roc-validator 0.2.0__tar.gz

roc_validator-0.2.0/LICENSE

@@ -0,0 +1,201 @@
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roc_validator-0.2.0/PKG-INFO

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+Metadata-Version: 2.1
+Name: roc-validator
+Version: 0.2.0
+Summary: A Python package to validate RO-Crates
+Author: Marco Enrico Piras
+Author-email: kikkomep@crs4.it
+Requires-Python: >=3.8.1,<4.0.0
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Requires-Dist: click (>=8.1.7,<9.0.0)
+Requires-Dist: colorlog (>=6.8,<7.0)
+Requires-Dist: inquirerpy (>=0.3.4,<0.4.0)
+Requires-Dist: pyshacl (>=0.26.0,<0.27.0)
+Requires-Dist: rdflib (>=7.0.0,<8.0.0)
+Requires-Dist: requests (>=2.32.3,<3.0.0)
+Requires-Dist: requests-cache (>=1.2.1,<2.0.0)
+Requires-Dist: rich (>=13.8.0,<14.0.0)
+Requires-Dist: rich-click (>=1.8.3,<2.0.0)
+Requires-Dist: toml (>=0.10.2,<0.11.0)
+Description-Content-Type: text/markdown
+
+# rocrate-validator
+
+[![main workflow](https://github.com/crs4/rocrate-validator/actions/workflows/testing.yaml/badge.svg)](https://github.com/crs4/rocrate-validator/actions/workflows/testing.yaml) [![License](https://img.shields.io/badge/License-Apache_2.0-blue.svg)](https://opensource.org/licenses/Apache-2.0)
+
+<!-- [![Build Status](https://repolab.crs4.it/lifemonitor/rocrate-validator/badges/develop/pipeline.svg)](https://repolab.crs4.it/lifemonitor/rocrate-validator/-/pipelines?page=1&scope=branches&ref=develop) -->
+
+<!-- [![PyPI version](https://badge.fury.io/py/rocrate-validator.svg)](https://badge.fury.io/py/rocrate-validator) -->
+
+<!-- [![codecov](https://codecov.io/gh/crs4/rocrate-validator/branch/main/graph/badge.svg?token=3ZQZQZQZQZ)](https://codecov.io/gh/crs4/rocrate-validator) -->
+
+A Python package to validate [RO-Crate](https://researchobject.github.io/ro-crate/) packages.
+
+* Supports CLI-based validation as well as programmatic validation (so it can
+  easily be used by Python code).
+* Implements an extensible validation framework to which new RO-Crate profiles
+  can be added.  Validation is based on SHACL shapes and Python code.
+* Currently, validations for the following profiles are implemented: RO-Crate
+  (base profile), [Workflow
+  RO-Crate](https://www.researchobject.org/ro-crate/specification/1.1/workflows.html),
+  [Process Run
+  Crate](https://www.researchobject.org/workflow-run-crate/profiles/0.1/process_run_crate.html).
+  More are being implemented.
+
+**Note**: this software is still work in progress. Feel free to try it out,
+report positive and negative feedback.  Do send a note (e.g., by opening an
+Issue) before starting to develop patches you would like to contribute.  The
+implementation of validation code for additional RO-Crate profiles would be
+particularly welcome.
+
+## Setup
+
+Follow these steps to set up the project:
+
+1. **Clone the repository**
+
+```bash
+git clone https://github.com/crs4/rocrate-validator.git
+cd rocrate-validator
+```
+
+2. **Set up a Python virtual environment (optional)**
+
+Set up a Python virtual environment using `venv`:
+
+```bash
+python3 -m venv .venv
+source .venv/bin/activate
+```
+
+Or using `virtualenv`:
+
+```bash
+virtualenv .venv
+source .venv/bin/activate
+```
+
+This step, while optional, is recommended for isolating your project dependencies. If skipped, Poetry will automatically create a virtual environment for you.
+
+3. **Install the project using Poetry**
+
+Ensure you have Poetry installed. If not, follow the instructions [here](https://python-poetry.org/docs/#installation). Then, install the project:
+
+```bash
+poetry install
+```
+
+## Usage
+
+After installation, you can use the main command `rocrate-validator` to validate ROCrates.
+
+### Using Poetry
+
+Run the validator using the following command:
+
+```bash
+poetry run rocrate-validator validate <path_to_rocrate>
+```
+
+Replace `<path_to_rocrate>` with the path to the RO-Crate you want to validate.
+
+Type `poetry run rocrate-validator --help` for more information.
+
+### Using the installed package on your virtual environment
+
+Activate the virtual environment:
+
+```bash
+source .venv/bin/activate
+```
+
+Then, run the validator using the following command:
+
+```bash
+rocrate-validator validate <path_to_rocrate>
+```
+
+Replace `<path_to_rocrate>` with the path to the RO-Crate you want to validate.
+
+Type `rocrate-validator --help` for more information.
+
+## Running the tests
+
+To run the tests, use the following command:
+
+```bash
+poetry run pytest
+```
+
+<!-- ## Contributing
+
+Contributions are welcome! Please read our [contributing guidelines](CONTRIBUTING.md) for details. -->
+
+## License
+
+This project is licensed under the terms of the Apache License 2.0. See the
+[LICENSE](LICENSE) file for details.
+
+## Acknowledgements
+
+This work has been partially funded by the following sources:
+
+* the [BY-COVID](https://by-covid.org/) project (HORIZON Europe grant agreement number 101046203);
+* the [LIFEMap](https://www.thelifemap.it/) project, funded by the Italian Ministry of Health (Piano Operative Salute, Trajectory 3).
+
+<img alt="Co-funded by the EU"
+    src="https://raw.githubusercontent.com/crs4/rocrate-validator/develop/docs/img/eu-logo/EN_Co-fundedbytheEU_RGB_POS.png"
+    width="250" align="right"/>
+

