diff --git a/crypt4gh_middleware/middleware.py b/crypt4gh_middleware/middleware.py new file mode 100644 index 0000000..3a86f4c --- /dev/null +++ b/crypt4gh_middleware/middleware.py @@ -0,0 +1,89 @@ +"""Crypt4GH middleware.""" +from pathlib import Path +import uuid + +import flask + +VOLUME_PATH = f"/vol/{str(uuid.uuid4().hex)}" +# mypy: disable-error-code="index" + +class PathNotAllowedException(ValueError): + """Raised when a path is not allowed.""" + +class EmptyPayloadException(ValueError): + """Raised when request has no JSON payload.""" + +class CryptMiddleware: + """Middleware class to handle Crypt4GH file inputs.""" + + def __init__(self): + self.original_input_paths = [] + + def _add_decryption_executor(self, request: flask.Request) -> flask.Request: + """Add the decryption executor to the executor list.""" + executor = { + "image": "athitheyag/crypt4gh:1.0", + "command": [ + "python3", + "decrypt.py" + ] + self.original_input_paths + [ + "--output-dir", + VOLUME_PATH + ] + } + request.json["executors"].insert(0, executor) + return request + + def _add_volume(self, request: flask.Request) -> flask.Request: + """Check volumes to ensure none start with VOLUME_PATH and add VOLUME_PATH. + + Raises: + PathNotAllowedError if volumes start with VOLUME_PATH. + """ + for volume in request.json["volumes"]: + if volume.startswith(VOLUME_PATH): + raise PathNotAllowedException(f"{VOLUME_PATH} is not allowed in volumes.") + request.json["volumes"].append(VOLUME_PATH) + return request + + def _change_executor_paths(self, request: flask.Request) -> flask.Request: + """Change original input file paths in executors to the output directory.""" + for executor_body in request.json["executors"]: + for i, path in enumerate(executor_body["command"]): + if path in self.original_input_paths: + executor_body["command"][i] = str(Path(VOLUME_PATH)/Path(path).name) + return request + + def _check_output_paths(self, request: flask.Request) -> None: + """Check if an input path is present in the output paths. Inplace + modifications are not allowed. + + Raises: + PathNotAllowedError if input path is present in output paths. + """ + for output_body in request.json["outputs"]: + path = output_body["path"] + if path in self.original_input_paths: + raise PathNotAllowedException(f"{path} is being modified inplace.") + + def _set_original_input_paths(self, request: flask.Request) -> None: + """Retrieve and store the original input file paths. + + Raises: + PathNotAllowedError if any path starts with VOLUME_PATH. + """ + for input_body in request.json["inputs"]: + if input_body["path"].startswith(VOLUME_PATH): + raise PathNotAllowedException(f"{VOLUME_PATH} is not allowed in input path.") + self.original_input_paths.append(input_body["path"]) + + def apply_middleware(self, request: flask.Request) -> flask.Request: + """Apply middleware to request.""" + if not request.json: + raise EmptyPayloadException("Request JSON has no payload.") + self._set_original_input_paths(request) + self._check_output_paths(request) + request = self._change_executor_paths(request) + request = self._add_volume(request) + request = self._add_decryption_executor(request) + return request diff --git a/poetry.lock b/poetry.lock index 0a55cf9..e61162e 100644 --- a/poetry.lock +++ b/poetry.lock @@ -54,6 +54,17 @@ files = [ tests = ["pytest (>=3.2.1,!=3.3.0)"] typecheck = ["mypy"] +[[package]] +name = "blinker" +version = "1.8.2" +description = "Fast, simple object-to-object and broadcast signaling" +optional = false +python-versions = ">=3.8" +files = [ + {file = "blinker-1.8.2-py3-none-any.whl", hash = "sha256:1779309f71bf239144b9399d06ae925637cf6634cf6bd131104184531bf67c01"}, + {file = "blinker-1.8.2.tar.gz", hash = "sha256:8f77b09d3bf7c795e969e9486f39c2c5e9c39d4ee07424be2bc594ece9642d83"}, +] + [[package]] name = "certifi" version = "2024.6.2" @@ -228,6 +239,20 @@ files = [ {file = "charset_normalizer-3.3.2-py3-none-any.whl", hash = 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