lib/SGN/Controller/AJAX/Transgenic.pm

   1 =head1 NAME
   2
   3 SGN::Controller::AJAX::Transgenic - a REST controller class for Vector Constructs.
   4
   5 =head1 DESCRIPTION
   6
   7 Synchronizes transgenic accessions into the database from the ETHZ CASS database.
   8
   9 =head1 AUTHOR
  10
  11 Nicolas Morales <nm529@cornell.edu>
  12
  13 =cut
  14
  15 package SGN::Controller::AJAX::Transgenic;
  16
  17 use Moose;
  18 use JSON -support_by_pp;
  19 use List::MoreUtils qw /any /;
  20 use Data::Dumper;
  21 use JSON;
  22 use SGN::Model::Cvterm;
  23
  24
  25 BEGIN { extends 'Catalyst::Controller::REST' }
  26
  27 __PACKAGE__->config(
  28     default   => 'application/json',
  29     stash_key => 'rest',
  30     map       => { 'application/json' => 'JSON', 'text/html' => 'JSON' },
  31    );
  32
  33
  34 sub sync_cass_transgenics : Path('/ajax/cass_transgenics/sync') Args(0) ActionClass('REST') { }
  35
  36 sub sync_cass_transgenics_POST {
  37     my $self = shift;
  38     my $c = shift;
  39     my $status = '';
  40     my $schema = $c->dbic_schema("Bio::Chado::Schema");
  41
  42     my $transgenic_names = decode_json($c->req->param("data"));
  43     my %transgenic_hash = %$transgenic_names;
  44     my $transgenics = $transgenic_hash{transgenic};
  45     my @transgenics_array = @$transgenics;
  46
  47     my $stock_type_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'accession', 'stock_type')->cvterm_id();
  48     my $stock_prop_type_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'transgenic', 'stock_property')->cvterm_id();
  49
  50     my $create_db = $schema->resultset("General::Db")->find_or_create({
  51         name => 'ETHZ_CASS',
  52         description => 'Internal ETHZ CASS DB',
  53         urlprefix => '',
  54         url => 'https://cass.pb.ethz.ch'
  55     });
  56
  57     foreach (@transgenics_array) {
  58         #print STDERR $_->{construct};
  59         #print STDERR $_->{construct_id};
  60         #print STDERR $_->{level};
  61
  62         my $create_stock = $schema->resultset("Stock::Stock")->find_or_create({
  63             uniquename => $_->{transgenic},
  64             name => $_->{transgenic},
  65             type_id => $stock_type_id,
  66         });
  67
  68         my $create_dbxref = $schema->resultset("General::Dbxref")->find_or_create({
  69                 db_id => $create_db->db_id(),
  70                 accession => $_->{transgenic_id},
  71                 version => 'transgenic',
  72                 description => 'ETHZ_CASS transgenic id'
  73         });
  74
  75         my $create_stock_dbxref = $schema->resultset("Stock::StockDbxref")->find_or_create({
  76                 stock_id => $create_stock->stock_id(),
  77                 dbxref_id => $create_dbxref->dbxref_id()
  78         });
  79
  80         my $create_stock_prop = $schema->resultset("Stock::Stockprop")->find_or_create({
  81                 stock_id => $create_stock->stock_id(),
  82                 type_id => $stock_prop_type_id,
  83                 value => 1
  84         });
  85     }
  86
  87     #print STDERR Dumper $transgenics;
  88     #print STDERR $status;
  89
  90     $c->stash->{rest} = {response=>$status};
  91 }
  92
  93 1;