ItemNotFoundException in Base1PluginExecuter if leaveStdin or leaveStdout is false

[Jari Häkkinen]

Result files and directories are created but obviously no transformation.

Stacktrace:

net.sf.basedb.core.ItemNotFoundException: Item not found: Transformation[id=0]
at net.sf.basedb.core.Transformation.getById(Transformation.java:106)
at net.sf.basedb.plugins.Base1PluginExecuter.run(Base1PluginExecuter.java:692)
at net.sf.basedb.core.PluginExecutionRequest.invoke(PluginExecutionRequest.java:106)
at net.sf.basedb.clients.jobagent.executors.ThreadJobExecutor.executeJob(ThreadJobExecutor.java:109)
at net.sf.basedb.clients.jobagent.executors.ThreadJobExecutor.main(ThreadJobExecutor.java:202)

[Nicklas Nordborg]

This happens when one of the "Leave stdin.txt" or "Leave stdout.txt" options is set to false. Set both to true and the problem should go away.

Here is how to do that:

1. Find the problematic plug-in configuration in Administrate -> Plugins -> Configurations and click on it.
2. Click on the "Configure" button.
3. In the first dialog, leave the "File" parameter empty, and click "Next".
4. Change the "Leave stdin.txt" and "Leave stdout.txt" options to true and click Next.
5. The settings should be saved. The plug-in should now work.

[Nicklas Nordborg]

(In [4721]) References #1227: ItemNotFoundException? in Base1PluginExecuter if leaveStdin or leaveStdout is false

Added a test case that has leaveStdin/leaveStdout = false

[Nicklas Nordborg]

(In [4722]) References #1227: ItemNotFoundException? in Base1PluginExecuter if leaveStdin or leaveStdout is false

Should be fixed now. As part of the fix some rearrangements were made so that leaveStdin and leaveStdout are respected even when there is some kind of problem with the plug-in.

[Jari Häkkinen]

Tested successfully.