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Restart Tomcat with Java

I need to restart the tomcat from Java code.
For eg, if a query is not executed for a certain time Period then it will restart the tomcat automatically.
I have tried the following shutdown and startup code, but when we shutdown the tomcat then the java code will not run and tomcat not started.
Note :- I am running this code from a application and restarting the same tomact which the same application is using.
Following the code
try {
PreparedStatement.setQueryTimeout(10);
rs = PreparedStatement.executeQuery();
} catch (SQLException ex) {
System.out.println("IN CATCH BLOCK FOR THE REFRESH INVOICE");
String shutcommand = "killall java";
Process shutchild = Runtime.getRuntime().exec(shutcommand);
System.out.println("JAVA PROCESS KILLED");
String locationCommand = "cd /root/cluster/tomcat6/bin";
Process locationChild = Runtime.getRuntime().exec(locationCommand);
String strtcommand = "./startup.sh";
Process strtchild = Runtime.getRuntime().exec(strtcommand);
}

Killing tomcat after SQLException this is not good idea to handle this exception. Probably the problem is on database site.
But if you are sure, that it is what you need you can kill this java proces in this section, but to run tomcat you should use for example bash and cron. Why? Beacues after killing your executing code will stop, so you don't achieve the line to start tomcat.
How to check tomcat: Is Tomcat running?

TL;DR
File binaryDir = new File(System.getProperty("catalina.home") + File.separator + "bin");
String restartCommand = "\"shutdown.bat & ping 0.0.0.0 -n 4 & C:\\WINDOWS\\system32\\net start Tomcat8\"";
new ProcessBuilder("cmd", "/c", restartCommand).directory(binaryDir).start();
Survive
Creating new process will survive JVM shutdown. If you combine commands in one line
it should work fine according to my tests and this.
shutdown.bat
You need to use shutdown.bat instead stopping windows service because it often fails on Windows with message Cannot stop service Apache Tomcat...
ping 0.0.0.0 -n 4
You need to wait some time after shutdown otherwise you will get Service is already starting. Try again later error message. Also note I use ping instead timeout because it causes problems on some systems.
C:\WINDOWS\system32\net start Tomcat8
I'm starting windows service because invoking startup.bat won't work for me. Also remember to replace Tomcat8 if you using different tomcat or custom service name for example Tomcat7
Redirect I/O
Don't redirect input or output of process instance or command will shutdown with JVM, and Tomcat won't start.

You can execute this native command using java
String command = "c:\program files\tomcat\bin\startup.bat";//for linux use .sh
Process child = Runtime.getRuntime().exec(command);

You should consider using ProcessBuilder instead of Runtime exec. Also, you should split all the arguments when you want to execute a command.
I suggest this :
ProcessBuilder shutcommand = new ProcessBuilder("killall", "java");
Process shutchild = shutcommand.start();
System.out.println("JAVA PROCESS KILLED");
ProcessBuilder strtcommand = new ProcessBuilder("/root/cluster/tomcat6/bin/startup.sh", "java");
Process strtchild = strtcommand.start();

Execute R Script from Web Application with Java

I have created a Web Application with Struts, and I would like to execute and R script from a Java class.
My script is in the directory: WebContent/script
The name is: rScript.R
I have checked that a way to execute is using this:
Runtime.getRuntime().exec("WebContent/script/rScript.R")
But this doesn't work. Does someone know how I have to put the sentence?
Cheers.

Try
Process process =Runtime.getRuntime().exec("RScript C:/.../WebContent/script/rScript.R")
process.waitFor();

Get working directory of another Java process

I can get working directory of current Java program using this code:
Path path = Paths.get(*ClassName*.class.getProtectionDomain().getCodeSource().getLocation().toURI());
Also I can get CommandLine parameters (but there is no directory in the output) of running Java processes using this command wmic process get CommandLine where name='java.exe' /value
It is possible to get working directory of another Java process (better programmatically)? Probably it can be solved with some jdk/bin utilities?

