lib/CXGN/BrAPI/v2/GenomeMaps.pm

   1 package CXGN::BrAPI::v2::GenomeMaps;
   2
   3 use Moose;
   4 use Data::Dumper;
   5 use SGN::Model::Cvterm;
   6 use JSON;
   7 use CXGN::Cview::MapFactory;
   8 use CXGN::BrAPI::Pagination;
   9 use CXGN::BrAPI::JSONResponse;
  10
  11 extends 'CXGN::BrAPI::v2::Common';
  12
  13 =head2 list
  14
  15  Usage:        $brapi->list()
  16  Desc:         lists all available maps.
  17  Ret:          returns a hash with all the map info
  18                for each map, the following keys are present:
  19                         mapDbId
  20                         name
  21                         species
  22                         type
  23                         unit
  24                         markerCount
  25                         comments
  26                         linkageGroupCount
  27                see brapi documentation for more information.
  28  Args:         usual brapi args (pageSize etc)
  29  Side Effects:
  30  Example:
  31
  32 =cut
  33
  34 sub list {
  35     my $self = shift;
  36     my $inputs = shift;
  37         my $page_size = $self->page_size;
  38         my $page = $self->page;
  39         my $status = $self->status;
  40
  41         my $crop_id = $inputs->{commonCropName} || ($inputs->{commonCropNames} || ());
  42     my $scientific_id = $inputs->{scientificName} || ($inputs->{scientificNames} || ());
  43     my $type_id = $inputs->{type} || ($inputs->{types} || ());
  44     my $map_id = $inputs->{mapDbId} || ($inputs->{mapDbIds} || ());
  45         # mapPUI
  46         # programDbId
  47         # trialDbId
  48         # studyDbId
  49         my @maps;
  50
  51         my $start = $page_size*$page;
  52         my $end = $page_size*($page+1)-1;
  53
  54         my $map_factory = CXGN::Cview::MapFactory->new($self->bcs_schema()->storage->dbh(), $inputs->{config});
  55
  56         if ( $map_id ) {
  57                 @maps = $map_factory->create( { map_id => $map_id->[0] });
  58         } else {
  59                 @maps = $map_factory->get_all_maps();
  60         }
  61
  62         my @data;
  63         my $passes_search;
  64
  65         my $query = "SELECT map_id, date_loaded, count(distinct(location_id)) FROM sgn.map_version JOIN marker_location using (map_version_id) WHERE map_version_id=? GROUP BY 1,2";
  66         my $sth = $self->bcs_schema->storage()->dbh()->prepare($query);
  67
  68         foreach my $m (@maps) {
  69         my $map_version_id = $m->get_id();
  70         if ($map_version_id =~ /\D/) { next; } # not a valid id
  71         $sth->execute($map_version_id);
  72         my ($map_id, $date_loaded, $marker_count) = $sth->fetchrow_array();
  73
  74         my $map_type = $m->get_type();
  75         my $map_units = $m->get_units();
  76         if ($map_type eq 'sequence'){
  77             $map_type = 'Physical';
  78             $map_units = 'Mb';
  79         } else {
  80             $map_type = 'Genetic';
  81             $map_units = 'cM';
  82         }
  83         my $scientific_name = $m->get_organism();
  84         my $common_name = $m->get_common_name();
  85
  86                 $passes_search = 1;
  87         if ( $crop_id && ! grep { $_ eq $common_name } @{$crop_id} ) { $passes_search = 0;};
  88         if ( $scientific_id && ! grep { $_ eq $scientific_name } @{$scientific_id} ) { $passes_search = 0;};
  89         if ( $type_id && ! grep { $_ eq $map_type } @{$type_id} ) { $passes_search = 0;};
  90
  91                 if ( $passes_search ){
  92                 my %map_info = (
  93                             additionalInfo => {name => $m->get_long_name()},
  94                                 comments => $m->get_abstract(),
  95                     commonCropName => $common_name,
  96                     documentationURL => "https://brapi.org",
  97                     linkageGroupCount => $m->get_chromosome_count(),
  98                     mapDbId =>  qq|$map_id|,
  99                     mapName => $m->get_short_name(),
 100                     mapPUI => undef,
 101                                 markerCount => $marker_count,
 102                     publishedDate => $date_loaded,
 103                     scientificName => $scientific_name,
 104                     type => $map_type,
 105                                 unit => $map_units,
 106                         );
 107                         push @data, \%map_info;
 108                 }
 109         }
 110
 111         my $total_count = scalar(@maps);
 112         my %result = (data => \@data);
 113         my @data_files;
 114         my $pagination = CXGN::BrAPI::Pagination->pagination_response($total_count,$page_size,$page);
 115
 116         return CXGN::BrAPI::JSONResponse->return_success(\%result, $pagination,
 117                                                          \@data_files, $status, 'Maps list result constructed');
 118 }
 119
 120
 121 =head2 detail
 122
 123  Usage:        $brapi->detail()
 124  Desc:         returns the detail information of a map in brapi format
 125  Ret:
 126  Args:
 127  Side Effects:
 128  Example:
 129
 130 =cut
 131
 132
 133 sub detail {
 134         my $self = shift;
