Dear Monks, I am trying to populate a table with a rather large (~60GB) file. I would like to ask if there is a way to populate the table, even if, say 1% of the lines are erroneous, without the script dying.
My code so far is: 
#!/usr/bin/perl

use strict;
use warnings;
use DBI;

my $numArgs = $#ARGV + 1;
die "Usage: ./upload_script.pl <CSV_FILE>" if ($numArgs != 1);

my $infile = $ARGV[0];
my $logfile = $infile.'.log';

my $driver  = "Pg"; 
my $database = "testdb";
my $dsn = "DBI:$driver:dbname = $database;port = 123456"; 
my $userid = "xxx";
my $password = "yyy";
my $dbh = DBI->connect($dsn, $userid, $password, { RaiseError => 1 }) 
   or die $DBI::errstr;

open LOG, ">$logfile";
print LOG "Opened database successfully\n";
my $count=0;

open (DB_IN, "<$infile" ) || die ("File not found: '$infile'\n");
readline DB_IN;    
while(<DB_IN>)
{
    my $input_line=$_;
        chomp $input_line;

    my @array_of_input = split(/\t/, $input_line);

    $count++;
    my $pid_field = $array_of_input[0];
    my $quantityid_field = $array_of_input[1];
    my $labid_field = $array_of_input[2];
    my $system_field = $array_of_input[3];
    my $component_field = $array_of_input[4];
    my $numericvalue_field = $array_of_input[6];
    my $ref_lower_field = $array_of_input[7];
    my $ref_upper_field = $array_of_input[8];
    my $shown_value_field = $array_of_input[9];
    my $date_field = $array_of_input[10];
    my $time_field = $array_of_input[11];
    my $database_field = $array_of_input[12];
    my $componentdb_field = $array_of_input[13];
    my $componenttranslationlookup_field = $array_of_input[14];
    my $testtype_field = $array_of_input[15];
    my $unitclean_field = $array_of_input[16];
    my $shownclean_field = $array_of_input[17];
    my $reflowerclean_field = $array_of_input[18];
    my $refupperclean_field = $array_of_input[19];
    my $intervaltype_field = $array_of_input[20];
    my $flag_field = $array_of_input[21];
    my $abo_field = $array_of_input[22];
    my $rhesus_field = $array_of_input[23];
    my $dob_field = $array_of_input[24];
    my $sex_field = $array_of_input[25];

    my $insert_stmt = "    INSERT INTO biochemical
                           VALUES (".$count.", 
                                   '".$pid_field."', 
                                   '".$quantityid_field."', 
                                   '".$labid_field."', 
                                   '".$system_field."', 
                                   '".$component_field."',
                                   '".$numericvalue_field."', 
                                   '".$ref_lower_field."', 
                                   '".$ref_upper_field."', 
                                   '".$shown_value_field."', 
                                '".$date_field."', 
                                   '".$time_field."', 
                                   '".$database_field."', 
                                   '".$componentdb_field."', 
                                   '".$componenttranslationlookup_fiel
+d."', 
                                   '".$testtype_field."', 
                                   '".$unitclean_field."', 
                                   '".$shownclean_field."', 
                                   '".$reflowerclean_field."', 
                                   '".$refupperclean_field."', 
                                   '".$intervaltype_field."', 
                                   '".$flag_field."', 
                                   '".$abo_field."', 
                                   '".$rhesus_field."', 
                                   '".$dob_field."', 
                                   '".$sex_field."')";

    my $rv = $dbh->do($insert_stmt);
    if(!$rv)
    {
        print "Problem inserting: $input_line\n";
    }
}
close DB_IN;
close LOG;

[download]
This code does work, but it dies as soon as an erroneous line is found. Ideally, I would like this line to just be thrown into my LOG and then the script continues to execute. Is there a way? In that way, I could leave the script run unattended and then check the lines that were not able to be inserted.

In reply to Skip problematic lines while populating database by Anonymous Monk

Title:
Use:  <p> text here (a paragraph) </p>
and:  <code> code here </code>
to format your post, it's "PerlMonks-approved HTML":


  • Posts are HTML formatted. Put <p> </p> tags around your paragraphs. Put <code> </code> tags around your code and data!
  • Titles consisting of a single word are discouraged, and in most cases are disallowed outright.
  • Read Where should I post X? if you're not absolutely sure you're posting in the right place.
  • Please read these before you post! —
  • Posts may use any of the Perl Monks Approved HTML tags:
    a, abbr, b, big, blockquote, br, caption, center, col, colgroup, dd, del, details, div, dl, dt, em, font, h1, h2, h3, h4, h5, h6, hr, i, ins, li, ol, p, pre, readmore, small, span, spoiler, strike, strong, sub, summary, sup, table, tbody, td, tfoot, th, thead, tr, tt, u, ul, wbr
  • You may need to use entities for some characters, as follows. (Exception: Within code tags, you can put the characters literally.)
            For:     Use:
    & &amp;
    < &lt;
    > &gt;
    [ &#91;
    ] &#93;
  • Link using PerlMonks shortcuts! What shortcuts can I use for linking?
  • See Writeup Formatting Tips and other pages linked from there for more info.