diff --git a/.devcontainer/Dockerfile b/.devcontainer/Dockerfile
index a3be4194..7eb17e2d 100644
--- a/.devcontainer/Dockerfile
+++ b/.devcontainer/Dockerfile
@@ -1,4 +1,4 @@
-FROM mcr.microsoft.com/vscode/devcontainers/python:3.9-bullseye
+FROM mcr.microsoft.com/devcontainers/python:1-3.12-bookworm
 
 ENV PYTHONUNBUFFERED 1
 
diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
index c49da2b5..b9b990e5 100644
--- a/.devcontainer/devcontainer.json
+++ b/.devcontainer/devcontainer.json
@@ -1,6 +1,5 @@
 // For format details, see https://aka.ms/devcontainer.json. For config options, see the README at:
 // https://github.com/microsoft/vscode-dev-containers/tree/v0.177.0/containers/python-3-postgres
-// Update the VARIANT arg in docker-compose.yml to pick a Python version: 3, 3.8, 3.7, 3.6
 {
 	"name": "${localWorkspaceFolderBasename}",
 	"dockerComposeFile": "docker-compose.yml",
@@ -20,13 +19,10 @@
 				"python.languageServer": "Pylance",
 				"python.analysis.typeCheckingMode": "basic",
 				"python.testing.pytestPath": "/usr/local/py-utils/bin/pytest",
-				"python.testing.pytestArgs": [
-					"--profile"
-				],
 				"python.testing.unittestEnabled": false,
 				"python.testing.pytestEnabled": true,
 				"editor.codeActionsOnSave": {
-					"source.organizeImports": true
+					"source.organizeImports": "explicit"
 				},
 				"editor.formatOnSave": true,
 				"editor.renderWhitespace": "all",
@@ -75,4 +71,4 @@
 		// details can be found here: https://github.com/devcontainers/features/tree/main/src/docker-outside-of-docker
 		"ghcr.io/devcontainers/features/docker-outside-of-docker:1": {}
 	}
-}
+}
\ No newline at end of file
diff --git a/.devcontainer/license_header.txt b/.devcontainer/license_header.txt
index 5757817f..3e70646f 100644
--- a/.devcontainer/license_header.txt
+++ b/.devcontainer/license_header.txt
@@ -1,4 +1,4 @@
-Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 for the German Human Genome-Phenome Archive (GHGA)
 
 Licensed under the Apache License, Version 2.0 (the "License");
diff --git a/.github/workflows/check_config_docs.yaml b/.github/workflows/check_config_docs.yaml
index bb88b574..b2d08c8e 100644
--- a/.github/workflows/check_config_docs.yaml
+++ b/.github/workflows/check_config_docs.yaml
@@ -1,17 +1,24 @@
-name: Check if the config schema and the example are up to date.
+name: Check if the config schema and the example are up to date
 
 on: push
 
 jobs:
   static-code-analysis:
+    name: Check config schema and example
+
     runs-on: ubuntu-latest
+
     steps:
-      - uses: actions/checkout@v3
+      - name: Checkout repository
+        id: checkout
+        uses: actions/checkout@v4
 
-      - id: common
-        uses: ghga-de/gh-action-common@v4
+      - name: Common steps
+        id: common
+        uses: ghga-de/gh-action-common@v6
 
       - name: Check config docs
+        id: check-config-docs
         run: |
           export ${{ steps.common.outputs.CONFIG_YAML_ENV_VAR_NAME }}="${{ steps.common.outputs.CONFIG_YAML }}"
 
diff --git a/.github/workflows/check_pyproject.yaml b/.github/workflows/check_pyproject.yaml
index d929c799..0c7abdc6 100644
--- a/.github/workflows/check_pyproject.yaml
+++ b/.github/workflows/check_pyproject.yaml
@@ -1,16 +1,23 @@
-name: Check if the config schema and the example are up to date.
+name: Check if pyproject.toml file is up to date
 
 on: push
 
 jobs:
   static-code-analysis:
+    name: Check pyproject file
+
     runs-on: ubuntu-latest
+
     steps:
-      - uses: actions/checkout@v3
+      - name: Checkout repository
+        id: checkout
+        uses: actions/checkout@v4
 
-      - id: common
-        uses: ghga-de/gh-action-common@v4
+      - name: Common steps
+        id: common
+        uses: ghga-de/gh-action-common@v6
 
       - name: Check pyproject.toml
+        id: check-pyproject
         run: |
           ./scripts/update_pyproject.py --check
diff --git a/.github/workflows/check_readme.yaml b/.github/workflows/check_readme.yaml
index 7414554d..5d06e3f1 100644
--- a/.github/workflows/check_readme.yaml
+++ b/.github/workflows/check_readme.yaml
@@ -1,16 +1,23 @@
-name: Check if the readme is up to date.
+name: Check if the README file is up to date
 
 on: push
 
 jobs:
   static-code-analysis:
+    name: Check README file
+
     runs-on: ubuntu-latest
+
     steps:
-      - uses: actions/checkout@v3
+      - name: Checkout repository
+        id: checkout
+        uses: actions/checkout@v4
 
-      - id: common
-        uses: ghga-de/gh-action-common@v4
+      - name: Common steps
+        id: common
+        uses: ghga-de/gh-action-common@v6
 
-      - name: Check readme
+      - name: Check README
+        id: check-readme
         run: |
           ./scripts/update_readme.py --check
diff --git a/.github/workflows/check_template_files.yaml b/.github/workflows/check_template_files.yaml
index 9fb5cbf0..e6b7e608 100644
--- a/.github/workflows/check_template_files.yaml
+++ b/.github/workflows/check_template_files.yaml
@@ -4,14 +4,23 @@ on: push
 
 jobs:
   check-template-files:
+    name: Check template files
+
     runs-on: ubuntu-latest
+
     steps:
-      - uses: actions/checkout@v3
-      - name: Set up Python 3.9
-        uses: actions/setup-python@v4
+      - name: Checkout repository
+        id: checkout
+        uses: actions/checkout@v4
+
+      - name: Set up Python 3.12
+        id: setup-python
+        uses: actions/setup-python@v5
         with:
-          python-version: 3.9
+          python-version: '3.12'
+
       - name: Check template files
+        id: check-template-files
         run: |
           if [ "${{ github.event.repository.name }}" == "microservice-repository-template" ]
           then
diff --git a/.github/workflows/ci_release.yaml b/.github/workflows/ci_release.yaml
index d8547b40..4a286247 100644
--- a/.github/workflows/ci_release.yaml
+++ b/.github/workflows/ci_release.yaml
@@ -6,7 +6,10 @@ on:
 
 jobs:
   push_to_docker_hub:
+    name: Push to Docker Hub
+
     runs-on: ubuntu-latest
+
     steps:
       - uses: ghga-de/gh-action-ci@v1
         with:
diff --git a/.github/workflows/ci_workflow_dispatch.yaml b/.github/workflows/ci_workflow_dispatch.yaml
index eab7d5a3..a49be97b 100644
--- a/.github/workflows/ci_workflow_dispatch.yaml
+++ b/.github/workflows/ci_workflow_dispatch.yaml
@@ -11,6 +11,7 @@ on:
 
 jobs:
   fetch-tag:
+    name: Fetch Tag
     runs-on: ubuntu-latest
     if:  github.event_name == 'workflow_dispatch' || ( github.event.action != 'labeled' && contains(github.event.pull_request.labels.*.name, 'build') ) || ( github.event.action == 'labeled' && github.event.label.name == 'build' )
     steps:
@@ -20,6 +21,7 @@ jobs:
       latest_tag: ${{ steps.fetch-tag.outputs.latest_tag }}
 
   push_to_docker_hub:
+    name: Push to Docker Hub
     needs: fetch-tag
     runs-on: ubuntu-latest
     steps:
diff --git a/.github/workflows/static_code_analysis.yaml b/.github/workflows/static_code_analysis.yaml
index 86a014df..052dfdcf 100644
--- a/.github/workflows/static_code_analysis.yaml
+++ b/.github/workflows/static_code_analysis.yaml
@@ -4,24 +4,36 @@ on: push
 
 jobs:
   static-code-analysis:
-    runs-on: ubuntu-latest
     name: Static Code Analysis
+
+    runs-on: ubuntu-latest
+
     steps:
-      - uses: actions/checkout@v3
+      - name: Checkout repository
+        id: checkout
+        uses: actions/checkout@v4
 
-      - id: common
-        uses: ghga-de/gh-action-common@v4
+      - name: Common steps
+        id: common
+        uses: ghga-de/gh-action-common@v6
 
-      - uses: pre-commit/action@v3.0.0
+      - name: Run pre-commit
+        uses: pre-commit/action@v3.0.1
         env:
           SKIP: no-commit-to-branch
-      - name: ruff
+
+      - name: Run ruff
+        id: ruff
         run: |
           ruff check --output-format=github .
           ruff format --check .
-      - name: mypy
+
+      - name: Run mypy
+        id: mypy
         run: |
           mypy .
+
       - name: Check license header and file
+        id: license-checker
         run: |
-          ./scripts/license_checker.py
+          ./scripts/check_license.py
diff --git a/.github/workflows/tests.yaml b/.github/workflows/tests.yaml
index dacc9f50..56a9c199 100644
--- a/.github/workflows/tests.yaml
+++ b/.github/workflows/tests.yaml
@@ -1,19 +1,24 @@
-name: Tests
+name: Run test suite and measure coverage
 
 on: push
 
 jobs:
   tests:
+    name: Run test suite
+
     runs-on: ubuntu-latest
-    name: Tests
 
     steps:
-      - uses: actions/checkout@v3
+      - name: Checkout repository
+        id: checkout
+        uses: actions/checkout@v4
 
-      - id: common
-        uses: ghga-de/gh-action-common@v4
+      - name: Common steps
+        id: common
+        uses: ghga-de/gh-action-common@v6
 
-      - id: pytest
+      - name: Run tests
+        id: pytest
         run: |
           export ${{ steps.common.outputs.CONFIG_YAML_ENV_VAR_NAME }}="${{ steps.common.outputs.CONFIG_YAML }}"
 
@@ -22,8 +27,8 @@ jobs:
             --cov-report=xml \
             tests
 
-      - id: coveralls
-        name: Upload coverage to coveralls
+      - name: Upload coverage to coveralls
+        id: coveralls
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         run: |
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 60c83522..63f041ad 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -1,10 +1,7 @@
 # See https://pre-commit.com for more information
 # See https://pre-commit.com/hooks.html for more hooks
 
-default_language_version:
-  python: python3.9
-
-minimum_pre_commit_version: 3.0.0
+minimum_pre_commit_version: 3.7.0
 
 repos:
   - repo: local
@@ -48,13 +45,13 @@ repos:
       - id: no-commit-to-branch
         args: [--branch, dev, --branch, int, --branch, main]
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.3.3
+    rev: v0.4.5
     hooks:
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix]
       - id: ruff-format
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.9.0
+    rev: v1.10.0
     hooks:
       - id: mypy
         args: [--no-warn-unused-ignores]
diff --git a/.pyproject_generation/README.md b/.pyproject_generation/README.md
index 93b988fe..4434a8ff 100644
--- a/.pyproject_generation/README.md
+++ b/.pyproject_generation/README.md
@@ -1,5 +1,5 @@
 <!--
- Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+ Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
  for the German Human Genome-Phenome Archive (GHGA)
 
  Licensed under the Apache License, Version 2.0 (the "License");
diff --git a/.pyproject_generation/pyproject_custom.toml b/.pyproject_generation/pyproject_custom.toml
index 3a457248..1af0a319 100644
--- a/.pyproject_generation/pyproject_custom.toml
+++ b/.pyproject_generation/pyproject_custom.toml
@@ -1,12 +1,12 @@
 [project]
 name = "metldata"
-version = "1.2.1"
+version = "1.3.0"
 description = "metldata - A framework for handling metadata based on ETL, CQRS, and event sourcing."
 dependencies = [
-    "hexkit[akafka,mongodb] >=2.1.1, <3",
+    "hexkit[akafka,mongodb] >=3, <4",
     "ghga-service-commons[api,auth] >=3.1.1, <4",
     "ghga-event-schemas >=3.0.0, <4",
-    "typer~=0.9.0",
+    "typer>=0.12",
     "linkml==1.6.1",
     "linkml-runtime==1.6.0",
     "linkml-validator==0.4.5",
diff --git a/.pyproject_generation/pyproject_template.toml b/.pyproject_generation/pyproject_template.toml
index a6201df9..07a11ffa 100644
--- a/.pyproject_generation/pyproject_template.toml
+++ b/.pyproject_generation/pyproject_template.toml
@@ -1,5 +1,5 @@
 [build-system]
-requires = ["setuptools>=67.7.2"]
+requires = ["setuptools>=69"]
 build-backend = "setuptools.build_meta"
 
 [project]
@@ -7,14 +7,13 @@ readme = "README.md"
 authors = [
     { name = "German Human Genome Phenome Archive (GHGA)", email = "contact@ghga.de" },
 ]
-requires-python = ">=3.9"
+requires-python = ">=3.12"
 license = { text = "Apache 2.0" }
 classifiers = [
     "Development Status :: 1 - Planning",
     "Operating System :: POSIX :: Linux",
-    "Programming Language :: Python :: 3.9",
-    "Programming Language :: Python :: 3.10",
-    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.12",
     "License :: OSI Approved :: Apache Software License",
     "Topic :: Internet :: WWW/HTTP :: HTTP Servers",
     "Topic :: Software Development :: Libraries",
@@ -34,7 +33,7 @@ exclude = [
 ]
 line-length = 88
 src = ["src", "tests", "examples", "scripts"]
-target-version = "py39"
+target-version = "py312"
 
 [tool.ruff.lint]
 fixable = [
@@ -43,8 +42,9 @@ fixable = [
     "D", # pydocstyle
 ]
 ignore = [
-    "E", # pycodestyle errors
-    "W", # pycodestyle warnings - pycodestyle covered by black
+    "E111", # indentation with invalid multiple (for formatter)
+    "E114", # indentation with invalid multiple comment (for formatter)
+    "E116", # over indentation (for formatter)
     "PLW", # pylint warnings
     "RUF001", # ambiguous unicode character strings
     "RUF010", # explicit conversion to string or repr: !s or !r
@@ -56,8 +56,9 @@ ignore = [
     "D400", # first doc line ends in period
     "D401", # non-imperative-mood
     "D107", # missing docstring in __init__
-    "D206", # indent-with-spaces (ignored for formatter)
-    "D300", # triple-single-quotes (ignored for formatter)
+    "D206", # indent-with-spaces (for formatter)
+    "D300", # triple-single-quotes (for formatter)
+    "UP040", # type statement (not yet supported by mypy)
 ]
 select = [
     "C90", # McCabe Complexity
@@ -98,12 +99,12 @@ check_untyped_defs = true
 no_site_packages = false
 
 [tool.pytest.ini_options]
-minversion = "7.1"
+minversion = "8.0"
 asyncio_mode = "strict"
 
 [tool.coverage.paths]
 source = [
-  "src",
-  "/workspace/src",
-  "**/lib/python*/site-packages",
+    "src",
+    "/workspace/src",
+    "**/lib/python*/site-packages",
 ]
diff --git a/.readme_generation/README.md b/.readme_generation/README.md
index ed2a2a79..725df747 100644
--- a/.readme_generation/README.md
+++ b/.readme_generation/README.md
@@ -1,5 +1,5 @@
 <!--
- Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+ Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
  for the German Human Genome-Phenome Archive (GHGA)
 
  Licensed under the Apache License, Version 2.0 (the "License");
diff --git a/.template/README.md b/.template/README.md
index 8a5e7cd6..56ada89f 100644
--- a/.template/README.md
+++ b/.template/README.md
@@ -1,5 +1,5 @@
 <!--
- Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+ Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
  for the German Human Genome-Phenome Archive (GHGA)
 
  Licensed under the Apache License, Version 2.0 (the "License");
diff --git a/.template/deprecated_files.txt b/.template/deprecated_files.txt
index df962efe..152ea266 100644
--- a/.template/deprecated_files.txt
+++ b/.template/deprecated_files.txt
@@ -13,6 +13,7 @@
 .github/workflows/cd.yaml
 
 scripts/check_mandatory_and_static_files.py
+scripts/license_checker.py
 scripts/update_static_files.py
 
 docs
diff --git a/.template/static_files.txt b/.template/static_files.txt
index 46e46bf6..1cf97905 100644
--- a/.template/static_files.txt
+++ b/.template/static_files.txt
@@ -15,10 +15,12 @@
 
 scripts/script_utils/__init__.py
 scripts/script_utils/cli.py
+scripts/script_utils/deps.py
+scripts/script_utils/lock_deps.py
 
 scripts/__init__.py
 scripts/update_all.py
-scripts/license_checker.py
+scripts/check_license.py
 scripts/get_package_name.py
 scripts/update_config_docs.py
 scripts/update_template_files.py
diff --git a/Dockerfile b/Dockerfile
index b7aea924..5728dd23 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -14,7 +14,7 @@
 # limitations under the License.
 
 ## creating building container
-FROM python:3.10.9-slim-bullseye AS builder
+FROM python:3.12-slim-bookworm AS builder
 # update and install dependencies
 RUN apt update
 RUN apt upgrade -y
@@ -26,7 +26,7 @@ WORKDIR /service
 RUN python -m build
 
 # creating running container
-FROM python:3.10.9-slim-bullseye
+FROM python:3.12-slim-bookworm
 # update and install dependencies
 RUN apt update
 RUN apt upgrade -y
diff --git a/LICENSE b/LICENSE
index ba3d39f3..f459a369 100644
--- a/LICENSE
+++ b/LICENSE
@@ -186,7 +186,7 @@
       same "printed page" as the copyright notice for easier
       identification within third-party archives.
 
-   Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+   Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
    for the German Human Genome-Phenome Archive (GHGA)
 
    Licensed under the Apache License, Version 2.0 (the "License");
diff --git a/README.md b/README.md
index 855d134f..c865a439 100644
--- a/README.md
+++ b/README.md
@@ -58,13 +58,13 @@ We recommend using the provided Docker container.
 
 A pre-build version is available at [docker hub](https://hub.docker.com/repository/docker/ghga/metldata):
 ```bash
-docker pull ghga/metldata:1.2.1
+docker pull ghga/metldata:1.3.0
 ```
 
 Or you can build the container yourself from the [`./Dockerfile`](./Dockerfile):
 ```bash
 # Execute in the repo's root dir:
-docker build -t ghga/metldata:1.2.1 .
+docker build -t ghga/metldata:1.3.0 .
 ```
 
 For production-ready deployment, we recommend using Kubernetes, however,
@@ -72,7 +72,7 @@ for simple use cases, you could execute the service using docker
 on a single server:
 ```bash
 # The entrypoint is preconfigured:
-docker run -p 8080:8080 ghga/metldata:1.2.1 --help
+docker run -p 8080:8080 ghga/metldata:1.3.0 --help
 ```
 
 If you prefer not to use containers, you may install the service from source:
@@ -143,7 +143,7 @@ The service requires the following configuration parameters:
 
 - **`kafka_ssl_keyfile`** *(string)*: Optional filename containing the client private key. Default: `""`.
 
-- **`kafka_ssl_password`** *(string)*: Optional password to be used for the client private key. Default: `""`.
+- **`kafka_ssl_password`** *(string, format: password)*: Optional password to be used for the client private key. Default: `""`.
 
 - **`generate_correlation_id`** *(boolean)*: A flag, which, if False, will result in an error when inbound requests don't possess a correlation ID. If True, requests without a correlation ID will be assigned a newly generated ID in the correlation ID middleware function. Default: `true`.
 
@@ -334,12 +334,55 @@ The service requires the following configuration parameters:
 
 - **`artifact_infos`** *(array)*: Information for artifacts to be queryable via the Artifacts REST API.
 
-  - **Items**: Refer to *[#/$defs/ArtifactInfo](#$defs/ArtifactInfo)*.
+  - **Items**: Refer to *[#/$defs/ArtifactInfo](#%24defs/ArtifactInfo)*.
 
 - **`loader_token_hashes`** *(array)*: Hashes of tokens used to authenticate for loading artifact.
 
   - **Items** *(string)*
 
+## Definitions
+
+
+- <a id="%24defs/AnchorPoint"></a>**`AnchorPoint`** *(object)*: A model for describing an anchor point for the specified target class.
+
+  - **`target_class`** *(string, required)*: The name of the class to be targeted.
+
+  - **`identifier_slot`** *(string, required)*: The name of the slot in the target class that is used as identifier.
+
+  - **`root_slot`** *(string, required)*: The name of the slot in the root class used to link to the target class.
+
+- <a id="%24defs/ArtifactInfo"></a>**`ArtifactInfo`** *(object)*: Model to describe general information on an artifact.
+Please note, it does not contain actual artifact instances derived from specific
+metadata.
+
+  - **`name`** *(string, required)*: The name of the artifact.
+
+  - **`description`** *(string, required)*: A description of the artifact.
+
+  - **`resource_classes`** *(object, required)*: A dictionary of resource classes for this artifact. The keys are the names of the classes. The values are the corresponding class models. Can contain additional properties.
+
+    - **Additional properties**: Refer to *[#/$defs/ArtifactResourceClass](#%24defs/ArtifactResourceClass)*.
+
+- <a id="%24defs/ArtifactResourceClass"></a>**`ArtifactResourceClass`** *(object)*: Model to describe a resource class of an artifact.
+
+  - **`name`** *(string, required)*: The name of the metadata class.
+
+  - **`description`**: A description of the metadata class. Default: `null`.
+
+    - **Any of**
+
+      - *string*
+
+      - *null*
+
+  - **`anchor_point`**: The anchor point for this metadata class.
+
+    - **All of**
+
+      - : Refer to *[#/$defs/AnchorPoint](#%24defs/AnchorPoint)*.
+
+  - **`json_schema`** *(object, required)*: The JSON schema for this metadata class.
+
 
 ### Usage:
 
diff --git a/config_schema.json b/config_schema.json
index bc06522f..dfb1a8ed 100644
--- a/config_schema.json
+++ b/config_schema.json
@@ -179,8 +179,10 @@
     "kafka_ssl_password": {
       "default": "",
       "description": "Optional password to be used for the client private key.",
+      "format": "password",
       "title": "Kafka Ssl Password",
-      "type": "string"
+      "type": "string",
+      "writeOnly": true
     },
     "generate_correlation_id": {
       "default": true,
diff --git a/lock/README.md b/lock/README.md
index fc255b55..090a32e4 100644
--- a/lock/README.md
+++ b/lock/README.md
@@ -1,5 +1,5 @@
 <!--
- Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+ Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
  for the German Human Genome-Phenome Archive (GHGA)
 
  Licensed under the Apache License, Version 2.0 (the "License");
diff --git a/lock/requirements-dev-template.in b/lock/requirements-dev-template.in
index b543188a..dd81066c 100644
--- a/lock/requirements-dev-template.in
+++ b/lock/requirements-dev-template.in
@@ -1,34 +1,32 @@
 # common requirements for development and testing of services
 
-pytest>=7.4.0
-pytest-asyncio>=0.23.0
-pytest-cov>=4.1.0
-pytest-profiling>=1.7.0
-snakeviz>=2.2.0
-logot>=1.2.0
+pytest>=8.2
+pytest-asyncio>=0.23.6
+pytest-cov>=5
+snakeviz>=2.2
+logot>=1.3
 
-pre-commit>=3.6.0
+pre-commit>=3.7
 
-mypy>=1.8.0
-mypy-extensions>=1.0.0
+mypy>=1.10
+mypy-extensions>=1.0
 
-ruff>=0.3.0
+ruff>=0.4
 
-click>=8.1.0
-typer>=0.9.0
+click>=8.1
+typer>=0.12
 
-httpx>=0.27.0
-pytest-httpx>=0.30.0
+httpx>=0.27
+pytest-httpx>=0.30
 
 urllib3>=1.26.18
-requests>=2.31.0
+requests>=2.31
 
-stringcase>=1.2.0
-jsonschema2md>=1.0.0
-setuptools>=69.1.0
+stringcase>=1.2
+jsonschema2md>=1.1
+setuptools>=69.5
 
 # required since switch to pyproject.toml and pip-tools
-tomli>=2.0.1
-tomli_w>=1.0.0
+tomli_w>=1.0
 
-uv>=0.1.21
+uv>=0.1.44
diff --git a/lock/requirements-dev.in b/lock/requirements-dev.in
index 4d48a8fd..0bf7a5f6 100644
--- a/lock/requirements-dev.in
+++ b/lock/requirements-dev.in
@@ -4,4 +4,4 @@
 -r requirements-dev-template.in
 
