bin/transfer_genome_project_info.pl

   1
   2
   3
   4 ####   {"genome_project_funding_agencies":"TraitGenetics Inc.","genome_project_contact_person":"Martin Ganal, ganal@traitgenetics.de","genome_project_sequencing_center":"TraitGenetics","genome_project_dates":"2012","genome_project_genbank_link":"","genome_project_url":"traitgenetics.com","genome_project_sequenced_accessions":"Ailsa Craig"}
   5
   6 use strict;
   7
   8 use Getopt::Std;
   9 use Data::Dumper;
  10 use Pod::Usage;
  11 use Bio::Chado::Schema;
  12 use CXGN::DB::InsertDBH;
  13 use JSON::Any;
  14
  15 our ($opt_H, $opt_D, $opt_i);
  16
  17 getopts('H:D:i:');
  18
  19 if (!$opt_H || !$opt_D ) {
  20     pod2usage(-verbose => 2, -message => "Must provide options -H (hostname), -D (database name), -i (input file) \n");
  21 }
  22
  23 my $dbhost = $opt_H;
  24 my $dbname = $opt_D;
  25
  26 my $dbh = CXGN::DB::InsertDBH->new({
  27         dbhost=>$dbhost,
  28         dbname=>$dbname,
  29         dbargs => {AutoCommit => 1, RaiseError => 1}
  30 });
  31
  32 my $schema= Bio::Chado::Schema->connect(  sub { $dbh->get_actual_dbh() });
  33
  34 my $q = "SELECT organismprop_id, organism_id, type_id, value from organismprop where type_id=(SELECT cvterm_id FROM cvterm where name='organism_sequencing_metadata')";
  35
  36 my $h = $dbh->prepare($q);
  37 $h->execute();
  38
  39 while (my ($organismprop_id, $organism_id, $type_id, $value)= $h->fetchrow_array()) {
  40     my $data = JSON::Any->decode($value);
  41
  42     my $row = $schema->resultset("Stock::Stock")->find( { organism_id => $organism_id, uniquename => $data->{genome_project_sequenced_accessions} });
  43
  44     if ($row) {
  45         print STDERR "accession $data->{genome_project_sequenced_accessions} FOUND in database!!!!\n";
  46         my $si = CXGN::Stock::SequencingInfo->new( { schema => $schema });
  47
  48         $si->funded_by($data->{genome_project_funding_agencies});
  49         $si->contact_email($data->{genome_project_contact_person});
  50         $si->organization($data->{genome_project_sequencing_center});
  51         $si->sequencing_year($data->{genome_project_dates});
  52         $si->genbank_accession($data->{genome_project_genbank_link});
  53         $si->website($data->{genome_project_url});
  54         $si->stock_id($row->stock_id());
  55         $si->store();
  56
  57     }
  58     else {
  59         print sTDERR "accession $data->{genome_project_sequenced_accessions} ***NOT*** FOUND in database!!!!\n";
  60
  61     }
  62 }