bin/delete_trials.pl

   1
   2 =head1 NAME
   3
   4 delete_trials.pl - script to delete trials
   5
   6 =head1 DESCRIPTION
   7
   8 perl delete_trials.pl -i trial_id -H host -D dbname -U dbuser -P dbpass -b basepath -r temp_file_nd_experiment_id
   9
  10 Deletes trials that whose ids are provided as a comma separated list for the -i parameter.
  11 First, it deletes metadata, then trial layouts, then phenotypes, and finally the trial entry in the project table. All deletes are hard deletes. There is no way of bringing the trial back, except from a backup. So be careful!
  12
  13 =head1 AUTHOR
  14
  15 Lukas Mueller <lam87@cornell.edu>
  16
  17 =cut
  18
  19 use strict;
  20
  21 use Getopt::Std;
  22 use Bio::Chado::Schema;
  23 use CXGN::Metadata::Schema;
  24 use CXGN::Phenome::Schema;
  25 use CXGN::DB::InsertDBH;
  26 use CXGN::Trial;
  27
  28 our ($opt_H, $opt_D, $opt_U, $opt_P, $opt_b, $opt_i, $opt_n, $opt_t, $opt_r);
  29
  30 getopts('H:D:U:P:b:i:t:r:n');
  31
  32 my $dbhost = $opt_H;
  33 my $dbname = $opt_D;
  34 my $dbuser = $opt_U;
  35 my $dbpass = $opt_P;
  36 my $trial_ids = $opt_i;
  37 my $trial_names = $opt_t;
  38 my $non_interactive = $opt_n;
  39
  40 my $dbh = CXGN::DB::InsertDBH->new( { dbhost=>$dbhost,
  41                                       dbname=>$dbname,
  42                                       dbargs => {AutoCommit => 0,
  43                                       RaiseError => 1}
  44                                     }
  45     );
  46
  47 print STDERR "Connecting to database...\n";
  48 my $schema= Bio::Chado::Schema->connect(  sub { $dbh->get_actual_dbh() } );
  49 my $metadata_schema = CXGN::Metadata::Schema->connect( sub { $dbh->get_actual_dbh() });
  50 my $phenome_schema = CXGN::Phenome::Schema->connect( sub { $dbh->get_actual_dbh() });
  51
  52 my @trial_ids = split ",", $trial_ids;
  53 my @trial_names = split ",", $trial_names;
  54
  55 foreach my $name (@trial_names) {
  56     my $trial = $schema->resultset("Project::Project")->find( { name => $name });
  57     if (!$trial) { print STDERR "Trial $name not found. Skipping...\n"; next; }
  58     push @trial_ids, $trial->project_id();
  59 }
  60
  61 foreach my $trial_id (@trial_ids) {
  62     print STDERR "Retrieving trial information for trial $trial_id...\n";
  63
  64     my $t = CXGN::Trial->new({
  65         bcs_schema => $schema,
  66         metadata_schema => $metadata_schema,
  67         phenome_schema => $phenome_schema,
  68         trial_id => $trial_id
  69     });
  70
  71     my $answer = "";
  72     if (!$non_interactive) {
  73         print $t->get_name().", ".$t->get_description().". Delete? ";
  74         $answer = <>;
  75     }
  76     if ($non_interactive || $answer =~ m/^y/i) {
  77         eval {
  78             delete_trial($metadata_schema, $phenome_schema, $t);
  79         };
  80         if ($@) {
  81             print STDERR "An error occurred trying to delete trial ".$t->get_name()." ($@)\n";
  82             $dbh->rollback();
  83         }
  84         else {
  85             $dbh->commit();
  86             print STDERR "Trial ".$t->get_name()." successfully deleted\n";
  87         }
  88
  89     }
  90
  91 }
  92
  93 $dbh->disconnect();
  94 print STDERR "Done with everything (though nd_experiment entry deletion may still be occuring asynchronously).\n";
  95
  96 sub delete_trial {
  97     my $metadata_schema = shift;
  98     my $phenome_schema = shift;
  99     my $t = shift;
 100
 101     print STDERR "Deleting trial ".$t->get_name()."\n";
 102     print STDERR "Delete metadata...\n";
 103     $t->delete_metadata();
 104     print STDERR "Deleting phenotypes...\n";
 105     $t->delete_phenotype_data($opt_b, $dbhost, $dbname, $dbuser, $dbpass, $opt_r);
 106     print STDERR "Deleting layout...\n";
 107     $t->delete_field_layout();
 108     print STDERR "Delete project entry...\n";
 109     $t->delete_project_entry();
 110 }
 111