update version to 1.3.11

.cspell.json

@@ -0,0 +1,26 @@
+{
+  "version": "0.2",
+  "language": "en,en-gb",
+  "ignoreWords": [
+    "followlinks",
+    "getframe",
+    "pycache",
+    "pydantic",
+    "toolbelt",
+    "UNLCK"
+  ],
+  "words": [
+    "chacl",
+    "kikan",
+    "mdrs",
+    "mdrsclient",
+    "neurodata",
+    "Neuroinformatics",
+    "orcid",
+    "RIKEN"
+  ],
+  "ignorePaths": [
+    ".env",
+    "__pycache__"
+  ]
+}

.editorconfig

@@ -0,0 +1,12 @@
+# editorconfig.org
+
+[*]
+charset = utf-8
+indent_style = space
+indent_size = 2
+end_of_line = lf
+insert_final_newline = true
+trim_trailing_whitespace = true
+
+[*.md]
+trim_trailing_whitespace = false

.gitignore

@@ -160,4 +160,5 @@ cython_debug/
 .idea/
 
 # mdrs-cli
-.neurodatacli.config
+.neurodatacli.config
+poetry.toml

.vscode/settings.json

@@ -1,7 +1,7 @@
 {
   "editor.formatOnSave": true,
   "editor.codeActionsOnSave": {
-    "source.organizeImports": true
+    "source.organizeImports": "explicit"
   },
   "[python]": {
     "editor.defaultFormatter": "ms-python.black-formatter"
@@ -15,9 +15,12 @@
   "[jsonc]": {
     "editor.defaultFormatter": "esbenp.prettier-vscode"
   },
+  // Extensions - Black Formatter
+  "black-formatter.args": ["--line-length=120"],
   // Extensions - Code Spell Checker
-  "cSpell.ignoreWords": ["getframe", "pydantic", "UNLCK"],
+  // - see: .cspell.json
-  "cSpell.words": ["chacl", "mdrs", "mdrsclient", "neurodata", "Neuroinformatics", "RIKEN"],
+  // Extensions - Flake8
+  "flake8.args": ["--max-line-length=120"],
   // Extensions - isort
   "isort.args": ["--profile=black"],
   // Extensions - Prettier
@@ -28,16 +31,6 @@
   "prettier.trailingComma": "all",
   // Extensions - Pylance
   "python.analysis.typeCheckingMode": "strict",
-  "python.analysis.exclude": ["api/migrations/[0-9]*.py"],
-  // Extensions - Python:black
-  "python.formatting.blackArgs": ["--line-length=120"],
-  "python.formatting.provider": "black",
-  // Extensions - Python:Flake8
-  "python.linting.enabled": true,
-  "python.linting.flake8Enabled": true,
-  "python.linting.flake8Args": ["--max-line-length=120"],
-  "python.linting.ignorePatterns": ["**/site-packages/**/*.py", ".vscode/*.py"],
-  "python.linting.lintOnSave": true,
   // Extensions - Python Docstring Generator configuration
   "autoDocstring.docstringFormat": "google"
 }

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

@@ -4,8 +4,8 @@ The mdrs-client-python is python library and a command-line client for up- and d
 
 ## Installing
 
-```
+```shell
-pip install -e .
+poetry install
 ```
 
 ## Example Usage
@@ -14,141 +14,146 @@ pip install -e .
 
 Create remote host configuration
 
-```
+```shell
-$ mdrs config create neurodata https://neurodata.riken.jp/api
+mdrs config create neurodata https://neurodata.riken.jp/api
 ```
 
 ### login
 
 Login to remote host
 
-```
+```shell
-$ mdrs login neurodata:
+mdrs login neurodata:
 Username: (enter your login name)
 Password: (enter your password)
+
+mdrs login -u USERNAME -p PASSWORD neurodata:
 ```
 
 ### logout
 
 Logout from remote host
 
-```
+```shell
-$ mdrs logout neurodata:
+mdrs logout neurodata:
 ```
 
 ### whoami
 
 Print current user name
 
-```
+```shell
-$ mdrs whoami neurodata:
+mdrs whoami neurodata:
 ```
 
 ### labs
 
 List all laboratories
 
-```
+```shell
-$ mdrs labs neurodata:
+mdrs labs neurodata:
 ```
 
 ### ls
 
 List the folder contents
 
-```
+```shell
-$ mdrs ls neurodata:/NIU/Repository/
+mdrs ls neurodata:/NIU/Repository/
-$ mdrs ls -p PW_OPEN_PASSWORD neurodata:/NIU/Repository/PW_Open/
+mdrs ls -p SHARING_PASSWORD neurodata:/NIU/Repository/PW_Open/
-$ mdrs ls -r neurodata:/NIU/Repository/Dataset1/
+mdrs ls -r neurodata:/NIU/Repository/Dataset1/
-$ mdrs ls -J -r neurodata:/NIU/Repository/Dataset1/
+mdrs ls -J -r neurodata:/NIU/Repository/Dataset1/
 ```
 
 ### mkdir
 
 Create a new folder
 
-```
+```shell
-$ mdrs mkdir neurodata:/NIU/Repository/TEST
+mdrs mkdir neurodata:/NIU/Repository/TEST
 ```
 
 ### upload
 
 Upload the file or directory
 
-```
+```shell
-$ mdrs upload ./sample.dat neurodata:/NIU/Repository/TEST/
+mdrs upload ./sample.dat neurodata:/NIU/Repository/TEST/
-$ mdrs upload -r ./dataset neurodata:/NIU/Repository/TEST/
+mdrs upload -r ./dataset neurodata:/NIU/Repository/TEST/
+mdrs upload -r --skip-if-exists ./dataset neurodata:/NIU/Repository/TEST/
 ```
 
 ### download
 
 Download the file or folder
 
-```
+```shell
-$ mdrs download neurodata:/NIU/Repository/TEST/sample.dat ./
+mdrs download neurodata:/NIU/Repository/TEST/sample.dat ./
-$ mdrs download -r neurodata:/NIU/Repository/TEST/dataset/ ./
+mdrs download -r neurodata:/NIU/Repository/TEST/dataset/ ./
-$ mdrs download -p PW_OPEN_PASSWORD neurodata:/NIU/Repository/PW_Open/Readme.dat ./
+mdrs download -p SHARING_PASSWORD neurodata:/NIU/Repository/PW_Open/Readme.dat ./
+mdrs download -r --exclude /NIU/Repository/TEST/dataset/skip neurodata:/NIU/Repository/TEST/dataset/ ./
+mdrs download -r --skip-if-exists neurodata:/NIU/Repository/TEST/dataset/ ./
 ```
 
