I'm in the final stages of a project and need to create a script that will run an executable a given number of times with varying input. One of the inputs is a file kept in a separate folder from the executable.
Before doing anything, I want to check whether the file exists. There are two possible file inputs that can be given, so I need to compare them. The possible inputs are
execute cancer 9
execute promoter 9
where cancer and promoters are the datasets to be used in the program and 9 is the number of times the script loop has to execute.
Here's what I've come up with:
#!/bin/bash
#Shell script to execute Proj 4 requirements while leaving the folder
#structure alone separated.
file1= "Data/BC/bc80-train-1"
file2= "Data/Promoters/p80-train-1"
if [ "$1" == "cancer" ] then #execute command on the cancer dataset
echo "Executing on the cancer dataset"
if [ -f "$file1" ] then
echo "$file1 file exists..."
else
echo "$file1 file Missing, cancelling execution"
echo "Dataset must be in ../Data/BC/ and file must be bc80-train-1"
fi
elif [ "$1" == "promoter" ] then #execute on the promoter dataset
echo "Executing on the promoter dataset"
if [ -f "$file2"] then
echo "$file2 file exists..."
else
echo "$file2 file missing, cancelling execution"
echo "Dataset must be in ~/Data/Promoters/ and file must be p80-train-1"
fi
fi
The problem with this is it opens the files and outputs them to terminal, where each line ends in : command not found
I thought the -f and -e flags were used to check whether a file exists. So why is the file content being output to the terminal?
Drop the space to the right of = in:
file1= "Data/BC/bc80-train-1"
file2= "Data/Promoters/p80-train-1"
Also the keyword then should be on a line by itself or if on the same line as if should have a ; before it:
if [ condition ] ; then
...
fi
OR
if [ condition ]
then
...
fi
Your error messages mix ../Data/ and ~/Data/, but your file1 and file2 don't have either .. or ~ in their definitions:
file1= "Data/BC/bc80-train-1"
file2= "Data/Promoters/p80-train-1"
Remove the space after the = in file1= and file2=
Don't repeat yourself, use a function:
#!/bin/bash
checkfile() {
echo "Executing on the $1 dataset"
file="$2/$3"
if [ -f "$file" ] then
echo "$file file exists..."
else
echo "$file file Missing, cancelling execution"
echo "Dataset must be in $2 and file must be $3"
fi
}
case $1 in
cancer)
checkfile $1 Data/BC bc80-train-1
;;
promoter)
checkfile $1 Data/Promoters p80-train-1
;;
*)
echo "Error: unknown dataset. Use 'cancer' or 'promoter'"
;;
esac
Related
So I started today taking a look at scripting using vim and I'm just so very lost and was looking for some help in a few areas.
For my first project,I want to process a file as a command line argument, and if a file isn't included when the user executes this script, then a usage message should be displayed, followed by exiting the program.
I have no clue where to even start with that, will I need and if ... then statement, or what?
Save vim for later and try to learn one thing at a time. A simpler text editor is called nano.
Now, as far as checking for a file as an argument, and showing a usage message otherwise, this is a typical pattern:
PROGNAME="$0"
function show_usage()
{
echo "Usage: ${PROGNAME} <filename>" >&2
echo "..." >&2
exit 1
}
if [[ $# -lt 1 ]]; then
show_usage
fi
echo "Contents of ${1}:"
cat "$1"
Let's break this down.
PROGNAME="$0"
$0 is the name of the script, as it was called on the command line.
function show_usage()
{
echo "Usage: ${PROGNAME} <filename>" >&2
echo "..." >&2
exit 1
}
This is the function that prints the "usage" message and exits with a failure status code. 0 is success, anything other than 0 is a failure. Note that we redirect our echo to &2--this prints the usage message on Standard Error rather than Standard Output.
if [[ $# -lt 1 ]]; then
show_usage
fi
$# is the number of arguments passed to the script. If that number is less than 1, print the usage message and exit.
