_anything/api/v1_api/namespace.py
@@ -1,6 +1,6 @@
 """Module containing the namespace API endpoints of the v1 API."""
 
-from datetime import datetime
+from datetime import datetime, timezone
 from http import HTTPStatus
 from typing import Any, List, Optional
 
@@ -396,7 +396,7 @@ def delete(self, namespace: str):
         # only actually delete when not already deleted
         if found_namespace.deleted_on is None:
             # soft delete namespace
-            found_namespace.deleted_on = datetime.utcnow()
+            found_namespace.deleted_on = datetime.now(timezone.utc)
             DB.session.add(found_namespace)
             DB.session.commit()
 
diff --git a/muse_for_anything/api/v1_api/ontology_objects.py b/muse_for_anything/api/v1_api/ontology_objects.py
index 2f9b60e..04f77bb 100644
--- a/muse_for_anything/api/v1_api/ontology_objects.py
+++ b/muse_for_anything/api/v1_api/ontology_objects.py
@@ -1,6 +1,6 @@
 """Module containing the object API endpoints of the v1 API."""
 
-from datetime import datetime
+from datetime import datetime, timezone
 from http import HTTPStatus
 from typing import Any, List, Optional
 
@@ -651,7 +651,7 @@ def delete(self, namespace: str, object_id: str):
         # only actually delete when not already deleted
         if found_object.deleted_on is None:
             # soft delete object
-            found_object.deleted_on = datetime.utcnow()
+            found_object.deleted_on = datetime.now(timezone.utc)
             # TODO soft delete komposition objects (also implement undelete…)
             DB.session.add(found_object)
             DB.session.commit()
diff --git a/muse_for_anything/api/v1_api/ontology_types.py b/muse_for_anything/api/v1_api/ontology_types.py
index ef873e1..ece023f 100644
--- a/muse_for_anything/api/v1_api/ontology_types.py
+++ b/muse_for_anything/api/v1_api/ontology_types.py
@@ -1,6 +1,6 @@
 """Module containing the type API endpoints of the v1 API."""
 
-from datetime import datetime
+from datetime import datetime, timezone
 from http import HTTPStatus
 from typing import Any, List, Optional
 
@@ -513,7 +513,7 @@ def delete(self, namespace: str, object_type: str):
         # only actually delete when not already deleted
         if found_object_type.deleted_on is None:
             # soft delete namespace
-            found_object_type.deleted_on = datetime.utcnow()
+            found_object_type.deleted_on = datetime.now(timezone.utc)
             DB.session.add(found_object_type)
             DB.session.commit()
 
diff --git a/muse_for_anything/api/v1_api/taxonomy.py b/muse_for_anything/api/v1_api/taxonomy.py
index efe6042..51f00fe 100644
--- a/muse_for_anything/api/v1_api/taxonomy.py
+++ b/muse_for_anything/api/v1_api/taxonomy.py
@@ -1,6 +1,6 @@
 """Module containing the taxonomy API endpoints of the v1 API."""
 
-from datetime import datetime
+from datetime import datetime, timezone
 from http import HTTPStatus
 from typing import Any, List, Optional
 
@@ -498,7 +498,7 @@ def delete(self, namespace: str, taxonomy: str):
         # only actually delete when not already deleted
         if found_taxonomy.deleted_on is None:
             # soft delete namespace
-            found_taxonomy.deleted_on = datetime.utcnow()
+            found_taxonomy.deleted_on = datetime.now(timezone.utc)
             DB.session.add(found_taxonomy)
             DB.session.commit()
 
diff --git a/muse_for_anything/api/v1_api/taxonomy_items.py b/muse_for_anything/api/v1_api/taxonomy_items.py
index dc24257..629b21b 100644
--- a/muse_for_anything/api/v1_api/taxonomy_items.py
+++ b/muse_for_anything/api/v1_api/taxonomy_items.py
@@ -1,6 +1,6 @@
 """Module containing the taxonomy items API endpoints of the v1 API."""
 
-from datetime import datetime
+from datetime import datetime, timezone
 from http import HTTPStatus
 from typing import Any, Dict, List, Optional, Sequence, Tuple, cast
 
@@ -423,7 +423,7 @@ def delete(self, namespace: str, taxonomy: str, taxonomy_item: str):  # restore
         # only actually delete when not already deleted
         if found_taxonomy_item.deleted_on is None:
             # delete taxonomy item
-            deleted_timestamp = datetime.utcnow()
+            deleted_timestamp = datetime.now(timezone.utc)
             found_taxonomy_item.deleted_on = deleted_timestamp
             # also delete incoming and outgoing relations to remove them
             # from relations of existing items
@@ -913,7 +913,7 @@ def delete(
         # only actually delete when not already deleted
         if found_relation.deleted_on is None:
             # delete taxonomy item relation
-            found_relation.deleted_on = datetime.utcnow()
+            found_relation.deleted_on = datetime.now(timezone.utc)
             DB.session.add(found_relation)
             DB.session.commit()
 
diff --git a/muse_for_anything/db/models/model_helpers.py b/muse_for_anything/db/models/model_helpers.py
index b8c8cfb..64fe18c 100644
--- a/muse_for_anything/db/models/model_helpers.py
+++ b/muse_for_anything/db/models/model_helpers.py
@@ -1,4 +1,4 @@
-from datetime import datetime
+from datetime import datetime, timezone
 from typing import Any, Sequence
 from sqlalchemy import DateTime
 from sqlalchemy.sql.elements import literal
@@ -33,21 +33,29 @@ class IdMixin:
 class NameDescriptionMixin:
     """Add a 'name' and 'description' column to the table."""
 
-    name: Mapped[str] = mapped_column(DB.Unicode, nullable=False, index=True, info={"collate": "NOCASE"})
+    name: Mapped[str] = mapped_column(
+        DB.Unicode, nullable=False, index=True, info={"collate": "NOCASE"}
+    )
     description: Mapped[str] = mapped_column(DB.UnicodeText, nullable=True, index=True)
 
 
 class UniqueNameDescriptionMixin:
     """Add a 'name' (with a unique constraint) and 'description' column to the table."""
 
-    name: Mapped[str] = mapped_column(DB.Unicode, nullable=False, unique=True, index=True, info={"collate": "NOCASE"})
+    name: Mapped[str] = mapped_column(
+        DB.Unicode, nullable=False, unique=True, index=True, info={"collate": "NOCASE"}
+    )
     description: Mapped[str] = mapped_column(DB.UnicodeText, nullable=True, index=True)
 
 
 class CreateDeleteMixin:
     """Add the columns 'created_on' and 'deleted_on' to track creation and deletion of immutable database entries."""
 
-    created_on: Mapped[datetime] = mapped_column(DateTime(timezone=True), default=datetime.utcnow, nullable=False)
+    created_on: Mapped[datetime] = mapped_column(
+        DateTime(timezone=True),
+        default_factory=lambda: datetime.now(timezone.utc),
+        nullable=False,
+    )
     deleted_on: Mapped[datetime] = mapped_column(DateTime(timezone=True), nullable=True)
 
     @property
@@ -58,7 +66,12 @@ def is_deleted(self) -> bool:
 class ChangesMixin(CreateDeleteMixin):
     """Add the columns 'created_on', 'updated_on' and 'deleted_on' to track changes to the database entries."""
 
-    updated_on: Mapped[datetime] = mapped_column(DateTime(timezone=True), default=datetime.utcnow, onupdate=datetime.utcnow, nullable=False)
+    updated_on: Mapped[datetime] = mapped_column(
+        DateTime(timezone=True),
+        default_factory=lambda: datetime.now(timezone.utc),
+        onupdate=lambda: datetime.now(timezone.utc),
+        nullable=False,
+    )
 
 
 __all__ = list(get_all_classes_of_module(__name__))

From 4ab6fe61123dd4c6767f2d64b864407492e4a1e1 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Fabian=20B=C3=BChler?=
 <fabian.buehler@iaas.uni-stuttgart.de>
Date: Tue, 23 Jul 2024 16:40:54 +0200
Subject: [PATCH 03/14] Format with current black version

---
 muse_for_anything/api/util.py                 |  1 +
 .../api/v1_api/generators/namespace.py        |  4 +-
 .../api/v1_api/generators/object.py           |  4 +-
 .../api/v1_api/generators/object_version.py   |  8 +-
 .../api/v1_api/generators/taxonomy.py         |  4 +-
 .../api/v1_api/generators/taxonomy_item.py    |  4 +-
 .../generators/taxonomy_item_relation.py      |  4 +-
 .../generators/taxonomy_item_version.py       |  4 +-
 .../api/v1_api/generators/user_management.py  |  8 +-
 .../api/v1_api/models/ontology.py             | 32 ++++++--
 .../api/v1_api/ontology_object_validation.py  | 12 +--
 .../api/v1_api/ontology_type_validation.py    | 12 +--
 .../api/v1_api/request_helpers.py             |  4 +-
 muse_for_anything/api/v1_api/root.py          |  9 ++-
 muse_for_anything/api/v1_api/schema.py        | 10 +--
 muse_for_anything/db/__init__.py              |  6 +-
 .../db/models/object_relation_tables.py       | 42 ++++++++---
 .../db/models/ontology_objects.py             | 74 ++++++++++++-------
 muse_for_anything/db/models/taxonomies.py     | 30 +++++---
 muse_for_anything/oso_helpers.py              | 51 +++++++------
 muse_for_anything/password_helpers.py         | 20 ++---
 muse_for_anything/util/config/__init__.py     |  1 +
 muse_for_anything/util/debug_routes/routes.py |  1 -
 23 files changed, 218 insertions(+), 127 deletions(-)

diff --git a/muse_for_anything/api/util.py b/muse_for_anything/api/util.py
index 3f48866..1cb6875 100644
--- a/muse_for_anything/api/util.py
+++ b/muse_for_anything/api/util.py
@@ -1,4 +1,5 @@
 """Module containing utilities for flask smorest APIs."""
+
 from typing import Any, Dict
 from flask import url_for
 from flask_smorest import Blueprint
diff --git a/muse_for_anything/api/v1_api/generators/namespace.py b/muse_for_anything/api/v1_api/generators/namespace.py
index 643642f..53aec04 100644
--- a/muse_for_anything/api/v1_api/generators/namespace.py
+++ b/muse_for_anything/api/v1_api/generators/namespace.py
@@ -335,7 +335,9 @@ def generate_api_object(
             return
 
         return NamespaceData(
-            self=LinkGenerator.get_link_of(resource, query_params=query_params, ignore_deleted=True),
+            self=LinkGenerator.get_link_of(
+                resource, query_params=query_params, ignore_deleted=True
+            ),
             name=resource.name,
             description=resource.description,
             created_on=resource.created_on,
diff --git a/muse_for_anything/api/v1_api/generators/object.py b/muse_for_anything/api/v1_api/generators/object.py
index 38e39c3..7507620 100644
--- a/muse_for_anything/api/v1_api/generators/object.py
+++ b/muse_for_anything/api/v1_api/generators/object.py
@@ -248,7 +248,9 @@ def generate_api_object(
             return
 
         return ObjectData(
-            self=LinkGenerator.get_link_of(resource, query_params=query_params, ignore_deleted=True),
+            self=LinkGenerator.get_link_of(
+                resource, query_params=query_params, ignore_deleted=True
+            ),
             name=resource.name,
             description=resource.description,
             created_on=resource.created_on,
diff --git a/muse_for_anything/api/v1_api/generators/object_version.py b/muse_for_anything/api/v1_api/generators/object_version.py
index 12264d9..dcd0ccf 100644
--- a/muse_for_anything/api/v1_api/generators/object_version.py
+++ b/muse_for_anything/api/v1_api/generators/object_version.py
@@ -158,9 +158,7 @@ def update_key(
         return key
 
