cgi-bin/search/unigene_build.pl

   1 #!/usr/bin/perl
   2
   3 =head1 NAME
   4
   5   unigene_build.pl
   6   Controller to show the web_page for unigene build 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
  31 use CXGN::MasonFactory;
  32 use CXGN::Page;
  33
  34
  35 use CXGN::DB::Connection;
  36 use CXGN::DB::DBICFactory;
  37
  38 use SGN::Schema;
  39 use CXGN::Transcript::Unigene;
  40
  41 ## Create mason object
  42
  43 my $m = CXGN::MasonFactory->new();
  44
  45 ## Use of CXGN::Page to take the arguments from the URL
  46
  47 my $page = CXGN::Page->new();
  48
  49 my %args = $page->get_all_encoded_arguments();
  50
  51 ## It create a MASON path and transmite it to let the dependient MASON
  52 ## code access to the MASON components (using the only mason dir give
  53 ## problems)
  54
  55 ## Create the gem schema object (used to get data from expression to samples)
  56
  57
  58
  59 ## There are one way to access to the page using id as integer. If use
  60 ## other combinations give an error message
  61
  62 my $psqlv = `psql --version`;
  63 chomp($psqlv);
  64
  65 my @schema_list = ('sgn');
  66 if ($psqlv =~ /8\.1/) {
  67     push @schema_list, 'tsearch2';
  68 }
  69
  70 my $schema = CXGN::DB::DBICFactory->open_schema( 'SGN::Schema', search_path => \@schema_list, );
  71
  72 my @schema_list2 = ('public');
  73 if ($psqlv =~ /8\.1/) {
  74     push @schema_list2, 'tsearch2';
  75 }
  76
  77 my $bcs = CXGN::DB::DBICFactory->open_schema( 'Bio::Chado::Schema', search_path => \@schema_list2, );
  78
  79 my $dbh = CXGN::DB::Connection->new();
  80
  81 ## Get unigene build object
  82
  83 my $unigene_build = CXGN::Transcript::UnigeneBuild->new($dbh);
  84 if (exists $args{'id'} && $args{'id'} =~ m/^\d+$/) {
  85     $unigene_build = CXGN::Transcript::UnigeneBuild->new($dbh, $args{'id'});
  86 }
  87
  88
  89 ## There are one way to access to the page using id as integer. If use other combinations give an error message
  90
  91 if (defined $unigene_build) {
  92     $m->exec('/transcript/unigene_build_detail.mas',
  93              bcs           => $bcs,
  94              schema        => $schema,
  95              unigene_build => $unigene_build );
  96 }
  97 else {
  98     $m->exec('/transcript/transcript_page_error.mas',
  99              object => $unigene_build );
 100 }