orrisroot
4c9954c1fd
flake8 reported 49 findings and pyright 10, and two of them were real bugs rather than matters of style. The rest were unused imports and four functions over the complexity limit. - Unlock a DOI folder with the id the DOI response carries, rather than an attribute the model does not have, which raised `AttributeError` on every locked DOI folder. - Size the `ls` Size column from the sub-folder on the row rather than from its parent, which pushed the later columns out of line. - Share the path resolution and the destination checks between `cp` and `mv`, and split the recursive download and the `ls` row printing, bringing all four functions under the complexity limit. - Accept a client built without a connection, which `config` and `version` rely on, and report the reason if one is then asked for. - Declare the config protocol's constructor for the type checker alone, so the protocol keeps its guard against being instantiated. - Remove 41 unused imports, and let flake8 accept black's spacing. - Point pyright at the project's own environment, without which it resolved no dependency and reported 124 findings that were not real. - Cover the two fixes and the shared `cp`/`mv` paths with new tests.
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.
Installation (Production)
It is recommended to use a virtual environment (venv) to keep your Python environment isolated.
Option 1: Using standard venv + pip
python3 -m venv .venv
source .venv/bin/activate # On Windows: .venv\Scripts\activate
pip install .
Option 2: Using uv
uv venv
source .venv/bin/activate # On Windows: .venv\Scripts\activate
uv pip install .
Development Setup
To set up a local development environment with development tools (testing, formatting, linting):
Option 1: Using standard venv + pip
python3 -m venv .venv
source .venv/bin/activate # On Windows: .venv\Scripts\activate
pip install -e ".[dev]"
Option 2: Using uv (Recommended for developers)
uv sync
CLI Usage
config create
Create remote host configuration
mdrs config create neurodata https://neurodata.riken.jp/api
config update
Update the URL of a registered remote host.
mdrs config update neurodata https://neurodata.riken.jp/api
config list
List registered remote hosts.
mdrs config list
mdrs config ls
config delete
Remove a registered remote host.
mdrs config delete neurodata
mdrs config rm neurodata
login
Login to remote host
mdrs login neurodata:
Username: (enter your login name)
Password: (enter your password)
mdrs login -u USERNAME -p PASSWORD neurodata:
logout
Logout from remote host
mdrs logout neurodata:
whoami
Print current user name
mdrs whoami neurodata:
labs
List all laboratories
mdrs labs neurodata:
ls
List the folder contents. You can also specify a DOI path in the form remote:10.xxxx/yyy.ID[/optional/subpath].
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
Create a new folder
mdrs mkdir neurodata:/NIU/Repository/TEST
upload
Upload the file or directory
mdrs upload ./sample.dat neurodata:/NIU/Repository/TEST/
mdrs upload -r ./dataset neurodata:/NIU/Repository/TEST/
mdrs upload -r --skip-if-exists ./dataset neurodata:/NIU/Repository/TEST/
download
Download the file or folder. You can also specify a DOI path.
mdrs download neurodata:/NIU/Repository/TEST/sample.dat ./
mdrs download -r neurodata:/NIU/Repository/TEST/dataset/ ./
mdrs download -p SHARING_PASSWORD neurodata:/NIU/Repository/PW_Open/Readme.dat ./
mdrs download -r --exclude /NIU/Repository/TEST/dataset/skip neurodata:/NIU/Repository/TEST/dataset/ ./
mdrs download -r --skip-if-exists neurodata:/NIU/Repository/TEST/dataset/ ./
# 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
Move or rename the file or folder
mdrs mv neurodata:/NIU/Repository/TEST/sample.dat neurodata:/NIU/Repository/TEST2/sample2.dat
mdrs mv neurodata:/NIU/Repository/TEST/dataset neurodata:/NIU/Repository/TEST2/
cp
Copy the file and folder
mdrs cp neurodata:/NIU/Repository/TEST/sample.dat neurodata:/NIU/Repository/TEST2/sample2.dat
mdrs cp -r neurodata:/NIU/Repository/TEST/dataset neurodata:/NIU/Repository/TEST2/
rm
Remove the file or folder
mdrs rm neurodata:/NIU/Repository/TEST/sample.dat
mdrs rm -r neurodata:/NIU/Repository/TEST/dataset
chacl
Change the folder access level
mdrs chacl private neurodata:/NIU/Repository/Private
mdrs chacl cbs_open -r neurodata:/NIU/Repository/CBS_Open
mdrs chacl pw_open -r -p SHARING_PASSWORD neurodata:/NIU/Repository/PW_Open
metadata
Get a folder metadata. You can also specify a DOI path.
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. You can also specify a DOI path.
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
Show the tool name and version number
mdrs version
help
Show the help message and exit
mdrs -h
Python API Usage
You can also use this package as a Python library to programmatically interact with MDRS repositories.
from mdrsclient.client import MdrsClient
from mdrsclient.cache import InMemoryCache
from mdrsclient.config import InMemoryConfig
# 1. Setup in-memory configuration and cache to avoid local state files (e.g., config.ini, cache/*.json)
config = InMemoryConfig("neurodata")
config.url = "https://neurodata.riken.jp/api"
cache = InMemoryCache()
# 2. Initialize client with custom configuration and cache
client = MdrsClient.from_remote("neurodata", cache=cache, config=config)
# 3. Login to the remote server
client.login("username", "password")
# 4. 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)
Testing
You can run the unit test suite using the standard library unittest discover runner:
.venv/bin/python -m unittest discover tests
Changelog
See CHANGELOG.md for the full change history.