 
-class ObjectVersionSelfLinkGenerator(
-    LinkGenerator, resource_type=OntologyObjectVersion
-):
+class ObjectVersionSelfLinkGenerator(LinkGenerator, resource_type=OntologyObjectVersion):
     def generate_link(
         self,
         resource: OntologyObjectVersion,
@@ -199,7 +197,9 @@ def generate_api_object(
             return
 
         return ObjectData(
-            self=LinkGenerator.get_link_of(resource, query_params=query_params, ignore_deleted=True),
+            self=LinkGenerator.get_link_of(
+                resource, query_params=query_params, ignore_deleted=True
+            ),
             name=resource.name,
             description=resource.description,
             created_on=resource.created_on,
diff --git a/muse_for_anything/api/v1_api/generators/taxonomy.py b/muse_for_anything/api/v1_api/generators/taxonomy.py
index e288f1b..aaad29b 100644
--- a/muse_for_anything/api/v1_api/generators/taxonomy.py
+++ b/muse_for_anything/api/v1_api/generators/taxonomy.py
@@ -194,7 +194,9 @@ def generate_api_object(
             return
 
         return TaxonomyData(
-            self=LinkGenerator.get_link_of(resource, query_params=query_params, ignore_deleted=True),
+            self=LinkGenerator.get_link_of(
+                resource, query_params=query_params, ignore_deleted=True
+            ),
             name=resource.name,
             description=resource.description,
             created_on=resource.created_on,
diff --git a/muse_for_anything/api/v1_api/generators/taxonomy_item.py b/muse_for_anything/api/v1_api/generators/taxonomy_item.py
index 32535f9..9beeb1b 100644
--- a/muse_for_anything/api/v1_api/generators/taxonomy_item.py
+++ b/muse_for_anything/api/v1_api/generators/taxonomy_item.py
@@ -447,7 +447,9 @@ def generate_api_object(
         ]
 
         return TaxonomyItemData(
-            self=LinkGenerator.get_link_of(resource, query_params=query_params, ignore_deleted=True),
+            self=LinkGenerator.get_link_of(
+                resource, query_params=query_params, ignore_deleted=True
+            ),
             name=resource.name,
             description=resource.description,
             sort_key=resource.sort_key,
diff --git a/muse_for_anything/api/v1_api/generators/taxonomy_item_relation.py b/muse_for_anything/api/v1_api/generators/taxonomy_item_relation.py
index 39afb20..66d872e 100644
--- a/muse_for_anything/api/v1_api/generators/taxonomy_item_relation.py
+++ b/muse_for_anything/api/v1_api/generators/taxonomy_item_relation.py
@@ -318,7 +318,9 @@ def generate_api_object(
             return
 
         return TaxonomyItemRelationData(
-            self=LinkGenerator.get_link_of(resource, query_params=query_params, ignore_deleted=True),
+            self=LinkGenerator.get_link_of(
+                resource, query_params=query_params, ignore_deleted=True
+            ),
             source_item=LinkGenerator.get_link_of(resource.taxonomy_item_source),
             target_item=LinkGenerator.get_link_of(resource.taxonomy_item_target),
             created_on=resource.created_on,
diff --git a/muse_for_anything/api/v1_api/generators/taxonomy_item_version.py b/muse_for_anything/api/v1_api/generators/taxonomy_item_version.py
index a37c657..f7ddf1b 100644
--- a/muse_for_anything/api/v1_api/generators/taxonomy_item_version.py
+++ b/muse_for_anything/api/v1_api/generators/taxonomy_item_version.py
@@ -282,7 +282,9 @@ def generate_api_object(
         ]
 
         return TaxonomyItemData(
-            self=LinkGenerator.get_link_of(resource, query_params=query_params, ignore_deleted=True),
+            self=LinkGenerator.get_link_of(
+                resource, query_params=query_params, ignore_deleted=True
+            ),
             name=resource.name,
             description=resource.description,
             sort_key=resource.sort_key,
diff --git a/muse_for_anything/api/v1_api/generators/user_management.py b/muse_for_anything/api/v1_api/generators/user_management.py
index 4211c73..98f9ec1 100644
--- a/muse_for_anything/api/v1_api/generators/user_management.py
+++ b/muse_for_anything/api/v1_api/generators/user_management.py
@@ -253,7 +253,9 @@ def generate_link(
             return
         link = LinkGenerator.get_link_of(CollectionResource(UserRole, resource=resource))
         link.rel = (CREATE_REL, POST_REL, REQUIRES_FRESH_LOGIN_REL)
-        link.schema = url_for(SCHEMA_RESOURCE, schema_id=USER_ROLE_POST_SCHEMA, _external=True)
+        link.schema = url_for(
+            SCHEMA_RESOURCE, schema_id=USER_ROLE_POST_SCHEMA, _external=True
+        )
         return link
 
 
@@ -271,7 +273,9 @@ def generate_api_object(
             return
 
         return UserData(
-            self=LinkGenerator.get_link_of(resource, query_params=query_params, ignore_deleted=True),
+            self=LinkGenerator.get_link_of(
+                resource, query_params=query_params, ignore_deleted=True
+            ),
             username=resource.username,
             e_mail=resource.e_mail,
         )
diff --git a/muse_for_anything/api/v1_api/models/ontology.py b/muse_for_anything/api/v1_api/models/ontology.py
index 591c4e6..412b482 100644
--- a/muse_for_anything/api/v1_api/models/ontology.py
+++ b/muse_for_anything/api/v1_api/models/ontology.py
@@ -48,7 +48,9 @@ class DeletedPageSchemaMixin:
     deleted = ma.fields.Boolean(required=False, allow_none=True, missing=False)
 
 
-class NamespacePageParamsSchema(SearchPageSchemaMixin, DeletedPageSchemaMixin, CursorPageArgumentsSchema):
+class NamespacePageParamsSchema(
+    SearchPageSchemaMixin, DeletedPageSchemaMixin, CursorPageArgumentsSchema
+):
     pass
 
 
@@ -128,11 +130,15 @@ class FileExportData(BaseApiObject):
     content_type: str = "application/xml"
 
 
-class ObjectTypePageParamsSchema(CursorPageArgumentsSchema, SearchPageSchemaMixin, DeletedPageSchemaMixin):
+class ObjectTypePageParamsSchema(
+    CursorPageArgumentsSchema, SearchPageSchemaMixin, DeletedPageSchemaMixin
+):
     pass
 
 
-class ObjectTypeVersionsPageParamsSchema(CursorPageArgumentsSchema, DeletedPageSchemaMixin):
+class ObjectTypeVersionsPageParamsSchema(
+    CursorPageArgumentsSchema, DeletedPageSchemaMixin
+):
     pass
 
 
@@ -171,15 +177,21 @@ class ObjectData(BaseApiObject, ChangesDataMixin, NameDescriptionMixin):
     data: Any
 
 
-class ObjectsCursorPageArgumentsSchema(CursorPageArgumentsSchema, DeletedPageSchemaMixin, SearchPageSchemaMixin):
+class ObjectsCursorPageArgumentsSchema(
+    CursorPageArgumentsSchema, DeletedPageSchemaMixin, SearchPageSchemaMixin
+):
     type_id = ma.fields.String(data_key="type-id", allow_none=True, load_only=True)
 
 
-class ObjectVersionsCursorPageArgumentsSchema(CursorPageArgumentsSchema, DeletedPageSchemaMixin):
+class ObjectVersionsCursorPageArgumentsSchema(
+    CursorPageArgumentsSchema, DeletedPageSchemaMixin
+):
     pass
 
 
-class TaxonomyPageParamsSchema(CursorPageArgumentsSchema, SearchPageSchemaMixin, DeletedPageSchemaMixin):
+class TaxonomyPageParamsSchema(
+    CursorPageArgumentsSchema, SearchPageSchemaMixin, DeletedPageSchemaMixin
+):
     pass
 
 
@@ -200,11 +212,15 @@ class TaxonomyData(BaseApiObject, ChangesDataMixin, NameDescriptionMixin):
     items: Sequence[ApiLink] = tuple()
 
 
-class TaxonomyItemPageParamsSchema(CursorPageArgumentsSchema, SearchPageSchemaMixin, DeletedPageSchemaMixin):
+class TaxonomyItemPageParamsSchema(
+    CursorPageArgumentsSchema, SearchPageSchemaMixin, DeletedPageSchemaMixin
+):
     pass
 
 
-class TaxonomyItemVersionsPageParamsSchema(CursorPageArgumentsSchema, DeletedPageSchemaMixin):
+class TaxonomyItemVersionsPageParamsSchema(
+    CursorPageArgumentsSchema, DeletedPageSchemaMixin
+):
     pass
 
 
diff --git a/muse_for_anything/api/v1_api/ontology_object_validation.py b/muse_for_anything/api/v1_api/ontology_object_validation.py
index 8e2be3f..2a587e7 100644
--- a/muse_for_anything/api/v1_api/ontology_object_validation.py
+++ b/muse_for_anything/api/v1_api/ontology_object_validation.py
@@ -62,12 +62,12 @@ def resolve_type_version_schema_url(url_string: str):
     version: str = params.get("version")
     if endpoint == "api-v1.TypeVersionView":
 
-        found_type_version: Optional[
-            OntologyObjectTypeVersion
-        ] = OntologyObjectTypeVersion.query.filter(
-            OntologyObjectTypeVersion.version == int(version),
-            OntologyObjectTypeVersion.object_type_id == int(object_type),
-        ).first()
+        found_type_version: Optional[OntologyObjectTypeVersion] = (
+            OntologyObjectTypeVersion.query.filter(
+                OntologyObjectTypeVersion.version == int(version),
+                OntologyObjectTypeVersion.object_type_id == int(object_type),
+            ).first()
+        )
 
         if found_type_version is None:
             raise DataVisitorException(f"Invalid schema ref! Schema '{url}' not found!")
diff --git a/muse_for_anything/api/v1_api/ontology_type_validation.py b/muse_for_anything/api/v1_api/ontology_type_validation.py
index 0c6afd0..5b34d21 100644
--- a/muse_for_anything/api/v1_api/ontology_type_validation.py
+++ b/muse_for_anything/api/v1_api/ontology_type_validation.py
@@ -211,12 +211,12 @@ def extract_type_reference(
                 namespace=namespace, object_type=object_type, version=version
             )
 
