bin/merge_stocks.pl

   1
   2 =head1 NAME
   3
   4 merge_stocks.pl - merge stocks using a file with stocks to merge
   5
   6 =head1 DESCRIPTION
   7
   8 merge_stocks.pl -H [database host] -D [database name]  [ -x ] mergefile.txt
   9
  10 Options:
  11
  12  -H the database host
  13  -D the database name
  14  -x flag; if present, delete the empty remaining accession
  15
  16 mergefile.txt: A file with three columns: first column is ignored, bad name, good name.
  17
  18 All the metadata of bad name will be transferred to good name.
  19 If -x is used, stock with name bad name will be deleted.
  20
  21 =head1 AUTHOR
  22
  23 Lukas Mueller <lam87@cornell.edu>
  24
  25 =cut
  26
  27 use strict;
  28
  29 use Getopt::Std;
  30 use CXGN::DB::InsertDBH;
  31 use CXGN::DB::Schemas;
  32 use CXGN::Chado::Stock;
  33
  34 our($opt_H, $opt_D, $opt_x);
  35 getopts('H:D:x');
  36
  37 my $dbh = CXGN::DB::InsertDBH->new(
  38     {
  39         dbhost => $opt_H,
  40         dbname => $opt_D ,
  41         dbargs => {
  42             AutoCommit => 0,
  43             RaiseError => 1,
  44             limit_dialect => 'LimitOffset',
  45         }
  46     });
  47
  48 my $delete_merged_stock = $opt_x;
  49
  50 print STDERR "Note: -x: Deleting stocks that have been merged into other stocks.\n";
  51
  52 my $s = CXGN::DB::Schemas->new({ dbh => $dbh });
  53 my $schema = $s->bcs_schema();
  54 my $file = shift;
  55
  56 open(my $F, "<", $file) || die "Can't open file $file.\n";
  57
  58 my $header = <$F>;
  59
  60 eval {
  61     while (<$F>) {
  62         chomp;
  63         my ($line_count, $merge_stock_name, $good_stock_name) = split /\t/;
  64
  65         my $stock_row = $schema->resultset("Stock::Stock")->find( { uniquename => $good_stock_name });
  66         if (!$stock_row) {
  67             print STDERR "Stock $good_stock_name not found. Skipping..\n";
  68             next();
  69         }
  70
  71         my $merge_row = $schema->resultset("Stock::Stock")->find( { uniquename => $merge_stock_name });
  72         if (!$merge_row) {
  73             print STDERR "Stock $merge_stock_name not available for merging. Skipping\n";
  74             next();
  75         }
  76
  77         my $good_stock = CXGN::Chado::Stock->new($schema, $stock_row->stock_id);
  78         my $merge_stock = CXGN::Chado::Stock->new($schema, $merge_row->stock_id);
  79
  80         print STDERR "Merging stock $merge_stock_name into $good_stock_name... ";
  81         $good_stock->merge($merge_stock->get_stock_id(), $delete_merged_stock);
  82         print STDERR "Done.\n";
  83     }
  84
  85 };
  86 if ($@) {
  87     print STDERR "An ERROR occurred ($@). Rolling back changes...\n";
  88     $dbh->rollback();
  89 }
  90 else {
  91     print STDERR "Script is done. Committing... ";
  92     $dbh->commit();
  93     print STDERR "Done.\n";
  94 }