Perl issues regarding mysql:Can't locate object method "connect" and Can't use string ("") as a HASH

Question

I'm currently trying to run NERVE a vaccine development program that is made up of Perl scripts and have trouble getting it to run properly. I've downloaded and installed all prerequisites but every time I reach the mysql step of the code, it crashes, and an error message says: Can't locate object method "connect" via package "Mysql" (perhaps you forgot to load "Mysql"?) at ./NERVE line 340, line 5. I took a look at the code and changed "use mysql" to "use DBI" and "use DBD:mysql" but then I get the error: Can't use string ("") as a HASH ref while "strict refs" in use at /usr/local/lib/perl/5.14.2/DBI.pm line 604, line 5.

I would appreciate if anyone could look the code over for the mysql section and give me advice on how to fix it so I can run the program properly. I tried emailing the developers but no response so I'm hoping you guys can help me.

Below is the perl code for NERVE for the mysql section.

    use mysql;
$db=Mysql->connect("$host","$database","$user","$password");
if(!$db || (!$host || !$database || !$user || !$password)){
    print "\nAttention: mysql connection parameters are missing or not correct!\n";
    print "I need you to specify: host, database, user, password;\n";
    print "You can do it now typing them right in that order and separeted only by comma;\n";
    print "For example:localhost,Pathogens,sandro,xvzhs\n";
    print "So, your Mysql connection settings are (type q to quit):";
    while (!($db && $mysql =~ /,/) & $mysql ne "q"){
        chomp($mysql = <STDIN>);
        die "Ok,let's quit this work! Call me when your mind is clearer about Mysql parameters! Bye :-)\n" if $mysql eq "q";
        ($host,$database,$user,$password) = split (',',$mysql);
        $db=Mysql->connect("$host","$database","$user","$password");
        last if($db && $mysql =~ /,/);
        print "\nMysql connection settings still not correct!\n";
        print "Remember: host, database, user, password, separeted only by comma.\n";
        print "For example:localhost,Pathogens,sandro,xvzhs\n";
        print "Please, try again:";
    }
    print "Ok, Mysql connection to \"$database\" database was successful!\n";
}

Answer 1

The error message is correct. You are attempting to use a module named , but you never loaded it. Change

use mysql;

to

use Mysql;

to use that module. In the comments, you mention that results in

Can't locate Mysql.pm in @INC 

Unless you have reason to believe the module is installed, that indicates it needs to be installed^[1]

That module used to be part of the DBD-mysql distribution, but it's obsolete. It's so ancient it was removed from DBD some years ago. To obtain it, you will need to downgrade your DBD-mysql distribution to version 3.0008.

That's pretty awful thing to do. The script should have DBI instead.

---

cjm points

since the Mysql.pm in 3.0008 is just a compatibility layer using DBI under the hood, you should be able to install Mysql.pm & Mysql/Statement.pm from that old dist along with a current DBD-mysql.

So if you extract Mysql.pm from the distro I linked above as /usr/lib/perl5/Mysql.pm and Mysql/Statement.pm as /usr/lib/perl5/Mysql/Statement.pm, you should have an easy pain-free solution.

---

1. In newer versions of Perl, the error message has been improved. It now reads as follows:

   Can't locate Mysql.pm in @INC (you may need to install the Mysql module)