package SGN::View::Mason::Commands;
use strict;
use vars qw($m $c);
HTML::Mason::Component::FileBased->new(
'code' => sub {
use utf8; local $SGN::View::Mason::Commands::m = $HTML::Mason::Commands::m;
HTML::Mason::Exception::Params->throw
    ( error =>
      "Odd number of parameters passed to component expecting name/value pairs"
    ) if @_ % 2;
my ( $organism_name, $organism_id, $taxon, $common_name, $description, $comment, @synonyms, $taxonomy, $accessions, $solcyc, $solcyc_link, $ploidy, $genome_size, $chromosome_number, $maps, $est_attribution, @libraries, $phenotypes, $onto_count, $trait_count, $loci, $qtl_data, $user_id, $privileged_user, $form, $static_data, $images );
{
    my %pos;
    for ( my $x = 0; $x < @_; $x += 2 )
    {
        $pos{ $_[$x] } = $x + 1;
    }

    foreach my $arg ( qw( organism_name organism_id common_name ) )
    {
        HTML::Mason::Exception::Params->throw
            ( error => "no value sent for required parameter '$arg'" )
                unless exists $pos{$arg};
    }
#line 3 "/home/production/cxgn/sgn/mason/organism/view_organism.mas"
    $organism_name = $_[ $pos{'organism_name'} ];
#line 4 "/home/production/cxgn/sgn/mason/organism/view_organism.mas"
    $organism_id = $_[ $pos{'organism_id'} ];
#line 5 "/home/production/cxgn/sgn/mason/organism/view_organism.mas"
     $taxon = exists $pos{'taxon'} ? $_[ $pos{'taxon'} ] :  '';
#line 6 "/home/production/cxgn/sgn/mason/organism/view_organism.mas"
    $common_name = $_[ $pos{'common_name'} ];
#line 7 "/home/production/cxgn/sgn/mason/organism/view_organism.mas"
     $description = exists $pos{'description'} ? $_[ $pos{'description'} ] :  '';
#line 8 "/home/production/cxgn/sgn/mason/organism/view_organism.mas"
     $comment = exists $pos{'comment'} ? $_[ $pos{'comment'} ] :  '';
#line 9 "/home/production/cxgn/sgn/mason/organism/view_organism.mas"
     @synonyms = exists $pos{'synonyms'} ? HTML::Mason::Tools::coerce_to_array( $_[ $pos{'synonyms'} ], '@synonyms') :  ();
#line 10 "/home/production/cxgn/sgn/mason/organism/view_organism.mas"
     $taxonomy = exists $pos{'taxonomy'} ? $_[ $pos{'taxonomy'} ] :  '';
#line 11 "/home/production/cxgn/sgn/mason/organism/view_organism.mas"
     $accessions = exists $pos{'accessions'} ? $_[ $pos{'accessions'} ] :  '';
#line 12 "/home/production/cxgn/sgn/mason/organism/view_organism.mas"
     $solcyc = exists $pos{'solcyc'} ? $_[ $pos{'solcyc'} ] :  '';
#line 13 "/home/production/cxgn/sgn/mason/organism/view_organism.mas"
     $solcyc_link = exists $pos{'solcyc_link'} ? $_[ $pos{'solcyc_link'} ] :  '';
#line 14 "/home/production/cxgn/sgn/mason/organism/view_organism.mas"
     $ploidy = exists $pos{'ploidy'} ? $_[ $pos{'ploidy'} ] :  '';
#line 15 "/home/production/cxgn/sgn/mason/organism/view_organism.mas"
     $genome_size = exists $pos{'genome_size'} ? $_[ $pos{'genome_size'} ] :  '';
#line 16 "/home/production/cxgn/sgn/mason/organism/view_organism.mas"
     $chromosome_number = exists $pos{'chromosome_number'} ? $_[ $pos{'chromosome_number'} ] :  '';
#line 17 "/home/production/cxgn/sgn/mason/organism/view_organism.mas"
     $maps = exists $pos{'maps'} ? $_[ $pos{'maps'} ] :  '';
#line 18 "/home/production/cxgn/sgn/mason/organism/view_organism.mas"
     $est_attribution = exists $pos{'est_attribution'} ? $_[ $pos{'est_attribution'} ] :  '';
#line 19 "/home/production/cxgn/sgn/mason/organism/view_organism.mas"
     @libraries = exists $pos{'libraries'} ? HTML::Mason::Tools::coerce_to_array( $_[ $pos{'libraries'} ], '@libraries') :  ();
#line 20 "/home/production/cxgn/sgn/mason/organism/view_organism.mas"
     $phenotypes = exists $pos{'phenotypes'} ? $_[ $pos{'phenotypes'} ] :  '';
#line 21 "/home/production/cxgn/sgn/mason/organism/view_organism.mas"
     $onto_count = exists $pos{'onto_count'} ? $_[ $pos{'onto_count'} ] :  '';
#line 22 "/home/production/cxgn/sgn/mason/organism/view_organism.mas"
     $trait_count = exists $pos{'trait_count'} ? $_[ $pos{'trait_count'} ] :  '';
#line 23 "/home/production/cxgn/sgn/mason/organism/view_organism.mas"
     $loci = exists $pos{'loci'} ? $_[ $pos{'loci'} ] :  '';
#line 24 "/home/production/cxgn/sgn/mason/organism/view_organism.mas"
     $qtl_data = exists $pos{'qtl_data'} ? $_[ $pos{'qtl_data'} ] :  undef;
#line 25 "/home/production/cxgn/sgn/mason/organism/view_organism.mas"
     $user_id = exists $pos{'user_id'} ? $_[ $pos{'user_id'} ] :  undef;
#line 26 "/home/production/cxgn/sgn/mason/organism/view_organism.mas"
     $privileged_user = exists $pos{'privileged_user'} ? $_[ $pos{'privileged_user'} ] :  undef;
#line 27 "/home/production/cxgn/sgn/mason/organism/view_organism.mas"
     $form = exists $pos{'form'} ? $_[ $pos{'form'} ] :  undef;;
#line 28 "/home/production/cxgn/sgn/mason/organism/view_organism.mas"
     $static_data = exists $pos{'static_data'} ? $_[ $pos{'static_data'} ] :  undef;;
#line 29 "/home/production/cxgn/sgn/mason/organism/view_organism.mas"
     $images = exists $pos{'images'} ? $_[ $pos{'images'} ] :  [];
}
$m->debug_hook( $m->current_comp->path ) if ( HTML::Mason::Compiler::IN_PERL_DB() );

