add VEP process management #7
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sheridancbio
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Jun 22, 2020
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sheridancbio
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| Process psProcess = psProcessBuilder.start(); | ||
| BufferedReader in = new BufferedReader(new InputStreamReader(psProcess.getInputStream())); | ||
| while (true) { | ||
| String line = in.readLine(); |
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isn't it equivalent to use:
while ((line = in.readLine()) != null)
...
?
I am hesitant to use true in the while statement
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i suppose the item being parsed would also need to be in the while statement check as well
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fixed as you suggested
| determineIfKillCommandIsAvailable(); | ||
| } | ||
| // ReaperDaemonThread | ||
| while (true) { |
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hesitant to use true here as well but at the same time there's a lot going on in this block so maybe just keeping it true is best to keep it simple?
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I have fixed this too. The reaper thread, once started, will continue to run as long as the application is running. So now the condition of the while statement checks whether a shutdown of the reaper was requested and exits if it sees such a request.
I have added a servlet configuration bean which will send the request for reaper shutdown as the servlet is exiting ... and will give a few seconds for the reaper to complete its work before exiting the application.
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Squashing and updating commit message |
- SystemProcessManager class now provides process management services for VEP
- uses UNIXProcess (if available) for determining a Process pid
- uses UNIXProcess (if available) for reaping zombies (via waitForProcessExit())
- determines availability of ps and kill commands on local system
- manages processes launched if needed tools are available
- starts ReaperDaemonThread when first VEP process is launched
- reaper will periodically check for orphaned child processes of a destroyed VEP process and kill them
- reaper will periodically check for zombie processes and reap them
- unix 'ps' command output parsing encapsulated in ProcessSurveyor class
- remove thread interruption in VepRunner - now StreamTransferrer threads will exit naturally when orphaned children are killed
- shut down reaper as application shuts down
Co-authored-by: Manda Wilson <1458628+mandawilson@users.noreply.github.com>
Co-authored-by: Robert Sheridan <7747489+sheridancbio@users.noreply.github.com>
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