lib/CXGN/BrAPI/v1/Germplasm.pm

   1 package CXGN::BrAPI::v1::Germplasm;
   2
   3 use Moose;
   4 use Data::Dumper;
   5 use SGN::Model::Cvterm;
   6 use CXGN::Trial;
   7 use CXGN::Chado::Stock;
   8 use CXGN::BrAPI::Pagination;
   9 use CXGN::BrAPI::ErrorResponse;
  10
  11 has 'bcs_schema' => (
  12         isa => 'Bio::Chado::Schema',
  13         is => 'rw',
  14         required => 1,
  15 );
  16
  17 has 'metadata_schema' => (
  18         isa => 'CXGN::Metadata::Schema',
  19         is => 'rw',
  20         required => 1,
  21 );
  22
  23 has 'phenome_schema' => (
  24         isa => 'CXGN::Phenome::Schema',
  25         is => 'rw',
  26         required => 1,
  27 );
  28
  29 has 'page_size' => (
  30         isa => 'Int',
  31         is => 'rw',
  32         required => 1,
  33 );
  34
  35 has 'page' => (
  36         isa => 'Int',
  37         is => 'rw',
  38         required => 1,
  39 );
  40
  41 has 'status' => (
  42         isa => 'ArrayRef[Maybe[HashRef]]',
  43         is => 'rw',
  44         required => 1,
  45 );
  46
  47 sub germplasm_search {
  48         my $self = shift;
  49         my $search_params = shift;
  50
  51         my $page_size = $self->page_size;
  52         my $page = $self->page;
  53         my $status = $self->status;
  54
  55         my @germplasm_names = $search_params->{germplasmName} ? @{$search_params->{germplasmName}} : ();
  56         my @accession_numbers = $search_params->{accessionNumber} ? @{$search_params->{accessionNumber}} : ();
  57         my @genus = $search_params->{germplasmGenus} ? @{$search_params->{germplasmGenus}} : ();
  58         my $subtaxa = $search_params->{germplasmSubTaxa}->[0];
  59         my @species = $search_params->{germplasmSpecies} ? @{$search_params->{germplasmSpecies}} : ();
  60         my @germplasm_ids = $search_params->{germplasmDbId} ? @{$search_params->{germplasmDbId}} : ();
  61         my @germplasm_puis = $search_params->{germplasmPUI} ? @{$search_params->{germplasmPUI}} : ();
  62         my $match_method = $search_params->{matchMethod}->[0];
  63         my %result;
  64
  65         if ($match_method && ($match_method ne 'exact' && $match_method ne 'wildcard')) {
  66                 push @$status, { 'error' => "matchMethod '$match_method' not recognized. Allowed matchMethods: wildcard, exact. Wildcard allows % or * for multiple characters and ? for single characters." };
  67         }
  68         my $total_count = 0;
  69
  70         my $accession_type_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($self->bcs_schema, 'accession', 'stock_type')->cvterm_id();
  71         my %search_params;
  72         my @join_params;
  73
  74         $search_params{'me.type_id'} = $accession_type_cvterm_id;
  75
  76         if (@germplasm_names && scalar(@germplasm_names)>0){
  77                 if (!$match_method || $match_method eq 'exact') {
  78                         $search_params{'me.uniquename'} = \@germplasm_names;
  79                 } elsif ($match_method eq 'wildcard') {
  80                         my @wildcard_names;
  81                         foreach (@germplasm_names) {
  82                                 $_ =~ tr/*?/%_/;
  83                                 push @wildcard_names, $_;
  84                         }
  85                         $search_params{'me.uniquename'} = { 'ilike' => \@wildcard_names };
  86                 }
  87         }
  88
  89         if (@germplasm_ids && scalar(@germplasm_ids)>0){
  90                 if (!$match_method || $match_method eq 'exact') {
  91                         $search_params{'me.stock_id'} = \@germplasm_ids;
  92                 } elsif ($match_method eq 'wildcard') {
  93                         my @wildcard_ids;
  94                         foreach (@germplasm_ids) {
  95                                 $_ =~ tr/*?/%_/;
  96                                 push @wildcard_ids, $_;
  97                         }
  98                         $search_params{'me.stock_id::varchar(255)'} = { 'ilike' => \@wildcard_ids };
  99                 }
 100         }
 101
 102         #print STDERR Dumper \%search_params;
 103         #$self->bcs_schema->storage->debug(1);
 104         my $accession_number_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($self->bcs_schema(), 'accession number', 'stock_property')->cvterm_id();
