refactor: extract MdrsClient service layer for library portability

To improve the tool's portability as a Python library, the core logic
has been decoupled from the CLI interface. This allows developers to
programmatically interact with MDRS without relying on CLI-specific
argument parsing or local file-based caches.

- Introduce `MdrsClient` service layer to handle core operations.
- Abstract authentication state using `CacheInterface` and `InMemoryCache`.
- Migrate all CLI commands to utilize `MdrsClient` for execution.
- Separate `Doi` data model from API responses and move to `models/doi.py`.
- Update `README.md` to include Python API usage examples.
- Bump package version to 1.3.17.

README.md

@@ -8,7 +8,7 @@ The mdrs-client-python is python library and a command-line client for up- and d
 poetry install
 ```
 
-## Example Usage
+## CLI Usage
 
 ### config create
 
@@ -82,13 +82,17 @@ mdrs labs neurodata:
 
 ### ls
 
-List the folder contents
+List the folder contents. You can also specify a DOI path in the form `remote:10.xxxx/yyy.ID[/optional/subpath]`.
 
 ```shell
 mdrs ls neurodata:/NIU/Repository/
 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/
+
+# DOI access examples:
+mdrs ls neurodata:10.60178/cbs.20260429-001
+mdrs ls "neurodata:10.60178/cbs.20260429-001/Figure 1"
 ```
 
 ### mkdir
@@ -111,7 +115,7 @@ mdrs upload -r --skip-if-exists ./dataset neurodata:/NIU/Repository/TEST/
 
 ### download
 
-Download the file or folder
+Download the file or folder. You can also specify a DOI path.
 
 ```shell
 mdrs download neurodata:/NIU/Repository/TEST/sample.dat ./
@@ -119,6 +123,10 @@ 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/ ./
+
+# DOI access examples:
+mdrs download neurodata:10.60178/cbs.20260429-001/README_NeuroData.md ./
+mdrs download -r "neurodata:10.60178/cbs.20260429-001/Figure 1" ./
 ```
 
 ### mv
@@ -160,20 +168,26 @@ mdrs chacl pw_open -r -p SHARING_PASSWORD neurodata:/NIU/Repository/PW_Open
 
 ### metadata
 
-Get a folder metadata
+Get a folder metadata. You can also specify a DOI path.
 
 ```shell
 mdrs metadata neurodata:/NIU/Repository/TEST/
 mdrs metadata -p SHARING_PASSWORD neurodata:/NIU/Repository/PW_Open/
+
+# DOI access examples:
+mdrs metadata neurodata:10.60178/cbs.20260429-001
 ```
 
 ### file-metadata
 
-Get the file metadata
+Get the file metadata. You can also specify a DOI path.
 
 ```shell
 mdrs file-metadata neurodata:/NIU/Repository/TEST/dataset/sample.dat
 mdrs file-metadata -p SHARING_PASSWORD neurodata:/NIU/Repository/PW_Open/Readme.txt
+
+# DOI access examples:
+mdrs file-metadata "neurodata:10.60178/cbs.20260429-001/Figure 1/Figure1v3.pdf"
 ```
 
 ### version
@@ -191,3 +205,28 @@ Show the help message and exit
 ```shell
 mdrs -h
 ```
+
+## Python API Usage
+
+You can also use this package as a Python library to programmatically interact with MDRS repositories.
+
+```python
+from mdrsclient.client import MdrsClient
+from mdrsclient.cache import InMemoryCache
+
+# 1. Setup client with an in-memory cache to avoid local `.mdrsclient` state files
+cache = InMemoryCache()
+client = MdrsClient.from_remote("neurodata", cache=cache)
+
+# 2. Login to the remote server
+client.login("username", "password")
+
+# 3. Use service methods
+labs = client.get_laboratories()
+metadata = client.metadata("neurodata:/NIU/Repository/")
+
+# Transfer files programmatically
+client.upload("/path/to/local/data", "neurodata:/NIU/Repository/TEST/", is_recursive=True)
+client.download("neurodata:/NIU/Repository/TEST/data", "/path/to/local", is_recursive=True)
+```
+

mdrsclient/__init__.py

@@ -1,3 +1,7 @@
 from mdrsclient.__version__ import __version__
 
 __all__ = ["__version__"]
+
+from mdrsclient.client import MdrsClient
+
+__all__ = ["MdrsClient"]

mdrsclient/__version__.py

@@ -1,5 +1,9 @@
-from importlib.metadata import version
+import importlib.metadata
+
+try:
+    __version__ = importlib.metadata.version("mdrs-client-python")
+except importlib.metadata.PackageNotFoundError:
+    __version__ = "0.0.0-dev"
 
-__version__ = version("mdrs-client-python")
 
 __all__ = ["__version__"]

mdrsclient/api/__init__.py

@@ -1,9 +1,11 @@
+from mdrsclient.api.doi import DoiApi
 from mdrsclient.api.files import FilesApi
 from mdrsclient.api.folders import FoldersApi
 from mdrsclient.api.laboratories import LaboratoriesApi
 from mdrsclient.api.users import UsersApi
 
 __all__ = [
+    "DoiApi",
     "FilesApi",
     "FoldersApi",
     "LaboratoriesApi",

mdrsclient/api/base.py

@@ -5,12 +5,7 @@ from pydantic import TypeAdapter
 from requests import Response
 
 from mdrsclient.connection import MDRSConnection
-from mdrsclient.exceptions import (
-    BadRequestException,
-    ForbiddenException,
-    UnauthorizedException,
-    UnexpectedException,
-)
+from mdrsclient.exceptions import BadRequestException, ForbiddenException, UnauthorizedException, UnexpectedException
 from mdrsclient.models.error import DRFStandardizedErrors
 
 

mdrsclient/api/doi.py

@@ -0,0 +1,33 @@
+from typing import Final
+
+from pydantic import TypeAdapter
+from pydantic.dataclasses import dataclass
+
+from mdrsclient.api.base import BaseApi
+from mdrsclient.api.utils import token_check
+from mdrsclient.models.doi import Doi
+
+
+@dataclass(frozen=True)
+class DoiRetrieveFolderRef:
+    id: str
+
+
+@dataclass(frozen=True)
+class DoiRetrieveResponse:
+    id: str
+    doi: str
+    folder: DoiRetrieveFolderRef
+
+
+class DoiApi(BaseApi):
+    ENTRYPOINT: Final[str] = "v3/doi/"
+
+    def retrieve(self, doi_id: str) -> Doi:
+        """Retrieve the folder associated with a DOI suffix ID (GET v3/doi/{id}/)."""
+        url = self.ENTRYPOINT + doi_id + "/"
+        token_check(self.connection)
+        response = self.connection.get(url)
+        self._raise_response_error(response)
+        api_resp = TypeAdapter(DoiRetrieveResponse).validate_python(response.json())
+        return Doi(id=api_resp.id, doi=api_resp.doi, folder_id=api_resp.folder.id)

mdrsclient/api/files.py

@@ -1,6 +1,7 @@
 import mimetypes
 import os
 from typing import Any, Final
+from unicodedata import normalize
 
 from pydantic import TypeAdapter
 from pydantic.dataclasses import dataclass
@@ -53,7 +54,10 @@ class FilesApi(BaseApi):
         try:
             with open(os.path.realpath(path), mode="rb") as fp:
                 data = MultipartEncoder(
-                    fields={"folder_id": folder_id, "file": (os.path.basename(path), fp, self._get_mime_type(path))}
+                    fields={
+                        "folder_id": folder_id,
+                        "file": (normalize("NFC", 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)
@@ -75,7 +79,9 @@ class FilesApi(BaseApi):
             # update file body
             try:
                 with open(os.path.realpath(path), mode="rb") as fp:
-                    data = MultipartEncoder(fields={"file": (os.path.basename(path), fp, self._get_mime_type(path))})
+                    data = MultipartEncoder(
+                        fields={"file": (normalize("NFC", 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.")

