This script should output a warning notification for the utilization of the main disk if over 50%, but it provides no output. My disk is currently sat at 60% so it should in theory work.
I have added an else statement to identify if the loop is not working but the else statement isnt triggered.
I'm provided no error so its hard to identify where i have gone wrong specifically.
#!/bin/bash
df -H | grep /dev/sda2 | awk '{ printf "%d", $5}' > diskOutput.txt
input="diskOutput.txt"
while IFS= read -r line
do
if [ $line -gt 50 ]
then
up="`uptime | cut -b 1-9`"
output="WARNING UTILISATION $line - $up"
echo "$output"
else
echo "no-in"
fi
done < $input
#rm diskOutput.txt
echo "finished"
Try this.
#!/bin/bash
df -H | grep /dev/sda2 | awk '{ printf "%d", $5}' > diskOutput.txt
echo "" >>diskOutput.txt
input="diskOutput.txt"
while IFS= read -r line
do
if [ $line -gt 50 ]
then
up="`uptime | cut -b 1-9`"
output="WARNING UTILISATION $line - $up"
echo "$output"
else
echo "no-in"
fi
done < $input
#rm diskOutput.txt
echo "finished"
You are setting an internal field separator as space here.
while IFS= read -r line
But when creating file, with %d you are removing all char except digits.
Related
Assume an input table (intable.csv) that contains ID numbers in its second column, and a fresh output table (outlist.csv) into which the input file - extended by one column - is to be written line by line.
echo -ne "foo,NC_045043\nbar,NC_045193\nbaz,n.a.\nqux,NC_045054\n" > intable.csv
echo -n "" > outtable.csv
Further assume that one or more third-party commands (here: esearch, efetch; both part of Entrez Direct) are employed to retrieve additional information for each ID number. This additional info is to form the third column of the output table.
while IFS="" read -r line || [[ -n "$line" ]]
do
echo -n "$line" >> outtable.csv
NCNUM=$(echo "$line" | awk -F"," '{print $2}')
if [[ $NCNUM == NC_* ]]
then
echo "$NCNUM"
RECORD=$(esearch -db nucleotide -query "$NCNUM" | efetch -format gb)
echo "$RECORD" | grep "^LOCUS" | awk '{print ","$3}' | \
tr -d "\n" >> outtable.csv
else
echo ",n.a." >> outtable.csv
fi
done < intable.csv
Why does the while loop iterate only over the first input table entry under the above code, whereas it iterates over all input table entries if the code lines starting with RECORD and echo "$RECORD" are commented out? How can I correct this behavior?
This would happen if esearch reads from standard input. It will inherit the input redirection from the while loop, so it will consume the rest of the input file.
The solution is to redirect is standard input elsewhere, e.g. /dev/null.
while IFS="" read -r line || [[ -n "$line" ]]
do
echo -n "$line" >> outtable.csv
NCNUM=$(echo "$line" | awk -F"," '{print $2}')
if [[ $NCNUM == NC_* ]]
then
echo "$NCNUM"
RECORD=$(esearch -db nucleotide -query "$NCNUM" </dev/null | efetch -format gb)
echo "$RECORD" | grep "^LOCUS" | awk '{print ","$3}' | \
tr -d "\n" >> outtable.csv
else
echo ",n.a." >> outtable.csv
fi
done < intable.csv
The error that I am getting is with the df command on mac, I would like to specify a value in gigabytes and perhaps allow the user to choose a different drive if / is full.
destination="$HOME/Desktop/sandbox"
if [ $(df -h --output=avail /|tail -n1) -lt 300000 ]; then
echo "There is less than 300GB available..." ;
exit
else
for files in *.tar ; do echo copying "$files" ; cp "$files" "$destination" ; read -n 1 -p "Press any key..." ; done
fi
Not sure if df -h / | tail -1 | awk '{print $4}' | sed 's/..$//' is a good option
destination="$HOME/Desktop/sandbox"
freespace="$(df -h / | tail -1 | awk '{print $4}' | sed 's/..$//')"
if [ "$freespace" -lt 300 ]; then
echo "There is less than 300GB available..." ;
exit
else
for files in *.sh ; do echo copying "$files" ; cp "$files" "$destination" ; read -n 1 -p "Press any key..." ; done
fi
The problem is that you are using dh -h what means "human readable" and always append unit after the number (M, G, k...). There is a lot of options how to cut it out by grep, awk, cut or sed. But perhaps the best way is to use different option e.g. df -m to have an output in megabytes and multiply the required space.
