lib/CXGN/BrAPI/v2/Plates.pm

   1 package CXGN::BrAPI::v2::Plates;
   2
   3 use Moose;
   4 use Data::Dumper;
   5 use SGN::Model::Cvterm;
   6 use CXGN::Genotype::Search;
   7 use JSON;
   8 use CXGN::BrAPI::FileResponse;
   9 use CXGN::BrAPI::Pagination;
  10 use CXGN::BrAPI::JSONResponse;
  11
  12 extends 'CXGN::BrAPI::v2::Common';
  13
  14 sub search {
  15     my $self = shift;
  16     my $params = shift;
  17     my $c = $self->context;
  18     my $page_size = $self->page_size;
  19     my $page = $self->page;
  20     my $status = $self->status;
  21
  22     my $plates_arrayref = $params->{plateDbId} || ($params->{plateDbIds} || ());
  23     my $program_id_list = $params->{programDbId} || ($params->{programDbIds} || ());
  24     my $program_list = $params->{programName} || ($params->{programNames} || ());
  25     my $trial_name_list = $params->{plateName} || ($params->{plateNames} || ());
  26     my $folder_id_list = $params->{studyDbId} || ($params->{studyDbIds} || ());
  27     my $folder_name_list = $params->{studyName} || ($params->{studyNames} || ());
  28
  29     my $sp_person_id = $c->user() ? $c->user->get_object()->get_sp_person_id() : undef;
  30     my $bcs_schema = $c->dbic_schema('Bio::Chado::Schema', 'sgn_chado', $sp_person_id);
  31
  32     my @trial_ids;
  33     if ($plates_arrayref){
  34         push @trial_ids, @{$plates_arrayref};
  35     }
  36
  37     my $trial_search = CXGN::Trial::Search->new({
  38         bcs_schema=>$bcs_schema,
  39         trial_design_list=>['genotyping_plate'],
  40         trial_id_list => \@trial_ids,
  41         program_list => $program_list,
  42         program_id_list => $program_id_list,
  43         trial_name_list => $trial_name_list,
  44         folder_id_list => $folder_id_list,
  45         folder_name_list => $folder_name_list,
  46         # location_list => $location_list,
  47         # location_id_list => $location_id_list,
  48         # year_list => $year_list,
  49         # trial_type_list => $trial_type_list,
  50         # trial_design_list => $trial_design_list,
  51         # trial_name_is_exact => $trial_name_is_exact,
  52         # accession_list => $accession_list,
  53         # accession_name_list => $accession_name_list,
  54         # trait_list => $trait_list,
  55     });
  56
  57     my ($data, $total_count) = $trial_search->search();
  58
  59     my @data;
  60
  61     foreach (@$data){
  62         push @data, {
  63                 additionalInfo => {},
  64                 externalReferences => [],
  65                 plateBarcode => undef,
  66                 plateFormat => $_->{genotyping_plate_format},
  67                 plateName => $_->{trial_name},
  68                 programDbId => qq|$_->{breeding_program_id}|,
  69                 sampleType => $_->{genotyping_plate_sample_type},
  70                 studyDbId => qq|$_->{trial_id}|,
  71                 trialDbId => qq|$_->{trial_id}|,
  72                 plateDbId => qq|$_->{trial_id}|,
  73         }
  74     }
  75
  76     my %result = (data=>\@data);
  77     my @data_files;
  78     my $pagination = CXGN::BrAPI::Pagination->pagination_response($total_count,$page_size,$page);
  79     return CXGN::BrAPI::JSONResponse->return_success(\%result, $pagination, \@data_files, $status, 'Plates result constructed');
  80 }
  81
  82 sub detail {
  83     my $self = shift;
  84     my $plate_id = shift;
  85     my $c = $self->context;
  86     my $page_size = $self->page_size;
  87     my $page = $self->page;
  88     my $status = $self->status;
  89
  90     my $sp_person_id = $c->user() ? $c->user->get_object()->get_sp_person_id() : undef;
  91     my $bcs_schema = $c->dbic_schema('Bio::Chado::Schema', 'sgn_chado', $sp_person_id);
  92
  93     my $trial_search = CXGN::Trial::Search->new({
  94         bcs_schema=>$bcs_schema,
  95         trial_design_list=>['genotyping_plate'],
  96         trial_id_list => [$plate_id]
  97     });
  98
  99     my ($data, $total_count) = $trial_search->search();
 100
 101     my @data;
 102
 103     foreach (@$data){
 104         push @data, {
 105                 additionalInfo => {},
 106                 externalReferences => [],
 107                 plateBarcode => undef,
 108                 plateFormat => $_->{genotyping_plate_format},
 109                 plateName => $_->{trial_name},
 110                 programDbId => qq|$_->{breeding_program_id}|,
 111                 sampleType => $_->{genotyping_plate_sample_type},
 112                 studyDbId => qq|$_->{trial_id}|,
 113                 trialDbId => qq|$_->{trial_id}|,
 114                 plateDbId => qq|$_->{trial_id}|,
 115         }
 116     }
 117
 118     my @data_files;
 119     my $pagination = CXGN::BrAPI::Pagination->pagination_response($total_count,$page_size,$page);
 120     return CXGN::BrAPI::JSONResponse->return_success(@data, $pagination, \@data_files, $status, 'Plates result constructed');
 121 }
 122
 123
 124
 125 1;