schemapack 1.0.0__tar.gz

schemapack-1.0.0/LICENSE

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+   Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+   for the German Human Genome-Phenome Archive (GHGA)
+
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schemapack-1.0.0/PKG-INFO

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+Metadata-Version: 2.1
+Name: schemapack
+Version: 1.0.0
+Summary: Make your JSON Schemas sociable and create linked data model.
+Author-email: "German Human Genome Phenome Archive (GHGA)" <contact@ghga.de>
+License: Apache 2.0
+Classifier: Development Status :: 1 - Planning
+Classifier: Operating System :: POSIX :: Linux
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: License :: OSI Approved :: Apache Software License
+Classifier: Topic :: Internet :: WWW/HTTP :: HTTP Servers
+Classifier: Topic :: Software Development :: Libraries
+Classifier: Intended Audience :: Developers
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: pydantic<3,>=2
+Requires-Dist: pydantic_settings<3,>=2
+Requires-Dist: PyYAML<7,>=6.0.1
+Requires-Dist: jsonschema<5,>=4.19.2
+Requires-Dist: immutabledict<4,>=3.0.0
+
+![tests](https://github.com/ghga-de/schemapack/actions/workflows/unit_and_int_tests.yaml/badge.svg)
+[![PyPI version shields.io](https://img.shields.io/pypi/v/schemapack.svg)](https://pypi.python.org/pypi/schemapack/)
+[![PyPI pyversions](https://img.shields.io/pypi/pyversions/schemapack.svg)](https://pypi.python.org/pypi/schemapack/)
+[![Coverage Status](https://coveralls.io/repos/github/ghga-de/schemapack/badge.svg?branch=main)](https://coveralls.io/github/ghga-de/schemapack?branch=main)
+
+# schemapack
+
+Make your JSON Schemas sociable and create linked data model.
+
+## Installation
+This package is available at PyPI:
+https://pypi.org/project/schemapack
+
+You can install it from there using:
+```
+pip install schemapack
+```
+
+## Development
+For setting up the development environment, we rely on the
+[devcontainer feature](https://code.visualstudio.com/docs/remote/containers) of vscode.
+
+To use it, you have to have Docker as well as vscode with its "Remote - Containers"
+extension (`ms-vscode-remote.remote-containers`) extension installed.
+Then, you just have to open this repo in vscode and run the command
+`Remote-Containers: Reopen in Container` from the vscode "Command Palette".
+
+This will give you a full-fledged, pre-configured development environment including:
+- infrastructural dependencies of the service (databases, etc.)
+- all relevant vscode extensions pre-installed
+- pre-configured linting and auto-formating
+- a pre-configured debugger
+- automatic license-header insertion
+
+Moreover, inside the devcontainer, there is follwing convenience command available
+(please type it in the integrated terminal of vscode):
+- `dev_install` - install the lib with all development dependencies and pre-commit hooks
+(please run that if you are starting the devcontainer for the first time
+or if added any python dependencies to the [`./setup.cfg`](./setup.cfg))
+
+## License
+This repository is free to use and modify according to the [Apache 2.0 License](./LICENSE).

