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Wrapper Creator

Introduction

A wrapper creator is a B-Fabric entity which contains the configuration of an executable with WRAPPERCREATOR context. This entity is considered as a "bridge entity" between the wrapper creator executable and the application. Depending on the configuration, the wrappers may be created in different ways. The examples below show how the new concept is used to ensure the compatibility of existing external applications.

Registration

Navigate to Admin / Application Data / Wrapper Creators and click on "Create Wrapper Creator". Select the submitter executable, modify the parameter setting and click on "Save".

"Resources Batch"

The application executable entity contains the absolute path to the executable file on the file system in the "program" attribute. Exactly one input file will be specified as input file. Copying of the input file to the scratch space is done by the the application executable, as well as copying of the output file to the storage.
Example Application: Peakplot - Label tandem mass specs
Example Wrapper 'Resources Batch'
#!/bin/bash -x

CONTACT="support@fgcz.uzh.ch"
declare -a ALLTEMPFILES
trap cleanTemp EXIT

WSTOOLSSET_DIRPATH="/home/bfabric/sgeworker_test/fgcz-bfabric-demo/webservicetools"
export PATH="$WSTOOLSSET_DIRPATH:$PATH"

SCRATCHSPACE="/scratch"
EXTERNALJOBID=3254
WORKUNITID=105789
STORAGEID=1
PROJECTID=474
CREATEDBY="amarko"
INPUT_RESOURCEID=81605
RESOURCE_NAME="F129304"

INPUT_PROTOCOL="scp"
INPUT_HOST="fgcz-c-064.fgcz-net.unizh.ch"
INPUT_FILEPATH="/usr/local/mascot/data/20101203/F129304.dat"
INPUT="$INPUT_PROTOCOL://$INPUT_HOST/$INPUT_FILEPATH"

OUTPUT_PROTOCOL="scp"
OUTPUT_HOST="fgcz-data.uzh.ch"
OUTPUT_BASEPATH="/home/bfabric/repos/"
OUTPUT_RELATIVEPATH="p474/Proteomics/Peakplot___Label_tandem_mass_specs/workunit_105789"
OUTPUT_DIRPATH="$OUTPUT_BASEPATH/$OUTPUT_RELATIVEPATH"
OUTPUT_FILENAME="F129304.zip"
OUTPUT_FILEPATH="$OUTPUT_DIRPATH/$OUTPUT_FILENAME"
OUTPUT="$OUTPUT_PROTOCOL://$OUTPUT_HOST/$OUTPUT_FILEPATH"

ORIGINAL_EXECUTABLE="/home/bfabric/sgeworker_test/bin/fgcz_sge_peakplot_ng"
EXECUTABLE="$SCRATCHSPACE/executable-$WORKUNITID-$EXTERNALJOBID"

addTemp() {
    local TEMPFILE="$1"
    test -e "$TEMPFILE" && ALLTEMPFILES[${#ALLTEMPFILES[*]}]=$TEMPFILE
}

cleanTemp() {
    if [[ ${#ALLTEMPFILES[*]} -gt 0 ]]; then
        for TEMPFILE in "${ALLTEMPFILES[@]}"
        do
            test -e "$TEMPFILE" && rm -rf $TEMPFILE
        done
    fi
}

die() {
    if [ -n "$JOB_ID" ]; then
        externaljobsave --id $EXTERNALJOBID \
        --status "failed" --logthis "$1" 
    fi
    local myDate=$( date "+%Y%m%d-%H%M%S")
    local myHost=$( hostname )
    echo -n "[$myDate @ $myHost] Error: "
    echo $*
    echo "Contact: $CONTACT"
    echo "exit 1"
    exit 1
}

logmessage() {
    local myDate=$( date "+%Y%m%d-%H%M%S" )
    local myHost=$( hostname )
    echo -n "[$myDate @ $myHost] Log: "
    echo $*
}

logmessage "BEGIN COMPUTENODE INFO"
logmessage $( date )
logmessage $( hostname )
logmessage $( netstat -i -e | grep -w inet | grep -v 127.0.0.1 | head -n1 | awk '{print $2}' | cut -d'/' -f1 | cut -d':' -f2 )
logmessage $( uptime )
logmessage "BASH_VERSION: $BASH_VERSION"
logmessage "END COMPUTENODE INFO"

test -e "$SCRATCHSPACE" || die "$SCRATCHSPACE does not exist!"
test -w "$SCRATCHSPACE" || die "$SCRATCHSPACE is not writable!"

