lib/CXGN/Genotype/GenotypingProject.pm

   1
   2 =head1 NAME
   3
   4 CXGN::Genotype::GenotypingProject - an object representing a genotyping project in the database
   5
   6 =head1 DESCRIPTION
   7
   8     my $genotyping_project = CXGN::Genotype::GenotypingProject->new( { schema => $schema, trial_id => 37347 });
   9
  10
  11 =head1 AUTHORS
  12
  13     Titima Tantikanjana
  14
  15 =head1 METHODS
  16
  17 =cut
  18 package CXGN::Genotype::GenotypingProject;
  19
  20 use Moose;
  21 use SGN::Model::Cvterm;
  22 use Data::Dumper;
  23 use JSON;
  24 use CXGN::Trial::Search;
  25 use Try::Tiny;
  26 use CXGN::Trial;
  27 use CXGN::Trial::TrialLayout;
  28
  29 has 'bcs_schema' => (
  30     isa => 'Bio::Chado::Schema',
  31     is => 'rw',
  32     required => 1,
  33 );
  34
  35 has 'project_id' => (
  36     isa => 'Int',
  37     is => 'rw',
  38     required => 1,
  39 );
  40
  41 has 'project_facility' => (isa => 'Str',
  42     is => 'rw',
  43     required => 0,
  44 );
  45
  46 has 'project_and_plate_relationship_cvterm_id' => (
  47     isa => 'Int',
  48     is => 'rw',
  49 );
  50
  51 has 'genotyping_plate_list' => (
  52     isa => 'ArrayRef[Int]|Undef',
  53     is => 'rw',
  54 );
  55
  56 has 'new_genotyping_plate_list' => (
  57     isa => 'ArrayRef[Int]|Undef',
  58     is => 'rw',
  59 );
  60
  61 sub BUILD {
  62
  63     my $self = shift;
  64     my $schema = $self->bcs_schema();
  65     my $genotyping_project_id = $self->project_id();
  66
  67     my $genotyping_project = CXGN::Trial->new( { bcs_schema => $schema, trial_id => $genotyping_project_id });
  68     my $project_facility = $genotyping_project->get_genotyping_facility();
  69
  70     my $genotyping_project_relationship_cvterm = SGN::Model::Cvterm->get_cvterm_row($schema, 'genotyping_project_and_plate_relationship', 'project_relationship');
  71     my $project_and_plate_relationship_cvterm_id = $genotyping_project_relationship_cvterm->cvterm_id();
  72     my $relationships_rs = $schema->resultset("Project::ProjectRelationship")->search ({
  73         object_project_id => $genotyping_project_id,
  74         type_id => $project_and_plate_relationship_cvterm_id
  75     });
  76
  77     my @plate_list;
  78     if ($relationships_rs) {
  79         while (my $each_relationship = $relationships_rs->next()) {
  80             push @plate_list, $each_relationship->subject_project_id();
  81         }
  82     }
  83     $self->project_facility($project_facility);
  84     $self->project_and_plate_relationship_cvterm_id($project_and_plate_relationship_cvterm_id);
  85     $self->genotyping_plate_list(\@plate_list);
  86
  87 }
  88
  89
  90 sub get_genotyping_plate_ids {
  91     my $self = shift;
  92     my $plate_list = $self->genotyping_plate_list();
  93     return $plate_list;
  94 }
  95
  96
  97 sub validate_relationship {
  98     my $self = shift;
  99     my $schema = $self->bcs_schema();
 100     my $new_plate_ids = $self->new_genotyping_plate_list();
 101     my $genotyping_project_id = $self->project_id();
 102     my $project_facility = $self->project_facility();
 103     my @plate_ids = @$new_plate_ids;
 104     my @genotyping_plate_errors;
 105
 106     foreach my $plate_id (@plate_ids) {
 107         my $genotyping_plate = CXGN::Trial->new( { bcs_schema => $schema, trial_id => $plate_id });
 108         my $plate_facility = $genotyping_plate->get_genotyping_facility();
 109
 110         if (($plate_facility ne 'None') && ($project_facility ne 'None')) {
 111             if ($plate_facility ne $project_facility) {
 112                 my $genotyping_plate_name = $genotyping_plate->get_name();
 113                 push @genotyping_plate_errors, $genotyping_plate_name;
 114             }
 115         }
 116     }
 117
 118     return {error_messages => \@genotyping_plate_errors}
 119 }
 120
 121
 122 sub set_project_for_genotyping_plate {
 123     my $self = shift;
 124     my $schema = $self->bcs_schema();
 125     my $genotyping_project_id = $self->project_id();
 126     my $new_genotyping_plate_list = $self->new_genotyping_plate_list();
 127     my @new_genotyping_plates = @$new_genotyping_plate_list;