schemapack-1.0.0/README.md

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+![tests](https://github.com/ghga-de/schemapack/actions/workflows/unit_and_int_tests.yaml/badge.svg)
+[![PyPI version shields.io](https://img.shields.io/pypi/v/schemapack.svg)](https://pypi.python.org/pypi/schemapack/)
+[![PyPI pyversions](https://img.shields.io/pypi/pyversions/schemapack.svg)](https://pypi.python.org/pypi/schemapack/)
+[![Coverage Status](https://coveralls.io/repos/github/ghga-de/schemapack/badge.svg?branch=main)](https://coveralls.io/github/ghga-de/schemapack?branch=main)
+
+# schemapack
+
+Make your JSON Schemas sociable and create linked data model.
+
+## Installation
+This package is available at PyPI:
+https://pypi.org/project/schemapack
+
+You can install it from there using:
+```
+pip install schemapack
+```
+
+## Development
+For setting up the development environment, we rely on the
+[devcontainer feature](https://code.visualstudio.com/docs/remote/containers) of vscode.
+
+To use it, you have to have Docker as well as vscode with its "Remote - Containers"
+extension (`ms-vscode-remote.remote-containers`) extension installed.
+Then, you just have to open this repo in vscode and run the command
+`Remote-Containers: Reopen in Container` from the vscode "Command Palette".
+
+This will give you a full-fledged, pre-configured development environment including:
+- infrastructural dependencies of the service (databases, etc.)
+- all relevant vscode extensions pre-installed
+- pre-configured linting and auto-formating
+- a pre-configured debugger
+- automatic license-header insertion
+
+Moreover, inside the devcontainer, there is follwing convenience command available
+(please type it in the integrated terminal of vscode):
+- `dev_install` - install the lib with all development dependencies and pre-commit hooks
+(please run that if you are starting the devcontainer for the first time
+or if added any python dependencies to the [`./setup.cfg`](./setup.cfg))
+
+## License
+This repository is free to use and modify according to the [Apache 2.0 License](./LICENSE).

schemapack-1.0.0/pyproject.toml

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+[build-system]
+requires = ["setuptools>=67.7.2"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "schemapack"
+version = "1.0.0"
+description = "Make your JSON Schemas sociable and create linked data model."
+readme = "README.md"
+authors = [
+    { name = "German Human Genome Phenome Archive (GHGA)", email = "contact@ghga.de" },
+]
+requires-python = ">=3.9"
+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",
+    "License :: OSI Approved :: Apache Software License",
+    "Topic :: Internet :: WWW/HTTP :: HTTP Servers",
+    "Topic :: Software Development :: Libraries",
+    "Intended Audience :: Developers",
+]
+dependencies = [
+    "pydantic >=2, <3",
+    "pydantic_settings >=2, <3",
+    "PyYAML >=6.0.1, <7",
+    "jsonschema >=4.19.2, <5",
+    "immutabledict >=3.0.0, <4",
+]
+
+[tool.setuptools.packages.find]
+where = ["src"]

schemapack-1.0.0/setup.cfg

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+[egg_info]
+tag_build = 
+tag_date = 0
+

schemapack-1.0.0/src/schemapack/__init__.py

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+# 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.
+
+"""A specification (plus tooling) for describing linked data models based on JSON schema."""
+
+from importlib.metadata import version
+
+__version__ = version(__package__)

schemapack-1.0.0/src/schemapack/__main__.py

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+# 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.
+
+"""Entrypoint of the package"""

