I'm not able to run the MVN goals through shell script - bash

I just used the below shell script in Post Build activity in JENKINS "Execute Shell" cmd
#!/bin/bash
mvn --version
export M2_HOME=/opt/maven/maven-3.3.3 # your Mavan home path
export PATH=$PATH:$M2_HOME/bin
mvn --version
echo $HOME
echo $WORKSPACE
file=$WORKSPACE/XXXX/XXXX-reports
cd $file
cp XXXX-1.html test.html
fail=`grep "test-method.*FAIL" results.xml | sed -e 's/^.*test-
instance-name="\(.*\) ' | tr '\n' ','`
echo $fail
count=0
while [ $count -lt 5 ]
do
if [ ! -z "$fail" -a "$fail" != " " ];
then
echo `$M2_HOME/bin/mvn clean test -f ../../pom.xml -DInclude=${fail}`
cp XXXX-report.html ReReport_$count.html
retry=`expr $count + 1`
fi
done
In the above shell script I'm trying to run the mvn command and continuing to run 5 times to increase pass count in UNIT script execution.
But It's not working. It's failed to execute the maven goals. So, I just comment the executable and added echo to debug.
But no luck.
Any leads

I suggest that you use this following script that modifies yours. Add your parameters there.
The product log file: mvn_jenkins.log will allow you to easily find problems as suggested by mjuarez:
#!/bin/bash
MVNCMD=$(command -v mvn)
MVNPARAMS=" -version" # replace with your appropriate params
LOGFILE="mvn_jenkins.log"
COUNT=0
while [ $COUNT -lt 5 ]; do
echo "Execute: $MVNCMD $MVNPARAMS" >> $LOGFILE
echo "-------" >> $LOGFILE
$MVNCMD $MVNPARAMS 2>&1>> $LOGFILE
echo "" >> $LOGFILE
COUNT=$((COUNT + 1))
done
Explanation:
MVNCMD=$(command -v mvn): put the full qualified name of maven execute file in MVNCMD var
$MVNCMD $MVNPARAMS 2>&1>> $LOGFILE: Execute mvn command with parameters and redirect error output messages (2) and regular output messages (1) to the log file.
About your maven parameters I don't understand why you use -DskipTests=true.

Related

Trying to create submit script to SGE

I'm trying to edit my working bash script to an SGE script in order to submit it as a job to the cluster.
Currently I have:
#!/bin/bash
# Perform fastqc on files in a specified directory.
for ((j=1; j <=17; j++))
do
directory=/data4/una/batch"$j"/
files=$""$directory"/*.fastq.gz"
batch=$"batch_"$j""
outfile=$""$batch"_submit_script.sh"
echo "#!/bin/bash">>$outfile;
echo "# Your job name">>$outfile;
echo "# -N $batch">>$outfile;
echo "# The job should be placed into the queue 'all.q'">>$outfile;
echo "#$ -q all.q">>$outfile;
echo "# Running in the current working directory">>$outfile;
echo "#$ -cwd">>$outfile;
echo "">>$outfile;
echo "# Export some necessary environment variables">>$outfile;
echo "#$ -S /bin/bash">>$outfile;
echo "#$ -v PATH">>$outfile;
echo "#$ -v LD_LIBRARY_PATH">>$outfile;
echo "#$ -v PYTHONPATH">>$outfile;
echo "# Finally, put your command here">>$outfile;
echo "">>$outfile;
echo "#$ for i in $files;">>$outfile;
echo "#$ do;">>$outfile;
echo "#$ fastqc -f fastq -o /data4/una/test/fastq/$i;">>$outfile;
echo "#$done">>$outfile;
echo "">>$outfile;
qsub $outfile;
done
But I'm getting an error:
Unable to read script file because of error: ERROR! invalid option argument "-f"
But
fastqc -f fastq -o /data4/una/test/fastq/$i
is a totally valid line in my bash script.
Thoughts?
Thanks!
It actually was poor formatting for my loop that was causing this error. I didn't need to start those lines with #$ at all, so those lines become:
echo "for i in $files;">>$outfile;
echo "do">>$outfile;
echo " fastqc -f fastq -o /data4/una/test/fastqc $i">>$outfile;
echo "done">>$outfile;
echo "">>$outfile;
qsub $outfile;

