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)
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