#!/usr/local/bin/perl

###############################################################################
# $Id$
#
# Description : This script authenticates the user, and then
#               displays the opening access 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.
#
###############################################################################


###############################################################################
# Get the script set up with everything it will need
###############################################################################
use strict;
use vars qw ($q $sbeams $atlas $PROG_NAME
             $current_contact_id $current_username);
use lib qw (../../lib/perl);
use CGI::Carp qw(fatalsToBrowser croak);

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

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

###############################################################################
# Global Variables
###############################################################################
$PROG_NAME = 'ViewSRMBuild';
$SBEAMS_SUBDIR = 'PeptideAtlas';


$sbeams = new SBEAMS::Connection;
$atlas = new SBEAMS::PeptideAtlas;
$atlas->setSBEAMS($sbeams);
my $peptide_selector = new SBEAMS::PeptideAtlas::BestPeptideSelector;
$peptide_selector->setAtlas( $atlas );
$peptide_selector->setSBEAMS( $sbeams );
my $GV = SBEAMS::Connection::GoogleVisualization->new();


my $instrument_map = $peptide_selector->getInstrumentMap();
$instrument_map->{Any} = 0;
my %code2instrument = reverse( %{$instrument_map} );

# Coverage hash keyed by build_id
my %builds;
my %current_build;
my %parameters;

main();


###############################################################################
# Main Program:
#
# Call $sbeams->Authentication and stop immediately if authentication
# fails else continue.
###############################################################################
sub main
{
    # Do the SBEAMS authentication and exit if a username is not returned
    exit unless ($current_username = $sbeams->Authenticate(
        permitted_work_groups_ref=>['PeptideAtlas_user','PeptideAtlas_admin',
        'PeptideAtlas_readonly', 'PeptideAtlas_exec'],
        #connect_read_only=>1,
        allow_anonymous_access=>1,
    ));
    $sbeams->setSessionAttribute( key => 'PA_resource', value => 'SRMAtlas' );


    # Read in the default input parameters
    my $n_params_found = $sbeams->parse_input_parameters(
        q=>$q,
        parameters_ref=>\%parameters
        );
    # Process generic "state" parameters before we start
    $sbeams->processStandardParameters(parameters_ref=>\%parameters);

    # This will look for mod-specific params and do the right thing
    $atlas->processModuleParameters(parameters_ref=>\%parameters);
    $parameters{cov_level} ||= 'cov_3';

    # get project_id
    my $project_id = $atlas->getProjectID(
        atlas_build_name => $parameters{atlas_build_name},
        atlas_build_id => $parameters{atlas_build_id}
        );

    $atlas->display_page_header(project_id => $project_id);

  my $atlas_build_id = $atlas->getCurrentAtlasBuildID(
    parameters_ref => \%parameters,
  );
	$parameters{atlas_build_id} = $atlas_build_id;

  # Will use passed build_id if any, then cached (cookie) id, then default
  # If user passed bogus value it should get sorted out here.
	my $pabst_build_id = $peptide_selector->get_pabst_build( %parameters );
	$parameters{pabst_build_id} = $pabst_build_id;

  #### Get the HTML to display the tabs
  my $tabMenu = $atlas->getTabMenu(
    parameters_ref => \%parameters,
    program_name => $PROG_NAME,
  );
  if ($sbeams->output_mode() eq 'html') {
    print "<script>document.title = 'SRMAtlas Builds list';</script>";
    print $tabMenu->asHTML();
    print "<BR>\n";
  }


    my $content = '';
		$content .= get_build_list(%parameters);
    $content .= "<BR>\n";
    $content .= $sbeams->makeInfoText( "Charts shows detailed coverage plots for selected build, use radio buttons in table (above) to switch <BR>" ); 
		$content .= get_build_details(%parameters);

    print "$content";

    $atlas->display_page_footer();
    $sbeams->setSessionAttribute( key => 'PA_resource', value => '' );


} # end main


###############################################################################
# Show the main welcome page
###############################################################################
sub get_build_details {
  my %parameters = @_;

  my $section_header = $atlas->encodeSectionHeader(
    LMTABS => 1,
    no_toggle => 1,
    text => "SRMAtlas Build: $builds{$parameters{pabst_build_id}}->{name} ($parameters{pabst_build_id})"
  );

  my @instruments = sort {$a <=> $b} keys( %{$builds{$parameters{pabst_build_id}}->{instruments}} );
  push @instruments, shift( @instruments );

  print "<PRE>";
#  print Dumper( @instruments );
  print "</PRE>";

  my @samples;
  my @csamples;

  if ( $current_build{instruments}->{0}->{cov_any} < 500 ) {
    $current_build{bioseq_cnt} = $current_build{instruments}->{0}->{cov_any};
  }

