version 1.0 API

.github/dependabot.yml

@@ -0,0 +1,6 @@
+version: 2
+updates:
+  - package-ecosystem: "pip"
+    directory: "/"
+    schedule:
+      interval: "weekly"

.github/workflows/test_docker.yml

@@ -0,0 +1,35 @@
+name: Integration Tests
+
+on:
+  pull_request:
+    branches: [ develop ]
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.11'
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install pytest requests minio docker
+
+      - name: Build Docker Compose Containers
+        run: |
+          cp example.env .env
+          docker compose -f docker-compose-develop.yml build 
+
+      - name: Spin Up Docker Compose and Run Tests
+        run: pytest -s -v tests/test_integration.py
+
+      - name: Ensure that Docker Compose is Shutdown
+        if: always()
+        run: docker compose down

.github/workflows/unit_tests.yml

@@ -0,0 +1,28 @@
+name: Unit Tests
+
+on:
+  pull_request:
+    branches: [ develop ]
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.11'
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -r requirements.txt
+          pip install pytest pytest-mock
+
+      - name: Run tests (excluding integration tests)
+        run: |
+          python -m pytest --ignore=tests/test_integration.py

README.md

@@ -70,12 +70,20 @@ For testing locally developed containers use the alternate Docker Compose file:
 
 ## Example Usage
 
-```
+Submission of validation of RO-Crate with the ID of `ro_crate_1`. No webhook is used here: 
+```bash
 curl -X 'POST' \
-  'http://localhost:5001/ro_crates/validate_by_id_no_webhook' \
+  'http://localhost:5001/ro_crates/v1/ro_crate_1/validation' \
+  -H 'accept: application/json' \
+  -H 'Content-Type: application/json' \
+  -d '{}'
+```
+
+Retrieval of validation result for RO-Crate `ro_crate_1`:
+```bash
+curl -X 'GET' \
+  'http://localhost:5001/ro_crates/v1/ro_crate_1/validation' \
   -H 'accept: application/json' \
   -H 'Content-Type: application/json' \
-  -d '{
-  "crate_id": "1"
-}'
+  -d '{}'
 ```

app/__init__.py

@@ -8,9 +8,9 @@
 
 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
+from app.ro_crates.routes import v1_post_bp, v1_get_bp
+from app.utils.config import DevelopmentConfig, ProductionConfig, InvalidAPIUsage, make_celery
+from flask import jsonify
 
 
 def create_app() -> APIFlask:
@@ -20,8 +20,12 @@ def create_app() -> APIFlask:
     :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")
+    app.register_blueprint(v1_post_bp, url_prefix="/v1/ro_crates")
+    app.register_blueprint(v1_get_bp, url_prefix="/v1/ro_crates")
+
+    @app.errorhandler(InvalidAPIUsage)
+    def invalid_api_usage(e):
+        return jsonify(e.to_dict()), e.status_code
 
     # Load configuration:
     if os.getenv("FLASK_ENV") == "production":

app/celery_worker.py

@@ -5,42 +5,6 @@
 # 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/ro_crates/routes/__init__.py

@@ -4,14 +4,8 @@
 # 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
+v1_post_bp = post_routes_bp
+v1_get_bp = get_routes_bp

app/ro_crates/routes/get_routes.py

@@ -5,25 +5,45 @@
 # Copyright (c) 2025 eScience Lab, The University of Manchester
 
 from apiflask import APIBlueprint, Schema
-from apiflask.fields import Integer, String
-from flask import request, Response
+from apiflask.fields import String, Boolean
+from marshmallow.fields import Nested
+from flask import Response
 
 from app.services.validation_service import get_ro_crate_validation_task
 
 get_routes_bp = APIBlueprint("get_routes", __name__)
 
-class validate_data(Schema):
-    crate_id = String(required=True)
 
+class MinioConfig(Schema):
+    endpoint = String(required=True)
+    accesskey = String(required=True)
+    secret = String(required=True)
+    ssl = Boolean(required=True)
+    bucket = String(required=True)
 
-@get_routes_bp.get("/get_validation_by_id")
-@get_routes_bp.input(validate_data(partial=True), location='json')
-def get_ro_crate_validation_by_id(json_data) -> tuple[Response, int]:
+
+class ValidateResult(Schema):
+    minio_config = Nested(MinioConfig, required=True)
+    root_path = String(required=False)
+
+
+@get_routes_bp.get("<string:crate_id>/validation")
+@get_routes_bp.input(ValidateResult(partial=False), location='json')
+def get_ro_crate_validation_by_id(json_data, crate_id) -> tuple[Response, int]:
     """
     Endpoint to obtain an RO-Crate validation result using its ID from MinIO.
 
-    Parameters:
-    - **crate_id**: The ID of the RO-Crate to validate. _Required_.
+    Path Parameters:
+    - **crate_id**: The RO-Crate ID. _Required_.
+
+    Request Body Parameters:
+    - **minio_config**: The MinIO bucket containing the RO-Crate. _Required_
+      - **endpoint**: Endpoint, e.g. 'localhost:9000'
+      - **accesskey**: Access key / username
+      - **secret**: Secret / password
+      - **ssl**: Use SSL encryption? True/False
+      - **bucket**: The MinIO bucket to access 
+    - **root_path**: The root path containing the RO-Crate. _Optional_
 
     Returns:
     - A tuple containing the validation result and an HTTP status code.
@@ -32,9 +52,11 @@ def get_ro_crate_validation_by_id(json_data) -> tuple[Response, int]:
     - KeyError: If required parameters (`crate_id`) are missing.
     """
 
-    try:
-        crate_id = json_data["crate_id"]
-    except:
-        raise KeyError("Missing required parameter: 'crate_id'")
+    minio_config = json_data["minio_config"]
+
+    if "root_path" in json_data:
+        root_path = json_data["root_path"]
+    else:
+        root_path = None
 
-    return get_ro_crate_validation_task(crate_id)
+    return get_ro_crate_validation_task(minio_config, crate_id, root_path)