Merge pull request #52 from eScienceLab/develop

v0.1 Release

Author: douglowe

.dockerignore

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+# Git
+**/.git
+**/.github
+**/.gitignore
+**/.gitattributes
+
+
+# Environments
+example.env
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# OSX files
+**/.DS_Store
+
+# Docker
+Dockerfile
+docker-compose*
+.dockerignore
+
+# Python
+**/__pycache__

.github/workflows/build.yml

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+#
+name: Create and publish a Docker image
+
+# Configures this workflow to run every time a tagged release is created.
+on:
+  release:
+    types: [published]
+  workflow_dispatch:
+
+env:
+  REGISTRY: ghcr.io
+  IMAGE_NAME: ${{ github.repository }}
+
+jobs:
+  build-and-push-image:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      packages: write
+      attestations: write
+      id-token: write
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+      - name: Log in to the Container registry
+        uses: docker/login-action@v3
+        with:
+          registry: ${{ env.REGISTRY }}
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+      # This step uses [docker/metadata-action](https://github.com/docker/metadata-action#about) to extract tags and labels that will be applied to the specified image. The `id` "meta" allows the output of this step to be referenced in a subsequent step. The `images` value provides the base name for the tags and labels.
+      - name: Extract metadata (tags, labels) for Docker
+        id: meta
+        uses: docker/metadata-action@v5
+        with:
+          images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
+      # This step uses the `docker/build-push-action` action to build the image, based on your repository's `Dockerfile`. If the build succeeds, it pushes the image to GitHub Packages.
+      # It uses the `context` parameter to define the build's context as the set of files located in the specified path. For more information, see [Usage](https://github.com/docker/build-push-action#usage) in the README of the `docker/build-push-action` repository.
+      # It uses the `tags` and `labels` parameters to tag and label the image with the output from the "meta" step.
+      - name: Build and push Docker image
+        id: push
+        uses: docker/build-push-action@v6
+        with:
+          context: .
+          push: true
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}
+      # This step generates an artifact attestation for the image, which is an unforgeable statement about where and how it was built. It increases supply chain security for people who consume the image. For more information, see [Using artifact attestations to establish provenance for builds](/actions/security-guides/using-artifact-attestations-to-establish-provenance-for-builds).
+      - name: Generate artifact attestation
+        uses: actions/attest-build-provenance@v2
+        with:
+          subject-name: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME}}
+          subject-digest: ${{ steps.push.outputs.digest }}
+          push-to-registry: true
+      

Dockerfile

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+FROM python:3.11-slim
+
+# Install required system packages, including git
+RUN apt-get update && apt-get install -y git && rm -rf /var/lib/apt/lists/*
+
+WORKDIR /app
+
+COPY requirements.txt .
+RUN pip install --upgrade pip
+RUN pip install --no-cache-dir -r requirements.txt
+
+COPY cratey.py LICENSE /app/
+COPY app /app/app
+
+RUN useradd -ms /bin/bash flaskuser
+RUN chown -R flaskuser:flaskuser /app
+
+USER flaskuser
+
+EXPOSE 5000
+
+CMD ["flask", "run", "--host=0.0.0.0"]
+
+LABEL org.opencontainers.image.source="https://github.com/eScienceLab/Cratey-Validator"

LICENSE

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+MIT License
+
+Copyright (c) 2025 eScience Lab, University of Manchester
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

README.md

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+# RO-Crate Validation Service
+
+This project presents a Flask-based API for validating RO-Crates.
+
+## Project Structure
+
+```
+app/
+├── ro_crates/
+│   ├── routes/
+│   │   ├── __init__.py         # Registers blueprints
+│   │   └── post_routes.py      # POST API routes
+│   └── __init__.py             
+├── services/
+│   ├── logging_service.py      # Centralised logging
+│   └── validation_service.py   # Queue RO-Crates for validation
+├── tasks/
+│   └── validation_tasks.py     # Validate RO-Crates
+├── utils/
+│   ├── config.py               # Configuration
+│   ├── minio_utils.py          # Methods for interacting with MinIO
+│   └── webhook_utils.py        # Methods for sending webhooks
+```
+
+## Setting up the project
+
+### Prerequisites
+
+- Docker with Docker Compose
+
+### Installation
+
+1. Clone the repository:
+    ```bash
+   git clone https://github.com/eScienceLab/Cratey-Validator.git
+   cd crate-validation-service
+   ```
+
+2. Create the `.env` file for shared environment information. An example environment file is included (`example.env`), which can be copied for this purpose. But make sure to change any security settings (username and passwords).
+
+3. Build and start the services using Docker Compose:
+    ```bash
+   docker compose up --build
+   ```
+
+4. Set up the MinIO bucket
+   1. Open the MinIO web interface at `http://localhost:9000`.  
+   2. Log in with your MinIO credentials.  
+   3. Create a new bucket named `ro-crates`.  
+   4. **Enable versioning** for the `ro-crates` bucket — this is important for tracking unique object versions.
+
+      ![Ensure MinIO versioning is enabled](docs/assets/minio-versioning-enabled.webp "Ensure MinIO versioning is enabled")
+
+   5. Upload your RO-Crate files to the `ro-crates` bucket.  
+   6. To verify that versioning is enabled:
+      - Select the uploaded RO-Crate object in the `ro-crates` bucket.
+      - Navigate to the **Actions** panel on the right.
+      - The **Display Object Versions** option should be clickable.
+
+      ![Validate MinIO versioning is enabled](docs/assets/validate-minio-versioning-enabled.webp "Validate MinIO versioning is enabled")
+
+
+## Development
+
+For standard usage the Docker Compose script uses prebuilt containers.
+For testing locally developed containers use the alternate Docker Compose file:
+```bash
+   docker compose --file docker-compose-develop.yml up --build
+``` 
+
+## Example Usage
+
+```
+curl -X 'POST' \
+  'http://localhost:5001/ro_crates/validate_by_id_no_webhook' \
+  -H 'accept: application/json' \
+  -H 'Content-Type: application/json' \
+  -d '{
+  "crate_id": "1"
+}'
+```

