db/00133/AddProtocoltoStoredNIRSRetroactively.pm

   1 #!/usr/bin/env perl
   2
   3
   4 =head1 NAME
   5
   6 AddProtocoltoStoredNIRSRetroactively
   7
   8 =head1 SYNOPSIS
   9
  10 mx-run AddProtocoltoStoredNIRSRetroactively [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 This patch retroactively adds a protocol for the uploaded NIRS data
  17 This subclass uses L<Moose>. The parent class uses L<MooseX::Runnable>
  18
  19 =head1 AUTHOR
  20
  21 =head1 COPYRIGHT & LICENSE
  22
  23 Copyright 2010 Boyce Thompson Institute for Plant Research
  24
  25 This program is free software; you can redistribute it and/or modify
  26 it under the same terms as Perl itself.
  27
  28 =cut
  29
  30
  31 package AddProtocoltoStoredNIRSRetroactively;
  32
  33 use Moose;
  34 use Bio::Chado::Schema;
  35 use Try::Tiny;
  36 use SGN::Model::Cvterm;
  37 use JSON;
  38 extends 'CXGN::Metadata::Dbpatch';
  39
  40
  41 has '+description' => ( default => <<'' );
  42 This patch retroactively adds a protocol for the uploaded NIRS data
  43
  44 has '+prereq' => (
  45         default => sub {
  46         [],
  47     },
  48
  49 );
  50
  51 sub patch {
  52     my $self=shift;
  53
  54     print STDOUT "Executing the patch:\n " .   $self->name . ".\n\nDescription:\n  ".  $self->description . ".\n\nExecuted by:\n " .  $self->username . " .";
  55
  56     print STDOUT "\nChecking if this db_patch was executed before or if previous db_patches have been executed.\n";
  57
  58     print STDOUT "\nExecuting the SQL commands.\n";
  59     my $schema = Bio::Chado::Schema->connect( sub { $self->dbh->clone } );
  60
  61     my $high_dim_nirs_protocol_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'high_dimensional_phenotype_nirs_protocol', 'protocol_type')->cvterm_id();
  62     my $high_dim_nirs_protocol_prop_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'high_dimensional_phenotype_protocol_properties', 'protocol_property')->cvterm_id();
  63
  64     my %nirs_protocol_prop = (device_type => 'SCIO');
  65
  66     my $protocol = $schema->resultset('NaturalDiversity::NdProtocol')->create({
  67         name => 'NIRS Protocol',
  68         type_id => $high_dim_nirs_protocol_cvterm_id,
  69         nd_protocolprops => [{type_id => $high_dim_nirs_protocol_prop_cvterm_id, value => encode_json \%nirs_protocol_prop}]
  70     });
  71     my $protocol_id = $protocol->nd_protocol_id();
  72
  73     my $desc_q = "UPDATE nd_protocol SET description=? WHERE nd_protocol_id=?;";
  74     my $desc_dbh = $schema->storage->dbh()->prepare($desc_q);
  75     $desc_dbh->execute('Default NIRS protocol', $protocol_id);
  76
  77     my $protocol_query = "INSERT INTO nd_experiment_protocol ( nd_experiment_id, nd_protocol_id) VALUES (?,?);";
  78     my $protocol_dbh = $schema->storage->dbh()->prepare($protocol_query);
  79
  80     my $q = "SELECT nd_experiment_id
  81         FROM phenome.nd_experiment_md_json
  82         JOIN metadata.md_json USING(json_id)
  83         WHERE json_type='nirs_spectra';";
  84     my $dbh = $schema->storage->dbh()->prepare($q);
  85     $dbh->execute();
  86     while (my ($nd_experiment_id) = $dbh->fetchrow_array()) {
  87         $protocol_dbh->execute($nd_experiment_id, $protocol_id);
  88     }
  89
  90     print "You're done!\n";
  91 }
  92
  93
  94 ####
  95 1; #
  96 ####