bin/transfer_genome_project_info.pl

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   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 use CXGN::Stock::SequencingInfo;
  15
  16 our ($opt_H, $opt_D);
  17
  18 getopts('H:D:');
  19
  20 if (!$opt_H || !$opt_D ) {
  21     pod2usage(-verbose => 2, -message => "Must provide options -H (hostname), -D (database name), -i (input file) \n");
  22 }
  23
  24 my $dbhost = $opt_H;
  25 my $dbname = $opt_D;
  26
  27 my $dbh = CXGN::DB::InsertDBH->new({
  28         dbhost=>$dbhost,
  29         dbname=>$dbname,
  30         dbargs => {AutoCommit => 1, RaiseError => 1}
  31 });
  32
  33 my $schema= Bio::Chado::Schema->connect(  sub { $dbh->get_actual_dbh() });
  34
  35 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')";
  36
  37 my $h = $dbh->prepare($q);
  38 $h->execute();
  39
  40 while (my ($organismprop_id, $organism_id, $type_id, $value)= $h->fetchrow_array()) {
  41     my $data = JSON::Any->decode($value);
  42
  43     my $row = $schema->resultset("Stock::Stock")->find( { organism_id => $organism_id, uniquename => $data->{genome_project_sequenced_accessions} });
  44
  45     if ($row) {
  46         print STDERR "accession $data->{genome_project_sequenced_accessions} FOUND in database!!!!\n";
  47         my $si = CXGN::Stock::SequencingInfo->new( { schema => $schema });
  48
  49         $si->funded_by($data->{genome_project_funding_agencies});
  50         $si->contact_email($data->{genome_project_contact_person});
  51         $si->organization($data->{genome_project_sequencing_center});
  52         $si->sequencing_year($data->{genome_project_dates});
  53         $si->genbank_accession($data->{genome_project_genbank_link});
  54         $si->website($data->{genome_project_url});
  55         $si->stock_id($row->stock_id());
  56         $si->store();
  57
  58     }
  59     else {
  60         print STDERR "accession $data->{genome_project_sequenced_accessions} ***NOT*** FOUND in database!!!!\n";
  61
  62     }
  63 }