first commit

.env.example

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+# CONFIG_DIR_PATH="~/.mdrs-client"
+# NUMBER_OF_PROCESS=10

.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+.python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/#use-with-ide
+.pdm.toml
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+.idea/
+
+# mdrs-cli
+.neurodatacli.config

.vscode/extensions.json

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+{
+    "recommendations": [
+        "ms-python.python",
+        "ms-python.black-formatter",
+        "ms-python.isort",
+        "ms-python.flake8",
+        "ms-python.vscode-pylance",
+        "esbenp.prettier-vscode",
+        "redhat.vscode-xml",
+        "njpwerner.autodocstring",
+        "mosapride.zenkaku",
+        "streetsidesoftware.code-spell-checker"
+    ]
+}

.vscode/settings.json

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+{
+    "editor.formatOnSave": true,
+    "editor.codeActionsOnSave": {
+        "source.organizeImports": true
+    },
+    "[python]": {
+        "editor.defaultFormatter": "ms-python.black-formatter"
+    },
+    "[xml]": {
+        "editor.defaultFormatter": "redhat.vscode-xml"
+    },
+    "[jsonc]": {
+        "editor.defaultFormatter": "esbenp.prettier-vscode"
+    },
+    // Extensions - Code Spell Checker
+    "cSpell.ignoreWords": ["getframe", "pydantic"],
+    "cSpell.words": ["mdrs", "mdrsclient", "neurodata", "Neuroinformatics", "RIKEN"],
+    // Extensions - isort
+    "isort.args": ["--profile=black"],
+    // Extensions - Prettier
+    "prettier.printWidth": 120,
+    "prettier.singleQuote": true,
+    "prettier.tabWidth": 4,
+    // Extensions - Pylance
+    "python.analysis.typeCheckingMode": "basic",
+    "python.analysis.exclude": ["api/migrations/[0-9]*.py"],
+    // Extensions - Python:black
+    "python.formatting.blackArgs": ["--line-length=120"],
+    "python.formatting.provider": "black",
+    // Extensions - Python:Flake8
+    "python.linting.enabled": true,
+    "python.linting.flake8Enabled": true,
+    "python.linting.flake8Args": ["--max-line-length=120"],
+    "python.linting.ignorePatterns": ["**/site-packages/**/*.py", ".vscode/*.py"],
+    "python.linting.lintOnSave": true,
+    // Extensions - Python Docstring Generator configuration
+    "autoDocstring.docstringFormat": "google"
+}

LICENSE

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+MIT License
+
+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
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

README.md

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+# mdrs-client-python
+The mdrs-client-python is python library and a command-line client for up- and downloading files to and from MDRS based repository.
+
+## Installing
+```
+pip install -e .
+```
+
+## Example Usage
+
+### config create
+Create remote host configuration
+```
+$ mdrs config create neurodata https://neurodata.riken.jp/api
+```
+
+### login
+login to remote host
+```
+$ mdrs login neurodata:
+Username: (enter your login name)
+Password: (enter your password)
+```
+
+### logout
+Logout from remote host
+```
+$ mdrs logout neurodata:
+```
+
+### whoami
+Print effective user name
+```
+$ mdrs whoami neurodata:
+```
+
+### labs
+List all laboratories
+```
+$ mdrs labs neurodata:
+```
+
+### ls
+List the folder contents
+```
+$ mdrs ls neurodata:/NIU/Repository/
+```
+
+### mkdir
+Create a new folder
+```
+$ mdrs mkdir neurodata:/NIU/Repository/TEST
+```
+
+### rmdir
+Remove a existing folder
+```
+$ mdrs rmdir neurodata:/NIU/Repository/TEST
+```
+
+### metadata
+Get a folder metadata
+```
+$ mdrs metadata neurodata:/NIU/Repository/TEST
+```
+
+### upload
+Upload the file or directories
+```
+$ mdrs upload ./sample.dat neurodata:/NIU/Repository/TEST/
+$ mdrs upload -r ./dataset neurodata:/NIU/Repository/TEST/
+```
+
+### download
+Download a file
+```
+$ mdrs download neurodata:/NIU/Repository/TEST/sample.dat ./
+```
+
+### move
+Move a file
+```
+$ mdrs move neurodata:/NIU/Repository/TEST/sample.dat neurodata:/NIU/Repository/TEST2/sample2.dat
+```
+
+### remove
+Remove a file
+```
+$ mdrs remove neurodata:/NIU/Repository/TEST2/sample2.dat
+```
+
+### file-metadata
+Get the file metadata
+```
+$ mdrs file-metadata neurodata:/NIU/Repository/TEST/dataset/sample.dat
+```
+
+### help
+Show the help message and exit
+```
+$ mdrs -h
+```

VERSION

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+1.0.0

mdrsclient/__main__.py

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+import argparse
+
+from mdrsclient.commands import (
+    ConfigCommand,
+    FileCommand,
+    FolderCommand,
+    LaboratoryCommand,
+    UserCommand,
+)
+from mdrsclient.exceptions import MDRSException
+
+
+def main() -> None:
+    description = """This is a command-line program to up files."""
+
+    parser = argparse.ArgumentParser(description=description, formatter_class=argparse.RawDescriptionHelpFormatter)
+    subparsers = parser.add_subparsers(title="subcommands")
+
+    ConfigCommand.register(subparsers)
+    UserCommand.register(subparsers)
+    LaboratoryCommand.register(subparsers)
+    FolderCommand.register(subparsers)
+    FileCommand.register(subparsers)
+
+    try:
+        args = parser.parse_args()
+        if hasattr(args, "func"):
+            args.func(args)
+        else:
+            parser.print_help()
+    except MDRSException as e:
+        print(f"Error: {e}")
+        exit(2)
+
+
+if __name__ == "__main__":
+    main()

mdrsclient/__version__.py

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+import os
+
+here = os.path.abspath(os.path.dirname(__file__))
+__all__ = ["__version__"]
+
+
+with open(os.path.join(os.path.dirname(here), "VERSION")) as version_file:
+    __version__ = version_file.read().strip()

mdrsclient/api/__init__.py

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+from mdrsclient.api.file import FileApi
+from mdrsclient.api.folder import FolderApi
+from mdrsclient.api.laboratory import LaboratoryApi
+from mdrsclient.api.user import UserApi
+
+__all__ = [
+    "FileApi",
+    "FolderApi",
+    "LaboratoryApi",
+    "UserApi",
+]

mdrsclient/api/base.py

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+from abc import ABC
+
+import requests
+from pydantic import parse_obj_as
+from requests import Response
+
+from mdrsclient.exceptions import (
+    BadRequestException,
+    ForbiddenException,
+    UnauthorizedException,
+    UnexpectedException,
+)
+from mdrsclient.models import DRFStandardizedErrors
+from mdrsclient.session import MDRSSession
+
+
+class BaseApi(ABC):
+    def __init__(self, session: MDRSSession) -> None:
+        self.session = session
+
+    def _get(self, url, *args, **kwargs) -> Response:
+        return self.session.get(self.__build_url(url), *args, **kwargs)
+
+    def _post(self, url, *args, **kwargs) -> Response:
+        return self.session.post(self.__build_url(url), *args, **kwargs)
+
+    def _put(self, url, *args, **kwargs) -> Response:
+        return self.session.put(self.__build_url(url), *args, **kwargs)
+
+    def _delete(self, url, *args, **kwargs) -> Response:
+        return self.session.delete(self.__build_url(url), *args, **kwargs)
+
+    def _patch(self, url, *args, **kwargs) -> Response:
+        return self.session.patch(self.__build_url(url), *args, **kwargs)
+
+    def _raise_response_error(self, response: Response) -> None:
+        if response.status_code >= 300:
+            if response.status_code < 400 or response.status_code >= 500:
+                raise UnexpectedException(f"Unexpected status code returned: {response.status_code}.")
+            errors = parse_obj_as(DRFStandardizedErrors, response.json())
+            if response.status_code == requests.codes.bad_request:
+                raise BadRequestException(errors.errors[0].detail)
+            elif response.status_code == requests.codes.unauthorized:
+                raise UnauthorizedException("Login required.")
+            elif response.status_code == requests.codes.forbidden:
+                raise ForbiddenException("You do not have enough permissions. Access is denied.")
+            else:
+                raise UnexpectedException(errors.errors[0].detail)
+
+    def __build_url(self, *args: tuple) -> str:
+        return self.session.build_url(*args)

