MetabolomicsHub Common Data Model and Utility Tools (mhd-model)

You can find documentation on Github

Development Environment

Development environment for linux or mac

# install python package manager uv
curl -LsSf https://astral.sh/uv/install.sh | sh

# add $HOME/.local/bin to your PATH, either restart your shell or run
export PATH=$HOME/.local/bin:$PATH

# install git from https://git-scm.com/downloads
# Linux command
apt update; apt install git -y

# Mac command
# brew install git

# clone project from github
git clone https://github.com/MetabolomicsHub/mhd_model.git

cd mhd-model

# install python if it is not installed
uv python install 3.12

# install python dependencies
uv sync

# install pre-commit to check repository integrity and format checking
uv run pre-commit

# open your IDE (vscode, pycharm, etc.) and set python interpreter as .venv/bin/python

Commandline (CLI) Tool Usage

# you can use any python version >= 3.12
pip install mhd-model

mhd-cli

Example API Usage

from mhd_model.mhd_client import MhdClient, MhdClientError

mhd_webservice_base_url = "https://www.metabolomicshub.org/test/api/submission"
api_token = "<your-api-token>"


def get_new_mhd_accession_example():
    mhd_client: MhdClient = MhdClient(mhd_webservice_base_url, api_token)

    try:
        accession = mhd_client.get_new_mhd_accession(
            dataset_repository_identifier="MTBLS1234567", accession_type="mhd"
        )
        print("Accession: %s" % accession)
    except MhdClientError as ex:
        print("Error: %s" % ex.message)


def get_new_test_mhd_accession_example():
    mhd_client: MhdClient = MhdClient(mhd_webservice_base_url, api_token)

    try:
        accession = mhd_client.get_new_mhd_accession(
            dataset_repository_identifier="MTBLS4444", accession_type="test"
        )
        print("Accession: %s" % accession)
    except MhdClientError as ex:
        print("Error: %s" % ex.message)


def submit_legacy_dataset_example():
    announcement_file_path = "MTBLS9876543.announcement.json"
    dataset_repository_id = "MTBLS9876543"
    announcement_reason = "Initial revision"
    mhd_client: MhdClient = MhdClient(mhd_webservice_base_url, api_token)

    try:
        revision: SubmittedRevision = mhd_client.submit_announcement_file(
            dataset_repository_id=dataset_repository_id,
            mhd_id=None,
            file_path=announcement_file_path,
            announcement_reason=announcement_reason,
        )
        print("Revision: %s" % revision.revision)
    except MhdClientError as ex:
        print("Error: %s" % ex.message)


def submit_mhd_dataset_example():
    announcement_file_path = "MTBLS9876543.announcement.json"
    mhd_id = "MHD0000001"
    dataset_repository_id = "MTBLS22222"
    announcement_reason = "Initial revision"
    mhd_client: MhdClient = MhdClient(mhd_webservice_base_url, api_token)

    try:
        revision: SubmittedRevision = mhd_client.submit_announcement_file(
            dataset_repository_id=dataset_repository_id,
            mhd_id=mhd_id,
            file_path=announcement_file_path,
            announcement_reason=announcement_reason,
        )
        print("Revision: %s" % revision.revision)
    except MhdClientError as ex:
        print("Error: %s" % ex.message)

Metadata

Release files for mhd-model 0.1.110

For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.

Source distribution (sdist)

Source distribution for mhd-model 0.1.110
File	Size	Uploaded
mhd_model-0.1.110.tar.gz	231.0 kB	Sep 21, 2026	Details

Built distribution (wheel)

Table of built distributions (wheels) for mhd-model 0.1.110
File	Interpreter	ABI	Platform	Reset
mhd_model-0.1.110-py3-none-any.whl 295.0 kB Sep 21, 2026	Python 3	none	any	Details

Total release size: 526.0 kB

Release files / mhd_model-0.1.110.tar.gz

Download URL	mhd_model-0.1.110.tar.gz
Size	231.0 kB
Tags	Source
SHA-256 checksum How to use checksums	`1970f107f3cfb663ed7d3b50f891fe2cf0d0aa21dd7e97be0cb477862b6ef5d7`
BLAKE2b-256 checksum How to use checksums	`d82ef6a35beeacfc49e614186dfc46c58fc3487e0ad5e664dac87eaa86e9b4f0`
Upload date	Sep 21, 2026
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`uv/0.12.17 {"installer":{"name":"uv","version":"0.12.17","subcommand":["publish"]},"python":null,"implementation":{"name":null,"version":null},"distro":{"name":"Ubuntu","version":"24.04","id":"noble","libc":null},"system":{"name":null,"release":null},"cpu":null,"openssl_version":null,"setuptools_version":null,"rustc_version":null,"ci":true}`

Release files / mhd_model-0.1.110-py3-none-any.whl

Download URL	mhd_model-0.1.110-py3-none-any.whl
Size	295.0 kB
Tags	Python 3
SHA-256 checksum How to use checksums	`092e5f8b3fad1f0b0c546056c443f490a3dfeebbffa6a4a2a772322249d7010b`
BLAKE2b-256 checksum How to use checksums	`03fc63b1450bbc3e66b7e9b860a0395fb1f246c703064fd4e483b5f2e1ff8c99`
Upload date	Sep 21, 2026
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`uv/0.12.17 {"installer":{"name":"uv","version":"0.12.17","subcommand":["publish"]},"python":null,"implementation":{"name":null,"version":null},"distro":{"name":"Ubuntu","version":"24.04","id":"noble","libc":null},"system":{"name":null,"release":null},"cpu":null,"openssl_version":null,"setuptools_version":null,"rustc_version":null,"ci":true}`