Interactors Core

Introduction

This project parses IntAct clustered interactions and save them into a lightweight database (SQLite). Once the database is created, the graph-importer will consume it and then interactor will be part of the Graph Database.

Clone and Package

• Clone project

git clone https://github.com/reactome/interactors-core.git
cd interactors-core
# Note: You must skip test because at this point the database hasn't been created yet.
mvn clean package -DskipTests

Main: IntactParser.java

Parameters:

• -d download the latest version 'intact-micluster.txt' from IntAct (see -t and -u)
• -f file to be parsed (cannot be used if -d is specified)
• -g database file (must be unique in the folder)
• -t folder to save the file when downloaded
• -u specify another ftp URL to download the file from IntAct.

Recommend:

java -jar target/InteractorsParser-exec.jar -g /path/to/interactors.db -d

Validate

• To validate the database creation the tests can be performed.

mvn package -Dinteractors.SQLite=interactors.db

Extras

• Logs: The logs are stored in logs/ directory
• parser-messages.txt: This file stores all the parser messages. Any oddity will be written on it.