app.py

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+"""Initialises and configures Flask, integrates Celery, and registers application blueprints."""
+
+# Author: Alexander Hambley
+# License: MIT
+# Copyright (c) 2025 eScience Lab, The University of Manchester
+
+import os
+
+from apiflask import APIFlask
+
+from app.celery_worker import make_celery, celery
+from app.ro_crates.routes import ro_crates_post_bp, ro_crates_get_bp
+from app.utils.config import DevelopmentConfig, ProductionConfig, make_celery
+
+
+def create_app() -> APIFlask:
+    """
+    Creates and configures Flask application.
+
+    :return: Flask: A configured Flask application instance.
+    """
+    app = APIFlask(__name__)
+    app.register_blueprint(ro_crates_post_bp, url_prefix="/ro_crates")
+    app.register_blueprint(ro_crates_get_bp, url_prefix="/ro_crates")
+
+    # Load configuration:
+    if os.getenv("FLASK_ENV") == "production":
+        app.config.from_object(ProductionConfig)
+    else:
+        # Development environment:
+        app.debug = True
+        print("URL Map:")
+        for rule in app.url_map.iter_rules():
+            print(rule)
+        app.config.from_object(DevelopmentConfig)
+
+    # Integrate Celery
+    make_celery(app)
+
+    return app

app/__init__.py

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+"""Configures and initialises a Celery instance for use with a Flask application."""
+
+# Author: Alexander Hambley
+# License: MIT
+# Copyright (c) 2025 eScience Lab, The University of Manchester
+
+from celery import Celery
+from flask import Flask
+
+
+def make_celery(app: Flask = None) -> Celery:
+    """
+    Create and configure a Celery instance using Flask configuration.
+
+    :param app: The Flask application. Configuration will be used to initialise Celery.
+    :return: Celery: A configured Celery instance.
+    :raises ValueError: If the Flask configuration values are not provided.
+    """
+    if not app:
+        raise ValueError(
+            "A Flask application instance must be provided to configure Celery."
+        )
+
+    if "CELERY_RESULT_BACKEND" not in app.config:
+        raise ValueError(
+            "Missing configuration: 'CELERY_RESULT_BACKEND' is not defined in the Flask app config."
+        )
+
+    if "CELERY_BROKER_URL" not in app.config:
+        raise ValueError(
+            "Missing configuration: 'CELERY_BROKER_URL' is not defined in the Flask app config."
+        )
+
+    celery_instance = Celery(
+        app.import_name,
+        backend=app.config["CELERY_RESULT_BACKEND"],
+        broker=app.config["CELERY_BROKER_URL"],
+    )
+
+    if app:
+        celery_instance.conf.update(app.config)
+
+    return celery_instance
+
+
+celery = Celery()

app/celery_worker.py

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+"""Defines main Blueprint and registers sub-Blueprints for organising related routes."""
+
+# Author: Alexander Hambley
+# License: MIT
+# Copyright (c) 2025 eScience Lab, The University of Manchester
+
+from apiflask import APIBlueprint
+
+from app.ro_crates.routes.post_routes import post_routes_bp
+from app.ro_crates.routes.get_routes import get_routes_bp
+
+#ro_crates_bp = APIBlueprint("ro_crates", __name__)
+
+#ro_crates_bp.register_blueprint(post_routes_bp, url_prefix="/post")
+
+ro_crates_post_bp = post_routes_bp
+ro_crates_get_bp = get_routes_bp