.cspell.json

@@ -16,11 +16,7 @@
     "mdrsclient",
     "neurodata",
     "Neuroinformatics",
-    "orcid",
     "RIKEN"
   ],
-  "ignorePaths": [
-    ".env",
-    "__pycache__"
-  ]
+  "ignorePaths": [".env", "__pycache__"]
 }

.gitignore

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

README.md

@@ -60,7 +60,7 @@ List the folder contents
 
 ```shell
 mdrs ls neurodata:/NIU/Repository/
-mdrs ls -p SHARING_PASSWORD neurodata:/NIU/Repository/PW_Open/
+mdrs ls -p PW_OPEN_PASSWORD neurodata:/NIU/Repository/PW_Open/
 mdrs ls -r neurodata:/NIU/Repository/Dataset1/
 mdrs ls -J -r neurodata:/NIU/Repository/Dataset1/
 ```
@@ -80,7 +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 --skip-if-exists ./dataset neurodata:/NIU/Repository/TEST/
+mdrs upload -r -s ./dataset neurodata:/NIU/Repository/TEST/
 ```
 
 ### download
@@ -90,9 +90,8 @@ Download the file or folder
 ```shell
 mdrs download neurodata:/NIU/Repository/TEST/sample.dat ./
 mdrs download -r neurodata:/NIU/Repository/TEST/dataset/ ./
-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/ ./
+mdrs download -p PW_OPEN_PASSWORD neurodata:/NIU/Repository/PW_Open/Readme.dat ./
+mdrs download -r  --exclude /NIU/Repository/TEST/dataset/skip neurodata:/NIU/Repository/TEST/dataset/ ./
 ```
 
 ### mv
@@ -129,7 +128,7 @@ 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 SHARING_PASSWORD neurodata:/NIU/Repository/PW_Open
+mdrs chacl pw_open -r -p PW_OPEN_PASSWORD neurodata:/NIU/Repository/PW_Open
 ```
 
 ### metadata
@@ -138,7 +137,7 @@ Get a folder metadata
 
 ```shell
 mdrs metadata neurodata:/NIU/Repository/TEST/
-mdrs metadata -p SHARING_PASSWORD neurodata:/NIU/Repository/PW_Open/
+mdrs metadata -p PW_OPEN_PASSWORD neurodata:/NIU/Repository/PW_Open/
 ```
 
 ### file-metadata
@@ -147,7 +146,7 @@ Get the file metadata
 
 ```shell
 mdrs file-metadata neurodata:/NIU/Repository/TEST/dataset/sample.dat
-mdrs file-metadata -p SHARING_PASSWORD neurodata:/NIU/Repository/PW_Open/Readme.txt
+mdrs file-metadata -p PW_OPEN_PASSWORD neurodata:/NIU/Repository/PW_Open/Readme.txt
 ```
 
 ### help

mdrsclient/VERSION

@@ -1 +1 @@
-1.3.11
+1.3.7

mdrsclient/__main__.py

@@ -1,6 +1,5 @@
 import argparse
 import sys
-from json import JSONDecodeError
 
 from mdrsclient.commands import (
     ChaclCommand,
@@ -53,9 +52,6 @@ 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/users.py

@@ -20,10 +20,8 @@ class UsersCurrentResponseLaboratory:
 class UsersApiCurrentResponse:
     id: int
     username: str
-    first_name: str
-    last_name: str
+    full_name: str
     email: str
-    orcid_id: str
     laboratories: list[UsersCurrentResponseLaboratory]
     is_staff: bool
     is_active: bool

mdrsclient/commands/download.py

@@ -22,7 +22,6 @@ class DownloadFileInfo:
 @dataclass
 class DownloadContext:
     hasError: bool
-    isSkipIfExists: bool
     files: list[DownloadFileInfo]
 
 
@@ -33,12 +32,6 @@ 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"
         )
@@ -52,20 +45,13 @@ 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
         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)
+        cls.download(remote_path, local_path, is_recursive, password, excludes)
 