-            found_type_version: Optional[
-                OntologyObjectTypeVersion
-            ] = OntologyObjectTypeVersion.query.filter(
-                OntologyObjectTypeVersion.version == version_number,
-                OntologyObjectTypeVersion.object_type_id == object_type_id,
-            ).first()
+            found_type_version: Optional[OntologyObjectTypeVersion] = (
+                OntologyObjectTypeVersion.query.filter(
+                    OntologyObjectTypeVersion.version == version_number,
+                    OntologyObjectTypeVersion.object_type_id == object_type_id,
+                ).first()
+            )
 
             if (
                 found_type_version is None
diff --git a/muse_for_anything/api/v1_api/request_helpers.py b/muse_for_anything/api/v1_api/request_helpers.py
index a1bdf68..3c8e83b 100644
--- a/muse_for_anything/api/v1_api/request_helpers.py
+++ b/muse_for_anything/api/v1_api/request_helpers.py
@@ -293,7 +293,9 @@ def default_generate_api_object(
         query_params: Optional[Dict[str, str]] = None,
     ) -> Optional[BaseApiObject]:
         return BaseApiObject(
-            self=LinkGenerator.get_link_of(resource, query_params=query_params, ignore_deleted=True)
+            self=LinkGenerator.get_link_of(
+                resource, query_params=query_params, ignore_deleted=True
+            )
         )
 
     def generate_api_object(
diff --git a/muse_for_anything/api/v1_api/root.py b/muse_for_anything/api/v1_api/root.py
index 3177bc7..add3220 100644
--- a/muse_for_anything/api/v1_api/root.py
+++ b/muse_for_anything/api/v1_api/root.py
@@ -149,7 +149,14 @@ def get(self):
                     rel=("collection", "page"),
                     resource_type="ont-object",
                     key=("namespaceId",),
-                    query_key=("item-count", "cursor", "sort", "type-id", "search", "deleted"),
+                    query_key=(
+                        "item-count",
+                        "cursor",
+                        "sort",
+                        "type-id",
+                        "search",
+                        "deleted",
+                    ),
                 ),
                 KeyedApiLink(
                     href=template_url_for(
diff --git a/muse_for_anything/api/v1_api/schema.py b/muse_for_anything/api/v1_api/schema.py
index a8f5458..e3c4ef0 100644
--- a/muse_for_anything/api/v1_api/schema.py
+++ b/muse_for_anything/api/v1_api/schema.py
@@ -313,11 +313,11 @@ def _get_object_type_version(self, schema_id: str) -> OntologyObjectTypeVersion:
             )
 
         type_version_id = int(schema_id)
-        found_object_type_version: Optional[
-            OntologyObjectTypeVersion
-        ] = OntologyObjectTypeVersion.query.filter(
-            OntologyObjectTypeVersion.id == type_version_id
-        ).first()
+        found_object_type_version: Optional[OntologyObjectTypeVersion] = (
+            OntologyObjectTypeVersion.query.filter(
+                OntologyObjectTypeVersion.id == type_version_id
+            ).first()
+        )
 
         if found_object_type_version is None:
             abort(HTTPStatus.NOT_FOUND, message=gettext("Schema id not found."))
diff --git a/muse_for_anything/db/__init__.py b/muse_for_anything/db/__init__.py
index e997ade..8776d00 100644
--- a/muse_for_anything/db/__init__.py
+++ b/muse_for_anything/db/__init__.py
@@ -11,9 +11,9 @@
 def register_db(app: Flask):
     """Register the sqlalchemy db and alembic migrations with the flask app."""
     if not app.config.get("SQLALCHEMY_DATABASE_URI"):
-        app.config[
-            "SQLALCHEMY_DATABASE_URI"
-        ] = f"sqlite:///{app.instance_path}/{app.import_name}.db"
+        app.config["SQLALCHEMY_DATABASE_URI"] = (
+            f"sqlite:///{app.instance_path}/{app.import_name}.db"
+        )
 
     DB.init_app(app)
     app.logger.info(f'Connected to db "{app.config["SQLALCHEMY_DATABASE_URI"]}".')
diff --git a/muse_for_anything/db/models/object_relation_tables.py b/muse_for_anything/db/models/object_relation_tables.py
index 7431259..317b099 100644
--- a/muse_for_anything/db/models/object_relation_tables.py
+++ b/muse_for_anything/db/models/object_relation_tables.py
@@ -30,10 +30,14 @@ class OntologyTypeVersionToTypeVersion(MODEL, IdMixin):
     __tablename__ = "TypeVersionToTypeVersion"
 
     # the type version importing
-    type_version_source_id: Mapped[int] = mapped_column(ForeignKey("OntologyObjectTypeVersion.id"), nullable=False)
-    
+    type_version_source_id: Mapped[int] = mapped_column(
+        ForeignKey("OntologyObjectTypeVersion.id"), nullable=False
+    )
+
     # the imported type version
-    type_version_target_id: Mapped[int] = mapped_column(ForeignKey("OntologyObjectTypeVersion.id"), nullable=False)
+    type_version_target_id: Mapped[int] = mapped_column(
+        ForeignKey("OntologyObjectTypeVersion.id"), nullable=False
+    )
 
     # relationships
     type_version_source: Mapped[OntologyObjectTypeVersion] = relationship(
@@ -62,8 +66,12 @@ class OntologyTypeVersionToType(MODEL, IdMixin):
 
     __tablename__ = "TypeVersionToType"
 
-    type_version_source_id: Mapped[int] = mapped_column(ForeignKey("OntologyObjectTypeVersion.id"), nullable=False)
-    type_target_id: Mapped[int] = mapped_column(ForeignKey("OntologyObjectType.id"), nullable=False)
+    type_version_source_id: Mapped[int] = mapped_column(
+        ForeignKey("OntologyObjectTypeVersion.id"), nullable=False
+    )
+    type_target_id: Mapped[int] = mapped_column(
+        ForeignKey("OntologyObjectType.id"), nullable=False
+    )
 
     # relationships
     type_version_source: Mapped[OntologyObjectTypeVersion] = relationship(
@@ -92,8 +100,12 @@ class OntologyTypeVersionToTaxonomy(MODEL, IdMixin):
 
     __tablename__ = "TypeVersionToTaxonomy"
 
-    type_version_source_id: Mapped[int] = mapped_column(ForeignKey("OntologyObjectTypeVersion.id"), nullable=False)
-    taxonomy_target_id: Mapped[int] = mapped_column(ForeignKey("Taxonomy.id"), nullable=False)
+    type_version_source_id: Mapped[int] = mapped_column(
+        ForeignKey("OntologyObjectTypeVersion.id"), nullable=False
+    )
+    taxonomy_target_id: Mapped[int] = mapped_column(
+        ForeignKey("Taxonomy.id"), nullable=False
+    )
 
     # relationships
     type_version_source: Mapped[OntologyObjectTypeVersion] = relationship(
@@ -122,8 +134,12 @@ class OntologyObjectVersionToObject(MODEL, IdMixin):
 
     __tablename__ = "ObjectVersionToObject"
 
-    object_version_source_id: Mapped[int] = mapped_column(ForeignKey("OntologyObjectTypeVersion.id"), nullable=False)
-    object_target_id: Mapped[int] = mapped_column(ForeignKey("OntologyObject.id"), nullable=False)
+    object_version_source_id: Mapped[int] = mapped_column(
+        ForeignKey("OntologyObjectTypeVersion.id"), nullable=False
+    )
+    object_target_id: Mapped[int] = mapped_column(
+        ForeignKey("OntologyObject.id"), nullable=False
+    )
 
     # relationships
     object_version_source: Mapped[OntologyObjectVersion] = relationship(
@@ -152,8 +168,12 @@ class OntologyObjectVersionToTaxonomyItem(MODEL, IdMixin):
 
     __tablename__ = "ObjectVersionToTaxonomyItem"
 
-    object_version_source_id: Mapped[int] = mapped_column(ForeignKey("OntologyObjectVersion.id"), nullable=False)
-    taxonomy_item_target_id: Mapped[int] = mapped_column(ForeignKey("TaxonomyItem.id"), nullable=False)
+    object_version_source_id: Mapped[int] = mapped_column(
+        ForeignKey("OntologyObjectVersion.id"), nullable=False
+    )
+    taxonomy_item_target_id: Mapped[int] = mapped_column(
+        ForeignKey("TaxonomyItem.id"), nullable=False
+    )
 
     # relationships
     object_version_source: Mapped[OntologyObjectVersion] = relationship(
diff --git a/muse_for_anything/db/models/ontology_objects.py b/muse_for_anything/db/models/ontology_objects.py
index b10b751..fab712e 100644
--- a/muse_for_anything/db/models/ontology_objects.py
+++ b/muse_for_anything/db/models/ontology_objects.py
@@ -24,9 +24,11 @@ class OntologyObjectType(MODEL, IdMixin, NameDescriptionMixin, ChangesMixin):
     __tablename__ = "Type"
 
     namespace_id: Mapped[int] = mapped_column(ForeignKey("Namespace.id"), nullable=False)
-    current_version_id: Mapped[int] = mapped_column(ForeignKey("TypeVesion.id"), nullable=True)
+    current_version_id: Mapped[int] = mapped_column(
+        ForeignKey("TypeVesion.id"), nullable=True
+    )
     is_toplevel_type: Mapped[int] = mapped_column(nullable=False)
-    
+
     # relationships
     namespace: Mapped[Namespace] = relationship(innerjoin=True, lazy="selectin")
     current_version: Mapped["OntologyObjectTypeVersion"] = relationship(
@@ -111,7 +113,9 @@ class OntologyObjectTypeVersion(MODEL, IdMixin, CreateDeleteMixin):
     __tablename__ = "TypeVersion"
 
     id: Mapped[int] = mapped_column(primary_key=True)
-    object_type_id: Mapped[int] = mapped_column(ForeignKey("OntologyObjectType.id"), nullable=False)
+    object_type_id: Mapped[int] = mapped_column(
+        ForeignKey("OntologyObjectType.id"), nullable=False
+    )
     version: Mapped[int] = mapped_column(nullable=False)
     data: Mapped[Text] = mapped_column(DB.JSON, nullable=False)
 
@@ -143,11 +147,13 @@ def __table_args__(cls):
         back_populates="type_version_source",
         primaryjoin="OntologyObjectTypeVersion.id == OntologyTypeVersionToTypeVersion.type_version_source_id",
     )
-    imported_by_types: Mapped[List["rel.OntologyTypeVersionToTypeVersion"]] = relationship(
-        lazy="select",
-        order_by="OntologyTypeVersionToTypeVersion.id",
-        back_populates="type_version_target",
-        primaryjoin="OntologyObjectTypeVersion.id == OntologyTypeVersionToTypeVersion.type_version_target_id",
+    imported_by_types: Mapped[List["rel.OntologyTypeVersionToTypeVersion"]] = (
+        relationship(
+            lazy="select",
+            order_by="OntologyTypeVersionToTypeVersion.id",
+            back_populates="type_version_target",
+            primaryjoin="OntologyObjectTypeVersion.id == OntologyTypeVersionToTypeVersion.type_version_target_id",
+        )
     )
 
     referenced_types: Mapped[List["rel.OntologyTypeVersionToType"]] = relationship(
@@ -157,11 +163,13 @@ def __table_args__(cls):
         primaryjoin="OntologyObjectTypeVersion.id == OntologyTypeVersionToType.type_version_source_id",
     )
 