 128     my $transaction_error;
 129
 130     my $coderef = sub {
 131
 132         foreach my $plate_id (@new_genotyping_plates) {
 133             my $relationship_rs = $schema->resultset("Project::ProjectRelationship")->find ({
 134                 subject_project_id => $plate_id,
 135                 type_id => $self->project_and_plate_relationship_cvterm_id()
 136             });
 137
 138             if($relationship_rs){
 139                 print STDERR "UPDATING...."."\n";
 140                 $relationship_rs->object_project_id($genotyping_project_id);
 141                 $relationship_rs->update();
 142             } else {
 143                 $relationship_rs = $schema->resultset('Project::ProjectRelationship')->create({
 144                             object_project_id => $genotyping_project_id,
 145                             subject_project_id => $plate_id,
 146                             type_id => $self->project_and_plate_relationship_cvterm_id()
 147                 });
 148                 $relationship_rs->insert();
 149             }
 150         }
 151     };
 152
 153     try {
 154         $schema->txn_do($coderef);
 155     } catch {
 156         $transaction_error =  $_;
 157     };
 158
 159     if ($transaction_error) {
 160         print STDERR "Transaction error associating genotyping plate: $transaction_error\n";
 161         return;
 162     }
 163
 164     return 1;
 165
 166 }
 167
 168
 169 sub get_plate_info {
 170     my $self = shift;
 171     my $schema = $self->bcs_schema();
 172     my $plate_list = $self->genotyping_plate_list();
 173     my $number_of_plates = scalar (@$plate_list);
 174     my $data;
 175     my $total_count;
 176     my @all_plates;
 177     my $number_of_samples;
 178     if ($number_of_plates > 0) {
 179         my $trial_search = CXGN::Trial::Search->new({
 180             bcs_schema => $schema,
 181             trial_design_list => ['genotyping_plate'],
 182             trial_id_list => $plate_list
 183         });
 184         ($data, $total_count) = $trial_search->search();
 185
 186         foreach my $plate (@$data){
 187             my $plate_layout = CXGN::Trial::TrialLayout->new({schema => $schema, trial_id => $plate->{trial_id}, experiment_type => 'genotyping_layout'});
 188             my $sample_names = $plate_layout->get_plot_names();
 189             my $number_of_samples = '';
 190             if ($sample_names){
 191                 $number_of_samples = scalar(@{$sample_names});
 192             }
 193
 194             push @all_plates, {
 195                 plate_id => $plate->{trial_id},
 196                 plate_name => $plate->{trial_name},
 197                 plate_description => $plate->{description},
 198                 plate_format => $plate->{genotyping_plate_format},
 199                 sample_type => $plate->{genotyping_plate_sample_type},
 200                 number_of_samples => $number_of_samples,
 201             };
 202         }
 203     }
 204
 205     return (\@all_plates, $number_of_plates);
 206
 207 }
 208
 209
 210 sub get_associated_protocol {
 211     my $self = shift;
 212     my $schema = $self->bcs_schema();
 213     my $genotyping_project_id = $self->project_id();
 214
 215     my $q = "SELECT DISTINCT nd_protocol.nd_protocol_id, nd_protocol.name
 216         FROM nd_experiment_project
 217         JOIN nd_experiment_genotype ON (nd_experiment_project.nd_experiment_id = nd_experiment_genotype.nd_experiment_id)
 218         JOIN nd_experiment_protocol ON (nd_experiment_project.nd_experiment_id = nd_experiment_protocol.nd_experiment_id)
 219         JOIN nd_protocol ON (nd_experiment_protocol.nd_protocol_id = nd_protocol.nd_protocol_id)
 220         WHERE nd_experiment_project.project_id = ?";
 221
 222     my $h = $schema->storage->dbh()->prepare($q);
 223     $h->execute($genotyping_project_id);
 224
 225     my @associated_protocol = ();
 226     while (my ($protocol_id, $protocol_name) = $h->fetchrow_array()){
 227         push @associated_protocol, [$protocol_id, $protocol_name]
 228     }
 229
 230     return \@associated_protocol;
 231
 232 }
 233
 234
 235
 236 1;