#!/usr/local/bin/perl

###############################################################################
# $Id$
#
# SBEAMS is Copyright (C) 2000-2007 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 ($sbeams);
use lib qw (../../lib/perl);
#use CGI::Carp qw(fatalsToBrowser croak);

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


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


###############################################################################
# Global Variables
###############################################################################
my $sbeams = new SBEAMS::Connection;
$sbeams->setSBEAMS_SUBDIR($SBEAMS_SUBDIR);
my $atlas = new SBEAMS::PeptideAtlas;
$atlas->setSBEAMS($sbeams);

# Read input parameters
my $params = process_params();
my $rs_params = { %$params };


my $atlas_build_id = '';
my $out_mode;

{ # Main 

    # Authenticate or exit
    my $username = $sbeams->Authenticate( permitted_work_groups_ref => 
                                                      ['PeptideAtlas_user',
                                                      'PeptideAtlas_admin', 
                                                      'PeptideAtlas_readonly', 'PeptideAtlas_exec'],
                                                      # connect_read_only=>1,
                                              ) || exit;

    $out_mode = $sbeams->output_mode();

    ## get current settings
    my $project_id = $sbeams->getCurrent_project_id();


    my $page = '';

    $page .= $sbeams->getGifSpacer( 700 ) . "<BR>\n" if $out_mode eq 'html';

  #### Get the HTML to display the tabs
    my $tabMenu = $atlas->getTabMenu(
      parameters_ref => $params,
      program_name => 'proteinListDetails',
    );
#
    $atlas_build_id = $params->{build_id} || $atlas->getCurrentAtlasBuildID(parameters_ref => $params);
    my $list_id = $params->{list_id};
    $list_id ||= $atlas->getDefaultProteinListID( build_id => $atlas_build_id);

    
  # Add general section 
  if ( $out_mode eq 'html' ) {
    $page .= get_list_overview ( $list_id );
    $page .= "<BR>\n";
  }

  $page .= get_list_entries ( list_id => $list_id );

#    my ( $sample_table, $sample_arrayref ) = get_sample_info( $build_id );
#    my ( $chart_div, $header ) = get_draw_chart_function( $sample_arrayref );

#    $page .= "<BR>$batch_help\n";
#    $page .= $sample_table;
  if ( $out_mode eq 'html' ) {
    $page .= "<BR>\n";
  }

    # Print what we already have, speed up apparent page loading time.

    $atlas->display_page_header(  project_id => $project_id, onload => 'sortables_init()', sortable => 1 );

		print $page;

#    my $build_path = get_build_path( build_id => $build_id );

		$atlas->display_page_footer();

} # end main

  
  
sub get_list_entries {
  my %args = @_; 

  my $content = '';

  if ( $out_mode eq 'html' ) {
    $content .= $atlas->encodeSectionHeader(
      LMTABS => 1,
      no_toggle => 1,
      text => 'Proteins',
      span => 4,
    );
  }

  my @column_array = (
    ["protein_name","PLP.protein_name","Accession"],
    ["Description","substring( PLP.protein_description, 1, 80 )","Description"],
    ["num_peps"," COUNT( distinct peptide_id )", "Num Peps"],
    ["num_obs","SUM(n_observations) ", "Num Obs"],
    ["key_accession","PLP.key_accession ", "Related"],
    ["length","len( CAST( B.biosequence_seq AS VARCHAR(2000) ) ) ", "Length"],
    ["Status","CASE WHEN order_status = 'D' THEN 'Delivered' ELSE 'Unknown' END", "Status"],
  );

  # Defalut to query mode
  $params->{apply_action} ||= 'QUERY';

  if ( $params->{apply_action} =~ /(QUERY|GO)/) {
    if ( 1 || $params->{show_nxst} ) {
      push @column_array, ["NxST","CASE WHEN CAST( Biosequence_seq AS VARCHAR(2000) ) LIKE '%N[^P][ST]%' THEN 'Yes' WHEN CAST( Biosequence_seq AS VARCHAR(2000) ) IS NULL THEN 'n/a' ELSE 'No' END ", "NxST"];
    }
    if ( 1 || $params->{show_cys} ) {
      push @column_array, ["Cys","CASE WHEN CAST( Biosequence_seq AS VARCHAR(2000) ) LIKE '%C%' THEN 'Yes' WHEN CAST( Biosequence_seq AS VARCHAR(2000) ) IS NULL THEN 'n/a' ELSE 'No' END ", "Cys"];
    }
  } else {
    push @column_array, ["NxST","CASE WHEN CAST( Biosequence_seq AS VARCHAR(2000) ) LIKE '%N[^P][ST]%' THEN 'Yes' WHEN biosequence_seq = '' THEN 'n/a' ELSE 'No' END ", "NxST"];
    push @column_array, ["Cys","CASE WHEN CAST( Biosequence_seq AS VARCHAR(2000) ) LIKE '%C%' THEN 'Yes' WHEN biosequence_seq = '' THEN 'n/a' ELSE 'No' END ", "Cys"];
  }