mdrsclient/api/file.py

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+import sys
+from typing import Final
+
+from pydantic import parse_obj_as
+from pydantic.dataclasses import dataclass
+
+from mdrsclient.api.base import BaseApi
+from mdrsclient.api.utils import token_check
+from mdrsclient.exceptions import UnexpectedException
+from mdrsclient.models import File
+
+
+@dataclass(frozen=True)
+class FileCreateResponse:
+    id: str
+
+
+class FileApi(BaseApi):
+    ENTRYPOINT: Final[str] = "v2/file/"
+
+    def retrieve(self, id: str) -> File:
+        print(self.__class__.__name__ + "::" + sys._getframe().f_code.co_name)
+        url = self.ENTRYPOINT + id + "/"
+        token_check(self.session)
+        response = self._get(url)
+        self._raise_response_error(response)
+        return parse_obj_as(File, response.json())
+
+    def create(self, folder_id: str, path: str) -> str:
+        print(self.__class__.__name__ + "::" + sys._getframe().f_code.co_name)
+        url = self.ENTRYPOINT
+        token_check(self.session)
+        data = {"folder_id": folder_id}
+        try:
+            with open(path, mode="rb") as fp:
+                response = self._post(url, data=data, files={"file": fp})
+                self._raise_response_error(response)
+                ret = parse_obj_as(FileCreateResponse, response.json())
+        except OSError:
+            raise UnexpectedException(f"Could not open `{path}` file.")
+        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.session)
+        if path is not None:
+            try:
+                with open(path, mode="rb") as fp:
+                    response = self._put(url, files={"file": fp})
+            except OSError:
+                raise UnexpectedException(f"Could not open `{path}` file.")
+        else:
+            data = {"name": file.name, "description": file.description}
+            response = self._put(url, data=data)
+        self._raise_response_error(response)
+        return True
+
+    def destroy(self, file: File) -> bool:
+        print(self.__class__.__name__ + "::" + sys._getframe().f_code.co_name)
+        url = self.ENTRYPOINT + file.id + "/"
+        token_check(self.session)
+        response = self._delete(url)
+        self._raise_response_error(response)
+        return True
+
+    def move(self, file: File, folder_id: str | None) -> bool:
+        print(self.__class__.__name__ + "::" + sys._getframe().f_code.co_name)
+        url = self.ENTRYPOINT + file.id + "/move/"
+        data = {"folder": folder_id}
+        token_check(self.session)
+        response = self._post(url, data=data)
+        self._raise_response_error(response)
+        return True
+
+    def metadata(self, file: File) -> dict:
+        print(self.__class__.__name__ + "::" + sys._getframe().f_code.co_name)
+        url = self.ENTRYPOINT + file.id + "/metadata/"
+        token_check(self.session)
+        response = self._get(url)
+        self._raise_response_error(response)
+        return response.json()

mdrsclient/api/folder.py

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+import sys
+from typing import Final
+
+from pydantic import parse_obj_as
+from pydantic.dataclasses import dataclass
+
+from mdrsclient.api.base import BaseApi
+from mdrsclient.api.utils import token_check
+from mdrsclient.models import Folder, FolderSimple
+
+
+@dataclass(frozen=True)
+class FolderCreateResponse:
+    id: str
+
+
+class FolderApi(BaseApi):
+    ENTRYPOINT: Final[str] = "v2/folder/"
+
+    def list(self, laboratory_id: int, path: str) -> list[FolderSimple]:
+        print(self.__class__.__name__ + "::" + sys._getframe().f_code.co_name)
+        url = self.ENTRYPOINT
+        params = {"path": path, "laboratory_id": laboratory_id}
+        token_check(self.session)
+        response = self._get(url, params=params)
+        self._raise_response_error(response)
+        ret: list[FolderSimple] = []
+        for data in response.json():
+            ret.append(parse_obj_as(FolderSimple, data))
+        return ret
+
+    def retrieve(self, id: str) -> Folder:
+        print(self.__class__.__name__ + "::" + sys._getframe().f_code.co_name)
+        url = self.ENTRYPOINT + id + "/"
+        token_check(self.session)
+        response = self._get(url)
+        self._raise_response_error(response)
+        ret = parse_obj_as(Folder, response.json())
+        return ret
+
+    def create(self, name: str, parent_id: str) -> str:
+        print(self.__class__.__name__ + "::" + sys._getframe().f_code.co_name)
+        url = self.ENTRYPOINT
+        data = {"name": name, "parent_id": parent_id, "description": "", "template_id": -1}
+        token_check(self.session)
+        response = self._post(url, data=data)
+        self._raise_response_error(response)
+        ret = parse_obj_as(FolderCreateResponse, response.json())
+        return ret.id
+
+    def update(self, folder: FolderSimple) -> bool:
+        print(self.__class__.__name__ + "::" + sys._getframe().f_code.co_name)
+        url = self.ENTRYPOINT
+        data = {
+            "name": folder.name,
+            "description": folder.description,
+        }
+        token_check(self.session)
+        response = self._put(url, data=data)
+        self._raise_response_error(response)
+        return True
+
+    def destroy(self, id: str) -> bool:
+        print(self.__class__.__name__ + "::" + sys._getframe().f_code.co_name)
+        url = self.ENTRYPOINT + id + "/"
+        token_check(self.session)
+        response = self._delete(url)
+        self._raise_response_error(response)
+        return True
+
+    def metadata(self, id: str) -> dict:
+        print(self.__class__.__name__ + "::" + sys._getframe().f_code.co_name)
+        url = self.ENTRYPOINT + id + "/metadata/"
+        token_check(self.session)
+        response = self._get(url)
+        self._raise_response_error(response)
+        return response.json()

mdrsclient/api/laboratory.py

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+import sys
+from typing import Final
+
+from pydantic import parse_obj_as
+
+from mdrsclient.api.base import BaseApi
+from mdrsclient.api.utils import token_check
+from mdrsclient.models import Laboratories, Laboratory
+
+
+class LaboratoryApi(BaseApi):
+    ENTRYPOINT: Final[str] = "v2/laboratory/"
+
+    def list(self) -> Laboratories:
+        print(self.__class__.__name__ + "::" + sys._getframe().f_code.co_name)
+        url = self.ENTRYPOINT
+        token_check(self.session)
+        response = self._get(url)
+        self._raise_response_error(response)
+        ret = Laboratories([])
+        for data in response.json():
+            ret.append(parse_obj_as(Laboratory, data))
+        return ret

