diff --git a/README.md b/README.md index bfafbac..2528c8b 100644 --- a/README.md +++ b/README.md @@ -12,6 +12,9 @@ these can also be read from a minIO instance (or AWS S3 for that matter). ## Environment Variables +Set `SERVICE_URL` to the base URL of the service (e.g. `https://bentov2.local/api/drop-box`). +This is used for file URI generation. + If using the current filesystem to serve file, you can use the `SERVICE_DATA` environment variable to point to some location (./data by default). diff --git a/bento_drop_box_service/app.py b/bento_drop_box_service/app.py index 4649baa..10aedce 100644 --- a/bento_drop_box_service/app.py +++ b/bento_drop_box_service/app.py @@ -26,6 +26,7 @@ SERVICE_ID=os.environ.get("SERVICE_ID", str(":".join(list(SERVICE_TYPE.values())[:2]))), SERVICE_DATA_SOURCE="minio" if MINIO_URL else "local", SERVICE_DATA=None if MINIO_URL else SERVICE_DATA, + SERVICE_URL=os.environ.get("SERVICE_URL", "http://127.0.0.1:5000"), # base URL to construct object URIs from MINIO_URL=MINIO_URL, MINIO_USERNAME=os.environ.get("MINIO_USERNAME") if MINIO_URL else None, MINIO_PASSWORD=os.environ.get("MINIO_PASSWORD") if MINIO_URL else None, diff --git a/bento_drop_box_service/backend.py b/bento_drop_box_service/backend.py index 7000f55..511bd5e 100644 --- a/bento_drop_box_service/backend.py +++ b/bento_drop_box_service/backend.py @@ -19,10 +19,10 @@ async def _get_backend() -> Optional[DropBoxBackend]: # Make data directory/ies if needed if current_app.config["SERVICE_DATA_SOURCE"] == "local": os.makedirs(current_app.config["SERVICE_DATA"], exist_ok=True) - return LocalBackend() + return LocalBackend(logger=current_app.logger) elif current_app.config["SERVICE_DATA_SOURCE"] == "minio": - return MinioBackend() + return MinioBackend(logger=current_app.logger) return None diff --git a/bento_drop_box_service/backends/base.py b/bento_drop_box_service/backends/base.py index 4e50223..781a27b 100644 --- a/bento_drop_box_service/backends/base.py +++ b/bento_drop_box_service/backends/base.py @@ -1,3 +1,4 @@ +import logging from abc import ABC, abstractmethod from typing import Tuple from werkzeug import Request, Response @@ -7,6 +8,9 @@ class DropBoxBackend(ABC): + def __init__(self, logger: logging.Logger): + self.logger = logger + @abstractmethod async def get_directory_tree(self) -> Tuple[dict]: pass diff --git a/bento_drop_box_service/backends/local.py b/bento_drop_box_service/backends/local.py index 7e6fa49..132a807 100644 --- a/bento_drop_box_service/backends/local.py +++ b/bento_drop_box_service/backends/local.py @@ -4,45 +4,69 @@ import aiofiles.os import aiofiles.ospath import os +import pathlib from bento_lib.responses.quart_errors import quart_bad_request_error, quart_not_found_error -from typing import TypedDict +from typing import Tuple, TypedDict from quart import current_app, send_file, Request, Response from werkzeug.utils import secure_filename from .base import DropBoxBackend +# TODO: py3.10: remove in favour of [str].removeprefix(...) +def _str_removeprefix_polyfill(s: str, prefix: str) -> str: + return s[len(prefix):] if s.startswith(prefix) else s + + # TODO: py3.11: individual optional fields class DropBoxEntry(TypedDict, total=False): name: str - path: str + filePath: str + uri: str size: int contents: tuple[DropBoxEntry, ...] class LocalBackend(DropBoxBackend): - async def _get_directory_tree(self, directory: str, level: int = 0) -> tuple[DropBoxEntry, ...]: + async def _get_directory_tree( + self, + root_path: pathlib.Path, + sub_path: Tuple[str, ...], + level: int = 0, + ) -> tuple[DropBoxEntry, ...]: + root_path = root_path.absolute() entries: list[DropBoxEntry] = [] - # for some reason this doesn't work as a comprehension + sub_path_str: str = "/".join(sub_path) + current_dir = (root_path / sub_path_str).absolute() # noinspection PyUnresolvedReferences - for entry in (await aiofiles.os.listdir(directory)): + for entry in (await aiofiles.os.listdir(current_dir)): if (level < current_app.config["TRAVERSAL_LIMIT"] or not ( - await aiofiles.ospath.isdir(os.path.join(directory, entry)))) and entry[0] != ".": + await aiofiles.ospath.isdir(current_dir))) and entry[0] != ".": + if "/" in entry: + self.logger.warning(f"Skipped entry with a '/' in its name: {entry}") + continue + entry_path = current_dir / entry entries.append({ "name": entry, - "path": os.path.abspath(os.path.join(directory, entry)), + "filePath": str(entry_path), **({ - "contents": await self._get_directory_tree(os.path.join(directory, entry), level=level + 1), - } if (await aiofiles.ospath.isdir(os.path.join(directory, entry))) else { - "size": await aiofiles.ospath.getsize(os.path.join(directory, entry)), + "contents": await self._get_directory_tree(root_path, (*sub_path, entry), level=level + 1), + } if (await aiofiles.ospath.isdir(entry_path)) else { + "size": await aiofiles.ospath.getsize(entry_path), + "uri": ( + current_app.config["SERVICE_URL"] + + "/objects" + + _str_removeprefix_polyfill(str(entry_path), str(root_path)) + ), }) }) return tuple(entries) async def get_directory_tree(self) -> tuple[DropBoxEntry, ...]: - return await self._get_directory_tree(current_app.config["SERVICE_DATA"]) + root_path: pathlib.Path = pathlib.Path(current_app.config["SERVICE_DATA"]) + return await self._get_directory_tree(root_path, (".",)) async def upload_to_path(self, request: Request, path: str, content_length: int) -> Response: # TODO: This might not be secure (ok for now due to permissions check) @@ -68,10 +92,14 @@ async def upload_to_path(self, request: Request, path: str, content_length: int) return current_app.response_class(status=204) async def retrieve_from_path(self, path: str) -> Response: + root_path: pathlib.Path = pathlib.Path(current_app.config["SERVICE_DATA"]).absolute() directory_items: tuple[DropBoxEntry, ...] = await self.get_directory_tree() + # Manually crawl through the tree to only return items which are explicitly in the tree. + # Otherwise, find the file if it exists and return it. - path_parts: list[str] = path.split("/") # TODO: Deal with slashes in file names + # TODO: Deal with slashes in file names + path_parts: list[str] = _str_removeprefix_polyfill(path, str(root_path)).lstrip("/").split("/") while len(path_parts) > 0: part = path_parts[0] @@ -87,8 +115,11 @@ async def retrieve_from_path(self, path: str) -> Response: if len(path_parts) > 0: return quart_bad_request_error("Cannot retrieve a directory") - return await send_file(node["path"], mimetype="application/octet-stream", as_attachment=True, - attachment_filename=node["name"]) + return await send_file( + node["filePath"], + mimetype="application/octet-stream", + as_attachment=True, + attachment_filename=node["name"]) directory_items = node["contents"] diff --git a/bento_drop_box_service/backends/minio.py b/bento_drop_box_service/backends/minio.py index eda80d6..5bcf767 100644 --- a/bento_drop_box_service/backends/minio.py +++ b/bento_drop_box_service/backends/minio.py @@ -1,4 +1,5 @@ import boto3 +import logging from typing import Tuple from botocore.exceptions import ClientError @@ -11,8 +12,8 @@ class MinioBackend(DropBoxBackend): - def __init__(self, resource=None): - super(MinioBackend, self).