lib/CXGN/Stock/TissueSample/Search.pm

   1 package CXGN::Stock::TissueSample::Search;
   2
   3 =head1 NAME
   4 CXGN::Stock::TissueSample::Search - an object to handle searching for tissue samples
   5 =head1 USAGE
   6 my $sample_search = CXGN::Stock::TissueSample::Search->new({
   7     bcs_schema=>$schema,
   8     tissue_sample_db_id_list => \@tissue_ids,
   9     tissue_sample_name_list => \@tissue_names,
  10     plate_db_id_list => \@geno_trial_ids,
  11     plate_name_list => \@geno_trial_names,
  12     germplasm_db_id_list => \@accession_ids,
  13     germplasm_name_list => \@accession_names,
  14     observation_unit_db_id_list => \@plot_ids,
  15     observation_unit_name_list => \@plot_names,
  16     order_by => '',
  17     limit => 10,
  18     offset => 0
  19 });
  20 my $result = $sample_search->search();
  21
  22 Modeled after brapi samples search call.
  23 observation_unit_db_id_list is for a list of source plot_ids, plant_ids, or tissue_sample_ids
  24 plate_db_id_list is for a list of genotyping_trial_ids
  25 germplasm_db_id_list is for a list of accession_ids
  26
  27 =head1 DESCRIPTION
  28 =head1 AUTHORS
  29
  30 =cut
  31
  32 use strict;
  33 use warnings;
  34 use Moose;
  35 use Try::Tiny;
  36 use Data::Dumper;
  37 use SGN::Model::Cvterm;
  38 use CXGN::Stock::TissueSample;
  39
  40 has 'bcs_schema' => (
  41     isa => 'Bio::Chado::Schema',
  42     is => 'rw',
  43     required => 1,
  44 );
  45
  46 has 'tissue_sample_db_id_list' => (
  47     isa => 'ArrayRef[Int]|Undef',
  48     is => 'rw'
  49 );
  50
  51 has 'tissue_sample_name_list' => (
  52     isa => 'ArrayRef[Str]|Undef',
  53     is => 'rw'
  54 );
  55
  56 has 'plate_db_id_list' => (
  57     isa => 'ArrayRef[Int]|Undef',
  58     is => 'rw'
  59 );
  60
  61 has 'plate_name_list' => (
  62     isa => 'ArrayRef[Str]|Undef',
  63     is => 'rw'
  64 );
  65
  66 has 'germplasm_db_id_list' => (
  67     isa => 'ArrayRef[Int]|Undef',
  68     is => 'rw'
  69 );
  70
  71 has 'germplasm_name_list' => (
  72     isa => 'ArrayRef[Str]|Undef',
  73     is => 'rw'
  74 );
  75
  76 has 'observation_unit_db_id_list' => (
  77     isa => 'ArrayRef[Int]|Undef',
  78     is => 'rw'
  79 );
  80
  81 has 'observation_unit_name_list' => (
  82     isa => 'ArrayRef[Str]|Undef',
  83     is => 'rw'
  84 );
  85
  86 has 'order_by' => (
  87     isa => 'Str|Undef',
  88     is => 'rw'
  89 );
  90
  91 has 'limit' => (
  92     isa => 'Int|Undef',
  93     is => 'rw',
  94 );
  95
  96 has 'offset' => (
  97     isa => 'Int|Undef',
  98     is => 'rw',
  99 );
 100
 101 sub search {
 102     my $self = shift;
 103     my $schema = $self->bcs_schema();
 104
 105     my $accession_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'accession', 'stock_type')->cvterm_id();
 106     my $plant_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'plant', 'stock_type')->cvterm_id();
 107     my $plot_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'plot', 'stock_type')->cvterm_id();
 108     my $tissue_sample_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'tissue_sample', 'stock_type')->cvterm_id();
 109     my $tissue_relationship_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'tissue_sample_of', 'stock_relationship')->cvterm_id();
 110     my $genotyping_experiment_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'genotyping_layout', 'experiment_type')->cvterm_id();
 111
 112     my %and_conditions;
 113     $and_conditions{'me.type_id'} = $tissue_sample_cvterm_id;
 114
 115     my $order_by = $self->order_by || 'me.uniquename';
 116
 117     my %join_clause = ('stock_relationship_subjects' => 'object');
 118     $and_conditions{'stock_relationship_subjects.type_id'} = $tissue_relationship_cvterm_id;
 119
 120     if ($self->tissue_sample_db_id_list() && scalar(@{$self->tissue_sample_db_id_list}) > 0){
 121         $and_conditions{'me.stock_id'} = {'-in' => $self->tissue_sample_db_id_list};
 122     }
 123     if ($self->tissue_sample_name_list() && scalar(@{$self->tissue_sample_name_list}) > 0){
 124         foreach (@{$self->tissue_sample_name_list}){
 125             push @{$and_conditions{'me.uniquename'}}, {'ilike' => '%'.$_.'%'};
 126         }
 127     }
 128
 129     if (($self->plate_db_id_list() && scalar(@{$self->plate_db_id_list}) > 0) || ($self->plate_name_list() && scalar(@{$self->plate_name_list}) > 0)){
 130         $join_clause{nd_experiment_stocks} = {nd_experiment => {nd_experiment_projects => 'project'} };
 131         $and_conditions{'nd_experiment.type_id'} = $genotyping_experiment_cvterm_id;
 132
 133         if ($self->plate_db_id_list() && scalar(@{$self->plate_db_id_list}) > 0){
 134             $and_conditions{'project.project_id'} = {'-in' => $self->plate_db_id_list};
 135         }
 136         if ($self->plate_name_list() && scalar(@{$self->plate_name_list}) > 0){
 137             $and_conditions{'project.name'} = {'-in' => $self->plate_name_list};
 138         }
 139     }
 140
