lib/CXGN/BreedersToolbox/Delete.pm

   1
   2 package CXGN::BreedersToolbox::Delete;
   3
   4 use Moose;
   5
   6 use Data::Dumper;
   7
   8 has bcs_schema => (is => 'rw');
   9 has metadata_schema => (is=> 'rw');
  10 has phenome_schema => (is => 'rw');
  11
  12 =head2 delete_experiments_by_file
  13  SEEMS TO BE DEPRECATED BECAUSE CRUCIAL FUNCTIONS WITHIN THIS CALL ARE COMMENTED OUT
  14
  15  Currently using SGN::Controller::AJAX::BreedersToolbox->delete_uploaded_phenotype_files to delete phenotype files from manage phenotype page
  16
  17  Usage:        $cpd->delete_experiments_by_file($user_id, $md_file_id);
  18  Desc:         deletes the phenotype information associated with file $md_file_id
  19  Ret:          a hash with deletion statistics
  20  Args:         a user_id (for privilege check),
  21                an md_file_id (primary key of metadata.md_files)
  22  Side Effects: connects to the database and deletes information (be careful!)
  23  Example:
  24
  25 =cut
  26
  27 # sub delete_experiments_by_file {
  28 #     my $self = shift;
  29 #     my $user_id = shift;
  30 #     my $md_file_id = shift;
  31 #
  32 #     print STDERR "Get the md_file entry... ";
  33 #     my $srs = $self->metadata_schema->resultset("MdFiles")->search( { file_id => $md_file_id } );
  34 #
  35 #     print STDERR "Retrieved ".$srs->count()." entries.\n";
  36 #     if ($srs->count() == 0) {
  37 #       return "The file specified does not exist."
  38 #     }
  39 #
  40 #     my $file_row = $srs->first();
  41 #     my $metadata_id = $file_row->metadata_id()->metadata_id();
  42 #
  43 #     print STDERR "Get the associated md_metadata info... ($metadata_id, $user_id)";
  44 #
  45 #     my $frs = $self->metadata_schema->resultset("MdMetadata")->search( { metadata_id => $metadata_id, create_person_id=>$user_id });
  46 #
  47 #     print STDERR "Retrieved ".$frs->count()." entries.\n";
  48 #     if ($frs->count()==0) {
  49 #       return "You don't have the necessary privileges to delete this file";
  50 #     }
  51 #
  52 #     print STDERR "Get the entries from the linking table... ";
  53 #     my $prs = $self->phenome_schema -> resultset("NdExperimentMdFiles")->search( { file_id => $md_file_id });
  54 #
  55 #     print STDERR "Retrieved ".$prs->count()." entries.\n";
  56 #     if ($prs->count() == 0) {
  57 #       print STDERR "No experiments have been loaded for file with md_file_id $md_file_id\n";
  58 #     }
  59 #     else {
  60 #       foreach my $prs_row ($prs->rows()) {
  61 #           print STDERR "Deleting the MdExperiment entries... ";
  62 #
  63 #           # first delete the entry in the linking table...
  64 #           #
  65 #           my $nd_experiment_id = $prs_row->nd_experiment_id();
  66 #           $prs_row->delete();
  67 #
  68 #           $self->_delete_phenotype_experiments($nd_experiment_id);
  69 #       }
  70 #     }
  71 #
  72 #     # set md_files and/or metadata to obsolote
  73 #     print STDERR "Update the md_file table to obsolete... ";
  74 #     my $mdmd_row = $self->metadata_schema->resultset("MdMetadata")->find( { metadata_id => $metadata_id } );
  75 #     if ($mdmd_row) {
  76 #       $mdmd_row -> update( { obsolete => 1 });
  77 #     }
  78 #     print STDERR "Done.\n";
  79 #     print STDERR "Delete complete.\n";
  80 #
  81 # }
  82
  83 # sub delete_phenotype_data_by_trial {
  84 #     my $self = shift;
  85 #     my $trial_id = shift;
  86
  87
  88 #     $self->bcs_schema->txn_do(
  89 #       sub {
  90 #           # first, delete metadata entries
  91 #           #
  92 #           $self->delete_metadata_by_trial($trial_id);
  93
  94 #           # delete phenotype data associated with trial
  95 #           #
  96 #           my $trial = $self->bcs_schema()->resultset("Project::Project")->search( { project_id => $trial_id });
  97
  98 #           my $nd_experiment_rs = $self->bcs_schema()->resultset("NaturalDiversity::NdExperimentProject")->search( { project_id => $trial_id });
  99 #           my @nd_experiment_ids = map { $_->nd_experiment_id } $nd_experiment_rs->all();
 100
 101 #           $self->_delete_phenotype_experiments(@nd_experiment_ids); # cascading deletes should take care of everything (IT DOESNT????)
