cgi-bin/gem/platform.pl

   1 #!/usr/bin/perl
   2
   3 =head1 NAME
   4
   5   platform.pl
   6   Controller to show the web_page for platform using MASON.
   7
   8 =cut
   9
  10 =head1 DESCRIPTION
  11
  12   This is the controller script to show the web_page using MASON
  13
  14 =cut
  15
  16 =head1 AUTHORS
  17
  18  Aureliano Bombarely Gomez
  19  (ab782@cornell.edu)
  20
  21 =cut
  22
  23
  24 use strict;
  25 use warnings;
  26
  27 use CXGN::MasonFactory;
  28 use CXGN::Page;
  29
  30 use CXGN::DB::Connection;
  31 use CXGN::DB::DBICFactory;
  32 use CXGN::GEM::Schema;
  33 use CXGN::GEM::Platform;
  34 use CXGN::GEM::Target;
  35
  36
  37 ## Create mason object
  38
  39 my $m = CXGN::MasonFactory->new();
  40
  41
  42 ## Create the schema object
  43
  44 my $psqlv = `psql --version`;
  45 chomp($psqlv);
  46
  47 my @schema_list = ('gem', 'biosource', 'metadata', 'public');
  48 if ($psqlv =~ /8\.1/) {
  49     push @schema_list, 'tsearch2';
  50 }
  51
  52 my $schema = CXGN::DB::DBICFactory->open_schema( 'CXGN::GEM::Schema', search_path => \@schema_list, );
  53
  54 ## Also it will create a dbi-connection object ($dbh) for all the methods that do not use schemas
  55 ## (as CXGN::People::Person) to not interfere with them
  56
  57 my $dbh = CXGN::DB::Connection->new();
  58
  59 ## Use of CXGN::Page to take the arguments from the URL
  60
  61 my %args = CXGN::Page->new()->get_all_encoded_arguments();
  62
  63 ## Now it will create a platform object (by default it will create an empty platform object)
  64
  65 my $platform = CXGN::GEM::Platform->new($schema);
  66
  67 if (exists $args{'id'} && $args{'id'} =~ m/^\d+$/) {
  68    $platform = CXGN::GEM::Platform->new($schema, $args{'id'});
  69 } elsif (exists $args{'name'}) {
  70    $platform = CXGN::GEM::Platform->new_by_name($schema, $args{'name'});
  71 }
  72
  73
  74 ## Other data that the controller will suply will be:
  75
  76 #### 1) @target_list with CXGN::GEM::Target objects for hybridizations
  77
  78 my @target_list = ();
  79
  80 if (defined $platform->get_platform_id() ) {
  81     my @hyb_rows = $schema->resultset('GeHybridization')
  82         ->search({ platform_id => $platform->get_platform_id() });
  83
  84     foreach my $hyb_row (@hyb_rows) {
  85         my $target_id = $hyb_row->get_column('target_id');
  86         my $target = CXGN::GEM::Target->new($schema, $target_id);
  87         push @target_list, $target;
  88     }
  89 }
  90
  91 #### 2) @template_list with template_rows for templates (use CXGN::GEM::Template is slow because template object get other data)
  92
  93 my @template_row_list = ();
  94
  95 if (defined $platform->get_platform_id() ) {
  96
  97     @template_row_list = $schema->resultset('GeTemplate')
  98                                 ->search( { platform_id => $platform->get_platform_id() } );
  99 }
 100
 101 #### 3) @pub_id_list, a list of pub ids to show the publications associated with this platform
 102
 103 my @pub_id_list = ();
 104
 105 if (defined $platform->get_platform_id() ) {
 106
 107     @pub_id_list = $platform->get_publication_list();
 108 }
 109
 110
 111 ## There are two ways to access to the page, using id=int or name=something. If use other combinations give an error message
 112
 113 if (defined $platform->get_platform_id() ) {
 114     $m->exec('/gem/platform_detail.mas',
 115              dbh           => $dbh,
 116              schema        => $schema,
 117              platform      => $platform,
 118              target_list   => \@target_list,
 119              template_list => \@template_row_list,
 120              pub_list      => \@pub_id_list    );
 121 } else {
 122     $m->exec('/gem/gem_page_error.mas',
 123              schema => $schema,
 124              object => $platform );
 125 }