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 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/api/submission"
api_key = "<your-api-key>"


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

    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_key)

    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_key)

    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_key)

    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 0.1.108

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 0.1.108
File	Size	Uploaded
mhd_model-0.1.108.tar.gz	223.6 kB	Sep 20, 2026	Details

Built distribution (wheel)

Table of built distributions (wheels) for mhd-model 0.1.108
File	Interpreter	ABI	Platform	Reset
mhd_model-0.1.108-py3-none-any.whl 280.2 kB Sep 20, 2026	Python 3	none	any	Details

Total release size: 503.8 kB

Release files / mhd_model-0.1.108.tar.gz

Download URL	mhd_model-0.1.108.tar.gz
Size	223.6 kB
Tags	Source
SHA-256 checksum How to use checksums	`0a7e0ea293364d8db154ffb96c0cf63962b66303b486b50650ced5c0610a6139`
BLAKE2b-256 checksum How to use checksums	`619bdabcddc2c4817d23379d2d5e791111983673932cd8227ed6fdc3637344d9`
Upload date	Sep 20, 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-0.1.108-py3-none-any.whl

Download URL	mhd_model-0.1.108-py3-none-any.whl
Size	280.2 kB
Tags	Python 3
SHA-256 checksum How to use checksums	`9a89d64ed0bde0b6e5725c5343ef9c734f3aeef44d8933c7e2e6351afd4b6941`
BLAKE2b-256 checksum How to use checksums	`9b9f895160744eb5800a1b6d4c95a102ea660bbe1d196b1b203fc31c5fe7a0ef`
Upload date	Sep 20, 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}`