 102
 103 #       });
 104
 105 # }
 106
 107 # sub delete_field_layout_by_trial {
 108 #     my $self = shift;
 109 #     my $trial_id = shift;
 110
 111 #     # first, delete metadata entries
 112 #     #
 113 #     $self->bcs_schema()->txn_do(
 114 #       sub {
 115 #           $self->delete_metadata_by_trial($trial_id);
 116
 117 #           my $trial = $self->bcs_schema()->resultset("Project::Project")->search( { project_id => $trial_id });
 118
 119 #           my $nd_experiment_rs = $self->bcs_schema()->resultset("NaturalDiversity::NdExperimentProject")->search( { project_id => $trial_id });
 120 #           my @nd_experiment_ids = map { $_->nd_experiment_id } $nd_experiment_rs->all();
 121
 122 #           print STDERR "ND EXPERIMENTS: ".(join ",", @nd_experiment_ids)."\n";
 123
 124 #           print STDERR "DELETING trial layout for trial id $trial_id...\n";
 125 #           return $self->_delete_field_layout_experiment($trial_id);
 126 #       }
 127 #       );
 128 # }
 129
 130 # sub delete_metadata_by_trial {
 131 #     my $self = shift;
 132 #     my $trial_id = shift;
 133
 134
 135 #     # first, deal with entries in the md_metadata table, which may reference nd_experiment (through linking table)
 136 #     my $q = "SELECT distinct(metadata_id) FROM nd_experiment_project JOIN phenome.nd_experiment_md_files using(nd_experiment_id) JOIN metadata.md_files using(file_id) JOIN metadata.md_metadata using(metadata_id) WHERE project_id=?";
 137 #     my $h = $self->bcs_schema->storage()->dbh()->prepare($q);
 138 #     $h->execute($trial_id);
 139
 140 #     while (my ($md_id) = $h->fetchrow_array()) {
 141 #       my $mdmd_row = $self->metadata_schema->resultset("MdMetadata")->find( { metadata_id => $md_id } );
 142 #       if ($mdmd_row) {
 143 #           print STDERR "Update the md_metadata table to obsolete... for $md_id";
 144 #           $mdmd_row -> update( { obsolete => 1 });
 145 #       }
 146 #     }
 147
 148 #     # delete the entries from the linking table...
 149 #     $q = "SELECT distinct(file_id) FROM nd_experiment_project JOIN phenome.nd_experiment_md_files using(nd_experiment_id) JOIN metadata.md_files using(file_id) JOIN metadata.md_metadata using(metadata_id) WHERE project_id=?";
 150 #     $h = $self->bcs_schema->storage()->dbh()->prepare($q);
 151 #     $h->execute($trial_id);
 152
 153 #     while (my ($file_id) = $h->fetchrow_array()) {
 154 #       my $ndemdf_rs = $self->phenome_schema->resultset("NdExperimentMdFiles")->search( { file_id=>$file_id });
 155 #       print STDERR "Delete phenome.nd_experiment_md_files row for file_id $file_id...\n";
 156 #       foreach my $row ($ndemdf_rs->all()) {
 157 #           $row->delete();
 158 #       }
 159 #     }
 160 # }
 161
 162
 163 # sub _delete_phenotype_experiments {
 164 #     my $self = shift;
 165 #     my @nd_experiment_ids = @_;
 166
 167
 168 #     print STDERR "Deleting the MdExperiment entries... ";
 169
 170 #     # retrieve the associated phenotype ids (they won't be deleted by the cascade)
 171 #     #
 172 #     my $phenotypes_deleted = 0;
 173 #     my $nd_experiments_deleted = 0;
 174
 175 #     my $phenotype_rs = $self->bcs_schema()->resultset("NaturalDiversity::NdExperimentPhenotype")->search( { nd_experiment_id=> { -in => [ @nd_experiment_ids ] }}, { join => 'phenotype' });
 176 #     if ($phenotype_rs->count() > 0) {
 177 #       foreach my $p ($phenotype_rs->all()) {
 178 #           print STDERR "Deleting phenotype_id ".$p->phenotype_id()."\n";
 179 #           $p->delete();
 180 #           $phenotypes_deleted++;
 181 #       }
 182 #     }
 183
 184 #     # delete the experiments
 185 #     #
 186 #     my $delete_rs = $self->bcs_schema()->resultset("NaturalDiversity::NdExperiment")->search({ nd_experiment_id => { -in => [ @nd_experiment_ids] }});
 187 #     $nd_experiments_deleted = $delete_rs->count();
 188 #     $delete_rs->delete_all();
 189 #     print STDERR "Done.\n";
 190
 191 #     return { phenotypes_deleted => $phenotypes_deleted,
 192 #            nd_experiments_deleted => $nd_experiments_deleted
 193 #     };
 194 # }
 195
 196 # =head2 _delete_field_layout_experiment
 197
 198 #  Usage:
 199 #  Desc:
 200 #  Ret:
 201 #  Args:
 202 #  Side Effects:
 203 #  Example:
 204
 205 # =cut
 206
 207 # sub _delete_field_layout_experiment {
 208 #     my $self = shift;
 209 #     my $trial_id = shift;
 210
 211 #     # check if there are still associated phenotypes...