mdrsclient/cache.py

@@ -2,6 +2,7 @@ import dataclasses
 import hashlib
 import json
 import os
+from typing import Protocol, runtime_checkable
 
 from pydantic import TypeAdapter, ValidationError
 from pydantic.dataclasses import dataclass
@@ -16,7 +17,7 @@ from mdrsclient.utils import FileLock
 class CacheData:
     user: User | None = None
     token: Token | None = None
-    laboratories: Laboratories = Laboratories()
+    laboratories: Laboratories = dataclasses.field(default_factory=Laboratories)
     digest: str = ""
 
     def clear(self) -> None:
@@ -43,6 +44,67 @@ class CacheData:
         ).hexdigest()
 
 
+@runtime_checkable
+class CacheInterface(Protocol):
+    @property
+    def token(self) -> Token | None: ...
+    @token.setter
+    def token(self, token: Token) -> None: ...
+    @token.deleter
+    def token(self) -> None: ...
+
+    @property
+    def user(self) -> User | None: ...
+    @user.setter
+    def user(self, user: User) -> None: ...
+    @user.deleter
+    def user(self) -> None: ...
+
+    @property
+    def laboratories(self) -> Laboratories: ...
+    @laboratories.setter
+    def laboratories(self, laboratories: Laboratories) -> None: ...
+
+
+class InMemoryCache:
+    def __init__(self) -> None:
+        self.__data = CacheData()
+
+    @property
+    def token(self) -> Token | None:
+        return self.__data.token
+
+    @token.setter
+    def token(self, token: Token) -> None:
+        self.__data.token = token
+
+    @token.deleter
+    def token(self) -> None:
+        if self.__data.token is not None:
+            self.__data.token = None
+
+    @property
+    def user(self) -> User | None:
+        return self.__data.user
+
+    @user.setter
+    def user(self, user: User) -> None:
+        self.__data.user = user
+
+    @user.deleter
+    def user(self) -> None:
+        if self.__data.user is not None:
+            self.__data.user = None
+
+    @property
+    def laboratories(self) -> Laboratories:
+        return self.__data.laboratories
+
+    @laboratories.setter
+    def laboratories(self, laboratories: Laboratories) -> None:
+        self.__data.laboratories = laboratories
+
+
 class CacheFile:
     __serial: int
     __cache_dir: str

mdrsclient/client.py

@@ -0,0 +1,266 @@
+import os
+from concurrent.futures import ThreadPoolExecutor
+from typing import Any
+from unicodedata import normalize
+
+from mdrsclient.api import DoiApi, FilesApi, FoldersApi, LaboratoriesApi, UsersApi
+from mdrsclient.commands.base import BaseCommand
+from mdrsclient.connection import MDRSConnection
+from mdrsclient.exceptions import IllegalArgumentException, MDRSException, UnauthorizedException, UnexpectedException
+from mdrsclient.models import File, Folder, Laboratory, Token, User
+from mdrsclient.models.file import find_file
+from mdrsclient.settings import CONCURRENT
+
+
+class MdrsClient:
+    """Service layer client for MDRS."""
+
+    def __init__(self, connection: MDRSConnection):
+        self.connection = connection
+
+    @classmethod
+    def from_remote(cls, remote: str) -> "MdrsClient":
+        return cls(BaseCommand._create_connection(remote))
+
+    def login(self, username: str, password: str) -> tuple[Token, User]:
+        user_api = UsersApi(self.connection)
+        token = user_api.token(username, password)
+        self.connection.token = token
+        user = user_api.current()
+        self.connection.user = user
+        return token, user
+
+    def logout(self) -> None:
+        self.connection.logout()
+
+    def whoami(self) -> User:
+        user_api = UsersApi(self.connection)
+        return user_api.current()
+
+    def get_laboratories(self) -> list[Laboratory]:
+        laboratory_api = LaboratoriesApi(self.connection)
+        labs = laboratory_api.list()
+        self.connection.laboratories = labs
+        return list(labs)
+
+    def mkdir(self, remote_path: str) -> None:
+        remote, laboratory_name, r_path = BaseCommand._parse_remote_host_with_path(remote_path)
+        r_path = r_path.rstrip("/")
+        r_dirname = os.path.dirname(r_path)
+        r_basename = os.path.basename(r_path)
+        laboratory = BaseCommand._find_laboratory(self.connection, laboratory_name)
+        parent_folder = BaseCommand._find_folder(self.connection, laboratory, r_dirname)
+        files = BaseCommand._find_files(self.connection, parent_folder.id)
+        if parent_folder.find_sub_folder(r_basename) is not None or find_file(files, r_basename) is not None:
+            raise IllegalArgumentException(f"Cannot create folder `{r_path}`: File exists.")
+        folder_api = FoldersApi(self.connection)
+        folder_api.create(normalize("NFC", r_basename), parent_folder.id)
+
+    def rm(self, remote_path: str, is_recursive: bool = False) -> None:
+        remote, laboratory_name, r_path = BaseCommand._parse_remote_host_with_path(remote_path)
+        r_path = r_path.rstrip("/")
+        r_dirname = os.path.dirname(r_path)
+        r_basename = os.path.basename(r_path)
+        laboratory = BaseCommand._find_laboratory(self.connection, laboratory_name)
+        parent_folder = BaseCommand._find_folder(self.connection, laboratory, r_dirname)
+        parent_files = BaseCommand._find_files(self.connection, parent_folder.id)
+        file = find_file(parent_files, r_basename)
+        if file is not None:
+            file_api = FilesApi(self.connection)
+            file_api.destroy(file)
+        else:
+            folder = parent_folder.find_sub_folder(r_basename)
+            if folder is None:
+                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 = FoldersApi(self.connection)
+            folder_api.destroy(folder.id, True)
+
+    def ls(self, remote_path: str, password: str | None = None) -> tuple[Folder, list[File]]:
+        folder, laboratory = BaseCommand._resolve_folder(self.connection, remote_path, password)
+        files = BaseCommand._find_files(self.connection, folder.id)
+        return folder, files
+
+    def cp(self, src_path: str, dest_path: str, is_recursive: bool = False) -> None:
+        s_remote, s_laboratory_name, s_path = BaseCommand._parse_remote_host_with_path(src_path)
+        d_remote, d_laboratory_name, d_path = BaseCommand._parse_remote_host_with_path(dest_path)
+        if s_remote != d_remote:
+            raise IllegalArgumentException("Remote host mismatched.")
+        if s_laboratory_name != d_laboratory_name:
+            raise IllegalArgumentException("Laboratory mismatched.")
+        s_path = s_path.rstrip("/")
+        s_dirname = os.path.dirname(s_path)
+        s_basename = os.path.basename(s_path)
+        if d_path.endswith("/"):
+            d_dirname = d_path
+            d_basename = s_basename
+        else:
+            d_dirname = os.path.dirname(d_path)
+            d_basename = os.path.basename(d_path)
+        laboratory = BaseCommand._find_laboratory(self.connection, s_laboratory_name)
+        s_parent_folder = BaseCommand._find_folder(self.connection, laboratory, s_dirname)
+        s_parent_files = BaseCommand._find_files(self.connection, s_parent_folder.id)
+        d_parent_folder = BaseCommand._find_folder(self.connection, laboratory, d_dirname)
+        d_parent_files = BaseCommand._find_files(self.connection, d_parent_folder.id)
+        s_file = find_file(s_parent_files, s_basename)
+        if s_file is not None:
+            d_file = find_file(d_parent_files, d_basename)
+            if d_file is not None:
+                raise IllegalArgumentException(f"File `{d_basename}` already exists.")
+            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 = FilesApi(self.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:
+            s_folder = s_parent_folder.find_sub_folder(s_basename)
+            if s_folder is None:
+                raise IllegalArgumentException(f"File or folder `{s_basename}` not found.")
+            if not is_recursive:
+                raise IllegalArgumentException(f"Cannot copy `{s_path}`: Is a folder.")
+            if find_file(d_parent_files, d_basename) is not None:
+                raise IllegalArgumentException(f"Cannot overwrite non-folder `{d_basename}` with folder `{s_path}`.")
+            d_folder = d_parent_folder.find_sub_folder(d_basename)
+            if d_folder is not None:
+                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 = FoldersApi(self.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))
+
+    def mv(self, src_path: str, dest_path: str) -> None:
+        s_remote, s_laboratory_name, s_path = BaseCommand._parse_remote_host_with_path(src_path)
+        d_remote, d_laboratory_name, d_path = BaseCommand._parse_remote_host_with_path(dest_path)
+        if s_remote != d_remote:
+            raise IllegalArgumentException("Remote host mismatched.")
