lib/SGN/Controller/AJAX/Transformation.pm

   1 package SGN::Controller::AJAX::Transformation;
   2
   3 use Moose;
   4 use Data::Dumper;
   5 use JSON;
   6 use CXGN::People::Person;
   7 use SGN::Image;
   8 use CXGN::Stock::StockLookup;
   9 use CXGN::Location::LocationLookup;
  10 use SGN::Model::Cvterm;
  11 use CXGN::List::Validate;
  12 use CXGN::List;
  13 use CXGN::Transformation::AddTransformationProject;
  14 use CXGN::Transformation::AddTransformationIdentifier;
  15 use List::MoreUtils qw /any /;
  16
  17
  18 BEGIN { extends 'Catalyst::Controller::REST' }
  19
  20 __PACKAGE__->config(
  21     default   => 'application/json',
  22     stash_key => 'rest',
  23     map       => { 'application/json' => 'JSON', 'text/html' => 'JSON' },
  24    );
  25
  26
  27 sub add_transformation_project : Path('/ajax/transformation/add_transformation_project') : ActionClass('REST') {}
  28
  29 sub add_transformation_project_POST :Args(0){
  30     my ($self, $c) = @_;
  31     my $schema = $c->dbic_schema('Bio::Chado::Schema', 'sgn_chado');
  32     my $dbh = $c->dbc->dbh;
  33     my $project_name = $c->req->param('project_name');
  34     my $breeding_program_id = $c->req->param('project_program_id');
  35     my $location = $c->req->param('project_location');
  36     my $year = $c->req->param('year');
  37     my $project_description = $c->req->param('project_description');
  38     $project_name =~ s/^\s+|\s+$//g;
  39
  40     print STDERR "PROJECT NAME =".Dumper($project_name)."\n";
  41     if (!$c->user()){
  42         $c->stash->{rest} = {error => "You need to be logged in to add a transformation project."};
  43         return;
  44     }
  45
  46     if (!any { $_ eq "curator" || $_ eq "submitter" } ($c->user()->roles)){
  47         $c->stash->{rest} = {error =>  "you have insufficient privileges to add a transformation project." };
  48         return;
  49     }
  50
  51     my $user_id = $c->user()->get_object()->get_sp_person_id();
  52
  53     my $geolocation_lookup = CXGN::Location::LocationLookup->new(schema =>$schema);
  54        $geolocation_lookup->set_location_name($location);
  55        if(!$geolocation_lookup->get_geolocation()){
  56            $c->stash->{rest}={error => "Location not found"};
  57            return;
  58        }
  59
  60     my $error;
  61     eval{
  62         my $add_transformation_project = CXGN::Transformation::AddTransformationProject->new({
  63             chado_schema => $schema,
  64             dbh => $dbh,
  65             breeding_program_id => $breeding_program_id,
  66             year => $year,
  67             project_description => $project_description,
  68             transformation_project_name => $project_name,
  69             nd_geolocation_id => $geolocation_lookup->get_geolocation()->nd_geolocation_id(),
  70             owner_id => $user_id
  71         });
  72
  73         my $return = $add_transformation_project->save_transformation_project();
  74         if ($return->{error}){
  75             $error = $return->{error};
  76         }
  77     };
  78
  79     if ($@) {
  80         $c->stash->{rest} = {error => $@};
  81         return;
  82     };
  83
  84     if ($error){
  85         $c->stash->{rest} = {error => $error};
  86     } else {
  87         $c->stash->{rest} = {success => 1};
  88     }
  89
  90 }
  91
  92
  93 sub add_transformation_identifier : Path('/ajax/transformation/add_transformation_identifier') : ActionClass('REST') {}
  94
  95 sub add_transformation_identifier_POST :Args(0){
  96     my ($self, $c) = @_;
  97     my $schema = $c->dbic_schema('Bio::Chado::Schema', 'sgn_chado');
  98     my $phenome_schema = $c->dbic_schema("CXGN::Phenome::Schema");
  99     my $dbh = $c->dbc->dbh;
 100     my $transformation_identifier = $c->req->param('transformation_identifier');
 101     my $plant_material = $c->req->param('plant_material');
 102     my $vector_construct = $c->req->param('vector_construct');
 103     my $notes = $c->req->param('notes');
 104     my $transformation_project_id = $c->req->param('transformation_project_id');
 105     $transformation_identifier =~ s/^\s+|\s+$//g;
 106
 107     print STDERR "TRANSFORMATION IDENTIFIER =".Dumper($transformation_identifier)."\n";
 108
 109     if (!$c->user()){
 110         $c->stash->{rest} = {error => "You need to be logged in to add a transformation transformation identifier."};
 111         return;
 112     }
 113
 114     if (!any { $_ eq "curator" || $_ eq "submitter" } ($c->user()->roles)){
 115         $c->stash->{rest} = {error =>  "you have insufficient privileges to add a transformation identifier." };
 116         return;
 117     }
 118
 119     my $user_id = $c->user()->get_object()->get_sp_person_id();
 120
 121     my $accession_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($schema,'accession', 'stock_type')->cvterm_id();
 122     my $vector_construct_cvterm_id = SGN::Model::Cvterm->get_cvterm_row($schema,'vector_construct', 'stock_type')->cvterm_id();
 123
 124     if ($schema->resultset("Stock::Stock")->find({uniquename => $transformation_identifier})){
 125         $c->stash->{rest} = {error =>  "Transformation identifier already exists." };
 126         return 0;
 127     }
 128
 129     if (! $schema->resultset("Stock::Stock")->find({uniquename => $plant_material, type_id => $accession_cvterm_id })){
 130         $c->stash->{rest} = {error =>  "Plant material does not exist or does not exist as accession uniquename." };
 131         return;
 132     }
 133
 134     if (! $schema->resultset("Stock::Stock")->find({uniquename => $vector_construct, type_id => $vector_construct_cvterm_id })){
 135         $c->stash->{rest} = {error =>  "vector construct does not exist or does not exist as vector construct uniquename." };
 136         return;
 137     }
 138
 139     eval {
 140         my $add_transformation = CXGN::Transformation::AddTransformationIdentifier->new({
 141             chado_schema => $schema,
 142             phenome_schema => $phenome_schema,
 143             dbh => $dbh,
 144             transformation_project_id => $transformation_project_id,
 145             transformation_identifier => $transformation_identifier,
 146             plant_material => $plant_material,
 147             vector_construct => $vector_construct,
 148             notes => $notes,
 149             owner_id => $user_id,
 150         });
 151
 152         $add_transformation->add_transformation_identifier();
 153     };
 154
 155     if ($@) {
 156         $c->stash->{rest} = { error => "An error occurred: $@"};
 157         return 0;
 158     }
 159     return 1;
 160
 161 }
 162
 163
 164
 165 ###
 166 1;#
 167 ###