lib/CXGN/BrAPI/v1/Phenotypes.pm

   1 package CXGN::BrAPI::v1::Phenotypes;
   2
   3 use Moose;
   4 use Data::Dumper;
   5 use SGN::Model::Cvterm;
   6 use CXGN::Trial;
   7 use CXGN::Trait;
   8 use CXGN::Phenotypes::SearchFactory;
   9 use CXGN::BrAPI::Pagination;
  10
  11 has 'bcs_schema' => (
  12         isa => 'Bio::Chado::Schema',
  13         is => 'rw',
  14         required => 1,
  15 );
  16
  17 has 'metadata_schema' => (
  18         isa => 'CXGN::Metadata::Schema',
  19         is => 'rw',
  20         required => 1,
  21 );
  22
  23 has 'phenome_schema' => (
  24         isa => 'CXGN::Phenome::Schema',
  25         is => 'rw',
  26         required => 1,
  27 );
  28
  29 has 'page_size' => (
  30         isa => 'Int',
  31         is => 'rw',
  32         required => 1,
  33 );
  34
  35 has 'page' => (
  36         isa => 'Int',
  37         is => 'rw',
  38         required => 1,
  39 );
  40
  41 has 'status' => (
  42         isa => 'ArrayRef[Maybe[HashRef]]',
  43         is => 'rw',
  44         required => 1,
  45 );
  46
  47
  48 sub search {
  49         my $self = shift;
  50         my $inputs = shift;
  51         my $data_level = $inputs->{data_level} || 'plot';
  52         my $search_type = $inputs->{search_type} || 'complete';
  53         my @trait_ids_array = $inputs->{trait_ids} ? @{$inputs->{trait_ids}} : ();
  54         my @accession_ids_array = $inputs->{accession_ids} ? @{$inputs->{accession_ids}} : ();
  55         my @study_ids_array = $inputs->{study_ids} ? @{$inputs->{study_ids}} : ();
  56         my @location_ids_array = $inputs->{location_ids} ? @{$inputs->{location_ids}} : ();
  57         my @years_array = $inputs->{years} ? @{$inputs->{years}} : ();
  58         my $page_size = $self->page_size;
  59         my $page = $self->page;
  60         my $status = $self->status;
  61
  62         my $factory_type;
  63     if ($search_type eq 'complete'){
  64         $factory_type = 'Native';
  65     }
  66     if ($search_type eq 'fast'){
  67         $factory_type = 'MaterializedView';
  68     }
  69     my $phenotypes_search = CXGN::Phenotypes::SearchFactory->instantiate(
  70         $factory_type,    #can be either 'MaterializedView', or 'Native'
  71         {
  72             bcs_schema=>$self->bcs_schema,
  73             data_level=>$data_level,
  74             trial_list=>\@study_ids_array,
  75                         trait_list=>\@trait_ids_array,
  76             include_timestamp=>1,
  77                 year_list=>\@years_array,
  78                 location_list=>\@location_ids_array,
  79                 accession_list=>\@accession_ids_array,
  80         }
  81     );
  82     my $data = $phenotypes_search->search();
  83     #print STDERR Dumper $data;
  84         my @data_window;
  85         my %obs_units;
  86         foreach (@$data){
  87                 if (exists($obs_units{$_->[14]})){
  88                         my $observations = $obs_units{$_->[14]}->{observations};
  89                         push @$observations, {
  90                                 observationDbId => $_->[19],
  91                                 observationVariableDbId => $_->[10],
  92                                 observationVariableName => $_->[4],
  93                                 observationTimestamp => $_->[15],
  94                                 season => $_->[0],
  95                                 collector => '',
  96                                 value => $_->[5],
  97                         };
  98                         $obs_units{$_->[14]}->{observations} = $observations;
  99                 } else {
 100                         $obs_units{$_->[14]} = {
 101                                 observationUnitDbId => $_->[14],
 102                                 observationLevel => $_->[18],
 103                                 observationLevels => $_->[18],
 104                                 plotNumber => $_->[9],
 105                                 plantNumber => '',
 106                                 blockNumber => $_->[8],
 107                                 replicate => $_->[7],
 108                                 observationUnitName => $_->[6],
 109                                 germplasmDbId => $_->[13],
 110                                 germplasmName => $_->[2],
 111                                 studyDbId => $_->[11],
 112                                 studyName => $_->[1],
 113                                 studyLocationDbId => $_->[12],
 114                                 studyLocation => $_->[3],
 115                                 programName => '',
 116                                 X => '',
 117                                 Y => '',
 118                                 entryType => '',
 119                                 entryNumber => '',
 120                                 treatments => [],
 121                                 observations => [{
 122                                         observationDbId => $_->[19],
 123                                         observationVariableDbId => $_->[10],
 124                                         observationVariableName => $_->[4],
 125                                         observationTimestamp => $_->[15],
 126                                         season => $_->[0],
 127                                         collector => '',
 128                                         value => $_->[5],
 129                                 }]
 130                         };
 131                 }
 132         }
 133         my $total_count = scalar(keys %obs_units);
 134         my $count = 0;
 135         my $offset = $page*$page_size;
 136         my $limit = $page_size*($page+1)-1;
 137         foreach my $obs_unit_id (sort keys %obs_units) {
 138                 if ($count >= $offset && $count <= ($offset+$limit)){
 139                         push @data_window, $obs_units{$obs_unit_id};
 140                 }
 141         }
 142         my %result = (data=>\@data_window);
 143         push @$status, { 'success' => 'Studies observations result constructed' };
 144         my $pagination = CXGN::BrAPI::Pagination->pagination_response($total_count,$page_size,$page);
 145         my $response = {
 146                 'status' => $status,
 147                 'pagination' => $pagination,
 148                 'result' => \%result,
 149                 'datafiles' => []
 150         };
 151         return $response;
 152 }
 153
 154 1;