+        if s_laboratory_name != d_laboratory_name:
+            raise IllegalArgumentException("Laboratory mismatched.")
+        s_path = s_path.rstrip("/")
+        s_dirname = os.path.dirname(s_path)
+        s_basename = os.path.basename(s_path)
+        if d_path.endswith("/"):
+            d_dirname = d_path
+            d_basename = s_basename
+        else:
+            d_dirname = os.path.dirname(d_path)
+            d_basename = os.path.basename(d_path)
+        laboratory = BaseCommand._find_laboratory(self.connection, s_laboratory_name)
+        s_parent_folder = BaseCommand._find_folder(self.connection, laboratory, s_dirname)
+        s_parent_files = BaseCommand._find_files(self.connection, s_parent_folder.id)
+        d_parent_folder = BaseCommand._find_folder(self.connection, laboratory, d_dirname)
+        d_parent_files = BaseCommand._find_files(self.connection, d_parent_folder.id)
+        s_file = find_file(s_parent_files, s_basename)
+        if s_file is not None:
+            d_file = find_file(d_parent_files, d_basename)
+            if d_file is not None:
+                raise IllegalArgumentException(f"File `{d_basename}` already exists.")
+            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 = FilesApi(self.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:
+            s_folder = s_parent_folder.find_sub_folder(s_basename)
+            if s_folder is None:
+                raise IllegalArgumentException(f"File or folder `{s_basename}` not found.")
+            if find_file(d_parent_files, d_basename) is not None:
+                raise IllegalArgumentException(f"Cannot overwrite non-folder `{d_basename}` with folder `{s_path}`.")
+            d_folder = d_parent_folder.find_sub_folder(d_basename)
+            if d_folder is not None:
+                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 = FoldersApi(self.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))
+
+    def chacl(
+        self, remote_path: str, access_level: int, is_recursive: bool = False, password: str | None = None
+    ) -> None:
+        remote, laboratory_name, r_path = BaseCommand._parse_remote_host_with_path(remote_path)
+        r_path = r_path.rstrip("/")
+        laboratory = BaseCommand._find_laboratory(self.connection, laboratory_name)
+        folder = BaseCommand._find_folder(self.connection, laboratory, r_path)
+        folder_api = FoldersApi(self.connection)
+        folder_api.acl(folder.id, access_level, is_recursive, password)
+
+    def metadata(self, remote_path: str, password: str | None = None) -> dict:
+        folder, laboratory = BaseCommand._resolve_folder(self.connection, remote_path, password)
+        folder_api = FoldersApi(self.connection)
+        return folder_api.metadata(folder.id)
+
+    def file_metadata(self, remote_path: str, password: str | None = None) -> dict:
+        folder, laboratory, r_basename = BaseCommand._resolve_file(self.connection, remote_path, password)
+        files = BaseCommand._find_files(self.connection, folder.id)
+        file = find_file(files, r_basename)
+        if file is None:
+            raise IllegalArgumentException(f"File `{r_basename}` not found.")
+        file_api = FilesApi(self.connection)
+        return file_api.metadata(file)
+
+    def _create_connection(self, remote: str):
+        return self.connection
+
+    def upload(
+        self, local_path: str, remote_path: str, is_recursive: bool = False, is_skip_if_exists: bool = False
+    ) -> None:
+        from mdrsclient.commands.upload import UploadCommand
+
+        UploadCommand._upload_logic(self.connection, local_path, remote_path, is_recursive, is_skip_if_exists)
+
+    def download(
+        self,
+        remote_path: str,
+        local_path: str,
+        is_recursive: bool = False,
+        is_skip_if_exists: bool = False,
+        password: str | None = None,
+        excludes: list[str] | None = None,
+    ) -> None:
+        from mdrsclient.commands.download import DownloadCommand
+
+        DownloadCommand._download_logic(
+            self.connection, remote_path, local_path, is_recursive, is_skip_if_exists, password, excludes or []
+        )
+
+    def ls_command(
+        self,
+        remote_path: str,
+        password: str | None = None,
+        is_json: bool = False,
+        is_recursive: bool = False,
+        is_quiet: bool = False,
+    ) -> None:
+        from mdrsclient.commands.ls import LsCommand
+
+        LsCommand._ls_logic(self.connection, remote_path, password, is_json, is_recursive, is_quiet)
+
+    def version(self) -> str:
+        from mdrsclient.__version__ import __version__
+
+        return f"mdrs {__version__}"
+
+    def config_create(self, remote: str, url: str) -> None:
+        from mdrsclient.commands.config import ConfigCommand
+
+        ConfigCommand.create(remote, url)
+
+    def config_update(self, remote: str, url: str) -> None:
+        from mdrsclient.commands.config import ConfigCommand
+
+        ConfigCommand.update(remote, url)
+
+    def config_list(self) -> list:
+        from mdrsclient.config import ConfigFile
+
+        config = ConfigFile("")
+        return config.list()
+
+    def config_delete(self, remote: str) -> None:
+        from mdrsclient.commands.config import ConfigCommand
+
+        ConfigCommand.delete(remote)

mdrsclient/commands/base.py

@@ -1,9 +1,10 @@
+import os
 import re
 from abc import ABC, abstractmethod
 from typing import Any
 from unicodedata import normalize
 
-from mdrsclient.api import FilesApi, FoldersApi, LaboratoriesApi
+from mdrsclient.api import DoiApi, FilesApi, FoldersApi, LaboratoriesApi
 from mdrsclient.config import ConfigFile
 from mdrsclient.connection import MDRSConnection
 from mdrsclient.exceptions import (
@@ -95,3 +96,172 @@ class BaseCommand(ABC):
             laboratory = folder_array.pop(0)
             folder = "/" + "/".join(folder_array)
         return (remote_host, laboratory, folder)
+
+    # ------------------------------------------------------------------
+    # DOI helpers
+    # ------------------------------------------------------------------
+
+    @staticmethod
+    def _is_doi(path_component: str) -> bool:
+        """Return True if path_component looks like a DOI string.
+
+        A DOI is recognised as a string that starts with ``10.`` and
+        contains a ``/``.
+        """
+        return path_component.startswith("10.") and "/" in path_component
+
+    @staticmethod
+    def _doi_suffix_id(doi: str) -> str:
+        """Extract the internal system ID from a full DOI string.
+
+        MDRS uses the segment after the last ``.`` in the suffix (the part
+        after the ``/``) as its identifier.
+        Example: ``10.xxxx/prefix.20230511-001`` → ``20230511-001``.
+        If there is no ``.`` in the suffix, the whole suffix is returned.
+        Trailing slashes are stripped before processing.
+        """
+        # Strip any trailing slash first.
+        doi = doi.rstrip("/")
+        slash_pos = doi.find("/")
+        if slash_pos == -1:
+            return doi
+        suffix = doi[slash_pos + 1 :]
+        dot_pos = suffix.rfind(".")
+        return suffix[dot_pos + 1 :] if dot_pos != -1 else suffix
+
+    @staticmethod
+    def _split_doi_and_subpath(doi_with_path: str) -> tuple[str, str]:
+        """Split a DOI-with-optional-path string into (doi, subpath)."""
+        # Find the first '/' that separates registrant from suffix.
+        first_slash = doi_with_path.find("/")
+        if first_slash != -1:
+            after_suffix_start = first_slash + 1
+            after_first = doi_with_path[after_suffix_start:]
+            # Find the next '/' inside the suffix portion — this starts the subpath.
+            second_slash = after_first.find("/")
+            if second_slash != -1:
+                doi_end = after_suffix_start + second_slash
+                doi = doi_with_path[:doi_end]
+                subpath = doi_with_path[doi_end:]  # begins with "/"
+                # Treat a bare trailing slash as no subpath (root of DOI folder).
+                if subpath == "/":
+                    return (doi, "")
+                else:
+                    return (doi, subpath)
+            else:
+                # No second slash — the whole string is the DOI, no subpath.
+                return (doi_with_path, "")
+        else:
+            return (doi_with_path, "")
+
+    @classmethod
+    def _parse_doi_remote_host(cls, path: str) -> tuple[str, str, str]:
+        """Parse ``remote:10.xxxx/prefix.ID[/optional/sub/path]`` into ``(remote, doi, subpath)``."""
