db/00047/UpdateSnpGenotypeCvterm.pm

   1
   2 #!/usr/bin/env perl
   3
   4
   5 =head1 NAME
   6
   7  UpdateSnpGenotypeCvterm
   8
   9 =head1 SYNOPSIS
  10
  11 mx-run ThisPackageName [options] -H hostname -D dbname -u username [-F]
  12
  13 this is a subclass of L<CXGN::Metadata::Dbpatch>
  14 see the perldoc of parent class for more details.
  15
  16 =head1 DESCRIPTION
  17
  18 This patch moves all genotypes and genotypeprops of cvterm type "snp genotype" and cv name 'local' ,  to a "snp genotype" cvterm  and genotype_property cv .
  19 This is done to eliminate duplicates of snp genotype cvterms loaded previously in the different databases using different cv terms (null, local, genotype_property), making the cvterm name for snp genotype more explicit.
  20 This also solves a potential conflict with the unique constraint in the dbxref table, since using the cvterm name "snp genotype" causes creating a dbxref.snp genotype of "autocreated:snp genotype" when creating properties using bio chado schema create_stock function.
  21 The same snp genotyping will be attempted to be created when autocreating another property with the name "snp genotype".
  22
  23 This subclass uses L<Moose>. The parent class uses L<MooseX::Runnable>
  24
  25 =head1 AUTHOR
  26
  27  Guillaume Bauchet<gjb99@cornell.edu>
  28
  29 =head1 COPYRIGHT & LICENSE
  30
  31 Copyright 2010 Boyce Thompson Institute for Plant Research
  32
  33 This program is free software; you can redistribute it and/or modify
  34 it under the same terms as Perl itself.
  35
  36 =cut
  37
  38
  39 package UpdateSnpGenotypeCvterm;
  40
  41 use Moose;
  42 use Bio::Chado::Schema;
  43 use Try::Tiny;
  44
  45 extends 'CXGN::Metadata::Dbpatch';
  46
  47
  48 has '+description' => ( default => <<'' );
  49 This patch will find_or_create a snp genotyping cvterm
  50 with cv of  genotype_property
  51 Then all genotypes and genotypeprops of type_id matching the word snp genotyping will be associated with the snp genotyping cvterm
  52 this is important for making the snp genotyping cvterm unified across the different databases and eliminating redundancy
  53
  54 has '+prereq' => (
  55     default => sub {
  56         [],
  57     },
  58   );
  59
  60 sub patch {
  61     my $self=shift;
  62
  63     print STDOUT "Executing the patch:\n " .   $self->name . ".\n\nDescription:\n  ".  $self->description . ".\n\nExecuted by:\n " .  $self->username . " .";
  64
  65     print STDOUT "\nChecking if this db_patch was executed before or if previous db_patches have been executed.\n";
  66
  67     print STDOUT "\nExecuting the SQL commands.\n";
  68     my $schema = Bio::Chado::Schema->connect( sub { $self->dbh->clone } );
  69
  70
  71 #find or create cvterm with snp genotyping name and genotype_property cv
  72 ##there might be an existing dbxref with snp genotyping = autocreated:snp genotyping
  73 #~
  74     my $coderef = sub {
  75
  76         my $snp_genotyping_cvterm = $schema->resultset("Cv::Cvterm")->create_with(
  77             { name   => 'snp genotyping',
  78               cv     => 'genotype_property',
  79             });
  80
  81         my $snp_genotyping_cvterm_id = $snp_genotyping_cvterm->cvterm_id;
  82         print "***snp_genotyping_cvterm_id is $snp_genotyping_cvterm_id \n";
  83
  84
  85 #find all genotypes and genotypeprops that have a type_id  ilike %snp_genotyping%' and change it to the
  86 #genotype_property  "snp genotyping" cvterm
  87 # delete the old cvterm
  88
  89         my $genotypeprop_rs = $schema->resultset("Genetic::Genotypeprop")->search(
  90             {
  91                 'type.name' => { ilike => 'snp%genotyping' },
  92                 'cv.name'   => 'local'
  93             },
  94             {
  95                 join =>  {'type' =>  'cv' },
  96             }
  97             );
  98
  99         print "** found " . $genotypeprop_rs->count . " genotypeprops with type_id of 'snp genotyping' and cv.name = 'local'  \n\n";
 100         print "**Changing genotypeprop.type_id to cvterm.name = 'snp genotyping' , cv= genotype_property ";
 101         $genotypeprop_rs->update( { type_id => $snp_genotyping_cvterm_id});
 102
 103
 104         my $genotype_rs = $schema->resultset("Genetic::Genotype")->search(
 105             {
 106                 'type.name' => { ilike => 'snp%genotyping' },
 107                 'cv.name'   => 'local'
 108             },
 109             {
 110                 join => { 'type' =>  'cv' },
 111             }
 112             );
 113
 114         print "** found " . $genotype_rs->count . " genotypes with type_id of 'snp genotyping' and cv.name = 'local'  \n\n";
 115         print "**Changing genotype.type_id to cvterm.name = 'snp genotyping' , cv= genotype_property ";
 116         $genotype_rs->update( { type_id => $snp_genotyping_cvterm_id });
 117
 118
 119
 120         my $old_cvterm = $schema->resultset("Cv::Cvterm")->search(
 121             {
 122                 'me.name' => 'snp genotyping',
 123                 'cv.name' => 'local' ,
 124             },
 125             {
 126                 join => 'cv'
 127             }
 128             );
 129
 130         $old_cvterm->delete();
 131
 132
 133         if ($self->trial) {
 134             print "Trial mode! Rolling back transaction\n\n";
 135             $schema->txn_rollback;
 136             return 0;
 137         }
 138         return 1;
 139     };
 140
 141     try {
 142         $schema->txn_do($coderef);
 143
 144     } catch {
 145         die "Load failed! " . $_ .  "\n" ;
 146     };
 147
 148
 149     print "You're done!\n";
 150 }
 151
 152
 153
 154
 155
 156 ####
 157 1; #
 158 ####