lib/CXGN/Pedigree/ParseUpload.pm

   1 package CXGN::Pedigree::ParseUpload;
   2
   3 use Moose;
   4 use MooseX::FollowPBP;
   5 use Moose::Util::TypeConstraints;
   6 use Bio::GeneticRelationships::Pedigree;
   7 use Bio::GeneticRelationships::Individual;
   8
   9 with 'MooseX::Object::Pluggable';
  10
  11
  12 has 'chado_schema' => (
  13                        is       => 'ro',
  14                        isa      => 'DBIx::Class::Schema',
  15                        required => 1,
  16                       );
  17
  18 has 'filename' => (
  19                    is => 'ro',
  20                    isa => 'Str',
  21                    required => 1,
  22                   );
  23
  24 has 'parse_errors' => (
  25                        is => 'ro',
  26                        isa => 'ArrayRef[Str]',
  27                        writer => '_set_parse_errors',
  28                        reader => 'get_parse_errors',
  29                        predicate => 'has_parse_errors',
  30                       );
  31
  32 has '_parsed_data' => (
  33                        is => 'ro',
  34                        isa => 'HashRef',
  35                        writer => '_set_parsed_data',
  36                        predicate => '_has_parsed_data',
  37                       );
  38
  39 sub parse {
  40   my $self = shift;
  41
  42   if (!$self->_validate_with_plugin()) {
  43     print STDERR "\nCould not validate cross file: ".$self->get_filename()."\n";
  44     return;
  45   }
  46
  47   if (!$self->_parse_with_plugin()) {
  48     print STDERR "\nCould not parse cross file: ".$self->get_filename()."\n";
  49     return;
  50   }
  51
  52   if (!$self->_has_parsed_data()) {
  53     print STDERR "\nNo parsed data for cross file: ".$self->get_filename()."\n";
  54     return;
  55   } else {
  56     return $self->_parsed_data();
  57   }
  58
  59   print STDERR "\nError parsing cross file: ".$self->get_filename()."\n";
  60   return;
  61 }
  62
  63
  64 1;