+        parts = path.split(":", 1)
+        if len(parts) != 2:
+            raise IllegalArgumentException("remote_path must be in the form 'remote:10.xxxx/prefix.ID'")
+        remote, doi_with_path = parts
+        if not cls._is_doi(doi_with_path):
+            raise IllegalArgumentException(
+                f"Path `{doi_with_path}` does not look like a DOI (must start with '10.' and contain '/')."
+            )
+        doi, subpath = cls._split_doi_and_subpath(doi_with_path)
+        return (remote, doi, subpath)
+
+    @classmethod
+    def _find_folder_by_doi(
+        cls,
+        connection: MDRSConnection,
+        doi: str,
+        password: str | None = None,
+    ) -> tuple[Folder, Laboratory]:
+        """Resolve a DOI to a (Folder, Laboratory) pair.
+
+        Calls GET v3/doi/{id}/ to look up the folder ID, retrieves the full
+        folder detail (which carries ``laboratory_id``), and resolves the
+        laboratory from that field.
+        """
+        doi_clean = doi.rstrip("/")
+        doi_id = cls._doi_suffix_id(doi_clean)
+        doi_api = DoiApi(connection)
+        doi_resp = doi_api.retrieve(doi_id)
+
+        # Verify the returned DOI matches the one supplied (case-insensitive).
+        returned_doi = doi_resp.doi.rstrip("/")
+        if returned_doi.lower() != doi_clean.lower():
+            raise IllegalArgumentException(
+                f"DOI mismatch: requested `{doi_clean}` but server returned `{returned_doi}`."
+            )
+
+        folder_api = FoldersApi(connection)
+
+        # Retrieve full folder detail directly by ID; laboratory_id is here.
+        folder = folder_api.retrieve(doi_resp.folder_id)
+
+        if folder.lock:
+            if password is None:
+                raise UnauthorizedException(f"Folder for DOI `{doi_clean}` is locked.")
+            folder_api.auth(doi_resp.folder.id, password)
+
+        # Resolve laboratory using laboratory_id from the full folder detail.
+        lab_api = LaboratoriesApi(connection)
+        labs = lab_api.list()
+        lab = labs.find_by_id(folder.laboratory_id)
+        if lab is None:
+            raise UnexpectedException(f"Laboratory with id {folder.laboratory_id} not found.")
+
+        connection.laboratories = labs
+        return (folder, lab)
+
+    @classmethod
+    def _resolve_folder(
+        cls,
+        connection: MDRSConnection,
+        remote_path: str,
+        password: str | None = None,
+    ) -> tuple[Folder, Laboratory]:
+        """Resolve any remote path (normal or DOI) into a (Folder, Laboratory) pair."""
+        path_component = remote_path.split(":", 1)[1] if ":" in remote_path else ""
+        if cls._is_doi(path_component):
+            remote, doi, subpath = cls._parse_doi_remote_host(remote_path)
+            doi_folder, laboratory = cls._find_folder_by_doi(connection, doi, password)
+            if not subpath:
+                return (doi_folder, laboratory)
+            else:
+                abs_path = doi_folder.path.rstrip("/") + subpath
+                folder = cls._find_folder(connection, laboratory, abs_path, password)
+                return (folder, laboratory)
+        else:
+            remote, laboratory_name, r_path = cls._parse_remote_host_with_path(remote_path)
+            laboratory = cls._find_laboratory(connection, laboratory_name)
+            folder = cls._find_folder(connection, laboratory, r_path, password)
+            return (folder, laboratory)
+
+    @classmethod
+    def _resolve_file(
+        cls,
+        connection: MDRSConnection,
+        remote_path: str,
+        password: str | None = None,
+    ) -> tuple[Folder, Laboratory, str]:
+        """Resolve a remote path pointing to a file into the parent Folder, its Laboratory, and the file's basename."""
+        path_component = remote_path.split(":", 1)[1] if ":" in remote_path else ""
+        if cls._is_doi(path_component):
+            remote, doi, subpath = cls._parse_doi_remote_host(remote_path)
+            doi_folder, laboratory = cls._find_folder_by_doi(connection, doi, password)
+            subpath_clean = subpath.rstrip("/")
+            if not subpath_clean:
+                raise IllegalArgumentException("DOI path must point to a file, not a folder.")
+            r_dirname = os.path.dirname(subpath_clean)
+            r_basename = os.path.basename(subpath_clean)
+            abs_path = doi_folder.path.rstrip("/") + r_dirname
+            parent_folder = cls._find_folder(connection, laboratory, abs_path, password)
+            return (parent_folder, laboratory, r_basename)
+        else:
+            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)
+            r_basename = os.path.basename(r_path)
+            laboratory = cls._find_laboratory(connection, laboratory_name)
+            parent_folder = cls._find_folder(connection, laboratory, r_dirname, password)
+            return (parent_folder, laboratory, r_basename)

mdrsclient/commands/chacl.py

@@ -31,10 +31,8 @@ class ChaclCommand(BaseCommand):
 
     @classmethod
     def chacl(cls, remote_path: str, access_level: int, is_recursive: bool, password: str | None) -> None:
-        (remote, laboratory_name, r_path) = cls._parse_remote_host_with_path(remote_path)
-        r_path = r_path.rstrip("/")
-        connection = cls._create_connection(remote)
-        laboratory = cls._find_laboratory(connection, laboratory_name)
-        folder = cls._find_folder(connection, laboratory, r_path)
-        folder_api = FoldersApi(connection)
-        folder_api.acl(folder.id, access_level, is_recursive, password)
+        remote = remote_path.split(":", 1)[0] if ":" in remote_path else ""
+        from mdrsclient.client import MdrsClient
+
+        client = MdrsClient.from_remote(remote)
+        client.chacl(remote_path, access_level, is_recursive, password)

mdrsclient/commands/config.py

@@ -28,7 +28,9 @@ class ConfigCommand(BaseCommand):
         list_parser = config_parsers.add_parser("list", help="list all the remote hosts", aliases=["ls"])
         list_parser.set_defaults(func=cls.func_list)
         # config delete
-        delete_parser = config_parsers.add_parser("delete", help="delete an existing remote host", aliases=["remove", "rm"])
+        delete_parser = config_parsers.add_parser(
+            "delete", help="delete an existing remote host", aliases=["remove", "rm"]
+        )
         delete_parser.add_argument("remote", help="label of remote host")
         delete_parser.set_defaults(func=cls.func_delete)
 
@@ -36,13 +38,17 @@ class ConfigCommand(BaseCommand):
     def func_create(cls, args: Namespace) -> None:
         remote = str(args.remote)
         url = str(args.url)
-        cls.create(remote, url)
+        from mdrsclient.client import MdrsClient
+
+        MdrsClient(None).config_create(remote, url)
 
     @classmethod
     def func_update(cls, args: Namespace) -> None:
         remote = str(args.remote)
         url = str(args.url)
-        cls.update(remote, url)
+        from mdrsclient.client import MdrsClient
+
+        MdrsClient(None).config_update(remote, url)
 
     @classmethod
     def func_list(cls, args: Namespace) -> None:
@@ -51,7 +57,9 @@ class ConfigCommand(BaseCommand):
     @classmethod
     def func_delete(cls, args: Namespace) -> None:
         remote = str(args.remote)
-        cls.delete(remote)
+        from mdrsclient.client import MdrsClient
+
+        MdrsClient(None).config_delete(remote)
 
     @classmethod
     def create(cls, remote: str, url: str) -> None:
@@ -73,8 +81,10 @@ class ConfigCommand(BaseCommand):
 
     @classmethod
     def list(cls) -> None:
-        config = ConfigFile("")
-        for remote, url in config.list():
+        from mdrsclient.client import MdrsClient
+
+        client = MdrsClient(None)
+        for remote, url in client.config_list():
             print(f"{remote}:\t{url}")
 
     @classmethod

mdrsclient/commands/cp.py

@@ -29,53 +29,8 @@ class CpCommand(BaseCommand):
 
     @classmethod
     def cp(cls, src_path: str, dest_path: str, is_recursive: bool) -> None:
-        (s_remote, s_laboratory_name, s_path) = cls._parse_remote_host_with_path(src_path)
-        (d_remote, d_laboratory_name, d_path) = cls._parse_remote_host_with_path(dest_path)
-        if s_remote != d_remote:
-            raise IllegalArgumentException("Remote host mismatched.")
