GenBankFactory

Data extraction and normalization pipeline used for bi-monthly GenBank data dumps.

Javadocs should be kept up to date here.

Dependencies:

• JDK 1.8.x
• Maven 3.x
• PostgreSQL 9.x for SQL Database
• Lucene 5.5.x for Lucene Index
• Java IDE, Spring Tool Suite is recommended

Setup:

1. Import the project into an IDE as "Existing Maven Project"

2. Create an GenBankFactory.local.properties file in the src folder with your SQL and Lucene details. Refer to GenBankFactory.local.properties.template

3. Run the build.sh script

4. The build should run successfully and generate a runnable jar in the target folder.

Usage

• Always double triple check parameters before building and running the .jar, as it may delete databases.
• Any changes to GenBankFactory.local.properties will only be reflected after running a new build.
• Allocate at minimum 6GB RAM, preferably 8GB.
• Typical usage scenario commands:
  • Fresh data dump: nohup java -Xms4G -Xmx8G -jar target/zoophy-genbank-factory-1.x.x-jar-with-dependencies.jar dump create -f gbvrl &
  • Re-Run data dump: nohup java -Xms4G -Xmx8G -jar target/zoophy-genbank-factory-1.x.x-jar-with-dependencies.jar dump clean -f gbvrl &
  • Rebuild Index: nohup java -Xms4G -Xmx8G -jar target/zoophy-genbank-factory-1.x.x-jar-with-dependencies.jar index &