db/00006/PopulateStockPub.pm

   1 #!/usr/bin/env perl
   2
   3
   4 =head1 NAME
   5
   6     PopulateStockPub.pm
   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 is a patch for populating the stockpub table , and granting web_usr permissions
  18
  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 PopulateStockPub;
  36
  37 use Moose;
  38 extends 'CXGN::Metadata::Dbpatch';
  39
  40 use Bio::Chado::Schema;
  41
  42 sub init_patch {
  43     my $self=shift;
  44     my $name = __PACKAGE__;
  45     print "dbpatch name is ':" .  $name . "\n\n";
  46     my $description = 'Populating stock_pub table';
  47     my @previous_requested_patches = (); #ADD HERE
  48     $self->name($name);
  49     $self->description($description);
  50     $self->prereq(\@previous_requested_patches);
  51 }
  52
  53 sub patch {
  54     my $self=shift;
  55
  56     print STDOUT "Executing the patch:\n " .   $self->name . ".\n\nDescription:\n  ".  $self->description . ".\n\nExecuted by:\n " .  $self->username . " .";
  57
  58     print STDOUT "\nChecking if this db_patch was executed before or if previous db_patches have been executed.\n";
  59
  60     print STDOUT "\nExecuting the SQL commands.\n";
  61     my $schema = Bio::Chado::Schema->connect( sub { $self->dbh->clone } );
  62
  63     my $stockdbxrefs = $schema->resultset("General::Db")->search( { name => 'PMID' } )
  64         ->search_related('dbxrefs')->search_related('stock_dbxrefs');
  65     my $result = $schema->txn_do( sub {
  66         while ( my $sd = $stockdbxrefs->next )  {
  67             $sd->stock->find_or_create_related('stock_pubs' , {
  68                 pub_id => $sd->dbxref->search_related('pub_dbxrefs')->search_related('pub')->first->pub_id
  69                                                }, );
  70             print "Added publication for stock " . $sd->stock->name . "\n";
  71         }
  72         if ( $self->trial ) {
  73             print "Trial mode! Rolling back transaction.\n\n";
  74             $schema->txn_rollback;
  75             return 0;
  76         } else {
  77             print "Committing.\n";
  78             return 1;
  79         }
  80     });
  81
  82
  83     $self->dbh->do(<<EOSQL);
  84 --do your SQL here
  85 --
  86 --grant permissions to web_usr
  87  grant ALL  on public.stock_pub to web_usr ;
  88  grant USAGE on public.stock_pub_stock_pub_id_seq TO  web_usr ;
  89
  90
  91 EOSQL
  92     print $result ? "Patch applied successfully.\n" : "Patch not applied.\n";
  93 }
  94
  95
  96 ####
  97 1; #
  98 ####
  99