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#
# fsl:exec execute a shell command with logging all setup
#
# Stephen Smith, FMRIB Image Analysis Group
#
# Copyright (C) 2000-2007 University of Oxford
#
# Part of FSL - FMRIB's Software Library
# http://www.fmrib.ox.ac.uk/fsl
# fsl@fmrib.ox.ac.uk
#
# Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance
# Imaging of the Brain), Department of Clinical Neurology, Oxford
# University, Oxford, UK
#
#
# LICENCE
#
# FMRIB Software Library, Release 5.0 (c) 2012, The University of
# Oxford (the "Software")
#
# The Software remains the property of the University of Oxford ("the
# University").
#
# The Software is distributed "AS IS" under this Licence solely for
# non-commercial use in the hope that it will be useful, but in order
# that the University as a charitable foundation protects its assets for
# the benefit of its educational and research purposes, the University
# makes clear that no condition is made or to be implied, nor is any
# warranty given or to be implied, as to the accuracy of the Software,
# or that it will be suitable for any particular purpose or for use
# under any specific conditions. Furthermore, the University disclaims
# all responsibility for the use which is made of the Software. It
# further disclaims any liability for the outcomes arising from using
# the Software.
#
# The Licensee agrees to indemnify the University and hold the
# University harmless from and against any and all claims, damages and
# liabilities asserted by third parties (including claims for
# negligence) which arise directly or indirectly from the use of the
# Software or the sale of any products based on the Software.
#
# No part of the Software may be reproduced, modified, transmitted or
# transferred in any form or by any means, electronic or mechanical,
# without the express permission of the University. The permission of
# the University is not required if the said reproduction, modification,
# transmission or transference is done without financial return, the
# conditions of this Licence are imposed upon the receiver of the
# product, and all original and amended source code is included in any
# transmitted product. You may be held legally responsible for any
# copyright infringement that is caused or encouraged by your failure to
# abide by these terms and conditions.
#
# You are not permitted under this Licence to use this Software
# commercially. Use for which any financial return is received shall be
# defined as commercial use, and includes (1) integration of all or part
# of the source code or the Software into a product for sale or license
# by or on behalf of Licensee to third parties or (2) use of the
# Software or any derivative of it for research with the final aim of
# developing software products for sale or license to a third party or
# (3) use of the Software or any derivative of it for research with the
# final aim of developing non-software products for sale or license to a
# third party, or (4) use of the Software to provide any service to an
# external organisation for which payment is received. If you are
# interested in using the Software commercially, please contact Isis
# Innovation Limited ("Isis"), the technology transfer company of the
# University, to negotiate a licence. Contact details are:
# innovation@isis.ox.ac.uk quoting reference DE/9564.
#
# usage: fsl:echo <filename> "string" [-o]
# -o : overwrite instead of appending
#
proc fsl:echo { thefilename thestring args } {
if { $thefilename != "" } {
if { [ llength $args ] != 0 } {
catch { exec sh -c "echo \"$thestring\" > $thefilename" >& /dev/null } putserr
} else {
catch { exec sh -c "echo \"$thestring\" >> $thefilename" >& /dev/null } putserr
}
} else {
catch { puts $thestring } putserr
}
if { [ glob -nocomplain logs/* ] != "" } {
catch { exec sh -c "cat logs/* > report_log.html" } putserr
}
}
# usage: fsl:exec "the command" [options]
# note the double-quotes round "the command"
# -n : don't output logging information
# -b <job_duration> : submit to SGE (if available) and return immediately; otherwise wait to return until <command> has finished
# job_duration is in minutes, set 0 for unknown
# -f : "the command" is a filename to be treated as a parallel batch job (one command per line)
# -h <job-hold-id> : ID of SGE job that must finish before this job gets run
# -N <job_name> : the job will have the name <job_name> on the SGE submission
# -l <logdir> : output logs in <logdir>
# -i : ignore errors ( return exit status 0 to calling script )
proc fsl:exec { thecommand args } {
global logout comout FSLDIR FD SGEID
# process args
set do_logout 1
set do_runfsl 0
set do_runfsl_command ""
set do_parallel ""
set job_holds ""
set job_name ""
set runtime 300
set ignoreErrors 0
set args [ join $args ]
set logdir ""
for { set argindex 0 } { $argindex < [ llength $args ] } { incr argindex 1 } {
set thearg [ lindex $args $argindex ]
if { $thearg == "-n" } {
set do_logout 0
}
if { $thearg == "-f" } {
set do_parallel "-t"
}
if { $thearg == "-h" } {
incr argindex 1
set theid [ lindex $args $argindex ]
if { $theid > 0 } {
if { $job_holds == "" } {
set job_holds "-j $theid"
} else {
set job_holds "${job_holds},$theid"
}
}
}
if { $thearg == "-N" } {
incr argindex 1
set job_name "-N [ lindex $args $argindex ]"
}
if { $thearg == "-l" } {
incr argindex 1
set logdir "-l [ lindex $args $argindex ]"
}
if { $thearg == "-b" } {
set do_runfsl 1
incr argindex 1
set runtime [ lindex $args $argindex ]
}
if { $thearg == "-i" } {
set ignoreErrors 1
}
}
# add runfsl call if required
if { $do_runfsl } {
set thecommand "${FSLDIR}/bin/fsl_sub -T $runtime $logdir $job_name $job_holds $do_parallel $thecommand"
}
# save just the command to report.com if it has been setup
if { [ info exists comout ] && $comout != "" } {
fsl:echo $comout "$thecommand\n"
}
# if logout doesn't exist, set empty so that logging will go to screen
if { ! [ info exists logout ] } {
set logout ""
}
if { ! [ info exists ::errorCode ] } { set ::errorCode "NONE" }
# run and log the actual command
if { $do_logout } {
fsl:echo $logout "\n$thecommand"
if { $logout != "" } {
set errorCode [ catch { exec sh -c $thecommand >>& $logout } errmsg ]
set actualCode [lindex $::errorCode 0]
if { $errorCode != 0 && $actualCode ne "NONE" && $ignoreErrors != 1 } {
} else {
# Trim errmsg to final line
set errmsg [ exec sh -c "tail -n 1 $logout" ]
}
} else {
set errorCode [ catch { exec sh -c $thecommand } errmsg ]
set actualCode [lindex $::errorCode 0]
catch { puts $errmsg } putserr
}
} else {
set errorCode [ catch { exec sh -c $thecommand } errmsg ]
set actualCode [lindex $::errorCode 0]
}
if { $errorCode != 0 && $actualCode ne "NONE" && $ignoreErrors != 1 } {
if { $do_logout } {
fsl:echo $logout "\nFATAL ERROR ENCOUNTERED:\nCOMMAND:\n$thecommand\nERROR MESSAGE:\n$errmsg\nEND OF ERROR MESSAGE"
}
} else {
set errorCode 0
}
# now return errmsg in case the exec call needs to know the output
return -code $errorCode $errmsg
}
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