You can get this information via the Attach API. To use it, you have to add the tools.jar of your jdk to your class path. Then, the following code will print the current working directories of all recognized JVM processes:
for(VirtualMachineDescriptor d: VirtualMachine.list()) {
System.out.println(d.id()+"\t"+d.displayName());
try {
VirtualMachine vm = VirtualMachine.attach(d);
try(Closeable c = vm::detach) {
System.out.println("\tcurrent dir: "+vm.getSystemProperties().get("user.dir"));
}
}
catch(AttachNotSupportedException|IOException ex) {
System.out.println("\t"+ex);
}
}

Running shell script on tomcat7

I have been breaking my head for two days trying to fix the file permissions for my tomcat7 server. I have a library class (.jar file included in myapp/WEB-INF) which needs to run a shell script. The library is written by me and works fine within NetBeans ie. no hassle in creating,reading and deleting files. That is because NetBeans runs the program as blumonkey(my username on my Ubuntu System). But when I import this into tomcat and run it, tomcat "executes" the command, produces no definite output, tries to check for a file(which will be generated when the script succeeds) and throws a FileNotFoundException.
More Details as follows:
Tomcat7 installed using apt-get, has its data in 2 locations - /var/lib/tomcat7 with conf and webapps folders and /usr/share/tomcat7 with the bin and lib folders
The user uploads a .zip file which is stores to /home/blumonkey/data. Rest of the program runs on the documents stored here. All new folders/files uploaded by tomcat have, obviously, tomcat7 as the owner.
I have tried things like changing the ownership to blumonkey, adding tomcat7 to blumonkey user group but none of the methods worked (Somewhere around here I probably messed up changing permissions carelessly :/ ). Apparently tomcat7 is unable to process on the files it owns.(How can this be?).
The script works when I run it in the terminal. But it doesn't work when I do a sudo -u tomcat7 script.sh, ie run it as tomcat7. It just exits with no message. I doubt that this it what is happening as I have tried to debug by redirecting the errors and outputs in ProcessBuilder but they came empty.
Any help regarding how to fix the issue and get the script running would be greatly appreciated. Please comment if you need any more info.
The code for script execution
private static void RunShellCommandFromJava(String command,String fn, String arg1,String arg2) throws Exception
{
try
{
System.out.println(System.getProperty("user.name"));
ProcessBuilder pbuilder = new ProcessBuilder("/bin/bash",command,fn,arg1,arg2);
System.out.println(pbuilder.command());
pbuilder.redirectErrorStream(true);
Process p = pbuilder.start();
p.waitFor();
}
catch(Exception ie)
{
throw ie;
}
}
The command which needs to be executed
"/bin/bash /abs/path/to/script.sh /abs/path/to/doc/in/data-folder maxpages=30 maxsearches=3"
PS : I have followed this question but it didn't help. I also tried other options like Runtime.exec(), bash,/bin/bash/ and /bin/bash/ -c, some of them don't work at all, others give no results.

Try to use Runtime and check standard error to find out what was the problem (probably permissions or paths):
// run command
String[] fixCmd = new String[] { "/bin/bash", "/abs/path/to/script.sh", "/abs/path/to/doc/in/data-folder", "maxpages=30", "maxsearches=3" };
Process start = Runtime.getRuntime().exec(fixCmd);
// monitor standard error to find out what's wrong
BufferedReader r = new BufferedReader(new InputStreamReader(start.getErrorStream()));
String line = null;
while ((line = r.readLine()) != null) {
System.out.println(line);
}

Invoking a Remote .bat file over http

I have a .bat file on a remote machine. I want to invoke it through http call. I dont want to make any changes on the remote machine. Is there a way to do it using java and http?
String command = "cmd /C start C:/Users/abc/Desktop/test.bat";
Runtime rt = Runtime.getRuntime();
Process pr = rt.exec(command);
The above works good to invoke a .bat file on local machine. I would not mind considering other ways too, but invoking it through http would be the first choice.
EDIT:
I am using paramiko to do this now. However,I am unable to run the remote commands on the command prompt.
ssh = paramiko.SSHClient()
print "Enter the IP address"
ip = raw_input("ip>")
print "Enter the username"
user = raw_input("username>")
print "Enter the password"
pwd = raw_input("password>")
ssh.set_missing_host_key_policy(paramiko.AutoAddPolicy())
ssh.connect(ip, username=user, password=pwd, allow_agent = False)
print "connection successfull"
i, o, e = ssh.exec_command("echo test") # example command
s = e.read()
if s: # an error occurred
raise RuntimeError, s
result = o.read()
print result
Somehow it says AllowDesktopAccess failed

You need a service on the remote machine, for example an http server that is configured to run this script on demand (eg via cgi) or an ssh server you can connect to to issue the command.
Since you're using windows (I assume) then PsExec may be the service you need.
http://technet.microsoft.com/en-us/sysinternals/bb897553