  #### Build the columns part of the SQL statement
  ## Sends @column_array_ref to build_SQL_columns_list, which
  ## (1) appends the 2nd element in array to $columns_clause
  ## (2) fills %colnameidx_ref as a hash with key = 1st element
  ## and value = 3rd element, and (3) fills @column_titles_ref
  ## array with the 3rd element

  my %colnameidx;
  my @column_titles;
  my $columns_clause = $sbeams->build_SQL_columns_list(
    column_array_ref=>\@column_array,
    colnameidx_ref=>\%colnameidx,
    column_titles_ref=>\@column_titles
  );

#  protein_name, protein_description, COUNT( distinct peptide_id ) num_peptides, key_accession SUM( n_observations ) num_obs,

  my $sql = qq~
  SELECT DISTINCT $columns_clause
  FROM $TBAT_PROTEIN_LIST_PROTEIN PLP
  LEFT JOIN $TBAT_BIOSEQUENCE B 
    ON ( PLP.protein_name = B.biosequence_name OR B.biosequence_name IS NULL )
  LEFT JOIN $TBAT_PEPTIDE_MAPPING PM 
    ON B.biosequence_id = PM.matched_biosequence_id
  LEFT JOIN $TBAT_PEPTIDE_INSTANCE PI 
  ON PI.peptide_instance_id = PM.peptide_instance_id 
  WHERE ( atlas_build_id = 217 OR atlas_build_id IS NULL )

  AND protein_list_id = $args{list_id}
  AND protein_name = key_accession  -- For now, limit to 'primary' accession
  AND protein_name NOT LIKE '%-1'
  GROUP BY protein_name, protein_description, key_accession, CAST( biosequence_seq AS VARCHAR(2000) ), order_status 
  ORDER BY key_accession ASC 
  ~;
 
  my $resultset_ref = {};

  my $hidden_cols = { biosequence_seq => 1 };
#  my $trim_width_ref = { Description => 40 };

  my $url_cols = { 'Accession' => "$CGI_BASE_DIR/PeptideAtlas/GetProtein?show_synthpep_track=1;atlas_build_id=$atlas_build_id;protein_name=%V&action=GO;show_aa_content=1",
                   'Related' => "$CGI_BASE_DIR/PeptideAtlas/compareProteins?build_id=$atlas_build_id;protein_list_id=$args{list_id};key_accession=%V&action=QUERY" };

  my $query_name = "$SBEAMS_SUBDIR/proteinListDetails";
  my $base_url = "$CGI_BASE_DIR/$SBEAMS_SUBDIR/proteinListDetails";

  if ( $params->{apply_action} =~ /(QUERY|GO)/) {

    #### Fetch the results from the database server
    $sbeams->fetchResultSet(
      sql_query=>$sql,
      resultset_ref=>$resultset_ref,
    );

    #### Store the resultset and parameters to disk resultset cache
    $rs_params->{set_name} = "SETME";
    $sbeams->writeResultSet(
        resultset_file_ref => \$rs_params->{set_name},
             resultset_ref => $resultset_ref,
      query_parameters_ref => $params,
      resultset_params_ref => $rs_params,
      query_name=> $query_name
    );


  } elsif ( $params->{apply_action} eq "VIEWRESULTSET") {

    $sbeams->readResultSet(
      resultset_file       => $params->{set_name},
      resultset_ref        => $resultset_ref,
      query_parameters_ref => $params,
      resultset_params_ref => $rs_params,
    );
  }



  $log->info( "Base URL is $base_url" );

  $sbeams->collectSTDOUT();
  
  $rs_params->{page_size} ||= 50;

  # Display the resultset
  $sbeams->displayResultSet(
      resultset_ref=>$resultset_ref,
      query_parameters_ref=>$params,
      rs_params_ref=>$rs_params,
      url_cols_ref=>$url_cols,
      hidden_cols_ref=>$hidden_cols,
#      trim_width_ref=> $trim_width_ref,
      column_titles_ref=>\@column_titles,
      base_url=> $base_url,
      no_escape => 1
    );

