refactor: ♻️ transfer validation api to codefair repo

[slugb0t]

Summary by Sourcery

Transfer the validation API to the codefair repository, introducing a new API for CWL validation and setting up the necessary infrastructure for development, testing, and deployment.

New Features:

• Introduce a new API for CWL validation with endpoints for validating CWL and CITATION.cff files.

Enhancements:

• Refactor the project structure to include a new 'validator-api' directory with configuration files for linting, testing, and building.

Build:

• Add a Dockerfile for building the validator API image with necessary dependencies and configurations.

CI:

• Create a GitHub Actions workflow for building and deploying the validator API Docker image to Azure Container Registry.

Documentation:

• Add a README file with setup instructions, prerequisites, and usage guidelines for the CWL validator API.

[fairdataihub-bot]

Thank you for submitting this pull request! We appreciate your contribution to the project. Before we can merge it, we need to review the changes you've made to ensure they align with our code standards and meet the requirements of the project. We'll get back to you as soon as we can with feedback. Thanks again!

[sourcery-ai]

Reviewer's Guide by Sourcery

This PR transfers the CWL validation API to the codefair repository. The implementation includes a Flask-based REST API with endpoints for validating CWL and CITATION.cff files, along with configuration files for development, testing, and deployment.

Class diagram for the CWL Validator API

classDiagram
    class Api {
        +title: str
        +description: str
        +doc: str
        +init_app(app: Flask)
    }
    class HelloEverynyan {
        +get() str
    }
    class ValidateCWL {
        +post() dict
    }
    class ValidateCitation {
        +post() dict
    }
    Api <|-- HelloEverynyan
    Api <|-- ValidateCWL
    Api <|-- ValidateCitation
    class Flask {
        +config: dict
    }
    class CORS {
        +init_app(app: Flask)
    }
    Flask <|-- Api
    Flask <|-- CORS

Loading

File-Level Changes

Change	Details	Files
Set up Flask REST API with validation endpoints	Created Flask application with CORS support and configuration Implemented /validate-cwl endpoint for CWL file validation Implemented /validate-citation endpoint for CITATION.cff validation Added basic /echo endpoint for health checks	validator-api/apis/__init__.py validator-api/app.py
Added Docker containerization support	Created Dockerfile with Python 3.10 Alpine base image Added Poetry for dependency management Configured container to install cwltool and cffconvert Set up docker-compose for local development	validator-api/Dockerfile validator-api/docker-compose.yaml
Configured development environment and tooling	Set up Poetry project configuration with dependencies Added linting configurations for pylint, flake8, and pydocstyle Configured pytest for testing Added GitHub workflow for building and deploying to Azure Container Registry	validator-api/pyproject.toml validator-api/.pylint.ini validator-api/.pydocstyle.ini validator-api/.github/workflows/build-and-deploy.yml

---

Tips and commands

Interacting with Sourcery

• Trigger a new review: Comment @sourcery-ai review on the pull request.
• Continue discussions: Reply directly to Sourcery's review comments.
• Generate a GitHub issue from a review comment: Ask Sourcery to create an
  issue from a review comment by replying to it.
• Generate a pull request title: Write @sourcery-ai anywhere in the pull
  request title to generate a title at any time.
• Generate a pull request summary: Write @sourcery-ai summary anywhere in
  the pull request body to generate a PR summary at any time. You can also use
  this command to specify where the summary should be inserted.

Customizing Your Experience

Access your dashboard to:

• Enable or disable review features such as the Sourcery-generated pull request
  summary, the reviewer's guide, and others.
• Change the review language.
• Add, remove or edit custom review instructions.
• Adjust other review settings.

Getting Help

• Contact our support team for questions or feedback.
• Visit our documentation for detailed guides and information.
• Keep in touch with the Sourcery team by following us on X/Twitter, LinkedIn or GitHub.

[fairdataihub-bot]

Thanks for making updates to your pull request. Our team will take a look and provide feedback as soon as possible. Please wait for any GitHub Actions to complete before editing your pull request. If you have any additional questions or concerns, feel free to let us know. Thank you for your contributions!

[fairdataihub-bot]

Thanks for closing this pull request! If you have any further questions, please feel free to open a new issue. We are always happy to help!

[sourcery-ai]

Hey @slugb0t - I've reviewed your changes - here's some feedback:

Overall Comments:

• Consider reviewing the extensive list of disabled pylint checks in .pylint.ini - some of these like 'missing-docstring' and 'too-many-arguments' could help improve code quality if enabled

Here's what I looked at during the review

• 🟡 General issues: 2 issues found
• 🟢 Security: all looks good
• 🟢 Testing: all looks good
• 🟢 Complexity: all looks good
• 🟢 Documentation: all looks good

---

Sourcery is free for open source - if you like our reviews please consider sharing them ✨

• X
• Mastodon
• LinkedIn
• Facebook

_{Help me be more useful! Please click 👍 or 👎 on each comment and I'll use the feedback to improve your reviews.}

[sourcery-ai]

suggestion (typo): Consider capitalizing 'API' as it's an acronym

Suggested change

	If you would like to update the api, please follow the instructions below.
	If you would like to update the API, please follow the instructions below.

[sourcery-ai]

suggestion: Consider explaining what 'poe' is when first introducing it

It would be helpful to briefly mention that 'poe' commands come from poethepoet, or include a reference to the tool's documentation.

# Using poethepoet task runner (https://github.com/nat-n/poethepoet)
poe format

[sourcery-ai]

suggestion (code-quality): Replace m.group(x) with m[x] for re.Match objects (use-getitem-for-re-match-groups)

Suggested change

	stderr_clean = match.group(0) if match else "Unknown error"
	stderr_clean = match[0] if match else "Unknown error"