Installation

Prepare the environment

To use SciAssist, first clone the project and create a conda environment for it:

# clone project
git clone https://github.com/WING-NUS/SciAssist
cd SciAssist

# [OPTIONAL] create conda environment
conda create -n myenv python=3.8
conda activate myenv

# install pytorch according to instructions
# https://pytorch.org/get-started/

# install requirements
pip install -r requirements.txt

Set up PDF parsing engine s2orc-doc2json

The current doc2json tool uses Grobid to first process each PDF into XML, then extracts paper components from the XML. If you fail to install Doc2Json or Grobid with bin/doc2json/scripts/run.sh , try to execute the following command:

cd bin/doc2json
python setup.py develop
cd ../..

This will setup Doc2Json.

Install Grobid

You will need to have Java installed on your machine. Then, you can install your own version of Grobid and get it running, or you can run the following script:

bash bin/doc2json/scripts/setup_grobid.sh

This will setup Grobid, currently hard-coded as version 0.6.1. Then run:

bash bin/doc2json/scripts/run_grobid.sh

to start the Grobid server. Don’t worry if it gets stuck at 87%; this is normal and means Grobid is ready to process PDFs.