db/00046/DeleteNullLocalSynonyms.pm

   1 #!/usr/bin/env perl
   2
   3
   4 =head1 NAME
   5
   6  DeleteMullLocalSynonyms
   7
   8 =head1 SYNOPSIS
   9
  10 mx-run ThisPackageName [options] -H hostname -D dbname -u username [-F]
  11
  12 this is a subclass of L<CXGN::Metadata::Dbpatch>
  13 see the perldoc of parent class for more details.
  14
  15 =head1 DESCRIPTION
  16
  17 This patch deletes the ubiquitous 'synonym' cvterms with cv_id of 'null' or 'local'
  18 synonyms should be loaded with an explicit cv_id providing the right context, e.g. cvterm.name = stock_synoym cv_id = stock_property, organism_synonym cv_id = organism_property
  19 This subclass uses L<Moose>. The parent class uses L<MooseX::Runnable>
  20
  21 =head1 AUTHOR
  22
  23  Naama Menda<nm249@cornell.edu>
  24
  25 =head1 COPYRIGHT & LICENSE
  26
  27 Copyright 2010 Boyce Thompson Institute for Plant Research
  28
  29 This program is free software; you can redistribute it and/or modify
  30 it under the same terms as Perl itself.
  31
  32 =cut
  33
  34
  35 package DeleteNullLocalSynonyms ;
  36
  37 use Moose;
  38 use Bio::Chado::Schema;
  39 use Try::Tiny;
  40
  41 extends 'CXGN::Metadata::Dbpatch';
  42
  43
  44 has '+description' => ( default => <<'' );
  45 This patch will find cvterms with name ilike synonyms and cv.name
  46 local or null and will delete those.
  47 this is important for using only synonyms with an explicit cvterm.name and cv.name.
  48
  49 has '+prereq' => (
  50     default => sub {
  51         ['UpdateOrganismSynonymCvterms', 'UpdateStockSynonymCvterms' ],
  52     },
  53   );
  54
  55 sub patch {
  56     my $self=shift;
  57
  58     print STDOUT "Executing the patch:\n " .   $self->name . ".\n\nDescription:\n  ".  $self->description . ".\n\nExecuted by:\n " .  $self->username . " .";
  59
  60     print STDOUT "\nChecking if this db_patch was executed before or if previous db_patches have been executed.\n";
  61
  62     print STDOUT "\nExecuting the SQL commands.\n";
  63     my $schema = Bio::Chado::Schema->connect( sub { $self->dbh->clone } );
  64
  65
  66 #find or create cvterm with name stock_synonym
  67 #make sure it has a dbxref of autocreated:stock_synonym and db = null
  68 ##there might be an existing dbxref with accession = autocreated:synonym
  69 #we will not be using that one anymore for distincting between synonyms of different entities.
  70     my $coderef = sub {
  71
  72
  73 ###########################
  74
  75 #find all cvterms with name  ilike 'synonym%' and cv.name = local
  76 # delete the cvterm of name = synonym and cv name = "local" or "null"
  77
  78         my $local_syn_cvterms = $schema->resultset("Cv::Cvterm")->search(
  79             {
  80                 'me.name' => { ilike => 'synonym%' },
  81                 'cv.name' => 'local'
  82             },
  83             {
  84                 join => 'cv'
  85             }
  86             );
  87
  88         print "** found " . $local_syn_cvterms->count . " cv.name=local cvterms \n\n";
  89
  90         if ($local_syn_cvterms ) {
  91             print "**Deleting ... \n";
  92             $local_syn_cvterms->delete;
  93         }
  94 #############################
  95
  96         my $null_syn_cvterms = $schema->resultset("Cv::Cvterm")->search(
  97             {
  98                 'me.name' => { ilike => 'synonym%' },
  99                 'cv.name' => 'null'
 100             },
 101             {
 102                 join => 'cv'
 103             }
 104             );
 105
 106         print "** found " . $null_syn_cvterms->count . " cv.name=null cvterms \n\n";
 107
 108         if ($null_syn_cvterms) {
 109             print "**Deleting ... \n";
 110             $null_syn_cvterms->delete;
 111         }
 112
 113 ###############################
 114
 115         if ($self->trial) {
 116             print "Trial mode! Rolling back transaction\n\n";
 117             $schema->txn_rollback;
 118             return 0;
 119         }
 120         return 1;
 121     };
 122
 123     try {
 124         $schema->txn_do($coderef);
 125
 126     } catch {
 127         die "Load failed! " . $_ .  "\n" ;
 128     };
 129
 130
 131     print "You're done!\n";
 132 }
 133
 134
 135 ####
 136 1; #
 137 ####