lib/CXGN/Pedigree/AddCrossInfo.pm

   1 package CXGN::Pedigree::AddCrossInfo;
   2
   3 =head1 NAME
   4
   5 CXGN::Pedigree::AddCrossInfo - a module to add cross information such as date of pollination, number of flowers pollinated, number of fruits set as stock properties for cross.
   6
   7 =head1 USAGE
   8
   9 my $cross_add_info = CXGN::Pedigree::AddCrossInfo->new({ chado_schema => $chado_schema, cross_name => $cross_name, key => $info_type, value => $value, data_type => $data_type} );
  10 $cross_add_info->add_info();
  11
  12 =head1 DESCRIPTION
  13
  14 Adds cross properties in json string format to stock of type cross. The cross must already exist in the database. This module is intended to be used in independent loading scripts and interactive dialogs.
  15
  16 =head1 AUTHORS
  17
  18 Jeremy D. Edwards (jde22@cornell.edu)
  19 Titima Tantikanjana (tt15@cornell.edu)
  20
  21 =cut
  22
  23 use Moose;
  24 use MooseX::FollowPBP;
  25 use Moose::Util::TypeConstraints;
  26 use Try::Tiny;
  27 use CXGN::Stock::StockLookup;
  28 use SGN::Model::Cvterm;
  29 use Data::Dumper;
  30 use JSON;
  31
  32 has 'chado_schema' => (
  33             is       => 'rw',
  34                 isa      => 'DBIx::Class::Schema',
  35                 predicate => 'has_chado_schema',
  36                 required => 1,
  37         );
  38 has 'cross_name' => (isa =>'Str', is => 'rw', predicate => 'has_cross_name', required => 1,);
  39 has 'key' => (isa =>'Str', is => 'rw', predicate => 'has_key', required => 1,);
  40 has 'value' => (isa =>'Str', is => 'rw', predicate => 'has_value', required => 1,);
  41 has 'data_type' => (isa =>'Str', is => 'rw', predicate => 'has_type', required => 1,);
  42
  43 sub add_info {
  44     my $self = shift;
  45     my $schema = $self->get_chado_schema();
  46     my $transaction_error;
  47
  48     #add all cross info in a single transaction
  49     my $coderef = sub {
  50
  51         #get cross (stock of type cross)
  52         my $cross_stock = $self->_get_cross($self->get_cross_name());
  53         if (!$cross_stock) {
  54             print STDERR "Cross could not be found\n";
  55             return;
  56         }
  57
  58         # get cvterm of cross info type (crossing_metadata_json or cross_additional_info)
  59         my $cross_info_type = $self->get_data_type();
  60 #        print STDERR "DATA TYPE =".Dumper($cross_info_type)."\n";
  61         my $cross_info_cvterm;
  62         if (($cross_info_type eq 'crossing_metadata_json') || ($cross_info_type eq 'cross_additional_info')) {
  63                         $cross_info_cvterm = SGN::Model::Cvterm->get_cvterm_row($schema, $cross_info_type, 'stock_property');
  64         } else {
  65                         print STDERR "Invalid type"."\n";
  66             return;
  67         }
  68
  69         my $cross_json_string;
  70         my $cross_json_hash = {};
  71         my $previous_stockprop_rs = $cross_stock->stockprops({type_id=>$cross_info_cvterm->cvterm_id});
  72         if ($previous_stockprop_rs->count == 1){
  73             $cross_json_string = $previous_stockprop_rs->first->value();
  74             $cross_json_hash = decode_json $cross_json_string;
  75             $cross_json_string = _generate_property_hash($self->get_key, $self->get_value, $cross_json_hash);
  76             $previous_stockprop_rs->first->update({value=>$cross_json_string});
  77         } elsif ($previous_stockprop_rs->count > 1) {
  78             print STDERR "More than one found!\n";
  79             return;
  80         } else {
  81             $cross_json_string = _generate_property_hash($self->get_key, $self->get_value, $cross_json_hash);
  82             $cross_stock->create_stockprops({$cross_info_cvterm->name() => $cross_json_string});
  83         }
  84 #        print STDERR "CROSS JSON STRING =".Dumper($cross_json_string)."\n";
  85     };
  86
  87     #try to add all cross info in a transaction
  88     try {
  89         $schema->txn_do($coderef);
  90     } catch {
  91         $transaction_error =  $_;
  92     };
  93
  94     if ($transaction_error) {
  95         print STDERR "Transaction error storing information for cross: $transaction_error\n";
  96         return;
  97     }
  98
  99     return 1;
 100 }
 101
 102 sub _generate_property_hash {
 103     my $key = shift;
 104     my $value = shift;
 105     my $cross_json_hash = shift;
 106     $cross_json_hash->{$key} = $value;
 107     #print STDERR Dumper $cross_json_hash;
 108     my $cross_json_string = encode_json $cross_json_hash;
 109     return $cross_json_string;
 110 }
 111
 112
 113 sub _get_cross {
 114     my $self = shift;
 115     my $cross_name = shift;
 116     my $schema = $self->get_chado_schema();
 117     my $stock_lookup = CXGN::Stock::StockLookup->new(schema => $schema);
 118     my $stock;
 119     my $cross_cvterm =  SGN::Model::Cvterm->get_cvterm_row($schema, 'cross', 'stock_type');
 120
 121     $stock_lookup->set_stock_name($cross_name);
 122     $stock = $stock_lookup->get_cross_exact();
 123
 124     if (!$stock) {
 125         print STDERR "Cross name does not exist\n";
 126         return;
 127     }
 128     return $stock;
 129 }
 130
 131 #######
 132 1;
 133 #######