 105         if (@accession_numbers && scalar(@accession_numbers)>0) {
 106                 $search_params{'stockprops.type_id'} = $accession_number_cvterm_id;
 107                 $search_params{'stockprops.value'} = \@accession_numbers;
 108                 push @join_params, 'stockprops';
 109         }
 110         my $accession_pui_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($self->bcs_schema(), 'PUI', 'stock_property')->cvterm_id();
 111         if (@germplasm_puis && scalar(@germplasm_puis)>0) {
 112                 $search_params{'stockprops.type_id'} = $accession_pui_cvterm_id;
 113                 $search_params{'stockprops.value'} = \@germplasm_puis;
 114                 push @join_params, 'stockprops';
 115         }
 116         if (@genus && scalar(@genus)>0) {
 117                 $search_params{'organism.genus'} = \@genus;
 118         }
 119         if (@species && scalar(@species)>0) {
 120                 $search_params{'organism.species'} = \@species;
 121         }
 122
 123         push @join_params, 'organism';
 124         my $rs = $self->bcs_schema()->resultset("Stock::Stock")->search( \%search_params, {join=>\@join_params, '+select'=>['organism.genus', 'organism.species', 'organism.common_name'], '+as'=>['genus','species','common_name'], order_by=>'me.uniquename'} );
 125
 126         my @data;
 127         if ($rs) {
 128                 $total_count = $rs->count();
 129                 my $rs_slice = $rs->slice($page_size*$page, $page_size*($page+1)-1);
 130                 while (my $stock = $rs_slice->next()) {
 131                         my $stockprop_hash = CXGN::Chado::Stock->new($self->bcs_schema, $stock->stock_id)->get_stockprop_hash();
 132                         my @donor_array;
 133                         my $donor_accessions = $stockprop_hash->{'donor'} ? $stockprop_hash->{'donor'} : [];
 134                         my $donor_institutes = $stockprop_hash->{'donor institute'} ? $stockprop_hash->{'donor institute'} : [];
 135                         my $donor_puis = $stockprop_hash->{'donor PUI'} ? $stockprop_hash->{'donor PUI'} : [];
 136                         for (0 .. scalar(@$donor_accessions)){
 137                                 push @donor_array, { 'donorGermplasmName'=>$donor_accessions->[$_], 'donorAccessionNumber'=>$donor_accessions->[$_], 'donorInstituteCode'=>$donor_institutes->[$_], 'germplasmPUI'=>$donor_puis->[$_] };
 138                         }
 139                         push @data, {
 140                                 germplasmDbId=>$stock->stock_id,
 141                                 defaultDisplayName=>$stock->uniquename,
 142                                 germplasmName=>$stock->uniquename,
 143                                 accessionNumber=>$stockprop_hash->{'accession number'} ? join ',', @{$stockprop_hash->{'accession number'}} : '',
 144                                 germplasmPUI=>$stockprop_hash->{'PUI'} ? join ',', @{$stockprop_hash->{'PUI'}} : '',
 145                                 pedigree=>$self->germplasm_pedigree_string($stock->stock_id),
 146                                 germplasmSeedSource=>$stockprop_hash->{'seed source'} ? join ',', @{$stockprop_hash->{'seed source'}} : '',
 147                                 synonyms=> $stockprop_hash->{'stock_synonym'} ? join ',', @{$stockprop_hash->{'stock_synonym'}} : '',
 148                                 commonCropName=>$stock->get_column('common_name'),
 149                                 instituteCode=>$stockprop_hash->{'institute code'} ? join ',', @{$stockprop_hash->{'institute code'}} : '',
 150                                 instituteName=>$stockprop_hash->{'institute name'} ? join ',', @{$stockprop_hash->{'institute name'}} : '',
 151                                 biologicalStatusOfAccessionCode=>$stockprop_hash->{'biological status of accession code'} ? join ',', @{$stockprop_hash->{'biological status of accession code'}} : '',
 152                                 countryOfOriginCode=>$stockprop_hash->{'country of origin'} ? join ',', @{$stockprop_hash->{'country of origin'}} : '',
 153                                 typeOfGermplasmStorageCode=>$stockprop_hash->{'type of germplasm storage code'} ? join ',', @{$stockprop_hash->{'type of germplasm storage code'}} : '',