-        if s_laboratory_name != d_laboratory_name:
-            raise IllegalArgumentException("Laboratory mismatched.")
-        s_path = s_path.rstrip("/")
-        s_dirname = os.path.dirname(s_path)
-        s_basename = os.path.basename(s_path)
-        if d_path.endswith("/"):
-            d_dirname = d_path
-            d_basename = s_basename
-        else:
-            d_dirname = os.path.dirname(d_path)
-            d_basename = os.path.basename(d_path)
-        connection = cls._create_connection(s_remote)
-        laboratory = cls._find_laboratory(connection, s_laboratory_name)
-        s_parent_folder = cls._find_folder(connection, laboratory, s_dirname)
-        s_parent_files = cls._find_files(connection, s_parent_folder.id)
-        d_parent_folder = cls._find_folder(connection, laboratory, d_dirname)
-        d_parent_files = cls._find_files(connection, d_parent_folder.id)
-        s_file = find_file(s_parent_files, s_basename)
-        if s_file is not None:
-            # source is file
-            d_file = find_file(d_parent_files, d_basename)
-            if d_file is not None:
-                raise IllegalArgumentException(f"File `{d_basename}` already exists.")
-            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 = 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:
-            s_folder = s_parent_folder.find_sub_folder(s_basename)
-            if s_folder is None:
-                raise IllegalArgumentException(f"File or folder `{s_basename}` not found.")
-            # source is folder
-            if not is_recursive:
-                raise IllegalArgumentException(f"Cannot copy `{s_path}`: Is a folder.")
-            if find_file(d_parent_files, d_basename) is not None:
-                raise IllegalArgumentException(f"Cannot overwrite non-folder `{d_basename}` with folder `{s_path}`.")
-            d_folder = d_parent_folder.find_sub_folder(d_basename)
-            if d_folder is not None:
-                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 = 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))
+        remote = src_path.split(":", 1)[0] if ":" in src_path else ""
+        from mdrsclient.client import MdrsClient
+
+        client = MdrsClient.from_remote(remote)
+        client.cp(src_path, dest_path, is_recursive)

mdrsclient/commands/download.py

@@ -68,11 +68,83 @@ class DownloadCommand(BaseCommand):
         password: str | None,
         excludes: list[str],
     ) -> None:
-        (remote, laboratory_name, r_path) = cls._parse_remote_host_with_path(remote_path)
+        remote = remote_path.split(":", 1)[0] if ":" in remote_path else ""
+        from mdrsclient.client import MdrsClient
+
+        client = MdrsClient.from_remote(remote)
+        client.download(remote_path, local_path, is_recursive, is_skip_if_exists, password, excludes)
+        return
+
+    @classmethod
+    def _download_logic(
+        cls,
+        connection: MDRSConnection,
+        remote_path: str,
+        local_path: str,
+        is_recursive: bool,
+        is_skip_if_exists: bool,
+        password: str | None,
+        excludes: list[str],
+    ) -> None:
+        # Detect DOI path: "remote:10.xxxx/prefix.ID[/optional/sub/path]"
+        path_component = remote_path.split(":", 1)[1] if ":" in remote_path else ""
+        if cls._is_doi(path_component):
+            remote, doi, subpath = cls._parse_doi_remote_host(remote_path)
+
+            l_dirname = os.path.realpath(local_path)
+            if not os.path.isdir(l_dirname):
+                raise IllegalArgumentException(f"Local directory `{local_path}` not found.")
+            doi_folder, laboratory = cls._find_folder_by_doi(connection, doi, password)
+
+            subpath_clean = subpath.rstrip("/")
+            if not subpath_clean:
+                folder = doi_folder
+                is_folder = True
+            else:
+                r_dirname = os.path.dirname(subpath_clean)
+                r_basename = os.path.basename(subpath_clean)
+                abs_parent_path = doi_folder.path.rstrip("/") + r_dirname
+                r_parent_folder = cls._find_folder(connection, laboratory, abs_parent_path, password)
+                r_parent_files = cls._find_files(connection, r_parent_folder.id)
+                file = find_file(r_parent_files, r_basename)
+                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)
+                    context.files.append(DownloadFileInfo(file, l_path))
+                    cls.__multiple_download(connection, context)
+                    return
+                else:
+                    folder_simple = r_parent_folder.find_sub_folder(r_basename)
+                    if folder_simple is None:
+                        raise IllegalArgumentException(f"File or folder `{subpath_clean}` not found.")
+                    folder = FoldersApi(connection).retrieve(folder_simple.id)
+                    is_folder = True
+
+            # For a DOI target the whole folder is the download target.
+            if not is_recursive:
+                # Non-recursive: download only the files at the top level of the DOI folder.
+                files = cls._find_files(connection, folder.id)
+                context = DownloadContext(False, is_skip_if_exists, [])
+                for file in files:
+                    if cls.__check_excludes(excludes, laboratory, folder, file):
+                        continue
+                    l_path = os.path.join(l_dirname, file.name)
+                    context.files.append(DownloadFileInfo(file, l_path))
+                cls.__multiple_download(connection, context)
+                return
+            folder_api = FoldersApi(connection)
+            cls.__multiple_download_pickup_recursive_files(
+                connection, folder_api, laboratory, folder.id, l_dirname, excludes, is_skip_if_exists
+            )
+            return
+
+        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)
         r_basename = os.path.basename(r_path)
-        connection = cls._create_connection(remote)
+
         l_dirname = os.path.realpath(local_path)
         if not os.path.isdir(l_dirname):
             raise IllegalArgumentException(f"Local directory `{local_path}` not found.")

mdrsclient/commands/file_metadata.py

@@ -25,17 +25,9 @@ class FileMetadataCommand(BaseCommand):
 
     @classmethod
     def file_metadata(cls, remote_path: str, password: str | None) -> 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)
-        r_basename = os.path.basename(r_path)
-        connection = cls._create_connection(remote)
-        laboratory = cls._find_laboratory(connection, laboratory_name)
-        folder = cls._find_folder(connection, laboratory, r_dirname, password)
-        files = cls._find_files(connection, folder.id)
-        file = find_file(files, r_basename)
-        if file is None:
-            raise IllegalArgumentException(f"File `{r_basename}` not found.")
-        file_api = FilesApi(connection)
-        metadata = file_api.metadata(file)
+        remote = remote_path.split(":", 1)[0] if ":" in remote_path else ""
+        from mdrsclient.client import MdrsClient
+
+        client = MdrsClient.from_remote(remote)
+        metadata = client.file_metadata(remote_path, password)
         print(json.dumps(metadata, ensure_ascii=False))

mdrsclient/commands/labs.py

@@ -19,11 +19,11 @@ class LabsCommand(BaseCommand):
 
     @classmethod
     def labs(cls, remote: str) -> None:
-        remote = cls._parse_remote_host(remote)
-        connection = cls._create_connection(remote)
-        laboratory_api = LaboratoriesApi(connection)
-        laboratories = laboratory_api.list()
-        connection.laboratories = laboratories
+        remote_host = cls._parse_remote_host(remote)
+        from mdrsclient.client import MdrsClient
+
+        client = MdrsClient.from_remote(remote_host)
+        laboratories = client.get_laboratories()
         label = {"id": "ID", "name": "Name", "pi_name": "PI", "full_name": "Laboratory"}
         length: dict[str, int] = {}
         for key in label.keys():
@@ -34,7 +34,6 @@ class LabsCommand(BaseCommand):
             length["pi_name"] = max(length["pi_name"], len(laboratory.pi_name))
             length["full_name"] = max(length["full_name"], len(laboratory.full_name))
         header = (
-            # f"{label['id']:{length['id']}}\t{label['name']:{length['name']}}\t"
             f"{label['name']:{length['name']}}\t"
             f"{label['pi_name']:{length['pi_name']}}\t{label['full_name']:{length['full_name']}}"
         )
@@ -42,7 +41,6 @@ class LabsCommand(BaseCommand):
         print("-" * len(header.expandtabs()))
         for laboratory in laboratories:
             print(
-                # f"{laboratory.id:{length['id']}}\t{laboratory.name:{length['name']}}\t"
                 f"{laboratory.name:{length['name']}}\t"
                 f"{laboratory.pi_name:{length['pi_name']}}\t{laboratory.full_name:{length['full_name']}}"
             )

mdrsclient/commands/login.py

@@ -21,20 +21,15 @@ class LoginCommand(BaseCommand):
     @classmethod
     def func(cls, args: Namespace) -> None:
         remote = str(args.remote)
-        username = str(args.username) if args.password else input("Username: ").strip()
+        username = str(args.username) if args.username else input("Username: ").strip()
         password = str(args.password) if args.password else getpass.getpass("Password: ").strip()
         cls.login(remote, username, password)
 
     @classmethod
     def login(cls, remote: str, username: str, password: str) -> None:
-        remote = cls._parse_remote_host(remote)
-        config = ConfigFile(remote)
-        if config.url is None:
-            raise MissingConfigurationException(f"Remote host `{remote}` is not found.")