-    referenced_taxonomies: Mapped[List["rel.OntologyTypeVersionToTaxonomy"]] = relationship(
-        lazy="select",
-        order_by="OntologyTypeVersionToTaxonomy.id",
-        back_populates="type_version_source",
-        primaryjoin="OntologyObjectTypeVersion.id == OntologyTypeVersionToTaxonomy.type_version_source_id",
+    referenced_taxonomies: Mapped[List["rel.OntologyTypeVersionToTaxonomy"]] = (
+        relationship(
+            lazy="select",
+            order_by="OntologyTypeVersionToTaxonomy.id",
+            back_populates="type_version_source",
+            primaryjoin="OntologyObjectTypeVersion.id == OntologyTypeVersionToTaxonomy.type_version_source_id",
+        )
     )
 
     @property
@@ -207,8 +215,12 @@ class OntologyObject(MODEL, IdMixin, NameDescriptionMixin, ChangesMixin):
     __tablename__ = "Object"
 
     namespace_id: Mapped[int] = mapped_column(ForeignKey("Namespace.id"), nullable=False)
-    object_type_id: Mapped[int] = mapped_column(ForeignKey("OnotologyObjectType.id"), nullable=False)
-    current_version_id: Mapped[int] = mapped_column(ForeignKey("ObjectVersion.id"), nullable=True)
+    object_type_id: Mapped[int] = mapped_column(
+        ForeignKey("OnotologyObjectType.id"), nullable=False
+    )
+    current_version_id: Mapped[int] = mapped_column(
+        ForeignKey("ObjectVersion.id"), nullable=True
+    )
 
     # relationships
     namespace: Mapped[Namespace] = relationship(innerjoin=True, lazy="selectin")
@@ -231,11 +243,13 @@ class OntologyObject(MODEL, IdMixin, NameDescriptionMixin, ChangesMixin):
         primaryjoin="OntologyObject.id == OntologyObjectVersion.object_id",
     )
 
-    referenced_by_objects: Mapped[List["rel.OntologyObjectVersionToObject"]] = relationship(
-        lazy="select",
-        order_by="OntologyObjectVersionToObject.id",
-        back_populates="object_target",
-        primaryjoin="OntologyObject.id == OntologyObjectVersionToObject.object_target_id",
+    referenced_by_objects: Mapped[List["rel.OntologyObjectVersionToObject"]] = (
+        relationship(
+            lazy="select",
+            order_by="OntologyObjectVersionToObject.id",
+            back_populates="object_target",
+            primaryjoin="OntologyObject.id == OntologyObjectVersionToObject.object_target_id",
+        )
     )
 
     @property
@@ -285,9 +299,13 @@ class OntologyObjectVersion(MODEL, IdMixin, NameDescriptionMixin, CreateDeleteMi
 
     __tablename__ = "ObjectVersion"
 
-    object_id: Mapped[int] = mapped_column(ForeignKey("OntologyObject.id"), nullable=False)
+    object_id: Mapped[int] = mapped_column(
+        ForeignKey("OntologyObject.id"), nullable=False
+    )
     version: Mapped[int] = mapped_column(nullable=False)
-    object_type_version_id: Mapped[int] = mapped_column(ForeignKey("OntologyObjectTypeVersion.id"), nullable=False)
+    object_type_version_id: Mapped[int] = mapped_column(
+        ForeignKey("OntologyObjectTypeVersion.id"), nullable=False
+    )
     data: Mapped[Text] = mapped_column(DB.JSON, nullable=False)
 
     @declared_attr
@@ -318,11 +336,13 @@ def __table_args__(cls):
         primaryjoin="OntologyObjectVersion.id == OntologyObjectVersionToObject.object_version_source_id",
     )
 
-    referenced_taxonomy_items: Mapped[List["rel.OntologyObjectVersionToTaxonomyItem"]] = relationship(
-        lazy="select",
-        order_by="OntologyObjectVersionToTaxonomyItem.id",
-        back_populates="object_version_source",
-        primaryjoin="OntologyObjectVersion.id == OntologyObjectVersionToTaxonomyItem.object_version_source_id",
+    referenced_taxonomy_items: Mapped[List["rel.OntologyObjectVersionToTaxonomyItem"]] = (
+        relationship(
+            lazy="select",
+            order_by="OntologyObjectVersionToTaxonomyItem.id",
+            back_populates="object_version_source",
+            primaryjoin="OntologyObjectVersion.id == OntologyObjectVersionToTaxonomyItem.object_version_source_id",
+        )
     )
 
     @property
diff --git a/muse_for_anything/db/models/taxonomies.py b/muse_for_anything/db/models/taxonomies.py
index 4f136d1..8884bdf 100644
--- a/muse_for_anything/db/models/taxonomies.py
+++ b/muse_for_anything/db/models/taxonomies.py
@@ -81,7 +81,9 @@ class TaxonomyItem(MODEL, IdMixin, ChangesMixin):
     __tablename__ = "TaxonomyItem"
 
     taxonomy_id: Mapped[int] = mapped_column(ForeignKey("Taxonomy.id"), nullable=False)
-    current_version_id: Mapped[int] = mapped_column(ForeignKey("TaxonomyItemVersion.id"), nullable=True)
+    current_version_id: Mapped[int] = mapped_column(
+        ForeignKey("TaxonomyItemVersion.id"), nullable=True
+    )
 
     # relationships
     taxonomy: Mapped[Taxonomy] = relationship(
@@ -127,11 +129,13 @@ class TaxonomyItem(MODEL, IdMixin, ChangesMixin):
         primaryjoin="and_(TaxonomyItem.id == TaxonomyItemRelation.taxonomy_item_target_id, TaxonomyItemRelation.deleted_on == None)",
     )
 
-    referenced_by_objects: Mapped[List["rel.OntologyObjectVersionToTaxonomyItem"]] = relationship(
-        lazy="select",
-        order_by="OntologyObjectVersionToTaxonomyItem.id",
-        back_populates="taxonomy_item_target",
-        primaryjoin="TaxonomyItem.id == OntologyObjectVersionToTaxonomyItem.taxonomy_item_target_id",
+    referenced_by_objects: Mapped[List["rel.OntologyObjectVersionToTaxonomyItem"]] = (
+        relationship(
+            lazy="select",
+            order_by="OntologyObjectVersionToTaxonomyItem.id",
+            back_populates="taxonomy_item_target",
+            primaryjoin="TaxonomyItem.id == OntologyObjectVersionToTaxonomyItem.taxonomy_item_target_id",
+        )
     )
 
     @property
@@ -174,10 +178,12 @@ class TaxonomyItemVersion(MODEL, IdMixin, NameDescriptionMixin, CreateDeleteMixi
 
     __tablename__ = "TaxonomyItemVersion"
 
-    taxonomy_item_id: Mapped[int] = mapped_column(ForeignKey("TaxonomyItem.id"), nullable=False)
+    taxonomy_item_id: Mapped[int] = mapped_column(
+        ForeignKey("TaxonomyItem.id"), nullable=False
+    )
     version: Mapped[int] = mapped_column(nullable=False)
     sort_key: Mapped[float] = mapped_column(nullable=True)
-    
+
     @declared_attr
     def __table_args__(cls):
         return (
@@ -224,9 +230,13 @@ class TaxonomyItemRelation(MODEL, IdMixin, CreateDeleteMixin):
 
     __tablename__ = "TaxonomyItemRelation"
 
-    taxonomy_item_source_id: Mapped[int] = mapped_column(ForeignKey("TaxonomyItem.id"), nullable=False)
+    taxonomy_item_source_id: Mapped[int] = mapped_column(
+        ForeignKey("TaxonomyItem.id"), nullable=False
+    )
 
-    taxonomy_item_target_id: Mapped[int] = mapped_column(ForeignKey("TaxonomyItem.id"), nullable=False)
+    taxonomy_item_target_id: Mapped[int] = mapped_column(
+        ForeignKey("TaxonomyItem.id"), nullable=False
+    )
 
     # relationships
     taxonomy_item_source: Mapped[TaxonomyItem] = relationship(
diff --git a/muse_for_anything/oso_helpers.py b/muse_for_anything/oso_helpers.py
index 2cd11fb..679d93c 100644
--- a/muse_for_anything/oso_helpers.py
+++ b/muse_for_anything/oso_helpers.py
@@ -57,7 +57,7 @@ class OsoResource:
     arguments: Optional[Dict[str, Any]] = None
 
 
-class CustomFlaskOso():
+class CustomFlaskOso:
 
     _oso: Oso
     _app: Flask
@@ -66,19 +66,19 @@ class CustomFlaskOso():
     def __init__(self, oso: Optional[Oso] = None, app: Optional[Flask] = None) -> None:
         self._app = app
         self._oso = None
-        
+
         def unauthorized() -> NoReturn:
             raise Forbidden("Unauthorized")
-        
+
         self._unauthorized_action = unauthorized
-        
+
         self._get_actor = lambda: g.current_user
-        
+
         if self._app is not None:
             self.init_app(self._app)
         if oso is not None:
             self.set_oso(oso)
-        
+
         self._allowed_methods = None
 
     def set_oso(self, oso: Oso) -> None:
@@ -94,7 +94,7 @@ def init_app(self, app: Flask):
 
     def teardown(self, exception):
         pass
-    
+
     def _provide_oso(self) -> None:
         top = _app_context()
         if not hasattr(top, "oso_flask_oso"):
@@ -105,30 +105,26 @@ def _clear_old_cache(
     ):
         self._allowed_methods = None
 
-    def set_get_actor(self, func:Callable[[], Any]) -> None:
+    def set_get_actor(self, func: Callable[[], Any]) -> None:
         self._get_actor = func
-        
-    def set_unauthorize_action(self, func:Callable[[], Any]) -> None:
+
+    def set_unauthorize_action(self, func: Callable[[], Any]) -> None:
         self._unauthorized_action = func
-        
-    def require_authorization(self, app:Optional[Flask] = None) -> None:
+
+    def require_authorization(self, app: Optional[Flask] = None) -> None:
         if app is None:
             app = self._app
         if app is None:
-            raise OsoError(
-                "Cannot require authorization without Flask app object"
-            )
+            raise OsoError("Cannot require authorization without Flask app object")
         app.after_request(self._require_authorization)
-        
+
     def perform_route_authorization(self, app: Optional[Flask] = None) -> None:
         if app is None:
             app = self._app
         if app is None:
-            raise OsoError(
-                "Cannot perform route authorization without Flask app object"
-            )
+            raise OsoError("Cannot perform route authorization without Flask app object")
         app.before_request(self.perform_route_authorization)
-        
+
     def skip_authorization(self, reason: Optional[str] = None) -> None:
         _authorize_called()
 
