How to execute this project with docker

First you have to make sure that you have your xmls ready so you can execute the Python scripts using Docker containers, for this, follow the next steps:

How to get the xmls from your own pdfs

  1. Make sure you have GROBID server running, you can do this using Docker, make sure you have it installed and the run the next commands in your terminal:

  • Pull the GROBID image:

docker pull lfoppiano/grobid:0.7.2

  • Run the image:

docker run -t --rm -p 8070:8070 lfoppiano/grobid:0.7.2

The web service will be running in http://localhost:8070/

  1. Now copy and paste your pdfs into the directory called ‘Papers’, that you’ll find inside the directory called ‘compose’, which location is: ‘./AIandOpenScienceInResearchSoftwareEngineering-main/Docker/compose’.

    The next image shows a flow for you to identify where the Papers directory is in an easier way:

docker:

  1. Now in your terminal, make sure that you are inside the directory ‘compose’ which location is: ‘./AIandOpenScienceInResearchSoftwareEngineering-main/Docker/compose’, and run the next command:

python request_grobid.py

terminalseven:

This runs a Python script that’ll connect to the GROBID server using the Grobid Python client and download all of the XML of the pdfs inside the ‘Papers’ directory, this might take a few minutes (if it takes way too long, just delete the container, create it again an rerun the python script).

After request_grobid.py has finished executing, check that all of the XMLs are inside the ‘Papers’ directory and continue with the next steps:

Now that you have all of your XMLs, run the Python scripts with Docker compose

For this project Docker compose was the easiest way of containerizing my Python files, because it allows for all of them to run at the same time and also adding a bind mount which is used to retrieve the output files that each Python file creates and stores them in a directory in the host machine so the user can see the output since containers don’t have a graphic enviroment.

For it to run in your computer, follow the next steps:

IMPORTANT: Make sure that you have docker compose downloaded on your machine so you can execute this project correctly.

  1. Open your console and change directories until you are inside the directory named ‘Docker’ and then change directories once more to the directory inside ‘Docker’ called ‘compose’ (‘./AIandOpenScienceInResearchSoftwareEngineering-main/Docker/compose)’.

cd /AIandOpenScienceInResearchSoftwareEngineering-main/Docker/compose

For example:

terminalfive:

  1. Once you are inside the ‘compose’ directory, run the next command on your terminal:

docker-compose up --build

It’ll look something like this:

terminalsix:

And when it’s executed succesfully it’ll look like this:

terminalsixtwo:

  1. After you’ve run the prior command all of the output files from each of the Python files should be found on the directory called ‘result_files’ that can be found inside the directory ‘compose’.

    The result_files directory will look like this with all of the output files:

output:

  1. Now, type the next command:

docker-compose down

And that’s it! Now you have all of the output files in your computer :)