mdrsclient/api/user.py

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+import sys
+from typing import Final
+
+import requests
+from pydantic import parse_obj_as
+from pydantic.dataclasses import dataclass
+
+from mdrsclient.api.base import BaseApi
+from mdrsclient.exceptions import UnauthorizedException
+from mdrsclient.models import Token, User
+
+
+@dataclass(frozen=True)
+class UserAuthResponse(Token):
+    laboratory: str
+    lab_id: int
+
+
+class UserApi(BaseApi):
+    ENTRYPOINT: Final[str] = "v2/"
+
+    def auth(self, username: str, password: str) -> tuple[User, Token]:
+        print(self.__class__.__name__ + "::" + sys._getframe().f_code.co_name)
+        url = self.ENTRYPOINT + "auth/"
+        data = {"username": username, "password": password}
+        response = self._post(url, data=data)
+        if response.status_code == requests.codes.unauthorized:
+            raise UnauthorizedException("Invalid username or password.")
+        self._raise_response_error(response)
+        obj = parse_obj_as(UserAuthResponse, response.json())
+        token = Token(access=obj.access, refresh=obj.refresh)
+        user = User(id=token.user_id, username=username, laboratory_id=obj.lab_id, laboratory=obj.laboratory)
+        return (user, token)
+
+    def refresh(self, token: Token) -> Token:
+        print(self.__class__.__name__ + "::" + sys._getframe().f_code.co_name)
+        url = self.ENTRYPOINT + "refresh/"
+        data = {"refresh": token.refresh}
+        response = self._post(url, data=data)
+        if response.status_code == requests.codes.unauthorized:
+            raise UnauthorizedException("Token is invalid or expired.")
+        self._raise_response_error(response)
+        token = parse_obj_as(Token, response.json())
+        return token

mdrsclient/api/utils.py

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+from mdrsclient.api.user import UserApi
+from mdrsclient.exceptions import UnauthorizedException
+from mdrsclient.session import MDRSSession
+
+
+def token_check(session: MDRSSession) -> None:
+    if session.token is not None:
+        if session.token.is_refresh_required:
+            user_api = UserApi(session)
+            try:
+                session.token = user_api.refresh(session.token)
+            except UnauthorizedException:
+                session.logout()
+        elif session.token.is_expired:
+            session.logout()

mdrsclient/cache.py

@@ -0,0 +1,113 @@
+import dataclasses
+import fcntl
+import json
+import os
+
+from pydantic import ValidationError
+from pydantic.dataclasses import dataclass
+from pydantic.tools import parse_obj_as
+
+from mdrsclient.models import Laboratories, Token, User
+from mdrsclient.settings import CONFIG_DIR_PATH
+
+
+@dataclass
+class CacheData:
+    user: User | None
+    token: Token | None
+    laboratories: Laboratories
+
+
+class CacheFile:
+    serial: int
+    cache_dir: str
+    cache_file: str
+    data: CacheData
+
+    def __init__(self, remote: str) -> None:
+        self.serial = -1
+        self.cache_dir = os.path.join(CONFIG_DIR_PATH, "cache")
+        self.cache_file = os.path.join(self.cache_dir, remote + ".json")
+        self.data = CacheData(user=None, token=None, laboratories=Laboratories([]))
+
+    def dump(self) -> CacheData | None:
+        self.__load()
+        return self.data
+
+    @property
+    def token(self) -> Token | None:
+        self.__load()
+        return self.data.token
+
+    @token.setter
+    def token(self, token: Token) -> None:
+        self.__load()
+        self.data.token = token
+        self.__save()
+
+    @token.deleter
+    def token(self) -> None:
+        if self.data.token is not None:
+            self.__clear()
+
+    @property
+    def user(self) -> User | None:
+        return self.data.user
+
+    @user.setter
+    def user(self, user: User) -> None:
+        self.__load()
+        self.data.user = user
+        self.__save()
+
+    @user.deleter
+    def user(self) -> None:
+        if self.data.user is not None:
+            self.__clear()
+
+    @property
+    def laboratories(self) -> Laboratories:
+        return self.data.laboratories
+
+    @laboratories.setter
+    def laboratories(self, laboratories: Laboratories) -> None:
+        self.__load()
+        self.data.laboratories = laboratories
+        self.__save()
+
+    def __clear(self) -> None:
+        self.data.user = None
+        self.data.token = None
+        self.data.laboratories.clear()
+        self.__save()
+
+    def __load(self) -> None:
+        if os.path.isfile(self.cache_file):
+            stat = os.stat(self.cache_file)
+            serial = hash((stat.st_uid, stat.st_gid, stat.st_mode, stat.st_size, stat.st_mtime))
+            if self.serial != serial:
+                try:
+                    with open(self.cache_file) as f:
+                        self.data = parse_obj_as(CacheData, json.load(f))
+                except ValidationError:
+                    self.__clear()
+                    self.__save()
+                else:
+                    self.serial = serial
+        else:
+            self.data.token = None
+            self.serial = -1
+
+    def __save(self) -> None:
+        self.__ensure_cache_dir()
+        with open(self.cache_file, "w") as f:
+            fcntl.flock(f, fcntl.LOCK_EX)
+            f.write(json.dumps(dataclasses.asdict(self.data)))
+        # ensure file is secure.
+        os.chmod(self.cache_file, 0o600)
+
+    def __ensure_cache_dir(self) -> None:
+        if not os.path.exists(self.cache_dir):
+            os.makedirs(self.cache_dir)
+        # ensure directory is secure.
+        os.chmod(self.cache_dir, 0o700)

mdrsclient/commands/__init__.py

@@ -0,0 +1,13 @@
+from mdrsclient.commands.config import ConfigCommand
+from mdrsclient.commands.file import FileCommand
+from mdrsclient.commands.folder import FolderCommand
+from mdrsclient.commands.laboratory import LaboratoryCommand
+from mdrsclient.commands.user import UserCommand
+
+__all__ = [
+    "ConfigCommand",
+    "FileCommand",
+    "FolderCommand",
+    "LaboratoryCommand",
+    "UserCommand",
+]

mdrsclient/commands/base.py

@@ -0,0 +1,11 @@
+from abc import ABC, abstractmethod
+from argparse import _SubParsersAction
+
+from mdrsclient.exceptions import UnexpectedException
+
+
+class BaseCommand(ABC):
+    @staticmethod
+    @abstractmethod
+    def register(top_level_subparsers: _SubParsersAction) -> None:
+        raise UnexpectedException("Not implemented.")

