PubMed Connections is a web application that facilitates the analysis of the relationships between authors in the PubMed database.

Config

The app/config.py file is used to hold user specific settings for the project. This includes secret keys or email addresses. These values should not be committed to the GitHub repository, but by default git will want to include them in commits. The following command can be used to keep your changes to config.py out of your commits,

git update-index --skip-worktree config.py

However, sometimes you may wish to push changes that include changes within config.py. In these cases, you should first manually remove all private information from app/config.py. After you have done this, you can use the following command to allow config.py to be included in commits,

git update-index --no-skip-worktree config.py

Once you have committed the changes to config.py, you can mark the file using skip-worktree again, and add your private information back.

Conda Environment

This project uses a conda environment to manage its dependencies. Instructions to install conda can be found in the conda documentation.

1. Creating the environment

This only has to be done once. This command will create a new conda environment that can be used to run the website locally.

conda env create -f environment.yml

2. Activating the environment

This will activate the environment so that you can run the website with all its dependencies loaded.

conda activate pubmed-connections

3. Updating the environment

This will update the environment to include any new dependencies that were added to the environment.yml file.

conda env update --name pubmed-connections --file environment.yml --prune

Neo4J Configuration

Neo4J stores recent transactions in a log by default, but this can use up huge amounts of disk-space when we create the entire database. Therefore, adding the following options to your Neo4J configuration will disable storing more than one transaction at a time, which will greatly reduce the size of the Neo4J database on-disk after its extraction.

# Retention policy for transaction logs needed to perform recovery and backups.
dbms.tx_log.rotation.retention_policy=1 files
dbms.tx_log.rotation.size=56M
dbms.tx_log.rotation.retention_policy=keep_none

Example Graph

An example graph that was generated from academics at the University of Western Australia is shown below.