roc_validator-0.2.0/README.md

@@ -0,0 +1,127 @@
+# rocrate-validator
+
+[![main workflow](https://github.com/crs4/rocrate-validator/actions/workflows/testing.yaml/badge.svg)](https://github.com/crs4/rocrate-validator/actions/workflows/testing.yaml) [![License](https://img.shields.io/badge/License-Apache_2.0-blue.svg)](https://opensource.org/licenses/Apache-2.0)
+
+<!-- [![Build Status](https://repolab.crs4.it/lifemonitor/rocrate-validator/badges/develop/pipeline.svg)](https://repolab.crs4.it/lifemonitor/rocrate-validator/-/pipelines?page=1&scope=branches&ref=develop) -->
+
+<!-- [![PyPI version](https://badge.fury.io/py/rocrate-validator.svg)](https://badge.fury.io/py/rocrate-validator) -->
+
+<!-- [![codecov](https://codecov.io/gh/crs4/rocrate-validator/branch/main/graph/badge.svg?token=3ZQZQZQZQZ)](https://codecov.io/gh/crs4/rocrate-validator) -->
+
+A Python package to validate [RO-Crate](https://researchobject.github.io/ro-crate/) packages.
+
+* Supports CLI-based validation as well as programmatic validation (so it can
+  easily be used by Python code).
+* Implements an extensible validation framework to which new RO-Crate profiles
+  can be added.  Validation is based on SHACL shapes and Python code.
+* Currently, validations for the following profiles are implemented: RO-Crate
+  (base profile), [Workflow
+  RO-Crate](https://www.researchobject.org/ro-crate/specification/1.1/workflows.html),
+  [Process Run
+  Crate](https://www.researchobject.org/workflow-run-crate/profiles/0.1/process_run_crate.html).
+  More are being implemented.
+
+**Note**: this software is still work in progress. Feel free to try it out,
+report positive and negative feedback.  Do send a note (e.g., by opening an
+Issue) before starting to develop patches you would like to contribute.  The
+implementation of validation code for additional RO-Crate profiles would be
+particularly welcome.
+
+## Setup
+
+Follow these steps to set up the project:
+
+1. **Clone the repository**
+
+```bash
+git clone https://github.com/crs4/rocrate-validator.git
+cd rocrate-validator
+```
+
+2. **Set up a Python virtual environment (optional)**
+
+Set up a Python virtual environment using `venv`:
+
+```bash
+python3 -m venv .venv
+source .venv/bin/activate
+```
+
+Or using `virtualenv`:
+
+```bash
+virtualenv .venv
+source .venv/bin/activate
+```
+
+This step, while optional, is recommended for isolating your project dependencies. If skipped, Poetry will automatically create a virtual environment for you.
+
+3. **Install the project using Poetry**
+
+Ensure you have Poetry installed. If not, follow the instructions [here](https://python-poetry.org/docs/#installation). Then, install the project:
+
+```bash
+poetry install
+```
+
+## Usage
+
+After installation, you can use the main command `rocrate-validator` to validate ROCrates.
+
+### Using Poetry
+
+Run the validator using the following command:
+
+```bash
+poetry run rocrate-validator validate <path_to_rocrate>
+```
+
+Replace `<path_to_rocrate>` with the path to the RO-Crate you want to validate.
+
+Type `poetry run rocrate-validator --help` for more information.
+
+### Using the installed package on your virtual environment
+
+Activate the virtual environment:
+
+```bash
+source .venv/bin/activate
+```
+
+Then, run the validator using the following command:
+
+```bash
+rocrate-validator validate <path_to_rocrate>
+```
+
+Replace `<path_to_rocrate>` with the path to the RO-Crate you want to validate.
+
+Type `rocrate-validator --help` for more information.
+
+## Running the tests
+
+To run the tests, use the following command:
+
+```bash
+poetry run pytest
+```
+
+<!-- ## Contributing
+
+Contributions are welcome! Please read our [contributing guidelines](CONTRIBUTING.md) for details. -->
+
+## License
+
+This project is licensed under the terms of the Apache License 2.0. See the
+[LICENSE](LICENSE) file for details.
+
+## Acknowledgements
+
+This work has been partially funded by the following sources:
+
+* the [BY-COVID](https://by-covid.org/) project (HORIZON Europe grant agreement number 101046203);
+* the [LIFEMap](https://www.thelifemap.it/) project, funded by the Italian Ministry of Health (Piano Operative Salute, Trajectory 3).
+
+<img alt="Co-funded by the EU"
+    src="https://raw.githubusercontent.com/crs4/rocrate-validator/develop/docs/img/eu-logo/EN_Co-fundedbytheEU_RGB_POS.png"
+    width="250" align="right"/>