 212 #     #
 213 #     if ($self->trial_has_phenotype_data()) {
 214 #       print STDERR "Attempt to delete field layout that still has associated phenotype data.\n";
 215 #       return { error => "Trial still has associated phenotyping experiment, cannot delete." };
 216 #     }
 217
 218 #     my $field_layout_type_id = $self->bcs_schema->resultset("Cv::Cvterm")->find( { name => "field_layout" })->cvterm_id();
 219 #     print STDERR "Field layout type id = $field_layout_type_id\n";
 220
 221 #     my $plot_type_id = $self->bcs_schema->resultset("Cv::Cvterm")->find( { name => 'plot' })->cvterm_id();
 222 #     print STDERR "Plot type id = $plot_type_id\n";
 223
 224 #     my $q = "SELECT stock_id FROM nd_experiment_project JOIN nd_experiment USING (nd_experiment_id) JOIN nd_experiment_stock ON (nd_experiment.nd_experiment_id = nd_experiment_stock.nd_experiment_id) JOIN stock USING(stock_id) WHERE nd_experiment.type_id=? AND project_id=? AND stock.type_id=?";
 225 #     my $h = $self->bcs_schema->storage()->dbh()->prepare($q);
 226 #     $h->execute($field_layout_type_id, $trial_id, $plot_type_id);
 227
 228 #     my $plots_deleted = 0;
 229 #     while (my ($plot_id) = $h->fetchrow_array()) {
 230 #       my $plot = $self->bcs_schema()->resultset("Stock::Stock")->find( { stock_id => $plot_id });
 231 #       print STDERR "Deleting associated plot ".$plot->name()." (".$plot->stock_id().") \n";
 232 #       $plots_deleted++;
 233 #       $plot->delete();
 234 #     }
 235
 236 #     $q = "SELECT nd_experiment_id FROM nd_experiment JOIN nd_experiment_project USING(nd_experiment_id) WHERE nd_experiment.type_id=? AND project_id=?";
 237 #     $h = $self->bcs_schema->storage()->dbh()->prepare($q);
 238 #     $h->execute($field_layout_type_id, $trial_id);
 239
 240 #     my ($nd_experiment_id) = $h->fetchrow_array();
 241 #     if ($nd_experiment_id) {
 242 #       print STDERR "Delete corresponding nd_experiment entry  ($nd_experiment_id)...\n";
 243 #       my $nde = $self->bcs_schema()->resultset("NaturalDiversity::NdExperiment")->find( { nd_experiment_id => $nd_experiment_id });
 244 #       $nde->delete();
 245 #     }
 246
 247
 248 #     #return { success => $plots_deleted };
 249 #     return { success => 1 };
 250 # }
 251
 252 # sub trial_has_phenotype_data {
 253 #     my $self = shift;
 254 #     my $trial_id = shift;
 255
 256 #     my $phenotyping_experiment_type_id = $self->bcs_schema->resultset("Cv::Cvterm")->find( { name => 'phenotyping_experiment' })->cvterm_id();
 257
 258 #     my $phenotype_experiment_rs = $self->bcs_schema()->resultset("NaturalDiversity::NdExperimentProject")->search(
 259 #       {
 260 #           project_id => $trial_id, 'nd_experiment.type_id' => $phenotyping_experiment_type_id},
 261 #       {
 262 #           join => 'nd_experiment'
 263 #       }
 264 #       );
 265
 266 #     return $phenotype_experiment_rs->count();
 267
 268 # }
 269
 270 sub plot_has_phenotype_data {
 271     my $self = shift;
 272     my $plot_id = shift;
 273
 274     my $phenotype_rs = $self->bcs_schema->resultset("Stock::Stock")->search( { stock_id => $plot_id }, { join => { 'phenotypes' }});
 275
 276     if ($phenotype_rs->count() > 0) {
 277         return 1;
 278     }
 279     return 0;
 280 }
 281
 282 1;