if [ -n "$JOB_ID" ]; then
    which externaljobsave || die "externaljobsave not available!"
    which resourcesave || die "resourcesave not available!"
    which curl || die "curl not available!"
    which mktemp || die "mktemp not available!"
    which xmlstarlet || die "xmlstarlet not available!"
fi

test -e "$ORIGINAL_EXECUTABLE" || die "$ORIGINAL_EXECUTABLE does not exits!"
test -x "$ORIGINAL_EXECUTABLE" || die "$ORIGINAL_EXECUTABLE can't be executed!"

if [ -n "$JOB_ID" ]; then
    export STATFILE="/tmp/statfile-$WORKUNITID-$EXTERNALJOBID"
    touch $STATFILE
    addTemp $STATFILE
fi    

cp "$ORIGINAL_EXECUTABLE" "$EXECUTABLE"
addTemp "$EXECUTABLE"
chmod 700 "$EXECUTABLE"
$EXECUTABLE \
--input="$INPUT" \
--output="$OUTPUT" \
--createdby=$CREATEDBY \
--projectid=$PROJECTID \
--workunitid=$WORKUNITID
test $? -eq 0 || die "execution failed"

if [ -n "$JOB_ID" ]; then
    FILESIZE="$( cat $STATFILE | grep 'SIZE' | awk '{print $2}' )"
    FILECHECKSUM="$( cat $STATFILE | grep 'MD5SUM' | awk '{print $2}')"
fi

if [ -n "$JOB_ID" ]; then
    set -x
    resourcesave \
    --workunitid $WORKUNITID \
    --storageid $STORAGEID \
    --relativepath "$OUTPUT_RELATIVEPATH/$OUTPUT_FILENAME" \
    --inputresourceid $INPUT_RESOURCEID \
    --size $FILESIZE \
    --filechecksum "$FILECHECKSUM" \
    --name "$RESOURCE_NAME" \
    --status "available"
    test $? -eq 0 || die "failed to create resource in B-Fabric"

    set -x
    externaljobsave \
    --id $EXTERNALJOBID \
    --status done  \
    --logthis "execution finished successfully" 
    test $? -eq 0 || die "failed to update external job in B-Fabric"
fi

exit 0

"Resources Non-Batch"

The application executable entity contains the absolute path to the executable file on the file system in the "program" attribute. One or more input file will be specified as input file. Copying of the input file to the scratch space is done by the the application executable, as well as copying of the output file to the storage.
Example Application: Scaffold, mudpit
Example Wrapper 'Resources Non-Batch'
#!/bin/bash -x

CONTACT="support@fgcz.uzh.ch"
declare -a ALLTEMPFILES
trap cleanTemp EXIT

WSTOOLSSET_DIRPATH="/home/bfabric/sgeworker_test/fgcz-bfabric-demo/webservicetools"
export PATH="$WSTOOLSSET_DIRPATH:$PATH"

SCRATCHSPACE="/scratch"
EXTERNALJOBID=3328
WORKUNITID=105826
STORAGEID=1
PROJECTID=474
CREATEDBY="barkows"
RESOURCE_NAME="Scaffold, no mudPit"

INPUT="scp://fgcz-c-064.fgcz-net.unizh.ch/usr/local/mascot/data/20101202/F129284.dat,scp://fgcz-c-064.fgcz-net.unizh.ch/usr/local/mascot/data/20101202/F129277.dat"
OUTPUT_PROTOCOL="scp"
OUTPUT_HOST="fgcz-data.uzh.ch"
OUTPUT_BASEPATH="/home/bfabric/repos/"
OUTPUT_RELATIVEPATH="p474/Proteomics/Scaffold__no_mudPit/workunit_105826"
OUTPUT_DIRPATH="$OUTPUT_BASEPATH/$OUTPUT_RELATIVEPATH"
OUTPUT_FILENAME="Scaffold__no_mudPit.sf3"
OUTPUT_FILEPATH="$OUTPUT_DIRPATH/$OUTPUT_FILENAME"
OUTPUT="$OUTPUT_PROTOCOL://$OUTPUT_HOST/$OUTPUT_FILEPATH"