 # additional requirements can be listed here
-testcontainers[kafka,mongo]>=3.4.1
+testcontainers[kafka,mongo]>=4.4.1, <5
diff --git a/lock/requirements-dev.txt b/lock/requirements-dev.txt
index 94bfeced..16b2cf8a 100644
--- a/lock/requirements-dev.txt
+++ b/lock/requirements-dev.txt
@@ -1,31 +1,35 @@
-# This file was autogenerated by uv via the following command:
-#    uv pip compile --refresh --generate-hashes --output-file /workspace/lock/requirements-dev.txt /tmp/tmphyx3y5vn/pyproject.toml /workspace/lock/requirements-dev.in
-aiokafka==0.8.1 \
-    --hash=sha256:1e24839088fd6d3ff481cc09a48ea487b997328df11630bc0a1b88255edbcfe9 \
-    --hash=sha256:1f43d2afd7d3e4407ada8d754895fad7c344ca00648a8a38418d76564eaaf6cd \
-    --hash=sha256:1f6044ed270b946d31f265903b5eb101940ed0ff3a902eaf8178103c943bbcc9 \
-    --hash=sha256:24373bb2d519abac036d5b04ebc43452ef4ad1916953b6678b9801a9c93ba237 \
-    --hash=sha256:2fa54b8b068d9d8735cb6757a0f48168f8cf9be68860b0bae6b3ed1684cef49b \
-    --hash=sha256:3816bcfc3c57dfa4ed77fe1dc3a9a464e17b6400061348155115f282c8150c47 \
-    --hash=sha256:45cd28af6590d6a999bb706803166570121ba8a5a0d06c51ebd8a59fab53593c \
-    --hash=sha256:4693fbe3c10f125bf3e2df8a8ccbca3eff2bdaaa6589d28c7532c10e7d84598b \
-    --hash=sha256:4fccd599ab6b3fda4f4187d854b343f153b40d05d6774be9acf238618da50031 \
-    --hash=sha256:6421ee81084532f915501074a132acb2afc8cb88bf5ddb11e584230a30f6f006 \
-    --hash=sha256:673c163dee62dfe45146d5250af0e395da5cc92b63f8878c592abc7dc1862899 \
-    --hash=sha256:7d327d66b41c4e3bafff7f9efb71936a08f940aa665680717e20862e4272a068 \
-    --hash=sha256:7f09784322c0d2c4fcc222add4337a5ac394aa30a248eb4e0e4587a125573c75 \
-    --hash=sha256:90960356513f3979754261b132b12a96b0d9e3c6eb44420e3a90a7c31156a81a \
-    --hash=sha256:935da8c4da9a00a1e16020d88e578206097b4bb72ebc2a25fbd2cb817907ef28 \
-    --hash=sha256:9f19d90b7360bc2239fcd8b147508ae39c3e5b1acfc8e6a2a9b0f306070f7ffe \
-    --hash=sha256:a8a641a8102c51422afe111d4bc70c51f335f38fc5906e4c839bd17afeaf3cb2 \
-    --hash=sha256:af6df9a41e08b61d7e62c0a416feeabd81bad76fa5c70d499b083d6af9ce72c3 \
-    --hash=sha256:b2bf97548fa77ad31062ca580368d346b16ba9fdca5856c435f256f3699ab12b \
-    --hash=sha256:bbffc431d9285328c0bc108949132ae11cec863f1dd5a43a1fc3d45a69ffb8a9 \
-    --hash=sha256:bf7473c55dc7959d4b7f9d750fa6017b325813d6cb761e488c2d9ea44e922954 \
-    --hash=sha256:c4332d37cb9d52181cfda4236566b4028c7c188549277f87bcc3027577d72b1b \
-    --hash=sha256:d300188e358cd29989c817f6ee2a2965a039e5a71de8ade6f80f02ebb9bd07b8 \
-    --hash=sha256:fd8f9e17bc9cd2ea664a7f5133aede39a8fffebffe0c450252d475dbdedb4a35 \
-    --hash=sha256:ff318d29ecbeea8c58d69c91c24d48d7ed4a8d3e829b607e670d118a9a35d5ba
+aiokafka==0.10.0 \
+    --hash=sha256:007f1c51f440cc07155d2491f4deea6536492324153296aa73736a74cd833d3e \
+    --hash=sha256:05c4a7ced5d6f3dbc289767574d6a5d9b31e1c243e992dcecd34dbc40fcbbf9b \
+    --hash=sha256:06060708a4bcf062be496c8641fca382c88782d3c381a34ccb5ac8677bdac695 \
+    --hash=sha256:12d703317812262feac6577ff488f2ccddc4408da0ff608a5454062782b5a80d \
+    --hash=sha256:1509c1b29cd1d4d920a649f257d72109bbc3d61431135505b8e0d8d488796ff2 \
+    --hash=sha256:1fe0194ea72524df37369a8cf0837263b55194ac20616e612f0ab7bfb568b76b \
+    --hash=sha256:22299f8d5269dcb00b1b53fdee44dbe729091d4038e1bb63d0bb2f5cdf9af47a \
+    --hash=sha256:5efb63686562809f0f9bf0fa6d1e52f222af2d8f8441f8c412b156f15c98da43 \
+    --hash=sha256:6e10fdee4189fe7eed36d602df822e9ff4f19535c0a514cf015f78308d206c1a \
+    --hash=sha256:7068f0beb8478cde09618dcc9a833cc18ff37bd14864fa8b60ad4e4c3dad6489 \
+    --hash=sha256:74229a57c95e2efccec95d9b42554dc168c97a263f013e3e983202bd33ca189d \
+    --hash=sha256:781ab300214681e40667185a402abf6b31b4c4b8f1cdabbdc3549d8cf383b34d \
+    --hash=sha256:7ce35563f955490b43190e3389b5f3d92d50e22b32d1a40772fd14fb1d50c5db \
+    --hash=sha256:82a75ea13d7e6e11c7ee2fb9419e9ea3541744648c69ab27b56fb6bca5b319c1 \
+    --hash=sha256:8b74aeacfb8ced9764002c63b58e4c78c94809131d89000cb936c25c298ffb1e \
+    --hash=sha256:9728c523f10ac4bb46719cc64f3c1d47625898872bc3901b22b9d48b6e401d1c \
+    --hash=sha256:99127ab680f9b08b0213d00b7d1e0480c6d08601f52ad42e829350f9599db301 \
+    --hash=sha256:b91109dc25f79be4d27454cc766239a5368d18b26682d4b5c6b913ca92691220 \
+    --hash=sha256:c23ec22fbf26e2f84678f0589076bea1ff26ae6dfd3c601e6de10ad00d605261 \
+    --hash=sha256:cf4a47659517000a8fe88e0fb353898b718ee214e21f62a2a949be9bf801cd9e \
+    --hash=sha256:cf9e241766b7f4c305807763330dacf8c220ad9e8fc7f2b22730a2db66fad61d \
+    --hash=sha256:d52c25f3d0db7dd340a5d08108da302db1ba64c2190970dbdb768b79629d6add \
+    --hash=sha256:de56c503b3d64e24a5b6705e55bc524a8357b0495402f859f921a71d65274cb1 \
+    --hash=sha256:e16d8a23f0e173e5ca86c2d1c270e25a529a0eed973c77d7e8a0dfc868699aa4 \
+    --hash=sha256:e833e4ef7fc5f3f637ba5fb4210acc7e5ea916bb7107e4b619b1b1a3e361bc62 \
+    --hash=sha256:ebe5be9f578e89e6db961121070f7c35662924abee00ba4ccf64557e2cdd7edf \
+    --hash=sha256:f069bda1f31e466d815b631a07bc6fad5190b29dfff5f117bcbf1948cd7a38aa \
+    --hash=sha256:f2f19dee69c69389f5911e6b23c361c5285366d237f782eaae118d12acc42d7f \
+    --hash=sha256:f4b22a31f40493cea50dddb4dfc92750dfb273635ccb094a16fde9678eb38958 \
+    --hash=sha256:fafc95bdaed9e1810fcd80b02ac117e51c72681ffe50353e5d61e2170609e1fc \
+    --hash=sha256:ffc30e4c6bfcb00356a002f623c93a51d8336ca67687ea069dd11822da07379c
     # via hexkit
 annotated-types==0.6.0 \
     --hash=sha256:0641064de18ba7a25dee8f96403ebc39113d0cb953a01429249d5c7564666a43 \
@@ -233,6 +237,7 @@ click==8.1.7 \
     --hash=sha256:ae74fb96c20a0277a1d615f1e4d73c8414f5a98db8b799a7931d1582f3390c28 \
     --hash=sha256:ca9853ad459e787e2192211578cc907e7594e294c7ccc834310722b41b9ca6de
     # via
+    #   -r lock/requirements-dev-template.in
     #   json-flattener
     #   linkml
     #   linkml-runtime
@@ -334,10 +339,6 @@ deprecated==1.2.14 \
     --hash=sha256:6fac8b097794a90302bdbb17b9b815e732d3c4720583ff1b198499d78470466c \
     --hash=sha256:e5323eb936458dccc2582dc6f9c322c852a775a27065ff2b0c4970b9d53d01b3
     # via linkml-runtime
-deprecation==2.1.0 \
-    --hash=sha256:72b3bde64e5d778694b0cf68178aed03d15e15477116add3fb773e581f9518ff \
-    --hash=sha256:a10811591210e1fb0e768a8c25517cabeabcba6f0bf96564f8ff45189f90b14a
-    # via testcontainers
 distlib==0.3.8 \
     --hash=sha256:034db59a0b96f8ca18035f36290806a9a6e6bd9d1ff91e45a7f172eb17e51784 \
     --hash=sha256:1530ea13e350031b6312d8580ddb6b27a104275a31106523b8f123787f494f64
@@ -355,21 +356,21 @@ docker==7.0.0 \
 email-validator==2.1.0.post1 \
     --hash=sha256:a4b0bd1cf55f073b924258d19321b1f3aa74b4b5a71a42c305575dba920e1a44 \
     --hash=sha256:c973053efbeddfef924dc0bd93f6e77a1ea7ee0fce935aea7103c7a3d6d2d637
-    # via pydantic
+    # via
+    #   fastapi
+    #   pydantic
 et-xmlfile==1.1.0 \
     --hash=sha256:8eb9e2bc2f8c97e37a2dc85a09ecdcdec9d8a396530a6d5a33b30b9a92da0c5c \
     --hash=sha256:a2ba85d1d6a74ef63837eed693bcb89c3f752169b0e3e7ae5b16ca5e1b3deada
     # via openpyxl
-exceptiongroup==1.2.0 \
-    --hash=sha256:4bfd3996ac73b41e9b9628b04e079f193850720ea5945fc96a08633c66912f14 \
-    --hash=sha256:91f5c769735f051a4290d52edd0858999b57e5876e9f85937691bd4c9fa3ed68
-    # via
-    #   anyio
-    #   pytest
-fastapi==0.110.0 \
-    --hash=sha256:266775f0dcc95af9d3ef39bad55cff525329a931d5fd51930aadd4f428bf7ff3 \
-    --hash=sha256:87a1f6fb632a218222c5984be540055346a8f5d8a68e8f6fb647b1dc9934de4b
+fastapi==0.111.0 \
+    --hash=sha256:97ecbf994be0bcbdadedf88c3150252bed7b2087075ac99735403b1b76cc8fc0 \
+    --hash=sha256:b9db9dd147c91cb8b769f7183535773d8741dd46f9dc6676cd82eab510228cd7
     # via ghga-service-commons
+fastapi-cli==0.0.4 \
+    --hash=sha256:a2552f3a7ae64058cdbb530be6fa6dbfc975dc165e4fa66d224c3d396e25e809 \
+    --hash=sha256:e2e9ffaffc1f7767f488d6da34b6f5a377751c996f397902eb6abb99a67bde32
+    # via fastapi
 filelock==3.13.1 \
     --hash=sha256:521f5f56c50f8426f5e03ad3b281b490a87ef15bc6c526f168290f0c7148d44e \
     --hash=sha256:57dbda9b35157b05fb3e58ee91448612eb674172fab98ee235ccb0b5bee19a1c
@@ -383,13 +384,11 @@ fqdn==1.5.1 \
 ghga-event-schemas==3.0.0 \
     --hash=sha256:67dce9db2d45be862f69a58a903fac43416997ad50fd4f1f1d25822533a187d1 \
     --hash=sha256:7a8952e37bd935809f324aa21653b008e01a5ea920d36217734ee35776d92602
-ghga-service-commons==3.1.1 \
-    --hash=sha256:6f758721a2673ac9c594d9cd052e0204b79950bf9f3e828ca5d870a6637d81b6 \
-    --hash=sha256:b4e696c350f14a983d9447c43b16a954f0d2bf0a057c3ecdf0a95e3f115c89b4
-gprof2dot==2022.7.29 \
-    --hash=sha256:45b4d298bd36608fccf9511c3fd88a773f7a1abc04d6cd39445b11ba43133ec5 \
-    --hash=sha256:f165b3851d3c52ee4915eb1bd6cca571e5759823c2cd0f71a79bda93c2dc85d6
-    # via pytest-profiling
+    # via metldata (pyproject.toml)
+ghga-service-commons==3.1.4 \
+    --hash=sha256:63450bed2f0ca7431f064b640d35e15a29f93b7f4c67b5fd3b812afc8ced5151 \
+    --hash=sha256:eb78042aeb17bb70e17f7c7185fbcf87a54968a410de99f968a7e944cd0f6f78
+    # via metldata (pyproject.toml)
 graphviz==0.20.1 \
     --hash=sha256:587c58a223b51611c0cf461132da386edd896a029524ca61a1462b880bf97977 \
     --hash=sha256:8c58f14adaa3b947daf26c19bc1e98c4e0702cdc31cf99153e6f06904d492bf8
@@ -467,10 +466,12 @@ hbreader==0.9.1 \
     #   jsonasobj2
     #   linkml
     #   linkml-runtime
-hexkit==2.1.1 \
-    --hash=sha256:1f0a0e20a6d56fe4fa5e0b1c798df4720d2f84e20cbe7f16464bd5107e109c90 \
-    --hash=sha256:3ec0f9690eb573125e22bce0c662019c9708cd17f8d2353396dc4496577718c3
-    # via ghga-service-commons
+hexkit==3.1.0 \
+    --hash=sha256:3f96ede959b4d81a6b78637ebf47019787e5d3321bd01f9abe82cb8118bada66 \
+    --hash=sha256:b922c048091f622798ccf25a767fe3d64ff8ee000d1c3cf18967b6b6de8f2592
+    # via
+    #   metldata (pyproject.toml)
+    #   ghga-service-commons
 httpcore==1.0.2 \
     --hash=sha256:096cc05bca73b8e459a1fc3dcf585148f63e534eae4339559c9b8a8d6399acc7 \
     --hash=sha256:9fc092e4799b26174648e54b74ed5f683132a464e95643b226e00c2ed2fa6535
@@ -516,7 +517,10 @@ httptools==0.6.1 \
 httpx==0.27.0 \
     --hash=sha256:71d5465162c13681bff01ad59b2cc68dd838ea1f10e51574bac27103f00c91a5 \
     --hash=sha256:a0cb88a46f32dc874e04ee956e4c2764aba2aa228f650b06788ba6bda2962ab5
-    # via pytest-httpx
+    # via
+    #   -r lock/requirements-dev-template.in
+    #   fastapi
+    #   pytest-httpx
 identify==2.5.33 \
     --hash=sha256:161558f9fe4559e1557e1bff323e8631f6a0e4837f7497767c1782832f16b62d \
     --hash=sha256:d40ce5fcd762817627670da8a7d8d8e65f24342d14539c59488dc603bf662e34
@@ -548,6 +552,7 @@ jinja2==3.1.2 \
     --hash=sha256:31351a702a408a9e7595a8fc6150fc3f43bb6bf7e319770cbc0db9df9437e852 \
     --hash=sha256:6088930bfe239f0e6710546ab9c19c9ef35e29792895fed6e6e31a023a182a61
     # via
+    #   fastapi
     #   linkml
     #   linkml-dataops
 json-flattener==0.1.9 \
@@ -580,9 +585,9 @@ jsonpointer==2.4 \
     # via
     #   jsonpatch
     #   jsonschema
-jsonschema==4.20.0 \
-    --hash=sha256:4f614fd46d8d61258610998997743ec5492a648b33cf478c1ddc23ed4598a5fa \
-    --hash=sha256:ed6231f0429ecf966f5bc8dfef245998220549cbbcf140f913b7464c52c3b6b3
+jsonschema==4.22.0 \
+    --hash=sha256:5b22d434a45935119af990552c862e5d6d564e8f6601206b305a61fdf661a2b7 \
+    --hash=sha256:ff4cfd6b1367a40e7bc6411caec72effadd3db0bbe5017de188f2d6108335802
     # via
     #   ghga-event-schemas
     #   hexkit
@@ -592,22 +597,20 @@ jsonschema-specifications==2023.11.2 \
     --hash=sha256:9472fc4fea474cd74bea4a2b190daeccb5a9e4db2ea80efcf7a1b582fc9a81b8 \
     --hash=sha256:e74ba7c0a65e8cb49dc26837d6cfe576557084a8b423ed16a420984228104f93
     # via jsonschema
-jsonschema2md==1.0.0 \
-    --hash=sha256:01e18693c8dcdd643aa79ce757c5896877c590493422d23fd0bd76562fbc424b \
-    --hash=sha256:1d1333cb6d55a152ce10051b05651bc71122c0ec5e572b3433046825661569d4
-jwcrypto==1.5.4 \
-    --hash=sha256:0815fbab613db99bad85691da5f136f8860423396667728a264bcfa6e1db36b0
+jsonschema2md==1.1.0 \
+    --hash=sha256:2386fc4d119330686db3989ea497ab96a4defb6388386fc0ceff756b5c1a66a7 \
+    --hash=sha256:e89edf2de1bc7fc3e842915c7c29b7b70888555a87002eccc06350c0412a1458
+    # via -r lock/requirements-dev-template.in
+jwcrypto==1.5.6 \
+    --hash=sha256:150d2b0ebbdb8f40b77f543fb44ffd2baeff48788be71f67f03566692fd55789 \
+    --hash=sha256:771a87762a0c081ae6166958a954f80848820b2ab066937dc8b8379d65b1b039
     # via ghga-service-commons
-kafka-python==2.0.2 \
-    --hash=sha256:04dfe7fea2b63726cd6f3e79a2d86e709d608d74406638c5da33a01d45a9d7e3 \
-    --hash=sha256:2d92418c7cb1c298fa6c7f0fb3519b520d0d7526ac6cb7ae2a4fc65a51a94b6e
-    # via
-    #   aiokafka
-    #   testcontainers
 linkml==1.6.1 \
     --hash=sha256:65f73cf29a77518972238e71e91e012c081cf2e43d71d8965ca414c78c11e08e \
     --hash=sha256:7501cb9c7b2c13ca78fc7121ae8b5457fb5771138714da31cc11f971062070ee
-    # via linkml-validator
+    # via
+    #   metldata (pyproject.toml)
+    #   linkml-validator
 linkml-dataops==0.1.0 \
     --hash=sha256:193cf7f659e5f07946d2c2761896910d5f7151d91282543b1363801f68307f4c \
     --hash=sha256:4550eab65e78b70dc3b9c651724a94ac2b1d1edb2fbe576465f1d6951a54ed04
@@ -616,15 +619,22 @@ linkml-runtime==1.6.0 \
     --hash=sha256:1b6b698f8cf23d63ff833ae0be8055b2e945e1c0ef06a1ed6db359247194a2eb \
     --hash=sha256:a06df7431a9b929afe242598800d99cec83bb31cbdc1f5d2d70e6b26c67dc337
     # via
+    #   metldata (pyproject.toml)
     #   linkml
     #   linkml-dataops
     #   linkml-validator
 linkml-validator==0.4.5 \
     --hash=sha256:7a9799830cba3e1df203cde86263d8ea85f9ed9f6a45a218e3f752483abac030 \
     --hash=sha256:bce72053c1593a678ccefd28ed5cf4b39a878e78da884b5b41fef65610a23867
-logot==1.2.0 \
-    --hash=sha256:e4972cc1569322ed6d1e25e8c4507c3d9ebb4fdd93058c420f800bf223bc5f90 \
-    --hash=sha256:ed994e50e30fed2378965a859def1eff1c62d97255479196de33f6de7cec2866
+    # via metldata (pyproject.toml)
+logot==1.3.0 \
+    --hash=sha256:bb2e8cf8ca949015e1e096e45023095ebd5df06ea4627f5df47d53dcdf62b74e \
+    --hash=sha256:de392d182308828a0a9a442120e25e4ad2258fef52c4ed275e012aaffb0514a5
+    # via -r lock/requirements-dev-template.in
+markdown-it-py==3.0.0 \
+    --hash=sha256:355216845c60bd96232cd8d8c40e8f9765cc86f46880e43a8fd22dc1a1a8cab1 \
+    --hash=sha256:e3f60a94fa066dc52ec76661e37c851cb232d92f9886b15cb560aaada2df8feb
+    # via rich
 markupsafe==2.1.3 \
     --hash=sha256:05fb21170423db021895e1ea1e1f3ab3adb85d1c2333cbc2310f2a26bc77272e \
     --hash=sha256:0a4e4a1aff6c7ac4cd55792abf96c915634c2b97e3cc1c7129578aa68ebd754e \
@@ -687,42 +697,49 @@ markupsafe==2.1.3 \
     --hash=sha256:fec21693218efe39aa7f8599346e90c705afa52c5b31ae019b2e57e8f6542bb2 \
     --hash=sha256:ffcc3f7c66b5f5b7931a5aa68fc9cecc51e685ef90282f4a82f0f5e9b704ad11
     # via jinja2
-motor==3.3.2 \
-    --hash=sha256:6fe7e6f0c4f430b9e030b9d22549b732f7c2226af3ab71ecc309e4a1b7d19953 \
-    --hash=sha256:d2fc38de15f1c8058f389c1a44a4d4105c0405c48c061cd492a654496f7bc26a
+mdurl==0.1.2 \
+    --hash=sha256:84008a41e51615a49fc9966191ff91509e3c40b939176e643fd50a5c2196b8f8 \
+    --hash=sha256:bb413d29f5eea38f31dd4754dd7377d4465116fb207585f97bf925588687c1ba
+    # via markdown-it-py
+motor==3.4.0 \
+    --hash=sha256:4b1e1a0cc5116ff73be2c080a72da078f2bb719b53bc7a6bb9e9a2f7dcd421ed \
+    --hash=sha256:c89b4e4eb2e711345e91c7c9b122cb68cce0e5e869ed0387dd0acb10775e3131
     # via hexkit
-mypy==1.9.0 \
-    --hash=sha256:0235391f1c6f6ce487b23b9dbd1327b4ec33bb93934aa986efe8a9563d9349e6 \
-    --hash=sha256:190da1ee69b427d7efa8aa0d5e5ccd67a4fb04038c380237a0d96829cb157913 \
-    --hash=sha256:2418488264eb41f69cc64a69a745fad4a8f86649af4b1041a4c64ee61fc61129 \
-    --hash=sha256:3a3c007ff3ee90f69cf0a15cbcdf0995749569b86b6d2f327af01fd1b8aee9dc \
-    --hash=sha256:3cc5da0127e6a478cddd906068496a97a7618a21ce9b54bde5bf7e539c7af974 \
-    --hash=sha256:48533cdd345c3c2e5ef48ba3b0d3880b257b423e7995dada04248725c6f77374 \
-    --hash=sha256:49c87c15aed320de9b438ae7b00c1ac91cd393c1b854c2ce538e2a72d55df150 \
-    --hash=sha256:4d3dbd346cfec7cb98e6cbb6e0f3c23618af826316188d587d1c1bc34f0ede03 \
-    --hash=sha256:571741dc4194b4f82d344b15e8837e8c5fcc462d66d076748142327626a1b6e9 \
-    --hash=sha256:587ce887f75dd9700252a3abbc9c97bbe165a4a630597845c61279cf32dfbf02 \
-    --hash=sha256:5d741d3fc7c4da608764073089e5f58ef6352bedc223ff58f2f038c2c4698a89 \
-    --hash=sha256:5e6061f44f2313b94f920e91b204ec600982961e07a17e0f6cd83371cb23f5c2 \
-    --hash=sha256:61758fabd58ce4b0720ae1e2fea5cfd4431591d6d590b197775329264f86311d \
-    --hash=sha256:653265f9a2784db65bfca694d1edd23093ce49740b2244cde583aeb134c008f3 \
-    --hash=sha256:68edad3dc7d70f2f17ae4c6c1b9471a56138ca22722487eebacfd1eb5321d612 \
-    --hash=sha256:81a10926e5473c5fc3da8abb04119a1f5811a236dc3a38d92015cb1e6ba4cb9e \
-    --hash=sha256:85ca5fcc24f0b4aeedc1d02f93707bccc04733f21d41c88334c5482219b1ccb3 \
-    --hash=sha256:a260627a570559181a9ea5de61ac6297aa5af202f06fd7ab093ce74e7181e43e \
-    --hash=sha256:aceb1db093b04db5cd390821464504111b8ec3e351eb85afd1433490163d60cd \
-    --hash=sha256:b685154e22e4e9199fc95f298661deea28aaede5ae16ccc8cbb1045e716b3e04 \
-    --hash=sha256:d357423fa57a489e8c47b7c85dfb96698caba13d66e086b412298a1a0ea3b0ed \
-    --hash=sha256:d4d5ddc13421ba3e2e082a6c2d74c2ddb3979c39b582dacd53dd5d9431237185 \
-    --hash=sha256:e49499be624dead83927e70c756970a0bc8240e9f769389cdf5714b0784ca6bf \
-    --hash=sha256:e54396d70be04b34f31d2edf3362c1edd023246c82f1730bbf8768c28db5361b \
-    --hash=sha256:f88566144752999351725ac623471661c9d1cd8caa0134ff98cceeea181789f4 \
-    --hash=sha256:f8a67616990062232ee4c3952f41c779afac41405806042a8126fe96e098419f \
-    --hash=sha256:fe28657de3bfec596bbeef01cb219833ad9d38dd5393fc649f4b366840baefe6
+mypy==1.10.0 \
+    --hash=sha256:075cbf81f3e134eadaf247de187bd604748171d6b79736fa9b6c9685b4083061 \
+    --hash=sha256:12b6bfc1b1a66095ab413160a6e520e1dc076a28f3e22f7fb25ba3b000b4ef99 \
+    --hash=sha256:1ec404a7cbe9fc0e92cb0e67f55ce0c025014e26d33e54d9e506a0f2d07fe5de \
+    --hash=sha256:28d0e038361b45f099cc086d9dd99c15ff14d0188f44ac883010e172ce86c38a \
+    --hash=sha256:2b0695d605ddcd3eb2f736cd8b4e388288c21e7de85001e9f85df9187f2b50f9 \
+    --hash=sha256:3236a4c8f535a0631f85f5fcdffba71c7feeef76a6002fcba7c1a8e57c8be1ec \
+    --hash=sha256:3be66771aa5c97602f382230165b856c231d1277c511c9a8dd058be4784472e1 \
+    --hash=sha256:3d087fcbec056c4ee34974da493a826ce316947485cef3901f511848e687c131 \
+    --hash=sha256:3f298531bca95ff615b6e9f2fc0333aae27fa48052903a0ac90215021cdcfa4f \
+    --hash=sha256:4a2b5cdbb5dd35aa08ea9114436e0d79aceb2f38e32c21684dcf8e24e1e92821 \
+    --hash=sha256:4cf18f9d0efa1b16478c4c129eabec36148032575391095f73cae2e722fcf9d5 \
+    --hash=sha256:8b2cbaca148d0754a54d44121b5825ae71868c7592a53b7292eeb0f3fdae95ee \
+    --hash=sha256:8f55583b12156c399dce2df7d16f8a5095291354f1e839c252ec6c0611e86e2e \
+    --hash=sha256:92f93b21c0fe73dc00abf91022234c79d793318b8a96faac147cd579c1671746 \
+    --hash=sha256:9e36fb078cce9904c7989b9693e41cb9711e0600139ce3970c6ef814b6ebc2b2 \
+    --hash=sha256:9fd50226364cd2737351c79807775136b0abe084433b55b2e29181a4c3c878c0 \
+    --hash=sha256:a781f6ad4bab20eef8b65174a57e5203f4be627b46291f4589879bf4e257b97b \
+    --hash=sha256:a87dbfa85971e8d59c9cc1fcf534efe664d8949e4c0b6b44e8ca548e746a8d53 \
+    --hash=sha256:b808e12113505b97d9023b0b5e0c0705a90571c6feefc6f215c1df9381256e30 \
+    --hash=sha256:bc6ac273b23c6b82da3bb25f4136c4fd42665f17f2cd850771cb600bdd2ebeda \
+    --hash=sha256:cd777b780312ddb135bceb9bc8722a73ec95e042f911cc279e2ec3c667076051 \
+    --hash=sha256:da1cbf08fb3b851ab3b9523a884c232774008267b1f83371ace57f412fe308c2 \
+    --hash=sha256:e22e1527dc3d4aa94311d246b59e47f6455b8729f4968765ac1eacf9a4760bc7 \
+    --hash=sha256:f8c083976eb530019175aabadb60921e73b4f45736760826aa1689dda8208aee \
+    --hash=sha256:f90cff89eea89273727d8783fef5d4a934be2fdca11b47def50cf5d311aff727 \
+    --hash=sha256:fa7ef5244615a2523b56c034becde4e9e3f9b034854c93639adb667ec9ec2976 \
+    --hash=sha256:fcfc70599efde5c67862a07a1aaf50e55bce629ace26bb19dc17cece5dd31ca4
+    # via -r lock/requirements-dev-template.in
 mypy-extensions==1.0.0 \
     --hash=sha256:4392f6c0eb8a5668a69e23d168ffa70f0be9ccfd32b5cc2d26a34ae5b844552d \
     --hash=sha256:75dbf8955dc00442a438fc4d0666508a9a97b6bd41aa2f0ffe9d2f2725af0782
-    # via mypy
+    # via
+    #   -r lock/requirements-dev-template.in
+    #   mypy
 nodeenv==1.8.0 \
     --hash=sha256:d51e0c37e64fbf47d017feac3145cdbb58836d7eee8c6f6d3b6880c5456227d2 \
     --hash=sha256:df865724bb3c3adc86b3876fa209771517b0cfe596beff01a92700e0e8be4cec
@@ -731,12 +748,59 @@ openpyxl==3.1.2 \
     --hash=sha256:a6f5977418eff3b2d5500d54d9db50c8277a368436f4e4f8ddb1be3422870184 \
     --hash=sha256:f91456ead12ab3c6c2e9491cf33ba6d08357d802192379bb482f1033ade496f5
     # via linkml
+orjson==3.10.3 \
+    --hash=sha256:0943a96b3fa09bee1afdfccc2cb236c9c64715afa375b2af296c73d91c23eab2 \
+    --hash=sha256:0a62f9968bab8a676a164263e485f30a0b748255ee2f4ae49a0224be95f4532b \
+    --hash=sha256:16bda83b5c61586f6f788333d3cf3ed19015e3b9019188c56983b5a299210eb5 \
+    --hash=sha256:1770e2a0eae728b050705206d84eda8b074b65ee835e7f85c919f5705b006c9b \
+    --hash=sha256:17e0713fc159abc261eea0f4feda611d32eabc35708b74bef6ad44f6c78d5ea0 \
+    --hash=sha256:18566beb5acd76f3769c1d1a7ec06cdb81edc4d55d2765fb677e3eaa10fa99e0 \
+    --hash=sha256:1952c03439e4dce23482ac846e7961f9d4ec62086eb98ae76d97bd41d72644d7 \
+    --hash=sha256:1bd2218d5a3aa43060efe649ec564ebedec8ce6ae0a43654b81376216d5ebd42 \
+    --hash=sha256:1c23dfa91481de880890d17aa7b91d586a4746a4c2aa9a145bebdbaf233768d5 \
+    --hash=sha256:252124b198662eee80428f1af8c63f7ff077c88723fe206a25df8dc57a57b1fa \
+    --hash=sha256:2b166507acae7ba2f7c315dcf185a9111ad5e992ac81f2d507aac39193c2c818 \
+    --hash=sha256:2e5e176c994ce4bd434d7aafb9ecc893c15f347d3d2bbd8e7ce0b63071c52e25 \
+    --hash=sha256:3582b34b70543a1ed6944aca75e219e1192661a63da4d039d088a09c67543b08 \
+    --hash=sha256:382e52aa4270a037d41f325e7d1dfa395b7de0c367800b6f337d8157367bf3a7 \
+    --hash=sha256:416b195f78ae461601893f482287cee1e3059ec49b4f99479aedf22a20b1098b \
+    --hash=sha256:4ad1f26bea425041e0a1adad34630c4825a9e3adec49079b1fb6ac8d36f8b754 \
+    --hash=sha256:4c895383b1ec42b017dd2c75ae8a5b862fc489006afde06f14afbdd0309b2af0 \
+    --hash=sha256:5102f50c5fc46d94f2033fe00d392588564378260d64377aec702f21a7a22912 \
+    --hash=sha256:520de5e2ef0b4ae546bea25129d6c7c74edb43fc6cf5213f511a927f2b28148b \
+    --hash=sha256:544a12eee96e3ab828dbfcb4d5a0023aa971b27143a1d35dc214c176fdfb29b3 \
+    --hash=sha256:73100d9abbbe730331f2242c1fc0bcb46a3ea3b4ae3348847e5a141265479700 \
+    --hash=sha256:831c6ef73f9aa53c5f40ae8f949ff7681b38eaddb6904aab89dca4d85099cb78 \
+    --hash=sha256:8bc7a4df90da5d535e18157220d7915780d07198b54f4de0110eca6b6c11e290 \
+    --hash=sha256:8d0b84403d287d4bfa9bf7d1dc298d5c1c5d9f444f3737929a66f2fe4fb8f134 \
+    --hash=sha256:8d40c7f7938c9c2b934b297412c067936d0b54e4b8ab916fd1a9eb8f54c02294 \
+    --hash=sha256:9059d15c30e675a58fdcd6f95465c1522b8426e092de9fff20edebfdc15e1cb0 \
+    --hash=sha256:93433b3c1f852660eb5abdc1f4dd0ced2be031ba30900433223b28ee0140cde5 \
+    --hash=sha256:978be58a68ade24f1af7758626806e13cff7748a677faf95fbb298359aa1e20d \
+    --hash=sha256:99b880d7e34542db89f48d14ddecbd26f06838b12427d5a25d71baceb5ba119d \
+    --hash=sha256:9a7bc9e8bc11bac40f905640acd41cbeaa87209e7e1f57ade386da658092dc16 \
+    --hash=sha256:9e253498bee561fe85d6325ba55ff2ff08fb5e7184cd6a4d7754133bd19c9195 \
+    --hash=sha256:9f3e87733823089a338ef9bbf363ef4de45e5c599a9bf50a7a9b82e86d0228da \
+    --hash=sha256:9fb6c3f9f5490a3eb4ddd46fc1b6eadb0d6fc16fb3f07320149c3286a1409dd8 \
+    --hash=sha256:a39aa73e53bec8d410875683bfa3a8edf61e5a1c7bb4014f65f81d36467ea098 \
+    --hash=sha256:b69a58a37dab856491bf2d3bbf259775fdce262b727f96aafbda359cb1d114d8 \
+    --hash=sha256:b8d4d1a6868cde356f1402c8faeb50d62cee765a1f7ffcfd6de732ab0581e063 \
+    --hash=sha256:ba7f67aa7f983c4345eeda16054a4677289011a478ca947cd69c0a86ea45e534 \
+    --hash=sha256:be2719e5041e9fb76c8c2c06b9600fe8e8584e6980061ff88dcbc2691a16d20d \
+    --hash=sha256:be2aab54313752c04f2cbaab4515291ef5af8c2256ce22abc007f89f42f49109 \
+    --hash=sha256:c0403ed9c706dcd2809f1600ed18f4aae50be263bd7112e54b50e2c2bc3ebd6d \
+    --hash=sha256:c8334c0d87103bb9fbbe59b78129f1f40d1d1e8355bbed2ca71853af15fa4ed3 \
+    --hash=sha256:cb0175a5798bdc878956099f5c54b9837cb62cfbf5d0b86ba6d77e43861bcec2 \
+    --hash=sha256:ccaa0a401fc02e8828a5bedfd80f8cd389d24f65e5ca3954d72c6582495b4bcf \
+    --hash=sha256:cf20465e74c6e17a104ecf01bf8cd3b7b252565b4ccee4548f18b012ff2f8069 \
+    --hash=sha256:d4a654ec1de8fdaae1d80d55cee65893cb06494e124681ab335218be6a0691e7 \
+    --hash=sha256:e852baafceff8da3c9defae29414cc8513a1586ad93e45f27b89a639c68e8176
+    # via fastapi
 packaging==23.2 \
     --hash=sha256:048fb0e9405036518eaaf48a55953c750c11e1a1b68e0dd1a9d62ed0c092cfc5 \
     --hash=sha256:8c491190033a9af7e1d931d0b5dacc2ef47509b34dd0de67ed209b5203fc88c7
     # via
     #   aiokafka
-    #   deprecation
     #   docker
     #   pyproject-api
     #   pytest
@@ -751,9 +815,9 @@ platformdirs==4.1.0 \
     # via
     #   tox
     #   virtualenv
-pluggy==1.3.0 \
-    --hash=sha256:cf61ae8f126ac6f7c451172cf30e3e43d3ca77615509771b3a984a0730651e12 \
-    --hash=sha256:d89c696a773f8bd377d18e5ecda92b7a3793cbe66c87060a6fb58c7b6e1061f7
+pluggy==1.5.0 \
+    --hash=sha256:2cffa88e94fdc978c4c574f15f9e59b7f4201d439195c3715ca9e2486f1d0cf1 \
+    --hash=sha256:44e1ad92c8ca002de6377e165f3e0f1be63266ab4d554740532335b9d75ea669
     # via
     #   pytest
     #   tox
@@ -761,9 +825,10 @@ ply==3.11 \
     --hash=sha256:00c7c1aaa88358b9c765b6d3000c6eec0ba42abca5351b095321aef446081da3 \
     --hash=sha256:096f9b8350b65ebd2fd1346b12452efe5b9607f7482813ffca50c22722a807ce
     # via jsonpath-ng
-pre-commit==3.6.0 \
-    --hash=sha256:c255039ef399049a5544b6ce13d135caba8f2c28c3b4033277a788f434308376 \
-    --hash=sha256:d30bad9abf165f7785c15a21a1f46da7d0677cb00ee7ff4c579fd38922efe15d
+pre-commit==3.7.1 \
+    --hash=sha256:8ca3ad567bc78a4972a3f1a477e94a79d4597e8140a6e0b651c5e33899c3654a \
+    --hash=sha256:fae36fd1d7ad7d6a5a1c0b0d5adb2ed1a3bda5a21bf6c3e5372073d7a11cd4c5
+    # via -r lock/requirements-dev-template.in
 prefixcommons==0.1.12 \
     --hash=sha256:16dbc0a1f775e003c724f19a694fcfa3174608f5c8b0e893d494cf8098ac7f8b \
     --hash=sha256:22c4e2d37b63487b3ab48f0495b70f14564cb346a15220f23919eb0c1851f69f
@@ -905,6 +970,10 @@ pydantic-settings==2.1.0 \
     --hash=sha256:26b1492e0a24755626ac5e6d715e9077ab7ad4fb5f19a8b7ed7011d52f36141c \
     --hash=sha256:7621c0cb5d90d1140d2f0ef557bdf03573aac7035948109adf2574770b77605a
     # via hexkit
+pygments==2.18.0 \
+    --hash=sha256:786ff802f32e91311bff3889f6e9a86e81505fe99f2735bb6d60ae0c5004f199 \
+    --hash=sha256:b8e6aca0523f3ab76fee51799c488e38782ac06eafcf95e7ba832985c8e7b13a
+    # via rich
 pyjsg==0.11.10 \
     --hash=sha256:10af60ff42219be7e85bf7f11c19b648715b0b29eb2ddbd269e87069a7c3f26d \
     --hash=sha256:4bd6e3ff2833fa2b395bbe803a2d72a5f0bab5b7285bccd0da1a1bc0aee88bfa
@@ -995,9 +1064,7 @@ pymongo==4.6.1 \
     --hash=sha256:f9756f1d25454ba6a3c2f1ef8b7ddec23e5cdeae3dc3c3377243ae37a383db00 \
     --hash=sha256:ff62ba8ff70f01ab4fe0ae36b2cb0b5d1f42e73dfc81ddf0758cd9f77331ad25 \
     --hash=sha256:ff925f1cca42e933376d09ddc254598f8c5fcd36efc5cac0118bb36c36217c41
-    # via
-    #   motor
-    #   testcontainers
+    # via motor
 pyparsing==3.1.1 \
     --hash=sha256:32c7c0b711493c72ff18a981d24f28aaf9c1fb7ed5e9667c9e84e3db623bdbfb \
     --hash=sha256:ede28a1a32462f5a9705e07aea48001a08f7cf81a021585011deba701581a0db
@@ -1016,30 +1083,30 @@ pyshexc==0.9.1 \
     # via
     #   linkml
     #   pyshex
-pytest==7.4.3 \
-    --hash=sha256:0d009c083ea859a71b76adf7c1d502e4bc170b80a8ef002da5806527b9591fac \
-    --hash=sha256:d989d136982de4e3b29dabcc838ad581c64e8ed52c11fbe86ddebd9da0818cd5
+pytest==8.2.1 \
+    --hash=sha256:5046e5b46d8e4cac199c373041f26be56fdb81eb4e67dc11d4e10811fc3408fd \
+    --hash=sha256:faccc5d332b8c3719f40283d0d44aa5cf101cec36f88cde9ed8f2bc0538612b1
     # via
+    #   -r lock/requirements-dev-template.in
     #   pytest-asyncio
     #   pytest-cov
     #   pytest-httpx
     #   pytest-logging
-    #   pytest-profiling
-pytest-asyncio==0.23.5 \
-    --hash=sha256:3a048872a9c4ba14c3e90cc1aa20cbc2def7d01c7c8db3777ec281ba9c057675 \
-    --hash=sha256:4e7093259ba018d58ede7d5315131d21923a60f8a6e9ee266ce1589685c89eac
-pytest-cov==4.1.0 \
-    --hash=sha256:3904b13dfbfec47f003b8e77fd5b589cd11904a21ddf1ab38a64f204d6a10ef6 \
-    --hash=sha256:6ba70b9e97e69fcc3fb45bfeab2d0a138fb65c4d0d6a41ef33983ad114be8c3a
+pytest-asyncio==0.23.7 \
+    --hash=sha256:009b48127fbe44518a547bddd25611551b0e43ccdbf1e67d12479f569832c20b \
+    --hash=sha256:5f5c72948f4c49e7db4f29f2521d4031f1c27f86e57b046126654083d4770268
+    # via -r lock/requirements-dev-template.in
+pytest-cov==5.0.0 \
+    --hash=sha256:4f0764a1219df53214206bf1feea4633c3b558a2925c8b59f144f682861ce652 \
+    --hash=sha256:5837b58e9f6ebd335b0f8060eecce69b662415b16dc503883a02f45dfeb14857
+    # via -r lock/requirements-dev-template.in
 pytest-httpx==0.30.0 \
     --hash=sha256:6d47849691faf11d2532565d0c8e0e02b9f4ee730da31687feae315581d7520c \
     --hash=sha256:755b8edca87c974dd4f3605c374fda11db84631de3d163b99c0df5807023a19a
+    # via -r lock/requirements-dev-template.in
 pytest-logging==2015.11.4 \
     --hash=sha256:cec5c85ecf18aab7b2ead5498a31b9f758680ef5a902b9054ab3f2bdbb77c896
     # via prefixcommons
-pytest-profiling==1.7.0 \
-    --hash=sha256:93938f147662225d2b8bd5af89587b979652426a8a6ffd7e73ec4a23e24b7f29 \
-    --hash=sha256:999cc9ac94f2e528e3f5d43465da277429984a1c237ae9818f8cfd0b06acb019
 python-dateutil==2.8.2 \
     --hash=sha256:0123cacc1627ae19ddf3c27a5de5bd67ee4586fbdd6440d9748f8abb483d3e86 \
     --hash=sha256:961d03dc3453ebbc59dbdea9e4e11c5651520a876d0f4db161e8674aae935da9
@@ -1052,6 +1119,10 @@ python-dotenv==1.0.0 \
     # via
     #   pydantic-settings
     #   uvicorn
+python-multipart==0.0.9 \
+    --hash=sha256:03f54688c663f1b7977105f021043b0793151e4cb1c1a9d4a11fc13d622c4026 \
+    --hash=sha256:97ca7b8ea7b05f977dc3849c3ba99d51689822fab725c3703af7c866a0c2b215
+    # via fastapi
 pytrie==0.4.0 \
     --hash=sha256:8f4488f402d3465993fb6b6efa09866849ed8cda7903b50647b7d0342b805379 \
     --hash=sha256:f687c224ee8c66cda8e8628a903011b692635ffbb08d4b39c5f92b18eb78c950
@@ -1150,6 +1221,7 @@ requests==2.31.0 \
     --hash=sha256:58cd2187c01e70e6e26505bca751777aa9f2ee0b7f4300988b709f44e013003f \
     --hash=sha256:942c5a758f98d790eaed1a29cb6eefc7ffb0d1cf7af05c3d2791656dbd6ad1e1
     # via
+    #   -r lock/requirements-dev-template.in
     #   curies
     #   docker
     #   linkml
@@ -1164,6 +1236,10 @@ rfc3987==1.3.8 \
     --hash=sha256:10702b1e51e5658843460b189b185c0366d2cf4cff716f13111b0ea9fd2dce53 \
     --hash=sha256:d3c4d257a560d544e9826b38bc81db676890c79ab9d7ac92b39c7a253d5ca733
     # via jsonschema
+rich==13.7.1 \
+    --hash=sha256:4edbae314f59eb482f54e9e30bf00d33350aaa94f4bfcd4e9e3110e64d0d7222 \
+    --hash=sha256:9be308cb1fe2f1f57d67ce99e95af38a1e2bc71ad9813b0e247cf7ffbcc3a432
+    # via typer
 rpds-py==0.13.2 \
     --hash=sha256:06d218e4464d31301e943b65b2c6919318ea6f69703a351961e1baaf60347276 \
     --hash=sha256:12ecf89bd54734c3c2c79898ae2021dca42750c7bcfb67f8fb3315453738ac8f \
@@ -1323,28 +1399,35 @@ ruamel-yaml-clib==0.2.8 \
     --hash=sha256:f481f16baec5290e45aebdc2a5168ebc6d35189ae6fea7a58787613a25f6e875 \
     --hash=sha256:fff3573c2db359f091e1589c3d7c5fc2f86f5bdb6f24252c2d8e539d4e45f412
     # via ruamel-yaml
-ruff==0.3.3 \
-    --hash=sha256:0171aab5fecdc54383993389710a3d1227f2da124d76a2784a7098e818f92d61 \
-    --hash=sha256:0da458989ce0159555ef224d5b7c24d3d2e4bf4c300b85467b08c3261c6bc6a8 \
-    --hash=sha256:1eca7ff7a47043cf6ce5c7f45f603b09121a7cc047447744b029d1b719278eb5 \
-    --hash=sha256:2700a804d5336bcffe063fd789ca2c7b02b552d2e323a336700abb8ae9e6a3f8 \
-    --hash=sha256:352e95ead6964974b234e16ba8a66dad102ec7bf8ac064a23f95371d8b198aab \
-    --hash=sha256:38671be06f57a2f8aba957d9f701ea889aa5736be806f18c0cd03d6ff0cbca8d \
-    --hash=sha256:45817af234605525cdf6317005923bf532514e1ea3d9270acf61ca2440691376 \
-    --hash=sha256:5a6cbf216b69c7090f0fe4669501a27326c34e119068c1494f35aaf4cc683778 \
-    --hash=sha256:79bca3a03a759cc773fca69e0bdeac8abd1c13c31b798d5bb3c9da4a03144a9f \
-    --hash=sha256:8d6ab88c81c4040a817aa432484e838aaddf8bfd7ca70e4e615482757acb64f8 \
-    --hash=sha256:973a0e388b7bc2e9148c7f9be8b8c6ae7471b9be37e1cc732f8f44a6f6d7720d \
-    --hash=sha256:b24c19e8598916d9c6f5a5437671f55ee93c212a2c4c569605dc3842b6820386 \
-    --hash=sha256:be90bcae57c24d9f9d023b12d627e958eb55f595428bafcb7fec0791ad25ddfc \
-    --hash=sha256:cfa60d23269d6e2031129b053fdb4e5a7b0637fc6c9c0586737b962b2f834493 \
-    --hash=sha256:e7d3f6762217c1da954de24b4a1a70515630d29f71e268ec5000afe81377642d \
-    --hash=sha256:f2831ec6a580a97f1ea82ea1eda0401c3cdf512cf2045fa3c85e8ef109e87de0 \
-    --hash=sha256:fd66469f1a18fdb9d32e22b79f486223052ddf057dc56dea0caaf1a47bdfaf4e
-setuptools==69.2.0 \
-    --hash=sha256:0ff4183f8f42cd8fa3acea16c45205521a4ef28f73c6391d8a25e92893134f2e \
-    --hash=sha256:c21c49fb1042386df081cb5d86759792ab89efca84cf114889191cd09aacc80c
-    # via nodeenv
+ruff==0.4.5 \
+    --hash=sha256:1169e47e9c4136c997f08f9857ae889d614c5035d87d38fda9b44b4338909cdf \
+    --hash=sha256:25f483ad9d50b00e7fd577f6d0305aa18494c6af139bce7319c68a17180087f4 \
+    --hash=sha256:286eabd47e7d4d521d199cab84deca135557e6d1e0f0d01c29e757c3cb151b54 \
+    --hash=sha256:441dab55c568e38d02bbda68a926a3d0b54f5510095c9de7f95e47a39e0168aa \
+    --hash=sha256:63fde3bf6f3ad4e990357af1d30e8ba2730860a954ea9282c95fc0846f5f64af \
+    --hash=sha256:6e1b139b45e2911419044237d90b60e472f57285950e1492c757dfc88259bb06 \
+    --hash=sha256:755ac9ac2598a941512fc36a9070a13c88d72ff874a9781493eb237ab02d75df \
+    --hash=sha256:75a426506a183d9201e7e5664de3f6b414ad3850d7625764106f7b6d0486f0a1 \
+    --hash=sha256:78e3ba4620dee27f76bbcad97067766026c918ba0f2d035c2fc25cbdd04d9c97 \
+    --hash=sha256:84dd157474e16e3a82745d2afa1016c17d27cb5d52b12e3d45d418bcc6d49264 \
+    --hash=sha256:8f58e615dec58b1a6b291769b559e12fdffb53cc4187160a2fc83250eaf54e96 \
+    --hash=sha256:9d15de3425f53161b3f5a5658d4522e4eee5ea002bf2ac7aa380743dd9ad5fba \
+    --hash=sha256:a6f29a8221d2e3d85ff0c7b4371c0e37b39c87732c969b4d90f3dad2e721c5b1 \
+    --hash=sha256:aed8166c18b1a169a5d3ec28a49b43340949e400665555b51ee06f22813ef062 \
+    --hash=sha256:b0b03c619d2b4350b4a27e34fd2ac64d0dabe1afbf43de57d0f9d8a05ecffa45 \
+    --hash=sha256:d6ef817124d72b54cc923f3444828ba24fa45c3164bc9e8f1813db2f3d3a8a11 \
+    --hash=sha256:f4b02a65985be2b34b170025a8b92449088ce61e33e69956ce4d316c0fe7cce0
+    # via -r lock/requirements-dev-template.in
+setuptools==70.0.0 \
+    --hash=sha256:54faa7f2e8d2d11bcd2c07bed282eef1046b5c080d1c32add737d7b5817b1ad4 \
+    --hash=sha256:f211a66637b8fa059bb28183da127d4e86396c991a942b028c6650d4319c3fd0
+    # via
+    #   -r lock/requirements-dev-template.in
+    #   nodeenv
+shellingham==1.5.4 \
+    --hash=sha256:7ecfff8f2fd72616f7481040475a65b2bf8af90a56c89140852d1120324e8686 \
+    --hash=sha256:8dbca0739d487e5bd35ab3ca4b36e11c4078f3a234bfce294b0a0291363404de
+    # via typer
 shexjsg==0.8.2 \
     --hash=sha256:3b0d8432dd313bee9e1343382c5e02e9908dd941a7dd7342bf8c0200fe523766 \
     --hash=sha256:f17a629fc577fa344382bdee143cd9ff86588537f9f811f66cea6f63cdbcd0b6
@@ -1356,12 +1439,12 @@ six==1.16.0 \
     --hash=sha256:8abb2f1d86890a2dfb989f9a77cfcfd3e47c2a354b01111771326f8aa26e0254
     # via
     #   isodate
-    #   pytest-profiling
     #   python-dateutil
     #   rfc3339-validator
 snakeviz==2.2.0 \
     --hash=sha256:569e2d71c47f80a886aa6e70d6405cb6d30aa3520969ad956b06f824c5f02b8e \
     --hash=sha256:7bfd00be7ae147eb4a170a471578e1cd3f41f803238958b6b8efcf2c698a6aa9
+    # via -r lock/requirements-dev-template.in
 sniffio==1.3.0 \
     --hash=sha256:e60305c5e5d314f5389259b7f22aaa33d8f7dee49763119234af3755c55b9101 \
     --hash=sha256:eecefdce1e5bbfb7ad2eeaabf7c1eeb404d7757c379bd1f7e5cce9d8bf425384
@@ -1433,27 +1516,23 @@ sqlalchemy==2.0.23 \
     --hash=sha256:f508ba8f89e0a5ecdfd3761f82dda2a3d7b678a626967608f4273e0dba8f07ac \
     --hash=sha256:fd54601ef9cc455a0c61e5245f690c8a3ad67ddb03d3b91c361d076def0b4c60
     # via linkml
-starlette==0.36.3 \
-    --hash=sha256:13d429aa93a61dc40bf503e8c801db1f1bca3dc706b10ef2434a36123568f044 \
-    --hash=sha256:90a671733cfb35771d8cc605e0b679d23b992f8dcfad48cc60b38cb29aeb7080
+starlette==0.37.2 \
+    --hash=sha256:6fe59f29268538e5d0d182f2791a479a0c64638e6935d1c6989e63fb2699c6ee \
+    --hash=sha256:9af890290133b79fc3db55474ade20f6220a364a0402e0b556e7cd5e1e093823
     # via fastapi
 stringcase==1.2.0 \
     --hash=sha256:48a06980661908efe8d9d34eab2b6c13aefa2163b3ced26972902e3bdfd87008
-    # via linkml-validator
-testcontainers==3.7.1 \
-    --hash=sha256:7f48cef4bf0ccd78f1a4534d4b701a003a3bace851f24eae58a32f9e3f0aeba0
-tomli==2.0.1 \
-    --hash=sha256:939de3e7a6161af0c887ef91b7d41a53e7c5a1ca976325f429cb46ea9bc30ecc \
-    --hash=sha256:de526c12914f0c550d15924c62d72abc48d6fe7364aa87328337a31007fe8a4f
     # via
-    #   coverage
-    #   mypy
-    #   pyproject-api
-    #   pytest
-    #   tox
+    #   -r lock/requirements-dev-template.in
+    #   linkml-validator
+testcontainers==4.5.0 \
+    --hash=sha256:6833df7db4cf8403feb1e4daf69b02a091d9da37aa3e8e808c756abbddb41cf3 \
+    --hash=sha256:e8610985cae2f0bc4bc3991896a47d5547f3ed896192970826151059a75f4ac2
+    # via -r lock/requirements-dev.in
 tomli-w==1.0.0 \
     --hash=sha256:9f2a07e8be30a0729e533ec968016807069991ae2fd921a78d42f429ae5f4463 \
     --hash=sha256:f463434305e0336248cac9c2dc8076b707d8a12d019dd349f5c1e382dd1ae1b9
+    # via -r lock/requirements-dev-template.in
 tornado==6.4 \
     --hash=sha256:02ccefc7d8211e5a7f9e8bc3f9e5b0ad6262ba2fbb683a6443ecc804e5224ce0 \
     --hash=sha256:10aeaa8006333433da48dec9fe417877f8bcc21f48dda8d661ae79da357b2a63 \
@@ -1471,9 +1550,13 @@ tox==4.11.4 \
     --hash=sha256:2adb83d68f27116812b69aa36676a8d6a52249cb0d173649de0e7d0c2e3e7229 \
     --hash=sha256:73a7240778fabf305aeb05ab8ea26e575e042ab5a18d71d0ed13e343a51d6ce1
     # via prefixmaps
-typer==0.9.0 \
-    --hash=sha256:50922fd79aea2f4751a8e0408ff10d2662bd0c8bbfa84755a699f3bada2978b2 \
-    --hash=sha256:5d96d986a21493606a358cae4461bd8cdf83cbf33a5aa950ae629ca3b51467ee
+typer==0.12.3 \
+    --hash=sha256:070d7ca53f785acbccba8e7d28b08dcd88f79f1fbda035ade0aecec71ca5c914 \
+    --hash=sha256:49e73131481d804288ef62598d97a1ceef3058905aa536a1134f90891ba35482
+    # via
+    #   -r lock/requirements-dev-template.in
+    #   metldata (pyproject.toml)
+    #   fastapi-cli
 types-python-dateutil==2.8.19.14 \
     --hash=sha256:1f4f10ac98bb8b16ade9dbee3518d9ace017821d94b057a425b069f834737f4b \
     --hash=sha256:f977b8de27787639986b4e28963263fd0e5158942b3ecef91b9335c130cb1ce9
@@ -1484,14 +1567,92 @@ typing-extensions==4.9.0 \
     # via
     #   fastapi
     #   jwcrypto
-    #   logot
     #   mypy
     #   pydantic
     #   pydantic-core
     #   sqlalchemy
-    #   starlette
+    #   testcontainers
     #   typer
-    #   uvicorn
+ujson==5.10.0 \
+    --hash=sha256:0de4971a89a762398006e844ae394bd46991f7c385d7a6a3b93ba229e6dac17e \
+    --hash=sha256:129e39af3a6d85b9c26d5577169c21d53821d8cf68e079060602e861c6e5da1b \
+    --hash=sha256:22cffecf73391e8abd65ef5f4e4dd523162a3399d5e84faa6aebbf9583df86d6 \
+    --hash=sha256:232cc85f8ee3c454c115455195a205074a56ff42608fd6b942aa4c378ac14dd7 \
+    --hash=sha256:2544912a71da4ff8c4f7ab5606f947d7299971bdd25a45e008e467ca638d13c9 \
+    --hash=sha256:2601aa9ecdbee1118a1c2065323bda35e2c5a2cf0797ef4522d485f9d3ef65bd \
+    --hash=sha256:26b0e2d2366543c1bb4fbd457446f00b0187a2bddf93148ac2da07a53fe51569 \
+    --hash=sha256:2987713a490ceb27edff77fb184ed09acdc565db700ee852823c3dc3cffe455f \
+    --hash=sha256:29b443c4c0a113bcbb792c88bea67b675c7ca3ca80c3474784e08bba01c18d51 \
+    --hash=sha256:2a890b706b64e0065f02577bf6d8ca3b66c11a5e81fb75d757233a38c07a1f20 \
+    --hash=sha256:2aff2985cef314f21d0fecc56027505804bc78802c0121343874741650a4d3d1 \
+    --hash=sha256:348898dd702fc1c4f1051bc3aacbf894caa0927fe2c53e68679c073375f732cf \
+    --hash=sha256:38665e7d8290188b1e0d57d584eb8110951a9591363316dd41cf8686ab1d0abc \
+    --hash=sha256:38d5d36b4aedfe81dfe251f76c0467399d575d1395a1755de391e58985ab1c2e \
+    --hash=sha256:3ff201d62b1b177a46f113bb43ad300b424b7847f9c5d38b1b4ad8f75d4a282a \
+    --hash=sha256:4573fd1695932d4f619928fd09d5d03d917274381649ade4328091ceca175539 \
+    --hash=sha256:4734ee0745d5928d0ba3a213647f1c4a74a2a28edc6d27b2d6d5bd9fa4319e27 \
+    --hash=sha256:4c4fc16f11ac1612f05b6f5781b384716719547e142cfd67b65d035bd85af165 \
+    --hash=sha256:502bf475781e8167f0f9d0e41cd32879d120a524b22358e7f205294224c71126 \
+    --hash=sha256:57aaf98b92d72fc70886b5a0e1a1ca52c2320377360341715dd3933a18e827b1 \
+    --hash=sha256:59e02cd37bc7c44d587a0ba45347cc815fb7a5fe48de16bf05caa5f7d0d2e816 \
+    --hash=sha256:5b6fee72fa77dc172a28f21693f64d93166534c263adb3f96c413ccc85ef6e64 \
+    --hash=sha256:5b91b5d0d9d283e085e821651184a647699430705b15bf274c7896f23fe9c9d8 \
+    --hash=sha256:604a046d966457b6cdcacc5aa2ec5314f0e8c42bae52842c1e6fa02ea4bda42e \
+    --hash=sha256:618efd84dc1acbd6bff8eaa736bb6c074bfa8b8a98f55b61c38d4ca2c1f7f287 \
+    --hash=sha256:61d0af13a9af01d9f26d2331ce49bb5ac1fb9c814964018ac8df605b5422dcb3 \
+    --hash=sha256:61e1591ed9376e5eddda202ec229eddc56c612b61ac6ad07f96b91460bb6c2fb \
+    --hash=sha256:621e34b4632c740ecb491efc7f1fcb4f74b48ddb55e65221995e74e2d00bbff0 \
+    --hash=sha256:6627029ae4f52d0e1a2451768c2c37c0c814ffc04f796eb36244cf16b8e57043 \
+    --hash=sha256:67079b1f9fb29ed9a2914acf4ef6c02844b3153913eb735d4bf287ee1db6e557 \
+    --hash=sha256:6dea1c8b4fc921bf78a8ff00bbd2bfe166345f5536c510671bccececb187c80e \
+    --hash=sha256:6e32abdce572e3a8c3d02c886c704a38a1b015a1fb858004e03d20ca7cecbb21 \
+    --hash=sha256:7223f41e5bf1f919cd8d073e35b229295aa8e0f7b5de07ed1c8fddac63a6bc5d \
+    --hash=sha256:73814cd1b9db6fc3270e9d8fe3b19f9f89e78ee9d71e8bd6c9a626aeaeaf16bd \
+    --hash=sha256:7490655a2272a2d0b072ef16b0b58ee462f4973a8f6bbe64917ce5e0a256f9c0 \
+    --hash=sha256:7663960f08cd5a2bb152f5ee3992e1af7690a64c0e26d31ba7b3ff5b2ee66337 \
+    --hash=sha256:78778a3aa7aafb11e7ddca4e29f46bc5139131037ad628cc10936764282d6753 \
+    --hash=sha256:7c10f4654e5326ec14a46bcdeb2b685d4ada6911050aa8baaf3501e57024b804 \
+    --hash=sha256:7ec0ca8c415e81aa4123501fee7f761abf4b7f386aad348501a26940beb1860f \
+    --hash=sha256:924f7318c31874d6bb44d9ee1900167ca32aa9b69389b98ecbde34c1698a250f \
+    --hash=sha256:94a87f6e151c5f483d7d54ceef83b45d3a9cca7a9cb453dbdbb3f5a6f64033f5 \
+    --hash=sha256:98ba15d8cbc481ce55695beee9f063189dce91a4b08bc1d03e7f0152cd4bbdd5 \
+    --hash=sha256:a245d59f2ffe750446292b0094244df163c3dc96b3ce152a2c837a44e7cda9d1 \
+    --hash=sha256:a5b366812c90e69d0f379a53648be10a5db38f9d4ad212b60af00bd4048d0f00 \
+    --hash=sha256:a65b6af4d903103ee7b6f4f5b85f1bfd0c90ba4eeac6421aae436c9988aa64a2 \
+    --hash=sha256:a984a3131da7f07563057db1c3020b1350a3e27a8ec46ccbfbf21e5928a43050 \
+    --hash=sha256:a9d2edbf1556e4f56e50fab7d8ff993dbad7f54bac68eacdd27a8f55f433578e \
+    --hash=sha256:ab13a2a9e0b2865a6c6db9271f4b46af1c7476bfd51af1f64585e919b7c07fd4 \
+    --hash=sha256:ac56eb983edce27e7f51d05bc8dd820586c6e6be1c5216a6809b0c668bb312b8 \
+    --hash=sha256:ad88ac75c432674d05b61184178635d44901eb749786c8eb08c102330e6e8996 \
+    --hash=sha256:b0111b27f2d5c820e7f2dbad7d48e3338c824e7ac4d2a12da3dc6061cc39c8e6 \
+    --hash=sha256:b3cd8f3c5d8c7738257f1018880444f7b7d9b66232c64649f562d7ba86ad4bc1 \
+    --hash=sha256:b9500e61fce0cfc86168b248104e954fead61f9be213087153d272e817ec7b4f \
+    --hash=sha256:ba17799fcddaddf5c1f75a4ba3fd6441f6a4f1e9173f8a786b42450851bd74f1 \
+    --hash=sha256:ba43cc34cce49cf2d4bc76401a754a81202d8aa926d0e2b79f0ee258cb15d3a4 \
+    --hash=sha256:baed37ea46d756aca2955e99525cc02d9181de67f25515c468856c38d52b5f3b \
+    --hash=sha256:beeaf1c48e32f07d8820c705ff8e645f8afa690cca1544adba4ebfa067efdc88 \
+    --hash=sha256:c18610b9ccd2874950faf474692deee4223a994251bc0a083c114671b64e6518 \
+    --hash=sha256:c66962ca7565605b355a9ed478292da628b8f18c0f2793021ca4425abf8b01e5 \
+    --hash=sha256:caf270c6dba1be7a41125cd1e4fc7ba384bf564650beef0df2dd21a00b7f5770 \
+    --hash=sha256:cc6139531f13148055d691e442e4bc6601f6dba1e6d521b1585d4788ab0bfad4 \
+    --hash=sha256:d2c75269f8205b2690db4572a4a36fe47cd1338e4368bc73a7a0e48789e2e35a \
+    --hash=sha256:d47ebb01bd865fdea43da56254a3930a413f0c5590372a1241514abae8aa7c76 \
+    --hash=sha256:d4dc2fd6b3067c0782e7002ac3b38cf48608ee6366ff176bbd02cf969c9c20fe \
+    --hash=sha256:d7d0e0ceeb8fe2468c70ec0c37b439dd554e2aa539a8a56365fd761edb418988 \
+    --hash=sha256:d8640fb4072d36b08e95a3a380ba65779d356b2fee8696afeb7794cf0902d0a1 \
+    --hash=sha256:dee5e97c2496874acbf1d3e37b521dd1f307349ed955e62d1d2f05382bc36dd5 \
+    --hash=sha256:dfef2814c6b3291c3c5f10065f745a1307d86019dbd7ea50e83504950136ed5b \
+    --hash=sha256:e1402f0564a97d2a52310ae10a64d25bcef94f8dd643fcf5d310219d915484f7 \
+    --hash=sha256:e7ce306a42b6b93ca47ac4a3b96683ca554f6d35dd8adc5acfcd55096c8dfcb8 \
+    --hash=sha256:e82d4bb2138ab05e18f089a83b6564fee28048771eb63cdecf4b9b549de8a2cc \
+    --hash=sha256:ecb24f0bdd899d368b715c9e6664166cf694d1e57be73f17759573a6986dd95a \
+    --hash=sha256:f00ea7e00447918ee0eff2422c4add4c5752b1b60e88fcb3c067d4a21049a720 \
+    --hash=sha256:f3caf9cd64abfeb11a3b661329085c5e167abbe15256b3b68cb5d914ba7396f3 \
+    --hash=sha256:f44bd4b23a0e723bf8b10628288c2c7c335161d6840013d4d5de20e48551773b \
+    --hash=sha256:f77b74475c462cb8b88680471193064d3e715c7c6074b1c8c412cb526466efe9 \
+    --hash=sha256:f8ccb77b3e40b151e20519c6ae6d89bfe3f4c14e8e210d910287f778368bb3d1 \
+    --hash=sha256:fbd8fd427f57a03cff3ad6574b5e299131585d9727c8c366da4624a9069ed746
+    # via fastapi
 uri-template==1.3.0 \
     --hash=sha256:0e00f8eb65e18c7de20d595a14336e9f337ead580c70934141624b6d1ffdacc7 \
     --hash=sha256:a44a133ea12d44a0c0f06d7d42a52d71282e77e2f937d8abd5655b8d56fc1363
@@ -1500,31 +1661,36 @@ urllib3==2.1.0 \
     --hash=sha256:55901e917a5896a349ff771be919f8bd99aff50b79fe58fec595eb37bbc56bb3 \
     --hash=sha256:df7aa8afb0148fa78488e7899b2c59b5f4ffcfa82e6c54ccb9dd37c1d7b52d54
     # via
+    #   -r lock/requirements-dev-template.in
     #   docker
     #   pyshex
     #   requests
-uv==0.1.22 \
-    --hash=sha256:144ffabe5f2519bf371bfd3db074b3d0952db31263fbd9b5b9a18efbc90ee772 \
-    --hash=sha256:23ce9a081e046d40ea9582824f1ec1a64830e7292f5885b42526baa0d9d834e1 \
-    --hash=sha256:275892300f842170eb03e15ee077d9f2327966d3e12048568230a13cd8de7ba5 \
-    --hash=sha256:28ea7dd1e9048610a13b47976c3f45ab1cc99e96f085c9e6659f024b46dad870 \
-    --hash=sha256:4936331140392c057e56e29751bcf0461ba5ec92592bf2082f7a85e8170c4051 \
-    --hash=sha256:4d23fa6693d5026b45df75b996a3f43166d10caa690925f9ee55e2d5ff61cfa9 \
-    --hash=sha256:6ae068131fd255bf55f48c077e54558184a1a23fcefbb78de3189853d121cf29 \
-    --hash=sha256:94f45b92d48489867c2b07a5ec2b1ead6994d46573f9066d3473e08a04f662e4 \
-    --hash=sha256:9b0d5d062484dcf97e191d4a28de23974ba6a384315300f9a439268506460b7d \
-    --hash=sha256:9c238d417a67aab57c2d407778c86078f92e12d127bc4076f5565a9203f3e4f5 \
-    --hash=sha256:b86f7c1ccbffa34cf82d2b5ff6b8650d3a66f4b9496b8fd07b18420ae232ebd7 \
-    --hash=sha256:baf5c2c0a1097dc29da6ab610c90b798d5e5e97aaace2e66cb474a8e2c1e0361 \
-    --hash=sha256:dee413bac546c359a37065e9b8ef1d48210517763000e569ed577745da11c321 \
-    --hash=sha256:e83c858770ad2eced9750bd6b7aed320d74e4a35a9408895de506bbc7b11343c \
-    --hash=sha256:f350292267f361c0aeb8c68f81e81d18e7eb383d8323dd10017ee93747471deb \
-    --hash=sha256:fa0f0eb1306082c65f042c4c54d6a7c1078b9b3ad65da4af7df11fba91848e21 \
-    --hash=sha256:fefb107a2fb4eac874cdf1066f8cc40c5112853890fa49520e13975a6ad2778a
-uvicorn==0.27.1 \
-    --hash=sha256:3d9a267296243532db80c83a959a3400502165ade2c1338dea4e67915fd4745a \
-    --hash=sha256:5c89da2f3895767472a35556e539fd59f7edbe9b1e9c0e1c99eebeadc61838e4
-    # via ghga-service-commons
+    #   testcontainers
+uv==0.2.4 \
+    --hash=sha256:097ccebb62f78a6da83c317d3e853afb382989a56154cfda57cffb8315a11784 \
+    --hash=sha256:25e2838d41bbce8eacd994b84e0cb2e3cac53c6044911675eb6d7d8292940039 \
+    --hash=sha256:26c2b4cec6e1ddc21c3dc49a328cab811971f16ed65860c5283d155ce68baa84 \
+    --hash=sha256:2a9d4211f60bb6fb2d6920628f70492ee825832e0cb30c62f49d2732b0c9a69d \
+    --hash=sha256:52aea379296cc82e1738955c00158108b8291d3112c0d037a28977c646940560 \
+    --hash=sha256:54ef0ef828a72c9b07b40d667e2a7a4db99db5fe6b4942aa7973e2b252b9ac1b \
+    --hash=sha256:550234196199b9bb046e036f13b05b869334c21f84665557f502217c56e31794 \
+    --hash=sha256:6f4c0ea371ad7ca6c8a8a7299b65cc0287d489cc45286254ddc1c25c23f69969 \
+    --hash=sha256:6f7cfc189fd4e5a2f6e24171ce911a2ef95d1827323975c39e6cd1436a9eaab9 \
+    --hash=sha256:7b48df5f0426fd4ee4e1d3d0f23ffc25945f2a62335a613eeef175f73d578d96 \
+    --hash=sha256:7f68ca7b3e53076d41bbfab74318ae3c5af93a58e409fe35fbe1f1d251017f4c \
+    --hash=sha256:8d67bf132d828d6f9e4936f9935c9426731d27b31ebe8797420a0c4459184363 \
+    --hash=sha256:9d0e58753a841f1260cca74c6e5baaced387e84ccc5b97931adc0061d9615a3a \
+    --hash=sha256:a4d4632179961f31fbecaeaf100903a76707547874f087d0461b6db01bce5ef3 \
+    --hash=sha256:ac07eeef96a83ff7dd5ff171441135436b3590d04f62cd273322b5e14fa32e7e \
+    --hash=sha256:b7cb9d8d71914e608358de43b1f54db5c435dd079665d7b2ab9d1724468a691f \
+    --hash=sha256:ea84d56c968205efe1f6e8a232a6bc1f10236fa3bd788c3e4d32e2bb7a70303f
+    # via -r lock/requirements-dev-template.in
+uvicorn==0.29.0 \
+    --hash=sha256:2c2aac7ff4f4365c206fd773a39bf4ebd1047c238f8b8268ad996829323473de \
+    --hash=sha256:6a69214c0b6a087462412670b3ef21224fa48cae0e452b5883e8e8bdfdd11dd0
+    # via
+    #   fastapi
+    #   ghga-service-commons
 uvloop==0.19.0 \
     --hash=sha256:0246f4fd1bf2bf702e06b0d45ee91677ee5c31242f39aab4ea6fe0c51aedd0fd \
     --hash=sha256:02506dc23a5d90e04d4f65c7791e65cf44bd91b37f24cfc3ef6cf2aff05dc7ec \
diff --git a/lock/requirements.txt b/lock/requirements.txt
index bc51fba1..9399132a 100644
--- a/lock/requirements.txt
+++ b/lock/requirements.txt
@@ -1,39 +1,48 @@
-# This file was autogenerated by uv via the following command:
-#    uv pip compile --refresh --generate-hashes --output-file /workspace/lock/requirements.txt /tmp/tmphyx3y5vn/pyproject.toml -c /workspace/lock/requirements-dev.txt
-aiokafka==0.8.1 \
-    --hash=sha256:1e24839088fd6d3ff481cc09a48ea487b997328df11630bc0a1b88255edbcfe9 \
-    --hash=sha256:1f43d2afd7d3e4407ada8d754895fad7c344ca00648a8a38418d76564eaaf6cd \
-    --hash=sha256:1f6044ed270b946d31f265903b5eb101940ed0ff3a902eaf8178103c943bbcc9 \
-    --hash=sha256:24373bb2d519abac036d5b04ebc43452ef4ad1916953b6678b9801a9c93ba237 \
-    --hash=sha256:2fa54b8b068d9d8735cb6757a0f48168f8cf9be68860b0bae6b3ed1684cef49b \
-    --hash=sha256:3816bcfc3c57dfa4ed77fe1dc3a9a464e17b6400061348155115f282c8150c47 \
-    --hash=sha256:45cd28af6590d6a999bb706803166570121ba8a5a0d06c51ebd8a59fab53593c \
-    --hash=sha256:4693fbe3c10f125bf3e2df8a8ccbca3eff2bdaaa6589d28c7532c10e7d84598b \
-    --hash=sha256:4fccd599ab6b3fda4f4187d854b343f153b40d05d6774be9acf238618da50031 \
-    --hash=sha256:6421ee81084532f915501074a132acb2afc8cb88bf5ddb11e584230a30f6f006 \
-    --hash=sha256:673c163dee62dfe45146d5250af0e395da5cc92b63f8878c592abc7dc1862899 \
-    --hash=sha256:7d327d66b41c4e3bafff7f9efb71936a08f940aa665680717e20862e4272a068 \
-    --hash=sha256:7f09784322c0d2c4fcc222add4337a5ac394aa30a248eb4e0e4587a125573c75 \
-    --hash=sha256:90960356513f3979754261b132b12a96b0d9e3c6eb44420e3a90a7c31156a81a \
-    --hash=sha256:935da8c4da9a00a1e16020d88e578206097b4bb72ebc2a25fbd2cb817907ef28 \
-    --hash=sha256:9f19d90b7360bc2239fcd8b147508ae39c3e5b1acfc8e6a2a9b0f306070f7ffe \
-    --hash=sha256:a8a641a8102c51422afe111d4bc70c51f335f38fc5906e4c839bd17afeaf3cb2 \
-    --hash=sha256:af6df9a41e08b61d7e62c0a416feeabd81bad76fa5c70d499b083d6af9ce72c3 \
-    --hash=sha256:b2bf97548fa77ad31062ca580368d346b16ba9fdca5856c435f256f3699ab12b \
-    --hash=sha256:bbffc431d9285328c0bc108949132ae11cec863f1dd5a43a1fc3d45a69ffb8a9 \
-    --hash=sha256:bf7473c55dc7959d4b7f9d750fa6017b325813d6cb761e488c2d9ea44e922954 \
-    --hash=sha256:c4332d37cb9d52181cfda4236566b4028c7c188549277f87bcc3027577d72b1b \
-    --hash=sha256:d300188e358cd29989c817f6ee2a2965a039e5a71de8ade6f80f02ebb9bd07b8 \
-    --hash=sha256:fd8f9e17bc9cd2ea664a7f5133aede39a8fffebffe0c450252d475dbdedb4a35 \
-    --hash=sha256:ff318d29ecbeea8c58d69c91c24d48d7ed4a8d3e829b607e670d118a9a35d5ba
-    # via hexkit
+aiokafka==0.10.0 \
+    --hash=sha256:007f1c51f440cc07155d2491f4deea6536492324153296aa73736a74cd833d3e \
+    --hash=sha256:05c4a7ced5d6f3dbc289767574d6a5d9b31e1c243e992dcecd34dbc40fcbbf9b \
+    --hash=sha256:06060708a4bcf062be496c8641fca382c88782d3c381a34ccb5ac8677bdac695 \
+    --hash=sha256:12d703317812262feac6577ff488f2ccddc4408da0ff608a5454062782b5a80d \
+    --hash=sha256:1509c1b29cd1d4d920a649f257d72109bbc3d61431135505b8e0d8d488796ff2 \
+    --hash=sha256:1fe0194ea72524df37369a8cf0837263b55194ac20616e612f0ab7bfb568b76b \
+    --hash=sha256:22299f8d5269dcb00b1b53fdee44dbe729091d4038e1bb63d0bb2f5cdf9af47a \
+    --hash=sha256:5efb63686562809f0f9bf0fa6d1e52f222af2d8f8441f8c412b156f15c98da43 \