  for my $instrument ( @instruments ) {
    my @inst_row = ( $code2instrument{$instrument} );
    my @cumulative_row = ( $code2instrument{$instrument} );

    my $cov_0 = $current_build{instruments}->{$instrument}->{cov_0};


    if ( $current_build{bioseq_cnt} < 1000 ) {
      $cov_0 = $current_build{instruments}->{$instrument}->{cov_any} - $current_build{bioseq_cnt};
      $cov_0 = 0 if $cov_0 < 1;
    }
    # Format
    $cov_0 = sprintf( "%0.1f", 100*($cov_0/$current_build{bioseq_cnt})) if $cov_0;

    push @inst_row, $cov_0;
    push @cumulative_row, $cov_0;

    my $cumulative;
    my @individual;
    my @cumulative;
    for my $cov ( reverse( qw( cov_1 cov_2 cov_3 cov_4 cov_5 ) ) ) {
      $cumulative += $current_build{instruments}->{$instrument}->{$cov};

      my $currcum = ( $cumulative ) ? sprintf( "%0.1f", 100*($cumulative/$current_build{bioseq_cnt}) ) : 0;
      push @cumulative, $currcum;

      my $currval = $current_build{instruments}->{$instrument}->{$cov};
      $currval = sprintf( "%0.1f", 100*($currval/$current_build{bioseq_cnt}) ) if $currval;
      push @individual, $currval; 
    }
    push @inst_row, reverse( @individual );
    push @cumulative_row, reverse( @cumulative );
    push @samples, \@inst_row;
    push @csamples, \@cumulative_row;
  }

  my $ichart = make_individual_chart_function( \@samples );
  my $cchart = make_cumulative_chart_function( \@csamples );

	my $header = $GV->getHeaderInfo();

  my $content = qq~
  <TABLE width="600">
  $section_header
  </TABLE>
  $header
  <BR>
  <H4>Percent peptide per protein coverage (cumulative) for $builds{$parameters{pabst_build_id}}->{name}</H4>
  $cchart
  <BR>
  <BR>
  <H4>Percent peptide per protein coverage (detailed) for $builds{$parameters{pabst_build_id}}->{name}</H4>
  $ichart
  ~;
#  <TR><TD><TABLE>
#  </TD></TR></TABLE>

  return "$content";
}

sub make_individual_chart_function {
	my $samples = shift || return '';

  my ( $chart ) = $GV->setDrawBarChart(  samples => $samples,
                                    	data_types => [ 'string', 'number', 'number', 'number', 'number', 'number', 'number' ],
                                      	headings => [ 'Instrument', '0', '1', '2', '3', '4', '5+' ],
                                      show_table => 0,
                                 truncate_labels => 24,
                                         options =>  "hAxis: {title: 'Percentage'}"

 	);
  return ( $chart );
}

sub make_cumulative_chart_function {
	my $samples = shift || return '';

  my ( $chart ) = $GV->setDrawBarChart(  samples => $samples,
                                    	data_types => [ 'string', 'number', 'number', 'number', 'number', 'number', 'number' ],
                                      	headings => [ 'Instrument', '0', '1+', '2+', '3+', '4+', '5+' ],
                                      show_table => 0,
                                 truncate_labels => 24
 	);
  return ( $chart );
}



sub get_build_list {
  my %parameters = @_;
  my $content = '';

  my $atlas_build_id = $parameters{atlas_build_id};

  #### Read in the standard form values
  my $apply_action  = $parameters{'action'} || $parameters{'apply_action'};
  my $TABLE_NAME = $parameters{'QUERY_NAME'};


  #### Set some specific settings for this program
  my $PROGRAM_FILE_NAME = $PROG_NAME;
  my $base_url = "$CGI_BASE_DIR/$SBEAMS_SUBDIR/$PROGRAM_FILE_NAME";
  my $help_url = "$CGI_BASE_DIR/help_popup.cgi";


  #### Get a list of accessible project_ids
  my @accessible_project_ids = $sbeams->getAccessibleProjects();
  my $accessible_project_ids = join( ",", @accessible_project_ids ) || '0';

  # Get and cache all build stats
  my $stats_sql = qq~
  SELECT PBS.* 
  FROM $TBAT_PABST_BUILD_STATISTICS PBS
  JOIN $TBAT_PABST_BUILD PB
    ON PB.pabst_build_id = PBS.build_id
  WHERE project_id IN ( $accessible_project_ids )
  ~;

  my $sth = $sbeams->get_statement_handle( $stats_sql );
  use Data::Dumper;
  my %f;
  my $cnt;
  for my $f ( @{$sth->{NAME}} ) {
    $f{$f} = $cnt++;
  }
#  die Dumper( %f );

