diff --git a/.cruft.json b/.cruft.json index a5de21c..0bc1c0d 100644 --- a/.cruft.json +++ b/.cruft.json @@ -8,7 +8,7 @@ "author_email": "cloud-service@elixir-europe.org", "development_status": "1 - Planning", "short_description": "File handler utilizing TUS and MinIO with DRS-Filer integration.", - "project_name": "tus-storagehandler", + "project_name": "tus_storagehandler", "project_slug": "tus_storagehandler", "github_username": "elixir-cloud-aai", "python_version": "3.11", diff --git a/.github/ISSUE_TEMPLATE/general-purpose.md b/.github/ISSUE_TEMPLATE/general-purpose.md index 8f6f2cf..21868c7 100644 --- a/.github/ISSUE_TEMPLATE/general-purpose.md +++ b/.github/ISSUE_TEMPLATE/general-purpose.md @@ -46,4 +46,4 @@ bug in --> - Operating System and version (desktop or mobile): - Link to your project: -[issue-tracker]: https://github.com/elixir-cloud-aai/tus-storagehandler/issues +[issue-tracker]: https://github.com/elixir-cloud-aai/tus_storagehandler/issues diff --git a/.github/workflows/run-application.yaml b/.github/workflows/run-application.yaml new file mode 100644 index 0000000..509b034 --- /dev/null +++ b/.github/workflows/run-application.yaml @@ -0,0 +1,48 @@ +--- +name: Run Application + +on: + push: + branches: + - main + pull_request: + branches: + - main + +jobs: + build: + runs-on: ubuntu-latest + + steps: + - name: Checkout code + uses: actions/checkout@v3 + + - name: Set up Python + uses: actions/setup-python@v4 + with: + python-version: '3.11' + + - name: Install Poetry + run: | + curl -sSL https://install.python-poetry.org | python3 - + echo "$HOME/.local/bin" >> $GITHUB_PATH + + - name: Activate environment and install dependencies + run: | + make v + source .venv/bin/activate + make i + + - name: Start server in the background + run: | + tus_storagehandler & + echo $! > server.pid + + - name: Run tests + run: | + poetry run pytest tests/test_integration + + - name: Stop server + run: | + kill $(cat server.pid) || true +... diff --git a/.markdownlint.yaml b/.markdownlint.yaml index a051501..b452f0d 100644 --- a/.markdownlint.yaml +++ b/.markdownlint.yaml @@ -65,7 +65,7 @@ MD037: true # Spaces inside emphasis markers MD038: true # Spaces inside code span elements MD039: true # Spaces inside link elements MD040: true # Fenced code blocks should have a language specified -MD041: false # First line need not be h1 +MD041: false # First line need not be h1 MD046: true # Code block style MD047: true # Files should end with a single newline character MD048: true # Code fence style diff --git a/README.md b/README.md index a18000a..7d619c2 100644 --- a/README.md +++ b/README.md @@ -18,6 +18,7 @@ File handler utilizing TUS and MinIO with DRS-Filer integration. - [Basic Usage](#basic-usage) - [Installation](#installation) - [Development](#development) +- [Environment Variables](#environment-variables) - [Contributing](#contributing) - [Code of Conduct](#code-of-conduct) - [Versioning](#versioning) @@ -25,7 +26,10 @@ File handler utilizing TUS and MinIO with DRS-Filer integration. - [Contact](#contact) ## Synopsis -This application provides endpoints for uploading, downloading, and listing files in a MinIO bucket, with TUS protocol support for uploads, and CORS enabled for cross-origin requests. + +This application provides endpoints for uploading, downloading, and listing +files in a MinIO bucket, with TUS protocol support for uploads, and CORS enabled +for cross-origin requests. ## Basic Usage @@ -33,9 +37,11 @@ This application provides endpoints for uploading, downloading, and listing file ### Prerequisites -This flask application requires a running instance of [minio](https://min.io/download) +This Flask application requires a running instance of +[MinIO](https://min.io/download). -Run the minio instance by executing the following command in the location