notify-send from within a bash script

I'd like to use notify-send from within a bash script that is running in the background to inform the user about the progress of the script. More specifically this is a script that automagically runs when a USB flash drive is inserted and runs a scan with ClamAV.
Specifically at line 30 and line 66. So far, I'm not having any luck. Can someone give me some advice/help? Thanks.
#!/bin/bash
#doOnUSBinsert_0.2.sh
#Author : Totti
# Make it executable by running 'sudo chmod x doOnUSBinsert_0.2.sh'
if ! [ -f /etc/udev/rules.d/80-doOnUSBinsert.rules ]
then # rule not added
cp "$0" /usr/bin/doOnUSBinsert
chmod u x /usr/bin/doOnUSBinsert
# echo 'SUBSYSTEM=="usb", ACTION=="add", RUN ="/path/to/script.sh"' | sudo tee /etc/udev/rules.d/80-clamscan.rules
echo 'SUBSYSTEM=="usb", ACTION=="add", RUN ="/usr/bin/doOnUSBinsert & "' | tee /etc/udev/rules.d/80-doOnUSBinsert.rules
if [ $? -eq 0 ]
then
echo 'Rule Successfully added. See file "/usr/bin/doOnUSBinsert" if you wish to edit the command'
exit 0
else
echo 'ERROR while adding rule'
exit 1
fi
fi
lfile="/tmp/doOnUSBinsert.log" # udev
lfile2="/tmp/clamscanFromUdev.log" # clamscan
lfile3="/tmp/doOnUSBinsert_mount.log" # mount
notify-send "USB SCAN ON INSERT" "Currently scanning with ClamAV"
main ()
{
sleep 12 # let the partitions to mount
#cat /proc/$$/environ | tr '�' 'n' >> /tmp/udevEnvirn.txt
echo "found $ID_SERIAL" >> "$lfile"
cat /etc/mtab | grep "^$part_c" >> "$lfile.3"
if [ "$ID_SERIAL"x = 'x' ]
then
echo "Exiting on empty ID_SERIAL" >> "$lfile"
exit 1
fi
#Eg: ID_SERIAL --> /dev/disk/by-id/usb-sandisk....42343254343543
#i=0
echo 'searching partitions' >> "$lfile"
for partitionPath in $( find /dev/disk/by-id/ -name "*$ID_SERIAL*part*" )
do
echo "current partition = $partitionPath" >> "$lfile"
# part[i ]="$( readlink -f "$partition" )" # Eg Output: /dev/sdb1 , /dev/sdb2
part_c="$( readlink -f $partitionPath )"
mpoint="$( cat /etc/mtab | grep "^$part_c" | awk '{print $2}' )"
echo "partitionPath= $partitionPath, part = $part_c, mountpoint= $mpoint" >> "$lfile"
echo "Scaning --> $mpoint" >> "$lfile.2"
############################################
clamscan -r --bell "$mpoint"/* >> "$lfile.2"
#############################################
done
}
notify-send "USB SCAN ON INSERT" "Finished scanning with ClamAV"
main &
echo ______________________________________ >> "$lfile"
exit 0
I'm pretty new to the linux world, but while looking for a solution for a similar project I found THIS
Tip: An overview on the available icons can be found here. To send
desktop notification from a background script running as root (replace
X_user and X_userid with the user and userid running X respectively):
sudo -u X_user DISPLAY=:0 DBUS_SESSION_BUS_ADDRESS=unix:path=/run/user/X_userid/bus notify-send 'Hello world!' 'This is an example notification.'
Hope this will help others.
Depending on how you are running the script it may not have access to the display variable. Try running export DISPLAY=:0.0 prior to the command.
If you are running the script as a different user, ie root, then you may also need to run it as su - <logged in user> -c notify-send ... (I usually don't need to do this, but I remember having to at one point - but I cant recall which distro or version I was on at the time.)

