chore: set up FOCA

deployment/Dockerfile

@@ -0,0 +1,21 @@
+##### BASE IMAGE #####
+FROM elixircloud/foca:20240711-py3.12
+
+##### METADATA ##### 
+LABEL software="Cloud Storage Handler"
+LABEL software.description="API for handling files on a cloud storage service"
+LABEL software.website="https://github.com/elixir-cloud-aai/tus-storagehandler"
+LABEL maintainer.organisation="ELIXIR Cloud & AAI"
+
+## Copy app files
+COPY ./tus_storage_handler /app
+
+## Install app
+RUN cd /app \
+  && poetry install \
+  && poetry shell \
+  && python app.py    
+
+WORKDIR /app
+
+CMD ["python", "tus_storage_handler/app.py"]

deployment/docker-compose.yaml

@@ -0,0 +1,11 @@
+version: '3.6'
+services:
+
+    cloud-registry:
+        image: elixircloud/csh:0.1.0
+        build:
+            context: .
+            dockerfile: Dockerfile
+        restart: unless-stopped
+        ports:
+            - "8080:8080"

pyproject.toml

@@ -23,7 +23,14 @@ repository = "https://github.com/elixir-cloud-aai/tus-storagehandler"
 version = "0.1.0"
 
 [tool.poetry.dependencies]
-python = ">=3.11"
+python = ">=3.11,<4.0"
+foca = "^0.13.0"
+connexion = "2.14.2"
+multipart = "^0.2.5"
+python-multipart = "^0.0.9"
+python-dotenv = "^1.0.1"
+pytest = "^8.3.2"
+requests = "^2.32.3"
 
 [tool.poetry.group.code_quality]
 optional = true

tests/test_integration/test_operations.py

@@ -0,0 +1,21 @@
+"""Integration tests for operations in the service."""
+
+import pytest
+import requests
+
+SUCCESS_STATUS_CODE = 200
+
+
+@pytest.fixture
+def base_url():
+    """Return the base URL for the service."""
+    return "http://localhost:8080"
+
+
+def test_get_root(base_url):
+    """Test the root endpoint of the service."""
+    response = requests.get(f"{base_url}/elixircoud/csh/v1")
+
+    assert (
+        response.status_code == SUCCESS_STATUS_CODE
+    ), f"Expected status code 200, got {response.status_code}"

tus_storagehandler/__init__.py

@@ -1 +1 @@
-"""This package contains module for the tus_storagehandler."""
+"""Cloud Storage Handler."""

tus_storagehandler/api/__init__.py

@@ -0,0 +1 @@
+"""API package."""

tus_storagehandler/api/elixircloud/__init__.py

@@ -0,0 +1 @@
+"""Elixircloud API package."""

tus_storagehandler/api/elixircloud/csh/__init__.py

@@ -0,0 +1 @@
+"""Cloud Storage Handler API package."""

tus_storagehandler/api/elixircloud/csh/controllers.py

@@ -0,0 +1,12 @@
+"""Cloud Storage Handler controllers."""
+
+import logging
+
+from flask import jsonify
+
+logger = logging.getLogger(__name__)
+
+
+def home():
+    """Endpoint to return a welcome message."""
+    return jsonify({"message": "Welcome to the Cloud Storage Handler server!"}), 200

tus_storagehandler/app.py

@@ -0,0 +1,57 @@
+"""API server entry point."""
+
+import logging
+import os
+from pathlib import Path
+
+from connexion import FlaskApp  # type: ignore
+from dotenv import load_dotenv  # type: ignore
+from foca import Foca
+
+load_dotenv()
+logger = logging.getLogger(__name__)
+
+
+def init_app() -> FlaskApp:
+    """Initialize and return the FOCA app.
+
+    This function initializes the FOCA app by loading the configuration
+    from the environment variable `TUS_FOCA_CONFIG_PATH` if set, or from
+    the default path if not. It raises a `FileNotFoundError` if the
+    configuration file is not found.
+
+    Returns:
+        A Connexion application instance.
+
+    Raises:
+        FileNotFoundError: If the configuration file is not found.
+    """
+    # Determine the configuration path
+    config_path_env1 = os.getenv("TUS_FOCA_CONFIG_PATH")
+    print(config_path_env1)
+    if config_path_env := os.getenv("TUS_FOCA_CONFIG_PATH"):
+        print(config_path_env)
+        config_path = Path(config_path_env).resolve()
+    else:
+        config_path = (
+            Path(__file__).parents[1] / "deployment" / "config.yaml"
+        ).resolve()
+
+    # Check if the configuration file exists
+    if not config_path.exists():
+        raise FileNotFoundError(f"Config file not found at: {config_path}")
+
+    foca = Foca(
+        config_file=config_path,
+    )
+    return foca.create_app()
+
+
+def main() -> None:
+    """Run FOCA application."""
+    app = init_app()
+    app.run(port=app.port)
+
+
+if __name__ == "__main__":
+    main()

tus_storagehandler/config.yaml

@@ -0,0 +1,40 @@
+server:
+    host: '0.0.0.0'
+    port: 8080
+    debug: False
+    environment: development
+    testing: False
+    use_reloader: True
+
+security:
+    auth:
+        required: True
+        add_key_to_claims: True
+        allow_expired: False
+        audience: null
+        claim_identity: sub
+        claim_issuer: iss
+        algorithms:
+          - RS256
+        validation_methods:
+          - userinfo
+          - public_key
+        validation_checks: all
+
+api:
+    specs:
+        - path: storage_handler.yaml
+          append: null
+          add_operation_fields:
+              x-openapi-router-controller: tus_storagehandler.api.elixircloud.csh.controllers 
+          connexion:
+              strict_validation: True
+              validate_responses: False
+              options:
+                  swagger_ui: True
+                  serve_spec: True
+
+exceptions:
+    required_members: [['message'], ['code']]
+    status_member: ['code']
+    exceptions: exceptions.exceptions

tus_storagehandler/exceptions.py

@@ -0,0 +1,22 @@
+"""Tus Storage Handler exceptions."""
+
+from werkzeug.exceptions import BadRequest, InternalServerError, NotFound
+
+exceptions = {
+    Exception: {
+        "message": "An unexpected error occurred. Please try again.",
+        "code": 500,
+    },
+    BadRequest: {
+        "message": "Invalid request. Please check your input and try again.",
+        "code": 400,
+    },
+    NotFound: {
+        "message": "The requested resource could not be found.",
+        "code": 404,
+    },
+    InternalServerError: {
+        "message": "An internal server error occurred in the tus storage handler",
+        "code": 500,
+    },
+}

tus_storagehandler/storage_handler.yaml

@@ -0,0 +1,34 @@
+openapi: 3.0.2
+info:
+  version: 1.0.0
+  title: Cloud Storage Handler
+  description: API for handling files on a cloud storage service
+  contact:
+    name: ELIXIR Cloud & AAI
+    email: [email protected]
+  license:
+    name: Apache 2.0
+    url: 'https://github.com/elixir-cloud-aai/tus-storagehandler/blob/main/LICENSE'
+servers:
+  - url: /elixircoud/csh/v1
+paths:
+  /:
+    get:
+      description: |
+        Returns a welcome message
+      operationId: home
+      responses:
+        '200':
+          description: basic response
+          content:
+            application/json:
+              schema:
+                type: object
+                properties:
+                  message:
+                    type: string
+                    example: "Welcome to Tus Storage Handler API"
+        '400':
+          description: The request is malformed.
+        '500':
+          description: An unexpected error occurred.