mdrsclient/commands/config.py

@@ -0,0 +1,69 @@
+from argparse import Namespace, _SubParsersAction
+
+from mdrsclient.commands.base import BaseCommand
+from mdrsclient.commands.utils import parse_remote_host
+from mdrsclient.config import ConfigFile
+from mdrsclient.exceptions import IllegalArgumentException
+
+
+class ConfigCommand(BaseCommand):
+    @staticmethod
+    def register(top_level_subparsers: _SubParsersAction) -> None:
+        # config
+        parser = top_level_subparsers.add_parser("config", help="configure remote hosts")
+        parser.set_defaults(func=lambda x: parser.print_help())
+        subparsers = parser.add_subparsers(title="config subcommands")
+        # config create
+        create_parser = subparsers.add_parser("create", help="create a new remote host")
+        create_parser.add_argument("remote", help="Label of remote host")
+        create_parser.add_argument("url", help="API entrypoint url of remote host")
+        create_parser.set_defaults(func=ConfigCommand.create)
+        # config update
+        update_parser = subparsers.add_parser("update", help="update a new remote host")
+        update_parser.add_argument("remote", help="Label of remote host")
+        update_parser.add_argument("url", help="API entrypoint url of remote host")
+        update_parser.set_defaults(func=ConfigCommand.update)
+        # config list
+        list_parser = subparsers.add_parser("list", help="list all the remote hosts")
+        list_parser.add_argument("-l", "--long", help="Show the api url", action="store_true")
+        list_parser.set_defaults(func=ConfigCommand.list)
+        # config delete
+        delete_parser = subparsers.add_parser("delete", help="delete an existing remote host")
+        delete_parser.add_argument("remote", help="Label of remote host")
+        delete_parser.set_defaults(func=ConfigCommand.delete)
+
+    @staticmethod
+    def create(args: Namespace) -> None:
+        remote = parse_remote_host(args.remote)
+        config = ConfigFile(remote=remote)
+        if config.url is not None:
+            raise IllegalArgumentException(f"Remote host `{remote}` is already exists.")
+        else:
+            config.url = args.url
+
+    @staticmethod
+    def update(args: Namespace) -> None:
+        remote = parse_remote_host(args.remote)
+        config = ConfigFile(remote=remote)
+        if config.url is None:
+            raise IllegalArgumentException(f"Remote host `{remote}` is not exists.")
+        else:
+            config.url = args.url
+
+    @staticmethod
+    def list(args: Namespace) -> None:
+        config = ConfigFile("")
+        for remote, url in config.list():
+            line = f"{remote}:"
+            if args.long:
+                line += f"\t{url}"
+            print(line)
+
+    @staticmethod
+    def delete(args: Namespace) -> None:
+        remote = parse_remote_host(args.remote)
+        config = ConfigFile(remote=remote)
+        if config.url is None:
+            raise IllegalArgumentException(f"Remote host `{remote}` is not exists.")
+        else:
+            del config.url

mdrsclient/commands/file.py

@@ -0,0 +1,231 @@
+import dataclasses
+import os
+from argparse import Namespace, _SubParsersAction
+from multiprocessing import Process
+
+from pydantic import parse_obj_as
+from pydantic.dataclasses import dataclass
+
+from mdrsclient.api import FileApi, FolderApi
+from mdrsclient.commands.base import BaseCommand
+from mdrsclient.commands.utils import (
+    create_session,
+    find_folder,
+    find_laboratory,
+    parse_remote_host_with_path,
+)
+from mdrsclient.exceptions import (
+    IllegalArgumentException,
+    MDRSException,
+    UnexpectedException,
+)
+from mdrsclient.models import File, Folder
+from mdrsclient.session import MDRSSession
+from mdrsclient.settings import NUMBER_OF_PROCESS
+
+
+@dataclass(frozen=True)
+class UploadFile:
+    folder: Folder
+    path: str
+
+
+class FileCommand(BaseCommand):
+    @staticmethod
+    def register(top_level_subparsers: _SubParsersAction) -> None:
+        # upload
+        upload_parser = top_level_subparsers.add_parser("upload", help="upload the file or directories")
+        upload_parser.add_argument(
+            "-r", "--recursive", help="Upload directories and their contents recursive", action="store_true"
+        )
+        upload_parser.add_argument("local_path", help="Local file path (/foo/bar/data.txt)")
+        upload_parser.add_argument("remote_path", help="Remote folder path (remote:/lab/path/)")
+        upload_parser.set_defaults(func=FileCommand.upload)
+        # download
+        download_parser = top_level_subparsers.add_parser("download", help="download a file")
+        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/)")
+        download_parser.set_defaults(func=FileCommand.download)
+        # move
+        move_parser = top_level_subparsers.add_parser("move", help="move a file")
+        move_parser.add_argument("src_path", help="Source remote file path (remote:/lab/path/file)")
+        move_parser.add_argument("dest_path", help="Destination remote file path (remote:/lab/path/file)")
+        move_parser.set_defaults(func=FileCommand.move)
+        # remove
+        remove_parser = top_level_subparsers.add_parser("remove", help="remove a file")
+        remove_parser.add_argument("remote_path", help="Remote file path (remote:/lab/path/file)")
+        remove_parser.set_defaults(func=FileCommand.remove)
+        # file-metadata
+        metadata_parser = top_level_subparsers.add_parser("file-metadata", help="get the file metadata")
+        metadata_parser.add_argument("remote_path", help="Remote file path (remote:/lab/path/file)")
+        metadata_parser.set_defaults(func=FileCommand.metadata)
+
+    @staticmethod
+    def upload(args: Namespace) -> None:
+        (remote, laboratory_name, path) = parse_remote_host_with_path(args.remote_path)
+        local_path = os.path.realpath(args.local_path)
+        if not os.path.exists(local_path):
+            raise IllegalArgumentException(f"File or directory `{args.local_path}` not found.")
+        session = create_session(remote)
+        laboratory = find_laboratory(session, laboratory_name)
+        folder = find_folder(session, laboratory, path)
+        upload_files: list[UploadFile] = []
+        if os.path.isdir(local_path):
+            if not args.recursive:
+                raise IllegalArgumentException(f"Cannot upload `{args.local_path}`: Is a directory.")
+            folder_api = FolderApi(session)
+            folders: dict[str, Folder] = {}
+            folders[path] = folder
+            local_basename = os.path.basename(local_path)
+            for dirpath, dirnames, filenames in os.walk(local_path):
+                sub = (
+                    local_basename
+                    if dirpath == local_path
+                    else os.path.join(local_basename, os.path.relpath(dirpath, local_path))
+                )
+                dest_folder_path = os.path.join(path, sub)
+                dest_folder_name = os.path.basename(dest_folder_path)
+                # prepare destination parent path
