Remove field fillers

db/00204/AddFillerPlotStockprop.pm

@@ -0,0 +1,83 @@
+#!/usr/bin/env perl
+
+
+=head1 NAME
+
+ AddFillerPlotStockprop.pm
+
+=head1 SYNOPSIS
+
+mx-run AddFillerPlotStockprop [options] -H hostname -D dbname -u username [-F]
+
+this is a subclass of L<CXGN::Metadata::Dbpatch>
+see the perldoc of parent class for more details.
+
+=head1 DESCRIPTION
+
+This is a test dummy patch.
+This subclass uses L<Moose>. The parent class uses L<MooseX::Runnable>
+
+=head1 AUTHOR
+
+ Ben Maza <bm743@cornell.edu>
+
+=head1 COPYRIGHT & LICENSE
+
+Copyright 2010 Boyce Thompson Institute for Plant Research
+
+This program is free software; you can redistribute it and/or modify
+it under the same terms as Perl itself.
+
+=cut
+
+
+package AddFillerPlotStockprop;
+
+use Moose;
+use Bio::Chado::Schema;
+use Try::Tiny;
+extends 'CXGN::Metadata::Dbpatch';
+
+
+has '+description' => ( default => <<'' );
+This patch will find_or_create a cvterm for plots
+
+has '+prereq' => (
+    default => sub {
+        [],
+    },
+  );
+
+sub patch {
+    my $self=shift;
+
+    print STDOUT "Executing the patch:\n " .   $self->name . ".\n\nDescription:\n  ".  $self->description . ".\n\nExecuted by:\n " .  $self->username . " .";
+
+    print STDOUT "\nChecking if this db_patch was executed before or if previous db_patches have been executed.\n";
+
+    print STDOUT "\nExecuting the SQL commands.\n";
+
+    my $schema = Bio::Chado::Schema->connect( sub { $self->dbh->clone } );
+
+    my $coderef = sub {
+
+        my $plot_stockprop_filler_plot_cvterm = $schema->resultset("Cv::Cvterm")->create_with({
+            name => 'filler_plot', 
+            cv   => 'stock_property',
+        });
+    };
+
+    try {
+        $schema->txn_do($coderef);
+
+    } catch {
+        die "Load failed! " . $_ .  "\n" ;
+    };
+
+    print "You're done!\n";
+}
+
+
+####
+1; #
+####

js/source/entries/fieldmap.js

@@ -83,6 +83,7 @@ export function init() {
             for (let plot of this.plot_arr.filter((plot) => plot.type == "filler")) {
                 brapi_post_plots.push({
                     additionalInfo: {
+                        filler_plot: 1,
                         invert_row_checkmark: document.getElementById(
                             "invert_row_checkmark"
                         ).checked,

lib/CXGN/Trial/TrialDesignStore/AbstractTrial.pm

@@ -417,6 +417,7 @@ sub store {
     my $stock_rel_type_id = $self->get_stock_relationship_type_id();
     my $additional_info_type_id = SGN::Model::Cvterm->get_cvterm_row($chado_schema, 'stock_additional_info', 'stock_property')->cvterm_id();
     my $intercrop_rel_type_id = SGN::Model::Cvterm->get_cvterm_row($chado_schema, 'intercrop_plot_of', 'stock_relationship')->cvterm_id();
+    my $filler_plot_cvterm_id = SGN::Model::Cvterm->get_cvterm_row( $chado_schema, 'filler_plot', 'stock_property' )->cvterm_id();
 
     my @source_stock_types = @{$self->get_source_stock_types()};
 
@@ -630,6 +631,8 @@ sub store {
             }
             my $additional_info = $design{$key}->{additional_info} ? encode_json $design{$key}->{additional_info} : undef;
 
+            my $is_filler = $design{$key}->{additional_info}->{filler_plot};
+
             my $facility_identifier;
             if ($design{$key}->{facility_identifier}) {
                 $facility_identifier = $design{$key}->{facility_identifier};
@@ -721,6 +724,10 @@ sub store {
                     push @plot_stock_props, { type_id => $self->get_facility_identifier_cvterm_id, value => $facility_identifier };
                 }
 
+                if ($is_filler) {
+                    push @plot_stock_props, { type_id => $filler_plot_cvterm_id, value => $is_filler };
+                }
+
                 my @plot_subjects;
                 my @plot_objects;
 

lib/SGN/Controller/AJAX/TrialMetadata.pm

@@ -2528,6 +2528,71 @@ sub trial_plots : Chained('trial') PathPart('plots') Args(0) {
     $c->stash->{rest} = { plots => \@data };
 }
 