-        connection = MDRSConnection(config.remote, config.url)
-        user_api = UsersApi(connection)
-        token = user_api.token(username, password)
-        connection.token = token
-        user = user_api.current()
-        connection.user = user
+        remote_host = cls._parse_remote_host(remote)
+        from mdrsclient.client import MdrsClient
+
+        client = MdrsClient.from_remote(remote_host)
+        client.login(username, password)
         print("Login Successful")

mdrsclient/commands/logout.py

@@ -21,9 +21,8 @@ class LogoutCommand(BaseCommand):
 
     @classmethod
     def logout(cls, remote: str) -> None:
-        remote = cls._parse_remote_host(remote)
-        config = ConfigFile(remote)
-        if config.url is None:
-            raise MissingConfigurationException(f"Remote host `{remote}` is not found.")
-        connection = MDRSConnection(config.remote, config.url)
-        connection.logout()
+        remote_host = cls._parse_remote_host(remote)
+        from mdrsclient.client import MdrsClient
+
+        client = MdrsClient.from_remote(remote_host)
+        client.logout()

mdrsclient/commands/ls.py

@@ -54,9 +54,22 @@ class LsCommand(BaseCommand):
 
     @classmethod
     def ls(cls, remote_path: str, password: str | None, is_json: bool, is_recursive: bool, is_quiet: bool) -> None:
-        (remote, laboratory_name, r_path) = cls._parse_remote_host_with_path(remote_path)
-        connection = cls._create_connection(remote)
-        laboratory = cls._find_laboratory(connection, laboratory_name)
+        remote = remote_path.split(":", 1)[0] if ":" in remote_path else ""
+        from mdrsclient.client import MdrsClient
+
+        client = MdrsClient.from_remote(remote)
+        client.ls_command(remote_path, password, is_json, is_recursive, is_quiet)
+        return
+
+    @classmethod
+    def _ls_logic(
+        cls, connection, remote_path: str, password: str | None, is_json: bool, is_recursive: bool, is_quiet: bool
+    ) -> None:
+        remote = remote_path.split(":", 1)[0] if ":" in remote_path else ""
+
+        folder, laboratory = cls._resolve_folder(connection, remote_path, password)
+        laboratory_name = laboratory.name
+        files = cls._find_files(connection, folder.id)
         context = LsCommandContext(
             f"{remote}:/{laboratory_name}",
             connection,
@@ -66,8 +79,6 @@ class LsCommand(BaseCommand):
             is_quiet,
             is_recursive,
         )
-        folder = cls._find_folder(connection, laboratory, r_path, password)
-        files = cls._find_files(connection, folder.id)
         if context.is_json:
             cls._ls_json(context, folder, files)
         else:

mdrsclient/commands/metadata.py

@@ -22,10 +22,9 @@ class MetadataCommand(BaseCommand):
 
     @classmethod
     def metadata(cls, remote_path: str, password: str | None) -> None:
-        (remote, laboratory_name, r_path) = cls._parse_remote_host_with_path(remote_path)
-        connection = cls._create_connection(remote)
-        laboratory = cls._find_laboratory(connection, laboratory_name)
-        folder = cls._find_folder(connection, laboratory, r_path, password)
-        folder_api = FoldersApi(connection)
-        metadata = folder_api.metadata(folder.id)
+        remote = remote_path.split(":", 1)[0] if ":" in remote_path else ""
+        from mdrsclient.client import MdrsClient
+
+        client = MdrsClient.from_remote(remote)
+        metadata = client.metadata(remote_path, password)
         print(json.dumps(metadata, ensure_ascii=False))

mdrsclient/commands/mkdir.py

@@ -23,15 +23,8 @@ class MkdirCommand(BaseCommand):
 
     @classmethod
     def mkdir(cls, remote_path: 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)
-        r_basename = os.path.basename(r_path)
-        connection = cls._create_connection(remote)
-        laboratory = cls._find_laboratory(connection, laboratory_name)
-        parent_folder = cls._find_folder(connection, laboratory, r_dirname)
-        files = cls._find_files(connection, parent_folder.id)
-        if parent_folder.find_sub_folder(r_basename) is not None or find_file(files, r_basename) is not None:
-            raise IllegalArgumentException(f"Cannot create folder `{r_path}`: File exists.")
-        folder_api = FoldersApi(connection)
-        folder_api.create(normalize("NFC", r_basename), parent_folder.id)
+        remote = remote_path.split(":", 1)[0] if ":" in remote_path else ""
+        from mdrsclient.client import MdrsClient
+
+        client = MdrsClient.from_remote(remote)
+        client.mkdir(remote_path)

mdrsclient/commands/mv.py

@@ -25,51 +25,8 @@ class MvCommand(BaseCommand):
 
     @classmethod
     def mv(cls, src_path: str, dest_path: str) -> None:
-        (s_remote, s_laboratory_name, s_path) = cls._parse_remote_host_with_path(src_path)
-        (d_remote, d_laboratory_name, d_path) = cls._parse_remote_host_with_path(dest_path)
-        if s_remote != d_remote:
-            raise IllegalArgumentException("Remote host mismatched.")
-        if s_laboratory_name != d_laboratory_name:
-            raise IllegalArgumentException("Laboratory mismatched.")
-        s_path = s_path.rstrip("/")
-        s_dirname = os.path.dirname(s_path)
-        s_basename = os.path.basename(s_path)
-        if d_path.endswith("/"):
-            d_dirname = d_path
-            d_basename = s_basename
-        else:
-            d_dirname = os.path.dirname(d_path)
-            d_basename = os.path.basename(d_path)
-        connection = cls._create_connection(s_remote)
-        laboratory = cls._find_laboratory(connection, s_laboratory_name)
-        s_parent_folder = cls._find_folder(connection, laboratory, s_dirname)
-        s_parent_files = cls._find_files(connection, s_parent_folder.id)
-        d_parent_folder = cls._find_folder(connection, laboratory, d_dirname)
-        d_parent_files = cls._find_files(connection, d_parent_folder.id)
-        s_file = find_file(s_parent_files, s_basename)
-        if s_file is not None:
-            # source is file
-            d_file = find_file(d_parent_files, d_basename)
-            if d_file is not None:
-                raise IllegalArgumentException(f"File `{d_basename}` already exists.")
-            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 = 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:
-            s_folder = s_parent_folder.find_sub_folder(s_basename)
-            if s_folder is None:
-                raise IllegalArgumentException(f"File or folder `{s_basename}` not found.")
-            # source is folder
-            if find_file(d_parent_files, d_basename) is not None:
-                raise IllegalArgumentException(f"Cannot overwrite non-folder `{d_basename}` with folder `{s_path}`.")