where minio is installed +Run the MinIO instance by executing the following command in the location where +MinIO is installed: ```sh minio server /data --console-address ":9001" @@ -43,28 +49,45 @@ minio server /data --console-address ":9001" ### Install Dependencies using Poetry -1. **Download the required dependencies** +1. **Clone the Repository** + + To get started, first, clone the repository using the following command: + + ```sh + git clone https://github.com/elixir-cloud-aai/tus-storagehandler.git + ``` + +1. **Navigate to the package folder** + + Navigate to the folder `tus_storagehandler`: + + ```sh + cd tus_storagehandler + ``` - Navigate to the folder `tus_storagehandler`. +1. **Install Poetry** -2. **Install Poetry** + If you haven't already, install Poetry by following the instructions on the + [Poetry website](https://python-poetry.org/docs/#installation). - If you haven't already, install Poetry by following the instructions on the [Poetry website](https://python-poetry.org/docs/#installation). +1. **Create and Activate a Virtual Environment (optional)** -3. **Create and Activate a Virtual Environment (optional)** + Poetry automatically creates and manages a virtual environment for your + project. You can activate it using: - Poetry automatically creates and manages a virtual environment for your project. You can activate it using: ```sh poetry shell ``` -4. **Install Dependencies** +1. **Install Dependencies** + + Run the following command to install the dependencies defined in the + `pyproject.toml` file: - Run the following command to install the dependencies defined in the `pyproject.toml` file: ```sh poetry install ``` - + ## Development For ease of use, certain scripts have been abbreviated in `Makefile`, make sure @@ -157,6 +180,16 @@ make u > **Note**: This is not the complete list of commands, run `make` to find out if > more have been added. +## Environment Variables + + + +| **Environment Variable** | **Description** | **Usage** | **Error Handling** | +|--|--|--|--| +| `CSH_FOCA_CONFIG_PATH` | Specifies the path to the configuration file for the FOCA app. | The FOCA app uses this environment variable to locate the configuration file. If not set, it defaults to `dev`. | If the configuration file is not found at the specified or default path, a `FileNotFoundError` will be raised. | + + + ## Contributing This project is a community effort and lives off _your_ contributions, be it in diff --git a/deployment/config.yaml b/deployment/config.yaml new file mode 100644 index 0000000..abd7679 --- /dev/null +++ b/deployment/config.yaml @@ -0,0 +1,42 @@ +--- +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: tus_storagehandler/api/specs/specs.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: tus_storagehandler.exceptions.exceptions +... diff --git a/docs/source/pages/tus_storagehandler.api.elixircloud.csh.rst b/docs/source/pages/tus_storagehandler.api.elixircloud.csh.rst new file mode 100644 index 0000000..5f59f96 --- /dev/null +++ b/docs/source/pages/tus_storagehandler.api.elixircloud.csh.rst @@ -0,0 +1,21 @@ +tus\_storagehandler.api.elixircloud.csh package +=============================================== + +Submodules +---------- + +tus\_storagehandler.api.elixircloud.csh.controllers module +---------------------------------------------------------- + +.. automodule:: tus_storagehandler.api.elixircloud.csh.controllers + :members: + :undoc-members: + :show-inheritance: + +Module contents +--------------- + +.. automodule:: tus_storagehandler.api.elixircloud.csh + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/source/pages/tus_storagehandler.api.elixircloud.rst b/docs/source/pages/tus_storagehandler.api.elixircloud.rst new file mode 100644 index 0000000..013bba5 --- /dev/null +++ b/docs/source/pages/tus_storagehandler.api.elixircloud.rst @@ -0,0 +1,18 @@ +tus\_storagehandler.api.elixircloud package +=========================================== + +Subpackages +----------- + +.. toctree:: + :maxdepth: 4 + + tus_storagehandler.api.elixircloud.csh + +Module contents +--------------- + +.. automodule:: tus_storagehandler.api.elixircloud + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/source/pages/tus_storagehandler.api.rst b/docs/source/pages/tus_storagehandler.api.rst new file mode 100644 index 0000000..b645718 --- /dev/null +++ b/docs/source/pages/tus_storagehandler.api.rst @@ -0,0 +1,18 @@ +tus\_storagehandler.api package +=============================== + +Subpackages +----------- + +.. toctree:: + :maxdepth: 4 + + tus_storagehandler.api.elixircloud + +Module contents +--------------- + +.. automodule:: tus_storagehandler.api + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/source/pages/tus_storagehandler.rst b/docs/source/pages/tus_storagehandler.rst index 50d75ff..8dc0616 100644 --- a/docs/source/pages/tus_storagehandler.rst +++ b/docs/source/pages/tus_storagehandler.rst @@ -1,13 +1,29 @@ tus\_storagehandler package =========================== +Subpackages +----------- + +.. toctree:: + :maxdepth: 4 + + tus_storagehandler.api + Submodules ---------- -tus\_storagehandler.main module -------------------------------- +tus\_storagehandler.app module +------------------------------ + +.. automodule:: tus_storagehandler.app + :members: + :undoc-members: + :show-inheritance: + +tus\_storagehandler.exceptions module +------------------------------------- -.. automodule:: tus_storagehandler.main +.. automodule:: tus_storagehandler.exceptions :members: :undoc-members: 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"sha256:90c079ff05e549f6bf50e02e910210b98b8ff1ebdd18e19c873cd237737c1358"}, + {file = "types_requests-2.32.0.20240712-py3-none-any.whl", hash = "sha256:f754283e152c752e46e70942fa2a146b5bc70393522257bb85bd1ef7e019dcc3"}, +] + +[package.dependencies] +urllib3 = ">=2" + +[[package]] +name = "typing" +version = "3.7.4.3" +description = "Type Hints for Python" +optional = false +python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" +files = [ + {file = "typing-3.7.4.3-py2-none-any.whl", hash = "sha256:283d868f5071ab9ad873e5e52268d611e851c870a2ba354193026f2dfb29d8b5"}, + {file = "typing-3.7.4.3.tar.gz", hash = "sha256:1187fb9c82fd670d10aa07bbb6cfcfe4bdda42d6fab8d5134f04e8c4d0b71cc9"}, +] + [[package]] name = "typing-extensions" version = "4.12.2" @@ -1846,6 +2560,17 @@ files = [ {file = "typos-1.23.6.tar.gz", hash = "sha256:2691988d2a15cde2cdd4f2fa5fd32880765b2a68ed6ccd48d6dc693c44447bcf"}, ] +[[package]] +name = "tzdata" +version = "2024.1" +description = "Provider of IANA time zone data" +optional = false +python-versions = ">=2" +files = [ + {file = "tzdata-2024.1-py2.py3-none-any.whl", hash = "sha256:9068bc196136463f5245e51efda838afa15aaeca9903f49050dfa2679db4d252"}, + {file = "tzdata-2024.1.tar.gz", hash = "sha256:2674120f8d891909751c38abcdfd386ac0a5a1127954fbc332af6b5ceae07efd"}, +] + [[package]] name = "urllib3" version = "2.2.2" @@ -1863,6 +2588,17 @@ h2 = ["h2 (>=4,<5)"] socks = ["pysocks (>=1.5.6,!=1.5.7,<2.0)"] zstd = ["zstandard (>=0.18.0)"] +[[package]] +name = "vine" +version = "5.1.0" +description = "Python promises." +optional = false +python-versions = ">=3.6" +files = [ + {file = "vine-5.1.0-py3-none-any.whl", hash = "sha256:40fdf3c48b2cfe1c38a49e9ae2da6fda88e4794c810050a728bd7413811fb1dc"}, + {file = "vine-5.1.0.tar.gz", hash = "sha256:8b62e981d35c41049211cf62a0a1242d8c1ee9bd15bb196ce38aefd6799e61e0"}, +] + [[package]] name = "virtualenv" version = "20.26.3" @@ -1883,7 +2619,35 @@ platformdirs = ">=3.9.1,<5" docs = ["furo (>=2023.7.26)", "proselint (>=0.13)", "sphinx (>=7.1.2,!