cgi-bin/gem/template.pl

   1 #!/usr/bin/perl
   2
   3 =head1 NAME
   4
   5   template.pl
   6   Controller to show the web_page for template using MASON.
   7
   8 =cut
   9
  10 =head1 SYNOPSIS
  11
  12
  13 =head1 DESCRIPTION
  14
  15   This is the script controller to show the template 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::Page;
  32
  33 use CXGN::DB::Connection;
  34 use CXGN::DB::DBICFactory;
  35 use CXGN::GEM::Schema;
  36 use CXGN::GEM::Template;
  37 use CXGN::GEM::Expression;
  38
  39 ## Create the mason object
  40
  41 my $m = CXGN::MasonFactory->new();
  42
  43
  44 ## Create the schema object
  45
  46 my $psqlv = `psql --version`;
  47 chomp($psqlv);
  48
  49 my @schema_list = ('gem', 'biosource', 'metadata', 'public');
  50 if ($psqlv =~ /8\.1/) {
  51     push @schema_list, 'tsearch2';
  52 }
  53
  54 my $schema = CXGN::DB::DBICFactory->open_schema( 'CXGN::GEM::Schema', search_path => \@schema_list, );
  55
  56 ## Another schema to create is a schema that use sgn as schema
  57
  58 my $sgn_schema = CXGN::DB::DBICFactory->open_schema( 'SGN::Schema', search_path => ['sgn'], );
  59
  60
  61 ## Also it will create a dbi-connection object ($dbh) for all the methods that do not use schemas
  62 ## (as CXGN::People::Person) to not interfiere with them
  63
  64 my $dbh = CXGN::DB::Connection->new();
  65
  66
  67 ## Use of CXGN::Page to take the arguments from the URL
  68
  69
  70 my $page = CXGN::Page->new();
  71
  72 my %args = $page->get_all_encoded_arguments();
  73
  74
  75 ## Get template object (by default it will create an empty template object)
  76
  77 my $template = CXGN::GEM::Template->new($schema);
  78
  79 if (exists $args{'id'}) {
  80    $template = CXGN::GEM::Template->new($schema, $args{'id'});
  81 } elsif (exists $args{'name'}) {
  82    $template = CXGN::GEM::Template->new_by_name($schema, $args{'name'});
  83 }
  84
  85 ## Get the unigene list associated with this template to use with the annotations
  86
  87 my @unigene_ids = ();
  88 if (defined $template->get_template_id) {
  89     @unigene_ids = $template->get_internal_accessions('unigene');
  90 }
  91
  92 ## Add expression object
  93
  94 my $expression = CXGN::GEM::Expression->new($schema);
  95
  96 if (defined $template->get_template_id()) {
  97     $expression = CXGN::GEM::Expression->new($schema, $template->get_template_id());
  98 }
  99
 100
 101
 102 ## There are two ways to access to the page, using id=int or name=something. If use other combinations give an error message
 103
 104 if (defined $template->get_template_id() or defined $template->get_template_name() ) {
 105     $m->exec( '/gem/template_detail.mas',
 106               dbh          => $dbh,
 107               schema       => $schema,
 108               sgn_schema   => $sgn_schema,
 109               template     => $template,
 110               expression   => $expression,
 111               unigene_list => \@unigene_ids
 112             );
 113 } else {
 114     $m->exec('/gem/gem_page_error.mas',
 115              schema => $schema,
 116              object => $template );
 117 }