lib/SGN/Controller/AJAX/GenotypingTrial.pm

   1
   2 package SGN::Controller::AJAX::GenotypingTrial;
   3
   4 use Moose;
   5 use JSON;
   6 use Data::Dumper;
   7 use CXGN::Trial::TrialDesign;
   8 use Try::Tiny;
   9 use List::MoreUtils qw /any /;
  10 use CXGN::People::Person;
  11 use CXGN::Login;
  12
  13 BEGIN { extends 'Catalyst::Controller::REST' }
  14
  15 __PACKAGE__->config(
  16     default   => 'application/json',
  17     stash_key => 'rest',
  18     map       => { 'application/json' => 'JSON', 'text/html' => 'JSON' },
  19 );
  20
  21 sub generate_genotype_trial : Path('/ajax/breeders/generategenotypetrial') ActionClass('REST') {}
  22 sub generate_genotype_trial_POST : Args(0) {
  23     my $self = shift;
  24     my $c = shift;
  25
  26     if (!($c->user()->check_roles('curator') || $c->user()->check_roles('submitter'))) {
  27         $c->stash->{rest} = { error => 'You do not have the required privileges to create a genotyping trial.' };
  28         $c->detach();
  29     }
  30
  31     my $schema = $c->dbic_schema("Bio::Chado::Schema");
  32     my $plate_info = decode_json $c->req->param("plate_data");
  33     print STDERR Dumper $plate_info;
  34
  35     if ( !$plate_info->{elements} || !$plate_info->{genotyping_facility_submit} || !$plate_info->{project_name} || !$plate_info->{description} || !$plate_info->{location} || !$plate_info->{year} || !$plate_info->{name} || !$plate_info->{breeding_program} || !$plate_info->{genotyping_facility} || !$plate_info->{sample_type} || !$plate_info->{plate_format} ) {
  36         $c->stash->{rest} = { error => "Please provide all parameters in the plate information section" };
  37         $c->detach();
  38     }
  39
  40     if ( $plate_info->{genotyping_facility} eq 'igd' && $plate_info->{genotyping_facility_submit} eq 'yes' && $plate_info->{blank_well} eq ''){
  41         $c->stash->{rest} = { error => "To submit to Cornell IGD you need to provide the blank well!" };
  42         $c->detach();
  43     }
  44
  45     my $location = $schema->resultset("NaturalDiversity::NdGeolocation")->find( { nd_geolocation_id => $plate_info->{location} } );
  46     if (!$location) {
  47         $c->stash->{rest} = { error => "Unknown location" };
  48         $c->detach();
  49     }
  50
  51     my $breeding_program = $schema->resultset("Project::Project")->find( { project_id => $plate_info->{breeding_program} });
  52     if (!$breeding_program) {
  53         $c->stash->{rest} = { error => "Unknown breeding program" };
  54         $c->detach();
  55     }
  56
  57     my $td = CXGN::Trial::TrialDesign->new( { schema => $schema });
  58
  59     $td->set_stock_list($plate_info->{elements});
  60     $td->set_block_size($plate_info->{plate_format});
  61     $td->set_blank($plate_info->{blank_well});
  62     $td->set_trial_name($plate_info->{name});
  63     $td->set_design_type("genotyping_plate");
  64
  65     eval {
  66         $td->calculate_design();
  67     };
  68
  69     if ($@) {
  70         $c->stash->{rest} = { error => "Design failed. Error: $@" };
  71         print STDERR "Design failed because of $@\n";
  72         $c->detach();
  73     }
  74
  75     my $design = $td->get_design();
  76
  77     if (exists($design->{error})) {
  78         $c->stash->{rest} = $design;
  79         $c->detach();
  80     }
  81
  82     #Add common answers from form to all wells
  83     foreach (values %$design){
  84         $_->{concentration} = $plate_info->{well_concentration};
  85         $_->{volume} = $plate_info->{well_volume};
  86         $_->{tissue_type} = $plate_info->{well_tissue};
  87         $_->{dna_person} = $plate_info->{well_dna_person};
  88         $_->{extraction} = $plate_info->{well_extraction};
  89         $_->{acquisition_date} = $plate_info->{well_date};
  90         $_->{notes} = $plate_info->{well_notes};
  91         $_->{ncbi_taxonomy_id} = $plate_info->{ncbi_taxonomy_id};
  92     }
  93     #print STDERR Dumper($design);
  94
  95     $c->stash->{rest} = {success => 1, design=>$design};
  96 }
  97
  98
  99 sub parse_genotype_trial_file : Path('/ajax/breeders/parsegenotypetrial') : ActionClass('REST') { }
 100 sub parse_genotype_trial_file_POST : Args(0) {
 101     my ($self, $c) = @_;
 102
 103     my $chado_schema = $c->dbic_schema('Bio::Chado::Schema', 'sgn_chado');
