refactor: take request in as parameter

crypt4gh_middleware/middleware.py

@@ -11,11 +11,9 @@ 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) -> None:
+    def _add_decryption_executor(self, request: flask.Request) -> flask.Request:
         """Add the decryption executor to the executor list."""
         executor = {
             "image": "athitheyag/crypt4gh:1.0",
@@ -24,57 +22,58 @@ def _add_decryption_executor(self) -> None:
                 "decrypt.py"
             ] + self.original_input_paths + [
                 "--output-dir",
-                str(self.output_dir)
+                "/vol/crypt/"
             ]
         }
-        self.request.json["executors"].insert(0, executor)
+        request.json["executors"].insert(0, executor)
+        return request
 
-    def _change_executor_paths(self) -> None:
+    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 self.request.json["executors"]:
+        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(self.output_dir/Path(path).name)
+                    executor_body["command"][i] = str(Path("/vol/crypt")/Path(path).name)
+        return request
 
-    def _change_output_paths(self) -> None:
+    def _change_output_paths(self, request: flask.Request) -> flask.Request:
         """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"]:
+        for output_body in request.json["outputs"]:
             path = output_body["path"]
             if path in self.original_input_paths:
-                output_body["path"] = str(self.output_dir/Path(path).name)
+                output_body["path"] = str(Path("/vol/crypt")/Path(path).name)
+        return request
 
-    def _check_volumes(self) -> None:
+    def _check_volumes(self, request: flask.Request) -> None:
         """Check volumes to ensure none start with /vol/crypt.
         
         Raises:
             ValueError if volumes start with /vol/crypt.
         """
-        for volume in self.request.json["volumes"]:
+        for volume in request.json["volumes"]:
             if volume.startswith("/vol/crypt"):
-                raise PathNotAllowedError("/vol/crypt/ is not allowed in volumes.")
+                raise PathNotAllowedError("/vol/crypt is not allowed in volumes.")
 
-    def _set_original_input_paths(self) -> None:
+    def _set_original_input_paths(self, request: flask.Request) -> None:
         """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"]:
+        for input_body in request.json["inputs"]:
             if input_body["path"].startswith("/vol/crypt"):
                 raise PathNotAllowedError("/vol/crypt/ 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."""
-        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
+        self._set_original_input_paths(request)
+        self._check_volumes(request)
+        request = self._change_executor_paths(request)
+        request = self._change_output_paths(request)
+        request = self._add_decryption_executor(request)
+        return request