Running a python code using process builder Java - java

I need some help.
I am trying to run a python script called mantime.py from a directory. I've tried to google it and found several ways to do it. Yet, I still got 2 as the exit value, which I expect it 0 (terminate normally). Here is my code:
public int performedManTime() throws IOException, InterruptedException{
ProcessBuilder pb = new ProcessBuilder("/usr/bin/python","/Users/ab/Downloads/ManTIME/mantime.py","-ppp","test",inputDir.getAbsolutePath(),"i2b2");
Map<String,String>env = pb.environment();
env.put("MANTIME_CRF_TRAIN", "/usr/local/Cellar/crf++/0.58/bin/crf_learn");
env.put("MANTIME_CRF_TEST", "/usr/local/Cellar/crf++/0.58/bin/crf_test");
env.put("MANTIME_CORENLP_FOLDER","/Users/ab/Downloads/ManTIME/externals/stanford-corenlp-full-2014-08-27");
Process process = pb.start();
process.waitFor();
System.out.println("Exit Value: "+process.exitValue());
return process.exitValue();
}
-ppp, test, input.dir and i2b2 are the arguments for the mantime.py
I tried to set up the environment as we can see above. Does anyone knows what are the problems? Any comment or suggestion would be really appreciated. Thank you
EDIT: I suspect since the python is on different directory with my tool (/usr/local/python). After I put the code bellow, somehow it works.
ProcessBuilder("/usr/bin/python","/Users/ab/Downloads/ManTIME/mantime.py","-ppp","test",inputDir.getAbsolutePath(),"i2b2");
pb.directory(/myToolsDir)

I suspect since the python is on different directory with my tool (/usr/local/python). After I put the code bellow, somehow it works. Thank you guys
ProcessBuilder("/usr/bin/python","/Users/ab/Downloads/ManTIME/mantime.py","-ppp","test",inputDir.getAbsolutePath(),"i2b2");
pb.directory(/myToolsDir)

Related

How can i call cpprofiler in choco-solver for contrainst programming profiling

I found this on choco-solver documentation but i do not know how use it with provided choco-solver sample program in order to profile.
NB: I already install cpprofiller in my machine and launch it. So it start a tcp server on port 6565.
Need help please.
First, make sure your code looks like:
try (CPProfiler profiler = new CPProfiler(s1.getSolver(), true)) {
solver.findSolution();
}
Then, you should start CPProfiler first and then run run Java program.
Once you go back to the CPProfiler interface, you should see the search tree being updated.

How to execute a python script from a Java program using jython? [duplicate]