 104     my $metadata_schema = $c->dbic_schema("CXGN::Metadata::Schema");
 105     my $phenome_schema = $c->dbic_schema("CXGN::Phenome::Schema");
 106     my $dbh = $c->dbc->dbh;
 107     my $upload_xls = $c->req->upload('genotyping_trial_layout_upload');
 108     my $upload_coordinate = $c->req->upload('genotyping_trial_layout_upload_coordinate');
 109     if ($upload_xls && $upload_coordinate){
 110         $c->stash->{rest} = {error => "Do not upload both XLS and Coordinate file at the same time!" };
 111         return;
 112     }
 113     if (!$upload_xls && !$upload_coordinate){
 114         $c->stash->{rest} = {error => "You must upload a genotyping trial file!" };
 115         return;
 116     }
 117     my $parser;
 118     my $parsed_data;
 119     my $upload;
 120     my $upload_type;
 121     if ($upload_xls){
 122         $upload = $upload_xls;
 123         $upload_type = 'GenotypeTrialXLS';
 124     }
 125     if ($upload_coordinate){
 126         $upload = $upload_coordinate;
 127         $upload_type = 'GenotypeTrialCoordinate';
 128     }
 129     my $upload_original_name = $upload->filename();
 130     my $upload_tempfile = $upload->tempname;
 131     my $subdirectory = "genotyping_trial_upload";
 132     my $archived_filename_with_path;
 133     my $md5;
 134     my $validate_file;
 135     my $parsed_file;
 136     my $parse_errors;
 137     my %parsed_data;
 138     my %upload_metadata;
 139     my $time = DateTime->now();
 140     my $timestamp = $time->ymd()."_".$time->hms();
 141     my $error;
 142
 143     if ($upload_original_name =~ /\s/ || $upload_original_name =~ /\// || $upload_original_name =~ /\\/ ) {
 144         print STDERR "File name must not have spaces or slashes.\n";
 145         $c->stash->{rest} = {error => "Uploaded file name must not contain spaces or slashes." };
 146         return;
 147     }
 148
 149     my $user_id;
 150     my $user_name;
 151     my $user_role;
 152     my $session_id = $c->req->param("sgn_session_id");
 153
 154     if ($session_id){
 155         my $dbh = $c->dbc->dbh;
 156         my @user_info = CXGN::Login->new($dbh)->query_from_cookie($session_id);
 157         if (!$user_info[0]){
 158             $c->stash->{rest} = {error=>'You must be logged in to upload genotyping trial!'};
 159             $c->detach();
 160         }
 161         $user_id = $user_info[0];
 162         $user_role = $user_info[1];
 163         my $p = CXGN::People::Person->new($dbh, $user_id);
 164         $user_name = $p->get_username;
 165     } else{
 166         if (!$c->user){
 167             $c->stash->{rest} = {error=>'You must be logged in to upload a genotyping trial!'};
 168             $c->detach();
 169         }
 170         $user_id = $c->user()->get_object()->get_sp_person_id();
 171         $user_name = $c->user()->get_object()->get_username();
 172         $user_role = $c->user->get_object->get_user_type();
 173     }
 174
 175     if ($user_role ne 'curator' && $user_role ne 'submitter') {
 176         $c->stash->{rest} = {error =>  "You have insufficient privileges to upload a genotyping trial." };
 177         $c->detach();
 178     }
 179
 180     ## Store uploaded temporary file in archive
 181     my $uploader = CXGN::UploadFile->new({
 182         tempfile => $upload_tempfile,
 183         subdirectory => $subdirectory,
 184         archive_path => $c->config->{archive_path},
 185         archive_filename => $upload_original_name,
 186         timestamp => $timestamp,
 187         user_id => $user_id,
 188         user_role => $user_role
 189     });
 190     $archived_filename_with_path = $uploader->archive();
 191     $md5 = $uploader->get_md5($archived_filename_with_path);
 192     if (!$archived_filename_with_path) {
 193         $c->stash->{rest} = {error => "Could not save file $upload_original_name in archive",};
 194         return;
 195     }
 196     unlink $upload_tempfile;
 197
 198     #parse uploaded file with appropriate plugin
 199     $parser = CXGN::Trial::ParseUpload->new(chado_schema => $chado_schema, filename => $archived_filename_with_path);
 200     $parser->load_plugin($upload_type);
 201     $parsed_data = $parser->parse();
 202
 203     if (!$parsed_data) {
 204         my $return_error = '';
 205
 206         if (! $parser->has_parse_errors() ){
 207             $return_error = "Could not get parsing errors";
 208             $c->stash->{rest} = {error_string => $return_error,};