Crontab will not execute .sh but crontab will execute a command

This issue is currently driving me nuts.
I setup a crontab with sudo crontab -e
The contents are 1 * * * * /home/bolte/bin/touchtest.sh
The contents of that file are:
#!/bin/bash
touch /home/bolte/bin/test.log
It creates the file. But the below script will not run.
#!/bin/bash
# CHANGE THESE
auth_email="11111111#live.co.uk"
auth_key="11111111111111111" # found in cloudflare
account settings
zone_name="11111.io"
record_name="11111.bolte.io"
# MAYBE CHANGE THESE
ip=$(curl -s http://ipv4.icanhazip.com)
ip_file="/home/bolte/ip.txt"
id_file="/home/bolte/cloudflare.ids"
log_file="/home/bolte/cloudflare.log"
# LOGGER
log() {
if [ "$1" ]; then
echo -e "[$(date)] - $1" >> $log_file
fi
}
# SCRIPT START
log "Check Initiated"
if [ -f $ip_file ]; then
old_ip=$(cat $ip_file)
if [ $ip == $old_ip ]; then
echo "IP has not changed."
exit 0
fi
fi
if [ -f $id_file ] && [ $(wc -l $id_file | cut -d " " -f 1) == 2 ]; then
zone_identifier=$(head -1 $id_file)
record_identifier=$(tail -1 $id_file)
else
zone_identifier=$(curl -s -X GET "https://api.cloudflare.com/client/v4/zones?name=$zone_name" -H "X-Auth-E$
record_identifier=$(curl -s -X GET "https://api.cloudflare.com/client/v4/zones/$zone_identifier/dns_record$
echo "$zone_identifier" > $id_file
echo "$record_identifier" >> $id_file
fi
update=$(curl -s -X PUT "https://api.cloudflare.com/client/v4/zones/$zone_identifier/dns_records/$record_ident$
[ Read 55 lines (Warning: No write permission) ]
^G Get Help ^O Write Out ^W Where Is ^K Cut Text ^J Justify ^C Cur Pos ^Y Prev Page
^X Exit ^R Read File ^\ Replace ^U Uncut Text ^T To Linter ^_ Go To Line ^V Next Page
I've been trying to troubleshoot why this code will not run every minute, there doesn't seem to be any output in the same folder as the script, which is located at /home/bolte/cloudflare-update-record.sh
Ok so the answer to this was, I was editing crontab with sudo, and the files were located in my users home folder. This is why they weren't working. Resolved my own issue.
If you have this issue just use $ crontab -e rather than sudo crontab -e, and specify full paths for your file outputs, unless you are putting the proper path variables in your script.

