#!/usr/local/bin/perl

###############################################################################
# Program     : UploadProteinList
# Author      : Nichole King
#
# Description : Upload a protein list, format it, and pass to
#               GetPeptides
#
###############################################################################


###############################################################################
# Set up all needed modules and objects
###############################################################################
use strict;
use Getopt::Long;
use FindBin;

use lib "$FindBin::Bin/../../lib/perl";

use vars qw ($sbeams $sbeamsMOD $q $current_contact_id $current_username
             $PROG_NAME $USAGE %OPTIONS $QUIET $VERBOSE $DEBUG $DATABASE
             $TABLE_NAME $PROGRAM_FILE_NAME $CATEGORY $DB_TABLE_NAME
             @MENU_OPTIONS);

use SBEAMS::Connection qw($q $log);
use SBEAMS::Connection::Settings;
use SBEAMS::Connection::Tables;
use SBEAMS::Connection::TabMenu;

use SBEAMS::PeptideAtlas;
use SBEAMS::PeptideAtlas::Settings;
use SBEAMS::PeptideAtlas::Tables;

$sbeams = new SBEAMS::Connection;
$sbeamsMOD = new SBEAMS::PeptideAtlas;
$sbeamsMOD->setSBEAMS($sbeams);
$sbeams->setSBEAMS_SUBDIR($SBEAMS_SUBDIR);

#$CGI::DISABLE_UPLOADS = 0; ##enable uploads

## USAGE:
$PROG_NAME = $FindBin::Script;
$USAGE = <<EOU;
Usage: $PROG_NAME [OPTIONS] key=value key=value ...
Options:
  --verbose n         Set verbosity level.  default is 0
  --quiet             Set flag to print nothing at all except errors
  --debug n           Set debug flag

 e.g.:  $PROG_NAME [OPTIONS] [keyword=value],...

EOU

#### Process options
unless (GetOptions(\%OPTIONS,"verbose:s","quiet","debug:s")) 
{
    print "$USAGE";
    exit;
}

$VERBOSE = $OPTIONS{"verbose"} || 0;
$QUIET = $OPTIONS{"quiet"} || 0;
$DEBUG = $OPTIONS{"debug"} || 0;

if ($DEBUG) 
{
    print "Options settings:\n";
    print "  VERBOSE = $VERBOSE\n";
    print "  QUIET = $QUIET\n";
    print "  DEBUG = $DEBUG\n";
}


###############################################################################
# Set Global Variables and execute main()
###############################################################################
main();
exit(0);


###############################################################################
# Main Program:
#
# Call $sbeams->Authenticate() and exit if it fails or continue if it works.
###############################################################################
sub main 
{
    ##authenticate and exit if unsuccessful
    exit unless ($current_username = $sbeams->Authenticate(
        permitted_work_groups_ref=>['PeptideAtlas_user','PeptideAtlas_admin',
        'PeptideAtlas_readonly', 'PeptideAtlas_exec'], allow_anonymous_access=>1,
    ));

    #### Read in the default input parameters
    my %parameters;

    my $n_params_found = $sbeams->parse_input_parameters(
        q=>$q,parameters_ref=>\%parameters);

    #$sbeams->printDebuggingInfo($q);


    #### Process generic "state" parameters before we start
    $sbeams->processStandardParameters(parameters_ref=>\%parameters);

    #### Decide what action to take based on information so far
    if ($parameters{action} eq "???") 
    { 
        # Some action
    } else 
    {
        my $project_id = $sbeamsMOD->getProjectID(
            atlas_build_id => $parameters{atlas_build_id}
        );

        $sbeamsMOD->display_page_header(project_id => $project_id);
  
        handle_request(ref_parameters=>\%parameters);
  
        $sbeamsMOD->display_page_footer();
    }

} # end main


###############################################################################
# Handle Request
###############################################################################
sub handle_request 
{
    my %args = @_;

    #### Process the arguments list
    my $ref_parameters = $args{'ref_parameters'}
        || die "ref_parameters not passed";
    my %parameters = %{$ref_parameters};

    print "<BR>\n";

    my $CATEGORY="UploadProteinList";
    my $PROGRAM_FILE_NAME = $PROG_NAME;
    my $base_url = "$CGI_BASE_DIR/$SBEAMS_SUBDIR/$PROGRAM_FILE_NAME";

    if ($sbeams->output_mode() eq 'html') 
    {
        print "<table>";

        print $q->start_multipart_form(
            -method=>"POST", 
            -action=>"$base_url",
            -enctype =>"multipart/form-data"
        );

        print "<tr><td><b>File of Proteins To Upload:</b>&nbsp;&nbsp;&nbsp;</td>";
        print"<td><input type='file' name='upload_file'></td>";
        print "</tr>";

        print "<tr><td><b>Mass (m/z in Da):</b>&nbsp;&nbsp;&nbsp;</td>";
        print "<td><input type='text' name='mass_constraint'></td>";
        print "</tr>";

        print "<tr><td><b>Best Probability Constraint:</b>&nbsp;&nbsp;&nbsp;</td>";
        print "<td><input type='text' name='best_prob_constraint'></td>";
        print "</tr>";

        print "<tr><td><b>Number of Observations:</b>&nbsp;&nbsp;&nbsp;</td>";
        print "<td><input type='text' name='n_obs_constraint'></td>";
        print "</tr>";

        print "<tr><td><b>Number of Protein Id's w/ a Peptide:</b>&nbsp;&nbsp;&nbsp;</td>";
        print "<td><input type='text' name='n_prot_constraint'></td>";
        print "</tr>";


        print "<tr><td>&nbsp;</td></tr>";

        print "<tr><td colspan=2><center>";
        print $q->submit(-name => "query", 
                         -value => 'QUERY',
                         -label => 'QUERY');
        print "</center></td></tr>";

        print $q->end_multipart_form;

        print "</table>";
    } 

    ## upload the file to a file handler
    my $fh = $q->upload('upload_file');

    if (!$fh && $q->cgi_error)
    {
        print $q->header(-status=>$q->cgi_error);
    }

    ## size constraint of 10 MB
    ## restrict $count < 30000 
    if ( (-T $fh) && (-s $fh < 1000000))
    {
        my $count = 0;

        my $read_file=0;

        ## protein list
        my %protein_hash;

        while (<$fh>)
        {
            my $str=$_;
            chomp($str);
            $protein_hash{$str} = $str;
            $count = $count + 1;

            last if ($count > 30000);
        }

        my $n_proteins = keys %protein_hash;
        print "<br>uploaded $count entries (= $n_proteins proteins). <br/>";

        ## join with a semi-colon:
        my $protein_list = join("%3B", %protein_hash);

#       ## construct redirect url root using $ENV{HTTP_REFERER}
#       my $http_referer = $ENV{HTTP_REFERER};
#       my $redirect_url;
#
#       my $queryString = "biosequence_name_constraint=$protein_list";
#
#       ## assume it's an sbeams 
#       if ($http_referer =~ /$HOSTNAME/)
#       {
#           ## remove end of URL:
#           $http_referer =~ s/(.*)\/(.*)$/$1/;
#           $redirect_url = "$http_referer/GetPeptides?$queryString";
#       } else
#       {
#           ## this will kick user out of secure connection
#           $redirect_url = "http://$HOSTNAME/$CGI_BASE_DIR/$SBEAMS_SUBDIR/GetPeptides?" .
#               "$queryString";
#       }
#
#       ## redirect to GetPeptides
#       print "<meta http-equiv=\"refresh\" content=\"0;URL=$redirect_url\">";
#
#       exit;

    } else
    {
#       print "looks like binary or file is too big<br/>";
    }

}