# builds is a global object
#  my %builds;

  my %cover;
	while ( my $row = $sth->fetchrow_hashref() ) {
    $builds{$row->{build_id}} ||= {};
    $builds{$row->{build_id}}->{bioseq_id} = $row->{ref_db};
    $builds{$row->{build_id}}->{bioseq_cnt} = $row->{ref_db_cnt};
    $builds{$row->{build_id}}->{instruments} ||= {}; 
    $builds{$row->{build_id}}->{instruments}->{$row->{instrument_id}} ||= {};;

    for my $cov ( qw( cov_0 cov_1 cov_2 cov_3 cov_4 cov_5 cov_any ) ) {
      $cover{$cov} ||= {};
      $cover{$cov}->{$row->{instrument_id}} ||= {};
      $cover{$cov}->{$row->{instrument_id}}->{$row->{build_id}} = $row->{$cov};
      $builds{$row->{build_id}}->{instruments}->{$row->{instrument_id}}->{$cov} = $row->{$cov};
    }

  }

  # Copy data prior to making it 'cumulative'
  my $curr = $builds{$parameters{pabst_build_id}};
  $current_build{bioseq_id} = $curr->{bioseq_id};
  $current_build{bioseq_cnt} = $curr->{bioseq_cnt};
  $current_build{instruments} = {};
  for my $inst ( keys( %{$curr->{instruments}} ) ) {
    for my $cov (  qw( cov_0 cov_1 cov_2 cov_3 cov_4 cov_5 cov_any ) ) { 
      $current_build{instruments}->{$inst}->{$cov} = $curr->{instruments}->{$inst}->{$cov};
    }
  }



  for my $bid ( keys( %builds ) ) {
    for my $instr ( keys( %{$builds{$bid}->{instruments}} ) ) {
      my $above = 0;
      for my $cov ( qw( cov_5 cov_4 cov_3 cov_2 cov_1 ) ) {
        my $incr = $above;
        $above += $builds{$bid}->{instruments}->{$instr}->{$cov};
        $builds{$bid}->{instruments}->{$instr}->{$cov} += $incr if $incr;
      }
    }
  }
  my @instruments = sort {$a <=> $b} keys( %{$cover{cov_any}} );
  push @instruments, shift( @instruments );

  my $sql = qq~
    SELECT pabst_build_id, build_name, build_comment
		FROM $TBAT_PABST_BUILD PB 
		JOIN $TB_ORGANISM O ON O.organism_id = PB.organism_id
    WHERE PB.project_id IN ( $accessible_project_ids )
    ORDER BY organism_name ASC, build_name ASC
    ~;
    my @atlas_builds = $sbeams->selectSeveralColumns($sql);

    #### If the output_mode is HTML, then display the form
    if ($sbeams->output_mode() eq 'html') {

    $content .= qq~
      <script LANGUAGE="Javascript">
        function switchBuild() {
          document.BuildList.apply_action.value = "GO";
          document.BuildList.submit();
        }
      </script>
      ~;

    $content .= $q->start_form(-method=>"POST",
                           -action=>"$base_url",
		                         -name=>"BuildList",
                          );
    }


    my $table = SBEAMS::Connection::DataTable->new();

    my @inst_headings = @code2instrument{@instruments};
    my $headings = [ '', 'Build Name', 'RefDB proteins', @inst_headings, 'Comment' ];
    my $heading_defs = { '' => 'Build Selector', 'Build Name' => 'Name of SRMAtlas build',
                'RefDB proteins' => 'Number of entries in source proteome - some builds cover only a sub-proteome',
                   'Comment' => 'Description of SRMAtlas build' };

    for my $inst ( @instruments ) {
      $heading_defs->{$code2instrument{$inst}} = "Number of proteins seen with $code2instrument{$inst} at specified coverage";
    }

    my $full_headings = $atlas->make_annotation_text( label_hash => $heading_defs, label_order => $headings );

    my %cov_defs = ( cov_1 => "Proteins covered by 1 or more peptides on specified instrument",
                     cov_2 => "Proteins covered by 2 or more peptides on specified instrument",
                     cov_3 => "Proteins covered by 3 or more peptides on specified instrument",
                     cov_4 => "Proteins covered by 4 or more peptides on specified instrument",
                     cov_5 => "Proteins covered by 5 or more peptides on specified instrument" );
 
