Hi I'm creating a bash script to improve my job. If I have some files in a directory such as
file1.dat
file2.dat
file3.dat
file1.inp
file2.inp
file3.fal
I must digit in a shell the following command
PBS_nastran ver=20101 mem=48Gb mod=i8 i=file1.dat
PBS_nastran ver=20101 mem=48Gb mod=i8 i=file2.dat
PBS_nastran ver=20101 mem=48Gb mod=i8 i=file3.dat
PBS_abaqus ver=6133 ncpu=16 j=file1.inp
PBS_abaqus ver=6133 ncpu=16 j=file2.inp
PBS_falancs j=file1.fal
I've created a symple script
code='nastran'
case $code in
abaqus) command="PBS_abaqus ver=6133 ncpu=16 j="
ext=".inp";;
nastran) command="PBS_nastran ver=20101 mem=48Gb mod=i8 i="
ext=".dat";;
falancs) command="PBS_falancs j="
ext=".fal";;
esac
file_list=$(ls * | grep "$ext$")
file_list=${file_list//"./"/}
file_list=$(echo $file_list | tr " " "\n")
for file in $file_list
do
command=$command$file
eval $command
done
this it's ok and work correctly. The next step in a optimization process it's to put the code in a *.sh file and I create this
#!/bin/bash
case $1 in
abaqus) command='PBS_abaqus ver=6133 ncpu=$3 j='
ext='.inp';;
nastran) command='PBS_nastran ver=20101 mem=48Gb mod=i8 i='
ext='.dat';;
falancs) command='PBS_falancs j='
ext='.fal';;
esac
if [ -z $2 ]
then
file_list=$(ls | grep -E "[0-9]{8}_[[:alnum:]].*_RUN_[[:alnum:]].*${ext}$")
file_list=${file_list//"./"/}
file_list=$(echo $file_list | tr " " "\n")
else
file_list=$2
fi
for file in $file_list
do
command=$command$file
eval "$command"
done
but if I lunch script "./script.sh nastran" there is an error:
./lancia.sh: line26: PBS_nastran: command not found
I think that the problem is in the interpretation of blank space but I don't understand the way to fix it.
Thank for your help
You should rarely need to use eval, and this is no exception. You can store a command name in a variable, but you should not store an entire command line. Put the arguments in an array to ensure they remain properly quoted.
Also, do not try to parse the output of ls; use patterns to match the files you want. (It is unfortunate, though, that you can't use bracket expressions like {8} with patterns.)
#!/bin/bash
num_cpus=${3:-1}
case $1 in
abaqus)
cmd_name=PBS_abaqus
cmd_options=( ver=6133 "ncpu=$num_cpus")
file_option="j"
ext='.inp'
;;
nastran)
cmd_name=PBS_nastran
cmd_options=( ver=20101 mem=48Gb mod=i8)
file_option="i"
ext='.dat'
;;
falancs)
cmd_name=PBS_falancs
cmd_options=()
file_option="j"
ext='.fal'
;;
*) echo "Unrecognized name '$1', aborting" >&2
exit 1
esac
if [ -z "$2" ]; then
file_list=( [[:digit:]][[:digit:]][[:digit:]][[:digit:]][[:digit:]][[:digit:]][[:digit:]][[:digit:]]_[[:alnum:]]*_RUN_[[:alnum:]]*$ext )
else
file_list=( $2 ) # I'm assuming here $2 is intended to be a pattern
fi
for file in "${file_list[#]}"; do
do
"$cmd_name" "${cmd_options[#]}" "$file_option=$file"
done
Related
Here is the code, I want to run this command
Getting the test.log input, then convert it to text type, then store it on the output.txt file
./small.sh test.log -t text -o output.txt
#!/usr/bin/env bash
usage() { echo "$0 usage:" && grep " .)\ #" $0; exit 0; }
[ $# -eq 0 ] && usage
parse()
{
local file=$1
local type=$2
local output=$3
echo "file: ${file}, type: ${type}, output: ${output}"
}
while getopts ":ht:o:" arg; do
case $arg in
t) # specify type.
type=${OPTARG} ;;
o) # specify directory.
output=${OPTARG} ;;
h | *) # Display help.
usage
exit 0
;;
esac
done
shift $(( OPTIND - 1))
parse "${file}" "${type}" "${output}"
with this code i can only get filename when i put it in unsort order like this
./small.sh -t text -o output.txt test.log
How can I get filename and argument with getopts
./small.sh test.log -t text -o output.txt
It is not possible. getopts only supports positional arguments after option arguments.