__init__() + def __init__(self, logger: logging.Logger, resource=None): + super(MinioBackend, self).__init__(logger) if resource: self.minio = resource diff --git a/bento_drop_box_service/routes.py b/bento_drop_box_service/routes.py index 4b12455..00280e9 100644 --- a/bento_drop_box_service/routes.py +++ b/bento_drop_box_service/routes.py @@ -1,10 +1,11 @@ +import asyncio from quart import Blueprint, current_app, jsonify, request, Response from bento_lib.auth.quart_decorators import quart_permissions_owner from bento_lib.responses.quart_errors import ( quart_bad_request_error, quart_internal_server_error ) -from bento_lib.types import GA4GHServiceInfo +from bento_lib.types import GA4GHServiceInfo, BentoExtraServiceInfo from bento_drop_box_service import __version__ from bento_drop_box_service.backend import get_backend from bento_drop_box_service.constants import BENTO_SERVICE_KIND, SERVICE_NAME, SERVICE_TYPE @@ -46,9 +47,37 @@ async def drop_box_retrieve(path) -> Response: return await backend.retrieve_from_path(path) +async def _git_stdout(*args) -> str: + git_proc = await asyncio.create_subprocess_exec( + "git", *args, stdout=asyncio.subprocess.PIPE, stderr=asyncio.subprocess.PIPE) + res, _ = await git_proc.communicate() + return res.decode().rstrip() + + @drop_box_service.route("/service-info", methods=["GET"]) async def service_info() -> Response: # Spec: https://github.com/ga4gh-discovery/ga4gh-service-info + + bento_info: BentoExtraServiceInfo = { + "serviceKind": BENTO_SERVICE_KIND + } + + debug_mode = current_app.config["BENTO_DEBUG"] + if debug_mode: + try: + if res_tag := await _git_stdout("describe", "--tags", "--abbrev=0"): + # noinspection PyTypeChecker + bento_info["gitTag"] = res_tag + if res_branch := await _git_stdout("branch", "--show-current"): + # noinspection PyTypeChecker + bento_info["gitBranch"] = res_branch + if res_commit := await _git_stdout("rev-parse", "HEAD"): + # noinspection PyTypeChecker + bento_info["gitCommit"] = res_commit + + except Exception as e: + current_app.logger.error(f"Error retrieving git information: {type(e).__name__}") + # Do a little type checking info: GA4GHServiceInfo = { "id": current_app.config["SERVICE_ID"], @@ -62,8 +91,7 @@ async def service_info() -> Response: "contactUrl": "mailto:info@c3g.ca", "version": __version__, "environment": "dev" if current_app.config["BENTO_DEBUG"] else "prod", - "bento": { - "serviceKind": BENTO_SERVICE_KIND, - }, + "bento": bento_info, } + return jsonify(info) diff --git a/poetry.lock b/poetry.lock index ede1faa..0f99c2b 100644 --- a/poetry.lock +++ b/poetry.lock @@ -169,14 +169,14 @@ tests-no-zope = ["cloudpickle", "cloudpickle", "hypothesis", "hypothesis", "mypy [[package]] name = "bento-lib" -version = "5.2.0" +version = "5.4.0" description = "A set of common utilities and helpers for Bento platform services." category = "main" optional = false python-versions = ">=3.8" files = [ - {file = "bento_lib-5.2.0-py3-none-any.whl", hash = "sha256:b8a84cbd4d0dd150ed187ddb93ea05fb7e36f6554be3fa09f6d8dca9309dbb72"}, - {file = "bento_lib-5.2.0.tar.gz", hash = "sha256:c2dec47bdb56caee982c1d526f3926cc98818a923b5d9c8d6a90d3a0e202e28d"}, + {file = "bento_lib-5.4.0-py3-none-any.whl", hash = "sha256:4bba8fa2a8510d16dcec6800354096a218b1320858175b0e90719af85f584a13"}, + {file = "bento_lib-5.4.0.tar.gz", hash = "sha256:db21a35d5135ad58ad1cb49c4c66b0637d500d52ee188ed5db0df1fdc09b0727"}, ] [package.dependencies] @@ -207,18 +207,18 @@ files = [ [[package]] name = "boto3" -version = "1.26.49" +version = "1.26.65" description = "The AWS SDK for Python" category = "main" optional = false python-versions = ">= 3.7" files = [ - {file = 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= "1.5.0" description = "API to interact with the python pyproject.toml based projects" category = "dev" optional = false python-versions = ">=3.7" files = [ - {file = "pyproject_api-1.4.0-py3-none-any.whl", hash = "sha256:c34226297781efdd1ba4dfb74ce21076d9a8360e2125ea31803c1a02c76b2460"}, - {file = "pyproject_api-1.4.0.tar.gz", hash = "sha256:ac85c1f82e0291dbae5a7739dbb9a990e11ee4034c9b5599ea714f07a24ecd71"}, + {file = "pyproject_api-1.5.0-py3-none-any.whl", hash = "sha256:4c111277dfb96bcd562c6245428f27250b794bfe3e210b8714c4f893952f2c17"}, + {file = "pyproject_api-1.5.0.tar.gz", hash = "sha256:0962df21f3e633b8ddb9567c011e6c1b3dcdfc31b7860c0ede7e24c5a1200fbe"}, ] [package.dependencies] @@ -1338,14 +1349,14 @@ files = [ [[package]] name = "pytest" -version = "7.2.0" +version = "7.2.1" description = "pytest: simple powerful testing with Python" category = "dev" optional = false python-versions = ">=3.7" files = [ - {file = "pytest-7.2.0-py3-none-any.whl", hash = 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"sha256:1195820ca35b141ce5ab040c9dfad8f03de6897c9bd867c6151dfb7dc58e64cd"}, + {file = "tox-4.4.4.tar.gz", hash = "sha256:e1ef01d9e9503b1218511f74517dc3f0008c8b5e0cc53ab7f51ff3c2ca63b349"}, ] [package.dependencies] @@ -1572,7 +1583,7 @@ filelock = ">=3.9" packaging = ">=23" platformdirs = ">=2.6.2" pluggy = ">=1" -pyproject-api = ">=1.4" +pyproject-api = ">=1.5" tomli = {version = ">=2.0.1", markers = "python_version < \"3.11\""} virtualenv = ">=20.17.1" @@ -1582,14 +1593,14 @@ testing = ["build[virtualenv] (>=0.9)", "covdefaults (>=2.2.2)", "devpi-process [[package]] name = "types-toml" -version = "0.10.8.1" +version = "0.10.8.3" description = "Typing stubs for toml" category = "dev" optional = false python-versions = "*" files = [ - {file = "types-toml-0.10.8.1.tar.gz", hash = "sha256:171bdb3163d79a520560f24ba916a9fc9bff81659c5448a9fea89240923722be"}, - {file = "types_toml-0.10.8.1-py3-none-any.whl", hash = "sha256:b7b5c4977f96ab7b5ac06d8a6590d17c0bf252a96efc03b109c2711fb3e0eafd"}, + {file = "types-toml-0.10.8.3.tar.gz", hash = "sha256:f37244eff4cd7eace9cb70d0bac54d3eba77973aa4ef26c271ac3d1c6503a48e"}, + {file = "types_toml-0.10.8.3-py3-none-any.whl", hash = "sha256:a2286a053aea6ab6ff814659272b1d4a05d86a1dd52b807a87b23511993b46c5"}, ] [[package]] @@ -1611,24 +1622,24 @@ socks = ["PySocks (>=1.5.6,!=1.5.7,<2.0)"] [[package]] name = "virtualenv" -version = "20.17.1" +version = "20.19.0" description = "Virtual Python Environment builder" category = "dev" optional = false -python-versions = ">=3.6" +python-versions = ">=3.7" files = [ - {file = "virtualenv-20.17.1-py3-none-any.whl", hash = "sha256:ce3b1684d6e1a20a3e5ed36795a97dfc6af29bc3970ca8dab93e11ac6094b3c4"}, - {file = "virtualenv-20.17.1.tar.gz", hash = "sha256:f8b927684efc6f1cc206c9db297a570ab9ad0e51c16fa9e45487d36d1905c058"}, + {file = "virtualenv-20.19.0-py3-none-any.whl", hash = "sha256:54eb59e7352b573aa04d53f80fc9736ed0ad5143af445a1e539aada6eb947dd1"}, + {file = "virtualenv-20.19.0.tar.gz", hash = "sha256:37a640ba82ed40b226599c522d411e4be5edb339a0c0de030c0dc7b646d61590"}, ] [package.dependencies] distlib = ">=0.3.6,<1" filelock = ">=3.4.1,<4" -platformdirs = ">=2.4,<3" +platformdirs = ">=2.4,<4" [package.extras] -docs = ["proselint (>=0.13)", "sphinx (>=5.3)", "sphinx-argparse (>=0.3.2)", "sphinx-rtd-theme (>=1)", "towncrier (>=22.8)"] -testing = ["coverage (>=6.2)", "coverage-enable-subprocess (>=1)", "flaky (>=3.7)", "packaging (>=21.3)", "pytest (>=7.0.1)", "pytest-env (>=0.6.2)", "pytest-freezegun (>=0.4.2)", "pytest-mock (>=3.6.1)", "pytest-randomly (>=3.10.3)", "pytest-timeout (>=2.1)"] +docs = ["furo (>=2022.12.7)", "proselint (>=0.13)", "sphinx (>=6.1.3)", "sphinx-argparse (>=0.4)", "sphinxcontrib-towncrier (>=0.2.1a0)", "towncrier (>=22.12)"] +test = ["covdefaults (>=2.2.2)", "coverage (>=7.1)", "coverage-enable-subprocess (>=1)", "flaky (>=3.7)", "packaging (>=23)", "pytest (>=7.2.1)", "pytest-env (>=0.8.1)", "pytest-freezegun (>=0.4.2)", "pytest-mock (>=3.10)", "pytest-randomly (>=3.12)", "pytest-timeout (>=2.1)"] [[package]] name = "werkzeug" @@ -1765,21 +1776,21 @@ multidict = ">=4.0" [[package]] name = "zipp" -version = "3.11.0" +version = "3.12.1" description = "Backport of pathlib-compatible object wrapper for zip files" category = "main" optional = false python-versions = ">=3.7" files = [ - {file = "zipp-3.11.0-py3-none-any.whl", hash = "sha256:83a28fcb75844b5c0cdaf5aa4003c2d728c77e05f5aeabe8e95e56727005fbaa"}, - {file = "zipp-3.11.0.tar.gz", hash = "sha256:a7a22e05929290a67401440b39690ae6563279bced5f314609d9d03798f56766"}, + {file = "zipp-3.12.1-py3-none-any.whl", hash = "sha256:6c4fe274b8f85ec73c37a8e4e3fa00df9fb9335da96fb789e3b96b318e5097b3"}, + {file = "zipp-3.12.1.tar.gz", hash = "sha256:a3cac813d40993596b39ea9e93a18e8a2076d5c378b8bc88ec32ab264e04ad02"}, ] [package.extras] -docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)"] +docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"] testing = ["flake8 (<5)", "func-timeout", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=1.3)", "pytest-flake8", "pytest-mypy (>=0.9.1)"] [metadata] lock-version = "2.0" -python-versions = "^3.8" -content-hash = "a21fd65501733464f0326605c41988a9ec3e382f1e5aa28058c7834380ba86d1" +python-versions = "^3.8.1" +content-hash = "9e7bb2cf7bb322fe4fbbc6e728443492d7cd2c131a3832183b069d9abc4c9981" diff --git a/pyproject.toml b/pyproject.toml index 5f564f6..8969514 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -4,7 +4,7 @@ build-backend = "poetry.core.masonry.api" [tool.poetry] name = "bento_drop_box_service" -version = "0.7.0" +version = "0.8.0" description = "Drop box and basic file management service for the Bento platform." authors = ["David Lougheed ", "Simon Chénard "] readme = "README.md" @@ -18,19 +18,19 @@ classifiers = [ ] [tool.poetry.dependencies] -python = "^3.8" -boto3 = "^1.26.4" +python = "^3.8.1" +boto3 = "^1.26.65" quart = "^0.18.3" -bento-lib = {extras = ["quart"], version = "^5.2.0"} +bento-lib = {extras = ["quart"], version = "^5.4.0"} aiofiles = "^22.1.0" [tool.poetry.group.dev.dependencies] -tox = "^4.2.8" +tox = "^4.4.4" codecov = "^2.1.12" coverage = "^6.5.0" -pytest = "^7.2.0" +pytest = "^7.2.1" pytest-cov = "^4.0.0" -moto = "^4.0.9" -flake8 = "^5.0.4" +moto = "^4.1.2" +flake8 = "^6.0.0" pytest-asyncio = "^0.20.1" debugpy = "^1.6.5"