From 01eb95cf689ae66e6afedda57946110adaafeb84 Mon Sep 17 00:00:00 2001
From: sbilge <bilge.sueruen@uni-tuebingen.de>
Date: Wed, 11 Dec 2024 11:11:24 +0000
Subject: [PATCH] custom types added

---
 .../common/custom_types.py                    | 25 +++++++++++++++++++
 .../common/instruction.py                     |  2 +-
 .../count_content_values/data_transform.py    | 24 ++++++++++++------
 3 files changed, 43 insertions(+), 8 deletions(-)
 create mode 100644 src/metldata/builtin_transformations/common/custom_types.py

diff --git a/src/metldata/builtin_transformations/common/custom_types.py b/src/metldata/builtin_transformations/common/custom_types.py
new file mode 100644
index 0000000..2ce3b76
--- /dev/null
+++ b/src/metldata/builtin_transformations/common/custom_types.py
@@ -0,0 +1,25 @@
+# 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");
+# 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.
+
+
+"""A collection of custom types used for builtin transformations."""
+
+from typing import Any, TypeAlias
+
+ResourceId: TypeAlias = str
+MutableDatapack: TypeAlias = dict[str, Any]
+MutableResource: TypeAlias = dict[str, dict]
+MutableClassResources: TypeAlias = dict[ResourceId, MutableResource]
+MutableResourceContent: TypeAlias = dict[str, Any]
diff --git a/src/metldata/builtin_transformations/common/instruction.py b/src/metldata/builtin_transformations/common/instruction.py
index 05591cd..c53d1b0 100644
--- a/src/metldata/builtin_transformations/common/instruction.py
+++ b/src/metldata/builtin_transformations/common/instruction.py
@@ -17,7 +17,7 @@
 
 from typing import Protocol, TypeVar
 
-from metldata.builtin_transformations.common.contentschema import NewContentSchemaPath
+from metldata.builtin_transformations.common import NewContentSchemaPath
 
 
 class InstructionProtocol(Protocol):
diff --git a/src/metldata/builtin_transformations/count_content_values/data_transform.py b/src/metldata/builtin_transformations/count_content_values/data_transform.py
index d2fe549..0cc6353 100644
--- a/src/metldata/builtin_transformations/count_content_values/data_transform.py
+++ b/src/metldata/builtin_transformations/count_content_values/data_transform.py
@@ -16,7 +16,6 @@
 """Data transformation logic for count content values transformation."""
 
 from collections import Counter
-from typing import Any
 
 from schemapack._internals.spec.custom_types import ResourceId
 from schemapack._internals.spec.datapack import ResourceIdSet
@@ -25,6 +24,12 @@
 from metldata.builtin_transformations.add_content_properties.path import (
     resolve_data_object_path,
 )
+from metldata.builtin_transformations.common.custom_types import (
+    MutableClassResources,
+    MutableDatapack,
+    MutableResource,
+    MutableResourceContent,
+)
 from metldata.builtin_transformations.common.path.path_utils import (
     get_directly_referenced_class,
 )
@@ -37,7 +42,9 @@
 )
 
 
-def get_class_resources(*, data: dict, class_name: str) -> dict:
+def get_class_resources(
+    *, data: MutableDatapack, class_name: str
+) -> MutableClassResources:
     """Extract the resources of a given class from the dictionary."""
     resources = data.get("resources", {}).get(class_name)
     if not resources:
@@ -61,7 +68,10 @@ def count_content(
 
 
 def transform_class(
-    *, class_name: str, data: dict, instructions: list[CountContentValueInstruction]
+    *,
+    class_name: str,
+    data: MutableDatapack,
+    instructions: list[CountContentValueInstruction],
 ):
     """Apply the count content value transformations to the specified class."""
     # the target prefix refers to resources that will be modified by the transformation
@@ -88,8 +98,8 @@ def transform_class(
 
 def transform_resource(
     *,
-    referenced_resources: dict[str, Any],
-    target_resource: dict,
+    referenced_resources: MutableClassResources,
+    target_resource: MutableResource,
     relation_name: str,
     instruction: CountContentValueInstruction,
 ):
@@ -117,7 +127,7 @@ def transform_resource(
 def get_values_to_count(
     *,
     relation_target_ids: ResourceId | ResourceIdSet,
-    referenced_resources: dict[str, Any],
+    referenced_resources: MutableClassResources,
     content_path: str,
 ):
     """Get countable properties from all resources referred to by the relation."""
@@ -131,7 +141,7 @@ def get_values_to_count(
 
 
 def get_modification_target(
-    *, data: dict[str, Any], instruction: CountContentValueInstruction
+    *, data: MutableResourceContent, instruction: CountContentValueInstruction
 ):
     """Get the json object that is to be modified."""
     path = instruction.target_content.object_path