lib/CXGN/BrAPI/v1/ObservationUnits.pm

   1 package CXGN::BrAPI::v1::ObservationUnits;
   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 use Try::Tiny;
  12 use CXGN::Phenotypes::PhenotypeMatrix;
  13 use CXGN::List::Transform;
  14
  15 extends 'CXGN::BrAPI::v1::Common';
  16
  17 sub search {
  18     my $self = shift;
  19     my $params = shift;
  20     my $page_size = $self->page_size;
  21     my $page = $self->page;
  22     my $status = $self->status;
  23     my @data_files;
  24
  25     my $data_level = $params->{observationLevel}->[0] || 'all';
  26     my $years_arrayref = $params->{seasonDbId} || ($params->{seasonDbIds} || ());
  27     my $location_ids_arrayref = $params->{locationDbId} || ($params->{locationDbIds} || ());
  28     my $study_ids_arrayref = $params->{studyDbId} || ($params->{studyDbIds} || ());
  29     my $accession_ids_arrayref = $params->{germplasmDbId} || ($params->{germplasmDbIds} || ());
  30     my $observation_unit_names_list = $params->{observationUnitName} || ($params->{observationUnitNames} || ());
  31     my $trait_list_arrayref = $params->{observationVariableDbId} || ($params->{observationVariableDbIds} || ());
  32     my $program_ids_arrayref = $params->{programDbId} || ($params->{programDbIds} || ());
  33     my $folder_ids_arrayref = $params->{trialDbId} || ($params->{trialDbIds} || ());
  34     my $start_time = $params->{observationTimeStampRangeStart}->[0] || undef;
  35     my $end_time = $params->{observationTimeStampRangeEnd}->[0] || undef;
  36
  37     # not part of brapi standard yet
  38     # my $phenotype_min_value = $params->{phenotype_min_value};
  39     # my $phenotype_max_value = $params->{phenotype_max_value};
  40     # my $exclude_phenotype_outlier = $params->{exclude_phenotype_outlier} || 0;
  41     # my $search_type = $params->{search_type}->[0] || 'MaterializedViewTable';
  42
  43     my $lt = CXGN::List::Transform->new();
  44     my $trait_ids_arrayref = $lt->transform($self->bcs_schema, "traits_2_trait_ids", $trait_list_arrayref)->{transform};
  45
  46     my $limit = $page_size*($page+1)-1;
  47     my $offset = $page_size*$page;
  48
  49     my $phenotypes_search = CXGN::Phenotypes::SearchFactory->instantiate(
  50         'MaterializedViewTable',
  51         {
  52             bcs_schema=>$self->bcs_schema,
  53             data_level=>$data_level,
  54             trial_list=>$study_ids_arrayref,
  55             trait_list=>$trait_ids_arrayref,
  56             include_timestamp=>1,
  57             year_list=>$years_arrayref,
  58             location_list=>$location_ids_arrayref,
  59             accession_list=>$accession_ids_arrayref,
  60             folder_list=>$folder_ids_arrayref,
  61             program_list=>$program_ids_arrayref,
  62             observation_unit_names_list=>$observation_unit_names_list,
  63             limit=>$limit,
  64             offset=>$offset,
  65             # # Order by plot_number, account for non-numeric plot numbers
  66             # order_by=>'NULLIF(regexp_replace(plot_number, \'\D\', \'\', \'g\'), \'\')::int',
  67             # phenotype_min_value=>$phenotype_min_value,
  68             # phenotype_max_value=>$phenotype_max_value,
  69             # exclude_phenotype_outlier=>$exclude_phenotype_outlier
  70         }
  71     );
  72     my ($data, $unique_traits) = $phenotypes_search->search();
  73     # print STDERR Dumper $data;
  74
  75     my @data_window;
  76     my $total_count = 0;
  77     foreach my $obs_unit (@$data){
  78         my @brapi_observations;
  79         my $observations = $obs_unit->{observations};
  80         foreach (@$observations){
  81             my $obs_timestamp = $_->{collect_date} ? $_->{collect_date} : $_->{timestamp};
  82             if ( $start_time && $obs_timestamp < $start_time ) { next; } #skip observations before date range
  83             if ( $end_time && $obs_timestamp > $end_time ) { next; } #skip observations after date range
  84             push @brapi_observations, {
  85                 observationDbId => qq|$_->{phenotype_id}|,
  86                 observationVariableDbId => qq|$_->{trait_id}|,
  87                 observationVariableName => $_->{trait_name},
  88                 observationTimeStamp => $obs_timestamp,
  89                 season => $obs_unit->{year},
  90                 collector => $_->{operator},
  91                 value => qq|$_->{value}|,
  92             };
  93         }
  94         my @brapi_treatments;
  95         my $treatments = $obs_unit->{treatments};
  96         while (my ($factor, $modality) = each %$treatments){
  97             my $modality = $modality ? $modality : '';
  98             push @brapi_treatments, {
  99                 factor => $factor,
 100                 modality => $modality,
 101             };
 102         }
 103         my $entry_type = $obs_unit->{obsunit_is_a_control} ? 'check' : 'test';
 104         push @data_window, {
 105             observationUnitDbId => qq|$obs_unit->{observationunit_stock_id}|,
 106             observationLevel => $obs_unit->{observationunit_type_name},
 107             observationLevels => $obs_unit->{observationunit_type_name},
 108             plotNumber => $obs_unit->{obsunit_plot_number},
 109             plantNumber => $obs_unit->{obsunit_plant_number},
 110             blockNumber => $obs_unit->{obsunit_block},
 111             replicate => $obs_unit->{obsunit_rep},
 112             observationUnitName => $obs_unit->{observationunit_uniquename},
 113             germplasmDbId => qq|$obs_unit->{germplasm_stock_id}|,
 114             germplasmName => $obs_unit->{germplasm_uniquename},
 115             studyDbId => qq|$obs_unit->{trial_id}|,
 116             studyName => $obs_unit->{trial_name},
 117             studyLocationDbId => qq|$obs_unit->{trial_location_id}|,
 118             studyLocation => $obs_unit->{trial_location_name},
 119             programName => $obs_unit->{breeding_program_name},
 120             X => $obs_unit->{obsunit_col_number},
 121             Y => $obs_unit->{obsunit_row_number},
 122             entryType => $entry_type,
 123             entryNumber => '',
 124             treatments => \@brapi_treatments,
 125             observations => \@brapi_observations,
 126             observationUnitXref => [],
 127             pedigree => undef
 128         };
 129         $total_count = $obs_unit->{full_count};
 130     }
 131
 132     my %result = (data=>\@data_window);
 133     my $pagination = CXGN::BrAPI::Pagination->pagination_response($total_count,$page_size,$page);
 134     return CXGN::BrAPI::JSONResponse->return_success(\%result, $pagination, \@data_files, $status, 'Phenotype search result constructed');
 135 }
 136
 137 1;