ORIGINAL_EXECUTABLE="/home/bfabric/sgeworker_test/bin/fgcz_sge_scaffold_no_mudPit_ng"
EXECUTABLE="$SCRATCHSPACE/executable-$WORKUNITID"

addTemp() {
    local TEMPFILE="$1"
    test -e "$TEMPFILE" && ALLTEMPFILES[${#ALLTEMPFILES[*]}]=$TEMPFILE
}

cleanTemp() {
    if [[ ${#ALLTEMPFILES[*]} -gt 0 ]]; then
        for TEMPFILE in "${ALLTEMPFILES[@]}"
        do
            test -e "$TEMPFILE" && rm -rf $TEMPFILE
        done
    fi
}

die() {
    if [ -n "$JOB_ID" ]; then
        externaljobsave --id $EXTERNALJOBID \
        --status "failed" --logthis "$1" 
    fi
    local myDate=$( date "+%Y%m%d-%H%M%S")
    local myHost=$( hostname )
    echo -n "[$myDate @ $myHost] Error: "
    echo $*
    echo "Contact: $CONTACT"
    echo "exit 1"
    exit 1
}

logmessage() {
    local myDate=$( date "+%Y%m%d-%H%M%S" )
    local myHost=$( hostname )
    echo -n "[$myDate @ $myHost] Log: "
    echo $*
}

logmessage "BEGIN COMPUTENODE INFO"
logmessage $( date )
logmessage $( hostname )
logmessage $( netstat -i -e | grep -w inet | grep -v 127.0.0.1 | head -n1 | awk '{print $2}' | cut -d'/' -f1 | cut -d':' -f2 )
logmessage $( uptime )
logmessage "BASH_VERSION: $BASH_VERSION"
logmessage "END COMPUTENODE INFO"

test -e "$SCRATCHSPACE" || die "$SCRATCHSPACE does not exist!"
test -w "$SCRATCHSPACE" || die "$SCRATCHSPACE is not writable!"

if [ -n "$JOB_ID" ]; then
    which externaljobsave || die "externaljobsave not available!"
    which resourcesave || die "resourcesave not available!"
    which curl || die "curl not available!"
    which mktemp || die "mktemp not available!"
    which xmlstarlet || die "xmlstarlet not available!"
fi

test -e "$ORIGINAL_EXECUTABLE" || die "$ORIGINAL_EXECUTABLE does not exits!"
test -x "$ORIGINAL_EXECUTABLE" || die "$ORIGINAL_EXECUTABLE can't be executed!"

if [ -n "$JOB_ID" ]; then
    export STATFILE="/tmp/statfile-$WORKUNITID-$EXTERNALJOBID"
    touch $STATFILE
    addTemp $STATFILE
fi    

cp "$ORIGINAL_EXECUTABLE" "$EXECUTABLE"
addTemp "$EXECUTABLE"
chmod 700 "$EXECUTABLE"
$EXECUTABLE \
--input="$INPUT" \
--output="$OUTPUT" \
--createdby=$CREATEDBY \
--projectid=$PROJECTID \
--workunitid=$WORKUNITID
test $? -eq 0 || die "execution failed"

if [ -n "$JOB_ID" ]; then
    FILESIZE="$( cat $STATFILE | grep 'SIZE' | awk '{print $2}' )"
    FILECHECKSUM="$( cat $STATFILE | grep 'MD5SUM' | awk '{print $2}')"
fi

if [ -n "$JOB_ID" ]; then
    set -x
    resourcesave \
    --workunitid $WORKUNITID \
    --storageid $STORAGEID \
    --relativepath "$OUTPUT_RELATIVEPATH/$OUTPUT_FILENAME" \
    --size $FILESIZE \
    --filechecksum "$FILECHECKSUM" \
    --name "$RESOURCE_NAME" \
    --status "available"
    test $? -eq 0 || die "failed to create resource in B-Fabric"

    set -x
    externaljobsave \
    --id $EXTERNALJOBID \
    --status done  \
    --logthis "execution finished successfully" 
    test $? -eq 0 || die "failed to update external job in B-Fabric"
fi

exit 0

"R Server"

The application executable entity contains the name of the R Script in the "program" attribute. The config.r and SampleAnnotation.txt configuration files are created according to the selected experiment definition. Copying of the input file to the scratch space is done by the the application executable, copying of the output file to the storage is done by the wrapper.
Example Application: Affymetrix QC Report
#!/bin/bash -x