    # Display the resultset controls
  if ( $out_mode eq 'html' ) {
    $sbeams->displayResultSetControls(
      resultset_ref=>$resultset_ref,
      query_parameters_ref=> $params,
      rs_params_ref=> $rs_params,
      base_url=> $base_url,
    );
  }
  $content .= $sbeams->fetchSTDOUT();
  return $content;

}


# General build info, date, name, organism, specialty, default
#

sub get_list_overview {

  my $list_id = shift;
# 0 protein_list_id
# 1 protein_list_name
# 2 contributor_name
# 3 contributor_contact_id
# 4 protein_list_description
# 5 project_id    

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

  my $list_sql = qq~
  SELECT protein_list_id, protein_list_name, contributor_name, protein_list_description, project_id 
  FROM $TBAT_PROTEIN_LIST 
  WHERE protein_list_id = $list_id
  AND project_id IN ( $project_ids )
  ORDER BY protein_list_id DESC
  ~;

  my $list_info = $sbeams->selectrow_hashref( $list_sql );
      
  my $prot_count = $sbeams->selectrow_hashref( <<"  PEP" );
  SELECT COUNT(*) cnt, COUNT(DISTINCT key_accession) dist
  FROM   $TBAT_PROTEIN_LIST_PROTEIN
  WHERE protein_list_id = $list_id
  PEP

  my $table = "<TABLE WIDTH=800>\n";

  my ( $tr, $link ) = $sbeams->make_table_toggle( name    => 'list_overview',
                                                  visible => 1,
                                                  tooltip => 'Show/Hide Section',
                                                  imglink => 1,
                                                  sticky  => 1 );

  $table .= $atlas->encodeSectionHeader(
      LMTABS => 1,
      no_toggle => 1,
      text => 'List Overview',
      span => 4,
      link => $link
  );

  my $spc = $sbeams->getGifSpacer(500);

  $table .= $atlas->encodeSectionItem( key   => 'List Name', tr_info => $tr,
                            value => $list_info->{protein_list_name} . $spc, vspan => 3 ) . "\n";
  $table .= $atlas->encodeSectionItem( key   => 'List Description', tr_info => $tr,
                            value => $list_info->{protein_list_description}, vspan => 3 ) . "\n";
  $table .= $atlas->encodeSectionItem( key   => 'Contributor', tr_info => $tr,
                            value => $list_info->{contributor_name} ) . "\n";
  $table .= $atlas->encodeSectionItem( key   => '# List Entries', tr_info => $tr,
                            value => $prot_count->{dist}, align => 'right' ) . "\n";
  $table .= $atlas->encodeSectionItem( key   => '# Mapped Proteins', tr_info => $tr,
                            value => $prot_count->{cnt}, align => 'right' ) . "\n";

  $table .= "</TABLE>\n";
  return $table;

}



sub process_params {
  my $params = {};
  $sbeams->parse_input_parameters( q => $q, parameters_ref => $params );
  $sbeams->processStandardParameters( parameters_ref => $params );
  $sbeams->processStandardParameters( parameters_ref => $params );
  my %rs_params = $sbeams->parseResultSetParams(q=>$q);
  for my $key ( keys %rs_params ) {
    $params->{$key} = $rs_params{$key};
  }
  return( $params );
}

sub get_build_path {
  my %args = @_;
  return unless $args{build_id};
  my $path = $atlas->getAtlasBuildDirectory( atlas_build_id => $args{build_id} );
  $path =~ s/DATA_FILES//;
  return $path;
}

sub get_draw_chart_function {
	my $sample_arrayref = shift || return '';

	my @samples;
	for my $s ( @{$sample_arrayref} ) {
		push @samples, [ $s->[1], $s->[4], $s->[7] ];
	}
	my $GV = SBEAMS::Connection::GoogleVisualization->new();
  my ( $chart ) = $GV->setDrawBarChart(  samples => \@samples,
                                    	data_types => [ 'string', 'number', 'number' ],
                                      	headings => [ 'Sample', 'Distinct peptides (n_obs > 1)', 'Cumulative peptides (n_obs > 1)' ],
                                      show_table => 0,
                                 truncate_labels => 24
 	);
	my $header = $GV->getHeaderInfo();
  return ( $chart, $header );
}