i have an issue with my bash script
t='Hostname\cfg;'
echo "Header" > $DST
for i in *
do
t="$i;"
egrep -v "(^$|^#)" $IPLIST | while read ii
do
if grep -q "$ii" $i
then
t=$t"y;"
else
t=$t"n;"
fi
echo "$t"
done
echo "x$t"
n=$(($n + 1))
echo "$n"
#echo "$ii;$t" # >> $DST
#t=""
done
Produces the following output:
h0010001.conf;y;
h0010001.conf;y;y;
<ommited>
h0010001.conf;y;y;y;y;y;y;y;y;y;y;y;y;y;y;y;y;y;y;y;y;n;n;y;y;y;y;y;y;y;y;y;y;y;y;n;y;y;y;y;y;y;n;y;y;y;y;y;y;y;y;y;n;n;
xh0010001.conf;
So for some reason the t Variable is empty after the inner loop has completed.
What I want to achieve is, to write t - after the second loop into a file.
#Barmar was spot on. Here's a typical workaround.
Change the while loop to run in the parent shell:
while read ii
do
if grep -q "$ii" $i
then
t=$t"y;"
else
t=$t"n;"
fi
echo "$t"
done < <(egrep -v "(^$|^#)" $IPLIST)
Related
Running another script in bash script while loop runs but the loop breaks!
N.B. The script I mentioned just loops over files in current directory and just run mpirun.
Here's my bash script:
#!/bin/bash
np="$1"
bin="$2"
ref="$3"
query="$4"
word_size="$5"
i=1;
input="$query"
while read line; do
echo $line
if [[ "${line:0:1}" == ">" ]] ; then
header="$line"
echo "$header" >> seq_"${i}".fasta
else
seq="$line"
echo "$seq" >> seq_"${i}".fasta
if ! (( i % 5)) ; then
./run.sh $np $bin $ref $word_size
^^^^^^^^
#for filename in *.fasta; do
# mpirun -np "${np}" "${bin}" -d "${ref}" -ql "${filename}" -k "${word_size}" -b > log
# rm $filename
#done
fi
((i++))
fi
done < $input
The problem is that your run.sh script is passing no parameters to mpirun. That script passes the variables ${np} ${bin} ${ref} ${filename} ${word_size} to mpirun, but those variables are local to your main script and are undefined in run.sh. You could export those variables in the main script so that they are available to all child processes, but a better solution would be to use positional parameters in run.sh:
for filename in *.fasta; do
mpirun -np "${1}" "${2}" -d "${3}" -ql "${4}" -k "${5}" -b > log
rm $filename
done
I don't know about mpirun, but if you have anything inside your loop that reads from stdin, the loop will break.
Please explain to me why the very last echo statement is blank? I expect that XCODE is incremented in the while loop to a value of 1:
#!/bin/bash
OUTPUT="name1 ip ip status" # normally output of another command with multi line output
if [ -z "$OUTPUT" ]
then
echo "Status WARN: No messages from SMcli"
exit $STATE_WARNING
else
echo "$OUTPUT"|while read NAME IP1 IP2 STATUS
do
if [ "$STATUS" != "Optimal" ]
then
echo "CRIT: $NAME - $STATUS"
echo $((++XCODE))
else
echo "OK: $NAME - $STATUS"
fi
done
fi
echo $XCODE
I've tried using the following statement instead of the ++XCODE method
XCODE=`expr $XCODE + 1`
and it too won't print outside of the while statement. I think I'm missing something about variable scope here, but the ol' man page isn't showing it to me.
Because you're piping into the while loop, a sub-shell is created to run the while loop.
Now this child process has its own copy of the environment and can't pass any
variables back to its parent (as in any unix process).
Therefore you'll need to restructure so that you're not piping into the loop.
Alternatively you could run in a function, for example, and echo the value you
want returned from the sub-process.
http://tldp.org/LDP/abs/html/subshells.html#SUBSHELL
The problem is that processes put together with a pipe are executed in subshells (and therefore have their own environment). Whatever happens within the while does not affect anything outside of the pipe.
Your specific example can be solved by rewriting the pipe to
while ... do ... done <<< "$OUTPUT"
or perhaps
while ... do ... done < <(echo "$OUTPUT")
This should work as well (because echo and while are in same subshell):
#!/bin/bash
cat /tmp/randomFile | (while read line
do
LINE="$LINE $line"
done && echo $LINE )
One more option:
#!/bin/bash
cat /some/file | while read line
do
var="abc"
echo $var | xsel -i -p # redirect stdin to the X primary selection
done
var=$(xsel -o -p) # redirect back to stdout
echo $var
EDIT:
Here, xsel is a requirement (install it).
Alternatively, you can use xclip:
xclip -i -selection clipboard
instead of
xsel -i -p
I got around this when I was making my own little du:
ls -l | sed '/total/d ; s/ */\t/g' | cut -f 5 |
( SUM=0; while read SIZE; do SUM=$(($SUM+$SIZE)); done; echo "$(($SUM/1024/1024/1024))GB" )
The point is that I make a subshell with ( ) containing my SUM variable and the while, but I pipe into the whole ( ) instead of into the while itself, which avoids the gotcha.