 ### mv
 
 Move or rename the file or folder
 
-```
+```shell
-$ mdrs mv neurodata:/NIU/Repository/TEST/sample.dat neurodata:/NIU/Repository/TEST2/sample2.dat
+mdrs mv neurodata:/NIU/Repository/TEST/sample.dat neurodata:/NIU/Repository/TEST2/sample2.dat
-$ mdrs mv neurodata:/NIU/Repository/TEST/dataset neurodata:/NIU/Repository/TEST2/
+mdrs mv neurodata:/NIU/Repository/TEST/dataset neurodata:/NIU/Repository/TEST2/
 ```
 
 ### cp
 
 Copy the file and folder
 
-```
+```shell
-$ mdrs cp neurodata:/NIU/Repository/TEST/sample.dat neurodata:/NIU/Repository/TEST2/sample2.dat
+mdrs cp neurodata:/NIU/Repository/TEST/sample.dat neurodata:/NIU/Repository/TEST2/sample2.dat
-$ mdrs cp -r neurodata:/NIU/Repository/TEST/dataset neurodata:/NIU/Repository/TEST2/
+mdrs cp -r neurodata:/NIU/Repository/TEST/dataset neurodata:/NIU/Repository/TEST2/
 ```
 
 ### rm
 
 Remove the file or folder
 
-```
+```shell
-$ mdrs rm neurodata:/NIU/Repository/TEST2/sample2.dat
+mdrs rm neurodata:/NIU/Repository/TEST/sample.dat
-$ mdrs rm -r neurodata:/NIU/Repository/TEST2/dataset
+mdrs rm -r neurodata:/NIU/Repository/TEST/dataset
 ```
 
 ### chacl
 
 Change the folder access level
 
-```
+```shell
-$ mdrs chacl private neurodata:/NIU/Repository/Private
+mdrs chacl private neurodata:/NIU/Repository/Private
-$ mdrs chacl cbs_open -r neurodata:/NIU/Repository/CBS_Open
+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 SHARING_PASSWORD neurodata:/NIU/Repository/PW_Open
 ```
 
 ### metadata
 
 Get a folder metadata
 
-```
+```shell
-$ mdrs metadata neurodata:/NIU/Repository/TEST/
+mdrs metadata neurodata:/NIU/Repository/TEST/
-$ mdrs metadata -p PW_OPEN_PASSWORD neurodata:/NIU/Repository/PW_Open/
+mdrs metadata -p SHARING_PASSWORD neurodata:/NIU/Repository/PW_Open/
 ```
 
 ### file-metadata
 
 Get the file metadata
 
-```
+```shell
-$ mdrs file-metadata neurodata:/NIU/Repository/TEST/dataset/sample.dat
+mdrs file-metadata neurodata:/NIU/Repository/TEST/dataset/sample.dat
-$ mdrs file-metadata -p PW_OPEN_PASSWORD neurodata:/NIU/Repository/PW_Open/Readme.txt
+mdrs file-metadata -p SHARING_PASSWORD neurodata:/NIU/Repository/PW_Open/Readme.txt
 ```
 