Bash sub script redirects input to /dev/null mistakenly

I'm working on a script to automate the creation of a .gitconfig file.
This is my main script that calls a function which in turn execute another file.
dotfile.sh
COMMAND_NAME=$1
shift
ARG_NAME=$#
set +a
fail() {
echo "";
printf "\r[${RED}FAIL${RESET}] $1\n";
echo "";
exit 1;
}
set -a
sub_setup() {
info "This may overwrite existing files in your computer. Are you sure? (y/n)";
read -p "" -n 1;
echo "";
if [[ $REPLY =~ ^[Yy]$ ]]; then
for ARG in $ARG_NAME; do
local SCRIPT="~/dotfiles/setup/${ARG}.sh";
[ -f "$SCRIPT" ] && echo "Applying '$ARG'" && . "$SCRIPT" || fail "Unable to find script '$ARG'";
done;
fi;
}
case $COMMAND_NAME in
"" | "-h" | "--help")
sub_help;
;;
*)
CMD=${COMMAND_NAME/*-/}
sub_${CMD} $ARG_NAME 2> /dev/null;
if [ $? = 127 ]; then
fail "'$CMD' is not a known command or has errors.";
fi;
;;
esac;
git.sh
git_config() {
if [ ! -f "~/dotfiles/git/gitconfig_template" ]; then
fail "No gitconfig_template file found in ~/dotfiles/git/";
elif [ -f "~/dotfiles/.gitconfig" ]; then
fail ".gitconfig already exists. Delete the file and retry.";
else
echo "Setting up .gitconfig";
GIT_CREDENTIAL="cache"
[ "$(uname -s)" == "Darwin" ] && GIT_CREDENTIAL="osxkeychain";
user " - What is your GitHub author name?";
read -e GIT_AUTHORNAME;
user " - What is your GitHub author email?";
read -e GIT_AUTHOREMAIL;
user " - What is your GitHub username?";
read -e GIT_USERNAME;
if sed -e "s/AUTHORNAME/$GIT_AUTHORNAME/g" \
-e "s/AUTHOREMAIL/$GIT_AUTHOREMAIL/g" \
-e "s/USERNAME/$GIT_USERNAME/g" \
-e "s/GIT_CREDENTIAL_HELPER/$GIT_CREDENTIAL/g" \
"~/dotfiles/git/gitconfig_template" > "~/dotfiles/.gitconfig"; then
success ".gitconfig has been setup";
else
fail ".gitconfig has not been setup";
fi;
fi;
}
git_config
In the console
$ ./dotfile.sh --setup git
[ ?? ] This may overwrite existing files in your computer. Are you sure? (y/n)
y
Applying 'git'
Setting up .gitconfig
[ .. ] - What is your GitHub author name?
Then I cannot see what I'm typing...
At the bottom of dotfile.sh, I redirect any error that occurs during my function call to /dev/null. But I should normally see what I'm typing. If I remove 2> /dev/null from this line sub_${CMD} $ARG_NAME 2> /dev/null;, it works!! But I don't understand why.
I need this line to prevent my script to echo an error in case my command doesn't exists. I only want my own message.
e.g.
$ ./dotfile --blahblah
./dotfiles: line 153: sub_blahblah: command not found
[FAIL] 'blahblah' is not a known command or has errors
I really don't understand why the input in my sub script is redirected to /dev/null as I mentioned only stderr to be redirected to /dev/null.
Thanks
Do you need the -e option in your read statements?
I did a quick test in an interactive shell. The following command does not echo characters :
read -e TEST 2>/dev/null
The following does echo the characters
read TEST 2>/dev/null

BASH script not work properly in crontab

Below line of my bash script not write output of /tmp/DPE_SC/LoadUnits/ttx/bin/deasn9 -b -a cdrr6 $fnames to file $dst_dir"/"$fstat"-"$fnames".txt when I execute from crontab.
It only creates empty file named $dst_dir"/"$fstat"-"$fnames".txt
Sure it works properly from command line manually.
/tmp/DPE_SC/LoadUnits/ttx/bin/deasn9 -b -a cdrr6 $fnames > $dst_dir/$fstat-$fnames.txt
What is my mistake?
This is my whole script
#!/bin/bash
export PATH=/tmp/DPE_SC/LoadUnits/ttx/bin:/usr/local/bin:/usr/bin:/bin:/usr/local/sbin:/usr/sbin:/sbin:/tmp/DPE_SC/Tools:/usr/X11R6/bin
src_dir=/charging/chsLog/ready
dst_dir=/Core/cdr
cd $src_dir
lastfile=cat $dst_dir/last_cdr.txt
filenames=ls -t | grep ^chsLog
fcounter=1
for fnames in $filenames
do
fstat=`stat -c %y ${fnames} | cut -d '.' -f1`
fstat=`echo ${fstat//[^0-9]/}`
if [[ $fstat -gt $lastfile ]]
then
if [[ $fcounter -eq 1 ]]
then
echo $fstat > $dst_dir/last_cdr.txt
let "fcounter = $fcounter + 1"
fi
deasn9 -b -a cdrr6 ${fnames} > $dst_dir/$fstat-${fnames}.txt
fi
done
Remember that your .profile, .bashrc, et. al. are not available from inside cron.
Environment variables have to be defined directly in the crontab.
e.g.
fstat=myValue
fname=aName
#hourly myJob ${fstat} ${fname}
I found what I mistaken. cdrr6 was not only option. It is cdr formatting library. Then I exported LIB path from scipt.
Now it worked perfectly.

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