#!/usr/local/bin/perl -w

###############################################################################
# Program     : GetPeptideLocations
#
# Description : Get locations for user-defined set of peptides
###############################################################################

$|++;

## Setup objects and globals 
use strict;
use Getopt::Long;
use FindBin;

use lib "$FindBin::Bin/../../lib/perl";
use vars qw ( $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;

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

# Set up Atlas objects
my $sbeams = new SBEAMS::Connection;
my $atlas = new SBEAMS::PeptideAtlas;
$atlas->setSBEAMS($sbeams);
$sbeams->setSBEAMS_SUBDIR( 'PeptideAtlas' );
my $best_peptide = new SBEAMS::PeptideAtlas::BestPeptideSelector;
$best_peptide->setAtlas( $atlas );
$best_peptide->setSBEAMS( $sbeams );
my $pabst_build_id;

my $is_html = 0;

main();
exit(0);

# Main Program
sub main 
{
  # Authenticate and exit if a username is not returned
  my $current_username = $sbeams->Authenticate( allow_anonymous_access => 0 );
  exit unless $current_username;

  $is_html = ( $sbeams->output_mode() eq 'html' ) ? 1 : 0;

  #### 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);


  # 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);

  # Decide what action to take based on information so far
  print $sbeams->get_http_header( mode => 'html'  );
	print_style();

#  $sbeams->printCGIParams($q);
  if ( $parameters{peptides} || $parameters{plates} ) {
    print_locations( \%parameters );
  }
  print_form( %parameters );

} # end main


sub print_form {

  my %args = @_;

  my $fuzz_checked = ( $args{fuzzy} ) ? 'checked' : '';

  my $tmp_checked = ( $args{tmp_plate} ) ? 'checked' : '';


  my %type_checked = ( m => 'checked', w => '', b => '' );
  if ( $args{type} eq 'Both' ) {
    $type_checked{m} = '';
    $type_checked{b} = 'checked';
  } elsif ( $args{type} eq 'Working' ) {
    $type_checked{m} = '';
    $type_checked{w} = 'checked';
  }
  my $order_select = get_order_select();

  print qq~
	
<div class="form-container">
 <form name=GetPlates method=POST>
  <fieldset>
   <legend>Search Peptides</legend>
    <div>
     <span class=label>Sequences:</span>
     <textarea id="peptides" name="peptides" cols="30" rows="8">$args{peptides}</textarea>
    </div>
  </fieldset>
  <fieldset>
   <legend>Search Plates</legend>
    <div>
     <span class=label>Plate Names:</span>
     <textarea id="plates" name="plates" cols="30" rows="6">$args{plates}</textarea>
     <br>
     <span class=label>Plate type:</span>
     <input type=radio id="type" name="type" value='Master' align=left $type_checked{m} >Master</input>
     <input type=radio id="type" name="type" value='Working' align=left $type_checked{w}>Working</input>
     <input type=radio id="type" name="type" value='Both' align=left $type_checked{b}>Both</input>
     <br>
    </div>
    <div>
     <span class=label>Add tmp well?:</span>
     <input type=checkbox id="tmp_plate" name="tmp_plate" $tmp_checked></input>
    </div>
    <div>
     <span class=label>Fuzzy Match?:</span>
     <input type=checkbox id="fuzzy" name="fuzzy" $fuzz_checked></input>
    </div>
    <div>
     <span class=label>Restrict Order:</span>
     $order_select
    </div>
  </fieldset>
 
  <div class="buttonrow">
   <input type="submit" value="Search" class="button" />
   <input type="reset" value="Clear" class="button" />
  </div>
 </form>
</div>
  ~;




} # end handle_request

sub print_style {
	print qq~
<style>
	div.form-container form p { margin: 0; }
	div.form-container form p.note { margin-left: 170px; font-size: 90%; color: #333; }
	div.form-container form fieldset { margin: 10px 0; padding: 10px; border: #DDD 1px solid; }
	div.form-container form legend { font-weight: bold; color: #666; }
	div.form-container form fieldset div { padding: 0.25em 0; }
	div.form-container label, 
	div.form-container span.label { margin-right: 10px; padding-right: 10px; width: 150px; display: block; float: left; text-align: right; position: relative; }
	div.form-container label.error, 
	div.form-container span.error { color: #C00; }
	div.form-container label em, 
	div.form-container span.label em { position: absolute; right: 0; font-size: 120%; font-style: normal; color: #C00; }
	div.form-container input.error { border-color: #C00; background-color: #FEF; }
	div.form-container input:focus,
	div.form-container input.error:focus, 
	div.form-container textarea:focus {	background-color: #EFF; border-color: #FC6; }
	div.form-container div.controlset label, 
	div.form-container div.controlset input { display: inline; float: none; }
	div.form-container div.controlset div { margin-left: 170px; }
	div.form-container div.buttonrow { margin-left: 180px; }

