#!/usr/local/bin/perl

###############################################################################
# Program     : GetSELExperiments
# Author      : Terry Farrah
# Description : Javascipt browser for SRM experiments
#
# 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 Getopt::Long;
use FindBin;
use POSIX qw(ceil floor);
use LWP::Simple;
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::Connection::Tables;
use SBEAMS::Connection::TabMenu;

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

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

use  SBEAMS::PeptideAtlas::PASSEL;
use SBEAMS::Connection::PubMedFetcher;

###############################################################################
# Set program name and usage banner for command line 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";
}


###############################################################################
# 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 {
  # This script is very simple.
  # Display PeptideAtlas header and footer.
  # In between, sandwich some static HTML.
  # Also create the static data file.

  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;

  $parameters{uploaded_file_not_saved} = 1;

  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);
    if(defined $parameters{SEL_experiment_id}){
      showSELExperiment(ref_parameters=>\%parameters);
    }else{ 
      handle_request(ref_parameters=>\%parameters);
    }
    $sbeamsMOD->display_page_footer();

  }


} # end main


###############################################################################
# Handle Request
###############################################################################
sub showSELExperiment{
  my %args = @_;
  my $ref_parameters = $args{'ref_parameters'}
    || die "ref_parameters not passed";
  my %parameters = %{$ref_parameters};
  my $SEL_experiment_id = $parameters{SEL_experiment_id};
  my $passel = new SBEAMS::PeptideAtlas::PASSEL;
  my $json = new JSON;

  # Collect a JSON hash containing data from all of the experiments.
  # Store also in string form to use for searching, sorting.
  my $json_filename_all = "$PHYSICAL_BASE_DIR/tmp/PASSEL_experiments_all.json";
  $passel->srm_experiments_2_json_all() if (! -e $json_filename_all);
  open (JSONFILE, "$json_filename_all") ||
    die "Can't open $json_filename_all for reading\n";
  my $json_href = $json->decode(join(" ",<JSONFILE>));
  close JSONFILE;

  my $tabMenu = $sbeamsMOD->getTabMenu(
    parameters_ref => \%parameters,
    program_name => $PROG_NAME,
  );
  
  my %labels = (
     experiment_title => 'Experiment Title',
     comment => 'Experiment Description',
     description => 'Sample Description',
     publication_name => 'Publication',
     abstract => 'Abstract',
     sample_date => 'Sample Date',
     contributors => 'Contributors',
     taxonomy => 'Organism',
     instrumentation => 'Instrument',
     spikein => 'Spikein',
     
  );

  if ($sbeams->output_mode() eq 'html'){
    print $tabMenu->asHTML() ; 
    print "<TABLE width=\"800\"><TR><TD><BR>\n";
    #print "<B>Metadata:</B><P>\n";
		foreach my $sample (@{$json_href->{"MS_QueryResponse"}{samples}}){
			next if($sample->{SEL_experiment_id} != $SEL_experiment_id);
			my $datasetIdentifier = $sample->{datasetIdentifier};
      print "<div align=\"center\"><font size=3><B>$datasetIdentifier</B></font></div>\n";
      my $link = "http://www.PeptideAtlas.org/PASS/$datasetIdentifier"; #$HTML_BASE_DIR ."/PASS/$datasetIdentifier";

      print qq~ <B><font color=blue>
            <a href="$link">
            Download raw data and supporting files
            </a>       
            </font></B><BR><BR>
            ~;

