[kepler-users] problem using ExternalExecution actor to query MySQL from R

[David LeBauer]

Hello,

I have a workflow that is contained in a series of bash scripts, and
these scripts use R to query MySQL.

The first bash script works when called from the command line, but not
through the External Execution actor, and the error is below.

what works:
in a shell, I run:
cd ~/pecantest
./bash/pecan.ma.sh $pft 15000 500

what doesnt:
in the External Execution actor, I have set the command to
./bash/pecan.ma.sh $pft 15000 500
and the directory to $HOME/pecantest/

I get the error pasted below.

the ./bash/pecan.ma.sh contains the following:
#!/bin/bash
env PFT=$1 ITER=$2 ENSN=$3 R --vanilla < ./rscripts/pecan.start.R
R --vanilla < ./rscripts/pecan.MA.runscript.R

Thank you for your help.

-David

ptolemy.kernel.util.IllegalActionException: Executing command
"./bash/pecan.ma.sh 'ebifarm.c4crop'  15000 500" returned a non-zero
return value of 1.
The last input was: null.
The standard output was:
R version 2.7.0 (2008-04-22)
Copyright (C) 2008 The R Foundation for Statistical Computing
ISBN 3-900051-07-0

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> ##input variables
> pft   <- system("echo $PFT", intern = TRUE)
> ITER  <- as.numeric(system("echo $ITER", intern = TRUE))
> M     <- as.numeric(system("echo $ENSN", intern = TRUE))
> print(cat("PECAn run with ",pft,
+           "\nmeta-analysis has",ITER,"iterations",
+           "\nensemble has",M,"config files"))
PECAn run with  'ebifarm.c4crop'
meta-analysis has 15000 iterations
ensemble has 500 config filesNULL
> save.image(file='pecan.start.Rdata')
>

R version 2.7.0 (2008-04-22)
Copyright (C) 2008 The R Foundation for Statistical Computing
ISBN 3-900051-07-0

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(PECAn, lib.loc = '~/lib/R')
loading JAGS module
   basemod
   bugs
> load('pecan.start.Rdata')
> ## 1. get species list based on pft
> spp <- query.bety.pft_species(pft)

The error output was: Loading required package: RMySQL
Loading required package: DBI
Loading required package: rjags
Loading required package: coda
Loading required package: lattice
Loading Tcl/Tk interface ... done
Loading required package: XML
Loading required package: MASS
Loading required package: ggplot2
Loading required package: proto
Loading required package: grid
Loading required package: reshape
Loading required package: plyr
Loading required package: digest
Loading required package: randtoolbox
Loading required package: rngWELL
Loading required package: hdf5
Warning messages:
1: package 'DBI' was built under R version 2.8.1
2: package 'rjags' was built under R version 2.8.1
3: package 'XML' was built under R version 2.8.1
Error in mysqlExecStatement(conn, statement, ...) :
  RS-DBI driver: (could not run statement: You have an error in your
SQL syntax; check the manual that corresponds to your MySQL server
version for the right syntax to use near 'ebifarm.c4crop''))' at line
1)
Calls: query.bety.pft_species ... .valueClassTest -> is -> is ->
mysqlExecStatement -> .Call
Execution halted

  in .ITER.External Execution
	at ptolemy.actor.lib.Exec.fire(Exec.java:376)
	at ptolemy.actor.AtomicActor.iterate(AtomicActor.java:469)
	at ptolemy.actor.sched.StaticSchedulingDirector.fire(StaticSchedulingDirector.java:188)
	at ptolemy.actor.CompositeActor.fire(CompositeActor.java:458)
	at ptolemy.actor.Manager.iterate(Manager.java:749)
	at ptolemy.actor.Manager.execute(Manager.java:351)
	at ptolemy.actor.Manager.run(Manager.java:1162)
	at ptolemy.actor.Manager$3.run(Manager.java:1215)

-- 
David LeBauer, PhD
Energy Biosciences Institute
University of Illinois Urbana-Champaign
1206 W. Gregory Drive
Urbana, IL  61801, U.S.A.