Also I would propose to add a grep $destination (mountpoint visible in df output) to filter the required FS and to not rely that it's always last line in the output.
Try something like this:
destination="$HOME/Desktop/sandbox"
free_space=$(df -h | grep $destination | awk '{print $4}')
if [ $free_space -lt $((300 * 1024)) ]; then
echo "There is less than 300GB available..." ;
exit
else
for files in *.tar; do
echo copying "$files"
cp "$files" "$destination"
read -n 1 -p "Press any key..."
done
fi
Complete novice in Bash. Trying to iterate thru 1000 gzip files, may be GNU parallel is the solution??
#!/bin/bash
ctr=0
echo "file_name,symbol,record_count" > $1
dir="/data/myfolder"
for f in "$dir"/*.gz; do
gunzip -c $f | while read line;
do
str=`echo $line | cut -d"|" -f1`
if [ "$str" == "H" ]; then
if [ $ctr -gt 0 ]; then
echo "$f,$sym,$ctr" >> $1
fi
ctr=0
sym=`echo $line | cut -d"|" -f3`
echo $sym
else
ctr=$((ctr+1))
fi
done
done
Any help to speed the process will be greatly appreciated !!!
#!/bin/bash
ctr=0
export ctr
echo "file_name,symbol,record_count" > $1
dir="/data/myfolder"
export dir
doit() {
f="$1"
gunzip -c $f | while read line;
do
str=`echo $line | cut -d"|" -f1`
if [ "$str" == "H" ]; then
if [ $ctr -gt 0 ]; then
echo "$f,$sym,$ctr"
fi
ctr=0
sym=`echo $line | cut -d"|" -f3`
echo $sym >&2
else
ctr=$((ctr+1))
fi
done
}
export -f doit
parallel doit ::: *gz 2>&1 > $1
The Bash while read loop is probably your main bottleneck here. Calling multiple external processes for simple field splitting will exacerbate the problem. Briefly,
while IFS="|" read -r first second third rest; do ...
leverages the shell's built-in field splitting functionality, but you probably want to convert the whole thing to a simple Awk script anyway.
echo "file_name,symbol,record_count" > "$1"
for f in "/data/myfolder"/*.gz; do
gunzip -c "$f" |
awk -F "\|" -v f="$f" -v OFS="," '
/H/ { if(ctr) print f, sym, ctr
ctr=0; sym=$3;
print sym >"/dev/stderr"
next }
{ ++ctr }'
done >>"$1"
This vaguely assumes that printing the lone sym is just for diagnostics. It should hopefully not be hard to see how this can be refactored if this is an incorrect assumption.
My aim is to transform the output (the last 2 lines) of the ping command in a CSV style.
Here are some examples:
In case there is a packet loss lower than 100% <
URL, PacketLoss, Min, Average, Max, Deviation
In case there is packet loss equal to 100%
URL, 100, -1, -1, -1, -1
My script is below, but when the packet loss is 100% the output is:
URL, 100,
So the problem is at the if statement, as it does not enter in elif, I use the same syntax as checking if the address is full or not (with "www." or not).
Can you please have a look because I tried multiple things and it did not work.
My script:
#!/bin/bash
declare site=''
declare result='';
if [[ "$1" == "www."* ]]; then
site="$1";
else
site="www.$1";
fi
result="$site";
pingOutput=$(ping $site -c10 -i0.2 -q| tail -n2);
fl=true;
while IFS= read -r line
do
# !!! The problem is here, the if statement is not working properly and I do not know why !!!
if [ "$fl" == "true" ]; then
result="$result $(echo "$line" | cut -d',' -f3 | cut -d" " -f2 | sed -r 's/%//g')";
fl=false;
elif [[ "$line" == "ms"* ]]; then
result="$result $(echo "$line" | cut -d' ' -f4 | sed -r 's/\// /g')";
else
result="$result -1 -1 -1 -1";
fi
done <<< "$pingOutput"
echo "$result";
This is a pretty old question but I've just stumbled upon it today. Below I paste a slight modified version of the above script that fixes the if issue and works on Mac OS.