CONTACT="support@fgcz.uzh.ch"
declare -a ALLTEMPFILES
trap cleanTemp EXIT

WSTOOLSSET_DIRPATH="/home/bfabric/sgeworker_test/fgcz-bfabric-demo/webservicetools"
export PATH="$WSTOOLSSET_DIRPATH:$PATH"
SCRATCHSPACE="/scratch/bfabric"
EXTERNALJOBID=3232
WORKUNITID=105783
STORAGEID=1
PROJECTID=403
CREATEDBY="amarko"
RESOURCE_NAME="tutorial day demo"
REXECUTABLE="/usr/local/ngseq/bin/R"
RCMD="$REXECUTABLE --no-save"
ZIPCMD="zip -r -q"

OUTPUT_PROTOCOL="scp"
OUTPUT_HOST="fgcz-data.uzh.ch"
OUTPUT_BASEPATH="/home/bfabric/repos/"
OUTPUT_RELATIVEPATH="p403/Transcriptomics/Affymetrix_QC_Report/workunit_105783"
OUTPUT_DIRPATH="$OUTPUT_BASEPATH/$OUTPUT_RELATIVEPATH"
OUTPUT_FILENAME="tutorial_day_demo.zip"
OUTPUT_FILEPATH="$OUTPUT_DIRPATH/$OUTPUT_FILENAME"
OUTPUT="$OUTPUT_PROTOCOL://$OUTPUT_HOST/$OUTPUT_FILEPATH"

WORKINGDIR="$SCRATCHSPACE/workunit-$WORKUNITID-$EXTERNALJOBID"

addTemp() {
    local TEMPFILE="$1"
    test -e "$TEMPFILE" && ALLTEMPFILES[${#ALLTEMPFILES[*]}]=$TEMPFILE
}

cleanTemp() {
    if [[ ${#ALLTEMPFILES[*]} -gt 0 ]]; then
        for TEMPFILE in "${ALLTEMPFILES[@]}"
        do
            test -e "$TEMPFILE" && rm -rf $TEMPFILE
        done
    fi
}

die() {
    if [ -n "$JOB_ID" ]; then
        externaljobsave --id $EXTERNALJOBID \
        --status "failed" --logthis "$1" 
    fi
    local myDate=$( date "+%Y%m%d-%H%M%S")
    local myHost=$( hostname )
    echo -n "[$myDate @ $myHost] Error: "
    echo $*
    echo "Contact: $CONTACT"
    echo "exit 1"
    exit 1
}

logmessage() {
    local myDate=$( date "+%Y%m%d-%H%M%S" )
    local myHost=$( hostname )
    echo -n "[$myDate @ $myHost] Log: "
    echo $*
}

printSampleAnnotation() {
cat <<ENDOFSAMPLEANNOTATION
Data Resource	Sample	Extract	Species	Treatment
p403/Transcriptomics/Affymetrix/LightStimulus/caquinof_20090312_dark_2_ATH1.CEL	dark_2_	dark_2_	Arabidopsis thaliana (thale cress)	light deprivation
p403/Transcriptomics/Affymetrix/LightStimulus/caquinof_20090312_sdlg_1_ATH1.CEL	sdlg_1_	sdlg_1_	Arabidopsis thaliana (thale cress)	light treatment
p403/Transcriptomics/Affymetrix/LightStimulus/caquinof_20090312_sdlg_3_ATH1.CEL	sdlg_3_	sdlg_3_	Arabidopsis thaliana (thale cress)	light treatment
p403/Transcriptomics/Affymetrix/LightStimulus/caquinof_20090313_dark_1_ATH1.CEL	dark_1_	dark_1_	Arabidopsis thaliana (thale cress)	light deprivation
p403/Transcriptomics/Affymetrix/LightStimulus/caquinof_20090313_dark_3_ATH1.CEL	dark_3_	dark_3_	Arabidopsis thaliana (thale cress)	light deprivation
p403/Transcriptomics/Affymetrix/LightStimulus/caquinof_20090313_sdlg_2_ATH1.CEL	sdlg_2_	sdlg_2_	Arabidopsis thaliana (thale cress)	light treatment
ENDOFSAMPLEANNOTATION
}