+                dest_parent_folder_path = os.path.dirname(dest_folder_path)
+                if folders.get(dest_parent_folder_path) is None:
+                    res = folder_api.list(laboratory.id, dest_parent_folder_path)
+                    if len(res) != 1:
+                        raise UnexpectedException(f"Remote folder `{dest_parent_folder_path}` not found.")
+                    folders[dest_parent_folder_path] = folder_api.retrieve(res[0].id)
+                # prepare destination path
+                if folders.get(dest_folder_path) is None:
+                    dest_folder_simple = folders[dest_parent_folder_path].find_sub_folder(dest_folder_name)
+                    if dest_folder_simple is None:
+                        dest_folder_id = folder_api.create(dest_folder_name, folders[dest_parent_folder_path].id)
+                    else:
+                        dest_folder_id = dest_folder_simple.id
+                    folders[dest_folder_path] = folder_api.retrieve(dest_folder_id)
+                    if dest_folder_simple is None:
+                        folders[dest_parent_folder_path].sub_folders.append(folders[dest_folder_path])
+                # register upload file list
+                for filename in filenames:
+                    upload_files.append(UploadFile(folders[dest_folder_path], os.path.join(dirpath, filename)))
+        else:
+            upload_files.append(UploadFile(folder, local_path))
+        FileCommand._multiple_upload(session, upload_files)
+
+    @staticmethod
+    def download(args: Namespace) -> None:
+        (remote, laboratory_name, path) = parse_remote_host_with_path(args.remote_path)
+        path = path.rstrip("/")
+        parent_path = os.path.dirname(path)
+        file_name = os.path.basename(path)
+        session = create_session(remote)
+        if not os.path.isdir(args.local_path):
+            raise IllegalArgumentException(f"Local directory `{args.local_path}` not found.")
+        local_file = os.path.join(args.local_path, file_name)
+        laboratory = find_laboratory(session, laboratory_name)
+        folder = find_folder(session, laboratory, parent_path)
+        file = folder.find_file(file_name)
+        if file is None:
+            raise IllegalArgumentException(f"File `{file_name}` not found.")
+        r = session.get(session.build_url("v2/" + file.download_url), stream=True)
+        try:
+            with open(local_file, "wb") as f:
+                for chunk in r.iter_content(chunk_size=4096):
+                    if chunk:
+                        f.write(chunk)
+                        f.flush()
+        except PermissionError:
+            raise IllegalArgumentException(f"Cannot create file `{local_file}`: Permission denied.")
+
+    @staticmethod
+    def move(args: Namespace) -> None:
+        (src_remote, src_laboratory_name, src_path) = parse_remote_host_with_path(args.src_path)
+        (dest_remote, dest_laboratory_name, dest_path) = parse_remote_host_with_path(args.dest_path)
+        if src_remote != dest_remote:
+            raise IllegalArgumentException("Remote host mismatched.")
+        if src_laboratory_name != dest_laboratory_name:
+            raise IllegalArgumentException("Laboratory mismatched.")
+        src_path = src_path.rstrip("/")
+        src_dirpath = os.path.dirname(src_path)
+        src_filename = os.path.basename(src_path)
+        if dest_path.endswith("/"):
+            dest_dirpath = dest_path
+            dest_filename = src_filename
+        else:
+            dest_dirpath = os.path.dirname(dest_path)
+            dest_filename = os.path.basename(dest_path)
+        session = create_session(src_remote)
+        laboratory = find_laboratory(session, src_laboratory_name)
+        src_folder = find_folder(session, laboratory, src_dirpath)
+        dest_folder = find_folder(session, laboratory, dest_dirpath)
+        src_file = src_folder.find_file(src_filename)
+        if src_file is None:
+            raise IllegalArgumentException(f"File `{src_filename}` not found.")
+        dest_file = dest_folder.find_file(dest_filename)
+        if dest_file is not None:
+            raise IllegalArgumentException(f"File `{dest_filename}` already exists.")
+        file_api = FileApi(session)
+        if src_folder.id != dest_folder.id:
+            file_api.move(src_file, dest_folder.id)
+        if dest_filename != src_filename:
+            dest_file_dict = dataclasses.asdict(src_file) | {"name": dest_filename}
+            dest_file = parse_obj_as(File, dest_file_dict)
+            file_api.update(dest_file, None)
+
+    @staticmethod
+    def remove(args: Namespace) -> None:
+        (remote, laboratory_name, path) = parse_remote_host_with_path(args.remote_path)
+        path = path.rstrip("/")
+        parent_path = os.path.dirname(path)
+        file_name = os.path.basename(path)
+        session = create_session(remote)
+        laboratory = find_laboratory(session, laboratory_name)
+        folder = find_folder(session, laboratory, parent_path)
+        file = folder.find_file(file_name)
+        if file is None:
+            raise IllegalArgumentException(f"File `{file_name}` not found.")
+        file_api = FileApi(session)
+        file_api.destroy(file)
+
+    @staticmethod
+    def metadata(args: Namespace) -> None:
+        (remote, laboratory_name, path) = parse_remote_host_with_path(args.remote_path)
+        path = path.rstrip("/")
+        parent_path = os.path.dirname(path)
+        file_name = os.path.basename(path)
+        session = create_session(remote)
+        laboratory = find_laboratory(session, laboratory_name)
+        folder = find_folder(session, laboratory, parent_path)
+        file = folder.find_file(file_name)
+        if file is None:
+            raise IllegalArgumentException(f"File `{file_name}` not found.")
+        file_api = FileApi(session)
+        metadata = file_api.metadata(file)
+        print(metadata)
+
+    @staticmethod
+    def _multiple_upload(session: MDRSSession, upload_files: list[UploadFile]) -> None:
+        processes: list[Process] = []
+        for idx in range(NUMBER_OF_PROCESS):
+            processes.append(
+                Process(
+                    target=FileCommand._multiple_upload_worker,
+                    args=(session, upload_files, idx, NUMBER_OF_PROCESS),
+                )
+            )
+        for process in processes:
+            process.start()
+        for process in processes:
+            process.join()
+
+    @staticmethod
+    def _multiple_upload_worker(session: MDRSSession, upload_files: list[UploadFile], idx: int, num_proc: int) -> None:
+        file_api = FileApi(session)
+        for upload_file in upload_files[idx::num_proc]:
+            file_name = os.path.basename(upload_file.path)
+            file = next((x for x in upload_file.folder.files if x.name == file_name), None)
+            try:
+                if file is None:
+                    file_api.create(upload_file.folder.id, upload_file.path)
+                else:
+                    file_api.update(file, upload_file.path)
+                pass
+            except MDRSException as e:
+                print(f"API Error: {e}")

