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Stop Java from killing Bash script that started it

I've spent the past couple days working on this, and at this point I am super stuck. I have a Java program that must be run not as a service. This program must also be capable of updating itself when a new file is given for updating.
As a result, I have a script that is started with Linux that starts the Java application and then checks every 5 seconds if the application has been terminated. If the application has been terminated, it should check if there is an update and then start appropriately.
This is the code for that script:
#!/bin/bash
JAVA_HOME=/usr/lib/jvm/java-16-openjdk-amd64
WORKING_DIR=~/Data
LOG=$WORKING_DIR/logs/Bash.log
rm $LOG
echo "Script started" > $LOG
while true; do
source $WORKING_DIR/Server.pid
if ! kill -0 $AppPID; then
echo "App must be started" >> $LOG
source $WORKING_DIR/UpdateStatus
if [ "$UpdateReady" -eq "1" ]; then
echo "Moving files for update" >> $LOG
mv $WORKING_DIR/Server.jar $WORKING_DIR/old.jar
mv $WORKING_DIR/new.jar $WORKING_DIR/Server.jar
fi
nohup ${JAVA_HOME}/bin/java -jar ${WORKING_DIR}/Server.jar &
echo AppPID="$!" > $WORKING_DIR/Server.pid
echo "Server started" >> $LOG
if [ "$UpdateReady" -eq "1" ]; then
echo "Checking for safe update" >> $LOG
source $WORKING_DIR/Server.pid
echo UpdateReady="0" > $WORKING_DIR/UpdateStatus
sleep 5;
if kill -0 $AppPID; then
echo "Update successful" >> $LOG
rm $WORKING_DIR/old.jar
else
echo "Update failed, restarting old jar" >> $LOG
rm $WORKING_DIR/Server.jar
mv $WORKING_DIR/old.jar $WORKING_DIR/Server.jar
nohup ${JAVA_HOME}/bin/java -jar ${WORKING_DIR}/Server.jar &
echo AppPID="$!" > $WORKING_DIR/Server.pid
fi
fi
echo "Server start process finished, going into idle state" >> $LOG
fi
sleep 5
echo "5 seconds idle passed" >> $LOG
done
To initialize the update, I have tried a couple of different things, both with the same result. First I had set UpdateReady="1" through Java, then used exit(0);. I have also tried having Java call a Bash script which also sets UpdateReady="1" but uses kill $AppPID to shutdown the java application.
The result is that both the Java application and the Bash script stop executing causing the update and restart to fail! I have looked through a significant amount of Stack Overflow questions and answers finding things such as nohup, all to no avail.
I will once again state that the Java application cannot be run as a service. No packages other than what is included in Java or made by Apache can be used, and no programs can be installed to Linux. I would prefer to solve the problem with Bash.
Upon testing some things mentioned in comments, I may have missed something that turns out to be important. While all other runs of the startup script will be run by the startup applications manager, the initial run is not.
The install is taken care of remotely with an SSH connection sending the following command string:
cd /home/UserName; unzip -u -o Server.zip; chmod 777 install.sh; bash install.sh &; exit
install.sh is as follows:
#!/bin/bash
INSTALL_DIR=~/Data
mkdir ${INSTALL_DIR}
mkdir ${INSTALL_DIR}/logs
mkdir ${INSTALL_DIR}/data
cp Server.jar ${INSTALL_DIR}/Server.jar
cp service-start.sh ${INSTALL_DIR}/service-start.sh
chmod 777 ${INSTALL_DIR}/service-start.sh
rm Server.jar
rm service-start.sh
rm Server.zip
nohup bash $INSTALL_DIR/service-start.sh &
Upon rebooting my machine, I noticed that this problem goes away! This means that there must be a problem with the initial setup script. When the shell command is run, it does seem to be sticky and not actually let go after the bash install.sh &. I have tried putting nohup at the beginning of this, however the entire line will not run in that case for reasons I am not able to determine.
I would prefer to not have the user be forced to restart after install and can't seem to find any way to force the Startup Application manager to start an application at any time other than startup.

Well, after a lot of searching and some prompting from the comments, I found that the issue lied with how the program was initially being started.
As mentioned in the update, the first run is always started by an ssh connection. I knew there was a slight problem with this ssh connection, as it seemed to hold onto the connection no matter what I did. It turns out that this was causing the problem that resulted in the Bash instance and the Java instance remaining attached.
The solution for this problem was found here: jsch ChannelExec run a .sh script with nohup "lose" some commands
After managing to get the initial setup to start with nohup properly, the issue has gone away.