 ### help
 
 Show the help message and exit
 
-```
+```shell
-$ mdrs -h
+mdrs -h
 ```

mdrsclient/VERSION

@@ -1 +1 @@
-1.1.1
+1.3.11

mdrsclient/__main__.py

@@ -1,5 +1,6 @@
 import argparse
 import sys
+from json import JSONDecodeError
 
 from mdrsclient.commands import (
     ChaclCommand,
@@ -52,6 +53,9 @@ def main() -> None:
     except MDRSException as e:
         print(f"Error: {e}")
         sys.exit(2)
+    except JSONDecodeError:
+        print("Unexpected response returned. Please check the configuration or the server's operational status.")
+        sys.exit(2)
     except KeyboardInterrupt:
         sys.exit(130)
 

mdrsclient/api/__init__.py

@@ -1,11 +1,11 @@
-from mdrsclient.api.file import FileApi
+from mdrsclient.api.files import FilesApi
-from mdrsclient.api.folder import FolderApi
+from mdrsclient.api.folders import FoldersApi
-from mdrsclient.api.laboratory import LaboratoryApi
+from mdrsclient.api.laboratories import LaboratoriesApi
-from mdrsclient.api.user import UserApi
+from mdrsclient.api.users import UsersApi
 
 __all__ = [
-    "FileApi",
+    "FilesApi",
-    "FolderApi",
+    "FoldersApi",
-    "LaboratoryApi",
+    "LaboratoriesApi",
-    "UserApi",
+    "UsersApi",
 ]

mdrsclient/api/files.py

@@ -1,7 +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
@@ -10,12 +13,13 @@ from mdrsclient.models import File
 
 
 @dataclass(frozen=True)
-class FileCreateResponse:
+class FilesApiCreateResponse:
     id: str
 
 
-class FileApi(BaseApi):
+class FilesApi(BaseApi):
-    ENTRYPOINT: Final[str] = "v2/file/"
+    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)
@@ -29,30 +33,43 @@ class FileApi(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(path, mode="rb") as fp:
+            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(FileCreateResponse).validate_python(response.json())
+                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:
+            raise UnexpectedException("Unspecified error.") from 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(path, mode="rb") as fp:
+                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.")
+            except Exception as e:
+                raise UnexpectedException("Unspecified error.") from e
         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
@@ -93,7 +110,8 @@ class FileApi(BaseApi):
 
     def download(self, file: File, path: str) -> bool:
         # print(self.__class__.__name__ + "::" + sys._getframe().f_code.co_name)
-        url = "v2/" + file.download_url
+        url = file.download_url
+        token_check(self.connection)
         response = self.connection.get(url, stream=True)
         self._raise_response_error(response)
         try:
@@ -105,3 +123,9 @@ class FileApi(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/api/folders.py

@@ -11,12 +11,12 @@ from mdrsclient.models import Folder, FolderSimple
 
 
 @dataclass(frozen=True)
-class FolderCreateResponse:
+class FoldersApiCreateResponse:
     id: str
 
 
-class FolderApi(BaseApi):
+class FoldersApi(BaseApi):
-    ENTRYPOINT: Final[str] = "v2/folder/"
+    ENTRYPOINT: Final[str] = "v3/folders/"
 
     def list(self, laboratory_id: int, path: str) -> list[FolderSimple]:
         # print(self.__class__.__name__ + "::" + sys._getframe().f_code.co_name)
@@ -46,7 +46,7 @@ class FolderApi(BaseApi):
         token_check(self.connection)
         response = self.connection.post(url, data=data)
         self._raise_response_error(response)
-        ret = TypeAdapter(FolderCreateResponse).validate_python(response.json())
+        ret = TypeAdapter(FoldersApiCreateResponse).validate_python(response.json())
         return ret.id
 
     def update(self, folder: FolderSimple) -> bool:

mdrsclient/api/laboratories.py

@@ -7,8 +7,8 @@ from mdrsclient.api.utils import token_check
 from mdrsclient.models import Laboratories, Laboratory
 
 
-class LaboratoryApi(BaseApi):
+class LaboratoriesApi(BaseApi):
-    ENTRYPOINT: Final[str] = "v2/laboratory/"
+    ENTRYPOINT: Final[str] = "v3/laboratories/"
 
     def list(self) -> Laboratories:
         # print(self.__class__.__name__ + "::" + sys._getframe().f_code.co_name)

mdrsclient/api/user.py

@@ -1,46 +0,0 @@
-from typing import Final
-
-import requests
-from pydantic import TypeAdapter
-from pydantic.dataclasses import dataclass
-
-from mdrsclient.api.base import BaseApi
-from mdrsclient.exceptions import UnauthorizedException
-from mdrsclient.models import Token, User
-
-
-@dataclass(frozen=True)
-class UserAuthResponse(Token):
-    is_reviewer: bool | None = None
-    laboratory: str | None = None
-    lab_id: int | None = None
-
-
-class UserApi(BaseApi):
-    ENTRYPOINT: Final[str] = "v2/"
-
-    def auth(self, username: str, password: str) -> tuple[User, Token]:
-        # print(self.__class__.__name__ + "::" + sys._getframe().f_code.co_name)
-        url = self.ENTRYPOINT + "auth/"
-        data: dict[str, str | int] = {"username": username, "password": password}
-        response = self.connection.post(url, data=data)
-        if response.status_code == requests.codes.unauthorized:
-            raise UnauthorizedException("Invalid username or password.")
-        self._raise_response_error(response)
-        obj = TypeAdapter(UserAuthResponse).validate_python(response.json())
-        token = Token(access=obj.access, refresh=obj.refresh)
-        laboratory_ids = [obj.lab_id] if obj.lab_id is not None else []
-        is_reviewer = obj.is_reviewer if obj.is_reviewer is not None else False
-        user = User(id=token.user_id, username=username, laboratory_ids=laboratory_ids, is_reviewer=is_reviewer)
-        return (user, token)
-
-    def refresh(self, token: Token) -> Token:
-        # print(self.__class__.__name__ + "::" + sys._getframe().f_code.co_name)
-        url = self.ENTRYPOINT + "refresh/"
-        data: dict[str, str | int] = {"refresh": token.refresh}
-        response = self.connection.post(url, data=data)
-        if response.status_code == requests.codes.unauthorized:
-            raise UnauthorizedException("Token is invalid or expired.")
-        self._raise_response_error(response)
-        token = TypeAdapter(Token).validate_python(response.json())
-        return token

mdrsclient/api/users.py

@@ -0,0 +1,69 @@
+from typing import Final
+
+import requests
+from pydantic import TypeAdapter
+from pydantic.dataclasses import dataclass
+
+from mdrsclient.api.base import BaseApi
+from mdrsclient.exceptions import UnauthorizedException
+from mdrsclient.models import Token, User
+
+
+@dataclass(frozen=True)
+class UsersCurrentResponseLaboratory:
+    id: int
+    name: str
+    role: int
+
+
+@dataclass(frozen=True)
+class UsersApiCurrentResponse:
+    id: int
+    username: str
+    first_name: str
+    last_name: str
+    email: str
+    orcid_id: str
+    laboratories: list[UsersCurrentResponseLaboratory]
+    is_staff: bool
+    is_active: bool
+    is_superuser: bool
+    is_reviewer: bool
+    last_login: str  # ISO8601
+    date_joined: str  # ISO8601
+
+
+class UsersApi(BaseApi):
+    ENTRYPOINT: Final[str] = "v3/users/"
+
+    def current(self) -> User:
+        # print(self.__class__.__name__ + "::" + sys._getframe().f_code.co_name)
+        url = self.ENTRYPOINT + "current/"
+        response = self.connection.get(url)
+        self._raise_response_error(response)
