test_proc_website.pm

package test_proc_website;
use Dancer ':syntax';
use Dancer::Plugin::Email;
use Dancer::Plugin::Database;
use DBI;
use Try::Tiny;
use File::Temp;
use File::Slurp;
use Data::Table;
use Data::Dumper;
use Time::Piece;
use Time::HiRes qw(gettimeofday);
use Cwd;
use Statistics::R;
use Archive::Zip qw(:ERROR_CODES);
use Number::Bytes::Human qw(format_bytes);
use Proc::Simple;
#use Proc::Background;
use feature qw(say);

our $VERSION = '0.1';

my $UPLOAD_FILE_SIZE = 450000000;                               #450MB file
my $TEMP_DIR = "/Users/tushardave26/Documents/Perl/Dancer/test_proc_website/tmp";
my $LOG_FILE = "/tmp/edn_log.csv";

get '/' => sub {
    template 'index';
};

get '/qqPlot' => sub {
    template 'qqPlot.tt';
};

post '/qqPlot' => sub {

        my $script_start_time = gettimeofday;
        my $temp_dir_template = "Q-QPlot"."_".localtime->ymd("")."_".localtime->time("")."_".$$."_"."XXXX";
        my ($name,$email,$y_limit,$xy_limit,$chart_title,$plot_name,$output_format,$pval_col,$log_line);
        my $email_mess = "Thank you so much for submitting your request for Q-Q plot utility. Your Q-Q plot is attached to this email. If you have any question regarding your plot, please contact Tushar Dave (Bioinforamtics Analyst 1) at tdave\@medicine.umaryland.edu.\n\nRegards,\nEDN Team";

        my $file = request->upload('upload-file');
        my $size = $file->size;
    my $filename = $file->filename;
        my $type = $file->type;

        my $size_readable = format_bytes($size);

        if ($size > $UPLOAD_FILE_SIZE) {
                template 'upload_file_size_error.tt', {size => $size};
        } else {

                $pval_col = params->{'p-val-col'};
                #$y_limit = params->{'y-limit'} ? params->{'y-limit'} : 100;
                #$xy_limit = params->{'xy-limit'} ? params->{'xy-limit'} : 100;
                $chart_title = params->{'chart-title'} ? params->{'chart-title'} : "";
                $output_format = params->{'output-file-type'} ? params->{'output-file-type'} : "png";
                $plot_name = params->{'output-file'} ? params->{'output-file'}.".".$output_format : "Q_Q_Plot".localtime->ymd("")."_".localtime->time("")."_".$$.".".$output_format;
                #my $zip_file_name = params->{'output-file'} ? params->{'output-file'} : "Q_Q_Plot".localtime->ymd("")."_".localtime->time("")."_".$$;

                my $temp_dir = File::Temp->newdir($temp_dir_template,
                                          CLEANUP => 0,
                                          DIR => $TEMP_DIR);

                chdir($temp_dir);

                $file->copy_to("$temp_dir/$filename");

                my $process = Proc::Simple->new();                      # creates a new process object
                Proc::Simple::debug(0);
                open my $f, ">", "test.txt" or die "Can not open test file $!";
                my $c = 0;

                #change made was to add full path to test_qqPlot.pl
                $process->start("perl /Users/tushardave26/Documents/Perl/Dancer/test_proc_website/scripts/test_qqPlot.pl --tempdir $temp_dir --filename $filename --filetype $type --pvalcol $pval_col --charttitle $chart_title --outputformat $output_format --plotname $plot_name");

                while ($process->poll()) {
                       template 'processing.tt';
                       sleep 10;
                }
                close $f;

                try {
                        email {
                                from    => '[email protected]',
                                to      => params->{'email'},
                                subject => 'Q-Q Plot Result from EDN Bioinformatics Toolkit',
                                body    => $email_mess,
                                #attach  => "$temp_dir/$zip_file"
                                attach => "$temp_dir/$plot_name"
                        };
                } catch {
                        error "Could not send email: $_";
                };

                template 'qqplot_submit.tt', {email => params->{'email'},
                                              image => "$temp_dir/$plot_name"};
        }
};

true;