cgi-bin/biosource/sample.pl

   1 #!/usr/bin/perl
   2
   3 =head1 NAME
   4
   5   sample.pl
   6   Controller to show the web_page for sample information using MASON.
   7
   8 =cut
   9
  10 =head1 SYNOPSIS
  11
  12
  13 =head1 DESCRIPTION
  14
  15   This is the script to show the web_page using MASON
  16
  17 =cut
  18
  19 =head1 AUTHORS
  20
  21  Aureliano Bombarely Gomez
  22  (ab782@cornell.edu)
  23
  24 =cut
  25
  26
  27 use strict;
  28 use warnings;
  29
  30 use CXGN::MasonFactory;
  31 use CXGN::DB::DBICFactory;
  32 use CXGN::DB::Connection;
  33 use CXGN::Biosource::Schema;
  34 use CXGN::Biosource::Sample;
  35 use CXGN::GEM::Schema;
  36 use CXGN::GEM::Target;
  37 use CXGN::DB::Connection;
  38
  39 use CXGN::Page;
  40 use CXGN::Page::FormattingHelpers  qw/ info_section_html info_table_html columnar_table_html page_title_html html_break_string /;
  41
  42
  43 ## Create the mason object
  44
  45 my $m = CXGN::MasonFactory->new();
  46
  47 ## Use of CXGN::Page to take the arguments from the URL
  48
  49 my %args = CXGN::Page->new()
  50                      ->get_all_encoded_arguments();
  51
  52 ## Create the schema used for the mason components
  53
  54 my $psqlv = `psql --version`;
  55 chomp($psqlv);
  56
  57 my $schema_list = 'biosource,metadata,public';
  58 if ($psqlv =~ /8\.1/) {
  59     $schema_list .= ',tsearch2';
  60 }
  61
  62 my @schema_list = split(/,/, $schema_list);
  63 my $schema = CXGN::DB::DBICFactory->open_schema( 'CXGN::Biosource::Schema', search_path => \@schema_list, );
  64
  65
  66 ## Get the sample data for sample specific mason components
  67
  68 my $sample;
  69 if (exists $args{'id'} && $args{'id'} =~ m/^\d+$/) {
  70     $sample = CXGN::Biosource::Sample->new($schema, $args{'id'});
  71 } elsif (exists $args{'name'}) {
  72     $sample = CXGN::Biosource::Sample->new_by_name($schema, $args{'name'});
  73 } else {
  74     $sample = CXGN::Biosource::Sample->new($schema);
  75 }
  76
  77 ## Get a publication list for common mason components
  78
  79 my @pubs = ();
  80 if (defined $sample) {
  81    @pubs = $sample->get_publication_list();
  82 }
  83
  84 ## The sample can be associated expression data (search sample_id in gem.ge_target_element table)
  85
  86 my @targets = ();
  87 if ($sample->get_sample_id() ) {
  88
  89     ## First create an schema that contains gem schema
  90     my @gem_schema_list = ('gem', @schema_list);
  91
  92     my $gemschema = CXGN::DB::DBICFactory->open_schema( 'CXGN::GEM::Schema', search_path => \@gem_schema_list, );
  93
  94     my @sample_el_rows = $gemschema->resultset('GeTargetElement')
  95                                    ->search({ sample_id => $sample->get_sample_id() });
  96
  97     foreach my $sample_el_row (@sample_el_rows) {
  98         my $target_id = $sample_el_row->get_column('target_id');
  99         my $target = CXGN::GEM::Target->new($gemschema, $target_id);
 100         push @targets, $target;
 101     }
 102 }
 103
 104 ## Get the sample relationship
 105
 106 my %sample_relations = $sample->get_relationship();
 107
 108 ## Depending if the $sample has or not id, it call a mason page (error when does not exists sample in the database)
 109
 110 ## There are two ways to access to the page, using id=int or name=something. If use other combinations give an error message
 111
 112 if (defined $sample->get_sample_id() ) {
 113     $m->exec('/biosource/sample_detail.mas', schema => $schema, sample => $sample, sample_relations_href => \%sample_relations, pub_list => \@pubs, target_list => \@targets );
 114 } else {
 115     $m->exec('/biosource/biosource_page_error.mas', schema => $schema, object => $sample );
 116 }
 117
 118