bin/load_field_coords.pl

   1 #!/usr/bin/perl
   2
   3 use strict;
   4 use warnings;
   5 use Bio::Chado::Schema;
   6 use Getopt::Std;
   7 use CXGN::DB::InsertDBH;
   8
   9
  10 our ($opt_H, $opt_D);
  11 getopts("H:D:");
  12 my $dbhost = $opt_H;
  13 my $dbname = $opt_D;
  14 my $file = shift;
  15
  16
  17
  18 my $dbh = CXGN::DB::InsertDBH->new( { dbhost=>$dbhost,
  19                                    dbname=>$dbname,
  20                                    dbargs => {AutoCommit => 1,
  21                                               RaiseError => 1,
  22                                    }
  23
  24                                  } );
  25
  26
  27 my $schema= Bio::Chado::Schema->connect( sub { $dbh->get_actual_dbh() });
  28
  29
  30 open (my $file_fh, "<", $file ) || die ("\nERROR: the file $file could not be found\n" );
  31
  32 my $header = <$file_fh>;
  33 while (my $line = <$file_fh>) {
  34     chomp $line;
  35     my ($plot,$row,$col) = split("\t", $line);
  36
  37
  38     my $rs = $schema->resultset("Stock::Stock")->search({uniquename=> $plot });
  39
  40     if ($rs->count()== 1) {
  41         my $r =  $rs->first();
  42         print STDERR "The plots $plot was found.\n Loading row $row col $col\n";
  43         $r->create_stockprops({row_number => $row, col_number => $col}, {autocreate => 1});
  44     }
  45
  46     else {
  47
  48         print STDERR "WARNING! $plot was not found in the database.\n";
  49
  50     }
  51
  52 }
  53
  54
  55
  56