template files for count references transformation

src/metldata/builtin_transformations/infer_relations/path/path.py → src/metldata/builtin_transformations/common/path/path.py

@@ -18,7 +18,7 @@
 
 from pydantic import GetJsonSchemaHandler, ValidationInfo
 
-from metldata.builtin_transformations.infer_relations.path.path_str import (
+from metldata.builtin_transformations.common.path.path_str import (
     PATH_PATTERN,
     ValidationError,
     clean_path_str,

src/metldata/builtin_transformations/infer_relations/path/path_str.py → src/metldata/builtin_transformations/common/path/path_str.py

@@ -18,7 +18,7 @@
 
 import re
 
-from metldata.builtin_transformations.infer_relations.path.path_elements import (
+from metldata.builtin_transformations.common.path.path_elements import (
     RelationPathElement,
     RelationPathElementType,
 )

src/metldata/builtin_transformations/count_references/__init__.py

@@ -0,0 +1,20 @@
+# 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 transformation to count the references."""
+
+# shortcuts:
+from metldata.builtin_transformations.count_references.main import (  # noqa: F401
+    COUNT_REFERENCES_TRANSFORMATION,
+)

src/metldata/builtin_transformations/count_references/assumptions.py

@@ -0,0 +1,63 @@
+# 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.
+
+"Assumptions for count references transformation"
+
+from typing import Any
+
+from schemapack.spec.schemapack import SchemaPack
+
+from metldata.builtin_transformations.common.path.path import RelationPath
+from metldata.builtin_transformations.common.path.path_elements import (
+    RelationPathElementType,
+)
+from metldata.transform.base import ModelAssumptionError
+
+
+def assert_path_classes_and_relations_exist(model: SchemaPack, path: RelationPath):
+    """Make sure that all classes and relations defined in the provided path exist in
+    the provided model.
+
+    Raises:
+        ModelAssumptionError:
+            if the model does not fulfill the assumptions.
+    """
+    for path_element in path.elements:
+        if path_element.source not in model.classes:
+            raise ModelAssumptionError(
+                f"Class {path_element.source} not found in model."
+            )
+
+        if path_element.target not in model.classes:
+            raise ModelAssumptionError(
+                f"Class {path_element.target} not found in model."
+            )
+
+        if path_element.type_ == RelationPathElementType.ACTIVE:
+            if (
+                path_element.property
+                not in model.classes[path_element.source].relations
+            ):
+                raise ModelAssumptionError(
+                    f"Relation property {path_element.property} not found in class"
+                    f" {path_element.source}."
+                )
+
+            return
+
+
+def check_model_assumptions(schema: SchemaPack, instructions_by_class: Any) -> None:
+    """Check the model assumptions for the count references transformation."""
+    return None

src/metldata/builtin_transformations/count_references/config.py

@@ -0,0 +1,32 @@
+# 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.
+"""Models used to describe count content properties that shall be calculated and added."""
+
+from typing import Any
+
+from pydantic import Field
+from pydantic_settings import BaseSettings, SettingsConfigDict
+
+
+class CountReferencesConfig(BaseSettings):
+    """Config containing content properties to be deleted from models and data."""
+
+    model_config = SettingsConfigDict(extra="forbid")
+
+    count_references: Any = Field(
+        ...,
+        description=("description"),
+        examples=[],
+    )

src/metldata/builtin_transformations/count_references/data_transform.py

@@ -0,0 +1,37 @@
+# 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.
+
+"""Logic for transforming data."""
+
+from schemapack.spec.datapack import DataPack
+
+# from metldata.transform.base import EvitableTransformationError
+
+
+def count_references(*, data: DataPack) -> DataPack:
+    """Count
+
+    Args:
+        data:
+
+
+    Returns:
+        The data with
+    """
+    modified_data = data.model_copy(deep=True)
+
+    # TODO modifications
+
+    return modified_data