+    --hash=sha256:6e10fdee4189fe7eed36d602df822e9ff4f19535c0a514cf015f78308d206c1a \
+    --hash=sha256:7068f0beb8478cde09618dcc9a833cc18ff37bd14864fa8b60ad4e4c3dad6489 \
+    --hash=sha256:74229a57c95e2efccec95d9b42554dc168c97a263f013e3e983202bd33ca189d \
+    --hash=sha256:781ab300214681e40667185a402abf6b31b4c4b8f1cdabbdc3549d8cf383b34d \
+    --hash=sha256:7ce35563f955490b43190e3389b5f3d92d50e22b32d1a40772fd14fb1d50c5db \
+    --hash=sha256:82a75ea13d7e6e11c7ee2fb9419e9ea3541744648c69ab27b56fb6bca5b319c1 \
+    --hash=sha256:8b74aeacfb8ced9764002c63b58e4c78c94809131d89000cb936c25c298ffb1e \
+    --hash=sha256:9728c523f10ac4bb46719cc64f3c1d47625898872bc3901b22b9d48b6e401d1c \
+    --hash=sha256:99127ab680f9b08b0213d00b7d1e0480c6d08601f52ad42e829350f9599db301 \
+    --hash=sha256:b91109dc25f79be4d27454cc766239a5368d18b26682d4b5c6b913ca92691220 \
+    --hash=sha256:c23ec22fbf26e2f84678f0589076bea1ff26ae6dfd3c601e6de10ad00d605261 \
+    --hash=sha256:cf4a47659517000a8fe88e0fb353898b718ee214e21f62a2a949be9bf801cd9e \
+    --hash=sha256:cf9e241766b7f4c305807763330dacf8c220ad9e8fc7f2b22730a2db66fad61d \
+    --hash=sha256:d52c25f3d0db7dd340a5d08108da302db1ba64c2190970dbdb768b79629d6add \
+    --hash=sha256:de56c503b3d64e24a5b6705e55bc524a8357b0495402f859f921a71d65274cb1 \
+    --hash=sha256:e16d8a23f0e173e5ca86c2d1c270e25a529a0eed973c77d7e8a0dfc868699aa4 \
+    --hash=sha256:e833e4ef7fc5f3f637ba5fb4210acc7e5ea916bb7107e4b619b1b1a3e361bc62 \
+    --hash=sha256:ebe5be9f578e89e6db961121070f7c35662924abee00ba4ccf64557e2cdd7edf \
+    --hash=sha256:f069bda1f31e466d815b631a07bc6fad5190b29dfff5f117bcbf1948cd7a38aa \
+    --hash=sha256:f2f19dee69c69389f5911e6b23c361c5285366d237f782eaae118d12acc42d7f \
+    --hash=sha256:f4b22a31f40493cea50dddb4dfc92750dfb273635ccb094a16fde9678eb38958 \
+    --hash=sha256:fafc95bdaed9e1810fcd80b02ac117e51c72681ffe50353e5d61e2170609e1fc \
+    --hash=sha256:ffc30e4c6bfcb00356a002f623c93a51d8336ca67687ea069dd11822da07379c
+    # via
+    #   -c lock/requirements-dev.txt
+    #   hexkit
 annotated-types==0.6.0 \
     --hash=sha256:0641064de18ba7a25dee8f96403ebc39113d0cb953a01429249d5c7564666a43 \
     --hash=sha256:563339e807e53ffd9c267e99fc6d9ea23eb8443c08f112651963e24e22f84a5d
-    # via pydantic
+    # via
+    #   -c lock/requirements-dev.txt
+    #   pydantic
 antlr4-python3-runtime==4.9.3 \
     --hash=sha256:f224469b4168294902bb1efa80a8bf7855f24c99aef99cbefc1bcd3cce77881b
     # via
+    #   -c lock/requirements-dev.txt
     #   linkml
     #   pyjsg
     #   pyshexc
@@ -41,30 +50,43 @@ anyio==3.7.1 \
     --hash=sha256:44a3c9aba0f5defa43261a8b3efb97891f2bd7d804e0e1f56419befa1adfc780 \
     --hash=sha256:91dee416e570e92c64041bd18b900d1d6fa78dff7048769ce5ac5ddad004fbb5
     # via
+    #   -c lock/requirements-dev.txt
+    #   httpx
     #   starlette
     #   watchfiles
 arrow==1.3.0 \
     --hash=sha256:c728b120ebc00eb84e01882a6f5e7927a53960aa990ce7dd2b10f39005a67f80 \
     --hash=sha256:d4540617648cb5f895730f1ad8c82a65f2dad0166f57b75f3ca54759c4d67a85
-    # via isoduration
+    # via
+    #   -c lock/requirements-dev.txt
+    #   isoduration
 async-timeout==4.0.3 \
     --hash=sha256:4640d96be84d82d02ed59ea2b7105a0f7b33abe8703703cd0ab0bf87c427522f \
     --hash=sha256:7405140ff1230c310e51dc27b3145b9092d659ce68ff733fb0cefe3ee42be028
-    # via aiokafka
+    # via
+    #   -c lock/requirements-dev.txt
+    #   aiokafka
 attrs==23.1.0 \
     --hash=sha256:1f28b4522cdc2fb4256ac1a020c78acf9cba2c6b461ccd2c126f3aa8e8335d04 \
     --hash=sha256:6279836d581513a26f1bf235f9acd333bc9115683f14f7e8fae46c98fc50e015
     # via
+    #   -c lock/requirements-dev.txt
     #   jsonschema
     #   referencing
 cachetools==5.3.2 \
     --hash=sha256:086ee420196f7b2ab9ca2db2520aca326318b68fe5ba8bc4d49cca91add450f2 \
     --hash=sha256:861f35a13a451f94e301ce2bec7cac63e881232ccce7ed67fab9b5df4d3beaa1
-    # via tox
+    # via
+    #   -c lock/requirements-dev.txt
+    #   tox
 certifi==2023.11.17 \
     --hash=sha256:9b469f3a900bf28dc19b8cfbf8019bf47f7fdd1a65a1d4ffb98fc14166beb4d1 \
     --hash=sha256:e036ab49d5b79556f99cfc2d9320b34cfbe5be05c5871b51de9329f0603b0474
-    # via requests
+    # via
+    #   -c lock/requirements-dev.txt
+    #   httpcore
+    #   httpx
+    #   requests
 cffi==1.16.0 \
     --hash=sha256:0c9ef6ff37e974b73c25eecc13952c55bceed9112be2d9d938ded8e856138bcc \
     --hash=sha256:131fd094d1065b19540c3d72594260f118b231090295d8c34e19a7bbcf2e860a \
@@ -118,14 +140,19 @@ cffi==1.16.0 \
     --hash=sha256:ee07e47c12890ef248766a6e55bd38ebfb2bb8edd4142d56db91b21ea68b7627 \
     --hash=sha256:fa3a0128b152627161ce47201262d3140edb5a5c3da88d73a1b790a959126956 \
     --hash=sha256:fcc8eb6d5902bb1cf6dc4f187ee3ea80a1eba0a89aba40a5cb20a5087d961357
-    # via cryptography
+    # via
+    #   -c lock/requirements-dev.txt
+    #   cryptography
 cfgraph==0.2.1 \
     --hash=sha256:b57fe7044a10b8ff65aa3a8a8ddc7d4cd77bf511b42e57289cd52cbc29f8fe74
-    # via pyshex
+    # via
+    #   -c lock/requirements-dev.txt
+    #   pyshex
 chardet==5.2.0 \
     --hash=sha256:1b3b6ff479a8c414bc3fa2c0852995695c4a026dcd6d0633b2dd092ca39c1cf7 \
     --hash=sha256:e1cf59446890a00105fe7b7912492ea04b6e6f06d4b742b2c788469e34c82970
     # via
+    #   -c lock/requirements-dev.txt
     #   pyshex
     #   pyshexc
     #   tox
@@ -220,11 +247,14 @@ charset-normalizer==3.3.2 \
     --hash=sha256:fb69256e180cb6c8a894fee62b3afebae785babc1ee98b81cdf68bbca1987f33 \
     --hash=sha256:fd1abc0d89e30cc4e02e4064dc67fcc51bd941eb395c502aac3ec19fab46b519 \
     --hash=sha256:ff8fa367d09b717b2a17a052544193ad76cd49979c805768879cb63d9ca50561
-    # via requests
+    # via
+    #   -c lock/requirements-dev.txt
+    #   requests
 click==8.1.7 \
     --hash=sha256:ae74fb96c20a0277a1d615f1e4d73c8414f5a98db8b799a7931d1582f3390c28 \
     --hash=sha256:ca9853ad459e787e2192211578cc907e7594e294c7ccc834310722b41b9ca6de
     # via
+    #   -c lock/requirements-dev.txt
     #   json-flattener
     #   linkml
     #   linkml-runtime
@@ -236,7 +266,9 @@ click==8.1.7 \
 colorama==0.4.6 \
     --hash=sha256:08695f5cb7ed6e0531a20572697297273c47b8cae5a63ffc6d6ed5c201be6e44 \
     --hash=sha256:4f1d9991f5acc0ca119f9d443620b77f9d6b33703e51011c16baf57afb285fc6
-    # via tox
+    # via
+    #   -c lock/requirements-dev.txt
+    #   tox
 cryptography==41.0.7 \
     --hash=sha256:079b85658ea2f59c4f43b70f8119a52414cdb7be34da5d019a77bf96d473b960 \
     --hash=sha256:09616eeaef406f99046553b8a40fbf8b1e70795a91885ba4c96a70793de5504a \
@@ -261,65 +293,91 @@ cryptography==41.0.7 \
     --hash=sha256:d6c391c021ab1f7a82da5d8d0b3cee2f4b2c455ec86c8aebbc84837a631ff309 \
     --hash=sha256:e3114da6d7f95d2dee7d3f4eec16dacff819740bbab931aff8648cb13c5ff5e7 \
     --hash=sha256:f983596065a18a2183e7f79ab3fd4c475205b839e02cbc0efbbf9666c4b3083d
-    # via jwcrypto
+    # via
+    #   -c lock/requirements-dev.txt
+    #   jwcrypto
 curies==0.7.4 \
     --hash=sha256:478f1818345988933d8bc6060f80a985401331f856ff8cf9bd98fa00d178ad39 \
     --hash=sha256:d3aaf16644b26ac2605ff83c565ec7df0ba0b5f7425516047666e609ec5fb718
     # via
+    #   -c lock/requirements-dev.txt
     #   linkml-runtime
     #   prefixmaps
 deprecated==1.2.14 \
     --hash=sha256:6fac8b097794a90302bdbb17b9b815e732d3c4720583ff1b198499d78470466c \
     --hash=sha256:e5323eb936458dccc2582dc6f9c322c852a775a27065ff2b0c4970b9d53d01b3
-    # via linkml-runtime
+    # via
+    #   -c lock/requirements-dev.txt
+    #   linkml-runtime
 distlib==0.3.8 \
     --hash=sha256:034db59a0b96f8ca18035f36290806a9a6e6bd9d1ff91e45a7f172eb17e51784 \
     --hash=sha256:1530ea13e350031b6312d8580ddb6b27a104275a31106523b8f123787f494f64
-    # via virtualenv
+    # via
+    #   -c lock/requirements-dev.txt
+    #   virtualenv
 dnspython==2.4.2 \
     --hash=sha256:57c6fbaaeaaf39c891292012060beb141791735dbb4004798328fc2c467402d8 \
     --hash=sha256:8dcfae8c7460a2f84b4072e26f1c9f4101ca20c071649cb7c34e8b6a93d58984
     # via
+    #   -c lock/requirements-dev.txt
     #   email-validator
     #   pymongo
 email-validator==2.1.0.post1 \
     --hash=sha256:a4b0bd1cf55f073b924258d19321b1f3aa74b4b5a71a42c305575dba920e1a44 \
     --hash=sha256:c973053efbeddfef924dc0bd93f6e77a1ea7ee0fce935aea7103c7a3d6d2d637
-    # via pydantic
+    # via
+    #   -c lock/requirements-dev.txt
+    #   fastapi
+    #   pydantic
 et-xmlfile==1.1.0 \
     --hash=sha256:8eb9e2bc2f8c97e37a2dc85a09ecdcdec9d8a396530a6d5a33b30b9a92da0c5c \
     --hash=sha256:a2ba85d1d6a74ef63837eed693bcb89c3f752169b0e3e7ae5b16ca5e1b3deada
-    # via openpyxl
-exceptiongroup==1.2.0 \
-    --hash=sha256:4bfd3996ac73b41e9b9628b04e079f193850720ea5945fc96a08633c66912f14 \
-    --hash=sha256:91f5c769735f051a4290d52edd0858999b57e5876e9f85937691bd4c9fa3ed68
     # via
-    #   anyio
-    #   pytest
-fastapi==0.110.0 \
-    --hash=sha256:266775f0dcc95af9d3ef39bad55cff525329a931d5fd51930aadd4f428bf7ff3 \
-    --hash=sha256:87a1f6fb632a218222c5984be540055346a8f5d8a68e8f6fb647b1dc9934de4b
-    # via ghga-service-commons
+    #   -c lock/requirements-dev.txt
+    #   openpyxl
+fastapi==0.111.0 \
+    --hash=sha256:97ecbf994be0bcbdadedf88c3150252bed7b2087075ac99735403b1b76cc8fc0 \
+    --hash=sha256:b9db9dd147c91cb8b769f7183535773d8741dd46f9dc6676cd82eab510228cd7
+    # via
+    #   -c lock/requirements-dev.txt
+    #   ghga-service-commons
+fastapi-cli==0.0.4 \
+    --hash=sha256:a2552f3a7ae64058cdbb530be6fa6dbfc975dc165e4fa66d224c3d396e25e809 \
+    --hash=sha256:e2e9ffaffc1f7767f488d6da34b6f5a377751c996f397902eb6abb99a67bde32
+    # via
+    #   -c lock/requirements-dev.txt
+    #   fastapi
 filelock==3.13.1 \
     --hash=sha256:521f5f56c50f8426f5e03ad3b281b490a87ef15bc6c526f168290f0c7148d44e \
     --hash=sha256:57dbda9b35157b05fb3e58ee91448612eb674172fab98ee235ccb0b5bee19a1c
     # via
+    #   -c lock/requirements-dev.txt
     #   tox
     #   virtualenv
 fqdn==1.5.1 \
     --hash=sha256:105ed3677e767fb5ca086a0c1f4bb66ebc3c100be518f0e0d755d9eae164d89f \
     --hash=sha256:3a179af3761e4df6eb2e026ff9e1a3033d3587bf980a0b1b2e1e5d08d7358014
-    # via jsonschema
+    # via
+    #   -c lock/requirements-dev.txt
+    #   jsonschema
 ghga-event-schemas==3.0.0 \
     --hash=sha256:67dce9db2d45be862f69a58a903fac43416997ad50fd4f1f1d25822533a187d1 \
     --hash=sha256:7a8952e37bd935809f324aa21653b008e01a5ea920d36217734ee35776d92602
-ghga-service-commons==3.1.1 \
-    --hash=sha256:6f758721a2673ac9c594d9cd052e0204b79950bf9f3e828ca5d870a6637d81b6 \
-    --hash=sha256:b4e696c350f14a983d9447c43b16a954f0d2bf0a057c3ecdf0a95e3f115c89b4
+    # via
+    #   -c lock/requirements-dev.txt
+    #   metldata (pyproject.toml)
+ghga-service-commons==3.1.4 \
+    --hash=sha256:63450bed2f0ca7431f064b640d35e15a29f93b7f4c67b5fd3b812afc8ced5151 \
+    --hash=sha256:eb78042aeb17bb70e17f7c7185fbcf87a54968a410de99f968a7e944cd0f6f78
+    # via
+    #   -c lock/requirements-dev.txt
+    #   metldata (pyproject.toml)
 graphviz==0.20.1 \
     --hash=sha256:587c58a223b51611c0cf461132da386edd896a029524ca61a1462b880bf97977 \
     --hash=sha256:8c58f14adaa3b947daf26c19bc1e98c4e0702cdc31cf99153e6f06904d492bf8
-    # via linkml
+    # via
+    #   -c lock/requirements-dev.txt
+    #   linkml
 greenlet==3.0.2 \
     --hash=sha256:006c1028ac0cfcc4e772980cfe73f5476041c8c91d15d64f52482fc571149d46 \
     --hash=sha256:0acadbc3f72cb0ee85070e8d36bd2a4673d2abd10731ee73c10222cf2dd4713c \
@@ -379,22 +437,37 @@ greenlet==3.0.2 \
     --hash=sha256:fb5d60805057d8948065338be6320d35e26b0a72f45db392eb32b70dd6dc9227 \
     --hash=sha256:fc14dd9554f88c9c1fe04771589ae24db76cd56c8f1104e4381b383d6b71aff8 \
     --hash=sha256:fefd5eb2c0b1adffdf2802ff7df45bfe65988b15f6b972706a0e55d451bffaea
-    # via sqlalchemy
+    # via
+    #   -c lock/requirements-dev.txt
+    #   sqlalchemy
 h11==0.14.0 \
     --hash=sha256:8f19fbbe99e72420ff35c00b27a34cb9937e902a8b810e2c88300c6f0a3b699d \
     --hash=sha256:e3fe4ac4b851c468cc8363d500db52c2ead036020723024a109d37346efaa761
-    # via uvicorn
+    # via
+    #   -c lock/requirements-dev.txt
+    #   httpcore
+    #   uvicorn
 hbreader==0.9.1 \
     --hash=sha256:9a6e76c9d1afc1b977374a5dc430a1ebb0ea0488205546d4678d6e31cc5f6801 \
     --hash=sha256:d2c132f8ba6276d794c66224c3297cec25c8079d0a4cf019c061611e0a3b94fa
     # via
+    #   -c lock/requirements-dev.txt
     #   jsonasobj2
     #   linkml
     #   linkml-runtime
-hexkit==2.1.1 \
-    --hash=sha256:1f0a0e20a6d56fe4fa5e0b1c798df4720d2f84e20cbe7f16464bd5107e109c90 \
-    --hash=sha256:3ec0f9690eb573125e22bce0c662019c9708cd17f8d2353396dc4496577718c3
-    # via ghga-service-commons
+hexkit==3.1.0 \
+    --hash=sha256:3f96ede959b4d81a6b78637ebf47019787e5d3321bd01f9abe82cb8118bada66 \
+    --hash=sha256:b922c048091f622798ccf25a767fe3d64ff8ee000d1c3cf18967b6b6de8f2592
+    # via
+    #   -c lock/requirements-dev.txt
+    #   metldata (pyproject.toml)
+    #   ghga-service-commons
+httpcore==1.0.2 \
+    --hash=sha256:096cc05bca73b8e459a1fc3dcf585148f63e534eae4339559c9b8a8d6399acc7 \
+    --hash=sha256:9fc092e4799b26174648e54b74ed5f683132a464e95643b226e00c2ed2fa6535
+    # via
+    #   -c lock/requirements-dev.txt
+    #   httpx
 httptools==0.6.1 \
     --hash=sha256:00d5d4b68a717765b1fabfd9ca755bd12bf44105eeb806c03d1962acd9b8e563 \
     --hash=sha256:0ac5a0ae3d9f4fe004318d64b8a854edd85ab76cffbf7ef5e32920faef62f142 \
@@ -432,69 +505,96 @@ httptools==0.6.1 \
     --hash=sha256:e0b281cf5a125c35f7f6722b65d8542d2e57331be573e9e88bc8b0115c4a7a81 \
     --hash=sha256:e57997ac7fb7ee43140cc03664de5f268813a481dff6245e0075925adc6aa185 \
     --hash=sha256:fe467eb086d80217b7584e61313ebadc8d187a4d95bb62031b7bab4b205c3ba3
-    # via uvicorn
+    # via
+    #   -c lock/requirements-dev.txt
+    #   uvicorn
+httpx==0.27.0 \
+    --hash=sha256:71d5465162c13681bff01ad59b2cc68dd838ea1f10e51574bac27103f00c91a5 \
+    --hash=sha256:a0cb88a46f32dc874e04ee956e4c2764aba2aa228f650b06788ba6bda2962ab5
+    # via
+    #   -c lock/requirements-dev.txt
+    #   fastapi
 idna==3.6 \
     --hash=sha256:9ecdbbd083b06798ae1e86adcbfe8ab1479cf864e4ee30fe4e46a003d12491ca \
     --hash=sha256:c05567e9c24a6b9faaa835c4821bad0590fbb9d5779e7caa6e1cc4978e7eb24f
     # via
+    #   -c lock/requirements-dev.txt
     #   anyio
     #   email-validator
+    #   httpx
     #   jsonschema
     #   requests
 iniconfig==2.0.0 \
     --hash=sha256:2d91e135bf72d31a410b17c16da610a82cb55f6b0477d1a902134b24a455b8b3 \
     --hash=sha256:b6a85871a79d2e3b22d2d1b94ac2824226a63c6b741c88f7ae975f18b6778374
-    # via pytest
+    # via
+    #   -c lock/requirements-dev.txt
+    #   pytest
 isodate==0.6.1 \
     --hash=sha256:0751eece944162659049d35f4f549ed815792b38793f07cf73381c1c87cbed96 \
     --hash=sha256:48c5881de7e8b0a0d648cb024c8062dc84e7b840ed81e864c7614fd3c127bde9
     # via
+    #   -c lock/requirements-dev.txt
     #   linkml
     #   rdflib
 isoduration==20.11.0 \
     --hash=sha256:ac2f9015137935279eac671f94f89eb00584f940f5dc49462a0c4ee692ba1bd9 \
     --hash=sha256:b2904c2a4228c3d44f409c8ae8e2370eb21a26f7ac2ec5446df141dde3452042
-    # via jsonschema
+    # via
+    #   -c lock/requirements-dev.txt
+    #   jsonschema
 jinja2==3.1.2 \
     --hash=sha256:31351a702a408a9e7595a8fc6150fc3f43bb6bf7e319770cbc0db9df9437e852 \
     --hash=sha256:6088930bfe239f0e6710546ab9c19c9ef35e29792895fed6e6e31a023a182a61
     # via
+    #   -c lock/requirements-dev.txt
+    #   fastapi
     #   linkml
     #   linkml-dataops
 json-flattener==0.1.9 \
     --hash=sha256:6b027746f08bf37a75270f30c6690c7149d5f704d8af1740c346a3a1236bc941 \
     --hash=sha256:84cf8523045ffb124301a602602201665fcb003a171ece87e6f46ed02f7f0c15
-    # via linkml-runtime
+    # via
+    #   -c lock/requirements-dev.txt
+    #   linkml-runtime
 jsonasobj==1.3.1 \
     --hash=sha256:b9e329dc1ceaae7cf5d5b214684a0b100e0dad0be6d5bbabac281ec35ddeca65 \
     --hash=sha256:d52e0544a54a08f6ea3f77fa3387271e3648655e0eace2f21e825c26370e44a2
     # via
+    #   -c lock/requirements-dev.txt
     #   pyjsg
     #   pyshexc
 jsonasobj2==1.0.4 \
     --hash=sha256:12e86f86324d54fcf60632db94ea74488d5314e3da554c994fe1e2c6f29acb79 \
     --hash=sha256:f50b1668ef478004aa487b2d2d094c304e5cb6b79337809f4a1f2975cc7fbb4e
     # via
+    #   -c lock/requirements-dev.txt
     #   linkml
     #   linkml-runtime
 jsonpatch==1.33 \
     --hash=sha256:0ae28c0cd062bbd8b8ecc26d7d164fbbea9652a1a3693f3b956c1eae5145dade \
     --hash=sha256:9fcd4009c41e6d12348b4a0ff2563ba56a2923a7dfee731d004e212e1ee5030c
-    # via linkml-dataops
+    # via
+    #   -c lock/requirements-dev.txt
+    #   linkml-dataops
 jsonpath-ng==1.6.0 \
     --hash=sha256:5483f8e9d74c39c9abfab554c070ae783c1c8cbadf5df60d561bc705ac68a07e \
     --hash=sha256:6fd04833412c4b3d9299edf369542f5e67095ca84efa17cbb7f06a34958adc9f
-    # via linkml-dataops
+    # via
+    #   -c lock/requirements-dev.txt
+    #   linkml-dataops
 jsonpointer==2.4 \
     --hash=sha256:15d51bba20eea3165644553647711d150376234112651b4f1811022aecad7d7a \
     --hash=sha256:585cee82b70211fa9e6043b7bb89db6e1aa49524340dde8ad6b63206ea689d88
     # via
+    #   -c lock/requirements-dev.txt
     #   jsonpatch
     #   jsonschema
-jsonschema==4.20.0 \
-    --hash=sha256:4f614fd46d8d61258610998997743ec5492a648b33cf478c1ddc23ed4598a5fa \
-    --hash=sha256:ed6231f0429ecf966f5bc8dfef245998220549cbbcf140f913b7464c52c3b6b3
+jsonschema==4.22.0 \
+    --hash=sha256:5b22d434a45935119af990552c862e5d6d564e8f6601206b305a61fdf661a2b7 \
+    --hash=sha256:ff4cfd6b1367a40e7bc6411caec72effadd3db0bbe5017de188f2d6108335802
     # via
+    #   -c lock/requirements-dev.txt
     #   ghga-event-schemas
     #   hexkit
     #   linkml
@@ -502,32 +602,49 @@ jsonschema==4.20.0 \
 jsonschema-specifications==2023.11.2 \
     --hash=sha256:9472fc4fea474cd74bea4a2b190daeccb5a9e4db2ea80efcf7a1b582fc9a81b8 \
     --hash=sha256:e74ba7c0a65e8cb49dc26837d6cfe576557084a8b423ed16a420984228104f93
-    # via jsonschema
-jwcrypto==1.5.4 \
-    --hash=sha256:0815fbab613db99bad85691da5f136f8860423396667728a264bcfa6e1db36b0
-    # via ghga-service-commons
-kafka-python==2.0.2 \
-    --hash=sha256:04dfe7fea2b63726cd6f3e79a2d86e709d608d74406638c5da33a01d45a9d7e3 \
-    --hash=sha256:2d92418c7cb1c298fa6c7f0fb3519b520d0d7526ac6cb7ae2a4fc65a51a94b6e
-    # via aiokafka
+    # via
+    #   -c lock/requirements-dev.txt
+    #   jsonschema
+jwcrypto==1.5.6 \
+    --hash=sha256:150d2b0ebbdb8f40b77f543fb44ffd2baeff48788be71f67f03566692fd55789 \
+    --hash=sha256:771a87762a0c081ae6166958a954f80848820b2ab066937dc8b8379d65b1b039
+    # via
+    #   -c lock/requirements-dev.txt
+    #   ghga-service-commons
 linkml==1.6.1 \
     --hash=sha256:65f73cf29a77518972238e71e91e012c081cf2e43d71d8965ca414c78c11e08e \
     --hash=sha256:7501cb9c7b2c13ca78fc7121ae8b5457fb5771138714da31cc11f971062070ee
-    # via linkml-validator
+    # via
+    #   -c lock/requirements-dev.txt
+    #   metldata (pyproject.toml)
+    #   linkml-validator
 linkml-dataops==0.1.0 \
     --hash=sha256:193cf7f659e5f07946d2c2761896910d5f7151d91282543b1363801f68307f4c \
     --hash=sha256:4550eab65e78b70dc3b9c651724a94ac2b1d1edb2fbe576465f1d6951a54ed04
-    # via linkml
+    # via
+    #   -c lock/requirements-dev.txt
+    #   linkml
 linkml-runtime==1.6.0 \
     --hash=sha256:1b6b698f8cf23d63ff833ae0be8055b2e945e1c0ef06a1ed6db359247194a2eb \
     --hash=sha256:a06df7431a9b929afe242598800d99cec83bb31cbdc1f5d2d70e6b26c67dc337
     # via
+    #   -c lock/requirements-dev.txt
+    #   metldata (pyproject.toml)
     #   linkml
     #   linkml-dataops
     #   linkml-validator
 linkml-validator==0.4.5 \
     --hash=sha256:7a9799830cba3e1df203cde86263d8ea85f9ed9f6a45a218e3f752483abac030 \
     --hash=sha256:bce72053c1593a678ccefd28ed5cf4b39a878e78da884b5b41fef65610a23867
+    # via
+    #   -c lock/requirements-dev.txt
+    #   metldata (pyproject.toml)
+markdown-it-py==3.0.0 \
+    --hash=sha256:355216845c60bd96232cd8d8c40e8f9765cc86f46880e43a8fd22dc1a1a8cab1 \
+    --hash=sha256:e3f60a94fa066dc52ec76661e37c851cb232d92f9886b15cb560aaada2df8feb
+    # via
+    #   -c lock/requirements-dev.txt
+    #   rich
 markupsafe==2.1.3 \
     --hash=sha256:05fb21170423db021895e1ea1e1f3ab3adb85d1c2333cbc2310f2a26bc77272e \
     --hash=sha256:0a4e4a1aff6c7ac4cd55792abf96c915634c2b97e3cc1c7129578aa68ebd754e \
@@ -589,19 +706,82 @@ markupsafe==2.1.3 \
     --hash=sha256:f698de3fd0c4e6972b92290a45bd9b1536bffe8c6759c62471efaa8acb4c37bc \
     --hash=sha256:fec21693218efe39aa7f8599346e90c705afa52c5b31ae019b2e57e8f6542bb2 \
     --hash=sha256:ffcc3f7c66b5f5b7931a5aa68fc9cecc51e685ef90282f4a82f0f5e9b704ad11
-    # via jinja2
-motor==3.3.2 \
-    --hash=sha256:6fe7e6f0c4f430b9e030b9d22549b732f7c2226af3ab71ecc309e4a1b7d19953 \
-    --hash=sha256:d2fc38de15f1c8058f389c1a44a4d4105c0405c48c061cd492a654496f7bc26a
-    # via hexkit
+    # via
+    #   -c lock/requirements-dev.txt
+    #   jinja2
+mdurl==0.1.2 \
+    --hash=sha256:84008a41e51615a49fc9966191ff91509e3c40b939176e643fd50a5c2196b8f8 \
+    --hash=sha256:bb413d29f5eea38f31dd4754dd7377d4465116fb207585f97bf925588687c1ba
+    # via
+    #   -c lock/requirements-dev.txt
+    #   markdown-it-py
+motor==3.4.0 \
+    --hash=sha256:4b1e1a0cc5116ff73be2c080a72da078f2bb719b53bc7a6bb9e9a2f7dcd421ed \
+    --hash=sha256:c89b4e4eb2e711345e91c7c9b122cb68cce0e5e869ed0387dd0acb10775e3131
+    # via
+    #   -c lock/requirements-dev.txt
+    #   hexkit
 openpyxl==3.1.2 \
     --hash=sha256:a6f5977418eff3b2d5500d54d9db50c8277a368436f4e4f8ddb1be3422870184 \
     --hash=sha256:f91456ead12ab3c6c2e9491cf33ba6d08357d802192379bb482f1033ade496f5
-    # via linkml
+    # via
+    #   -c lock/requirements-dev.txt
+    #   linkml
+orjson==3.10.3 \
+    --hash=sha256:0943a96b3fa09bee1afdfccc2cb236c9c64715afa375b2af296c73d91c23eab2 \
+    --hash=sha256:0a62f9968bab8a676a164263e485f30a0b748255ee2f4ae49a0224be95f4532b \
+    --hash=sha256:16bda83b5c61586f6f788333d3cf3ed19015e3b9019188c56983b5a299210eb5 \
+    --hash=sha256:1770e2a0eae728b050705206d84eda8b074b65ee835e7f85c919f5705b006c9b \
+    --hash=sha256:17e0713fc159abc261eea0f4feda611d32eabc35708b74bef6ad44f6c78d5ea0 \
+    --hash=sha256:18566beb5acd76f3769c1d1a7ec06cdb81edc4d55d2765fb677e3eaa10fa99e0 \
+    --hash=sha256:1952c03439e4dce23482ac846e7961f9d4ec62086eb98ae76d97bd41d72644d7 \
+    --hash=sha256:1bd2218d5a3aa43060efe649ec564ebedec8ce6ae0a43654b81376216d5ebd42 \
+    --hash=sha256:1c23dfa91481de880890d17aa7b91d586a4746a4c2aa9a145bebdbaf233768d5 \
+    --hash=sha256:252124b198662eee80428f1af8c63f7ff077c88723fe206a25df8dc57a57b1fa \
+    --hash=sha256:2b166507acae7ba2f7c315dcf185a9111ad5e992ac81f2d507aac39193c2c818 \
+    --hash=sha256:2e5e176c994ce4bd434d7aafb9ecc893c15f347d3d2bbd8e7ce0b63071c52e25 \
+    --hash=sha256:3582b34b70543a1ed6944aca75e219e1192661a63da4d039d088a09c67543b08 \
+    --hash=sha256:382e52aa4270a037d41f325e7d1dfa395b7de0c367800b6f337d8157367bf3a7 \
+    --hash=sha256:416b195f78ae461601893f482287cee1e3059ec49b4f99479aedf22a20b1098b \
+    --hash=sha256:4ad1f26bea425041e0a1adad34630c4825a9e3adec49079b1fb6ac8d36f8b754 \
+    --hash=sha256:4c895383b1ec42b017dd2c75ae8a5b862fc489006afde06f14afbdd0309b2af0 \
+    --hash=sha256:5102f50c5fc46d94f2033fe00d392588564378260d64377aec702f21a7a22912 \
+    --hash=sha256:520de5e2ef0b4ae546bea25129d6c7c74edb43fc6cf5213f511a927f2b28148b \
+    --hash=sha256:544a12eee96e3ab828dbfcb4d5a0023aa971b27143a1d35dc214c176fdfb29b3 \
+    --hash=sha256:73100d9abbbe730331f2242c1fc0bcb46a3ea3b4ae3348847e5a141265479700 \
+    --hash=sha256:831c6ef73f9aa53c5f40ae8f949ff7681b38eaddb6904aab89dca4d85099cb78 \
+    --hash=sha256:8bc7a4df90da5d535e18157220d7915780d07198b54f4de0110eca6b6c11e290 \
+    --hash=sha256:8d0b84403d287d4bfa9bf7d1dc298d5c1c5d9f444f3737929a66f2fe4fb8f134 \
+    --hash=sha256:8d40c7f7938c9c2b934b297412c067936d0b54e4b8ab916fd1a9eb8f54c02294 \
+    --hash=sha256:9059d15c30e675a58fdcd6f95465c1522b8426e092de9fff20edebfdc15e1cb0 \
+    --hash=sha256:93433b3c1f852660eb5abdc1f4dd0ced2be031ba30900433223b28ee0140cde5 \
+    --hash=sha256:978be58a68ade24f1af7758626806e13cff7748a677faf95fbb298359aa1e20d \
+    --hash=sha256:99b880d7e34542db89f48d14ddecbd26f06838b12427d5a25d71baceb5ba119d \
+    --hash=sha256:9a7bc9e8bc11bac40f905640acd41cbeaa87209e7e1f57ade386da658092dc16 \
+    --hash=sha256:9e253498bee561fe85d6325ba55ff2ff08fb5e7184cd6a4d7754133bd19c9195 \
+    --hash=sha256:9f3e87733823089a338ef9bbf363ef4de45e5c599a9bf50a7a9b82e86d0228da \
+    --hash=sha256:9fb6c3f9f5490a3eb4ddd46fc1b6eadb0d6fc16fb3f07320149c3286a1409dd8 \
+    --hash=sha256:a39aa73e53bec8d410875683bfa3a8edf61e5a1c7bb4014f65f81d36467ea098 \
+    --hash=sha256:b69a58a37dab856491bf2d3bbf259775fdce262b727f96aafbda359cb1d114d8 \
+    --hash=sha256:b8d4d1a6868cde356f1402c8faeb50d62cee765a1f7ffcfd6de732ab0581e063 \
+    --hash=sha256:ba7f67aa7f983c4345eeda16054a4677289011a478ca947cd69c0a86ea45e534 \
+    --hash=sha256:be2719e5041e9fb76c8c2c06b9600fe8e8584e6980061ff88dcbc2691a16d20d \
+    --hash=sha256:be2aab54313752c04f2cbaab4515291ef5af8c2256ce22abc007f89f42f49109 \
+    --hash=sha256:c0403ed9c706dcd2809f1600ed18f4aae50be263bd7112e54b50e2c2bc3ebd6d \
+    --hash=sha256:c8334c0d87103bb9fbbe59b78129f1f40d1d1e8355bbed2ca71853af15fa4ed3 \
+    --hash=sha256:cb0175a5798bdc878956099f5c54b9837cb62cfbf5d0b86ba6d77e43861bcec2 \
+    --hash=sha256:ccaa0a401fc02e8828a5bedfd80f8cd389d24f65e5ca3954d72c6582495b4bcf \
+    --hash=sha256:cf20465e74c6e17a104ecf01bf8cd3b7b252565b4ccee4548f18b012ff2f8069 \
+    --hash=sha256:d4a654ec1de8fdaae1d80d55cee65893cb06494e124681ab335218be6a0691e7 \
+    --hash=sha256:e852baafceff8da3c9defae29414cc8513a1586ad93e45f27b89a639c68e8176
+    # via
+    #   -c lock/requirements-dev.txt
+    #   fastapi
 packaging==23.2 \
     --hash=sha256:048fb0e9405036518eaaf48a55953c750c11e1a1b68e0dd1a9d62ed0c092cfc5 \
     --hash=sha256:8c491190033a9af7e1d931d0b5dacc2ef47509b34dd0de67ed209b5203fc88c7
     # via
+    #   -c lock/requirements-dev.txt
     #   aiokafka
     #   pyproject-api
     #   pytest
@@ -609,43 +789,54 @@ packaging==23.2 \
 parse==1.20.0 \
     --hash=sha256:5e171b001452fa9f004c5a58a93525175468daf69b493e9fa915347ed7ff6968 \
     --hash=sha256:bd28bae37714b45d5894d77160a16e2be36b64a3b618c81168b3684676aa498b
-    # via linkml
+    # via
+    #   -c lock/requirements-dev.txt
+    #   linkml
 platformdirs==4.1.0 \
     --hash=sha256:11c8f37bcca40db96d8144522d925583bdb7a31f7b0e37e3ed4318400a8e2380 \
     --hash=sha256:906d548203468492d432bcb294d4bc2fff751bf84971fbb2c10918cc206ee420
     # via
+    #   -c lock/requirements-dev.txt
     #   tox
     #   virtualenv
-pluggy==1.3.0 \
-    --hash=sha256:cf61ae8f126ac6f7c451172cf30e3e43d3ca77615509771b3a984a0730651e12 \
-    --hash=sha256:d89c696a773f8bd377d18e5ecda92b7a3793cbe66c87060a6fb58c7b6e1061f7
+pluggy==1.5.0 \
+    --hash=sha256:2cffa88e94fdc978c4c574f15f9e59b7f4201d439195c3715ca9e2486f1d0cf1 \
+    --hash=sha256:44e1ad92c8ca002de6377e165f3e0f1be63266ab4d554740532335b9d75ea669
     # via
+    #   -c lock/requirements-dev.txt
     #   pytest
     #   tox
 ply==3.11 \
     --hash=sha256:00c7c1aaa88358b9c765b6d3000c6eec0ba42abca5351b095321aef446081da3 \
     --hash=sha256:096f9b8350b65ebd2fd1346b12452efe5b9607f7482813ffca50c22722a807ce
-    # via jsonpath-ng
+    # via
+    #   -c lock/requirements-dev.txt
+    #   jsonpath-ng
 prefixcommons==0.1.12 \
     --hash=sha256:16dbc0a1f775e003c724f19a694fcfa3174608f5c8b0e893d494cf8098ac7f8b \
     --hash=sha256:22c4e2d37b63487b3ab48f0495b70f14564cb346a15220f23919eb0c1851f69f
     # via
+    #   -c lock/requirements-dev.txt
     #   linkml
     #   linkml-runtime
 prefixmaps==0.2.0 \
     --hash=sha256:0e3fdabf90b991e1f44a2b455e9042f6ba0e498fa7a769ffd8a6ad248f43af0c \
     --hash=sha256:a0f87077ac1651f1b386c178b80cd2edc294a6b7b628b30143ac98a1dae6f0b7
     # via
+    #   -c lock/requirements-dev.txt
     #   linkml
     #   linkml-runtime
 pycparser==2.21 \
     --hash=sha256:8ee45429555515e1f6b185e78100aea234072576aa43ab53aefcae078162fca9 \
     --hash=sha256:e644fdec12f7872f86c58ff790da456218b10f863970249516d60a5eaca77206
-    # via cffi
+    # via
+    #   -c lock/requirements-dev.txt
+    #   cffi
 pydantic==2.5.2 \
     --hash=sha256:80c50fb8e3dcecfddae1adbcc00ec5822918490c99ab31f6cf6140ca1c1429f0 \
     --hash=sha256:ff177ba64c6faf73d7afa2e8cad38fd456c0dbe01c9954e71038001cd15a6edd
     # via
+    #   -c lock/requirements-dev.txt
     #   curies
     #   fastapi
     #   ghga-event-schemas
@@ -762,15 +953,26 @@ pydantic-core==2.14.5 \
     --hash=sha256:f5e412d717366e0677ef767eac93566582518fe8be923361a5c204c1a62eaafe \
     --hash=sha256:fb2ed8b3fe4bf4506d6dab3b93b83bbc22237e230cba03866d561c3577517d18 \
     --hash=sha256:fe0a5a1025eb797752136ac8b4fa21aa891e3d74fd340f864ff982d649691867
-    # via pydantic
+    # via
+    #   -c lock/requirements-dev.txt
+    #   pydantic
 pydantic-settings==2.1.0 \
     --hash=sha256:26b1492e0a24755626ac5e6d715e9077ab7ad4fb5f19a8b7ed7011d52f36141c \
     --hash=sha256:7621c0cb5d90d1140d2f0ef557bdf03573aac7035948109adf2574770b77605a
-    # via hexkit
+    # via
+    #   -c lock/requirements-dev.txt
+    #   hexkit
+pygments==2.18.0 \
+    --hash=sha256:786ff802f32e91311bff3889f6e9a86e81505fe99f2735bb6d60ae0c5004f199 \
+    --hash=sha256:b8e6aca0523f3ab76fee51799c488e38782ac06eafcf95e7ba832985c8e7b13a
+    # via
+    #   -c lock/requirements-dev.txt
+    #   rich
 pyjsg==0.11.10 \
     --hash=sha256:10af60ff42219be7e85bf7f11c19b648715b0b29eb2ddbd269e87069a7c3f26d \
     --hash=sha256:4bd6e3ff2833fa2b395bbe803a2d72a5f0bab5b7285bccd0da1a1bc0aee88bfa
     # via
+    #   -c lock/requirements-dev.txt
     #   linkml
     #   pyshexc
     #   shexjsg
@@ -857,48 +1059,71 @@ pymongo==4.6.1 \
     --hash=sha256:f9756f1d25454ba6a3c2f1ef8b7ddec23e5cdeae3dc3c3377243ae37a383db00 \
     --hash=sha256:ff62ba8ff70f01ab4fe0ae36b2cb0b5d1f42e73dfc81ddf0758cd9f77331ad25 \
     --hash=sha256:ff925f1cca42e933376d09ddc254598f8c5fcd36efc5cac0118bb36c36217c41
-    # via motor
+    # via
+    #   -c lock/requirements-dev.txt
+    #   motor
 pyparsing==3.1.1 \
     --hash=sha256:32c7c0b711493c72ff18a981d24f28aaf9c1fb7ed5e9667c9e84e3db623bdbfb \
     --hash=sha256:ede28a1a32462f5a9705e07aea48001a08f7cf81a021585011deba701581a0db
-    # via rdflib
+    # via
+    #   -c lock/requirements-dev.txt
+    #   rdflib
 pyproject-api==1.6.1 \
     --hash=sha256:1817dc018adc0d1ff9ca1ed8c60e1623d5aaca40814b953af14a9cf9a5cae538 \
     --hash=sha256:4c0116d60476b0786c88692cf4e325a9814965e2469c5998b830bba16b183675
-    # via tox
+    # via
+    #   -c lock/requirements-dev.txt
+    #   tox
 pyshex==0.8.1 \
     --hash=sha256:3c5c4d45fe27faaadae803cb008c41acf8ee784da7868b04fd84967e75be70d0 \
     --hash=sha256:6da1b10123e191abf8dcb6bf3e54aa3e1fcf771df5d1a0ed453217c8900c8e6a
-    # via linkml
+    # via
+    #   -c lock/requirements-dev.txt
+    #   linkml
 pyshexc==0.9.1 \
     --hash=sha256:35a9975d4b9afeb20ef710fb6680871756381d0c39fbb5470b3b506581a304d3 \
     --hash=sha256:efc55ed5cb2453e9df569b03e282505e96bb06597934288f3b23dd980ef10028
     # via
+    #   -c lock/requirements-dev.txt
     #   linkml
     #   pyshex
-pytest==7.4.3 \
-    --hash=sha256:0d009c083ea859a71b76adf7c1d502e4bc170b80a8ef002da5806527b9591fac \
-    --hash=sha256:d989d136982de4e3b29dabcc838ad581c64e8ed52c11fbe86ddebd9da0818cd5
-    # via pytest-logging
+pytest==8.2.1 \
+    --hash=sha256:5046e5b46d8e4cac199c373041f26be56fdb81eb4e67dc11d4e10811fc3408fd \
+    --hash=sha256:faccc5d332b8c3719f40283d0d44aa5cf101cec36f88cde9ed8f2bc0538612b1
+    # via
+    #   -c lock/requirements-dev.txt
+    #   pytest-logging
 pytest-logging==2015.11.4 \
     --hash=sha256:cec5c85ecf18aab7b2ead5498a31b9f758680ef5a902b9054ab3f2bdbb77c896
-    # via prefixcommons
+    # via
+    #   -c lock/requirements-dev.txt
+    #   prefixcommons
 python-dateutil==2.8.2 \
     --hash=sha256:0123cacc1627ae19ddf3c27a5de5bd67ee4586fbdd6440d9748f8abb483d3e86 \
     --hash=sha256:961d03dc3453ebbc59dbdea9e4e11c5651520a876d0f4db161e8674aae935da9
     # via
+    #   -c lock/requirements-dev.txt
     #   arrow
     #   linkml
 python-dotenv==1.0.0 \
     --hash=sha256:a8df96034aae6d2d50a4ebe8216326c61c3eb64836776504fcca410e5937a3ba \
     --hash=sha256:f5971a9226b701070a4bf2c38c89e5a3f0d64de8debda981d1db98583009122a
     # via
+    #   -c lock/requirements-dev.txt
     #   pydantic-settings
     #   uvicorn
+python-multipart==0.0.9 \
+    --hash=sha256:03f54688c663f1b7977105f021043b0793151e4cb1c1a9d4a11fc13d622c4026 \
+    --hash=sha256:97ca7b8ea7b05f977dc3849c3ba99d51689822fab725c3703af7c866a0c2b215
+    # via
+    #   -c lock/requirements-dev.txt
+    #   fastapi
 pytrie==0.4.0 \
     --hash=sha256:8f4488f402d3465993fb6b6efa09866849ed8cda7903b50647b7d0342b805379 \
     --hash=sha256:f687c224ee8c66cda8e8628a903011b692635ffbb08d4b39c5f92b18eb78c950
-    # via curies
+    # via
+    #   -c lock/requirements-dev.txt
+    #   curies
 pyyaml==6.0.1 \
     --hash=sha256:04ac92ad1925b2cff1db0cfebffb6ffc43457495c9b3c39d3fcae417d7125dc5 \
     --hash=sha256:062582fca9fabdd2c8b54a3ef1c978d786e0f6b3a1510e0ac93ef59e0ddae2bc \
@@ -952,6 +1177,7 @@ pyyaml==6.0.1 \
     --hash=sha256:fd1592b3fdf65fff2ad0004b5e363300ef59ced41c2e6b3a99d4089fa8c5435d \
     --hash=sha256:fd66fc5d0da6d9815ba2cebeb4205f95818ff4b79c3ebe268e75d961704af52f
     # via
+    #   -c lock/requirements-dev.txt
     #   hexkit
     #   json-flattener
     #   linkml
@@ -963,6 +1189,7 @@ rdflib==7.0.0 \
     --hash=sha256:0438920912a642c866a513de6fe8a0001bd86ef975057d6962c79ce4771687cd \
     --hash=sha256:9995eb8569428059b8c1affd26b25eac510d64f5043d9ce8c84e0d0036e995ae
     # via
+    #   -c lock/requirements-dev.txt
     #   cfgraph
     #   linkml
     #   linkml-runtime
@@ -973,11 +1200,14 @@ rdflib==7.0.0 \
 rdflib-jsonld==0.6.1 \
     --hash=sha256:bcf84317e947a661bae0a3f2aee1eced697075fc4ac4db6065a3340ea0f10fc2 \
     --hash=sha256:eda5a42a2e09f80d4da78e32b5c684bccdf275368f1541e6b7bcddfb1382a0e0
-    # via rdflib-shim
+    # via
+    #   -c lock/requirements-dev.txt
+    #   rdflib-shim
 rdflib-shim==1.0.3 \
     --hash=sha256:7a853e7750ef1e9bf4e35dea27d54e02d4ed087de5a9e0c329c4a6d82d647081 \
     --hash=sha256:d955d11e2986aab42b6830ca56ac6bc9c893abd1d049a161c6de2f1b99d4fc0d
     # via
+    #   -c lock/requirements-dev.txt
     #   pyshex
     #   pyshexc
     #   sparqlslurper
@@ -985,12 +1215,14 @@ referencing==0.32.0 \
     --hash=sha256:689e64fe121843dcfd57b71933318ef1f91188ffb45367332700a86ac8fd6161 \
     --hash=sha256:bdcd3efb936f82ff86f993093f6da7435c7de69a3b3a5a06678a6050184bee99
     # via
+    #   -c lock/requirements-dev.txt
     #   jsonschema
     #   jsonschema-specifications
 requests==2.31.0 \
     --hash=sha256:58cd2187c01e70e6e26505bca751777aa9f2ee0b7f4300988b709f44e013003f \
     --hash=sha256:942c5a758f98d790eaed1a29cb6eefc7ffb0d1cf7af05c3d2791656dbd6ad1e1
     # via
+    #   -c lock/requirements-dev.txt
     #   curies
     #   linkml
     #   linkml-runtime
@@ -999,11 +1231,21 @@ requests==2.31.0 \
 rfc3339-validator==0.1.4 \
     --hash=sha256:138a2abdf93304ad60530167e51d2dfb9549521a836871b88d7f4695d0022f6b \
     --hash=sha256:24f6ec1eda14ef823da9e36ec7113124b39c04d50a4d3d3a3c2859577e7791fa
-    # via jsonschema
+    # via
+    #   -c lock/requirements-dev.txt
+    #   jsonschema
 rfc3987==1.3.8 \
     --hash=sha256:10702b1e51e5658843460b189b185c0366d2cf4cff716f13111b0ea9fd2dce53 \
     --hash=sha256:d3c4d257a560d544e9826b38bc81db676890c79ab9d7ac92b39c7a253d5ca733
-    # via jsonschema
+    # via
+    #   -c lock/requirements-dev.txt
+    #   jsonschema
+rich==13.7.1 \
+    --hash=sha256:4edbae314f59eb482f54e9e30bf00d33350aaa94f4bfcd4e9e3110e64d0d7222 \
+    --hash=sha256:9be308cb1fe2f1f57d67ce99e95af38a1e2bc71ad9813b0e247cf7ffbcc3a432
+    # via
+    #   -c lock/requirements-dev.txt
+    #   typer
 rpds-py==0.13.2 \
     --hash=sha256:06d218e4464d31301e943b65b2c6919318ea6f69703a351961e1baaf60347276 \
     --hash=sha256:12ecf89bd54734c3c2c79898ae2021dca42750c7bcfb67f8fb3315453738ac8f \
@@ -1105,12 +1347,15 @@ rpds-py==0.13.2 \
     --hash=sha256:f8eae66a1304de7368932b42d801c67969fd090ddb1a7a24f27b435ed4bed68f \
     --hash=sha256:fdb82eb60d31b0c033a8e8ee9f3fc7dfbaa042211131c29da29aea8531b4f18f
     # via
+    #   -c lock/requirements-dev.txt
     #   jsonschema
     #   referencing
 ruamel-yaml==0.18.5 \
     --hash=sha256:61917e3a35a569c1133a8f772e1226961bf5a1198bea7e23f06a0841dea1ab0e \
     --hash=sha256:a013ac02f99a69cdd6277d9664689eb1acba07069f912823177c5eced21a6ada
-    # via linkml-dataops
+    # via
+    #   -c lock/requirements-dev.txt
+    #   linkml-dataops
 ruamel-yaml-clib==0.2.8 \
     --hash=sha256:024cfe1fc7c7f4e1aff4a81e718109e13409767e4f871443cbff3dba3578203d \
     --hash=sha256:03d1162b6d1df1caa3a4bd27aa51ce17c9afc2046c31b0ad60a0a96ec22f8001 \
@@ -1162,36 +1407,54 @@ ruamel-yaml-clib==0.2.8 \
     --hash=sha256:edaef1c1200c4b4cb914583150dcaa3bc30e592e907c01117c08b13a07255ec2 \
     --hash=sha256:f481f16baec5290e45aebdc2a5168ebc6d35189ae6fea7a58787613a25f6e875 \
     --hash=sha256:fff3573c2db359f091e1589c3d7c5fc2f86f5bdb6f24252c2d8e539d4e45f412
-    # via ruamel-yaml
+    # via
+    #   -c lock/requirements-dev.txt
+    #   ruamel-yaml
+shellingham==1.5.4 \
+    --hash=sha256:7ecfff8f2fd72616f7481040475a65b2bf8af90a56c89140852d1120324e8686 \
+    --hash=sha256:8dbca0739d487e5bd35ab3ca4b36e11c4078f3a234bfce294b0a0291363404de
+    # via
+    #   -c lock/requirements-dev.txt
+    #   typer
 shexjsg==0.8.2 \
     --hash=sha256:3b0d8432dd313bee9e1343382c5e02e9908dd941a7dd7342bf8c0200fe523766 \
     --hash=sha256:f17a629fc577fa344382bdee143cd9ff86588537f9f811f66cea6f63cdbcd0b6
     # via
+    #   -c lock/requirements-dev.txt
     #   pyshex
     #   pyshexc
 six==1.16.0 \
     --hash=sha256:1e61c37477a1626458e36f7b1d82aa5c9b094fa4802892072e49de9c60c4c926 \
     --hash=sha256:8abb2f1d86890a2dfb989f9a77cfcfd3e47c2a354b01111771326f8aa26e0254
     # via
+    #   -c lock/requirements-dev.txt
     #   isodate
     #   python-dateutil
     #   rfc3339-validator
 sniffio==1.3.0 \
     --hash=sha256:e60305c5e5d314f5389259b7f22aaa33d8f7dee49763119234af3755c55b9101 \
     --hash=sha256:eecefdce1e5bbfb7ad2eeaabf7c1eeb404d7757c379bd1f7e5cce9d8bf425384
-    # via anyio
+    # via
+    #   -c lock/requirements-dev.txt
+    #   anyio
+    #   httpx
 sortedcontainers==2.4.0 \
     --hash=sha256:25caa5a06cc30b6b83d11423433f65d1f9d76c4c6a0c90e3379eaa43b9bfdb88 \
     --hash=sha256:a163dcaede0f1c021485e957a39245190e74249897e2ae4b2aa38595db237ee0
-    # via pytrie
+    # via
+    #   -c lock/requirements-dev.txt
+    #   pytrie
 sparqlslurper==0.5.1 \
     --hash=sha256:9282ebb064fc6152a58269d194cb1e7b275b0f095425a578d75b96dcc851f546 \
     --hash=sha256:ae49b2d8ce3dd38df7a40465b228ad5d33fb7e11b3f248d195f9cadfc9cfff87
-    # via pyshex
+    # via
+    #   -c lock/requirements-dev.txt
+    #   pyshex
 sparqlwrapper==2.0.0 \
     --hash=sha256:3fed3ebcc77617a4a74d2644b86fd88e0f32e7f7003ac7b2b334c026201731f1 \
     --hash=sha256:c99a7204fff676ee28e6acef327dc1ff8451c6f7217dcd8d49e8872f324a8a20
     # via
+    #   -c lock/requirements-dev.txt
     #   pyshex
     #   sparqlslurper
 sqlalchemy==2.0.23 \
@@ -1244,58 +1507,152 @@ sqlalchemy==2.0.23 \
     --hash=sha256:f48ed89dd11c3c586f45e9eec1e437b355b3b6f6884ea4a4c3111a3358fd0c18 \
     --hash=sha256:f508ba8f89e0a5ecdfd3761f82dda2a3d7b678a626967608f4273e0dba8f07ac \
     --hash=sha256:fd54601ef9cc455a0c61e5245f690c8a3ad67ddb03d3b91c361d076def0b4c60
-    # via linkml
-starlette==0.36.3 \
-    --hash=sha256:13d429aa93a61dc40bf503e8c801db1f1bca3dc706b10ef2434a36123568f044 \
-    --hash=sha256:90a671733cfb35771d8cc605e0b679d23b992f8dcfad48cc60b38cb29aeb7080
-    # via fastapi
+    # via
+    #   -c lock/requirements-dev.txt
+    #   linkml
+starlette==0.37.2 \
+    --hash=sha256:6fe59f29268538e5d0d182f2791a479a0c64638e6935d1c6989e63fb2699c6ee \
+    --hash=sha256:9af890290133b79fc3db55474ade20f6220a364a0402e0b556e7cd5e1e093823
+    # via
+    #   -c lock/requirements-dev.txt
+    #   fastapi
 stringcase==1.2.0 \
     --hash=sha256:48a06980661908efe8d9d34eab2b6c13aefa2163b3ced26972902e3bdfd87008
-    # via linkml-validator
-tomli==2.0.1 \
-    --hash=sha256:939de3e7a6161af0c887ef91b7d41a53e7c5a1ca976325f429cb46ea9bc30ecc \
-    --hash=sha256:de526c12914f0c550d15924c62d72abc48d6fe7364aa87328337a31007fe8a4f
     # via
-    #   pyproject-api
-    #   pytest
-    #   tox
+    #   -c lock/requirements-dev.txt
+    #   linkml-validator
 tox==4.11.4 \
     --hash=sha256:2adb83d68f27116812b69aa36676a8d6a52249cb0d173649de0e7d0c2e3e7229 \
     --hash=sha256:73a7240778fabf305aeb05ab8ea26e575e042ab5a18d71d0ed13e343a51d6ce1
-    # via prefixmaps
-typer==0.9.0 \
-    --hash=sha256:50922fd79aea2f4751a8e0408ff10d2662bd0c8bbfa84755a699f3bada2978b2 \
-    --hash=sha256:5d96d986a21493606a358cae4461bd8cdf83cbf33a5aa950ae629ca3b51467ee
+    # via
+    #   -c lock/requirements-dev.txt
+    #   prefixmaps
+typer==0.12.3 \
+    --hash=sha256:070d7ca53f785acbccba8e7d28b08dcd88f79f1fbda035ade0aecec71ca5c914 \
+    --hash=sha256:49e73131481d804288ef62598d97a1ceef3058905aa536a1134f90891ba35482
+    # via
+    #   -c lock/requirements-dev.txt
+    #   metldata (pyproject.toml)
+    #   fastapi-cli
 types-python-dateutil==2.8.19.14 \
     --hash=sha256:1f4f10ac98bb8b16ade9dbee3518d9ace017821d94b057a425b069f834737f4b \
     --hash=sha256:f977b8de27787639986b4e28963263fd0e5158942b3ecef91b9335c130cb1ce9
-    # via arrow
+    # via
+    #   -c lock/requirements-dev.txt
+    #   arrow
 typing-extensions==4.9.0 \
     --hash=sha256:23478f88c37f27d76ac8aee6c905017a143b0b1b886c3c9f66bc2fd94f9f5783 \
     --hash=sha256:af72aea155e91adfc61c3ae9e0e342dbc0cba726d6cba4b6c72c1f34e47291cd
     # via
+    #   -c lock/requirements-dev.txt
     #   fastapi
     #   jwcrypto
     #   pydantic
     #   pydantic-core
     #   sqlalchemy
-    #   starlette
     #   typer
-    #   uvicorn
+ujson==5.10.0 \
+    --hash=sha256:0de4971a89a762398006e844ae394bd46991f7c385d7a6a3b93ba229e6dac17e \
+    --hash=sha256:129e39af3a6d85b9c26d5577169c21d53821d8cf68e079060602e861c6e5da1b \
+    --hash=sha256:22cffecf73391e8abd65ef5f4e4dd523162a3399d5e84faa6aebbf9583df86d6 \
+    --hash=sha256:232cc85f8ee3c454c115455195a205074a56ff42608fd6b942aa4c378ac14dd7 \
+    --hash=sha256:2544912a71da4ff8c4f7ab5606f947d7299971bdd25a45e008e467ca638d13c9 \
+    --hash=sha256:2601aa9ecdbee1118a1c2065323bda35e2c5a2cf0797ef4522d485f9d3ef65bd \
+    --hash=sha256:26b0e2d2366543c1bb4fbd457446f00b0187a2bddf93148ac2da07a53fe51569 \
+    --hash=sha256:2987713a490ceb27edff77fb184ed09acdc565db700ee852823c3dc3cffe455f \
+    --hash=sha256:29b443c4c0a113bcbb792c88bea67b675c7ca3ca80c3474784e08bba01c18d51 \
+    --hash=sha256:2a890b706b64e0065f02577bf6d8ca3b66c11a5e81fb75d757233a38c07a1f20 \
+    --hash=sha256:2aff2985cef314f21d0fecc56027505804bc78802c0121343874741650a4d3d1 \
+    --hash=sha256:348898dd702fc1c4f1051bc3aacbf894caa0927fe2c53e68679c073375f732cf \
+    --hash=sha256:38665e7d8290188b1e0d57d584eb8110951a9591363316dd41cf8686ab1d0abc \
+    --hash=sha256:38d5d36b4aedfe81dfe251f76c0467399d575d1395a1755de391e58985ab1c2e \
+    --hash=sha256:3ff201d62b1b177a46f113bb43ad300b424b7847f9c5d38b1b4ad8f75d4a282a \
+    --hash=sha256:4573fd1695932d4f619928fd09d5d03d917274381649ade4328091ceca175539 \
+    --hash=sha256:4734ee0745d5928d0ba3a213647f1c4a74a2a28edc6d27b2d6d5bd9fa4319e27 \
+    --hash=sha256:4c4fc16f11ac1612f05b6f5781b384716719547e142cfd67b65d035bd85af165 \
+    --hash=sha256:502bf475781e8167f0f9d0e41cd32879d120a524b22358e7f205294224c71126 \
+    --hash=sha256:57aaf98b92d72fc70886b5a0e1a1ca52c2320377360341715dd3933a18e827b1 \
+    --hash=sha256:59e02cd37bc7c44d587a0ba45347cc815fb7a5fe48de16bf05caa5f7d0d2e816 \
+    --hash=sha256:5b6fee72fa77dc172a28f21693f64d93166534c263adb3f96c413ccc85ef6e64 \
+    --hash=sha256:5b91b5d0d9d283e085e821651184a647699430705b15bf274c7896f23fe9c9d8 \
+    --hash=sha256:604a046d966457b6cdcacc5aa2ec5314f0e8c42bae52842c1e6fa02ea4bda42e \
+    --hash=sha256:618efd84dc1acbd6bff8eaa736bb6c074bfa8b8a98f55b61c38d4ca2c1f7f287 \
+    --hash=sha256:61d0af13a9af01d9f26d2331ce49bb5ac1fb9c814964018ac8df605b5422dcb3 \
+    --hash=sha256:61e1591ed9376e5eddda202ec229eddc56c612b61ac6ad07f96b91460bb6c2fb \
+    --hash=sha256:621e34b4632c740ecb491efc7f1fcb4f74b48ddb55e65221995e74e2d00bbff0 \
+    --hash=sha256:6627029ae4f52d0e1a2451768c2c37c0c814ffc04f796eb36244cf16b8e57043 \
+    --hash=sha256:67079b1f9fb29ed9a2914acf4ef6c02844b3153913eb735d4bf287ee1db6e557 \
+    --hash=sha256:6dea1c8b4fc921bf78a8ff00bbd2bfe166345f5536c510671bccececb187c80e \
+    --hash=sha256:6e32abdce572e3a8c3d02c886c704a38a1b015a1fb858004e03d20ca7cecbb21 \
+    --hash=sha256:7223f41e5bf1f919cd8d073e35b229295aa8e0f7b5de07ed1c8fddac63a6bc5d \
+    --hash=sha256:73814cd1b9db6fc3270e9d8fe3b19f9f89e78ee9d71e8bd6c9a626aeaeaf16bd \
+    --hash=sha256:7490655a2272a2d0b072ef16b0b58ee462f4973a8f6bbe64917ce5e0a256f9c0 \
+    --hash=sha256:7663960f08cd5a2bb152f5ee3992e1af7690a64c0e26d31ba7b3ff5b2ee66337 \
+    --hash=sha256:78778a3aa7aafb11e7ddca4e29f46bc5139131037ad628cc10936764282d6753 \
+    --hash=sha256:7c10f4654e5326ec14a46bcdeb2b685d4ada6911050aa8baaf3501e57024b804 \
+    --hash=sha256:7ec0ca8c415e81aa4123501fee7f761abf4b7f386aad348501a26940beb1860f \
+    --hash=sha256:924f7318c31874d6bb44d9ee1900167ca32aa9b69389b98ecbde34c1698a250f \
+    --hash=sha256:94a87f6e151c5f483d7d54ceef83b45d3a9cca7a9cb453dbdbb3f5a6f64033f5 \
+    --hash=sha256:98ba15d8cbc481ce55695beee9f063189dce91a4b08bc1d03e7f0152cd4bbdd5 \
+    --hash=sha256:a245d59f2ffe750446292b0094244df163c3dc96b3ce152a2c837a44e7cda9d1 \
+    --hash=sha256:a5b366812c90e69d0f379a53648be10a5db38f9d4ad212b60af00bd4048d0f00 \
+    --hash=sha256:a65b6af4d903103ee7b6f4f5b85f1bfd0c90ba4eeac6421aae436c9988aa64a2 \
+    --hash=sha256:a984a3131da7f07563057db1c3020b1350a3e27a8ec46ccbfbf21e5928a43050 \
+    --hash=sha256:a9d2edbf1556e4f56e50fab7d8ff993dbad7f54bac68eacdd27a8f55f433578e \
+    --hash=sha256:ab13a2a9e0b2865a6c6db9271f4b46af1c7476bfd51af1f64585e919b7c07fd4 \
+    --hash=sha256:ac56eb983edce27e7f51d05bc8dd820586c6e6be1c5216a6809b0c668bb312b8 \
+    --hash=sha256:ad88ac75c432674d05b61184178635d44901eb749786c8eb08c102330e6e8996 \
+    --hash=sha256:b0111b27f2d5c820e7f2dbad7d48e3338c824e7ac4d2a12da3dc6061cc39c8e6 \
+    --hash=sha256:b3cd8f3c5d8c7738257f1018880444f7b7d9b66232c64649f562d7ba86ad4bc1 \
+    --hash=sha256:b9500e61fce0cfc86168b248104e954fead61f9be213087153d272e817ec7b4f \
+    --hash=sha256:ba17799fcddaddf5c1f75a4ba3fd6441f6a4f1e9173f8a786b42450851bd74f1 \
+    --hash=sha256:ba43cc34cce49cf2d4bc76401a754a81202d8aa926d0e2b79f0ee258cb15d3a4 \
+    --hash=sha256:baed37ea46d756aca2955e99525cc02d9181de67f25515c468856c38d52b5f3b \
+    --hash=sha256:beeaf1c48e32f07d8820c705ff8e645f8afa690cca1544adba4ebfa067efdc88 \
+    --hash=sha256:c18610b9ccd2874950faf474692deee4223a994251bc0a083c114671b64e6518 \
+    --hash=sha256:c66962ca7565605b355a9ed478292da628b8f18c0f2793021ca4425abf8b01e5 \
+    --hash=sha256:caf270c6dba1be7a41125cd1e4fc7ba384bf564650beef0df2dd21a00b7f5770 \
+    --hash=sha256:cc6139531f13148055d691e442e4bc6601f6dba1e6d521b1585d4788ab0bfad4 \
+    --hash=sha256:d2c75269f8205b2690db4572a4a36fe47cd1338e4368bc73a7a0e48789e2e35a \
+    --hash=sha256:d47ebb01bd865fdea43da56254a3930a413f0c5590372a1241514abae8aa7c76 \
+    --hash=sha256:d4dc2fd6b3067c0782e7002ac3b38cf48608ee6366ff176bbd02cf969c9c20fe \
+    --hash=sha256:d7d0e0ceeb8fe2468c70ec0c37b439dd554e2aa539a8a56365fd761edb418988 \
+    --hash=sha256:d8640fb4072d36b08e95a3a380ba65779d356b2fee8696afeb7794cf0902d0a1 \
+    --hash=sha256:dee5e97c2496874acbf1d3e37b521dd1f307349ed955e62d1d2f05382bc36dd5 \
+    --hash=sha256:dfef2814c6b3291c3c5f10065f745a1307d86019dbd7ea50e83504950136ed5b \
+    --hash=sha256:e1402f0564a97d2a52310ae10a64d25bcef94f8dd643fcf5d310219d915484f7 \
+    --hash=sha256:e7ce306a42b6b93ca47ac4a3b96683ca554f6d35dd8adc5acfcd55096c8dfcb8 \
+    --hash=sha256:e82d4bb2138ab05e18f089a83b6564fee28048771eb63cdecf4b9b549de8a2cc \
+    --hash=sha256:ecb24f0bdd899d368b715c9e6664166cf694d1e57be73f17759573a6986dd95a \
+    --hash=sha256:f00ea7e00447918ee0eff2422c4add4c5752b1b60e88fcb3c067d4a21049a720 \
+    --hash=sha256:f3caf9cd64abfeb11a3b661329085c5e167abbe15256b3b68cb5d914ba7396f3 \
+    --hash=sha256:f44bd4b23a0e723bf8b10628288c2c7c335161d6840013d4d5de20e48551773b \
+    --hash=sha256:f77b74475c462cb8b88680471193064d3e715c7c6074b1c8c412cb526466efe9 \
+    --hash=sha256:f8ccb77b3e40b151e20519c6ae6d89bfe3f4c14e8e210d910287f778368bb3d1 \
+    --hash=sha256:fbd8fd427f57a03cff3ad6574b5e299131585d9727c8c366da4624a9069ed746
+    # via
+    #   -c lock/requirements-dev.txt
+    #   fastapi
 uri-template==1.3.0 \
     --hash=sha256:0e00f8eb65e18c7de20d595a14336e9f337ead580c70934141624b6d1ffdacc7 \
     --hash=sha256:a44a133ea12d44a0c0f06d7d42a52d71282e77e2f937d8abd5655b8d56fc1363
-    # via jsonschema
+    # via
+    #   -c lock/requirements-dev.txt
+    #   jsonschema
 urllib3==2.1.0 \
     --hash=sha256:55901e917a5896a349ff771be919f8bd99aff50b79fe58fec595eb37bbc56bb3 \
     --hash=sha256:df7aa8afb0148fa78488e7899b2c59b5f4ffcfa82e6c54ccb9dd37c1d7b52d54
     # via
+    #   -c lock/requirements-dev.txt
     #   pyshex
     #   requests
-uvicorn==0.27.1 \
-    --hash=sha256:3d9a267296243532db80c83a959a3400502165ade2c1338dea4e67915fd4745a \
-    --hash=sha256:5c89da2f3895767472a35556e539fd59f7edbe9b1e9c0e1c99eebeadc61838e4
-    # via ghga-service-commons
+uvicorn==0.29.0 \
+    --hash=sha256:2c2aac7ff4f4365c206fd773a39bf4ebd1047c238f8b8268ad996829323473de \
+    --hash=sha256:6a69214c0b6a087462412670b3ef21224fa48cae0e452b5883e8e8bdfdd11dd0
+    # via
+    #   -c lock/requirements-dev.txt
+    #   fastapi
+    #   ghga-service-commons
 uvloop==0.19.0 \
     --hash=sha256:0246f4fd1bf2bf702e06b0d45ee91677ee5c31242f39aab4ea6fe0c51aedd0fd \
     --hash=sha256:02506dc23a5d90e04d4f65c7791e65cf44bd91b37f24cfc3ef6cf2aff05dc7ec \
@@ -1328,11 +1685,15 @@ uvloop==0.19.0 \
     --hash=sha256:de4313d7f575474c8f5a12e163f6d89c0a878bc49219641d49e6f1444369a90e \
     --hash=sha256:e27f100e1ff17f6feeb1f33968bc185bf8ce41ca557deee9d9bbbffeb72030b7 \
     --hash=sha256:f467a5fd23b4fc43ed86342641f3936a68ded707f4627622fa3f82a120e18256
-    # via uvicorn
+    # via
+    #   -c lock/requirements-dev.txt
+    #   uvicorn
 virtualenv==20.25.0 \
     --hash=sha256:4238949c5ffe6876362d9c0180fc6c3a824a7b12b80604eeb8085f2ed7460de3 \
     --hash=sha256:bf51c0d9c7dd63ea8e44086fa1e4fb1093a31e963b86959257378aef020e1f1b
-    # via tox
+    # via
+    #   -c lock/requirements-dev.txt
+    #   tox
 watchdog==3.0.0 \
     --hash=sha256:0e06ab8858a76e1219e68c7573dfeba9dd1c0219476c5a44d5333b01d7e1743a \
     --hash=sha256:13bbbb462ee42ec3c5723e1205be8ced776f05b100e4737518c67c8325cf6100 \
@@ -1361,7 +1722,9 @@ watchdog==3.0.0 \
     --hash=sha256:c9d8c8ec7efb887333cf71e328e39cffbf771d8f8f95d308ea4125bf5f90ba64 \
     --hash=sha256:d00e6be486affb5781468457b21a6cbe848c33ef43f9ea4a73b4882e5f188a44 \
     --hash=sha256:d429c2430c93b7903914e4db9a966c7f2b068dd2ebdd2fa9b9ce094c7d459f33
-    # via linkml
+    # via
+    #   -c lock/requirements-dev.txt
+    #   linkml
 watchfiles==0.21.0 \
     --hash=sha256:02b73130687bc3f6bb79d8a170959042eb56eb3a42df3671c79b428cd73f17cc \
     --hash=sha256:02d91cbac553a3ad141db016e3350b03184deaafeba09b9d6439826ee594b365 \
@@ -1438,11 +1801,15 @@ watchfiles==0.21.0 \
     --hash=sha256:ec8c8900dc5c83650a63dd48c4d1d245343f904c4b64b48798c67a3767d7e165 \
     --hash=sha256:f564bf68404144ea6b87a78a3f910cc8de216c6b12a4cf0b27718bf4ec38d303 \
     --hash=sha256:fd7ac678b92b29ba630d8c842d8ad6c555abda1b9ef044d6cc092dacbfc9719d
-    # via uvicorn
+    # via
+    #   -c lock/requirements-dev.txt
+    #   uvicorn
 webcolors==1.13 \
     --hash=sha256:29bc7e8752c0a1bd4a1f03c14d6e6a72e93d82193738fa860cbff59d0fcc11bf \
     --hash=sha256:c225b674c83fa923be93d235330ce0300373d02885cef23238813b0d5668304a
-    # via jsonschema
+    # via
+    #   -c lock/requirements-dev.txt
+    #   jsonschema
 websockets==12.0 \
     --hash=sha256:00700340c6c7ab788f176d118775202aadea7602c5cc6be6ae127761c16d6b0b \
     --hash=sha256:0bee75f400895aef54157b36ed6d3b308fcab62e5260703add87f44cee9c82a6 \
@@ -1516,7 +1883,9 @@ websockets==12.0 \
     --hash=sha256:f764ba54e33daf20e167915edc443b6f88956f37fb606449b4a5b10ba42235a5 \
     --hash=sha256:fc4e7fa5414512b481a2483775a8e8be7803a35b30ca805afa4998a84f9fd9e8 \
     --hash=sha256:ffefa1374cd508d633646d51a8e9277763a9b78ae71324183693959cf94635a7
-    # via uvicorn
+    # via
+    #   -c lock/requirements-dev.txt
+    #   uvicorn
 wrapt==1.16.0 \
     --hash=sha256:0d2691979e93d06a95a26257adb7bfd0c93818e89b1406f5a28f36e0d8c1e1fc \
     --hash=sha256:14d7dc606219cdd7405133c713f2c218d4252f2a469003f8c46bb92d5d095d81 \
@@ -1588,4 +1957,6 @@ wrapt==1.16.0 \
     --hash=sha256:f6b2d0c6703c988d334f297aa5df18c45e97b0af3679bb75059e0e0bd8b1069d \
     --hash=sha256:f8212564d49c50eb4565e502814f694e240c55551a5f1bc841d4fcaabb0a9b8a \
     --hash=sha256:ffa565331890b90056c01db69c0fe634a776f8019c143a5ae265f9c6bc4bd6d4
-    # via deprecated
+    # via
+    #   -c lock/requirements-dev.txt
+    #   deprecated
diff --git a/pyproject.toml b/pyproject.toml
index 30687873..a26afc94 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [build-system]
 requires = [
-    "setuptools>=67.7.2",
+    "setuptools>=69",
 ]
 build-backend = "setuptools.build_meta"
 
