This repository contains a series of tools that are being used by the AIACE project in the data integration process.

This toolkit makes mainly use of the following requirements:

• bash (shell for scripting)
• unzip (deal with zip compressed archives)
• Miller (CSV manipulation CLI toolkit)
• DuckDB (embedded SQL OLAP DBMS)

For example, on Ubuntu the first three requirements can be installed by using the package manager:

$ sudo apt install bash unzip miller

DuckDB has many APIs, in our case we are using the CLI interface. In order to install the binary version visit the releases page and download the most appropriate version for your use case.

Our workflow was tested on Ubuntu 22.04 LTS, with version 0.5.1 of DuckDB.

Let us begin by saying that the pipeline is tailored to the research needs of the AIACE project and thus scripts and programs are specific to the file hierarchy and the configuration of the machine that was used for the data analysis process.

Nonetheless, there is a well defined thought scheme behind the way the process unfolds and here we will point out its main features.

TODO: expand Pipeline section

TODO: docker image yet to be uploaded

The image can be pulled from the Github Containers Repository.

$ docker pull ghcr.io/shoyip/aiace_data_integrator

Then it can be run as follows.

$ docker run -v [host data folder]:/app/data --env-file .env -i -t ghcr.io/shoyip/aiace_data_integrator

where the host data folder has to be an absolute path pointing to the directory of the host machine where we would like the data to be downloaded.

The image can be built by issuing the following command.

$ docker build -t data_integrator

Once the image is built, the Bulk Downloader tool can be run as follows.

$ docker run -v [host data folder]:/app/data --env-file .env -i -t data_integrator

where the host data folder has to be an absolute path pointing to the directory of the host machine where we would like the data to be downloaded.

The .env file should contain the informations as pointed out previously. DOWNLOAD_FOLDER should be set to /app/data.

Shoichi Yip // 2022

This tool contributes to the AIACE project (UniTrento).

• Principal Investigator: prof. Luca Tubiana
• Postdoctoral Student: dr. Jules Morand
• Research Assistant: Shoichi Yip