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)

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

mhd_model-0.1.91.tar.gz (188.8 kB view details)

Uploaded Jul 17, 2026 Source

Built Distribution

If you're not sure about the file name format, learn more about wheel file names.

The dropdown lists show the available interpreters, ABIs, and platforms. Enable javascript to be able to filter the list of wheel files.

mhd_model-0.1.91-py3-none-any.whl (245.4 kB view details)

Uploaded Jul 17, 2026 Python 3

File details

Details for the file mhd_model-0.1.91.tar.gz.

File metadata

Download URL: mhd_model-0.1.91.tar.gz
Upload date: Jul 17, 2026
Size: 188.8 kB
Tags: Source
Uploaded using Trusted Publishing? No
Uploaded via: uv/0.11.29 {"installer":{"name":"uv","version":"0.11.29","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}

File hashes

Hashes for mhd_model-0.1.91.tar.gz
Algorithm	Hash digest
SHA256	`7f35e589c819773df743518afaa32050d84fcd2ac12d28a87db3d31fb1545f28`
MD5	`3d9b777c313f987154426b638da2e643`
BLAKE2b-256	`0a089abaa8be0f3cfb83bbde796c7f20c6c3f48ac786e7736de052833a4832b6`

See more details on using hashes here.

File details

Details for the file mhd_model-0.1.91-py3-none-any.whl.

File metadata

Download URL: mhd_model-0.1.91-py3-none-any.whl
Upload date: Jul 17, 2026
Size: 245.4 kB
Tags: Python 3
Uploaded using Trusted Publishing? No
Uploaded via: uv/0.11.29 {"installer":{"name":"uv","version":"0.11.29","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}

File hashes

Hashes for mhd_model-0.1.91-py3-none-any.whl
Algorithm	Hash digest
SHA256	`748ebf87d9bb52fec62787761d757d3dcae2b435d1d70ccfe377f78c123c9a2a`
MD5	`cab572fca56ca51a00b86d9b6c2c3fde`
BLAKE2b-256	`7a04e89e54aa0ffd56eb50f4fa06033c6d964b18557c2b55a605b9373a7962ea`