schemapack-1.0.0/src/schemapack/exceptions.py

@@ -0,0 +1,202 @@
+# 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.
+#
+
+"""Collection of package-specific exceptions"""
+
+from abc import ABC
+from dataclasses import dataclass
+from typing import Optional
+
+import pydantic_core
+
+
+class BaseError(ABC, Exception):
+    """Base class for all schemapack errors."""
+
+
+class SpecError(BaseError, ValueError):
+    """An error indicating that an instance was not valid against the specification."""
+
+    def __init__(self, message: str, *, details: list[pydantic_core.ErrorDetails]):
+        """Initiate a SpecError.
+
+        Args:
+            message: A human-readable message describing the error.
+            details: Details on which fields of the instance are invalid.
+        """
+        super().__init__(message)
+        self.message = message
+        self.details = details
+
+
+class SchemaPackSpecError(SpecError):
+    """An error indicating that the provided data is not valid against the schemapack
+    specification.
+    """
+
+    def __init__(self, message: str, *, details: list[pydantic_core.ErrorDetails]):
+        """Initiate a SchemaPackSpecError.
+
+        Args:
+            message: A human-readable message describing the error.
+            details: Details on which fields of the instance are invalid.
+        """
+        message = (
+            "The provided object was not compatible with the schemapack"
+            + f" specification: {message}"
+        )
+        super().__init__(message, details=details)
+
+
+class DataPackSpecError(SpecError):
+    """An error indicating that the provided data is not valid against the datapack
+    specification (this is independent of validation done using a schemapack).
+    """
+
+    def __init__(self, message: str, *, details: list[pydantic_core.ErrorDetails]):
+        """Initiate a SchemaPackSpecError.
+
+        Args:
+            message: A human-readable message describing the error.
+            details: Details on which fields of the instance are invalid.
+        """
+        message = (
+            "The provided object was not compatible with the datapack"
+            + f" specification: {message}"
+        )
+        super().__init__(message, details=details)
+
+
+class ValidationPluginError(BaseError, ValueError):
+    """Raised by a ValidationPlugin."""
+
+    def __init__(
+        self, *, type_: str, message: str, details: Optional[dict[str, object]] = None
+    ):
+        """Initiate a ValidationPluginError.
+
+        Args:
+            type: A preferably short type label.
+            message: A human-readable message describing the error.
+            details: A dictionary for transporting additional machine-readable details.
+        """
+        super().__init__(message)
+        self.type_ = type_
+        self.message = message
+        self.details = details if details else {}
+
+
+@dataclass
+class ValidationErrorRecord:
+    """A record of an Error occuring during validation on a specific context
+    (e.g. a specific resource) regarding a specific validation aspect.
+
+    Attributes:
+        subject_class:
+            If relevant, the name of the subject class as per the schemapack.
+        subject_resource:
+            If relevant, the ID or the subject resource of the subject class.
+        type:
+            A preferably short type label.
+        message:
+            A human-readable message describing the error.
+        details:
+            A dictionary for transporting additional machine-readable details.
+    """
+
+    subject_class: Optional[str]
+    subject_resource: Optional[str]
+    type: str
+    message: str
+    details: dict[str, object]
+
+
+def _val_record_to_str(record: ValidationErrorRecord) -> str:
+    """Translate a ValidationErrorRecords into a human-readable message
+    to be displayed to the user on the terminal.
+    """
+    if record.subject_class:
+        if record.subject_resource:
+            context = f"resource '{record.subject_class}.{record.subject_resource}'"
+        else:
+            context = "class '{record.subject_class}'"
+    else:
+        context = "global datapack"
+
+    return (
+        f"Error in {context}:"
+        + f"\n\tType: {record.type}"
+        + f"\n\tMessage: {record.message}"
+    )
+
+
+def _sorted_val_records(
+    records: list[ValidationErrorRecord],
+) -> list[ValidationErrorRecord]:
+    """Sort a set of ValidationErrorRecords."""
+    return sorted(records, key=lambda r: (r.subject_class, r.subject_resource, r.type))
+
+
+class ValidationError(BaseError, ValueError):
+    """A collection of ValidationErrorRecords raised when a datapack fails validation
+    against a schemapack.
+    """
+
+    def __init__(self, records: list[ValidationErrorRecord]):
+        """Initiate a ValidationError.
+
+        Args:
+            records: A list of ValidationErrorRecords.
+        """
+        if not records:
+            raise ValueError("ValidationError must be raised with at least one record.")
+
+        self.records = _sorted_val_records(records)
+        n_records = len(self.records)
+        record_messages = "\n".join(_val_record_to_str(r) for r in self.records)
+        message = f"Validation failed with {n_records} issue(s):\n{record_messages}"
+
+        super().__init__(message)
+
+
+class ValidationAssumptionError(BaseError, RuntimeError):
+    """This is raised when a unit of code assumes to work with a datapack that has
+    already been validated against a specific schemapack, however, it became apparent
+    that this assumption was not correct. The error should not contain the details on
+    which aspect is invalid. These details can be retrieved by performing a validation
+    and receiving a ValidationError.
+    """
+
+    def __init__(self, *, context: str):
+        """Initiate a ValidationAssumptionError.
+
+        Args:
+            context: Some context to be included in the error message.
+        """
+        message = (
+            "It was assumed that the provided datapack has already been validated"
+            + " against the provided schemapack, however, this assumption failed in"
+            + f" the context of {context}. Please validate the datapack against the"
+            + " schemapack to get further details."
+        )
+        super().__init__(message)
+        self.message = message
+
+
+class CircularRelationError(BaseError, ValueError):
+    """Raised when a circular relation between resources is detected, but the requested
+    operation cannot be performed on datapacks with circular relations.
+    """