Merge pull request #3549 from solgenomics/bug/brapi-studies-fixes-add…

…itions

bug/brapi studies fixes additions

db/00139/AddMiscellaneousTrialType.pm

@@ -0,0 +1,84 @@
+#!/usr/bin/env perl
+
+
+=head1 NAME
+
+ AddMiscellaneousTrialType
+
+=head1 SYNOPSIS
+
+mx-run ThisPackageName [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 add a sytem cvterm that is used to store miscellaneous trial types for trials.
+
+This subclass uses L<Moose>. The parent class uses L<MooseX::Runnable>
+
+=head1 AUTHOR
+
+ Chris Tucker<[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 AddMiscellaneousTrialType;
+
+use Moose;
+use Try::Tiny;
+use Bio::Chado::Schema;
+
+extends 'CXGN::Metadata::Dbpatch';
+
+
+has '+description' => ( default => <<'' );
+This patch add a sytem cvterm that is used to store miscellaneous trial types for trials.
+
+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 $new_cvterm = $schema->resultset("Cv::Cvterm")->create_with(
+            {
+                name => 'misc_trial',
+                definition => 'A trial type that holds any trial type',
+                cv   => 'project_type',
+            });
+    };
+
+    try {
+        $schema->txn_do($coderef);
+
+    } catch {
+        die "Load failed! " . $_ .  "\n" ;
+    };
+
+    print "You're done!\n";
+}
+
+####
+1; #
+####

lib/CXGN/BrAPI/v2/ObservationUnits.pm

@@ -598,7 +598,7 @@ sub observationunits_store {
     my $project = $self->bcs_schema->resultset("Project::Project")->find( { project_id => $trial_id });
     my $design_prop =  $project->projectprops->find( { 'type.name' => 'design' },{ join => 'type'}); #there should be only one design prop.
     if (!$design_prop) {
-        return CXGN::BrAPI::JSONResponse->return_error($self->status, sprintf('Study doe not have a proper Study type.'));
+        return CXGN::BrAPI::JSONResponse->return_error($self->status, sprintf('Study does not have a proper Study type.'));
     }
     my $design_type = $design_prop->value;