=7.3)", "sphinx-argparse (>=0.4)", "sphinxcontrib-towncrier (>=0.2.1a0)", "towncrier (>=23.6)"] test = ["covdefaults (>=2.3)", "coverage (>=7.2.7)", "coverage-enable-subprocess (>=1)", "flaky (>=3.7)", "packaging (>=23.1)", "pytest (>=7.4)", "pytest-env (>=0.8.2)", "pytest-freezer (>=0.4.8)", "pytest-mock (>=3.11.1)", "pytest-randomly (>=3.12)", "pytest-timeout (>=2.1)", "setuptools (>=68)", "time-machine (>=2.10)"] +[[package]] +name = "wcwidth" +version = "0.2.13" +description = "Measures the displayed width of unicode strings in a terminal" +optional = false +python-versions = "*" +files = [ + {file = "wcwidth-0.2.13-py2.py3-none-any.whl", hash = "sha256:3da69048e4540d84af32131829ff948f1e022c1c6bdb8d6102117aac784f6859"}, + {file = "wcwidth-0.2.13.tar.gz", hash = "sha256:72ea0c06399eb286d978fdedb6923a9eb47e1c486ce63e9b4e64fc18303972b5"}, +] + +[[package]] +name = "werkzeug" +version = "2.3.8" +description = "The comprehensive WSGI web application library." +optional = false +python-versions = ">=3.8" +files = [ + {file = "werkzeug-2.3.8-py3-none-any.whl", hash = "sha256:bba1f19f8ec89d4d607a3bd62f1904bd2e609472d93cd85e9d4e178f472c3748"}, + {file = "werkzeug-2.3.8.tar.gz", hash = "sha256:554b257c74bbeb7a0d254160a4f8ffe185243f52a52035060b761ca62d977f03"}, +] + +[package.dependencies] +MarkupSafe = ">=2.1.1" + +[package.extras] +watchdog = ["watchdog (>=2.3)"] + [metadata] lock-version = "2.0" -python-versions = ">=3.11" -content-hash = "4027347a21d17f010b9a18def7ea8f7a3983138948ac5e98cb24f4292b2cadab" +python-versions = ">=3.11,<4.0" +content-hash = "43ba118188416b06b0408c02bfd4def3b77f632639bf22d168dfb645cc323c36" diff --git a/pyproject.toml b/pyproject.toml index c5d5c59..6a11168 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -6,6 +6,13 @@ requires = ["poetry-core"] warn_return_any = true warn_unused_configs = true +[[tool.mypy.overrides]] +ignore_missing_imports = true +module = [ + "connexion.*", + "foca", +] + [tool.poetry] authors = ["ELIXIR Cloud AAI "] classifiers = [ @@ -19,11 +26,14 @@ license = "Apache-2.0" maintainers = ["ELIXIR Cloud AAI "] name = "tus_storagehandler" readme = "README.md" -repository = "https://github.com/elixir-cloud-aai/tus-storagehandler" +repository = "https://github.com/elixir-cloud-aai/tus_storagehandler" version = "0.1.0" [tool.poetry.dependencies] -python = ">=3.11" +flask = "2.2.3" +foca = "^0.13.0" +python = ">=3.11,<4.0" +sphinx = "^8.0.2" [tool.poetry.group.code_quality] optional = true @@ -34,7 +44,7 @@ ruff = ">=0.4.10" typos = ">=1.22.8" [tool.poetry.group.docs] -optional = true +optional = false [tool.poetry.group.docs.dependencies] added-value = ">=0.24.0" @@ -64,6 +74,7 @@ pytest-cov = ">=5.0.0,<=6.0.0" optional = true [tool.poetry.group.types.dependencies] +types-requests = "^2.32.0.20240712" [tool.poetry.group.vulnerability] optional = true @@ -73,7 +84,7 @@ bandit = ">=1.7.8,<2.0.0" safety = ">=3.2.0,<4.0.0" [tool.poetry.scripts] -tus_storagehandler = "tus_storagehandler.main:main" +tus_storagehandler = "tus_storagehandler.app:main" [tool.ruff] indent-width = 4 diff --git a/tests/test_integration/test_operations.py b/tests/test_integration/test_operations.py new file mode 100644 index 0000000..51b6d3c --- /dev/null +++ b/tests/test_integration/test_operations.py @@ -0,0 +1,29 @@ +"""Test operations for the tus-storagehandler service.""" + +from http import HTTPStatus +from unittest import mock + +import requests + + +def test_get_root(): + """Test the root endpoint of the service with a mocked response.""" + print("Starting test_get_root...") + + server_url = "http://localhost:8080/elixircoud/csh/v1" + + with mock.patch("requests.get") as mock_get: + mock_response = mock.Mock() + mock_response.status_code = HTTPStatus.OK + mock_get.return_value = mock_response + + response = requests.get(server_url) + print(f"Response status code: {response.status_code}") + + assert ( + response.status_code == HTTPStatus.OK + ), f"Expected status code 200, got {response.status_code}" + + mock_get.assert_called_once_with(server_url) + + print("Finished test_get_root") diff --git a/tus_storagehandler/__init__.py b/tus_storagehandler/__init__.py index 9f8346a..795090d 100644 --- a/tus_storagehandler/__init__.py +++ b/tus_storagehandler/__init__.py @@ -1 +1 @@ -"""This package contains module for the tus_storagehandler.""" +"""Cloud Storage Handler.""" diff --git a/tus_storagehandler/api/__init__.py b/tus_storagehandler/api/__init__.py new file mode 100644 index 0000000..dff53e5 --- /dev/null +++ b/tus_storagehandler/api/__init__.py @@ -0,0 +1 @@ +"""API package.""" diff --git a/tus_storagehandler/api/elixircloud/__init__.py b/tus_storagehandler/api/elixircloud/__init__.py new file mode 100644 index 0000000..355afdf --- /dev/null +++ b/tus_storagehandler/api/elixircloud/__init__.py @@ -0,0 +1 @@ +"""ELIXIR Cloud API package.""" diff --git a/tus_storagehandler/api/elixircloud/csh/__init__.py b/tus_storagehandler/api/elixircloud/csh/__init__.py new file mode 100644 index 0000000..d4a6564 --- /dev/null +++ b/tus_storagehandler/api/elixircloud/csh/__init__.py @@ -0,0 +1 @@ +"""ELIXIR Cloud Storage Handler API package.""" diff --git a/tus_storagehandler/api/elixircloud/csh/controllers.py b/tus_storagehandler/api/elixircloud/csh/controllers.py new file mode 100644 index 0000000..b70a045 --- /dev/null +++ b/tus_storagehandler/api/elixircloud/csh/controllers.py @@ -0,0 +1,15 @@ +"""Cloud Storage Handler controllers.""" + +import logging +from http import HTTPStatus + +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!"} + ), HTTPStatus.OK diff --git a/tus_storagehandler/api/specs/specs.yaml b/tus_storagehandler/api/specs/specs.yaml new file mode 100644 index 0000000..cf3af80 --- /dev/null +++ b/tus_storagehandler/api/specs/specs.yaml @@ -0,0 +1,38 @@ +--- +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: cloud-service@elixir-europe.org + 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. +... diff --git a/tus_storagehandler/app.py b/tus_storagehandler/app.py new file mode 100644 index 0000000..c7d499c --- /dev/null +++ b/tus_storagehandler/app.py @@ -0,0 +1,53 @@ +"""API server entry point.""" + +import logging +import os +from pathlib import Path + +from connexion import FlaskApp +from foca import Foca + +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 `CSH_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 + if config_path_env := os.getenv("CSH_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() diff --git a/tus_storagehandler/exceptions.py b/tus_storagehandler/exceptions.py new file mode 100644 index 0000000..26b784b --- /dev/null +++ b/tus_storagehandler/exceptions.py @@ -0,0 +1,24 @@ +"""Tus Storage Handler exceptions.""" + +from http import HTTPStatus + +from werkzeug.exceptions import BadRequest, InternalServerError, NotFound + +exceptions = { + Exception: { + "message": "An unexpected error occurred. Please try again.", + "code": HTTPStatus.INTERNAL_SERVER_ERROR, # 500 + }, + BadRequest: { + "message": "Invalid request. Please check your input and try again.", + "code": HTTPStatus.BAD_REQUEST, # 400 + }, + NotFound: { + "message": "The requested resource could not be found.", + "code": HTTPStatus.NOT_FOUND, # 404 + }, + InternalServerError: { + "message": "An internal server error occurred in the tus storage handler", + "code": HTTPStatus.INTERNAL_SERVER_ERROR, # 500 + }, +} diff --git a/tus_storagehandler/main.py b/tus_storagehandler/main.py deleted file mode 100644 index c1c8f60..0000000 --- a/tus_storagehandler/main.py +++ /dev/null @@ -1,10 +0,0 @@ -"""Entry point for tus_storagehandler.""" - - -def main(): - """Main entry point for tus_storagehandler.""" - print("Hello from tus_storagehandler!") - - -if __name__ == "__main__": - main()