@@ -9,26 +9,25 @@ readme = "README.md"
 authors = [
     { name = "German Human Genome Phenome Archive (GHGA)", email = "contact@ghga.de" },
 ]
-requires-python = ">=3.9"
+requires-python = ">=3.12"
 classifiers = [
     "Development Status :: 1 - Planning",
     "Operating System :: POSIX :: Linux",
-    "Programming Language :: Python :: 3.9",
-    "Programming Language :: Python :: 3.10",
-    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.12",
     "License :: OSI Approved :: Apache Software License",
     "Topic :: Internet :: WWW/HTTP :: HTTP Servers",
     "Topic :: Software Development :: Libraries",
     "Intended Audience :: Developers",
 ]
 name = "metldata"
-version = "1.2.1"
+version = "1.3.0"
 description = "metldata - A framework for handling metadata based on ETL, CQRS, and event sourcing."
 dependencies = [
-    "hexkit[akafka,mongodb] >=2.1.1, <3",
+    "hexkit[akafka,mongodb] >=3, <4",
     "ghga-service-commons[api,auth] >=3.1.1, <4",
     "ghga-event-schemas >=3.0.0, <4",
-    "typer~=0.9.0",
+    "typer>=0.12",
     "linkml==1.6.1",
     "linkml-runtime==1.6.0",
     "linkml-validator==0.4.5",
@@ -63,7 +62,7 @@ src = [
     "examples",
     "scripts",
 ]
-target-version = "py39"
+target-version = "py312"
 