+        obj = TypeAdapter(UsersApiCurrentResponse).validate_python(response.json())
+        laboratory_ids = list(map(lambda x: x.id, obj.laboratories))
+        user = User(id=obj.id, username=obj.username, laboratory_ids=laboratory_ids, is_reviewer=obj.is_reviewer)
+        return user
+
+    def token(self, username: str, password: str) -> Token:
+        # print(self.__class__.__name__ + "::" + sys._getframe().f_code.co_name)
+        url = self.ENTRYPOINT + "token/"
+        data: dict[str, str | int] = {"username": username, "password": password}
+        response = self.connection.post(url, data=data)
+        if response.status_code == requests.codes.unauthorized:
+            raise UnauthorizedException("Invalid username or password.")
+        self._raise_response_error(response)
+        token = TypeAdapter(Token).validate_python(response.json())
+        return token
+
+    def tokenRefresh(self, token: Token) -> Token:
+        # print(self.__class__.__name__ + "::" + sys._getframe().f_code.co_name)
+        url = self.ENTRYPOINT + "token/refresh/"
+        data: dict[str, str | int] = {"refresh": token.refresh}
+        response = self.connection.post(url, data=data)
+        if response.status_code == requests.codes.unauthorized:
+            raise UnauthorizedException("Token is invalid or expired.")
+        self._raise_response_error(response)
+        token = TypeAdapter(Token).validate_python(response.json())
+        return token

mdrsclient/api/utils.py

@@ -1,4 +1,4 @@
-from mdrsclient.api.user import UserApi
+from mdrsclient.api.users import UsersApi
 from mdrsclient.connection import MDRSConnection
 from mdrsclient.exceptions import UnauthorizedException
 
@@ -8,9 +8,9 @@ def token_check(connection: MDRSConnection) -> None:
         connection.lock.acquire()
         if connection.token is not None:
             if connection.token.is_refresh_required:
-                user_api = UserApi(connection)
+                user_api = UsersApi(connection)
                 try:
-                    connection.token = user_api.refresh(connection.token)
+                    connection.token = user_api.tokenRefresh(connection.token)
                 except UnauthorizedException:
                     connection.logout()
             elif connection.token.is_expired:

mdrsclient/commands/base.py

@@ -3,7 +3,7 @@ from abc import ABC, abstractmethod
 from typing import Any
 from unicodedata import normalize
 
-from mdrsclient.api import FolderApi, LaboratoryApi
+from mdrsclient.api import FoldersApi, LaboratoriesApi
 from mdrsclient.config import ConfigFile
 from mdrsclient.connection import MDRSConnection
 from mdrsclient.exceptions import (
@@ -31,7 +31,7 @@ class BaseCommand(ABC):
     @classmethod
     def _find_laboratory(cls, connection: MDRSConnection, name: str) -> Laboratory:
         if connection.laboratories.empty() or connection.token is not None and connection.token.is_expired:
-            laboratory_api = LaboratoryApi(connection)
+            laboratory_api = LaboratoriesApi(connection)
             connection.laboratories = laboratory_api.list()
         laboratory = connection.laboratories.find_by_name(name)
         if laboratory is None:
@@ -42,7 +42,7 @@ class BaseCommand(ABC):
     def _find_folder(
         cls, connection: MDRSConnection, laboratory: Laboratory, path: str, password: str | None = None
     ) -> Folder:
-        folder_api = FolderApi(connection)
+        folder_api = FoldersApi(connection)
         folders = folder_api.list(laboratory.id, normalize("NFC", path))
         if len(folders) != 1:
             raise UnexpectedException(f"Folder `{path}` not found.")

mdrsclient/commands/chacl.py

@@ -1,7 +1,7 @@
 from argparse import Namespace
 from typing import Any
 
-from mdrsclient.api import FolderApi
+from mdrsclient.api import FoldersApi
 from mdrsclient.commands.base import BaseCommand
 from mdrsclient.exceptions import IllegalArgumentException
 from mdrsclient.models import FolderAccessLevel
@@ -36,5 +36,5 @@ class ChaclCommand(BaseCommand):
         connection = cls._create_connection(remote)
         laboratory = cls._find_laboratory(connection, laboratory_name)
         folder = cls._find_folder(connection, laboratory, r_path)
-        folder_api = FolderApi(connection)
+        folder_api = FoldersApi(connection)
         folder_api.acl(folder.id, access_level, is_recursive, password)

mdrsclient/commands/config.py

@@ -25,11 +25,11 @@ class ConfigCommand(BaseCommand):
         update_parser.add_argument("url", help="API entrypoint url of remote host")
         update_parser.set_defaults(func=cls.func_update)
         # config list
-        list_parser = config_parsers.add_parser("list", help="list all the remote hosts")
+        list_parser = config_parsers.add_parser("list", help="list all the remote hosts", aliases=["ls"])
         list_parser.add_argument("-l", "--long", help="show the api url", action="store_true")
         list_parser.set_defaults(func=cls.func_list)
         # config delete
-        delete_parser = config_parsers.add_parser("delete", help="delete an existing remote host")
+        delete_parser = config_parsers.add_parser("delete", help="delete an existing remote host", aliases=["remove"])
         delete_parser.add_argument("remote", help="label of remote host")
         delete_parser.set_defaults(func=cls.func_delete)
 

mdrsclient/commands/cp.py

@@ -3,7 +3,7 @@ from argparse import Namespace
 from typing import Any
 from unicodedata import normalize
 
-from mdrsclient.api import FileApi, FolderApi
+from mdrsclient.api import FilesApi, FoldersApi
 from mdrsclient.commands.base import BaseCommand
 from mdrsclient.exceptions import IllegalArgumentException
 
@@ -56,7 +56,7 @@ class CpCommand(BaseCommand):
             d_sub_folder = d_parent_folder.find_sub_folder(d_basename)
             if d_sub_folder is not None:
                 raise IllegalArgumentException(f"Cannot overwrite non-folder `{d_basename}` with folder `{d_path}`.")
-            file_api = FileApi(connection)
+            file_api = FilesApi(connection)
             if s_parent_folder.id != d_parent_folder.id or d_basename != s_basename:
                 file_api.copy(s_file, d_parent_folder.id, normalize("NFC", d_basename))
         else:
@@ -73,6 +73,6 @@ class CpCommand(BaseCommand):
                 if d_folder.id == s_folder.id:
                     raise IllegalArgumentException(f"`{s_path}` and `{s_path}` are the same folder.")
                 raise IllegalArgumentException(f"Cannot move `{s_path}` to `{d_path}`: Folder not empty.")
-            folder_api = FolderApi(connection)
+            folder_api = FoldersApi(connection)
             if s_parent_folder.id != d_parent_folder.id or s_basename != d_basename:
                 folder_api.copy(s_folder, d_parent_folder.id, normalize("NFC", d_basename))

mdrsclient/commands/download.py

@@ -5,11 +5,11 @@ from typing import Any
 
 from pydantic.dataclasses import dataclass
 
-from mdrsclient.api import FileApi, FolderApi
+from mdrsclient.api import FilesApi, FoldersApi
 from mdrsclient.commands.base import BaseCommand
 from mdrsclient.connection import MDRSConnection
-from mdrsclient.exceptions import IllegalArgumentException
+from mdrsclient.exceptions import IllegalArgumentException, UnexpectedException
-from mdrsclient.models import File
+from mdrsclient.models import File, Folder, Laboratory