 154                                 genus=>$stock->get_column('genus'),
 155                                 species=>$stock->get_column('species'),
 156                                 speciesAuthority=>'',
 157                                 subtaxa=>'',
 158                                 subtaxaAuthority=>'',
 159                                 donors=>\@donor_array,
 160                                 acquisitionDate=>'',
 161                         };
 162                 }
 163         }
 164
 165         %result = (data => \@data);
 166         push @$status, { 'success' => 'Germplasm-search result constructed' };
 167         my $pagination = CXGN::BrAPI::Pagination->pagination_response($total_count,$page_size,$page);
 168         my $response = {
 169                 'status' => $status,
 170                 'pagination' => $pagination,
 171                 'result' => \%result,
 172                 'datafiles' => []
 173         };
 174         return $response;
 175 }
 176
 177 sub germplasm_pedigree_string {
 178         my $self = shift;
 179         my $stock_id = shift;
 180         my $s = CXGN::Chado::Stock->new($self->bcs_schema, $stock_id);
 181         my $pedigree_root = $s->get_parents('1');
 182         my $pedigree_string = $pedigree_root ? $pedigree_root->get_pedigree_string('1') : '';
 183         return $pedigree_string;
 184 }
 185
 186 sub germplasm_detail {
 187         my $self = shift;
 188         my $stock_id = shift;
 189         my $status = $self->status;
 190         my %result;
 191
 192         my $verify_id = $self->bcs_schema->resultset('Stock::Stock')->find({stock_id=>$stock_id});
 193         my $stock = CXGN::Chado::Stock->new($self->bcs_schema(), $stock_id);
 194
 195         my $total_count = 0;
 196         if ($verify_id) {
 197                 $total_count = 1;
 198         } else {
 199                 push @$status, { 'error' => 'GermplasmDbId does not exist in the database' };
 200                 return CXGN::BrAPI::ErrorResponse->return_error($status);
 201         }
 202         my $stockprop_hash = $stock->get_stockprop_hash();
 203
 204         my @donor_array;
 205         my $donor_accessions = $stockprop_hash->{'donor'} ? $stockprop_hash->{'donor'} : [];
 206         my $donor_institutes = $stockprop_hash->{'donor institute'} ? $stockprop_hash->{'donor institute'} : [];
 207         my $donor_puis = $stockprop_hash->{'donor PUI'} ? $stockprop_hash->{'donor PUI'} : [];
 208         for (0 .. scalar(@$donor_accessions)){
 209                 push @donor_array, { 'donorGermplasmName'=>$donor_accessions->[$_], 'donorAccessionNumber'=>$donor_accessions->[$_], 'donorInstituteCode'=>$donor_institutes->[$_], 'germplasmPUI'=>$donor_puis->[$_] };
 210         }
 211
 212         %result = (
 213                 germplasmDbId=>$stock_id,
 214                 defaultDisplayName=>$stock->get_name(),
 215                 germplasmName=>$stock->get_uniquename(),
 216                 accessionNumber=>$stock->get_uniquename(),
 217                 germplasmPUI=>$stock->get_uniquename(),
 218                 pedigree=>$self->germplasm_pedigree_string($stock_id),
 219                 germplasmSeedSource=>$stockprop_hash->{'seed source'} ? join ',', @{$stockprop_hash->{'seed source'}} : '',
 220                 synonyms=>$stockprop_hash->{'stock_synonym'} ? join ',', @{$stockprop_hash->{'stock_synonym'}} : '',
 221                 commonCropName=>$stock->get_organism->common_name(),
 222                 instituteCode=>$stockprop_hash->{'institute code'} ? join ',', @{$stockprop_hash->{'institute code'}} : '',
 223                 instituteName=>$stockprop_hash->{'institute name'} ? join ',', @{$stockprop_hash->{'institute name'}} : '',
 224                 biologicalStatusOfAccessionCode=>$stockprop_hash->{'biological status of accession code'} ? join ',', @{$stockprop_hash->{'biological status of accession code'}} : '',
 225                 countryOfOriginCode=>$stockprop_hash->{'country of origin'} ? join ',', @{$stockprop_hash->{'country of origin'}} : '',
 226                 typeOfGermplasmStorageCode=>$stockprop_hash->{'type of germplasm storage code'} ? join ',', @{$stockprop_hash->{'type of germplasm storage code'}} : '',
 227                 genus=>$stock->get_organism->genus(),
