lib/CXGN/Transformation/CreateAutogeneratedNames.pm

   1 package CXGN::Transformation::CreateAutogeneratedNames;
   2
   3 =head1 NAME
   4
   5 CXGN::Transformation::CreateAutogeneratedNames - a module to create autogenerated names based on autogenerated name metadata.
   6
   7 =head1 USAGE
   8
   9
  10 =head1 DESCRIPTION
  11
  12
  13 =head1 AUTHORS
  14
  15 Titima Tantikanjana (tt15@cornell.edu)
  16
  17 =cut
  18
  19 use Moose;
  20 use MooseX::FollowPBP;
  21 use Moose::Util::TypeConstraints;
  22 use Try::Tiny;
  23 use CXGN::Stock::StockLookup;
  24 use SGN::Model::Cvterm;
  25 use Data::Dumper;
  26 use JSON;
  27
  28 has 'schema' => (
  29     is => 'rw',
  30     isa => 'DBIx::Class::Schema',
  31         predicate => 'has_schema',
  32         required => 1,
  33 );
  34
  35 has 'dbh' => (
  36     is  => 'rw',
  37     predicate => 'has_dbh',
  38     required => 1,
  39 );
  40
  41 has 'breeding_program_id' => (
  42     isa =>'Int',
  43     is => 'rw',
  44     predicate => 'has_breeding_program_id',
  45     required => 1,
  46 );
  47
  48 has 'name_format' => (
  49     isa =>'Str',
  50     is => 'rw',
  51     predicate => 'has_name_format',
  52     required => 1,
  53 );
  54
  55 has 'number_of_names' => (
  56     isa => 'Int',
  57     is => 'rw',
  58     predicate => 'has_number_of_names',
  59     required => 1,
  60 );
  61
  62 has 'source_info' => (
  63     isa => 'Str',
  64     is => 'rw',
  65     predicate => 'has_source_info',
  66     required => 1,
  67 );
  68
  69
  70 sub create_names {
  71
  72     my $self = shift;
  73     my $schema = $self->get_schema();
  74     my $breeding_program_id = $self->get_breeding_program_id();
  75     my $name_format = $self->get_name_format();
  76     my $number_of_names = $self->get_number_of_names();
  77     my $source_info_string = $self->get_source_info();
  78     my $source_info = decode_json $source_info_string;
  79
  80     my @autogenerated_names;
  81     my $name_metadata_hash = {};
  82
  83     my $autogenerated_name_metadata_cvterm = SGN::Model::Cvterm->get_cvterm_row($schema, 'autogenerated_name_metadata', 'project_property');
  84     my $program = $schema->resultset('Project::Project')->find({ project_id => $breeding_program_id});
  85     if (!$program) {
  86         return {error => "Breeding Program not found!\n"};
  87     }
  88
  89     my $name_metadata_projectprop_rs = $program->projectprops({type_id => $autogenerated_name_metadata_cvterm->cvterm_id});
  90     if ($name_metadata_projectprop_rs->count == 1){
  91         my $name_metadata_string = $name_metadata_projectprop_rs->first->value();
  92         $name_metadata_hash = decode_json $name_metadata_string;
  93     } else {
  94         return {error => "Error retrieving autogenerated name metadata!\n"};
  95     }
  96     my $name_format_metadata = $name_metadata_hash->{$name_format};
  97     my $name_attributes = $name_format_metadata->{'name_attributes'};
  98     my $last_serial_number = $name_format_metadata->{'last_serial_number'};
  99
 100     my @new_autogenerated_names;
 101     my $prefix;
 102     foreach my $n (1..$number_of_names) {
 103         my @all_name_components = ();
 104         my $new_name = '';
 105         my $incremented_number = $n + $last_serial_number;
 106         foreach my $attribute (@$name_attributes) {
 107             my $name_info;
 108             my %text_hash = ();
 109             if (ref $attribute eq ref {}) {
 110                 %text_hash = %{$attribute};
 111                 $name_info = $text_hash{'text'};
 112                 push @all_name_components, $name_info;
 113             } else {
 114                 $name_info = $source_info->{$attribute};
 115                 push @all_name_components, $name_info;
 116             }
 117         }
 118         $new_name = join("_", @all_name_components).$incremented_number;
 119         push @new_autogenerated_names, $new_name;
 120     }
 121
 122     my $rs = $schema->resultset("Stock::Stock")->search({
 123         'is_obsolete' => { '!=' => 't' },
 124         'uniquename' => { -in => \@new_autogenerated_names }
 125     });
 126
 127     my @invalid_names = ();
 128     while (my $r=$rs->next){
 129         push @invalid_names, $r->uniquename;
 130     }
 131
 132     if (scalar(@invalid_names) >= 1) {
 133         my $names = join(",", @invalid_names);
 134         return {error => "Invalid Names: $names!\n"};
 135     }
 136
 137     my $new_last_serial_number = $last_serial_number + $number_of_names;
 138
 139     my $new_names_info = {};
 140     $new_names_info->{'new_autogenerated_names'} = \@new_autogenerated_names;
 141     $new_names_info->{'new_last_serial_number'} = $new_last_serial_number;
 142
 143     return {new_names => $new_names_info};
 144
 145 }
 146
 147
 148
 149 #######
 150 1;
 151 #######