#!/usr/local/bin/perl

###############################################################################
# Program     : EvalProtEvidence
# Author      : Terry Farrah <tfarrah@systemsbiology.org>
# $Id: main.cgi 6972 2012-02-28 06:50:02Z dcampbel $
#
# Description : Interface for manual evaluation of protein evidence.
#
# SBEAMS is Copyright (C) 2000-2013 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 $sbeamsMOD $PROG_NAME
             $current_contact_id $current_username);
use lib qw (../../lib/perl);
use CGI::Carp qw(fatalsToBrowser croak);
use FindBin;
use lib "$FindBin::Bin/../../lib/perl";

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

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


###############################################################################
# Global Variables
###############################################################################
$PROG_NAME = 'EvalProtEvidence';
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,
    ));


    #### Read in the default input parameters
    my %parameters;
    my $n_params_found = $sbeams->parse_input_parameters(
        q=>$q,
        parameters_ref=>\%parameters
        );

    if ( $parameters{reset_id} && $parameters{reset_id} eq 'true' ) {
      $sbeamsMOD->clearBuildSettings();
    }

    ## get project_id to send to HTMLPrinter display
    my $project_id = $sbeamsMOD->getProjectID(
        atlas_build_name => $parameters{atlas_build_name},
        atlas_build_id => $parameters{atlas_build_id}
        );


    #### Process generic "state" parameters before we start
    $sbeams->processStandardParameters(parameters_ref=>\%parameters);
#    $sbeams->printCGIParams($q);


    #### Decide what action to take based on information so far
    if ($parameters{action} eq "???") {

        # Some action
 
    } else {

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

        handle_request(ref_parameters=>\%parameters);

        $sbeamsMOD->display_page_footer();

    }




} # end main


###############################################################################
# Show the main welcome page
###############################################################################
sub handle_request {

    my %args = @_;

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

    my %parameters = %{$ref_parameters};


  #### Get the current atlas_build_id based on parameters or session
  my $atlas_build_id = $sbeamsMOD->getCurrentAtlasBuildID(
    parameters_ref => \%parameters,
  );
  if (defined($atlas_build_id) && $atlas_build_id < 0) {
    #### Don't return. Let the user pick from a valid one.
    #return;
  }


  #### 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 "<BR>\n";
    print $tabMenu->asHTML() if ($sbeams->output_mode() eq 'html');
    print "<BR>\n";
  }


    #### 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';

    my $ATLAS_BUILD_ID = $parameters{atlas_build_id} || 393; 

    #### Get a list of putative proteins
    my $sql = qq~
      select
      bs.biosequence_name,
      pprot.spectrum_annotation_level_id,
      pprot.added_to_nextprot,
      pprot.added_to_nextprot,
      pid.protein_group_number,
      bs.biosequence_id,
      count(ppp.putative_protein_id) as n_novel_peps,
      count(distinct pia.protein_identification_annotation_id),
      avg(sal.level_probability)

      from $TBAT_PUTATIVE_PROTEIN pprot
      join $TBAT_BIOSEQUENCE bs
      on bs.biosequence_id = pprot.biosequence_id
      join $TBAT_PROTEIN_IDENTIFICATION pid
      on pid.biosequence_id = bs.biosequence_id
	and pid.atlas_build_id = $ATLAS_BUILD_ID
      join $TBAT_PUTATIVE_PROTEIN_PEPTIDE ppp
      on ppp.putative_protein_id = pprot.putative_protein_id
      left join $TBAT_PROTEIN_IDENTIFICATION_ANNOTATION pia
      on pia.protein_identification_id = pid.protein_identification_id
      left join $TBAT_SPECTRUM_ANNOTATION_LEVEL sal
      on sal.spectrum_annotation_level_id =
         pia.spectrum_annotation_level_id

        group by
	  bs.biosequence_name,
	  pprot.spectrum_annotation_level_id,
	  pprot.added_to_nextprot,
	  pid.protein_group_number,
	  bs.biosequence_id
	order by
	  bs.biosequence_name
  ~;
  my @results = $sbeams->selectSeveralColumns($sql);

  ### Get biosequence descriptions (they are of type text, so can't
  ### be retrieved in the above query due to the GROUP BY)
  $sql = qq~
    select
    bs.biosequence_name, bs.biosequence_desc
      from $TBAT_PUTATIVE_PROTEIN pprot
      join $TBAT_BIOSEQUENCE bs
      on bs.biosequence_id = pprot.biosequence_id
      join $TBAT_PROTEIN_IDENTIFICATION pid
      on pid.biosequence_id = bs.biosequence_id
	and pid.atlas_build_id = $ATLAS_BUILD_ID
    ~;
  my %descr;
  my @results_descr = $sbeams->selectSeveralColumns($sql);
  foreach my $result_aref ( @results_descr ) {
    $descr{$result_aref->[0]} = $result_aref->[1];
  }