-            d_folder = d_parent_folder.find_sub_folder(d_basename)
-            if d_folder is not None:
-                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 = 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))
+        remote = src_path.split(":", 1)[0] if ":" in src_path else ""
+        from mdrsclient.client import MdrsClient
+
+        client = MdrsClient.from_remote(remote)
+        client.mv(src_path, dest_path)

mdrsclient/commands/rm.py

@@ -26,23 +26,8 @@ class RmCommand(BaseCommand):
 
     @classmethod
     def rm(cls, remote_path: str, is_recursive: bool) -> 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)
-        r_basename = os.path.basename(r_path)
-        connection = cls._create_connection(remote)
-        laboratory = cls._find_laboratory(connection, laboratory_name)
-        parent_folder = cls._find_folder(connection, laboratory, r_dirname)
-        parent_files = cls._find_files(connection, parent_folder.id)
-        file = find_file(parent_files, r_basename)
-        if file is not None:
-            file_api = FilesApi(connection)
-            file_api.destroy(file)
-        else:
-            folder = parent_folder.find_sub_folder(r_basename)
-            if folder is None:
-                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 = FoldersApi(connection)
-            folder_api.destroy(folder.id, True)
+        remote = remote_path.split(":", 1)[0] if ":" in remote_path else ""
+        from mdrsclient.client import MdrsClient
+
+        client = MdrsClient.from_remote(remote)
+        client.rm(remote_path, is_recursive)

mdrsclient/commands/upload.py

@@ -2,6 +2,7 @@ import os
 from argparse import Namespace
 from concurrent.futures import ThreadPoolExecutor
 from typing import Any
+from unicodedata import normalize
 
 from pydantic.dataclasses import dataclass
 
@@ -48,11 +49,22 @@ class UploadCommand(BaseCommand):
 
     @classmethod
     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)
+        remote = remote_path.split(":", 1)[0] if ":" in remote_path else ""
+        from mdrsclient.client import MdrsClient
+
+        client = MdrsClient.from_remote(remote)
+        client.upload(local_path, remote_path, is_recursive, is_skip_if_exists)
+        return
+
+    @classmethod
+    def _upload_logic(
+        cls, connection, 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.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)
+
         laboratory = cls._find_laboratory(connection, laboratory_name)
         folder = cls._find_folder(connection, laboratory, r_path)
         files = cls._find_files(connection, folder.id)
@@ -81,7 +93,7 @@ class UploadCommand(BaseCommand):
                 if folder_map.get(d_dirname) is None:
                     d_folder = folder_map[d_parent_dirname].find_sub_folder(d_basename)
                     if d_folder is None:
-                        d_folder_id = folder_api.create(d_basename, folder_map[d_parent_dirname].id)
+                        d_folder_id = folder_api.create(normalize("NFC", d_basename), folder_map[d_parent_dirname].id)
                     else:
                         d_folder_id = d_folder.id
                     print(d_dirname)

mdrsclient/commands/version.py

@@ -17,4 +17,8 @@ class VersionCommand(BaseCommand):
 
     @classmethod
     def version(cls) -> None:
-        print(f"mdrs {__version__}")
+        from mdrsclient.client import MdrsClient
+
+        # Client initialization is not strictly needed for version, but for consistency:
+        client = MdrsClient(None)
+        print(client.version())

mdrsclient/commands/whoami.py

@@ -23,12 +23,15 @@ class WhoamiCommand(BaseCommand):
 
     @classmethod
     def whoami(cls, remote: str) -> None:
-        remote = cls._parse_remote_host(remote)
-        config = ConfigFile(remote)
-        if config.url is None:
-            raise MissingConfigurationException(f"Remote host `{remote}` is not found.")
-        connection = MDRSConnection(config.remote, config.url)
-        if connection.token is not None and connection.token.is_expired:
-            connection.logout()
-        username = connection.user.username if connection.user is not None else cls.ANONYMOUS_USERNAME
+        remote_host = cls._parse_remote_host(remote)
+        from mdrsclient.client import MdrsClient
+
+        client = MdrsClient.from_remote(remote_host)
+        if client.connection.token is not None and client.connection.token.is_expired:
+            client.logout()
+        try:
+            user = client.whoami()
+            username = user.username if user is not None else cls.ANONYMOUS_USERNAME
+        except Exception:
+            username = cls.ANONYMOUS_USERNAME
         print(username)

mdrsclient/connection.py

@@ -9,7 +9,7 @@ from requests_toolbelt.multipart.encoder import MultipartEncoder
 from typing_extensions import Unpack
 
 from mdrsclient.__version__ import __version__
-from mdrsclient.cache import CacheFile
+from mdrsclient.cache import CacheFile, CacheInterface
 from mdrsclient.exceptions import MissingConfigurationException
 from mdrsclient.models import Laboratories, Token, User
 
@@ -39,14 +39,14 @@ class MDRSConnection:
     url: str
     session: Session
     lock: threading.Lock
-    __cache: CacheFile
+    __cache: CacheInterface
 
-    def __init__(self, remote: str, url: str) -> None:
+    def __init__(self, remote: str, url: str, cache: CacheInterface | None = None) -> None:
         super().__init__()
         self.url = url
         self.session = Session()
         self.lock = threading.Lock()
-        self.__cache = CacheFile(remote)
+        self.__cache = cache if cache is not None else CacheFile(remote)
         self.__prepare_headers()
 
     def get(self, url: str, **kwargs: Unpack[_KwArgsMDRSConnectionGet]) -> Response:
@@ -92,6 +92,8 @@ class MDRSConnection:
         self.__cache.laboratories = laboratories
 
     def __build_url(self, path: str) -> str:
+        if path.startswith("http://") or path.startswith("https://"):
+            return path
         if self.url == "":
             raise MissingConfigurationException("remote host is not configured")
         return f"{self.url}/{path}"

mdrsclient/models/__init__.py

@@ -1,3 +1,4 @@
+from mdrsclient.models.doi import Doi
 from mdrsclient.models.error import DRFStandardizedErrors
 from mdrsclient.models.file import File
 from mdrsclient.models.folder import Folder, FolderAccessLevel, FolderSimple
@@ -6,6 +7,7 @@ from mdrsclient.models.user import Token, User
 
 __all__ = [
     "DRFStandardizedErrors",
+    "Doi",
     "File",
     "Folder",
     "FolderAccessLevel",

mdrsclient/models/doi.py

@@ -0,0 +1,11 @@
+from pydantic.dataclasses import dataclass
+
+
+@dataclass(frozen=True)
+class Doi:
+    """Model representing a DOI entity (Response from GET v3/doi/{id}/)."""
+
+    # The internal DOI suffix ID returned as a string (e.g. "20260429-001").
+    id: str
+    doi: str
+    folder_id: str

mdrsclient/services.py

@@ -0,0 +1,223 @@
+from typing import Any
+import os
+import re
+from unicodedata import normalize
+
+from mdrsclient.api import DoiApi, FilesApi, FoldersApi, LaboratoriesApi, UsersApi
+from mdrsclient.config import ConfigFile
+from mdrsclient.connection import MDRSConnection
+from mdrsclient.exceptions import (
+    IllegalArgumentException,
+    MissingConfigurationException,
+    UnauthorizedException,
+    UnexpectedException,
+)
+from mdrsclient.models import File, Folder, Laboratory, Token, User
+from mdrsclient.utils import page_num_from_url
+
+
+class MdrsService:
+    def __init__(self, connection: MDRSConnection):
+        self.connection = connection
+
+    @classmethod
+    def create_connection(cls, remote: str) -> MDRSConnection:
+        config = ConfigFile(remote)
+        if config.url is None:
+            raise MissingConfigurationException(f"Remote host `{remote}` is not found.")
+        return MDRSConnection(config.remote, config.url)
+
+    def login(self, username: str, password: str) -> tuple[Token, User]:
+        user_api = UsersApi(self.connection)
+        token = user_api.token(username, password)
+        self.connection.token = token
+        user = user_api.current()
+        self.connection.user = user
+        return token, user
+
+    def logout(self) -> None:
+        self.connection.logout()
+
+    def whoami(self) -> User:
+        user_api = UsersApi(self.connection)
+        return user_api.current()
+
+    def get_laboratories(self) -> list[Laboratory]:
+        laboratory_api = LaboratoriesApi(self.connection)
+        labs = laboratory_api.list()
+        self.connection.laboratories = labs
+        return list(labs)
+
+    def find_laboratory(self, name: str) -> Laboratory:
+        if self.connection.laboratories.empty() or (self.connection.token and self.connection.token.is_expired):
+            self.get_laboratories()
+        laboratory = self.connection.laboratories.find_by_name(name)
+        if laboratory is None:
+            raise IllegalArgumentException(f"Laboratory `{name}` not found.")
+        return laboratory
+
+    def find_folder(self, laboratory: Laboratory, path: str, password: str | None = None) -> Folder:
+        folder_api = FoldersApi(self.connection)
+        folders = folder_api.list(laboratory.id, normalize("NFC", path))
+        if len(folders) != 1:
+            raise UnexpectedException(f"Folder `{path}` not found.")