     @classmethod
     def download(
-        cls,
-        remote_path: str,
-        local_path: str,
-        is_recursive: bool,
-        is_skip_if_exists: bool,
-        password: str | None,
-        excludes: list[str],
+        cls, remote_path: str, local_path: str, is_recursive: 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("/")
@@ -81,7 +67,7 @@ class DownloadCommand(BaseCommand):
         if file is not None:
             if cls.__check_excludes(excludes, laboratory, r_parent_folder, file):
                 return
-            context = DownloadContext(False, is_skip_if_exists, [])
+            context = DownloadContext(False, [])
             l_path = os.path.join(l_dirname, r_basename)
             context.files.append(DownloadFileInfo(file, l_path))
             cls.__multiple_download(connection, context)
@@ -93,7 +79,7 @@ class DownloadCommand(BaseCommand):
                 raise IllegalArgumentException(f"Cannot download `{r_path}`: Is a folder.")
             folder_api = FoldersApi(connection)
             cls.__multiple_download_pickup_recursive_files(
-                connection, folder_api, laboratory, folder.id, l_dirname, excludes, is_skip_if_exists
+                connection, folder_api, laboratory, folder.id, l_dirname, excludes
             )
 
     @classmethod
@@ -105,9 +91,8 @@ class DownloadCommand(BaseCommand):
         folder_id: str,
         basedir: str,
         excludes: list[str],
-        is_skip_if_exists: bool,
     ) -> None:
-        context = DownloadContext(False, is_skip_if_exists, [])
+        context = DownloadContext(False, [])
         folder = folder_api.retrieve(folder_id)
         dirname = os.path.join(basedir, folder.name)
         if cls.__check_excludes(excludes, laboratory, folder, None):
@@ -125,34 +110,28 @@ class DownloadCommand(BaseCommand):
             raise UnexpectedException("Some files failed to download.")
         for sub_folder in folder.sub_folders:
             cls.__multiple_download_pickup_recursive_files(
-                connection, folder_api, laboratory, sub_folder.id, dirname, excludes, is_skip_if_exists
+                connection, folder_api, laboratory, sub_folder.id, dirname, excludes
             )
 
     @classmethod
     def __multiple_download(cls, connection: MDRSConnection, context: DownloadContext) -> None:
         file_api = FilesApi(connection)
         with ThreadPoolExecutor(max_workers=CONCURRENT) as pool:
-            results = pool.map(
-                lambda x: cls.__multiple_download_worker(file_api, x, context.isSkipIfExists), context.files
-            )
+            results = pool.map(lambda x: cls.__multiple_download_worker(file_api, x), 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: FilesApi, info: DownloadFileInfo, is_skip_if_exists: bool) -> bool:
-        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
+    def __multiple_download_worker(cls, file_api: FilesApi, info: DownloadFileInfo) -> bool:
+        try:
+            file_api.download(info.file, info.path)
+        except Exception:
+            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()
+        path = f"/{laboratory.name}{folder.path}{file.name if file is not None else ""}".rstrip("/").lower()
         return path in excludes

mdrsclient/config.py

@@ -2,7 +2,7 @@ import configparser
 import os
 from typing import Final
 
-import validators
+import validators  # type: ignore
 
 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):
+        if not validators.url(url):  # type: ignore
             raise IllegalArgumentException("malformed URI sequence")
         self.__load()
         if self.__config.has_section(self.remote):

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "mdrs-client-python"
-version = "1.3.11"
+version = "1.3.7"
 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"
@@ -13,7 +13,6 @@ classifiers=[
     "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",
 ]
@@ -26,17 +25,17 @@ 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"
+pydantic = "^2.8.2"
+pydantic-settings = "^2.3.4"
+PyJWT = "^2.8.0"
+validators = "^0.33.0"
 
 [tool.poetry.group.dev.dependencies]
-black = "^24.10.0"
-flake8 = "^7.1.1"
+black = "^24.2.2"
+flake8 = "^7.1.0"
 Flake8-pyproject = "^1.2.3"
 isort = "^5.13.2"
-pyright = "^1.1.391"
+pyright = "^1.1.372"
 
 [tool.poetry.scripts]
 mdrs = 'mdrsclient.__main__:main'