lib/CXGN/Phenotypes/HighDimensionalPhenotypesSearch.pm

   1 package CXGN::Phenotypes::HighDimensionalPhenotypesSearch;
   2
   3 =head1 NAME
   4
   5 CXGN::Phenotypes::HighDimensionalPhenotypesSearch - an object to handle searching high dim phenotypes (NIRS, Trnascriptomics, Metabolomics) across database.
   6
   7 =head1 USAGE
   8
   9 my $phenotypes_search = CXGN::Phenotypes::HighDimensionalPhenotypesSearch->new({
  10     bcs_schema=>$schema,
  11     nd_protocol_id=>$nd_protocol_id,
  12     high_dimensional_phenotype_type=>$high_dimensional_phenotype_type, #NIRS, Transcriptomics, or Metabolomics
  13     high_dimensional_phenotype_identifier_list=>\@high_dimensional_phenotype_identifier_list,
  14     query_associated_stocks=>$query_associated_stocks, #Query associated plots, plants, tissue samples, etc for accessions that are given
  15     accession_list=>$accession_ids,
  16     plot_list=>$plot_ids,
  17     plant_list=>$plant_ids,
  18 });
  19 my (\%data, \%identifier_metadata, \@identifier_names) = $phenotypes_search->search();
  20
  21 =head1 DESCRIPTION
  22
  23
  24 =head1 AUTHORS
  25
  26
  27 =cut
  28
  29 use strict;
  30 use warnings;
  31 use Moose;
  32 use Try::Tiny;
  33 use Data::Dumper;
  34 use SGN::Model::Cvterm;
  35 use CXGN::Stock::StockLookup;
  36 use CXGN::Trial::TrialLayout;
  37 use CXGN::Calendar;
  38 use JSON;
  39 use CXGN::Phenotypes::HighDimensionalPhenotypeProtocol;
  40
  41 has 'bcs_schema' => (
  42     isa => 'Bio::Chado::Schema',
  43     is => 'rw',
  44     required => 1
  45 );
  46
  47 has 'high_dimensional_phenotype_type' => (
  48     isa => 'Str',
  49     is => 'rw',
  50     required => 1
  51 );
  52
  53 has 'nd_protocol_id' => (
  54     isa => 'Int',
  55     is => 'rw',
  56     required => 1
  57 );
  58
  59 has 'query_associated_stocks' => (
  60     isa => 'Bool|Undef',
  61     is => 'ro',
  62     default => 1
  63 );
  64
  65 has 'high_dimensional_phenotype_identifier_list' => (
  66     isa => 'ArrayRef[Str]|Undef',
  67     is => 'rw',
  68 );
  69
  70 has 'accession_list' => (
  71     isa => 'ArrayRef[Int]|Undef',
  72     is => 'rw',
  73 );
  74
  75 has 'plot_list' => (
  76     isa => 'ArrayRef[Int]|Undef',
  77     is => 'rw',
  78 );
  79
  80 has 'plant_list' => (
  81     isa => 'ArrayRef[Int]|Undef',
  82     is => 'rw',
  83 );
  84
  85 sub search {
  86     my $self = shift;
  87     my $schema = $self->bcs_schema();
  88     my $nd_protocol_id = $self->nd_protocol_id();
  89     my $high_dimensional_phenotype_type = $self->high_dimensional_phenotype_type();
  90     my $high_dimensional_phenotype_identifier_list = $self->high_dimensional_phenotype_identifier_list();
  91     my $accession_ids = $self->accession_list();
  92     my $plot_ids = $self->plot_list();
  93     my $plant_ids = $self->plant_list();
  94     my $query_associated_stocks = $self->query_associated_stocks();
  95     my $dbh = $schema->storage->dbh();
  96
  97     if (!$accession_ids && !$plot_ids && !$plant_ids) {
  98         return { error => "No accessions or plots or plants in your selected dataset!" };
  99     }
 100
 101     my @all_stock_ids;
 102     if ($query_associated_stocks) {
 103         if ($accession_ids && scalar(@$accession_ids) > 0) {
 104             push @all_stock_ids, @$accession_ids;
 105         }
 106         if ($plot_ids && scalar(@$plot_ids) > 0) {
 107             push @all_stock_ids, @$plot_ids;
 108         }
 109         if ($plant_ids && scalar(@$plant_ids) > 0) {
 110             push @all_stock_ids, @$plant_ids;
 111         }
 112
 113         my $accession_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'accession', 'stock_type')->cvterm_id();
 114         my $plot_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'plot', 'stock_type')->cvterm_id();
 115         my $plant_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'plant', 'stock_type')->cvterm_id();