+        if folders[0].lock:
+            if password is None:
+                raise UnauthorizedException(f"Folder `{path}` is locked.")
+            folder_api.auth(folders[0].id, password)
+        return folder_api.retrieve(folders[0].id)
+
+    def find_files(self, folder_id: str) -> list[File]:
+        files_api = FilesApi(self.connection)
+        page = 1
+        results_file = []
+        while page:
+            result = files_api.list(folder_id, page)
+            results_file.extend(result.results)
+            page = 0
+            if result.next:
+                page = page_num_from_url(result.next)
+        return results_file
+
+    @staticmethod
+    def is_doi(path_component: str) -> bool:
+        return path_component.startswith("10.") and "/" in path_component
+
+    @staticmethod
+    def doi_suffix_id(doi: str) -> str:
+        doi = doi.rstrip("/")
+        slash_pos = doi.find("/")
+        if slash_pos == -1:
+            return doi
+        suffix = doi[slash_pos + 1 :]
+        dot_pos = suffix.rfind(".")
+        return suffix[dot_pos + 1 :] if dot_pos != -1 else suffix
+
+    @staticmethod
+    def split_doi_and_subpath(doi_with_path: str) -> tuple[str, str]:
+        first_slash = doi_with_path.find("/")
+        if first_slash != -1:
+            after_suffix_start = first_slash + 1
+            after_first = doi_with_path[after_suffix_start:]
+            second_slash = after_first.find("/")
+            if second_slash != -1:
+                doi_end = after_suffix_start + second_slash
+                doi = doi_with_path[:doi_end]
+                subpath = doi_with_path[doi_end:]
+                if subpath == "/":
+                    return (doi, "")
+                else:
+                    return (doi, subpath)
+            else:
+                return (doi_with_path, "")
+        else:
+            return (doi_with_path, "")
+
+    @classmethod
+    def parse_remote_host(cls, path: str) -> str:
+        path_array = path.split(":")
+        remote_host = path_array[0]
+        if len(path_array) == 2 and path_array[1] != "" or len(path_array) > 2:
+            raise IllegalArgumentException("Invalid remote host")
+        return remote_host
+
+    @classmethod
+    def parse_remote_host_with_path(cls, path: str) -> tuple[str, str, str]:
+        path = re.sub(r"//+|/\./+|/\.$", "/", path)
+        if re.search(r"/\.\./|/\.\.$", path) is not None:
+            raise IllegalArgumentException("Path traversal found.")
+        path_array = path.split(":")
+        if len(path_array) != 2:
+            raise IllegalArgumentException("Invalid remote host.")
+        remote_host = path_array[0]
+        folder_array = path_array[1].split("/")
+        is_absolute_path = folder_array[0] == ""
+        if not is_absolute_path:
+            raise IllegalArgumentException("Must be absolute paths.")
+        del folder_array[0]
+        if len(folder_array) == 0:
+            laboratory = ""
+            folder = ""
+        else:
+            laboratory = folder_array.pop(0)
+            folder = "/" + "/".join(folder_array)
+        return (remote_host, laboratory, folder)
+
+    @classmethod
+    def parse_doi_remote_host(cls, path: str) -> tuple[str, str, str]:
+        parts = path.split(":", 1)
+        if len(parts) != 2:
+            raise IllegalArgumentException("remote_path must be in the form 'remote:10.xxxx/prefix.ID'")
+        remote, doi_with_path = parts
+        if not cls.is_doi(doi_with_path):
+            raise IllegalArgumentException(f"Path `{doi_with_path}` does not look like a DOI.")
+        doi, subpath = cls.split_doi_and_subpath(doi_with_path)
+        return (remote, doi, subpath)
+
+    def find_folder_by_doi(self, doi: str, password: str | None = None) -> tuple[Folder, Laboratory]:
+        doi_clean = doi.rstrip("/")
+        doi_id = self.doi_suffix_id(doi_clean)
+        doi_api = DoiApi(self.connection)
+        doi_resp = doi_api.retrieve(doi_id)
+
+        returned_doi = doi_resp.doi.rstrip("/")
+        if returned_doi.lower() != doi_clean.lower():
+            raise IllegalArgumentException(
+                f"DOI mismatch: requested `{doi_clean}` but server returned `{returned_doi}`."
+            )
+
+        folder_api = FoldersApi(self.connection)
+        folder = folder_api.retrieve(doi_resp.folder_id)
+
+        if folder.lock:
+            if password is None:
+                raise UnauthorizedException(f"Folder for DOI `{doi_clean}` is locked.")
+            folder_api.auth(doi_resp.folder.id, password)
+
+        lab_api = LaboratoriesApi(self.connection)
+        labs = lab_api.list()
+        lab = labs.find_by_id(folder.laboratory_id)
+        if lab is None:
+            raise UnexpectedException(f"Laboratory with id {folder.laboratory_id} not found.")
+
+        self.connection.laboratories = labs
+        return (folder, lab)
+
+    def resolve_folder(self, remote_path: str, password: str | None = None) -> tuple[Folder, Laboratory]:
+        path_component = remote_path.split(":", 1)[1] if ":" in remote_path else ""
+        if self.is_doi(path_component):
+            remote, doi, subpath = self.parse_doi_remote_host(remote_path)
+            doi_folder, laboratory = self.find_folder_by_doi(doi, password)
+            if not subpath:
+                return (doi_folder, laboratory)
+            else:
+                abs_path = doi_folder.path.rstrip("/") + subpath
+                folder = self.find_folder(laboratory, abs_path, password)
+                return (folder, laboratory)
+        else:
+            remote, laboratory_name, r_path = self.parse_remote_host_with_path(remote_path)
+            laboratory = self.find_laboratory(laboratory_name)
+            folder = self.find_folder(laboratory, r_path, password)
+            return (folder, laboratory)
+
+    def resolve_file(self, remote_path: str, password: str | None = None) -> tuple[Folder, Laboratory, str]:
+        path_component = remote_path.split(":", 1)[1] if ":" in remote_path else ""
+        if self.is_doi(path_component):
+            remote, doi, subpath = self.parse_doi_remote_host(remote_path)
+            doi_folder, laboratory = self.find_folder_by_doi(doi, password)
+            subpath_clean = subpath.rstrip("/")
+            if not subpath_clean:
+                raise IllegalArgumentException("DOI path must point to a file, not a folder.")
+            r_dirname = os.path.dirname(subpath_clean)
+            r_basename = os.path.basename(subpath_clean)
+            abs_path = doi_folder.path.rstrip("/") + r_dirname
+            parent_folder = self.find_folder(laboratory, abs_path, password)
+            return (parent_folder, laboratory, r_basename)
+        else:
+            remote, laboratory_name, r_path = self.parse_remote_host_with_path(remote_path)
+            r_path = r_path.rstrip("/")
+            r_dirname = os.path.dirname(r_path)
+            r_basename = os.path.basename(r_path)
+            laboratory = self.find_laboratory(laboratory_name)
+            parent_folder = self.find_folder(laboratory, r_dirname, password)
+            return (parent_folder, laboratory, r_basename)

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "mdrs-client-python"
-version = "1.3.14"
+version = "1.3.17"
 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"
@@ -24,20 +24,20 @@ packages = [
 
 [tool.poetry.dependencies]
 python = "^3.10"
-requests = "^2.32.3"
+requests = "^2.34.2"
 requests-toolbelt = "^1.0.0"
 python-dotenv = "^1.1.0"
-pydantic = "^2.11.4"
-pydantic-settings = "^2.9.1"
-PyJWT = "^2.10.1"
-validators = "^0.34.0"
+pydantic = "^2.13.4"
+pydantic-settings = "^2.14.1"
+PyJWT = "^2.13.0"
+validators = "^0.35.0"
 
 [tool.poetry.group.dev.dependencies]
-black = "^24.10.0"
+black = "^26.5.1"
 flake8 = "^7.2.0"
 Flake8-pyproject = "^1.2.3"
-isort = "^5.13.2"
-pyright = "^1.1.400"
+isort = "^8.0.1"
+pyright = "^1.1.401"
 
 [tool.poetry.scripts]
 mdrs = 'mdrsclient.__main__:main'