db/00009/ApplyPopulationTypes.pm

   1
   2 package ApplyPopulationTypes;
   3
   4 use Moose;
   5 extends 'CXGN::Metadata::Dbpatch';
   6
   7 use Bio::Chado::Schema;
   8
   9 sub init_patch {
  10
  11     my $self=shift;
  12     my $name = __PACKAGE__;
  13     print "dbpatch name is ':" .  $name . "\n\n";
  14     my $description = 'Adding explicit population types to stocks of type population';
  15     my @previous_requested_patches = ('LoadPhenomeInStock'); #ADD HERE
  16     $self->name($name);
  17     $self->description($description);
  18     $self->prereq(\@previous_requested_patches);
  19 }
  20
  21 sub patch {
  22     my $self=shift;
  23
  24     print STDOUT "Executing the patch:\n " .   $self->name . ".\n\nDescription:\n  ".  $self->description . ".\n\nExecuted by:\n " .  $self->username . " .";
  25
  26     print STDOUT "\nChecking if this db_patch was executed before or if previous db_patches have been executed.\n";
  27
  28     print STDOUT "\nExecuting the SQL commands.\n";
  29
  30     my $schema = Bio::Chado::Schema->connect( sub { $self->dbh->clone } );
  31
  32     my $coderef = sub {
  33         my $cvterm_rs = $schema->resultset('Cv::Cvterm');
  34         my $f2_cvterm = $cvterm_rs->create_with( {
  35             name => 'f2 population',
  36             cv   => 'stock type', }
  37             );
  38         my $bc_cvterm = $cvterm_rs->create_with( {
  39             name => 'backcross population',
  40             cv   => 'stock type', }
  41             );
  42         my $mutant_cvterm = $cvterm_rs->create_with( {
  43             name => 'mutant population',
  44             cv   => 'stock type', }
  45             );
  46         my $population_stocks = $schema->resultset('Cv::Cvterm')->search( { 'me.name' => 'population' } )->
  47             search_related('stocks');
  48         while (my $population = $population_stocks->next) {
  49             my $population_name = $population->name;
  50             print "Looking at population $population_name..\n";
  51             if ( grep {  /F2/i  } ($population_name) ) {
  52                 print "updating type to " . $f2_cvterm->name . "\n";
  53                 $population->update( { type_id=>$f2_cvterm->cvterm_id } );
  54             }
  55             if ( grep {  /Backcross/i  } ($population_name) ) {
  56                 print "updating type to " . $bc_cvterm->name . "\n";
  57                 $population->update( { type_id=>$bc_cvterm->cvterm_id } );
  58             }
  59             if ( grep {  /mutant/i  } ($population_name) ) {
  60                 print "updating type to " . $mutant_cvterm->name . "\n";
  61                 $population->update( { type_id=>$mutant_cvterm->cvterm_id } );
  62             }
  63         }
  64         if ($self->trial) {
  65             print "Trial mode! Rolling back transaction\n\n";
  66             $schema->txn_rollback;
  67         }
  68         return 1;
  69     };
  70
  71     try {
  72         $schema->txn_do($coderef);
  73         print "Data committed! \n";
  74     } catch {
  75         die "Load failed! " . $_ .  "\n" ;
  76     };
  77
  78     print "You're done!\n";
  79 }
  80
  81
  82 ####
  83 1; #
  84 ####
  85