db/00007/AddQtlMarkers.pm

   1 package AddQtlMarkers;
   2
   3 use Moose;
   4 extends 'CXGN::Metadata::Dbpatch';
   5
   6 use Bio::Chado::Schema;
   7
   8 sub init_patch {
   9     my $self=shift;
  10     my $name = __PACKAGE__;
  11     print "dbpatch name is ':" .  $name . "\n\n";
  12     my $description = 'Adding QTL marker and map types, and flanking positions to marker_location';
  13     my @previous_requested_patches = (); #ADD HERE
  14     $self->name($name);
  15     $self->description($description);
  16     $self->prereq(\@previous_requested_patches);
  17 }
  18
  19 sub patch {
  20     my $self=shift;
  21
  22     print STDOUT "Executing the patch:\n " .   $self->name . ".\n\nDescription:\n  ".  $self->description . ".\n\nExecuted by:\n " .  $self->username . " .";
  23
  24     print STDOUT "\nChecking if this db_patch was executed before or if previous db_patches have been executed.\n";
  25
  26     print STDOUT "\nExecuting the SQL commands.\n";
  27
  28     $self->dbh->do( <<EOT );
  29     ALTER TABLE sgn.map DROP CONSTRAINT map_map_type_check;
  30     ALTER TABLE sgn.map ADD CONSTRAINT map_map_type_check CHECK
  31         (map_type = 'genetic'::text OR map_type = 'fish'::text OR map_type = 'sequence'::text OR map_type = 'QTL');
  32
  33     ALTER TABLE sgn.marker_experiment DROP CONSTRAINT marker_experiment_protocol_check;
  34     ALTER TABLE sgn.marker_experiment ADD CONSTRAINT marker_experiment_protocol_check CHECK (protocol = 'AFLP'::text OR protocol = 'CAPS'::text OR protocol = 'RAPD'::text OR protocol = 'SNP'::text OR protocol = 'SSR'::text OR protocol = 'RFLP'::text OR protocol = 'PCR'::text OR protocol = 'dCAPS'::text OR protocol = 'DART'::text OR protocol = 'OPA'::text OR protocol = 'unknown'::text OR protocol = 'ASPE'::text OR protocol = 'INDEL'::text OR protocol = 'QTL'::text);
  35
  36     ALTER TABLE sgn.marker_location ADD COLUMN position_north numeric(8,5);
  37     ALTER TABLE sgn.marker_location ADD COLUMN position_south numeric(8,5);
  38
  39 EOT
  40
  41     print "You're done!\n";
  42
  43 }
  44
  45
  46 ####
  47 1; #
  48 ####
  49