lib/CXGN/Genotype/CreatePlateOrder.pm

   1 package CXGN::Genotype::CreatePlateOrder;
   2 =head1 NAME
   3
   4 CXGN::Genotype::CreatePlateOrder - an object to submit genotyping plates to facilities
   5
   6 =head1 USAGE
   7
   8 PLEASE BE AWARE THAT THE DEFAULT OPTIONS FOR genotypeprop_hash_select, protocolprop_top_key_select, protocolprop_marker_hash_select ARE PRONE TO EXCEEDING THE MEMORY LIMITS OF VM. CHECK THE MOOSE ATTRIBUTES BELOW TO SEE THE DEFAULTS, AND ADJUST YOUR MOOSE INSTANTIATION ACCORDINGLY
   9
  10 my $create_order = CXGN::Genotype::CreatePlateOrder->new({
  11     bcs_schema=>$schema,
  12     people_schema=>$people_schema,
  13     client_id=>$client_id,
  14     order_id=>$order_id,
  15     extract_dna=>$extract_dna,
  16     service_id_list=>$service_id_list,
  17     plate_id => $plate_id,
  18 });
  19 my $errors = $submit_samples->validate();
  20 $submit_samples->send();
  21
  22
  23 # RECOMMENDED
  24 If you just want to send genotyping plates with different volume per well
  25
  26 =head1 DESCRIPTION
  27
  28
  29 =head1 AUTHORS
  30
  31  Mirella Flores <mrf252@cornell.edu>
  32  Lukas Mueller <lam87@cornell.edu>
  33
  34 =cut
  35
  36 use strict;
  37 use warnings;
  38 use Moose;
  39 use Try::Tiny;
  40 use Data::Dumper;
  41 use SGN::Model::Cvterm;
  42 use CXGN::Stock::TissueSample::Search;
  43 use JSON;
  44
  45 has 'bcs_schema' => (
  46     isa => 'Bio::Chado::Schema',
  47     is => 'rw',
  48     required => 1,
  49 );
  50
  51
  52 has 'client_id' => (
  53     is => 'ro',
  54     isa => 'Str',
  55     required => 1,
  56 );
  57
  58
  59 has 'requeriments' => (
  60     isa => 'HashRef|Undef',
  61     is => 'rw',
  62     required => 0,
  63 );
  64
  65 has 'service_id_list' => (
  66     isa => 'ArrayRef[Str]|Undef',
  67     is => 'ro',
  68     required => 1,
  69 );
  70
  71 has 'plate_id' => (
  72     isa => 'Str',
  73     is => 'ro',
  74     required => 1,
  75 );
  76
  77 has 'facility_id' => (
  78     isa => 'Str',
  79     is => 'ro',
  80     required => 0,
  81 );
  82
  83 has 'organism_name' => (
  84     isa => 'Str',
  85     is => 'ro',
  86     required => 1,
  87 );
  88
  89 # sub BUILD {
  90 #     my $self = shift;
  91 # }
  92
  93 =head2 validate()
  94
  95 Function for validating data before sending to facilities
  96
  97 my $submit_samples = CXGN::Genotype::CreatePlateOrder->new({
  98     bcs_schema=>$schema,
  99     etc...
 100 });
 101 my $get_errors = $submit_samples->validate();
 102
 103 =cut
 104
 105 sub validate {
 106     my $self = shift;
 107     # my $schema = $self->bcs_schema;
 108     # my $dbh = $schema->storage->dbh;
 109 }
 110
 111 =head2 submit()
 112
 113 Function for submit genotyping plates to facilities
 114
 115 my $create_order = CXGN::Genotype::CreatePlateOrder->new({
 116     bcs_schema=>$schema,
 117     etc...
 118 });
 119 my $errors = $submit_samples->submit();
 120
 121 =cut
 122
 123 sub create {
 124     my $self = shift;
 125     my $c = shift;
 126
 127     my $schema= $self->bcs_schema;
 128
 129     my $plate_id = $self->plate_id;
 130     my $facility_id = $self->facility_id;
 131     my $client_id = $self->client_id;
 132     my $get_requeriments = $self->requeriments;
 133     my $service_id_list = $self->service_id_list;
 134     my $requeriments = $get_requeriments ? $get_requeriments : {};
 135     my $organism_name = $self->organism_name;
 136
 137     my $genotyping_trial;
 138     eval {
 139         $genotyping_trial = CXGN::Trial->new( { bcs_schema => $schema, trial_id => $plate_id });
 140     };
 141
 142     my $sample_type = $genotyping_trial->get_genotyping_plate_sample_type;
 143
 144     my $plate_format = 'PLATE_96' if ($genotyping_trial->get_genotyping_plate_format eq 96);
 145
 146     my $samples = _formated_samples($schema,$plate_id,$organism_name);
 147
 148     my $plate;
 149     push @$plate, {
 150         clientPlateBarcode=> $genotyping_trial->get_name(),
 151         clientPlateId=> $plate_id,
 152         sampleSubmissionFormat=> $plate_format,
 153         samples=> $samples
 154     };
 155
 156     my $order =  {
 157                 clientId=>qq|$client_id|,
 158                 numberOfSamples=>scalar @$samples,
 159                 plates=>$plate,
 160                 requiredServiceInfo => $requeriments,
 161                 sampleType=>$sample_type,
 162                 serviceIds=>$service_id_list,
 163             };
 164
 165     return $order;
 166 }
 167
 168 sub _formated_samples {
 169     my $schema = shift;
 170     my $plate_id = shift;
 171     my $organism_name = shift;
 172
 173     if (!$plate_id || !$organism_name){
 174         return
 175     }
 176
 177     my $concent_unit = 'ng';
 178     my $volume_unit =  'ul';
 179
 180     my $sample_search = CXGN::Stock::TissueSample::Search->new({
 181         bcs_schema=>$schema,
 182         plate_db_id_list => [$plate_id],
 183         order_by => '',
 184     });
 185
 186     my ($results, $total_count) = $sample_search->search();
 187     my @samples;
 188
 189     foreach my $result (@$results){
 190          if ($result->{germplasmName} ne 'BLANK'){
 191             push @samples, {
 192                         clientSampleBarCode=> $result->{sampleName},
 193                         clientSampleId=> qq|$result->{sampleDbId}|,
 194                         column=> $result->{col_number} + 0,
 195                         row=> $result->{row_number},
 196                         comments=> $result->{notes},
 197                         concentration=> {
 198                             units=> $concent_unit,
 199                             value=> ($result->{concentration} eq 'NA' || $result->{concentration} eq '') ? 0 : $result->{concentration} + 0,
 200                         },
 201                         tissueType=> $result->{tissue_type},
 202                         volume=> {
 203                             units=> $volume_unit,
 204                             value=> ($result->{volume} eq 'NA' || $result->{volume} eq '') ? 0 : $result->{volume} + 0,
 205                         },
 206                         well=> $result->{well} ? $result->{well} : $result->{row_number} . $result->{col_number},
 207                         organismName=> $organism_name,
 208                         speciesName=> $result->{species} ? $result->{species} : "",
 209                         taxonomyOntologyReference=> {},
 210                         tissueTypeOntologyReference=> {},
 211                     };
 212             }
 213     }
 214
 215     return \@samples;
 216 }
 217
 218 1;