printConfigR(){
cat <<EOFCONFIGR
scriptDir = "/usr/local/ngseq/bfab_scripts"
rScripts = list.files(path=scriptDir, pattern='.*\\\\.r', recursive=TRUE,full.names=TRUE)
for (rs in rScripts){ message(rs); source(rs)}
annoFile = "SampleAnnotation.txt"
config = list()
config[["Name"]] = "Affymetrix QC Report"
config[["Project ID"]] = "403"
config[["Project Name"]] = "Informatics Test Project"
affyQC(annoFile, config=config)
EOFCONFIGR
}

logmessage "BEGIN COMPUTENODE INFO"
logmessage $( date )
logmessage $( hostname )
logmessage $( netstat -i -e | grep -w inet | grep -v 127.0.0.1 | head -n1 | awk '{print $2}' | cut -d'/' -f1 | cut -d':' -f2 )
logmessage $( uptime )
logmessage "BASH_VERSION: $BASH_VERSION"
logmessage "END COMPUTENODE INFO"

test -e "$SCRATCHSPACE" || die "$SCRATCHSPACE does not exist!"
test -w "$SCRATCHSPACE" || die "$SCRATCHSPACE is not writable!"

if [ -n "$JOB_ID" ]; then
    which externaljobsave || die "externaljobsave not available!"
    which resourcesave || die "resourcesave not available!"
    which curl || die "curl not available!"
    which mktemp || die "mktemp not available!"
    which xmlstarlet || die "xmlstarlet not available!"
fi

set -x
if [ -n "$JOB_ID" ]; then
    echo "checking tool(s) for copying directory contents to the storage host"
    which scp || die "scp not available!"
    which ssh || die "ssh not available!"
    which rsync || die "rsync not available!"
fi

# checking execution tools
test -e "$REXECUTABLE" || die "$REXECUTABLE does not exits!"
test -x "$REXECUTABLE" || die "$REXECUTABLE can't be executed!"
which zip || die "zip not available!"

if [ -n "$JOB_ID" ]; then
    set -x
    STARTING=$( echo "Starting execution on $HOSTNAME;     JOB_ID: "$JOB_ID"; JOB_NAME: $JOB_NAME" )
    externaljobsave --id $EXTERNALJOBID --status running --logthis "$STARTING"
    set -x
fi

# create the working directory
mkdir -p "$WORKINGDIR"
test $? -eq 0 || die "failed to create workint directory: $WORKINGDIR"
if [ -n "$JOB_ID" ]; then
    addTemp "$WORKINGDIR"
fi

# change into the working dir, print config files and run R
cd "$WORKINGDIR"
printConfigR > config.r
printSampleAnnotation > SampleAnnotation.txt
$RCMD < config.r
test $? -eq 0 || die "R execution failed"
test -r "$WORKINGDIR/00index.html" || die "R processing finished without success!"

# zip the content of the working dir
cd "$WORKINGDIR"
$ZIPCMD "$OUTPUT_FILENAME" .
test $? -eq 0 || die "zip command failed"

# determine the filesize and the file checksum
FILESIZE="$( stat -c %s $OUTPUT_FILENAME )"
FILECHECKSUM="$( md5sum $OUTPUT_FILENAME | awk '{print $1}' )"

# copy the content of the working directory to the storage
if [ -n "$JOB_ID" ]; then
    ssh $OUTPUT_HOST "mkdir -p $OUTPUT_DIRPATH"
    test $? -eq 0 || die "creating workunit directory failed"
    rsync -av -e ssh "$WORKINGDIR/" "$OUTPUT_HOST:$OUTPUT_DIRPATH/"
    test $? -eq 0 || die "rsync failed to copy data to storage"
fi


# update B-Fabric
if [ -n "$JOB_ID" ]; then
    set -x
    resourcesave \
    --workunitid $WORKUNITID \
    --storageid $STORAGEID \
    --relativepath "$OUTPUT_RELATIVEPATH/$OUTPUT_FILENAME" \
    --size $FILESIZE \
    --filechecksum "$FILECHECKSUM" \
    --name "$RESOURCE_NAME" \
    --status "available"
    test $? -eq 0 || die "failed to create resource in B-Fabric"

    set -x
    externaljobsave \
    --id $EXTERNALJOBID \
    --status done  \
    --logthis "execution finished successfully" 
    test $? -eq 0 || die "failed to update external job in B-Fabric"
fi

exit 0

"program $OPTIONS $INPUT $OUTPUT"

The application executable contains the command or the absolute path in the "program" attribute. The options are composed from parameters: if a parameter is of type "string" then "key value" will be added to the variable OPTIONS; in case of parameters of type "boolean" only "key" will be attached. The order is not guaranteed. The wrapper will copy the input file from the storage to the the scratch; INPUT will contain the path of the local input file, OUTPUT will contain the output path to the local output file.
Currently, there is no application which utilizes this wrapper creator.