 209         }
 210         else {
 211             $parse_errors = $parser->get_parse_errors();
 212             #print STDERR Dumper $parse_errors;
 213
 214             foreach my $error_string (@{$parse_errors->{'error_messages'}}){
 215                 $return_error=$return_error.$error_string."<br>";
 216             }
 217         }
 218
 219         $c->stash->{rest} = {error_string => $return_error, missing_accessions => $parse_errors->{'missing_accessions'}};
 220         return;
 221     }
 222     #print STDERR Dumper $parsed_data;
 223
 224     #Turn parased data into same format as generate_genotype_trial above
 225     my %design;
 226     foreach (sort keys %$parsed_data){
 227         my $val = $parsed_data->{$_};
 228         $design{$val->{well}} = {
 229             plot_name => $val->{sample_id},
 230             stock_name => $val->{source_stock_uniquename},
 231             plot_number => $val->{well},
 232             row_number => $val->{row},
 233             col_number => $val->{column},
 234             is_blank => $val->{is_blank},
 235             concentration => $val->{concentration},
 236             volume => $val->{volume},
 237             tissue_type => $val->{tissue_type},
 238             dna_person => $val->{dna_person},
 239             extraction => $val->{extraction},
 240             acquisition_date => $val->{date},
 241             notes => $val->{notes},
 242             ncbi_taxonomy_id => $val->{ncbi_taxonomy_id}
 243         };
 244     }
 245
 246     $c->stash->{rest} = {success => "1", design=>\%design};
 247 }
 248
 249 sub store_genotype_trial : Path('/ajax/breeders/storegenotypetrial') ActionClass('REST') {}
 250 sub store_genotype_trial_POST : Args(0) {
 251     my $self = shift;
 252     my $c = shift;
 253
 254     my $user_id;
 255     my $user_name;
 256     my $user_role;
 257     my $session_id = $c->req->param("sgn_session_id");
 258
 259     if ($session_id){
 260         my $dbh = $c->dbc->dbh;
 261         my @user_info = CXGN::Login->new($dbh)->query_from_cookie($session_id);
 262         if (!$user_info[0]){
 263             $c->stash->{rest} = {error=>'You must be logged in to upload genotyping trial!'};
 264             $c->detach();
 265         }
 266         $user_id = $user_info[0];
 267         $user_role = $user_info[1];
 268         my $p = CXGN::People::Person->new($dbh, $user_id);
 269         $user_name = $p->get_username;
 270     } else{
 271         if (!$c->user){
 272             $c->stash->{rest} = {error=>'You must be logged in to upload a genotyping trial!'};
 273             $c->detach();
 274         }
 275         $user_id = $c->user()->get_object()->get_sp_person_id();
 276         $user_name = $c->user()->get_object()->get_username();
 277         $user_role = $c->user->get_object->get_user_type();
 278     }
 279
 280     if ($user_role ne 'curator' && $user_role ne 'submitter') {
 281         $c->stash->{rest} = {error =>  "You have insufficient privileges to upload a genotyping trial." };
 282         $c->detach();
 283     }
 284
 285     my $schema = $c->dbic_schema("Bio::Chado::Schema");
 286     my $plate_info = decode_json $c->req->param("plate_data");
 287     #print STDERR Dumper $plate_info;
 288
 289     if ( !$plate_info->{design} || !$plate_info->{genotyping_facility_submit} || !$plate_info->{project_name} || !$plate_info->{description} || !$plate_info->{location} || !$plate_info->{year} || !$plate_info->{name} || !$plate_info->{breeding_program} || !$plate_info->{genotyping_facility} || !$plate_info->{sample_type} || !$plate_info->{plate_format} ) {
 290         $c->stash->{rest} = { error => "Please provide all parameters in the plate information section" };
 291         $c->detach();
 292     }
 293
 294     my $location = $schema->resultset("NaturalDiversity::NdGeolocation")->find( { nd_geolocation_id => $plate_info->{location} } );
 295     if (!$location) {
 296         $c->stash->{rest} = { error => "Unknown location" };
 297         $c->detach();
 298     }
 299
 300     my $breeding_program = $schema->resultset("Project::Project")->find( { project_id => $plate_info->{breeding_program} });
 301     if (!$breeding_program) {
 302         $c->stash->{rest} = { error => "Unknown breeding program" };
 303         $c->detach();
 304     }
 305
 306     print STDERR "Creating the genotyping trial...\n";
