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 0.1.101

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 0.1.101
File	Size	Uploaded
mhd_model-0.1.101.tar.gz	222.8 kB	Sep 15, 2026	Details

Built distribution (wheel)

Table of built distributions (wheels) for mhd-model 0.1.101
File	Interpreter	ABI	Platform	Reset
mhd_model-0.1.101-py3-none-any.whl 279.5 kB Sep 15, 2026	Python 3	none	any	Details

Total release size: 502.3 kB

Release files / mhd_model-0.1.101.tar.gz

Download URL	mhd_model-0.1.101.tar.gz
Size	222.8 kB
Tags	Source
SHA-256 checksum How to use checksums	`5090aa4f0ec6d13992b48ddc39c47b319995e6b54bf341717d6df5c47d3b38a7`
BLAKE2b-256 checksum How to use checksums	`b4a5bfcfb3b38f41cbfcf65607bdf75517e39e864a172b0b4fd662da97f21c2c`
Upload date	Sep 15, 2026
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`uv/0.12.14 {"installer":{"name":"uv","version":"0.12.14","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-0.1.101-py3-none-any.whl

Download URL	mhd_model-0.1.101-py3-none-any.whl
Size	279.5 kB
Tags	Python 3
SHA-256 checksum How to use checksums	`b11bd2a5c11d1b4c07fee9dbf05a5b94c66414e069ed4a1a179c7d32fd7b3858`
BLAKE2b-256 checksum How to use checksums	`b56952731f0e828e1b5a58ac9bfe1639870998e7185f111ae4482d0bf3c1c66a`
Upload date	Sep 15, 2026
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`uv/0.12.14 {"installer":{"name":"uv","version":"0.12.14","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}`