 141     if (($self->germplasm_db_id_list() && scalar(@{$self->germplasm_db_id_list}) > 0) || ($self->germplasm_name_list() && scalar(@{$self->germplasm_name_list}) > 0)){
 142         $and_conditions{'object.type_id'} = $accession_cvterm_id;
 143
 144         if ($self->germplasm_db_id_list() && scalar(@{$self->germplasm_db_id_list}) > 0){
 145             $and_conditions{'object.stock_id'} = {'-in' => $self->germplasm_db_id_list};
 146         }
 147         if ($self->germplasm_name_list() && scalar(@{$self->germplasm_name_list}) > 0){
 148             foreach (@{$self->germplasm_name_list}){
 149                 push @{$and_conditions{'object.uniquename'}}, {'ilike' => '%'.$_.'%'};
 150             }
 151         }
 152     }
 153
 154     if (($self->observation_unit_db_id_list() && scalar(@{$self->observation_unit_db_id_list}) > 0) || ($self->observation_unit_name_list() && scalar(@{$self->observation_unit_name_list}) > 0)){
 155         $and_conditions{'object.type_id'} = [$plot_cvterm_id, $plant_cvterm_id, $tissue_sample_cvterm_id];
 156
 157         if ($self->observation_unit_db_id_list() && scalar(@{$self->observation_unit_db_id_list}) > 0){
 158             $and_conditions{'object.stock_id'} = {'-in' => $self->observation_unit_db_id_list};
 159         }
 160         if ($self->observation_unit_name_list() && scalar(@{$self->observation_unit_name_list}) > 0){
 161             foreach (@{$self->observation_unit_name_list}){
 162                 push @{$and_conditions{'object.uniquename'}}, {'ilike' => '%'.$_.'%'};
 163             }
 164         }
 165     }
 166
 167     #$schema->storage->debug(1);
 168     my $sample_rs = $schema->resultset("Stock::Stock")->search(
 169         \%and_conditions,
 170         {
 171             join => \%join_clause,
 172             order_by => { '-asc' => $order_by },
 173             distinct => 1
 174         }
 175     );
 176
 177     my @result;
 178
 179     my $limit = $self->limit;
 180     my $offset = $self->offset;
 181     my $records_total = $sample_rs->count();
 182     if (defined($limit) && defined($offset)){
 183         $sample_rs = $sample_rs->slice($offset, $limit);
 184     }
 185
 186     while ( my $t = $sample_rs->next() ) {
 187         my $s = CXGN::Stock::TissueSample->new(schema=>$self->bcs_schema, tissue_sample_id=>$t->stock_id);
 188         my $accession_id = $s->get_accession ? $s->get_accession->[0] : undef;
 189         my $accession_name = $s->get_accession ? $s->get_accession->[1] : undef;
 190         my $source_plot_id = $s->get_source_plot ? $s->get_source_plot->[0] : undef;
 191         my $source_plot_name = $s->get_source_plot ? $s->get_source_plot->[1] : undef;
 192         my $source_plant_id = $s->get_source_plant ? $s->get_source_plant->[0] : undef;
 193         my $source_plant_name = $s->get_source_plant ? $s->get_source_plant->[1] : undef;
 194         my $source_sample_id = $s->get_source_tissue_sample ? $s->get_source_tissue_sample->[0] : undef;
 195         my $source_sample_name = $s->get_source_tissue_sample ? $s->get_source_tissue_sample->[1] : undef;
 196         my $source_obs_id = $s->source_observation_unit ? $s->source_observation_unit->[0] : undef;
 197         my $source_obs_name = $s->source_observation_unit ? $s->source_observation_unit->[1] : undef;
 198         my $source_obs_type = $s->source_observation_unit ? $s->source_observation_unit->[2] : undef;
 199         my $plate_id = $s->get_plate ? $s->get_plate->[0] : undef;
 200         my $plate_name = $s->get_plate ? $s->get_plate->[1] : undef;
 201         my $trial_id = $s->get_trial ? $s->get_trial->[0] : undef;
 202         my $trial_name = $s->get_trial ? $s->get_trial->[1] : undef;
 203
 204         push @result, {
 205             sampleDbId => $t->stock_id,
 206             sampleName => $t->uniquename,
 207             observationUnitDbId => $source_obs_id,
 208             observationUnitName => $source_obs_name,
 209             observationUnitType => $source_obs_type,
 210             germplasmDbId => $accession_id,
 211             germplasmName => $accession_name,
 212             studyDbId => $trial_id,
 213             studyName => $trial_name,
 214             plotDbId => $source_plot_id,
 215             plotName => $source_plot_name,
 216             plantDbId => $source_plant_id,
 217             plantName => $source_plant_name,
 218             sourceSampleDbId => $source_sample_id,
 219             sourceSampleName => $source_sample_name,
 220             plateDbId => $plate_id,
 221             plateName => $plate_name,
 222             plateIndex => 0,
 223             dna_person => $s->dna_person,
 224             acquisition_date => $s->acquisition_date,
 225             tissue_type => $s->tissue_type,
 226             extraction => $s->extraction,
 227             notes => $s->notes,
 228             well => $s->well,
 229             concentration => $s->concentration,
 230             volume => $s->volume,
 231             is_blank => $s->is_blank
 232         };
 233     }
 234     #print STDERR Dumper \@result;
 235
 236     return (\@result, $records_total);
 237 }
 238
 239 1;