FrozenDict content schema handling (#36)

* FrozenDict content schema handling

* Template update

* Version increase

* Update src/schemapack/_internals/utils.py

Co-authored-by: Thomas Zajac <[email protected]>

---------

Co-authored-by: Thomas Zajac <[email protected]>

.devcontainer/Dockerfile

@@ -1,4 +1,4 @@
-FROM mcr.microsoft.com/devcontainers/python:1-3.12-bullseye
+FROM mcr.microsoft.com/devcontainers/python:1-3.12-bookworm
 
 ENV PYTHONUNBUFFERED 1
 
@@ -8,7 +8,7 @@ ARG USER_GID=$USER_UID
 RUN if [ "$USER_GID" != "1000" ] || [ "$USER_UID" != "1000" ]; then groupmod --gid $USER_GID vscode && usermod --uid $USER_UID --gid $USER_GID vscode; fi
 
 # [Option] Install Node.js
-ARG INSTALL_NODE="true"
+ARG INSTALL_NODE="false"
 ARG NODE_VERSION="lts/*"
 RUN if [ "${INSTALL_NODE}" = "true" ]; then su vscode -c "umask 0002 && . /usr/local/share/nvm/nvm.sh && nvm install ${NODE_VERSION} 2>&1"; fi
 

.pre-commit-config.yaml

@@ -48,12 +48,12 @@ repos:
       - id: debug-statements
       - id: debug-statements
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.4.4
+    rev: v0.8.2
     hooks:
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix]
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.10.0
+    rev: v1.13.0
     hooks:
       - id: mypy
         args: [--no-warn-unused-ignores]

.pyproject_generation/pyproject_custom.toml

@@ -1,7 +1,7 @@
 
 [project]
 name = "schemapack"
-version = "2.0.0-alpha.4"
+version = "2.0.0-alpha.5"
 description = "Make your JSON Schemas sociable and create linked data model."
 dependencies = [
     "pydantic >=2, <3",

.pyproject_generation/pyproject_template.toml

@@ -40,6 +40,7 @@ fixable = [
     "UP", # e.g. List -> list
     "I", # sort imports
     "D", # pydocstyle
+    "RUF022", # sort items in __all__
 ]
 ignore = [
     "E111", # indentation with invalid multiple (for formatter)
@@ -59,6 +60,7 @@ ignore = [
     "D206", # indent-with-spaces (for formatter)
     "D300", # triple-single-quotes (for formatter)
     "UP040", # type statement (not yet supported by mypy)
+    "PLC0206", # Extracting value from dictionary without calling `.items()`
 ]
 select = [
     "C90", # McCabe Complexity

.template/mandatory_files.txt

@@ -23,6 +23,7 @@ lock/requirements-dev.txt
 lock/requirements.txt
 
 Dockerfile
+Dockerfile.debian
 config_schema.json
 example_config.yaml
 LICENSE

.template/mandatory_files_ignore.txt

@@ -3,10 +3,6 @@
 
 .devcontainer/docker-compose.yml
 
-.github/workflows/cd.yaml
-.github/workflows/dev_cd.yaml
-.github/workflows/check_openapi_spec.yaml
-
 scripts/script_utils/fastapi_app_location.py
 
 Dockerfile

Dockerfile.debian

@@ -0,0 +1,48 @@
+# 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.
+
+## creating building container
+FROM python:3.12-slim-bookworm AS builder
+# update and install dependencies
+RUN apt update
+RUN apt upgrade -y
+RUN pip install build
+# copy code
+COPY . /service
+WORKDIR /service
+# build wheel
+RUN python -m build
+
+# creating running container
+FROM python:3.12-slim-bookworm
+# update and install dependencies
+RUN apt update
+RUN apt upgrade -y
+# copy and install requirements and wheel
+WORKDIR /service
+COPY --from=builder /service/lock/requirements.txt /service
+RUN pip install --no-deps -r requirements.txt
+RUN rm requirements.txt
+COPY --from=builder /service/dist/ /service
+RUN pip install --no-deps *.whl
+RUN rm *.whl
+# create new user and execute as that user
+RUN useradd --create-home appuser
+WORKDIR /home/appuser
+USER appuser
+# set environment
+ENV PYTHONUNBUFFERED=1
+# Please adapt to package name:
+ENTRYPOINT ["my-microservice"]

lock/requirements-dev-template.in

@@ -1,7 +1,7 @@
 # common requirements for development and testing of services
 
 pytest>=8.2
-pytest-asyncio>=0.23.6
+pytest-asyncio>=0.23.7
 pytest-cov>=5
 snakeviz>=2.2
 logot>=1.3
@@ -29,4 +29,4 @@ setuptools>=69.5
 # required since switch to pyproject.toml and pip-tools
 tomli_w>=1.0
 
