This is the Java implementation of the GuestLanguage protocol in eHive.

It allows to write Runnables in Java and add them to standard eHive pipelines, potentially alongside Perl and Python Runnables.

Like in Perl, analyses are given a module name, which must contain a class of the same name. The class must inherit from org.ensembl.hive.BaseRunnable (see org.ensembl.hive.longmult.DigitFactory for an example) and implement the abstract fetchInput(), run() and writeOutput() methods. The stub preCleanUp() and postCleanUp() methods may also be overridden as required.

Job information is encapsulated in the org.ensembl.hive.Job and parameters in org.ensembl.hive.ParamContainer. Currently, parameter handling does not support dynamic parameter expansion using #expr markup

Due to the use of JSON for parent-child communication, params, input and output are handled as Map<String,Object>.