lib/CXGN/BrAPI/v1/ObservationTables.pm

   1 package CXGN::BrAPI::v1::ObservationTables;
   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 $trait_list_arrayref = $params->{observationVariableDbId} || ($params->{observationVariableDbIds} || ());
  31     my $program_ids_arrayref = $params->{programDbId} || ($params->{programDbIds} || ());
  32     my $folder_ids_arrayref = $params->{trialDbId} || ($params->{trialDbIds} || ());
  33     my $start_time = $params->{observationTimeStampRangeStart}->[0] || undef;
  34     my $end_time = $params->{observationTimeStampRangeEnd}->[0] || undef;
  35
  36     # not part of brapi standard yet
  37     # my $phenotype_min_value = $params->{phenotype_min_value};
  38     # my $phenotype_max_value = $params->{phenotype_max_value};
  39     # my $exclude_phenotype_outlier = $params->{exclude_phenotype_outlier} || 0;
  40     # my $search_type = $params->{search_type}->[0] || 'MaterializedViewTable';
  41
  42     my $lt = CXGN::List::Transform->new();
  43     my $trait_ids_arrayref = $lt->transform($self->bcs_schema, "traits_2_trait_ids", $trait_list_arrayref)->{transform};
  44
  45     my $phenotypes_search = CXGN::Phenotypes::PhenotypeMatrix->new(
  46         bcs_schema=>$self->bcs_schema,
  47         data_level=>$data_level,
  48         search_type=>'MaterializedViewTable',
  49         trial_list=>$study_ids_arrayref,
  50         trait_list=>$trait_ids_arrayref,
  51         include_timestamp=>1,
  52         year_list=>$years_arrayref,
  53         location_list=>$location_ids_arrayref,
  54         accession_list=>$accession_ids_arrayref,
  55         folder_list=>$folder_ids_arrayref,
  56         program_list=>$program_ids_arrayref,
  57         # phenotype_min_value=>$phenotype_min_value,
  58         # phenotype_max_value=>$phenotype_max_value,
  59         # exclude_phenotype_outlier=>$exclude_phenotype_outlier
  60     );
  61     my @data;
  62     try {
  63         @data = $phenotypes_search->get_phenotype_matrix();
  64     }
  65     catch {
  66         return CXGN::BrAPI::JSONResponse->return_error($status, 'An Error Occured During Phenotype Search Table');
  67     }
  68
  69     my @data_files;
  70     my $total_count = scalar(@data)-1;
  71     my @header_names = @{$data[0]};
  72     my @trait_names = @header_names[39 .. $#header_names];
  73     my @header_ids;
  74     foreach my $t (@trait_names) {
  75         if ($t eq 'notes') { next; }
  76         push @header_ids, SGN::Model::Cvterm->get_cvterm_row_from_trait_name($self->bcs_schema, $t)->cvterm_id();
  77     }
  78
  79     my $start = $page_size*$page;
  80     my $end = $page_size*($page+1)-1;
  81     my @data_window;
  82     for (my $line = $start; $line < $end; $line++) {
  83         if ($data[$line]) {
  84             my $columns = $data[$line];
  85             push @data_window, $columns;
  86         }
  87     }
  88
  89     #print STDERR Dumper \@data_window;
  90
  91     my %result = (
  92         headerRow => ['studyYear', 'programDbId', 'programName', 'programDescription', 'studyDbId', 'studyName', 'studyDescription', 'studyDesign', 'plotWidth', 'plotLength', 'fieldSize', 'fieldTrialIsPlannedToBeGenotyped', 'fieldTrialIsPlannedToCross', 'plantingDate', 'harvestDate', 'locationDbId', 'locationName', 'germplasmDbId', 'germplasmName', 'germplasmSynonyms', 'observationLevel', 'observationUnitDbId', 'observationUnitName', 'replicate', 'blockNumber', 'plotNumber', 'rowNumber', 'colNumber', 'entryType', 'plantNumber', 'plantedSeedlotStockDbId', 'plantedSeedlotStockUniquename', 'plantedSeedlotCurrentCount', 'plantedSeedlotCurrentWeightGram', 'plantedSeedlotBoxName', 'plantedSeedlotTransactionCount', 'plantedSeedlotTransactionWeight', 'plantedSeedlotTransactionDescription', 'availableGermplasmSeedlotUniquenames'],
  93         observationVariableDbIds => \@header_ids,
  94         observationVariableNames => \@trait_names,
  95         data=>\@data_window
  96     );
  97
  98     my $pagination = CXGN::BrAPI::Pagination->pagination_response($total_count,$page_size,$page);
  99     return CXGN::BrAPI::JSONResponse->return_success(\%result, $pagination, \@data_files, $status, 'Phenotype-search table result constructed');
 100 }
 101
 102 1;