lib/CXGN/Genotype/ParseUpload.pm

   1 package CXGN::Genotype::ParseUpload;
   2
   3 use Moose;
   4 use Data::Dumper;
   5 use MooseX::FollowPBP;
   6 use Moose::Util::TypeConstraints;
   7
   8 with 'MooseX::Object::Pluggable';
   9
  10
  11 has 'chado_schema' => (
  12     is => 'ro',
  13     isa => 'DBIx::Class::Schema',
  14     required => 1,
  15 );
  16
  17 has 'filename' => (
  18     is => 'ro',
  19     isa => 'Str',
  20     required => 1,
  21 );
  22
  23 has 'filename_intertek_marker_info' => (
  24     is => 'ro',
  25     isa => 'Str|Undef',
  26 );
  27
  28 has 'nd_protocol_id' => (
  29     is => 'ro',
  30     isa => 'Int|Undef',
  31 );
  32
  33 has 'observation_unit_type_name' => ( #Can be accession, plot, plant, tissue_sample
  34     isa => 'Str',
  35     is => 'ro',
  36     required => 1,
  37 );
  38
  39 has 'organism_id' => (
  40     isa => 'Int',
  41     is => 'ro',
  42     required => 0,
  43 );
  44
  45 has 'create_missing_observation_units_as_accessions' => (
  46     isa => 'Bool',
  47     is => 'ro',
  48     default => 0,
  49 );
  50
  51 has 'igd_numbers_included' => (
  52     isa => 'Bool',
  53     is => 'ro',
  54     default => 0,
  55 );
  56
  57 has 'parse_errors' => (
  58     is => 'ro',
  59     isa => 'HashRef',
  60     writer => '_set_parse_errors',
  61     reader => 'get_parse_errors',
  62     predicate => 'has_parse_errors',
  63 );
  64
  65 has '_parsed_data' => (
  66     is => 'ro',
  67     isa => 'HashRef',
  68     writer => '_set_parsed_data',
  69     predicate => '_has_parsed_data',
  70 );
  71
  72 sub parse {
  73     my $self = shift;
  74
  75     if (!$self->_validate_with_plugin()) {
  76         my $errors = $self->get_parse_errors();
  77         #print STDERR "\nCould not validate genotypes file: ".$self->get_filename()."\nError:".Dumper($errors)."\n";
  78         return;
  79     }
  80
  81     if (!$self->_parse_with_plugin()) {
  82         my $errors = $self->get_parse_errors();
  83         #print STDERR "\nCould not parse genotypes file: ".$self->get_filename()."\nError:".Dumper($errors)."\n";
  84         return;
  85     }
  86
  87     if (!$self->_has_parsed_data()) {
  88         my $errors = $self->get_parse_errors();
  89         #print STDERR "\nNo parsed data for genotypes file: ".$self->get_filename()."\nError:".Dumper($errors)."\n";
  90         return;
  91     } else {
  92         return $self->_parsed_data();
  93     }
  94
  95     my $errors = $self->get_parse_errors();
  96     #print STDERR "\nError parsing genotypes file: ".$self->get_filename()."\nError:".Dumper($errors)."\n";
  97     return;
  98 }
  99
 100 sub parse_with_iterator {
 101     my $self = shift;
 102
 103     if (!$self->_validate_with_plugin()) {
 104         my $errors = $self->get_parse_errors();
 105         #print STDERR "\nCould not validate genotypes file: ".$self->get_filename()."\nError:".Dumper($errors)."\n";
 106         return;
 107     }
 108
 109     if (!$self->_parse_with_plugin()) {
 110         my $errors = $self->get_parse_errors();
 111         #print STDERR "\nCould not parse genotypes file: ".$self->get_filename()."\nError:".Dumper($errors)."\n";
 112         return 1;
 113     }
 114 }
 115
 116 sub next {
 117     my $self = shift;
 118
 119     return $self->next_genotype();
 120 }
 121
 122 1;