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 CXGN::Transformation::Transformation;
  16 use CXGN::Transformation::AddTransformant;
  17 use List::MoreUtils qw /any /;
  18
  19
  20 BEGIN { extends 'Catalyst::Controller::REST' }
  21
  22 __PACKAGE__->config(
  23     default   => 'application/json',
  24     stash_key => 'rest',
  25     map       => { 'application/json' => 'JSON', 'text/html' => 'JSON' },
  26    );
  27
  28
  29 sub add_transformation_project : Path('/ajax/transformation/add_transformation_project') : ActionClass('REST') {}
  30
  31 sub add_transformation_project_POST :Args(0){
  32     my ($self, $c) = @_;
  33     my $schema = $c->dbic_schema('Bio::Chado::Schema', 'sgn_chado');
  34     my $dbh = $c->dbc->dbh;
  35     my $project_name = $c->req->param('project_name');
  36     my $breeding_program_id = $c->req->param('project_program_id');
  37     my $location = $c->req->param('project_location');
  38     my $year = $c->req->param('year');
  39     my $project_description = $c->req->param('project_description');
  40     $project_name =~ s/^\s+|\s+$//g;
  41
  42     print STDERR "PROJECT NAME =".Dumper($project_name)."\n";
  43     if (!$c->user()){
  44         $c->stash->{rest} = {error => "You need to be logged in to add a transformation project."};
  45         return;
  46     }
  47
  48     if (!any { $_ eq "curator" || $_ eq "submitter" } ($c->user()->roles)){
  49         $c->stash->{rest} = {error =>  "you have insufficient privileges to add a transformation project." };
  50         return;
  51     }
  52
  53     my $user_id = $c->user()->get_object()->get_sp_person_id();
  54
  55     my $geolocation_lookup = CXGN::Location::LocationLookup->new(schema =>$schema);
  56        $geolocation_lookup->set_location_name($location);
  57        if(!$geolocation_lookup->get_geolocation()){
  58            $c->stash->{rest}={error => "Location not found"};
  59            return;
  60        }
  61
  62     my $error;
  63     eval{
  64         my $add_transformation_project = CXGN::Transformation::AddTransformationProject->new({
  65             chado_schema => $schema,
  66             dbh => $dbh,
  67             breeding_program_id => $breeding_program_id,
  68             year => $year,
  69             project_description => $project_description,
  70             transformation_project_name => $project_name,
  71             nd_geolocation_id => $geolocation_lookup->get_geolocation()->nd_geolocation_id(),
  72             owner_id => $user_id
  73         });
  74
  75         my $return = $add_transformation_project->save_transformation_project();
  76         if ($return->{error}){
  77             $error = $return->{error};
  78         }
  79     };
  80
  81     if ($@) {
  82         $c->stash->{rest} = {error => $@};
  83         return;
  84     };
  85
  86     if ($error){
  87         $c->stash->{rest} = {error => $error};
  88     } else {
  89         $c->stash->{rest} = {success => 1};
  90     }
  91
  92 }
  93
  94
  95 sub add_transformation_identifier : Path('/ajax/transformation/add_transformation_identifier') : ActionClass('REST') {}
  96
  97 sub add_transformation_identifier_POST :Args(0){
  98     my ($self, $c) = @_;
  99     my $schema = $c->dbic_schema('Bio::Chado::Schema', 'sgn_chado');
 100     my $phenome_schema = $c->dbic_schema("CXGN::Phenome::Schema");
 101     my $dbh = $c->dbc->dbh;
 102     my $transformation_identifier = $c->req->param('transformation_identifier');
 103     my $plant_material = $c->req->param('plant_material');
 104     my $vector_construct = $c->req->param('vector_construct');
 105     my $notes = $c->req->param('notes');
 106     my $transformation_project_id = $c->req->param('transformation_project_id');
 107     $transformation_identifier =~ s/^\s+|\s+$//g;
 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} = { success => 0, error => $@ };