-uv>=0.1.39
+uv>=0.2.13

pyproject.toml

@@ -21,7 +21,7 @@ classifiers = [
     "Intended Audience :: Developers",
 ]
 name = "schemapack"
-version = "2.0.0-alpha.4"
+version = "2.0.0-alpha.5"
 description = "Make your JSON Schemas sociable and create linked data model."
 dependencies = [
     "pydantic >=2, <3",
@@ -68,6 +68,7 @@ fixable = [
     "UP",
     "I",
     "D",
+    "RUF022",
 ]
 ignore = [
     "E111",
@@ -87,6 +88,7 @@ ignore = [
     "D206",
     "D300",
     "UP040",
+    "PLC0206",
 ]
 select = [
     "C90",

src/schemapack/__init__.py

@@ -28,18 +28,18 @@
 from ._internals.validation import SchemaPackValidator
 
 __all__ = [
+    "SchemaPackValidator",
+    "denormalize",
+    "dump_schemapack",
+    "dumps_datapack",
+    "dumps_schemapack",
     "export_mermaid",
-    "load_and_validate",
-    "load_datapack",
-    "load_schemapack",
     "isolate",
     "isolate_class",
     "isolate_resource",
-    "denormalize",
-    "SchemaPackValidator",
-    "dumps_datapack",
-    "dump_schemapack",
-    "dumps_schemapack",
+    "load_and_validate",
+    "load_datapack",
+    "load_schemapack",
 ]
 
 __version__ = version(__package__)

src/schemapack/_internals/isolate.py

@@ -33,7 +33,7 @@
 from schemapack.spec.schemapack import SchemaPack
 
 
-def identify_resource_dependencies(  # noqa: C901, PLR0912
+def identify_resource_dependencies(  # noqa: C901
     *,
     datapack: DataPack,
     class_name: ClassName,
@@ -92,7 +92,7 @@ def identify_resource_dependencies(  # noqa: C901, PLR0912
     resource_blacklist: dict[ClassName, set[ResourceId]] = defaultdict(set)
     resource_blacklist[class_name].add(resource_id)
     if _resource_blacklist:
-        for class_name, resource_ids in _resource_blacklist.items():
+        for class_name, resource_ids in _resource_blacklist.items():  # noqa: PLR1704
             resource_blacklist[class_name].update(resource_ids)
 
     dependencies_by_class: dict[ClassName, set[ResourceId]] = defaultdict(set)

src/schemapack/_internals/spec/custom_types.py

@@ -18,6 +18,7 @@
 
 from typing import Annotated, TypeAlias
 
+from arcticfreeze import FrozenDict
 from pydantic import Field as _Field
 
 _NonEmptyStr: TypeAlias = Annotated[str, _Field(..., min_length=1)]
@@ -26,3 +27,5 @@
 RelationPropertyName: TypeAlias = _NonEmptyStr
 ContentPropertyName: TypeAlias = _NonEmptyStr
 IdPropertyName: TypeAlias = _NonEmptyStr
+FrozenType: TypeAlias = FrozenDict[str, "str | FrozenType | tuple"]
+ThawedType: TypeAlias = dict[str, "str | ThawedType | list"]

src/schemapack/_internals/utils.py

@@ -32,8 +32,10 @@
 import jsonschema.protocols
 import jsonschema.validators
 import ruamel.yaml
+from arcticfreeze import FrozenDict
 from pydantic import BaseModel
 
+from schemapack._internals.spec.custom_types import FrozenType, ThawedType
 from schemapack.exceptions import ParsingError
 
 yaml = ruamel.yaml.YAML(typ="rt")
@@ -79,7 +81,8 @@ def assert_valid_json_schema(schema: Mapping[str, Any]) -> None:
     cls: type[jsonschema.protocols.Validator] = jsonschema.validators.validator_for(
         schema
     )
-
+    if isinstance(schema, FrozenDict):
+        schema = thaw_frozendict(schema)
     try:
         cls.check_schema(schema)
     except jsonschema.exceptions.SchemaError as error:
@@ -109,6 +112,18 @@ def model_to_serializable_dict(
     return json.loads(model.model_dump_json(exclude_defaults=True))
 