#!/bin/bash
OUTPUT="name1 ip ip status"
+export XCODE=0;
if [ -z "$OUTPUT" ]
----
echo "CRIT: $NAME - $STATUS"
- echo $((++XCODE))
+ export XCODE=$(( $XCODE + 1 ))
else
echo $XCODE
see if those changes help
Another option is to output the results into a file from the subshell and then read it in the parent shell. something like
#!/bin/bash
EXPORTFILE=/tmp/exportfile${RANDOM}
cat /tmp/randomFile | while read line
do
LINE="$LINE $line"
echo $LINE > $EXPORTFILE
done
LINE=$(cat $EXPORTFILE)
I am trying to do the following in bash:
get my external IP
read first line of a file
compare both values
if it is not the same, delete the file and recreate it with the current address
I really don't know why this fails, all my script does is to output my current address and the first line of the file (which by the way is simply "asd" for testing)
#!/bin/bash
IP= curl http://ipecho.net/plain
OLD= head -n 1 /Users/emse/Downloads/IP/IP.txt
if [ "$IP" = "$OLD" ]; then
exit
else
rm /Users/emse/Downloads/IP/IP.txt
$IP> /Users/emse/Downloads/IP/IP.txt
exit
fi
Some obvious problems in your script:
Don't put spaces on either side of equal sign if you want to do assignment
You want the output of curl, head so wrap them in backticks (`)
You want to write $IP into the file, not to execute the content of it as a command, so echo it
The script becomes:
#!/bin/bash
IP=`curl http://ipecho.net/plain`
OLD=`head -n 1 /Users/emse/Downloads/IP/IP.txt`
if [ "$IP" = "$OLD" ]; then
exit
else
rm /Users/emse/Downloads/IP/IP.txt
echo $IP > /Users/emse/Downloads/IP/IP.txt
exit
fi
Excellent answer qingbo, just a tad bit of refinement:
#!/bin/bash
IP=`curl http://ipecho.net/plain`
OLD=`head -n 1 /Users/emse/Downloads/IP/IP.txt`
if [ "$IP" != "$OLD" ]; then
echo $IP > /Users/emse/Downloads/IP/IP.txt # > creates/truncates/replaces IP.txt
fi
I'm trying to merge the second field of the csv with all the id's in the diff file. codes.csv has 2 fields: ID,Description. I keep getting an error on the second cat.
cat: codes.cvs: No such file or directory.
The file does exist and I'm running the script from the same directory as codes.csv.
for i in `cat diff.txt`;
do
for j in `cat codes.cvs`;
do
id = `sed "$j"`;
desc = `sed "?=$j"`;
if [$i == $id]
then
echo "$id $desc"
fi
done;
done;
Any ideas what I am doing wrong here?
Looks like a simple typo. codes.cvs should be codes.csv as you indicated the name was everywhere else.
for i in `cat diff.txt`;
do
for j in `cat codes.csv`;
do
id=`sed "$j"`;
desc=`sed "?=$j"`;
if [ $i == $id ]
then
echo "$id $desc"
fi
done;
done;
Please explain to me why the very last echo statement is blank? I expect that XCODE is incremented in the while loop to a value of 1:
#!/bin/bash
OUTPUT="name1 ip ip status" # normally output of another command with multi line output
if [ -z "$OUTPUT" ]
then
echo "Status WARN: No messages from SMcli"
exit $STATE_WARNING
else
echo "$OUTPUT"|while read NAME IP1 IP2 STATUS
do
if [ "$STATUS" != "Optimal" ]
then
echo "CRIT: $NAME - $STATUS"
echo $((++XCODE))
else
echo "OK: $NAME - $STATUS"
fi
done
fi
echo $XCODE
I've tried using the following statement instead of the ++XCODE method
XCODE=`expr $XCODE + 1`
and it too won't print outside of the while statement. I think I'm missing something about variable scope here, but the ol' man page isn't showing it to me.
Because you're piping into the while loop, a sub-shell is created to run the while loop.
Now this child process has its own copy of the environment and can't pass any
variables back to its parent (as in any unix process).
Therefore you'll need to restructure so that you're not piping into the loop.
Alternatively you could run in a function, for example, and echo the value you
want returned from the sub-process.
http://tldp.org/LDP/abs/html/subshells.html#SUBSHELL
The problem is that processes put together with a pipe are executed in subshells (and therefore have their own environment). Whatever happens within the while does not affect anything outside of the pipe.
Your specific example can be solved by rewriting the pipe to
while ... do ... done <<< "$OUTPUT"
or perhaps
while ... do ... done < <(echo "$OUTPUT")
This should work as well (because echo and while are in same subshell):
#!/bin/bash
cat /tmp/randomFile | (while read line
do
LINE="$LINE $line"
done && echo $LINE )
One more option:
#!/bin/bash
cat /some/file | while read line
do
var="abc"
echo $var | xsel -i -p # redirect stdin to the X primary selection
done
var=$(xsel -o -p) # redirect back to stdout
echo $var
EDIT:
Here, xsel is a requirement (install it).
Alternatively, you can use xclip:
xclip -i -selection clipboard
instead of
xsel -i -p
I got around this when I was making my own little du:
ls -l | sed '/total/d ; s/ */\t/g' | cut -f 5 |
( SUM=0; while read SIZE; do SUM=$(($SUM+$SIZE)); done; echo "$(($SUM/1024/1024/1024))GB" )
The point is that I make a subshell with ( ) containing my SUM variable and the while, but I pipe into the whole ( ) instead of into the while itself, which avoids the gotcha.
#!/bin/bash
OUTPUT="name1 ip ip status"
+export XCODE=0;
if [ -z "$OUTPUT" ]
----
echo "CRIT: $NAME - $STATUS"
- echo $((++XCODE))
+ export XCODE=$(( $XCODE + 1 ))
else
echo $XCODE
see if those changes help
Another option is to output the results into a file from the subshell and then read it in the parent shell. something like
#!/bin/bash
EXPORTFILE=/tmp/exportfile${RANDOM}
cat /tmp/randomFile | while read line
do
LINE="$LINE $line"
echo $LINE > $EXPORTFILE
done
LINE=$(cat $EXPORTFILE)