 157         print STDERR "An error condition occurred, was not able to create transformation identifier. ($@).\n";
 158         return;
 159     }
 160
 161     $c->stash->{rest} = { success => 1 };
 162
 163 }
 164
 165
 166 sub get_transformations_in_project :Path('/ajax/transformation/transformations_in_project') :Args(1) {
 167     my $self = shift;
 168     my $c = shift;
 169     my $project_id = shift;
 170     my $schema = $c->dbic_schema("Bio::Chado::Schema");
 171     my $dbh = $c->dbc->dbh;
 172
 173     my $transformation_obj = CXGN::Transformation::Transformation->new({schema=>$schema, dbh=>$dbh, project_id=>$project_id});
 174
 175     my $result = $transformation_obj->get_transformations_in_project();
 176 #    print STDERR "RESULT =".Dumper($result)."\n";
 177     my @transformations;
 178     foreach my $r (@$result){
 179         my ($transformation_id, $transformation_name, $plant_id, $plant_name, $vector_id, $vector_name) =@$r;
 180         push @transformations, [qq{<a href="/transformation/$transformation_id">$transformation_name</a>}, qq{<a href="/stock/$plant_id/view">$plant_name</a>}, qq{<a href="/stock/$vector_id/view">$vector_name</a>},'' , ''];
 181     }
 182
 183     $c->stash->{rest} = { data => \@transformations };
 184
 185 }
 186
 187
 188 sub add_transformants : Path('/ajax/transformation/add_transformants') : ActionClass('REST') {}
 189
 190 sub add_transformants_POST :Args(0){
 191     my ($self, $c) = @_;
 192     my $schema = $c->dbic_schema('Bio::Chado::Schema', 'sgn_chado');
 193     my $phenome_schema = $c->dbic_schema("CXGN::Phenome::Schema");
 194     my $dbh = $c->dbc->dbh;
 195     my $transformation_name = $c->req->param('transformation_name');
 196     my $transformation_stock_id = $c->req->param('transformation_stock_id');
 197     my $new_name_count = $c->req->param('new_name_count');
 198     print STDERR "TRANSFORMATION NAME =".Dumper($transformation_name)."\n";
 199     print STDERR "COUNT =".Dumper($new_name_count)."\n";
 200
 201     if (!$c->user()){
 202         $c->stash->{rest} = {error => "You need to be logged in to add new transformants."};
 203         return;
 204     }
 205
 206     if (!any { $_ eq "curator" || $_ eq "submitter" } ($c->user()->roles)){
 207         $c->stash->{rest} = {error =>  "you have insufficient privileges to add new transformants." };
 208         return;
 209     }
 210
 211     my $user_id = $c->user()->get_object()->get_sp_person_id();
 212     my $start_number = 1;
 213     my $basename = $transformation_name.'_T';
 214     my @new_transformant_names = ();
 215     foreach my $n (1..$new_name_count) {
 216         push @new_transformant_names, $basename. (sprintf "%04d", $n + $start_number -1);
 217     }
 218
 219     foreach my $new_name (@new_transformant_names) {
 220         my $validate_new_name_rs = $schema->resultset("Stock::Stock")->search({uniquename=> $new_name});
 221         if ($validate_new_name_rs->count() > 0) {
 222             $c->stash->{rest} = {error_string => "Error creating new transformant name",};
 223             return;
 224         }
 225     }
 226
 227     eval {
 228         my $add_transformants = CXGN::Transformation::AddTransformant->new({
 229             schema => $schema,
 230             phenome_schema => $phenome_schema,
 231             dbh => $dbh,
 232             transformation_stock_id => $transformation_stock_id,
 233             transformant_names => \@new_transformant_names,
 234             owner_id => $user_id,
 235         });
 236
 237         $add_transformants->add_transformant();
 238     };
 239
 240     if ($@) {
 241         $c->stash->{rest} = { success => 0, error => $@ };
 242         print STDERR "An error condition occurred, was not able to create transformation identifier. ($@).\n";
 243         return;
 244     }
 245
 246     $c->stash->{rest} = { success => 1 };
 247
 248 }
 249
 250
 251
 252 ###
 253 1;#
 254 ###