sub upload {
        my $self = shift;
        my $q = $self->query;
        if(untaintFile($q->param('file')) && $q->upload('file')) {
                my $filename=untaintFile($q->param('file'));
                ($filename) = $filename =~ /([[:ascii:]]+)/;
                my $file = $q->upload('file');
                my $data;
                while(<$file>) {
                        $data .= $_;
                }
                if($data) {
                        my $thisfile = File->parse($data);
                        
                        if(my $format_error = $thisfile->check_formatt
+ing()) {
                                ...warn the user if there are any file
+ format errors...
                                return;
                        }
                        my $file_id = $self->file_upload({name => $fil
+ename, data => $data});
                }
        }

        $self->header_type('redirect');
        $self->header_props(-url => "$CONFIG{userbase}/user.pl");
        return;
}

sub parse {
        my $proto = shift;
        my $origfile = shift;
        my @lines = ();
        my $file = $origfile;
        LINE: while(length($file) >= 94) {
                $file =~ s/^\D*//;
                push @lines, substr($file, 0, 94, '');
                if(@lines && substr($lines[-1], 0, 1) eq '9') {
                        last LINE; # Don't need to parse any more afte
+r the file control record
                }
        }

        my @batches = ();
        for(my $i = 0; $i < @lines; $i++) {
                if(substr($lines[$i], 0, 1) eq '5') { # Batch Header
                        my @tempbatch = ();
                        for(; $i < @lines; $i++) {
                                push @tempbatch, $lines[$i];
                                if(substr($lines[$i], 0, 1) eq '8') { 
+# Batch Control
                                        last;
                                }
                        }
                        push @batches, File::Batches->new(\@tempbatch)
+;
                }
        }

        my $self = {
                file            => $origfile,
                lines           => \@lines,
                batches         => \@batches,
                total_subtract     => substr($lines[-1], 31, 12),
                total_add    => substr($lines[-1], 43, 12),
        };

        bless $self, $proto;
        return $self;
}
sub file_upload {
        my $self = shift;

        my %params = validate(@_, {
                name    => { type => SCALAR },
                data    => { type => SCALAR },
        });

        my $thisFile = File->parse($params{data});

        my @effective_dates;
        tie @effective_dates, 'Array::Unique';

        @effective_dates = $thisFile->get_effective_dates;

        ...insert data into database...

        return $id; #return the primary key
}
[download]

No browser will send a full path for input type file.

IE does...

Here's a few checks you could easily add:

• Was a file name entered?
• Does this file contain data?
• Is the data of the expected size/type/format?

It looks like you're assuming that it's a text file, and you read it into memory line by line. But what if someone accidentally sends you a large binary file (maybe it's the correct file, only it's been zipped)?

Here's a revised version of your upload() function that uses read() to read the file into a buffer 1kb at a time, and abort if it looks too big (you can set your own limit).

sub upload {
  my $self = shift;
  my $q = $self->query;
  if(untaintFile($q->param('file')) && $q->upload('file')) {
    my $filename=untaintFile($q->param('file'));
    ($filename) = $filename =~ /([[:ascii:]]+)/;

    unless($filename) {
      croak "no filename given!";
    }

    my $file = $q->upload('file');

    unless($file) {
      croak "can't get filehandle for upload!";
    }

    my $data;
    my $buffer;
    my $bytesread = 0;
    my $totalbytes = 0;

    while($bytesread = read($file, $buffer, 1024)) {
      $totalbytes += $bytesread;
      if($totalbytes > $MAX_DATA_LIMIT) {
        croak "upload file too big!";
      }
      $data .= $buffer;
    }

    unless ($data) {
      croak "no data!";
    } else {
      my $thisfile = File->parse($data);
                        
      if(my $format_error = $thisfile->check_formatting()) {
        # warn if any format errors found
      return;
                        }
      my $file_id = $self->file_upload({
        name => $filename, 
        data => $data,
      });
    }
  }
  $self->header_type('redirect');
  $self->header_props(-url => "$CONFIG{userbase}/user.pl");
  return;
}
[download]

Thanks for the input. I'll try that. What about taint? Will that satisfy taint?