src/metldata/builtin_transformations/count_references/main.py

@@ -0,0 +1,77 @@
+# 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 transformation to count references."""
+
+from schemapack.spec.datapack import DataPack
+from schemapack.spec.schemapack import SchemaPack
+
+from metldata.builtin_transformations.count_references.assumptions import (
+    check_model_assumptions,
+)
+from metldata.builtin_transformations.count_references.config import (
+    CountReferencesConfig,
+)
+from metldata.builtin_transformations.count_references.data_transform import (
+    count_references,
+)
+from metldata.builtin_transformations.count_references.model_transform import (
+    add_count_references,
+)
+from metldata.transform.base import DataTransformer, TransformationDefinition
+
+
+class CountReferencesTransformer(DataTransformer[CountReferencesConfig]):
+    """A transformer that counts the references and adds them to content properties."""
+
+    def transform(self, data: DataPack) -> DataPack:
+        """Transforms data.
+
+        Args:
+            data: The data as DataPack to be transformed.
+        """
+        return count_references(data=data)
+
+
+def check_model_assumptions_wrapper(
+    model: SchemaPack, config: CountReferencesConfig
+) -> None:
+    """Check the assumptions of the model.
+
+    Raises:
+        ModelAssumptionError:
+            if the model does not fulfill the assumptions.
+    """
+    check_model_assumptions(schema=model, instructions_by_class=config.count_references)
+
+
+def transform_model(model: SchemaPack, config: CountReferencesConfig) -> SchemaPack:
+    """Transform the data model.
+
+    Raises:
+        DataModelTransformationError:
+            if the transformation fails.
+    """
+    return add_count_references(
+        model=model, instructions_by_class=config.count_references
+    )
+
+
+COUNT_REFERENCES_TRANSFORMATION = TransformationDefinition[CountReferencesConfig](
+    config_cls=CountReferencesConfig,
+    check_model_assumptions=check_model_assumptions_wrapper,
+    transform_model=transform_model,
+    data_transformer_factory=CountReferencesTransformer,
+)

src/metldata/builtin_transformations/count_references/model_transform.py

@@ -0,0 +1,38 @@
+# 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.
+"""Model transformation logic for the 'count references' transformation"""
+
+from schemapack.spec.schemapack import (
+    # ClassDefinition,
+    SchemaPack,
+)
+
+# from metldata.transform.base import EvitableTransformationError
+
+
+def add_count_references(
+    *, model: SchemaPack, instructions_by_class: dict[str, list[str]]
+) -> SchemaPack:
+    """Delete content properties from a model.
+
+    Args:
+        model:
+            The model based on SchemaPack to
+    Returns:
+        The model with the
+    """
+    # TODO model transform logic for count references
+
+    return model

src/metldata/builtin_transformations/infer_relations/assumptions.py

@@ -18,10 +18,10 @@
 
 from schemapack.spec.schemapack import SchemaPack
 
-from metldata.builtin_transformations.infer_relations.path.path import (
+from metldata.builtin_transformations.common.path.path import (
     RelationPath,
 )
-from metldata.builtin_transformations.infer_relations.path.path_elements import (
+from metldata.builtin_transformations.common.path.path_elements import (
     RelationPathElementType,
 )
 from metldata.builtin_transformations.infer_relations.relations import (

src/metldata/builtin_transformations/infer_relations/relations.py

@@ -18,7 +18,7 @@
 
 from pydantic import BaseModel, ConfigDict, Field, model_validator
 
-from metldata.builtin_transformations.infer_relations.path.path import (
+from metldata.builtin_transformations.common.path.path import (
     RelationPath,
 )
 

tests/fixtures/example_transformations/count_references/multiple/config.yaml

@@ -0,0 +1,31 @@
+# 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.
+
+count_references:
+- class_name: Dataset
+  target_content:
+    object_path: "file_summary"
+    property_name: "count"
+  source_relation_path: "Dataset(files)>File"
+- class_name: Sample
+  target_content:
+    object_path: "file_summary"
+    property_name: "count"
+  source_relation_path: "Sample(files)>File"
+- class_name: Experiment
+  target_content:
+    object_path: "sample_summary"
+    property_name: "count"
+  source_relation_path: "Experiment(samples)>Sample"