#!/usr/local/bin/perl

###############################################################################
# Program     : uploadTransitions
# $Id: $
#
# SBEAMS is Copyright (C) 2000-2008 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.
#
###############################################################################


use strict;
use lib qw (../../lib/perl);
use File::Basename;

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

use SBEAMS::PeptideAtlas;
use SBEAMS::PeptideAtlas::Settings;
use SBEAMS::PeptideAtlas::TraMLParser;

## Globals ##
my $sbeams = new SBEAMS::Connection;
my $pepatlas = new SBEAMS::PeptideAtlas;
$pepatlas->setSBEAMS($sbeams);
my $program = basename( $0 );

main();


sub main { 
  my $current_username = $sbeams->Authenticate( allow_anonymous_access => 1) || die "Authentication failed";

  my $params = process_params();
  $params->{apply_action} ||= 'show form';

  for my $param ( keys( %$params ) ) { $log->info("Params say: $param => $params->{$param}"); }

  if ( $params->{apply_action} eq 'Upload file' ) {
    upload_transitions( $params );
    print $q->redirect( $q->self_url() );
  } elsif ( $params->{apply_action} eq 'show form' ) {
    $pepatlas->printPageHeader( force_header => 1 );
    print_upload_form( $params );

  }
  $pepatlas->printPageFooter();

} # end main


sub upload_transitions {
  my $params = shift;

  # read file
  $pepatlas->validate_transition_data( %$params );
  # Insert transitions
  my $ids = $pepatlas->insert_transition_data( set_name => $params->{transition_set} );
#  my $ids = [1,2,3,4];
  # print table of transitions
  if ( $ids ) {
    $sbeams->set_page_message( msg => 'Saved ' . scalar( @$ids ) . ' transitions', type => 'Info' );
#    print_results( $ids );
  } else {
    $sbeams->set_page_message( msg => 'No transitions saved', type => 'Error' );
  }

  # exit
  if ( $params->{output_mode} eq 'tsv' ) {
    $pepatlas->printPageHeader( force_header => 1 );
    print "Success\t".scalar(@$ids)." transitions uploaded\n";
    exit;
  } else {
    return;
  }
  exit;
}


sub process_params {
  my $params = {};
  
  # Process parameters
  $sbeams->parse_input_parameters( parameters_ref => $params,
                                                 q => $q
                                 );
  # Process "state" parameters
  $sbeams->processStandardParameters( parameters_ref => $params );

#  for my $param ( keys( %$params ) ) { $log->debug( "Params say: $param => $params->{$param}" ); }

  $q->delete( 'apply_action' );
  my $error_text;
  $params->{transition_set} ||= 'Uploaded_set_' . time();
  $params->{type} ||= 'tabtext';
  for my $required ( qw(transition_file transition_set ) ) {
    if ( !defined $required ) {
      my $sep = ( $error_text ) ? ', ' : '';
      $error_text ||= 'Missing required parameters: ';
      $error_text .= $sep . $required;
    }
  }
  show_error( $error_text ) if $error_text;
  
  my $uploaded_file = $q->param( 'transition_file' );
  my @transition_file;
  while ( my $line = <$uploaded_file> ) {
    push @transition_file, $line;
  }
  $log->info( "file has $#transition_file elements" );
  $params->{transition_file_data} = \@transition_file;
#  for my $p ( keys (%$params ) ) { $log->debug( "$p => $params->{$p}" ); }

  return $params;
}

sub show_error {
  print STDERR "Foshizzle\n";
  exit;
  $sbeams->set_page_message( msg => 'This functionality is not yet complete', type => 'Error' );
  print $q->redirect( $q->self_url() );
}

sub print_upload_form {
  my $params = shift;
  $sbeams->printUserContext();
  
  my $pad = '&nbsp;' x 5;
  my $excel = "<A HREF=$HTML_BASE_DIR/doc/PeptideAtlas/transition_template.xls>(template)</A>";
  my $tsv = "<A HREF=$HTML_BASE_DIR/doc/PeptideAtlas/transition_template.tsv>(template)</A>";
  my $traml = "<A HREF=http://psidev.info/index.php?q=node/405i>(information)</A>";