#line 1 "/home/production/cxgn/sgn/mason/organism/view_organism.mas"
$m->print( '
' );
#line 31 "/home/production/cxgn/sgn/mason/organism/view_organism.mas"
$m->print( '
' );
#line 32 "/home/production/cxgn/sgn/mason/organism/view_organism.mas"

my $this_page = "/organism/$organism_id/view/";
my $image_subtitle =
!$privileged_user ?
"<span class= \"ghosted\">[Add new image]</span> "
: " <a href=\"/image/add?type_id=$organism_id&type=organism&action=new&refering_page=$this_page\">[ Add new image]</a>" ;
#line 39 "/home/production/cxgn/sgn/mason/organism/view_organism.mas"
$m->print( '
' );
#line 40 "/home/production/cxgn/sgn/mason/organism/view_organism.mas"
$m->comp(   '/util/import_javascript.mas', classes => ["jquery", "thickbox", "CXGN.Page.FormattingHelpers"]   
); #line 40 "/home/production/cxgn/sgn/mason/organism/view_organism.mas"
$m->print( '


' );
#line 43 "/home/production/cxgn/sgn/mason/organism/view_organism.mas"
$m->comp(   '/page/page_title.mas', title=>"Details for $taxon <i>$organism_name</i>"   
); #line 43 "/home/production/cxgn/sgn/mason/organism/view_organism.mas"
$m->print( '

' );
#line 45 "/home/production/cxgn/sgn/mason/organism/view_organism.mas"
$m->comp( { content => sub {
#line 45 "/home/production/cxgn/sgn/mason/organism/view_organism.mas"
$m->print( '
' );
#line 46 "/home/production/cxgn/sgn/mason/organism/view_organism.mas"
$m->comp(   '/organism/basic_info.mas', name=>$organism_name, common_name=>$common_name, description=>$description, comment=>$comment, synonyms=> \@synonyms   
); #line 46 "/home/production/cxgn/sgn/mason/organism/view_organism.mas"
$m->print( '
' );
#line 47 "/home/production/cxgn/sgn/mason/organism/view_organism.mas"
} }, '/page/info_section.mas', title=>'Basic information'
 );
#line 47 "/home/production/cxgn/sgn/mason/organism/view_organism.mas"
$m->print( '