 
+def thaw_frozendict(frozen_dict: FrozenType) -> ThawedType:
+    """Recursively thaws a FrozenDict into a standard dictionary."""
+    return {
+        key: (
+            thaw_frozendict(val)
+            if isinstance(val, FrozenDict)
+            else (list(val) if isinstance(val, tuple) else val)
+        )
+        for key, val in frozen_dict.items()
+    }
+
+
 def dumps_model(
     model: BaseModel,
     *,

src/schemapack/_internals/validation/__init__.py

@@ -24,8 +24,8 @@
 )
 
 __all__ = [
-    "SchemaPackValidator",
-    "GlobalValidationPlugin",
     "ClassValidationPlugin",
+    "GlobalValidationPlugin",
     "ResourceValidationPlugin",
+    "SchemaPackValidator",
 ]

src/schemapack/_internals/validation/plugins/__init__.py

@@ -61,14 +61,14 @@
     "ContentSchemaValidationPlugin",
     "ExpectedRootValidationPlugin",
     "MissingClassSlotValidationPlugin",
-    "MissingRelationValidationPlugin",
+    "MissingMandatoryOriginValidationPlugin",
     "MissingMandatoryTargetValidationPlugin",
+    "MissingRelationValidationPlugin",
     "MultipleTargetValidationPlugin",
-    "TargetOverlapValidationPlugin",
     "TargetIdValidationPlugin",
+    "TargetOverlapValidationPlugin",
     "UnexpectedRootValidationPlugin",
     "UnknownClassSlotValidationPlugin",
     "UnknownRelationValidationPlugin",
     "UnkownRootResourceValidationPlugin",
-    "MissingMandatoryOriginValidationPlugin",
 ]

src/schemapack/exceptions.py

@@ -33,15 +33,15 @@
 
 __all__ = [
     "BaseError",
-    "SpecError",
+    "CircularRelationError",
+    "ClassNotFoundError",
+    "DataPackSpecError",
     "ParsingError",
+    "ResourceNotFoundError",
+    "SchemaPackSpecError",
+    "SpecError",
+    "ValidationAssumptionError",
     "ValidationError",
     "ValidationErrorRecord",
-    "DataPackSpecError",
-    "SchemaPackSpecError",
-    "CircularRelationError",
     "ValidationPluginError",
-    "ValidationAssumptionError",
-    "ResourceNotFoundError",
-    "ClassNotFoundError",
 ]

src/schemapack/plugins.py

@@ -23,7 +23,7 @@
 )
 
 __all__ = [
-    "GlobalValidationPlugin",
     "ClassValidationPlugin",
+    "GlobalValidationPlugin",
     "ResourceValidationPlugin",
 ]

src/schemapack/spec/custom_types.py

@@ -26,8 +26,8 @@
 
 __all__ = [
     "ClassName",
-    "ResourceId",
-    "RelationPropertyName",
     "ContentPropertyName",
     "IdPropertyName",
+    "RelationPropertyName",
+    "ResourceId",
 ]

src/schemapack/spec/datapack.py

@@ -24,8 +24,8 @@
 )
 
 __all__ = [
+    "SUPPORTED_DATA_PACK_VERSIONS",
     "DataPack",
     "Resource",
     "SupportedDataPackVersions",
-    "SUPPORTED_DATA_PACK_VERSIONS",
 ]

src/schemapack/spec/schemapack.py

@@ -29,11 +29,11 @@
 
 __all__ = [
     "SUPPORTED_SCHEMA_PACK_VERSIONS",
-    "SchemaPack",
     "ClassDefinition",
     "IDSpec",
     "MandatoryRelationSpec",
     "MultipleRelationSpec",
     "Relation",
+    "SchemaPack",
     "SupportedSchemaPackVersions",
 ]

src/schemapack/utils.py

@@ -22,4 +22,4 @@
     read_json_or_yaml_mapping,
 )
 
-__all__ = ["read_json_or_yaml_mapping", "model_to_serializable_dict"]
+__all__ = ["model_to_serializable_dict", "read_json_or_yaml_mapping"]