@@ -183,21 +179,21 @@ def authorize(
             resource = request._get_currect_object()
         if self.oso is None:
             raise OsoError("Cannot perform authorization without oso instance")
-        
+
         allowed = self.oso.is_allowed(actor, action, resource)
         _authorize_called()
-        
+
         if not allowed:
             self._unauthorized_action()
-        
+
     @property
     def app(self) -> Flask:
         return self._app or current_app
-    
+
     @property
     def oso(self) -> Optional[Oso]:
         return self._oso
-    
+
     @property
     def current_actor(self) -> Any:
         return self._get_actor()
@@ -206,7 +202,7 @@ def _perform_route_authorization(self) -> None:
         if not request.url_rule:
             return
         self.authorize(resource=request)
-        
+
     def _require_authorization(self, response: Response) -> Response:
         if not request.url_rule:
             return Response
@@ -273,9 +269,11 @@ def get_allowed_actions(
 
 FLASK_OSO = CustomFlaskOso(oso=OSO)
 
+
 def _authorize_called() -> None:
     _app_context().oso_flask_authorize_called = True
 
+
 def _app_context():
     top = request_ctx
     if top is None:
@@ -285,6 +283,7 @@ def _app_context():
         )
     return top
 
+
 def register_oso(app: Flask):
     """Register oso to enable access management for this app."""
     from .db.models.namespace import Namespace
diff --git a/muse_for_anything/password_helpers.py b/muse_for_anything/password_helpers.py
index e80f9c8..e56fb78 100644
--- a/muse_for_anything/password_helpers.py
+++ b/muse_for_anything/password_helpers.py
@@ -447,8 +447,8 @@ def check_current_settings(self) -> bool:
             end = time_ns()
             results.append(end - start)
 
-        min_time = min(results) / (10 ** 9)
-        max_time = max(results) / (10 ** 9)
+        min_time = min(results) / (10**9)
+        max_time = max(results) / (10**9)
 
         if min_time < 0.1:
             if self._app:
@@ -536,12 +536,12 @@ def calibrate(self, echo_results: bool = False) -> Dict[str, Dict[int, List[int]
                     timings.append(end - start)
                 results_bcrypt[rounds] = timings
                 if echo_results:
-                    min_time = min(timings) / (10 ** 9)
-                    max_time = max(timings) / (10 ** 9)
+                    min_time = min(timings) / (10**9)
+                    max_time = max(timings) / (10**9)
                     click.echo(
                         f"Log Rounds {rounds: 4}: Min {min_time:<8.3} s  Max {max_time:<8.3} s"
                     )
-                if max(timings) > 1 * (10 ** 9):
+                if max(timings) > 1 * (10**9):
                     break
 
         if echo_results:
@@ -567,12 +567,12 @@ def calibrate(self, echo_results: bool = False) -> Dict[str, Dict[int, List[int]
                 timings.append(end - start)
             results_pbkdf2[rounds] = timings
             if echo_results:
-                min_time = min(timings) / (10 ** 9)
-                max_time = max(timings) / (10 ** 9)
+                min_time = min(timings) / (10**9)
+                max_time = max(timings) / (10**9)
                 click.echo(
                     f"Rounds {rounds:13_}: Min {min_time:<6.3} s  Max {max_time:<6.3} s"
                 )
-            if max(timings) > 1 * (10 ** 9):
+            if max(timings) > 1 * (10**9):
                 break
 
         results = {
@@ -613,8 +613,8 @@ def generate_calibration_data():
     data = FLASK_PASSWORD.calibrate(True)
     click.echo("\nDetermining good settings from calibration results:\n")
 
-    min_threshold_ns = 0.2 * (10 ** 9)
-    max_threshold_ns = 1.2 * (10 ** 9)
+    min_threshold_ns = 0.2 * (10**9)
+    max_threshold_ns = 1.2 * (10**9)
 
     for key, name in (("bcrypt", "Bcrypt"), ("pbkdf2", "PBKDF2")):
         calibration_data = data.get(key)
diff --git a/muse_for_anything/util/config/__init__.py b/muse_for_anything/util/config/__init__.py
index 02261b2..31fd610 100644
--- a/muse_for_anything/util/config/__init__.py
+++ b/muse_for_anything/util/config/__init__.py
@@ -1,4 +1,5 @@
 """Module containing default config values."""
+
 from logging import INFO, WARNING
 from os import urandom
 
diff --git a/muse_for_anything/util/debug_routes/routes.py b/muse_for_anything/util/debug_routes/routes.py
index 2618d64..f047ae7 100644
--- a/muse_for_anything/util/debug_routes/routes.py
+++ b/muse_for_anything/util/debug_routes/routes.py
@@ -4,7 +4,6 @@
 from .root import DEBUG_BLP
 
 
-
 @DEBUG_BLP.route("/routes")
 def routes():
     """Render all registered routes."""

From 60cff315d0ae8bee015e8d46c4a6ac42fec56747 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Fabian=20B=C3=BChler?=
 <fabian.buehler@iaas.uni-stuttgart.de>
Date: Tue, 23 Jul 2024 16:50:27 +0200
Subject: [PATCH 04/14] Fix missing import url_parse

---
 .../api/v1_api/ontology_type_validation.py    | 29 ++++++++++---------
 1 file changed, 16 insertions(+), 13 deletions(-)

diff --git a/muse_for_anything/api/v1_api/ontology_type_validation.py b/muse_for_anything/api/v1_api/ontology_type_validation.py
index 5b34d21..65c8f90 100644
--- a/muse_for_anything/api/v1_api/ontology_type_validation.py
+++ b/muse_for_anything/api/v1_api/ontology_type_validation.py
@@ -1,27 +1,25 @@
 """Module containing validation functions for object types."""
 
 from dataclasses import dataclass
-from muse_for_anything.db.models.taxonomies import Taxonomy
-from flask.globals import request_ctx
-from werkzeug.urls import url_parse
-from werkzeug.routing import MapAdapter
-
 from http import HTTPStatus
-
-from muse_for_anything.api.json_schema.schema_tools import SchemaWalker
 from typing import Any, Callable, Deque, Dict, Optional, Sequence, Set, Tuple
-from flask_babel import gettext
-from jsonschema import Draft7Validator
+from urllib.parse import urlparse
 
+from flask.globals import request_ctx
+from flask_babel import gettext
 from flask_smorest import abort
+from jsonschema import Draft7Validator
+from werkzeug.routing import MapAdapter
 
+from muse_for_anything.api.json_schema.schema_tools import SchemaWalker
 from muse_for_anything.db.models.ontology_objects import (
     OntologyObjectType,
     OntologyObjectTypeVersion,
 )
-from .models.schema import TYPE_SCHEMA
-from ..json_schema import DataWalker, DataWalkerVisitor, DataVisitorException
+from muse_for_anything.db.models.taxonomies import Taxonomy
 
+from ..json_schema import DataVisitorException, DataWalker, DataWalkerVisitor
+from .models.schema import TYPE_SCHEMA
 
 SCHEMA_VALIDATOR = Draft7Validator(TYPE_SCHEMA)
 
@@ -150,14 +148,19 @@ def visit(self, data, walker: SchemaWalker) -> None:
                     f"Unknown local schema reference '{ref}'! No schema with matching id!"
                 )
         else:
-            url = url_parse(data["$ref"])
+            url = urlparse(data["$ref"])
 
             ctx = request_ctx
             if ctx is None:
                 raise DataVisitorException(
                     "No request context to check schema url against!"
                 )
-            url_adapter: MapAdapter = ctx.url_adapter
+            url_adapter: Optional[MapAdapter] = ctx.url_adapter
+            if url_adapter is None:
+                raise DataVisitorException(
+                    "No url adapter found in request context! Unable to check URL."
+                    f"URL: '{url}'"
+                )
             if url.netloc != url_adapter.get_host(None):
                 raise DataVisitorException(
                     "Only references to schemas on the same MUSE4Anything instance allowed! "

From ea869d3b99228df8ffa9893c9a300e91318360cc Mon Sep 17 00:00:00 2001
From: Jan Weber <st157366@stud.uni-stuttgart.de>
Date: Thu, 25 Jul 2024 12:09:42 +0200
Subject: [PATCH 05/14] Fix url_parse and request_ctx

---
 .../api/v1_api/ontology_object_validation.py     | 16 +++++++++++-----
 1 file changed, 11 insertions(+), 5 deletions(-)

diff --git a/muse_for_anything/api/v1_api/ontology_object_validation.py b/muse_for_anything/api/v1_api/ontology_object_validation.py
index 2a587e7..e4a9dd7 100644
--- a/muse_for_anything/api/v1_api/ontology_object_validation.py
+++ b/muse_for_anything/api/v1_api/ontology_object_validation.py
@@ -2,9 +2,10 @@
 
 from dataclasses import dataclass
 
+from urllib.parse import urlparse
+
 from muse_for_anything.db.models.taxonomies import TaxonomyItem
-from flask.globals import _request_ctx_stack
-from werkzeug.urls import url_parse
+from flask.globals import request_ctx
 from werkzeug.routing import MapAdapter
 
 from http import HTTPStatus
@@ -36,12 +37,17 @@ class ObjectMetadata:
 def resolve_type_version_schema_url(url_string: str):
     """Resolver url references without creating any http request by directly querying the database."""
     # TODO use url cache
-    url = url_parse(url_string)
+    url = urlparse(url_string)
     # url should already be from a validated type!
-    ctx = _request_ctx_stack.top
+    ctx = request_ctx
     if ctx is None:
         raise DataVisitorException("No request context to check schema url against!")
-    url_adapter: MapAdapter = ctx.url_adapter
+    url_adapter: Optional[MapAdapter] = ctx.url_adapter
+    if url_adapter is None:
+                raise DataVisitorException(
+                    "No url adapter found in request context! Unable to check URL."
+                    f"URL: '{url}'"
+                )
     if url.netloc != url_adapter.get_host(None):
         raise DataVisitorException(
             "Only references to schemas on the same MUSE4Anything instance allowed! "

From f19c5b85dfef03b48b7176ea64b4b8c09cb4399a Mon Sep 17 00:00:00 2001
From: Jan Weber <st157366@stud.uni-stuttgart.de>
Date: Thu, 25 Jul 2024 12:12:07 +0200
Subject: [PATCH 06/14] Fix locale_selector for Babel

---
 muse_for_anything/babel.py | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/muse_for_anything/babel.py b/muse_for_anything/babel.py
index c85be82..f461f83 100644
--- a/muse_for_anything/babel.py
+++ b/muse_for_anything/babel.py
@@ -11,7 +11,6 @@
 BABEL = Babel()
 
 
-@BABEL.localeselector
 def get_locale():
     if "lang" in g:
         # check LanguageAccept option in g context
@@ -47,4 +46,4 @@ def inject_lang_from_header():
 
 def register_babel(app: Flask):
     """Register babel to enable translations for this app."""
-    BABEL.init_app(app)
+    BABEL.init_app(app, locale_selector=get_locale)

