Add web service for adding organisms to sessions

Refs #1447

lib/Canto/Controller/Curs.pm

@@ -2554,6 +2554,22 @@ sub ws_add_gene : Chained('top') PathPart('ws/gene/add')
   $c->forward('View::JSON');
 }
 
+sub ws_add_organism : Chained('top') PathPart('ws/organism/add')
+{
+  my ($self, $c, $taxonid) = @_;
+
+  my $st = $c->stash();
+  my $schema = $st->{schema};
+
+
+  my $service_utils = Canto::Curs::ServiceUtils->new(curs_schema => $schema,
+                                                     config => $c->config());
+
+  $st->{json_data} = $service_utils->add_organism_by_taxonid($taxonid);
+
+  $c->forward('View::JSON');
+}
+
 sub ws_settings_get_all : Chained('top') PathPart('ws/settings/get_all')
 {
   my ($self, $c) = @_;

lib/Canto/Curs/OrganismManager.pm

@@ -0,0 +1,71 @@
+package Canto::Curs::OrganismManager;
+
+=head1 NAME
+
+Canto::Curs::OrganismManager - Manage adding and removing session organism
+
+=head1 SYNOPSIS
+
+=head1 AUTHOR
+
+Kim Rutherford C<< <kmr44@cam.ac.uk> >>
+
+=head1 BUGS
+
+Please report any bugs or feature requests to C<kmr44@cam.ac.uk>.
+
+=head1 SUPPORT
+
+You can find documentation for this module with the perldoc command.
+
+    perldoc Canto::Curs::OrganismManager
+
+=over 4
+
+=back
+
+=head1 COPYRIGHT & LICENSE
+
+Copyright 2013 Kim Rutherford, all rights reserved.
+
+This program is free software; you can redistribute it and/or modify it
+under the same terms as Perl itself.
+
+=head1 FUNCTIONS
+
+=cut
+
+use Carp;
+use Moose;
+
+use Canto::Track;
+use Canto::CursDB::Organism;
+
+has curs_schema => (is => 'rw', isa => 'Canto::CursDB', required => 1);
+has organism_lookup => (is => 'ro', init_arg => undef, lazy_build => 1);
+
+with 'Canto::Role::Configurable';
+
+sub _build_organism_lookup
+{
+  my $self = shift;
+
+  return Canto::Track::get_adaptor($self->config(), 'organism');
+}
+
+sub add_organism_by_taxonid
+{
+  my $self = shift;
+
+  my $taxonid = shift;
+
+  my $organism_details = $self->organism_lookup->lookup_by_taxonid($taxonid);
+
+  if ($organism_details) {
+    return Canto::CursDB::Organism::get_organism($self->curs_schema(), $taxonid);
+  } else {
+    return undef;
+  }
+}
+
+1;

lib/Canto/Curs/ServiceUtils.pm

@@ -51,13 +51,15 @@ use Canto::Curs::GeneProxy;
 use Canto::Curs::Utils;
 use Canto::Curs::ConditionUtil;
 use Canto::Curs::MetadataStorer;
+use Canto::Curs::OrganismManager;
 
 has curs_schema => (is => 'ro', isa => 'Canto::CursDB', required => 1);
 
 has ontology_lookup => (is => 'ro', init_arg => undef, lazy_build => 1);
 has allele_lookup => (is => 'ro', init_arg => undef, lazy_build => 1);
 has genotype_lookup => (is => 'ro', init_arg => undef, lazy_build => 1);
 has organism_lookup => (is => 'ro', init_arg => undef, lazy_build => 1);
+has organism_manager => (is => 'ro', init_arg => undef, lazy_build => 1);
 
 has state => (is => 'rw', init_arg => undef,
               isa => 'Canto::Curs::State', lazy_build => 1);
@@ -112,6 +114,14 @@ sub _build_organism_lookup
   return Canto::Track::get_adaptor($self->config(), 'organism');
 }
 
+sub _build_organism_manager
+{
+  my $self = shift;
+
+  return Canto::Curs::OrganismManager->new(config => $self->config(),
+                                           curs_schema => $self->curs_schema());
+}
+
 sub _build_curator_manager
 {
   my $self = shift;
@@ -1306,4 +1316,48 @@ sub add_gene_by_identifier
   }
 }
 
+
+=head2 add_organism_by_taxonid
+
+ Usage   : $service_utils->add_organism_by_taxonid($taxonid);
+ Function: Add the given organism to the session
+ Args    : $taxonid
+ Return  : a hash, with keys:
+              status - "success" or "error"
+              message - on error, the error message
+
+=cut
+
+sub add_organism_by_taxonid
+{
+  my $self = shift;
+  my $taxonid = shift;
+
+  my $curs_schema = $self->curs_schema();
+
+  my $organism_manager = $self->organism_manager();
+
+  try {
+    $curs_schema->txn_begin();
+
+    my $organism = $organism_manager->add_organism_by_taxonid($taxonid);
+
+    if ($organism) {
+      $curs_schema->txn_commit();
+      return {
+        status => 'success',
+      };
+    } else {
+      return {
+        status => 'error',
+        message => "organism with taxonid $taxonid not found",
+      };
+    }
+  } catch {
+    $curs_schema->txn_rollback();
+    chomp $_;
+    return _make_error($_);
+  }
+}
+
 1;

t/80_curs_service_utils_organism.t

@@ -1,6 +1,6 @@
 use strict;
 use warnings;
-use Test::More tests => 3;
+use Test::More tests => 8;
 use Test::Deep;
 use JSON;
 
@@ -26,3 +26,15 @@ my $res = $service_utils->list_for_service('organism');
 is (@$res, 1);
 is ($res->[0]->{full_name}, "Schizosaccharomyces pombe");
 is ($res->[0]->{gene_count}, 4);
+
+
+# add an organism
+$service_utils->add_organism_by_taxonid(4932);
+
+$res = $service_utils->list_for_service('organism');
+
+is (@$res, 2);
+is ($res->[0]->{full_name}, "Schizosaccharomyces pombe");
+is ($res->[0]->{gene_count}, 4);
+is ($res->[1]->{full_name}, "Saccharomyces cerevisiae");
+is ($res->[1]->{gene_count}, 0);