 from mdrsclient.settings import CONCURRENT
 
 
@@ -19,6 +19,13 @@ class DownloadFileInfo:
     path: str
 
 
+@dataclass
+class DownloadContext:
+    hasError: bool
+    isSkipIfExists: bool
+    files: list[DownloadFileInfo]
+
+
 class DownloadCommand(BaseCommand):
     @classmethod
     def register(cls, parsers: Any) -> None:
@@ -26,6 +33,15 @@ class DownloadCommand(BaseCommand):
         download_parser.add_argument(
             "-r", "--recursive", help="download folders and their contents recursive", action="store_true"
         )
+        download_parser.add_argument(
+            "-s",
+            "--skip-if-exists",
+            help="skip the download if file is already downloaded and file size is the same",
+            action="store_true",
+        )
+        download_parser.add_argument(
+            "-e", "--exclude", help="exclude to download path matched file or folders", action="append"
+        )
         download_parser.add_argument("-p", "--password", help="password to use when open locked folder")
         download_parser.add_argument("remote_path", help="remote file path (remote:/lab/path/file)")
         download_parser.add_argument("local_path", help="local folder path (/foo/bar/)")
@@ -36,11 +52,21 @@ class DownloadCommand(BaseCommand):
         remote_path = str(args.remote_path)
         local_path = str(args.local_path)
         is_recursive = bool(args.recursive)
+        is_skip_if_exists = bool(args.skip_if_exists)
         password = str(args.password) if args.password else None
-        cls.download(remote_path, local_path, is_recursive, password)
+        excludes = list(map(lambda x: str(x).rstrip("/").lower(), args.exclude)) if args.exclude is not None else []
+        cls.download(remote_path, local_path, is_recursive, is_skip_if_exists, password, excludes)
 
     @classmethod
-    def download(cls, remote_path: str, local_path: str, is_recursive: bool, password: str | None) -> None:
+    def download(
+        cls,
+        remote_path: str,
+        local_path: str,
+        is_recursive: bool,
+        is_skip_if_exists: bool,
+        password: str | None,
+        excludes: list[str],
+    ) -> None:
         (remote, laboratory_name, r_path) = cls._parse_remote_host_with_path(remote_path)
         r_path = r_path.rstrip("/")
         r_dirname = os.path.dirname(r_path)
@@ -52,42 +78,81 @@ class DownloadCommand(BaseCommand):
         laboratory = cls._find_laboratory(connection, laboratory_name)
         r_parent_folder = cls._find_folder(connection, laboratory, r_dirname, password)
         file = r_parent_folder.find_file(r_basename)
-        download_files: list[DownloadFileInfo] = []
         if file is not None:
+            if cls.__check_excludes(excludes, laboratory, r_parent_folder, file):
+                return
+            context = DownloadContext(False, is_skip_if_exists, [])
             l_path = os.path.join(l_dirname, r_basename)
-            download_files.append(DownloadFileInfo(file, l_path))
+            context.files.append(DownloadFileInfo(file, l_path))
+            cls.__multiple_download(connection, context)
         else:
             folder = r_parent_folder.find_sub_folder(r_basename)
             if folder is None:
                 raise IllegalArgumentException(f"File or folder `{r_path}` not found.")
             if not is_recursive:
                 raise IllegalArgumentException(f"Cannot download `{r_path}`: Is a folder.")
-            folder_api = FolderApi(connection)
+            folder_api = FoldersApi(connection)
-            cls.__multiple_download_pickup_recursive_files(folder_api, download_files, folder.id, l_dirname)
+            cls.__multiple_download_pickup_recursive_files(
-        cls.__multiple_download(connection, download_files)
+                connection, folder_api, laboratory, folder.id, l_dirname, excludes, is_skip_if_exists
+            )
 
     @classmethod
     def __multiple_download_pickup_recursive_files(
-        cls, folder_api: FolderApi, infolist: list[DownloadFileInfo], folder_id: str, basedir: str
+        cls,
+        connection: MDRSConnection,
+        folder_api: FoldersApi,
+        laboratory: Laboratory,
+        folder_id: str,
+        basedir: str,
+        excludes: list[str],
+        is_skip_if_exists: bool,
     ) -> None:
+        context = DownloadContext(False, is_skip_if_exists, [])
         folder = folder_api.retrieve(folder_id)
         dirname = os.path.join(basedir, folder.name)
+        if cls.__check_excludes(excludes, laboratory, folder, None):
+            return
         if not os.path.exists(dirname):
             os.makedirs(dirname)
         print(dirname)
         for file in folder.files:
+            if cls.__check_excludes(excludes, laboratory, folder, file):
+                continue
             path = os.path.join(dirname, file.name)
-            infolist.append(DownloadFileInfo(file, path))
+            context.files.append(DownloadFileInfo(file, path))
+        cls.__multiple_download(connection, context)
+        if context.hasError:
+            raise UnexpectedException("Some files failed to download.")
         for sub_folder in folder.sub_folders:
-            cls.__multiple_download_pickup_recursive_files(folder_api, infolist, sub_folder.id, dirname)
+            cls.__multiple_download_pickup_recursive_files(
+                connection, folder_api, laboratory, sub_folder.id, dirname, excludes, is_skip_if_exists
+            )
 
     @classmethod
-    def __multiple_download(cls, connection: MDRSConnection, infolist: list[DownloadFileInfo]) -> None:
+    def __multiple_download(cls, connection: MDRSConnection, context: DownloadContext) -> None:
-        file_api = FileApi(connection)
+        file_api = FilesApi(connection)
         with ThreadPoolExecutor(max_workers=CONCURRENT) as pool:
-            pool.map(lambda x: cls.__multiple_download_worker(file_api, x), infolist)
+            results = pool.map(
+                lambda x: cls.__multiple_download_worker(file_api, x, context.isSkipIfExists), context.files
+            )
+            hasError = next(filter(lambda x: x is False, results), None)
+            if hasError is not None:
+                context.hasError = True
 
     @classmethod
-    def __multiple_download_worker(cls, file_api: FileApi, info: DownloadFileInfo) -> None:
+    def __multiple_download_worker(cls, file_api: FilesApi, info: DownloadFileInfo, is_skip_if_exists: bool) -> bool:
-        file_api.download(info.file, info.path)
+        if not is_skip_if_exists or os.path.exists(info.path) and info.file.size != os.path.getsize(info.path):
+            try:
+                file_api.download(info.file, info.path)
+            except Exception:
+                print(f"Failed: ${info.path}")
+                if os.path.isfile(info.path):
+                    os.remove(info.path)
+                return False
         print(info.path)
+        return True
+
+    @classmethod
+    def __check_excludes(cls, excludes: list[str], laboratory: Laboratory, folder: Folder, file: File | None) -> bool:
+        path = f"/{laboratory.name}{folder.path}{file.name if file is not None else ''}".rstrip("/").lower()
+        return path in excludes

mdrsclient/commands/file_metadata.py

@@ -3,7 +3,7 @@ import os
 from argparse import Namespace
 from typing import Any
 
-from mdrsclient.api import FileApi
