#!/usr/local/bin/perl

###############################################################################
# Program     : PASS_Summary
# Author      : Zhi Sun
# Description : This script shows the PeptideAtlas passel_submission page
#
# SBEAMS is Copyright (C) 2000-2021 Institute for Systems Biology
# This program is governed by the terms of the GNU General Public License (GPL)
# version 2 as published by the Free Software Foundation.  It is provided
# WITHOUT ANY WARRANTY.  See the full description of GPL terms in the
# LICENSE file distributed with this software.
#
###############################################################################
use strict;
use CGI::Carp qw(fatalsToBrowser croak);
use FindBin;
use Getopt::Long;

use POSIX qw(ceil floor);
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::Authenticator;

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);

###############################################################################
# Set program name and usage banner for command like use
###############################################################################
$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";
}

my @datasetTypes = ( 'MSMS' => 'MS/MS dataset',
	'SRM' => 'SRM dataset',
	'MS1' => 'MS1 dataset',
	'QC' => 'Ongoing QC dataset',
	'Other' => 'Other',
);
###############################################################################
# Set Global Variables and execute main()
###############################################################################
main();
exit(0);

###############################################################################
# Main Program:
#
# Call $sbeams->Authenticate() and exit if it fails or continue if it works.
###############################################################################
sub main {
  exit unless ($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
        );

    #### Do the SBEAMS authentication and exit if a username is not returned
    exit unless ($current_username = $sbeams->Authenticate(
        permitted_work_groups_ref=>['PeptideAtlas_user','PeptideAtlas_admin',
        'PeptideAtlas_readonly', 'PeptideAtlas_exec'],
        #connect_read_only=>1,
        allow_anonymous_access=>1,
    ));

    #### 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,
                                        init_tooltip => 1);

        handle_request(ref_parameters=>\%parameters);

        $sbeamsMOD->display_page_footer();
    }
    $sbeams->profile_sql( list => 0 );

} # end main
###############################################################################
# Handle Request
###############################################################################
sub handle_request {
  my %args = @_;
  $log->debug( "Start page " . time() );

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

  my %parameters = %{$ref_parameters};

  #### Show current user context information
  #$sbeams->printUserContext();

  #### Get the HTML to display the tabs
  my $tabMenu = $sbeamsMOD->getTabMenu(
     parameters_ref => \%parameters,
     program_name => $PROG_NAME,
  );

  if ($sbeams->output_mode() eq 'html') {
    print "<script>document.title = 'PASSEL Datasets';</script>";
    print $tabMenu->asHTML().'<br>';
  }

  my $html = qq~
		</head>
		<body class="datagrid">
		<br>
		<script type='text/javascript' src="$CGI_BASE_DIR/../usr/javascript/passel/js/portal.js"></script>
		<script type="text/javascript" src="$CGI_BASE_DIR/../usr/javascript/passel/js/jig.min.js"></script> 

		<link rel="stylesheet" type="text/css" href="$CGI_BASE_DIR/../usr/javascript/passel/css/ext-all.css" />
		<script type="text/javascript" src="$CGI_BASE_DIR/../usr/javascript/passel/js/ext-big.js"></script>
		<script type="text/javascript" src="$CGI_BASE_DIR/../usr/javascript/passel_submission/js/grid_passel.js"></script>
		<script type="text/javascript">
							var browseAttributes = {
							sample: '',
							}
		</script>

		<B><font color="#b00">Email address</B></font>
		 <input type="text" id="email" value="" size=50 maxlength=80/>
		 &nbsp;&nbsp;&nbsp;&nbsp;

		 <B><font color="#b00">Password</B></font>
		 <input type="password" id="password" value="" size=10 maxlength=50/>
		 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
		<input type="button" id="login" value="LOGIN" />
    <p id="msg" style="width: 430px; padding: 5"></p>
		<BR>
		<HR>
		<br>   

		<form style="width: 1000px;overflow:auto;padding: 5px;-ro-width: auto;" enctype="application/x-www-form-urlencoded" action="/" name="EntrezForm" method="post" onsubmit="return false;" id="EntrezForm">
		<div>
		</div>
		<div class="search">
		<span>&nbsp;&nbsp;Search:&nbsp;</span>
		<select id="selectedTitle" name="selectedTitle" style="font-size:92%">
		<option value="all" selected="selected">&nbsp;All </option>
		<option value="id" >&nbsp;Identifier</option>
		<option value="title" >&nbsp;Dataset Title</option>
		<option value="tag" >&nbsp;Dataset Tag</option>
    <option value="type" >&nbsp;Dataset Type</option>
		<option value="submitter" >&nbsp;Submitter</option>
		<option value="email" >&nbsp;Email</option>
		<!--<option value="date" >&nbsp;Release Date</option>-->
		</select>
		<span>for</span>
		<input type="text" size="38" id="searchq" name="searchq"  >
		<input type="button" id="searchbtn" name="searchbtn" class="sarchBtnOK" value="Search" >

		<span>&nbsp;&nbsp;Select:&nbsp;</span>
		<select id="selectFileType" name="selectFileType" style="font-size:92%">
		<option value="all" selected="selected">&nbsp;All </option>
		<option value="raw" >&nbsp;RAW</option>
		<option value="mzXML/mzML" >&nbsp;mzXML/mzML</option>
		<option value="description" >&nbsp;Description File</option>
		</select>
		<span>to</span>
		<input type="button" id="downloadbtn" name="downloadbtn" value="Get Download List">
		&nbsp;&nbsp; 
		<input type="button" id="downloadbtn2" name="downloadbtn2" value="Download Table">

		</div>

		<table cellpadding="0" width="100%" cellspacing="0" id="br1owseWrapper">                    
		<tr>
			<td valign="top">
			 <div class="datagrid"> 
				<div id="sample-layout"></div>
				<div id="tabsPanel"></div>
				<div id="center"></div>
				<div id="samplestudyWrapper">
				 <div id="browse"> 
					<div id="toolbar"></div>
					<div id="prot-grid"></div>
				 </div>  <!--"browse"  -->
				</div>   <!-- "samplestudyWrapper" -->
				</div> <!-- "datagrid" -->
			</td>
			</tr>
		</table>
		</form>
		<br><br>
		</body>
 ~;

  print $html;
}