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Webapp that runs process won't complete
@Entity
public class Job implements Runnable {

    @Id @GeneratedValue
    private Long id;

    //getters and setters

    @Override
    public void run() {
         Process p = null;

        try {
            BufferedWriter bw = new BufferedWriter(new FileWriter("/opt/condor/bin/datafile"));
            bw.write(this.getName());
            bw.close();

            p = new ProcessBuilder("/opt/condor/bin/scripts/create-filter.sh").start();
            jobHelper(p);

            List<String> dates = datesBetween();
            status = "Running Master";

            for(String temp : dates) {
                String[] splitDate = temp.split("-");
                String tmpYear = splitDate[0];
                String tmpMonth = splitDate[1];
                String tmpDay = splitDate[2];

                log.info("Running Master script: master.sh " + this.getCustomer() + ", " + this.getProject() + ", " + tmpYear + ", " + tmpMonth + ", " + tmpDay);

                p = new ProcessBuilder("/opt/condor/bin/scripts/master.sh", this.getCustomer(), this.getProject(), tmpYear, tmpMonth, tmpDay).start();
                log.info("Entering job helper");
                jobHelper(p);
                log.info("exited job helper");
            }

        status = "Finished Master";
        log.info("Finished Master");
    } catch (IOException ioe) {
        log.error("IO Error: " , ioe);
        ioe.printStackTrace();
    }

    log.info("Done running script");

    endTime = Long.toString(System.currentTimeMillis());

    status = "Ended";

    JobManager.FinishJob(this);
    }

private boolean jobHelper(Process p) {
                log.info("inside job helper");
    BufferedReader br = new BufferedReader(new InputStreamReader(p.getInputStream()));
    String line;

    try {
        while ((line = br.readLine()) != null) {
            log.info(line);

            if(line.contains("Uh oh!"))
                return true;
        }

    boolean running = true;
    while(running) {
                          log.info("waiting...");
        p.waitFor();
                          log.info("done waiting");
        running = false;
    }

    } catch (IOException e) {
        log.error("IO Error: " , e);
        e.printStackTrace();
    } catch (InterruptedException e) {
        log.error("Interrupted Exception: ", e);
        e.printStackTrace();
        p.destroy();
    }

    return false;
}

}