+from mdrsclient.api import FilesApi
 from mdrsclient.commands.base import BaseCommand
 from mdrsclient.exceptions import IllegalArgumentException
 
@@ -34,6 +34,6 @@ class FileMetadataCommand(BaseCommand):
         file = folder.find_file(r_basename)
         if file is None:
             raise IllegalArgumentException(f"File `{r_basename}` not found.")
-        file_api = FileApi(connection)
+        file_api = FilesApi(connection)
         metadata = file_api.metadata(file)
         print(json.dumps(metadata, ensure_ascii=False))

mdrsclient/commands/labs.py

@@ -1,7 +1,7 @@
 from argparse import Namespace
 from typing import Any
 
-from mdrsclient.api import LaboratoryApi
+from mdrsclient.api import LaboratoriesApi
 from mdrsclient.commands.base import BaseCommand
 
 
@@ -21,7 +21,7 @@ class LabsCommand(BaseCommand):
     def labs(cls, remote: str) -> None:
         remote = cls._parse_remote_host(remote)
         connection = cls._create_connection(remote)
-        laboratory_api = LaboratoryApi(connection)
+        laboratory_api = LaboratoriesApi(connection)
         laboratories = laboratory_api.list()
         connection.laboratories = laboratories
         label = {"id": "ID", "name": "Name", "pi_name": "PI", "full_name": "Laboratory"}

mdrsclient/commands/login.py

@@ -2,7 +2,7 @@ import getpass
 from argparse import Namespace
 from typing import Any
 
-from mdrsclient.api import UserApi
+from mdrsclient.api import UsersApi
 from mdrsclient.commands.base import BaseCommand
 from mdrsclient.config import ConfigFile
 from mdrsclient.connection import MDRSConnection
@@ -13,14 +13,16 @@ class LoginCommand(BaseCommand):
     @classmethod
     def register(cls, parsers: Any) -> None:
         login_parser = parsers.add_parser("login", help="login to remote host")
+        login_parser.add_argument("-u", "--username", help="login username")
+        login_parser.add_argument("-p", "--password", help="login password")
         login_parser.add_argument("remote", help="label of remote host")
         login_parser.set_defaults(func=cls.func)
 
     @classmethod
     def func(cls, args: Namespace) -> None:
         remote = str(args.remote)
-        username = input("Username: ").strip()
+        username = str(args.username) if args.password else input("Username: ").strip()
-        password = getpass.getpass("Password: ").strip()
+        password = str(args.password) if args.password else getpass.getpass("Password: ").strip()
         cls.login(remote, username, password)
 
     @classmethod
@@ -30,8 +32,9 @@ class LoginCommand(BaseCommand):
         if config.url is None:
             raise MissingConfigurationException(f"Remote host `{remote}` is not found.")
         connection = MDRSConnection(config.remote, config.url)
-        user_api = UserApi(connection)
+        user_api = UsersApi(connection)
-        (user, token) = user_api.auth(username, password)
+        token = user_api.token(username, password)
-        print("Login Successful")
-        connection.user = user
         connection.token = token
+        user = user_api.current()
+        connection.user = user
+        print("Login Successful")

mdrsclient/commands/ls.py

@@ -4,7 +4,7 @@ from typing import Any
 
 from pydantic.dataclasses import dataclass
 
-from mdrsclient.api import FolderApi
+from mdrsclient.api import FoldersApi
 from mdrsclient.commands.base import BaseCommand
 from mdrsclient.connection import MDRSConnection
 from mdrsclient.exceptions import UnauthorizedException
@@ -82,7 +82,7 @@ class LsCommand(BaseCommand):
             "type": "Type",
             "acl": "Access",
             "laboratory": "Laboratory",
-            "size": "Lock/Size",
+            "size": "Size",
             "date": "Date",
             "name": "Name",
         }
@@ -90,11 +90,11 @@ class LsCommand(BaseCommand):
         for key in label.keys():
             length[key] = len(label[key]) if not context.is_quick else 0
         for sub_folder in folder.sub_folders:
-            sub_laboratory = context.connection.laboratories.find_by_id(sub_folder.lab_id)
+            sub_laboratory = context.connection.laboratories.find_by_id(sub_folder.laboratory_id)
             sub_laboratory_name = sub_laboratory.name if sub_laboratory is not None else "(invalid)"
             length["acl"] = max(length["acl"], len(sub_folder.access_level_name))
             length["laboratory"] = max(length["laboratory"], len(sub_laboratory_name))
-            length["size"] = max(length["size"], len(sub_folder.lock_name))
+            length["size"] = max(length["size"], len(str(folder.size)))
             length["date"] = max(length["date"], len(sub_folder.updated_at_name))
             length["name"] = max(length["name"], len(sub_folder.name))
         for file in folder.files:
@@ -118,10 +118,11 @@ class LsCommand(BaseCommand):
             print("-" * len(header.expandtabs()))
 
         for sub_folder in sorted(folder.sub_folders, key=lambda x: x.name):
-            sub_laboratory_name = cls._laboratory_name(context, sub_folder.lab_id)
+            sub_laboratory_name = cls._laboratory_name(context, sub_folder.laboratory_id)
+            sub_folder_type = "[d]" if sub_folder.lock is False else "[l]"
             print(
-                f"{'[d]':{length['type']}}\t{sub_folder.access_level_name:{length['acl']}}\t"
+                f"{sub_folder_type:{length['type']}}\t{sub_folder.access_level_name:{length['acl']}}\t"
-                f"{sub_laboratory_name:{length['laboratory']}}\t{sub_folder.lock_name:{length['size']}}\t"
+                f"{sub_laboratory_name:{length['laboratory']}}\t{sub_folder.size:{length['size']}}\t"
                 f"{sub_folder.updated_at_name:{length['date']}}\t{sub_folder.name:{length['name']}}"
             )
         for file in sorted(folder.files, key=lambda x: x.name):
@@ -134,7 +135,7 @@ class LsCommand(BaseCommand):
         if context.is_recursive:
             print("")
             for sub_folder in sorted(folder.sub_folders, key=lambda x: x.name):
-                folder_api = FolderApi(context.connection)
+                folder_api = FoldersApi(context.connection)
                 try:
                     if sub_folder.lock:
                         folder_api.auth(sub_folder.id, context.password)
@@ -149,15 +150,16 @@ class LsCommand(BaseCommand):
             "id": folder.id,
             "pid": folder.pid,
             "name": folder.name,
+            "size": folder.size,
             "access_level": folder.access_level_name,
             "lock": folder.lock,
-            "laboratory": cls._laboratory_name(context, folder.lab_id),
+            "laboratory": cls._laboratory_name(context, folder.laboratory_id),
             "description": folder.description,
             "created_at": folder.created_at,
             "updated_at": folder.updated_at,
         }
         if isinstance(folder, Folder):
-            folder_api = FolderApi(context.connection)
+            folder_api = FoldersApi(context.connection)
             data["metadata"] = folder_api.metadata(folder.id)
             if context.is_recursive:
                 sub_folders: list[dict[str, Any]] = []
@@ -187,7 +189,7 @@ class LsCommand(BaseCommand):
             # "thumbnail": file.thumbnail,
             "description": file.description,
             "metadata": file.metadata,