P.S. You can uncomment the # prctg=100.0% line to see the if working.
#!/bin/bash
declare site=''
declare result=''
declare prctg=''
[[ "$1" == "www."* ]] && site="$1" || site="www.$1"
result="$site"
pingOutput=$(ping $site -c10 -i0.2 -q | tail -n2)
fl=true
while IFS= read -r line
do
#echo $line
if [ "$fl" == "true" ]
then
prctg=$(echo "$line" | grep -Eo "[.[:digit:]]{1,10}%")
result="$result,$prctg"
fl=false
# prctg=100.0%
else
if [ "$prctg" == "100.0%" ]
then
result="$result,-1,-1,-1,-1"
else
result="$result,$(echo "$line" | cut -d' ' -f4 | sed -E 's/\//,/g')"
fi
fi
done <<< "$pingOutput"
echo "$result"
I hope it helps someone from the future! :)
Since the second line of the pingOutput was never processed (the loop ended before) the action of adding the -1 to the output was never performed.
Due to this problem I decided to capture the percentage of failure and act when no packets were returned (100%), I also simplified some expressions you used initially.
I investigated the script and came up with the following solution:
#!/bin/bash
declare site=''
declare result=''
declare prctg=''
[[ "$1" == "www."* ]] && site="$1" || site="www.$1"
result="$site"
pingOutput=$(ping $site -c10 -i0.2 -q| tail -n2)
fl=true
while IFS= read -r line
do
# !!! The problem is here, the if statement is not working properly and I do not know why !!!
echo $line
if [ "$fl" == "true" ]
then
prctg=$(echo "$line" | grep -Po "[0-9]{0,3}(?=%)")
result="$result $prctg"
fl=false
fi
if [ "$prctg" == "100" ]
then
result="$result -1 -1 -1 -1"
else
result="$result $(echo "$line" | cut -d' ' -f4 | sed -r 's/\// /g')"
fi
done <<< "$pingOutput"
echo "$result"
I have the following code
for ip in $(ifconfig | awk -F ":" '/inet addr/{split($2,a," ");print a[1]}')
do
bytesin=0; bytesout=0;
while read line
do
if [[ $(echo ${line} | awk '{print $1}') == ${ip} ]]
then
increment=$(echo ${line} | awk '{print $4}')
bytesout=$((${bytesout} + ${increment}))
else
increment=$(echo ${line} | awk '{print $4}')
bytesin=$((${bytesin} + ${increment}))
fi
done < <(pmacct -s | grep ${ip})
echo "${ip} ${bytesin} ${bytesout}" >> /tmp/bwacct.txt
done
Which I would like to print the incremented values to bwacct.txt, but instead the file is full of zeroes:
91.227.223.66 0 0
91.227.221.126 0 0
127.0.0.1 0 0
My understanding of Bash is that a redirected for loop should preserve variables. What am I doing wrong?
First of all, simplify your script! Usually there are many better ways in bash. Also most of the time you can rely on pure bash solutions instead of running awk or other tools.
Then add some debbuging!
Here is a bit refactored script with debugging
#!/bin/bash
for ip in "$(ifconfig | grep -oP 'inet addr:\K[0-9.]+')"
do
bytesin=0
bytesout=0
while read -r line
do
read -r subIp _ _ increment _ <<< "$line"
if [[ $subIp == "$ip" ]]
then
((bytesout+=increment))
else
((bytesin+=increment))
fi
# some debugging
echo "line: $line"
echo "subIp: $subIp"
echo "bytesin: $bytesin"
echo "bytesout: $bytesout"
done <<< "$(pmacct -s | grep "$ip")"
echo "$ip $bytesin $bytesout" >> /tmp/bwacct.txt
done
Much clearer now, huh? :)