= Job Monitoring =

Job execution is monitored by reading a log file of the job. A job consists of a number of steps which consists of a number of operations ([http://www.molgenis.org/wiki/ComputeStartDataModel MCF Data Model]). A step of the job can be started when all operations of a previous step are finished. Operations in a step can be executed in parallel. Every operation writes to a job log file. Monitoring is implemented by reading job log files. Monitoring is called from [http://www.molgenis.org/svn/sandbox/molgenis_processing/3.3.galaxy/ScriptbasedComputePlatform/src/scriptserver/PipelineThread.java PipelineThread] after step is submitted for execution:

{{{
private LoggingReader monitor = new LoggingReader();

...

int numberOfSteps = pipeline.getNumberOfSteps();

for (int i = 0; i < numberOfSteps; i++)
{
	Step step = pipeline.getStep(i);

    //here, step is submitted for execution
    
    ...
    
    monitor.setStep(step);

	while (!monitor.isNotFinishedStep())
    {
    	monitor.checkStepStatus();

        try
        {
        	Thread.sleep(5000);
        }
		...
	//continue to a next step  	
 	...
}}}