lib/CXGN/BrAPI/v1/GenomeMaps.pm

   1 package CXGN::BrAPI::v1::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::v1::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 $start = $page_size*$page;
  42         my $end = $page_size*($page+1)-1;
  43
  44         my $map_factory = CXGN::Cview::MapFactory->new($self->bcs_schema()->storage->dbh(), $inputs->{config});
  45
  46         my @maps = $map_factory->get_all_maps();
  47         my @data;
  48
  49   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";
  50         my $sth = $self->bcs_schema->storage()->dbh()->prepare($query);
  51
  52         foreach my $m (@maps) {
  53         my $map_version_id = $m->get_id();
  54         if ($map_version_id =~ /\D/) { next; } # not a valid id
  55         $sth->execute($map_version_id);
  56         my ($map_id, $date_loaded, $marker_count) = $sth->fetchrow_array();
  57         my $map_type = $m->get_type();
  58         my $map_units = $m->get_units();
  59         if ($map_type eq 'sequence'){
  60             $map_type = 'Physical';
  61             $map_units = 'Mb';
  62         } else {
  63             $map_type = 'Genetic';
  64             $map_units = 'cM';
  65         }
  66         my $scientific_name = $m->get_organism();
  67         my ($genus,$species) = undef;
  68         if ($scientific_name) { ($genus,$species) = split(" ", $scientific_name) };
  69         my %map_info = (
  70                     mapDbId =>  qq|$map_id|,
  71                         name => $m->get_long_name(),
  72                         species => $species,
  73                         type => $map_type,
  74                         unit => $map_units,
  75                         markerCount => $marker_count,
  76                         comments => $m->get_abstract(),
  77                         linkageGroupCount => $m->get_chromosome_count(),
  78             commonCropName => $m->get_common_name(),
  79             documentationURL => "https://brapi.org",
  80             mapName => $m->get_short_name(),
  81             publishedDate => $date_loaded,
  82             scientificName => $scientific_name,
  83                 );
  84
  85                 push @data, \%map_info;
  86         }
  87
  88         my $total_count = scalar(@maps);
  89         my %result = (data => \@data);
  90         my @data_files;
  91         my $pagination = CXGN::BrAPI::Pagination->pagination_response($total_count,$page_size,$page);
  92
  93         return CXGN::BrAPI::JSONResponse->return_success(\%result, $pagination,
  94                                                          \@data_files, $status, 'Maps list result constructed');
  95 }
  96
  97
  98 =head2 detail
  99
 100  Usage:        $brapi->detail()
 101  Desc:         returns the detail information of a map in brapi format
 102  Ret:
 103  Args:
 104  Side Effects:
 105  Example:
 106
 107 =cut
 108
 109 sub detail {
 110         my $self = shift;
 111         my $map_id = shift;
 112         my $page_size = $self->page_size;
 113         my $page = $self->page;
 114         my $status = $self->status;
 115
 116         my $map_factory = CXGN::Cview::MapFactory->new($self->bcs_schema->storage()->dbh());
 117
 118         my $map = $map_factory->create( { map_id => $map_id });
 119     my $map_type = $map->get_type();
 120     my $map_units = $map->get_units();
 121     if ($map_type eq 'sequence'){
 122         $map_type = 'Physical';
 123         $map_units = 'Mb';
 124     } else {
 125         $map_type = 'Genetic';
 126         $map_units = 'cM';
 127     }
 128
 129         my @data = ();
 130
 131         foreach my $chr ($map->get_chromosomes()) {
 132             push @data, {
 133             linkageGroupName => $chr->get_name(),
 134                           markerCount => scalar($chr->get_markers()),
 135                           maxPosition => $chr->get_length()
 136             };
 137         }
 138             my ($data_window, $pagination) = CXGN::BrAPI::Pagination->paginate_array(\@data,$page_size,$page);
 139
 140         my %result = (
