NCATS Translator

Data Quality Assessment Implementation | Docker + RDFUnit

A Dockerization of the NCATS Translator for Data Quality Analysis.
The purpose of this project is to provide automation of the NCATS Translator stand-alone implementation in order to escalate on more general data quality assessment.

Prerequisites

Docker for Mac and Windows

Usage

Clone the repository

    git clone https://github.com/amalic/NCATS-Translator-DQA-Docker.git && \
    cd NCATS-Translator-DQA-Docker

Build the Docker image

    docker build -t translator_dqa .

Run the Docker container

Options

1. Run translator and show usage text

    docker run -it --rm -p 7200:7200  \
    -v ~/NCATS-Translator-DQA-Docker/data/Input:/root/NCATS-Translator-DQA/Input/ \
    -v ~/NCATS-Translator-DQA-Docker/data/Output:/root/NCATS-Translator-DQA/Output/ \
    translator_dqa -h

2. Run translator with a URL

    docker run -it --rm -p 7200:7200  \
    -v "$PWD"/data/Input:/root/NCATS-Translator-DQA/Input/ \
    -v "$PWD"/data/Output:/root/NCATS-Translator-DQA/Output/ \
    translator_dqa -f https://biosharing.org/biodbcore-000015

On this option you have to make shure that change the url for your dataset url, we expect 2 outputs here "$PWD"/data/Output

3. Run translator with a local file

    docker run -it --rm -p 7200:7200 \
    -v "$PWD"/data/Input:/root/NCATS-Translator-DQA/Input/ \
    -v "$PWD"/data/Output:/root/NCATS-Translator-DQA/Output/ \
    translator_dqa -d /root/NCATS-Translator-DQA/Input/kegg-drug.ttl

We provide a dataset for testing, but you can manually put your .ttl files on the Input folder "$PWD"/data/Input

4. Build the container and keep it running

    docker run -it -p 7200:7200 \
    -v "$PWD"/data/Input:/root/NCATS-Translator-DQA/Input/ \
    -v "$PWD"/data/Output:/root/NCATS-Translator-DQA/Output/ \
    --name=dqa_box --entrypoint /bin/bash translator_dqa

We need to start the GraphDB service service graphdb start
In case you want to keep the container running you can make more than one task inside the container, the running command:

    ./translator_dqa.py -d /root/NCATS-Translator-DQA/Input/kegg-drug.ttl

(exit the container exit)

In case you want to run again an existing container

    docker start -ai dqa_box

Notice that we choose dqa_box a default name for the container, furthermore, you want to remove it docker rm dqa_box

GraphDB is available on http://localhost:7200/

Licence

The MIT License (MIT) 2017

amalic/NCATS-Translator-DQA-Docker