' );
#line 49 "/home/production/cxgn/sgn/mason/organism/view_organism.mas"
$m->comp(   '/organism/taxonomy.mas', taxonomy=>$taxonomy   
); #line 49 "/home/production/cxgn/sgn/mason/organism/view_organism.mas"
$m->print( '

' );
#line 51 "/home/production/cxgn/sgn/mason/organism/view_organism.mas"
$m->comp( { content => sub {
#line 51 "/home/production/cxgn/sgn/mason/organism/view_organism.mas"
$m->print( '
' );
#line 52 "/home/production/cxgn/sgn/mason/organism/view_organism.mas"
$m->comp(   '/image/print_images.mas', images => $images   
); #line 52 "/home/production/cxgn/sgn/mason/organism/view_organism.mas"
$m->print( '
' );
#line 53 "/home/production/cxgn/sgn/mason/organism/view_organism.mas"
} }, '/page/info_section.mas', title=>"Images" , subtitle=>$image_subtitle
 );
#line 53 "/home/production/cxgn/sgn/mason/organism/view_organism.mas"
$m->print( '


' );
#line 56 "/home/production/cxgn/sgn/mason/organism/view_organism.mas"
$m->comp(   '/organism/accessions.mas', accessions => $accessions   
); #line 56 "/home/production/cxgn/sgn/mason/organism/view_organism.mas"
$m->print( '

' );
#line 58 "/home/production/cxgn/sgn/mason/organism/view_organism.mas"
 if ($taxon ne 'species' && $taxon ne 'subspecies') { return; }
$m->print( '
' );
#line 60 "/home/production/cxgn/sgn/mason/organism/view_organism.mas"
$m->comp( { content => sub {
#line 60 "/home/production/cxgn/sgn/mason/organism/view_organism.mas"
$m->print( '
' );
#line 61 "/home/production/cxgn/sgn/mason/organism/view_organism.mas"
$m->print(  $solcyc_link  );
#line 61 "/home/production/cxgn/sgn/mason/organism/view_organism.mas"
$m->print( '
' );
#line 62 "/home/production/cxgn/sgn/mason/organism/view_organism.mas"
} }, '/page/info_section.mas', title=>'Metabolic details'
 );
#line 62 "/home/production/cxgn/sgn/mason/organism/view_organism.mas"
$m->print( '

' );
#line 64 "/home/production/cxgn/sgn/mason/organism/view_organism.mas"
$m->comp( { content => sub {
#line 64 "/home/production/cxgn/sgn/mason/organism/view_organism.mas"
$m->print( '
' );
#line 65 "/home/production/cxgn/sgn/mason/organism/view_organism.mas"
$m->comp(   '/organism/genomic_details.mas', ploidy => $ploidy, genome_size=>$genome_size, chromosome_number => $chromosome_number, loci=>$loci, maps=>$maps   
); #line 65 "/home/production/cxgn/sgn/mason/organism/view_organism.mas"
$m->print( '


' );
#line 68 "/home/production/cxgn/sgn/mason/organism/view_organism.mas"
} }, '/page/info_section.mas', title=>'Genome data', collapsible=>1
 );
#line 68 "/home/production/cxgn/sgn/mason/organism/view_organism.mas"
$m->print( '

' );
#line 70 "/home/production/cxgn/sgn/mason/organism/view_organism.mas"
$m->comp( { content => sub {
#line 70 "/home/production/cxgn/sgn/mason/organism/view_organism.mas"
$m->print( '

' );
#line 72 "/home/production/cxgn/sgn/mason/organism/view_organism.mas"
 my @links = map { qq|<a href="/content/library_info.pl?library=$_">$_</a>| } @libraries;
$m->print( '
' );
#line 74 "/home/production/cxgn/sgn/mason/organism/view_organism.mas"
$m->comp(   '/page/info_table.mas',
   data => [
  'Libraries ('.scalar(@links).')' => (join ", ", (@links)),
  Attribution => $est_attribution ], border => 0
   
); #line 78 "/home/production/cxgn/sgn/mason/organism/view_organism.mas"
$m->print( '
' );
#line 79 "/home/production/cxgn/sgn/mason/organism/view_organism.mas"
} }, '/page/info_section.mas', title=>'Transcript Information', collapsible => 1
 );
#line 79 "/home/production/cxgn/sgn/mason/organism/view_organism.mas"
$m->print( '


' );
#line 82 "/home/production/cxgn/sgn/mason/organism/view_organism.mas"
$m->comp( { content => sub {
#line 82 "/home/production/cxgn/sgn/mason/organism/view_organism.mas"
$m->print( '