You can:
accept the limitation
use something elsem, like GNU getopt.
write your own option parsing code
I want to create a utility function for bash to remove duplicate lines. I am using function
function remove_empty_lines() {
if ! command -v awk &> /dev/null
then
echo '[x] ERR: "awk" command not found'
return
fi
if [[ -z "$1" ]]
then
echo "usage: remove_empty_lines <file-name> [--replace]"
echo
echo "Arguments:"
echo -e "\t--replace\t (Optional) If not passed, the result will be redirected to stdout"
return
fi
if [[ ! -f "$1" ]]
then
echo "[x] ERR: \"$1\" file not found"
return
fi
echo $0
local CMD="awk '!seen[$0]++' $1"
if [[ "$2" = '--reload' ]]
then
CMD+=" > $1"
fi
echo $CMD
}
If I am running the main awk command directly, it is working. But when i execute the same $CMD in the function, I am getting this error
$ remove_empty_lines app.js
/bin/bash
awk '!x[/bin/bash]++' app.js
The original code is broken in several ways:
When used with --reload, it would truncate the output file's contents before awk could ever read those contents (see How can I use a file in a command and redirect output to the same file without truncating it?)
It didn't ever actually run the command, and for the reasons described in BashFAQ #50, storing a shell command in a string is inherently buggy (one can work around some of those issues with eval; BashFAQ #48 describes why doing so introduces security bugs).
It wrote error messages (and other "diagnostic content") to stdout instead of stderr; this means that if your function's output was redirected to a file, you could never see its errors -- they'd end up jumbled into the output.
Error cases were handled with a return even in cases where $? would be zero; this means that return itself would return a zero/successful/truthy status, not revealing to the caller that any error had taken place.
Presumably the reason you were storing your output in CMD was to be able to perform a redirection conditionally, but that can be done other ways: Below, we always create a file descriptor out_fd, but point it to either stdout (when called without --reload), or to a temporary file (if called with --reload); if-and-only-if awk succeeds, we then move the temporary file over the output file, thus replacing it as an atomic operation.
remove_empty_lines() {
local out_fd rc=0 tempfile=
command -v awk &>/dev/null || { echo '[x] ERR: "awk" command not found' >&2; return 1; }
if [[ -z "$1" ]]; then
printf '%b\n' >&2 \
'usage: remove_empty_lines <file-name> [--replace]' \
'' \
'Arguments:' \
'\t--replace\t(Optional) If not passed, the result will be redirected to stdout'
return 1
fi
[[ -f "$1" ]] || { echo "[x] ERR: \"$1\" file not found" >&2; return 1; }
if [ "$2" = --reload ]; then
tempfile=$(mktemp -t "$1.XXXXXX") || return
exec {out_fd}>"$tempfile" || { rc=$?; rm -f "$tempfile"; return "$rc"; }
else
exec {out_fd}>&1
fi
awk '!seen[$0]++' <"$1" >&$out_fd || { rc=$?; rm -f "$tempfile"; return "$rc"; }
exec {out_fd}>&- # close our file descriptor
if [[ $tempfile ]]; then
mv -- "$tempfile" "$1" || return
fi
}
First off the output from your function call is not an error but rather the output of two echo commands (echo $0 and echo $CMD).
And as Charles Duffy has pointed out ... at no point is the function actually running the $CMD.
As for the inclusion of /bin/bash in your function's echo output ... the main problem is the reference to $0; by definition $0 is the name of the running process, which in the case of a function is the shell under which the function is being called. Consider the following when run from a bash command prompt:
$ echo $0
-bash
As you can see from your output this generates /bin/bash in your environment. See this and this for more details.
On a related note, the reference to $0 within double quotes causes the $0 to be evaluated, so this:
local CMD="awk '!seen[$0]++' $1"
becomes
local CMD="awk '!seen[/bin/bash]++' app.js"
I'm thinking what you want is something like:
echo $1 # the name of the file to be processed
local CMD="awk '!seen[\$0]++' $1" # escape the '$' in '$0'
becomes
local CMD="awk '!seen[$0]++' app.js"
That should fix the issues shown in your function's output; as for the other issues ... you're getting a good bit of feedback in the various comments ...
Please explain to me why the very last echo statement is blank? I expect that XCODE is incremented in the while loop to a value of 1:
#!/bin/bash
OUTPUT="name1 ip ip status" # normally output of another command with multi line output
if [ -z "$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 $EXPORTFILE)
How do I check if file exists in bash?
When I try to do it like this:
FILE1="${#:$OPTIND:1}"
if [ ! -e "$FILE1" ]
then
echo "requested file doesn't exist" >&2
exit 1
elif
<more code follows>
I always get following output:
requested file doesn't exist
The program is used like this:
script.sh [-g] [-p] [-r FUNCTION_ID|-d FUNCTION_ID] FILE
Any ideas please?
I will be glad for any help.
P.S. I wish I could show the entire file without the risk of being fired from school for having a duplicate. If there is a private method of communication I will happily oblige.