From 5714d02f4893fb591b7853a598d7593a0ad88d14 Mon Sep 17 00:00:00 2001
From: Jan Weber <st157366@stud.uni-stuttgart.de>
Date: Thu, 25 Jul 2024 12:26:57 +0200
Subject: [PATCH 07/14] Update SQLAlchemy models

---
 .../db/models/object_relation_tables.py       | 20 ++++++++---------
 .../db/models/ontology_objects.py             | 22 +++++++++++++------
 muse_for_anything/db/models/taxonomies.py     | 20 ++++++++++++-----
 muse_for_anything/db/models/users.py          |  4 ++--
 4 files changed, 42 insertions(+), 24 deletions(-)

diff --git a/muse_for_anything/db/models/object_relation_tables.py b/muse_for_anything/db/models/object_relation_tables.py
index 317b099..74d9f11 100644
--- a/muse_for_anything/db/models/object_relation_tables.py
+++ b/muse_for_anything/db/models/object_relation_tables.py
@@ -31,12 +31,12 @@ class OntologyTypeVersionToTypeVersion(MODEL, IdMixin):
 
     # the type version importing
     type_version_source_id: Mapped[int] = mapped_column(
-        ForeignKey("OntologyObjectTypeVersion.id"), nullable=False
+        ForeignKey(OntologyObjectTypeVersion.id), nullable=False
     )
 
     # the imported type version
     type_version_target_id: Mapped[int] = mapped_column(
-        ForeignKey("OntologyObjectTypeVersion.id"), nullable=False
+        ForeignKey(OntologyObjectTypeVersion.id), nullable=False
     )
 
     # relationships
@@ -67,10 +67,10 @@ class OntologyTypeVersionToType(MODEL, IdMixin):
     __tablename__ = "TypeVersionToType"
 
     type_version_source_id: Mapped[int] = mapped_column(
-        ForeignKey("OntologyObjectTypeVersion.id"), nullable=False
+        ForeignKey(OntologyObjectTypeVersion.id), nullable=False
     )
     type_target_id: Mapped[int] = mapped_column(
-        ForeignKey("OntologyObjectType.id"), nullable=False
+        ForeignKey(OntologyObjectType.id), nullable=False
     )
 
     # relationships
@@ -101,10 +101,10 @@ class OntologyTypeVersionToTaxonomy(MODEL, IdMixin):
     __tablename__ = "TypeVersionToTaxonomy"
 
     type_version_source_id: Mapped[int] = mapped_column(
-        ForeignKey("OntologyObjectTypeVersion.id"), nullable=False
+        ForeignKey(OntologyObjectTypeVersion.id), nullable=False
     )
     taxonomy_target_id: Mapped[int] = mapped_column(
-        ForeignKey("Taxonomy.id"), nullable=False
+        ForeignKey(Taxonomy.id), nullable=False
     )
 
     # relationships
@@ -135,10 +135,10 @@ class OntologyObjectVersionToObject(MODEL, IdMixin):
     __tablename__ = "ObjectVersionToObject"
 
     object_version_source_id: Mapped[int] = mapped_column(
-        ForeignKey("OntologyObjectTypeVersion.id"), nullable=False
+        ForeignKey(OntologyObjectVersion.id), nullable=False
     )
     object_target_id: Mapped[int] = mapped_column(
-        ForeignKey("OntologyObject.id"), nullable=False
+        ForeignKey(OntologyObject.id), nullable=False
     )
 
     # relationships
@@ -169,10 +169,10 @@ class OntologyObjectVersionToTaxonomyItem(MODEL, IdMixin):
     __tablename__ = "ObjectVersionToTaxonomyItem"
 
     object_version_source_id: Mapped[int] = mapped_column(
-        ForeignKey("OntologyObjectVersion.id"), nullable=False
+        ForeignKey(OntologyObjectVersion.id), nullable=False
     )
     taxonomy_item_target_id: Mapped[int] = mapped_column(
-        ForeignKey("TaxonomyItem.id"), nullable=False
+        ForeignKey(TaxonomyItem.id), nullable=False
     )
 
     # relationships
diff --git a/muse_for_anything/db/models/ontology_objects.py b/muse_for_anything/db/models/ontology_objects.py
index fab712e..4de603a 100644
--- a/muse_for_anything/db/models/ontology_objects.py
+++ b/muse_for_anything/db/models/ontology_objects.py
@@ -23,9 +23,9 @@ class OntologyObjectType(MODEL, IdMixin, NameDescriptionMixin, ChangesMixin):
 
     __tablename__ = "Type"
 
-    namespace_id: Mapped[int] = mapped_column(ForeignKey("Namespace.id"), nullable=False)
+    namespace_id: Mapped[int] = mapped_column(ForeignKey(Namespace.id), nullable=False)
     current_version_id: Mapped[int] = mapped_column(
-        ForeignKey("TypeVesion.id"), nullable=True
+        ForeignKey("TypeVersion.id"), nullable=True
     )
     is_toplevel_type: Mapped[int] = mapped_column(nullable=False)
 
@@ -50,6 +50,7 @@ class OntologyObjectType(MODEL, IdMixin, NameDescriptionMixin, ChangesMixin):
     )
 
     referenced_by_types: Mapped[List["rel.OntologyTypeVersionToType"]] = relationship(
+        "OntologyTypeVersionToType",
         lazy="select",
         order_by="OntologyTypeVersionToType.id",
         back_populates="type_target",
@@ -114,7 +115,7 @@ class OntologyObjectTypeVersion(MODEL, IdMixin, CreateDeleteMixin):
 
     id: Mapped[int] = mapped_column(primary_key=True)
     object_type_id: Mapped[int] = mapped_column(
-        ForeignKey("OntologyObjectType.id"), nullable=False
+        ForeignKey(OntologyObjectType.id), nullable=False
     )
     version: Mapped[int] = mapped_column(nullable=False)
     data: Mapped[Text] = mapped_column(DB.JSON, nullable=False)
@@ -142,6 +143,7 @@ def __table_args__(cls):
     )
 
     imported_types: Mapped[List["rel.OntologyTypeVersionToTypeVersion"]] = relationship(
+        "OntologyTypeVersionToTypeVersion",
         lazy="select",
         order_by="OntologyTypeVersionToTypeVersion.id",
         back_populates="type_version_source",
@@ -149,6 +151,7 @@ def __table_args__(cls):
     )
     imported_by_types: Mapped[List["rel.OntologyTypeVersionToTypeVersion"]] = (
         relationship(
+            "OntologyTypeVersionToTypeVersion",
             lazy="select",
             order_by="OntologyTypeVersionToTypeVersion.id",
             back_populates="type_version_target",
@@ -157,6 +160,7 @@ def __table_args__(cls):
     )
 
     referenced_types: Mapped[List["rel.OntologyTypeVersionToType"]] = relationship(
+        "OntologyTypeVersionToType",
         lazy="select",
         order_by="OntologyTypeVersionToType.id",
         back_populates="type_version_source",
@@ -165,6 +169,7 @@ def __table_args__(cls):
 
     referenced_taxonomies: Mapped[List["rel.OntologyTypeVersionToTaxonomy"]] = (
         relationship(
+            "OntologyTypeVersionToTaxonomy",
             lazy="select",
             order_by="OntologyTypeVersionToTaxonomy.id",
             back_populates="type_version_source",
@@ -214,9 +219,9 @@ class OntologyObject(MODEL, IdMixin, NameDescriptionMixin, ChangesMixin):
 
     __tablename__ = "Object"
 
-    namespace_id: Mapped[int] = mapped_column(ForeignKey("Namespace.id"), nullable=False)
+    namespace_id: Mapped[int] = mapped_column(ForeignKey(Namespace.id), nullable=False)
     object_type_id: Mapped[int] = mapped_column(
-        ForeignKey("OnotologyObjectType.id"), nullable=False
+        ForeignKey(OntologyObjectType.id), nullable=False
     )
     current_version_id: Mapped[int] = mapped_column(
         ForeignKey("ObjectVersion.id"), nullable=True
@@ -245,6 +250,7 @@ class OntologyObject(MODEL, IdMixin, NameDescriptionMixin, ChangesMixin):
 
     referenced_by_objects: Mapped[List["rel.OntologyObjectVersionToObject"]] = (
         relationship(
+            "OntologyObjectVersionToObject",
             lazy="select",
             order_by="OntologyObjectVersionToObject.id",
             back_populates="object_target",
@@ -300,11 +306,11 @@ class OntologyObjectVersion(MODEL, IdMixin, NameDescriptionMixin, CreateDeleteMi
     __tablename__ = "ObjectVersion"
 
     object_id: Mapped[int] = mapped_column(
-        ForeignKey("OntologyObject.id"), nullable=False
+        ForeignKey(OntologyObject.id), nullable=False
     )
     version: Mapped[int] = mapped_column(nullable=False)
     object_type_version_id: Mapped[int] = mapped_column(
-        ForeignKey("OntologyObjectTypeVersion.id"), nullable=False
+        ForeignKey(OntologyObjectTypeVersion.id), nullable=False
     )
     data: Mapped[Text] = mapped_column(DB.JSON, nullable=False)
 
@@ -330,6 +336,7 @@ def __table_args__(cls):
     )
 
     referenced_objects: Mapped[List["rel.OntologyObjectVersionToObject"]] = relationship(
+        "OntologyObjectVersionToObject",
         lazy="select",
         order_by="OntologyObjectVersionToObject.id",
         back_populates="object_version_source",
@@ -338,6 +345,7 @@ def __table_args__(cls):
 
     referenced_taxonomy_items: Mapped[List["rel.OntologyObjectVersionToTaxonomyItem"]] = (
         relationship(
+            "OntologyObjectVersionToTaxonomyItem",
             lazy="select",
             order_by="OntologyObjectVersionToTaxonomyItem.id",
             back_populates="object_version_source",
diff --git a/muse_for_anything/db/models/taxonomies.py b/muse_for_anything/db/models/taxonomies.py
index 8884bdf..29a3539 100644
--- a/muse_for_anything/db/models/taxonomies.py
+++ b/muse_for_anything/db/models/taxonomies.py
@@ -23,18 +23,20 @@ class Taxonomy(MODEL, IdMixin, NameDescriptionMixin, ChangesMixin):
 
     __tablename__ = "Taxonomy"
 
-    namespace_id: Mapped[int] = mapped_column(ForeignKey("Namespace.id"), nullable=False)
+    namespace_id: Mapped[int] = mapped_column(ForeignKey(Namespace.id), nullable=False)
 
