d2s 0.1.9

A Command Line Interface to orchestrate the integration of heterogenous data and the deployment of services consuming the integrated data. See https://d2s.semanticscience.org

A commandline interface to orchestrate the integration of heterogenous data sources under a common RDF Knowledge Graph using CWL workflows, and the deployment of user-facing services over the integrated data using Docker.

Install

See the d2s documentation website.

With pip

pip install d2s cwlref-runner

Use pip, pip3 or pipx depending on your system preferences.

Requirements:

• docker-compose
• git
• curl

Enable autocompletion

Enable commandline autocompletion in the terminal

Highly recommended, it makes d2s much more user-friendly

• Bash: add the import autocomplete line to .bashrc

echo 'eval "$(_D2S_COMPLETE=source d2s)"' >> ~/.bashrc

nano .bashrc if issues with the import

• ZSH: add the import autocomplete line to .zshrc

echo 'eval "$(_D2S_COMPLETE=source_zsh d2s)"' >> ~/.zshrc

nano .zshrc if issues with the import

Try it

Display the default help command

d2s

Create a d2s project in the current directory

d2s init

Development setup

# Add new package
pip install package && pip freeze > requirements.txt

Install for dev

Install d2s as cli in local for dev. d2s will be updated directly on change.

pip3 install --editable .

Recommended script to build and publish automatically using Docker:

./publish_pip.sh

Or do it locally

# Build packages in dist/
python3 setup.py sdist bdist_wheel
# Publish the built dist/ directory
twine upload --repository-url https://upload.pypi.org/legacy/ dist/*

You might need to install twine

pipx install twine

If you experience issues with Bash or ZSH because d2s is not defined when installing for dev. Then add pip3 install --editable develop/d2s-cli to .zshrc

You might need to install Python3.7

sudo apt-get install python3.7 python3.7-venv python3.7-dev
# Set python3 to use 3.7
sudo update-alternatives --install /usr/bin/python3 python3 /usr/bin/python3.7 1
sudo update-alternatives --config python3

If you face issue uploading the package on pypi

twine check dist/d2s-*-py3-none-any.whl