My mistake. Fas forcing a binary file into a wrong place. Thanks for everyone's help.
Little trick to debugging problems like this. Add these lines to the top of your script:
export PS4="\$LINENO: "
set -xv
The set -xv will print out each line before it is executed, and then the line once the shell interpolates variables, etc. The $PS4 is the prompt used by set -xv. This will print the line number of the shell script as it executes. You'll be able to follow what is going on and where you may have problems.
Here's an example of a test script:
#! /bin/bash
export PS4="\$LINENO: "
set -xv
FILE1="${#:$OPTIND:1}" # Line 6
if [ ! -e "$FILE1" ] # Line 7
then
echo "requested file doesn't exist" >&2
exit 1
else
echo "Found File $FILE1" # Line 12
fi
And here's what I get when I run it:
$ ./test.sh .profile
FILE1="${#:$OPTIND:1}"
6: FILE1=.profile
if [ ! -e "$FILE1" ]
then
echo "requested file doesn't exist" >&2
exit 1
else
echo "Found File $FILE1"
fi
7: [ ! -e .profile ]
12: echo 'Found File .profile'
Found File .profile
Here, I can see that I set $FILE1 to .profile, and that my script understood that ${#:$OPTIND:1}. The best thing about this is that it works on all shells down to the original Bourne shell. That means if you aren't running Bash as you think you might be, you'll see where your script is failing, and maybe fix the issue.
I suspect you might not be running your script in Bash. Did you put #! /bin/bash on the top?
script.sh [-g] [-p] [-r FUNCTION_ID|-d FUNCTION_ID] FILE
You may want to use getopts to parse your parameters:
#! /bin/bash
USAGE=" Usage:
script.sh [-g] [-p] [-r FUNCTION_ID|-d FUNCTION_ID] FILE
"
while getopts gpr:d: option
do
case $option in
g) g_opt=1;;
p) p_opt=1;;
r) rfunction_id="$OPTARG";;
d) dfunction_id="$OPTARG";;
[?])
echo "Invalid Usage" 1>&2
echo "$USAGE" 1>&2
exit 2
;;
esac
done
if [[ -n $rfunction_id && -n $dfunction_id ]]
then
echo "Invalid Usage: You can't specify both -r and -d" 1>&2
echo "$USAGE" >2&
exit 2
fi
shift $(($OPTIND - 1))
[[ -n $g_opt ]] && echo "-g was set"
[[ -n $p_opt ]] && echo "-p was set"
[[ -n $rfunction_id ]] && echo "-r was set to $rfunction_id"
[[ -n $dfunction_id ]] && echo "-d was set to $dfunction_id"
[[ -n $1 ]] && echo "File is $1"
To (recap) and add to #DavidW.'s excellent answer:
Check the shebang line (first line) of your script to ensure that it's executed by bash: is it #!/bin/bash or #!/usr/bin/env bash?
Inspect your script file for hidden control characters (such as \r) that can result in unexpected behavior; run cat -v scriptFile | fgrep ^ - it should produce NO output; if the file does contain \r chars., they would show as ^M.
To remove the \r instances (more accurately, to convert Windows-style \r\n newline sequences to Unix \n-only sequences), you can use dos2unix file to convert in place; if you don't have this utility, you can use sed 's/'$'\r''$//' file > outfile (CAVEAT: use a DIFFERENT output file, otherwise you'll destroy your input file); to remove all \r instances (even if not followed by \n), use tr -d '\r' < file > outfile (CAVEAT: use a DIFFERENT output file, otherwise you'll destroy your input file).
In addition to #DavidW.'s great debugging technique, you can add the following to visually inspect all arguments passed to your script:
i=0; for a; do echo "\$$((i+=1))=[$a]"; done
(The purpose of enclosing the value in [...] (for example), is to see the exact boundaries of the values.)
This will yield something like:
$1=[-g]
$2=[input.txt]
...
Note, though, that nothing at all is printed if no arguments were passed.
Try to print FILE1 to see if it has the value you want, if it is not the problem, here is a simple script (site below):
#!/bin/bash
file="${#:$OPTIND:1}"
if [ -f "$file" ]
then
echo "$file found."
else
echo "$file not found."
fi
http://www.cyberciti.biz/faq/unix-linux-test-existence-of-file-in-bash/
Instead of plucking an item out of "$#" in a tricky way, why don't you shift off the args you've processed with getopts:
while getopts ...
done
shift $(( OPTIND - 1 ))
FILE1=$1
Please explain to me why the very last echo statement is blank? I expect that XCODE is incremented in the while loop to a value of 1:
#!/bin/bash
OUTPUT="name1 ip ip status" # normally output of another command with multi line output
if [ -z "$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)