Job agent can't execute plug-ins

[Nicklas Nordborg]

It doesn't work for any plug-in. If the job agent uses the ProcessJobExecutor the stacktrace is:

java.lang.Exception: 08:59:50,681 ERROR ThreadJobExecutor:104 - Error executing job: Job[id=1; name=Run plugin: Affymetrix CDF probeset importer]
net.sf.basedb.core.ConnectionClosedException: The connection has been closed.
at net.sf.basedb.core.DbControl.getItem(DbControl.java:718)
at net.sf.basedb.core.JobAgentSettings.getJobAgent(JobAgentSettings.java:172)
at net.sf.basedb.core.Job.execute(Job.java:1215)
at net.sf.basedb.clients.jobagent.executors.ThreadJobExecutor.executeJob(ThreadJobExecutor.java:98)
at net.sf.basedb.clients.jobagent.executors.ThreadJobExecutor.main(ThreadJobExecutor.java:193)
08:59:50,747 ERROR ThreadJobExecutor:197 - Error executing job with ID: 1
java.lang.NullPointerException
at net.sf.basedb.clients.jobagent.executors.ThreadJobExecutor.executeJob(ThreadJobExecutor.java:106)
at net.sf.basedb.clients.jobagent.executors.ThreadJobExecutor.main(ThreadJobExecutor.java:193)

at net.sf.basedb.clients.jobagent.executors.ProcessJobExecutor.executeJob(ProcessJobExecutor.java:226)
at net.sf.basedb.clients.jobagent.JobRunner.run(JobRunner.java:126)
at java.lang.Thread.run(Thread.java:619)

If the job agent uses the ThreadJobExecutor the stacktrace is:

java.lang.NullPointerException
at net.sf.basedb.clients.jobagent.executors.ThreadJobExecutor.executeJob(ThreadJobExecutor.java:106)
at net.sf.basedb.clients.jobagent.JobRunner.run(JobRunner.java:126)
at java.lang.Thread.run(Thread.java:619)

The only workaround is to execute jobs with the internal job queue.

[Nicklas Nordborg]

(In [4497]) Fixes #1115: Job agent can't execute plug-ins