db/00139/AddSequenceMetadataTypes.pm

   1 #!/usr/bin/env perl
   2
   3
   4 =head1 NAME
   5
   6 AddSequenceMetadataTypes.pm
   7
   8 =head1 SYNOPSIS
   9
  10 mx-run AddSequenceMetadataTypes [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 patch adds the CV and CVTerms for the Sequence Metadata Types (used by the featureprop_json table)
  18 This subclass uses L<Moose>. The parent class uses L<MooseX::Runnable>
  19
  20 =head1 AUTHOR
  21
  22 =head1 COPYRIGHT & LICENSE
  23
  24 Copyright 2010 Boyce Thompson Institute for Plant Research
  25
  26 This program is free software; you can redistribute it and/or modify
  27 it under the same terms as Perl itself.
  28
  29 =cut
  30
  31
  32 package AddSequenceMetadataTypes;
  33
  34 use Moose;
  35 use Bio::Chado::Schema;
  36 use Try::Tiny;
  37 extends 'CXGN::Metadata::Dbpatch';
  38
  39
  40 has '+description' => ( default => <<'' );
  41 This patch adds the CV and CVTerms for the Sequence Metadata Types (used by the featureprop_json table)
  42
  43 has '+prereq' => (
  44         default => sub {
  45         [],
  46     },
  47
  48 );
  49
  50 sub patch {
  51     my $self=shift;
  52
  53     print STDOUT "Executing the patch:\n " .   $self->name . ".\n\nDescription:\n  ".  $self->description . ".\n\nExecuted by:\n " .  $self->username . " .";
  54
  55     print STDOUT "\nChecking if this db_patch was executed before or if previous db_patches have been executed.\n";
  56
  57     print STDOUT "\nExecuting the SQL commands.\n";
  58     my $schema = Bio::Chado::Schema->connect( sub { $self->dbh->clone } );
  59     my $cvterm_rs = $schema->resultset("Cv::Cvterm");
  60         my $cv_rs = $schema->resultset("Cv::Cv");
  61
  62     print STDERR "CREATING CV...\n";
  63     my $cv = $cv_rs->find_or_create({ name => 'sequence_metadata_types' });
  64
  65     print STDERR "ADDING CVTERMS...\n";
  66     $cvterm_rs->create_with({
  67                 name => 'Gene Annotation',
  68                 cv => 'sequence_metadata_types'
  69         });
  70     $cvterm_rs->create_with({
  71                 name => 'GWAS Results',
  72                 cv => 'sequence_metadata_types'
  73         });
  74     $cvterm_rs->create_with({
  75                 name => 'MNase',
  76                 cv => 'sequence_metadata_types'
  77         });
  78
  79     print STDERR "UPDATING DEFINITIONS...\n";
  80     $self->dbh->do(<<EOSQL);
  81 UPDATE public.cvterm SET definition = 'Provides sequence features (gene, mRNA, UTR, exon, CDS) and annotations based on alignments of biological evidence.'
  82 WHERE name = 'Gene Annotation' AND cv_id = (SELECT cv_id FROM cv WHERE name = 'sequence_metadata_types');
  83
  84 UPDATE public.cvterm SET definition = 'Report of quantitative trait loci (QTLs) indentified by running rrBLUP analysis on phenotype trials and genotype trials within the T3 database.'
  85 WHERE name = 'GWAS Results' AND cv_id = (SELECT cv_id FROM cv WHERE name = 'sequence_metadata_types');
  86
  87 UPDATE public.cvterm SET definition = 'Report of chromatine accessibility score.  The report can be used to prioritize genomic variants and explain phenotypes. (https://genomebiology.biomedcentral.com/track/pdf/10.1186/s13059-020-02093-1)'
  88 WHERE name = 'MNase' AND cv_id = (SELECT cv_id FROM cv WHERE name = 'sequence_metadata_types');
  89 EOSQL
  90
  91     print "You're done!\n";
  92 }
  93
  94
  95 ####
  96 1; #
  97 ####