 135         my $map_id = shift;
 136         my $page_size = $self->page_size;
 137         my $page = $self->page;
 138         my $status = $self->status;
 139         my %result;
 140
 141         my $map_factory = CXGN::Cview::MapFactory->new($self->bcs_schema->storage()->dbh());
 142         my $map = $map_factory->create( { map_id => $map_id });
 143
 144         if ($map){
 145             my $map_type = $map->get_type();
 146             my $map_units = $map->get_units();
 147             if ($map_type eq 'sequence'){
 148                 $map_type = 'Physical';
 149                 $map_units = 'Mb';
 150             } else {
 151                 $map_type = 'Genetic';
 152                 $map_units = 'cM';
 153             }
 154
 155                 my $scientific_name = $map->get_organism();
 156
 157             my $query = "SELECT map_id, date_loaded, count(distinct(location_id)) FROM sgn.map_version JOIN marker_location using (map_version_id) WHERE map_version_id=? GROUP BY 1,2";
 158                 my $sth = $self->bcs_schema->storage()->dbh()->prepare($query);
 159             my $map_version_id = $map->get_id();
 160                 if ($map_version_id =~ /\D/) { next; }
 161                 $sth->execute($map_version_id);
 162                 my ($map_id1, $date_loaded, $marker_count) = $sth->fetchrow_array();
 163
 164                 %result = (
 165                         additionalInfo => { name => $map->get_long_name() },
 166                         comments => $map->get_abstract(),
 167                 commonCropName => $map->get_common_name(),
 168                 documentationURL => "https://brapi.org",
 169                 linkageGroupCount => $map->get_chromosome_count(),
 170                 mapDbId =>  qq|$map_id|,
 171                 mapName => $map->get_short_name(),
 172                 mapPUI => undef,
 173                         markerCount => $marker_count,
 174                 publishedDate => $date_loaded,
 175                 scientificName => $scientific_name,
 176                 type => $map_type,
 177                         unit => $map_units,
 178                 );
 179         }
 180
 181         my @data_files;
 182         my $pagination = CXGN::BrAPI::Pagination->pagination_response(1,$page_size,$page);
 183
 184         return CXGN::BrAPI::JSONResponse->return_success(\%result, $pagination, \@data_files, $status, 'Maps detail result constructed');
 185 }
 186
 187
 188 sub linkagegroups {
 189         my $self = shift;
 190         my $inputs = shift;
 191         my $map_id = $inputs->{map_id};
 192         my $page_size = $self->page_size;
 193         my $page = $self->page;
 194         my $status = $self->status;
 195         my $total_count = 0;
 196         my @data = ();
 197
 198         my $map_factory = CXGN::Cview::MapFactory->new($self->bcs_schema->storage()->dbh());
 199         my $map = $map_factory->create( { map_id => $map_id });
 200
 201         if ($map){
 202                 foreach my $chr ($map->get_chromosomes()) {
 203                     push @data, {
 204                                 additionalInfo => {},
 205                                 linkageGroupName => $chr->get_name(),
 206                                 markerCount => scalar($chr->get_markers()),
 207                                 maxPosition => $chr->get_length()
 208                     };
 209                     $total_count++;
 210                 }
 211         }
 212
 213         my @data_files;
 214         my %result = (data => \@data);
 215         my $pagination = CXGN::BrAPI::Pagination->pagination_response($total_count,$page_size,$page);
 216
 217         return CXGN::BrAPI::JSONResponse->return_success(\%result, $pagination, \@data_files, $status, 'Maps detail result constructed');
 218 }
 219
 220 # =head2 genosort
 221
 222 #  Usage:        genosort($a_chr, $a_pos, $b_chr, $b_pos)
 223 #  Desc:         sorts marker coordinates according to position for marker names
 224 #                of the format S(\d+)_(.*)
 225 #  Ret:
 226 #  Args:
 227 #  Side Effects:
 228 #  Example:
 229
 230 # =cut
 231
 232 # sub genosort {
 233 #     my ($a_chr, $a_pos, $b_chr, $b_pos);
 234 #     if ($a =~ m/S(\d+)\_(.*)/) {
 235 #       $a_chr = $1;
 236 #       $a_pos = $2;
 237 #     }
 238 #     if ($b =~ m/S(\d+)\_(.*)/) {
 239 #       $b_chr = $1;
 240 #       $b_pos = $2;
 241 #     }
 242
 243 #     if ($a_chr && $b_chr) {
 244 #       if ($a_chr == $b_chr) {
 245 #           return $a_pos <=> $b_pos;
 246 #       }
 247 #       return $a_chr <=> $b_chr;
 248 #     } else {
 249 #       return -1;
 250 #     }
 251 # }
 252
 253 # sub get_protocolprop_hash {
 254 #       my $self = shift;
 255 #       my $nd_protocol_id = shift;
 256 #       my $prop_rs = $self->bcs_schema->resultset('NaturalDiversity::NdProtocolprop')->search({'me.nd_protocol_id' => $nd_protocol_id}, {join=>['type'], +select=>['type.name', 'me.value'], +as=>['name', 'value']});
 257 #       my $prop_hash;
 258 #       while (my $r = $prop_rs->next()){
 259 #               push @{ $prop_hash->{$r->get_column('name')} }, $r->get_column('value');
 260 #       }
 261
 262 #       return $prop_hash;
 263 # }
 264
 265 1;