 [tool.ruff.lint]
 fixable = [
@@ -72,8 +71,9 @@ fixable = [
     "D",
 ]
 ignore = [
-    "E",
-    "W",
+    "E111",
+    "E114",
+    "E116",
     "PLW",
     "RUF001",
     "RUF010",
@@ -87,6 +87,7 @@ ignore = [
     "D107",
     "D206",
     "D300",
+    "UP040",
 ]
 select = [
     "C90",
@@ -146,7 +147,7 @@ check_untyped_defs = true
 no_site_packages = false
 
 [tool.pytest.ini_options]
-minversion = "7.1"
+minversion = "8.0"
 asyncio_mode = "strict"
 
 [tool.coverage.paths]
diff --git a/scripts/__init__.py b/scripts/__init__.py
index 6222ab0b..f05ff703 100644
--- a/scripts/__init__.py
+++ b/scripts/__init__.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
diff --git a/scripts/license_checker.py b/scripts/check_license.py
similarity index 88%
rename from scripts/license_checker.py
rename to scripts/check_license.py
index b6a718df..37103d88 100755
--- a/scripts/license_checker.py
+++ b/scripts/check_license.py
@@ -1,6 +1,6 @@
 #!/usr/bin/env python3
 
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -24,7 +24,6 @@
 import sys
 from datetime import date
 from pathlib import Path
-from typing import Optional, Union
 
 # root directory of the package:
 ROOT_DIR = Path(__file__).parent.parent.resolve()
@@ -34,42 +33,45 @@
 
 # exclude files and dirs from license header check:
 EXCLUDE = [
+    ".coveragerc",
     ".devcontainer",
-    "eggs",
+    ".editorconfig",
     ".eggs",
-    "dist",
-    "build",
-    "develop-eggs",
-    "lib",
-    "lib62",
-    "parts",
-    "sdist",
-    "wheels",
-    "pip-wheel-metadata",
-    ".coveragerc",
     ".git",
     ".github",
     ".flake8",
     ".gitignore",
-    ".pylintrc",
-    ".ruff.toml",
-    ".ruff_cache",
-    "example_config.yaml",
-    "config_schema.json",
-    "LICENSE",  # is checked but not for the license header
-    ".pre-commit-config.yaml",
-    "docs",
-    ".vscode",
     ".mypy_cache",
     ".mypy.ini",
+    ".pylintrc",
     ".pytest_cache",
-    ".editorconfig",
+    ".ruff.toml",
+    ".ruff_cache",
     ".template/.static_files.txt",
     ".template/.static_files_ignore.txt",
     ".template/.mandatory_files.txt",
     ".template/.mandatory_files_ignore.txt",
     ".template/.deprecated_files.txt",
     ".template/.deprecated_files_ignore.txt",
+    ".tox",
+    ".venv",
+    ".vscode",
+    "eggs",
+    "build",
+    "config_schema.json",
+    "dist",
+    "docs",
+    "develop-eggs",
+    "example_config.yaml",
+    "htmlcov",
+    "lib",
+    "lib62",
+    "parts",
+    "pip-wheel-metadata",
+    "sdist",
+    "venv",
+    "wheels",
+    "LICENSE",  # is checked but not for the license header
 ]
 
 # exclude file by file ending from license header check:
@@ -82,6 +84,8 @@
     "md",
     "pub",
     "pyc",
+    "pyd",
+    "typed",
     "sec",
     "toml",
     "txt",
@@ -111,8 +115,8 @@
 See the License for the specific language governing permissions and
 limitations under the License."""
 