  my @buttons = $sbeams->getFormButtons( name => 'apply_action', 
                                        value => 'Upload file', 
                                        types => [ qw(submit reset) ] );
  my $buttons = join $pad, @buttons;
  my $info_text = get_info_text();
#  <TR><TD ALIGN=RIGHT><B>Download template:</B></TD><TD>$template_links</TD></TR>

  print <<"  END";
  <H1>Upload The Transitions</H1>
  <FORM ENCTYPE="multipart/form-data" METHOD=POST>
  <TABLE BORDER=0>
  <TR><TD ALIGN=RIGHT><B>Transition set name:</B></TD><TD><INPUT TYPE=TEXT NAME=transition_set SIZE=30></TD></TR>
  <TR><TD ALIGN=RIGHT><B>Transitions file:</B></TD><TD><INPUT TYPE=FILE NAME=transition_file SIZE=30></TD></TR>
  <TR><TD ALIGN=RIGHT><B>Type:</B></TD>
    <TD><INPUT TYPE=RADIO NAME=type CHECKED VALUE=xls></INPUT> Excel $excel |
     <INPUT TYPE=RADIO NAME=type VALUE=tabtext> </INPUT> TSV $tsv |
     <INPUT TYPE=RADIO NAME=type VALUE=traml> </INPUT> TraML $traml  </TD>
  </TR>
  <TR><TD></TD><TD ALIGN=LEFT>$buttons</TD></TR>
  <TR><TD ALIGN=RIGHT></TD><TD></TD></TR>
  </TABLE>
  </FORM>
	<BR>
  $info_text 
  END
#<TR><TD COLSPAN=2 ALIGN=CENTER>$buttons</TD>

} # end showMainPage

sub get_info_text {
  my $content =<<"  END";
  <PRE>
   <DIV class=info_box ID=help>
    This form allows you to upload a file of 'validated' transitions, rather than
    entering them manually one at a time.  You can download a template file in 
    Excel, TSV, or TraML format from the links above, and enter your data in the
    columns provided, as described in the table below.


    <TABLE BORDER=10 BGCOLOR=white>
     <TR><TD>modified_peptide_sequence</TD><TD>Sequence of the peptide including any modifications in standard notation, e.g. THC[160]AAHR</TD></TR>
     <TR><TD>peptide_charge</TD><TD>Charge on the precursor ion</TD></TR>
     <TR><TD>q1_mz</TD><TD>parent mass to charge ratio: q1</TD></TR>
     <TR><TD>q3_mz</TD><TD>product ion mass to charge ratio: q3</TD></TR>
     <TR><TD>q3_ion_label</TD><TD>Label for the product ion (e.g. y1-7, b2-6, etc.)</TD></TR>
     <TR><TD>transition_suitability_level_id</TD><TD>User-specified quality metric.  Permissible values are Best, OK, and No, all others will be stored as 'OK'</TD></TR>
     <TR><TD>publication_id</TD><TD>Article title of publication related to this entry, if any</TD></TR>
     <TR><TD>annotator_name</TD><TD>Name of person uploading transitions</TD></TR>
     <TR><TD>collision_energy</TD><TD>Collision energy setting used during validation run, or best CE setting if multiple runs were performed</TD></TR>
     <TR><TD>retention_time</TD><TD>Retention time (in minutes) of parent peptide</TD></TR>
     <TR><TD>instrument</TD><TD>Instrument used for analysis of transition pair</TD></TR>
     <TR><TD>comment</TD><TD>Any additional comments or information you wish to provide</TD></TR>
    </TABLE>

    
   </DIV>
  </PRE>
  END
  my @toggle = $sbeams->make_toggle_section( textlink => 1,
                                       hidetext => "Hide Explanation",
                                       showtext => "Show Explanation", 
                                      box_style => 1,
                                       content => $content );

  return "$toggle[1]<BR><BR>$toggle[0]";
}