db/00046/UpdateStockSynonymCvterms.pm

   1 #!/usr/bin/env perl
   2
   3
   4 =head1 NAME
   5
   6  UpdateStockSynonymCvterms
   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 moves all stockprops of cvterm type "synonym" to a "stock_synonym" cvterm, "stock_property" cv , and "autocreated:stock_synonym" dbxref.
  18 This is done to eliminate redundant usage of synonym-like cvterms loaded in the different databases using different cv terms (null, local, stock_property), making the cvterm name for stock synonyms more explicit: "stock_synonym" instead of "synonym" which may be used for other CVs such as organism_property.
  19 This also solves a potential conflict with the unique constraint in the dbxref table, since using the cvterm name "synonym" causes creating a dbxref.accession of "autocreated:synonym" when creating properties using BCS create_stockprops function. The same accession will be attempted to be created when autocreating another property with the name "synonym", e.g. create_organismprop (organism_synonym will be taken care of in another db_patch)
  20
  21 This subclass uses L<Moose>. The parent class uses L<MooseX::Runnable>
  22
  23 =head1 AUTHOR
  24
  25  Naama Menda<nm249@cornell.edu>
  26
  27 =head1 COPYRIGHT & LICENSE
  28
  29 Copyright 2010 Boyce Thompson Institute for Plant Research
  30
  31 This program is free software; you can redistribute it and/or modify
  32 it under the same terms as Perl itself.
  33
  34 =cut
  35
  36
  37 package UpdateStockSynonymCvterms;
  38
  39 use Moose;
  40 use Bio::Chado::Schema;
  41 use Try::Tiny;
  42
  43 extends 'CXGN::Metadata::Dbpatch';
  44
  45
  46 has '+description' => ( default => <<'' );
  47 This patch will find_or_create a cvterm name stock_synonym
  48 with cv of stock_property and dbxref of autocreated:stock_synonym
  49 Then all stockprop of type_id matching the word synonym will be associated with
  50 the stock_synonym cvterm
  51 this is important for making stock synonyms unified across the different databases and eliminating redundancy of cvterms with name = synonym
  52
  53 has '+prereq' => (
  54     default => sub {
  55         [],
  56     },
  57   );
  58
  59 sub patch {
  60     my $self=shift;
  61
  62     print STDOUT "Executing the patch:\n " .   $self->name . ".\n\nDescription:\n  ".  $self->description . ".\n\nExecuted by:\n " .  $self->username . " .";
  63
  64     print STDOUT "\nChecking if this db_patch was executed before or if previous db_patches have been executed.\n";
  65
  66     print STDOUT "\nExecuting the SQL commands.\n";
  67     my $schema = Bio::Chado::Schema->connect( sub { $self->dbh->clone } );
  68
  69
  70 #find or create cvterm with name stock_synonym
  71 #make sure it has a dbxref of autocreated:stock_synonym and db = null
  72 ##there might be an existing dbxref with accession = autocreated:synonym
  73 #we will not be using that one anymore for distincting between synonyms of different entities.
  74     my $coderef = sub {
  75
  76         my $stock_synonym_cvterm = $schema->resultset("Cv::Cvterm")->create_with( {
  77             name => 'stock_synonym',
  78             cv   => 'stock_property', }
  79             );
  80
  81         my $stock_synonym_cvterm_id = $stock_synonym_cvterm->cvterm_id;
  82         print "***stock_synonym_cvterm_id is $stock_synonym_cvterm_id \n";
  83 #find all stockprops that have a type_id  ilike %synonym%' and change it to the
  84 #stock_synonym cvterm
  85 # delete the cvterm of name = synonym and cv name = "local" or "null"
  86
  87         my $stockprops = $schema->resultset("Stock::Stockprop")->search(
  88             {
  89                 'type.name' => { ilike => 'synonym%' },
  90             },
  91             {
  92                 join => 'type'
  93             }
  94             );
  95
  96         print "** found " . $stockprops->count . " stockprops \n\n";
  97         print "**Changing cvterm name of stock synonyms to stock_synonym , cv= stock_property ";
  98         $stockprops->update( { type_id => $stock_synonym_cvterm_id } ) ;
  99
 100         if ($self->trial) {
 101             print "Trial mode! Rolling back transaction\n\n";
 102             $schema->txn_rollback;
 103             return 0;
 104         }
 105         return 1;
 106     };
 107
 108     try {
 109         $schema->txn_do($coderef);
 110
 111     } catch {
 112         die "Load failed! " . $_ .  "\n" ;
 113     };
 114
 115
 116     print "You're done!\n";
 117 }
 118
 119
 120 ####
 121 1; #
 122 ####