mdrsclient/commands/folder.py

@@ -0,0 +1,117 @@
+import os
+from argparse import Namespace, _SubParsersAction
+
+from mdrsclient.api import FolderApi
+from mdrsclient.commands.base import BaseCommand
+from mdrsclient.commands.utils import (
+    create_session,
+    find_folder,
+    find_laboratory,
+    parse_remote_host_with_path,
+)
+
+
+class FolderCommand(BaseCommand):
+    @staticmethod
+    def register(top_level_subparsers: _SubParsersAction) -> None:
+        # ls
+        ls_parser = top_level_subparsers.add_parser("ls", help="list the folder contents")
+        ls_parser.add_argument("remote_path", help="Remote folder path (remote:/lab/path/)")
+        ls_parser.set_defaults(func=FolderCommand.list)
+        # mkdir
+        mkdir_parser = top_level_subparsers.add_parser("mkdir", help="create a new folder")
+        mkdir_parser.add_argument("remote_path", help="Remote folder path (remote:/lab/path/)")
+        mkdir_parser.set_defaults(func=FolderCommand.mkdir)
+        # rmdir
+        rmdir_parser = top_level_subparsers.add_parser("rmdir", help="remove a existing folder")
+        rmdir_parser.add_argument("remote_path", help="Remote folder path (remote:/lab/path/)")
+        rmdir_parser.set_defaults(func=FolderCommand.rmdir)
+        # metadata
+        metadata_parser = top_level_subparsers.add_parser("metadata", help="get a folder metadata")
+        metadata_parser.add_argument("remote_path", help="Remote folder path (remote:/lab/path/)")
+        metadata_parser.set_defaults(func=FolderCommand.metadata)
+
+    @staticmethod
+    def list(args: Namespace) -> None:
+        (remote, laboratory_name, path) = parse_remote_host_with_path(args.remote_path)
+        session = create_session(remote)
+        laboratory = find_laboratory(session, laboratory_name)
+        folder = find_folder(session, laboratory, path)
+        label = {
+            "type": "Type",
+            "acl": "Access",
+            "laboratory": "Laboratory",
+            "size": "Lock/Size",
+            "date": "Date",
+            "name": "Name",
+        }
+        length: dict[str, int] = {}
+        for key in label.keys():
+            length[key] = len(label[key])
+        for sub_folder in folder.sub_folders:
+            sub_laboratory = session.laboratories.find_by_id(sub_folder.lab_id)
+            sub_laboratory_name = sub_laboratory.name if sub_laboratory is not None else "(invalid)"
+            length["acl"] = max(length["acl"], len(sub_folder.access_level_name))
+            length["laboratory"] = max(length["laboratory"], len(sub_laboratory_name))
+            length["size"] = max(length["size"], len(sub_folder.lock_name))
+            length["date"] = max(length["date"], len(sub_folder.updated_at_name))
+            length["name"] = max(length["name"], len(sub_folder.name))
+        for file in folder.files:
+            length["size"] = max(length["size"], len(str(file.size)))
+            length["date"] = max(length["date"], len(file.updated_at_name))
+            length["name"] = max(length["name"], len(file.name))
+        length["acl"] = max(length["acl"], len(folder.access_level_name))
+        length["laboratory"] = max(length["laboratory"], len(laboratory.name))
+        header = (
+            f"{label['type']:{length['type']}}\t{label['acl']:{length['acl']}}\t"
+            f"{label['laboratory']:{length['laboratory']}}\t{label['size']:{length['size']}}\t"
+            f"{label['date']:{length['date']}}\t{label['name']:{length['name']}}"
+        )
+        print(header)
+        print("-" * len(header.expandtabs()))
+
+        for sub_folder in sorted(folder.sub_folders, key=lambda x: x.name):
+            sub_laboratory = session.laboratories.find_by_id(sub_folder.lab_id)
+            sub_laboratory_name = sub_laboratory.name if sub_laboratory is not None else "(invalid)"
+            print(
+                f"{'[d]':{length['type']}}\t{sub_folder.access_level_name:{length['acl']}}\t"
+                f"{sub_laboratory_name:{length['laboratory']}}\t{sub_folder.lock_name:{length['size']}}\t"
+                f"{sub_folder.updated_at_name:{length['date']}}\t{sub_folder.name:{length['name']}}"
+            )
+        for file in sorted(folder.files, key=lambda x: x.name):
+            print(
+                f"{'[f]':{length['type']}}\t{folder.access_level_name:{length['acl']}}\t"
+                f"{laboratory.name:{length['laboratory']}}\t{file.size:{length['size']}}\t"
+                f"{file.updated_at_name:{length['date']}}\t{file.name:{length['name']}}"
+            )
+
+    @staticmethod
+    def mkdir(args: Namespace) -> None:
+        (remote, laboratory_name, path) = parse_remote_host_with_path(args.remote_path)
+        path = path.rstrip("/")
+        parent_path = os.path.dirname(path)
+        folder_name = os.path.basename(path)
+        session = create_session(remote)
+        laboratory = find_laboratory(session, laboratory_name)
+        folder = find_folder(session, laboratory, parent_path)
+        folder_api = FolderApi(session)
+        folder_api.create(folder_name, folder.id)
+
+    @staticmethod
+    def rmdir(args: Namespace) -> None:
+        (remote, laboratory_name, path) = parse_remote_host_with_path(args.remote_path)
+        session = create_session(remote)
+        laboratory = find_laboratory(session, laboratory_name)
+        folder = find_folder(session, laboratory, path)
+        folder_api = FolderApi(session)
+        folder_api.destroy(folder.id)
+
+    @staticmethod
+    def metadata(args: Namespace) -> None:
+        (remote, laboratory_name, path) = parse_remote_host_with_path(args.remote_path)
+        session = create_session(remote)
+        laboratory = find_laboratory(session, laboratory_name)
+        folder = find_folder(session, laboratory, path)
+        folder_api = FolderApi(session)
+        metadata = folder_api.metadata(folder.id)
+        print(metadata)

mdrsclient/commands/laboratory.py

@@ -0,0 +1,42 @@
+from argparse import Namespace, _SubParsersAction
+
+from mdrsclient.api import LaboratoryApi
+from mdrsclient.commands.base import BaseCommand
+from mdrsclient.commands.utils import create_session, parse_remote_host
+
+
+class LaboratoryCommand(BaseCommand):
+    @staticmethod
+    def register(top_level_subparsers: _SubParsersAction) -> None:
+        # labs
+        lls_parser = top_level_subparsers.add_parser("labs", help="list all laboratories")
+        lls_parser.add_argument("remote", help="Label of remote host")
+        lls_parser.set_defaults(func=LaboratoryCommand.list)
+
+    @staticmethod
+    def list(args: Namespace) -> None:
+        remote = parse_remote_host(args.remote)
+        session = create_session(remote)
+        laboratory_api = LaboratoryApi(session)
+        laboratories = laboratory_api.list()
+        session.laboratories = laboratories
+        label = {"id": "ID", "name": "Name", "pi_name": "PI", "full_name": "Laboratory"}
+        length: dict[str, int] = {}
+        for key in label.keys():
+            length[key] = len(label[key])
+        for laboratory in laboratories:
+            length["id"] = max(length["id"], len(str(laboratory.id)))
+            length["name"] = max(length["name"], len(laboratory.name))
+            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['pi_name']:{length['pi_name']}}\t{label['full_name']:{length['full_name']}}"
+        )
+        print(header)
+        print("-" * len(header.expandtabs()))
+        for laboratory in laboratories:
+            print(
+                f"{laboratory.id:{length['id']}}\t{laboratory.name:{length['name']}}\t"
+                f"{laboratory.pi_name:{length['pi_name']}}\t{laboratory.full_name:{length['full_name']}}"
+            )

mdrsclient/commands/user.py

@@ -0,0 +1,61 @@
+import getpass
+from argparse import Namespace, _SubParsersAction
+
+from mdrsclient.api import UserApi
+from mdrsclient.commands.base import BaseCommand
+from mdrsclient.commands.utils import parse_remote_host
+from mdrsclient.config import ConfigFile
+from mdrsclient.exceptions import MissingConfigurationException
+from mdrsclient.session import MDRSSession
+
+
+class UserCommand(BaseCommand):
+    @staticmethod
+    def register(top_level_subparsers: _SubParsersAction) -> None:
+        # login
+        login_parser = top_level_subparsers.add_parser("login", help="login to remote host")
+        login_parser.add_argument("remote", help="Label of remote host")
+        login_parser.set_defaults(func=UserCommand.login)
+        # logout
+        logout_parser = top_level_subparsers.add_parser("logout", help="logout from remote host")
+        logout_parser.add_argument("remote", help="Label of remote host")
+        logout_parser.set_defaults(func=UserCommand.logout)
+        # whoami
+        whoami_parser = top_level_subparsers.add_parser("whoami", help="show current user name")
+        whoami_parser.add_argument("remote", help="Label of remote host")
+        whoami_parser.set_defaults(func=UserCommand.whoami)
+
+    @staticmethod
+    def login(args: Namespace) -> None:
+        remote = parse_remote_host(args.remote)
+        config = ConfigFile(remote)
+        if config.url is None:
+            raise MissingConfigurationException(f"Remote host `{remote}` is not found.")
+        session = MDRSSession(config.remote, config.url)
+        username = input("Username: ").strip()
+        password = getpass.getpass("Password: ").strip()
+        user_api = UserApi(session)
+        (user, token) = user_api.auth(username, password)
+        session.user = user
+        session.token = token
+
+    @staticmethod
+    def logout(args: Namespace) -> None:
+        remote = parse_remote_host(args.remote)
+        config = ConfigFile(remote)
+        if config.url is None:
+            raise MissingConfigurationException(f"Remote host `{remote}` is not found.")
+        session = MDRSSession(config.remote, config.url)
+        session.logout()
+
+    @staticmethod
+    def whoami(args: Namespace) -> None:
+        remote = parse_remote_host(args.remote)
+        config = ConfigFile(remote)
+        if config.url is None:
+            raise MissingConfigurationException(f"Remote host `{remote}` is not found.")
+        session = MDRSSession(config.remote, config.url)
+        if session.token is not None and session.token.is_expired:
+            session.logout()
+        username = session.user.username if session.user is not None else "(Anonymous)"
+        print(username)