Ansible terminates my app with "nohup"

I have a task in Ansible playbook that executes a .jar file in the background, but after finishing that task, the (java) app terminates.
- name: Run Java app in the background
shell: nohup java -jar app.jar &
I need the app running for tasks further down in the playbook. Any ideas??
NOTE: When I run it in Putty ssh session it runs smoothly and the app stays in background.

The most likely reason is attached IO. Try:
- name: Run Java app in the background
shell: nohup java -jar app.jar </dev/null >/dev/null 2>&1 &

Ok So I had this issue today and my script is a tad different but essentially doing the same thing so this is what I have, running on Oracle, Centos and RHEL.
in script start_service.sh I have this, this script is executed not sourced.
#!/bin/sh
DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd)"
nohup java -jar ${DIR}/$1 --spring.config.location=${DIR}/application.yml --logging.config=${DIR}/logging.xml > ${DIR}/log/output.log 2>&1 &
In my playbook I have:
- name: run service
shell: "{{ service_install_location }}/application_name/start-service.sh application_name-{{ application_version }}.jar"
args:
chdir: "{{ service_install_location }}/application_name"
executable: /bin/bash
Now, the BASH_SOURCE argument is specific to bash so if you are running plain old sh then you need $0. nohup is required so when the ssh connection terminates your background task does not get killed (turn on -vvv for ansible to see connections being made to understand how this happens on a remote machine).
I should point out we are doing this temporarily as this should really be installed as a service to be under the control of service/init.d but for now, this answers your question

why doesn't jenkins start my java program?

This is extremely annoying but I have a script launch.sh like:
#!/bin/bash -x
java -jar foo.jar &
If I run it by hand, my java program starts up. However in Jenkins I configured that just does execute shell: $HUDSON_HOME/launch.sh >& out
I see from out file that it looks like it started java, but when I do a ps I don't see it there. How do I configure jenkins appropriately?

https://wiki.jenkins-ci.org/display/JENKINS/ProcessTreeKiller
add
export BUILD_ID=dontKillMe
to shell script

Running Scrapy from bash (shell script)

I have developed a web app in Java which uses Scrapy to get some data. To reach that, I invoke a shell script from Java:
Process p = Runtime.getRuntime().exec("sh myPath/myScript.sh");
p.waitFor();
which contains
#!/bin/bash
cd mySpiderPath
echo "We are going tu run scrapy"
scrapy crawl mySpider
echo "done!"
After running it, both "echo" are printed but scrapy does nothing. If I run myScript.sh from shell it works perfectly... I'm confused!
What can I do to try to debug this strange behavior?
EDIT
I have changed myScript.sh to run python version instead of scrapy command, and it doesn't work... so, the conclusion is that is not an "scrapy problem" but it is a bash script problem when it's invoked from Java...any ideas? (if I execute myScript.sh from shell it works fine)
#!/bin/bash
cd mySpiderPath
echo "We are going tu run scrapy"
python --version
echo "done!"

Try changing:
Process p = Runtime.getRuntime().exec("sh myPath/myScript.sh");
to:
Process p = Runtime.getRuntime().exec("bash myPath/myScript.sh");
This will probably run the script with /bin/bash instead of /bin/sh, that often points to a simpler shell.

How to create a script to restart a JAR file and get output in a terminal?

I have used the following scripting for start and stop a jar file.
**start.sh**
#!/bin/bash
nohup nice java -jar Server.jar > ./Server.out 2>&1 &
**stop.sh**
#!/bin/bash
kill `ps -ef | grep Server.jar | grep -v grep | awk '{ print $2 }'`
Now I want to merge both scripts and create a new restart script. I also want this script output in a terminal instead of a text file(Server.out).
Would appreciate any kind of input/help.

You can either put the commands of the two sripts after each other (kill first, java second) or just call the two scipts in the appropriate order.
The idea is that restart is basically equivalent to killing the current running version and starting a new one.
To avoid the output to a file, remove the > ./Server.out part.
Edit: removed note about removing the redirection part as I misread the grep part of the kill script
Update: Missed the nohup part of the script: with nohup you need to redirect output to a file, because the process is detached from the terminal (see documentation). If you do want to see the output in the terminal, remove nohup as well as the redirection to the file