-            "download_url": f"{context.connection.url}/v2/{file.download_url}",
+            "download_url": f"{context.connection.url}/{file.download_url}",
             "created_at": file.created_at,
             "updated_at": file.updated_at,
         }

mdrsclient/commands/metadata.py

@@ -2,7 +2,7 @@ import json
 from argparse import Namespace
 from typing import Any
 
-from mdrsclient.api import FolderApi
+from mdrsclient.api import FoldersApi
 from mdrsclient.commands.base import BaseCommand
 
 
@@ -26,6 +26,6 @@ class MetadataCommand(BaseCommand):
         connection = cls._create_connection(remote)
         laboratory = cls._find_laboratory(connection, laboratory_name)
         folder = cls._find_folder(connection, laboratory, r_path, password)
-        folder_api = FolderApi(connection)
+        folder_api = FoldersApi(connection)
         metadata = folder_api.metadata(folder.id)
         print(json.dumps(metadata, ensure_ascii=False))

mdrsclient/commands/mkdir.py

@@ -3,7 +3,7 @@ from argparse import Namespace
 from typing import Any
 from unicodedata import normalize
 
-from mdrsclient.api import FolderApi
+from mdrsclient.api import FoldersApi
 from mdrsclient.commands.base import BaseCommand
 from mdrsclient.exceptions import IllegalArgumentException
 
@@ -31,5 +31,5 @@ class MkdirCommand(BaseCommand):
         parent_folder = cls._find_folder(connection, laboratory, r_dirname)
         if parent_folder.find_sub_folder(r_basename) is not None or parent_folder.find_file(r_basename) is not None:
             raise IllegalArgumentException(f"Cannot create folder `{r_path}`: File exists.")
-        folder_api = FolderApi(connection)
+        folder_api = FoldersApi(connection)
         folder_api.create(normalize("NFC", r_basename), parent_folder.id)

mdrsclient/commands/mv.py

@@ -3,7 +3,7 @@ from argparse import Namespace
 from typing import Any
 from unicodedata import normalize
 
-from mdrsclient.api import FileApi, FolderApi
+from mdrsclient.api import FilesApi, FoldersApi
 from mdrsclient.commands.base import BaseCommand
 from mdrsclient.exceptions import IllegalArgumentException
 
@@ -52,7 +52,7 @@ class MvCommand(BaseCommand):
             d_sub_folder = d_parent_folder.find_sub_folder(d_basename)
             if d_sub_folder is not None:
                 raise IllegalArgumentException(f"Cannot overwrite non-folder `{d_basename}` with folder `{d_path}`.")
-            file_api = FileApi(connection)
+            file_api = FilesApi(connection)
             if s_parent_folder.id != d_parent_folder.id or d_basename != s_basename:
                 file_api.move(s_file, d_parent_folder.id, normalize("NFC", d_basename))
         else:
@@ -67,6 +67,6 @@ class MvCommand(BaseCommand):
                 if d_folder.id == s_folder.id:
                     raise IllegalArgumentException(f"`{s_path}` and `{s_path}` are the same folder.")
                 raise IllegalArgumentException(f"Cannot move `{s_path}` to `{d_path}`: Folder not empty.")
-            folder_api = FolderApi(connection)
+            folder_api = FoldersApi(connection)
             if s_parent_folder.id != d_parent_folder.id or d_basename != s_basename:
                 folder_api.move(s_folder, d_parent_folder.id, normalize("NFC", d_basename))

mdrsclient/commands/rm.py

@@ -2,7 +2,7 @@ import os
 from argparse import Namespace
 from typing import Any
 
-from mdrsclient.api import FileApi, FolderApi
+from mdrsclient.api import FilesApi, FoldersApi
 from mdrsclient.commands.base import BaseCommand
 from mdrsclient.exceptions import IllegalArgumentException
 
@@ -34,7 +34,7 @@ class RmCommand(BaseCommand):
         parent_folder = cls._find_folder(connection, laboratory, r_dirname)
         file = parent_folder.find_file(r_basename)
         if file is not None:
-            file_api = FileApi(connection)
+            file_api = FilesApi(connection)
             file_api.destroy(file)
         else:
             folder = parent_folder.find_sub_folder(r_basename)
@@ -42,5 +42,5 @@ class RmCommand(BaseCommand):
                 raise IllegalArgumentException(f"Cannot remove `{r_path}`: No such file or folder.")
             if not is_recursive:
                 raise IllegalArgumentException(f"Cannot remove `{r_path}`: Is a folder.")
-            folder_api = FolderApi(connection)
+            folder_api = FoldersApi(connection)
             folder_api.destroy(folder.id, True)

mdrsclient/commands/upload.py

@@ -5,7 +5,7 @@ from typing import Any
 
 from pydantic.dataclasses import dataclass
 
-from mdrsclient.api import FileApi, FolderApi
+from mdrsclient.api import FilesApi, FoldersApi
 from mdrsclient.commands.base import BaseCommand
 from mdrsclient.connection import MDRSConnection
 from mdrsclient.exceptions import IllegalArgumentException, MDRSException
@@ -26,6 +26,12 @@ class UploadCommand(BaseCommand):
         upload_parser.add_argument(
             "-r", "--recursive", help="upload directories and their contents recursive", action="store_true"
         )
+        upload_parser.add_argument(
+            "-s",
+            "--skip-if-exists",
+            help="skip the upload if file is already uploaded and file size is the same",
+            action="store_true",
+        )
         upload_parser.add_argument("local_path", help="local file path (/foo/bar/data.txt)")
         upload_parser.add_argument("remote_path", help="remote folder path (remote:/lab/path/)")
         upload_parser.set_defaults(func=cls.func)
@@ -35,12 +41,13 @@ class UploadCommand(BaseCommand):
         local_path = str(args.local_path)
         remote_path = str(args.remote_path)
         is_recursive = bool(args.recursive)
-        cls.upload(local_path, remote_path, is_recursive)
+        is_skip_if_exists = bool(args.skip_if_exists)
+        cls.upload(local_path, remote_path, is_recursive, is_skip_if_exists)
 
     @classmethod
-    def upload(cls, local_path: str, remote_path: str, is_recursive: bool) -> None:
+    def upload(cls, local_path: str, remote_path: str, is_recursive: bool, is_skip_if_exists: bool) -> None:
         (remote, laboratory_name, r_path) = cls._parse_remote_host_with_path(remote_path)
-        l_path = os.path.realpath(local_path)
+        l_path = os.path.abspath(local_path)
         if not os.path.exists(l_path):
             raise IllegalArgumentException(f"File or directory `{local_path}` not found.")
         connection = cls._create_connection(remote)
@@ -50,11 +57,11 @@ class UploadCommand(BaseCommand):
         if os.path.isdir(l_path):
             if not is_recursive:
                 raise IllegalArgumentException(f"Cannot upload `{local_path}`: Is a directory.")
-            folder_api = FolderApi(connection)
+            folder_api = FoldersApi(connection)
             folder_map: dict[str, Folder] = {}
             folder_map[r_path] = folder
             l_basename = os.path.basename(l_path)
-            for dirpath, _, filenames in os.walk(l_path):
+            for dirpath, _, filenames in os.walk(l_path, followlinks=True):
                 sub = l_basename if dirpath == l_path else os.path.join(l_basename, os.path.relpath(dirpath, l_path))
                 d_dirname = os.path.join(r_path, sub)
                 d_basename = os.path.basename(d_dirname)
@@ -78,23 +85,25 @@ class UploadCommand(BaseCommand):
                     infos.append(UploadFileInfo(folder_map[d_dirname], os.path.join(dirpath, filename)))
