bin/load_composed_cvprops.pl

   1 #!/usr/bin/env perl
   2
   3 =head1
   4
   5 load_composed_cvprops.pl
   6
   7 =head1 SYNOPSIS
   8
   9 load_composed_cvprops.pl -H [dbhost] -D [dbname]  -T [trait_ontology cv name] -c [composed_trait_ontology cv name] -o [object_ontology cv name] -a [attribute_ontology cv name] -m [method_ontology cv name] -u [unit_ontology cv name] -t [time_ontology cv name]
  10
  11 =head1 COMMAND-LINE OPTIONS
  12
  13  -H  host name
  14  -D  database name
  15
  16  optional:
  17  -T [trait_ontology cv name]
  18  -c [composed_trait_ontology cv name]
  19  -o [object_ontology cv name]
  20  -a [attribute_ontology cv name]
  21  -m [method_ontology cv name]
  22  -u [unit_ontology cv name]
  23  -t [time_ontology cv name]
  24
  25 =head2 DESCRIPTION
  26
  27
  28 =head2 AUTHOR
  29
  30 Bryan Ellerbrock (bje24@cornell.edu)
  31
  32 Feb 2017
  33
  34 =cut
  35
  36 use strict;
  37 use warnings;
  38 use Data::Dumper;
  39 use Getopt::Std;
  40 use Bio::Chado::Schema;
  41 use CXGN::DB::InsertDBH;
  42 use CXGN::DB::Connection;
  43 use Try::Tiny;
  44
  45 our ( $opt_H, $opt_D, $opt_T, $opt_c, $opt_o, $opt_a, $opt_m, $opt_u, $opt_t );
  46 getopts('H:D:T:c:o:a:m:u:t:');
  47
  48 sub print_help {
  49     print STDERR
  50 "A script to load composed cvprops\nUsage: load_composed_cvprops.pl -H [dbhost] -D [dbname]  -T [trait_ontology cv name] -c [composed_trait_ontology cv name] -o [object_ontology cv name] -a [attribute_ontology cv name] -m [method_ontology cv name] -u [unit_ontology cv name] -t [time_ontology cv name] \n";
  51 }
  52
  53 if ( !$opt_D || !$opt_H ) {
  54     print_help();
  55     die("Exiting: -H [dbhost] and -D [dbname] options missing\n");
  56 }
  57
  58 my $dbh = CXGN::DB::InsertDBH->new(
  59     {
  60         dbname => $opt_D,
  61         dbhost => $opt_H,
  62         dbargs => {
  63             AutoCommit => 1,
  64             RaiseError => 1
  65         },
  66     }
  67 );
  68
  69 my $schema = Bio::Chado::Schema->connect( sub { $dbh->get_actual_dbh() } );
  70
  71 my %cvprop_hash = (
  72     trait_ontology          => $opt_T,
  73     composed_trait_ontology => $opt_c,
  74     object_ontology         => $opt_o,
  75     attribute_ontology      => $opt_a,
  76     method_ontology         => $opt_m,
  77     unit_ontology           => $opt_u,
  78     time_ontology           => $opt_t
  79 );
  80
  81 my $coderef = sub {
  82
  83     my $composable_cvtypes =
  84       $schema->resultset("Cv::Cv")->find( { name => 'composable_cvtypes' } );
  85     if ( !$composable_cvtypes ) {
  86         print STDERR
  87 "No cv found for composable_cvtypes in database '$opt_D'.\n Run patch AddComposedCvtypeCv.pm on this database to load missing composable_cvtype cv.";
  88     }
  89
  90     my ( $ontology, $ontology_cvtype, $new_ontology_cvprop );
  91     while ( my ( $key, $value ) = each %cvprop_hash ) {
  92
  93         if ($value) {
  94             $ontology =
  95               $schema->resultset("Cv::Cv")->find( { name => $value } );
  96
  97             if ( !$ontology ) {
  98                 print STDERR
  99 "No cv was found with the name '$value' in database '$opt_D'.\n";
 100             }
 101
 102             $ontology_cvtype = $schema->resultset("Cv::Cvterm")->find(
 103                 {
 104                     name  => $key,
 105                     cv_id => $composable_cvtypes->cv_id()
 106                 }
 107             );
 108
 109             if ( !$ontology_cvtype ) {
 110                 print STDERR
 111 "No term found for composable_cvtype '$key' in database '$opt_D'.\n Skipping cv '$value'.\n Run patch AddComposedCvtypeCv.pm on this database to load missing composable_cvtypes.\n";
 112                 next;
 113             }
 114
 115             $new_ontology_cvprop =
 116               $schema->resultset("Cv::Cvprop")->find_or_new(
 117                 {
 118                     cv_id   => $ontology->cv_id(),
 119                     type_id => $ontology_cvtype->cvterm_id()
 120                 }
 121               );
 122
 123             if ( !$new_ontology_cvprop->in_storage ) {
 124                 print STDERR
 125                   "Giving cv with name '$value' the cvprop '$key'... \n";
 126                 $new_ontology_cvprop->insert;
 127             }
 128             else {
 129                 print STDERR
 130 "The Cv with name '$value' already has the cvprop '$key'... \n";
 131             }
 132
 133         }
 134     }
 135 };
 136
 137 try {
 138     $schema->txn_do($coderef);
 139
 140 }
 141 catch {
 142     die "Load failed! " . $_ . "\n";
 143 };
 144
 145 print "You're done!\n";