bin/drone_image_frame_shift_change.pl

   1 #!/usr/bin/perl
   2
   3 =head1
   4
   5 drone_image_frame_shift_change.pl
   6
   7 =head1 SYNOPSIS
   8
   9     load_locations.pl -H [dbhost] -D [dbname] -i [infile] -j [drone run id]
  10
  11 =head1 COMMAND-LINE OPTIONS
  12   ARGUMENTS
  13  -H host name (required) e.g. "localhost"
  14  -D database name (required) e.g. "cxgn_cassava"
  15  -i path to infile (required)
  16  -j drone run project id (required)
  17
  18 =head1 DESCRIPTION
  19
  20 The format is .csv
  21
  22 =head1 AUTHOR
  23
  24  Nicolas Morales (nm529@cornell.edu)
  25
  26 =cut
  27
  28 use strict;
  29
  30 use Getopt::Std;
  31 use Data::Dumper;
  32 use Carp qw /croak/ ;
  33 use Pod::Usage;
  34 use Bio::Chado::Schema;
  35 use CXGN::DB::InsertDBH;
  36 use CXGN::DroneImagery::ImagesSearch;
  37
  38 our ($opt_H, $opt_D, $opt_i, $opt_j);
  39
  40 getopts('H:D:i:j:');
  41
  42 if (!$opt_H || !$opt_D || !$opt_i || !$opt_j) {
  43     pod2usage(-verbose => 2, -message => "Must provide options -H (hostname), -D (database name), -i (input file) \n");
  44 }
  45
  46 my $dbhost = $opt_H;
  47 my $dbname = $opt_D;
  48
  49 my $dbh = CXGN::DB::InsertDBH->new({
  50         dbhost=>$dbhost,
  51         dbname=>$dbname,
  52         dbargs => {AutoCommit => 1, RaiseError => 1}
  53 });
  54
  55 my $schema= Bio::Chado::Schema->connect(  sub { $dbh->get_actual_dbh() } );
  56 $dbh->do('SET search_path TO public,sgn');
  57
  58 my $q = "UPDATE phenome.stock_image SET stock_id = ? WHERE stock_image_id = ?;";
  59 my $q2 = "UPDATE metadata.md_image SET obsolete='t' WHERE image_id = ?;";
  60 my $h = $schema->storage->dbh()->prepare($q);
  61 my $h2 = $schema->storage->dbh()->prepare($q2);
  62
  63 open(my $F, "<", $opt_i) || die " Can't open file $opt_i\n";
  64 while (my $line = <$F>) {
  65     chomp $line;
  66     my @row = split ',', $line;
  67     my $plot_name_old = $row[0];
  68     my $plot_name_new = $row[1];
  69
  70     my $old_plot_id = $schema->resultset("Stock::Stock")->find({uniquename=>$plot_name_old})->stock_id();
  71     #my $new_plot_id = $schema->resultset("Stock::Stock")->find({uniquename=>$plot_name_new})->stock_id();
  72
  73     my $images_search = CXGN::DroneImagery::ImagesSearch->new({
  74         bcs_schema=>$schema,
  75         drone_run_project_id_list=>[$opt_j],
  76         stock_id_list=>[$old_plot_id]
  77     });
  78     my ($result, $total_count) = $images_search->search();
  79
  80     foreach (@$result) {
  81         print STDERR Dumper $_->{drone_run_band_project_name};
  82         print STDERR Dumper $_->{project_image_type_name};
  83         print STDERR Dumper $_->{stock_uniquename};
  84
  85         my $image_id = $_->{image_id};
  86         my $stock_image_id = $_->{stock_image_id};
  87         $h->execute($new_plot_id, $stock_image_id);
  88         #$h2->execute($image_id);
  89     }
  90 }
  91 close($F);
  92
  93 print STDERR "Script Complete.\n";