lib/CXGN/Trial/ParseUpload.pm

   1 package CXGN::Trial::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 'parse_warnings' => (
  24     is => 'ro',
  25     isa => 'HashRef',
  26     writer => '_set_parse_warnings',
  27     reader => 'get_parse_warnings',
  28     predicate => 'has_parse_warnings'
  29 );
  30
  31 has 'parse_errors' => (
  32     is => 'ro',
  33     isa => 'HashRef',
  34     writer => '_set_parse_errors',
  35     reader => 'get_parse_errors',
  36     predicate => 'has_parse_errors'
  37 );
  38
  39 has '_parsed_data' => (
  40     is => 'ro',
  41     isa => 'HashRef',
  42     writer => '_set_parsed_data',
  43     predicate => '_has_parsed_data'
  44 );
  45
  46 has 'trial_stock_type' => (
  47     isa => 'Str',
  48     is => 'rw',
  49     predicate => 'has_trial_stock_type',
  50     required => 0,
  51     default => 'accession'
  52 );
  53
  54 sub parse {
  55   my $self = shift;
  56   my $args = shift;
  57
  58   if (!$self->_validate_with_plugin($args)) {
  59                 my $errors = $self->get_parse_errors();
  60     print STDERR "\nCould not validate trial file: ".$self->get_filename()."\nError:".Dumper($errors)."\n";
  61     return;
  62   }
  63
  64   # print STDERR "Check 3.1: ".localtime();
  65
  66   if (!$self->_parse_with_plugin($args)) {
  67                 my $errors = $self->get_parse_errors();
  68     print STDERR "\nCould not parse trial file: ".$self->get_filename()."\nError:".Dumper($errors)."\n";
  69     return;
  70   }
  71
  72   # print STDERR "Check 3.2: ".localtime();
  73
  74   if (!$self->_has_parsed_data()) {
  75                 my $errors = $self->get_parse_errors();
  76     print STDERR "\nNo parsed data for trial file: ".$self->get_filename()."\nError:".Dumper($errors)."\n";
  77     return;
  78   } else {
  79     return $self->_parsed_data();
  80   }
  81
  82   #print STDERR "Check 3.3: ".localtime();
  83
  84         my $errors = $self->get_parse_errors();
  85   print STDERR "\nError parsing trial file: ".$self->get_filename()."\nError:".Dumper($errors)."\n";
  86   return;
  87 }
  88
  89
  90 1;