MVRS has asked for the wisdom of the Perl Monks concerning the following question:

hi Monks ,Am trying to run system command which takes input from the user

#!/usr/bin/perl
use strict;

print "Enter the Rast Username\n";
my $username = <>;

print "Enter the Rast Password\n";
my $Password = <>;

print "Enter the fasta file Name\n";
my $fasta = <>;

print "Enter the Domain Name\n";
my $domain= <>;

print "Enter Genetic_Code\n";
my $Genetic_code = <> ;


system (qq("svr_submit_RAST_job --user "$username" --passwd "$Password
+" --fasta "$fasta" --domain "$domain" --genetic_code "$Genetic_code")
+);

[download]

if same job submitted as following, it works

system("svr_submit_RAST_job --user "=xxxxxx --passwd ******** --fasta seq.fasta --domain bacteria --genetic_code 11)

it works , why iam unable make with $xxxxx script please help me in solving this problem

Replies are listed 'Best First'.
Re: Perl calling Linux commands
by tobyink (Canon) on Mar 08, 2013 at 10:17 UTC 
    chomp(my $username = <>);
# ... etc

    [download]

    See chomp.

    package Cow { use Moo; has name => (is => 'lazy', default => sub { 'Mooington' }) } say Cow->new->name
[reply]
[d/l]
Re: Perl calling Linux commands
by marto (Cardinal) on Mar 08, 2013 at 10:17 UTC

    Read the advice you got in your previous post about using chomp when reading input input from users.

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[d/l]
Re: Perl calling Linux commands
by tmharish (Friar) on Mar 08, 2013 at 11:06 UTC

    If you had printed the system command that you were running you would have figured this out.

    Update

    Just to show what I meant consider what happens when your code is modified like so: 

    
my $command = qq("svr_submit_RAST_job --user "$username" --passwd "$Pa
+ssword" --fasta "$fasta" --domain "$domain" --genetic_code "$Genetic_
+code") ;

print "\n\n\nGoing to run the following through system:\n $command\n";

    [download]
    Output 
    Enter the Rast Username
username
Enter the Rast Password
password
Enter the fasta file Name
filename
Enter the Domain Name
domainname
Enter Genetic_Code
geneticcode



Going to run the following through system:
 "svr_submit_RAST_job --user "username
" --passwd "password
" --fasta "filename
" --domain "domainname
" --genetic_code "geneticcode
"

    [download]

    And the newlines are there for you to see, as plain as daylight.

[reply]
[d/l]
[select]

      Additionally you need to look at tainted variables.

      Its a really bad idea to take user input and throw it to system ( or a database ) - What if the username input was: 

      " || ls && 0 &&

      [download]

      Of course you could replace ls with whatever exciting nefarious command you choose but thats the idea ...

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[d/l]
[select]
Re: Perl calling Linux commands
by vinoth.ree (Monsignor) on Mar 08, 2013 at 11:07 UTC
[reply]
[reply]
Re: Perl calling Linux commands
by Anonymous Monk on Mar 09, 2013 at 01:26 UTC
[reply]

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