  .info_box { background: #F0F0F0; border: #000 1px solid; padding: 4px; width: 80%; color: #444444 }
	.clear_info_box { border: #000 1px solid; padding: 4px; width: 80%; color: #444444 }
  .sortheader{background-color: #888888; font-size: 10pt; font-weight: bold; color:white; line-height: 25px;}
	.sortarrow { font-size: 12pt; font-weight: bold }

</style>
~;

}

sub annotate {

  my %parameters = @_;

# 0 ID
# 1 Tran_Plate
# 2 Tran_well
# 3 Plate
# 4 well
# 5 Symbol
# 6 QC_Positive
# 7 Lysate_SKU
# 8 protein_mw
# 9 RCclone
# 10 ProteinID
# 11 Accn
# 12 locus_id
# 13 swissprot
  if ( $parameters{upload_file} ) {

    my %map;
    while ( my $line = <DATA> ) {
      chomp $line;
      my @line = split( "\t", $line, -1 );
      my $map_acc = $line[9];
      $map_acc =~ s/RC2//;
      $map{$map_acc} = $line[13] || $line[12] || 'na';
    }
    my $basename = $parameters{upload_file};
    if ( $basename =~ /\.\w+$/ ) {
      $basename =~ s/\.\w+/\.map/;
    } else {
      $basename .= '.map';
    }


    ## upload the file to a file handler
    my $fh = $q->upload('upload_file');

    if (!$fh && $q->cgi_error && $is_html) {
#      print $q->header(-status=>$q->cgi_error);
    }

    my $max_cnt = 100000;
    my $cnt = 0;

#    print $header;
    while ( my $line = <$fh> ) {
      chomp $line;
			$line =~ s/\r//g;
      my @line = split( "\t", $line, -1 );
      if ( $cnt++ ) {
        my $map_id = $line[0];
        $map_id =~ s/TP3//;
        my $sp_id = $map{$map_id} || 'NoMap';
        push @line, $sp_id;
      } else {
        push @line, 'SwissProt';
      }
      print join( "\t", @line ) . "\n";
    }
  } else {
    print_form();
  }
  exit;

} # annotate fetch_peptides;

sub print_locations {
  my $params = shift;

  if ( !$params->{peptides} && !$params->{plates} ) {
    die "Choans";
    print "<div class=warning_msg>Must provide either peptides or plates to search</div><br>\n";
  }

	my $peptides = $params->{peptides};
	$params->{peptide_string} = '';

	$peptides =~ s/\s+/ /gm;
	my @peptides = split /\s+/, $peptides;
	my %peptides;
	for my $peptide ( @peptides ) {
		$peptides{$peptide}++;
	}

  my $peptide_and = '';
  if ( $params->{peptides} && $params->{peptides} =~ /\w/ ) {
    $peptide_and = 'AND sequence IN (';
    my $sep = '';
  	for my $seq ( keys( %peptides ) ) {
	  	$peptide_and .= $sep . "'$seq'";
		  $sep = ',';
  		$params->{peptide_string} .= "$seq\n";
  	}
	  $peptide_and .= ")\n";
  }

	my $plates = $params->{plates};
	$params->{plate_string} = '';
	$plates =~ s/\s+/ /gm;
	my @plates = split /\s+/, $plates;
	my %plates;
	for my $plate ( @plates ) {
		$plates{$plate}++;
	}

  my $plate_and = '';
  if ( $params->{plates} && $params->{plates} =~ /\w/ ) {
    my $sep = '';
  	for my $plate ( keys( %plates ) ) {
      if ( $params->{fuzzy} ) {
        if ( !$sep ) {
          $plate_and .= "AND plate_barcode_id LIKE '%" . $plate . "'\n";
        } else {
          $plate_and .= "OR plate_barcode_id LIKE '%" . $plate . "'\n";
        }
      } else {
        if ( !$sep ) {
          $plate_and .= 'AND plate_barcode_id IN (';
        }
  	  	$plate_and .= $sep . "'$plate'";
  	  	$params->{plate_string} .= "$plate\n";
      }
	  	$sep = ',';
  	}
	  $plate_and .= ")\n" unless $params->{fuzzy};
  }

  my $order_and = '';
  if ( $params->{Order} && $params->{Order} ne 'All' ) {
    $order_and = "AND orders.name = '$params->{Order}'";
  }


  open PEPS, "/net/db/projects/PeptideAtlas/MRMAtlas/current_libs/peptides2proteins.tsv" || die "Unable to open peptide file";
  my %pep2prot;
  while ( my $line = <PEPS> ) {
	  chomp $line;
    my @line = split( /\t/, $line );
    $pep2prot{$line[0]} = $line[1];
  }

  my $driver = 'DBI:mysql:mrmatlas_lims:mslims';
  my $user = 'mrm_ro';
  my $pass = 'Tsr3#@gfA356!&5';
  my %error = ( PrintError => 1, RaiseError => 1);
  my $dbh = DBI->connect($driver,$user,$pass,\%error);

  my @headings = qw( sequence well_barcode_id freezer shelf rack box row col mw ssr isb_index peptides.status orders.name plate_barcode_id plate_type conc amountMol  );
	my $heading_str = join( ', ', @headings );
  my $sql = qq~
  SELECT $heading_str 
  FROM plates JOIN orders ON plates.order_id = orders.id
  JOIN locations ON locations.id = plates.location_id
  JOIN plate_peptides ON plate_peptides.plate_id = plates.id
  JOIN peptides  ON peptides.id = plate_peptides.peptide_id
  LEFT JOIN vendor_plate_detail  ON vendor_plate_detail.plate_peptide_id = plate_peptides.id
  WHERE 1 = 1
  $peptide_and
  $plate_and
  $order_and
  ORDER BY orders.id ASC, plate_barcode_id ASC, row, col
  ~;