     # relationships
     namespace = relationship(Namespace, innerjoin=True, lazy="selectin")
 
     items: Mapped[List["TaxonomyItem"]] = relationship(
+        "TaxonomyItem",
         lazy="select",  # do not always load this
         order_by="TaxonomyItem.id",
         back_populates="taxonomy",
         primaryjoin="Taxonomy.id == TaxonomyItem.taxonomy_id",
     )
     current_items: Mapped[List["TaxonomyItem"]] = relationship(
+        "TaxonomyItem",
         viewonly=True,
         # lazy="select",  # do not always load this
         order_by="TaxonomyItem.id",
@@ -43,6 +45,7 @@ class Taxonomy(MODEL, IdMixin, NameDescriptionMixin, ChangesMixin):
     )
 
     referenced_by_types: Mapped[List["rel.OntologyTypeVersionToTaxonomy"]] = relationship(
+        "OntologyTypeVersionToTaxonomy",
         lazy="select",
         order_by="OntologyTypeVersionToTaxonomy.id",
         back_populates="taxonomy_target",
@@ -80,7 +83,7 @@ class TaxonomyItem(MODEL, IdMixin, ChangesMixin):
 
     __tablename__ = "TaxonomyItem"
 
-    taxonomy_id: Mapped[int] = mapped_column(ForeignKey("Taxonomy.id"), nullable=False)
+    taxonomy_id: Mapped[int] = mapped_column(ForeignKey(Taxonomy.id), nullable=False)
     current_version_id: Mapped[int] = mapped_column(
         ForeignKey("TaxonomyItemVersion.id"), nullable=True
     )
@@ -93,36 +96,42 @@ class TaxonomyItem(MODEL, IdMixin, ChangesMixin):
         sync_backref=False,
     )
     current_version: Mapped["TaxonomyItemVersion"] = relationship(
+        "TaxonomyItemVersion",
         post_update=True,
         innerjoin=True,
         lazy="joined",
         primaryjoin="TaxonomyItem.current_version_id == TaxonomyItemVersion.id",
     )
     versions: Mapped[List["TaxonomyItemVersion"]] = relationship(
+        "TaxonomyItemVersion",
         lazy="select",
         order_by="TaxonomyItemVersion.version",
         back_populates="taxonomy_item",
         primaryjoin="TaxonomyItem.id == TaxonomyItemVersion.taxonomy_item_id",
     )
     related: Mapped[List["TaxonomyItemRelation"]] = relationship(
+        "TaxonomyItemRelation",
         lazy="select",
         order_by="TaxonomyItemRelation.id",
         back_populates="taxonomy_item_source",
         primaryjoin="TaxonomyItem.id == TaxonomyItemRelation.taxonomy_item_source_id",
     )
     ancestors: Mapped[List["TaxonomyItemRelation"]] = relationship(
+        "TaxonomyItemRelation",
         lazy="select",
         order_by="TaxonomyItemRelation.id",
         back_populates="taxonomy_item_target",
         primaryjoin="TaxonomyItem.id == TaxonomyItemRelation.taxonomy_item_target_id",
     )
     current_related: Mapped[List["TaxonomyItemRelation"]] = relationship(
+        "TaxonomyItemRelation",
         viewonly=True,
         lazy="selectin",  # deals better with multiple levels of hierarchy
         order_by="TaxonomyItemRelation.id",
         primaryjoin="and_(TaxonomyItem.id == TaxonomyItemRelation.taxonomy_item_source_id, TaxonomyItemRelation.deleted_on == None)",
     )
     current_ancestors: Mapped[List["TaxonomyItemRelation"]] = relationship(
+        "TaxonomyItemRelation",
         viewonly=True,
         lazy="selectin",  # deals better with multiple levels of hierarchy
         order_by="TaxonomyItemRelation.id",
@@ -131,6 +140,7 @@ class TaxonomyItem(MODEL, IdMixin, ChangesMixin):
 
     referenced_by_objects: Mapped[List["rel.OntologyObjectVersionToTaxonomyItem"]] = (
         relationship(
+            "OntologyObjectVersionToTaxonomyItem",
             lazy="select",
             order_by="OntologyObjectVersionToTaxonomyItem.id",
             back_populates="taxonomy_item_target",
@@ -179,7 +189,7 @@ class TaxonomyItemVersion(MODEL, IdMixin, NameDescriptionMixin, CreateDeleteMixi
     __tablename__ = "TaxonomyItemVersion"
 
     taxonomy_item_id: Mapped[int] = mapped_column(
-        ForeignKey("TaxonomyItem.id"), nullable=False
+        ForeignKey(TaxonomyItem.id), nullable=False
     )
     version: Mapped[int] = mapped_column(nullable=False)
     sort_key: Mapped[float] = mapped_column(nullable=True)
@@ -231,11 +241,11 @@ class TaxonomyItemRelation(MODEL, IdMixin, CreateDeleteMixin):
     __tablename__ = "TaxonomyItemRelation"
 
     taxonomy_item_source_id: Mapped[int] = mapped_column(
-        ForeignKey("TaxonomyItem.id"), nullable=False
+        ForeignKey(TaxonomyItem.id), nullable=False
     )
 
     taxonomy_item_target_id: Mapped[int] = mapped_column(
-        ForeignKey("TaxonomyItem.id"), nullable=False
+        ForeignKey(TaxonomyItem.id), nullable=False
     )
 
     # relationships
diff --git a/muse_for_anything/db/models/users.py b/muse_for_anything/db/models/users.py
index cd6297a..d4c7e38 100644
--- a/muse_for_anything/db/models/users.py
+++ b/muse_for_anything/db/models/users.py
@@ -158,7 +158,7 @@ class UserRole(MODEL, IdMixin):
 
     __tablename__ = "UserRole"
 
-    user_id: Mapped[int] = mapped_column(ForeignKey("User.id"), nullable=False)
+    user_id: Mapped[int] = mapped_column(ForeignKey(User.id), nullable=False)
     role: Mapped[str] = mapped_column(DB.String(64))
 
     # references
@@ -247,7 +247,7 @@ class UserGrant(MODEL, IdMixin):
 
     __tablename__ = "UserGrant"
 
-    user_id: Mapped[int] = mapped_column(ForeignKey("User.id"), nullable=True)
+    user_id: Mapped[int] = mapped_column(ForeignKey(User.id), nullable=True)
     role: Mapped[str] = mapped_column(DB.String(64), index=True)
     resource_type: Mapped[str] = mapped_column(DB.String(64), index=True)
     resource_id: Mapped[int] = mapped_column(index=True)

From 03d91bb353a0ffade7b70006c2a966bd4faef7bf Mon Sep 17 00:00:00 2001
From: Jan Weber <st157366@stud.uni-stuttgart.de>
Date: Thu, 25 Jul 2024 13:09:49 +0200
Subject: [PATCH 08/14] Fixed default for updated_on and created_on

---
 muse_for_anything/db/models/model_helpers.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/muse_for_anything/db/models/model_helpers.py b/muse_for_anything/db/models/model_helpers.py
index 64fe18c..e66bd66 100644
--- a/muse_for_anything/db/models/model_helpers.py
+++ b/muse_for_anything/db/models/model_helpers.py
@@ -52,8 +52,8 @@ class CreateDeleteMixin:
     """Add the columns 'created_on' and 'deleted_on' to track creation and deletion of immutable database entries."""
 
     created_on: Mapped[datetime] = mapped_column(
-        DateTime(timezone=True),
-        default_factory=lambda: datetime.now(timezone.utc),
+        DB.DateTime,
+        default=lambda: datetime.now(timezone.utc),
         nullable=False,
     )
     deleted_on: Mapped[datetime] = mapped_column(DateTime(timezone=True), nullable=True)
@@ -67,8 +67,8 @@ class ChangesMixin(CreateDeleteMixin):
     """Add the columns 'created_on', 'updated_on' and 'deleted_on' to track changes to the database entries."""
 
     updated_on: Mapped[datetime] = mapped_column(
-        DateTime(timezone=True),
-        default_factory=lambda: datetime.now(timezone.utc),
+        DB.DateTime,
+        default=lambda: datetime.now(timezone.utc),
         onupdate=lambda: datetime.now(timezone.utc),
         nullable=False,
     )

From 1f3261122b17ca60056560b477e3026c1b78ee54 Mon Sep 17 00:00:00 2001
From: Jan Weber <st157366@stud.uni-stuttgart.de>
Date: Fri, 26 Jul 2024 10:18:26 +0200
Subject: [PATCH 09/14] Add timezoned columns again

---
 muse_for_anything/db/models/model_helpers.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/muse_for_anything/db/models/model_helpers.py b/muse_for_anything/db/models/model_helpers.py
index e66bd66..a82f542 100644
--- a/muse_for_anything/db/models/model_helpers.py
+++ b/muse_for_anything/db/models/model_helpers.py
@@ -52,7 +52,7 @@ class CreateDeleteMixin:
     """Add the columns 'created_on' and 'deleted_on' to track creation and deletion of immutable database entries."""
 
     created_on: Mapped[datetime] = mapped_column(
-        DB.DateTime,
+        DateTime(timezone=True),
         default=lambda: datetime.now(timezone.utc),
         nullable=False,
     )
@@ -67,7 +67,7 @@ class ChangesMixin(CreateDeleteMixin):
     """Add the columns 'created_on', 'updated_on' and 'deleted_on' to track changes to the database entries."""
 
     updated_on: Mapped[datetime] = mapped_column(
-        DB.DateTime,
+        DateTime(timezone=True),
         default=lambda: datetime.now(timezone.utc),
         onupdate=lambda: datetime.now(timezone.utc),
         nullable=False,

From 05c9538ae419202bf63ae7dc3cc35bc8782ba78f Mon Sep 17 00:00:00 2001
From: Jan Weber <st157366@stud.uni-stuttgart.de>
Date: Fri, 26 Jul 2024 10:41:00 +0200
Subject: [PATCH 10/14] Format with current black version

---
 .../api/v1_api/ontology_object_validation.py              | 8 ++++----
 muse_for_anything/db/models/ontology_objects.py           | 4 +---
 2 files changed, 5 insertions(+), 7 deletions(-)

diff --git a/muse_for_anything/api/v1_api/ontology_object_validation.py b/muse_for_anything/api/v1_api/ontology_object_validation.py
index e4a9dd7..eb09023 100644
--- a/muse_for_anything/api/v1_api/ontology_object_validation.py
+++ b/muse_for_anything/api/v1_api/ontology_object_validation.py
@@ -44,10 +44,10 @@ def resolve_type_version_schema_url(url_string: str):
         raise DataVisitorException("No request context to check schema url against!")
     url_adapter: Optional[MapAdapter] = ctx.url_adapter
     if url_adapter is None:
-                raise DataVisitorException(
-                    "No url adapter found in request context! Unable to check URL."
-                    f"URL: '{url}'"
-                )
+        raise DataVisitorException(
+            "No url adapter found in request context! Unable to check URL."
+            f"URL: '{url}'"
+        )
     if url.netloc != url_adapter.get_host(None):
         raise DataVisitorException(
             "Only references to schemas on the same MUSE4Anything instance allowed! "
diff --git a/muse_for_anything/db/models/ontology_objects.py b/muse_for_anything/db/models/ontology_objects.py
index 4de603a..bdcfa74 100644
--- a/muse_for_anything/db/models/ontology_objects.py
+++ b/muse_for_anything/db/models/ontology_objects.py
@@ -305,9 +305,7 @@ class OntologyObjectVersion(MODEL, IdMixin, NameDescriptionMixin, CreateDeleteMi
 
