lib/CXGN/Insitu/Organism.pm

   1
   2 use strict;
   3 use CXGN::Insitu::Experiment;
   4
   5
   6 package CXGN::Insitu::Organism;
   7
   8 use base qw / CXGN::Insitu::DB /;
   9
  10 =head2 new
  11
  12  Usage:
  13  Desc:
  14  Ret:
  15  Args:
  16  Side Effects:
  17  Example:
  18
  19 =cut
  20
  21 sub new {
  22     my $class = shift;
  23     my $dbh = shift;
  24     my $id = shift;
  25     my $self  = $class -> SUPER::new($dbh);
  26
  27     if ($id) {
  28         $self->set_organism_id($id);
  29         $self->fetch_organism();
  30     }
  31     return $self;
  32 }
  33
  34 sub fetch_organism {
  35     my $self = shift;
  36     my $query = "SELECT is_organism_id,
  37                         name,
  38                         common_name,
  39                         description,
  40                         user_id
  41                    FROM insitu.is_organism
  42                   WHERE is_organism_id=?";
  43     my $sth = $self->get_dbh()->prepare($query);
  44     $sth->execute($self->get_organism_id());
  45     my ($organism_id, $name, $common_name, $description, $user_id) =
  46         $sth->fetchrow_array();
  47     $self->set_organism_id($organism_id);
  48     $self->set_name($name);
  49     $self->set_common_name($common_name);
  50     $self->set_description($description);
  51     $self->set_user_id($user_id);
  52 }
  53
  54 =head2 store
  55
  56  Usage:
  57  Desc:
  58  Ret:
  59  Args:
  60  Side Effects:
  61  Example:
  62
  63 =cut
  64
  65 sub store {
  66     my $self = shift;
  67     if ($self->get_organism_id()) {
  68         my $query = "UPDATE insitu.is_organism SET
  69                         name=?,
  70                         common_name=?,
  71                         description=?,
  72                         user_id=?
  73                      WHERE is_organism_id=?";
  74         my $sth = $self->get_dbh()->prepare($query);
  75         $sth->execute(
  76                       $self->get_name(),
  77                       $self->get_common_name(),
  78                       $self->get_description(),
  79                       $self->get_organism_id(),
  80                       $self->get_user_id()
  81
  82                       );
  83     }
  84     else {
  85         my $query = "INSERT INTO insitu.is_organism
  86                                  (name, common_name, description, user_id)
  87                           VALUES (?, ?, ?, ?)";
  88         my $sth = $self->get_dbh()->prepare($query);
  89         $sth->execute(
  90                       $self->get_name(),
  91                       $self->get_common_name(),
  92                       $self->get_description(),
  93                       $self->get_user_id()
  94                       );
  95         return $self->get_dbh()->last_insert_id("is_organism");
  96     }
  97 }
  98
  99 =head2 get_all_organisms
 100
 101  Usage:        my ($names_ref, $ids_ref) = CXGN::Insitu::Organism::get_all_organisms($dbh);
 102  Desc:         This is a static function.
 103  Ret:          Returns to arrayrefs. One array contains all the
 104                organism names, and the other all the organism ids
 105                with corresponding array indices.
 106  Args:         a database handle
 107  Side Effects:
 108  Example:
 109
 110 =cut
 111
 112 sub get_all_organisms {
 113     my $dbh = shift;
 114     my $query = "SELECT name, is_organism_id
 115                    FROM insitu.is_organism";
 116     my $sth = $dbh->prepare($query);
 117     $sth->execute();
 118     my @names = ();
 119     my @ids = ();
 120     while (my($name, $organism_id) = $sth->fetchrow_array()) {
 121         push @names, $name;
 122         push @ids, $organism_id;
 123     }
 124     return (\@names, \@ids);
 125 }
 126
 127
 128
 129 =head2 get_organism_id
 130
 131  Usage:
 132  Desc:
 133  Ret:
 134  Args:
 135  Side Effects:
 136  Example:
 137
 138 =cut
 139
 140 sub get_organism_id {
 141   my $self=shift;
 142   return $self->{organism_id};
 143
 144 }
 145
 146 =head2 set_organism_id
 147
 148  Usage:
 149  Desc:
 150  Ret:
 151  Args:
 152  Side Effects:
 153  Example:
 154
 155 =cut
 156
 157 sub set_organism_id {
 158   my $self=shift;
 159   $self->{organism_id}=shift;
 160 }
 161
 162 =head2 get_name
 163
 164  Usage:
 165  Desc:
 166  Ret:
 167  Args:
 168  Side Effects:
 169  Example:
 170
 171 =cut
 172
 173 sub get_name {
 174   my $self=shift;
 175   return $self->{name};
 176
 177 }
 178
 179 =head2 set_name
 180
 181  Usage:
 182  Desc:
 183  Ret:
 184  Args:
 185  Side Effects:
 186  Example:
 187
 188 =cut
 189
 190 sub set_name {
 191   my $self=shift;
 192   $self->{name}=shift;
 193 }
 194
 195 =head2 get_common_name
 196
 197  Usage:
 198  Desc:
 199  Ret:
 200  Args:
 201  Side Effects:
 202  Example:
 203
 204 =cut
 205
 206 sub get_common_name {
 207   my $self=shift;
 208   return $self->{common_name};
 209
 210 }
 211
 212 =head2 set_common_name
 213
 214  Usage:
 215  Desc:
 216  Ret:
 217  Args:
 218  Side Effects:
 219  Example:
 220
 221 =cut
 222
 223 sub set_common_name {
 224   my $self=shift;
 225   $self->{common_name}=shift;
 226 }
 227
 228 =head2 get_description
 229
 230  Usage:
 231  Desc:
 232  Ret:
 233  Args:
 234  Side Effects:
 235  Example:
 236
 237 =cut
 238
 239 sub get_description {
 240   my $self=shift;
 241   return $self->{description};
 242
 243 }
 244
 245 =head2 set_description
 246
 247  Usage:
 248  Desc:
 249  Ret:
 250  Args:
 251  Side Effects:
 252  Example:
 253
 254 =cut
 255
 256 sub set_description {
 257   my $self=shift;
 258   $self->{description}=shift;
 259 }
 260
 261 =head2 get_user_id
 262
 263  Usage:
 264  Desc:
 265  Ret:
 266  Args:
 267  Side Effects:
 268  Example:
 269
 270 =cut
 271
 272 sub get_user_id {
 273   my $self=shift;
 274   return $self->{user_id};
 275
 276 }
 277
 278 =head2 set_user_id
 279
 280  Usage:
 281  Desc:
 282  Ret:
 283  Args:
 284  Side Effects:
 285  Example:
 286
 287 =cut
 288
 289 sub set_user_id {
 290   my $self=shift;
 291   $self->{user_id}=shift;
 292 }
 293
 294
 295
 296
 297 =head2 get_associated_experiments
 298
 299  Usage:
 300  Desc:
 301  Ret:
 302  Args:
 303  Side Effects:
 304  Example:
 305
 306 =cut
 307
 308 sub get_associated_experiments {
 309     my $self = shift;
 310     my $query = "SELECT experiment.experiment_id FROM insitu.experiment
 311                   WHERE is_organism_id=?";
 312     my $sth = $self->get_dbh()->prepare($query);
 313     $sth->execute($self->get_organism_id());
 314     my @experiments = ();
 315     while (my ($experiment_id) = $sth->fetchrow_array()) {
 316         push @experiments, CXGN::Insitu::Experiment->new($self->get_dbh(), $experiment_id);
 317     }
 318     return @experiments;
 319
 320 }
 321
 322
 323
 324
 325 return 1;
 326