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Dev-Test

Set up Python Virtual Environment

You can set up a Python development environment with a virtual environment:

python3 -m venv py3

Make sure that you have the virtual environment activated:

. py3/bin/activate

Install poetry

To use the latest code in this repo (or to develop new features) you can clone this repo, install poetry:

curl -sSL https://raw.githubusercontent.com/python-poetry/poetry/master/get-poetry.py | python -

and then use poetry to install this package:

poetry install -vv

Setup and run tests

Local development like this:

poetry shell
poetry install -vv
python3 -m pytest

There are various ways to select a subset of python unit-tests - see: https://stackoverflow.com/questions/36456920/is-there-a-way-to-specify-which-pytest-tests-to-run-from-a-file

Manual Testing

You can also set up credentials to submit data to the graph in your data commons. This assumes that you can get API access by downloading your credentials.json.

Make sure that your python virtual environment and dependencies are updated. Also, check that your credentials have appropriate permissions to make the service calls too.

COMMONS_URL = "https://mycommons.azurefd.net"
PROGRAM_NAME = "MyProgram"
PROJECT_NAME = "MyProject"
CREDENTIALS_FILE_PATH = "credentials.json"
gen3_node_json = {
  "projects": {"code": PROJECT_NAME},
  "type": "core_metadata_collection",
  "submitter_id": "core_metadata_collection_myid123456",
}
auth = Gen3Auth(endpoint=COMMONS_URL, refresh_file=CREDENTIALS_FILE_PATH)
sheepdog_client = Gen3Submission(COMMONS_URL, auth)
json_result = sheepdog_client.submit_record(PROGRAM_NAME, PROJECT_NAME, gen3_node_json)

CLI

If the gen3 cli is not in your path, or is overwritten by a shell function, then you can still invoke the cli:

python -m gen3.cli --help
or
poetry run gen3 --help