     __tablename__ = "ObjectVersion"
 
-    object_id: Mapped[int] = mapped_column(
-        ForeignKey(OntologyObject.id), nullable=False
-    )
+    object_id: Mapped[int] = mapped_column(ForeignKey(OntologyObject.id), nullable=False)
     version: Mapped[int] = mapped_column(nullable=False)
     object_type_version_id: Mapped[int] = mapped_column(
         ForeignKey(OntologyObjectTypeVersion.id), nullable=False

From 5b03b6e33447113b40acedc43dd4a0f8f58a8f99 Mon Sep 17 00:00:00 2001
From: Jan Weber <st157366@stud.uni-stuttgart.de>
Date: Fri, 26 Jul 2024 16:41:56 +0200
Subject: [PATCH 11/14] Add todos for safety check with request context

---
 muse_for_anything/api/v1_api/ontology_object_validation.py | 1 +
 muse_for_anything/oso_helpers.py                           | 1 +
 2 files changed, 2 insertions(+)

diff --git a/muse_for_anything/api/v1_api/ontology_object_validation.py b/muse_for_anything/api/v1_api/ontology_object_validation.py
index eb09023..7c152c5 100644
--- a/muse_for_anything/api/v1_api/ontology_object_validation.py
+++ b/muse_for_anything/api/v1_api/ontology_object_validation.py
@@ -40,6 +40,7 @@ def resolve_type_version_schema_url(url_string: str):
     url = urlparse(url_string)
     # url should already be from a validated type!
     ctx = request_ctx
+    # TODO Safety check will probably never trigger
     if ctx is None:
         raise DataVisitorException("No request context to check schema url against!")
     url_adapter: Optional[MapAdapter] = ctx.url_adapter
diff --git a/muse_for_anything/oso_helpers.py b/muse_for_anything/oso_helpers.py
index 679d93c..891c1fc 100644
--- a/muse_for_anything/oso_helpers.py
+++ b/muse_for_anything/oso_helpers.py
@@ -276,6 +276,7 @@ def _authorize_called() -> None:
 
 def _app_context():
     top = request_ctx
+    # TODO Safety check will probably never trigger
     if top is None:
         raise OsoError(
             "Application context doesn't exist. Did you use oso outside the context of a request? "

From 5385ddffb2dc392a5e91f068935097bbd8603df5 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Fabian=20B=C3=BChler?=
 <fabian.buehler@iaas.uni-stuttgart.de>
Date: Fri, 26 Jul 2024 17:06:43 +0200
Subject: [PATCH 12/14] Fix resource_ctx usage and fix typing problems in flask
 oso

---
 .../api/v1_api/ontology_object_validation.py  |  6 ++--
 .../api/v1_api/ontology_type_validation.py    |  5 ++--
 muse_for_anything/oso_helpers.py              | 28 +++++++++++--------
 3 files changed, 23 insertions(+), 16 deletions(-)

diff --git a/muse_for_anything/api/v1_api/ontology_object_validation.py b/muse_for_anything/api/v1_api/ontology_object_validation.py
index 7c152c5..15950d2 100644
--- a/muse_for_anything/api/v1_api/ontology_object_validation.py
+++ b/muse_for_anything/api/v1_api/ontology_object_validation.py
@@ -39,9 +39,9 @@ def resolve_type_version_schema_url(url_string: str):
     # TODO use url cache
     url = urlparse(url_string)
     # url should already be from a validated type!
-    ctx = request_ctx
-    # TODO Safety check will probably never trigger
-    if ctx is None:
+    try:
+        ctx = request_ctx._get_current_object()
+    except RuntimeError:
         raise DataVisitorException("No request context to check schema url against!")
     url_adapter: Optional[MapAdapter] = ctx.url_adapter
     if url_adapter is None:
diff --git a/muse_for_anything/api/v1_api/ontology_type_validation.py b/muse_for_anything/api/v1_api/ontology_type_validation.py
index 65c8f90..8d8a3e8 100644
--- a/muse_for_anything/api/v1_api/ontology_type_validation.py
+++ b/muse_for_anything/api/v1_api/ontology_type_validation.py
@@ -150,8 +150,9 @@ def visit(self, data, walker: SchemaWalker) -> None:
         else:
             url = urlparse(data["$ref"])
 
-            ctx = request_ctx
-            if ctx is None:
+            try:
+                ctx = request_ctx._get_current_object()
+            except RuntimeError:
                 raise DataVisitorException(
                     "No request context to check schema url against!"
                 )
diff --git a/muse_for_anything/oso_helpers.py b/muse_for_anything/oso_helpers.py
index 891c1fc..f83b764 100644
--- a/muse_for_anything/oso_helpers.py
+++ b/muse_for_anything/oso_helpers.py
@@ -3,7 +3,7 @@
 from dataclasses import dataclass
 from typing import Any, Callable, Dict, NoReturn, Optional, Sequence, Type
 
-from flask import Flask, current_app, g, request
+from flask import Flask, current_app
 from flask.globals import request_ctx, g, request
 from flask.wrappers import Request, Response
 from oso import Oso
@@ -59,8 +59,8 @@ class OsoResource:
 
 class CustomFlaskOso:
 
-    _oso: Oso
-    _app: Flask
+    _oso: Optional[Oso]
+    _app: Optional[Flask]
     _allowed_methods: Optional[Sequence[str]]
 
     def __init__(self, oso: Optional[Oso] = None, app: Optional[Flask] = None) -> None:
@@ -205,7 +205,7 @@ def _perform_route_authorization(self) -> None:
 
     def _require_authorization(self, response: Response) -> Response:
         if not request.url_rule:
-            return Response
+            return response
         if not getattr(_app_context(), "oso_flask_authorize_called", False):
             raise OsoError("Authorize not called.")
         return response
@@ -222,7 +222,9 @@ def is_admin(
         if actor is None:
             actor = self._get_current_actor()
 
-        oso: Oso = self.oso
+        oso = self.oso
+        if oso is None:
+            raise ValueError("No instance of oso set!")
         return oso.query_rule("is_admin", resource)
 
     def is_allowed(
@@ -241,7 +243,9 @@ def is_allowed(
         if action is None:
             action = request.method
 
-        oso: Oso = self.oso
+        oso = self.oso
+        if oso is None:
+            raise ValueError("No instance of oso set!")
         return oso.is_allowed(actor, action, resource)
 
     def get_allowed_actions(
@@ -258,7 +262,9 @@ def get_allowed_actions(
         if actor is None:
             actor = self._get_current_actor()
 
-        oso: Oso = self.oso
+        oso = self.oso
+        if oso is None:
+            raise ValueError("No instance of oso set!")
         result = oso.get_allowed_actions(actor, resource, allow_wildcard=allow_wildcard)
         if should_cache_result:
             self._allowed_methods = result
@@ -275,14 +281,14 @@ def _authorize_called() -> None:
 
 
 def _app_context():
-    top = request_ctx
-    # TODO Safety check will probably never trigger
-    if top is None:
+    try:
+        context = request_ctx._get_current_object()
+    except RuntimeError:
         raise OsoError(
             "Application context doesn't exist. Did you use oso outside the context of a request? "
             "See https://flask.palletsprojects.com/en/1.1.x/appcontext/#manually-push-a-context"
         )
-    return top
+    return context
 
 
 def register_oso(app: Flask):

From 9aa86fc56049df2179c525bb645aee1c26a9c059 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Fabian=20B=C3=BChler?=
 <fabian.buehler@iaas.uni-stuttgart.de>
Date: Mon, 29 Jul 2024 10:52:28 +0200
Subject: [PATCH 13/14] Fix alembic migrations not working

---
 migrations/env.py | 15 ++++++++-------
 1 file changed, 8 insertions(+), 7 deletions(-)

diff --git a/migrations/env.py b/migrations/env.py
index 84702be..90d268f 100644
--- a/migrations/env.py
+++ b/migrations/env.py
@@ -3,10 +3,8 @@
 import logging
 from logging.config import fileConfig
 
-from sqlalchemy import engine_from_config
-from sqlalchemy import pool
-
 from alembic import context
+from sqlalchemy import engine_from_config, pool
 
 # this is the Alembic Config object, which provides
 # access to the values within the .ini file in use.
@@ -23,9 +21,8 @@
 # target_metadata = mymodel.Base.metadata
 from flask import current_app
 
-current_app.config[
-    "SQLITE_FOREIGN_KEYS"
-] = False  # do NOT use foreign key checking when updating DB
+# do NOT use foreign key checking when updating DB
+current_app.config["SQLITE_FOREIGN_KEYS"] = False
 config.set_main_option(
     "sqlalchemy.url",
     str(current_app.extensions["migrate"].db.engine.url).replace("%", "%%"),
@@ -84,13 +81,17 @@ def process_revision_directives(context, revision, directives):
     )
 
     with connectable.connect() as connection:
+        extra_kwargs = dict(current_app.extensions["migrate"].configure_args)
+        # remove duplicate args from extra config
+        extra_kwargs.pop("compare_type", None)
+        extra_kwargs.pop("render_as_batch", None)
         context.configure(
             connection=connection,
             target_metadata=target_metadata,
             process_revision_directives=process_revision_directives,
             render_as_batch=True,
             compare_type=True,
-            **current_app.extensions["migrate"].configure_args
+            **extra_kwargs,
         )
 
         with context.begin_transaction():

From 476abf5ac799ad3714d2f5e159f808ea6f285c5c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Fabian=20B=C3=BChler?=
 <fabian.buehler@iaas.uni-stuttgart.de>
Date: Mon, 29 Jul 2024 10:56:51 +0200
Subject: [PATCH 14/14] Run black 24 on migration and conf.py

---
 docs/conf.py                                          | 6 +++---
 migrations/versions/a18bebd2bb1a_initial_migration.py | 1 +
 2 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/docs/conf.py b/docs/conf.py
index 4981d13..11b2e81 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -91,9 +91,9 @@
 autosectionlabel_prefix_document = False
 autosectionlabel_maxdepth = None
 
-intersphinx_mapping: Optional[
-    Dict[str, Tuple[str, Union[Optional[str], Tuple[str]]]]
-] = None
+intersphinx_mapping: Optional[Dict[str, Tuple[str, Union[Optional[str], Tuple[str]]]]] = (
+    None
+)
 intersphinx_timeout = 30
 
 source_suffix = {
diff --git a/migrations/versions/a18bebd2bb1a_initial_migration.py b/migrations/versions/a18bebd2bb1a_initial_migration.py
index 5963d15..a8147f9 100644
--- a/migrations/versions/a18bebd2bb1a_initial_migration.py
+++ b/migrations/versions/a18bebd2bb1a_initial_migration.py
@@ -3,6 +3,7 @@
 Revision ID: a18bebd2bb1a
 Create Date: 2021-09-19 20:16:31.258752
 """
+
 from alembic import op
 import sqlalchemy as sa