UPGRADE_NOTES.md

Upgrade notes to BridgeDb 2.0

1. Initialing data sources

Replace

BioDataSource.init();

with

DataSourceTxt.init();

2. Getting DataSource's

Replace

DataSource ds = DataSource.getBySystemCode("Ck");

with

DataSource ds = DataSource.getExistingBySystemCode("Ck");

Similarly, and more important:

DataSource ds = DataSource.getByFullName("PubChem-compound");

with

DataSource ds = DataSource.getExistingByFullName("PubChem-compound");

The latter two new methods throw an IllegalArgumentException if the DataSource does not exist. Use one of the following two methods to check first:

DataSource.systemCodeExists("Ck");
DataSource.fullNameExists("PubChem-compound");