db/00046/UpdateOrganismSynonymCvterms.pm

   1 #!/usr/bin/env perl
   2
   3
   4 =head1 NAME
   5
   6  UpdateOrganismSynonymCvterms
   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 organismprops of cvterm type "synonym" to a "organism_synonym" cvterm, "orgnaism_property" cv,
  18 and "autocreated:organism_synonym" dbxref.
  19 This is done to eliminate redundant usage of synonym-like cvterms loaded in the different databases
  20 using different cv terms (null, local, stock_property), making the cvterm name for organism synonyms more explicit:
  21 "orgnaism_synonym" instead of "synonym"
  22 This also solves a potential conflict with the unique constraint in the dbxref table, since using the cvterm name "synonym"
  23 causes creating a dbxref.accession of "autocreated:synonym" when creating properties using BCS create_stockprops function.
  24 The same accession will be attempted to be created when autocreating another property with the name "synonym", e.g.
  25 create_stockprops (stock_synonym is take care of in db_patch UpdateStockSynonymCvterms )
  26
  27 This subclass uses L<Moose>. The parent class uses L<MooseX::Runnable>
  28
  29 =head1 AUTHOR
  30
  31  Naama Menda<nm249@cornell.edu>
  32
  33 =head1 COPYRIGHT & LICENSE
  34
  35 Copyright 2010 Boyce Thompson Institute for Plant Research
  36
  37 This program is free software; you can redistribute it and/or modify
  38 it under the same terms as Perl itself.
  39
  40 =cut
  41
  42
  43 package UpdateOrganismSynonymCvterms;
  44
  45 use Moose;
  46 use Bio::Chado::Schema;
  47 use Try::Tiny;
  48
  49 extends 'CXGN::Metadata::Dbpatch';
  50
  51
  52 has '+description' => ( default => <<'' );
  53 This patch will find_or_create a cvterm name organism_synonym
  54 with cv of organism_property and dbxref of autocreated:organism_synonym
  55 Then all organismprops of type_id matching the word synonym will be associated with
  56 the organism_synonym cvterm
  57 this is important for making organism synonyms unified across the different databases and eliminating redundancy of cvterms with name = synonym
  58
  59 has '+prereq' => (
  60     default => sub {
  61         [],
  62     },
  63   );
  64
  65 sub patch {
  66     my $self=shift;
  67
  68     print STDOUT "Executing the patch:\n " .   $self->name . ".\n\nDescription:\n  ".  $self->description . ".\n\nExecuted by:\n " .  $self->username . " .";
  69
  70     print STDOUT "\nChecking if this db_patch was executed before or if previous db_patches have been executed.\n";
  71
  72     print STDOUT "\nExecuting the SQL commands.\n";
  73     my $schema = Bio::Chado::Schema->connect( sub { $self->dbh->clone } );
  74
  75
  76 #find or create cvterm with name organism_synonym
  77 #make sure it has a dbxref of autocreated:organism_synonym and db = null
  78 ##there might be an existing dbxref with accession = autocreated:synonym
  79 #we will not be using that one anymore for distincting between synonyms of different entities.
  80     my $coderef = sub {
  81
  82         my $organism_synonym_cvterm = $schema->resultset("Cv::Cvterm")->create_with( {
  83             name => 'organism_synonym',
  84             cv   => 'organism_property', }
  85             );
  86
  87         my $organism_synonym_cvterm_id = $organism_synonym_cvterm->cvterm_id;
  88         print "***organism_synonym_cvterm_id is $organism_synonym_cvterm_id \n";
  89 #find all organismprops that have a type_id  ilike %synonym%' and change it to the
  90 #organism_synonym cvterm
  91 # delete the cvterm of name = synonym and cv name = "local" or "null"
  92
  93         my $organismprops = $schema->resultset("Organism::Organismprop")->search(
  94             {
  95                 'type.name' => { ilike => '%synonym%' },
  96             },
  97             {
  98                 join => 'type'
  99             }
 100             );
 101
 102         print "** found " . $organismprops->count . " organismprops \n\n";
 103         print "**Changing cvterm name of organism synonyms to organism_synonym , cv= organism_property ";
 104         $organismprops->update( { type_id => $organism_synonym_cvterm_id } ) ;
 105
 106         if ($self->trial) {
 107             print "Trial mode! Rolling back transaction\n\n";
 108             $schema->txn_rollback;
 109             return 0;
 110         }
 111         return 1;
 112     };
 113
 114     try {
 115         $schema->txn_do($coderef);
 116
 117     } catch {
 118         die "Load failed! " . $_ .  "\n" ;
 119     };
 120
 121
 122     print "You're done!\n";
 123 }
 124
 125
 126 ####
 127 1; #
 128 ####