Passing variable between scripts

Question

I've created a variable $date in Main.pl script that I would like to pass to Annotator.pl script. I use shell script to execute Annotator.pl. I can't figure out how to pass $date to Annotator.pl. When I run my $date = $ARGV[0]; in Annotator.pl I get the name of the current directory, however, $date = $ARGV[1]; returns nothing.

Please see the code below. The date is important because it has to be exact and I can't figure out how to pass it to Annotator.pl. Thanks for your help.

Main.pl Script:

#!/usr/bin/perl -w
    use strict;
    use warnings;

    my $sec; my $min; my $hour; my $mday; my $mon; my $year; my $wday; my $yday;    my $isdst;
    ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst) = localtime();
    $mon=$mon+1; $year = 1900+$year;
    if (length($mon)==1) {$mon="0".$mon;}
    if (length($mday)==1) {$mday="0".$mday;}
    if (length($hour)==1) {$hour="0".$hour;}
    if (length($min)==1) {$min="0".$min;}
    if (length($sec)==1) {$sec="0".$sec;}

    my $date = "$mon"."_"."$mday"."_"."$year"."-".$hour.$min.$sec;

    my $cmd5 = `perl MDL_unzip_annotate.sh /data/test_all_runs pVCF $date`;   print "$cmd5";

Shell script: MDL_unzip_annotate.sh that executes Annotator.pl

home="/data/test_all_runs" #location of the run directory from which the program is launched
   scripts="/data/test_scripts"  

     datapath=$1 #this is called in Main.pl as [test_all_runs]
     process=$2 #the process  

    if [[ "$process" == "pVCF" ]];then
            cd $datapath
            folders="$(ls)"
            cd $scripts
        for ff in $folders; do
            dname=$ff
                echo $dname
                if [  ! -f $dname ];then

                    cmd2="perl Annotator.pl $dname"
                    echo $cmd2

                    cmd2=`perl Annotator.pl $dname`
                    echo $cmd2
                fi
            done    
    done          

    fi

Annotator.pl script:

#!perl
    use strict;
    use warnings;

    my $date = $ARGV[1]; print "the date is######## ".$date."\n";

perl MDL_unzip_annotate.sh /data/test_all_runs pVCF $date is wildly dangerous -- concatenating your command into a string means you're calling system(), which runs sh -c with that string as an argument, which means you're vulnerable to shell injection attacks. Don't do that. — Charles Duffy
– Charles Duffy, Commented Jul 19, 2016 at 19:56
I'm a novice... please suggest how to pass $date to Annotator.pl. Thanks — user3781528
– user3781528, Commented Jul 19, 2016 at 19:58
Think about what happens if you populate your year from user input rather than the local time -- if the user runs the program with 1994$(rm -rf $HOME) as the year, you don't want the system to actually invoke rm, but that's what'll happen if that string is passed to a shell -- and literal quoting is easy to work around. — Charles Duffy
– Charles Duffy, Commented Jul 19, 2016 at 19:58
Run your shell component through shellcheck.net, and fix the bugs it identifies. — Charles Duffy
– Charles Duffy, Commented Jul 19, 2016 at 19:58

user3781528 · Accepted Answer · 2016-07-19 21:08:30Z

1

Instead of using shell script I will use the following code to capture the name of the folder in a specific directory:

opendir my $dir, "/data/test_all_runs" or die "Cannot open directory: $!";
my @run_folder = readdir $dir;
closedir $dir;
my $last_one = pop @run_folder; print "The folder is".$last_one."\n";

Thanks for your suggestions.

answered Jul 19, 2016 at 21:08

user3781528

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1 Comment

zdim Over a year ago

Great :) Please note, readdir returns files without any path. So to get workable lists you should prepend path as needed. For example, @filenames = map { "$path/$_" } readdir $dir. Or you can chdir $dirname and then work with bare names. But then do not forget that your script's working directory is $dirname.

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