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Adapting replace_plots.pl to get plot id #4774

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Jan 9, 2024
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Adapting replace_plots.pl to get plot id #4774

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14 changes: 9 additions & 5 deletions bin/replace_plots.pl
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Original file line number Diff line number Diff line change
Expand Up @@ -21,7 +21,7 @@ =head1 DESCRIPTION

The infile provided has three columns:

1) the stock_id of the plot that needs to be changed.
1) the plot name that needs to be changed.
2) the stock uniquename as it is in the database that is currently associated
3) the new stock uniquename (needs to be in the database).
4) optional: a new plot name
Expand Down Expand Up @@ -51,6 +51,7 @@ =head1 AUTHOR
use Bio::Chado::Schema;
use CXGN::DB::InsertDBH;
use Try::Tiny;
use SGN::Model::Cvterm;

our ($opt_H, $opt_D, $opt_i, $opt_t);

Expand Down Expand Up @@ -94,13 +95,16 @@ =head1 AUTHOR
for my $row ( 0 .. $row_max ) {

my $plot_name = $worksheet->get_cell($row, 0)->value();
my $plot_id = $worksheet->get_cell($row, 1)->value();
my $db_uniquename = $worksheet->get_cell($row,2)->value();
my $new_uniquename = $worksheet->get_cell($row,3)->value();
my $plot_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'plot', 'stock_type')->cvterm_id();
my $plot_id = $schema->resultset('Stock::Stock')->find({uniquename=>$plot_name, type_id=>$plot_cvterm_id})->stock_id();

# my $plot_id = $worksheet->get_cell($row, 1)->value();
my $db_uniquename = $worksheet->get_cell($row,1)->value();
my $new_uniquename = $worksheet->get_cell($row,2)->value();

my $new_plotname = "";
eval {
$new_plotname = $worksheet->get_cell($row, 4)->value();
$new_plotname = $worksheet->get_cell($row, 3)->value();
};

if ($@) {
Expand Down
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