-# A list of all chars that may be used to introduce a comment:
-COMMENT_CHARS = ["#"]
+# A list of strings that may be used to introduce a line comment:
+LINE_COMMENTS = ["#"]
 
 AUTHOR = """Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 for the German Human Genome-Phenome Archive (GHGA)"""
@@ -135,11 +139,11 @@ class GlobalCopyrightNotice:
     """
 
     def __init__(self):
-        self._text: Optional[str] = None
-        self._n_lines: Optional[int] = None
+        self._text: str | None = None
+        self._n_lines: int | None = None
 
     @property
-    def text(self) -> Optional[str]:
+    def text(self) -> str | None:
         return self._text
 
     @text.setter
@@ -162,7 +166,7 @@ def n_lines(self) -> int:
 class UnexpectedBinaryFileError(RuntimeError):
     """Thrown when trying to read a binary file."""
 
-    def __init__(self, file_path: Union[str, Path]):
+    def __init__(self, file_path: str | Path):
         message = f"The file could not be read because it is binary: {str(file_path)}"
         super().__init__(message)
 
@@ -176,13 +180,13 @@ def get_target_files(
     """Get target files that are not match the exclude conditions.
     Args:
         target_dir (pathlib.Path): The target dir to search.
-        exclude (List[str], optional):
+        exclude (list[str], optional):
             Overwrite default list of file/dir paths relative to
             the target dir that shall be excluded.
-        exclude_endings (List[str], optional):
+        exclude_endings (list[str], optional):
             Overwrite default list of file endings that shall
             be excluded.
-        exclude_pattern (List[str], optional):
+        exclude_pattern (list[str], optional):
             Overwrite default list of regex patterns match file path
             for exclusion.
     """
@@ -198,24 +202,25 @@ def get_target_files(
         file_
         for file_ in all_files
         if not (
-            any([file_.is_relative_to(excl) for excl in exclude_normalized])
-            or any([str(file_).endswith(ending) for ending in exclude_endings])
-            or any([re.match(pattern, str(file_)) for pattern in exclude_pattern])
+            any(file_.is_relative_to(excl) for excl in exclude_normalized)
+            or any(str(file_).endswith(ending) for ending in exclude_endings)
+            or any(re.match(pattern, str(file_)) for pattern in exclude_pattern)
         )
     ]
     return target_files
 
 
-def normalized_line(line: str, chars_to_trim: list[str] = COMMENT_CHARS) -> str:
-    norm_line = line.strip()
-
-    for char in chars_to_trim:
-        norm_line = norm_line.strip(char)
+def normalized_line(line: str, line_comments: list[str] = LINE_COMMENTS) -> str:
+    line = line.strip()
+    for line_comment in line_comments:
+        line_without_comment = line.removeprefix(line_comment)
+        if line_without_comment != line:
+            line = line_without_comment.lstrip()
+            break
+    return line
 
-    return norm_line.strip("\n").strip("\t").strip()
 
-
-def normalized_text(text: str, chars_to_trim: list[str] = COMMENT_CHARS) -> str:
+def normalized_text(text: str, line_comments: list[str] = LINE_COMMENTS) -> str:
     "Normalize a license header text."
     lines = text.split("\n")
 
@@ -227,7 +232,7 @@ def normalized_text(text: str, chars_to_trim: list[str] = COMMENT_CHARS) -> str:
         if stripped_line.startswith("#!"):
             continue
 
-        norm_line = normalized_line(stripped_line)
+        norm_line = normalized_line(stripped_line, line_comments=line_comments)
 
         # exclude empty lines:
         if norm_line == "":
@@ -245,22 +250,17 @@ def format_copyright_template(copyright_template: str, author: str) -> str:
     return normalized_text(copyright_template.replace("{author}", author))
 
 
-def is_commented_line(line: str, comment_chars: list[str] = COMMENT_CHARS) -> bool:
+def is_commented_line(line: str, line_comments: list[str] = LINE_COMMENTS) -> bool:
     """Checks whether a line is a comment."""
-    line_stripped = line.strip()
-    for comment_char in comment_chars:
-        if line_stripped.startswith(comment_char):
-            return True
-
-    return False
+    return line.lstrip().startswith(tuple(line_comments))
 
 
 def is_empty_line(line: str) -> bool:
     """Checks whether a line is empty."""
-    return line.strip("\n").strip("\t").strip() == ""
+    return not line.strip()
 
 
-def get_header(file_path: Path, comment_chars: list[str] = COMMENT_CHARS):
+def get_header(file_path: Path, line_comments: list[str] = LINE_COMMENTS):
     """Extracts the header from a file and normalizes it."""
     header_lines: list[str] = []
 
@@ -268,7 +268,7 @@ def get_header(file_path: Path, comment_chars: list[str] = COMMENT_CHARS):
         with open(file_path) as file:
             for line in file:
                 if is_commented_line(
-                    line, comment_chars=comment_chars
+                    line, line_comments=line_comments
                 ) or is_empty_line(line):
                     header_lines.append(line)
                 else:
@@ -278,7 +278,7 @@ def get_header(file_path: Path, comment_chars: list[str] = COMMENT_CHARS):
 
     # normalize the lines:
     header = "".join(header_lines)
-    return normalized_text(header, chars_to_trim=comment_chars)
+    return normalized_text(header, line_comments=line_comments)
 
 
 def validate_year_string(year_string: str, min_year: int = MIN_YEAR) -> bool:
@@ -291,8 +291,8 @@ def validate_year_string(year_string: str, min_year: int = MIN_YEAR) -> bool:
     if year_string.isnumeric():
         return int(year_string) == current_year
 
-    # Otherwise, a range (e.g. 2021 - 2023) is expected:
-    match = re.match("(\d+) - (\d+)", year_string)
+    # Otherwise, a range (e.g. 2021 - 2024) is expected:
+    match = re.match(r"(\d+) - (\d+)", year_string)
 
     if not match:
         return False
@@ -313,7 +313,7 @@ def check_copyright_notice(
     global_copyright: GlobalCopyrightNotice,
     copyright_template: str = COPYRIGHT_TEMPLATE,
     author: str = AUTHOR,
-    comment_chars: list[str] = COMMENT_CHARS,
+    line_comments: list[str] = LINE_COMMENTS,
     min_year: int = MIN_YEAR,
 ) -> bool:
     """Checks the specified copyright text against a template.
@@ -381,7 +381,7 @@ def check_file_headers(
     exclude: list[str] = EXCLUDE,
     exclude_endings: list[str] = EXCLUDE_ENDINGS,
     exclude_pattern: list[str] = EXCLUDE_PATTERN,
-    comment_chars: list[str] = COMMENT_CHARS,
+    line_comments: list[str] = LINE_COMMENTS,
     min_year: int = MIN_YEAR,
 ) -> tuple[list[Path], list[Path]]:
     """Check files for presence of a license header and verify that
@@ -402,13 +402,13 @@ def check_file_headers(
             The author that shall be included in the license header.
             It will replace any appearance of "{author}" in the license
             header. This defaults to an author info for GHGA.
-        exclude (List[str], optional):
+        exclude (list[str], optional):
             Overwrite default list of file/dir paths relative to
             the target dir that shall be excluded.
-        exclude_endings (List[str], optional):
+        exclude_endings (list[str], optional):
             Overwrite default list of file endings that shall
             be excluded.
-        exclude_pattern (List[str], optional):
+        exclude_pattern (list[str], optional):
             Overwrite default list of regex patterns match file path
             for exclusion.
     """
@@ -425,13 +425,13 @@ def check_file_headers(
 
     for target_file in target_files:
         try:
-            header = get_header(target_file, comment_chars=comment_chars)
+            header = get_header(target_file, line_comments=line_comments)
             if check_copyright_notice(
                 copyright=header,
                 global_copyright=global_copyright,
                 copyright_template=copyright_template,
                 author=author,
-                comment_chars=comment_chars,
+                line_comments=line_comments,
                 min_year=min_year,
             ):
                 passed_files.append(target_file)
@@ -449,7 +449,7 @@ def check_license_file(
     global_copyright: GlobalCopyrightNotice,
     copyright_template: str = COPYRIGHT_TEMPLATE,
     author: str = AUTHOR,
-    comment_chars: list[str] = COMMENT_CHARS,
+    line_comments: list[str] = LINE_COMMENTS,
     min_year: int = MIN_YEAR,
 ) -> bool:
     """Currently only checks if the copyright notice in the
@@ -491,7 +491,7 @@ def check_license_file(
         global_copyright=global_copyright,
         copyright_template=copyright_template,
         author=author,
-        comment_chars=comment_chars,
+        line_comments=line_comments,
         min_year=min_year,
     )
 
diff --git a/scripts/get_package_name.py b/scripts/get_package_name.py
index 84d15fd9..505a9211 100755
--- a/scripts/get_package_name.py
+++ b/scripts/get_package_name.py
@@ -1,6 +1,6 @@
 #!/usr/bin/env python3
 
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
diff --git a/scripts/list_outdated_dependencies.py b/scripts/list_outdated_dependencies.py
index 0546abb1..894818c9 100755
--- a/scripts/list_outdated_dependencies.py
+++ b/scripts/list_outdated_dependencies.py
@@ -1,6 +1,6 @@
 #!/usr/bin/env python3
 
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -139,12 +139,14 @@ def print_table(
     header_lengths = [len(header) for header in headers]
 
     # Find the maximum length of each column
-    col_widths = [max(len(str(cell)) for cell in col) for col in zip(*rows)]
+    col_widths = [
+        max(len(str(cell)) for cell in col) for col in zip(*rows, strict=True)
+    ]
 
     # Create a row format based on the maximum column widths
     row_format = delimiter.join(
         f"{{:<{max(width, header_len)}}}"
-        for width, header_len in zip(col_widths, header_lengths)
+        for width, header_len in zip(col_widths, header_lengths, strict=True)
     )
 
     print("  " + row_format.format(*headers))
diff --git a/scripts/script_utils/__init__.py b/scripts/script_utils/__init__.py
index 56e52b5e..d0b0aa97 100644
--- a/scripts/script_utils/__init__.py
+++ b/scripts/script_utils/__init__.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
diff --git a/scripts/script_utils/cli.py b/scripts/script_utils/cli.py
index 75c127ff..c7d6af43 100644
--- a/scripts/script_utils/cli.py
+++ b/scripts/script_utils/cli.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -26,6 +26,13 @@ def echo_success(message: str):
     typer.echo(styled_message)
 
 
+def echo_warning(message: str):
+    """Print a warning message."""
+
+    styled_message = typer.style(text=message, fg=typer.colors.YELLOW)
+    typer.echo(styled_message)
+
+
 def echo_failure(message: str):
     """Print a failure message."""
 
diff --git a/scripts/script_utils/deps.py b/scripts/script_utils/deps.py
index cd84c93e..4e2f8e78 100644
--- a/scripts/script_utils/deps.py
+++ b/scripts/script_utils/deps.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -15,12 +15,12 @@
 #
 """Contains utils for working with dependencies, lock files, etc."""
 
+import tomllib
 from copy import deepcopy
 from pathlib import Path
 from typing import Any
 
 import stringcase
-import tomli
 
 
 def exclude_from_dependency_list(*, package_name: str, dependencies: list) -> list:
@@ -69,7 +69,7 @@ def remove_self_dependencies(pyproject: dict) -> dict:
 def get_modified_pyproject(pyproject_toml_path: Path) -> dict[str, Any]:
     """Get a copy of pyproject.toml with any self-referencing dependencies removed."""
     with open(pyproject_toml_path, "rb") as pyproject_toml:
-        pyproject = tomli.load(pyproject_toml)
+        pyproject = tomllib.load(pyproject_toml)
 
     modified_pyproject = remove_self_dependencies(pyproject)
     return modified_pyproject
diff --git a/scripts/script_utils/lock_deps.py b/scripts/script_utils/lock_deps.py
index 6dca8226..f800d143 100644
--- a/scripts/script_utils/lock_deps.py
+++ b/scripts/script_utils/lock_deps.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -17,14 +17,13 @@
 
 import re
 from pathlib import Path
-from typing import Optional
 
 from packaging.requirements import Requirement
 
 
 def get_lock_file_deps(
     lock_file_path: Path,
-    exclude: Optional[set[str]] = None,
+    exclude: set[str] | None = None,
 ) -> list[Requirement]:
     """Inspect the lock file to get the dependencies.
 
diff --git a/scripts/update_all.py b/scripts/update_all.py
index f319faef..856253f3 100755
--- a/scripts/update_all.py
+++ b/scripts/update_all.py
@@ -1,6 +1,6 @@
 #!/usr/bin/env python3
 
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
diff --git a/scripts/update_config_docs.py b/scripts/update_config_docs.py
index 90c12081..8156192d 100755
--- a/scripts/update_config_docs.py
+++ b/scripts/update_config_docs.py
@@ -1,6 +1,6 @@
 #!/usr/bin/env python3
 
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
diff --git a/scripts/update_hook_revs.py b/scripts/update_hook_revs.py
index 0422de2e..c915cb05 100755
--- a/scripts/update_hook_revs.py
+++ b/scripts/update_hook_revs.py
@@ -1,6 +1,6 @@
 #!/usr/bin/env python3
 
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
diff --git a/scripts/update_lock.py b/scripts/update_lock.py
index 5def8076..2f263a3d 100755
--- a/scripts/update_lock.py
+++ b/scripts/update_lock.py
@@ -1,6 +1,6 @@
 #!/usr/bin/env python3
 
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -100,13 +100,7 @@ def compile_lock_file(
 
     print(f"Updating '{output.name}'...")
 
-    command = [
-        "uv",
-        "pip",
-        "compile",
-        "--refresh",
-        "--generate-hashes",
-    ]
+    command = ["uv", "pip", "compile", "--refresh", "--generate-hashes", "--no-header"]
 
     if upgrade:
         command.append("--upgrade")
diff --git a/scripts/update_pyproject.py b/scripts/update_pyproject.py
index b68d43da..a09c6f05 100755
--- a/scripts/update_pyproject.py
+++ b/scripts/update_pyproject.py
@@ -1,6 +1,6 @@
 #!/usr/bin/env python3
 
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -19,9 +19,9 @@
 """A script to update the pyproject.toml."""
 
 import sys
+import tomllib
 from pathlib import Path
 
-import tomli
 import tomli_w
 
 from script_utils import cli
@@ -37,33 +37,33 @@
 def read_template_pyproject() -> dict[str, object]:
     """Read the pyproject_template.toml."""
     with open(PYPROJECT_TEMPLATE_PATH, "rb") as file:
-        return tomli.load(file)
+        return tomllib.load(file)
 
 
 def read_custom_pyproject() -> dict[str, object]:
     """Read the pyproject_custom.toml."""
     with open(PYPROJECT_CUSTOM_PATH, "rb") as file:
-        return tomli.load(file)
+        return tomllib.load(file)
 
 
 def read_current_pyproject() -> dict[str, object]:
     """Read the current pyproject.toml."""
     with open(PYPROJECT_TOML, "rb") as file:
-        return tomli.load(file)
+        return tomllib.load(file)
 
 
 def write_pyproject(pyproject: dict[str, object]) -> None:
     """Write the given pyproject dict into the pyproject.toml."""
     with open(PYPROJECT_TOML, "wb") as file:
-        tomli_w.dump(pyproject, file)
+        tomli_w.dump(pyproject, file, multiline_strings=True)
 
 
 def merge_fields(*, source: dict[str, object], dest: dict[str, object]):
     """Merge fields existing in both custom and template pyproject definitions.
 
     If a given field is a dictionary, merge or assign depending on if it's found in dest.
-    If the field is anything else either assign the value or exit with a message if a
-    conflict exists.
+    If the field is anything else either assign the value or exit with an error message
+    if the values have different types.
     """
     for field, value in source.items():
         if isinstance(value, dict):
@@ -72,11 +72,13 @@ def merge_fields(*, source: dict[str, object], dest: dict[str, object]):
             else:
                 dest[field] = value
         else:
-            if field in dest and value != dest[field]:
-                cli.echo_failure(f"Conflicting values for '{field}'")
-                exit(1)
-            elif field not in dest:
-                dest[field] = value
+            if field in dest:
+                if type(value) == type(dest[field]):
+                    cli.echo_warning(f"Overriding value for '{field}'...")
+                else:
+                    cli.echo_failure(f"Conflicting types for '{field}'...")
+                    sys.exit(1)
+            dest[field] = value
 
 
 def merge_pyprojects(inputs: list[dict[str, object]]) -> dict[str, object]:
@@ -85,10 +87,10 @@ def merge_pyprojects(inputs: list[dict[str, object]]) -> dict[str, object]:
 
     for input in inputs[1:]:
         for field, value in input.items():
-            if field not in pyproject:
-                pyproject[field] = value
-            else:
+            if field in pyproject:
                 merge_fields(source=value, dest=pyproject[field])  # type: ignore
+            else:
+                pyproject[field] = value
 
     return pyproject
 
diff --git a/scripts/update_readme.py b/scripts/update_readme.py
index b8273b02..41052d25 100755
--- a/scripts/update_readme.py
+++ b/scripts/update_readme.py
@@ -1,6 +1,6 @@
 #!/usr/bin/env python3
 
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -20,11 +20,11 @@
 import json
 import subprocess  # nosec
 import sys
+import tomllib
 from pathlib import Path
 from string import Template
 
 import jsonschema2md
-import tomli
 from pydantic import BaseModel, Field
 from stringcase import spinalcase, titlecase
 
@@ -97,7 +97,7 @@ def read_toml_package_header() -> PackageHeader:
     """Read basic information about the package from the pyproject.toml"""
 
     with open(PYPROJECT_TOML_PATH, "rb") as pyproject_toml:
-        pyproject = tomli.load(pyproject_toml)
+        pyproject = tomllib.load(pyproject_toml)
         pyproject_project = pyproject["project"]
         return PackageHeader(
             shortname=pyproject_project["name"],
diff --git a/scripts/update_template_files.py b/scripts/update_template_files.py
index fe29d575..0df6a745 100755
--- a/scripts/update_template_files.py
+++ b/scripts/update_template_files.py
@@ -1,6 +1,6 @@
 #!/usr/bin/env python3
 
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
diff --git a/src/metldata/__init__.py b/src/metldata/__init__.py
index c5d79541..ba8dbe50 100644
--- a/src/metldata/__init__.py
+++ b/src/metldata/__init__.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
diff --git a/src/metldata/__main__.py b/src/metldata/__main__.py
index 233538f7..3f14fe0d 100644
--- a/src/metldata/__main__.py
+++ b/src/metldata/__main__.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
diff --git a/src/metldata/accession_registry/__init__.py b/src/metldata/accession_registry/__init__.py
index b778cb28..f49cdf39 100644
--- a/src/metldata/accession_registry/__init__.py
+++ b/src/metldata/accession_registry/__init__.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
diff --git a/src/metldata/accession_registry/accession_registry.py b/src/metldata/accession_registry/accession_registry.py
index 24701d88..cf9291ff 100644
--- a/src/metldata/accession_registry/accession_registry.py
+++ b/src/metldata/accession_registry/accession_registry.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
diff --git a/src/metldata/accession_registry/accession_store.py b/src/metldata/accession_registry/accession_store.py
index 4501ce63..ca209219 100644
--- a/src/metldata/accession_registry/accession_store.py
+++ b/src/metldata/accession_registry/accession_store.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
diff --git a/src/metldata/accession_registry/config.py b/src/metldata/accession_registry/config.py
index c7f6a1c5..44e36333 100644
--- a/src/metldata/accession_registry/config.py
+++ b/src/metldata/accession_registry/config.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
diff --git a/src/metldata/artifacts_rest/__init__.py b/src/metldata/artifacts_rest/__init__.py
index 643a46c5..7076091a 100644
--- a/src/metldata/artifacts_rest/__init__.py
+++ b/src/metldata/artifacts_rest/__init__.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
diff --git a/src/metldata/artifacts_rest/api_factory.py b/src/metldata/artifacts_rest/api_factory.py
index 1eaab54e..2254f1d9 100644
--- a/src/metldata/artifacts_rest/api_factory.py
+++ b/src/metldata/artifacts_rest/api_factory.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
diff --git a/src/metldata/artifacts_rest/artifact_dao.py b/src/metldata/artifacts_rest/artifact_dao.py
index 9d8bb475..9267cc4d 100644
--- a/src/metldata/artifacts_rest/artifact_dao.py
+++ b/src/metldata/artifacts_rest/artifact_dao.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -16,8 +16,9 @@
 
 """DAO for managing artifacts."""
 
+from typing import TypeAlias
+
 from hexkit.protocols.dao import DaoFactoryProtocol, DaoNaturalId
-from typing_extensions import TypeAlias
 
 from metldata.artifacts_rest.artifact_info import get_artifact_info_dict
 from metldata.artifacts_rest.models import ArtifactInfo, ArtifactResource
diff --git a/src/metldata/artifacts_rest/artifact_info.py b/src/metldata/artifacts_rest/artifact_info.py
index 61c5d566..8fa5967a 100644
--- a/src/metldata/artifacts_rest/artifact_info.py
+++ b/src/metldata/artifacts_rest/artifact_info.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -17,7 +17,6 @@
 """Logic for handling information on artifacts."""
 
 import json
-from typing import Optional
 
 from linkml.generators.jsonschemagen import JsonSchemaGenerator
 from linkml_runtime.linkml_model.annotations import Annotation
@@ -114,9 +113,7 @@ def subset_json_schema_for_class(*, global_json_schema: Json, class_name: str) -
     }
 
 
-def load_description_for_class(
-    *, model: MetadataModel, class_name: str
-) -> Optional[str]:
+def load_description_for_class(*, model: MetadataModel, class_name: str) -> str | None:
     """Load the description for the specified class of the metadata model."""
     return model.schema_view.get_class(class_name, strict=True).description
 
diff --git a/src/metldata/artifacts_rest/config.py b/src/metldata/artifacts_rest/config.py
index d3de7a00..5a57f5c8 100644
--- a/src/metldata/artifacts_rest/config.py
+++ b/src/metldata/artifacts_rest/config.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
diff --git a/src/metldata/artifacts_rest/load_resources.py b/src/metldata/artifacts_rest/load_resources.py
index 3d0f6585..cd74c407 100644
--- a/src/metldata/artifacts_rest/load_resources.py
+++ b/src/metldata/artifacts_rest/load_resources.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -185,7 +185,7 @@ async def process_new_or_changed_resources(
             )
 
 
-async def process_resource_upsert(  # pylint: disable=too-many-locals
+async def process_resource_upsert(
     *,
     artifact_info_dict: dict[str, ArtifactInfo],
     artifact_name: str,
diff --git a/src/metldata/artifacts_rest/models.py b/src/metldata/artifacts_rest/models.py
index 11faf9ce..2dafdf78 100644
--- a/src/metldata/artifacts_rest/models.py
+++ b/src/metldata/artifacts_rest/models.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -16,8 +16,6 @@
 
 """Data models."""
 
-from typing import Optional
-
 from ghga_service_commons.utils.utc_dates import UTCDatetime
 from pydantic import BaseModel, Field, field_validator
 from typing_extensions import TypedDict
@@ -26,9 +24,9 @@
 from metldata.model_utils.anchors import AnchorPoint
 
 try:  # workaround for https://github.com/pydantic/pydantic/issues/5821
-    from typing_extensions import Literal
+    from typing import Literal
 except ImportError:
-    from typing import Literal  # type: ignore
+    from typing import Literal
 
 
 class ArtifactResource(BaseModel):
@@ -45,7 +43,7 @@ class ArtifactResourceClass(BaseModel):
     """Model to describe a resource class of an artifact."""
 
     name: str = Field(..., description="The name of the metadata class.")
-    description: Optional[str] = Field(
+    description: str | None = Field(
         None, description="A description of the metadata class."
     )
     anchor_point: AnchorPoint = Field(
diff --git a/src/metldata/artifacts_rest/query_resources.py b/src/metldata/artifacts_rest/query_resources.py
index c2091aac..2bed7b6c 100644
--- a/src/metldata/artifacts_rest/query_resources.py
+++ b/src/metldata/artifacts_rest/query_resources.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
diff --git a/src/metldata/builtin_transformations/__init__.py b/src/metldata/builtin_transformations/__init__.py
index 0d36155a..e417aad6 100644
--- a/src/metldata/builtin_transformations/__init__.py
+++ b/src/metldata/builtin_transformations/__init__.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
diff --git a/src/metldata/builtin_transformations/add_accessions/__init__.py b/src/metldata/builtin_transformations/add_accessions/__init__.py
index e8a80b5b..75005f1c 100644
--- a/src/metldata/builtin_transformations/add_accessions/__init__.py
+++ b/src/metldata/builtin_transformations/add_accessions/__init__.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -17,7 +17,6 @@
 """A transformation to add accessions to metadata."""
 
 # shortcuts:
-# pylint: disable=unused-import
 from metldata.builtin_transformations.add_accessions.main import (  # noqa: F401
     ACCESSION_ADDITION_TRANSFORMATION,
     AccessionAdditionConfig,
diff --git a/src/metldata/builtin_transformations/add_accessions/config.py b/src/metldata/builtin_transformations/add_accessions/config.py
index 38ca599e..152f1034 100644
--- a/src/metldata/builtin_transformations/add_accessions/config.py
+++ b/src/metldata/builtin_transformations/add_accessions/config.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
diff --git a/src/metldata/builtin_transformations/add_accessions/main.py b/src/metldata/builtin_transformations/add_accessions/main.py
index f42606f5..4c1a5b7a 100644
--- a/src/metldata/builtin_transformations/add_accessions/main.py
+++ b/src/metldata/builtin_transformations/add_accessions/main.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -81,7 +81,7 @@ def transform(self, *, metadata: Json, annotation: SubmissionAnnotation) -> Json
 
 def check_model_assumptions(
     model: MetadataModel,
-    config: AccessionAdditionConfig,  # pylint: disable=unused-argument
+    config: AccessionAdditionConfig,
 ) -> None:
     """Check the assumptions of the model.
 
diff --git a/src/metldata/builtin_transformations/add_accessions/metadata_transform.py b/src/metldata/builtin_transformations/add_accessions/metadata_transform.py
index 0e2e0ae0..73989b7c 100644
--- a/src/metldata/builtin_transformations/add_accessions/metadata_transform.py
+++ b/src/metldata/builtin_transformations/add_accessions/metadata_transform.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -17,9 +17,9 @@
 """Logic for transforming metadata."""
 
 from collections import defaultdict
+from typing import TypeAlias
 
 from pydantic import Json
-from typing_extensions import TypeAlias
 
 from metldata.metadata_utils import lookup_self_id
 from metldata.model_utils.anchors import AnchorPoint, lookup_anchor_point
diff --git a/src/metldata/builtin_transformations/add_accessions/model_transform.py b/src/metldata/builtin_transformations/add_accessions/model_transform.py
index 7d599714..39a1aa2a 100644
--- a/src/metldata/builtin_transformations/add_accessions/model_transform.py
+++ b/src/metldata/builtin_transformations/add_accessions/model_transform.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -17,7 +17,7 @@
 """Logic for transforming metadata models."""
 
 from copy import deepcopy
-from typing import Optional, cast
+from typing import cast
 
 from linkml_runtime.linkml_model.meta import ClassDefinition, SlotDefinition
 
@@ -29,7 +29,7 @@
 
 
 def unset_identifier(
-    *, class_definition: ClassDefinition, class_identifiers: dict[str, Optional[str]]
+    *, class_definition: ClassDefinition, class_identifiers: dict[str, str | None]
 ) -> ClassDefinition:
     """Get a modified copy of the provided class definition with the identifier being
     unset.
@@ -74,7 +74,7 @@ def add_accessions_to_class(
     *,
     class_definition: ClassDefinition,
     accession_slot_name: str,
-    class_identifiers: dict[str, Optional[str]],
+    class_identifiers: dict[str, str | None],
 ) -> ClassDefinition:
     """Get a modified copy of the provided class definition with the accession slot
     being added as identifier.
diff --git a/src/metldata/builtin_transformations/aggregate/__init__.py b/src/metldata/builtin_transformations/aggregate/__init__.py
index 7c4d37c7..8696864d 100644
--- a/src/metldata/builtin_transformations/aggregate/__init__.py
+++ b/src/metldata/builtin_transformations/aggregate/__init__.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -17,7 +17,6 @@
 """Aggregate transformation for metadata."""
 
 # shortcuts:
-# pylint: disable=unused-import
 from metldata.builtin_transformations.aggregate.config import (  # noqa: F401
     AggregateConfig,
 )
diff --git a/src/metldata/builtin_transformations/aggregate/cached_model.py b/src/metldata/builtin_transformations/aggregate/cached_model.py
index 787b932f..22c421ea 100644
--- a/src/metldata/builtin_transformations/aggregate/cached_model.py
+++ b/src/metldata/builtin_transformations/aggregate/cached_model.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
diff --git a/src/metldata/builtin_transformations/aggregate/config.py b/src/metldata/builtin_transformations/aggregate/config.py
index 50dd3f39..3426f28c 100644
--- a/src/metldata/builtin_transformations/aggregate/config.py
+++ b/src/metldata/builtin_transformations/aggregate/config.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -16,8 +16,6 @@
 
 """Config for aggregate transformations"""
 
-from typing import Optional
-
 from pydantic import BaseModel, model_validator
 from pydantic_settings import BaseSettings
 
@@ -34,7 +32,7 @@ class AggregationOperation(BaseModel):
 
     input_paths: list[str]
     output_path: str
-    visit_only_once: Optional[list[str]] = None
+    visit_only_once: list[str] | None = None
     function: type[AggregationFunction]
 
     @model_validator(mode="before")
diff --git a/src/metldata/builtin_transformations/aggregate/data_subgraph.py b/src/metldata/builtin_transformations/aggregate/data_subgraph.py
index 7159e7d9..f4221953 100644
--- a/src/metldata/builtin_transformations/aggregate/data_subgraph.py
+++ b/src/metldata/builtin_transformations/aggregate/data_subgraph.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -20,7 +20,7 @@
 
 from collections import defaultdict
 from collections.abc import Iterator
-from typing import Any, Optional
+from typing import Any
 
 from linkml_runtime.linkml_model import SlotDefinition
 
@@ -72,7 +72,7 @@ class DataSubgraph:
 
     _model: MetadataModel
     _paths: list[list[SlotDefinition]]
-    _class_identifiers: dict[str, Optional[str]]
+    _class_identifiers: dict[str, str | None]
     _all_classes: list[str]
     _anchor_points: dict[str, AnchorPoint]
 
@@ -222,7 +222,7 @@ def __init__(  # noqa: PLR0913
         submission_data: Json,
         origin: str,
         path_strings: list[str],
-        visit_once_classes: Optional[list[str]] = None,
+        visit_once_classes: list[str] | None = None,
     ):
         """Creates a new DataSubgraph object.
 
diff --git a/src/metldata/builtin_transformations/aggregate/expanding_dict.py b/src/metldata/builtin_transformations/aggregate/expanding_dict.py
index 55861661..413ba186 100644
--- a/src/metldata/builtin_transformations/aggregate/expanding_dict.py
+++ b/src/metldata/builtin_transformations/aggregate/expanding_dict.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
diff --git a/src/metldata/builtin_transformations/aggregate/func.py b/src/metldata/builtin_transformations/aggregate/func.py
index b739c6cb..93e6e987 100644
--- a/src/metldata/builtin_transformations/aggregate/func.py
+++ b/src/metldata/builtin_transformations/aggregate/func.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -20,7 +20,7 @@
 from collections import Counter
 from collections.abc import Iterable
 from operator import itemgetter
-from typing import Any, Optional
+from typing import Any
 
 from metldata.builtin_transformations.aggregate.models import (
     MinimalClass,
@@ -37,7 +37,7 @@ class AggregationFunction(ABC):
     result_range_name: str
     """The name of the range of the data produced by func."""
 
-    result_range_cls_def: Optional[MinimalClass]
+    result_range_cls_def: MinimalClass | None
     """The class definition of the data produced by func. None if the function
     result range is a type rather than a class."""
 
diff --git a/src/metldata/builtin_transformations/aggregate/main.py b/src/metldata/builtin_transformations/aggregate/main.py
index cbc2c253..45199682 100644
--- a/src/metldata/builtin_transformations/aggregate/main.py
+++ b/src/metldata/builtin_transformations/aggregate/main.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -73,7 +73,7 @@ def transform(self, *, metadata: Json, annotation: SubmissionAnnotation) -> Json
 
 def check_model_assumptions(
     model: MetadataModel,
-    config: AggregateConfig,  # pylint: disable=unused-argument
+    config: AggregateConfig,
 ) -> None:
     """Check the assumptions of the model.
 
diff --git a/src/metldata/builtin_transformations/aggregate/metadata_transform.py b/src/metldata/builtin_transformations/aggregate/metadata_transform.py
index dfbfe175..d9342989 100644
--- a/src/metldata/builtin_transformations/aggregate/metadata_transform.py
+++ b/src/metldata/builtin_transformations/aggregate/metadata_transform.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -25,7 +25,6 @@
 from metldata.model_utils.anchors import AnchorPoint
 
 
-# pylint: disable=unused-argument
 def execute_aggregation(
     *,
     original_model: CachedMetadataModel,
diff --git a/src/metldata/builtin_transformations/aggregate/model_transform.py b/src/metldata/builtin_transformations/aggregate/model_transform.py
index 665baddf..60f9744f 100644
--- a/src/metldata/builtin_transformations/aggregate/model_transform.py
+++ b/src/metldata/builtin_transformations/aggregate/model_transform.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -20,7 +20,6 @@
 from collections import defaultdict
 from collections.abc import Iterable
 from dataclasses import asdict
-from typing import Optional
 
 from linkml_runtime.linkml_model import ClassDefinition, SlotDefinition
 from stringcase import snakecase
@@ -41,7 +40,7 @@
 from metldata.model_utils.manipulate import add_anchor_point, upsert_class_slot
 from metldata.transform.base import MetadataModelTransformationError
 
-Path = tuple[Optional[str], ...]
+Path = tuple[str | None, ...]
 
 
 class PathMatrix:
@@ -81,7 +80,7 @@ def load_leaf_slots(self, leaf_slots: list[MinimalSlot]) -> None:
         """
         self.leaf_slots = [
             MinimalNamedSlot(slot_name=slot_name, **asdict(slot))
-            for slot_name, slot in zip(self.path_leaves(), leaf_slots)
+            for slot_name, slot in zip(self.path_leaves(), leaf_slots, strict=False)
         ]
 
     @property
@@ -203,7 +202,7 @@ def add_aggregation(min_model: MinimalLinkMLModel, aggregation: Aggregation) ->
         path_strings=path_strings,
         leaf_slots=[
             MinimalSlot(range=slot_range, multivalued=mv)
-            for slot_range, mv in zip(leaf_ranges, leaf_multivalued)
+            for slot_range, mv in zip(leaf_ranges, leaf_multivalued, strict=False)
         ],
     )
 
diff --git a/src/metldata/builtin_transformations/aggregate/models.py b/src/metldata/builtin_transformations/aggregate/models.py
index 829fec9c..e60d56e1 100644
--- a/src/metldata/builtin_transformations/aggregate/models.py
+++ b/src/metldata/builtin_transformations/aggregate/models.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
diff --git a/src/metldata/builtin_transformations/custom_embeddings/__init__.py b/src/metldata/builtin_transformations/custom_embeddings/__init__.py
index ce6f9c73..99e07dc4 100644
--- a/src/metldata/builtin_transformations/custom_embeddings/__init__.py
+++ b/src/metldata/builtin_transformations/custom_embeddings/__init__.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -17,7 +17,6 @@
 """A transformation to generate custom embeddings for classes of a metadata model."""
 
