Merge pull request #5191 from solgenomics/topic/quality_control

Phenotype Quality Control

db/00187/AddBreederRole.pm

@@ -0,0 +1,77 @@
+#!/usr/bin/env perl
+
+
+=head1 NAME
+
+AddBreederRole
+
+=head1 SYNOPSIS
+
+mx-run AddBreederRole [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 patch adds vendor role on sgn_people.sp_roles
+
+This subclass uses L<Moose>. The parent class uses L<MooseX::Runnable>
+
+=head1 AUTHOR
+
+ Chris Simoes < [email protected] >
+
+=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 AddBreederRole;
+
+use Moose;
+
+extends 'CXGN::Metadata::Dbpatch';
+
+
+has '+description' => ( default => <<'' );
+This patch adds vendor role on sgn_people.sp_roles
+
+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";
+
+
+
+   $self->dbh->do(<<EOSQL);
+--do your SQL here
+--
+INSERT INTO sgn_people.sp_roles(name) VALUES ('breeder');
+
+EOSQL
+
+
+    print "You're done!\n";
+
+}
+
+
+####
+1; #
+####

db/00187/AddValidatePhenotypeCvterm.pm

@@ -0,0 +1,86 @@
+#!/usr/bin/env perl
+
+
+=head1 NAME
+
+ AddValidatePhenotypeCvterm
+
+=head1 SYNOPSIS
+
+mx-run AddValidadePhenotypeCvterm [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 patch adds phenotype_property cvterm for storing a suppressed plot phenotype.
+This subclass uses L<Moose>. The parent class uses L<MooseX::Runnable>
+
+=head1 AUTHOR
+
+Chris Simoes <[email protected]>
+
+=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 AddValidatePhenotypeCvterm;
+
+use Moose;
+use Bio::Chado::Schema;
+use Try::Tiny;
+extends 'CXGN::Metadata::Dbpatch';
+
+
+has '+description' => ( default => <<'' );
+This patch adds phenotype_property cvterm for storing a suppressed plot phenotype.
+
+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 } );
+
+
+    print STDERR "INSERTING CV TERMS...\n";
+
+    my $terms = {
+        'project_property' => [
+            'validated_phenotype',
+        ]
+    };
+
+	foreach my $t (keys %$terms){
+		foreach (@{$terms->{$t}}){
+			$schema->resultset("Cv::Cvterm")->create_with({
+				name => $_,
+				cv => $t
+			});
+		}
+	}
+
+
+print "You're done!\n";
+}
+
+
+####
+1; #
+####

js/source/entries/mixedmodels.js

@@ -103,10 +103,12 @@ export function init(main_div) {
     $('#mixed_model_analysis_prepare_button').click(function () {
 
         dataset_id = get_dataset_id();
+        var dataset_trait_outliers = $('#dataset_trait_outliers').is(':checked') ? 1 : 0;
+
         if (dataset_id != false) {
             $.ajax({
                 url: '/ajax/mixedmodels/prepare',
-                data: { 'dataset_id': get_dataset_id() },
+                data: { 'dataset_id': get_dataset_id(),'dataset_trait_outliers': dataset_trait_outliers, },
                 success: function (r) {
                     if (r.error) {
                         alert(r.error);