			foreach my $key (qw(experiment_title
                          comment
													description
													publication_name
													abstract
													taxonomy
													instrumentation
													spikein
													counts
                          contributors
													sample_date)){ 
        if($key !~ /(publication|counts)/){
          if($sample->{$key} ne ''){
				    print "<B><font color=blue>$labels{$key}:</font></B> $sample->{$key}<BR>\n";
          }
        }elsif($key =~ /count/){
          print qq~
                <B><font color=blue>Experiment Summary:</font></B>
                <ul>
                <li>Transition Group Measured: $sample->{counts}{"transition_groups"} 
                <a href="$CGI_BASE_DIR/PeptideAtlas/GetSELTransitions?SEL_experiments=$SEL_experiment_id\&row_limit=5000\&QUERY_NAME=AT_GetSELTransitions\&action=QUERY\&apply_action=QUERY">[Explore Transition Groups]</a></li>
                <li>Number of Ms Runs: $sample->{counts}{"runs"}</li>
                <li>Number of Proteins: $sample->{counts}{"prots"}</li>
                <li>Distinct Peptide Sequences: $sample->{counts}{"peps"}</li>
                </ul>
                ~;
        }elsif($key =~ /publication/){
           if(defined $sample->{publication}{ids}){
             my @ids = @{$sample->{publication}{ids}};
             print "<B><font color=blue>Publication:</font></B>";
             foreach my $id (@ids){
                #### Get the XML data from NCBI
                my $url = "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?".
                  "db=pubmed&id=$id&retmode=text&rettype=abstract";
                my $content = get $url or die "Couldn't get $url";
                my $ref = '';
                if($content !~ /Cannot process ID/){
                   my @lines = split("\n", $content);
                   shift @lines;
                   $ref = shift @lines;
                   $ref =~ s/^\d+\.\s+//;
                   shift @lines;
                   $ref = $lines[0] . " ". $ref;
                    print qq~ $ref
                             <a href="http://www.ncbi.nlm.nih.gov/pubmed/?term=$id">$id</a>
                             <BR>
                          ~;
                }else{ 
                  if(defined $sample->{publication_name}){
                    print " $sample->{publication_name}<BR>";
                  }
               }
             }
			    }else{
            if(defined $sample->{publication_name}){
              print "<B><font color=blue>Publication:</font></B> $sample->{publication_name}<BR>";
            }

          }
		    }
       }
     }
		print "<BR>\n";
		print "</TR></TD></TABLE>\n";
  }
}


sub handle_request {
  my %args = @_;

  #### 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,
  );
  print $tabMenu->asHTML() if ($sbeams->output_mode() eq 'html');


  my $html;

  # Javascript stuff
  $html = qq~

    <head xmlns:xi="http://www.w3.org/2001/XInclude">
		  <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
					  
		  <title>Repository</title>

		  <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/js/grid_ISB.js"></script>

	  <!--[if IE]>
			  <style>div#ext-gen27 {height:0px; }</style>
			  <![endif]-->
		  <style>
			  #south-panel .x-tool-collapse-south {
			  background-position:0 -210px;
			  }
			  #south-panel .x-tool-collapse-south-over {
			  background-position:-15px -210px;
			  }
			  #south-panel-xcollapsed .x-tool-expand-south {
			  background-position:0 -195px;
			  }
			  #south-panel-xcollapsed .x-tool-expand-south-over {
			  background-position:-15px -195px;
			  }
			  .x-grid3-header-offset{padding-left:1px;width:auto !important;}
			  ul.x-tab-strip {        
					  width:auto !important;
			  }
			  #contentbox-left {width: 99% !important;}
			  #contentbox-right {width: 1px !important; display:none; margin-right:0px !important;}
			  div#display_bar1 { display: none;}
		  </style>

		  <script type="text/javascript">
		  document.title = 'PASSEL Experiment Repository';
		  var browseAttributes = {
			  sample: '',
		  }
		  </script>

		  </head>
  ~;
  print $html;

  # Text at the top of the window
  $html = qq~
	  <body class="datagrid">

	   <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>
	  <br>
	  <h1>SRM Experiments Available in PASSEL</h1>
	  <br>
					  <p class="rep">
  <b>Please wait a few seconds for table to display.</b><br>Then, click individual experiments
  for detailed info and links to raw data.<br>Click TxGrps link for PASSEL
  transition group tables.

					  </p>
					  </p>

	  <br>
	  </div>
  ~;
  print $html;

#  Filter experiments using Search, then click individual experiments
#  for detailed info and links to transition lists and experimental results.

  # Search boxes and buttons
  $html = qq~
	  <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="title" >&nbsp;Experiment Title</option>
	    <option value="organism" >&nbsp;Organism</option>
	    <option value="tag" >&nbsp;Sample Tag</option>
	    <option value="instrument" >&nbsp;Instrument</option>
	    <option value="publication" >&nbsp;Publication</option>
	    <option value="abstract" >&nbsp;Abstract</option>
	    <option value="contributors" >&nbsp;Contributors</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" >

	  &nbsp;&nbsp; 
	  <input type="button" id="downloadbtn" name="downloadbtn" value="Download Table">

	  </div>
  ~;
  print $html;

  # Display of data table
  $html = qq~

		 <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;

}