d2s 0.1.7

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](https://www.w3.org/RDF/) using [CWL workflows](https://www.commonwl.org/), and the deployment of user-facing services over the integrated data using [Docker](https://www.docker.com/).

## Install

See the [d2s documentation website](https://d2s.semanticscience.org/docs/d2s-installation).

### With pip

`bash pip install d2s cwlref-runner `

> Use [pip](https://pypi.org/project/pip/), pip3 or [pipx](https://pipxproject.github.io/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

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

> nano .bashrc if issues with the import

• ZSH: add the import autocomplete line to .zshrc

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

> nano .zshrc if issues with the import

## Try it

Display the default help command

`bash d2s `

Create a d2s project in the current directory

`bash d2s init `

# Development setup

`bash # 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.

`bash pip3 install --editable . `

Script to build and publish automatically:

`bash ./publish_pip.sh `

Or do it manually:

`bash # Build packages 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

`bash 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

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