echo "Contents of ${1}:"
cat "$1"
$1 is out filename--the first argument of the script. We can do whatever processing we want to here, with $1 being the filename. Hope this helps!
i think you're asking how to write a bash script that requires a file as a command-line argument, and exits with a usage message if there's a problem with that:
#!/bin/bash
# check if user provided exactly one command-line argument:
if [ $# -ne 1 ]; then
echo "Usage: `basename "$0"` file"
exit 1
# now check if the provided argument corresponds to a real file
elif [ ! -f "$1" ]; then
echo "Error: couldn't find $1."
exit 1
fi
# do things with the file...
stat "$1"
head "$1"
tail "$1"
grep 'xyz' "$1"
I have a shell script where I pass (2) parameters, one to pass a dbname, the other to call one of (2) filenames. I want to check if either filename exists, then proceed with calling that script, else exit because the user can enter the wrong string and construct my_foo.sql which I don't want. I don't think I have the condition for setting "or" correctly since putting the correct param still produces error. Is there a better way to write this?
Here is what I have so far.
#/usr/bin/ksh
if [ $# != 2 ]; then
echo "Usage: test.sh <dbname> <test|live>" 2>&1
exit 1
fi
# Check actual file name
CHKSCRIPT1=/tmp/my_test.sql;
CHKSCRIPT2=/tmp/my_live.sql;
if [ -f "CHKSCRIPT1" ] || [ -f "CHKSCRIPT2" ]
then
/bin/sqlplus -s foo/bar #/my_$2.sql
else
echo "Correct sql script does not exist. Enter test or live"
exit 1
fi
Your issue is that you're not referencing your variables correctly:
if [ -f "$CHKSCRIPT1" ] || [ -f "$CHKSCRIPT2" ]
...
fi
edit: Per #chepner, you shouldn't use -o
In addition to the problem you had with expanding the parameters, you should separate what the user types from what files need to exist. If the user enters "live", the only thing that matters is whether or not /tmp/my_live.sql exists. If the user enters "injection_attack", your script should not execute /tmp/my_injection_attack.sql (which presumably was created without your knowledge). The right thing to do is to first verify that a valid command was entered, then check if the appropriate file exists.
if [ $# != 2 ]; then
echo "Usage: test.sh <dbname> <test|live>" 2>&1
exit 1
fi
case $2 in
test|live)
filename="/tmp/my_{$2}.sql"
;;
*) echo "Must enter test or live"
exit 1
;;
esac
if [ -f "$filename" ]; then
/bin/sqlplus -s foo/bar #/my_$2.sql
else
echo "SQL script $filename does not exist."
exit 1
fi
How do I check if file exists in bash?
When I try to do it like this:
FILE1="${#:$OPTIND:1}"
if [ ! -e "$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
Create a script to backup a file or directory tree by making a zip of the file(s) and copying it $HOME/Backups. The zipfile name should include what it is backing up, and the date the file was created. The script should take a random number of arguments specifying what to backup. If it is not given at least one item to include in the backup, it should complain. Ive got most of it to work but im having issues with multiple files ie file1 file2 to backup at the same time
#!/bin/bash
clear
echo
echo "Use this script to backup files to your home/backups directory"
echo
ls -la
echo
echo "================================================================"
echo
echo -n "Input file(s)/dir to backup: " ; read filez
while [ "$filez" == "" ] ; do
echo -n "You didnt input a filename, try again: " ; read filez
done
while [ ! -e "$filez" ] ; do
echo -n "No such file/dir, try again: " ; read filez
while [ "$filez" == "" ] ; do
echo -n "You didnt input a filename, try again: " ; read filez
done
done
echo
echo "================================================================"
echo
echo -n "Input name of backup file you wish to create(date automatically included): " ; read filezname
while [ "$filezname" == "" ] ; do
echo -n "You didnt input a filename, try again: " ; read filezname
done
zip -r $HOME/backups/$filezname"_$(date +%F)" $filez
Personally, I'm a fan of bash scripts taking arguments right from the command line:
script arg1 arg2 arg3 ...
