db/00027/AddBlastDbBlastDbGroupLinkingTable.pm

   1 #!/usr/bin/env perl
   2
   3
   4 =head1 NAME
   5
   6  AddBlastDbBlastDbGroupLinkingTable.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 subclass uses L<Moose>. The parent class uses L<MooseX::Runnable>
  18
  19 =head1 AUTHOR
  20
  21  Lukas Mueller<lam87@cornell.edu>
  22
  23 =head1 COPYRIGHT & LICENSE
  24
  25 Copyright 2010 Boyce Thompson Institute for Plant Research
  26
  27 This program is free software; you can redistribute it and/or modify
  28 it under the same terms as Perl itself.
  29
  30 =cut
  31
  32
  33 package AddBlastDbBlastDbGroupLinkingTable;
  34
  35 use Moose;
  36 extends 'CXGN::Metadata::Dbpatch';
  37
  38
  39 has '+description' => ( default => <<'' );
  40 Adds a linking table between the blast_db and blast_db_group table
  41
  42 has '+prereq' => (
  43     default => sub {
  44         [ ],
  45     },
  46   );
  47
  48 sub patch {
  49     my $self=shift;
  50
  51     print STDOUT "Executing the patch:\n " .   $self->name . ".\n\nDescription:\n  ".  $self->description . ".\n\nExecuted by:\n " .  $self->username . " .";
  52
  53     print STDOUT "\nChecking if this db_patch was executed before or if previous db_patches have been executed.\n";
  54
  55     print STDOUT "\nExecuting the SQL commands.\n";
  56
  57     $self->dbh->do(<<EOSQL);
  58 --do your SQL here
  59 --
  60
  61 create table blast_db_blast_db_group (
  62     blast_db_blast_db_group_id serial primary key,
  63     blast_db_id bigint REFERENCES blast_db,
  64     blast_db_group_id bigint REFERENCES blast_db_group
  65 );
  66
  67 -- populate table with current data from blast_db table
  68
  69 insert into sgn.blast_db_blast_db_group (blast_db_id, blast_db_group_id) SELECT blast_db_id, blast_db_group_id FROM sgn.blast_db;
  70
  71 -- also add blast_db_organism table
  72
  73 create table blast_db_organism (
  74     blast_db_organism_id serial primary key,
  75     blast_db_id bigint references sgn.blast_db,
  76     organism_id bigint references public.organism
  77 );
  78
  79     GRANT select ON sgn.blast_db_organism TO web_usr;
  80     GRANT select ON sgn.blast_db_blast_db_group TO web_usr;
  81
  82
  83 EOSQL
  84
  85 print "You're done!\n";
  86 }
  87
  88
  89 ####
  90 1; #
  91 ####