I have a simple script with while loop, but cannot understand, why it breaks after first line, from $vault_list variable:
#!/bin/bash
tech_login="$1"
vault_list=$(docker exec -i tmgnt_vault_1 vault list secret/${tech_login}-terminals | sed 1,2d)
while IFS= read -r terminal
do
echo "line is $terminal"
key_values=$(docker exec -i tmgnt_vault_1 vault read secret/${tech_login}-terminals/$terminal )
done <<< "$vault_list"
If I remove $key_values from while loop, it returns all values in echo "line is $terminal".
Can anyone point me, what is the problem with while loop? I assume, that this can be a problem with output, but not sure.
Hopefully this will help others.
ssh might be the command that is eating stdin.
It was for me.
e.g. ssh inside a while loop was causing the loop to exit after first iteration.
LIST="cid1 10.10.0.1 host1
cid2 10.10.0.2 host1
cid3 10.10.0.3 host2"
# this while loop exits after first iteration
# ssh has eaten rest of stdin
echo "$LIST" |while read -r cid cip chost; do
echo $cid;
PSINFO=$(ssh $chost docker exec -i $cid "ps -e -orss=,pid=,args=,cmd=" |grep java );
echo PSINFO=$PSINFO;
done;
SOLVED by directing ssh to take stdin from /dev/null using </dev/null:
# this while loop keeps on running
# ssh directed to take stdin from /dev/null
echo "$LIST" |while read -r cid cip chost; do
echo $cid;
PSINFO=$(ssh $chost docker exec -i $cid "ps -e -orss=,pid=,args=,cmd=" </dev/null |grep java );
echo PSINFO=$PSINFO;
done;
With hint from #choroba I found right syntax for $key_values:
key_values=$(docker exec -i tmgnt_vault_1 vault read secret/${tech_login}-terminals/$terminal <<<$terminal)
I was need to pass the $terminal variable explicitly to the docker command, which can be done with a here-string, "<<
Related
I have a script which watches dmesg and kills a process after a specific log message
#!/bin/bash
while sleep 1;
do
# dmesg -w | grep --max-count=1 -q 'protocol'
dmesg -w | sed '/protocol/Q'
mkdir -p /home/user/dmesg/
eval "dmesg -T > /home/user/dmesg/dmesg-`date +%d_%m_%Y-%H:%M`.log";
eval "dmesg -c";
pkill -x -9 programm
done
The Problem is that sed as well as grep only trigger after two messages.
So the script will not continue after only one message.
Is there anything I am missing?
You have a script that periodically executes dmesg. Instead, write a script that watches the output of dmesg.
dmesg | while IFS= read -r line; do
case "$line" in
*protocol*)
echo "do something when line has protocol"
;;
esac
done
Consider reading https://mywiki.wooledge.org/BashFAQ/001 .
I'm trying to run this command over multiple machines
sshpass -p 'nico' ssh -o 'StrictHostKeyChecking=no' nico#x.x.x.x "mkdir test"
The IPs are stored in the following .txt file
$ cat ips.txt
10.0.2.15
10.0.2.5
I created a bash script that reads this file line by line. If I run it with an echo:
#!/bin/bash
input="ips.txt"
while IFS= read -r line
do
echo "$line"
#sshpass -p 'nico' ssh -o 'StrictHostKeyChecking=no' nico#$line "mkdir test"
done < "$input"
It prints every line:
$ ./variables.sh
10.0.2.15
10.0.2.5
This makes me understand that the script is working as intended. However, when I replace the echo line with the command I want to run for each line:
#!/bin/bash
input="ips.txt"
while IFS= read -r line
do
#echo "$line"
sshpass -p 'nico' ssh -o 'StrictHostKeyChecking=no' nico#$line "mkdir test"
done < "$input"
It only performs the action for the first IP on the file, then stops. Why?
Managed to solve this by using a for instead of a while. Script ended up looking like this:
for file in $(cat ips.txt)
do
sshpass -p 'nico' ssh -o 'StrictHostKeyChecking=no' nico#$file "mkdir test"
done
While your example is a solution that works, it's not the explanation.
Your could find the explanation here : ssh breaks out of while-loop in bash
In two words :
"while" loop continue reading from the same file-descriptor that defined in the loop header ( $input in your case )
ssh (or sshpass) read data from stdin (but in your case from file descriptor $input). And here is the point that hide the things as we didn't exect "ssh" to read the data.
Just to understand the problem you could have same strange experience for example using commands like "ffmpeg" or "mplayer" in while loop. Mplayer and ffmpeg use the keyboards while they are running, so they will consume all the the file-descriptor.
Another good and funny example :
#!/bin/bash
{
echo first
for ((i=0; i < 16384; i++)); do echo "testing"; done
echo "second"
} > test_file
while IFS= read -r line
do
echo "Read $line"
cat | uptime > /dev/null
done < test_file
At first part we write 1st line : first
16384 lines : testing
then last line : second
16384 lines "testing" are equal to 128Kb buffer
At the second part, the command "cat | uptime" will consume exactly 128Kb buffer, so our script will give
Read first
Read second
As solution, as you did, we could use "for" loop.