 # shortcuts:
-# pylint: disable=unused-import
 from metldata.builtin_transformations.custom_embeddings.main import (  # noqa: F401
     CUSTOM_EMBEDDING_TRANSFORMATION,
     CustomEmbeddingConfig,
diff --git a/src/metldata/builtin_transformations/custom_embeddings/config.py b/src/metldata/builtin_transformations/custom_embeddings/config.py
index 4bf18c5e..1fc22146 100644
--- a/src/metldata/builtin_transformations/custom_embeddings/config.py
+++ b/src/metldata/builtin_transformations/custom_embeddings/config.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -52,7 +52,6 @@ class CustomEmbeddingConfig(BaseSettings):
         ),
     )
 
-    # pylint: disable=no-self-argument
     @field_validator("embedding_profiles")
     def check_embedding_profiles_unique(
         cls,  # noqa: N805
diff --git a/src/metldata/builtin_transformations/custom_embeddings/embedding_profile.py b/src/metldata/builtin_transformations/custom_embeddings/embedding_profile.py
index 6214011b..a90b5531 100644
--- a/src/metldata/builtin_transformations/custom_embeddings/embedding_profile.py
+++ b/src/metldata/builtin_transformations/custom_embeddings/embedding_profile.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
diff --git a/src/metldata/builtin_transformations/custom_embeddings/main.py b/src/metldata/builtin_transformations/custom_embeddings/main.py
index d53eecdc..01f4634d 100644
--- a/src/metldata/builtin_transformations/custom_embeddings/main.py
+++ b/src/metldata/builtin_transformations/custom_embeddings/main.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -73,7 +73,7 @@ def transform(self, *, metadata: Json, annotation: SubmissionAnnotation) -> Json
 
 def check_model_assumptions(
     model: MetadataModel,
-    config: CustomEmbeddingConfig,  # pylint: disable=unused-argument
+    config: CustomEmbeddingConfig,
 ) -> None:
     """Check the assumptions of the model.
 
diff --git a/src/metldata/builtin_transformations/custom_embeddings/metadata_transform.py b/src/metldata/builtin_transformations/custom_embeddings/metadata_transform.py
index 213d4c97..5d2199c9 100644
--- a/src/metldata/builtin_transformations/custom_embeddings/metadata_transform.py
+++ b/src/metldata/builtin_transformations/custom_embeddings/metadata_transform.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -16,7 +16,7 @@
 
 """Logic for transforming metadata."""
 
-from typing import Union, cast
+from typing import cast
 
 from metldata.builtin_transformations.custom_embeddings.embedding_profile import (
     EmbeddingProfile,
@@ -53,7 +53,7 @@ def is_slot_multivalued(
 
 def resolve_target_resource(
     target_resource_id: str,
-    target: Union[str, EmbeddingProfile],
+    target: str | EmbeddingProfile,
     global_metadata: Json,
     model: MetadataModel,
     anchor_points_by_target: dict,
diff --git a/src/metldata/builtin_transformations/custom_embeddings/model_transform.py b/src/metldata/builtin_transformations/custom_embeddings/model_transform.py
index bfb8de3b..cb6bc6d1 100644
--- a/src/metldata/builtin_transformations/custom_embeddings/model_transform.py
+++ b/src/metldata/builtin_transformations/custom_embeddings/model_transform.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -17,7 +17,6 @@
 """Logic for transforming metadata models."""
 
 from copy import deepcopy
-from typing import Union
 
 from linkml_runtime.linkml_model.meta import ClassDefinition, SlotDefinition
 from stringcase import snakecase
@@ -51,7 +50,7 @@ def get_embedded_reference_slot(
     class_: ClassDefinition,
     schema_view: ExportableSchemaView,
     reference_slot_name: str,
-    target: Union[str, EmbeddingProfile],
+    target: str | EmbeddingProfile,
 ) -> SlotDefinition:
     """Update the slot definition of an embedded reference."""
     if not class_.slots or reference_slot_name not in class_.slots:
diff --git a/src/metldata/builtin_transformations/delete_slots/__init__.py b/src/metldata/builtin_transformations/delete_slots/__init__.py
index 0ba7dddd..be2fcd19 100644
--- a/src/metldata/builtin_transformations/delete_slots/__init__.py
+++ b/src/metldata/builtin_transformations/delete_slots/__init__.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -17,7 +17,6 @@
 """A transformation that deletes slots from models and associated metadata."""
 
 # shortcuts:
-# pylint: disable=unused-import
 from metldata.builtin_transformations.delete_slots.main import (  # noqa: F401
     SLOT_DELETION_TRANSFORMATION,
     SlotDeletionConfig,
diff --git a/src/metldata/builtin_transformations/delete_slots/assumptions.py b/src/metldata/builtin_transformations/delete_slots/assumptions.py
index 1118a8f4..34e33795 100644
--- a/src/metldata/builtin_transformations/delete_slots/assumptions.py
+++ b/src/metldata/builtin_transformations/delete_slots/assumptions.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
diff --git a/src/metldata/builtin_transformations/delete_slots/config.py b/src/metldata/builtin_transformations/delete_slots/config.py
index 09679b6a..ce42951f 100644
--- a/src/metldata/builtin_transformations/delete_slots/config.py
+++ b/src/metldata/builtin_transformations/delete_slots/config.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
diff --git a/src/metldata/builtin_transformations/delete_slots/main.py b/src/metldata/builtin_transformations/delete_slots/main.py
index ab67d1ef..cf398c47 100644
--- a/src/metldata/builtin_transformations/delete_slots/main.py
+++ b/src/metldata/builtin_transformations/delete_slots/main.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
diff --git a/src/metldata/builtin_transformations/delete_slots/metadata_transform.py b/src/metldata/builtin_transformations/delete_slots/metadata_transform.py
index 094074b0..b300cc65 100644
--- a/src/metldata/builtin_transformations/delete_slots/metadata_transform.py
+++ b/src/metldata/builtin_transformations/delete_slots/metadata_transform.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
diff --git a/src/metldata/builtin_transformations/delete_slots/model_transform.py b/src/metldata/builtin_transformations/delete_slots/model_transform.py
index 211c7a6f..b18b8360 100644
--- a/src/metldata/builtin_transformations/delete_slots/model_transform.py
+++ b/src/metldata/builtin_transformations/delete_slots/model_transform.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
diff --git a/src/metldata/builtin_transformations/infer_references/__init__.py b/src/metldata/builtin_transformations/infer_references/__init__.py
index 9752d6a6..9b6c831a 100644
--- a/src/metldata/builtin_transformations/infer_references/__init__.py
+++ b/src/metldata/builtin_transformations/infer_references/__init__.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -17,7 +17,6 @@
 """A transformation to infer references based on existing ones in the metadata model."""
 
 # shortcuts:
-# pylint: disable=unused-import
 from metldata.builtin_transformations.infer_references.main import (  # noqa: F401
     REFERENCE_INFERENCE_TRANSFORMATION,
     ReferenceInferenceConfig,
diff --git a/src/metldata/builtin_transformations/infer_references/config.py b/src/metldata/builtin_transformations/infer_references/config.py
index 9362b17a..c553c912 100644
--- a/src/metldata/builtin_transformations/infer_references/config.py
+++ b/src/metldata/builtin_transformations/infer_references/config.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
diff --git a/src/metldata/builtin_transformations/infer_references/main.py b/src/metldata/builtin_transformations/infer_references/main.py
index e5233322..385bde3d 100644
--- a/src/metldata/builtin_transformations/infer_references/main.py
+++ b/src/metldata/builtin_transformations/infer_references/main.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -74,7 +74,7 @@ def transform(self, *, metadata: Json, annotation: SubmissionAnnotation) -> Json
 
 def check_model_assumptions(
     model: MetadataModel,
-    config: ReferenceInferenceConfig,  # pylint: disable=unused-argument
+    config: ReferenceInferenceConfig,
 ) -> None:
     """Check the assumptions of the model.
 
diff --git a/src/metldata/builtin_transformations/infer_references/metadata_transform.py b/src/metldata/builtin_transformations/infer_references/metadata_transform.py
index 0c3533ed..2ec75159 100644
--- a/src/metldata/builtin_transformations/infer_references/metadata_transform.py
+++ b/src/metldata/builtin_transformations/infer_references/metadata_transform.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
diff --git a/src/metldata/builtin_transformations/infer_references/model_transform.py b/src/metldata/builtin_transformations/infer_references/model_transform.py
index ee8becce..ed0ac61a 100644
--- a/src/metldata/builtin_transformations/infer_references/model_transform.py
+++ b/src/metldata/builtin_transformations/infer_references/model_transform.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
diff --git a/src/metldata/builtin_transformations/infer_references/path/__init__.py b/src/metldata/builtin_transformations/infer_references/path/__init__.py
index c813d562..27b862df 100644
--- a/src/metldata/builtin_transformations/infer_references/path/__init__.py
+++ b/src/metldata/builtin_transformations/infer_references/path/__init__.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
diff --git a/src/metldata/builtin_transformations/infer_references/path/path.py b/src/metldata/builtin_transformations/infer_references/path/path.py
index 1f2e567a..f06903b6 100644
--- a/src/metldata/builtin_transformations/infer_references/path/path.py
+++ b/src/metldata/builtin_transformations/infer_references/path/path.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
diff --git a/src/metldata/builtin_transformations/infer_references/path/path_elements.py b/src/metldata/builtin_transformations/infer_references/path/path_elements.py
index bc9ac902..2ad53a72 100644
--- a/src/metldata/builtin_transformations/infer_references/path/path_elements.py
+++ b/src/metldata/builtin_transformations/infer_references/path/path_elements.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
diff --git a/src/metldata/builtin_transformations/infer_references/path/path_str.py b/src/metldata/builtin_transformations/infer_references/path/path_str.py
index d5bbdbc8..42d56134 100644
--- a/src/metldata/builtin_transformations/infer_references/path/path_str.py
+++ b/src/metldata/builtin_transformations/infer_references/path/path_str.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -17,7 +17,6 @@
 """Data models"""
 
 import re
-from typing import Optional
 
 from metldata.builtin_transformations.infer_references.path.path_elements import (
     ReferencePathElement,
@@ -107,7 +106,7 @@ def get_target_class(*, path_str: str) -> str:
     return match.group(1)
 
 
-def split_first_element(*, path_str: str) -> tuple[str, Optional[str]]:
+def split_first_element(*, path_str: str) -> tuple[str, str | None]:
     """Return a tuple of the first element and the remaining path string.
     Thereby, the target class of the first element is set as the source class of the
     remaining path.
diff --git a/src/metldata/builtin_transformations/infer_references/path/resolve.py b/src/metldata/builtin_transformations/infer_references/path/resolve.py
index f8fc2ad0..88a74716 100644
--- a/src/metldata/builtin_transformations/infer_references/path/resolve.py
+++ b/src/metldata/builtin_transformations/infer_references/path/resolve.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
diff --git a/src/metldata/builtin_transformations/infer_references/reference.py b/src/metldata/builtin_transformations/infer_references/reference.py
index f1b15858..e7e0c345 100644
--- a/src/metldata/builtin_transformations/infer_references/reference.py
+++ b/src/metldata/builtin_transformations/infer_references/reference.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
diff --git a/src/metldata/builtin_transformations/merge_slots/__init__.py b/src/metldata/builtin_transformations/merge_slots/__init__.py
index c644c723..ad5b0451 100644
--- a/src/metldata/builtin_transformations/merge_slots/__init__.py
+++ b/src/metldata/builtin_transformations/merge_slots/__init__.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -17,7 +17,6 @@
 """A transformation that merges multiple slots of a class into a single one."""
 
 # shortcuts:
-# pylint: disable=unused-import
 from metldata.builtin_transformations.merge_slots.main import (  # noqa: F401
     SLOT_MERGING_TRANSFORMATION,
     SlotMergingConfig,
diff --git a/src/metldata/builtin_transformations/merge_slots/assumptions.py b/src/metldata/builtin_transformations/merge_slots/assumptions.py
index 376f306f..5c0aef2f 100644
--- a/src/metldata/builtin_transformations/merge_slots/assumptions.py
+++ b/src/metldata/builtin_transformations/merge_slots/assumptions.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
diff --git a/src/metldata/builtin_transformations/merge_slots/config.py b/src/metldata/builtin_transformations/merge_slots/config.py
index 319728fe..9492f0fb 100644
--- a/src/metldata/builtin_transformations/merge_slots/config.py
+++ b/src/metldata/builtin_transformations/merge_slots/config.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
diff --git a/src/metldata/builtin_transformations/merge_slots/main.py b/src/metldata/builtin_transformations/merge_slots/main.py
index d8b672e4..b3118e6a 100644
--- a/src/metldata/builtin_transformations/merge_slots/main.py
+++ b/src/metldata/builtin_transformations/merge_slots/main.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
diff --git a/src/metldata/builtin_transformations/merge_slots/metadata_transform.py b/src/metldata/builtin_transformations/merge_slots/metadata_transform.py
index 3b55a4d5..0229d8b2 100644
--- a/src/metldata/builtin_transformations/merge_slots/metadata_transform.py
+++ b/src/metldata/builtin_transformations/merge_slots/metadata_transform.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
diff --git a/src/metldata/builtin_transformations/merge_slots/model_transform.py b/src/metldata/builtin_transformations/merge_slots/model_transform.py
index e2b6ec4d..4deb2afc 100644
--- a/src/metldata/builtin_transformations/merge_slots/model_transform.py
+++ b/src/metldata/builtin_transformations/merge_slots/model_transform.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
diff --git a/src/metldata/builtin_transformations/merge_slots/models.py b/src/metldata/builtin_transformations/merge_slots/models.py
index 2bbff3a8..4c63f5e4 100644
--- a/src/metldata/builtin_transformations/merge_slots/models.py
+++ b/src/metldata/builtin_transformations/merge_slots/models.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -16,8 +16,6 @@
 
 """Models to describe slot merging instructions."""
 
-from typing import Optional
-
 from pydantic import BaseModel, Field, model_validator
 
 
@@ -33,7 +31,7 @@ class SlotMergeInstruction(BaseModel):
     target_slot: str = Field(
         ..., description="The slot into which the source slots should be merged."
     )
-    target_description: Optional[str] = Field(
+    target_description: str | None = Field(
         None,
         description="A description of the target slot.",
     )
diff --git a/src/metldata/builtin_transformations/normalize_model/__init__.py b/src/metldata/builtin_transformations/normalize_model/__init__.py
index 5dcf04ca..5df97b22 100644
--- a/src/metldata/builtin_transformations/normalize_model/__init__.py
+++ b/src/metldata/builtin_transformations/normalize_model/__init__.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
diff --git a/src/metldata/builtin_transformations/normalize_model/config.py b/src/metldata/builtin_transformations/normalize_model/config.py
index 1119afd9..750ba3ff 100644
--- a/src/metldata/builtin_transformations/normalize_model/config.py
+++ b/src/metldata/builtin_transformations/normalize_model/config.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
diff --git a/src/metldata/builtin_transformations/normalize_model/main.py b/src/metldata/builtin_transformations/normalize_model/main.py
index f11960af..9d6352fb 100644
--- a/src/metldata/builtin_transformations/normalize_model/main.py
+++ b/src/metldata/builtin_transformations/normalize_model/main.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -26,12 +26,10 @@
 from metldata.transform.base import MetadataTransformer, TransformationDefinition
 
 
-# pylint: disable=unused-argument
 def check_model_assumptions(model: MetadataModel, config: NormalizationConfig):
     """Check that the classes and slots specified in the config exist in the model."""
 
 
-# pylint: disable=unused-argument
 def transform_model(model: MetadataModel, config: NormalizationConfig) -> MetadataModel:
     """Normalize the model."""
     return normalize_model(model)
diff --git a/src/metldata/builtin_transformations/normalize_model/model_transform.py b/src/metldata/builtin_transformations/normalize_model/model_transform.py
index abd4395e..f25a62a9 100644
--- a/src/metldata/builtin_transformations/normalize_model/model_transform.py
+++ b/src/metldata/builtin_transformations/normalize_model/model_transform.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
diff --git a/src/metldata/builtin_workflows/__init__.py b/src/metldata/builtin_workflows/__init__.py
index 1867ef27..946da494 100644
--- a/src/metldata/builtin_workflows/__init__.py
+++ b/src/metldata/builtin_workflows/__init__.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
diff --git a/src/metldata/builtin_workflows/ghga_archive.py b/src/metldata/builtin_workflows/ghga_archive.py
index 6394476a..5d42919f 100644
--- a/src/metldata/builtin_workflows/ghga_archive.py
+++ b/src/metldata/builtin_workflows/ghga_archive.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
diff --git a/src/metldata/cli.py b/src/metldata/cli.py
index 559e6a57..700ba449 100644
--- a/src/metldata/cli.py
+++ b/src/metldata/cli.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
diff --git a/src/metldata/combined.py b/src/metldata/combined.py
index 28e742ce..00cb463a 100644
--- a/src/metldata/combined.py
+++ b/src/metldata/combined.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
diff --git a/src/metldata/config.py b/src/metldata/config.py
index 2f0c426b..8e9cade9 100644
--- a/src/metldata/config.py
+++ b/src/metldata/config.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -17,16 +17,12 @@
 
 from hexkit.config import config_from_yaml
 
-# pylint: disable=unused-import
 from metldata.accession_registry.config import Config as AccessionRegistryConfig
 from metldata.artifacts_rest.config import ArtifactsRestConfig
-
-# pylint: disable=unused-import
 from metldata.load.config import ArtifactLoaderAPIConfig
 from metldata.submission_registry.config import Config as SubmissionRegistryConfig
 
 
-# pylint: disable=too-many-ancestors
 @config_from_yaml(prefix="metl_sub")
 class SubmissionConfig(AccessionRegistryConfig, SubmissionRegistryConfig):
     """Config parameters and their defaults."""
diff --git a/src/metldata/custom_types.py b/src/metldata/custom_types.py
index b762072d..6ea19461 100644
--- a/src/metldata/custom_types.py
+++ b/src/metldata/custom_types.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -16,9 +16,7 @@
 
 """A collection of custom types."""
 
-from typing import Any
-
-from typing_extensions import TypeAlias
+from typing import Any, TypeAlias
 
 Json: TypeAlias = dict[str, Any]
 
diff --git a/src/metldata/event_handling/__init__.py b/src/metldata/event_handling/__init__.py
index ce5cccb9..6b99f9e3 100644
--- a/src/metldata/event_handling/__init__.py
+++ b/src/metldata/event_handling/__init__.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
diff --git a/src/metldata/event_handling/artifact_events.py b/src/metldata/event_handling/artifact_events.py
index f84ac1ca..e8c25f0f 100644
--- a/src/metldata/event_handling/artifact_events.py
+++ b/src/metldata/event_handling/artifact_events.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
diff --git a/src/metldata/event_handling/event_handling.py b/src/metldata/event_handling/event_handling.py
index 9b56f235..b792227b 100644
--- a/src/metldata/event_handling/event_handling.py
+++ b/src/metldata/event_handling/event_handling.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -19,7 +19,6 @@
 import json
 from collections.abc import Iterator
 from pathlib import Path
-from typing import Optional
 
 from hexkit.base import InboundProviderBase
 from hexkit.custom_types import Ascii, JsonObject
@@ -165,7 +164,7 @@ async def run(self, forever: bool = True) -> None:
             event_store_path=self._config.event_store_path,
         ):
             await self._translator.consume(
-                payload=event.payload, type_=event.type_, topic=event.topic
+                payload=event.payload, type_=event.type_, topic=event.topic, key=""
             )
 
 
@@ -180,7 +179,7 @@ def __init__(self, *, config: FileSystemEventConfig):
         self._config = config
 
     def collect_events(
-        self, *, topic: str, types: Optional[list[str]] = None
+        self, *, topic: str, types: list[str] | None = None
     ) -> Iterator[Event]:
         """Collect all events for the given types from the given topic."""
         events = read_events_from_topic(
diff --git a/src/metldata/event_handling/models.py b/src/metldata/event_handling/models.py
index 787a13ce..e8252007 100644
--- a/src/metldata/event_handling/models.py
+++ b/src/metldata/event_handling/models.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
diff --git a/src/metldata/event_handling/submission_events.py b/src/metldata/event_handling/submission_events.py
index d48e9dc0..209bde1b 100644
--- a/src/metldata/event_handling/submission_events.py
+++ b/src/metldata/event_handling/submission_events.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
diff --git a/src/metldata/load/__init__.py b/src/metldata/load/__init__.py
index 6926c580..5bd5d464 100644
--- a/src/metldata/load/__init__.py
+++ b/src/metldata/load/__init__.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
diff --git a/src/metldata/load/aggregator.py b/src/metldata/load/aggregator.py
index e112bc5f..5870b33d 100644
--- a/src/metldata/load/aggregator.py
+++ b/src/metldata/load/aggregator.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
diff --git a/src/metldata/load/api.py b/src/metldata/load/api.py
index be71c6a0..d9016e52 100644
--- a/src/metldata/load/api.py
+++ b/src/metldata/load/api.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -16,8 +16,6 @@
 
 """API for loading artifacts into running services."""
 
-from typing import Optional
-
 from fastapi import Depends, HTTPException, Response, Security
 from fastapi.routing import APIRouter
 from fastapi.security import HTTPAuthorizationCredentials, HTTPBearer
@@ -59,7 +57,7 @@ def __init__(self, *, token_hashes: list[str]):
         """Initialize the loader token auth provider."""
         self._token_hashes = token_hashes
 
-    async def get_context(self, token: str) -> Optional[LoaderTokenAuthContext]:
+    async def get_context(self, token: str) -> LoaderTokenAuthContext | None:
         """Get a loader token auth context."""
         if not token:
             return None
diff --git a/src/metldata/load/auth.py b/src/metldata/load/auth.py
index bba402db..cf45e6a9 100644
--- a/src/metldata/load/auth.py
+++ b/src/metldata/load/auth.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
diff --git a/src/metldata/load/client.py b/src/metldata/load/client.py
index 95154749..d658e6ce 100644
--- a/src/metldata/load/client.py
+++ b/src/metldata/load/client.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
diff --git a/src/metldata/load/collect.py b/src/metldata/load/collect.py
index 1ba0d7d5..fdd90a19 100644
--- a/src/metldata/load/collect.py
+++ b/src/metldata/load/collect.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -66,6 +66,6 @@ def collect_artifacts(
             content = event.payload.get("content")
             if not content:
                 raise RuntimeError("Artifact does not contain 'content' field.")
-            artifact_resources[artifact_type].append(content)
+            artifact_resources[artifact_type].append(content)  # type: ignore
 
     return artifact_resources
diff --git a/src/metldata/load/config.py b/src/metldata/load/config.py
index 1b812cb2..d6535c6f 100644
--- a/src/metldata/load/config.py
+++ b/src/metldata/load/config.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -27,7 +27,7 @@
 from metldata.load.event_publisher import EventPubTranslatorConfig
 
 
-class ArtifactLoaderAPIConfig(  # pylint: disable=too-many-ancestors
+class ArtifactLoaderAPIConfig(
     ArtifactsRestConfig,
     ApiConfigBase,
     EventPubTranslatorConfig,
diff --git a/src/metldata/load/event_publisher.py b/src/metldata/load/event_publisher.py
index ee309d67..b34d805d 100644
--- a/src/metldata/load/event_publisher.py
+++ b/src/metldata/load/event_publisher.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
diff --git a/src/metldata/load/load.py b/src/metldata/load/load.py
index 5a952465..07d64240 100644
--- a/src/metldata/load/load.py
+++ b/src/metldata/load/load.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -82,7 +82,7 @@ async def load_artifacts_using_dao(
     )
 
 
-async def _get_changed_resources(  # pylint: disable=too-many-locals
+async def _get_changed_resources(
     artifact_resources: ArtifactResourceDict,
     artifact_info_dict: dict[str, ArtifactInfo],
     dao_collection: ArtifactDaoCollection,
diff --git a/src/metldata/load/main.py b/src/metldata/load/main.py
index f209b57b..c7042f7f 100644
--- a/src/metldata/load/main.py
+++ b/src/metldata/load/main.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
diff --git a/src/metldata/load/models.py b/src/metldata/load/models.py
index 1c799dbd..18f4a0be 100644
--- a/src/metldata/load/models.py
+++ b/src/metldata/load/models.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -16,7 +16,7 @@
 
 """Data models."""
 
-from typing_extensions import TypeAlias
+from typing import TypeAlias
 
 from metldata.custom_types import Json
 
diff --git a/src/metldata/load/stats.py b/src/metldata/load/stats.py
index 83a65847..a1fea68c 100644
--- a/src/metldata/load/stats.py
+++ b/src/metldata/load/stats.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -17,7 +17,7 @@
 """Generate global summary statistics."""
 
 from operator import itemgetter
-from typing import Any, Optional, cast
+from typing import Any, cast
 
 from ghga_service_commons.utils.utc_dates import now_as_utc
 
@@ -32,7 +32,7 @@
 STATS_COLLECTION_NAME = "stats"
 
 
-def get_stat_slot(resource_class: str) -> Optional[str]:
+def get_stat_slot(resource_class: str) -> str | None:
     """Get the name of the slot that shall be used as grouping key."""
     if resource_class.endswith("File"):
         return "format"
diff --git a/src/metldata/metadata_utils.py b/src/metldata/metadata_utils.py
index f3e3b671..b0792b7d 100644
--- a/src/metldata/metadata_utils.py
+++ b/src/metldata/metadata_utils.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -17,7 +17,7 @@
 """Utilities for handling metadata."""
 
 from copy import deepcopy
-from typing import Union, cast
+from typing import cast
 
 from metldata.custom_types import Json
 from metldata.model_utils.anchors import AnchorPoint, lookup_anchor_point
@@ -278,9 +278,7 @@ def upsert_resources_in_metadata(
     return {**global_metadata_copy, anchor_point.root_slot: resources}
 
 
-def lookup_slot_in_resource(
-    *, resource: Json, slot_name: str
-) -> Union[Json, list[Json]]:
+def lookup_slot_in_resource(*, resource: Json, slot_name: str) -> Json | list[Json]:
     """Lookup a slot in a resource. Raises an error if the slot does not exist."""
     content = resource.get(slot_name)
 
diff --git a/src/metldata/model_utils/__init__.py b/src/metldata/model_utils/__init__.py
index 2c7c8478..cd62492a 100644
--- a/src/metldata/model_utils/__init__.py
+++ b/src/metldata/model_utils/__init__.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
diff --git a/src/metldata/model_utils/anchors.py b/src/metldata/model_utils/anchors.py
index d9c27671..15fc7bcf 100644
--- a/src/metldata/model_utils/anchors.py
+++ b/src/metldata/model_utils/anchors.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
diff --git a/src/metldata/model_utils/assumptions.py b/src/metldata/model_utils/assumptions.py
index a3d4bcd6..5b96a7e4 100644
--- a/src/metldata/model_utils/assumptions.py
+++ b/src/metldata/model_utils/assumptions.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -16,8 +16,6 @@
 
 """Logic to check basic assumptions about the metadata model."""
 
-from typing import Optional
-
 from metldata.model_utils.anchors import (
     AnchorPointNotFoundError,
     InvalidAnchorPointError,
@@ -92,9 +90,7 @@ def check_root_class_existence(model: MetadataModel) -> None:
         )
 
 
-def check_anchor_points(
-    model: MetadataModel, classes: Optional[list[str]] = None
-) -> None:
+def check_anchor_points(model: MetadataModel, classes: list[str] | None = None) -> None:
     """Checks the anchor points of the root class. If classes is specified, also checks
     that anchor points for the classes exist.
 
diff --git a/src/metldata/model_utils/config.py b/src/metldata/model_utils/config.py
index 19f72620..ee51a168 100644
--- a/src/metldata/model_utils/config.py
+++ b/src/metldata/model_utils/config.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
diff --git a/src/metldata/model_utils/essentials.py b/src/metldata/model_utils/essentials.py
index cfe9d489..9a054a0e 100644
--- a/src/metldata/model_utils/essentials.py
+++ b/src/metldata/model_utils/essentials.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -73,7 +73,6 @@ def __eq__(self, other: object):
 
         return self.as_dict() == other.as_dict()
 
-    # pylint: disable=too-many-nested-blocks,too-many-branches
     def as_dict(self, essential: bool = True):  # noqa: PLR0912, C901
         """Get a dictionary representation of the model. If essential set to True, the
         dictionary will be cleaned of all fields that are not essential.
diff --git a/src/metldata/model_utils/identifiers.py b/src/metldata/model_utils/identifiers.py
index 7946379a..37261ca6 100644
--- a/src/metldata/model_utils/identifiers.py
+++ b/src/metldata/model_utils/identifiers.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -16,12 +16,10 @@
 
 """Handling identifiers of classes in a metadata model."""
 
-from typing import Optional
-
 from metldata.model_utils.essentials import ROOT_CLASS, MetadataModel
 
 
-def get_class_identifier(model: MetadataModel, class_name: str) -> Optional[str]:
+def get_class_identifier(model: MetadataModel, class_name: str) -> str | None:
     """Get the identifier of a class in a metadata model.
 
     Returns:
@@ -37,7 +35,7 @@ def get_class_identifier(model: MetadataModel, class_name: str) -> Optional[str]
     return None
 
 
-def get_class_identifiers(model: MetadataModel) -> dict[str, Optional[str]]:
+def get_class_identifiers(model: MetadataModel) -> dict[str, str | None]:
     """Get the identifiers of all classes in a metadata model.
 
     Returns:
@@ -46,7 +44,7 @@ class does not have an identifier, the value is None.
     """
     schema_view = model.schema_view
 
-    identifiers_by_class: dict[str, Optional[str]] = {}
+    identifiers_by_class: dict[str, str | None] = {}
     for class_name in schema_view.all_classes():
         if class_name == ROOT_CLASS:
             continue  # Root class does not have an identifier
diff --git a/src/metldata/model_utils/manipulate.py b/src/metldata/model_utils/manipulate.py
index 8f7d3015..5261e614 100644
--- a/src/metldata/model_utils/manipulate.py
+++ b/src/metldata/model_utils/manipulate.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -19,7 +19,6 @@
 """
 
 from copy import deepcopy
-from typing import Optional, Union
 
 import jsonasobj2
 from linkml_runtime.linkml_model.meta import ClassDefinition, SlotDefinition
@@ -50,7 +49,7 @@ def __init__(
         class_name: str,
         slot_name: str,
         direct: bool = False,
-        context: Optional[str] = None,
+        context: str | None = None,
     ):
         message = (
             f"The slot '{slot_name}' does not exist"
@@ -181,7 +180,7 @@ def add_slot_usage_annotation(
     slot_name: str,
     class_name: str,
     annotation_key: str,
-    annotation_value: Union[str, bool, int, float],
+    annotation_value: str | bool | int | float,
 ) -> ExportableSchemaView:
     """Add annotations to a slot in the context of a class.
     For more details see:
@@ -250,7 +249,7 @@ def add_anchor_point(
     *,
     schema_view: ExportableSchemaView,
     anchor_point: AnchorPoint,
-    description: Optional[str] = None,
+    description: str | None = None,
 ) -> ExportableSchemaView:
     """Add an anchor point for a class to the tree root of the model."""
     class_ = schema_view.get_class(class_name=anchor_point.target_class)
diff --git a/src/metldata/model_utils/metadata_validator.py b/src/metldata/model_utils/metadata_validator.py
index 40b861f4..25df266d 100644
--- a/src/metldata/model_utils/metadata_validator.py
+++ b/src/metldata/model_utils/metadata_validator.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
diff --git a/src/metldata/submission_registry/__init__.py b/src/metldata/submission_registry/__init__.py
index 7b1978bb..958c9cc5 100644
--- a/src/metldata/submission_registry/__init__.py
+++ b/src/metldata/submission_registry/__init__.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
diff --git a/src/metldata/submission_registry/config.py b/src/metldata/submission_registry/config.py
index 0d887295..a3642e38 100644
--- a/src/metldata/submission_registry/config.py
+++ b/src/metldata/submission_registry/config.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -20,7 +20,6 @@
 from metldata.submission_registry.submission_store import SubmissionStoreConfig
 
 
-# pylint: disable=too-many-ancestors
 class Config(
     SubmissionStoreConfig,
     SubmissionRegistryConfig,
diff --git a/src/metldata/submission_registry/event_publisher.py b/src/metldata/submission_registry/event_publisher.py
index e3554b5e..966d2254 100644
--- a/src/metldata/submission_registry/event_publisher.py
+++ b/src/metldata/submission_registry/event_publisher.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
diff --git a/src/metldata/submission_registry/identifiers.py b/src/metldata/submission_registry/identifiers.py
index 347f39f9..2b78a279 100644
--- a/src/metldata/submission_registry/identifiers.py
+++ b/src/metldata/submission_registry/identifiers.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -18,7 +18,6 @@
 
 from collections.abc import Iterable
 from functools import partial
-from typing import Optional
 from uuid import uuid4
 
 from pydantic import Json
@@ -45,7 +44,7 @@ def lookup_accession(
     anchor: str,
     alias: str,
     accession_map: AccessionMap,
-) -> Optional[str]:
+) -> str | None:
     """Lookup the accession for a resource with the provided user-defined alias of
     the class with the provided anchor. If no accession exists, None is returned.
     """
@@ -103,7 +102,7 @@ def get_aliases_for_resources(
 def generate_accession_map(
     *,
     content: SubmissionContent,
-    existing_accession_map: Optional[AccessionMap] = None,
+    existing_accession_map: AccessionMap | None = None,
     accession_registry: AccessionRegistry,
     anchor_points_by_target: dict[str, AnchorPoint],
 ) -> AccessionMap:
diff --git a/src/metldata/submission_registry/models.py b/src/metldata/submission_registry/models.py
index 491cc319..3c11f04f 100644
--- a/src/metldata/submission_registry/models.py
+++ b/src/metldata/submission_registry/models.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -18,11 +18,10 @@
 
 from enum import Enum
 from operator import attrgetter
-from typing import Optional
+from typing import TypeAlias
 
 from ghga_service_commons.utils.utc_dates import UTCDatetime, now_as_utc
 from pydantic import BaseModel, Field, field_validator
-from typing_extensions import TypeAlias
 
 from metldata.custom_types import SubmissionContent
 
@@ -55,7 +54,7 @@ class SubmissionHeader(BaseModel):
     """Basic information provided for a submission."""
 
     title: str = Field(..., description="A descriptive title for this submission.")
-    description: Optional[str] = Field(None, description="An optional description.")
+    description: str | None = Field(None, description="An optional description.")
 
 
 class Submission(SubmissionHeader):
@@ -63,7 +62,7 @@ class Submission(SubmissionHeader):
 
     id: str
 
-    content: Optional[SubmissionContent] = Field(
+    content: SubmissionContent | None = Field(
         None,
         description=(
             "The metadata content of the submission. Keys on the top level correspond to"
diff --git a/src/metldata/submission_registry/submission_registry.py b/src/metldata/submission_registry/submission_registry.py
index dd97eef5..e2f660ba 100644
--- a/src/metldata/submission_registry/submission_registry.py
+++ b/src/metldata/submission_registry/submission_registry.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
diff --git a/src/metldata/submission_registry/submission_store.py b/src/metldata/submission_registry/submission_store.py
index f23a838a..3f7cb183 100644
--- a/src/metldata/submission_registry/submission_store.py
+++ b/src/metldata/submission_registry/submission_store.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
diff --git a/src/metldata/transform/__init__.py b/src/metldata/transform/__init__.py
index 6b39eff7..80fa438f 100644
--- a/src/metldata/transform/__init__.py
+++ b/src/metldata/transform/__init__.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
diff --git a/src/metldata/transform/artifact_publisher.py b/src/metldata/transform/artifact_publisher.py
index 23abc115..2db4b1e0 100644
--- a/src/metldata/transform/artifact_publisher.py
+++ b/src/metldata/transform/artifact_publisher.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
diff --git a/src/metldata/transform/base.py b/src/metldata/transform/base.py
index 0acc9f20..31c6e70e 100644
--- a/src/metldata/transform/base.py
+++ b/src/metldata/transform/base.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -18,9 +18,10 @@
 
 from abc import ABC, abstractmethod
 from collections import defaultdict
+from collections.abc import Callable
 from dataclasses import dataclass
 from graphlib import CycleError, TopologicalSorter
-from typing import Callable, Generic, Optional, TypeVar
+from typing import Generic, TypeVar
 
 from pydantic import (
     BaseModel,
@@ -35,7 +36,6 @@
 from metldata.event_handling.models import SubmissionAnnotation
 
 # shortcuts:
-# pylint: disable=unused-import
 from metldata.model_utils.assumptions import MetadataModelAssumptionError  # noqa: F401
 from metldata.model_utils.essentials import MetadataModel
 
@@ -122,7 +122,7 @@ class WorkflowStepBase(BaseModel, ABC):
 
     model_config = ConfigDict(frozen=True)
     description: str = Field(..., description="A description of the step.")
-    input: Optional[str] = Field(
+    input: str | None = Field(
         ...,
         description=(
             "The name of the workflow step from which the output is used as input"
@@ -161,7 +161,6 @@ class WorkflowDefinition(BaseModel):
         ),
     )
 
-    # pylint: disable=no-self-argument
     @field_validator("steps", mode="after")
     def validate_step_references(
         cls,  # noqa: N805
diff --git a/src/metldata/transform/config.py b/src/metldata/transform/config.py
index 66002541..9fb94a25 100644
--- a/src/metldata/transform/config.py
+++ b/src/metldata/transform/config.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -21,7 +21,6 @@
 from metldata.transform.source_event_subscriber import SourceEventSubscriberConfig
 
 
-# pylint: disable=too-many-ancestors
 class TransformationEventHandlingConfig(
     FileSystemEventConfig, ArtifactEventPublisherConfig, SourceEventSubscriberConfig
 ):
diff --git a/src/metldata/transform/handling.py b/src/metldata/transform/handling.py
index cef518e1..5b97e93e 100644
--- a/src/metldata/transform/handling.py
+++ b/src/metldata/transform/handling.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
diff --git a/src/metldata/transform/main.py b/src/metldata/transform/main.py
index d9de2f6a..9806875a 100644
--- a/src/metldata/transform/main.py
+++ b/src/metldata/transform/main.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -16,8 +16,7 @@
 
 """Main logic for running a transformation workflow on submissions."""
 
