feat: add middleware class

crypt4gh_middleware/middleware.py

@@ -0,0 +1,77 @@
+"""Crypt4GH middleware."""
+
+from pathlib import Path
+
+import flask
+
+class CryptMiddleware:
+    """Middleware class to handle Crypt4GH file inputs."""
+
+    def __init__(self):
+        self.request = None
+        self.original_input_paths = []
+        self.output_dir = Path("/vol/crypt/")
+
+    def _add_decryption_executor(self):
+        """Add the decryption executor to the executor list."""
+        executor = {
+            "image": "athitheyag/crypt4gh:1.0",
+            "command": [
+                "python3",
+                "decrypt.py"
+            ] + self.original_input_paths + [
+                "--output-dir",
+                self.output_dir.as_posix()
+            ]
+        }
+        self.request.json["executors"].insert(0, executor)
+
+    def _change_executor_paths(self):
+        """Change original input file paths in executors to the output directory."""
+        for executor_body in self.request.json["executors"]:
+            for i, path in enumerate(executor_body["command"]):
+                if path in self.original_input_paths:
+                    executor_body["command"][i] = (self.output_dir/path.split("/")[-1]).as_posix()
+
+    def _change_output_paths(self):
+        """Change original output file paths to the output directory if the output path is
+        the same as an input path.
+
+        Accounts for case where input file is modified in place in a TES request.
+        """
+        for output_body in self.request.json["outputs"]:
+            path = output_body["path"]
+            if path in self.original_input_paths:
+                output_body["path"] = (self.output_dir/path.split("/")[-1]).as_posix()
+
+    def _check_volumes(self):
+        """Check volumes to ensure none start with /vol/crypt.
+
+        Raises:
+            ValueError if volumes start with /vol/crypt.
+        """
+        for volume in self.request.json["volumes"]:
+            if volume.startswith("/vol/crypt"):
+                raise ValueError("/vol/crypt/ is not allowed in volumes.")
+
+    def _set_original_input_paths(self):
+        """Retrieve and store the original input file paths.
+
+        Raises:
+            ValueError if any path starts with /vol/crypt.
+        """
+        for input_body in self.request.json["inputs"]:
+            if input_body["path"].startswith("/vol/crypt"):
+                raise ValueError("/vol/crypt/ is not allowed in input path.")
+            self.original_input_paths.append(input_body["path"])
+
+    def apply_middleware(self, request: flask.Request):
+        """Apply middleware to request."""
+        self.request = request
+        self._set_original_input_paths()
+        self._check_volumes()
+        self._change_executor_paths()
+        self._change_output_paths()
+        self._add_decryption_executor()
+
+        return self.request

pyproject.toml

@@ -21,5 +21,8 @@ ruff = "*"
 pylint = "*"
 mypy = "*"
 
+[tool.poetry.group.middleware.dependencies]
+flask = "*"
+
 [tool.pylint."MESSAGES CONTROL"]
-disable = ["logging-fstring-interpolation", "missing-timeout"]
+disable = ["logging-fstring-interpolation", "missing-timeout", "too-few-public-methods"]