  #### Get a list of putative peptides mapping to a each protein
  my $sql = qq~
    select
    bs.biosequence_id,
    p.peptide_sequence
    from $TBAT_PUTATIVE_PROTEIN pprot
    join $TBAT_BIOSEQUENCE bs
    on bs.biosequence_id = pprot.biosequence_id
    join $TBAT_PUTATIVE_PROTEIN_PEPTIDE ppp
    on ppp.putative_protein_id = pprot.putative_protein_id
    join $TBAT_PEPTIDE p
    on p.peptide_id = ppp.peptide_id
  ~;
  my %peps;
  my @results_pep = $sbeams->selectSeveralColumns($sql);
  foreach my $result_aref ( @results_pep ) {
    #print "Hashing $result_aref->[0] to $result_aref->[1]<br>\n";
    $peps{$result_aref->[0]}->{$result_aref->[1]} = 1;
  }

  #### If the output_mode is HTML, then display the form
  if ($sbeams->output_mode() eq 'html') {
    my $table = SBEAMS::Connection::DataTable->new();
    my $rows = $table->getRowNum();

    # Can add Comments back once I change their datatype from text to
    # varchar in the schema! need to add back to SELECT and GROUP BY
    # as well.
    $table->addRow( [  'Biosequence', 'Status', 'in NP?', 'Comments', 'Novel Peptides', 'Protein Group', 'Algn w/SP in grp', 'N Evals', 'Avg Eval', 'Description' ] );
    $table->setRowAttr(  COLS => [1..7], ROWS => [1], BGCOLOR => '#bbbbbb', ALIGN=>'CENTER' );
    $table->setHeaderAttr( BOLD => 1 );

    foreach my $result_aref ( @results ) {
       my @row;
       my @trinfo;
       my $bgcolor = '#dddddd';

       my $bioseq_name = $result_aref->[0];
       my $bioseq_id = $result_aref->[5];
 
       $row[0] =<<"      END";
       <A HREF=GetProtein?atlas_build_id=$ATLAS_BUILD_ID&protein_name=$result_aref->[0]&action=GO&apply_action=QUERY&ann=1>
       $result_aref->[0]</A>
      END

       $row[1] = $result_aref->[1];
       $row[2] = $result_aref->[2];
       #$row[3] = $sbeams->truncateStringWithMouseover( string => $result_aref->[3], len => 50 );
       $row[4] =<<"      END";
       <A HREF=EvalPepEvidence?biosequence_id=$bioseq_id>
       $result_aref->[6]</A>
      END
       $row[5] =<<"      END";
       <A HREF=GetProteins?atlas_build_id=$ATLAS_BUILD_ID&protein_group_number_constraint=$result_aref->[4]&apply_action=QUERY>
       $result_aref->[4]</A>
      END
       my $pepseq_csv = join(',', keys %{$peps{$bioseq_id}});
       $row[6] =<<"      END";
       <A HREF=compareProteins?bioseq_id=$bioseq_id&swiss_prot_only=1&protein_group_number=$result_aref->[4]&pepseq=${pepseq_csv}&eval_prot_evidence=1><IMG BORDER="0" SRC="/sbeams/images/compareProteins.png"></A>
      END


#       $row[4] = ( !$atlas_build->[3] ) ? 'N' : ( $row[4] ) ?
# 		"<SPAN CLASS=popup_help TITLE='$atlas_build->[4]'>Y</SPAN>" : 'Y';
      $row[7] = $result_aref->[7];
      $row[8] = sprintf "%0.2f", $result_aref->[8];

      my $biosequence_description = $descr{$result_aref->[0]};
       $row[9] = $sbeams->truncateStringWithMouseover( string => $biosequence_description, len => 50 );

      $table->addRow( \@row );
      $rows = $table->getRowNum();
      $table->setRowAttr(  COLS => [1..8], ROWS => [$rows], BGCOLOR => $bgcolor, @trinfo );
    }

    $table->setColAttr(  COLS => [1..8], ROWS => [1..$rows], NOWRAP => 1 );
    $table->setColAttr(  COLS => [3], ROWS => [1..$rows], ALIGN => 'RIGHT' );
    $table->setColAttr(  COLS => [4,5], ROWS => [1..$rows], ALIGN => 'CENTER' );
    print "$table";
    print $q->hidden( "apply_action", '');
    print $q->end_form;

  }


} # end showMainPage