java

When used for the pipeline, this directory is expected to contain at least the following files:

• jdkLogConfig.properties: a JAVA property file allowing to configure logging messages using the package java.util.logging
• log4j.properties: a JAVA property file allowing to configure logging messages using the library log4j
• log4j2.xml: a XML file allowing to configure logging messages using the library log4j2
• a fat JAR of the Bgee pipeline, shipping all its dependencies

The default configuration of java.util.logging will be overridden using jdkLogConfig.properties.
If you do not want this behavior to take place, use the system property java.util.logging.config.file to point to a different configuration file.

The default logging level of the SLF4J SimpleLogger will be set to error. Use the system property org.slf4j.simpleLogger.defaultLogLevel to change this value.

The configuration of log4j and log4j2 are simply retrieved from the associated configuration files.

This will cover all loggers used by the dependencies of Bgee (SLF4J SimpleLogger, JDK java.util.logging package, log4, log4j2).

System properties specific to Bgee

• bgee.dao.jdbc.username: username to connect to the Bgee database using JDBC
• bgee.dao.jdbc.password: password to connect to the Bgee database using JDBC
• bgee.dao.jdbc.driver.names: comma-separated list of classnames of the JDBC Driver implementations to use, e.g.: com.mysql.jdbc.Driver,net.sf.log4jdbc.sql.jdbcapi.DriverSpy
• bgee.dao.jdbc.url: the JDBC connection URL; it should NOT contain the username and password