fixed bug to upload large file.

.cspell.json

@@ -1,7 +1,14 @@
 {
   "version": "0.2",
   "language": "en,en-gb",
-  "ignoreWords": ["followlinks", "getframe", "pycache", "pydantic", "UNLCK"],
+  "ignoreWords": [
+    "followlinks",
+    "getframe",
+    "pycache",
+    "pydantic",
+    "toolbelt",
+    "UNLCK"
+  ],
   "words": [
     "chacl",
     "kikan",

LICENSE.txt

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2023 Neuroinformatics Unit, RIKEN CBS
+Copyright (c) 2023- Neuroinformatics Unit, RIKEN CBS
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

README.md

@@ -80,6 +80,7 @@ Upload the file or directory
 ```shell
 mdrs upload ./sample.dat neurodata:/NIU/Repository/TEST/
 mdrs upload -r ./dataset neurodata:/NIU/Repository/TEST/
+mdrs upload -r -s ./dataset neurodata:/NIU/Repository/TEST/
 ```
 
 ### download
@@ -115,8 +116,8 @@ mdrs cp -r neurodata:/NIU/Repository/TEST/dataset neurodata:/NIU/Repository/TEST
 Remove the file or folder
 
 ```shell
-mdrs rm neurodata:/NIU/Repository/TEST2/sample2.dat
-mdrs rm -r neurodata:/NIU/Repository/TEST2/dataset
+mdrs rm neurodata:/NIU/Repository/TEST/sample.dat
+mdrs rm -r neurodata:/NIU/Repository/TEST/dataset
 ```
 
 ### chacl
@@ -126,7 +127,7 @@ Change the folder access level
 ```shell
 mdrs chacl private neurodata:/NIU/Repository/Private
 mdrs chacl cbs_open -r neurodata:/NIU/Repository/CBS_Open
-mdrs chacl pw_open -r -p FOLDER_PASSWORD neurodata:/NIU/Repository/PW_Open
+mdrs chacl pw_open -r -p PW_OPEN_PASSWORD neurodata:/NIU/Repository/PW_Open
 ```
 
 ### metadata

mdrsclient/VERSION

@@ -1 +1 @@
-1.3.1
+1.3.4

mdrsclient/api/files.py

@@ -1,8 +1,10 @@
+import mimetypes
 import os
 from typing import Any, Final
 
 from pydantic import TypeAdapter
 from pydantic.dataclasses import dataclass
+from requests_toolbelt.multipart.encoder import MultipartEncoder
 
 from mdrsclient.api.base import BaseApi
 from mdrsclient.api.utils import token_check
@@ -17,6 +19,7 @@ class FilesApiCreateResponse:
 
 class FilesApi(BaseApi):
     ENTRYPOINT: Final[str] = "v3/files/"
+    FALLBACK_MIMETYPE: Final[str] = "application/octet-stream"
 
     def retrieve(self, id: str) -> File:
         # print(self.__class__.__name__ + "::" + sys._getframe().f_code.co_name)
@@ -30,30 +33,42 @@ class FilesApi(BaseApi):
         # print(self.__class__.__name__ + "::" + sys._getframe().f_code.co_name)
         url = self.ENTRYPOINT
         token_check(self.connection)
-        data: dict[str, str | int] = {"folder_id": folder_id}
+        data: dict[str, str | int] | MultipartEncoder = {}
         try:
             with open(os.path.realpath(path), mode="rb") as fp:
-                response = self.connection.post(url, data=data, files={"file": fp})
+                data = MultipartEncoder(
+                    fields={"folder_id": folder_id, "file": (os.path.basename(path), fp, self._get_mime_type(path))}
+                )
+                response = self.connection.post(url, data=data, headers={"Content-Type": data.content_type})
                 self._raise_response_error(response)
                 ret = TypeAdapter(FilesApiCreateResponse).validate_python(response.json())
         except OSError:
             raise UnexpectedException(f"Could not open `{path}` file.")
+        except MemoryError:
+            raise UnexpectedException("Out of memory.")
+        except Exception as e:
+            print(e)
+            raise UnexpectedException(e)
         return ret.id
 