    $content .= $sbeams->makeInfoText( "Table shows $cov_defs{$parameters{cov_level}}, coverage can be changed using SELECT list below the table.<BR>" );
        

    my $help_text = $atlas->make_table_help( 
                                               entries => $full_headings,
                                          );
#                                               footnote => $cover_def
    $content .= $help_text;

    my $bioseq_sets = $atlas->getBiosequenceSets();

    my @builds = ( $headings );
    # build has id, name, comment
    # %builds has the rest, keyed by build_id->instr->cov_depth
    foreach my $build ( @atlas_builds ) {
#			next unless $build->[9];
# [ '', 'Build Name', 'RefDB', 'RefDB proteins', @inst_headings, 'Comment' ];

      $builds{$build->[0]}->{name} = $build->[1];
      my $selected = '';
      my $bgcolor = '#dddddd';
      if ($build->[0] == $parameters{pabst_build_id} ) {
        $selected = 'CHECKED ';
      }
      my $radio = qq~
        <INPUT $selected TYPE="radio" NAME="pabst_build_id" VALUE="$build->[0]" onClick=blur() onChange="switchBuild()">
      ~;

      $build->[2] = $sbeams->truncateStringWithMouseover( len => 60, 
                                                       string => $build->[2],
                                                  add_elipses => 1,
                                               suppress_class => 1 );

#          $bioseq_sets->{$builds{$build->[0]}->{bioseq_id}},

      my $ref_db_cnt = $builds{$build->[0]}->{bioseq_cnt};
      my $ref_supp = '';
      # Sub proteome!
      if ( $builds{$build->[0]}->{instruments}->{0}->{cov_any} < 1000 ) {
        $ref_db_cnt = $builds{$build->[0]}->{instruments}->{0}->{cov_any};
        $builds{$build->[0]}->{bioseq_cnt} = $ref_db_cnt;
        $ref_supp = ' (sub-proteome)';
      }

      my @build_row = ( $radio, $build->[1], $ref_db_cnt . $ref_supp );

      print "<PRE>";
      for my $id ( @instruments ) {
        my $cnt = '&nbsp;-&nbsp;';
        if ( $builds{$build->[0]}->{instruments}->{$id} ) {
#          print "we have $id for $build->[0]\n";
          if ( $builds{$build->[0]}->{instruments}->{$id}->{$parameters{cov_level}} ) {
#            print "we have $parameters{cov_level}!!\n";
#            $cnt = sprintf( "%0.1f", 100*$builds{$build->[0]}->{instruments}->{$id}->{$parameters{cov_level}}/$ref_db_cnt ) . '%'; 
            $cnt = sprintf( "%0.1f", 100*$builds{$build->[0]}->{instruments}->{$id}->{$parameters{cov_level}}/$ref_db_cnt ) . '%'; 
          }
        }
        push @build_row, $cnt;
      }
#      print "build is $build->[0], cov is $parameters{cov_level}";
#      print Dumper( $builds{$build->[0]} );
      print "</PRE>";

      push @build_row, $build->[2];

      push @builds, \@build_row;
    }

    my ( $html, $rs_name ) = $atlas->encodeSectionTable( header => 1,
                                                        width => '600',
                                                         rows => \@builds,
                                                 rows_to_show => 5000,
                                                     max_rows => 5000,
                                                    help_text => '',
                                                        align => [ qw( center left right right right right right right right left ) ],
                                                     bg_color => '#EAEAEA',
                                                     sortable => 0,
                                                     table_id => 'SRMAtlas',
                                                     );

#   $table->setColAttr(  COLS => [2..8], ROWS => [1..$table->getRowNum()], ALIGN => 'RIGHT' );
#  $html =~ s/TABLE NOOP/TABLE style="display:none" NOOP/gm;


  $content .= "<TABLE>$html</TABLE>";

  $content .= get_cover_select(); 
  $content .= $q->hidden( "apply_action", '');
  $content .= $q->end_form;

  return $content;
} # get_build_list 

sub get_cover_select {

  my %selected = ( cov_1 => '', cov_2 => '', cov_3 => '', cov_4 => '', cov_5 => '' );
  $selected{$parameters{cov_level}} = 'selected';

  my $select = qq~
  <SELECT NAME=cov_level onChange="submit()">
  <OPTION VALUE=cov_1 $selected{cov_1}> Covered by one or more peptide(s) </OPTION>
  <OPTION VALUE=cov_2 $selected{cov_2}> Covered by two or more peptides </OPTION>
  <OPTION VALUE=cov_3 $selected{cov_3}> Covered by three or more peptides </OPTION>
  <OPTION VALUE=cov_4 $selected{cov_4}> Covered by four or more peptides </OPTION>
  <OPTION VALUE=cov_5 $selected{cov_5}> Covered by five or more peptides </OPTION>
  </SELECT>
  ~;
  return $select;
}