+sub remove_filler_plots : Chained('trial') PathPart('remove_fillers') Args(0) {
+    my $self = shift;
+    my $c = shift;
+    my $sp_person_id = $c->user() ? $c->user->get_object()->get_sp_person_id() : undef;
+    my $schema = $c->dbic_schema("Bio::Chado::Schema", undef, $sp_person_id);
+    my $trial = $c->stash->{trial};
+    my $trial_id = $c->stash->{trial_id};
+
+    my $stocks_rs = $schema->resultset('Stock::Stock')->search(
+        {
+            'project.project_id' => $trial_id,
+            'stockprops.type_id' => SGN::Model::Cvterm->get_cvterm_row(
+                $schema,
+                'filler_plot',
+                'stock_property'
+            )->cvterm_id(),
+        },
+        {
+            join => [
+                {
+                    nd_experiment_stocks => {
+                        nd_experiment => {
+                            nd_experiment_projects => 'project'
+                        }
+                    }
+                },
+                'stockprops'
+            ],
+            distinct => 1,
+        }
+    );
+
+    my @stock_ids = $stocks_rs->get_column('stock_id')->all;
+
+    my $trial_layout_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($schema, 'trial_layout_json', 'project_property')->cvterm_id();
+
+    if (@stock_ids) {
+        $schema->resultset('Stock::Stock')->search({
+            stock_id => { -in => \@stock_ids }
+        })->delete;
+
+        my $pp_rs = $schema->resultset('Project::Projectprop')->search({
+            project_id => $trial_id,
+            type_id    => $trial_layout_cvterm_id,
+        });
+
+        while (my $row = $pp_rs->next) {
+            my $layout = decode_json($row->value);
+
+            # Remove filler plot numbers from projectprop.value json
+            my %filler_ids = map { $_ => 1 } @stock_ids;
+
+            foreach my $plot_number (keys %$layout) {
+                if ($filler_ids{ $layout->{$plot_number}->{plot_id} }) {
+                    delete $layout->{$plot_number};
+                }
+            }
+
+            $row->value(encode_json($layout));
+            $row->update;
+        }
+    }
+    $c->stash->{rest} = { success => 1, deleted => scalar(@stock_ids) };
+}
+
 sub trial_has_data_levels : Chained('trial') PathPart('has_data_levels') Args(0) {
     my $self = shift;
     my $c = shift;

mason/breeders_toolbox/trial/phenotype_heatmap.mas

@@ -226,6 +226,7 @@ $trial_stock_type => undef
         <div class="interactive_fieldmap_buttons">
             <button type="button" class="btn btn-primary fieldmap_edit" id="transpose_fieldmap">Transpose</button>
             <button type="button" class="btn btn-primary fieldmap_edit" id="change_dimensions_button">Change Dimensions</button>
+            <button type="button" class="btn btn-primary fieldmap_edit" id ="remove_fillers">Remove Filler Plots</button>
             <button type="button" id="print_fieldmap" name="print_fieldmap" class="btn btn-primary fieldmap_edit">Print Fieldmap</button>
             <button type="button" id="submit_fieldmap" name="submit_fieldmap" class="btn btn-success fieldmap_edit">Submit Field Layout</button>
         </div>
@@ -703,6 +704,28 @@ $trial_stock_type => undef
     </div>
 </div>
 
+<div class="modal  fade" id="delete_filler_plots_confirm_message" name="delete_filler_dialog_confirm_message" tabindex="-1" role="dialog" aria-labelledby="DeleteFillerPlotsDialog">
+    <div class="modal-dialog " role="document">
+        <div class="modal-content">
+            <div class="modal-header" style="text-align: center">
+                <button type="button" class="close" data-dismiss="modal" aria-label="Close"><span aria-hidden="true">&times;</span></button>
+                <h4 class="modal-title" id="DeleteFillerPlotsDialog">Remove Filler Plots</h4>
+            </div>
+            <div class="modal-body">
+                <div class="container-fluid">
+
+                    <p3>This will remove all filler plots in this trial. Do you want to continue?</p3> </br></br>
+
+                </div>
+            </div>
+            <div class="modal-footer">
+                <button id="close_delete_filler_dialog" type="button" class="btn btn-default" data-dismiss="modal">Cancel</button>
+                <button type="button" class="btn btn-primary" name="delete_filler_plots_dialog_submit" id="remove_filler_plots_dialog_submit">Remove Fillers</button>
+            </div>
+        </div>
+    </div>
+</div>
+
 <%perl>
 my $dbh = $stockref->{dbh};
 my $image_ids =  $stockref->{image_ids} || [] ;
@@ -1053,6 +1076,38 @@ jQuery(document).ready( function() {
         }
     })
 
+    jQuery("#remove_fillers").click(function() {
+        jQuery('#delete_filler_plots_confirm_message').modal("show");
+    });
+
+    jQuery("#remove_filler_plots_dialog_submit").click(function() {
+        remove_fillers();
+    });
+
+    function remove_fillers() {
+        jQuery.ajax({
+            url: '/ajax/breeders/trial/<% $trial_id %>/remove_fillers',
+            type: "POST",
+            dataType: "json",
+            beforeSend: function(){
+                jQuery('#delete_filler_plots_confirm_message').modal("hide");
+                jQuery("#working_modal").modal("show");
+            },
+            success: function(response) {
+                if (response.success) {
+                    alert(`Removed ${response.deleted} filler plot(s)`);
+                    location.reload();
+                } else {
+                    alert("Failed to remove filler plots");
+                }
+            },
+            error: function(err) {
+                console.error(err);
+                alert("Error removing filler plots");
+            }
+        });
+    }
+
     jQuery("#border_accession_form").submit( function() {
         event.preventDefault();
     });