 228                 species=>$stock->get_organism->species(),
 229                 speciesAuthority=>'',
 230                 subtaxa=>'',
 231                 subtaxaAuthority=>'',
 232                 donors=>\@donor_array,
 233                 acquisitionDate=>'',
 234         );
 235         push @$status, { 'success' => 'Germplasm-search result constructed' };
 236         my $pagination = CXGN::BrAPI::Pagination->pagination_response($total_count,1,0);
 237         my $response = {
 238                 'status' => $status,
 239                 'pagination' => $pagination,
 240                 'result' => \%result,
 241                 'datafiles' => []
 242         };
 243         return $response;
 244 }
 245
 246 sub germplasm_pedigree {
 247         my $self = shift;
 248         my $inputs = shift;
 249         my $stock_id = $inputs->{stock_id};
 250         my $notation = $inputs->{notation};
 251         my $status = $self->status;
 252         if ($notation) {
 253                 push @$status, { 'info' => 'Notation not yet implemented. Returns a simple parent1/parent2 string.' };
 254                 if ($notation ne 'purdy') {
 255                         push @$status, { 'error' => 'Unsupported notation code. Allowed notation: purdy' };
 256                 }
 257         }
 258
 259         my %result;
 260         my $total_count = 0;
 261         my $s = CXGN::Chado::Stock->new($self->bcs_schema(), $stock_id);
 262         if ($s) {
 263                 $total_count = 1;
 264                 my @direct_parents = $s->get_direct_parents();
 265                 %result = (
 266                         germplasmDbId=>$stock_id,
 267                         pedigree=>$self->germplasm_pedigree_string($stock_id),
 268                         parent1Id=>$direct_parents[0][0],
 269                         parent2Id=>$direct_parents[1][0]
 270                 );
 271         }
 272
 273         push @$status, { 'success' => 'Germplasm-pedigree result constructed' };
 274         my $pagination = CXGN::BrAPI::Pagination->pagination_response($total_count,1,0);
 275         my $response = {
 276                 'status' => $status,
 277                 'pagination' => $pagination,
 278                 'result' => \%result,
 279                 'datafiles' => []
 280         };
 281         return $response;
 282 }
 283
 284 sub germplasm_markerprofiles {
 285         my $self = shift;
 286         my $stock_id = shift;
 287
 288         my $page_size = $self->page_size;
 289         my $page = $self->page;
 290         my $status = $self->status;
 291         my @marker_profiles;
 292
 293         my $snp_genotyping_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($self->bcs_schema, 'snp genotyping', 'genotype_property')->cvterm_id();
 294
 295         my $rs = $self->bcs_schema->resultset('NaturalDiversity::NdExperiment')->search(
 296                 {'genotypeprops.type_id' => $snp_genotyping_cvterm_id, 'stock.stock_id'=>$stock_id},
 297                 {join=> [{'nd_experiment_genotypes' => {'genotype' => 'genotypeprops'} }, {'nd_experiment_protocols' => 'nd_protocol' }, {'nd_experiment_stocks' => 'stock'} ],
 298                 select=> ['genotypeprops.genotypeprop_id'],
 299                 as=> ['genotypeprop_id'],
 300                 order_by=>{ -asc=>'genotypeprops.genotypeprop_id' }
 301                 }
 302         );
 303
 304         my $rs_slice = $rs->slice($page_size*$page, $page_size*($page+1)-1);
 305         while (my $gt = $rs_slice->next()) {
 306                 push @marker_profiles, $gt->get_column('genotypeprop_id');
 307         }
 308         my $total_count = scalar(@marker_profiles);
 309         my %result = (
 310                 germplasmDbId=>$stock_id,
 311                 markerProfiles=>\@marker_profiles
 312         );
 313         push @$status, { 'success' => 'Germplasm-markerprofiles result constructed' };
 314         my $pagination = CXGN::BrAPI::Pagination->pagination_response($total_count,$page_size,$page);
 315         my $response = {
 316                 'status' => $status,
 317                 'pagination' => $pagination,
 318                 'result' => \%result,
 319                 'datafiles' => []
 320         };
 321         return $response;
 322 }
 323
 324
 325 1;