Or use "ssh -n"
Or playing with some file descriptor - you could find the example in the link that I gave.
Here is the chunk of code for reference:-
Output:
I have checked the variable values using echo and those looks fine.
But what I want do achieve is searching logs on remote hosts using grep which does not give any output.
for dir in ${log_path}
do
for host in ${Host}
do
if [[ "${userinputserverhost}" == "${host}" ]]
then
ssh -q -T username#userinputserverhost "bash -s" <<-'EOF' 2>&1 | tee -a ${LogFile}
echo -e "Fetching details: \n"
`\$(grep -A 5 -s "\${ID}" "\${dir}"/archive/*.log)`
EOF
fi
break
done
done
First, remove all the crap around the grep.
Second, you're overquoting your vars.
Third, skip the "bash -s" if you can.
ssh -q -T username#userinputserverhost <<-'EOF' 2>&1 | tee -a ${LogFile}
echo -e "Fetching details: \n"
grep -A 5 -s "${ID}" "${dir}"/archive/*.log
EOF
Fourth, I don't see where $ID is set...so if that's being loaded on the remote system by the login or something, then that one would need the dollar sign backslashed.
Finally, be aware that here-docs are great, but sometimes here-strings are simpler if you can spare the quotes.
$: ssh 2>&1 dudeling#sandbox-server '
> date
> whoami
> ' | tee -a foo.txt
Fri Apr 30 09:23:09 EDT 2021
dudeling
$: cat foo.txt
Fri Apr 30 09:23:09 EDT 2021
dudeling
That one is more a matter of taste. Even better, if you can, write your remote-script to a local file & use that. And of course, you can always add set -vx into the script to see what gets remotely executed.
cat >tmpScript <<-'EOF'
echo -e "Fetching details: \n"
set -vx
grep -A 5 -s "${ID}" "${dir}"/archive/*.log
EOF
ssh <tmpScript 2>&1 -q -T username#userinputserverhost | tee -a ${LogFile}
Now you have an exact copy of what was issued for debugging.
Thanks Paul for spending time and coming up with suggestions/solutions.
I have managed to get it working couple of days back. Would have felt happy to say that your solution worked 100% but even satisfied that I got it sorted on my own as it helped me learn some new stuff.
FYI - grep -A 5 -s "${ID}" "${dir}"/archive/*.log - this will work but only by using shell built-in 'declare -p' to declare the variables within EOF. Also, I read somewhere and it is recommended to use EOF unqouted as it caters variable expansion to remote hosts without any trouble.
Below piece of code is working for me in bash:
ssh -q -T username#userinputserverhost <<-EOF 2>&1 | tee -a ${LogFile}
echo -e "Fetching details: \n"
$(declare -p ID)
$(declare -p dir)
grep -A 5 -s "${ID}" "${dir}"/archive/*.log
EOF
I was trying to break a loop I created with
ctrl+C while reading a file.
Instead it was just stopping the specific iteration and not
the whole loop.
How can I stop it completely instead of having to ctrl+C all the iterations?
The whole script can be found here
An example file is like that:
echo -e "SRR7637893\nSRR7637894\nSRR7637895\nSRR7637896" > filenames.txt
The specific code chunk that probably makes the issue is the while loop here(set -xv; has been added afterwards as suggested from markp-fuso in comments):
set -xv;
while read -r line; do
echo "Now downloading "${line}"\n"
docker run --rm -v "$OUTPUT_DIR":/data -w /data inutano/sra-toolkit:v2.9.2 fasterq-dump "${line}" -t /data/shm -e $PROCESSORS
if [[ -s $OUTPUT_DIR/${line}.fastq ]]; then
echo "Using pigz on ${line}.fastq"
pigz --best $OUTPUT_DIR/"${line}*.fastq"
else
echo "$OUTPUT_DIR/${line}.fastq not found"
fi
done < "$INPUT_txt"; set +xv
I'm working on a simple bash script daemon that uses Unix domain sockets. I have a loop like this:
#!/bin/bash
while true
do
rm /var/run/mysock.sock
command=`nc -Ul /var/run/mysock.sock`
echo $command > /tmp/command
done
I'm echoing the command out to /tmp/command just for debugging purposes.
Is this the best way to do this?
Looks like I'm late to the party. Anyway, here is my suggestion I employ successfully for one-shot messages with response:
INPUT=$(mktemp -u)
mkfifo -m 600 "$INPUT"
OUTPUT=$(mktemp -u)
mkfifo -m 600 "$OUTPUT"
(cat "$INPUT" | nc -U "$SKT_PATH" > "$OUTPUT") &
NCPID=$!
exec 4>"$INPUT"
exec 5<"$OUTPUT"
echo "$POST_LINE" >&4
read -u 5 -r RESPONSE;
echo "Response: '$RESPONSE'"
Here I use two FIFOs to talk to nc (1) and fetch it's response.
You can use a single file also to use bidirectional.
mkfifo communicate_pipe
exec 3<> communicate_pipe
cat communicate_pipe - | python socket.py 127.0.0.1:8002 | while read line; do
cmd="./something.sh '${line}' > communicate_pipe";
eval $cmd;
fi;
done