"program $OPTIONS $INPUT > $OUTPUT"

The application executable contains the command or the absolute path in the "program" attribute. The options are composed from parameters: if a parameter is of type "string" then "key value" will be added to the variable OPTIONS; in case of parameters of type "boolean" only "key" will be attached. The order is not guaranteed. The wrapper will copy the input file from the storage to the the scratch; INPUT will contain the local path. It is assumed that the application writes the output to STDOUT, so this will be piped into the file described by the OUTPUT variable.
Example Application: Head Tool
program $OPTIONS $INPUT $OUTPUT
#!/bin/bash -x

CONTACT="support@fgcz.uzh.ch"
declare -a ALLTEMPFILES
trap cleanTemp EXIT

WSTOOLSSET_DIRPATH="/home/bfabric/sgeworker_test/fgcz-bfabric-demo/webservicetools"
export PATH="$WSTOOLSSET_DIRPATH:$PATH"

SCRATCHSPACE="/scratch"
EXTERNALJOBID=3381
WORKUNITID=105851
STORAGEID=1
PROJECTID=474
CREATEDBY="amarko"
INPUT_RESOURCEID=81600
RESOURCE_NAME="F129283"

INPUT_PROTOCOL="scp"
INPUT_HOST="fgcz-c-064.fgcz-net.unizh.ch"
INPUT_FILEPATH="/usr/local/mascot/data/20101202/F129283.dat"
INPUT_FILENAME="F129283.dat"
INPUT="$INPUT_PROTOCOL://$INPUT_HOST/$INPUT_FILEPATH"

OUTPUT_PROTOCOL="scp"
OUTPUT_HOST="fgcz-data.uzh.ch"
OUTPUT_BASEPATH="/home/bfabric/repos"
OUTPUT_RELATIVEPATH="p474/General/Head_Tool/workunit_105851"
OUTPUT_DIRPATH="$OUTPUT_BASEPATH/$OUTPUT_RELATIVEPATH"
OUTPUT_FILENAME="F129283.zip"
OUTPUT_FILEPATH="$OUTPUT_DIRPATH/$OUTPUT_FILENAME"
OUTPUT="$OUTPUT_PROTOCOL://$OUTPUT_HOST/$OUTPUT_FILEPATH"
OUTPUT_FILENAME_UNZIPPED="F129283.txt"

ZIPCMD="zip -r -q"
EXECUTABLE="/usr/bin/head"
OPTIONS="-n 40 "

WORKINGDIR="$SCRATCHSPACE/workunit-$WORKUNITID-$EXTERNALJOBID"
INPUT_FILEPATH_LOCAL="$WORKINGDIR/$INPUT_FILENAME"
OUTPUT_FILEPATH_LOCAL="$WORKINGDIR/$OUTPUT_FILENAME"
OUTPUT_FILEPATH_LOCAL_UNZIPPED="$WORKINGDIR/$OUTPUT_FILENAME_UNZIPPED"

addTemp() {
    local TEMPFILE="$1"
    test -e "$TEMPFILE" && ALLTEMPFILES[${#ALLTEMPFILES[*]}]=$TEMPFILE
}

cleanTemp() {
    if [[ ${#ALLTEMPFILES[*]} -gt 0 ]]; then
        for TEMPFILE in "${ALLTEMPFILES[@]}"
        do
            test -e "$TEMPFILE" && rm -rf $TEMPFILE
        done
    fi
}

die() {
    if [ -n "$JOB_ID" ]; then
        externaljobsave --id $EXTERNALJOBID \
        --status "failed" --logthis "$1" 
    fi
    local myDate=$( date "+%Y%m%d-%H%M%S")
    local myHost=$( hostname )
    echo -n "[$myDate @ $myHost] Error: "
    echo $*
    echo "Contact: $CONTACT"
    echo "exit 1"
    exit 1
}