mdrsclient/commands/utils.py

@@ -0,0 +1,69 @@
+import re
+
+from mdrsclient.api import FolderApi, LaboratoryApi
+from mdrsclient.config import ConfigFile
+from mdrsclient.exceptions import (
+    IllegalArgumentException,
+    MissingConfigurationException,
+    UnauthorizedException,
+    UnexpectedException,
+)
+from mdrsclient.models import Folder, Laboratory
+from mdrsclient.session import MDRSSession
+
+
+def create_session(remote: str) -> MDRSSession:
+    config = ConfigFile(remote)
+    if config.url is None:
+        raise MissingConfigurationException(f"Remote host `{remote}` is not found.")
+    return MDRSSession(config.remote, config.url)
+
+
+def find_laboratory(session: MDRSSession, laboratory_name: str) -> Laboratory:
+    if session.laboratories.empty():
+        laboratory_api = LaboratoryApi(session)
+        session.laboratories = laboratory_api.list()
+    laboratory = session.laboratories.find_by_name(laboratory_name)
+    if laboratory is None:
+        raise IllegalArgumentException(f"Laboratory `{laboratory_name}` not found.")
+    return laboratory
+
+
+def find_folder(session: MDRSSession, laboratory: Laboratory, path: str) -> Folder:
+    folder_api = FolderApi(session)
+    folders = folder_api.list(laboratory.id, path)
+    if len(folders) != 1:
+        raise UnexpectedException(f"Folder `{path}` not found.")
+    if folders[0].lock:
+        raise UnauthorizedException(f"Folder `{path}` is locked.")
+    return folder_api.retrieve(folders[0].id)
+
+
+def parse_remote_host(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
+
+
+def parse_remote_host_with_path(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)

mdrsclient/config.py

@@ -0,0 +1,80 @@
+import configparser
+import os
+from typing import Final
+
+import validators
+
+from mdrsclient.exceptions import IllegalArgumentException
+from mdrsclient.settings import CONFIG_FILE_PATH
+
+
+class ConfigFile:
+    OPTION_URL: Final[str] = "url"
+
+    serial: int
+    config_file: str
+    config_dir: str
+    remote: str
+    config: configparser.ConfigParser
+
+    def __init__(self, remote: str) -> None:
+        self.serial = -1
+        self.config_file = CONFIG_FILE_PATH
+        self.config_dir = os.path.dirname(CONFIG_FILE_PATH)
+        self.remote = remote
+        self.config = configparser.ConfigParser()
+
+    def list(self) -> list[tuple[str, str]]:
+        ret: list[tuple[str, str]] = []
+        self.__load()
+        for remote in self.config.sections():
+            url = self.config.get(remote, self.OPTION_URL)
+            ret.append((remote, url))
+        return ret
+
+    @property
+    def url(self) -> str | None:
+        if not self.__exists(self.remote):
+            return None
+        return self.config.get(self.remote, self.OPTION_URL)
+
+    @url.setter
+    def url(self, url: str) -> None:
+        if not validators.url(url):  # type: ignore
+            raise IllegalArgumentException("malformed URI sequence")
+        self.__load()
+        if self.config.has_section(self.remote):
+            self.config.remove_section(self.remote)
+        self.config.add_section(self.remote)
+        self.config.set(self.remote, self.OPTION_URL, url)
+        self.__save()
+
+    @url.deleter
+    def url(self) -> None:
+        if self.__exists(self.remote):
+            self.config.remove_section(self.remote)
+            self.__save()
+
+    def __exists(self, section: str) -> bool:
+        self.__load()
+        return self.config.has_option(section, self.OPTION_URL)
+
+    def __load(self) -> None:
+        if os.path.isfile(self.config_file):
+            stat = os.stat(self.config_file)
+            serial = hash(stat)
+            if self.serial != serial:
+                self.config.read(self.config_file, encoding="utf8")
+                self.serial = serial
+
+    def __save(self) -> None:
+        self.__ensure_cache_dir()
+        with open(self.config_file, "w") as f:
+            self.config.write(f)
+        os.chmod(self.config_file, 0o600)
+
+    def __ensure_cache_dir(self) -> None:
+        if not os.path.exists(self.config_dir):
+            os.makedirs(self.config_dir)
+        # ensure directory is secure.
+        os.chmod(self.config_dir, 0o700)

mdrsclient/exceptions.py

@@ -0,0 +1,40 @@
+class MDRSException(Exception):
+    """Thrown when some kind of errors occurred"""
+
+    pass
+
+
+class IllegalArgumentException(MDRSException):
+    """Thrown when something wrong with the argument is passed to a method"""
+
+    pass
+
+
+class MissingConfigurationException(MDRSException):
+    """Thrown when wrong or missing system configuration"""
+
+    pass
+
+
+class BadRequestException(MDRSException):
+    """Thrown when the request does not contain valid parameter"""
+
+    pass
+
+
+class UnauthorizedException(MDRSException):
+    """Thrown when the current user not allowed to perform an operation on the resource"""
+
+    pass
+
+
+class ForbiddenException(MDRSException):
+    """Thrown when the current user does not have enough privileges to access the resource"""
+
+    pass
+
+
+class UnexpectedException(MDRSException):
+    """Thrown when unexpected error occurred"""
+
+    pass

mdrsclient/models/__init__.py

@@ -0,0 +1,16 @@
+from mdrsclient.models.error import DRFStandardizedErrors
+from mdrsclient.models.file import File
+from mdrsclient.models.folder import Folder, FolderSimple
+from mdrsclient.models.laboratory import Laboratories, Laboratory
+from mdrsclient.models.user import Token, User
+
+__all__ = [
+    "DRFStandardizedErrors",
+    "File",
+    "Folder",
+    "FolderSimple",
+    "Laboratories",
+    "Laboratory",
+    "Token",
+    "User",
+]

mdrsclient/models/error.py

@@ -0,0 +1,14 @@
+from pydantic.dataclasses import dataclass
+
+
+@dataclass(frozen=True)
+class DRFStandardizedError:
+    code: str
+    detail: str
+    attr: str | None
+
+
+@dataclass(frozen=True)
+class DRFStandardizedErrors:
+    type: str
+    errors: list[DRFStandardizedError]

mdrsclient/models/file.py

@@ -0,0 +1,25 @@
+from pydantic.dataclasses import dataclass
+
+from mdrsclient.models.utils import iso8601_to_user_friendly
+
+
+@dataclass(frozen=True)
+class File:
+    id: str
+    name: str
+    type: str
+    size: int
+    thumbnail: str | None
+    description: str
+    metadata: dict
+    download_url: str
+    created_at: str
+    updated_at: str
+
+    @property
+    def created_at_name(self) -> str:
+        return iso8601_to_user_friendly(self.created_at)
+
+    @property
+    def updated_at_name(self) -> str:
+        return iso8601_to_user_friendly(self.updated_at)