Bash takes arguments using the special array $#, and you can do arguments processing with shift. Something like this:
#!/bin/bash
filezname=$1
shift
filez=""
for file in "$#"
do
filez="$filez $file"
done
if [[ $filez == "" ]]
then
echo "Give me argz! Nom nom nom!"
exit 0
fi
# Do stuff
What this does is it takes the first argument, takes it as the name of the zip file, and then slurps the rest of the filenames you want to zip up into a big long space-separated string that you can play with.
I have below script but I can't find the error. Somebody an help me ?
In concrete I split a big file in different then compress any file, move it and send by ftp rename destination filename.
Something not work :(
in line:
put ${file} ${7}.T${j}(+1)
I try to rename the file with (+1) ended new filename
Kind regards
#!/bin/bash
# configuration stuff
# ${1} absolute path file
# ${2} num_files
# ${3} output_filename
# ${4} ipMainframe ip to put files
# ${5} FTP username
# ${6} FTP password
# ${7} destination filename
if [ ! $# == 7 ]; then
#number of parameter different of two
echo "Number of parameter incorrect"
echo "Command use: LLP_split_gzip_sendFTPandTrigger.sh absolute_path_file number_of_pieces output_filename ipMainframe userFTP pwdFTP destinationFilename"
exit 1
fi
if [ -f ${1} ]; then
# If file exists
if [[ ${2} =~ ^[\-0-9]+$ ]] && (( ${2} > 0)); then
# if number of pieces is an integer > 0
#Remove old files
echo "home directory = $HOME"
CMD=`rm -f '"$HOME"/"$3"*'`
if [ $? != 0 ]; then
echo "Impossible to remove old files $home/llp_tmp* $home/"$3"* in home directory"
echo $CMD
fi
# Calculate line for every file splitted
total_lines=$(cat ${1} | wc -l)
((lines_per_file = (total_lines + ${2} - 1) / ${2}))
# Split the actual file, maintaining lines.
CMD=`split -l "$lines_per_file" "$1" "$HOME"/llp_tmp`
if [ $? != 0 ]; then
echo "SPLITTING FILE ERROR: problem to split file."
echo $CMD
exit 3
fi
#For every file splitted rename and zip it
i=1
for file in $HOME/llp_tmp*; do
CMD=`mv "$file" "$3"."$i"`
if [ $? != 0 ]; then
echo "Impossible to rename file"
echo $CMD
exit 5
fi
CMD=`gzip "$3"."$i"`
if [ $? != 0 ]; then
echo "Impossible to compress file $3.$i"
echo $CMD
exit 6
fi
i=`expr $i + 1`
done
ftp -n ${4} << EOF
j=1
user ${5} ${6}
for file in $3.*; do
put ${file} ${7}.T${j}(+1)
j=`expr $j + 1`
done
quit
else
echo "number of pieces second parameter must be more than 0."
exit 2
fi
else
echo "absolute path first paramater doesnt exist"
exit 1
fi
exit 0
You are not terminating your here document. When I run your script I get:
gash.sh: line 72: warning: here-document at line 54 delimited by end-of-file (wanted `EOF')
gash.sh: line 73: syntax error: unexpected end of file
ftp -n ${4} << EOF is the issue. Where is your here document?
The warning says it all, you don't have an EOF marker. Note that this MUST NOT BE INDENTED! The EOF must be in "column 0" and have no trailing characters, including whitespace.
Edit: It appears you want to use program constructs within a single FTP session - I don't know of a way of doing that in Bash. Perl has an easy to use FTP module where you can do it, simple example:
use strict;
use Net::FTP;
my $ftp = Net::FTP->new ("hostname");
$ftp->login ("username", "password");
$ftp->binary ();
for my $file (glob("$ENV{HOME}/llp_tmp*")) {
$ftp->put ($file);
}
$ftp->quit();
You don't need parentheses around +1.
Change it to:
put "${file}" "${7}.T${j}+1"
It's good practice to quote variables.
Another tip: Instead of j=`expr $j + 1`, you can simply use ((j++)).