 141                 mapDbId =>  qq|$map_id|,
 142                 mapName => $map->get_short_name(),
 143                 type => $map_type,
 144                 unit => $map_units,
 145         comments => $map->get_abstract(),
 146         documentationURL => "https://brapi.org",
 147                 data => $data_window,
 148         );
 149
 150         my @data_files;
 151         return CXGN::BrAPI::JSONResponse->return_success(\%result, $pagination, \@data_files, $status, 'Maps detail result constructed');
 152 }
 153
 154 =head2 positions
 155
 156  Usage:        $brapi->positions()
 157  Desc:         returns all the positions and marker scores for a given
 158                map and chromosome
 159  Ret:
 160  Args:
 161  Side Effects:
 162  Example:
 163
 164 =cut
 165
 166 sub positions {
 167         my $self = shift;
 168         my $inputs = shift;
 169         my $map_id = $inputs->{map_id};
 170         my $min = $inputs->{min};
 171         my $max = $inputs->{max};
 172         my @linkage_group_ids = $inputs->{linkage_group_ids} ? @{$inputs->{linkage_group_ids}} : ();
 173         my $page_size = $self->page_size;
 174         my $page = $self->page;
 175         my $status = $self->status;
 176
 177         my $map_factory = CXGN::Cview::MapFactory->new($self->bcs_schema->storage()->dbh());
 178
 179         my $map = $map_factory->create( { map_id => $map_id });
 180
 181         my @data = ();
 182
 183         foreach my $chr ($map->get_chromosomes()) {
 184             foreach my $m ($chr->get_markers()) {
 185                 if (@linkage_group_ids) {
 186                     if (grep $_ eq $chr->get_name(), @linkage_group_ids) {
 187                         push @data, {
 188                             markerDbId => $m->get_id(),
 189                             markerName => $m->get_name(),
 190                             location => $m->get_offset(),
 191                             linkageGroupName => $chr->get_name(),
 192                         };
 193                     }
 194                 }
 195                 else {
 196                     push @data, {
 197                             markerDbId => $m->get_id(),
 198                             markerName => $m->get_name(),
 199                             location => $m->get_offset(),
 200                             linkageGroupName => $chr->get_name()
 201                     }
 202                 }
 203             }
 204         }
 205     my $marker_count = scalar(@data);
 206         my ($data_window, $pagination) = CXGN::BrAPI::Pagination->paginate_array(\@data,$marker_count,$page); #set page size to total number of markers
 207
 208         my %result = ( data => $data_window );
 209         my @data_files;
 210         return CXGN::BrAPI::JSONResponse->return_success(\%result, $pagination, \@data_files, $status, 'Maps detail result constructed');
 211 }
 212
 213 =head2 genosort
 214
 215  Usage:        genosort($a_chr, $a_pos, $b_chr, $b_pos)
 216  Desc:         sorts marker coordinates according to position for marker names
 217                of the format S(\d+)_(.*)
 218  Ret:
 219  Args:
 220  Side Effects:
 221  Example:
 222
 223 =cut
 224
 225 sub genosort {
 226     my ($a_chr, $a_pos, $b_chr, $b_pos);
 227     if ($a =~ m/S(\d+)\_(.*)/) {
 228         $a_chr = $1;
 229         $a_pos = $2;
 230     }
 231     if ($b =~ m/S(\d+)\_(.*)/) {
 232         $b_chr = $1;
 233         $b_pos = $2;
 234     }
 235
 236     if ($a_chr && $b_chr) {
 237       if ($a_chr == $b_chr) {
 238           return $a_pos <=> $b_pos;
 239       }
 240       return $a_chr <=> $b_chr;
 241     } else {
 242       return -1;
 243     }
 244 }
 245
 246 sub get_protocolprop_hash {
 247         my $self = shift;
 248         my $nd_protocol_id = shift;
 249         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']});
 250         my $prop_hash;
 251         while (my $r = $prop_rs->next()){
 252                 push @{ $prop_hash->{$r->get_column('name')} }, $r->get_column('value');
 253         }
 254
 255         return $prop_hash;
 256 }
 257
 258 1;