mdrsclient/models/folder.py

@@ -0,0 +1,58 @@
+from typing import Final
+
+from pydantic.dataclasses import dataclass
+
+from mdrsclient.models import File
+from mdrsclient.models.utils import iso8601_to_user_friendly
+
+ACCESS_LEVEL_NAMES: Final[dict[int, str]] = {
+    -1: "Storage",
+    0: "Private",
+    1: "CBS Open",
+    2: "PW Open",
+    3: "Public",
+}
+
+
+@dataclass(frozen=True)
+class FolderSimple:
+    id: str
+    pid: str | None
+    name: str
+    access_level: int
+    lock: bool
+    lab_id: int
+    description: str
+    created_at: str
+    updated_at: str
+    restrict_opened_at: str | None
+
+    @property
+    def access_level_name(self) -> str:
+        return ACCESS_LEVEL_NAMES[self.access_level]
+
+    @property
+    def lock_name(self) -> str:
+        return "locked" if self.lock else "unlocked"
+
+    @property
+    def created_at_name(self) -> str:
+        return iso8601_to_user_friendly(self.created_at)
+
+    @property
+    def updated_at_name(self) -> str:
+        return iso8601_to_user_friendly(self.updated_at)
+
+
+@dataclass(frozen=True)
+class Folder(FolderSimple):
+    metadata: list[dict]
+    sub_folders: list[FolderSimple]
+    files: list[File]
+    path: str
+
+    def find_sub_folder(self, name: str) -> FolderSimple | None:
+        return next((x for x in self.sub_folders if x.name == name), None)
+
+    def find_file(self, name: str) -> File | None:
+        return next((x for x in self.files if x.name == name), None)

mdrsclient/models/laboratory.py

@@ -0,0 +1,34 @@
+from typing import Generator
+
+from pydantic.dataclasses import dataclass
+
+
+@dataclass(frozen=True)
+class Laboratory:
+    id: int
+    name: str
+    pi_name: str
+    full_name: str
+
+
+@dataclass(frozen=True)
+class Laboratories:
+    items: list[Laboratory]
+
+    def __iter__(self) -> Generator[Laboratory, None, None]:
+        yield from self.items
+
+    def empty(self) -> bool:
+        return len(self.items) == 0
+
+    def clear(self) -> None:
+        self.items.clear()
+
+    def append(self, item: Laboratory) -> None:
+        self.items.append(item)
+
+    def find_by_id(self, id: int) -> Laboratory | None:
+        return next((x for x in self.items if x.id == id), None)
+
+    def find_by_name(self, name: str) -> Laboratory | None:
+        return next((x for x in self.items if x.name == name), None)

mdrsclient/models/user.py

@@ -0,0 +1,50 @@
+import time
+
+import jwt
+from pydantic import parse_obj_as
+from pydantic.dataclasses import dataclass
+
+
+@dataclass(frozen=True)
+class DecodedJWT:
+    token_type: str
+    exp: int
+    iat: int
+    jti: str
+    user_id: int
+
+
+@dataclass(frozen=True)
+class Token:
+    access: str
+    refresh: str
+
+    @property
+    def user_id(self) -> int:
+        access_decoded = self.__decode(self.access)
+        return access_decoded.user_id
+
+    @property
+    def is_expired(self) -> bool:
+        now = int(time.time()) + 10
+        refresh_decoded = self.__decode(self.refresh)
+        return now > refresh_decoded.exp
+
+    @property
+    def is_refresh_required(self) -> bool:
+        now = int(time.time()) + 10
+        access_decoded = self.__decode(self.access)
+        refresh_decoded = self.__decode(self.refresh)
+        return now > access_decoded.exp and now < refresh_decoded.exp
+
+    def __decode(self, token: str) -> DecodedJWT:
+        data = jwt.decode(token, options={"verify_signature": False})
+        return parse_obj_as(DecodedJWT, data)
+
+
+@dataclass(frozen=True)
+class User:
+    id: int
+    username: str
+    laboratory_id: int
+    laboratory: str

mdrsclient/models/utils.py

@@ -0,0 +1,5 @@
+import datetime
+
+
+def iso8601_to_user_friendly(text: str) -> str:
+    return datetime.datetime.fromisoformat(text).strftime("%Y/%m/%d %H:%M:%S")

mdrsclient/session.py

@@ -0,0 +1,58 @@
+import requests
+
+from mdrsclient.cache import CacheFile
+from mdrsclient.exceptions import MissingConfigurationException
+from mdrsclient.models import Laboratories, Token, User
+
+
+class MDRSSession(requests.Session):
+    url: str
+    __cache: CacheFile
+
+    def __init__(self, remote: str, url: str) -> None:
+        super().__init__()
+        self.url = url
+        self.__cache = CacheFile(remote)
+        self.__prepare_headers()
+
+    def build_url(self, *args) -> str:
+        if self.url == "":
+            raise MissingConfigurationException("remote host is not configured")
+        parts = [self.url]
+        parts.extend(args)
+        return "/".join(parts)
+
+    def logout(self) -> None:
+        del self.__cache.user
+        del self.__cache.token
+        self.headers.update({"Authorization": ""})
+
+    @property
+    def user(self) -> User | None:
+        return self.__cache.user
+
+    @user.setter
+    def user(self, user: User) -> None:
+        self.__cache.user = user
+
+    @property
+    def token(self) -> Token | None:
+        return self.__cache.token
+
+    @token.setter
+    def token(self, token: Token) -> None:
+        self.__cache.token = token
+        self.__prepare_headers()
+
+    @property
+    def laboratories(self) -> Laboratories:
+        return self.__cache.laboratories
+
+    @laboratories.setter
+    def laboratories(self, laboratories: Laboratories) -> None:
+        self.__cache.laboratories = laboratories
+
+    def __prepare_headers(self) -> None:
+        self.headers.update({"accept": "application/json"})
+        if self.token is not None:
+            self.headers.update({"Authorization": f"Bearer {self.token.access}"})

mdrsclient/settings.py

@@ -0,0 +1,20 @@
+import os
+
+from pydantic import BaseSettings
+
+
+class Settings(BaseSettings):
+    config_dir_path: str = "~/.mdrs-client"
+    number_of_process: int = 10
+
+    class Config:
+        env_file = ".env"
+        env_file_encoding = "utf-8"
+
+
+settings = Settings()
+
+NUMBER_OF_PROCESS = settings.number_of_process
+
+CONFIG_DIR_PATH = os.path.expanduser(settings.config_dir_path)
+CONFIG_FILE_PATH = os.path.join(CONFIG_DIR_PATH, "config.ini")

requirements.txt

@@ -0,0 +1,5 @@
+requests
+python-dotenv
+pydantic
+PyJWT
+validators

setup.py

@@ -0,0 +1,46 @@
+import os
+from typing import Final
+
+from setuptools import find_packages, setup
+
+BASE_DIR: Final[str] = os.path.abspath(os.path.dirname(__file__))
+
+with open(os.path.join(BASE_DIR, "VERSION")) as f:
+    __version__ = f.read().strip()
+
+with open(os.path.join(BASE_DIR, "requirements.txt")) as f:
+    __requirements__ = f.read().splitlines()
+
+with open(os.path.join(BASE_DIR, "README.md")) as f:
+    __readme__ = f.read()
+
+setup(
+    name="mdrsclient",
+    version=__version__,
+    description="A MDRS command-line tool",
+    long_description=__readme__,
+    author="Neuroinformatics Unit, RIKEN CBS",
+    license="MIT",
+    classifiers=[
+        "Development Status :: 3 - Alpha",
+        "Environment :: Console",
+        "Intended Audience :: Developers",
+        "Intended Audience :: Science/Research",
+        "Programming Language :: Python :: 3.10",
+        "Programming Language :: Python :: 3.11",
+        "OSI Approved :: MIT License",
+        "Topic :: Utilities",
+    ],
+    packages=find_packages(),
+    include_package_data=True,
+    package_data={
+        "": [
+            os.path.join(BASE_DIR, "README.md"),
+            os.path.join(BASE_DIR, "LICENSE"),
+            os.path.join(BASE_DIR, "VERSION"),
+            os.path.join(BASE_DIR, "requirements.txt"),
+        ]
+    },
+    install_requires=__requirements__,
+    entry_points={"console_scripts": ["mdrs=mdrsclient.__main__:main"]},
+)