     def update(self, file: File, path: str | None) -> bool:
         # print(self.__class__.__name__ + "::" + sys._getframe().f_code.co_name)
         url = self.ENTRYPOINT + file.id + "/"
         token_check(self.connection)
+        data: dict[str, str | int] | MultipartEncoder = {}
         if path is not None:
             # update file body
             try:
                 with open(os.path.realpath(path), mode="rb") as fp:
-                    response = self.connection.put(url, files={"file": fp})
+                    data = MultipartEncoder(fields={"file": (os.path.basename(path), fp, self._get_mime_type(path))})
+                    response = self.connection.put(url, data=data, headers={"Content-Type": data.content_type})
             except OSError:
                 raise UnexpectedException(f"Could not open `{path}` file.")
+            except MemoryError:
+                raise UnexpectedException("Out of memory.")
         else:
             # update metadata
-            data: dict[str, str | int] = {"name": file.name, "description": file.description}
+            data = {"name": file.name, "description": file.description}
             response = self.connection.put(url, data=data)
         self._raise_response_error(response)
         return True
@@ -106,3 +121,9 @@ class FilesApi(BaseApi):
         except PermissionError:
             print(f"Cannot create file `{path}`: Permission denied.")
         return True
+
+    def _get_mime_type(self, path: str) -> str:
+        mt = mimetypes.guess_type(path)
+        if mt:
+            return mt[0] or self.FALLBACK_MIMETYPE
+        return self.FALLBACK_MIMETYPE

mdrsclient/commands/upload.py

@@ -106,4 +106,4 @@ class UploadCommand(BaseCommand):
                 file_api.update(file, info.path)
             print(os.path.join(info.folder.path, basename))
         except MDRSException as e:
-            print(f"API Error: {e}")
+            print(f"Error: {e}")

mdrsclient/connection.py

@@ -1,9 +1,9 @@
 import platform
 import threading
-from io import BufferedReader
 from typing import TypedDict
 
 from requests import Response, Session
+from requests_toolbelt.multipart.encoder import MultipartEncoder
 
 # Unpack is new in 3.11
 from typing_extensions import Unpack
@@ -21,14 +21,14 @@ class _KwArgsMDRSConnectionGet(TypedDict, total=False):
 
 class _KwArgsMDRSConnectionPost(TypedDict, total=False):
     params: dict[str, str | int]
-    data: dict[str, str | int]
-    files: dict[str, BufferedReader]
+    data: dict[str, str | int] | MultipartEncoder
+    headers: dict[str, str]
 
 
 class _KwArgsMDRSConnectionPut(TypedDict, total=False):
     params: dict[str, str | int]
-    data: dict[str, str | int]
-    files: dict[str, BufferedReader]
+    data: dict[str, str | int] | MultipartEncoder
+    headers: dict[str, str]
 
 
 class _KwArgsMDRSConnectionDelete(TypedDict, total=False):

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "mdrs-client-python"
-version = "1.3.3"
+version = "1.3.4"
 description = "The mdrs-client-python is python library and a command-line client for up- and downloading files to and from MDRS based repository."
 authors = ["Yoshihiro OKUMURA <yoshihiro.okumura@riken.jp>"]
 license = "MIT"
@@ -22,19 +22,20 @@ packages = [
 
 [tool.poetry.dependencies]
 python = "^3.10"
-requests = "^2.31.0"
+requests = "^2.32.3"
+requests-toolbelt = "^1.0.0"
 python-dotenv = "^1.0.1"
-pydantic = "^2.6.1"
-pydantic-settings = "^2.1.0"
+pydantic = "^2.8.2"
+pydantic-settings = "^2.3.4"
 PyJWT = "^2.8.0"
 validators = "^0.22.0"
 
 [tool.poetry.group.dev.dependencies]
-black = "^24.2.0"
-flake8 = "^7.0.0"
+black = "^24.2.2"
+flake8 = "^7.1.0"
 Flake8-pyproject = "^1.2.3"
 isort = "^5.13.2"
-pyright = "^1.1.350"
+pyright = "^1.1.370"
 
 [tool.poetry.scripts]
 mdrs = 'mdrsclient.__main__:main'