db/00021/MarkerPositionSize.pm

   1 #!/usr/bin/env perl
   2
   3
   4 =head1 NAME
   5
   6  MarkerPositionSize.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 Change the sgn.marker_location.position type from numeric(8,5) to numeric(9,6)
  18 to accomodate full genome location in bp
  19
  20 This subclass uses L<Moose>. The parent class uses L<MooseX::Runnable>
  21
  22 =head1 AUTHOR
  23
  24  Naama Menda<nm249@cornell.edu>
  25
  26 =head1 COPYRIGHT & LICENSE
  27
  28 Copyright 2012 Boyce Thompson Institute for Plant Research
  29
  30 This program is free software; you can redistribute it and/or modify
  31 it under the same terms as Perl itself.
  32
  33 =cut
  34
  35
  36 package MarkerPositionSize;
  37
  38 use Moose;
  39 extends 'CXGN::Metadata::Dbpatch';
  40
  41
  42 has '+description' => ( default => <<'' );
  43 Change the sgn.marker_location.position type from numeric(8,5) to numeric(9,6)
  44 to accomodate full genome location in bp
  45
  46
  47 sub patch {
  48     my $self=shift;
  49
  50     print STDOUT "Executing the patch:\n " .   $self->name . ".\n\nDescription:\n  ".  $self->description . ".\n\nExecuted by:\n " .  $self->username . " .";
  51
  52     print STDOUT "\nChecking if this db_patch was executed before or if previous db_patches have been executed.\n";
  53
  54     print STDOUT "\nExecuting the SQL commands.\n";
  55
  56     $self->dbh->do(<<EOSQL);
  57 DROP VIEW sgn.marker_to_map;
  58 ALTER TABLE sgn.marker_location ALTER COLUMN position TYPE numeric(9,6);
  59
  60 CREATE VIEW sgn.marker_to_map AS
  61 SELECT m.marker_id, me.protocol, ml.location_id, linkage_group.lg_name, linkage_group.lg_order, ml."position", ml.confidence_id, ml.subscript, ml.map_version_id, map.map_id, map.parent_1, map.parent_2, map_version.current_version
  62    FROM marker m
  63    LEFT JOIN marker_experiment me USING (marker_id)
  64    LEFT JOIN marker_location ml USING (location_id)
  65    LEFT JOIN map_version USING (map_version_id)
  66    LEFT JOIN map USING (map_id)
  67    LEFT JOIN linkage_group USING (lg_id)
  68   WHERE map_version.current_version = true;
  69
  70 GRANT select ON sgn.marker_to_map TO web_usr;
  71
  72 EOSQL
  73
  74 print "You're done!\n";
  75 }
  76
  77
  78 ####
  79 1; #
  80 ####