roc_validator-0.2.0/pyproject.toml

@@ -0,0 +1,63 @@
+[tool.poetry]
+name = "roc-validator"
+version = "0.2.0"
+description = "A Python package to validate RO-Crates"
+authors = [
+    "Marco Enrico Piras <kikkomep@crs4.it>",
+    "Luca Pireddu <luca.pireddu@crs4.it>",
+    "Simone Leo <simleo@crs4.it>",
+]
+readme = "README.md"
+packages = [{ include = "rocrate_validator", from = "." }]
+include = [
+    { path = "pyproject.toml", format = [
+        "sdist",
+        "wheel",
+    ] },
+    { path = "README.md", format = [
+        "sdist",
+        "wheel",
+    ] },
+    { path = "LICENSE", format = [
+        "sdist",
+        "wheel",
+    ] }
+]
+
+[tool.poetry.dependencies]
+python = "^3.8.1"
+rdflib = "^7.0.0"
+pyshacl = "^0.26.0"
+click = "^8.1.7"
+rich = "^13.8.0"
+toml = "^0.10.2"
+rich-click = "^1.8.3"
+colorlog = "^6.8"
+requests = "^2.32.3"
+requests-cache = "^1.2.1"
+inquirerpy = "^0.3.4"
+
+[tool.poetry.group.dev.dependencies]
+pyproject-flake8 = "^6.1.0"
+pylint = "^3.1.0"
+ipykernel = "^6.29.3"
+
+[tool.poetry.group.test.dependencies]
+pytest-cov = "^5.0.0"
+pytest-xdist = "^3.6.1"
+
+[tool.flake8]
+max-line-length = 120
+
+[build-system]
+requires = ["poetry-core"]
+build-backend = "poetry.core.masonry.api"
+
+[tool.poetry.scripts]
+rocrate-validator = "rocrate_validator.cli:cli"
+
+[tool.rocrate_validator]
+skip_dirs = [".git", ".github", ".vscode"]
+
+[tool.pytest.ini_options]
+testpaths = ["tests"]

roc_validator-0.2.0/rocrate_validator/__init__.py

@@ -0,0 +1,20 @@
+# Copyright (c) 2024 CRS4
+#
+# 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.
+
+def get_version():
+    from rocrate_validator.utils import get_version
+    return get_version()
+
+
+__version__ = get_version()

roc_validator-0.2.0/rocrate_validator/cli/__init__.py

@@ -0,0 +1,18 @@
+# Copyright (c) 2024 CRS4
+#
+# 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.
+
+from .commands import profiles, validate
+from .main import cli
+
+__all__ = ["cli", "profiles", "validate"]

roc_validator-0.2.0/rocrate_validator/cli/commands/errors.py

@@ -0,0 +1,58 @@
+# Copyright (c) 2024 CRS4
+#
+# 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.
+
+import sys
+import textwrap
+
+from rich.console import Console
+
+import rocrate_validator.log as logging
+from rocrate_validator.errors import InvalidProfilePath, ProfileNotFound, ProfilesDirectoryNotFound
+
+# Create a logger for this module
+logger = logging.getLogger(__name__)
+
+
+def handle_error(e: Exception, console: Console) -> None:
+    error_message = ""
+    if isinstance(e, ProfilesDirectoryNotFound):
+        error_message = f"""
+        The profile folder could not be located at the specified path: [red]{e.profiles_path}[/red].
+        Please ensure that the path is correct and try again.
+        """
+    elif isinstance(e, ProfileNotFound):
+        error_message = f"""The profile with the identifier "[red bold]{e.profile_name}[/red bold]" could not be found.
+        Please ensure that the profile exists and try again.
+
+        To see the available profiles, run:
+        [cyan bold]rocrate-validator profiles list[/cyan bold]
+        """
+    elif isinstance(e, InvalidProfilePath):
+        error_message = f"""The profile path "[red bold]{e.profile_path}[/red bold]" is not valid.
+        Please ensure that the profile exists and try again.
+
+        To see the available profiles, run:
+        [cyan bold]rocrate-validator profiles list[/cyan bold]
+        """
+    else:
+        error_message = f"\n\n[bold][[red]FAILED[/red]] Unexpected error: {e} !!![/bold]\n"
+        if logger.isEnabledFor(logging.DEBUG):
+            console.print_exception()
+        console.print(textwrap.indent("This error may be due to a bug.\n"
+                                      "Please report it to the issue tracker "
+                                      "along with the following stack trace:\n", ' ' * 9))
+        console.print_exception()
+
+    console.print(f"\n\n[bold][[red]ERROR[/red]] {error_message}[/bold]\n", style="white")
+    sys.exit(2)