What's the easiest way to execute a Python script from Java, and receive the output of that script? I've looked for different libraries like Jepp or Jython, but most appear out of date. Another problem with the libraries is that I need to be able to easily include a library with the source code (though I don't need to source for the library itself) if I use a library.
Because of this, would the easiest/most effective way be to simply do something like call the script with runtime.exec, and then somehow capture printed output? Or, even though it would be very painful for me, I could also just have the Python script output to a temporary text file, then read the file in Java.
Note: the actual communication between Java and Python is not a requirement of the problem I am trying to solve. This is, however, the only way I can think of to easily perform what needs to be done.
Not sure if I understand your question correctly, but provided that you can call the Python executable from the console and just want to capture its output in Java, you can use the exec() method in the Java Runtime class.
Process p = Runtime.getRuntime().exec("python yourapp.py");
You can read up on how to actually read the output from this resource:
http://www.devdaily.com/java/edu/pj/pj010016
import java.io.*;
public class JavaRunCommand {
public static void main(String args[]) {
String s = null;
try {
// run the Unix "ps -ef" command
// using the Runtime exec method:
Process p = Runtime.getRuntime().exec("ps -ef");
BufferedReader stdInput = new BufferedReader(new
InputStreamReader(p.getInputStream()));
BufferedReader stdError = new BufferedReader(new
InputStreamReader(p.getErrorStream()));
// read the output from the command
System.out.println("Here is the standard output of the command:\n");
while ((s = stdInput.readLine()) != null) {
System.out.println(s);
}
// read any errors from the attempted command
System.out.println("Here is the standard error of the command (if any):\n");
while ((s = stdError.readLine()) != null) {
System.out.println(s);
}
System.exit(0);
}
catch (IOException e) {
System.out.println("exception happened - here's what I know: ");
e.printStackTrace();
System.exit(-1);
}
}
}
There is also an Apache library (the Apache exec project) that can help you with this. You can read more about it here:
http://www.devdaily.com/java/java-exec-processbuilder-process-1
http://commons.apache.org/exec/
You can include the Jython library in your Java Project. You can download the source code from the Jython project itself.
Jython does offers support for JSR-223 which basically lets you run a Python script from Java.
You can use a ScriptContext to configure where you want to send your output of the execution.
For instance, let's suppose you have the following Python script in a file named numbers.py:
for i in range(1,10):
print(i)
So, you can run it from Java as follows:
public static void main(String[] args) throws ScriptException, IOException {
StringWriter writer = new StringWriter(); //ouput will be stored here
ScriptEngineManager manager = new ScriptEngineManager();
ScriptContext context = new SimpleScriptContext();
context.setWriter(writer); //configures output redirection
ScriptEngine engine = manager.getEngineByName("python");
engine.eval(new FileReader("numbers.py"), context);
System.out.println(writer.toString());
}
And the output will be:
1
2
3
4
5
6
7
8
9
As long as your Python script is compatible with Python 2.5 you will not have any problems running this with Jython.
I met the same problem before, also read the answers here, but doesn't found any satisfy solution can balance the compatibility, performance and well format output, the Jython can't work with extend C packages and slower than CPython. So finally I decided to invent the wheel myself, it took my 5 nights, I hope it can help you too: jpserve(https://github.com/johnhuang-cn/jpserve).
JPserve provides a simple way to call Python and exchange the result by well format JSON, few performance loss. The following is the sample code.
At first, start jpserve on Python side
>>> from jpserve.jpserve import JPServe
>>> serve = JPServe(("localhost", 8888))
>>> serve.start()
INFO:JPServe:JPServe starting...
INFO:JPServe:JPServe listening in localhost 8888
Then call Python from JAVA side:
PyServeContext.init("localhost", 8888);
PyExecutor executor = PyServeContext.getExecutor();
script = "a = 2\n"
+ "b = 3\n"
+ "_result_ = a * b";
PyResult rs = executor.exec(script);
System.out.println("Result: " + rs.getResult());
---
Result: 6
Jep is anther option. It embeds CPython in Java through JNI.
import jep.Jep;
//...
try(Jep jep = new Jep(false)) {
jep.eval("s = 'hello world'");
jep.eval("print(s)");
jep.eval("a = 1 + 2");
Long a = (Long) jep.getValue("a");
}
I've looked for different libraries like Jepp or Jython, but most seem to be very out of date.
Jython is not "a library"; it's an implementation of the Python language on top of the Java Virtual Machine. It is definitely not out of date; the most recent release was Feb. 24 of this year. It implements Python 2.5, which means you will be missing a couple of more recent features, but it is honestly not much different from 2.7.
Note: the actual communication between Java and Python is not a requirement of the aforementioned assignment, so this isn't doing my homework for me. This is, however, the only way I can think of to easily perform what needs to be done.
This seems extremely unlikely for a school assignment. Please tell us more about what you're really trying to do. Usually, school assignments specify exactly what languages you'll be using for what, and I've never heard of one that involved more than one language at all. If it did, they'd tell you if you needed to set up this kind of communication, and how they intended you to do it.
Jython approach
Java is supposed to be platform independent, and to call a native application (like python) isn't very platform independent.
There is a version of Python (Jython) which is written in Java, which allow us to embed Python in our Java programs. As usually, when you are going to use external libraries, one hurdle is to compile and to run it correctly, therefore we go through the process of building and running a simple Java program with Jython.
We start by getting hold of jython jar file:
https://www.jython.org/download.html
I copied jython-2.5.3.jar to the directory where my Java program was going to be. Then I typed in the following program, which do the same as the previous two; take two numbers, sends them to python, which adds them, then python returns it back to our Java program, where the number is outputted to the screen:
import org.python.util.PythonInterpreter;
import org.python.core.*;
class test3{
public static void main(String a[]){
PythonInterpreter python = new PythonInterpreter();
int number1 = 10;
int number2 = 32;
python.set("number1", new PyInteger(number1));
python.set("number2", new PyInteger(number2));
python.exec("number3 = number1+number2");
PyObject number3 = python.get("number3");
System.out.println("val : "+number3.toString());
}
}
I call this file "test3.java", save it, and do the following to compile it:
javac -classpath jython-2.5.3.jar test3.java
The next step is to try to run it, which I do the following way:
java -classpath jython-2.5.3.jar:. test3
Now, this allows us to use Python from Java, in a platform independent manner. It is kind of slow. Still, it's kind of cool, that it is a Python interpreter written in Java.
ProcessBuilder is very easy to use.
ProcessBuilder pb = new ProcessBuilder("python","Your python file",""+Command line arguments if any);
Process p = pb.start();
This should call python. Refer to the process approach here for full example!
https://bytes.com/topic/python/insights/949995-three-ways-run-python-programs-java
You can try using groovy. It runs on the JVM and it comes with great support for running external processes and extracting the output:
http://groovy.codehaus.org/Executing+External+Processes+From+Groovy
You can see in this code taken from the same link how groovy makes it easy to get the status of the process:
println "return code: ${ proc.exitValue()}"
println "stderr: ${proc.err.text}"
println "stdout: ${proc.in.text}" // *out* from the external program is *in* for groovy
First I would recommend to use ProcessBuilder ( since 1.5 )
Simple usage is described here
https://stackoverflow.com/a/14483787
For more complex example refer to
http://www.javaworld.com/article/2071275/core-java/when-runtime-exec---won-t.html
I've encountered problem when launching Python script from Java, script
was producing too much output to standard out and everything went bad.
The best way to achieve would be to use Apache Commons Exec as I use it for production without problems even for Java 8 environment because of the fact that it lets you execute any external process (including python, bash etc) in synchronous and asynchronous way by using watchdogs.
CommandLine cmdLine = new CommandLine("python");
cmdLine.addArgument("/my/python/script/script.py");
DefaultExecuteResultHandler resultHandler = new DefaultExecuteResultHandler();
ExecuteWatchdog watchdog = new ExecuteWatchdog(60*1000);
Executor executor = new DefaultExecutor();
executor.setExitValue(1);
executor.setWatchdog(watchdog);
executor.execute(cmdLine, resultHandler);
// some time later the result handler callback was invoked so we
// can safely request the exit value
resultHandler.waitFor();
Complete source code for a small but complete POC is shared here that addresses another concern in this post;
https://github.com/raohammad/externalprocessfromjava.git