 116         my $tissue_sample_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'tissue_sample', 'stock_type')->cvterm_id();
 117
 118         my $plot_of_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'plot_of', 'stock_relationship')->cvterm_id();
 119         my $plant_of_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'plant_of', 'stock_relationship')->cvterm_id();
 120         my $tissue_sample_of_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'tissue_sample_of', 'stock_relationship')->cvterm_id();
 121
 122         if ($accession_ids && scalar(@$accession_ids) > 0) {
 123             my $accession_ids_sql = join ',', @$accession_ids;
 124             my $accession_q = "SELECT subject_id FROM stock_relationship WHERE object_id IN ($accession_ids_sql) AND type_id IN ($plot_of_cvterm_id, $plant_of_cvterm_id, $tissue_sample_of_cvterm_id);";
 125             my $accession_h = $dbh->prepare($accession_q);
 126             $accession_h->execute();
 127             while (my ($stock_id) = $accession_h->fetchrow_array()) {
 128                 push @all_stock_ids, $stock_id;
 129             }
 130         }
 131         if ( ($plot_ids && scalar(@$plot_ids) > 0) || ($plant_ids && scalar(@$plant_ids) > 0) ) {
 132             my @plot_plant_ids;
 133             if ($plot_ids && scalar(@$plot_ids) > 0) {
 134                 push @plot_plant_ids, @$plot_ids;
 135             }
 136             if ($plant_ids && scalar(@$plant_ids) > 0) {
 137                 push @plot_plant_ids, @$plant_ids;
 138             }
 139             my $plot_ids_sql = join ',', @plot_plant_ids;
 140             my $plot_q = "SELECT object_id FROM stock_relationship WHERE subject_id IN ($plot_ids_sql) AND type_id IN ($plot_of_cvterm_id, $plant_of_cvterm_id, $tissue_sample_of_cvterm_id);";
 141             my $plot_h = $dbh->prepare($plot_q);
 142             $plot_h->execute();
 143             while (my ($stock_id) = $plot_h->fetchrow_array()) {
 144                 push @all_stock_ids, $stock_id;
 145             }
 146
 147             my $accession_ids_sql = join ',', @all_stock_ids;
 148             my $accession_q = "SELECT subject_id FROM stock_relationship WHERE object_id IN ($accession_ids_sql) AND type_id IN ($plot_of_cvterm_id, $plant_of_cvterm_id, $tissue_sample_of_cvterm_id);";
 149             my $accession_h = $dbh->prepare($accession_q);
 150             $accession_h->execute();
 151             while (my ($stock_id) = $accession_h->fetchrow_array()) {
 152                 push @all_stock_ids, $stock_id;
 153             }
 154         }
 155     }
 156     else {
 157         if ($accession_ids && scalar(@$accession_ids) > 0) {
 158             push @all_stock_ids, @$accession_ids;
 159         }
 160         if ($plot_ids && scalar(@$plot_ids) > 0) {
 161             push @all_stock_ids, @$plot_ids;
 162         }
 163         if ($plant_ids && scalar(@$plant_ids) > 0) {
 164             push @all_stock_ids, @$plant_ids;
 165         }
 166     }
 167
 168     # print STDERR Dumper \@all_stock_ids;
 169     my $stock_ids_sql = join ',', @all_stock_ids;
 170
 171     my %data_matrix;
 172     my $protocol_type_cvterm_id;
 173
 174     if ($high_dimensional_phenotype_type eq 'NIRS') {
 175         my $q = "SELECT stock.uniquename, stock.stock_id, metadata.md_json.json->>'spectra', metadata.md_json.json->>'device_type'
 176             FROM stock
 177             JOIN nd_experiment_stock USING(stock_id)
 178             JOIN nd_experiment USING(nd_experiment_id)
 179             JOIN nd_experiment_protocol USING(nd_experiment_id)
 180             JOIN phenome.nd_experiment_md_json USING(nd_experiment_id)
 181             JOIN metadata.md_json USING(json_id)
 182             WHERE stock.stock_id IN ($stock_ids_sql) AND nd_experiment_protocol.nd_protocol_id = ? AND metadata.md_json.json_type = 'nirs_spectra';";
