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