-from collections.abc import Awaitable
-from typing import Callable
+from collections.abc import Awaitable, Callable
 
 from metldata.event_handling.event_handling import (
     FileSystemEventPublisher,
diff --git a/src/metldata/transform/source_event_subscriber.py b/src/metldata/transform/source_event_subscriber.py
index 8537e76a..d0c335be 100644
--- a/src/metldata/transform/source_event_subscriber.py
+++ b/src/metldata/transform/source_event_subscriber.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -16,8 +16,7 @@
 
 """Logic for subscribing to source events."""
 
-from collections.abc import Awaitable
-from typing import Callable
+from collections.abc import Awaitable, Callable
 
 from hexkit.custom_types import Ascii, JsonObject
 from hexkit.protocols.eventsub import EventSubscriberProtocol
@@ -44,9 +43,8 @@ def __init__(
         self.types_of_interest = [config.source_event_type]
         self._run_workflow_func = run_workflow_func
 
-    # pylint: disable=unused-argument
     async def _consume_validated(
-        self, *, payload: JsonObject, type_: Ascii, topic: Ascii
+        self, *, payload: JsonObject, type_: Ascii, topic: Ascii, key: Ascii
     ) -> None:
         """
         Receive and process an event with already validated topic and type.
@@ -56,5 +54,5 @@ async def _consume_validated(
             type_ (str): The type of the event.
             topic (str): Name of the topic the event was published to.
         """
-        submission_event_payload = SubmissionEventPayload(**payload)
+        submission_event_payload = SubmissionEventPayload(**payload)  # type: ignore
         await self._run_workflow_func(submission_event_payload)
diff --git a/tests/__init__.py b/tests/__init__.py
index 6f368976..a0473377 100644
--- a/tests/__init__.py
+++ b/tests/__init__.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
diff --git a/tests/accession_registry/__init__.py b/tests/accession_registry/__init__.py
index afc1fcb0..dfacd52e 100644
--- a/tests/accession_registry/__init__.py
+++ b/tests/accession_registry/__init__.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
diff --git a/tests/accession_registry/test_accession_registry.py b/tests/accession_registry/test_accession_registry.py
index 89dc851b..83662f6e 100644
--- a/tests/accession_registry/test_accession_registry.py
+++ b/tests/accession_registry/test_accession_registry.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
diff --git a/tests/accession_registry/test_accession_store.py b/tests/accession_registry/test_accession_store.py
index cfb2a359..d6563bad 100644
--- a/tests/accession_registry/test_accession_store.py
+++ b/tests/accession_registry/test_accession_store.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
diff --git a/tests/artifact_rest/__init__.py b/tests/artifact_rest/__init__.py
index f5c81d1e..3c7e4b9b 100644
--- a/tests/artifact_rest/__init__.py
+++ b/tests/artifact_rest/__init__.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
diff --git a/tests/artifact_rest/test_api_factory.py b/tests/artifact_rest/test_api_factory.py
index 4a171216..9695632c 100644
--- a/tests/artifact_rest/test_api_factory.py
+++ b/tests/artifact_rest/test_api_factory.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -22,6 +22,7 @@
 from ghga_service_commons.api.testing import AsyncTestClient
 from ghga_service_commons.utils.utc_dates import UTCDatetime, now_as_utc
 from hexkit.protocols.dao import DaoFactoryProtocol
+from hexkit.providers.mongodb.testutils import MongoDbFixture
 
 from metldata.artifacts_rest.api_factory import rest_api_factory
 from metldata.artifacts_rest.artifact_info import ArtifactInfo, get_artifact_info_dict
@@ -29,13 +30,10 @@
 from metldata.load.stats import create_stats_using_aggregator
 from tests.artifact_rest.test_load_artifacts import load_example_artifact_resources
 from tests.fixtures.artifact_info import EXAMPLE_ARTIFACT_INFOS, MINIMAL_ARTIFACT_INFO
-from tests.fixtures.mongodb import (  # noqa: F401; pylint: disable=unused-import
-    MongoDbFixture,
-    mongodb_fixture,
-)
+
+pytestmark = pytest.mark.asyncio()
 
 
-@pytest.mark.asyncio
 async def get_example_app_client(
     dao_factory: DaoFactoryProtocol,
     artifact_infos: list[ArtifactInfo] = EXAMPLE_ARTIFACT_INFOS,
@@ -50,30 +48,20 @@ async def get_example_app_client(
     return AsyncTestClient(app)
 
 
-@pytest.mark.asyncio
-async def test_health_check(
-    mongodb_fixture: MongoDbFixture,  # noqa: F811
-):
+async def test_health_check(mongodb: MongoDbFixture):
     """Test that the health check endpoint works."""
-    async with await get_example_app_client(
-        dao_factory=mongodb_fixture.dao_factory
-    ) as client:
+    async with await get_example_app_client(dao_factory=mongodb.dao_factory) as client:
         response = await client.get("/health")
 
     assert response.status_code == 200
     assert response.json() == {"status": "OK"}
 
 
-@pytest.mark.asyncio
-async def test_artifacts_info_endpoint(
-    mongodb_fixture: MongoDbFixture,  # noqa: F811
-):
+async def test_artifacts_info_endpoint(mongodb: MongoDbFixture):
     """Test happy path of using the artifacts info endpoint."""
     expected_infos = EXAMPLE_ARTIFACT_INFOS
 
-    async with await get_example_app_client(
-        dao_factory=mongodb_fixture.dao_factory
-    ) as client:
+    async with await get_example_app_client(dao_factory=mongodb.dao_factory) as client:
         response = await client.options("/artifacts")
 
     response_json = response.json()
@@ -82,7 +70,6 @@ async def test_artifacts_info_endpoint(
     assert observed_infos == expected_infos
 
 
-@pytest.mark.asyncio
 @pytest.mark.parametrize(
     "artifact_name, expected_info",
     [(info.name, info) for info in EXAMPLE_ARTIFACT_INFOS],
@@ -90,32 +77,27 @@ async def test_artifacts_info_endpoint(
 async def test_artifact_info_endpoint(
     artifact_name: str,
     expected_info: ArtifactInfo,
-    mongodb_fixture: MongoDbFixture,  # noqa: F811
+    mongodb: MongoDbFixture,
 ):
     """Test happy path of using the artifact info endpoint."""
-    async with await get_example_app_client(
-        dao_factory=mongodb_fixture.dao_factory
-    ) as client:
+    async with await get_example_app_client(dao_factory=mongodb.dao_factory) as client:
         response = await client.options(f"/artifacts/{artifact_name}")
 
     observed_info = ArtifactInfo(**response.json())
     assert observed_info == expected_info
 
 
-@pytest.mark.asyncio
-async def test_get_artifact_resource_endpoint(
-    mongodb_fixture: MongoDbFixture,  # noqa: F811
-):
+async def test_get_artifact_resource_endpoint(mongodb: MongoDbFixture):
     """Test happy path of using the get artifact resource endpoint."""
     # load example resources and prepare client:
-    await load_example_artifact_resources(dao_factory=mongodb_fixture.dao_factory)
+    await load_example_artifact_resources(dao_factory=mongodb.dao_factory)
 
     # Get an example resource:
     artifact_name = MINIMAL_ARTIFACT_INFO.name
     class_name = "File"
     resource_id = "test_sample_01_R1"
     async with await get_example_app_client(
-        dao_factory=mongodb_fixture.dao_factory,
+        dao_factory=mongodb.dao_factory,
         artifact_infos=[MINIMAL_ARTIFACT_INFO],
     ) as client:
         response = await client.get(
@@ -133,25 +115,22 @@ async def test_get_artifact_resource_endpoint(
     assert observed_resource["alias"] == resource_id
 
 
-@pytest.mark.asyncio
-async def test_get_stats_endpoint(
-    mongodb_fixture: MongoDbFixture,  # noqa: F811
-):
+async def test_get_stats_endpoint(mongodb: MongoDbFixture):
     """Test happy path of using the get stats endpoint."""
     # load example resources and prepare client:
-    await load_example_artifact_resources(dao_factory=mongodb_fixture.dao_factory)
+    await load_example_artifact_resources(dao_factory=mongodb.dao_factory)
 
     artifact_infos = [MINIMAL_ARTIFACT_INFO]
 
     await create_stats_using_aggregator(
         artifact_infos=get_artifact_info_dict(artifact_infos=artifact_infos),
         primary_artifact_name=artifact_infos[-1].name,
-        db_aggregator=MongoDbAggregator(config=mongodb_fixture.config),
+        db_aggregator=MongoDbAggregator(config=mongodb.config),
     )
 
     # Get the global summary statistics:
     async with await get_example_app_client(
-        dao_factory=mongodb_fixture.dao_factory,
+        dao_factory=mongodb.dao_factory,
         artifact_infos=artifact_infos,
     ) as client:
         response = await client.get("/stats")
diff --git a/tests/artifact_rest/test_artifact_info.py b/tests/artifact_rest/test_artifact_info.py
index a3810493..92411017 100644
--- a/tests/artifact_rest/test_artifact_info.py
+++ b/tests/artifact_rest/test_artifact_info.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
diff --git a/tests/artifact_rest/test_load_artifacts.py b/tests/artifact_rest/test_load_artifacts.py
index 86c82379..eda0faef 100644
--- a/tests/artifact_rest/test_load_artifacts.py
+++ b/tests/artifact_rest/test_load_artifacts.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -18,16 +18,15 @@
 
 import pytest
 from hexkit.protocols.dao import DaoFactoryProtocol
+from hexkit.providers.mongodb.testutils import MongoDbFixture
 
 from metldata.artifacts_rest.artifact_dao import ArtifactDaoCollection
 from metldata.artifacts_rest.load_resources import load_artifact_resources
 from metldata.artifacts_rest.models import ArtifactResource
 from tests.fixtures.artifact_info import MINIMAL_ARTIFACT_INFO
 from tests.fixtures.metadata import VALID_MINIMAL_METADATA_EXAMPLE
-from tests.fixtures.mongodb import (  # noqa: F401; pylint: disable=unused-import
-    MongoDbFixture,
-    mongodb_fixture,
-)
+
+pytestmark = pytest.mark.asyncio()
 
 
 async def load_example_artifact_resources(
@@ -52,13 +51,10 @@ async def load_example_artifact_resources(
     return dao_collection
 
 
-@pytest.mark.asyncio
-async def test_load_artifact_resources(
-    mongodb_fixture: MongoDbFixture,  # noqa: F811
-):
+async def test_load_artifact_resources(mongodb: MongoDbFixture):
     """Test happy path of using load_artifact_resources function."""
     dao_collection = await load_example_artifact_resources(
-        dao_factory=mongodb_fixture.dao_factory,
+        dao_factory=mongodb.dao_factory,
     )
 
     # check that artifact resources have been persisted to the database by testing for
diff --git a/tests/artifact_rest/test_query_resources.py b/tests/artifact_rest/test_query_resources.py
index d2fdec64..654952fa 100644
--- a/tests/artifact_rest/test_query_resources.py
+++ b/tests/artifact_rest/test_query_resources.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -17,24 +17,20 @@
 """Test the query_resource module."""
 
 import pytest
+from hexkit.providers.mongodb.testutils import MongoDbFixture
 
 from metldata.artifacts_rest.query_resources import query_artifact_resource
 from tests.artifact_rest.test_load_artifacts import load_example_artifact_resources
 from tests.fixtures.artifact_info import MINIMAL_ARTIFACT_INFO
-from tests.fixtures.mongodb import (  # noqa: F401; pylint: disable=unused-import
-    MongoDbFixture,
-    mongodb_fixture,
-)
 
+pytestmark = pytest.mark.asyncio()
 
-@pytest.mark.asyncio
-async def test_query_artifact_resource(
-    mongodb_fixture: MongoDbFixture,  # noqa: F811
-):
+
+async def test_query_artifact_resource(mongodb: MongoDbFixture):
     """Test happy path of using the query_artifact_resource function."""
     # load example resources and prepare client:
     dao_collection = await load_example_artifact_resources(
-        dao_factory=mongodb_fixture.dao_factory
+        dao_factory=mongodb.dao_factory
     )
 
     # Get an example resource:
diff --git a/tests/builtin_tranformations/__init__.py b/tests/builtin_tranformations/__init__.py
index e01cef3b..8a072fe4 100644
--- a/tests/builtin_tranformations/__init__.py
+++ b/tests/builtin_tranformations/__init__.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
diff --git a/tests/builtin_tranformations/aggregate/conftest.py b/tests/builtin_tranformations/aggregate/conftest.py
index b9c38ea6..e183dc0a 100644
--- a/tests/builtin_tranformations/aggregate/conftest.py
+++ b/tests/builtin_tranformations/aggregate/conftest.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
diff --git a/tests/builtin_tranformations/aggregate/test_data_subgraph.py b/tests/builtin_tranformations/aggregate/test_data_subgraph.py
index 6de58744..5b2fa442 100644
--- a/tests/builtin_tranformations/aggregate/test_data_subgraph.py
+++ b/tests/builtin_tranformations/aggregate/test_data_subgraph.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
diff --git a/tests/builtin_tranformations/aggregate/test_model_generator.py b/tests/builtin_tranformations/aggregate/test_model_generator.py
index e2758808..ade898f7 100644
--- a/tests/builtin_tranformations/aggregate/test_model_generator.py
+++ b/tests/builtin_tranformations/aggregate/test_model_generator.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -14,7 +14,6 @@
 # limitations under the License.
 #
 
-# pylint: disable=redefined-outer-name
 
 """Test the model generation"""
 
diff --git a/tests/builtin_tranformations/infer_references/__init__.py b/tests/builtin_tranformations/infer_references/__init__.py
index aafb25d1..cc888dd7 100644
--- a/tests/builtin_tranformations/infer_references/__init__.py
+++ b/tests/builtin_tranformations/infer_references/__init__.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
diff --git a/tests/builtin_tranformations/infer_references/path/__init__.py b/tests/builtin_tranformations/infer_references/path/__init__.py
index 762a33f4..65aed342 100644
--- a/tests/builtin_tranformations/infer_references/path/__init__.py
+++ b/tests/builtin_tranformations/infer_references/path/__init__.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
diff --git a/tests/builtin_tranformations/infer_references/path/test_config.py b/tests/builtin_tranformations/infer_references/path/test_config.py
index 9f01daf6..24ab9e69 100644
--- a/tests/builtin_tranformations/infer_references/path/test_config.py
+++ b/tests/builtin_tranformations/infer_references/path/test_config.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
diff --git a/tests/builtin_tranformations/infer_references/path/test_path.py b/tests/builtin_tranformations/infer_references/path/test_path.py
index 70d61510..b690c6cb 100644
--- a/tests/builtin_tranformations/infer_references/path/test_path.py
+++ b/tests/builtin_tranformations/infer_references/path/test_path.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
diff --git a/tests/builtin_tranformations/infer_references/path/test_path_str.py b/tests/builtin_tranformations/infer_references/path/test_path_str.py
index 857c9618..f461c166 100644
--- a/tests/builtin_tranformations/infer_references/path/test_path_str.py
+++ b/tests/builtin_tranformations/infer_references/path/test_path_str.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -17,7 +17,6 @@
 """Test reference utils."""
 
 from contextlib import nullcontext
-from typing import Optional
 
 import pytest
 
@@ -132,7 +131,7 @@ def test_get_target_class(path_str: str, expected_target_class: str):
     ],
 )
 def test_split_first_element(
-    path_str: str, expected_first_element: str, expected_remaining_path: Optional[str]
+    path_str: str, expected_first_element: str, expected_remaining_path: str | None
 ):
     """Test the split_first_element method."""
     observed_first_element, observed_remaining_path = split_first_element(
diff --git a/tests/builtin_tranformations/merge_slots/__init__.py b/tests/builtin_tranformations/merge_slots/__init__.py
index 43d68b6a..da5a8996 100644
--- a/tests/builtin_tranformations/merge_slots/__init__.py
+++ b/tests/builtin_tranformations/merge_slots/__init__.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
diff --git a/tests/builtin_tranformations/merge_slots/test_config.py b/tests/builtin_tranformations/merge_slots/test_config.py
index 78bf88bd..9e208607 100644
--- a/tests/builtin_tranformations/merge_slots/test_config.py
+++ b/tests/builtin_tranformations/merge_slots/test_config.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
diff --git a/tests/builtin_tranformations/merge_slots/test_models.py b/tests/builtin_tranformations/merge_slots/test_models.py
index 2115b914..0d87d61a 100644
--- a/tests/builtin_tranformations/merge_slots/test_models.py
+++ b/tests/builtin_tranformations/merge_slots/test_models.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
diff --git a/tests/builtin_tranformations/test_happy.py b/tests/builtin_tranformations/test_happy.py
index fd61dd0a..8150f509 100644
--- a/tests/builtin_tranformations/test_happy.py
+++ b/tests/builtin_tranformations/test_happy.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
diff --git a/tests/builtin_workflows/__init__.py b/tests/builtin_workflows/__init__.py
index e5b236ca..18bc0622 100644
--- a/tests/builtin_workflows/__init__.py
+++ b/tests/builtin_workflows/__init__.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
diff --git a/tests/builtin_workflows/test_happy.py b/tests/builtin_workflows/test_happy.py
index fd544e58..2e35d6ac 100644
--- a/tests/builtin_workflows/test_happy.py
+++ b/tests/builtin_workflows/test_happy.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
diff --git a/tests/conftest.py b/tests/conftest.py
index 435e0090..3a65bd27 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -16,21 +16,15 @@
 
 """Shared fixtures"""
 
-import asyncio
-
-import pytest
-from hexkit.providers.mongodb.testutils import get_mongodb_fixture
-
-
-def event_loop_fixture():
-    """Event loop fixture for when an event loop is needed beyond function scope."""
-    loop = asyncio.get_event_loop_policy().new_event_loop()
-    asyncio.set_event_loop(loop)
-    yield loop
-    loop.close()
-    asyncio.set_event_loop(None)
-
-
-event_loop = pytest.fixture(fixture_function=event_loop_fixture, scope="session")
-
-mongodb_session = get_mongodb_fixture(scope="session")
+# The container fixtures persist across the whole session.
+# The kafka- and mongodb_fixtures reset the underlying container state for each test,
+# and they only have a function scope
+# The default fixture names for kafka_fixture and mongodb_fixture are kafka and mongodb
+from hexkit.providers.akafka.testutils import (  # noqa: F401
+    kafka_container_fixture,
+    kafka_fixture,
+)
+from hexkit.providers.mongodb.testutils import (  # noqa: F401
+    mongodb_container_fixture,
+    mongodb_fixture,
+)
diff --git a/tests/fixtures/__init__.py b/tests/fixtures/__init__.py
index b8a4adb5..955d32d5 100644
--- a/tests/fixtures/__init__.py
+++ b/tests/fixtures/__init__.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
diff --git a/tests/fixtures/artifact_info.py b/tests/fixtures/artifact_info.py
index a2f698ad..c7a32848 100644
--- a/tests/fixtures/artifact_info.py
+++ b/tests/fixtures/artifact_info.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
diff --git a/tests/fixtures/config.py b/tests/fixtures/config.py
index 736960ad..a3e58035 100644
--- a/tests/fixtures/config.py
+++ b/tests/fixtures/config.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
diff --git a/tests/fixtures/event_handling.py b/tests/fixtures/event_handling.py
index 01f28595..856081c4 100644
--- a/tests/fixtures/event_handling.py
+++ b/tests/fixtures/event_handling.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
diff --git a/tests/fixtures/load/__init__.py b/tests/fixtures/load/__init__.py
index 3f457cfc..c42268ec 100644
--- a/tests/fixtures/load/__init__.py
+++ b/tests/fixtures/load/__init__.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
diff --git a/tests/fixtures/load/config.py b/tests/fixtures/load/config.py
index d2ae80c4..1ea9f8cc 100644
--- a/tests/fixtures/load/config.py
+++ b/tests/fixtures/load/config.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -17,7 +17,6 @@
 """Config fixture for testing the loader"""
 
 from pathlib import Path
-from typing import Optional, Union
 
 import yaml
 from pydantic_settings import BaseSettings
@@ -29,7 +28,7 @@
 
 
 def get_config(
-    sources: Optional[list[Union[BaseSettings, dict]]] = None,
+    sources: list[BaseSettings | dict] | None = None,
     default_config_yaml: Path = TEST_CONFIG_YAML,
 ) -> ArtifactLoaderAPIConfig:
     """Merges parameters from the default TEST_CONFIG_YAML with params inferred
diff --git a/tests/fixtures/load/joint.py b/tests/fixtures/load/joint.py
index 593382fe..aee45fdd 100644
--- a/tests/fixtures/load/joint.py
+++ b/tests/fixtures/load/joint.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -22,6 +22,7 @@
 
 from ghga_service_commons.api.testing import AsyncTestClient
 from hexkit.providers.akafka.testutils import KafkaFixture
+from hexkit.providers.mongodb.testutils import MongoDbFixture
 from pytest_asyncio import fixture
 
 from metldata.artifacts_rest.artifact_info import ArtifactInfo, load_artifact_info
@@ -33,10 +34,6 @@
 from metldata.model_utils.essentials import MetadataModel
 from tests.fixtures.load.config import get_config
 from tests.fixtures.load.utils import BASE_DIR
-from tests.fixtures.mongodb import (  # noqa: F401; pylint: disable=unused-import
-    MongoDbFixture,
-    mongodb_fixture,
-)
 
 ARTIFACT_INFOS_PATH = BASE_DIR / "example_models" / "artifact_infos.json"
 ARTIFACT_NAME = "embedded_public"
@@ -63,10 +60,7 @@ class JointFixture:
 
 
 @fixture
-async def joint_fixture(
-    kafka_fixture: KafkaFixture,
-    mongodb_fixture: MongoDbFixture,  # noqa: F811
-) -> JointFixture:
+async def joint_fixture(kafka: KafkaFixture, mongodb: MongoDbFixture) -> JointFixture:
     """Get a tuple of a configured test client together with a corresponding token."""
     artifact_infos = [
         load_artifact_info(
@@ -90,8 +84,8 @@ async def joint_fixture(
                 "artifact_infos": artifact_infos,
                 "loader_token_hashes": [token_hash],
             },
-            kafka_fixture.config,
-            mongodb_fixture.config,
+            kafka.config,
+            mongodb.config,
         ]
     )
 
@@ -109,7 +103,7 @@ async def joint_fixture(
         config=config,
         expected_file_resource_content=expected_file_resource_content,
         expected_embedded_dataset_resource_content=expected_embedded_dataset_resource_content,
-        kafka=kafka_fixture,
-        mongodb=mongodb_fixture,
+        kafka=kafka,
+        mongodb=mongodb,
         token=token,
     )
diff --git a/tests/fixtures/load/utils.py b/tests/fixtures/load/utils.py
index 3e648ff4..85997a97 100644
--- a/tests/fixtures/load/utils.py
+++ b/tests/fixtures/load/utils.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
diff --git a/tests/fixtures/metadata.py b/tests/fixtures/metadata.py
index 37d08659..ed478311 100644
--- a/tests/fixtures/metadata.py
+++ b/tests/fixtures/metadata.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
diff --git a/tests/fixtures/metadata_models.py b/tests/fixtures/metadata_models.py
index 3228c1ee..2b1295e0 100644
--- a/tests/fixtures/metadata_models.py
+++ b/tests/fixtures/metadata_models.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
diff --git a/tests/fixtures/mongodb.py b/tests/fixtures/mongodb.py
deleted file mode 100644
index 8f3221f8..00000000
--- a/tests/fixtures/mongodb.py
+++ /dev/null
@@ -1,29 +0,0 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
-# for the German Human Genome-Phenome Archive (GHGA)
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-#     http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-#
-
-"""Fixture for using the MongoDB."""
-
-from hexkit.providers.mongodb.testutils import MongoDbFixture
-from pytest import fixture
-
-
-@fixture
-def mongodb_fixture(  # pylint: disable=redefined-outer-name
-    mongodb_session: MongoDbFixture,
-) -> MongoDbFixture:
-    """Fixture that gets an empty MongoDB."""
-    mongodb_session.empty_collections()
-    return mongodb_session
diff --git a/tests/fixtures/transformations.py b/tests/fixtures/transformations.py
index 94111e81..6152b31e 100644
--- a/tests/fixtures/transformations.py
+++ b/tests/fixtures/transformations.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
diff --git a/tests/fixtures/utils.py b/tests/fixtures/utils.py
index f0f7c24c..fb1cbc0d 100644
--- a/tests/fixtures/utils.py
+++ b/tests/fixtures/utils.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
diff --git a/tests/fixtures/workflows.py b/tests/fixtures/workflows.py
index 2366b5f4..f8ededfe 100644
--- a/tests/fixtures/workflows.py
+++ b/tests/fixtures/workflows.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
diff --git a/tests/load/__init__.py b/tests/load/__init__.py
index 8d0aed92..443a1dcf 100644
--- a/tests/load/__init__.py
+++ b/tests/load/__init__.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
diff --git a/tests/load/test_client.py b/tests/load/test_client.py
index 65c97d91..48fb16a2 100644
--- a/tests/load/test_client.py
+++ b/tests/load/test_client.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
diff --git a/tests/load/test_main.py b/tests/load/test_main.py
index aa80060e..f5d3fd7f 100644
--- a/tests/load/test_main.py
+++ b/tests/load/test_main.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -22,10 +22,6 @@
 import pytest
 from ghga_service_commons.utils.utc_dates import now_as_utc
 from hexkit.protocols.dao import ResourceNotFoundError
-from hexkit.providers.akafka.testutils import (  # noqa: F401; pylint: disable=unused-import
-    KafkaFixture,
-    kafka_fixture,
-)
 
 from metldata.artifacts_rest.artifact_dao import ArtifactDaoCollection
 from metldata.artifacts_rest.load_resources import (
@@ -35,22 +31,17 @@
 from metldata.artifacts_rest.models import ArtifactResource, GlobalStats
 from metldata.load.auth import generate_token
 from metldata.load.stats import STATS_COLLECTION_NAME
-from tests.fixtures.load.joint import (  # noqa: F401; pylint: disable=unused-import
+from tests.fixtures.load.joint import (
     EMBEDDED_DATASET_TEST_PATH,
     JointFixture,
-    joint_fixture,
-)
-from tests.fixtures.mongodb import (  # noqa: F401; pylint: disable=unused-import
-    MongoDbFixture,
-    mongodb_fixture,
+    joint_fixture,  # noqa: F401
 )
 from tests.fixtures.workflows import EXAMPLE_ARTIFACTS
 
+pytestmark = pytest.mark.asyncio()
 
-@pytest.mark.asyncio
-async def test_load_artifacts_endpoint_happy(
-    joint_fixture: JointFixture,  # noqa: F811
-):
+
+async def test_load_artifacts_endpoint_happy(joint_fixture: JointFixture):  # noqa: F811
     """Test the happy path of using the load artifacts endpoint."""
     async with joint_fixture.kafka.record_events(
         in_topic=joint_fixture.config.dataset_change_event_topic
@@ -211,7 +202,6 @@ async def test_load_artifacts_endpoint_happy(
         await dao.get_by_id(changed_accession)
 
 
-@pytest.mark.asyncio
 async def test_load_artifacts_endpoint_invalid_resources(
     joint_fixture: JointFixture,  # noqa: F811
 ):
@@ -228,7 +218,6 @@ async def test_load_artifacts_endpoint_invalid_resources(
     assert response.status_code == 422
 
 
-@pytest.mark.asyncio
 async def test_load_artifacts_endpoint_invalid_token(
     joint_fixture: JointFixture,  # noqa: F811
 ):
@@ -244,10 +233,7 @@ async def test_load_artifacts_endpoint_invalid_token(
     assert response.status_code == 401
 
 
-@pytest.mark.asyncio
-async def test_file_slot_transformation(
-    joint_fixture: JointFixture,  # noqa: F811
-):
+async def test_file_slot_transformation(joint_fixture: JointFixture):  # noqa: F811
     """Test that file slots are discovered and file extensions are extracted correctly"""
     with open(EMBEDDED_DATASET_TEST_PATH, encoding="utf-8") as file:
         embedded_datasets = json.load(file)
diff --git a/tests/model_utils/__init__.py b/tests/model_utils/__init__.py
index 20826764..e6b80c17 100644
--- a/tests/model_utils/__init__.py
+++ b/tests/model_utils/__init__.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
diff --git a/tests/model_utils/test_anchor.py b/tests/model_utils/test_anchor.py
index 8f4795b1..bed0d7c9 100644
--- a/tests/model_utils/test_anchor.py
+++ b/tests/model_utils/test_anchor.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
diff --git a/tests/model_utils/test_assumptions.py b/tests/model_utils/test_assumptions.py
index d05e555c..cd2310cd 100644
--- a/tests/model_utils/test_assumptions.py
+++ b/tests/model_utils/test_assumptions.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
diff --git a/tests/model_utils/test_config.py b/tests/model_utils/test_config.py
index 583cb922..5c5cc743 100644
--- a/tests/model_utils/test_config.py
+++ b/tests/model_utils/test_config.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
diff --git a/tests/model_utils/test_essentials.py b/tests/model_utils/test_essentials.py
index 0453aef0..351aafc8 100644
--- a/tests/model_utils/test_essentials.py
+++ b/tests/model_utils/test_essentials.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
diff --git a/tests/model_utils/test_identifiers.py b/tests/model_utils/test_identifiers.py
index 85cd3326..ae859212 100644
--- a/tests/model_utils/test_identifiers.py
+++ b/tests/model_utils/test_identifiers.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
diff --git a/tests/model_utils/test_manipulate.py b/tests/model_utils/test_manipulate.py
index 414556d6..5975b830 100644
--- a/tests/model_utils/test_manipulate.py
+++ b/tests/model_utils/test_manipulate.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
diff --git a/tests/model_utils/test_metadata_validator.py b/tests/model_utils/test_metadata_validator.py
index ccb94acb..1bb9b6fd 100644
--- a/tests/model_utils/test_metadata_validator.py
+++ b/tests/model_utils/test_metadata_validator.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
diff --git a/tests/submission_registry/__init__.py b/tests/submission_registry/__init__.py
index 327be0b7..5d5bfa00 100644
--- a/tests/submission_registry/__init__.py
+++ b/tests/submission_registry/__init__.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
diff --git a/tests/submission_registry/test_event_publisher.py b/tests/submission_registry/test_event_publisher.py
index 3d44726d..2fafe7f3 100644
--- a/tests/submission_registry/test_event_publisher.py
+++ b/tests/submission_registry/test_event_publisher.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
diff --git a/tests/submission_registry/test_identifiers.py b/tests/submission_registry/test_identifiers.py
index 199bb887..196fa440 100644
--- a/tests/submission_registry/test_identifiers.py
+++ b/tests/submission_registry/test_identifiers.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
diff --git a/tests/submission_registry/test_models.py b/tests/submission_registry/test_models.py
index 2cbad8f7..af730f69 100644
--- a/tests/submission_registry/test_models.py
+++ b/tests/submission_registry/test_models.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
diff --git a/tests/submission_registry/test_submission_registry.py b/tests/submission_registry/test_submission_registry.py
index 6ebc146a..bfd41c2c 100644
--- a/tests/submission_registry/test_submission_registry.py
+++ b/tests/submission_registry/test_submission_registry.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
diff --git a/tests/submission_registry/test_submission_store.py b/tests/submission_registry/test_submission_store.py
index 9ecee9d4..5c17d54d 100644
--- a/tests/submission_registry/test_submission_store.py
+++ b/tests/submission_registry/test_submission_store.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
diff --git a/tests/test_event_handling.py b/tests/test_event_handling.py
index fe7fbccc..c6afb04d 100644
--- a/tests/test_event_handling.py
+++ b/tests/test_event_handling.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -80,11 +80,11 @@ class MockSubscriberTranslator(EventSubscriberProtocol):
 
         def __init__(self):
             self.consumed_events: set[ConsumedEvent] = set()
-            self.topics_of_interest = {"topic1"}
-            self.types_of_interest = {"type1", "type2"}
+            self.topics_of_interest = {"topic1"}  # type: ignore
+            self.types_of_interest = {"type1", "type2"}  # type: ignore
 
         async def _consume_validated(
-            self, *, payload: JsonObject, type_: Ascii, topic: Ascii
+            self, *, payload: JsonObject, type_: Ascii, topic: Ascii, key: Ascii
         ) -> None:
             self.consumed_events.add(
                 ConsumedEvent(topic=topic, type_=type_, payload=json.dumps(payload))
diff --git a/tests/test_metadata_utils.py b/tests/test_metadata_utils.py
index 8f839539..cbb591dc 100644
--- a/tests/test_metadata_utils.py
+++ b/tests/test_metadata_utils.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
diff --git a/tests/transform/__init__.py b/tests/transform/__init__.py
index 46489375..33c14b9f 100644
--- a/tests/transform/__init__.py
+++ b/tests/transform/__init__.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
diff --git a/tests/transform/test_base.py b/tests/transform/test_base.py
index 669607cb..f110ef4d 100644
--- a/tests/transform/test_base.py
+++ b/tests/transform/test_base.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
diff --git a/tests/transform/test_handling.py b/tests/transform/test_handling.py
index c666a1a6..bebda0fa 100644
--- a/tests/transform/test_handling.py
+++ b/tests/transform/test_handling.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
diff --git a/tests/transform/test_main.py b/tests/transform/test_main.py
index 4ee9afbb..c8defe0d 100644
--- a/tests/transform/test_main.py
+++ b/tests/transform/test_main.py
@@ -1,4 +1,4 @@
-# Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+# Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
 # for the German Human Genome-Phenome Archive (GHGA)
 #
 # Licensed under the Apache License, Version 2.0 (the "License");