d2s 0.1.22

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 Command Line 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 (SPARQL, GraphQL-LD, OpenAPI, Web UI).

Installation

Complete documentation about the d2s-cli on the d2s documentation website 📖

Install with pipx

pipx install d2s cwlref-runner

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

Requirements:

• Python 3.6
• docker-compose
• git, curl, time (bash)

Enable autocompletion

Enable commandline autocompletion in the terminal

Highly recommended, it makes d2s much more user-friendly

• ZSH: add the import autocomplete line to the ~/.zshrc file.

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

Set your terminal to use ZSH by default:

chsh -s /bin/zsh

A oh-my-zsh theme can be easily chosen for a personalized experience. See the zsh-theme-biradate to easily install a simple theme and configure your terminal in a few minutes.

• Bash: add the import autocomplete line to the ~/.bashrc file.

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

To be tested.

Upgrade package

With pipx:

pipx uninstall d2s
pipx install d2s

With pip:

pip install --upgrade d2s 

Try it

Display the default help command

d2s

Create a d2s project in the given folder

d2s init project-folder-name

All d2s commands are designed to be run from the project folder, move to it

cd project-folder-name/

Project settings stored if .d2sconfig file.

Development setup

Install package and add it to requirements.txt:

pip install package && pip freeze > requirements.txt

Install for dev

Install d2s as executable in local for development. d2s will be updated directly on change in the code.

pip install --editable .

To publish a new version, upgrade the version in setup.py and use the following script to build and publish automatically using Docker:

./publish_pip.sh

Or do it locally:

# Build packages in dist/ folder
python3 setup.py sdist bdist_wheel
# Publish packages previously built in the dist/ folder
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 pip install --editable develop/d2s-cli to .zshrc

You might need to install Python3.6 for dev (dev with python3.6 should work though)

sudo apt-get install python3.6 python3.6-venv python3.6-dev
# Set python3 to use 3.6
sudo update-alternatives --install /usr/bin/python3 python3 /usr/bin/python3.6 1
sudo update-alternatives --config python3

vim /usr/bin/gnome-terminal

#!/usr/bin/python3.6

If you face issue uploading the package on pypi:

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