         else:
             infos.append(UploadFileInfo(folder, l_path))
-        cls.__multiple_upload(connection, infos)
+        cls.__multiple_upload(connection, infos, is_skip_if_exists)
 
     @classmethod
-    def __multiple_upload(cls, connection: MDRSConnection, infos: list[UploadFileInfo]) -> None:
+    def __multiple_upload(
-        file_api = FileApi(connection)
+        cls, connection: MDRSConnection, infos: list[UploadFileInfo], is_skip_if_exists: bool
+    ) -> None:
+        file_api = FilesApi(connection)
         with ThreadPoolExecutor(max_workers=CONCURRENT) as pool:
-            pool.map(lambda x: cls.__multiple_upload_worker(file_api, x), infos)
+            pool.map(lambda x: cls.__multiple_upload_worker(file_api, x, is_skip_if_exists), infos)
 
     @classmethod
-    def __multiple_upload_worker(cls, file_api: FileApi, info: UploadFileInfo) -> None:
+    def __multiple_upload_worker(cls, file_api: FilesApi, info: UploadFileInfo, is_skip_if_exists: bool) -> None:
         basename = os.path.basename(info.path)
         file = info.folder.find_file(basename)
         try:
             if file is None:
                 file_api.create(info.folder.id, info.path)
-            else:
+            elif not is_skip_if_exists or file.size != os.path.getsize(info.path):
                 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/config.py

@@ -2,7 +2,7 @@ import configparser
 import os
 from typing import Final
 
-import validators  # type: ignore
+import validators
 
 from mdrsclient.exceptions import IllegalArgumentException
 from mdrsclient.settings import CONFIG_DIRNAME
@@ -41,7 +41,7 @@ class ConfigFile:
 
     @url.setter
     def url(self, url: str) -> None:
-        if not validators.url(url):  # type: ignore
+        if not validators.url(url):
             raise IllegalArgumentException("malformed URI sequence")
         self.__load()
         if self.__config.has_section(self.remote):

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]
+    data: dict[str, str | int] | MultipartEncoder
-    files: dict[str, BufferedReader]
+    headers: dict[str, str]
 
 
 class _KwArgsMDRSConnectionPut(TypedDict, total=False):
     params: dict[str, str | int]
-    data: dict[str, str | int]
+    data: dict[str, str | int] | MultipartEncoder
-    files: dict[str, BufferedReader]
+    headers: dict[str, str]
 
 
 class _KwArgsMDRSConnectionDelete(TypedDict, total=False):

mdrsclient/models/folder.py

@@ -8,28 +8,37 @@ from mdrsclient.models.utils import iso8601_to_user_friendly
 
 
 class FolderAccessLevelItem(NamedTuple):
-    id: int
+    mask: int
     key: str
     label: str
 
 
 class FolderAccessLevel:
+    # Bit Mask
+    # - bit 0: Is Private
+    # - bit 1: Is Public
+    # - bit 2: With Password
+    # - bit 3-7: (Reserved)
+    # - bit 8-15: Restricted Open
     ACCESS_LEVELS: Final[list[FolderAccessLevelItem]] = [
-        FolderAccessLevelItem(-1, "storage", "Storage"),
+        FolderAccessLevelItem(0x0204, "5kikan_or_pw_open", "5Kikan or PW Open"),
-        FolderAccessLevelItem(0, "private", "Private"),
+        FolderAccessLevelItem(0x0104, "cbs_or_pw_open", "CBS or PW Open"),
-        FolderAccessLevelItem(1, "cbs_open", "CBS Open"),
+        FolderAccessLevelItem(0x0200, "5kikan_open", "5Kikan Open"),
-        FolderAccessLevelItem(2, "pw_open", "PW Open"),
+        FolderAccessLevelItem(0x0100, "cbs_open", "CBS Open"),
-        FolderAccessLevelItem(3, "public", "Public"),
+        FolderAccessLevelItem(0x0004, "pw_open", "PW Open"),
+        FolderAccessLevelItem(0x0002, "public", "Public"),
+        FolderAccessLevelItem(0x0001, "private", "Private"),
+        FolderAccessLevelItem(0x0000, "storage", "Storage"),
     ]
 
     @staticmethod
     def key2id(key: str) -> int | None:
         acl = next((x for x in FolderAccessLevel.ACCESS_LEVELS if x.key == key), None)
-        return acl.id if acl is not None else None
+        return acl.mask if acl is not None else None
 
     @staticmethod
     def id2label(id: int) -> str | None:
-        acl = next((x for x in FolderAccessLevel.ACCESS_LEVELS if x.id == id), None)
+        acl = next((x for x in FolderAccessLevel.ACCESS_LEVELS if (x.mask & id) == x.mask), None)
         return acl.label if acl is not None else None
 
 
@@ -40,7 +49,8 @@ class FolderSimple:
     name: str
     access_level: int
     lock: bool
-    lab_id: int
+    size: int
+    laboratory_id: int
     description: str
     created_at: str
     updated_at: str

pyproject.toml

@@ -0,0 +1,76 @@
+[tool.poetry]
+name = "mdrs-client-python"
+version = "1.3.11"
+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"
+readme = "README.md"
+classifiers=[
+    "Development Status :: 3 - Alpha",
+    "Environment :: Console",
+    "Intended Audience :: Developers",
+    "Intended Audience :: Science/Research",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
+    "OSI Approved :: MIT License",
+    "Topic :: Utilities",
+]
+packages = [
+    { include = "mdrsclient" }
+]
+
+[tool.poetry.dependencies]
+python = "^3.10"
+requests = "^2.32.3"
+requests-toolbelt = "^1.0.0"
+python-dotenv = "^1.0.1"
+pydantic = "^2.10.5"
+pydantic-settings = "^2.7.1"
+PyJWT = "^2.10.1"
+validators = "^0.34.0"
+
+[tool.poetry.group.dev.dependencies]
+black = "^24.10.0"
+flake8 = "^7.1.1"
+Flake8-pyproject = "^1.2.3"
+isort = "^5.13.2"
+pyright = "^1.1.391"
+
+[tool.poetry.scripts]
+mdrs = 'mdrsclient.__main__:main'
+
+[build-system]
+requires = ["poetry-core"]
+build-backend = "poetry.core.masonry.api"
+
+[tool.black]
+line-length = 120
+target-version = ['py310']
+include = '\.pyi?$'
+exclude = '''
+/(
+    \.git
+  | \.venv
+  | __pycache__
+  | dist
+)/
+'''
+
+[tool.flake8]
+exclude = ".git, .venv, __pycache__, dist"
+max-complexity = 10
+max-line-length = 120
+
+[tool.isort]
+profile = "black"
+line_length = 120
+
+[tool.mypy]
+
+[tool.pyright]
+typeCheckingMode = "basic"
+exclude = ["**/__pycache__", "**/.*", "dist"]
+#reportUnknownMemberType = "warning"
+#reportUnknownVariableType = "warning"

requirements.txt

@@ -1,6 +0,0 @@
-requests
-python-dotenv
-pydantic
-pydantic-settings
-PyJWT
-validators

setup.py

@@ -1,40 +0,0 @@
-import os
-from typing import Final
-
-from setuptools import find_packages, setup
-
-from mdrsclient import __version__
-
-BASE_DIR: Final[str] = os.path.realpath(os.path.dirname(__file__))
-
-with open(os.path.join(BASE_DIR, "requirements.txt")) as f:
-    __requirements__ = f.read().splitlines()
-
-with open(os.path.join(BASE_DIR, "README.md")) as f:
-    __readme__ = f.read()
-
-setup(
-    name="mdrsclient",
-    version=__version__,
-    description="A MDRS command-line tool",
-    long_description=__readme__,
-    author="Neuroinformatics Unit, RIKEN CBS",
-    license="MIT",
-    classifiers=[
-        "Development Status :: 3 - Alpha",
-        "Environment :: Console",
-        "Intended Audience :: Developers",
-        "Intended Audience :: Science/Research",
-        "Programming Language :: Python :: 3.10",
-        "Programming Language :: Python :: 3.11",
-        "OSI Approved :: MIT License",
-        "Topic :: Utilities",
-    ],
-    packages=find_packages(),
-    include_package_data=True,
-    package_data={
-        "mdrsclient": ["VERSION"],
-    },
-    install_requires=__requirements__,
-    entry_points={"console_scripts": ["mdrs=mdrsclient.__main__:main"]},
-)