update version to 1.3.11

.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",
@@ -9,7 +16,11 @@
     "mdrsclient",
     "neurodata",
     "Neuroinformatics",
+    "orcid",
     "RIKEN"
   ],
-  "ignorePaths": [".env", "__pycache__"]
+  "ignorePaths": [
+    ".env",
+    "__pycache__"
+  ]
 }

.gitignore

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

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

@@ -60,7 +60,7 @@ List the folder contents
 
 ```shell
 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 -J -r neurodata:/NIU/Repository/Dataset1/
 ```
@@ -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 --skip-if-exists ./dataset neurodata:/NIU/Repository/TEST/
 ```
 
 ### download
@@ -89,7 +90,9 @@ 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 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
@@ -115,8 +118,8 @@ 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 neurodata:/NIU/Repository/TEST/sample.dat
-mdrs rm -r neurodata:/NIU/Repository/TEST2/dataset
+mdrs rm -r neurodata:/NIU/Repository/TEST/dataset
 ```
 
 ### chacl
@@ -126,7 +129,7 @@ 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 SHARING_PASSWORD neurodata:/NIU/Repository/PW_Open
 ```
 
 ### metadata
@@ -135,7 +138,7 @@ Get a folder metadata
 
 ```shell
 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
@@ -144,7 +147,7 @@ Get the file metadata
 
 ```shell
 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

mdrsclient/VERSION

@@ -1 +1 @@
-1.3.1
+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/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 +33,43 @@ 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:
+            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(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
@@ -95,6 +111,7 @@ class FilesApi(BaseApi):
     def download(self, file: File, path: str) -> bool:
         # print(self.__class__.__name__ + "::" + sys._getframe().f_code.co_name)
         url = file.download_url
+        token_check(self.connection)
         response = self.connection.get(url, stream=True)
         self._raise_response_error(response)
         try:
@@ -106,3 +123,9 @@ 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/api/users.py

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

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/download.py

@@ -8,8 +8,8 @@ from pydantic.dataclasses import dataclass
 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)
@@ -52,10 +78,13 @@ 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:
@@ -63,31 +92,67 @@ class DownloadCommand(BaseCommand):
             if not is_recursive:
                 raise IllegalArgumentException(f"Cannot download `{r_path}`: Is a folder.")
             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: FoldersApi, 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 = 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: FilesApi, 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/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/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):

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "mdrs-client-python"
-version = "1.3.3"
+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"
@@ -13,6 +13,7 @@ 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",
 ]
@@ -22,19 +23,20 @@ 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 = "^2.10.5"
-pydantic-settings = "^2.1.0"
+pydantic-settings = "^2.7.1"
-PyJWT = "^2.8.0"
+PyJWT = "^2.10.1"
-validators = "^0.22.0"
+validators = "^0.34.0"
 
 [tool.poetry.group.dev.dependencies]
-black = "^24.2.0"
+black = "^24.10.0"
-flake8 = "^7.0.0"
+flake8 = "^7.1.1"
 Flake8-pyproject = "^1.2.3"
 isort = "^5.13.2"
-pyright = "^1.1.350"
+pyright = "^1.1.391"
 
 [tool.poetry.scripts]
 mdrs = 'mdrsclient.__main__:main'