logmessage() {
    local myDate=$( date "+%Y%m%d-%H%M%S" )
    local myHost=$( hostname )
    echo -n "[$myDate @ $myHost] Log: "
    echo $*
}

logmessage "BEGIN COMPUTENODE INFO"
logmessage $( date )
logmessage $( hostname )
logmessage $( netstat -i -e | grep -w inet | grep -v 127.0.0.1 | head -n1 | awk '{print $2}' | cut -d'/' -f1 | cut -d':' -f2 )
logmessage $( uptime )
logmessage "BASH_VERSION: $BASH_VERSION"
logmessage "END COMPUTENODE INFO"

test -e "$SCRATCHSPACE" || die "$SCRATCHSPACE does not exist!"
test -w "$SCRATCHSPACE" || die "$SCRATCHSPACE is not writable!"

if [ -n "$JOB_ID" ]; then
    which externaljobsave || die "externaljobsave not available!"
    which resourcesave || die "resourcesave not available!"
    which curl || die "curl not available!"
    which mktemp || die "mktemp not available!"
    which xmlstarlet || die "xmlstarlet not available!"
fi

if [ -n "$JOB_ID" ]; then
    set -x
    STARTING=$( echo "Starting execution on $HOSTNAME;     JOB_ID: "$JOB_ID"; JOB_NAME: $JOB_NAME" )
    externaljobsave --id $EXTERNALJOBID --status running --logthis "$STARTING"
    set -x
fi

set -x
echo "checking tool(s) for copying input file from the storage host"
which scp || die "scp not available!"
which ssh || die "ssh not available!"
if [ -n "$JOB_ID" ]; then
    echo "checking tool(s) for copying output file to the storage host"
    which scp || die "scp not available!"
    which ssh || die "ssh not available!"
fi


mkdir -p "$WORKINGDIR"
test $? -eq 0 || die "unable to create working directory: $WORKINGDIR"
if [ -n "$JOB_ID" ]; then
    addTemp "$WORKINGDIR"
fi

scp -o StrictHostKeyChecking=no -o VerifyHostKeyDNS=no -c arcfour "$INPUT_HOST:$INPUT_FILEPATH" "$WORKINGDIR"
test $? -eq 0 || die "copying input files failed"

cd "$WORKINGDIR"
$EXECUTABLE $OPTIONS $INPUT_FILEPATH_LOCAL > $OUTPUT_FILEPATH_LOCAL_UNZIPPED
test $? -eq 0 || die "execution failed"

cd "$WORKINGDIR"
$ZIPCMD $OUTPUT_FILENAME $OUTPUT_FILENAME_UNZIPPED
test $? -eq "0" || die "zip command failed"
FILESIZE="$( stat -c %s $OUTPUT_FILENAME )"
FILECHECKSUM="$( md5sum $OUTPUT_FILENAME | awk '{print $1}' )"

if [ -n "$JOB_ID" ]; then
    ssh $OUTPUT_HOST "mkdir -p $OUTPUT_DIRPATH"
    test $? -eq 0 || die "creating workunit directory failed"
    scp -o StrictHostKeyChecking=no -o VerifyHostKeyDNS=no -c arcfour "$OUTPUT_FILEPATH_LOCAL" "$OUTPUT_HOST:$OUTPUT_DIRPATH "
    test $? -eq 0 || die "scp failed to copy data to storage"
fi

if [ -n "$JOB_ID" ]; then
    set -x
    resourcesave \
    --workunitid $WORKUNITID \
    --storageid $STORAGEID \
    --relativepath "$OUTPUT_RELATIVEPATH/$OUTPUT_FILENAME" \
    --inputresourceid $INPUT_RESOURCEID \
    --size $FILESIZE \
    --filechecksum "$FILECHECKSUM" \
    --name "$RESOURCE_NAME" \
    --status "available"
    test $? -eq 0 || die "failed to create resource in B-Fabric"

    set -x
    externaljobsave \
    --id $EXTERNALJOBID \
    --status done  \
    --logthis "execution finished successfully" 
    test $? -eq 0 || die "failed to update external job in B-Fabric"
fi
exit 0


Created by amarko. Last Modification: Friday February 2, 2024 13:34:48 CET by tuerker.