 183         print STDERR Dumper $q;
 184         my $h = $dbh->prepare($q);
 185         $h->execute($nd_protocol_id);
 186         while (my ($stock_uniquename, $stock_id, $spectra, $device_type) = $h->fetchrow_array()) {
 187             eval {
 188                 $spectra = decode_json $spectra;
 189                 $data_matrix{$stock_id}->{spectra} = $spectra;
 190                 $data_matrix{$stock_id}->{device_type} = $device_type;
 191             };
 192         }
 193
 194         $protocol_type_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'high_dimensional_phenotype_nirs_protocol', 'protocol_type')->cvterm_id();
 195     }
 196     elsif ($high_dimensional_phenotype_type eq 'Transcriptomics') {
 197         my $q = "SELECT stock.uniquename, stock.stock_id, metadata.md_json.json
 198             FROM stock
 199             JOIN nd_experiment_stock USING(stock_id)
 200             JOIN nd_experiment USING(nd_experiment_id)
 201             JOIN nd_experiment_protocol USING(nd_experiment_id)
 202             JOIN phenome.nd_experiment_md_json USING(nd_experiment_id)
 203             JOIN metadata.md_json USING(json_id)
 204             WHERE stock.stock_id IN ($stock_ids_sql) AND nd_experiment_protocol.nd_protocol_id = ? AND metadata.md_json.json_type = 'transcriptomics';";
 205         print STDERR Dumper $q;
 206         my $h = $dbh->prepare($q);
 207         $h->execute($nd_protocol_id);
 208         while (my ($stock_uniquename, $stock_id, $transcriptomics) = $h->fetchrow_array()) {
 209             eval {
 210                 $transcriptomics = decode_json $transcriptomics;
 211                 $data_matrix{$stock_id}->{transcriptomics} = $transcriptomics;
 212             };
 213         }
 214
 215         $protocol_type_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'high_dimensional_phenotype_transcriptomics_protocol', 'protocol_type')->cvterm_id();
 216     }
 217     elsif ($high_dimensional_phenotype_type eq 'Metabolomics') {
 218         my $q = "SELECT stock.uniquename, stock.stock_id, metadata.md_json.json
 219             FROM stock
 220             JOIN nd_experiment_stock USING(stock_id)
 221             JOIN nd_experiment USING(nd_experiment_id)
 222             JOIN nd_experiment_protocol USING(nd_experiment_id)
 223             JOIN phenome.nd_experiment_md_json USING(nd_experiment_id)
 224             JOIN metadata.md_json USING(json_id)
 225             WHERE stock.stock_id IN ($stock_ids_sql) AND nd_experiment_protocol.nd_protocol_id = ? AND metadata.md_json.json_type = 'metabolomics';";
 226         print STDERR Dumper $q;
 227         my $h = $dbh->prepare($q);
 228         $h->execute($nd_protocol_id);
 229         while (my ($stock_uniquename, $stock_id, $metabolomics) = $h->fetchrow_array()) {
 230             eval {
 231                 $metabolomics = decode_json $metabolomics;
 232                 $data_matrix{$stock_id}->{metabolomics} = $metabolomics;
 233             };
 234         }
 235
 236         $protocol_type_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'high_dimensional_phenotype_metabolomics_protocol', 'protocol_type')->cvterm_id();
 237     }
 238     else {
 239         die "NOT A VALID HIGHDIMENSIONAL PHENOTYPE TYPE $high_dimensional_phenotype_type\n";
 240     }
 241
 242     my $protocol = CXGN::Phenotypes::HighDimensionalPhenotypeProtocol->new({
 243         bcs_schema => $schema,
 244         nd_protocol_id => $nd_protocol_id,
 245         nd_protocol_type_id => $protocol_type_cvterm_id
 246     });
 247     my $identifier_metadata = $protocol->header_column_details;
 248     my $identifier_names = $protocol->header_column_names;
 249
 250     # print STDERR Dumper \%data_matrix;
 251     # print STDERR Dumper $identifier_metadata;
 252     # print STDERR Dumper $identifier_names;
 253     return (\%data_matrix, $identifier_metadata, $identifier_names);
 254 }
 255
 256 1;