[kepler-dev] Running Shell Scripts inside Kepler

[Dan Higgins]

Christopher,
    I was also surprised also that the "bin/sh" technique did not work. 
In any case, changing it fixed things on both the Mac and on Linux ! 
Maybe there is something specific in the R script?

Dan

Christopher Brooks wrote:

>BTW - My hack for the exec command in ptjacl (a 100% Java
>implementation of a subset of Tcl)
>was to add a -sh command line argument.  If -sh is present, then
>we use /bin/sh, if not, then we use cmd under Windows etc.
>
>The ptjacl exec command is written in Java and uses the
>Runtime.exec(), so it is very similar to CommandLine.
>
>I'm not sure if this would help with CommandLine.  It seems dumb
>to have to tell the tool whether to use /bin/sh or not, but at
>the time it seemed like the quickest solution.  It looks
>like the problem for here is that sometimes you want /bin/sh,
>sometimes you don't.  I'm surprised that under Linux and
>the Mac, the following did not work for you.
>
>              commandArray[0] = "/bin/sh";
>              commandArray[1] = "-c";
>              commandArray[2] = "R";
>              commandArray[3] = "--silent";
>              commandArray[4] = "--no-restore";
>              commandArray[5] = "--no-save";
>
>BTW - Under Windows the ptjacl exec command writes out two files
>c:/temp/jacl1.bat and c:/temp/jacl2.bat
>
>jacl1.bat looks like:
>--start--
>@echo off
>cmd.exe /C C:\TEMP\jacl2.bat
>--end--
>
>--start--
>@echo off
>C:
>cd \cxh\ptII\ptolemy\copernicus\java\test
>make "-C" "../cg/ComplexDivide" "MODEL=ComplexDivide"
>"SOURCECLASS=../../../../ptolemy/actor/lib/test/auto/ComplexDivide.xml"
>"smokeTest" 
>--end--
>
>This seems a litle byzantine, but it works.
>
>_Christopher
>
>
>
>--------
>
>    Hi Ilkay (and others)
>    
>    A few weeks ago, you were asking if I had experience/problems with 
>    running shell scripts using the CommandLine actor. At the time, I did 
>    not, but that situation changed with some recent work on the RExpression 
>    actor. And I discovered some problems (and solutions) which may be of 
>    interest.
>    
>    In the commandLine actor (and Java in general), the runtime.exec() 
>    method is used to create subprocesses; e.g.
>    
>              _process = runtime.exec(commandArray);
>    
>    where, for the Windows OS, the commandArray might be something like
>    
>              commandArray[0] = "cmd.exe";
>              commandArray[1] = "/C";
>              commandArray[2] = "R";
>              commandArray[3] = "--silent";
>              commandArray[4] = "--no-restore";
>              commandArray[5] = "--no-save";
>p    
>    In this case, the Windows command line processor 'cmd.exe' is used to 
>    execute the 'R' program. This works fine on a Windows machine and use of 
>    'cmd' to launch the R program means that the PATH system variable is 
>    used to find R. Thus no need for specifying the absolute path.
>    
>    Now, on Linux or MacOSX, the commandArray (for the CommandLine actor) 
>    uses /bin/sh to execute the command line; e.g.
>    
>              commandArray[0] = "/bin/sh";
>              commandArray[1] = "-c";
>              commandArray[2] = "R";
>              commandArray[3] = "--silent";
>              commandArray[4] = "--no-restore";
>              commandArray[5] = "--no-save";
>    
>    Now here is where I ran into trouble!!! On Linux and the Mac, 'R' is a 
>    shell script, not a simple executable! And apparently, the Java 
>    runtime.exec() method WILL NOT START A SUBPROCESS SET UP THIS WAY WITH A 
>    SHELL SCRIPT!!!
>    
>    So what I discovered was that on Unix machines, I can change the 
>    commandArray to directly call the shell script (i.e. not call the shell 
>    to launch it). In this case, the commandArray is just
>    
>              commandArray[0] = "R";
>              commandArray[1] = "--silent";
>              commandArray[2] = "--no-restore";
>              commandArray[3] = "--no-save";
>    
>    This worked on both Linux and the MacOSX and the OS still can find a 
>    shell script using PATH (which is cannot do under Windows).
>    
>    So this solved my problem, but I am not sure exactly how it might work 
>    for the CommandLine actor where it is not obvious whether or not one is 
>    trying to run a shell script. Maybe, we can just drop the '/bin/sh' part 
>    of the commandArray for executables AND shell scripts?
>    
>    Dan
>    
>    -- 
>    *******************************************************************
>    Dan Higgins                                  higgins at nceas.ucsb.edu
>    http://www.nceas.ucsb.edu/    Ph: 805-893-5127
>    National Center for Ecological Analysis and Synthesis (NCEAS) 
>    Marine Science Building - Room 3405
>    Santa Barbara, CA 93195
>    *******************************************************************
>    
>    _______________________________________________
>    Kepler-dev mailing list
>    Kepler-dev at ecoinformatics.org
>    http://mercury.nceas.ucsb.edu/ecoinformatics/mailman/listinfo/kepler-dev
>--------
>  
>


-- 
*******************************************************************
Dan Higgins                                  higgins at nceas.ucsb.edu
http://www.nceas.ucsb.edu/    Ph: 805-893-5127
National Center for Ecological Analysis and Synthesis (NCEAS) 
Marine Science Building - Room 3405
Santa Barbara, CA 93195
*******************************************************************