Number of phenotyped lines : ' );
#line 84 "/home/production/cxgn/sgn/mason/organism/view_organism.mas"
$m->print(  $phenotypes  );
#line 84 "/home/production/cxgn/sgn/mason/organism/view_organism.mas"
$m->print( '
<br />
Number of traits scored  : ' );
#line 86 "/home/production/cxgn/sgn/mason/organism/view_organism.mas"
$m->print(  $trait_count  );
#line 86 "/home/production/cxgn/sgn/mason/organism/view_organism.mas"
$m->print( '
<br />
Number of ontology annotations : ' );
#line 88 "/home/production/cxgn/sgn/mason/organism/view_organism.mas"
$m->print(  $onto_count  );
#line 88 "/home/production/cxgn/sgn/mason/organism/view_organism.mas"
$m->print( '
<br /><br />


' );
#line 92 "/home/production/cxgn/sgn/mason/organism/view_organism.mas"
$m->comp( { content => sub {
#line 92 "/home/production/cxgn/sgn/mason/organism/view_organism.mas"
$m->print( '

' );
#line 94 "/home/production/cxgn/sgn/mason/organism/view_organism.mas"
 if ($qtl_data) {
$m->print( '  ' );
#line 95 "/home/production/cxgn/sgn/mason/organism/view_organism.mas"
$m->comp(   '/page/columnar_table.mas',
    data => $qtl_data,
    headings => [ 'Name', 'Traits' ],
    __alt_freq   => 2,
    __alt_width  => 1,
    __alt_offset => 3,
    __align      => 'l'   
); #line 101 "/home/production/cxgn/sgn/mason/organism/view_organism.mas"
$m->print( '
' );
#line 102 "/home/production/cxgn/sgn/mason/organism/view_organism.mas"
}
$m->print( ' ' );
#line 103 "/home/production/cxgn/sgn/mason/organism/view_organism.mas"
} }, '/page/info_section.mas', title=>'QTL data', is_subsection=>1
 );
#line 103 "/home/production/cxgn/sgn/mason/organism/view_organism.mas"
$m->print( '
' );
#line 104 "/home/production/cxgn/sgn/mason/organism/view_organism.mas"
} }, '/page/info_section.mas', title=>'Phenomic Details', collapsible=>1
 );
#line 104 "/home/production/cxgn/sgn/mason/organism/view_organism.mas"
$m->print( '



' );
#line 108 "/home/production/cxgn/sgn/mason/organism/view_organism.mas"
$m->comp(   '/organism/project_metadata.mas', organism_id=>$organism_id   
); #line 108 "/home/production/cxgn/sgn/mason/organism/view_organism.mas"
$m->print( '



' );
#line 112 "/home/production/cxgn/sgn/mason/organism/view_organism.mas"
$m->comp(   '/page/comments.mas', object_type=>"organism", object_id=>$organism_id, referer=>$this_page   
); #line 112 "/home/production/cxgn/sgn/mason/organism/view_organism.mas"
$m->print( '

' );
;return;
},
'declared_args' => {
  '$accessions' => { default => ' \'\'' },
  '$chromosome_number' => { default => ' \'\'' },
  '$comment' => { default => ' \'\'' },
  '$common_name' => { default => undef },
  '$description' => { default => ' \'\'' },
  '$est_attribution' => { default => ' \'\'' },
  '$form' => { default => ' undef;' },
  '$genome_size' => { default => ' \'\'' },
  '$images' => { default => ' []' },
  '$loci' => { default => ' \'\'' },
  '$maps' => { default => ' \'\'' },
  '$onto_count' => { default => ' \'\'' },
  '$organism_id' => { default => undef },
  '$organism_name' => { default => undef },
  '$phenotypes' => { default => ' \'\'' },
  '$ploidy' => { default => ' \'\'' },
  '$privileged_user' => { default => ' undef' },
  '$qtl_data' => { default => ' undef' },
  '$solcyc' => { default => ' \'\'' },
  '$solcyc_link' => { default => ' \'\'' },
  '$static_data' => { default => ' undef;' },
  '$taxon' => { default => ' \'\'' },
  '$taxonomy' => { default => ' \'\'' },
  '$trait_count' => { default => ' \'\'' },
  '$user_id' => { default => ' undef' },
  '@libraries' => { default => ' ()' },
  '@synonyms' => { default => ' ()' }
},
'load_time' => 1763108195,

)
;