#!/usr/local/bin/perl

###############################################################################
# Program     : GetTransitionLists
# $Id$
#
# Description : Returns transitions lists info in PeptideAtlas
#
# 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.
#
###############################################################################


###############################################################################
# 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;
$sbeams = new SBEAMS::Connection;

use SBEAMS::BioLink;
my $biolink = SBEAMS::BioLink->new();
$biolink->setSBEAMS($sbeams);

use SBEAMS::BioLink;
my $biolink = new SBEAMS::BioLink;

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

use SBEAMS::PeptideAtlas::KeySearch;
my $keySearch = new SBEAMS::PeptideAtlas::KeySearch;
$keySearch->setSBEAMS($sbeams);
my @coverage;  # Global sequence coverage array, will be populated post-graphic


###############################################################################
# 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";
}



###############################################################################
# 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 {

  #### 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,
  ));


  #### 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, init_tooltip => 1);
      handle_request(ref_parameters=>\%parameters);
      $sbeamsMOD->display_page_footer();
  }


} # end main



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

  my $spacer = $sbeams->getGifSpacer( 900 );
  my $htmlmode = ( $sbeams->output_mode() eq 'html' ) ? 1 : 0;


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

  my %parameters = %{$ref_parameters};


  #### 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 $tabMenu->asHTML();
    print "<script>document.title = 'Download Public SRM Transition Lists from PeptideAtlas';</script>";
  }

  #### SHOW ALL LISTS
  ##
  my $transitionsHTML = &display_transitions_lists('all');
  print "<TABLE><BR>$transitionsHTML</TABLE>\n" if ($htmlmode);


  #### SHOW USER-UPLOADED LISTS
  ##
  if ( $sbeams->isGuestUser() ) {

      if ($htmlmode) {
	  my $login_link = "$SERVER_BASE_DIR$ENV{REQUEST_URI}";
	  if ($login_link =~ /\?/) {
	      $login_link .= "&force_login=yes";
	  } else {
	      $login_link .= "?force_login=yes";
	  }

	  print "<HR NOSHADE /><B>Please <A HREF=$login_link>log in to PeptideAtlas</A> in order to Upload your Transitions Lists</B>\n<BR/>(Please contact us if you need an account to PeptideAtlas)";

      }
  } else {

      $transitionsHTML = &display_transitions_lists('user');
      print "<TABLE><BR>$transitionsHTML</TABLE>\n" if ($htmlmode);

      if ($htmlmode) {
	  my $upload_link = "ManageTable.cgi?TABLE_NAME=AT_srm_transition_set&ShowEntryForm=1";
	  print "<HR NOSHADE /><B><A HREF=$upload_link>Upload your Transitions List to PeptideAtlas</A></B>\n";
      }
  }


#  if ($sbeams->output_mode() eq 'xml' ) {
#      $transitionsXML .= "</transition_lists>\n\n";
#      print $transitionsXML;
#  }


} # end handle_request



# Helper sub to avoid copy/paste proliferation
sub display_transitions_lists {
    my $context = shift || 'all';  # 'user' or 'all'

    #### SHOW UPLOADED LISTS
    ##
    ##
    #### Widget to allow show/hide of section
    my ( $tr, $link ) = $sbeams->make_table_toggle( name => "gettransitions_lists_$context",
						    visible => 1,
						    tooltip => 'Show/Hide Section',
						    imglink => 1,
						    sticky => 1,
						    );

    #### Display the section header
    # $transitionsXML = '<?xml version="1.0" encoding="ISO-8859-1"?><transition_lists><base_download_url>http://www.peptideatlas.org/cgi/fileDownloader.pl/</base_download_url>';
    my $transitionsHTML =  ($context eq 'user') ?
	"<H2>View and Download SRM Transition Lists Uploaded by <font color=red>$current_username</font></H2>\n" :
	"<h1>Download Public SRM Transition Lists from PeptideAtlas</h1>\n";

    $transitionsHTML .= $sbeamsMOD->encodeSectionHeader(
      LMTABS => 1,
      no_toggle => 1,
      text => 'Uploaded Transitions Lists',
      link => $link
	);

#  my $trans_help = get_table_help( 'annotated_transitions' );
#  my $transitions_lists = $sbeamsMOD->get_transitions_lists();
    my $transitions_lists = get_transitions_lists($context);

    #### If a result is returned
    if ( scalar @$transitions_lists ) {
    
	### Download and Manage links here!
	my $link_pre = "ManageTable.cgi/";
	my $link_post= "?TABLE_NAME=AT_srm_transition_set&GetFile=upload_file&srm_transition_set_id=";

	my $link_manage = "?TABLE_NAME=AT_srm_transition_set&srm_transition_set_id=";

	my $link_pubmed = "http://www.ncbi.nlm.nih.gov/pubmed/";

	#### Loops through resultset and do formatting
	for my $list ( @$transitions_lists ) {
	    $list->[6] = "<A HREF=$link_pre" . $list->[6] . "$link_post". $list->[0] . ">$list->[6]</A>";

	    my $patrId = sprintf("PATR%05d", $list->[0]);

	    if ($context eq 'user') {
		$list->[0] = "<A HREF=$link_pre$link_manage". $list->[0] . ">$patrId</A>";
	    } else {
		$list->[0] = $patrId;
	    }

	    if ($list->[4] && $list->[5]) {
		$list->[4] = "<A TARGET='_blank' HREF=$link_pubmed" . $list->[5] . ">$list->[4]</A>";
	    }

	    if ($sbeams->output_mode() eq 'xml' ) {
		#$transitionsXML .= "<element>$list->[0]</element>\n";
	    }

	    # remove PMID
	    splice(@{$list},5,1);

	}
	my @labels = ( 'Accession','Set Tag', 'Title', 'Organism', 'Publication', 'Download File');
	push @labels, ('Is Public?','Go Live Date') if ($context eq 'user');

	#### Add table column headings
	unshift @$transitions_lists, \@labels;

	#### Format table
	$transitionsHTML .= $sbeamsMOD->encodeSectionTable( header => 1, 
							    tr_info => $tr,
							    set_download => 0,
							    chg_bkg_idx => 1,
							    align  => [qw(left left left center left left left center)],
							    rows => $transitions_lists );
    }

    return $transitionsHTML;
}


sub get_transitions_lists {
  my $context = shift;

  my $ispub  = ($context eq 'user') ? ', TS.is_public' : '';
  my $golive = ($context eq 'user') ? ', TS.golive_date' : '';

  my $ispub2 = ($context ne 'user') ? "AND TS.is_public = 'Y'" : '';
  my $isuser = ($context eq 'user') ? 'AND TS.created_by_id = '. $sbeams->getCurrent_contact_id() : '';

  my $sql =<<"  END";
  SELECT
      TS.srm_transition_set_id,
      TS.set_tag,
      TS.set_title,
      O.organism_name,
      TS.publication_name,
      TS.pubmed_ID,
      TS.upload_file
      $ispub
      $golive
   FROM $TBAT_SRM_TRANSITION_SET TS
   LEFT JOIN $TB_ORGANISM O
        ON ( O.organism_id = TS.organism_id )
   WHERE
      TS.record_status = 'N'
      $ispub2
      $isuser
   ORDER BY
      TS.date_created, TS.srm_transition_set_id DESC
  END

  my @rows = $sbeams->selectSeveralColumns($sql);
  return \@rows;
}