How to call a bash script from GWT-RPC server (Java)

I want to call a bash script from GWT server
I coded up my first application with GWT/RPC, and I need to call a bash script on the server side (from MyOwnServiceImpl extends RemoteServiceServlet implements MyOwnService).
ProcessBuilder doesn't work
To do that, I confess that I am using java.lang.ProcessBuilder, which is apparently "not supported by GAE" (I just ignored the warning). As it is running on the server side, it seemed to me that it should work anyways. I feel that I am missing something.
Something seems to be preventing the call from being executed, even though the required packages are correctly imported, the binaries are found, the execution doesn't crash. But the call is just not successful (for example even mkdir is not executed on the server).
Related posts weren't much help...
How to execute a Unix shell script via GWT? (does not give a complete answer, and I could not simply comment on the answer)
GWT + ProcessBuilder (mentions precisely the solution I implemented which is not working for me, see above)
Any thoughts on this would be much appreciated, thanks!
In a GWT application without GAE you can use Runtime.getRuntime().exec("some command");
If you want to read out the result of the command, you can use:
Process p = Runtime.getRuntime().exec("A command");
BufferedReader in = new BufferedReader(new InputStreamReader(p.getErrorStream()));
StringBuilder builder = new StringBuilder();
String line = null;
while ((line = in.readLine()) != null) {
builder.append(line + "\n");
}
String result = builder.toString();
If the command above should not work, i guess you have to remove GAE from your project to run a bash script.
you can call bash script with GWT,if your servet side on your computer.
the limit is GAE for secury. no way to cross this limit.

Use Java to start a Windows exe

I want to find out how to open any exe in Windows using Java code. I have searched Google before and they only show me part of the code that they use, I think, because it doesn't seem to compile.
I have downloaded JDK 7 to compile. I don't use Eclipse at the moment and also explaining what I had to do to get it to work in detail would help a lot.
to what Sri Harsha Chilakapati said: would i need to create a class for the code?
Thanks to those who answered but i didn't quite get what you meant but i did however manage to find a website which had what i was after:
http://www.rgagnon.com/javadetails/java-0014.html
public class Test {
public static void main(String[] args) throws Exception {
Process p = Runtime.getRuntime().exec(
"\"c:/program files/windows/notepad.exe\"");
p.waitFor();
}
}
the above was what i was after but thanks again anyway to the people who answered.
Try this.
String myExe = "C:\\MyExe.exe";
String args = "";
Runtime.getRuntime().exec(myExe + " " + args);
Hope this helps.
I would recommend the ProcessBuilder, especially for additional arguments.

Executing linux commands from inside java program

I am trying to create a GUI using java swing. From there I have to run linux system commands. I tried using exec(). But the exec() function is unable to parse the string if it contains single quotes. The code which I have used is as follows-
Process p = Runtime.getRuntime().exec("cpabe-enc pub_key message.txt '( it_department or ( marketing and manager ) )'")
BufferedReader stdInput = new BufferedReader(new InputStreamReader(p.getInputStream()));
But I am getting error when I run the program as--syntax error at "'(".
The same command runs when I write
Process p = Runtime.getRuntime().exec("cpabe-enc pub_key message.txt default")
Please help. Thanks in advance for your help.
Split up the parameters into an array instead, one string for each argument, and use the exec-method that takes as String[] instead, that generally works better for arguments.
Somethign along the lines of:
Runtime.getRuntime().exec(new String[] {"cpabe-enc", "pub_key", "message.txt", "( it_department or ( marketing and manager ) )"});
or whatever what your exact parameters are.
Its because the runtime does not interpret the '(...)' as a single parameter like you intend.
Try using ProcessBuilder instead:
http://docs.oracle.com/javase/1.5.0/docs/api/java/lang/ProcessBuilder.html
I recently got this kind of problem solved. I was using javaFX to call shell scripts on button click .. which is very much similar to your swing application scenario...
Here are the links hope it might help you...
How to code in java to run unix shell script which use rSync internally in windows environment using cygwin?
Getting error in calling shell script in windows environment using java code and cygwin...!
Happy coding... :)

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