transmart-schemas

Liquibase scripts

Create database transmartDev with TranSMART schemas

• Create a user sudo -u postgres psql -c "create role biomart_user with password 'biomart_user' login"
• Set environment variables:

  PGUSER=biomart_user
  PGPASSWORD=biomart_user
  PGDATABASE=transmartDev

• Build the jar file with gradle assemble
• Run prepare_database.sh

Development

# Build the jar file in build/libs
gradle assemble

# Run test scripts
gradle check

To add schema updates, create a new changelog file in db/changelog/changes and add a record in db.changelog-master.yaml.

How to autogenerate a changelog

• Download Liquibase
• Download postgresql-42.2.5.jre7.jar
• Create a file liquibase.properties:

  driver=org.postgresql.Driver
  classpath=postgresql-42.2.5.jre7.jar
  url=jdbc:postgresql://localhost:5432/transmart
  username=tm_cz
  password=tm_cz
  changeLogFile=db.changelog.xml

/path/to/liquibase --defaultSchemaName=i2b2demodata generateChangelog

This generates a changelog for the i2b2demodata schema in db.changelog.xml.