#SELECT sequence, mw, pp.volume as 'pp_vol', plate_barcode_id, o.name, vendor, amountMg, amountMol, conc, vpd.volume as 'vol'
#FROM peptides p JOIN plate_peptides pp ON p.id = pp.peptide_id
#                JOIN plates pl ON pl.id = pp.plate_id 
#                JOIN orders o ON o.id = pl.order_id 
#                JOIN vendor_plate_detail vpd ON vpd.plate_peptide_id = pp.id 
#limit 10 ;

  $headings[15] = 'mg/ml';
  $headings[16] = 'nmol';

   my @wells;
   if ( $params->{tmp_plate} ) {
     $headings[17] = 'tmp_well';
     for my $row ( 'A'..'H' ) {
       for my $col ( 1..12 ) {
         my $pcol = ( $col > 9 ) ? $col : '0' . $col;
         push @wells, $row . $pcol;
       }
     }
   }

  my $sth = $dbh->prepare( $sql );
  $sth->execute();
	my @peptides;
  push @headings, 'Protein ACC';
  my $tmp_plate = 1;
  while ( my @row = $sth->fetchrow_array() ) {
    my $prot = $pep2prot{$row[0]} || '';
		$row[10] = ucfirst( lc($row[10]) );

    if ( $params->{type} =~ /working/i ) {
	  	next if $row[14] =~ /master/i;
    } elsif ( $params->{type} =~ /master/i ) {
	  	next if $row[14] =~ /working/i;
    }
    
    if ( $params->{tmp_plate} ) {
      my $well = shift @wells;
      
      my $plate_well = $tmp_plate . '_' . $well;
      $tmp_plate++ if $well eq 'H12';

      push @row, $plate_well;
      push @wells, $well;
    }
	  push @peptides, [@row, $prot];

  }

unshift @peptides, \@headings;
my $align = [ qw( left right left right right left left left left left left left ) ];
my $help_text = '';
my $change_on = 12;

my ( $html, $rs_name ) = $atlas->encodeSectionTable( header => 1,
                                                      width => '600',
                                                      align  => $align,
                                                      rs_headings => \@headings,
                                                      rows => \@peptides,
                                                      rows_to_show => 25,
                                                      max_rows => 10,
                                                      help_text => $help_text,
                                                      chg_bkg_idx => $change_on,
                                                      set_download => 'Download peptides',
                                                      file_prefix => 'best_peptides_',
                                                      bg_color => '#EAEAEA',
                                                      sortable => 1,
                                                      table_id => 'pabst',
                                                      close_table => 1,
                                                      );
print qq~
  <fieldset>
   <legend>Results</legend>
    $rs_name
    <div>
		 $html
    </div>
  </fieldset>
	~;



}

sub get_order_select {
  my $driver = 'DBI:mysql:mrmatlas_lims:mslims';
  my $user = 'mrm_ro';
  my $pass = 'Tsr3#@gfA356!&5';
  my %error = ( PrintError => 1, RaiseError => 1);
  my $dbh = DBI->connect($driver,$user,$pass,\%error);
#DBI:mysql:$DB_DATABASE:$DB_SERVER
  my $sql = qq~
  SELECT DISTINCT orders.name
  FROM plates JOIN orders ON plates.order_id = orders.id
  JOIN plate_peptides ON plate_peptides.plate_id = plates.id
  JOIN peptides  ON peptides.id = plate_peptides.peptide_id
  WHERE plate_type = 'MASTER'
  ORDER BY orders.name ASC
  ~;
  my $sth = $dbh->prepare( $sql );
  $sth->execute();

  my $select = qq~
    <SELECT NAME=Order>
      <OPTION SELECTED> All </OPTION>
   ~;
#      <OPTION> All Thermo</OPTION>
#      <OPTION> All JPT</OPTION>
#      <OPTION> All Zurich</OPTION>

  while ( my @row = $sth->fetchrow_array() ) {
    $select .= "<OPTION>$row[0]</OPTION>\n";
  }
  $select .= "</SELECT>\n";
  $log->debug( $select );
  return $select;
  exit;

#  my $dbh = DBI->connect($DB_DRIVER,$DB_RO_USER,$DB_RO_PASS,\%error_attr);
# mysql -umrm_ro -hmslims -P3306 -p'Tsr3#@gfA356!&5' -Dmrmatlas_lims
}


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