 307
 308     my $message;
 309     my $coderef = sub {
 310
 311         my $ct = CXGN::Trial::TrialCreate->new( {
 312             chado_schema => $schema,
 313             dbh => $c->dbc->dbh(),
 314             user_name => $user_name, #not implemented,
 315             operator => $user_name,
 316             trial_year => $plate_info->{year},
 317             trial_location => $location->description(),
 318             program => $breeding_program->name(),
 319             trial_description => $plate_info->{description},
 320             design_type => 'genotyping_plate',
 321             design => $plate_info->{design},
 322             trial_name => $plate_info->{name},
 323             is_genotyping => 1,
 324             genotyping_user_id => $user_id,
 325             genotyping_project_name => $plate_info->{project_name},
 326             genotyping_facility_submitted => $plate_info->{genotyping_facility_submit},
 327             genotyping_facility => $plate_info->{genotyping_facility},
 328             genotyping_plate_format => $plate_info->{plate_format},
 329             genotyping_plate_sample_type => $plate_info->{sample_type},
 330         });
 331
 332         $message = $ct->save_trial();
 333     };
 334
 335     try {
 336         $schema->txn_do($coderef);
 337     } catch {
 338         print STDERR "Transaction Error: $_\n";
 339         $c->stash->{rest} = {error => "Error saving genotyping trial in the database: $_"};
 340         $c->detach;
 341     };
 342
 343     my $error;
 344     if ($message->{'error'}) {
 345         $error = $message->{'error'};
 346     }
 347     if ($error){
 348         $c->stash->{rest} = {error => "Error saving genotyping trial in the database: $error"};
 349         $c->detach;
 350     }
 351     #print STDERR Dumper(%message);
 352
 353     my $dbh = $c->dbc->dbh();
 354     my $bs = CXGN::BreederSearch->new( { dbh=>$dbh, dbname=>$c->config->{dbname}, } );
 355     my $refresh = $bs->refresh_matviews($c->config->{dbhost}, $c->config->{dbname}, $c->config->{dbuser}, $c->config->{dbpass}, 'stockprop');
 356
 357     my $saved_layout = CXGN::Trial::TrialLayout->new({schema => $schema, trial_id => $message->{trial_id}, experiment_type=>'genotyping_layout'});
 358     my $saved_design = $saved_layout->get_design();
 359     #print STDERR Dumper $saved_design;
 360
 361     my @brapi_samples;
 362     foreach (values %$saved_design){
 363         push @brapi_samples, {
 364             sampleDbId => $_->{plot_id},
 365             sampleName => $_->{plot_name},
 366             well => $_->{plot_number},
 367             row => $_->{row_number},
 368             column => $_->{col_number},
 369             concentration => $_->{concentration},
 370             volume => $_->{volume},
 371             tissueType => $_->{tissue_type},
 372             taxonId => {
 373                 sourceName => 'NCBI',
 374                 taxonId => $_->{ncbi_taxonomy_id}
 375             }
 376         };
 377     }
 378
 379     my $brapi_plate_data = {
 380         vendorProjectDbId => $plate_info->{project_name},
 381         clientPlateDbId => $message->{trial_id},
 382         clientPlateName => $plate_info->{name},
 383         plateFormat => $plate_info->{plate_format},
 384         sampleType => $plate_info->{sample_type},
 385         samples => \@brapi_samples
 386     };
 387
 388     $c->stash->{rest} = {
 389         message => "Successfully stored the genotyping trial.",
 390         trial_id => $message->{trial_id},
 391         plate_data => $brapi_plate_data
 392     };
 393 }
 394
 395 sub get_genotypingserver_credentials : Path('/ajax/breeders/genotyping_credentials') Args(0) {
 396     my $self = shift;
 397     my $c = shift;
 398
 399     if ($c->user && ($c->user->check_roles("submitter") || $c->user->check_roles("curator"))) {
 400         $c->stash->{rest} = {
 401             host => $c->config->{genotyping_server_host},
 402             username => $c->config->{genotyping_server_username},
 403             password => $c->config->{genotyping_server_password},
 404             token => $c->config->{genotyping_server_token},
 405         };
 406     }
 407     else {
 408         $c->stash->{rest} = {
 409             error => "Insufficient privileges for this operation."
 410         };
 411     }
 412 }
 413
 414 1;